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

Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 905 by tim, Wed Jan 7 19:26:12 2004 UTC vs.
Revision 910 by gezelter, Thu Jan 8 18:05:37 2004 UTC

#	Line 7 \| Line 7
7		#ifdef IS_MPI
8		#include <mpi.h>
9		#include "mpiSimulation.hpp"
10	–	#define TAKE_THIS_TAG_CHAR 15
11	–	#define TAKE_THIS_TAG_INT 20
10
11		namespace dWrite{
12	<	void nodeZeroError( void );
15	<	void anonymousNodeDie( void );
12	>	void DieDieDie( void );
13		}
14
15		using namespace dWrite;
#	Line 69 \| Line 66 \| void DumpWriter::writeDump( double currentTime ){
66		void DumpWriter::writeDump( double currentTime ){
67
68		const int BUFFERSIZE = 2000;
69	+	const int MINIBUFFERSIZE = 10;
70	+
71		char tempBuffer[BUFFERSIZE];
72		char writeLine[BUFFERSIZE];
73
74		int i;
75		#ifdef IS_MPI
76		int j, which_node, done, which_atom, local_index;
77	+	double atomTransData[6];
78	+	double atomOrientData[7];
79	+	int isDirectional;
80	+	char* atomTypeString;
81	+	char MPIatomTypeString[MINIBUFFERSIZE];
82	+	int me;
83	+	int atomTypeTag;
84	+	int atomIsDirectionalTag;
85	+	int atomTransDataTag;
86	+	int atomOrientDataTag;
87		#else //is_mpi
88		int nAtoms = entry_plug->n_atoms;
89		#endif //is_mpi
#	Line 84 \| Line 93 \| void DumpWriter::writeDump( double currentTime ){
93		Atom** atoms = entry_plug->atoms;
94		double pos[3], vel[3];
95
87	–
96		// write current frame to the eor file
97
98		this->writeFinal( currentTime );
#	Line 185 \| Line 193 \| void DumpWriter::writeDump( double currentTime ){
193
194		which_node = AtomToProcMap[i];
195
196	<	if (which_node == 0 ) {
196	>	if (which_node != 0) {
197	>
198	>	atomTypeTag = 4*i;
199	>	atomIsDirectionalTag = 4*i + 1;
200	>	atomTransDataTag = 4*i + 2;
201	>	atomOrientDataTag = 4*i + 3;
202
203	+	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
204	+	atomTypeTag, MPI_COMM_WORLD, &istatus);
205	+
206	+	strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
207	+
208	+	MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
209	+	atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
210	+
211	+	MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
212	+	atomTransDataTag, MPI_COMM_WORLD, &istatus);
213	+
214	+	if (isDirectional) {
215	+
216	+	MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
217	+	atomOrientDataTag, MPI_COMM_WORLD, &istatus);
218	+
219	+	}
220	+
221	+	} else {
222	+
223		haveError = 0;
224		which_atom = i;
225		local_index=-1;
226	+
227		for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
228		if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
229		}
230	+
231		if (local_index != -1) {
197	–	//format the line
232
233	+	atomTypeString = atoms[local_index]->getType();
234	+
235		atoms[local_index]->getPos(pos);
236		atoms[local_index]->getVel(vel);
237
238	<	sprintf( tempBuffer,
239	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
240	<	atoms[local_index]->getType(),
205	<	pos[0],
206	<	pos[1],
207	<	pos[2],
208	<	vel[0],
209	<	vel[1],
210	<	vel[2]); // check here.
211	<	strcpy( writeLine, tempBuffer );
238	>	atomTransData[0] = pos[0];
239	>	atomTransData[1] = pos[1];
240	>	atomTransData[2] = pos[2];
241
242	+	atomTransData[3] = vel[0];
243	+	atomTransData[4] = vel[1];
244	+	atomTransData[5] = vel[2];
245	+
246	+	isDirectional = 0;
247	+
248		if( atoms[local_index]->isDirectional() ){
249
250	+	isDirectional = 1;
251	+
252		dAtom = (DirectionalAtom *)atoms[local_index];
253		dAtom->getQ( q );
254	+
255	+	atomOrientData[0] = q[0];
256	+	atomOrientData[1] = q[1];
257	+	atomOrientData[2] = q[2];
258	+	atomOrientData[3] = q[3];
259
260	<	sprintf( tempBuffer,
261	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
262	<	q[0],
263	<	q[1],
222	<	q[2],
223	<	q[3],
224	<	dAtom->getJx(),
225	<	dAtom->getJy(),
226	<	dAtom->getJz());
227	<	strcat( writeLine, tempBuffer );
260	>	atomOrientData[4] = dAtom->getJx();
261	>	atomOrientData[5] = dAtom->getJy();
262	>	atomOrientData[6] = dAtom->getJz();
263	>	}
264
265	<	}
230	<	else
231	<	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
232	<	}
233	<	else {
265	>	} else {
266		sprintf(painCave.errMsg,
267		"Atom %d not found on processor %d\n",
268		i, worldRank );
#	Line 238 \| Line 270 \| void DumpWriter::writeDump( double currentTime ){
270		simError();
271		}
272
273	<	if(haveError) nodeZeroError();
273	>	if(haveError) DieDieDie();
274	>
275	>	// If we've survived to here, format the line:
276	>
277	>	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]);
286
287	<	}
244	<	else {
245	<	myStatus = 1;
246	<	MPI_Send(&myStatus, 1, MPI_INT, which_node,
247	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
248	<	MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
249	<	MPI_COMM_WORLD);
250	<	MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
251	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
252	<	MPI_Recv(&myStatus, 1, MPI_INT, which_node,
253	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
287	>	strcpy( writeLine, tempBuffer );
288
289	<	if(!myStatus) nodeZeroError();
289	>	if (isDirectional) {
290
291	<	}
291	>	sprintf( tempBuffer,
292	>	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
293	>	atomOrientData[0],
294	>	atomOrientData[1],
295	>	atomOrientData[2],
296	>	atomOrientData[3],
297	>	atomOrientData[4],
298	>	atomOrientData[5],
299	>	atomOrientData[6]);
300	>	strcat( writeLine, tempBuffer );
301
302	<	outFile << writeLine;
303	<	outFile.flush();
304	<	}
302	>	} else {
303	>	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
304	>	}
305
306	<	// kill everyone off:
307	<	myStatus = -1;
308	<	for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
266	<	MPI_Send(&myStatus, 1, MPI_INT, j,
267	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
306	>	outFile << writeLine;
307	>	outFile.flush();
308	>	}
309		}
310
311	+	outFile.flush();
312	+	sprintf( checkPointMsg,
313	+	"Sucessfully took a dump.\n");
314	+	MPIcheckPoint();
315	+
316		} else {
317
318	<	done = 0;
319	<	while (!done) {
318	>	// worldRank != 0, so I'm a remote node.
319	>
320	>	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
321	>
322	>	// Am I the node which has this atom?
323	>
324	>	if (AtomToProcMap[i] == worldRank) {
325
326	<	MPI_Recv(&myStatus, 1, MPI_INT, 0,
327	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
326	>	local_index=-1;
327	>	for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
328	>	if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
329	>	}
330	>	if (local_index != -1) {
331	>
332	>	atomTypeString = atoms[local_index]->getType();
333
334	<	if(!myStatus) anonymousNodeDie();
335	<
280	<	if(myStatus < 0) break;
334	>	atoms[local_index]->getPos(pos);
335	>	atoms[local_index]->getVel(vel);
336
337	<	MPI_Recv(&which_atom, 1, MPI_INT, 0,
338	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
337	>	atomTransData[0] = pos[0];
338	>	atomTransData[1] = pos[1];
339	>	atomTransData[2] = pos[2];
340
341	<	myStatus = 1;
342	<	local_index=-1;
343	<	for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
344	<	if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
345	<	}
290	<	if (local_index != -1) {
291	<	//format the line
341	>	atomTransData[3] = vel[0];
342	>	atomTransData[4] = vel[1];
343	>	atomTransData[5] = vel[2];
344	>
345	>	isDirectional = 0;
346
347	<	atoms[local_index]->getPos(pos);
294	<	atoms[local_index]->getVel(vel);
347	>	if( atoms[local_index]->isDirectional() ){
348
349	<	sprintf( tempBuffer,
350	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
351	<	atoms[local_index]->getType(),
352	<	pos[0],
353	<	pos[1],
354	<	pos[2],
355	<	vel[0],
356	<	vel[1],
357	<	vel[2]); // check here.
305	<	strcpy( writeLine, tempBuffer );
349	>	isDirectional = 1;
350	>
351	>	dAtom = (DirectionalAtom *)atoms[local_index];
352	>	dAtom->getQ( q );
353	>
354	>	atomOrientData[0] = q[0];
355	>	atomOrientData[1] = q[1];
356	>	atomOrientData[2] = q[2];
357	>	atomOrientData[3] = q[3];
358
359	<	if( atoms[local_index]->isDirectional() ){
359	>	atomOrientData[4] = dAtom->getJx();
360	>	atomOrientData[5] = dAtom->getJy();
361	>	atomOrientData[6] = dAtom->getJz();
362	>	}
363
364	<	dAtom = (DirectionalAtom *)atoms[local_index];
365	<	dAtom->getQ( q );
366	<
367	<	sprintf( tempBuffer,
368	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
369	<	q[0],
315	<	q[1],
316	<	q[2],
317	<	q[3],
318	<	dAtom->getJx(),
319	<	dAtom->getJy(),
320	<	dAtom->getJz());
321	<	strcat( writeLine, tempBuffer );
364	>	} else {
365	>	sprintf(painCave.errMsg,
366	>	"Atom %d not found on processor %d\n",
367	>	i, worldRank );
368	>	haveError= 1;
369	>	simError();
370		}
323	–	else{
324	–	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
325	–	}
326	–	}
327	–	else {
328	–	sprintf(painCave.errMsg,
329	–	"Atom %d not found on processor %d\n",
330	–	which_atom, worldRank );
331	–	myStatus = 0;
332	–	simError();
371
372	<	strcpy( writeLine, "Hello, I'm an error.\n");
335	<	}
372	>	// I've survived this far, so send off the data!
373
374	<	MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
375	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
376	<	MPI_Send( &myStatus, 1, MPI_INT, 0,
377	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
374	>	atomTypeTag = 4*i;
375	>	atomIsDirectionalTag = 4*i + 1;
376	>	atomTransDataTag = 4*i + 2;
377	>	atomOrientDataTag = 4*i + 3;
378	>
379	>
380	>	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
381	>
382	>	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
383	>	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	>	}
399		}
342	–	}
343	–	outFile.flush();
344	–	sprintf( checkPointMsg,
345	–	"Sucessfully took a dump.\n");
346	–	MPIcheckPoint();
400
401	<	// last thing last, enable fatalities.
401	>	sprintf( checkPointMsg,
402	>	"Sucessfully took a dump.\n");
403	>	MPIcheckPoint();
404	>
405	>	}
406	>
407		painCave.isEventLoop = 0;
408
409		#endif // is_mpi
#	Line 357 \| Line 415 \| void DumpWriter::writeFinal(double finalTime){
415		ofstream finalOut;
416
417		const int BUFFERSIZE = 2000;
418	+	const int MINIBUFFERSIZE = 10;
419		char tempBuffer[BUFFERSIZE];
420		char writeLine[BUFFERSIZE];
421
#	Line 366 \| Line 425 \| void DumpWriter::writeFinal(double finalTime){
425		int i;
426		#ifdef IS_MPI
427		int j, which_node, done, which_atom, local_index;
428	+	double atomTransData[6];
429	+	double atomOrientData[7];
430	+	int isDirectional;
431	+	char* atomTypeString;
432	+	char MPIatomTypeString[MINIBUFFERSIZE];
433	+	int atomTypeTag;
434	+	int atomIsDirectionalTag;
435	+	int atomTransDataTag;
436	+	int atomOrientDataTag;
437		#else //is_mpi
438		int nAtoms = entry_plug->n_atoms;
439		#endif //is_mpi
#	Line 472 \| Line 540 \| void DumpWriter::writeFinal(double finalTime){
540
541		// write out header and node 0's coordinates
542
475	–	haveError = 0;
543		if( worldRank == 0 ){
544		finalOut << mpiSim->getTotAtoms() << "\n";
545
546		finalOut << finalTime << ";\t"
547	<	<< entry_plug->Hmat[0][0] << "\t"
548	<	<< entry_plug->Hmat[1][0] << "\t"
549	<	<< entry_plug->Hmat[2][0] << ";\t"
547	>	<< entry_plug->Hmat[0][0] << "\t"
548	>	<< entry_plug->Hmat[1][0] << "\t"
549	>	<< entry_plug->Hmat[2][0] << ";\t"
550
551	<	<< entry_plug->Hmat[0][1] << "\t"
552	<	<< entry_plug->Hmat[1][1] << "\t"
553	<	<< entry_plug->Hmat[2][1] << ";\t"
551	>	<< entry_plug->Hmat[0][1] << "\t"
552	>	<< entry_plug->Hmat[1][1] << "\t"
553	>	<< entry_plug->Hmat[2][1] << ";\t"
554
555	<	<< entry_plug->Hmat[0][2] << "\t"
556	<	<< entry_plug->Hmat[1][2] << "\t"
557	<	<< entry_plug->Hmat[2][2] << ";";
555	>	<< entry_plug->Hmat[0][2] << "\t"
556	>	<< entry_plug->Hmat[1][2] << "\t"
557	>	<< entry_plug->Hmat[2][2] << ";";
558
492	–	//write out additional parameters, such as chi and eta
559		finalOut << entry_plug->the_integrator->getAdditionalParameters();
560		finalOut << endl;
561	<
561	>	finalOut.flush();
562		for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
563	<	// Get the Node number which has this molecule:
563	>	// Get the Node number which has this atom;
564
565		which_node = AtomToProcMap[i];
566
567	<	if (which_node == mpiSim->getMyNode()) {
567	>	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
574	+	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
575	+	atomTypeTag, MPI_COMM_WORLD, &istatus);
576	+
577	+	strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
578	+
579	+	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		which_atom = i;
596		local_index=-1;
597	+
598		for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
599		if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
600		}
601	+
602		if (local_index != -1) {
603
604	+	atomTypeString = atoms[local_index]->getType();
605	+
606		atoms[local_index]->getPos(pos);
607		atoms[local_index]->getVel(vel);
608
609	<	sprintf( tempBuffer,
610	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
611	<	atoms[local_index]->getType(),
516	<	pos[0],
517	<	pos[1],
518	<	pos[2],
519	<	vel[0],
520	<	vel[1],
521	<	vel[2]);
522	<	strcpy( writeLine, tempBuffer );
609	>	atomTransData[0] = pos[0];
610	>	atomTransData[1] = pos[1];
611	>	atomTransData[2] = pos[2];
612
613	<	if( atoms[local_index]->isDirectional() ){
613	>	atomTransData[3] = vel[0];
614	>	atomTransData[4] = vel[1];
615	>	atomTransData[5] = vel[2];
616	>
617	>	isDirectional = 0;
618
619	<	dAtom = (DirectionalAtom *)atoms[local_index];
527	<	dAtom->getQ( q );
619	>	if( atoms[local_index]->isDirectional() ){
620
621	<	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	<	else {
621	>	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		sprintf(painCave.errMsg,
638		"Atom %d not found on processor %d\n",
639		i, worldRank );
#	Line 548 \| Line 641 \| void DumpWriter::writeFinal(double finalTime){
641		simError();
642		}
643
644	<	if(haveError) nodeZeroError();
644	>	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
658	<	}
554	<	else {
658	>	strcpy( writeLine, tempBuffer );
659
660	<	myStatus = 1;
557	<	MPI_Send(&myStatus, 1, MPI_INT, which_node,
558	<	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	<	MPI_Recv(&myStatus, 1, MPI_INT, which_node,
564	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
660	>	if (isDirectional) {
661
662	<	if(!myStatus) nodeZeroError();
663	<	}
662	>	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
673	<	finalOut << writeLine;
674	<	}
673	>	} else {
674	>	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
675	>	}
676
677	<	// kill everyone off:
678	<	myStatus = -1;
679	<	for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
575	<	MPI_Send(&myStatus, 1, MPI_INT, j,
576	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
677	>	finalOut << writeLine;
678	>	finalOut.flush();
679	>	}
680		}
681
682	+	finalOut.flush();
683	+	sprintf( checkPointMsg,
684	+	"Sucessfully took a dump.\n");
685	+	MPIcheckPoint();
686	+
687		} else {
688
689	<	done = 0;
690	<	while (!done) {
689	>	// 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
697	<	MPI_Recv(&myStatus, 1, MPI_INT, 0,
698	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
697	>	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
705	<	if(!myStatus) anonymousNodeDie();
705	>	atoms[local_index]->getPos(pos);
706	>	atoms[local_index]->getVel(vel);
707
708	<	if(myStatus < 0) break;
708	>	atomTransData[0] = pos[0];
709	>	atomTransData[1] = pos[1];
710	>	atomTransData[2] = pos[2];
711
712	<	MPI_Recv(&which_atom, 1, MPI_INT, 0,
713	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
712	>	atomTransData[3] = vel[0];
713	>	atomTransData[4] = vel[1];
714	>	atomTransData[5] = vel[2];
715	>
716	>	isDirectional = 0;
717
718	<	myStatus = 1;
595	<	local_index=-1;
596	<	for (j=0; j < mpiSim->getMyNlocal(); j++) {
597	<	if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
598	<	}
599	<	if (local_index != -1) {
718	>	if( atoms[local_index]->isDirectional() ){
719
720	<	atoms[local_index]->getPos(pos);
721	<	atoms[local_index]->getVel(vel);
720	>	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
730	<	//format the line
731	<	sprintf( tempBuffer,
732	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
733	<	atoms[local_index]->getType(),
608	<	pos[0],
609	<	pos[1],
610	<	pos[2],
611	<	vel[0],
612	<	vel[1],
613	<	vel[2]); // check here.
614	<	strcpy( writeLine, tempBuffer );
730	>	atomOrientData[4] = dAtom->getJx();
731	>	atomOrientData[5] = dAtom->getJy();
732	>	atomOrientData[6] = dAtom->getJz();
733	>	}
734
735	<	if( atoms[local_index]->isDirectional() ){
735	>	} else {
736	>	sprintf(painCave.errMsg,
737	>	"Atom %d not found on processor %d\n",
738	>	i, worldRank );
739	>	haveError= 1;
740	>	simError();
741	>	}
742
743	<	dAtom = (DirectionalAtom *)atoms[local_index];
619	<	dAtom->getQ( q );
743	>	// I've survived this far, so send off the data!
744
745	<	sprintf( tempBuffer,
746	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
747	<	q[0],
748	<	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	<	}
636	<	else {
637	<	sprintf(painCave.errMsg,
638	<	"Atom %d not found on processor %d\n",
639	<	which_atom, worldRank );
640	<	myStatus = 0;
641	<	simError();
745	>	atomTypeTag = 4*i;
746	>	atomIsDirectionalTag = 4*i + 1;
747	>	atomTransDataTag = 4*i + 2;
748	>	atomOrientDataTag = 4*i + 3;
749
750	<	strcpy( writeLine, "Hello, I'm an error.\n");
644	<	}
750	>	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
751
752	<	MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
753	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
754	<	MPI_Send( &myStatus, 1, MPI_INT, 0,
755	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
752	>	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
753	>	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	>	}
769		}
770	+
771	+	sprintf( checkPointMsg,
772	+	"Sucessfully wrote final file.\n");
773	+	MPIcheckPoint();
774	+
775		}
776	<	finalOut.flush();
777	<	sprintf( checkPointMsg,
654	<	"Sucessfully took a dump.\n");
655	<	MPIcheckPoint();
776	>
777	>	painCave.isEventLoop = 0;
778
779		if( worldRank == 0 ) finalOut.close();
780		#endif // is_mpi
#	Line 664 \| Line 786 \| void dWrite::nodeZeroError( void ){
786
787		// a couple of functions to let us escape the write loop
788
789	<	void dWrite::nodeZeroError( void ){
668	<	int j, myStatus;
789	>	void dWrite::DieDieDie( void ){
790
670	–	myStatus = 0;
671	–	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
672	–	MPI_Send( &myStatus, 1, MPI_INT, j,
673	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
674	–	}
675	–
676	–
791		MPI_Finalize();
792		exit (0);
679	–
793		}
794
682	–	void dWrite::anonymousNodeDie( void ){
683	–
684	–	MPI_Finalize();
685	–	exit (0);
686	–	}
687	–
795		#endif //is_mpi

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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents): Revision 905 by tim, Wed Jan 7 19:26:12 2004 UTC vs. Revision 910 by gezelter, Thu Jan 8 18:05:37 2004 UTC

Diff Legend

Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 905 by tim, Wed Jan 7 19:26:12 2004 UTC vs.
Revision 910 by gezelter, Thu Jan 8 18:05:37 2004 UTC