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Comparing trunk/src/io/RestReader.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1407 by cli2, Wed Jan 20 16:04:40 2010 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]  Vardeman & Gezelter, in progress (2009).                        
40 > */
41  
42 < #define _LARGEFILE_SOURCE64
43 < #define _FILE_OFFSET_BITS 64
44 <
45 < #include <sys/types.h>
46 < #include <sys/stat.h>
47 <
48 < #include <iostream>
49 < #include <math.h>
50 <
51 < #include <stdio.h>
52 < #include <stdlib.h>
53 < #include <string.h>
54 <
55 < #include "primitives/Molecule.hpp"
56 < #include "utils/MemoryUtils.hpp"
42 >
43 > #include <sys/types.h>
44 > #include <sys/stat.h>
45 >
46 > #include <math.h>
47 > #include <string>
48 > #include <sstream>
49 > #include <iostream>
50 > #include <stdio.h>
51 > #include <stdlib.h>
52 > #include <string.h>
53 >
54 > #include "io/RestReader.hpp"
55 > #include "primitives/Molecule.hpp"
56 > #include "utils/simError.h"
57 > #include "utils/MemoryUtils.hpp"
58   #include "utils/StringTokenizer.hpp"
59 < #include "io/RestReader.hpp"
60 < #include "utils/simError.h"
59 > #include "restraints/ObjectRestraint.hpp"
60 > #include "restraints/MolecularRestraint.hpp"
61 >
62 > #ifdef IS_MPI
63 >
64 > #include <mpi.h>
65 > #endif
66  
67 < #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
67 > namespace OpenMD {
68  
69 < namespace oopse {
70 <  
71 <  RestReader::RestReader( SimInfo* info ) : info_(info){
69 >  void RestReader::scanFile(){
70 >    int lineNo = 0;
71 >    std::streampos prevPos;
72 >    std::streampos  currPos;
73      
74 <    idealName = "idealCrystal.in";
74 > #ifdef IS_MPI
75      
76 <    isScanned = false;
77 <    
78 < #ifdef IS_MPI
79 <    if (worldRank == 0) {
80 < #endif
76 >    if (worldRank == 0) {
77 > #endif // is_mpi
78 >
79 >      inFile_->clear();
80 >      currPos = inFile_->tellg();
81 >      prevPos = currPos;
82        
83 <      inIdealFile = fopen(idealName, "r");
84 <      if(inIdealFile == NULL){
85 <        sprintf(painCave.errMsg,
86 <                "RestReader: Cannot open file: %s\n", idealName);
87 <        painCave.isFatal = 1;
88 <        simError();
83 >      bool foundOpenSnapshotTag = false;
84 >      
85 >      while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) {
86 >        ++lineNo;
87 >        
88 >        std::string line = buffer;
89 >        currPos = inFile_->tellg();
90 >        if (line.find("<Snapshot>")!= std::string::npos) {
91 >          foundOpenSnapshotTag = true;
92 >          framePos_ = prevPos;
93 >        }
94 >        prevPos = currPos;
95        }
96        
97 <      inIdealFileName = idealName;
89 < #ifdef IS_MPI
97 > #ifdef IS_MPI
98      }
99 <    strcpy( checkPointMsg,
100 <            "File \"idealCrystal.in\" opened successfully for reading." );
101 <    MPIcheckPoint();
94 < #endif
99 >    MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD);
100 > #endif // is_mpi
101 >  }
102  
103 <    return;  
104 <  }
105 <  
106 <  RestReader :: ~RestReader( ){
107 < #ifdef IS_MPI
108 <    if (worldRank == 0) {
109 < #endif
110 <      int error;
111 <      error = fclose( inIdealFile );
103 >
104 >  void RestReader::readSet(){
105 >    std::string line;
106 >    
107 > #ifndef IS_MPI
108 >    
109 >    inFile_->clear();
110 >    inFile_->seekg(framePos_);
111 >    
112 >    std::istream& inputStream = *inFile_;
113 > #else
114 >    
115 >    int masterNode = 0;
116 >    std::stringstream sstream;
117 >    if (worldRank == masterNode) {
118 >      std::string sendBuffer;
119        
120 <      if( error ){
121 <        sprintf( painCave.errMsg,
122 <                 "Error closing %s\n", inIdealFileName.c_str());
123 <        simError();
120 >      inFile_->clear();  
121 >      inFile_->seekg(framePos_);
122 >      
123 >      while (inFile_->getline(buffer, bufferSize)) {
124 >        
125 >        line = buffer;
126 >        sendBuffer += line;
127 >        sendBuffer += '\n';
128 >        if (line.find("</Snapshot>") != std::string::npos) {
129 >          break;
130 >        }        
131        }
132        
133 <      MemoryUtils::deletePointers(framePos);
133 >      int sendBufferSize = sendBuffer.size();
134 >      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
135 >      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
136        
137 < #ifdef IS_MPI
138 <    }
139 <    strcpy( checkPointMsg, "Restraint file closed successfully." );
140 <    MPIcheckPoint();
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, MPI_COMM_WORLD);    
145 >      sstream.str(recvBuffer);
146 >      delete [] recvBuffer;
147 >    }      
148 >    
149 >    std::istream& inputStream = sstream;  
150   #endif
151      
152 <    return;
153 <  }
154 <  
155 <  
156 <  void RestReader :: readIdealCrystal(){
152 >    inputStream.getline(buffer, bufferSize);
153 >
154 >    line = buffer;
155 >    if (line.find("<Snapshot>") == std::string::npos) {
156 >      sprintf(painCave.errMsg,
157 >              "RestReader Error: can not find <Snapshot>\n");
158 >      painCave.isFatal = 1;
159 >      simError();
160 >    }
161      
162 <    int i;
163 <    unsigned int j;
162 >    //read frameData
163 >    readFrameProperties(inputStream);
164      
165 < #ifdef IS_MPI
166 <    int done, which_node, which_atom; // loop counter
131 < #endif //is_mpi
165 >    //read StuntDoubles
166 >    readStuntDoubles(inputStream);
167      
168 <    const int BUFFERSIZE = 2000; // size of the read buffer
169 <    int nTotObjs; // the number of atoms
170 <    char read_buffer[BUFFERSIZE]; //the line buffer for reading
168 >    inputStream.getline(buffer, bufferSize);
169 >    line = buffer;
170 >    if (line.find("</Snapshot>") == std::string::npos) {
171 >      sprintf(painCave.errMsg,
172 >              "RestReader Error: can not find </Snapshot>\n");
173 >      painCave.isFatal = 1;
174 >      simError();
175 >    }            
176 >  }
177      
178 <    char *eof_test; // ptr to see when we reach the end of the file
179 <    char *parseErr;
178 >  void RestReader::readReferenceStructure() {
179 >
180 >    // We need temporary storage to keep track of all StuntDouble positions
181 >    // in case some of the restraints are molecular (i.e. if they use
182 >    // multiple SD positions to determine restrained orientations or positions:
183 >
184 >    all_pos_.clear();
185 >    all_pos_.resize(info_->getNGlobalIntegrableObjects()) ;
186      
187 <    std::vector<StuntDouble*> integrableObjects;
188 <    
187 >    // Restraint files are just standard dump files, but with the reference
188 >    // structure stored in the first frame (frame 0).
189 >    // RestReader overloads readSet and explicitly handles all of the
190 >    // ObjectRestraints in that method:
191 >
192 >    scanFile();
193 >
194 >
195 >    readSet();
196 >
197 >
198 >    // all ObjectRestraints have been handled, now we have to worry about
199 >    // molecular restraints:
200 >
201 >    SimInfo::MoleculeIterator i;
202 >    Molecule::IntegrableObjectIterator j;
203      Molecule* mol;
204 <    StuntDouble* integrableObject;
144 <    SimInfo::MoleculeIterator mi;
145 <    Molecule::IntegrableObjectIterator ii;
204 >    StuntDouble* sd;
205      
206 < #ifndef IS_MPI
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 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
211 <    if( eof_test == NULL ){
151 <      sprintf( painCave.errMsg,
152 <               "RestraintReader error: error reading 1st line of \"%s\"\n",
153 <               inIdealFileName.c_str() );
154 <      painCave.isFatal = 1;
155 <      simError();
156 <    }
157 <    
158 <    nTotObjs = atoi( read_buffer );
159 <    
160 <    if( nTotObjs != info_->getNGlobalIntegrableObjects() ){
161 <      sprintf( painCave.errMsg,
162 <               "RestraintReader error. %s nIntegrable, %d, "
163 <               "does not match the meta-data file's nIntegrable, %d.\n",
164 <               inIdealFileName.c_str(), nTotObjs,
165 <               info_->getNGlobalIntegrableObjects());
166 <      painCave.isFatal = 1;
167 <      simError();
168 <    }
169 <    
170 <    // skip over the comment line
171 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
172 <    if(eof_test == NULL){
173 <      sprintf( painCave.errMsg,
174 <               "error in reading commment in %s\n", inIdealFileName.c_str());
175 <      painCave.isFatal = 1;
176 <      simError();
177 <    }
178 <    
179 <    // parse the ideal crystal lines
180 <    /*
181 <     * Note: we assume that there is a one-to-one correspondence between
182 <     * integrable objects and lines in the idealCrystal.in file.  Thermodynamic
183 <     * integration is only supported for simple rigid bodies.
184 <     */
185 <    for (mol = info_->beginMolecule(mi); mol != NULL;
186 <         mol = info_->nextMolecule(mi)) {
210 >    for (mol = info_->beginMolecule(i); mol != NULL;
211 >         mol = info_->nextMolecule(i)) {          
212        
213 <      for (integrableObject = mol->beginIntegrableObject(ii);
214 <           integrableObject != NULL;
215 <           integrableObject = mol->nextIntegrableObject(ii)) {    
213 >      // is this molecule restrained?    
214 >      GenericData* data = mol->getPropertyByName("Restraint");
215 >      
216 >      if (data != NULL) {
217          
218 <        eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
193 <        if(eof_test == NULL){
194 <          sprintf(painCave.errMsg,
195 <                  "RestReader Error: error in reading file %s\n"
196 <                  "natoms  = %d; index = %d\n"
197 <                  "error reading the line from the file.\n",
198 <                  inIdealFileName.c_str(), nTotObjs,
199 <                  integrableObject->getGlobalIndex() );
200 <          painCave.isFatal = 1;
201 <          simError();
202 <        }
218 >        // make sure we can reinterpret the generic data as restraint data:
219          
220 <        parseErr = parseIdealLine( read_buffer, integrableObject);
205 <        if( parseErr != NULL ){
206 <          strcpy( painCave.errMsg, parseErr );
207 <          painCave.isFatal = 1;
208 <          simError();
209 <        }
210 <      }
211 <    }
212 <    
213 <    // MPI Section of code..........
214 < #else //IS_MPI
215 <    
216 <    // first thing first, suspend fatalities.
217 <    painCave.isEventLoop = 1;
218 <    
219 <    int masterNode = 0;
220 <    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
221 <    
222 <    MPI_Status istatus;
223 <    int nCurObj;
224 <    int nitems;
225 <    int haveError;
226 <
227 <    nTotObjs = info_->getNGlobalIntegrableObjects();
228 <    haveError = 0;
229 <
230 <    if (worldRank == masterNode) {
231 <      eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
232 <      if( eof_test == NULL ){
233 <        sprintf( painCave.errMsg,
234 <                 "Error reading 1st line of %s \n ",inIdealFileName.c_str());
235 <        painCave.isFatal = 1;
236 <        simError();
237 <      }
238 <      
239 <      nitems = atoi( read_buffer );
240 <      
241 <      // Check to see that the number of integrable objects in the
242 <      // intial configuration file is the same as derived from the
243 <      // meta-data file.
244 <      if( nTotObjs != nitems){
245 <        sprintf( painCave.errMsg,
246 <                 "RestraintReader Error. %s nIntegrable, %d, "
247 <                 "does not match the meta-data file's nIntegrable, %d.\n",
248 <                 inIdealFileName.c_str(), nTotObjs,
249 <                 info_->getNGlobalIntegrableObjects());
250 <        painCave.isFatal = 1;
251 <        simError();
252 <      }
253 <      
254 <      // skip over the comment line
255 <      eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
256 <      if(eof_test == NULL){
257 <        sprintf( painCave.errMsg,
258 <                 "error in reading commment in %s\n", inIdealFileName.c_str());
259 <        painCave.isFatal = 1;
260 <        simError();
261 <      }
262 <
263 <      for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
264 <        int which_node = info_->getMolToProc(i);
220 >        RestraintData* restData= dynamic_cast<RestraintData*>(data);        
221          
222 <        if(which_node == masterNode){
267 <          //molecules belong to master node
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) {
272 <            sprintf(painCave.errMsg,
273 <                    "RestReader Error: Molecule not found on node %d!\n",
274 <                    worldRank);
275 <            painCave.isFatal = 1;
276 <            simError();
277 <          }
227 >          MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
228            
229 <          for (integrableObject = mol->beginIntegrableObject(ii);
280 <               integrableObject != NULL;
281 <               integrableObject = mol->nextIntegrableObject(ii)){
229 >          if (mRest != NULL) {          
230              
231 <            eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
231 >            // now we need to pack the stunt doubles for the reference
232 >            // structure:
233              
234 <            if(eof_test == NULL){
235 <              sprintf(painCave.errMsg,
236 <                      "RestReader Error: error in reading file %s\n"
237 <                      "natoms  = %d; index = %d\n"
289 <                      "error reading the line from the file.\n",
290 <                      inIdealFileName.c_str(), nTotObjs, i );
291 <              painCave.isFatal = 1;
292 <              simError();
293 <            }
294 <        
295 <            parseIdealLine(read_buffer, integrableObject);
296 <        
297 <          }
298 <        } else {
299 <          //molecule belongs to slave nodes
300 <          
301 <          MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
302 <                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
303 <          
304 <          for(j=0; j < nCurObj; j++){
234 >            std::vector<Vector3d> ref;
235 >            int count = 0;
236 >            RealType mass, mTot;
237 >            Vector3d COM(0.0);
238              
239 <            eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
307 <            if(eof_test == NULL){
308 <              sprintf(painCave.errMsg,
309 <                      "RestReader Error: error in reading file %s\n"
310 <                      "natoms  = %d; index = %d\n"
311 <                      "error reading the line from the file.\n",
312 <                      inIdealFileName.c_str(), nTotObjs, i );
313 <              painCave.isFatal = 1;
314 <              simError();
315 <            }
239 >            mTot = 0.0;
240              
241 <            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
242 <                     TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
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 >            COM /= mTot;
258 >            mRest->setReferenceStructure(ref, COM);        
259            }
260          }
261        }
262 <    } else {
263 <      //actions taken at slave nodes
264 <      for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
265 <        int which_node = info_->getMolToProc(i);
262 >    }
263 >  }
264 >
265 >  
266 >  
267 >  void RestReader::parseDumpLine(const std::string& line) {        
268 >
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 >  
284 >    if (index < 1116){
285 >      std::string type = tokenizer.nextToken();
286 >      
287 >      Vector3d pos;
288 >      
289 >      pos[0] = tokenizer.nextTokenAsDouble();
290 >      pos[1] = tokenizer.nextTokenAsDouble();
291 >      pos[2] = tokenizer.nextTokenAsDouble();
292 >      
293 >      all_pos_[index] = pos;
294 >    }else{
295 >      
296 >      bool exist = false;
297 >      int indexCount = 0;
298 >      
299 >      while ( (!exist) && (indexCount < stuntDoubleIndex_.size())){
300 >        if (index == stuntDoubleIndex_[indexCount])
301 >          exist = true;
302 >        indexCount++;
303 >      }
304 >      
305 >      StuntDouble* integrableObject;
306 >      
307 >      if (exist){
308          
309 <        if(which_node == worldRank){
310 <          //molecule with global index i belongs to this processor
311 <          
312 <          mol = info_->getMoleculeByGlobalIndex(i);
313 <          
314 <          if(mol == NULL) {
315 <            sprintf(painCave.errMsg,
316 <                    "RestReader Error: molecule not found on node %d\n",
317 <                    worldRank);
318 <            painCave.isFatal = 1;
319 <            simError();
320 <          }
321 <          
322 <          nCurObj = mol->getNIntegrableObjects();
323 <          
324 <          MPI_Send(&nCurObj, 1, MPI_INT, masterNode,
325 <                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
309 >        integrableObject = info_->getIOIndexToIntegrableObject(index);
310 >        
311 >        int compareindex = integrableObject->getGlobalIntegrableObjectIndex();
312 >        
313 >        if (integrableObject == NULL) {
314 >          return;
315 >        }  
316 >        
317 >        std::string type = tokenizer.nextToken();
318 >        
319 >        Vector3d pos;
320 >        
321 >        pos[0] = tokenizer.nextTokenAsDouble();
322 >        pos[1] = tokenizer.nextTokenAsDouble();
323 >        pos[2] = tokenizer.nextTokenAsDouble();
324 >        
325 >        Vector3d vel;
326 >        vel[0] = tokenizer.nextTokenAsDouble();
327 >        vel[1] = tokenizer.nextTokenAsDouble();
328 >        vel[2] = tokenizer.nextTokenAsDouble();
329 >        
330 >        
331 >        Quat4d q;
332 >        if (integrableObject->isDirectional()) {
333            
334 <          for (integrableObject = mol->beginIntegrableObject(ii);
335 <               integrableObject != NULL;
336 <               integrableObject = mol->nextIntegrableObject(ii)){
337 <            
338 <            MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode,
339 <                     TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
340 <            
341 <            parseErr = parseIdealLine(read_buffer, integrableObject);
342 <            
343 <            if( parseErr != NULL ){
344 <              strcpy( painCave.errMsg, parseErr );
345 <              simError();
334 >          q[0] = tokenizer.nextTokenAsDouble();
335 >          q[1] = tokenizer.nextTokenAsDouble();
336 >          q[2] = tokenizer.nextTokenAsDouble();
337 >          q[3] = tokenizer.nextTokenAsDouble();
338 >        }  
339 >        // keep the position in case we need it for a molecular restraint:
340 >        
341 >        all_pos_[index] = pos;
342 >        
343 >        // is this io restrained?
344 >        GenericData* data = integrableObject->getPropertyByName("Restraint");
345 >        ObjectRestraint* oRest;
346 >        
347 >        if (data != NULL) {
348 >          // make sure we can reinterpret the generic data as restraint data:
349 >          RestraintData* restData= dynamic_cast<RestraintData*>(data);        
350 >          if (restData != NULL) {
351 >            // make sure we can reinterpet the restraint data as a pointer to
352 >            // an ObjectRestraint:
353 >            oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
354 >            if (oRest != NULL) {          
355 >              if (integrableObject->isDirectional()) {
356 >                oRest->setReferenceStructure(pos, q.toRotationMatrix3());
357 >              } else {                          
358 >                oRest->setReferenceStructure(pos);
359 >              }
360              }
361            }
362          }
363        }
364      }
362 – #endif
365    }
366    
367 <  char* RestReader::parseIdealLine(char* readLine, StuntDouble* sd){
367 >  void  RestReader::readStuntDoubles(std::istream& inputStream) {
368      
369 <    char *foo; // the pointer to the current string token
369 >    inputStream.getline(buffer, bufferSize);
370 >    std::string line(buffer);
371      
372 <    double pos[3];        // position place holders
373 <    double q[4];          // the quaternions
374 <    double RfromQ[3][3];  // the rotation matrix
375 <    double normalize;     // to normalize the reference unit vector
376 <    double uX, uY, uZ;    // reference unit vector place holders
374 <    double uselessToken;
375 <    StringTokenizer tokenizer(readLine);
376 <    int nTokens;
377 <    
378 <    nTokens = tokenizer.countTokens();
379 <
380 <    if (nTokens < 14) {
381 <      sprintf(painCave.errMsg,
382 <              "RestReader Error: Not enough Tokens.\n");
383 <      painCave.isFatal = 1;
384 <      simError();
372 >    if (line.find("<StuntDoubles>") == std::string::npos) {
373 >      sprintf(painCave.errMsg,
374 >              "RestReader Error: Missing <StuntDoubles>\n");
375 >      painCave.isFatal = 1;
376 >      simError();
377      }
378      
379 <    std::string name = tokenizer.nextToken();
380 <
389 <    if (name != sd->getType()) {
379 >    while(inputStream.getline(buffer, bufferSize)) {
380 >      line = buffer;
381        
382 <      sprintf(painCave.errMsg,
383 <              "RestReader Error: Atom type [%s] in %s does not "
384 <              "match Atom Type [%s] in .md file.\n",
385 <              name.c_str(), inIdealFileName.c_str(),
386 <              sd->getType().c_str());
396 <      painCave.isFatal = 1;
397 <      simError();        
382 >      if(line.find("</StuntDoubles>") != std::string::npos) {
383 >        break;
384 >      }
385 >      
386 >      parseDumpLine(line);
387      }
388      
389 <    pos[0] = tokenizer.nextTokenAsDouble();
401 <    pos[1] = tokenizer.nextTokenAsDouble();
402 <    pos[2] = tokenizer.nextTokenAsDouble();
389 >  }
390  
391 <    // store the positions in the stuntdouble as generic data doubles
392 <    DoubleGenericData* refPosX = new DoubleGenericData();
393 <    refPosX->setID("refPosX");
394 <    refPosX->setData(pos[0]);
408 <    sd->addProperty(refPosX);
391 >  
392 >  void RestReader::readFrameProperties(std::istream& inputStream) {
393 >    inputStream.getline(buffer, bufferSize);
394 >    std::string line(buffer);
395  
396 <    DoubleGenericData* refPosY = new DoubleGenericData();
397 <    refPosY->setID("refPosY");
398 <    refPosY->setData(pos[1]);
399 <    sd->addProperty(refPosY);
400 <    
401 <    DoubleGenericData* refPosZ = new DoubleGenericData();
416 <    refPosZ->setID("refPosZ");
417 <    refPosZ->setData(pos[2]);
418 <    sd->addProperty(refPosZ);
396 >    if (line.find("<FrameData>") == std::string::npos) {
397 >      sprintf(painCave.errMsg,
398 >              "RestReader Error: Missing <FrameData>\n");
399 >      painCave.isFatal = 1;
400 >      simError();
401 >    }
402  
403 <    // we don't need the velocities
404 <    uselessToken = tokenizer.nextTokenAsDouble();
405 <    uselessToken = tokenizer.nextTokenAsDouble();
406 <    uselessToken = tokenizer.nextTokenAsDouble();
407 <    
408 <    if (sd->isDirectional()) {
403 >    // restraints don't care about frame data (unless we need to wrap
404 >    // coordinates, but we'll worry about that later), so
405 >    // we'll just scan ahead until the end of the frame data:
406 >
407 >    while(inputStream.getline(buffer, bufferSize)) {
408 >      line = buffer;
409        
410 <      q[0] = tokenizer.nextTokenAsDouble();
411 <      q[1] = tokenizer.nextTokenAsDouble();
429 <      q[2] = tokenizer.nextTokenAsDouble();
430 <      q[3] = tokenizer.nextTokenAsDouble();
431 <      
432 <      // now build the rotation matrix and find the unit vectors
433 <      RfromQ[0][0] = q[0]*q[0] + q[1]*q[1] - q[2]*q[2] - q[3]*q[3];
434 <      RfromQ[0][1] = 2*(q[1]*q[2] + q[0]*q[3]);
435 <      RfromQ[0][2] = 2*(q[1]*q[3] - q[0]*q[2]);
436 <      RfromQ[1][0] = 2*(q[1]*q[2] - q[0]*q[3]);
437 <      RfromQ[1][1] = q[0]*q[0] - q[1]*q[1] + q[2]*q[2] - q[3]*q[3];
438 <      RfromQ[1][2] = 2*(q[2]*q[3] + q[0]*q[1]);
439 <      RfromQ[2][0] = 2*(q[1]*q[3] + q[0]*q[2]);
440 <      RfromQ[2][1] = 2*(q[2]*q[3] - q[0]*q[1]);
441 <      RfromQ[2][2] = q[0]*q[0] - q[1]*q[1] - q[2]*q[2] + q[3]*q[3];
442 <      
443 <      normalize = sqrt(RfromQ[2][0]*RfromQ[2][0] + RfromQ[2][1]*RfromQ[2][1]
444 <                       + RfromQ[2][2]*RfromQ[2][2]);
445 <      uX = RfromQ[2][0]/normalize;
446 <      uY = RfromQ[2][1]/normalize;
447 <      uZ = RfromQ[2][2]/normalize;
448 <      
449 <      // store reference unit vectors as generic data in the stuntdouble
450 <      DoubleGenericData* refVectorX = new DoubleGenericData();
451 <      refVectorX->setID("refVectorX");
452 <      refVectorX->setData(uX);
453 <      sd->addProperty(refVectorX);
454 <      
455 <      DoubleGenericData* refVectorY = new DoubleGenericData();
456 <      refVectorY->setID("refVectorY");
457 <      refVectorY->setData(uY);
458 <      sd->addProperty(refVectorY);
459 <      
460 <      DoubleGenericData* refVectorZ = new DoubleGenericData();
461 <      refVectorZ->setID("refVectorZ");
462 <      refVectorZ->setData(uZ);
463 <      sd->addProperty(refVectorZ);
464 <    }
465 <    
466 <    // we don't need the angular velocities, so let's exit the line
467 <    return NULL;
468 <  }
469 <  
470 <  void RestReader::readZangle(){
471 <    
472 <    int i;
473 <    unsigned int j;
474 <    int isPresent;
475 <    
476 <    Molecule* mol;
477 <    StuntDouble* integrableObject;
478 <    SimInfo::MoleculeIterator mi;
479 <    Molecule::IntegrableObjectIterator ii;
480 <    
481 < #ifdef IS_MPI
482 <    int done, which_node, which_atom; // loop counter
483 <    int nProc;
484 <    MPI_Status istatus;
485 < #endif //is_mpi
486 <    
487 <    const int BUFFERSIZE = 2000; // size of the read buffer
488 <    int nTotObjs; // the number of atoms
489 <    char read_buffer[BUFFERSIZE]; //the line buffer for reading
490 <    
491 <    char *eof_test; // ptr to see when we reach the end of the file
492 <    char *parseErr;
493 <    
494 <    std::vector<StuntDouble*> vecParticles;
495 <    std::vector<double> tempZangs;
496 <      
497 <    inAngFileName = info_->getRestFileName();
498 <    
499 <    inAngFileName += "0";
500 <    
501 <    // open the omega value file for reading
502 < #ifdef IS_MPI
503 <    if (worldRank == 0) {
504 < #endif
505 <      isPresent = 1;
506 <      inAngFile = fopen(inAngFileName.c_str(), "r");
507 <      if(!inAngFile){
508 <        sprintf(painCave.errMsg,
509 <                "Restraints Warning: %s file is not present\n"
510 <                "\tAll omega values will be initialized to zero. If the\n"
511 <                "\tsimulation is starting from the idealCrystal.in reference\n"
512 <                "\tconfiguration, this is the desired action. If this is not\n"
513 <                "\tthe case, the energy calculations will be incorrect.\n",
514 <                inAngFileName.c_str());
515 <        painCave.severity = OOPSE_WARNING;
516 <        painCave.isFatal = 0;
517 <        simError();  
518 <        isPresent = 0;
410 >      if(line.find("</FrameData>") != std::string::npos) {
411 >        break;
412        }
520 –      
521 – #ifdef IS_MPI
522 –      // let the other nodes know the status of the file search
523 –      MPI_Bcast(&isPresent, 1, MPI_INT, 0, MPI_COMM_WORLD);
524 – #endif // is_mpi
525 –      
526 –      if (!isPresent) {
527 –        zeroZangle();
528 –        return;
529 –      }
530 –      
531 – #ifdef IS_MPI
532 –    }
533 –    
534 –    // listen to node 0 to see if we should exit this function
535 –    if (worldRank != 0) {
536 –      MPI_Bcast(&isPresent, 1, MPI_INT, 0, MPI_COMM_WORLD);
537 –      if (!isPresent) {
538 –        zeroZangle();
539 –        return;
540 –      }
541 –    }
542 –    
543 –    strcpy( checkPointMsg, "zAngle file opened successfully for reading." );
544 –    MPIcheckPoint();
545 – #endif
546 –    
547 – #ifndef IS_MPI
548 –    
549 –    eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
550 –    if( eof_test == NULL ){
551 –      sprintf( painCave.errMsg,
552 –               "RestraintReader error: error reading 1st line of \"%s\"\n",
553 –               inAngFileName.c_str() );
554 –      painCave.isFatal = 1;
555 –      simError();
556 –    }
557 –    
558 –    eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
559 –    while ( eof_test != NULL ) {
560 –      // check for and ignore blank lines
561 –      if ( read_buffer != NULL )
562 –        tempZangs.push_back( atof(read_buffer) );
563 –      eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
564 –    }
565 –    
566 –    nTotObjs = info_->getNGlobalIntegrableObjects();
567 –    
568 –    if( nTotObjs != tempZangs.size() ){
569 –      sprintf( painCave.errMsg,
570 –               "RestraintReader zAngle reading error. %s nIntegrable, %d, "
571 –               "does not match the meta-data file's nIntegrable, %d.\n",
572 –               inAngFileName.c_str(), tempZangs.size(), nTotObjs );
573 –      painCave.isFatal = 1;
574 –      simError();
575 –    }
576 –    
577 –    // load the zAngles into the integrable objects
578 –    i = 0;
579 –    for (mol = info_->beginMolecule(mi); mol != NULL;
580 –         mol = info_->nextMolecule(mi)) {
413        
582 –      for (integrableObject = mol->beginIntegrableObject(ii);
583 –           integrableObject != NULL;
584 –           integrableObject = mol->nextIntegrableObject(ii)) {    
585 –        
586 –        integrableObject->setZangle(tempZangs[i]);
587 –        i++;
588 –      }
414      }
415      
591 –    // MPI Section of code..........
592 – #else //IS_MPI
593 –    
594 –    // first thing first, suspend fatalities.
595 –    painCave.isEventLoop = 1;
596 –
597 –    int masterNode = 0;
598 –    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
599 –    int haveError;
600 –    int index;    
601 –
602 –    int nCurObj;
603 –    double angleTranfer;
604 –    
605 –    nTotObjs = info_->getNGlobalIntegrableObjects();
606 –    haveError = 0;
607 –
608 –    if (worldRank == masterNode) {
609 –      
610 –      eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
611 –      if( eof_test == NULL ){
612 –        sprintf( painCave.errMsg,
613 –                 "Error reading 1st line of %s \n ",inAngFileName.c_str());
614 –        haveError = 1;
615 –        simError();
616 –      }
617 –      
618 –      // let node 0 load the temporary angle vector
619 –      eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
620 –      while ( eof_test != NULL ) {
621 –        // check for and ignore blank lines
622 –        if ( read_buffer != NULL )
623 –          tempZangs.push_back( atof(read_buffer) );
624 –        eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
625 –      }
626 –      
627 –      // Check to see that the number of integrable objects in the
628 –      // intial configuration file is the same as derived from the
629 –      // meta-data file.
630 –      if( nTotObjs != tempZangs.size() ){
631 –        sprintf( painCave.errMsg,
632 –                 "RestraintReader zAngle reading Error. %s nIntegrable, %d, "
633 –                 "does not match the meta-data file's nIntegrable, %d.\n",
634 –                 inAngFileName.c_str(), tempZangs.size(), nTotObjs);
635 –        haveError= 1;
636 –        simError();
637 –      }
638 –      
639 –      // At this point, node 0 has a tempZangs vector completed, and
640 –      // everyone else has nada
641 –      index = 0;
642 –      
643 –      for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
644 –        // Get the Node number which has this atom
645 –        which_node = info_->getMolToProc(i);
646 –        
647 –        if (worldRank == masterNode) {
648 –          mol = info_->getMoleculeByGlobalIndex(i);
649 –          
650 –          if(mol == NULL) {
651 –            strcpy(painCave.errMsg, "Molecule not found on node 0!");
652 –            haveError = 1;
653 –            simError();
654 –          }
655 –          
656 –          for (integrableObject = mol->beginIntegrableObject(ii);
657 –               integrableObject != NULL;
658 –               integrableObject = mol->nextIntegrableObject(ii)){
659 –            
660 –            integrableObject->setZangle(tempZangs[index]);
661 –            index++;
662 –          }    
663 –          
664 –        } else {
665 –          // I am MASTER OF THE UNIVERSE, but I don't own this molecule
666 –          
667 –          MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
668 –                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
669 –          
670 –          for(j=0; j < nCurObj; j++){            
671 –            angleTransfer = tempZangs[index];
672 –            MPI_Send(&angleTransfer, 1, MPI_DOUBLE, which_node,
673 –                     TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);              
674 –            index++;
675 –          }
676 –          
677 –        }
678 –      }
679 –    } else {
680 –      // I am SLAVE TO THE MASTER
681 –      for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
682 –        int which_node = info_->getMolToProc(i);
683 –
684 –        if (which_node == worldRank) {
685 –          
686 –          // BUT I OWN THIS MOLECULE!!!
687 –          
688 –          mol = info_->getMoleculeByGlobalIndex(i);
689 –
690 –          if(mol == NULL) {
691 –            sprintf(painCave.errMsg,
692 –                    "RestReader Error: molecule not found on node %d\n",
693 –                    worldRank);
694 –            painCave.isFatal = 1;
695 –            simError();
696 –          }
697 –
698 –          nCurObj = mol->getNIntegrableObjects();
699 –        
700 –          MPI_Send(&nCurObj, 1, MPI_INT, 0,
701 –                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
702 –          
703 –          for (integrableObject = mol->beginIntegrableObject(ii);
704 –               integrableObject != NULL;
705 –               integrableObject = mol->nextIntegrableObject(ii)){
706 –            
707 –            MPI_Recv(&angleTransfer, 1, MPI_DOUBLE, 0,
708 –                     TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
709 –
710 –            integrableObject->setZangle(angleTransfer);
711 –          }    
712 –        }
713 –      }
714 –    }
715 – #endif
416    }
717 –  
718 –  void RestReader :: zeroZangle(){
719 –    
720 –    int i;
721 –    unsigned int j;
722 –    int nTotObjs; // the number of atoms
723 –    
724 –    Molecule* mol;
725 –    StuntDouble* integrableObject;
726 –    SimInfo::MoleculeIterator mi;
727 –    Molecule::IntegrableObjectIterator ii;
728 –    
729 –    std::vector<StuntDouble*> vecParticles;
730 –    
731 – #ifndef IS_MPI
732 –    // set all zAngles to 0.0
733 –    for (mol = info_->beginMolecule(mi); mol != NULL;
734 –         mol = info_->nextMolecule(mi))
735 –      
736 –      for (integrableObject = mol->beginIntegrableObject(ii);
737 –           integrableObject != NULL;
738 –           integrableObject = mol->nextIntegrableObject(ii))    
739 –        integrableObject->setZangle( 0.0 );
740 –    
741 –    
742 –    // MPI Section of code..........
743 – #else //IS_MPI
744 –    
745 –    // first thing first, suspend fatalities.
746 –    painCave.isEventLoop = 1;
747 –    
748 –    int masterNode = 0;
749 –    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
750 –    int haveError;
751 –    int which_node;
752 –    
753 –    MPI_Status istatus;
754 –    
755 –    int nCurObj;
756 –    double angleTranfer;
757 –    
758 –    nTotObjs = info_->getNGlobalIntegrableObjects();
759 –    haveError = 0;
760 –    if (worldRank == masterNode) {
417  
418 <      for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
419 <        // Get the Node number which has this atom
764 <        which_node = info_->getMolToProc(i);
765 <        
766 <        // let's let node 0 pass out constant values to all the processors
767 <        if (worldRank == masterNode) {
768 <          mol = info_->getMoleculeByGlobalIndex(i);
769 <          
770 <          if(mol == NULL) {
771 <            strcpy(painCave.errMsg, "Molecule not found on node 0!");
772 <            haveError = 1;
773 <            simError();
774 <          }
775 <          
776 <          for (integrableObject = mol->beginIntegrableObject(ii);
777 <               integrableObject != NULL;
778 <               integrableObject = mol->nextIntegrableObject(ii)){
779 <            
780 <            integrableObject->setZangle( 0.0 );
781 <            
782 <          }
783 <          
784 <        } else {
785 <          // I am MASTER OF THE UNIVERSE, but I don't own this molecule
786 <          
787 <          MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
788 <                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
789 <          
790 <          for(j=0; j < nCurObj; j++){            
791 <            angleTransfer = 0.0;
792 <            MPI_Send(&angleTransfer, 1, MPI_DOUBLE, which_node,
793 <                     TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);              
794 <            
795 <          }
796 <        }
797 <      }
798 <    } else {
799 <      // I am SLAVE TO THE MASTER
800 <      for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
801 <        int which_node = info_->getMolToProc(i);
802 <        
803 <        if (which_node == worldRank) {
804 <          
805 <          // BUT I OWN THIS MOLECULE!!!
806 <          mol = info_->getMoleculeByGlobalIndex(i);
807 <          
808 <          if(mol == NULL) {
809 <            sprintf(painCave.errMsg,
810 <                    "RestReader Error: molecule not found on node %d\n",
811 <                    worldRank);
812 <            painCave.isFatal = 1;
813 <            simError();
814 <          }
815 <          
816 <          nCurObj = mol->getNIntegrableObjects();
817 <          
818 <          MPI_Send(&nCurObj, 1, MPI_INT, 0,
819 <                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
820 <          
821 <          for (integrableObject = mol->beginIntegrableObject(ii);
822 <               integrableObject != NULL;
823 <               integrableObject = mol->nextIntegrableObject(ii)){
824 <            
825 <            MPI_Recv(&angleTransfer, 1, MPI_DOUBLE, 0,
826 <                     TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
827 <            vecParticles[j]->setZangle(angleTransfer);
828 <          }    
829 <        }
830 <      }
831 <    }
832 < #endif
833 <  }
834 <  
835 < } // end namespace oopse
418 >  
419 > }//end namespace OpenMD

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