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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 1714 by gezelter, Sat May 19 18:12:46 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();
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();
43	>	#define _LARGEFILE_SOURCE64
44	>	#define _FILE_OFFSET_BITS 64
45	>
46	>	#include <sys/types.h>
47	>	#include <sys/stat.h>
48	>
49	>	#include <iostream>
50	>	#include <math.h>
51	>
52	>	#include <stdio.h>
53	>	#include <stdlib.h>
54	>	#include <string.h>
55	>
56	>	#include "io/DumpReader.hpp"
57	>	#include "primitives/Molecule.hpp"
58	>	#include "utils/simError.h"
59	>	#include "utils/MemoryUtils.hpp"
60	>	#include "utils/StringTokenizer.hpp"
61	>
62	>	#ifdef IS_MPI
63	>
64	>	#include <mpi.h>
65	>	#define TAKE_THIS_TAG_CHAR 0
66	>	#define TAKE_THIS_TAG_INT 1
67	>
68	>	#endif // is_mpi
69	>
70	>
71	>	namespace OpenMD {
72	>
73	>	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
74	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
75	>
76	>	#ifdef IS_MPI
77	>
78	>	if (worldRank == 0) {
79	>	#endif
80	>
81	>	inFile_ = new std::ifstream(filename_.c_str());
82	>
83	>	if (inFile_->fail()) {
84	>	sprintf(painCave.errMsg,
85	>	"DumpReader: Cannot open file: %s\n",
86	>	filename_.c_str());
87	>	painCave.isFatal = 1;
88	>	simError();
89	>	}
90	>
91	>	#ifdef IS_MPI
92	>
93	>	}
94	>
95	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
96	>	errorCheckPoint();
97	>
98	>	#endif
99	>
100	>	return;
101	>	}
102
103	<	#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
103	>	DumpReader::~DumpReader() {
104
105	<	rewind( inFile );
105	>	#ifdef IS_MPI
106
107	<	currPos = new fpos_t;
108	<	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 ) ){
107	>	if (worldRank == 0) {
108	>	#endif
109
110	<	framePos.push_back(currPos);
114	<
115	<	i = atoi(readBuffer);
110	>	delete inFile_;
111
112	<	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	<	}
112	>	#ifdef IS_MPI
113
114	<	currPos = new fpos_t;
146	<	fgetpos( inFile, currPos );
147	<	fgets( readBuffer, sizeof( readBuffer ), inFile );
148	<	lineNum++;
149	<	}
114	>	}
115
116	<	delete currPos;
117	<	rewind( inFile );
116	>	strcpy(checkPointMsg, "Dump file closed successfully.");
117	>	errorCheckPoint();
118	>
119	>	#endif
120	>
121	>	return;
122	>	}
123	>
124	>	int DumpReader::getNFrames(void) {
125
126	<	isScanned = true;
127	<
128	<	#ifdef IS_MPI
129	<	}
130	<	strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
131	<	MPIcheckPoint();
132	<	#endif // is_mpi
133	<	}
134	<
135	<	void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
136	<
137	<	simnfo = the_simnfo;
138	<
139	<	this->readSet( whichFrame );
140	<	}
126	>	if (!isScanned_)
127	>	scanFile();
128	>
129	>	return nframes_;
130	>	}
131	>
132	>	void DumpReader::scanFile(void) {
133	>	int lineNo = 0;
134	>	std::streampos prevPos;
135	>	std::streampos  currPos;
136	>
137	>	#ifdef IS_MPI
138	>
139	>	if (worldRank == 0) {
140	>	#endif // is_mpi
141	>
142	>	currPos = inFile_->tellg();
143	>	prevPos = currPos;
144	>	bool foundOpenSnapshotTag = false;
145	>	bool foundClosedSnapshotTag = false;
146	>	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 || storageLayout & DataStorage::dslElectroFrame) {
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	+	if (needCOMprops_) {
246	+	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
247	+	Vector3d com;
248	+	Vector3d comvel;
249	+	Vector3d comw;
250	+	if (needPos_ && needVel_){
251	+	info_->getComAll(com, comvel);
252	+	comw = info_->getAngularMomentum();
253	+	}else{
254	+	com = info_->getCom();
255	+	comvel = 0.0;
256	+	comw   = 0.0;
257	+	}
258	+	s->setCOMprops(com, comvel, comw);
259	+	}
260
261	+	}
262	+
263	+	void DumpReader::readSet(int whichFrame) {
264	+	std::string line;
265
266	<	void DumpReader :: readSet( int whichFrame ){
266	>	#ifndef IS_MPI
267	>	inFile_->clear();
268	>	inFile_->seekg(framePos_[whichFrame]);
269
270	<	int i;
175	<	unsigned int j;
270	>	std::istream& inputStream = *inFile_;
271
272	<	#ifdef IS_MPI
273	<	int done, which_node, which_atom; // loop counter
274	<	#endif //is_mpi
272	>	#else
273	>	int masterNode = 0;
274	>	std::stringstream sstream;
275	>	if (worldRank == masterNode) {
276	>	std::string sendBuffer;
277
278	<	const int BUFFERSIZE = 2000; // size of the read buffer
279	<	int nTotObjs; // the number of atoms
280	<	char read_buffer[BUFFERSIZE]; //the line buffer for reading
278	>	inFile_->clear();
279	>	inFile_->seekg(framePos_[whichFrame]);
280	>
281	>	while (inFile_->getline(buffer, bufferSize)) {
282
283	<	char *eof_test; // ptr to see when we reach the end of the file
284	<	char *parseErr;
283	>	line = buffer;
284	>	sendBuffer += line;
285	>	sendBuffer += '\n';
286	>	if (line.find("</Snapshot>") != std::string::npos) {
287	>	break;
288	>	}
289	>	}
290
291	<	vector<StuntDouble*> integrableObjects;
291	>	int sendBufferSize = sendBuffer.size();
292	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
293	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
294	>
295	>	sstream.str(sendBuffer);
296	>	} else {
297	>	int sendBufferSize;
298	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
299	>	char * recvBuffer = new char[sendBufferSize+1];
300	>	assert(recvBuffer);
301	>	recvBuffer[sendBufferSize] = '\0';
302	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
303	>	sstream.str(recvBuffer);
304	>	delete [] recvBuffer;
305	>	}
306
307	+	std::istream& inputStream = sstream;
308	+	#endif
309
310	<	#ifndef IS_MPI
310	>	inputStream.getline(buffer, bufferSize);
311
312	<	fsetpos(inFile, framePos[whichFrame]);
313	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
314	<	if( eof_test == NULL ){
315	<	sprintf( painCave.errMsg,
316	<	"DumpReader error: error reading 1st line of \"%s\"\n",
317	<	inFileName.c_str() );
318	<	painCave.isFatal = 1;
319	<	simError();
320	<	}
312	>	line = buffer;
313	>	if (line.find("<Snapshot>") == std::string::npos) {
314	>	sprintf(painCave.errMsg,
315	>	"DumpReader Error: can not find <Snapshot>\n");
316	>	painCave.isFatal = 1;
317	>	simError();
318	>	}
319	>
320	>	//read frameData
321	>	readFrameProperties(inputStream);
322
323	<	nTotObjs = atoi( read_buffer );
323	>	//read StuntDoubles
324	>	readStuntDoubles(inputStream);
325
326	<	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
327	<	sprintf( painCave.errMsg,
328	<	"DumpReader error. %s nIntegrable, %d, "
329	<	"does not match the meta-data file's nIntegrable, %d.\n",
330	<	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
331	<	painCave.isFatal = 1;
332	<	simError();
333	<	}
326	>	inputStream.getline(buffer, bufferSize);
327	>	line = buffer;
328	>	if (line.find("</Snapshot>") == std::string::npos) {
329	>	sprintf(painCave.errMsg,
330	>	"DumpReader Error: can not find </Snapshot>\n");
331	>	painCave.isFatal = 1;
332	>	simError();
333	>	}
334	>
335	>	}
336	>
337	>	void DumpReader::parseDumpLine(const std::string& line) {
338
339	<	//read the box mat from the comment line
339	>
340	>	StringTokenizer tokenizer(line);
341	>	int nTokens;
342	>
343	>	nTokens = tokenizer.countTokens();
344	>
345	>	if (nTokens < 2) {
346	>	sprintf(painCave.errMsg,
347	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
348	>	painCave.isFatal = 1;
349	>	simError();
350	>	}
351
352	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
353	<	if(eof_test == NULL){
354	<	sprintf( painCave.errMsg,
219	<	"error in reading commment in %s\n", inFileName.c_str());
220	<	painCave.isFatal = 1;
221	<	simError();
222	<	}
352	>	int index = tokenizer.nextTokenAsInt();
353	>
354	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
355
356	<	parseErr = parseCommentLine( read_buffer, simnfo);
357	<	if( parseErr != NULL ){
358	<	strcpy( painCave.errMsg, parseErr );
359	<	painCave.isFatal = 1;
360	<	simError();
229	<	}
356	>	if (integrableObject == NULL) {
357	>	return;
358	>	}
359	>	std::string type = tokenizer.nextToken();
360	>	int size = type.size();
361
362	<	//parse dump lines
362	>	size_t found;
363	>
364	>	if (needPos_) {
365	>	found = type.find("p");
366	>	if (found == std::string::npos) {
367	>	sprintf(painCave.errMsg,
368	>	"DumpReader Error: StuntDouble %d has no Position\n"
369	>	"\tField (\"p\") specified.\n%s\n", index,
370	>	line.c_str());
371	>	painCave.isFatal = 1;
372	>	simError();
373	>	}
374	>	}
375	>
376	>	if (integrableObject->isDirectional()) {
377	>	if (needQuaternion_) {
378	>	found = type.find("q");
379	>	if (found == std::string::npos) {
380	>	sprintf(painCave.errMsg,
381	>	"DumpReader Error: Directional StuntDouble %d has no\n"
382	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
383	>	line.c_str());
384	>	painCave.isFatal = 1;
385	>	simError();
386	>	}
387	>	}
388	>	}
389
390	<	for( i=0; i < simnfo->n_mol; i++){
390	>	for(int i = 0; i < size; ++i) {
391	>	switch(type[i]) {
392	>
393	>	case 'p': {
394	>	Vector3d pos;
395	>	pos[0] = tokenizer.nextTokenAsDouble();
396	>	pos[1] = tokenizer.nextTokenAsDouble();
397	>	pos[2] = tokenizer.nextTokenAsDouble();
398	>	if (needPos_) {
399	>	integrableObject->setPos(pos);
400	>	}
401	>	break;
402	>	}
403	>	case 'v' : {
404	>	Vector3d vel;
405	>	vel[0] = tokenizer.nextTokenAsDouble();
406	>	vel[1] = tokenizer.nextTokenAsDouble();
407	>	vel[2] = tokenizer.nextTokenAsDouble();
408	>	if (needVel_) {
409	>	integrableObject->setVel(vel);
410	>	}
411	>	break;
412	>	}
413
414	<	integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
414	>	case 'q' : {
415	>	Quat4d q;
416	>	if (integrableObject->isDirectional()) {
417	>
418	>	q[0] = tokenizer.nextTokenAsDouble();
419	>	q[1] = tokenizer.nextTokenAsDouble();
420	>	q[2] = tokenizer.nextTokenAsDouble();
421	>	q[3] = tokenizer.nextTokenAsDouble();
422	>
423	>	RealType qlen = q.length();
424	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
425	>
426	>	sprintf(painCave.errMsg,
427	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
428	>	painCave.isFatal = 1;
429	>	simError();
430	>
431	>	}
432	>
433	>	q.normalize();
434	>	if (needQuaternion_) {
435	>	integrableObject->setQ(q);
436	>	}
437	>	}
438	>	break;
439	>	}
440	>	case 'j' : {
441	>	Vector3d ji;
442	>	if (integrableObject->isDirectional()) {
443	>	ji[0] = tokenizer.nextTokenAsDouble();
444	>	ji[1] = tokenizer.nextTokenAsDouble();
445	>	ji[2] = tokenizer.nextTokenAsDouble();
446	>	if (needAngMom_) {
447	>	integrableObject->setJ(ji);
448	>	}
449	>	}
450	>	break;
451	>	}
452	>	case 'f': {
453	>
454	>	Vector3d force;
455	>	force[0] = tokenizer.nextTokenAsDouble();
456	>	force[1] = tokenizer.nextTokenAsDouble();
457	>	force[2] = tokenizer.nextTokenAsDouble();
458	>	integrableObject->setFrc(force);
459	>	break;
460	>	}
461	>	case 't' : {
462	>
463	>	Vector3d torque;
464	>	torque[0] = tokenizer.nextTokenAsDouble();
465	>	torque[1] = tokenizer.nextTokenAsDouble();
466	>	torque[2] = tokenizer.nextTokenAsDouble();
467	>	integrableObject->setTrq(torque);
468	>	break;
469	>	}
470	>	case 'u' : {
471	>
472	>	RealType particlePot;
473	>	particlePot = tokenizer.nextTokenAsDouble();
474	>	integrableObject->setParticlePot(particlePot);
475	>	break;
476	>	}
477	>	case 'c' : {
478
479	<	for(j = 0; j < integrableObjects.size(); j++){
479	>	RealType flucQPos;
480	>	flucQPos = tokenizer.nextTokenAsDouble();
481	>	integrableObject->setFlucQPos(flucQPos);
482	>	break;
483	>	}
484	>	case 'w' : {
485
486	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
487	<	if(eof_test == NULL){
488	<	sprintf(painCave.errMsg,
489	<	"error in reading file %s\n"
490	<	"natoms  = %d; index = %d\n"
491	<	"error reading the line from the file.\n",
245	<	inFileName.c_str(), nTotObjs, i );
246	<	painCave.isFatal = 1;
247	<	simError();
248	<	}
249	<
250	<	parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
251	<	if( parseErr != NULL ){
252	<	strcpy( painCave.errMsg, parseErr );
253	<	painCave.isFatal = 1;
254	<	simError();
255	<	}
256	<	}
257	<	}
486	>	RealType flucQVel;
487	>	flucQVel = tokenizer.nextTokenAsDouble();
488	>	integrableObject->setFlucQVel(flucQVel);
489	>	break;
490	>	}
491	>	case 'g' : {
492
493	<	// MPI Section of code..........
494	<	#else //IS_MPI
493	>	RealType flucQFrc;
494	>	flucQFrc = tokenizer.nextTokenAsDouble();
495	>	integrableObject->setFlucQFrc(flucQFrc);
496	>	break;
497	>	}
498	>	case 'e' : {
499
500	<	// first thing first, suspend fatalities.
501	<	painCave.isEventLoop = 1;
500	>	Vector3d eField;
501	>	eField[0] = tokenizer.nextTokenAsDouble();
502	>	eField[1] = tokenizer.nextTokenAsDouble();
503	>	eField[2] = tokenizer.nextTokenAsDouble();
504	>	integrableObject->setElectricField(eField);
505	>	break;
506	>	}
507	>	default: {
508	>	sprintf(painCave.errMsg,
509	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
510	>	painCave.isFatal = 1;
511	>	simError();
512	>	break;
513	>	}
514
515	<	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();
515	>	}
516		}
517	+
518	+	}
519	+
520
521	<	nitems = atoi( read_buffer );
521	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
522
523	<	// Check to see that the number of integrable objects in the
524	<	// intial configuration file is the same as derived from the
525	<	// meta-data file.
526	<
527	<	if( nTotObjs != nitems){
528	<	sprintf( painCave.errMsg,
529	<	"DumpReader Error. %s nIntegrable, %d, "
530	<	"does not match the meta-data file's nIntegrable, %d.\n",
297	<	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
298	<	haveError= 1;
299	<	simError();
523	>	inputStream.getline(buffer, bufferSize);
524	>	std::string line(buffer);
525	>
526	>	if (line.find("<StuntDoubles>") == std::string::npos) {
527	>	sprintf(painCave.errMsg,
528	>	"DumpReader Error: Missing <StuntDoubles>\n");
529	>	painCave.isFatal = 1;
530	>	simError();
531		}
532
533	<	//read the boxMat from the comment line
534	<
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();
338	<	}
339	<
340	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
341	<	for(j=0; j < integrableObjects.size(); j++){
342	<
343	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
344	<	if(eof_test == NULL){
345	<	sprintf(painCave.errMsg,
346	<	"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	<
361	<	}
362	<	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);
533	>	while(inputStream.getline(buffer, bufferSize)) {
534	>	line = buffer;
535
536	<	for(j=0; j < nCurObj; j++){
537	<
370	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
371	<	if(eof_test == NULL){
372	<	sprintf(painCave.errMsg,
373	<	"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	<
536	>	if(line.find("</StuntDoubles>") != std::string::npos) {
537	>	break;
538		}
389	–
390	–	}
391	–
392	–	}
393	–	else{
394	–	//actions taken at slave nodes
395	–	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
539
540	<	parseErr = parseCommentLine( read_buffer, simnfo);
398	<
399	<	if( parseErr != NULL ){
400	<	strcpy( painCave.errMsg, parseErr );
401	<	haveError = 1;
402	<	simError();
540	>	parseDumpLine(line);
541		}
542
543	<	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);
543	>	}
544
545	<	if(localIndex == -1) {
414	<	sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
415	<	haveError = 1;
416	<	simError();
417	<	}
545	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
546
547	<	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
547	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
548	>	inputStream.getline(buffer, bufferSize);
549	>	std::string line(buffer);
550
551	<	nCurObj = integrableObjects.size();
552	<
553	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
554	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
551	>	if (line.find("<FrameData>") == std::string::npos) {
552	>	sprintf(painCave.errMsg,
553	>	"DumpReader Error: Missing <FrameData>\n");
554	>	painCave.isFatal = 1;
555	>	simError();
556	>	}
557
558	<	for(j = 0; j < integrableObjects.size(); j++){
559	<
560	<	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
561	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
562	<
431	<	parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
432	<
433	<	if( parseErr != NULL ){
434	<	strcpy( painCave.errMsg, parseErr );
435	<	simError();
436	<	}
437	<
438	<	}
439	<
558	>	while(inputStream.getline(buffer, bufferSize)) {
559	>	line = buffer;
560	>
561	>	if(line.find("</FrameData>") != std::string::npos) {
562	>	break;
563		}
564
565	<	}
566	<
567	<	}
568	<
569	<	#endif
570	<	}
571	<
449	<	char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
450	<
451	<	char *foo; // the pointer to the current string token
452	<
453	<	double pos[3]; // position place holders
454	<	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 );
565	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
566	>	if (!tokenizer.hasMoreTokens()) {
567	>	sprintf(painCave.errMsg,
568	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
569	>	painCave.isFatal = 1;
570	>	simError();
571	>	}
572
573	<	foo = strtok(NULL, " ,;\t");
574	<	if(foo == NULL){
575	<	sprintf( painCave.errMsg,
576	<	"error in reading postition z from %s\n",
577	<	inFileName.c_str());
578	<	return strdup( painCave.errMsg );
579	<	}
580	<	pos[2] = atof( foo );
581	<
582	<
583	<	// get the velocities
584	<
585	<	foo = strtok(NULL, " ,;\t");
586	<	if(foo == NULL){
587	<	sprintf( painCave.errMsg,
588	<	"error in reading velocity x from %s\n",
589	<	inFileName.c_str() );
590	<	return strdup( painCave.errMsg );
591	<	}
592	<	vel[0] = atof( foo );
593	<
594	<	foo = strtok(NULL, " ,;\t");
595	<	if(foo == NULL){
596	<	sprintf( painCave.errMsg,
597	<	"error in reading velocity x from %s\n",
598	<	inFileName.c_str() );
599	<	return strdup( painCave.errMsg );
600	<	}
601	<	vel[1] = atof( foo );
602	<
603	<	foo = strtok(NULL, " ,;\t");
604	<	if(foo == NULL){
605	<	sprintf( painCave.errMsg,
606	<	"error in reading velocity x from %s\n",
607	<	inFileName.c_str() );
608	<	return strdup( painCave.errMsg );
609	<	}
610	<	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 );
573	>	std::string propertyName = tokenizer.nextToken();
574	>	if (propertyName == "Time") {
575	>	RealType currTime = tokenizer.nextTokenAsDouble();
576	>	s->setTime(currTime);
577	>	} else if (propertyName == "Hmat"){
578	>	Mat3x3d hmat;
579	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
580	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
581	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
582	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
583	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
584	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
585	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
586	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
587	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
588	>	s->setHmat(hmat);
589	>	} else if (propertyName == "Thermostat") {
590	>	RealType chi = tokenizer.nextTokenAsDouble();
591	>	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
592	>	s->setChi(chi);
593	>	s->setIntegralOfChiDt(integralOfChiDt);
594	>	} else if (propertyName == "Barostat") {
595	>	Mat3x3d eta;
596	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
597	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
598	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
599	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
600	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
601	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
602	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
603	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
604	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
605	>	s->setEta(eta);
606	>	} else {
607	>	sprintf(painCave.errMsg,
608	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
609	>	painCave.isFatal = 0;
610	>	simError();
611		}
697	–	integralOfChidt = atof( foo );
612
699	–	//push chi and integralOfChidt into SimInfo::properties which can be
700	–	//retrieved by integrator later
701	–	DoubleGenericData* chiValue = new DoubleGenericData();
702	–	chiValue->setID(CHIVALUE_ID);
703	–	chiValue->setData(chi);
704	–	entry_plug->addProperty(chiValue);
705	–
706	–	DoubleGenericData* integralOfChidtValue = new DoubleGenericData();
707	–	integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
708	–	integralOfChidtValue->setData(integralOfChidt);
709	–	entry_plug->addProperty(integralOfChidtValue);
710	–
613		}
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	–	}
614
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);
615		}
616
617	<
618	<	MPI_Finalize();
756	<	exit (0);
757	<
758	<	}
759	<
760	<	void DumpReader::anonymousNodeDie( void ){
761	<
762	<	MPI_Finalize();
763	<	exit (0);
764	<	}
765	<	#endif
617	>
618	>	}//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 1714 by gezelter, Sat May 19 18:12:46 2012 UTC

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