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mmeineke |
723 |
#define _FILE_OFFSET_BITS 64 |
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gezelter |
829 |
#include <string.h> |
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mmeineke |
377 |
#include <iostream> |
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#include <fstream> |
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tim |
929 |
#include <algorithm> |
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#include <utility> |
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mmeineke |
377 |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#include "mpiSimulation.hpp" |
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mmeineke |
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namespace dWrite{ |
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gezelter |
907 |
void DieDieDie( void ); |
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mmeineke |
440 |
} |
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using namespace dWrite; |
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mmeineke |
377 |
#endif //is_mpi |
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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entry_plug = the_entry_plug; |
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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tim |
837 |
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tim |
929 |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
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tim |
837 |
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tim |
929 |
if( !dumpFile ){ |
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tim |
837 |
|
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mmeineke |
377 |
sprintf( painCave.errMsg, |
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"Could not open \"%s\" for dump output.\n", |
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tim |
929 |
entry_plug->sampleName); |
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mmeineke |
377 |
painCave.isFatal = 1; |
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simError(); |
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} |
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mmeineke |
469 |
|
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mmeineke |
377 |
//outFile.setf( ios::scientific ); |
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#ifdef IS_MPI |
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} |
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tim |
929 |
//sort the local atoms by global index |
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sortByGlobalIndex(); |
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mmeineke |
377 |
sprintf( checkPointMsg, |
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"Sucessfully opened output file for dumping.\n"); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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DumpWriter::~DumpWriter( ){ |
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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tim |
929 |
dumpFile.close(); |
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mmeineke |
377 |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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tim |
929 |
#ifdef IS_MPI |
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tim |
837 |
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tim |
929 |
/** |
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* A hook function to load balancing |
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*/ |
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void DumpWriter::update(){ |
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sortByGlobalIndex(); |
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} |
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/** |
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* Auxiliary sorting function |
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*/ |
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bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
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return p1.second < p2.second; |
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} |
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/** |
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* Sorting the local index by global index |
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*/ |
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void DumpWriter::sortByGlobalIndex(){ |
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Atom** atoms = entry_plug->atoms; |
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indexArray.clear(); |
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for(int i = 0; i < mpiSim->getMyNlocal();i++) |
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indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
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} |
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#endif |
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void DumpWriter::writeDump(double currentTime){ |
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// write to eor file |
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writeFinal(currentTime); |
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//write to dump file |
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writeFrame(dumpFile, currentTime); |
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} |
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void DumpWriter::writeFinal(double currentTime){ |
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ofstream finalOut; |
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//Open eor file |
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
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if( !finalOut ){ |
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for final dump output.\n", |
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entry_plug->finalName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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#ifdef IS_MPI |
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} |
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#endif |
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//write to eor file |
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writeFrame(finalOut, currentTime); |
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//close eor file |
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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finalOut.close(); |
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} |
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#endif // is_mpi |
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} |
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void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){ |
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mmeineke |
377 |
const int BUFFERSIZE = 2000; |
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gezelter |
912 |
const int MINIBUFFERSIZE = 100; |
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gezelter |
907 |
|
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mmeineke |
377 |
char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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156 |
mmeineke |
787 |
int i; |
157 |
gezelter |
916 |
|
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mmeineke |
787 |
#ifdef IS_MPI |
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gezelter |
916 |
|
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int *potatoes; |
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int myPotato; |
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int nProc; |
164 |
tim |
929 |
int j, which_node, done, which_atom, local_index, currentIndex; |
165 |
gezelter |
916 |
double atomData6[6]; |
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double atomData13[13]; |
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gezelter |
907 |
int isDirectional; |
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char* atomTypeString; |
169 |
gezelter |
910 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
170 |
gezelter |
916 |
|
171 |
mmeineke |
787 |
#else //is_mpi |
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int nAtoms = entry_plug->n_atoms; |
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#endif //is_mpi |
174 |
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175 |
mmeineke |
377 |
double q[4]; |
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DirectionalAtom* dAtom; |
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Atom** atoms = entry_plug->atoms; |
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mmeineke |
670 |
double pos[3], vel[3]; |
179 |
tim |
837 |
|
180 |
mmeineke |
377 |
#ifndef IS_MPI |
181 |
tim |
837 |
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182 |
mmeineke |
377 |
outFile << nAtoms << "\n"; |
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tim |
837 |
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outFile << currentTime << ";\t" |
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mmeineke |
590 |
<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
188 |
mmeineke |
572 |
|
189 |
mmeineke |
590 |
<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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mmeineke |
572 |
|
193 |
mmeineke |
590 |
<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
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//write out additional parameters, such as chi and eta |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
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outFile << endl; |
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200 |
mmeineke |
377 |
for( i=0; i<nAtoms; i++ ){ |
201 |
tim |
837 |
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mmeineke |
670 |
atoms[i]->getPos(pos); |
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atoms[i]->getVel(vel); |
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mmeineke |
377 |
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
208 |
mmeineke |
670 |
pos[0], |
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pos[1], |
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pos[2], |
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vel[0], |
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vel[1], |
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vel[2]); |
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mmeineke |
377 |
strcpy( writeLine, tempBuffer ); |
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216 |
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if( atoms[i]->isDirectional() ){ |
217 |
tim |
837 |
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218 |
mmeineke |
377 |
dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
220 |
tim |
837 |
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mmeineke |
377 |
sprintf( tempBuffer, |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[0], |
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q[1], |
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q[2], |
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q[3], |
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dAtom->getJx(), |
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dAtom->getJy(), |
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dAtom->getJz()); |
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strcat( writeLine, tempBuffer ); |
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} |
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else |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
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tim |
837 |
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mmeineke |
377 |
outFile << writeLine; |
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} |
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#else // is_mpi |
239 |
gezelter |
416 |
|
240 |
chuckv |
913 |
/* code to find maximum tag value */ |
241 |
tim |
919 |
|
242 |
tim |
920 |
int *tagub, flag, MAXTAG; |
243 |
chuckv |
913 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
244 |
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if (flag) { |
245 |
tim |
920 |
MAXTAG = *tagub; |
246 |
chuckv |
913 |
} else { |
247 |
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MAXTAG = 32767; |
248 |
gezelter |
916 |
} |
249 |
mmeineke |
440 |
|
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int haveError; |
251 |
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252 |
mmeineke |
447 |
MPI_Status istatus; |
253 |
gezelter |
416 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
254 |
tim |
837 |
|
255 |
mmeineke |
377 |
// write out header and node 0's coordinates |
256 |
tim |
837 |
|
257 |
mmeineke |
377 |
if( worldRank == 0 ){ |
258 |
gezelter |
916 |
|
259 |
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// Node 0 needs a list of the magic potatoes for each processor; |
260 |
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261 |
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nProc = mpiSim->getNumberProcessors(); |
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potatoes = new int[nProc]; |
263 |
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264 |
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for (i = 0; i < nProc; i++) |
265 |
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potatoes[i] = 0; |
266 |
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267 |
mmeineke |
377 |
outFile << mpiSim->getTotAtoms() << "\n"; |
268 |
tim |
837 |
|
269 |
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outFile << currentTime << ";\t" |
270 |
gezelter |
591 |
<< entry_plug->Hmat[0][0] << "\t" |
271 |
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<< entry_plug->Hmat[1][0] << "\t" |
272 |
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<< entry_plug->Hmat[2][0] << ";\t" |
273 |
tim |
837 |
|
274 |
gezelter |
591 |
<< entry_plug->Hmat[0][1] << "\t" |
275 |
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<< entry_plug->Hmat[1][1] << "\t" |
276 |
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<< entry_plug->Hmat[2][1] << ";\t" |
277 |
tim |
837 |
|
278 |
gezelter |
591 |
<< entry_plug->Hmat[0][2] << "\t" |
279 |
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<< entry_plug->Hmat[1][2] << "\t" |
280 |
tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
281 |
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282 |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
283 |
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outFile << endl; |
284 |
chuckv |
434 |
outFile.flush(); |
285 |
tim |
929 |
|
286 |
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currentIndex = 0; |
287 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
288 |
chuckv |
913 |
|
289 |
gezelter |
417 |
// Get the Node number which has this atom; |
290 |
chuckv |
913 |
|
291 |
tim |
837 |
which_node = AtomToProcMap[i]; |
292 |
chuckv |
913 |
|
293 |
gezelter |
907 |
if (which_node != 0) { |
294 |
gezelter |
916 |
|
295 |
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if (potatoes[which_node] + 3 >= MAXTAG) { |
296 |
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// The potato was going to exceed the maximum value, |
297 |
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// so wrap this processor potato back to 0: |
298 |
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299 |
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potatoes[which_node] = 0; |
300 |
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MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
301 |
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302 |
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} |
303 |
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304 |
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myPotato = potatoes[which_node]; |
305 |
gezelter |
907 |
|
306 |
gezelter |
910 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
307 |
gezelter |
916 |
myPotato, MPI_COMM_WORLD, &istatus); |
308 |
gezelter |
907 |
|
309 |
tim |
920 |
atomTypeString = MPIatomTypeString; |
310 |
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311 |
gezelter |
916 |
myPotato++; |
312 |
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313 |
gezelter |
907 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
314 |
gezelter |
916 |
myPotato, MPI_COMM_WORLD, &istatus); |
315 |
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316 |
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myPotato++; |
317 |
gezelter |
907 |
|
318 |
gezelter |
916 |
if (isDirectional) { |
319 |
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MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
320 |
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myPotato, MPI_COMM_WORLD, &istatus); |
321 |
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} else { |
322 |
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MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
323 |
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myPotato, MPI_COMM_WORLD, &istatus); |
324 |
gezelter |
907 |
} |
325 |
gezelter |
916 |
|
326 |
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myPotato++; |
327 |
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potatoes[which_node] = myPotato; |
328 |
gezelter |
907 |
|
329 |
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} else { |
330 |
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|
331 |
mmeineke |
440 |
haveError = 0; |
332 |
chuckv |
436 |
which_atom = i; |
333 |
gezelter |
916 |
|
334 |
tim |
929 |
local_index = indexArray[currentIndex].first; |
335 |
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|
336 |
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if (which_atom == indexArray[currentIndex].second) { |
337 |
gezelter |
916 |
|
338 |
gezelter |
907 |
atomTypeString = atoms[local_index]->getType(); |
339 |
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|
340 |
mmeineke |
670 |
atoms[local_index]->getPos(pos); |
341 |
gezelter |
916 |
atoms[local_index]->getVel(vel); |
342 |
mmeineke |
670 |
|
343 |
gezelter |
916 |
atomData6[0] = pos[0]; |
344 |
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atomData6[1] = pos[1]; |
345 |
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atomData6[2] = pos[2]; |
346 |
tim |
837 |
|
347 |
gezelter |
916 |
atomData6[3] = vel[0]; |
348 |
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atomData6[4] = vel[1]; |
349 |
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atomData6[5] = vel[2]; |
350 |
gezelter |
907 |
|
351 |
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isDirectional = 0; |
352 |
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|
353 |
chuckv |
436 |
if( atoms[local_index]->isDirectional() ){ |
354 |
tim |
837 |
|
355 |
gezelter |
907 |
isDirectional = 1; |
356 |
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|
357 |
chuckv |
436 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
358 |
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dAtom->getQ( q ); |
359 |
gezelter |
916 |
|
360 |
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for (int j = 0; j < 6 ; j++) |
361 |
|
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atomData13[j] = atomData6[j]; |
362 |
gezelter |
907 |
|
363 |
gezelter |
916 |
atomData13[6] = q[0]; |
364 |
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atomData13[7] = q[1]; |
365 |
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atomData13[8] = q[2]; |
366 |
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atomData13[9] = q[3]; |
367 |
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|
368 |
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atomData13[10] = dAtom->getJx(); |
369 |
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atomData13[11] = dAtom->getJy(); |
370 |
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atomData13[12] = dAtom->getJz(); |
371 |
gezelter |
907 |
} |
372 |
gezelter |
916 |
|
373 |
gezelter |
907 |
} else { |
374 |
mmeineke |
440 |
sprintf(painCave.errMsg, |
375 |
|
|
"Atom %d not found on processor %d\n", |
376 |
|
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i, worldRank ); |
377 |
|
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haveError= 1; |
378 |
|
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simError(); |
379 |
tim |
837 |
} |
380 |
gezelter |
916 |
|
381 |
gezelter |
907 |
if(haveError) DieDieDie(); |
382 |
gezelter |
916 |
|
383 |
tim |
929 |
currentIndex ++; |
384 |
tim |
926 |
} |
385 |
|
|
// If we've survived to here, format the line: |
386 |
|
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|
387 |
|
|
if (!isDirectional) { |
388 |
|
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|
389 |
tim |
929 |
sprintf( writeLine, |
390 |
tim |
926 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
391 |
|
|
atomTypeString, |
392 |
|
|
atomData6[0], |
393 |
|
|
atomData6[1], |
394 |
|
|
atomData6[2], |
395 |
|
|
atomData6[3], |
396 |
|
|
atomData6[4], |
397 |
|
|
atomData6[5]); |
398 |
tim |
929 |
|
399 |
tim |
926 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
400 |
|
|
|
401 |
|
|
} else { |
402 |
|
|
|
403 |
tim |
929 |
sprintf( writeLine, |
404 |
tim |
926 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
405 |
|
|
atomTypeString, |
406 |
|
|
atomData13[0], |
407 |
|
|
atomData13[1], |
408 |
|
|
atomData13[2], |
409 |
|
|
atomData13[3], |
410 |
|
|
atomData13[4], |
411 |
|
|
atomData13[5], |
412 |
|
|
atomData13[6], |
413 |
|
|
atomData13[7], |
414 |
|
|
atomData13[8], |
415 |
|
|
atomData13[9], |
416 |
|
|
atomData13[10], |
417 |
|
|
atomData13[11], |
418 |
|
|
atomData13[12]); |
419 |
gezelter |
907 |
|
420 |
|
|
} |
421 |
tim |
926 |
|
422 |
|
|
outFile << writeLine; |
423 |
mmeineke |
377 |
} |
424 |
tim |
926 |
|
425 |
mmeineke |
377 |
|
426 |
gezelter |
907 |
outFile.flush(); |
427 |
|
|
sprintf( checkPointMsg, |
428 |
|
|
"Sucessfully took a dump.\n"); |
429 |
|
|
MPIcheckPoint(); |
430 |
tim |
919 |
delete[] potatoes; |
431 |
gezelter |
415 |
} else { |
432 |
tim |
837 |
|
433 |
gezelter |
907 |
// worldRank != 0, so I'm a remote node. |
434 |
gezelter |
916 |
|
435 |
|
|
// Set my magic potato to 0: |
436 |
|
|
|
437 |
|
|
myPotato = 0; |
438 |
tim |
929 |
currentIndex = 0; |
439 |
gezelter |
907 |
|
440 |
|
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
441 |
|
|
|
442 |
|
|
// Am I the node which has this atom? |
443 |
|
|
|
444 |
|
|
if (AtomToProcMap[i] == worldRank) { |
445 |
tim |
837 |
|
446 |
gezelter |
916 |
if (myPotato + 3 >= MAXTAG) { |
447 |
|
|
|
448 |
|
|
// The potato was going to exceed the maximum value, |
449 |
|
|
// so wrap this processor potato back to 0 (and block until |
450 |
|
|
// node 0 says we can go: |
451 |
|
|
|
452 |
|
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
453 |
|
|
|
454 |
|
|
} |
455 |
tim |
919 |
which_atom = i; |
456 |
tim |
929 |
local_index = indexArray[currentIndex].first; |
457 |
tim |
920 |
|
458 |
tim |
929 |
if (which_atom == indexArray[currentIndex].second) { |
459 |
gezelter |
907 |
|
460 |
|
|
atomTypeString = atoms[local_index]->getType(); |
461 |
tim |
837 |
|
462 |
gezelter |
907 |
atoms[local_index]->getPos(pos); |
463 |
|
|
atoms[local_index]->getVel(vel); |
464 |
tim |
837 |
|
465 |
gezelter |
916 |
atomData6[0] = pos[0]; |
466 |
|
|
atomData6[1] = pos[1]; |
467 |
|
|
atomData6[2] = pos[2]; |
468 |
tim |
837 |
|
469 |
gezelter |
916 |
atomData6[3] = vel[0]; |
470 |
|
|
atomData6[4] = vel[1]; |
471 |
|
|
atomData6[5] = vel[2]; |
472 |
gezelter |
907 |
|
473 |
|
|
isDirectional = 0; |
474 |
tim |
837 |
|
475 |
gezelter |
907 |
if( atoms[local_index]->isDirectional() ){ |
476 |
mmeineke |
377 |
|
477 |
gezelter |
907 |
isDirectional = 1; |
478 |
|
|
|
479 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
480 |
|
|
dAtom->getQ( q ); |
481 |
|
|
|
482 |
gezelter |
916 |
for (int j = 0; j < 6 ; j++) |
483 |
|
|
atomData13[j] = atomData6[j]; |
484 |
|
|
|
485 |
|
|
atomData13[6] = q[0]; |
486 |
|
|
atomData13[7] = q[1]; |
487 |
|
|
atomData13[8] = q[2]; |
488 |
|
|
atomData13[9] = q[3]; |
489 |
mmeineke |
670 |
|
490 |
gezelter |
916 |
atomData13[10] = dAtom->getJx(); |
491 |
|
|
atomData13[11] = dAtom->getJy(); |
492 |
|
|
atomData13[12] = dAtom->getJz(); |
493 |
gezelter |
907 |
} |
494 |
tim |
837 |
|
495 |
gezelter |
907 |
} else { |
496 |
|
|
sprintf(painCave.errMsg, |
497 |
|
|
"Atom %d not found on processor %d\n", |
498 |
|
|
i, worldRank ); |
499 |
|
|
haveError= 1; |
500 |
|
|
simError(); |
501 |
|
|
} |
502 |
tim |
837 |
|
503 |
gezelter |
916 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
504 |
tim |
837 |
|
505 |
gezelter |
916 |
// null terminate the string before sending (just in case): |
506 |
|
|
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
507 |
tim |
837 |
|
508 |
gezelter |
910 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
509 |
gezelter |
916 |
myPotato, MPI_COMM_WORLD); |
510 |
gezelter |
907 |
|
511 |
gezelter |
916 |
myPotato++; |
512 |
|
|
|
513 |
gezelter |
907 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
514 |
gezelter |
916 |
myPotato, MPI_COMM_WORLD); |
515 |
gezelter |
907 |
|
516 |
gezelter |
916 |
myPotato++; |
517 |
|
|
|
518 |
gezelter |
907 |
if (isDirectional) { |
519 |
|
|
|
520 |
gezelter |
916 |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
521 |
|
|
myPotato, MPI_COMM_WORLD); |
522 |
gezelter |
907 |
|
523 |
gezelter |
916 |
} else { |
524 |
|
|
|
525 |
|
|
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
526 |
|
|
myPotato, MPI_COMM_WORLD); |
527 |
gezelter |
907 |
} |
528 |
gezelter |
916 |
|
529 |
tim |
929 |
myPotato++; |
530 |
|
|
currentIndex++; |
531 |
mmeineke |
377 |
} |
532 |
gezelter |
907 |
} |
533 |
mmeineke |
440 |
|
534 |
gezelter |
907 |
sprintf( checkPointMsg, |
535 |
gezelter |
916 |
"Sucessfully took a dump.\n"); |
536 |
gezelter |
907 |
MPIcheckPoint(); |
537 |
|
|
|
538 |
gezelter |
916 |
} |
539 |
gezelter |
907 |
|
540 |
mmeineke |
377 |
#endif // is_mpi |
541 |
|
|
} |
542 |
mmeineke |
440 |
|
543 |
|
|
#ifdef IS_MPI |
544 |
|
|
|
545 |
|
|
// a couple of functions to let us escape the write loop |
546 |
|
|
|
547 |
gezelter |
907 |
void dWrite::DieDieDie( void ){ |
548 |
tim |
837 |
|
549 |
mmeineke |
440 |
MPI_Finalize(); |
550 |
|
|
exit (0); |
551 |
|
|
} |
552 |
|
|
|
553 |
|
|
#endif //is_mpi |