ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 837 by tim, Wed Oct 29 00:19:10 2003 UTC

# Line 1 | Line 1
1 + #define _FILE_OFFSET_BITS 64
2   #include <iostream>
3 < #include <cmath>
3 > #include <math.h>
4  
5   #include <stdio.h>
6   #include <stdlib.h>
# Line 10 | Line 11
11  
12   #include "ReadWrite.hpp"
13   #include "simError.h"
14 + #include "GenericData.hpp"
15  
16   #ifdef IS_MPI
17   #include <mpi.h>
# Line 26 | Line 28 | InitializeFromFile :: InitializeFromFile( char *in_nam
28  
29   #endif // is_mpi
30  
31 < InitializeFromFile :: InitializeFromFile( char *in_name ){
31 > InitializeFromFile::InitializeFromFile( char *in_name ){
32 >
33   #ifdef IS_MPI
34    if (worldRank == 0) {
35   #endif
# Line 38 | Line 41 | InitializeFromFile :: InitializeFromFile( char *in_nam
41      painCave.isFatal = 1;
42      simError();
43    }
44 <  
44 >
45    strcpy( c_in_name, in_name);
46   #ifdef IS_MPI
47    }
48   strcpy( checkPointMsg, "Infile opened for reading successfully." );
49    MPIcheckPoint();
50   #endif
51 <  return;  
51 >  return;
52   }
53  
54 < InitializeFromFile :: ~InitializeFromFile( ){
54 > InitializeFromFile::~InitializeFromFile( ){
55   #ifdef IS_MPI
56    if (worldRank == 0) {
57   #endif
# Line 71 | Line 74 | void InitializeFromFile :: readInit( SimInfo* the_simn
74  
75   void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
76  
77 <  int i, j, done, which_node, which_atom; // loop counter
77 >  int i, j;
78  
79 + #ifdef IS_MPI
80 +  int done, which_node, which_atom; // loop counter
81 + #endif //is_mpi
82 +
83    const int BUFFERSIZE = 2000; // size of the read buffer
84    int n_atoms; // the number of atoms
85 <  char read_buffer[BUFFERSIZE]; //the line buffer for reading
79 < #ifdef IS_MPI
80 <  char send_buffer[BUFFERSIZE];
81 < #endif
85 >  char read_buffer[BUFFERSIZE]; //the line buffer for reading
86  
87 <  char *eof_test; // ptr to see when we reach the end of the file
87 >  char *eof_test; // ptr to see when we reach the end of the file
88    char *parseErr;
85 –  int procIndex;
86 –  double currTime;
87 –  double boxMat[9];
88 –  double theBoxMat3[3][3];
89  
90    simnfo = the_simnfo;
91  
# Line 102 | Line 102 | void InitializeFromFile :: readInit( SimInfo* the_simn
102  
103    n_atoms = atoi( read_buffer );
104  
105 –  Atom **atoms = simnfo->atoms;
106 –  DirectionalAtom* dAtom;
107 –
105    if( n_atoms != simnfo->n_atoms ){
106      sprintf( painCave.errMsg,
107               "Initialize from File error. %s n_atoms, %d, "
# Line 113 | Line 110 | void InitializeFromFile :: readInit( SimInfo* the_simn
110      painCave.isFatal = 1;
111      simError();
112    }
113 <  
114 <  //read the box mat from the comment line
115 <  
113 >
114 >  //read the box mat from the comment line
115 >
116    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
117    if(eof_test == NULL){
118      sprintf( painCave.errMsg,
# Line 124 | Line 121 | void InitializeFromFile :: readInit( SimInfo* the_simn
121      simError();
122    }
123  
124 <  parseErr = parseBoxLine( read_buffer, boxMat, currTime );
124 >
125 >
126 >  parseErr = parseCommentLine( read_buffer, simnfo);
127    if( parseErr != NULL ){
128      strcpy( painCave.errMsg, parseErr );
129      painCave.isFatal = 1;
130      simError();
131    }
132  
133 <  for(i=0;i<3;i++)
135 <    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
133 >  //parse dump lines
134  
137 –  simnfo->setBoxM( theBoxMat3 );
138 –  simnfo->setTime( currTime );
139 –
140 –
135    for( i=0; i < n_atoms; i++){
136 <    
136 >
137      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
138      if(eof_test == NULL){
139        sprintf(painCave.errMsg,
# Line 151 | Line 145 | void InitializeFromFile :: readInit( SimInfo* the_simn
145        simError();
146      }
147  
148 <    
148 >
149      parseErr = parseDumpLine( read_buffer, i );
150      if( parseErr != NULL ){
151        strcpy( painCave.errMsg, parseErr );
# Line 169 | Line 163 | void InitializeFromFile :: readInit( SimInfo* the_simn
163  
164    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
165    int haveError;
166 <  
166 >
167    MPI_Status istatus;
168    int *AtomToProcMap = mpiSim->getAtomToProcMap();
169  
170 <  
170 >
171    haveError = 0;
172    if (worldRank == 0) {
173  
174      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
175      if( eof_test == NULL ){
176        sprintf( painCave.errMsg,
177 <               "Error reading 1st line of %d \n ",c_in_name);
177 >               "Error reading 1st line of %s \n ",c_in_name);
178        haveError = 1;
179        simError();
180      }
181 <    
181 >
182      n_atoms = atoi( read_buffer );
183 <    
190 <    Atom **atoms = simnfo->atoms;
191 <    DirectionalAtom* dAtom;
192 <
183 >
184      // Check to see that the number of atoms in the intial configuration file is the
185      // same as declared in simBass.
186 <    
186 >
187      if( n_atoms != mpiSim->getTotAtoms() ){
188        sprintf( painCave.errMsg,
189                 "Initialize from File error. %s n_atoms, %d, "
# Line 201 | Line 192 | void InitializeFromFile :: readInit( SimInfo* the_simn
192        haveError= 1;
193        simError();
194      }
195 <    
196 <    //read the boxMat from the comment line
197 <    
195 >
196 >    //read the boxMat from the comment line
197 >
198      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
199      if(eof_test == NULL){
200        sprintf( painCave.errMsg,
# Line 211 | Line 202 | void InitializeFromFile :: readInit( SimInfo* the_simn
202        haveError = 1;
203        simError();
204      }
205 <    
206 <    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
205 >
206 >    //Every single processor will parse the comment line by itself
207 >    //By using this way, we might lose some efficiency, but if we want to add
208 >    //more parameters into comment line, we only need to modify function
209 >    //parseCommentLine
210 >
211 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
212 >
213 >    parseErr = parseCommentLine( read_buffer, simnfo);
214 >
215      if( parseErr != NULL ){
216        strcpy( painCave.errMsg, parseErr );
217        haveError = 1;
218        simError();
219      }
220  
222 –    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
223 –    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
224 –  
225 –    if(haveError) nodeZeroError();
226 –
221      for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
222 <      
222 >
223        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
224        if(eof_test == NULL){
225          sprintf(painCave.errMsg,
# Line 236 | Line 230 | void InitializeFromFile :: readInit( SimInfo* the_simn
230          haveError= 1;
231          simError();
232        }
233 <    
233 >
234        if(haveError) nodeZeroError();
235  
236        // Get the Node number which wants this atom:
237 <      which_node = AtomToProcMap[i];    
237 >      which_node = AtomToProcMap[i];
238        if (which_node == 0) {
239          parseErr = parseDumpLine( read_buffer, i );
240          if( parseErr != NULL ){
241            strcpy( painCave.errMsg, parseErr );
242            haveError = 1;
243            simError();
244 <        }    
244 >        }
245          if(haveError) nodeZeroError();
246 <      }
247 <      
246 >      }
247 >
248        else {
249 <      
249 >
250          myStatus = 1;
251 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
251 >        MPI_Send(&myStatus, 1, MPI_INT, which_node,
252                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
253 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
253 >        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,
257 >        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
258                   MPI_COMM_WORLD, &istatus);
259 <        
259 >
260          if(!myStatus) nodeZeroError();
261        }
262      }
263      myStatus = -1;
264 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
265 <      MPI_Send( &myStatus, 1, MPI_INT, j,
264 >    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
265 >      MPI_Send( &myStatus, 1, MPI_INT, j,
266                  TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
267      }
268 <    
268 >
269    } else {
276 –    
277 –    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
278 –    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
270  
271 +    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
272 +
273 +    parseErr = parseCommentLine( read_buffer, simnfo);
274 +
275 +    if( parseErr != NULL ){
276 +      strcpy( painCave.errMsg, parseErr );
277 +      haveError = 1;
278 +      simError();
279 +    }
280 +
281 +
282      done = 0;
283      while (!done) {
284  
285 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
285 >      MPI_Recv(&myStatus, 1, MPI_INT, 0,
286                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
287 <      
287 >
288        if(!myStatus) anonymousNodeDie();
289 <      
289 >
290        if(myStatus < 0) break;
291  
292 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
292 >      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,
294 >      MPI_Recv(&which_atom, 1, MPI_INT, 0,
295                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
296 <      
296 >
297        myStatus = 1;
298        parseErr = parseDumpLine( read_buffer, which_atom );
299        if( parseErr != NULL ){
# Line 299 | Line 301 | void InitializeFromFile :: readInit( SimInfo* the_simn
301          myStatus = 0;;
302          simError();
303        }
304 <      
305 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
304 >
305 >      MPI_Send( &myStatus, 1, MPI_INT, 0,
306                  TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
307 <      
307 >
308      }
309    }
310 <    
310 >
311   // last  thing last, enable  fatalities.
312    painCave.isEventLoop = 0;
313  
312 –  for(i=0;i<3;i++)
313 –    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
314  
315 –  simnfo->setBoxM( theBoxMat3 );
316 –  simnfo->setTime( currTime );
315  
318 –  
316   #endif
317   }
318  
319   char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
320  
321 <  char *foo; // the pointer to the current string token
322 <  
321 >  char *foo; // the pointer to the current string token
322 >
323    double pos[3]; // position place holders
324    double vel[3]; // velocity placeholders
325    double q[4]; // the quaternions
326    double jx, jy, jz; // angular velocity placeholders;
327    double qSqr, qLength; // needed to normalize the quaternion vector.
328 <  
328 >
329    Atom **atoms = simnfo->atoms;
330    DirectionalAtom* dAtom;
334 –  
335 –  int j, n_atoms, atomIndex;
331  
332 +  int n_atoms, atomIndex;
333 +
334   #ifdef IS_MPI
335 +  int j;
336 +
337    n_atoms = mpiSim->getTotAtoms();
338 <  atomIndex=-1;        
338 >  atomIndex=-1;
339    for (j=0; j < mpiSim->getMyNlocal(); j++) {
340      if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
341    }
# Line 346 | Line 345 | char* InitializeFromFile::parseDumpLine(char* readLine
345               "in file %s does not exist on processor %d .\n",
346               globalIndex, c_in_name, mpiSim->getMyNode() );
347      return strdup( painCave.errMsg );
348 <  }  
348 >  }
349   #else
350    n_atoms = simnfo->n_atoms;
351    atomIndex = globalIndex;
352   #endif // is_mpi
353  
354    // set the string tokenizer
355 <  
355 >
356    foo = strtok(readLine, " ,;\t");
357 <  
357 >
358    // check the atom name to the current atom
359 <  
359 >
360    if( strcmp( foo, atoms[atomIndex]->getType() ) ){
361      sprintf( painCave.errMsg,
362               "Initialize from file error. Atom %s at index %d "
# Line 366 | Line 365 | char* InitializeFromFile::parseDumpLine(char* readLine
365               foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
366      return strdup( painCave.errMsg );
367    }
368 <    
368 >
369    // get the positions
370  
371    foo = strtok(NULL, " ,;\t");
# Line 378 | Line 377 | char* InitializeFromFile::parseDumpLine(char* readLine
377      return strdup( painCave.errMsg );
378    }
379    pos[0] = atof( foo );
380 <  
380 >
381    foo = strtok(NULL, " ,;\t");
382    if(foo == NULL){
383      sprintf( painCave.errMsg,
# Line 388 | Line 387 | char* InitializeFromFile::parseDumpLine(char* readLine
387      return strdup( painCave.errMsg );
388    }
389    pos[1] = atof( foo );
390 <    
390 >
391    foo = strtok(NULL, " ,;\t");
392    if(foo == NULL){
393      sprintf( painCave.errMsg,
# Line 397 | Line 396 | char* InitializeFromFile::parseDumpLine(char* readLine
396               c_in_name, n_atoms, atomIndex );
397      return strdup( painCave.errMsg );
398    }
399 <  pos[2] = atof( foo );    
399 >  pos[2] = atof( foo );
400  
401  
402    // get the velocities
# Line 411 | Line 410 | char* InitializeFromFile::parseDumpLine(char* readLine
410      return strdup( painCave.errMsg );
411    }
412    vel[0] = atof( foo );
413 <    
413 >
414    foo = strtok(NULL, " ,;\t");
415    if(foo == NULL){
416      sprintf( painCave.errMsg,
# Line 421 | Line 420 | char* InitializeFromFile::parseDumpLine(char* readLine
420      return strdup( painCave.errMsg );
421    }
422    vel[1] = atof( foo );
423 <    
423 >
424    foo = strtok(NULL, " ,;\t");
425    if(foo == NULL){
426      sprintf( painCave.errMsg,
# Line 431 | Line 430 | char* InitializeFromFile::parseDumpLine(char* readLine
430      return strdup( painCave.errMsg );
431    }
432    vel[2] = atof( foo );
433 <    
434 <    
433 >
434 >
435    // get the quaternions
436 <    
436 >
437    if( atoms[atomIndex]->isDirectional() ){
438 <      
438 >
439      foo = strtok(NULL, " ,;\t");
440      if(foo == NULL){
441        sprintf(painCave.errMsg,
# Line 446 | Line 445 | char* InitializeFromFile::parseDumpLine(char* readLine
445        return strdup( painCave.errMsg );
446      }
447      q[0] = atof( foo );
448 <      
448 >
449      foo = strtok(NULL, " ,;\t");
450      if(foo == NULL){
451        sprintf( painCave.errMsg,
# Line 456 | Line 455 | char* InitializeFromFile::parseDumpLine(char* readLine
455        return strdup( painCave.errMsg );
456      }
457      q[1] = atof( foo );
458 <      
458 >
459      foo = strtok(NULL, " ,;\t");
460      if(foo == NULL){
461        sprintf( painCave.errMsg,
# Line 466 | Line 465 | char* InitializeFromFile::parseDumpLine(char* readLine
465        return strdup( painCave.errMsg );
466      }
467      q[2] = atof( foo );
468 <      
468 >
469      foo = strtok(NULL, " ,;\t");
470      if(foo == NULL){
471        sprintf( painCave.errMsg,
# Line 476 | Line 475 | char* InitializeFromFile::parseDumpLine(char* readLine
475        return strdup( painCave.errMsg );
476      }
477      q[3] = atof( foo );
478 <      
478 >
479      // get the angular velocities
480 <      
480 >
481      foo = strtok(NULL, " ,;\t");
482      if(foo == NULL){
483        sprintf( painCave.errMsg,
# Line 488 | Line 487 | char* InitializeFromFile::parseDumpLine(char* readLine
487        return strdup( painCave.errMsg );
488      }
489      jx = atof( foo );
490 <      
490 >
491      foo = strtok(NULL, " ,;\t");
492      if(foo == NULL){
493        sprintf( painCave.errMsg,
# Line 498 | Line 497 | char* InitializeFromFile::parseDumpLine(char* readLine
497        return strdup( painCave.errMsg );
498      }
499      jy = atof(foo );
500 <      
500 >
501      foo = strtok(NULL, " ,;\t");
502      if(foo == NULL){
503        sprintf( painCave.errMsg,
# Line 508 | Line 507 | char* InitializeFromFile::parseDumpLine(char* readLine
507        return strdup( painCave.errMsg );
508      }
509      jz = atof( foo );
510 <      
510 >
511      dAtom = ( DirectionalAtom* )atoms[atomIndex];
512  
513      // check that the quaternion vector is normalized
514  
515      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
516 <      
516 >
517      qLength = sqrt( qSqr );
518      q[0] = q[0] / qLength;
519      q[1] = q[1] / qLength;
520      q[2] = q[2] / qLength;
521      q[3] = q[3] / qLength;
522 <      
522 >
523      dAtom->setQ( q );
524 <      
524 >
525      // add the angular velocities
526  
527      dAtom->setJx( jx );
528      dAtom->setJy( jy );
529      dAtom->setJz( jz );
530    }
531 <    
531 >
532    // add the positions and velocities to the atom
533 <    
533 >
534    atoms[atomIndex]->setPos( pos );
535    atoms[atomIndex]->setVel( vel );
536  
# Line 539 | Line 538 | char* InitializeFromFile::parseBoxLine(char* readLine,
538   }
539  
540  
541 < char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
543 <                                       double &time ){
541 > char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
542  
543 <  char *foo; // the pointer to the current string token
544 <  int j;
543 >  double currTime;
544 >  double boxMat[9];
545 >  double theBoxMat3[3][3];
546 >  double chi;
547 >  double integralOfChidt;
548 >  double eta[9];
549  
550 +  char *foo; // the pointer to the current string token
551 +
552    // set the string tokenizer
553 <  
553 >
554    foo = strtok(readLine, " ,;\t");
555    // set the timeToken.
556  
# Line 556 | Line 560 | char* InitializeFromFile::parseBoxLine(char* readLine,
560               c_in_name );
561      return strdup( painCave.errMsg );
562    }
559 –  time = atof( foo );
563  
564 <  // get the Hx vector
564 >  currTime = atof( foo );
565 >  entry_plug->setTime( currTime );
566  
567 <  foo = strtok(NULL, " ,;\t");
568 <  if(foo == NULL){
569 <    sprintf( painCave.errMsg,
570 <             "error in reading Hx[0] from %s\n",
571 <             c_in_name );
572 <    return strdup( painCave.errMsg );
567 >  //get H-Matrix
568 >
569 >  for(int i = 0 ; i < 9; i++){
570 >    foo = strtok(NULL, " ,;\t");
571 >    if(foo == NULL){
572 >      sprintf( painCave.errMsg,
573 >               "error in reading H[%d] from %s\n", i, c_in_name );
574 >      return strdup( painCave.errMsg );
575 >    }
576 >    boxMat[i] = atof( foo );
577    }
570 –  boxMat[0] = atof( foo );
571 –  
572 –  foo = strtok(NULL, " ,;\t");
573 –  if(foo == NULL){
574 –    sprintf( painCave.errMsg,
575 –             "error in reading Hx[1] from %s\n",
576 –             c_in_name );
577 –    return strdup( painCave.errMsg );
578 –  }
579 –  boxMat[1] = atof( foo );
580 –    
581 –  foo = strtok(NULL, " ,;\t");
582 –  if(foo == NULL){
583 –    sprintf( painCave.errMsg,
584 –             "error in reading Hx[2] from %s\n",
585 –             c_in_name );
586 –    return strdup( painCave.errMsg );
587 –  }
588 –  boxMat[2] = atof( foo );    
578  
579 <  // get the Hy vector
579 >  for(int i=0;i<3;i++)
580 >    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
581  
582 <  foo = strtok(NULL, " ,;\t");
583 <  if(foo == NULL){
594 <    sprintf( painCave.errMsg,
595 <             "error in reading Hy[0] from %s\n",
596 <             c_in_name );
597 <    return strdup( painCave.errMsg );
598 <  }
599 <  boxMat[3] = atof( foo );
600 <  
601 <  foo = strtok(NULL, " ,;\t");
602 <  if(foo == NULL){
603 <    sprintf( painCave.errMsg,
604 <             "error in reading Hy[1] from %s\n",
605 <             c_in_name );
606 <    return strdup( painCave.errMsg );
607 <  }
608 <  boxMat[4] = atof( foo );
609 <    
610 <  foo = strtok(NULL, " ,;\t");
611 <  if(foo == NULL){
612 <    sprintf( painCave.errMsg,
613 <             "error in reading Hy[2] from %s\n",
614 <             c_in_name );
615 <    return strdup( painCave.errMsg );
616 <  }
617 <  boxMat[5] = atof( foo );    
582 >  //set H-Matrix
583 >  entry_plug->setBoxM( theBoxMat3 );
584  
585 <  // get the Hz vector
585 >  //get chi and integralOfChidt, they should appear by pair
586 >  foo = strtok(NULL, " ,;\t\n");
587 >  if(foo != NULL){
588 >    chi = atof(foo);
589  
590 <  foo = strtok(NULL, " ,;\t");
591 <  if(foo == NULL){
592 <    sprintf( painCave.errMsg,
593 <             "error in reading Hz[0] from %s\n",
594 <             c_in_name );
595 <    return strdup( painCave.errMsg );
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 <  boxMat[6] = atof( foo );
612 <  
613 <  foo = strtok(NULL, " ,;\t");
614 <  if(foo == NULL){
615 <    sprintf( painCave.errMsg,
616 <             "error in reading Hz[1] from %s\n",
617 <             c_in_name );
618 <    return strdup( painCave.errMsg );
611 >  else
612 >    return NULL;
613 >
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    }
637 –  boxMat[7] = atof( foo );
638 –    
639 –  foo = strtok(NULL, " ,;\t");
640 –  if(foo == NULL){
641 –    sprintf( painCave.errMsg,
642 –             "error in reading Hz[2] from %s\n",
643 –             c_in_name );
644 –    return strdup( painCave.errMsg );
645 –  }
646 –  boxMat[8] = atof( foo );    
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 +
634    return NULL;
635   }
636  
651 –
637   #ifdef IS_MPI
638  
639   // a couple of functions to let us escape the read loop
640  
641   void initFile::nodeZeroError( void ){
642    int j, myStatus;
643 <  
643 >
644    myStatus = 0;
645 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
646 <    MPI_Send( &myStatus, 1, MPI_INT, j,
645 >  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
646 >    MPI_Send( &myStatus, 1, MPI_INT, j,
647                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
648 <  }  
664 <  
648 >  }
649  
650 +
651    MPI_Finalize();
652    exit (0);
653 <  
653 >
654   }
655  
656   void initFile::anonymousNodeDie( void ){

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines