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root/OpenMD/branches/development/src/io/DumpReader.cpp

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1714 by gezelter, Sat May 19 18:12:46 2012 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1	>	/*
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42	+
43	+	#define _LARGEFILE_SOURCE64
44	+	#define _FILE_OFFSET_BITS 64
45
46	<	#define _LARGEFILE_SOURCE64
47	<	#define _FILE_OFFSET_BITS 64
46	>	#include <sys/types.h>
47	>	#include <sys/stat.h>
48	>
49	>	#include <iostream>
50	>	#include <math.h>
51	>
52	>	#include <stdio.h>
53	>	#include <stdlib.h>
54	>	#include <string.h>
55	>
56	>	#include "io/DumpReader.hpp"
57	>	#include "primitives/Molecule.hpp"
58	>	#include "utils/simError.h"
59	>	#include "utils/MemoryUtils.hpp"
60	>	#include "utils/StringTokenizer.hpp"
61	>
62	>	#ifdef IS_MPI
63	>
64	>	#include <mpi.h>
65	>	#define TAKE_THIS_TAG_CHAR 0
66	>	#define TAKE_THIS_TAG_INT 1
67	>
68	>	#endif // is_mpi
69	>
70	>
71	>	namespace OpenMD {
72	>
73	>	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
74	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
75	>
76	>	#ifdef IS_MPI
77	>
78	>	if (worldRank == 0) {
79	>	#endif
80	>
81	>	inFile_ = new std::ifstream(filename_.c_str());
82	>
83	>	if (inFile_->fail()) {
84	>	sprintf(painCave.errMsg,
85	>	"DumpReader: Cannot open file: %s\n",
86	>	filename_.c_str());
87	>	painCave.isFatal = 1;
88	>	simError();
89	>	}
90	>
91	>	#ifdef IS_MPI
92	>
93	>	}
94	>
95	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
96	>	errorCheckPoint();
97	>
98	>	#endif
99	>
100	>	return;
101	>	}
102	>
103	>	DumpReader::~DumpReader() {
104	>
105	>	#ifdef IS_MPI
106	>
107	>	if (worldRank == 0) {
108	>	#endif
109	>
110	>	delete inFile_;
111	>
112	>	#ifdef IS_MPI
113	>
114	>	}
115	>
116	>	strcpy(checkPointMsg, "Dump file closed successfully.");
117	>	errorCheckPoint();
118	>
119	>	#endif
120	>
121	>	return;
122	>	}
123	>
124	>	int DumpReader::getNFrames(void) {
125	>
126	>	if (!isScanned_)
127	>	scanFile();
128	>
129	>	return nframes_;
130	>	}
131	>
132	>	void DumpReader::scanFile(void) {
133	>	int lineNo = 0;
134	>	std::streampos prevPos;
135	>	std::streampos  currPos;
136	>
137	>	#ifdef IS_MPI
138	>
139	>	if (worldRank == 0) {
140	>	#endif // is_mpi
141	>
142	>	currPos = inFile_->tellg();
143	>	prevPos = currPos;
144	>	bool foundOpenSnapshotTag = false;
145	>	bool foundClosedSnapshotTag = false;
146	>	while(inFile_->getline(buffer, bufferSize)) {
147	>	++lineNo;
148	>
149	>	std::string line = buffer;
150	>	currPos = inFile_->tellg();
151	>	if (line.find("<Snapshot>")!= std::string::npos) {
152	>	if (foundOpenSnapshotTag) {
153	>	sprintf(painCave.errMsg,
154	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
155	>	filename_.c_str());
156	>	painCave.isFatal = 1;
157	>	simError();
158	>	}
159	>	foundOpenSnapshotTag = true;
160	>	foundClosedSnapshotTag = false;
161	>	framePos_.push_back(prevPos);
162	>
163	>	} else if (line.find("</Snapshot>") != std::string::npos){
164	>	if (!foundOpenSnapshotTag) {
165	>	sprintf(painCave.errMsg,
166	>	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
167	>	filename_.c_str());
168	>	painCave.isFatal = 1;
169	>	simError();
170	>	}
171	>
172	>	if (foundClosedSnapshotTag) {
173	>	sprintf(painCave.errMsg,
174	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
175	>	filename_.c_str());
176	>	painCave.isFatal = 1;
177	>	simError();
178	>	}
179	>	foundClosedSnapshotTag = true;
180	>	foundOpenSnapshotTag = false;
181	>	}
182	>	prevPos = currPos;
183	>	}
184	>
185	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
186	>	// it and give a warning message
187	>	if (foundOpenSnapshotTag) {
188	>	sprintf(painCave.errMsg,
189	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
190	>	painCave.isFatal = 0;
191	>	simError();
192	>	framePos_.pop_back();
193	>	}
194	>
195	>	nframes_ = framePos_.size();
196	>
197	>	if (nframes_ == 0) {
198	>	sprintf(painCave.errMsg,
199	>	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
200	>	painCave.isFatal = 1;
201	>	simError();
202	>	}
203	>	#ifdef IS_MPI
204	>	}
205	>
206	>	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
207	>
208	>	#endif // is_mpi
209	>
210	>	isScanned_ = true;
211	>	}
212	>
213	>	void DumpReader::readFrame(int whichFrame) {
214	>	if (!isScanned_)
215	>	scanFile();
216	>
217	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
218	>
219	>	if (storageLayout & DataStorage::dslPosition) {
220	>	needPos_ = true;
221	>	} else {
222	>	needPos_ = false;
223	>	}
224	>
225	>	if (storageLayout & DataStorage::dslVelocity) {
226	>	needVel_ = true;
227	>	} else {
228	>	needVel_ = false;
229	>	}
230	>
231	>	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
232	>	needQuaternion_ = true;
233	>	} else {
234	>	needQuaternion_ = false;
235	>	}
236	>
237	>	if (storageLayout & DataStorage::dslAngularMomentum) {
238	>	needAngMom_ = true;
239	>	} else {
240	>	needAngMom_ = false;
241	>	}
242	>
243	>	readSet(whichFrame);
244
245	<	#include <sys/types.h>
246	<	#include <sys/stat.h>
245	>	if (needCOMprops_) {
246	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
247	>	Vector3d com;
248	>	Vector3d comvel;
249	>	Vector3d comw;
250	>	if (needPos_ && needVel_){
251	>	info_->getComAll(com, comvel);
252	>	comw = info_->getAngularMomentum();
253	>	}else{
254	>	com = info_->getCom();
255	>	comvel = 0.0;
256	>	comw   = 0.0;
257	>	}
258	>	s->setCOMprops(com, comvel, comw);
259	>	}
260
261	<	#include <iostream>
262	<	#include <math.h>
261	>	}
262	>
263	>	void DumpReader::readSet(int whichFrame) {
264	>	std::string line;
265
266	<	#include <stdio.h>
267	<	#include <stdlib.h>
268	<	#include <string.h>
266	>	#ifndef IS_MPI
267	>	inFile_->clear();
268	>	inFile_->seekg(framePos_[whichFrame]);
269
270	<	#include "io/DumpReader.hpp"
56	<	#include "primitives/Molecule.hpp"
57	<	#include "utils/simError.h"
58	<	#include "utils/MemoryUtils.hpp"
59	<	#include "utils/StringTokenizer.hpp"
270	>	std::istream& inputStream = *inFile_;
271
272	<	#ifdef IS_MPI
272	>	#else
273	>	int masterNode = 0;
274	>	std::stringstream sstream;
275	>	if (worldRank == masterNode) {
276	>	std::string sendBuffer;
277
278	<	#include <mpi.h>
279	<	#define TAKE_THIS_TAG_CHAR 0
280	<	#define TAKE_THIS_TAG_INT 1
278	>	inFile_->clear();
279	>	inFile_->seekg(framePos_[whichFrame]);
280	>
281	>	while (inFile_->getline(buffer, bufferSize)) {
282
283	<	#endif // is_mpi
283	>	line = buffer;
284	>	sendBuffer += line;
285	>	sendBuffer += '\n';
286	>	if (line.find("</Snapshot>") != std::string::npos) {
287	>	break;
288	>	}
289	>	}
290
291	<
292	<	namespace oopse {
293	<
294	<	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
295	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
296	<
297	<	#ifdef IS_MPI
291	>	int sendBufferSize = sendBuffer.size();
292	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
293	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
294	>
295	>	sstream.str(sendBuffer);
296	>	} else {
297	>	int sendBufferSize;
298	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
299	>	char * recvBuffer = new char[sendBufferSize+1];
300	>	assert(recvBuffer);
301	>	recvBuffer[sendBufferSize] = '\0';
302	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
303	>	sstream.str(recvBuffer);
304	>	delete [] recvBuffer;
305	>	}
306
307	<	if (worldRank == 0) {
307	>	std::istream& inputStream = sstream;
308		#endif
309
310	<	inFile_ = fopen(filename_.c_str(), "r");
310	>	inputStream.getline(buffer, bufferSize);
311
312	<	if (inFile_ == NULL) {
313	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
314	<	painCave.isFatal = 1;
315	<	simError();
316	<	}
312	>	line = buffer;
313	>	if (line.find("<Snapshot>") == std::string::npos) {
314	>	sprintf(painCave.errMsg,
315	>	"DumpReader Error: can not find <Snapshot>\n");
316	>	painCave.isFatal = 1;
317	>	simError();
318	>	}
319	>
320	>	//read frameData
321	>	readFrameProperties(inputStream);
322
323	<	#ifdef IS_MPI
323	>	//read StuntDoubles
324	>	readStuntDoubles(inputStream);
325
326	+	inputStream.getline(buffer, bufferSize);
327	+	line = buffer;
328	+	if (line.find("</Snapshot>") == std::string::npos) {
329	+	sprintf(painCave.errMsg,
330	+	"DumpReader Error: can not find </Snapshot>\n");
331	+	painCave.isFatal = 1;
332	+	simError();
333	+	}
334	+
335	+	}
336	+
337	+	void DumpReader::parseDumpLine(const std::string& line) {
338	+
339	+
340	+	StringTokenizer tokenizer(line);
341	+	int nTokens;
342	+
343	+	nTokens = tokenizer.countTokens();
344	+
345	+	if (nTokens < 2) {
346	+	sprintf(painCave.errMsg,
347	+	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
348	+	painCave.isFatal = 1;
349	+	simError();
350	+	}
351	+
352	+	int index = tokenizer.nextTokenAsInt();
353	+
354	+	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
355	+
356	+	if (integrableObject == NULL) {
357	+	return;
358		}
359	+	std::string type = tokenizer.nextToken();
360	+	int size = type.size();
361
362	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
363	<	MPIcheckPoint();
362	>	size_t found;
363	>
364	>	if (needPos_) {
365	>	found = type.find("p");
366	>	if (found == std::string::npos) {
367	>	sprintf(painCave.errMsg,
368	>	"DumpReader Error: StuntDouble %d has no Position\n"
369	>	"\tField (\"p\") specified.\n%s\n", index,
370	>	line.c_str());
371	>	painCave.isFatal = 1;
372	>	simError();
373	>	}
374	>	}
375	>
376	>	if (integrableObject->isDirectional()) {
377	>	if (needQuaternion_) {
378	>	found = type.find("q");
379	>	if (found == std::string::npos) {
380	>	sprintf(painCave.errMsg,
381	>	"DumpReader Error: Directional StuntDouble %d has no\n"
382	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
383	>	line.c_str());
384	>	painCave.isFatal = 1;
385	>	simError();
386	>	}
387	>	}
388	>	}
389
390	<	#endif
390	>	for(int i = 0; i < size; ++i) {
391	>	switch(type[i]) {
392	>
393	>	case 'p': {
394	>	Vector3d pos;
395	>	pos[0] = tokenizer.nextTokenAsDouble();
396	>	pos[1] = tokenizer.nextTokenAsDouble();
397	>	pos[2] = tokenizer.nextTokenAsDouble();
398	>	if (needPos_) {
399	>	integrableObject->setPos(pos);
400	>	}
401	>	break;
402	>	}
403	>	case 'v' : {
404	>	Vector3d vel;
405	>	vel[0] = tokenizer.nextTokenAsDouble();
406	>	vel[1] = tokenizer.nextTokenAsDouble();
407	>	vel[2] = tokenizer.nextTokenAsDouble();
408	>	if (needVel_) {
409	>	integrableObject->setVel(vel);
410	>	}
411	>	break;
412	>	}
413
414	<	return;
415	<	}
414	>	case 'q' : {
415	>	Quat4d q;
416	>	if (integrableObject->isDirectional()) {
417	>
418	>	q[0] = tokenizer.nextTokenAsDouble();
419	>	q[1] = tokenizer.nextTokenAsDouble();
420	>	q[2] = tokenizer.nextTokenAsDouble();
421	>	q[3] = tokenizer.nextTokenAsDouble();
422	>
423	>	RealType qlen = q.length();
424	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
425	>
426	>	sprintf(painCave.errMsg,
427	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
428	>	painCave.isFatal = 1;
429	>	simError();
430	>
431	>	}
432	>
433	>	q.normalize();
434	>	if (needQuaternion_) {
435	>	integrableObject->setQ(q);
436	>	}
437	>	}
438	>	break;
439	>	}
440	>	case 'j' : {
441	>	Vector3d ji;
442	>	if (integrableObject->isDirectional()) {
443	>	ji[0] = tokenizer.nextTokenAsDouble();
444	>	ji[1] = tokenizer.nextTokenAsDouble();
445	>	ji[2] = tokenizer.nextTokenAsDouble();
446	>	if (needAngMom_) {
447	>	integrableObject->setJ(ji);
448	>	}
449	>	}
450	>	break;
451	>	}
452	>	case 'f': {
453
454	<	DumpReader::~DumpReader() {
454	>	Vector3d force;
455	>	force[0] = tokenizer.nextTokenAsDouble();
456	>	force[1] = tokenizer.nextTokenAsDouble();
457	>	force[2] = tokenizer.nextTokenAsDouble();
458	>	integrableObject->setFrc(force);
459	>	break;
460	>	}
461	>	case 't' : {
462
463	<	#ifdef IS_MPI
463	>	Vector3d torque;
464	>	torque[0] = tokenizer.nextTokenAsDouble();
465	>	torque[1] = tokenizer.nextTokenAsDouble();
466	>	torque[2] = tokenizer.nextTokenAsDouble();
467	>	integrableObject->setTrq(torque);
468	>	break;
469	>	}
470	>	case 'u' : {
471
472	<	if (worldRank == 0) {
473	<	#endif
472	>	RealType particlePot;
473	>	particlePot = tokenizer.nextTokenAsDouble();
474	>	integrableObject->setParticlePot(particlePot);
475	>	break;
476	>	}
477	>	case 'c' : {
478
479	<	int error;
480	<	error = fclose(inFile_);
479	>	RealType flucQPos;
480	>	flucQPos = tokenizer.nextTokenAsDouble();
481	>	integrableObject->setFlucQPos(flucQPos);
482	>	break;
483	>	}
484	>	case 'w' : {
485
486	<	if (error) {
487	<	sprintf(painCave.errMsg, "Error closing %s\n", filename_.c_str());
488	<	painCave.isFatal = 1;
489	<	simError();
486	>	RealType flucQVel;
487	>	flucQVel = tokenizer.nextTokenAsDouble();
488	>	integrableObject->setFlucQVel(flucQVel);
489	>	break;
490		}
491	+	case 'g' : {
492
493	<	MemoryUtils::deleteVectorOfPointer(framePos_);
493	>	RealType flucQFrc;
494	>	flucQFrc = tokenizer.nextTokenAsDouble();
495	>	integrableObject->setFlucQFrc(flucQFrc);
496	>	break;
497	>	}
498	>	case 'e' : {
499
500	<	#ifdef IS_MPI
500	>	Vector3d eField;
501	>	eField[0] = tokenizer.nextTokenAsDouble();
502	>	eField[1] = tokenizer.nextTokenAsDouble();
503	>	eField[2] = tokenizer.nextTokenAsDouble();
504	>	integrableObject->setElectricField(eField);
505	>	break;
506	>	}
507	>	default: {
508	>	sprintf(painCave.errMsg,
509	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
510	>	painCave.isFatal = 1;
511	>	simError();
512	>	break;
513	>	}
514
515	+	}
516		}
517	+
518	+	}
519	+
520
521	<	strcpy(checkPointMsg, "Dump file closed successfully.");
123	<	MPIcheckPoint();
521	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
522
523	<	#endif
523	>	inputStream.getline(buffer, bufferSize);
524	>	std::string line(buffer);
525	>
526	>	if (line.find("<StuntDoubles>") == std::string::npos) {
527	>	sprintf(painCave.errMsg,
528	>	"DumpReader Error: Missing <StuntDoubles>\n");
529	>	painCave.isFatal = 1;
530	>	simError();
531	>	}
532
533	<	return;
534	<	}
533	>	while(inputStream.getline(buffer, bufferSize)) {
534	>	line = buffer;
535	>
536	>	if(line.find("</StuntDoubles>") != std::string::npos) {
537	>	break;
538	>	}
539
540	<	int DumpReader::getNFrames(void) {
540	>	parseDumpLine(line);
541	>	}
542	>
543	>	}
544
545	<	if (!isScanned_)
133	<	scanFile();
545	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
546
547	<	return nframes_;
548	<	}
547	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
548	>	inputStream.getline(buffer, bufferSize);
549	>	std::string line(buffer);
550
551	<	void DumpReader::scanFile(void) {
552	<	int i, j;
553	<	int lineNum = 0;
554	<	char readBuffer[maxBufferSize];
555	<	fpos_t * currPos;
143	<
144	<	#ifdef IS_MPI
145	<
146	<	if (worldRank == 0) {
147	<	#endif // is_mpi
148	<
149	<	rewind(inFile_);
150	<
151	<	currPos = new fpos_t;
152	<	fgetpos(inFile_, currPos);
153	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
154	<	lineNum++;
155	<
156	<	if (feof(inFile_)) {
157	<	sprintf(painCave.errMsg,
158	<	"File \"%s\" ended unexpectedly at line %d\n",
159	<	filename_.c_str(),
160	<	lineNum);
161	<	painCave.isFatal = 1;
162	<	simError();
163	<	}
164	<
165	<	while (!feof(inFile_)) {
166	<	framePos_.push_back(currPos);
167	<
168	<	i = atoi(readBuffer);
169	<
170	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
171	<	lineNum++;
172	<
173	<	if (feof(inFile_)) {
174	<	sprintf(painCave.errMsg,
175	<	"File \"%s\" ended unexpectedly at line %d\n",
176	<	filename_.c_str(),
177	<	lineNum);
178	<	painCave.isFatal = 1;
179	<	simError();
180	<	}
181	<
182	<	for(j = 0; j < i; j++) {
183	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
184	<	lineNum++;
185	<
186	<	if (feof(inFile_)) {
187	<	sprintf(painCave.errMsg,
188	<	"File \"%s\" ended unexpectedly at line %d,"
189	<	" with atom %d\n", filename_.c_str(),
190	<	lineNum,
191	<	j);
192	<
193	<	painCave.isFatal = 1;
194	<	simError();
195	<	}
196	<	}
197	<
198	<	currPos = new fpos_t;
199	<	fgetpos(inFile_, currPos);
200	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
201	<	lineNum++;
202	<	}
203	<
204	<	delete currPos;
205	<	rewind(inFile_);
206	<
207	<	nframes_ = framePos_.size();
208	<	#ifdef IS_MPI
551	>	if (line.find("<FrameData>") == std::string::npos) {
552	>	sprintf(painCave.errMsg,
553	>	"DumpReader Error: Missing <FrameData>\n");
554	>	painCave.isFatal = 1;
555	>	simError();
556		}
557
558	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
558	>	while(inputStream.getline(buffer, bufferSize)) {
559	>	line = buffer;
560	>
561	>	if(line.find("</FrameData>") != std::string::npos) {
562	>	break;
563	>	}
564	>
565	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
566	>	if (!tokenizer.hasMoreTokens()) {
567	>	sprintf(painCave.errMsg,
568	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
569	>	painCave.isFatal = 1;
570	>	simError();
571	>	}
572
573	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
574	<	MPIcheckPoint();
575	<
576	<	#endif // is_mpi
577	<
578	<	isScanned_ = true;
579	<	}
580	<
581	<	void DumpReader::readFrame(int whichFrame) {
582	<	readSet(whichFrame);
583	<	}
584	<
585	<	void DumpReader::readSet(int whichFrame) {
586	<	int i;
587	<	int nTotObjs;                  // the number of atoms
588	<	char read_buffer[maxBufferSize];  //the line buffer for reading
589	<	char * eof_test;               // ptr to see when we reach the end of the file
590	<
591	<	Molecule* mol;
592	<	StuntDouble* integrableObject;
593	<	SimInfo::MoleculeIterator mi;
594	<	Molecule::IntegrableObjectIterator ii;
595	<
596	<	#ifndef IS_MPI
597	<
598	<	fsetpos(inFile_, framePos_[whichFrame]);
599	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
600	<
601	<	if (eof_test == NULL) {
602	<	sprintf(painCave.errMsg,
603	<	"DumpReader error: error reading 1st line of \"%s\"\n",
604	<	filename_.c_str());
605	<	painCave.isFatal = 1;
606	<	simError();
607	<	}
608	<
609	<	nTotObjs = atoi(read_buffer);
610	<
611	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
612	<	sprintf(painCave.errMsg,
253	<	"DumpReader error. %s nIntegrable, %d, "
254	<	"does not match the meta-data file's nIntegrable, %d.\n",
255	<	filename_.c_str(),
256	<	nTotObjs,
257	<	info_->getNGlobalIntegrableObjects());
258	<
259	<	painCave.isFatal = 1;
260	<	simError();
261	<	}
262	<
263	<	//read the box mat from the comment line
264	<
265	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
266	<
267	<	if (eof_test == NULL) {
268	<	sprintf(painCave.errMsg, "error in reading commment in %s\n",
269	<	filename_.c_str());
270	<	painCave.isFatal = 1;
271	<	simError();
272	<	}
273	<
274	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
275	<
276	<	//parse dump lines
277	<
278	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
279	<
280	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
281	<	integrableObject = mol->nextIntegrableObject(ii)) {
282	<
283	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
284	<
285	<	if (eof_test == NULL) {
286	<	sprintf(painCave.errMsg,
287	<	"error in reading file %s\n"
288	<	"natoms  = %d; index = %d\n"
289	<	"error reading the line from the file.\n",
290	<	filename_.c_str(),
291	<	nTotObjs,
292	<	i);
293	<
294	<	painCave.isFatal = 1;
295	<	simError();
296	<	}
297	<
298	<	parseDumpLine(read_buffer, integrableObject);
299	<
300	<	}
301	<	}
302	<
303	<	// MPI Section of code..........
304	<
305	<	#else //IS_MPI
306	<
307	<	// first thing first, suspend fatalities.
308	<	int masterNode = 0;
309	<	int nCurObj;
310	<	painCave.isEventLoop = 1;
311	<
312	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
313	<	int haveError;
314	<
315	<	MPI_Status istatus;
316	<	int nitems;
317	<
318	<	nTotObjs = info_->getNGlobalIntegrableObjects();
319	<	haveError = 0;
320	<
321	<	if (worldRank == masterNode) {
322	<	fsetpos(inFile_, framePos_[whichFrame]);
323	<
324	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
325	<
326	<	if (eof_test == NULL) {
327	<	sprintf(painCave.errMsg, "Error reading 1st line of %s \n ",
328	<	filename_.c_str());
329	<	painCave.isFatal = 1;
330	<	simError();
331	<	}
332	<
333	<	nitems = atoi(read_buffer);
334	<
335	<	// Check to see that the number of integrable objects in the
336	<	// intial configuration file is the same as derived from the
337	<	// meta-data file.
338	<
339	<	if (nTotObjs != nitems) {
340	<	sprintf(painCave.errMsg,
341	<	"DumpReader Error. %s nIntegrable, %d, "
342	<	"does not match the meta-data file's nIntegrable, %d.\n",
343	<	filename_.c_str(),
344	<	nTotObjs,
345	<	info_->getNGlobalIntegrableObjects());
346	<
347	<	painCave.isFatal = 1;
348	<	simError();
349	<	}
350	<
351	<	//read the boxMat from the comment line
352	<
353	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
354	<
355	<	if (eof_test == NULL) {
356	<	sprintf(painCave.errMsg, "error in reading commment in %s\n",
357	<	filename_.c_str());
358	<	painCave.isFatal = 1;
359	<	simError();
360	<	}
361	<
362	<	//Every single processor will parse the comment line by itself
363	<	//By using this way, we might lose some efficiency, but if we want to add
364	<	//more parameters into comment line, we only need to modify function
365	<	//parseCommentLine
366	<
367	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
368	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
369	<
370	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
371	<	int which_node = info_->getMolToProc(i);
372	<
373	<	if (which_node == masterNode) {
374	<	//molecules belong to master node
375	<
376	<	mol = info_->getMoleculeByGlobalIndex(i);
377	<
378	<	if (mol == NULL) {
379	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
380	<	painCave.isFatal = 1;
381	<	simError();
382	<	}
383	<
384	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
385	<	integrableObject = mol->nextIntegrableObject(ii)){
386	<
387	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
388	<
389	<	if (eof_test == NULL) {
390	<	sprintf(painCave.errMsg,
391	<	"error in reading file %s\n"
392	<	"natoms  = %d; index = %d\n"
393	<	"error reading the line from the file.\n",
394	<	filename_.c_str(),
395	<	nTotObjs,
396	<	i);
397	<
398	<	painCave.isFatal = 1;
399	<	simError();
400	<	}
401	<
402	<	parseDumpLine(read_buffer, integrableObject);
403	<	}
404	<	} else {
405	<	//molecule belongs to slave nodes
406	<
407	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
408	<	MPI_COMM_WORLD, &istatus);
409	<
410	<	for(int j = 0; j < nCurObj; j++) {
411	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
412	<
413	<	if (eof_test == NULL) {
414	<	sprintf(painCave.errMsg,
415	<	"error in reading file %s\n"
416	<	"natoms  = %d; index = %d\n"
417	<	"error reading the line from the file.\n",
418	<	filename_.c_str(),
419	<	nTotObjs,
420	<	i);
421	<
422	<	painCave.isFatal = 1;
423	<	simError();
424	<	}
425	<
426	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
427	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
428	<	}
429	<	}
430	<	}
431	<	} else {
432	<	//actions taken at slave nodes
433	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
434	<
435	<	/**@todo*/
436	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
437	<
438	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
439	<	int which_node = info_->getMolToProc(i);
440	<
441	<	if (which_node == worldRank) {
442	<	//molecule with global index i belongs to this processor
443	<
444	<	mol = info_->getMoleculeByGlobalIndex(i);
445	<	if (mol == NULL) {
446	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
447	<	painCave.isFatal = 1;
448	<	simError();
449	<	}
450	<
451	<	nCurObj = mol->getNIntegrableObjects();
452	<
453	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
454	<	MPI_COMM_WORLD);
455	<
456	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
457	<	integrableObject = mol->nextIntegrableObject(ii)){
458	<
459	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
460	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
461	<
462	<	parseDumpLine(read_buffer, integrableObject);
463	<	}
464	<
465	<	}
466	<
467	<	}
468	<
573	>	std::string propertyName = tokenizer.nextToken();
574	>	if (propertyName == "Time") {
575	>	RealType currTime = tokenizer.nextTokenAsDouble();
576	>	s->setTime(currTime);
577	>	} else if (propertyName == "Hmat"){
578	>	Mat3x3d hmat;
579	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
580	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
581	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
582	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
583	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
584	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
585	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
586	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
587	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
588	>	s->setHmat(hmat);
589	>	} else if (propertyName == "Thermostat") {
590	>	RealType chi = tokenizer.nextTokenAsDouble();
591	>	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
592	>	s->setChi(chi);
593	>	s->setIntegralOfChiDt(integralOfChiDt);
594	>	} else if (propertyName == "Barostat") {
595	>	Mat3x3d eta;
596	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
597	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
598	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
599	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
600	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
601	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
602	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
603	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
604	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
605	>	s->setEta(eta);
606	>	} else {
607	>	sprintf(painCave.errMsg,
608	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
609	>	painCave.isFatal = 0;
610	>	simError();
611	>	}
612	>
613		}
614
615	<	#endif
615	>	}
616
617	<	}
618	<
475	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
476	<
477	<	Vector3d pos;  // position place holders
478	<	Vector3d vel;  // velocity placeholders
479	<	Quat4d q;    // the quaternions
480	<	Vector3d ji;   // angular velocity placeholders;
481	<	StringTokenizer tokenizer(line);
482	<	int nTokens;
483	<
484	<	nTokens = tokenizer.countTokens();
485	<
486	<	if (nTokens < 14) {
487	<	sprintf(painCave.errMsg,
488	<	"Not enough Tokens.\n");
489	<	painCave.isFatal = 1;
490	<	simError();
491	<	}
492	<
493	<	std::string name = tokenizer.nextToken();
494	<
495	<	if (name != integrableObject->getType()) {
496	<
497	<	}
498	<
499	<	pos[0] = tokenizer.nextTokenAsDouble();
500	<	pos[1] = tokenizer.nextTokenAsDouble();
501	<	pos[2] = tokenizer.nextTokenAsDouble();
502	<	integrableObject->setPos(pos);
503	<
504	<	vel[0] = tokenizer.nextTokenAsDouble();
505	<	vel[1] = tokenizer.nextTokenAsDouble();
506	<	vel[2] = tokenizer.nextTokenAsDouble();
507	<	integrableObject->setVel(vel);
508	<
509	<	if (integrableObject->isDirectional()) {
510	<
511	<	q[0] = tokenizer.nextTokenAsDouble();
512	<	q[1] = tokenizer.nextTokenAsDouble();
513	<	q[2] = tokenizer.nextTokenAsDouble();
514	<	q[3] = tokenizer.nextTokenAsDouble();
515	<
516	<	double qlen = q.length();
517	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
518	<
519	<	sprintf(painCave.errMsg,
520	<	"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
521	<	painCave.isFatal = 1;
522	<	simError();
523	<
524	<	}
525	<
526	<	q.normalize();
527	<
528	<	integrableObject->setQ(q);
529	<
530	<	ji[0] = tokenizer.nextTokenAsDouble();
531	<	ji[1] = tokenizer.nextTokenAsDouble();
532	<	ji[2] = tokenizer.nextTokenAsDouble();
533	<	integrableObject->setJ(ji);
534	<	}
535	<
536	<	}
537	<
538	<
539	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
540	<	double currTime;
541	<	Mat3x3d hmat;
542	<	double chi;
543	<	double integralOfChiDt;
544	<	Mat3x3d eta;
545	<
546	<	StringTokenizer tokenizer(line);
547	<	int nTokens;
548	<
549	<	nTokens = tokenizer.countTokens();
550	<
551	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
552	<	if (nTokens < 10) {
553	<	sprintf(painCave.errMsg,
554	<	"Not enough tokens in comment line: %s", line);
555	<	painCave.isFatal = 1;
556	<	simError();
557	<	}
558	<
559	<	//read current time
560	<	currTime = tokenizer.nextTokenAsDouble();
561	<	s->setTime(currTime);
562	<
563	<	//read h-matrix
564	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
565	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
566	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
567	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
568	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
569	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
570	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
571	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
572	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
573	<	s->setHmat(hmat);
574	<
575	<	//read chi and integrablOfChidt, they should apprear in pair
576	<	if (tokenizer.countTokens() >= 2) {
577	<	chi = tokenizer.nextTokenAsDouble();
578	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
579	<
580	<	s->setChi(chi);
581	<	s->setIntegralOfChiDt(integralOfChiDt);
582	<	}
583	<
584	<	//read eta (eta is 3x3 matrix)
585	<	if (tokenizer.countTokens() >= 9) {
586	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
587	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
588	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
589	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
590	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
591	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
592	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
593	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
594	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
595	<
596	<	s->setEta(eta);
597	<	}
598	<
599	<
600	<	}
601	<
602	<	}//end namespace oopse
617	>
618	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1714 by gezelter, Sat May 19 18:12:46 2012 UTC

#	Line 0 | Line 1
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