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

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 381 by tim, Tue Mar 1 14:45:45 2005 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41	+
42	+	#define _LARGEFILE_SOURCE64
43	+	#define _FILE_OFFSET_BITS 64
44
45	<	#define _LARGEFILE_SOURCE64
46	<	#define _FILE_OFFSET_BITS 64
45	>	#include <sys/types.h>
46	>	#include <sys/stat.h>
47	>
48	>	#include <iostream>
49	>	#include <math.h>
50	>
51	>	#include <stdio.h>
52	>	#include <stdlib.h>
53	>	#include <string.h>
54	>
55	>	#include "io/DumpReader.hpp"
56	>	#include "primitives/Molecule.hpp"
57	>	#include "utils/simError.h"
58	>	#include "utils/MemoryUtils.hpp"
59	>	#include "utils/StringTokenizer.hpp"
60	>
61	>	#ifdef IS_MPI
62	>
63	>	#include <mpi.h>
64	>	#define TAKE_THIS_TAG_CHAR 0
65	>	#define TAKE_THIS_TAG_INT 1
66	>
67	>	#endif // is_mpi
68	>
69	>
70	>	namespace OpenMD {
71	>
72	>	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
74	>
75	>	#ifdef IS_MPI
76	>
77	>	if (worldRank == 0) {
78	>	#endif
79	>
80	>	inFile_ = new std::ifstream(filename_.c_str());
81	>
82	>	if (inFile_->fail()) {
83	>	sprintf(painCave.errMsg,
84	>	"DumpReader: Cannot open file: %s\n",
85	>	filename_.c_str());
86	>	painCave.isFatal = 1;
87	>	simError();
88	>	}
89	>
90	>	#ifdef IS_MPI
91	>
92	>	}
93	>
94	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95	>	errorCheckPoint();
96	>
97	>	#endif
98	>
99	>	return;
100	>	}
101	>
102	>	DumpReader::~DumpReader() {
103	>
104	>	#ifdef IS_MPI
105	>
106	>	if (worldRank == 0) {
107	>	#endif
108	>
109	>	delete inFile_;
110	>
111	>	#ifdef IS_MPI
112	>
113	>	}
114	>
115	>	strcpy(checkPointMsg, "Dump file closed successfully.");
116	>	errorCheckPoint();
117	>
118	>	#endif
119	>
120	>	return;
121	>	}
122	>
123	>	int DumpReader::getNFrames(void) {
124	>
125	>	if (!isScanned_)
126	>	scanFile();
127	>
128	>	return nframes_;
129	>	}
130	>
131	>	void DumpReader::scanFile(void) {
132	>	int lineNo = 0;
133	>	std::streampos prevPos;
134	>	std::streampos  currPos;
135	>
136	>	#ifdef IS_MPI
137	>
138	>	if (worldRank == 0) {
139	>	#endif // is_mpi
140	>
141	>	currPos = inFile_->tellg();
142	>	prevPos = currPos;
143	>	bool foundOpenSnapshotTag = false;
144	>	bool foundClosedSnapshotTag = false;
145	>	while(inFile_->getline(buffer, bufferSize)) {
146	>	++lineNo;
147	>
148	>	std::string line = buffer;
149	>	currPos = inFile_->tellg();
150	>	if (line.find("<Snapshot>")!= std::string::npos) {
151	>	if (foundOpenSnapshotTag) {
152	>	sprintf(painCave.errMsg,
153	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154	>	filename_.c_str());
155	>	painCave.isFatal = 1;
156	>	simError();
157	>	}
158	>	foundOpenSnapshotTag = true;
159	>	foundClosedSnapshotTag = false;
160	>	framePos_.push_back(prevPos);
161	>
162	>	} else if (line.find("</Snapshot>") != std::string::npos){
163	>	if (!foundOpenSnapshotTag) {
164	>	sprintf(painCave.errMsg,
165	>	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
166	>	filename_.c_str());
167	>	painCave.isFatal = 1;
168	>	simError();
169	>	}
170	>
171	>	if (foundClosedSnapshotTag) {
172	>	sprintf(painCave.errMsg,
173	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
174	>	filename_.c_str());
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	foundClosedSnapshotTag = true;
179	>	foundOpenSnapshotTag = false;
180	>	}
181	>	prevPos = currPos;
182	>	}
183	>
184	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
185	>	// it and give a warning message
186	>	if (foundOpenSnapshotTag) {
187	>	sprintf(painCave.errMsg,
188	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
189	>	painCave.isFatal = 0;
190	>	simError();
191	>	framePos_.pop_back();
192	>	}
193	>
194	>	nframes_ = framePos_.size();
195	>
196	>	if (nframes_ == 0) {
197	>	sprintf(painCave.errMsg,
198	>	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
199	>	painCave.isFatal = 1;
200	>	simError();
201	>	}
202	>	#ifdef IS_MPI
203	>	}
204	>
205	>	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206	>
207	>	#endif // is_mpi
208	>
209	>	isScanned_ = true;
210	>	}
211	>
212	>	void DumpReader::readFrame(int whichFrame) {
213	>	if (!isScanned_)
214	>	scanFile();
215	>
216	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
217	>
218	>	if (storageLayout & DataStorage::dslPosition) {
219	>	needPos_ = true;
220	>	} else {
221	>	needPos_ = false;
222	>	}
223	>
224	>	if (storageLayout & DataStorage::dslVelocity) {
225	>	needVel_ = true;
226	>	} else {
227	>	needVel_ = false;
228	>	}
229	>
230	>	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
231	>	needQuaternion_ = true;
232	>	} else {
233	>	needQuaternion_ = false;
234	>	}
235	>
236	>	if (storageLayout & DataStorage::dslAngularMomentum) {
237	>	needAngMom_ = true;
238	>	} else {
239	>	needAngMom_ = false;
240	>	}
241	>
242	>	readSet(whichFrame);
243
244	<	#include <sys/types.h>
245	<	#include <sys/stat.h>
244	>	if (needCOMprops_) {
245	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	>	Vector3d com;
247	>	Vector3d comvel;
248	>	Vector3d comw;
249	>	if (needPos_ && needVel_){
250	>	info_->getComAll(com, comvel);
251	>	comw = info_->getAngularMomentum();
252	>	}else{
253	>	com = info_->getCom();
254	>	comvel = 0.0;
255	>	comw   = 0.0;
256	>	}
257	>	s->setCOMprops(com, comvel, comw);
258	>	}
259
260	<	#include <iostream>
261	<	#include <math.h>
260	>	}
261	>
262	>	void DumpReader::readSet(int whichFrame) {
263	>	std::string line;
264
265	<	#include <stdio.h>
266	<	#include <stdlib.h>
267	<	#include <string.h>
265	>	#ifndef IS_MPI
266	>	inFile_->clear();
267	>	inFile_->seekg(framePos_[whichFrame]);
268
269	<	#include "io/DumpReader.hpp"
56	<	#include "primitives/Molecule.hpp"
57	<	#include "utils/simError.h"
58	<	#include "utils/MemoryUtils.hpp"
59	<	#include "utils/StringTokenizer.hpp"
269	>	std::istream& inputStream = *inFile_;
270
271	<	#ifdef IS_MPI
271	>	#else
272	>	int masterNode = 0;
273	>	std::stringstream sstream;
274	>	if (worldRank == masterNode) {
275	>	std::string sendBuffer;
276
277	<	#include <mpi.h>
278	<	#define TAKE_THIS_TAG_CHAR 0
279	<	#define TAKE_THIS_TAG_INT 1
277	>	inFile_->clear();
278	>	inFile_->seekg(framePos_[whichFrame]);
279	>
280	>	while (inFile_->getline(buffer, bufferSize)) {
281
282	<	#endif // is_mpi
283	<
284	<
285	<	namespace oopse {
286	<
287	<	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
288	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
74	<
75	<	#ifdef IS_MPI
282	>	line = buffer;
283	>	sendBuffer += line;
284	>	sendBuffer += '\n';
285	>	if (line.find("</Snapshot>") != std::string::npos) {
286	>	break;
287	>	}
288	>	}
289
290	<	if (worldRank == 0) {
290	>	int sendBufferSize = sendBuffer.size();
291	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
292	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
293	>
294	>	sstream.str(sendBuffer);
295	>	} else {
296	>	int sendBufferSize;
297	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
298	>	char * recvBuffer = new char[sendBufferSize+1];
299	>	assert(recvBuffer);
300	>	recvBuffer[sendBufferSize] = '\0';
301	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
302	>	sstream.str(recvBuffer);
303	>	delete [] recvBuffer;
304	>	}
305	>
306	>	std::istream& inputStream = sstream;
307		#endif
308
309	<	inFile_ = fopen(filename_.c_str(), "r");
309	>	inputStream.getline(buffer, bufferSize);
310
311	<	if (inFile_ == NULL) {
312	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
313	<	painCave.isFatal = 1;
314	<	simError();
315	<	}
311	>	line = buffer;
312	>	if (line.find("<Snapshot>") == std::string::npos) {
313	>	sprintf(painCave.errMsg,
314	>	"DumpReader Error: can not find <Snapshot>\n");
315	>	painCave.isFatal = 1;
316	>	simError();
317	>	}
318	>
319	>	//read frameData
320	>	readFrameProperties(inputStream);
321
322	<	#ifdef IS_MPI
322	>	//read StuntDoubles
323	>	readStuntDoubles(inputStream);
324
325	<	}
325	>	inputStream.getline(buffer, bufferSize);
326	>	line = buffer;
327	>	if (line.find("</Snapshot>") == std::string::npos) {
328	>	sprintf(painCave.errMsg,
329	>	"DumpReader Error: can not find </Snapshot>\n");
330	>	painCave.isFatal = 1;
331	>	simError();
332	>	}
333	>
334	>	}
335	>
336	>	void DumpReader::parseDumpLine(const std::string& line) {
337
338	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
339	<	MPIcheckPoint();
338	>
339	>	StringTokenizer tokenizer(line);
340	>	int nTokens;
341	>
342	>	nTokens = tokenizer.countTokens();
343	>
344	>	if (nTokens < 2) {
345	>	sprintf(painCave.errMsg,
346	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
347	>	painCave.isFatal = 1;
348	>	simError();
349	>	}
350
351	<	#endif
351	>	int index = tokenizer.nextTokenAsInt();
352	>
353	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
354
355	<	return;
356	<	}
355	>	if (integrableObject == NULL) {
356	>	return;
357	>	}
358	>	std::string type = tokenizer.nextToken();
359	>	int size = type.size();
360
361	<	DumpReader::~DumpReader() {
361	>	for(int i = 0; i < size; ++i) {
362	>	switch(type[i]) {
363	>
364	>	case 'p': {
365	>	Vector3d pos;
366	>	pos[0] = tokenizer.nextTokenAsDouble();
367	>	pos[1] = tokenizer.nextTokenAsDouble();
368	>	pos[2] = tokenizer.nextTokenAsDouble();
369	>	if (needPos_) {
370	>	integrableObject->setPos(pos);
371	>	}
372	>	break;
373	>	}
374	>	case 'v' : {
375	>	Vector3d vel;
376	>	vel[0] = tokenizer.nextTokenAsDouble();
377	>	vel[1] = tokenizer.nextTokenAsDouble();
378	>	vel[2] = tokenizer.nextTokenAsDouble();
379	>	if (needVel_) {
380	>	integrableObject->setVel(vel);
381	>	}
382	>	break;
383	>	}
384
385	<	#ifdef IS_MPI
385	>	case 'q' : {
386	>	Quat4d q;
387	>	if (integrableObject->isDirectional()) {
388	>
389	>	q[0] = tokenizer.nextTokenAsDouble();
390	>	q[1] = tokenizer.nextTokenAsDouble();
391	>	q[2] = tokenizer.nextTokenAsDouble();
392	>	q[3] = tokenizer.nextTokenAsDouble();
393	>
394	>	RealType qlen = q.length();
395	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
396	>
397	>	sprintf(painCave.errMsg,
398	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
399	>	painCave.isFatal = 1;
400	>	simError();
401	>
402	>	}
403	>
404	>	q.normalize();
405	>	if (needQuaternion_) {
406	>	integrableObject->setQ(q);
407	>	}
408	>	}
409	>	break;
410	>	}
411	>	case 'j' : {
412	>	Vector3d ji;
413	>	if (integrableObject->isDirectional()) {
414	>	ji[0] = tokenizer.nextTokenAsDouble();
415	>	ji[1] = tokenizer.nextTokenAsDouble();
416	>	ji[2] = tokenizer.nextTokenAsDouble();
417	>	if (needAngMom_) {
418	>	integrableObject->setJ(ji);
419	>	}
420	>	}
421	>	break;
422	>	}
423	>	case 'f': {
424
425	<	if (worldRank == 0) {
426	<	#endif
425	>	Vector3d force;
426	>	force[0] = tokenizer.nextTokenAsDouble();
427	>	force[1] = tokenizer.nextTokenAsDouble();
428	>	force[2] = tokenizer.nextTokenAsDouble();
429	>	integrableObject->setFrc(force);
430	>	break;
431	>	}
432	>	case 't' : {
433
434	<	int error;
435	<	error = fclose(inFile_);
436	<
437	<	if (error) {
438	<	sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
439	<	painCave.isFatal = 1;
113	<	simError();
434	>	Vector3d torque;
435	>	torque[0] = tokenizer.nextTokenAsDouble();
436	>	torque[1] = tokenizer.nextTokenAsDouble();
437	>	torque[2] = tokenizer.nextTokenAsDouble();
438	>	integrableObject->setTrq(torque);
439	>	break;
440		}
441	+	default: {
442	+	sprintf(painCave.errMsg,
443	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
444	+	painCave.isFatal = 1;
445	+	simError();
446	+	break;
447	+	}
448
449	<	MemoryUtils::deleteVectorOfPointer(framePos_);
449	>	}
450	>	}
451	>
452	>	}
453	>
454
455	<	#ifdef IS_MPI
455	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
456
457	+	inputStream.getline(buffer, bufferSize);
458	+	std::string line(buffer);
459	+
460	+	if (line.find("<StuntDoubles>") == std::string::npos) {
461	+	sprintf(painCave.errMsg,
462	+	"DumpReader Error: Missing <StuntDoubles>\n");
463	+	painCave.isFatal = 1;
464	+	simError();
465		}
466
467	<	strcpy(checkPointMsg, "Dump file closed successfully.");
468	<	MPIcheckPoint();
467	>	while(inputStream.getline(buffer, bufferSize)) {
468	>	line = buffer;
469	>
470	>	if(line.find("</StuntDoubles>") != std::string::npos) {
471	>	break;
472	>	}
473
474	<	#endif
474	>	parseDumpLine(line);
475	>	}
476	>
477	>	}
478
479	<	return;
128	<	}
479	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
480
481	<	int DumpReader::getNFrames(void) {
481	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
482	>	inputStream.getline(buffer, bufferSize);
483	>	std::string line(buffer);
484
485	<	if (!isScanned_)
486	<	scanFile();
485	>	if (line.find("<FrameData>") == std::string::npos) {
486	>	sprintf(painCave.errMsg,
487	>	"DumpReader Error: Missing <FrameData>\n");
488	>	painCave.isFatal = 1;
489	>	simError();
490	>	}
491
492	<	return nframes_;
493	<	}
492	>	while(inputStream.getline(buffer, bufferSize)) {
493	>	line = buffer;
494	>
495	>	if(line.find("</FrameData>") != std::string::npos) {
496	>	break;
497	>	}
498	>
499	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
500	>	if (!tokenizer.hasMoreTokens()) {
501	>	sprintf(painCave.errMsg,
502	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
503	>	painCave.isFatal = 1;
504	>	simError();
505	>	}
506
507	<	void DumpReader::scanFile(void) {
508	<	int i, j;
509	<	int lineNum = 0;
510	<	char readBuffer[maxBufferSize];
511	<	fpos_t * currPos;
512	<
513	<	#ifdef IS_MPI
514	<
515	<	if (worldRank == 0) {
516	<	#endif // is_mpi
517	<
518	<	rewind(inFile_);
519	<
520	<	currPos = new fpos_t;
521	<	fgetpos(inFile_, currPos);
522	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
523	<	lineNum++;
524	<
525	<	if (feof(inFile_)) {
526	<	sprintf(painCave.errMsg,
527	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
528	<	filename_.c_str(),
529	<	lineNum);
530	<	painCave.isFatal = 1;
531	<	simError();
532	<	}
533	<
534	<	while (!feof(inFile_)) {
535	<	framePos_.push_back(currPos);
536	<
537	<	i = atoi(readBuffer);
538	<
539	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
540	<	lineNum++;
541	<
542	<	if (feof(inFile_)) {
543	<	sprintf(painCave.errMsg,
544	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
545	<	filename_.c_str(),
546	<	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
507	>	std::string propertyName = tokenizer.nextToken();
508	>	if (propertyName == "Time") {
509	>	RealType currTime = tokenizer.nextTokenAsDouble();
510	>	s->setTime(currTime);
511	>	} else if (propertyName == "Hmat"){
512	>	Mat3x3d hmat;
513	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
514	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
515	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
516	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
517	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
518	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
519	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
520	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
521	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
522	>	s->setHmat(hmat);
523	>	} else if (propertyName == "Thermostat") {
524	>	RealType chi = tokenizer.nextTokenAsDouble();
525	>	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
526	>	s->setChi(chi);
527	>	s->setIntegralOfChiDt(integralOfChiDt);
528	>	} else if (propertyName == "Barostat") {
529	>	Mat3x3d eta;
530	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
531	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
532	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
533	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
534	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
535	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
536	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
537	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
538	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
539	>	s->setEta(eta);
540	>	} else {
541	>	sprintf(painCave.errMsg,
542	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
543	>	painCave.isFatal = 0;
544	>	simError();
545	>	}
546	>
547		}
548
549	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
549	>	}
550
551	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
552	<	MPIcheckPoint();
215	<
216	<	#endif // is_mpi
217	<
218	<	isScanned_ = true;
219	<	}
220	<
221	<	void DumpReader::readFrame(int whichFrame) {
222	<	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
223	<
224	<	if (storageLayout & DataStorage::dslPosition) {
225	<	needPos_ = true;
226	<	} else {
227	<	needPos_ = false;
228	<	}
229	<
230	<	if (storageLayout & DataStorage::dslVelocity) {
231	<	needVel_ = true;
232	<	} else {
233	<	needVel_ = false;
234	<	}
235	<
236	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
237	<	needQuaternion_ = true;
238	<	} else {
239	<	needQuaternion_ = false;
240	<	}
241	<
242	<	if (storageLayout & DataStorage::dslAngularMomentum) {
243	<	needAngMom_ = true;
244	<	} else {
245	<	needAngMom_ = false;
246	<	}
247	<
248	<	readSet(whichFrame);
249	<	}
250	<
251	<	void DumpReader::readSet(int whichFrame) {
252	<	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	<
495	<	}
496	<
497	<	#endif
498	<
499	<	}
500	<
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
551	>
552	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpReader.cpp (property svn:keywords):
Revision 381 by tim, Tue Mar 1 14:45:45 2005 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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