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root/group/branches/no-template-branch/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 2003 UTC

# Line 1 | Line 1
1   #include <iostream>
2 < #include <cmath>
2 > #include <math.h>
3  
4   #include <stdio.h>
5   #include <stdlib.h>
# Line 26 | Line 26 | using namespace initFile;
26  
27   #endif // is_mpi
28  
29 < InitializeFromFile :: InitializeFromFile( char *in_name ){
29 > InitializeFromFile::InitializeFromFile( char *in_name ){
30 >
31   #ifdef IS_MPI
32    if (worldRank == 0) {
33   #endif
# Line 48 | Line 49 | InitializeFromFile :: InitializeFromFile( char *in_nam
49    return;  
50   }
51  
52 < InitializeFromFile :: ~InitializeFromFile( ){
52 > InitializeFromFile::~InitializeFromFile( ){
53   #ifdef IS_MPI
54    if (worldRank == 0) {
55   #endif
# Line 69 | Line 70 | InitializeFromFile :: ~InitializeFromFile( ){
70   }
71  
72  
73 < void InitializeFromFile :: read_xyz( SimInfo* the_simnfo ){
73 > void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
74  
75 <  int i, j, done, which_node, which_atom; // loop counter
75 >  int i, j;
76 >  
77 > #ifdef IS_MPI
78 >  int done, which_node, which_atom; // loop counter
79 > #endif //is_mpi
80  
81    const int BUFFERSIZE = 2000; // size of the read buffer
82    int n_atoms; // the number of atoms
83    char read_buffer[BUFFERSIZE]; //the line buffer for reading
79 – #ifdef IS_MPI
80 –  char send_buffer[BUFFERSIZE];
81 – #endif
84  
85    char *eof_test; // ptr to see when we reach the end of the file
86    char *parseErr;
87 <  int procIndex;
87 >
88 >  double currTime;
89    double boxMat[9];
90 <  
90 >  double theBoxMat3[3][3];
91  
92    simnfo = the_simnfo;
93  
# Line 100 | Line 103 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
103    }
104  
105    n_atoms = atoi( read_buffer );
103 –
104 –  Atom **atoms = simnfo->atoms;
105 –  DirectionalAtom* dAtom;
106  
107    if( n_atoms != simnfo->n_atoms ){
108      sprintf( painCave.errMsg,
# Line 123 | Line 123 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
123      simError();
124    }
125  
126 <  parseErr = parseBoxLine( read_buffer, boxMat );
126 >  parseErr = parseBoxLine( read_buffer, boxMat, currTime );
127    if( parseErr != NULL ){
128      strcpy( painCave.errMsg, parseErr );
129      painCave.isFatal = 1;
130      simError();
131    }
132  
133 <  simnfo->setBoxM( boxMat );
133 >  for(i=0;i<3;i++)
134 >    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
135  
136 +  simnfo->setBoxM( theBoxMat3 );
137 +  simnfo->setTime( currTime );
138  
139 +
140    for( i=0; i < n_atoms; i++){
141      
142      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
# Line 175 | Line 179 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
179      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
180      if( eof_test == NULL ){
181        sprintf( painCave.errMsg,
182 <               "Error reading 1st line of %d \n ",c_in_name);
182 >               "Error reading 1st line of %s \n ",c_in_name);
183        haveError = 1;
184        simError();
185      }
186      
187      n_atoms = atoi( read_buffer );
188      
185 –    Atom **atoms = simnfo->atoms;
186 –    DirectionalAtom* dAtom;
187 –
189      // Check to see that the number of atoms in the intial configuration file is the
190      // same as declared in simBass.
191      
# Line 207 | Line 208 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
208        simError();
209      }
210      
211 <    parseErr = parseBoxLine( read_buffer, boxMat );
211 >    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
212      if( parseErr != NULL ){
213        strcpy( painCave.errMsg, parseErr );
214        haveError = 1;
# Line 215 | Line 216 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
216      }
217  
218      MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
219 +    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
220    
221      if(haveError) nodeZeroError();
222  
# Line 269 | Line 271 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
271    } else {
272      
273      MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
274 +    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
275  
276      done = 0;
277      while (!done) {
# Line 301 | Line 304 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
304      
305   // last  thing last, enable  fatalities.
306    painCave.isEventLoop = 0;
307 <  simnfo->setBoxM( boxMat );
307 >
308 >  for(i=0;i<3;i++)
309 >    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
310 >
311 >  simnfo->setBoxM( theBoxMat3 );
312 >  simnfo->setTime( currTime );
313  
314    
315   #endif
# Line 311 | Line 319 | char* InitializeFromFile::parseDumpLine(char* readLine
319  
320    char *foo; // the pointer to the current string token
321    
322 <  double rx, ry, rz; // position place holders
323 <  double vx, vy, vz; // velocity placeholders
322 >  double pos[3]; // position place holders
323 >  double vel[3]; // velocity placeholders
324    double q[4]; // the quaternions
325    double jx, jy, jz; // angular velocity placeholders;
326    double qSqr, qLength; // needed to normalize the quaternion vector.
# Line 320 | Line 328 | char* InitializeFromFile::parseDumpLine(char* readLine
328    Atom **atoms = simnfo->atoms;
329    DirectionalAtom* dAtom;
330    
331 <  int j, n_atoms, atomIndex;
331 >  int n_atoms, atomIndex;
332  
333   #ifdef IS_MPI
334 +  int j;
335 +
336    n_atoms = mpiSim->getTotAtoms();
337    atomIndex=-1;        
338    for (j=0; j < mpiSim->getMyNlocal(); j++) {
# Line 365 | Line 375 | char* InitializeFromFile::parseDumpLine(char* readLine
375               c_in_name, n_atoms, atomIndex );
376      return strdup( painCave.errMsg );
377    }
378 <  rx = atof( foo );
378 >  pos[0] = atof( foo );
379    
380    foo = strtok(NULL, " ,;\t");
381    if(foo == NULL){
# Line 375 | Line 385 | char* InitializeFromFile::parseDumpLine(char* readLine
385               c_in_name, n_atoms, atomIndex );
386      return strdup( painCave.errMsg );
387    }
388 <  ry = atof( foo );
388 >  pos[1] = atof( foo );
389      
390    foo = strtok(NULL, " ,;\t");
391    if(foo == NULL){
# Line 385 | Line 395 | char* InitializeFromFile::parseDumpLine(char* readLine
395               c_in_name, n_atoms, atomIndex );
396      return strdup( painCave.errMsg );
397    }
398 <  rz = atof( foo );    
398 >  pos[2] = atof( foo );    
399  
400  
401    // get the velocities
# Line 398 | Line 408 | char* InitializeFromFile::parseDumpLine(char* readLine
408               c_in_name, n_atoms, atomIndex );
409      return strdup( painCave.errMsg );
410    }
411 <  vx = atof( foo );
411 >  vel[0] = atof( foo );
412      
413    foo = strtok(NULL, " ,;\t");
414    if(foo == NULL){
# Line 408 | Line 418 | char* InitializeFromFile::parseDumpLine(char* readLine
418               c_in_name, n_atoms, atomIndex );
419      return strdup( painCave.errMsg );
420    }
421 <  vy = atof( foo );
421 >  vel[1] = atof( foo );
422      
423    foo = strtok(NULL, " ,;\t");
424    if(foo == NULL){
# Line 418 | Line 428 | char* InitializeFromFile::parseDumpLine(char* readLine
428               c_in_name, n_atoms, atomIndex );
429      return strdup( painCave.errMsg );
430    }
431 <  vz = atof( foo );
431 >  vel[2] = atof( foo );
432      
433      
434    // get the quaternions
# Line 520 | Line 530 | char* InitializeFromFile::parseDumpLine(char* readLine
530      
531    // add the positions and velocities to the atom
532      
533 <  atoms[atomIndex]->setX( rx );
534 <  atoms[atomIndex]->setY( ry );
525 <  atoms[atomIndex]->setZ( rz );
526 <    
527 <  atoms[atomIndex]->set_vx( vx );
528 <  atoms[atomIndex]->set_vy( vy );
529 <  atoms[atomIndex]->set_vz( vz );
533 >  atoms[atomIndex]->setPos( pos );
534 >  atoms[atomIndex]->setVel( vel );
535  
536    return NULL;
537   }
538  
539  
540 < char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){
540 > char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
541 >                                       double &time ){
542  
543    char *foo; // the pointer to the current string token
538 –  int j;
544  
545    // set the string tokenizer
546    
547    foo = strtok(readLine, " ,;\t");
548 <  // ignore the first token which is the time stamp.
548 >  // set the timeToken.
549  
550 +  if(foo == NULL){
551 +    sprintf( painCave.errMsg,
552 +             "error in reading Time from %s\n",
553 +             c_in_name );
554 +    return strdup( painCave.errMsg );
555 +  }
556 +  time = atof( foo );
557  
558    // get the Hx vector
559  

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