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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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tim |
905 |
#define TAKE_THIS_TAG_CHAR 15 |
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#define TAKE_THIS_TAG_INT 20 |
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mmeineke |
440 |
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namespace dWrite{ |
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void nodeZeroError( void ); |
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void anonymousNodeDie( void ); |
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} |
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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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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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#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 |
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|
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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 |
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<< 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 |
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 |
|
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mmeineke |
590 |
<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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tim |
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<< 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 |
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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 ); |
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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; |
148 |
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} |
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outFile.flush(); |
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#else // is_mpi |
152 |
gezelter |
416 |
|
153 |
mmeineke |
440 |
// first thing first, suspend fatalities. |
154 |
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painCave.isEventLoop = 1; |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
157 |
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int haveError; |
158 |
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mmeineke |
447 |
MPI_Status istatus; |
160 |
gezelter |
416 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
161 |
tim |
837 |
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mmeineke |
377 |
// write out header and node 0's coordinates |
163 |
tim |
837 |
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164 |
mmeineke |
377 |
if( worldRank == 0 ){ |
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outFile << mpiSim->getTotAtoms() << "\n"; |
166 |
tim |
837 |
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outFile << currentTime << ";\t" |
168 |
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" |
171 |
tim |
837 |
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172 |
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" |
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tim |
837 |
|
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gezelter |
591 |
<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
178 |
tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
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180 |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
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outFile << endl; |
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chuckv |
434 |
outFile.flush(); |
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gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
184 |
gezelter |
417 |
// Get the Node number which has this atom; |
185 |
tim |
837 |
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which_node = AtomToProcMap[i]; |
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chuckv |
436 |
if (which_node == 0 ) { |
189 |
tim |
837 |
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190 |
mmeineke |
440 |
haveError = 0; |
191 |
chuckv |
436 |
which_atom = i; |
192 |
tim |
837 |
local_index=-1; |
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chuckv |
436 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
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} |
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if (local_index != -1) { |
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//format the line |
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tim |
837 |
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mmeineke |
670 |
atoms[local_index]->getPos(pos); |
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atoms[local_index]->getVel(vel); |
201 |
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chuckv |
436 |
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[local_index]->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]); // check here. |
211 |
chuckv |
436 |
strcpy( writeLine, tempBuffer ); |
212 |
tim |
837 |
|
213 |
chuckv |
436 |
if( atoms[local_index]->isDirectional() ){ |
214 |
tim |
837 |
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chuckv |
436 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
216 |
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dAtom->getQ( q ); |
217 |
tim |
837 |
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chuckv |
436 |
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 ); |
228 |
tim |
837 |
|
229 |
chuckv |
436 |
} |
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else |
231 |
tim |
837 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
232 |
chuckv |
436 |
} |
233 |
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else { |
234 |
mmeineke |
440 |
sprintf(painCave.errMsg, |
235 |
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"Atom %d not found on processor %d\n", |
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i, worldRank ); |
237 |
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haveError= 1; |
238 |
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simError(); |
239 |
tim |
837 |
} |
240 |
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241 |
mmeineke |
440 |
if(haveError) nodeZeroError(); |
242 |
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243 |
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} |
244 |
chuckv |
436 |
else { |
245 |
mmeineke |
440 |
myStatus = 1; |
246 |
tim |
837 |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
247 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
248 |
tim |
837 |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
249 |
mmeineke |
447 |
MPI_COMM_WORLD); |
250 |
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MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
251 |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
252 |
tim |
837 |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
253 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
254 |
tim |
837 |
|
255 |
mmeineke |
440 |
if(!myStatus) nodeZeroError(); |
256 |
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257 |
mmeineke |
377 |
} |
258 |
tim |
837 |
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259 |
mmeineke |
377 |
outFile << writeLine; |
260 |
chuckv |
434 |
outFile.flush(); |
261 |
mmeineke |
377 |
} |
262 |
tim |
837 |
|
263 |
gezelter |
415 |
// kill everyone off: |
264 |
mmeineke |
440 |
myStatus = -1; |
265 |
tim |
905 |
for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
266 |
tim |
837 |
MPI_Send(&myStatus, 1, MPI_INT, j, |
267 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
268 |
mmeineke |
377 |
} |
269 |
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|
270 |
gezelter |
415 |
} else { |
271 |
tim |
837 |
|
272 |
gezelter |
415 |
done = 0; |
273 |
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while (!done) { |
274 |
tim |
837 |
|
275 |
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MPI_Recv(&myStatus, 1, MPI_INT, 0, |
276 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
277 |
mmeineke |
440 |
|
278 |
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if(!myStatus) anonymousNodeDie(); |
279 |
tim |
837 |
|
280 |
mmeineke |
440 |
if(myStatus < 0) break; |
281 |
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|
282 |
tim |
837 |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
283 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
284 |
tim |
837 |
|
285 |
mmeineke |
440 |
myStatus = 1; |
286 |
tim |
837 |
local_index=-1; |
287 |
mmeineke |
440 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
288 |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
289 |
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} |
290 |
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if (local_index != -1) { |
291 |
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//format the line |
292 |
mmeineke |
670 |
|
293 |
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atoms[local_index]->getPos(pos); |
294 |
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atoms[local_index]->getVel(vel); |
295 |
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|
296 |
mmeineke |
440 |
sprintf( tempBuffer, |
297 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
298 |
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atoms[local_index]->getType(), |
299 |
mmeineke |
670 |
pos[0], |
300 |
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pos[1], |
301 |
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pos[2], |
302 |
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vel[0], |
303 |
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vel[1], |
304 |
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vel[2]); // check here. |
305 |
mmeineke |
440 |
strcpy( writeLine, tempBuffer ); |
306 |
tim |
837 |
|
307 |
mmeineke |
440 |
if( atoms[local_index]->isDirectional() ){ |
308 |
tim |
837 |
|
309 |
mmeineke |
440 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
310 |
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dAtom->getQ( q ); |
311 |
tim |
837 |
|
312 |
mmeineke |
440 |
sprintf( tempBuffer, |
313 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
314 |
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q[0], |
315 |
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q[1], |
316 |
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q[2], |
317 |
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q[3], |
318 |
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dAtom->getJx(), |
319 |
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dAtom->getJy(), |
320 |
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dAtom->getJz()); |
321 |
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strcat( writeLine, tempBuffer ); |
322 |
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} |
323 |
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else{ |
324 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
325 |
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} |
326 |
tim |
837 |
} |
327 |
mmeineke |
440 |
else { |
328 |
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sprintf(painCave.errMsg, |
329 |
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"Atom %d not found on processor %d\n", |
330 |
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which_atom, worldRank ); |
331 |
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myStatus = 0; |
332 |
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simError(); |
333 |
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|
334 |
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strcpy( writeLine, "Hello, I'm an error.\n"); |
335 |
mmeineke |
377 |
} |
336 |
mmeineke |
440 |
|
337 |
tim |
837 |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
338 |
mmeineke |
447 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
339 |
tim |
837 |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
340 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
341 |
mmeineke |
377 |
} |
342 |
tim |
837 |
} |
343 |
gezelter |
415 |
outFile.flush(); |
344 |
|
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sprintf( checkPointMsg, |
345 |
|
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"Sucessfully took a dump.\n"); |
346 |
|
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MPIcheckPoint(); |
347 |
mmeineke |
440 |
|
348 |
|
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// last thing last, enable fatalities. |
349 |
|
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painCave.isEventLoop = 0; |
350 |
|
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|
351 |
mmeineke |
377 |
#endif // is_mpi |
352 |
|
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} |
353 |
|
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|
354 |
mmeineke |
572 |
void DumpWriter::writeFinal(double finalTime){ |
355 |
gezelter |
416 |
|
356 |
mmeineke |
377 |
char finalName[500]; |
357 |
|
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ofstream finalOut; |
358 |
gezelter |
416 |
|
359 |
|
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const int BUFFERSIZE = 2000; |
360 |
|
|
char tempBuffer[BUFFERSIZE]; |
361 |
tim |
837 |
char writeLine[BUFFERSIZE]; |
362 |
gezelter |
416 |
|
363 |
|
|
double q[4]; |
364 |
|
|
DirectionalAtom* dAtom; |
365 |
mmeineke |
787 |
Atom** atoms = entry_plug->atoms; |
366 |
|
|
int i; |
367 |
|
|
#ifdef IS_MPI |
368 |
|
|
int j, which_node, done, which_atom, local_index; |
369 |
|
|
#else //is_mpi |
370 |
gezelter |
416 |
int nAtoms = entry_plug->n_atoms; |
371 |
mmeineke |
787 |
#endif //is_mpi |
372 |
tim |
837 |
|
373 |
mmeineke |
670 |
double pos[3], vel[3]; |
374 |
tim |
837 |
|
375 |
mmeineke |
377 |
#ifdef IS_MPI |
376 |
|
|
if(worldRank == 0 ){ |
377 |
|
|
#endif // is_mpi |
378 |
tim |
837 |
|
379 |
mmeineke |
377 |
strcpy( finalName, entry_plug->finalName ); |
380 |
tim |
837 |
|
381 |
mmeineke |
377 |
finalOut.open( finalName, ios::out | ios::trunc ); |
382 |
|
|
if( !finalOut ){ |
383 |
|
|
sprintf( painCave.errMsg, |
384 |
|
|
"Could not open \"%s\" for final dump output.\n", |
385 |
|
|
finalName ); |
386 |
|
|
painCave.isFatal = 1; |
387 |
|
|
simError(); |
388 |
|
|
} |
389 |
tim |
837 |
|
390 |
mmeineke |
377 |
// finalOut.setf( ios::scientific ); |
391 |
tim |
837 |
|
392 |
mmeineke |
377 |
#ifdef IS_MPI |
393 |
|
|
} |
394 |
tim |
837 |
|
395 |
mmeineke |
377 |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
396 |
tim |
837 |
MPIcheckPoint(); |
397 |
|
|
|
398 |
mmeineke |
377 |
#endif //is_mpi |
399 |
|
|
|
400 |
tim |
837 |
|
401 |
mmeineke |
377 |
#ifndef IS_MPI |
402 |
tim |
837 |
|
403 |
mmeineke |
377 |
finalOut << nAtoms << "\n"; |
404 |
tim |
837 |
|
405 |
gezelter |
591 |
finalOut << finalTime << ";\t" |
406 |
mmeineke |
590 |
<< entry_plug->Hmat[0][0] << "\t" |
407 |
|
|
<< entry_plug->Hmat[1][0] << "\t" |
408 |
gezelter |
591 |
<< entry_plug->Hmat[2][0] << ";\t" |
409 |
tim |
837 |
|
410 |
mmeineke |
590 |
<< entry_plug->Hmat[0][1] << "\t" |
411 |
|
|
<< entry_plug->Hmat[1][1] << "\t" |
412 |
gezelter |
591 |
<< entry_plug->Hmat[2][1] << ";\t" |
413 |
tim |
837 |
|
414 |
mmeineke |
590 |
<< entry_plug->Hmat[0][2] << "\t" |
415 |
|
|
<< entry_plug->Hmat[1][2] << "\t" |
416 |
tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
417 |
|
|
|
418 |
|
|
//write out additional parameters, such as chi and eta |
419 |
|
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
420 |
|
|
finalOut << endl; |
421 |
|
|
|
422 |
mmeineke |
377 |
for( i=0; i<nAtoms; i++ ){ |
423 |
tim |
837 |
|
424 |
mmeineke |
670 |
atoms[i]->getPos(pos); |
425 |
|
|
atoms[i]->getVel(vel); |
426 |
tim |
837 |
|
427 |
mmeineke |
377 |
sprintf( tempBuffer, |
428 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
429 |
|
|
atoms[i]->getType(), |
430 |
mmeineke |
670 |
pos[0], |
431 |
|
|
pos[1], |
432 |
|
|
pos[2], |
433 |
|
|
vel[0], |
434 |
|
|
vel[1], |
435 |
|
|
vel[2]); |
436 |
mmeineke |
377 |
strcpy( writeLine, tempBuffer ); |
437 |
|
|
|
438 |
|
|
if( atoms[i]->isDirectional() ){ |
439 |
tim |
837 |
|
440 |
mmeineke |
377 |
dAtom = (DirectionalAtom *)atoms[i]; |
441 |
|
|
dAtom->getQ( q ); |
442 |
tim |
837 |
|
443 |
mmeineke |
377 |
sprintf( tempBuffer, |
444 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
445 |
|
|
q[0], |
446 |
|
|
q[1], |
447 |
|
|
q[2], |
448 |
|
|
q[3], |
449 |
|
|
dAtom->getJx(), |
450 |
|
|
dAtom->getJy(), |
451 |
|
|
dAtom->getJz()); |
452 |
|
|
strcat( writeLine, tempBuffer ); |
453 |
|
|
} |
454 |
|
|
else |
455 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
456 |
tim |
837 |
|
457 |
mmeineke |
377 |
finalOut << writeLine; |
458 |
|
|
} |
459 |
|
|
finalOut.flush(); |
460 |
gezelter |
415 |
finalOut.close(); |
461 |
mmeineke |
377 |
|
462 |
|
|
#else // is_mpi |
463 |
tim |
837 |
|
464 |
mmeineke |
440 |
// first thing first, suspend fatalities. |
465 |
|
|
painCave.isEventLoop = 1; |
466 |
|
|
|
467 |
|
|
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
468 |
|
|
int haveError; |
469 |
|
|
|
470 |
mmeineke |
447 |
MPI_Status istatus; |
471 |
gezelter |
416 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
472 |
|
|
|
473 |
mmeineke |
377 |
// write out header and node 0's coordinates |
474 |
tim |
837 |
|
475 |
mmeineke |
440 |
haveError = 0; |
476 |
mmeineke |
377 |
if( worldRank == 0 ){ |
477 |
|
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
478 |
tim |
837 |
|
479 |
gezelter |
591 |
finalOut << finalTime << ";\t" |
480 |
|
|
<< entry_plug->Hmat[0][0] << "\t" |
481 |
|
|
<< entry_plug->Hmat[1][0] << "\t" |
482 |
|
|
<< entry_plug->Hmat[2][0] << ";\t" |
483 |
tim |
837 |
|
484 |
gezelter |
591 |
<< entry_plug->Hmat[0][1] << "\t" |
485 |
|
|
<< entry_plug->Hmat[1][1] << "\t" |
486 |
|
|
<< entry_plug->Hmat[2][1] << ";\t" |
487 |
tim |
837 |
|
488 |
gezelter |
591 |
<< entry_plug->Hmat[0][2] << "\t" |
489 |
|
|
<< entry_plug->Hmat[1][2] << "\t" |
490 |
tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
491 |
|
|
|
492 |
|
|
//write out additional parameters, such as chi and eta |
493 |
|
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
494 |
|
|
finalOut << endl; |
495 |
|
|
|
496 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
497 |
gezelter |
415 |
// Get the Node number which has this molecule: |
498 |
tim |
837 |
|
499 |
|
|
which_node = AtomToProcMap[i]; |
500 |
|
|
|
501 |
gezelter |
416 |
if (which_node == mpiSim->getMyNode()) { |
502 |
chuckv |
437 |
|
503 |
|
|
which_atom = i; |
504 |
tim |
837 |
local_index=-1; |
505 |
chuckv |
437 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
506 |
|
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
507 |
|
|
} |
508 |
tim |
837 |
if (local_index != -1) { |
509 |
mmeineke |
670 |
|
510 |
|
|
atoms[local_index]->getPos(pos); |
511 |
|
|
atoms[local_index]->getVel(vel); |
512 |
tim |
837 |
|
513 |
chuckv |
437 |
sprintf( tempBuffer, |
514 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
515 |
|
|
atoms[local_index]->getType(), |
516 |
mmeineke |
670 |
pos[0], |
517 |
|
|
pos[1], |
518 |
|
|
pos[2], |
519 |
|
|
vel[0], |
520 |
|
|
vel[1], |
521 |
|
|
vel[2]); |
522 |
chuckv |
437 |
strcpy( writeLine, tempBuffer ); |
523 |
tim |
837 |
|
524 |
chuckv |
437 |
if( atoms[local_index]->isDirectional() ){ |
525 |
tim |
837 |
|
526 |
chuckv |
437 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
527 |
|
|
dAtom->getQ( q ); |
528 |
tim |
837 |
|
529 |
chuckv |
437 |
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 |
tim |
837 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
542 |
chuckv |
437 |
} |
543 |
|
|
else { |
544 |
mmeineke |
440 |
sprintf(painCave.errMsg, |
545 |
|
|
"Atom %d not found on processor %d\n", |
546 |
|
|
i, worldRank ); |
547 |
|
|
haveError= 1; |
548 |
|
|
simError(); |
549 |
tim |
837 |
} |
550 |
mmeineke |
440 |
|
551 |
|
|
if(haveError) nodeZeroError(); |
552 |
tim |
837 |
|
553 |
|
|
} |
554 |
mmeineke |
440 |
else { |
555 |
tim |
837 |
|
556 |
mmeineke |
440 |
myStatus = 1; |
557 |
tim |
837 |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
558 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
559 |
|
|
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
560 |
|
|
MPI_COMM_WORLD); |
561 |
|
|
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
562 |
|
|
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
563 |
tim |
837 |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
564 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
565 |
tim |
837 |
|
566 |
mmeineke |
440 |
if(!myStatus) nodeZeroError(); |
567 |
mmeineke |
377 |
} |
568 |
tim |
837 |
|
569 |
mmeineke |
377 |
finalOut << writeLine; |
570 |
|
|
} |
571 |
tim |
837 |
|
572 |
gezelter |
415 |
// kill everyone off: |
573 |
mmeineke |
440 |
myStatus = -1; |
574 |
tim |
905 |
for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
575 |
tim |
837 |
MPI_Send(&myStatus, 1, MPI_INT, j, |
576 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
577 |
mmeineke |
377 |
} |
578 |
|
|
|
579 |
gezelter |
415 |
} else { |
580 |
tim |
837 |
|
581 |
gezelter |
415 |
done = 0; |
582 |
|
|
while (!done) { |
583 |
mmeineke |
440 |
|
584 |
tim |
837 |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
585 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
586 |
tim |
837 |
|
587 |
mmeineke |
440 |
if(!myStatus) anonymousNodeDie(); |
588 |
tim |
837 |
|
589 |
mmeineke |
440 |
if(myStatus < 0) break; |
590 |
tim |
837 |
|
591 |
|
|
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
592 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
593 |
tim |
837 |
|
594 |
mmeineke |
440 |
myStatus = 1; |
595 |
tim |
837 |
local_index=-1; |
596 |
mmeineke |
440 |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
597 |
|
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
598 |
|
|
} |
599 |
|
|
if (local_index != -1) { |
600 |
mmeineke |
377 |
|
601 |
mmeineke |
670 |
atoms[local_index]->getPos(pos); |
602 |
|
|
atoms[local_index]->getVel(vel); |
603 |
|
|
|
604 |
mmeineke |
440 |
//format the line |
605 |
|
|
sprintf( tempBuffer, |
606 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
607 |
|
|
atoms[local_index]->getType(), |
608 |
mmeineke |
670 |
pos[0], |
609 |
|
|
pos[1], |
610 |
|
|
pos[2], |
611 |
|
|
vel[0], |
612 |
|
|
vel[1], |
613 |
|
|
vel[2]); // check here. |
614 |
mmeineke |
440 |
strcpy( writeLine, tempBuffer ); |
615 |
tim |
837 |
|
616 |
mmeineke |
440 |
if( atoms[local_index]->isDirectional() ){ |
617 |
tim |
837 |
|
618 |
mmeineke |
440 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
619 |
|
|
dAtom->getQ( q ); |
620 |
tim |
837 |
|
621 |
mmeineke |
440 |
sprintf( tempBuffer, |
622 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
623 |
|
|
q[0], |
624 |
|
|
q[1], |
625 |
|
|
q[2], |
626 |
|
|
q[3], |
627 |
|
|
dAtom->getJx(), |
628 |
|
|
dAtom->getJy(), |
629 |
|
|
dAtom->getJz()); |
630 |
|
|
strcat( writeLine, tempBuffer ); |
631 |
|
|
} |
632 |
|
|
else{ |
633 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
634 |
|
|
} |
635 |
tim |
837 |
} |
636 |
mmeineke |
440 |
else { |
637 |
|
|
sprintf(painCave.errMsg, |
638 |
|
|
"Atom %d not found on processor %d\n", |
639 |
|
|
which_atom, worldRank ); |
640 |
|
|
myStatus = 0; |
641 |
|
|
simError(); |
642 |
tim |
837 |
|
643 |
mmeineke |
440 |
strcpy( writeLine, "Hello, I'm an error.\n"); |
644 |
mmeineke |
377 |
} |
645 |
mmeineke |
440 |
|
646 |
tim |
837 |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
647 |
mmeineke |
447 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
648 |
tim |
837 |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
649 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
650 |
mmeineke |
377 |
} |
651 |
gezelter |
419 |
} |
652 |
gezelter |
415 |
finalOut.flush(); |
653 |
|
|
sprintf( checkPointMsg, |
654 |
|
|
"Sucessfully took a dump.\n"); |
655 |
|
|
MPIcheckPoint(); |
656 |
tim |
837 |
|
657 |
|
|
if( worldRank == 0 ) finalOut.close(); |
658 |
mmeineke |
377 |
#endif // is_mpi |
659 |
|
|
} |
660 |
mmeineke |
440 |
|
661 |
|
|
|
662 |
|
|
|
663 |
|
|
#ifdef IS_MPI |
664 |
|
|
|
665 |
|
|
// a couple of functions to let us escape the write loop |
666 |
|
|
|
667 |
|
|
void dWrite::nodeZeroError( void ){ |
668 |
|
|
int j, myStatus; |
669 |
tim |
837 |
|
670 |
mmeineke |
440 |
myStatus = 0; |
671 |
tim |
837 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
672 |
|
|
MPI_Send( &myStatus, 1, MPI_INT, j, |
673 |
mmeineke |
447 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
674 |
tim |
837 |
} |
675 |
mmeineke |
440 |
|
676 |
tim |
837 |
|
677 |
mmeineke |
440 |
MPI_Finalize(); |
678 |
|
|
exit (0); |
679 |
tim |
837 |
|
680 |
mmeineke |
440 |
} |
681 |
|
|
|
682 |
|
|
void dWrite::anonymousNodeDie( void ){ |
683 |
|
|
|
684 |
|
|
MPI_Finalize(); |
685 |
|
|
exit (0); |
686 |
|
|
} |
687 |
|
|
|
688 |
|
|
#endif //is_mpi |