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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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#ifdef IS_MPI |
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#include <mpi.h> |
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#include "mpiSimulation.hpp" |
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mmeineke |
440 |
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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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mmeineke |
377 |
strcpy( outName, entry_plug->sampleName ); |
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tim |
837 |
|
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mmeineke |
377 |
outFile.open(outName, ios::out | ios::trunc ); |
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tim |
837 |
|
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mmeineke |
377 |
if( !outFile ){ |
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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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outName); |
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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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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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outFile.close(); |
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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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void DumpWriter::writeDump( double currentTime ){ |
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tim |
837 |
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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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mmeineke |
787 |
int i; |
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#ifdef IS_MPI |
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int j, which_node, done, which_atom, local_index; |
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gezelter |
907 |
double atomTransData[6]; |
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double atomOrientData[7]; |
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int isDirectional; |
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char* atomTypeString; |
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gezelter |
910 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
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gezelter |
907 |
int me; |
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int atomTypeTag; |
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int atomIsDirectionalTag; |
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int atomTransDataTag; |
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int atomOrientDataTag; |
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mmeineke |
787 |
#else //is_mpi |
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int nAtoms = entry_plug->n_atoms; |
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#endif //is_mpi |
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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]; |
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tim |
837 |
|
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mmeineke |
804 |
// write current frame to the eor file |
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mmeineke |
377 |
|
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mmeineke |
804 |
this->writeFinal( currentTime ); |
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mmeineke |
377 |
#ifndef IS_MPI |
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tim |
837 |
|
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mmeineke |
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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" |
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mmeineke |
572 |
|
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mmeineke |
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<< 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 |
|
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mmeineke |
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<< 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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mmeineke |
377 |
for( i=0; i<nAtoms; i++ ){ |
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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(), |
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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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if( atoms[i]->isDirectional() ){ |
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tim |
837 |
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mmeineke |
377 |
dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
140 |
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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} |
152 |
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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" ); |
154 |
tim |
837 |
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mmeineke |
377 |
outFile << writeLine; |
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} |
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outFile.flush(); |
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#else // is_mpi |
160 |
gezelter |
416 |
|
161 |
chuckv |
913 |
/* code to find maximum tag value */ |
162 |
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int *tagub, flag, MAXTAG; |
163 |
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MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
164 |
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if (flag) { |
165 |
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MAXTAG = *tagub; |
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} else { |
167 |
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MAXTAG = 32767; |
168 |
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} |
169 |
mmeineke |
440 |
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170 |
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int haveError; |
171 |
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172 |
mmeineke |
447 |
MPI_Status istatus; |
173 |
gezelter |
416 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
174 |
tim |
837 |
|
175 |
mmeineke |
377 |
// write out header and node 0's coordinates |
176 |
tim |
837 |
|
177 |
mmeineke |
377 |
if( worldRank == 0 ){ |
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outFile << mpiSim->getTotAtoms() << "\n"; |
179 |
tim |
837 |
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180 |
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outFile << currentTime << ";\t" |
181 |
gezelter |
591 |
<< 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" |
184 |
tim |
837 |
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gezelter |
591 |
<< 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" |
188 |
tim |
837 |
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189 |
gezelter |
591 |
<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
191 |
tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
192 |
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193 |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
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outFile << endl; |
195 |
chuckv |
434 |
outFile.flush(); |
196 |
chuckv |
913 |
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tag = 0; |
198 |
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199 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
200 |
chuckv |
913 |
|
201 |
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if (tag + 2 >= MAXTAG) { |
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// The tag was going to exceed the maximum value, so wrap around to 0: |
203 |
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tag = 0; |
204 |
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// Send the newly zeroed tag on to the other nodes: |
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MPI_Bcast(&tag, 1, MPI_INT, 0, MPI_COMM_WORLD); |
206 |
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} |
207 |
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208 |
gezelter |
417 |
// Get the Node number which has this atom; |
209 |
chuckv |
913 |
|
210 |
tim |
837 |
which_node = AtomToProcMap[i]; |
211 |
chuckv |
913 |
|
212 |
gezelter |
907 |
if (which_node != 0) { |
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gezelter |
910 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
215 |
gezelter |
907 |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
216 |
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217 |
gezelter |
910 |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
218 |
gezelter |
912 |
|
219 |
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// Null terminate the atomTypeString just in case: |
220 |
gezelter |
910 |
|
221 |
gezelter |
912 |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
222 |
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223 |
gezelter |
907 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
224 |
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atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
225 |
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226 |
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MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
227 |
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atomTransDataTag, MPI_COMM_WORLD, &istatus); |
228 |
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229 |
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if (isDirectional) { |
230 |
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231 |
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MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
232 |
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atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
233 |
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234 |
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} |
235 |
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236 |
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} else { |
237 |
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238 |
mmeineke |
440 |
haveError = 0; |
239 |
chuckv |
436 |
which_atom = i; |
240 |
tim |
837 |
local_index=-1; |
241 |
gezelter |
907 |
|
242 |
chuckv |
436 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
243 |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
244 |
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} |
245 |
gezelter |
907 |
|
246 |
chuckv |
436 |
if (local_index != -1) { |
247 |
tim |
837 |
|
248 |
gezelter |
907 |
atomTypeString = atoms[local_index]->getType(); |
249 |
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250 |
mmeineke |
670 |
atoms[local_index]->getPos(pos); |
251 |
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atoms[local_index]->getVel(vel); |
252 |
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253 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
254 |
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atomTransData[1] = pos[1]; |
255 |
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atomTransData[2] = pos[2]; |
256 |
tim |
837 |
|
257 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
258 |
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atomTransData[4] = vel[1]; |
259 |
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atomTransData[5] = vel[2]; |
260 |
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261 |
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isDirectional = 0; |
262 |
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|
263 |
chuckv |
436 |
if( atoms[local_index]->isDirectional() ){ |
264 |
tim |
837 |
|
265 |
gezelter |
907 |
isDirectional = 1; |
266 |
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|
267 |
chuckv |
436 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
268 |
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dAtom->getQ( q ); |
269 |
gezelter |
907 |
|
270 |
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atomOrientData[0] = q[0]; |
271 |
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atomOrientData[1] = q[1]; |
272 |
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atomOrientData[2] = q[2]; |
273 |
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atomOrientData[3] = q[3]; |
274 |
tim |
837 |
|
275 |
gezelter |
907 |
atomOrientData[4] = dAtom->getJx(); |
276 |
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atomOrientData[5] = dAtom->getJy(); |
277 |
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atomOrientData[6] = dAtom->getJz(); |
278 |
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} |
279 |
tim |
837 |
|
280 |
gezelter |
907 |
} else { |
281 |
mmeineke |
440 |
sprintf(painCave.errMsg, |
282 |
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"Atom %d not found on processor %d\n", |
283 |
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i, worldRank ); |
284 |
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haveError= 1; |
285 |
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simError(); |
286 |
tim |
837 |
} |
287 |
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288 |
gezelter |
907 |
if(haveError) DieDieDie(); |
289 |
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290 |
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// If we've survived to here, format the line: |
291 |
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292 |
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sprintf( tempBuffer, |
293 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
294 |
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atomTypeString, |
295 |
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atomTransData[0], |
296 |
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atomTransData[1], |
297 |
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atomTransData[2], |
298 |
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atomTransData[3], |
299 |
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atomTransData[4], |
300 |
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atomTransData[5]); |
301 |
mmeineke |
440 |
|
302 |
gezelter |
907 |
strcpy( writeLine, tempBuffer ); |
303 |
tim |
837 |
|
304 |
gezelter |
907 |
if (isDirectional) { |
305 |
mmeineke |
440 |
|
306 |
gezelter |
907 |
sprintf( tempBuffer, |
307 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
308 |
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atomOrientData[0], |
309 |
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atomOrientData[1], |
310 |
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atomOrientData[2], |
311 |
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atomOrientData[3], |
312 |
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atomOrientData[4], |
313 |
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atomOrientData[5], |
314 |
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atomOrientData[6]); |
315 |
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strcat( writeLine, tempBuffer ); |
316 |
tim |
837 |
|
317 |
gezelter |
907 |
} else { |
318 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
319 |
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} |
320 |
tim |
837 |
|
321 |
gezelter |
907 |
outFile << writeLine; |
322 |
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outFile.flush(); |
323 |
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} |
324 |
mmeineke |
377 |
} |
325 |
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|
326 |
gezelter |
907 |
outFile.flush(); |
327 |
|
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sprintf( checkPointMsg, |
328 |
|
|
"Sucessfully took a dump.\n"); |
329 |
|
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MPIcheckPoint(); |
330 |
|
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|
331 |
gezelter |
415 |
} else { |
332 |
tim |
837 |
|
333 |
gezelter |
907 |
// worldRank != 0, so I'm a remote node. |
334 |
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|
335 |
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
336 |
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|
337 |
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// Am I the node which has this atom? |
338 |
|
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|
339 |
|
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if (AtomToProcMap[i] == worldRank) { |
340 |
tim |
837 |
|
341 |
gezelter |
907 |
local_index=-1; |
342 |
|
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for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
343 |
|
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
344 |
|
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} |
345 |
|
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if (local_index != -1) { |
346 |
|
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|
347 |
|
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atomTypeString = atoms[local_index]->getType(); |
348 |
mmeineke |
440 |
|
349 |
gezelter |
907 |
atoms[local_index]->getPos(pos); |
350 |
|
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atoms[local_index]->getVel(vel); |
351 |
tim |
837 |
|
352 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
353 |
|
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atomTransData[1] = pos[1]; |
354 |
|
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atomTransData[2] = pos[2]; |
355 |
mmeineke |
440 |
|
356 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
357 |
|
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atomTransData[4] = vel[1]; |
358 |
|
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atomTransData[5] = vel[2]; |
359 |
|
|
|
360 |
|
|
isDirectional = 0; |
361 |
tim |
837 |
|
362 |
gezelter |
907 |
if( atoms[local_index]->isDirectional() ){ |
363 |
mmeineke |
670 |
|
364 |
gezelter |
907 |
isDirectional = 1; |
365 |
|
|
|
366 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
367 |
|
|
dAtom->getQ( q ); |
368 |
|
|
|
369 |
|
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atomOrientData[0] = q[0]; |
370 |
|
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atomOrientData[1] = q[1]; |
371 |
|
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atomOrientData[2] = q[2]; |
372 |
|
|
atomOrientData[3] = q[3]; |
373 |
mmeineke |
670 |
|
374 |
gezelter |
907 |
atomOrientData[4] = dAtom->getJx(); |
375 |
|
|
atomOrientData[5] = dAtom->getJy(); |
376 |
|
|
atomOrientData[6] = dAtom->getJz(); |
377 |
|
|
} |
378 |
tim |
837 |
|
379 |
gezelter |
907 |
} else { |
380 |
|
|
sprintf(painCave.errMsg, |
381 |
|
|
"Atom %d not found on processor %d\n", |
382 |
|
|
i, worldRank ); |
383 |
|
|
haveError= 1; |
384 |
|
|
simError(); |
385 |
|
|
} |
386 |
tim |
837 |
|
387 |
gezelter |
907 |
// I've survived this far, so send off the data! |
388 |
tim |
837 |
|
389 |
gezelter |
907 |
atomTypeTag = 4*i; |
390 |
|
|
atomIsDirectionalTag = 4*i + 1; |
391 |
|
|
atomTransDataTag = 4*i + 2; |
392 |
|
|
atomOrientDataTag = 4*i + 3; |
393 |
mmeineke |
440 |
|
394 |
gezelter |
910 |
|
395 |
|
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
396 |
|
|
|
397 |
gezelter |
912 |
// null terminate the string before sending (just in case): |
398 |
|
|
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
399 |
|
|
|
400 |
gezelter |
910 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
401 |
gezelter |
907 |
atomTypeTag, MPI_COMM_WORLD); |
402 |
|
|
|
403 |
|
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
404 |
|
|
atomIsDirectionalTag, MPI_COMM_WORLD); |
405 |
|
|
|
406 |
|
|
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
407 |
|
|
atomTransDataTag, MPI_COMM_WORLD); |
408 |
|
|
|
409 |
|
|
if (isDirectional) { |
410 |
|
|
|
411 |
|
|
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
412 |
|
|
atomOrientDataTag, MPI_COMM_WORLD); |
413 |
|
|
|
414 |
|
|
} |
415 |
|
|
|
416 |
mmeineke |
377 |
} |
417 |
gezelter |
907 |
} |
418 |
mmeineke |
440 |
|
419 |
gezelter |
907 |
sprintf( checkPointMsg, |
420 |
|
|
"Sucessfully took a dump.\n"); |
421 |
|
|
MPIcheckPoint(); |
422 |
|
|
|
423 |
tim |
837 |
} |
424 |
gezelter |
907 |
|
425 |
mmeineke |
440 |
painCave.isEventLoop = 0; |
426 |
|
|
|
427 |
mmeineke |
377 |
#endif // is_mpi |
428 |
|
|
} |
429 |
|
|
|
430 |
mmeineke |
572 |
void DumpWriter::writeFinal(double finalTime){ |
431 |
gezelter |
416 |
|
432 |
mmeineke |
377 |
char finalName[500]; |
433 |
|
|
ofstream finalOut; |
434 |
gezelter |
416 |
|
435 |
|
|
const int BUFFERSIZE = 2000; |
436 |
gezelter |
912 |
const int MINIBUFFERSIZE = 100; |
437 |
gezelter |
416 |
char tempBuffer[BUFFERSIZE]; |
438 |
tim |
837 |
char writeLine[BUFFERSIZE]; |
439 |
gezelter |
416 |
|
440 |
|
|
double q[4]; |
441 |
|
|
DirectionalAtom* dAtom; |
442 |
mmeineke |
787 |
Atom** atoms = entry_plug->atoms; |
443 |
|
|
int i; |
444 |
|
|
#ifdef IS_MPI |
445 |
|
|
int j, which_node, done, which_atom, local_index; |
446 |
gezelter |
907 |
double atomTransData[6]; |
447 |
|
|
double atomOrientData[7]; |
448 |
|
|
int isDirectional; |
449 |
|
|
char* atomTypeString; |
450 |
gezelter |
910 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
451 |
gezelter |
907 |
int atomTypeTag; |
452 |
|
|
int atomIsDirectionalTag; |
453 |
|
|
int atomTransDataTag; |
454 |
|
|
int atomOrientDataTag; |
455 |
mmeineke |
787 |
#else //is_mpi |
456 |
gezelter |
416 |
int nAtoms = entry_plug->n_atoms; |
457 |
mmeineke |
787 |
#endif //is_mpi |
458 |
tim |
837 |
|
459 |
mmeineke |
670 |
double pos[3], vel[3]; |
460 |
tim |
837 |
|
461 |
mmeineke |
377 |
#ifdef IS_MPI |
462 |
|
|
if(worldRank == 0 ){ |
463 |
|
|
#endif // is_mpi |
464 |
tim |
837 |
|
465 |
mmeineke |
377 |
strcpy( finalName, entry_plug->finalName ); |
466 |
tim |
837 |
|
467 |
mmeineke |
377 |
finalOut.open( finalName, ios::out | ios::trunc ); |
468 |
|
|
if( !finalOut ){ |
469 |
|
|
sprintf( painCave.errMsg, |
470 |
|
|
"Could not open \"%s\" for final dump output.\n", |
471 |
|
|
finalName ); |
472 |
|
|
painCave.isFatal = 1; |
473 |
|
|
simError(); |
474 |
|
|
} |
475 |
tim |
837 |
|
476 |
mmeineke |
377 |
// finalOut.setf( ios::scientific ); |
477 |
tim |
837 |
|
478 |
mmeineke |
377 |
#ifdef IS_MPI |
479 |
|
|
} |
480 |
tim |
837 |
|
481 |
mmeineke |
377 |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
482 |
tim |
837 |
MPIcheckPoint(); |
483 |
|
|
|
484 |
mmeineke |
377 |
#endif //is_mpi |
485 |
|
|
|
486 |
tim |
837 |
|
487 |
mmeineke |
377 |
#ifndef IS_MPI |
488 |
tim |
837 |
|
489 |
mmeineke |
377 |
finalOut << nAtoms << "\n"; |
490 |
tim |
837 |
|
491 |
gezelter |
591 |
finalOut << finalTime << ";\t" |
492 |
mmeineke |
590 |
<< entry_plug->Hmat[0][0] << "\t" |
493 |
|
|
<< entry_plug->Hmat[1][0] << "\t" |
494 |
gezelter |
591 |
<< entry_plug->Hmat[2][0] << ";\t" |
495 |
tim |
837 |
|
496 |
mmeineke |
590 |
<< entry_plug->Hmat[0][1] << "\t" |
497 |
|
|
<< entry_plug->Hmat[1][1] << "\t" |
498 |
gezelter |
591 |
<< entry_plug->Hmat[2][1] << ";\t" |
499 |
tim |
837 |
|
500 |
mmeineke |
590 |
<< entry_plug->Hmat[0][2] << "\t" |
501 |
|
|
<< entry_plug->Hmat[1][2] << "\t" |
502 |
tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
503 |
|
|
|
504 |
|
|
//write out additional parameters, such as chi and eta |
505 |
|
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
506 |
|
|
finalOut << endl; |
507 |
|
|
|
508 |
mmeineke |
377 |
for( i=0; i<nAtoms; i++ ){ |
509 |
tim |
837 |
|
510 |
mmeineke |
670 |
atoms[i]->getPos(pos); |
511 |
|
|
atoms[i]->getVel(vel); |
512 |
tim |
837 |
|
513 |
mmeineke |
377 |
sprintf( tempBuffer, |
514 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
515 |
|
|
atoms[i]->getType(), |
516 |
mmeineke |
670 |
pos[0], |
517 |
|
|
pos[1], |
518 |
|
|
pos[2], |
519 |
|
|
vel[0], |
520 |
|
|
vel[1], |
521 |
|
|
vel[2]); |
522 |
mmeineke |
377 |
strcpy( writeLine, tempBuffer ); |
523 |
|
|
|
524 |
|
|
if( atoms[i]->isDirectional() ){ |
525 |
tim |
837 |
|
526 |
mmeineke |
377 |
dAtom = (DirectionalAtom *)atoms[i]; |
527 |
|
|
dAtom->getQ( q ); |
528 |
tim |
837 |
|
529 |
mmeineke |
377 |
sprintf( tempBuffer, |
530 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
531 |
|
|
q[0], |
532 |
|
|
q[1], |
533 |
|
|
q[2], |
534 |
|
|
q[3], |
535 |
|
|
dAtom->getJx(), |
536 |
|
|
dAtom->getJy(), |
537 |
|
|
dAtom->getJz()); |
538 |
|
|
strcat( writeLine, tempBuffer ); |
539 |
|
|
} |
540 |
|
|
else |
541 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
542 |
tim |
837 |
|
543 |
mmeineke |
377 |
finalOut << writeLine; |
544 |
|
|
} |
545 |
|
|
finalOut.flush(); |
546 |
gezelter |
415 |
finalOut.close(); |
547 |
mmeineke |
377 |
|
548 |
|
|
#else // is_mpi |
549 |
tim |
837 |
|
550 |
mmeineke |
440 |
// first thing first, suspend fatalities. |
551 |
|
|
painCave.isEventLoop = 1; |
552 |
|
|
|
553 |
|
|
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
554 |
|
|
int haveError; |
555 |
|
|
|
556 |
mmeineke |
447 |
MPI_Status istatus; |
557 |
gezelter |
416 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
558 |
|
|
|
559 |
mmeineke |
377 |
// write out header and node 0's coordinates |
560 |
tim |
837 |
|
561 |
mmeineke |
377 |
if( worldRank == 0 ){ |
562 |
|
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
563 |
tim |
837 |
|
564 |
gezelter |
591 |
finalOut << finalTime << ";\t" |
565 |
gezelter |
907 |
<< entry_plug->Hmat[0][0] << "\t" |
566 |
|
|
<< entry_plug->Hmat[1][0] << "\t" |
567 |
|
|
<< entry_plug->Hmat[2][0] << ";\t" |
568 |
tim |
837 |
|
569 |
gezelter |
907 |
<< entry_plug->Hmat[0][1] << "\t" |
570 |
|
|
<< entry_plug->Hmat[1][1] << "\t" |
571 |
|
|
<< entry_plug->Hmat[2][1] << ";\t" |
572 |
tim |
837 |
|
573 |
gezelter |
907 |
<< entry_plug->Hmat[0][2] << "\t" |
574 |
|
|
<< entry_plug->Hmat[1][2] << "\t" |
575 |
|
|
<< entry_plug->Hmat[2][2] << ";"; |
576 |
tim |
837 |
|
577 |
|
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
578 |
|
|
finalOut << endl; |
579 |
gezelter |
907 |
finalOut.flush(); |
580 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
581 |
gezelter |
907 |
// Get the Node number which has this atom; |
582 |
tim |
837 |
|
583 |
|
|
which_node = AtomToProcMap[i]; |
584 |
|
|
|
585 |
gezelter |
907 |
if (which_node != 0) { |
586 |
|
|
|
587 |
|
|
atomTypeTag = 4*i; |
588 |
|
|
atomIsDirectionalTag = 4*i + 1; |
589 |
|
|
atomTransDataTag = 4*i + 2; |
590 |
|
|
atomOrientDataTag = 4*i + 3; |
591 |
chuckv |
437 |
|
592 |
gezelter |
910 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
593 |
gezelter |
907 |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
594 |
|
|
|
595 |
gezelter |
910 |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
596 |
|
|
|
597 |
gezelter |
907 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
598 |
|
|
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
599 |
|
|
|
600 |
|
|
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
601 |
|
|
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
602 |
|
|
|
603 |
|
|
if (isDirectional) { |
604 |
|
|
|
605 |
|
|
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
606 |
|
|
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
607 |
|
|
|
608 |
|
|
} |
609 |
|
|
|
610 |
|
|
} else { |
611 |
|
|
|
612 |
|
|
haveError = 0; |
613 |
chuckv |
437 |
which_atom = i; |
614 |
tim |
837 |
local_index=-1; |
615 |
gezelter |
907 |
|
616 |
chuckv |
437 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
617 |
|
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
618 |
|
|
} |
619 |
gezelter |
907 |
|
620 |
tim |
837 |
if (local_index != -1) { |
621 |
mmeineke |
670 |
|
622 |
gezelter |
907 |
atomTypeString = atoms[local_index]->getType(); |
623 |
|
|
|
624 |
mmeineke |
670 |
atoms[local_index]->getPos(pos); |
625 |
|
|
atoms[local_index]->getVel(vel); |
626 |
tim |
837 |
|
627 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
628 |
|
|
atomTransData[1] = pos[1]; |
629 |
|
|
atomTransData[2] = pos[2]; |
630 |
tim |
837 |
|
631 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
632 |
|
|
atomTransData[4] = vel[1]; |
633 |
|
|
atomTransData[5] = vel[2]; |
634 |
|
|
|
635 |
|
|
isDirectional = 0; |
636 |
tim |
837 |
|
637 |
gezelter |
907 |
if( atoms[local_index]->isDirectional() ){ |
638 |
tim |
837 |
|
639 |
gezelter |
907 |
isDirectional = 1; |
640 |
|
|
|
641 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
642 |
|
|
dAtom->getQ( q ); |
643 |
|
|
|
644 |
|
|
atomOrientData[0] = q[0]; |
645 |
|
|
atomOrientData[1] = q[1]; |
646 |
|
|
atomOrientData[2] = q[2]; |
647 |
|
|
atomOrientData[3] = q[3]; |
648 |
|
|
|
649 |
|
|
atomOrientData[4] = dAtom->getJx(); |
650 |
|
|
atomOrientData[5] = dAtom->getJy(); |
651 |
|
|
atomOrientData[6] = dAtom->getJz(); |
652 |
|
|
} |
653 |
|
|
|
654 |
|
|
} else { |
655 |
mmeineke |
440 |
sprintf(painCave.errMsg, |
656 |
|
|
"Atom %d not found on processor %d\n", |
657 |
|
|
i, worldRank ); |
658 |
|
|
haveError= 1; |
659 |
|
|
simError(); |
660 |
tim |
837 |
} |
661 |
mmeineke |
440 |
|
662 |
gezelter |
907 |
if(haveError) DieDieDie(); |
663 |
|
|
|
664 |
|
|
// If we've survived to here, format the line: |
665 |
|
|
|
666 |
|
|
sprintf( tempBuffer, |
667 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
668 |
|
|
atomTypeString, |
669 |
|
|
atomTransData[0], |
670 |
|
|
atomTransData[1], |
671 |
|
|
atomTransData[2], |
672 |
|
|
atomTransData[3], |
673 |
|
|
atomTransData[4], |
674 |
|
|
atomTransData[5]); |
675 |
tim |
837 |
|
676 |
gezelter |
907 |
strcpy( writeLine, tempBuffer ); |
677 |
tim |
837 |
|
678 |
gezelter |
907 |
if (isDirectional) { |
679 |
tim |
837 |
|
680 |
gezelter |
907 |
sprintf( tempBuffer, |
681 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
682 |
|
|
atomOrientData[0], |
683 |
|
|
atomOrientData[1], |
684 |
|
|
atomOrientData[2], |
685 |
|
|
atomOrientData[3], |
686 |
|
|
atomOrientData[4], |
687 |
|
|
atomOrientData[5], |
688 |
|
|
atomOrientData[6]); |
689 |
|
|
strcat( writeLine, tempBuffer ); |
690 |
tim |
837 |
|
691 |
gezelter |
907 |
} else { |
692 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
693 |
|
|
} |
694 |
tim |
837 |
|
695 |
gezelter |
907 |
finalOut << writeLine; |
696 |
|
|
finalOut.flush(); |
697 |
|
|
} |
698 |
mmeineke |
377 |
} |
699 |
|
|
|
700 |
gezelter |
907 |
finalOut.flush(); |
701 |
|
|
sprintf( checkPointMsg, |
702 |
|
|
"Sucessfully took a dump.\n"); |
703 |
|
|
MPIcheckPoint(); |
704 |
|
|
|
705 |
gezelter |
415 |
} else { |
706 |
tim |
837 |
|
707 |
gezelter |
907 |
// worldRank != 0, so I'm a remote node. |
708 |
|
|
|
709 |
|
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
710 |
|
|
|
711 |
|
|
// Am I the node which has this atom? |
712 |
|
|
|
713 |
|
|
if (AtomToProcMap[i] == worldRank) { |
714 |
mmeineke |
440 |
|
715 |
gezelter |
907 |
local_index=-1; |
716 |
|
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
717 |
|
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
718 |
|
|
} |
719 |
|
|
if (local_index != -1) { |
720 |
|
|
|
721 |
|
|
atomTypeString = atoms[local_index]->getType(); |
722 |
tim |
837 |
|
723 |
gezelter |
907 |
atoms[local_index]->getPos(pos); |
724 |
|
|
atoms[local_index]->getVel(vel); |
725 |
tim |
837 |
|
726 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
727 |
|
|
atomTransData[1] = pos[1]; |
728 |
|
|
atomTransData[2] = pos[2]; |
729 |
tim |
837 |
|
730 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
731 |
|
|
atomTransData[4] = vel[1]; |
732 |
|
|
atomTransData[5] = vel[2]; |
733 |
|
|
|
734 |
|
|
isDirectional = 0; |
735 |
tim |
837 |
|
736 |
gezelter |
907 |
if( atoms[local_index]->isDirectional() ){ |
737 |
mmeineke |
377 |
|
738 |
gezelter |
907 |
isDirectional = 1; |
739 |
|
|
|
740 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
741 |
|
|
dAtom->getQ( q ); |
742 |
|
|
|
743 |
|
|
atomOrientData[0] = q[0]; |
744 |
|
|
atomOrientData[1] = q[1]; |
745 |
|
|
atomOrientData[2] = q[2]; |
746 |
|
|
atomOrientData[3] = q[3]; |
747 |
mmeineke |
670 |
|
748 |
gezelter |
907 |
atomOrientData[4] = dAtom->getJx(); |
749 |
|
|
atomOrientData[5] = dAtom->getJy(); |
750 |
|
|
atomOrientData[6] = dAtom->getJz(); |
751 |
|
|
} |
752 |
tim |
837 |
|
753 |
gezelter |
907 |
} else { |
754 |
|
|
sprintf(painCave.errMsg, |
755 |
|
|
"Atom %d not found on processor %d\n", |
756 |
|
|
i, worldRank ); |
757 |
|
|
haveError= 1; |
758 |
|
|
simError(); |
759 |
|
|
} |
760 |
tim |
837 |
|
761 |
gezelter |
907 |
// I've survived this far, so send off the data! |
762 |
tim |
837 |
|
763 |
gezelter |
907 |
atomTypeTag = 4*i; |
764 |
|
|
atomIsDirectionalTag = 4*i + 1; |
765 |
|
|
atomTransDataTag = 4*i + 2; |
766 |
|
|
atomOrientDataTag = 4*i + 3; |
767 |
tim |
837 |
|
768 |
gezelter |
910 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
769 |
|
|
|
770 |
|
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
771 |
gezelter |
907 |
atomTypeTag, MPI_COMM_WORLD); |
772 |
|
|
|
773 |
|
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
774 |
|
|
atomIsDirectionalTag, MPI_COMM_WORLD); |
775 |
|
|
|
776 |
|
|
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
777 |
|
|
atomTransDataTag, MPI_COMM_WORLD); |
778 |
|
|
|
779 |
|
|
if (isDirectional) { |
780 |
|
|
|
781 |
|
|
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
782 |
|
|
atomOrientDataTag, MPI_COMM_WORLD); |
783 |
|
|
|
784 |
|
|
} |
785 |
|
|
|
786 |
mmeineke |
377 |
} |
787 |
gezelter |
907 |
} |
788 |
mmeineke |
440 |
|
789 |
gezelter |
907 |
sprintf( checkPointMsg, |
790 |
|
|
"Sucessfully wrote final file.\n"); |
791 |
|
|
MPIcheckPoint(); |
792 |
|
|
|
793 |
gezelter |
419 |
} |
794 |
gezelter |
907 |
|
795 |
|
|
painCave.isEventLoop = 0; |
796 |
tim |
837 |
|
797 |
|
|
if( worldRank == 0 ) finalOut.close(); |
798 |
mmeineke |
377 |
#endif // is_mpi |
799 |
|
|
} |
800 |
mmeineke |
440 |
|
801 |
|
|
|
802 |
|
|
|
803 |
|
|
#ifdef IS_MPI |
804 |
|
|
|
805 |
|
|
// a couple of functions to let us escape the write loop |
806 |
|
|
|
807 |
gezelter |
907 |
void dWrite::DieDieDie( void ){ |
808 |
tim |
837 |
|
809 |
mmeineke |
440 |
MPI_Finalize(); |
810 |
|
|
exit (0); |
811 |
|
|
} |
812 |
|
|
|
813 |
|
|
#endif //is_mpi |