ViewVC Help

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

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

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 274 by tim, Tue Jan 25 21:59:18 2005 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1	>	/*
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41	+
42	+	#define _LARGEFILE_SOURCE64
43	+	#define _FILE_OFFSET_BITS 64
44
45	<	#define _LARGEFILE_SOURCE64
46	<	#define _FILE_OFFSET_BITS 64
45	>	#include <sys/types.h>
46	>	#include <sys/stat.h>
47	>
48	>	#include <iostream>
49	>	#include <math.h>
50	>
51	>	#include <stdio.h>
52	>	#include <stdlib.h>
53	>	#include <string.h>
54	>
55	>	#include "io/DumpReader.hpp"
56	>	#include "primitives/Molecule.hpp"
57	>	#include "utils/simError.h"
58	>	#include "utils/MemoryUtils.hpp"
59	>	#include "utils/StringTokenizer.hpp"
60	>
61	>	#ifdef IS_MPI
62	>
63	>	#include <mpi.h>
64	>	#define TAKE_THIS_TAG_CHAR 0
65	>	#define TAKE_THIS_TAG_INT 1
66	>
67	>	#endif // is_mpi
68	>
69	>
70	>	namespace OpenMD {
71	>
72	>	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
74	>
75	>	#ifdef IS_MPI
76	>
77	>	if (worldRank == 0) {
78	>	#endif
79	>
80	>	inFile_ = new std::ifstream(filename_.c_str());
81	>
82	>	if (inFile_->fail()) {
83	>	sprintf(painCave.errMsg,
84	>	"DumpReader: Cannot open file: %s\n",
85	>	filename_.c_str());
86	>	painCave.isFatal = 1;
87	>	simError();
88	>	}
89	>
90	>	#ifdef IS_MPI
91	>
92	>	}
93	>
94	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95	>	errorCheckPoint();
96	>
97	>	#endif
98	>
99	>	return;
100	>	}
101	>
102	>	DumpReader::~DumpReader() {
103	>
104	>	#ifdef IS_MPI
105	>
106	>	if (worldRank == 0) {
107	>	#endif
108	>
109	>	delete inFile_;
110	>
111	>	#ifdef IS_MPI
112	>
113	>	}
114	>
115	>	strcpy(checkPointMsg, "Dump file closed successfully.");
116	>	errorCheckPoint();
117	>
118	>	#endif
119	>
120	>	return;
121	>	}
122	>
123	>	int DumpReader::getNFrames(void) {
124	>
125	>	if (!isScanned_)
126	>	scanFile();
127	>
128	>	return nframes_;
129	>	}
130	>
131	>	void DumpReader::scanFile(void) {
132	>	int lineNo = 0;
133	>	std::streampos prevPos;
134	>	std::streampos  currPos;
135	>
136	>	#ifdef IS_MPI
137	>
138	>	if (worldRank == 0) {
139	>	#endif // is_mpi
140	>
141	>	currPos = inFile_->tellg();
142	>	prevPos = currPos;
143	>	bool foundOpenSnapshotTag = false;
144	>	bool foundClosedSnapshotTag = false;
145	>	while(inFile_->getline(buffer, bufferSize)) {
146	>	++lineNo;
147	>
148	>	std::string line = buffer;
149	>	currPos = inFile_->tellg();
150	>	if (line.find("<Snapshot>")!= std::string::npos) {
151	>	if (foundOpenSnapshotTag) {
152	>	sprintf(painCave.errMsg,
153	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154	>	filename_.c_str());
155	>	painCave.isFatal = 1;
156	>	simError();
157	>	}
158	>	foundOpenSnapshotTag = true;
159	>	foundClosedSnapshotTag = false;
160	>	framePos_.push_back(prevPos);
161	>
162	>	} else if (line.find("</Snapshot>") != std::string::npos){
163	>	if (!foundOpenSnapshotTag) {
164	>	sprintf(painCave.errMsg,
165	>	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
166	>	filename_.c_str());
167	>	painCave.isFatal = 1;
168	>	simError();
169	>	}
170	>
171	>	if (foundClosedSnapshotTag) {
172	>	sprintf(painCave.errMsg,
173	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
174	>	filename_.c_str());
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	foundClosedSnapshotTag = true;
179	>	foundOpenSnapshotTag = false;
180	>	}
181	>	prevPos = currPos;
182	>	}
183	>
184	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
185	>	// it and give a warning message
186	>	if (foundOpenSnapshotTag) {
187	>	sprintf(painCave.errMsg,
188	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
189	>	painCave.isFatal = 0;
190	>	simError();
191	>	framePos_.pop_back();
192	>	}
193	>
194	>	nframes_ = framePos_.size();
195	>
196	>	if (nframes_ == 0) {
197	>	sprintf(painCave.errMsg,
198	>	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
199	>	painCave.isFatal = 1;
200	>	simError();
201	>	}
202	>	#ifdef IS_MPI
203	>	}
204	>
205	>	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206	>
207	>	#endif // is_mpi
208	>
209	>	isScanned_ = true;
210	>	}
211	>
212	>	void DumpReader::readFrame(int whichFrame) {
213	>	if (!isScanned_)
214	>	scanFile();
215	>
216	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
217	>
218	>	if (storageLayout & DataStorage::dslPosition) {
219	>	needPos_ = true;
220	>	} else {
221	>	needPos_ = false;
222	>	}
223	>
224	>	if (storageLayout & DataStorage::dslVelocity) {
225	>	needVel_ = true;
226	>	} else {
227	>	needVel_ = false;
228	>	}
229	>
230	>	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
231	>	needQuaternion_ = true;
232	>	} else {
233	>	needQuaternion_ = false;
234	>	}
235	>
236	>	if (storageLayout & DataStorage::dslAngularMomentum) {
237	>	needAngMom_ = true;
238	>	} else {
239	>	needAngMom_ = false;
240	>	}
241	>
242	>	readSet(whichFrame);
243
244	<	#include <sys/types.h>
245	<	#include <sys/stat.h>
244	>	if (needCOMprops_) {
245	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	>	Vector3d com;
247	>	Vector3d comvel;
248	>	Vector3d comw;
249	>	if (needPos_ && needVel_){
250	>	info_->getComAll(com, comvel);
251	>	comw = info_->getAngularMomentum();
252	>	}else{
253	>	com = info_->getCom();
254	>	comvel = 0.0;
255	>	comw   = 0.0;
256	>	}
257	>	s->setCOMprops(com, comvel, comw);
258	>	}
259
260	<	#include <iostream>
261	<	#include <math.h>
260	>	}
261	>
262	>	void DumpReader::readSet(int whichFrame) {
263	>	std::string line;
264
265	<	#include <stdio.h>
266	<	#include <stdlib.h>
267	<	#include <string.h>
265	>	#ifndef IS_MPI
266	>	inFile_->clear();
267	>	inFile_->seekg(framePos_[whichFrame]);
268
269	<	#include "io/DumpReader.hpp"
56	<	#include "primitives/Molecule.hpp"
57	<	#include "utils/simError.h"
58	<	#include "utils/MemoryUtils.hpp"
59	<	#include "utils/StringTokenizer.hpp"
269	>	std::istream& inputStream = *inFile_;
270
271	<	#ifdef IS_MPI
271	>	#else
272	>	int masterNode = 0;
273	>	std::stringstream sstream;
274	>	if (worldRank == masterNode) {
275	>	std::string sendBuffer;
276
277	<	#include <mpi.h>
278	<	#define TAKE_THIS_TAG_CHAR 0
279	<	#define TAKE_THIS_TAG_INT 1
277	>	inFile_->clear();
278	>	inFile_->seekg(framePos_[whichFrame]);
279	>
280	>	while (inFile_->getline(buffer, bufferSize)) {
281
282	<	#endif // is_mpi
283	<
284	<
285	<	namespace oopse {
286	<
287	<	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
288	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
74	<
75	<	#ifdef IS_MPI
76	<
77	<	if (worldRank == 0) {
78	<	#endif
79	<
80	<	inFile_ = fopen(filename_.c_str(), "r");
282	>	line = buffer;
283	>	sendBuffer += line;
284	>	sendBuffer += '\n';
285	>	if (line.find("</Snapshot>") != std::string::npos) {
286	>	break;
287	>	}
288	>	}
289
290	<	if (inFile_ == NULL) {
291	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
292	<	painCave.isFatal = 1;
293	<	simError();
294	<	}
290	>	int sendBufferSize = sendBuffer.size();
291	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
292	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
293	>
294	>	sstream.str(sendBuffer);
295	>	} else {
296	>	int sendBufferSize;
297	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
298	>	char * recvBuffer = new char[sendBufferSize+1];
299	>	assert(recvBuffer);
300	>	recvBuffer[sendBufferSize] = '\0';
301	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
302	>	sstream.str(recvBuffer);
303	>	delete [] recvBuffer;
304	>	}
305
306	<	#ifdef IS_MPI
306	>	std::istream& inputStream = sstream;
307	>	#endif
308
309	<	}
309	>	inputStream.getline(buffer, bufferSize);
310
311	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
312	<	MPIcheckPoint();
311	>	line = buffer;
312	>	if (line.find("<Snapshot>") == std::string::npos) {
313	>	sprintf(painCave.errMsg,
314	>	"DumpReader Error: can not find <Snapshot>\n");
315	>	painCave.isFatal = 1;
316	>	simError();
317	>	}
318	>
319	>	//read frameData
320	>	readFrameProperties(inputStream);
321
322	<	#endif
322	>	//read StuntDoubles
323	>	readStuntDoubles(inputStream);
324
325	<	return;
326	<	}
325	>	inputStream.getline(buffer, bufferSize);
326	>	line = buffer;
327	>	if (line.find("</Snapshot>") == std::string::npos) {
328	>	sprintf(painCave.errMsg,
329	>	"DumpReader Error: can not find </Snapshot>\n");
330	>	painCave.isFatal = 1;
331	>	simError();
332	>	}
333	>
334	>	}
335	>
336	>	void DumpReader::parseDumpLine(const std::string& line) {
337
338	<	DumpReader::~DumpReader() {
338	>
339	>	StringTokenizer tokenizer(line);
340	>	int nTokens;
341	>
342	>	nTokens = tokenizer.countTokens();
343	>
344	>	if (nTokens < 2) {
345	>	sprintf(painCave.errMsg,
346	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
347	>	painCave.isFatal = 1;
348	>	simError();
349	>	}
350
351	<	#ifdef IS_MPI
351	>	int index = tokenizer.nextTokenAsInt();
352	>
353	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
354
355	<	if (worldRank == 0) {
356	<	#endif
355	>	if (integrableObject == NULL) {
356	>	return;
357	>	}
358	>	std::string type = tokenizer.nextToken();
359	>	int size = type.size();
360
361	<	int error;
362	<	error = fclose(inFile_);
361	>	size_t found;
362	>
363	>	if (needPos_) {
364	>	found = type.find("p");
365	>	if (found == std::string::npos) {
366	>	sprintf(painCave.errMsg,
367	>	"DumpReader Error: StuntDouble %d has no Position\n"
368	>	"\tField (\"p\") specified.\n%s\n", index,
369	>	line.c_str());
370	>	painCave.isFatal = 1;
371	>	simError();
372	>	}
373	>	}
374	>
375	>	if (integrableObject->isDirectional()) {
376	>	if (needQuaternion_) {
377	>	found = type.find("q");
378	>	if (found == std::string::npos) {
379	>	sprintf(painCave.errMsg,
380	>	"DumpReader Error: Directional StuntDouble %d has no\n"
381	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
382	>	line.c_str());
383	>	painCave.isFatal = 1;
384	>	simError();
385	>	}
386	>	}
387	>	}
388
389	<	if (error) {
390	<	sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
391	<	painCave.isFatal = 1;
392	<	simError();
389	>	for(int i = 0; i < size; ++i) {
390	>	switch(type[i]) {
391	>
392	>	case 'p': {
393	>	Vector3d pos;
394	>	pos[0] = tokenizer.nextTokenAsDouble();
395	>	pos[1] = tokenizer.nextTokenAsDouble();
396	>	pos[2] = tokenizer.nextTokenAsDouble();
397	>	if (needPos_) {
398	>	integrableObject->setPos(pos);
399	>	}
400	>	break;
401		}
402	+	case 'v' : {
403	+	Vector3d vel;
404	+	vel[0] = tokenizer.nextTokenAsDouble();
405	+	vel[1] = tokenizer.nextTokenAsDouble();
406	+	vel[2] = tokenizer.nextTokenAsDouble();
407	+	if (needVel_) {
408	+	integrableObject->setVel(vel);
409	+	}
410	+	break;
411	+	}
412
413	<	MemoryUtils::deleteVectorOfPointer(framePos_);
413	>	case 'q' : {
414	>	Quat4d q;
415	>	if (integrableObject->isDirectional()) {
416	>
417	>	q[0] = tokenizer.nextTokenAsDouble();
418	>	q[1] = tokenizer.nextTokenAsDouble();
419	>	q[2] = tokenizer.nextTokenAsDouble();
420	>	q[3] = tokenizer.nextTokenAsDouble();
421	>
422	>	RealType qlen = q.length();
423	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
424	>
425	>	sprintf(painCave.errMsg,
426	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
427	>	painCave.isFatal = 1;
428	>	simError();
429	>
430	>	}
431	>
432	>	q.normalize();
433	>	if (needQuaternion_) {
434	>	integrableObject->setQ(q);
435	>	}
436	>	}
437	>	break;
438	>	}
439	>	case 'j' : {
440	>	Vector3d ji;
441	>	if (integrableObject->isDirectional()) {
442	>	ji[0] = tokenizer.nextTokenAsDouble();
443	>	ji[1] = tokenizer.nextTokenAsDouble();
444	>	ji[2] = tokenizer.nextTokenAsDouble();
445	>	if (needAngMom_) {
446	>	integrableObject->setJ(ji);
447	>	}
448	>	}
449	>	break;
450	>	}
451	>	case 'f': {
452
453	<	#ifdef IS_MPI
453	>	Vector3d force;
454	>	force[0] = tokenizer.nextTokenAsDouble();
455	>	force[1] = tokenizer.nextTokenAsDouble();
456	>	force[2] = tokenizer.nextTokenAsDouble();
457	>	integrableObject->setFrc(force);
458	>	break;
459	>	}
460	>	case 't' : {
461
462	+	Vector3d torque;
463	+	torque[0] = tokenizer.nextTokenAsDouble();
464	+	torque[1] = tokenizer.nextTokenAsDouble();
465	+	torque[2] = tokenizer.nextTokenAsDouble();
466	+	integrableObject->setTrq(torque);
467	+	break;
468	+	}
469	+	case 'u' : {
470	+
471	+	RealType particlePot;
472	+	particlePot = tokenizer.nextTokenAsDouble();
473	+	integrableObject->setParticlePot(particlePot);
474	+	break;
475	+	}
476	+	default: {
477	+	sprintf(painCave.errMsg,
478	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
479	+	painCave.isFatal = 1;
480	+	simError();
481	+	break;
482	+	}
483	+
484	+	}
485		}
486	+
487	+	}
488	+
489
490	<	strcpy(checkPointMsg, "Dump file closed successfully.");
123	<	MPIcheckPoint();
490	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
491
492	<	#endif
492	>	inputStream.getline(buffer, bufferSize);
493	>	std::string line(buffer);
494	>
495	>	if (line.find("<StuntDoubles>") == std::string::npos) {
496	>	sprintf(painCave.errMsg,
497	>	"DumpReader Error: Missing <StuntDoubles>\n");
498	>	painCave.isFatal = 1;
499	>	simError();
500	>	}
501
502	<	return;
503	<	}
502	>	while(inputStream.getline(buffer, bufferSize)) {
503	>	line = buffer;
504	>
505	>	if(line.find("</StuntDoubles>") != std::string::npos) {
506	>	break;
507	>	}
508
509	<	int DumpReader::getNFrames(void) {
509	>	parseDumpLine(line);
510	>	}
511	>
512	>	}
513
514	<	if (!isScanned_)
133	<	scanFile();
514	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
515
516	<	return nframes_;
517	<	}
518	<
519	<	void DumpReader::scanFile(void) {
520	<	int i, j;
521	<	int lineNum = 0;
522	<	char readBuffer[maxBufferSize];
523	<	fpos_t * currPos;
524	<
144	<	#ifdef IS_MPI
145	<
146	<	if (worldRank == 0) {
147	<	#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();
163	<	}
164	<
165	<	while (!feof(inFile_)) {
166	<	framePos_.push_back(currPos);
167	<
168	<	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++;
202	<	}
203	<
204	<	delete currPos;
205	<	rewind(inFile_);
206	<
207	<	nframes_ = framePos_.size();
208	<	#ifdef IS_MPI
516	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
517	>	inputStream.getline(buffer, bufferSize);
518	>	std::string line(buffer);
519	>
520	>	if (line.find("<FrameData>") == std::string::npos) {
521	>	sprintf(painCave.errMsg,
522	>	"DumpReader Error: Missing <FrameData>\n");
523	>	painCave.isFatal = 1;
524	>	simError();
525		}
526
527	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
527	>	while(inputStream.getline(buffer, bufferSize)) {
528	>	line = buffer;
529	>
530	>	if(line.find("</FrameData>") != std::string::npos) {
531	>	break;
532	>	}
533	>
534	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
535	>	if (!tokenizer.hasMoreTokens()) {
536	>	sprintf(painCave.errMsg,
537	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
538	>	painCave.isFatal = 1;
539	>	simError();
540	>	}
541
542	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
543	<	MPIcheckPoint();
544	<
545	<	#endif // is_mpi
546	<
547	<	isScanned_ = true;
548	<	}
549	<
550	<	void DumpReader::readFrame(int whichFrame) {
551	<	readSet(whichFrame);
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
559	<
560	<	Molecule* mol;
561	<	StuntDouble* integrableObject;
562	<	SimInfo::MoleculeIterator mi;
563	<	Molecule::IntegrableObjectIterator ii;
564	<
565	<	#ifndef IS_MPI
566	<
567	<	fsetpos(inFile_, framePos_[whichFrame]);
568	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
569	<
570	<	if (eof_test == NULL) {
571	<	sprintf(painCave.errMsg,
572	<	"DumpReader error: error reading 1st line of \"%s\"\n",
573	<	filename_.c_str());
574	<	painCave.isFatal = 1;
575	<	simError();
576	<	}
577	<
578	<	nTotObjs = atoi(read_buffer);
579	<
580	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
581	<	sprintf(painCave.errMsg,
253	<	"DumpReader error. %s nIntegrable, %d, "
254	<	"does not match the meta-data file's nIntegrable, %d.\n",
255	<	filename_.c_str(),
256	<	nTotObjs,
257	<	info_->getNGlobalIntegrableObjects());
258	<
259	<	painCave.isFatal = 1;
260	<	simError();
261	<	}
262	<
263	<	//read the box mat from the comment line
264	<
265	<	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();
272	<	}
273	<
274	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
275	<
276	<	//parse dump lines
277	<
278	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
279	<
280	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
281	<	integrableObject = mol->nextIntegrableObject(ii)) {
282	<
283	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
284	<
285	<	if (eof_test == NULL) {
286	<	sprintf(painCave.errMsg,
287	<	"DumpReader Error: error in reading file %s\n"
288	<	"natoms  = %d; index = %d\n"
289	<	"error reading the line from the file.\n",
290	<	filename_.c_str(),
291	<	nTotObjs,
292	<	i);
293	<
294	<	painCave.isFatal = 1;
295	<	simError();
296	<	}
297	<
298	<	parseDumpLine(read_buffer, integrableObject);
299	<
300	<	}
301	<	}
302	<
303	<	// 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	<	}
332	<
333	<	nitems = atoi(read_buffer);
334	<
335	<	// Check to see that the number of integrable objects in the
336	<	// intial configuration file is the same as derived from the
337	<	// meta-data file.
338	<
339	<	if (nTotObjs != nitems) {
340	<	sprintf(painCave.errMsg,
341	<	"DumpReader Error. %s nIntegrable, %d, "
342	<	"does not match the meta-data file's nIntegrable, %d.\n",
343	<	filename_.c_str(),
344	<	nTotObjs,
345	<	info_->getNGlobalIntegrableObjects());
346	<
347	<	painCave.isFatal = 1;
348	<	simError();
349	<	}
350	<
351	<	//read the boxMat from the comment line
352	<
353	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
354	<
355	<	if (eof_test == NULL) {
356	<	sprintf(painCave.errMsg, "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	<
542	>	std::string propertyName = tokenizer.nextToken();
543	>	if (propertyName == "Time") {
544	>	RealType currTime = tokenizer.nextTokenAsDouble();
545	>	s->setTime(currTime);
546	>	} else if (propertyName == "Hmat"){
547	>	Mat3x3d hmat;
548	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
549	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
550	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
551	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
552	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
553	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
554	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
555	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
556	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
557	>	s->setHmat(hmat);
558	>	} else if (propertyName == "Thermostat") {
559	>	RealType chi = tokenizer.nextTokenAsDouble();
560	>	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
561	>	s->setChi(chi);
562	>	s->setIntegralOfChiDt(integralOfChiDt);
563	>	} else if (propertyName == "Barostat") {
564	>	Mat3x3d eta;
565	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
566	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
567	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
568	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
569	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
570	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
571	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
572	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
573	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
574	>	s->setEta(eta);
575	>	} else {
576	>	sprintf(painCave.errMsg,
577	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
578	>	painCave.isFatal = 0;
579	>	simError();
580	>	}
581	>
582		}
583
584	<	#endif
584	>	}
585
586	<	}
587	<
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
586	>
587	>	}//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.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

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

Diff Legend

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