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root/OpenMD/trunk/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.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

#	Line 1 | Line 1
1	<	#define _LARGEFILE_SOURCE64
2	<	#define _FILE_OFFSET_BITS 64
3	<
4	<	#include <sys/types.h>
5	<	#include <sys/stat.h>
6	<
7	<	#include <iostream>
8	<	#include <math.h>
9	<
10	<	#include <stdio.h>
11	<	#include <stdlib.h>
12	<	#include <string.h>
13	<
14	<
15	<	#include "ReadWrite.hpp"
16	<	#include "simError.h"
17	<
18	<	#ifdef IS_MPI
19	<	#include <mpi.h>
20	<	#include "mpiSimulation.hpp"
21	<	#define TAKE_THIS_TAG_CHAR 0
22	<	#define TAKE_THIS_TAG_INT 1
23	<	#endif // is_mpi
24	<
25	<
26	<	DumpReader :: DumpReader(const char *in_name ){
27	<
28	<	isScanned = false;
29	<
30	<	#ifdef IS_MPI
31	<	if (worldRank == 0) {
32	<	#endif
33	<
34	<	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	<	}
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	<	inFileName = in_name;
44	<	#ifdef IS_MPI
45	<	}
46	<	strcpy( checkPointMsg, "Dump file opened for reading successfully." );
47	<	MPIcheckPoint();
43	>	#define _LARGEFILE_SOURCE64
44	>	#define _FILE_OFFSET_BITS 64
45	>
46	>	#ifdef IS_MPI
47	>	#include <mpi.h>
48		#endif
49	<	return;
50	<	}
51	<
52	<	DumpReader :: ~DumpReader( ){
53	<	#ifdef IS_MPI
54	<	if (worldRank == 0) {
55	<	#endif
56	<	vector<fpos_t*>::iterator i;
57	<
58	<	int error;
59	<	error = fclose( inFile );
60	<	if( error ){
61	<	sprintf( painCave.errMsg,
62	<	"Error closing %s\n", inFileName.c_str());
63	<	simError();
64	<	}
65	<
66	<	for(i = framePos.begin(); i != framePos.end(); ++i)
67	<	delete *i;
68	<	framePos.clear();
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	<	#ifdef IS_MPI
70	<	}
71	<	strcpy( checkPointMsg, "Dump file closed successfully." );
72	<	MPIcheckPoint();
73	<	#endif
74	<
75	<	return;
76	<	}
77	<
78	<	int DumpReader::getNframes( void ){
79	<
80	<	if( !isScanned )
81	<	scanFile();
82	<	return framePos.size();
83	<	}
84	<
85	<	void DumpReader::scanFile( void ){
86	<
87	<	int i, j;
88	<	int lineNum = 0;
89	<	char readBuffer[2000];
90	<	fpos_t *currPos;
91	<
92	<	#ifdef IS_MPI
93	<	if( worldRank == 0 ){
94	<	#endif // is_mpi
101	>	DumpReader::~DumpReader() {
102
103	<	rewind( inFile );
103	>	#ifdef IS_MPI
104
105	<	currPos = new fpos_t;
106	<	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();
109	<	}
110	<
111	<	while( !feof( inFile ) ){
105	>	if (worldRank == 0) {
106	>	#endif
107
108	<	framePos.push_back(currPos);
114	<
115	<	i = atoi(readBuffer);
108	>	delete inFile_;
109
110	<	fgets( readBuffer, sizeof( readBuffer ), inFile );
118	<	lineNum++;
119	<	if( feof( inFile ) ){
120	<	sprintf( painCave.errMsg,
121	<	"File \"%s\" ended unexpectedly at line %d\n",
122	<	inFileName.c_str(),
123	<	lineNum );
124	<	painCave.isFatal = 1;
125	<	simError();
126	<	}
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	<	}
110	>	#ifdef IS_MPI
111
112	<	currPos = new fpos_t;
146	<	fgetpos( inFile, currPos );
147	<	fgets( readBuffer, sizeof( readBuffer ), inFile );
148	<	lineNum++;
149	<	}
112	>	}
113
114	<	delete currPos;
115	<	rewind( inFile );
114	>	strcpy(checkPointMsg, "Dump file closed successfully.");
115	>	errorCheckPoint();
116	>
117	>	#endif
118	>
119	>	return;
120	>	}
121	>
122	>	int DumpReader::getNFrames(void) {
123
124	<	isScanned = true;
124	>	if (!isScanned_)
125	>	scanFile();
126	>
127	>	return nframes_;
128	>	}
129	>
130	>	void DumpReader::scanFile(void) {
131
132	<	#ifdef IS_MPI
133	<	}
134	<	strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
135	<	MPIcheckPoint();
136	<	#endif // is_mpi
137	<	}
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	<	void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
146	<
147	<	simnfo = the_simnfo;
148	<
149	<	this->readSet( whichFrame );
150	<	}
151	<
152	<
153	<
154	<	void DumpReader :: readSet( int whichFrame ){
155	<
156	<	int i;
157	<	unsigned int j;
158	<
159	<	#ifdef IS_MPI
160	<	int done, which_node, which_atom; // loop counter
161	<	#endif //is_mpi
162	<
163	<	const int BUFFERSIZE = 2000; // size of the read buffer
164	<	int nTotObjs; // the number of atoms
165	<	char read_buffer[BUFFERSIZE]; //the line buffer for reading
166	<
167	<	char *eof_test; // ptr to see when we reach the end of the file
168	<	char *parseErr;
169	<
170	<	vector<StuntDouble*> integrableObjects;
171	<
172	<
173	<	#ifndef IS_MPI
174	<
175	<	fsetpos(inFile, framePos[whichFrame]);
176	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
177	<	if( eof_test == NULL ){
178	<	sprintf( painCave.errMsg,
179	<	"DumpReader error: error reading 1st line of \"%s\"\n",
180	<	inFileName.c_str() );
181	<	painCave.isFatal = 1;
182	<	simError();
183	<	}
184	<
185	<	nTotObjs = atoi( read_buffer );
186	<
187	<	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
188	<	sprintf( painCave.errMsg,
189	<	"DumpReader error. %s nIntegrable, %d, "
190	<	"does not match the meta-data file's nIntegrable, %d.\n",
191	<	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	//read the box mat from the comment line
197	<
198	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
199	<	if(eof_test == NULL){
200	<	sprintf( painCave.errMsg,
201	<	"error in reading commment in %s\n", inFileName.c_str());
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
205	<
206	<	parseErr = parseCommentLine( read_buffer, simnfo);
207	<	if( parseErr != NULL ){
208	<	strcpy( painCave.errMsg, parseErr );
209	<	painCave.isFatal = 1;
210	<	simError();
211	<	}
212	<
213	<	//parse dump lines
214	<
215	<	for( i=0; i < simnfo->n_mol; i++){
216	<
217	<	integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
218	<
219	<	for(j = 0; j < integrableObjects.size(); j++){
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	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
248	<	if(eof_test == NULL){
249	<	sprintf(painCave.errMsg,
250	<	"error in reading file %s\n"
251	<	"natoms  = %d; index = %d\n"
252	<	"error reading the line from the file.\n",
253	<	inFileName.c_str(), nTotObjs, i );
254	<	painCave.isFatal = 1;
255	<	simError();
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	>	#ifndef IS_MPI
267	>	inFile_->clear();
268	>	inFile_->seekg(framePos_[whichFrame]);
269	>
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	>	inFile_->clear();
279	>	inFile_->seekg(framePos_[whichFrame]);
280	>
281	>	while (inFile_->getline(buffer, bufferSize)) {
282	>
283	>	line = buffer;
284	>	sendBuffer += line;
285	>	sendBuffer += '\n';
286	>	if (line.find("</Snapshot>") != std::string::npos) {
287	>	break;
288	>	}
289		}
290	+
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	<	parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
297	<	if( parseErr != NULL ){
298	<	strcpy( painCave.errMsg, parseErr );
299	<	painCave.isFatal = 1;
300	<	simError();
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	>	std::istream& inputStream = sstream;
309	>	#endif
310	>
311	>	inputStream.getline(buffer, bufferSize);
312	>
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	>	//read StuntDoubles
325	>	readStuntDoubles(inputStream);
326	>
327	>	inputStream.getline(buffer, bufferSize);
328	>	line = buffer;
329	>
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	>
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 index = tokenizer.nextTokenAsInt();
359	>
360	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
361	>
362	>	if (sd == NULL) {
363	>	return;
364	>	}
365	>	std::string type = tokenizer.nextToken();
366	>	int size = type.size();
367	>
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		}
380		}
381	<	}
381	>
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	<	// MPI Section of code..........
397	<	#else //IS_MPI
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	<	// first thing first, suspend fatalities.
421	<	painCave.isEventLoop = 1;
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	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
461	<	int haveError;
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	<	MPI_Status istatus;
470	<	int *MolToProcMap = mpiSim->getMolToProcMap();
471	<	int localIndex;
472	<	int nCurObj;
473	<	int nitems;
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	<	nTotObjs = simnfo->getTotIntegrableObjects();
479	<	haveError = 0;
480	<	if (worldRank == 0) {
481	<	fsetpos(inFile,  framePos[whichFrame]);
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	>	RealType flucQVel;
493	>	flucQVel = tokenizer.nextTokenAsDouble();
494	>	sd->setFlucQVel(flucQVel);
495	>	break;
496	>	}
497	>	case 'g' : {
498	>
499	>	RealType flucQFrc;
500	>	flucQFrc = tokenizer.nextTokenAsDouble();
501	>	sd->setFlucQFrc(flucQFrc);
502	>	break;
503	>	}
504	>	case 'e' : {
505	>
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	>	case 's' : {
514
515	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
516	<	if( eof_test == NULL ){
517	<	sprintf( painCave.errMsg,
518	<	"Error reading 1st line of %s \n ",inFileName.c_str());
519	<	haveError = 1;
520	<	simError();
521	<	}
515	>	RealType sPot;
516	>	sPot = tokenizer.nextTokenAsDouble();
517	>	sd->setSitePotential(sPot);
518	>	break;
519	>	}
520	>	default: {
521	>	sprintf(painCave.errMsg,
522	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
523	>	painCave.isFatal = 1;
524	>	simError();
525	>	break;
526	>	}
527
528	<	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();
528	>	}
529		}
530	+	}
531	+
532
533	<	//read the boxMat from the comment line
533	>	void DumpReader::parseSiteLine(const std::string& line) {
534
535	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
536	<	if(eof_test == NULL){
537	<	sprintf( painCave.errMsg,
538	<	"error in reading commment in %s\n", inFileName.c_str());
539	<	haveError = 1;
540	<	simError();
541	<	}
535	>	StringTokenizer tokenizer(line);
536	>	int nTokens;
537	>
538	>	nTokens = tokenizer.countTokens();
539	>
540	>	if (nTokens < 2) {
541	>	sprintf(painCave.errMsg,
542	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
543	>	painCave.isFatal = 1;
544	>	simError();
545	>	}
546
547	<	//Every single processor will parse the comment line by itself
548	<	//By using this way, we might lose some efficiency, but if we want to add
549	<	//more parameters into comment line, we only need to modify function
315	<	//parseCommentLine
547	>	/**
548	>	* The first token is the global integrable object index.
549	>	*/
550
551	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
552	<
553	<	parseErr = parseCommentLine( read_buffer, simnfo);
554	<
321	<	if( parseErr != NULL ){
322	<	strcpy( painCave.errMsg, parseErr );
323	<	haveError = 1;
324	<	simError();
551	>	int index = tokenizer.nextTokenAsInt();
552	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
553	>	if (sd == NULL) {
554	>	return;
555		}
556
557	<	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
558	<	which_node = MolToProcMap[i];
559	<	if(which_node == 0){
560	<	//molecules belong to master node
557	>	/**
558	>	* Test to see if the next token is an integer or not.  If not,
559	>	* we've got data on the integrable object itself.  If there is an
560	>	* integer, we're parsing data for a site on a rigid body.
561	>	*/
562
563	<	localIndex = mpiSim->getGlobalToLocalMol(i);
563	>	std::string indexTest = tokenizer.peekNextToken();
564	>	std::istringstream i(indexTest);
565	>	int siteIndex;
566	>	if (i >> siteIndex) {
567	>	// chew up this token and parse as an int:
568	>	siteIndex = tokenizer.nextTokenAsInt();
569
570	<	if(localIndex == -1) {
571	<	strcpy(painCave.errMsg, "Molecule not found on node 0!");
572	<	haveError = 1;
337	<	simError();
570	>	if (sd->isRigidBody()) {
571	>	RigidBody* rb = static_cast<RigidBody*>(sd);
572	>	sd = rb->getAtoms()[siteIndex];
573		}
574	+	}
575
576	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
577	<	for(j=0; j < integrableObjects.size(); j++){
576	>	/**
577	>	* The next token contains information on what follows.
578	>	*/
579	>	std::string type = tokenizer.nextToken();
580	>	int size = type.size();
581	>
582	>	for(int i = 0; i < size; ++i) {
583	>	switch(type[i]) {
584
585	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
586	<	if(eof_test == NULL){
587	<	sprintf(painCave.errMsg,
588	<	"error in reading file %s\n"
589	<	"natoms  = %d; index = %d\n"
590	<	"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	<
585	>	case 'u' : {
586	>
587	>	RealType particlePot;
588	>	particlePot = tokenizer.nextTokenAsDouble();
589	>	sd->setParticlePot(particlePot);
590	>	break;
591		}
592	<	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++){
592	>	case 'c' : {
593
594	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
595	<	if(eof_test == NULL){
596	<	sprintf(painCave.errMsg,
597	<	"error in reading file %s\n"
374	<	"natoms  = %d; index = %d\n"
375	<	"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	<
594	>	RealType flucQPos;
595	>	flucQPos = tokenizer.nextTokenAsDouble();
596	>	sd->setFlucQPos(flucQPos);
597	>	break;
598		}
599	<
600	<	}
599	>	case 'w' : {
600	>
601	>	RealType flucQVel;
602	>	flucQVel = tokenizer.nextTokenAsDouble();
603	>	sd->setFlucQVel(flucQVel);
604	>	break;
605	>	}
606	>	case 'g' : {
607	>
608	>	RealType flucQFrc;
609	>	flucQFrc = tokenizer.nextTokenAsDouble();
610	>	sd->setFlucQFrc(flucQFrc);
611	>	break;
612	>	}
613	>	case 'e' : {
614	>
615	>	Vector3d eField;
616	>	eField[0] = tokenizer.nextTokenAsDouble();
617	>	eField[1] = tokenizer.nextTokenAsDouble();
618	>	eField[2] = tokenizer.nextTokenAsDouble();
619	>	sd->setElectricField(eField);
620	>	break;
621	>	}
622	>	case 's' : {
623	>
624	>	RealType sPot;
625	>	sPot = tokenizer.nextTokenAsDouble();
626	>	sd->setSitePotential(sPot);
627	>	break;
628	>	}
629	>	default: {
630	>	sprintf(painCave.errMsg,
631	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
632	>	painCave.isFatal = 1;
633	>	simError();
634	>	break;
635	>	}
636	>	}
637	>	}
638	>	}
639	>
640	>
641	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
642
643	<	}
644	<	else{
645	<	//actions taken at slave nodes
646	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
643	>	inputStream.getline(buffer, bufferSize);
644	>	std::string line(buffer);
645	>
646	>	if (line.find("<StuntDoubles>") == std::string::npos) {
647	>	sprintf(painCave.errMsg,
648	>	"DumpReader Error: Missing <StuntDoubles>\n");
649	>	painCave.isFatal = 1;
650	>	simError();
651	>	}
652
653	<	parseErr = parseCommentLine( read_buffer, simnfo);
653	>	while(inputStream.getline(buffer, bufferSize)) {
654	>	line = buffer;
655	>
656	>	if(line.find("</StuntDoubles>") != std::string::npos) {
657	>	break;
658	>	}
659
660	<	if( parseErr != NULL ){
400	<	strcpy( painCave.errMsg, parseErr );
401	<	haveError = 1;
402	<	simError();
660	>	parseDumpLine(line);
661		}
662
663	<	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);
663	>	}
664
665	<	if(localIndex == -1) {
414	<	sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
415	<	haveError = 1;
416	<	simError();
417	<	}
665	>	void  DumpReader::readSiteData(std::istream& inputStream) {
666
667	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
667	>	std::string line(buffer);
668
669	<	nCurObj = integrableObjects.size();
670	<
671	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
672	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
673	<
674	<	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	<	}
669	>	// We already found the starting <SiteData> tag or we wouldn't be
670	>	// here, so just start parsing until we get to the ending
671	>	// </SiteData> tag:
672	>
673	>	while(inputStream.getline(buffer, bufferSize)) {
674	>	line = buffer;
675
676	<	}
676	>	if(line.find("</SiteData>") != std::string::npos) {
677	>	break;
678	>	}
679
680	+	parseSiteLine(line);
681	+	}
682	+
683		}
684
685	<	#endif
447	<	}
685	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
686
687	<	char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
687	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
688	>	inputStream.getline(buffer, bufferSize);
689	>	std::string line(buffer);
690
691	<	char *foo; // the pointer to the current string token
691	>	if (line.find("<FrameData>") == std::string::npos) {
692	>	sprintf(painCave.errMsg,
693	>	"DumpReader Error: Missing <FrameData>\n");
694	>	painCave.isFatal = 1;
695	>	simError();
696	>	}
697
698	<	double pos[3]; // position place holders
699	<	double vel[3]; // velocity placeholders
700	<	double q[4]; // the quaternions
701	<	double ji[3]; // angular velocity placeholders;
702	<	double qSqr, qLength; // needed to normalize the quaternion vector.
703	<
704	<
705	<	// set the string tokenizer
706	<
707	<	foo = strtok(readLine, " ,;\t");
708	<
709	<	// check the atom name to the current atom
710	<
711	<	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
698	>	while(inputStream.getline(buffer, bufferSize)) {
699	>	line = buffer;
700	>
701	>	if(line.find("</FrameData>") != std::string::npos) {
702	>	break;
703	>	}
704	>
705	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
706	>	if (!tokenizer.hasMoreTokens()) {
707	>	sprintf(painCave.errMsg,
708	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
709	>	painCave.isFatal = 1;
710	>	simError();
711	>	}
712
713	<	foo = strtok(NULL, " ,;\t");
714	<	if(foo == NULL){
715	<	sprintf( painCave.errMsg,
716	<	"error in reading postition x from %s\n",
717	<	inFileName.c_str());
718	<	return strdup( painCave.errMsg );
719	<	}
720	<	pos[0] = atof( foo );
721	<
722	<	foo = strtok(NULL, " ,;\t");
723	<	if(foo == NULL){
724	<	sprintf( painCave.errMsg,
725	<	"error in reading postition y from %s\n",
726	<	inFileName.c_str());
727	<	return strdup( painCave.errMsg );
728	<	}
729	<	pos[1] = atof( foo );
730	<
731	<	foo = strtok(NULL, " ,;\t");
732	<	if(foo == NULL){
733	<	sprintf( painCave.errMsg,
734	<	"error in reading postition z from %s\n",
735	<	inFileName.c_str());
736	<	return strdup( painCave.errMsg );
737	<	}
738	<	pos[2] = atof( foo );
739	<
740	<
741	<	// get the velocities
742	<
743	<	foo = strtok(NULL, " ,;\t");
744	<	if(foo == NULL){
745	<	sprintf( painCave.errMsg,
746	<	"error in reading velocity x from %s\n",
747	<	inFileName.c_str() );
748	<	return strdup( painCave.errMsg );
749	<	}
750	<	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 );
713	>	std::string propertyName = tokenizer.nextToken();
714	>	if (propertyName == "Time") {
715	>	RealType currTime = tokenizer.nextTokenAsDouble();
716	>	s->setTime(currTime);
717	>	} else if (propertyName == "Hmat"){
718	>	Mat3x3d hmat;
719	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
720	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
721	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
722	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
723	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
724	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
725	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
726	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
727	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
728	>	s->setHmat(hmat);
729	>	} else if (propertyName == "Thermostat") {
730	>	pair<RealType, RealType> thermostat;
731	>	thermostat.first = tokenizer.nextTokenAsDouble();
732	>	thermostat.second = tokenizer.nextTokenAsDouble();
733	>	s->setThermostat(thermostat);
734	>	} else if (propertyName == "Barostat") {
735	>	Mat3x3d eta;
736	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
737	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
738	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
739	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
740	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
741	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
742	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
743	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
744	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
745	>	s->setBarostat(eta);
746	>	} else {
747	>	sprintf(painCave.errMsg,
748	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
749	>	painCave.isFatal = 0;
750	>	simError();
751		}
697	–	integralOfChidt = atof( foo );
752
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	–
753		}
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	–	}
754
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);
755		}
756
757	<
758	<	MPI_Finalize();
757	<	exit (0);
758	<
759	<	}
760	<
761	<	void DumpReader::anonymousNodeDie( void ){
762	<
763	<	MPI_Finalize();
764	<	exit (0);
765	<	}
766	<	#endif
757	>
758	>	}//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.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

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