Cloned SEACAS for EXODUS library with extra build files for internal package management.
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// Copyright(C) 1999-2023 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
#include "EJ_SystemInterface.h"
#include "EJ_Version.h" // for qainfo
#include "EJ_vector3d.h" // for vector3d
#include <SL_tokenize.h> // for tokenize
#include <algorithm> // for sort, find, transform
#include <cctype> // for tolower
#include <copyright.h>
#include <cstddef> // for size_t
#include <cstdlib> // for exit, strtod, strtoul, abs, etc
#include <cstring> // for strchr, strlen
#include <fmt/format.h>
#include <iosfwd> // for ostream
#include <utility> // for pair, make_pair
#include <vector> // for vector
namespace {
bool str_equal(const std::string &s1, const std::string &s2)
{
return (s1.size() == s2.size()) &&
std::equal(s1.begin(), s1.end(), s2.begin(),
[](char a, char b) { return std::tolower(a) == std::tolower(b); });
}
void parse_variable_names(const char *tokens, StringIdVector *variable_list);
void parse_variable_names(const char *tokens, StringIdVector *variable_list);
void parse_offset(const char *tokens, vector3d *offset);
void parse_integer_list(const char *tokens, std::vector<int> *list);
void parse_part_list(const char *tokens, std::vector<int> *list);
void parse_omissions(const char *tokens, Omissions *omissions, const std::string &basename,
bool require_ids);
} // namespace
SystemInterface::SystemInterface()
{
offset_.x = 0.0;
offset_.y = 0.0;
offset_.z = 0.0;
enroll_options();
}
SystemInterface::~SystemInterface() = default;
void SystemInterface::enroll_options()
{
options_.usage("[options] list_of_files_to_join");
options_.enroll("help", GetLongOption::NoValue, "Print this summary and exit", nullptr);
options_.enroll("version", GetLongOption::NoValue, "Print version and exit", nullptr);
options_.enroll("output", GetLongOption::MandatoryValue, "Name of output file to create",
"ejoin-out.e", nullptr, true);
options_.enroll(
"extract_blocks", GetLongOption::MandatoryValue,
"Use only the specified part/block pairs. The specification is\n"
"\t\tp#:block_id1:block_id2,p#:block_id1. For example, to\n"
"\t\tExtract block ids 1,3,4 from part 1; blocks 2 3 4 from part 2;\n"
"\t\tand block 8 from part5, specify\n"
"\t\t\t '-extract_blocks p1:1:3:4,p2:2:3:4,p5:8'\n"
"\t\tIf an extract is specified, then only that id(s) will be used for that part.",
nullptr);
options_.enroll("omit_blocks", GetLongOption::MandatoryValue,
"Omit the specified part/block pairs. The specification is\n"
"\t\tp#:block_id1:block_id2,p#:block_id1. For example, to\n"
"\t\tOmit block id 1,3,4 from part 1; block 2 3 4 from part 2;\n"
"\t\tand block 8 from part5, specify\n"
"\t\t\t '-omit_blocks p1:1:3:4,p2:2:3:4,p5:8'",
nullptr);
options_.enroll("omit_assemblies", GetLongOption::MandatoryValue,
"If no value, then don't transfer any assemblies to output file.\n"
"\t\tIf just p#,p#,... specified, then omit assemblies on specified parts\n"
"\t\tIf p#:id1:id2,p#:id2,id4... then omit the assemblies with the specified\n"
"\t\tid in the specified parts.",
nullptr, "ALL");
options_.enroll(
"omit_part_assemblies", GetLongOption::NoValue,
"Do not create an assembly for each input part containing the blocks in that part.\n"
"\t\tDefault is to create the part assemblies.",
nullptr);
options_.enroll("omit_nodesets", GetLongOption::OptionalValue,
"If no value, then don't transfer any nodesets to output file.\n"
"\t\tIf just p#,p#,... specified, then omit sets on specified parts\n"
"\t\tIf p#:id1:id2,p#:id2,id4... then omit the sets with the specified\n"
"\t\tid in the specified parts.",
nullptr, "ALL");
options_.enroll("omit_sidesets", GetLongOption::OptionalValue,
"If no value, then don't transfer any sidesets to output file.\n"
"\t\tIf just p#,p#,... specified, then omit sets on specified parts\n"
"\t\tIf p#:id1:id2,p#:id2,id4... then omit the sets with the specified\n"
"\t\tid in the specified parts.",
nullptr, "ALL");
options_.enroll("convert_nodal_to_nodesets", GetLongOption::MandatoryValue,
"For each part listed (or ALL),\n"
"\t\tcreate a nodeset containing the nodes of that part\n"
"\t\tand output the nodal fields as nodeset fields instead of nodal fields.\n"
"\t\tFormat is comma-separated list of parts (1-based), or ALL",
nullptr, nullptr, true);
options_.enroll("match_node_ids", GetLongOption::NoValue,
"Combine nodes if their global ids match.", nullptr);
options_.enroll("match_node_coordinates", GetLongOption::NoValue,
"Combine nodes if they are within tolerance distance of each other.", nullptr);
#if 0
options_.enroll("match_elem_ids", GetLongOption::NoValue,
"Combine elements if their global ids match and they are compatible.\n"
"\t\tCompatible = same element type, nodes of the two elements match",
nullptr);
options_.enroll("match_element_coordinates", GetLongOption::NoValue,
"Combine elements if their centroids are within tolerance distance\n"
"\t\tand they are compatible (same element type, nodes match).",
nullptr);
#endif
options_.enroll("tolerance", GetLongOption::MandatoryValue,
"Maximum distance between two nodes to be considered colocated.", nullptr,
nullptr, true);
options_.enroll(
"block_prefix", GetLongOption::MandatoryValue,
"Prefix used on the input block names of second and subsequent meshes to make them\n"
"\t\tunique. Default is 'p'. Example: block1, p2_block1, p3_block1.",
"p");
options_.enroll("offset", GetLongOption::MandatoryValue,
"Comma-separated x,y,z offset for coordinates of second and subsequent meshes.\n"
"\t\tThe offset will be multiplied by the part number-1 so:\n"
"\t\tP1: no offset; P2: 1x, 1y, 1z; P3: 2x, 2y, 2z; P(n+1): nx, ny, nz",
nullptr, nullptr, true);
options_.enroll("steps", GetLongOption::MandatoryValue,
"Specify subset of timesteps to transfer to output file.\n"
"\t\tFormat is beg:end:step. 1:10:2 --> 1,3,5,7,9\n"
"\t\tTo only transfer last step, use '-steps LAST'",
"1:");
options_.enroll("gvar", GetLongOption::MandatoryValue,
"Comma-separated list of global variables to be joined or ALL or NONE.", nullptr);
options_.enroll("evar", GetLongOption::MandatoryValue,
"Comma-separated list of element variables to be joined or ALL or NONE.\n"
"\t\tVariables can be limited to certain blocks by appending a\n"
"\t\tcolon followed by the block id. E.g. -evar sigxx:10:20",
nullptr);
options_.enroll("nvar", GetLongOption::MandatoryValue,
"Comma-separated list of nodal variables to be joined or ALL or NONE.", nullptr);
options_.enroll("nsetvar", GetLongOption::MandatoryValue,
"Comma-separated list of nodeset variables to be joined or ALL or NONE.\n"
"\t\tVariables can be limited to certain sets by appending a\n"
"\t\tcolon followed by the nodeset id. E.g. -nsetvar sigxx:10:20",
nullptr);
options_.enroll("ssetvar", GetLongOption::MandatoryValue,
"Comma-separated list of sideset variables to be joined or ALL or NONE.\n"
"\t\tVariables can be limited to certain sidesets by appending a\n"
"\t\tcolon followed by the sideset id. E.g. -ssetvar sigxx:10:20",
nullptr);
options_.enroll(
"info_records", GetLongOption::OptionalValue,
"If no value specified or not present,\n"
"\t\tthen don't transfer any information records to output file.\n"
"\t\tIf 'p#,p#,...' specified, then only transfer information records on specified parts\n"
"\t\tIf 'all' specified, then transfer all information records",
nullptr, "NONE");
options_.enroll("ignore_element_ids", GetLongOption::NoValue,
"Ignore the element id maps on the input database and just use a 1..#elements id "
"map on output.\n"
"\t\tMuch faster for large models if do not need specific element global ids",
nullptr, nullptr, true);
options_.enroll("netcdf4", GetLongOption::NoValue,
"Create output database using the HDF5-based "
"netcdf which allows for up to 2.1 GB "
"nodes and elements",
nullptr);
options_.enroll("64-bit", GetLongOption::NoValue,
"True if forcing the use of 64-bit integers for the output file", nullptr);
options_.enroll(
"zlib", GetLongOption::NoValue,
"Use the Zlib / libz compression method if compression is enabled (default) [exodus only].",
nullptr);
options_.enroll("szip", GetLongOption::NoValue,
"Use SZip compression. [exodus only, enables netcdf-4]", nullptr);
options_.enroll(
"compress", GetLongOption::MandatoryValue,
"Specify the hdf5 (netcdf4) compression level [0..9] to be used on the output file.",
nullptr);
options_.enroll("disable_field_recognition", GetLongOption::NoValue,
"Do not try to combine scalar fields into higher-order fields such as\n"
"\t\tvectors or tensors based on the field suffix",
nullptr);
options_.enroll("copyright", GetLongOption::NoValue, "Show copyright and license data.", nullptr);
}
bool SystemInterface::parse_options(int argc, char **argv)
{
int option_index = options_.parse(argc, argv);
if (option_index < 1) {
return false;
}
if (options_.retrieve("help") != nullptr) {
options_.usage();
fmt::print(
stderr,
"\n\tCan also set options via EJOIN_OPTIONS environment variable.\n"
"\n\tDocumentation: https://sandialabs.github.io/seacas-docs/sphinx/html/index.html#ejoin\n"
"\n\t->->-> Send email to gdsjaar@sandia.gov for ejoin support.<-<-<-\n");
exit(EXIT_SUCCESS);
}
if (options_.retrieve("version") != nullptr) {
// Version is printed up front, just exit...
exit(0);
}
if (options_.retrieve("copyright") != nullptr) {
fmt::print("{}", copyright("2010-2021"));
exit(EXIT_SUCCESS);
}
// Parse remaining options as directory paths.
// Note that inputFiles_.size() is the number of parts which can be used in
// parsing of other options...
if (option_index < argc) {
while (option_index < argc) {
inputFiles_.emplace_back(argv[option_index++]);
}
}
else {
fmt::print(stderr, "\nERROR: no files specified\n\n");
return false;
}
size_t part_count = inputFiles_.size();
blockOmissions_.resize(part_count);
blockInclusions_.resize(part_count);
nsetOmissions_.resize(part_count);
ssetOmissions_.resize(part_count);
assemblyOmissions_.resize(part_count);
// Get options from environment variable also...
char *options = getenv("EJOIN_OPTIONS");
if (options != nullptr) {
fmt::print(
stderr,
"\nThe following options were specified via the EJOIN_OPTIONS environment variable:\n"
"\t{}\n\n",
options);
options_.parse(options, options_.basename(*argv));
}
outputName_ = options_.get_option_value("output", outputName_);
blockPrefix_ = options_.get_option_value("block_prefix", blockPrefix_);
{
const char *temp = options_.retrieve("offset");
if (temp != nullptr) {
parse_offset(temp, &offset_);
}
}
tolerance_ = options_.get_option_value("tolerance", tolerance_);
{
const char *temp = options_.retrieve("steps");
if (temp != nullptr) {
parse_step_option(temp);
}
}
{
const char *temp = options_.retrieve("convert_nodal_to_nodesets");
if (temp != nullptr) {
parse_integer_list(temp, &nodesetConvertParts_);
std::sort(nodesetConvertParts_.begin(), nodesetConvertParts_.end());
}
}
{
const char *temp = options_.retrieve("info_records");
if (temp != nullptr) {
parse_part_list(temp, &infoRecordParts_);
std::sort(infoRecordParts_.begin(), infoRecordParts_.end());
}
}
{
const char *temp = options_.retrieve("omit_blocks");
if (temp != nullptr) {
parse_omissions(temp, &blockOmissions_, "block", true);
}
}
{
const char *temp = options_.retrieve("omit_assemblies");
if (temp != nullptr) {
parse_omissions(temp, &assemblyOmissions_, "assembly", true);
}
}
if (options_.retrieve("omit_part_assemblies") != nullptr) {
createAssemblies_ = false;
}
{
const char *temp = options_.retrieve("extract_blocks");
if (temp != nullptr) {
parse_omissions(temp, &blockInclusions_, "block", true);
}
}
{
const char *temp = options_.retrieve("omit_nodesets");
if (temp != nullptr) {
if (str_equal("ALL", temp)) {
omitNodesets_ = true;
}
else {
parse_omissions(temp, &nsetOmissions_, "nodelist", false);
}
}
else {
omitNodesets_ = false;
}
}
{
const char *temp = options_.retrieve("omit_sidesets");
if (temp != nullptr) {
if (str_equal("ALL", temp)) {
omitSidesets_ = true;
}
else {
parse_omissions(temp, &ssetOmissions_, "surface", false);
}
}
else {
omitSidesets_ = false;
}
}
{
const char *temp = options_.retrieve("gvar");
if (temp != nullptr) {
parse_variable_names(temp, &globalVarNames_);
}
}
{
const char *temp = options_.retrieve("nvar");
if (temp != nullptr) {
parse_variable_names(temp, &nodeVarNames_);
}
}
{
const char *temp = options_.retrieve("evar");
if (temp != nullptr) {
parse_variable_names(temp, &elemVarNames_);
}
}
{
const char *temp = options_.retrieve("nsetvar");
if (temp != nullptr) {
parse_variable_names(temp, &nsetVarNames_);
}
}
{
const char *temp = options_.retrieve("ssetvar");
if (temp != nullptr) {
parse_variable_names(temp, &ssetVarNames_);
}
}
disableFieldRecognition_ = options_.retrieve("disable_field_recognition") != nullptr;
useNetcdf4_ = options_.retrieve("netcdf4") != nullptr;
ignoreElementIds_ = options_.retrieve("ignore_element_ids") != nullptr;
if (options_.retrieve("64-bit") != nullptr) {
ints64bit_ = true;
}
if (options_.retrieve("szip") != nullptr) {
szip_ = true;
zlib_ = false;
}
zlib_ = (options_.retrieve("zlib") != nullptr);
if (szip_ && zlib_) {
fmt::print(stderr, "ERROR: Only one of 'szip' or 'zlib' can be specified.\n");
}
compressionLevel_ = options_.get_option_value("compress", compressionLevel_);
if (options_.retrieve("match_node_ids") != nullptr) {
matchNodeIds_ = true;
matchNodeXYZ_ = false;
}
else {
matchNodeIds_ = false;
}
if (options_.retrieve("match_node_coordinates") != nullptr) {
matchNodeXYZ_ = true;
matchNodeIds_ = false;
}
else {
matchNodeXYZ_ = false;
}
#if 0
if (options_.retrieve("match_elem_ids")) {
matchElemIds_ = true;
matchElemXYZ_ = false;
} else {
matchElemIds_ = false;
}
if (options_.retrieve("match_elem_coordinates")) {
matchElemXYZ_ = true;
matchElemIds_ = false;
} else {
matchElemXYZ_ = false;
}
#endif
return true;
}
bool SystemInterface::convert_nodes_to_nodesets(int part_number) const
{
if (nodesetConvertParts_.empty()) {
return false;
}
if (nodesetConvertParts_[0] == 0) {
return true;
}
else {
return std::find(nodesetConvertParts_.cbegin(), nodesetConvertParts_.cend(), part_number) !=
nodesetConvertParts_.cend();
}
}
void SystemInterface::parse_step_option(const char *tokens)
{
//: The defined formats for the count attribute are:<br>
//: <ul>
//: <li><missing> -- default -- 1 <= count <= oo (all steps)</li>
//: <li>"X" -- X <= count <= X (just step X). If X == LAST, last step
// only</li>
//: <li>"X:Y" -- X to Y by 1</li>
//: <li>"X:" -- X to oo by 1</li>
//: <li>":Y" -- 1 to Y by 1</li>
//: <li>"::Z" -- 1 to oo by Z</li>
//: <li>"LAST" -- last step only</li>
//: </ul>
//: The count and step must always be >= 0
// Break into tokens separated by ":"
// Default is given in constructor above...
if (tokens != nullptr) {
if (strchr(tokens, ':') != nullptr) {
// The string contains a separator
std::array<int, 3> vals{stepMin_, stepMax_, stepInterval_};
int j = 0;
for (auto &val : vals) {
// Parse 'i'th field
char tmp_str[128];
int k = 0;
while (tokens[j] != '\0' && tokens[j] != ':') {
tmp_str[k++] = tokens[j++];
}
tmp_str[k] = '\0';
if (strlen(tmp_str) > 0) {
val = strtoul(tmp_str, nullptr, 0);
}
if (tokens[j++] == '\0') {
break; // Reached end of string
}
}
stepMin_ = abs(vals[0]);
stepMax_ = abs(vals[1]);
stepInterval_ = abs(vals[2]);
}
else if (str_equal("LAST", tokens)) {
stepMin_ = stepMax_ = -1;
}
else {
// Does not contain a separator, min == max
stepMin_ = stepMax_ = strtol(tokens, nullptr, 0);
}
}
}
void SystemInterface::show_version()
{
fmt::print("EJoin\n"
"\t(A code for merging Exodus databases; with or without results data.)\n"
"\t(Version: {}) Modified: {}\n",
qainfo[2], qainfo[1]);
}
namespace {
std::string LowerCase(const std::string &name)
{
std::string s = name;
std::transform(s.begin(), s.end(), // source
s.begin(), // destination
::tolower); // operation
return s;
}
using StringVector = std::vector<std::string>;
void parse_variable_names(const char *tokens, StringIdVector *variable_list)
{
// Break into tokens separated by ","
if (tokens != nullptr) {
std::string token_string(tokens);
StringVector var_list = SLIB::tokenize(token_string, ",");
// At this point, var_list is either a single string, or a string
// separated from 1 or more block ids with ":" delimiter.
// For example, sigxx:1:10:100 would indicate that the variable
// "sigxx" should be written only for blocks with id 1, 10, and
// 100. "sigxx" would indicate that the variable should be
// written for all blocks.
auto I = var_list.begin();
while (I != var_list.end()) {
StringVector name_id = SLIB::tokenize(*I, ":");
std::string var_name = LowerCase(name_id[0]);
if (name_id.size() == 1) {
(*variable_list).emplace_back(var_name, 0);
}
else {
for (size_t i = 1; i < name_id.size(); i++) {
// Convert string to integer...
int id = std::stoi(name_id[i]);
(*variable_list).emplace_back(var_name, id);
}
}
++I;
}
// Sort the list...
std::sort(
variable_list->begin(), variable_list->end(),
[](const std::pair<std::string, size_t> &t1, const std::pair<std::string, size_t> &t2) {
return t1.first < t2.first || (!(t2.first < t1.first) && t1.second < t2.second);
});
}
}
void parse_offset(const char *tokens, vector3d *offset)
{
// Break into tokens separated by ","
if (tokens != nullptr) {
std::string token_string(tokens);
StringVector var_list = SLIB::tokenize(token_string, ",");
// At this point, var_list should contain 1,2,or 3 strings
// corresponding to the x, y, and z coordinate offsets.
if (var_list.size() != 3) {
fmt::print(stderr,
"ERROR: Incorrect number of offset components specified--3 required.\n\n");
offset->x = offset->y = offset->z = 0.0;
return;
}
std::string offx = var_list[0];
std::string offy = var_list[1];
std::string offz = var_list[2];
double x = std::stod(offx);
double y = std::stod(offy);
double z = std::stod(offz);
offset->x = x;
offset->y = y;
offset->z = z;
}
}
void parse_integer_list(const char *tokens, std::vector<int> *list)
{
// Break into tokens separated by ","
if (tokens != nullptr) {
if (LowerCase(tokens) == "all") {
(*list).push_back(0);
return;
}
std::string token_string(tokens);
StringVector part_list = SLIB::tokenize(token_string, ",");
auto I = part_list.begin();
while (I != part_list.end()) {
int id = std::stoi(*I);
(*list).push_back(id);
++I;
}
}
}
void parse_part_list(const char *tokens, std::vector<int> *list)
{
// Break into tokens separated by ","
// Tokens will be of the form "p$" or "all"
if (tokens != nullptr) {
if (LowerCase(tokens) == "all") {
(*list).push_back(0);
return;
}
std::string token_string(tokens);
StringVector part_list = SLIB::tokenize(token_string, ",");
auto I = part_list.begin();
while (I != part_list.end()) {
std::string part = *I;
if (part[0] == 'p' || part[0] == 'P') {
std::string part_id(part, 1);
int part_num = std::stoi(part_id);
list->push_back(part_num);
}
else {
fmt::print(stderr,
"ERROR: Bad syntax ({}) specifying part number. Use 'p'+ part_number\n"
" For example -info_records p1,p2,p7\n",
part);
exit(EXIT_FAILURE);
}
++I;
}
}
}
void parse_omissions(const char *tokens, Omissions *omissions, const std::string &basename,
bool require_ids)
{
// to Omit block id 1,3,4 from part 1; block 2 3 4 from part 2;
// and block 8 from part5, specify
// '-omit_blocks p1:1:3:4,p2:2:3:4,p5:8'
// Break into tokens separated by "," Each token will then be a
// ":" separated list of blocks to be omitted for the specified
// part.
// If "require_ids" is true, then there must be at least one id
// following the part specification. If false, then it is OK to
// just specify a part number and all entities (typically nset or
// sset) will be omitted on that part.
if (tokens == nullptr) {
return;
}
std::string token_string(tokens);
StringVector part_block_list = SLIB::tokenize(token_string, ",");
// Now, for each token in 'part_block_list', split by ":"
// The result should be a string starting with 'p' followed by an
// integer indicating the part followed by 1 or more strings which
// are the block ids of the blocks to be omitted for that part.
//
// Parts are 1-based. Store the results in the 'omissions' set as
// the pair (part#, block_id).
auto I = part_block_list.begin();
while (I != part_block_list.end()) {
StringVector part_block = SLIB::tokenize(*I, ":");
if (part_block.empty() || (part_block[0][0] != 'p' && part_block[0][0] != 'P')) {
fmt::print(stderr, "ERROR: Bad syntax specifying the part number. Use 'p' + part number\n"
" For example -omit_blocks p1:1:2:3,p2:2:3:4\n");
exit(EXIT_FAILURE);
}
if (require_ids && part_block.size() == 1) {
fmt::print(stderr,
"ERROR: No block ids were found following the part specification.\n"
" for part {}\n",
part_block[0]);
exit(EXIT_FAILURE);
}
// Extract the part number...
std::string part(part_block[0], 1);
int part_num = std::stoi(part) - 1;
// If no blocks specified for a part, then omit all entities for
// this part. Since don't know how many entities there are,
// store the id as '0' to signify all.
if (part_block.size() == 1) {
(*omissions)[part_num].emplace_back("ALL");
}
else {
// Get the list of blocks to omit for this part...
auto J = part_block.begin();
++J; // Skip p#
while (J != part_block.end()) {
std::string block = *J;
std::string name = basename + '_' + block;
(*omissions)[part_num].push_back(name);
++J;
}
}
++I;
}
}
} // namespace