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output_manager.cpp
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output_manager.cpp
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/* Copyright 2014 - Andrea Sgattoni, Luca Fedeli, Stefano Sinigardi */
/*******************************************************************************
This file is part of piccante.
piccante is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
piccante is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with piccante. If not, see <http://www.gnu.org/licenses/>.
*******************************************************************************/
#include "output_manager.h"
int is_big_endian()
{
union {
uint32_t i;
char c[4];
} bint = { 0x01020304 };
return bint.c[0] == 1;
}
emProbe::emProbe(){
coordinates[0] = coordinates[1] = coordinates[2] = 0;
name = "NONAME";
}
bool emProbe::compareProbes(emProbe *rhs){
return (coordinates[0] == rhs->coordinates[0] &&
coordinates[1] == rhs->coordinates[1] &&
coordinates[2] == rhs->coordinates[2] &&
name.c_str() == rhs->name.c_str());
}
void emProbe::setPointCoordinate(double X, double Y, double Z){
coordinates[0] = X;
coordinates[1] = Y;
coordinates[2] = Z;
}
void emProbe::setName(std::string iname){
name = iname;
}
outDomain::outDomain(){
coordinates[0] = coordinates[1] = coordinates[2] = 0;
name = "";
remainingCoord[0] = remainingCoord[1] = 1;
remainingCoord[2] = 1;
subselection = false;
overrideFlag = false;
followMovingWindowFlag = false;
rmin[0] = rmin[1] = rmin[2] = -1e10;
rmax[0] = rmax[1] = rmax[2] = +1e10;
}
void outDomain::followMovingWindow(){
followMovingWindowFlag = true;
}
bool outDomain::compareDomains(outDomain *rhs){
if (coordinates[0] == rhs->coordinates[0] &&
coordinates[1] == rhs->coordinates[1] &&
coordinates[2] == rhs->coordinates[2] &&
remainingCoord[0] == rhs->remainingCoord[0] &&
remainingCoord[1] == rhs->remainingCoord[1] &&
remainingCoord[2] == rhs->remainingCoord[2] &&
name.c_str() == rhs->name.c_str() &&
subselection == rhs->subselection&&
followMovingWindowFlag == rhs->followMovingWindowFlag&&
overrideFlag == rhs->overrideFlag){
if (!subselection)
return true;
else if (rmin[0] == rhs->rmin[0] &&
rmin[1] == rhs->rmin[1] &&
rmin[2] == rhs->rmin[2] &&
rmax[0] == rhs->rmax[0] &&
rmax[1] == rhs->rmax[1] &&
rmax[2] == rhs->rmax[2]){
return true;
}
}
return false;
}
void outDomain::setFreeDimensions(bool flagX, bool flagY, bool flagZ){
remainingCoord[0] = flagX;
remainingCoord[1] = flagY;
remainingCoord[2] = flagZ;
}
void outDomain::setPointCoordinate(double X, double Y, double Z){
coordinates[0] = X;
coordinates[1] = Y;
coordinates[2] = Z;
}
void outDomain::setName(std::string iname){
name = iname;
}
void outDomain::setXRange(double min, double max){
subselection = true;
rmin[0] = min;
rmax[0] = max;
}
void outDomain::setYRange(double min, double max){
subselection = true;
rmin[1] = min;
rmax[1] = max;
}
void outDomain::setZRange(double min, double max){
subselection = true;
rmin[2] = min;
rmax[2] = max;
}
bool requestCompTime(const request &first, const request &second){
if (first.itime != second.itime)
return (first.itime < second.itime);
else if (first.type != second.type)
return (first.type < second.type);
else if (first.target != second.target)
return (first.target < second.target);
else if (first.domain != second.domain)
return (first.domain < second.domain);
else
return false;
}
bool requestCompUnique(const request &first, const request &second){
return ((first.itime == second.itime) &&
(first.type == second.type) &&
(first.target == second.target) &&
(first.domain == second.domain));
}
bool compOutput(const reqOutput &first, const reqOutput &second){
if (first.p != second.p)
return (first.p < second.p);
else if (first.task != second.task)
return (first.task < second.task);
else
return false;
}
OUTPUT_MANAGER::OUTPUT_MANAGER(GRID* _mygrid, EM_FIELD* _myfield, CURRENT* _mycurrent, std::vector<SPECIE*> _myspecies){
mygrid = _mygrid;
isThereGrid = (mygrid != NULL) ? true : false;
myfield = _myfield;
isThereField = (myfield != NULL) ? true : false;
mycurrent = _mycurrent;
isThereCurrent = (mycurrent != NULL) ? true : false;
myspecies = _myspecies;
isThereSpecList = (myspecies.size() > 0) ? true : false;
amIInit = false;
isThereDiag = false;
isThereEMProbe =false;
outDomain *domain1 = new outDomain;
domain1->overrideFlag = true;
myDomains.push_back(domain1);
fieldGroupSize = FIELDS_GROUP_SIZE;
multifileGroupSize = MACRO_CPUGROUP_FOR_MULTIFILE;
particleGroupSize = PHASE_SPACE_GROUP_SIZE;
particleBufferSize = NPARTICLE_BUFFER_SIZE;
outputDir = "OUTPUT";
}
OUTPUT_MANAGER::~OUTPUT_MANAGER(){
for (std::vector<outDomain*>::iterator it = myDomains.begin(); it != myDomains.end(); ++it)
delete(*it);
}
void OUTPUT_MANAGER::setOutputPath(std::string dirName){
outputDir = dirName;
}
void OUTPUT_MANAGER::createDiagFile(){
if (checkGrid()){
if (mygrid->myid != mygrid->master_proc)
return;
}
else{
if (mygrid->myid != 0)
return;
}
std::ofstream of1;
diagFileName = outputDir + "/diag.dat";
of1.open(diagFileName.c_str(), std::ofstream::out | std::ofstream::trunc);
of1 << " " << std::setw(diagNarrowWidth) << "#istep" << " " << std::setw(diagWidth) << "time";
of1 << " " << std::setw(diagWidth) << "Etot";
of1 << " " << std::setw(diagWidth) << "Ex2" << " " << std::setw(diagWidth) << "Ey2" << " " << std::setw(diagWidth) << "Ez2";
of1 << " " << std::setw(diagWidth) << "Bx2" << " " << std::setw(diagWidth) << "By2" << " " << std::setw(diagWidth) << "Bz2";
std::vector<SPECIE*>::const_iterator spec_iterator;
for (spec_iterator = myspecies.begin(); spec_iterator != myspecies.end(); spec_iterator++){
of1 << " " << std::setw(diagWidth) << (*spec_iterator)->name;
}
of1 << std::endl;
of1.close();
}
void OUTPUT_MANAGER::createExtremaFiles(){
// if (checkGrid()){
if (mygrid->myid != mygrid->master_proc)
return;
if (checkEMField()){
extremaFieldFileName = outputDir + "/EXTREMES_EMfield.dat";
std::ofstream of0;
of0.open(extremaFieldFileName.c_str());
myfield->init_output_extrems(of0);
of0.close();
}
if (checkSpecies()){
for (std::vector<SPECIE*>::iterator it = myspecies.begin(); it != myspecies.end(); it++){
std::stringstream ss1;
ss1 << outputDir << "/EXTREMES_" << (*it)->name << ".dat";
extremaSpecFileNames.push_back(ss1.str());
std::ofstream of1;
of1.open(ss1.str().c_str());
(*it)->init_output_extrems(of1);
of1.close();
}
}
}
void OUTPUT_MANAGER::createEMProbeFiles(){
int ii = 0;
for (std::vector<emProbe*>::iterator it = myEMProbes.begin(); it != myEMProbes.end(); it++){
std::stringstream ss0;
ss0 << outputDir << "/EMProbe_" << (*it)->name << "_" << ii << ".txt";
(*it)->fileName = ss0.str();
ii++;
}
if (checkGrid()){
if (mygrid->myid != mygrid->master_proc)
return;
}
else{
if (mygrid->myid != 0)
return;
}
if (checkEMField()){
for (std::vector<emProbe*>::iterator it = myEMProbes.begin(); it != myEMProbes.end(); it++){
std::ofstream of0;
of0.open((*it)->fileName.c_str());
of0 << "# EM field probe at coordinates ";
of0 << (*it)->coordinates[0] << " ";
of0 << (*it)->coordinates[1] << " ";
of0 << (*it)->coordinates[2] << " ";
of0 << std::endl;
of0.close();
}
}
}
void OUTPUT_MANAGER::initialize(std::string _outputDir){
#if defined (USE_BOOST)
std::string _newoutputDir;
std::stringstream ss;
time_t timer;
std::time(&timer);
ss << _outputDir << "_" << (int)timer;
_newoutputDir = ss.str();
if (mygrid->myid == mygrid->master_proc){
if (!boost::filesystem::exists(_outputDir)){
boost::filesystem::create_directories(_outputDir);
}
else{
boost::filesystem::rename(_outputDir, _newoutputDir);
boost::filesystem::create_directories(_outputDir);
}
}
#endif
outputDir = _outputDir;
prepareOutputMap();
if (!checkGrid()){
return;
}
if (isThereDiag){
createDiagFile();
createExtremaFiles();
}
if (isThereEMProbe){
createEMProbeFiles();
}
amIInit = true;
}
void OUTPUT_MANAGER::initialize(){
#if defined (USE_BOOST)
std::string _newoutputDir;
std::stringstream ss;
time_t timer;
std::time(&timer);
ss << outputDir << "_" << (int)timer;
_newoutputDir = ss.str();
if (mygrid->myid == mygrid->master_proc){
if (!boost::filesystem::exists(outputDir)){
boost::filesystem::create_directories(outputDir);
}
else{
boost::filesystem::rename(outputDir, _newoutputDir);
boost::filesystem::create_directories(outputDir);
}
}
#endif
prepareOutputMap();
if (!checkGrid()){
return;
}
if (isThereDiag){
createDiagFile();
createExtremaFiles();
}
if (isThereEMProbe){
createEMProbeFiles();
}
amIInit = true;
}
void OUTPUT_MANAGER::close(){
}
bool OUTPUT_MANAGER::checkGrid(){
if (!isThereGrid){
if (mygrid->myid == mygrid->master_proc){
std::cout << "WARNING! No valid GRID pointer provided. Output request will be ignored." << std::endl;
}
}
return isThereGrid;
}
bool OUTPUT_MANAGER::checkEMField(){
if (!isThereField){
if (mygrid->myid == mygrid->master_proc){
std::cout << "WARNING! No valid FIELD pointer provided. Output request will be ignored." << std::endl;
}
}
return isThereField;
}
bool OUTPUT_MANAGER::checkCurrent(){
if (!isThereCurrent){
if (mygrid->myid == mygrid->master_proc){
std::cout << "WARNING! No valid CURRENT pointer provided. Output request will be ignored." << std::endl;
}
}
return isThereCurrent;
}
bool OUTPUT_MANAGER::checkSpecies(){
if (!isThereSpecList){
if (mygrid->myid == mygrid->master_proc){
std::cout << "WARNING! Empty SPECIES list provided. Output request will be ignored." << std::endl;
}
}
return isThereSpecList;
}
int OUTPUT_MANAGER::getIntegerTime(double dtime){
if (dtime == 0.0)
return 0;
int Nsteps = mygrid->getTotalNumberOfTimesteps();
int step = (int)floor(dtime / mygrid->dt + 0.5);
return (step <= Nsteps) ? (step) : (-1);
}
int OUTPUT_MANAGER::findSpecIndexInMyspeciesVector(std::string name){
int pos = 0;
for (std::vector<SPECIE*>::iterator it = myspecies.begin(); it != myspecies.end(); it++){
if ((*it)->getName() == name){
return pos;
}
pos++;
}
if (mygrid->myid == mygrid->master_proc){
std::cout << "WARNING! Species" << name << " not in species list !" << std::endl;
}
return -1;
}
int OUTPUT_MANAGER::findProbeIndexInMyprobeVector(emProbe *newProbe){
int pos = 0;
for (std::vector<emProbe*>::iterator it = myEMProbes.begin(); it != myEMProbes.end(); it++){
if ((*it)->compareProbes(newProbe)){
return pos;
}
pos++;
}
return -1;
}
int OUTPUT_MANAGER::findDomainIndexInMydomainsVector(outDomain *newDomain){
int pos = 0;
for (std::vector<outDomain*>::iterator it = myDomains.begin(); it != myDomains.end(); it++){
if ((*it)->compareDomains(newDomain)){
return pos;
}
pos++;
}
return -1;
}
void OUTPUT_MANAGER::addRequestToList(std::list<request>& reqList, diagType type, int target, int domain, double startTime, double frequency, double endTime){
std::list<request> tempList;
for (double ttime = startTime; ttime <= endTime; ttime += frequency){
request req;
req.dtime = ttime;
req.itime = getIntegerTime(ttime);
req.type = type;
req.target = target;
req.domain = domain;
tempList.push_back(req);
}
tempList.sort(requestCompTime);
reqList.merge(tempList, requestCompTime);
}
void OUTPUT_MANAGER::addEBFieldFrom(double startTime, double frequency){
addEBField(NULL, startTime, frequency, mygrid->getTotalTime(), WHICH_E_AND_B);
}
void OUTPUT_MANAGER::addEBFieldAt(double atTime){
addEBField(NULL, atTime, 1.0, atTime, WHICH_E_AND_B);
}
void OUTPUT_MANAGER::addEBFieldFromTo(double startTime, double frequency, double endTime){
addEBField(NULL, startTime, frequency, endTime, WHICH_E_AND_B);
}
void OUTPUT_MANAGER::addEBFieldFrom(outDomain* _domain, double startTime, double frequency){
addEBField(_domain, startTime, frequency, mygrid->getTotalTime(), WHICH_E_AND_B);
}
void OUTPUT_MANAGER::addEBFieldAt(outDomain* _domain, double atTime){
addEBField(_domain, atTime, 1.0, atTime, WHICH_E_AND_B);
}
void OUTPUT_MANAGER::addEBFieldFromTo(outDomain* _domain, double startTime, double frequency, double endTime){
addEBField(_domain, startTime, frequency, endTime, WHICH_E_AND_B);
}
void OUTPUT_MANAGER::addEFieldFrom(double startTime, double frequency){
addEBField(NULL, startTime, frequency, mygrid->getTotalTime(), WHICH_E_ONLY);
}
void OUTPUT_MANAGER::addEFieldAt(double atTime){
addEBField(NULL, atTime, 1.0, atTime, WHICH_E_ONLY);
}
void OUTPUT_MANAGER::addEFieldFromTo(double startTime, double frequency, double endTime){
addEBField(NULL, startTime, frequency, endTime, WHICH_E_ONLY);
}
void OUTPUT_MANAGER::addBFieldFrom(double startTime, double frequency){
addEBField(NULL, startTime, frequency, mygrid->getTotalTime(), WHICH_B_ONLY);
}
void OUTPUT_MANAGER::addBFieldAt(double atTime){
addEBField(NULL, atTime, 1.0, atTime, WHICH_B_ONLY);
}
void OUTPUT_MANAGER::addBFieldFromTo(double startTime, double frequency, double endTime){
addEBField(NULL, startTime, frequency, endTime, WHICH_B_ONLY);
}
// SELECTION
void OUTPUT_MANAGER::addEFieldFrom(outDomain* _domain, double startTime, double frequency){
addEBField(_domain, startTime, frequency, mygrid->getTotalTime(), WHICH_E_ONLY);
}
void OUTPUT_MANAGER::addEFieldAt(outDomain* _domain, double atTime){
addEBField(_domain, atTime, 1.0, atTime, WHICH_E_ONLY);
}
void OUTPUT_MANAGER::addEFieldFromTo(outDomain* _domain, double startTime, double frequency, double endTime){
addEBField(_domain, startTime, frequency, endTime, WHICH_E_ONLY);
}
void OUTPUT_MANAGER::addBFieldFrom(outDomain* _domain, double startTime, double frequency){
addEBField(_domain, startTime, frequency, mygrid->getTotalTime(), WHICH_B_ONLY);
}
void OUTPUT_MANAGER::addBFieldAt(outDomain* _domain, double atTime){
addEBField(_domain, atTime, 1.0, atTime, WHICH_B_ONLY);
}
void OUTPUT_MANAGER::addBFieldFromTo(outDomain* _domain, double startTime, double frequency, double endTime){
addEBField(_domain, startTime, frequency, endTime, WHICH_B_ONLY);
}
void OUTPUT_MANAGER::addEBField(outDomain* _domain, double startTime, double frequency, double endTime, whichFieldOut whichOut){
if (!(checkGrid() && checkEMField()))
return;
int domainID = 0;
if (_domain != NULL){
domainID = findDomainIndexInMydomainsVector(_domain);
if (domainID < 0){
myDomains.push_back(_domain);
domainID = myDomains.size() - 1;
}
}
if (whichOut == WHICH_E_AND_B){
addRequestToList(requestList, OUT_E_FIELD, 0, domainID, startTime, frequency, endTime);
addRequestToList(requestList, OUT_B_FIELD, 0, domainID, startTime, frequency, endTime);
}
else if (whichOut == WHICH_E_ONLY){
addRequestToList(requestList, OUT_E_FIELD, 0, domainID, startTime, frequency, endTime);
}
else if (whichOut == WHICH_B_ONLY){
addRequestToList(requestList, OUT_B_FIELD, 0, domainID, startTime, frequency, endTime);
}
}
// EM Probe ///////////////////////////////////////
void OUTPUT_MANAGER::addEBFieldProbeFrom(emProbe* Probe, double startTime, double frequency){
addEBFieldProbe(Probe, startTime, frequency, mygrid->getTotalTime());
}
void OUTPUT_MANAGER::addEBFieldProbeAt(emProbe* Probe, double atTime){
addEBFieldProbe(Probe, atTime, 1.0, atTime);
}
void OUTPUT_MANAGER::addEBFieldProbeFromTo(emProbe* Probe, double startTime, double frequency, double endTime){
addEBFieldProbe(Probe, startTime, frequency, endTime);
}
void OUTPUT_MANAGER::addEBFieldProbe(emProbe* Probe, double startTime, double frequency, double endTime){
if (!(checkGrid() && checkEMField()))
return;
int domainID = findProbeIndexInMyprobeVector(Probe);
if (domainID < 0){
myEMProbes.push_back(Probe);
isThereEMProbe = true;
domainID = myEMProbes.size() - 1;
}
addRequestToList(requestList, OUT_EB_PROBE, 0, domainID, startTime, frequency, endTime);
}
// ++++++++++++++++++++++++++++ species density
void OUTPUT_MANAGER::addSpeciesDensityFrom(std::string name, double startTime, double frequency){
addSpeciesDensity(NULL, name, startTime, frequency, mygrid->getTotalTime());
}
void OUTPUT_MANAGER::addSpeciesDensityAt(std::string name, double atTime){
addSpeciesDensity(NULL, name, atTime, 1.0, atTime);
}
void OUTPUT_MANAGER::addSpeciesDensityFromTo(std::string name, double startTime, double frequency, double endTime){
addSpeciesDensity(NULL, name, startTime, frequency, endTime);
}
void OUTPUT_MANAGER::addSpeciesDensityFrom(outDomain* domain_in, std::string name, double startTime, double frequency){
addSpeciesDensity(domain_in, name, startTime, frequency, mygrid->getTotalTime());
}
void OUTPUT_MANAGER::addSpeciesDensityAt(outDomain* domain_in, std::string name, double atTime){
addSpeciesDensity(domain_in, name, atTime, 1.0, atTime);
}
void OUTPUT_MANAGER::addSpeciesDensityFromTo(outDomain* domain_in, std::string name, double startTime, double frequency, double endTime){
addSpeciesDensity(domain_in, name, startTime, frequency, endTime);
}
void OUTPUT_MANAGER::addSpeciesDensity(outDomain* domain_in, std::string name, double startTime, double frequency, double endTime){
if (!(checkGrid() && checkSpecies() && checkCurrent()))
return;
int specNum = findSpecIndexInMyspeciesVector(name);
if (specNum < 0)
return;
int domainID = 0;
if (domain_in != NULL){
domainID = findDomainIndexInMydomainsVector(domain_in);
if (domainID < 0){
myDomains.push_back(domain_in);
domainID = myDomains.size() - 1;
}
}
addRequestToList(requestList, OUT_SPEC_DENSITY, specNum, domainID, startTime, frequency, endTime);
}
// ++++++++++++++++++++++++++++ current
void OUTPUT_MANAGER::addCurrentFrom(double startTime, double frequency){
addCurrent(NULL, startTime, frequency, mygrid->getTotalTime());
}
void OUTPUT_MANAGER::addCurrentAt(double atTime){
addCurrent(NULL, atTime, 1.0, atTime);
}
void OUTPUT_MANAGER::addCurrentFromTo(double startTime, double frequency, double endTime){
addCurrent(NULL, startTime, frequency, endTime);
}
void OUTPUT_MANAGER::addCurrentFrom(outDomain* domain_in, double startTime, double frequency){
addCurrent(domain_in, startTime, frequency, mygrid->getTotalTime());
}
void OUTPUT_MANAGER::addCurrentAt(outDomain* domain_in, double atTime){
addCurrent(domain_in, atTime, 1.0, atTime);
}
void OUTPUT_MANAGER::addCurrentFromTo(outDomain* domain_in, double startTime, double frequency, double endTime){
addCurrent(domain_in, startTime, frequency, endTime);
}
void OUTPUT_MANAGER::addCurrent(outDomain* domain_in, double startTime, double frequency, double endTime){
if (!(checkGrid() && checkCurrent()))
return;
int domainID = 0;
if (domain_in != NULL){
domainID = findDomainIndexInMydomainsVector(domain_in);
if (domainID < 0){
myDomains.push_back(domain_in);
domainID = myDomains.size() - 1;
}
}
addRequestToList(requestList, OUT_CURRENT, 0, domainID, startTime, frequency, endTime);
}
// ++++++++++++++++++++++++++++ species binary
void OUTPUT_MANAGER::addSpeciesPhaseSpaceFrom(std::string name, double startTime, double frequency){
addSpeciesPhaseSpace(NULL, name, startTime, frequency, mygrid->getTotalTime());
}
void OUTPUT_MANAGER::addSpeciesPhaseSpaceAt(std::string name, double atTime){
addSpeciesPhaseSpace(NULL, name, atTime, 1.0, atTime);
}
void OUTPUT_MANAGER::addSpeciesPhaseSpaceFromTo(std::string name, double startTime, double frequency, double endTime){
addSpeciesPhaseSpace(NULL, name, startTime, frequency, endTime);
}
void OUTPUT_MANAGER::addSpeciesPhaseSpaceFrom(outDomain* domain_in, std::string name, double startTime, double frequency){
addSpeciesPhaseSpace(domain_in, name, startTime, frequency, mygrid->getTotalTime());
}
void OUTPUT_MANAGER::addSpeciesPhaseSpaceAt(outDomain* domain_in, std::string name, double atTime){
addSpeciesPhaseSpace(domain_in, name, atTime, 1.0, atTime);
}
void OUTPUT_MANAGER::addSpeciesPhaseSpaceFromTo(outDomain* domain_in, std::string name, double startTime, double frequency, double endTime){
addSpeciesPhaseSpace(domain_in, name, startTime, frequency, endTime);
}
void OUTPUT_MANAGER::addSpeciesPhaseSpace(outDomain* domain_in, std::string name, double startTime, double frequency, double endTime){
if (!(checkGrid() && checkSpecies()))
return;
int specNum = findSpecIndexInMyspeciesVector(name);
if (specNum < 0)
return;
int domainID = 0;
if (domain_in != NULL){
domainID = findDomainIndexInMydomainsVector(domain_in);
if (domainID < 0){
myDomains.push_back(domain_in);
domainID = myDomains.size() - 1;
}
}
addRequestToList(requestList, OUT_SPEC_PHASE_SPACE, specNum, domainID, startTime, frequency, endTime);
}
// ++++++++++++++++++++++++++++ diag
void OUTPUT_MANAGER::addDiagFrom(double startTime, double frequency){
addDiag(startTime, frequency, mygrid->getTotalTime());
}
void OUTPUT_MANAGER::addDiagAt(double atTime){
addDiag(atTime, 1.0, atTime);
}
void OUTPUT_MANAGER::addDiagFromTo(double startTime, double frequency, double endTime){
addDiag(startTime, frequency, endTime);
}
void OUTPUT_MANAGER::addDiag(double startTime, double frequency, double endTime){
if (!(checkGrid() && checkCurrent() && checkEMField()))
return;
addRequestToList(requestList, OUT_DIAG, 0, 0, startTime, frequency, endTime);
isThereDiag = true;
}
void OUTPUT_MANAGER::prepareOutputMap(){
requestList.sort(requestCompTime);
requestList.unique(requestCompUnique);
std::map< int, std::vector<request> >::iterator itMap;
for (std::list<request>::iterator itList = requestList.begin(); itList != requestList.end(); itList++){
itMap = allOutputs.find(itList->itime);
if (itMap != allOutputs.end()){
itMap->second.push_back(*itList);
}
else{
std::vector<request> newTimeVec;
newTimeVec.push_back(*itList);
allOutputs.insert(std::pair<int, std::vector<request> >(itList->itime, newTimeVec));
timeList.push_back(itList->itime);
}
}
}
void OUTPUT_MANAGER::processOutputEntry(request req){
switch (req.type){
case OUT_E_FIELD:
callEMFieldDomain(req);
break;
case OUT_B_FIELD:
callEMFieldDomain(req);
break;
case OUT_EB_PROBE:
callEMFieldProbe(req);
break;
case OUT_SPEC_DENSITY:
callSpecDensity(req);
break;
case OUT_CURRENT:
callCurrent(req);
break;
case OUT_SPEC_PHASE_SPACE:
callSpecPhaseSpace(req);
break;
case OUT_DIAG:
callDiag(req);
break;
default:
break;
}
}
void OUTPUT_MANAGER::callDiags(int istep){
std::map< int, std::vector<request> >::iterator itMap;
itMap = allOutputs.find(istep);
if (itMap == allOutputs.end())
return;
std::vector<request> diagList = itMap->second;
for (std::vector<request>::iterator it = diagList.begin(); it != diagList.end(); it++){
processOutputEntry(*it);
}
}
std::string OUTPUT_MANAGER::composeOutputName(std::string dir, std::string out, std::string opt, double time, std::string ext){
std::stringstream ss;
ss << dir << "/"
<< out << "_";
if (opt != "")
ss << opt << "_";
ss << std::setw(OUTPUT_SIZE_TIME_DIAG) << std::setfill('0') << std::fixed << std::setprecision(3) << time;
ss << ext;
return ss.str();
}
std::string OUTPUT_MANAGER::composeOutputName(std::string dir, std::string out, std::string opt1, std::string opt2, int domain, double time, std::string ext){
std::stringstream ss;
ss << dir << "/"
<< out << "_";
if (opt1 != "")
ss << opt1 << "_";
if (opt2 != "")
ss << opt2 << "_";
if (domain != 0)
ss << domain << "_";
ss << std::setw(OUTPUT_SIZE_TIME_DIAG) << std::setfill('0') << std::fixed << std::setprecision(3) << time;
ss << ext;
return ss.str();
}
void OUTPUT_MANAGER::appendIDtoFileName(char *nomefile, std::string fileName, int ID){
std::stringstream myFileName;
myFileName << fileName << "." << std::setfill('0') << std::setw(3) << ID;
nomefile = new char[myFileName.str().size() + 1];
strcpy(nomefile, myFileName.str().c_str());
}
#if defined(USE_HDF5)
void OUTPUT_MANAGER::writeEMFieldBinaryHDF5(std::string fileName, request req){
int dimensionality = mygrid->accesso.dimensions;
int Ncomp = myfield->getNcomp();
MPI_Info info = MPI_INFO_NULL;
char nomi[6][3] = { "Ex", "Ey", "Ez", "Bx", "By", "Bz" };
char* nomefile = new char[fileName.size() + 4];
nomefile[fileName.size()] = 0;
sprintf(nomefile, "%s.h5", fileName.c_str());
hid_t file_id, dset_id[6]; /* file and dataset identifiers */
hid_t filespace[6], memspace[6]; /* file and memory dataspace identifiers */
hsize_t dimsf[3]; /* dataset dimensions */
hsize_t count[3]; /* hyperslab selection parameters */
hsize_t offset[3];
hid_t plist_id; /* property list identifier */
int i;
herr_t status;
/*
* Set up file access property list with parallel I/O access
*/
plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, info);
/*
* Create a new file collectively and release property list identifier.
*/
file_id = H5Fcreate(nomefile, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
H5Pclose(plist_id);
/*
* Create the dataspace for the dataset.
*/
if (dimensionality == 1){
dimsf[0] = mygrid->uniquePoints[0];
}
else if (dimensionality == 2){
dimsf[0] = mygrid->uniquePoints[1];
dimsf[1] = mygrid->uniquePoints[0];
}
else{
dimsf[0] = mygrid->uniquePoints[2];
dimsf[1] = mygrid->uniquePoints[1];
dimsf[2] = mygrid->uniquePoints[0];
}
for (int i = 0; i < 6; i++)
filespace[i] = H5Screate_simple(dimensionality, dimsf, NULL);
/*
* Create the dataset with default properties and close filespace.
*/
for (int i = 0; i < 6; i++){
dset_id[i] = H5Dcreate1(file_id, nomi[i], H5T_NATIVE_FLOAT, filespace[i],
H5P_DEFAULT);
H5Sclose(filespace[i]);
}
/*
* Each process defines dataset in memory and writes it to the hyperslab
* in the file.
*/
if (dimensionality == 1){
offset[0] = mygrid->rproc_imin[0][mygrid->rmyid[0]];
count[0] = mygrid->uniquePointsloc[0];
}
else if (dimensionality == 2){
offset[1] = mygrid->rproc_imin[0][mygrid->rmyid[0]];
offset[0] = mygrid->rproc_imin[1][mygrid->rmyid[1]];
count[1] = mygrid->uniquePointsloc[0];
count[0] = mygrid->uniquePointsloc[1];
}
else{
offset[2] = mygrid->rproc_imin[0][mygrid->rmyid[0]];
offset[1] = mygrid->rproc_imin[1][mygrid->rmyid[1]];
offset[0] = mygrid->rproc_imin[2][mygrid->rmyid[2]];
count[2] = mygrid->uniquePointsloc[0];
count[1] = mygrid->uniquePointsloc[1];
count[0] = mygrid->uniquePointsloc[2];
}
/*
* Select hyperslab in the file.
*/
for (int i = 0; i < 6; i++){
memspace[i] = H5Screate_simple(dimensionality, count, NULL);
filespace[i] = H5Dget_space(dset_id[i]);
H5Sselect_hyperslab(filespace[i], H5S_SELECT_SET, offset, NULL, count, NULL);
}
//+++++++++++ Start CPU Field Values +++++++++++++++++++++
{
float *Ex, *Ey, *Ez, *Bx, *By, *Bz;
int Nx, Ny, Nz;
Nx = mygrid->uniquePointsloc[0];
Ny = mygrid->uniquePointsloc[1];
Nz = mygrid->uniquePointsloc[2];
int size = Nx*Ny*Nz;
Ex = new float[size];
Ey = new float[size];
Ez = new float[size];
Bx = new float[size];
By = new float[size];
Bz = new float[size];
for (int k = 0; k < Nz; k++)
for (int j = 0; j < Ny; j++)
for (int i = 0; i < Nx; i++){
Ex[i + j*Nx + k*Ny*Nx] = (float)myfield->VEB(0, i, j, k);
Ey[i + j*Nx + k*Ny*Nx] = (float)myfield->VEB(1, i, j, k);
Ez[i + j*Nx + k*Ny*Nx] = (float)myfield->VEB(2, i, j, k);
Bx[i + j*Nx + k*Ny*Nx] = (float)myfield->VEB(3, i, j, k);
By[i + j*Nx + k*Ny*Nx] = (float)myfield->VEB(4, i, j, k);
Bz[i + j*Nx + k*Ny*Nx] = (float)myfield->VEB(5, i, j, k);
}
/*
* Create property list for collective dataset write.
*/
plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
status = H5Dwrite(dset_id[0], H5T_NATIVE_FLOAT, memspace[0], filespace[0],
plist_id, Ex);
status = H5Dwrite(dset_id[1], H5T_NATIVE_FLOAT, memspace[1], filespace[1],
plist_id, Ey);
status = H5Dwrite(dset_id[2], H5T_NATIVE_FLOAT, memspace[2], filespace[2],
plist_id, Ez);
status = H5Dwrite(dset_id[3], H5T_NATIVE_FLOAT, memspace[3], filespace[3],
plist_id, Bx);
status = H5Dwrite(dset_id[4], H5T_NATIVE_FLOAT, memspace[4], filespace[4],
plist_id, By);
status = H5Dwrite(dset_id[5], H5T_NATIVE_FLOAT, memspace[5], filespace[5],
plist_id, Bz);
delete[]Ex;
delete[]Ey;
delete[]Ez;
delete[]Bx;
delete[]By;
delete[]Bz;
}
for (int i = 0; i < 6; i++){
H5Dclose(dset_id[i]);
H5Sclose(filespace[i]);
H5Sclose(memspace[i]);
}
H5Pclose(plist_id);
H5Fclose(file_id);
delete[] nomefile;
//////////////////////////// END of collective binary file write
}
#endif
void OUTPUT_MANAGER::prepareIntegerBigHeader(int *itodo, int uniqueN[3], int slice_rNproc[], int Ncomp){
itodo[0] = is_big_endian();
itodo[1] = uniqueN[0];
itodo[2] = uniqueN[1];
itodo[3] = uniqueN[2];
itodo[4] = slice_rNproc[0];
itodo[5] = slice_rNproc[1];
itodo[6] = slice_rNproc[2];
itodo[7] = Ncomp;
}
void OUTPUT_MANAGER::prepareFloatCoordinatesHeader(float *fcir[3], int uniqueN[3], int imin[]){
for (int c = 0; c < 3; c++){
for (int m = 0; m < uniqueN[c]; m++){
fcir[c][m] = (float)mygrid->cir[c][m + imin[c]];
}
}
}
void OUTPUT_MANAGER::writeBigHeader(MPI_File thefile, int uniqueN[3], int imin[3], int slice_rNproc[3], int Ncomp){
MPI_Status status;
int itodo[8];
float *fcir[3];