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root/OpenMD/trunk/src/io/DumpReader.cpp

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 274 by tim, Tue Jan 25 21:59:18 2005 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1	>	/*
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42	+
43	+	#define _LARGEFILE_SOURCE64
44	+	#define _FILE_OFFSET_BITS 64
45
46	<	#define _LARGEFILE_SOURCE64
47	<	#define _FILE_OFFSET_BITS 64
46	>	#include <sys/types.h>
47	>	#include <sys/stat.h>
48	>
49	>	#include <iostream>
50	>	#include <math.h>
51	>
52	>	#include <stdio.h>
53	>	#include <stdlib.h>
54	>	#include <string.h>
55	>
56	>	#include "io/DumpReader.hpp"
57	>	#include "primitives/Molecule.hpp"
58	>	#include "utils/simError.h"
59	>	#include "utils/MemoryUtils.hpp"
60	>	#include "utils/StringTokenizer.hpp"
61	>	#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 || 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 <iostream>
245	<	#include <math.h>
244	>	if (needCOMprops_) {
245	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	>	Thermo thermo(info_);
247	>	Vector3d com;
248
249	<	#include <stdio.h>
250	<	#include <stdlib.h>
251	<	#include <string.h>
249	>	if (needPos_ && needVel_) {
250	>	Vector3d comvel;
251	>	Vector3d comw;
252	>	thermo.getComAll(com, comvel);
253	>	comw = thermo.getAngularMomentum();
254	>	} else {
255	>	com = thermo.getCom();
256	>	}
257	>	}
258	>	}
259	>
260	>	void DumpReader::readSet(int whichFrame) {
261	>	std::string line;
262
263	<	#include "io/DumpReader.hpp"
264	<	#include "primitives/Molecule.hpp"
265	<	#include "utils/simError.h"
58	<	#include "utils/MemoryUtils.hpp"
59	<	#include "utils/StringTokenizer.hpp"
263	>	#ifndef IS_MPI
264	>	inFile_->clear();
265	>	inFile_->seekg(framePos_[whichFrame]);
266
267	<	#ifdef IS_MPI
267	>	std::istream& inputStream = *inFile_;
268
269	<	#include <mpi.h>
270	<	#define TAKE_THIS_TAG_CHAR 0
271	<	#define TAKE_THIS_TAG_INT 1
269	>	#else
270	>	int masterNode = 0;
271	>	std::stringstream sstream;
272	>	if (worldRank == masterNode) {
273	>	std::string sendBuffer;
274
275	<	#endif // is_mpi
275	>	inFile_->clear();
276	>	inFile_->seekg(framePos_[whichFrame]);
277	>
278	>	while (inFile_->getline(buffer, bufferSize)) {
279
280	+	line = buffer;
281	+	sendBuffer += line;
282	+	sendBuffer += '\n';
283	+	if (line.find("</Snapshot>") != std::string::npos) {
284	+	break;
285	+	}
286	+	}
287
288	<	namespace oopse {
288	>	int sendBufferSize = sendBuffer.size();
289	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
290	>	MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
291	>	MPI::CHAR, masterNode);
292	>
293	>	sstream.str(sendBuffer);
294	>	} else {
295	>	int sendBufferSize;
296	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
297	>	char * recvBuffer = new char[sendBufferSize+1];
298	>	assert(recvBuffer);
299	>	recvBuffer[sendBufferSize] = '\0';
300	>	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
301	>	sstream.str(recvBuffer);
302	>	delete [] recvBuffer;
303	>	}
304
305	<	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) {
305	>	std::istream& inputStream = sstream;
306		#endif
307
308	<	inFile_ = fopen(filename_.c_str(), "r");
308	>	inputStream.getline(buffer, bufferSize);
309
310	<	if (inFile_ == NULL) {
311	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
312	<	painCave.isFatal = 1;
313	<	simError();
314	<	}
315	<
316	<	#ifdef IS_MPI
310	>	line = buffer;
311	>	if (line.find("<Snapshot>") == std::string::npos) {
312	>	sprintf(painCave.errMsg,
313	>	"DumpReader Error: can not find <Snapshot>\n");
314	>	painCave.isFatal = 1;
315	>	simError();
316	>	}
317	>
318	>	//read frameData
319	>	readFrameProperties(inputStream);
320
321	<	}
321	>	//read StuntDoubles
322	>	readStuntDoubles(inputStream);
323
324	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
325	<	MPIcheckPoint();
324	>	inputStream.getline(buffer, bufferSize);
325	>	line = buffer;
326
327	<	#endif
327	>	if (line.find("<SiteData>") != std::string::npos) {
328	>	//read SiteData
329	>	readSiteData(inputStream);
330	>	} else {
331	>	if (line.find("</Snapshot>") == std::string::npos) {
332	>	sprintf(painCave.errMsg,
333	>	"DumpReader Error: can not find </Snapshot>\n");
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338	>	}
339	>
340	>	void DumpReader::parseDumpLine(const std::string& line) {
341
342	<	return;
343	<	}
342	>
343	>	StringTokenizer tokenizer(line);
344	>	int nTokens;
345	>
346	>	nTokens = tokenizer.countTokens();
347	>
348	>	if (nTokens < 2) {
349	>	sprintf(painCave.errMsg,
350	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
351	>	painCave.isFatal = 1;
352	>	simError();
353	>	}
354
355	<	DumpReader::~DumpReader() {
355	>	int index = tokenizer.nextTokenAsInt();
356	>
357	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
358
359	<	#ifdef IS_MPI
359	>	if (sd == NULL) {
360	>	return;
361	>	}
362	>	std::string type = tokenizer.nextToken();
363	>	int size = type.size();
364
365	<	if (worldRank == 0) {
366	<	#endif
367	<
368	<	int error;
369	<	error = fclose(inFile_);
370	<
371	<	if (error) {
372	<	sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
373	<	painCave.isFatal = 1;
374	<	simError();
365	>	size_t found;
366	>
367	>	if (needPos_) {
368	>	found = type.find("p");
369	>	if (found == std::string::npos) {
370	>	sprintf(painCave.errMsg,
371	>	"DumpReader Error: StuntDouble %d has no Position\n"
372	>	"\tField (\"p\") specified.\n%s\n", index,
373	>	line.c_str());
374	>	painCave.isFatal = 1;
375	>	simError();
376	>	}
377	>	}
378	>
379	>	if (sd->isDirectional()) {
380	>	if (needQuaternion_) {
381	>	found = type.find("q");
382	>	if (found == std::string::npos) {
383	>	sprintf(painCave.errMsg,
384	>	"DumpReader Error: Directional StuntDouble %d has no\n"
385	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
386	>	line.c_str());
387	>	painCave.isFatal = 1;
388	>	simError();
389		}
390	<
116	<	MemoryUtils::deleteVectorOfPointer(framePos_);
117	<
118	<	#ifdef IS_MPI
119	<
390	>	}
391		}
392
393	<	strcpy(checkPointMsg, "Dump file closed successfully.");
394	<	MPIcheckPoint();
393	>	for(int i = 0; i < size; ++i) {
394	>	switch(type[i]) {
395	>
396	>	case 'p': {
397	>	Vector3d pos;
398	>	pos[0] = tokenizer.nextTokenAsDouble();
399	>	pos[1] = tokenizer.nextTokenAsDouble();
400	>	pos[2] = tokenizer.nextTokenAsDouble();
401	>	if (needPos_) {
402	>	sd->setPos(pos);
403	>	}
404	>	break;
405	>	}
406	>	case 'v' : {
407	>	Vector3d vel;
408	>	vel[0] = tokenizer.nextTokenAsDouble();
409	>	vel[1] = tokenizer.nextTokenAsDouble();
410	>	vel[2] = tokenizer.nextTokenAsDouble();
411	>	if (needVel_) {
412	>	sd->setVel(vel);
413	>	}
414	>	break;
415	>	}
416
417	<	#endif
417	>	case 'q' : {
418	>	Quat4d q;
419	>	if (sd->isDirectional()) {
420	>
421	>	q[0] = tokenizer.nextTokenAsDouble();
422	>	q[1] = tokenizer.nextTokenAsDouble();
423	>	q[2] = tokenizer.nextTokenAsDouble();
424	>	q[3] = tokenizer.nextTokenAsDouble();
425	>
426	>	RealType qlen = q.length();
427	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
428	>
429	>	sprintf(painCave.errMsg,
430	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
431	>	painCave.isFatal = 1;
432	>	simError();
433	>
434	>	}
435	>
436	>	q.normalize();
437	>	if (needQuaternion_) {
438	>	sd->setQ(q);
439	>	}
440	>	}
441	>	break;
442	>	}
443	>	case 'j' : {
444	>	Vector3d ji;
445	>	if (sd->isDirectional()) {
446	>	ji[0] = tokenizer.nextTokenAsDouble();
447	>	ji[1] = tokenizer.nextTokenAsDouble();
448	>	ji[2] = tokenizer.nextTokenAsDouble();
449	>	if (needAngMom_) {
450	>	sd->setJ(ji);
451	>	}
452	>	}
453	>	break;
454	>	}
455	>	case 'f': {
456
457	<	return;
458	<	}
457	>	Vector3d force;
458	>	force[0] = tokenizer.nextTokenAsDouble();
459	>	force[1] = tokenizer.nextTokenAsDouble();
460	>	force[2] = tokenizer.nextTokenAsDouble();
461	>	sd->setFrc(force);
462	>	break;
463	>	}
464	>	case 't' : {
465
466	<	int DumpReader::getNFrames(void) {
466	>	Vector3d torque;
467	>	torque[0] = tokenizer.nextTokenAsDouble();
468	>	torque[1] = tokenizer.nextTokenAsDouble();
469	>	torque[2] = tokenizer.nextTokenAsDouble();
470	>	sd->setTrq(torque);
471	>	break;
472	>	}
473	>	case 'u' : {
474
475	<	if (!isScanned_)
476	<	scanFile();
475	>	RealType particlePot;
476	>	particlePot = tokenizer.nextTokenAsDouble();
477	>	sd->setParticlePot(particlePot);
478	>	break;
479	>	}
480	>	case 'c' : {
481
482	<	return nframes_;
483	<	}
482	>	RealType flucQPos;
483	>	flucQPos = tokenizer.nextTokenAsDouble();
484	>	sd->setFlucQPos(flucQPos);
485	>	break;
486	>	}
487	>	case 'w' : {
488
489	<	void DumpReader::scanFile(void) {
490	<	int i, j;
491	<	int lineNum = 0;
492	<	char readBuffer[maxBufferSize];
493	<	fpos_t * currPos;
489	>	RealType flucQVel;
490	>	flucQVel = tokenizer.nextTokenAsDouble();
491	>	sd->setFlucQVel(flucQVel);
492	>	break;
493	>	}
494	>	case 'g' : {
495
496	<	#ifdef IS_MPI
497	<
498	<	if (worldRank == 0) {
499	<	#endif // is_mpi
148	<
149	<	rewind(inFile_);
150	<
151	<	currPos = new fpos_t;
152	<	fgetpos(inFile_, currPos);
153	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
154	<	lineNum++;
155	<
156	<	if (feof(inFile_)) {
157	<	sprintf(painCave.errMsg,
158	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
159	<	filename_.c_str(),
160	<	lineNum);
161	<	painCave.isFatal = 1;
162	<	simError();
496	>	RealType flucQFrc;
497	>	flucQFrc = tokenizer.nextTokenAsDouble();
498	>	sd->setFlucQFrc(flucQFrc);
499	>	break;
500		}
501	+	case 'e' : {
502
503	<	while (!feof(inFile_)) {
504	<	framePos_.push_back(currPos);
505	<
506	<	i = atoi(readBuffer);
507	<
508	<	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++;
503	>	Vector3d eField;
504	>	eField[0] = tokenizer.nextTokenAsDouble();
505	>	eField[1] = tokenizer.nextTokenAsDouble();
506	>	eField[2] = tokenizer.nextTokenAsDouble();
507	>	sd->setElectricField(eField);
508	>	break;
509		}
510	+	default: {
511	+	sprintf(painCave.errMsg,
512	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
513	+	painCave.isFatal = 1;
514	+	simError();
515	+	break;
516	+	}
517
518	<	delete currPos;
205	<	rewind(inFile_);
206	<
207	<	nframes_ = framePos_.size();
208	<	#ifdef IS_MPI
518	>	}
519		}
520	+
521	+	}
522	+
523
524	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
524	>	void DumpReader::parseSiteLine(const std::string& line) {
525
526	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
527	<	MPIcheckPoint();
526	>	StringTokenizer tokenizer(line);
527	>	int nTokens;
528	>
529	>	nTokens = tokenizer.countTokens();
530	>
531	>	if (nTokens < 2) {
532	>	sprintf(painCave.errMsg,
533	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
534	>	painCave.isFatal = 1;
535	>	simError();
536	>	}
537
538	<	#endif // is_mpi
538	>	/**
539	>	* The first token is the global integrable object index.
540	>	*/
541
542	<	isScanned_ = true;
543	<	}
542	>	int index = tokenizer.nextTokenAsInt();
543	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
544	>	if (sd == NULL) {
545	>	return;
546	>	}
547
548	<	void DumpReader::readFrame(int whichFrame) {
549	<	readSet(whichFrame);
550	<	}
548	>	/**
549	>	* Test to see if the next token is an integer or not.  If not,
550	>	* we've got data on the integrable object itself.  If there is an
551	>	* integer, we're parsing data for a site on a rigid body.
552	>	*/
553
554	<	void DumpReader::readSet(int whichFrame) {
555	<	int i;
556	<	int nTotObjs;                  // the number of atoms
557	<	char read_buffer[maxBufferSize];  //the line buffer for reading
558	<	char * eof_test;               // ptr to see when we reach the end of the file
554	>	std::string indexTest = tokenizer.peekNextToken();
555	>	std::istringstream i(indexTest);
556	>	int siteIndex;
557	>	if (i >> siteIndex) {
558	>	// chew up this token and parse as an int:
559	>	siteIndex = tokenizer.nextTokenAsInt();
560	>	RigidBody* rb = static_cast<RigidBody*>(sd);
561	>	sd = rb->getAtoms()[siteIndex];
562	>	}
563
564	<	Molecule* mol;
565	<	StuntDouble* integrableObject;
566	<	SimInfo::MoleculeIterator mi;
567	<	Molecule::IntegrableObjectIterator ii;
564	>	/**
565	>	* The next token contains information on what follows.
566	>	*/
567	>	std::string type = tokenizer.nextToken();
568	>	int size = type.size();
569	>
570	>	for(int i = 0; i < size; ++i) {
571	>	switch(type[i]) {
572	>
573	>	case 'u' : {
574	>
575	>	RealType particlePot;
576	>	particlePot = tokenizer.nextTokenAsDouble();
577	>	sd->setParticlePot(particlePot);
578	>	break;
579	>	}
580	>	case 'c' : {
581	>
582	>	RealType flucQPos;
583	>	flucQPos = tokenizer.nextTokenAsDouble();
584	>	sd->setFlucQPos(flucQPos);
585	>	break;
586	>	}
587	>	case 'w' : {
588	>
589	>	RealType flucQVel;
590	>	flucQVel = tokenizer.nextTokenAsDouble();
591	>	sd->setFlucQVel(flucQVel);
592	>	break;
593	>	}
594	>	case 'g' : {
595	>
596	>	RealType flucQFrc;
597	>	flucQFrc = tokenizer.nextTokenAsDouble();
598	>	sd->setFlucQFrc(flucQFrc);
599	>	break;
600	>	}
601	>	case 'e' : {
602	>
603	>	Vector3d eField;
604	>	eField[0] = tokenizer.nextTokenAsDouble();
605	>	eField[1] = tokenizer.nextTokenAsDouble();
606	>	eField[2] = tokenizer.nextTokenAsDouble();
607	>	sd->setElectricField(eField);
608	>	break;
609	>	}
610	>	default: {
611	>	sprintf(painCave.errMsg,
612	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
613	>	painCave.isFatal = 1;
614	>	simError();
615	>	break;
616	>	}
617	>	}
618	>	}
619	>	}
620	>
621	>
622	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
623	>
624	>	inputStream.getline(buffer, bufferSize);
625	>	std::string line(buffer);
626	>
627	>	if (line.find("<StuntDoubles>") == std::string::npos) {
628	>	sprintf(painCave.errMsg,
629	>	"DumpReader Error: Missing <StuntDoubles>\n");
630	>	painCave.isFatal = 1;
631	>	simError();
632	>	}
633
634	<	#ifndef IS_MPI
634	>	while(inputStream.getline(buffer, bufferSize)) {
635	>	line = buffer;
636	>
637	>	if(line.find("</StuntDoubles>") != std::string::npos) {
638	>	break;
639	>	}
640
641	<	fsetpos(inFile_, framePos_[whichFrame]);
239	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
240	<
241	<	if (eof_test == NULL) {
242	<	sprintf(painCave.errMsg,
243	<	"DumpReader error: error reading 1st line of \"%s\"\n",
244	<	filename_.c_str());
245	<	painCave.isFatal = 1;
246	<	simError();
641	>	parseDumpLine(line);
642		}
643	+
644	+	}
645
646	<	nTotObjs = atoi(read_buffer);
646	>	void  DumpReader::readSiteData(std::istream& inputStream) {
647
648	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
649	<	sprintf(painCave.errMsg,
650	<	"DumpReader error. %s nIntegrable, %d, "
651	<	"does not match the meta-data file's nIntegrable, %d.\n",
652	<	filename_.c_str(),
653	<	nTotObjs,
257	<	info_->getNGlobalIntegrableObjects());
258	<
259	<	painCave.isFatal = 1;
260	<	simError();
648	>	inputStream.getline(buffer, bufferSize);
649	>	std::string line(buffer);
650	>
651	>	if (line.find("<SiteData>") == std::string::npos) {
652	>	// site data isn't required for a simulation, so skip
653	>	return;
654		}
655
656	<	//read the box mat from the comment line
656	>	while(inputStream.getline(buffer, bufferSize)) {
657	>	line = buffer;
658	>
659	>	if(line.find("</SiteData>") != std::string::npos) {
660	>	break;
661	>	}
662
663	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
266	<
267	<	if (eof_test == NULL) {
268	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
269	<	filename_.c_str());
270	<	painCave.isFatal = 1;
271	<	simError();
663	>	parseSiteLine(line);
664		}
665	+
666	+	}
667
668	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
668	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
669
670	<	//parse dump lines
670	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
671	>	inputStream.getline(buffer, bufferSize);
672	>	std::string line(buffer);
673
674	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
674	>	if (line.find("<FrameData>") == std::string::npos) {
675	>	sprintf(painCave.errMsg,
676	>	"DumpReader Error: Missing <FrameData>\n");
677	>	painCave.isFatal = 1;
678	>	simError();
679	>	}
680
681	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
682	<	integrableObject = mol->nextIntegrableObject(ii)) {
681	>	while(inputStream.getline(buffer, bufferSize)) {
682	>	line = buffer;
683	>
684	>	if(line.find("</FrameData>") != std::string::npos) {
685	>	break;
686	>	}
687	>
688	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
689	>	if (!tokenizer.hasMoreTokens()) {
690	>	sprintf(painCave.errMsg,
691	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
692	>	painCave.isFatal = 1;
693	>	simError();
694	>	}
695
696	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
697	<
698	<	if (eof_test == NULL) {
699	<	sprintf(painCave.errMsg,
700	<	"DumpReader Error: error in reading file %s\n"
701	<	"natoms  = %d; index = %d\n"
702	<	"error reading the line from the file.\n",
703	<	filename_.c_str(),
704	<	nTotObjs,
705	<	i);
706	<
707	<	painCave.isFatal = 1;
708	<	simError();
709	<	}
710	<
711	<	parseDumpLine(read_buffer, integrableObject);
712	<
713	<	}
696	>	std::string propertyName = tokenizer.nextToken();
697	>	if (propertyName == "Time") {
698	>	RealType currTime = tokenizer.nextTokenAsDouble();
699	>	s->setTime(currTime);
700	>	} else if (propertyName == "Hmat"){
701	>	Mat3x3d hmat;
702	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
703	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
704	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
705	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
706	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
707	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
708	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
709	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
710	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
711	>	s->setHmat(hmat);
712	>	} else if (propertyName == "Thermostat") {
713	>	pair<RealType, RealType> thermostat;
714	>	thermostat.first = tokenizer.nextTokenAsDouble();
715	>	thermostat.second = tokenizer.nextTokenAsDouble();
716	>	s->setThermostat(thermostat);
717	>	} else if (propertyName == "Barostat") {
718	>	Mat3x3d eta;
719	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
720	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
721	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
722	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
723	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
724	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
725	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
726	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
727	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
728	>	s->setBarostat(eta);
729	>	} else {
730	>	sprintf(painCave.errMsg,
731	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
732	>	painCave.isFatal = 0;
733	>	simError();
734	>	}
735	>
736		}
737
738	<	// MPI Section of code..........
304	<
305	<	#else //IS_MPI
306	<
307	<	// first thing first, suspend fatalities.
308	<	int masterNode = 0;
309	<	int nCurObj;
310	<	painCave.isEventLoop = 1;
311	<
312	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
313	<	int haveError;
314	<
315	<	MPI_Status istatus;
316	<	int nitems;
317	<
318	<	nTotObjs = info_->getNGlobalIntegrableObjects();
319	<	haveError = 0;
320	<
321	<	if (worldRank == masterNode) {
322	<	fsetpos(inFile_, framePos_[whichFrame]);
323	<
324	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
325	<
326	<	if (eof_test == NULL) {
327	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
328	<	filename_.c_str());
329	<	painCave.isFatal = 1;
330	<	simError();
331	<	}
738	>	}
739
740	<	nitems = atoi(read_buffer);
741	<
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, "DumpReader Error: 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, "DumpReader Error: 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	<	"DumpReader Error: 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	<	"DumpReader Error: 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, "DumpReader Error: 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	<	"DumpReader Error: 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	<	sprintf(painCave.errMsg,
498	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
499	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
500	<	painCave.isFatal = 1;
501	<	simError();
502	<	}
503	<
504	<	pos[0] = tokenizer.nextTokenAsDouble();
505	<	pos[1] = tokenizer.nextTokenAsDouble();
506	<	pos[2] = tokenizer.nextTokenAsDouble();
507	<	integrableObject->setPos(pos);
508	<
509	<	vel[0] = tokenizer.nextTokenAsDouble();
510	<	vel[1] = tokenizer.nextTokenAsDouble();
511	<	vel[2] = tokenizer.nextTokenAsDouble();
512	<	integrableObject->setVel(vel);
513	<
514	<	if (integrableObject->isDirectional()) {
515	<
516	<	q[0] = tokenizer.nextTokenAsDouble();
517	<	q[1] = tokenizer.nextTokenAsDouble();
518	<	q[2] = tokenizer.nextTokenAsDouble();
519	<	q[3] = tokenizer.nextTokenAsDouble();
520	<
521	<	double qlen = q.length();
522	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
523	<
524	<	sprintf(painCave.errMsg,
525	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
526	<	painCave.isFatal = 1;
527	<	simError();
528	<
529	<	}
530	<
531	<	q.normalize();
532	<
533	<	integrableObject->setQ(q);
534	<
535	<	ji[0] = tokenizer.nextTokenAsDouble();
536	<	ji[1] = tokenizer.nextTokenAsDouble();
537	<	ji[2] = tokenizer.nextTokenAsDouble();
538	<	integrableObject->setJ(ji);
539	<	}
540	<
541	<	}
542	<
543	<
544	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
545	<	double currTime;
546	<	Mat3x3d hmat;
547	<	double chi;
548	<	double integralOfChiDt;
549	<	Mat3x3d eta;
550	<
551	<	StringTokenizer tokenizer(line);
552	<	int nTokens;
553	<
554	<	nTokens = tokenizer.countTokens();
555	<
556	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
557	<	if (nTokens < 10) {
558	<	sprintf(painCave.errMsg,
559	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
560	<	painCave.isFatal = 1;
561	<	simError();
562	<	}
563	<
564	<	//read current time
565	<	currTime = tokenizer.nextTokenAsDouble();
566	<	s->setTime(currTime);
567	<
568	<	//read h-matrix
569	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
570	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
571	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
572	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
573	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
574	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
575	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
576	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
577	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
578	<	s->setHmat(hmat);
579	<
580	<	//read chi and integrablOfChidt, they should apprear in pair
581	<	if (tokenizer.countTokens() >= 2) {
582	<	chi = tokenizer.nextTokenAsDouble();
583	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
584	<
585	<	s->setChi(chi);
586	<	s->setIntegralOfChiDt(integralOfChiDt);
587	<	}
588	<
589	<	//read eta (eta is 3x3 matrix)
590	<	if (tokenizer.countTokens() >= 9) {
591	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
592	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
593	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
594	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
595	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
596	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
597	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
598	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
599	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
600	<
601	<	s->setEta(eta);
602	<	}
603	<
604	<
605	<	}
606	<
607	<	}//end namespace oopse
740	>
741	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpReader.cpp (property svn:keywords):
Revision 274 by tim, Tue Jan 25 21:59:18 2005 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

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