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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 1198 by tim, Thu May 27 00:48:12 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 +
224      parseErr = parseCommentLine( read_buffer, simnfo);
225  
226      if( parseErr != NULL ){
# Line 218 | Line 229 | void InitializeFromFile :: readInit( SimInfo* the_simn
229        simError();
230      }
231  
232 <    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
232 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
233 >      which_node = MolToProcMap[i];
234 >      if(which_node == 0){
235 >       //molecules belong to master node
236  
237 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
238 <      if(eof_test == NULL){
239 <        sprintf(painCave.errMsg,
240 <                "error in reading file %s\n"
241 <                "natoms  = %d; index = %d\n"
242 <                "error reading the line from the file.\n",
229 <                c_in_name, n_atoms, i );
230 <        haveError= 1;
231 <        simError();
237 >      localIndex = mpiSim->getGlobalToLocalMol(i);
238 >
239 >      if(localIndex == -1) {
240 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
241 >        haveError = 1;
242 >        simError();
243        }
244  
245 <      if(haveError) nodeZeroError();
245 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
246 >       for(j=0; j < integrableObjects.size(); j++){
247 >        
248 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
249 >          if(eof_test == NULL){
250 >                sprintf(painCave.errMsg,
251 >                    "error in reading file %s\n"
252 >                    "natoms  = %d; index = %d\n"
253 >                    "error reading the line from the file.\n",
254 >                    c_in_name, nTotObjs, i );
255 >                haveError= 1;
256 >                simError();
257 >          }
258 >          
259 >          if(haveError) nodeZeroError();
260  
261 <      // Get the Node number which wants this atom:
262 <      which_node = AtomToProcMap[i];
263 <      if (which_node == 0) {
264 <        parseErr = parseDumpLine( read_buffer, i );
265 <        if( parseErr != NULL ){
241 <          strcpy( painCave.errMsg, parseErr );
242 <          haveError = 1;
243 <          simError();
244 <        }
245 <        if(haveError) nodeZeroError();
261 >          parseDumpLine(read_buffer, integrableObjects[j]);
262 >          
263 >       }
264 >
265 >
266        }
267 +      else{
268 +      //molecule belongs to slave nodes
269  
270 <      else {
270 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
271 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
272  
273 <        myStatus = 1;
274 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
275 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
276 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
277 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
278 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
279 <                 MPI_COMM_WORLD);
280 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
281 <                 MPI_COMM_WORLD, &istatus);
273 >       for(j=0; j < nCurObj; j++){
274 >        
275 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
276 >          if(eof_test == NULL){
277 >                sprintf(painCave.errMsg,
278 >                    "error in reading file %s\n"
279 >                    "natoms  = %d; index = %d\n"
280 >                    "error reading the line from the file.\n",
281 >                    c_in_name, nTotObjs, i );
282 >                haveError= 1;
283 >                simError();
284 >          }
285 >          
286 >          if(haveError) nodeZeroError();
287  
288 <        if(!myStatus) nodeZeroError();
288 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
289 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
290 >
291 >       }
292 >
293        }
294 +      
295      }
296 <    myStatus = -1;
297 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
298 <      MPI_Send( &myStatus, 1, MPI_INT, j,
299 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
267 <    }
296 >    
297 >  }
298 >  else{
299 >  //actions taken at slave nodes
300  
269 –  } else {
270 –
301      MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
302  
303      parseErr = parseCommentLine( read_buffer, simnfo);
# Line 277 | Line 307 | void InitializeFromFile :: readInit( SimInfo* the_simn
307        haveError = 1;
308        simError();
309      }
310 +  
311 +    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
312 +      which_node = MolToProcMap[i];
313 +      
314 +      if(which_node == worldRank){
315 +      //molecule with global index i belongs to this processor
316 +      
317 +        localIndex = mpiSim->getGlobalToLocalMol(i);
318  
319 +        if(localIndex == -1) {
320 +          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
321 +          haveError = 1;
322 +          simError();
323 +        }
324  
325 <    done = 0;
283 <    while (!done) {
325 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
326  
327 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
328 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
327 >        nCurObj = integrableObjects.size();
328 >        
329 >        MPI_Send(&nCurObj, 1, MPI_INT, 0,
330 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
331  
332 <      if(!myStatus) anonymousNodeDie();
332 >        for(j = 0; j < integrableObjects.size(); j++){
333  
334 <      if(myStatus < 0) break;
334 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
335 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
336  
337 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
293 <               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);
337 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
338  
339 <      myStatus = 1;
340 <      parseErr = parseDumpLine( read_buffer, which_atom );
341 <      if( parseErr != NULL ){
342 <        strcpy( painCave.errMsg, parseErr );
301 <        myStatus = 0;;
302 <        simError();
303 <      }
339 >          if( parseErr != NULL ){
340 >                strcpy( painCave.errMsg, parseErr );
341 >                simError();
342 >          }
343  
344 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
345 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
346 <
344 >        }
345 >          
346 >      }
347 >      
348      }
309 –  }
349  
350 < // last  thing last, enable  fatalities.
312 <  painCave.isEventLoop = 0;
313 <
314 <
315 <
350 >  }
351   #endif
352   }
353  
354 < char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
354 > char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
355  
356    char *foo; // the pointer to the current string token
357  
358    double pos[3]; // position place holders
359    double vel[3]; // velocity placeholders
360    double q[4]; // the quaternions
361 <  double jx, jy, jz; // angular velocity placeholders;
361 >  double ji[3]; // angular velocity placeholders;
362    double qSqr, qLength; // needed to normalize the quaternion vector.
363  
329 –  Atom **atoms = simnfo->atoms;
330 –  DirectionalAtom* dAtom;
364  
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 –
365    // set the string tokenizer
366  
367    foo = strtok(readLine, " ,;\t");
368  
369    // check the atom name to the current atom
370  
371 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
371 >  if( strcmp( foo, sd->getType() ) ){
372      sprintf( painCave.errMsg,
373 <             "Initialize from file error. Atom %s at index %d "
363 <             "in file %s does not"
373 >             "Initialize from file error.  Does not"
374               " match the BASS atom %s.\n",
375 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
375 >             sd->getType() );
376      return strdup( painCave.errMsg );
377    }
378  
# Line 371 | Line 381 | char* InitializeFromFile::parseDumpLine(char* readLine
381    foo = strtok(NULL, " ,;\t");
382    if(foo == NULL){
383      sprintf( painCave.errMsg,
384 <             "error in reading postition x from %s\n"
385 <             "natoms  = %d, index = %d\n",
376 <             c_in_name, n_atoms, atomIndex );
384 >             "error in reading postition x from %s\n",
385 >             c_in_name);
386      return strdup( painCave.errMsg );
387    }
388    pos[0] = atof( foo );
# Line 381 | Line 390 | char* InitializeFromFile::parseDumpLine(char* readLine
390    foo = strtok(NULL, " ,;\t");
391    if(foo == NULL){
392      sprintf( painCave.errMsg,
393 <             "error in reading postition y from %s\n"
394 <             "natoms  = %d, index = %d\n",
386 <             c_in_name, n_atoms, atomIndex );
393 >             "error in reading postition y from %s\n",
394 >             c_in_name);
395      return strdup( painCave.errMsg );
396    }
397    pos[1] = atof( foo );
# Line 391 | Line 399 | char* InitializeFromFile::parseDumpLine(char* readLine
399    foo = strtok(NULL, " ,;\t");
400    if(foo == NULL){
401      sprintf( painCave.errMsg,
402 <             "error in reading postition z from %s\n"
403 <             "natoms  = %d, index = %d\n",
396 <             c_in_name, n_atoms, atomIndex );
402 >             "error in reading postition z from %s\n",
403 >             c_in_name);
404      return strdup( painCave.errMsg );
405    }
406    pos[2] = atof( foo );
# Line 404 | Line 411 | char* InitializeFromFile::parseDumpLine(char* readLine
411    foo = strtok(NULL, " ,;\t");
412    if(foo == NULL){
413      sprintf( painCave.errMsg,
414 <             "error in reading velocity x from %s\n"
415 <             "natoms  = %d, index = %d\n",
409 <             c_in_name, n_atoms, atomIndex );
414 >             "error in reading velocity x from %s\n",
415 >             c_in_name );
416      return strdup( painCave.errMsg );
417    }
418    vel[0] = atof( foo );
# Line 414 | Line 420 | char* InitializeFromFile::parseDumpLine(char* readLine
420    foo = strtok(NULL, " ,;\t");
421    if(foo == NULL){
422      sprintf( painCave.errMsg,
423 <             "error in reading velocity y from %s\n"
424 <             "natoms  = %d, index = %d\n",
419 <             c_in_name, n_atoms, atomIndex );
423 >             "error in reading velocity x from %s\n",
424 >             c_in_name );
425      return strdup( painCave.errMsg );
426    }
427    vel[1] = atof( foo );
# Line 424 | Line 429 | char* InitializeFromFile::parseDumpLine(char* readLine
429    foo = strtok(NULL, " ,;\t");
430    if(foo == NULL){
431      sprintf( painCave.errMsg,
432 <             "error in reading velocity z from %s\n"
433 <             "natoms  = %d, index = %d\n",
429 <             c_in_name, n_atoms, atomIndex );
432 >             "error in reading velocity x from %s\n",
433 >             c_in_name );
434      return strdup( painCave.errMsg );
435    }
436    vel[2] = atof( foo );
437  
438  
439 +  // add the positions and velocities to the atom
440 +
441 +  sd->setPos( pos );
442 +  sd->setVel( vel );
443 +
444 +  if (!sd->isDirectional())
445 +    return NULL;
446 +
447    // get the quaternions
448  
449 <  if( atoms[atomIndex]->isDirectional() ){
449 >  if( sd->isDirectional() ){
450  
451      foo = strtok(NULL, " ,;\t");
452      if(foo == NULL){
453 <      sprintf(painCave.errMsg,
454 <              "error in reading quaternion 0 from %s\n"
455 <              "natoms  = %d, index = %d\n",
444 <              c_in_name, n_atoms, atomIndex );
453 >      sprintf( painCave.errMsg,
454 >                     "error in reading velocity x from %s\n",
455 >                      c_in_name );
456        return strdup( painCave.errMsg );
457      }
458      q[0] = atof( foo );
# Line 449 | Line 460 | char* InitializeFromFile::parseDumpLine(char* readLine
460      foo = strtok(NULL, " ,;\t");
461      if(foo == NULL){
462        sprintf( painCave.errMsg,
463 <               "error in reading quaternion 1 from %s\n"
464 <               "natoms  = %d, index = %d\n",
454 <               c_in_name, n_atoms, atomIndex );
463 >                     "error in reading velocity x from %s\n",
464 >                      c_in_name );
465        return strdup( painCave.errMsg );
466      }
467      q[1] = atof( foo );
# Line 459 | Line 469 | char* InitializeFromFile::parseDumpLine(char* readLine
469      foo = strtok(NULL, " ,;\t");
470      if(foo == NULL){
471        sprintf( painCave.errMsg,
472 <               "error in reading quaternion 2 from %s\n"
473 <               "natoms  = %d, index = %d\n",
464 <               c_in_name, n_atoms, atomIndex );
472 >                     "error in reading velocity x from %s\n",
473 >                      c_in_name );
474        return strdup( painCave.errMsg );
475      }
476      q[2] = atof( foo );
# Line 469 | Line 478 | char* InitializeFromFile::parseDumpLine(char* readLine
478      foo = strtok(NULL, " ,;\t");
479      if(foo == NULL){
480        sprintf( painCave.errMsg,
481 <               "error in reading quaternion 3 from %s\n"
482 <               "natoms  = %d, index = %d\n",
474 <               c_in_name, n_atoms, atomIndex );
481 >                     "error in reading velocity x from %s\n",
482 >                      c_in_name );
483        return strdup( painCave.errMsg );
484      }
485      q[3] = atof( foo );
# Line 481 | Line 489 | char* InitializeFromFile::parseDumpLine(char* readLine
489      foo = strtok(NULL, " ,;\t");
490      if(foo == NULL){
491        sprintf( painCave.errMsg,
492 <               "error in reading angular momentum jx from %s\n"
493 <               "natoms  = %d, index = %d\n",
486 <               c_in_name, n_atoms, atomIndex );
492 >                     "error in reading velocity x from %s\n",
493 >                      c_in_name );
494        return strdup( painCave.errMsg );
495      }
496 <    jx = atof( foo );
496 >    ji[0] = atof( foo );
497  
498      foo = strtok(NULL, " ,;\t");
499      if(foo == NULL){
500        sprintf( painCave.errMsg,
501 <               "error in reading angular momentum jy from %s\n"
502 <               "natoms  = %d, index = %d\n",
496 <               c_in_name, n_atoms, atomIndex );
501 >                     "error in reading velocity x from %s\n",
502 >                      c_in_name );
503        return strdup( painCave.errMsg );
504      }
505 <    jy = atof(foo );
505 >    ji[1] = atof(foo );
506  
507      foo = strtok(NULL, " ,;\t");
508      if(foo == NULL){
509        sprintf( painCave.errMsg,
510 <               "error in reading angular momentum jz from %s\n"
511 <               "natoms  = %d, index = %d\n",
506 <               c_in_name, n_atoms, atomIndex );
510 >                     "error in reading velocity x from %s\n",
511 >                      c_in_name );
512        return strdup( painCave.errMsg );
513      }
514 <    jz = atof( foo );
514 >    ji[2] = atof( foo );
515  
511 –    dAtom = ( DirectionalAtom* )atoms[atomIndex];
516  
517      // check that the quaternion vector is normalized
518  
# Line 520 | Line 524 | char* InitializeFromFile::parseDumpLine(char* readLine
524      q[2] = q[2] / qLength;
525      q[3] = q[3] / qLength;
526  
527 <    dAtom->setQ( q );
527 >    // add quaternion and angular velocities
528  
529 <    // add the angular velocities
530 <
527 <    dAtom->setJx( jx );
528 <    dAtom->setJy( jy );
529 <    dAtom->setJz( jz );
529 >    sd->setQ( q );
530 >    sd->setJ( ji );
531    }
532  
532 –  // add the positions and velocities to the atom
533  
534 –  atoms[atomIndex]->setPos( pos );
535 –  atoms[atomIndex]->setVel( vel );
534  
535    return NULL;
536   }
# Line 583 | Line 581 | char* InitializeFromFile::parseCommentLine(char* readL
581    entry_plug->setBoxM( theBoxMat3 );
582  
583    //get chi and integralOfChidt, they should appear by pair
586 –  foo = strtok(NULL, " ,;\t\n");
587 –  if(foo != NULL){
588 –    chi = atof(foo);
584  
585 +  if( entry_plug->useInitXSstate ){
586      foo = strtok(NULL, " ,;\t\n");
587 <    if(foo == NULL){
588 <      sprintf( painCave.errMsg,
589 <               "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
590 <      return strdup( painCave.errMsg );
587 >    if(foo != NULL){
588 >      chi = atof(foo);
589 >      
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 );
595 >      }
596 >      integralOfChidt = atof( foo );
597 >      
598 >      //push chi and integralOfChidt into SimInfo::properties which can be
599 >      //retrieved by integrator later
600 >      DoubleData* chiValue = new DoubleData();
601 >      chiValue->setID(CHIVALUE_ID);
602 >      chiValue->setData(chi);
603 >      entry_plug->addProperty(chiValue);
604 >      
605 >      DoubleData* integralOfChidtValue = new DoubleData();
606 >      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
607 >      integralOfChidtValue->setData(integralOfChidt);
608 >      entry_plug->addProperty(integralOfChidtValue);
609 >      
610      }
611 <    integralOfChidt = atof( foo );
612 <
613 <    //push chi and integralOfChidt into SimInfo::properties which can be
611 >    else
612 >      return NULL;
613 >    
614 >    //get eta
615 >    foo = strtok(NULL, " ,;\t\n");
616 >    if(foo != NULL ){
617 >  
618 >      for(int i = 0 ; i < 9; i++){
619 >        
620 >        if(foo == NULL){
621 >          sprintf( painCave.errMsg,
622 >                   "error in reading eta[%d] from %s\n", i, c_in_name );
623 >          return strdup( painCave.errMsg );
624 >        }
625 >        eta[i] = atof( foo );
626 >        foo = strtok(NULL, " ,;\t\n");
627 >      }
628 >    }
629 >    else
630 >      return NULL;
631 >    
632 >    //push eta into SimInfo::properties which can be
633      //retrieved by integrator later
634 <    DoubleData* chiValue = new DoubleData();
635 <    chiValue->setID(CHIVALUE_ID);
636 <    chiValue->setData(chi);
637 <    entry_plug->addProperty(chiValue);
638 <
605 <    DoubleData* integralOfChidtValue = new DoubleData();
606 <    integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
607 <    integralOfChidtValue->setData(integralOfChidt);
608 <    entry_plug->addProperty(integralOfChidtValue);
609 <
634 >    
635 >    DoubleArrayData* etaValue = new DoubleArrayData();
636 >    etaValue->setID(ETAVALUE_ID);
637 >    etaValue->setData(eta, 9);
638 >    entry_plug->addProperty(etaValue);
639    }
611 –  else
612 –    return NULL;
640  
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 –
641    return NULL;
642   }
643  
# Line 642 | Line 649 | void initFile::nodeZeroError( void ){
649    int j, myStatus;
650  
651    myStatus = 0;
652 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
652 >  for (j = 0; j < mpiSim->getNprocessors(); j++) {
653      MPI_Send( &myStatus, 1, MPI_INT, j,
654                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
655    }

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