ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 1825 by gezelter, Wed Jan 9 19:27:52 2013 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	>	#include "brains/Thermo.hpp"
62	>
63	>	#ifdef IS_MPI
64	>	#include <mpi.h>
65	>	#endif
66	>
67	>
68	>	namespace OpenMD {
69	>
70	>	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
71	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
72	>
73	>	#ifdef IS_MPI
74	>
75	>	if (worldRank == 0) {
76	>	#endif
77	>
78	>	inFile_ = new std::ifstream(filename_.c_str(),
79	>	ifstream::in | ifstream::binary);
80	>
81	>	if (inFile_->fail()) {
82	>	sprintf(painCave.errMsg,
83	>	"DumpReader: Cannot open file: %s\n",
84	>	filename_.c_str());
85	>	painCave.isFatal = 1;
86	>	simError();
87	>	}
88	>
89	>	#ifdef IS_MPI
90	>
91	>	}
92	>
93	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
94	>	errorCheckPoint();
95	>
96	>	#endif
97	>
98	>	return;
99	>	}
100	>
101	>	DumpReader::~DumpReader() {
102	>
103	>	#ifdef IS_MPI
104	>
105	>	if (worldRank == 0) {
106	>	#endif
107	>
108	>	delete inFile_;
109	>
110	>	#ifdef IS_MPI
111	>
112	>	}
113	>
114	>	strcpy(checkPointMsg, "Dump file closed successfully.");
115	>	errorCheckPoint();
116	>
117	>	#endif
118	>
119	>	return;
120	>	}
121	>
122	>	int DumpReader::getNFrames(void) {
123	>
124	>	if (!isScanned_)
125	>	scanFile();
126	>
127	>	return nframes_;
128	>	}
129	>
130	>	void DumpReader::scanFile(void) {
131	>	int lineNo = 0;
132	>	std::streampos prevPos;
133	>	std::streampos  currPos;
134	>
135	>	#ifdef IS_MPI
136	>
137	>	if (worldRank == 0) {
138	>	#endif // is_mpi
139	>
140	>	currPos = inFile_->tellg();
141	>	prevPos = currPos;
142	>	bool foundOpenSnapshotTag = false;
143	>	bool foundClosedSnapshotTag = false;
144
145	<	#include <sys/types.h>
146	<	#include <sys/stat.h>
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::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0);
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 ||
231	>	storageLayout & DataStorage::dslDipole ||
232	>	storageLayout & DataStorage::dslQuadrupole) {
233	>	needQuaternion_ = true;
234	>	} else {
235	>	needQuaternion_ = false;
236	>	}
237	>
238	>	if (storageLayout & DataStorage::dslAngularMomentum) {
239	>	needAngMom_ = true;
240	>	} else {
241	>	needAngMom_ = false;
242	>	}
243	>
244	>	readSet(whichFrame);
245
246	<	#include <iostream>
247	<	#include <math.h>
246	>	if (needCOMprops_) {
247	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
248	>	Thermo thermo(info_);
249	>	Vector3d com;
250
251	<	#include <stdio.h>
252	<	#include <stdlib.h>
253	<	#include <string.h>
251	>	if (needPos_ && needVel_) {
252	>	Vector3d comvel;
253	>	Vector3d comw;
254	>	thermo.getComAll(com, comvel);
255	>	comw = thermo.getAngularMomentum();
256	>	} else {
257	>	com = thermo.getCom();
258	>	}
259	>	}
260	>	}
261	>
262	>	void DumpReader::readSet(int whichFrame) {
263	>	std::string line;
264
265	<	#include "io/DumpReader.hpp"
266	<	#include "primitives/Molecule.hpp"
267	<	#include "utils/simError.h"
58	<	#include "utils/MemoryUtils.hpp"
59	<	#include "utils/StringTokenizer.hpp"
265	>	#ifndef IS_MPI
266	>	inFile_->clear();
267	>	inFile_->seekg(framePos_[whichFrame]);
268
269	<	#ifdef IS_MPI
269	>	std::istream& inputStream = *inFile_;
270
271	<	#include <mpi.h>
272	<	#define TAKE_THIS_TAG_CHAR 0
273	<	#define TAKE_THIS_TAG_INT 1
271	>	#else
272	>	int masterNode = 0;
273	>	std::stringstream sstream;
274	>	if (worldRank == masterNode) {
275	>	std::string sendBuffer;
276
277	<	#endif // is_mpi
277	>	inFile_->clear();
278	>	inFile_->seekg(framePos_[whichFrame]);
279	>
280	>	while (inFile_->getline(buffer, bufferSize)) {
281
282	+	line = buffer;
283	+	sendBuffer += line;
284	+	sendBuffer += '\n';
285	+	if (line.find("</Snapshot>") != std::string::npos) {
286	+	break;
287	+	}
288	+	}
289
290	<	namespace oopse {
290	>	int sendBufferSize = sendBuffer.size();
291	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
292	>	MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
293	>	MPI::CHAR, masterNode);
294	>
295	>	sstream.str(sendBuffer);
296	>	} else {
297	>	int sendBufferSize;
298	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
299	>	char * recvBuffer = new char[sendBufferSize+1];
300	>	assert(recvBuffer);
301	>	recvBuffer[sendBufferSize] = '\0';
302	>	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
303	>	sstream.str(recvBuffer);
304	>	delete [] recvBuffer;
305	>	}
306
307	<	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
74	<
75	<	#ifdef IS_MPI
76	<
77	<	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	<	}
317	<
318	<	#ifdef IS_MPI
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	<	}
323	>	//read StuntDoubles
324	>	readStuntDoubles(inputStream);
325
326	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
327	<	MPIcheckPoint();
326	>	inputStream.getline(buffer, bufferSize);
327	>	line = buffer;
328
329	<	#endif
329	>	if (line.find("<SiteData>") != std::string::npos) {
330	>	//read SiteData
331	>	readSiteData(inputStream);
332	>	} else {
333	>	if (line.find("</Snapshot>") == std::string::npos) {
334	>	sprintf(painCave.errMsg,
335	>	"DumpReader Error: can not find </Snapshot>\n");
336	>	painCave.isFatal = 1;
337	>	simError();
338	>	}
339	>	}
340	>	}
341	>
342	>	void DumpReader::parseDumpLine(const std::string& line) {
343
344	<	return;
345	<	}
344	>
345	>	StringTokenizer tokenizer(line);
346	>	int nTokens;
347	>
348	>	nTokens = tokenizer.countTokens();
349	>
350	>	if (nTokens < 2) {
351	>	sprintf(painCave.errMsg,
352	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
353	>	painCave.isFatal = 1;
354	>	simError();
355	>	}
356
357	<	DumpReader::~DumpReader() {
357	>	int index = tokenizer.nextTokenAsInt();
358	>
359	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
360
361	<	#ifdef IS_MPI
361	>	if (sd == NULL) {
362	>	return;
363	>	}
364	>	std::string type = tokenizer.nextToken();
365	>	int size = type.size();
366
367	<	if (worldRank == 0) {
368	<	#endif
369	<
370	<	int error;
371	<	error = fclose(inFile_);
372	<
373	<	if (error) {
374	<	sprintf(painCave.errMsg, "Error closing %s\n", filename_.c_str());
375	<	painCave.isFatal = 1;
376	<	simError();
367	>	size_t found;
368	>
369	>	if (needPos_) {
370	>	found = type.find("p");
371	>	if (found == std::string::npos) {
372	>	sprintf(painCave.errMsg,
373	>	"DumpReader Error: StuntDouble %d has no Position\n"
374	>	"\tField (\"p\") specified.\n%s\n", index,
375	>	line.c_str());
376	>	painCave.isFatal = 1;
377	>	simError();
378	>	}
379	>	}
380	>
381	>	if (sd->isDirectional()) {
382	>	if (needQuaternion_) {
383	>	found = type.find("q");
384	>	if (found == std::string::npos) {
385	>	sprintf(painCave.errMsg,
386	>	"DumpReader Error: Directional StuntDouble %d has no\n"
387	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
388	>	line.c_str());
389	>	painCave.isFatal = 1;
390	>	simError();
391		}
392	<
116	<	MemoryUtils::deleteVectorOfPointer(framePos_);
117	<
118	<	#ifdef IS_MPI
119	<
392	>	}
393		}
394
395	<	strcpy(checkPointMsg, "Dump file closed successfully.");
396	<	MPIcheckPoint();
395	>	for(int i = 0; i < size; ++i) {
396	>	switch(type[i]) {
397	>
398	>	case 'p': {
399	>	Vector3d pos;
400	>	pos[0] = tokenizer.nextTokenAsDouble();
401	>	pos[1] = tokenizer.nextTokenAsDouble();
402	>	pos[2] = tokenizer.nextTokenAsDouble();
403	>	if (needPos_) {
404	>	sd->setPos(pos);
405	>	}
406	>	break;
407	>	}
408	>	case 'v' : {
409	>	Vector3d vel;
410	>	vel[0] = tokenizer.nextTokenAsDouble();
411	>	vel[1] = tokenizer.nextTokenAsDouble();
412	>	vel[2] = tokenizer.nextTokenAsDouble();
413	>	if (needVel_) {
414	>	sd->setVel(vel);
415	>	}
416	>	break;
417	>	}
418
419	<	#endif
419	>	case 'q' : {
420	>	Quat4d q;
421	>	if (sd->isDirectional()) {
422	>
423	>	q[0] = tokenizer.nextTokenAsDouble();
424	>	q[1] = tokenizer.nextTokenAsDouble();
425	>	q[2] = tokenizer.nextTokenAsDouble();
426	>	q[3] = tokenizer.nextTokenAsDouble();
427	>
428	>	RealType qlen = q.length();
429	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
430	>
431	>	sprintf(painCave.errMsg,
432	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
433	>	painCave.isFatal = 1;
434	>	simError();
435	>
436	>	}
437	>
438	>	q.normalize();
439	>	if (needQuaternion_) {
440	>	sd->setQ(q);
441	>	}
442	>	}
443	>	break;
444	>	}
445	>	case 'j' : {
446	>	Vector3d ji;
447	>	if (sd->isDirectional()) {
448	>	ji[0] = tokenizer.nextTokenAsDouble();
449	>	ji[1] = tokenizer.nextTokenAsDouble();
450	>	ji[2] = tokenizer.nextTokenAsDouble();
451	>	if (needAngMom_) {
452	>	sd->setJ(ji);
453	>	}
454	>	}
455	>	break;
456	>	}
457	>	case 'f': {
458
459	<	return;
460	<	}
459	>	Vector3d force;
460	>	force[0] = tokenizer.nextTokenAsDouble();
461	>	force[1] = tokenizer.nextTokenAsDouble();
462	>	force[2] = tokenizer.nextTokenAsDouble();
463	>	sd->setFrc(force);
464	>	break;
465	>	}
466	>	case 't' : {
467
468	<	int DumpReader::getNFrames(void) {
468	>	Vector3d torque;
469	>	torque[0] = tokenizer.nextTokenAsDouble();
470	>	torque[1] = tokenizer.nextTokenAsDouble();
471	>	torque[2] = tokenizer.nextTokenAsDouble();
472	>	sd->setTrq(torque);
473	>	break;
474	>	}
475	>	case 'u' : {
476
477	<	if (!isScanned_)
478	<	scanFile();
477	>	RealType particlePot;
478	>	particlePot = tokenizer.nextTokenAsDouble();
479	>	sd->setParticlePot(particlePot);
480	>	break;
481	>	}
482	>	case 'c' : {
483
484	<	return nframes_;
485	<	}
484	>	RealType flucQPos;
485	>	flucQPos = tokenizer.nextTokenAsDouble();
486	>	sd->setFlucQPos(flucQPos);
487	>	break;
488	>	}
489	>	case 'w' : {
490
491	<	void DumpReader::scanFile(void) {
492	<	int i, j;
493	<	int lineNum = 0;
494	<	char readBuffer[maxBufferSize];
495	<	fpos_t * currPos;
491	>	RealType flucQVel;
492	>	flucQVel = tokenizer.nextTokenAsDouble();
493	>	sd->setFlucQVel(flucQVel);
494	>	break;
495	>	}
496	>	case 'g' : {
497
498	<	#ifdef IS_MPI
498	>	RealType flucQFrc;
499	>	flucQFrc = tokenizer.nextTokenAsDouble();
500	>	sd->setFlucQFrc(flucQFrc);
501	>	break;
502	>	}
503	>	case 'e' : {
504
505	<	if (worldRank == 0) {
506	<	#endif // is_mpi
507	<
508	<	rewind(inFile_);
509	<
510	<	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();
505	>	Vector3d eField;
506	>	eField[0] = tokenizer.nextTokenAsDouble();
507	>	eField[1] = tokenizer.nextTokenAsDouble();
508	>	eField[2] = tokenizer.nextTokenAsDouble();
509	>	sd->setElectricField(eField);
510	>	break;
511		}
512	+	default: {
513	+	sprintf(painCave.errMsg,
514	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
515	+	painCave.isFatal = 1;
516	+	simError();
517	+	break;
518	+	}
519
520	<	while (!feof(inFile_)) {
521	<	framePos_.push_back(currPos);
520	>	}
521	>	}
522	>
523	>	}
524	>
525
526	<	i = atoi(readBuffer);
526	>	void DumpReader::parseSiteLine(const std::string& line) {
527
528	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
529	<	lineNum++;
530	<
531	<	if (feof(inFile_)) {
532	<	sprintf(painCave.errMsg,
533	<	"File \"%s\" ended unexpectedly at line %d\n",
534	<	filename_.c_str(),
535	<	lineNum);
536	<	painCave.isFatal = 1;
537	<	simError();
538	<	}
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
209	<	}
528	>	StringTokenizer tokenizer(line);
529	>	int nTokens;
530	>
531	>	nTokens = tokenizer.countTokens();
532	>
533	>	if (nTokens < 2) {
534	>	sprintf(painCave.errMsg,
535	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
536	>	painCave.isFatal = 1;
537	>	simError();
538	>	}
539
540	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
540	>	/**
541	>	* The first token is the global integrable object index.
542	>	*/
543
544	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
545	<	MPIcheckPoint();
544	>	int index = tokenizer.nextTokenAsInt();
545	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
546	>	if (sd == NULL) {
547	>	return;
548	>	}
549
550	<	#endif // is_mpi
550	>	/**
551	>	* Test to see if the next token is an integer or not.  If not,
552	>	* we've got data on the integrable object itself.  If there is an
553	>	* integer, we're parsing data for a site on a rigid body.
554	>	*/
555
556	<	isScanned_ = true;
557	<	}
556	>	std::string indexTest = tokenizer.peekNextToken();
557	>	std::istringstream i(indexTest);
558	>	int siteIndex;
559	>	if (i >> siteIndex) {
560	>	// chew up this token and parse as an int:
561	>	siteIndex = tokenizer.nextTokenAsInt();
562	>	RigidBody* rb = static_cast<RigidBody*>(sd);
563	>	sd = rb->getAtoms()[siteIndex];
564	>	}
565
566	<	void DumpReader::readFrame(int whichFrame) {
567	<	readSet(whichFrame);
568	<	}
566	>	/**
567	>	* The next token contains information on what follows.
568	>	*/
569	>	std::string type = tokenizer.nextToken();
570	>	int size = type.size();
571	>
572	>	for(int i = 0; i < size; ++i) {
573	>	switch(type[i]) {
574	>
575	>	case 'u' : {
576	>
577	>	RealType particlePot;
578	>	particlePot = tokenizer.nextTokenAsDouble();
579	>	sd->setParticlePot(particlePot);
580	>	break;
581	>	}
582	>	case 'c' : {
583	>
584	>	RealType flucQPos;
585	>	flucQPos = tokenizer.nextTokenAsDouble();
586	>	sd->setFlucQPos(flucQPos);
587	>	break;
588	>	}
589	>	case 'w' : {
590	>
591	>	RealType flucQVel;
592	>	flucQVel = tokenizer.nextTokenAsDouble();
593	>	sd->setFlucQVel(flucQVel);
594	>	break;
595	>	}
596	>	case 'g' : {
597	>
598	>	RealType flucQFrc;
599	>	flucQFrc = tokenizer.nextTokenAsDouble();
600	>	sd->setFlucQFrc(flucQFrc);
601	>	break;
602	>	}
603	>	case 'e' : {
604	>
605	>	Vector3d eField;
606	>	eField[0] = tokenizer.nextTokenAsDouble();
607	>	eField[1] = tokenizer.nextTokenAsDouble();
608	>	eField[2] = tokenizer.nextTokenAsDouble();
609	>	sd->setElectricField(eField);
610	>	break;
611	>	}
612	>	default: {
613	>	sprintf(painCave.errMsg,
614	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
615	>	painCave.isFatal = 1;
616	>	simError();
617	>	break;
618	>	}
619	>	}
620	>	}
621	>	}
622	>
623	>
624	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
625	>
626	>	inputStream.getline(buffer, bufferSize);
627	>	std::string line(buffer);
628	>
629	>	if (line.find("<StuntDoubles>") == std::string::npos) {
630	>	sprintf(painCave.errMsg,
631	>	"DumpReader Error: Missing <StuntDoubles>\n");
632	>	painCave.isFatal = 1;
633	>	simError();
634	>	}
635
636	<	void DumpReader::readSet(int whichFrame) {
637	<	int i;
638	<	int nTotObjs;                  // the number of atoms
639	<	char read_buffer[maxBufferSize];  //the line buffer for reading
640	<	char * eof_test;               // ptr to see when we reach the end of the file
636	>	while(inputStream.getline(buffer, bufferSize)) {
637	>	line = buffer;
638	>
639	>	if(line.find("</StuntDoubles>") != std::string::npos) {
640	>	break;
641	>	}
642
643	<	Molecule* mol;
644	<	StuntDouble* integrableObject;
645	<	SimInfo::MoleculeIterator mi;
646	<	Molecule::IntegrableObjectIterator ii;
643	>	parseDumpLine(line);
644	>	}
645	>
646	>	}
647
648	<	#ifndef IS_MPI
648	>	void  DumpReader::readSiteData(std::istream& inputStream) {
649
650	<	fsetpos(inFile_, framePos_[whichFrame]);
651	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
652	<
653	<	if (eof_test == NULL) {
654	<	sprintf(painCave.errMsg,
655	<	"DumpReader error: error reading 1st line of \"%s\"\n",
244	<	filename_.c_str());
245	<	painCave.isFatal = 1;
246	<	simError();
650	>	inputStream.getline(buffer, bufferSize);
651	>	std::string line(buffer);
652	>
653	>	if (line.find("<SiteData>") == std::string::npos) {
654	>	// site data isn't required for a simulation, so skip
655	>	return;
656		}
657
658	<	nTotObjs = atoi(read_buffer);
658	>	while(inputStream.getline(buffer, bufferSize)) {
659	>	line = buffer;
660	>
661	>	if(line.find("</SiteData>") != std::string::npos) {
662	>	break;
663	>	}
664
665	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
252	<	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();
665	>	parseSiteLine(line);
666		}
667	+
668	+	}
669
670	<	//read the box mat from the comment line
670	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
671
672	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
672	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
673	>	inputStream.getline(buffer, bufferSize);
674	>	std::string line(buffer);
675
676	<	if (eof_test == NULL) {
677	<	sprintf(painCave.errMsg, "error in reading commment in %s\n",
678	<	filename_.c_str());
679	<	painCave.isFatal = 1;
680	<	simError();
676	>	if (line.find("<FrameData>") == std::string::npos) {
677	>	sprintf(painCave.errMsg,
678	>	"DumpReader Error: Missing <FrameData>\n");
679	>	painCave.isFatal = 1;
680	>	simError();
681		}
682
683	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
683	>	while(inputStream.getline(buffer, bufferSize)) {
684	>	line = buffer;
685	>
686	>	if(line.find("</FrameData>") != std::string::npos) {
687	>	break;
688	>	}
689	>
690	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
691	>	if (!tokenizer.hasMoreTokens()) {
692	>	sprintf(painCave.errMsg,
693	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
694	>	painCave.isFatal = 1;
695	>	simError();
696	>	}
697
698	<	//parse dump lines
699	<
700	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
701	<
702	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
703	<	integrableObject = mol->nextIntegrableObject(ii)) {
704	<
705	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
706	<
707	<	if (eof_test == NULL) {
708	<	sprintf(painCave.errMsg,
709	<	"error in reading file %s\n"
710	<	"natoms  = %d; index = %d\n"
711	<	"error reading the line from the file.\n",
712	<	filename_.c_str(),
713	<	nTotObjs,
714	<	i);
715	<
716	<	painCave.isFatal = 1;
717	<	simError();
718	<	}
719	<
720	<	parseDumpLine(read_buffer, integrableObject);
721	<
722	<	}
698	>	std::string propertyName = tokenizer.nextToken();
699	>	if (propertyName == "Time") {
700	>	RealType currTime = tokenizer.nextTokenAsDouble();
701	>	s->setTime(currTime);
702	>	} else if (propertyName == "Hmat"){
703	>	Mat3x3d hmat;
704	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
705	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
706	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
707	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
708	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
709	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
710	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
711	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
712	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
713	>	s->setHmat(hmat);
714	>	} else if (propertyName == "Thermostat") {
715	>	pair<RealType, RealType> thermostat;
716	>	thermostat.first = tokenizer.nextTokenAsDouble();
717	>	thermostat.second = tokenizer.nextTokenAsDouble();
718	>	s->setThermostat(thermostat);
719	>	} else if (propertyName == "Barostat") {
720	>	Mat3x3d eta;
721	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
722	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
723	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
724	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
725	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
726	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
727	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
728	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
729	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
730	>	s->setBarostat(eta);
731	>	} else {
732	>	sprintf(painCave.errMsg,
733	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
734	>	painCave.isFatal = 0;
735	>	simError();
736	>	}
737	>
738		}
739
740	<	// MPI Section of code..........
740	>	}
741
742	<	#else //IS_MPI
743	<
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	<
469	<	}
470	<
471	<	#endif
472	<
473	<	}
474	<
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
742	>
743	>	}//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 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

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

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines