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

Comparing trunk/src/io/RestReader.cpp (file contents):
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	<	*
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. 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	<	*/
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
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 "primitives/Molecule.hpp"
57	<	#include "utils/MemoryUtils.hpp"
43	>
44	>	#include <sys/types.h>
45	>	#include <sys/stat.h>
46	>
47	>	#include <math.h>
48	>	#include <string>
49	>	#include <sstream>
50	>	#include <iostream>
51	>	#include <stdio.h>
52	>	#include <stdlib.h>
53	>	#include <string.h>
54	>
55	>	#include "io/RestReader.hpp"
56	>	#include "primitives/Molecule.hpp"
57	>	#include "utils/simError.h"
58	>	#include "utils/MemoryUtils.hpp"
59		#include "utils/StringTokenizer.hpp"
60	<	#include "io/RestReader.hpp"
61	<	#include "utils/simError.h"
60	>	#include "restraints/ObjectRestraint.hpp"
61	>	#include "restraints/MolecularRestraint.hpp"
62	>
63	>	#ifdef IS_MPI
64	>
65	>	#include <mpi.h>
66	>	#endif
67
68	<	#ifdef IS_MPI
62	<	#include <mpi.h>
63	<	#define TAKE_THIS_TAG_CHAR 0
64	<	#define TAKE_THIS_TAG_INT 1
65	<	#define TAKE_THIS_TAG_DOUBLE 2
66	<	#endif // is_mpi
68	>	namespace OpenMD {
69
70	<	namespace oopse {
71	<
72	<	RestReader::RestReader( SimInfo* info ) : info_(info){
70	>	void RestReader::scanFile(){
71	>	int lineNo = 0;
72	>	std::streampos prevPos;
73	>	std::streampos  currPos;
74
75	<	idealName = "idealCrystal.in";
76	<
77	<	#ifdef IS_MPI
78	<	if (worldRank == 0) {
76	<	#endif
75	>	#ifdef IS_MPI
76	>
77	>	if (worldRank == 0) {
78	>	#endif // is_mpi
79
80	<	inIdealFile = new std::ifstream(idealName.c_str());
81	<
82	<	if(inIdealFile->fail()){
83	<	sprintf(painCave.errMsg,
84	<	"RestReader: Cannot open file: %s\n",
85	<	idealName.c_str());
86	<	painCave.isFatal = 1;
87	<	simError();
80	>	inFile_->clear();
81	>	currPos = inFile_->tellg();
82	>	prevPos = currPos;
83	>
84	>	bool foundOpenSnapshotTag = false;
85	>
86	>	while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) {
87	>	++lineNo;
88	>
89	>	std::string line = buffer;
90	>	currPos = inFile_->tellg();
91	>	if (line.find("<Snapshot>")!= std::string::npos) {
92	>	foundOpenSnapshotTag = true;
93	>	framePos_ = prevPos;
94	>	}
95	>	prevPos = currPos;
96		}
97
98	<	#ifdef IS_MPI
98	>	#ifdef IS_MPI
99		}
100	<	strcpy( checkPointMsg,
101	<	"File \"idealCrystal.in\" opened successfully for reading." );
102	<	errorCheckPoint();
93	<	#endif
100	>	MPI::COMM_WORLD.Bcast(&framePos_, 1, MPI::INT, 0);
101	>	#endif // is_mpi
102	>	}
103
95	–	return;
96	–	}
97	–
98	–	RestReader :: ~RestReader( ){
99	–	#ifdef IS_MPI
100	–	if (worldRank == 0) {
101	–	#endif
104
105	<	delete inIdealFile;
106	<	delete inAngFile;
105	<
106	<	#ifdef IS_MPI
107	<	}
108	<	strcpy( checkPointMsg,
109	<	"File idealCrystal.in (and .zang0 if present) closed successfully." );
110	<	errorCheckPoint();
111	<	#endif
105	>	void RestReader::readSet(){
106	>	std::string line;
107
108	<	return;
114	<	}
115	<
116	<
117	<	void RestReader :: readIdealCrystal(){
118	<
119	<	#ifdef IS_MPI
120	<	int which_node;
121	<	int i, j;
122	<	#endif //is_mpi
108	>	#ifndef IS_MPI
109
110	<	const int BUFFERSIZE = 2000; // size of the read buffer
111	<	int nTotObjs; // the number of atoms
126	<	char read_buffer[BUFFERSIZE]; //the line buffer for reading
110	>	inFile_->clear();
111	>	inFile_->seekg(framePos_);
112
113	<	char *parseErr;
113	>	std::istream& inputStream = *inFile_;
114	>	#else
115
116	<	std::vector<StuntDouble*> integrableObjects;
116	>	int masterNode = 0;
117	>	std::stringstream sstream;
118	>	if (worldRank == masterNode) {
119	>	std::string sendBuffer;
120	>
121	>	inFile_->clear();
122	>	inFile_->seekg(framePos_);
123	>
124	>	while (inFile_->getline(buffer, bufferSize)) {
125	>
126	>	line = buffer;
127	>	sendBuffer += line;
128	>	sendBuffer += '\n';
129	>	if (line.find("</Snapshot>") != std::string::npos) {
130	>	break;
131	>	}
132	>	}
133	>
134	>	int sendBufferSize = sendBuffer.size();
135	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
136	>	MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
137	>	MPI::CHAR, masterNode);
138	>
139	>	sstream.str(sendBuffer);
140	>	} else {
141	>	int sendBufferSize;
142	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
143	>	char * recvBuffer = new char[sendBufferSize+1];
144	>	assert(recvBuffer);
145	>	recvBuffer[sendBufferSize] = '\0';
146	>	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
147	>	sstream.str(recvBuffer);
148	>	delete [] recvBuffer;
149	>	}
150
151	<	Molecule* mol;
152	<	StuntDouble* integrableObject;
134	<	SimInfo::MoleculeIterator mi;
135	<	Molecule::IntegrableObjectIterator ii;
151	>	std::istream& inputStream = sstream;
152	>	#endif
153
154	<	#ifndef IS_MPI
138	<
139	<	inIdealFile->getline(read_buffer, sizeof(read_buffer));
154	>	inputStream.getline(buffer, bufferSize);
155
156	<	if( inIdealFile->eof() ){
157	<	sprintf( painCave.errMsg,
158	<	"RestraintReader error: error reading 1st line of \"%s\"\n",
159	<	idealName.c_str() );
160	<	painCave.isFatal = 1;
161	<	simError();
162	<	}
156	>	line = buffer;
157	>	if (line.find("<Snapshot>") == std::string::npos) {
158	>	sprintf(painCave.errMsg,
159	>	"RestReader Error: can not find <Snapshot>\n");
160	>	painCave.isFatal = 1;
161	>	simError();
162	>	}
163
164	<	nTotObjs = atoi( read_buffer );
164	>	//read frameData
165	>	readFrameProperties(inputStream);
166
167	<	if( nTotObjs != info_->getNGlobalIntegrableObjects() ){
168	<	sprintf( painCave.errMsg,
153	<	"RestraintReader error. %s nIntegrable, %d, "
154	<	"does not match the meta-data file's nIntegrable, %d.\n",
155	<	idealName.c_str(),
156	<	nTotObjs,
157	<	info_->getNGlobalIntegrableObjects());
158	<	painCave.isFatal = 1;
159	<	simError();
160	<	}
167	>	//read StuntDoubles
168	>	readStuntDoubles(inputStream);
169
170	<	// skip over the comment line
171	<	inIdealFile->getline(read_buffer, sizeof(read_buffer));
172	<
173	<	if( inIdealFile->eof() ){
174	<	sprintf( painCave.errMsg,
175	<	"error in reading commment in %s\n",
176	<	idealName.c_str());
177	<	painCave.isFatal = 1;
178	<	simError();
171	<	}
170	>	inputStream.getline(buffer, bufferSize);
171	>	line = buffer;
172	>	if (line.find("</Snapshot>") == std::string::npos) {
173	>	sprintf(painCave.errMsg,
174	>	"RestReader Error: can not find </Snapshot>\n");
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	}
179
180	<	// parse the ideal crystal lines
174	<	/*
175	<	* Note: we assume that there is a one-to-one correspondence between
176	<	* integrable objects and lines in the idealCrystal.in file.  Thermodynamic
177	<	* integration is only supported for simple rigid bodies.
178	<	*/
179	<	for (mol = info_->beginMolecule(mi); mol != NULL;
180	<	mol = info_->nextMolecule(mi)) {
181	<
182	<	for (integrableObject = mol->beginIntegrableObject(ii);
183	<	integrableObject != NULL;
184	<	integrableObject = mol->nextIntegrableObject(ii)) {
180	>	void RestReader::readReferenceStructure() {
181
182	<	inIdealFile->getline(read_buffer, sizeof(read_buffer));
182	>	// We need temporary storage to keep track of all StuntDouble positions
183	>	// in case some of the restraints are molecular (i.e. if they use
184	>	// multiple SD positions to determine restrained orientations or positions:
185
186	<	if( inIdealFile->eof() ){
187	<	sprintf(painCave.errMsg,
190	<	"RestReader Error: error in reading file %s\n"
191	<	"natoms  = %d; index = %d\n"
192	<	"error reading the line from the file.\n",
193	<	idealName.c_str(), nTotObjs,
194	<	integrableObject->getGlobalIndex() );
195	<	painCave.isFatal = 1;
196	<	simError();
197	<	}
198	<
199	<	parseErr = parseIdealLine( read_buffer, integrableObject);
200	<	if( parseErr != NULL ){
201	<	strcpy( painCave.errMsg, parseErr );
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
205	<	}
206	<	}
186	>	all_pos_.clear();
187	>	all_pos_.resize(info_->getNGlobalIntegrableObjects()) ;
188
189	<	// MPI Section of code..........
190	<	#else //IS_MPI
191	<
192	<	// first thing first, suspend fatalities.
212	<	painCave.isEventLoop = 1;
213	<
214	<	int masterNode = 0;
215	<
216	<	MPI_Status istatus;
217	<	int nCurObj;
218	<	int nitems;
219	<	int haveError;
189	>	// Restraint files are just standard dump files, but with the reference
190	>	// structure stored in the first frame (frame 0).
191	>	// RestReader overloads readSet and explicitly handles all of the
192	>	// ObjectRestraints in that method:
193
194	<	nTotObjs = info_->getNGlobalIntegrableObjects();
222	<	haveError = 0;
194	>	scanFile();
195
196	<	if (worldRank == masterNode) {
225	<	inIdealFile->getline(read_buffer, sizeof(read_buffer));
196	>	readSet();
197
227	–	if( inIdealFile->eof() ){
228	–	sprintf( painCave.errMsg,
229	–	"Error reading 1st line of %s \n ",idealName.c_str());
230	–	painCave.isFatal = 1;
231	–	simError();
232	–	}
233	–
234	–	nitems = atoi( read_buffer );
235	–
236	–	// Check to see that the number of integrable objects in the
237	–	// intial configuration file is the same as derived from the
238	–	// meta-data file.
239	–	if( nTotObjs != nitems){
240	–	sprintf( painCave.errMsg,
241	–	"RestraintReader Error. %s nIntegrable, %d, "
242	–	"does not match the meta-data file's nIntegrable, %d.\n",
243	–	idealName.c_str(), nTotObjs,
244	–	info_->getNGlobalIntegrableObjects());
245	–	painCave.isFatal = 1;
246	–	simError();
247	–	}
248	–
249	–	// skip over the comment line
250	–	inIdealFile->getline(read_buffer, sizeof(read_buffer));
198
199	<	if( inIdealFile->eof() ){
200	<	sprintf( painCave.errMsg,
254	<	"error in reading commment in %s\n", idealName.c_str());
255	<	painCave.isFatal = 1;
256	<	simError();
257	<	}
199	>	// all ObjectRestraints have been handled, now we have to worry about
200	>	// molecular restraints:
201
202	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode, MPI_COMM_WORLD);
203	<
204	<	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
205	<	which_node = info_->getMolToProc(i);
202	>	SimInfo::MoleculeIterator i;
203	>	Molecule::IntegrableObjectIterator j;
204	>	Molecule* mol;
205	>	StuntDouble* sd;
206	>
207	>	// no need to worry about parallel molecules, as molecules are not
208	>	// split across processor boundaries.  Just loop over all molecules
209	>	// we know about:
210	>
211	>	for (mol = info_->beginMolecule(i); mol != NULL;
212	>	mol = info_->nextMolecule(i)) {
213	>
214	>	// is this molecule restrained?
215	>	GenericData* data = mol->getPropertyByName("Restraint");
216	>
217	>	if (data != NULL) {
218
219	<	if(which_node == masterNode){
220	<	//molecules belong to master node
219	>	// make sure we can reinterpret the generic data as restraint data:
220	>
221	>	RestraintData* restData= dynamic_cast<RestraintData*>(data);
222	>
223	>	if (restData != NULL) {
224
225	<	mol = info_->getMoleculeByGlobalIndex(i);
225	>	// make sure we can reinterpet the restraint data as a
226	>	// pointer to a MolecularRestraint:
227
228	<	if(mol == NULL) {
270	<	sprintf(painCave.errMsg,
271	<	"RestReader Error: Molecule not found on node %d!\n",
272	<	worldRank);
273	<	painCave.isFatal = 1;
274	<	simError();
275	<	}
228	>	MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
229
230	<	for (integrableObject = mol->beginIntegrableObject(ii);
278	<	integrableObject != NULL;
279	<	integrableObject = mol->nextIntegrableObject(ii)){
230	>	if (mRest != NULL) {
231
232	<	inIdealFile->getline(read_buffer, sizeof(read_buffer));
232	>	// now we need to pack the stunt doubles for the reference
233	>	// structure:
234
235	<	if( inIdealFile->eof() ){
236	<	sprintf(painCave.errMsg,
237	<	"RestReader Error: error in reading file %s\n"
238	<	"natoms  = %d; index = %d\n"
239	<	"error reading the line from the file.\n",
240	<	idealName.c_str(), nTotObjs, i );
241	<	painCave.isFatal = 1;
242	<	simError();
235	>	std::vector<Vector3d> ref;
236	>	int count = 0;
237	>	RealType mass, mTot;
238	>	Vector3d COM(0.0);
239	>
240	>	mTot = 0.0;
241	>
242	>	// loop over the stunt doubles in this molecule in the order we
243	>	// will be looping them in the restraint code:
244	>
245	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
246	>	sd = mol->nextIntegrableObject(j)) {
247	>
248	>	// push back the reference positions of the stunt
249	>	// doubles from the *globally* sorted array of
250	>	// positions:
251	>
252	>	ref.push_back( all_pos_[sd->getGlobalIntegrableObjectIndex()] );
253	>	mass = sd->getMass();
254	>	COM = COM + mass * ref[count];
255	>	mTot = mTot + mass;
256	>	count = count + 1;
257		}
258	<
259	<	parseIdealLine(read_buffer, integrableObject);
294	<
258	>	COM /= mTot;
259	>	mRest->setReferenceStructure(ref, COM);
260		}
296	–
297	–	} else {
298	–	//molecule belongs to slave nodes
299	–
300	–	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
301	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
302	–
303	–	for(j = 0; j < nCurObj; j++){
304	–	inIdealFile->getline(read_buffer, sizeof(read_buffer));
305	–
306	–	if( inIdealFile->eof() ){
307	–	sprintf(painCave.errMsg,
308	–	"RestReader Error: error in reading file %s\n"
309	–	"natoms  = %d; index = %d\n"
310	–	"error reading the line from the file.\n",
311	–	idealName.c_str(), nTotObjs, i );
312	–	painCave.isFatal = 1;
313	–	simError();
314	–	}
315	–
316	–	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
317	–	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
318	–	}
261		}
262		}
263	<	} else {
264	<	//actions taken at slave nodes
323	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode, MPI_COMM_WORLD);
263	>	}
264	>	}
265
266	<	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
267	<	int which_node = info_->getMolToProc(i);
266	>
267	>
268	>	void RestReader::parseDumpLine(const std::string& line) {
269
270	<	if(which_node == worldRank){
271	<	//molecule with global index i belongs to this processor
270	>	StringTokenizer tokenizer(line);
271	>	int nTokens;
272	>
273	>	nTokens = tokenizer.countTokens();
274	>
275	>	if (nTokens < 2) {
276	>	sprintf(painCave.errMsg,
277	>	"RestReader Error: Not enough Tokens.\n%s\n", line.c_str());
278	>	painCave.isFatal = 1;
279	>	simError();
280	>	}
281	>
282	>	int index = tokenizer.nextTokenAsInt();
283	>
284	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
285	>
286	>	if (sd == NULL) {
287	>	return;
288	>	}
289	>
290	>	std::string type = tokenizer.nextToken();
291	>	int size = type.size();
292	>
293	>	Vector3d pos;
294	>	Quat4d q;
295	>
296	>	for(int i = 0; i < size; ++i) {
297	>	switch(type[i]) {
298	>
299	>	case 'p': {
300	>	pos[0] = tokenizer.nextTokenAsDouble();
301	>	pos[1] = tokenizer.nextTokenAsDouble();
302	>	pos[2] = tokenizer.nextTokenAsDouble();
303	>	break;
304	>	}
305	>	case 'v' : {
306	>	Vector3d vel;
307	>	vel[0] = tokenizer.nextTokenAsDouble();
308	>	vel[1] = tokenizer.nextTokenAsDouble();
309	>	vel[2] = tokenizer.nextTokenAsDouble();
310	>	break;
311	>	}
312	>
313	>	case 'q' : {
314	>	if (sd->isDirectional()) {
315
316	<	mol = info_->getMoleculeByGlobalIndex(i);
316	>	q[0] = tokenizer.nextTokenAsDouble();
317	>	q[1] = tokenizer.nextTokenAsDouble();
318	>	q[2] = tokenizer.nextTokenAsDouble();
319	>	q[3] = tokenizer.nextTokenAsDouble();
320
321	<	if(mol == NULL) {
322	<	sprintf(painCave.errMsg,
335	<	"RestReader Error: molecule not found on node %d\n",
336	<	worldRank);
337	<	painCave.isFatal = 1;
338	<	simError();
339	<	}
340	<
341	<	nCurObj = mol->getNIntegrableObjects();
342	<
343	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode,
344	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
345	<
346	<	for (integrableObject = mol->beginIntegrableObject(ii);
347	<	integrableObject != NULL;
348	<	integrableObject = mol->nextIntegrableObject(ii)){
349	<
350	<	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode,
351	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
321	>	RealType qlen = q.length();
322	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
323
324	<	parseErr = parseIdealLine(read_buffer, integrableObject);
325	<
326	<	if( parseErr != NULL ){
327	<	strcpy( painCave.errMsg, parseErr );
328	<	simError();
324	>	sprintf(painCave.errMsg,
325	>	"RestReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
326	>	painCave.isFatal = 1;
327	>	simError();
328	>	}
329	>
330	>	q.normalize();
331	>	}
332	>	break;
333	>	}
334	>	case 'j' : {
335	>	Vector3d ji;
336	>	if (sd->isDirectional()) {
337	>	ji[0] = tokenizer.nextTokenAsDouble();
338	>	ji[1] = tokenizer.nextTokenAsDouble();
339	>	ji[2] = tokenizer.nextTokenAsDouble();
340	>	}
341	>	break;
342	>	}
343	>	case 'f': {
344	>	Vector3d force;
345	>	force[0] = tokenizer.nextTokenAsDouble();
346	>	force[1] = tokenizer.nextTokenAsDouble();
347	>	force[2] = tokenizer.nextTokenAsDouble();
348	>	break;
349	>	}
350	>	case 't' : {
351	>	Vector3d torque;
352	>	torque[0] = tokenizer.nextTokenAsDouble();
353	>	torque[1] = tokenizer.nextTokenAsDouble();
354	>	torque[2] = tokenizer.nextTokenAsDouble();
355	>	break;
356	>	}
357	>	default: {
358	>	sprintf(painCave.errMsg,
359	>	"RestReader Error: %s is an unrecognized type\n", type.c_str());
360	>	painCave.isFatal = 1;
361	>	simError();
362	>	break;
363	>	}
364	>	}
365	>	// keep the position in case we need it for a molecular restraint:
366	>
367	>	all_pos_[index] = pos;
368	>
369	>	// is this io restrained?
370	>	GenericData* data = sd->getPropertyByName("Restraint");
371	>	ObjectRestraint* oRest;
372	>
373	>	if (data != NULL) {
374	>	// make sure we can reinterpret the generic data as restraint data:
375	>	RestraintData* restData= dynamic_cast<RestraintData*>(data);
376	>	if (restData != NULL) {
377	>	// make sure we can reinterpet the restraint data as a pointer to
378	>	// an ObjectRestraint:
379	>	oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
380	>	if (oRest != NULL) {
381	>	if (sd->isDirectional()) {
382	>	oRest->setReferenceStructure(pos, q.toRotationMatrix3());
383	>	} else {
384	>	oRest->setReferenceStructure(pos);
385		}
386		}
387		}
388		}
389		}
363	–	#endif
390		}
391
392	<	char* RestReader::parseIdealLine(char* readLine, StuntDouble* sd){
392	>	void  RestReader::readStuntDoubles(std::istream& inputStream) {
393
394	<	RealType pos[3];        // position place holders
395	<	RealType q[4];          // the quaternions
370	<	RealType RfromQ[3][3];  // the rotation matrix
371	<	RealType normalize;     // to normalize the reference unit vector
372	<	RealType uX, uY, uZ;    // reference unit vector place holders
373	<	RealType uselessToken;
374	<	StringTokenizer tokenizer(readLine);
375	<	int nTokens;
394	>	inputStream.getline(buffer, bufferSize);
395	>	std::string line(buffer);
396
397	<	nTokens = tokenizer.countTokens();
398	<
399	<	if (nTokens < 14) {
400	<	sprintf(painCave.errMsg,
401	<	"RestReader Error: Not enough Tokens.\n");
382	<	painCave.isFatal = 1;
383	<	simError();
397	>	if (line.find("<StuntDoubles>") == std::string::npos) {
398	>	sprintf(painCave.errMsg,
399	>	"RestReader Error: Missing <StuntDoubles>\n");
400	>	painCave.isFatal = 1;
401	>	simError();
402		}
403
404	<	std::string name = tokenizer.nextToken();
405	<
388	<	if (name != sd->getType()) {
404	>	while(inputStream.getline(buffer, bufferSize)) {
405	>	line = buffer;
406
407	<	sprintf(painCave.errMsg,
408	<	"RestReader Error: Atom type [%s] in %s does not "
409	<	"match Atom Type [%s] in .md file.\n",
393	<	name.c_str(), idealName.c_str(),
394	<	sd->getType().c_str());
395	<	painCave.isFatal = 1;
396	<	simError();
397	<	}
398	<
399	<	pos[0] = tokenizer.nextTokenAsDouble();
400	<	pos[1] = tokenizer.nextTokenAsDouble();
401	<	pos[2] = tokenizer.nextTokenAsDouble();
402	<
403	<	// store the positions in the stuntdouble as generic data doubles
404	<	DoubleGenericData* refPosX = new DoubleGenericData();
405	<	refPosX->setID("refPosX");
406	<	refPosX->setData(pos[0]);
407	<	sd->addProperty(refPosX);
408	<
409	<	DoubleGenericData* refPosY = new DoubleGenericData();
410	<	refPosY->setID("refPosY");
411	<	refPosY->setData(pos[1]);
412	<	sd->addProperty(refPosY);
413	<
414	<	DoubleGenericData* refPosZ = new DoubleGenericData();
415	<	refPosZ->setID("refPosZ");
416	<	refPosZ->setData(pos[2]);
417	<	sd->addProperty(refPosZ);
418	<
419	<	// we don't need the velocities
420	<	uselessToken = tokenizer.nextTokenAsDouble();
421	<	uselessToken = tokenizer.nextTokenAsDouble();
422	<	uselessToken = tokenizer.nextTokenAsDouble();
423	<
424	<	if (sd->isDirectional()) {
407	>	if(line.find("</StuntDoubles>") != std::string::npos) {
408	>	break;
409	>	}
410
411	<	q[0] = tokenizer.nextTokenAsDouble();
427	<	q[1] = tokenizer.nextTokenAsDouble();
428	<	q[2] = tokenizer.nextTokenAsDouble();
429	<	q[3] = tokenizer.nextTokenAsDouble();
430	<
431	<	// now build the rotation matrix and find the unit vectors
432	<	RfromQ[0][0] = q[0]*q[0] + q[1]*q[1] - q[2]*q[2] - q[3]*q[3];
433	<	RfromQ[0][1] = 2*(q[1]*q[2] + q[0]*q[3]);
434	<	RfromQ[0][2] = 2*(q[1]*q[3] - q[0]*q[2]);
435	<	RfromQ[1][0] = 2*(q[1]*q[2] - q[0]*q[3]);
436	<	RfromQ[1][1] = q[0]*q[0] - q[1]*q[1] + q[2]*q[2] - q[3]*q[3];
437	<	RfromQ[1][2] = 2*(q[2]*q[3] + q[0]*q[1]);
438	<	RfromQ[2][0] = 2*(q[1]*q[3] + q[0]*q[2]);
439	<	RfromQ[2][1] = 2*(q[2]*q[3] - q[0]*q[1]);
440	<	RfromQ[2][2] = q[0]*q[0] - q[1]*q[1] - q[2]*q[2] + q[3]*q[3];
441	<
442	<	normalize = sqrt(RfromQ[2][0]*RfromQ[2][0] + RfromQ[2][1]*RfromQ[2][1]
443	<	+ RfromQ[2][2]*RfromQ[2][2]);
444	<	uX = RfromQ[2][0]/normalize;
445	<	uY = RfromQ[2][1]/normalize;
446	<	uZ = RfromQ[2][2]/normalize;
447	<
448	<	// store reference unit vectors as generic data in the stuntdouble
449	<	DoubleGenericData* refVectorX = new DoubleGenericData();
450	<	refVectorX->setID("refVectorX");
451	<	refVectorX->setData(uX);
452	<	sd->addProperty(refVectorX);
453	<
454	<	DoubleGenericData* refVectorY = new DoubleGenericData();
455	<	refVectorY->setID("refVectorY");
456	<	refVectorY->setData(uY);
457	<	sd->addProperty(refVectorY);
458	<
459	<	DoubleGenericData* refVectorZ = new DoubleGenericData();
460	<	refVectorZ->setID("refVectorZ");
461	<	refVectorZ->setData(uZ);
462	<	sd->addProperty(refVectorZ);
411	>	parseDumpLine(line);
412		}
413
465	–	// we don't need the angular velocities, so let's exit the line
466	–	return NULL;
414		}
415	+
416
417	<	void RestReader::readZangle(){
418	<
419	<	int i;
472	<	int isPresent;
473	<
474	<	Molecule* mol;
475	<	StuntDouble* integrableObject;
476	<	SimInfo::MoleculeIterator mi;
477	<	Molecule::IntegrableObjectIterator ii;
478	<
479	<	#ifdef IS_MPI
480	<	int which_node;
481	<	MPI_Status istatus;
482	<	#endif //is_mpi
483	<
484	<	const int BUFFERSIZE = 2000; // size of the read buffer
485	<	unsigned int nTotObjs; // the number of atoms
486	<	char read_buffer[BUFFERSIZE]; //the line buffer for reading
487	<
488	<	std::vector<StuntDouble*> vecParticles;
489	<	std::vector<RealType> tempZangs;
490	<
491	<	angFile = info_->getRestFileName();
492	<
493	<	angFile += "0";
494	<
495	<	// open the omega value file for reading
496	<	#ifdef IS_MPI
497	<	if (worldRank == 0) {
498	<	#endif
499	<	isPresent = 1;
500	<
501	<	inAngFile = new std::ifstream(angFile.c_str());
502	<
503	<	if(inAngFile->fail()){
504	<	sprintf(painCave.errMsg,
505	<	"Restraints Warning: %s file is not present\n"
506	<	"\tAll omega values will be initialized to zero. If the\n"
507	<	"\tsimulation is starting from the idealCrystal.in reference\n"
508	<	"\tconfiguration, this is the desired action. If this is not\n"
509	<	"\tthe case, the energy calculations will be incorrect.\n",
510	<	angFile.c_str());
511	<	painCave.severity = OOPSE_WARNING;
512	<	painCave.isFatal = 0;
513	<	simError();
514	<	isPresent = 0;
515	<	}
516	<
517	<	#ifdef IS_MPI
518	<	// let the other nodes know the status of the file search
519	<	MPI_Bcast(&isPresent, 1, MPI_INT, 0, MPI_COMM_WORLD);
520	<	#endif // is_mpi
521	<
522	<	if (!isPresent) {
523	<	zeroZangle();
524	<	return;
525	<	}
526	<
527	<	#ifdef IS_MPI
528	<	if (!isPresent) {
529	<	// master node zeroes out its zAngles if .zang0 isn't present
530	<	zeroZangle();
531	<	return;
532	<	}
417	>	void RestReader::readFrameProperties(std::istream& inputStream) {
418	>	inputStream.getline(buffer, bufferSize);
419	>	std::string line(buffer);
420
421	+	if (line.find("<FrameData>") == std::string::npos) {
422	+	sprintf(painCave.errMsg,
423	+	"RestReader Error: Missing <FrameData>\n");
424	+	painCave.isFatal = 1;
425	+	simError();
426		}
427	<
428	<	// listen to node 0 to see if we should exit this function
429	<	if (worldRank != 0) {
430	<	MPI_Bcast(&isPresent, 1, MPI_INT, 0, MPI_COMM_WORLD);
431	<	if (!isPresent) {
432	<	zeroZangle();
433	<	return;
427	>
428	>	// restraints don't care about frame data (unless we need to wrap
429	>	// coordinates, but we'll worry about that later), so
430	>	// we'll just scan ahead until the end of the frame data:
431	>
432	>	while(inputStream.getline(buffer, bufferSize)) {
433	>	line = buffer;
434	>
435	>	if(line.find("</FrameData>") != std::string::npos) {
436	>	break;
437		}
543	–	}
544	–
545	–	strcpy( checkPointMsg, "zAngle file opened successfully for reading." );
546	–	errorCheckPoint();
547	–	#endif
548	–
549	–	#ifndef IS_MPI
550	–
551	–	// read the first line and die if there is a failure
552	–	inAngFile->getline(read_buffer, sizeof(read_buffer));
553	–
554	–	if( inAngFile->eof() ){
555	–	sprintf( painCave.errMsg,
556	–	"RestraintReader error: error reading 1st line of \"%s\"\n",
557	–	angFile.c_str() );
558	–	painCave.isFatal = 1;
559	–	simError();
560	–	}
561	–
562	–	// read the file and load the values into a vector
563	–	inAngFile->getline(read_buffer, sizeof(read_buffer));
564	–
565	–	while ( !inAngFile->eof() ) {
566	–	// check for and ignore blank lines
567	–	if ( read_buffer != NULL )
568	–	tempZangs.push_back( atof(read_buffer) );
569	–
570	–	inAngFile->getline(read_buffer, sizeof(read_buffer));
571	–	}
572	–
573	–	nTotObjs = info_->getNGlobalIntegrableObjects();
574	–
575	–	if( nTotObjs != tempZangs.size() ){
576	–	sprintf( painCave.errMsg,
577	–	"RestraintReader zAngle reading error. %s nIntegrable, %d, "
578	–	"does not match the meta-data file's nIntegrable, %i.\n",
579	–	angFile.c_str(),
580	–	tempZangs.size(),
581	–	nTotObjs );
582	–	painCave.isFatal = 1;
583	–	simError();
584	–	}
585	–
586	–	// load the zAngles into the integrable objects
587	–	i = 0;
588	–	for (mol = info_->beginMolecule(mi); mol != NULL;
589	–	mol = info_->nextMolecule(mi)) {
438
591	–	for (integrableObject = mol->beginIntegrableObject(ii);
592	–	integrableObject != NULL;
593	–	integrableObject = mol->nextIntegrableObject(ii)) {
594	–
595	–	integrableObject->setZangle(tempZangs[i]);
596	–	i++;
597	–	}
439		}
440
600	–	// MPI Section of code..........
601	–	#else //IS_MPI
602	–
603	–	// first thing first, suspend fatalities.
604	–	painCave.isEventLoop = 1;
605	–
606	–	int masterNode = 0;
607	–
608	–	int haveError;
609	–	int intObjIndex;
610	–	int intObjIndexTransfer;
611	–
612	–	int j;
613	–	int nCurObj;
614	–	RealType angleTransfer;
615	–
616	–	nTotObjs = info_->getNGlobalIntegrableObjects();
617	–	haveError = 0;
618	–
619	–	if (worldRank == masterNode) {
620	–
621	–	inAngFile->getline(read_buffer, sizeof(read_buffer));
622	–
623	–	if( inAngFile->eof() ){
624	–	sprintf( painCave.errMsg,
625	–	"Error reading 1st line of %s \n ",angFile.c_str());
626	–	haveError = 1;
627	–	simError();
628	–	}
629	–
630	–	// let the master node read the file and load the temporary angle vector
631	–	inAngFile->getline(read_buffer, sizeof(read_buffer));
632	–
633	–	while ( !inAngFile->eof() ) {
634	–	// check for and ignore blank lines
635	–	if ( read_buffer != NULL )
636	–	tempZangs.push_back( atof(read_buffer) );
637	–
638	–	inAngFile->getline(read_buffer, sizeof(read_buffer));
639	–	}
640	–
641	–	// Check to see that the number of integrable objects in the
642	–	// intial configuration file is the same as derived from the
643	–	// meta-data file.
644	–	if( nTotObjs != tempZangs.size() ){
645	–	sprintf( painCave.errMsg,
646	–	"RestraintReader zAngle reading Error. %s nIntegrable, %d, "
647	–	"does not match the meta-data file's nIntegrable, %d.\n",
648	–	angFile.c_str(),
649	–	tempZangs.size(),
650	–	nTotObjs);
651	–	haveError= 1;
652	–	simError();
653	–	}
654	–
655	–	// At this point, node 0 has a tempZangs vector completed, and
656	–	// everyone else has nada
657	–
658	–	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
659	–	// Get the Node number which has this atom
660	–	which_node = info_->getMolToProc(i);
661	–
662	–	if (which_node == masterNode) {
663	–	mol = info_->getMoleculeByGlobalIndex(i);
664	–
665	–	if(mol == NULL) {
666	–	strcpy(painCave.errMsg, "Molecule not found on node 0!");
667	–	haveError = 1;
668	–	simError();
669	–	}
670	–
671	–	for (integrableObject = mol->beginIntegrableObject(ii);
672	–	integrableObject != NULL;
673	–	integrableObject = mol->nextIntegrableObject(ii)){
674	–	intObjIndex = integrableObject->getGlobalIntegrableObjectIndex();
675	–	integrableObject->setZangle(tempZangs[intObjIndex]);
676	–	}
677	–
678	–	} else {
679	–	// I am MASTER OF THE UNIVERSE, but I don't own this molecule
680	–	// listen for the number of integrableObjects in the molecule
681	–	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
682	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
683	–
684	–	for(j=0; j < nCurObj; j++){
685	–	// listen for which integrableObject we need to send the value for
686	–	MPI_Recv(&intObjIndexTransfer, 1, MPI_INT, which_node,
687	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
688	–	angleTransfer = tempZangs[intObjIndexTransfer];
689	–	// send the value to the node so it can initialize the object
690	–	MPI_Send(&angleTransfer, 1, MPI_REALTYPE, which_node,
691	–	TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);
692	–	}
693	–	}
694	–	}
695	–	} else {
696	–	// I am SLAVE TO THE MASTER
697	–	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
698	–	which_node = info_->getMolToProc(i);
699	–
700	–	if (which_node == worldRank) {
701	–
702	–	// BUT I OWN THIS MOLECULE!!!
703	–
704	–	mol = info_->getMoleculeByGlobalIndex(i);
705	–
706	–	if(mol == NULL) {
707	–	sprintf(painCave.errMsg,
708	–	"RestReader Error: molecule not found on node %d\n",
709	–	worldRank);
710	–	painCave.isFatal = 1;
711	–	simError();
712	–	}
713	–
714	–	nCurObj = mol->getNIntegrableObjects();
715	–	// send the number of integrableObjects in the molecule
716	–	MPI_Send(&nCurObj, 1, MPI_INT, 0,
717	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
718	–
719	–	for (integrableObject = mol->beginIntegrableObject(ii);
720	–	integrableObject != NULL;
721	–	integrableObject = mol->nextIntegrableObject(ii)){
722	–	intObjIndexTransfer = integrableObject->getGlobalIntegrableObjectIndex();
723	–	// send the global index of the integrableObject
724	–	MPI_Send(&intObjIndexTransfer, 1, MPI_INT, 0,
725	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
726	–	// listen for the value we want to set locally
727	–	MPI_Recv(&angleTransfer, 1, MPI_REALTYPE, 0,
728	–	TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
729	–
730	–	integrableObject->setZangle(angleTransfer);
731	–	}
732	–	}
733	–	}
734	–	}
735	–	#endif
441		}
737	–
738	–	void RestReader :: zeroZangle(){
739	–
740	–	Molecule* mol;
741	–	StuntDouble* integrableObject;
742	–	SimInfo::MoleculeIterator mi;
743	–	Molecule::IntegrableObjectIterator ii;
442
443	<	#ifndef IS_MPI
444	<	// set all zAngles to 0.0
747	<	for (mol = info_->beginMolecule(mi); mol != NULL;
748	<	mol = info_->nextMolecule(mi))
749	<
750	<	for (integrableObject = mol->beginIntegrableObject(ii);
751	<	integrableObject != NULL;
752	<	integrableObject = mol->nextIntegrableObject(ii))
753	<	integrableObject->setZangle( 0.0 );
754	<
755	<
756	<	// MPI Section of code..........
757	<	#else //IS_MPI
758	<
759	<	// first thing first, suspend fatalities.
760	<	painCave.isEventLoop = 1;
761	<
762	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
763	<	int haveError;
764	<	int which_node;
765	<
766	<	haveError = 0;
767	<
768	<	for (int i=0 ; i < info_->getNGlobalMolecules(); i++) {
769	<
770	<	// Get the Node number which has this atom
771	<	which_node = info_->getMolToProc(i);
772	<
773	<	// each processor zeroes its own integrable objects
774	<	if (which_node == worldRank) {
775	<	mol = info_->getMoleculeByGlobalIndex(i);
776	<
777	<	if(mol == NULL) {
778	<	sprintf( painCave.errMsg,
779	<	"Molecule not found on node %i!",
780	<	which_node );
781	<	haveError = 1;
782	<	simError();
783	<	}
784	<
785	<	for (integrableObject = mol->beginIntegrableObject(ii);
786	<	integrableObject != NULL;
787	<	integrableObject = mol->nextIntegrableObject(ii)){
788	<
789	<	integrableObject->setZangle( 0.0 );
790	<
791	<	}
792	<	}
793	<	}
794	<
795	<	#endif
796	<	}
797	<
798	<	} // end namespace oopse
443	>
444	>	}//end namespace OpenMD

Comparing trunk/src/io/RestReader.cpp (property svn:keywords):
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

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