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root/OpenMD/branches/development/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.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
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 {
42
43	<	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
44	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
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
76	>	#ifdef IS_MPI
77
78	<	if (worldRank == 0) {
79	<	#endif
78	>	if (worldRank == 0) {
79	>	#endif
80
81	<	inFile_ = fopen(filename_.c_str(), "r");
81	>	inFile_ = new std::ifstream(filename_.c_str());
82
83	<	if (inFile_ == NULL) {
84	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
85	<	painCave.isFatal = 1;
86	<	simError();
87	<	}
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
91	>	#ifdef IS_MPI
92
93	<	}
93	>	}
94
95	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
96	<	MPIcheckPoint();
95	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
96	>	errorCheckPoint();
97
98	<	#endif
98	>	#endif
99
100	<	return;
101	<	}
100	>	return;
101	>	}
102
103	<	DumpReader::~DumpReader() {
103	>	DumpReader::~DumpReader() {
104
105	<	#ifdef IS_MPI
105	>	#ifdef IS_MPI
106
107	<	if (worldRank == 0) {
108	<	#endif
107	>	if (worldRank == 0) {
108	>	#endif
109
110	<	int error;
108	<	error = fclose(inFile_);
110	>	delete inFile_;
111
112	<	if (error) {
111	<	sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
112	<	painCave.isFatal = 1;
113	<	simError();
114	<	}
112	>	#ifdef IS_MPI
113
114	<	MemoryUtils::deletePointers(framePos_);
117	<
118	<	#ifdef IS_MPI
119	<
120	<	}
114	>	}
115
116	<	strcpy(checkPointMsg, "Dump file closed successfully.");
117	<	MPIcheckPoint();
116	>	strcpy(checkPointMsg, "Dump file closed successfully.");
117	>	errorCheckPoint();
118
119	<	#endif
119	>	#endif
120
121	<	return;
122	<	}
121	>	return;
122	>	}
123
124	<	int DumpReader::getNFrames(void) {
124	>	int DumpReader::getNFrames(void) {
125	>
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	<	if (!isScanned_)
133	<	scanFile();
137	>	#ifdef IS_MPI
138
139	<	return nframes_;
140	<	}
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
139	>	if (worldRank == 0) {
140	>	#endif // is_mpi
141
142	<	rewind(inFile_);
143	<
144	<	currPos = new fpos_t;
145	<	fgetpos(inFile_, currPos);
146	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
147	<	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);
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	<	i = atoi(readBuffer);
150	<
151	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
152	<	lineNum++;
153	<
154	<	if (feof(inFile_)) {
155	<	sprintf(painCave.errMsg,
156	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
157	<	filename_.c_str(),
158	<	lineNum);
159	<	painCave.isFatal = 1;
160	<	simError();
161	<	}
181	<
182	<	for(j = 0; j < i; j++) {
183	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
184	<	lineNum++;
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	<	if (feof(inFile_)) {
164	<	sprintf(painCave.errMsg,
165	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
166	<	" with atom %d\n", filename_.c_str(),
167	<	lineNum,
168	<	j);
169	<
193	<	painCave.isFatal = 1;
194	<	simError();
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	<
198	<	currPos = new fpos_t;
199	<	fgetpos(inFile_, currPos);
200	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
201	<	lineNum++;
182	>	prevPos = currPos;
183		}
184
185	<	delete currPos;
186	<	rewind(inFile_);
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();
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());
195	>	nframes_ = framePos_.size();
196
197	<	painCave.isFatal = 1;
198	<	simError();
199	<	}
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	<	//read the box mat from the comment line
208	>	#endif // is_mpi
209
210	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
211	<
212	<	if (eof_test == NULL) {
213	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
214	<	filename_.c_str());
215	<	painCave.isFatal = 1;
216	<	simError();
217	<	}
218	<
219	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
220	<
221	<	//parse dump lines
222	<
223	<	i = 0;
224	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
225	<
226	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
227	<	integrableObject = mol->nextIntegrableObject(ii)) {
228	<
229	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
230	<
231	<	if (eof_test == NULL) {
232	<	sprintf(painCave.errMsg,
233	<	"DumpReader Error: error in reading file %s\n"
234	<	"natoms  = %d; index = %d\n"
235	<	"error reading the line from the file.\n",
236	<	filename_.c_str(),
237	<	nTotObjs,
238	<	i);
239	<
240	<	painCave.isFatal = 1;
241	<	simError();
242	<	}
243	<
244	<	parseDumpLine(read_buffer, integrableObject);
245	<	i++;
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	<	// MPI Section of code..........
262	<
263	<	#else //IS_MPI
264	<
265	<	// first thing first, suspend fatalities.
260	>
261	>	}
262	>
263	>	void DumpReader::readSet(int whichFrame) {
264	>	std::string line;
265	>
266	>	#ifndef IS_MPI
267	>	inFile_->clear();
268	>	inFile_->seekg(framePos_[whichFrame]);
269	>
270	>	std::istream& inputStream = *inFile_;
271	>
272	>	#else
273		int masterNode = 0;
274	<	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	<
274	>	std::stringstream sstream;
275		if (worldRank == masterNode) {
276	<	fsetpos(inFile_, framePos_[whichFrame]);
277	<
278	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
279	<
353	<	if (eof_test == NULL) {
354	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
355	<	filename_.c_str());
356	<	painCave.isFatal = 1;
357	<	simError();
358	<	}
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
276	>	std::string sendBuffer;
277	>
278	>	inFile_->clear();
279	>	inFile_->seekg(framePos_[whichFrame]);
280
281	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
282	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
283	<
284	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
285	<	int which_node = info_->getMolToProc(i);
286	<
287	<	if (which_node == masterNode) {
288	<	//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	<	}
281	>	while (inFile_->getline(buffer, bufferSize)) {
282	>
283	>	line = buffer;
284	>	sendBuffer += line;
285	>	sendBuffer += '\n';
286	>	if (line.find("</Snapshot>") != std::string::npos) {
287	>	break;
288	>	}
289		}
290	<	} else {
291	<	//actions taken at slave nodes
292	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
290	>
291	>	int sendBufferSize = sendBuffer.size();
292	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
293	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
294
295	<	/**@todo*/
296	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
297	<
298	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
299	<	int which_node = info_->getMolToProc(i);
300	<
301	<	if (which_node == worldRank) {
302	<	//molecule with global index i belongs to this processor
303	<
304	<	mol = info_->getMoleculeByGlobalIndex(i);
305	<	if (mol == NULL) {
306	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
307	<	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	<
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	+	inputStream.getline(buffer, bufferSize);
311	+
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	<	}
321	<
322	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
323	<
324	<	Vector3d pos;  // position place holders
325	<	Vector3d vel;  // velocity placeholders
326	<	Quat4d q;    // the quaternions
327	<	Vector3d ji;   // angular velocity placeholders;
328	<	StringTokenizer tokenizer(line);
329	<	int nTokens;
330	<
331	<	nTokens = tokenizer.countTokens();
332	<
333	<	if (nTokens < 14) {
334	<	sprintf(painCave.errMsg,
335	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
336	<	painCave.isFatal = 1;
337	<	simError();
320	>	//read frameData
321	>	readFrameProperties(inputStream);
322	>
323	>	//read StuntDoubles
324	>	readStuntDoubles(inputStream);
325	>
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	>
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	>	int index = tokenizer.nextTokenAsInt();
353	>
354	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
355	>
356	>	if (integrableObject == NULL) {
357	>	return;
358		}
359	+	std::string type = tokenizer.nextToken();
360	+	int size = type.size();
361	+
362	+	size_t found;
363
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();
364		if (needPos_) {
365	<	integrableObject->setPos(pos);
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
538	–	vel[0] = tokenizer.nextTokenAsDouble();
539	–	vel[1] = tokenizer.nextTokenAsDouble();
540	–	vel[2] = tokenizer.nextTokenAsDouble();
541	–	if (needVel_) {
542	–	integrableObject->setVel(vel);
543	–	}
544	–
376		if (integrableObject->isDirectional()) {
377	<
378	<	q[0] = tokenizer.nextTokenAsDouble();
379	<	q[1] = tokenizer.nextTokenAsDouble();
380	<	q[2] = tokenizer.nextTokenAsDouble();
381	<	q[3] = tokenizer.nextTokenAsDouble();
382	<
383	<	double qlen = q.length();
384	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
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(int i = 0; i < size; ++i) {
391	>	switch(type[i]) {
392
393	<	sprintf(painCave.errMsg,
394	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
395	<	painCave.isFatal = 1;
396	<	simError();
397	<
398	<	}
399	<
400	<	q.normalize();
401	<	if (needQuaternion_) {
402	<	integrableObject->setQ(q);
403	<	}
404	<
405	<	ji[0] = tokenizer.nextTokenAsDouble();
406	<	ji[1] = tokenizer.nextTokenAsDouble();
407	<	ji[2] = tokenizer.nextTokenAsDouble();
408	<	if (needAngMom_) {
409	<	integrableObject->setJ(ji);
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	>	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	>	default: {
478	>	sprintf(painCave.errMsg,
479	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
480	>	painCave.isFatal = 1;
481	>	simError();
482	>	break;
483	>	}
484	>
485		}
486		}
487	+
488	+	}
489	+
490	+
491	+	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
492	+
493	+	inputStream.getline(buffer, bufferSize);
494	+	std::string line(buffer);
495
496	<	}
497	<
498	<
499	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
500	<	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();
496	>	if (line.find("<StuntDoubles>") == std::string::npos) {
497	>	sprintf(painCave.errMsg,
498	>	"DumpReader Error: Missing <StuntDoubles>\n");
499	>	painCave.isFatal = 1;
500	>	simError();
501		}
502	<
503	<	//read current time
504	<	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();
502	>
503	>	while(inputStream.getline(buffer, bufferSize)) {
504	>	line = buffer;
505
506	<	s->setChi(chi);
507	<	s->setIntegralOfChiDt(integralOfChiDt);
506	>	if(line.find("</StuntDoubles>") != std::string::npos) {
507	>	break;
508	>	}
509	>
510	>	parseDumpLine(line);
511		}
512	<
513	<	//read eta (eta is 3x3 matrix)
514	<	if (tokenizer.countTokens() >= 9) {
515	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
516	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
517	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
518	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
519	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
520	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
521	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
522	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
523	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
512	>
513	>	}
514	>
515	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
516	>
517	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
518	>	inputStream.getline(buffer, bufferSize);
519	>	std::string line(buffer);
520	>
521	>	if (line.find("<FrameData>") == std::string::npos) {
522	>	sprintf(painCave.errMsg,
523	>	"DumpReader Error: Missing <FrameData>\n");
524	>	painCave.isFatal = 1;
525	>	simError();
526	>	}
527	>
528	>	while(inputStream.getline(buffer, bufferSize)) {
529	>	line = buffer;
530
531	<	s->setEta(eta);
531	>	if(line.find("</FrameData>") != std::string::npos) {
532	>	break;
533	>	}
534	>
535	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
536	>	if (!tokenizer.hasMoreTokens()) {
537	>	sprintf(painCave.errMsg,
538	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
539	>	painCave.isFatal = 1;
540	>	simError();
541	>	}
542	>
543	>	std::string propertyName = tokenizer.nextToken();
544	>	if (propertyName == "Time") {
545	>	RealType currTime = tokenizer.nextTokenAsDouble();
546	>	s->setTime(currTime);
547	>	} else if (propertyName == "Hmat"){
548	>	Mat3x3d hmat;
549	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
550	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
551	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
552	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
553	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
554	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
555	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
556	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
557	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
558	>	s->setHmat(hmat);
559	>	} else if (propertyName == "Thermostat") {
560	>	RealType chi = tokenizer.nextTokenAsDouble();
561	>	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
562	>	s->setChi(chi);
563	>	s->setIntegralOfChiDt(integralOfChiDt);
564	>	} else if (propertyName == "Barostat") {
565	>	Mat3x3d eta;
566	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
567	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
568	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
569	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
570	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
571	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
572	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
573	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
574	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
575	>	s->setEta(eta);
576	>	} else {
577	>	sprintf(painCave.errMsg,
578	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
579	>	painCave.isFatal = 0;
580	>	simError();
581	>	}
582	>
583		}
584	<
638	<
584	>
585		}
586	<
587	<	}//end namespace oopse
586	>
587	>
588	>	}//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.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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