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root/group/trunk/OOPSE-4/src/io/DumpReader.cpp
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Comparing trunk/OOPSE-4/src/io/DumpReader.cpp (file contents):
Revision 1625 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 3102 by gezelter, Fri Dec 29 21:43:18 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 "io/ReadWrite.hpp"
16 < #include "utils/simError.h"
17 <
18 < #ifdef IS_MPI
19 < #include <mpi.h>
20 < #include "brains/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), needCOMprops_(false) {
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 +    if (needCOMprops_) {
245 +      Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246 +      Vector3d com;
247 +      Vector3d comvel;
248 +      Vector3d comw;
249 +      info_->getComAll(com, comvel);
250 +      comw = info_->getAngularMomentum();
251 +      s->setCOMprops(com, comvel, comw);      
252 +    }
253  
254 +  }
255 +  
256 +  void DumpReader::readSet(int whichFrame) {    
257 +    std::string line;
258  
259 < void DumpReader :: readSet( int whichFrame ){
259 > #ifndef IS_MPI
260  
261 <  int i;
262 <  unsigned int j;
261 >    inFile_->clear();  
262 >    inFile_->seekg(framePos_[whichFrame]);
263  
264 < #ifdef IS_MPI
178 <  int done, which_node, which_atom; // loop counter
179 < #endif //is_mpi
264 >    std::istream& inputStream = *inFile_;    
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 > #else
267 >    int masterNode = 0;
268 >    std::stringstream sstream;
269 >    if (worldRank == masterNode) {
270 >      std::string sendBuffer;
271  
272 <  char *eof_test; // ptr to see when we reach the end of the file
273 <  char *parseErr;
272 >      inFile_->clear();  
273 >      inFile_->seekg(framePos_[whichFrame]);
274 >      
275 >      while (inFile_->getline(buffer, bufferSize)) {
276  
277 <  vector<StuntDouble*> integrableObjects;
277 >        line = buffer;
278 >        sendBuffer += line;
279 >        sendBuffer += '\n';
280 >        if (line.find("</Snapshot>") != std::string::npos) {
281 >          break;
282 >        }        
283 >      }
284  
285 +      int sendBufferSize = sendBuffer.size();
286 +      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
287 +      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
288 +      
289 +      sstream.str(sendBuffer);
290 +    } else {
291 +      int sendBufferSize;
292 +      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
293 +      char * recvBuffer = new char[sendBufferSize+1];
294 +      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
295 +      sstream.str(recvBuffer);
296 +    }      
297  
298 < #ifndef IS_MPI
298 >    std::istream& inputStream = sstream;  
299 > #endif
300  
301 <  fsetpos(inFile, framePos[whichFrame]);
194 <  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 <  }
301 >    inputStream.getline(buffer, bufferSize);
302  
303 <  nTotObjs = atoi( read_buffer );
303 >    line = buffer;
304 >    if (line.find("<Snapshot>") == std::string::npos) {
305 >      sprintf(painCave.errMsg,
306 >              "DumpReader Error: can not find <Snapshot>\n");
307 >      painCave.isFatal = 1;
308 >      simError();
309 >    }
310 >    
311 >    //read frameData
312 >    readFrameProperties(inputStream);
313  
314 <  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
315 <    sprintf( painCave.errMsg,
207 <             "DumpReader error. %s nIntegrable, %d, "
208 <             "does not match the meta-data file's nIntegrable, %d.\n",
209 <             inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
210 <    painCave.isFatal = 1;
211 <    simError();
212 <  }
314 >    //read StuntDoubles
315 >    readStuntDoubles(inputStream);    
316  
317 <  //read the box mat from the comment line
317 >    inputStream.getline(buffer, bufferSize);
318 >    line = buffer;
319 >    if (line.find("</Snapshot>") == std::string::npos) {
320 >      sprintf(painCave.errMsg,
321 >              "DumpReader Error: can not find </Snapshot>\n");
322 >      painCave.isFatal = 1;
323 >      simError();
324 >    }        
325 >  
326 >  }
327 >  
328 >  void DumpReader::parseDumpLine(const std::string& line) {
329  
330 <  eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
331 <  if(eof_test == NULL){
332 <    sprintf( painCave.errMsg,
333 <             "error in reading commment in %s\n", inFileName.c_str());
334 <    painCave.isFatal = 1;
335 <    simError();
336 <  }
330 >      
331 >    StringTokenizer tokenizer(line);
332 >    int nTokens;
333 >    
334 >    nTokens = tokenizer.countTokens();
335 >    
336 >    if (nTokens < 2) {
337 >      sprintf(painCave.errMsg,
338 >              "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
339 >      painCave.isFatal = 1;
340 >      simError();
341 >    }
342  
343 <  parseErr = parseCommentLine( read_buffer, simnfo);
344 <  if( parseErr != NULL ){
345 <    strcpy( painCave.errMsg, parseErr );
227 <    painCave.isFatal = 1;
228 <    simError();
229 <  }
343 >    int index = tokenizer.nextTokenAsInt();
344 >
345 >    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
346  
347 <  //parse dump lines
347 >    if (integrableObject == NULL) {
348 >      return;
349 >    }
350 >    std::string type = tokenizer.nextToken();
351 >    int size = type.size();
352  
353 <  for( i=0; i < simnfo->n_mol; i++){
353 >    for(int i = 0; i < size; ++i) {
354 >      switch(type[i]) {
355 >        
356 >        case 'p': {
357 >            Vector3d pos;
358 >            pos[0] = tokenizer.nextTokenAsDouble();
359 >            pos[1] = tokenizer.nextTokenAsDouble();
360 >            pos[2] = tokenizer.nextTokenAsDouble();
361 >            if (needPos_) {
362 >              integrableObject->setPos(pos);
363 >            }            
364 >            break;
365 >        }
366 >        case 'v' : {
367 >            Vector3d vel;
368 >            vel[0] = tokenizer.nextTokenAsDouble();
369 >            vel[1] = tokenizer.nextTokenAsDouble();
370 >            vel[2] = tokenizer.nextTokenAsDouble();
371 >            if (needVel_) {
372 >              integrableObject->setVel(vel);
373 >            }
374 >            break;
375 >        }
376  
377 <    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
377 >        case 'q' : {
378 >           Quat4d q;
379 >           if (integrableObject->isDirectional()) {
380 >              
381 >             q[0] = tokenizer.nextTokenAsDouble();
382 >             q[1] = tokenizer.nextTokenAsDouble();
383 >             q[2] = tokenizer.nextTokenAsDouble();
384 >             q[3] = tokenizer.nextTokenAsDouble();
385 >              
386 >             RealType qlen = q.length();
387 >             if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
388 >                
389 >               sprintf(painCave.errMsg,
390 >                       "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
391 >               painCave.isFatal = 1;
392 >               simError();
393 >                
394 >             }  
395 >              
396 >             q.normalize();
397 >             if (needQuaternion_) {            
398 >               integrableObject->setQ(q);
399 >             }              
400 >           }            
401 >           break;
402 >        }  
403 >        case 'j' : {
404 >          Vector3d ji;
405 >          if (integrableObject->isDirectional()) {
406 >             ji[0] = tokenizer.nextTokenAsDouble();
407 >             ji[1] = tokenizer.nextTokenAsDouble();
408 >             ji[2] = tokenizer.nextTokenAsDouble();
409 >             if (needAngMom_) {
410 >               integrableObject->setJ(ji);
411 >             }
412 >          }
413 >          break;
414 >        }  
415 >        case 'f': {
416  
417 <    for(j = 0; j < integrableObjects.size(); j++){
417 >          Vector3d force;
418 >          force[0] = tokenizer.nextTokenAsDouble();
419 >          force[1] = tokenizer.nextTokenAsDouble();
420 >          force[2] = tokenizer.nextTokenAsDouble();          
421 >          integrableObject->setFrc(force);
422 >          break;
423 >        }
424 >        case 't' : {
425 >
426 >           Vector3d torque;
427 >           torque[0] = tokenizer.nextTokenAsDouble();
428 >           torque[1] = tokenizer.nextTokenAsDouble();
429 >           torque[2] = tokenizer.nextTokenAsDouble();          
430 >           integrableObject->setTrq(torque);          
431 >           break;
432 >        }
433 >        default: {
434 >               sprintf(painCave.errMsg,
435 >                       "DumpReader Error: %s is an unrecognized type\n", type.c_str());
436 >               painCave.isFatal = 1;
437 >               simError();
438 >          break;  
439 >        }
440  
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();
441        }
249 –      
250 –      parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
251 –      if( parseErr != NULL ){
252 –        strcpy( painCave.errMsg, parseErr );
253 –        painCave.isFatal = 1;
254 –        simError();
255 –      }
442      }
443 <  }
443 >    
444 >  }
445 >  
446  
447 <  // MPI Section of code..........
260 < #else //IS_MPI
447 >  void  DumpReader::readStuntDoubles(std::istream& inputStream) {
448  
449 <  // first thing first, suspend fatalities.
450 <  painCave.isEventLoop = 1;
451 <
452 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
453 <  int haveError;
454 <
455 <  MPI_Status istatus;
456 <  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();
449 >    inputStream.getline(buffer, bufferSize);
450 >    std::string line(buffer);
451 >    
452 >    if (line.find("<StuntDoubles>") == std::string::npos) {
453 >      sprintf(painCave.errMsg,
454 >              "DumpReader Error: Missing <StuntDoubles>\n");
455 >      painCave.isFatal = 1;
456 >      simError();
457      }
458  
459 <    nitems = atoi( read_buffer );
460 <
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);
459 >    while(inputStream.getline(buffer, bufferSize)) {
460 >      line = buffer;
461        
462 <       for(j=0; j < nCurObj; j++){
463 <        
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 <
462 >      if(line.find("</StuntDoubles>") != std::string::npos) {
463 >        break;
464        }
389 –      
390 –    }
391 –    
392 –  }
393 –  else{
394 –  //actions taken at slave nodes
395 –    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
465  
466 <    parseErr = parseCommentLine( read_buffer, simnfo);
398 <
399 <    if( parseErr != NULL ){
400 <      strcpy( painCave.errMsg, parseErr );
401 <      haveError = 1;
402 <      simError();
466 >      parseDumpLine(line);
467      }
468    
469 <    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);
469 >  }
470  
471 <        if(localIndex == -1) {
414 <          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
415 <          haveError = 1;
416 <          simError();
417 <        }
471 >  void DumpReader::readFrameProperties(std::istream& inputStream) {
472  
473 <        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
473 >    Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
474 >    inputStream.getline(buffer, bufferSize);
475 >    std::string line(buffer);
476  
477 <        nCurObj = integrableObjects.size();
478 <        
479 <        MPI_Send(&nCurObj, 1, MPI_INT, 0,
480 <                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
477 >    if (line.find("<FrameData>") == std::string::npos) {
478 >      sprintf(painCave.errMsg,
479 >              "DumpReader Error: Missing <FrameData>\n");
480 >      painCave.isFatal = 1;
481 >      simError();
482 >    }
483  
484 <        for(j = 0; j < integrableObjects.size(); j++){
485 <
486 <          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
487 <                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
488 <
431 <          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
432 <
433 <          if( parseErr != NULL ){
434 <                strcpy( painCave.errMsg, parseErr );
435 <                simError();
436 <          }
437 <
438 <        }
439 <          
484 >    while(inputStream.getline(buffer, bufferSize)) {
485 >      line = buffer;
486 >      
487 >      if(line.find("</FrameData>") != std::string::npos) {
488 >        break;
489        }
490        
491 <    }
491 >      StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
492 >      if (!tokenizer.hasMoreTokens()) {
493 >        sprintf(painCave.errMsg,
494 >                "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
495 >        painCave.isFatal = 1;
496 >        simError();      
497 >      }
498  
499 <  }
500 <
501 < #endif
502 < }
503 <
504 < char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
505 <
506 <  char *foo; // the pointer to the current string token
507 <
508 <  double pos[3]; // position place holders
509 <  double vel[3]; // velocity placeholders
510 <  double q[4]; // the quaternions
511 <  double ji[3]; // angular velocity placeholders;
512 <  double qSqr, qLength; // needed to normalize the quaternion vector.
513 <
514 <
515 <  // set the string tokenizer
516 <
517 <  foo = strtok(readLine, " ,;\t");
518 <
519 <  // check the atom name to the current atom
520 <
521 <  if( strcmp( foo, sd->getType() ) ){
522 <    sprintf( painCave.errMsg,
523 <             "DumpReader error.  Does not"
524 <             " match the meta-data atom %s.\n",
525 <             sd->getType() );
526 <    return strdup( painCave.errMsg );
527 <  }
528 <
529 <  // get the positions
530 <
531 <  foo = strtok(NULL, " ,;\t");
532 <  if(foo == NULL){
533 <    sprintf( painCave.errMsg,
534 <             "error in reading postition x from %s\n",
535 <             inFileName.c_str());
536 <    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 );
552 <    }
553 <    q[0] = atof( foo );
554 <
555 <    foo = strtok(NULL, " ,;\t");
556 <    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);
690 <      
691 <      foo = strtok(NULL, " ,;\t\n");
692 <      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 );
499 >      std::string propertyName = tokenizer.nextToken();
500 >      if (propertyName == "Time") {
501 >        RealType currTime = tokenizer.nextTokenAsDouble();
502 >        s->setTime(currTime);
503 >      } else if (propertyName == "Hmat"){
504 >        Mat3x3d hmat;
505 >        hmat(0, 0) = tokenizer.nextTokenAsDouble();
506 >        hmat(0, 1) = tokenizer.nextTokenAsDouble();
507 >        hmat(0, 2) = tokenizer.nextTokenAsDouble();
508 >        hmat(1, 0) = tokenizer.nextTokenAsDouble();
509 >        hmat(1, 1) = tokenizer.nextTokenAsDouble();
510 >        hmat(1, 2) = tokenizer.nextTokenAsDouble();
511 >        hmat(2, 0) = tokenizer.nextTokenAsDouble();
512 >        hmat(2, 1) = tokenizer.nextTokenAsDouble();
513 >        hmat(2, 2) = tokenizer.nextTokenAsDouble();
514 >        s->setHmat(hmat);      
515 >      } else if (propertyName == "Thermostat") {
516 >        RealType chi = tokenizer.nextTokenAsDouble();
517 >        RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
518 >        s->setChi(chi);
519 >        s->setIntegralOfChiDt(integralOfChiDt);        
520 >     } else if (propertyName == "Barostat") {
521 >        Mat3x3d eta;
522 >        eta(0, 0) = tokenizer.nextTokenAsDouble();
523 >        eta(0, 1) = tokenizer.nextTokenAsDouble();
524 >        eta(0, 2) = tokenizer.nextTokenAsDouble();
525 >        eta(1, 0) = tokenizer.nextTokenAsDouble();
526 >        eta(1, 1) = tokenizer.nextTokenAsDouble();
527 >        eta(1, 2) = tokenizer.nextTokenAsDouble();
528 >        eta(2, 0) = tokenizer.nextTokenAsDouble();
529 >        eta(2, 1) = tokenizer.nextTokenAsDouble();
530 >        eta(2, 2) = tokenizer.nextTokenAsDouble();
531 >        s->setEta(eta);
532 >      } else {
533 >        sprintf(painCave.errMsg,
534 >                "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
535 >        painCave.isFatal = 0;
536 >        simError();        
537        }
697 –      integralOfChidt = atof( foo );
538        
699 –      //push chi and integralOfChidt into SimInfo::properties which can be
700 –      //retrieved by integrator later
701 –      DoubleGenericData* chiValue = new DoubleGenericData();
702 –      chiValue->setID(CHIVALUE_ID);
703 –      chiValue->setData(chi);
704 –      entry_plug->addProperty(chiValue);
705 –      
706 –      DoubleGenericData* integralOfChidtValue = new DoubleGenericData();
707 –      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
708 –      integralOfChidtValue->setData(integralOfChidt);
709 –      entry_plug->addProperty(integralOfChidtValue);
710 –      
539      }
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 –    DoubleVectorGenericData* etaValue = new DoubleVectorGenericData(ETAVALUE_ID);
737 –    etaValue->insert(etaValue->end(), eta, eta+9);
738 –    entry_plug->addProperty(etaValue);
739 –  }
540  
741 –  return NULL;
742 – }
743 –
744 – #ifdef IS_MPI
745 – void DumpReader::nodeZeroError( void ){
746 –  int j, myStatus;
747 –
748 –  myStatus = 0;
749 –  for (j = 0; j < mpiSim->getNProcessors(); j++) {
750 –    MPI_Send( &myStatus, 1, MPI_INT, j,
751 –              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
541    }
542  
543 <
544 <  MPI_Finalize();
756 <  exit (0);
757 <
758 < }
759 <
760 < void DumpReader::anonymousNodeDie( void ){
761 <
762 <  MPI_Finalize();
763 <  exit (0);
764 < }
765 < #endif
543 >  
544 > }//end namespace oopse

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