[ViewVC] Diff of: group/trunk/OOPSE/libmdtools/DumpWriter.cpp

Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 929 by tim, Tue Jan 13 15:46:49 2004 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 2004 UTC

#	Line 1 \| Line 1
1	+	#define _LARGEFILE_SOURCE64
2		#define _FILE_OFFSET_BITS 64
3
4		#include <string.h>
#	Line 28 \| Line 29 \| *DumpWriter::DumpWriter( SimInfo the_entry_plug ){**
29		if(worldRank == 0 ){
30		#endif // is_mpi
31
31	–
32		dumpFile.open(entry_plug->sampleName, ios::out \| ios::trunc );
33
34		if( !dumpFile ){
#	Line 40 \| Line 40 \| *DumpWriter::DumpWriter( SimInfo the_entry_plug ){**
40		simError();
41		}
42
43	–	//outFile.setf( ios::scientific );
44	–
43		#ifdef IS_MPI
44		}
45
#	Line 90 \| Line 88 \| void DumpWriter::sortByGlobalIndex(){
88		*/
89
90		void DumpWriter::sortByGlobalIndex(){
91	<	Atom** atoms = entry_plug->atoms;
94	<
91	>	Molecule* mols = entry_plug->molecules;
92		indexArray.clear();
93
94	<	for(int i = 0; i < mpiSim->getMyNlocal();i++)
95	<	indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
94	>	for(int i = 0; i < entry_plug->n_mol;i++)
95	>	indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
96
97		sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
98		}
99	+
100		#endif
101
102		void DumpWriter::writeDump(double currentTime){
105	–
106	–	// write to eor file
107	–	writeFinal(currentTime);
103
104	<	//write to dump file
105	<	writeFrame(dumpFile, currentTime);
104	>	ofstream finalOut;
105	>	vector<ofstream*> fileStreams;
106	>
107	>	#ifdef IS_MPI
108	>	if(worldRank == 0 ){
109	>	#endif
110	>	finalOut.open( entry_plug->finalName, ios::out \| ios::trunc );
111	>	if( !finalOut ){
112	>	sprintf( painCave.errMsg,
113	>	"Could not open \"%s\" for final dump output.\n",
114	>	entry_plug->finalName );
115	>	painCave.isFatal = 1;
116	>	simError();
117	>	}
118	>	#ifdef IS_MPI
119	>	}
120	>	#endif // is_mpi
121	>
122	>	fileStreams.push_back(&finalOut);
123	>	fileStreams.push_back(&dumpFile);
124	>
125	>	writeFrame(fileStreams, currentTime);
126	>
127	>	#ifdef IS_MPI
128	>	finalOut.close();
129	>	#endif
130
131		}
132
133		void DumpWriter::writeFinal(double currentTime){
134
135	<	ofstream finalOut;
136	<
137	<	//Open eor file
135	>	ofstream finalOut;
136	>	vector<ofstream*> fileStreams;
137	>
138		#ifdef IS_MPI
139		if(worldRank == 0 ){
140		#endif // is_mpi
141
142		finalOut.open( entry_plug->finalName, ios::out \| ios::trunc );
143	+
144		if( !finalOut ){
145		sprintf( painCave.errMsg,
146		"Could not open \"%s\" for final dump output.\n",
#	Line 128 \| Line 148 \| void DumpWriter::writeFinal(double currentTime){
148		painCave.isFatal = 1;
149		simError();
150		}
151	<
151	>
152		#ifdef IS_MPI
153		}
134	–	#endif
135	–
136	–	//write to eor file
137	–	writeFrame(finalOut, currentTime);
138	–
139	–	//close eor file
140	–	#ifdef IS_MPI
141	–	if(worldRank == 0 ){
142	–	finalOut.close();
143	–	}
154		#endif // is_mpi
155	+
156	+	fileStreams.push_back(&finalOut);
157	+	writeFrame(fileStreams, currentTime);
158
159	+	#ifdef IS_MPI
160	+	finalOut.close();
161	+	#endif
162	+
163		}
164
165	<	void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
165	>	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166
167		const int BUFFERSIZE = 2000;
168		const int MINIBUFFERSIZE = 100;
169
170	<	char tempBuffer[BUFFERSIZE];
170	>	char tempBuffer[BUFFERSIZE];
171		char writeLine[BUFFERSIZE];
172
173	<	int i;
173	>	int i, k;
174
175		#ifdef IS_MPI
176
177	+	/*********************************************************************
178	+	* Documentation? You want DOCUMENTATION?
179	+	*
180	+	* Why all the potatoes below?
181	+	*
182	+	* To make a long story short, the original version of DumpWriter
183	+	* worked in the most inefficient way possible. Node 0 would
184	+	* poke each of the node for an individual atom's formatted data
185	+	* as node 0 worked its way down the global index. This was particularly
186	+	* inefficient since the method blocked all processors at every atom
187	+	* (and did it twice!).
188	+	*
189	+	* An intermediate version of DumpWriter could be described from Node
190	+	* zero's perspective as follows:
191	+	*
192	+	* 1) Have 100 of your friends stand in a circle.
193	+	* 2) When you say go, have all of them start tossing potatoes at
194	+	* you (one at a time).
195	+	* 3) Catch the potatoes.
196	+	*
197	+	* It was an improvement, but MPI has buffers and caches that could
198	+	* best be described in this analogy as "potato nets", so there's no
199	+	* need to block the processors atom-by-atom.
200	+	*
201	+	* This new and improved DumpWriter works in an even more efficient
202	+	* way:
203	+	*
204	+	* 1) Have 100 of your friend stand in a circle.
205	+	* 2) When you say go, have them start tossing 5-pound bags of
206	+	* potatoes at you.
207	+	* 3) Once you've caught a friend's bag of potatoes,
208	+	* toss them a spud to let them know they can toss another bag.
209	+	*
210	+	* How's THAT for documentation?
211	+	*
212	+	*********************************************************************/
213	+
214		int *potatoes;
215		int myPotato;
216
217		int nProc;
218		int j, which_node, done, which_atom, local_index, currentIndex;
219	<	double atomData6[6];
166	<	double atomData13[13];
219	>	double atomData[13];
220		int isDirectional;
221		char* atomTypeString;
222		char MPIatomTypeString[MINIBUFFERSIZE];
223	<
224	<	#else //is_mpi
172	<	int nAtoms = entry_plug->n_atoms;
223	>	int nObjects;
224	>	int msgLen; // the length of message actually recieved at master nodes
225		#endif //is_mpi
226
227	<	double q[4];
227	>	double q[4], ji[3];
228		DirectionalAtom* dAtom;
177	–	Atom** atoms = entry_plug->atoms;
229		double pos[3], vel[3];
230	<
230	>	int nTotObjects;
231	>	StuntDouble* sd;
232	>	char* molName;
233	>	vector<StuntDouble*> integrableObjects;
234	>	vector<StuntDouble*>::iterator iter;
235	>	nTotObjects = entry_plug->getTotIntegrableObjects();
236		#ifndef IS_MPI
237	+
238	+	for(k = 0; k < outFile.size(); k++){
239	+	*outFile[k] << nTotObjects << "\n";
240
241	<	outFile << nAtoms << "\n";
241	>	*outFile[k] << currentTime << ";\t"
242	>	<< entry_plug->Hmat[0][0] << "\t"
243	>	<< entry_plug->Hmat[1][0] << "\t"
244	>	<< entry_plug->Hmat[2][0] << ";\t"
245	>
246	>	<< entry_plug->Hmat[0][1] << "\t"
247	>	<< entry_plug->Hmat[1][1] << "\t"
248	>	<< entry_plug->Hmat[2][1] << ";\t"
249
250	<	outFile << currentTime << ";\t"
251	<	<< entry_plug->Hmat[0][0] << "\t"
252	<	<< entry_plug->Hmat[1][0] << "\t"
187	<	<< entry_plug->Hmat[2][0] << ";\t"
250	>	<< entry_plug->Hmat[0][2] << "\t"
251	>	<< entry_plug->Hmat[1][2] << "\t"
252	>	<< entry_plug->Hmat[2][2] << ";";
253
254	<	<< entry_plug->Hmat[0][1] << "\t"
255	<	<< entry_plug->Hmat[1][1] << "\t"
256	<	<< entry_plug->Hmat[2][1] << ";\t"
254	>	//write out additional parameters, such as chi and eta
255	>	*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
256	>	}
257	>
258	>	for( i=0; i< entry_plug->n_mol; i++ ){
259
260	<	<< entry_plug->Hmat[0][2] << "\t"
261	<	<< entry_plug->Hmat[1][2] << "\t"
262	<	<< entry_plug->Hmat[2][2] << ";";
263	<	//write out additional parameters, such as chi and eta
264	<	outFile << entry_plug->the_integrator->getAdditionalParameters();
265	<	outFile << endl;
260	>	integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
261	>	molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
262	>
263	>	for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){
264	>	sd = *iter;
265	>	sd->getPos(pos);
266	>	sd->getVel(vel);
267
268	<	for( i=0; i<nAtoms; i++ ){
269	<
270	<	atoms[i]->getPos(pos);
271	<	atoms[i]->getVel(vel);
268	>	sprintf( tempBuffer,
269	>	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
270	>	sd->getType(),
271	>	pos[0],
272	>	pos[1],
273	>	pos[2],
274	>	vel[0],
275	>	vel[1],
276	>	vel[2]);
277	>	strcpy( writeLine, tempBuffer );
278
279	<	sprintf( tempBuffer,
206	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
207	<	atoms[i]->getType(),
208	<	pos[0],
209	<	pos[1],
210	<	pos[2],
211	<	vel[0],
212	<	vel[1],
213	<	vel[2]);
214	<	strcpy( writeLine, tempBuffer );
279	>	if( sd->isDirectional() ){
280
281	<	if( atoms[i]->isDirectional() ){
281	>	sd->getQ( q );
282	>	sd->getJ( ji );
283
284	<	dAtom = (DirectionalAtom *)atoms[i];
285	<	dAtom->getQ( q );
286	<
287	<	sprintf( tempBuffer,
288	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
289	<	q[0],
290	<	q[1],
291	<	q[2],
292	<	q[3],
293	<	dAtom->getJx(),
294	<	dAtom->getJy(),
295	<	dAtom->getJz());
296	<	strcat( writeLine, tempBuffer );
284	>	sprintf( tempBuffer,
285	>	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
286	>	q[0],
287	>	q[1],
288	>	q[2],
289	>	q[3],
290	>	ji[0],
291	>	ji[1],
292	>	ji[2]);
293	>	strcat( writeLine, tempBuffer );
294	>	}
295	>	else
296	>	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
297		}
232	–	else
233	–	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298
299	<	outFile << writeLine;
300	<	}
299	>
300	>	for(k = 0; k < outFile.size(); k++)
301	>	*outFile[k] << writeLine;
302	>	}
303
304		#else // is_mpi
305
#	Line 250 \| Line 316 \| void DumpWriter::writeFrame( ofstream& outFile, double
316		int haveError;
317
318		MPI_Status istatus;
319	<	int *AtomToProcMap = mpiSim->getAtomToProcMap();
319	>	int nCurObj;
320	>	int *MolToProcMap = mpiSim->getMolToProcMap();
321
322		// write out header and node 0's coordinates
323
#	Line 258 \| Line 325 \| void DumpWriter::writeFrame( ofstream& outFile, double
325
326		// Node 0 needs a list of the magic potatoes for each processor;
327
328	<	nProc = mpiSim->getNumberProcessors();
328	>	nProc = mpiSim->getNprocessors();
329		potatoes = new int[nProc];
330
331	+	//write out the comment lines
332		for (i = 0; i < nProc; i++)
333		potatoes[i] = 0;
334
335	<	outFile << mpiSim->getTotAtoms() << "\n";
335	>	for(k = 0; k < outFile.size(); k++){
336	>	*outFile[k] << nTotObjects << "\n";
337
338	<	outFile << currentTime << ";\t"
339	<	<< entry_plug->Hmat[0][0] << "\t"
340	<	<< entry_plug->Hmat[1][0] << "\t"
341	<	<< entry_plug->Hmat[2][0] << ";\t"
338	>	*outFile[k] << currentTime << ";\t"
339	>	<< entry_plug->Hmat[0][0] << "\t"
340	>	<< entry_plug->Hmat[1][0] << "\t"
341	>	<< entry_plug->Hmat[2][0] << ";\t"
342
343	<	<< entry_plug->Hmat[0][1] << "\t"
344	<	<< entry_plug->Hmat[1][1] << "\t"
345	<	<< entry_plug->Hmat[2][1] << ";\t"
343	>	<< entry_plug->Hmat[0][1] << "\t"
344	>	<< entry_plug->Hmat[1][1] << "\t"
345	>	<< entry_plug->Hmat[2][1] << ";\t"
346
347	<	<< entry_plug->Hmat[0][2] << "\t"
348	<	<< entry_plug->Hmat[1][2] << "\t"
349	<	<< entry_plug->Hmat[2][2] << ";";
347	>	<< entry_plug->Hmat[0][2] << "\t"
348	>	<< entry_plug->Hmat[1][2] << "\t"
349	>	<< entry_plug->Hmat[2][2] << ";";
350	>
351	>	*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
352	>	}
353
282	–	outFile << entry_plug->the_integrator->getAdditionalParameters();
283	–	outFile << endl;
284	–	outFile.flush();
285	–
354		currentIndex = 0;
355	<	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
355	>
356	>	for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
357
358		// Get the Node number which has this atom;
359
360	<	which_node = AtomToProcMap[i];
360	>	which_node = MolToProcMap[i];
361
362		if (which_node != 0) {
363	<
364	<	if (potatoes[which_node] + 3 >= MAXTAG) {
363	>
364	>	if (potatoes[which_node] + 1 >= MAXTAG) {
365		// The potato was going to exceed the maximum value,
366		// so wrap this processor potato back to 0:
367
368		potatoes[which_node] = 0;
369	<	MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
369	>	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370
371		}
372
373		myPotato = potatoes[which_node];
305	–
306	–	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
307	–	myPotato, MPI_COMM_WORLD, &istatus);
308	–
309	–	atomTypeString = MPIatomTypeString;
310	–
311	–	myPotato++;
374
375	<	MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
375	>	//recieve the number of integrableObject in current molecule
376	>	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
377		myPotato, MPI_COMM_WORLD, &istatus);
315	–
378		myPotato++;
379	+
380	+	for(int l = 0; l < nCurObj; l++){
381
382	<	if (isDirectional) {
383	<	MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
384	<	myPotato, MPI_COMM_WORLD, &istatus);
385	<	} else {
386	<	MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
387	<	myPotato, MPI_COMM_WORLD, &istatus);
382	>	if (potatoes[which_node] + 2 >= MAXTAG) {
383	>	// The potato was going to exceed the maximum value,
384	>	// so wrap this processor potato back to 0:
385	>
386	>	potatoes[which_node] = 0;
387	>	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
388	>
389	>	}
390	>
391	>	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
392	>	myPotato, MPI_COMM_WORLD, &istatus);
393	>
394	>	atomTypeString = MPIatomTypeString;
395	>
396	>	myPotato++;
397	>
398	>	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
399	>	myPotato++;
400	>
401	>	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
402	>
403	>	if(msgLen == 13)
404	>	isDirectional = 1;
405	>	else
406	>	isDirectional = 0;
407	>
408		}
325	–
326	–	myPotato++;
409		potatoes[which_node] = myPotato;
410
411		} else {
412
413	<	haveError = 0;
332	<	which_atom = i;
413	>	haveError = 0;
414
415	<	local_index = indexArray[currentIndex].first;
335	<
336	<	if (which_atom == indexArray[currentIndex].second) {
337	<
338	<	atomTypeString = atoms[local_index]->getType();
415	>	local_index = indexArray[currentIndex].first;
416
417	<	atoms[local_index]->getPos(pos);
341	<	atoms[local_index]->getVel(vel);
417	>	integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
418
419	<	atomData6[0] = pos[0];
420	<	atomData6[1] = pos[1];
421	<	atomData6[2] = pos[2];
419	>	for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){
420	>	sd = *iter;
421	>	atomTypeString = sd->getType();
422	>
423	>	sd->getPos(pos);
424	>	sd->getVel(vel);
425	>
426	>	atomData[0] = pos[0];
427	>	atomData[1] = pos[1];
428	>	atomData[2] = pos[2];
429
430	<	atomData6[3] = vel[0];
431	<	atomData6[4] = vel[1];
432	<	atomData6[5] = vel[2];
433	<
434	<	isDirectional = 0;
430	>	atomData[3] = vel[0];
431	>	atomData[4] = vel[1];
432	>	atomData[5] = vel[2];
433	>
434	>	isDirectional = 0;
435
436	<	if( atoms[local_index]->isDirectional() ){
436	>	if( sd->isDirectional() ){
437
438	<	isDirectional = 1;
439	<
440	<	dAtom = (DirectionalAtom *)atoms[local_index];
441	<	dAtom->getQ( q );
438	>	isDirectional = 1;
439	>
440	>	sd->getQ( q );
441	>	sd->getJ( ji );
442
443	<	for (int j = 0; j < 6 ; j++)
444	<	atomData13[j] = atomData6[j];
443	>	for (int j = 0; j < 6 ; j++)
444	>	atomData[j] = atomData[j];
445	>
446	>	atomData[6] = q[0];
447	>	atomData[7] = q[1];
448	>	atomData[8] = q[2];
449	>	atomData[9] = q[3];
450	>
451	>	atomData[10] = ji[0];
452	>	atomData[11] = ji[1];
453	>	atomData[12] = ji[2];
454	>	}
455
456	<	atomData13[6] = q[0];
364	<	atomData13[7] = q[1];
365	<	atomData13[8] = q[2];
366	<	atomData13[9] = q[3];
367	<
368	<	atomData13[10] = dAtom->getJx();
369	<	atomData13[11] = dAtom->getJy();
370	<	atomData13[12] = dAtom->getJz();
371	<	}
372	<
373	<	} else {
374	<	sprintf(painCave.errMsg,
375	<	"Atom %d not found on processor %d\n",
376	<	i, worldRank );
377	<	haveError= 1;
378	<	simError();
379	<	}
456	>	}
457
458	<	if(haveError) DieDieDie();
382	<
383	<	currentIndex ++;
458	>	currentIndex++;
459		}
460		// If we've survived to here, format the line:
461
462		if (!isDirectional) {
463
464	<	sprintf( writeLine,
464	>	sprintf( writeLine,
465		"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
466		atomTypeString,
467	<	atomData6[0],
468	<	atomData6[1],
469	<	atomData6[2],
470	<	atomData6[3],
471	<	atomData6[4],
472	<	atomData6[5]);
473	<
467	>	atomData[0],
468	>	atomData[1],
469	>	atomData[2],
470	>	atomData[3],
471	>	atomData[4],
472	>	atomData[5]);
473	>
474		strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
475
476		} else {
#	Line 403 \| Line 478 \| void DumpWriter::writeFrame( ofstream& outFile, double
478		sprintf( writeLine,
479		"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
480		atomTypeString,
481	<	atomData13[0],
482	<	atomData13[1],
483	<	atomData13[2],
484	<	atomData13[3],
485	<	atomData13[4],
486	<	atomData13[5],
487	<	atomData13[6],
488	<	atomData13[7],
489	<	atomData13[8],
490	<	atomData13[9],
491	<	atomData13[10],
492	<	atomData13[11],
493	<	atomData13[12]);
481	>	atomData[0],
482	>	atomData[1],
483	>	atomData[2],
484	>	atomData[3],
485	>	atomData[4],
486	>	atomData[5],
487	>	atomData[6],
488	>	atomData[7],
489	>	atomData[8],
490	>	atomData[9],
491	>	atomData[10],
492	>	atomData[11],
493	>	atomData[12]);
494
495		}
496
497	<	outFile << writeLine;
497	>	for(k = 0; k < outFile.size(); k++)
498	>	*outFile[k] << writeLine;
499		}
500
501	<
502	<	outFile.flush();
501	>	for(k = 0; k < outFile.size(); k++)
502	>	outFile[k]->flush();
503	>
504		sprintf( checkPointMsg,
505		"Sucessfully took a dump.\n");
506	+
507		MPIcheckPoint();
508	+
509		delete[] potatoes;
510	+
511		} else {
512
513		// worldRank != 0, so I'm a remote node.
#	Line 437 \| Line 517 \| void DumpWriter::writeFrame( ofstream& outFile, double
517		myPotato = 0;
518		currentIndex = 0;
519
520	<	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
520	>	for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
521
522	<	// Am I the node which has this atom?
522	>	// Am I the node which has this integrableObject?
523
524	<	if (AtomToProcMap[i] == worldRank) {
524	>	if (MolToProcMap[i] == worldRank) {
525
446	–	if (myPotato + 3 >= MAXTAG) {
526
527	+	if (myPotato + 1 >= MAXTAG) {
528	+
529		// The potato was going to exceed the maximum value,
530		// so wrap this processor potato back to 0 (and block until
531		// node 0 says we can go:
532	<
532	>
533		MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
534
535		}
455	–	which_atom = i;
456	–	local_index = indexArray[currentIndex].first;
457	–
458	–	if (which_atom == indexArray[currentIndex].second) {
459	–
460	–	atomTypeString = atoms[local_index]->getType();
536
537	<	atoms[local_index]->getPos(pos);
538	<	atoms[local_index]->getVel(vel);
464	<
465	<	atomData6[0] = pos[0];
466	<	atomData6[1] = pos[1];
467	<	atomData6[2] = pos[2];
468	<
469	<	atomData6[3] = vel[0];
470	<	atomData6[4] = vel[1];
471	<	atomData6[5] = vel[2];
537	>	local_index = indexArray[currentIndex].first;
538	>	integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
539
540	<	isDirectional = 0;
540	>	nCurObj = integrableObjects.size();
541	>
542	>	MPI_Send(&nCurObj, 1, MPI_INT, 0,
543	>	myPotato, MPI_COMM_WORLD);
544	>	myPotato++;
545
546	<	if( atoms[local_index]->isDirectional() ){
546	>	for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){
547
548	<	isDirectional = 1;
548	>	if (myPotato + 2 >= MAXTAG) {
549	>
550	>	// The potato was going to exceed the maximum value,
551	>	// so wrap this processor potato back to 0 (and block until
552	>	// node 0 says we can go:
553	>
554	>	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
555	>
556	>	}
557
558	<	dAtom = (DirectionalAtom *)atoms[local_index];
480	<	dAtom->getQ( q );
558	>	sd = *iter;
559
560	<	for (int j = 0; j < 6 ; j++)
483	<	atomData13[j] = atomData6[j];
484	<
485	<	atomData13[6] = q[0];
486	<	atomData13[7] = q[1];
487	<	atomData13[8] = q[2];
488	<	atomData13[9] = q[3];
560	>	atomTypeString = sd->getType();
561
562	<	atomData13[10] = dAtom->getJx();
563	<	atomData13[11] = dAtom->getJy();
492	<	atomData13[12] = dAtom->getJz();
493	<	}
562	>	sd->getPos(pos);
563	>	sd->getVel(vel);
564
565	<	} else {
566	<	sprintf(painCave.errMsg,
567	<	"Atom %d not found on processor %d\n",
498	<	i, worldRank );
499	<	haveError= 1;
500	<	simError();
501	<	}
565	>	atomData[0] = pos[0];
566	>	atomData[1] = pos[1];
567	>	atomData[2] = pos[2];
568
569	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
569	>	atomData[3] = vel[0];
570	>	atomData[4] = vel[1];
571	>	atomData[5] = vel[2];
572	>
573	>	isDirectional = 0;
574
575	<	// null terminate the string before sending (just in case):
506	<	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
575	>	if( sd->isDirectional() ){
576
577	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578	<	myPotato, MPI_COMM_WORLD);
579	<
580	<	myPotato++;
577	>	isDirectional = 1;
578	>
579	>	sd->getQ( q );
580	>	sd->getJ( ji );
581	>
582	>
583	>	atomData[6] = q[0];
584	>	atomData[7] = q[1];
585	>	atomData[8] = q[2];
586	>	atomData[9] = q[3];
587	>
588	>	atomData[10] = ji[0];
589	>	atomData[11] = ji[1];
590	>	atomData[12] = ji[2];
591	>	}
592
593	<	MPI_Send(&isDirectional, 1, MPI_INT, 0,
594	<	myPotato, MPI_COMM_WORLD);
515	<
516	<	myPotato++;
517	<
518	<	if (isDirectional) {
593	>
594	>	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
595
596	<	MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
597	<	myPotato, MPI_COMM_WORLD);
522	<
523	<	} else {
596	>	// null terminate the string before sending (just in case):
597	>	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
598
599	<	MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
600	<	myPotato, MPI_COMM_WORLD);
601	<	}
599	>	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
600	>	myPotato, MPI_COMM_WORLD);
601	>
602	>	myPotato++;
603	>
604	>	if (isDirectional) {
605
606	<	myPotato++;
607	<	currentIndex++;
606	>	MPI_Send(atomData, 13, MPI_DOUBLE, 0,
607	>	myPotato, MPI_COMM_WORLD);
608	>
609	>	} else {
610	>
611	>	MPI_Send(atomData, 6, MPI_DOUBLE, 0,
612	>	myPotato, MPI_COMM_WORLD);
613	>	}
614	>
615	>	myPotato++;
616	>
617	>	}
618	>
619	>	currentIndex++;
620	>
621	>	}
622	>
623		}
532	–	}
624
625		sprintf( checkPointMsg,
626		"Sucessfully took a dump.\n");
627	<	MPIcheckPoint();
627	>	MPIcheckPoint();
628
629	<	}
629	>	}
630	>
631	>
632
633		#endif // is_mpi
634		}

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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents): Revision 929 by tim, Tue Jan 13 15:46:49 2004 UTC vs. Revision 1198 by tim, Thu May 27 00:48:12 2004 UTC

Diff Legend

Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 929 by tim, Tue Jan 13 15:46:49 2004 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 2004 UTC