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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 830 by gezelter, Tue Oct 28 16:20:28 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 26 | Line 27 | using namespace initFile;
27  
28   #endif // is_mpi
29  
30 < InitializeFromFile :: InitializeFromFile( char *in_name ){
30 > InitializeFromFile::InitializeFromFile( char *in_name ){
31 >
32   #ifdef IS_MPI
33    if (worldRank == 0) {
34   #endif
# Line 48 | Line 50 | InitializeFromFile :: InitializeFromFile( char *in_nam
50    return;  
51   }
52  
53 < InitializeFromFile :: ~InitializeFromFile( ){
53 > InitializeFromFile::~InitializeFromFile( ){
54   #ifdef IS_MPI
55    if (worldRank == 0) {
56   #endif
# Line 71 | Line 73 | void InitializeFromFile :: readInit( SimInfo* the_simn
73  
74   void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
75  
76 <  int i, j, done, which_node, which_atom; // loop counter
76 >  int i, j;
77 >  
78 > #ifdef IS_MPI
79 >  int done, which_node, which_atom; // loop counter
80 > #endif //is_mpi
81  
82    const int BUFFERSIZE = 2000; // size of the read buffer
83    int n_atoms; // the number of atoms
84    char read_buffer[BUFFERSIZE]; //the line buffer for reading
79 – #ifdef IS_MPI
80 –  char send_buffer[BUFFERSIZE];
81 – #endif
85  
86    char *eof_test; // ptr to see when we reach the end of the file
87    char *parseErr;
88 <  int procIndex;
88 >
89 >  double currTime;
90    double boxMat[9];
91    double theBoxMat3[3][3];
92  
# Line 101 | Line 105 | void InitializeFromFile :: readInit( SimInfo* the_simn
105  
106    n_atoms = atoi( read_buffer );
107  
104 –  Atom **atoms = simnfo->atoms;
105 –  DirectionalAtom* dAtom;
106 –
108    if( n_atoms != simnfo->n_atoms ){
109      sprintf( painCave.errMsg,
110               "Initialize from File error. %s n_atoms, %d, "
# Line 123 | Line 124 | void InitializeFromFile :: readInit( SimInfo* the_simn
124      simError();
125    }
126  
127 <  parseErr = parseBoxLine( read_buffer, boxMat );
127 >  parseErr = parseBoxLine( read_buffer, boxMat, currTime );
128    if( parseErr != NULL ){
129      strcpy( painCave.errMsg, parseErr );
130      painCave.isFatal = 1;
# Line 134 | Line 135 | void InitializeFromFile :: readInit( SimInfo* the_simn
135      for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
136  
137    simnfo->setBoxM( theBoxMat3 );
138 +  simnfo->setTime( currTime );
139  
140  
141    for( i=0; i < n_atoms; i++){
# Line 178 | Line 180 | void InitializeFromFile :: readInit( SimInfo* the_simn
180      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
181      if( eof_test == NULL ){
182        sprintf( painCave.errMsg,
183 <               "Error reading 1st line of %d \n ",c_in_name);
183 >               "Error reading 1st line of %s \n ",c_in_name);
184        haveError = 1;
185        simError();
186      }
187      
188      n_atoms = atoi( read_buffer );
189      
188 –    Atom **atoms = simnfo->atoms;
189 –    DirectionalAtom* dAtom;
190 –
190      // Check to see that the number of atoms in the intial configuration file is the
191      // same as declared in simBass.
192      
# Line 210 | Line 209 | void InitializeFromFile :: readInit( SimInfo* the_simn
209        simError();
210      }
211      
212 <    parseErr = parseBoxLine( read_buffer, boxMat );
212 >    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
213      if( parseErr != NULL ){
214        strcpy( painCave.errMsg, parseErr );
215        haveError = 1;
# Line 218 | Line 217 | void InitializeFromFile :: readInit( SimInfo* the_simn
217      }
218  
219      MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
220 +    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
221    
222      if(haveError) nodeZeroError();
223  
# Line 272 | Line 272 | void InitializeFromFile :: readInit( SimInfo* the_simn
272    } else {
273      
274      MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
275 +    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
276  
277      done = 0;
278      while (!done) {
# Line 309 | Line 310 | void InitializeFromFile :: readInit( SimInfo* the_simn
310      for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
311  
312    simnfo->setBoxM( theBoxMat3 );
313 +  simnfo->setTime( currTime );
314  
315    
316   #endif
# Line 318 | Line 320 | char* InitializeFromFile::parseDumpLine(char* readLine
320  
321    char *foo; // the pointer to the current string token
322    
323 <  double rx, ry, rz; // position place holders
324 <  double vx, vy, vz; // velocity placeholders
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.
# Line 327 | Line 329 | char* InitializeFromFile::parseDumpLine(char* readLine
329    Atom **atoms = simnfo->atoms;
330    DirectionalAtom* dAtom;
331    
332 <  int j, n_atoms, atomIndex;
332 >  int n_atoms, atomIndex;
333  
334   #ifdef IS_MPI
335 +  int j;
336 +
337    n_atoms = mpiSim->getTotAtoms();
338    atomIndex=-1;        
339    for (j=0; j < mpiSim->getMyNlocal(); j++) {
# Line 372 | Line 376 | char* InitializeFromFile::parseDumpLine(char* readLine
376               c_in_name, n_atoms, atomIndex );
377      return strdup( painCave.errMsg );
378    }
379 <  rx = atof( foo );
379 >  pos[0] = atof( foo );
380    
381    foo = strtok(NULL, " ,;\t");
382    if(foo == NULL){
# Line 382 | Line 386 | char* InitializeFromFile::parseDumpLine(char* readLine
386               c_in_name, n_atoms, atomIndex );
387      return strdup( painCave.errMsg );
388    }
389 <  ry = atof( foo );
389 >  pos[1] = atof( foo );
390      
391    foo = strtok(NULL, " ,;\t");
392    if(foo == NULL){
# Line 392 | Line 396 | char* InitializeFromFile::parseDumpLine(char* readLine
396               c_in_name, n_atoms, atomIndex );
397      return strdup( painCave.errMsg );
398    }
399 <  rz = atof( foo );    
399 >  pos[2] = atof( foo );    
400  
401  
402    // get the velocities
# Line 405 | Line 409 | char* InitializeFromFile::parseDumpLine(char* readLine
409               c_in_name, n_atoms, atomIndex );
410      return strdup( painCave.errMsg );
411    }
412 <  vx = atof( foo );
412 >  vel[0] = atof( foo );
413      
414    foo = strtok(NULL, " ,;\t");
415    if(foo == NULL){
# Line 415 | Line 419 | char* InitializeFromFile::parseDumpLine(char* readLine
419               c_in_name, n_atoms, atomIndex );
420      return strdup( painCave.errMsg );
421    }
422 <  vy = atof( foo );
422 >  vel[1] = atof( foo );
423      
424    foo = strtok(NULL, " ,;\t");
425    if(foo == NULL){
# Line 425 | Line 429 | char* InitializeFromFile::parseDumpLine(char* readLine
429               c_in_name, n_atoms, atomIndex );
430      return strdup( painCave.errMsg );
431    }
432 <  vz = atof( foo );
432 >  vel[2] = atof( foo );
433      
434      
435    // get the quaternions
# Line 527 | Line 531 | char* InitializeFromFile::parseDumpLine(char* readLine
531      
532    // add the positions and velocities to the atom
533      
534 <  atoms[atomIndex]->setX( rx );
535 <  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 );
534 >  atoms[atomIndex]->setPos( pos );
535 >  atoms[atomIndex]->setVel( vel );
536  
537    return NULL;
538   }
539  
540  
541 < char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){
541 > char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
542 >                                       double &time ){
543  
544    char *foo; // the pointer to the current string token
545 –  int j;
545  
546    // set the string tokenizer
547    
# Line 555 | Line 554 | char* InitializeFromFile::parseBoxLine(char* readLine,
554               c_in_name );
555      return strdup( painCave.errMsg );
556    }
557 <  simnfo->setTime( atof( foo ) );
557 >  time = atof( foo );
558  
559    // get the Hx vector
560  

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