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

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 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
19	<	*    notice, this list of conditions and the following disclaimer.
20	<	*
21	<	* 3. Redistributions in binary form must reproduce the above copyright
22	<	*    notice, this list of conditions and the following disclaimer in the
23	<	*    documentation and/or other materials provided with the
24	<	*    distribution.
25	<	*
26	<	* This software is provided "AS IS," without a warranty of any
27	<	* kind. All express or implied conditions, representations and
28	<	* warranties, including any implied warranty of merchantability,
29	<	* fitness for a particular purpose or non-infringement, are hereby
30	<	* excluded.  The University of Notre Dame and its licensors shall not
31	<	* be liable for any damages suffered by licensee as a result of
32	<	* using, modifying or distributing the software or its
33	<	* derivatives. In no event will the University of Notre Dame or its
34	<	* licensors be liable for any lost revenue, profit or data, or for
35	<	* direct, indirect, special, consequential, incidental or punitive
36	<	* damages, however caused and regardless of the theory of liability,
37	<	* arising out of the use of or inability to use software, even if the
38	<	* University of Notre Dame has been advised of the possibility of
39	<	* such damages.
40	<	*/
1	>	/*
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42
43		#define _LARGEFILE_SOURCE64
44		#define _FILE_OFFSET_BITS 64
#	Line 57 | Line 58
58		#include "utils/simError.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/StringTokenizer.hpp"
61	+	#include "brains/Thermo.hpp"
62
63		#ifdef IS_MPI
62	–
64		#include <mpi.h>
65	<	#define TAKE_THIS_TAG_CHAR 0
65	<	#define TAKE_THIS_TAG_INT 1
65	>	#endif
66
67	–	#endif // is_mpi
67
68	<
70	<	namespace oopse {
68	>	namespace OpenMD {
69
70		DumpReader::DumpReader(SimInfo* info, const std::string& filename)
71	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
72	<
71	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
72	>
73		#ifdef IS_MPI
74	<
75	<	if (worldRank == 0) {
74	>
75	>	if (worldRank == 0) {
76		#endif
77	<
78	<	inFile_ = new std::ifstream(filename_.c_str());
79	<
80	<	if (inFile_->fail()) {
81	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
82	<	painCave.isFatal = 1;
83	<	simError();
84	<	}
85	<
86	<	#ifdef IS_MPI
89	<
77	>
78	>	inFile_ = new std::ifstream(filename_.c_str(),
79	>	ifstream::in | ifstream::binary);
80	>
81	>	if (inFile_->fail()) {
82	>	sprintf(painCave.errMsg,
83	>	"DumpReader: Cannot open file: %s\n",
84	>	filename_.c_str());
85	>	painCave.isFatal = 1;
86	>	simError();
87		}
88	<
89	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
90	<	MPIcheckPoint();
94	<
95	<	#endif
96	<
97	<	return;
88	>
89	>	#ifdef IS_MPI
90	>
91		}
92	<
92	>
93	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
94	>	errorCheckPoint();
95	>
96	>	#endif
97	>
98	>	return;
99	>	}
100	>
101		DumpReader::~DumpReader() {
102	<
102	>
103		#ifdef IS_MPI
104	<
104	>
105		if (worldRank == 0) {
106		#endif
107	<
107	>
108		delete inFile_;
109	<
109	>
110		#ifdef IS_MPI
111	<
111	>
112		}
113	<
113	>
114		strcpy(checkPointMsg, "Dump file closed successfully.");
115	<	MPIcheckPoint();
116	<
115	>	errorCheckPoint();
116	>
117		#endif
118	<
118	>
119		return;
120		}
121	<
121	>
122		int DumpReader::getNFrames(void) {
123
124		if (!isScanned_)
#	Line 127 | Line 128 | namespace oopse {
128		}
129
130		void DumpReader::scanFile(void) {
131	<	int i, j;
132	<	int lineNum = 0;
132	<	char readBuffer[maxBufferSize];
131	>	int lineNo = 0;
132	>	std::streampos prevPos;
133		std::streampos  currPos;
134	<
134	>
135		#ifdef IS_MPI
136	<
136	>
137		if (worldRank == 0) {
138		#endif // is_mpi
139	<
140	<	inFile_->seekg (0, std::ios::beg);
141	<
142	<
143	<	currPos = inFile_->tellg();
144	<	inFile_->getline(readBuffer, sizeof(readBuffer));
145	<	lineNum++;
146	<
147	<	if (inFile_->eof()) {
148	<	sprintf(painCave.errMsg,
149	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
150	<	filename_.c_str(),
151	<	lineNum);
152	<	painCave.isFatal = 1;
153	<	simError();
154	<	}
155	<
156	<	while (!inFile_->eof()) {
157	<	framePos_.push_back(currPos);
158	<
159	<	i = atoi(readBuffer);
160	<
161	<	inFile_->getline(readBuffer, sizeof(readBuffer));
162	<	lineNum++;
163	<
164	<	if (inFile_->eof()) {
165	<	sprintf(painCave.errMsg,
166	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
167	<	filename_.c_str(),
168	<	lineNum);
169	<	painCave.isFatal = 1;
170	<	simError();
171	<	}
172	<
173	<	for(j = 0; j < i; j++) {
174	<	inFile_->getline(readBuffer, sizeof(readBuffer));
175	<	lineNum++;
176	<
177	<	if (inFile_->eof()) {
139	>
140	>	currPos = inFile_->tellg();
141	>	prevPos = currPos;
142	>	bool foundOpenSnapshotTag = false;
143	>	bool foundClosedSnapshotTag = false;
144	>	bool foundOpenSiteDataTag = false;
145	>	while(inFile_->getline(buffer, bufferSize)) {
146	>	++lineNo;
147	>
148	>	std::string line = buffer;
149	>	currPos = inFile_->tellg();
150	>	if (line.find("<Snapshot>")!= std::string::npos) {
151	>	if (foundOpenSnapshotTag) {
152		sprintf(painCave.errMsg,
153	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
154	<	" with atom %d\n", filename_.c_str(),
181	<	lineNum,
182	<	j);
183	<
153	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154	>	filename_.c_str());
155		painCave.isFatal = 1;
156	+	simError();
157	+	}
158	+	foundOpenSnapshotTag = true;
159	+	foundClosedSnapshotTag = false;
160	+	framePos_.push_back(prevPos);
161	+
162	+	} else if (line.find("</Snapshot>") != std::string::npos){
163	+	if (!foundOpenSnapshotTag) {
164	+	sprintf(painCave.errMsg,
165	+	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
166	+	filename_.c_str());
167	+	painCave.isFatal = 1;
168		simError();
169	<	}
170	<	}
171	<
172	<	currPos = inFile_->tellg();
173	<	inFile_->getline(readBuffer, sizeof(readBuffer));
174	<	lineNum++;
175	<	}
176	<
177	<	inFile_->seekg (0, std::ios::beg);
178	<
169	>	}
170	>
171	>	if (foundClosedSnapshotTag) {
172	>	sprintf(painCave.errMsg,
173	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
174	>	filename_.c_str());
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	foundClosedSnapshotTag = true;
179	>	foundOpenSnapshotTag = false;
180	>	}
181	>	prevPos = currPos;
182	>	}
183	>
184	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
185	>	// it and give a warning message
186	>	if (foundOpenSnapshotTag) {
187	>	sprintf(painCave.errMsg,
188	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
189	>	painCave.isFatal = 0;
190	>	simError();
191	>	framePos_.pop_back();
192	>	}
193	>
194		nframes_ = framePos_.size();
195	+
196	+	if (nframes_ == 0) {
197	+	sprintf(painCave.errMsg,
198	+	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
199	+	painCave.isFatal = 1;
200	+	simError();
201	+	}
202		#ifdef IS_MPI
203		}
204
205		MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206	<
202	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
203	<	MPIcheckPoint();
204	<
206	>
207		#endif // is_mpi
208	<
208	>
209		isScanned_ = true;
210		}
211
#	Line 238 | Line 240 | namespace oopse {
240		}
241
242		readSet(whichFrame);
243	+
244	+	if (needCOMprops_) {
245	+	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	+	Thermo thermo(info_);
247	+	Vector3d com;
248	+
249	+	if (needPos_ && needVel_) {
250	+	Vector3d comvel;
251	+	Vector3d comw;
252	+	thermo.getComAll(com, comvel);
253	+	comw = thermo.getAngularMomentum();
254	+	} else {
255	+	com = thermo.getCom();
256	+	}
257	+	}
258		}
259
260	<	void DumpReader::readSet(int whichFrame) {
261	<	int i;
262	<	int nTotObjs;                  // the number of atoms
246	<	char read_buffer[maxBufferSize];  //the line buffer for reading
247	<	char * eof_test;               // ptr to see when we reach the end of the file
248	<
249	<	Molecule* mol;
250	<	StuntDouble* integrableObject;
251	<	SimInfo::MoleculeIterator mi;
252	<	Molecule::IntegrableObjectIterator ii;
253	<
260	>	void DumpReader::readSet(int whichFrame) {
261	>	std::string line;
262	>
263		#ifndef IS_MPI
264		inFile_->clear();
265		inFile_->seekg(framePos_[whichFrame]);
266	<
267	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
266	>
267	>	std::istream& inputStream = *inFile_;
268	>
269	>	#else
270	>	int masterNode = 0;
271	>	std::stringstream sstream;
272	>	if (worldRank == masterNode) {
273	>	std::string sendBuffer;
274	>
275	>	inFile_->clear();
276	>	inFile_->seekg(framePos_[whichFrame]);
277	>
278	>	while (inFile_->getline(buffer, bufferSize)) {
279	>
280	>	line = buffer;
281	>	sendBuffer += line;
282	>	sendBuffer += '\n';
283	>	if (line.find("</Snapshot>") != std::string::npos) {
284	>	break;
285	>	}
286	>	}
287	>
288	>	int sendBufferSize = sendBuffer.size();
289	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
290	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
291	>
292	>	sstream.str(sendBuffer);
293	>	} else {
294	>	int sendBufferSize;
295	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
296	>	char * recvBuffer = new char[sendBufferSize+1];
297	>	assert(recvBuffer);
298	>	recvBuffer[sendBufferSize] = '\0';
299	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
300	>	sstream.str(recvBuffer);
301	>	delete [] recvBuffer;
302	>	}
303	>
304	>	std::istream& inputStream = sstream;
305	>	#endif
306	>
307	>	inputStream.getline(buffer, bufferSize);
308	>
309	>	line = buffer;
310	>	if (line.find("<Snapshot>") == std::string::npos) {
311		sprintf(painCave.errMsg,
312	<	"DumpReader error: error reading 1st line of \"%s\"\n",
261	<	filename_.c_str());
312	>	"DumpReader Error: can not find <Snapshot>\n");
313		painCave.isFatal = 1;
314		simError();
315		}
316	+
317	+	//read frameData
318	+	readFrameProperties(inputStream);
319	+
320	+	//read StuntDoubles
321	+	readStuntDoubles(inputStream);
322	+
323	+	inputStream.getline(buffer, bufferSize);
324	+	line = buffer;
325	+
326	+	if (line.find("<SiteData>") != std::string::npos) {
327	+	//read SiteData
328	+	readSiteData(inputStream);
329	+	} else {
330	+	if (line.find("</Snapshot>") == std::string::npos) {
331	+	sprintf(painCave.errMsg,
332	+	"DumpReader Error: can not find </Snapshot>\n");
333	+	painCave.isFatal = 1;
334	+	simError();
335	+	}
336	+	}
337	+	}
338	+
339	+	void DumpReader::parseDumpLine(const std::string& line) {
340	+
341	+
342	+	StringTokenizer tokenizer(line);
343	+	int nTokens;
344
345	<	nTotObjs = atoi(read_buffer);
345	>	nTokens = tokenizer.countTokens();
346
347	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
347	>	if (nTokens < 2) {
348		sprintf(painCave.errMsg,
349	<	"DumpReader error. %s nIntegrable, %d, "
271	<	"does not match the meta-data file's nIntegrable, %d.\n",
272	<	filename_.c_str(),
273	<	nTotObjs,
274	<	info_->getNGlobalIntegrableObjects());
275	<
349	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
350		painCave.isFatal = 1;
351		simError();
352		}
353	<
354	<	//read the box mat from the comment line
355	<
356	<
357	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
358	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
359	<	filename_.c_str());
360	<	painCave.isFatal = 1;
361	<	simError();
362	<	}
363	<
364	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
365	<
366	<	//parse dump lines
367	<
368	<	i = 0;
295	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
296	<
297	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
298	<	integrableObject = mol->nextIntegrableObject(ii)) {
299	<
300	<
301	<
302	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
303	<	sprintf(painCave.errMsg,
304	<	"DumpReader Error: error in reading file %s\n"
305	<	"natoms  = %d; index = %d\n"
306	<	"error reading the line from the file.\n",
307	<	filename_.c_str(),
308	<	nTotObjs,
309	<	i);
310	<
311	<	painCave.isFatal = 1;
312	<	simError();
313	<	}
314	<
315	<	parseDumpLine(read_buffer, integrableObject);
316	<	i++;
317	<	}
318	<	}
319	<
320	<	// MPI Section of code..........
321	<
322	<	#else //IS_MPI
323	<
324	<	// first thing first, suspend fatalities.
325	<	int masterNode = 0;
326	<	int nCurObj;
327	<	painCave.isEventLoop = 1;
328	<
329	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
330	<	int haveError;
331	<
332	<	MPI_Status istatus;
333	<	int nitems;
334	<
335	<	nTotObjs = info_->getNGlobalIntegrableObjects();
336	<	haveError = 0;
337	<
338	<	if (worldRank == masterNode) {
339	<	inFile_->clear();
340	<	inFile_->seekg(framePos_[whichFrame]);
341	<
342	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
343	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
344	<	filename_.c_str());
345	<	painCave.isFatal = 1;
346	<	simError();
347	<	}
348	<
349	<	nitems = atoi(read_buffer);
350	<
351	<	// Check to see that the number of integrable objects in the
352	<	// intial configuration file is the same as derived from the
353	<	// meta-data file.
354	<
355	<	if (nTotObjs != nitems) {
353	>
354	>	int index = tokenizer.nextTokenAsInt();
355	>
356	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
357	>
358	>	if (sd == NULL) {
359	>	return;
360	>	}
361	>	std::string type = tokenizer.nextToken();
362	>	int size = type.size();
363	>
364	>	size_t found;
365	>
366	>	if (needPos_) {
367	>	found = type.find("p");
368	>	if (found == std::string::npos) {
369		sprintf(painCave.errMsg,
370	<	"DumpReader Error. %s nIntegrable, %d, "
371	<	"does not match the meta-data file's nIntegrable, %d.\n",
372	<	filename_.c_str(),
360	<	nTotObjs,
361	<	info_->getNGlobalIntegrableObjects());
362	<
370	>	"DumpReader Error: StuntDouble %d has no Position\n"
371	>	"\tField (\"p\") specified.\n%s\n", index,
372	>	line.c_str());
373		painCave.isFatal = 1;
374		simError();
375	<	}
376	<
377	<	//read the boxMat from the comment line
378	<
379	<
380	<
381	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
382	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
383	<	filename_.c_str());
384	<	painCave.isFatal = 1;
385	<	simError();
386	<	}
387	<
388	<	//Every single processor will parse the comment line by itself
389	<	//By using this way, we might lose some efficiency, but if we want to add
390	<	//more parameters into comment line, we only need to modify function
391	<	//parseCommentLine
392	<
393	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
394	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
395	<
396	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
397	<	int which_node = info_->getMolToProc(i);
398	<
399	<	if (which_node == masterNode) {
400	<	//molecules belong to master node
401	<
402	<	mol = info_->getMoleculeByGlobalIndex(i);
403	<
404	<	if (mol == NULL) {
405	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
406	<	painCave.isFatal = 1;
407	<	simError();
408	<	}
409	<
410	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
411	<	integrableObject = mol->nextIntegrableObject(ii)){
402	<
403	<
404	<
405	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
406	<	sprintf(painCave.errMsg,
407	<	"DumpReader Error: error in reading file %s\n"
408	<	"natoms  = %d; index = %d\n"
409	<	"error reading the line from the file.\n",
410	<	filename_.c_str(),
411	<	nTotObjs,
412	<	i);
413	<
414	<	painCave.isFatal = 1;
415	<	simError();
375	>	}
376	>	}
377	>
378	>	if (sd->isDirectional()) {
379	>	if (needQuaternion_) {
380	>	found = type.find("q");
381	>	if (found == std::string::npos) {
382	>	sprintf(painCave.errMsg,
383	>	"DumpReader Error: Directional StuntDouble %d has no\n"
384	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
385	>	line.c_str());
386	>	painCave.isFatal = 1;
387	>	simError();
388	>	}
389	>	}
390	>	}
391	>
392	>	for(int i = 0; i < size; ++i) {
393	>	switch(type[i]) {
394	>
395	>	case 'p': {
396	>	Vector3d pos;
397	>	pos[0] = tokenizer.nextTokenAsDouble();
398	>	pos[1] = tokenizer.nextTokenAsDouble();
399	>	pos[2] = tokenizer.nextTokenAsDouble();
400	>	if (needPos_) {
401	>	sd->setPos(pos);
402	>	}
403	>	break;
404	>	}
405	>	case 'v' : {
406	>	Vector3d vel;
407	>	vel[0] = tokenizer.nextTokenAsDouble();
408	>	vel[1] = tokenizer.nextTokenAsDouble();
409	>	vel[2] = tokenizer.nextTokenAsDouble();
410	>	if (needVel_) {
411	>	sd->setVel(vel);
412		}
413	<
414	<	parseDumpLine(read_buffer, integrableObject);
415	<	}
416	<	} else {
417	<	//molecule belongs to slave nodes
418	<
419	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
420	<	MPI_COMM_WORLD, &istatus);
421	<
422	<	for(int j = 0; j < nCurObj; j++) {
423	<
424	<
425	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
426	<	sprintf(painCave.errMsg,
427	<	"DumpReader Error: error in reading file %s\n"
428	<	"natoms  = %d; index = %d\n"
429	<	"error reading the line from the file.\n",
430	<	filename_.c_str(),
431	<	nTotObjs,
432	<	i);
433	<
434	<	painCave.isFatal = 1;
435	<	simError();
436	<	}
437	<
438	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
439	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
440	<	}
441	<	}
442	<	}
443	<	} else {
444	<	//actions taken at slave nodes
445	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
446	<
447	<	/**@todo*/
448	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
449	<
450	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
451	<	int which_node = info_->getMolToProc(i);
452	<
453	<	if (which_node == worldRank) {
454	<	//molecule with global index i belongs to this processor
455	<
456	<	mol = info_->getMoleculeByGlobalIndex(i);
457	<	if (mol == NULL) {
458	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
459	<	painCave.isFatal = 1;
460	<	simError();
461	<	}
462	<
463	<	nCurObj = mol->getNIntegrableObjects();
464	<
465	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
466	<	MPI_COMM_WORLD);
467	<
468	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
469	<	integrableObject = mol->nextIntegrableObject(ii)){
470	<
471	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
472	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
473	<
474	<	parseDumpLine(read_buffer, integrableObject);
475	<	}
476	<
477	<	}
478	<
479	<	}
480	<
481	<	}
413	>	break;
414	>	}
415	>
416	>	case 'q' : {
417	>	Quat4d q;
418	>	if (sd->isDirectional()) {
419	>
420	>	q[0] = tokenizer.nextTokenAsDouble();
421	>	q[1] = tokenizer.nextTokenAsDouble();
422	>	q[2] = tokenizer.nextTokenAsDouble();
423	>	q[3] = tokenizer.nextTokenAsDouble();
424	>
425	>	RealType qlen = q.length();
426	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
427	>
428	>	sprintf(painCave.errMsg,
429	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
430	>	painCave.isFatal = 1;
431	>	simError();
432	>
433	>	}
434	>
435	>	q.normalize();
436	>	if (needQuaternion_) {
437	>	sd->setQ(q);
438	>	}
439	>	}
440	>	break;
441	>	}
442	>	case 'j' : {
443	>	Vector3d ji;
444	>	if (sd->isDirectional()) {
445	>	ji[0] = tokenizer.nextTokenAsDouble();
446	>	ji[1] = tokenizer.nextTokenAsDouble();
447	>	ji[2] = tokenizer.nextTokenAsDouble();
448	>	if (needAngMom_) {
449	>	sd->setJ(ji);
450	>	}
451	>	}
452	>	break;
453	>	}
454	>	case 'f': {
455	>
456	>	Vector3d force;
457	>	force[0] = tokenizer.nextTokenAsDouble();
458	>	force[1] = tokenizer.nextTokenAsDouble();
459	>	force[2] = tokenizer.nextTokenAsDouble();
460	>	sd->setFrc(force);
461	>	break;
462	>	}
463	>	case 't' : {
464	>
465	>	Vector3d torque;
466	>	torque[0] = tokenizer.nextTokenAsDouble();
467	>	torque[1] = tokenizer.nextTokenAsDouble();
468	>	torque[2] = tokenizer.nextTokenAsDouble();
469	>	sd->setTrq(torque);
470	>	break;
471	>	}
472	>	case 'u' : {
473	>
474	>	RealType particlePot;
475	>	particlePot = tokenizer.nextTokenAsDouble();
476	>	sd->setParticlePot(particlePot);
477	>	break;
478	>	}
479	>	case 'c' : {
480	>
481	>	RealType flucQPos;
482	>	flucQPos = tokenizer.nextTokenAsDouble();
483	>	sd->setFlucQPos(flucQPos);
484	>	break;
485	>	}
486	>	case 'w' : {
487	>
488	>	RealType flucQVel;
489	>	flucQVel = tokenizer.nextTokenAsDouble();
490	>	sd->setFlucQVel(flucQVel);
491	>	break;
492	>	}
493	>	case 'g' : {
494	>
495	>	RealType flucQFrc;
496	>	flucQFrc = tokenizer.nextTokenAsDouble();
497	>	sd->setFlucQFrc(flucQFrc);
498	>	break;
499	>	}
500	>	case 'e' : {
501	>
502	>	Vector3d eField;
503	>	eField[0] = tokenizer.nextTokenAsDouble();
504	>	eField[1] = tokenizer.nextTokenAsDouble();
505	>	eField[2] = tokenizer.nextTokenAsDouble();
506	>	sd->setElectricField(eField);
507	>	break;
508	>	}
509	>	default: {
510	>	sprintf(painCave.errMsg,
511	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
512	>	painCave.isFatal = 1;
513	>	simError();
514	>	break;
515	>	}
516	>
517	>	}
518	>	}
519
487	–	#endif
488	–
520		}
521
522	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
523	<
524	<	Vector3d pos;  // position place holders
494	<	Vector3d vel;  // velocity placeholders
495	<	Quat4d q;    // the quaternions
496	<	Vector3d ji;   // angular velocity placeholders;
522	>
523	>	void DumpReader::parseSiteLine(const std::string& line) {
524	>
525		StringTokenizer tokenizer(line);
526		int nTokens;
527
528		nTokens = tokenizer.countTokens();
529
530	<	if (nTokens < 14) {
530	>	if (nTokens < 2) {
531		sprintf(painCave.errMsg,
532	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
532	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
533		painCave.isFatal = 1;
534		simError();
535		}
536	<
537	<	std::string name = tokenizer.nextToken();
538	<
539	<	if (name != integrableObject->getType()) {
540	<
541	<	sprintf(painCave.errMsg,
542	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
543	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
544	<	painCave.isFatal = 1;
545	<	simError();
546	<	}
547	<
548	<	pos[0] = tokenizer.nextTokenAsDouble();
549	<	pos[1] = tokenizer.nextTokenAsDouble();
550	<	pos[2] = tokenizer.nextTokenAsDouble();
551	<	if (needPos_) {
552	<	integrableObject->setPos(pos);
553	<	}
554	<
555	<	vel[0] = tokenizer.nextTokenAsDouble();
556	<	vel[1] = tokenizer.nextTokenAsDouble();
557	<	vel[2] = tokenizer.nextTokenAsDouble();
558	<	if (needVel_) {
559	<	integrableObject->setVel(vel);
560	<	}
561	<
562	<	if (integrableObject->isDirectional()) {
563	<
564	<	q[0] = tokenizer.nextTokenAsDouble();
565	<	q[1] = tokenizer.nextTokenAsDouble();
566	<	q[2] = tokenizer.nextTokenAsDouble();
567	<	q[3] = tokenizer.nextTokenAsDouble();
568	<
569	<	RealType qlen = q.length();
570	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
571	<
536	>
537	>	/**
538	>	* The first token is the global integrable object index.
539	>	*/
540	>
541	>	int index = tokenizer.nextTokenAsInt();
542	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
543	>	if (sd == NULL) {
544	>	return;
545	>	}
546	>
547	>	/**
548	>	* Test to see if the next token is an integer or not.  If not,
549	>	* we've got data on the integrable object itself.  If there is an
550	>	* integer, we're parsing data for a site on a rigid body.
551	>	*/
552	>
553	>	std::string indexTest = tokenizer.peekNextToken();
554	>	std::istringstream i(indexTest);
555	>	int siteIndex;
556	>	if (i >> siteIndex) {
557	>	// chew up this token and parse as an int:
558	>	siteIndex = tokenizer.nextTokenAsInt();
559	>	RigidBody* rb = static_cast<RigidBody*>(sd);
560	>	sd = rb->getAtoms()[siteIndex];
561	>	}
562	>
563	>	/**
564	>	* The next token contains information on what follows.
565	>	*/
566	>	std::string type = tokenizer.nextToken();
567	>	int size = type.size();
568	>
569	>	for(int i = 0; i < size; ++i) {
570	>	switch(type[i]) {
571	>
572	>	case 'u' : {
573	>
574	>	RealType particlePot;
575	>	particlePot = tokenizer.nextTokenAsDouble();
576	>	sd->setParticlePot(particlePot);
577	>	break;
578	>	}
579	>	case 'c' : {
580	>
581	>	RealType flucQPos;
582	>	flucQPos = tokenizer.nextTokenAsDouble();
583	>	sd->setFlucQPos(flucQPos);
584	>	break;
585	>	}
586	>	case 'w' : {
587	>
588	>	RealType flucQVel;
589	>	flucQVel = tokenizer.nextTokenAsDouble();
590	>	sd->setFlucQVel(flucQVel);
591	>	break;
592	>	}
593	>	case 'g' : {
594	>
595	>	RealType flucQFrc;
596	>	flucQFrc = tokenizer.nextTokenAsDouble();
597	>	sd->setFlucQFrc(flucQFrc);
598	>	break;
599	>	}
600	>	case 'e' : {
601	>
602	>	Vector3d eField;
603	>	eField[0] = tokenizer.nextTokenAsDouble();
604	>	eField[1] = tokenizer.nextTokenAsDouble();
605	>	eField[2] = tokenizer.nextTokenAsDouble();
606	>	sd->setElectricField(eField);
607	>	break;
608	>	}
609	>	default: {
610		sprintf(painCave.errMsg,
611	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0\n");
611	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
612		painCave.isFatal = 1;
613		simError();
614	<
615	<	}
616	<
617	<	q.normalize();
552	<	if (needQuaternion_) {
553	<	integrableObject->setQ(q);
554	<	}
555	<
556	<	ji[0] = tokenizer.nextTokenAsDouble();
557	<	ji[1] = tokenizer.nextTokenAsDouble();
558	<	ji[2] = tokenizer.nextTokenAsDouble();
559	<	if (needAngMom_) {
560	<	integrableObject->setJ(ji);
561	<	}
562	<	}
563	<
614	>	break;
615	>	}
616	>	}
617	>	}
618		}
619	<
620	<
621	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
622	<	RealType currTime;
623	<	Mat3x3d hmat;
624	<	RealType chi;
625	<	RealType integralOfChiDt;
626	<	Mat3x3d eta;
573	<
574	<	StringTokenizer tokenizer(line);
575	<	int nTokens;
576	<
577	<	nTokens = tokenizer.countTokens();
578	<
579	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
580	<	if (nTokens < 10) {
619	>
620	>
621	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
622	>
623	>	inputStream.getline(buffer, bufferSize);
624	>	std::string line(buffer);
625	>
626	>	if (line.find("<StuntDoubles>") == std::string::npos) {
627		sprintf(painCave.errMsg,
628	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
628	>	"DumpReader Error: Missing <StuntDoubles>\n");
629		painCave.isFatal = 1;
630	<	simError();
631	<	}
632	<
633	<	//read current time
634	<	currTime = tokenizer.nextTokenAsDouble();
635	<	s->setTime(currTime);
636	<
637	<	//read h-matrix
638	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
639	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
640	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
641	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
642	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
643	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
644	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
645	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
646	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
647	<	s->setHmat(hmat);
648	<
649	<	//read chi and integralOfChidt, they should apprear in pair
650	<	if (tokenizer.countTokens() >= 2) {
651	<	chi = tokenizer.nextTokenAsDouble();
652	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
653	<
654	<	s->setChi(chi);
655	<	s->setIntegralOfChiDt(integralOfChiDt);
656	<	}
657	<
658	<	//read eta (eta is 3x3 matrix)
659	<	if (tokenizer.countTokens() >= 9) {
660	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
661	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
662	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
663	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
664	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
665	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
666	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
667	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
668	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
669	<
670	<	s->setEta(eta);
671	<	}
672	<
673	<
674	<	}
630	>	simError();
631	>	}
632	>
633	>	while(inputStream.getline(buffer, bufferSize)) {
634	>	line = buffer;
635	>
636	>	if(line.find("</StuntDoubles>") != std::string::npos) {
637	>	break;
638	>	}
639	>
640	>	parseDumpLine(line);
641	>	}
642	>
643	>	}
644	>
645	>	void  DumpReader::readSiteData(std::istream& inputStream) {
646	>
647	>	inputStream.getline(buffer, bufferSize);
648	>	std::string line(buffer);
649	>
650	>	if (line.find("<SiteData>") == std::string::npos) {
651	>	// site data isn't required for a simulation, so skip
652	>	return;
653	>	}
654	>
655	>	while(inputStream.getline(buffer, bufferSize)) {
656	>	line = buffer;
657	>
658	>	if(line.find("</SiteData>") != std::string::npos) {
659	>	break;
660	>	}
661	>
662	>	parseSiteLine(line);
663	>	}
664	>
665	>	}
666	>
667	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
668	>
669	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
670	>	inputStream.getline(buffer, bufferSize);
671	>	std::string line(buffer);
672	>
673	>	if (line.find("<FrameData>") == std::string::npos) {
674	>	sprintf(painCave.errMsg,
675	>	"DumpReader Error: Missing <FrameData>\n");
676	>	painCave.isFatal = 1;
677	>	simError();
678	>	}
679	>
680	>	while(inputStream.getline(buffer, bufferSize)) {
681	>	line = buffer;
682	>
683	>	if(line.find("</FrameData>") != std::string::npos) {
684	>	break;
685	>	}
686	>
687	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
688	>	if (!tokenizer.hasMoreTokens()) {
689	>	sprintf(painCave.errMsg,
690	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
691	>	painCave.isFatal = 1;
692	>	simError();
693	>	}
694	>
695	>	std::string propertyName = tokenizer.nextToken();
696	>	if (propertyName == "Time") {
697	>	RealType currTime = tokenizer.nextTokenAsDouble();
698	>	s->setTime(currTime);
699	>	} else if (propertyName == "Hmat"){
700	>	Mat3x3d hmat;
701	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
702	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
703	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
704	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
705	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
706	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
707	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
708	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
709	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
710	>	s->setHmat(hmat);
711	>	} else if (propertyName == "Thermostat") {
712	>	pair<RealType, RealType> thermostat;
713	>	thermostat.first = tokenizer.nextTokenAsDouble();
714	>	thermostat.second = tokenizer.nextTokenAsDouble();
715	>	s->setThermostat(thermostat);
716	>	} else if (propertyName == "Barostat") {
717	>	Mat3x3d eta;
718	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
719	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
720	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
721	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
722	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
723	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
724	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
725	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
726	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
727	>	s->setBarostat(eta);
728	>	} else {
729	>	sprintf(painCave.errMsg,
730	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
731	>	painCave.isFatal = 0;
732	>	simError();
733	>	}
734	>
735	>	}
736	>
737	>	}
738	>
739
740	<	}//end namespace oopse
740	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpReader.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC

#	Line 0 | Line 1
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