forked from lijiext/lammps
707 lines
22 KiB
C++
707 lines
22 KiB
C++
#include <string>
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#include <fstream>
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#include <stdio.h>
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#include <sstream>
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#include "OutputManager.h"
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#include "ATC_Error.h"
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//#define EXTENDED_ERROR_CHECKING
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namespace ATC {
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static const int kFieldPrecison = 12;
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static const int kFieldWidth = kFieldPrecison + 6;
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static const int kFileNameSize = 26;
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static string tensor_component_names[9] = {"11","12","13",
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"21","22","23",
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"31","32","33"};
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static string sym_tensor_component_names[6] = {"11","22","33","12","13","23"};
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static string vector_component_names[3] = {"_X","_Y","_Z"};
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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"};
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string* get_component_names(int type) {
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string* componentNames = list_component_names;
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if (type==VECTOR_OUTPUT)
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componentNames = vector_component_names;
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else if (type == SYM_TENSOR_OUTPUT)
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componentNames = sym_tensor_component_names;
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else if (type == TENSOR_OUTPUT)
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componentNames = tensor_component_names;
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return componentNames;
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}
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//-----------------------------------------------------------------------------
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//*
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//-----------------------------------------------------------------------------
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OutputManager::OutputManager(string outputPrefix, OutputType otype)
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: outputPrefix_(outputPrefix),
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dataType_(POINT),
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outputType_(otype),
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firstStep_(true),
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writeGlobalsHeader_(true),
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firstGlobalsWrite_(true),
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tensorToComponents_(false), // paraview does not support tensors
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vectorToComponents_(false),
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initialized_(false)
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{}
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//-----------------------------------------------------------------------------
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//*
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//-----------------------------------------------------------------------------
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OutputManager::OutputManager()
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: outputPrefix_("NULL"),
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dataType_(POINT),
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outputType_(ENSIGHT),
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firstStep_(true),
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writeGlobalsHeader_(true),
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firstGlobalsWrite_(true),
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tensorToComponents_(false), // paraview does not support tensors
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vectorToComponents_(false),
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initialized_(false)
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{}
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//-----------------------------------------------------------------------------
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//*
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//-----------------------------------------------------------------------------
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OutputManager::~OutputManager() {}
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//-----------------------------------------------------------------------------
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//*
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//-----------------------------------------------------------------------------
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void OutputManager::set_option(OutputOption option, bool value) {
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if (option == OUTPUT_VECTOR_COMPONENTS) vectorToComponents_ = value;
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else if (option == OUTPUT_TENSOR_COMPONENTS) tensorToComponents_ = value;
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else throw ATC_Error(0,"unsupported output option");
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};
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//-----------------------------------------------------------------------------
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//*
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//-----------------------------------------------------------------------------
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void OutputManager::initialize(string outputPrefix, OutputType otype)
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{
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if (outputPrefix_ != outputPrefix ) { // new stream with existing object
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outputPrefix_ = outputPrefix;
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initialized_ = false;
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}
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outputTimes_.clear();
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outputType_ = otype;
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firstStep_ = true;
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firstGlobalsWrite_ = true;
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writeGlobalsHeader_ = true;
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}
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//-----------------------------------------------------------------------------
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//*
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//-----------------------------------------------------------------------------
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// Dump text-based fields to disk for later restart
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void OutputManager::write_restart_file(string fileName, OUTPUT_LIST *data)
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{
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FILE * fp=NULL;
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fp=fopen(fileName.c_str(),"wb"); // open
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OUTPUT_LIST::iterator iter;
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for (iter = data->begin(); iter != data->end(); iter++) {
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const MATRIX* field_data = iter->second;
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for (int i = 0; i < field_data->nRows(); ++i) {
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for (int j = 0; j < field_data->nCols(); ++j) {
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double x = (*field_data)(i,j);
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fwrite(&x,sizeof(double),1,fp);
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}
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}
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}
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fclose(fp);
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}
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//-----------------------------------------------------------------------------
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//*
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//-----------------------------------------------------------------------------
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// Read a file corresponding to a write by write_restart_file
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void OutputManager::read_restart_file(string fileName, OUTPUT_LIST *data)
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{
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FILE * fp=NULL;
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fp=fopen(fileName.c_str(),"rb"); // open
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OUTPUT_LIST::iterator iter;
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for (iter = data->begin(); iter != data->end(); iter++) {
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MATRIX* field_data = iter->second;
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for (int i = 0; i < field_data->nRows(); ++i) {
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for (int j = 0; j < field_data->nCols(); ++j) {
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double myVal;
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fread(&myVal,sizeof(double),1,fp);
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(*field_data)(i,j) = myVal;
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}
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}
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}
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fclose(fp);
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}
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//-----------------------------------------------------------------------------
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//*
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//-----------------------------------------------------------------------------
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void OutputManager::write_globals(void)
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{
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if ( outputPrefix_ == "NULL") return;
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string file = outputPrefix_ + ".GLOBALS";
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ofstream text;
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if ( firstGlobalsWrite_ ) text.open(file.c_str(),ios_base::out);
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else text.open(file.c_str(),ios_base::app);
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firstGlobalsWrite_ = false;
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map<string, double>::iterator iter;
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// header
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if ( firstStep_ || writeGlobalsHeader_) {
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text << "# time:1 ";
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int index = 2;
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for (iter = globalData_.begin(); iter != globalData_.end(); iter++)
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{
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string name = iter->first;
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string str; stringstream out; out << ":" << index++;
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str = out.str();
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name.append(str);
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text.width(kFieldWidth); text << name << " ";
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}
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text << '\n';
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}
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writeGlobalsHeader_ = false;
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// data
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text.width(kFieldWidth); text << outputTimes_[outputTimes_.size()-1] << " ";
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for (iter = globalData_.begin();
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iter != globalData_.end(); iter++) {
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double value = iter->second;
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text << setw(kFieldWidth) << std::scientific << std::setprecision(kFieldPrecison) << value << " ";
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}
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text << "\n";
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}
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//-----------------------------------------------------------------------------
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//*
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//-----------------------------------------------------------------------------
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void OutputManager::write_geometry(const MATRIX &coordinates,
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const Array2D<int> *connectivities)
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{
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if ( outputPrefix_ == "NULL") return;
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// geometry based on a reference configuration
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string geom_file_name = outputPrefix_ + ".geo";
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string geom_file_text = outputPrefix_ + ".XYZ";
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// open file
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FILE * fp=NULL;
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ofstream text;
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char buffer[80];
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if ( ! initialized_ ) {
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fp=fopen(geom_file_name.c_str(),"wb"); // open
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strcpy(buffer,"C Binary");
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fwrite(buffer,sizeof(char),80,fp);
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// write geometry once
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if (outputType_ == GNUPLOT) text.open(geom_file_text.c_str(),ios_base::out);
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}
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else {
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fp=fopen(geom_file_name.c_str(),"ab"); // append
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// if (outputType_ == GNUPLOT) text.open(geom_file_text.c_str(),ios_base::app);
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}
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if (fp == NULL) {
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throw ATC_Error(0,"can not create Ensight geometry file");
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}
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// write preamble
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strcpy(buffer,"BEGIN TIME STEP");
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fwrite(buffer,sizeof(char),80,fp);
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strcpy(buffer,"Ensight geometry file");
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fwrite(buffer,sizeof(char),80,fp);
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strcpy(buffer,"description");
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fwrite(buffer,sizeof(char),80,fp);
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strcpy(buffer,"node id assign");
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fwrite(buffer,sizeof(char),80,fp);
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strcpy(buffer,"element id assign");
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fwrite(buffer,sizeof(char),80,fp);
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// per part
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strcpy(buffer,"part");
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fwrite(buffer,sizeof(char),80,fp);
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int part_number=1;
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fwrite(&part_number,sizeof(int),1,fp);
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strcpy(buffer,"description");
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fwrite(buffer,sizeof(char),80,fp);
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// write coordinates
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strcpy(buffer,"coordinates");
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fwrite(buffer,sizeof(char),80,fp);
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number_of_nodes_ = coordinates.nCols();
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fwrite(&number_of_nodes_,sizeof(int),1,fp);
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int number_of_spatial_dimensions = coordinates.nRows();
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if (number_of_spatial_dimensions != 3)
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throw ATC_Error(0,"Ensight writer needs a 3D geometry");
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for (int i = 0; i < number_of_spatial_dimensions; ++i)
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{
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for (int j = 0; j < number_of_nodes_; ++j)
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{
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float x = (float) coordinates(i,j);
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fwrite(&x,sizeof(float),1,fp);
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}
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}
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// write mesh connectivities or point "connectivities"
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if (connectivities)
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{
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dataType_ = MESH;
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strcpy(buffer,"hexa8");
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fwrite(buffer,sizeof(char),80,fp);
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int number_of_elements = connectivities->nCols();
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fwrite(&number_of_elements,sizeof(int),1,fp);
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int number_of_nodes_per_element = connectivities->nRows();
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for (int j = 0; j < number_of_elements; ++j)
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{
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for (int i = 0; i < number_of_nodes_per_element; ++i)
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{
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int inode = (*connectivities)(i,j) +1; // 1 based numbering
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fwrite(&inode,sizeof(int),1,fp);
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}
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}
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}
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else
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{
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strcpy(buffer,"point");
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fwrite(buffer,sizeof(char),80,fp);
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int number_of_elements = number_of_nodes_;
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fwrite(&number_of_elements,sizeof(int),1,fp);
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int number_of_nodes_per_element = 1;
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for (int j = 0; j < number_of_elements; ++j)
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{
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int inode = j +1; // 1 based numbering
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fwrite(&inode,sizeof(int),1,fp);
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}
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}
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// end per part
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strcpy(buffer,"END TIME STEP");
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fwrite(buffer,sizeof(char),80,fp);
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fclose(fp);
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// text output
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if (outputType_ == GNUPLOT )
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{
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for (int j = 0; j < number_of_nodes_; ++j)
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{
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for (int i = 0; i < number_of_spatial_dimensions; ++i)
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{
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text << setw(kFieldWidth) << std::scientific << std::setprecision(kFieldPrecison) << coordinates(i,j) << " ";
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}
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text << "\n";
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}
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text << "\n";
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}
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if (!initialized_) initialized_ = true;
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}
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//-----------------------------------------------------------------------------
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//*
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//-----------------------------------------------------------------------------
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void OutputManager::write_geometry(OUTPUT_LIST &part_coordinates)
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{
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if ( outputPrefix_ == "NULL") return;
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// geometry based on a reference configuration
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string geom_file_name = outputPrefix_ + ".geo";
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string geom_file_text = outputPrefix_ + ".XYZ";
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// open file
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FILE * fp =NULL;
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ofstream text;
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char buffer[80];
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if ( ! initialized_ )
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{
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fp=fopen(geom_file_name.c_str(),"wb"); // open
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strcpy(buffer,"C Binary");
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fwrite(buffer,sizeof(char),80,fp);
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if (outputType_ == GNUPLOT) text.open(geom_file_text.c_str(),ios_base::out);
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}
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else
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{
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fp=fopen(geom_file_name.c_str(),"ab"); // append
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if (outputType_ == GNUPLOT) text.open(geom_file_text.c_str(),ios_base::app);
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}
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if (fp == NULL) {
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throw ATC_Error(0,"can not create Ensight geometry file");
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}
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// write preamble
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strcpy(buffer,"BEGIN TIME STEP");
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fwrite(buffer,sizeof(char),80,fp);
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strcpy(buffer,"Ensight geometry file");
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fwrite(buffer,sizeof(char),80,fp);
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strcpy(buffer,"description");
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fwrite(buffer,sizeof(char),80,fp);
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strcpy(buffer,"node id assign");
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fwrite(buffer,sizeof(char),80,fp);
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strcpy(buffer,"element id assign");
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fwrite(buffer,sizeof(char),80,fp);
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// per part
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int part_number=1;
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OUTPUT_LIST::iterator iter;
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for (iter = part_coordinates.begin(); iter != part_coordinates.end(); iter++)
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{
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string part_name = iter->first;
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DenseMatrix<double> coordinates = *(iter->second);
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strcpy(buffer,"part");
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fwrite(buffer,sizeof(char),80,fp);
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fwrite(&part_number,sizeof(int),1,fp);
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strcpy(buffer,part_name.c_str());
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fwrite(buffer,sizeof(char),80,fp);
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// write coordinates
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strcpy(buffer,"coordinates");
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fwrite(buffer,sizeof(char),80,fp);
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number_of_nodes_ = coordinates.nCols();
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fwrite(&number_of_nodes_,sizeof(int),1,fp);
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int number_of_spatial_dimensions = coordinates.nRows();
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if (number_of_spatial_dimensions != 3)
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{
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throw ATC_Error(0,"Ensight writer needs a 3D geometry");
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}
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for (int i=0; i<number_of_spatial_dimensions; i++)
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{
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for (int j=0; j<number_of_nodes_; j++)
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{
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float x = (float)coordinates(i,j);
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fwrite(&x,sizeof(float),1,fp);
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}
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}
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// write mesh connectivities or point "connectivities"
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strcpy(buffer,"point");
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fwrite(buffer,sizeof(char),80,fp);
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int number_of_elements = number_of_nodes_;
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fwrite(&number_of_elements,sizeof(int),1,fp);
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int number_of_nodes_per_element = 1;
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for (int j = 0; j < number_of_elements; ++j)
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{
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int inode = j +1; // 1 based numbering
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fwrite(&inode,sizeof(int),1,fp);
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}
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++part_number;
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}
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strcpy(buffer,"END TIME STEP");
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fwrite(buffer,sizeof(char),80,fp);
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fclose(fp);
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if (!initialized_) initialized_ = true;
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}
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//-----------------------------------------------------------------------------
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/** pack "soln" into data */
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//-----------------------------------------------------------------------------
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void OutputManager::write_data(double time, FIELDS *soln, OUTPUT_LIST *data, const int *node_map)
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{
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// pack
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OUTPUT_LIST combined_data;
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if (soln)
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{
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FIELDS::iterator iter;
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for (iter = soln->begin(); iter != soln->end(); iter++)
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{
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FieldName field_index = iter->first;
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MATRIX* field_data = &(iter->second);
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string field_name = field_to_string(field_index);
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combined_data[field_name] = field_data;
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}
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}
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if (data)
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{
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OUTPUT_LIST::iterator iter;
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for (iter = data->begin(); iter != data->end(); iter++)
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{
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string field_name = iter->first;
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MATRIX* field_data = iter->second;
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combined_data[field_name] = field_data;
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}
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}
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write_data(time, &(combined_data), node_map);
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};
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//-----------------------------------------------------------------------------
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/** write (ensight gold format "C" binary) data */
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//-----------------------------------------------------------------------------
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void OutputManager::write_data(double time, OUTPUT_LIST *data, const int *node_map)
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{
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if (! initialized_) throw ATC_Error(0,"must write geometry before data");
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// write data
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OUTPUT_LIST::iterator iter;
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for (iter = data->begin(); iter != data->end(); iter++)
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{
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string field_name = iter->first;
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const MATRIX* field_data = iter->second;
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write_data(field_name, field_data, node_map);
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}
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// write dictionary
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write_dictionary(time,data);
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// write text dump
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if (outputType_ == GNUPLOT) {
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write_text(data);
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if (firstStep_ && node_map) {
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string map_file_text = outputPrefix_ + ".MAP";
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ofstream text;
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text.open(map_file_text.c_str(),ios_base::out);
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for (int i=0; i< number_of_nodes_ ; i++) {
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text << node_map[i] << "\n";
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}
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text.close();
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}
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}
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// global variables
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if (! globalData_.empty()) write_globals();
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if (firstStep_) firstStep_ = false;
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}
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//-----------------------------------------------------------------------------
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/** write (ensight gold format "C" binary) data */
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//-----------------------------------------------------------------------------
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void OutputManager::write_data(string field_name, const MATRIX *field_data, const int *node_map)
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{
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int ndof = field_data->nCols();
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int col_start = 0;
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int col_end = ndof;
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string filenames[kFileNameSize];
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int nfiles = 1;
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filenames[0] = outputPrefix_ + "." + field_name;
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int type = data_type(ndof);
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if (use_component_names(type)){
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nfiles = ndof;
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string* component_names = get_component_names(type);
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for (int ifile = 0; ifile < nfiles; ++ifile)
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{
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string comp_name = field_name + component_names[ifile];
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filenames[ifile] = outputPrefix_ + "." + comp_name;
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}
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}
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for (int ifile = 0; ifile < nfiles; ++ifile)
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{
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// for vector/tensor to components
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if ( nfiles > 1 )
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{
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col_start = ifile;
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col_end = ifile+1;
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}
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// open or append data file
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string data_file_name = filenames[ifile];
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FILE * fp;
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if ( outputTimes_.size() == 0 ) {
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fp=fopen(data_file_name.c_str(),"wb"); // open
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}
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else {
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fp=fopen(data_file_name.c_str(),"ab"); // append
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}
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if (fp == NULL) {
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throw ATC_Error(0,"can not create Ensight data file: "+data_file_name);
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}
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// write data
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char buffer[80];
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strcpy(buffer,"BEGIN TIME STEP");
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fwrite(buffer,sizeof(char),80,fp);
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strcpy(buffer,"field name"); // NOTE could be the field name
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fwrite(buffer,sizeof(char),80,fp);
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// per part
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strcpy(buffer,"part");
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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
|
|
|
|
|