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 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1787 by gezelter, Wed Aug 29 18:13:11 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	>	#include "brains/Thermo.hpp"
62	>
63	>	#ifdef IS_MPI
64	>	#include <mpi.h>
65	>	#endif
66	>
67	>
68	>	namespace OpenMD {
69	>
70	>	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
71	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
72	>
73	>	#ifdef IS_MPI
74	>
75	>	if (worldRank == 0) {
76	>	#endif
77	>
78	>	inFile_ = new std::ifstream(filename_.c_str());
79	>
80	>	if (inFile_->fail()) {
81	>	sprintf(painCave.errMsg,
82	>	"DumpReader: Cannot open file: %s\n",
83	>	filename_.c_str());
84	>	painCave.isFatal = 1;
85	>	simError();
86	>	}
87	>
88	>	#ifdef IS_MPI
89	>
90	>	}
91	>
92	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
93	>	errorCheckPoint();
94	>
95	>	#endif
96	>
97	>	return;
98	>	}
99	>
100	>	DumpReader::~DumpReader() {
101	>
102	>	#ifdef IS_MPI
103	>
104	>	if (worldRank == 0) {
105	>	#endif
106	>
107	>	delete inFile_;
108	>
109	>	#ifdef IS_MPI
110	>
111	>	}
112	>
113	>	strcpy(checkPointMsg, "Dump file closed successfully.");
114	>	errorCheckPoint();
115	>
116	>	#endif
117	>
118	>	return;
119	>	}
120	>
121	>	int DumpReader::getNFrames(void) {
122	>
123	>	if (!isScanned_)
124	>	scanFile();
125	>
126	>	return nframes_;
127	>	}
128	>
129	>	void DumpReader::scanFile(void) {
130	>	int lineNo = 0;
131	>	std::streampos prevPos;
132	>	std::streampos  currPos;
133	>
134	>	#ifdef IS_MPI
135	>
136	>	if (worldRank == 0) {
137	>	#endif // is_mpi
138	>
139	>	currPos = inFile_->tellg();
140	>	prevPos = currPos;
141	>	bool foundOpenSnapshotTag = false;
142	>	bool foundClosedSnapshotTag = false;
143	>	bool foundOpenSiteDataTag = false;
144	>	while(inFile_->getline(buffer, bufferSize)) {
145	>	++lineNo;
146	>
147	>	std::string line = buffer;
148	>	currPos = inFile_->tellg();
149	>	if (line.find("<Snapshot>")!= std::string::npos) {
150	>	if (foundOpenSnapshotTag) {
151	>	sprintf(painCave.errMsg,
152	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
153	>	filename_.c_str());
154	>	painCave.isFatal = 1;
155	>	simError();
156	>	}
157	>	foundOpenSnapshotTag = true;
158	>	foundClosedSnapshotTag = false;
159	>	framePos_.push_back(prevPos);
160	>
161	>	} else if (line.find("</Snapshot>") != std::string::npos){
162	>	if (!foundOpenSnapshotTag) {
163	>	sprintf(painCave.errMsg,
164	>	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
165	>	filename_.c_str());
166	>	painCave.isFatal = 1;
167	>	simError();
168	>	}
169	>
170	>	if (foundClosedSnapshotTag) {
171	>	sprintf(painCave.errMsg,
172	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
173	>	filename_.c_str());
174	>	painCave.isFatal = 1;
175	>	simError();
176	>	}
177	>	foundClosedSnapshotTag = true;
178	>	foundOpenSnapshotTag = false;
179	>	}
180	>	prevPos = currPos;
181	>	}
182	>
183	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
184	>	// it and give a warning message
185	>	if (foundOpenSnapshotTag) {
186	>	sprintf(painCave.errMsg,
187	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
188	>	painCave.isFatal = 0;
189	>	simError();
190	>	framePos_.pop_back();
191	>	}
192	>
193	>	nframes_ = framePos_.size();
194	>
195	>	if (nframes_ == 0) {
196	>	sprintf(painCave.errMsg,
197	>	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
198	>	painCave.isFatal = 1;
199	>	simError();
200	>	}
201	>	#ifdef IS_MPI
202	>	}
203	>
204	>	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
205	>
206	>	#endif // is_mpi
207	>
208	>	isScanned_ = true;
209	>	}
210	>
211	>	void DumpReader::readFrame(int whichFrame) {
212	>	if (!isScanned_)
213	>	scanFile();
214	>
215	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
216	>
217	>	if (storageLayout & DataStorage::dslPosition) {
218	>	needPos_ = true;
219	>	} else {
220	>	needPos_ = false;
221	>	}
222	>
223	>	if (storageLayout & DataStorage::dslVelocity) {
224	>	needVel_ = true;
225	>	} else {
226	>	needVel_ = false;
227	>	}
228	>
229	>	if (storageLayout & DataStorage::dslAmat ||
230	>	storageLayout & DataStorage::dslDipole ||
231	>	storageLayout & DataStorage::dslQuadrupole) {
232	>	needQuaternion_ = true;
233	>	} else {
234	>	needQuaternion_ = false;
235	>	}
236	>
237	>	if (storageLayout & DataStorage::dslAngularMomentum) {
238	>	needAngMom_ = true;
239	>	} else {
240	>	needAngMom_ = false;
241	>	}
242	>
243	>	readSet(whichFrame);
244
245	<	#include <sys/types.h>
246	<	#include <sys/stat.h>
245	>	if (needCOMprops_) {
246	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
247	>	Thermo thermo(info_);
248	>	Vector3d com;
249
250	<	#include <iostream>
251	<	#include <math.h>
250	>	if (needPos_ && needVel_) {
251	>	Vector3d comvel;
252	>	Vector3d comw;
253	>	thermo.getComAll(com, comvel);
254	>	comw = thermo.getAngularMomentum();
255	>	} else {
256	>	com = thermo.getCom();
257	>	}
258	>	}
259	>	}
260	>
261	>	void DumpReader::readSet(int whichFrame) {
262	>	std::string line;
263
264	<	#include <stdio.h>
265	<	#include <stdlib.h>
266	<	#include <string.h>
264	>	#ifndef IS_MPI
265	>	inFile_->clear();
266	>	inFile_->seekg(framePos_[whichFrame]);
267
268	+	std::istream& inputStream = *inFile_;
269
270	<	#include "ReadWrite.hpp"
271	<	#include "simError.h"
270	>	#else
271	>	int masterNode = 0;
272	>	std::stringstream sstream;
273	>	if (worldRank == masterNode) {
274	>	std::string sendBuffer;
275
276	<	#ifdef IS_MPI
277	<	#include <mpi.h>
278	<	#include "mpiSimulation.hpp"
279	<	#define TAKE_THIS_TAG_CHAR 0
22	<	#define TAKE_THIS_TAG_INT 1
23	<	#endif // is_mpi
276	>	inFile_->clear();
277	>	inFile_->seekg(framePos_[whichFrame]);
278	>
279	>	while (inFile_->getline(buffer, bufferSize)) {
280
281	+	line = buffer;
282	+	sendBuffer += line;
283	+	sendBuffer += '\n';
284	+	if (line.find("</Snapshot>") != std::string::npos) {
285	+	break;
286	+	}
287	+	}
288
289	<	DumpReader :: DumpReader(const char *in_name ){
289	>	int sendBufferSize = sendBuffer.size();
290	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
291	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
292	>
293	>	sstream.str(sendBuffer);
294	>	} else {
295	>	int sendBufferSize;
296	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
297	>	char * recvBuffer = new char[sendBufferSize+1];
298	>	assert(recvBuffer);
299	>	recvBuffer[sendBufferSize] = '\0';
300	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
301	>	sstream.str(recvBuffer);
302	>	delete [] recvBuffer;
303	>	}
304
305	<	isScanned = false;
29	<
30	<	#ifdef IS_MPI
31	<	if (worldRank == 0) {
305	>	std::istream& inputStream = sstream;
306		#endif
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();
47	<	#endif
48	<	return;
49	<	}
308	>	inputStream.getline(buffer, bufferSize);
309
310	<	DumpReader :: ~DumpReader( ){
311	<	#ifdef IS_MPI
312	<	if (worldRank == 0) {
313	<	#endif
314	<	vector<fpos_t*>::iterator i;
310	>	line = buffer;
311	>	if (line.find("<Snapshot>") == std::string::npos) {
312	>	sprintf(painCave.errMsg,
313	>	"DumpReader Error: can not find <Snapshot>\n");
314	>	painCave.isFatal = 1;
315	>	simError();
316	>	}
317	>
318	>	//read frameData
319	>	readFrameProperties(inputStream);
320
321	<	int error;
322	<	error = fclose( inFile );
59	<	if( error ){
60	<	sprintf( painCave.errMsg,
61	<	"Error closing %s\n", inFileName.c_str());
62	<	simError();
63	<	}
321	>	//read StuntDoubles
322	>	readStuntDoubles(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
74	<
75	<	return;
76	<	}
324	>	inputStream.getline(buffer, bufferSize);
325	>	line = buffer;
326
327	<	int DumpReader::getNframes( void ){
327	>	if (line.find("<SiteData>") != std::string::npos) {
328	>	//read SiteData
329	>	readSiteData(inputStream);
330	>	} else {
331	>	if (line.find("</Snapshot>") == std::string::npos) {
332	>	sprintf(painCave.errMsg,
333	>	"DumpReader Error: can not find </Snapshot>\n");
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338	>	}
339	>
340	>	void DumpReader::parseDumpLine(const std::string& line) {
341
342	<	if( !isScanned )
343	<	scanFile();
344	<	return framePos.size();
345	<	}
342	>
343	>	StringTokenizer tokenizer(line);
344	>	int nTokens;
345	>
346	>	nTokens = tokenizer.countTokens();
347	>
348	>	if (nTokens < 2) {
349	>	sprintf(painCave.errMsg,
350	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
351	>	painCave.isFatal = 1;
352	>	simError();
353	>	}
354
355	<	void DumpReader::scanFile( void ){
355	>	int index = tokenizer.nextTokenAsInt();
356	>
357	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
358
359	<	int i, j;
360	<	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();
359	>	if (sd == NULL) {
360	>	return;
361		}
362	+	std::string type = tokenizer.nextToken();
363	+	int size = type.size();
364
365	<	while( !feof( inFile ) ){
366	<
367	<	framePos.push_back(currPos);
368	<
369	<	i = atoi(readBuffer);
370	<
371	<	fgets( readBuffer, sizeof( readBuffer ), inFile );
372	<	lineNum++;
373	<	if( feof( inFile ) ){
374	<	sprintf( painCave.errMsg,
375	<	"File \"%s\" ended unexpectedly at line %d\n",
122	<	inFileName.c_str(),
123	<	lineNum );
124	<	painCave.isFatal = 1;
125	<	simError();
365	>	size_t found;
366	>
367	>	if (needPos_) {
368	>	found = type.find("p");
369	>	if (found == std::string::npos) {
370	>	sprintf(painCave.errMsg,
371	>	"DumpReader Error: StuntDouble %d has no Position\n"
372	>	"\tField (\"p\") specified.\n%s\n", index,
373	>	line.c_str());
374	>	painCave.isFatal = 1;
375	>	simError();
376		}
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++;
377		}
378
379	<	delete currPos;
380	<	rewind( inFile );
381	<
382	<	isScanned = true;
379	>	if (sd->isDirectional()) {
380	>	if (needQuaternion_) {
381	>	found = type.find("q");
382	>	if (found == std::string::npos) {
383	>	sprintf(painCave.errMsg,
384	>	"DumpReader Error: Directional StuntDouble %d has no\n"
385	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
386	>	line.c_str());
387	>	painCave.isFatal = 1;
388	>	simError();
389	>	}
390	>	}
391	>	}
392
393	<	#ifdef IS_MPI
394	<	}
395	<	strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
396	<	MPIcheckPoint();
397	<	#endif // is_mpi
398	<	}
393	>	for(int i = 0; i < size; ++i) {
394	>	switch(type[i]) {
395	>
396	>	case 'p': {
397	>	Vector3d pos;
398	>	pos[0] = tokenizer.nextTokenAsDouble();
399	>	pos[1] = tokenizer.nextTokenAsDouble();
400	>	pos[2] = tokenizer.nextTokenAsDouble();
401	>	if (needPos_) {
402	>	sd->setPos(pos);
403	>	}
404	>	break;
405	>	}
406	>	case 'v' : {
407	>	Vector3d vel;
408	>	vel[0] = tokenizer.nextTokenAsDouble();
409	>	vel[1] = tokenizer.nextTokenAsDouble();
410	>	vel[2] = tokenizer.nextTokenAsDouble();
411	>	if (needVel_) {
412	>	sd->setVel(vel);
413	>	}
414	>	break;
415	>	}
416
417	<	void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
417	>	case 'q' : {
418	>	Quat4d q;
419	>	if (sd->isDirectional()) {
420	>
421	>	q[0] = tokenizer.nextTokenAsDouble();
422	>	q[1] = tokenizer.nextTokenAsDouble();
423	>	q[2] = tokenizer.nextTokenAsDouble();
424	>	q[3] = tokenizer.nextTokenAsDouble();
425	>
426	>	RealType qlen = q.length();
427	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
428	>
429	>	sprintf(painCave.errMsg,
430	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
431	>	painCave.isFatal = 1;
432	>	simError();
433	>
434	>	}
435	>
436	>	q.normalize();
437	>	if (needQuaternion_) {
438	>	sd->setQ(q);
439	>	}
440	>	}
441	>	break;
442	>	}
443	>	case 'j' : {
444	>	Vector3d ji;
445	>	if (sd->isDirectional()) {
446	>	ji[0] = tokenizer.nextTokenAsDouble();
447	>	ji[1] = tokenizer.nextTokenAsDouble();
448	>	ji[2] = tokenizer.nextTokenAsDouble();
449	>	if (needAngMom_) {
450	>	sd->setJ(ji);
451	>	}
452	>	}
453	>	break;
454	>	}
455	>	case 'f': {
456
457	<	simnfo = the_simnfo;
457	>	Vector3d force;
458	>	force[0] = tokenizer.nextTokenAsDouble();
459	>	force[1] = tokenizer.nextTokenAsDouble();
460	>	force[2] = tokenizer.nextTokenAsDouble();
461	>	sd->setFrc(force);
462	>	break;
463	>	}
464	>	case 't' : {
465
466	<	this->readSet( whichFrame );
467	<	}
466	>	Vector3d torque;
467	>	torque[0] = tokenizer.nextTokenAsDouble();
468	>	torque[1] = tokenizer.nextTokenAsDouble();
469	>	torque[2] = tokenizer.nextTokenAsDouble();
470	>	sd->setTrq(torque);
471	>	break;
472	>	}
473	>	case 'u' : {
474
475	+	RealType particlePot;
476	+	particlePot = tokenizer.nextTokenAsDouble();
477	+	sd->setParticlePot(particlePot);
478	+	break;
479	+	}
480	+	case 'c' : {
481
482	+	RealType flucQPos;
483	+	flucQPos = tokenizer.nextTokenAsDouble();
484	+	sd->setFlucQPos(flucQPos);
485	+	break;
486	+	}
487	+	case 'w' : {
488
489	<	void DumpReader :: readSet( int whichFrame ){
489	>	RealType flucQVel;
490	>	flucQVel = tokenizer.nextTokenAsDouble();
491	>	sd->setFlucQVel(flucQVel);
492	>	break;
493	>	}
494	>	case 'g' : {
495
496	<	int i;
497	<	unsigned int j;
496	>	RealType flucQFrc;
497	>	flucQFrc = tokenizer.nextTokenAsDouble();
498	>	sd->setFlucQFrc(flucQFrc);
499	>	break;
500	>	}
501	>	case 'e' : {
502
503	<	#ifdef IS_MPI
504	<	int done, which_node, which_atom; // loop counter
505	<	#endif //is_mpi
503	>	Vector3d eField;
504	>	eField[0] = tokenizer.nextTokenAsDouble();
505	>	eField[1] = tokenizer.nextTokenAsDouble();
506	>	eField[2] = tokenizer.nextTokenAsDouble();
507	>	sd->setElectricField(eField);
508	>	break;
509	>	}
510	>	default: {
511	>	sprintf(painCave.errMsg,
512	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
513	>	painCave.isFatal = 1;
514	>	simError();
515	>	break;
516	>	}
517
518	<	const int BUFFERSIZE = 2000; // size of the read buffer
519	<	int nTotObjs; // the number of atoms
520	<	char read_buffer[BUFFERSIZE]; //the line buffer for reading
518	>	}
519	>	}
520	>
521	>	}
522	>
523
524	<	char *eof_test; // ptr to see when we reach the end of the file
186	<	char *parseErr;
524	>	void DumpReader::parseSiteLine(const std::string& line) {
525
526	<	vector<StuntDouble*> integrableObjects;
526	>	StringTokenizer tokenizer(line);
527	>	int nTokens;
528	>
529	>	nTokens = tokenizer.countTokens();
530	>
531	>	if (nTokens < 2) {
532	>	sprintf(painCave.errMsg,
533	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
534	>	painCave.isFatal = 1;
535	>	simError();
536	>	}
537
538	+	/**
539	+	* The first token is the global integrable object index.
540	+	*/
541
542	<	#ifndef IS_MPI
542	>	int index = tokenizer.nextTokenAsInt();
543	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
544	>	if (sd == NULL) {
545	>	return;
546	>	}
547
548	<	fsetpos(inFile, framePos[whichFrame]);
549	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
550	<	if( eof_test == NULL ){
551	<	sprintf( painCave.errMsg,
552	<	"DumpReader error: error reading 1st line of \"%s\"\n",
198	<	inFileName.c_str() );
199	<	painCave.isFatal = 1;
200	<	simError();
201	<	}
548	>	/**
549	>	* Test to see if the next token is an integer or not.  If not,
550	>	* we've got data on the integrable object itself.  If there is an
551	>	* integer, we're parsing data for a site on a rigid body.
552	>	*/
553
554	<	nTotObjs = atoi( read_buffer );
554	>	std::string indexTest = tokenizer.peekNextToken();
555	>	std::istringstream i(indexTest);
556	>	int siteIndex;
557	>	if (i >> siteIndex) {
558	>	// chew up this token and parse as an int:
559	>	siteIndex = tokenizer.nextTokenAsInt();
560	>	RigidBody* rb = static_cast<RigidBody*>(sd);
561	>	sd = rb->getAtoms()[siteIndex];
562	>	}
563
564	<	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
565	<	sprintf( painCave.errMsg,
566	<	"DumpReader error. %s nIntegrable, %d, "
567	<	"does not match the meta-data file's nIntegrable, %d.\n",
568	<	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
569	<	painCave.isFatal = 1;
570	<	simError();
571	<	}
572	<
573	<	//read the box mat from the comment line
574	<
575	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
576	<	if(eof_test == NULL){
577	<	sprintf( painCave.errMsg,
578	<	"error in reading commment in %s\n", inFileName.c_str());
220	<	painCave.isFatal = 1;
221	<	simError();
222	<	}
223	<
224	<	parseErr = parseCommentLine( read_buffer, simnfo);
225	<	if( parseErr != NULL ){
226	<	strcpy( painCave.errMsg, parseErr );
227	<	painCave.isFatal = 1;
228	<	simError();
229	<	}
230	<
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();
564	>	/**
565	>	* The next token contains information on what follows.
566	>	*/
567	>	std::string type = tokenizer.nextToken();
568	>	int size = type.size();
569	>
570	>	for(int i = 0; i < size; ++i) {
571	>	switch(type[i]) {
572	>
573	>	case 'u' : {
574	>
575	>	RealType particlePot;
576	>	particlePot = tokenizer.nextTokenAsDouble();
577	>	sd->setParticlePot(particlePot);
578	>	break;
579		}
580	<
581	<	parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
582	<	if( parseErr != NULL ){
583	<	strcpy( painCave.errMsg, parseErr );
584	<	painCave.isFatal = 1;
585	<	simError();
580	>	case 'c' : {
581	>
582	>	RealType flucQPos;
583	>	flucQPos = tokenizer.nextTokenAsDouble();
584	>	sd->setFlucQPos(flucQPos);
585	>	break;
586		}
587	<	}
588	<	}
589	<
590	<	// MPI Section of code..........
591	<	#else //IS_MPI
592	<
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();
587	>	case 'w' : {
588	>
589	>	RealType flucQVel;
590	>	flucQVel = tokenizer.nextTokenAsDouble();
591	>	sd->setFlucQVel(flucQVel);
592	>	break;
593		}
594	<
340	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
341	<	for(j=0; j < integrableObjects.size(); j++){
594	>	case 'g' : {
595
596	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
597	<	if(eof_test == NULL){
598	<	sprintf(painCave.errMsg,
599	<	"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	<
596	>	RealType flucQFrc;
597	>	flucQFrc = tokenizer.nextTokenAsDouble();
598	>	sd->setFlucQFrc(flucQFrc);
599	>	break;
600		}
601	<	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++){
601	>	case 'e' : {
602
603	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
604	<	if(eof_test == NULL){
605	<	sprintf(painCave.errMsg,
606	<	"error in reading file %s\n"
607	<	"natoms  = %d; index = %d\n"
608	<	"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	<
603	>	Vector3d eField;
604	>	eField[0] = tokenizer.nextTokenAsDouble();
605	>	eField[1] = tokenizer.nextTokenAsDouble();
606	>	eField[2] = tokenizer.nextTokenAsDouble();
607	>	sd->setElectricField(eField);
608	>	break;
609		}
610	<
611	<	}
610	>	default: {
611	>	sprintf(painCave.errMsg,
612	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
613	>	painCave.isFatal = 1;
614	>	simError();
615	>	break;
616	>	}
617	>	}
618	>	}
619	>	}
620	>
621	>
622	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
623
624	<	}
625	<	else{
626	<	//actions taken at slave nodes
627	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
624	>	inputStream.getline(buffer, bufferSize);
625	>	std::string line(buffer);
626	>
627	>	if (line.find("<StuntDoubles>") == std::string::npos) {
628	>	sprintf(painCave.errMsg,
629	>	"DumpReader Error: Missing <StuntDoubles>\n");
630	>	painCave.isFatal = 1;
631	>	simError();
632	>	}
633
634	<	parseErr = parseCommentLine( read_buffer, simnfo);
634	>	while(inputStream.getline(buffer, bufferSize)) {
635	>	line = buffer;
636	>
637	>	if(line.find("</StuntDoubles>") != std::string::npos) {
638	>	break;
639	>	}
640
641	<	if( parseErr != NULL ){
400	<	strcpy( painCave.errMsg, parseErr );
401	<	haveError = 1;
402	<	simError();
641	>	parseDumpLine(line);
642		}
643
644	<	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);
644	>	}
645
646	<	if(localIndex == -1) {
414	<	sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
415	<	haveError = 1;
416	<	simError();
417	<	}
646	>	void  DumpReader::readSiteData(std::istream& inputStream) {
647
648	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
648	>	inputStream.getline(buffer, bufferSize);
649	>	std::string line(buffer);
650	>
651	>	if (line.find("<SiteData>") == std::string::npos) {
652	>	// site data isn't required for a simulation, so skip
653	>	return;
654	>	}
655
656	<	nCurObj = integrableObjects.size();
657	<
423	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
424	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
425	<
426	<	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	<	}
656	>	while(inputStream.getline(buffer, bufferSize)) {
657	>	line = buffer;
658
659	<	}
659	>	if(line.find("</SiteData>") != std::string::npos) {
660	>	break;
661	>	}
662
663	+	parseSiteLine(line);
664	+	}
665	+
666		}
667
668	<	#endif
447	<	}
668	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
669
670	<	char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
670	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
671	>	inputStream.getline(buffer, bufferSize);
672	>	std::string line(buffer);
673
674	<	char *foo; // the pointer to the current string token
675	<
676	<	double pos[3]; // position place holders
677	<	double vel[3]; // velocity placeholders
678	<	double q[4]; // the quaternions
679	<	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 );
674	>	if (line.find("<FrameData>") == std::string::npos) {
675	>	sprintf(painCave.errMsg,
676	>	"DumpReader Error: Missing <FrameData>\n");
677	>	painCave.isFatal = 1;
678	>	simError();
679	>	}
680
681	<	foo = strtok(NULL, " ,;\t");
682	<	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);
681	>	while(inputStream.getline(buffer, bufferSize)) {
682	>	line = buffer;
683
684	<	foo = strtok(NULL, " ,;\t\n");
685	<	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 );
684	>	if(line.find("</FrameData>") != std::string::npos) {
685	>	break;
686		}
697	–	integralOfChidt = atof( foo );
687
688	<	//push chi and integralOfChidt into SimInfo::properties which can be
689	<	//retrieved by integrator later
690	<	DoubleData* chiValue = new DoubleData();
691	<	chiValue->setID(CHIVALUE_ID);
692	<	chiValue->setData(chi);
693	<	entry_plug->addProperty(chiValue);
688	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
689	>	if (!tokenizer.hasMoreTokens()) {
690	>	sprintf(painCave.errMsg,
691	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
692	>	painCave.isFatal = 1;
693	>	simError();
694	>	}
695	>
696	>	std::string propertyName = tokenizer.nextToken();
697	>	if (propertyName == "Time") {
698	>	RealType currTime = tokenizer.nextTokenAsDouble();
699	>	s->setTime(currTime);
700	>	} else if (propertyName == "Hmat"){
701	>	Mat3x3d hmat;
702	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
703	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
704	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
705	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
706	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
707	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
708	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
709	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
710	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
711	>	s->setHmat(hmat);
712	>	} else if (propertyName == "Thermostat") {
713	>	pair<RealType, RealType> thermostat;
714	>	thermostat.first = tokenizer.nextTokenAsDouble();
715	>	thermostat.second = tokenizer.nextTokenAsDouble();
716	>	s->setThermostat(thermostat);
717	>	} else if (propertyName == "Barostat") {
718	>	Mat3x3d eta;
719	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
720	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
721	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
722	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
723	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
724	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
725	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
726	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
727	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
728	>	s->setBarostat(eta);
729	>	} else {
730	>	sprintf(painCave.errMsg,
731	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
732	>	painCave.isFatal = 0;
733	>	simError();
734	>	}
735
706	–	DoubleData* integralOfChidtValue = new DoubleData();
707	–	integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
708	–	integralOfChidtValue->setData(integralOfChidt);
709	–	entry_plug->addProperty(integralOfChidtValue);
710	–
736		}
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	–	}
737
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);
738		}
739
740	<
741	<	MPI_Finalize();
757	<	exit (0);
758	<
759	<	}
760	<
761	<	void DumpReader::anonymousNodeDie( void ){
762	<
763	<	MPI_Finalize();
764	<	exit (0);
765	<	}
766	<	#endif
740	>
741	>	}//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 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

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

Diff Legend

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