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

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 381 by tim, Tue Mar 1 14:45:45 2005 UTC vs.
Revision 1790 by gezelter, Thu Aug 30 17:18:22 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	>	bool foundOpenSiteDataTag = false;
145	>	while(inFile_->getline(buffer, bufferSize)) {
146	>	++lineNo;
147	>
148	>	std::string line = buffer;
149	>	currPos = inFile_->tellg();
150	>	if (line.find("<Snapshot>")!= std::string::npos) {
151	>	if (foundOpenSnapshotTag) {
152	>	sprintf(painCave.errMsg,
153	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154	>	filename_.c_str());
155	>	painCave.isFatal = 1;
156	>	simError();
157	>	}
158	>	foundOpenSnapshotTag = true;
159	>	foundClosedSnapshotTag = false;
160	>	framePos_.push_back(prevPos);
161	>
162	>	} else if (line.find("</Snapshot>") != std::string::npos){
163	>	if (!foundOpenSnapshotTag) {
164	>	sprintf(painCave.errMsg,
165	>	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
166	>	filename_.c_str());
167	>	painCave.isFatal = 1;
168	>	simError();
169	>	}
170	>
171	>	if (foundClosedSnapshotTag) {
172	>	sprintf(painCave.errMsg,
173	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
174	>	filename_.c_str());
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	foundClosedSnapshotTag = true;
179	>	foundOpenSnapshotTag = false;
180	>	}
181	>	prevPos = currPos;
182	>	}
183	>
184	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
185	>	// it and give a warning message
186	>	if (foundOpenSnapshotTag) {
187	>	sprintf(painCave.errMsg,
188	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
189	>	painCave.isFatal = 0;
190	>	simError();
191	>	framePos_.pop_back();
192	>	}
193	>
194	>	nframes_ = framePos_.size();
195	>
196	>	if (nframes_ == 0) {
197	>	sprintf(painCave.errMsg,
198	>	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
199	>	painCave.isFatal = 1;
200	>	simError();
201	>	}
202	>	#ifdef IS_MPI
203	>	}
204	>
205	>	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206	>
207	>	#endif // is_mpi
208	>
209	>	isScanned_ = true;
210	>	}
211	>
212	>	void DumpReader::readFrame(int whichFrame) {
213	>	if (!isScanned_)
214	>	scanFile();
215	>
216	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
217	>
218	>	if (storageLayout & DataStorage::dslPosition) {
219	>	needPos_ = true;
220	>	} else {
221	>	needPos_ = false;
222	>	}
223	>
224	>	if (storageLayout & DataStorage::dslVelocity) {
225	>	needVel_ = true;
226	>	} else {
227	>	needVel_ = false;
228	>	}
229	>
230	>	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
231	>	needQuaternion_ = true;
232	>	} else {
233	>	needQuaternion_ = false;
234	>	}
235	>
236	>	if (storageLayout & DataStorage::dslAngularMomentum) {
237	>	needAngMom_ = true;
238	>	} else {
239	>	needAngMom_ = false;
240	>	}
241	>
242	>	readSet(whichFrame);
243
244	<	#include <sys/types.h>
245	<	#include <sys/stat.h>
244	>	if (needCOMprops_) {
245	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	>	Thermo thermo(info_);
247	>	Vector3d com;
248
249	<	#include <iostream>
250	<	#include <math.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 <stdio.h>
264	<	#include <stdlib.h>
265	<	#include <string.h>
263	>	#ifndef IS_MPI
264	>	inFile_->clear();
265	>	inFile_->seekg(framePos_[whichFrame]);
266
267	<	#include "io/DumpReader.hpp"
56	<	#include "primitives/Molecule.hpp"
57	<	#include "utils/simError.h"
58	<	#include "utils/MemoryUtils.hpp"
59	<	#include "utils/StringTokenizer.hpp"
267	>	std::istream& inputStream = *inFile_;
268
269	<	#ifdef IS_MPI
269	>	#else
270	>	int masterNode = 0;
271	>	std::stringstream sstream;
272	>	if (worldRank == masterNode) {
273	>	std::string sendBuffer;
274
275	<	#include <mpi.h>
276	<	#define TAKE_THIS_TAG_CHAR 0
277	<	#define TAKE_THIS_TAG_INT 1
275	>	inFile_->clear();
276	>	inFile_->seekg(framePos_[whichFrame]);
277	>
278	>	while (inFile_->getline(buffer, bufferSize)) {
279
280	<	#endif // is_mpi
280	>	line = buffer;
281	>	sendBuffer += line;
282	>	sendBuffer += '\n';
283	>	if (line.find("</Snapshot>") != std::string::npos) {
284	>	break;
285	>	}
286	>	}
287
288	+	int sendBufferSize = sendBuffer.size();
289	+	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
290	+	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
291	+
292	+	sstream.str(sendBuffer);
293	+	} else {
294	+	int sendBufferSize;
295	+	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
296	+	char * recvBuffer = new char[sendBufferSize+1];
297	+	assert(recvBuffer);
298	+	recvBuffer[sendBufferSize] = '\0';
299	+	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
300	+	sstream.str(recvBuffer);
301	+	delete [] recvBuffer;
302	+	}
303
304	<	namespace oopse {
71	<
72	<	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) {
304	>	std::istream& inputStream = sstream;
305		#endif
306
307	<	inFile_ = fopen(filename_.c_str(), "r");
307	>	inputStream.getline(buffer, bufferSize);
308
309	<	if (inFile_ == NULL) {
310	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
311	<	painCave.isFatal = 1;
312	<	simError();
313	<	}
314	<
315	<	#ifdef IS_MPI
309	>	line = buffer;
310	>	if (line.find("<Snapshot>") == std::string::npos) {
311	>	sprintf(painCave.errMsg,
312	>	"DumpReader Error: can not find <Snapshot>\n");
313	>	painCave.isFatal = 1;
314	>	simError();
315	>	}
316	>
317	>	//read frameData
318	>	readFrameProperties(inputStream);
319
320	<	}
320	>	//read StuntDoubles
321	>	readStuntDoubles(inputStream);
322
323	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
324	<	MPIcheckPoint();
323	>	inputStream.getline(buffer, bufferSize);
324	>	line = buffer;
325
326	<	#endif
326	>	if (line.find("<SiteData>") != std::string::npos) {
327	>	//read SiteData
328	>	readSiteData(inputStream);
329	>	} else {
330	>	if (line.find("</Snapshot>") == std::string::npos) {
331	>	sprintf(painCave.errMsg,
332	>	"DumpReader Error: can not find </Snapshot>\n");
333	>	painCave.isFatal = 1;
334	>	simError();
335	>	}
336	>	}
337	>	}
338	>
339	>	void DumpReader::parseDumpLine(const std::string& line) {
340
341	<	return;
342	<	}
341	>
342	>	StringTokenizer tokenizer(line);
343	>	int nTokens;
344	>
345	>	nTokens = tokenizer.countTokens();
346	>
347	>	if (nTokens < 2) {
348	>	sprintf(painCave.errMsg,
349	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
350	>	painCave.isFatal = 1;
351	>	simError();
352	>	}
353
354	<	DumpReader::~DumpReader() {
354	>	int index = tokenizer.nextTokenAsInt();
355	>
356	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
357
358	<	#ifdef IS_MPI
358	>	if (sd == NULL) {
359	>	return;
360	>	}
361	>	std::string type = tokenizer.nextToken();
362	>	int size = type.size();
363
364	<	if (worldRank == 0) {
365	<	#endif
366	<
367	<	int error;
368	<	error = fclose(inFile_);
369	<
370	<	if (error) {
371	<	sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
372	<	painCave.isFatal = 1;
373	<	simError();
364	>	size_t found;
365	>
366	>	if (needPos_) {
367	>	found = type.find("p");
368	>	if (found == std::string::npos) {
369	>	sprintf(painCave.errMsg,
370	>	"DumpReader Error: StuntDouble %d has no Position\n"
371	>	"\tField (\"p\") specified.\n%s\n", index,
372	>	line.c_str());
373	>	painCave.isFatal = 1;
374	>	simError();
375	>	}
376	>	}
377	>
378	>	if (sd->isDirectional()) {
379	>	if (needQuaternion_) {
380	>	found = type.find("q");
381	>	if (found == std::string::npos) {
382	>	sprintf(painCave.errMsg,
383	>	"DumpReader Error: Directional StuntDouble %d has no\n"
384	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
385	>	line.c_str());
386	>	painCave.isFatal = 1;
387	>	simError();
388		}
389	<
116	<	MemoryUtils::deleteVectorOfPointer(framePos_);
117	<
118	<	#ifdef IS_MPI
119	<
389	>	}
390		}
391
392	<	strcpy(checkPointMsg, "Dump file closed successfully.");
393	<	MPIcheckPoint();
392	>	for(int i = 0; i < size; ++i) {
393	>	switch(type[i]) {
394	>
395	>	case 'p': {
396	>	Vector3d pos;
397	>	pos[0] = tokenizer.nextTokenAsDouble();
398	>	pos[1] = tokenizer.nextTokenAsDouble();
399	>	pos[2] = tokenizer.nextTokenAsDouble();
400	>	if (needPos_) {
401	>	sd->setPos(pos);
402	>	}
403	>	break;
404	>	}
405	>	case 'v' : {
406	>	Vector3d vel;
407	>	vel[0] = tokenizer.nextTokenAsDouble();
408	>	vel[1] = tokenizer.nextTokenAsDouble();
409	>	vel[2] = tokenizer.nextTokenAsDouble();
410	>	if (needVel_) {
411	>	sd->setVel(vel);
412	>	}
413	>	break;
414	>	}
415
416	<	#endif
416	>	case 'q' : {
417	>	Quat4d q;
418	>	if (sd->isDirectional()) {
419	>
420	>	q[0] = tokenizer.nextTokenAsDouble();
421	>	q[1] = tokenizer.nextTokenAsDouble();
422	>	q[2] = tokenizer.nextTokenAsDouble();
423	>	q[3] = tokenizer.nextTokenAsDouble();
424	>
425	>	RealType qlen = q.length();
426	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
427	>
428	>	sprintf(painCave.errMsg,
429	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
430	>	painCave.isFatal = 1;
431	>	simError();
432	>
433	>	}
434	>
435	>	q.normalize();
436	>	if (needQuaternion_) {
437	>	sd->setQ(q);
438	>	}
439	>	}
440	>	break;
441	>	}
442	>	case 'j' : {
443	>	Vector3d ji;
444	>	if (sd->isDirectional()) {
445	>	ji[0] = tokenizer.nextTokenAsDouble();
446	>	ji[1] = tokenizer.nextTokenAsDouble();
447	>	ji[2] = tokenizer.nextTokenAsDouble();
448	>	if (needAngMom_) {
449	>	sd->setJ(ji);
450	>	}
451	>	}
452	>	break;
453	>	}
454	>	case 'f': {
455
456	<	return;
457	<	}
456	>	Vector3d force;
457	>	force[0] = tokenizer.nextTokenAsDouble();
458	>	force[1] = tokenizer.nextTokenAsDouble();
459	>	force[2] = tokenizer.nextTokenAsDouble();
460	>	sd->setFrc(force);
461	>	break;
462	>	}
463	>	case 't' : {
464
465	<	int DumpReader::getNFrames(void) {
465	>	Vector3d torque;
466	>	torque[0] = tokenizer.nextTokenAsDouble();
467	>	torque[1] = tokenizer.nextTokenAsDouble();
468	>	torque[2] = tokenizer.nextTokenAsDouble();
469	>	sd->setTrq(torque);
470	>	break;
471	>	}
472	>	case 'u' : {
473
474	<	if (!isScanned_)
475	<	scanFile();
474	>	RealType particlePot;
475	>	particlePot = tokenizer.nextTokenAsDouble();
476	>	sd->setParticlePot(particlePot);
477	>	break;
478	>	}
479	>	case 'c' : {
480
481	<	return nframes_;
482	<	}
481	>	RealType flucQPos;
482	>	flucQPos = tokenizer.nextTokenAsDouble();
483	>	sd->setFlucQPos(flucQPos);
484	>	break;
485	>	}
486	>	case 'w' : {
487
488	<	void DumpReader::scanFile(void) {
489	<	int i, j;
490	<	int lineNum = 0;
491	<	char readBuffer[maxBufferSize];
492	<	fpos_t * currPos;
488	>	RealType flucQVel;
489	>	flucQVel = tokenizer.nextTokenAsDouble();
490	>	sd->setFlucQVel(flucQVel);
491	>	break;
492	>	}
493	>	case 'g' : {
494
495	<	#ifdef IS_MPI
496	<
497	<	if (worldRank == 0) {
498	<	#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();
495	>	RealType flucQFrc;
496	>	flucQFrc = tokenizer.nextTokenAsDouble();
497	>	sd->setFlucQFrc(flucQFrc);
498	>	break;
499		}
500	+	case 'e' : {
501
502	<	while (!feof(inFile_)) {
503	<	framePos_.push_back(currPos);
504	<
505	<	i = atoi(readBuffer);
506	<
507	<	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++;
502	>	Vector3d eField;
503	>	eField[0] = tokenizer.nextTokenAsDouble();
504	>	eField[1] = tokenizer.nextTokenAsDouble();
505	>	eField[2] = tokenizer.nextTokenAsDouble();
506	>	sd->setElectricField(eField);
507	>	break;
508		}
509	+	default: {
510	+	sprintf(painCave.errMsg,
511	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
512	+	painCave.isFatal = 1;
513	+	simError();
514	+	break;
515	+	}
516
517	<	delete currPos;
205	<	rewind(inFile_);
206	<
207	<	nframes_ = framePos_.size();
208	<	#ifdef IS_MPI
517	>	}
518		}
519	+
520	+	}
521	+
522
523	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
523	>	void DumpReader::parseSiteLine(const std::string& line) {
524
525	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
526	<	MPIcheckPoint();
527	<
528	<	#endif // is_mpi
529	<
530	<	isScanned_ = true;
531	<	}
532	<
533	<	void DumpReader::readFrame(int whichFrame) {
534	<	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
525	>	StringTokenizer tokenizer(line);
526	>	int nTokens;
527	>
528	>	nTokens = tokenizer.countTokens();
529	>
530	>	if (nTokens < 2) {
531	>	sprintf(painCave.errMsg,
532	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
533	>	painCave.isFatal = 1;
534	>	simError();
535	>	}
536
537	<	if (storageLayout & DataStorage::dslPosition) {
538	<	needPos_ = true;
539	<	} else {
227	<	needPos_ = false;
228	<	}
537	>	/**
538	>	* The first token is the global integrable object index.
539	>	*/
540
541	<	if (storageLayout & DataStorage::dslVelocity) {
542	<	needVel_ = true;
543	<	} else {
544	<	needVel_ = false;
541	>	int index = tokenizer.nextTokenAsInt();
542	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
543	>	if (sd == NULL) {
544	>	return;
545		}
546
547	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
548	<	needQuaternion_ = true;
549	<	} else {
550	<	needQuaternion_ = false;
547	>	/**
548	>	* Test to see if the next token is an integer or not.  If not,
549	>	* we've got data on the integrable object itself.  If there is an
550	>	* integer, we're parsing data for a site on a rigid body.
551	>	*/
552	>
553	>	std::string indexTest = tokenizer.peekNextToken();
554	>	std::istringstream i(indexTest);
555	>	int siteIndex;
556	>	if (i >> siteIndex) {
557	>	// chew up this token and parse as an int:
558	>	siteIndex = tokenizer.nextTokenAsInt();
559	>	RigidBody* rb = static_cast<RigidBody*>(sd);
560	>	sd = rb->getAtoms()[siteIndex];
561		}
562
563	<	if (storageLayout & DataStorage::dslAngularMomentum) {
564	<	needAngMom_ = true;
565	<	} else {
566	<	needAngMom_ = false;
563	>	/**
564	>	* The next token contains information on what follows.
565	>	*/
566	>	std::string type = tokenizer.nextToken();
567	>	int size = type.size();
568	>
569	>	for(int i = 0; i < size; ++i) {
570	>	switch(type[i]) {
571	>
572	>	case 'u' : {
573	>
574	>	RealType particlePot;
575	>	particlePot = tokenizer.nextTokenAsDouble();
576	>	sd->setParticlePot(particlePot);
577	>	break;
578	>	}
579	>	case 'c' : {
580	>
581	>	RealType flucQPos;
582	>	flucQPos = tokenizer.nextTokenAsDouble();
583	>	sd->setFlucQPos(flucQPos);
584	>	break;
585	>	}
586	>	case 'w' : {
587	>
588	>	RealType flucQVel;
589	>	flucQVel = tokenizer.nextTokenAsDouble();
590	>	sd->setFlucQVel(flucQVel);
591	>	break;
592	>	}
593	>	case 'g' : {
594	>
595	>	RealType flucQFrc;
596	>	flucQFrc = tokenizer.nextTokenAsDouble();
597	>	sd->setFlucQFrc(flucQFrc);
598	>	break;
599	>	}
600	>	case 'e' : {
601	>
602	>	Vector3d eField;
603	>	eField[0] = tokenizer.nextTokenAsDouble();
604	>	eField[1] = tokenizer.nextTokenAsDouble();
605	>	eField[2] = tokenizer.nextTokenAsDouble();
606	>	sd->setElectricField(eField);
607	>	break;
608	>	}
609	>	default: {
610	>	sprintf(painCave.errMsg,
611	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
612	>	painCave.isFatal = 1;
613	>	simError();
614	>	break;
615	>	}
616	>	}
617	>	}
618	>	}
619	>
620	>
621	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
622	>
623	>	inputStream.getline(buffer, bufferSize);
624	>	std::string line(buffer);
625	>
626	>	if (line.find("<StuntDoubles>") == std::string::npos) {
627	>	sprintf(painCave.errMsg,
628	>	"DumpReader Error: Missing <StuntDoubles>\n");
629	>	painCave.isFatal = 1;
630	>	simError();
631		}
632
633	<	readSet(whichFrame);
634	<	}
633	>	while(inputStream.getline(buffer, bufferSize)) {
634	>	line = buffer;
635	>
636	>	if(line.find("</StuntDoubles>") != std::string::npos) {
637	>	break;
638	>	}
639
640	<	void DumpReader::readSet(int whichFrame) {
641	<	int i;
642	<	int nTotObjs;                  // the number of atoms
643	<	char read_buffer[maxBufferSize];  //the line buffer for reading
255	<	char * eof_test;               // ptr to see when we reach the end of the file
640	>	parseDumpLine(line);
641	>	}
642	>
643	>	}
644
645	<	Molecule* mol;
258	<	StuntDouble* integrableObject;
259	<	SimInfo::MoleculeIterator mi;
260	<	Molecule::IntegrableObjectIterator ii;
645	>	void  DumpReader::readSiteData(std::istream& inputStream) {
646
647	<	#ifndef IS_MPI
648	<
649	<	fsetpos(inFile_, framePos_[whichFrame]);
650	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
651	<
652	<	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();
647	>	inputStream.getline(buffer, bufferSize);
648	>	std::string line(buffer);
649	>
650	>	if (line.find("<SiteData>") == std::string::npos) {
651	>	// site data isn't required for a simulation, so skip
652	>	return;
653		}
654
655	<	nTotObjs = atoi(read_buffer);
655	>	while(inputStream.getline(buffer, bufferSize)) {
656	>	line = buffer;
657	>
658	>	if(line.find("</SiteData>") != std::string::npos) {
659	>	break;
660	>	}
661
662	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
278	<	sprintf(painCave.errMsg,
279	<	"DumpReader error. %s nIntegrable, %d, "
280	<	"does not match the meta-data file's nIntegrable, %d.\n",
281	<	filename_.c_str(),
282	<	nTotObjs,
283	<	info_->getNGlobalIntegrableObjects());
284	<
285	<	painCave.isFatal = 1;
286	<	simError();
662	>	parseSiteLine(line);
663		}
664	+
665	+	}
666
667	<	//read the box mat from the comment line
667	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
668
669	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
669	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
670	>	inputStream.getline(buffer, bufferSize);
671	>	std::string line(buffer);
672
673	<	if (eof_test == NULL) {
674	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
675	<	filename_.c_str());
676	<	painCave.isFatal = 1;
677	<	simError();
673	>	if (line.find("<FrameData>") == std::string::npos) {
674	>	sprintf(painCave.errMsg,
675	>	"DumpReader Error: Missing <FrameData>\n");
676	>	painCave.isFatal = 1;
677	>	simError();
678		}
679
680	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
680	>	while(inputStream.getline(buffer, bufferSize)) {
681	>	line = buffer;
682	>
683	>	if(line.find("</FrameData>") != std::string::npos) {
684	>	break;
685	>	}
686	>
687	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
688	>	if (!tokenizer.hasMoreTokens()) {
689	>	sprintf(painCave.errMsg,
690	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
691	>	painCave.isFatal = 1;
692	>	simError();
693	>	}
694
695	<	//parse dump lines
696	<
697	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
698	<
699	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
700	<	integrableObject = mol->nextIntegrableObject(ii)) {
701	<
702	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
703	<
704	<	if (eof_test == NULL) {
705	<	sprintf(painCave.errMsg,
706	<	"DumpReader Error: error in reading file %s\n"
707	<	"natoms  = %d; index = %d\n"
708	<	"error reading the line from the file.\n",
709	<	filename_.c_str(),
710	<	nTotObjs,
711	<	i);
712	<
713	<	painCave.isFatal = 1;
714	<	simError();
715	<	}
716	<
717	<	parseDumpLine(read_buffer, integrableObject);
718	<
719	<	}
695	>	std::string propertyName = tokenizer.nextToken();
696	>	if (propertyName == "Time") {
697	>	RealType currTime = tokenizer.nextTokenAsDouble();
698	>	s->setTime(currTime);
699	>	} else if (propertyName == "Hmat"){
700	>	Mat3x3d hmat;
701	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
702	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
703	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
704	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
705	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
706	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
707	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
708	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
709	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
710	>	s->setHmat(hmat);
711	>	} else if (propertyName == "Thermostat") {
712	>	pair<RealType, RealType> thermostat;
713	>	thermostat.first = tokenizer.nextTokenAsDouble();
714	>	thermostat.second = tokenizer.nextTokenAsDouble();
715	>	s->setThermostat(thermostat);
716	>	} else if (propertyName == "Barostat") {
717	>	Mat3x3d eta;
718	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
719	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
720	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
721	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
722	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
723	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
724	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
725	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
726	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
727	>	s->setBarostat(eta);
728	>	} else {
729	>	sprintf(painCave.errMsg,
730	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
731	>	painCave.isFatal = 0;
732	>	simError();
733	>	}
734	>
735		}
736
737	<	// MPI Section of code..........
330	<
331	<	#else //IS_MPI
332	<
333	<	// first thing first, suspend fatalities.
334	<	int masterNode = 0;
335	<	int nCurObj;
336	<	painCave.isEventLoop = 1;
337	<
338	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
339	<	int haveError;
340	<
341	<	MPI_Status istatus;
342	<	int nitems;
343	<
344	<	nTotObjs = info_->getNGlobalIntegrableObjects();
345	<	haveError = 0;
346	<
347	<	if (worldRank == masterNode) {
348	<	fsetpos(inFile_, framePos_[whichFrame]);
349	<
350	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
737	>	}
738
739	<	if (eof_test == NULL) {
740	<	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
739	>
740	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpReader.cpp (property svn:keywords):
Revision 381 by tim, Tue Mar 1 14:45:45 2005 UTC vs.
Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC

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