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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 837 by tim, Wed Oct 29 00:19:10 2003 UTC vs.
Revision 1130 by tim, Thu Apr 22 14:55:17 2004 UTC

# Line 16 | Line 16
16   #ifdef IS_MPI
17   #include <mpi.h>
18   #include "mpiSimulation.hpp"
19 < #define TAKE_THIS_TAG_CHAR 0
20 < #define TAKE_THIS_TAG_INT 1
19 > #define TAKE_THIS_TAG_CHAR 3134
20 > #define TAKE_THIS_TAG_INT 3135
21  
22   namespace initFile{
23    void nodeZeroError( void );
# Line 45 | Line 45 | InitializeFromFile::InitializeFromFile( char *in_name
45    strcpy( c_in_name, in_name);
46   #ifdef IS_MPI
47    }
48 < strcpy( checkPointMsg, "Infile opened for reading successfully." );
48 >  else{
49 >          sprintf( c_in_name, "mpiNodeParser_%d", worldRank );
50 >  }
51 >  
52 >  strcpy( checkPointMsg, "Infile opened for reading successfully." );
53    MPIcheckPoint();
54   #endif
55    return;
# Line 81 | Line 85 | void InitializeFromFile :: readInit( SimInfo* the_simn
85   #endif //is_mpi
86  
87    const int BUFFERSIZE = 2000; // size of the read buffer
88 <  int n_atoms; // the number of atoms
88 >  int nTotObjs; // the number of atoms
89    char read_buffer[BUFFERSIZE]; //the line buffer for reading
90  
91    char *eof_test; // ptr to see when we reach the end of the file
92    char *parseErr;
93  
94 +  vector<StuntDouble*> integrableObjects;
95 +
96    simnfo = the_simnfo;
97  
98  
# Line 100 | Line 106 | void InitializeFromFile :: readInit( SimInfo* the_simn
106      simError();
107    }
108  
109 <  n_atoms = atoi( read_buffer );
109 >  nTotObjs = atoi( read_buffer );
110  
111 <  if( n_atoms != simnfo->n_atoms ){
111 >  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
112      sprintf( painCave.errMsg,
113               "Initialize from File error. %s n_atoms, %d, "
114               "does not match the BASS file's n_atoms, %d.\n",
115 <             c_in_name, n_atoms, simnfo->n_atoms );
115 >             c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
116      painCave.isFatal = 1;
117      simError();
118    }
# Line 121 | Line 127 | void InitializeFromFile :: readInit( SimInfo* the_simn
127      simError();
128    }
129  
124 –
125 –
130    parseErr = parseCommentLine( read_buffer, simnfo);
131    if( parseErr != NULL ){
132      strcpy( painCave.errMsg, parseErr );
# Line 132 | Line 136 | void InitializeFromFile :: readInit( SimInfo* the_simn
136  
137    //parse dump lines
138  
139 <  for( i=0; i < n_atoms; i++){
139 >  for( i=0; i < simnfo->n_mol; i++){
140  
141 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
138 <    if(eof_test == NULL){
139 <      sprintf(painCave.errMsg,
140 <              "error in reading file %s\n"
141 <              "natoms  = %d; index = %d\n"
142 <              "error reading the line from the file.\n",
143 <              c_in_name, n_atoms, i );
144 <      painCave.isFatal = 1;
145 <      simError();
146 <    }
141 >    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
142  
143 +    for(j = 0; j < integrableObjects.size(); j++){
144  
145 <    parseErr = parseDumpLine( read_buffer, i );
146 <    if( parseErr != NULL ){
147 <      strcpy( painCave.errMsg, parseErr );
148 <      painCave.isFatal = 1;
149 <      simError();
145 >      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
146 >      if(eof_test == NULL){
147 >        sprintf(painCave.errMsg,
148 >              "error in reading file %s\n"
149 >              "natoms  = %d; index = %d\n"
150 >              "error reading the line from the file.\n",
151 >              c_in_name, nTotObjs, i );
152 >        painCave.isFatal = 1;
153 >        simError();
154 >      }
155 >      
156 >      parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
157 >      if( parseErr != NULL ){
158 >        strcpy( painCave.errMsg, parseErr );
159 >        painCave.isFatal = 1;
160 >        simError();
161 >      }
162      }
163    }
164  
157 –
165    // MPI Section of code..........
166   #else //IS_MPI
167  
# Line 165 | Line 172 | void InitializeFromFile :: readInit( SimInfo* the_simn
172    int haveError;
173  
174    MPI_Status istatus;
175 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
175 >  int *MolToProcMap = mpiSim->getMolToProcMap();
176 >  int localIndex;
177 >  int nCurObj;
178 >  int nItems;
179  
180 <
180 >  nTotObjs = simnfo->getTotIntegrableObjects();
181    haveError = 0;
182    if (worldRank == 0) {
183  
# Line 179 | Line 189 | void InitializeFromFile :: readInit( SimInfo* the_simn
189        simError();
190      }
191  
192 <    n_atoms = atoi( read_buffer );
192 >    nItems = atoi( read_buffer );
193  
194 <    // Check to see that the number of atoms in the intial configuration file is the
194 >    // Check to see that the number of integrable objects  in the intial configuration file is the
195      // same as declared in simBass.
196  
197 <    if( n_atoms != mpiSim->getTotAtoms() ){
197 >    if( nTotObjs != nItems){
198        sprintf( painCave.errMsg,
199                 "Initialize from File error. %s n_atoms, %d, "
200                 "does not match the BASS file's n_atoms, %d.\n",
201 <               c_in_name, n_atoms, simnfo->n_atoms );
201 >               c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
202        haveError= 1;
203        simError();
204      }
# Line 210 | Line 220 | void InitializeFromFile :: readInit( SimInfo* the_simn
220  
221      MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
222  
223 +    cerr << "node " << worldRank << " finished  MPI_Bcast" << endl;
224 +
225      parseErr = parseCommentLine( read_buffer, simnfo);
226  
227      if( parseErr != NULL ){
# Line 218 | Line 230 | void InitializeFromFile :: readInit( SimInfo* the_simn
230        simError();
231      }
232  
233 <    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
233 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
234 >      which_node = MolToProcMap[i];
235 >      if(which_node == 0){
236 >       //molecules belong to master node
237  
238 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
239 <      if(eof_test == NULL){
240 <        sprintf(painCave.errMsg,
241 <                "error in reading file %s\n"
242 <                "natoms  = %d; index = %d\n"
243 <                "error reading the line from the file.\n",
229 <                c_in_name, n_atoms, i );
230 <        haveError= 1;
231 <        simError();
238 >      localIndex = mpiSim->getGlobalToLocalMol(i);
239 >
240 >      if(localIndex == -1) {
241 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
242 >        haveError = 1;
243 >        simError();
244        }
245  
246 <      if(haveError) nodeZeroError();
246 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
247 >       for(j=0; j < integrableObjects.size(); j++){
248 >        
249 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
250 >          if(eof_test == NULL){
251 >                sprintf(painCave.errMsg,
252 >                    "error in reading file %s\n"
253 >                    "natoms  = %d; index = %d\n"
254 >                    "error reading the line from the file.\n",
255 >                    c_in_name, nTotObjs, i );
256 >                haveError= 1;
257 >                simError();
258 >          }
259 >          
260 >          if(haveError) nodeZeroError();
261  
262 <      // Get the Node number which wants this atom:
263 <      which_node = AtomToProcMap[i];
264 <      if (which_node == 0) {
265 <        parseErr = parseDumpLine( read_buffer, i );
266 <        if( parseErr != NULL ){
241 <          strcpy( painCave.errMsg, parseErr );
242 <          haveError = 1;
243 <          simError();
244 <        }
245 <        if(haveError) nodeZeroError();
262 >          parseDumpLine(read_buffer, integrableObjects[j]);
263 >          
264 >       }
265 >
266 >
267        }
268 +      else{
269 +      //molecule belongs to slave nodes
270  
271 <      else {
271 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
272 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
273 >         cerr << "node " << worldRank << " finished  MPI_Send" << endl;  
274 >       for(j=0; j < nCurObj; j++){
275 >        
276 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
277 >          if(eof_test == NULL){
278 >                sprintf(painCave.errMsg,
279 >                    "error in reading file %s\n"
280 >                    "natoms  = %d; index = %d\n"
281 >                    "error reading the line from the file.\n",
282 >                    c_in_name, nTotObjs, i );
283 >                haveError= 1;
284 >                simError();
285 >          }
286 >          
287 >          if(haveError) nodeZeroError();
288  
289 <        myStatus = 1;
290 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
291 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
292 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
254 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
255 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
256 <                 MPI_COMM_WORLD);
257 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
258 <                 MPI_COMM_WORLD, &istatus);
289 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
290 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
291 >           cerr << "node " << worldRank << " finished  MPI_Send" << endl;
292 >       }
293  
260 –        if(!myStatus) nodeZeroError();
294        }
295 +      
296      }
297 <    myStatus = -1;
298 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
299 <      MPI_Send( &myStatus, 1, MPI_INT, j,
300 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
267 <    }
297 >    
298 >  }
299 >  else{
300 >  //actions taken at slave nodes
301  
269 –  } else {
270 –
302      MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
303  
304 +    cerr << "node " << worldRank << " finished  MPI_Bcast" << endl;
305      parseErr = parseCommentLine( read_buffer, simnfo);
306  
307      if( parseErr != NULL ){
# Line 277 | Line 309 | void InitializeFromFile :: readInit( SimInfo* the_simn
309        haveError = 1;
310        simError();
311      }
312 +  
313 +    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
314 +      which_node = MolToProcMap[i];
315 +      
316 +      if(which_node == worldRank){
317 +      //molecule with global index i belongs to this processor
318 +      
319 +        localIndex = mpiSim->getGlobalToLocalMol(i);
320  
321 +        if(localIndex == -1) {
322 +          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
323 +          haveError = 1;
324 +          simError();
325 +        }
326  
327 <    done = 0;
283 <    while (!done) {
327 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
328  
329 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
330 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
329 >        nCurObj = integrableObjects.size();
330 >        
331 >        MPI_Send(&nCurObj, 1, MPI_INT, 0,
332 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
333  
334 <      if(!myStatus) anonymousNodeDie();
334 >        cerr << "node " << worldRank << " finished  MPI_Send" << endl;
335 >        for(j = 0; j < integrableObjects.size(); j++){
336  
337 <      if(myStatus < 0) break;
337 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
338 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
339  
340 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
341 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
294 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
295 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
340 >        cerr << "node " << worldRank << " finished  MPI_Recv" << endl;
341 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
342  
343 <      myStatus = 1;
344 <      parseErr = parseDumpLine( read_buffer, which_atom );
345 <      if( parseErr != NULL ){
346 <        strcpy( painCave.errMsg, parseErr );
301 <        myStatus = 0;;
302 <        simError();
303 <      }
343 >          if( parseErr != NULL ){
344 >                strcpy( painCave.errMsg, parseErr );
345 >                simError();
346 >          }
347  
348 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
349 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
350 <
348 >        }
349 >          
350 >      }
351 >      
352      }
309 –  }
353  
354 < // last  thing last, enable  fatalities.
312 <  painCave.isEventLoop = 0;
313 <
314 <
315 <
354 >  }
355   #endif
356   }
357  
358 < char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
358 > char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
359  
360    char *foo; // the pointer to the current string token
361  
362    double pos[3]; // position place holders
363    double vel[3]; // velocity placeholders
364    double q[4]; // the quaternions
365 <  double jx, jy, jz; // angular velocity placeholders;
365 >  double ji[3]; // angular velocity placeholders;
366    double qSqr, qLength; // needed to normalize the quaternion vector.
367  
329 –  Atom **atoms = simnfo->atoms;
330 –  DirectionalAtom* dAtom;
368  
332 –  int n_atoms, atomIndex;
333 –
334 – #ifdef IS_MPI
335 –  int j;
336 –
337 –  n_atoms = mpiSim->getTotAtoms();
338 –  atomIndex=-1;
339 –  for (j=0; j < mpiSim->getMyNlocal(); j++) {
340 –    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
341 –  }
342 –  if (atomIndex == -1) {
343 –    sprintf( painCave.errMsg,
344 –             "Initialize from file error. Atom at index %d "
345 –             "in file %s does not exist on processor %d .\n",
346 –             globalIndex, c_in_name, mpiSim->getMyNode() );
347 –    return strdup( painCave.errMsg );
348 –  }
349 – #else
350 –  n_atoms = simnfo->n_atoms;
351 –  atomIndex = globalIndex;
352 – #endif // is_mpi
353 –
369    // set the string tokenizer
370  
371    foo = strtok(readLine, " ,;\t");
372  
373    // check the atom name to the current atom
374  
375 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
375 >  if( strcmp( foo, sd->getType() ) ){
376      sprintf( painCave.errMsg,
377 <             "Initialize from file error. Atom %s at index %d "
363 <             "in file %s does not"
377 >             "Initialize from file error.  Does not"
378               " match the BASS atom %s.\n",
379 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
379 >             sd->getType() );
380      return strdup( painCave.errMsg );
381    }
382  
# Line 371 | Line 385 | char* InitializeFromFile::parseDumpLine(char* readLine
385    foo = strtok(NULL, " ,;\t");
386    if(foo == NULL){
387      sprintf( painCave.errMsg,
388 <             "error in reading postition x from %s\n"
389 <             "natoms  = %d, index = %d\n",
376 <             c_in_name, n_atoms, atomIndex );
388 >             "error in reading postition x from %s\n",
389 >             c_in_name);
390      return strdup( painCave.errMsg );
391    }
392    pos[0] = atof( foo );
# Line 381 | Line 394 | char* InitializeFromFile::parseDumpLine(char* readLine
394    foo = strtok(NULL, " ,;\t");
395    if(foo == NULL){
396      sprintf( painCave.errMsg,
397 <             "error in reading postition y from %s\n"
398 <             "natoms  = %d, index = %d\n",
386 <             c_in_name, n_atoms, atomIndex );
397 >             "error in reading postition y from %s\n",
398 >             c_in_name);
399      return strdup( painCave.errMsg );
400    }
401    pos[1] = atof( foo );
# Line 391 | Line 403 | char* InitializeFromFile::parseDumpLine(char* readLine
403    foo = strtok(NULL, " ,;\t");
404    if(foo == NULL){
405      sprintf( painCave.errMsg,
406 <             "error in reading postition z from %s\n"
407 <             "natoms  = %d, index = %d\n",
396 <             c_in_name, n_atoms, atomIndex );
406 >             "error in reading postition z from %s\n",
407 >             c_in_name);
408      return strdup( painCave.errMsg );
409    }
410    pos[2] = atof( foo );
# Line 404 | Line 415 | char* InitializeFromFile::parseDumpLine(char* readLine
415    foo = strtok(NULL, " ,;\t");
416    if(foo == NULL){
417      sprintf( painCave.errMsg,
418 <             "error in reading velocity x from %s\n"
419 <             "natoms  = %d, index = %d\n",
409 <             c_in_name, n_atoms, atomIndex );
418 >             "error in reading velocity x from %s\n",
419 >             c_in_name );
420      return strdup( painCave.errMsg );
421    }
422    vel[0] = atof( foo );
# Line 414 | Line 424 | char* InitializeFromFile::parseDumpLine(char* readLine
424    foo = strtok(NULL, " ,;\t");
425    if(foo == NULL){
426      sprintf( painCave.errMsg,
427 <             "error in reading velocity y from %s\n"
428 <             "natoms  = %d, index = %d\n",
419 <             c_in_name, n_atoms, atomIndex );
427 >             "error in reading velocity x from %s\n",
428 >             c_in_name );
429      return strdup( painCave.errMsg );
430    }
431    vel[1] = atof( foo );
# Line 424 | Line 433 | char* InitializeFromFile::parseDumpLine(char* readLine
433    foo = strtok(NULL, " ,;\t");
434    if(foo == NULL){
435      sprintf( painCave.errMsg,
436 <             "error in reading velocity z from %s\n"
437 <             "natoms  = %d, index = %d\n",
429 <             c_in_name, n_atoms, atomIndex );
436 >             "error in reading velocity x from %s\n",
437 >             c_in_name );
438      return strdup( painCave.errMsg );
439    }
440    vel[2] = atof( foo );
441  
442  
443 +  // add the positions and velocities to the atom
444 +
445 +  sd->setPos( pos );
446 +  sd->setVel( vel );
447 +
448 +  if (!sd->isDirectional())
449 +    return NULL;
450 +
451    // get the quaternions
452  
453 <  if( atoms[atomIndex]->isDirectional() ){
453 >  if( sd->isDirectional() ){
454  
455      foo = strtok(NULL, " ,;\t");
456      if(foo == NULL){
457 <      sprintf(painCave.errMsg,
458 <              "error in reading quaternion 0 from %s\n"
459 <              "natoms  = %d, index = %d\n",
444 <              c_in_name, n_atoms, atomIndex );
457 >      sprintf( painCave.errMsg,
458 >                     "error in reading velocity x from %s\n",
459 >                      c_in_name );
460        return strdup( painCave.errMsg );
461      }
462      q[0] = atof( foo );
# Line 449 | Line 464 | char* InitializeFromFile::parseDumpLine(char* readLine
464      foo = strtok(NULL, " ,;\t");
465      if(foo == NULL){
466        sprintf( painCave.errMsg,
467 <               "error in reading quaternion 1 from %s\n"
468 <               "natoms  = %d, index = %d\n",
454 <               c_in_name, n_atoms, atomIndex );
467 >                     "error in reading velocity x from %s\n",
468 >                      c_in_name );
469        return strdup( painCave.errMsg );
470      }
471      q[1] = atof( foo );
# Line 459 | Line 473 | char* InitializeFromFile::parseDumpLine(char* readLine
473      foo = strtok(NULL, " ,;\t");
474      if(foo == NULL){
475        sprintf( painCave.errMsg,
476 <               "error in reading quaternion 2 from %s\n"
477 <               "natoms  = %d, index = %d\n",
464 <               c_in_name, n_atoms, atomIndex );
476 >                     "error in reading velocity x from %s\n",
477 >                      c_in_name );
478        return strdup( painCave.errMsg );
479      }
480      q[2] = atof( foo );
# Line 469 | Line 482 | char* InitializeFromFile::parseDumpLine(char* readLine
482      foo = strtok(NULL, " ,;\t");
483      if(foo == NULL){
484        sprintf( painCave.errMsg,
485 <               "error in reading quaternion 3 from %s\n"
486 <               "natoms  = %d, index = %d\n",
474 <               c_in_name, n_atoms, atomIndex );
485 >                     "error in reading velocity x from %s\n",
486 >                      c_in_name );
487        return strdup( painCave.errMsg );
488      }
489      q[3] = atof( foo );
# Line 481 | Line 493 | char* InitializeFromFile::parseDumpLine(char* readLine
493      foo = strtok(NULL, " ,;\t");
494      if(foo == NULL){
495        sprintf( painCave.errMsg,
496 <               "error in reading angular momentum jx from %s\n"
497 <               "natoms  = %d, index = %d\n",
486 <               c_in_name, n_atoms, atomIndex );
496 >                     "error in reading velocity x from %s\n",
497 >                      c_in_name );
498        return strdup( painCave.errMsg );
499      }
500 <    jx = atof( foo );
500 >    ji[0] = atof( foo );
501  
502      foo = strtok(NULL, " ,;\t");
503      if(foo == NULL){
504        sprintf( painCave.errMsg,
505 <               "error in reading angular momentum jy from %s\n"
506 <               "natoms  = %d, index = %d\n",
496 <               c_in_name, n_atoms, atomIndex );
505 >                     "error in reading velocity x from %s\n",
506 >                      c_in_name );
507        return strdup( painCave.errMsg );
508      }
509 <    jy = atof(foo );
509 >    ji[1] = atof(foo );
510  
511      foo = strtok(NULL, " ,;\t");
512      if(foo == NULL){
513        sprintf( painCave.errMsg,
514 <               "error in reading angular momentum jz from %s\n"
515 <               "natoms  = %d, index = %d\n",
506 <               c_in_name, n_atoms, atomIndex );
514 >                     "error in reading velocity x from %s\n",
515 >                      c_in_name );
516        return strdup( painCave.errMsg );
517      }
518 <    jz = atof( foo );
518 >    ji[2] = atof( foo );
519  
511 –    dAtom = ( DirectionalAtom* )atoms[atomIndex];
520  
521      // check that the quaternion vector is normalized
522  
# Line 520 | Line 528 | char* InitializeFromFile::parseDumpLine(char* readLine
528      q[2] = q[2] / qLength;
529      q[3] = q[3] / qLength;
530  
531 <    dAtom->setQ( q );
531 >    // add quaternion and angular velocities
532  
533 <    // add the angular velocities
534 <
527 <    dAtom->setJx( jx );
528 <    dAtom->setJy( jy );
529 <    dAtom->setJz( jz );
533 >    sd->setQ( q );
534 >    sd->setJ( ji );
535    }
536  
532 –  // add the positions and velocities to the atom
537  
534 –  atoms[atomIndex]->setPos( pos );
535 –  atoms[atomIndex]->setVel( vel );
538  
539    return NULL;
540   }
# Line 583 | Line 585 | char* InitializeFromFile::parseCommentLine(char* readL
585    entry_plug->setBoxM( theBoxMat3 );
586  
587    //get chi and integralOfChidt, they should appear by pair
586 –  foo = strtok(NULL, " ,;\t\n");
587 –  if(foo != NULL){
588 –    chi = atof(foo);
588  
589 +  if( entry_plug->useInitXSstate ){
590      foo = strtok(NULL, " ,;\t\n");
591 <    if(foo == NULL){
592 <      sprintf( painCave.errMsg,
593 <               "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
594 <      return strdup( painCave.errMsg );
591 >    if(foo != NULL){
592 >      chi = atof(foo);
593 >      
594 >      foo = strtok(NULL, " ,;\t\n");
595 >      if(foo == NULL){
596 >        sprintf( painCave.errMsg,
597 >                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
598 >        return strdup( painCave.errMsg );
599 >      }
600 >      integralOfChidt = atof( foo );
601 >      
602 >      //push chi and integralOfChidt into SimInfo::properties which can be
603 >      //retrieved by integrator later
604 >      DoubleData* chiValue = new DoubleData();
605 >      chiValue->setID(CHIVALUE_ID);
606 >      chiValue->setData(chi);
607 >      entry_plug->addProperty(chiValue);
608 >      
609 >      DoubleData* integralOfChidtValue = new DoubleData();
610 >      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
611 >      integralOfChidtValue->setData(integralOfChidt);
612 >      entry_plug->addProperty(integralOfChidtValue);
613 >      
614      }
615 <    integralOfChidt = atof( foo );
616 <
617 <    //push chi and integralOfChidt into SimInfo::properties which can be
615 >    else
616 >      return NULL;
617 >    
618 >    //get eta
619 >    foo = strtok(NULL, " ,;\t\n");
620 >    if(foo != NULL ){
621 >  
622 >      for(int i = 0 ; i < 9; i++){
623 >        
624 >        if(foo == NULL){
625 >          sprintf( painCave.errMsg,
626 >                   "error in reading eta[%d] from %s\n", i, c_in_name );
627 >          return strdup( painCave.errMsg );
628 >        }
629 >        eta[i] = atof( foo );
630 >        foo = strtok(NULL, " ,;\t\n");
631 >      }
632 >    }
633 >    else
634 >      return NULL;
635 >    
636 >    //push eta into SimInfo::properties which can be
637      //retrieved by integrator later
638 <    DoubleData* chiValue = new DoubleData();
639 <    chiValue->setID(CHIVALUE_ID);
640 <    chiValue->setData(chi);
641 <    entry_plug->addProperty(chiValue);
642 <
605 <    DoubleData* integralOfChidtValue = new DoubleData();
606 <    integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
607 <    integralOfChidtValue->setData(integralOfChidt);
608 <    entry_plug->addProperty(integralOfChidtValue);
609 <
638 >    
639 >    DoubleArrayData* etaValue = new DoubleArrayData();
640 >    etaValue->setID(ETAVALUE_ID);
641 >    etaValue->setData(eta, 9);
642 >    entry_plug->addProperty(etaValue);
643    }
611 –  else
612 –    return NULL;
644  
614 –  //get eta
615 –  for(int i = 0 ; i < 9; i++){
616 –    foo = strtok(NULL, " ,;\t");
617 –    if(foo == NULL){
618 –      sprintf( painCave.errMsg,
619 –               "error in reading eta[%d] from %s\n", i, c_in_name );
620 –      return strdup( painCave.errMsg );
621 –    }
622 –    eta[i] = atof( foo );
623 –  }
624 –
625 –  //push eta into SimInfo::properties which can be
626 –  //retrieved by integrator later
627 –  //entry_plug->setBoxM( theBoxMat3 );
628 –  DoubleArrayData* etaValue = new DoubleArrayData();
629 –  etaValue->setID(ETAVALUE_ID);
630 –  etaValue->setData(eta, 9);
631 –  entry_plug->addProperty(etaValue);
632 –
633 –
645    return NULL;
646   }
647  

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