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root/OpenMD/trunk/src/io/DumpReader.cpp
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Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC

# Line 1 | Line 1
1 < #define _LARGEFILE_SOURCE64
2 < #define _FILE_OFFSET_BITS 64
3 <
4 < #include <sys/types.h>
5 < #include <sys/stat.h>
6 <
7 < #include <iostream>
8 < #include <math.h>
9 <
10 < #include <stdio.h>
11 < #include <stdlib.h>
12 < #include <string.h>
13 <
14 <
15 < #include "ReadWrite.hpp"
16 < #include "simError.h"
17 <
18 < #ifdef IS_MPI
19 < #include <mpi.h>
20 < #include "mpiSimulation.hpp"
21 < #define TAKE_THIS_TAG_CHAR 0
22 < #define TAKE_THIS_TAG_INT 1
23 < #endif // is_mpi
24 <
25 <
26 < DumpReader :: DumpReader(const char *in_name ){
27 <
28 <  isScanned = false;
29 <
30 < #ifdef IS_MPI
31 <  if (worldRank == 0) {
32 < #endif
33 <
34 <  inFile = fopen(in_name, "r");
35 <  if(inFile == NULL){
36 <    sprintf(painCave.errMsg,
37 <            "Cannot open file: %s\n", in_name);
38 <    painCave.isFatal = 1;
39 <    simError();
40 <  }
1 > /*
2 > * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 > *
4 > * The University of Notre Dame grants you ("Licensee") a
5 > * non-exclusive, royalty free, license to use, modify and
6 > * redistribute this software in source and binary code form, provided
7 > * that the following conditions are met:
8 > *
9 > * 1. Acknowledgement of the program authors must be made in any
10 > *    publication of scientific results based in part on use of the
11 > *    program.  An acceptable form of acknowledgement is citation of
12 > *    the article in which the program was described (Matthew
13 > *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 > *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 > *    Parallel Simulation Engine for Molecular Dynamics,"
16 > *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 > *
18 > * 2. Redistributions of source code must retain the above copyright
19 > *    notice, this list of conditions and the following disclaimer.
20 > *
21 > * 3. Redistributions in binary form must reproduce the above copyright
22 > *    notice, this list of conditions and the following disclaimer in the
23 > *    documentation and/or other materials provided with the
24 > *    distribution.
25 > *
26 > * This software is provided "AS IS," without a warranty of any
27 > * kind. All express or implied conditions, representations and
28 > * warranties, including any implied warranty of merchantability,
29 > * fitness for a particular purpose or non-infringement, are hereby
30 > * excluded.  The University of Notre Dame and its licensors shall not
31 > * be liable for any damages suffered by licensee as a result of
32 > * using, modifying or distributing the software or its
33 > * derivatives. In no event will the University of Notre Dame or its
34 > * licensors be liable for any lost revenue, profit or data, or for
35 > * direct, indirect, special, consequential, incidental or punitive
36 > * damages, however caused and regardless of the theory of liability,
37 > * arising out of the use of or inability to use software, even if the
38 > * University of Notre Dame has been advised of the possibility of
39 > * such damages.
40 > */
41    
42 <  inFileName = in_name;
43 < #ifdef IS_MPI
44 <  }
45 <  strcpy( checkPointMsg, "Dump file opened for reading successfully." );
46 <  MPIcheckPoint();
47 < #endif
48 <  return;  
49 < }
50 <
51 < DumpReader :: ~DumpReader( ){
52 < #ifdef IS_MPI
53 <  if (worldRank == 0) {
54 < #endif
55 <  vector<fpos_t*>::iterator i;
56 <
57 <  int error;
58 <  error = fclose( inFile );
59 <  if( error ){
60 <    sprintf( painCave.errMsg,
61 <             "Error closing %s\n", inFileName.c_str());
62 <    simError();
63 <  }
64 <
65 <  for(i = framePos.begin(); i != framePos.end(); ++i)
66 <    delete *i;
67 <  framePos.clear();
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 "io/DumpReader.hpp"
56 > #include "primitives/Molecule.hpp"
57 > #include "utils/simError.h"
58 > #include "utils/MemoryUtils.hpp"
59 > #include "utils/StringTokenizer.hpp"
60 >
61 > #ifdef IS_MPI
62 >
63 > #include <mpi.h>
64 > #define TAKE_THIS_TAG_CHAR 0
65 > #define TAKE_THIS_TAG_INT 1
66 >
67 > #endif // is_mpi
68 >
69 >
70 > namespace oopse {
71 >  
72 >  DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73 >    : info_(info), filename_(filename), isScanned_(false), nframes_(0) {
74 >    
75 > #ifdef IS_MPI
76 >    
77 >    if (worldRank == 0) {
78 > #endif
79 >      
80 >      inFile_ = new std::ifstream(filename_.c_str());
81 >      
82 >      if (inFile_->fail()) {
83 >        sprintf(painCave.errMsg,
84 >                "DumpReader: Cannot open file: %s\n",
85 >                filename_.c_str());
86 >        painCave.isFatal = 1;
87 >        simError();
88 >      }
89 >      
90 > #ifdef IS_MPI
91 >      
92 >    }
93 >    
94 >    strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95 >    MPIcheckPoint();
96 >    
97 > #endif
98 >    
99 >    return;
100 >  }
101    
102 < #ifdef IS_MPI
70 <  }
71 <  strcpy( checkPointMsg, "Dump file closed successfully." );
72 <  MPIcheckPoint();
73 < #endif
74 <
75 <  return;
76 < }
77 <
78 < int DumpReader::getNframes( void ){
79 <
80 <  if( !isScanned )
81 <    scanFile();
82 <  return framePos.size();
83 < }
84 <
85 < void DumpReader::scanFile( void ){
86 <
87 <  int i, j;
88 <  int lineNum = 0;
89 <  char readBuffer[2000];
90 <  fpos_t *currPos;
91 <
92 < #ifdef IS_MPI
93 <  if( worldRank == 0 ){
94 < #endif // is_mpi
102 >  DumpReader::~DumpReader() {
103      
104 <    rewind( inFile );
104 > #ifdef IS_MPI
105      
106 <    currPos = new fpos_t;
107 <    fgetpos( inFile, currPos );
100 <    fgets( readBuffer, sizeof( readBuffer ), inFile );
101 <    lineNum++;
102 <    if( feof( inFile ) ){
103 <      sprintf( painCave.errMsg,
104 <               "File \"%s\" ended unexpectedly at line %d\n",
105 <               inFileName.c_str(),
106 <               lineNum );
107 <      painCave.isFatal = 1;
108 <      simError();
109 <    }
110 <
111 <    while( !feof( inFile ) ){
106 >    if (worldRank == 0) {
107 > #endif
108        
109 <      framePos.push_back(currPos);
114 <
115 <      i = atoi(readBuffer);
109 >      delete inFile_;
110        
111 <      fgets( readBuffer, sizeof( readBuffer ), inFile );
118 <      lineNum++;    
119 <      if( feof( inFile ) ){
120 <        sprintf( painCave.errMsg,
121 <                 "File \"%s\" ended unexpectedly at line %d\n",
122 <                 inFileName.c_str(),
123 <                 lineNum );
124 <        painCave.isFatal = 1;
125 <        simError();
126 <      }
127 <            
128 <      for(j=0; j<i; j++){
129 <        
130 <        fgets( readBuffer, sizeof( readBuffer ), inFile );
131 <        lineNum++;    
132 <        if( feof( inFile ) ){
133 <          sprintf( painCave.errMsg,
134 <                   "File \"%s\" ended unexpectedly at line %d,"
135 <                   " with atom %d\n",
136 <                   inFileName.c_str(),
137 <                   lineNum,
138 <                   j );
139 <          painCave.isFatal = 1;
140 <          simError();
141 <        }
142 <        
143 <      }
111 > #ifdef IS_MPI
112        
113 <      currPos = new fpos_t;
146 <      fgetpos( inFile, currPos );
147 <      fgets( readBuffer, sizeof( readBuffer ), inFile );
148 <      lineNum++;
149 <    }
113 >    }
114      
115 <    delete currPos;
116 <    rewind( inFile );
115 >    strcpy(checkPointMsg, "Dump file closed successfully.");
116 >    MPIcheckPoint();
117 >    
118 > #endif
119 >    
120 >    return;
121 >  }
122 >  
123 >  int DumpReader::getNFrames(void) {
124      
125 <    isScanned = true;
126 <
127 < #ifdef IS_MPI
128 <  }
129 <  strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
130 <  MPIcheckPoint();
131 < #endif // is_mpi
132 < }
133 <
134 < void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
135 <
136 <  simnfo = the_simnfo;
137 <
138 <  this->readSet( whichFrame );
139 < }
125 >    if (!isScanned_)
126 >      scanFile();
127 >    
128 >    return nframes_;
129 >  }
130 >  
131 >  void DumpReader::scanFile(void) {
132 >    int lineNo = 0;
133 >    std::streampos prevPos;
134 >    std::streampos  currPos;
135 >    
136 > #ifdef IS_MPI
137 >    
138 >    if (worldRank == 0) {
139 > #endif // is_mpi
140 >      
141 >      currPos = inFile_->tellg();
142 >      prevPos = currPos;
143 >      bool foundOpenSnapshotTag = false;
144 >      bool foundClosedSnapshotTag = false;
145 >      while(inFile_->getline(buffer, bufferSize)) {
146 >        ++lineNo;
147 >        
148 >        std::string line = buffer;
149 >        currPos = inFile_->tellg();
150 >        if (line.find("<Snapshot>")!= std::string::npos) {
151 >          if (foundOpenSnapshotTag) {
152 >            sprintf(painCave.errMsg,
153 >                    "DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154 >                    filename_.c_str());
155 >            painCave.isFatal = 1;
156 >            simError();          
157 >          }
158 >          foundOpenSnapshotTag = true;
159 >          foundClosedSnapshotTag = false;
160 >          framePos_.push_back(prevPos);
161 >          
162 >        } else if (line.find("</Snapshot>") != std::string::npos){
163 >          if (!foundOpenSnapshotTag) {
164 >            sprintf(painCave.errMsg,
165 >                    "DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
166 >                    filename_.c_str());
167 >            painCave.isFatal = 1;
168 >            simError();
169 >          }
170 >          
171 >          if (foundClosedSnapshotTag) {
172 >            sprintf(painCave.errMsg,
173 >                    "DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
174 >                    filename_.c_str());
175 >            painCave.isFatal = 1;
176 >            simError();
177 >          }
178 >          foundClosedSnapshotTag = true;
179 >          foundOpenSnapshotTag = false;
180 >        }
181 >        prevPos = currPos;
182 >      }
183 >      
184 >      // only found <Snapshot> for the last frame means the file is corrupted, we should discard
185 >      // it and give a warning message
186 >      if (foundOpenSnapshotTag) {
187 >        sprintf(painCave.errMsg,
188 >                "DumpReader: last frame in %s is invalid\n", filename_.c_str());
189 >        painCave.isFatal = 0;
190 >        simError();      
191 >        framePos_.pop_back();
192 >      }
193 >      
194 >      nframes_ = framePos_.size();
195 >      
196 >      if (nframes_ == 0) {
197 >        sprintf(painCave.errMsg,
198 >                "DumpReader: %s does not contain a valid frame\n", filename_.c_str());
199 >        painCave.isFatal = 1;
200 >        simError();      
201 >      }
202 > #ifdef IS_MPI
203 >    }
204 >    
205 >    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206 >    
207 > #endif // is_mpi
208 >    
209 >    isScanned_ = true;
210 >  }
211 >  
212 >  void DumpReader::readFrame(int whichFrame) {
213 >    if (!isScanned_)
214 >      scanFile();
215 >        
216 >    int storageLayout = info_->getSnapshotManager()->getStorageLayout();
217 >    
218 >    if (storageLayout & DataStorage::dslPosition) {
219 >      needPos_ = true;
220 >    } else {
221 >      needPos_ = false;
222 >    }
223 >    
224 >    if (storageLayout & DataStorage::dslVelocity) {
225 >      needVel_ = true;
226 >    } else {
227 >      needVel_ = false;
228 >    }
229 >    
230 >    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
231 >      needQuaternion_ = true;
232 >    } else {
233 >      needQuaternion_ = false;
234 >    }
235 >    
236 >    if (storageLayout & DataStorage::dslAngularMomentum) {
237 >      needAngMom_ = true;
238 >    } else {
239 >      needAngMom_ = false;    
240 >    }
241 >    
242 >    readSet(whichFrame);
243 >  }
244 >  
245 >  void DumpReader::readSet(int whichFrame) {    
246 >    std::string line;
247  
248 + #ifndef IS_MPI
249  
250 +    inFile_->clear();  
251 +    inFile_->seekg(framePos_[whichFrame]);
252  
253 < void DumpReader :: readSet( int whichFrame ){
253 >    std::istream& inputStream = *inFile_;    
254  
255 <  int i;
256 <  unsigned int j;
255 > #else
256 >    int masterNode = 0;
257 >    std::stringstream sstream;
258 >    if (worldRank == masterNode) {
259 >      std::string sendBuffer;
260  
261 < #ifdef IS_MPI
262 <  int done, which_node, which_atom; // loop counter
263 < #endif //is_mpi
261 >      inFile_->clear();  
262 >      inFile_->seekg(framePos_[whichFrame]);
263 >      
264 >      while (inFile_->getline(buffer, bufferSize)) {
265  
266 <  const int BUFFERSIZE = 2000; // size of the read buffer
267 <  int nTotObjs; // the number of atoms
268 <  char read_buffer[BUFFERSIZE]; //the line buffer for reading
266 >        line = buffer;
267 >        sendBuffer += line;
268 >        sendBuffer += '\n';
269 >        if (line.find("</Snapshot>") != std::string::npos) {
270 >          break;
271 >        }        
272 >      }
273  
274 <  char *eof_test; // ptr to see when we reach the end of the file
275 <  char *parseErr;
274 >      int sendBufferSize = sendBuffer.size();
275 >      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
276 >      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
277 >      
278 >      sstream.str(sendBuffer);
279 >      std::cerr << sendBuffer;
280 >    } else {
281 >      int sendBufferSize;
282 >      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
283 >      char * recvBuffer = new char[sendBufferSize+1];
284 >      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
285 >      sstream.str(recvBuffer);
286 >    }      
287  
288 <  vector<StuntDouble*> integrableObjects;
288 >    std::istream& inputStream = sstream;  
289 > #endif
290  
291 +    inputStream.getline(buffer, bufferSize);
292  
293 < #ifndef IS_MPI
293 >    line = buffer;
294 >    if (line.find("<Snapshot>") == std::string::npos) {
295 >      sprintf(painCave.errMsg,
296 >              "DumpReader Error: can not find <Snapshot>\n");
297 >      painCave.isFatal = 1;
298 >      simError();
299 >    }
300 >    
301 >    //read frameData
302 >    readFrameProperties(inputStream);
303  
304 <  fsetpos(inFile, framePos[whichFrame]);
305 <  eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
195 <  if( eof_test == NULL ){
196 <    sprintf( painCave.errMsg,
197 <             "DumpReader error: error reading 1st line of \"%s\"\n",
198 <             inFileName.c_str() );
199 <    painCave.isFatal = 1;
200 <    simError();
201 <  }
304 >    //read StuntDoubles
305 >    readStuntDoubles(inputStream);    
306  
307 <  nTotObjs = atoi( read_buffer );
307 >    inputStream.getline(buffer, bufferSize);
308 >    line = buffer;
309 >    if (line.find("</Snapshot>") == std::string::npos) {
310 >      sprintf(painCave.errMsg,
311 >              "DumpReader Error: can not find </Snapshot>\n");
312 >      painCave.isFatal = 1;
313 >      simError();
314 >    }        
315 >  
316 >  }
317 >  
318 >  void DumpReader::parseDumpLine(const std::string& line) {
319  
320 <  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
321 <    sprintf( painCave.errMsg,
322 <             "DumpReader error. %s nIntegrable, %d, "
323 <             "does not match the meta-data file's nIntegrable, %d.\n",
324 <             inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
325 <    painCave.isFatal = 1;
326 <    simError();
327 <  }
320 >      
321 >    StringTokenizer tokenizer(line);
322 >    int nTokens;
323 >    
324 >    nTokens = tokenizer.countTokens();
325 >    
326 >    if (nTokens < 2) {
327 >      sprintf(painCave.errMsg,
328 >              "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
329 >      painCave.isFatal = 1;
330 >      simError();
331 >    }
332  
333 <  //read the box mat from the comment line
333 >    int index = tokenizer.nextTokenAsInt();
334 >
335 >    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
336  
337 <  eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
338 <  if(eof_test == NULL){
339 <    sprintf( painCave.errMsg,
340 <             "error in reading commment in %s\n", inFileName.c_str());
341 <    painCave.isFatal = 1;
342 <    simError();
343 <  }
337 >    if (integrableObject == NULL) {
338 >      return;
339 >    }
340 >    std::string type = tokenizer.nextToken();
341 >    int size = type.size();
342 >    for(int i = 0; i < size; ++i) {
343 >      switch(type[i]) {
344 >        
345 >        case 'p': {
346 >            Vector3d pos;
347 >            pos[0] = tokenizer.nextTokenAsDouble();
348 >            pos[1] = tokenizer.nextTokenAsDouble();
349 >            pos[2] = tokenizer.nextTokenAsDouble();
350 >            if (needPos_) {
351 >              integrableObject->setPos(pos);
352 >            }            
353 >            break;
354 >        }
355 >        case 'v' : {
356 >            Vector3d vel;
357 >            vel[0] = tokenizer.nextTokenAsDouble();
358 >            vel[1] = tokenizer.nextTokenAsDouble();
359 >            vel[2] = tokenizer.nextTokenAsDouble();
360 >            if (needVel_) {
361 >              integrableObject->setVel(vel);
362 >            }
363 >            break;
364 >        }
365  
366 <  parseErr = parseCommentLine( read_buffer, simnfo);
367 <  if( parseErr != NULL ){
368 <    strcpy( painCave.errMsg, parseErr );
369 <    painCave.isFatal = 1;
370 <    simError();
371 <  }
366 >        case 'q' : {
367 >           Quat4d q;
368 >           if (integrableObject->isDirectional()) {
369 >              
370 >             q[0] = tokenizer.nextTokenAsDouble();
371 >             q[1] = tokenizer.nextTokenAsDouble();
372 >             q[2] = tokenizer.nextTokenAsDouble();
373 >             q[3] = tokenizer.nextTokenAsDouble();
374 >              
375 >             RealType qlen = q.length();
376 >             if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
377 >                
378 >               sprintf(painCave.errMsg,
379 >                       "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
380 >               painCave.isFatal = 1;
381 >               simError();
382 >                
383 >             }  
384 >              
385 >             q.normalize();
386 >             if (needQuaternion_) {            
387 >               integrableObject->setQ(q);
388 >             }              
389 >           }            
390 >           break;
391 >        }  
392 >        case 'j' : {
393 >          Vector3d ji;
394 >          if (integrableObject->isDirectional()) {
395 >             ji[0] = tokenizer.nextTokenAsDouble();
396 >             ji[1] = tokenizer.nextTokenAsDouble();
397 >             ji[2] = tokenizer.nextTokenAsDouble();
398 >             if (needAngMom_) {
399 >               integrableObject->setJ(ji);
400 >             }
401 >          }
402 >        }  
403 >        case 'f': {
404  
405 <  //parse dump lines
405 >          Vector3d force;
406 >          force[0] = tokenizer.nextTokenAsDouble();
407 >          force[1] = tokenizer.nextTokenAsDouble();
408 >          force[2] = tokenizer.nextTokenAsDouble();          
409 >          integrableObject->setFrc(force);
410 >          break;
411 >        }
412 >        case 't' : {
413  
414 <  for( i=0; i < simnfo->n_mol; i++){
415 <
416 <    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
417 <
418 <    for(j = 0; j < integrableObjects.size(); j++){
414 >           Vector3d torque;
415 >           torque[0] = tokenizer.nextTokenAsDouble();
416 >           torque[1] = tokenizer.nextTokenAsDouble();
417 >           torque[2] = tokenizer.nextTokenAsDouble();          
418 >           integrableObject->setTrq(torque);          
419 >           break;
420 >        }
421 >        default: {
422 >               sprintf(painCave.errMsg,
423 >                       "DumpReader Error: %s is an unrecognized type\n", type.c_str());
424 >               painCave.isFatal = 1;
425 >               simError();
426 >          break;  
427 >        }
428  
239 –      eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
240 –      if(eof_test == NULL){
241 –        sprintf(painCave.errMsg,
242 –              "error in reading file %s\n"
243 –              "natoms  = %d; index = %d\n"
244 –              "error reading the line from the file.\n",
245 –              inFileName.c_str(), nTotObjs, i );
246 –        painCave.isFatal = 1;
247 –        simError();
429        }
249 –      
250 –      parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
251 –      if( parseErr != NULL ){
252 –        strcpy( painCave.errMsg, parseErr );
253 –        painCave.isFatal = 1;
254 –        simError();
255 –      }
430      }
431 <  }
431 >    
432 >  }
433 >  
434  
435 <  // MPI Section of code..........
260 < #else //IS_MPI
435 >  void  DumpReader::readStuntDoubles(std::istream& inputStream) {
436  
437 <  // first thing first, suspend fatalities.
438 <  painCave.isEventLoop = 1;
439 <
440 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
441 <  int haveError;
442 <
443 <  MPI_Status istatus;
444 <  int *MolToProcMap = mpiSim->getMolToProcMap();
270 <  int localIndex;
271 <  int nCurObj;
272 <  int nitems;
273 <
274 <  nTotObjs = simnfo->getTotIntegrableObjects();
275 <  haveError = 0;
276 <  if (worldRank == 0) {
277 <     fsetpos(inFile,  framePos[whichFrame]);
278 <
279 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
280 <    if( eof_test == NULL ){
281 <      sprintf( painCave.errMsg,
282 <               "Error reading 1st line of %s \n ",inFileName.c_str());
283 <      haveError = 1;
284 <      simError();
437 >    inputStream.getline(buffer, bufferSize);
438 >    std::string line(buffer);
439 >    
440 >    if (line.find("<StuntDoubles>") == std::string::npos) {
441 >      sprintf(painCave.errMsg,
442 >              "DumpReader Error: Missing <StuntDoubles>\n");
443 >      painCave.isFatal = 1;
444 >      simError();
445      }
446  
447 <    nitems = atoi( read_buffer );
448 <
289 <    // Check to see that the number of integrable objects in the
290 <    // intial configuration file is the same as derived from the
291 <    // meta-data file.
292 <
293 <    if( nTotObjs != nitems){
294 <      sprintf( painCave.errMsg,
295 <               "DumpReader Error. %s nIntegrable, %d, "
296 <               "does not match the meta-data file's nIntegrable, %d.\n",
297 <               inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
298 <      haveError= 1;
299 <      simError();
300 <    }
301 <
302 <    //read the boxMat from the comment line
303 <
304 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
305 <    if(eof_test == NULL){
306 <      sprintf( painCave.errMsg,
307 <               "error in reading commment in %s\n", inFileName.c_str());
308 <      haveError = 1;
309 <      simError();
310 <    }
311 <
312 <    //Every single processor will parse the comment line by itself
313 <    //By using this way, we might lose some efficiency, but if we want to add
314 <    //more parameters into comment line, we only need to modify function
315 <    //parseCommentLine
316 <
317 <    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
318 <
319 <    parseErr = parseCommentLine( read_buffer, simnfo);
320 <
321 <    if( parseErr != NULL ){
322 <      strcpy( painCave.errMsg, parseErr );
323 <      haveError = 1;
324 <      simError();
325 <    }
326 <
327 <    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
328 <      which_node = MolToProcMap[i];
329 <      if(which_node == 0){
330 <       //molecules belong to master node
331 <
332 <      localIndex = mpiSim->getGlobalToLocalMol(i);
333 <
334 <      if(localIndex == -1) {
335 <        strcpy(painCave.errMsg, "Molecule not found on node 0!");
336 <        haveError = 1;
337 <        simError();
338 <      }
339 <
340 <       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
341 <       for(j=0; j < integrableObjects.size(); j++){
342 <        
343 <          eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
344 <          if(eof_test == NULL){
345 <                sprintf(painCave.errMsg,
346 <                    "error in reading file %s\n"
347 <                    "natoms  = %d; index = %d\n"
348 <                    "error reading the line from the file.\n",
349 <                    inFileName.c_str(), nTotObjs, i );
350 <                haveError= 1;
351 <                simError();
352 <          }
353 <          
354 <          if(haveError) nodeZeroError();
355 <
356 <          parseDumpLine(read_buffer, integrableObjects[j]);
357 <          
358 <       }
359 <
360 <
361 <      }
362 <      else{
363 <      //molecule belongs to slave nodes
364 <
365 <        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
366 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
447 >    while(inputStream.getline(buffer, bufferSize)) {
448 >      line = buffer;
449        
450 <       for(j=0; j < nCurObj; j++){
451 <        
370 <          eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
371 <          if(eof_test == NULL){
372 <                sprintf(painCave.errMsg,
373 <                    "error in reading file %s\n"
374 <                    "natoms  = %d; index = %d\n"
375 <                    "error reading the line from the file.\n",
376 <                    inFileName.c_str(), nTotObjs, i );
377 <                haveError= 1;
378 <                simError();
379 <          }
380 <          
381 <          if(haveError) nodeZeroError();
382 <
383 <            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
384 <                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
385 <          
386 <       }
387 <
450 >      if(line.find("</StuntDoubles>") != std::string::npos) {
451 >        break;
452        }
389 –      
390 –    }
391 –    
392 –  }
393 –  else{
394 –  //actions taken at slave nodes
395 –    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
453  
454 <    parseErr = parseCommentLine( read_buffer, simnfo);
398 <
399 <    if( parseErr != NULL ){
400 <      strcpy( painCave.errMsg, parseErr );
401 <      haveError = 1;
402 <      simError();
454 >      parseDumpLine(line);
455      }
456    
405 –    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
406 –      which_node = MolToProcMap[i];
407 –      
408 –      if(which_node == worldRank){
409 –      //molecule with global index i belongs to this processor
410 –      
411 –        localIndex = mpiSim->getGlobalToLocalMol(i);
412 –
413 –        if(localIndex == -1) {
414 –          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
415 –          haveError = 1;
416 –          simError();
417 –        }
418 –
419 –        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
420 –
421 –        nCurObj = integrableObjects.size();
422 –        
423 –        MPI_Send(&nCurObj, 1, MPI_INT, 0,
424 –                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
425 –
426 –        for(j = 0; j < integrableObjects.size(); j++){
427 –
428 –          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
429 –                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
430 –
431 –          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
432 –
433 –          if( parseErr != NULL ){
434 –                strcpy( painCave.errMsg, parseErr );
435 –                simError();
436 –          }
437 –
438 –        }
439 –          
440 –      }
441 –      
442 –    }
443 –
457    }
458  
459 < #endif
447 < }
459 >  void DumpReader::readFrameProperties(std::istream& inputStream) {
460  
461 < char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
461 >    Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
462 >    inputStream.getline(buffer, bufferSize);
463 >    std::string line(buffer);
464  
465 <  char *foo; // the pointer to the current string token
466 <
467 <  double pos[3]; // position place holders
468 <  double vel[3]; // velocity placeholders
469 <  double q[4]; // the quaternions
456 <  double ji[3]; // angular velocity placeholders;
457 <  double qSqr, qLength; // needed to normalize the quaternion vector.
458 <
459 <
460 <  // set the string tokenizer
461 <
462 <  foo = strtok(readLine, " ,;\t");
463 <
464 <  // check the atom name to the current atom
465 <
466 <  if( strcmp( foo, sd->getType() ) ){
467 <    sprintf( painCave.errMsg,
468 <             "DumpReader error.  Does not"
469 <             " match the meta-data atom %s.\n",
470 <             sd->getType() );
471 <    return strdup( painCave.errMsg );
472 <  }
473 <
474 <  // get the positions
475 <
476 <  foo = strtok(NULL, " ,;\t");
477 <  if(foo == NULL){
478 <    sprintf( painCave.errMsg,
479 <             "error in reading postition x from %s\n",
480 <             inFileName.c_str());
481 <    return strdup( painCave.errMsg );
482 <  }
483 <  pos[0] = atof( foo );
484 <
485 <  foo = strtok(NULL, " ,;\t");
486 <  if(foo == NULL){
487 <    sprintf( painCave.errMsg,
488 <             "error in reading postition y from %s\n",
489 <             inFileName.c_str());
490 <    return strdup( painCave.errMsg );
491 <  }
492 <  pos[1] = atof( foo );
493 <
494 <  foo = strtok(NULL, " ,;\t");
495 <  if(foo == NULL){
496 <    sprintf( painCave.errMsg,
497 <             "error in reading postition z from %s\n",
498 <             inFileName.c_str());
499 <    return strdup( painCave.errMsg );
500 <  }
501 <  pos[2] = atof( foo );
502 <
503 <
504 <  // get the velocities
505 <
506 <  foo = strtok(NULL, " ,;\t");
507 <  if(foo == NULL){
508 <    sprintf( painCave.errMsg,
509 <             "error in reading velocity x from %s\n",
510 <             inFileName.c_str() );
511 <    return strdup( painCave.errMsg );
512 <  }
513 <  vel[0] = atof( foo );
514 <
515 <  foo = strtok(NULL, " ,;\t");
516 <  if(foo == NULL){
517 <    sprintf( painCave.errMsg,
518 <             "error in reading velocity x from %s\n",
519 <             inFileName.c_str() );
520 <    return strdup( painCave.errMsg );
521 <  }
522 <  vel[1] = atof( foo );
523 <
524 <  foo = strtok(NULL, " ,;\t");
525 <  if(foo == NULL){
526 <    sprintf( painCave.errMsg,
527 <             "error in reading velocity x from %s\n",
528 <             inFileName.c_str() );
529 <    return strdup( painCave.errMsg );
530 <  }
531 <  vel[2] = atof( foo );
532 <
533 <
534 <  // add the positions and velocities to the atom
535 <
536 <  sd->setPos( pos );
537 <  sd->setVel( vel );
538 <
539 <  if (!sd->isDirectional())
540 <    return NULL;
541 <
542 <  // get the quaternions
543 <
544 <  if( sd->isDirectional() ){
545 <
546 <    foo = strtok(NULL, " ,;\t");
547 <    if(foo == NULL){
548 <      sprintf( painCave.errMsg,
549 <                     "error in reading velocity x from %s\n",
550 <                      inFileName.c_str() );
551 <      return strdup( painCave.errMsg );
465 >    if (line.find("<FrameData>") == std::string::npos) {
466 >      sprintf(painCave.errMsg,
467 >              "DumpReader Error: Missing <FrameData>\n");
468 >      painCave.isFatal = 1;
469 >      simError();
470      }
553 –    q[0] = atof( foo );
471  
472 <    foo = strtok(NULL, " ,;\t");
473 <    if(foo == NULL){
557 <      sprintf( painCave.errMsg,
558 <                     "error in reading velocity x from %s\n",
559 <                      inFileName.c_str() );
560 <      return strdup( painCave.errMsg );
561 <    }
562 <    q[1] = atof( foo );
563 <
564 <    foo = strtok(NULL, " ,;\t");
565 <    if(foo == NULL){
566 <      sprintf( painCave.errMsg,
567 <                     "error in reading velocity x from %s\n",
568 <                      inFileName.c_str() );
569 <      return strdup( painCave.errMsg );
570 <    }
571 <    q[2] = atof( foo );
572 <
573 <    foo = strtok(NULL, " ,;\t");
574 <    if(foo == NULL){
575 <      sprintf( painCave.errMsg,
576 <                     "error in reading velocity x from %s\n",
577 <                      inFileName.c_str() );
578 <      return strdup( painCave.errMsg );
579 <    }
580 <    q[3] = atof( foo );
581 <
582 <    // get the angular velocities
583 <
584 <    foo = strtok(NULL, " ,;\t");
585 <    if(foo == NULL){
586 <      sprintf( painCave.errMsg,
587 <                     "error in reading velocity x from %s\n",
588 <                      inFileName.c_str() );
589 <      return strdup( painCave.errMsg );
590 <    }
591 <    ji[0] = atof( foo );
592 <
593 <    foo = strtok(NULL, " ,;\t");
594 <    if(foo == NULL){
595 <      sprintf( painCave.errMsg,
596 <                     "error in reading velocity x from %s\n",
597 <                      inFileName.c_str() );
598 <      return strdup( painCave.errMsg );
599 <    }
600 <    ji[1] = atof(foo );
601 <
602 <    foo = strtok(NULL, " ,;\t");
603 <    if(foo == NULL){
604 <      sprintf( painCave.errMsg,
605 <                     "error in reading velocity x from %s\n",
606 <                      inFileName.c_str() );
607 <      return strdup( painCave.errMsg );
608 <    }
609 <    ji[2] = atof( foo );
610 <
611 <
612 <    // check that the quaternion vector is normalized
613 <
614 <    qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
615 <
616 <    if (fabs(qSqr) < 1e-6) {
617 <      sprintf(painCave.errMsg,
618 <          "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
619 <       return strdup(painCave.errMsg);
620 <    }
621 <
622 <    qLength = sqrt( qSqr );
623 <    q[0] = q[0] / qLength;
624 <    q[1] = q[1] / qLength;
625 <    q[2] = q[2] / qLength;
626 <    q[3] = q[3] / qLength;
627 <
628 <    // add quaternion and angular velocities
629 <
630 <    sd->setQ( q );
631 <    sd->setJ( ji );
632 <  }
633 <
634 <
635 <
636 <  return NULL;
637 < }
638 <
639 <
640 < char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){
641 <
642 <  double currTime;
643 <  double boxMat[9];
644 <  double theBoxMat3[3][3];
645 <  double chi;
646 <  double integralOfChidt;
647 <  double eta[9];
648 <
649 <  char *foo; // the pointer to the current string token
650 <
651 <  // set the string tokenizer
652 <
653 <  foo = strtok(readLine, " ,;\t");
654 <  // set the timeToken.
655 <
656 <  if(foo == NULL){
657 <    sprintf( painCave.errMsg,
658 <             "error in reading Time from %s\n",
659 <             inFileName.c_str() );
660 <    return strdup( painCave.errMsg );
661 <  }
662 <
663 <  currTime = atof( foo );
664 <  entry_plug->setTime( currTime );
665 <
666 <  //get H-Matrix
667 <
668 <  for(int i = 0 ; i < 9; i++){
669 <    foo = strtok(NULL, " ,;\t");
670 <    if(foo == NULL){
671 <      sprintf( painCave.errMsg,
672 <               "error in reading H[%d] from %s\n", i, inFileName.c_str() );
673 <      return strdup( painCave.errMsg );
674 <    }
675 <    boxMat[i] = atof( foo );
676 <  }
677 <
678 <  for(int i=0;i<3;i++)
679 <    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
680 <
681 <  //set H-Matrix
682 <  entry_plug->setBoxM( theBoxMat3 );
683 <
684 <  //get chi and integralOfChidt, they should appear by pair
685 <
686 <  if( entry_plug->useInitXSstate ){
687 <    foo = strtok(NULL, " ,;\t\n");
688 <    if(foo != NULL){
689 <      chi = atof(foo);
472 >    while(inputStream.getline(buffer, bufferSize)) {
473 >      line = buffer;
474        
475 <      foo = strtok(NULL, " ,;\t\n");
476 <      if(foo == NULL){
693 <        sprintf( painCave.errMsg,
694 <                 "chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() );
695 <        return strdup( painCave.errMsg );
475 >      if(line.find("</FrameData>") != std::string::npos) {
476 >        break;
477        }
697 –      integralOfChidt = atof( foo );
478        
479 <      //push chi and integralOfChidt into SimInfo::properties which can be
480 <      //retrieved by integrator later
481 <      DoubleData* chiValue = new DoubleData();
482 <      chiValue->setID(CHIVALUE_ID);
483 <      chiValue->setData(chi);
484 <      entry_plug->addProperty(chiValue);
479 >      StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
480 >      if (!tokenizer.hasMoreTokens()) {
481 >        sprintf(painCave.errMsg,
482 >                "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
483 >        painCave.isFatal = 1;
484 >        simError();      
485 >      }
486 >
487 >      std::string propertyName = tokenizer.nextToken();
488 >      if (propertyName == "Time") {
489 >        RealType currTime = tokenizer.nextTokenAsDouble();
490 >        s->setTime(currTime);
491 >      } else if (propertyName == "Hmat"){
492 >        Mat3x3d hmat;
493 >        hmat(0, 0) = tokenizer.nextTokenAsDouble();
494 >        hmat(0, 1) = tokenizer.nextTokenAsDouble();
495 >        hmat(0, 2) = tokenizer.nextTokenAsDouble();
496 >        hmat(1, 0) = tokenizer.nextTokenAsDouble();
497 >        hmat(1, 1) = tokenizer.nextTokenAsDouble();
498 >        hmat(1, 2) = tokenizer.nextTokenAsDouble();
499 >        hmat(2, 0) = tokenizer.nextTokenAsDouble();
500 >        hmat(2, 1) = tokenizer.nextTokenAsDouble();
501 >        hmat(2, 2) = tokenizer.nextTokenAsDouble();
502 >        s->setHmat(hmat);      
503 >      } else if (propertyName == "Thermostat") {
504 >        RealType chi = tokenizer.nextTokenAsDouble();
505 >        RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
506 >        s->setChi(chi);
507 >        s->setIntegralOfChiDt(integralOfChiDt);        
508 >     } else if (propertyName == "Barostat") {
509 >        Mat3x3d eta;
510 >        eta(0, 0) = tokenizer.nextTokenAsDouble();
511 >        eta(0, 1) = tokenizer.nextTokenAsDouble();
512 >        eta(0, 2) = tokenizer.nextTokenAsDouble();
513 >        eta(1, 0) = tokenizer.nextTokenAsDouble();
514 >        eta(1, 1) = tokenizer.nextTokenAsDouble();
515 >        eta(1, 2) = tokenizer.nextTokenAsDouble();
516 >        eta(2, 0) = tokenizer.nextTokenAsDouble();
517 >        eta(2, 1) = tokenizer.nextTokenAsDouble();
518 >        eta(2, 2) = tokenizer.nextTokenAsDouble();
519 >        s->setEta(eta);
520 >      } else {
521 >        sprintf(painCave.errMsg,
522 >                "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
523 >        painCave.isFatal = 0;
524 >        simError();        
525 >      }
526        
706 –      DoubleData* integralOfChidtValue = new DoubleData();
707 –      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
708 –      integralOfChidtValue->setData(integralOfChidt);
709 –      entry_plug->addProperty(integralOfChidtValue);
710 –      
527      }
712 –    else
713 –      return NULL;
714 –    
715 –    //get eta
716 –    foo = strtok(NULL, " ,;\t\n");
717 –    if(foo != NULL ){
718 –  
719 –      for(int i = 0 ; i < 9; i++){
720 –        
721 –        if(foo == NULL){
722 –          sprintf( painCave.errMsg,
723 –                   "error in reading eta[%d] from %s\n", i, inFileName.c_str() );
724 –          return strdup( painCave.errMsg );
725 –        }
726 –        eta[i] = atof( foo );
727 –        foo = strtok(NULL, " ,;\t\n");
728 –      }
729 –    }
730 –    else
731 –      return NULL;
732 –    
733 –    //push eta into SimInfo::properties which can be
734 –    //retrieved by integrator later
735 –    //entry_plug->setBoxM( theBoxMat3 );
736 –    DoubleArrayData* etaValue = new DoubleArrayData();
737 –    etaValue->setID(ETAVALUE_ID);
738 –    etaValue->setData(eta, 9);
739 –    entry_plug->addProperty(etaValue);
740 –  }
528  
742 –  return NULL;
743 – }
744 –
745 – #ifdef IS_MPI
746 – void DumpReader::nodeZeroError( void ){
747 –  int j, myStatus;
748 –
749 –  myStatus = 0;
750 –  for (j = 0; j < mpiSim->getNProcessors(); j++) {
751 –    MPI_Send( &myStatus, 1, MPI_INT, j,
752 –              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
529    }
530  
531 <
532 <  MPI_Finalize();
757 <  exit (0);
758 <
759 < }
760 <
761 < void DumpReader::anonymousNodeDie( void ){
762 <
763 <  MPI_Finalize();
764 <  exit (0);
765 < }
766 < #endif
531 >  
532 > }//end namespace oopse

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