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root/group/trunk/OOPSE/libmdtools/DumpReader.cpp
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Comparing trunk/OOPSE/libmdtools/DumpReader.cpp (file contents):
Revision 829 by gezelter, Tue Oct 28 16:03:37 2003 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <sys/types.h>
# Line 21 | Line 22
22   #define TAKE_THIS_TAG_INT 1
23   #endif // is_mpi
24  
24 – namespace dumpRead{
25  
26 < #ifdef IS_MPI
27 <  void nodeZeroError( void );
28 <  void anonymousNodeDie( void );
29 < #endif // is_mpi
30 <  
31 < }
26 > DumpReader :: DumpReader(const char *in_name ){
27  
33 – using namespace dumpRead;
34 –
35 –
36 – DumpReader :: DumpReader( char *in_name ){
37 –
28    isScanned = false;
39 –  headFP = new FilePos;
29  
30   #ifdef IS_MPI
31    if (worldRank == 0) {
# Line 50 | Line 39 | DumpReader :: DumpReader( char *in_name ){
39      simError();
40    }
41    
42 <  strcpy( inName, in_name);
42 >  inFileName = in_name;
43   #ifdef IS_MPI
44    }
45    strcpy( checkPointMsg, "Dump file opened for reading successfully." );
# Line 63 | Line 52 | 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", inName );
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();
68 +  
69   #ifdef IS_MPI
70    }
71    strcpy( checkPointMsg, "Dump file closed successfully." );
# Line 81 | Line 77 | int DumpReader::getNframes( void ){
77  
78   int DumpReader::getNframes( void ){
79  
80 <  if( !isScanned ) scanFile();
81 <  return nFrames;
80 >  if( !isScanned )
81 >    scanFile();
82 >  return framePos.size();
83   }
84  
85   void DumpReader::scanFile( void ){
86  
87 <  int vectorSize;
91 <  int i, j, k;
87 >  int i, j;
88    int lineNum = 0;
89    char readBuffer[2000];
94 –  char* foo;
90    fpos_t *currPos;
96 –  double time;
91  
98 –  FilePos *currFP;
99 –
100 –
92   #ifdef IS_MPI
93    if( worldRank == 0 ){
94   #endif // is_mpi
# Line 111 | Line 102 | void DumpReader::scanFile( void ){
102      if( feof( inFile ) ){
103        sprintf( painCave.errMsg,
104                 "File \"%s\" ended unexpectedly at line %d\n",
105 <               inName,
105 >               inFileName.c_str(),
106                 lineNum );
107        painCave.isFatal = 1;
108        simError();
109      }
110 <    
120 <    nFrames = 0;
110 >
111      while( !feof( inFile ) ){
112 +      
113 +      framePos.push_back(currPos);
114  
123 –      headFP->add( currPos );
124 –      nFrames++;
125 –
115        i = atoi(readBuffer);
116        
117        fgets( readBuffer, sizeof( readBuffer ), inFile );
# Line 130 | Line 119 | void DumpReader::scanFile( void ){
119        if( feof( inFile ) ){
120          sprintf( painCave.errMsg,
121                   "File \"%s\" ended unexpectedly at line %d\n",
122 <                 inName,
122 >                 inFileName.c_str(),
123                   lineNum );
124          painCave.isFatal = 1;
125          simError();
126        }
127 <      
139 < //       if(outTime){
140 < //      foo = strtok( readBuffer, " ,;\t" );
141 < //      time = atof( foo );
142 < //       }
143 <      
127 >            
128        for(j=0; j<i; j++){
129          
130          fgets( readBuffer, sizeof( readBuffer ), inFile );
# Line 149 | Line 133 | void DumpReader::scanFile( void ){
133            sprintf( painCave.errMsg,
134                     "File \"%s\" ended unexpectedly at line %d,"
135                     " with atom %d\n",
136 <                   inName,
136 >                   inFileName.c_str(),
137                     lineNum,
138                     j );
139            painCave.isFatal = 1;
# Line 166 | Line 150 | void DumpReader::scanFile( void ){
150      
151      delete currPos;
152      rewind( inFile );
153 <    
170 <    frameStart = new FilePos*[nFrames];
171 <    currFP = headFP;
172 <    for(i=0; i<nFrames; i++){
173 <      
174 <      currFP = currFP->getNext();
175 <      if( currFP == NULL ){
176 <        sprintf( painCave.errMsg,
177 <                 "DumpReader error: scanFile FilePos mismatch at "
178 <                 "nFrames = %d\n",
179 <                 i );
180 <        painCave.isFatal = 1;
181 <        simError();
182 <      }
183 <      
184 <      frameStart[i] = currFP;
185 <    }
186 <
153 >    
154      isScanned = true;
155  
156   #ifdef IS_MPI
# Line 204 | Line 171 | void DumpReader :: readSet( int whichFrame ){
171  
172   void DumpReader :: readSet( int whichFrame ){
173  
174 <  int i, j, done, which_node, which_atom; // loop counter
174 >  int i;
175 >  unsigned int j;
176  
209 –  const int BUFFERSIZE = 2000; // size of the read buffer
210 –  int n_atoms; // the number of atoms
211 –  char read_buffer[BUFFERSIZE]; //the line buffer for reading
177   #ifdef IS_MPI
178 <  char send_buffer[BUFFERSIZE];
179 < #endif
178 >  int done, which_node, which_atom; // loop counter
179 > #endif //is_mpi
180  
181 <  char *eof_test; // ptr to see when we reach the end of the file
181 >  const int BUFFERSIZE = 2000; // size of the read buffer
182 >  int nTotObjs; // the number of atoms
183 >  char read_buffer[BUFFERSIZE]; //the line buffer for reading
184 >
185 >  char *eof_test; // ptr to see when we reach the end of the file
186    char *parseErr;
218 –  int procIndex;
219 –  double boxMat[9];
220 –  double theBoxMat3[3][3];
221 –  double time;
187  
188 <  fpos_t *framePos;
224 <  
225 < #ifndef IS_MPI
226 <  
227 <  framePos = frameStart[whichFrame]->getPos();
188 >  vector<StuntDouble*> integrableObjects;
189  
229 –  
190  
191 + #ifndef IS_MPI
192  
193 +  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 <             inName );
198 >             inFileName.c_str() );
199      painCave.isFatal = 1;
200      simError();
201    }
240 –  
241 –  n_atoms = atoi( read_buffer );
202  
203 <  Atom **atoms = simnfo->atoms;
244 <  DirectionalAtom* dAtom;
203 >  nTotObjs = atoi( read_buffer );
204  
205 <  if( n_atoms != simnfo->n_atoms ){
205 >  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
206      sprintf( painCave.errMsg,
207               "DumpReader error. %s n_atoms, %d, "
208               "does not match the BASS file's n_atoms, %d.\n",
209 <             inName, n_atoms, simnfo->n_atoms );
209 >             inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
210      painCave.isFatal = 1;
211      simError();
212    }
213 <  
214 <  //read the box mat from the comment line
215 <  
213 >
214 >  //read the box mat from the comment line
215 >
216    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
217    if(eof_test == NULL){
218      sprintf( painCave.errMsg,
219 <             "error in reading commment in %s\n", inName);
219 >             "error in reading commment in %s\n", inFileName.c_str());
220      painCave.isFatal = 1;
221      simError();
222    }
223  
224 <  parseErr = parseCommentLine( read_buffer, time, boxMat );
224 >  parseErr = parseCommentLine( read_buffer, simnfo);
225    if( parseErr != NULL ){
226      strcpy( painCave.errMsg, parseErr );
227      painCave.isFatal = 1;
228      simError();
229    }
230  
231 <  simnfo->setTime( time );
273 <  
274 <  for(i=0;i<3;i++)
275 <    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
276 <  
231 >  //parse dump lines
232  
233 <  simnfo->setBoxM( theBoxMat3 );
279 <  
233 >  for( i=0; i < simnfo->n_mol; i++){
234  
235 <  for( i=0; i < n_atoms; i++){
282 <    
283 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
284 <    if(eof_test == NULL){
285 <      sprintf(painCave.errMsg,
286 <              "error in reading file %s\n"
287 <              "natoms  = %d; index = %d\n"
288 <              "error reading the line from the file.\n",
289 <              inName, n_atoms, i );
290 <      painCave.isFatal = 1;
291 <      simError();
292 <    }
235 >    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
236  
237 <    
238 <    parseErr = parseDumpLine( read_buffer, i );
239 <    if( parseErr != NULL ){
240 <      strcpy( painCave.errMsg, parseErr );
241 <      painCave.isFatal = 1;
242 <      simError();
237 >    for(j = 0; j < integrableObjects.size(); j++){
238 >
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();
248 >      }
249 >      
250 >      parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
251 >      if( parseErr != NULL ){
252 >        strcpy( painCave.errMsg, parseErr );
253 >        painCave.isFatal = 1;
254 >        simError();
255 >      }
256      }
257    }
258  
303 –
259    // MPI Section of code..........
260   #else //IS_MPI
261  
# Line 309 | Line 264 | void DumpReader :: readSet( int whichFrame ){
264  
265    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
266    int haveError;
267 <  
267 >
268    MPI_Status istatus;
269 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
269 >  int *MolToProcMap = mpiSim->getMolToProcMap();
270 >  int localIndex;
271 >  int nCurObj;
272 >  int nitems;
273  
274 <  
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 %d \n ",inName);
282 >               "Error reading 1st line of %s \n ",inFileName.c_str());
283        haveError = 1;
284        simError();
285      }
286 <    
287 <    n_atoms = atoi( read_buffer );
288 <    
289 <    Atom **atoms = simnfo->atoms;
331 <    DirectionalAtom* dAtom;
332 <
333 <    // Check to see that the number of atoms in the intial configuration file is the
286 >
287 >    nitems = atoi( read_buffer );
288 >
289 >    // Check to see that the number of integrable objects  in the intial configuration file is the
290      // same as declared in simBass.
291 <    
292 <    if( n_atoms != mpiSim->getTotAtoms() ){
291 >
292 >    if( nTotObjs != nitems){
293        sprintf( painCave.errMsg,
294 <               "Initialize from File error. %s n_atoms, %d, "
294 >               "DumpReadererror. %s n_atoms, %d, "
295                 "does not match the BASS file's n_atoms, %d.\n",
296 <               inName, n_atoms, simnfo->n_atoms );
296 >               inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
297        haveError= 1;
298        simError();
299      }
300 <    
301 <    //read the time and boxMat from the comment line
302 <    
300 >
301 >    //read the boxMat from the comment line
302 >
303      eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
304      if(eof_test == NULL){
305        sprintf( painCave.errMsg,
306 <               "error in reading commment in %s\n", inName);
307 <      haveError = 1;
308 <      simError();
309 <    }
310 <    
311 <    parseErr = parseCommentLine( read_buffer, time, boxMat );
306 >               "error in reading commment in %s\n", inFileName.c_str());
307 >      haveError = 1;
308 >      simError();
309 >    }
310 >
311 >    //Every single processor will parse the comment line by itself
312 >    //By using this way, we might lose some efficiency, but if we want to add
313 >    //more parameters into comment line, we only need to modify function
314 >    //parseCommentLine
315 >
316 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
317 >
318 >    parseErr = parseCommentLine( read_buffer, simnfo);
319 >
320      if( parseErr != NULL ){
321        strcpy( painCave.errMsg, parseErr );
322        haveError = 1;
323        simError();
324      }
325  
326 <    MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
327 <    
328 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
329 <    
330 <    if(haveError) nodeZeroError();
331 <    
332 <    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
333 <      
334 <      eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
335 <      if(eof_test == NULL){
336 <        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 <                inName, n_atoms, i );
377 <        haveError= 1;
378 <        simError();
326 >    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
327 >      which_node = MolToProcMap[i];
328 >      if(which_node == 0){
329 >       //molecules belong to master node
330 >
331 >      localIndex = mpiSim->getGlobalToLocalMol(i);
332 >
333 >      if(localIndex == -1) {
334 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
335 >        haveError = 1;
336 >        simError();
337        }
380 –    
381 –      if(haveError) nodeZeroError();
338  
339 <      // Get the Node number which wants this atom:
340 <      which_node = AtomToProcMap[i];    
341 <      if (which_node == 0) {
342 <        parseErr = parseDumpLine( read_buffer, i );
343 <        if( parseErr != NULL ){
344 <          strcpy( painCave.errMsg, parseErr );
345 <          haveError = 1;
346 <          simError();
347 <        }    
348 <        if(haveError) nodeZeroError();
349 <      }
339 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
340 >       for(j=0; j < integrableObjects.size(); j++){
341 >        
342 >          eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
343 >          if(eof_test == NULL){
344 >                sprintf(painCave.errMsg,
345 >                    "error in reading file %s\n"
346 >                    "natoms  = %d; index = %d\n"
347 >                    "error reading the line from the file.\n",
348 >                    inFileName.c_str(), nTotObjs, i );
349 >                haveError= 1;
350 >                simError();
351 >          }
352 >          
353 >          if(haveError) nodeZeroError();
354 >
355 >          parseDumpLine(read_buffer, integrableObjects[j]);
356 >          
357 >       }
358 >
359 >
360 >      }
361 >      else{
362 >      //molecule belongs to slave nodes
363 >
364 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
365 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
366        
367 <      else {
368 <      
369 <        myStatus = 1;
370 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
371 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
372 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
373 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
374 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
375 <                 MPI_COMM_WORLD);
376 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
377 <                 MPI_COMM_WORLD, &istatus);
378 <        
379 <        if(!myStatus) nodeZeroError();
367 >       for(j=0; j < nCurObj; j++){
368 >        
369 >          eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
370 >          if(eof_test == NULL){
371 >                sprintf(painCave.errMsg,
372 >                    "error in reading file %s\n"
373 >                    "natoms  = %d; index = %d\n"
374 >                    "error reading the line from the file.\n",
375 >                    inFileName.c_str(), nTotObjs, i );
376 >                haveError= 1;
377 >                simError();
378 >          }
379 >          
380 >          if(haveError) nodeZeroError();
381 >
382 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
383 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
384 >          
385 >       }
386 >
387        }
388 +      
389      }
410 –    myStatus = -1;
411 –    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
412 –      MPI_Send( &myStatus, 1, MPI_INT, j,
413 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
414 –    }
390      
391 <  } else {
392 <    
393 <    MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
394 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
391 >  }
392 >  else{
393 >  //actions taken at slave nodes
394 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
395  
396 <    done = 0;
422 <    while (!done) {
396 >    parseErr = parseCommentLine( read_buffer, simnfo);
397  
398 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
399 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
398 >    if( parseErr != NULL ){
399 >      strcpy( painCave.errMsg, parseErr );
400 >      haveError = 1;
401 >      simError();
402 >    }
403 >  
404 >    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
405 >      which_node = MolToProcMap[i];
406        
407 <      if(!myStatus) anonymousNodeDie();
407 >      if(which_node == worldRank){
408 >      //molecule with global index i belongs to this processor
409        
410 <      if(myStatus < 0) break;
410 >        localIndex = mpiSim->getGlobalToLocalMol(i);
411  
412 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
413 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
414 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
415 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
416 <      
417 <      myStatus = 1;
418 <      parseErr = parseDumpLine( read_buffer, which_atom );
419 <      if( parseErr != NULL ){
420 <        strcpy( painCave.errMsg, parseErr );
421 <        myStatus = 0;;
422 <        simError();
412 >        if(localIndex == -1) {
413 >          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
414 >          haveError = 1;
415 >          simError();
416 >        }
417 >
418 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
419 >
420 >        nCurObj = integrableObjects.size();
421 >        
422 >        MPI_Send(&nCurObj, 1, MPI_INT, 0,
423 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
424 >
425 >        for(j = 0; j < integrableObjects.size(); j++){
426 >
427 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
428 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
429 >
430 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
431 >
432 >          if( parseErr != NULL ){
433 >                strcpy( painCave.errMsg, parseErr );
434 >                simError();
435 >          }
436 >
437 >        }
438 >          
439        }
440        
444 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
445 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
446 –      
441      }
442 +
443    }
449 –    
450 – // last  thing last, enable  fatalities.
451 –  painCave.isEventLoop = 0;
444  
453 –  simnfo->setTime( time );
454 –
455 –  for(i=0;i<3;i++)
456 –    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
457 –
458 –  simnfo->setBoxM( theBoxMat3 );
459 –
460 –  
445   #endif
446   }
447  
448 < char* DumpReader::parseDumpLine(char* readLine, int globalIndex){
448 > char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
449  
450 <  char *foo; // the pointer to the current string token
451 <  
450 >  char *foo; // the pointer to the current string token
451 >
452    double pos[3]; // position place holders
453    double vel[3]; // velocity placeholders
454    double q[4]; // the quaternions
455 <  double jx, jy, jz; // angular velocity placeholders;
455 >  double ji[3]; // angular velocity placeholders;
456    double qSqr, qLength; // needed to normalize the quaternion vector.
473 –  
474 –  Atom **atoms = simnfo->atoms;
475 –  DirectionalAtom* dAtom;
476 –  
477 –  int j, n_atoms, atomIndex;
457  
479 – #ifdef IS_MPI
480 –  n_atoms = mpiSim->getTotAtoms();
481 –  atomIndex=-1;        
482 –  for (j=0; j < mpiSim->getMyNlocal(); j++) {
483 –    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
484 –  }
485 –  if (atomIndex == -1) {
486 –    sprintf( painCave.errMsg,
487 –             "Initialize from file error. Atom at index %d "
488 –             "in file %s does not exist on processor %d .\n",
489 –             globalIndex, inName, mpiSim->getMyNode() );
490 –    return strdup( painCave.errMsg );
491 –  }  
492 – #else
493 –  n_atoms = simnfo->n_atoms;
494 –  atomIndex = globalIndex;
495 – #endif // is_mpi
458  
459    // set the string tokenizer
460 <  
460 >
461    foo = strtok(readLine, " ,;\t");
462 <  
462 >
463    // check the atom name to the current atom
464 <  
465 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
464 >
465 >  if( strcmp( foo, sd->getType() ) ){
466      sprintf( painCave.errMsg,
467 <             "Initialize from file error. Atom %s at index %d "
506 <             "in file %s does not"
467 >             "DumpReader error.  Does not"
468               " match the BASS atom %s.\n",
469 <             foo, atomIndex, inName, atoms[atomIndex]->getType() );
469 >             sd->getType() );
470      return strdup( painCave.errMsg );
471    }
472 <    
472 >
473    // get the positions
474  
475    foo = strtok(NULL, " ,;\t");
476    if(foo == NULL){
477      sprintf( painCave.errMsg,
478 <             "error in reading postition x from %s\n"
479 <             "natoms  = %d, index = %d\n",
519 <             inName, n_atoms, atomIndex );
478 >             "error in reading postition x from %s\n",
479 >             inFileName.c_str());
480      return strdup( painCave.errMsg );
481    }
482    pos[0] = atof( foo );
483 <  
483 >
484    foo = strtok(NULL, " ,;\t");
485    if(foo == NULL){
486      sprintf( painCave.errMsg,
487 <             "error in reading postition y from %s\n"
488 <             "natoms  = %d, index = %d\n",
529 <             inName, n_atoms, atomIndex );
487 >             "error in reading postition y from %s\n",
488 >             inFileName.c_str());
489      return strdup( painCave.errMsg );
490    }
491    pos[1] = atof( foo );
492 <    
492 >
493    foo = strtok(NULL, " ,;\t");
494    if(foo == NULL){
495      sprintf( painCave.errMsg,
496 <             "error in reading postition z from %s\n"
497 <             "natoms  = %d, index = %d\n",
539 <             inName, n_atoms, atomIndex );
496 >             "error in reading postition z from %s\n",
497 >             inFileName.c_str());
498      return strdup( painCave.errMsg );
499    }
500 <  pos[2] = atof( foo );    
500 >  pos[2] = atof( foo );
501  
502  
503    // get the velocities
# Line 547 | Line 505 | char* DumpReader::parseDumpLine(char* readLine, int gl
505    foo = strtok(NULL, " ,;\t");
506    if(foo == NULL){
507      sprintf( painCave.errMsg,
508 <             "error in reading velocity x from %s\n"
509 <             "natoms  = %d, index = %d\n",
552 <             inName, n_atoms, atomIndex );
508 >             "error in reading velocity x from %s\n",
509 >             inFileName.c_str() );
510      return strdup( painCave.errMsg );
511    }
512    vel[0] = atof( foo );
513 <    
513 >
514    foo = strtok(NULL, " ,;\t");
515    if(foo == NULL){
516      sprintf( painCave.errMsg,
517 <             "error in reading velocity y from %s\n"
518 <             "natoms  = %d, index = %d\n",
562 <             inName, n_atoms, atomIndex );
517 >             "error in reading velocity x from %s\n",
518 >             inFileName.c_str() );
519      return strdup( painCave.errMsg );
520    }
521    vel[1] = atof( foo );
522 <    
522 >
523    foo = strtok(NULL, " ,;\t");
524    if(foo == NULL){
525      sprintf( painCave.errMsg,
526 <             "error in reading velocity z from %s\n"
527 <             "natoms  = %d, index = %d\n",
572 <             inName, n_atoms, atomIndex );
526 >             "error in reading velocity x from %s\n",
527 >             inFileName.c_str() );
528      return strdup( painCave.errMsg );
529    }
530    vel[2] = atof( foo );
531 <    
532 <    
531 >
532 >
533 >  // add the positions and velocities to the atom
534 >
535 >  sd->setPos( pos );
536 >  sd->setVel( vel );
537 >
538 >  if (!sd->isDirectional())
539 >    return NULL;
540 >
541    // get the quaternions
542 <    
543 <  if( atoms[atomIndex]->isDirectional() ){
544 <      
542 >
543 >  if( sd->isDirectional() ){
544 >
545      foo = strtok(NULL, " ,;\t");
546      if(foo == NULL){
547 <      sprintf(painCave.errMsg,
548 <              "error in reading quaternion 0 from %s\n"
549 <              "natoms  = %d, index = %d\n",
587 <              inName, n_atoms, atomIndex );
547 >      sprintf( painCave.errMsg,
548 >                     "error in reading velocity x from %s\n",
549 >                      inFileName.c_str() );
550        return strdup( painCave.errMsg );
551      }
552      q[0] = atof( foo );
553 <      
553 >
554      foo = strtok(NULL, " ,;\t");
555      if(foo == NULL){
556        sprintf( painCave.errMsg,
557 <               "error in reading quaternion 1 from %s\n"
558 <               "natoms  = %d, index = %d\n",
597 <               inName, n_atoms, atomIndex );
557 >                     "error in reading velocity x from %s\n",
558 >                      inFileName.c_str() );
559        return strdup( painCave.errMsg );
560      }
561      q[1] = atof( foo );
562 <      
562 >
563      foo = strtok(NULL, " ,;\t");
564      if(foo == NULL){
565        sprintf( painCave.errMsg,
566 <               "error in reading quaternion 2 from %s\n"
567 <               "natoms  = %d, index = %d\n",
607 <               inName, n_atoms, atomIndex );
566 >                     "error in reading velocity x from %s\n",
567 >                      inFileName.c_str() );
568        return strdup( painCave.errMsg );
569      }
570      q[2] = atof( foo );
571 <      
571 >
572      foo = strtok(NULL, " ,;\t");
573      if(foo == NULL){
574        sprintf( painCave.errMsg,
575 <               "error in reading quaternion 3 from %s\n"
576 <               "natoms  = %d, index = %d\n",
617 <               inName, n_atoms, atomIndex );
575 >                     "error in reading velocity x from %s\n",
576 >                      inFileName.c_str() );
577        return strdup( painCave.errMsg );
578      }
579      q[3] = atof( foo );
580 <      
580 >
581      // get the angular velocities
582 <      
582 >
583      foo = strtok(NULL, " ,;\t");
584      if(foo == NULL){
585        sprintf( painCave.errMsg,
586 <               "error in reading angular momentum jx from %s\n"
587 <               "natoms  = %d, index = %d\n",
629 <               inName, n_atoms, atomIndex );
586 >                     "error in reading velocity x from %s\n",
587 >                      inFileName.c_str() );
588        return strdup( painCave.errMsg );
589      }
590 <    jx = atof( foo );
591 <      
590 >    ji[0] = atof( foo );
591 >
592      foo = strtok(NULL, " ,;\t");
593      if(foo == NULL){
594        sprintf( painCave.errMsg,
595 <               "error in reading angular momentum jy from %s\n"
596 <               "natoms  = %d, index = %d\n",
639 <               inName, n_atoms, atomIndex );
595 >                     "error in reading velocity x from %s\n",
596 >                      inFileName.c_str() );
597        return strdup( painCave.errMsg );
598      }
599 <    jy = atof(foo );
600 <      
599 >    ji[1] = atof(foo );
600 >
601      foo = strtok(NULL, " ,;\t");
602      if(foo == NULL){
603        sprintf( painCave.errMsg,
604 <               "error in reading angular momentum jz from %s\n"
605 <               "natoms  = %d, index = %d\n",
649 <               inName, n_atoms, atomIndex );
604 >                     "error in reading velocity x from %s\n",
605 >                      inFileName.c_str() );
606        return strdup( painCave.errMsg );
607      }
608 <    jz = atof( foo );
653 <      
654 <    dAtom = ( DirectionalAtom* )atoms[atomIndex];
608 >    ji[2] = atof( foo );
609  
610 +
611      // check that the quaternion vector is normalized
612  
613      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
614 <      
614 >
615 >    if (fabs(qSqr) < 1e-6) {
616 >      sprintf(painCave.errMsg,
617 >          "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
618 >       return strdup(painCave.errMsg);
619 >    }
620 >
621      qLength = sqrt( qSqr );
622      q[0] = q[0] / qLength;
623      q[1] = q[1] / qLength;
624      q[2] = q[2] / qLength;
625      q[3] = q[3] / qLength;
665 –      
666 –    dAtom->setQ( q );
667 –      
668 –    // add the angular velocities
626  
627 <    dAtom->setJx( jx );
628 <    dAtom->setJy( jy );
629 <    dAtom->setJz( jz );
627 >    // add quaternion and angular velocities
628 >
629 >    sd->setQ( q );
630 >    sd->setJ( ji );
631    }
674 –    
675 –  // add the positions and velocities to the atom
632  
677 –  atoms[atomIndex]->setPos( pos );
678 –  atoms[atomIndex]->setVel( vel );
633  
634 +
635    return NULL;
636   }
637  
638  
639 < char* DumpReader::parseCommentLine(char* readLine, double &time,
685 <                                   double boxMat[9]){
639 > char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){
640  
641 <  char *foo; // the pointer to the current string token
642 <  int j;
641 >  double currTime;
642 >  double boxMat[9];
643 >  double theBoxMat3[3][3];
644 >  double chi;
645 >  double integralOfChidt;
646 >  double eta[9];
647  
648 +  char *foo; // the pointer to the current string token
649 +
650    // set the string tokenizer
651 <  
651 >
652    foo = strtok(readLine, " ,;\t");
653 +  // set the timeToken.
654 +
655    if(foo == NULL){
656      sprintf( painCave.errMsg,
657 <             "error in reading time from %s\n",
658 <             inName );
657 >             "error in reading Time from %s\n",
658 >             inFileName.c_str() );
659      return strdup( painCave.errMsg );
660    }
699 –  time = atof( foo );
661  
662 <  // get the Hx vector
662 >  currTime = atof( foo );
663 >  entry_plug->setTime( currTime );
664  
665 <  foo = strtok(NULL, " ,;\t");
666 <  if(foo == NULL){
667 <    sprintf( painCave.errMsg,
668 <             "error in reading Hx[0] from %s\n",
669 <             inName );
670 <    return strdup( painCave.errMsg );
665 >  //get H-Matrix
666 >
667 >  for(int i = 0 ; i < 9; i++){
668 >    foo = strtok(NULL, " ,;\t");
669 >    if(foo == NULL){
670 >      sprintf( painCave.errMsg,
671 >               "error in reading H[%d] from %s\n", i, inFileName.c_str() );
672 >      return strdup( painCave.errMsg );
673 >    }
674 >    boxMat[i] = atof( foo );
675    }
710 –  boxMat[0] = atof( foo );
711 –  
712 –  foo = strtok(NULL, " ,;\t");
713 –  if(foo == NULL){
714 –    sprintf( painCave.errMsg,
715 –             "error in reading Hx[1] from %s\n",
716 –             inName );
717 –    return strdup( painCave.errMsg );
718 –  }
719 –  boxMat[1] = atof( foo );
720 –    
721 –  foo = strtok(NULL, " ,;\t");
722 –  if(foo == NULL){
723 –    sprintf( painCave.errMsg,
724 –             "error in reading Hx[2] from %s\n",
725 –             inName );
726 –    return strdup( painCave.errMsg );
727 –  }
728 –  boxMat[2] = atof( foo );    
676  
677 <  // get the Hy vector
677 >  for(int i=0;i<3;i++)
678 >    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
679  
680 <  foo = strtok(NULL, " ,;\t");
681 <  if(foo == NULL){
734 <    sprintf( painCave.errMsg,
735 <             "error in reading Hy[0] from %s\n",
736 <             inName );
737 <    return strdup( painCave.errMsg );
738 <  }
739 <  boxMat[3] = atof( foo );
740 <  
741 <  foo = strtok(NULL, " ,;\t");
742 <  if(foo == NULL){
743 <    sprintf( painCave.errMsg,
744 <             "error in reading Hy[1] from %s\n",
745 <             inName );
746 <    return strdup( painCave.errMsg );
747 <  }
748 <  boxMat[4] = atof( foo );
749 <    
750 <  foo = strtok(NULL, " ,;\t");
751 <  if(foo == NULL){
752 <    sprintf( painCave.errMsg,
753 <             "error in reading Hy[2] from %s\n",
754 <             inName );
755 <    return strdup( painCave.errMsg );
756 <  }
757 <  boxMat[5] = atof( foo );    
680 >  //set H-Matrix
681 >  entry_plug->setBoxM( theBoxMat3 );
682  
683 <  // get the Hz vector
683 >  //get chi and integralOfChidt, they should appear by pair
684  
685 <  foo = strtok(NULL, " ,;\t");
686 <  if(foo == NULL){
687 <    sprintf( painCave.errMsg,
688 <             "error in reading Hz[0] from %s\n",
689 <             inName );
690 <    return strdup( painCave.errMsg );
685 >  if( entry_plug->useInitXSstate ){
686 >    foo = strtok(NULL, " ,;\t\n");
687 >    if(foo != NULL){
688 >      chi = atof(foo);
689 >      
690 >      foo = strtok(NULL, " ,;\t\n");
691 >      if(foo == NULL){
692 >        sprintf( painCave.errMsg,
693 >                 "chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() );
694 >        return strdup( painCave.errMsg );
695 >      }
696 >      integralOfChidt = atof( foo );
697 >      
698 >      //push chi and integralOfChidt into SimInfo::properties which can be
699 >      //retrieved by integrator later
700 >      DoubleData* chiValue = new DoubleData();
701 >      chiValue->setID(CHIVALUE_ID);
702 >      chiValue->setData(chi);
703 >      entry_plug->addProperty(chiValue);
704 >      
705 >      DoubleData* integralOfChidtValue = new DoubleData();
706 >      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
707 >      integralOfChidtValue->setData(integralOfChidt);
708 >      entry_plug->addProperty(integralOfChidtValue);
709 >      
710 >    }
711 >    else
712 >      return NULL;
713 >    
714 >    //get eta
715 >    foo = strtok(NULL, " ,;\t\n");
716 >    if(foo != NULL ){
717 >  
718 >      for(int i = 0 ; i < 9; i++){
719 >        
720 >        if(foo == NULL){
721 >          sprintf( painCave.errMsg,
722 >                   "error in reading eta[%d] from %s\n", i, inFileName.c_str() );
723 >          return strdup( painCave.errMsg );
724 >        }
725 >        eta[i] = atof( foo );
726 >        foo = strtok(NULL, " ,;\t\n");
727 >      }
728 >    }
729 >    else
730 >      return NULL;
731 >    
732 >    //push eta into SimInfo::properties which can be
733 >    //retrieved by integrator later
734 >    //entry_plug->setBoxM( theBoxMat3 );
735 >    DoubleArrayData* etaValue = new DoubleArrayData();
736 >    etaValue->setID(ETAVALUE_ID);
737 >    etaValue->setData(eta, 9);
738 >    entry_plug->addProperty(etaValue);
739    }
768 –  boxMat[6] = atof( foo );
769 –  
770 –  foo = strtok(NULL, " ,;\t");
771 –  if(foo == NULL){
772 –    sprintf( painCave.errMsg,
773 –             "error in reading Hz[1] from %s\n",
774 –             inName );
775 –    return strdup( painCave.errMsg );
776 –  }
777 –  boxMat[7] = atof( foo );
778 –    
779 –  foo = strtok(NULL, " ,;\t");
780 –  if(foo == NULL){
781 –    sprintf( painCave.errMsg,
782 –             "error in reading Hz[2] from %s\n",
783 –             inName );
784 –    return strdup( painCave.errMsg );
785 –  }
786 –  boxMat[8] = atof( foo );    
740  
741    return NULL;
742   }
743  
791 –
744   #ifdef IS_MPI
745 <
794 < // a couple of functions to let us escape the read loop
795 <
796 < void dumpRead::nodeZeroError( void ){
745 > void DumpReader::nodeZeroError( void ){
746    int j, myStatus;
747 <  
747 >
748    myStatus = 0;
749 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
750 <    MPI_Send( &myStatus, 1, MPI_INT, j,
749 >  for (j = 0; j < mpiSim->getNProcessors(); j++) {
750 >    MPI_Send( &myStatus, 1, MPI_INT, j,
751                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
752 <  }  
804 <  
752 >  }
753  
754 +
755    MPI_Finalize();
756    exit (0);
757 <  
757 >
758   }
759  
760 < void dumpRead::anonymousNodeDie( void ){
760 > void DumpReader::anonymousNodeDie( void ){
761  
762    MPI_Finalize();
763    exit (0);
764   }
765 <
817 < #endif //is_mpi
765 > #endif

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