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

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trunk/src/io/DumpReader.cpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC

#	Line 1 | Line 1
1	<	#define _LARGEFILE_SOURCE64
2	<	#define _FILE_OFFSET_BITS 64
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. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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	>	#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	>
62	>	#ifdef IS_MPI
63	>
64	>	#include <mpi.h>
65	>	#define TAKE_THIS_TAG_CHAR 0
66	>	#define TAKE_THIS_TAG_INT 1
67	>
68	>	#endif // is_mpi
69	>
70	>
71	>	namespace OpenMD {
72	>
73	>	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
74	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
75	>
76	>	#ifdef IS_MPI
77	>
78	>	if (worldRank == 0) {
79	>	#endif
80	>
81	>	inFile_ = new std::ifstream(filename_.c_str());
82	>
83	>	if (inFile_->fail()) {
84	>	sprintf(painCave.errMsg,
85	>	"DumpReader: Cannot open file: %s\n",
86	>	filename_.c_str());
87	>	painCave.isFatal = 1;
88	>	simError();
89	>	}
90	>
91	>	#ifdef IS_MPI
92	>
93	>	}
94	>
95	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
96	>	errorCheckPoint();
97	>
98	>	#endif
99	>
100	>	return;
101	>	}
102	>
103	>	DumpReader::~DumpReader() {
104	>
105	>	#ifdef IS_MPI
106	>
107	>	if (worldRank == 0) {
108	>	#endif
109	>
110	>	delete inFile_;
111	>
112	>	#ifdef IS_MPI
113	>
114	>	}
115	>
116	>	strcpy(checkPointMsg, "Dump file closed successfully.");
117	>	errorCheckPoint();
118	>
119	>	#endif
120	>
121	>	return;
122	>	}
123	>
124	>	int DumpReader::getNFrames(void) {
125	>
126	>	if (!isScanned_)
127	>	scanFile();
128	>
129	>	return nframes_;
130	>	}
131	>
132	>	void DumpReader::scanFile(void) {
133	>	int lineNo = 0;
134	>	std::streampos prevPos;
135	>	std::streampos  currPos;
136	>
137	>	#ifdef IS_MPI
138	>
139	>	if (worldRank == 0) {
140	>	#endif // is_mpi
141	>
142	>	currPos = inFile_->tellg();
143	>	prevPos = currPos;
144	>	bool foundOpenSnapshotTag = false;
145	>	bool foundClosedSnapshotTag = false;
146	>	bool foundOpenSiteDataTag = false;
147	>	while(inFile_->getline(buffer, bufferSize)) {
148	>	++lineNo;
149	>
150	>	std::string line = buffer;
151	>	currPos = inFile_->tellg();
152	>	if (line.find("<Snapshot>")!= std::string::npos) {
153	>	if (foundOpenSnapshotTag) {
154	>	sprintf(painCave.errMsg,
155	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
156	>	filename_.c_str());
157	>	painCave.isFatal = 1;
158	>	simError();
159	>	}
160	>	foundOpenSnapshotTag = true;
161	>	foundClosedSnapshotTag = false;
162	>	framePos_.push_back(prevPos);
163	>
164	>	} else if (line.find("</Snapshot>") != std::string::npos){
165	>	if (!foundOpenSnapshotTag) {
166	>	sprintf(painCave.errMsg,
167	>	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
168	>	filename_.c_str());
169	>	painCave.isFatal = 1;
170	>	simError();
171	>	}
172	>
173	>	if (foundClosedSnapshotTag) {
174	>	sprintf(painCave.errMsg,
175	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
176	>	filename_.c_str());
177	>	painCave.isFatal = 1;
178	>	simError();
179	>	}
180	>	foundClosedSnapshotTag = true;
181	>	foundOpenSnapshotTag = false;
182	>	}
183	>	prevPos = currPos;
184	>	}
185	>
186	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
187	>	// it and give a warning message
188	>	if (foundOpenSnapshotTag) {
189	>	sprintf(painCave.errMsg,
190	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
191	>	painCave.isFatal = 0;
192	>	simError();
193	>	framePos_.pop_back();
194	>	}
195	>
196	>	nframes_ = framePos_.size();
197	>
198	>	if (nframes_ == 0) {
199	>	sprintf(painCave.errMsg,
200	>	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
201	>	painCave.isFatal = 1;
202	>	simError();
203	>	}
204	>	#ifdef IS_MPI
205	>	}
206	>
207	>	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
208	>
209	>	#endif // is_mpi
210	>
211	>	isScanned_ = true;
212	>	}
213	>
214	>	void DumpReader::readFrame(int whichFrame) {
215	>	if (!isScanned_)
216	>	scanFile();
217	>
218	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
219	>
220	>	if (storageLayout & DataStorage::dslPosition) {
221	>	needPos_ = true;
222	>	} else {
223	>	needPos_ = false;
224	>	}
225	>
226	>	if (storageLayout & DataStorage::dslVelocity) {
227	>	needVel_ = true;
228	>	} else {
229	>	needVel_ = false;
230	>	}
231	>
232	>	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
233	>	needQuaternion_ = true;
234	>	} else {
235	>	needQuaternion_ = false;
236	>	}
237	>
238	>	if (storageLayout & DataStorage::dslAngularMomentum) {
239	>	needAngMom_ = true;
240	>	} else {
241	>	needAngMom_ = false;
242	>	}
243	>
244	>	readSet(whichFrame);
245
246	<	#include <sys/types.h>
247	<	#include <sys/stat.h>
246	>	if (needCOMprops_) {
247	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
248	>	Vector3d com;
249	>	Vector3d comvel;
250	>	Vector3d comw;
251	>	if (needPos_ && needVel_){
252	>	info_->getComAll(com, comvel);
253	>	comw = info_->getAngularMomentum();
254	>	}else{
255	>	com = info_->getCom();
256	>	comvel = 0.0;
257	>	comw   = 0.0;
258	>	}
259	>	s->setCOMprops(com, comvel, comw);
260	>	}
261
262	<	#include <iostream>
263	<	#include <math.h>
262	>	}
263	>
264	>	void DumpReader::readSet(int whichFrame) {
265	>	std::string line;
266
267	<	#include <stdio.h>
268	<	#include <stdlib.h>
269	<	#include <string.h>
267	>	#ifndef IS_MPI
268	>	inFile_->clear();
269	>	inFile_->seekg(framePos_[whichFrame]);
270
271	+	std::istream& inputStream = *inFile_;
272
273	<	#include "ReadWrite.hpp"
274	<	#include "simError.h"
273	>	#else
274	>	int masterNode = 0;
275	>	std::stringstream sstream;
276	>	if (worldRank == masterNode) {
277	>	std::string sendBuffer;
278
279	<	#ifdef IS_MPI
280	<	#include <mpi.h>
281	<	#include "mpiSimulation.hpp"
282	<	#define TAKE_THIS_TAG_CHAR 0
22	<	#define TAKE_THIS_TAG_INT 1
23	<	#endif // is_mpi
279	>	inFile_->clear();
280	>	inFile_->seekg(framePos_[whichFrame]);
281	>
282	>	while (inFile_->getline(buffer, bufferSize)) {
283
284	+	line = buffer;
285	+	sendBuffer += line;
286	+	sendBuffer += '\n';
287	+	if (line.find("</Snapshot>") != std::string::npos) {
288	+	break;
289	+	}
290	+	}
291
292	<	DumpReader :: DumpReader(const char *in_name ){
292	>	int sendBufferSize = sendBuffer.size();
293	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
294	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
295	>
296	>	sstream.str(sendBuffer);
297	>	} else {
298	>	int sendBufferSize;
299	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
300	>	char * recvBuffer = new char[sendBufferSize+1];
301	>	assert(recvBuffer);
302	>	recvBuffer[sendBufferSize] = '\0';
303	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
304	>	sstream.str(recvBuffer);
305	>	delete [] recvBuffer;
306	>	}
307
308	<	isScanned = false;
29	<
30	<	#ifdef IS_MPI
31	<	if (worldRank == 0) {
308	>	std::istream& inputStream = sstream;
309		#endif
310
311	<	inFile = fopen(in_name, "r");
35	<	if(inFile == NULL){
36	<	sprintf(painCave.errMsg,
37	<	"Cannot open file: %s\n", in_name);
38	<	painCave.isFatal = 1;
39	<	simError();
40	<	}
41	<
42	<	inFileName = in_name;
43	<	#ifdef IS_MPI
44	<	}
45	<	strcpy( checkPointMsg, "Dump file opened for reading successfully." );
46	<	MPIcheckPoint();
47	<	#endif
48	<	return;
49	<	}
311	>	inputStream.getline(buffer, bufferSize);
312
313	<	DumpReader :: ~DumpReader( ){
314	<	#ifdef IS_MPI
315	<	if (worldRank == 0) {
316	<	#endif
317	<	vector<fpos_t*>::iterator i;
313	>	line = buffer;
314	>	if (line.find("<Snapshot>") == std::string::npos) {
315	>	sprintf(painCave.errMsg,
316	>	"DumpReader Error: can not find <Snapshot>\n");
317	>	painCave.isFatal = 1;
318	>	simError();
319	>	}
320	>
321	>	//read frameData
322	>	readFrameProperties(inputStream);
323
324	<	int error;
325	<	error = fclose( inFile );
59	<	if( error ){
60	<	sprintf( painCave.errMsg,
61	<	"Error closing %s\n", inFileName.c_str());
62	<	simError();
63	<	}
324	>	//read StuntDoubles
325	>	readStuntDoubles(inputStream);
326
327	<	for(i = framePos.begin(); i != framePos.end(); ++i)
328	<	delete *i;
67	<	framePos.clear();
68	<
69	<	#ifdef IS_MPI
70	<	}
71	<	strcpy( checkPointMsg, "Dump file closed successfully." );
72	<	MPIcheckPoint();
73	<	#endif
74	<
75	<	return;
76	<	}
327	>	inputStream.getline(buffer, bufferSize);
328	>	line = buffer;
329
330	<	int DumpReader::getNframes( void ){
330	>	if (line.find("<SiteData>") != std::string::npos) {
331	>	//read SiteData
332	>	readSiteData(inputStream);
333	>	} else {
334	>	if (line.find("</Snapshot>") == std::string::npos) {
335	>	sprintf(painCave.errMsg,
336	>	"DumpReader Error: can not find </Snapshot>\n");
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340	>	}
341	>	}
342	>
343	>	void DumpReader::parseDumpLine(const std::string& line) {
344
345	<	if( !isScanned )
346	<	scanFile();
347	<	return framePos.size();
348	<	}
345	>
346	>	StringTokenizer tokenizer(line);
347	>	int nTokens;
348	>
349	>	nTokens = tokenizer.countTokens();
350	>
351	>	if (nTokens < 2) {
352	>	sprintf(painCave.errMsg,
353	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
354	>	painCave.isFatal = 1;
355	>	simError();
356	>	}
357
358	<	void DumpReader::scanFile( void ){
358	>	int index = tokenizer.nextTokenAsInt();
359	>
360	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
361
362	<	int i, j;
363	<	int lineNum = 0;
89	<	char readBuffer[2000];
90	<	fpos_t *currPos;
91	<
92	<	#ifdef IS_MPI
93	<	if( worldRank == 0 ){
94	<	#endif // is_mpi
95	<
96	<	rewind( inFile );
97	<
98	<	currPos = new fpos_t;
99	<	fgetpos( inFile, currPos );
100	<	fgets( readBuffer, sizeof( readBuffer ), inFile );
101	<	lineNum++;
102	<	if( feof( inFile ) ){
103	<	sprintf( painCave.errMsg,
104	<	"File \"%s\" ended unexpectedly at line %d\n",
105	<	inFileName.c_str(),
106	<	lineNum );
107	<	painCave.isFatal = 1;
108	<	simError();
362	>	if (integrableObject == NULL) {
363	>	return;
364		}
365	+	std::string type = tokenizer.nextToken();
366	+	int size = type.size();
367
368	<	while( !feof( inFile ) ){
369	<
370	<	framePos.push_back(currPos);
371	<
372	<	i = atoi(readBuffer);
373	<
374	<	fgets( readBuffer, sizeof( readBuffer ), inFile );
375	<	lineNum++;
376	<	if( feof( inFile ) ){
377	<	sprintf( painCave.errMsg,
378	<	"File \"%s\" ended unexpectedly at line %d\n",
122	<	inFileName.c_str(),
123	<	lineNum );
124	<	painCave.isFatal = 1;
125	<	simError();
368	>	size_t found;
369	>
370	>	if (needPos_) {
371	>	found = type.find("p");
372	>	if (found == std::string::npos) {
373	>	sprintf(painCave.errMsg,
374	>	"DumpReader Error: StuntDouble %d has no Position\n"
375	>	"\tField (\"p\") specified.\n%s\n", index,
376	>	line.c_str());
377	>	painCave.isFatal = 1;
378	>	simError();
379		}
127	–
128	–	for(j=0; j<i; j++){
129	–
130	–	fgets( readBuffer, sizeof( readBuffer ), inFile );
131	–	lineNum++;
132	–	if( feof( inFile ) ){
133	–	sprintf( painCave.errMsg,
134	–	"File \"%s\" ended unexpectedly at line %d,"
135	–	" with atom %d\n",
136	–	inFileName.c_str(),
137	–	lineNum,
138	–	j );
139	–	painCave.isFatal = 1;
140	–	simError();
141	–	}
142	–
143	–	}
144	–
145	–	currPos = new fpos_t;
146	–	fgetpos( inFile, currPos );
147	–	fgets( readBuffer, sizeof( readBuffer ), inFile );
148	–	lineNum++;
380		}
381
382	<	delete currPos;
383	<	rewind( inFile );
384	<
385	<	isScanned = true;
382	>	if (integrableObject->isDirectional()) {
383	>	if (needQuaternion_) {
384	>	found = type.find("q");
385	>	if (found == std::string::npos) {
386	>	sprintf(painCave.errMsg,
387	>	"DumpReader Error: Directional StuntDouble %d has no\n"
388	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
389	>	line.c_str());
390	>	painCave.isFatal = 1;
391	>	simError();
392	>	}
393	>	}
394	>	}
395
396	<	#ifdef IS_MPI
397	<	}
398	<	strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
399	<	MPIcheckPoint();
400	<	#endif // is_mpi
401	<	}
396	>	for(int i = 0; i < size; ++i) {
397	>	switch(type[i]) {
398	>
399	>	case 'p': {
400	>	Vector3d pos;
401	>	pos[0] = tokenizer.nextTokenAsDouble();
402	>	pos[1] = tokenizer.nextTokenAsDouble();
403	>	pos[2] = tokenizer.nextTokenAsDouble();
404	>	if (needPos_) {
405	>	integrableObject->setPos(pos);
406	>	}
407	>	break;
408	>	}
409	>	case 'v' : {
410	>	Vector3d vel;
411	>	vel[0] = tokenizer.nextTokenAsDouble();
412	>	vel[1] = tokenizer.nextTokenAsDouble();
413	>	vel[2] = tokenizer.nextTokenAsDouble();
414	>	if (needVel_) {
415	>	integrableObject->setVel(vel);
416	>	}
417	>	break;
418	>	}
419
420	<	void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
420	>	case 'q' : {
421	>	Quat4d q;
422	>	if (integrableObject->isDirectional()) {
423	>
424	>	q[0] = tokenizer.nextTokenAsDouble();
425	>	q[1] = tokenizer.nextTokenAsDouble();
426	>	q[2] = tokenizer.nextTokenAsDouble();
427	>	q[3] = tokenizer.nextTokenAsDouble();
428	>
429	>	RealType qlen = q.length();
430	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
431	>
432	>	sprintf(painCave.errMsg,
433	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
434	>	painCave.isFatal = 1;
435	>	simError();
436	>
437	>	}
438	>
439	>	q.normalize();
440	>	if (needQuaternion_) {
441	>	integrableObject->setQ(q);
442	>	}
443	>	}
444	>	break;
445	>	}
446	>	case 'j' : {
447	>	Vector3d ji;
448	>	if (integrableObject->isDirectional()) {
449	>	ji[0] = tokenizer.nextTokenAsDouble();
450	>	ji[1] = tokenizer.nextTokenAsDouble();
451	>	ji[2] = tokenizer.nextTokenAsDouble();
452	>	if (needAngMom_) {
453	>	integrableObject->setJ(ji);
454	>	}
455	>	}
456	>	break;
457	>	}
458	>	case 'f': {
459
460	<	simnfo = the_simnfo;
460	>	Vector3d force;
461	>	force[0] = tokenizer.nextTokenAsDouble();
462	>	force[1] = tokenizer.nextTokenAsDouble();
463	>	force[2] = tokenizer.nextTokenAsDouble();
464	>	integrableObject->setFrc(force);
465	>	break;
466	>	}
467	>	case 't' : {
468
469	<	this->readSet( whichFrame );
470	<	}
469	>	Vector3d torque;
470	>	torque[0] = tokenizer.nextTokenAsDouble();
471	>	torque[1] = tokenizer.nextTokenAsDouble();
472	>	torque[2] = tokenizer.nextTokenAsDouble();
473	>	integrableObject->setTrq(torque);
474	>	break;
475	>	}
476	>	case 'u' : {
477
478	+	RealType particlePot;
479	+	particlePot = tokenizer.nextTokenAsDouble();
480	+	integrableObject->setParticlePot(particlePot);
481	+	break;
482	+	}
483	+	case 'c' : {
484
485	+	RealType flucQPos;
486	+	flucQPos = tokenizer.nextTokenAsDouble();
487	+	integrableObject->setFlucQPos(flucQPos);
488	+	break;
489	+	}
490	+	case 'w' : {
491
492	<	void DumpReader :: readSet( int whichFrame ){
492	>	RealType flucQVel;
493	>	flucQVel = tokenizer.nextTokenAsDouble();
494	>	integrableObject->setFlucQVel(flucQVel);
495	>	break;
496	>	}
497	>	case 'g' : {
498
499	<	int i;
500	<	unsigned int j;
499	>	RealType flucQFrc;
500	>	flucQFrc = tokenizer.nextTokenAsDouble();
501	>	integrableObject->setFlucQFrc(flucQFrc);
502	>	break;
503	>	}
504	>	case 'e' : {
505
506	<	#ifdef IS_MPI
507	<	int done, which_node, which_atom; // loop counter
508	<	#endif //is_mpi
506	>	Vector3d eField;
507	>	eField[0] = tokenizer.nextTokenAsDouble();
508	>	eField[1] = tokenizer.nextTokenAsDouble();
509	>	eField[2] = tokenizer.nextTokenAsDouble();
510	>	integrableObject->setElectricField(eField);
511	>	break;
512	>	}
513	>	default: {
514	>	sprintf(painCave.errMsg,
515	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
516	>	painCave.isFatal = 1;
517	>	simError();
518	>	break;
519	>	}
520
521	<	const int BUFFERSIZE = 2000; // size of the read buffer
522	<	int nTotObjs; // the number of atoms
523	<	char read_buffer[BUFFERSIZE]; //the line buffer for reading
521	>	}
522	>	}
523	>
524	>	}
525	>
526
527	<	char *eof_test; // ptr to see when we reach the end of the file
186	<	char *parseErr;
527	>	void DumpReader::parseSiteLine(const std::string& line) {
528
529	<	vector<StuntDouble*> integrableObjects;
529	>	StringTokenizer tokenizer(line);
530	>	int nTokens;
531	>
532	>	nTokens = tokenizer.countTokens();
533	>
534	>	if (nTokens < 2) {
535	>	sprintf(painCave.errMsg,
536	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
537	>	painCave.isFatal = 1;
538	>	simError();
539	>	}
540
541	+	/**
542	+	* The first token is the global integrable object index.
543	+	*/
544
545	<	#ifndef IS_MPI
545	>	int index = tokenizer.nextTokenAsInt();
546	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
547	>	if (integrableObject == NULL) {
548	>	return;
549	>	}
550	>	StuntDouble* sd = integrableObject;
551
552	<	fsetpos(inFile, framePos[whichFrame]);
553	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
554	<	if( eof_test == NULL ){
555	<	sprintf( painCave.errMsg,
556	<	"DumpReader error: error reading 1st line of \"%s\"\n",
198	<	inFileName.c_str() );
199	<	painCave.isFatal = 1;
200	<	simError();
201	<	}
552	>	/**
553	>	* Test to see if the next token is an integer or not.  If not,
554	>	* we've got data on the integrable object itself.  If there is an
555	>	* integer, we're parsing data for a site on a rigid body.
556	>	*/
557
558	<	nTotObjs = atoi( read_buffer );
559	<
560	<	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
561	<	sprintf( painCave.errMsg,
562	<	"DumpReader error. %s nIntegrable, %d, "
563	<	"does not match the meta-data file's nIntegrable, %d.\n",
564	<	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
565	<	painCave.isFatal = 1;
566	<	simError();
212	<	}
213	<
214	<	//read the box mat from the comment line
558	>	std::string indexTest = tokenizer.peekNextToken();
559	>	std::istringstream i(indexTest);
560	>	int siteIndex;
561	>	if (i >> siteIndex) {
562	>	// chew up this token and parse as an int:
563	>	siteIndex = tokenizer.nextTokenAsInt();
564	>	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
565	>	sd = rb->getAtoms()[siteIndex];
566	>	}
567
568	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
569	<	if(eof_test == NULL){
570	<	sprintf( painCave.errMsg,
571	<	"error in reading commment in %s\n", inFileName.c_str());
572	<	painCave.isFatal = 1;
573	<	simError();
574	<	}
575	<
576	<	parseErr = parseCommentLine( read_buffer, simnfo);
577	<	if( parseErr != NULL ){
578	<	strcpy( painCave.errMsg, parseErr );
579	<	painCave.isFatal = 1;
580	<	simError();
581	<	}
582	<
231	<	//parse dump lines
232	<
233	<	for( i=0; i < simnfo->n_mol; i++){
234	<
235	<	integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
236	<
237	<	for(j = 0; j < integrableObjects.size(); j++){
238	<
239	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
240	<	if(eof_test == NULL){
241	<	sprintf(painCave.errMsg,
242	<	"error in reading file %s\n"
243	<	"natoms  = %d; index = %d\n"
244	<	"error reading the line from the file.\n",
245	<	inFileName.c_str(), nTotObjs, i );
246	<	painCave.isFatal = 1;
247	<	simError();
568	>	/**
569	>	* The next token contains information on what follows.
570	>	*/
571	>	std::string type = tokenizer.nextToken();
572	>	int size = type.size();
573	>
574	>	for(int i = 0; i < size; ++i) {
575	>	switch(type[i]) {
576	>
577	>	case 'u' : {
578	>
579	>	RealType particlePot;
580	>	particlePot = tokenizer.nextTokenAsDouble();
581	>	sd->setParticlePot(particlePot);
582	>	break;
583		}
584	<
585	<	parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
586	<	if( parseErr != NULL ){
587	<	strcpy( painCave.errMsg, parseErr );
588	<	painCave.isFatal = 1;
589	<	simError();
584	>	case 'c' : {
585	>
586	>	RealType flucQPos;
587	>	flucQPos = tokenizer.nextTokenAsDouble();
588	>	sd->setFlucQPos(flucQPos);
589	>	break;
590		}
591	<	}
592	<	}
593	<
594	<	// MPI Section of code..........
595	<	#else //IS_MPI
596	<
262	<	// first thing first, suspend fatalities.
263	<	painCave.isEventLoop = 1;
264	<
265	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
266	<	int haveError;
267	<
268	<	MPI_Status istatus;
269	<	int *MolToProcMap = mpiSim->getMolToProcMap();
270	<	int localIndex;
271	<	int nCurObj;
272	<	int nitems;
273	<
274	<	nTotObjs = simnfo->getTotIntegrableObjects();
275	<	haveError = 0;
276	<	if (worldRank == 0) {
277	<	fsetpos(inFile,  framePos[whichFrame]);
278	<
279	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
280	<	if( eof_test == NULL ){
281	<	sprintf( painCave.errMsg,
282	<	"Error reading 1st line of %s \n ",inFileName.c_str());
283	<	haveError = 1;
284	<	simError();
285	<	}
286	<
287	<	nitems = atoi( read_buffer );
288	<
289	<	// Check to see that the number of integrable objects in the
290	<	// intial configuration file is the same as derived from the
291	<	// meta-data file.
292	<
293	<	if( nTotObjs != nitems){
294	<	sprintf( painCave.errMsg,
295	<	"DumpReader Error. %s nIntegrable, %d, "
296	<	"does not match the meta-data file's nIntegrable, %d.\n",
297	<	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
298	<	haveError= 1;
299	<	simError();
300	<	}
301	<
302	<	//read the boxMat from the comment line
303	<
304	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
305	<	if(eof_test == NULL){
306	<	sprintf( painCave.errMsg,
307	<	"error in reading commment in %s\n", inFileName.c_str());
308	<	haveError = 1;
309	<	simError();
310	<	}
311	<
312	<	//Every single processor will parse the comment line by itself
313	<	//By using this way, we might lose some efficiency, but if we want to add
314	<	//more parameters into comment line, we only need to modify function
315	<	//parseCommentLine
316	<
317	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
318	<
319	<	parseErr = parseCommentLine( read_buffer, simnfo);
320	<
321	<	if( parseErr != NULL ){
322	<	strcpy( painCave.errMsg, parseErr );
323	<	haveError = 1;
324	<	simError();
325	<	}
326	<
327	<	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
328	<	which_node = MolToProcMap[i];
329	<	if(which_node == 0){
330	<	//molecules belong to master node
331	<
332	<	localIndex = mpiSim->getGlobalToLocalMol(i);
333	<
334	<	if(localIndex == -1) {
335	<	strcpy(painCave.errMsg, "Molecule not found on node 0!");
336	<	haveError = 1;
337	<	simError();
591	>	case 'w' : {
592	>
593	>	RealType flucQVel;
594	>	flucQVel = tokenizer.nextTokenAsDouble();
595	>	sd->setFlucQVel(flucQVel);
596	>	break;
597		}
598	<
340	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
341	<	for(j=0; j < integrableObjects.size(); j++){
598	>	case 'g' : {
599
600	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
601	<	if(eof_test == NULL){
602	<	sprintf(painCave.errMsg,
603	<	"error in reading file %s\n"
347	<	"natoms  = %d; index = %d\n"
348	<	"error reading the line from the file.\n",
349	<	inFileName.c_str(), nTotObjs, i );
350	<	haveError= 1;
351	<	simError();
352	<	}
353	<
354	<	if(haveError) nodeZeroError();
355	<
356	<	parseDumpLine(read_buffer, integrableObjects[j]);
357	<
358	<	}
359	<
360	<
600	>	RealType flucQFrc;
601	>	flucQFrc = tokenizer.nextTokenAsDouble();
602	>	sd->setFlucQFrc(flucQFrc);
603	>	break;
604		}
605	<	else{
363	<	//molecule belongs to slave nodes
364	<
365	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
366	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
367	<
368	<	for(j=0; j < nCurObj; j++){
605	>	case 'e' : {
606
607	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
608	<	if(eof_test == NULL){
609	<	sprintf(painCave.errMsg,
610	<	"error in reading file %s\n"
611	<	"natoms  = %d; index = %d\n"
612	<	"error reading the line from the file.\n",
376	<	inFileName.c_str(), nTotObjs, i );
377	<	haveError= 1;
378	<	simError();
379	<	}
380	<
381	<	if(haveError) nodeZeroError();
382	<
383	<	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
384	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
385	<
386	<	}
387	<
607	>	Vector3d eField;
608	>	eField[0] = tokenizer.nextTokenAsDouble();
609	>	eField[1] = tokenizer.nextTokenAsDouble();
610	>	eField[2] = tokenizer.nextTokenAsDouble();
611	>	sd->setElectricField(eField);
612	>	break;
613		}
614	<
615	<	}
614	>	default: {
615	>	sprintf(painCave.errMsg,
616	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
617	>	painCave.isFatal = 1;
618	>	simError();
619	>	break;
620	>	}
621	>	}
622	>	}
623	>	}
624	>
625	>
626	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
627
628	<	}
629	<	else{
630	<	//actions taken at slave nodes
631	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
628	>	inputStream.getline(buffer, bufferSize);
629	>	std::string line(buffer);
630	>
631	>	if (line.find("<StuntDoubles>") == std::string::npos) {
632	>	sprintf(painCave.errMsg,
633	>	"DumpReader Error: Missing <StuntDoubles>\n");
634	>	painCave.isFatal = 1;
635	>	simError();
636	>	}
637
638	<	parseErr = parseCommentLine( read_buffer, simnfo);
638	>	while(inputStream.getline(buffer, bufferSize)) {
639	>	line = buffer;
640	>
641	>	if(line.find("</StuntDoubles>") != std::string::npos) {
642	>	break;
643	>	}
644
645	<	if( parseErr != NULL ){
400	<	strcpy( painCave.errMsg, parseErr );
401	<	haveError = 1;
402	<	simError();
645	>	parseDumpLine(line);
646		}
647
648	<	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
406	<	which_node = MolToProcMap[i];
407	<
408	<	if(which_node == worldRank){
409	<	//molecule with global index i belongs to this processor
410	<
411	<	localIndex = mpiSim->getGlobalToLocalMol(i);
648	>	}
649
650	<	if(localIndex == -1) {
414	<	sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
415	<	haveError = 1;
416	<	simError();
417	<	}
650	>	void  DumpReader::readSiteData(std::istream& inputStream) {
651
652	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
652	>	inputStream.getline(buffer, bufferSize);
653	>	std::string line(buffer);
654	>
655	>	if (line.find("<SiteData>") == std::string::npos) {
656	>	// site data isn't required for a simulation, so skip
657	>	return;
658	>	}
659
660	<	nCurObj = integrableObjects.size();
661	<
662	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
663	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
660	>	while(inputStream.getline(buffer, bufferSize)) {
661	>	line = buffer;
662	>
663	>	if(line.find("</SiteData>") != std::string::npos) {
664	>	break;
665	>	}
666
667	<	for(j = 0; j < integrableObjects.size(); j++){
667	>	parseSiteLine(line);
668	>	}
669	>
670	>	}
671
672	<	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
429	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
672	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
673
674	<	parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
674	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
675	>	inputStream.getline(buffer, bufferSize);
676	>	std::string line(buffer);
677
678	<	if( parseErr != NULL ){
679	<	strcpy( painCave.errMsg, parseErr );
680	<	simError();
681	<	}
678	>	if (line.find("<FrameData>") == std::string::npos) {
679	>	sprintf(painCave.errMsg,
680	>	"DumpReader Error: Missing <FrameData>\n");
681	>	painCave.isFatal = 1;
682	>	simError();
683	>	}
684
685	<	}
686	<
685	>	while(inputStream.getline(buffer, bufferSize)) {
686	>	line = buffer;
687	>
688	>	if(line.find("</FrameData>") != std::string::npos) {
689	>	break;
690		}
691
692	<	}
692	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
693	>	if (!tokenizer.hasMoreTokens()) {
694	>	sprintf(painCave.errMsg,
695	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
696	>	painCave.isFatal = 1;
697	>	simError();
698	>	}
699
700	<	}
701	<
702	<	#endif
703	<	}
704	<
705	<	char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
706	<
707	<	char *foo; // the pointer to the current string token
708	<
709	<	double pos[3]; // position place holders
710	<	double vel[3]; // velocity placeholders
711	<	double q[4]; // the quaternions
712	<	double ji[3]; // angular velocity placeholders;
713	<	double qSqr, qLength; // needed to normalize the quaternion vector.
714	<
715	<
716	<	// set the string tokenizer
717	<
718	<	foo = strtok(readLine, " ,;\t");
719	<
720	<	// check the atom name to the current atom
721	<
722	<	if( strcmp( foo, sd->getType() ) ){
723	<	sprintf( painCave.errMsg,
724	<	"DumpReader error.  Does not"
725	<	" match the meta-data atom %s.\n",
726	<	sd->getType() );
727	<	return strdup( painCave.errMsg );
728	<	}
729	<
730	<	// get the positions
731	<
732	<	foo = strtok(NULL, " ,;\t");
733	<	if(foo == NULL){
734	<	sprintf( painCave.errMsg,
735	<	"error in reading postition x from %s\n",
736	<	inFileName.c_str());
737	<	return strdup( painCave.errMsg );
482	<	}
483	<	pos[0] = atof( foo );
484	<
485	<	foo = strtok(NULL, " ,;\t");
486	<	if(foo == NULL){
487	<	sprintf( painCave.errMsg,
488	<	"error in reading postition y from %s\n",
489	<	inFileName.c_str());
490	<	return strdup( painCave.errMsg );
491	<	}
492	<	pos[1] = atof( foo );
493	<
494	<	foo = strtok(NULL, " ,;\t");
495	<	if(foo == NULL){
496	<	sprintf( painCave.errMsg,
497	<	"error in reading postition z from %s\n",
498	<	inFileName.c_str());
499	<	return strdup( painCave.errMsg );
500	<	}
501	<	pos[2] = atof( foo );
502	<
503	<
504	<	// get the velocities
505	<
506	<	foo = strtok(NULL, " ,;\t");
507	<	if(foo == NULL){
508	<	sprintf( painCave.errMsg,
509	<	"error in reading velocity x from %s\n",
510	<	inFileName.c_str() );
511	<	return strdup( painCave.errMsg );
512	<	}
513	<	vel[0] = atof( foo );
514	<
515	<	foo = strtok(NULL, " ,;\t");
516	<	if(foo == NULL){
517	<	sprintf( painCave.errMsg,
518	<	"error in reading velocity x from %s\n",
519	<	inFileName.c_str() );
520	<	return strdup( painCave.errMsg );
521	<	}
522	<	vel[1] = atof( foo );
523	<
524	<	foo = strtok(NULL, " ,;\t");
525	<	if(foo == NULL){
526	<	sprintf( painCave.errMsg,
527	<	"error in reading velocity x from %s\n",
528	<	inFileName.c_str() );
529	<	return strdup( painCave.errMsg );
530	<	}
531	<	vel[2] = atof( foo );
532	<
533	<
534	<	// add the positions and velocities to the atom
535	<
536	<	sd->setPos( pos );
537	<	sd->setVel( vel );
538	<
539	<	if (!sd->isDirectional())
540	<	return NULL;
541	<
542	<	// get the quaternions
543	<
544	<	if( sd->isDirectional() ){
545	<
546	<	foo = strtok(NULL, " ,;\t");
547	<	if(foo == NULL){
548	<	sprintf( painCave.errMsg,
549	<	"error in reading velocity x from %s\n",
550	<	inFileName.c_str() );
551	<	return strdup( painCave.errMsg );
552	<	}
553	<	q[0] = atof( foo );
554	<
555	<	foo = strtok(NULL, " ,;\t");
556	<	if(foo == NULL){
557	<	sprintf( painCave.errMsg,
558	<	"error in reading velocity x from %s\n",
559	<	inFileName.c_str() );
560	<	return strdup( painCave.errMsg );
561	<	}
562	<	q[1] = atof( foo );
563	<
564	<	foo = strtok(NULL, " ,;\t");
565	<	if(foo == NULL){
566	<	sprintf( painCave.errMsg,
567	<	"error in reading velocity x from %s\n",
568	<	inFileName.c_str() );
569	<	return strdup( painCave.errMsg );
570	<	}
571	<	q[2] = atof( foo );
572	<
573	<	foo = strtok(NULL, " ,;\t");
574	<	if(foo == NULL){
575	<	sprintf( painCave.errMsg,
576	<	"error in reading velocity x from %s\n",
577	<	inFileName.c_str() );
578	<	return strdup( painCave.errMsg );
579	<	}
580	<	q[3] = atof( foo );
581	<
582	<	// get the angular velocities
583	<
584	<	foo = strtok(NULL, " ,;\t");
585	<	if(foo == NULL){
586	<	sprintf( painCave.errMsg,
587	<	"error in reading velocity x from %s\n",
588	<	inFileName.c_str() );
589	<	return strdup( painCave.errMsg );
590	<	}
591	<	ji[0] = atof( foo );
592	<
593	<	foo = strtok(NULL, " ,;\t");
594	<	if(foo == NULL){
595	<	sprintf( painCave.errMsg,
596	<	"error in reading velocity x from %s\n",
597	<	inFileName.c_str() );
598	<	return strdup( painCave.errMsg );
599	<	}
600	<	ji[1] = atof(foo );
601	<
602	<	foo = strtok(NULL, " ,;\t");
603	<	if(foo == NULL){
604	<	sprintf( painCave.errMsg,
605	<	"error in reading velocity x from %s\n",
606	<	inFileName.c_str() );
607	<	return strdup( painCave.errMsg );
608	<	}
609	<	ji[2] = atof( foo );
610	<
611	<
612	<	// check that the quaternion vector is normalized
613	<
614	<	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
615	<
616	<	if (fabs(qSqr) < 1e-6) {
617	<	sprintf(painCave.errMsg,
618	<	"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
619	<	return strdup(painCave.errMsg);
620	<	}
621	<
622	<	qLength = sqrt( qSqr );
623	<	q[0] = q[0] / qLength;
624	<	q[1] = q[1] / qLength;
625	<	q[2] = q[2] / qLength;
626	<	q[3] = q[3] / qLength;
627	<
628	<	// add quaternion and angular velocities
629	<
630	<	sd->setQ( q );
631	<	sd->setJ( ji );
632	<	}
633	<
634	<
635	<
636	<	return NULL;
637	<	}
638	<
639	<
640	<	char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){
641	<
642	<	double currTime;
643	<	double boxMat[9];
644	<	double theBoxMat3[3][3];
645	<	double chi;
646	<	double integralOfChidt;
647	<	double eta[9];
648	<
649	<	char *foo; // the pointer to the current string token
650	<
651	<	// set the string tokenizer
652	<
653	<	foo = strtok(readLine, " ,;\t");
654	<	// set the timeToken.
655	<
656	<	if(foo == NULL){
657	<	sprintf( painCave.errMsg,
658	<	"error in reading Time from %s\n",
659	<	inFileName.c_str() );
660	<	return strdup( painCave.errMsg );
661	<	}
662	<
663	<	currTime = atof( foo );
664	<	entry_plug->setTime( currTime );
665	<
666	<	//get H-Matrix
667	<
668	<	for(int i = 0 ; i < 9; i++){
669	<	foo = strtok(NULL, " ,;\t");
670	<	if(foo == NULL){
671	<	sprintf( painCave.errMsg,
672	<	"error in reading H[%d] from %s\n", i, inFileName.c_str() );
673	<	return strdup( painCave.errMsg );
674	<	}
675	<	boxMat[i] = atof( foo );
676	<	}
677	<
678	<	for(int i=0;i<3;i++)
679	<	for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
680	<
681	<	//set H-Matrix
682	<	entry_plug->setBoxM( theBoxMat3 );
683	<
684	<	//get chi and integralOfChidt, they should appear by pair
685	<
686	<	if( entry_plug->useInitXSstate ){
687	<	foo = strtok(NULL, " ,;\t\n");
688	<	if(foo != NULL){
689	<	chi = atof(foo);
690	<
691	<	foo = strtok(NULL, " ,;\t\n");
692	<	if(foo == NULL){
693	<	sprintf( painCave.errMsg,
694	<	"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() );
695	<	return strdup( painCave.errMsg );
700	>	std::string propertyName = tokenizer.nextToken();
701	>	if (propertyName == "Time") {
702	>	RealType currTime = tokenizer.nextTokenAsDouble();
703	>	s->setTime(currTime);
704	>	} else if (propertyName == "Hmat"){
705	>	Mat3x3d hmat;
706	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
707	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
708	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
709	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
710	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
711	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
712	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
713	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
714	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
715	>	s->setHmat(hmat);
716	>	} else if (propertyName == "Thermostat") {
717	>	RealType chi = tokenizer.nextTokenAsDouble();
718	>	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
719	>	s->setChi(chi);
720	>	s->setIntegralOfChiDt(integralOfChiDt);
721	>	} else if (propertyName == "Barostat") {
722	>	Mat3x3d eta;
723	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
724	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
725	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
726	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
727	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
728	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
729	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
730	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
731	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
732	>	s->setEta(eta);
733	>	} else {
734	>	sprintf(painCave.errMsg,
735	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
736	>	painCave.isFatal = 0;
737	>	simError();
738		}
697	–	integralOfChidt = atof( foo );
739
699	–	//push chi and integralOfChidt into SimInfo::properties which can be
700	–	//retrieved by integrator later
701	–	DoubleData* chiValue = new DoubleData();
702	–	chiValue->setID(CHIVALUE_ID);
703	–	chiValue->setData(chi);
704	–	entry_plug->addProperty(chiValue);
705	–
706	–	DoubleData* integralOfChidtValue = new DoubleData();
707	–	integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
708	–	integralOfChidtValue->setData(integralOfChidt);
709	–	entry_plug->addProperty(integralOfChidtValue);
710	–
740		}
712	–	else
713	–	return NULL;
714	–
715	–	//get eta
716	–	foo = strtok(NULL, " ,;\t\n");
717	–	if(foo != NULL ){
718	–
719	–	for(int i = 0 ; i < 9; i++){
720	–
721	–	if(foo == NULL){
722	–	sprintf( painCave.errMsg,
723	–	"error in reading eta[%d] from %s\n", i, inFileName.c_str() );
724	–	return strdup( painCave.errMsg );
725	–	}
726	–	eta[i] = atof( foo );
727	–	foo = strtok(NULL, " ,;\t\n");
728	–	}
729	–	}
730	–	else
731	–	return NULL;
732	–
733	–	//push eta into SimInfo::properties which can be
734	–	//retrieved by integrator later
735	–	//entry_plug->setBoxM( theBoxMat3 );
736	–	DoubleArrayData* etaValue = new DoubleArrayData();
737	–	etaValue->setID(ETAVALUE_ID);
738	–	etaValue->setData(eta, 9);
739	–	entry_plug->addProperty(etaValue);
740	–	}
741
742	–	return NULL;
743	–	}
744	–
745	–	#ifdef IS_MPI
746	–	void DumpReader::nodeZeroError( void ){
747	–	int j, myStatus;
748	–
749	–	myStatus = 0;
750	–	for (j = 0; j < mpiSim->getNProcessors(); j++) {
751	–	MPI_Send( &myStatus, 1, MPI_INT, j,
752	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
742		}
743
744	<
745	<	MPI_Finalize();
757	<	exit (0);
758	<
759	<	}
760	<
761	<	void DumpReader::anonymousNodeDie( void ){
762	<
763	<	MPI_Finalize();
764	<	exit (0);
765	<	}
766	<	#endif
744	>
745	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC

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