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root/OpenMD/trunk/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.
Revision 2000 by gezelter, Sat May 31 22:35:05 2014 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, 234107 (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	>	#ifdef IS_MPI
47	>	#include <mpi.h>
48	>	#endif
49	>
50	>	#include <sys/types.h>
51	>	#include <sys/stat.h>
52	>
53	>	#include <iostream>
54	>	#include <math.h>
55	>
56	>	#include <stdio.h>
57	>	#include <stdlib.h>
58	>	#include <string.h>
59	>
60	>	#include "io/DumpReader.hpp"
61	>	#include "primitives/Molecule.hpp"
62	>	#include "utils/simError.h"
63	>	#include "utils/MemoryUtils.hpp"
64	>	#include "utils/StringTokenizer.hpp"
65	>	#include "brains/Thermo.hpp"
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	<	#include <sys/types.h>
109	<	#include <sys/stat.h>
108	>	inFile_->~istream();
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
132	<	#include <iostream>
133	<	#include <math.h>
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 <stdio.h>
146	<	#include <stdlib.h>
147	<	#include <string.h>
145	>	int lineNo = 0;
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 ||
232	>	storageLayout & DataStorage::dslDipole ||
233	>	storageLayout & DataStorage::dslQuadrupole) {
234	>	needQuaternion_ = true;
235	>	} else {
236	>	needQuaternion_ = false;
237	>	}
238	>
239	>	if (storageLayout & DataStorage::dslAngularMomentum) {
240	>	needAngMom_ = true;
241	>	} else {
242	>	needAngMom_ = false;
243	>	}
244	>
245	>	readSet(whichFrame);
246
247	<	#include "io/DumpReader.hpp"
248	<	#include "primitives/Molecule.hpp"
249	<	#include "utils/simError.h"
250	<	#include "utils/MemoryUtils.hpp"
59	<	#include "utils/StringTokenizer.hpp"
247	>	if (needCOMprops_) {
248	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
249	>	Thermo thermo(info_);
250	>	Vector3d com;
251
252	<	#ifdef IS_MPI
252	>	if (needPos_ && needVel_) {
253	>	Vector3d comvel;
254	>	Vector3d comw;
255	>	thermo.getComAll(com, comvel);
256	>	comw = thermo.getAngularMomentum();
257	>	} else {
258	>	com = thermo.getCom();
259	>	}
260	>	}
261	>	}
262	>
263	>	void DumpReader::readSet(int whichFrame) {
264	>	std::string line;
265
266	<	#include <mpi.h>
267	<	#define TAKE_THIS_TAG_CHAR 0
268	<	#define TAKE_THIS_TAG_INT 1
266	>	#ifndef IS_MPI
267	>	inFile_->clear();
268	>	inFile_->seekg(framePos_[whichFrame]);
269
270	<	#endif // is_mpi
270	>	std::istream& inputStream = *inFile_;
271
272	+	#else
273	+	int masterNode = 0;
274	+	std::stringstream sstream;
275	+	if (worldRank == masterNode) {
276	+	std::string sendBuffer;
277
278	<	namespace oopse {
278	>	inFile_->clear();
279	>	inFile_->seekg(framePos_[whichFrame]);
280	>
281	>	while (inFile_->getline(buffer, bufferSize)) {
282
283	<	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
284	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
283	>	line = buffer;
284	>	sendBuffer += line;
285	>	sendBuffer += '\n';
286	>	if (line.find("</Snapshot>") != std::string::npos) {
287	>	break;
288	>	}
289	>	}
290
291	<	#ifdef IS_MPI
291	>	int sendBufferSize = sendBuffer.size();
292	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
293	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize,
294	>	MPI_CHAR, masterNode, MPI_COMM_WORLD);
295	>
296	>	sstream.str(sendBuffer);
297	>	} else {
298	>	int sendBufferSize;
299	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
300	>	char * recvBuffer = new char[sendBufferSize+1];
301	>	assert(recvBuffer);
302	>	recvBuffer[sendBufferSize] = '\0';
303	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
304	>	sstream.str(recvBuffer);
305	>	delete [] recvBuffer;
306	>	}
307
308	<	if (worldRank == 0) {
308	>	std::istream& inputStream = sstream;
309		#endif
310
311	<	inFile_ = fopen(filename_.c_str(), "r");
311	>	inputStream.getline(buffer, bufferSize);
312
313	<	if (inFile_ == NULL) {
314	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
315	<	painCave.isFatal = 1;
316	<	simError();
317	<	}
313	>	line = buffer;
314	>	if (line.find("<Snapshot>") == std::string::npos) {
315	>	sprintf(painCave.errMsg,
316	>	"DumpReader Error: can not find <Snapshot>\n");
317	>	painCave.isFatal = 1;
318	>	simError();
319	>	}
320	>
321	>	//read frameData
322	>	readFrameProperties(inputStream);
323
324	<	#ifdef IS_MPI
325	<
324	>	//read StuntDoubles
325	>	readStuntDoubles(inputStream);
326	>
327	>	inputStream.getline(buffer, bufferSize);
328	>	line = buffer;
329	>
330	>	if (line.find("<SiteData>") != std::string::npos) {
331	>	//read SiteData
332	>	readSiteData(inputStream);
333	>	} else {
334	>	if (line.find("</Snapshot>") == std::string::npos) {
335	>	sprintf(painCave.errMsg,
336	>	"DumpReader Error: can not find </Snapshot>\n");
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340		}
341	+	}
342	+
343	+	void DumpReader::parseDumpLine(const std::string& line) {
344
345	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
346	<	MPIcheckPoint();
345	>
346	>	StringTokenizer tokenizer(line);
347	>	int nTokens;
348	>
349	>	nTokens = tokenizer.countTokens();
350	>
351	>	if (nTokens < 2) {
352	>	sprintf(painCave.errMsg,
353	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
354	>	painCave.isFatal = 1;
355	>	simError();
356	>	}
357
358	<	#endif
358	>	int index = tokenizer.nextTokenAsInt();
359	>
360	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
361
362	<	return;
363	<	}
362	>	if (sd == NULL) {
363	>	return;
364	>	}
365	>	std::string type = tokenizer.nextToken();
366	>	int size = type.size();
367
368	<	DumpReader::~DumpReader() {
369	<
370	<	#ifdef IS_MPI
371	<
372	<	if (worldRank == 0) {
373	<	#endif
374	<
375	<	int error;
376	<	error = fclose(inFile_);
377	<
378	<	if (error) {
379	<	sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
380	<	painCave.isFatal = 1;
381	<	simError();
368	>	size_t found;
369	>
370	>	if (needPos_) {
371	>	found = type.find("p");
372	>	if (found == std::string::npos) {
373	>	sprintf(painCave.errMsg,
374	>	"DumpReader Error: StuntDouble %d has no Position\n"
375	>	"\tField (\"p\") specified.\n%s\n", index,
376	>	line.c_str());
377	>	painCave.isFatal = 1;
378	>	simError();
379	>	}
380	>	}
381	>
382	>	if (sd->isDirectional()) {
383	>	if (needQuaternion_) {
384	>	found = type.find("q");
385	>	if (found == std::string::npos) {
386	>	sprintf(painCave.errMsg,
387	>	"DumpReader Error: Directional StuntDouble %d has no\n"
388	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
389	>	line.c_str());
390	>	painCave.isFatal = 1;
391	>	simError();
392		}
393	<
116	<	MemoryUtils::deletePointers(framePos_);
117	<
118	<	#ifdef IS_MPI
119	<
393	>	}
394		}
395
396	<	strcpy(checkPointMsg, "Dump file closed successfully.");
397	<	MPIcheckPoint();
396	>	for(int i = 0; i < size; ++i) {
397	>	switch(type[i]) {
398	>
399	>	case 'p': {
400	>	Vector3d pos;
401	>	pos[0] = tokenizer.nextTokenAsDouble();
402	>	pos[1] = tokenizer.nextTokenAsDouble();
403	>	pos[2] = tokenizer.nextTokenAsDouble();
404	>	if (needPos_) {
405	>	sd->setPos(pos);
406	>	}
407	>	break;
408	>	}
409	>	case 'v' : {
410	>	Vector3d vel;
411	>	vel[0] = tokenizer.nextTokenAsDouble();
412	>	vel[1] = tokenizer.nextTokenAsDouble();
413	>	vel[2] = tokenizer.nextTokenAsDouble();
414	>	if (needVel_) {
415	>	sd->setVel(vel);
416	>	}
417	>	break;
418	>	}
419
420	<	#endif
420	>	case 'q' : {
421	>	Quat4d q;
422	>	if (sd->isDirectional()) {
423	>
424	>	q[0] = tokenizer.nextTokenAsDouble();
425	>	q[1] = tokenizer.nextTokenAsDouble();
426	>	q[2] = tokenizer.nextTokenAsDouble();
427	>	q[3] = tokenizer.nextTokenAsDouble();
428	>
429	>	RealType qlen = q.length();
430	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
431	>
432	>	sprintf(painCave.errMsg,
433	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
434	>	painCave.isFatal = 1;
435	>	simError();
436	>
437	>	}
438	>
439	>	q.normalize();
440	>	if (needQuaternion_) {
441	>	sd->setQ(q);
442	>	}
443	>	}
444	>	break;
445	>	}
446	>	case 'j' : {
447	>	Vector3d ji;
448	>	if (sd->isDirectional()) {
449	>	ji[0] = tokenizer.nextTokenAsDouble();
450	>	ji[1] = tokenizer.nextTokenAsDouble();
451	>	ji[2] = tokenizer.nextTokenAsDouble();
452	>	if (needAngMom_) {
453	>	sd->setJ(ji);
454	>	}
455	>	}
456	>	break;
457	>	}
458	>	case 'f': {
459
460	<	return;
461	<	}
460	>	Vector3d force;
461	>	force[0] = tokenizer.nextTokenAsDouble();
462	>	force[1] = tokenizer.nextTokenAsDouble();
463	>	force[2] = tokenizer.nextTokenAsDouble();
464	>	sd->setFrc(force);
465	>	break;
466	>	}
467	>	case 't' : {
468
469	<	int DumpReader::getNFrames(void) {
469	>	Vector3d torque;
470	>	torque[0] = tokenizer.nextTokenAsDouble();
471	>	torque[1] = tokenizer.nextTokenAsDouble();
472	>	torque[2] = tokenizer.nextTokenAsDouble();
473	>	sd->setTrq(torque);
474	>	break;
475	>	}
476	>	case 'u' : {
477
478	<	if (!isScanned_)
479	<	scanFile();
478	>	RealType particlePot;
479	>	particlePot = tokenizer.nextTokenAsDouble();
480	>	sd->setParticlePot(particlePot);
481	>	break;
482	>	}
483	>	case 'c' : {
484
485	<	return nframes_;
486	<	}
485	>	RealType flucQPos;
486	>	flucQPos = tokenizer.nextTokenAsDouble();
487	>	sd->setFlucQPos(flucQPos);
488	>	break;
489	>	}
490	>	case 'w' : {
491
492	<	void DumpReader::scanFile(void) {
493	<	int i, j;
494	<	int lineNum = 0;
495	<	char readBuffer[maxBufferSize];
496	<	fpos_t * currPos;
492	>	RealType flucQVel;
493	>	flucQVel = tokenizer.nextTokenAsDouble();
494	>	sd->setFlucQVel(flucQVel);
495	>	break;
496	>	}
497	>	case 'g' : {
498
499	<	#ifdef IS_MPI
499	>	RealType flucQFrc;
500	>	flucQFrc = tokenizer.nextTokenAsDouble();
501	>	sd->setFlucQFrc(flucQFrc);
502	>	break;
503	>	}
504	>	case 'e' : {
505
506	<	if (worldRank == 0) {
507	<	#endif // is_mpi
508	<
509	<	rewind(inFile_);
510	<
511	<	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();
506	>	Vector3d eField;
507	>	eField[0] = tokenizer.nextTokenAsDouble();
508	>	eField[1] = tokenizer.nextTokenAsDouble();
509	>	eField[2] = tokenizer.nextTokenAsDouble();
510	>	sd->setElectricField(eField);
511	>	break;
512		}
513	+	case 's' : {
514
515	<	while (!feof(inFile_)) {
516	<	framePos_.push_back(currPos);
517	<
518	<	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++;
515	>	RealType sPot;
516	>	sPot = tokenizer.nextTokenAsDouble();
517	>	sd->setSitePotential(sPot);
518	>	break;
519		}
520	+	default: {
521	+	sprintf(painCave.errMsg,
522	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
523	+	painCave.isFatal = 1;
524	+	simError();
525	+	break;
526	+	}
527
528	<	delete currPos;
205	<	rewind(inFile_);
206	<
207	<	nframes_ = framePos_.size();
208	<	#ifdef IS_MPI
528	>	}
529		}
530	+	}
531	+
532
533	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
533	>	void DumpReader::parseSiteLine(const std::string& line) {
534
535	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
536	<	MPIcheckPoint();
537	<
538	<	#endif // is_mpi
539	<
540	<	isScanned_ = true;
541	<	}
542	<
543	<	void DumpReader::readFrame(int whichFrame) {
544	<	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
535	>	StringTokenizer tokenizer(line);
536	>	int nTokens;
537	>
538	>	nTokens = tokenizer.countTokens();
539	>
540	>	if (nTokens < 2) {
541	>	sprintf(painCave.errMsg,
542	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
543	>	painCave.isFatal = 1;
544	>	simError();
545	>	}
546
547	<	if (storageLayout & DataStorage::dslPosition) {
548	<	needPos_ = true;
549	<	} else {
227	<	needPos_ = false;
228	<	}
547	>	/**
548	>	* The first token is the global integrable object index.
549	>	*/
550
551	<	if (storageLayout & DataStorage::dslVelocity) {
552	<	needVel_ = true;
553	<	} else {
554	<	needVel_ = false;
551	>	int index = tokenizer.nextTokenAsInt();
552	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
553	>	if (sd == NULL) {
554	>	return;
555		}
556
557	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
558	<	needQuaternion_ = true;
559	<	} else {
560	<	needQuaternion_ = false;
561	<	}
557	>	/**
558	>	* Test to see if the next token is an integer or not.  If not,
559	>	* we've got data on the integrable object itself.  If there is an
560	>	* integer, we're parsing data for a site on a rigid body.
561	>	*/
562
563	<	if (storageLayout & DataStorage::dslAngularMomentum) {
564	<	needAngMom_ = true;
565	<	} else {
566	<	needAngMom_ = false;
567	<	}
563	>	std::string indexTest = tokenizer.peekNextToken();
564	>	std::istringstream i(indexTest);
565	>	int siteIndex;
566	>	if (i >> siteIndex) {
567	>	// chew up this token and parse as an int:
568	>	siteIndex = tokenizer.nextTokenAsInt();
569
570	<	readSet(whichFrame);
571	<	}
572	<
573	<	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();
570	>	if (sd->isRigidBody()) {
571	>	RigidBody* rb = static_cast<RigidBody*>(sd);
572	>	sd = rb->getAtoms()[siteIndex];
573	>	}
574		}
575
576	<	nTotObjs = atoi(read_buffer);
577	<
578	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
579	<	sprintf(painCave.errMsg,
580	<	"DumpReader error. %s nIntegrable, %d, "
581	<	"does not match the meta-data file's nIntegrable, %d.\n",
582	<	filename_.c_str(),
583	<	nTotObjs,
584	<	info_->getNGlobalIntegrableObjects());
585	<
586	<	painCave.isFatal = 1;
587	<	simError();
576	>	/**
577	>	* The next token contains information on what follows.
578	>	*/
579	>	std::string type = tokenizer.nextToken();
580	>	int size = type.size();
581	>
582	>	for(int i = 0; i < size; ++i) {
583	>	switch(type[i]) {
584	>
585	>	case 'u' : {
586	>
587	>	RealType particlePot;
588	>	particlePot = tokenizer.nextTokenAsDouble();
589	>	sd->setParticlePot(particlePot);
590	>	break;
591	>	}
592	>	case 'c' : {
593	>
594	>	RealType flucQPos;
595	>	flucQPos = tokenizer.nextTokenAsDouble();
596	>	sd->setFlucQPos(flucQPos);
597	>	break;
598	>	}
599	>	case 'w' : {
600	>
601	>	RealType flucQVel;
602	>	flucQVel = tokenizer.nextTokenAsDouble();
603	>	sd->setFlucQVel(flucQVel);
604	>	break;
605	>	}
606	>	case 'g' : {
607	>
608	>	RealType flucQFrc;
609	>	flucQFrc = tokenizer.nextTokenAsDouble();
610	>	sd->setFlucQFrc(flucQFrc);
611	>	break;
612	>	}
613	>	case 'e' : {
614	>
615	>	Vector3d eField;
616	>	eField[0] = tokenizer.nextTokenAsDouble();
617	>	eField[1] = tokenizer.nextTokenAsDouble();
618	>	eField[2] = tokenizer.nextTokenAsDouble();
619	>	sd->setElectricField(eField);
620	>	break;
621	>	}
622	>	case 's' : {
623	>
624	>	RealType sPot;
625	>	sPot = tokenizer.nextTokenAsDouble();
626	>	sd->setSitePotential(sPot);
627	>	break;
628	>	}
629	>	default: {
630	>	sprintf(painCave.errMsg,
631	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
632	>	painCave.isFatal = 1;
633	>	simError();
634	>	break;
635	>	}
636	>	}
637	>	}
638	>	}
639	>
640	>
641	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
642	>
643	>	inputStream.getline(buffer, bufferSize);
644	>	std::string line(buffer);
645	>
646	>	if (line.find("<StuntDoubles>") == std::string::npos) {
647	>	sprintf(painCave.errMsg,
648	>	"DumpReader Error: Missing <StuntDoubles>\n");
649	>	painCave.isFatal = 1;
650	>	simError();
651		}
652
653	<	//read the box mat from the comment line
653	>	while(inputStream.getline(buffer, bufferSize)) {
654	>	line = buffer;
655	>
656	>	if(line.find("</StuntDoubles>") != std::string::npos) {
657	>	break;
658	>	}
659
660	<	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();
660	>	parseDumpLine(line);
661		}
662	+
663	+	}
664
665	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
665	>	void  DumpReader::readSiteData(std::istream& inputStream) {
666
667	<	//parse dump lines
667	>	std::string line(buffer);
668
669	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
669	>	// We already found the starting <SiteData> tag or we wouldn't be
670	>	// here, so just start parsing until we get to the ending
671	>	// </SiteData> tag:
672	>
673	>	while(inputStream.getline(buffer, bufferSize)) {
674	>	line = buffer;
675	>
676	>	if(line.find("</SiteData>") != std::string::npos) {
677	>	break;
678	>	}
679
680	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
681	<	integrableObject = mol->nextIntegrableObject(ii)) {
680	>	parseSiteLine(line);
681	>	}
682	>
683	>	}
684
685	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
685	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
686
687	<	if (eof_test == NULL) {
688	<	sprintf(painCave.errMsg,
689	<	"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);
687	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
688	>	inputStream.getline(buffer, bufferSize);
689	>	std::string line(buffer);
690
691	<	painCave.isFatal = 1;
692	<	simError();
693	<	}
694	<
695	<	parseDumpLine(read_buffer, integrableObject);
325	<
326	<	}
691	>	if (line.find("<FrameData>") == std::string::npos) {
692	>	sprintf(painCave.errMsg,
693	>	"DumpReader Error: Missing <FrameData>\n");
694	>	painCave.isFatal = 1;
695	>	simError();
696		}
697
698	<	// MPI Section of code..........
698	>	while(inputStream.getline(buffer, bufferSize)) {
699	>	line = buffer;
700	>
701	>	if(line.find("</FrameData>") != std::string::npos) {
702	>	break;
703	>	}
704	>
705	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
706	>	if (!tokenizer.hasMoreTokens()) {
707	>	sprintf(painCave.errMsg,
708	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
709	>	painCave.isFatal = 1;
710	>	simError();
711	>	}
712
713	<	#else //IS_MPI
713	>	std::string propertyName = tokenizer.nextToken();
714	>	if (propertyName == "Time") {
715	>	RealType currTime = tokenizer.nextTokenAsDouble();
716	>	s->setTime(currTime);
717	>	} else if (propertyName == "Hmat"){
718	>	Mat3x3d hmat;
719	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
720	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
721	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
722	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
723	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
724	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
725	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
726	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
727	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
728	>	s->setHmat(hmat);
729	>	} else if (propertyName == "Thermostat") {
730	>	pair<RealType, RealType> thermostat;
731	>	thermostat.first = tokenizer.nextTokenAsDouble();
732	>	thermostat.second = tokenizer.nextTokenAsDouble();
733	>	s->setThermostat(thermostat);
734	>	} else if (propertyName == "Barostat") {
735	>	Mat3x3d eta;
736	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
737	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
738	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
739	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
740	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
741	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
742	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
743	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
744	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
745	>	s->setBarostat(eta);
746	>	} else {
747	>	sprintf(painCave.errMsg,
748	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
749	>	painCave.isFatal = 0;
750	>	simError();
751	>	}
752	>
753	>	}
754
755	<	// first thing first, suspend fatalities.
334	<	int masterNode = 0;
335	<	int nCurObj;
336	<	painCave.isEventLoop = 1;
755	>	}
756
757	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
758	<	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
757	>
758	>	}//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.
Revision 2000 by gezelter, Sat May 31 22:35:05 2014 UTC

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