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root/group/trunk/OOPSE/libmdtools/DumpReader.cpp
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Comparing trunk/OOPSE/libmdtools/DumpReader.cpp (file contents):
Revision 637 by gezelter, Thu Jul 17 21:50:01 2003 UTC vs.
Revision 1078 by tim, Tue Mar 2 20:32:40 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2 + #define _FILE_OFFSET_BITS 64
3 +
4 + #include <sys/types.h>
5 + #include <sys/stat.h>
6 +
7   #include <iostream>
8 < #include <cmath>
8 > #include <math.h>
9  
10   #include <stdio.h>
11   #include <stdlib.h>
12   #include <string.h>
7 – #include <unistd.h>
8 – #include <sys/types.h>
9 – #include <sys/stat.h>
13  
14 +
15   #include "ReadWrite.hpp"
16   #include "simError.h"
17  
# Line 16 | Line 20
20   #include "mpiSimulation.hpp"
21   #define TAKE_THIS_TAG_CHAR 0
22   #define TAKE_THIS_TAG_INT 1
23 + #endif // is_mpi
24  
25   namespace dumpRead{
26 +
27 + #ifdef IS_MPI
28    void nodeZeroError( void );
29    void anonymousNodeDie( void );
30 + #endif // is_mpi
31 +  
32   }
33  
34   using namespace dumpRead;
35  
27 – #endif // is_mpi
36  
37 < DumpReader :: DumpReader( char *in_name ){
37 > DumpReader :: DumpReader(const char *in_name ){
38 >
39 >  isScanned = false;
40 >  headFP = new FilePos;
41 >
42   #ifdef IS_MPI
43    if (worldRank == 0) {
44   #endif
45  
46 <  c_in_file = fopen(in_name, "r");
47 <  if(c_in_file == NULL){
46 >  inFile = fopen(in_name, "r");
47 >  if(inFile == NULL){
48      sprintf(painCave.errMsg,
49              "Cannot open file: %s\n", in_name);
50      painCave.isFatal = 1;
51      simError();
52    }
53    
54 <  strcpy( c_in_name, in_name);
54 >  strcpy( inName, in_name);
55   #ifdef IS_MPI
56    }
57    strcpy( checkPointMsg, "Dump file opened for reading successfully." );
# Line 53 | Line 65 | DumpReader :: ~DumpReader( ){
65    if (worldRank == 0) {
66   #endif
67    int error;
68 <  error = fclose( c_in_file );
68 >  error = fclose( inFile );
69    if( error ){
70      sprintf( painCave.errMsg,
71 <             "Error closing %s\n", c_in_name );
71 >             "Error closing %s\n", inName );
72      simError();
73    }
74   #ifdef IS_MPI
# Line 68 | Line 80 | DumpReader :: ~DumpReader( ){
80    return;
81   }
82  
83 + int DumpReader::getNframes( void ){
84  
85 < void DumpReader :: getFrame( SimInfo* the_simnfo, int whichFrame){
85 >  if( !isScanned ) scanFile();
86 >  return nFrames;
87 > }
88  
89 + void DumpReader::scanFile( void ){
90 +
91 +  int vectorSize;
92 +  int i, j, k;
93 +  int lineNum = 0;
94 +  char readBuffer[2000];
95 +  char* foo;
96 +  fpos_t *currPos;
97 +  double time;
98 +
99 +  FilePos *currFP;
100 +
101 +
102 + #ifdef IS_MPI
103 +  if( worldRank == 0 ){
104 + #endif // is_mpi
105 +    
106 +    rewind( inFile );
107 +    
108 +    currPos = new fpos_t;
109 +    fgetpos( inFile, currPos );
110 +    fgets( readBuffer, sizeof( readBuffer ), inFile );
111 +    lineNum++;
112 +    if( feof( inFile ) ){
113 +      sprintf( painCave.errMsg,
114 +               "File \"%s\" ended unexpectedly at line %d\n",
115 +               inName,
116 +               lineNum );
117 +      painCave.isFatal = 1;
118 +      simError();
119 +    }
120 +    
121 +    nFrames = 0;
122 +    while( !feof( inFile ) ){
123 +
124 +      headFP->add( currPos );
125 +      nFrames++;
126 +
127 +      i = atoi(readBuffer);
128 +      
129 +      fgets( readBuffer, sizeof( readBuffer ), inFile );
130 +      lineNum++;    
131 +      if( feof( inFile ) ){
132 +        sprintf( painCave.errMsg,
133 +                 "File \"%s\" ended unexpectedly at line %d\n",
134 +                 inName,
135 +                 lineNum );
136 +        painCave.isFatal = 1;
137 +        simError();
138 +      }
139 +      
140 + //       if(outTime){
141 + //      foo = strtok( readBuffer, " ,;\t" );
142 + //      time = atof( foo );
143 + //       }
144 +      
145 +      for(j=0; j<i; j++){
146 +        
147 +        fgets( readBuffer, sizeof( readBuffer ), inFile );
148 +        lineNum++;    
149 +        if( feof( inFile ) ){
150 +          sprintf( painCave.errMsg,
151 +                   "File \"%s\" ended unexpectedly at line %d,"
152 +                   " with atom %d\n",
153 +                   inName,
154 +                   lineNum,
155 +                   j );
156 +          painCave.isFatal = 1;
157 +          simError();
158 +        }
159 +        
160 +      }
161 +      
162 +      currPos = new fpos_t;
163 +      fgetpos( inFile, currPos );
164 +      fgets( readBuffer, sizeof( readBuffer ), inFile );
165 +      lineNum++;
166 +    }
167 +    
168 +    delete currPos;
169 +    rewind( inFile );
170 +    
171 +    frameStart = new FilePos*[nFrames];
172 +    currFP = headFP;
173 +    for(i=0; i<nFrames; i++){
174 +      
175 +      currFP = currFP->getNext();
176 +      if( currFP == NULL ){
177 +        sprintf( painCave.errMsg,
178 +                 "DumpReader error: scanFile FilePos mismatch at "
179 +                 "nFrames = %d\n",
180 +                 i );
181 +        painCave.isFatal = 1;
182 +        simError();
183 +      }
184 +      
185 +      frameStart[i] = currFP;
186 +    }
187 +
188 +    isScanned = true;
189 +
190 + #ifdef IS_MPI
191 +  }
192 +  strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
193 +  MPIcheckPoint();
194 + #endif // is_mpi
195 + }
196 +
197 + void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
198 +
199 +  simnfo = the_simnfo;
200 +
201 +  this->readSet( whichFrame );
202 + }
203 +
204 +
205 +
206 + void DumpReader :: readSet( int whichFrame ){
207 +
208    int i, j, done, which_node, which_atom; // loop counter
209  
210    const int BUFFERSIZE = 2000; // size of the read buffer
# Line 85 | Line 219 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
219    int procIndex;
220    double boxMat[9];
221    double theBoxMat3[3][3];
222 +  double time;
223  
224 <  simnfo = the_simnfo;
225 <
224 >  fpos_t *framePos;
225 >  
226   #ifndef IS_MPI
227 <  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
227 >  
228 >  framePos = frameStart[whichFrame]->getPos();
229 >
230 >  fsetpos(inFile, framePos);
231 >  
232 >
233 >  eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
234    if( eof_test == NULL ){
235      sprintf( painCave.errMsg,
236               "DumpReader error: error reading 1st line of \"%s\"\n",
237 <             c_in_name );
237 >             inName );
238      painCave.isFatal = 1;
239      simError();
240    }
# Line 107 | Line 248 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
248      sprintf( painCave.errMsg,
249               "DumpReader error. %s n_atoms, %d, "
250               "does not match the BASS file's n_atoms, %d.\n",
251 <             c_in_name, n_atoms, simnfo->n_atoms );
251 >             inName, n_atoms, simnfo->n_atoms );
252      painCave.isFatal = 1;
253      simError();
254    }
255    
256    //read the box mat from the comment line
257    
258 <  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
258 >  eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
259    if(eof_test == NULL){
260      sprintf( painCave.errMsg,
261 <             "error in reading commment in %s\n", c_in_name);
261 >             "error in reading commment in %s\n", inName);
262      painCave.isFatal = 1;
263      simError();
264    }
# Line 140 | Line 281 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
281  
282    for( i=0; i < n_atoms; i++){
283      
284 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
284 >    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
285      if(eof_test == NULL){
286        sprintf(painCave.errMsg,
287                "error in reading file %s\n"
288                "natoms  = %d; index = %d\n"
289                "error reading the line from the file.\n",
290 <              c_in_name, n_atoms, i );
290 >              inName, n_atoms, i );
291        painCave.isFatal = 1;
292        simError();
293      }
# Line 176 | Line 317 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
317    
318    haveError = 0;
319    if (worldRank == 0) {
320 <
321 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
320 >    fsetpos(inFile, framePos);
321 >    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
322      if( eof_test == NULL ){
323        sprintf( painCave.errMsg,
324 <               "Error reading 1st line of %d \n ",c_in_name);
324 >               "Error reading 1st line of %d \n ",inName);
325        haveError = 1;
326        simError();
327      }
# Line 197 | Line 338 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
338        sprintf( painCave.errMsg,
339                 "Initialize from File error. %s n_atoms, %d, "
340                 "does not match the BASS file's n_atoms, %d.\n",
341 <               c_in_name, n_atoms, simnfo->n_atoms );
341 >               inName, n_atoms, simnfo->n_atoms );
342        haveError= 1;
343        simError();
344      }
345      
346      //read the time and boxMat from the comment line
347      
348 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
348 >    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
349      if(eof_test == NULL){
350        sprintf( painCave.errMsg,
351 <               "error in reading commment in %s\n", c_in_name);
351 >               "error in reading commment in %s\n", inName);
352        haveError = 1;
353        simError();
354      }
# Line 219 | Line 360 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
360        simError();
361      }
362  
363 <    MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
363 >    MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
364      
365      MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
366      
# Line 227 | Line 368 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
368      
369      for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
370        
371 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
371 >      eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
372        if(eof_test == NULL){
373          sprintf(painCave.errMsg,
374                  "error in reading file %s\n"
375                  "natoms  = %d; index = %d\n"
376                  "error reading the line from the file.\n",
377 <                c_in_name, n_atoms, i );
377 >                inName, n_atoms, i );
378          haveError= 1;
379          simError();
380        }
# Line 275 | Line 416 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
416      
417    } else {
418      
419 <    MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
419 >    MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
420      MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
421  
422      done = 0;
# Line 325 | Line 466 | char* DumpReader::parseDumpLine(char* readLine, int gl
466  
467    char *foo; // the pointer to the current string token
468    
469 <  double rx, ry, rz; // position place holders
470 <  double vx, vy, vz; // velocity placeholders
469 >  double pos[3]; // position place holders
470 >  double vel[3]; // velocity placeholders
471    double q[4]; // the quaternions
472    double jx, jy, jz; // angular velocity placeholders;
473    double qSqr, qLength; // needed to normalize the quaternion vector.
# Line 346 | Line 487 | char* DumpReader::parseDumpLine(char* readLine, int gl
487      sprintf( painCave.errMsg,
488               "Initialize from file error. Atom at index %d "
489               "in file %s does not exist on processor %d .\n",
490 <             globalIndex, c_in_name, mpiSim->getMyNode() );
490 >             globalIndex, inName, mpiSim->getMyNode() );
491      return strdup( painCave.errMsg );
492    }  
493   #else
# Line 357 | Line 498 | char* DumpReader::parseDumpLine(char* readLine, int gl
498    // set the string tokenizer
499    
500    foo = strtok(readLine, " ,;\t");
501 <  
501 >  atoms[atomIndex]->setType(foo);
502    // check the atom name to the current atom
503    
504 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
505 <    sprintf( painCave.errMsg,
506 <             "Initialize from file error. Atom %s at index %d "
507 <             "in file %s does not"
508 <             " match the BASS atom %s.\n",
509 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
510 <    return strdup( painCave.errMsg );
511 <  }
504 >  //if( strcmp( foo, atoms[atomIndex]->getType() ) ){
505 >  //  sprintf( painCave.errMsg,
506 >  //    "Initialize from file error. Atom %s at index %d "
507 >  //     "in file %s does not"
508 >  //     " match the BASS atom %s.\n",
509 >  //     foo, atomIndex, inName, atoms[atomIndex]->getType() );
510 >  //  return strdup( painCave.errMsg );
511 >  //}
512      
513    // get the positions
514  
# Line 376 | Line 517 | char* DumpReader::parseDumpLine(char* readLine, int gl
517      sprintf( painCave.errMsg,
518               "error in reading postition x from %s\n"
519               "natoms  = %d, index = %d\n",
520 <             c_in_name, n_atoms, atomIndex );
520 >             inName, n_atoms, atomIndex );
521      return strdup( painCave.errMsg );
522    }
523 <  rx = atof( foo );
523 >  pos[0] = atof( foo );
524    
525    foo = strtok(NULL, " ,;\t");
526    if(foo == NULL){
527      sprintf( painCave.errMsg,
528               "error in reading postition y from %s\n"
529               "natoms  = %d, index = %d\n",
530 <             c_in_name, n_atoms, atomIndex );
530 >             inName, n_atoms, atomIndex );
531      return strdup( painCave.errMsg );
532    }
533 <  ry = atof( foo );
533 >  pos[1] = atof( foo );
534      
535    foo = strtok(NULL, " ,;\t");
536    if(foo == NULL){
537      sprintf( painCave.errMsg,
538               "error in reading postition z from %s\n"
539               "natoms  = %d, index = %d\n",
540 <             c_in_name, n_atoms, atomIndex );
540 >             inName, n_atoms, atomIndex );
541      return strdup( painCave.errMsg );
542    }
543 <  rz = atof( foo );    
543 >  pos[2] = atof( foo );    
544  
545  
546    // get the velocities
# Line 409 | Line 550 | char* DumpReader::parseDumpLine(char* readLine, int gl
550      sprintf( painCave.errMsg,
551               "error in reading velocity x from %s\n"
552               "natoms  = %d, index = %d\n",
553 <             c_in_name, n_atoms, atomIndex );
553 >             inName, n_atoms, atomIndex );
554      return strdup( painCave.errMsg );
555    }
556 <  vx = atof( foo );
556 >  vel[0] = atof( foo );
557      
558    foo = strtok(NULL, " ,;\t");
559    if(foo == NULL){
560      sprintf( painCave.errMsg,
561               "error in reading velocity y from %s\n"
562               "natoms  = %d, index = %d\n",
563 <             c_in_name, n_atoms, atomIndex );
563 >             inName, n_atoms, atomIndex );
564      return strdup( painCave.errMsg );
565    }
566 <  vy = atof( foo );
566 >  vel[1] = atof( foo );
567      
568    foo = strtok(NULL, " ,;\t");
569    if(foo == NULL){
570      sprintf( painCave.errMsg,
571               "error in reading velocity z from %s\n"
572               "natoms  = %d, index = %d\n",
573 <             c_in_name, n_atoms, atomIndex );
573 >             inName, n_atoms, atomIndex );
574      return strdup( painCave.errMsg );
575    }
576 <  vz = atof( foo );
576 >  vel[2] = atof( foo );
577      
578      
579    // get the quaternions
# Line 444 | Line 585 | char* DumpReader::parseDumpLine(char* readLine, int gl
585        sprintf(painCave.errMsg,
586                "error in reading quaternion 0 from %s\n"
587                "natoms  = %d, index = %d\n",
588 <              c_in_name, n_atoms, atomIndex );
588 >              inName, n_atoms, atomIndex );
589        return strdup( painCave.errMsg );
590      }
591      q[0] = atof( foo );
# Line 454 | Line 595 | char* DumpReader::parseDumpLine(char* readLine, int gl
595        sprintf( painCave.errMsg,
596                 "error in reading quaternion 1 from %s\n"
597                 "natoms  = %d, index = %d\n",
598 <               c_in_name, n_atoms, atomIndex );
598 >               inName, n_atoms, atomIndex );
599        return strdup( painCave.errMsg );
600      }
601      q[1] = atof( foo );
# Line 464 | Line 605 | char* DumpReader::parseDumpLine(char* readLine, int gl
605        sprintf( painCave.errMsg,
606                 "error in reading quaternion 2 from %s\n"
607                 "natoms  = %d, index = %d\n",
608 <               c_in_name, n_atoms, atomIndex );
608 >               inName, n_atoms, atomIndex );
609        return strdup( painCave.errMsg );
610      }
611      q[2] = atof( foo );
# Line 474 | Line 615 | char* DumpReader::parseDumpLine(char* readLine, int gl
615        sprintf( painCave.errMsg,
616                 "error in reading quaternion 3 from %s\n"
617                 "natoms  = %d, index = %d\n",
618 <               c_in_name, n_atoms, atomIndex );
618 >               inName, n_atoms, atomIndex );
619        return strdup( painCave.errMsg );
620      }
621      q[3] = atof( foo );
# Line 486 | Line 627 | char* DumpReader::parseDumpLine(char* readLine, int gl
627        sprintf( painCave.errMsg,
628                 "error in reading angular momentum jx from %s\n"
629                 "natoms  = %d, index = %d\n",
630 <               c_in_name, n_atoms, atomIndex );
630 >               inName, n_atoms, atomIndex );
631        return strdup( painCave.errMsg );
632      }
633      jx = atof( foo );
# Line 496 | Line 637 | char* DumpReader::parseDumpLine(char* readLine, int gl
637        sprintf( painCave.errMsg,
638                 "error in reading angular momentum jy from %s\n"
639                 "natoms  = %d, index = %d\n",
640 <               c_in_name, n_atoms, atomIndex );
640 >               inName, n_atoms, atomIndex );
641        return strdup( painCave.errMsg );
642      }
643      jy = atof(foo );
# Line 506 | Line 647 | char* DumpReader::parseDumpLine(char* readLine, int gl
647        sprintf( painCave.errMsg,
648                 "error in reading angular momentum jz from %s\n"
649                 "natoms  = %d, index = %d\n",
650 <               c_in_name, n_atoms, atomIndex );
650 >               inName, n_atoms, atomIndex );
651        return strdup( painCave.errMsg );
652      }
653      jz = atof( foo );
# Line 533 | Line 674 | char* DumpReader::parseDumpLine(char* readLine, int gl
674    }
675      
676    // add the positions and velocities to the atom
536 –    
537 –  atoms[atomIndex]->setX( rx );
538 –  atoms[atomIndex]->setY( ry );
539 –  atoms[atomIndex]->setZ( rz );
540 –    
541 –  atoms[atomIndex]->set_vx( vx );
542 –  atoms[atomIndex]->set_vy( vy );
543 –  atoms[atomIndex]->set_vz( vz );
677  
678 +  atoms[atomIndex]->setPos( pos );
679 +  atoms[atomIndex]->setVel( vel );
680 +
681    return NULL;
682   }
683  
684  
685 < char* DumpReader::parseCommentLine(char* readLine, double time,
685 > char* DumpReader::parseCommentLine(char* readLine, double &time,
686                                     double boxMat[9]){
687  
688    char *foo; // the pointer to the current string token
689    int j;
690 +  double chi, integralOfChidt;
691 +  double eta[9];
692  
693    // set the string tokenizer
694    
# Line 558 | Line 696 | char* DumpReader::parseCommentLine(char* readLine, dou
696    if(foo == NULL){
697      sprintf( painCave.errMsg,
698               "error in reading time from %s\n",
699 <             c_in_name );
699 >             inName );
700      return strdup( painCave.errMsg );
701    }
702    time = atof( foo );
# Line 569 | Line 707 | char* DumpReader::parseCommentLine(char* readLine, dou
707    if(foo == NULL){
708      sprintf( painCave.errMsg,
709               "error in reading Hx[0] from %s\n",
710 <             c_in_name );
710 >             inName );
711      return strdup( painCave.errMsg );
712    }
713    boxMat[0] = atof( foo );
# Line 578 | Line 716 | char* DumpReader::parseCommentLine(char* readLine, dou
716    if(foo == NULL){
717      sprintf( painCave.errMsg,
718               "error in reading Hx[1] from %s\n",
719 <             c_in_name );
719 >             inName );
720      return strdup( painCave.errMsg );
721    }
722    boxMat[1] = atof( foo );
# Line 587 | Line 725 | char* DumpReader::parseCommentLine(char* readLine, dou
725    if(foo == NULL){
726      sprintf( painCave.errMsg,
727               "error in reading Hx[2] from %s\n",
728 <             c_in_name );
728 >             inName );
729      return strdup( painCave.errMsg );
730    }
731    boxMat[2] = atof( foo );    
# Line 598 | Line 736 | char* DumpReader::parseCommentLine(char* readLine, dou
736    if(foo == NULL){
737      sprintf( painCave.errMsg,
738               "error in reading Hy[0] from %s\n",
739 <             c_in_name );
739 >             inName );
740      return strdup( painCave.errMsg );
741    }
742    boxMat[3] = atof( foo );
# Line 607 | Line 745 | char* DumpReader::parseCommentLine(char* readLine, dou
745    if(foo == NULL){
746      sprintf( painCave.errMsg,
747               "error in reading Hy[1] from %s\n",
748 <             c_in_name );
748 >             inName );
749      return strdup( painCave.errMsg );
750    }
751    boxMat[4] = atof( foo );
# Line 616 | Line 754 | char* DumpReader::parseCommentLine(char* readLine, dou
754    if(foo == NULL){
755      sprintf( painCave.errMsg,
756               "error in reading Hy[2] from %s\n",
757 <             c_in_name );
757 >             inName );
758      return strdup( painCave.errMsg );
759    }
760    boxMat[5] = atof( foo );    
# Line 627 | Line 765 | char* DumpReader::parseCommentLine(char* readLine, dou
765    if(foo == NULL){
766      sprintf( painCave.errMsg,
767               "error in reading Hz[0] from %s\n",
768 <             c_in_name );
768 >             inName );
769      return strdup( painCave.errMsg );
770    }
771    boxMat[6] = atof( foo );
# Line 636 | Line 774 | char* DumpReader::parseCommentLine(char* readLine, dou
774    if(foo == NULL){
775      sprintf( painCave.errMsg,
776               "error in reading Hz[1] from %s\n",
777 <             c_in_name );
777 >             inName );
778      return strdup( painCave.errMsg );
779    }
780    boxMat[7] = atof( foo );
# Line 645 | Line 783 | char* DumpReader::parseCommentLine(char* readLine, dou
783    if(foo == NULL){
784      sprintf( painCave.errMsg,
785               "error in reading Hz[2] from %s\n",
786 <             c_in_name );
786 >             inName );
787      return strdup( painCave.errMsg );
788    }
789    boxMat[8] = atof( foo );    
790  
791    return NULL;
792 +
793 +  //get chi and integralOfChidt, they should appear by pair
794 +  foo = strtok(NULL, " ,;\t\n");
795 +  if(foo != NULL){
796 +    chi = atof(foo);
797 +    
798 +    foo = strtok(NULL, " ,;\t\n");
799 +    if(foo == NULL){
800 +      sprintf( painCave.errMsg,
801 +               "chi and integralOfChidt should appear by pair in %s\n", inName );
802 +      return strdup( painCave.errMsg );
803 +    }
804 +    integralOfChidt = atof( foo );
805 +    
806 +    //push chi and integralOfChidt into SimInfo::properties which can be
807 +    //retrieved by integrator later
808 +    DoubleData* chiValue = new DoubleData();
809 +    chiValue->setID(CHIVALUE_ID);
810 +    chiValue->setData(chi);
811 +    simnfo->addProperty(chiValue);
812 +    
813 +    DoubleData* integralOfChidtValue = new DoubleData();
814 +    integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
815 +    integralOfChidtValue->setData(integralOfChidt);
816 +    simnfo->addProperty(integralOfChidtValue);
817 +    
818 +  }
819 +  else
820 +    return NULL;
821 +  
822 +  //get eta
823 +  for(int i = 0 ; i < 9; i++){
824 +    foo = strtok(NULL, " ,;\t");
825 +    if(foo == NULL){
826 +      sprintf( painCave.errMsg,
827 +               "error in reading eta[%d] from %s\n", i, inName );
828 +      return strdup( painCave.errMsg );
829 +    }
830 +    eta[i] = atof( foo );
831 +  }
832 +  
833 +  //push eta into SimInfo::properties which can be
834 +  //retrieved by integrator later
835 +  //simnfo->setBoxM( theBoxMat3 );
836 +  DoubleArrayData* etaValue = new DoubleArrayData();
837 +  etaValue->setID(ETAVALUE_ID);
838 +  etaValue->setData(eta, 9);
839 +  simnfo->addProperty(etaValue);
840 +  
841 +  
842 +  return NULL;
843 +  
844 +  
845 +
846   }
847  
848  
# Line 658 | Line 850 | char* DumpReader::parseCommentLine(char* readLine, dou
850  
851   // a couple of functions to let us escape the read loop
852  
853 < void initFile::nodeZeroError( void ){
853 > void dumpRead::nodeZeroError( void ){
854    int j, myStatus;
855    
856    myStatus = 0;
# Line 673 | Line 865 | void initFile::nodeZeroError( void ){
865    
866   }
867  
868 < void initFile::anonymousNodeDie( void ){
868 > void dumpRead::anonymousNodeDie( void ){
869  
870    MPI_Finalize();
871    exit (0);

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