Fix: add HybridMesher as normal source folder (not submodule)

HybridMesher

@@ -1 +0,0 @@
-Subproject commit 30f75424f6f8b54d5ae32510d714ad1c506e58ac

HybridMesher/Makefile

@@ -0,0 +1,125 @@
+CC := g++-10
+NVCC := nvcc
+CFLAGS := -std=c++17 -fpic -MMD -Wall -fopenmp
+NVCC_FLAGS := -std=c++17 -fpic -MMD -Xcudafe="--diag_suppress=20012 --diag_suppress=20236" -Xcompiler -fopenmp
+
+INCLUDE := libraries/include libraries/include/NetCDF-C
+LIBS_DIR := libraries/lib
+LIBS_DIR_GPU := /usr/local/cuda/lib64
+LIBS := exodus netcdf hdf5_hl hdf5 z tet dl zip
+LIBS_GPU := cuda cudart cublas
+
+TARGET = Geometry
+SRC_DIR = src
+BUILD_DIR = build
+
+# Should not need to modify below.
+
+CPU_BUILD_DIR = $(BUILD_DIR)/cpu
+GPU_BUILD_DIR = $(BUILD_DIR)/gpu
+PY_CPU_BUILD_DIR = $(BUILD_DIR)/py_cpu
+
+SRC = $(wildcard $(SRC_DIR)/*/*.cpp) $(wildcard $(SRC_DIR)/*.cpp)
+
+# Get source files and object files.
+GCC_SRC = $(filter-out %.cu.cpp ,$(SRC))
+NVCC_SRC = $(filter %.cu.cpp, $(SRC))
+GCC_OBJ = $(GCC_SRC:$(SRC_DIR)/%.cpp=%.o)
+NVCC_OBJ = $(NVCC_SRC:$(SRC_DIR)/%.cpp=%.o)
+
+# If compiling for CPU, all go to GCC. Otherwise, they are split.
+CPU_OBJ = $(addprefix $(CPU_BUILD_DIR)/,$(GCC_OBJ)) $(addprefix $(CPU_BUILD_DIR)/,$(NVCC_OBJ))
+GPU_GCC_OBJ = $(addprefix $(GPU_BUILD_DIR)/,$(GCC_OBJ))
+GPU_NVCC_OBJ = $(addprefix $(GPU_BUILD_DIR)/,$(NVCC_OBJ))
+
+PY_CPU_OBJ = $(addprefix $(PY_CPU_BUILD_DIR)/,$(GCC_OBJ)) $(addprefix $(PY_CPU_BUILD_DIR)/,$(NVCC_OBJ))
+
+# $(info $$GCC_SRC is [${GCC_SRC}])
+# $(info $$NVCC_SRC is [${NVCC_SRC}])
+# $(info $$GCC_OBJ is [${GCC_OBJ}])
+# $(info $$NVCC_OBJ is [${NVCC_OBJ}])
+
+# $(info $$CPU_OBJ is [${CPU_OBJ}])
+# $(info $$GPU_GCC_OBJ is [${GPU_GCC_OBJ}])
+# $(info $$GPU_NVCC_OBJ is [${GPU_NVCC_OBJ}])
+
+HEADER = $(wildcard $(SRC_DIR)/*/*.h) $(wildcard $(SRC_DIR)/*.h)
+CPU_DEPS = $(wildcard $(CPU_BUILD_DIR)/*.d)
+GPU_DEPS = $(wildcard $(GPU_BUILD_DIR)/*.d)
+
+SPACE := $(subst ,, )
+COMMA := ,
+
+INC := $(INCLUDE:%=-I%)
+LIB := $(LIBS_DIR:%=-L%)
+RPATH := $(subst $(SPACE),$(COMMA),$(LIBS_DIR))
+LIB_GPU := $(LIBS_DIR_GPU:%=-L%)
+LD := $(LIBS:%=-l%)
+LD_GPU := $(LIBS_GPU:%=-l%)
+
+PY_EXT := $(shell python3-config --extension-suffix)
+PY_INC := $(shell python3-config --includes)
+
+
+# Reminder:
+# $< = first prerequisite
+# $@ = the target which matched the rule
+# $^ = all prerequisites
+
+.PHONY: all docs clean
+
+all : cpu gpu python docs
+
+cpu: $(TARGET)CPU
+gpu: $(TARGET)GPU
+python: $(TARGET)PY
+
+docs: SHELL:=/bin/bash
+docs:
+	if [ ! -d "docs/.venv" ]; then python3 -m venv "docs/.venv"; fi
+	( \
+		source docs/.venv/bin/activate;\
+		pip install -r docs/requirements.txt; \
+		doxygen docs/Doxyfile; \
+		sphinx-build -b html docs/source docs/build/html; \
+		deactivate \
+	)
+
+# CPU ONLY
+$(TARGET)CPU: $(CPU_OBJ)
+	$(CC) $(CFLAGS) $^ -o $@ $(LIB) $(LD) -Wl,-rpath,$(RPATH)
+
+$(CPU_BUILD_DIR)/%.o $(CPU_BUILD_DIR)/%.cu.o: $(SRC_DIR)/%.cpp | $(CPU_BUILD_DIR)
+	$(CC) $(CFLAGS) -c -o $@ $< $(INC) $(PY_INC)
+
+# GPU ONLY
+# For GPU, we need to build the NVCC objects, the NVCC linked object, and the
+# regular ones. Then, we link them all together.
+$(TARGET)GPU: $(GPU_BUILD_DIR)/link.o $(GPU_GCC_OBJ) | $(GPU_BUILD_DIR)
+	$(CC) -g -DCUDA $(CFLAGS) $(GPU_NVCC_OBJ) $^ -o $@ $(INC) $(LIB) $(LIB_GPU) $(LD) $(LD_GPU)  -Wl,-rpath,$(RPATH)
+
+$(GPU_BUILD_DIR)/link.o: $(GPU_NVCC_OBJ) | $(GPU_BUILD_DIR)
+	$(NVCC) --device-link $^ -o $@
+
+$(GPU_BUILD_DIR)/%.cu.o: $(SRC_DIR)/%.cu.cpp | $(GPU_BUILD_DIR)
+	$(NVCC) $(NVCC_FLAGS) -DCUDA -x cu --device-c -o $@ $< $(INC)
+
+$(GPU_BUILD_DIR)/%.o: $(SRC_DIR)/%.cpp | $(GPU_BUILD_DIR)
+	$(CC) $(CFLAGS) -g -DCUDA -c -o $@ $< $(INC)
+
+# PYTHON CPU
+
+$(TARGET)PY: $(PY_CPU_OBJ)
+	$(CC) $(CFLAGS) $^ -shared -o $(TARGET)$(PY_EXT) $(LIB) -Wl,--whole-archive $(LD) -Wl,--no-whole-archive
+
+$(PY_CPU_BUILD_DIR)/%.o $(PY_CPU_BUILD_DIR)/%.cu.o: $(SRC_DIR)/%.cpp | $(PY_CPU_BUILD_DIR)
+	$(CC) $(CFLAGS) -DPYTHON -c -o $@ $< $(INC) $(PY_INC)
+
+-include $(CPU_DEPS)
+-include $(GPU_DEPS)
+
+$(CPU_BUILD_DIR) $(GPU_BUILD_DIR) $(PY_CPU_BUILD_DIR):
+	mkdir -p $@
+
+clean:
+	rm -Rf $(BUILD_DIR) $(TARGET)* docs/build docs/.venv

HybridMesher/PRE_SETUP

@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+
+import os
+import subprocess
+from pathlib import Path
+
+def main():
+    libraries_dir = "libraries"
+    
+    # Unzip lib.zip in the libraries directory
+    subprocess.run(["unzip", "libs.zip"], cwd=libraries_dir, check=True)
+
+    # Make clone directory
+    subprocess.run(["mkdir", "-p", "clone"], cwd=libraries_dir)
+
+    # Move everything except 'libs.zip'
+    directories = [f.name for f in Path(libraries_dir).iterdir() if f.is_dir()]
+    
+    for dir in directories:
+        if(dir != "clone"):
+            subprocess.run(["mv", dir, "clone/"], cwd=libraries_dir)
+
+
+if __name__ == "__main__":
+    main()

HybridMesher/README.rst

@@ -0,0 +1,36 @@
+========
+Geometry
+========
+This repository contains code for the Geometry library, which is available both as a
+C++ library and a Python module. The documentation is up `here <https://acem.ece.illinois.edu/docs/Geometry/>`__.
+
+Building
+--------
+All that is required is a working Python installation. First, clone the repository
+
+.. code-block:: sh
+
+    $ git clone https://git.acem.ece.illinois.edu/gonzalo9/HybridMesher.git
+    $ cd HybridMesher
+
+You may also need to install a few other tools, such as ``m4`` and ``cmake`` if they are not
+already installed. A new version of ``cmake`` is needed. Next, we build the dependencies by running
+
+.. code-block:: sh
+
+    $ ./PRE_SETUP
+    $ ./SETUP
+
+Lastly, you can build the Python module by running the Makefile
+
+.. code-block:: sh
+
+    $ make python
+
+Documentation
+-------------
+To build the documentation, you simply only need to run the Makefile
+
+.. code-block:: sh
+
+    $ make docs

HybridMesher/SETUP

@@ -0,0 +1,258 @@
+#!/usr/bin/env python3
+
+from __future__ import annotations
+import argparse, subprocess, shutil, os
+from enum import Enum
+from pathlib import Path
+
+LIB_DIR = Path("libraries/clone")
+INSTALL_DIR = Path("libraries")
+SYSTEM_INSTALL_DIR = Path("/usr/local")
+Compatibility = Enum('Compatibility', ['Equal', 'AtLeast', 'AtMost'])
+CompatSymbol = {Compatibility.Equal: '==', Compatibility.AtLeast: ">=", Compatibility.AtMost: "<="}
+SymbolCompat = {'==': Compatibility.Equal, ">=": Compatibility.AtLeast, "<=": Compatibility.AtMost}
+
+
+def make_box(string: str):
+    length = len(string) - 3
+    print("╔" + "="*(length-2) + "╗")
+    print(f"┇   {string}   ┇")
+    print("╚" + "="*(length-2) + "╝ ")
+
+
+def error(predicate: bool, error: str):
+    if predicate:
+        print(f'[\033[1;31mERROR\033[0m] {error}')
+        quit()
+
+class Library:
+    def __init__(self, name: str, version: str, compatibility: Compatibility):
+        self.name = name
+        self.version = [int(x) for x in version.split(".")]
+        self.compatibility = compatibility
+        self.id = name if version == "0.0.0" else f'{name}-{version}'
+
+    def exists(self):
+        return (INSTALL_DIR / self.id).is_dir()
+
+    def is_satisfied_by(self, dep: Library):
+        if self.compatibility == Compatibility.Equal:
+            return self.version == dep.version
+        elif self.compatibility == Compatibility.AtLeast:
+            return self.version <= dep.version
+        elif self.compatibility == Compatibility.AtMost:
+            return self.version >= dep.version
+
+    @staticmethod
+    def from_name(name: str) -> Library:
+        ind = name.rfind("-")
+        if ind == -1:
+            return Library(name, "0.0.0", Compatibility.Equal)
+        else:
+            error(not name[ind+1].isnumeric(), f"The library '{name}' has an invalid name.")
+            return Library(name[:ind], name[ind+1:], Compatibility.Equal)
+
+    @staticmethod
+    def from_line(line: str) -> Library:
+        line = line.split(" ")
+        if len(line) == 1:
+            return Library(line[0], "0.0.0", Compatibility.AtLeast)
+        try:
+            return Library(line[0], line[2], SymbolCompat[line[1]])
+        except (KeyError, IndexError):
+            error(True, f"The dependency line '{line}' is formatted improperly.")
+
+class Node:
+    def __init__(self, lib: Library):
+        self.lib = lib
+        self.parent = None
+        self.dependencies = []
+        self.visited = False
+
+    def build(self, prefix: Path, verbose: bool) -> int:
+        head = "  ──  "
+        space = "       "
+        ok = " [\033[1;32mOK\033[0m] "
+        err = " [\033[1;31mERR\033[0m] "
+
+        lib_prefix = prefix / self.lib.id
+        setup = LIB_DIR / self.lib.id / "SETUP"
+        error(not setup.is_file(), f"The library '{self.lib.id}' does not have a SETUP file.")
+
+        make_box(f"Building '\033[1;96m{self.lib.id}\033[0m'")
+        if lib_prefix.is_dir():
+            print(f"{ok}Library is already built, installation at '{lib_prefix}'\n")
+            return 0
+
+        deps = " ".join([str(prefix / dep) for dep in self.dependencies])
+        commands = f"{setup} {lib_prefix} {deps}".split(" ")
+        if verbose:
+            p = subprocess.Popen(commands, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True)
+        else:
+            p = subprocess.Popen(commands, stdout=subprocess.DEVNULL, stderr=subprocess.PIPE, text=True)
+
+        rows, _ = shutil.get_terminal_size((80, 20))
+        s = rows - 10 - len(head)
+        for line in (p.stdout if verbose else p.stderr):
+            line = "\n".join([(head if i == 0 else space) + line[i: i + s] for i in range(0, len(line), s)])
+            print(line, end="")
+
+        returncode = p.poll()
+        if returncode == 0:
+            print(f"{ok}Finished building library, installation at '{lib_prefix}'\n")
+            return 0
+        else:
+            print(f"{err}Error while building library. Return code: {returncode}\n")
+            return 1
+
+
+class DependencyTree:
+    def __init__(self):
+        self.all_deps = dict()
+        self.roots = []
+
+    def add_library(self, lib_dir: Path):
+        lib = Library.from_name(lib_dir.name)
+        if lib.id not in self.all_deps:
+            self.all_deps[lib.id] = Node(lib)
+        else:
+            error(True, "Duplicate libaries, shouldn't be possible.")
+
+        dep_file = lib_dir / "DEPENDENCIES"
+        error(not dep_file.is_file(), f"The library '{lib.id}' does not have a DEPENDENCIES file.")
+        lib_deps = open(dep_file, "r").read().splitlines()
+        for dep_line in lib_deps:
+            lib_dep = Library.from_line(dep_line)
+            self.all_deps[lib.id].dependencies.append(lib_dep)
+
+    def build(self):
+        # Validate dependencies and build tree.
+        for node in self.all_deps.values():
+            satisfied_deps = []
+            for dep in node.dependencies:
+                fails = ""
+                satisfied = False
+                for node_check in self.all_deps.values():
+                    if node_check.lib.name != dep.name:
+                        continue
+                    if dep.is_satisfied_by(node_check.lib):
+                        satisfied = True
+                        satisfied_deps.append(node_check.lib.id)
+                        node_check.parent = node.lib.id
+                        break
+                    else:
+                        fails += f', {node_check.lib.id}'
+
+                if not satisfied:
+                    vers = ".".join([str(x) for x in dep.version])
+                    dep_line = f'{dep.name} {CompatSymbol[dep.compatibility]} {vers}'
+                    error(True, f"Dependency '{dep_line}' from '{node.lib.id}' is not satisfied "\
+                                    f"by any of the following:{fails[1:]}")
+
+            self.all_deps[node.lib.id].dependencies = satisfied_deps
+
+        # Get roots of the tree.
+        for node in self.all_deps.values():
+            if node.parent is None:
+                self.roots.append(node.lib.id)
+
+    def __repr__(self):
+        return self.string_helper(0, self.roots)[:-1]
+
+    def string_helper(self, layer, deps):
+        line = ""
+        for i, node_id in enumerate(deps):
+            node = self.all_deps[node_id]
+            line += "│    "*layer + f"├─{node.lib.id}\n"
+            line += self.string_helper(layer+1, node.dependencies)
+        return line
+
+    def reverse_traversal(self) -> List[Node]:
+        rt = self.reverse_helper(self.roots)[::-1]
+        seen = set()
+        return [x for x in rt if not (x in seen or seen.add(x))]
+
+    def reverse_helper(self, libs):
+        traversal = []
+        for node_id in libs:
+            node = self.all_deps[node_id]
+            traversal.append(node_id)
+            traversal += self.reverse_helper(node.dependencies)
+
+        return traversal
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Sets up the libraries necessary in " \
+                                      "the local 'libraries/' environment, unless otherwise specified. " \
+                                      "Searches the 'libraries/clone' to install libaries.")
+
+    parser.add_argument("--verbose", help="Output all setup information.", action="store_true")
+    parser.add_argument("--tree", help="Visualize the dependency tree.", action="store_true")
+    parser.add_argument("--system", help="Install packages to the system '/usr/local' folder.", action="store_true")
+
+    args = parser.parse_args()
+
+    tree = DependencyTree()
+    for lib_dir in LIB_DIR.iterdir():
+        tree.add_library(lib_dir)
+    tree.build()
+
+
+
+    # Build libraries
+    lib_build_order = tree.reverse_traversal()
+    
+    if args.tree:
+        print(lib_build_order)
+        quit()
+    failed = 0
+    for lib_id in lib_build_order:
+        prefix = SYSTEM_INSTALL_DIR if args.system else INSTALL_DIR
+        failed += tree.all_deps[lib_id].build(prefix.resolve(), args.verbose)
+
+    total = len(lib_build_order)
+    print("Building process finished:")
+    if not failed:
+        print(f" [\033[1;32mPASS\033[0m] ({total - failed}/{total})")
+
+        inc_dir, lib_dir = INSTALL_DIR / "include", INSTALL_DIR / "lib"
+        inc_dir.mkdir(exist_ok=True)
+        lib_dir.mkdir(exist_ok=True)
+        for sym in inc_dir.iterdir():
+            sym.unlink()
+        for sym in lib_dir.iterdir():
+            if not sym.is_dir(): sym.unlink()
+
+        lib_names = dict() # name, id
+        for lib_id in lib_build_order:
+            name = tree.all_deps[lib_id].lib.name
+            if name in lib_names: # Name already exists, so include version in name.
+                if lib_names[name] != 0: # Name hasn't been marked as duplicate.
+                    lib_names[lib_names[name]] = lib_names[name] # Make old id as a new pair.
+                    lib_names[name] = 0 # Mark the old name as 0.
+                lib_names[lib_id] = lib_id # Add the new one as an id pair.
+            else: # Make (name, id) pair.
+                lib_names[name] = lib_id
+
+        # Apply include symlinks.
+        for lib_name, lib_id in lib_names.items():
+            (inc_dir / lib_name).symlink_to(INSTALL_DIR.resolve() / lib_id / "include", target_is_directory=True)
+
+        # Apply lib symlinks.
+        for lib_id in lib_build_order:
+            library_lib_dir = INSTALL_DIR / lib_id / "lib"
+            if not library_lib_dir.is_dir(): continue
+            for f in library_lib_dir.iterdir():
+                if f.suffix == ".a": (lib_dir / f.name).symlink_to(f.resolve())
+
+        print("Applied symlinks in 'libraries/include' and 'libraries/lib'")
+    else:
+        print(f" [\033[1;31mFAIL\033[0m] ({total - failed}/{total})")
+
+
+
+
+if __name__ == "__main__":
+    main()
+    main()

HybridMesher/SingaporeVersion.py

@@ -0,0 +1,240 @@
+import sys
+sys.path.append('.')
+
+import Geometry as geo
+import numpy as np
+import pandas as pd
+from numpy import linalg as la
+
+#######################################################
+#######################################################
+##                                                   ##
+##                  PART TO MODIFY                   ##
+##                                                   ##
+#######################################################
+#######################################################
+
+directory = "/home/user/Projects/problems/testCylinder/" # Absolute path to the model files  
+fileName = "test_cylinder"                               # Name of the .g and .json files
+
+unit = 1.0                                               # Unit of the input (in meters) -> 1.0 for meters or 2.54e-2 for inches
+mesh_size = 0.08                                         # Mesh size in the unit used
+unit2trunc = 4                                           # Number of significant digits in the regular mesh
+
+PEC = 1                                                  # PEC in the .bc file
+ABC = 2                                                  # PW  in the .bc file
+
+
+#######################################################
+#######################################################
+##                                                   ##
+##              DO NOT CHANGE FROM HERE              ##
+##                                                   ##
+#######################################################
+#######################################################
+
+########################################
+##        AUXILIARY FUNCTIONS         ##
+########################################
+def floor(number, sig_figs):
+  return np.trunc(number * (10 ** sig_figs)) / (10 ** sig_figs)
+
+def truncate_to_significant_figures(number, sig_figs):
+  isNumber = False
+  if not isinstance(number, np.ndarray):
+    number = np.array([number])
+    isNumber = True
+
+  maskLower = number < 0
+  maskGreater = number > 0
+  
+  order_of_magnitude = np.zeros_like(number)
+  order_of_magnitude[maskGreater] = np.floor(np.log10(number[maskGreater]))
+  order_of_magnitude[maskLower] = np.floor(np.log10(-number[maskLower]))
+  
+  if isNumber:
+    return floor(number, -(order_of_magnitude - sig_figs + 1))[0]
+
+  return floor(number, -(order_of_magnitude - sig_figs + 1))
+
+
+########################################
+##            MAIN FUNCTION           ##
+########################################
+def main():
+  name = f"{directory}/{fileName}"
+
+  regularElementSize = truncate_to_significant_figures(mesh_size, 4)
+
+  print(f"Using {directory}/{fileName}.g")
+
+  mesh = geo.VolumeMesh.from_exodus(f"{directory}/{fileName}.g")
+  config = mesh.apply_config(f"{directory}/{fileName}.json")
+  BC = geo.BoundaryCondition
+
+  regular = mesh.make_grid_mesh(regularElementSize, mesh.face_sets_with_bc(BC.PEC))
+  irregular = mesh.make_hybrid_mesh(regularElementSize, mesh.face_sets_with_bc(BC.PEC), max_volume=pow(regularElementSize,3)*np.sqrt(2)/12)
+
+  surfs = irregular.extract_surfaces(irregular.face_sets_with_bc(BC.PEC))
+  surfs.save_stl(f"{name}_pec_surfaces.stl")  
+  surfs = regular.extract_surfaces(regular.face_sets_with_bc(BC.NCB))
+  surfs.save_stl(f"{name}_ncbc_surfaces.stl")
+  surfs = regular.extract_surfaces(regular.face_sets_with_bc(BC.ABC))
+  surfs.save_stl(f"{name}_acb_surfaces.stl")
+
+  regularVertices = regular.vertices.shape[1]
+  regVertices = np.array(regular.vertices)
+
+  referenceNode = regular.vertices[:,0]
+  center = referenceNode - np.floor((np.absolute(referenceNode) + (regularElementSize / 2.0)) / regularElementSize) * regularElementSize * np.sign(referenceNode)
+  center = floor(center, unit2trunc)
+
+  regVertices = np.floor((np.absolute(regVertices - center.reshape((3,1))) + (regularElementSize / 2.0)) / regularElementSize) * regularElementSize * np.sign(regVertices) + center.reshape((3,1))
+  regVertices = regVertices.T
+
+  totalNodes = np.vstack((np.array(regular.vertices).T, np.array(irregular.vertices).T))
+
+  totalNodes, indices, verticesMap, _ = np.unique(totalNodes, axis=0, return_index=True, return_inverse=True, return_counts=True)
+  np.savetxt(f'{name}.node', totalNodes, newline="\n3 0 0\n" , fmt='%f', header=f"{unit}\n{totalNodes.shape[0]}", comments='')
+  totalNodes = np.vstack((regVertices, np.array(irregular.vertices).T))[indices, :]
+
+
+  ########################################
+  ##          REGULAR ELEMENTS          ##
+  ########################################
+
+  dimRegular = (regular.info.num_elems, 4)
+  regularFacesBC = np.zeros(dimRegular)
+
+  NCBC = 1000
+
+  for i in range(regular.info.num_face_sets):
+    bcValue = 0
+    if (regular.get_face_set_bc(i) == BC.PEC):
+      bcValue = PEC
+    elif (regular.get_face_set_bc(i) == BC.ABC):
+      bcValue = ABC
+    elif (regular.get_face_set_bc(i) == BC.NCB):
+      bcValue = NCBC
+    else:
+      bcValue = 0
+      
+    for j in range(len(regular.face_set(i))):
+      regularFacesBC[regular.face_set(i)[j] // 4][regular.face_set(i)[j] % 4] = int(bcValue)
+
+  elementArray = np.empty((regular.info.num_elems, 4), dtype=np.int64)
+  bcArray = np.zeros((regular.info.num_elems, 4), dtype=np.int64)
+
+  nElements = 0
+
+  for i in range(regular.info.num_elem_sets):
+    elemSet = np.array(regular.elem_set(i))
+    num_elements = elemSet.shape[1]
+    row_range = range(nElements, nElements + num_elements)
+
+    elementArray[row_range, :] = verticesMap[elemSet].T
+    bcArray[row_range, :] = regularFacesBC[row_range][:, [3, 1, 2, 0]]
+
+    nElements += num_elements
+
+  sorted_indices = np.argsort(elementArray, axis=1)
+
+  elementArray = np.take_along_axis(elementArray, sorted_indices, axis=1)
+  bcArray = np.take_along_axis(bcArray, sorted_indices, axis=1)
+
+  #################################
+  ##       GROUP REGULARS        ##
+  #################################
+
+  nodesArray = np.empty((regular.info.num_elems, 4, 3))
+  nodesArray[:,0,:] = [totalNodes[i][:3] for i in elementArray[:, 0]]
+  nodesArray[:,1,:] = [totalNodes[i][:3] for i in elementArray[:, 1]]
+  nodesArray[:,2,:] = [totalNodes[i][:3] for i in elementArray[:, 2]]
+  nodesArray[:,3,:] = [totalNodes[i][:3] for i in elementArray[:, 3]]
+
+  edgesArray = np.empty((regular.info.num_elems, 3, 3))
+  edgesArray[:,0,:] = nodesArray[:,0,:] - nodesArray[:,1,:]
+  edgesArray[:,1,:] = nodesArray[:,0,:] - nodesArray[:,2,:]
+  edgesArray[:,2,:] = nodesArray[:,0,:] - nodesArray[:,3,:]
+
+  tolerance = 1e-10
+  _, indices = np.unique(np.round(edgesArray / tolerance) * tolerance, axis=0, return_inverse=True)
+  indices = indices + np.ones_like(indices)
+
+  indices[np.any(bcArray != 0, axis=1)] = 0
+  
+  uniqueValues, indices = np.unique(indices, axis=0, return_inverse=True)
+  
+  indices = np.hstack((indices, np.zeros((irregular.info.num_elems,),dtype=np.int64)))
+  
+  ########################################
+  ##         IRREGULAR ELEMENTS         ##
+  ########################################
+
+  dimIrregular = (irregular.info.num_elems, 4)
+  irregularFacesBC = np.zeros(dimIrregular)
+
+  for i in range(irregular.info.num_face_sets):
+    bcValue = 0
+    if (irregular.get_face_set_bc(i) == BC.PEC):
+      bcValue = PEC
+    elif (irregular.get_face_set_bc(i) == BC.ABC):
+      bcValue = ABC
+    elif (irregular.get_face_set_bc(i) == BC.NCB):
+      bcValue = NCBC
+    else:
+      bcValue = 0
+      
+    for j in range(len(irregular.face_set(i))):
+      irregularFacesBC[irregular.face_set(i)[j] // 4][irregular.face_set(i)[j] % 4] = int(bcValue)
+
+  irregularElementArray = np.empty((irregular.info.num_elems, 4), dtype=np.int64)
+  irregularBcArray = np.zeros((irregular.info.num_elems, 4), dtype=np.int64)
+
+  nElements = 0
+
+  for i in range(irregular.info.num_elem_sets):
+    elemSet = np.array(irregular.elem_set(i))
+    num_elements = elemSet.shape[1]
+    row_range = range(nElements, nElements + num_elements)
+
+    irregularElementArray[row_range, :] = verticesMap[elemSet + regularVertices].T
+    irregularBcArray[row_range, :] = irregularFacesBC[row_range][:, [3, 1, 2, 0]]
+
+    nElements += num_elements
+
+  ########################################
+  ##                JOIN                ##
+  ########################################
+  elementArray = np.vstack((elementArray, irregularElementArray))
+  bcArray = np.vstack((bcArray, irregularBcArray))
+
+  np.savetxt(f'{name}.regular', indices, fmt='%d', header=str(uniqueValues.shape[0]), comments='')
+
+  bcArray[bcArray == NCBC] = 0
+
+  print(f"The number of elements is {bcArray.shape[0]}")
+
+  ########################################
+  ##                PRINT               ##
+  ########################################
+  c_with_extra = np.ones((2 * (regular.info.num_elems + irregular.info.num_elems), 4 + 1), dtype=np.int64) * (-1)
+  c_with_extra[::2] = np.hstack((np.ones(((regular.info.num_elems + irregular.info.num_elems),1), dtype=np.int64) * 0, elementArray))
+  c_with_extra[1::2, 1:] = bcArray
+
+  df = pd.DataFrame(c_with_extra, dtype=np.int64)
+
+  mask = df != -1
+  df = df.where(mask, other=np.nan)
+
+  new_row = pd.Series([(regular.info.num_elems + irregular.info.num_elems)] + [np.nan] * (df.shape[1] - 1), index=df.columns)
+
+  # Insert the new row at the top
+  df = pd.concat([new_row.to_frame().T, df], ignore_index=True)
+
+  df = df.astype('Int64')
+  df.to_csv(f'{name}.tetra', sep=' ', index=False, header=False)
+
+
+if __name__ == '__main__':
+	main()

HybridMesher/build/cpu/IO.d

@@ -0,0 +1,9 @@
+build/cpu/IO.o: src/IO.cpp libraries/include/nlohmann-json/json.hpp \
+ src/Geometry.hpp src/IO.hpp libraries/include/EXODUS/exodusII.h \
+ libraries/include/EXODUS/exodus_config.h \
+ libraries/include/NetCDF-C/netcdf.h \
+ libraries/include/NetCDF-C/netcdf_meta.h src/Types.hpp \
+ libraries/include/CudaTools/Array.h libraries/include/CudaTools/Core.h \
+ libraries/include/CudaTools/Macros.h libraries/include/CudaTools/Types.h \
+ libraries/include/CudaTools/Core.h libraries/include/CudaTools/Macros.h \
+ libraries/include/CudaTools/Types.h

HybridMesher/build/cpu/MeshAlgorithms.d

@@ -0,0 +1,10 @@
+build/cpu/MeshAlgorithms.o: src/MeshAlgorithms.cpp \
+ libraries/include/TetGen/tetgen.h src/Geometry.hpp src/IO.hpp \
+ libraries/include/EXODUS/exodusII.h \
+ libraries/include/EXODUS/exodus_config.h \
+ libraries/include/NetCDF-C/netcdf.h \
+ libraries/include/NetCDF-C/netcdf_meta.h src/Types.hpp \
+ libraries/include/CudaTools/Array.h libraries/include/CudaTools/Core.h \
+ libraries/include/CudaTools/Macros.h libraries/include/CudaTools/Types.h \
+ libraries/include/CudaTools/Core.h libraries/include/CudaTools/Macros.h \
+ libraries/include/CudaTools/Types.h

HybridMesher/build/cpu/PyBind.d

@@ -0,0 +1 @@
+build/cpu/PyBind.o: src/PyBind.cpp

HybridMesher/build/py_cpu/Geometry.cu.d

@@ -0,0 +1,124 @@
+build/py_cpu/Geometry.cu.o: src/Geometry.cu.cpp \
+ libraries/include/CudaTools/Core.h libraries/include/CudaTools/Macros.h \
+ src/Geometry.hpp libraries/include/pybind11/numpy.h \
+ libraries/include/pybind11/pybind11.h \
+ libraries/include/pybind11/detail/class.h \
+ libraries/include/pybind11/detail/../attr.h \
+ libraries/include/pybind11/detail/../detail/common.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/Python.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/patchlevel.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymacconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyport.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/exports.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymacro.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymath.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pytime.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/object.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/object.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymem.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pymem.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/objimpl.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/objimpl.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/typeslots.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyhash.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pydebug.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bytearrayobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/bytearrayobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bytesobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/bytesobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/unicodeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/unicodeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/longobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/longintrepr.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/boolobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/floatobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/complexobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/rangeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/memoryobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/tupleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/tupleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/listobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/listobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/dictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/dictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/odictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/enumobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/setobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/methodobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/methodobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/moduleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/funcobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/classobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/fileobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/fileobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pycapsule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/code.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/code.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyframe.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/traceback.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/traceback.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/sliceobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cellobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/iterobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/initconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/genobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystate.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pystate.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/descrobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/genericaliasobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/warnings.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/weakrefobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/structseq.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/namespaceobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/picklebufobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/codecs.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyerrors.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pyerrors.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythread.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/context.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyarena.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/modsupport.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/compile.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythonrun.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pylifecycle.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pylifecycle.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/ceval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/ceval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/sysmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/sysmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/osmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/intrcheck.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/import.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/import.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/abstract.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/abstract.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bltinmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/eval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyctype.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystrtod.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystrcmp.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/fileutils.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/fileutils.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyfpe.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/tracemalloc.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/frameobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/frameobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythread.h \
+ libraries/include/pybind11/detail/../cast.h \
+ libraries/include/pybind11/detail/../detail/descr.h \
+ libraries/include/pybind11/detail/../detail/type_caster_base.h \
+ libraries/include/pybind11/detail/../detail/../pytypes.h \
+ libraries/include/pybind11/detail/../detail/../buffer_info.h \
+ libraries/include/pybind11/detail/../detail/internals.h \
+ libraries/include/pybind11/detail/../detail/typeid.h \
+ libraries/include/pybind11/detail/../options.h \
+ libraries/include/pybind11/detail/init.h \
+ libraries/include/pybind11/gil.h libraries/include/pybind11/complex.h \
+ src/IO.hpp libraries/include/EXODUS/exodusII.h \
+ libraries/include/EXODUS/exodus_config.h \
+ libraries/include/NetCDF-C/netcdf.h \
+ libraries/include/NetCDF-C/netcdf_meta.h src/Types.hpp \
+ libraries/include/CudaTools/Array.h libraries/include/CudaTools/Core.h \
+ libraries/include/CudaTools/Types.h libraries/include/CudaTools/Macros.h \
+ libraries/include/CudaTools/Types.h

HybridMesher/build/py_cpu/IO.d

@@ -0,0 +1,124 @@
+build/py_cpu/IO.o: src/IO.cpp libraries/include/nlohmann-json/json.hpp \
+ src/Geometry.hpp libraries/include/pybind11/numpy.h \
+ libraries/include/pybind11/pybind11.h \
+ libraries/include/pybind11/detail/class.h \
+ libraries/include/pybind11/detail/../attr.h \
+ libraries/include/pybind11/detail/../detail/common.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/Python.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/patchlevel.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymacconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyport.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/exports.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymacro.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymath.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pytime.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/object.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/object.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymem.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pymem.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/objimpl.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/objimpl.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/typeslots.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyhash.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pydebug.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bytearrayobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/bytearrayobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bytesobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/bytesobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/unicodeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/unicodeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/longobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/longintrepr.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/boolobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/floatobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/complexobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/rangeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/memoryobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/tupleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/tupleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/listobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/listobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/dictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/dictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/odictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/enumobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/setobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/methodobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/methodobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/moduleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/funcobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/classobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/fileobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/fileobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pycapsule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/code.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/code.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyframe.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/traceback.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/traceback.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/sliceobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cellobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/iterobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/initconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/genobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystate.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pystate.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/descrobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/genericaliasobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/warnings.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/weakrefobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/structseq.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/namespaceobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/picklebufobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/codecs.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyerrors.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pyerrors.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythread.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/context.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyarena.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/modsupport.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/compile.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythonrun.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pylifecycle.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pylifecycle.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/ceval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/ceval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/sysmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/sysmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/osmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/intrcheck.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/import.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/import.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/abstract.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/abstract.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bltinmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/eval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyctype.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystrtod.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystrcmp.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/fileutils.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/fileutils.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyfpe.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/tracemalloc.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/frameobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/frameobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythread.h \
+ libraries/include/pybind11/detail/../cast.h \
+ libraries/include/pybind11/detail/../detail/descr.h \
+ libraries/include/pybind11/detail/../detail/type_caster_base.h \
+ libraries/include/pybind11/detail/../detail/../pytypes.h \
+ libraries/include/pybind11/detail/../detail/../buffer_info.h \
+ libraries/include/pybind11/detail/../detail/internals.h \
+ libraries/include/pybind11/detail/../detail/typeid.h \
+ libraries/include/pybind11/detail/../options.h \
+ libraries/include/pybind11/detail/init.h \
+ libraries/include/pybind11/gil.h libraries/include/pybind11/complex.h \
+ src/IO.hpp libraries/include/EXODUS/exodusII.h \
+ libraries/include/EXODUS/exodus_config.h \
+ libraries/include/NetCDF-C/netcdf.h \
+ libraries/include/NetCDF-C/netcdf_meta.h src/Types.hpp \
+ libraries/include/CudaTools/Array.h libraries/include/CudaTools/Core.h \
+ libraries/include/CudaTools/Macros.h libraries/include/CudaTools/Types.h \
+ libraries/include/CudaTools/Core.h libraries/include/CudaTools/Macros.h \
+ libraries/include/CudaTools/Types.h

HybridMesher/build/py_cpu/MeshAlgorithms.d

@@ -0,0 +1,124 @@
+build/py_cpu/MeshAlgorithms.o: src/MeshAlgorithms.cpp \
+ libraries/include/TetGen/tetgen.h src/Geometry.hpp \
+ libraries/include/pybind11/numpy.h libraries/include/pybind11/pybind11.h \
+ libraries/include/pybind11/detail/class.h \
+ libraries/include/pybind11/detail/../attr.h \
+ libraries/include/pybind11/detail/../detail/common.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/Python.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/patchlevel.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymacconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyport.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/exports.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymacro.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymath.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pytime.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/object.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/object.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymem.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pymem.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/objimpl.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/objimpl.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/typeslots.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyhash.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pydebug.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bytearrayobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/bytearrayobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bytesobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/bytesobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/unicodeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/unicodeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/longobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/longintrepr.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/boolobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/floatobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/complexobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/rangeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/memoryobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/tupleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/tupleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/listobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/listobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/dictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/dictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/odictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/enumobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/setobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/methodobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/methodobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/moduleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/funcobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/classobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/fileobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/fileobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pycapsule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/code.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/code.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyframe.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/traceback.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/traceback.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/sliceobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cellobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/iterobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/initconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/genobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystate.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pystate.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/descrobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/genericaliasobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/warnings.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/weakrefobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/structseq.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/namespaceobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/picklebufobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/codecs.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyerrors.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pyerrors.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythread.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/context.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyarena.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/modsupport.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/compile.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythonrun.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pylifecycle.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pylifecycle.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/ceval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/ceval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/sysmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/sysmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/osmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/intrcheck.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/import.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/import.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/abstract.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/abstract.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bltinmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/eval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyctype.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystrtod.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystrcmp.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/fileutils.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/fileutils.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyfpe.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/tracemalloc.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/frameobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/frameobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythread.h \
+ libraries/include/pybind11/detail/../cast.h \
+ libraries/include/pybind11/detail/../detail/descr.h \
+ libraries/include/pybind11/detail/../detail/type_caster_base.h \
+ libraries/include/pybind11/detail/../detail/../pytypes.h \
+ libraries/include/pybind11/detail/../detail/../buffer_info.h \
+ libraries/include/pybind11/detail/../detail/internals.h \
+ libraries/include/pybind11/detail/../detail/typeid.h \
+ libraries/include/pybind11/detail/../options.h \
+ libraries/include/pybind11/detail/init.h \
+ libraries/include/pybind11/gil.h libraries/include/pybind11/complex.h \
+ src/IO.hpp libraries/include/EXODUS/exodusII.h \
+ libraries/include/EXODUS/exodus_config.h \
+ libraries/include/NetCDF-C/netcdf.h \
+ libraries/include/NetCDF-C/netcdf_meta.h src/Types.hpp \
+ libraries/include/CudaTools/Array.h libraries/include/CudaTools/Core.h \
+ libraries/include/CudaTools/Macros.h libraries/include/CudaTools/Types.h \
+ libraries/include/CudaTools/Core.h libraries/include/CudaTools/Macros.h \
+ libraries/include/CudaTools/Types.h

HybridMesher/build/py_cpu/PyBind.d

@@ -0,0 +1,124 @@
+build/py_cpu/PyBind.o: src/PyBind.cpp libraries/include/pybind11/numpy.h \
+ libraries/include/pybind11/pybind11.h \
+ libraries/include/pybind11/detail/class.h \
+ libraries/include/pybind11/detail/../attr.h \
+ libraries/include/pybind11/detail/../detail/common.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/Python.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/patchlevel.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymacconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyport.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/exports.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymacro.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymath.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pytime.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/object.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/object.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pymem.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pymem.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/objimpl.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/objimpl.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/typeslots.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyhash.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pydebug.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bytearrayobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/bytearrayobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bytesobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/bytesobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/unicodeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/unicodeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/longobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/longintrepr.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/boolobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/floatobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/complexobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/rangeobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/memoryobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/tupleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/tupleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/listobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/listobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/dictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/dictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/odictobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/enumobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/setobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/methodobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/methodobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/moduleobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/funcobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/classobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/fileobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/fileobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pycapsule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/code.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/code.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyframe.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/traceback.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/traceback.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/sliceobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cellobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/iterobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/initconfig.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/genobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystate.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pystate.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/descrobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/genericaliasobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/warnings.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/weakrefobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/structseq.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/namespaceobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/picklebufobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/codecs.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyerrors.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pyerrors.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythread.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/context.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyarena.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/modsupport.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/compile.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythonrun.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pylifecycle.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/pylifecycle.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/ceval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/ceval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/sysmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/sysmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/osmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/intrcheck.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/import.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/import.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/abstract.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/abstract.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/bltinmodule.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/eval.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyctype.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystrtod.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pystrcmp.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/fileutils.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/fileutils.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pyfpe.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/tracemalloc.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/frameobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/cpython/frameobject.h \
+ /opt/intel/oneapi/intelpython/python3.9/include/python3.9/pythread.h \
+ libraries/include/pybind11/detail/../cast.h \
+ libraries/include/pybind11/detail/../detail/descr.h \
+ libraries/include/pybind11/detail/../detail/type_caster_base.h \
+ libraries/include/pybind11/detail/../detail/../pytypes.h \
+ libraries/include/pybind11/detail/../detail/../buffer_info.h \
+ libraries/include/pybind11/detail/../detail/internals.h \
+ libraries/include/pybind11/detail/../detail/typeid.h \
+ libraries/include/pybind11/detail/../options.h \
+ libraries/include/pybind11/detail/init.h \
+ libraries/include/pybind11/gil.h libraries/include/pybind11/complex.h \
+ libraries/include/pybind11/operators.h libraries/include/pybind11/stl.h \
+ src/Geometry.hpp src/IO.hpp libraries/include/EXODUS/exodusII.h \
+ libraries/include/EXODUS/exodus_config.h \
+ libraries/include/NetCDF-C/netcdf.h \
+ libraries/include/NetCDF-C/netcdf_meta.h src/Types.hpp \
+ libraries/include/CudaTools/Array.h libraries/include/CudaTools/Core.h \
+ libraries/include/CudaTools/Macros.h libraries/include/CudaTools/Types.h \
+ libraries/include/CudaTools/Core.h libraries/include/CudaTools/Macros.h \
+ libraries/include/CudaTools/Types.h

HybridMesher/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

HybridMesher/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

HybridMesher/docs/requirements.txt

@@ -0,0 +1,4 @@
+Sphinx>=5.1.1
+sphinx-rtd-theme>=1.0.0
+sphinxcontrib-bibtex>=2.5.0
+breathe>=4.34.0

HybridMesher/docs/source/.auctex-auto/refs.el

@@ -0,0 +1,14 @@
+(TeX-add-style-hook
+ "refs"
+ (lambda ()
+   (LaTeX-add-bibitems
+    ""
+    "alvarez_2014"
+    "rognes_2010"
+    "sevilla_2014"
+    "tian_2017"
+    "webb_1999"
+    "dunavant_1985"
+    "fezoui_2005"))
+ :bibtex)
+

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HybridMesher/docs/source/_static/js/mathjax-config.js

@@ -0,0 +1,39 @@
+sections = {
+  "mesh_prep": 1,
+  "matrix_assembly": 2,
+  "bc_calc": 3,
+  "timestep": 4,
+}
+
+
+window.MathJax = {
+  loader: {load: ['[tex]/tagformat', '[tex]/ams']},
+  tex: {
+    packages: {'[+]': ['tagformat', 'ams']},
+    macros: {
+      dd: "{\\, \\mathrm{d}}",
+      E: "{\\mathbf{E}}",
+      H: "{\\mathbf{H}}",
+      J: "{\\mathbf{J}}",
+      D: "{\\mathbf{D}}",
+      B: "{\\mathbf{B}}",
+      M: "{\\mathbf{M}}",
+      tbE: "{\\tilde{\\E}}",
+      tbH: "{\\tilde{\\H}}",
+      tE: "{\\tilde{E}}",
+      tH: "{\\tilde{H}}",
+      tphi: "{\\tilde{\\phi}}",
+      curl: ["{\\nabla \\times {#1}}", 1],
+      div: ["{\\nabla \\cdot {#1}}", 1],
+      tens: ["{\\bar{\\bar{{#1}}}}", 1],
+    },
+    tags: 'ams',
+    tagformat: {
+      number: (n) => sections[window.location.pathname.split("/").pop().split(".")[0]] + '.' + n,
+    },
+    ams: {
+      multilineWidth: '100%',
+      multilineIndent: '50em'
+    }
+  },
+}

HybridMesher/docs/source/classes.rst

@@ -0,0 +1,81 @@
+=======
+Classes
+=======
+
+There are a few classes used for storing mesh data. All of the classes are stored under
+the namespace ``Geometry``, and hence is ommitted from now on.
+
+.. note::
+
+   Most functions are also available in the Python module, however, the ``camelCase``
+   naming is replaced with ``snake_case``. For example, in C++, one would write
+   ``mesh.exportFacesSTL(...)``, but in Python, ``mesh.export_faces_stl(...)`` would be
+   correct.
+
+There are two main components:
+
+#. :ref:`Mesh Related`
+#. :ref:`IO Related`
+
+Mesh Related
+============
+These classes relate primarily to the actual geometry mesh data itself.
+
+ThreeVector<T>
+--------------
+.. doxygenclass:: Geometry::ThreeVector
+    :members:
+    :allow-dot-graphs:
+
+.. doxygentypedef:: Geometry::Vector
+.. doxygentypedef:: Geometry::Indices
+
+Face
+----
+.. doxygenclass:: Geometry::Face
+    :members:
+
+Element
+-------
+.. doxygenclass:: Geometry::Element
+    :members:
+
+
+BoundaryCondition
+-----------------
+.. doxygenenum:: Geometry::BoundaryCondition
+
+VolumeMeshInfo
+--------------
+.. doxygenstruct:: Geometry::VolumeMeshInfo
+    :members:
+
+VolumeMesh
+----------
+.. doxygenclass:: Geometry::VolumeMesh
+    :members:
+    :allow-dot-graphs:
+
+
+IO Related
+==========
+
+EXODUS
+------
+.. doxygenclass:: Geometry::IO::EXODUS
+    :members:
+
+JSON
+----
+
+.. doxygenstruct:: Geometry::IO::JSON::ElementSet
+    :members:
+
+.. doxygenstruct:: Geometry::IO::JSON::FaceSet
+    :members:
+
+.. doxygenstruct:: Geometry::IO::JSON::HybridMesh
+    :members:
+
+.. doxygenstruct:: Geometry::IO::JSON::Config
+    :members:

HybridMesher/docs/source/conf.py

@@ -0,0 +1,54 @@
+# Configuration file for the Sphinx documentation builder.
+
+# -- Project information
+
+project = 'Geometry'
+copyright = '2023'
+author = 'Kenneth Jao'
+
+release = '0.1'
+version = '0.1.0'
+
+# -- General configuration
+
+html_static_path = ["_static"]
+html_js_files = ["js/mathjax-config.js"]
+
+extensions = [
+    'sphinx.ext.duration',
+    'sphinx.ext.doctest',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.autosectionlabel',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.graphviz',
+    'sphinxcontrib.bibtex',
+    'breathe',
+]
+
+breathe_projects = {}
+breathe_projects[project] = "../build/xml"
+breathe_default_project = project
+
+bibtex_bibfiles = ['refs.bib']
+
+mathjax_path = "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
+}
+intersphinx_disabled_domains = ['std']
+
+templates_path = ['_templates']
+
+# -- Options for HTML output
+
+html_theme = 'sphinx_rtd_theme'
+html_theme_options = {
+    'collapse_navigation': False,
+}
+
+# -- Options for EPUB output
+epub_show_urls = 'footnote'

HybridMesher/docs/source/index.rst

@@ -0,0 +1,21 @@
+========
+Geometry
+========
+
+This is the documentation for Geometry, a module which processes volumetric mesh data,
+available both as a C++ library or as a Python module. To get started, please head over to the
+:doc:`usage` section. If you're a developer and working this project, please
+refer to the :doc:`classes` for detailed code documentation.
+
+.. note::
+
+   If you would like to contribute, please visit the `git page <https://git.acem.ece.illinois.edu/kjao/Geometry>`__.
+
+Contents
+========
+
+.. toctree::
+   :maxdepth: 2
+
+   usage
+   classes

HybridMesher/docs/source/refs.bib

@@ -0,0 +1,85 @@
+@Book{
+    jin_2014, 
+    place={Hoboken}, 
+    title={The finite element method in electromagnetics},
+    publisher={Wiley},
+    author={Jin, Jian-Ming},
+    year={2014}
+}
+
+@book{alvarez_2014,
+  title={A discontinuous Galerkin finite element method for the time-domain solution of Maxwell equations},
+  author={{\'A}lvarez Gonz{\'a}lez, Jes{\'u}s and others},
+  year={2014},
+  publisher={Universidad de Granada}
+}
+
+@article{rognes_2010,
+author = {Rognes, Marie E. and Kirby, Robert C. and Logg, Anders},
+title = {Efficient Assembly of H(div) and H(curl) Conforming Finite Elements},
+journal = {SIAM Journal on Scientific Computing},
+volume = {31},
+number = {6},
+pages = {4130-4151},
+year = {2010},
+doi = {https://doi.org/10.1137/08073901X},
+}
+
+@article{sevilla_2014,
+title = {The use of hybrid meshes to improve the efficiency of a discontinuous Galerkin method for the solution of Maxwell’s equations},
+journal = {Computers & Structures},
+volume = {137},
+pages = {2-13},
+year = {2014},
+note = {Special Issue Title: UK Association for Computational Mechanics in Engineering},
+issn = {0045-7949},
+doi = {https://doi.org/10.1016/j.compstruc.2013.01.014},
+url = {https://www.sciencedirect.com/science/article/pii/S0045794913000357},
+author = {Ruben Sevilla and Oubay Hassan and Kenneth Morgan},
+}
+
+@article{tian_2017,
+  author={Tian, Cheng-Yi and Shi, Yan and Liang, Chang-Hong},
+  journal={IEEE Microwave and Wireless Components Letters},
+  title={A Low-Storage Discontinuous Galerkin Time-Domain Method},
+  year={2017},
+  volume={27},
+  number={1},
+  pages={1-3},
+  doi={10.1109/LMWC.2016.2629959}
+}
+
+@article{webb_1999,
+  author={Webb, J.P.},
+  journal={IEEE Transactions on Antennas and Propagation},
+  title={Hierarchal vector basis functions of arbitrary order for triangular and tetrahedral finite elements},
+  year={1999},
+  volume={47},
+  number={8},
+  pages={1244-1253},
+  doi={10.1109/8.791939}
+}
+
+@article{dunavant_1985,
+Author = {Dunavant, D.A.},
+ISSN = {10970207},
+Journal = {International Journal for Numerical Methods in Engineering},
+Number = {6},
+Pages = {1129-1148 - 1148},
+Title = {High degree efficient symmetrical Gaussian quadrature rules for the triangle.},
+Volume = {21},
+URL = {https://proxy2.library.illinois.edu/login?url=https://search.ebscohost.com/login.aspx?direct=true&db=edselc&AN=edselc.2-52.0-0022076980&site=eds-live&scope=site},
+Year = {1985},
+}
+
+@article{fezoui_2005,
+author = {{Fezoui, Loula} and {Lanteri, St\'ephane} and {Lohrengel, St\'ephanie} and {Piperno, Serge}},
+title = {Convergence and stability of a discontinuous Galerkin time-domain method for the 3D heterogeneous Maxwell equations on unstructured meshes},
+DOI= "10.1051/m2an:2005049",
+url= "https://doi.org/10.1051/m2an:2005049",
+journal = {ESAIM: M2AN},
+year = 2005,
+volume = 39,
+number = 6,
+pages = "1149-1176",
+}

HybridMesher/docs/source/usage.rst

@@ -0,0 +1,132 @@
+==================
+Usage and Examples
+==================
+This module is very basic, mainly involving the :ref:`VolumeMesh` class.
+The usage of this libary will be illustrated through examples, and further details
+can be found in the other sections. The full examples are given in the `samples <https://git.acem.ece.illinois.edu/kjao/Geometry/src/branch/main/samples>`__ folder.
+We show the examples in Python, but as the module is built from C++, it should be a direct
+translation if needed. Refer to :doc:`classes` for more information.
+
+
+Mesh Structure
+==============
+The mesh is composed of three main parts: vertices, elements, and marked faces.
+We group elements and marked faces with element and face sets, respectively. We may want to
+assign attributes or conditions onto these element or face sets. This is accomplished by
+creating a JSON file. For example,
+
+.. code-block:: json
+
+    {
+        "Element Sets": [
+            {
+                "index": 0,
+                "attribute": "air"
+            }
+        ],
+        "Face Sets": [
+            {
+                "index": 0,
+                "boundary": "PEC"
+            },
+            {
+                "index": 1,
+                "boundary": "ABC"
+            }
+        ],
+        "Hybrid Mesh": {
+            "enable": true,
+            "holes": [
+                [0, 0, 0], [7, -7, 0]
+            ]
+        }
+    }
+
+These three main sections *must* be present in the JSON file for it to be read properly.
+Currently, the supported boundary conditions are
+
+* [0] PEC (Perfect Electric Conductor)
+* [1] PMC (Perfect Magnetic Conductor)
+* [2] ABC (Absorbing Boundary Condition)
+* [3] PML (Perfectly Matched Layer)
+* [4] None
+* [5] None
+* [6] None
+* [7] NCB (Perfect Magnetic Conductor)
+
+Loading
+=======
+This example shows how to load a EXODUS (.g) mesh file and access its information.
+
+.. code-block:: python
+
+    import Geometry as geo
+
+    mesh_path = "../mesh/Cylinder.g"
+    json_path = "../mesh/Cylinder.json"
+
+    mesh = geo.VolumeMesh.from_exodus(mesh_path)
+    mesh.apply_config(json_path)
+    print(mesh.info)
+    print()
+
+    print("Vertex Array:")
+    print(mesh.vertices)
+    print()
+
+    print("Vertex Indices of Element Set 0:")
+    print(mesh.elem_set(0))
+    print()
+
+    print("Face Indices of Face Set 0:")
+    print(mesh.face_set(0))
+    print()
+
+    print("Element Operations:")
+    elem = mesh.element(0)
+    print("Volume:", elem.volume())
+    for face_num in range(4):
+        print(f"Face {face_num}:")
+        print(elem.face(face_num))
+        print("Area:", elem.face(face_num).normal().norm() / 2)
+    print()
+
+    print("Element Set 0 Attribute:", mesh.get_elem_set_attribute(0))
+    print("Face Set 0 Boundary Condition:",  mesh.get_face_set_bc(0))
+    print()
+
+
+Exporting STLs
+==============
+Following from there, we can also export mesh data. We can export all the elements
+as faces, or specific face sets.
+
+.. code-block:: python
+
+    BC = geo.BoundaryCondition # Shorthand
+
+    mesh.save_exodus("CylinderVolume") # Export EXODUS (.g) file.
+    mesh.extract_surfaces().save_stl("CylinderBoundary") # Export STL file.
+    # Only export the ABC Boundary.
+    mesh.extract_surfaces(mesh.face_sets_with_bc(BC.ABC)).save_stl("CylinderABC")
+
+Hybrid Mesh Generation
+======================
+To utilize the hybrid mesh generation functionality, we need only
+call a few functions.
+
+.. code-block:: python
+
+    mesh = geo.VolumeMesh.from_exodus(mesh_path)
+    config = mesh.apply_config(json_path) # Get the config data.
+
+    BC = geo.BoundaryCondition # Shorthand
+
+    # Generate the grid mesh with each cube's side being 1.4.
+    # Ignore ABC face sets when generating the regular mesh.
+    hybrid = mesh.create_hybrid_mesh(1.4, mesh.face_sets_with_bc(BC.ABC))
+    hybrid.export_exodus("HybridCylinder")
+
+    hybrid_surfs = hybrid.extractSurfaces()
+    hybrid_surfs.save_stl("InnerCylinderPEC", inner.face_sets_with_bc(BC.PEC))
+    hybrid_surfs.save_stl("InnerCylinderNCB", inner.face_sets_with_bc(BC.NCB))

HybridMesher/libraries/CudaTools/include/Array.h

@@ -0,0 +1,845 @@
+#ifndef CUDATOOLS_ARRAY_H
+#define CUDATOOLS_ARRAY_H
+
+#include "Core.h"
+#include "Macros.h"
+#include "Types.h"
+
+#include <cmath>
+#include <complex>
+#include <cstdlib>
+#include <iomanip>
+#include <random>
+#include <type_traits>
+
+#ifdef CUDATOOLS_USE_EIGEN
+#include <Eigen/Dense>
+#endif
+
+#ifdef CUDATOOLS_USE_PYTHON
+#include <pybind11/numpy.h>
+#include <pybind11/pybind11.h>
+namespace py = pybind11;
+#endif
+
+#ifdef DEVICE
+#define POINTER pDevice
+#else
+#define POINTER pHost
+#endif
+
+using namespace CudaTools::Types;
+
+namespace CudaTools {
+
+#ifdef CUDATOOLS_USE_EIGEN
+template <typename T>
+using EigenMat = Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic, Eigen::ColMajor>;
+template <typename T> using EigenMapMat = Eigen::Map<EigenMat<T>>;
+template <typename T> using ConstEigenMapMat = Eigen::Map<const EigenMat<T>>;
+
+template <typename T> struct EigenAdaptConst_S { typedef EigenMapMat<T> type; };
+template <typename T> struct EigenAdaptConst_S<const T> { typedef ConstEigenMapMat<T> type; };
+template <typename T> using EigenAdaptConst = typename EigenAdaptConst_S<T>::type;
+#endif
+
+template <typename T> class Array;
+
+struct Slice {
+    uint32_t first;
+    uint32_t second;
+    HD Slice(const std::initializer_list<uint32_t> i)
+        : first(*i.begin()), second(*(i.begin() + 1)) {}
+};
+
+template <typename T> class ArrayIterator {
+  private:
+    template <typename U>
+    friend std::ostream& operator<<(std::ostream& out, const ArrayIterator<U>& it);
+    T* pData;
+    Shape mShape;
+    uint32_t mIndices[CUDATOOLS_ARRAY_MAX_AXES] = {0};
+
+  public:
+    HD ArrayIterator(T* p, const Shape& shape) : pData(p), mShape(shape){};
+
+    /**
+     * Moves the iterator to the next value.
+     */
+    HD void next() {
+        bool carry = false;
+        uint32_t offset = 0;
+        for (uint32_t iAxis = mShape.axes() - 1; iAxis < mShape.axes(); --iAxis) {
+            if (mIndices[iAxis] == mShape.dim(iAxis) - 1) {
+                mIndices[iAxis] = 0;
+                offset += mShape.stride(iAxis) * (mShape.dim(iAxis) - 1);
+                carry = true;
+            } else {
+                pData += mShape.stride(iAxis);
+                mIndices[iAxis] += 1;
+                carry = false;
+            }
+
+            if (not carry) {
+                pData -= offset;
+                return;
+            }
+        }
+        pData += 1; // "Overflow" occured, so we reached end of array.
+    }
+
+    /**
+     * Moves the iterator to the previous value.
+     */
+    HD void prev() {
+        bool carry = false;
+        uint32_t offset = 0;
+        for (uint32_t iAxis = mShape.axes() - 1; iAxis < mShape.axes(); --iAxis) {
+            if (mIndices[iAxis] == 0) {
+                mIndices[iAxis] = mShape.dim(iAxis) - 1;
+                offset += mShape.stride(iAxis) * (mShape.dim(iAxis) - 1);
+                carry = true;
+            } else {
+                pData -= mShape.stride(iAxis);
+                mIndices[iAxis] += 1;
+                carry = false;
+            }
+            if (not carry) {
+                pData += offset;
+                return;
+            }
+        }
+        pData -= 1;
+    }
+
+    /**
+     * Moves the iterator a specified value away.
+     * \param amount the amount to advance by
+     */
+    HD void advance(const int32_t amount) {
+        if (amount < 0) {
+            for (uint32_t i = 0; i < std::abs(amount); ++i) {
+                prev();
+            }
+        } else {
+            for (uint32_t i = 0; i < std::abs(amount); ++i) {
+                next();
+            }
+        }
+    }
+
+    HD void operator++() { next(); }; /**< Prefix increment operator. */
+    HD void operator--() { prev(); }; /**< Prefix decrement operator. */
+
+    /**< Addition operator. */
+    HD ArrayIterator<T> operator+(const int32_t v) const {
+        ArrayIterator<T> it = *this;
+        it.advance(v);
+        return it;
+    };
+
+    /** Subtraction operator.*/
+    HD ArrayIterator<T> operator-(const int32_t v) const {
+        ArrayIterator<T> it = *this;
+        it.advance(-v);
+        return it;
+    };
+    HD void operator+=(const int32_t v) { advance(v); };
+    HD void operator-=(const int32_t v) { advance(-v); };
+
+    HD T& operator*() { return *pData; };             /**< Dereference operator. */
+    HD const T& operator*() const { return *pData; }; /**< Const dereference operator. */
+
+    /**
+     * Equals operator.
+     */
+    HD bool operator==(const ArrayIterator<T>& it) { return pData == it.pData; }
+
+    /**
+     * Not equals operator.
+     */
+    HD bool operator!=(const ArrayIterator<T>& it) { return pData != it.pData; }
+};
+
+template <typename T> std::ostream& operator<<(std::ostream& out, const ArrayIterator<T>& it) {
+    return out << it.pData;
+}
+
+template <typename T> class ArrayLoader {
+  private:
+    ArrayIterator<T> mIterator;
+    ArrayIterator<T> mIteratorEnd;
+
+  public:
+    HD ArrayLoader(const ArrayIterator<T>& it, const ArrayIterator<T>& it_end)
+        : mIterator(it), mIteratorEnd(it_end){};
+    HD ArrayLoader &operator,(const T value) {
+        CT_ERROR_IF(mIterator, ==, mIteratorEnd, "Cannot assign more values than Array size");
+        *mIterator = value;
+        ++mIterator;
+        return *this;
+    }
+};
+
+/**
+ * A container that holds a N-dimensional array, stored column major. To set the
+ * maximum N, there is a compiler macro CUDATOOLS_ARRAY_MAX_DIM whose default value is 4.
+ * It adapts to operations between host and device to ease memory management.
+ */
+template <typename T> class Array {
+  private:
+    template <typename U> friend std::ostream& operator<<(std::ostream&, const Array<U>&);
+
+    Shape mShape;
+    T* pHost = nullptr;
+    T* pDevice = nullptr;
+
+    bool mIsView = false;
+    bool mIsSlice = false;
+
+    uint32_t mEndOffset = 0;
+
+    HD void freeArrays() {
+#ifndef DEVICE
+        if (not mIsView) {
+            if (pDevice != nullptr) CudaTools::free(pDevice);
+            if (pHost != nullptr) delete[] pHost;
+        }
+#endif
+    };
+
+    HD void calcEnd() {
+        uint32_t offset = 0;
+        for (uint32_t i = 0; i < shape().axes(); ++i) {
+            offset += (shape().dim(i) - 1) * shape().stride(i);
+        }
+        mEndOffset = offset + 1;
+    };
+
+  public:
+    HD Array() = default;
+
+    /**
+     * Constructor for an Array that creates an allocates an array with
+     * the specified Shape. Construction in this format is disabled on the device.
+     * \brief Host only
+     * \param shape the shape of the array
+     * \param noDevice whether to initialize the array on the device
+     */
+    Array(const Shape& shape, const bool noDevice = false) : mShape(shape), mIsView(false) {
+        pHost = new T[shape.items()];
+        calcEnd();
+        if (noDevice) return;
+        pDevice = reinterpret_cast<T*>(CudaTools::malloc(shape.items() * sizeof(T)));
+    };
+
+    /**
+     * Constructor for an Array from an existing (preallocated) pointer.
+     * \param pointer the pointer to use
+     * \param shape the shape of the array
+     * \param noDevice whether to initialize the array on the device
+     */
+    HD Array(T* const pointer, const Shape& shape, const bool noDevice = false)
+        : mShape(shape), mIsView(true), mIsSlice(false) {
+        POINTER = pointer;
+        calcEnd();
+#ifndef DEVICE
+        if (noDevice) return;
+        pDevice = reinterpret_cast<T*>(CudaTools::malloc(shape.items() * sizeof(T)));
+#endif
+    };
+
+    /**
+     * Constructor for making a Array view from another Array,
+     * given an offset and shape.
+     * \param arr the original Array
+     * \param shape the shape of the new array
+     * \param offset the index where to start the a view of the array
+     */
+    HD Array(const Array& arr, const Shape& shape, const uint32_t offset = 0)
+        : mShape(shape), pHost(arr.pHost), pDevice(arr.pDevice), mIsView(true),
+          mIsSlice(arr.mIsSlice) {
+        calcEnd();
+        if (pHost != nullptr) pHost += offset;
+        if (pDevice != nullptr) pDevice += offset;
+    };
+
+    /**
+     * The copy-constructor for a Array. If this is not a view, a deep copy
+     * of the data will be performed on both host and device. On the device, it is always
+     * treated like a view.
+     */
+    HD Array(const Array& arr) : mShape(arr.mShape), mIsView(arr.mIsView), mIsSlice(arr.mIsSlice) {
+        calcEnd();
+        if (mIsView) { // If the other array was a view (and now this one), just assign.
+            pHost = arr.pHost;
+            pDevice = arr.pDevice;
+            return;
+        }
+
+        // Otherwise, we assume this is needs to own data.
+        pHost = new T[mShape.items()];
+        auto arr_it = arr.begin();
+        for (auto it = begin(); it != end(); ++it) {
+            *it = *arr_it;
+            ++arr_it;
+        }
+
+#ifndef DEVICE
+        if (arr.pDevice != nullptr) {
+            pDevice = (T*)CudaTools::malloc(mShape.items() * sizeof(T));
+        }
+#endif
+    };
+
+    /**
+     *  The move-constructor for a Array.
+     */
+    HD Array(Array&& arr)
+        : mShape(arr.mShape), pHost(arr.pHost), pDevice(arr.pDevice), mIsView(arr.mIsView),
+          mIsSlice(arr.mIsSlice) {
+        calcEnd();
+        // Make other object empty.
+        arr.pHost = nullptr;
+        arr.pDevice = nullptr;
+        arr.mIsView = true;
+    };
+
+    HD ~Array() { freeArrays(); };
+
+    /**
+     * The copy-assignment operator for a Array. If this is not a view,
+     * then the currently owned data will be freed, and a deep copy of the data will
+     * be performed on both host and device. On the device, it is always treated like a view.
+     */
+    HD Array& operator=(const Array& arr) {
+        if (this == &arr) return *this;
+
+        if (mIsView) { // If this array is a view, we assign data from the right-hand side.
+            auto arr_it = arr.begin();
+            for (auto it = begin(); it != end() and arr_it != arr.end(); ++it) {
+                *it = *arr_it;
+                ++arr_it;
+            }
+            return *this;
+        }
+
+        // Otherwise, it is implied to be object reassignment.
+        mShape = arr.mShape;
+        mIsView = arr.mIsView;
+        mIsSlice = arr.mIsSlice;
+        calcEnd();
+
+        // Regardless if the right-hand side is a view, we create a new copy.
+        // In case that the right-hand side is a view of this array, we
+        // allocate memory to copy first. Keep in mind that the right-hand side
+        // array will then become undefined.
+
+        // We can only do this on the host.
+#ifndef DEVICE
+        T* new_pDevice = nullptr;
+        if (pDevice != nullptr) {
+            new_pDevice = (T*)CudaTools::malloc(mShape.items() * sizeof(T));
+        }
+
+        T* new_pHost = new T[mShape.items()];
+        memcpy(new_pHost, arr.pHost, mShape.items() * sizeof(T));
+
+        freeArrays();
+        pHost = new_pHost;
+        pDevice = new_pDevice;
+#else
+        pHost = arr.pHost;
+        pDevice = arr.pDevice;
+#endif
+        return *this;
+    };
+
+    /**
+     * The move-assignment operator for a Array.
+     */
+    HD Array& operator=(Array&& arr) {
+        if (this == &arr) return *this;
+
+        if (mIsView) { // If this array is a view, we assign data from the right-hand side.
+            auto arr_it = arr.begin();
+            for (auto it = begin(); it != end() and arr_it != arr.end(); ++it) {
+                *it = *arr_it;
+                ++arr_it;
+            }
+            return *this;
+        }
+
+        CT_ERROR(arr.mIsView,
+                 "Cannot move-assign view to a non-view (owner). This would lead to undefined "
+                 "behavior.");
+
+        // Otherwise, it is implied to be object reassignment.
+        freeArrays();
+        mShape = arr.mShape;
+        pHost = arr.pHost;
+        pDevice = arr.pDevice;
+        mIsView = arr.mIsView;
+        mIsSlice = arr.mIsSlice;
+        calcEnd();
+
+        // Make other array empty.
+        arr.pHost = nullptr;
+        arr.pDevice = nullptr;
+        arr.mIsView = true;
+        return *this;
+    };
+
+    /**
+     * Used for indexing the Array.
+     * \param index index of the first dimension
+     */
+    HD Array operator[](const uint32_t index) const {
+        CT_ERROR_IF(index, >=, shape().dim(0), "Index exceeds axis size");
+        return Array(*this, shape().subshape(1), index * shape().stride(0));
+    };
+
+    /**
+     * Used for indexing the Array.
+     * \param indices a list of indices to index the Array
+     */
+    HD Array operator[](const std::initializer_list<uint32_t> indices) const {
+        CT_ERROR_IF(indices.size(), >, shape().axes(),
+                    "Number of indices cannot exceed number of axes");
+        auto it = indices.begin();
+        uint offset = 0;
+        for (uint32_t i = 0; i < indices.size(); ++i) {
+            uint32_t index = *it;
+            CT_ERROR_IF(index, >=, shape().dim(i), "Index exceeds axis size");
+            offset += index * shape().stride(i);
+            ++it;
+        }
+        return Array(*this, shape().subshape(indices.size()), offset);
+    };
+
+    HD ArrayLoader<T> operator<<(const T value) {
+        auto it = begin();
+        *it = value;
+        ++it;
+        return ArrayLoader<T>(it, end());
+    };
+
+    HD T operator=(const T& value) { return POINTER[0] = value; };
+    HD operator T&() { return POINTER[0]; };
+    HD operator const T&() const { return POINTER[0]; };
+
+    /**
+     * Used to create slices of the Array.
+     * \param slices a list of slices to slice the Array
+     */
+    HD Array slice(const std::initializer_list<Slice> slices) const {
+        CT_ERROR_IF(slices.size(), >, shape().axes(),
+                    "Number of slices cannot exceed number of axes");
+
+        uint offset = 0;
+        Shape new_shape = mShape;
+        auto it = slices.begin();
+        for (uint32_t i = 0; i < slices.size(); ++i) {
+            uint32_t from_index = it->first;
+            uint32_t to_index = it->second;
+            CT_ERROR_IF(from_index, >, to_index,
+                        "Slice start cannot be greater than than slice end");
+            CT_ERROR_IF(from_index, >=, shape().dim(i), "Slice start exceeds axis size");
+            CT_ERROR_IF(to_index - 1, >=, shape().dim(i), "Slice end exceeds axis size");
+
+            offset += from_index * shape().stride(i);
+            new_shape.mAxisDim[i] = to_index - from_index;
+            ++it;
+        }
+        new_shape.mItems = 1;
+        for (uint32_t i = 0; i < shape().axes(); ++i) {
+            new_shape.mItems *= new_shape.dim(i);
+        }
+
+        Array<T> arr(*this, new_shape, offset);
+        arr.mIsSlice = true;
+        return arr;
+    };
+
+    /**
+     * Returns this Array with a different Shape. Its self assigning version is reshape.
+     * If this Array is a slice of another, then it will perform a deep copy, and return
+     * a new non-view array.
+     */
+    HD Array reshaped(const Shape& new_shape) const {
+        CT_ERROR_IF(shape().items(), !=, new_shape.items(),
+                    "New shape cannot have a different number of terms");
+        CT_ERROR(mIsSlice, "Cannot reshape slice, a new array must be made. (Try copy first)")
+        Array<T> arr = view();
+        arr.mShape = new_shape;
+        return arr;
+    };
+
+    HD void reshape(const Shape& new_shape) {
+        CT_ERROR_IF(shape().items(), !=, new_shape.items(),
+                    "New shape cannot have a different number of terms");
+        CT_ERROR(mIsSlice, "Cannot reshape slice, a new array must be made. (Try copy first)")
+        mShape = new_shape;
+    };
+
+    /**
+     * Gets a view that is has at least two dimensions. Useful for promoting
+     * single vectors to their 2D counterparts.
+     */
+    HD Array atLeast2D() const {
+        return (shape().axes() == 1) ? reshaped({shape().length(), 1}) : view();
+    };
+
+    /**
+     * Reshapes this array, making it at least 2D. Useful for promoting
+     * single vectors to their 2D counterparts.
+     */
+    HD void asAtLeast2D() {
+        if (shape().axes() == 1) reshape({shape().length(), 1});
+    };
+
+    /**
+     * Returns a view of this Array that has been flattened into one dimension.
+     */
+    HD Array flattened() const { return reshaped({mShape.mItems}); };
+
+    /**
+     * Flattens this Array into one dimension.
+     */
+    HD void flatten() { reshape({mShape.mItems}); };
+
+#ifdef CUDATOOLS_USE_EIGEN
+    /**
+     * Returns the Eigen::Map of this Array.
+     */
+    EigenAdaptConst<ComplexConversion<T>> eigenMap() const {
+        uint32_t total_dim = mShape.mAxes;
+        CT_ERROR(mIsSlice, "Mapping to an Eigen array cannot occur on slices")
+        CT_ERROR_IF(total_dim, !=, 2,
+                    "Mapping to an Eigen array can only occur on two-dimensional arrays");
+        return EigenAdaptConst<ComplexConversion<T>>((ComplexConversion<T>*)POINTER, mShape.rows(),
+                                                     mShape.cols());
+    };
+#endif
+
+    /**
+     * Gets the Shape of the Array.
+     */
+    HD Shape shape() const { return mShape; };
+
+    /**
+     * Gets the pointer to this array, depending on host or device.
+     */
+    HD ComplexConversion<T>* data() const { return (ComplexConversion<T>*)POINTER; };
+
+    /**
+     * Returns the device pointer regardless of host or device.
+     */
+    HD T* dataDevice() const { return pDevice; };
+
+    HD bool isView() const { return mIsView; };   /**< Gets whether this Array is a view. */
+    HD bool isSlice() const { return mIsSlice; }; /**< Gets whether this Array is a slice. */
+
+    /**
+     * Gets a view of this Array.
+     */
+    HD Array view() const { return Array(*this, mShape); }
+
+    /**
+     * Copies this Array and returns a new Array with the same memory.
+     */
+    Array copy() const {
+        Array<T> arr(mShape, (pDevice == nullptr));
+
+        auto arr_it = arr.begin();
+        for (auto it = begin(); it != end(); ++it) {
+            *arr_it = *it;
+            ++arr_it;
+        }
+#ifndef DEVICE
+        if (pDevice != nullptr) {
+            CudaTools::copy(pDevice, arr.dataDevice(), mShape.items() * sizeof(T)).wait();
+        }
+#endif
+        return arr;
+    };
+
+    /**
+     * Gets the iterator to the beginning of this Array.
+     */
+    HD ArrayIterator<T> begin() const { return ArrayIterator<T>(POINTER, mShape); };
+
+    /**
+     * Gets the iterator to the end of this Array.
+     */
+    HD ArrayIterator<T> end() const { return ArrayIterator<T>(POINTER + mEndOffset, mShape); };
+
+    /**
+     * Sets the values of the entire Array to a constant. This is restricted to numerical types.
+     */
+    HD void setConstant(const T value) const {
+        static_assert(is_host_num<T>, "Function only available on host-compatible numeric types.");
+        for (auto it = begin(); it != end(); ++it) {
+            *it = value;
+        }
+    };
+
+    /**
+     * Sets the Array values with uniform random values in a specified range. This is restricted to
+     * numerical types.
+     * \brief Host only
+     */
+    void setRandom(const T min, const T max) const {
+        static_assert(is_host_num<T>, "Function only available on host-compatible numeric types.");
+        if constexpr (is_complex<T>) {
+            CT_ERROR_IF(max.real(), <, min.real(),
+                        "Upper bound of range cannot be larger than lower bound");
+            CT_ERROR_IF(max.imag(), <, min.imag(),
+                        "Upper bound of range cannot be larger than lower bound");
+        } else {
+            CT_ERROR_IF(max, <, min, "Upper bound of range cannot be larger than lower bound");
+        }
+        std::random_device rd;
+        std::mt19937 mt(rd());
+        if constexpr (is_int<T>) {
+            std::uniform_int_distribution<T> dist(min, max);
+            for (auto it = begin(); it != end(); ++it) {
+                *it = dist(mt);
+            }
+        } else if constexpr (is_float<T>) {
+            std::uniform_real_distribution<T> dist(min, max);
+            for (auto it = begin(); it != end(); ++it) {
+                *it = dist(mt);
+            }
+        } else if constexpr (is_complex<T>) {
+            std::uniform_real_distribution<ComplexUnderlying<T>> distr(min.real(), max.real());
+            std::uniform_real_distribution<ComplexUnderlying<T>> disti(min.imag(), max.imag());
+            for (auto it = begin(); it != end(); ++it) {
+                *it = T(distr(mt), disti(mt));
+            }
+        }
+    };
+
+    /**
+     * Sets the Array values to start from a value and increment by a specified step. This is
+     * restricted to numerical types.
+     */
+    HD void setRange(T min, const T step = 1) const {
+        static_assert(is_host_num<T>, "Function only available on host-compatible numeric types.");
+        for (auto it = begin(); it != end(); ++it) {
+            *it = min;
+            min += step;
+        }
+    }
+    /**
+     * Sets the Array values to be evenly spaced numbers over a given interval. This is restricted
+     * to floating point types.
+     */
+    HD void setLinspace(const T min, const T max) const {
+        static_assert(is_float<T>, "Function only available on numeric floating types.");
+        CT_ERROR_IF(max, <, min, "Upper bound of range cannot be larger than lower bound");
+        T i = 0;
+        T d = max - min;
+        T items = (T)(shape().items() - 1);
+        for (auto it = begin(); it != end(); ++it) {
+            *it = min + d * (i / items);
+            i += 1;
+        }
+    };
+
+    /**
+     * Returns array of given shape with constant values. This is restricted to numerical types.
+     * \brief Host only
+     */
+    static Array constant(const Shape& shape, const T value) {
+        static_assert(is_host_num<T>, "Function only available on host-compatible numeric types.");
+        Array<T> arr(shape);
+        arr.setConstant(value);
+        return arr;
+    };
+
+    /**
+     * Returns array of given shape with random values in given interval. This is restricted to
+     * numerical types.
+     * \brief Host only
+     */
+    static Array random(const Shape& shape, const T min, const T max) {
+        static_assert(is_host_num<T>, "Function only available on host-compatible numeric types.");
+        Array<T> arr(shape);
+        arr.setRandom(min, max);
+        return arr;
+    };
+
+    /**
+     * Returns evenly spaced values within a given interval. This is restricted to numerical types.
+     * \brief Host only
+     */
+    static Array range(const T min, const T max, const T step = 1) {
+        static_assert(is_host_num<T>, "Function only available on host-compatible numeric types.");
+        CT_ERROR_IF(max, <, min, "Upper bound of range cannot be larger than lower bound");
+        Array<T> arr({(uint32_t)((max - min) / step)});
+        arr.setRange(min, step);
+        return arr;
+    }
+
+    /**
+     * Returns evenly spaced values within a given interval. This is restricted to floating point
+     * types.
+     * \brief Host only
+     */
+    static Array linspace(const T min, const T max, const uint32_t size) {
+        static_assert(is_float<T>, "Function only available on numeric floating types.");
+        Array<T> arr({size});
+        arr.setLinspace(min, max);
+        return arr;
+    }
+
+    /**
+     * Transposes the internal data and returns the corresponding new Array.
+     * Its self assigning version is transpose. This is restricted to numerical types.
+     * \brief Host only
+     */
+
+#ifdef CUDATOOLS_USE_EIGEN
+    Array transposed() const {
+        static_assert(is_host_num<T>, "Function only available on host-compatible numeric types.");
+        CT_ERROR_IF(shape().axes(), !=, 2, "Tranpose can only occur on two-dimensional arrays");
+        Array<T> new_arr({mShape.rows(), mShape.cols()});
+        new_arr.eigenMap() = this->eigenMap().transpose().eval();
+        return new_arr;
+    };
+
+    /**
+     * Transposes the intenal data. Its self assigning version is transpose.
+     * This is restricted to numerical types.
+     * \brief Host only
+     */
+    void transpose() {
+        static_assert(is_host_num<T>, "Function only available on host-compatible numeric types.");
+        CT_ERROR_IF(shape().axes(), !=, 2, "Tranpose can only occur on two-dimensional arrays");
+        Array<T> new_arr(*this, {mShape.cols(), mShape.rows()});
+        new_arr.eigenMap() = this->eigenMap().transpose().eval();
+        mShape = Shape({mShape.cols(), mShape.rows()});
+    };
+
+    void inverse() const {
+        static_assert(is_float<T>, "Function only available on floating numeric types.");
+        CT_ERROR_IF(shape().axes(), !=, 2, "Inverse can only occur on two-dimensional arrays");
+        CT_ERROR_IF(shape().rows(), !=, shape().cols(),
+                    "Inverse can only occur on square matrices");
+        Array<T> inv(shape());
+        inv.eigenMap() = this->eigenMap().inverse();
+    };
+#endif
+
+    /**
+     * Pins the memory (page locks) for faster memory transfer in concurrent
+     * transfers.
+     * \brief Host only
+     */
+    void pinMemory() const { CudaTools::pin(pHost, mShape.items() * sizeof(T)); };
+
+    /**
+     * Updates the host copy by copying the device data back to the host.
+     * \brief Host only
+     */
+    StreamID updateHost(const StreamID& stream = DEF_MEM_STREAM) const {
+        CT_ERROR(mIsSlice, "Cannot update host copy on a slice");
+        return CudaTools::copy(pDevice, pHost, mShape.items() * sizeof(T), stream);
+    };
+
+    /**
+     * Updates the device copy by copying the host data to the device.
+     * \brief Host only
+     */
+    StreamID updateDevice(const StreamID& stream = DEF_MEM_STREAM) const {
+        CT_ERROR(mIsSlice, "Cannot update device copy on a slice");
+        return CudaTools::copy(pHost, pDevice, mShape.items() * sizeof(T), stream);
+    };
+
+#ifdef CUDATOOLS_USE_PYTHON
+    /**
+     * Returns a py::array for making an Array available as a Python numpy array.
+     */
+    py::array pyArray() const {
+        std::vector<py::ssize_t> dims, strides;
+        for (uint iAxis = 0; iAxis < mShape.axes(); ++iAxis) {
+            dims.push_back(static_cast<py::ssize_t>(mShape.dim(iAxis)));
+            strides.push_back(sizeof(T) * static_cast<py::ssize_t>(mShape.stride(iAxis)));
+        }
+        return py::array_t<T, py::array::f_style>(
+            py::buffer_info((void*)pHost, sizeof(T), py::format_descriptor<T>::format(),
+                            static_cast<py::ssize_t>(mShape.axes()), dims, strides));
+    };
+#endif
+};
+
+template <typename T>
+void printAxis(std::ostream& out, const Array<T>& arr, const uint32_t axis, size_t width) {
+    std::string space = std::string(2 * axis, ' ');
+    if (arr.shape().axes() == 1) {
+        out << "[";
+        for (uint32_t i = 0; i < arr.shape().items(); ++i) {
+            if constexpr (std::is_floating_point<T>::value) {
+                out << std::scientific << std::setprecision(6);
+            }
+            if (width == 0) {
+                out << ((i == 0) ? "" : " ");
+            } else {
+                out << std::setw((i == 0) ? width - 1 : width);
+            }
+            out << static_cast<T>(arr[i]) << ((i == arr.shape().items() - 1) ? "]" : ",");
+        }
+    } else if (arr.shape().axes() == 2) {
+        for (uint32_t i = 0; i < arr.shape().dim(0); ++i) {
+            out << space << ((i == 0) ? "[" : " ");
+            printAxis(out, arr[i], axis + 1, width);
+            out << ((i == arr.shape().dim(0) - 1) ? "]" : ",\n");
+        }
+    } else {
+        out << space << "[\n";
+        for (uint32_t i = 0; i < arr.shape().dim(0); ++i) {
+            printAxis(out, arr[i], axis + 1, width);
+            out << ((i == arr.shape().dim(0) - 1) ? "\n" : ",\n\n");
+        }
+        out << space << "]";
+    }
+}
+
+template <typename T> std::ostream& operator<<(std::ostream& out, const Array<T>& arr) {
+    size_t width = 0;
+    if constexpr (is_int<T>) {
+        T max_val = 0;
+        bool negative = false;
+        for (auto it = arr.begin(); it != arr.end(); ++it) {
+            T val = *it;
+            if constexpr (not std::is_unsigned<T>::value) {
+                if (*it < 0) {
+                    negative = true;
+                    val *= -1;
+                }
+            }
+            max_val = (val > max_val) ? val : max_val;
+        }
+        width = std::to_string(max_val).size() + 1;
+        width += (negative) ? 1 : 0;
+    } else if constexpr (is_float<T>) {
+        T max_val = 0;
+        bool negative = false;
+        for (auto it = arr.begin(); it != arr.end(); ++it) {
+            if (*it < 0) negative = true;
+            int exp = 0;
+            frexp(*it, &exp);
+            max_val = (exp > max_val) ? exp : max_val;
+        }
+        width = std::to_string(max_val).size() + 5;
+        width += (negative) ? 1 : 0;
+    }
+
+    printAxis<T>(out, arr, 0, (arr.shape().axes() == 1) ? 0 : width);
+    return out;
+}
+
+}; // namespace CudaTools
+
+#endif // ARRAY_H

HybridMesher/libraries/CudaTools/include/BLAS.h

@@ -0,0 +1,627 @@
+#ifndef CUDATOOLS_BLAS_H
+#define CUDATOOLS_BLAS_H
+
+#ifndef CUDATOOLS_USE_EIGEN
+#error "Cannot use CudaTools BLAS.h header without Eigen."
+#endif
+
+#include "Array.h"
+#include "Core.h"
+#include "Macros.h"
+#include "Types.h"
+
+using namespace CudaTools::Types;
+
+namespace CudaTools {
+namespace BLAS {
+
+struct BatchInfo {
+    uint32_t strideA, strideB, strideC;
+    uint32_t size;
+};
+
+struct Check {
+    template <typename T>
+    static void isAtLeast2D(const Array<T>& arr, const std::string& name = "Array") {
+        CT_ERROR_IF(arr.shape().axes(), <, 2, (name + " needs to be at least 2D").c_str());
+    };
+
+    template <typename T>
+    static void isSquare(const Array<T>& arr, const std::string& name = "Array") {
+        isAtLeast2D(arr, name);
+        CT_ERROR_IF(arr.shape().rows(), !=, arr.shape().cols(), (name + " is not square").c_str())
+    };
+
+    template <typename T, typename U, typename V>
+    static void isValidMatmul(const Array<T>& A, const Array<U>& B, const Array<V>& C,
+                              const std::string& nameA = "A", const std::string& nameB = "B",
+                              const std::string nameC = "C") {
+        isAtLeast2D(A, nameA);
+        isAtLeast2D(B, nameB);
+        isAtLeast2D(C, nameB);
+        CT_ERROR_IF(A.shape().cols(), !=, B.shape().rows(),
+                    (nameA + nameB + " is not a valid matrix multiplication").c_str());
+
+        Shape ABshape({A.shape().rows(), B.shape().cols()});
+        Shape Cshape({C.shape().rows(), C.shape().cols()});
+
+        CT_ERROR_IF(
+            ABshape, !=, Cshape,
+            ("The shape of " + nameA + nameB + " does not match the shape of " + nameC).c_str());
+    };
+
+    template <typename T> static uint32_t getUpperItems(const Array<T>& arr) {
+        uint32_t upperItems = 1;
+        for (uint32_t iAxis = 0; iAxis < arr.shape().axes() - 2; ++iAxis) {
+            upperItems *= arr.shape().dim(iAxis);
+        }
+        return upperItems;
+    };
+
+    template <typename T, typename U>
+    static void matchUpperShape(const Array<T>& A, const Array<U>& B,
+                                const std::string& nameA = "A", const std::string& nameB = "B") {
+        CT_ERROR_IF(A.shape().axes(), !=, B.shape().axes(),
+                    (nameA + " and " + nameB + " shapes do not match for broadcasting").c_str());
+        for (uint32_t iAxis = 0; iAxis < A.shape().axes() - 2; ++iAxis) {
+            uint32_t Adim = A.shape().dim(iAxis);
+            uint32_t Bdim = B.shape().dim(iAxis);
+            CT_ERROR_IF(
+                Adim, !=, Bdim,
+                (nameA + " and " + nameB + " shapes do not match for broadcasting").c_str());
+        }
+    };
+
+    template <typename T, typename U, typename V>
+    static BatchInfo isBroadcastable(const Array<T>& A, const Array<U>& B, const Array<V>& C,
+                                     const std::string& nameA = "A", const std::string& nameB = "B",
+                                     const std::string nameC = "C") {
+        isValidMatmul(A, B, C, nameA, nameB, nameC);
+        uint32_t itemsA = getUpperItems(A);
+        uint32_t itemsB = getUpperItems(B);
+        uint32_t itemsC = getUpperItems(C);
+
+        uint32_t Asize = A.shape().rows() * A.shape().cols();
+        uint32_t Bsize = B.shape().rows() * B.shape().cols();
+        uint32_t Csize = C.shape().rows() * C.shape().cols();
+
+        if (itemsA == itemsB) {
+            CT_ERROR_IF(itemsA, !=, itemsC,
+                        ("Incorrect dimensions to broadcast to output " + nameC).c_str());
+            matchUpperShape(A, B, nameA, nameB);
+            matchUpperShape(A, C, nameA, nameC);
+            return BatchInfo{Asize, Bsize, Csize, itemsC};
+        } else if (itemsA > itemsB) {
+            CT_ERROR_IF(
+                itemsB, !=, 1,
+                ("Cannot broadcast operation to " + nameB + " with non-matching " + nameA).c_str());
+            CT_ERROR_IF(itemsA, !=, itemsC,
+                        ("Incorrect dimensions to broadcast to output " + nameC).c_str());
+            matchUpperShape(A, C, nameA, nameC);
+            return BatchInfo{Asize, 0, Csize, itemsC};
+        } else {
+            CT_ERROR_IF(
+                itemsA, !=, 1,
+                ("Cannot broadcast operation to " + nameA + " with non-matching " + nameB).c_str());
+            CT_ERROR_IF(itemsA, !=, itemsC,
+                        ("Incorrect dimensions to broadcast to output " + nameC).c_str());
+            matchUpperShape(B, C, nameB, nameC);
+            return BatchInfo{0, Bsize, Csize, itemsC};
+        }
+    };
+};
+
+/**
+ * Represents a Batch of Arrays with the same shape. Mainly used for cuBLAS functions.
+ */
+template <typename T> class Batch {
+  protected:
+    Array<T*> mBatch;
+    Shape mShape;
+
+    uint32_t mCount = 0;
+    uint32_t mBatchSize;
+
+  public:
+    Batch() = delete;
+
+    /**
+     * Constructs a batch from a given size.
+     */
+    Batch(const uint32_t size) : mBatchSize(size){};
+
+    /**
+     * Constructs a batch from a non-view Array.
+     */
+    Batch(const Array<T>& arr) {
+        CT_ERROR(arr.isView(), "Array cannot be a view");
+        mShape = Shape({arr.shape().rows(), arr.shape().cols()});
+        mBatchSize = mCount = Check::getUpperItems(arr);
+
+        mBatch = Array<T*>({mBatchSize});
+
+        Array<T> batch = arr.reshaped({mBatchSize, mShape.rows(), mShape.cols()});
+        for (uint32_t i = 0; i < mBatchSize; ++i) {
+#ifdef CUDACC
+            mBatch[i] = batch[i].dataDevice();
+#else
+            mBatch[i] = batch[i].data();
+#endif
+        }
+
+        mBatch.updateDevice().wait();
+    };
+
+    /**
+     * Adds a matrix to the batch. Array must be a view.
+     */
+    void add(const Array<T>& arr) {
+        CT_ERROR(not arr.isView(), "Cannot add non-view Arrays");
+        CT_ERROR_IF(mCount, ==, mBatchSize, "Batch is full, cannot add more arrays");
+#ifdef CUDACC
+        mBatch[mCount] = arr.dataDevice();
+#else
+        mBatch[mCount] = arr.data();
+#endif
+        if (mCount == 0) {
+            mShape = arr.shape();
+            mBatchSize = mCount = Check::getUpperItems(arr);
+        } else {
+            CT_ERROR_IF(arr.shape(), !=, mShape, "Cannot add matrix of different shape to batch");
+        }
+        ++mCount;
+
+        if (mCount == mBatchSize) {
+            mBatch.updateDevice().wait();
+        }
+    };
+
+    /**
+     * Indexing operator which returns a view of the Array in the Batch at the given index.
+     */
+    Array<T> operator[](const uint32_t index) const {
+        CT_ERROR_IF(index, >=, mBatchSize, "Index exceeds batch size");
+        return Array<T>(mBatch[index], {mShape.rows(), mShape.cols()});
+    };
+
+    /**
+     * Returns the batch Array of pointers.
+     */
+    Array<T*> batch() const { return mBatch.view(); };
+    Shape shape() const { return mShape; } /**< Gets the shape of the matrices in the batch. */
+    uint32_t size() const { return mBatchSize; }        /**< Gets the batch size.*/
+    bool full() const { return mBatchSize == mCount; }; /**< Gets if the batch is full. */
+};
+
+////////////////
+// cuBLAS API //
+////////////////
+
+template <typename T> struct CudaComplexConversion_S { typedef T type; };
+#ifdef CUDACC
+template <> struct CudaComplexConversion_S<complex64> { typedef cuComplex type; };
+template <> struct CudaComplexConversion_S<complex128> { typedef cuDoubleComplex type; };
+#else
+
+#endif
+
+template <typename T> using CudaComplexConversion = typename CudaComplexConversion_S<T>::type;
+
+template <typename T> struct CublasTypeLetter_S { char letter; };
+template <> struct CublasTypeLetter_S<real32> { char letter = 'S'; };
+template <> struct CublasTypeLetter_S<real64> { char letter = 'D'; };
+template <> struct CublasTypeLetter_S<complex64> { char letter = 'C'; };
+template <> struct CublasTypeLetter_S<complex128> { char letter = 'Z'; };
+#ifdef CUDACC
+template <> struct CublasTypeLetter_S<real16> { char letter = 'H'; };
+#endif
+
+template <typename T> char CublasTypeLetter = CublasTypeLetter_S<T>::letter;
+
+// Shorthands to reduce clutter.
+
+#define CAST(var) reinterpret_cast<CudaComplexConversion<T>*>(var)
+#define DCAST(var) reinterpret_cast<CudaComplexConversion<T>**>(var)
+
+#define cublas(T, func) cublas##CublasTypeLetter<T>##func
+
+template <typename T, typename F1, typename F2, typename F3, typename F4, typename... Args>
+constexpr void invoke(F1 f1, F2 f2, F3 f3, F4 f4, Args&&... args) {
+    if constexpr (std::is_same<T, real32>::value) {
+        CUBLAS_CHECK(f1(args...));
+    } else if constexpr (std::is_same<T, real64>::value) {
+        CUBLAS_CHECK(f2(args...));
+    } else if constexpr (std::is_same<T, complex64>::value) {
+        CUBLAS_CHECK(f3(args...));
+    } else if constexpr (std::is_same<T, complex128>::value) {
+        CUBLAS_CHECK(f4(args...));
+    } else {
+        CT_ERROR(true, "This BLAS function is not callable with that type");
+    }
+}
+
+// If someone can think of a better solution, please tell me.
+template <typename T, typename F1, typename F2, typename F3, typename F4, typename F5,
+          typename... Args>
+constexpr void invoke5(F1 f1, F2 f2, F3 f3, F4 f4, F5 f5, Args&&... args) {
+    if constexpr (std::is_same<T, real32>::value) {
+        CUBLAS_CHECK(f1(args...));
+    } else if constexpr (std::is_same<T, real64>::value) {
+        CUBLAS_CHECK(f2(args...));
+    } else if constexpr (std::is_same<T, complex64>::value) {
+        CUBLAS_CHECK(f3(args...));
+    } else if constexpr (std::is_same<T, complex128>::value) {
+        CUBLAS_CHECK(f4(args...));
+    } else if constexpr (std::is_same<T, real16>::value) {
+        CUBLAS_CHECK(f5(args...));
+    } else {
+        CT_ERROR(true, "This BLAS function is not callable with that type");
+    }
+}
+
+/**
+ * Computes the matrix-vector product: \f$ y = \alpha Ax + \beta y \f$. It will automatically
+ * broadcast the operation if applicable.
+ */
+template <typename T>
+StreamID GEMV(const T alpha, const Array<T>& A, const Array<T>& x, const T beta, const Array<T>& y,
+              const StreamID& stream = DEF_CUBLAS_STREAM) {
+
+    BatchInfo bi = Check::isBroadcastable(A, x, y, "A", "x", "y");
+    CT_ERROR_IF(x.shape().cols(), !=, 1, "x must be a column vector");
+    CT_ERROR_IF(y.shape().cols(), !=, 1, "x must be a column vector");
+
+    uint32_t rows = A.shape().rows();
+    uint32_t cols = A.shape().cols();
+    T a = alpha, b = beta;
+#ifdef CUDACC
+    CUBLAS_CHECK(cublasSetStream(Manager::get()->cublasHandle(), Manager::get()->stream(stream)));
+    if (bi.size == 1) {
+        invoke<T>(cublasSgemv, cublasDgemv, cublasCgemv, cublasZgemv,
+                  Manager::get()->cublasHandle(), CUBLAS_OP_N, rows, cols, CAST(&a),
+                  CAST(A.dataDevice()), rows, CAST(x.dataDevice()), 1, CAST(&b),
+                  CAST(y.dataDevice()), 1);
+    } else { // Greater than 2, so broadcast.
+        invoke<T>(cublasSgemvStridedBatched, cublasDgemvStridedBatched, cublasCgemvStridedBatched,
+                  cublasZgemvStridedBatched, Manager::get()->cublasHandle(), CUBLAS_OP_N, rows,
+                  cols, CAST(&a), CAST(A.dataDevice()), rows, bi.strideA, CAST(x.dataDevice()), 1,
+                  bi.strideB, CAST(&b), CAST(y.dataDevice()), 1, bi.strideC, bi.size);
+    }
+
+#else
+    if (bi.size == 1) {
+        y.eigenMap() = a * (A.eigenMap() * x.eigenMap()) + b * y.eigenMap();
+    } else { // Greater than 2, so broadcast.
+#pragma omp parallel for
+        for (uint32_t i = 0; i < bi.size; ++i) {
+            auto Ai = Array<T>(A, {rows, cols}, i * bi.strideA).eigenMap();
+            auto xi = Array<T>(x, {cols, 1}, i * bi.strideB).eigenMap();
+            auto yi = Array<T>(y, {rows, 1}, i * bi.strideC).eigenMap();
+            yi = a * (Ai * xi) + b * yi;
+        }
+    }
+#endif
+    return StreamID{stream};
+}
+
+/**
+ * Computes the matrix-matrix product: \f$ C = \alpha AB + \beta C \f$. It will automatically
+ * broadcast the operation if applicable.
+ */
+template <typename T>
+StreamID GEMM(const T alpha, const Array<T>& A, const Array<T>& B, const T beta, const Array<T>& C,
+              const StreamID& stream = DEF_CUBLAS_STREAM) {
+
+    BatchInfo bi = Check::isBroadcastable(A, B, C, "A", "B", "C");
+    // A is m x k, B is k x n.
+    uint32_t m = A.shape().rows();
+    uint32_t k = A.shape().cols();
+    uint32_t n = B.shape().cols();
+
+    T a = alpha, b = beta;
+#ifdef CUDACC
+    CUBLAS_CHECK(cublasSetStream(Manager::get()->cublasHandle(), Manager::get()->stream(stream)));
+
+    if (bi.size == 1) {
+        invoke5<T>(cublasSgemm, cublasDgemm, cublasCgemm, cublasZgemm, cublasHgemm,
+                   Manager::get()->cublasHandle(), CUBLAS_OP_N, CUBLAS_OP_N, m, n, k, CAST(&a),
+                   CAST(A.dataDevice()), m, CAST(B.dataDevice()), k, CAST(&b), CAST(C.dataDevice()),
+                   m);
+
+    } else { // Greater than 2, so broadcast.
+        invoke5<T>(cublasSgemmStridedBatched, cublasDgemmStridedBatched, cublasCgemmStridedBatched,
+                   cublasZgemmStridedBatched, cublasHgemmStridedBatched,
+                   Manager::get()->cublasHandle(), CUBLAS_OP_N, CUBLAS_OP_N, m, n, k, CAST(&a),
+                   CAST(A.dataDevice()), m, bi.strideA, CAST(B.dataDevice()), k, bi.strideB,
+                   CAST(&b), CAST(C.dataDevice()), m, bi.strideC, bi.size);
+    }
+
+#else
+    if (bi.size == 1) {
+        C.eigenMap() = a * (A.eigenMap() * B.eigenMap()) + b * C.eigenMap();
+    } else { // Greater than 2, so broadcast.
+#pragma omp parallel for
+        for (uint32_t i = 0; i < bi.size; ++i) {
+            auto Ai = Array<T>(A, {m, k}, i * bi.strideA).eigenMap();
+            auto Bi = Array<T>(B, {k, n}, i * bi.strideB).eigenMap();
+            auto Ci = Array<T>(C, {m, n}, i * bi.strideC).eigenMap();
+            Ci = a * (Ai * Bi) + b * Ci;
+        }
+    }
+#endif
+    return StreamID{stream};
+}
+
+/**
+ * Computes the diagonal matrix multiplication: \f$ C = A\mathrm{diag}(X) \f$, or \f$ C =
+ * \mathrm{diag}(X)A \f$ if left = true.
+ */
+template <typename T>
+StreamID DGMM(const Array<T>& A, const Array<T>& X, const Array<T>& C, const bool left = false,
+              const StreamID& stream = DEF_CUBLAS_STREAM) {
+    CT_ERROR_IF(X.shape().cols(), !=, 1, "'x' must be a column vector.");
+    if (left) {
+        CT_ERROR_IF(A.shape().rows(), !=, X.shape().rows(),
+                    "Rows of 'A' and length of 'x' need to match.");
+    } else {
+        CT_ERROR_IF(A.shape().cols(), !=, X.shape().rows(),
+                    "Columns of 'A' and length of 'x' need to match.");
+    }
+    CT_ERROR_IF(A.shape().rows(), !=, C.shape().rows(),
+                "Rows of 'A' and rows() of 'C' need to  match.");
+    CT_ERROR_IF(A.shape().cols(), !=, C.shape().cols(),
+                "Rows of 'A' and columns of 'C' need to match.");
+
+#ifdef CUDACC
+    uint32_t m = C.shape().rows();
+    uint32_t n = C.shape().cols();
+    auto mode = (left) ? CUBLAS_SIDE_LEFT : CUBLAS_SIDE_RIGHT;
+    CUBLAS_CHECK(cublasSetStream(Manager::get()->cublasHandle(), Manager::get()->stream(stream)));
+    invoke<T>(cublasSdgmm, cublasDdgmm, cublasCdgmm, cublasZdgmm, Manager::get()->cublasHandle(), m,
+              n, CAST(A.dataDevice()), A.shape().rows(), CAST(X.dataDevice()), 1,
+              CAST(C.dataDevice()), m);
+#else
+    if (left) {
+        C.eigenMap() = X.eigenMap().asDiagonal() * A.eigenMap();
+    } else {
+        C.eigenMap() = A.eigenMap() * X.eigenMap().asDiagonal();
+    }
+#endif
+    return StreamID{stream};
+}
+
+//////////////////////////////
+// PLUArray Related Objects //
+//////////////////////////////
+
+///////////////////////////
+// PartialPivLU Wrapper  //
+///////////////////////////
+
+// This class is just a workaround to use Eigen's internals directly.
+template <typename T> class PartialPivLU;
+namespace internal {
+template <typename T> static Array<T> empty({1, 1});
+template <typename T> static EigenMapMat<T> empty_map = empty<T>.eigenMap();
+}; // namespace internal
+
+template <typename T, std::enable_if_t<is_float<T> or is_complex<T>, bool> = true> class PLUArray;
+// This is a wrapper class for Eigen's class so we have more controlled access to
+// the underlying data.
+template <typename T> class PartialPivLU : public Eigen::PartialPivLU<Eigen::Ref<EigenMat<T>>> {
+  private:
+    using Base = Eigen::PartialPivLU<Eigen::Ref<EigenMat<T>>>;
+    template <typename U, std::enable_if_t<is_float<U> or is_complex<U>, bool>>
+    friend class PLUArray;
+
+    EigenMapMat<T> mMapLU;
+    EigenMapMat<int32_t> mMapPivots;
+
+  public:
+    PartialPivLU()
+        : Base(internal::empty_map<T>), mMapLU(internal::empty_map<T>),
+          mMapPivots(internal::empty_map<int32_t>){};
+
+    void make(const Array<T>& lu, const Array<int32_t>& pivots) {
+
+        new (&mMapLU) EigenMapMat<T>(lu.eigenMap());
+        new (&mMapPivots) EigenMapMat<int32_t>(pivots.atLeast2D().eigenMap());
+
+        new (&this->m_lu) decltype(Base::m_lu)(mMapLU.derived());
+        new (&this->m_p) decltype(Base::m_p)(mMapPivots.derived());
+
+        // new (&this->m_rowsTranspositions) decltype(Base::m_rowsTranspositions)(
+        //     mMapPivots.derived());
+
+        this->m_l1_norm = 0;
+        this->m_det_p = 0;
+        this->m_isInitialized = true;
+    };
+};
+
+namespace internal {
+// We only create one and copy-construct to avoid the re-initialization.
+template <typename T> static PartialPivLU<T> BlankPPLU = PartialPivLU<T>();
+}; // namespace internal
+
+/**
+ * Class for storing the PLU decomposition an Array. This is restricted to floating point types.
+ */
+template <typename T, std::enable_if_t<is_float<T> or is_complex<T>, bool>> class PLUArray {
+  private:
+    Array<T> mLU;
+    Array<int32_t> mPivots;
+    PartialPivLU<T> mPPLU = internal::BlankPPLU<T>;
+
+  public:
+    PLUArray() = delete;
+
+    /**
+     * Constructor for a PLUArray given the matrix dimension.
+     */
+    PLUArray(const uint32_t n) : mLU({n, n}), mPivots({n}) { mPPLU.make(mLU, mPivots); };
+
+    /**
+     * Constructor for a PLUArray given an existing array.
+     */
+    PLUArray(const Array<T>& arr)
+        : mLU((arr.isView()) ? arr.view() : arr), mPivots({arr.shape().rows()}) {
+        CT_ERROR_IF(mLU.shape().axes(), !=, 2, "Array must be a 2D matrix");
+        CT_ERROR_IF(mLU.shape().rows(), !=, mLU.shape().cols(), "Matrix must be square");
+        mPPLU.make(mLU, mPivots);
+    };
+
+    /**
+     * Constructor for a PLUArray given an existing location in memory for both the matrix and
+     * the pivots.
+     */
+    PLUArray(const Array<T>& arr, const Array<int32_t> pivots)
+        : mLU(arr.view()), mPivots(pivots.view()) {
+        CT_ERROR_IF(mLU.shape().axes(), !=, 2, "Array must be a 2D matrix");
+        CT_ERROR_IF(mLU.shape().rows(), !=, mLU.shape().cols(), "Matrix must be square");
+        mPPLU.make(mLU, mPivots);
+    };
+
+    uint32_t rank() { return mLU.shape().rows(); }; /**< Gets the rank of the LU matrix. */
+    Array<T> LU() const { return mLU.view(); };     /**< Gets the LU matrix. */
+    Array<int32_t> pivots() const { return mPivots.view(); }; /**< Gets the LU matrix. */
+
+    /**
+     * Comptues the inplace LU factorization for this array on CPU.
+     */
+    void computeLU() {
+        mPPLU.compute();
+        mPPLU.mMapPivots = mPPLU.permutationP().indices();
+    };
+
+    /**
+     * Solves the system \f$ LUx = b \f$ and returns \f$x\f$.
+     */
+    Array<T> solve(const Array<T>& b) {
+        Array<T> x(b.shape());
+        x.eigenMap() = mPPLU.solve(b.eigenMap());
+        return x;
+    };
+};
+
+/**
+ * This is a batch version of PLUArray, to enable usage of the cuBLAS API. This is restricted to
+ * floating point types.
+ */
+template <typename T, std::enable_if_t<is_float<T> or is_complex<T>, bool> = true>
+class PLUBatch : public Batch<T> {
+  private:
+    Array<int32_t> mPivotsBatch;
+    Array<int32_t> mInfoLU;
+    int32_t mInfoSolve;
+
+    bool mInitialized = false;
+
+  public:
+    /**
+     * Constructor of a PLUBatch from a given batch size.
+     */
+    PLUBatch(const uint32_t size) : Batch<T>(size), mInfoLU({size}){};
+
+    /**
+     * Constructor of a PLUBatch from a multi-dimensional array, batched across upper dimensions.
+     */
+    PLUBatch(const Array<T>& arr) : Batch<T>(arr) {
+        Check::isSquare(arr, "LU Array");
+
+        mPivotsBatch = Array<int32_t>({this->mBatchSize * this->mShape.rows()});
+        mInfoLU = Array<int32_t>({this->mBatchSize});
+    };
+
+    /**
+     * Indexing operator which returns the PLUArray in the PLUBatch at the given index.
+     */
+    PLUArray<T> operator[](const uint32_t index) const {
+        CT_ERROR_IF(index, >=, this->mBatchSize, "Index exceeds batch size");
+        Array<T> lu(this->mBatch[index], {this->mShape.rows(), this->mShape.cols()});
+        Array<int32_t> pivots(mPivotsBatch.data() + index * this->mShape.rows(),
+                              {this->mShape.rows()});
+        return PLUArray<T>(lu, pivots);
+    };
+
+    /**
+     * Computes the inplace PLU decomposition of batch of arrays.
+     */
+    StreamID computeLU(const StreamID& stream = DEF_CUBLAS_STREAM) {
+#ifdef CUDACC
+        uint32_t n = this->mShape.rows();
+        CUBLAS_CHECK(
+            cublasSetStream(Manager::get()->cublasHandle(), Manager::get()->stream(stream)));
+        invoke<T>(cublasSgetrfBatched, cublasDgetrfBatched, cublasCgetrfBatched,
+                  cublasZgetrfBatched, Manager::get()->cublasHandle(), n,
+                  DCAST(this->mBatch.dataDevice()), n, mPivotsBatch.dataDevice(),
+                  mInfoLU.dataDevice(), this->mBatchSize);
+
+#else
+#pragma omp parallel for
+        for (uint32_t i = 0; i < this->mBatchSize; ++i) {
+            (*this)[i].computeLU();
+        }
+#endif
+        mInitialized = true;
+        return stream;
+    };
+
+    /**
+     * Solves the batched system \f$LUx = b\f$ inplace. The solution \f$x\f$ is written back into
+     * \f$b\f$.
+     */
+    StreamID solve(const Batch<T>& b, const StreamID& stream = DEF_CUBLAS_STREAM) {
+        CT_ERROR(not mInitialized,
+                 "Cannot solve system if PLUBatch has not yet computed its LU decomposition");
+        CT_ERROR_IF(b.size(), !=, this->mBatchSize,
+                    "Upper dimensions of b do not match batch size");
+        CT_ERROR_IF(b.shape().rows(), !=, this->mShape.rows(),
+                    "The length of each column of b must match the matrix rank");
+
+#ifdef CUDACC
+        uint32_t n = b.shape().rows();
+        uint32_t nrhs = b.shape().cols();
+        CUBLAS_CHECK(
+            cublasSetStream(Manager::get()->cublasHandle(), Manager::get()->stream(stream)));
+        invoke<T>(cublasSgetrsBatched, cublasDgetrsBatched, cublasCgetrsBatched,
+                  cublasZgetrsBatched, Manager::get()->cublasHandle(), CUBLAS_OP_N, n, nrhs,
+                  DCAST(this->mBatch.dataDevice()), n, mPivotsBatch.dataDevice(),
+                  DCAST(b.batch().dataDevice()), n, &mInfoSolve, this->mBatchSize);
+
+#else
+#pragma omp parallel for
+        for (uint32_t i = 0; i < this->mBatchSize; ++i) {
+            b[i] = (*this)[i].solve(b[i]);
+        }
+#endif
+        return stream;
+    };
+
+    /**
+     * Gets the pivots data from the device to the host. Does nothing for CPU.
+     */
+    StreamID getPivots(const StreamID& stream = DEF_MEM_STREAM) const {
+        mPivotsBatch.updateHost(stream);
+        return stream;
+    };
+
+    /**
+     * Gets the info array for the LU decomposition for the device to the host. Does not
+     * return useful information for CPU.
+     */
+    Array<int32_t> getLUInfo() const {
+        mInfoLU.updateHost().wait();
+        return mInfoLU;
+    };
+
+    /**
+     * Checks validity of the solve operation. Does not return useful information for CPU.
+     */
+    int32_t validSolve() const { return mInfoSolve == 0; }
+};
+
+}; // namespace BLAS
+}; // namespace CudaTools
+
+#endif

HybridMesher/libraries/CudaTools/include/Core.h

@@ -0,0 +1,683 @@
+#ifndef CUDATOOLS_H
+#define CUDATOOLS_H
+
+#include "Macros.h"
+#include <functional>
+#include <iostream>
+#include <string>
+#include <tuple>
+#include <unordered_map>
+#include <vector>
+
+namespace CudaTools {
+
+struct Event;
+/**
+ * Simple wrapper for the name of a stream. Its purposes is to allow for
+ * 'streams' to be passed on host code, and allowing for simple syntax
+ * for waiting.
+ */
+struct StreamID {
+  public:
+    std::string mId;
+    StreamID() : mId(""){};
+    /**
+     * The constructor for a StreamID.
+     */
+    StreamID(const std::string& id_) : mId(id_){};
+    StreamID(const char* id_) : mId(id_){};
+
+    void wait() const; /**< Makes host wait for this stream. */
+    /**
+     * Makes this stream wait for this event. Does not block the host.
+     */
+    void wait(const Event& event) const;
+};
+
+static const StreamID DEF_MEM_STREAM = StreamID{"defaultMemory"};
+static const StreamID DEF_CUBLAS_STREAM = StreamID{"defaultCublas"};
+static const StreamID DEF_KERNEL_STREAM = StreamID{"defaultKernel"};
+
+/**
+ * Allocates memory on the device.
+ */
+void* malloc(const size_t size);
+
+/**
+ * Frees memory on the device.
+ */
+void free(void* const pDevice);
+
+/**
+ * Copies memory from the source pointer to the dest pointer.
+ */
+StreamID copy(void* const source, void* const dest, const size_t size,
+              const StreamID& stream = DEF_MEM_STREAM);
+/**
+ * Initializes or sets device memory to a value.
+ */
+StreamID memset(void* const pDevice, int value, const size_t size,
+                const StreamID& stream = DEF_MEM_STREAM);
+/**
+ * Pins memory on the host.
+ */
+void pin(void* const pHost, const size_t size);
+
+#ifdef CUDACC
+cudaDeviceProp getDeviceProp();
+static cudaDeviceProp DeviceProperties = getDeviceProp();
+const char* cublasGetErrorString(cublasStatus_t status);
+#endif
+
+/**
+ * A class that manages various CUDA Runtime components, such as
+ * streams, events, and handles.
+ */
+class Manager {
+  private:
+    static Manager mManagerInstance;
+    Manager(const std::vector<std::string>& names);
+    ~Manager();
+#ifdef CUDACC
+    std::unordered_map<std::string, cudaStream_t> mStreams;
+    cublasHandle_t mCublas;
+    // cusparseHandle_t mCusparse;
+#endif
+  public:
+    /**
+     * Used to get the global CudaTools::Manager instance.
+     */
+    static Manager* get() { return &mManagerInstance; };
+
+    void waitFor(const StreamID& stream) const; /**< Waits for the stream provided. */
+    void sync() const;                          /**< Waits until all device code has finished. */
+    void addStream(const std::string& name);    /**< Creates a stream with the given name. */
+#ifdef CUDACC
+    cudaStream_t stream(const StreamID& stream) const;
+    cublasHandle_t cublasHandle() const;
+    // cusparseHandle_t cusparseHandle() const;
+#endif
+};
+
+namespace Kernel {
+
+/**
+ * A struct that contains the kernel launch parameters.
+ */
+struct Settings {
+  public:
+#ifdef CUDACC
+    dim3 blockGrid;
+    dim3 threadBlock;
+    size_t sharedMemoryBytes = 0;
+#else
+    size_t threads;
+#endif
+    StreamID stream;
+
+    Settings() = default;
+
+    void setGridDim(const size_t x);                 /**< Sets the Grid dimensions. */
+    void setGridDim(const size_t x, const size_t y); /**< Sets the Grid dimensions. */
+    void setGridDim(const size_t x, const size_t y,
+                    const size_t z);                  /**< Sets the Grid dimensions. */
+    void setBlockDim(const size_t x);                 /**< Sets the Thread Block dimensions. */
+    void setBlockDim(const size_t x, const size_t y); /**< Sets the Thread Block dimensions. */
+    void setBlockDim(const size_t x, const size_t y,
+                     const size_t z); /**< Sets the Thread Block dimensions. */
+
+    void setSharedMemSize(const size_t bytes); /**< Sets the static shared memory size. */
+    void setStream(const StreamID& stream);    /**< Sets the stream. */
+};
+
+/**
+ * Returns a kernel launch parameters based on the number of threads, and optionally
+ * a stream. Should only be used for 'embarassingly parallel' situations, or where
+ * each thread corresponds some sort of index.
+ */
+Settings basic(const size_t threads, const StreamID& stream = DEF_KERNEL_STREAM);
+
+/**
+ * Launches a kernel with the provided function, settings and its arguments.
+ */
+
+template <typename F, typename... Args>
+StreamID launch(F func, const Kernel::Settings& sett, Args... args) {
+#ifdef CUDACC
+    func<<<sett.blockGrid, sett.threadBlock, sett.sharedMemoryBytes,
+           Manager::get()->stream(sett.stream.mId)>>>(args...);
+#else
+    func(args...);
+#endif
+    return sett.stream;
+}
+}; // namespace Kernel
+
+template <typename T> class Array;
+
+/**
+ * A class that holds information about an Array.
+ */
+class Shape {
+  private:
+    template <typename T> friend class Array;
+    uint32_t mAxes;
+    uint32_t mItems;
+    uint32_t mAxisDim[CUDATOOLS_ARRAY_MAX_AXES] = {0};
+    uint32_t mStride[CUDATOOLS_ARRAY_MAX_AXES] = {0};
+
+  public:
+    HD Shape() : mAxes(0), mItems(1){};
+    /**
+     * The constructor for a Shape.
+     * \param dims an initializer list of the dimensions.
+     */
+    HD Shape(const std::initializer_list<uint32_t> dims);
+
+    HD uint32_t axes() const;  /**< Gets the number of axes. */
+    HD uint32_t items() const; /**< Gets the total number of items. */
+
+    HD uint32_t length() const; /**< For 1D shapes, gets the length. In general, gets the
+                                   dimension of the last axis. */
+    HD uint32_t rows() const;   /**< For 2D shapes, gets the number of rows. In general, gets the
+                                   dimension of the second to last axis. */
+    HD uint32_t cols() const;   /**< For 2D shapes, gets the number of columns. In general, gets
+                                   the dimension of the second to last axis. */
+
+    HD uint32_t
+    dim(const uint32_t axis) const; /**< Gets the dimension size of the specified axis. */
+    HD uint32_t stride(const uint32_t axis) const; /**< Gets the stride of the specified axis. */
+
+    /**
+     * Gets the shape at a specific axis of this shape.
+     * \param axis the axis of where the new shape starts.
+     */
+    HD Shape subshape(const uint32_t axis) const;
+
+    HD bool operator==(const Shape& s) const; /**< Equals operator. */
+    HD bool operator!=(const Shape& s) const; /**< Not equals operator. */
+};
+
+std::ostream& operator<<(std::ostream& out, const Shape& s);
+
+/**
+ * A simple class that manages a CUDA Event.
+ */
+struct Event {
+#ifdef CUDACC
+    cudaEvent_t mEvent;
+#endif
+    Event();
+    ~Event();
+    void record(const StreamID& stream); /**< Records a event from a stream. */
+};
+
+template <typename F, typename... Args> struct FuncHolder {
+    F mFunc;
+    std::tuple<Args...> mArgs;
+    FuncHolder() = delete;
+    FuncHolder(F func, Args... args) : mFunc(func), mArgs(std::make_tuple(args...)){};
+    static void run(void* data) {
+        FuncHolder<F, Args...>* fh = (FuncHolder<F, Args...>*)(data);
+        std::apply([fh](auto&&... args) { fh->mFunc(args...); }, fh->mArgs);
+    };
+};
+
+/**
+ * A class that manages CUDA Graphs.
+ */
+template <typename F, typename... Args> class Graph {
+  private:
+#ifdef CUDACC
+    cudaGraph_t mGraph;
+    cudaGraphExec_t mInstance;
+#endif
+    FuncHolder<F, Args...> mFuncHolder;
+    StreamID mStream;
+
+  public:
+    Graph() = delete;
+    /**
+     * The constructor for a Graph, which captures the function.
+     * \param func the function to capture.
+     * \param stream the origin stream to use.
+     * \param args the arguments of the function.
+     */
+    Graph(const StreamID& stream, F func, Args... args)
+        : mFuncHolder(func, args...), mStream(stream) {
+#ifdef CUDACC
+        CUDA_CHECK(
+            cudaStreamBeginCapture(Manager::get()->stream(mStream), cudaStreamCaptureModeGlobal));
+        mFuncHolder.run((void*)&mFuncHolder);
+        CUDA_CHECK(cudaStreamEndCapture(Manager::get()->stream(mStream), &mGraph));
+        CUDA_CHECK(cudaGraphInstantiate(&mInstance, mGraph, NULL, NULL, 0));
+#endif
+    };
+
+    ~Graph() {
+#ifdef CUDACC
+        cudaGraphDestroy(mGraph);
+        cudaGraphExecDestroy(mInstance);
+#endif
+    };
+
+    /**
+     * Executes the instantiated graph, or simply runs the function with provided
+     * arguments if compiling for CPU.
+     */
+    StreamID execute() const {
+#ifdef CUDACC
+        cudaGraphLaunch(mInstance, Manager::get()->stream(mStream));
+#else
+        mFuncHolder.run((void*)&mFuncHolder);
+#endif
+        return mStream;
+    }
+};
+
+/**
+ * A struct to facilitate other CUDA Graphs functionality like creating branches and host callbacks.
+ */
+struct GraphManager {
+    std::vector<void*> mHostData;
+    std::vector<Event*> mEvents;
+
+    ~GraphManager();
+
+    /**
+     * Within a function that is being stream captured, launch a host function that can
+     * be captured into the graph.
+     */
+
+    template <typename F, typename... Args>
+    void launchHostFunction(const StreamID& stream, F func, Args&&... args) {
+#ifdef CUDACC
+        FuncHolder<F, Args...>* fh = new FuncHolder<F, Args...>(func, args...);
+        mHostData.push_back((void*)fh);
+        cudaHostFn_t run_func = fh->run;
+        CUDA_CHECK(cudaLaunchHostFunc(Manager::get()->stream(stream), run_func, fh));
+#else
+        func(args...);
+#endif
+    }
+
+    /**
+     * Makes a new branch in the graph to be run in parallel by a new stream.
+     * \param orig_stream the original stream to branch from.
+     * \param branch_stream the stream of the new branch.
+     */
+    void makeBranch(const StreamID& orig_stream, const StreamID& branch_stream);
+    /**
+     * Joins a existing branch in the graph to collapse a parallel block.
+     * \param orig_stream the original stream to join the branch to.
+     * \param branch_stream the stream of the branch to join.
+     */
+    void joinBranch(const StreamID& orig_stream, const StreamID& branch_stream);
+};
+
+}; // namespace CudaTools
+#endif // CUDATOOLS_H
+
+#ifdef CUDATOOLS_IMPLEMENTATION
+#ifndef __CUDATOOLS_IMPLEMENTED__
+#define __CUDATOOLS_IMPLEMENTED__
+namespace CudaTools {
+
+//////////////////////
+// StreamID Methods //
+//////////////////////
+
+void StreamID::wait() const { Manager::get()->waitFor(mId); }
+
+void StreamID::wait(const Event& event) const {
+#ifdef CUDACC
+    CUDA_CHECK(cudaStreamWaitEvent(Manager::get()->stream(mId), event.mEvent, 0));
+#endif
+}
+
+////////////////////
+// Memory Methods //
+////////////////////
+
+void* malloc(const size_t size) {
+#ifdef CUDACC
+    void* pDevice;
+    CUDA_CHECK(cudaMalloc(&pDevice, size));
+    return pDevice;
+#else
+    return nullptr;
+#endif
+}
+
+void free(void* const pDevice) {
+#ifdef CUDACC
+    if (pDevice != nullptr) CUDA_CHECK(cudaFree(pDevice));
+#endif
+}
+
+StreamID copy(void* const source, void* const dest, const size_t size, const StreamID& stream) {
+#ifdef CUDACC
+    CUDA_CHECK(
+        cudaMemcpyAsync(dest, source, size, cudaMemcpyDefault, Manager::get()->stream(stream)));
+#endif
+    return stream;
+}
+
+StreamID memset(void* const pDevice, const int value, const size_t size, const StreamID& stream) {
+#ifdef CUDACC
+    CUDA_CHECK(cudaMemsetAsync(pDevice, value, size, Manager::get()->stream(stream)));
+#endif
+    return stream;
+}
+
+void pin(void* const pHost, const size_t size) {
+#ifdef CUDACC
+    CUDA_CHECK(cudaHostRegister(pHost, size, cudaHostRegisterDefault));
+#endif
+}
+
+#ifdef CUDACC
+cudaDeviceProp getDeviceProp() {
+    cudaSetDevice(0);
+    cudaDeviceProp deviceProp;
+    cudaGetDeviceProperties(&deviceProp, 0);
+    return deviceProp;
+}
+#endif
+
+/////////////////////
+// Manager Methods //
+/////////////////////
+
+Manager::Manager(const std::vector<std::string>& names) {
+#ifdef CUDACC
+    for (auto name : names) {
+        addStream(name);
+    }
+    CUBLAS_CHECK(cublasCreate(&mCublas));
+    // CUSPARSE_CHECK(cusparseCreate(&mCusparse));
+#endif
+}
+
+Manager::~Manager() {
+#ifdef CUDACC
+    for (auto& it : mStreams) {
+        cudaStreamDestroy(it.second);
+    }
+    cublasDestroy(mCublas);
+    // CUSPARSE_CHECK(cusparseDestroy(mCusparse));
+#endif
+}
+
+void Manager::waitFor(const StreamID& stream) const {
+#ifdef CUDACC
+    auto it = mStreams.find(stream.mId);
+    if (it != mStreams.end()) {
+        CUDA_CHECK(cudaStreamSynchronize(it->second));
+    } else {
+        CT_ERROR(true, ("Invalid stream " + stream.mId).c_str());
+    }
+#endif
+}
+
+void Manager::sync() const {
+#ifdef CUDACC
+    CUDA_CHECK(cudaDeviceSynchronize());
+#endif
+}
+
+void Manager::addStream(const std::string& name) {
+#ifdef CUDACC
+    cudaStream_t s;
+    CUDA_CHECK(cudaStreamCreate(&s));
+    mStreams[name] = s;
+#endif
+}
+
+#ifdef CUDACC
+cudaStream_t Manager::stream(const StreamID& stream) const {
+    auto it = mStreams.find(stream.mId);
+    if (it != mStreams.end()) {
+        return it->second;
+    } else {
+        CT_ERROR(true, ("Invalid stream " + stream.mId).c_str());
+    }
+}
+
+cublasHandle_t Manager::cublasHandle() const { return mCublas; };
+// cusparseHandle_t Manager::cusparseHandle() const { return mCusparse; };
+
+Manager Manager::mManagerInstance = Manager({"defaultMemory", "defaultCublas", "defaultKernel"});
+#else
+Manager Manager::mManagerInstance = Manager({""});
+#endif
+
+////////////////////
+// Kernel Methods //
+////////////////////
+
+namespace Kernel {
+
+void Settings::setGridDim(const size_t x) {
+#ifdef CUDACC
+    CT_ERROR_IF(x, >, DeviceProperties.maxGridSize[0], "Total grid size too large")
+    blockGrid.x = x;
+    blockGrid.y = 1;
+    blockGrid.z = 1;
+#endif
+}
+
+void Settings::setGridDim(const size_t x, const size_t y) {
+#ifdef CUDACC
+    CT_ERROR_IF(x * y, >, DeviceProperties.maxGridSize[0], "Total grid size too large.");
+    CT_ERROR_IF(x, >, DeviceProperties.maxGridSize[0], "Grid dimension 'x' too large.");
+    CT_ERROR_IF(y, >, DeviceProperties.maxGridSize[1], "Grid dimension 'y' too large.");
+    blockGrid.x = x;
+    blockGrid.y = y;
+    blockGrid.z = 1;
+#endif
+}
+
+void Settings::setGridDim(const size_t x, const size_t y, const size_t z) {
+#ifdef CUDACC
+    CT_ERROR_IF(x * y * z, >, DeviceProperties.maxGridSize[0], "Total grid size too large.");
+    CT_ERROR_IF(x, >, DeviceProperties.maxGridSize[0], "Grid dimension 'x' too large.");
+    CT_ERROR_IF(y, >, DeviceProperties.maxGridSize[1], "Grid dimension 'y' too large.");
+    CT_ERROR_IF(z, >, DeviceProperties.maxGridSize[2], "Grid dimension 'z' too large.");
+    blockGrid.x = x;
+    blockGrid.y = y;
+    blockGrid.z = z;
+#endif
+}
+
+void Settings::setBlockDim(const size_t x) {
+#ifdef CUDACC
+    CT_ERROR_IF(x, >, DeviceProperties.maxThreadsDim[0], "Total block size too large.");
+    threadBlock.x = x;
+    threadBlock.y = 1;
+    threadBlock.z = 1;
+#endif
+}
+
+void Settings::setBlockDim(const size_t x, const size_t y) {
+#ifdef CUDACC
+    CT_ERROR_IF(x * y, >, DeviceProperties.maxThreadsDim[0], "Total block size too large.");
+    CT_ERROR_IF(x, >, DeviceProperties.maxThreadsDim[0], "Block dimension 'x' too large.");
+    CT_ERROR_IF(y, >, DeviceProperties.maxThreadsDim[1], "Block dimension 'y' too large.");
+    threadBlock.x = x;
+    threadBlock.y = y;
+    threadBlock.z = 1;
+#endif
+}
+
+void Settings::setBlockDim(const size_t x, const size_t y, const size_t z) {
+#ifdef CUDACC
+    CT_ERROR_IF(x * y * z, >, DeviceProperties.maxThreadsDim[0], "Total block size too large.");
+    CT_ERROR_IF(x, >, DeviceProperties.maxThreadsDim[0], "Block dimension 'x' too large.");
+    CT_ERROR_IF(y, >, DeviceProperties.maxThreadsDim[1], "Block dimension 'y' too large.");
+    CT_ERROR_IF(z, >, DeviceProperties.maxThreadsDim[2], "Block dimension 'z' too large.");
+    threadBlock.x = x;
+    threadBlock.y = y;
+    threadBlock.z = z;
+#endif
+}
+
+void Settings::setSharedMemSize(const size_t bytes) {
+#ifdef CUDACC
+    sharedMemoryBytes = bytes;
+#endif
+}
+
+void Settings::setStream(const StreamID& stream_) {
+#ifdef CUDACC
+    stream = stream_;
+#endif
+}
+
+Settings basic(const size_t threads, const StreamID& stream) {
+    Settings sett;
+#ifdef CUDACC
+    auto max_threads = DeviceProperties.maxThreadsPerBlock;
+    size_t grid_blocks = (threads + max_threads - 1) / max_threads;   // ceil(threads / max_threads)
+    size_t block_threads = (threads + grid_blocks - 1) / grid_blocks; // ceil(threads / grid_blocks)
+    sett.setGridDim(grid_blocks);
+    sett.setBlockDim(block_threads);
+    sett.setStream(stream);
+#else
+    sett.threads = threads;
+#endif
+    return sett;
+}
+
+}; // namespace Kernel
+
+/////////////////////
+// Shape Functions //
+/////////////////////
+
+HD Shape::Shape(const std::initializer_list<uint32_t> dims) : mAxes(dims.size()), mItems(1) {
+    CT_ERROR_IF(dims.size(), >, CUDATOOLS_ARRAY_MAX_AXES, "Number of axes exceeds max axes");
+    mAxes = dims.size();
+    if (mAxes == 0) return;
+
+    auto it = dims.end() - 1;
+    mItems = 1;
+    for (uint32_t iAxis = mAxes - 1; iAxis < mAxes; --iAxis) {
+        uint32_t dim = *it;
+        CT_ERROR_IF(dim, ==, 0, "Axis dimension cannot be 0");
+
+        mAxisDim[iAxis] = dim;
+        mStride[iAxis] = mItems;
+        mItems *= dim;
+        --it;
+    }
+
+    if (mAxes == 1) return;
+    // Swap last two, for column major storage.
+    mStride[mAxes - 2] = 1;
+    mStride[mAxes - 1] = mAxisDim[mAxes - 2];
+}
+
+HD uint32_t Shape::axes() const { return mAxes; };
+HD uint32_t Shape::items() const { return mItems; };
+HD uint32_t Shape::length() const { return mAxisDim[mAxes - 1]; }
+
+HD uint32_t Shape::rows() const { return mAxisDim[mAxes - 2]; }
+
+HD uint32_t Shape::cols() const { return mAxisDim[mAxes - 1]; }
+
+HD uint32_t Shape::dim(const uint32_t axis) const { return mAxisDim[axis]; }
+HD uint32_t Shape::stride(const uint32_t axis) const { return mStride[axis]; }
+
+HD bool Shape::operator==(const Shape& s) const {
+    if (mAxes != s.mAxes) {
+        return false;
+    }
+    for (uint32_t iAxis = 0; iAxis < mAxes; ++iAxis) {
+        if (mAxisDim[iAxis] != s.mAxisDim[iAxis]) {
+            return false;
+        }
+    }
+    return true;
+}
+
+HD bool Shape::operator!=(const Shape& s) const { return not(*this == s); }
+
+HD Shape Shape::subshape(const uint32_t axis) const {
+    CT_ERROR_IF(axis, >, mAxes, "Axis number exceeds number of axes.");
+    if (axis == mAxes) return Shape({1});
+
+    Shape new_shape({});
+    new_shape.mAxes = mAxes - axis;
+    new_shape.mItems = mItems;
+
+    for (uint32_t iAxis = 0; iAxis < axis; iAxis++) {
+        new_shape.mItems /= mAxisDim[iAxis];
+    }
+    for (uint32_t iAxis = axis; iAxis < mAxes; iAxis++) {
+        new_shape.mAxisDim[iAxis - axis] = mAxisDim[iAxis];
+        new_shape.mStride[iAxis - axis] = mStride[iAxis];
+    }
+    return new_shape;
+}
+
+std::ostream& operator<<(std::ostream& out, const Shape& s) {
+    out << "(";
+    if (s.axes() == 0) return out << ")";
+    for (uint32_t iAxis = 0; iAxis < s.axes() - 1; ++iAxis) {
+        out << s.dim(iAxis) << ", ";
+    }
+    return out << s.dim(s.axes() - 1) << ")";
+}
+
+///////////////////
+// Event Methods //
+///////////////////
+
+Event::Event() {
+#ifdef CUDACC
+    CUDA_CHECK(cudaEventCreate(&mEvent));
+#endif
+}
+
+Event::~Event() {
+#ifdef CUDACC
+    cudaEventDestroy(mEvent);
+#endif
+}
+
+void Event::record(const StreamID& stream) {
+#ifdef CUDACC
+    CUDA_CHECK(cudaEventRecord(mEvent, Manager::get()->stream(stream)));
+#endif
+}
+
+//////////////////////////
+// GraphManager Methods //
+//////////////////////////
+
+GraphManager::~GraphManager() {
+#ifdef CUDACC
+    for (Event* event : mEvents) {
+        delete event;
+    }
+#endif
+}
+
+void GraphManager::makeBranch(const StreamID& orig_stream, const StreamID& branch_stream) {
+    Event* event = new Event();
+    event->record(orig_stream);
+    mEvents.push_back(event);
+    branch_stream.wait(*event);
+}
+
+void GraphManager::joinBranch(const StreamID& orig_stream, const StreamID& branch_stream) {
+    Event* event = new Event();
+    event->record(branch_stream);
+    mEvents.push_back(event);
+    orig_stream.wait(*event);
+}
+
+};     // namespace CudaTools
+#endif
+#endif // CUDATOOLS_IMPLEMENTATION

HybridMesher/libraries/CudaTools/include/Macros.h

@@ -0,0 +1,311 @@
+#ifndef MACROS_H
+#define MACROS_H
+
+#include <exception>
+#include <sstream>
+#include <stdarg.h>
+
+#if defined(CUDA) && defined(__CUDACC__)
+#define CUDACC
+#endif
+
+#if defined(__CUDA_ARCH__) && (__CUDA_ARCH__ > 0)
+#define DEVICE
+#endif
+
+#ifdef CUDATOOLS_DOXYGEN
+/**
+ * \def CUDACC
+ * This macro is defined when this code is being compiled by nvcc and the CUDA compilation
+ * flag is set. This should be used to enclose code where CUDA specific libraries and syntax are
+ * being used.
+ */
+#define CUDACC
+
+/**
+ * \def DEVICE
+ * This macro is defined when this code is being compiled for the device. The difference between
+ * this and CUDACC is that this should exclusively be used to dcide if code is being compiled
+ * to execute on the device. CUDACC is only determines what compiler is being used.
+ */
+#define DEVICE
+
+/**
+ * \def HD
+ * Mark a function in front with this if it needs to be callable on both the
+ * CPU and CUDA device.
+ */
+#define HD
+
+/**
+ * \def DEVICE_FUNC
+ * Mark a function in front with this if it is only callable on the CUDA device.
+ */
+#define DEVICE_FUNC
+
+/**
+ * \def SHARED
+ * Mark a variable as static shared memory.
+ */
+#define SHARED
+
+/**
+ * \def CUDATOOLS_USE_EIGEN
+ * Compile the CudaTools library with Eigen support.
+ */
+#define CUDATOOLS_USE_EIGEN
+
+/**
+ * \def CUDATOOLS_USE_PYTHON
+ * Compile the CudaTools library with Python support.
+ */
+#define CUDATOOLS_USE_PYTHON
+
+/**
+ * \def KERNEL(call, settings, ...)
+ * Used to call a CUDA kernel.
+ * \param call the name of the kernel
+ * \param settings the associated CudaTools::Kernel::Settings to initialize the kernel with
+ * \param ... the arguments of the kernel
+ */
+#define KERNEL(call, settings, ...)
+
+/**
+ * \def BASIC_LOOP(N)
+ * Can be used in conjunction with CudaTools::Kernel::Basic, which is mainly used for embarassingly
+ * parallel situations. Exposes the loop/thread number as iThread.
+ * \param N number of iterations
+ */
+#define BASIC_LOOP(N)
+
+/**
+ * \def DEVICE_COPY(name)
+ * Can be used inside a class declaration (header) which generates boilerplate code to allow this
+ * class to be used on the device.
+ *
+ * This macro creates a few functions:\n
+ * name* that(): returns the pointer to this instance on the device.
+ *
+ * void allocateDevice(): allocates the memory on the device for this class instance.
+ *
+ * void freeDevice(): frees the memory on the device for this class instance.
+ *
+ * CudaTools::StreamID updateHost(const CudaTools::StreamID& stream): updates the host instance
+ * of the class.
+ *
+ * CudaTools::StreamID updateDevice(const CudaTools::StreamID& stream): updates
+ * the device instance of the class.
+ * \param name the name of the class
+ */
+#define DEVICE_COPY(name)
+
+/**
+ * \def CT_ERROR_IF(a, op, b, msg)
+ * Used for throwing runtime errors given a condition with an operator.
+ */
+#define CT_ERROR_IF(a, op, b, msg)
+
+/**
+ * \def CT_ERROR(a, msg)
+ * Used for throwing runtime errors given a bool.
+ */
+#define CT_ERROR(a, msg)
+
+/**
+ * \def CUDA_CHECK(call)
+ * Gets the error generated by a CUDA function call if there is one.
+ * \param call CUDA function to check if there are errors when running.
+ */
+#define CUDA_CHECK(call)
+
+/**
+ * \def CUBLAS_CHECK(call)
+ * Gets the error generated by a cuBLAS function call if there is one.
+ * \param call cuBLAS function to check if there are errors when running.
+ */
+#define CUBLAS_CHECK(call)
+
+/**
+ * \def CUDA_MEM(call)
+ * Gets the GPU memory used from function call if there is one.
+ * \param call function to measure memory usage.
+ * \param name an identifier to use as a variable and when printing. Must satisfy variable naming.
+ */
+#define CUDA_MEM(call, name)
+#endif
+
+///////////////////
+// KERNEL MACROS //
+///////////////////
+
+#ifdef CUDACC
+
+#include <cublas_v2.h>
+#include <cuda_bf16.h>
+#include <cuda_fp16.h>
+#include <cuda_runtime.h>
+//#include <cusparse.h>
+
+#define DEVICE_FUNC __device__
+#define HD __host__ __device__
+#define SHARED __shared__
+
+#define KERNEL(call, ...) __global__ void call(__VA_ARGS__)
+
+#else
+#define DEVICE_FUNC
+#define HD
+#define SHARED
+
+#define KERNEL(call, ...) void call(__VA_ARGS__)
+
+#endif // CUDACC
+
+///////////////////
+// DEVICE MACROS //
+///////////////////
+
+#ifdef DEVICE
+
+#define BASIC_LOOP(N)                                                                              \
+    uint32_t iThread = blockIdx.x * blockDim.x + threadIdx.x;                                      \
+    if (iThread < N)
+#else
+#define BASIC_LOOP(N) _Pragma("omp parallel for") for (uint32_t iThread = 0; iThread < N; ++iThread)
+
+#endif
+
+//////////////////
+// CLASS MACROS //
+//////////////////
+
+#define UPDATE_FUNC(name)                                                                          \
+    inline CudaTools::StreamID updateHost(const CudaTools::StreamID& stream =                      \
+                                              CudaTools::DEF_MEM_STREAM) {                         \
+        return CudaTools::copy(that(), this, sizeof(name));                                        \
+    };                                                                                             \
+    inline CudaTools::StreamID updateDevice(const CudaTools::StreamID& stream =                    \
+                                                CudaTools::DEF_MEM_STREAM) {                       \
+        return CudaTools::copy(this, that(), sizeof(name));                                        \
+    }
+
+#ifdef CUDACC
+
+#define DEVICE_COPY(name)                                                                          \
+  private:                                                                                         \
+    name* __deviceInstance__ = nullptr;                                                            \
+                                                                                                   \
+  public:                                                                                          \
+    inline name* that() { return __deviceInstance__; };                                            \
+    inline void allocateDevice() { __deviceInstance__ = (name*)CudaTools::malloc(sizeof(name)); }; \
+    inline void freeDevice() { CudaTools::free(__deviceInstance__); };                             \
+    UPDATE_FUNC(name)
+
+#else
+#define DEVICE_COPY(name)                                                                          \
+  public:                                                                                          \
+    inline name* that() { return this; };                                                          \
+    inline void allocateDevice(){};                                                                \
+    inline void freeDevice(){};                                                                    \
+    UPDATE_FUNC(name)
+
+#endif
+
+#ifndef CUDATOOLS_ARRAY_MAX_AXES
+/**
+ * \def CUDATOOLS_ARRAY_MAX_AXES
+ * The maximum number of axes/dimensions an
+ * CudaTools::Array can have. The default is set
+ * to 4, but can be manully set fit the program
+ * needs.
+ */
+#define CUDATOOLS_ARRAY_MAX_AXES 4
+#endif
+
+////////////////////
+// Error Checking //
+////////////////////
+
+#ifndef NO_DIMENSION_CHECK
+#ifdef DEVICE
+#define CT_ERROR_IF(a, op, b, msg)                                                                 \
+    if (a op b) {                                                                                  \
+        printf("\033[1;31m[CudaTools]\033[0m %s:%d\n | %s: (" #a ") " #op " (" #b ").\n",          \
+               __FILE__, __LINE__, msg);                                                           \
+    }
+
+#define CT_ERROR(a, msg)                                                                           \
+    if (a) {                                                                                       \
+        printf("\033[1;31m[CudaTools]\033[0m %s:%d\n | %s: " #a ".\n", __FILE__, __LINE__, msg);   \
+    }
+#else
+
+#define CT_ERROR_IF(a, op, b, msg)                                                                 \
+    if (a op b) {                                                                                  \
+        std::ostringstream os_a;                                                                   \
+        std::ostringstream os_b;                                                                   \
+        os_a << a;                                                                                 \
+        os_b << b;                                                                                 \
+        printf("\033[1;31m[CudaTools]\033[0m %s:%d\n | %s: (" #a ")%s " #op " (" #b ")%s.\n",      \
+               __FILE__, __LINE__, msg, os_a.str().c_str(), os_b.str().c_str());                   \
+        throw std::exception();                                                                    \
+    }
+
+#define CT_ERROR(a, msg)                                                                           \
+    if (a) {                                                                                       \
+        printf("\033[1;31m[CudaTools]\033[0m %s:%d\n | %s: " #a ".\n", __FILE__, __LINE__, msg);   \
+        throw std::exception();                                                                    \
+    }
+#endif
+
+#endif // NO_DIMENSION_CHECK
+
+#if defined(CUDACC) && !defined(NO_CUDA_CHECK)
+
+#define CUDA_CHECK(call)                                                                           \
+    do {                                                                                           \
+        cudaError_t err = (call);                                                                  \
+        if (err != cudaSuccess) {                                                                  \
+            printf("\033[1;31m[CUDA]\033[0m %s:%d\n | %s\n", __FILE__, __LINE__,                   \
+                   cudaGetErrorString(err));                                                       \
+            throw std::exception();                                                                \
+        }                                                                                          \
+    } while (0)
+
+#define CUBLAS_CHECK(call)                                                                         \
+    do {                                                                                           \
+        cublasStatus_t err = (call);                                                               \
+        if (err != CUBLAS_STATUS_SUCCESS) {                                                        \
+            printf("\033[1;31m[cuBLAS]\033[0m %s:%d\n | %s\n", __FILE__, __LINE__,                 \
+                   cublasGetStatusName(err));                                                      \
+            throw std::exception();                                                                \
+        }                                                                                          \
+    } while (0)
+
+/*
+#define CUSPARSE_CHECK(call)                                                                       \
+    do {                                                                                           \
+        cusparseStatus_t err = (call);                                                             \
+        if (err != CUSPARSE_STATUS_SUCCESS) {                                                      \
+            printf("[cuSPARSE] %s:%d\n | %s\n", __FILE__, __LINE__, cusparseGetErrorName(err));    \
+            throw std::exception();                                                                \
+        }                                                                                          \
+    } while (0)
+*/
+
+#define CUDA_MEM(call, name)                                                                       \
+    size_t free_bef_##name, free_aft_##name;                                                       \
+    cudaMemGetInfo(&free_bef_##name, NULL);                                                        \
+    call;                                                                                          \
+    CudaTools::Manager::get()->sync();                                                             \
+    cudaMemGetInfo(&free_aft_##name, NULL);                                                        \
+    printf("[%s] GPU Memory Usage: %iMiB\n", #name,                                                \
+           (free_bef_##name - free_aft_##name) / (1024 * 1024));
+
+#else
+#define CUDA_CHECK(call) (call)
+#define CUBLAS_CHECK(call) (call)
+#define CUDA_MEM(call, name) (call)
+#endif
+
+#endif // MACROS_H

HybridMesher/libraries/CudaTools/include/Types.h

@@ -0,0 +1,166 @@
+#ifndef CUDATOOLS_COMPLEX_H
+#define CUDATOOLS_COMPLEX_H
+
+#include "Macros.h"
+#include <cmath>
+#include <complex>
+
+/**
+ * This is directly adapated from cuComplex.h, except placed into a C++ friendly format.
+ */
+
+namespace CudaTools {
+
+namespace Types {
+
+using real32 = float;  /**< Type alias for 32-bit floating point datatype. */
+using real64 = double; /**< Type alias for 64-bit floating point datatype. */
+
+#ifdef CUDACC
+
+using real16 = __half;         /**< Type alias for 16-bit floating point datatype, when using GPU.
+                                 Otherwise, defaults to float. */
+using realb16 = __nv_bfloat16; /**< Type alias for the 16-bit bfloat datatype, when using GPU.
+                                  Otherwise, defaults to float. */
+
+#else
+
+using real16 = float;
+using realb16 = float;
+
+#endif // CUDACC
+
+template <typename T> class complex {
+  private:
+    T r = 0;
+    T i = 0;
+
+  public:
+    HD complex() = default;
+    HD complex(T real, T imag) : r(real), i(imag){};
+    HD complex(T x) : r(x), i(0){};
+
+    HD complex<T> operator+(const complex<T> z) const { return complex(r + z.r, i + z.i); };
+    HD complex<T> operator-(const complex<T> z) const { return complex(r - z.r, i - z.i); };
+    HD complex<T> operator*(const T y) const { return complex(r * y, i * y); };
+    HD complex<T> operator/(const T y) const { return complex(r / y, i / y); };
+
+    HD complex<T> operator*(const complex<T> z) const {
+        return complex(r * z.r - i * z.i, r * z.i + i * z.r);
+    };
+    HD complex<T> operator/(const complex<T> z) const {
+        T s = std::abs(z.r) + std::abs(z.i);
+        T oos = 1.0f / s;
+        T ars = r * oos, ais = i * oos, brs = z.r * oos, bis = z.i * oos;
+        s = (brs * brs) + (bis * bis);
+        oos = 1.0f / s;
+        return complex(ars * brs + ais * bis, ais * brs - ars * bis) * oos;
+    };
+
+    HD void operator+=(const complex<T> z) {
+        r += z.r;
+        i += z.i;
+    };
+    HD void operator-=(const complex<T> z) {
+        r -= z.r;
+        i -= z.i;
+    };
+    HD void operator*=(const T y) {
+        r *= y;
+        i *= y;
+    };
+    HD void operator/=(const T y) {
+        r /= y;
+        i /= y;
+    };
+
+    HD void operator*=(const complex<T> z) {
+        T a = r * z.r - i * z.i, b = r * z.i + i * z.r;
+        r = a;
+        i = b;
+    }
+
+    HD void operator/=(const complex<T> z) {
+        T s = std::abs(z.r) + std::abs(z.i);
+        T oos = 1.0f / s;
+        T ars = r * oos, ais = i * oos, brs = z.r * oos, bis = z.i * oos;
+        s = (brs * brs) + (bis * bis);
+        oos = 1.0f / s;
+        r = (ars * brs + ais * bis) * oos;
+        i = (ais * brs - ars * bis) * oos;
+    };
+
+    HD T abs() const {
+        T a = std::abs(r), b = std::abs(i);
+        T v, w;
+        if (a > b) {
+            v = a;
+            w = b;
+        } else {
+            v = b;
+            w = a;
+        }
+        T t = w / v;
+        t = 1.0f + t * t;
+        t = v * std::sqrt(t);
+        if ((v == 0.0f) || (v > 3.402823466e38f) || (w > 3.402823466e38f)) {
+            t = v + w;
+        }
+        return t;
+    }
+
+    HD complex<T> conj() const { return complex(r, -1 * i); }
+
+    HD T real() const { return r; };
+    HD T imag() const { return i; };
+};
+
+template class complex<real32>;
+template class complex<real64>;
+
+template <class T> complex<T> operator*(const T y, const complex<T> z) { return z * y; };
+template <class T> complex<T> operator/(const T y, const complex<T> z) { return z / y; };
+
+template complex<real32> operator*<real32>(const real32, const complex<real32>);
+template complex<real64> operator*<real64>(const real64, const complex<real64>);
+template complex<real32> operator/<real32>(const real32, const complex<real32>);
+template complex<real64> operator/<real64>(const real64, const complex<real64>);
+
+#ifdef CUDACC
+using complex64 = complex<real32>; /**< Type alias for 64-bit complex floating point datatype.
+                                    * This adapts depending on the CUDA compilation flag, and
+                                    * will automatically switch std::complex<real32>. */
+
+using complex128 = complex<real64>; /**< Type alias for 128-bit complex floating point datatype.
+                                     * This adapts depending on the CUDA compilation flag, and will
+                                     * automatically switch std::complex<real64>. */
+
+#else
+using complex64 = std::complex<real32>;
+using complex128 = std::complex<real64>;
+#endif
+
+/** Type alises and lots of metaprogramming definitions, primarily dealing with
+ * the different numeric types and overrides. */
+
+template <typename T> struct ComplexUnderlying_S { typedef T type; };
+template <> struct ComplexUnderlying_S<complex64> { typedef float type; };
+template <> struct ComplexUnderlying_S<complex128> { typedef double type; };
+template <typename T> using ComplexUnderlying = typename ComplexUnderlying_S<T>::type;
+
+template <typename T> struct ComplexConversion_S { typedef T type; };
+template <> struct ComplexConversion_S<complex64> { typedef std::complex<float> type; };
+template <> struct ComplexConversion_S<complex128> { typedef std::complex<double> type; };
+template <typename T> using ComplexConversion = typename ComplexConversion_S<T>::type;
+
+template <typename T> inline constexpr bool is_int = std::is_integral<T>::value;
+template <typename T> inline constexpr bool is_float = std::is_floating_point<T>::value;
+template <typename T>
+inline constexpr bool is_complex =
+    std::is_same<T, complex64>::value or std::is_same<T, complex128>::value;
+template <typename T> inline constexpr bool is_host_num = is_int<T> or is_float<T> or is_complex<T>;
+
+}; // namespace Types
+}; // namespace CudaTools
+
+#endif

HybridMesher/libraries/EXODUS/include/SeacasConfig.cmake

@@ -0,0 +1,66 @@
+# @HEADER
+# ************************************************************************
+#
+#            TriBITS: Tribal Build, Integrate, and Test System
+#                    Copyright 2013 Sandia Corporation
+#
+#
+# Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+# the U.S. Government retains certain rights in this software.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# ************************************************************************
+# @HEADER
+
+get_filename_component(_Seacas_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
+get_filename_component(_Seacas_PREFIX "${_Seacas_DIR}" PATH)
+set(Seacas_DIR "${_Seacas_PREFIX}/lib/cmake/Seacas")
+message(WARNING "SeacasConfig.cmake has moved.  "
+  "It now exists at a location under the installation prefix where the "
+  "find_package command looks by default (<prefix>/lib/cmake/Seacas).  "
+  "This compatibility file exists at the old location (<prefix>/include) "
+  "to present this message and load the file from its new location."
+  "\n"
+  "The find_package() call that loaded this file did so because its "
+  "cached result variable, Seacas_DIR, is set to\n"
+  "  ${_Seacas_DIR}\n"
+  "I'm locally setting Seacas_DIR to\n"
+  "  ${Seacas_DIR}\n"
+  "and loading SeacasConfig.cmake from its new location.  "
+  "One may suppress this warning by setting the above value in the cache.  "
+  "However, the application needs modification permanently fix the issue.  "
+  "The find_package() call that loaded this file may have the form\n"
+  "  find_package(Seacas REQUIRED PATHS \${Seacas_PATH}/include)\n"
+  "Change it to the form\n"
+  "  set(CMAKE_PREFIX_PATH \${Seacas_PATH} \${CMAKE_PREFIX_PATH})\n"
+  "  find_package(Seacas REQUIRED)\n"
+  "to find SeacasConfig.cmake in its new location in future builds "
+  "while still honoring the Seacas_PATH option for this application."
+  )
+include(${Seacas_DIR}/SeacasConfig.cmake)

HybridMesher/libraries/EXODUS/include/Seacas_version_date.h

@@ -0,0 +1,36 @@
+/* SEACAS_VERSION_DATE
+ *
+ * This macro gives the version date of the Seacas git repository at
+ * the time it was configured.  It gives the date YYYY-MM-DD and the 2-digit
+ * (24) hour hh of the commit as a 10-digit integer:
+ *
+ *   YYYYYMMDDhh
+ *
+ * As long as the branch for the git repo is not hard reset, the first-parent
+ * history should give a monotonically increasing 10-digit integer.  This
+ * 10-digit date/time integer YYYYMMDDhh will fit in a signed 32-bit integer
+ * with a maximum value of 2^32 / 2 - 1 = 2147483647.  Therefore, the maximum
+ * date that can be handled is the year 2147 with the max date/time of 2147 12
+ * 31 23 = 2147123123.  Modern C/C++ compilers (and other implementations of
+ * the C preprocessor) should be able to handle 32-bit integers.
+ * 
+ * This header file is meant to be included by downstream codes to determine
+ * the version of Seacas being used and allows
+ * SEACAS_VERSION_DATE to be used in C/C++ ifdefs like:
+ *
+ * #if defined(SEACAS_VERSION_DATE) && SEACAS_VERSION_DATE >= 2019032704
+ *   // The version is newer than 2019-03-27 04:00:00 UTC
+ *   ...
+ * #else
+ *   // The version is older than 2019-03-27 04:00:00 UTC
+ *     ...
+ *  #endif
+ *
+ * This allows downstream codes to know the fine-grained version of
+ * Seacas at configure and build time to adjust for the addition of
+ * new features, deprecation of code, or breaks in backward compatibility
+ * (which occur in specific commits with unique commit dates).
+ *
+ */
+
+#undef SEACAS_VERSION_DATE

HybridMesher/libraries/EXODUS/include/exodusII_int.h

@@ -0,0 +1,892 @@
+/*
+
+ * Copyright(C) 1999-2020, 2022, 2023 National Technology & Engineering Solutions
+ * of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
+ * NTESS, the U.S. Government retains certain rights in this software.
+ *
+ * See packages/seacas/LICENSE for details
+ */
+/*****************************************************************************
+ *
+ * exodusII_int.h - ExodusII header file for internal Exodus call use only
+ *
+ */
+#pragma once
+
+#include <stdbool.h>
+
+#include "exodus_config.h"
+
+#if defined(EXODUS_THREADSAFE)
+#include <pthread.h>
+#endif
+
+#include "netcdf.h"
+#if defined(NC_HAVE_META_H)
+#include "netcdf_meta.h"
+#endif
+
+#if defined(_WIN32) && defined(_MSC_VER) && _MSC_VER < 1900
+#define PRId64 "I64d"
+#else
+#include <inttypes.h>
+#endif
+
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+
+#ifndef __APPLE__
+#if defined __STDC__ || defined __cplusplus
+#include <stdlib.h>
+#endif
+#endif
+
+#ifdef _MSC_VER
+#pragma warning(disable : 4127)
+#pragma warning(disable : 4706)
+#pragma warning(disable : 4701)
+#endif
+
+#if defined(__BORLANDC__)
+#pragma warn - 8004 /* "assigned a value that is never used" */
+#endif
+
+#include <stdio.h>
+
+#if defined(_MSC_VER) && _MSC_VER < 1900
+#define __func__ __FUNCTION__
+#define snprintf _snprintf
+#endif
+
+#define snprintf_nowarn(...) (snprintf(__VA_ARGS__) < 0 ? abort() : (void)0)
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**
+ * \defgroup Internal Internal Functions and Defines
+ * \internal
+ *
+ * Variables and functions used internally in the library
+ *@{
+ */
+#define MAX_VAR_NAME_LENGTH 32 /**< Internal use only */
+
+/* Default "filesize" for newly created files.
+ * Set to 0 for normal filesize setting.
+ * Set to 1 for EXODUS_LARGE_MODEL setting to be the default
+ */
+#define EXODUS_DEFAULT_SIZE 1
+
+/* Used to map between root (file id) and group ids when using groups */
+#define EX_FILE_ID_MASK (0xffff0000) /**< Must match FILE_ID_MASK in NetCDF nc4internal.h */
+#define EX_GRP_ID_MASK  (0x0000ffff) /**< Must match GRP_ID_MASK in NetCDF nc4internal.h */
+
+void ex__reset_error_status(void);
+
+#if defined(EXODUS_THREADSAFE)
+#if !defined(exerrval)
+/* In both exodusII.h and exodusII_int.h */
+typedef struct EX_errval
+{
+  int  errval;
+  char last_pname[MAX_ERR_LENGTH];
+  char last_errmsg[MAX_ERR_LENGTH];
+  int  last_err_num;
+} EX_errval_t;
+
+EXODUS_EXPORT EX_errval_t *ex_errval;
+#define exerrval ex_errval->errval
+#endif
+
+extern pthread_once_t EX_first_init_g;
+
+typedef struct EX_mutex_struct
+{
+  pthread_mutex_t     atomic_lock; /**< lock for atomicity of new mechanism */
+  pthread_mutexattr_t attribute;
+} EX_mutex_t;
+
+extern EX_mutex_t   EX_g;
+extern int          ex__mutex_lock(EX_mutex_t *mutex);
+extern int          ex__mutex_unlock(EX_mutex_t *mutex, const char *func, int line);
+extern void         ex__pthread_first_thread_init(void);
+extern EX_errval_t *exerrval_get();
+
+#define EX_FUNC_ENTER()                                                                            \
+  do {                                                                                             \
+    /* Initialize the thread-safe code */                                                          \
+    pthread_once(&EX_first_init_g, ex__pthread_first_thread_init);                                 \
+                                                                                                   \
+    /* Grab the mutex for the library */                                                           \
+    ex__mutex_lock(&EX_g);                                                                         \
+    ex_errval               = exerrval_get();                                                      \
+    exerrval                = 0;                                                                   \
+    ex_errval->last_err_num = 0;                                                                   \
+  } while (0)
+
+#define EX_FUNC_ENTER_INT()                                                                        \
+  do {                                                                                             \
+    /* Initialize the thread-safe code */                                                          \
+    pthread_once(&EX_first_init_g, ex__pthread_first_thread_init);                                 \
+                                                                                                   \
+    /* Grab the mutex for the library */                                                           \
+    ex__mutex_lock(&EX_g);                                                                         \
+    ex_errval = exerrval_get();                                                                    \
+  } while (0)
+
+#define EX_FUNC_LEAVE(error)                                                                       \
+  do {                                                                                             \
+    ex__mutex_unlock(&EX_g, __func__, __LINE__);                                                   \
+    return error;                                                                                  \
+  } while (0)
+
+#define EX_FUNC_VOID()                                                                             \
+  do {                                                                                             \
+    ex__mutex_unlock(&EX_g, __func__, __LINE__);                                                   \
+    return;                                                                                        \
+  } while (0)
+
+#define EX_FUNC_UNLOCK()                                                                           \
+  do {                                                                                             \
+    ex__mutex_unlock(&EX_g, __func__, __LINE__);                                                   \
+  } while (0)
+
+#else
+
+/* Enable this to output tracing information from the API functions */
+#if 0
+EXODUS_EXPORT int indent;
+#define EX_FUNC_ENTER()                                                                            \
+  do {                                                                                             \
+    ex__reset_error_status();                                                                      \
+    fprintf(stderr, "%d Enter: %s\n", indent, __func__);                                           \
+    indent++;                                                                                      \
+  } while (0)
+#define EX_FUNC_ENTER_INT()                                                                        \
+  do {                                                                                             \
+    fprintf(stderr, "%d Enter: %s\n", indent, __func__);                                           \
+    indent++;                                                                                      \
+  } while (0)
+#define EX_FUNC_LEAVE(error)                                                                       \
+  do {                                                                                             \
+    indent--;                                                                                      \
+    fprintf(stderr, "%d Leave: %s\n", indent, __func__);                                           \
+    return error;                                                                                  \
+  } while (0)
+#define EX_FUNC_VOID()                                                                             \
+  do {                                                                                             \
+    indent--;                                                                                      \
+    fprintf(stderr, "%d Leave: %s\n", indent, __func__);                                           \
+    return;                                                                                        \
+  } while (0)
+#define EX_FUNC_UNLOCK()                                                                           \
+  do {                                                                                             \
+    indent--;                                                                                      \
+    fprintf(stderr, "%d Unlock: %s\n", indent, __func__);                                          \
+  } while (0)
+#else
+#define EX_FUNC_ENTER()                                                                            \
+  do {                                                                                             \
+    ex__reset_error_status();                                                                      \
+  } while (0)
+#define EX_FUNC_ENTER_INT()
+#define EX_FUNC_LEAVE(error) return error
+#define EX_FUNC_VOID()       return
+#define EX_FUNC_UNLOCK()
+#endif
+#endif
+
+#define EX_UNUSED(A)                                                                               \
+  do {                                                                                             \
+    (void)(A);                                                                                     \
+  } while (0)
+
+/*
+ * This file contains defined constants that are used internally in the
+ * EXODUS API.
+ *
+ * The first group of constants refer to NetCDF variables, attributes, or
+ * dimensions in which the EXODUS data are stored.  Using the defined
+ * constants will allow the names of the NetCDF entities to be changed easily
+ * in the future if needed.  The first three letters of the constant identify
+ * the NetCDF entity as a variable (VAR), dimension (DIM), or attribute (ATT).
+ *
+ * NOTE: The entity name should not have any blanks in it.  Blanks are
+ *       technically legal but some NetCDF utilities (ncgen in particular)
+ *       fail when they encounter a blank in a name.
+ *
+ */
+#define ATT_TITLE       "title"       /**< the database title        */
+#define ATT_API_VERSION "api_version" /**< the EXODUS api vers number  */
+/*! the EXODUS api vers # used for db version 2.01 and earlier              */
+#define ATT_API_VERSION_BLANK "api version"
+#define ATT_VERSION           "version"   /**< the EXODUS file vers number */
+#define ATT_FILESIZE          "file_size" /**< 1=large, 0=normal */
+/*! word size of floating point numbers in file     */
+#define ATT_FLT_WORDSIZE "floating_point_word_size"
+/*! word size of floating point numbers in file used for db version
+   2.01 and earlier */
+#define ATT_FLT_WORDSIZE_BLANK "floating point word size"
+#define ATT_MAX_NAME_LENGTH    "maximum_name_length"
+#define ATT_INT64_STATUS       "int64_status"
+#define ATT_NEM_API_VERSION    "nemesis_api_version"
+#define ATT_NEM_FILE_VERSION   "nemesis_file_version"
+#define ATT_PROCESSOR_INFO     "processor_info"
+#define ATT_LAST_WRITTEN_TIME  "last_written_time"
+
+#define DIM_NUM_ASSEMBLY             "num_assembly" /**< number of assemblies       */
+#define DIM_NUM_BLOB                 "num_blob"     /**< number of blobs       */
+#define DIM_NUM_NODES                "num_nodes"    /**< number of nodes                */
+#define DIM_NUM_DIM                  "num_dim"      /**< number of dimensions; 2- or 3-d*/
+#define DIM_NUM_EDGE                 "num_edge"     /**< number of edges (over all blks)*/
+#define DIM_NUM_FACE                 "num_face"     /**< number of faces (over all blks)*/
+#define DIM_NUM_ELEM                 "num_elem"     /**< number of elements             */
+#define DIM_NUM_EL_BLK               "num_el_blk"   /**< number of element blocks       */
+#define DIM_NUM_ED_BLK               "num_ed_blk"   /**< number of edge blocks          */
+#define DIM_NUM_FA_BLK               "num_fa_blk"   /**< number of face blocks          */
+#define VAR_COORD                    "coord"        /**< nodal coordinates         */
+#define VAR_COORD_X                  "coordx"       /**< X-dimension coordinate    */
+#define VAR_COORD_Y                  "coordy"       /**< Y-dimension coordinate    */
+#define VAR_COORD_Z                  "coordz"       /**< Z-dimension coordinate    */
+#define VAR_NAME_COOR                "coor_names"   /**< names of coordinates      */
+#define VAR_NAME_EL_BLK              "eb_names"     /**< names of element blocks   */
+#define VAR_NAME_NS                  "ns_names"     /**< names of node sets        */
+#define VAR_NAME_SS                  "ss_names"     /**< names of side sets        */
+#define VAR_NAME_EM                  "emap_names"   /**< names of element maps     */
+#define VAR_NAME_EDM                 "edmap_names"  /**< names of edge    maps     */
+#define VAR_NAME_FAM                 "famap_names"  /**< names of face    maps     */
+#define VAR_NAME_NM                  "nmap_names"   /**< names of node    maps     */
+#define VAR_NAME_ED_BLK              "ed_names"     /**< names of edge    blocks   */
+#define VAR_NAME_FA_BLK              "fa_names"     /**< names of face    blocks   */
+#define VAR_NAME_ES                  "es_names"     /**< names of edge    sets     */
+#define VAR_NAME_FS                  "fs_names"     /**< names of face    sets     */
+#define VAR_NAME_ELS                 "els_names"    /**< names of element sets     */
+#define VAR_STAT_EL_BLK              "eb_status"    /**< element block status      */
+#define VAR_STAT_ECONN               "econn_status" /**< element block edge status */
+#define VAR_STAT_FCONN               "fconn_status" /**< element block face status */
+#define VAR_STAT_ED_BLK              "ed_status"    /**< edge    block status      */
+#define VAR_STAT_FA_BLK              "fa_status"    /**< face    block status      */
+#define VAR_ID_EL_BLK                "eb_prop1"     /**< element block ids props   */
+#define VAR_ID_ED_BLK                "ed_prop1"     /**< edge    block ids props   */
+#define VAR_ID_FA_BLK                "fa_prop1"     /**< face    block ids props   */
+#define DIM_NUM_ENTITY_ASSEMBLY(num) ex__catstr("num_entity_assembly", num)
+#define VAR_ENTITY_ASSEMBLY(num)     ex__catstr("assembly_entity", num)
+#define DIM_NUM_VALUES_BLOB(num)     ex__catstr("num_values_blob", num)
+#define VAR_ENTITY_BLOB(num)         ex__catstr("blob_entity", num)
+#define EX_ATTRIBUTE_TYPE            "_type"
+#define EX_ATTRIBUTE_TYPENAME        "_typename"
+#define EX_ATTRIBUTE_NAME            "_name"
+#define EX_ATTRIBUTE_ID              "_id"
+
+/*! element type names for each element block      */
+#define ATT_NAME_ELB "elem_type"
+/*! number of elements in element  block num               */
+#define DIM_NUM_EL_IN_BLK(num) ex__catstr("num_el_in_blk", num)
+/*! number of nodes per element in element block num       */
+#define DIM_NUM_NOD_PER_EL(num) ex__catstr("num_nod_per_el", num)
+/*! number of attributes in element block num               */
+#define DIM_NUM_ATT_IN_BLK(num) ex__catstr("num_att_in_blk", num)
+/*! number of edges in edge block num               */
+#define DIM_NUM_ED_IN_EBLK(num) ex__catstr("num_ed_in_blk", num)
+/*! number of nodes per edge in edge block num          */
+#define DIM_NUM_NOD_PER_ED(num) ex__catstr("num_nod_per_ed", num)
+/*! number of edges per element in element block num       */
+#define DIM_NUM_EDG_PER_EL(num) ex__catstr("num_edg_per_el", num)
+/*! number of attributes in edge block num               */
+#define DIM_NUM_ATT_IN_EBLK(num) ex__catstr("num_att_in_eblk", num)
+/*! number of faces in face block num               */
+#define DIM_NUM_FA_IN_FBLK(num) ex__catstr("num_fa_in_blk", num)
+/*! number of nodes per face in face block num          */
+#define DIM_NUM_NOD_PER_FA(num) ex__catstr("num_nod_per_fa", num)
+/*! number of faces per element in element block num       */
+#define DIM_NUM_FAC_PER_EL(num) ex__catstr("num_fac_per_el", num)
+/*! number of attributes in face block num               */
+#define DIM_NUM_ATT_IN_FBLK(num) ex__catstr("num_att_in_fblk", num)
+/*! element connectivity for element block num       */
+#define VAR_CONN(num) ex__catstr("connect", num)
+/*! array containing number of entity per */
+/*  entity for n-sided face/element blocks */
+#define VAR_EBEPEC(num) ex__catstr("ebepecnt", num)
+/*! list of attributes for element block num       */
+#define VAR_ATTRIB(num) ex__catstr("attrib", num)
+/*! list of attribute names for element block num     */
+#define VAR_NAME_ATTRIB(num) ex__catstr("attrib_name", num)
+/*! list of the numth property for all element blocks  */
+#define VAR_EB_PROP(num) ex__catstr("eb_prop", num)
+/*! edge connectivity for element block num       */
+#define VAR_ECONN(num) ex__catstr("edgconn", num)
+/*! edge connectivity for edge block num          */
+#define VAR_EBCONN(num) ex__catstr("ebconn", num)
+/*! list of attributes for edge block num          */
+#define VAR_EATTRIB(num) ex__catstr("eattrb", num)
+/*! list of attribute names for edge block num        */
+#define VAR_NAME_EATTRIB(num) ex__catstr("eattrib_name", num)
+#define VAR_NATTRIB           "nattrb"
+#define VAR_NAME_NATTRIB      "nattrib_name"
+#define DIM_NUM_ATT_IN_NBLK   "num_att_in_nblk"
+
+#define VAR_NSATTRIB(num)      ex__catstr("nsattrb", num)
+#define VAR_NAME_NSATTRIB(num) ex__catstr("nsattrib_name", num)
+#define DIM_NUM_ATT_IN_NS(num) ex__catstr("num_att_in_ns", num)
+
+#define VAR_SSATTRIB(num)      ex__catstr("ssattrb", num)
+#define VAR_NAME_SSATTRIB(num) ex__catstr("ssattrib_name", num)
+#define DIM_NUM_ATT_IN_SS(num) ex__catstr("num_att_in_ss", num)
+
+#define VAR_ESATTRIB(num)      ex__catstr("esattrb", num)
+#define VAR_NAME_ESATTRIB(num) ex__catstr("esattrib_name", num)
+#define DIM_NUM_ATT_IN_ES(num) ex__catstr("num_att_in_es", num)
+
+#define VAR_FSATTRIB(num)      ex__catstr("fsattrb", num)
+#define VAR_NAME_FSATTRIB(num) ex__catstr("fsattrib_name", num)
+#define DIM_NUM_ATT_IN_FS(num) ex__catstr("num_att_in_fs", num)
+
+#define VAR_ELSATTRIB(num)      ex__catstr("elsattrb", num)
+#define VAR_NAME_ELSATTRIB(num) ex__catstr("elsattrib_name", num)
+#define DIM_NUM_ATT_IN_ELS(num) ex__catstr("num_att_in_els", num)
+
+/*! list of the numth property for all edge blocks     */
+#define VAR_ED_PROP(num) ex__catstr("ed_prop", num)
+/*! face connectivity for element block num       */
+#define VAR_FCONN(num) ex__catstr("facconn", num)
+/*! face connectivity for face block num          */
+#define VAR_FBCONN(num) ex__catstr("fbconn", num)
+/*! array containing number of entity per entity for n-sided face/element blocks */
+#define VAR_FBEPEC(num) ex__catstr("fbepecnt", num)
+/*! list of attributes for face block num          */
+#define VAR_FATTRIB(num) ex__catstr("fattrb", num)
+/*! list of attribute names for face block num        */
+#define VAR_NAME_FATTRIB(num) ex__catstr("fattrib_name", num)
+/*! list of the numth property for all face blocks     */
+#define VAR_FA_PROP(num) ex__catstr("fa_prop", num)
+/*! name attached to element block, node set, side set, element map,
+    or map properties */
+#define ATT_PROP_NAME "name"
+#define VAR_MAP       "elem_map"      /**< element order map         */
+#define DIM_NUM_SS    "num_side_sets" /**< number of side sets            */
+#define VAR_SS_STAT   "ss_status"     /**< side set status           */
+#define VAR_SS_IDS    "ss_prop1"      /**< side set id properties    */
+/*! number of sides in side set num*/
+#define DIM_NUM_SIDE_SS(num) ex__catstr("num_side_ss", num)
+/*! number of distribution factors in side set num           */
+#define DIM_NUM_DF_SS(num) ex__catstr("num_df_ss", num)
+/*! the distribution factors for each node in side set num */
+#define VAR_FACT_SS(num) ex__catstr("dist_fact_ss", num)
+/*! list of elements in side set num                 */
+#define VAR_ELEM_SS(num) ex__catstr("elem_ss", num)
+/*! list of sides in side set */
+#define VAR_SIDE_SS(num) ex__catstr("side_ss", num)
+/*! list of the numth property for all side sets       */
+#define VAR_SS_PROP(num) ex__catstr("ss_prop", num)
+#define DIM_NUM_ES       "num_edge_sets" /**< number of edge sets            */
+#define VAR_ES_STAT      "es_status"     /**< edge set status           */
+#define VAR_ES_IDS       "es_prop1"      /**< edge set id properties    */
+/*! number of edges in edge set num*/
+#define DIM_NUM_EDGE_ES(num) ex__catstr("num_edge_es", num)
+/*! number of distribution factors in edge set num           */
+#define DIM_NUM_DF_ES(num) ex__catstr("num_df_es", num)
+/*! the distribution factors for each node in edge set num */
+#define VAR_FACT_ES(num) ex__catstr("dist_fact_es", num)
+/*! list of edges in edge set num                 */
+#define VAR_EDGE_ES(num) ex__catstr("edge_es", num)
+/*! list of orientations in the edge set.            */
+#define VAR_ORNT_ES(num) ex__catstr("ornt_es", num)
+/*! list of the numth property for all edge sets       */
+#define VAR_ES_PROP(num) ex__catstr("es_prop", num)
+#define DIM_NUM_FS       "num_face_sets" /**< number of face sets            */
+#define VAR_FS_STAT      "fs_status"     /**< face set status           */
+#define VAR_FS_IDS       "fs_prop1"      /**< face set id properties    */
+/*! number of faces in side set num*/
+#define DIM_NUM_FACE_FS(num) ex__catstr("num_face_fs", num)
+/*! number of distribution factors in face set num           */
+#define DIM_NUM_DF_FS(num) ex__catstr("num_df_fs", num)
+/*! the distribution factors for each node in face set num                 */
+#define VAR_FACT_FS(num) ex__catstr("dist_fact_fs", num)
+/*! list of elements in face set num                 */
+#define VAR_FACE_FS(num) ex__catstr("face_fs", num)
+/*! list of sides in side set */
+#define VAR_ORNT_FS(num) ex__catstr("ornt_fs", num)
+/*! list of the numth property for all face sets       */
+#define VAR_FS_PROP(num) ex__catstr("fs_prop", num)
+#define DIM_NUM_ELS      "num_elem_sets" /**< number of elem sets            */
+/*! number of elements in elem set num                     */
+#define DIM_NUM_ELE_ELS(num) ex__catstr("num_ele_els", num)
+/*! number of distribution factors in element set num        */
+#define DIM_NUM_DF_ELS(num) ex__catstr("num_df_els", num)
+#define VAR_ELS_STAT        "els_status" /**< elem set status           */
+#define VAR_ELS_IDS         "els_prop1"  /**< elem set id properties    */
+/*! list of elements in elem set num                 */
+#define VAR_ELEM_ELS(num) ex__catstr("elem_els", num)
+/*! list of distribution factors in elem set num */
+#define VAR_FACT_ELS(num) ex__catstr("dist_fact_els", num)
+/*! list of the numth property for all elem sets       */
+#define VAR_ELS_PROP(num) ex__catstr("els_prop", num)
+#define DIM_NUM_NS        "num_node_sets" /**< number of node sets            */
+/*! number of nodes in node set num                     */
+#define DIM_NUM_NOD_NS(num) ex__catstr("num_nod_ns", num)
+/*! number of distribution factors in node set num           */
+#define DIM_NUM_DF_NS(num) ex__catstr("num_df_ns", num)
+#define VAR_NS_STAT        "ns_status" /**< node set status           */
+#define VAR_NS_IDS         "ns_prop1"  /**< node set id properties    */
+/*! list of nodes in node set num                     */
+#define VAR_NODE_NS(num) ex__catstr("node_ns", num)
+/*! list of distribution factors in node set num */
+#define VAR_FACT_NS(num) ex__catstr("dist_fact_ns", num)
+/*! list of the numth property for all node sets       */
+#define VAR_NS_PROP(num) ex__catstr("ns_prop", num)
+#define DIM_NUM_QA       "num_qa_rec"       /**< number of QA records           */
+#define VAR_QA_TITLE     "qa_records"       /**< QA records                */
+#define DIM_NUM_INFO     "num_info"         /**< number of information records  */
+#define VAR_INFO         "info_records"     /**< information records       */
+#define VAR_WHOLE_TIME   "time_whole"       /**< simulation times for whole time steps */
+#define VAR_ASSEMBLY_TAB "assembly_var_tab" /**< assembly variable truth table */
+#define VAR_BLOB_TAB     "blob_var_tab"     /**< blob variable truth table */
+#define VAR_ELEM_TAB     "elem_var_tab"     /**< element variable truth table */
+#define VAR_EBLK_TAB     "edge_var_tab"     /**< edge variable truth table */
+#define VAR_FBLK_TAB     "face_var_tab"     /**< face variable truth table */
+#define VAR_ELSET_TAB    "elset_var_tab"    /**< elemset variable truth table */
+#define VAR_SSET_TAB     "sset_var_tab"     /**< sideset variable truth table */
+#define VAR_FSET_TAB     "fset_var_tab"     /**< faceset variable truth table */
+#define VAR_ESET_TAB     "eset_var_tab"     /**< edgeset variable truth table */
+#define VAR_NSET_TAB     "nset_var_tab"     /**< nodeset variable truth table */
+#define DIM_NUM_GLO_VAR  "num_glo_var"      /**< number of global variables */
+#define VAR_NAME_GLO_VAR "name_glo_var"     /**< names of global variables */
+#define VAR_GLO_VAR      "vals_glo_var"     /**< values of global variables*/
+#define DIM_NUM_NOD_VAR  "num_nod_var"      /**< number of nodal variables      */
+#define VAR_NAME_NOD_VAR "name_nod_var"     /**< names of nodal variables  */
+#define VAR_NOD_VAR      "vals_nod_var"     /**< values of nodal variables \deprecated */
+/*! values of nodal variables */
+#define VAR_NOD_VAR_NEW(num) ex__catstr("vals_nod_var", num)
+
+#define DIM_NUM_ASSEMBLY_VAR         "num_assembly_var"  /**< number of assembly variables    */
+#define VAR_NAME_ASSEMBLY_VAR        "name_assembly_var" /**< names of assembly variables*/
+#define VAR_ASSEMBLY_VAR(num1, num2) ex__catstr2("vals_assembly_var", num1, "assembly", num2)
+
+#define DIM_NUM_BLOB_VAR         "num_blob_var"  /**< number of blob variables    */
+#define VAR_NAME_BLOB_VAR        "name_blob_var" /**< names of blob variables*/
+#define VAR_BLOB_VAR(num1, num2) ex__catstr2("vals_blob_var", num1, "blob", num2)
+
+#define DIM_NUM_ELE_VAR  "num_elem_var"  /**< number of element variables    */
+#define VAR_NAME_ELE_VAR "name_elem_var" /**< names of element variables*/
+/*! values of element variable num1 in element block num2                    */
+#define VAR_ELEM_VAR(num1, num2) ex__catstr2("vals_elem_var", num1, "eb", num2)
+#define DIM_NUM_EDG_VAR          "num_edge_var"  /**< number of edge variables       */
+#define VAR_NAME_EDG_VAR         "name_edge_var" /**< names of edge variables   */
+/*! values of edge variable num1 in edge block num2 */
+#define VAR_EDGE_VAR(num1, num2) ex__catstr2("vals_edge_var", num1, "eb", num2)
+#define DIM_NUM_FAC_VAR          "num_face_var"  /**< number of face variables       */
+#define VAR_NAME_FAC_VAR         "name_face_var" /**< names of face variables   */
+/*! values of face variable num1 in face block num2 */
+#define VAR_FACE_VAR(num1, num2) ex__catstr2("vals_face_var", num1, "fb", num2)
+
+#define DIM_NUM_NSET_VAR  "num_nset_var"  /**< number of nodeset variables    */
+#define VAR_NAME_NSET_VAR "name_nset_var" /**< names of nodeset variables*/
+/*! values of nodeset variable num1 in nodeset num2    */
+#define VAR_NS_VAR(num1, num2) ex__catstr2("vals_nset_var", num1, "ns", num2)
+#define DIM_NUM_ESET_VAR       "num_eset_var" /**< number of edgeset variables    */
+/*! values of edgeset variable num1 in edgeset num2    */
+#define VAR_NAME_ESET_VAR      "name_eset_var" /**< names of edgeset variables*/
+#define VAR_ES_VAR(num1, num2) ex__catstr2("vals_eset_var", num1, "es", num2)
+#define DIM_NUM_FSET_VAR       "num_fset_var"  /**< number of faceset variables    */
+#define VAR_NAME_FSET_VAR      "name_fset_var" /**< names of faceset variables*/
+/*! values of faceset variable num1 in faceset num2    */
+#define VAR_FS_VAR(num1, num2) ex__catstr2("vals_fset_var", num1, "fs", num2)
+#define DIM_NUM_SSET_VAR       "num_sset_var"  /**< number of sideset variables    */
+#define VAR_NAME_SSET_VAR      "name_sset_var" /**< names of sideset variables*/
+/*! values of sideset variable num1 in sideset num2    */
+#define VAR_SS_VAR(num1, num2) ex__catstr2("vals_sset_var", num1, "ss", num2)
+#define DIM_NUM_ELSET_VAR      "num_elset_var"  /**< number of element set variables*/
+#define VAR_NAME_ELSET_VAR     "name_elset_var" /**< names of elemset variables*/
+/*! values of elemset variable num1 in elemset num2    */
+#define VAR_ELS_VAR(num1, num2) ex__catstr2("vals_elset_var", num1, "es", num2)
+
+/**
+ * \defgroup ReductionVariables Variables controlling storage of reduction variables
+ *@{
+ */
+#define DIM_NUM_ASSEMBLY_RED_VAR  "num_assembly_red_var"  /**< number of assembly variables    */
+#define VAR_NAME_ASSEMBLY_RED_VAR "name_assembly_red_var" /**< names of assembly variables*/
+#define VAR_ASSEMBLY_RED_VAR(num) ex__catstr("vals_red_var_assembly", num)
+
+#define DIM_NUM_BLOB_RED_VAR  "num_blob_red_var"  /**< number of blob variables    */
+#define VAR_NAME_BLOB_RED_VAR "name_blob_red_var" /**< names of blob variables*/
+#define VAR_BLOB_RED_VAR(num) ex__catstr("vals_red_var_blob", num)
+
+#define DIM_NUM_ELE_RED_VAR  "num_elem_red_var"  /**< number of element variables    */
+#define VAR_NAME_ELE_RED_VAR "name_elem_red_var" /**< names of element variables*/
+/*! values of element variable num in element block num                    */
+#define VAR_ELEM_RED_VAR(num) ex__catstr("vals_red_var_eb", num)
+
+#define DIM_NUM_EDG_RED_VAR  "num_edge_red_var"  /**< number of edge variables       */
+#define VAR_NAME_EDG_RED_VAR "name_edge_red_var" /**< names of edge variables   */
+/*! values of edge variable num in edge block num */
+#define VAR_EDGE_RED_VAR(num) ex__catstr("vals_red_var_edb", num)
+
+#define DIM_NUM_FAC_RED_VAR  "num_face_red_var"  /**< number of face variables       */
+#define VAR_NAME_FAC_RED_VAR "name_face_red_var" /**< names of face variables   */
+/*! values of face variable num in face block num */
+#define VAR_FACE_RED_VAR(num) ex__catstr("vals_red_var_fb", num)
+
+#define DIM_NUM_NSET_RED_VAR  "num_nset_red_var"  /**< number of nodeset variables    */
+#define VAR_NAME_NSET_RED_VAR "name_nset_red_var" /**< names of nodeset variables*/
+/*! values of nodeset variable num in nodeset num    */
+#define VAR_NS_RED_VAR(num) ex__catstr("vals_red_var_nset", num)
+
+#define DIM_NUM_ESET_RED_VAR "num_eset_red_var" /**< number of edgeset variables    */
+/*! values of edgeset variable num in edgeset num    */
+#define VAR_NAME_ESET_RED_VAR "name_eset_red_var" /**< names of edgeset variables*/
+#define VAR_ES_RED_VAR(num)   ex__catstr("vals_red_var_eset", num)
+
+#define DIM_NUM_FSET_RED_VAR  "num_fset_red_var"  /**< number of faceset variables    */
+#define VAR_NAME_FSET_RED_VAR "name_fset_red_var" /**< names of faceset variables*/
+/*! values of faceset variable num in faceset num    */
+#define VAR_FS_RED_VAR(num) ex__catstr("vals_red_var_fset", num)
+
+#define DIM_NUM_SSET_RED_VAR  "num_sset_red_var"  /**< number of sideset variables    */
+#define VAR_NAME_SSET_RED_VAR "name_sset_red_var" /**< names of sideset variables*/
+/*! values of sideset variable num in sideset num    */
+#define VAR_SS_RED_VAR(num) ex__catstr("vals_red_var_sset", num)
+
+#define DIM_NUM_ELSET_RED_VAR  "num_elset_red_var"  /**< number of element set variables*/
+#define VAR_NAME_ELSET_RED_VAR "name_elset_red_var" /**< names of elemset variables*/
+/*! values of elemset variable num in elemset num    */
+#define VAR_ELS_RED_VAR(num) ex__catstr("vals_red_var_elset", num)
+/** @}*/
+
+/*! general dimension of length MAX_STR_LENGTH used for some string lengths   */
+#define DIM_STR "len_string"
+/*! general dimension of length MAX_NAME_LENGTH used for name lengths   */
+#define DIM_STR_NAME "len_name"
+/*! general dimension of length MAX_LINE_LENGTH used for long strings   */
+#define DIM_LIN "len_line"
+#define DIM_N4  "four"
+#define DIM_N1  "blob_entity"
+/*! unlimited (expandable) dimension for time steps*/
+#define DIM_TIME         "time_step"
+#define VAR_ELEM_NUM_MAP "elem_num_map"  /**< element numbering map     */
+#define VAR_FACE_NUM_MAP "face_num_map"  /**< face numbering map     */
+#define VAR_EDGE_NUM_MAP "edge_num_map"  /**< edge numbering map     */
+#define VAR_NODE_NUM_MAP "node_num_map"  /**< node numbering map        */
+#define DIM_NUM_EM       "num_elem_maps" /**< number of element maps         */
+/*! the numth element map     */
+#define VAR_ELEM_MAP(num) ex__catstr("elem_map", num)
+/*! list of the numth property for all element maps    */
+#define VAR_EM_PROP(num) ex__catstr("em_prop", num)
+#define DIM_NUM_EDM      "num_edge_maps" /**< number of edge maps            */
+/*! the numth edge map        */
+#define VAR_EDGE_MAP(num) ex__catstr("edge_map", num)
+/* list of the numth property for all edge maps       */
+#define VAR_EDM_PROP(num) ex__catstr("edm_prop", num)
+#define DIM_NUM_FAM       "num_face_maps" /**< number of face maps            */
+/*! the numth face map        */
+#define VAR_FACE_MAP(num) ex__catstr("face_map", num)
+/*! list of the numth property for all face maps       */
+#define VAR_FAM_PROP(num) ex__catstr("fam_prop", num)
+#define DIM_NUM_NM        "num_node_maps" /**< number of node maps            */
+/*! the numth node map        */
+#define VAR_NODE_MAP(num) ex__catstr("node_map", num)
+/*! list of the numth property for all node maps       */
+#define VAR_NM_PROP(num) ex__catstr("nm_prop", num)
+/*! list of the numth property for all assemblies      */
+#define VAR_ASSEMBLY_PROP(num) ex__catstr("assembly_prop", num)
+#define VAR_BLOB_PROP(num)     ex__catstr("blob_prop", num)
+
+#define DIM_NUM_CFRAMES  "num_cframes"
+#define DIM_NUM_CFRAME9  "num_cframes_9"
+#define VAR_FRAME_COORDS "frame_coordinates"
+#define VAR_FRAME_IDS    "frame_ids"
+#define VAR_FRAME_TAGS   "frame_tags"
+
+#define VAR_ELBLK_IDS_GLOBAL   "el_blk_ids_global"
+#define VAR_ELBLK_CNT_GLOBAL   "el_blk_cnt_global"
+#define VAR_NS_IDS_GLOBAL      "ns_ids_global"
+#define VAR_NS_NODE_CNT_GLOBAL "ns_node_cnt_global"
+#define VAR_NS_DF_CNT_GLOBAL   "ns_df_cnt_global"
+#define VAR_SS_IDS_GLOBAL      "ss_ids_global"
+#define VAR_SS_SIDE_CNT_GLOBAL "ss_side_cnt_global"
+#define VAR_SS_DF_CNT_GLOBAL   "ss_df_cnt_global"
+#define VAR_FILE_TYPE          "nem_ftype"
+#define VAR_COMM_MAP           "comm_map"
+#define VAR_NODE_MAP_INT       "node_mapi"
+#define VAR_NODE_MAP_INT_IDX   "node_mapi_idx"
+#define VAR_NODE_MAP_BOR       "node_mapb"
+#define VAR_NODE_MAP_BOR_IDX   "node_mapb_idx"
+#define VAR_NODE_MAP_EXT       "node_mape"
+#define VAR_NODE_MAP_EXT_IDX   "node_mape_idx"
+#define VAR_ELEM_MAP_INT       "elem_mapi"
+#define VAR_ELEM_MAP_INT_IDX   "elem_mapi_idx"
+#define VAR_ELEM_MAP_BOR       "elem_mapb"
+#define VAR_ELEM_MAP_BOR_IDX   "elem_mapb_idx"
+#define VAR_INT_N_STAT         "int_n_stat"
+#define VAR_BOR_N_STAT         "bor_n_stat"
+#define VAR_EXT_N_STAT         "ext_n_stat"
+#define VAR_INT_E_STAT         "int_e_stat"
+#define VAR_BOR_E_STAT         "bor_e_stat"
+#define VAR_N_COMM_IDS         "n_comm_ids"
+#define VAR_N_COMM_STAT        "n_comm_stat"
+#define VAR_N_COMM_INFO_IDX    "n_comm_info_idx"
+#define VAR_E_COMM_IDS         "e_comm_ids"
+#define VAR_E_COMM_STAT        "e_comm_stat"
+#define VAR_E_COMM_INFO_IDX    "e_comm_info_idx"
+#define VAR_N_COMM_NIDS        "n_comm_nids"
+#define VAR_N_COMM_PROC        "n_comm_proc"
+#define VAR_N_COMM_DATA_IDX    "n_comm_data_idx"
+#define VAR_E_COMM_EIDS        "e_comm_eids"
+#define VAR_E_COMM_SIDS        "e_comm_sids"
+#define VAR_E_COMM_PROC        "e_comm_proc"
+#define VAR_E_COMM_DATA_IDX    "e_comm_data_idx"
+
+#define DIM_NUM_INT_NODES    "num_int_node"
+#define DIM_NUM_BOR_NODES    "num_bor_node"
+#define DIM_NUM_EXT_NODES    "num_ext_node"
+#define DIM_NUM_INT_ELEMS    "num_int_elem"
+#define DIM_NUM_BOR_ELEMS    "num_bor_elem"
+#define DIM_NUM_PROCS        "num_processors"
+#define DIM_NUM_PROCS_F      "num_procs_file"
+#define DIM_NUM_NODES_GLOBAL "num_nodes_global"
+#define DIM_NUM_ELEMS_GLOBAL "num_elems_global"
+#define DIM_NUM_NS_GLOBAL    "num_ns_global"
+#define DIM_NUM_SS_GLOBAL    "num_ss_global"
+#define DIM_NUM_ELBLK_GLOBAL "num_el_blk_global"
+#define DIM_NUM_N_CMAPS      "num_n_cmaps"
+#define DIM_NUM_E_CMAPS      "num_e_cmaps"
+#define DIM_NCNT_CMAP        "ncnt_cmap"
+#define DIM_ECNT_CMAP        "ecnt_cmap"
+
+enum ex__element_type {
+  EX_EL_UNK          = -1, /**< unknown entity */
+  EX_EL_NULL_ELEMENT = 0,
+  EX_EL_TRIANGLE     = 1,  /**< Triangle entity */
+  EX_EL_QUAD         = 2,  /**< Quad entity */
+  EX_EL_HEX          = 3,  /**< Hex entity */
+  EX_EL_WEDGE        = 4,  /**< Wedge entity */
+  EX_EL_TETRA        = 5,  /**< Tetra entity */
+  EX_EL_TRUSS        = 6,  /**< Truss entity */
+  EX_EL_BEAM         = 7,  /**< Beam entity */
+  EX_EL_SHELL        = 8,  /**< Shell entity */
+  EX_EL_SPHERE       = 9,  /**< Sphere entity */
+  EX_EL_CIRCLE       = 10, /**< Circle entity */
+  EX_EL_TRISHELL     = 11, /**< Triangular Shell entity */
+  EX_EL_PYRAMID      = 12  /**< Pyramid entity */
+};
+typedef enum ex__element_type ex__element_type;
+
+/* Internal structure declarations */
+
+struct ex__file_item
+{
+  int          file_id;
+  nc_type      netcdf_type_code;
+  int          int64_status;
+  int          maximum_name_length;
+  int          time_varid; /* Store to avoid lookup each timestep */
+  unsigned int assembly_count;
+  unsigned int blob_count;
+  unsigned int
+      compression_algorithm : 2;      /**< GZIP/ZLIB, SZIP, more may be supported by NetCDF soon */
+  unsigned int compression_level : 6; /**< 0 (disabled) to 9 (maximum) compression level for
+                                         gzip, 4..32 and even for szip; NetCDF-4 only */
+  unsigned int user_compute_wordsize : 1; /**< 0 for 4 byte or 1 for 8 byte reals */
+  unsigned int shuffle : 1;               /**< 1 true, 0 false */
+  unsigned int
+      file_type : 2; /**< 0 - classic, 1 -- 64 bit classic, 2 --NetCDF4,  3 --NetCDF4 classic */
+  unsigned int          is_write : 1;    /**< for output or append */
+  unsigned int          is_parallel : 1; /**< 1 true, 0 false */
+  unsigned int          is_hdf5 : 1;     /**< 1 true, 0 false */
+  unsigned int          is_pnetcdf : 1;  /**< 1 true, 0 false */
+  unsigned int          has_nodes : 1;   /**< for input only at this time */
+  unsigned int          has_edges : 1;   /**< for input only at this time */
+  unsigned int          has_faces : 1;   /**< for input only at this time */
+  unsigned int          has_elems : 1;   /**< for input only at this time */
+  struct ex__file_item *next;
+};
+
+struct ex__elem_blk_parm
+{
+  char             elem_type[33];
+  int64_t          elem_blk_id;
+  int64_t          num_elem_in_blk;
+  int              num_nodes_per_elem;
+  int              num_sides;
+  int              num_nodes_per_side[6];
+  int              num_attr;
+  int64_t          elem_ctr;
+  ex__element_type elem_type_val;
+};
+
+/* Used in exo_jack.c for fortran interface */
+enum ex__coordinate_frame_type {
+  EX_CF_RECTANGULAR = 1,
+  EX_CF_CYLINDRICAL = 2,
+  EX_CF_SPHERICAL   = 3
+};
+typedef enum ex__coordinate_frame_type ex__coordinate_frame_type;
+
+struct ex__list_item
+{ /* for use with ex_get_file_item */
+  int                   exo_id;
+  int                   value;
+  struct ex__list_item *next;
+};
+
+struct ex__obj_stats
+{
+  int64_t              *id_vals;
+  int                  *stat_vals;
+  size_t                num;
+  int                   exoid;
+  char                  valid_ids;
+  char                  valid_stat;
+  char                  sequential;
+  struct ex__obj_stats *next;
+};
+
+#ifndef EXODUS_EXPORT
+#define EXODUS_EXPORT extern
+#endif /* EXODUS_EXPORT */
+
+EXODUS_EXPORT void ex__iqsort(int v[], int iv[], size_t N);
+EXODUS_EXPORT void ex__iqsort64(int64_t v[], int64_t iv[], int64_t N);
+
+EXODUS_EXPORT char *ex__catstr(const char * /*string*/, int /*num*/);
+EXODUS_EXPORT char *ex__catstr2(const char * /*string1*/, int /*num1*/, const char * /*string2*/,
+                                int /*num2*/);
+EXODUS_EXPORT char *ex__dim_num_entries_in_object(ex_entity_type /*obj_type*/, int /*idx*/);
+EXODUS_EXPORT char *ex__dim_num_objects(ex_entity_type obj_type);
+EXODUS_EXPORT char *ex__name_var_of_object(ex_entity_type /*obj_type*/, int /*i*/, int /*j*/);
+EXODUS_EXPORT char *ex__name_red_var_of_object(ex_entity_type /*obj_type*/, int /*indx*/);
+EXODUS_EXPORT char *ex__name_of_map(ex_entity_type /*map_type*/, int /*map_index*/);
+
+EXODUS_EXPORT int ex__conv_init(int exoid, int *comp_wordsize, int *io_wordsize, int file_wordsize,
+                                int int64_status, bool is_parallel, bool is_hdf5, bool is_pnetcdf,
+                                bool is_write);
+
+EXODUS_EXPORT void ex__conv_exit(int exoid);
+
+EXODUS_EXPORT nc_type nc_flt_code(int exoid);
+EXODUS_EXPORT int     ex__comp_ws(int exoid);
+EXODUS_EXPORT int     ex__get_cpu_ws(void);
+EXODUS_EXPORT int     ex__is_parallel(int exoid);
+
+EXODUS_EXPORT struct ex__list_item **ex__get_counter_list(ex_entity_type obj_type);
+EXODUS_EXPORT int  ex__get_file_item(int /*exoid*/, struct ex__list_item  **/*list_ptr*/);
+EXODUS_EXPORT int  ex__inc_file_item(int /*exoid*/, struct ex__list_item  **/*list_ptr*/);
+EXODUS_EXPORT void ex__rm_file_item(int /*exoid*/, struct ex__list_item ** /*list_ptr*/);
+
+extern struct ex__obj_stats *exoII_eb;
+extern struct ex__obj_stats *exoII_ed;
+extern struct ex__obj_stats *exoII_fa;
+extern struct ex__obj_stats *exoII_ns;
+extern struct ex__obj_stats *exoII_es;
+extern struct ex__obj_stats *exoII_fs;
+extern struct ex__obj_stats *exoII_ss;
+extern struct ex__obj_stats *exoII_els;
+extern struct ex__obj_stats *exoII_em;
+extern struct ex__obj_stats *exoII_edm;
+extern struct ex__obj_stats *exoII_fam;
+extern struct ex__obj_stats *exoII_nm;
+
+struct ex__file_item *ex__find_file_item(int exoid);
+struct ex__file_item *ex__add_file_item(int exoid);
+struct ex__obj_stats *ex__get_stat_ptr(int exoid, struct ex__obj_stats **obj_ptr);
+
+EXODUS_EXPORT void ex__rm_stat_ptr(int exoid, struct ex__obj_stats **obj_ptr);
+
+EXODUS_EXPORT void ex__set_compact_storage(int exoid, int varid);
+EXODUS_EXPORT void ex__compress_variable(int exoid, int varid, int type);
+EXODUS_EXPORT int  ex__id_lkup(int exoid, ex_entity_type id_type, ex_entity_id num);
+EXODUS_EXPORT int  ex__check_valid_file_id(
+     int exoid, const char *func); /** Return fatal error if exoid does not refer to valid file */
+EXODUS_EXPORT int   ex__check_multiple_open(const char *path, int mode, const char *func);
+EXODUS_EXPORT int   ex__check_file_type(const char *path, int *type);
+EXODUS_EXPORT char *ex__canonicalize_filename(const char *path);
+EXODUS_EXPORT int   ex__get_dimension(int exoid, const char *DIMENSION, const char *label,
+                                      size_t *count, int *dimid, const char *routine);
+
+EXODUS_EXPORT int ex__get_nodal_var(int exoid, int time_step, int nodal_var_index,
+                                    int64_t num_nodes, void *nodal_var_vals);
+
+EXODUS_EXPORT int ex__put_nodal_var(int exoid, int time_step, int nodal_var_index,
+                                    int64_t num_nodes, const void *nodal_var_vals);
+
+EXODUS_EXPORT int ex__get_nodal_var_time(int exoid, int nodal_var_index, int64_t node_number,
+                                         int beg_time_step, int end_time_step,
+                                         void *nodal_var_vals);
+
+EXODUS_EXPORT int ex__get_partial_nodal_var(int exoid, int time_step, int nodal_var_index,
+                                            int64_t start_node, int64_t num_nodes, void *var_vals);
+
+EXODUS_EXPORT int ex__put_partial_nodal_var(int exoid, int time_step, int nodal_var_index,
+                                            int64_t start_node, int64_t num_nodes,
+                                            const void *nodal_var_vals);
+EXODUS_EXPORT int ex__get_glob_vars(int exoid, int time_step, int num_glob_vars,
+                                    void *glob_var_vals);
+
+EXODUS_EXPORT int ex__get_glob_var_time(int exoid, int glob_var_index, int beg_time_step,
+                                        int end_time_step, void *glob_var_vals);
+
+EXODUS_EXPORT int  ex__get_name(int exoid, int varid, size_t index, char *name, int name_size,
+                                ex_entity_type obj_type, const char *routine);
+EXODUS_EXPORT int  ex__get_names(int exoid, int varid, size_t num_entity, char **names,
+                                 ex_entity_type obj_type, const char *routine);
+EXODUS_EXPORT int  ex__put_name(int exoid, int varid, size_t index, const char *name,
+                                ex_entity_type obj_type, const char *subtype, const char *routine);
+EXODUS_EXPORT int  ex__put_names(int exoid, int varid, size_t num_entity, char *const *names,
+                                 ex_entity_type obj_type, const char *subtype, const char *routine);
+EXODUS_EXPORT void ex__trim(char *name);
+EXODUS_EXPORT void ex__update_max_name_length(int exoid, int length);
+EXODUS_EXPORT int  ex__leavedef(int         exoid,    /* NemesisI file ID         */
+                                const char *call_rout /* Name of calling function */
+ );
+
+EXODUS_EXPORT int ex__check_version(int run_version);
+EXODUS_EXPORT int ex__handle_mode(unsigned int my_mode, int is_parallel, int run_version);
+EXODUS_EXPORT int ex__populate_header(int exoid, const char *path, int my_mode, int is_parallel,
+                                      int *comp_ws, int *io_ws);
+
+EXODUS_EXPORT int ex__get_block_param(int exoid, ex_entity_id id, int ndim,
+                                      struct ex__elem_blk_parm *elem_blk_parm);
+
+EXODUS_EXPORT int ex__get_file_type(int exoid, char *ftype);
+
+EXODUS_EXPORT int ex__put_nemesis_version(int exoid);
+
+EXODUS_EXPORT int ex__put_homogenous_block_params(int exoid, size_t block_count,
+                                                  const struct ex_block *blocks);
+
+EXODUS_EXPORT int ne__check_file_version(int exoid);
+
+EXODUS_EXPORT int ne__id_lkup(int          exoid,       /* NetCDF/Exodus file ID */
+                              const char  *ne_var_name, /* Nemesis variable name */
+                              int64_t     *idx,         /* index variable for variable, length 2 */
+                              ex_entity_id ne_var_id    /* NetCDF variable ID */
+);
+
+/**
+ * For output databases, the maximum length of any entity, variable,
+ * property, attribute, or coordinate name to be written (not
+ * including the NULL terminator). If a name is longer than this
+ * value, a warning message will be output to stderr and the name
+ * will be truncated.  Must be set (via call to
+ * ex_set_max_name_length()(exoid, int len) prior to calling ex_create().
+ *
+ * For input databases, the size of the name arrays that the client
+ * code will be passing to API routines that retrieve names (not
+ * including the NULL terminator). This defaults to 32 for
+ * compatibility with older clients. The value used at the time of
+ * creation of the database can be queried by ex_inquire with the
+ * #EX_INQ_DB_MAX_ALLOWED_NAME_LENGTH argument. The current value for this
+ * variable can be queried with #EX_INQ_MAX_READ_NAME_LENGTH argument.
+ *
+ * Note that this is a global setting for all databases. If you are
+ * accessing multiple databases, they will all use the same value.
+ */
+EXODUS_EXPORT int ex__default_max_name_length;
+/*! @} */
+
+#ifdef __cplusplus
+}
+#endif

HybridMesher/libraries/EXODUS/include/exodusII_par.h

@@ -0,0 +1,18 @@
+/*
+ * Copyright(C) 1999-2020, 2022 National Technology & Engineering Solutions
+ * of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
+ * NTESS, the U.S. Government retains certain rights in this software.
+ *
+ * See packages/seacas/LICENSE for details
+ */
+/*
+ * NOTE: Contents of this include file have been moved to exodusII.h
+ * Retained here just for backward compatibility
+ */
+#pragma once
+
+#include "exodusII.h"
+
+#if !defined(PARALLEL_AWARE_EXODUS)
+#error "Parallel-aware exodusII_par.h included in non-parallel context"
+#endif

HybridMesher/libraries/EXODUS/include/exodus_config.h

@@ -0,0 +1,22 @@
+#pragma once
+/* #undef EXODUS_THREADSAFE */
+
+#ifndef SEACAS_DEPRECATED
+#  if (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
+#    define SEACAS_DEPRECATED  __attribute__((__deprecated__))
+#  else
+#    define SEACAS_DEPRECATED
+#  endif
+#endif
+
+#ifndef SEACAS_DEPRECATED_MSG
+#  if (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 5))
+#    define SEACAS_DEPRECATED_MSG(MSG)  __attribute__((__deprecated__ (#MSG) ))
+#  elif (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
+#    define SEACAS_DEPRECATED_MSG(MSG)  __attribute__((__deprecated__))
+#  else
+#    define SEACAS_DEPRECATED_MSG(MSG)
+#  endif
+#endif
+
+

HybridMesher/libraries/EXODUS/lib/cmake/SEACAS/SEACASConfig.cmake

@@ -0,0 +1,222 @@
+# @HEADER
+# ************************************************************************
+#
+#            TriBITS: Tribal Build, Integrate, and Test System
+#                    Copyright 2013 Sandia Corporation
+#
+# Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+# the U.S. Government retains certain rights in this software.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# ************************************************************************
+# @HEADER
+
+##############################################################################
+#
+# CMake variable for use by Seacas/SEACAS clients.
+#
+# Do not edit: This file was generated automatically by CMake.
+#
+##############################################################################
+
+if(CMAKE_VERSION VERSION_LESS 3.3)
+  set(${CMAKE_FIND_PACKAGE_NAME}_NOT_FOUND_MESSAGE
+    "SEACAS requires CMake 3.3 or later for 'if (... IN_LIST ...)'"
+    )
+  set(${CMAKE_FIND_PACKAGE_NAME}_FOUND FALSE)
+  return()
+endif()
+cmake_minimum_required(VERSION 3.3...3.22.0)
+
+## ---------------------------------------------------------------------------
+## Compilers used by Seacas/SEACAS build
+## ---------------------------------------------------------------------------
+
+set(SEACAS_CXX_COMPILER "/usr/lib/ccache/g++")
+
+set(SEACAS_C_COMPILER "/usr/lib/ccache/gcc")
+
+set(SEACAS_Fortran_COMPILER "gfortran")
+# Deprecated!
+set(SEACAS_FORTRAN_COMPILER "gfortran") 
+
+
+## ---------------------------------------------------------------------------
+## Compiler flags used by Seacas/SEACAS build
+## ---------------------------------------------------------------------------
+
+## Give the build type
+set(SEACAS_CMAKE_BUILD_TYPE "RELEASE")
+
+## Set compiler flags, including those determined by build type
+set(SEACAS_CXX_FLAGS [[ -O3 -DNDEBUG]])
+
+set(SEACAS_C_FLAGS [[  -Wall -Wunused -pedantic -std=c11 -fPIC -O3 -DNDEBUG]])
+
+set(SEACAS_Fortran_FLAGS [[ ]])
+# Deprecated
+set(SEACAS_FORTRAN_FLAGS [[ ]])
+
+## Extra link flags (e.g., specification of fortran libraries)
+set(SEACAS_EXTRA_LD_FLAGS [[]])
+
+## This is the command-line entry used for setting rpaths. In a build
+## with static libraries it will be empty.
+set(SEACAS_SHARED_LIB_RPATH_COMMAND "-Wl,-rpath,/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/EXODUS/lib")
+set(SEACAS_BUILD_SHARED_LIBS "YES")
+
+set(SEACAS_LINKER /usr/bin/ld)
+set(SEACAS_AR /usr/bin/ar)
+
+## ---------------------------------------------------------------------------
+## Set library specifications and paths
+## ---------------------------------------------------------------------------
+
+## Base install location (if not in the build tree)
+set(SEACAS_INSTALL_DIR "/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/EXODUS")
+
+## List of package libraries
+set(SEACAS_LIBRARIES SEACAS::all_libs)
+
+## ---------------------------------------------------------------------------
+## MPI specific variables
+##   These variables are provided to make it easier to get the mpi libraries
+##   and includes on systems that do not use the mpi wrappers for compiling
+## ---------------------------------------------------------------------------
+
+set(SEACAS_MPI_LIBRARIES "")
+set(SEACAS_MPI_LIBRARY_DIRS "")
+set(SEACAS_MPI_INCLUDE_DIRS "")
+set(SEACAS_MPI_EXEC "")
+set(SEACAS_MPI_EXEC_MAX_NUMPROCS "")
+set(SEACAS_MPI_EXEC_NUMPROCS_FLAG "")
+
+## ---------------------------------------------------------------------------
+## Set useful general variables
+## ---------------------------------------------------------------------------
+
+# Enables/Disables for upstream package dependencies
+set(SEACAS_ENABLE_SEACASExodus ON)
+set(SEACAS_ENABLE_SEACASIoss OFF)
+set(SEACAS_ENABLE_SEACASExodus_for OFF)
+set(SEACAS_ENABLE_SEACASExoIIv2for32 OFF)
+set(SEACAS_ENABLE_SEACASNemesis OFF)
+set(SEACAS_ENABLE_SEACASChaco OFF)
+set(SEACAS_ENABLE_SEACASAprepro_lib OFF)
+set(SEACAS_ENABLE_SEACASSupes OFF)
+set(SEACAS_ENABLE_SEACASSuplib OFF)
+set(SEACAS_ENABLE_SEACASSuplibC OFF)
+set(SEACAS_ENABLE_SEACASSuplibCpp OFF)
+set(SEACAS_ENABLE_SEACASSVDI OFF)
+set(SEACAS_ENABLE_SEACASPLT OFF)
+set(SEACAS_ENABLE_SEACASAlgebra OFF)
+set(SEACAS_ENABLE_SEACASAprepro OFF)
+set(SEACAS_ENABLE_SEACASBlot OFF)
+set(SEACAS_ENABLE_SEACASConjoin OFF)
+set(SEACAS_ENABLE_SEACASEjoin OFF)
+set(SEACAS_ENABLE_SEACASEpu OFF)
+set(SEACAS_ENABLE_SEACASCpup OFF)
+set(SEACAS_ENABLE_SEACASExo2mat OFF)
+set(SEACAS_ENABLE_SEACASExodiff OFF)
+set(SEACAS_ENABLE_SEACASExomatlab OFF)
+set(SEACAS_ENABLE_SEACASExotxt OFF)
+set(SEACAS_ENABLE_SEACASExo_format OFF)
+set(SEACAS_ENABLE_SEACASEx1ex2v2 OFF)
+set(SEACAS_ENABLE_SEACASExotec2 OFF)
+set(SEACAS_ENABLE_SEACASFastq OFF)
+set(SEACAS_ENABLE_SEACASGjoin OFF)
+set(SEACAS_ENABLE_SEACASGen3D OFF)
+set(SEACAS_ENABLE_SEACASGenshell OFF)
+set(SEACAS_ENABLE_SEACASGrepos OFF)
+set(SEACAS_ENABLE_SEACASExplore OFF)
+set(SEACAS_ENABLE_SEACASMapvarlib OFF)
+set(SEACAS_ENABLE_SEACASMapvar OFF)
+set(SEACAS_ENABLE_SEACASMapvar-kd OFF)
+set(SEACAS_ENABLE_SEACASMat2exo OFF)
+set(SEACAS_ENABLE_SEACASNas2exo OFF)
+set(SEACAS_ENABLE_SEACASZellij OFF)
+set(SEACAS_ENABLE_SEACASNemslice OFF)
+set(SEACAS_ENABLE_SEACASNemspread OFF)
+set(SEACAS_ENABLE_SEACASNumbers OFF)
+set(SEACAS_ENABLE_SEACASSlice OFF)
+set(SEACAS_ENABLE_SEACASTxtexo OFF)
+set(SEACAS_ENABLE_SEACASEx2ex1v2 OFF)
+set(SEACAS_ENABLE_MPI OFF)
+
+# Exported cache variables
+set(SEACAS_ENABLE_DEBUG "OFF")
+set(HAVE_SEACAS_DEBUG "OFF")
+set(SEACASExodus_ENABLE_THREADSAFE "NO")
+set(EXODUS_THREADSAFE "OFF")
+set(SEACASExodus_ENABLE_STATIC "YES")
+set(EXODUS_STATIC "ON")
+set(SEACASExodus_ENABLE_SHARED "OFF")
+set(EXODUS_SHARED "OFF")
+set(SEACASIoss_ENABLE_THREADSAFE "OFF")
+set(IOSS_THREADSAFE "OFF")
+
+# Include configuration of dependent packages
+if (NOT TARGET SEACASExodus::all_libs)
+  include("${CMAKE_CURRENT_LIST_DIR}/../SEACASExodus/SEACASExodusConfig.cmake")
+endif()
+
+# Import SEACAS targets
+include("${CMAKE_CURRENT_LIST_DIR}/SEACASTargets.cmake")
+
+# Standard TriBITS-compliant external package variables
+set(SEACAS_IS_TRIBITS_COMPLIANT TRUE)
+set(SEACAS_TRIBITS_COMPLIANT_PACKAGE_CONFIG_FILE "${CMAKE_CURRENT_LIST_FILE}")
+set(SEACAS_TRIBITS_COMPLIANT_PACKAGE_CONFIG_FILE_DIR "${CMAKE_CURRENT_LIST_DIR}")
+
+
+## ----------------------------------------------------------------------------
+## Create deprecated non-namespaced library targets for backwards compatibility
+## ----------------------------------------------------------------------------
+
+set(SEACAS_EXPORTED_PACKAGE_LIBS_NAMES "exodus")
+
+foreach(libname IN LISTS SEACAS_EXPORTED_PACKAGE_LIBS_NAMES)
+  if (NOT TARGET ${libname})
+    add_library(${libname} INTERFACE IMPORTED)
+    target_link_libraries(${libname}
+       INTERFACE SEACAS::${libname})
+    set(deprecationMessage
+      "WARNING: The non-namespaced target '${libname}' is deprecated!"
+      "  If always using newer versions of the project 'Seacas', then use the"
+      " new namespaced target 'SEACAS::${libname}', or better yet,"
+      " 'SEACAS::all_libs' to be less sensitive to changes in the definition"
+      " of targets in the package 'SEACAS'.  Or, to maintain compatibility with"
+      " older or newer versions the project 'Seacas', instead link against the"
+      " libraries specified by the variable 'SEACAS_LIBRARIES'."
+      )
+    string(REPLACE ";" "" deprecationMessage "${deprecationMessage}")
+    set_target_properties(${libname}
+      PROPERTIES DEPRECATION "${deprecationMessage}" )
+  endif()
+endforeach()

HybridMesher/libraries/EXODUS/lib/cmake/SEACAS/SEACASTargets.cmake

@@ -0,0 +1,123 @@
+# Generated by CMake
+
+if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" LESS 2.8)
+   message(FATAL_ERROR "CMake >= 2.8.0 required")
+endif()
+if(CMAKE_VERSION VERSION_LESS "2.8.3")
+   message(FATAL_ERROR "CMake >= 2.8.3 required")
+endif()
+cmake_policy(PUSH)
+cmake_policy(VERSION 2.8.3...3.22)
+#----------------------------------------------------------------
+# Generated CMake target import file.
+#----------------------------------------------------------------
+
+# Commands may need to know the format version.
+set(CMAKE_IMPORT_FILE_VERSION 1)
+
+# Protect against multiple inclusion, which would fail when already imported targets are added once more.
+set(_cmake_targets_defined "")
+set(_cmake_targets_not_defined "")
+set(_cmake_expected_targets "")
+foreach(_cmake_expected_target IN ITEMS SEACAS::all_libs)
+  list(APPEND _cmake_expected_targets "${_cmake_expected_target}")
+  if(TARGET "${_cmake_expected_target}")
+    list(APPEND _cmake_targets_defined "${_cmake_expected_target}")
+  else()
+    list(APPEND _cmake_targets_not_defined "${_cmake_expected_target}")
+  endif()
+endforeach()
+unset(_cmake_expected_target)
+if(_cmake_targets_defined STREQUAL _cmake_expected_targets)
+  unset(_cmake_targets_defined)
+  unset(_cmake_targets_not_defined)
+  unset(_cmake_expected_targets)
+  unset(CMAKE_IMPORT_FILE_VERSION)
+  cmake_policy(POP)
+  return()
+endif()
+if(NOT _cmake_targets_defined STREQUAL "")
+  string(REPLACE ";" ", " _cmake_targets_defined_text "${_cmake_targets_defined}")
+  string(REPLACE ";" ", " _cmake_targets_not_defined_text "${_cmake_targets_not_defined}")
+  message(FATAL_ERROR "Some (but not all) targets in this export set were already defined.\nTargets Defined: ${_cmake_targets_defined_text}\nTargets not yet defined: ${_cmake_targets_not_defined_text}\n")
+endif()
+unset(_cmake_targets_defined)
+unset(_cmake_targets_not_defined)
+unset(_cmake_expected_targets)
+
+
+# Compute the installation prefix relative to this file.
+get_filename_component(_IMPORT_PREFIX "${CMAKE_CURRENT_LIST_FILE}" PATH)
+get_filename_component(_IMPORT_PREFIX "${_IMPORT_PREFIX}" PATH)
+get_filename_component(_IMPORT_PREFIX "${_IMPORT_PREFIX}" PATH)
+get_filename_component(_IMPORT_PREFIX "${_IMPORT_PREFIX}" PATH)
+if(_IMPORT_PREFIX STREQUAL "/")
+  set(_IMPORT_PREFIX "")
+endif()
+
+# Create imported target SEACAS::all_libs
+add_library(SEACAS::all_libs INTERFACE IMPORTED)
+
+set_target_properties(SEACAS::all_libs PROPERTIES
+  INTERFACE_INCLUDE_DIRECTORIES "${_IMPORT_PREFIX}/include"
+  INTERFACE_LINK_LIBRARIES "SEACASExodus::exodus"
+)
+
+if(CMAKE_VERSION VERSION_LESS 3.0.0)
+  message(FATAL_ERROR "This file relies on consumers using CMake 3.0.0 or greater.")
+endif()
+
+# Load information for each installed configuration.
+file(GLOB _cmake_config_files "${CMAKE_CURRENT_LIST_DIR}/SEACASTargets-*.cmake")
+foreach(_cmake_config_file IN LISTS _cmake_config_files)
+  include("${_cmake_config_file}")
+endforeach()
+unset(_cmake_config_file)
+unset(_cmake_config_files)
+
+# Cleanup temporary variables.
+set(_IMPORT_PREFIX)
+
+# Loop over all imported files and verify that they actually exist
+foreach(_cmake_target IN LISTS _cmake_import_check_targets)
+  foreach(_cmake_file IN LISTS "_cmake_import_check_files_for_${_cmake_target}")
+    if(NOT EXISTS "${_cmake_file}")
+      message(FATAL_ERROR "The imported target \"${_cmake_target}\" references the file
+   \"${_cmake_file}\"
+but this file does not exist.  Possible reasons include:
+* The file was deleted, renamed, or moved to another location.
+* An install or uninstall procedure did not complete successfully.
+* The installation package was faulty and contained
+   \"${CMAKE_CURRENT_LIST_FILE}\"
+but not all the files it references.
+")
+    endif()
+  endforeach()
+  unset(_cmake_file)
+  unset("_cmake_import_check_files_for_${_cmake_target}")
+endforeach()
+unset(_cmake_target)
+unset(_cmake_import_check_targets)
+
+# Make sure the targets which have been exported in some other
+# export set exist.
+unset(${CMAKE_FIND_PACKAGE_NAME}_NOT_FOUND_MESSAGE_targets)
+foreach(_target "SEACASExodus::exodus" )
+  if(NOT TARGET "${_target}" )
+    set(${CMAKE_FIND_PACKAGE_NAME}_NOT_FOUND_MESSAGE_targets "${${CMAKE_FIND_PACKAGE_NAME}_NOT_FOUND_MESSAGE_targets} ${_target}")
+  endif()
+endforeach()
+
+if(DEFINED ${CMAKE_FIND_PACKAGE_NAME}_NOT_FOUND_MESSAGE_targets)
+  if(CMAKE_FIND_PACKAGE_NAME)
+    set( ${CMAKE_FIND_PACKAGE_NAME}_FOUND FALSE)
+    set( ${CMAKE_FIND_PACKAGE_NAME}_NOT_FOUND_MESSAGE "The following imported targets are referenced, but are missing: ${${CMAKE_FIND_PACKAGE_NAME}_NOT_FOUND_MESSAGE_targets}")
+  else()
+    message(FATAL_ERROR "The following imported targets are referenced, but are missing: ${${CMAKE_FIND_PACKAGE_NAME}_NOT_FOUND_MESSAGE_targets}")
+  endif()
+endif()
+unset(${CMAKE_FIND_PACKAGE_NAME}_NOT_FOUND_MESSAGE_targets)
+
+# Commands beyond this point should not need to know the version.
+set(CMAKE_IMPORT_FILE_VERSION)
+cmake_policy(POP)

HybridMesher/libraries/EXODUS/lib/cmake/SEACASExodus/SEACASExodusConfig.cmake

@@ -0,0 +1,181 @@
+# @HEADER
+# ************************************************************************
+#
+#            TriBITS: Tribal Build, Integrate, and Test System
+#                    Copyright 2013 Sandia Corporation
+#
+# Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+# the U.S. Government retains certain rights in this software.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# ************************************************************************
+# @HEADER
+
+##############################################################################
+#
+# CMake variable for use by Seacas/SEACASExodus clients.
+#
+# Do not edit: This file was generated automatically by CMake.
+#
+##############################################################################
+
+if(CMAKE_VERSION VERSION_LESS 3.3)
+  set(${CMAKE_FIND_PACKAGE_NAME}_NOT_FOUND_MESSAGE
+    "SEACASExodus requires CMake 3.3 or later for 'if (... IN_LIST ...)'"
+    )
+  set(${CMAKE_FIND_PACKAGE_NAME}_FOUND FALSE)
+  return()
+endif()
+cmake_minimum_required(VERSION 3.3...3.22.0)
+
+## ---------------------------------------------------------------------------
+## Compilers used by Seacas/SEACASExodus build
+## ---------------------------------------------------------------------------
+
+set(SEACASExodus_CXX_COMPILER "/usr/lib/ccache/g++")
+
+set(SEACASExodus_C_COMPILER "/usr/lib/ccache/gcc")
+
+set(SEACASExodus_Fortran_COMPILER "gfortran")
+# Deprecated!
+set(SEACASExodus_FORTRAN_COMPILER "gfortran") 
+
+
+## ---------------------------------------------------------------------------
+## Compiler flags used by Seacas/SEACASExodus build
+## ---------------------------------------------------------------------------
+
+## Give the build type
+set(SEACASExodus_CMAKE_BUILD_TYPE "RELEASE")
+
+## Set compiler flags, including those determined by build type
+set(SEACASExodus_CXX_FLAGS [[ -O3 -DNDEBUG]])
+
+set(SEACASExodus_C_FLAGS [[  -Wall -Wunused -pedantic -std=c11 -fPIC -O3 -DNDEBUG]])
+
+set(SEACASExodus_Fortran_FLAGS [[ ]])
+# Deprecated
+set(SEACASExodus_FORTRAN_FLAGS [[ ]])
+
+## Extra link flags (e.g., specification of fortran libraries)
+set(SEACASExodus_EXTRA_LD_FLAGS [[]])
+
+## This is the command-line entry used for setting rpaths. In a build
+## with static libraries it will be empty.
+set(SEACASExodus_SHARED_LIB_RPATH_COMMAND "-Wl,-rpath,/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/EXODUS/lib")
+set(SEACASExodus_BUILD_SHARED_LIBS "YES")
+
+set(SEACASExodus_LINKER /usr/bin/ld)
+set(SEACASExodus_AR /usr/bin/ar)
+
+## ---------------------------------------------------------------------------
+## Set library specifications and paths
+## ---------------------------------------------------------------------------
+
+## Base install location (if not in the build tree)
+set(SEACASExodus_INSTALL_DIR "/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/EXODUS")
+
+## List of package libraries
+set(SEACASExodus_LIBRARIES SEACASExodus::all_libs)
+
+## ---------------------------------------------------------------------------
+## MPI specific variables
+##   These variables are provided to make it easier to get the mpi libraries
+##   and includes on systems that do not use the mpi wrappers for compiling
+## ---------------------------------------------------------------------------
+
+set(SEACASExodus_MPI_LIBRARIES "")
+set(SEACASExodus_MPI_LIBRARY_DIRS "")
+set(SEACASExodus_MPI_INCLUDE_DIRS "")
+set(SEACASExodus_MPI_EXEC "")
+set(SEACASExodus_MPI_EXEC_MAX_NUMPROCS "")
+set(SEACASExodus_MPI_EXEC_NUMPROCS_FLAG "")
+
+## ---------------------------------------------------------------------------
+## Set useful general variables
+## ---------------------------------------------------------------------------
+
+# Enables/Disables for upstream package dependencies
+set(SEACASExodus_ENABLE_Netcdf ON)
+set(SEACASExodus_ENABLE_Pthread OFF)
+set(SEACASExodus_ENABLE_HDF5 OFF)
+set(SEACASExodus_ENABLE_Pnetcdf OFF)
+set(SEACASExodus_ENABLE_MPI OFF)
+
+# Exported cache variables
+set(SEACAS_ENABLE_DEBUG "OFF")
+set(HAVE_SEACAS_DEBUG "OFF")
+set(SEACASExodus_ENABLE_THREADSAFE "NO")
+set(EXODUS_THREADSAFE "OFF")
+set(SEACASExodus_ENABLE_STATIC "YES")
+set(EXODUS_STATIC "ON")
+set(SEACASExodus_ENABLE_SHARED "OFF")
+set(EXODUS_SHARED "OFF")
+set(SEACASIoss_ENABLE_THREADSAFE "OFF")
+set(IOSS_THREADSAFE "OFF")
+
+# Include configuration of dependent packages
+if (NOT TARGET Netcdf::all_libs)
+  include("${CMAKE_CURRENT_LIST_DIR}/../../external_packages/Netcdf/NetcdfConfig.cmake")
+endif()
+
+# Import SEACASExodus targets
+include("${CMAKE_CURRENT_LIST_DIR}/SEACASExodusTargets.cmake")
+
+# Standard TriBITS-compliant external package variables
+set(SEACASExodus_IS_TRIBITS_COMPLIANT TRUE)
+set(SEACASExodus_TRIBITS_COMPLIANT_PACKAGE_CONFIG_FILE "${CMAKE_CURRENT_LIST_FILE}")
+set(SEACASExodus_TRIBITS_COMPLIANT_PACKAGE_CONFIG_FILE_DIR "${CMAKE_CURRENT_LIST_DIR}")
+
+
+## ----------------------------------------------------------------------------
+## Create deprecated non-namespaced library targets for backwards compatibility
+## ----------------------------------------------------------------------------
+
+set(SEACASExodus_EXPORTED_PACKAGE_LIBS_NAMES "exodus")
+
+foreach(libname IN LISTS SEACASExodus_EXPORTED_PACKAGE_LIBS_NAMES)
+  if (NOT TARGET ${libname})
+    add_library(${libname} INTERFACE IMPORTED)
+    target_link_libraries(${libname}
+       INTERFACE SEACASExodus::${libname})
+    set(deprecationMessage
+      "WARNING: The non-namespaced target '${libname}' is deprecated!"
+      "  If always using newer versions of the project 'Seacas', then use the"
+      " new namespaced target 'SEACASExodus::${libname}', or better yet,"
+      " 'SEACASExodus::all_libs' to be less sensitive to changes in the definition"
+      " of targets in the package 'SEACASExodus'.  Or, to maintain compatibility with"
+      " older or newer versions the project 'Seacas', instead link against the"
+      " libraries specified by the variable 'SEACASExodus_LIBRARIES'."
+      )
+    string(REPLACE ";" "" deprecationMessage "${deprecationMessage}")
+    set_target_properties(${libname}
+      PROPERTIES DEPRECATION "${deprecationMessage}" )
+  endif()
+endforeach()

HybridMesher/libraries/EXODUS/lib/cmake/SEACASExodus/SEACASExodusTargets-release.cmake

@@ -0,0 +1,19 @@
+#----------------------------------------------------------------
+# Generated CMake target import file for configuration "RELEASE".
+#----------------------------------------------------------------
+
+# Commands may need to know the format version.
+set(CMAKE_IMPORT_FILE_VERSION 1)
+
+# Import target "SEACASExodus::exodus" for configuration "RELEASE"
+set_property(TARGET SEACASExodus::exodus APPEND PROPERTY IMPORTED_CONFIGURATIONS RELEASE)
+set_target_properties(SEACASExodus::exodus PROPERTIES
+  IMPORTED_LOCATION_RELEASE "${_IMPORT_PREFIX}/lib/libexodus.so.2.0"
+  IMPORTED_SONAME_RELEASE "libexodus.so.2"
+  )
+
+list(APPEND _cmake_import_check_targets SEACASExodus::exodus )
+list(APPEND _cmake_import_check_files_for_SEACASExodus::exodus "${_IMPORT_PREFIX}/lib/libexodus.so.2.0" )
+
+# Commands beyond this point should not need to know the version.
+set(CMAKE_IMPORT_FILE_VERSION)

HybridMesher/libraries/EXODUS/lib/cmake/SEACASExodus/SEACASExodusTargets.cmake

@@ -0,0 +1,116 @@
+# Generated by CMake
+
+if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" LESS 2.8)
+   message(FATAL_ERROR "CMake >= 2.8.0 required")
+endif()
+if(CMAKE_VERSION VERSION_LESS "2.8.3")
+   message(FATAL_ERROR "CMake >= 2.8.3 required")
+endif()
+cmake_policy(PUSH)
+cmake_policy(VERSION 2.8.3...3.22)
+#----------------------------------------------------------------
+# Generated CMake target import file.
+#----------------------------------------------------------------
+
+# Commands may need to know the format version.
+set(CMAKE_IMPORT_FILE_VERSION 1)
+
+# Protect against multiple inclusion, which would fail when already imported targets are added once more.
+set(_cmake_targets_defined "")
+set(_cmake_targets_not_defined "")
+set(_cmake_expected_targets "")
+foreach(_cmake_expected_target IN ITEMS SEACASExodus::exodus SEACASExodus::all_libs)
+  list(APPEND _cmake_expected_targets "${_cmake_expected_target}")
+  if(TARGET "${_cmake_expected_target}")
+    list(APPEND _cmake_targets_defined "${_cmake_expected_target}")
+  else()
+    list(APPEND _cmake_targets_not_defined "${_cmake_expected_target}")
+  endif()
+endforeach()
+unset(_cmake_expected_target)
+if(_cmake_targets_defined STREQUAL _cmake_expected_targets)
+  unset(_cmake_targets_defined)
+  unset(_cmake_targets_not_defined)
+  unset(_cmake_expected_targets)
+  unset(CMAKE_IMPORT_FILE_VERSION)
+  cmake_policy(POP)
+  return()
+endif()
+if(NOT _cmake_targets_defined STREQUAL "")
+  string(REPLACE ";" ", " _cmake_targets_defined_text "${_cmake_targets_defined}")
+  string(REPLACE ";" ", " _cmake_targets_not_defined_text "${_cmake_targets_not_defined}")
+  message(FATAL_ERROR "Some (but not all) targets in this export set were already defined.\nTargets Defined: ${_cmake_targets_defined_text}\nTargets not yet defined: ${_cmake_targets_not_defined_text}\n")
+endif()
+unset(_cmake_targets_defined)
+unset(_cmake_targets_not_defined)
+unset(_cmake_expected_targets)
+
+
+# Compute the installation prefix relative to this file.
+get_filename_component(_IMPORT_PREFIX "${CMAKE_CURRENT_LIST_FILE}" PATH)
+get_filename_component(_IMPORT_PREFIX "${_IMPORT_PREFIX}" PATH)
+get_filename_component(_IMPORT_PREFIX "${_IMPORT_PREFIX}" PATH)
+get_filename_component(_IMPORT_PREFIX "${_IMPORT_PREFIX}" PATH)
+if(_IMPORT_PREFIX STREQUAL "/")
+  set(_IMPORT_PREFIX "")
+endif()
+
+# Create imported target SEACASExodus::exodus
+add_library(SEACASExodus::exodus SHARED IMPORTED)
+
+set_target_properties(SEACASExodus::exodus PROPERTIES
+  INTERFACE_COMPILE_FEATURES "cxx_std_11"
+  INTERFACE_INCLUDE_DIRECTORIES "${_IMPORT_PREFIX}/include"
+  INTERFACE_LINK_LIBRARIES "Netcdf::all_libs"
+)
+
+# Create imported target SEACASExodus::all_libs
+add_library(SEACASExodus::all_libs INTERFACE IMPORTED)
+
+set_target_properties(SEACASExodus::all_libs PROPERTIES
+  INTERFACE_INCLUDE_DIRECTORIES "${_IMPORT_PREFIX}/include"
+  INTERFACE_LINK_LIBRARIES "SEACASExodus::exodus"
+)
+
+if(CMAKE_VERSION VERSION_LESS 3.0.0)
+  message(FATAL_ERROR "This file relies on consumers using CMake 3.0.0 or greater.")
+endif()
+
+# Load information for each installed configuration.
+file(GLOB _cmake_config_files "${CMAKE_CURRENT_LIST_DIR}/SEACASExodusTargets-*.cmake")
+foreach(_cmake_config_file IN LISTS _cmake_config_files)
+  include("${_cmake_config_file}")
+endforeach()
+unset(_cmake_config_file)
+unset(_cmake_config_files)
+
+# Cleanup temporary variables.
+set(_IMPORT_PREFIX)
+
+# Loop over all imported files and verify that they actually exist
+foreach(_cmake_target IN LISTS _cmake_import_check_targets)
+  foreach(_cmake_file IN LISTS "_cmake_import_check_files_for_${_cmake_target}")
+    if(NOT EXISTS "${_cmake_file}")
+      message(FATAL_ERROR "The imported target \"${_cmake_target}\" references the file
+   \"${_cmake_file}\"
+but this file does not exist.  Possible reasons include:
+* The file was deleted, renamed, or moved to another location.
+* An install or uninstall procedure did not complete successfully.
+* The installation package was faulty and contained
+   \"${CMAKE_CURRENT_LIST_FILE}\"
+but not all the files it references.
+")
+    endif()
+  endforeach()
+  unset(_cmake_file)
+  unset("_cmake_import_check_files_for_${_cmake_target}")
+endforeach()
+unset(_cmake_target)
+unset(_cmake_import_check_targets)
+
+# This file does not depend on other imported targets which have
+# been exported from the same project but in a separate export set.
+
+# Commands beyond this point should not need to know the version.
+set(CMAKE_IMPORT_FILE_VERSION)
+cmake_policy(POP)

HybridMesher/libraries/EXODUS/lib/cmake/Seacas/SeacasConfig.cmake

@@ -0,0 +1,202 @@
+# @HEADER
+# ************************************************************************
+#
+#            TriBITS: Tribal Build, Integrate, and Test System
+#                    Copyright 2013 Sandia Corporation
+#
+#
+# Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+# the U.S. Government retains certain rights in this software.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# ************************************************************************
+# @HEADER
+
+##############################################################################
+#
+# CMake variable for use by Seacas clients. 
+#
+# Do not edit: This file was generated automatically by CMake.
+#
+##############################################################################
+
+if(CMAKE_VERSION VERSION_LESS 3.3)
+  set(${CMAKE_FIND_PACKAGE_NAME}_NOT_FOUND_MESSAGE
+    "Seacas requires CMake 3.3 or later for 'if (... IN_LIST ...)'"
+    )
+  set(${CMAKE_FIND_PACKAGE_NAME}_FOUND FALSE)
+  return()
+endif()
+cmake_minimum_required(VERSION 3.3...3.22.0)
+
+## ---------------------------------------------------------------------------
+## Compilers used by Seacas build
+## ---------------------------------------------------------------------------
+
+set(Seacas_CXX_COMPILER "/usr/lib/ccache/g++")
+
+set(Seacas_C_COMPILER "/usr/lib/ccache/gcc")
+
+set(Seacas_Fortran_COMPILER "gfortran")
+
+## ---------------------------------------------------------------------------
+## Compiler flags used by Seacas build
+## ---------------------------------------------------------------------------
+
+set(Seacas_CMAKE_BUILD_TYPE "RELEASE")
+
+set(Seacas_CXX_COMPILER_FLAGS [[  -Wall -Wunused -pedantic -fPIC -O3 -DNDEBUG]])
+
+set(Seacas_C_COMPILER_FLAGS [[  -Wall -Wunused -pedantic -std=c11 -fPIC -O3 -DNDEBUG]])
+
+set(Seacas_Fortran_COMPILER_FLAGS [[   ]])
+
+## Extra link flags (e.g., specification of fortran libraries)
+set(Seacas_EXTRA_LD_FLAGS [[]])
+
+## This is the command-line entry used for setting rpaths. In a build
+## with static libraries it will be empty. 
+set(Seacas_SHARED_LIB_RPATH_COMMAND "-Wl,-rpath,/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/EXODUS/lib")
+set(Seacas_BUILD_SHARED_LIBS "YES")
+
+set(Seacas_LINKER /usr/bin/ld)
+set(Seacas_AR /usr/bin/ar)
+
+
+## ---------------------------------------------------------------------------
+## Set library specifications and paths 
+## ---------------------------------------------------------------------------
+
+## The project version number
+set(Seacas_VERSION "2.0")
+
+# For best practices in handling of components, see
+# <http://www.cmake.org/cmake/help/v3.2/manual/cmake-developer.7.html#find-modules>.
+#
+# If components were requested, include only those. If not, include all of
+# Trilinos.
+if (Seacas_FIND_COMPONENTS)
+  set(COMPONENTS_LIST ${Seacas_FIND_COMPONENTS})
+else()
+  set(COMPONENTS_LIST SEACAS;SEACASExodus)
+endif()
+
+# Initialize Seacas_FOUND with true, and set it to FALSE if any of
+# the required components wasn't found.
+set(Seacas_FOUND TRUE)
+set(Seacas_NOT_FOUND_MESSAGE "")
+set(selectedComponentsFound "")
+foreach (comp IN ITEMS ${COMPONENTS_LIST})
+  set(compPkgConfigFile
+    ${CMAKE_CURRENT_LIST_DIR}/../${comp}/${comp}Config.cmake
+    )
+  if (EXISTS ${compPkgConfigFile})
+    # Set Seacas_<component>_FOUND.
+    set(Seacas_${comp}_FOUND TRUE)
+    # Include the package file.
+    include(${compPkgConfigFile})
+    # Add variables to lists.
+    list(APPEND Seacas_LIBRARIES ${${comp}_LIBRARIES})
+    list(APPEND selectedComponentsFound ${comp})
+  else()
+    set(Seacas_${comp}_FOUND FALSE)
+    if(Seacas_FIND_REQUIRED_${comp})
+      string(APPEND Seacas_NOT_FOUND_MESSAGE
+        "ERROR: Could not find component '${comp}'!\n")
+      set(Seacas_FOUND FALSE)
+    endif()
+  endif()
+endforeach()
+
+# Deprecated (see #299)!
+set(Seacas_INCLUDE_DIRS "/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/EXODUS/include")
+
+# Remove duplicates in Seacas_LIBRARIES
+list(REMOVE_DUPLICATES Seacas_LIBRARIES)
+
+## ---------------------------------------------------------------------------
+## MPI specific variables
+##   These variables are provided to make it easier to get the mpi libraries
+##   and includes on systems that do not use the mpi wrappers for compiling
+## ---------------------------------------------------------------------------
+
+set(Seacas_INSTALL_DIR "/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/EXODUS")
+set(Seacas_MPI_LIBRARIES "")
+set(Seacas_MPI_LIBRARY_DIRS "")
+set(Seacas_MPI_INCLUDE_DIRS "")
+set(Seacas_MPI_EXEC "")
+set(Seacas_MPI_EXEC_PRE_NUMPROCS_FLAGS "")
+set(Seacas_MPI_EXEC_MAX_NUMPROCS "")
+set(Seacas_MPI_EXEC_POST_NUMPROCS_FLAGS "")
+set(Seacas_MPI_EXEC_NUMPROCS_FLAG "")
+
+## ---------------------------------------------------------------------------
+## Compiler vendor identifications
+## ---------------------------------------------------------------------------
+set(Seacas_SYSTEM_NAME "Linux")
+set(Seacas_CXX_COMPILER_ID "GNU")
+set(Seacas_C_COMPILER_ID "GNU")
+set(Seacas_Fortran_COMPILER_ID "")
+set(Seacas_Fortran_IMPLICIT_LINK_LIBRARIES "")
+
+## ---------------------------------------------------------------------------
+## Set useful general variables 
+## ---------------------------------------------------------------------------
+
+## The packages enabled for this project
+set(Seacas_PACKAGE_LIST "SEACAS;SEACASExodus")
+
+## The selected packages for this project
+set(Seacas_SELECTED_PACKAGE_LIST "${selectedComponentsFound}")
+
+## ---------------------------------------------------------------------------
+## Modern CMake (IMPORTED) targets
+## ---------------------------------------------------------------------------
+
+# Seacas::all_libs  (Does *not* depend on COMPONENTS)
+if (NOT TARGET Seacas::all_libs)
+  set(Seacas_ALL_PACKAGES_TARGETS)
+  foreach (pkg IN ITEMS SEACAS;SEACASExodus)
+    list(APPEND Seacas_ALL_PACKAGES_TARGETS ${pkg}::all_libs)
+  endforeach()
+  add_library(Seacas::all_libs IMPORTED INTERFACE GLOBAL)
+  target_link_libraries(Seacas::all_libs
+  INTERFACE ${Seacas_ALL_PACKAGES_TARGETS} )
+endif()
+
+# Seacas::all_selected_libs  (Depend on COMPONENTS)
+if (NOT TARGET Seacas::all_selected_libs)
+  set(Seacas_ALL_SELECTED_PACKAGES_TARGETS)
+  foreach (pkg IN ITEMS ${selectedComponentsFound})
+    list(APPEND Seacas_ALL_SELECTED_PACKAGES_TARGETS ${pkg}::all_libs)
+  endforeach()
+  add_library(Seacas::all_selected_libs IMPORTED INTERFACE GLOBAL)
+  target_link_libraries(Seacas::all_selected_libs
+    INTERFACE ${Seacas_ALL_SELECTED_PACKAGES_TARGETS} )
+endif()

HybridMesher/libraries/EXODUS/lib/cmake/Seacas/SeacasConfigVersion.cmake

@@ -0,0 +1,70 @@
+# This is a basic version file for the Config-mode of find_package().
+# It is used by write_basic_package_version_file() as input file for configure_file()
+# to create a version-file which can be installed along a config.cmake file.
+#
+# The created file sets PACKAGE_VERSION_EXACT if the current version string and
+# the requested version string are exactly the same and it sets
+# PACKAGE_VERSION_COMPATIBLE if the current version is >= requested version,
+# but only if the requested major version is the same as the current one.
+# The variable CVF_VERSION must be set before calling configure_file().
+
+
+set(PACKAGE_VERSION "2.0")
+
+if(PACKAGE_VERSION VERSION_LESS PACKAGE_FIND_VERSION)
+  set(PACKAGE_VERSION_COMPATIBLE FALSE)
+else()
+
+  if("2.0" MATCHES "^([0-9]+)\\.")
+    set(CVF_VERSION_MAJOR "${CMAKE_MATCH_1}")
+    if(NOT CVF_VERSION_MAJOR VERSION_EQUAL 0)
+      string(REGEX REPLACE "^0+" "" CVF_VERSION_MAJOR "${CVF_VERSION_MAJOR}")
+    endif()
+  else()
+    set(CVF_VERSION_MAJOR "2.0")
+  endif()
+
+  if(PACKAGE_FIND_VERSION_RANGE)
+    # both endpoints of the range must have the expected major version
+    math (EXPR CVF_VERSION_MAJOR_NEXT "${CVF_VERSION_MAJOR} + 1")
+    if (NOT PACKAGE_FIND_VERSION_MIN_MAJOR STREQUAL CVF_VERSION_MAJOR
+        OR ((PACKAGE_FIND_VERSION_RANGE_MAX STREQUAL "INCLUDE" AND NOT PACKAGE_FIND_VERSION_MAX_MAJOR STREQUAL CVF_VERSION_MAJOR)
+          OR (PACKAGE_FIND_VERSION_RANGE_MAX STREQUAL "EXCLUDE" AND NOT PACKAGE_FIND_VERSION_MAX VERSION_LESS_EQUAL CVF_VERSION_MAJOR_NEXT)))
+      set(PACKAGE_VERSION_COMPATIBLE FALSE)
+    elseif(PACKAGE_FIND_VERSION_MIN_MAJOR STREQUAL CVF_VERSION_MAJOR
+        AND ((PACKAGE_FIND_VERSION_RANGE_MAX STREQUAL "INCLUDE" AND PACKAGE_VERSION VERSION_LESS_EQUAL PACKAGE_FIND_VERSION_MAX)
+        OR (PACKAGE_FIND_VERSION_RANGE_MAX STREQUAL "EXCLUDE" AND PACKAGE_VERSION VERSION_LESS PACKAGE_FIND_VERSION_MAX)))
+      set(PACKAGE_VERSION_COMPATIBLE TRUE)
+    else()
+      set(PACKAGE_VERSION_COMPATIBLE FALSE)
+    endif()
+  else()
+    if(PACKAGE_FIND_VERSION_MAJOR STREQUAL CVF_VERSION_MAJOR)
+      set(PACKAGE_VERSION_COMPATIBLE TRUE)
+    else()
+      set(PACKAGE_VERSION_COMPATIBLE FALSE)
+    endif()
+
+    if(PACKAGE_FIND_VERSION STREQUAL PACKAGE_VERSION)
+      set(PACKAGE_VERSION_EXACT TRUE)
+    endif()
+  endif()
+endif()
+
+
+# if the installed project requested no architecture check, don't perform the check
+if("FALSE")
+  return()
+endif()
+
+# if the installed or the using project don't have CMAKE_SIZEOF_VOID_P set, ignore it:
+if("${CMAKE_SIZEOF_VOID_P}" STREQUAL "" OR "8" STREQUAL "")
+  return()
+endif()
+
+# check that the installed version has the same 32/64bit-ness as the one which is currently searching:
+if(NOT CMAKE_SIZEOF_VOID_P STREQUAL "8")
+  math(EXPR installedBits "8 * 8")
+  set(PACKAGE_VERSION "${PACKAGE_VERSION} (${installedBits}bit)")
+  set(PACKAGE_VERSION_UNSUITABLE TRUE)
+endif()

HybridMesher/libraries/EXODUS/lib/exodus.py

@@ -0,0 +1 @@
+exodus3.py

HybridMesher/libraries/EXODUS/lib/exomerge.py

@@ -0,0 +1 @@
+exomerge3.py

HybridMesher/libraries/EXODUS/lib/external_packages/DLlib/DLlibConfig.cmake

@@ -0,0 +1,23 @@
+# Package config file for external package/TPL 'DLlib'
+#
+# Generated by CMake, do not edit!
+
+# Guard against multiple inclusion
+if (TARGET DLlib::all_libs)
+  return()
+endif()
+
+add_library(tribits::DLlib::dl IMPORTED UNKNOWN)
+set_target_properties(tribits::DLlib::dl PROPERTIES
+  IMPORTED_LOCATION "/usr/lib/x86_64-linux-gnu/libdl.so")
+
+add_library(DLlib::all_libs INTERFACE IMPORTED)
+target_link_libraries(DLlib::all_libs
+  INTERFACE tribits::DLlib::dl
+  )
+
+
+# Standard TriBITS-compliant external package variables
+set(DLlib_IS_TRIBITS_COMPLIANT TRUE)
+set(DLlib_TRIBITS_COMPLIANT_PACKAGE_CONFIG_FILE "${CMAKE_CURRENT_LIST_FILE}")
+set(DLlib_TRIBITS_COMPLIANT_PACKAGE_CONFIG_FILE_DIR "${CMAKE_CURRENT_LIST_DIR}")

HybridMesher/libraries/EXODUS/lib/external_packages/DLlib/DLlibConfigVersion.cmake

@@ -0,0 +1,14 @@
+# Package config file for external package/TPL 'DLlib'
+#
+# Generated by CMake, do not edit!
+
+if (TRIBITS_FINDING_RAW_DLlib_PACKAGE_FIRST)
+  set(PACKAGE_VERSION_COMPATIBLE FALSE)
+  set(PACKAGE_VERSION_UNSUITABLE TRUE)
+else()
+  set(PACKAGE_VERSION_COMPATIBLE TRUE)
+endif()
+
+# Currently there is no version information
+set(PACKAGE_VERSION UNKNOWN)
+set(PACKAGE_VERSION_EXACT FALSE)

HybridMesher/libraries/EXODUS/lib/external_packages/Netcdf/NetcdfConfig.cmake

@@ -0,0 +1,62 @@
+# Package config file for external package/TPL 'Netcdf'
+#
+# Generated by CMake, do not edit!
+
+# Guard against multiple inclusion
+if (TARGET Netcdf::all_libs)
+  return()
+endif()
+
+add_library(tribits::Netcdf::m IMPORTED UNKNOWN)
+set_target_properties(tribits::Netcdf::m PROPERTIES
+  IMPORTED_LOCATION "/usr/lib/x86_64-linux-gnu/libm.so")
+
+add_library(tribits::Netcdf::dl IMPORTED UNKNOWN)
+set_target_properties(tribits::Netcdf::dl PROPERTIES
+  IMPORTED_LOCATION "/usr/lib/x86_64-linux-gnu/libdl.so")
+target_link_libraries(tribits::Netcdf::dl
+  INTERFACE tribits::Netcdf::m)
+
+add_library(tribits::Netcdf::z IMPORTED UNKNOWN)
+set_target_properties(tribits::Netcdf::z PROPERTIES
+  IMPORTED_LOCATION "/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/zlib-1.2.13/lib/libz.so")
+target_link_libraries(tribits::Netcdf::z
+  INTERFACE tribits::Netcdf::dl)
+
+add_library(tribits::Netcdf::hdf5 IMPORTED UNKNOWN)
+set_target_properties(tribits::Netcdf::hdf5 PROPERTIES
+  IMPORTED_LOCATION "/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/HDF5-1.14.1/lib/libhdf5.so")
+target_link_libraries(tribits::Netcdf::hdf5
+  INTERFACE tribits::Netcdf::z)
+
+add_library(tribits::Netcdf::hdf5_hl IMPORTED UNKNOWN)
+set_target_properties(tribits::Netcdf::hdf5_hl PROPERTIES
+  IMPORTED_LOCATION "/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/HDF5-1.14.1/lib/libhdf5_hl.so")
+target_link_libraries(tribits::Netcdf::hdf5_hl
+  INTERFACE tribits::Netcdf::hdf5)
+
+add_library(tribits::Netcdf::netcdf IMPORTED UNKNOWN)
+set_target_properties(tribits::Netcdf::netcdf PROPERTIES
+  IMPORTED_LOCATION "/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/NetCDF-C-4.9.2/lib/libnetcdf.so")
+target_link_libraries(tribits::Netcdf::netcdf
+  INTERFACE tribits::Netcdf::hdf5_hl)
+
+add_library(Netcdf::all_libs INTERFACE IMPORTED)
+target_link_libraries(Netcdf::all_libs
+  INTERFACE tribits::Netcdf::m
+  INTERFACE tribits::Netcdf::dl
+  INTERFACE tribits::Netcdf::z
+  INTERFACE tribits::Netcdf::hdf5
+  INTERFACE tribits::Netcdf::hdf5_hl
+  INTERFACE tribits::Netcdf::netcdf
+  )
+target_include_directories(Netcdf::all_libs SYSTEM
+  INTERFACE "/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/NetCDF-C-4.9.2/include"
+  INTERFACE "/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/HDF5-1.14.1/include"
+  )
+
+
+# Standard TriBITS-compliant external package variables
+set(Netcdf_IS_TRIBITS_COMPLIANT TRUE)
+set(Netcdf_TRIBITS_COMPLIANT_PACKAGE_CONFIG_FILE "${CMAKE_CURRENT_LIST_FILE}")
+set(Netcdf_TRIBITS_COMPLIANT_PACKAGE_CONFIG_FILE_DIR "${CMAKE_CURRENT_LIST_DIR}")

HybridMesher/libraries/EXODUS/lib/external_packages/Netcdf/NetcdfConfigVersion.cmake

@@ -0,0 +1,14 @@
+# Package config file for external package/TPL 'Netcdf'
+#
+# Generated by CMake, do not edit!
+
+if (TRIBITS_FINDING_RAW_Netcdf_PACKAGE_FIRST)
+  set(PACKAGE_VERSION_COMPATIBLE FALSE)
+  set(PACKAGE_VERSION_UNSUITABLE TRUE)
+else()
+  set(PACKAGE_VERSION_COMPATIBLE TRUE)
+endif()
+
+# Currently there is no version information
+set(PACKAGE_VERSION UNKNOWN)
+set(PACKAGE_VERSION_EXACT FALSE)

HybridMesher/libraries/EXODUS/lib/libexoIIv2c.a

@@ -0,0 +1 @@
+libexodus.a

HybridMesher/libraries/EXODUS/lib/libexodus.so

@@ -0,0 +1 @@
+libexodus.so.2

HybridMesher/libraries/EXODUS/lib/libexodus.so.2

@@ -0,0 +1 @@
+libexodus.so.2.0

HybridMesher/libraries/EXODUS/lib/tests/test_exodus3.py

@@ -0,0 +1,379 @@
+#!/usr/bin/env python
+"""
+Copyright(C) 1999-2022 National Technology & Engineering Solutions
+of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
+NTESS, the U.S. Government retains certain rights in this software.
+
+See packages/seacas/LICENSE for details
+
+"""
+
+import unittest
+import sys
+import os
+import tempfile
+import ctypes
+from contextlib import contextmanager
+
+ACCESS = os.getenv("ACCESS", "/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/EXODUS")
+sys.path.append(os.path.join(ACCESS, "lib"))
+import exodus as exo
+
+
+class TestExodus(unittest.TestCase):
+    def setUp(self):
+        input_dir = os.path.dirname(__file__)
+        self.tempdir = tempfile.TemporaryDirectory()
+        self.temp_exo_path = os.path.join(self.tempdir.name, "temp-test-assembly.exo")
+        with exo.exodus(
+            os.path.join(input_dir, "test-assembly.exo"), mode="r"
+        ) as exofile:
+            self.exofile = exofile
+            with self.exofile.copy(self.temp_exo_path, True) as temp_exofile:
+                self.temp_exofile = temp_exofile
+
+    def tearDown(self):
+        self.tempdir.cleanup()
+
+    def test_ex_obj_to_inq(self):
+        self.assertEqual("EX_INQ_ASSEMBLY", exo.ex_obj_to_inq("EX_ASSEMBLY"))
+
+    def test_ex_obj_to_inq_wrong_obj_type(self):
+        self.assertEqual(-1, exo.ex_obj_to_inq("fake_obj"))
+
+    def test_ex_entity_type_to_objType(self):
+        self.assertEqual(
+            "assembly",
+            exo.ex_entity_type_to_objType(exo.get_entity_type("EX_ASSEMBLY")),
+        )
+
+    def test_ex_entity_type_to_objType_wrong_entity_type(self):
+        self.assertEqual("EX_INVALID", exo.ex_entity_type_to_objType("fake_entity"))
+
+    def test_exodus_context_manager_reraises_exceptions(self):
+        with self.assertRaises(AssertionError):
+            with exo.exodus(self.temp_exo_path, mode="r"):
+                self.assertFalse(True)
+
+    def test_copy_opened_in_append_mode(self):
+        new = exo.assembly(
+            name="Unit_test", type=exo.ex_entity_type.EX_ASSEMBLY, id=444
+        )
+        new.entity_list = [100, 222]
+        temp_exo_path2 = f"{self.temp_exo_path}2"
+        with exo.exodus(self.temp_exo_path, mode="r") as temp_exofile:
+            expected = list(temp_exofile.get_ids("EX_ASSEMBLY"))
+            with temp_exofile.copy(temp_exo_path2, True, mode="a") as temp_exofile2:
+                temp_exofile2.put_assembly(new)
+                copied_output = list(temp_exofile2.get_ids("EX_ASSEMBLY"))
+                self.assertNotEqual(temp_exofile.modeChar, temp_exofile2.modeChar)
+        self.assertNotEqual(expected, copied_output)
+
+    def test_copy_opened_in_read_mode(self):
+        temp_exo_path2 = f"{self.temp_exo_path}2"
+        with exo.exodus(self.temp_exo_path, mode="r") as temp_exofile:
+            with temp_exofile.copy(temp_exo_path2, True, mode="r") as temp_exofile2:
+                expected = list(temp_exofile.get_ids("EX_ASSEMBLY"))
+                copied_output = list(temp_exofile2.get_ids("EX_ASSEMBLY"))
+                self.assertEqual(temp_exofile.modeChar, temp_exofile2.modeChar)
+        self.assertEqual(expected, copied_output)
+
+    def test_setup_ex_assembly(self):
+        assem = exo.assembly(name="Unit_test", type="EX_ASSEMBLY", id=444)
+        assem.entity_list = [100, 222]
+        ctype_assem = exo.setup_ex_assembly(assem)
+        self.assertIsInstance(ctype_assem, exo.ex_assembly)
+        self.assertIsInstance(
+            ctype_assem.entity_list, ctypes.POINTER(ctypes.c_longlong)
+        )
+
+    def test_get_name_assembly(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            assembly_ids = temp_exofile.get_ids("EX_ASSEMBLY")
+            names = [
+                temp_exofile.get_name("EX_ASSEMBLY", assembly)
+                for assembly in assembly_ids
+            ]
+        self.assertEqual(
+            ["Root", "Child2", "Child3", "Child4", "NewAssembly", "FromPython"], names
+        )
+
+    def test_inquire_assembly(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            assem_count = temp_exofile.inquire("EX_INQ_ASSEMBLY")
+        self.assertEqual(6, assem_count)
+
+    def test_get_block_id_map(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            elem_ids = temp_exofile.get_ids("EX_ELEM_BLOCK")
+            expected = [1, 2, 3, 4, 5, 6, 7]
+            outputs = []
+            for val in elem_ids:
+                outputs.extend(temp_exofile.get_block_id_map("EX_ELEM_BLOCK", val))
+        self.assertListEqual(expected, outputs)
+
+    def test_get_assembly(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            assembly_ids = temp_exofile.get_ids("EX_ASSEMBLY")
+            assemblies = [
+                temp_exofile.get_assembly(assembly) for assembly in assembly_ids
+            ]
+        root = exo.assembly(name="Root", type="EX_ASSEMBLY", id=100)
+        root.entity_list = [200, 300, 400]
+        self.assertEqual(str(root), str(assemblies[0]))
+
+    def test_get_entity_count(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            elem_ids = temp_exofile.get_ids("EX_ELEM_BLOCK")
+            elems = [temp_exofile.get_entity_count("EX_ELEM_BLOCK", elem) for elem in elem_ids]
+        self.assertListEqual([1, 1, 1, 1, 1, 1, 1], elems)
+
+    def test_get_elem_attr_values(self):
+        names = ["Scale", "Units"]
+        temp_copy = os.path.join(self.tempdir.name, "temp_copy.exo")
+        with exo.copy_mesh(self.temp_exo_path, temp_copy, additionalElementAttributes=names) as temp_exofile:
+            for elem_id in temp_exofile.get_ids("EX_ELEM_BLOCK"):
+                attrs = [[3.14159], [1]]
+                for name, values in zip(names, attrs):
+                    temp_exofile.put_elem_attr_values(elem_id, name, values)
+                self.assertEqual(3.14159, temp_exofile.get_elem_attr_values(elem_id, "Scale")[0])
+                self.assertEqual(1.0, temp_exofile.get_elem_attr_values(elem_id, "Units")[0])
+
+    def test_get_assemblies(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            assembly_ids = temp_exofile.get_ids("EX_ASSEMBLY")
+            assemblies = temp_exofile.get_assemblies(assembly_ids)
+        expected = [
+            exo.assembly(name="Root", type="EX_ASSEMBLY", id=100),
+            exo.assembly(name="Child2", type="EX_ELEM_BLOCK", id=200),
+            exo.assembly(name="Child3", type="EX_ELEM_BLOCK", id=300),
+            exo.assembly(name="Child4", type="EX_ELEM_BLOCK", id=400),
+            exo.assembly(name="NewAssembly", type="EX_ASSEMBLY", id=222),
+            exo.assembly(name="FromPython", type="EX_ASSEMBLY", id=333),
+        ]
+        entity_lists = [
+            [200, 300, 400],
+            [10, 11, 12, 13],
+            [14, 15, 16],
+            [10, 16],
+            [100, 200, 300, 400],
+            [100, 222],
+        ]
+        for i, x in enumerate(expected):
+            x.entity_list = entity_lists[i]
+        self.maxDiff = None
+        self.assertEqual(str(expected), str(assemblies))
+
+    def test_get_attributes_assembly(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            count = temp_exofile.get_attribute_count("EX_ASSEMBLY", 100)
+            self.assertEqual(count, 2)
+
+            attributes = temp_exofile.get_attributes("EX_ASSEMBLY", 100)
+            expected = [
+                exo.attribute("Scale", "EX_ASSEMBLY", 100),
+                exo.attribute("Units", "EX_ASSEMBLY", 100),
+            ]
+            expected[0].values = [1.5]
+            expected[1].values = [1, 0, 0, -1]
+
+            self.maxDiff = None
+            self.assertEqual(str(expected[0]), str(attributes["Scale"]))
+            self.assertEqual(str(expected[1]), str(attributes["Units"]))
+
+    def test_put_attributes_assembly(self):
+        with exo.exodus(self.temp_exo_path, mode="a") as temp_exofile:
+
+            new = [
+                exo.attribute("Scale", "EX_ASSEMBLY", 222),
+                exo.attribute("Units", "EX_ASSEMBLY", 333),
+            ]
+            new[0].values = [3.14159]
+            new[1].values = [0, 1, -1, 0]
+
+            temp_exofile.put_attribute(new[0])
+            temp_exofile.put_attribute(new[1])
+            att1 = temp_exofile.get_attributes("EX_ASSEMBLY", 222)
+            att2 = temp_exofile.get_attributes("EX_ASSEMBLY", 333)
+
+            self.maxDiff = None
+            self.assertEqual(str(att1["Scale"]), str(new[0]))
+            self.assertEqual(str(att2["Units"]), str(new[1]))
+
+    def test_put_qa(self):
+        new = [("name", "1.2.3-4", "20220801", "12:34:56")]
+        with exo.exodus(self.temp_exo_path, mode="a") as temp_exofile:
+            temp_exofile.put_qa_records(new)
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            self.assertEqual(new, temp_exofile.get_qa_records())
+
+    def test_copy_file(self):
+        new = [("name", "1.2.3-4", "20220801", "12:34:56")]
+        new_path = os.path.join(self.tempdir.name, "temp-test-assembly_new.exo")
+        with exo.exodus(self.temp_exo_path) as exofile:
+            qa_recs = exofile.get_qa_records()
+        with exo.exodus(new_path, mode="w+") as exofile:
+            exofile.put_qa_records(qa_recs + new)
+            with exo.exodus(self.temp_exo_path) as orig:
+                orig.copy_file(exofile.fileId, include_transient=True)
+                self.assertIn(new[0], exofile.get_qa_records())
+
+    def test_put_assembly(self):
+        new = exo.assembly(
+            name="Unit_test", type=exo.ex_entity_type.EX_ASSEMBLY, id=444
+        )
+        new.entity_list = [100, 222]
+        with exo.exodus(self.temp_exo_path, mode="a") as temp_exofile:
+            temp_exofile.put_assembly(new)
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            assembly_ids = temp_exofile.get_ids("EX_ASSEMBLY")
+            assemblies = [
+                temp_exofile.get_assembly(assembly) for assembly in assembly_ids
+            ]
+        self.assertEqual(new.name, assemblies[6].name)
+        self.assertEqual(16, assemblies[6].type)
+        self.assertEqual(new.id, assemblies[6].id)
+        self.assertEqual(new.entity_list, assemblies[6].entity_list)
+
+    def test_get_reduction_variables_assembly(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            red_var = temp_exofile.get_reduction_variable_number("EX_ASSEMBLY")
+            names = temp_exofile.get_reduction_variable_names("EX_ASSEMBLY")
+        self.assertEqual(4, red_var)
+        self.assertIn("Momentum_X", names)
+        self.assertIn("Momentum_Y", names)
+        self.assertIn("Momentum_Z", names)
+        self.assertIn("Kinetic_Energy", names)
+
+    def test_get_reduction_variables_assembly_enum(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            red_var = temp_exofile.get_reduction_variable_number(
+                exo.ex_entity_type.EX_ASSEMBLY
+            )
+            names = temp_exofile.get_reduction_variable_names(
+                exo.ex_entity_type.EX_ASSEMBLY
+            )
+        self.assertEqual(4, red_var)
+        self.assertIn("Momentum_X", names)
+        self.assertIn("Momentum_Y", names)
+        self.assertIn("Momentum_Z", names)
+        self.assertIn("Kinetic_Energy", names)
+
+    def test_get_reduction_variable_assembly(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            red_var = temp_exofile.get_reduction_variable_number("EX_ASSEMBLY")
+            name = temp_exofile.get_reduction_variable_name("EX_ASSEMBLY", 1)
+        self.assertEqual(4, red_var)
+        self.assertIn("Momentum_X", name)
+
+    def test_get_reduction_variable_assembly_enum(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            red_var = temp_exofile.get_reduction_variable_number(
+                exo.ex_entity_type.EX_ASSEMBLY
+            )
+            name = temp_exofile.get_reduction_variable_name(
+                exo.ex_entity_type.EX_ASSEMBLY, 1
+            )
+        self.assertEqual(4, red_var)
+        self.assertIn("Momentum_X", name)
+
+    def test_get_reduction_variable_values_assembly(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            assembly_ids = temp_exofile.get_ids("EX_ASSEMBLY")
+            assemblies = [
+                temp_exofile.get_assembly(assembly) for assembly in assembly_ids
+            ]
+            values = temp_exofile.get_reduction_variable_values(
+                "EX_ASSEMBLY", assemblies[0].id, 1
+            )
+        self.assertListEqual([0.02, 0.03, 0.04, 0.05], list(values))
+
+    def test_get_reduction_variable_values_assembly_no_values(self):
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            assembly_ids = temp_exofile.get_ids("EX_ASSEMBLY")
+            assemblies = [
+                temp_exofile.get_assembly(assembly) for assembly in assembly_ids
+            ]
+            values = temp_exofile.get_reduction_variable_values(
+                "EX_ASSEMBLY", assemblies[5].id, 1
+            )
+        self.assertListEqual([0.00, 0.00, 0.00, 0.00], list(values))
+
+    def test_put_assemblies(self):
+        new = exo.assembly(name="Unit_test", type="EX_ASSEMBLY", id=444)
+        new.entity_list = [100, 222]
+        with exo.exodus(self.temp_exo_path, mode="a") as temp_exofile:
+            temp_exofile.put_assemblies([new])
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            assembly_ids = temp_exofile.get_ids("EX_ASSEMBLY")
+            assemblies = [
+                temp_exofile.get_assembly(assembly) for assembly in assembly_ids
+            ]
+        self.assertEqual(new.name, assemblies[6].name)
+        self.assertEqual(16, assemblies[6].type)
+        self.assertEqual(new.id, assemblies[6].id)
+        self.assertEqual(new.entity_list, assemblies[6].entity_list)
+
+    def test_put_assemblies_multiple_assemblies(self):
+        new = exo.assembly(name="Unit_test1", type="EX_ASSEMBLY", id=444)
+        new.entity_list = [100, 222]
+        new2 = exo.assembly(name="Unit_test2", type="EX_ASSEMBLY", id=448)
+        new2.entity_list = [102, 224]
+        with exo.exodus(self.temp_exo_path, mode="a") as temp_exofile:
+            temp_exofile.put_assemblies([new, new2])
+        with exo.exodus(self.temp_exo_path) as temp_exofile:
+            assembly_ids = temp_exofile.get_ids("EX_ASSEMBLY")
+            assemblies = [
+                temp_exofile.get_assembly(assembly) for assembly in assembly_ids
+            ]
+        self.assertEqual(new.name, assemblies[6].name)
+        self.assertEqual(16, assemblies[6].type)
+        self.assertEqual(new.id, assemblies[6].id)
+        self.assertEqual(new.entity_list, assemblies[6].entity_list)
+
+        self.assertEqual(new2.name, assemblies[7].name)
+        self.assertEqual(16, assemblies[7].type)
+        self.assertEqual(new2.id, assemblies[7].id)
+        self.assertEqual(new2.entity_list, assemblies[7].entity_list)
+
+
+class TestExodusUtilities(unittest.TestCase):
+    def setUp(self):
+        self.tempdir = tempfile.TemporaryDirectory()
+
+    def tearDown(self):
+        self.tempdir.cleanup()
+
+    def test_basename(self):
+        self.assertEqual("test", exo.basename("test.e"))
+        self.assertEqual("fake/path/to/test", exo.basename("fake/path/to/test.e"))
+
+    def test_getExodusVersion(self):
+        include_path = os.path.join(self.tempdir.name, "include")
+        os.makedirs(include_path)
+        with open(os.path.join(include_path, "exodusII.h"), "w") as fptr:
+            fptr.write("#define EXODUS_VERSION_MAJOR 1\n")
+            fptr.write("#define EXODUS_VERSION_MINOR 22\n")
+        with swap_ACCESS_value(self.tempdir.name):
+            self.assertEqual(122, exo.getExodusVersion())
+
+    def test_getExodusVersion_not_found(self):
+        include_path = os.path.join(self.tempdir.name, "include")
+        os.makedirs(include_path)
+        with open(os.path.join(include_path, "exodusII.h"), "w") as fptr:
+            fptr.write("#define NOT_EXODUS_VERSION 1\n")
+            fptr.write("#define ALSO_NOT_EXODUS_VERSION 22\n")
+        with swap_ACCESS_value(self.tempdir.name):
+            self.assertEqual(0, exo.getExodusVersion())
+
+
+@contextmanager
+def swap_ACCESS_value(new_access_value):
+    old_value = exo.ACCESS
+    exo.ACCESS = new_access_value
+    yield
+    exo.ACCESS = old_value
+
+
+if __name__ == "__main__":
+    unittest.main()

HybridMesher/libraries/HDF5-1.14.1/bin/h5cc

@@ -0,0 +1,391 @@
+#! /bin/sh
+##
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://www.hdfgroup.org/licenses.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+##
+
+# This tool is adapted from the mpicc command of the MPICH Software.
+
+############################################################################
+##                                                                        ##
+## Things You May Have to Modify:                                         ##
+##                                                                        ##
+## If the following paths don't point to the place were HDF5 is installed ##
+## on your system (i.e., you received a binary distribution or moved the  ##
+## files from the originally installed directory to another directory)    ##
+## then modify them accordingly to represent the new paths.               ##
+##                                                                        ##
+############################################################################
+prefix="/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/HDF5-1.14.1"
+exec_prefix="${prefix}"
+libdir="${exec_prefix}/lib"
+includedir="${prefix}/include"
+HL="hl"
+
+############################################################################
+##                                                                        ##
+## Things You Can Modify to Override HDF5 Library Build Components:       ##
+##                                                                        ##
+## (Advanced usage - know what you're doing - you're on your own here.)   ##
+## The four variables below can be used to insert paths and flags in      ##
+## CPPFLAGS, CFLAGS, LDFLAGS, or LIBS in the h5cc compile line:           ##
+##    $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS   ##
+##    $LIBS $clibpath $link_objs $link_args $shared_link                  ##
+##                                                                        ##
+## These settings can be overridden by setting HDF5_CFLAGS,               ##
+## HDF5_CPPFLAGS, HDF5_LDFLAGS, or HDF5_LIBS in the environment.          ##
+##                                                                        ##
+############################################################################
+CFLAGSBASE=""
+CPPFLAGSBASE=""
+LDFLAGSBASE=""
+LIBSBASE=""
+
+############################################################################
+##                                                                        ##
+## You shouldn't have to modify anything below this line.                 ##
+##                                                                        ##
+############################################################################
+
+# Constants definitions
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+
+host_os="linux-gnu"
+
+prog_name="`basename $0`"
+
+allargs=""
+compile_args=""
+libraries=""
+link_args=""
+link_objs=""
+clibpath=""
+
+do_link="yes"
+do_compile="no"
+dash_o="no"
+dash_c="no"
+get_output_file="no"
+
+SHOW="eval"
+CCBASE="gcc"
+CLINKERBASE="gcc"
+
+# CFLAGS, CPPFLAGS and LDFLAGS are reserved for use by the script user.
+# FLAGS brought from the hdf5 build are put in H5BLD_*FLAGS.
+
+# User's CPPFLAGS and CFLAGS come after their H5BLD counterparts.  User's
+# LDFLAGS come just before clibpath, user's LIBS come after $link_objs and
+# before the hdf5 libraries in $link_args, followed by any external library
+# paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
+# from the hdf5 build. The order of the flags is intended to give precedence
+# to the user's flags.
+H5BLD_CFLAGS=" -fPIC"
+H5BLD_CPPFLAGS=" -I/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/zlib-1.2.13/include "
+H5BLD_LDFLAGS=" -L/media/digitalstorm/edf2449b-a566-40a2-8d0f-393bbe8ea1c0/maxwell_td_hybrid_mesher/HybridMesher/libraries/zlib-1.2.13/lib "
+H5BLD_LIBS="-lz -ldl -lm "
+
+CC="${HDF5_CC:-$CCBASE}"
+CLINKER="${HDF5_CLINKER:-$CLINKERBASE}"
+CFLAGS="${HDF5_CFLAGS:-$CFLAGSBASE}"
+CPPFLAGS="${HDF5_CPPFLAGS:-$CPPFLAGSBASE}"
+LDFLAGS="${HDF5_LDFLAGS:-$LDFLAGSBASE}"
+LIBS="${HDF5_LIBS:-$LIBSBASE}"
+
+# If a static library is available, the default will be to use it.  If the only
+# available library is shared, it will be used by default.  The user can
+# override either default, although choosing an unavailable library will result
+# in link errors.
+STATIC_AVAILABLE="yes"
+if test "${STATIC_AVAILABLE}" = "yes"; then
+  USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
+else
+  USE_SHARED_LIB="${HDF5_USE_SHLIB:-yes}"
+fi
+
+
+usage() {
+  # A wonderfully informative "usage" message.
+  echo "usage: $prog_name [OPTIONS] <compile line>"
+  echo "  OPTIONS:"
+  echo "    -help        This help message."
+  echo "    -echo        Show all the shell commands executed"
+  echo "    -prefix=DIR  Prefix directory to find HDF5 lib/ and include/"
+  echo "                   subdirectories [default: $prefix]"
+  echo "    -show        Show the commands without executing them"
+  echo "    -showconfig  Show the HDF5 library configuration summary"
+  echo "    -shlib       Compile with shared HDF5 libraries [default for hdf5 built"
+  echo "                                                     without static libraries]"
+  echo "    -noshlib     Compile with static HDF5 libraries [default for hdf5 built"
+  echo "                                                     with static libraries]"
+  echo " "
+  echo "  <compile line>  - the normal compile line options for your compiler."
+  echo "                    $prog_name uses the same compiler you used to compile"
+  echo "                    HDF5. Check with your compiler's man pages for more"
+  echo "                    information on which options are needed."
+  echo " "
+  echo " You can override the compiler, linker, and whether or not to use static"
+  echo " or shared libraries to compile your program by setting the following"
+  echo " environment variables accordingly:"
+  echo " "
+  echo "   HDF5_CC                  -  use a different C compiler"
+  echo "   HDF5_CLINKER             -  use a different linker"
+  echo "   HDF5_USE_SHLIB=[yes|no]  -  use shared or static version of the HDF5 library"
+  echo "                                 [default: no except when built with only"
+  echo "                                           shared libraries]"
+  echo " "
+  echo " You can also add or change paths and flags to the compile line using"
+  echo " the following environment variables or by assigning them to their counterparts"
+  echo " in the 'Things You Can Modify to Override...'" section of $prog_name
+  echo " "
+  echo "  Variable              Current value to be replaced"
+  echo "  HDF5_CPPFLAGS         \"$CPPFLAGSBASE\""
+  echo "  HDF5_CFLAGS           \"$CFLAGSBASE\""
+  echo "  HDF5_LDFLAGS          \"$LDFLAGSBASE\""
+  echo "  HDF5_LIBS             \"$LIBSBASE\""
+  echo " "
+  echo " Note that adding library paths to HDF5_LDFLAGS where another hdf5 version"
+  echo " is located may link your program with that other hdf5 library version."
+  echo " "
+  exit $EXIT_FAILURE
+}
+
+# Show the configuration summary of the library recorded in the
+# libhdf5.settings file reside in the lib directory.
+showconfigure()
+{
+  cat ${libdir}/libhdf5.settings
+  status=$?
+}
+
+# Main
+status=$EXIT_SUCCESS
+
+if test "$#" = "0"; then
+  # No parameters specified, issue usage statement and exit.
+  usage
+fi
+
+case "$CC" in
+  gcc)
+    kind="gcc"
+    ;;
+  mpicc|mpcc|mpicc_r)
+    # Is this gcc masquarading as an MPI compiler?
+    if test "`${CC} -v 2>&1 | sed -n 2p | cut -c1-3`" = "gcc"; then
+      kind="gcc"
+    else
+      # Nope
+      kind="$host_os"
+    fi
+    ;;
+  *)
+    kind="$host_os"
+    ;;
+esac
+
+for arg in $@ ; do
+  if test "x$get_output_file" = "xyes"; then
+    link_args="$link_args $arg"
+    output_file="$arg"
+    get_output_file="no"
+    continue
+  fi
+
+  case "$arg" in
+    -c)
+      allargs="$allargs $arg"
+      compile_args="$compile_args $arg"
+
+      if test "x$do_link" = "xyes" -a -n "$output_file"; then
+        compile_args="$compile_args -o $output_file"
+      fi
+
+      do_link="no"
+      dash_c="yes"
+      ;;
+    -o)
+      allargs="$allargs $arg"
+      dash_o="yes"
+
+      if test "x$dash_c" = "xyes"; then
+        compile_args="$compile_args $arg"
+      else
+        link_args="$link_args $arg"
+        do_link="yes"
+        get_output_file="yes"
+      fi
+      ;;
+    -E|-M|-MT)
+      allargs="$allargs $arg"
+      compile_args="$compile_args $arg"
+      dash_c="yes"
+      do_link="no"
+      ;;
+    -l*)
+      libraries=" $libraries $arg "
+      allargs="$allargs $arg"
+      ;;
+    -prefix=*)
+      prefix="`expr "$arg" : '-prefix=\(.*\)'`"
+      ;;
+    -echo)
+      set -x
+      ;;
+    -show)
+      SHOW="echo"
+      ;;
+    -showconfig)
+      showconfigure
+      exit $status
+      ;;
+    -shlib)
+      USE_SHARED_LIB="yes"
+      ;;
+    -noshlib)
+      USE_SHARED_LIB="no"
+      ;;
+    -help)
+      usage
+      ;;
+    *\"*)
+      qarg="'"$arg"'"
+      allargs="$allargs $qarg"
+      ;;
+    *\'*)
+      qarg='\"'"$arg"'\"'
+      allargs="$allargs $qarg"
+      ;;
+    *)
+      allargs="$allargs $qarg"
+
+      if test -s "$arg"; then
+        ext=`expr "$arg" : '.*\(\..*\)'`
+
+        if test "x$ext" = "x.c"; then
+          do_compile="yes"
+          compile_args="$compile_args $arg"
+          fname=`basename $arg .c`
+          link_objs="$link_objs $fname.o"
+        elif test "x$ext" = "x.o"; then
+          if test "x$dash_c" = "xyes"; then
+            compile_args="$compile_args $arg"
+          else
+            do_link="yes"
+            link_objs="$link_objs $arg"
+          fi
+        elif test "x$ext" = "x.a"; then
+          # This is an archive that we're linking in
+          libraries=" $libraries $arg "
+        else
+          compile_args="$compile_args $arg"
+          link_args="$link_args $arg"
+        fi
+      else
+        compile_args="$compile_args $arg"
+        link_args="$link_args $arg"
+      fi
+      ;;
+  esac
+done
+
+if test "$dash_c" = "yes" -a "$do_compile" = no -a "$do_link" = no ; then
+    # -c was specified.  Force do_compile on.
+    do_compile=yes
+fi
+
+if test "x$do_compile" = "xyes"; then
+  if test "x$dash_c" != "xyes"; then
+    compile_args="-c $compile_args"
+  fi
+
+  $SHOW $CC -I$includedir $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $compile_args
+  status=$?
+
+  if test "$status" != "0"; then
+    exit $status
+  fi
+fi
+
+if test "x$do_link" = "xyes"; then
+  shared_link=""
+# conditionally link with the hl library
+  if test "X$HL" = "Xhl"; then
+   libraries=" $libraries -lhdf5_hl -lhdf5 "
+  else
+   libraries=" $libraries  -lhdf5 "
+  fi
+  link_args="$link_args -L${libdir}"
+
+  case "$kind" in
+    gcc|linux*)
+      # MacOS X doesn't support the "-Wl,-rpath -Wl," style of linker flags.
+      # It appears to want none of them specified.
+      case "$host_os" in
+        darwin*)          flag="" ;;
+        *)                flag="-Wl,-rpath -Wl," ;;
+      esac
+      ;;
+    hpux*)                flag="-Wl,+b -Wl," ;;
+    freebsd*|solaris*)    flag="-R" ;;
+    rs6000*|aix*)         flag="-L" ;;
+    sgi)                  flag="-rpath " ;;
+    *)                    flag="" ;;
+  esac
+
+  if test -n "$flag"; then
+    shared_link="${flag}${libdir}"
+  fi
+
+  if test "x$USE_SHARED_LIB" != "xyes"; then
+    # The "-lhdf5" & "-lhdf5_hl" flags are in here already...This is a static
+    # compile though, so change it to the static version (.a) of the library.
+    new_libraries=""
+    for lib in $libraries; do
+      case "$lib" in
+        -lhdf5)
+          new_libraries="$new_libraries ${libdir}/libhdf5.a"
+          ;;
+        -lhdf5_hl)
+          new_libraries="$new_libraries ${libdir}/libhdf5_hl.a"
+          ;;
+        *)
+          new_libraries="$new_libraries $lib"
+          ;;
+      esac
+    done
+    libraries="$new_libraries"
+  fi
+
+  for lib in $libraries; do
+    if echo $link_args | grep " $lib " > /dev/null ||
+       echo $link_args | grep " $lib$" > /dev/null; then
+      :
+    else
+      link_args="$link_args $lib "
+    fi
+  done
+
+  # The LIBS are just a bunch of -l* libraries necessary for the HDF5
+  # module. It's okay if they're included twice in the compile line.
+  link_args="$link_args $H5BLD_LDFLAGS $H5BLD_LIBS"
+
+  # User's CPPFLAGS and CFLAGS come after their H5BLD counterparts.  User's
+  # LDFLAGS come just before clibpath, user's LIBS come after $link_objs and
+  # before the hdf5 libraries in $link_args, followed by any external library
+  # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
+  # from the hdf5 build. The order of the flags is intended to give precedence
+  # to the user's flags.
+  $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link
+  status=$?
+fi
+
+exit $status

HybridMesher/libraries/HDF5-1.14.1/bin/h5redeploy

@@ -0,0 +1,215 @@
+#! /bin/sh
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://www.hdfgroup.org/licenses.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+#
+
+## Update HDF5 compiler tools after the HDF5 software has been installed  ##
+## in a new location.							  ##
+## For help page, use "h5redeploy -help"				  ##
+##									  ##
+
+# Constants definitions
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+
+# Function definitions
+
+# show help page
+usage() {
+  # A wonderfully informative "usage" message.
+  echo "usage: $prog_name [OPTIONS]"
+  echo "  OPTIONS:"
+  echo "    -help|help        This help message"
+  echo "    -echo             Show all the shell commands executed"
+  echo "    -force            No prompt, just do it"
+  echo "    -prefix=DIR       New directory to find HDF5 lib/ and include/"
+  echo "                        subdirectories [default: current directory]"
+  echo "    -exec-prefix=DIR  New directory to find HDF5 lib/"
+  echo "                        subdirectory [default: <prefix>]"
+  echo "    -libdir=DIR       New directory for the HDF5 lib directory"
+  echo "                        [default: <exec-prefix>/lib]"
+  echo "    -includedir=DIR   New directory for the HDF5 header files"
+  echo "                        [default: <prefix>/include]"
+  echo "    -tool=TOOL        Tool to update. TOOL must be in the current"
+  echo "                        directory and writable. [default: $h5tools]"
+  echo "    -show             Show the commands without executing them"
+  echo " "
+  exit $EXIT_FAILURE
+}
+
+# display variable values
+dump_vars(){
+    echo "====Showing all variable values====="
+    echo prefix=$prefix
+    echo h5tools=$h5tools
+    echo "====End Showing====="
+}
+
+# show actions to be taken
+show_action()
+{
+    echo "Update the following tools because they are now installed at a new directory"
+    for t in $foundtools; do
+	echo "${t}:"
+	echo "   current setting=`sed -e '/^prefix=/s/prefix=//p' -e d $t`"
+	echo "   new     setting="\""$prefix"\"
+    done
+}
+
+
+# Report Error message
+ERROR()
+{
+    echo "***ERROR***"
+    echo "$1"
+}
+
+# Main
+#
+############################################################################
+## Installation directories:						  ##
+## prefix	architecture-independent files.				  ##
+## exec_prefix	architecture-dependent files, default is <prefix>.	  ##
+## libdir	libraries, default is <exec_prefix>/lib.		  ##
+## includedir	header files, default is <prefix/include>.		  ##
+## Not used here:							  ##
+## bindir	executables, <exec_prefix/bin>.				  ##
+############################################################################
+# Initialization
+h5tools="h5cc h5pcc h5fc h5pfc h5c++"	# possible hdf5 tools
+foundtools=		# tools found and will be modified
+fmode=			# force mode, default is off
+prefix=
+exec_prefix=
+libdir=
+includedir=
+
+# Parse options
+for arg in $@ ; do
+  case "$arg" in
+    -prefix=*)
+      prefix="`echo $arg | cut -f2 -d=`"
+      ;;
+    -exec-prefix=*)
+      exec_prefix="`echo $arg | cut -f2 -d=`"
+      ;;
+    -libdir=*)
+      libdir="`echo $arg | cut -f2 -d=`"
+      ;;
+    -includedir=*)
+      includedir="`echo $arg | cut -f2 -d=`"
+      ;;
+    -echo)
+      set -x
+      ;;
+    -show)
+      SHOW="echo"
+      ;;
+    -tool=*)
+      h5tools="`echo $arg | cut -f2 -d=`"
+      ;;
+    -help|help)
+      usage
+      ;;
+    -force)
+      fmode=yes
+      ;;
+    *)
+      ERROR "Unknown Option($arg)"
+      usage
+      exit $EXIT_FAILURE
+      ;;
+  esac
+done
+
+# Set to default value, one above where i am, if not given by user
+if [ -z "$prefix" ]; then
+    prefix=`(cd ..;pwd)`
+fi
+if [ -z "$exec_prefix" ]; then
+    exec_prefix='${prefix}'		# use single quotes to prevent expansion of $
+fi
+if [ -z "$libdir" ]; then
+    libdir='${exec_prefix}'/lib	# use single quotes to prevent expansion of $
+fi
+if [ -z "$includedir" ]; then
+    includedir='${prefix}'/include # use single quotes to prevent expansion of $
+fi
+
+for x in $h5tools; do
+    if [ -f $x ]; then
+	foundtools="$foundtools $x"
+	if [ ! -w $x ]; then
+	    ERROR "h5tool($x) is not writable"
+	    exit $EXIT_FAILURE
+	fi
+    fi
+done
+
+if [ -z "$foundtools" ]; then
+    ERROR "found no tools to modify"
+    exit $EXIT_FAILURE
+fi
+
+# Show actions to be taken and get consent
+show_action
+# Ask confirmation unless fmode is on
+if [ x-$fmode = x- ]; then
+    echo "Continue? (yes/no)"
+    read ansx
+    ans=`echo $ansx | tr "[A-Z]" "[a-z]"`
+    if [ x-$ans != x-yes ]; then
+	echo ABORT.  No tools changed.
+	exit $EXIT_FAILURE
+    fi
+fi
+
+
+# Create the update commands
+CMDFILE=/tmp/h5redeploy.$$
+touch $CMDFILE
+chmod 0600 $CMDFILE
+echo "/^prefix=/c"                    >> $CMDFILE
+echo prefix=\""$prefix"\"             >> $CMDFILE
+echo .                                >> $CMDFILE
+echo "/^exec_prefix=/c"               >> $CMDFILE
+echo exec_prefix=\""$exec_prefix"\"   >> $CMDFILE
+echo .                                >> $CMDFILE
+echo "/^libdir=/c"                    >> $CMDFILE
+echo libdir=\""$libdir"\"             >> $CMDFILE
+echo .                                >> $CMDFILE
+echo "/^includedir=/c"                >> $CMDFILE
+echo includedir=\""$includedir"\"     >> $CMDFILE
+echo .                                >> $CMDFILE
+(echo w; echo q)                      >> $CMDFILE
+
+
+# Update them
+if [ "$SHOW" = "echo" ]; then
+    echo "===Update commands are:===="
+    cat $CMDFILE
+    echo "===End Update commands====="
+fi
+
+for t in $foundtools; do
+    echo Update $t ...
+    COMMAND="ed - $t"
+    if [ "$SHOW" = "echo" ]; then
+	echo $COMMAND
+    else
+	$COMMAND < $CMDFILE
+    fi
+done
+
+
+# Cleanup
+rm -f $CMDFILE
+exit $EXIT_SUCCESS

HybridMesher/libraries/HDF5-1.14.1/include/H5ACpublic.h

@@ -0,0 +1,781 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*-------------------------------------------------------------------------
+ *
+ * Created:             H5ACpublic.h
+ *                      Jul 10 1997
+ *                      Robb Matzke
+ *
+ * Purpose:             Public include file for cache functions.
+ *
+ *-------------------------------------------------------------------------
+ */
+#ifndef H5ACpublic_H
+#define H5ACpublic_H
+
+/* Public headers needed by this file */
+#include "H5public.h"
+#include "H5Cpublic.h"
+
+/****************************************************************************
+ *
+ * structure H5AC_cache_config_t
+ *
+ * H5AC_cache_config_t is a public structure intended for use in public APIs.
+ * At least in its initial incarnation, it is basically a copy of struct
+ * H5C_auto_size_ctl_t, minus the report_fcn field, and plus the
+ * dirty_bytes_threshold field.
+ *
+ * The report_fcn field is omitted, as including it would require us to
+ * make H5C_t structure public.
+ *
+ * The dirty_bytes_threshold field does not appear in H5C_auto_size_ctl_t,
+ * as synchronization between caches on different processes is handled at
+ * the H5AC level, not at the level of H5C.  Note however that there is
+ * considerable interaction between this value and the other fields in this
+ * structure.
+ *
+ * Similarly, the open_trace_file, close_trace_file, and trace_file_name
+ * fields do not appear in H5C_auto_size_ctl_t, as most trace file
+ * issues are handled at the H5AC level.  The one exception is storage of
+ * the pointer to the trace file, which is handled by H5C.
+ *
+ * The structure is in H5ACpublic.h as we may wish to allow different
+ * configuration options for metadata and raw data caches.
+ *
+ * The fields of the structure are discussed individually below:
+ *
+ * version: Integer field containing the version number of this version
+ *      of the H5AC_cache_config_t structure.  Any instance of
+ *      H5AC_cache_config_t passed to the cache must have a known
+ *      version number, or an error will be flagged.
+ *
+ * rpt_fcn_enabled: Boolean field used to enable and disable the default
+ *    reporting function.  This function is invoked every time the
+ *    automatic cache resize code is run, and reports on its activities.
+ *
+ *    This is a debugging function, and should normally be turned off.
+ *
+ * open_trace_file: Boolean field indicating whether the trace_file_name
+ *     field should be used to open a trace file for the cache.
+ *
+ *      *** DEPRECATED *** Use H5Fstart/stop logging functions instead
+ *
+ *     The trace file is a debugging feature that allow the capture of
+ *     top level metadata cache requests for purposes of debugging and/or
+ *     optimization.  This field should normally be set to FALSE, as
+ *     trace file collection imposes considerable overhead.
+ *
+ *     This field should only be set to TRUE when the trace_file_name
+ *     contains the full path of the desired trace file, and either
+ *     there is no open trace file on the cache, or the close_trace_file
+ *     field is also TRUE.
+ *
+ * close_trace_file: Boolean field indicating whether the current trace
+ *     file (if any) should be closed.
+ *
+ *      *** DEPRECATED *** Use H5Fstart/stop logging functions instead
+ *
+ *     See the above comments on the open_trace_file field.  This field
+ *     should be set to FALSE unless there is an open trace file on the
+ *     cache that you wish to close.
+ *
+ * trace_file_name: Full path of the trace file to be opened if the
+ *     open_trace_file field is TRUE.
+ *
+ *      *** DEPRECATED *** Use H5Fstart/stop logging functions instead
+ *
+ *     In the parallel case, an ascii representation of the mpi rank of
+ *     the process will be appended to the file name to yield a unique
+ *     trace file name for each process.
+ *
+ *     The length of the path must not exceed H5AC__MAX_TRACE_FILE_NAME_LEN
+ *     characters.
+ *
+ * evictions_enabled:  Boolean field used to either report the current
+ *     evictions enabled status of the cache, or to set the cache's
+ *    evictions enabled status.
+ *
+ *     In general, the metadata cache should always be allowed to
+ *     evict entries.  However, in some cases it is advantageous to
+ *     disable evictions briefly, and thereby postpone metadata
+ *     writes.  However, this must be done with care, as the cache
+ *     can grow quickly.  If you do this, re-enable evictions as
+ *     soon as possible and monitor cache size.
+ *
+ *     At present, evictions can only be disabled if automatic
+ *     cache resizing is also disabled (that is, ( incr_mode ==
+ *    H5C_incr__off ) && ( decr_mode == H5C_decr__off )).  There
+ *    is no logical reason why this should be so, but it simplifies
+ *    implementation and testing, and I can't think of any reason
+ *    why it would be desirable.  If you can think of one, I'll
+ *    revisit the issue.
+ *
+ * set_initial_size: Boolean flag indicating whether the size of the
+ *      initial size of the cache is to be set to the value given in
+ *      the initial_size field.  If set_initial_size is FALSE, the
+ *      initial_size field is ignored.
+ *
+ * initial_size: If enabled, this field contain the size the cache is
+ *      to be set to upon receipt of this structure.  Needless to say,
+ *      initial_size must lie in the closed interval [min_size, max_size].
+ *
+ * min_clean_fraction: double in the range 0 to 1 indicating the fraction
+ *      of the cache that is to be kept clean.  This field is only used
+ *      in parallel mode.  Typical values are 0.1 to 0.5.
+ *
+ * max_size: Maximum size to which the cache can be adjusted.  The
+ *      supplied value must fall in the closed interval
+ *      [MIN_MAX_CACHE_SIZE, MAX_MAX_CACHE_SIZE].  Also, max_size must
+ *      be greater than or equal to min_size.
+ *
+ * min_size: Minimum size to which the cache can be adjusted.  The
+ *      supplied value must fall in the closed interval
+ *      [H5C__MIN_MAX_CACHE_SIZE, H5C__MAX_MAX_CACHE_SIZE].  Also, min_size
+ *      must be less than or equal to max_size.
+ *
+ * epoch_length: Number of accesses on the cache over which to collect
+ *      hit rate stats before running the automatic cache resize code,
+ *      if it is enabled.
+ *
+ *      At the end of an epoch, we discard prior hit rate data and start
+ *      collecting afresh.  The epoch_length must lie in the closed
+ *      interval [H5C__MIN_AR_EPOCH_LENGTH, H5C__MAX_AR_EPOCH_LENGTH].
+ *
+ *
+ * Cache size increase control fields:
+ *
+ * incr_mode: Instance of the H5C_cache_incr_mode enumerated type whose
+ *      value indicates how we determine whether the cache size should be
+ *      increased.  At present there are two possible values:
+ *
+ *      H5C_incr__off:  Don't attempt to increase the size of the cache
+ *              automatically.
+ *
+ *              When this increment mode is selected, the remaining fields
+ *              in the cache size increase section ar ignored.
+ *
+ *      H5C_incr__threshold: Attempt to increase the size of the cache
+ *              whenever the average hit rate over the last epoch drops
+ *              below the value supplied in the lower_hr_threshold
+ *              field.
+ *
+ *              Note that this attempt will fail if the cache is already
+ *              at its maximum size, or if the cache is not already using
+ *              all available space.
+ *
+ *      Note that you must set decr_mode to H5C_incr__off if you
+ *      disable metadata cache entry evictions.
+ *
+ * lower_hr_threshold: Lower hit rate threshold.  If the increment mode
+ *      (incr_mode) is H5C_incr__threshold and the hit rate drops below the
+ *      value supplied in this field in an epoch, increment the cache size by
+ *      size_increment.  Note that cache size may not be incremented above
+ *      max_size, and that the increment may be further restricted by the
+ *      max_increment field if it is enabled.
+ *
+ *      When enabled, this field must contain a value in the range [0.0, 1.0].
+ *      Depending on the incr_mode selected, it may also have to be less than
+ *      upper_hr_threshold.
+ *
+ * increment:  Double containing the multiplier used to derive the new
+ *      cache size from the old if a cache size increment is triggered.
+ *      The increment must be greater than 1.0, and should not exceed 2.0.
+ *
+ *      The new cache size is obtained my multiplying the current max cache
+ *      size by the increment, and then clamping to max_size and to stay
+ *      within the max_increment as necessary.
+ *
+ * apply_max_increment:  Boolean flag indicating whether the max_increment
+ *      field should be used to limit the maximum cache size increment.
+ *
+ * max_increment: If enabled by the apply_max_increment field described
+ *      above, this field contains the maximum number of bytes by which the
+ *      cache size can be increased in a single re-size.
+ *
+ * flash_incr_mode:  Instance of the H5C_cache_flash_incr_mode enumerated
+ *      type whose value indicates whether and by which algorithm we should
+ *      make flash increases in the size of the cache to accommodate insertion
+ *      of large entries and large increases in the size of a single entry.
+ *
+ *      The addition of the flash increment mode was occasioned by performance
+ *      problems that appear when a local heap is increased to a size in excess
+ *      of the current cache size.  While the existing re-size code dealt with
+ *      this eventually, performance was very bad for the remainder of the
+ *      epoch.
+ *
+ *      At present, there are two possible values for the flash_incr_mode:
+ *
+ *      H5C_flash_incr__off:  Don't perform flash increases in the size of
+ *              the cache.
+ *
+ *      H5C_flash_incr__add_space:  Let x be either the size of a newly
+ *              newly inserted entry, or the number of bytes by which the
+ *              size of an existing entry has been increased.
+ *
+ *              If
+ *                      x > flash_threshold * current max cache size,
+ *
+ *              increase the current maximum cache size by x * flash_multiple
+ *              less any free space in the cache, and star a new epoch.  For
+ *              now at least, pay no attention to the maximum increment.
+ *
+ *      In both of the above cases, the flash increment pays no attention to
+ *      the maximum increment (at least in this first incarnation), but DOES
+ *      stay within max_size.
+ *
+ *      With a little thought, it should be obvious that the above flash
+ *      cache size increase algorithm is not sufficient for all circumstances
+ *      -- for example, suppose the user round robins through
+ *      (1/flash_threshold) +1 groups, adding one data set to each on each
+ *      pass.  Then all will increase in size at about the same time, requiring
+ *      the max cache size to at least double to maintain acceptable
+ *      performance, however the above flash increment algorithm will not be
+ *      triggered.
+ *
+ *      Hopefully, the add space algorithms detailed above will be sufficient
+ *      for the performance problems encountered to date.  However, we should
+ *      expect to revisit the issue.
+ *
+ * flash_multiple: Double containing the multiple described above in the
+ *      H5C_flash_incr__add_space section of the discussion of the
+ *      flash_incr_mode section.  This field is ignored unless flash_incr_mode
+ *      is H5C_flash_incr__add_space.
+ *
+ * flash_threshold: Double containing the factor by which current max cache
+ *      size is multiplied to obtain the size threshold for the add_space flash
+ *      increment algorithm.  The field is ignored unless flash_incr_mode is
+ *      H5C_flash_incr__add_space.
+ *
+ *
+ * Cache size decrease control fields:
+ *
+ * decr_mode: Instance of the H5C_cache_decr_mode enumerated type whose
+ *      value indicates how we determine whether the cache size should be
+ *      decreased.  At present there are four possibilities.
+ *
+ *      H5C_decr__off:  Don't attempt to decrease the size of the cache
+ *              automatically.
+ *
+ *              When this increment mode is selected, the remaining fields
+ *              in the cache size decrease section are ignored.
+ *
+ *      H5C_decr__threshold: Attempt to decrease the size of the cache
+ *              whenever the average hit rate over the last epoch rises
+ *              above the value supplied in the upper_hr_threshold
+ *              field.
+ *
+ *      H5C_decr__age_out:  At the end of each epoch, search the cache for
+ *              entries that have not been accessed for at least the number
+ *              of epochs specified in the epochs_before_eviction field, and
+ *              evict these entries.  Conceptually, the maximum cache size
+ *              is then decreased to match the new actual cache size.  However,
+ *              this reduction may be modified by the min_size, the
+ *              max_decrement, and/or the empty_reserve.
+ *
+ *      H5C_decr__age_out_with_threshold:  Same as age_out, but we only
+ *              attempt to reduce the cache size when the hit rate observed
+ *              over the last epoch exceeds the value provided in the
+ *              upper_hr_threshold field.
+ *
+ *      Note that you must set decr_mode to H5C_decr__off if you
+ *      disable metadata cache entry evictions.
+ *
+ * upper_hr_threshold: Upper hit rate threshold.  The use of this field
+ *      varies according to the current decr_mode:
+ *
+ *      H5C_decr__off or H5C_decr__age_out:  The value of this field is
+ *              ignored.
+ *
+ *      H5C_decr__threshold:  If the hit rate exceeds this threshold in any
+ *              epoch, attempt to decrement the cache size by size_decrement.
+ *
+ *              Note that cache size may not be decremented below min_size.
+ *
+ *              Note also that if the upper_threshold is 1.0, the cache size
+ *              will never be reduced.
+ *
+ *      H5C_decr__age_out_with_threshold:  If the hit rate exceeds this
+ *              threshold in any epoch, attempt to reduce the cache size
+ *              by evicting entries that have not been accessed for more
+ *              than the specified number of epochs.
+ *
+ * decrement: This field is only used when the decr_mode is
+ *      H5C_decr__threshold.
+ *
+ *      The field is a double containing the multiplier used to derive the
+ *      new cache size from the old if a cache size decrement is triggered.
+ *      The decrement must be in the range 0.0 (in which case the cache will
+ *      try to contract to its minimum size) to 1.0 (in which case the
+ *      cache will never shrink).
+ *
+ * apply_max_decrement:  Boolean flag used to determine whether decrements
+ *      in cache size are to be limited by the max_decrement field.
+ *
+ * max_decrement: Maximum number of bytes by which the cache size can be
+ *      decreased in a single re-size.  Note that decrements may also be
+ *      restricted by the min_size of the cache, and (in age out modes) by
+ *      the empty_reserve field.
+ *
+ * epochs_before_eviction:  Integer field used in H5C_decr__age_out and
+ *      H5C_decr__age_out_with_threshold decrement modes.
+ *
+ *      This field contains the number of epochs an entry must remain
+ *      unaccessed before it is evicted in an attempt to reduce the
+ *      cache size.  If applicable, this field must lie in the range
+ *      [1, H5C__MAX_EPOCH_MARKERS].
+ *
+ * apply_empty_reserve:  Boolean field controlling whether the empty_reserve
+ *      field is to be used in computing the new cache size when the
+ *      decr_mode is H5C_decr__age_out or H5C_decr__age_out_with_threshold.
+ *
+ * empty_reserve:  To avoid a constant racheting down of cache size by small
+ *      amounts in the H5C_decr__age_out and H5C_decr__age_out_with_threshold
+ *      modes, this field allows one to require that any cache size
+ *      reductions leave the specified fraction of unused space in the cache.
+ *
+ *      The value of this field must be in the range [0.0, 1.0].  I would
+ *      expect typical values to be in the range of 0.01 to 0.1.
+ *
+ *
+ * Parallel Configuration Fields:
+ *
+ * In PHDF5, all operations that modify metadata must be executed collectively.
+ *
+ * We used to think that this was enough to ensure consistency across the
+ * metadata caches, but since we allow processes to read metadata individually,
+ * the order of dirty entries in the LRU list can vary across processes,
+ * which can result in inconsistencies between the caches.
+ *
+ * PHDF5 uses several strategies to prevent such inconsistencies in metadata,
+ * all of which use the fact that the same stream of dirty metadata is seen
+ * by all processes for purposes of synchronization.  This is done by
+ * having each process count the number of bytes of dirty metadata generated,
+ * and then running a "sync point" whenever this count exceeds a user
+ * specified threshold (see dirty_bytes_threshold below).
+ *
+ * The current metadata write strategy is indicated by the
+ * metadata_write_strategy field.  The possible values of this field, along
+ * with the associated metadata write strategies are discussed below.
+ *
+ * dirty_bytes_threshold:  Threshold of dirty byte creation used to
+ *     synchronize updates between caches. (See above for outline and
+ *    motivation.)
+ *
+ *    This value MUST be consistent across all processes accessing the
+ *    file.  This field is ignored unless HDF5 has been compiled for
+ *    parallel.
+ *
+ * metadata_write_strategy: Integer field containing a code indicating the
+ *    desired metadata write strategy.  The valid values of this field
+ *    are enumerated and discussed below:
+ *
+ *
+ *    H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY:
+ *
+ *    When metadata_write_strategy is set to this value, only process
+ *    zero is allowed to write dirty metadata to disk.  All other
+ *    processes must retain dirty metadata until they are informed at
+ *    a sync point that the dirty metadata in question has been written
+ *    to disk.
+ *
+ *    When the sync point is reached (or when there is a user generated
+ *    flush), process zero flushes sufficient entries to bring it into
+ *    compliance with its min clean size (or flushes all dirty entries in
+ *    the case of a user generated flush), broad casts the list of
+ *    entries just cleaned to all the other processes, and then exits
+ *    the sync point.
+ *
+ *    Upon receipt of the broadcast, the other processes mark the indicated
+ *    entries as clean, and leave the sync point as well.
+ *
+ *
+ *    H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED:
+ *
+ *    In the distributed metadata write strategy, process zero still makes
+ *    the decisions as to what entries should be flushed, but the actual
+ *    flushes are distributed across the processes in the computation to
+ *    the extent possible.
+ *
+ *    In this strategy, when a sync point is triggered (either by dirty
+ *    metadata creation or manual flush), all processes enter a barrier.
+ *
+ *    On the other side of the barrier, process 0 constructs an ordered
+ *    list of the entries to be flushed, and then broadcasts this list
+ *    to the caches in all the processes.
+ *
+ *    All processes then scan the list of entries to be flushed, flushing
+ *    some, and marking the rest as clean.  The algorithm for this purpose
+ *    ensures that each entry in the list is flushed exactly once, and
+ *    all are marked clean in each cache.
+ *
+ *    Note that in the case of a flush of the cache, no message passing
+ *    is necessary, as all processes have the same list of dirty entries,
+ *    and all of these entries must be flushed.  Thus in this case it is
+ *    sufficient for each process to sort its list of dirty entries after
+ *    leaving the initial barrier, and use this list as if it had been
+ *    received from process zero.
+ *
+ *    To avoid possible messages from the past/future, all caches must
+ *    wait until all caches are done before leaving the sync point.
+ *
+ ****************************************************************************/
+
+#define H5AC__CURR_CACHE_CONFIG_VERSION 1
+#define H5AC__MAX_TRACE_FILE_NAME_LEN   1024
+
+#define H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY 0
+#define H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED    1
+
+/**
+ * H5AC_cache_config_t is a public structure intended for use in public APIs.
+ * At least in its initial incarnation, it is basically a copy of \c struct
+ * \c H5C_auto_size_ctl_t, minus the \c report_fcn field, and plus the
+ * \c dirty_bytes_threshold field.
+ *
+ * The \c report_fcn field is omitted, as including it would require us to make
+ * \c H5C_t structure public.
+ *
+ * The \c dirty_bytes_threshold field does not appear in \c H5C_auto_size_ctl_t,
+ * as synchronization between caches on different processes is handled at the \c
+ * H5AC level, not at the level of \c H5C.  Note however that there is
+ * considerable interaction between this value and the other fields in this
+ * structure.
+ *
+ * Similarly, the \c open_trace_file, \c close_trace_file, and \c
+ * trace_file_name fields do not appear in \c H5C_auto_size_ctl_t, as most trace
+ * file issues are handled at the \c H5AC level.  The one exception is storage
+ * of the pointer to the trace file, which is handled by \c H5C.
+ *
+ * The structure is in H5ACpublic.h as we may wish to allow different
+ * configuration options for metadata and raw data caches.
+ */
+
+//! <!-- [H5AC_cache_config_t_snip] -->
+typedef struct H5AC_cache_config_t {
+    /* general configuration fields: */
+    //! <!-- [H5AC_cache_config_t_general_snip] -->
+    int version;
+    /**< Integer field indicating the version of the H5AC_cache_config_t
+     * in use. This field should be set to #H5AC__CURR_CACHE_CONFIG_VERSION
+     * (defined in H5ACpublic.h). */
+
+    hbool_t rpt_fcn_enabled;
+    /**< Boolean flag indicating whether the adaptive cache resize report
+     * function is enabled. This field should almost always be set to disabled
+     * (0). Since resize algorithm activity is reported via stdout, it MUST be
+     * set to disabled (0) on Windows machines.\n
+     * The report function is not supported code, and can be expected to change
+     * between versions of the library. Use it at your own risk. */
+
+    hbool_t open_trace_file;
+    /**< Boolean field indicating whether the
+     * \ref H5AC_cache_config_t.trace_file_name "trace_file_name"
+     * field should be used to open a trace file for the cache.\n
+     * The trace file is a debugging feature that allows the capture
+     * of top level metadata cache requests for purposes of debugging
+     * and/or optimization. This field should normally be set to 0, as
+     * trace file collection imposes considerable overhead.\n
+     * This field should only be set to 1 when the
+     * \ref H5AC_cache_config_t.trace_file_name "trace_file_name"
+     * contains the full path of the desired trace file, and either
+     * there is no open trace file on the cache, or the
+     * \ref H5AC_cache_config_t.close_trace_file "close_trace_file"
+     * field is also 1.\n
+     * The trace file feature is unsupported unless used at the
+     * direction of The HDF Group. It is intended to allow The HDF
+     * Group to collect a trace of cache activity in cases of occult
+     * failures and/or poor performance seen in the field, so as to aid
+     * in reproduction in the lab. If you use it absent the direction
+     * of The HDF Group, you are on your own. */
+
+    hbool_t close_trace_file;
+    /**< Boolean field indicating whether the current trace file
+     *(if any) should be closed.\n
+     * See the above comments on the \ref H5AC_cache_config_t.open_trace_file
+     * "open_trace_file" field. This field should be set to 0 unless there is
+     * an open trace file on the cache that you wish to close.\n
+     * The trace file feature is unsupported unless used at the direction of
+     * The HDF Group. It is intended to allow The HDF Group to collect a trace
+     * of cache activity in cases of occult failures and/or poor performance
+     * seen in the field, so as to aid in reproduction in the lab. If you use
+     * it absent the direction of The HDF Group, you are on your own. */
+
+    char trace_file_name[H5AC__MAX_TRACE_FILE_NAME_LEN + 1];
+    /**< Full path of the trace file to be opened if the
+     * \ref H5AC_cache_config_t.open_trace_file "open_trace_file" field is set
+     * to 1.\n
+     * In the parallel case, an ascii representation of the MPI rank of the
+     * process will be appended to the file name to yield a unique trace file
+     * name for each process.\n
+     * The length of the path must not exceed #H5AC__MAX_TRACE_FILE_NAME_LEN
+     * characters.\n
+     * The trace file feature is unsupported unless used at the direction of
+     * The HDF Group. It is intended to allow The HDF Group to collect a trace
+     * of cache activity in cases of occult failures and/or poor performance
+     * seen in the field, so as to aid in reproduction in the lab. If you use
+     * it absent the direction of The HDF Group, you are on your own. */
+
+    hbool_t evictions_enabled;
+    /**< A boolean flag indicating whether evictions from the metadata cache
+     * are enabled. This flag is initially set to enabled (1).\n
+     * In rare circumstances, the raw data throughput quirements may be so high
+     * that the user wishes to postpone metadata writes so as to reserve I/O
+     * throughput for raw data. The \p evictions_enabled field exists to allow
+     * this. However, this is an extreme step, and you have no business doing
+     * it unless you have read the User Guide section on metadata caching, and
+     * have considered all other options carefully.\n
+     * The \p evictions_enabled field may not be set to disabled (0)
+     * unless all adaptive cache resizing code is disabled via the
+     * \ref H5AC_cache_config_t.incr_mode "incr_mode",
+     * \ref H5AC_cache_config_t.flash_incr_mode "flash_incr_mode",
+     * \ref H5AC_cache_config_t.decr_mode "decr_mode" fields.\n
+     * When this flag is set to disabled (\c 0), the metadata cache will not
+     * attempt to evict entries to make space for new entries, and thus will
+     * grow without bound.\n
+     * Evictions will be re-enabled when this field is set back to \c 1.
+     * This should be done as soon as possible. */
+
+    hbool_t set_initial_size;
+    /**< Boolean flag indicating whether the cache should be created
+     * with a user specified initial size. */
+
+    size_t initial_size;
+    /**< If \ref H5AC_cache_config_t.set_initial_size "set_initial_size"
+     * is set to 1, \p initial_size must contain he desired initial size in
+     * bytes. This value must lie in the closed interval
+     * [ \p min_size, \p max_size ]. (see below) */
+
+    double min_clean_fraction;
+    /**< This field specifies the minimum fraction of the cache
+     * that must be kept either clean or empty.\n
+     * The value must lie in the interval [0.0, 1.0]. 0.01 is a good place to
+     * start in the serial case. In the parallel case, a larger value is needed
+     * -- see the overview of the metadata cache in the
+     * “Metadata Caching in HDF5” section of the -- <em>\ref UG</em>
+     * for details. */
+
+    size_t max_size;
+    /**< Upper bound (in bytes) on the range of values that the
+     * adaptive cache resize code can select as the maximum cache size. */
+
+    size_t min_size;
+    /**< Lower bound (in bytes) on the range of values that the
+     * adaptive cache resize code can select as the minimum cache * size. */
+
+    long int epoch_length;
+    /**< Number of cache accesses between runs of the adaptive cache resize
+     * code. 50,000 is a good starting number. */
+    //! <!-- [H5AC_cache_config_t_general_snip] -->
+
+    /* size increase control fields: */
+    //! <!-- [H5AC_cache_config_t_incr_snip] -->
+    enum H5C_cache_incr_mode incr_mode;
+    /**< Enumerated value indicating the operational mode of the automatic
+     * cache size increase code. At present, only two values listed in
+     * #H5C_cache_incr_mode are legal. */
+
+    double lower_hr_threshold;
+    /**< Hit rate threshold used by the hit rate threshold cache size
+     * increment algorithm.\n
+     * When the hit rate over an epoch is below this threshold and the cache
+     * is full, the maximum size of the cache is multiplied by increment
+     * (below), and then clipped as necessary to stay within \p max_size, and
+     * possibly \p max_increment.\n
+     * This field must lie in the interval [0.0, 1.0]. 0.8 or 0.9 is a good
+     * place to start. */
+
+    double increment;
+    /**< Factor by which the hit rate threshold cache size increment
+     * algorithm multiplies the current cache max size to obtain a tentative
+     * new cache size.\n
+     * The actual cache size increase will be clipped to satisfy the \p max_size
+     * specified in the general configuration, and possibly max_increment
+     * below.\n
+     * The parameter must be greater than or equal to 1.0 -- 2.0 is a reasonable
+     * value.\n
+     * If you set it to 1.0, you will effectively disable cache size increases.
+     */
+
+    hbool_t apply_max_increment;
+    /**< Boolean flag indicating whether an upper limit should be applied to
+     * the size of cache size increases. */
+
+    size_t max_increment;
+    /**< Maximum number of bytes by which cache size can be increased in a
+     * single step -- if applicable. */
+
+    enum H5C_cache_flash_incr_mode flash_incr_mode;
+    /**< Enumerated value indicating the operational mode of the flash cache
+     * size increase code. At present, only two listed  values in
+     * #H5C_cache_flash_incr_mode are legal.*/
+
+    double flash_multiple;
+    /**< The factor by which the size of the triggering entry / entry size
+     * increase is multiplied to obtain the initial cache size increment. This
+     * increment may be reduced to reflect existing free space in the cache and
+     * the \p max_size field above.\n
+     * The parameter must lie in the interval [0.0, 1.0]. 0.1 or 0.05 is a good
+     * place to start.\n
+     * At present, this field must lie in the range [0.1, 10.0]. */
+
+    double flash_threshold;
+    /**< The factor by which the current maximum cache size is multiplied to
+     * obtain the minimum size entry / entry size increase which may trigger a
+     * flash cache size increase. \n
+     * At present, this value must lie in the range [0.1, 1.0]. */
+    //! <!-- [H5AC_cache_config_t_incr_snip] -->
+
+    /* size decrease control fields: */
+    //! <!-- [H5AC_cache_config_t_decr_snip] -->
+    enum H5C_cache_decr_mode decr_mode;
+    /**< Enumerated value indicating the operational mode of the tomatic
+     * cache size decrease code. At present, the values listed in
+     * #H5C_cache_decr_mode are legal.*/
+
+    double upper_hr_threshold;
+    /**< Hit rate threshold for the hit rate threshold and ageout with hit
+     * rate threshold cache size decrement algorithms.\n
+     * When \p decr_mode is #H5C_decr__threshold, and the hit rate over a given
+     * epoch exceeds the supplied threshold, the current maximum cache
+     * size is multiplied by decrement to obtain a tentative new (and smaller)
+     * maximum cache size.\n
+     * When \p decr_mode is #H5C_decr__age_out_with_threshold, there is
+     * no attempt to find and evict aged out entries unless the hit rate in
+     * the previous epoch exceeded the supplied threshold.\n
+     * This field must lie in the interval [0.0, 1.0].\n
+     * For #H5C_incr__threshold, .9995 or .99995 is a good place to start.\n
+     * For #H5C_decr__age_out_with_threshold, .999 might be more useful.*/
+
+    double decrement;
+    /**< In the hit rate threshold cache size decrease algorithm, this
+     * parameter contains the factor by which the current max cache size is
+     * multiplied to produce a tentative new cache size.\n
+     * The actual cache size decrease will be clipped to satisfy the
+     * \ref H5AC_cache_config_t.min_size "min_size" specified in the general
+     * configuration, and possibly \ref H5AC_cache_config_t.max_decrement
+     * "max_decrement".\n
+     * The parameter must be be in the interval [0.0, 1.0].\n
+     * If you set it to 1.0, you will effectively
+     * disable cache size decreases. 0.9 is a reasonable starting point. */
+
+    hbool_t apply_max_decrement;
+    /**< Boolean flag indicating ether an upper limit should be applied to
+     * the size of cache size decreases. */
+
+    size_t max_decrement;
+    /**< Maximum number of bytes by which the maximum cache size can be
+     * decreased in any single step -- if applicable.*/
+
+    int epochs_before_eviction;
+    /**< In the ageout based cache size reduction algorithms, this field
+     * contains the minimum number of epochs an entry must remain unaccessed in
+     * cache before the cache size reduction algorithm tries to evict it. 3 is a
+     * reasonable value. */
+
+    hbool_t apply_empty_reserve;
+    /**< Boolean flag indicating whether the ageout based decrement
+     * algorithms will maintain a empty reserve when decreasing cache size. */
+
+    double empty_reserve;
+    /**< Empty reserve as a fraction maximum cache size if applicable.\n When
+     * so directed, the ageout based algorithms will not decrease the maximum
+     * cache size unless the empty reserve can be met.\n The parameter must lie
+     * in the interval [0.0, 1.0]. 0.1 or 0.05 is a good place to start. */
+    //! <!-- [H5AC_cache_config_t_decr_snip] -->
+
+    /* parallel configuration fields: */
+    //! <!-- [H5AC_cache_config_t_parallel_snip] -->
+    size_t dirty_bytes_threshold;
+    /**< Threshold number of bytes of dirty metadata generation for
+     * triggering synchronizations of the metadata caches serving the target
+     * file in the parallel case.\n Synchronization occurs whenever the number
+     * of bytes of dirty metadata created since the last synchronization exceeds
+     * this limit.\n This field only applies to the parallel case. While it is
+     * ignored elsewhere, it can still draw a value out of bounds error.\n It
+     * must be consistent across all caches on any given file.\n By default,
+     * this field is set to 256 KB. It shouldn't be more than half the current
+     * max cache size times the min clean fraction. */
+
+    int metadata_write_strategy;
+    /**< Desired metadata write strategy. The valid values for this field
+     * are:\n #H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY: Specifies the only
+     * process zero is allowed to write dirty metadata to disk.\n
+     * #H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED: Specifies that process zero
+     * still makes the decisions as to what entries should be flushed, but the
+     * actual flushes are distributed across the processes in the computation to
+     * the extent possible.\n The src/H5ACpublic.h include file in the HDF5
+     * library has detailed information on each strategy. */
+    //! <!-- [H5AC_cache_config_t_parallel_snip] -->
+} H5AC_cache_config_t;
+//! <!-- [H5AC_cache_config_t_snip] -->
+
+#define H5AC__CURR_CACHE_IMAGE_CONFIG_VERSION 1
+
+#define H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE -1
+#define H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX  100
+
+//! <!-- [H5AC_cache_image_config_t_snip] -->
+/**
+ * H5AC_cache_image_config_t is a public structure intended for use in public
+ * APIs.  At least in its initial incarnation, it is a copy of \c struct \c
+ * H5C_cache_image_ctl_t.
+ */
+
+typedef struct H5AC_cache_image_config_t {
+    int version;
+    /**< Integer field containing the version number of this version of the \c
+     *  H5C_image_ctl_t structure.  Any instance of \c H5C_image_ctl_t passed
+     *  to the cache must have a known version number, or an error will be
+     *  flagged.
+     */
+    hbool_t generate_image;
+    /**< Boolean flag indicating whether a cache image should be created on file
+     *   close.
+     */
+    hbool_t save_resize_status;
+    /**< Boolean flag indicating whether the cache image should include the
+     *  adaptive cache resize configuration and status.  Note that this field
+     *  is ignored at present.
+     */
+    int entry_ageout;
+    /**< Integer field indicating the maximum number of times a
+     *   prefetched entry can appear in subsequent cache images.  This field
+     *   exists to allow the user to avoid the buildup of infrequently used
+     *   entries in long sequences of cache images.
+     *
+     *   The value of this field must lie in the range \ref
+     *   H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE (-1) to \ref
+     *   H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX (100).
+     *
+     *   \ref H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE means that no limit is
+     *   imposed on number of times a prefetched entry can appear in subsequent
+     *   cache images.
+     *
+     *   A value of 0 prevents prefetched entries from being included in cache
+     *   images.
+     *
+     *   Positive integers restrict prefetched entries to the specified number
+     *   of appearances.
+     *
+     *   Note that the number of subsequent cache images that a prefetched entry
+     *   has appeared in is tracked in an 8 bit field.  Thus, while \ref
+     *   H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX can be increased from its current
+     *   value, any value in excess of 255 will be the functional equivalent of
+     *   \ref H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE.
+     */
+} H5AC_cache_image_config_t;
+
+//! <!-- [H5AC_cache_image_config_t_snip] -->
+
+#endif

HybridMesher/libraries/HDF5-1.14.1/include/H5Cpublic.h

@@ -0,0 +1,59 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*-------------------------------------------------------------------------
+ *
+ * Created:	H5Cpublic.h
+ *              June 4, 2005
+ *              John Mainzer
+ *
+ * Purpose:     Public include file for cache functions.
+ *
+ *-------------------------------------------------------------------------
+ */
+#ifndef H5Cpublic_H
+#define H5Cpublic_H
+
+/* Public headers needed by this file */
+#include "H5public.h"
+
+enum H5C_cache_incr_mode {
+    H5C_incr__off,
+    /**<Automatic cache size increase is disabled, and the remaining increment fields are ignored.*/
+
+    H5C_incr__threshold
+    /**<Automatic cache size increase is enabled using the hit rate threshold algorithm.*/
+};
+
+enum H5C_cache_flash_incr_mode {
+    H5C_flash_incr__off,
+    /**<Flash cache size increase is disabled.*/
+
+    H5C_flash_incr__add_space
+    /**<Flash cache size increase is enabled using the add space algorithm.*/
+};
+
+enum H5C_cache_decr_mode {
+    H5C_decr__off,
+    /**<Automatic cache size decrease is disabled.*/
+
+    H5C_decr__threshold,
+    /**<Automatic cache size decrease is enabled  using the hit rate threshold algorithm.*/
+
+    H5C_decr__age_out,
+    /**<Automatic cache size decrease is enabled using the ageout algorithm. */
+
+    H5C_decr__age_out_with_threshold
+    /**<Automatic cache size decrease is enabled using the ageout with hit rate threshold algorithm.*/
+};
+
+#endif

HybridMesher/libraries/HDF5-1.14.1/include/H5DOpublic.h

@@ -0,0 +1,250 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#ifndef H5DOpublic_H
+#define H5DOpublic_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/** \page H5DO_UG The HDF5 High Level Optimizations
+ * @todo Under Construction
+ */
+
+/**\defgroup H5DO HDF5 Optimizations APIs (H5DO)
+ *
+ * <em>Bypassing default HDF5 behavior in order to optimize for specific
+ * use cases (H5DO)</em>
+ *
+ * HDF5 functions described is this section are implemented in the HDF5 High-level
+ * library as optimized functions. These functions generally require careful setup
+ * and testing as they enable an application to bypass portions of the HDF5
+ * library’s I/O pipeline for performance purposes.
+ *
+ * These functions are distributed in the standard HDF5 distribution and are
+ * available any time the HDF5 High-level library is available.
+ *
+ * - \ref H5DOappend
+ *    \n Appends data to a dataset along a specified dimension.
+ * - \ref H5DOread_chunk
+ *   \n Reads a raw data chunk directly from a dataset in a file into a buffer (DEPRECATED)
+ * - \ref H5DOwrite_chunk
+ *   \n  Writes a raw data chunk from a buffer directly to a dataset in a file (DEPRECATED)
+ *
+ */
+
+/*-------------------------------------------------------------------------
+ *
+ * "Optimized dataset" routines.
+ *
+ *-------------------------------------------------------------------------
+ */
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DO
+ *
+ * \brief Appends data to a dataset along a specified dimension.
+ *
+ * \param[in] dset_id   Dataset identifier
+ * \param[in] dxpl_id   Dataset transfer property list identifier
+ * \param[in] axis      Dataset Dimension (0-based) for the append
+ * \param[in] extension Number of elements to append for the
+ *                      axis-th dimension
+ * \param[in] memtype   The memory datatype identifier
+ * \param[in] buf       Buffer with data for the append
+ *
+ * \return \herr_t
+ *
+ * \details The H5DOappend() routine extends a dataset by \p extension
+ *          number of elements along a dimension specified by a
+ *          dimension \p axis and writes \p buf of elements to the
+ *          dataset. Dimension \p axis is 0-based. Elements’ type
+ *          is described by \p memtype.
+ *
+ *          This routine combines calling H5Dset_extent(),
+ *          H5Sselect_hyperslab(), and H5Dwrite() into a single routine
+ *          that simplifies application development for the common case
+ *          of appending elements to an existing dataset.
+ *
+ *          For a multi-dimensional dataset, appending to one dimension
+ *          will write a contiguous hyperslab over the other dimensions.
+ *          For example, if a 3-D dataset has dimension sizes (3, 5, 8),
+ *          extending the 0th dimension (currently of size 3) by 3 will
+ *          append 3*5*8 = 120 elements (which must be pointed to by the
+ *          \p buffer parameter) to the dataset, making its final
+ *          dimension sizes (6, 5, 8).
+ *
+ *          If a dataset has more than one unlimited dimension, any of
+ *          those dimensions may be appended to, although only along
+ *          one dimension per call to H5DOappend().
+ *
+ * \since   1.10.0
+ *
+ */
+H5_HLDLL herr_t H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis, size_t extension, hid_t memtype,
+                           const void *buf);
+
+/* Symbols defined for compatibility with previous versions of the HDF5 API.
+ *
+ * Use of these symbols is deprecated.
+ */
+#ifndef H5_NO_DEPRECATED_SYMBOLS
+
+/* Compatibility wrappers for functionality moved to H5D */
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DO
+ *
+ * \brief Writes a raw data chunk from a buffer directly to a dataset in a file.
+ *
+ * \param[in] dset_id       Identifier for the dataset to write to
+ * \param[in] dxpl_id       Transfer property list identifier for
+ *                          this I/O operation
+ * \param[in] filters       Mask for identifying the filters in use
+ * \param[in] offset        Logical position of the chunk’s first element
+ *                          in the dataspace
+ * \param[in] data_size     Size of the actual data to be written in bytes
+ * \param[in] buf           Buffer containing data to be written to the chunk
+ *
+ * \return \herr_t
+ *
+ * \deprecated This function was deprecated in favor of the function
+ *             H5Dwrite_chunk() of HDF5-1.10.3.
+ *             The functionality of H5DOwrite_chunk() was moved
+ *             to H5Dwrite_chunk().
+ * \deprecated For compatibility, this API call has been left as a stub which
+ *             simply calls H5Dwrite_chunk(). New code should use H5Dwrite_chunk().
+ *
+ * \details The H5DOwrite_chunk() writes a raw data chunk as specified by its
+ *          logical \p offset in a chunked dataset \p dset_id from the application
+ *          memory buffer \p buf to the dataset in the file. Typically, the data
+ *          in \p buf is preprocessed in memory by a custom transformation, such as
+ *          compression. The chunk will bypass the library’s internal data
+ *          transfer pipeline, including filters, and will be written directly to the file.
+ *
+ *          \p dxpl_id is a data transfer property list identifier.
+ *
+ *          \p filters is a mask providing a record of which filters are used
+ *          with the chunk. The default value of the mask is zero (\c 0),
+ *          indicating that all enabled filters are applied. A filter is skipped
+ *          if the bit corresponding to the filter’s position in the pipeline
+ *          (<tt>0 ≤ position < 32</tt>) is turned on. This mask is saved
+ *          with the chunk in the file.
+ *
+ *          \p offset is an array specifying the logical position of the first
+ *          element of the chunk in the dataset’s dataspace. The length of the
+ *          offset array must equal the number of dimensions, or rank, of the
+ *          dataspace. The values in \p offset must not exceed the dimension limits
+ *          and must specify a point that falls on a dataset chunk boundary.
+ *
+ *          \p data_size is the size in bytes of the chunk, representing the number of
+ *          bytes to be read from the buffer \p buf. If the data chunk has been
+ *          precompressed, \p data_size should be the size of the compressed data.
+ *
+ *          \p buf is the memory buffer containing data to be written to the chunk in the file.
+ *
+ * \attention   Exercise caution when using H5DOread_chunk() and H5DOwrite_chunk(),
+ *              as they read and write data chunks directly in a file.
+ *              H5DOwrite_chunk() bypasses hyperslab selection, the conversion of data
+ *              from one datatype to another, and the filter pipeline to write the chunk.
+ *              Developers should have experience with these processes before
+ *              using this function. Please see
+ *              <a href="https://portal.hdfgroup.org/display/HDF5/Using+the+Direct+Chunk+Write+Function">
+ *              Using the Direct Chunk Write Function</a>
+ *              for more information.
+ *
+ * \note    H5DOread_chunk() and H5DOwrite_chunk() are not
+ *          supported under parallel and do not support variable length types.
+ *
+ * \par Example
+ * The following code illustrates the use of H5DOwrite_chunk to write
+ * an entire dataset, chunk by chunk:
+ * \snippet H5DO_examples.c H5DOwrite
+ *
+ * \version 1.10.3  Function deprecated in favor of H5Dwrite_chunk.
+ *
+ * \since   1.8.11
+ */
+H5_HLDLL herr_t H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset,
+                                size_t data_size, const void *buf);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DO
+ *
+ * \brief Reads a raw data chunk directly from a dataset in a file into a buffer.
+ *
+ * \param[in] dset_id           Identifier for the dataset to be read
+ * \param[in] dxpl_id           Transfer property list identifier for
+ *                              this I/O operation
+ * \param[in] offset            Logical position of the chunk’s first
+                                element in the dataspace
+ * \param[in,out] filters       Mask for identifying the filters used
+ *                              with the chunk
+ * \param[in] buf               Buffer containing the chunk read from
+ *                              the dataset
+ *
+ * \return \herr_t
+ *
+ * \deprecated This function was deprecated in favor of the function
+ *             H5Dread_chunk() as of HDF5-1.10.3.
+ *             In HDF5 1.10.3, the functionality of H5DOread_chunk()
+ *             was moved to H5Dread_chunk().
+ * \deprecated For compatibility, this API call has been left as a stub which
+ *             simply calls H5Dread_chunk().  New code should use H5Dread_chunk().
+ *
+ * \details The H5DOread_chunk() reads a raw data chunk as specified
+ *          by its logical \p offset in a chunked dataset \p dset_id
+ *          from the dataset in the file into the application memory
+ *          buffer \p buf. The data in \p buf is read directly from the file
+ *          bypassing the library’s internal data transfer pipeline,
+ *          including filters.
+ *
+ *          \p dxpl_id is a data transfer property list identifier.
+ *
+ *          The mask \p filters indicates which filters are used with the
+ *          chunk when written. A zero value indicates that all enabled filters
+ *          are applied on the chunk. A filter is skipped if the bit corresponding
+ *          to the filter’s position in the pipeline
+ *          (<tt>0 ≤ position < 32</tt>) is turned on.
+ *
+ *          \p offset is an array specifying the logical position of the first
+ *          element of the chunk in the dataset’s dataspace. The length of the
+ *          offset array must equal the number of dimensions, or rank, of the
+ *          dataspace. The values in \p offset must not exceed the dimension
+ *          limits and must specify a point that falls on a dataset chunk boundary.
+ *
+ *          \p buf is the memory buffer containing the chunk read from the dataset
+ *          in the file.
+ *
+ * \par Example
+ * The following code illustrates the use of H5DOread_chunk()
+ * to read a chunk from a dataset:
+ * \snippet H5DO_examples.c H5DOread
+ *
+ * \version 1.10.3  Function deprecated in favor of H5Dread_chunk.
+ *
+ * \since   1.10.2, 1.8.19
+ */
+H5_HLDLL herr_t H5DOread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters /*out*/,
+                               void *buf /*out*/);
+
+#endif /* H5_NO_DEPRECATED_SYMBOLS */
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

HybridMesher/libraries/HDF5-1.14.1/include/H5DSpublic.h

@@ -0,0 +1,413 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#ifndef H5DSpublic_H
+#define H5DSpublic_H
+
+#define DIMENSION_SCALE_CLASS "DIMENSION_SCALE"
+#define DIMENSION_LIST        "DIMENSION_LIST"
+#define REFERENCE_LIST        "REFERENCE_LIST"
+#define DIMENSION_LABELS      "DIMENSION_LABELS"
+
+/**
+ * \brief Prototype for H5DSiterate_scales() operator
+ *
+ */
+//! <!-- [H5DS_iterate_t_snip] -->
+typedef herr_t (*H5DS_iterate_t)(hid_t dset, unsigned dim, hid_t scale, void *visitor_data);
+//! <!-- [H5DS_iterate_t_snip] -->
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/** \page H5DS_UG The HDF5 High Level Dimension Scales
+ * @todo Under Construction
+ */
+
+/**\defgroup H5DS HDF5 Dimension Scales APIs (H5DS)
+ *
+ * <em>Creating and manipulating HDF5 datasets that are associated with
+ * the dimension of another HDF5 dataset (H5DS)</em>
+ *
+ * \note \Bold{Programming hints:}
+ * \note To use any of these functions or subroutines,
+ *       you must first include the relevant include file (C) or
+ *       module (Fortran) in your application.
+ * \note The following line includes the HDF5 Dimension Scale package,
+ *       H5DS, in C applications:
+ *       \code #include "hdf5_hl.h" \endcode
+ * \note This line includes the H5DS module in Fortran applications:
+ *       \code use h5ds \endcode
+ *
+ * - \ref H5DSwith_new_ref
+ *   \n Determines if new references are used with dimension scales.
+ * - \ref H5DSattach_scale
+ *   \n Attach dimension scale dsid to dimension idx of dataset did.
+ * - \ref H5DSdetach_scale
+ *   \n Detach dimension scale dsid from the dimension idx of Dataset did.
+ * - \ref H5DSget_label
+ *   \n Read the label for dimension idx of did into buffer label.
+ * - \ref H5DSget_num_scales
+ *   \n Determines how many Dimension Scales are attached
+ *      to dimension idx of did.
+ * - \ref H5DSget_scale_name
+ *   \n Retrieves name of scale did into buffer name.
+ * - \ref H5DSis_attached
+ *   \n Report if dimension scale dsid is currently attached
+ *      to dimension idx of dataset did.
+ * - \ref H5DSis_scale
+ *   \n Determines whether dset is a Dimension Scale.
+ * - \ref H5DSiterate_scales
+ *   \n Iterates the operation visitor through the scales
+ *      attached to dimension dim.
+ * - \ref H5DSset_label
+ *   \n Set label for the dimension idx of did to the value label.
+ * - \ref H5DSset_scale
+ *   \n Convert dataset dsid to a dimension scale,
+ *      with optional name, dimname.
+ *
+ */
+
+/* THIS IS A NEW ROUTINE NOT ON OLD PORTAL */
+/**
+ *  --------------------------------------------------------------------------
+ *  \ingroup H5DS
+ *
+ *  \brief Determines if new references are used with dimension scales.
+ *
+ *  \param[in] obj_id        Object identifier
+ *  \param[out] with_new_ref New references are used or not
+ *
+ *  \return \herr_t
+ *
+ *  \details H5DSwith_new_ref() takes any object identifier and checks
+ *           if new references are used for dimension scales. Currently,
+ *           new references are used when non-native VOL connector is
+ *           used or when H5_DIMENSION_SCALES_WITH_NEW_REF is set up
+ *           via configure option.
+ *
+ */
+H5_HLDLL herr_t H5DSwith_new_ref(hid_t obj_id, hbool_t *with_new_ref);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DS
+ *
+ * \brief Attach dimension scale \p dsid to dimension \p idx of
+ *        dataset did.
+ *
+ * \param[in] did   The dataset
+ * \param[in] dsid  The scale to be attached
+ * \param[in] idx   The dimension of \p did that \p dsid is associated with
+ *
+ * \return \herr_t
+ *
+ * \details Define Dimension Scale \p dsid to be associated with
+ *          dimension \p idx of dataset \p did.
+ *
+ *          Entries are created in the #DIMENSION_LIST and
+ *          #REFERENCE_LIST attributes, as defined in section 4.2 of
+ *          <a href="https://support.hdfgroup.org/HDF5/doc/HL/H5DS_Spec.pdf">
+ *          HDF5 Dimension Scale Specification</a>.
+ *
+ *          Fails if:
+ *          - Bad arguments
+ *          - If \p dsid is not a Dimension Scale
+ *          - If \p did is a Dimension Scale
+ *            (A Dimension Scale cannot have scales.)
+ *
+ * \note The Dimension Scale \p dsid can be attached to the
+ *       same dimension more than once, which has no effect.
+ */
+H5_HLDLL herr_t H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DS
+ *
+ * \brief Detach dimension scale \p dsid from the dimension \p idx of dataset \p did.
+ *
+ * \param[in] did   The dataset
+ * \param[in] dsid  The scale to be detached
+ * \param[in] idx   The dimension of \p did to detach
+ *
+ * \return \herr_t
+ *
+ * \details If possible, deletes association of Dimension Scale \p dsid with
+ *          dimension \p idx of dataset \p did. This deletes the entries in the
+ *          #DIMENSION_LIST and #REFERENCE_LIST attributes,
+ *          as defined in section 4.2 of
+ *          <a href="https://support.hdfgroup.org/HDF5/doc/HL/H5DS_Spec.pdf">
+ *          HDF5 Dimension Scale Specification</a>.
+ *
+ *          Fails if:
+ *          - Bad arguments
+ *          - The dataset \p did or \p dsid do not exist
+ *          - The \p dsid is not a Dimension Scale
+ *          - \p dsid is not attached to \p did
+ *
+ * \note A scale may be associated with more than dimension of the
+ *       same dataset. If so, the detach operation only deletes one
+ *       of the associations, for \p did.
+ *
+ */
+H5_HLDLL herr_t H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DS
+ *
+ * \brief Convert dataset \p dsid to a dimension scale,
+ *        with optional name, \p dimname.
+ *
+ * \param[in] dsid      The dataset to be made a Dimemsion Scale
+ * \param[in] dimname   The dimension name (optional), NULL if the
+ *                      dimension has no name.
+ *
+ * \return \herr_t
+ *
+ * \details The dataset \p dsid is converted to a Dimension Scale dataset,
+ *          as defined above. Creates the CLASS attribute, set to the value
+ *          "DIMENSION_SCALE" and an empty #REFERENCE_LIST attribute,
+ *          as described in
+ *          <a href="https://support.hdfgroup.org/HDF5/doc/HL/H5DS_Spec.pdf">
+ *          HDF5 Dimension Scale Specification</a>.
+ *          (PDF, see section 4.2).
+ *
+ *          If \p dimname is specified, then an attribute called NAME
+ *          is created, with the value \p dimname.
+ *
+ *          Fails if:
+ *          - Bad arguments
+ *          - If \p dsid is already a scale
+ *          - If \p dsid is a dataset which already has dimension scales
+ *
+ *          If the dataset was created with the Table, Image, or Palette interface [9],
+ *          it is not recommended to convert to a Dimension Scale.
+ *          (These Datasets will have a CLASS Table, Image, or Palette.)
+ *
+ * \todo what is [9] after Palette interface?
+ */
+H5_HLDLL herr_t H5DSset_scale(hid_t dsid, const char *dimname);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DS
+ *
+ * \brief Determines how many Dimension Scales are attached
+ *        to dimension \p idx of \p did.
+ *
+ * \param[in] did   The dataset to query
+ * \param[in] idx   The dimension of \p did to query
+ *
+ * \return Returns the number of Dimension Scales associated
+ *         with \p did, if successful, otherwise returns a
+ *         negative value.
+ *
+ * \details H5DSget_num_scales() determines how many Dimension
+ *          Scales are attached to dimension \p idx of
+ *          dataset \p did.
+ *
+ */
+H5_HLDLL int H5DSget_num_scales(hid_t did, unsigned int idx);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DS
+ *
+ * \brief Set label for the dimension \p idx of \p did
+ *        to the value \p label.
+ *
+ * \param[in] did   The dataset
+ * \param[in] idx   The dimension
+ * \param[in] label The label
+ *
+ * \return  \herr_t
+ *
+ * \details Sets the #DIMENSION_LABELS for dimension \p idx of
+ *          dataset \p did. If the dimension had a label,
+ *          the new value replaces the old.
+ *
+ *          Fails if:
+ *          - Bad arguments
+ *
+ */
+H5_HLDLL herr_t H5DSset_label(hid_t did, unsigned int idx, const char *label);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DS
+ *
+ * \brief Read the label for dimension \p idx of \p did into buffer \p label.
+ *
+ * \param[in] did       The dataset
+ * \param[in] idx       The dimension
+ * \param[out] label    The label
+ * \param[in] size      The length of the label buffer
+ *
+ * \return  Upon success, size of label or zero if no label found.
+ *          Negative if fail.
+ *
+ * \details Returns the value of the #DIMENSION_LABELS for
+ *          dimension \p idx of dataset \p did, if set.
+ *          Up to \p size characters of the name are copied into
+ *          the buffer \p label.  If the label is longer than
+ *          \p size, it will be truncated to fit.  The parameter
+ *          \p size is set to the size of the returned \p label.
+ *
+ *          If \p did has no label, the return value of
+ *          \p label is NULL.
+ *
+ *          Fails if:
+ *          - Bad arguments
+ *
+ */
+H5_HLDLL ssize_t H5DSget_label(hid_t did, unsigned int idx, char *label, size_t size);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DS
+ *
+ * \brief Retrieves name of scale \p did into buffer \p name.
+ *
+ * \param[in] did       Dimension scale identifier
+ * \param[out] name     Buffer to contain the returned name
+ * \param[in] size      Size in bytes, of the \p name buffer
+ *
+ * \return  Upon success, the length of the scale name or zero if no name found.
+ *          Negative if fail.
+ *
+ * \details H5DSget_scale_name() retrieves the name attribute
+ *          for scale \p did.
+ *
+ *          Up to \p size characters of the scale name are returned
+ *          in \p name; additional characters, if any, are not returned
+ *          to the user application.
+ *
+ *          If the length of the name, which determines the required value of
+ *          \p size, is unknown, a preliminary H5DSget_scale_name() call can
+ *          be made by setting \p name to NULL. The return value of this call
+ *          will be the size of the scale name; that value plus one (1) can then
+ *          be assigned to \p size for a second H5DSget_scale_name() call,
+ *          which will retrieve the actual name.  (The value passed in with the
+ *          parameter \p size must be one greater than size in bytes of the actual
+ *          name in order to accommodate the null terminator;
+ *          if \p size is set to the exact size of the name, the last byte
+ *          passed back will contain the null terminator and the last character
+ *          will be missing from the name passed back to the calling application.)
+ */
+H5_HLDLL ssize_t H5DSget_scale_name(hid_t did, char *name, size_t size);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DS
+ *
+ * \brief Determines whether \p did is a Dimension Scale.
+ *
+ * \param[in] did   The dataset to query
+ *
+ * \return  \htri_t
+ *
+ * \details H5DSis_scale() determines if \p did is a Dimension Scale,
+ *          i.e., has class="DIMENSION_SCALE").
+ *
+ */
+H5_HLDLL htri_t H5DSis_scale(hid_t did);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DS
+ *
+ * \brief Iterates the operation visitor through the scales
+ *        attached to dimension \p dim.
+ *
+ * \param[in]       did             The dataset
+ * \param[in]       dim             The dimension of dataset \p did
+ * \param[in,out]   idx             Input the index to start iterating,
+ *                                  output the next index to visit.
+ *                                  If NULL, start at the first position.
+ * \param[in]       visitor         The visitor function
+ * \param[in]       visitor_data    Arbitrary data to pass to the
+ *                                  visitor function
+ *
+ * \return  Returns the return value of the last operator if it was
+ *          non-zero, or zero if all scales were processed.
+ *
+ * \details H5DSiterate_scales() iterates over the scales attached to
+ *          dimension \p dim of dataset \p did. For each scale in the
+ *          list, the \p visitor_data and some additional information,
+ *          specified below, are passed to the \p visitor function.
+ *          The iteration begins with the \p idx object in the
+ *          group and the next element to be processed by the operator
+ *          is returned in \p idx. If \p idx is NULL, then the
+ *          iterator starts at the first group member; since no
+ *          stopping point is returned in this case,
+ *          the iterator cannot be restarted if one of the calls
+ *          to its operator returns non-zero.
+ *
+ *          The prototype for \ref H5DS_iterate_t is:
+ *          \snippet this H5DS_iterate_t_snip
+ *
+ *          The operation receives the Dimension Scale dataset
+ *          identifier, \p scale, and the pointer to the operator
+ *          data passed in to H5DSiterate_scales(), \p visitor_data.
+ *
+ *          The return values from an operator are:
+ *
+ *          - Zero causes the iterator to continue, returning zero
+ *            when all group members have been processed.
+ *          - Positive causes the iterator to immediately return that
+ *            positive value, indicating short-circuit success.
+ *            The iterator can be restarted at the next group member.
+ *          - Negative causes the iterator to immediately return
+ *            that value, indicating failure. The iterator can be
+ *            restarted at the next group member.
+ *
+ *          H5DSiterate_scales() assumes that the scales of the
+ *          dimension identified by \p dim remain unchanged through
+ *          the iteration. If the membership changes during the iteration,
+ *          the function's behavior is undefined.
+ */
+H5_HLDLL herr_t H5DSiterate_scales(hid_t did, unsigned int dim, int *idx, H5DS_iterate_t visitor,
+                                   void *visitor_data);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5DS
+ *
+ * \brief Report if dimension scale \p dsid is currently attached to
+ *        dimension \p idx of dataset \p did.
+ *
+ * \param[in] did   The dataset
+ * \param[in] dsid  The scale to be attached
+ * \param[in] idx   The dimension of \p did that \p dsid is associated with
+ *
+ * \return  \htri_t
+ *
+ * \details Report if dimension scale \p dsid is currently attached to
+ *          dimension \p idx of dataset \p did.
+ *
+ *          Fails if:
+ *          - Bad arguments
+ *          - If \p dsid is not a Dimension Scale
+ *          - The \p dsid is not a Dimension Scale
+ *          - If \p did is a Dimension Scale (A Dimension Scale cannot have scales.)
+ *
+ */
+H5_HLDLL htri_t H5DSis_attached(hid_t did, hid_t dsid, unsigned int idx);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

HybridMesher/libraries/HDF5-1.14.1/include/H5ESdevelop.h

@@ -0,0 +1,52 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * This file contains public declarations for the H5ES (event set) developer
+ *      support routines.
+ */
+
+#ifndef H5ESdevelop_H
+#define H5ESdevelop_H
+
+/* Include package's public header */
+#include "H5ESpublic.h"
+
+/*****************/
+/* Public Macros */
+/*****************/
+
+/*******************/
+/* Public Typedefs */
+/*******************/
+
+/********************/
+/* Public Variables */
+/********************/
+
+/*********************/
+/* Public Prototypes */
+/*********************/
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+H5_DLL herr_t H5ESinsert_request(hid_t es_id, hid_t connector_id, void *request);
+H5_DLL herr_t H5ESget_requests(hid_t es_id, H5_iter_order_t order, hid_t *connector_ids, void **requests,
+                               size_t array_len, size_t *count);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* H5ESdevelop_H */

HybridMesher/libraries/HDF5-1.14.1/include/H5ESpublic.h

@@ -0,0 +1,384 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * This file contains public declarations for the H5ES (event set) module.
+ */
+
+#ifndef H5ESpublic_H
+#define H5ESpublic_H
+
+/* Public headers needed by this file */
+#include "H5public.h" /* Generic Functions                    */
+
+/*****************/
+/* Public Macros */
+/*****************/
+
+/* Default value for "no event set" / synchronous execution */
+#define H5ES_NONE 0 /* (hid_t) */
+
+/* Special "wait" timeout values */
+#define H5ES_WAIT_FOREVER (UINT64_MAX) /* Wait until all operations complete */
+#define H5ES_WAIT_NONE                                                                                       \
+    (0) /* Don't wait for operations to complete,                                                            \
+         *  just check their status.                                                                         \
+         *  (this allows H5ESwait to behave                                                                  \
+         *   like a 'test' operation)                                                                        \
+         */
+
+/*******************/
+/* Public Typedefs */
+/*******************/
+
+/**
+ * Asynchronous operation status
+ */
+typedef enum H5ES_status_t {
+    H5ES_STATUS_IN_PROGRESS, /**< Operation(s) have not yet completed         */
+    H5ES_STATUS_SUCCEED,     /**< Operation(s) have completed, successfully   */
+    H5ES_STATUS_CANCELED,    /**< Operation(s) has been canceled              */
+    H5ES_STATUS_FAIL         /**< An operation has completed, but failed      */
+} H5ES_status_t;
+
+/**
+ * Information about operations in an event set
+ */
+typedef struct H5ES_op_info_t {
+    /* API call info */
+    const char *api_name; /**< Name of HDF5 API routine called */
+    char       *api_args; /**< "Argument string" for arguments to HDF5 API routine called */
+
+    /* Application info */
+    const char *app_file_name; /**< Name of source file where the HDF5 API routine was called */
+    const char *app_func_name; /**< Name of function where the HDF5 API routine was called */
+    unsigned    app_line_num;  /**< Line # of source file where the HDF5 API routine was called */
+
+    /* Operation info */
+    uint64_t op_ins_count; /**< Counter of operation's insertion into event set */
+    uint64_t op_ins_ts;    /**< Timestamp for when the operation was inserted into the event set */
+    uint64_t op_exec_ts;   /**< Timestamp for when the operation began execution */
+    uint64_t op_exec_time; /**< Execution time for operation (in ns) */
+} H5ES_op_info_t;
+
+//! <!-- [H5ES_err_info_t_snip] -->
+/**
+ * Information about failed operations in event set
+ */
+typedef struct H5ES_err_info_t {
+    /* API call info */
+    char *api_name; /**< Name of HDF5 API routine called */
+    char *api_args; /**< "Argument string" for arguments to HDF5 API routine called */
+
+    /* Application info */
+    char    *app_file_name; /**< Name of source file where the HDF5 API routine was called */
+    char    *app_func_name; /**< Name of function where the HDF5 API routine was called */
+    unsigned app_line_num;  /**< Line # of source file where the HDF5 API routine was called */
+
+    /* Operation info */
+    uint64_t op_ins_count; /**< Counter of operation's insertion into event set */
+    uint64_t op_ins_ts;    /**< Timestamp for when the operation was inserted into the event set */
+    uint64_t op_exec_ts;   /**< Timestamp for when the operation began execution */
+    uint64_t op_exec_time; /**< Execution time for operation (in ns) */
+
+    /* Error info */
+    hid_t err_stack_id; /**< ID for error stack from failed operation */
+} H5ES_err_info_t;
+//! <!-- [H5ES_err_info_t_snip] -->
+
+/*
+More Possible Info for H5ES_op_info_t:
+    Parent Operation's request token (*) -> "parent event count"? -- Could be
+        used to "prune" child operations from reported errors, with flag
+        to H5ESget_err_info?
+
+Possible debugging routines:  (Should also be configured from Env Var)
+    H5ESdebug_signal(hid_t es_id, signal_t sig, uint64_t <event count>);
+    H5ESdebug_err_trace_log(hid_t es_id, const char *filename);
+    H5ESdebug_err_trace_fh(hid_t es_id, FILE *fh);
+    H5ESdebug_err_signal(hid_t es_id, signal_t sig);
+[Possibly option to allow operations to be inserted into event set with error?]
+
+    Example usage:
+        es_id = H5EScreate();
+        H5ESdebug...(es_id, ...);
+        ...
+        H5Dwrite_async(..., es_id);
+
+How to Trace Async Operations?
+    <Example of stacking Logging VOL Connector w/Async VOL Connector>
+
+*/
+
+/**
+ * Callback for H5ESregister_insert_func()
+ */
+typedef int (*H5ES_event_insert_func_t)(const H5ES_op_info_t *op_info, void *ctx);
+
+/**
+ * Callback for H5ESregister_complete_func()
+ */
+typedef int (*H5ES_event_complete_func_t)(const H5ES_op_info_t *op_info, H5ES_status_t status,
+                                          hid_t err_stack, void *ctx);
+
+/********************/
+/* Public Variables */
+/********************/
+
+/*********************/
+/* Public Prototypes */
+/*********************/
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**
+ * \ingroup H5ES
+ *
+ * \brief Creates an event set
+ *
+ * \returns \hid_t{event set}
+ *
+ * \details H5EScreate() creates a new event set and returns a corresponding
+ *          event set identifier.
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL hid_t H5EScreate(void);
+
+/**
+ * \ingroup H5ES
+ *
+ * \brief Waits for operations in event set to complete
+ *
+ * \es_id
+ * \param[in] timeout Total time in nanoseconds to wait for all operations in
+ *            the event set to complete
+ * \param[out] num_in_progress The number of operations still in progress
+ * \param[out] err_occurred Flag if an operation in the event set failed
+ * \returns \herr_t
+ *
+ * \details H5ESwait() waits for operations in an event set \p es_id to wait
+ *          with \p timeout.
+ *
+ *          Timeout value is in nanoseconds, and is for the H5ESwait() call and
+ *          not for each individual operation in the event set. For example, if
+ *          "10" is passed as a timeout value and the event set waited 4
+ *          nanoseconds for the first operation to complete, the remaining
+ *          operations would be allowed to wait for at most 6 nanoseconds more,
+ *          i.e., the timeout value used across all operations in the event set
+ *          until it reaches 0, then any remaining operations are only checked
+ *          for completion, not waited on.
+ *
+ *          This call will stop waiting on operations and will return
+ *          immediately if an operation fails. If a failure occurs, the value
+ *          returned for the number of operations in progress may be inaccurate.
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL herr_t H5ESwait(hid_t es_id, uint64_t timeout, size_t *num_in_progress, hbool_t *err_occurred);
+
+/**
+ * \ingroup H5ES
+ *
+ * \brief Attempt to cancel operations in an event set
+ *
+ * \es_id
+ * \param[out] num_not_canceled The number of events not canceled
+ * \param[out] err_occurred Status indicating if error is present in the event set
+ * \returns \herr_t
+ *
+ * \details H5EScancel() attempts to cancel operations in an event set specified
+ *          by \p es_id. H5ES_NONE is a valid value for \p es_id, but functions as a no-op.
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL herr_t H5EScancel(hid_t es_id, size_t *num_not_canceled, hbool_t *err_occurred);
+
+/**
+ * \ingroup H5ES
+ *
+ * \brief Retrieves number of events in an event set
+ *
+ * \es_id
+ * \param[out] count The number of events in the event set
+ * \returns \herr_t
+ *
+ * \details H5ESget_count() retrieves number of events in an event set specified
+ *          by \p es_id.
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL herr_t H5ESget_count(hid_t es_id, size_t *count);
+
+/**
+ * \ingroup H5ES
+ *
+ * \brief Retrieves the accumulative operation counter for an event set
+ *
+ * \es_id
+ * \param[out] counter The accumulative counter value for an event set
+ * \returns \herr_t
+ *
+ * \details H5ESget_op_counter() retrieves the current accumulative count of
+ *          event set operations since the event set creation of \p es_id.
+ *
+ * \note This is designed for wrapper libraries mainly, to use as a mechanism
+ *       for matching operations inserted into the event set with possible
+ *       errors that occur.
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL herr_t H5ESget_op_counter(hid_t es_id, uint64_t *counter);
+
+/**
+ * \ingroup H5ES
+ *
+ * \brief Checks for failed operations
+ *
+ * \es_id
+ * \param[out] err_occurred Status indicating if error is present in the event
+ *             set
+ * \returns \herr_t
+ *
+ * \details H5ESget_err_status() checks if event set specified by es_id has
+ *          failed operations.
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL herr_t H5ESget_err_status(hid_t es_id, hbool_t *err_occurred);
+
+/**
+ * \ingroup H5ES
+ *
+ * \brief Retrieves the number of failed operations
+ *
+ * \es_id
+ * \param[out] num_errs Number of errors
+ * \returns \herr_t
+ *
+ * \details H5ESget_err_count() retrieves the number of failed operations in an
+ *          event set specified by \p es_id.
+ *
+ *          The function does not wait for active operations to complete, so
+ *          count may not include all failures.
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL herr_t H5ESget_err_count(hid_t es_id, size_t *num_errs);
+
+/**
+ * \ingroup H5ES
+ *
+ * \brief Retrieves information about failed operations
+ *
+ * \es_id
+ * \param[in] num_err_info The number of elements in \p err_info array
+ * \param[out] err_info Array of structures
+ * \param[out] err_cleared Number of cleared errors
+ * \returns \herr_t
+ *
+ * \details H5ESget_err_info() retrieves information about failed operations in
+ *          an event set specified by \p es_id.  The strings retrieved for each
+ *          error info must be released by calling H5free_memory().
+ *
+ *          Below is the description of the \ref H5ES_err_info_t structure:
+ *          \snippet this H5ES_err_info_t_snip
+ *          \click4more
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL herr_t H5ESget_err_info(hid_t es_id, size_t num_err_info, H5ES_err_info_t err_info[],
+                               size_t *err_cleared);
+/**
+ * \ingroup H5ES
+ *
+ * \brief Convenience routine to free an array of H5ES_err_info_t structs
+ *
+ * \param[in] num_err_info The number of elements in \p err_info array
+ * \param[in] err_info Array of structures
+ * \returns \herr_t
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL herr_t H5ESfree_err_info(size_t num_err_info, H5ES_err_info_t err_info[]);
+
+/**
+ * \ingroup H5ES
+ *
+ * \brief Registers a callback to invoke when a new operation is inserted into
+ *        an event set
+ *
+ * \es_id
+ * \param[in] func The insert function to register
+ * \param[in] ctx User-specified information (context) to pass to \p func
+ * \returns \herr_t
+ *
+ * \details Only one insert callback can be registered for each event set.
+ *          Registering a new callback will replace the existing one.
+ *          H5ES_NONE is a valid value for 'es_id', but functions as a no-op
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL herr_t H5ESregister_insert_func(hid_t es_id, H5ES_event_insert_func_t func, void *ctx);
+
+/**
+ * \ingroup H5ES
+ *
+ * \brief Registers a callback to invoke when an operation completes within an
+ *        event set
+ *
+ * \es_id
+ * \param[in] func The completion function to register
+ * \param[in] ctx User-specified information (context) to pass to \p func
+ * \returns \herr_t
+ *
+ * \details Only one complete callback can be registered for each event set.
+ *          Registering a new callback will replace the existing one.
+ *          H5ES_NONE is a valid value for 'es_id', but functions as a no-op
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL herr_t H5ESregister_complete_func(hid_t es_id, H5ES_event_complete_func_t func, void *ctx);
+
+/**
+ * \ingroup H5ES
+ *
+ * \brief Terminates access to an event set
+ *
+ * \es_id
+ * \returns \herr_t
+ *
+ * \details H5ESclose() terminates access to an event set specified by \p es_id.
+ *
+ * \since 1.14.0
+ *
+ */
+H5_DLL herr_t H5ESclose(hid_t es_id);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* H5ESpublic_H */

HybridMesher/libraries/HDF5-1.14.1/include/H5Epubgen.h

@@ -0,0 +1,441 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/* Generated automatically by bin/make_err -- do not edit */
+/* Add new errors to H5err.txt file */
+
+
+#ifndef H5Epubgen_H
+#define H5Epubgen_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*********************/
+/* Major error codes */
+/*********************/
+
+#define H5E_FUNC             (H5OPEN H5E_FUNC_g)
+#define H5E_FILE             (H5OPEN H5E_FILE_g)
+#define H5E_VOL              (H5OPEN H5E_VOL_g)
+#define H5E_SOHM             (H5OPEN H5E_SOHM_g)
+#define H5E_SYM              (H5OPEN H5E_SYM_g)
+#define H5E_PLUGIN           (H5OPEN H5E_PLUGIN_g)
+#define H5E_VFL              (H5OPEN H5E_VFL_g)
+#define H5E_INTERNAL         (H5OPEN H5E_INTERNAL_g)
+#define H5E_BTREE            (H5OPEN H5E_BTREE_g)
+#define H5E_REFERENCE        (H5OPEN H5E_REFERENCE_g)
+#define H5E_DATASPACE        (H5OPEN H5E_DATASPACE_g)
+#define H5E_RESOURCE         (H5OPEN H5E_RESOURCE_g)
+#define H5E_EVENTSET         (H5OPEN H5E_EVENTSET_g)
+#define H5E_ID               (H5OPEN H5E_ID_g)
+#define H5E_RS               (H5OPEN H5E_RS_g)
+#define H5E_FARRAY           (H5OPEN H5E_FARRAY_g)
+#define H5E_HEAP             (H5OPEN H5E_HEAP_g)
+#define H5E_MAP              (H5OPEN H5E_MAP_g)
+#define H5E_ATTR             (H5OPEN H5E_ATTR_g)
+#define H5E_IO               (H5OPEN H5E_IO_g)
+#define H5E_EFL              (H5OPEN H5E_EFL_g)
+#define H5E_TST              (H5OPEN H5E_TST_g)
+#define H5E_LIB              (H5OPEN H5E_LIB_g)
+#define H5E_PAGEBUF          (H5OPEN H5E_PAGEBUF_g)
+#define H5E_FSPACE           (H5OPEN H5E_FSPACE_g)
+#define H5E_DATASET          (H5OPEN H5E_DATASET_g)
+#define H5E_STORAGE          (H5OPEN H5E_STORAGE_g)
+#define H5E_LINK             (H5OPEN H5E_LINK_g)
+#define H5E_PLIST            (H5OPEN H5E_PLIST_g)
+#define H5E_DATATYPE         (H5OPEN H5E_DATATYPE_g)
+#define H5E_OHDR             (H5OPEN H5E_OHDR_g)
+#define H5E_NONE_MAJOR       (H5OPEN H5E_NONE_MAJOR_g)
+#define H5E_SLIST            (H5OPEN H5E_SLIST_g)
+#define H5E_ARGS             (H5OPEN H5E_ARGS_g)
+#define H5E_CONTEXT          (H5OPEN H5E_CONTEXT_g)
+#define H5E_EARRAY           (H5OPEN H5E_EARRAY_g)
+#define H5E_PLINE            (H5OPEN H5E_PLINE_g)
+#define H5E_ERROR            (H5OPEN H5E_ERROR_g)
+#define H5E_CACHE            (H5OPEN H5E_CACHE_g)
+H5_DLLVAR hid_t H5E_FUNC_g;          /* Function entry/exit */
+H5_DLLVAR hid_t H5E_FILE_g;          /* File accessibility */
+H5_DLLVAR hid_t H5E_VOL_g;           /* Virtual Object Layer */
+H5_DLLVAR hid_t H5E_SOHM_g;          /* Shared Object Header Messages */
+H5_DLLVAR hid_t H5E_SYM_g;           /* Symbol table */
+H5_DLLVAR hid_t H5E_PLUGIN_g;        /* Plugin for dynamically loaded library */
+H5_DLLVAR hid_t H5E_VFL_g;           /* Virtual File Layer */
+H5_DLLVAR hid_t H5E_INTERNAL_g;      /* Internal error (too specific to document in detail) */
+H5_DLLVAR hid_t H5E_BTREE_g;         /* B-Tree node */
+H5_DLLVAR hid_t H5E_REFERENCE_g;     /* References */
+H5_DLLVAR hid_t H5E_DATASPACE_g;     /* Dataspace */
+H5_DLLVAR hid_t H5E_RESOURCE_g;      /* Resource unavailable */
+H5_DLLVAR hid_t H5E_EVENTSET_g;      /* Event Set */
+H5_DLLVAR hid_t H5E_ID_g;            /* Object ID */
+H5_DLLVAR hid_t H5E_RS_g;            /* Reference Counted Strings */
+H5_DLLVAR hid_t H5E_FARRAY_g;        /* Fixed Array */
+H5_DLLVAR hid_t H5E_HEAP_g;          /* Heap */
+H5_DLLVAR hid_t H5E_MAP_g;           /* Map */
+H5_DLLVAR hid_t H5E_ATTR_g;          /* Attribute */
+H5_DLLVAR hid_t H5E_IO_g;            /* Low-level I/O */
+H5_DLLVAR hid_t H5E_EFL_g;           /* External file list */
+H5_DLLVAR hid_t H5E_TST_g;           /* Ternary Search Trees */
+H5_DLLVAR hid_t H5E_LIB_g;           /* General library infrastructure */
+H5_DLLVAR hid_t H5E_PAGEBUF_g;       /* Page Buffering */
+H5_DLLVAR hid_t H5E_FSPACE_g;        /* Free Space Manager */
+H5_DLLVAR hid_t H5E_DATASET_g;       /* Dataset */
+H5_DLLVAR hid_t H5E_STORAGE_g;       /* Data storage */
+H5_DLLVAR hid_t H5E_LINK_g;          /* Links */
+H5_DLLVAR hid_t H5E_PLIST_g;         /* Property lists */
+H5_DLLVAR hid_t H5E_DATATYPE_g;      /* Datatype */
+H5_DLLVAR hid_t H5E_OHDR_g;          /* Object header */
+H5_DLLVAR hid_t H5E_NONE_MAJOR_g;    /* No error */
+H5_DLLVAR hid_t H5E_SLIST_g;         /* Skip Lists */
+H5_DLLVAR hid_t H5E_ARGS_g;          /* Invalid arguments to routine */
+H5_DLLVAR hid_t H5E_CONTEXT_g;       /* API Context */
+H5_DLLVAR hid_t H5E_EARRAY_g;        /* Extensible Array */
+H5_DLLVAR hid_t H5E_PLINE_g;         /* Data filters */
+H5_DLLVAR hid_t H5E_ERROR_g;         /* Error API */
+H5_DLLVAR hid_t H5E_CACHE_g;         /* Object cache */
+
+/*********************/
+/* Minor error codes */
+/*********************/
+
+/* Object ID related errors */
+#define H5E_BADID            (H5OPEN H5E_BADID_g)
+#define H5E_BADGROUP         (H5OPEN H5E_BADGROUP_g)
+#define H5E_CANTREGISTER     (H5OPEN H5E_CANTREGISTER_g)
+#define H5E_CANTINC          (H5OPEN H5E_CANTINC_g)
+#define H5E_CANTDEC          (H5OPEN H5E_CANTDEC_g)
+#define H5E_NOIDS            (H5OPEN H5E_NOIDS_g)
+H5_DLLVAR hid_t H5E_BADID_g;         /* Unable to find ID information (already closed?) */
+H5_DLLVAR hid_t H5E_BADGROUP_g;      /* Unable to find ID group information */
+H5_DLLVAR hid_t H5E_CANTREGISTER_g;  /* Unable to register new ID */
+H5_DLLVAR hid_t H5E_CANTINC_g;       /* Unable to increment reference count */
+H5_DLLVAR hid_t H5E_CANTDEC_g;       /* Unable to decrement reference count */
+H5_DLLVAR hid_t H5E_NOIDS_g;         /* Out of IDs for group */
+
+/* Generic low-level file I/O errors */
+#define H5E_SEEKERROR        (H5OPEN H5E_SEEKERROR_g)
+#define H5E_READERROR        (H5OPEN H5E_READERROR_g)
+#define H5E_WRITEERROR       (H5OPEN H5E_WRITEERROR_g)
+#define H5E_CLOSEERROR       (H5OPEN H5E_CLOSEERROR_g)
+#define H5E_OVERFLOW         (H5OPEN H5E_OVERFLOW_g)
+#define H5E_FCNTL            (H5OPEN H5E_FCNTL_g)
+H5_DLLVAR hid_t H5E_SEEKERROR_g;     /* Seek failed */
+H5_DLLVAR hid_t H5E_READERROR_g;     /* Read failed */
+H5_DLLVAR hid_t H5E_WRITEERROR_g;    /* Write failed */
+H5_DLLVAR hid_t H5E_CLOSEERROR_g;    /* Close failed */
+H5_DLLVAR hid_t H5E_OVERFLOW_g;      /* Address overflowed */
+H5_DLLVAR hid_t H5E_FCNTL_g;         /* File control (fcntl) failed */
+
+/* Resource errors */
+#define H5E_NOSPACE          (H5OPEN H5E_NOSPACE_g)
+#define H5E_CANTALLOC        (H5OPEN H5E_CANTALLOC_g)
+#define H5E_CANTCOPY         (H5OPEN H5E_CANTCOPY_g)
+#define H5E_CANTFREE         (H5OPEN H5E_CANTFREE_g)
+#define H5E_ALREADYEXISTS    (H5OPEN H5E_ALREADYEXISTS_g)
+#define H5E_CANTLOCK         (H5OPEN H5E_CANTLOCK_g)
+#define H5E_CANTUNLOCK       (H5OPEN H5E_CANTUNLOCK_g)
+#define H5E_CANTGC           (H5OPEN H5E_CANTGC_g)
+#define H5E_CANTGETSIZE      (H5OPEN H5E_CANTGETSIZE_g)
+#define H5E_OBJOPEN          (H5OPEN H5E_OBJOPEN_g)
+H5_DLLVAR hid_t H5E_NOSPACE_g;       /* No space available for allocation */
+H5_DLLVAR hid_t H5E_CANTALLOC_g;     /* Can't allocate space */
+H5_DLLVAR hid_t H5E_CANTCOPY_g;      /* Unable to copy object */
+H5_DLLVAR hid_t H5E_CANTFREE_g;      /* Unable to free object */
+H5_DLLVAR hid_t H5E_ALREADYEXISTS_g; /* Object already exists */
+H5_DLLVAR hid_t H5E_CANTLOCK_g;      /* Unable to lock object */
+H5_DLLVAR hid_t H5E_CANTUNLOCK_g;    /* Unable to unlock object */
+H5_DLLVAR hid_t H5E_CANTGC_g;        /* Unable to garbage collect */
+H5_DLLVAR hid_t H5E_CANTGETSIZE_g;   /* Unable to compute size */
+H5_DLLVAR hid_t H5E_OBJOPEN_g;       /* Object is already open */
+
+/* Heap errors */
+#define H5E_CANTRESTORE      (H5OPEN H5E_CANTRESTORE_g)
+#define H5E_CANTCOMPUTE      (H5OPEN H5E_CANTCOMPUTE_g)
+#define H5E_CANTEXTEND       (H5OPEN H5E_CANTEXTEND_g)
+#define H5E_CANTATTACH       (H5OPEN H5E_CANTATTACH_g)
+#define H5E_CANTUPDATE       (H5OPEN H5E_CANTUPDATE_g)
+#define H5E_CANTOPERATE      (H5OPEN H5E_CANTOPERATE_g)
+H5_DLLVAR hid_t H5E_CANTRESTORE_g;   /* Can't restore condition */
+H5_DLLVAR hid_t H5E_CANTCOMPUTE_g;   /* Can't compute value */
+H5_DLLVAR hid_t H5E_CANTEXTEND_g;    /* Can't extend heap's space */
+H5_DLLVAR hid_t H5E_CANTATTACH_g;    /* Can't attach object */
+H5_DLLVAR hid_t H5E_CANTUPDATE_g;    /* Can't update object */
+H5_DLLVAR hid_t H5E_CANTOPERATE_g;   /* Can't operate on object */
+
+/* Map related errors */
+#define H5E_CANTPUT          (H5OPEN H5E_CANTPUT_g)
+H5_DLLVAR hid_t H5E_CANTPUT_g;       /* Can't put value */
+
+/* Function entry/exit interface errors */
+#define H5E_CANTINIT         (H5OPEN H5E_CANTINIT_g)
+#define H5E_ALREADYINIT      (H5OPEN H5E_ALREADYINIT_g)
+#define H5E_CANTRELEASE      (H5OPEN H5E_CANTRELEASE_g)
+H5_DLLVAR hid_t H5E_CANTINIT_g;      /* Unable to initialize object */
+H5_DLLVAR hid_t H5E_ALREADYINIT_g;   /* Object already initialized */
+H5_DLLVAR hid_t H5E_CANTRELEASE_g;   /* Unable to release object */
+
+/* Property list errors */
+#define H5E_CANTGET          (H5OPEN H5E_CANTGET_g)
+#define H5E_CANTSET          (H5OPEN H5E_CANTSET_g)
+#define H5E_DUPCLASS         (H5OPEN H5E_DUPCLASS_g)
+#define H5E_SETDISALLOWED    (H5OPEN H5E_SETDISALLOWED_g)
+H5_DLLVAR hid_t H5E_CANTGET_g;       /* Can't get value */
+H5_DLLVAR hid_t H5E_CANTSET_g;       /* Can't set value */
+H5_DLLVAR hid_t H5E_DUPCLASS_g;      /* Duplicate class name in parent class */
+H5_DLLVAR hid_t H5E_SETDISALLOWED_g; /* Disallowed operation */
+
+/* Asynchronous operation errors */
+#define H5E_CANTWAIT         (H5OPEN H5E_CANTWAIT_g)
+#define H5E_CANTCANCEL       (H5OPEN H5E_CANTCANCEL_g)
+H5_DLLVAR hid_t H5E_CANTWAIT_g;      /* Can't wait on operation */
+H5_DLLVAR hid_t H5E_CANTCANCEL_g;    /* Can't cancel operation */
+
+/* Free space errors */
+#define H5E_CANTMERGE        (H5OPEN H5E_CANTMERGE_g)
+#define H5E_CANTREVIVE       (H5OPEN H5E_CANTREVIVE_g)
+#define H5E_CANTSHRINK       (H5OPEN H5E_CANTSHRINK_g)
+H5_DLLVAR hid_t H5E_CANTMERGE_g;     /* Can't merge objects */
+H5_DLLVAR hid_t H5E_CANTREVIVE_g;    /* Can't revive object */
+H5_DLLVAR hid_t H5E_CANTSHRINK_g;    /* Can't shrink container */
+
+/* Object header related errors */
+#define H5E_LINKCOUNT        (H5OPEN H5E_LINKCOUNT_g)
+#define H5E_VERSION          (H5OPEN H5E_VERSION_g)
+#define H5E_ALIGNMENT        (H5OPEN H5E_ALIGNMENT_g)
+#define H5E_BADMESG          (H5OPEN H5E_BADMESG_g)
+#define H5E_CANTDELETE       (H5OPEN H5E_CANTDELETE_g)
+#define H5E_BADITER          (H5OPEN H5E_BADITER_g)
+#define H5E_CANTPACK         (H5OPEN H5E_CANTPACK_g)
+#define H5E_CANTRESET        (H5OPEN H5E_CANTRESET_g)
+#define H5E_CANTRENAME       (H5OPEN H5E_CANTRENAME_g)
+H5_DLLVAR hid_t H5E_LINKCOUNT_g;     /* Bad object header link count */
+H5_DLLVAR hid_t H5E_VERSION_g;       /* Wrong version number */
+H5_DLLVAR hid_t H5E_ALIGNMENT_g;     /* Alignment error */
+H5_DLLVAR hid_t H5E_BADMESG_g;       /* Unrecognized message */
+H5_DLLVAR hid_t H5E_CANTDELETE_g;    /* Can't delete message */
+H5_DLLVAR hid_t H5E_BADITER_g;       /* Iteration failed */
+H5_DLLVAR hid_t H5E_CANTPACK_g;      /* Can't pack messages */
+H5_DLLVAR hid_t H5E_CANTRESET_g;     /* Can't reset object */
+H5_DLLVAR hid_t H5E_CANTRENAME_g;    /* Unable to rename object */
+
+/* System level errors */
+#define H5E_SYSERRSTR        (H5OPEN H5E_SYSERRSTR_g)
+H5_DLLVAR hid_t H5E_SYSERRSTR_g;     /* System error message */
+
+/* I/O pipeline errors */
+#define H5E_NOFILTER         (H5OPEN H5E_NOFILTER_g)
+#define H5E_CALLBACK         (H5OPEN H5E_CALLBACK_g)
+#define H5E_CANAPPLY         (H5OPEN H5E_CANAPPLY_g)
+#define H5E_SETLOCAL         (H5OPEN H5E_SETLOCAL_g)
+#define H5E_NOENCODER        (H5OPEN H5E_NOENCODER_g)
+#define H5E_CANTFILTER       (H5OPEN H5E_CANTFILTER_g)
+H5_DLLVAR hid_t H5E_NOFILTER_g;      /* Requested filter is not available */
+H5_DLLVAR hid_t H5E_CALLBACK_g;      /* Callback failed */
+H5_DLLVAR hid_t H5E_CANAPPLY_g;      /* Error from filter 'can apply' callback */
+H5_DLLVAR hid_t H5E_SETLOCAL_g;      /* Error from filter 'set local' callback */
+H5_DLLVAR hid_t H5E_NOENCODER_g;     /* Filter present but encoding disabled */
+H5_DLLVAR hid_t H5E_CANTFILTER_g;    /* Filter operation failed */
+
+/* Group related errors */
+#define H5E_CANTOPENOBJ      (H5OPEN H5E_CANTOPENOBJ_g)
+#define H5E_CANTCLOSEOBJ     (H5OPEN H5E_CANTCLOSEOBJ_g)
+#define H5E_COMPLEN          (H5OPEN H5E_COMPLEN_g)
+#define H5E_PATH             (H5OPEN H5E_PATH_g)
+H5_DLLVAR hid_t H5E_CANTOPENOBJ_g;   /* Can't open object */
+H5_DLLVAR hid_t H5E_CANTCLOSEOBJ_g;  /* Can't close object */
+H5_DLLVAR hid_t H5E_COMPLEN_g;       /* Name component is too long */
+H5_DLLVAR hid_t H5E_PATH_g;          /* Problem with path to object */
+
+/* No error */
+#define H5E_NONE_MINOR       (H5OPEN H5E_NONE_MINOR_g)
+H5_DLLVAR hid_t H5E_NONE_MINOR_g;    /* No error */
+
+/* Plugin errors */
+#define H5E_OPENERROR        (H5OPEN H5E_OPENERROR_g)
+H5_DLLVAR hid_t H5E_OPENERROR_g;     /* Can't open directory or file */
+
+/* File accessibility errors */
+#define H5E_FILEEXISTS       (H5OPEN H5E_FILEEXISTS_g)
+#define H5E_FILEOPEN         (H5OPEN H5E_FILEOPEN_g)
+#define H5E_CANTCREATE       (H5OPEN H5E_CANTCREATE_g)
+#define H5E_CANTOPENFILE     (H5OPEN H5E_CANTOPENFILE_g)
+#define H5E_CANTCLOSEFILE    (H5OPEN H5E_CANTCLOSEFILE_g)
+#define H5E_NOTHDF5          (H5OPEN H5E_NOTHDF5_g)
+#define H5E_BADFILE          (H5OPEN H5E_BADFILE_g)
+#define H5E_TRUNCATED        (H5OPEN H5E_TRUNCATED_g)
+#define H5E_MOUNT            (H5OPEN H5E_MOUNT_g)
+#define H5E_UNMOUNT          (H5OPEN H5E_UNMOUNT_g)
+#define H5E_CANTDELETEFILE   (H5OPEN H5E_CANTDELETEFILE_g)
+#define H5E_CANTLOCKFILE     (H5OPEN H5E_CANTLOCKFILE_g)
+#define H5E_CANTUNLOCKFILE   (H5OPEN H5E_CANTUNLOCKFILE_g)
+H5_DLLVAR hid_t H5E_FILEEXISTS_g;    /* File already exists */
+H5_DLLVAR hid_t H5E_FILEOPEN_g;      /* File already open */
+H5_DLLVAR hid_t H5E_CANTCREATE_g;    /* Unable to create file */
+H5_DLLVAR hid_t H5E_CANTOPENFILE_g;  /* Unable to open file */
+H5_DLLVAR hid_t H5E_CANTCLOSEFILE_g; /* Unable to close file */
+H5_DLLVAR hid_t H5E_NOTHDF5_g;       /* Not an HDF5 file */
+H5_DLLVAR hid_t H5E_BADFILE_g;       /* Bad file ID accessed */
+H5_DLLVAR hid_t H5E_TRUNCATED_g;     /* File has been truncated */
+H5_DLLVAR hid_t H5E_MOUNT_g;         /* File mount error */
+H5_DLLVAR hid_t H5E_UNMOUNT_g;       /* File unmount error */
+H5_DLLVAR hid_t H5E_CANTDELETEFILE_g; /* Unable to delete file */
+H5_DLLVAR hid_t H5E_CANTLOCKFILE_g;  /* Unable to lock file */
+H5_DLLVAR hid_t H5E_CANTUNLOCKFILE_g; /* Unable to unlock file */
+
+/* Cache related errors */
+#define H5E_CANTFLUSH        (H5OPEN H5E_CANTFLUSH_g)
+#define H5E_CANTUNSERIALIZE  (H5OPEN H5E_CANTUNSERIALIZE_g)
+#define H5E_CANTSERIALIZE    (H5OPEN H5E_CANTSERIALIZE_g)
+#define H5E_CANTTAG          (H5OPEN H5E_CANTTAG_g)
+#define H5E_CANTLOAD         (H5OPEN H5E_CANTLOAD_g)
+#define H5E_PROTECT          (H5OPEN H5E_PROTECT_g)
+#define H5E_NOTCACHED        (H5OPEN H5E_NOTCACHED_g)
+#define H5E_SYSTEM           (H5OPEN H5E_SYSTEM_g)
+#define H5E_CANTINS          (H5OPEN H5E_CANTINS_g)
+#define H5E_CANTPROTECT      (H5OPEN H5E_CANTPROTECT_g)
+#define H5E_CANTUNPROTECT    (H5OPEN H5E_CANTUNPROTECT_g)
+#define H5E_CANTPIN          (H5OPEN H5E_CANTPIN_g)
+#define H5E_CANTUNPIN        (H5OPEN H5E_CANTUNPIN_g)
+#define H5E_CANTMARKDIRTY    (H5OPEN H5E_CANTMARKDIRTY_g)
+#define H5E_CANTMARKCLEAN    (H5OPEN H5E_CANTMARKCLEAN_g)
+#define H5E_CANTMARKUNSERIALIZED (H5OPEN H5E_CANTMARKUNSERIALIZED_g)
+#define H5E_CANTMARKSERIALIZED (H5OPEN H5E_CANTMARKSERIALIZED_g)
+#define H5E_CANTDIRTY        (H5OPEN H5E_CANTDIRTY_g)
+#define H5E_CANTCLEAN        (H5OPEN H5E_CANTCLEAN_g)
+#define H5E_CANTEXPUNGE      (H5OPEN H5E_CANTEXPUNGE_g)
+#define H5E_CANTRESIZE       (H5OPEN H5E_CANTRESIZE_g)
+#define H5E_CANTDEPEND       (H5OPEN H5E_CANTDEPEND_g)
+#define H5E_CANTUNDEPEND     (H5OPEN H5E_CANTUNDEPEND_g)
+#define H5E_CANTNOTIFY       (H5OPEN H5E_CANTNOTIFY_g)
+#define H5E_LOGGING          (H5OPEN H5E_LOGGING_g)
+#define H5E_CANTCORK         (H5OPEN H5E_CANTCORK_g)
+#define H5E_CANTUNCORK       (H5OPEN H5E_CANTUNCORK_g)
+H5_DLLVAR hid_t H5E_CANTFLUSH_g;     /* Unable to flush data from cache */
+H5_DLLVAR hid_t H5E_CANTUNSERIALIZE_g; /* Unable to mark metadata as unserialized */
+H5_DLLVAR hid_t H5E_CANTSERIALIZE_g; /* Unable to serialize data from cache */
+H5_DLLVAR hid_t H5E_CANTTAG_g;       /* Unable to tag metadata in the cache */
+H5_DLLVAR hid_t H5E_CANTLOAD_g;      /* Unable to load metadata into cache */
+H5_DLLVAR hid_t H5E_PROTECT_g;       /* Protected metadata error */
+H5_DLLVAR hid_t H5E_NOTCACHED_g;     /* Metadata not currently cached */
+H5_DLLVAR hid_t H5E_SYSTEM_g;        /* Internal error detected */
+H5_DLLVAR hid_t H5E_CANTINS_g;       /* Unable to insert metadata into cache */
+H5_DLLVAR hid_t H5E_CANTPROTECT_g;   /* Unable to protect metadata */
+H5_DLLVAR hid_t H5E_CANTUNPROTECT_g; /* Unable to unprotect metadata */
+H5_DLLVAR hid_t H5E_CANTPIN_g;       /* Unable to pin cache entry */
+H5_DLLVAR hid_t H5E_CANTUNPIN_g;     /* Unable to un-pin cache entry */
+H5_DLLVAR hid_t H5E_CANTMARKDIRTY_g; /* Unable to mark a pinned entry as dirty */
+H5_DLLVAR hid_t H5E_CANTMARKCLEAN_g; /* Unable to mark a pinned entry as clean */
+H5_DLLVAR hid_t H5E_CANTMARKUNSERIALIZED_g; /* Unable to mark an entry as unserialized */
+H5_DLLVAR hid_t H5E_CANTMARKSERIALIZED_g; /* Unable to mark an entry as serialized */
+H5_DLLVAR hid_t H5E_CANTDIRTY_g;     /* Unable to mark metadata as dirty */
+H5_DLLVAR hid_t H5E_CANTCLEAN_g;     /* Unable to mark metadata as clean */
+H5_DLLVAR hid_t H5E_CANTEXPUNGE_g;   /* Unable to expunge a metadata cache entry */
+H5_DLLVAR hid_t H5E_CANTRESIZE_g;    /* Unable to resize a metadata cache entry */
+H5_DLLVAR hid_t H5E_CANTDEPEND_g;    /* Unable to create a flush dependency */
+H5_DLLVAR hid_t H5E_CANTUNDEPEND_g;  /* Unable to destroy a flush dependency */
+H5_DLLVAR hid_t H5E_CANTNOTIFY_g;    /* Unable to notify object about action */
+H5_DLLVAR hid_t H5E_LOGGING_g;       /* Failure in the cache logging framework */
+H5_DLLVAR hid_t H5E_CANTCORK_g;      /* Unable to cork an object */
+H5_DLLVAR hid_t H5E_CANTUNCORK_g;    /* Unable to uncork an object */
+
+/* Link related errors */
+#define H5E_TRAVERSE         (H5OPEN H5E_TRAVERSE_g)
+#define H5E_NLINKS           (H5OPEN H5E_NLINKS_g)
+#define H5E_NOTREGISTERED    (H5OPEN H5E_NOTREGISTERED_g)
+#define H5E_CANTMOVE         (H5OPEN H5E_CANTMOVE_g)
+#define H5E_CANTSORT         (H5OPEN H5E_CANTSORT_g)
+H5_DLLVAR hid_t H5E_TRAVERSE_g;      /* Link traversal failure */
+H5_DLLVAR hid_t H5E_NLINKS_g;        /* Too many soft links in path */
+H5_DLLVAR hid_t H5E_NOTREGISTERED_g; /* Link class not registered */
+H5_DLLVAR hid_t H5E_CANTMOVE_g;      /* Can't move object */
+H5_DLLVAR hid_t H5E_CANTSORT_g;      /* Can't sort objects */
+
+/* Parallel MPI errors */
+#define H5E_MPI              (H5OPEN H5E_MPI_g)
+#define H5E_MPIERRSTR        (H5OPEN H5E_MPIERRSTR_g)
+#define H5E_CANTRECV         (H5OPEN H5E_CANTRECV_g)
+#define H5E_CANTGATHER       (H5OPEN H5E_CANTGATHER_g)
+#define H5E_NO_INDEPENDENT   (H5OPEN H5E_NO_INDEPENDENT_g)
+H5_DLLVAR hid_t H5E_MPI_g;           /* Some MPI function failed */
+H5_DLLVAR hid_t H5E_MPIERRSTR_g;     /* MPI Error String */
+H5_DLLVAR hid_t H5E_CANTRECV_g;      /* Can't receive data */
+H5_DLLVAR hid_t H5E_CANTGATHER_g;    /* Can't gather data */
+H5_DLLVAR hid_t H5E_NO_INDEPENDENT_g; /* Can't perform independent IO */
+
+/* Dataspace errors */
+#define H5E_CANTCLIP         (H5OPEN H5E_CANTCLIP_g)
+#define H5E_CANTCOUNT        (H5OPEN H5E_CANTCOUNT_g)
+#define H5E_CANTSELECT       (H5OPEN H5E_CANTSELECT_g)
+#define H5E_CANTNEXT         (H5OPEN H5E_CANTNEXT_g)
+#define H5E_BADSELECT        (H5OPEN H5E_BADSELECT_g)
+#define H5E_CANTCOMPARE      (H5OPEN H5E_CANTCOMPARE_g)
+#define H5E_INCONSISTENTSTATE (H5OPEN H5E_INCONSISTENTSTATE_g)
+#define H5E_CANTAPPEND       (H5OPEN H5E_CANTAPPEND_g)
+H5_DLLVAR hid_t H5E_CANTCLIP_g;      /* Can't clip hyperslab region */
+H5_DLLVAR hid_t H5E_CANTCOUNT_g;     /* Can't count elements */
+H5_DLLVAR hid_t H5E_CANTSELECT_g;    /* Can't select hyperslab */
+H5_DLLVAR hid_t H5E_CANTNEXT_g;      /* Can't move to next iterator location */
+H5_DLLVAR hid_t H5E_BADSELECT_g;     /* Invalid selection */
+H5_DLLVAR hid_t H5E_CANTCOMPARE_g;   /* Can't compare objects */
+H5_DLLVAR hid_t H5E_INCONSISTENTSTATE_g; /* Internal states are inconsistent */
+H5_DLLVAR hid_t H5E_CANTAPPEND_g;    /* Can't append object */
+
+/* Argument errors */
+#define H5E_UNINITIALIZED    (H5OPEN H5E_UNINITIALIZED_g)
+#define H5E_UNSUPPORTED      (H5OPEN H5E_UNSUPPORTED_g)
+#define H5E_BADTYPE          (H5OPEN H5E_BADTYPE_g)
+#define H5E_BADRANGE         (H5OPEN H5E_BADRANGE_g)
+#define H5E_BADVALUE         (H5OPEN H5E_BADVALUE_g)
+H5_DLLVAR hid_t H5E_UNINITIALIZED_g; /* Information is uinitialized */
+H5_DLLVAR hid_t H5E_UNSUPPORTED_g;   /* Feature is unsupported */
+H5_DLLVAR hid_t H5E_BADTYPE_g;       /* Inappropriate type */
+H5_DLLVAR hid_t H5E_BADRANGE_g;      /* Out of range */
+H5_DLLVAR hid_t H5E_BADVALUE_g;      /* Bad value */
+
+/* B-tree related errors */
+#define H5E_NOTFOUND         (H5OPEN H5E_NOTFOUND_g)
+#define H5E_EXISTS           (H5OPEN H5E_EXISTS_g)
+#define H5E_CANTENCODE       (H5OPEN H5E_CANTENCODE_g)
+#define H5E_CANTDECODE       (H5OPEN H5E_CANTDECODE_g)
+#define H5E_CANTSPLIT        (H5OPEN H5E_CANTSPLIT_g)
+#define H5E_CANTREDISTRIBUTE (H5OPEN H5E_CANTREDISTRIBUTE_g)
+#define H5E_CANTSWAP         (H5OPEN H5E_CANTSWAP_g)
+#define H5E_CANTINSERT       (H5OPEN H5E_CANTINSERT_g)
+#define H5E_CANTLIST         (H5OPEN H5E_CANTLIST_g)
+#define H5E_CANTMODIFY       (H5OPEN H5E_CANTMODIFY_g)
+#define H5E_CANTREMOVE       (H5OPEN H5E_CANTREMOVE_g)
+#define H5E_CANTFIND         (H5OPEN H5E_CANTFIND_g)
+H5_DLLVAR hid_t H5E_NOTFOUND_g;      /* Object not found */
+H5_DLLVAR hid_t H5E_EXISTS_g;        /* Object already exists */
+H5_DLLVAR hid_t H5E_CANTENCODE_g;    /* Unable to encode value */
+H5_DLLVAR hid_t H5E_CANTDECODE_g;    /* Unable to decode value */
+H5_DLLVAR hid_t H5E_CANTSPLIT_g;     /* Unable to split node */
+H5_DLLVAR hid_t H5E_CANTREDISTRIBUTE_g; /* Unable to redistribute records */
+H5_DLLVAR hid_t H5E_CANTSWAP_g;      /* Unable to swap records */
+H5_DLLVAR hid_t H5E_CANTINSERT_g;    /* Unable to insert object */
+H5_DLLVAR hid_t H5E_CANTLIST_g;      /* Unable to list node */
+H5_DLLVAR hid_t H5E_CANTMODIFY_g;    /* Unable to modify record */
+H5_DLLVAR hid_t H5E_CANTREMOVE_g;    /* Unable to remove object */
+H5_DLLVAR hid_t H5E_CANTFIND_g;      /* Unable to check for record */
+
+/* Datatype conversion errors */
+#define H5E_CANTCONVERT      (H5OPEN H5E_CANTCONVERT_g)
+#define H5E_BADSIZE          (H5OPEN H5E_BADSIZE_g)
+H5_DLLVAR hid_t H5E_CANTCONVERT_g;   /* Can't convert datatypes */
+H5_DLLVAR hid_t H5E_BADSIZE_g;       /* Bad size for object */
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* H5Epubgen_H */

HybridMesher/libraries/HDF5-1.14.1/include/H5Epublic.h

@@ -0,0 +1,946 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * This file contains public declarations for the H5E module.
+ */
+#ifndef H5Epublic_H
+#define H5Epublic_H
+
+#include <stdio.h> /*FILE arg of H5Eprint()                     */
+
+/* Public headers needed by this file */
+#include "H5public.h"
+#include "H5Ipublic.h"
+
+/* Value for the default error stack */
+#define H5E_DEFAULT 0 /* (hid_t) */
+
+/**
+ * Different kinds of error information
+ */
+typedef enum H5E_type_t { H5E_MAJOR, H5E_MINOR } H5E_type_t;
+
+/**
+ * Information about an error; element of error stack
+ */
+typedef struct H5E_error2_t {
+    hid_t cls_id;
+    /**< Class ID                           */
+    hid_t maj_num;
+    /**< Major error ID                        */
+    hid_t min_num;
+    /**< Minor error number                    */
+    unsigned line;
+    /**< Line in file where error occurs    */
+    const char *func_name;
+    /**< Function in which error occurred   */
+    const char *file_name;
+    /**< File in which error occurred       */
+    const char *desc;
+    /**< Optional supplied description      */
+} H5E_error2_t;
+
+/* When this header is included from a private header, don't make calls to H5open() */
+#undef H5OPEN
+#ifndef H5private_H
+#define H5OPEN H5open(),
+#else /* H5private_H */
+#define H5OPEN
+#endif /* H5private_H */
+
+/* HDF5 error class */
+/* Extern "C" block needed to compile C++ filter plugins with some compilers */
+#ifdef __cplusplus
+extern "C" {
+#endif
+#define H5E_ERR_CLS (H5OPEN H5E_ERR_CLS_g)
+H5_DLLVAR hid_t H5E_ERR_CLS_g;
+#ifdef __cplusplus
+}
+#endif
+
+/* Include the automatically generated public header information */
+/* (This includes the list of major and minor error codes for the library) */
+#include "H5Epubgen.h"
+
+/*
+ * One often needs to temporarily disable automatic error reporting when
+ * trying something that's likely or expected to fail.  The code to try can
+ * be nested between calls to H5Eget_auto() and H5Eset_auto(), but it's
+ * easier just to use this macro like:
+ *     H5E_BEGIN_TRY {
+ *        ...stuff here that's likely to fail...
+ *      } H5E_END_TRY;
+ *
+ * Warning: don't break, return, or longjmp() from the body of the loop or
+ *        the error reporting won't be properly restored!
+ *
+ * These two macros still use the old API functions for backward compatibility
+ * purpose.
+ */
+#ifndef H5_NO_DEPRECATED_SYMBOLS
+#define H5E_BEGIN_TRY                                                                                        \
+    {                                                                                                        \
+        unsigned H5E_saved_is_v2;                                                                            \
+        union {                                                                                              \
+            H5E_auto1_t efunc1;                                                                              \
+            H5E_auto2_t efunc2;                                                                              \
+        } H5E_saved;                                                                                         \
+        void *H5E_saved_edata;                                                                               \
+                                                                                                             \
+        (void)H5Eauto_is_v2(H5E_DEFAULT, &H5E_saved_is_v2);                                                  \
+        if (H5E_saved_is_v2) {                                                                               \
+            (void)H5Eget_auto2(H5E_DEFAULT, &H5E_saved.efunc2, &H5E_saved_edata);                            \
+            (void)H5Eset_auto2(H5E_DEFAULT, NULL, NULL);                                                     \
+        }                                                                                                    \
+        else {                                                                                               \
+            (void)H5Eget_auto1(&H5E_saved.efunc1, &H5E_saved_edata);                                         \
+            (void)H5Eset_auto1(NULL, NULL);                                                                  \
+        }
+
+#define H5E_END_TRY                                                                                          \
+    if (H5E_saved_is_v2)                                                                                     \
+        (void)H5Eset_auto2(H5E_DEFAULT, H5E_saved.efunc2, H5E_saved_edata);                                  \
+    else                                                                                                     \
+        (void)H5Eset_auto1(H5E_saved.efunc1, H5E_saved_edata);                                               \
+    }
+#else /* H5_NO_DEPRECATED_SYMBOLS */
+#define H5E_BEGIN_TRY                                                                                        \
+    {                                                                                                        \
+        H5E_auto2_t saved_efunc;                                                                             \
+        void       *H5E_saved_edata;                                                                         \
+                                                                                                             \
+        (void)H5Eget_auto2(H5E_DEFAULT, &saved_efunc, &H5E_saved_edata);                                     \
+        (void)H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
+#define H5E_END_TRY                                                                                          \
+    (void)H5Eset_auto2(H5E_DEFAULT, saved_efunc, H5E_saved_edata);                                           \
+    }
+#endif /* H5_NO_DEPRECATED_SYMBOLS */
+
+/*
+ * Public API Convenience Macros for Error reporting - Documented
+ */
+/* Use the Standard C __FILE__ & __LINE__ macros instead of typing them in */
+#define H5Epush_sim(func, cls, maj, min, str)                                                                \
+    H5Epush2(H5E_DEFAULT, __FILE__, func, __LINE__, cls, maj, min, str)
+
+/*
+ * Public API Convenience Macros for Error reporting - Undocumented
+ */
+/* Use the Standard C __FILE__ & __LINE__ macros instead of typing them in */
+/*  And return after pushing error onto stack */
+#define H5Epush_ret(func, cls, maj, min, str, ret)                                                           \
+    do {                                                                                                     \
+        H5Epush2(H5E_DEFAULT, __FILE__, func, __LINE__, cls, maj, min, str);                                 \
+        return (ret);                                                                                        \
+    } while (0)
+
+/* Use the Standard C __FILE__ & __LINE__ macros instead of typing them in
+ * And goto a label after pushing error onto stack.
+ */
+#define H5Epush_goto(func, cls, maj, min, str, label)                                                        \
+    {                                                                                                        \
+        H5Epush2(H5E_DEFAULT, __FILE__, func, __LINE__, cls, maj, min, str);                                 \
+        goto label;                                                                                          \
+    }
+
+/**
+ * Error stack traversal direction
+ */
+typedef enum H5E_direction_t {
+    H5E_WALK_UPWARD   = 0, /**< begin w/ most specific error, end at API function */
+    H5E_WALK_DOWNWARD = 1  /**< begin at API function, end w/ most specific error */
+} H5E_direction_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* Error stack traversal callback function pointers */
+//! <!-- [H5E_walk2_t_snip] -->
+/**
+ * \brief Callback function for H5Ewalk2()
+ *
+ * \param[in] n Indexed error position in the stack
+ * \param[in] err_desc Pointer to a data structure describing the error
+ * \param[in] client_data Pointer to client data in the format expected by the
+ *                        user-defined function
+ * \return \herr_t
+ */
+typedef herr_t (*H5E_walk2_t)(unsigned n, const H5E_error2_t *err_desc, void *client_data);
+//! <!-- [H5E_walk2_t_snip] -->
+
+//! <!-- [H5E_auto2_t_snip] -->
+/**
+ * \brief Callback function for H5Eset_auto2()
+ *
+ * \estack_id{estack}
+ * \param[in] client_data Pointer to client data in the format expected by the
+ *                        user-defined function
+ * \return \herr_t
+ */
+typedef herr_t (*H5E_auto2_t)(hid_t estack, void *client_data);
+//! <!-- [H5E_auto2_t_snip] -->
+
+/* Public API functions */
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Registers a client library or application program to the HDF5 error API
+ *
+ * \param[in] cls_name Name of the error class
+ * \param[in] lib_name Name of the client library or application to which the error class belongs
+ * \param[in] version Version of the client library or application to which the
+              error class belongs. It can be \c NULL.
+ * \return Returns a class identifier on success; otherwise returns H5I_INVALID_ID.
+ *
+ * \details H5Eregister_class() registers a client library or application
+ *          program to the HDF5 error API so that the client library or
+ *          application program can report errors together with the HDF5
+ *          library. It receives an identifier for this error class for further
+ *          error operations. The library name and version number will be
+ *          printed out in the error message as a preamble.
+ *
+ * \since 1.8.0
+ */
+H5_DLL hid_t H5Eregister_class(const char *cls_name, const char *lib_name, const char *version);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Removes an error class
+ *
+ * \param[in] class_id Error class identifier.
+ * \return \herr_t
+ *
+ * \details H5Eunregister_class() removes the error class specified by \p
+ *          class_id. All the major and minor errors in this class will also be
+ *          closed.
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Eunregister_class(hid_t class_id);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Closes an error message
+ *
+ * \param[in] err_id An error message identifier
+ * \return \herr_t
+ *
+ * \details H5Eclose_msg() closes an error message identifier, which can be
+ *          either a major or minor message.
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Eclose_msg(hid_t err_id);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Adds a major error message to an error class
+ *
+ * \param[in] cls An error class identifier
+ * \param[in] msg_type The type of the error message
+ * \param[in] msg Major error message
+ * \return \herr_t
+ *
+ * \details H5Ecreate_msg() adds an error message to an error class defined by
+ *          client library or application program. The error message can be
+ *          either major or minor as indicated by the parameter \p msg_type.
+ *
+ *          Use H5Eclose_msg() to close the message identifier returned by this
+ *          function.
+ *
+ * \since 1.8.0
+ */
+H5_DLL hid_t H5Ecreate_msg(hid_t cls, H5E_type_t msg_type, const char *msg);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Creates a new, empty error stack
+ *
+ * \return \hid_ti{error stack}
+ *
+ * \details H5Ecreate_stack() creates a new empty error stack and returns the
+ *          new stack’s identifier. Use H5Eclose_stack() to close the error stack
+ *          identifier returned by this function.
+ *
+ * \since 1.8.0
+ */
+H5_DLL hid_t H5Ecreate_stack(void);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Returns a copy of the current error stack
+ *
+ * \return \hid_ti{error stack}
+ *
+ * \details H5Eget_current_stack() copies the current error stack and returns an
+ *          error stack identifier for the new copy.
+ *
+ * \since 1.8.0
+ */
+H5_DLL hid_t H5Eget_current_stack(void);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Appends one error stack to another, optionally closing the source
+ *        stack.
+ *
+ * \estack_id{dst_stack_id}
+ * \estack_id{src_stack_id}
+ * \param[in] close_source_stack Flag to indicate whether to close the source stack
+ * \return \herr_t
+ *
+ * \details H5Eappend_stack() appends the messages from error stack
+ *          \p src_stack_id to the error stack \p dst_stack_id.
+ *          If \p close_source_stack is \c TRUE, the source error stack
+ *          will be closed.
+ *
+ * \since 1.14.0
+ */
+H5_DLL herr_t H5Eappend_stack(hid_t dst_stack_id, hid_t src_stack_id, hbool_t close_source_stack);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Closes an error stack handle
+ *
+ * \estack_id{stack_id}
+ *
+ * \return \herr_t
+ *
+ * \details H5Eclose_stack() closes the error stack handle \p stack_id
+ *          and releases its resources. #H5E_DEFAULT cannot be closed.
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Eclose_stack(hid_t stack_id);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Retrieves error class name
+ *
+ * \param[in] class_id Error class identifier
+ * \param[out] name Buffer for the error class name
+ * \param[in] size The maximum number of characters of the class name to be returned
+ *            by this function in \p name.
+ * \return Returns non-negative value as on success; otherwise returns negative value.
+ *
+ * \details H5Eget_class_name() retrieves the name of the error class specified
+ *          by the class identifier. If a non-NULL pointer is passed in for \p
+ *          name and \p size is greater than zero, the class name of \p size
+ *          long is returned. The length of the error class name is also
+ *          returned. If NULL is passed in as \p name, only the length of class
+ *          name is returned. If zero is returned, it means no name. The user is
+ *          responsible for allocating sufficient buffer space for the name.
+ *
+ * \since 1.8.0
+ */
+H5_DLL ssize_t H5Eget_class_name(hid_t class_id, char *name, size_t size);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Replaces the current error stack
+ *
+ * \estack_id{err_stack_id}
+ *
+ * \return \herr_t
+ *
+ * \details H5Eset_current_stack() replaces the content of the current error
+ *          stack with a copy of the content of the error stack specified by
+ *          \p err_stack_id, and it closes the error stack specified by
+ *          \p err_stack_id.
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Eset_current_stack(hid_t err_stack_id);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Pushes a new error record onto an error stack
+ *
+ * \estack_id{err_stack}. If the identifier is #H5E_DEFAULT, the error record
+ *                        will be pushed to the current stack.
+ * \param[in] file Name of the file in which the error was detected
+ * \param[in] func Name of the function in which the error was detected
+ * \param[in] line Line number in the file where the error was detected
+ * \param[in] cls_id Error class identifier
+ * \param[in] maj_id Major error identifier
+ * \param[in] min_id Minor error identifier
+ * \param[in] msg Error description string
+ * \return \herr_t
+ *
+ * \details H5Epush2() pushes a new error record onto the error stack specified
+ *          by \p err_stack.\n
+ *          The error record contains the error class identifier \p cls_id, the
+ *          major and minor message identifiers \p maj_id and \p min_id, the
+ *          function name \p func where the error was detected, the file name \p
+ *          file and line number \p line in the file where the error was
+ *          detected, and an error description \p msg.\n
+ *          The major and minor errors must be in the same error class.\n
+ *          The function name, filename, and error description strings must be
+ *          statically allocated.\n
+ *          \p msg can be a format control string with additional
+ *          arguments. This design of appending additional arguments is similar
+ *          to the system and C functions printf() and fprintf().
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Epush2(hid_t err_stack, const char *file, const char *func, unsigned line, hid_t cls_id,
+                       hid_t maj_id, hid_t min_id, const char *msg, ...);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Deletes specified number of error messages from the error stack
+ *
+ * \estack_id{err_stack}
+ * \param[in] count The number of error messages to be deleted from the top
+ *                  of error stack
+ * \return \herr_t
+ *
+ * \details H5Epop() deletes the number of error records specified in \p count
+ *          from the top of the error stack specified by \p err_stack (including
+ *          major, minor messages and description). The number of error messages
+ *          to be deleted is specified by \p count.
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Epop(hid_t err_stack, size_t count);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Prints the specified error stack in a default manner
+ *
+ * \estack_id{err_stack}
+ * \param[in] stream File pointer, or \c NULL for \c stderr
+ * \return \herr_t
+ *
+ * \details H5Eprint2() prints the error stack specified by \p err_stack on the
+ *          specified stream, \p stream. Even if the error stack is empty, a
+ *          one-line message of the following form will be printed:
+ *          \code{.unparsed}
+ *          HDF5-DIAG: Error detected in HDF5 library version: 1.5.62 thread 0.
+ *          \endcode
+ *
+ *          A similar line will appear before the error messages of each error
+ *          class stating the library name, library version number, and thread
+ *          identifier.
+ *
+ *          If \p err_stack is #H5E_DEFAULT, the current error stack will be
+ *          printed.
+ *
+ *          H5Eprint2() is a convenience function for H5Ewalk2() with a function
+ *          that prints error messages. Users are encouraged to write their own
+ *          more specific error handlers.
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Eprint2(hid_t err_stack, FILE *stream);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Walks the specified error stack, calling the specified function
+ *
+ * \estack_id{err_stack}
+ * \param[in] direction Direction in which the error stack is to be walked
+ * \param[in] func Function to be called for each error encountered
+ * \param[in] client_data Data to be passed to \p func
+ * \return \herr_t
+ *
+ * \details H5Ewalk2() walks the error stack specified by err_stack for the
+ *          current thread and calls the function specified in \p func for each
+ *          error along the way.
+ *
+ *          If the value of \p err_stack is #H5E_DEFAULT, then H5Ewalk2() walks
+ *          the current error stack.
+ *
+ *          \p direction specifies whether the stack is walked from the inside
+ *          out or the outside in. A value of #H5E_WALK_UPWARD means to begin
+ *          with the most specific error and end at the API; a value of
+ *          #H5E_WALK_DOWNWARD means to start at the API and end at the
+ *          innermost function where the error was first detected.
+ *
+ *          \p func, a function conforming to the #H5E_walk2_t prototype, will
+ *          be called for each error in the error stack. Its arguments will
+ *          include an index number \c n (beginning at zero regardless of stack
+ *          traversal direction), an error stack entry \c err_desc, and the \c
+ *          client_data pointer passed to H5Eprint(). The #H5E_walk2_t prototype
+ *          is as follows:
+ *          \snippet this H5E_walk2_t_snip
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Ewalk2(hid_t err_stack, H5E_direction_t direction, H5E_walk2_t func, void *client_data);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Returns the settings for the automatic error stack traversal
+ *        function and its data
+ *
+ * \estack_id
+ * \param[out] func The function currently set to be called upon an error condition
+ * \param[out] client_data Data currently set to be passed to the error function
+ * \return \herr_t
+ *
+ * \details H5Eget_auto2() returns the settings for the automatic error stack
+ *          traversal function, \p func, and its data, \p client_data, that are
+ *          associated with the error stack specified by \p estack_id.
+ *
+ *          Either or both of the \p func and \p client_data arguments may be
+ *          \c NULL, in which case the value is not returned.
+ *
+ *          The library initializes its default error stack traversal functions
+ *          to H5Eprint1() and H5Eprint2(). A call to H5Eget_auto2() returns
+ *          H5Eprint2() or the user-defined function passed in through
+ *          H5Eset_auto2(). A call to H5Eget_auto1() returns H5Eprint1() or the
+ *          user-defined function passed in through H5Eset_auto1(). However, if
+ *          the application passes in a user-defined function through
+ *          H5Eset_auto1(), it should call H5Eget_auto1() to query the traversal
+ *          function. If the application passes in a user-defined function
+ *          through H5Eset_auto2(), it should call H5Eget_auto2() to query the
+ *          traversal function.
+ *
+ *          Mixing the new style and the old style functions will cause a
+ *          failure. For example, if the application sets a user-defined
+ *          old-style traversal function through H5Eset_auto1(), a call to
+ *          H5Eget_auto2() will fail and will indicate that the application has
+ *          mixed H5Eset_auto1() and H5Eget_auto2(). On the other hand, mixing
+ *          H5Eset_auto2() and H5Eget_auto1() will also cause a failure. But if
+ *          the traversal functions are the library’s default H5Eprint1() or
+ *          H5Eprint2(), mixing H5Eset_auto1() and H5Eget_auto2() or mixing
+ *          H5Eset_auto2() and H5Eget_auto1() does not fail.
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Eget_auto2(hid_t estack_id, H5E_auto2_t *func, void **client_data);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Turns automatic error printing on or off
+ *
+ * \estack_id
+ * \param[in] func Function to be called upon an error condition
+ * \param[in] client_data Data passed to the error function
+ * \return \herr_t
+ *
+ * \details H5Eset_auto2() turns on or off automatic printing of errors for the
+ *          error stack specified with \p estack_id. An \p estack_id value of
+ *          #H5E_DEFAULT indicates the current stack.
+ *
+ *          When automatic printing is turned on, by the use of a non-null \p func
+ *          pointer, any API function which returns an error indication will
+ *          first call \p func, passing it \p client_data as an argument.
+ *
+ *          \p func, a function compliant with the #H5E_auto2_t prototype, is
+ *          defined in the H5Epublic.h source code file as:
+ *          \snippet this H5E_auto2_t_snip
+ *
+ *          When the library is first initialized, the auto printing function is
+ *          set to H5Eprint2() (cast appropriately) and \p client_data is the
+ *          standard error stream pointer, \c stderr.
+ *
+ *          Automatic stack traversal is always in the #H5E_WALK_DOWNWARD
+ *          direction.
+ *
+ *          Automatic error printing is turned off with a H5Eset_auto2() call
+ *          with a \c NULL \p func pointer.
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Eset_auto2(hid_t estack_id, H5E_auto2_t func, void *client_data);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Clears the specified error stack or the error stack for the current thread
+ *
+ * \estack_id{err_stack}
+ * \return \herr_t
+ *
+ * \details H5Eclear2() clears the error stack specified by \p err_stack, or, if
+ *          \p err_stack is set to #H5E_DEFAULT, the error stack for the current
+ *          thread.
+ *
+ *          \p err_stack is an error stack identifier, such as that returned by
+ *          H5Eget_current_stack().
+ *
+ *          The current error stack is also cleared whenever an API function is
+ *          called, with certain exceptions (for instance, H5Eprint1() or
+ *          H5Eprint2()).
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Eclear2(hid_t err_stack);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Determines the type of error stack
+ *
+ * \estack_id{err_stack}
+ * \param[out] is_stack A flag indicating which error stack \c typedef the
+ *                      specified error stack conforms to
+ *
+ * \return \herr_t
+ *
+ * \details H5Eauto_is_v2() determines whether the error auto reporting function
+ *          for an error stack conforms to the #H5E_auto2_t \c typedef or the
+ *          #H5E_auto1_t \c typedef.
+ *
+ *          The \p is_stack parameter is set to 1 if the error stack conforms to
+ *          #H5E_auto2_t and 0 if it conforms to #H5E_auto1_t.
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Eauto_is_v2(hid_t err_stack, unsigned *is_stack);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Retrieves an error message
+ *
+ * \param[in] msg_id Error message identifier
+ * \param[out] type The type of the error message Valid values are #H5E_MAJOR
+ *                  and #H5E_MINOR.
+ * \param[out] msg Error message buffer
+ * \param[in] size The length of error message to be returned by this function
+ * \return Returns the size of the error message in bytes on success; otherwise
+ *         returns a negative value.
+ *
+ * \details H5Eget_msg() retrieves the error message including its length and
+ *          type. The error message is specified by \p msg_id. The user is
+ *          responsible for passing in sufficient buffer space for the
+ *          message. If \p msg is not NULL and \p size is greater than zero, the
+ *          error message of \p size long is returned. The length of the message
+ *          is also returned. If NULL is passed in as \p msg, only the length
+ *          and type of the message is returned. If the return value is zero, it
+ *          means there is no message.
+ *
+ * \since 1.8.0
+ */
+H5_DLL ssize_t H5Eget_msg(hid_t msg_id, H5E_type_t *type, char *msg, size_t size);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Retrieves the number of error messages in an error stack
+ *
+ * \estack_id{error_stack_id}
+ * \return Returns a non-negative value on success; otherwise returns a negative value.
+ *
+ * \details H5Eget_num() retrieves the number of error records in the error
+ *          stack specified by \p error_stack_id (including major, minor
+ *          messages and description).
+ *
+ * \since 1.8.0
+ */
+H5_DLL ssize_t H5Eget_num(hid_t error_stack_id);
+
+/* Symbols defined for compatibility with previous versions of the HDF5 API.
+ *
+ * Use of these symbols is deprecated.
+ */
+#ifndef H5_NO_DEPRECATED_SYMBOLS
+
+/* Typedefs */
+
+/* Alias major & minor error types to hid_t's, for compatibility with new
+ *      error API in v1.8
+ */
+typedef hid_t H5E_major_t;
+typedef hid_t H5E_minor_t;
+
+/**
+ * Information about an error element of error stack.
+ */
+typedef struct H5E_error1_t {
+    H5E_major_t maj_num;   /**< major error number                 */
+    H5E_minor_t min_num;   /**< minor error number                 */
+    const char *func_name; /**< function in which error occurred   */
+    const char *file_name; /**< file in which error occurred       */
+    unsigned    line;      /**< line in file where error occurs    */
+    const char *desc;      /**< optional supplied description      */
+} H5E_error1_t;
+
+/* Error stack traversal callback function pointers */
+//! <!-- [H5E_walk1_t_snip] -->
+/**
+ * \brief Callback function for H5Ewalk1()
+ *
+ * \param[in] n Indexed error position in the stack
+ * \param[in] err_desc Pointer to a data structure describing the error
+ * \param[in] client_data Pointer to client data in the format expected by the
+ *                        user-defined function
+ * \return \herr_t
+ */
+typedef herr_t (*H5E_walk1_t)(int n, H5E_error1_t *err_desc, void *client_data);
+//! <!-- [H5E_walk1_t_snip] -->
+
+//! <!-- [H5E_auto1_t_snip] -->
+/**
+ * \brief Callback function for H5Eset_auto1()
+ *
+ * \param[in] client_data Pointer to client data in the format expected by the
+ *                        user-defined function
+ * \return \herr_t
+ */
+typedef herr_t (*H5E_auto1_t)(void *client_data);
+//! <!-- [H5E_auto1_t_snip] -->
+
+/* Function prototypes */
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Clears the error stack for the current thread
+ *
+ * \return \herr_t
+ *
+ * \deprecated 1.8.0 Function H5Eclear() renamed to H5Eclear1() and deprecated
+ *                   in this release.
+ *
+ * \details H5Eclear1() clears the error stack for the current thread.\n
+ *          The stack is also cleared whenever an API function is called, with
+ *          certain exceptions (for instance, H5Eprint1()).
+ *
+ */
+H5_DLL herr_t H5Eclear1(void);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Returns the current settings for the automatic error stack traversal
+ *        function and its data
+ *
+ * \param[out] func Current setting for the function to be called upon an error
+ *                  condition
+ * \param[out] client_data Current setting for the data passed to the error
+ *                         function
+ * \return \herr_t
+ *
+ * \deprecated 1.8.0 Function H5Eget_auto() renamed to H5Eget_auto1() and
+ *                   deprecated in this release.
+ *
+ * \details H5Eget_auto1() returns the current settings for the automatic error
+ *          stack traversal function, \p func, and its data,
+ *          \p client_data. Either or both arguments may be \c NULL, in which case the
+ *          value is not returned.
+ *
+ *          The library initializes its default error stack traversal functions
+ *          to H5Eprint1() and H5Eprint2(). A call to H5Eget_auto2() returns
+ *          H5Eprint2() or the user-defined function passed in through
+ *          H5Eset_auto2(). A call to H5Eget_auto1() returns H5Eprint1() or the
+ *          user-defined function passed in through H5Eset_auto1(). However, if
+ *          the application passes in a user-defined function through
+ *          H5Eset_auto1(), it should call H5Eget_auto1() to query the traversal
+ *          function. If the application passes in a user-defined function
+ *          through H5Eset_auto2(), it should call H5Eget_auto2() to query the
+ *          traversal function.
+ *
+ *          Mixing the new style and the old style functions will cause a
+ *          failure. For example, if the application sets a user-defined
+ *          old-style traversal function through H5Eset_auto1(), a call to
+ *          H5Eget_auto2() will fail and will indicate that the application has
+ *          mixed H5Eset_auto1() and H5Eget_auto2(). On the other hand, mixing
+ *          H5Eset_auto2() and H5Eget_auto1() will also cause a failure. But if
+ *          the traversal functions are the library’s default H5Eprint1() or
+ *          H5Eprint2(), mixing H5Eset_auto1() and H5Eget_auto2() or mixing
+ *          H5Eset_auto2() and H5Eget_auto1() does not fail.
+ *
+ */
+H5_DLL herr_t H5Eget_auto1(H5E_auto1_t *func, void **client_data);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Pushes a new error record onto the error stack
+ *
+ * \param[in] file Name of the file in which the error was detected
+ * \param[in] func Name of the function in which the error was detected
+ * \param[in] line Line number in the file where the error was detected
+ * \param[in] maj Major error identifier
+ * \param[in] min Minor error identifier
+ * \param[in] str Error description string
+ * \return \herr_t
+ *
+ * \deprecated 1.8.0 Function H5Epush() renamed to H5Epush1() and
+ *                   deprecated in this release.
+ *
+ * \details H5Epush1() pushes a new error record onto the error stack for the
+ *          current thread.\n
+ *          The error has major and minor numbers \p maj_num
+ *          and \p min_num, the function \p func where the error was detected, the
+ *          name of the file \p file where the error was detected, the line \p line
+ *          within that file, and an error description string \p str.\n
+ *          The function name, filename, and error description strings must be statically
+ *          allocated.
+ *
+ * \since 1.4.0
+ */
+H5_DLL herr_t H5Epush1(const char *file, const char *func, unsigned line, H5E_major_t maj, H5E_minor_t min,
+                       const char *str);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Prints the current error stack in a default manner
+ *
+ * \param[in] stream File pointer, or \c NULL for \c stderr
+ * \return \herr_t
+ *
+ * \deprecated 1.8.0 Function H5Eprint() renamed to H5Eprint1() and
+ *                   deprecated in this release.
+ *
+ * \details H5Eprint1() prints the error stack for the current thread
+ *          on the specified stream, \p stream. Even if the error stack is empty, a
+ *          one-line message of the following form will be printed:
+ *          \code{.unparsed}
+ *          HDF5-DIAG: Error detected in thread 0.
+ *          \endcode
+ *          H5Eprint1() is a convenience function for H5Ewalk1() with a function
+ *          that prints error messages. Users are encouraged to write their own
+ *          more specific error handlers.
+ *
+ */
+H5_DLL herr_t H5Eprint1(FILE *stream);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Turns automatic error printing on or off
+ *
+ * \param[in] func Function to be called upon an error condition
+ * \param[in] client_data Data passed to the error function
+ * \return \herr_t
+ *
+ * \deprecated 1.8.0 Function H5Eset_auto() renamed to H5Eset_auto1() and
+ *                   deprecated in this release.
+ *
+ * \details H5Eset_auto1() turns on or off automatic printing of errors. When
+ *          turned on (non-null \p func pointer), any API function which returns
+ *          an error indication will first call \p func, passing it \p
+ *          client_data as an argument.
+ *
+ *          \p func, a function conforming to the #H5E_auto1_t prototype, is
+ *          defined in the H5Epublic.h source code file as:
+ *          \snippet this H5E_auto1_t_snip
+ *
+ *          When the library is first initialized, the auto printing function is
+ *          set to H5Eprint1() (cast appropriately) and \p client_data is the
+ *          standard error stream pointer, \c stderr.
+ *
+ *          Automatic stack traversal is always in the #H5E_WALK_DOWNWARD
+ *          direction.
+ *
+ */
+H5_DLL herr_t H5Eset_auto1(H5E_auto1_t func, void *client_data);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Walks the current error stack, calling the specified function
+ *
+ * \param[in] direction Direction in which the error stack is to be walked
+ * \param[in] func Function to be called for each error encountered
+ * \param[in] client_data Data to be passed to \p func
+ * \return \herr_t
+ *
+ * \deprecated 1.8.0 Function H5Ewalk() renamed to H5Ewalk1() and
+ *                   deprecated in this release.
+ *
+ * \details H5Ewalk1() walks the error stack for the current thread and calls
+ *          the function specified in \p func for each error along the way.
+ *
+ *          \p direction specifies whether the stack is walked from the inside
+ *          out or the outside in. A value of #H5E_WALK_UPWARD means to begin
+ *          with the most specific error and end at the API; a value of
+ *          #H5E_WALK_DOWNWARD means to start at the API and end at the
+ *          innermost function where the error was first detected.
+ *
+ *          \p func, a function conforming to the #H5E_walk1_t prototype, will
+ *          be called for each error in the error stack. Its arguments will
+ *          include an index number \c n (beginning at zero regardless of stack
+ *          traversal direction), an error stack entry \c err_desc, and the \c
+ *          client_data pointer passed to H5Eprint(). The #H5E_walk1_t prototype
+ *          is as follows:
+ *          \snippet this H5E_walk1_t_snip
+ *
+ */
+H5_DLL herr_t H5Ewalk1(H5E_direction_t direction, H5E_walk1_t func, void *client_data);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Returns a character string describing an error specified by a major
+ *        error number
+ *
+ * \param[in] maj Major error number
+ * \return \herr_t
+ *
+ * \deprecated 1.8.0 Function deprecated in this release.
+ *
+ * \details H5Eget_major() returns a constant
+ *          character string that describes the error, given a major error number.
+ *
+ * \attention This function returns a dynamically allocated string (\c char
+ *            array). An application calling this function must free the memory
+ *            associated with the return value to prevent a memory leak.
+ *
+ */
+H5_DLL char *H5Eget_major(H5E_major_t maj);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5E
+ *
+ * \brief Returns a character string describing an error specified by a minor
+ *        error number
+ *
+ * \param[in] min Minor error number
+ * \return \herr_t
+ *
+ * \deprecated 1.8.0 Function deprecated and return type changed in this release.
+ *
+ * \details H5Eget_minor() returns a constant
+ *          character string that describes the error, given a minor error number.
+ *
+ * \attention In the Release 1.8.x series, H5Eget_minor() returns a string of
+ *            dynamic allocated \c char array. An application calling this
+ *            function from an HDF5 library of Release 1.8.0 or later must free
+ *            the memory associated with the return value to prevent a memory
+ *            leak. This is a change from the 1.6.x release series.
+ *
+ */
+H5_DLL char *H5Eget_minor(H5E_minor_t min);
+#endif /* H5_NO_DEPRECATED_SYMBOLS */
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* end H5Epublic_H */