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abaqus_io.C
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abaqus_io.C
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// The libMesh Finite Element Library.
// Copyright (C) 2002-2024 Benjamin S. Kirk, John W. Peterson, Roy H. Stogner
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
// Local includes
#include "libmesh/abaqus_io.h"
#include "libmesh/point.h"
#include "libmesh/elem.h"
#include "libmesh/enum_to_string.h"
#include "libmesh/boundary_info.h"
#include "libmesh/utility.h"
// gzstream for reading compressed files as a stream
#ifdef LIBMESH_HAVE_GZSTREAM
# include "libmesh/ignore_warnings.h" // shadowing in gzstream.h
# include "gzstream.h"
# include "libmesh/restore_warnings.h"
#endif
// C++ includes
#include <unordered_map>
#include <string>
#include <cstdlib> // std::strtol
#include <sstream>
#include <cctype> // isspace
// Anonymous namespace to hold mapping Data for Abaqus/libMesh element types
namespace
{
using namespace libMesh;
/**
* Data structure used for mapping Abaqus IDs to libMesh IDs, and
* eventually (possibly) vice-versa.
*/
struct ElementDefinition
{
// Maps (zero-based!) Abaqus local node numbers to libmesh local node numbers
std::vector<unsigned> abaqus_zero_based_node_id_to_libmesh_node_id;
// Maps (zero-based!) Abaqus side numbers to libmesh side numbers
std::vector<unsigned short> abaqus_zero_based_side_id_to_libmesh_side_id;
};
/**
* Locally-available map containing all element data.
*/
std::map<ElemType, ElementDefinition> eletypes;
/**
* Helper function to fill up eletypes map
*/
void add_eletype_entry(ElemType libmesh_elem_type,
const unsigned * node_map,
unsigned node_map_size,
const unsigned short * side_map,
unsigned side_map_size)
{
// If map entry does not exist, this will create it
ElementDefinition & map_entry = eletypes[libmesh_elem_type];
// Use the "swap trick" from Scott Meyer's "Effective STL" to swap
// an unnamed temporary vector into the map_entry's vector. Note:
// the vector(iter, iter) constructor is used.
std::vector<unsigned>
(node_map, node_map+node_map_size).swap
(map_entry.abaqus_zero_based_node_id_to_libmesh_node_id);
std::vector<unsigned short>
(side_map, side_map+side_map_size).swap
(map_entry.abaqus_zero_based_side_id_to_libmesh_side_id);
}
/**
* Helper function to initialize the eletypes map.
*/
void init_eletypes ()
{
// This should happen only once. The first time this method is
// called the eletypes data structure will be empty, and we will
// fill it. Any subsequent calls will find an initialized
// eletypes map and will do nothing.
if (eletypes.empty())
{
{
// NODEELEM
const unsigned int node_map[] = {0}; // identity
const unsigned short side_map[] = {0}; // identity
add_eletype_entry(NODEELEM, node_map, 1, side_map, 1);
}
{
// EDGE2
const unsigned int node_map[] = {0,1}; // identity
const unsigned short side_map[] = {0,1}; // identity
add_eletype_entry(EDGE2, node_map, 2, side_map, 2);
}
{
// TRI3
const unsigned int node_map[] = {0,1,2}; // identity
const unsigned short side_map[] = {0,1,2}; // identity
add_eletype_entry(TRI3, node_map, 3, side_map, 3);
}
{
// TRI6
const unsigned int node_map[] = {0,1,2,3,4,5}; // identity
const unsigned short side_map[] = {0,1,2}; // identity
add_eletype_entry(TRI6, node_map, 6, side_map, 3);
}
{
// QUAD4
const unsigned int node_map[] = {0,1,2,3}; // identity
const unsigned short side_map[] = {0,1,2,3}; // identity
add_eletype_entry(QUAD4, node_map, 4, side_map, 4);
}
{
// QUAD8
const unsigned int node_map[] = {0,1,2,3,4,5,6,7}; // identity
const unsigned short side_map[] = {0,1,2,3}; // identity
add_eletype_entry(QUAD8, node_map, 8, side_map, 4);
}
{
// TET4
const unsigned int node_map[] = {0,1,2,3}; // identity
const unsigned short side_map[] = {0,1,2,3}; // identity
add_eletype_entry(TET4, node_map, 4, side_map, 4);
}
{
// TET10
const unsigned int node_map[] = {0,1,2,3,4,5,6,7,8,9}; // identity
const unsigned short side_map[] = {0,1,2,3}; // identity
add_eletype_entry(TET10, node_map, 10, side_map, 4);
}
{
// HEX8
const unsigned int node_map[] = {0,1,2,3,4,5,6,7}; // identity
const unsigned short side_map[] = {0,5,1,2,3,4}; // inverse = 0,2,3,4,5,1
add_eletype_entry(HEX8, node_map, 8, side_map, 6);
}
{
// HEX20
const unsigned int node_map[] = // map is its own inverse
{0,1,2,3,4,5,6,7,8,9,10,11,16,17,18,19,12,13,14,15};
const unsigned short side_map[] = // inverse = 0,2,3,4,5,1
{0,5,1,2,3,4};
add_eletype_entry(HEX20, node_map, 20, side_map, 6);
}
{
// HEX27
const unsigned int node_map[] = // inverse = ...,21,23,24,25,26,22,20
{0,1,2,3,4,5,6,7,8,9,10,11,16,17,18,19,12,13,14,15,26,20,25,21,22,23,24};
const unsigned short side_map[] = // inverse = 0,2,3,4,5,1
{0,5,1,2,3,4};
add_eletype_entry(HEX27, node_map, 27, side_map, 6);
}
{
// PRISM6
const unsigned int node_map[] = {0,1,2,3,4,5}; // identity
const unsigned short side_map[] = {0,4,1,2,3}; // inverse = 0,2,3,4,1
add_eletype_entry(PRISM6, node_map, 6, side_map, 5);
}
{
// PRISM15
const unsigned int node_map[] = // map is its own inverse
{0,1,2,3,4,5,6,7,8,12,13,14,9,10,11};
const unsigned short side_map[] = // inverse = 0,2,3,4,1
{0,4,1,2,3};
add_eletype_entry(PRISM15, node_map, 15, side_map, 5);
}
{
// PRISM18
const unsigned int node_map[] = // map is its own inverse
{0,1,2,3,4,5,6,7,8,12,13,14,9,10,11,15,16,17};
const unsigned short side_map[] = // inverse = 0,2,3,4,1
{0,4,1,2,3};
add_eletype_entry(PRISM18, node_map, 18, side_map, 5);
}
} // if (eletypes.empty())
}
} // anonymous namespace
namespace libMesh
{
AbaqusIO::AbaqusIO (MeshBase & mesh_in) :
MeshInput<MeshBase> (mesh_in),
build_sidesets_from_nodesets(false),
_already_seen_part(false)
{
}
AbaqusIO::~AbaqusIO () = default;
void AbaqusIO::read (const std::string & fname)
{
// Get a reference to the mesh we are reading
MeshBase & the_mesh = MeshInput<MeshBase>::mesh();
// Clear any existing mesh data
the_mesh.clear();
// Open stream for reading
const bool gzipped_file = (fname.rfind(".gz") == fname.size() - 3);
if (gzipped_file)
{
#ifdef LIBMESH_HAVE_GZSTREAM
auto inf = std::make_unique<igzstream>();
libmesh_assert(inf);
inf->open(fname.c_str(), std::ios::in);
_in = std::move(inf); // class takes ownership as base class pointer
#else
libmesh_error_msg("ERROR: need gzstream to handle .gz files!!!");
#endif
}
else
{
auto inf = std::make_unique<std::ifstream>();
libmesh_assert(inf);
std::string new_name = Utility::unzip_file(fname);
inf->open(new_name.c_str(), std::ios::in);
libmesh_assert(inf->good());
_in = std::move(inf); // class takes ownership as base class pointer
}
// Initialize the elems_of_dimension array. We will use this in a
// "1-based" manner so that elems_of_dimension[d]==true means
// elements of dimension d have been seen.
elems_of_dimension.resize(4, false);
// Read file line-by-line... this is based on a set of different
// test input files. I have not looked at the full input file
// specs for Abaqus.
std::string s;
while (true)
{
// Try to read something. This may set EOF!
std::getline(*_in, s);
if (*_in)
{
// Process s...
//
// There are many sections in Abaqus files, we read some
// but others are just ignored... Some sections may occur
// more than once. For example for a hybrid grid, you
// will have multiple *Element sections...
// Some Abaqus files use all upper-case for section names,
// so we will just convert s to uppercase
std::string upper(s);
std::transform(upper.begin(), upper.end(), upper.begin(), ::toupper);
// 0.) Look for the "*Part" section
if (upper.find("*PART") == static_cast<std::string::size_type>(0))
{
libmesh_error_msg_if
(_already_seen_part,
"We currently don't support reading Abaqus files with multiple PART sections");
_already_seen_part = true;
}
// 1.) Look for the "*Nodes" section
if (upper.find("*NODE") == static_cast<std::string::size_type>(0))
{
// Some sections that begin with *NODE are actually
// "*NODE OUTPUT" sections which we want to skip. I
// have only seen this with a single space, but it would
// probably be more robust to remove whitespace before
// making this check.
if (upper.find("*NODE OUTPUT") == static_cast<std::string::size_type>(0))
continue;
// Some *Node sections also specify an Nset name on the same line.
// Look for one here.
std::string nset_name = this->parse_label(s, "nset");
// Process any lines of comments that may be present
this->process_and_discard_comments();
// Read a block of nodes
this->read_nodes(nset_name);
}
// 2.) Look for the "*Element" section
else if (upper.find("*ELEMENT,") == static_cast<std::string::size_type>(0))
{
// Some sections that begin with *ELEMENT are actually
// "*ELEMENT OUTPUT" sections which we want to skip. I
// have only seen this with a single space, but it would
// probably be more robust to remove whitespace before
// making this check.
if (upper.find("*ELEMENT OUTPUT") == static_cast<std::string::size_type>(0))
continue;
// Some *Element sections also specify an Elset name on the same line.
// Look for one here.
std::string elset_name = this->parse_label(s, "elset");
// Process any lines of comments that may be present
this->process_and_discard_comments();
// Read a block of elements
this->read_elements(upper, elset_name);
}
// 3.) Look for a Nodeset section
else if (upper.find("*NSET") == static_cast<std::string::size_type>(0))
{
std::string nset_name = this->parse_label(s, "nset");
// I haven't seen an unnamed nset yet, but let's detect it
// just in case...
libmesh_error_msg_if(nset_name == "", "Unnamed nset encountered!");
// Is this a "generated" nset, i.e. one which has three
// entries corresponding to (first, last, stride)?
bool is_generated = this->detect_generated_set(upper);
// Process any lines of comments that may be present
this->process_and_discard_comments();
// Read the IDs, storing them in _nodeset_ids
if (is_generated)
this->generate_ids(nset_name, _nodeset_ids);
else
this->read_ids(nset_name, _nodeset_ids);
} // *Nodeset
// 4.) Look for an Elset section
else if (upper.find("*ELSET") == static_cast<std::string::size_type>(0))
{
std::string elset_name = this->parse_label(s, "elset");
// I haven't seen an unnamed elset yet, but let's detect it
// just in case...
libmesh_error_msg_if(elset_name == "", "Unnamed elset encountered!");
// Is this a "generated" elset, i.e. one which has three
// entries corresponding to (first, last, stride)?
bool is_generated = this->detect_generated_set(upper);
// Process any lines of comments that may be present
this->process_and_discard_comments();
// Read the IDs, storing them in _elemset_ids
if (is_generated)
this->generate_ids(elset_name, _elemset_ids);
else
this->read_ids(elset_name, _elemset_ids);
} // *Elset
// 5.) Look for a Surface section. Need to be a little
// careful, since there are also "surface interaction"
// sections we don't want to read here.
else if (upper.find("*SURFACE,") == static_cast<std::string::size_type>(0))
{
// Get the name from the Name=Foo label. This will be the map key.
std::string sideset_name = this->parse_label(s, "name");
// Some (all?) surfaces also declare a type, which can
// help us figure out how they should be parsed, so we
// pass this to the read_sideset() function.
std::string sideset_type = this->parse_label(s, "type");
// Process any lines of comments that may be present
this->process_and_discard_comments();
// Read the sideset IDs
this->read_sideset(sideset_name, sideset_type, _sideset_ids);
}
// Derived classes could override this to add support for additional sections
extended_parsing(upper);
continue;
} // if (*_in)
// If !file, check to see if EOF was set. If so, break out
// of while loop.
if (_in->eof())
break;
// If !in and !in.eof(), stream is in a bad state!
libmesh_error_msg("Stream is bad! Perhaps the file: " << fname << " does not exist?");
} // while
// Set the Mesh dimension based on the highest dimension element seen.
the_mesh.set_mesh_dimension(this->max_elem_dimension_seen());
// Set element IDs based on the element sets.
this->assign_subdomain_ids();
// Assign nodeset values to the BoundaryInfo object
this->assign_boundary_node_ids();
// Assign sideset values in the BoundaryInfo object
this->assign_sideset_ids();
// If the Abaqus file contains only nodesets, we can have libmesh
// generate sidesets from them. This BoundaryInfo function currently
// *overwrites* existing sidesets in surprising ways, so we don't
// call it if there are already sidesets present in the original file.
if (build_sidesets_from_nodesets && the_mesh.get_boundary_info().n_boundary_conds() == 0)
the_mesh.get_boundary_info().build_side_list_from_node_list();
// Delete lower-dimensional elements from the Mesh. We assume these
// were only used for setting BCs, and aren't part of the actual
// Mesh.
{
unsigned char max_dim = this->max_elem_dimension_seen();
for (auto & elem : the_mesh.element_ptr_range())
if (elem->dim() < max_dim)
the_mesh.delete_elem(elem);
}
}
void AbaqusIO::read_nodes(std::string nset_name)
{
// Get a reference to the mesh we are reading
MeshBase & the_mesh = MeshInput<MeshBase>::mesh();
// In the input files I have, Abaqus neither tells what
// the mesh dimension is nor how many nodes it has...
//
// The node line format is:
// id, x, y, z
// and you do have to parse out the commas.
// The z-coordinate will only be present for 3D meshes
// Temporary variables for parsing lines of text
char c;
std::string line;
// We need to duplicate some of the read_ids code if this *NODE
// section also defines an NSET. We'll set up the id_storage
// pointer and push back IDs into this vector in the loop below...
std::vector<dof_id_type> * id_storage = nullptr;
if (nset_name != "")
id_storage = &(_nodeset_ids[nset_name]);
// We will read nodes until the next line begins with *, since that will be the
// next section.
// TODO: Is Abaqus guaranteed to start the line with '*' or can there be leading white space?
while (_in->peek() != '*' && _in->peek() != EOF)
{
// Read an entire line which corresponds to a single point's id
// and (x,y,z) values.
std::getline(*_in, line);
// Remove all whitespace characters from the line. This way we
// can do the remaining parsing without worrying about tabs,
// different numbers of spaces, etc.
strip_ws(line);
// Make a stream out of the modified line so we can stream values
// from it in the usual way.
std::stringstream ss(line);
// Values to be read in from file
dof_id_type abaqus_node_id=0;
Real x=0, y=0, z=0;
// Note: we assume *at least* 2D points here, should we worry about
// trying to read 1D Abaqus meshes?
ss >> abaqus_node_id >> c >> x >> c >> y;
// Peek at the next character. If it is a comma, then there is another
// value to read!
if (ss.peek() == ',')
ss >> c >> z;
// If this *NODE section defines an NSET, also store the abaqus ID in id_storage
if (id_storage)
id_storage->push_back(abaqus_node_id);
// Convert from Abaqus 1-based to libMesh 0-based numbering
libmesh_error_msg_if(abaqus_node_id < 1,
"Invalid Abaqus node ID found");
const dof_id_type libmesh_node_id = abaqus_node_id-1;
libmesh_error_msg_if(the_mesh.query_node_ptr(libmesh_node_id),
"Duplicate Abaqus node ID found");
// Add the point to the mesh using libmesh's numbering,
// and post-increment the libmesh node counter.
the_mesh.add_point(Point(x,y,z), libmesh_node_id);
} // while
}
void AbaqusIO::read_elements(std::string upper, std::string elset_name)
{
// Get a reference to the mesh we are reading
MeshBase & the_mesh = MeshInput<MeshBase>::mesh();
// initialize the eletypes map (eletypes is a file-global variable)
init_eletypes();
ElemType elem_type = INVALID_ELEM;
unsigned n_nodes_per_elem = 0;
// Within s, we should have "type=XXXX"
if (upper.find("T3D2") != std::string::npos ||
upper.find("B31") != std::string::npos)
{
elem_type = EDGE2;
n_nodes_per_elem = 2;
elems_of_dimension[1] = true;
}
else if (upper.find("B32") != std::string::npos)
{
elem_type = EDGE3;
n_nodes_per_elem = 3;
elems_of_dimension[1] = true;
}
else if (upper.find("S3") != std::string::npos ||
upper.find("CPE3") != std::string::npos ||
upper.find("2D3") != std::string::npos)
{
elem_type = TRI3;
n_nodes_per_elem = 3;
elems_of_dimension[2] = true;
}
else if (upper.find("CPE4") != std::string::npos ||
upper.find("S4") != std::string::npos ||
upper.find("CPEG4") != std::string::npos ||
upper.find("2D4") != std::string::npos)
{
elem_type = QUAD4;
n_nodes_per_elem = 4;
elems_of_dimension[2] = true;
}
else if (upper.find("CPE6") != std::string::npos ||
upper.find("S6") != std::string::npos ||
upper.find("CPEG6") != std::string::npos ||
upper.find("2D6") != std::string::npos)
{
elem_type = TRI6;
n_nodes_per_elem = 6;
elems_of_dimension[2] = true;
}
else if (upper.find("CPE8") != std::string::npos ||
upper.find("S8") != std::string::npos ||
upper.find("CPEG8") != std::string::npos ||
upper.find("2D8") != std::string::npos)
{
elem_type = QUAD8;
n_nodes_per_elem = 8;
elems_of_dimension[2] = true;
}
else if (upper.find("3D8") != std::string::npos)
{
elem_type = HEX8;
n_nodes_per_elem = 8;
elems_of_dimension[3] = true;
}
else if (upper.find("3D4") != std::string::npos)
{
elem_type = TET4;
n_nodes_per_elem = 4;
elems_of_dimension[3] = true;
}
else if (upper.find("3D20") != std::string::npos)
{
elem_type = HEX20;
n_nodes_per_elem = 20;
elems_of_dimension[3] = true;
}
else if (upper.find("3D27") != std::string::npos)
{
elem_type = HEX27;
n_nodes_per_elem = 27;
elems_of_dimension[3] = true;
}
else if (upper.find("3D6") != std::string::npos)
{
elem_type = PRISM6;
n_nodes_per_elem = 6;
elems_of_dimension[3] = true;
}
else if (upper.find("3D15") != std::string::npos)
{
elem_type = PRISM15;
n_nodes_per_elem = 15;
elems_of_dimension[3] = true;
}
else if (upper.find("3D10") != std::string::npos)
{
elem_type = TET10;
n_nodes_per_elem = 10;
elems_of_dimension[3] = true;
}
else if (upper.find("MASS") != std::string::npos)
{
// "MASS" elements are used to indicate point masses in Abaqus
// models. These are mapped to NODEELEMs in libmesh.
elem_type = NODEELEM;
n_nodes_per_elem = 1;
elems_of_dimension[0] = true;
}
else
libmesh_error_msg("Unrecognized element type: " << upper);
// Insert the elem type we detected into the set of all elem types for this mesh
_elem_types.insert(elem_type);
// Grab a reference to the element definition for this element type
const ElementDefinition & eledef = eletypes[elem_type];
// If the element definition was not found, the call above would have
// created one with an uninitialized struct. Check for that here...
libmesh_error_msg_if
(eledef.abaqus_zero_based_node_id_to_libmesh_node_id.size() == 0,
"No Abaqus->LibMesh mapping information for ElemType "
<< Utility::enum_to_string(elem_type) << "!");
// We will read elements until the next line begins with *, since that will be the
// next section.
while (_in->peek() != '*' && _in->peek() != EOF)
{
// Read the element ID, it is the first number on each line. It is
// followed by a comma, so read that also. We will need this ID later
// when we try to assign subdomain IDs
dof_id_type abaqus_elem_id = 0;
char c;
*_in >> abaqus_elem_id >> c;
// Add an element of the appropriate type to the Mesh, with the
// abaqus element ID.
std::unique_ptr<Elem> new_elem = Elem::build(elem_type);
new_elem->set_id() = abaqus_elem_id-1;
Elem * elem = the_mesh.add_elem(std::move(new_elem));
// The count of the total number of IDs read for the current element.
unsigned id_count=0;
// Continue reading line-by-line until we have read enough nodes for this element
while (id_count < n_nodes_per_elem)
{
// Read entire line (up to carriage return) of comma-separated values
std::string csv_line;
std::getline(*_in, csv_line);
// Create a stream object out of the current line
std::stringstream line_stream(csv_line);
// Process the comma-separated values
std::string cell;
while (std::getline(line_stream, cell, ','))
{
dof_id_type abaqus_global_node_id;
bool success = string_to_num(cell, abaqus_global_node_id);
if (success)
{
// Map the id'th element ID (Abaqus 1-based numbering) to LibMesh numbering
libmesh_error_msg_if(abaqus_global_node_id < 1,
"Invalid Abaqus node ID found");
const dof_id_type libmesh_global_node_id = abaqus_global_node_id-1;
// Grab the node pointer from the mesh for this ID
Node * node = the_mesh.node_ptr(libmesh_global_node_id);
// If node_ptr() returns nullptr, it may mean we have not yet read the
// *Nodes section, though I assumed that always came before the *Elements section...
libmesh_error_msg_if
(node == nullptr,
"Error! Mesh::node_ptr() returned nullptr. Either no node exists with ID "
<< libmesh_global_node_id
<< " or perhaps this input file has *Elements defined before *Nodes?");
// Note: id_count is the zero-based abaqus (elem local) node index. We therefore map
// it to a libmesh elem local node index using the element definition map
unsigned libmesh_elem_local_node_id =
eledef.abaqus_zero_based_node_id_to_libmesh_node_id[id_count];
// Set this node pointer within the element.
elem->set_node(libmesh_elem_local_node_id) = node;
// Increment the count of IDs read for this element
id_count++;
} // end if (success)
} // end while getline(',')
} // end while (id_count)
// Ensure that we read *exactly* as many nodes as we were expecting to, no more.
libmesh_error_msg_if
(id_count != n_nodes_per_elem,
"Error: Needed to read "
<< n_nodes_per_elem
<< " nodes, but read "
<< id_count
<< " instead!");
// If we are recording Elset IDs, add this element to the correct set for later processing.
// Make sure to add it with the Abaqus ID, not the libmesh one!
if (elset_name != "")
_elemset_ids[elset_name].push_back(abaqus_elem_id);
} // end while (peek)
}
std::string AbaqusIO::parse_label(std::string line, std::string label_name) const
{
// Handle files which have weird line endings from e.g. windows.
// You can check what kind of line endings you have with 'cat -vet'.
// For example, some files may have two kinds of line endings like:
//
// 4997,^I496,^I532,^I487,^I948^M$
//
// and we don't want to deal with this when extracting a label, so
// just remove all the space characters, which should include all
// kinds of remaining newlines. (I don't think Abaqus allows
// whitespace in label names.)
strip_ws(line);
// Do all string comparisons in upper-case
std::string
upper_line(line),
upper_label_name(label_name);
std::transform(upper_line.begin(), upper_line.end(), upper_line.begin(), ::toupper);
std::transform(upper_label_name.begin(), upper_label_name.end(), upper_label_name.begin(), ::toupper);
// Get index of start of "label="
size_t label_index = upper_line.find(upper_label_name + "=");
if (label_index != std::string::npos)
{
// Location of the first comma following "label="
size_t comma_index = upper_line.find(",", label_index);
// Construct iterators from which to build the sub-string.
// Note: The +1 while initializing beg is to skip past the "=" which follows the label name
std::string::iterator
beg = line.begin() + label_name.size() + 1 + label_index,
end = (comma_index == std::string::npos) ? line.end() : line.begin() + comma_index;
return std::string(beg, end);
}
// The label index was not found, return the empty string
return std::string("");
}
bool AbaqusIO::detect_generated_set(std::string upper) const
{
// Avoid issues with weird line endings, spaces before commas, etc.
strip_ws(upper);
// Check each comma-separated value in "upper" to see if it is the generate flag.
std::string cell;
std::stringstream line_stream(upper);
while (std::getline(line_stream, cell, ','))
if (cell == "GENERATE")
return true;
return false;
}
void AbaqusIO::read_ids(std::string set_name, container_t & container)
{
// Grab a reference to a vector that will hold all the IDs
std::vector<dof_id_type> & id_storage = container[set_name];
// Read until the start of another section is detected, or EOF is encountered
while (_in->peek() != '*' && _in->peek() != EOF)
{
// Read entire comma-separated line into a string
std::string csv_line;
std::getline(*_in, csv_line);
// On that line, use std::getline again to parse each
// comma-separated entry.
std::string cell;
std::stringstream line_stream(csv_line);
while (std::getline(line_stream, cell, ','))
{
dof_id_type id;
bool success = string_to_num(cell, id);
// Note that lists of comma-separated values in abaqus also
// *end* with a comma, so the last call to getline on a given
// line will get an empty string, which we must detect.
if (success)
id_storage.push_back(id);
}
}
}
void AbaqusIO::generate_ids(std::string set_name, container_t & container)
{
// Grab a reference to a vector that will hold all the IDs
std::vector<dof_id_type> & id_storage = container[set_name];
// Read until the start of another section is detected, or EOF is
// encountered. "generate" sections seem to only have one line,
// although I suppose it's possible they could have more.
while (_in->peek() != '*' && _in->peek() != EOF)
{
// Read entire comma-separated line into a string
std::string csv_line;
std::getline(*_in, csv_line);
// Remove all whitespaces from csv_line.
strip_ws(csv_line);
// Create a new stringstream object from the string, and stream
// in the comma-separated values.
char c;
dof_id_type start, end, stride;
std::stringstream line_stream(csv_line);
line_stream >> start >> c >> end >> c >> stride;
// Generate entries in the id_storage. Note: each element can
// only belong to a single Elset (since this corresponds to the
// subdomain_id) so if an element appears in multiple Elsets,
// the "last" one (alphabetically, based on set name) in the
// _elemset_ids map will "win".
for (dof_id_type current = start; current <= end; current += stride)
id_storage.push_back(current);
}
}
void AbaqusIO::read_sideset(const std::string & sideset_name,
const std::string & sideset_type,
sideset_container_t & container)
{
// Grab a reference to a vector that will hold all the IDs
std::vector<std::pair<dof_id_type, unsigned>> & id_storage = container[sideset_name];
// Variables for storing values read in from file
unsigned side_id=0;
char c;
std::string elem_id_or_set, dummy;
// Read until the start of another section is detected, or EOF is encountered
while (_in->peek() != '*' && _in->peek() != EOF)
{
// Read first string up to and including the comma, which is discarded.
std::getline(*_in, elem_id_or_set, ',');
// Strip any leading or trailing trailing whitespace from this
// string, since some Abaqus files may have this.
strip_ws(elem_id_or_set);
// Handle sidesets of type "NODE"
if (sideset_type == "NODE")
{
// Create a sideset from a nodeset. This is not currently
// supported, so print a warning and keep going.
if (_nodeset_ids.count(elem_id_or_set))
libMesh::out << "Warning: skipped creating a sideset from a "
<< "nodeset, this is not yet supported."
<< std::endl;
}
// Otherwise, we assume it's a sideset of the form: "391, S2" or "Elset_1, S3".
// If it's not one of these forms, we'll throw an error instead
// of letting the stream get into a bad state.
else // sideset_type != "NODE"
{
// Read the character "S", followed by the side id. Note: the >> operator
// eats whitespace until it reaches a valid character, so this should work
// whether or not there is a space after the previous comma.
*_in >> c >> side_id;
// Try to convert first string to an integer.
dof_id_type elem_id;
bool success = string_to_num(elem_id_or_set, elem_id);
if (success)
{
// if the side set is of the form of "391, S2"
id_storage.emplace_back(elem_id, side_id);
}
if (!success)
{
// if the side set is of the form of "Elset_1, S3"
const auto & vec = libmesh_map_find(_elemset_ids, elem_id_or_set);
for (const auto & elem_id_in_elset : vec)
id_storage.emplace_back(elem_id_in_elset, side_id);
}
}
// Successful or not, we extract the remaining characters on the
// line, including the newline, to (hopefully) go to the next section.
std::getline(*_in, dummy);
} // while
}
void AbaqusIO::assign_subdomain_ids()
{
// Get a reference to the mesh we are reading
MeshBase & the_mesh = MeshInput<MeshBase>::mesh();
// The number of elemsets we've found while reading
std::size_t n_elemsets = _elemset_ids.size();
// Fill in a temporary map with (ElemType, index) pairs based on the _elem_types set. This
// will allow us to easily look up this index in the loop below.
std::map<ElemType, unsigned> elem_types_map;
{
unsigned ctr=0;
for (const auto & type : _elem_types)
elem_types_map[type] = ctr++;
}
// Loop over each Elemset and assign subdomain IDs to Mesh elements
{
// The maximum element dimension seen while reading the Mesh
unsigned char max_dim = this->max_elem_dimension_seen();
// The elemset_id counter assigns a logical numbering to the _elemset_ids keys
container_t::iterator it = _elemset_ids.begin(), end = _elemset_ids.end();
for (unsigned elemset_id=0; it != end; ++it, ++elemset_id)
{
// Grab a reference to the vector of IDs
std::vector<dof_id_type> & id_vector = it->second;
// Loop over this vector
for (const auto & id : id_vector)
{
// Map the id'th element ID (Abaqus 1-based numbering) to LibMesh numbering
libmesh_error_msg_if(id < 1,
"Invalid Abaqus element ID found");
const dof_id_type libmesh_elem_id = id-1;