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45eec9f73b66596a87f16632dc62035e1bb9ca42
mfem/fem/datacollection.cpp
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// Copyright (c) 2010-2023, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#include "fem.hpp"
#include "../mesh/nurbs.hpp"
#include "../mesh/vtk.hpp"
#include "../general/binaryio.hpp"
#include "../general/text.hpp"
#include "picojson.h"
#include <cerrno> // errno
#include <sstream>
#include <regex>
#ifndef _WIN32
#include <sys/stat.h> // mkdir
#else
#include <direct.h> // _mkdir
#define mkdir(dir, mode) _mkdir(dir)
#endif
namespace mfem
{
// static method
int DataCollection::create_directory(const std::string &dir_name,
const Mesh *mesh, int myid)
{
// create directories recursively
const char path_delim = '/';
std::string::size_type pos = 0;
int err_flag;
#ifdef MFEM_USE_MPI
const ParMesh *pmesh = dynamic_cast<const ParMesh*>(mesh);
#endif
do
{
pos = dir_name.find(path_delim, pos+1);
std::string subdir = dir_name.substr(0, pos);
#ifndef MFEM_USE_MPI
err_flag = mkdir(subdir.c_str(), 0777);
err_flag = (err_flag && (errno != EEXIST)) ? 1 : 0;
#else
if (myid == 0 || pmesh == NULL)
{
err_flag = mkdir(subdir.c_str(), 0777);
err_flag = (err_flag && (errno != EEXIST)) ? 1 : 0;
}
#endif
}
while ( pos != std::string::npos );
#ifdef MFEM_USE_MPI
if (pmesh)
{
MPI_Bcast(&err_flag, 1, MPI_INT, 0, pmesh->GetComm());
}
#endif
return err_flag;
}
// class DataCollection implementation
DataCollection::DataCollection(const std::string& collection_name, Mesh *mesh_)
{
std::string::size_type pos = collection_name.find_last_of('/');
if (pos == std::string::npos)
{
name = collection_name;
// leave prefix_path empty
}
else
{
prefix_path = collection_name.substr(0, pos+1);
name = collection_name.substr(pos+1);
}
mesh = mesh_;
myid = 0;
num_procs = 1;
serial = true;
appendRankToFileName = false;
#ifdef MFEM_USE_MPI
m_comm = MPI_COMM_NULL;
ParMesh *par_mesh = dynamic_cast<ParMesh*>(mesh);
if (par_mesh)
{
myid = par_mesh->GetMyRank();
num_procs = par_mesh->GetNRanks();
m_comm = par_mesh->GetComm();
serial = false;
appendRankToFileName = true;
}
#endif
own_data = false;
cycle = -1;
time = 0.0;
time_step = 0.0;
precision = precision_default;
pad_digits_cycle = pad_digits_rank = pad_digits_default;
format = SERIAL_FORMAT; // use serial mesh format
compression = 0;
error = No_Error;
}
void DataCollection::SetMesh(Mesh *new_mesh)
{
if (own_data && new_mesh != mesh) { delete mesh; }
mesh = new_mesh;
myid = 0;
num_procs = 1;
serial = true;
appendRankToFileName = false;
#ifdef MFEM_USE_MPI
m_comm = MPI_COMM_NULL;
ParMesh *par_mesh = dynamic_cast<ParMesh*>(mesh);
if (par_mesh)
{
myid = par_mesh->GetMyRank();
num_procs = par_mesh->GetNRanks();
m_comm = par_mesh->GetComm();
serial = false;
appendRankToFileName = true;
}
#endif
}
#ifdef MFEM_USE_MPI
void DataCollection::SetMesh(MPI_Comm comm, Mesh *new_mesh)
{
// This seems to be the cleanest way to accomplish this
// and avoid duplicating fine grained details:
SetMesh(new_mesh);
m_comm = comm;
MPI_Comm_rank(comm, &myid);
MPI_Comm_size(comm, &num_procs);
}
#endif
void DataCollection::SetFormat(int fmt)
{
switch (fmt)
{
case SERIAL_FORMAT: break;
#ifdef MFEM_USE_MPI
case PARALLEL_FORMAT: break;
#endif
default: MFEM_ABORT("unknown format: " << fmt);
}
format = fmt;
}
void DataCollection::SetCompression(bool comp)
{
compression = comp;
#ifndef MFEM_USE_ZLIB
MFEM_VERIFY(!compression, "ZLib not enabled in MFEM build.");
#endif
}
void DataCollection::SetPrefixPath(const std::string& prefix)
{
if (!prefix.empty())
{
prefix_path = prefix;
if (!prefix_path.empty() && prefix_path[prefix_path.size()-1] != '/')
{
prefix_path += '/';
}
}
else
{
prefix_path.clear();
}
}
void DataCollection::Load(int cycle_)
{
MFEM_ABORT("this method is not implemented");
}
void DataCollection::Save()
{
SaveMesh();
if (error) { return; }
for (FieldMapIterator it = field_map.begin(); it != field_map.end(); ++it)
{
SaveOneField(it);
// Even if there is an error, try saving the other fields
}
for (QFieldMapIterator it = q_field_map.begin(); it != q_field_map.end();
++it)
{
SaveOneQField(it);
}
}
void DataCollection::SaveMesh()
{
std::string dir_name = prefix_path + name;
if (cycle != -1)
{
dir_name += "_" + to_padded_string(cycle, pad_digits_cycle);
}
int error_code = create_directory(dir_name, mesh, myid);
if (error_code)
{
error = WRITE_ERROR;
MFEM_WARNING("Error creating directory: " << dir_name);
return; // do not even try to write the mesh
}
std::string mesh_name = GetMeshFileName();
mfem::ofgzstream mesh_file(mesh_name, compression);
mesh_file.precision(precision);
#ifdef MFEM_USE_MPI
const ParMesh *pmesh = dynamic_cast<const ParMesh*>(mesh);
if (pmesh && format == PARALLEL_FORMAT)
{
pmesh->ParPrint(mesh_file);
}
else
#endif
{
mesh->Print(mesh_file);
}
if (!mesh_file)
{
error = WRITE_ERROR;
MFEM_WARNING("Error writing mesh to file: " << mesh_name);
}
}
std::string DataCollection::GetMeshShortFileName() const
{
return (serial || format == SERIAL_FORMAT) ? "mesh" : "pmesh";
}
std::string DataCollection::GetMeshFileName() const
{
return GetFieldFileName(GetMeshShortFileName());
}
std::string DataCollection::GetFieldFileName(const std::string &field_name)
const
{
std::string dir_name = prefix_path + name;
if (cycle != -1)
{
dir_name += "_" + to_padded_string(cycle, pad_digits_cycle);
}
std::string file_name = dir_name + "/" + field_name;
if (appendRankToFileName)
{
file_name += "." + to_padded_string(myid, pad_digits_rank);
}
return file_name;
}
void DataCollection::SaveOneField(const FieldMapIterator &it)
{
mfem::ofgzstream field_file(GetFieldFileName(it->first), compression);
field_file.precision(precision);
(it->second)->Save(field_file);
if (!field_file)
{
error = WRITE_ERROR;
MFEM_WARNING("Error writing field to file: " << it->first);
}
}
void DataCollection::SaveOneQField(const QFieldMapIterator &it)
{
mfem::ofgzstream q_field_file(GetFieldFileName(it->first), compression);
q_field_file.precision(precision);
(it->second)->Save(q_field_file);
if (!q_field_file)
{
error = WRITE_ERROR;
MFEM_WARNING("Error writing q-field to file: " << it->first);
}
}
void DataCollection::SaveField(const std::string &field_name)
{
FieldMapIterator it = field_map.find(field_name);
if (it != field_map.end())
{
SaveOneField(it);
}
}
void DataCollection::SaveQField(const std::string &q_field_name)
{
QFieldMapIterator it = q_field_map.find(q_field_name);
if (it != q_field_map.end())
{
SaveOneQField(it);
}
}
void DataCollection::DeleteData()
{
if (own_data) { delete mesh; }
mesh = NULL;
field_map.DeleteData(own_data);
q_field_map.DeleteData(own_data);
own_data = false;
}
void DataCollection::DeleteAll()
{
DeleteData();
field_map.clear();
q_field_map.clear();
}
DataCollection::~DataCollection()
{
DeleteData();
}
// class VisItDataCollection implementation
void VisItDataCollection::UpdateMeshInfo()
{
if (mesh)
{
spatial_dim = mesh->SpaceDimension();
topo_dim = mesh->Dimension();
if (mesh->NURBSext)
{
visit_levels_of_detail =
std::max(visit_levels_of_detail, mesh->NURBSext->GetOrder());
}
}
else
{
spatial_dim = 0;
topo_dim = 0;
}
}
VisItDataCollection::VisItDataCollection(const std::string& collection_name,
Mesh *mesh)
: DataCollection(collection_name, mesh)
{
appendRankToFileName = true; // always include rank in file names
cycle = 0; // always include cycle in directory names
visit_levels_of_detail = 1;
visit_max_levels_of_detail = 32;
UpdateMeshInfo();
}
#ifdef MFEM_USE_MPI
VisItDataCollection::VisItDataCollection(MPI_Comm comm,
const std::string& collection_name,
Mesh *mesh)
: DataCollection(collection_name, mesh)
{
m_comm = comm;
MPI_Comm_rank(comm, &myid);
MPI_Comm_size(comm, &num_procs);
appendRankToFileName = true; // always include rank in file names
cycle = 0; // always include cycle in directory names
visit_levels_of_detail = 1;
visit_max_levels_of_detail = 32;
UpdateMeshInfo();
}
#endif
void VisItDataCollection::SetMesh(Mesh *new_mesh)
{
DataCollection::SetMesh(new_mesh);
appendRankToFileName = true;
UpdateMeshInfo();
}
#ifdef MFEM_USE_MPI
void VisItDataCollection::SetMesh(MPI_Comm comm, Mesh *new_mesh)
{
// use VisItDataCollection's custom SetMesh, then set MPI info
SetMesh(new_mesh);
m_comm = comm;
MPI_Comm_rank(comm, &myid);
MPI_Comm_size(comm, &num_procs);
}
#endif
void VisItDataCollection::RegisterField(const std::string& name,
GridFunction *gf)
{
int LOD = 1;
if (gf->FESpace()->GetNURBSext())
{
LOD = gf->FESpace()->GetNURBSext()->GetOrder();
}
else
{
for (int e=0; e<gf->FESpace()->GetNE(); e++)
{
LOD = std::max(LOD,gf->FESpace()->GetFE(e)->GetOrder());
}
}
DataCollection::RegisterField(name, gf);
field_info_map[name] = VisItFieldInfo("nodes", gf->VectorDim(), LOD);
visit_levels_of_detail = std::max(visit_levels_of_detail, LOD);
}
void VisItDataCollection::RegisterQField(const std::string& name,
QuadratureFunction *qf)
{
int LOD = -1;
Mesh *mesh = qf->GetSpace()->GetMesh();
for (int e=0; e<qf->GetSpace()->GetNE(); e++)
{
int locLOD = GlobGeometryRefiner.GetRefinementLevelFromElems(
mesh->GetElementBaseGeometry(e),
qf->GetIntRule(e).GetNPoints());
LOD = std::max(LOD,locLOD);
}
DataCollection::RegisterQField(name, qf);
field_info_map[name] = VisItFieldInfo("elements", 1, LOD);
visit_levels_of_detail = std::max(visit_levels_of_detail, LOD);
}
void VisItDataCollection::SetLevelsOfDetail(int levels_of_detail)
{
visit_levels_of_detail = levels_of_detail;
}
void VisItDataCollection::SetMaxLevelsOfDetail(int max_levels_of_detail)
{
visit_max_levels_of_detail = max_levels_of_detail;
}
void VisItDataCollection::DeleteAll()
{
field_info_map.clear();
DataCollection::DeleteAll();
}
void VisItDataCollection::Save()
{
DataCollection::Save();
SaveRootFile();
}
void VisItDataCollection::SaveRootFile()
{
if (myid != 0) { return; }
std::string root_name = prefix_path + name + "_" +
to_padded_string(cycle, pad_digits_cycle) +
".mfem_root";
std::ofstream root_file(root_name);
root_file << GetVisItRootString();
if (!root_file)
{
error = WRITE_ERROR;
MFEM_WARNING("Error writing VisIt root file: " << root_name);
}
}
void VisItDataCollection::Load(int cycle_)
{
DeleteAll();
time_step = 0.0;
error = No_Error;
cycle = cycle_;
std::string root_name = prefix_path + name + "_" +
to_padded_string(cycle, pad_digits_cycle) +
".mfem_root";
LoadVisItRootFile(root_name);
if (format != SERIAL_FORMAT || num_procs > 1)
{
#ifndef MFEM_USE_MPI
MFEM_WARNING("Cannot load parallel VisIt root file in serial.");
error = READ_ERROR;
#else
if (m_comm == MPI_COMM_NULL)
{
MFEM_WARNING("Cannot load parallel VisIt root file without MPI"
" communicator");
error = READ_ERROR;
}
else
{
// num_procs was read from the root file, check for consistency with
// the associated MPI_Comm, m_comm:
int comm_size;
MPI_Comm_size(m_comm, &comm_size);
if (comm_size != num_procs)
{
MFEM_WARNING("Processor number mismatch: VisIt root file: "
<< num_procs << ", MPI_comm: " << comm_size);
error = READ_ERROR;
}
else
{
// myid was set when setting m_comm
}
}
#endif
}
if (!error)
{
LoadMesh(); // sets own_data to true, when there is no error
}
if (!error)
{
LoadFields();
}
if (error)
{
DeleteAll();
}
}
void VisItDataCollection::LoadVisItRootFile(const std::string& root_name)
{
std::ifstream root_file(root_name);
std::stringstream buffer;
buffer << root_file.rdbuf();
if (!buffer)
{
error = READ_ERROR;
MFEM_WARNING("Error reading the VisIt root file: " << root_name);
}
else
{
ParseVisItRootString(buffer.str());
}
}
void VisItDataCollection::LoadMesh()
{
// GetMeshFileName() uses 'serial', so we need to set it in advance.
serial = (format == SERIAL_FORMAT);
std::string mesh_fname = GetMeshFileName();
named_ifgzstream file(mesh_fname);
// TODO: in parallel, check for errors on all processors
if (!file)
{
error = READ_ERROR;
MFEM_WARNING("Unable to open mesh file: " << mesh_fname);
return;
}
// TODO: 1) load parallel mesh on one processor
if (format == SERIAL_FORMAT)
{
mesh = new Mesh(file, 1, 0, false);
serial = true;
}
else
{
#ifdef MFEM_USE_MPI
mesh = new ParMesh(m_comm, file);
serial = false;
#else
error = READ_ERROR;
MFEM_WARNING("Reading parallel format in serial is not supported");
return;
#endif
}
spatial_dim = mesh->SpaceDimension();
topo_dim = mesh->Dimension();
own_data = true;
}
void VisItDataCollection::LoadFields()
{
std::string path_left = prefix_path + name + "_" +
to_padded_string(cycle, pad_digits_cycle) + "/";
std::string path_right = "." + to_padded_string(myid, pad_digits_rank);
field_map.clear();
for (FieldInfoMapIterator it = field_info_map.begin();
it != field_info_map.end(); ++it)
{
std::string fname = path_left + it->first + path_right;
mfem::ifgzstream file(fname);
// TODO: in parallel, check for errors on all processors
if (!file)
{
error = READ_ERROR;
MFEM_WARNING("Unable to open field file: " << fname);
return;
}
// TODO: 1) load parallel GridFunction on one processor
if (serial)
{
if ((it->second).association == "nodes")
{
field_map.Register(it->first, new GridFunction(mesh, file), own_data);
}
else if ((it->second).association == "elements")
{
q_field_map.Register(it->first, new QuadratureFunction(mesh, file), own_data);
}
}
else
{
#ifdef MFEM_USE_MPI
if ((it->second).association == "nodes")
{
field_map.Register(
it->first,
new ParGridFunction(dynamic_cast<ParMesh*>(mesh), file), own_data);
}
else if ((it->second).association == "elements")
{
q_field_map.Register(it->first, new QuadratureFunction(mesh, file), own_data);
}
#else
error = READ_ERROR;
MFEM_WARNING("Reading parallel format in serial is not supported");
return;
#endif
}
}
}
std::string VisItDataCollection::GetVisItRootString()
{
// Get the path string (relative to where the root file is, i.e. no prefix).
std::string path_str =
name + "_" + to_padded_string(cycle, pad_digits_cycle) + "/";
// We have to build the json tree inside out to get all the values in there
picojson::object top, dsets, main, mesh, fields, field, mtags, ftags;
// Build the mesh data
std::string file_ext_format = ".%0" + to_string(pad_digits_rank) + "d";
mtags["spatial_dim"] = picojson::value(to_string(spatial_dim));
mtags["topo_dim"] = picojson::value(to_string(topo_dim));
mtags["max_lods"] = picojson::value(to_string(visit_max_levels_of_detail));
mesh["path"] = picojson::value(path_str + GetMeshShortFileName() +
file_ext_format);
mesh["tags"] = picojson::value(mtags);
mesh["format"] = picojson::value(to_string(format));
// Build the fields data entries
for (FieldInfoMapIterator it = field_info_map.begin();
it != field_info_map.end(); ++it)
{
ftags["assoc"] = picojson::value((it->second).association);
ftags["comps"] = picojson::value(to_string((it->second).num_components));
ftags["lod"] = picojson::value(to_string((it->second).lod));
field["path"] = picojson::value(path_str + it->first + file_ext_format);
field["tags"] = picojson::value(ftags);
fields[it->first] = picojson::value(field);
}
main["cycle"] = picojson::value(double(cycle));
main["time"] = picojson::value(time);
main["time_step"] = picojson::value(time_step);
main["domains"] = picojson::value(double(num_procs));
main["mesh"] = picojson::value(mesh);
if (!field_info_map.empty())
{
main["fields"] = picojson::value(fields);
}
dsets["main"] = picojson::value(main);
top["dsets"] = picojson::value(dsets);
return picojson::value(top).serialize(true);
}
void VisItDataCollection::ParseVisItRootString(const std::string& json)
{
picojson::value top, dsets, main, mesh, fields;
std::string parse_err = picojson::parse(top, json);
if (!parse_err.empty())
{
error = READ_ERROR;
MFEM_WARNING("Unable to parse VisIt root data.");
return;
}
// Process "main"
dsets = top.get("dsets");
main = dsets.get("main");
cycle = int(main.get("cycle").get<double>());
time = main.get("time").get<double>();
if (main.contains("time_step"))
{
time_step = main.get("time_step").get<double>();
}
num_procs = int(main.get("domains").get<double>());
mesh = main.get("mesh");
fields = main.get("fields");
// ... Process "mesh"
// Set the DataCollection::name using the mesh path
std::string path = mesh.get("path").get<std::string>();
size_t right_sep = path.rfind('_');
if (right_sep == std::string::npos)
{
error = READ_ERROR;
MFEM_WARNING("Unable to parse VisIt root data.");
return;
}
name = path.substr(0, right_sep);
if (mesh.contains("format"))
{
format = to_int(mesh.get("format").get<std::string>());
}
spatial_dim = to_int(mesh.get("tags").get("spatial_dim").get<std::string>());
topo_dim = to_int(mesh.get("tags").get("topo_dim").get<std::string>());
visit_max_levels_of_detail =
to_int(mesh.get("tags").get("max_lods").get<std::string>());
// ... Process "fields"
field_info_map.clear();
if (fields.is<picojson::object>())
{
picojson::object fields_obj = fields.get<picojson::object>();
for (picojson::object::iterator it = fields_obj.begin();
it != fields_obj.end(); ++it)
{
picojson::value tags = it->second.get("tags");
field_info_map[it->first] =
VisItFieldInfo(tags.get("assoc").get<std::string>(),
to_int(tags.get("comps").get<std::string>()));
}
}
}
ParaViewDataCollection::ParaViewDataCollection(const std::string&
collection_name,
Mesh *mesh_)
: DataCollection(collection_name, mesh_),
levels_of_detail(1),
pv_data_format(VTKFormat::BINARY),
high_order_output(false),
restart_mode(false)
{
cycle = 0; // always include a valid cycle index in file names
compression_level = -1; // default zlib compression level, equivalent to 6
#ifdef MFEM_USE_ZLIB
compression = true; // if we have zlib, enable compression
#else
compression = false; // otherwise, disable compression
#endif
}
void ParaViewDataCollection::SetLevelsOfDetail(int levels_of_detail_)
{
levels_of_detail = levels_of_detail_;
}
void ParaViewDataCollection::Load(int )
{
MFEM_WARNING("ParaViewDataCollection::Load() is not implemented!");
}
std::string ParaViewDataCollection::GenerateCollectionPath()
{
return prefix_path + DataCollection::GetCollectionName();
}
std::string ParaViewDataCollection::GeneratePVTUPath()
{
return "Cycle" + to_padded_string(cycle,pad_digits_cycle);
}
std::string ParaViewDataCollection::GenerateVTUPath()
{
return GeneratePVTUPath();
}
std::string ParaViewDataCollection::GeneratePVDFileName()
{
return GetCollectionName() + ".pvd";
}
std::string ParaViewDataCollection::GeneratePVTUFileName(
const std::string &prefix)
{
return prefix + ".pvtu";
}
std::string ParaViewDataCollection::GenerateVTUFileName(
const std::string &prefix, int rank)
{
return prefix + to_padded_string(rank, pad_digits_rank) + ".vtu";
}
void ParaViewDataCollection::Save()
{
// add a new collection to the PDV file
std::string col_path = GenerateCollectionPath();
// check if the directories are created
{
std::string path = col_path + "/" + GenerateVTUPath();
int error_code = create_directory(path, mesh, myid);
if (error_code)
{
error = WRITE_ERROR;
MFEM_WARNING("Error creating directory: " << path);
return; // do not even try to write the mesh
}
}
// the directory is created
// create pvd file if needed. If we are not in restart mode, a new pvd file
// is always created. In restart mode, we keep any previously defined
// timestep values as long as they are less than the currently defined time.
if (myid == 0 && !pvd_stream.is_open())
{
std::string pvdname = col_path + "/" + GeneratePVDFileName();
bool write_header = true;
std::ifstream pvd_in;
if (restart_mode && (pvd_in.open(pvdname,std::ios::binary),pvd_in.good()))
{
// PVD file exists and restart mode enabled: preserve existing time
// steps less than the current time.
std::fstream::pos_type pos_begin = pvd_in.tellg();
std::fstream::pos_type pos_end = pos_begin;
std::regex regexp("timestep=\"([^[:space:]]+)\".*file=\"Cycle(\\d+)");
std::smatch match;
std::string line;
while (getline(pvd_in,line))
{
if (regex_search(line,match,regexp))
{
MFEM_ASSERT(match.size() == 3, "Unable to parse DataSet");
double tvalue = std::stod(match[1]);
if (tvalue >= GetTime()) { break; }
int cvalue = std::stoi(match[2]);
MFEM_VERIFY(cvalue < GetCycle(), "Cycle " << GetCycle() <<
" is too small for restart mode: trying to overwrite"
" existing data.");
pos_end = pvd_in.tellg();
}
}
// Since pvd_in is opened in binary mode, count will store the number
// of bytes from the beginning of the file until the desired insertion
// point (in text mode on Windows this is not the case).
size_t count = pos_end - pos_begin;
if (count != 0)
{
write_header = false;
std::vector<char> buf(count);
// Read the contents of the PVD file, from the beginning to the
// insertion point.
pvd_in.clear();
pvd_in.seekg(pos_begin);
pvd_in.read(buf.data(), count);
pvd_in.close();
// Open the PVD file in truncate mode to delete the previous
// contents. Open in binary mode to write the data buffer without
// converting \r\n to \r\r\n on Windows.
pvd_stream.open(pvdname,std::ios::out|std::ios::trunc|std::ios::binary);
pvd_stream.write(buf.data(), count);
// Close and reopen the file in text mode, appending to the end.
pvd_stream.close();
pvd_stream.open(pvdname,std::ios::in|std::ios::out|std::ios::ate);
}
}
if (write_header)
{
// Initialize new pvd file.
pvd_stream.open(pvdname,std::ios::out|std::ios::trunc);
pvd_stream << "<?xml version=\"1.0\"?>\n";
pvd_stream << "<VTKFile type=\"Collection\" version=\"0.1\"";
pvd_stream << " byte_order=\"" << VTKByteOrder() << "\">\n";
pvd_stream << "<Collection>" << std::endl;
}
}
std::string vtu_prefix = col_path + "/" + GenerateVTUPath() + "/";
// Save the local part of the mesh and grid functions fields to the local
// VTU file
{
std::ofstream os(vtu_prefix + GenerateVTUFileName("proc", myid));
os.precision(precision);
SaveDataVTU(os, levels_of_detail);
}
// Save the local part of the quadrature function fields
for (const auto &qfield : q_field_map)
{
const std::string &field_name = qfield.first;
std::ofstream os(vtu_prefix + GenerateVTUFileName(field_name, myid));
qfield.second->SaveVTU(os, pv_data_format, GetCompressionLevel());
}
// MPI rank 0 also creates a "PVTU" file that points to all of the separately
// written VTU files.
// This file path is then appended to the PVD file.
if (myid == 0)
{
// Create the main PVTU file
{
std::ofstream pvtu_out(vtu_prefix + GeneratePVTUFileName("data"));
WritePVTUHeader(pvtu_out);
// Grid function fields
pvtu_out << "<PPointData>\n";
for (auto &field_it : field_map)
{
int vec_dim = field_it.second->VectorDim();
pvtu_out << "<PDataArray type=\"" << GetDataTypeString()
<< "\" Name=\"" << field_it.first
<< "\" NumberOfComponents=\"" << vec_dim << "\" "
<< "format=\"" << GetDataFormatString() << "\" />\n";
}
pvtu_out << "</PPointData>\n";
// Element attributes
pvtu_out << "<PCellData>\n";
pvtu_out << "\t<PDataArray type=\"Int32\" Name=\"" << "attribute"
<< "\" NumberOfComponents=\"1\""
<< " format=\"" << GetDataFormatString() << "\"/>\n";
pvtu_out << "</PCellData>\n";
WritePVTUFooter(pvtu_out, "proc");
}
// Add the latest PVTU to the PVD
pvd_stream << "<DataSet timestep=\"" << GetTime()
<< "\" group=\"\" part=\"" << 0 << "\" file=\""
<< GeneratePVTUPath() + "/" + GeneratePVTUFileName("data")
<< "\" name=\"mesh\"/>\n";
// Create PVTU files for each quadrature field and add them to the PVD
// file
for (auto &q_field : q_field_map)
{
const std::string &q_field_name = q_field.first;
std::string q_fname = GeneratePVTUPath() + "/"
+ GeneratePVTUFileName(q_field_name);
std::ofstream pvtu_out(col_path + "/" + q_fname);
WritePVTUHeader(pvtu_out);
int vec_dim = q_field.second->GetVDim();
pvtu_out << "<PPointData>\n";
pvtu_out << "<PDataArray type=\"" << GetDataTypeString()
<< "\" Name=\"" << q_field_name
<< "\" NumberOfComponents=\"" << vec_dim << "\" "
<< "format=\"" << GetDataFormatString() << "\" />\n";
pvtu_out << "</PPointData>\n";
WritePVTUFooter(pvtu_out, q_field_name);
pvd_stream << "<DataSet timestep=\"" << GetTime()
<< "\" group=\"\" part=\"" << 0 << "\" file=\""
<< q_fname << "\" name=\"" << q_field_name << "\"/>\n";
}
pvd_stream.flush();
// Move the insertion point before the closing collection tag, so that
// the PVD file is valid even when writing incrementally.
std::fstream::pos_type pos = pvd_stream.tellp();
pvd_stream << "</Collection>\n";
pvd_stream << "</VTKFile>" << std::endl;
pvd_stream.seekp(pos);
}
}
void ParaViewDataCollection::WritePVTUHeader(std::ostream &os)
{
os << "<?xml version=\"1.0\"?>\n";
os << "<VTKFile type=\"PUnstructuredGrid\"";
os << " version =\"0.1\" byte_order=\"" << VTKByteOrder() << "\">\n";
os << "<PUnstructuredGrid GhostLevel=\"0\">\n";
os << "<PPoints>\n";
os << "\t<PDataArray type=\"" << GetDataTypeString() << "\" ";
os << " Name=\"Points\" NumberOfComponents=\"3\""
<< " format=\"" << GetDataFormatString() << "\"/>\n";
os << "</PPoints>\n";
os << "<PCells>\n";
os << "\t<PDataArray type=\"Int32\" ";
os << " Name=\"connectivity\" NumberOfComponents=\"1\""
<< " format=\"" << GetDataFormatString() << "\"/>\n";
os << "\t<PDataArray type=\"Int32\" ";
os << " Name=\"offsets\" NumberOfComponents=\"1\""
<< " format=\"" << GetDataFormatString() << "\"/>\n";
os << "\t<PDataArray type=\"UInt8\" ";
os << " Name=\"types\" NumberOfComponents=\"1\""
<< " format=\"" << GetDataFormatString() << "\"/>\n";
os << "</PCells>\n";
}
void ParaViewDataCollection::WritePVTUFooter(std::ostream &os,
const std::string &vtu_prefix)
{
for (int ii=0; ii<num_procs; ii++)
{
std::string vtu_filename = GenerateVTUFileName(vtu_prefix, ii);
os << "<Piece Source=\"" << vtu_filename << "\"/>\n";
}
os << "</PUnstructuredGrid>\n";
os << "</VTKFile>\n";
}
void ParaViewDataCollection::SaveDataVTU(std::ostream &os, int ref)
{
os << "<VTKFile type=\"UnstructuredGrid\"";
if (GetCompressionLevel() != 0)
{
os << " compressor=\"vtkZLibDataCompressor\"";
}
os << " version=\"0.1\" byte_order=\"" << VTKByteOrder() << "\">\n";
os << "<UnstructuredGrid>\n";
mesh->PrintVTU(os,ref,pv_data_format,high_order_output,GetCompressionLevel());
// dump out the grid functions as point data
os << "<PointData >\n";
// save the grid functions
// iterate over all grid functions
for (FieldMapIterator it=field_map.begin(); it!=field_map.end(); ++it)
{
SaveGFieldVTU(os,ref,it);
}
os << "</PointData>\n";
// close the mesh
os << "</Piece>\n"; // close the piece open in the PrintVTU method
os << "</UnstructuredGrid>\n";
os << "</VTKFile>" << std::endl;
}
void ParaViewDataCollection::SaveGFieldVTU(std::ostream &os, int ref_,
const FieldMapIterator &it)
{
RefinedGeometry *RefG;
Vector val;
DenseMatrix vval, pmat;
std::vector<char> buf;
int vec_dim = it->second->VectorDim();
os << "<DataArray type=\"" << GetDataTypeString()
<< "\" Name=\"" << it->first
<< "\" NumberOfComponents=\"" << vec_dim << "\""
<< " format=\"" << GetDataFormatString() << "\" >" << '\n';
if (vec_dim == 1)
{
// scalar data
for (int i = 0; i < mesh->GetNE(); i++)
{
RefG = GlobGeometryRefiner.Refine(
mesh->GetElementBaseGeometry(i), ref_, 1);
it->second->GetValues(i, RefG->RefPts, val, pmat);
for (int j = 0; j < val.Size(); j++)
{
WriteBinaryOrASCII(os, buf, val(j), "\n", pv_data_format);
}
}
}
else
{
// vector data
for (int i = 0; i < mesh->GetNE(); i++)
{
RefG = GlobGeometryRefiner.Refine(
mesh->GetElementBaseGeometry(i), ref_, 1);
it->second->GetVectorValues(i, RefG->RefPts, vval, pmat);
for (int jj = 0; jj < vval.Width(); jj++)
{
for (int ii = 0; ii < vval.Height(); ii++)
{
WriteBinaryOrASCII(os, buf, vval(ii,jj), " ", pv_data_format);
}
if (pv_data_format == VTKFormat::ASCII) { os << '\n'; }
}
}
}
if (IsBinaryFormat())
{
WriteVTKEncodedCompressed(os,buf.data(),buf.size(),GetCompressionLevel());
os << '\n';
}
os << "</DataArray>" << std::endl;
}
void ParaViewDataCollection::SetDataFormat(VTKFormat fmt)
{
pv_data_format = fmt;
}
bool ParaViewDataCollection::IsBinaryFormat() const
{
return pv_data_format != VTKFormat::ASCII;
}
void ParaViewDataCollection::SetHighOrderOutput(bool high_order_output_)
{
high_order_output = high_order_output_;
}
void ParaViewDataCollection::SetCompressionLevel(int compression_level_)
{
MFEM_ASSERT(compression_level_ >= -1 && compression_level_ <= 9,
"Compression level must be between -1 and 9 (inclusive).");
compression_level = compression_level_;
compression = compression_level_ != 0;
}
void ParaViewDataCollection::SetCompression(bool compression_)
{
compression = compression_;
}
void ParaViewDataCollection::UseRestartMode(bool restart_mode_)
{
restart_mode = restart_mode_;
}
const char *ParaViewDataCollection::GetDataFormatString() const
{
if (pv_data_format == VTKFormat::ASCII)
{
return "ascii";
}
else
{
return "binary";
}
}
const char *ParaViewDataCollection::GetDataTypeString() const
{
if (pv_data_format==VTKFormat::ASCII || pv_data_format==VTKFormat::BINARY)
{
return "Float64";
}
else
{
return "Float32";
}
}
int ParaViewDataCollection::GetCompressionLevel() const
{
return compression ? compression_level : 0;
}
} // end namespace MFEM
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