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

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 601 by tim, Thu Sep 15 19:17:04 2005 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 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++;
148	<
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	>	bool foundOpenSiteDataTag = false;
147	>	while(inFile_->getline(buffer, bufferSize)) {
148	>	++lineNo;
149
150	<	i = atoi(readBuffer);
151	<
152	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
153	<	lineNum++;
154	<
155	<	if (feof(inFile_)) {
156	<	sprintf(painCave.errMsg,
157	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
158	<	filename_.c_str(),
159	<	lineNum);
160	<	painCave.isFatal = 1;
161	<	simError();
162	<	}
181	<
182	<	for(j = 0; j < i; j++) {
183	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
184	<	lineNum++;
150	>	std::string line = buffer;
151	>	currPos = inFile_->tellg();
152	>	if (line.find("<Snapshot>")!= std::string::npos) {
153	>	if (foundOpenSnapshotTag) {
154	>	sprintf(painCave.errMsg,
155	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
156	>	filename_.c_str());
157	>	painCave.isFatal = 1;
158	>	simError();
159	>	}
160	>	foundOpenSnapshotTag = true;
161	>	foundClosedSnapshotTag = false;
162	>	framePos_.push_back(prevPos);
163
164	<	if (feof(inFile_)) {
165	<	sprintf(painCave.errMsg,
166	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
167	<	" with atom %d\n", filename_.c_str(),
168	<	lineNum,
169	<	j);
170	<
193	<	painCave.isFatal = 1;
194	<	simError();
164	>	} else if (line.find("</Snapshot>") != std::string::npos){
165	>	if (!foundOpenSnapshotTag) {
166	>	sprintf(painCave.errMsg,
167	>	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
168	>	filename_.c_str());
169	>	painCave.isFatal = 1;
170	>	simError();
171		}
172	+
173	+	if (foundClosedSnapshotTag) {
174	+	sprintf(painCave.errMsg,
175	+	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
176	+	filename_.c_str());
177	+	painCave.isFatal = 1;
178	+	simError();
179	+	}
180	+	foundClosedSnapshotTag = true;
181	+	foundOpenSnapshotTag = false;
182		}
183	<
198	<	currPos = new fpos_t;
199	<	fgetpos(inFile_, currPos);
200	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
201	<	lineNum++;
183	>	prevPos = currPos;
184		}
185
186	<	delete currPos;
187	<	rewind(inFile_);
186	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
187	>	// it and give a warning message
188	>	if (foundOpenSnapshotTag) {
189	>	sprintf(painCave.errMsg,
190	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
191	>	painCave.isFatal = 0;
192	>	simError();
193	>	framePos_.pop_back();
194	>	}
195
196	<	nframes_ = framePos_.size();
197	<	#ifdef IS_MPI
198	<	}
196	>	nframes_ = framePos_.size();
197	>
198	>	if (nframes_ == 0) {
199	>	sprintf(painCave.errMsg,
200	>	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
201	>	painCave.isFatal = 1;
202	>	simError();
203	>	}
204	>	#ifdef IS_MPI
205	>	}
206	>
207	>	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
208
209	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
209	>	#endif // is_mpi
210
211	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
212	<	MPIcheckPoint();
213	<
214	<	#endif // is_mpi
215	<
216	<	isScanned_ = true;
217	<	}
218	<
219	<	void DumpReader::readFrame(int whichFrame) {
220	<	if (!isScanned_)
221	<	scanFile();
222	<
223	<	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
224	<
225	<	if (storageLayout & DataStorage::dslPosition) {
226	<	needPos_ = true;
227	<	} else {
228	<	needPos_ = false;
211	>	isScanned_ = true;
212	>	}
213	>
214	>	void DumpReader::readFrame(int whichFrame) {
215	>	if (!isScanned_)
216	>	scanFile();
217	>
218	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
219	>
220	>	if (storageLayout & DataStorage::dslPosition) {
221	>	needPos_ = true;
222	>	} else {
223	>	needPos_ = false;
224	>	}
225	>
226	>	if (storageLayout & DataStorage::dslVelocity) {
227	>	needVel_ = true;
228	>	} else {
229	>	needVel_ = false;
230	>	}
231	>
232	>	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
233	>	needQuaternion_ = true;
234	>	} else {
235	>	needQuaternion_ = false;
236	>	}
237	>
238	>	if (storageLayout & DataStorage::dslAngularMomentum) {
239	>	needAngMom_ = true;
240	>	} else {
241	>	needAngMom_ = false;
242	>	}
243	>
244	>	readSet(whichFrame);
245	>
246	>	if (needCOMprops_) {
247	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
248	>	Vector3d com;
249	>	Vector3d comvel;
250	>	Vector3d comw;
251	>	if (needPos_ && needVel_){
252	>	info_->getComAll(com, comvel);
253	>	comw = info_->getAngularMomentum();
254	>	}else{
255	>	com = info_->getCom();
256	>	comvel = 0.0;
257	>	comw   = 0.0;
258	>	}
259	>	s->setCOMprops(com, comvel, comw);
260		}
261	<
262	<	if (storageLayout & DataStorage::dslVelocity) {
263	<	needVel_ = true;
261	>
262	>	}
263	>
264	>	void DumpReader::readSet(int whichFrame) {
265	>	std::string line;
266	>
267	>	#ifndef IS_MPI
268	>	inFile_->clear();
269	>	inFile_->seekg(framePos_[whichFrame]);
270	>
271	>	std::istream& inputStream = *inFile_;
272	>
273	>	#else
274	>	int masterNode = 0;
275	>	std::stringstream sstream;
276	>	if (worldRank == masterNode) {
277	>	std::string sendBuffer;
278	>
279	>	inFile_->clear();
280	>	inFile_->seekg(framePos_[whichFrame]);
281	>
282	>	while (inFile_->getline(buffer, bufferSize)) {
283	>
284	>	line = buffer;
285	>	sendBuffer += line;
286	>	sendBuffer += '\n';
287	>	if (line.find("</Snapshot>") != std::string::npos) {
288	>	break;
289	>	}
290	>	}
291	>
292	>	int sendBufferSize = sendBuffer.size();
293	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
294	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
295	>
296	>	sstream.str(sendBuffer);
297		} else {
298	<	needVel_ = false;
299	<	}
298	>	int sendBufferSize;
299	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
300	>	char * recvBuffer = new char[sendBufferSize+1];
301	>	assert(recvBuffer);
302	>	recvBuffer[sendBufferSize] = '\0';
303	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
304	>	sstream.str(recvBuffer);
305	>	delete [] recvBuffer;
306	>	}
307	>
308	>	std::istream& inputStream = sstream;
309	>	#endif
310	>
311	>	inputStream.getline(buffer, bufferSize);
312	>
313	>	line = buffer;
314	>	if (line.find("<Snapshot>") == std::string::npos) {
315	>	sprintf(painCave.errMsg,
316	>	"DumpReader Error: can not find <Snapshot>\n");
317	>	painCave.isFatal = 1;
318	>	simError();
319	>	}
320
321	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
322	<	needQuaternion_ = true;
321	>	//read frameData
322	>	readFrameProperties(inputStream);
323	>
324	>	//read StuntDoubles
325	>	readStuntDoubles(inputStream);
326	>
327	>	inputStream.getline(buffer, bufferSize);
328	>	line = buffer;
329	>
330	>	if (line.find("<SiteData>") != std::string::npos) {
331	>	//read SiteData
332	>	readSiteData(inputStream);
333		} else {
334	<	needQuaternion_ = false;
334	>	if (line.find("</Snapshot>") == std::string::npos) {
335	>	sprintf(painCave.errMsg,
336	>	"DumpReader Error: can not find </Snapshot>\n");
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340		}
341	<
342	<	if (storageLayout & DataStorage::dslAngularMomentum) {
343	<	needAngMom_ = true;
344	<	} else {
345	<	needAngMom_ = false;
341	>	}
342	>
343	>	void DumpReader::parseDumpLine(const std::string& line) {
344	>
345	>
346	>	StringTokenizer tokenizer(line);
347	>	int nTokens;
348	>
349	>	nTokens = tokenizer.countTokens();
350	>
351	>	if (nTokens < 2) {
352	>	sprintf(painCave.errMsg,
353	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
354	>	painCave.isFatal = 1;
355	>	simError();
356	>	}
357	>
358	>	int index = tokenizer.nextTokenAsInt();
359	>
360	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
361	>
362	>	if (integrableObject == NULL) {
363	>	return;
364		}
365	+	std::string type = tokenizer.nextToken();
366	+	int size = type.size();
367	+
368	+	size_t found;
369
370	<	readSet(whichFrame);
371	<	}
372	<
373	<	void DumpReader::readSet(int whichFrame) {
374	<	int i;
375	<	int nTotObjs;                  // the number of atoms
376	<	char read_buffer[maxBufferSize];  //the line buffer for reading
377	<	char * eof_test;               // ptr to see when we reach the end of the file
378	<
379	<	Molecule* mol;
261	<	StuntDouble* integrableObject;
262	<	SimInfo::MoleculeIterator mi;
263	<	Molecule::IntegrableObjectIterator ii;
264	<
265	<	#ifndef IS_MPI
266	<
267	<	fsetpos(inFile_, framePos_[whichFrame]);
268	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
269	<
270	<	if (eof_test == NULL) {
271	<	sprintf(painCave.errMsg,
272	<	"DumpReader error: error reading 1st line of \"%s\"\n",
273	<	filename_.c_str());
274	<	painCave.isFatal = 1;
275	<	simError();
370	>	if (needPos_) {
371	>	found = type.find("p");
372	>	if (found == std::string::npos) {
373	>	sprintf(painCave.errMsg,
374	>	"DumpReader Error: StuntDouble %d has no Position\n"
375	>	"\tField (\"p\") specified.\n%s\n", index,
376	>	line.c_str());
377	>	painCave.isFatal = 1;
378	>	simError();
379	>	}
380		}
381
382	<	nTotObjs = atoi(read_buffer);
383	<
384	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
385	<	sprintf(painCave.errMsg,
386	<	"DumpReader error. %s nIntegrable, %d, "
387	<	"does not match the meta-data file's nIntegrable, %d.\n",
388	<	filename_.c_str(),
389	<	nTotObjs,
390	<	info_->getNGlobalIntegrableObjects());
391	<
392	<	painCave.isFatal = 1;
393	<	simError();
382	>	if (integrableObject->isDirectional()) {
383	>	if (needQuaternion_) {
384	>	found = type.find("q");
385	>	if (found == std::string::npos) {
386	>	sprintf(painCave.errMsg,
387	>	"DumpReader Error: Directional StuntDouble %d has no\n"
388	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
389	>	line.c_str());
390	>	painCave.isFatal = 1;
391	>	simError();
392	>	}
393	>	}
394		}
395	<
396	<	//read the box mat from the comment line
397	<
294	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
295	<
296	<	if (eof_test == NULL) {
297	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
298	<	filename_.c_str());
299	<	painCave.isFatal = 1;
300	<	simError();
301	<	}
302	<
303	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
304	<
305	<	//parse dump lines
306	<
307	<	i = 0;
308	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
309	<
310	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
311	<	integrableObject = mol->nextIntegrableObject(ii)) {
395	>
396	>	for(int i = 0; i < size; ++i) {
397	>	switch(type[i]) {
398
399	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
400	<
401	<	if (eof_test == NULL) {
402	<	sprintf(painCave.errMsg,
403	<	"DumpReader Error: error in reading file %s\n"
404	<	"natoms  = %d; index = %d\n"
405	<	"error reading the line from the file.\n",
406	<	filename_.c_str(),
407	<	nTotObjs,
322	<	i);
323	<
324	<	painCave.isFatal = 1;
325	<	simError();
399	>	case 'p': {
400	>	Vector3d pos;
401	>	pos[0] = tokenizer.nextTokenAsDouble();
402	>	pos[1] = tokenizer.nextTokenAsDouble();
403	>	pos[2] = tokenizer.nextTokenAsDouble();
404	>	if (needPos_) {
405	>	integrableObject->setPos(pos);
406	>	}
407	>	break;
408		}
409	<
410	<	parseDumpLine(read_buffer, integrableObject);
411	<	i++;
409	>	case 'v' : {
410	>	Vector3d vel;
411	>	vel[0] = tokenizer.nextTokenAsDouble();
412	>	vel[1] = tokenizer.nextTokenAsDouble();
413	>	vel[2] = tokenizer.nextTokenAsDouble();
414	>	if (needVel_) {
415	>	integrableObject->setVel(vel);
416	>	}
417	>	break;
418	>	}
419	>
420	>	case 'q' : {
421	>	Quat4d q;
422	>	if (integrableObject->isDirectional()) {
423	>
424	>	q[0] = tokenizer.nextTokenAsDouble();
425	>	q[1] = tokenizer.nextTokenAsDouble();
426	>	q[2] = tokenizer.nextTokenAsDouble();
427	>	q[3] = tokenizer.nextTokenAsDouble();
428	>
429	>	RealType qlen = q.length();
430	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
431	>
432	>	sprintf(painCave.errMsg,
433	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
434	>	painCave.isFatal = 1;
435	>	simError();
436	>
437	>	}
438	>
439	>	q.normalize();
440	>	if (needQuaternion_) {
441	>	integrableObject->setQ(q);
442	>	}
443	>	}
444	>	break;
445	>	}
446	>	case 'j' : {
447	>	Vector3d ji;
448	>	if (integrableObject->isDirectional()) {
449	>	ji[0] = tokenizer.nextTokenAsDouble();
450	>	ji[1] = tokenizer.nextTokenAsDouble();
451	>	ji[2] = tokenizer.nextTokenAsDouble();
452	>	if (needAngMom_) {
453	>	integrableObject->setJ(ji);
454	>	}
455	>	}
456	>	break;
457	>	}
458	>	case 'f': {
459	>
460	>	Vector3d force;
461	>	force[0] = tokenizer.nextTokenAsDouble();
462	>	force[1] = tokenizer.nextTokenAsDouble();
463	>	force[2] = tokenizer.nextTokenAsDouble();
464	>	integrableObject->setFrc(force);
465	>	break;
466	>	}
467	>	case 't' : {
468	>
469	>	Vector3d torque;
470	>	torque[0] = tokenizer.nextTokenAsDouble();
471	>	torque[1] = tokenizer.nextTokenAsDouble();
472	>	torque[2] = tokenizer.nextTokenAsDouble();
473	>	integrableObject->setTrq(torque);
474	>	break;
475	>	}
476	>	case 'u' : {
477	>
478	>	RealType particlePot;
479	>	particlePot = tokenizer.nextTokenAsDouble();
480	>	integrableObject->setParticlePot(particlePot);
481	>	break;
482	>	}
483	>	case 'c' : {
484	>
485	>	RealType flucQPos;
486	>	flucQPos = tokenizer.nextTokenAsDouble();
487	>	integrableObject->setFlucQPos(flucQPos);
488	>	break;
489	>	}
490	>	case 'w' : {
491	>
492	>	RealType flucQVel;
493	>	flucQVel = tokenizer.nextTokenAsDouble();
494	>	integrableObject->setFlucQVel(flucQVel);
495	>	break;
496	>	}
497	>	case 'g' : {
498	>
499	>	RealType flucQFrc;
500	>	flucQFrc = tokenizer.nextTokenAsDouble();
501	>	integrableObject->setFlucQFrc(flucQFrc);
502	>	break;
503	>	}
504	>	case 'e' : {
505	>
506	>	Vector3d eField;
507	>	eField[0] = tokenizer.nextTokenAsDouble();
508	>	eField[1] = tokenizer.nextTokenAsDouble();
509	>	eField[2] = tokenizer.nextTokenAsDouble();
510	>	integrableObject->setElectricField(eField);
511	>	break;
512	>	}
513	>	default: {
514	>	sprintf(painCave.errMsg,
515	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
516	>	painCave.isFatal = 1;
517	>	simError();
518	>	break;
519	>	}
520	>
521		}
522		}
523	+
524	+	}
525	+
526	+
527	+	void DumpReader::parseSiteLine(const std::string& line) {
528	+
529	+	StringTokenizer tokenizer(line);
530	+	int nTokens;
531	+
532	+	nTokens = tokenizer.countTokens();
533	+
534	+	if (nTokens < 2) {
535	+	sprintf(painCave.errMsg,
536	+	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
537	+	painCave.isFatal = 1;
538	+	simError();
539	+	}
540	+
541	+	/**
542	+	* The first token is the global integrable object index.
543	+	*/
544	+
545	+	int index = tokenizer.nextTokenAsInt();
546	+	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
547	+	if (integrableObject == NULL) {
548	+	return;
549	+	}
550	+	StuntDouble* sd = integrableObject;
551	+
552	+	/**
553	+	* Test to see if the next token is an integer or not.  If not,
554	+	* we've got data on the integrable object itself.  If there is an
555	+	* integer, we're parsing data for a site on a rigid body.
556	+	*/
557	+
558	+	std::string indexTest = tokenizer.peekNextToken();
559	+	std::istringstream i(indexTest);
560	+	int siteIndex;
561	+	if (i >> siteIndex) {
562	+	// chew up this token and parse as an int:
563	+	siteIndex = tokenizer.nextTokenAsInt();
564	+	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
565	+	sd = rb->getAtoms()[siteIndex];
566	+	}
567	+
568	+	/**
569	+	* The next token contains information on what follows.
570	+	*/
571	+	std::string type = tokenizer.nextToken();
572	+	int size = type.size();
573
574	<	// MPI Section of code..........
575	<
576	<	#else //IS_MPI
577	<
578	<	// first thing first, suspend fatalities.
579	<	int masterNode = 0;
580	<	int nCurObj;
581	<	painCave.isEventLoop = 1;
582	<
342	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
343	<	int haveError;
344	<
345	<	MPI_Status istatus;
346	<	int nitems;
347	<
348	<	nTotObjs = info_->getNGlobalIntegrableObjects();
349	<	haveError = 0;
350	<
351	<	if (worldRank == masterNode) {
352	<	fsetpos(inFile_, framePos_[whichFrame]);
353	<
354	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
355	<
356	<	if (eof_test == NULL) {
357	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
358	<	filename_.c_str());
359	<	painCave.isFatal = 1;
360	<	simError();
574	>	for(int i = 0; i < size; ++i) {
575	>	switch(type[i]) {
576	>
577	>	case 'u' : {
578	>
579	>	RealType particlePot;
580	>	particlePot = tokenizer.nextTokenAsDouble();
581	>	sd->setParticlePot(particlePot);
582	>	break;
583		}
584	<
363	<	nitems = atoi(read_buffer);
364	<
365	<	// Check to see that the number of integrable objects in the
366	<	// intial configuration file is the same as derived from the
367	<	// meta-data file.
368	<
369	<	if (nTotObjs != nitems) {
370	<	sprintf(painCave.errMsg,
371	<	"DumpReader Error. %s nIntegrable, %d, "
372	<	"does not match the meta-data file's nIntegrable, %d.\n",
373	<	filename_.c_str(),
374	<	nTotObjs,
375	<	info_->getNGlobalIntegrableObjects());
584	>	case 'c' : {
585
586	<	painCave.isFatal = 1;
587	<	simError();
586	>	RealType flucQPos;
587	>	flucQPos = tokenizer.nextTokenAsDouble();
588	>	sd->setFlucQPos(flucQPos);
589	>	break;
590		}
591	<
592	<	//read the boxMat from the comment line
593	<
594	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
595	<
596	<	if (eof_test == NULL) {
386	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
387	<	filename_.c_str());
388	<	painCave.isFatal = 1;
389	<	simError();
591	>	case 'w' : {
592	>
593	>	RealType flucQVel;
594	>	flucQVel = tokenizer.nextTokenAsDouble();
595	>	sd->setFlucQVel(flucQVel);
596	>	break;
597		}
598	<
392	<	//Every single processor will parse the comment line by itself
393	<	//By using this way, we might lose some efficiency, but if we want to add
394	<	//more parameters into comment line, we only need to modify function
395	<	//parseCommentLine
396	<
397	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
398	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
399	<
400	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
401	<	int which_node = info_->getMolToProc(i);
598	>	case 'g' : {
599
600	<	if (which_node == masterNode) {
601	<	//molecules belong to master node
602	<
603	<	mol = info_->getMoleculeByGlobalIndex(i);
407	<
408	<	if (mol == NULL) {
409	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
410	<	painCave.isFatal = 1;
411	<	simError();
412	<	}
413	<
414	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
415	<	integrableObject = mol->nextIntegrableObject(ii)){
416	<
417	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
418	<
419	<	if (eof_test == NULL) {
420	<	sprintf(painCave.errMsg,
421	<	"DumpReader Error: error in reading file %s\n"
422	<	"natoms  = %d; index = %d\n"
423	<	"error reading the line from the file.\n",
424	<	filename_.c_str(),
425	<	nTotObjs,
426	<	i);
427	<
428	<	painCave.isFatal = 1;
429	<	simError();
430	<	}
431	<
432	<	parseDumpLine(read_buffer, integrableObject);
433	<	}
434	<	} else {
435	<	//molecule belongs to slave nodes
436	<
437	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
438	<	MPI_COMM_WORLD, &istatus);
439	<
440	<	for(int j = 0; j < nCurObj; j++) {
441	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
442	<
443	<	if (eof_test == NULL) {
444	<	sprintf(painCave.errMsg,
445	<	"DumpReader Error: error in reading file %s\n"
446	<	"natoms  = %d; index = %d\n"
447	<	"error reading the line from the file.\n",
448	<	filename_.c_str(),
449	<	nTotObjs,
450	<	i);
451	<
452	<	painCave.isFatal = 1;
453	<	simError();
454	<	}
455	<
456	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
457	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
458	<	}
459	<	}
600	>	RealType flucQFrc;
601	>	flucQFrc = tokenizer.nextTokenAsDouble();
602	>	sd->setFlucQFrc(flucQFrc);
603	>	break;
604		}
605	<	} else {
462	<	//actions taken at slave nodes
463	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
464	<
465	<	/**@todo*/
466	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
467	<
468	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
469	<	int which_node = info_->getMolToProc(i);
605	>	case 'e' : {
606
607	<	if (which_node == worldRank) {
608	<	//molecule with global index i belongs to this processor
609	<
610	<	mol = info_->getMoleculeByGlobalIndex(i);
611	<	if (mol == NULL) {
612	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
477	<	painCave.isFatal = 1;
478	<	simError();
479	<	}
480	<
481	<	nCurObj = mol->getNIntegrableObjects();
482	<
483	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
484	<	MPI_COMM_WORLD);
485	<
486	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
487	<	integrableObject = mol->nextIntegrableObject(ii)){
488	<
489	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
490	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
491	<
492	<	parseDumpLine(read_buffer, integrableObject);
493	<	}
494	<
495	<	}
496	<
607	>	Vector3d eField;
608	>	eField[0] = tokenizer.nextTokenAsDouble();
609	>	eField[1] = tokenizer.nextTokenAsDouble();
610	>	eField[2] = tokenizer.nextTokenAsDouble();
611	>	sd->setElectricField(eField);
612	>	break;
613		}
614	<
615	<	}
616	<
617	<	#endif
618	<
619	<	}
614	>	default: {
615	>	sprintf(painCave.errMsg,
616	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
617	>	painCave.isFatal = 1;
618	>	simError();
619	>	break;
620	>	}
621	>	}
622	>	}
623	>	}
624
625	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
625	>
626	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
627
628	<	Vector3d pos;  // position place holders
629	<	Vector3d vel;  // velocity placeholders
509	<	Quat4d q;    // the quaternions
510	<	Vector3d ji;   // angular velocity placeholders;
511	<	StringTokenizer tokenizer(line);
512	<	int nTokens;
628	>	inputStream.getline(buffer, bufferSize);
629	>	std::string line(buffer);
630
631	<	nTokens = tokenizer.countTokens();
632	<
633	<	if (nTokens < 14) {
634	<	sprintf(painCave.errMsg,
635	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
519	<	painCave.isFatal = 1;
520	<	simError();
631	>	if (line.find("<StuntDoubles>") == std::string::npos) {
632	>	sprintf(painCave.errMsg,
633	>	"DumpReader Error: Missing <StuntDoubles>\n");
634	>	painCave.isFatal = 1;
635	>	simError();
636		}
637	<
638	<	std::string name = tokenizer.nextToken();
639	<
525	<	if (name != integrableObject->getType()) {
637	>
638	>	while(inputStream.getline(buffer, bufferSize)) {
639	>	line = buffer;
640
641	<	sprintf(painCave.errMsg,
642	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
643	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
644	<	painCave.isFatal = 1;
645	<	simError();
641	>	if(line.find("</StuntDoubles>") != std::string::npos) {
642	>	break;
643	>	}
644	>
645	>	parseDumpLine(line);
646		}
647	+
648	+	}
649	+
650	+	void  DumpReader::readSiteData(std::istream& inputStream) {
651	+
652	+	inputStream.getline(buffer, bufferSize);
653	+	std::string line(buffer);
654
655	<	pos[0] = tokenizer.nextTokenAsDouble();
656	<	pos[1] = tokenizer.nextTokenAsDouble();
657	<	pos[2] = tokenizer.nextTokenAsDouble();
537	<	if (needPos_) {
538	<	integrableObject->setPos(pos);
655	>	if (line.find("<SiteData>") == std::string::npos) {
656	>	// site data isn't required for a simulation, so skip
657	>	return;
658		}
659	<
660	<	vel[0] = tokenizer.nextTokenAsDouble();
661	<	vel[1] = tokenizer.nextTokenAsDouble();
543	<	vel[2] = tokenizer.nextTokenAsDouble();
544	<	if (needVel_) {
545	<	integrableObject->setVel(vel);
546	<	}
547	<
548	<	if (integrableObject->isDirectional()) {
659	>
660	>	while(inputStream.getline(buffer, bufferSize)) {
661	>	line = buffer;
662
663	<	q[0] = tokenizer.nextTokenAsDouble();
664	<	q[1] = tokenizer.nextTokenAsDouble();
552	<	q[2] = tokenizer.nextTokenAsDouble();
553	<	q[3] = tokenizer.nextTokenAsDouble();
554	<
555	<	double qlen = q.length();
556	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
557	<
558	<	sprintf(painCave.errMsg,
559	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
560	<	painCave.isFatal = 1;
561	<	simError();
562	<
563	<	}
564	<
565	<	q.normalize();
566	<	if (needQuaternion_) {
567	<	integrableObject->setQ(q);
663	>	if(line.find("</SiteData>") != std::string::npos) {
664	>	break;
665		}
666	<
667	<	ji[0] = tokenizer.nextTokenAsDouble();
571	<	ji[1] = tokenizer.nextTokenAsDouble();
572	<	ji[2] = tokenizer.nextTokenAsDouble();
573	<	if (needAngMom_) {
574	<	integrableObject->setJ(ji);
575	<	}
666	>
667	>	parseSiteLine(line);
668		}
577	–
578	–	}
669
670	<
671	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
672	<	double currTime;
673	<	Mat3x3d hmat;
674	<	double chi;
675	<	double integralOfChiDt;
676	<	Mat3x3d eta;
677	<
678	<	StringTokenizer tokenizer(line);
679	<	int nTokens;
680	<
681	<	nTokens = tokenizer.countTokens();
682	<
593	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
594	<	if (nTokens < 10) {
595	<	sprintf(painCave.errMsg,
596	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
597	<	painCave.isFatal = 1;
598	<	simError();
670	>	}
671	>
672	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
673	>
674	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
675	>	inputStream.getline(buffer, bufferSize);
676	>	std::string line(buffer);
677	>
678	>	if (line.find("<FrameData>") == std::string::npos) {
679	>	sprintf(painCave.errMsg,
680	>	"DumpReader Error: Missing <FrameData>\n");
681	>	painCave.isFatal = 1;
682	>	simError();
683		}
684	<
685	<	//read current time
686	<	currTime = tokenizer.nextTokenAsDouble();
603	<	s->setTime(currTime);
604	<
605	<	//read h-matrix
606	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
607	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
608	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
609	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
610	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
611	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
612	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
613	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
614	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
615	<	s->setHmat(hmat);
616	<
617	<	//read chi and integralOfChidt, they should apprear in pair
618	<	if (tokenizer.countTokens() >= 2) {
619	<	chi = tokenizer.nextTokenAsDouble();
620	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
684	>
685	>	while(inputStream.getline(buffer, bufferSize)) {
686	>	line = buffer;
687
688	<	s->setChi(chi);
689	<	s->setIntegralOfChiDt(integralOfChiDt);
690	<	}
625	<
626	<	//read eta (eta is 3x3 matrix)
627	<	if (tokenizer.countTokens() >= 9) {
628	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
629	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
630	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
631	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
632	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
633	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
634	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
635	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
636	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
688	>	if(line.find("</FrameData>") != std::string::npos) {
689	>	break;
690	>	}
691
692	<	s->setEta(eta);
692	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
693	>	if (!tokenizer.hasMoreTokens()) {
694	>	sprintf(painCave.errMsg,
695	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
696	>	painCave.isFatal = 1;
697	>	simError();
698	>	}
699	>
700	>	std::string propertyName = tokenizer.nextToken();
701	>	if (propertyName == "Time") {
702	>	RealType currTime = tokenizer.nextTokenAsDouble();
703	>	s->setTime(currTime);
704	>	} else if (propertyName == "Hmat"){
705	>	Mat3x3d hmat;
706	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
707	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
708	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
709	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
710	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
711	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
712	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
713	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
714	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
715	>	s->setHmat(hmat);
716	>	} else if (propertyName == "Thermostat") {
717	>	RealType chi = tokenizer.nextTokenAsDouble();
718	>	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
719	>	s->setChi(chi);
720	>	s->setIntegralOfChiDt(integralOfChiDt);
721	>	} else if (propertyName == "Barostat") {
722	>	Mat3x3d eta;
723	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
724	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
725	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
726	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
727	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
728	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
729	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
730	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
731	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
732	>	s->setEta(eta);
733	>	} else {
734	>	sprintf(painCave.errMsg,
735	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
736	>	painCave.isFatal = 0;
737	>	simError();
738	>	}
739	>
740		}
741	<
641	<
741	>
742		}
743	<
744	<	}//end namespace oopse
743	>
744	>
745	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 601 by tim, Thu Sep 15 19:17:04 2005 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC

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