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

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42	>
43	>	#define _LARGEFILE_SOURCE64
44	>	#define _FILE_OFFSET_BITS 64
45	>
46	>	#ifdef IS_MPI
47	>	#include <mpi.h>
48	>	#endif
49	>
50	>	#include <sys/types.h>
51	>	#include <sys/stat.h>
52	>
53	>	#include <iostream>
54	>	#include <math.h>
55	>
56	>	#include <stdio.h>
57	>	#include <stdlib.h>
58	>	#include <string.h>
59	>
60	>	#include "io/DumpReader.hpp"
61	>	#include "primitives/Molecule.hpp"
62	>	#include "utils/simError.h"
63	>	#include "utils/MemoryUtils.hpp"
64	>	#include "utils/StringTokenizer.hpp"
65	>	#include "brains/Thermo.hpp"
66	>
67	>
68	>	namespace OpenMD {
69	>
70	>	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
71	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
72	>
73	>	#ifdef IS_MPI
74	>
75	>	if (worldRank == 0) {
76	>	#endif
77	>
78	>	inFile_ = new std::ifstream(filename_.c_str(),
79	>	ifstream::in | ifstream::binary);
80	>
81	>	if (inFile_->fail()) {
82	>	sprintf(painCave.errMsg,
83	>	"DumpReader: Cannot open file: %s\n",
84	>	filename_.c_str());
85	>	painCave.isFatal = 1;
86	>	simError();
87	>	}
88	>
89	>	#ifdef IS_MPI
90	>
91	>	}
92	>
93	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
94	>	errorCheckPoint();
95	>
96	>	#endif
97	>
98	>	return;
99	>	}
100	>
101	>	DumpReader::~DumpReader() {
102	>
103	>	#ifdef IS_MPI
104	>
105	>	if (worldRank == 0) {
106	>	#endif
107	>
108	>	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
132	<	#include <sys/types.h>
133	<	#include <sys/stat.h>
132	>	std::streampos prevPos;
133	>	std::streampos  currPos;
134	>
135	>	#ifdef IS_MPI
136	>
137	>	if (worldRank == 0) {
138	>	#endif // is_mpi
139	>
140	>	currPos = inFile_->tellg();
141	>	prevPos = currPos;
142	>	bool foundOpenSnapshotTag = false;
143	>	bool foundClosedSnapshotTag = false;
144
145	<	#include <iostream>
146	<	#include <math.h>
145	>	int lineNo = 0;
146	>	while(inFile_->getline(buffer, bufferSize)) {
147	>	++lineNo;
148	>
149	>	std::string line = buffer;
150	>	currPos = inFile_->tellg();
151	>	if (line.find("<Snapshot>")!= std::string::npos) {
152	>	if (foundOpenSnapshotTag) {
153	>	sprintf(painCave.errMsg,
154	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
155	>	filename_.c_str());
156	>	painCave.isFatal = 1;
157	>	simError();
158	>	}
159	>	foundOpenSnapshotTag = true;
160	>	foundClosedSnapshotTag = false;
161	>	framePos_.push_back(prevPos);
162	>
163	>	} else if (line.find("</Snapshot>") != std::string::npos){
164	>	if (!foundOpenSnapshotTag) {
165	>	sprintf(painCave.errMsg,
166	>	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
167	>	filename_.c_str());
168	>	painCave.isFatal = 1;
169	>	simError();
170	>	}
171	>
172	>	if (foundClosedSnapshotTag) {
173	>	sprintf(painCave.errMsg,
174	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
175	>	filename_.c_str());
176	>	painCave.isFatal = 1;
177	>	simError();
178	>	}
179	>	foundClosedSnapshotTag = true;
180	>	foundOpenSnapshotTag = false;
181	>	}
182	>	prevPos = currPos;
183	>	}
184	>
185	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
186	>	// it and give a warning message
187	>	if (foundOpenSnapshotTag) {
188	>	sprintf(painCave.errMsg,
189	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
190	>	painCave.isFatal = 0;
191	>	simError();
192	>	framePos_.pop_back();
193	>	}
194	>
195	>	nframes_ = framePos_.size();
196	>
197	>	if (nframes_ == 0) {
198	>	sprintf(painCave.errMsg,
199	>	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
200	>	painCave.isFatal = 1;
201	>	simError();
202	>	}
203	>	#ifdef IS_MPI
204	>	}
205	>
206	>	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
207	>
208	>	#endif // is_mpi
209	>
210	>	isScanned_ = true;
211	>	}
212	>
213	>	void DumpReader::readFrame(int whichFrame) {
214	>	if (!isScanned_)
215	>	scanFile();
216	>
217	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
218	>
219	>	if (storageLayout & DataStorage::dslPosition) {
220	>	needPos_ = true;
221	>	} else {
222	>	needPos_ = false;
223	>	}
224	>
225	>	if (storageLayout & DataStorage::dslVelocity) {
226	>	needVel_ = true;
227	>	} else {
228	>	needVel_ = false;
229	>	}
230	>
231	>	if (storageLayout & DataStorage::dslAmat ||
232	>	storageLayout & DataStorage::dslDipole ||
233	>	storageLayout & DataStorage::dslQuadrupole) {
234	>	needQuaternion_ = true;
235	>	} else {
236	>	needQuaternion_ = false;
237	>	}
238	>
239	>	if (storageLayout & DataStorage::dslAngularMomentum) {
240	>	needAngMom_ = true;
241	>	} else {
242	>	needAngMom_ = false;
243	>	}
244	>
245	>	readSet(whichFrame);
246
247	<	#include <stdio.h>
248	<	#include <stdlib.h>
249	<	#include <string.h>
247	>	if (needCOMprops_) {
248	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
249	>	Thermo thermo(info_);
250	>	Vector3d com;
251
252	+	if (needPos_ && needVel_) {
253	+	Vector3d comvel;
254	+	Vector3d comw;
255	+	thermo.getComAll(com, comvel);
256	+	comw = thermo.getAngularMomentum();
257	+	} else {
258	+	com = thermo.getCom();
259	+	}
260	+	}
261	+	}
262	+
263	+	void DumpReader::readSet(int whichFrame) {
264	+	std::string line;
265
266	<	#include "io/ReadWrite.hpp"
267	<	#include "utils/simError.h"
266	>	#ifndef IS_MPI
267	>	inFile_->clear();
268	>	inFile_->seekg(framePos_[whichFrame]);
269
270	<	#ifdef IS_MPI
19	<	#include <mpi.h>
20	<	#include "brains/mpiSimulation.hpp"
21	<	#define TAKE_THIS_TAG_CHAR 0
22	<	#define TAKE_THIS_TAG_INT 1
23	<	#endif // is_mpi
270	>	std::istream& inputStream = *inFile_;
271
272	+	#else
273	+	int masterNode = 0;
274	+	std::stringstream sstream;
275	+	if (worldRank == masterNode) {
276	+	std::string sendBuffer;
277
278	<	DumpReader :: DumpReader(const char *in_name ){
278	>	inFile_->clear();
279	>	inFile_->seekg(framePos_[whichFrame]);
280	>
281	>	while (inFile_->getline(buffer, bufferSize)) {
282
283	<	isScanned = false;
283	>	line = buffer;
284	>	sendBuffer += line;
285	>	sendBuffer += '\n';
286	>	if (line.find("</Snapshot>") != std::string::npos) {
287	>	break;
288	>	}
289	>	}
290
291	<	#ifdef IS_MPI
292	<	if (worldRank == 0) {
293	<	#endif
291	>	int sendBufferSize = sendBuffer.size();
292	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
293	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize,
294	>	MPI_CHAR, masterNode, MPI_COMM_WORLD);
295	>
296	>	sstream.str(sendBuffer);
297	>	} else {
298	>	int sendBufferSize;
299	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
300	>	char * recvBuffer = new char[sendBufferSize+1];
301	>	assert(recvBuffer);
302	>	recvBuffer[sendBufferSize] = '\0';
303	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
304	>	sstream.str(recvBuffer);
305	>	delete [] recvBuffer;
306	>	}
307
308	<	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();
308	>	std::istream& inputStream = sstream;
309		#endif
48	–	return;
49	–	}
310
311	<	DumpReader :: ~DumpReader( ){
52	<	#ifdef IS_MPI
53	<	if (worldRank == 0) {
54	<	#endif
55	<	vector<fpos_t*>::iterator i;
311	>	inputStream.getline(buffer, bufferSize);
312
313	<	int error;
314	<	error = fclose( inFile );
315	<	if( error ){
316	<	sprintf( painCave.errMsg,
317	<	"Error closing %s\n", inFileName.c_str());
318	<	simError();
319	<	}
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	<	for(i = framePos.begin(); i != framePos.end(); ++i)
325	<	delete *i;
67	<	framePos.clear();
68	<
69	<	#ifdef IS_MPI
70	<	}
71	<	strcpy( checkPointMsg, "Dump file closed successfully." );
72	<	MPIcheckPoint();
73	<	#endif
324	>	//read StuntDoubles
325	>	readStuntDoubles(inputStream);
326
327	<	return;
328	<	}
77	<
78	<	int DumpReader::getNframes( void ){
327	>	inputStream.getline(buffer, bufferSize);
328	>	line = buffer;
329
330	<	if( !isScanned )
331	<	scanFile();
332	<	return framePos.size();
333	<	}
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	<	void DumpReader::scanFile( void ){
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	<	int i, j;
359	<	int lineNum = 0;
360	<	char readBuffer[2000];
90	<	fpos_t *currPos;
358	>	int index = tokenizer.nextTokenAsInt();
359	>
360	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
361
362	<	#ifdef IS_MPI
363	<	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 (sd == 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 (sd->isDirectional()) {
383	>	if (needQuaternion_) {
384	>	found = type.find("q");
385	>	if (found == std::string::npos) {
386	>	sprintf(painCave.errMsg,
387	>	"DumpReader Error: Directional StuntDouble %d has no\n"
388	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
389	>	line.c_str());
390	>	painCave.isFatal = 1;
391	>	simError();
392	>	}
393	>	}
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	>	sd->setPos(pos);
406	>	}
407	>	break;
408	>	}
409	>	case 'v' : {
410	>	Vector3d vel;
411	>	vel[0] = tokenizer.nextTokenAsDouble();
412	>	vel[1] = tokenizer.nextTokenAsDouble();
413	>	vel[2] = tokenizer.nextTokenAsDouble();
414	>	if (needVel_) {
415	>	sd->setVel(vel);
416	>	}
417	>	break;
418	>	}
419
420	<	void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
420	>	case 'q' : {
421	>	Quat4d q;
422	>	if (sd->isDirectional()) {
423	>
424	>	q[0] = tokenizer.nextTokenAsDouble();
425	>	q[1] = tokenizer.nextTokenAsDouble();
426	>	q[2] = tokenizer.nextTokenAsDouble();
427	>	q[3] = tokenizer.nextTokenAsDouble();
428	>
429	>	RealType qlen = q.length();
430	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
431	>
432	>	sprintf(painCave.errMsg,
433	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
434	>	painCave.isFatal = 1;
435	>	simError();
436	>
437	>	}
438	>
439	>	q.normalize();
440	>	if (needQuaternion_) {
441	>	sd->setQ(q);
442	>	}
443	>	}
444	>	break;
445	>	}
446	>	case 'j' : {
447	>	Vector3d ji;
448	>	if (sd->isDirectional()) {
449	>	ji[0] = tokenizer.nextTokenAsDouble();
450	>	ji[1] = tokenizer.nextTokenAsDouble();
451	>	ji[2] = tokenizer.nextTokenAsDouble();
452	>	if (needAngMom_) {
453	>	sd->setJ(ji);
454	>	}
455	>	}
456	>	break;
457	>	}
458	>	case 'f': {
459
460	<	simnfo = the_simnfo;
460	>	Vector3d force;
461	>	force[0] = tokenizer.nextTokenAsDouble();
462	>	force[1] = tokenizer.nextTokenAsDouble();
463	>	force[2] = tokenizer.nextTokenAsDouble();
464	>	sd->setFrc(force);
465	>	break;
466	>	}
467	>	case 't' : {
468
469	<	this->readSet( whichFrame );
470	<	}
469	>	Vector3d torque;
470	>	torque[0] = tokenizer.nextTokenAsDouble();
471	>	torque[1] = tokenizer.nextTokenAsDouble();
472	>	torque[2] = tokenizer.nextTokenAsDouble();
473	>	sd->setTrq(torque);
474	>	break;
475	>	}
476	>	case 'u' : {
477
478	+	RealType particlePot;
479	+	particlePot = tokenizer.nextTokenAsDouble();
480	+	sd->setParticlePot(particlePot);
481	+	break;
482	+	}
483	+	case 'c' : {
484
485	+	RealType flucQPos;
486	+	flucQPos = tokenizer.nextTokenAsDouble();
487	+	sd->setFlucQPos(flucQPos);
488	+	break;
489	+	}
490	+	case 'w' : {
491
492	<	void DumpReader :: readSet( int whichFrame ){
492	>	RealType flucQVel;
493	>	flucQVel = tokenizer.nextTokenAsDouble();
494	>	sd->setFlucQVel(flucQVel);
495	>	break;
496	>	}
497	>	case 'g' : {
498
499	<	int i;
500	<	unsigned int j;
499	>	RealType flucQFrc;
500	>	flucQFrc = tokenizer.nextTokenAsDouble();
501	>	sd->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	>	sd->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	<	char *eof_test; // ptr to see when we reach the end of the file
186	<	char *parseErr;
526	>	void DumpReader::parseSiteLine(const std::string& line) {
527
528	<	vector<StuntDouble*> integrableObjects;
528	>	StringTokenizer tokenizer(line);
529	>	int nTokens;
530	>
531	>	nTokens = tokenizer.countTokens();
532	>
533	>	if (nTokens < 2) {
534	>	sprintf(painCave.errMsg,
535	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
536	>	painCave.isFatal = 1;
537	>	simError();
538	>	}
539
540	+	/**
541	+	* The first token is the global integrable object index.
542	+	*/
543
544	<	#ifndef IS_MPI
544	>	int index = tokenizer.nextTokenAsInt();
545	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
546	>	if (sd == NULL) {
547	>	return;
548	>	}
549
550	<	fsetpos(inFile, framePos[whichFrame]);
551	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
552	<	if( eof_test == NULL ){
553	<	sprintf( painCave.errMsg,
554	<	"DumpReader error: error reading 1st line of \"%s\"\n",
198	<	inFileName.c_str() );
199	<	painCave.isFatal = 1;
200	<	simError();
201	<	}
550	>	/**
551	>	* Test to see if the next token is an integer or not.  If not,
552	>	* we've got data on the integrable object itself.  If there is an
553	>	* integer, we're parsing data for a site on a rigid body.
554	>	*/
555
556	<	nTotObjs = atoi( read_buffer );
556	>	std::string indexTest = tokenizer.peekNextToken();
557	>	std::istringstream i(indexTest);
558	>	int siteIndex;
559	>	if (i >> siteIndex) {
560	>	// chew up this token and parse as an int:
561	>	siteIndex = tokenizer.nextTokenAsInt();
562
563	<	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
564	<	sprintf( painCave.errMsg,
565	<	"DumpReader error. %s nIntegrable, %d, "
566	<	"does not match the meta-data file's nIntegrable, %d.\n",
567	<	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
213	<
214	<	//read the box mat from the comment line
563	>	if (sd->isRigidBody()) {
564	>	RigidBody* rb = static_cast<RigidBody*>(sd);
565	>	sd = rb->getAtoms()[siteIndex];
566	>	}
567	>	}
568
569	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
570	<	if(eof_test == NULL){
571	<	sprintf( painCave.errMsg,
572	<	"error in reading commment in %s\n", inFileName.c_str());
573	<	painCave.isFatal = 1;
574	<	simError();
575	<	}
576	<
577	<	parseErr = parseCommentLine( read_buffer, simnfo);
578	<	if( parseErr != NULL ){
579	<	strcpy( painCave.errMsg, parseErr );
580	<	painCave.isFatal = 1;
581	<	simError();
582	<	}
583	<
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();
569	>	/**
570	>	* The next token contains information on what follows.
571	>	*/
572	>	std::string type = tokenizer.nextToken();
573	>	int size = type.size();
574	>
575	>	for(int i = 0; i < size; ++i) {
576	>	switch(type[i]) {
577	>
578	>	case 'u' : {
579	>
580	>	RealType particlePot;
581	>	particlePot = tokenizer.nextTokenAsDouble();
582	>	sd->setParticlePot(particlePot);
583	>	break;
584		}
585	<
586	<	parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
587	<	if( parseErr != NULL ){
588	<	strcpy( painCave.errMsg, parseErr );
589	<	painCave.isFatal = 1;
590	<	simError();
585	>	case 'c' : {
586	>
587	>	RealType flucQPos;
588	>	flucQPos = tokenizer.nextTokenAsDouble();
589	>	sd->setFlucQPos(flucQPos);
590	>	break;
591		}
592	<	}
593	<	}
594	<
595	<	// MPI Section of code..........
596	<	#else //IS_MPI
597	<
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();
592	>	case 'w' : {
593	>
594	>	RealType flucQVel;
595	>	flucQVel = tokenizer.nextTokenAsDouble();
596	>	sd->setFlucQVel(flucQVel);
597	>	break;
598		}
599	<
340	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
341	<	for(j=0; j < integrableObjects.size(); j++){
599	>	case 'g' : {
600
601	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
602	<	if(eof_test == NULL){
603	<	sprintf(painCave.errMsg,
604	<	"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	<
601	>	RealType flucQFrc;
602	>	flucQFrc = tokenizer.nextTokenAsDouble();
603	>	sd->setFlucQFrc(flucQFrc);
604	>	break;
605		}
606	<	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++){
606	>	case 'e' : {
607
608	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
609	<	if(eof_test == NULL){
610	<	sprintf(painCave.errMsg,
611	<	"error in reading file %s\n"
612	<	"natoms  = %d; index = %d\n"
613	<	"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	<
608	>	Vector3d eField;
609	>	eField[0] = tokenizer.nextTokenAsDouble();
610	>	eField[1] = tokenizer.nextTokenAsDouble();
611	>	eField[2] = tokenizer.nextTokenAsDouble();
612	>	sd->setElectricField(eField);
613	>	break;
614		}
615	<
616	<	}
615	>	default: {
616	>	sprintf(painCave.errMsg,
617	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
618	>	painCave.isFatal = 1;
619	>	simError();
620	>	break;
621	>	}
622	>	}
623	>	}
624	>	}
625	>
626	>
627	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
628
629	<	}
630	<	else{
631	<	//actions taken at slave nodes
632	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
629	>	inputStream.getline(buffer, bufferSize);
630	>	std::string line(buffer);
631	>
632	>	if (line.find("<StuntDoubles>") == std::string::npos) {
633	>	sprintf(painCave.errMsg,
634	>	"DumpReader Error: Missing <StuntDoubles>\n");
635	>	painCave.isFatal = 1;
636	>	simError();
637	>	}
638
639	<	parseErr = parseCommentLine( read_buffer, simnfo);
639	>	while(inputStream.getline(buffer, bufferSize)) {
640	>	line = buffer;
641	>
642	>	if(line.find("</StuntDoubles>") != std::string::npos) {
643	>	break;
644	>	}
645
646	<	if( parseErr != NULL ){
400	<	strcpy( painCave.errMsg, parseErr );
401	<	haveError = 1;
402	<	simError();
646	>	parseDumpLine(line);
647		}
648
649	<	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);
649	>	}
650
651	<	if(localIndex == -1) {
414	<	sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
415	<	haveError = 1;
416	<	simError();
417	<	}
651	>	void  DumpReader::readSiteData(std::istream& inputStream) {
652
653	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
653	>	std::string line(buffer);
654
655	<	nCurObj = integrableObjects.size();
656	<
657	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
658	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
659	<
660	<	for(j = 0; j < integrableObjects.size(); j++){
427	<
428	<	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
429	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
430	<
431	<	parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
432	<
433	<	if( parseErr != NULL ){
434	<	strcpy( painCave.errMsg, parseErr );
435	<	simError();
436	<	}
437	<
438	<	}
439	<
440	<	}
655	>	// We already found the starting <SiteData> tag or we wouldn't be
656	>	// here, so just start parsing until we get to the ending
657	>	// </SiteData> tag:
658	>
659	>	while(inputStream.getline(buffer, bufferSize)) {
660	>	line = buffer;
661
662	<	}
662	>	if(line.find("</SiteData>") != std::string::npos) {
663	>	break;
664	>	}
665
666	+	parseSiteLine(line);
667	+	}
668	+
669		}
670
671	<	#endif
447	<	}
671	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
672
673	<	char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
673	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
674	>	inputStream.getline(buffer, bufferSize);
675	>	std::string line(buffer);
676
677	<	char *foo; // the pointer to the current string token
677	>	if (line.find("<FrameData>") == std::string::npos) {
678	>	sprintf(painCave.errMsg,
679	>	"DumpReader Error: Missing <FrameData>\n");
680	>	painCave.isFatal = 1;
681	>	simError();
682	>	}
683
684	<	double pos[3]; // position place holders
685	<	double vel[3]; // velocity placeholders
455	<	double q[4]; // the quaternions
456	<	double ji[3]; // angular velocity placeholders;
457	<	double qSqr, qLength; // needed to normalize the quaternion vector.
458	<
459	<
460	<	// set the string tokenizer
461	<
462	<	foo = strtok(readLine, " ,;\t");
463	<
464	<	// check the atom name to the current atom
465	<
466	<	if( strcmp( foo, sd->getType() ) ){
467	<	sprintf( painCave.errMsg,
468	<	"DumpReader error.  Does not"
469	<	" match the meta-data atom %s.\n",
470	<	sd->getType() );
471	<	return strdup( painCave.errMsg );
472	<	}
473	<
474	<	// get the positions
475	<
476	<	foo = strtok(NULL, " ,;\t");
477	<	if(foo == NULL){
478	<	sprintf( painCave.errMsg,
479	<	"error in reading postition x from %s\n",
480	<	inFileName.c_str());
481	<	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);
684	>	while(inputStream.getline(buffer, bufferSize)) {
685	>	line = buffer;
686
687	<	foo = strtok(NULL, " ,;\t\n");
688	<	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 );
687	>	if(line.find("</FrameData>") != std::string::npos) {
688	>	break;
689		}
697	–	integralOfChidt = atof( foo );
690
691	<	//push chi and integralOfChidt into SimInfo::properties which can be
692	<	//retrieved by integrator later
693	<	DoubleData* chiValue = new DoubleData();
694	<	chiValue->setID(CHIVALUE_ID);
695	<	chiValue->setData(chi);
696	<	entry_plug->addProperty(chiValue);
691	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
692	>	if (!tokenizer.hasMoreTokens()) {
693	>	sprintf(painCave.errMsg,
694	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
695	>	painCave.isFatal = 1;
696	>	simError();
697	>	}
698	>
699	>	std::string propertyName = tokenizer.nextToken();
700	>	if (propertyName == "Time") {
701	>	RealType currTime = tokenizer.nextTokenAsDouble();
702	>	s->setTime(currTime);
703	>	} else if (propertyName == "Hmat"){
704	>	Mat3x3d hmat;
705	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
706	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
707	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
708	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
709	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
710	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
711	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
712	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
713	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
714	>	s->setHmat(hmat);
715	>	} else if (propertyName == "Thermostat") {
716	>	pair<RealType, RealType> thermostat;
717	>	thermostat.first = tokenizer.nextTokenAsDouble();
718	>	thermostat.second = tokenizer.nextTokenAsDouble();
719	>	s->setThermostat(thermostat);
720	>	} else if (propertyName == "Barostat") {
721	>	Mat3x3d eta;
722	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
723	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
724	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
725	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
726	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
727	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
728	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
729	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
730	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
731	>	s->setBarostat(eta);
732	>	} else {
733	>	sprintf(painCave.errMsg,
734	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
735	>	painCave.isFatal = 0;
736	>	simError();
737	>	}
738
706	–	DoubleData* integralOfChidtValue = new DoubleData();
707	–	integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
708	–	integralOfChidtValue->setData(integralOfChidt);
709	–	entry_plug->addProperty(integralOfChidtValue);
710	–
739		}
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	–	}
740
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);
741		}
742
743	<
744	<	MPI_Finalize();
757	<	exit (0);
758	<
759	<	}
760	<
761	<	void DumpReader::anonymousNodeDie( void ){
762	<
763	<	MPI_Finalize();
764	<	exit (0);
765	<	}
766	<	#endif
743	>
744	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpReader.cpp (property svn:keywords):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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