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

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 132 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1794 by gezelter, Thu Sep 6 19:44:06 2012 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 "io/ReadWrite.hpp"
16	<	#include "utils/simError.h"
17	<
18	<	#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
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, 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	<	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	>	#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	<	return;
67	<	}
68	<
69	<	DumpReader :: ~DumpReader( ){
70	<	#ifdef IS_MPI
71	<	if (worldRank == 0) {
72	<	#endif
73	<	vector<fpos_t*>::iterator i;
74	<
75	<	int error;
76	<	error = fclose( inFile );
77	<	if( error ){
78	<	sprintf( painCave.errMsg,
79	<	"Error closing %s\n", inFileName.c_str());
80	<	simError();
81	<	}
82	<
83	<	for(i = framePos.begin(); i != framePos.end(); ++i)
84	<	delete *i;
85	<	framePos.clear();
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;
125	<
126	<	#ifdef IS_MPI
127	<	}
128	<	strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
129	<	MPIcheckPoint();
130	<	#endif // is_mpi
131	<	}
132	<
133	<	void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
134	<
135	<	simnfo = the_simnfo;
136	<
137	<	this->readSet( whichFrame );
138	<	}
139	<
140	<
141	<
142	<	void DumpReader :: readSet( int whichFrame ){
143	<
144	<	int i;
145	<	unsigned int j;
146	<
147	<	#ifdef IS_MPI
148	<	int done, which_node, which_atom; // loop counter
149	<	#endif //is_mpi
150	<
151	<	const int BUFFERSIZE = 2000; // size of the read buffer
152	<	int nTotObjs; // the number of atoms
153	<	char read_buffer[BUFFERSIZE]; //the line buffer for reading
154	<
155	<	char *eof_test; // ptr to see when we reach the end of the file
156	<	char *parseErr;
157	<
158	<	vector<StuntDouble*> integrableObjects;
159	<
160	<
161	<	#ifndef IS_MPI
162	<
163	<	fsetpos(inFile, framePos[whichFrame]);
164	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
165	<	if( eof_test == NULL ){
166	<	sprintf( painCave.errMsg,
167	<	"DumpReader error: error reading 1st line of \"%s\"\n",
168	<	inFileName.c_str() );
169	<	painCave.isFatal = 1;
170	<	simError();
171	<	}
172	<
173	<	nTotObjs = atoi( read_buffer );
174	<
175	<	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
176	<	sprintf( painCave.errMsg,
177	<	"DumpReader error. %s nIntegrable, %d, "
178	<	"does not match the meta-data file's nIntegrable, %d.\n",
179	<	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
180	<	painCave.isFatal = 1;
181	<	simError();
212	<	}
213	<
214	<	//read the box mat from the comment line
215	<
216	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
217	<	if(eof_test == NULL){
218	<	sprintf( painCave.errMsg,
219	<	"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();
124	>	if (!isScanned_)
125	>	scanFile();
126	>
127	>	return nframes_;
128	>	}
129	>
130	>	void DumpReader::scanFile(void) {
131	>	int lineNo = 0;
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	>	bool foundOpenSiteDataTag = false;
145	>	while(inFile_->getline(buffer, bufferSize)) {
146	>	++lineNo;
147	>
148	>	std::string line = buffer;
149	>	currPos = inFile_->tellg();
150	>	if (line.find("<Snapshot>")!= std::string::npos) {
151	>	if (foundOpenSnapshotTag) {
152	>	sprintf(painCave.errMsg,
153	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154	>	filename_.c_str());
155	>	painCave.isFatal = 1;
156	>	simError();
157	>	}
158	>	foundOpenSnapshotTag = true;
159	>	foundClosedSnapshotTag = false;
160	>	framePos_.push_back(prevPos);
161	>
162	>	} else if (line.find("</Snapshot>") != std::string::npos){
163	>	if (!foundOpenSnapshotTag) {
164	>	sprintf(painCave.errMsg,
165	>	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
166	>	filename_.c_str());
167	>	painCave.isFatal = 1;
168	>	simError();
169	>	}
170	>
171	>	if (foundClosedSnapshotTag) {
172	>	sprintf(painCave.errMsg,
173	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
174	>	filename_.c_str());
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	foundClosedSnapshotTag = true;
179	>	foundOpenSnapshotTag = false;
180	>	}
181	>	prevPos = currPos;
182		}
183
184	<	parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
185	<	if( parseErr != NULL ){
186	<	strcpy( painCave.errMsg, parseErr );
187	<	painCave.isFatal = 1;
188	<	simError();
184	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
185	>	// it and give a warning message
186	>	if (foundOpenSnapshotTag) {
187	>	sprintf(painCave.errMsg,
188	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
189	>	painCave.isFatal = 0;
190	>	simError();
191	>	framePos_.pop_back();
192		}
193	+
194	+	nframes_ = framePos_.size();
195	+
196	+	if (nframes_ == 0) {
197	+	sprintf(painCave.errMsg,
198	+	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
199	+	painCave.isFatal = 1;
200	+	simError();
201	+	}
202	+	#ifdef IS_MPI
203	+	}
204	+
205	+	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206	+
207	+	#endif // is_mpi
208	+
209	+	isScanned_ = true;
210	+	}
211	+
212	+	void DumpReader::readFrame(int whichFrame) {
213	+	if (!isScanned_)
214	+	scanFile();
215	+
216	+	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
217	+
218	+	if (storageLayout & DataStorage::dslPosition) {
219	+	needPos_ = true;
220	+	} else {
221	+	needPos_ = false;
222	+	}
223	+
224	+	if (storageLayout & DataStorage::dslVelocity) {
225	+	needVel_ = true;
226	+	} else {
227	+	needVel_ = false;
228	+	}
229	+
230	+	if (storageLayout & DataStorage::dslAmat ||
231	+	storageLayout & DataStorage::dslDipole ||
232	+	storageLayout & DataStorage::dslQuadrupole) {
233	+	needQuaternion_ = true;
234	+	} else {
235	+	needQuaternion_ = false;
236	+	}
237	+
238	+	if (storageLayout & DataStorage::dslAngularMomentum) {
239	+	needAngMom_ = true;
240	+	} else {
241	+	needAngMom_ = false;
242	+	}
243	+
244	+	readSet(whichFrame);
245	+
246	+	if (needCOMprops_) {
247	+	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
248	+	Thermo thermo(info_);
249	+	Vector3d com;
250	+
251	+	if (needPos_ && needVel_) {
252	+	Vector3d comvel;
253	+	Vector3d comw;
254	+	thermo.getComAll(com, comvel);
255	+	comw = thermo.getAngularMomentum();
256	+	} else {
257	+	com = thermo.getCom();
258	+	}
259		}
260	<	}
260	>	}
261	>
262	>	void DumpReader::readSet(int whichFrame) {
263	>	std::string line;
264
265	<	// MPI Section of code..........
266	<	#else //IS_MPI
265	>	#ifndef IS_MPI
266	>	inFile_->clear();
267	>	inFile_->seekg(framePos_[whichFrame]);
268
269	<	// first thing first, suspend fatalities.
263	<	painCave.isEventLoop = 1;
269	>	std::istream& inputStream = *inFile_;
270
271	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
272	<	int haveError;
271	>	#else
272	>	int masterNode = 0;
273	>	std::stringstream sstream;
274	>	if (worldRank == masterNode) {
275	>	std::string sendBuffer;
276
277	<	MPI_Status istatus;
278	<	int *MolToProcMap = mpiSim->getMolToProcMap();
279	<	int localIndex;
280	<	int nCurObj;
272	<	int nitems;
277	>	inFile_->clear();
278	>	inFile_->seekg(framePos_[whichFrame]);
279	>
280	>	while (inFile_->getline(buffer, bufferSize)) {
281
282	<	nTotObjs = simnfo->getTotIntegrableObjects();
283	<	haveError = 0;
284	<	if (worldRank == 0) {
285	<	fsetpos(inFile,  framePos[whichFrame]);
282	>	line = buffer;
283	>	sendBuffer += line;
284	>	sendBuffer += '\n';
285	>	if (line.find("</Snapshot>") != std::string::npos) {
286	>	break;
287	>	}
288	>	}
289
290	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
291	<	if( eof_test == NULL ){
292	<	sprintf( painCave.errMsg,
293	<	"Error reading 1st line of %s \n ",inFileName.c_str());
294	<	haveError = 1;
295	<	simError();
290	>	int sendBufferSize = sendBuffer.size();
291	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
292	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
293	>
294	>	sstream.str(sendBuffer);
295	>	} else {
296	>	int sendBufferSize;
297	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
298	>	char * recvBuffer = new char[sendBufferSize+1];
299	>	assert(recvBuffer);
300	>	recvBuffer[sendBufferSize] = '\0';
301	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
302	>	sstream.str(recvBuffer);
303	>	delete [] recvBuffer;
304	>	}
305	>
306	>	std::istream& inputStream = sstream;
307	>	#endif
308	>
309	>	inputStream.getline(buffer, bufferSize);
310	>
311	>	line = buffer;
312	>	if (line.find("<Snapshot>") == std::string::npos) {
313	>	sprintf(painCave.errMsg,
314	>	"DumpReader Error: can not find <Snapshot>\n");
315	>	painCave.isFatal = 1;
316	>	simError();
317	>	}
318	>
319	>	//read frameData
320	>	readFrameProperties(inputStream);
321	>
322	>	//read StuntDoubles
323	>	readStuntDoubles(inputStream);
324	>
325	>	inputStream.getline(buffer, bufferSize);
326	>	line = buffer;
327	>
328	>	if (line.find("<SiteData>") != std::string::npos) {
329	>	//read SiteData
330	>	readSiteData(inputStream);
331	>	} else {
332	>	if (line.find("</Snapshot>") == std::string::npos) {
333	>	sprintf(painCave.errMsg,
334	>	"DumpReader Error: can not find </Snapshot>\n");
335	>	painCave.isFatal = 1;
336	>	simError();
337	>	}
338		}
339	+	}
340	+
341	+	void DumpReader::parseDumpLine(const std::string& line) {
342
343	<	nitems = atoi( read_buffer );
343	>
344	>	StringTokenizer tokenizer(line);
345	>	int nTokens;
346	>
347	>	nTokens = tokenizer.countTokens();
348	>
349	>	if (nTokens < 2) {
350	>	sprintf(painCave.errMsg,
351	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
352	>	painCave.isFatal = 1;
353	>	simError();
354	>	}
355
356	<	// Check to see that the number of integrable objects in the
357	<	// intial configuration file is the same as derived from the
358	<	// meta-data file.
356	>	int index = tokenizer.nextTokenAsInt();
357	>
358	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
359	>
360	>	if (sd == NULL) {
361	>	return;
362	>	}
363	>	std::string type = tokenizer.nextToken();
364	>	int size = type.size();
365	>
366	>	size_t found;
367	>
368	>	if (needPos_) {
369	>	found = type.find("p");
370	>	if (found == std::string::npos) {
371	>	sprintf(painCave.errMsg,
372	>	"DumpReader Error: StuntDouble %d has no Position\n"
373	>	"\tField (\"p\") specified.\n%s\n", index,
374	>	line.c_str());
375	>	painCave.isFatal = 1;
376	>	simError();
377	>	}
378	>	}
379	>
380	>	if (sd->isDirectional()) {
381	>	if (needQuaternion_) {
382	>	found = type.find("q");
383	>	if (found == std::string::npos) {
384	>	sprintf(painCave.errMsg,
385	>	"DumpReader Error: Directional StuntDouble %d has no\n"
386	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
387	>	line.c_str());
388	>	painCave.isFatal = 1;
389	>	simError();
390	>	}
391	>	}
392	>	}
393	>
394	>	for(int i = 0; i < size; ++i) {
395	>	switch(type[i]) {
396	>
397	>	case 'p': {
398	>	Vector3d pos;
399	>	pos[0] = tokenizer.nextTokenAsDouble();
400	>	pos[1] = tokenizer.nextTokenAsDouble();
401	>	pos[2] = tokenizer.nextTokenAsDouble();
402	>	if (needPos_) {
403	>	sd->setPos(pos);
404	>	}
405	>	break;
406	>	}
407	>	case 'v' : {
408	>	Vector3d vel;
409	>	vel[0] = tokenizer.nextTokenAsDouble();
410	>	vel[1] = tokenizer.nextTokenAsDouble();
411	>	vel[2] = tokenizer.nextTokenAsDouble();
412	>	if (needVel_) {
413	>	sd->setVel(vel);
414	>	}
415	>	break;
416	>	}
417	>
418	>	case 'q' : {
419	>	Quat4d q;
420	>	if (sd->isDirectional()) {
421	>
422	>	q[0] = tokenizer.nextTokenAsDouble();
423	>	q[1] = tokenizer.nextTokenAsDouble();
424	>	q[2] = tokenizer.nextTokenAsDouble();
425	>	q[3] = tokenizer.nextTokenAsDouble();
426	>
427	>	RealType qlen = q.length();
428	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
429	>
430	>	sprintf(painCave.errMsg,
431	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
432	>	painCave.isFatal = 1;
433	>	simError();
434	>
435	>	}
436	>
437	>	q.normalize();
438	>	if (needQuaternion_) {
439	>	sd->setQ(q);
440	>	}
441	>	}
442	>	break;
443	>	}
444	>	case 'j' : {
445	>	Vector3d ji;
446	>	if (sd->isDirectional()) {
447	>	ji[0] = tokenizer.nextTokenAsDouble();
448	>	ji[1] = tokenizer.nextTokenAsDouble();
449	>	ji[2] = tokenizer.nextTokenAsDouble();
450	>	if (needAngMom_) {
451	>	sd->setJ(ji);
452	>	}
453	>	}
454	>	break;
455	>	}
456	>	case 'f': {
457	>
458	>	Vector3d force;
459	>	force[0] = tokenizer.nextTokenAsDouble();
460	>	force[1] = tokenizer.nextTokenAsDouble();
461	>	force[2] = tokenizer.nextTokenAsDouble();
462	>	sd->setFrc(force);
463	>	break;
464	>	}
465	>	case 't' : {
466	>
467	>	Vector3d torque;
468	>	torque[0] = tokenizer.nextTokenAsDouble();
469	>	torque[1] = tokenizer.nextTokenAsDouble();
470	>	torque[2] = tokenizer.nextTokenAsDouble();
471	>	sd->setTrq(torque);
472	>	break;
473	>	}
474	>	case 'u' : {
475	>
476	>	RealType particlePot;
477	>	particlePot = tokenizer.nextTokenAsDouble();
478	>	sd->setParticlePot(particlePot);
479	>	break;
480	>	}
481	>	case 'c' : {
482	>
483	>	RealType flucQPos;
484	>	flucQPos = tokenizer.nextTokenAsDouble();
485	>	sd->setFlucQPos(flucQPos);
486	>	break;
487	>	}
488	>	case 'w' : {
489
490	<	if( nTotObjs != nitems){
491	<	sprintf( painCave.errMsg,
492	<	"DumpReader Error. %s nIntegrable, %d, "
493	<	"does not match the meta-data file's nIntegrable, %d.\n",
494	<	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
495	<	haveError= 1;
299	<	simError();
300	<	}
490	>	RealType flucQVel;
491	>	flucQVel = tokenizer.nextTokenAsDouble();
492	>	sd->setFlucQVel(flucQVel);
493	>	break;
494	>	}
495	>	case 'g' : {
496
497	<	//read the boxMat from the comment line
497	>	RealType flucQFrc;
498	>	flucQFrc = tokenizer.nextTokenAsDouble();
499	>	sd->setFlucQFrc(flucQFrc);
500	>	break;
501	>	}
502	>	case 'e' : {
503
504	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
505	<	if(eof_test == NULL){
506	<	sprintf( painCave.errMsg,
507	<	"error in reading commment in %s\n", inFileName.c_str());
508	<	haveError = 1;
509	<	simError();
504	>	Vector3d eField;
505	>	eField[0] = tokenizer.nextTokenAsDouble();
506	>	eField[1] = tokenizer.nextTokenAsDouble();
507	>	eField[2] = tokenizer.nextTokenAsDouble();
508	>	sd->setElectricField(eField);
509	>	break;
510	>	}
511	>	default: {
512	>	sprintf(painCave.errMsg,
513	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
514	>	painCave.isFatal = 1;
515	>	simError();
516	>	break;
517	>	}
518	>
519	>	}
520		}
521	+
522	+	}
523	+
524
525	<	//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
525	>	void DumpReader::parseSiteLine(const std::string& line) {
526
527	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
527	>	StringTokenizer tokenizer(line);
528	>	int nTokens;
529	>
530	>	nTokens = tokenizer.countTokens();
531	>
532	>	if (nTokens < 2) {
533	>	sprintf(painCave.errMsg,
534	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
535	>	painCave.isFatal = 1;
536	>	simError();
537	>	}
538
539	<	parseErr = parseCommentLine( read_buffer, simnfo);
539	>	/**
540	>	* The first token is the global integrable object index.
541	>	*/
542
543	<	if( parseErr != NULL ){
544	<	strcpy( painCave.errMsg, parseErr );
545	<	haveError = 1;
546	<	simError();
543	>	int index = tokenizer.nextTokenAsInt();
544	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
545	>	if (sd == NULL) {
546	>	return;
547		}
548
549	<	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
550	<	which_node = MolToProcMap[i];
551	<	if(which_node == 0){
552	<	//molecules belong to master node
549	>	/**
550	>	* Test to see if the next token is an integer or not.  If not,
551	>	* we've got data on the integrable object itself.  If there is an
552	>	* integer, we're parsing data for a site on a rigid body.
553	>	*/
554
555	<	localIndex = mpiSim->getGlobalToLocalMol(i);
555	>	std::string indexTest = tokenizer.peekNextToken();
556	>	std::istringstream i(indexTest);
557	>	int siteIndex;
558	>	if (i >> siteIndex) {
559	>	// chew up this token and parse as an int:
560	>	siteIndex = tokenizer.nextTokenAsInt();
561	>	RigidBody* rb = static_cast<RigidBody*>(sd);
562	>	sd = rb->getAtoms()[siteIndex];
563	>	}
564
565	<	if(localIndex == -1) {
566	<	strcpy(painCave.errMsg, "Molecule not found on node 0!");
567	<	haveError = 1;
568	<	simError();
565	>	/**
566	>	* The next token contains information on what follows.
567	>	*/
568	>	std::string type = tokenizer.nextToken();
569	>	int size = type.size();
570	>
571	>	for(int i = 0; i < size; ++i) {
572	>	switch(type[i]) {
573	>
574	>	case 'u' : {
575	>
576	>	RealType particlePot;
577	>	particlePot = tokenizer.nextTokenAsDouble();
578	>	sd->setParticlePot(particlePot);
579	>	break;
580		}
581	<
340	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
341	<	for(j=0; j < integrableObjects.size(); j++){
581	>	case 'c' : {
582
583	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
584	<	if(eof_test == NULL){
585	<	sprintf(painCave.errMsg,
586	<	"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	<
583	>	RealType flucQPos;
584	>	flucQPos = tokenizer.nextTokenAsDouble();
585	>	sd->setFlucQPos(flucQPos);
586	>	break;
587		}
588	<	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++){
588	>	case 'w' : {
589
590	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
591	<	if(eof_test == NULL){
592	<	sprintf(painCave.errMsg,
593	<	"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	<
590	>	RealType flucQVel;
591	>	flucQVel = tokenizer.nextTokenAsDouble();
592	>	sd->setFlucQVel(flucQVel);
593	>	break;
594		}
595	<
596	<	}
595	>	case 'g' : {
596	>
597	>	RealType flucQFrc;
598	>	flucQFrc = tokenizer.nextTokenAsDouble();
599	>	sd->setFlucQFrc(flucQFrc);
600	>	break;
601	>	}
602	>	case 'e' : {
603	>
604	>	Vector3d eField;
605	>	eField[0] = tokenizer.nextTokenAsDouble();
606	>	eField[1] = tokenizer.nextTokenAsDouble();
607	>	eField[2] = tokenizer.nextTokenAsDouble();
608	>	sd->setElectricField(eField);
609	>	break;
610	>	}
611	>	default: {
612	>	sprintf(painCave.errMsg,
613	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
614	>	painCave.isFatal = 1;
615	>	simError();
616	>	break;
617	>	}
618	>	}
619	>	}
620	>	}
621	>
622	>
623	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
624
625	<	}
626	<	else{
627	<	//actions taken at slave nodes
628	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
625	>	inputStream.getline(buffer, bufferSize);
626	>	std::string line(buffer);
627	>
628	>	if (line.find("<StuntDoubles>") == std::string::npos) {
629	>	sprintf(painCave.errMsg,
630	>	"DumpReader Error: Missing <StuntDoubles>\n");
631	>	painCave.isFatal = 1;
632	>	simError();
633	>	}
634
635	<	parseErr = parseCommentLine( read_buffer, simnfo);
635	>	while(inputStream.getline(buffer, bufferSize)) {
636	>	line = buffer;
637	>
638	>	if(line.find("</StuntDoubles>") != std::string::npos) {
639	>	break;
640	>	}
641
642	<	if( parseErr != NULL ){
400	<	strcpy( painCave.errMsg, parseErr );
401	<	haveError = 1;
402	<	simError();
642	>	parseDumpLine(line);
643		}
644
645	<	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);
645	>	}
646
647	<	if(localIndex == -1) {
414	<	sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
415	<	haveError = 1;
416	<	simError();
417	<	}
647	>	void  DumpReader::readSiteData(std::istream& inputStream) {
648
649	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
649	>	inputStream.getline(buffer, bufferSize);
650	>	std::string line(buffer);
651	>
652	>	if (line.find("<SiteData>") == std::string::npos) {
653	>	// site data isn't required for a simulation, so skip
654	>	return;
655	>	}
656
657	<	nCurObj = integrableObjects.size();
658	<
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	<	}
657	>	while(inputStream.getline(buffer, bufferSize)) {
658	>	line = buffer;
659
660	<	}
660	>	if(line.find("</SiteData>") != std::string::npos) {
661	>	break;
662	>	}
663
664	+	parseSiteLine(line);
665	+	}
666	+
667		}
668
669	<	#endif
447	<	}
669	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
670
671	<	char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
671	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
672	>	inputStream.getline(buffer, bufferSize);
673	>	std::string line(buffer);
674
675	<	char *foo; // the pointer to the current string token
675	>	if (line.find("<FrameData>") == std::string::npos) {
676	>	sprintf(painCave.errMsg,
677	>	"DumpReader Error: Missing <FrameData>\n");
678	>	painCave.isFatal = 1;
679	>	simError();
680	>	}
681
682	<	double pos[3]; // position place holders
683	<	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);
682	>	while(inputStream.getline(buffer, bufferSize)) {
683	>	line = buffer;
684
685	<	foo = strtok(NULL, " ,;\t\n");
686	<	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 );
685	>	if(line.find("</FrameData>") != std::string::npos) {
686	>	break;
687		}
697	–	integralOfChidt = atof( foo );
688
689	<	//push chi and integralOfChidt into SimInfo::properties which can be
690	<	//retrieved by integrator later
691	<	DoubleGenericData* chiValue = new DoubleGenericData();
692	<	chiValue->setID(CHIVALUE_ID);
693	<	chiValue->setData(chi);
694	<	entry_plug->addProperty(chiValue);
689	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
690	>	if (!tokenizer.hasMoreTokens()) {
691	>	sprintf(painCave.errMsg,
692	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
693	>	painCave.isFatal = 1;
694	>	simError();
695	>	}
696	>
697	>	std::string propertyName = tokenizer.nextToken();
698	>	if (propertyName == "Time") {
699	>	RealType currTime = tokenizer.nextTokenAsDouble();
700	>	s->setTime(currTime);
701	>	} else if (propertyName == "Hmat"){
702	>	Mat3x3d hmat;
703	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
704	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
705	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
706	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
707	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
708	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
709	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
710	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
711	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
712	>	s->setHmat(hmat);
713	>	} else if (propertyName == "Thermostat") {
714	>	pair<RealType, RealType> thermostat;
715	>	thermostat.first = tokenizer.nextTokenAsDouble();
716	>	thermostat.second = tokenizer.nextTokenAsDouble();
717	>	s->setThermostat(thermostat);
718	>	} else if (propertyName == "Barostat") {
719	>	Mat3x3d eta;
720	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
721	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
722	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
723	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
724	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
725	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
726	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
727	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
728	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
729	>	s->setBarostat(eta);
730	>	} else {
731	>	sprintf(painCave.errMsg,
732	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
733	>	painCave.isFatal = 0;
734	>	simError();
735	>	}
736
706	–	DoubleGenericData* integralOfChidtValue = new DoubleGenericData();
707	–	integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
708	–	integralOfChidtValue->setData(integralOfChidt);
709	–	entry_plug->addProperty(integralOfChidtValue);
710	–
737		}
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	–	DoubleVectorGenericData* etaValue = new DoubleVectorGenericData(ETAVALUE_ID);
737	–	etaValue->insert(etaValue->end(), eta, eta+9);
738	–	entry_plug->addProperty(etaValue);
739	–	}
738
741	–	return NULL;
742	–	}
743	–
744	–	#ifdef IS_MPI
745	–	void DumpReader::nodeZeroError( void ){
746	–	int j, myStatus;
747	–
748	–	myStatus = 0;
749	–	for (j = 0; j < mpiSim->getNProcessors(); j++) {
750	–	MPI_Send( &myStatus, 1, MPI_INT, j,
751	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
739		}
740
741	<
742	<	MPI_Finalize();
756	<	exit (0);
757	<
758	<	}
759	<
760	<	void DumpReader::anonymousNodeDie( void ){
761	<
762	<	MPI_Finalize();
763	<	exit (0);
764	<	}
765	<	#endif
741	>
742	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 132 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1794 by gezelter, Thu Sep 6 19:44:06 2012 UTC

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