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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 644 by mmeineke, Tue Jul 22 16:41:08 2003 UTC vs.
Revision 874 by mmeineke, Fri Nov 21 20:10:02 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 | using namespace initFile;
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." );
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;  
55 >  return;
56   }
57  
58 < InitializeFromFile :: ~InitializeFromFile( ){
58 > InitializeFromFile::~InitializeFromFile( ){
59   #ifdef IS_MPI
60    if (worldRank == 0) {
61   #endif
# Line 71 | Line 78 | void InitializeFromFile :: readInit( SimInfo* the_simn
78  
79   void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
80  
81 <  int i, j, done, which_node, which_atom; // loop counter
81 >  int i, j;
82  
83 + #ifdef IS_MPI
84 +  int done, which_node, which_atom; // loop counter
85 + #endif //is_mpi
86 +
87    const int BUFFERSIZE = 2000; // size of the read buffer
88    int n_atoms; // the number of atoms
89 <  char read_buffer[BUFFERSIZE]; //the line buffer for reading
79 < #ifdef IS_MPI
80 <  char send_buffer[BUFFERSIZE];
81 < #endif
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
91 >  char *eof_test; // ptr to see when we reach the end of the file
92    char *parseErr;
85 –  int procIndex;
86 –  double currTime;
87 –  double boxMat[9];
88 –  double theBoxMat3[3][3];
93  
94    simnfo = the_simnfo;
95  
# Line 102 | Line 106 | void InitializeFromFile :: readInit( SimInfo* the_simn
106  
107    n_atoms = atoi( read_buffer );
108  
105 –  Atom **atoms = simnfo->atoms;
106 –  DirectionalAtom* dAtom;
107 –
109    if( n_atoms != simnfo->n_atoms ){
110      sprintf( painCave.errMsg,
111               "Initialize from File error. %s n_atoms, %d, "
# Line 113 | Line 114 | void InitializeFromFile :: readInit( SimInfo* the_simn
114      painCave.isFatal = 1;
115      simError();
116    }
117 <  
118 <  //read the box mat from the comment line
119 <  
117 >
118 >  //read the box mat from the comment line
119 >
120    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
121    if(eof_test == NULL){
122      sprintf( painCave.errMsg,
# Line 124 | Line 125 | void InitializeFromFile :: readInit( SimInfo* the_simn
125      simError();
126    }
127  
128 <  parseErr = parseBoxLine( read_buffer, boxMat, currTime );
128 >
129 >
130 >  parseErr = parseCommentLine( read_buffer, simnfo);
131    if( parseErr != NULL ){
132      strcpy( painCave.errMsg, parseErr );
133      painCave.isFatal = 1;
134      simError();
135    }
136  
137 <  for(i=0;i<3;i++)
135 <    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
137 >  //parse dump lines
138  
137 –  simnfo->setBoxM( theBoxMat3 );
138 –  simnfo->setTime( currTime );
139 –
140 –
139    for( i=0; i < n_atoms; i++){
140 <    
140 >
141      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
142      if(eof_test == NULL){
143        sprintf(painCave.errMsg,
# Line 151 | Line 149 | void InitializeFromFile :: readInit( SimInfo* the_simn
149        simError();
150      }
151  
152 <    
152 >
153      parseErr = parseDumpLine( read_buffer, i );
154      if( parseErr != NULL ){
155        strcpy( painCave.errMsg, parseErr );
# Line 169 | Line 167 | void InitializeFromFile :: readInit( SimInfo* the_simn
167  
168    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
169    int haveError;
170 <  
170 >
171    MPI_Status istatus;
172    int *AtomToProcMap = mpiSim->getAtomToProcMap();
173  
174 <  
174 >
175    haveError = 0;
176    if (worldRank == 0) {
177  
178      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
179      if( eof_test == NULL ){
180        sprintf( painCave.errMsg,
181 <               "Error reading 1st line of %d \n ",c_in_name);
181 >               "Error reading 1st line of %s \n ",c_in_name);
182        haveError = 1;
183        simError();
184      }
185 <    
185 >
186      n_atoms = atoi( read_buffer );
187 <    
190 <    Atom **atoms = simnfo->atoms;
191 <    DirectionalAtom* dAtom;
192 <
187 >
188      // Check to see that the number of atoms in the intial configuration file is the
189      // same as declared in simBass.
190 <    
190 >
191      if( n_atoms != mpiSim->getTotAtoms() ){
192        sprintf( painCave.errMsg,
193                 "Initialize from File error. %s n_atoms, %d, "
# Line 201 | Line 196 | void InitializeFromFile :: readInit( SimInfo* the_simn
196        haveError= 1;
197        simError();
198      }
199 <    
200 <    //read the boxMat from the comment line
201 <    
199 >
200 >    //read the boxMat from the comment line
201 >
202      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
203      if(eof_test == NULL){
204        sprintf( painCave.errMsg,
# Line 211 | Line 206 | void InitializeFromFile :: readInit( SimInfo* the_simn
206        haveError = 1;
207        simError();
208      }
209 <    
210 <    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
209 >
210 >    //Every single processor will parse the comment line by itself
211 >    //By using this way, we might lose some efficiency, but if we want to add
212 >    //more parameters into comment line, we only need to modify function
213 >    //parseCommentLine
214 >
215 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
216 >
217 >    parseErr = parseCommentLine( read_buffer, simnfo);
218 >
219      if( parseErr != NULL ){
220        strcpy( painCave.errMsg, parseErr );
221        haveError = 1;
222        simError();
223      }
224  
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 –
225      for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
226 <      
226 >
227        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
228        if(eof_test == NULL){
229          sprintf(painCave.errMsg,
# Line 236 | Line 234 | void InitializeFromFile :: readInit( SimInfo* the_simn
234          haveError= 1;
235          simError();
236        }
237 <    
237 >
238        if(haveError) nodeZeroError();
239  
240        // Get the Node number which wants this atom:
241 <      which_node = AtomToProcMap[i];    
241 >      which_node = AtomToProcMap[i];
242        if (which_node == 0) {
243          parseErr = parseDumpLine( read_buffer, i );
244          if( parseErr != NULL ){
245            strcpy( painCave.errMsg, parseErr );
246            haveError = 1;
247            simError();
248 <        }    
248 >        }
249          if(haveError) nodeZeroError();
250 <      }
251 <      
250 >      }
251 >
252        else {
253 <      
253 >
254          myStatus = 1;
255 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
255 >        MPI_Send(&myStatus, 1, MPI_INT, which_node,
256                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
257 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
257 >        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
258                   TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
259          MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
260                   MPI_COMM_WORLD);
261 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
261 >        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
262                   MPI_COMM_WORLD, &istatus);
263 <        
263 >
264          if(!myStatus) nodeZeroError();
265        }
266      }
267      myStatus = -1;
268 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
269 <      MPI_Send( &myStatus, 1, MPI_INT, j,
268 >    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
269 >      MPI_Send( &myStatus, 1, MPI_INT, j,
270                  TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
271      }
272 <    
272 >
273    } else {
276 –    
277 –    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
278 –    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
274  
275 +    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
276 +
277 +    parseErr = parseCommentLine( read_buffer, simnfo);
278 +
279 +    if( parseErr != NULL ){
280 +      strcpy( painCave.errMsg, parseErr );
281 +      haveError = 1;
282 +      simError();
283 +    }
284 +
285 +
286      done = 0;
287      while (!done) {
288  
289 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
289 >      MPI_Recv(&myStatus, 1, MPI_INT, 0,
290                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
291 <      
291 >
292        if(!myStatus) anonymousNodeDie();
293 <      
293 >
294        if(myStatus < 0) break;
295  
296 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
296 >      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
297                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
298 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
298 >      MPI_Recv(&which_atom, 1, MPI_INT, 0,
299                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
300 <      
300 >
301        myStatus = 1;
302        parseErr = parseDumpLine( read_buffer, which_atom );
303        if( parseErr != NULL ){
# Line 299 | Line 305 | void InitializeFromFile :: readInit( SimInfo* the_simn
305          myStatus = 0;;
306          simError();
307        }
308 <      
309 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
308 >
309 >      MPI_Send( &myStatus, 1, MPI_INT, 0,
310                  TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
311 <      
311 >
312      }
313    }
314 <    
314 >
315   // last  thing last, enable  fatalities.
316    painCave.isEventLoop = 0;
317  
312 –  for(i=0;i<3;i++)
313 –    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
318  
315 –  simnfo->setBoxM( theBoxMat3 );
316 –  simnfo->setTime( currTime );
319  
318 –  
320   #endif
321   }
322  
323   char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
324  
325 <  char *foo; // the pointer to the current string token
326 <  
327 <  double rx, ry, rz; // position place holders
328 <  double vx, vy, vz; // velocity placeholders
325 >  char *foo; // the pointer to the current string token
326 >
327 >  double pos[3]; // position place holders
328 >  double vel[3]; // velocity placeholders
329    double q[4]; // the quaternions
330    double jx, jy, jz; // angular velocity placeholders;
331    double qSqr, qLength; // needed to normalize the quaternion vector.
332 <  
332 >
333    Atom **atoms = simnfo->atoms;
334    DirectionalAtom* dAtom;
334 –  
335 –  int j, n_atoms, atomIndex;
335  
336 +  int n_atoms, atomIndex;
337 +
338   #ifdef IS_MPI
339 +  int j;
340 +
341    n_atoms = mpiSim->getTotAtoms();
342 <  atomIndex=-1;        
342 >  atomIndex=-1;
343    for (j=0; j < mpiSim->getMyNlocal(); j++) {
344      if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
345    }
# Line 346 | Line 349 | char* InitializeFromFile::parseDumpLine(char* readLine
349               "in file %s does not exist on processor %d .\n",
350               globalIndex, c_in_name, mpiSim->getMyNode() );
351      return strdup( painCave.errMsg );
352 <  }  
352 >  }
353   #else
354    n_atoms = simnfo->n_atoms;
355    atomIndex = globalIndex;
356   #endif // is_mpi
357  
358    // set the string tokenizer
359 <  
359 >
360    foo = strtok(readLine, " ,;\t");
361 <  
361 >
362    // check the atom name to the current atom
363 <  
363 >
364    if( strcmp( foo, atoms[atomIndex]->getType() ) ){
365      sprintf( painCave.errMsg,
366               "Initialize from file error. Atom %s at index %d "
# Line 366 | Line 369 | char* InitializeFromFile::parseDumpLine(char* readLine
369               foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
370      return strdup( painCave.errMsg );
371    }
372 <    
372 >
373    // get the positions
374  
375    foo = strtok(NULL, " ,;\t");
# Line 377 | Line 380 | char* InitializeFromFile::parseDumpLine(char* readLine
380               c_in_name, n_atoms, atomIndex );
381      return strdup( painCave.errMsg );
382    }
383 <  rx = atof( foo );
384 <  
383 >  pos[0] = atof( foo );
384 >
385    foo = strtok(NULL, " ,;\t");
386    if(foo == NULL){
387      sprintf( painCave.errMsg,
# Line 387 | Line 390 | char* InitializeFromFile::parseDumpLine(char* readLine
390               c_in_name, n_atoms, atomIndex );
391      return strdup( painCave.errMsg );
392    }
393 <  ry = atof( foo );
394 <    
393 >  pos[1] = atof( foo );
394 >
395    foo = strtok(NULL, " ,;\t");
396    if(foo == NULL){
397      sprintf( painCave.errMsg,
# Line 397 | Line 400 | char* InitializeFromFile::parseDumpLine(char* readLine
400               c_in_name, n_atoms, atomIndex );
401      return strdup( painCave.errMsg );
402    }
403 <  rz = atof( foo );    
403 >  pos[2] = atof( foo );
404  
405  
406    // get the velocities
# Line 410 | Line 413 | char* InitializeFromFile::parseDumpLine(char* readLine
413               c_in_name, n_atoms, atomIndex );
414      return strdup( painCave.errMsg );
415    }
416 <  vx = atof( foo );
417 <    
416 >  vel[0] = atof( foo );
417 >
418    foo = strtok(NULL, " ,;\t");
419    if(foo == NULL){
420      sprintf( painCave.errMsg,
# Line 420 | Line 423 | char* InitializeFromFile::parseDumpLine(char* readLine
423               c_in_name, n_atoms, atomIndex );
424      return strdup( painCave.errMsg );
425    }
426 <  vy = atof( foo );
427 <    
426 >  vel[1] = atof( foo );
427 >
428    foo = strtok(NULL, " ,;\t");
429    if(foo == NULL){
430      sprintf( painCave.errMsg,
# Line 430 | Line 433 | char* InitializeFromFile::parseDumpLine(char* readLine
433               c_in_name, n_atoms, atomIndex );
434      return strdup( painCave.errMsg );
435    }
436 <  vz = atof( foo );
437 <    
438 <    
436 >  vel[2] = atof( foo );
437 >
438 >
439    // get the quaternions
440 <    
440 >
441    if( atoms[atomIndex]->isDirectional() ){
442 <      
442 >
443      foo = strtok(NULL, " ,;\t");
444      if(foo == NULL){
445        sprintf(painCave.errMsg,
# Line 446 | Line 449 | char* InitializeFromFile::parseDumpLine(char* readLine
449        return strdup( painCave.errMsg );
450      }
451      q[0] = atof( foo );
452 <      
452 >
453      foo = strtok(NULL, " ,;\t");
454      if(foo == NULL){
455        sprintf( painCave.errMsg,
# Line 456 | Line 459 | char* InitializeFromFile::parseDumpLine(char* readLine
459        return strdup( painCave.errMsg );
460      }
461      q[1] = atof( foo );
462 <      
462 >
463      foo = strtok(NULL, " ,;\t");
464      if(foo == NULL){
465        sprintf( painCave.errMsg,
# Line 466 | Line 469 | char* InitializeFromFile::parseDumpLine(char* readLine
469        return strdup( painCave.errMsg );
470      }
471      q[2] = atof( foo );
472 <      
472 >
473      foo = strtok(NULL, " ,;\t");
474      if(foo == NULL){
475        sprintf( painCave.errMsg,
# Line 476 | Line 479 | char* InitializeFromFile::parseDumpLine(char* readLine
479        return strdup( painCave.errMsg );
480      }
481      q[3] = atof( foo );
482 <      
482 >
483      // get the angular velocities
484 <      
484 >
485      foo = strtok(NULL, " ,;\t");
486      if(foo == NULL){
487        sprintf( painCave.errMsg,
# Line 488 | Line 491 | char* InitializeFromFile::parseDumpLine(char* readLine
491        return strdup( painCave.errMsg );
492      }
493      jx = atof( foo );
494 <      
494 >
495      foo = strtok(NULL, " ,;\t");
496      if(foo == NULL){
497        sprintf( painCave.errMsg,
# Line 498 | Line 501 | char* InitializeFromFile::parseDumpLine(char* readLine
501        return strdup( painCave.errMsg );
502      }
503      jy = atof(foo );
504 <      
504 >
505      foo = strtok(NULL, " ,;\t");
506      if(foo == NULL){
507        sprintf( painCave.errMsg,
# Line 508 | Line 511 | char* InitializeFromFile::parseDumpLine(char* readLine
511        return strdup( painCave.errMsg );
512      }
513      jz = atof( foo );
514 <      
514 >
515      dAtom = ( DirectionalAtom* )atoms[atomIndex];
516  
517      // check that the quaternion vector is normalized
518  
519      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
520 <      
520 >
521      qLength = sqrt( qSqr );
522      q[0] = q[0] / qLength;
523      q[1] = q[1] / qLength;
524      q[2] = q[2] / qLength;
525      q[3] = q[3] / qLength;
526 <      
526 >
527      dAtom->setQ( q );
528 <      
528 >
529      // add the angular velocities
530  
531      dAtom->setJx( jx );
532      dAtom->setJy( jy );
533      dAtom->setJz( jz );
534    }
535 <    
535 >
536    // add the positions and velocities to the atom
534 –    
535 –  atoms[atomIndex]->setX( rx );
536 –  atoms[atomIndex]->setY( ry );
537 –  atoms[atomIndex]->setZ( rz );
538 –    
539 –  atoms[atomIndex]->set_vx( vx );
540 –  atoms[atomIndex]->set_vy( vy );
541 –  atoms[atomIndex]->set_vz( vz );
537  
538 +  atoms[atomIndex]->setPos( pos );
539 +  atoms[atomIndex]->setVel( vel );
540 +
541    return NULL;
542   }
543  
544  
545 < char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
548 <                                       double &time ){
545 > char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
546  
547 <  char *foo; // the pointer to the current string token
548 <  int j;
547 >  double currTime;
548 >  double boxMat[9];
549 >  double theBoxMat3[3][3];
550 >  double chi;
551 >  double integralOfChidt;
552 >  double eta[9];
553  
554 +  char *foo; // the pointer to the current string token
555 +
556    // set the string tokenizer
557 <  
557 >
558    foo = strtok(readLine, " ,;\t");
559    // set the timeToken.
560  
# Line 561 | Line 564 | char* InitializeFromFile::parseBoxLine(char* readLine,
564               c_in_name );
565      return strdup( painCave.errMsg );
566    }
564 –  time = atof( foo );
567  
568 <  // get the Hx vector
568 >  currTime = atof( foo );
569 >  entry_plug->setTime( currTime );
570  
571 <  foo = strtok(NULL, " ,;\t");
572 <  if(foo == NULL){
573 <    sprintf( painCave.errMsg,
574 <             "error in reading Hx[0] from %s\n",
575 <             c_in_name );
576 <    return strdup( painCave.errMsg );
571 >  //get H-Matrix
572 >
573 >  for(int i = 0 ; i < 9; i++){
574 >    foo = strtok(NULL, " ,;\t");
575 >    if(foo == NULL){
576 >      sprintf( painCave.errMsg,
577 >               "error in reading H[%d] from %s\n", i, c_in_name );
578 >      return strdup( painCave.errMsg );
579 >    }
580 >    boxMat[i] = atof( foo );
581    }
575 –  boxMat[0] = atof( foo );
576 –  
577 –  foo = strtok(NULL, " ,;\t");
578 –  if(foo == NULL){
579 –    sprintf( painCave.errMsg,
580 –             "error in reading Hx[1] from %s\n",
581 –             c_in_name );
582 –    return strdup( painCave.errMsg );
583 –  }
584 –  boxMat[1] = atof( foo );
585 –    
586 –  foo = strtok(NULL, " ,;\t");
587 –  if(foo == NULL){
588 –    sprintf( painCave.errMsg,
589 –             "error in reading Hx[2] from %s\n",
590 –             c_in_name );
591 –    return strdup( painCave.errMsg );
592 –  }
593 –  boxMat[2] = atof( foo );    
582  
583 <  // get the Hy vector
583 >  for(int i=0;i<3;i++)
584 >    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
585  
586 <  foo = strtok(NULL, " ,;\t");
587 <  if(foo == NULL){
599 <    sprintf( painCave.errMsg,
600 <             "error in reading Hy[0] from %s\n",
601 <             c_in_name );
602 <    return strdup( painCave.errMsg );
603 <  }
604 <  boxMat[3] = atof( foo );
605 <  
606 <  foo = strtok(NULL, " ,;\t");
607 <  if(foo == NULL){
608 <    sprintf( painCave.errMsg,
609 <             "error in reading Hy[1] from %s\n",
610 <             c_in_name );
611 <    return strdup( painCave.errMsg );
612 <  }
613 <  boxMat[4] = atof( foo );
614 <    
615 <  foo = strtok(NULL, " ,;\t");
616 <  if(foo == NULL){
617 <    sprintf( painCave.errMsg,
618 <             "error in reading Hy[2] from %s\n",
619 <             c_in_name );
620 <    return strdup( painCave.errMsg );
621 <  }
622 <  boxMat[5] = atof( foo );    
586 >  //set H-Matrix
587 >  entry_plug->setBoxM( theBoxMat3 );
588  
589 <  // get the Hz vector
589 >  //get chi and integralOfChidt, they should appear by pair
590 >  foo = strtok(NULL, " ,;\t\n");
591 >  if(foo != NULL){
592 >    chi = atof(foo);
593  
594 <  foo = strtok(NULL, " ,;\t");
595 <  if(foo == NULL){
596 <    sprintf( painCave.errMsg,
597 <             "error in reading Hz[0] from %s\n",
598 <             c_in_name );
599 <    return strdup( painCave.errMsg );
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 <  boxMat[6] = atof( foo );
616 <  
617 <  foo = strtok(NULL, " ,;\t");
618 <  if(foo == NULL){
619 <    sprintf( painCave.errMsg,
620 <             "error in reading Hz[1] from %s\n",
621 <             c_in_name );
622 <    return strdup( painCave.errMsg );
615 >  else
616 >    return NULL;
617 >
618 >  //get eta
619 >  for(int i = 0 ; i < 9; i++){
620 >    foo = strtok(NULL, " ,;\t");
621 >    if(foo == NULL){
622 >      sprintf( painCave.errMsg,
623 >               "error in reading eta[%d] from %s\n", i, c_in_name );
624 >      return strdup( painCave.errMsg );
625 >    }
626 >    eta[i] = atof( foo );
627    }
642 –  boxMat[7] = atof( foo );
643 –    
644 –  foo = strtok(NULL, " ,;\t");
645 –  if(foo == NULL){
646 –    sprintf( painCave.errMsg,
647 –             "error in reading Hz[2] from %s\n",
648 –             c_in_name );
649 –    return strdup( painCave.errMsg );
650 –  }
651 –  boxMat[8] = atof( foo );    
628  
629 +  //push eta into SimInfo::properties which can be
630 +  //retrieved by integrator later
631 +  //entry_plug->setBoxM( theBoxMat3 );
632 +  DoubleArrayData* etaValue = new DoubleArrayData();
633 +  etaValue->setID(ETAVALUE_ID);
634 +  etaValue->setData(eta, 9);
635 +  entry_plug->addProperty(etaValue);
636 +
637 +
638    return NULL;
639   }
640  
656 –
641   #ifdef IS_MPI
642  
643   // a couple of functions to let us escape the read loop
644  
645   void initFile::nodeZeroError( void ){
646    int j, myStatus;
647 <  
647 >
648    myStatus = 0;
649 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
650 <    MPI_Send( &myStatus, 1, MPI_INT, j,
649 >  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
650 >    MPI_Send( &myStatus, 1, MPI_INT, j,
651                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
652 <  }  
669 <  
652 >  }
653  
654 +
655    MPI_Finalize();
656    exit (0);
657 <  
657 >
658   }
659  
660   void initFile::anonymousNodeDie( void ){

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