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

Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 910 by gezelter, Thu Jan 8 18:05:37 2004 UTC vs.
Revision 919 by tim, Sat Jan 10 02:15:35 2004 UTC

#	Line 66 \| Line 66 \| void DumpWriter::writeDump( double currentTime ){
66		void DumpWriter::writeDump( double currentTime ){
67
68		const int BUFFERSIZE = 2000;
69	<	const int MINIBUFFERSIZE = 10;
69	>	const int MINIBUFFERSIZE = 100;
70
71		char tempBuffer[BUFFERSIZE];
72		char writeLine[BUFFERSIZE];
73
74		int i;
75	+
76		#ifdef IS_MPI
77	+
78	+	int *potatoes;
79	+	int myPotato;
80	+
81	+	int nProc;
82		int j, which_node, done, which_atom, local_index;
83	<	double atomTransData[6];
84	<	double atomOrientData[7];
83	>	double atomData6[6];
84	>	double atomData13[13];
85		int isDirectional;
86		char* atomTypeString;
87		char MPIatomTypeString[MINIBUFFERSIZE];
88	<	int me;
83	<	int atomTypeTag;
84	<	int atomIsDirectionalTag;
85	<	int atomTransDataTag;
86	<	int atomOrientDataTag;
88	>
89		#else //is_mpi
90		int nAtoms = entry_plug->n_atoms;
91		#endif //is_mpi
#	Line 158 \| Line 160 \| void DumpWriter::writeDump( double currentTime ){
160
161		#else // is_mpi
162
163	<	// first thing first, suspend fatalities.
164	<	painCave.isEventLoop = 1;
163	>	cout << "master" <<endl;
164	>	/* code to find maximum tag value */
165	>
166	>	int tagub, flag, MAXTAG;
167	>	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
168	>	if (flag) {
169	>	MAXTAG = tagub;
170	>	} else {
171	>	MAXTAG = 32767;
172	>	}
173
164	–	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
174		int haveError;
175
176		MPI_Status istatus;
#	Line 170 \| Line 179 \| void DumpWriter::writeDump( double currentTime ){
179		// write out header and node 0's coordinates
180
181		if( worldRank == 0 ){
182	+
183	+	// Node 0 needs a list of the magic potatoes for each processor;
184	+
185	+	nProc = mpiSim->getNumberProcessors();
186	+	potatoes = new int[nProc];
187	+
188	+	for (i = 0; i < nProc; i++)
189	+	potatoes[i] = 0;
190	+
191		outFile << mpiSim->getTotAtoms() << "\n";
192
193		outFile << currentTime << ";\t"
#	Line 188 \| Line 206 \| void DumpWriter::writeDump( double currentTime ){
206		outFile << entry_plug->the_integrator->getAdditionalParameters();
207		outFile << endl;
208		outFile.flush();
209	+
210		for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
211	+
212		// Get the Node number which has this atom;
213	<
213	>
214		which_node = AtomToProcMap[i];
215	<
215	>
216		if (which_node != 0) {
197	–
198	–	atomTypeTag = 4*i;
199	–	atomIsDirectionalTag = 4*i + 1;
200	–	atomTransDataTag = 4*i + 2;
201	–	atomOrientDataTag = 4*i + 3;
217
218	+	if (potatoes[which_node] + 3 >= MAXTAG) {
219	+	// The potato was going to exceed the maximum value,
220	+	// so wrap this processor potato back to 0:
221	+
222	+	potatoes[which_node] = 0;
223	+	MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
224	+
225	+	}
226	+
227	+	myPotato = potatoes[which_node];
228	+
229		MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
230	<	atomTypeTag, MPI_COMM_WORLD, &istatus);
230	>	myPotato, MPI_COMM_WORLD, &istatus);
231
232		strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
207	–
208	–	MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
209	–	atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
233
234	<	MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
212	<	atomTransDataTag, MPI_COMM_WORLD, &istatus);
234	>	// Null terminate the atomTypeString just in case:
235
236	<	if (isDirectional) {
236	>	atomTypeString[strlen(atomTypeString) - 1] = '\0';
237
238	<	MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
217	<	atomOrientDataTag, MPI_COMM_WORLD, &istatus);
238	>	myPotato++;
239
240	+	MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
241	+	myPotato, MPI_COMM_WORLD, &istatus);
242	+
243	+	myPotato++;
244	+
245	+	if (isDirectional) {
246	+	MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
247	+	myPotato, MPI_COMM_WORLD, &istatus);
248	+	} else {
249	+	MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
250	+	myPotato, MPI_COMM_WORLD, &istatus);
251		}
252	+
253	+	myPotato++;
254	+	potatoes[which_node] = myPotato;
255
256		} else {
257
258		haveError = 0;
259		which_atom = i;
260		local_index=-1;
261	<
261	>
262		for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
263		if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
264		}
265	<
265	>
266		if (local_index != -1) {
267	<
267	>
268		atomTypeString = atoms[local_index]->getType();
269
270		atoms[local_index]->getPos(pos);
271	<	atoms[local_index]->getVel(vel);
271	>	atoms[local_index]->getVel(vel);
272
273	<	atomTransData[0] = pos[0];
274	<	atomTransData[1] = pos[1];
275	<	atomTransData[2] = pos[2];
273	>	atomData6[0] = pos[0];
274	>	atomData6[1] = pos[1];
275	>	atomData6[2] = pos[2];
276
277	<	atomTransData[3] = vel[0];
278	<	atomTransData[4] = vel[1];
279	<	atomTransData[5] = vel[2];
277	>	atomData6[3] = vel[0];
278	>	atomData6[4] = vel[1];
279	>	atomData6[5] = vel[2];
280
281		isDirectional = 0;
282
#	Line 251 \| Line 286 \| void DumpWriter::writeDump( double currentTime ){
286
287		dAtom = (DirectionalAtom *)atoms[local_index];
288		dAtom->getQ( q );
254	–
255	–	atomOrientData[0] = q[0];
256	–	atomOrientData[1] = q[1];
257	–	atomOrientData[2] = q[2];
258	–	atomOrientData[3] = q[3];
289
290	<	atomOrientData[4] = dAtom->getJx();
291	<	atomOrientData[5] = dAtom->getJy();
292	<	atomOrientData[6] = dAtom->getJz();
290	>	for (int j = 0; j < 6 ; j++)
291	>	atomData13[j] = atomData6[j];
292	>
293	>	atomData13[6] = q[0];
294	>	atomData13[7] = q[1];
295	>	atomData13[8] = q[2];
296	>	atomData13[9] = q[3];
297	>
298	>	atomData13[10] = dAtom->getJx();
299	>	atomData13[11] = dAtom->getJy();
300	>	atomData13[12] = dAtom->getJz();
301		}
302	<
302	>
303		} else {
304		sprintf(painCave.errMsg,
305		"Atom %d not found on processor %d\n",
#	Line 269 \| Line 307 \| void DumpWriter::writeDump( double currentTime ){
307		haveError= 1;
308		simError();
309		}
310	<
310	>
311		if(haveError) DieDieDie();
312	<
312	>
313		// If we've survived to here, format the line:
314
315	<	sprintf( tempBuffer,
278	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
279	<	atomTypeString,
280	<	atomTransData[0],
281	<	atomTransData[1],
282	<	atomTransData[2],
283	<	atomTransData[3],
284	<	atomTransData[4],
285	<	atomTransData[5]);
315	>	if (!isDirectional) {
316
317	<	strcpy( writeLine, tempBuffer );
318	<
319	<	if (isDirectional) {
317	>	sprintf( tempBuffer,
318	>	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
319	>	atomTypeString,
320	>	atomData6[0],
321	>	atomData6[1],
322	>	atomData6[2],
323	>	atomData6[3],
324	>	atomData6[4],
325	>	atomData6[5]);
326	>
327	>	strcpy( writeLine, tempBuffer );
328	>	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
329
330	+	} else {
331	+
332		sprintf( tempBuffer,
333	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
334	<	atomOrientData[0],
335	<	atomOrientData[1],
336	<	atomOrientData[2],
337	<	atomOrientData[3],
338	<	atomOrientData[4],
339	<	atomOrientData[5],
340	<	atomOrientData[6]);
333	>	"%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",
334	>	atomTypeString,
335	>	atomData13[0],
336	>	atomData13[1],
337	>	atomData13[2],
338	>	atomData13[3],
339	>	atomData13[4],
340	>	atomData13[5],
341	>	atomData13[6],
342	>	atomData13[7],
343	>	atomData13[8],
344	>	atomData13[9],
345	>	atomData13[10],
346	>	atomData13[11],
347	>	atomData13[12]);
348	>
349		strcat( writeLine, tempBuffer );
350	<
302	<	} else {
303	<	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
350	>
351		}
352	<
352	>
353		outFile << writeLine;
354		outFile.flush();
355		}
#	Line 312 \| Line 359 \| void DumpWriter::writeDump( double currentTime ){
359		sprintf( checkPointMsg,
360		"Sucessfully took a dump.\n");
361		MPIcheckPoint();
362	<
362	>	delete[] potatoes;
363		} else {
364
365		// worldRank != 0, so I'm a remote node.
366	+
367	+	// Set my magic potato to 0:
368	+
369	+	myPotato = 0;
370
371		for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
372
#	Line 323 \| Line 374 \| void DumpWriter::writeDump( double currentTime ){
374
375		if (AtomToProcMap[i] == worldRank) {
376
377	<	local_index=-1;
377	>	if (myPotato + 3 >= MAXTAG) {
378	>
379	>	// The potato was going to exceed the maximum value,
380	>	// so wrap this processor potato back to 0 (and block until
381	>	// node 0 says we can go:
382	>
383	>	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
384	>
385	>	}
386	>	which_atom = i;
387	>	local_index=-1;
388		for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
389		if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
390		}
#	Line 334 \| Line 395 \| void DumpWriter::writeDump( double currentTime ){
395		atoms[local_index]->getPos(pos);
396		atoms[local_index]->getVel(vel);
397
398	<	atomTransData[0] = pos[0];
399	<	atomTransData[1] = pos[1];
400	<	atomTransData[2] = pos[2];
398	>	atomData6[0] = pos[0];
399	>	atomData6[1] = pos[1];
400	>	atomData6[2] = pos[2];
401
402	<	atomTransData[3] = vel[0];
403	<	atomTransData[4] = vel[1];
404	<	atomTransData[5] = vel[2];
402	>	atomData6[3] = vel[0];
403	>	atomData6[4] = vel[1];
404	>	atomData6[5] = vel[2];
405
406		isDirectional = 0;
407
#	Line 351 \| Line 412 \| void DumpWriter::writeDump( double currentTime ){
412		dAtom = (DirectionalAtom *)atoms[local_index];
413		dAtom->getQ( q );
414
415	<	atomOrientData[0] = q[0];
416	<	atomOrientData[1] = q[1];
417	<	atomOrientData[2] = q[2];
418	<	atomOrientData[3] = q[3];
415	>	for (int j = 0; j < 6 ; j++)
416	>	atomData13[j] = atomData6[j];
417	>
418	>	atomData13[6] = q[0];
419	>	atomData13[7] = q[1];
420	>	atomData13[8] = q[2];
421	>	atomData13[9] = q[3];
422
423	<	atomOrientData[4] = dAtom->getJx();
424	<	atomOrientData[5] = dAtom->getJy();
425	<	atomOrientData[6] = dAtom->getJz();
423	>	atomData13[10] = dAtom->getJx();
424	>	atomData13[11] = dAtom->getJy();
425	>	atomData13[12] = dAtom->getJz();
426		}
427
428		} else {
#	Line 369 \| Line 433 \| void DumpWriter::writeDump( double currentTime ){
433		simError();
434		}
435
372	–	// I've survived this far, so send off the data!
373	–
374	–	atomTypeTag = 4*i;
375	–	atomIsDirectionalTag = 4*i + 1;
376	–	atomTransDataTag = 4*i + 2;
377	–	atomOrientDataTag = 4*i + 3;
378	–
379	–
436		strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
437
438	+	// null terminate the string before sending (just in case):
439	+	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
440	+
441		MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
442	<	atomTypeTag, MPI_COMM_WORLD);
442	>	myPotato, MPI_COMM_WORLD);
443
444	+	myPotato++;
445	+
446		MPI_Send(&isDirectional, 1, MPI_INT, 0,
447	<	atomIsDirectionalTag, MPI_COMM_WORLD);
447	>	myPotato, MPI_COMM_WORLD);
448
449	<	MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
450	<	atomTransDataTag, MPI_COMM_WORLD);
390	<
449	>	myPotato++;
450	>
451		if (isDirectional) {
452
453	<	MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
454	<	atomOrientDataTag, MPI_COMM_WORLD);
453	>	MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
454	>	myPotato, MPI_COMM_WORLD);
455
456	+	} else {
457	+
458	+	MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
459	+	myPotato, MPI_COMM_WORLD);
460		}
461	<
461	>
462	>	myPotato++;
463		}
464		}
465
#	Line 402 \| Line 467 \| void DumpWriter::writeDump( double currentTime ){
467		"Sucessfully took a dump.\n");
468		MPIcheckPoint();
469
470	<	}
470	>	}
471
407	–	painCave.isEventLoop = 0;
408	–
472		#endif // is_mpi
473		}
474
#	Line 415 \| Line 478 \| void DumpWriter::writeFinal(double finalTime){
478		ofstream finalOut;
479
480		const int BUFFERSIZE = 2000;
481	<	const int MINIBUFFERSIZE = 10;
481	>	const int MINIBUFFERSIZE = 100;
482		char tempBuffer[BUFFERSIZE];
483		char writeLine[BUFFERSIZE];
484
#	Line 424 \| Line 487 \| void DumpWriter::writeFinal(double finalTime){
487		Atom** atoms = entry_plug->atoms;
488		int i;
489		#ifdef IS_MPI
490	+
491	+	int *potatoes;
492	+	int myPotato;
493	+
494	+	int nProc;
495		int j, which_node, done, which_atom, local_index;
496	<	double atomTransData[6];
497	<	double atomOrientData[7];
496	>	double atomData6[6];
497	>	double atomData13[13];
498		int isDirectional;
499		char* atomTypeString;
500		char MPIatomTypeString[MINIBUFFERSIZE];
501	<	int atomTypeTag;
434	<	int atomIsDirectionalTag;
435	<	int atomTransDataTag;
436	<	int atomOrientDataTag;
501	>
502		#else //is_mpi
503		int nAtoms = entry_plug->n_atoms;
504		#endif //is_mpi
#	Line 529 \| Line 594 \| void DumpWriter::writeFinal(double finalTime){
594
595		#else // is_mpi
596
597	<	// first thing first, suspend fatalities.
598	<	painCave.isEventLoop = 1;
597	>	/* code to find maximum tag value */
598	>	int *tagub, flag, MAXTAG;
599	>	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
600	>	if (flag) {
601	>	MAXTAG = *tagub;
602	>	} else {
603	>	MAXTAG = 32767;
604	>	}
605
535	–	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
606		int haveError;
607
608		MPI_Status istatus;
#	Line 541 \| Line 611 \| void DumpWriter::writeFinal(double finalTime){
611		// write out header and node 0's coordinates
612
613		if( worldRank == 0 ){
614	+
615	+	// Node 0 needs a list of the magic potatoes for each processor;
616	+
617	+	nProc = mpiSim->getNumberProcessors();
618	+	potatoes = new int[nProc];
619	+
620	+	for (i = 0; i < nProc; i++)
621	+	potatoes[i] = 0;
622	+
623		finalOut << mpiSim->getTotAtoms() << "\n";
624
625		finalOut << finalTime << ";\t"
#	Line 559 \| Line 638 \| void DumpWriter::writeFinal(double finalTime){
638		finalOut << entry_plug->the_integrator->getAdditionalParameters();
639		finalOut << endl;
640		finalOut.flush();
641	+
642		for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
643	+
644		// Get the Node number which has this atom;
645	<
645	>
646		which_node = AtomToProcMap[i];
647	<
647	>
648		if (which_node != 0) {
568	–
569	–	atomTypeTag = 4*i;
570	–	atomIsDirectionalTag = 4*i + 1;
571	–	atomTransDataTag = 4*i + 2;
572	–	atomOrientDataTag = 4*i + 3;
649
650	+	if (potatoes[which_node] + 3 >= MAXTAG) {
651	+	// The potato was going to exceed the maximum value,
652	+	// so wrap this processor potato back to 0:
653	+
654	+	potatoes[which_node] = 0;
655	+	MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
656	+
657	+	}
658	+
659	+	myPotato = potatoes[which_node];
660	+
661		MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
662	<	atomTypeTag, MPI_COMM_WORLD, &istatus);
662	>	myPotato, MPI_COMM_WORLD, &istatus);
663
664		strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
578	–
579	–	MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
580	–	atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
665
666	<	MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
583	<	atomTransDataTag, MPI_COMM_WORLD, &istatus);
666	>	// Null terminate the atomTypeString just in case:
667
668	<	if (isDirectional) {
668	>	atomTypeString[strlen(atomTypeString) - 1] = '\0';
669
670	<	MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
588	<	atomOrientDataTag, MPI_COMM_WORLD, &istatus);
670	>	myPotato++;
671
672	+	MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
673	+	myPotato, MPI_COMM_WORLD, &istatus);
674	+
675	+	myPotato++;
676	+
677	+	if (isDirectional) {
678	+	MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
679	+	myPotato, MPI_COMM_WORLD, &istatus);
680	+	} else {
681	+	MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
682	+	myPotato, MPI_COMM_WORLD, &istatus);
683		}
684	+
685	+	myPotato++;
686	+	potatoes[which_node] = myPotato;
687
688		} else {
689
690		haveError = 0;
691		which_atom = i;
692		local_index=-1;
693	<
693	>
694		for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
695		if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
696		}
697	<
697	>
698		if (local_index != -1) {
699	<
699	>
700		atomTypeString = atoms[local_index]->getType();
701
702		atoms[local_index]->getPos(pos);
703	<	atoms[local_index]->getVel(vel);
703	>	atoms[local_index]->getVel(vel);
704
705	<	atomTransData[0] = pos[0];
706	<	atomTransData[1] = pos[1];
707	<	atomTransData[2] = pos[2];
705	>	atomData6[0] = pos[0];
706	>	atomData6[1] = pos[1];
707	>	atomData6[2] = pos[2];
708
709	<	atomTransData[3] = vel[0];
710	<	atomTransData[4] = vel[1];
711	<	atomTransData[5] = vel[2];
709	>	atomData6[3] = vel[0];
710	>	atomData6[4] = vel[1];
711	>	atomData6[5] = vel[2];
712
713		isDirectional = 0;
714
#	Line 622 \| Line 718 \| void DumpWriter::writeFinal(double finalTime){
718
719		dAtom = (DirectionalAtom *)atoms[local_index];
720		dAtom->getQ( q );
625	–
626	–	atomOrientData[0] = q[0];
627	–	atomOrientData[1] = q[1];
628	–	atomOrientData[2] = q[2];
629	–	atomOrientData[3] = q[3];
721
722	<	atomOrientData[4] = dAtom->getJx();
723	<	atomOrientData[5] = dAtom->getJy();
724	<	atomOrientData[6] = dAtom->getJz();
722	>	for (int j = 0; j < 6 ; j++)
723	>	atomData13[j] = atomData6[j];
724	>
725	>	atomData13[6] = q[0];
726	>	atomData13[7] = q[1];
727	>	atomData13[8] = q[2];
728	>	atomData13[9] = q[3];
729	>
730	>	atomData13[10] = dAtom->getJx();
731	>	atomData13[11] = dAtom->getJy();
732	>	atomData13[12] = dAtom->getJz();
733		}
734	<
734	>
735		} else {
736		sprintf(painCave.errMsg,
737		"Atom %d not found on processor %d\n",
#	Line 640 \| Line 739 \| void DumpWriter::writeFinal(double finalTime){
739		haveError= 1;
740		simError();
741		}
742	<
742	>
743		if(haveError) DieDieDie();
744	<
744	>
745		// If we've survived to here, format the line:
746
747	<	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]);
747	>	if (!isDirectional) {
748
749	<	strcpy( writeLine, tempBuffer );
750	<
751	<	if (isDirectional) {
749	>	sprintf( tempBuffer,
750	>	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
751	>	atomTypeString,
752	>	atomData6[0],
753	>	atomData6[1],
754	>	atomData6[2],
755	>	atomData6[3],
756	>	atomData6[4],
757	>	atomData6[5]);
758	>
759	>	strcpy( writeLine, tempBuffer );
760	>	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
761
762	+	} else {
763	+
764		sprintf( tempBuffer,
765	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
766	<	atomOrientData[0],
767	<	atomOrientData[1],
768	<	atomOrientData[2],
769	<	atomOrientData[3],
770	<	atomOrientData[4],
771	<	atomOrientData[5],
772	<	atomOrientData[6]);
765	>	"%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",
766	>	atomTypeString,
767	>	atomData13[0],
768	>	atomData13[1],
769	>	atomData13[2],
770	>	atomData13[3],
771	>	atomData13[4],
772	>	atomData13[5],
773	>	atomData13[6],
774	>	atomData13[7],
775	>	atomData13[8],
776	>	atomData13[9],
777	>	atomData13[10],
778	>	atomData13[11],
779	>	atomData13[12]);
780	>
781		strcat( writeLine, tempBuffer );
782	<
673	<	} else {
674	<	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
782	>
783		}
784	<
784	>
785		finalOut << writeLine;
786		finalOut.flush();
787		}
#	Line 682 \| Line 790 \| void DumpWriter::writeFinal(double finalTime){
790		finalOut.flush();
791		sprintf( checkPointMsg,
792		"Sucessfully took a dump.\n");
793	+	delete[] potatoes;
794	+
795		MPIcheckPoint();
796
797		} else {
798
799		// worldRank != 0, so I'm a remote node.
800	+
801	+	// Set my magic potato to 0:
802	+
803	+	myPotato = 0;
804
805		for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
806
#	Line 694 \| Line 808 \| void DumpWriter::writeFinal(double finalTime){
808
809		if (AtomToProcMap[i] == worldRank) {
810
811	+	if (myPotato + 3 >= MAXTAG) {
812	+
813	+	// The potato was going to exceed the maximum value,
814	+	// so wrap this processor potato back to 0 (and block until
815	+	// node 0 says we can go:
816	+
817	+	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
818	+
819	+	}
820	+	which_atom = i;
821		local_index=-1;
822		for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
823		if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
#	Line 705 \| Line 829 \| void DumpWriter::writeFinal(double finalTime){
829		atoms[local_index]->getPos(pos);
830		atoms[local_index]->getVel(vel);
831
832	<	atomTransData[0] = pos[0];
833	<	atomTransData[1] = pos[1];
834	<	atomTransData[2] = pos[2];
832	>	atomData6[0] = pos[0];
833	>	atomData6[1] = pos[1];
834	>	atomData6[2] = pos[2];
835
836	<	atomTransData[3] = vel[0];
837	<	atomTransData[4] = vel[1];
838	<	atomTransData[5] = vel[2];
836	>	atomData6[3] = vel[0];
837	>	atomData6[4] = vel[1];
838	>	atomData6[5] = vel[2];
839
840		isDirectional = 0;
841
#	Line 722 \| Line 846 \| void DumpWriter::writeFinal(double finalTime){
846		dAtom = (DirectionalAtom *)atoms[local_index];
847		dAtom->getQ( q );
848
849	<	atomOrientData[0] = q[0];
850	<	atomOrientData[1] = q[1];
851	<	atomOrientData[2] = q[2];
852	<	atomOrientData[3] = q[3];
849	>	for (int j = 0; j < 6 ; j++)
850	>	atomData13[j] = atomData6[j];
851	>
852	>	atomData13[6] = q[0];
853	>	atomData13[7] = q[1];
854	>	atomData13[8] = q[2];
855	>	atomData13[9] = q[3];
856
857	<	atomOrientData[4] = dAtom->getJx();
858	<	atomOrientData[5] = dAtom->getJy();
859	<	atomOrientData[6] = dAtom->getJz();
857	>	atomData13[10] = dAtom->getJx();
858	>	atomData13[11] = dAtom->getJy();
859	>	atomData13[12] = dAtom->getJz();
860		}
861
862		} else {
#	Line 740 \| Line 867 \| void DumpWriter::writeFinal(double finalTime){
867		simError();
868		}
869
743	–	// I've survived this far, so send off the data!
744	–
745	–	atomTypeTag = 4*i;
746	–	atomIsDirectionalTag = 4*i + 1;
747	–	atomTransDataTag = 4*i + 2;
748	–	atomOrientDataTag = 4*i + 3;
749	–
870		strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
871
872	+	// null terminate the string before sending (just in case):
873	+	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
874	+
875		MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
876	<	atomTypeTag, MPI_COMM_WORLD);
876	>	myPotato, MPI_COMM_WORLD);
877
878	+	myPotato++;
879	+
880		MPI_Send(&isDirectional, 1, MPI_INT, 0,
881	<	atomIsDirectionalTag, MPI_COMM_WORLD);
881	>	myPotato, MPI_COMM_WORLD);
882
883	<	MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
884	<	atomTransDataTag, MPI_COMM_WORLD);
760	<
883	>	myPotato++;
884	>
885		if (isDirectional) {
886
887	<	MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
888	<	atomOrientDataTag, MPI_COMM_WORLD);
887	>	MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
888	>	myPotato, MPI_COMM_WORLD);
889
890	+	} else {
891	+
892	+	MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
893	+	myPotato, MPI_COMM_WORLD);
894		}
895	<
895	>
896	>	myPotato++;
897		}
898		}
899
900		sprintf( checkPointMsg,
901	<	"Sucessfully wrote final file.\n");
901	>	"Sucessfully took a dump.\n");
902		MPIcheckPoint();
903
904	<	}
904	>	}
905
777	–	painCave.isEventLoop = 0;
778	–
906		if( worldRank == 0 ) finalOut.close();
907		#endif // is_mpi
908		}

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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents): Revision 910 by gezelter, Thu Jan 8 18:05:37 2004 UTC vs. Revision 919 by tim, Sat Jan 10 02:15:35 2004 UTC

Diff Legend

Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 910 by gezelter, Thu Jan 8 18:05:37 2004 UTC vs.
Revision 919 by tim, Sat Jan 10 02:15:35 2004 UTC