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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 643 by mmeineke, Mon Jul 21 21:27:40 2003 UTC vs.
Revision 689 by tim, Tue Aug 12 19:56:49 2003 UTC

# Line 26 | Line 26 | InitializeFromFile :: InitializeFromFile( char *in_nam
26  
27   #endif // is_mpi
28  
29 < InitializeFromFile :: InitializeFromFile( char *in_name ){
29 > InitializeFromFile::InitializeFromFile( char *in_name ){
30 >
31 >  std::cerr << "Hello from Initialize from file.\n";
32 >
33   #ifdef IS_MPI
34    if (worldRank == 0) {
35   #endif
# Line 48 | Line 51 | InitializeFromFile :: ~InitializeFromFile( ){
51    return;  
52   }
53  
54 < InitializeFromFile :: ~InitializeFromFile( ){
54 > InitializeFromFile::~InitializeFromFile( ){
55   #ifdef IS_MPI
56    if (worldRank == 0) {
57   #endif
# Line 83 | Line 86 | void InitializeFromFile :: readInit( SimInfo* the_simn
86    char *eof_test; // ptr to see when we reach the end of the file
87    char *parseErr;
88    int procIndex;
89 +  double currTime;
90    double boxMat[9];
91    double theBoxMat3[3][3];
92  
# Line 123 | Line 127 | void InitializeFromFile :: readInit( SimInfo* the_simn
127      simError();
128    }
129  
130 <  parseErr = parseBoxLine( read_buffer, boxMat );
130 >  parseErr = parseBoxLine( read_buffer, boxMat, currTime );
131    if( parseErr != NULL ){
132      strcpy( painCave.errMsg, parseErr );
133      painCave.isFatal = 1;
# Line 134 | Line 138 | void InitializeFromFile :: readInit( SimInfo* the_simn
138      for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
139  
140    simnfo->setBoxM( theBoxMat3 );
141 +  simnfo->setTime( currTime );
142  
143  
144    for( i=0; i < n_atoms; i++){
# Line 210 | Line 215 | void InitializeFromFile :: readInit( SimInfo* the_simn
215        simError();
216      }
217      
218 <    parseErr = parseBoxLine( read_buffer, boxMat );
218 >    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
219      if( parseErr != NULL ){
220        strcpy( painCave.errMsg, parseErr );
221        haveError = 1;
# Line 218 | Line 223 | void InitializeFromFile :: readInit( SimInfo* the_simn
223      }
224  
225      MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
226 +    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
227    
228      if(haveError) nodeZeroError();
229  
# Line 272 | Line 278 | void InitializeFromFile :: readInit( SimInfo* the_simn
278    } else {
279      
280      MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
281 +    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
282  
283      done = 0;
284      while (!done) {
# Line 309 | Line 316 | void InitializeFromFile :: readInit( SimInfo* the_simn
316      for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
317  
318    simnfo->setBoxM( theBoxMat3 );
319 +  simnfo->setTime( currTime );
320  
321    
322   #endif
# Line 318 | Line 326 | char* InitializeFromFile::parseDumpLine(char* readLine
326  
327    char *foo; // the pointer to the current string token
328    
329 <  double rx, ry, rz; // position place holders
330 <  double vx, vy, vz; // velocity placeholders
329 >  double pos[3]; // position place holders
330 >  double vel[3]; // velocity placeholders
331    double q[4]; // the quaternions
332    double jx, jy, jz; // angular velocity placeholders;
333    double qSqr, qLength; // needed to normalize the quaternion vector.
# Line 372 | Line 380 | char* InitializeFromFile::parseDumpLine(char* readLine
380               c_in_name, n_atoms, atomIndex );
381      return strdup( painCave.errMsg );
382    }
383 <  rx = atof( foo );
383 >  pos[0] = atof( foo );
384    
385    foo = strtok(NULL, " ,;\t");
386    if(foo == NULL){
# Line 382 | Line 390 | char* InitializeFromFile::parseDumpLine(char* readLine
390               c_in_name, n_atoms, atomIndex );
391      return strdup( painCave.errMsg );
392    }
393 <  ry = atof( foo );
393 >  pos[1] = atof( foo );
394      
395    foo = strtok(NULL, " ,;\t");
396    if(foo == NULL){
# Line 392 | 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 405 | Line 413 | char* InitializeFromFile::parseDumpLine(char* readLine
413               c_in_name, n_atoms, atomIndex );
414      return strdup( painCave.errMsg );
415    }
416 <  vx = atof( foo );
416 >  vel[0] = atof( foo );
417      
418    foo = strtok(NULL, " ,;\t");
419    if(foo == NULL){
# Line 415 | Line 423 | char* InitializeFromFile::parseDumpLine(char* readLine
423               c_in_name, n_atoms, atomIndex );
424      return strdup( painCave.errMsg );
425    }
426 <  vy = atof( foo );
426 >  vel[1] = atof( foo );
427      
428    foo = strtok(NULL, " ,;\t");
429    if(foo == NULL){
# Line 425 | Line 433 | char* InitializeFromFile::parseDumpLine(char* readLine
433               c_in_name, n_atoms, atomIndex );
434      return strdup( painCave.errMsg );
435    }
436 <  vz = atof( foo );
436 >  vel[2] = atof( foo );
437      
438      
439    // get the quaternions
# Line 527 | Line 535 | char* InitializeFromFile::parseDumpLine(char* readLine
535      
536    // add the positions and velocities to the atom
537      
538 <  atoms[atomIndex]->setX( rx );
539 <  atoms[atomIndex]->setY( ry );
532 <  atoms[atomIndex]->setZ( rz );
533 <    
534 <  atoms[atomIndex]->set_vx( vx );
535 <  atoms[atomIndex]->set_vy( vy );
536 <  atoms[atomIndex]->set_vz( vz );
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]){
545 > char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
546 >                                       double &time ){
547  
548    char *foo; // the pointer to the current string token
549    int j;
# Line 555 | Line 559 | char* InitializeFromFile::parseBoxLine(char* readLine,
559               c_in_name );
560      return strdup( painCave.errMsg );
561    }
562 <  simnfo->setTime( atof( foo ) );
562 >  time = atof( foo );
563  
564    // get the Hx vector
565  

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