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

Comparing trunk/src/io/RestReader.cpp (file contents):
Revision 1030 by chrisfen, Fri Sep 1 14:15:05 2006 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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	<	*/
32	<
33	<	#define _LARGEFILE_SOURCE64
34	<	#define _FILE_OFFSET_BITS 64
35	<
36	<	#include <sys/types.h>
37	<	#include <sys/stat.h>
38	<
39	<	#include <iostream>
40	<	#include <math.h>
41	<
42	<	#include <stdio.h>
43	<	#include <stdlib.h>
44	<	#include <string.h>
45	<
46	<	#include "primitives/Molecule.hpp"
47	<	#include "utils/MemoryUtils.hpp"
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, 234107 (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	>	#ifdef IS_MPI
44	>	#include <mpi.h>
45	>	#endif
46	>
47	>	#include <sys/types.h>
48	>	#include <sys/stat.h>
49	>
50	>	#include <math.h>
51	>	#include <string>
52	>	#include <sstream>
53	>	#include <iostream>
54	>	#include <stdio.h>
55	>	#include <stdlib.h>
56	>	#include <string.h>
57	>
58	>	#include "io/RestReader.hpp"
59	>	#include "primitives/Molecule.hpp"
60	>	#include "utils/simError.h"
61	>	#include "utils/MemoryUtils.hpp"
62		#include "utils/StringTokenizer.hpp"
63	<	#include "io/RestReader.hpp"
64	<	#include "utils/simError.h"
63	>	#include "restraints/ObjectRestraint.hpp"
64	>	#include "restraints/MolecularRestraint.hpp"
65
66	<	#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
66	>	namespace OpenMD {
67
68	<	namespace oopse {
69	<
70	<	RestReader::RestReader( SimInfo* info ) : info_(info){
68	>	void RestReader::scanFile(){
69	>
70	>	std::streampos prevPos;
71	>	std::streampos  currPos;
72
73	<	idealName = "idealCrystal.in";
74	<
75	<	#ifdef IS_MPI
76	<	if (worldRank == 0) {
76	<	#endif
73	>	#ifdef IS_MPI
74	>
75	>	if (worldRank == 0) {
76	>	#endif // is_mpi
77
78	<	inIdealFile = new std::ifstream(idealName.c_str());
79	<
80	<	if(inIdealFile->fail()){
81	<	sprintf(painCave.errMsg,
82	<	"RestReader: Cannot open file: %s\n",
83	<	idealName.c_str());
84	<	painCave.isFatal = 1;
85	<	simError();
78	>	inFile_->clear();
79	>	currPos = inFile_->tellg();
80	>	prevPos = currPos;
81	>
82	>	bool foundOpenSnapshotTag = false;
83	>	int lineNo = 0;
84	>	while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) {
85	>	++lineNo;
86	>
87	>	std::string line = buffer;
88	>	currPos = inFile_->tellg();
89	>	if (line.find("<Snapshot>")!= std::string::npos) {
90	>	foundOpenSnapshotTag = true;
91	>	framePos_ = prevPos;
92	>	}
93	>	prevPos = currPos;
94		}
95
96	<	#ifdef IS_MPI
96	>	#ifdef IS_MPI
97		}
98	<	strcpy( checkPointMsg,
99	<	"File \"idealCrystal.in\" opened successfully for reading." );
100	<	MPIcheckPoint();
93	<	#endif
98	>	MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD);
99	>	#endif // is_mpi
100	>	}
101
95	–	return;
96	–	}
97	–
98	–	RestReader :: ~RestReader( ){
99	–	#ifdef IS_MPI
100	–	if (worldRank == 0) {
101	–	#endif
102
103	<	delete inIdealFile;
104	<	delete inAngFile;
105	<
106	<	#ifdef IS_MPI
107	<	}
108	<	strcpy( checkPointMsg,
109	<	"File idealCrystal.in (and .zang0 if present) closed successfully." );
110	<	MPIcheckPoint();
111	<	#endif
103	>	void RestReader::readSet(){
104	>	std::string line;
105
106	<	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
106	>	#ifndef IS_MPI
107
108	<	const int BUFFERSIZE = 2000; // size of the read buffer
109	<	int nTotObjs; // the number of atoms
126	<	char read_buffer[BUFFERSIZE]; //the line buffer for reading
108	>	inFile_->clear();
109	>	inFile_->seekg(framePos_);
110
111	<	char *parseErr;
111	>	std::istream& inputStream = *inFile_;
112	>	#else
113
114	<	std::vector<StuntDouble*> integrableObjects;
114	>	int masterNode = 0;
115	>	std::stringstream sstream;
116	>	if (worldRank == masterNode) {
117	>	std::string sendBuffer;
118	>
119	>	inFile_->clear();
120	>	inFile_->seekg(framePos_);
121	>
122	>	while (inFile_->getline(buffer, bufferSize)) {
123	>
124	>	line = buffer;
125	>	sendBuffer += line;
126	>	sendBuffer += '\n';
127	>	if (line.find("</Snapshot>") != std::string::npos) {
128	>	break;
129	>	}
130	>	}
131	>
132	>	int sendBufferSize = sendBuffer.size();
133	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
134	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize,
135	>	MPI_CHAR, masterNode, MPI_COMM_WORLD);
136	>
137	>	sstream.str(sendBuffer);
138	>	} else {
139	>	int sendBufferSize;
140	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
141	>	char * recvBuffer = new char[sendBufferSize+1];
142	>	assert(recvBuffer);
143	>	recvBuffer[sendBufferSize] = '\0';
144	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode,
145	>	MPI_COMM_WORLD);
146	>	sstream.str(recvBuffer);
147	>	delete [] recvBuffer;
148	>	}
149
150	<	Molecule* mol;
151	<	StuntDouble* integrableObject;
134	<	SimInfo::MoleculeIterator mi;
135	<	Molecule::IntegrableObjectIterator ii;
150	>	std::istream& inputStream = sstream;
151	>	#endif
152
153	<	#ifndef IS_MPI
138	<
139	<	inIdealFile->getline(read_buffer, sizeof(read_buffer));
153	>	inputStream.getline(buffer, bufferSize);
154
155	<	if( inIdealFile->eof() ){
156	<	sprintf( painCave.errMsg,
157	<	"RestraintReader error: error reading 1st line of \"%s\"\n",
158	<	idealName.c_str() );
159	<	painCave.isFatal = 1;
160	<	simError();
161	<	}
155	>	line = buffer;
156	>	if (line.find("<Snapshot>") == std::string::npos) {
157	>	sprintf(painCave.errMsg,
158	>	"RestReader Error: can not find <Snapshot>\n");
159	>	painCave.isFatal = 1;
160	>	simError();
161	>	}
162
163	<	nTotObjs = atoi( read_buffer );
163	>	//read frameData
164	>	readFrameProperties(inputStream);
165
166	<	if( nTotObjs != info_->getNGlobalIntegrableObjects() ){
167	<	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	<	}
166	>	//read StuntDoubles
167	>	readStuntDoubles(inputStream);
168
169	<	// skip over the comment line
170	<	inIdealFile->getline(read_buffer, sizeof(read_buffer));
171	<
172	<	if( inIdealFile->eof() ){
173	<	sprintf( painCave.errMsg,
174	<	"error in reading commment in %s\n",
175	<	idealName.c_str());
176	<	painCave.isFatal = 1;
177	<	simError();
171	<	}
169	>	inputStream.getline(buffer, bufferSize);
170	>	line = buffer;
171	>	if (line.find("</Snapshot>") == std::string::npos) {
172	>	sprintf(painCave.errMsg,
173	>	"RestReader Error: can not find </Snapshot>\n");
174	>	painCave.isFatal = 1;
175	>	simError();
176	>	}
177	>	}
178
179	<	// 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)) {
179	>	void RestReader::readReferenceStructure() {
180
181	<	inIdealFile->getline(read_buffer, sizeof(read_buffer));
181	>	// We need temporary storage to keep track of all StuntDouble positions
182	>	// in case some of the restraints are molecular (i.e. if they use
183	>	// multiple SD positions to determine restrained orientations or positions:
184
185	<	if( inIdealFile->eof() ){
186	<	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	<	}
185	>	all_pos_.clear();
186	>	all_pos_.resize(info_->getNGlobalIntegrableObjects()) ;
187
188	<	// MPI Section of code..........
189	<	#else //IS_MPI
190	<
191	<	// 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;
188	>	// Restraint files are just standard dump files, but with the reference
189	>	// structure stored in the first frame (frame 0).
190	>	// RestReader overloads readSet and explicitly handles all of the
191	>	// ObjectRestraints in that method:
192
193	<	nTotObjs = info_->getNGlobalIntegrableObjects();
222	<	haveError = 0;
193	>	scanFile();
194
195	<	if (worldRank == masterNode) {
225	<	inIdealFile->getline(read_buffer, sizeof(read_buffer));
195	>	readSet();
196
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));
197
198	<	if( inIdealFile->eof() ){
199	<	sprintf( painCave.errMsg,
254	<	"error in reading commment in %s\n", idealName.c_str());
255	<	painCave.isFatal = 1;
256	<	simError();
257	<	}
198	>	// all ObjectRestraints have been handled, now we have to worry about
199	>	// molecular restraints:
200
201	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode, MPI_COMM_WORLD);
202	<
203	<	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
204	<	which_node = info_->getMolToProc(i);
201	>	SimInfo::MoleculeIterator i;
202	>	Molecule::IntegrableObjectIterator j;
203	>	Molecule* mol;
204	>	StuntDouble* sd;
205	>
206	>	// no need to worry about parallel molecules, as molecules are not
207	>	// split across processor boundaries.  Just loop over all molecules
208	>	// we know about:
209	>
210	>	for (mol = info_->beginMolecule(i); mol != NULL;
211	>	mol = info_->nextMolecule(i)) {
212	>
213	>	// is this molecule restrained?
214	>	GenericData* data = mol->getPropertyByName("Restraint");
215	>
216	>	if (data != NULL) {
217
218	<	if(which_node == masterNode){
219	<	//molecules belong to master node
218	>	// make sure we can reinterpret the generic data as restraint data:
219	>
220	>	RestraintData* restData= dynamic_cast<RestraintData*>(data);
221	>
222	>	if (restData != NULL) {
223
224	<	mol = info_->getMoleculeByGlobalIndex(i);
224	>	// make sure we can reinterpet the restraint data as a
225	>	// pointer to a MolecularRestraint:
226
227	<	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	<	}
227	>	MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
228
229	<	for (integrableObject = mol->beginIntegrableObject(ii);
278	<	integrableObject != NULL;
279	<	integrableObject = mol->nextIntegrableObject(ii)){
229	>	if (mRest != NULL) {
230
231	<	inIdealFile->getline(read_buffer, sizeof(read_buffer));
231	>	// now we need to pack the stunt doubles for the reference
232	>	// structure:
233
234	<	if( inIdealFile->eof() ){
235	<	sprintf(painCave.errMsg,
236	<	"RestReader Error: error in reading file %s\n"
237	<	"natoms  = %d; index = %d\n"
238	<	"error reading the line from the file.\n",
239	<	idealName.c_str(), nTotObjs, i );
240	<	painCave.isFatal = 1;
241	<	simError();
234	>	std::vector<Vector3d> ref;
235	>	int count = 0;
236	>	RealType mass, mTot;
237	>	Vector3d COM(0.0);
238	>
239	>	mTot = 0.0;
240	>
241	>	// loop over the stunt doubles in this molecule in the order we
242	>	// will be looping them in the restraint code:
243	>
244	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
245	>	sd = mol->nextIntegrableObject(j)) {
246	>
247	>	// push back the reference positions of the stunt
248	>	// doubles from the *globally* sorted array of
249	>	// positions:
250	>
251	>	ref.push_back( all_pos_[sd->getGlobalIntegrableObjectIndex()] );
252	>	mass = sd->getMass();
253	>	COM = COM + mass * ref[count];
254	>	mTot = mTot + mass;
255	>	count = count + 1;
256		}
257	<
258	<	parseIdealLine(read_buffer, integrableObject);
294	<
257	>	COM /= mTot;
258	>	mRest->setReferenceStructure(ref, COM);
259		}
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	–	}
260		}
261		}
262	<	} else {
263	<	//actions taken at slave nodes
323	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode, MPI_COMM_WORLD);
262	>	}
263	>	}
264
265	<	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
266	<	int which_node = info_->getMolToProc(i);
265	>
266	>
267	>	void RestReader::parseDumpLine(const std::string& line) {
268
269	<	if(which_node == worldRank){
270	<	//molecule with global index i belongs to this processor
269	>	StringTokenizer tokenizer(line);
270	>	int nTokens;
271	>
272	>	nTokens = tokenizer.countTokens();
273	>
274	>	if (nTokens < 2) {
275	>	sprintf(painCave.errMsg,
276	>	"RestReader Error: Not enough Tokens.\n%s\n", line.c_str());
277	>	painCave.isFatal = 1;
278	>	simError();
279	>	}
280	>
281	>	int index = tokenizer.nextTokenAsInt();
282	>
283	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
284	>
285	>	if (sd == NULL) {
286	>	return;
287	>	}
288	>
289	>	std::string type = tokenizer.nextToken();
290	>	int size = type.size();
291	>
292	>	Vector3d pos;
293	>	Quat4d q;
294	>
295	>	for(int i = 0; i < size; ++i) {
296	>	switch(type[i]) {
297	>
298	>	case 'p': {
299	>	pos[0] = tokenizer.nextTokenAsDouble();
300	>	pos[1] = tokenizer.nextTokenAsDouble();
301	>	pos[2] = tokenizer.nextTokenAsDouble();
302	>	break;
303	>	}
304	>	case 'v' : {
305	>	Vector3d vel;
306	>	vel[0] = tokenizer.nextTokenAsDouble();
307	>	vel[1] = tokenizer.nextTokenAsDouble();
308	>	vel[2] = tokenizer.nextTokenAsDouble();
309	>	break;
310	>	}
311	>
312	>	case 'q' : {
313	>	if (sd->isDirectional()) {
314
315	<	mol = info_->getMoleculeByGlobalIndex(i);
315	>	q[0] = tokenizer.nextTokenAsDouble();
316	>	q[1] = tokenizer.nextTokenAsDouble();
317	>	q[2] = tokenizer.nextTokenAsDouble();
318	>	q[3] = tokenizer.nextTokenAsDouble();
319
320	<	if(mol == NULL) {
321	<	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);
320	>	RealType qlen = q.length();
321	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
322
323	<	parseErr = parseIdealLine(read_buffer, integrableObject);
324	<
325	<	if( parseErr != NULL ){
326	<	strcpy( painCave.errMsg, parseErr );
327	<	simError();
323	>	sprintf(painCave.errMsg,
324	>	"RestReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
325	>	painCave.isFatal = 1;
326	>	simError();
327	>	}
328	>
329	>	q.normalize();
330	>	}
331	>	break;
332	>	}
333	>	case 'j' : {
334	>	Vector3d ji;
335	>	if (sd->isDirectional()) {
336	>	ji[0] = tokenizer.nextTokenAsDouble();
337	>	ji[1] = tokenizer.nextTokenAsDouble();
338	>	ji[2] = tokenizer.nextTokenAsDouble();
339	>	}
340	>	break;
341	>	}
342	>	case 'f': {
343	>	Vector3d force;
344	>	force[0] = tokenizer.nextTokenAsDouble();
345	>	force[1] = tokenizer.nextTokenAsDouble();
346	>	force[2] = tokenizer.nextTokenAsDouble();
347	>	break;
348	>	}
349	>	case 't' : {
350	>	Vector3d torque;
351	>	torque[0] = tokenizer.nextTokenAsDouble();
352	>	torque[1] = tokenizer.nextTokenAsDouble();
353	>	torque[2] = tokenizer.nextTokenAsDouble();
354	>	break;
355	>	}
356	>	default: {
357	>	sprintf(painCave.errMsg,
358	>	"RestReader Error: %s is an unrecognized type\n", type.c_str());
359	>	painCave.isFatal = 1;
360	>	simError();
361	>	break;
362	>	}
363	>	}
364	>	// keep the position in case we need it for a molecular restraint:
365	>
366	>	all_pos_[index] = pos;
367	>
368	>	// is this io restrained?
369	>	GenericData* data = sd->getPropertyByName("Restraint");
370	>
371	>	if (data != NULL) {
372	>	// make sure we can reinterpret the generic data as restraint data:
373	>	RestraintData* restData= dynamic_cast<RestraintData*>(data);
374	>	if (restData != NULL) {
375	>	// make sure we can reinterpet the restraint data as a pointer to
376	>	// an ObjectRestraint:
377	>	ObjectRestraint* oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
378	>	if (oRest != NULL) {
379	>	if (sd->isDirectional()) {
380	>	oRest->setReferenceStructure(pos, q.toRotationMatrix3());
381	>	} else {
382	>	oRest->setReferenceStructure(pos);
383		}
384		}
385		}
386		}
387		}
363	–	#endif
388		}
389
390	<	char* RestReader::parseIdealLine(char* readLine, StuntDouble* sd){
390	>	void  RestReader::readStuntDoubles(std::istream& inputStream) {
391
392	<	RealType pos[3];        // position place holders
393	<	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;
392	>	inputStream.getline(buffer, bufferSize);
393	>	std::string line(buffer);
394
395	<	nTokens = tokenizer.countTokens();
396	<
397	<	if (nTokens < 14) {
398	<	sprintf(painCave.errMsg,
399	<	"RestReader Error: Not enough Tokens.\n");
382	<	painCave.isFatal = 1;
383	<	simError();
395	>	if (line.find("<StuntDoubles>") == std::string::npos) {
396	>	sprintf(painCave.errMsg,
397	>	"RestReader Error: Missing <StuntDoubles>\n");
398	>	painCave.isFatal = 1;
399	>	simError();
400		}
401
402	<	std::string name = tokenizer.nextToken();
403	<
388	<	if (name != sd->getType()) {
402	>	while(inputStream.getline(buffer, bufferSize)) {
403	>	line = buffer;
404
405	<	sprintf(painCave.errMsg,
406	<	"RestReader Error: Atom type [%s] in %s does not "
407	<	"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()) {
405	>	if(line.find("</StuntDoubles>") != std::string::npos) {
406	>	break;
407	>	}
408
409	<	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);
409	>	parseDumpLine(line);
410		}
411
465	–	// we don't need the angular velocities, so let's exit the line
466	–	return NULL;
412		}
413	+
414
415	<	void RestReader::readZangle(){
416	<
417	<	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	<	}
415	>	void RestReader::readFrameProperties(std::istream& inputStream) {
416	>	inputStream.getline(buffer, bufferSize);
417	>	std::string line(buffer);
418
419	+	if (line.find("<FrameData>") == std::string::npos) {
420	+	sprintf(painCave.errMsg,
421	+	"RestReader Error: Missing <FrameData>\n");
422	+	painCave.isFatal = 1;
423	+	simError();
424		}
425	<
426	<	// listen to node 0 to see if we should exit this function
427	<	if (worldRank != 0) {
428	<	MPI_Bcast(&isPresent, 1, MPI_INT, 0, MPI_COMM_WORLD);
429	<	if (!isPresent) {
430	<	zeroZangle();
431	<	return;
425	>
426	>	// restraints don't care about frame data (unless we need to wrap
427	>	// coordinates, but we'll worry about that later), so
428	>	// we'll just scan ahead until the end of the frame data:
429	>
430	>	while(inputStream.getline(buffer, bufferSize)) {
431	>	line = buffer;
432	>
433	>	if(line.find("</FrameData>") != std::string::npos) {
434	>	break;
435		}
543	–	}
544	–
545	–	strcpy( checkPointMsg, "zAngle file opened successfully for reading." );
546	–	MPIcheckPoint();
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)) {
436
591	–	for (integrableObject = mol->beginIntegrableObject(ii);
592	–	integrableObject != NULL;
593	–	integrableObject = mol->nextIntegrableObject(ii)) {
594	–
595	–	integrableObject->setZangle(tempZangs[i]);
596	–	i++;
597	–	}
437		}
438
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
439		}
737	–
738	–	void RestReader :: zeroZangle(){
739	–
740	–	Molecule* mol;
741	–	StuntDouble* integrableObject;
742	–	SimInfo::MoleculeIterator mi;
743	–	Molecule::IntegrableObjectIterator ii;
440
441	<	#ifndef IS_MPI
442	<	// 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
441	>
442	>	}//end namespace OpenMD

Comparing trunk/src/io/RestReader.cpp (property svn:keywords):
Revision 1030 by chrisfen, Fri Sep 1 14:15:05 2006 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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