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

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trunk/src/io/DumpReader.cpp (file contents), Revision 996 by chrisfen, Wed Jun 28 14:35:14 2006 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1764 by gezelter, Tue Jul 3 18:32:27 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) {
71	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
72
73		#ifdef IS_MPI
74
#	Line 92 | Line 90 | namespace oopse {
90		}
91
92		strcpy(checkPointMsg, "Dump file opened for reading successfully.");
93	<	MPIcheckPoint();
93	>	errorCheckPoint();
94
95		#endif
96
#	Line 113 | Line 111 | namespace oopse {
111		}
112
113		strcpy(checkPointMsg, "Dump file closed successfully.");
114	<	MPIcheckPoint();
114	>	errorCheckPoint();
115
116		#endif
117
#	Line 129 | Line 127 | namespace oopse {
127		}
128
129		void DumpReader::scanFile(void) {
130	<	int i, j;
131	<	int lineNum = 0;
134	<	char readBuffer[maxBufferSize];
130	>	int lineNo = 0;
131	>	std::streampos prevPos;
132		std::streampos  currPos;
133	<
133	>
134		#ifdef IS_MPI
135	<
135	>
136		if (worldRank == 0) {
137		#endif // is_mpi
138	<
139	<	inFile_->seekg (0, std::ios::beg);
140	<
141	<
142	<	currPos = inFile_->tellg();
143	<	inFile_->getline(readBuffer, sizeof(readBuffer));
144	<	lineNum++;
145	<
146	<	if (inFile_->eof()) {
147	<	sprintf(painCave.errMsg,
148	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
149	<	filename_.c_str(),
150	<	lineNum);
154	<	painCave.isFatal = 1;
155	<	simError();
156	<	}
157	<
158	<	while (!inFile_->eof()) {
159	<	framePos_.push_back(currPos);
160	<
161	<	i = atoi(readBuffer);
162	<
163	<	inFile_->getline(readBuffer, sizeof(readBuffer));
164	<	lineNum++;
165	<
166	<	if (inFile_->eof()) {
167	<	sprintf(painCave.errMsg,
168	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
169	<	filename_.c_str(),
170	<	lineNum);
171	<	painCave.isFatal = 1;
172	<	simError();
173	<	}
174	<
175	<	for(j = 0; j < i; j++) {
176	<	inFile_->getline(readBuffer, sizeof(readBuffer));
177	<	lineNum++;
178	<
179	<	if (inFile_->eof()) {
138	>
139	>	currPos = inFile_->tellg();
140	>	prevPos = currPos;
141	>	bool foundOpenSnapshotTag = false;
142	>	bool foundClosedSnapshotTag = false;
143	>	bool foundOpenSiteDataTag = false;
144	>	while(inFile_->getline(buffer, bufferSize)) {
145	>	++lineNo;
146	>
147	>	std::string line = buffer;
148	>	currPos = inFile_->tellg();
149	>	if (line.find("<Snapshot>")!= std::string::npos) {
150	>	if (foundOpenSnapshotTag) {
151		sprintf(painCave.errMsg,
152	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
153	<	" with atom %d\n", filename_.c_str(),
183	<	lineNum,
184	<	j);
185	<
152	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
153	>	filename_.c_str());
154		painCave.isFatal = 1;
155	+	simError();
156	+	}
157	+	foundOpenSnapshotTag = true;
158	+	foundClosedSnapshotTag = false;
159	+	framePos_.push_back(prevPos);
160	+
161	+	} else if (line.find("</Snapshot>") != std::string::npos){
162	+	if (!foundOpenSnapshotTag) {
163	+	sprintf(painCave.errMsg,
164	+	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
165	+	filename_.c_str());
166	+	painCave.isFatal = 1;
167		simError();
168	<	}
169	<	}
170	<
171	<	currPos = inFile_->tellg();
172	<	inFile_->getline(readBuffer, sizeof(readBuffer));
173	<	lineNum++;
174	<	}
175	<
176	<	inFile_->seekg (0, std::ios::beg);
177	<
168	>	}
169	>
170	>	if (foundClosedSnapshotTag) {
171	>	sprintf(painCave.errMsg,
172	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
173	>	filename_.c_str());
174	>	painCave.isFatal = 1;
175	>	simError();
176	>	}
177	>	foundClosedSnapshotTag = true;
178	>	foundOpenSnapshotTag = false;
179	>	}
180	>	prevPos = currPos;
181	>	}
182	>
183	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
184	>	// it and give a warning message
185	>	if (foundOpenSnapshotTag) {
186	>	sprintf(painCave.errMsg,
187	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
188	>	painCave.isFatal = 0;
189	>	simError();
190	>	framePos_.pop_back();
191	>	}
192	>
193		nframes_ = framePos_.size();
194	+
195	+	if (nframes_ == 0) {
196	+	sprintf(painCave.errMsg,
197	+	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
198	+	painCave.isFatal = 1;
199	+	simError();
200	+	}
201		#ifdef IS_MPI
202		}
203
204		MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
205	<
204	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
205	<	MPIcheckPoint();
206	<
205	>
206		#endif // is_mpi
207	<
207	>
208		isScanned_ = true;
209		}
210
#	Line 240 | Line 239 | namespace oopse {
239		}
240
241		readSet(whichFrame);
242	+
243	+	if (needCOMprops_) {
244	+	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
245	+	Thermo thermo(info_);
246	+	Vector3d com;
247	+
248	+	if (needPos_ && needVel_) {
249	+	Vector3d comvel;
250	+	Vector3d comw;
251	+	thermo.getComAll(com, comvel);
252	+	comw = thermo.getAngularMomentum();
253	+	} else {
254	+	com = thermo.getCom();
255	+	}
256	+	}
257		}
258
259	<	void DumpReader::readSet(int whichFrame) {
260	<	int i;
261	<	int nTotObjs;                  // the number of atoms
248	<	char read_buffer[maxBufferSize];  //the line buffer for reading
249	<	char * eof_test;               // ptr to see when we reach the end of the file
250	<
251	<	Molecule* mol;
252	<	StuntDouble* integrableObject;
253	<	SimInfo::MoleculeIterator mi;
254	<	Molecule::IntegrableObjectIterator ii;
255	<
259	>	void DumpReader::readSet(int whichFrame) {
260	>	std::string line;
261	>
262		#ifndef IS_MPI
263		inFile_->clear();
264		inFile_->seekg(framePos_[whichFrame]);
265	<
266	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
265	>
266	>	std::istream& inputStream = *inFile_;
267	>
268	>	#else
269	>	int masterNode = 0;
270	>	std::stringstream sstream;
271	>	if (worldRank == masterNode) {
272	>	std::string sendBuffer;
273	>
274	>	inFile_->clear();
275	>	inFile_->seekg(framePos_[whichFrame]);
276	>
277	>	while (inFile_->getline(buffer, bufferSize)) {
278	>
279	>	line = buffer;
280	>	sendBuffer += line;
281	>	sendBuffer += '\n';
282	>	if (line.find("</Snapshot>") != std::string::npos) {
283	>	break;
284	>	}
285	>	}
286	>
287	>	int sendBufferSize = sendBuffer.size();
288	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
289	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
290	>
291	>	sstream.str(sendBuffer);
292	>	} else {
293	>	int sendBufferSize;
294	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
295	>	char * recvBuffer = new char[sendBufferSize+1];
296	>	assert(recvBuffer);
297	>	recvBuffer[sendBufferSize] = '\0';
298	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
299	>	sstream.str(recvBuffer);
300	>	delete [] recvBuffer;
301	>	}
302	>
303	>	std::istream& inputStream = sstream;
304	>	#endif
305	>
306	>	inputStream.getline(buffer, bufferSize);
307	>
308	>	line = buffer;
309	>	if (line.find("<Snapshot>") == std::string::npos) {
310		sprintf(painCave.errMsg,
311	<	"DumpReader error: error reading 1st line of \"%s\"\n",
263	<	filename_.c_str());
311	>	"DumpReader Error: can not find <Snapshot>\n");
312		painCave.isFatal = 1;
313		simError();
314		}
315	+
316	+	//read frameData
317	+	readFrameProperties(inputStream);
318	+
319	+	//read StuntDoubles
320	+	readStuntDoubles(inputStream);
321	+
322	+	inputStream.getline(buffer, bufferSize);
323	+	line = buffer;
324	+
325	+	if (line.find("<SiteData>") != std::string::npos) {
326	+	//read SiteData
327	+	readSiteData(inputStream);
328	+	} else {
329	+	if (line.find("</Snapshot>") == std::string::npos) {
330	+	sprintf(painCave.errMsg,
331	+	"DumpReader Error: can not find </Snapshot>\n");
332	+	painCave.isFatal = 1;
333	+	simError();
334	+	}
335	+	}
336	+	}
337	+
338	+	void DumpReader::parseDumpLine(const std::string& line) {
339	+
340	+
341	+	StringTokenizer tokenizer(line);
342	+	int nTokens;
343
344	<	nTotObjs = atoi(read_buffer);
344	>	nTokens = tokenizer.countTokens();
345
346	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
346	>	if (nTokens < 2) {
347		sprintf(painCave.errMsg,
348	<	"DumpReader error. %s nIntegrable, %d, "
273	<	"does not match the meta-data file's nIntegrable, %d.\n",
274	<	filename_.c_str(),
275	<	nTotObjs,
276	<	info_->getNGlobalIntegrableObjects());
277	<
348	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
349		painCave.isFatal = 1;
350		simError();
351		}
352	<
353	<	//read the box mat from the comment line
354	<
355	<
356	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
357	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
358	<	filename_.c_str());
359	<	painCave.isFatal = 1;
360	<	simError();
361	<	}
362	<
363	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
364	<
365	<	//parse dump lines
366	<
367	<	i = 0;
297	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
298	<
299	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
300	<	integrableObject = mol->nextIntegrableObject(ii)) {
301	<
302	<
303	<
304	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
305	<	sprintf(painCave.errMsg,
306	<	"DumpReader Error: error in reading file %s\n"
307	<	"natoms  = %d; index = %d\n"
308	<	"error reading the line from the file.\n",
309	<	filename_.c_str(),
310	<	nTotObjs,
311	<	i);
312	<
313	<	painCave.isFatal = 1;
314	<	simError();
315	<	}
316	<
317	<	parseDumpLine(read_buffer, integrableObject);
318	<	i++;
319	<	}
320	<	}
321	<
322	<	// MPI Section of code..........
323	<
324	<	#else //IS_MPI
325	<
326	<	// first thing first, suspend fatalities.
327	<	int masterNode = 0;
328	<	int nCurObj;
329	<	painCave.isEventLoop = 1;
330	<
331	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
332	<	int haveError;
333	<
334	<	MPI_Status istatus;
335	<	int nitems;
336	<
337	<	nTotObjs = info_->getNGlobalIntegrableObjects();
338	<	haveError = 0;
339	<
340	<	if (worldRank == masterNode) {
341	<	inFile_->clear();
342	<	inFile_->seekg(framePos_[whichFrame]);
343	<
344	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
345	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
346	<	filename_.c_str());
347	<	painCave.isFatal = 1;
348	<	simError();
349	<	}
350	<
351	<	nitems = atoi(read_buffer);
352	<
353	<	// Check to see that the number of integrable objects in the
354	<	// intial configuration file is the same as derived from the
355	<	// meta-data file.
356	<
357	<	if (nTotObjs != nitems) {
352	>
353	>	int index = tokenizer.nextTokenAsInt();
354	>
355	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
356	>
357	>	if (integrableObject == NULL) {
358	>	return;
359	>	}
360	>	std::string type = tokenizer.nextToken();
361	>	int size = type.size();
362	>
363	>	size_t found;
364	>
365	>	if (needPos_) {
366	>	found = type.find("p");
367	>	if (found == std::string::npos) {
368		sprintf(painCave.errMsg,
369	<	"DumpReader Error. %s nIntegrable, %d, "
370	<	"does not match the meta-data file's nIntegrable, %d.\n",
371	<	filename_.c_str(),
362	<	nTotObjs,
363	<	info_->getNGlobalIntegrableObjects());
364	<
369	>	"DumpReader Error: StuntDouble %d has no Position\n"
370	>	"\tField (\"p\") specified.\n%s\n", index,
371	>	line.c_str());
372		painCave.isFatal = 1;
373		simError();
374	<	}
375	<
376	<	//read the boxMat from the comment line
377	<
378	<
379	<
380	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
381	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
382	<	filename_.c_str());
383	<	painCave.isFatal = 1;
384	<	simError();
385	<	}
386	<
387	<	//Every single processor will parse the comment line by itself
388	<	//By using this way, we might lose some efficiency, but if we want to add
389	<	//more parameters into comment line, we only need to modify function
390	<	//parseCommentLine
391	<
392	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
393	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
394	<
395	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
396	<	int which_node = info_->getMolToProc(i);
397	<
398	<	if (which_node == masterNode) {
399	<	//molecules belong to master node
400	<
401	<	mol = info_->getMoleculeByGlobalIndex(i);
402	<
403	<	if (mol == NULL) {
404	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
405	<	painCave.isFatal = 1;
406	<	simError();
407	<	}
408	<
409	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
410	<	integrableObject = mol->nextIntegrableObject(ii)){
404	<
405	<
406	<
407	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
408	<	sprintf(painCave.errMsg,
409	<	"DumpReader Error: error in reading file %s\n"
410	<	"natoms  = %d; index = %d\n"
411	<	"error reading the line from the file.\n",
412	<	filename_.c_str(),
413	<	nTotObjs,
414	<	i);
415	<
416	<	painCave.isFatal = 1;
417	<	simError();
418	<	}
419	<
420	<	parseDumpLine(read_buffer, integrableObject);
421	<	}
422	<	} else {
423	<	//molecule belongs to slave nodes
424	<
425	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
426	<	MPI_COMM_WORLD, &istatus);
427	<
428	<	for(int j = 0; j < nCurObj; j++) {
429	<
430	<
431	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
432	<	sprintf(painCave.errMsg,
433	<	"DumpReader Error: error in reading file %s\n"
434	<	"natoms  = %d; index = %d\n"
435	<	"error reading the line from the file.\n",
436	<	filename_.c_str(),
437	<	nTotObjs,
438	<	i);
439	<
440	<	painCave.isFatal = 1;
441	<	simError();
374	>	}
375	>	}
376	>
377	>	if (integrableObject->isDirectional()) {
378	>	if (needQuaternion_) {
379	>	found = type.find("q");
380	>	if (found == std::string::npos) {
381	>	sprintf(painCave.errMsg,
382	>	"DumpReader Error: Directional StuntDouble %d has no\n"
383	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
384	>	line.c_str());
385	>	painCave.isFatal = 1;
386	>	simError();
387	>	}
388	>	}
389	>	}
390	>
391	>	for(int i = 0; i < size; ++i) {
392	>	switch(type[i]) {
393	>
394	>	case 'p': {
395	>	Vector3d pos;
396	>	pos[0] = tokenizer.nextTokenAsDouble();
397	>	pos[1] = tokenizer.nextTokenAsDouble();
398	>	pos[2] = tokenizer.nextTokenAsDouble();
399	>	if (needPos_) {
400	>	integrableObject->setPos(pos);
401	>	}
402	>	break;
403	>	}
404	>	case 'v' : {
405	>	Vector3d vel;
406	>	vel[0] = tokenizer.nextTokenAsDouble();
407	>	vel[1] = tokenizer.nextTokenAsDouble();
408	>	vel[2] = tokenizer.nextTokenAsDouble();
409	>	if (needVel_) {
410	>	integrableObject->setVel(vel);
411		}
412	<
413	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
414	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
415	<	}
416	<	}
417	<	}
418	<	} else {
419	<	//actions taken at slave nodes
420	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
421	<
422	<	/**@todo*/
423	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
424	<
425	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
426	<	int which_node = info_->getMolToProc(i);
427	<
428	<	if (which_node == worldRank) {
429	<	//molecule with global index i belongs to this processor
430	<
431	<	mol = info_->getMoleculeByGlobalIndex(i);
432	<	if (mol == NULL) {
433	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
434	<	painCave.isFatal = 1;
435	<	simError();
436	<	}
437	<
438	<	nCurObj = mol->getNIntegrableObjects();
439	<
440	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
441	<	MPI_COMM_WORLD);
442	<
443	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
444	<	integrableObject = mol->nextIntegrableObject(ii)){
445	<
446	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
447	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
448	<
449	<	parseDumpLine(read_buffer, integrableObject);
450	<	}
451	<
452	<	}
453	<
454	<	}
455	<
456	<	}
412	>	break;
413	>	}
414	>
415	>	case 'q' : {
416	>	Quat4d q;
417	>	if (integrableObject->isDirectional()) {
418	>
419	>	q[0] = tokenizer.nextTokenAsDouble();
420	>	q[1] = tokenizer.nextTokenAsDouble();
421	>	q[2] = tokenizer.nextTokenAsDouble();
422	>	q[3] = tokenizer.nextTokenAsDouble();
423	>
424	>	RealType qlen = q.length();
425	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
426	>
427	>	sprintf(painCave.errMsg,
428	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
429	>	painCave.isFatal = 1;
430	>	simError();
431	>
432	>	}
433	>
434	>	q.normalize();
435	>	if (needQuaternion_) {
436	>	integrableObject->setQ(q);
437	>	}
438	>	}
439	>	break;
440	>	}
441	>	case 'j' : {
442	>	Vector3d ji;
443	>	if (integrableObject->isDirectional()) {
444	>	ji[0] = tokenizer.nextTokenAsDouble();
445	>	ji[1] = tokenizer.nextTokenAsDouble();
446	>	ji[2] = tokenizer.nextTokenAsDouble();
447	>	if (needAngMom_) {
448	>	integrableObject->setJ(ji);
449	>	}
450	>	}
451	>	break;
452	>	}
453	>	case 'f': {
454	>
455	>	Vector3d force;
456	>	force[0] = tokenizer.nextTokenAsDouble();
457	>	force[1] = tokenizer.nextTokenAsDouble();
458	>	force[2] = tokenizer.nextTokenAsDouble();
459	>	integrableObject->setFrc(force);
460	>	break;
461	>	}
462	>	case 't' : {
463	>
464	>	Vector3d torque;
465	>	torque[0] = tokenizer.nextTokenAsDouble();
466	>	torque[1] = tokenizer.nextTokenAsDouble();
467	>	torque[2] = tokenizer.nextTokenAsDouble();
468	>	integrableObject->setTrq(torque);
469	>	break;
470	>	}
471	>	case 'u' : {
472	>
473	>	RealType particlePot;
474	>	particlePot = tokenizer.nextTokenAsDouble();
475	>	integrableObject->setParticlePot(particlePot);
476	>	break;
477	>	}
478	>	case 'c' : {
479	>
480	>	RealType flucQPos;
481	>	flucQPos = tokenizer.nextTokenAsDouble();
482	>	integrableObject->setFlucQPos(flucQPos);
483	>	break;
484	>	}
485	>	case 'w' : {
486	>
487	>	RealType flucQVel;
488	>	flucQVel = tokenizer.nextTokenAsDouble();
489	>	integrableObject->setFlucQVel(flucQVel);
490	>	break;
491	>	}
492	>	case 'g' : {
493	>
494	>	RealType flucQFrc;
495	>	flucQFrc = tokenizer.nextTokenAsDouble();
496	>	integrableObject->setFlucQFrc(flucQFrc);
497	>	break;
498	>	}
499	>	case 'e' : {
500	>
501	>	Vector3d eField;
502	>	eField[0] = tokenizer.nextTokenAsDouble();
503	>	eField[1] = tokenizer.nextTokenAsDouble();
504	>	eField[2] = tokenizer.nextTokenAsDouble();
505	>	integrableObject->setElectricField(eField);
506	>	break;
507	>	}
508	>	default: {
509	>	sprintf(painCave.errMsg,
510	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
511	>	painCave.isFatal = 1;
512	>	simError();
513	>	break;
514	>	}
515	>
516	>	}
517	>	}
518
489	–	#endif
490	–
519		}
520
521	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
522	<
523	<	Vector3d pos;  // position place holders
496	<	Vector3d vel;  // velocity placeholders
497	<	Quat4d q;    // the quaternions
498	<	Vector3d ji;   // angular velocity placeholders;
521	>
522	>	void DumpReader::parseSiteLine(const std::string& line) {
523	>
524		StringTokenizer tokenizer(line);
525		int nTokens;
526
527		nTokens = tokenizer.countTokens();
528
529	<	if (nTokens < 14) {
529	>	if (nTokens < 2) {
530		sprintf(painCave.errMsg,
531	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
531	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
532		painCave.isFatal = 1;
533		simError();
534		}
535	<
536	<	std::string name = tokenizer.nextToken();
537	<
538	<	if (name != integrableObject->getType()) {
539	<
540	<	sprintf(painCave.errMsg,
541	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
542	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
543	<	painCave.isFatal = 1;
544	<	simError();
545	<	}
546	<
547	<	pos[0] = tokenizer.nextTokenAsDouble();
548	<	pos[1] = tokenizer.nextTokenAsDouble();
549	<	pos[2] = tokenizer.nextTokenAsDouble();
550	<	if (needPos_) {
551	<	integrableObject->setPos(pos);
552	<	}
553	<
554	<	vel[0] = tokenizer.nextTokenAsDouble();
555	<	vel[1] = tokenizer.nextTokenAsDouble();
556	<	vel[2] = tokenizer.nextTokenAsDouble();
557	<	if (needVel_) {
558	<	integrableObject->setVel(vel);
559	<	}
560	<
561	<	if (integrableObject->isDirectional()) {
562	<
563	<	q[0] = tokenizer.nextTokenAsDouble();
564	<	q[1] = tokenizer.nextTokenAsDouble();
565	<	q[2] = tokenizer.nextTokenAsDouble();
566	<	q[3] = tokenizer.nextTokenAsDouble();
567	<
568	<	RealType qlen = q.length();
569	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
570	<
535	>
536	>	/**
537	>	* The first token is the global integrable object index.
538	>	*/
539	>
540	>	int index = tokenizer.nextTokenAsInt();
541	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
542	>	if (integrableObject == NULL) {
543	>	return;
544	>	}
545	>	StuntDouble* sd = integrableObject;
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*>(integrableObject);
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();
554	<	if (needQuaternion_) {
555	<	integrableObject->setQ(q);
556	<	}
557	<
558	<	ji[0] = tokenizer.nextTokenAsDouble();
559	<	ji[1] = tokenizer.nextTokenAsDouble();
560	<	ji[2] = tokenizer.nextTokenAsDouble();
561	<	if (needAngMom_) {
562	<	integrableObject->setJ(ji);
563	<	}
564	<	}
565	<
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;
575	<
576	<	StringTokenizer tokenizer(line);
577	<	int nTokens;
578	<
579	<	nTokens = tokenizer.countTokens();
580	<
581	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
582	<	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 996 by chrisfen, Wed Jun 28 14:35:14 2006 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

#	Line 0 | Line 1
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