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

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 398 by tim, Mon Mar 7 22:39:33 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
48	<
49	<	#include <sys/types.h>
50	<	#include <sys/stat.h>
51	<
52	<	#include <iostream>
53	<	#include <math.h>
54	<
55	<	#include <stdio.h>
56	<	#include <stdlib.h>
57	<	#include <string.h>
58	<
59	<	#include "io/DumpReader.hpp"
60	<	#include "primitives/Molecule.hpp"
61	<	#include "utils/simError.h"
62	<	#include "utils/MemoryUtils.hpp"
63	<	#include "utils/StringTokenizer.hpp"
64	<
65	<	#ifdef IS_MPI
66	<
67	<	#include <mpi.h>
68	<	#define TAKE_THIS_TAG_CHAR 0
69	<	#define TAKE_THIS_TAG_INT 1
70	<
71	<	#endif // is_mpi
72	<
73	<
74	<	namespace oopse {
75	<
76	<	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
77	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
78	<
79	<	#ifdef IS_MPI
80	<
81	<	if (worldRank == 0) {
82	<	#endif
83	<
84	<	inFile_ = fopen(filename_.c_str(), "r");
85	<
86	<	if (inFile_ == NULL) {
87	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
88	<	painCave.isFatal = 1;
89	<	simError();
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	<	#ifdef IS_MPI
246	<
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	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
262	<	MPIcheckPoint();
261	>	}
262	>
263	>	void DumpReader::readSet(int whichFrame) {
264	>	std::string line;
265
266	<	#endif
266	>	#ifndef IS_MPI
267	>	inFile_->clear();
268	>	inFile_->seekg(framePos_[whichFrame]);
269
270	<	return;
98	<	}
270	>	std::istream& inputStream = *inFile_;
271
272	<	DumpReader::~DumpReader() {
272	>	#else
273	>	int masterNode = 0;
274	>	std::stringstream sstream;
275	>	if (worldRank == masterNode) {
276	>	std::string sendBuffer;
277
278	<	#ifdef IS_MPI
278	>	inFile_->clear();
279	>	inFile_->seekg(framePos_[whichFrame]);
280	>
281	>	while (inFile_->getline(buffer, bufferSize)) {
282
283	<	if (worldRank == 0) {
283	>	line = buffer;
284	>	sendBuffer += line;
285	>	sendBuffer += '\n';
286	>	if (line.find("</Snapshot>") != std::string::npos) {
287	>	break;
288	>	}
289	>	}
290	>
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	>	std::istream& inputStream = sstream;
308		#endif
309
310	<	int error;
108	<	error = fclose(inFile_);
310	>	inputStream.getline(buffer, bufferSize);
311
312	<	if (error) {
313	<	sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
314	<	painCave.isFatal = 1;
315	<	simError();
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	>	//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	>	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	<	MemoryUtils::deletePointers(framePos_);
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	<	#ifdef IS_MPI
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	+	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	+	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	+	RealType particlePot;
473	+	particlePot = tokenizer.nextTokenAsDouble();
474	+	integrableObject->setParticlePot(particlePot);
475	+	break;
476	+	}
477	+	case 'c' : {
478	+
479	+	RealType flucQPos;
480	+	flucQPos = tokenizer.nextTokenAsDouble();
481	+	integrableObject->setFlucQPos(flucQPos);
482	+	break;
483	+	}
484	+	case 'w' : {
485	+
486	+	RealType flucQVel;
487	+	flucQVel = tokenizer.nextTokenAsDouble();
488	+	integrableObject->setFlucQVel(flucQVel);
489	+	break;
490	+	}
491	+	case 'g' : {
492	+
493	+	RealType flucQFrc;
494	+	flucQFrc = tokenizer.nextTokenAsDouble();
495	+	integrableObject->setFlucQFrc(flucQFrc);
496	+	break;
497	+	}
498	+	case 'e' : {
499	+
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	<	"DumpReader Error: 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	<	"DumpReader Error: 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	<	"DumpReader Error: 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	<	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
583	<
584	<	if (storageLayout & DataStorage::dslPosition) {
585	<	needPos_ = true;
586	<	} else {
587	<	needPos_ = false;
588	<	}
589	<
590	<	if (storageLayout & DataStorage::dslVelocity) {
591	<	needVel_ = true;
592	<	} else {
593	<	needVel_ = false;
594	<	}
595	<
596	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
597	<	needQuaternion_ = true;
598	<	} else {
599	<	needQuaternion_ = false;
600	<	}
601	<
602	<	if (storageLayout & DataStorage::dslAngularMomentum) {
603	<	needAngMom_ = true;
604	<	} else {
605	<	needAngMom_ = false;
606	<	}
607	<
608	<	readSet(whichFrame);
609	<	}
610	<
611	<	void DumpReader::readSet(int whichFrame) {
612	<	int i;
253	<	int nTotObjs;                  // the number of atoms
254	<	char read_buffer[maxBufferSize];  //the line buffer for reading
255	<	char * eof_test;               // ptr to see when we reach the end of the file
256	<
257	<	Molecule* mol;
258	<	StuntDouble* integrableObject;
259	<	SimInfo::MoleculeIterator mi;
260	<	Molecule::IntegrableObjectIterator ii;
261	<
262	<	#ifndef IS_MPI
263	<
264	<	fsetpos(inFile_, framePos_[whichFrame]);
265	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
266	<
267	<	if (eof_test == NULL) {
268	<	sprintf(painCave.errMsg,
269	<	"DumpReader error: error reading 1st line of \"%s\"\n",
270	<	filename_.c_str());
271	<	painCave.isFatal = 1;
272	<	simError();
273	<	}
274	<
275	<	nTotObjs = atoi(read_buffer);
276	<
277	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
278	<	sprintf(painCave.errMsg,
279	<	"DumpReader error. %s nIntegrable, %d, "
280	<	"does not match the meta-data file's nIntegrable, %d.\n",
281	<	filename_.c_str(),
282	<	nTotObjs,
283	<	info_->getNGlobalIntegrableObjects());
284	<
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
288	<
289	<	//read the box mat from the comment line
290	<
291	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
292	<
293	<	if (eof_test == NULL) {
294	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
295	<	filename_.c_str());
296	<	painCave.isFatal = 1;
297	<	simError();
298	<	}
299	<
300	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
301	<
302	<	//parse dump lines
303	<
304	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
305	<
306	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
307	<	integrableObject = mol->nextIntegrableObject(ii)) {
308	<
309	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
310	<
311	<	if (eof_test == NULL) {
312	<	sprintf(painCave.errMsg,
313	<	"DumpReader Error: error in reading file %s\n"
314	<	"natoms  = %d; index = %d\n"
315	<	"error reading the line from the file.\n",
316	<	filename_.c_str(),
317	<	nTotObjs,
318	<	i);
319	<
320	<	painCave.isFatal = 1;
321	<	simError();
322	<	}
323	<
324	<	parseDumpLine(read_buffer, integrableObject);
325	<
326	<	}
327	<	}
328	<
329	<	// MPI Section of code..........
330	<
331	<	#else //IS_MPI
332	<
333	<	// first thing first, suspend fatalities.
334	<	int masterNode = 0;
335	<	int nCurObj;
336	<	painCave.isEventLoop = 1;
337	<
338	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
339	<	int haveError;
340	<
341	<	MPI_Status istatus;
342	<	int nitems;
343	<
344	<	nTotObjs = info_->getNGlobalIntegrableObjects();
345	<	haveError = 0;
346	<
347	<	if (worldRank == masterNode) {
348	<	fsetpos(inFile_, framePos_[whichFrame]);
349	<
350	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
351	<
352	<	if (eof_test == NULL) {
353	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
354	<	filename_.c_str());
355	<	painCave.isFatal = 1;
356	<	simError();
357	<	}
358	<
359	<	nitems = atoi(read_buffer);
360	<
361	<	// Check to see that the number of integrable objects in the
362	<	// intial configuration file is the same as derived from the
363	<	// meta-data file.
364	<
365	<	if (nTotObjs != nitems) {
366	<	sprintf(painCave.errMsg,
367	<	"DumpReader Error. %s nIntegrable, %d, "
368	<	"does not match the meta-data file's nIntegrable, %d.\n",
369	<	filename_.c_str(),
370	<	nTotObjs,
371	<	info_->getNGlobalIntegrableObjects());
372	<
373	<	painCave.isFatal = 1;
374	<	simError();
375	<	}
376	<
377	<	//read the boxMat from the comment line
378	<
379	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
380	<
381	<	if (eof_test == NULL) {
382	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
383	<	filename_.c_str());
384	<	painCave.isFatal = 1;
385	<	simError();
386	<	}
387	<
388	<	//Every single processor will parse the comment line by itself
389	<	//By using this way, we might lose some efficiency, but if we want to add
390	<	//more parameters into comment line, we only need to modify function
391	<	//parseCommentLine
392	<
393	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
394	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
395	<
396	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
397	<	int which_node = info_->getMolToProc(i);
398	<
399	<	if (which_node == masterNode) {
400	<	//molecules belong to master node
401	<
402	<	mol = info_->getMoleculeByGlobalIndex(i);
403	<
404	<	if (mol == NULL) {
405	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
406	<	painCave.isFatal = 1;
407	<	simError();
408	<	}
409	<
410	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
411	<	integrableObject = mol->nextIntegrableObject(ii)){
412	<
413	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
414	<
415	<	if (eof_test == NULL) {
416	<	sprintf(painCave.errMsg,
417	<	"DumpReader Error: error in reading file %s\n"
418	<	"natoms  = %d; index = %d\n"
419	<	"error reading the line from the file.\n",
420	<	filename_.c_str(),
421	<	nTotObjs,
422	<	i);
423	<
424	<	painCave.isFatal = 1;
425	<	simError();
426	<	}
427	<
428	<	parseDumpLine(read_buffer, integrableObject);
429	<	}
430	<	} else {
431	<	//molecule belongs to slave nodes
432	<
433	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
434	<	MPI_COMM_WORLD, &istatus);
435	<
436	<	for(int j = 0; j < nCurObj; j++) {
437	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
438	<
439	<	if (eof_test == NULL) {
440	<	sprintf(painCave.errMsg,
441	<	"DumpReader Error: error in reading file %s\n"
442	<	"natoms  = %d; index = %d\n"
443	<	"error reading the line from the file.\n",
444	<	filename_.c_str(),
445	<	nTotObjs,
446	<	i);
447	<
448	<	painCave.isFatal = 1;
449	<	simError();
450	<	}
451	<
452	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
453	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
454	<	}
455	<	}
456	<	}
457	<	} else {
458	<	//actions taken at slave nodes
459	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
460	<
461	<	/**@todo*/
462	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
463	<
464	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
465	<	int which_node = info_->getMolToProc(i);
466	<
467	<	if (which_node == worldRank) {
468	<	//molecule with global index i belongs to this processor
469	<
470	<	mol = info_->getMoleculeByGlobalIndex(i);
471	<	if (mol == NULL) {
472	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
473	<	painCave.isFatal = 1;
474	<	simError();
475	<	}
476	<
477	<	nCurObj = mol->getNIntegrableObjects();
478	<
479	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
480	<	MPI_COMM_WORLD);
481	<
482	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
483	<	integrableObject = mol->nextIntegrableObject(ii)){
484	<
485	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
486	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
487	<
488	<	parseDumpLine(read_buffer, integrableObject);
489	<	}
490	<
491	<	}
492	<
493	<	}
494	<
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	<
501	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
502	<
503	<	Vector3d pos;  // position place holders
504	<	Vector3d vel;  // velocity placeholders
505	<	Quat4d q;    // the quaternions
506	<	Vector3d ji;   // angular velocity placeholders;
507	<	StringTokenizer tokenizer(line);
508	<	int nTokens;
509	<
510	<	nTokens = tokenizer.countTokens();
511	<
512	<	if (nTokens < 14) {
513	<	sprintf(painCave.errMsg,
514	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
515	<	painCave.isFatal = 1;
516	<	simError();
517	<	}
518	<
519	<	std::string name = tokenizer.nextToken();
520	<
521	<	if (name != integrableObject->getType()) {
522	<
523	<	sprintf(painCave.errMsg,
524	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
525	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
526	<	painCave.isFatal = 1;
527	<	simError();
528	<	}
529	<
530	<	pos[0] = tokenizer.nextTokenAsDouble();
531	<	pos[1] = tokenizer.nextTokenAsDouble();
532	<	pos[2] = tokenizer.nextTokenAsDouble();
533	<	if (needPos_) {
534	<	integrableObject->setPos(pos);
535	<	}
536	<
537	<	vel[0] = tokenizer.nextTokenAsDouble();
538	<	vel[1] = tokenizer.nextTokenAsDouble();
539	<	vel[2] = tokenizer.nextTokenAsDouble();
540	<	if (needVel_) {
541	<	integrableObject->setVel(vel);
542	<	}
543	<
544	<	if (integrableObject->isDirectional()) {
545	<
546	<	q[0] = tokenizer.nextTokenAsDouble();
547	<	q[1] = tokenizer.nextTokenAsDouble();
548	<	q[2] = tokenizer.nextTokenAsDouble();
549	<	q[3] = tokenizer.nextTokenAsDouble();
550	<
551	<	double qlen = q.length();
552	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
553	<
554	<	sprintf(painCave.errMsg,
555	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
556	<	painCave.isFatal = 1;
557	<	simError();
558	<
559	<	}
560	<
561	<	q.normalize();
562	<	if (needQuaternion_) {
563	<	integrableObject->setQ(q);
564	<	}
565	<
566	<	ji[0] = tokenizer.nextTokenAsDouble();
567	<	ji[1] = tokenizer.nextTokenAsDouble();
568	<	ji[2] = tokenizer.nextTokenAsDouble();
569	<	if (needAngMom_) {
570	<	integrableObject->setJ(ji);
571	<	}
572	<	}
573	<
574	<	}
575	<
576	<
577	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
578	<	double currTime;
579	<	Mat3x3d hmat;
580	<	double chi;
581	<	double integralOfChiDt;
582	<	Mat3x3d eta;
583	<
584	<	StringTokenizer tokenizer(line);
585	<	int nTokens;
586	<
587	<	nTokens = tokenizer.countTokens();
588	<
589	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
590	<	if (nTokens < 10) {
591	<	sprintf(painCave.errMsg,
592	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
593	<	painCave.isFatal = 1;
594	<	simError();
595	<	}
596	<
597	<	//read current time
598	<	currTime = tokenizer.nextTokenAsDouble();
599	<	s->setTime(currTime);
600	<
601	<	//read h-matrix
602	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
603	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
604	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
605	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
606	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
607	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
608	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
609	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
610	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
611	<	s->setHmat(hmat);
612	<
613	<	//read chi and integralOfChidt, they should apprear in pair
614	<	if (tokenizer.countTokens() >= 2) {
615	<	chi = tokenizer.nextTokenAsDouble();
616	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
617	<
618	<	s->setChi(chi);
619	<	s->setIntegralOfChiDt(integralOfChiDt);
620	<	}
621	<
622	<	//read eta (eta is 3x3 matrix)
623	<	if (tokenizer.countTokens() >= 9) {
624	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
625	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
626	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
627	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
628	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
629	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
630	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
631	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
632	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
633	<
634	<	s->setEta(eta);
635	<	}
636	<
637	<
638	<	}
639	<
640	<	}//end namespace oopse
617	>
618	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 398 by tim, Mon Mar 7 22:39:33 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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>	Changed lines