1 |
mmeineke |
723 |
#define _FILE_OFFSET_BITS 64 |
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3 |
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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11 |
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namespace dWrite{ |
12 |
gezelter |
907 |
void DieDieDie( void ); |
13 |
mmeineke |
440 |
} |
14 |
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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 ); |
30 |
tim |
837 |
|
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mmeineke |
377 |
outFile.open(outName, ios::out | ios::trunc ); |
32 |
tim |
837 |
|
33 |
mmeineke |
377 |
if( !outFile ){ |
34 |
tim |
837 |
|
35 |
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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} |
41 |
mmeineke |
469 |
|
42 |
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 ){ |
67 |
tim |
837 |
|
68 |
mmeineke |
377 |
const int BUFFERSIZE = 2000; |
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gezelter |
907 |
const int MINIBUFFERSIZE = 10; |
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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; |
87 |
mmeineke |
787 |
#else //is_mpi |
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int nAtoms = entry_plug->n_atoms; |
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#endif //is_mpi |
90 |
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91 |
mmeineke |
377 |
double q[4]; |
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DirectionalAtom* dAtom; |
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Atom** atoms = entry_plug->atoms; |
94 |
mmeineke |
670 |
double pos[3], vel[3]; |
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tim |
837 |
|
96 |
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 |
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" |
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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 |
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; |
119 |
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mmeineke |
377 |
for( i=0; i<nAtoms; i++ ){ |
121 |
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", |
127 |
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atoms[i]->getType(), |
128 |
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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136 |
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if( atoms[i]->isDirectional() ){ |
137 |
tim |
837 |
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138 |
mmeineke |
377 |
dAtom = (DirectionalAtom *)atoms[i]; |
139 |
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dAtom->getQ( q ); |
140 |
tim |
837 |
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141 |
mmeineke |
377 |
sprintf( tempBuffer, |
142 |
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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()); |
150 |
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strcat( writeLine, tempBuffer ); |
151 |
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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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155 |
mmeineke |
377 |
outFile << writeLine; |
156 |
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} |
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outFile.flush(); |
158 |
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159 |
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#else // is_mpi |
160 |
gezelter |
416 |
|
161 |
mmeineke |
440 |
// first thing first, suspend fatalities. |
162 |
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painCave.isEventLoop = 1; |
163 |
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164 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
165 |
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int haveError; |
166 |
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167 |
mmeineke |
447 |
MPI_Status istatus; |
168 |
gezelter |
416 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
169 |
tim |
837 |
|
170 |
mmeineke |
377 |
// write out header and node 0's coordinates |
171 |
tim |
837 |
|
172 |
mmeineke |
377 |
if( worldRank == 0 ){ |
173 |
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outFile << mpiSim->getTotAtoms() << "\n"; |
174 |
tim |
837 |
|
175 |
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outFile << currentTime << ";\t" |
176 |
gezelter |
591 |
<< entry_plug->Hmat[0][0] << "\t" |
177 |
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<< entry_plug->Hmat[1][0] << "\t" |
178 |
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<< entry_plug->Hmat[2][0] << ";\t" |
179 |
tim |
837 |
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180 |
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" |
183 |
tim |
837 |
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184 |
gezelter |
591 |
<< entry_plug->Hmat[0][2] << "\t" |
185 |
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<< entry_plug->Hmat[1][2] << "\t" |
186 |
tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
187 |
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188 |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
189 |
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outFile << endl; |
190 |
chuckv |
434 |
outFile.flush(); |
191 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
192 |
gezelter |
417 |
// Get the Node number which has this atom; |
193 |
tim |
837 |
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194 |
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which_node = AtomToProcMap[i]; |
195 |
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196 |
gezelter |
907 |
if (which_node != 0) { |
197 |
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atomTypeTag = 4*i; |
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atomIsDirectionalTag = 4*i + 1; |
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atomTransDataTag = 4*i + 2; |
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atomOrientDataTag = 4*i + 3; |
202 |
tim |
837 |
|
203 |
gezelter |
910 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
204 |
gezelter |
907 |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
205 |
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206 |
gezelter |
910 |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
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208 |
gezelter |
907 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
209 |
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atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
210 |
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211 |
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MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
212 |
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atomTransDataTag, MPI_COMM_WORLD, &istatus); |
213 |
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214 |
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if (isDirectional) { |
215 |
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216 |
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MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
217 |
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atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
218 |
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} |
220 |
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} else { |
222 |
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223 |
mmeineke |
440 |
haveError = 0; |
224 |
chuckv |
436 |
which_atom = i; |
225 |
tim |
837 |
local_index=-1; |
226 |
gezelter |
907 |
|
227 |
chuckv |
436 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
228 |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
229 |
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} |
230 |
gezelter |
907 |
|
231 |
chuckv |
436 |
if (local_index != -1) { |
232 |
tim |
837 |
|
233 |
gezelter |
907 |
atomTypeString = atoms[local_index]->getType(); |
234 |
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235 |
mmeineke |
670 |
atoms[local_index]->getPos(pos); |
236 |
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atoms[local_index]->getVel(vel); |
237 |
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238 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
239 |
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atomTransData[1] = pos[1]; |
240 |
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atomTransData[2] = pos[2]; |
241 |
tim |
837 |
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242 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
243 |
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atomTransData[4] = vel[1]; |
244 |
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atomTransData[5] = vel[2]; |
245 |
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246 |
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isDirectional = 0; |
247 |
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248 |
chuckv |
436 |
if( atoms[local_index]->isDirectional() ){ |
249 |
tim |
837 |
|
250 |
gezelter |
907 |
isDirectional = 1; |
251 |
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|
252 |
chuckv |
436 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
253 |
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dAtom->getQ( q ); |
254 |
gezelter |
907 |
|
255 |
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atomOrientData[0] = q[0]; |
256 |
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atomOrientData[1] = q[1]; |
257 |
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atomOrientData[2] = q[2]; |
258 |
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atomOrientData[3] = q[3]; |
259 |
tim |
837 |
|
260 |
gezelter |
907 |
atomOrientData[4] = dAtom->getJx(); |
261 |
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atomOrientData[5] = dAtom->getJy(); |
262 |
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atomOrientData[6] = dAtom->getJz(); |
263 |
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} |
264 |
tim |
837 |
|
265 |
gezelter |
907 |
} else { |
266 |
mmeineke |
440 |
sprintf(painCave.errMsg, |
267 |
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"Atom %d not found on processor %d\n", |
268 |
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i, worldRank ); |
269 |
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haveError= 1; |
270 |
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simError(); |
271 |
tim |
837 |
} |
272 |
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273 |
gezelter |
907 |
if(haveError) DieDieDie(); |
274 |
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275 |
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// If we've survived to here, format the line: |
276 |
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277 |
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sprintf( tempBuffer, |
278 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
279 |
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atomTypeString, |
280 |
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atomTransData[0], |
281 |
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atomTransData[1], |
282 |
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atomTransData[2], |
283 |
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atomTransData[3], |
284 |
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atomTransData[4], |
285 |
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atomTransData[5]); |
286 |
mmeineke |
440 |
|
287 |
gezelter |
907 |
strcpy( writeLine, tempBuffer ); |
288 |
tim |
837 |
|
289 |
gezelter |
907 |
if (isDirectional) { |
290 |
mmeineke |
440 |
|
291 |
gezelter |
907 |
sprintf( tempBuffer, |
292 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
293 |
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atomOrientData[0], |
294 |
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atomOrientData[1], |
295 |
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atomOrientData[2], |
296 |
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atomOrientData[3], |
297 |
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atomOrientData[4], |
298 |
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atomOrientData[5], |
299 |
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atomOrientData[6]); |
300 |
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strcat( writeLine, tempBuffer ); |
301 |
tim |
837 |
|
302 |
gezelter |
907 |
} else { |
303 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
304 |
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} |
305 |
tim |
837 |
|
306 |
gezelter |
907 |
outFile << writeLine; |
307 |
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outFile.flush(); |
308 |
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} |
309 |
mmeineke |
377 |
} |
310 |
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|
311 |
gezelter |
907 |
outFile.flush(); |
312 |
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sprintf( checkPointMsg, |
313 |
|
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"Sucessfully took a dump.\n"); |
314 |
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MPIcheckPoint(); |
315 |
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|
316 |
gezelter |
415 |
} else { |
317 |
tim |
837 |
|
318 |
gezelter |
907 |
// worldRank != 0, so I'm a remote node. |
319 |
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|
320 |
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
321 |
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|
322 |
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// Am I the node which has this atom? |
323 |
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324 |
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if (AtomToProcMap[i] == worldRank) { |
325 |
tim |
837 |
|
326 |
gezelter |
907 |
local_index=-1; |
327 |
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for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
328 |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
329 |
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} |
330 |
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if (local_index != -1) { |
331 |
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|
332 |
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atomTypeString = atoms[local_index]->getType(); |
333 |
mmeineke |
440 |
|
334 |
gezelter |
907 |
atoms[local_index]->getPos(pos); |
335 |
|
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atoms[local_index]->getVel(vel); |
336 |
tim |
837 |
|
337 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
338 |
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atomTransData[1] = pos[1]; |
339 |
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atomTransData[2] = pos[2]; |
340 |
mmeineke |
440 |
|
341 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
342 |
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atomTransData[4] = vel[1]; |
343 |
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atomTransData[5] = vel[2]; |
344 |
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|
345 |
|
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isDirectional = 0; |
346 |
tim |
837 |
|
347 |
gezelter |
907 |
if( atoms[local_index]->isDirectional() ){ |
348 |
mmeineke |
670 |
|
349 |
gezelter |
907 |
isDirectional = 1; |
350 |
|
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|
351 |
|
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dAtom = (DirectionalAtom *)atoms[local_index]; |
352 |
|
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dAtom->getQ( q ); |
353 |
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|
354 |
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atomOrientData[0] = q[0]; |
355 |
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atomOrientData[1] = q[1]; |
356 |
|
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atomOrientData[2] = q[2]; |
357 |
|
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atomOrientData[3] = q[3]; |
358 |
mmeineke |
670 |
|
359 |
gezelter |
907 |
atomOrientData[4] = dAtom->getJx(); |
360 |
|
|
atomOrientData[5] = dAtom->getJy(); |
361 |
|
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atomOrientData[6] = dAtom->getJz(); |
362 |
|
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} |
363 |
tim |
837 |
|
364 |
gezelter |
907 |
} else { |
365 |
|
|
sprintf(painCave.errMsg, |
366 |
|
|
"Atom %d not found on processor %d\n", |
367 |
|
|
i, worldRank ); |
368 |
|
|
haveError= 1; |
369 |
|
|
simError(); |
370 |
|
|
} |
371 |
tim |
837 |
|
372 |
gezelter |
907 |
// I've survived this far, so send off the data! |
373 |
tim |
837 |
|
374 |
gezelter |
907 |
atomTypeTag = 4*i; |
375 |
|
|
atomIsDirectionalTag = 4*i + 1; |
376 |
|
|
atomTransDataTag = 4*i + 2; |
377 |
|
|
atomOrientDataTag = 4*i + 3; |
378 |
mmeineke |
440 |
|
379 |
gezelter |
910 |
|
380 |
|
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
381 |
|
|
|
382 |
|
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
383 |
gezelter |
907 |
atomTypeTag, MPI_COMM_WORLD); |
384 |
|
|
|
385 |
|
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
386 |
|
|
atomIsDirectionalTag, MPI_COMM_WORLD); |
387 |
|
|
|
388 |
|
|
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
389 |
|
|
atomTransDataTag, MPI_COMM_WORLD); |
390 |
|
|
|
391 |
|
|
if (isDirectional) { |
392 |
|
|
|
393 |
|
|
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
394 |
|
|
atomOrientDataTag, MPI_COMM_WORLD); |
395 |
|
|
|
396 |
|
|
} |
397 |
|
|
|
398 |
mmeineke |
377 |
} |
399 |
gezelter |
907 |
} |
400 |
mmeineke |
440 |
|
401 |
gezelter |
907 |
sprintf( checkPointMsg, |
402 |
|
|
"Sucessfully took a dump.\n"); |
403 |
|
|
MPIcheckPoint(); |
404 |
|
|
|
405 |
tim |
837 |
} |
406 |
gezelter |
907 |
|
407 |
mmeineke |
440 |
painCave.isEventLoop = 0; |
408 |
|
|
|
409 |
mmeineke |
377 |
#endif // is_mpi |
410 |
|
|
} |
411 |
|
|
|
412 |
mmeineke |
572 |
void DumpWriter::writeFinal(double finalTime){ |
413 |
gezelter |
416 |
|
414 |
mmeineke |
377 |
char finalName[500]; |
415 |
|
|
ofstream finalOut; |
416 |
gezelter |
416 |
|
417 |
|
|
const int BUFFERSIZE = 2000; |
418 |
gezelter |
907 |
const int MINIBUFFERSIZE = 10; |
419 |
gezelter |
416 |
char tempBuffer[BUFFERSIZE]; |
420 |
tim |
837 |
char writeLine[BUFFERSIZE]; |
421 |
gezelter |
416 |
|
422 |
|
|
double q[4]; |
423 |
|
|
DirectionalAtom* dAtom; |
424 |
mmeineke |
787 |
Atom** atoms = entry_plug->atoms; |
425 |
|
|
int i; |
426 |
|
|
#ifdef IS_MPI |
427 |
|
|
int j, which_node, done, which_atom, local_index; |
428 |
gezelter |
907 |
double atomTransData[6]; |
429 |
|
|
double atomOrientData[7]; |
430 |
|
|
int isDirectional; |
431 |
|
|
char* atomTypeString; |
432 |
gezelter |
910 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
433 |
gezelter |
907 |
int atomTypeTag; |
434 |
|
|
int atomIsDirectionalTag; |
435 |
|
|
int atomTransDataTag; |
436 |
|
|
int atomOrientDataTag; |
437 |
mmeineke |
787 |
#else //is_mpi |
438 |
gezelter |
416 |
int nAtoms = entry_plug->n_atoms; |
439 |
mmeineke |
787 |
#endif //is_mpi |
440 |
tim |
837 |
|
441 |
mmeineke |
670 |
double pos[3], vel[3]; |
442 |
tim |
837 |
|
443 |
mmeineke |
377 |
#ifdef IS_MPI |
444 |
|
|
if(worldRank == 0 ){ |
445 |
|
|
#endif // is_mpi |
446 |
tim |
837 |
|
447 |
mmeineke |
377 |
strcpy( finalName, entry_plug->finalName ); |
448 |
tim |
837 |
|
449 |
mmeineke |
377 |
finalOut.open( finalName, ios::out | ios::trunc ); |
450 |
|
|
if( !finalOut ){ |
451 |
|
|
sprintf( painCave.errMsg, |
452 |
|
|
"Could not open \"%s\" for final dump output.\n", |
453 |
|
|
finalName ); |
454 |
|
|
painCave.isFatal = 1; |
455 |
|
|
simError(); |
456 |
|
|
} |
457 |
tim |
837 |
|
458 |
mmeineke |
377 |
// finalOut.setf( ios::scientific ); |
459 |
tim |
837 |
|
460 |
mmeineke |
377 |
#ifdef IS_MPI |
461 |
|
|
} |
462 |
tim |
837 |
|
463 |
mmeineke |
377 |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
464 |
tim |
837 |
MPIcheckPoint(); |
465 |
|
|
|
466 |
mmeineke |
377 |
#endif //is_mpi |
467 |
|
|
|
468 |
tim |
837 |
|
469 |
mmeineke |
377 |
#ifndef IS_MPI |
470 |
tim |
837 |
|
471 |
mmeineke |
377 |
finalOut << nAtoms << "\n"; |
472 |
tim |
837 |
|
473 |
gezelter |
591 |
finalOut << finalTime << ";\t" |
474 |
mmeineke |
590 |
<< entry_plug->Hmat[0][0] << "\t" |
475 |
|
|
<< entry_plug->Hmat[1][0] << "\t" |
476 |
gezelter |
591 |
<< entry_plug->Hmat[2][0] << ";\t" |
477 |
tim |
837 |
|
478 |
mmeineke |
590 |
<< entry_plug->Hmat[0][1] << "\t" |
479 |
|
|
<< entry_plug->Hmat[1][1] << "\t" |
480 |
gezelter |
591 |
<< entry_plug->Hmat[2][1] << ";\t" |
481 |
tim |
837 |
|
482 |
mmeineke |
590 |
<< entry_plug->Hmat[0][2] << "\t" |
483 |
|
|
<< entry_plug->Hmat[1][2] << "\t" |
484 |
tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
485 |
|
|
|
486 |
|
|
//write out additional parameters, such as chi and eta |
487 |
|
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
488 |
|
|
finalOut << endl; |
489 |
|
|
|
490 |
mmeineke |
377 |
for( i=0; i<nAtoms; i++ ){ |
491 |
tim |
837 |
|
492 |
mmeineke |
670 |
atoms[i]->getPos(pos); |
493 |
|
|
atoms[i]->getVel(vel); |
494 |
tim |
837 |
|
495 |
mmeineke |
377 |
sprintf( tempBuffer, |
496 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
497 |
|
|
atoms[i]->getType(), |
498 |
mmeineke |
670 |
pos[0], |
499 |
|
|
pos[1], |
500 |
|
|
pos[2], |
501 |
|
|
vel[0], |
502 |
|
|
vel[1], |
503 |
|
|
vel[2]); |
504 |
mmeineke |
377 |
strcpy( writeLine, tempBuffer ); |
505 |
|
|
|
506 |
|
|
if( atoms[i]->isDirectional() ){ |
507 |
tim |
837 |
|
508 |
mmeineke |
377 |
dAtom = (DirectionalAtom *)atoms[i]; |
509 |
|
|
dAtom->getQ( q ); |
510 |
tim |
837 |
|
511 |
mmeineke |
377 |
sprintf( tempBuffer, |
512 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
513 |
|
|
q[0], |
514 |
|
|
q[1], |
515 |
|
|
q[2], |
516 |
|
|
q[3], |
517 |
|
|
dAtom->getJx(), |
518 |
|
|
dAtom->getJy(), |
519 |
|
|
dAtom->getJz()); |
520 |
|
|
strcat( writeLine, tempBuffer ); |
521 |
|
|
} |
522 |
|
|
else |
523 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
524 |
tim |
837 |
|
525 |
mmeineke |
377 |
finalOut << writeLine; |
526 |
|
|
} |
527 |
|
|
finalOut.flush(); |
528 |
gezelter |
415 |
finalOut.close(); |
529 |
mmeineke |
377 |
|
530 |
|
|
#else // is_mpi |
531 |
tim |
837 |
|
532 |
mmeineke |
440 |
// first thing first, suspend fatalities. |
533 |
|
|
painCave.isEventLoop = 1; |
534 |
|
|
|
535 |
|
|
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
536 |
|
|
int haveError; |
537 |
|
|
|
538 |
mmeineke |
447 |
MPI_Status istatus; |
539 |
gezelter |
416 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
540 |
|
|
|
541 |
mmeineke |
377 |
// write out header and node 0's coordinates |
542 |
tim |
837 |
|
543 |
mmeineke |
377 |
if( worldRank == 0 ){ |
544 |
|
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
545 |
tim |
837 |
|
546 |
gezelter |
591 |
finalOut << finalTime << ";\t" |
547 |
gezelter |
907 |
<< entry_plug->Hmat[0][0] << "\t" |
548 |
|
|
<< entry_plug->Hmat[1][0] << "\t" |
549 |
|
|
<< entry_plug->Hmat[2][0] << ";\t" |
550 |
tim |
837 |
|
551 |
gezelter |
907 |
<< entry_plug->Hmat[0][1] << "\t" |
552 |
|
|
<< entry_plug->Hmat[1][1] << "\t" |
553 |
|
|
<< entry_plug->Hmat[2][1] << ";\t" |
554 |
tim |
837 |
|
555 |
gezelter |
907 |
<< entry_plug->Hmat[0][2] << "\t" |
556 |
|
|
<< entry_plug->Hmat[1][2] << "\t" |
557 |
|
|
<< entry_plug->Hmat[2][2] << ";"; |
558 |
tim |
837 |
|
559 |
|
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
560 |
|
|
finalOut << endl; |
561 |
gezelter |
907 |
finalOut.flush(); |
562 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
563 |
gezelter |
907 |
// Get the Node number which has this atom; |
564 |
tim |
837 |
|
565 |
|
|
which_node = AtomToProcMap[i]; |
566 |
|
|
|
567 |
gezelter |
907 |
if (which_node != 0) { |
568 |
|
|
|
569 |
|
|
atomTypeTag = 4*i; |
570 |
|
|
atomIsDirectionalTag = 4*i + 1; |
571 |
|
|
atomTransDataTag = 4*i + 2; |
572 |
|
|
atomOrientDataTag = 4*i + 3; |
573 |
chuckv |
437 |
|
574 |
gezelter |
910 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
575 |
gezelter |
907 |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
576 |
|
|
|
577 |
gezelter |
910 |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
578 |
|
|
|
579 |
gezelter |
907 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
580 |
|
|
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
581 |
|
|
|
582 |
|
|
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
583 |
|
|
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
584 |
|
|
|
585 |
|
|
if (isDirectional) { |
586 |
|
|
|
587 |
|
|
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
588 |
|
|
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
589 |
|
|
|
590 |
|
|
} |
591 |
|
|
|
592 |
|
|
} else { |
593 |
|
|
|
594 |
|
|
haveError = 0; |
595 |
chuckv |
437 |
which_atom = i; |
596 |
tim |
837 |
local_index=-1; |
597 |
gezelter |
907 |
|
598 |
chuckv |
437 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
599 |
|
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
600 |
|
|
} |
601 |
gezelter |
907 |
|
602 |
tim |
837 |
if (local_index != -1) { |
603 |
mmeineke |
670 |
|
604 |
gezelter |
907 |
atomTypeString = atoms[local_index]->getType(); |
605 |
|
|
|
606 |
mmeineke |
670 |
atoms[local_index]->getPos(pos); |
607 |
|
|
atoms[local_index]->getVel(vel); |
608 |
tim |
837 |
|
609 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
610 |
|
|
atomTransData[1] = pos[1]; |
611 |
|
|
atomTransData[2] = pos[2]; |
612 |
tim |
837 |
|
613 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
614 |
|
|
atomTransData[4] = vel[1]; |
615 |
|
|
atomTransData[5] = vel[2]; |
616 |
|
|
|
617 |
|
|
isDirectional = 0; |
618 |
tim |
837 |
|
619 |
gezelter |
907 |
if( atoms[local_index]->isDirectional() ){ |
620 |
tim |
837 |
|
621 |
gezelter |
907 |
isDirectional = 1; |
622 |
|
|
|
623 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
624 |
|
|
dAtom->getQ( q ); |
625 |
|
|
|
626 |
|
|
atomOrientData[0] = q[0]; |
627 |
|
|
atomOrientData[1] = q[1]; |
628 |
|
|
atomOrientData[2] = q[2]; |
629 |
|
|
atomOrientData[3] = q[3]; |
630 |
|
|
|
631 |
|
|
atomOrientData[4] = dAtom->getJx(); |
632 |
|
|
atomOrientData[5] = dAtom->getJy(); |
633 |
|
|
atomOrientData[6] = dAtom->getJz(); |
634 |
|
|
} |
635 |
|
|
|
636 |
|
|
} else { |
637 |
mmeineke |
440 |
sprintf(painCave.errMsg, |
638 |
|
|
"Atom %d not found on processor %d\n", |
639 |
|
|
i, worldRank ); |
640 |
|
|
haveError= 1; |
641 |
|
|
simError(); |
642 |
tim |
837 |
} |
643 |
mmeineke |
440 |
|
644 |
gezelter |
907 |
if(haveError) DieDieDie(); |
645 |
|
|
|
646 |
|
|
// If we've survived to here, format the line: |
647 |
|
|
|
648 |
|
|
sprintf( tempBuffer, |
649 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
650 |
|
|
atomTypeString, |
651 |
|
|
atomTransData[0], |
652 |
|
|
atomTransData[1], |
653 |
|
|
atomTransData[2], |
654 |
|
|
atomTransData[3], |
655 |
|
|
atomTransData[4], |
656 |
|
|
atomTransData[5]); |
657 |
tim |
837 |
|
658 |
gezelter |
907 |
strcpy( writeLine, tempBuffer ); |
659 |
tim |
837 |
|
660 |
gezelter |
907 |
if (isDirectional) { |
661 |
tim |
837 |
|
662 |
gezelter |
907 |
sprintf( tempBuffer, |
663 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
664 |
|
|
atomOrientData[0], |
665 |
|
|
atomOrientData[1], |
666 |
|
|
atomOrientData[2], |
667 |
|
|
atomOrientData[3], |
668 |
|
|
atomOrientData[4], |
669 |
|
|
atomOrientData[5], |
670 |
|
|
atomOrientData[6]); |
671 |
|
|
strcat( writeLine, tempBuffer ); |
672 |
tim |
837 |
|
673 |
gezelter |
907 |
} else { |
674 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
675 |
|
|
} |
676 |
tim |
837 |
|
677 |
gezelter |
907 |
finalOut << writeLine; |
678 |
|
|
finalOut.flush(); |
679 |
|
|
} |
680 |
mmeineke |
377 |
} |
681 |
|
|
|
682 |
gezelter |
907 |
finalOut.flush(); |
683 |
|
|
sprintf( checkPointMsg, |
684 |
|
|
"Sucessfully took a dump.\n"); |
685 |
|
|
MPIcheckPoint(); |
686 |
|
|
|
687 |
gezelter |
415 |
} else { |
688 |
tim |
837 |
|
689 |
gezelter |
907 |
// worldRank != 0, so I'm a remote node. |
690 |
|
|
|
691 |
|
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
692 |
|
|
|
693 |
|
|
// Am I the node which has this atom? |
694 |
|
|
|
695 |
|
|
if (AtomToProcMap[i] == worldRank) { |
696 |
mmeineke |
440 |
|
697 |
gezelter |
907 |
local_index=-1; |
698 |
|
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
699 |
|
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
700 |
|
|
} |
701 |
|
|
if (local_index != -1) { |
702 |
|
|
|
703 |
|
|
atomTypeString = atoms[local_index]->getType(); |
704 |
tim |
837 |
|
705 |
gezelter |
907 |
atoms[local_index]->getPos(pos); |
706 |
|
|
atoms[local_index]->getVel(vel); |
707 |
tim |
837 |
|
708 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
709 |
|
|
atomTransData[1] = pos[1]; |
710 |
|
|
atomTransData[2] = pos[2]; |
711 |
tim |
837 |
|
712 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
713 |
|
|
atomTransData[4] = vel[1]; |
714 |
|
|
atomTransData[5] = vel[2]; |
715 |
|
|
|
716 |
|
|
isDirectional = 0; |
717 |
tim |
837 |
|
718 |
gezelter |
907 |
if( atoms[local_index]->isDirectional() ){ |
719 |
mmeineke |
377 |
|
720 |
gezelter |
907 |
isDirectional = 1; |
721 |
|
|
|
722 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
723 |
|
|
dAtom->getQ( q ); |
724 |
|
|
|
725 |
|
|
atomOrientData[0] = q[0]; |
726 |
|
|
atomOrientData[1] = q[1]; |
727 |
|
|
atomOrientData[2] = q[2]; |
728 |
|
|
atomOrientData[3] = q[3]; |
729 |
mmeineke |
670 |
|
730 |
gezelter |
907 |
atomOrientData[4] = dAtom->getJx(); |
731 |
|
|
atomOrientData[5] = dAtom->getJy(); |
732 |
|
|
atomOrientData[6] = dAtom->getJz(); |
733 |
|
|
} |
734 |
tim |
837 |
|
735 |
gezelter |
907 |
} else { |
736 |
|
|
sprintf(painCave.errMsg, |
737 |
|
|
"Atom %d not found on processor %d\n", |
738 |
|
|
i, worldRank ); |
739 |
|
|
haveError= 1; |
740 |
|
|
simError(); |
741 |
|
|
} |
742 |
tim |
837 |
|
743 |
gezelter |
907 |
// I've survived this far, so send off the data! |
744 |
tim |
837 |
|
745 |
gezelter |
907 |
atomTypeTag = 4*i; |
746 |
|
|
atomIsDirectionalTag = 4*i + 1; |
747 |
|
|
atomTransDataTag = 4*i + 2; |
748 |
|
|
atomOrientDataTag = 4*i + 3; |
749 |
tim |
837 |
|
750 |
gezelter |
910 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
751 |
|
|
|
752 |
|
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
753 |
gezelter |
907 |
atomTypeTag, MPI_COMM_WORLD); |
754 |
|
|
|
755 |
|
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
756 |
|
|
atomIsDirectionalTag, MPI_COMM_WORLD); |
757 |
|
|
|
758 |
|
|
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
759 |
|
|
atomTransDataTag, MPI_COMM_WORLD); |
760 |
|
|
|
761 |
|
|
if (isDirectional) { |
762 |
|
|
|
763 |
|
|
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
764 |
|
|
atomOrientDataTag, MPI_COMM_WORLD); |
765 |
|
|
|
766 |
|
|
} |
767 |
|
|
|
768 |
mmeineke |
377 |
} |
769 |
gezelter |
907 |
} |
770 |
mmeineke |
440 |
|
771 |
gezelter |
907 |
sprintf( checkPointMsg, |
772 |
|
|
"Sucessfully wrote final file.\n"); |
773 |
|
|
MPIcheckPoint(); |
774 |
|
|
|
775 |
gezelter |
419 |
} |
776 |
gezelter |
907 |
|
777 |
|
|
painCave.isEventLoop = 0; |
778 |
tim |
837 |
|
779 |
|
|
if( worldRank == 0 ) finalOut.close(); |
780 |
mmeineke |
377 |
#endif // is_mpi |
781 |
|
|
} |
782 |
mmeineke |
440 |
|
783 |
|
|
|
784 |
|
|
|
785 |
|
|
#ifdef IS_MPI |
786 |
|
|
|
787 |
|
|
// a couple of functions to let us escape the write loop |
788 |
|
|
|
789 |
gezelter |
907 |
void dWrite::DieDieDie( void ){ |
790 |
tim |
837 |
|
791 |
mmeineke |
440 |
MPI_Finalize(); |
792 |
|
|
exit (0); |
793 |
|
|
} |
794 |
|
|
|
795 |
|
|
#endif //is_mpi |