Homec4science
Diffusion lammps (master) Browse

lammps/lib/atc/OutputManager.cpp
dfb38392c991master

Last Change
Raw File

OutputManager.cpp
View Options

#include <string>
#include <fstream>
#include <stdio.h>
#include <sstream>
#include "OutputManager.h"
#include "ATC_Error.h"
//#define EXTENDED_ERROR_CHECKING
namespace ATC {
static const int kFieldPrecison = 12;
static const int kFieldWidth = kFieldPrecison + 6;
static const int kFileNameSize = 26;
static string tensor_component_names[9] = {"11","12","13",
"21","22","23",
"31","32","33"};
static string sym_tensor_component_names[6] = {"11","22","33","12","13","23"};
static string vector_component_names[3] = {"_X","_Y","_Z"};
static string list_component_names[26] = {"_a","_b","_c","_d","_e","_f","_g","_h","_i","_j","_k","_l","_m","_n","_o","_p","_q","_r","_s","_t","_u","_v","_w","_x","_y","_z"};
string* get_component_names(int type) {
string* componentNames = list_component_names;
if (type==VECTOR_OUTPUT)
componentNames = vector_component_names;
else if (type == SYM_TENSOR_OUTPUT)
componentNames = sym_tensor_component_names;
else if (type == TENSOR_OUTPUT)
componentNames = tensor_component_names;
return componentNames;
}
//-----------------------------------------------------------------------------
//*
//-----------------------------------------------------------------------------
OutputManager::OutputManager(string outputPrefix, OutputType otype)
: outputPrefix_(outputPrefix),
dataType_(POINT),
outputType_(otype),
firstStep_(true),
writeGlobalsHeader_(true),
firstGlobalsWrite_(true),
tensorToComponents_(false), // paraview does not support tensors
vectorToComponents_(false),
initialized_(false)
{}
//-----------------------------------------------------------------------------
//*
//-----------------------------------------------------------------------------
OutputManager::OutputManager()
: outputPrefix_("NULL"),
dataType_(POINT),
outputType_(ENSIGHT),
firstStep_(true),
writeGlobalsHeader_(true),
firstGlobalsWrite_(true),
tensorToComponents_(false), // paraview does not support tensors
vectorToComponents_(false),
initialized_(false)
{}
//-----------------------------------------------------------------------------
//*
//-----------------------------------------------------------------------------
OutputManager::~OutputManager() {}
//-----------------------------------------------------------------------------
//*
//-----------------------------------------------------------------------------
void OutputManager::set_option(OutputOption option, bool value) {
if (option == OUTPUT_VECTOR_COMPONENTS) vectorToComponents_ = value;
else if (option == OUTPUT_TENSOR_COMPONENTS) tensorToComponents_ = value;
else throw ATC_Error(0,"unsupported output option");
};
//-----------------------------------------------------------------------------
//*
//-----------------------------------------------------------------------------
void OutputManager::initialize(string outputPrefix, OutputType otype)
{
if (outputPrefix_ != outputPrefix ) { // new stream with existing object
outputPrefix_ = outputPrefix;
initialized_ = false;
}
outputTimes_.clear();
outputType_ = otype;
firstStep_ = true;
firstGlobalsWrite_ = true;
writeGlobalsHeader_ = true;
}
//-----------------------------------------------------------------------------
//*
//-----------------------------------------------------------------------------
// Dump text-based fields to disk for later restart
void OutputManager::write_restart_file(string fileName, OUTPUT_LIST *data)
{
FILE * fp=NULL;
fp=fopen(fileName.c_str(),"wb"); // open
OUTPUT_LIST::iterator iter;
for (iter = data->begin(); iter != data->end(); iter++) {
const MATRIX* field_data = iter->second;
for (int i = 0; i < field_data->nRows(); ++i) {
for (int j = 0; j < field_data->nCols(); ++j) {
double x = (*field_data)(i,j);
fwrite(&x,sizeof(double),1,fp);
}
}
}
fclose(fp);
}
//-----------------------------------------------------------------------------
//*
//-----------------------------------------------------------------------------
// Read a file corresponding to a write by write_restart_file
void OutputManager::read_restart_file(string fileName, OUTPUT_LIST *data)
{
FILE * fp=NULL;
fp=fopen(fileName.c_str(),"rb"); // open
OUTPUT_LIST::iterator iter;
for (iter = data->begin(); iter != data->end(); iter++) {
MATRIX* field_data = iter->second;
for (int i = 0; i < field_data->nRows(); ++i) {
for (int j = 0; j < field_data->nCols(); ++j) {
double myVal;
fread(&myVal,sizeof(double),1,fp);
(*field_data)(i,j) = myVal;
}
}
}
fclose(fp);
}
//-----------------------------------------------------------------------------
//*
//-----------------------------------------------------------------------------
void OutputManager::write_globals(void)
{
if ( outputPrefix_ == "NULL") return;
string file = outputPrefix_ + ".GLOBALS";
ofstream text;
if ( firstGlobalsWrite_ ) text.open(file.c_str(),ios_base::out);
else text.open(file.c_str(),ios_base::app);
firstGlobalsWrite_ = false;
map<string, double>::iterator iter;
// header
if ( firstStep_ || writeGlobalsHeader_) {
text << "# time:1 ";
int index = 2;
for (iter = globalData_.begin(); iter != globalData_.end(); iter++)
{
string name = iter->first;
string str; stringstream out; out << ":" << index++;
str = out.str();
name.append(str);
text.width(kFieldWidth); text << name << " ";
}
text << '\n';
}
writeGlobalsHeader_ = false;
// data
text.width(kFieldWidth); text << outputTimes_[outputTimes_.size()-1] << " ";
for (iter = globalData_.begin();
iter != globalData_.end(); iter++) {
double value = iter->second;
text << setw(kFieldWidth) << std::scientific << std::setprecision(kFieldPrecison) << value << " ";
}
text << "\n";
}
//-----------------------------------------------------------------------------
//*
//-----------------------------------------------------------------------------
void OutputManager::write_geometry(const MATRIX &coordinates,
const Array2D<int> *connectivities)
{
if ( outputPrefix_ == "NULL") return;
// geometry based on a reference configuration
string geom_file_name = outputPrefix_ + ".geo";
string geom_file_text = outputPrefix_ + ".XYZ";
// open file
FILE * fp=NULL;
ofstream text;
char buffer[80];
if ( ! initialized_ ) {
fp=fopen(geom_file_name.c_str(),"wb"); // open
strcpy(buffer,"C Binary");
fwrite(buffer,sizeof(char),80,fp);
// write geometry once
if (outputType_ == GNUPLOT) text.open(geom_file_text.c_str(),ios_base::out);
}
else {
fp=fopen(geom_file_name.c_str(),"ab"); // append
// if (outputType_ == GNUPLOT) text.open(geom_file_text.c_str(),ios_base::app);
}
if (fp == NULL) {
throw ATC_Error(0,"can not create Ensight geometry file");
}
// write preamble
strcpy(buffer,"BEGIN TIME STEP");
fwrite(buffer,sizeof(char),80,fp);
strcpy(buffer,"Ensight geometry file");
fwrite(buffer,sizeof(char),80,fp);
strcpy(buffer,"description");
fwrite(buffer,sizeof(char),80,fp);
strcpy(buffer,"node id assign");
fwrite(buffer,sizeof(char),80,fp);
strcpy(buffer,"element id assign");
fwrite(buffer,sizeof(char),80,fp);
// per part
strcpy(buffer,"part");
fwrite(buffer,sizeof(char),80,fp);
int part_number=1;
fwrite(&part_number,sizeof(int),1,fp);
strcpy(buffer,"description");
fwrite(buffer,sizeof(char),80,fp);
// write coordinates
strcpy(buffer,"coordinates");
fwrite(buffer,sizeof(char),80,fp);
number_of_nodes_ = coordinates.nCols();
fwrite(&number_of_nodes_,sizeof(int),1,fp);
int number_of_spatial_dimensions = coordinates.nRows();
if (number_of_spatial_dimensions != 3)
throw ATC_Error(0,"Ensight writer needs a 3D geometry");
for (int i = 0; i < number_of_spatial_dimensions; ++i)
{
for (int j = 0; j < number_of_nodes_; ++j)
{
float x = (float) coordinates(i,j);
fwrite(&x,sizeof(float),1,fp);
}
}
// write mesh connectivities or point "connectivities"
if (connectivities)
{
dataType_ = MESH;
strcpy(buffer,"hexa8");
fwrite(buffer,sizeof(char),80,fp);
int number_of_elements = connectivities->nCols();
fwrite(&number_of_elements,sizeof(int),1,fp);
int number_of_nodes_per_element = connectivities->nRows();
for (int j = 0; j < number_of_elements; ++j)
{
for (int i = 0; i < number_of_nodes_per_element; ++i)
{
int inode = (*connectivities)(i,j) +1; // 1 based numbering
fwrite(&inode,sizeof(int),1,fp);
}
}
}
else
{
strcpy(buffer,"point");
fwrite(buffer,sizeof(char),80,fp);
int number_of_elements = number_of_nodes_;
fwrite(&number_of_elements,sizeof(int),1,fp);
int number_of_nodes_per_element = 1;
for (int j = 0; j < number_of_elements; ++j)
{
int inode = j +1; // 1 based numbering
fwrite(&inode,sizeof(int),1,fp);
}
}
// end per part
strcpy(buffer,"END TIME STEP");
fwrite(buffer,sizeof(char),80,fp);
fclose(fp);
// text output
if (outputType_ == GNUPLOT )
{
for (int j = 0; j < number_of_nodes_; ++j)
{
for (int i = 0; i < number_of_spatial_dimensions; ++i)
{
text << setw(kFieldWidth) << std::scientific << std::setprecision(kFieldPrecison) << coordinates(i,j) << " ";
}
text << "\n";
}
text << "\n";
}
if (!initialized_) initialized_ = true;
}
//-----------------------------------------------------------------------------
//*
//-----------------------------------------------------------------------------
void OutputManager::write_geometry(OUTPUT_LIST &part_coordinates)
{
if ( outputPrefix_ == "NULL") return;
// geometry based on a reference configuration
string geom_file_name = outputPrefix_ + ".geo";
string geom_file_text = outputPrefix_ + ".XYZ";
// open file
FILE * fp =NULL;
ofstream text;
char buffer[80];
if ( ! initialized_ )
{
fp=fopen(geom_file_name.c_str(),"wb"); // open
strcpy(buffer,"C Binary");
fwrite(buffer,sizeof(char),80,fp);
if (outputType_ == GNUPLOT) text.open(geom_file_text.c_str(),ios_base::out);
}
else
{
fp=fopen(geom_file_name.c_str(),"ab"); // append
if (outputType_ == GNUPLOT) text.open(geom_file_text.c_str(),ios_base::app);
}
if (fp == NULL) {
throw ATC_Error(0,"can not create Ensight geometry file");
}
// write preamble
strcpy(buffer,"BEGIN TIME STEP");
fwrite(buffer,sizeof(char),80,fp);
strcpy(buffer,"Ensight geometry file");
fwrite(buffer,sizeof(char),80,fp);
strcpy(buffer,"description");
fwrite(buffer,sizeof(char),80,fp);
strcpy(buffer,"node id assign");
fwrite(buffer,sizeof(char),80,fp);
strcpy(buffer,"element id assign");
fwrite(buffer,sizeof(char),80,fp);
// per part
int part_number=1;
OUTPUT_LIST::iterator iter;
for (iter = part_coordinates.begin(); iter != part_coordinates.end(); iter++)
{
string part_name = iter->first;
DenseMatrix<double> coordinates = *(iter->second);
strcpy(buffer,"part");
fwrite(buffer,sizeof(char),80,fp);
fwrite(&part_number,sizeof(int),1,fp);
strcpy(buffer,part_name.c_str());
fwrite(buffer,sizeof(char),80,fp);
// write coordinates
strcpy(buffer,"coordinates");
fwrite(buffer,sizeof(char),80,fp);
number_of_nodes_ = coordinates.nCols();
fwrite(&number_of_nodes_,sizeof(int),1,fp);
int number_of_spatial_dimensions = coordinates.nRows();
if (number_of_spatial_dimensions != 3)
{
throw ATC_Error(0,"Ensight writer needs a 3D geometry");
}
for (int i=0; i<number_of_spatial_dimensions; i++)
{
for (int j=0; j<number_of_nodes_; j++)
{
float x = (float)coordinates(i,j);
fwrite(&x,sizeof(float),1,fp);
}
}
// write mesh connectivities or point "connectivities"
strcpy(buffer,"point");
fwrite(buffer,sizeof(char),80,fp);
int number_of_elements = number_of_nodes_;
fwrite(&number_of_elements,sizeof(int),1,fp);
int number_of_nodes_per_element = 1;
for (int j = 0; j < number_of_elements; ++j)
{
int inode = j +1; // 1 based numbering
fwrite(&inode,sizeof(int),1,fp);
}
++part_number;
}
strcpy(buffer,"END TIME STEP");
fwrite(buffer,sizeof(char),80,fp);
fclose(fp);
if (!initialized_) initialized_ = true;
}
//-----------------------------------------------------------------------------
/** pack "soln" into data */
//-----------------------------------------------------------------------------
void OutputManager::write_data(double time, FIELDS *soln, OUTPUT_LIST *data, const int *node_map)
{
// pack
OUTPUT_LIST combined_data;
if (soln)
{
FIELDS::iterator iter;
for (iter = soln->begin(); iter != soln->end(); iter++)
{
FieldName field_index = iter->first;
MATRIX* field_data = &(iter->second);
string field_name = field_to_string(field_index);
combined_data[field_name] = field_data;
}
}
if (data)
{
OUTPUT_LIST::iterator iter;
for (iter = data->begin(); iter != data->end(); iter++)
{
string field_name = iter->first;
MATRIX* field_data = iter->second;
combined_data[field_name] = field_data;
}
}
write_data(time, &(combined_data), node_map);
};
//-----------------------------------------------------------------------------
/** write (ensight gold format "C" binary) data */
//-----------------------------------------------------------------------------
void OutputManager::write_data(double time, OUTPUT_LIST *data, const int *node_map)
{
if (! initialized_) throw ATC_Error(0,"must write geometry before data");
// write data
OUTPUT_LIST::iterator iter;
for (iter = data->begin(); iter != data->end(); iter++)
{
string field_name = iter->first;
const MATRIX* field_data = iter->second;
write_data(field_name, field_data, node_map);
}
// write dictionary
write_dictionary(time,data);
// write text dump
if (outputType_ == GNUPLOT) {
write_text(data);
if (firstStep_ && node_map) {
string map_file_text = outputPrefix_ + ".MAP";
ofstream text;
text.open(map_file_text.c_str(),ios_base::out);
for (int i=0; i< number_of_nodes_ ; i++) {
text << node_map[i] << "\n";
}
text.close();
}
}
// global variables
if (! globalData_.empty()) write_globals();
if (firstStep_) firstStep_ = false;
}
//-----------------------------------------------------------------------------
/** write (ensight gold format "C" binary) data */
//-----------------------------------------------------------------------------
void OutputManager::write_data(string field_name, const MATRIX *field_data, const int *node_map)
{
int ndof = field_data->nCols();
int col_start = 0;
int col_end = ndof;
string filenames[kFileNameSize];
int nfiles = 1;
filenames[0] = outputPrefix_ + "." + field_name;
int type = data_type(ndof);
if (use_component_names(type)){
nfiles = ndof;
string* component_names = get_component_names(type);
for (int ifile = 0; ifile < nfiles; ++ifile)
{
string comp_name = field_name + component_names[ifile];
filenames[ifile] = outputPrefix_ + "." + comp_name;
}
}
for (int ifile = 0; ifile < nfiles; ++ifile)
{
// for vector/tensor to components
if ( nfiles > 1 )
{
col_start = ifile;
col_end = ifile+1;
}
// open or append data file
string data_file_name = filenames[ifile];
FILE * fp;
if ( outputTimes_.size() == 0 ) {
fp=fopen(data_file_name.c_str(),"wb"); // open
}
else {
fp=fopen(data_file_name.c_str(),"ab"); // append
}
if (fp == NULL) {
throw ATC_Error(0,"can not create Ensight data file: "+data_file_name);
}
// write data
char buffer[80];
strcpy(buffer,"BEGIN TIME STEP");
fwrite(buffer,sizeof(char),80,fp);
strcpy(buffer,"field name"); // NOTE could be the field name
fwrite(buffer,sizeof(char),80,fp);
// per part
strcpy(buffer,"part");
fwrite(buffer,sizeof(char),80,fp);
int part_number = 1;
fwrite(&part_number,sizeof(int),1,fp);
strcpy(buffer,"coordinates");
fwrite(buffer,sizeof(char),80,fp);
if (node_map)
{
for (int j = col_start; j < col_end; ++j)
{
for (int i = 0; i < number_of_nodes_; ++i)
{
int inode = node_map[i];
float x = (float) (*field_data)(inode,j);
fwrite(&x,sizeof(float),1,fp);
}
}
}
else
{
for (int j = col_start; j < col_end; ++j)
{
for (int i = 0; i < field_data->nRows(); ++i)
{
float x = (float) (*field_data)(i,j);
fwrite(&x,sizeof(float),1,fp);
}
}
}
// end per part
strcpy(buffer,"END TIME STEP");
fwrite(buffer,sizeof(char),80,fp);
fclose(fp);
}
}
void OutputManager::write_text(OUTPUT_LIST *data)
{
string data_file_text = outputPrefix_ + ".DATA";
ofstream text;
if (firstStep_) text.open(data_file_text.c_str(),ios_base::out);
else text.open(data_file_text.c_str(),ios_base::app);
// write data label header
if (firstStep_)
{
text.width(6); text << "# index:1" << " "; // give an ordinate for gnuplot
text.width(10); text << " step:2" << " ";
int k =3;
if (data)
{
OUTPUT_LIST::iterator iter;
for (iter = data->begin(); iter != data->end(); iter++)
{
int ncols = iter->second->nCols();
string field_name = iter->first;
if (ncols == 1) {
string str; stringstream out; out << ":" << k; str = out.str();
field_name.append(str);
text.width(kFieldWidth); text << field_name << " ";
k++;
}
else {
for (int i = 1; i <= ncols; i++) {
string str; stringstream out; out <<"_"<<i<<":"<<k; str = out.str();
string name = field_name;
name.append(str);
text.width(kFieldWidth); text << name << " ";
k++;
}
}
}
} else { throw ATC_Error(0," data missing from output");}
text << "\n";
}
text << "# timestep " << outputTimes_.size() << " : "
<< outputTimes_[outputTimes_.size()-1] << "\n";
int nrows = 0;
OUTPUT_LIST::iterator iter;
iter = data->begin();
const MATRIX* field_data = iter->second;
nrows = field_data->nRows();
for (int i = 0; i < nrows; ++i)
{
text.width(6); text << i << " "; // give an ordinate for gnuplot
text.width(10); text << outputTimes_.size() << " ";
OUTPUT_LIST::iterator iter;
for (iter = data->begin(); iter != data->end(); iter++)
{
const MATRIX* field_data = iter->second;
for (int j = 0; j < field_data->nCols(); ++j)
{
text.width(kFieldWidth);
text << setw(kFieldWidth) << std::scientific << std::setprecision(kFieldPrecison) << (*field_data)(i,j) << " ";
}
}
text <<"\n";
}
text <<"\n";
}
/** write (ensight gold : ASCII "C" format) dictionary */
void OutputManager::write_dictionary(double time, OUTPUT_LIST *data)
{
// store the time step value
outputTimes_.push_back(time);
// file names
string dict_file_name = outputPrefix_ + ".case";
string geom_file_name = outputPrefix_ + ".geo";
// open file
FILE * fp;
if ((fp=fopen(dict_file_name.c_str(),"w")) == NULL)
{
throw ATC_Error(0,"can not create Ensight case file");
}
// write file
fprintf(fp,"FORMAT\n");
fprintf(fp,"type: ensight gold\n");
fprintf(fp,"GEOMETRY\n");
if ( dataType_ == POINT) {
fprintf(fp,"model: 1 1 %s change_coords_only\n", geom_file_name.c_str());
} else {
fprintf(fp,"model: %s\n", geom_file_name.c_str());
}
fprintf(fp,"VARIABLE\n");
// data types
if (!data) throw ATC_Error(0,"no data for output");
OUTPUT_LIST::iterator iter;
int ncols = 0;
for (iter = data->begin(); iter != data->end(); iter++) {
string field_name = iter->first;
string field_file = outputPrefix_ + "." + field_name;
const MATRIX* field_data = iter->second;
int fieldCols = field_data->nCols();
ncols += fieldCols;
int type = data_type(fieldCols);
if (use_component_names(type)){
string* component_names = get_component_names(type);
for (int j = 0; j < fieldCols; ++j)
{
string comp_name = field_name + component_names[j];
string comp_file = outputPrefix_ + "." + comp_name;
fprintf(fp,"scalar per node: 1 1 %s %s\n",
comp_name.c_str(),comp_file.c_str());
}
}
else if (type == VECTOR_OUTPUT) {
fprintf(fp,"vector per node: 1 1 %s %s\n",
field_name.c_str(),field_file.c_str());
}
else if (type == SYM_TENSOR_OUTPUT) {
fprintf(fp,"tensor symm per node: 1 1 %s %s\n",
field_name.c_str(),field_file.c_str());
}
else if (type == TENSOR_OUTPUT) {
fprintf(fp,"tensor asymm per node: 1 1 %s %s\n",
field_name.c_str(),field_file.c_str());
}
else {
fprintf(fp,"scalar per node: 1 1 %s %s\n",
field_name.c_str(),field_file.c_str());
}
}
if (!firstStep_ && ncols != nDataCols_) {
throw ATC_Error(0,"number of columns of data has changed: start new output");
}
nDataCols_ = ncols;
int nsteps = outputTimes_.size();
fprintf(fp,"TIME\n");
fprintf(fp,"time set: 1\n");
fprintf(fp,"number of steps: %10d\n",nsteps);
if ( dataType_ == POINT) {
fprintf(fp,"filename start number: 0\n");
fprintf(fp,"filename increment: 1\n");
}
fprintf(fp,"time values:\n");
for (int j = 0; j < nsteps; ++j) {
double t = outputTimes_[j];
fprintf(fp,"%12.5e",t);
if ((j+1)%6 == 0) fprintf(fp,"\n");
}
fprintf(fp,"\n");
fprintf(fp,"FILE\n");
fprintf(fp,"file set: 1\n");
fprintf(fp,"number of steps: %10d\n",nsteps);
fclose(fp);
};
} // end ATC namespace
c4science · Help