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

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1450 by gezelter, Thu Jun 17 19:11:37 2010 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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]  Vardeman & Gezelter, in progress (2009).
40		*/
41	–
42	–	#define _LARGEFILE_SOURCE64
43	–	#define _FILE_OFFSET_BITS 64
44	–
45	–	#include <sys/types.h>
46	–	#include <sys/stat.h>
47	–
48	–	#include <iostream>
49	–	#include <math.h>
50	–
51	–	#include <stdio.h>
52	–	#include <stdlib.h>
53	–	#include <string.h>
54	–
55	–	#include "io/DumpReader.hpp"
56	–	#include "primitives/Molecule.hpp"
57	–	#include "utils/simError.h"
58	–	#include "utils/MemoryUtils.hpp"
59	–	#include "utils/StringTokenizer.hpp"
60	–
61	–	#ifdef IS_MPI
62	–
63	–	#include <mpi.h>
64	–	#define TAKE_THIS_TAG_CHAR 0
65	–	#define TAKE_THIS_TAG_INT 1
66	–
67	–	#endif // is_mpi
68	–
69	–
70	–	namespace oopse {
41
42	<	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
43	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
42	>	#define _LARGEFILE_SOURCE64
43	>	#define _FILE_OFFSET_BITS 64
44	>
45	>	#include <sys/types.h>
46	>	#include <sys/stat.h>
47	>
48	>	#include <iostream>
49	>	#include <math.h>
50	>
51	>	#include <stdio.h>
52	>	#include <stdlib.h>
53	>	#include <string.h>
54	>
55	>	#include "io/DumpReader.hpp"
56	>	#include "primitives/Molecule.hpp"
57	>	#include "utils/simError.h"
58	>	#include "utils/MemoryUtils.hpp"
59	>	#include "utils/StringTokenizer.hpp"
60	>
61	>	#ifdef IS_MPI
62	>
63	>	#include <mpi.h>
64	>	#define TAKE_THIS_TAG_CHAR 0
65	>	#define TAKE_THIS_TAG_INT 1
66	>
67	>	#endif // is_mpi
68	>
69	>
70	>	namespace OpenMD {
71	>
72	>	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
74
75	<	#ifdef IS_MPI
75	>	#ifdef IS_MPI
76
77	<	if (worldRank == 0) {
78	<	#endif
77	>	if (worldRank == 0) {
78	>	#endif
79
80	<	inFile_ = fopen(filename_.c_str(), "r");
80	>	inFile_ = new std::ifstream(filename_.c_str());
81
82	<	if (inFile_ == NULL) {
83	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
84	<	painCave.isFatal = 1;
85	<	simError();
86	<	}
82	>	if (inFile_->fail()) {
83	>	sprintf(painCave.errMsg,
84	>	"DumpReader: Cannot open file: %s\n",
85	>	filename_.c_str());
86	>	painCave.isFatal = 1;
87	>	simError();
88	>	}
89
90	<	#ifdef IS_MPI
90	>	#ifdef IS_MPI
91
92	<	}
92	>	}
93
94	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95	<	MPIcheckPoint();
94	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95	>	errorCheckPoint();
96
97	<	#endif
97	>	#endif
98
99	<	return;
100	<	}
99	>	return;
100	>	}
101
102	<	DumpReader::~DumpReader() {
102	>	DumpReader::~DumpReader() {
103
104	<	#ifdef IS_MPI
104	>	#ifdef IS_MPI
105
106	<	if (worldRank == 0) {
107	<	#endif
106	>	if (worldRank == 0) {
107	>	#endif
108
109	<	int error;
108	<	error = fclose(inFile_);
109	>	delete inFile_;
110
111	<	if (error) {
111	<	sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
112	<	painCave.isFatal = 1;
113	<	simError();
114	<	}
111	>	#ifdef IS_MPI
112
113	<	MemoryUtils::deletePointers(framePos_);
117	<
118	<	#ifdef IS_MPI
119	<
120	<	}
113	>	}
114
115	<	strcpy(checkPointMsg, "Dump file closed successfully.");
116	<	MPIcheckPoint();
115	>	strcpy(checkPointMsg, "Dump file closed successfully.");
116	>	errorCheckPoint();
117
118	<	#endif
118	>	#endif
119
120	<	return;
121	<	}
120	>	return;
121	>	}
122
123	<	int DumpReader::getNFrames(void) {
123	>	int DumpReader::getNFrames(void) {
124	>
125	>	if (!isScanned_)
126	>	scanFile();
127	>
128	>	return nframes_;
129	>	}
130	>
131	>	void DumpReader::scanFile(void) {
132	>	int lineNo = 0;
133	>	std::streampos prevPos;
134	>	std::streampos  currPos;
135
136	<	if (!isScanned_)
133	<	scanFile();
136	>	#ifdef IS_MPI
137
138	<	return nframes_;
139	<	}
137	<
138	<	void DumpReader::scanFile(void) {
139	<	int i, j;
140	<	int lineNum = 0;
141	<	char readBuffer[maxBufferSize];
142	<	fpos_t * currPos;
143	<
144	<	#ifdef IS_MPI
145	<
146	<	if (worldRank == 0) {
147	<	#endif // is_mpi
138	>	if (worldRank == 0) {
139	>	#endif // is_mpi
140
141	<	rewind(inFile_);
142	<
143	<	currPos = new fpos_t;
144	<	fgetpos(inFile_, currPos);
145	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
146	<	lineNum++;
155	<
156	<	if (feof(inFile_)) {
157	<	sprintf(painCave.errMsg,
158	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
159	<	filename_.c_str(),
160	<	lineNum);
161	<	painCave.isFatal = 1;
162	<	simError();
163	<	}
164	<
165	<	while (!feof(inFile_)) {
166	<	framePos_.push_back(currPos);
141	>	currPos = inFile_->tellg();
142	>	prevPos = currPos;
143	>	bool foundOpenSnapshotTag = false;
144	>	bool foundClosedSnapshotTag = false;
145	>	while(inFile_->getline(buffer, bufferSize)) {
146	>	++lineNo;
147
148	<	i = atoi(readBuffer);
149	<
150	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
151	<	lineNum++;
152	<
153	<	if (feof(inFile_)) {
154	<	sprintf(painCave.errMsg,
155	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
156	<	filename_.c_str(),
157	<	lineNum);
158	<	painCave.isFatal = 1;
159	<	simError();
160	<	}
181	<
182	<	for(j = 0; j < i; j++) {
183	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
184	<	lineNum++;
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	<	if (feof(inFile_)) {
163	<	sprintf(painCave.errMsg,
164	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
165	<	" with atom %d\n", filename_.c_str(),
166	<	lineNum,
167	<	j);
168	<
193	<	painCave.isFatal = 1;
194	<	simError();
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	<
198	<	currPos = new fpos_t;
199	<	fgetpos(inFile_, currPos);
200	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
201	<	lineNum++;
181	>	prevPos = currPos;
182		}
183
184	<	delete currPos;
185	<	rewind(inFile_);
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();
208	<	#ifdef IS_MPI
209	<	}
210	<
211	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
212	<
213	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
214	<	MPIcheckPoint();
215	<
216	<	#endif // is_mpi
217	<
218	<	isScanned_ = true;
219	<	}
220	<
221	<	void DumpReader::readFrame(int whichFrame) {
222	<	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
223	<
224	<	if (storageLayout & DataStorage::dslPosition) {
225	<	needPos_ = true;
226	<	} else {
227	<	needPos_ = false;
228	<	}
229	<
230	<	if (storageLayout & DataStorage::dslVelocity) {
231	<	needVel_ = true;
232	<	} else {
233	<	needVel_ = false;
234	<	}
235	<
236	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
237	<	needQuaternion_ = true;
238	<	} else {
239	<	needQuaternion_ = false;
240	<	}
241	<
242	<	if (storageLayout & DataStorage::dslAngularMomentum) {
243	<	needAngMom_ = true;
244	<	} else {
245	<	needAngMom_ = false;
246	<	}
247	<
248	<	readSet(whichFrame);
249	<	}
250	<
251	<	void DumpReader::readSet(int whichFrame) {
252	<	int i;
253	<	int nTotObjs;                  // the number of atoms
254	<	char read_buffer[maxBufferSize];  //the line buffer for reading
255	<	char * eof_test;               // ptr to see when we reach the end of the file
256	<
257	<	Molecule* mol;
258	<	StuntDouble* integrableObject;
259	<	SimInfo::MoleculeIterator mi;
260	<	Molecule::IntegrableObjectIterator ii;
261	<
262	<	#ifndef IS_MPI
263	<
264	<	fsetpos(inFile_, framePos_[whichFrame]);
265	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
266	<
267	<	if (eof_test == NULL) {
268	<	sprintf(painCave.errMsg,
269	<	"DumpReader error: error reading 1st line of \"%s\"\n",
270	<	filename_.c_str());
271	<	painCave.isFatal = 1;
272	<	simError();
273	<	}
274	<
275	<	nTotObjs = atoi(read_buffer);
276	<
277	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
278	<	sprintf(painCave.errMsg,
279	<	"DumpReader error. %s nIntegrable, %d, "
280	<	"does not match the meta-data file's nIntegrable, %d.\n",
281	<	filename_.c_str(),
282	<	nTotObjs,
283	<	info_->getNGlobalIntegrableObjects());
194	>	nframes_ = framePos_.size();
195
196	<	painCave.isFatal = 1;
197	<	simError();
198	<	}
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	<	//read the box mat from the comment line
207	>	#endif // is_mpi
208
209	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
210	<
211	<	if (eof_test == NULL) {
212	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
213	<	filename_.c_str());
214	<	painCave.isFatal = 1;
215	<	simError();
216	<	}
217	<
218	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
219	<
220	<	//parse dump lines
221	<
222	<	i = 0;
223	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
224	<
225	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
226	<	integrableObject = mol->nextIntegrableObject(ii)) {
227	<
228	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
229	<
230	<	if (eof_test == NULL) {
231	<	sprintf(painCave.errMsg,
232	<	"DumpReader Error: error in reading file %s\n"
233	<	"natoms  = %d; index = %d\n"
234	<	"error reading the line from the file.\n",
235	<	filename_.c_str(),
236	<	nTotObjs,
237	<	i);
238	<
239	<	painCave.isFatal = 1;
240	<	simError();
241	<	}
242	<
243	<	parseDumpLine(read_buffer, integrableObject);
244	<	i++;
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 || storageLayout & DataStorage::dslElectroFrame) {
231	>	needQuaternion_ = true;
232	>	} else {
233	>	needQuaternion_ = false;
234	>	}
235	>
236	>	if (storageLayout & DataStorage::dslAngularMomentum) {
237	>	needAngMom_ = true;
238	>	} else {
239	>	needAngMom_ = false;
240	>	}
241	>
242	>	readSet(whichFrame);
243	>
244	>	if (needCOMprops_) {
245	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	>	Vector3d com;
247	>	Vector3d comvel;
248	>	Vector3d comw;
249	>	if (needPos_ && needVel_){
250	>	info_->getComAll(com, comvel);
251	>	comw = info_->getAngularMomentum();
252	>	}else{
253	>	com = info_->getCom();
254	>	comvel = 0.0;
255	>	comw   = 0.0;
256		}
257	+	s->setCOMprops(com, comvel, comw);
258		}
259	<
260	<	// MPI Section of code..........
261	<
262	<	#else //IS_MPI
263	<
264	<	// first thing first, suspend fatalities.
259	>
260	>	}
261	>
262	>	void DumpReader::readSet(int whichFrame) {
263	>	std::string line;
264	>
265	>	#ifndef IS_MPI
266	>	inFile_->clear();
267	>	inFile_->seekg(framePos_[whichFrame]);
268	>
269	>	std::istream& inputStream = *inFile_;
270	>
271	>	#else
272		int masterNode = 0;
273	<	int nCurObj;
337	<	painCave.isEventLoop = 1;
338	<
339	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
340	<	int haveError;
341	<
342	<	MPI_Status istatus;
343	<	int nitems;
344	<
345	<	nTotObjs = info_->getNGlobalIntegrableObjects();
346	<	haveError = 0;
347	<
273	>	std::stringstream sstream;
274		if (worldRank == masterNode) {
275	<	fsetpos(inFile_, framePos_[whichFrame]);
275	>	std::string sendBuffer;
276	>
277	>	inFile_->clear();
278	>	inFile_->seekg(framePos_[whichFrame]);
279
280	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
281	<
282	<	if (eof_test == NULL) {
283	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
284	<	filename_.c_str());
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
359	<
360	<	nitems = atoi(read_buffer);
361	<
362	<	// Check to see that the number of integrable objects in the
363	<	// intial configuration file is the same as derived from the
364	<	// meta-data file.
365	<
366	<	if (nTotObjs != nitems) {
367	<	sprintf(painCave.errMsg,
368	<	"DumpReader Error. %s nIntegrable, %d, "
369	<	"does not match the meta-data file's nIntegrable, %d.\n",
370	<	filename_.c_str(),
371	<	nTotObjs,
372	<	info_->getNGlobalIntegrableObjects());
373	<
374	<	painCave.isFatal = 1;
375	<	simError();
376	<	}
377	<
378	<	//read the boxMat from the comment line
379	<
380	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
381	<
382	<	if (eof_test == NULL) {
383	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
384	<	filename_.c_str());
385	<	painCave.isFatal = 1;
386	<	simError();
387	<	}
388	<
389	<	//Every single processor will parse the comment line by itself
390	<	//By using this way, we might lose some efficiency, but if we want to add
391	<	//more parameters into comment line, we only need to modify function
392	<	//parseCommentLine
393	<
394	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
395	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
396	<
397	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
398	<	int which_node = info_->getMolToProc(i);
399	<
400	<	if (which_node == masterNode) {
401	<	//molecules belong to master node
402	<
403	<	mol = info_->getMoleculeByGlobalIndex(i);
404	<
405	<	if (mol == NULL) {
406	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
407	<	painCave.isFatal = 1;
408	<	simError();
409	<	}
410	<
411	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
412	<	integrableObject = mol->nextIntegrableObject(ii)){
413	<
414	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
415	<
416	<	if (eof_test == NULL) {
417	<	sprintf(painCave.errMsg,
418	<	"DumpReader Error: error in reading file %s\n"
419	<	"natoms  = %d; index = %d\n"
420	<	"error reading the line from the file.\n",
421	<	filename_.c_str(),
422	<	nTotObjs,
423	<	i);
424	<
425	<	painCave.isFatal = 1;
426	<	simError();
427	<	}
428	<
429	<	parseDumpLine(read_buffer, integrableObject);
430	<	}
431	<	} else {
432	<	//molecule belongs to slave nodes
433	<
434	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
435	<	MPI_COMM_WORLD, &istatus);
436	<
437	<	for(int j = 0; j < nCurObj; j++) {
438	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
439	<
440	<	if (eof_test == NULL) {
441	<	sprintf(painCave.errMsg,
442	<	"DumpReader Error: error in reading file %s\n"
443	<	"natoms  = %d; index = %d\n"
444	<	"error reading the line from the file.\n",
445	<	filename_.c_str(),
446	<	nTotObjs,
447	<	i);
448	<
449	<	painCave.isFatal = 1;
450	<	simError();
451	<	}
452	<
453	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
454	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
455	<	}
456	<	}
280	>	while (inFile_->getline(buffer, bufferSize)) {
281	>
282	>	line = buffer;
283	>	sendBuffer += line;
284	>	sendBuffer += '\n';
285	>	if (line.find("</Snapshot>") != std::string::npos) {
286	>	break;
287	>	}
288		}
289	<	} else {
290	<	//actions taken at slave nodes
291	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
289	>
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	<	/**@todo*/
295	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
296	<
297	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
298	<	int which_node = info_->getMolToProc(i);
299	<
300	<	if (which_node == worldRank) {
301	<	//molecule with global index i belongs to this processor
302	<
303	<	mol = info_->getMoleculeByGlobalIndex(i);
304	<	if (mol == NULL) {
305	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
306	<	painCave.isFatal = 1;
475	<	simError();
476	<	}
477	<
478	<	nCurObj = mol->getNIntegrableObjects();
479	<
480	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
481	<	MPI_COMM_WORLD);
482	<
483	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
484	<	integrableObject = mol->nextIntegrableObject(ii)){
485	<
486	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
487	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
488	<
489	<	parseDumpLine(read_buffer, integrableObject);
490	<	}
491	<
492	<	}
493	<
494	<	}
495	<
496	<	}
497	<
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	<	}
320	<
321	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
322	<
323	<	Vector3d pos;  // position place holders
324	<	Vector3d vel;  // velocity placeholders
325	<	Quat4d q;    // the quaternions
326	<	Vector3d ji;   // angular velocity placeholders;
327	<	StringTokenizer tokenizer(line);
328	<	int nTokens;
329	<
330	<	nTokens = tokenizer.countTokens();
331	<
332	<	if (nTokens < 14) {
333	<	sprintf(painCave.errMsg,
334	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
335	<	painCave.isFatal = 1;
336	<	simError();
319	>	//read frameData
320	>	readFrameProperties(inputStream);
321	>
322	>	//read StuntDoubles
323	>	readStuntDoubles(inputStream);
324	>
325	>	inputStream.getline(buffer, bufferSize);
326	>	line = buffer;
327	>	if (line.find("</Snapshot>") == std::string::npos) {
328	>	sprintf(painCave.errMsg,
329	>	"DumpReader Error: can not find </Snapshot>\n");
330	>	painCave.isFatal = 1;
331	>	simError();
332	>	}
333	>
334	>	}
335	>
336	>	void DumpReader::parseDumpLine(const std::string& line) {
337	>
338	>
339	>	StringTokenizer tokenizer(line);
340	>	int nTokens;
341	>
342	>	nTokens = tokenizer.countTokens();
343	>
344	>	if (nTokens < 2) {
345	>	sprintf(painCave.errMsg,
346	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
347	>	painCave.isFatal = 1;
348	>	simError();
349	>	}
350	>
351	>	int index = tokenizer.nextTokenAsInt();
352	>
353	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
354	>
355	>	if (integrableObject == NULL) {
356	>	return;
357		}
358	+	std::string type = tokenizer.nextToken();
359	+	int size = type.size();
360	+
361	+	size_t found;
362
520	–	std::string name = tokenizer.nextToken();
521	–
522	–	if (name != integrableObject->getType()) {
523	–
524	–	sprintf(painCave.errMsg,
525	–	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
526	–	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
527	–	painCave.isFatal = 1;
528	–	simError();
529	–	}
530	–
531	–	pos[0] = tokenizer.nextTokenAsDouble();
532	–	pos[1] = tokenizer.nextTokenAsDouble();
533	–	pos[2] = tokenizer.nextTokenAsDouble();
363		if (needPos_) {
364	<	integrableObject->setPos(pos);
364	>	found = type.find("p");
365	>	if (found == std::string::npos) {
366	>	sprintf(painCave.errMsg,
367	>	"DumpReader Error: StuntDouble %d has no Position\n"
368	>	"\tField (\"p\") specified.\n%s\n", index,
369	>	line.c_str());
370	>	painCave.isFatal = 1;
371	>	simError();
372	>	}
373		}
374
538	–	vel[0] = tokenizer.nextTokenAsDouble();
539	–	vel[1] = tokenizer.nextTokenAsDouble();
540	–	vel[2] = tokenizer.nextTokenAsDouble();
541	–	if (needVel_) {
542	–	integrableObject->setVel(vel);
543	–	}
544	–
375		if (integrableObject->isDirectional()) {
376	<
377	<	q[0] = tokenizer.nextTokenAsDouble();
378	<	q[1] = tokenizer.nextTokenAsDouble();
379	<	q[2] = tokenizer.nextTokenAsDouble();
380	<	q[3] = tokenizer.nextTokenAsDouble();
381	<
382	<	double qlen = q.length();
383	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
384	<
385	<	sprintf(painCave.errMsg,
386	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
387	<	painCave.isFatal = 1;
388	<	simError();
389	<
390	<	}
391	<
392	<	q.normalize();
393	<	if (needQuaternion_) {
394	<	integrableObject->setQ(q);
395	<	}
396	<
397	<	ji[0] = tokenizer.nextTokenAsDouble();
398	<	ji[1] = tokenizer.nextTokenAsDouble();
399	<	ji[2] = tokenizer.nextTokenAsDouble();
400	<	if (needAngMom_) {
401	<	integrableObject->setJ(ji);
376	>	if (needQuaternion_) {
377	>	found = type.find("q");
378	>	if (found == std::string::npos) {
379	>	sprintf(painCave.errMsg,
380	>	"DumpReader Error: Directional StuntDouble %d has no\n"
381	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
382	>	line.c_str());
383	>	painCave.isFatal = 1;
384	>	simError();
385	>	}
386	>	}
387	>	}
388	>
389	>	for(int i = 0; i < size; ++i) {
390	>	switch(type[i]) {
391	>
392	>	case 'p': {
393	>	Vector3d pos;
394	>	pos[0] = tokenizer.nextTokenAsDouble();
395	>	pos[1] = tokenizer.nextTokenAsDouble();
396	>	pos[2] = tokenizer.nextTokenAsDouble();
397	>	if (needPos_) {
398	>	integrableObject->setPos(pos);
399	>	}
400	>	break;
401	>	}
402	>	case 'v' : {
403	>	Vector3d vel;
404	>	vel[0] = tokenizer.nextTokenAsDouble();
405	>	vel[1] = tokenizer.nextTokenAsDouble();
406	>	vel[2] = tokenizer.nextTokenAsDouble();
407	>	if (needVel_) {
408	>	integrableObject->setVel(vel);
409	>	}
410	>	break;
411	>	}
412	>
413	>	case 'q' : {
414	>	Quat4d q;
415	>	if (integrableObject->isDirectional()) {
416	>
417	>	q[0] = tokenizer.nextTokenAsDouble();
418	>	q[1] = tokenizer.nextTokenAsDouble();
419	>	q[2] = tokenizer.nextTokenAsDouble();
420	>	q[3] = tokenizer.nextTokenAsDouble();
421	>
422	>	RealType qlen = q.length();
423	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
424	>
425	>	sprintf(painCave.errMsg,
426	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
427	>	painCave.isFatal = 1;
428	>	simError();
429	>
430	>	}
431	>
432	>	q.normalize();
433	>	if (needQuaternion_) {
434	>	integrableObject->setQ(q);
435	>	}
436	>	}
437	>	break;
438	>	}
439	>	case 'j' : {
440	>	Vector3d ji;
441	>	if (integrableObject->isDirectional()) {
442	>	ji[0] = tokenizer.nextTokenAsDouble();
443	>	ji[1] = tokenizer.nextTokenAsDouble();
444	>	ji[2] = tokenizer.nextTokenAsDouble();
445	>	if (needAngMom_) {
446	>	integrableObject->setJ(ji);
447	>	}
448	>	}
449	>	break;
450	>	}
451	>	case 'f': {
452	>
453	>	Vector3d force;
454	>	force[0] = tokenizer.nextTokenAsDouble();
455	>	force[1] = tokenizer.nextTokenAsDouble();
456	>	force[2] = tokenizer.nextTokenAsDouble();
457	>	integrableObject->setFrc(force);
458	>	break;
459	>	}
460	>	case 't' : {
461	>
462	>	Vector3d torque;
463	>	torque[0] = tokenizer.nextTokenAsDouble();
464	>	torque[1] = tokenizer.nextTokenAsDouble();
465	>	torque[2] = tokenizer.nextTokenAsDouble();
466	>	integrableObject->setTrq(torque);
467	>	break;
468	>	}
469	>	default: {
470	>	sprintf(painCave.errMsg,
471	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
472	>	painCave.isFatal = 1;
473	>	simError();
474	>	break;
475	>	}
476	>
477		}
478		}
479	+
480	+	}
481	+
482	+
483	+	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
484	+
485	+	inputStream.getline(buffer, bufferSize);
486	+	std::string line(buffer);
487
488	<	}
489	<
490	<
491	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
492	<	double currTime;
580	<	Mat3x3d hmat;
581	<	double chi;
582	<	double integralOfChiDt;
583	<	Mat3x3d eta;
584	<
585	<	StringTokenizer tokenizer(line);
586	<	int nTokens;
587	<
588	<	nTokens = tokenizer.countTokens();
589	<
590	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
591	<	if (nTokens < 10) {
592	<	sprintf(painCave.errMsg,
593	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
594	<	painCave.isFatal = 1;
595	<	simError();
488	>	if (line.find("<StuntDoubles>") == std::string::npos) {
489	>	sprintf(painCave.errMsg,
490	>	"DumpReader Error: Missing <StuntDoubles>\n");
491	>	painCave.isFatal = 1;
492	>	simError();
493		}
494	<
495	<	//read current time
496	<	currTime = tokenizer.nextTokenAsDouble();
600	<	s->setTime(currTime);
601	<
602	<	//read h-matrix
603	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
604	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
605	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
606	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
607	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
608	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
609	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
610	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
611	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
612	<	s->setHmat(hmat);
613	<
614	<	//read chi and integralOfChidt, they should apprear in pair
615	<	if (tokenizer.countTokens() >= 2) {
616	<	chi = tokenizer.nextTokenAsDouble();
617	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
494	>
495	>	while(inputStream.getline(buffer, bufferSize)) {
496	>	line = buffer;
497
498	<	s->setChi(chi);
499	<	s->setIntegralOfChiDt(integralOfChiDt);
498	>	if(line.find("</StuntDoubles>") != std::string::npos) {
499	>	break;
500	>	}
501	>
502	>	parseDumpLine(line);
503		}
504	<
505	<	//read eta (eta is 3x3 matrix)
506	<	if (tokenizer.countTokens() >= 9) {
507	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
508	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
509	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
510	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
511	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
512	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
513	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
514	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
515	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
504	>
505	>	}
506	>
507	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
508	>
509	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
510	>	inputStream.getline(buffer, bufferSize);
511	>	std::string line(buffer);
512	>
513	>	if (line.find("<FrameData>") == std::string::npos) {
514	>	sprintf(painCave.errMsg,
515	>	"DumpReader Error: Missing <FrameData>\n");
516	>	painCave.isFatal = 1;
517	>	simError();
518	>	}
519	>
520	>	while(inputStream.getline(buffer, bufferSize)) {
521	>	line = buffer;
522
523	<	s->setEta(eta);
523	>	if(line.find("</FrameData>") != std::string::npos) {
524	>	break;
525	>	}
526	>
527	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
528	>	if (!tokenizer.hasMoreTokens()) {
529	>	sprintf(painCave.errMsg,
530	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
531	>	painCave.isFatal = 1;
532	>	simError();
533	>	}
534	>
535	>	std::string propertyName = tokenizer.nextToken();
536	>	if (propertyName == "Time") {
537	>	RealType currTime = tokenizer.nextTokenAsDouble();
538	>	s->setTime(currTime);
539	>	} else if (propertyName == "Hmat"){
540	>	Mat3x3d hmat;
541	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
542	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
543	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
544	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
545	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
546	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
547	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
548	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
549	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
550	>	s->setHmat(hmat);
551	>	} else if (propertyName == "Thermostat") {
552	>	RealType chi = tokenizer.nextTokenAsDouble();
553	>	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
554	>	s->setChi(chi);
555	>	s->setIntegralOfChiDt(integralOfChiDt);
556	>	} else if (propertyName == "Barostat") {
557	>	Mat3x3d eta;
558	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
559	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
560	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
561	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
562	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
563	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
564	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
565	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
566	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
567	>	s->setEta(eta);
568	>	} else {
569	>	sprintf(painCave.errMsg,
570	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
571	>	painCave.isFatal = 0;
572	>	simError();
573	>	}
574	>
575		}
576	<
638	<
576	>
577		}
578	<
579	<	}//end namespace oopse
578	>
579	>
580	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpReader.cpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1450 by gezelter, Thu Jun 17 19:11:37 2010 UTC

#	Line 0 | Line 1
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