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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 419 by gezelter, Thu Mar 27 15:07:29 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

# Line 13 | Line 13
13  
14   #ifdef IS_MPI
15   #include <mpi.h>
16 – #include <mpi++.h>
16   #include "mpiSimulation.hpp"
17 < #define TAKE_THIS_TAG 0
17 > #define TAKE_THIS_TAG_CHAR 0
18 > #define TAKE_THIS_TAG_INT 1
19 >
20 > namespace initFile{
21 >  void nodeZeroError( void );
22 >  void anonymousNodeDie( void );
23 > }
24 >
25 > 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 40 | Line 49 | InitializeFromFile :: ~InitializeFromFile( ){
49    return;  
50   }
51  
52 < InitializeFromFile :: ~InitializeFromFile( ){
52 > InitializeFromFile::~InitializeFromFile( ){
53   #ifdef IS_MPI
54    if (worldRank == 0) {
55   #endif
# Line 61 | Line 70 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
70   }
71  
72  
73 < void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
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
71 – #ifdef IS_MPI
72 –  char send_buffer[BUFFERSIZE];
73 – #endif
84  
85    char *eof_test; // ptr to see when we reach the end of the file
86    char *parseErr;
77 –  int procIndex;
87  
88 <  entry_plug = the_entry_plug;
88 >  double currTime;
89 >  double boxMat[9];
90 >  double theBoxMat3[3][3];
91  
92 +  simnfo = the_simnfo;
93  
94 +
95   #ifndef IS_MPI
96    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
97    if( eof_test == NULL ){
# Line 91 | Line 104 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
104  
105    n_atoms = atoi( read_buffer );
106  
107 <  Atom **atoms = entry_plug->atoms;
95 <  DirectionalAtom* dAtom;
96 <
97 <  if( n_atoms != entry_plug->n_atoms ){
107 >  if( n_atoms != simnfo->n_atoms ){
108      sprintf( painCave.errMsg,
109               "Initialize from File error. %s n_atoms, %d, "
110               "does not match the BASS file's n_atoms, %d.\n",
111 <             c_in_name, n_atoms, entry_plug->n_atoms );
111 >             c_in_name, n_atoms, simnfo->n_atoms );
112      painCave.isFatal = 1;
113      simError();
114    }
115    
116 <  //read and toss the comment line
116 >  //read the box mat from the comment line
117    
118    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
119    if(eof_test == NULL){
# Line 113 | Line 123 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
123      simError();
124    }
125  
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 +  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 132 | Line 156 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
156        strcpy( painCave.errMsg, parseErr );
157        painCave.isFatal = 1;
158        simError();
159 <    }    
159 >    }
160    }
161  
162  
163    // MPI Section of code..........
164   #else //IS_MPI
165  
166 <  MPI::Status istatus;
166 >  // first thing first, suspend fatalities.
167 >  painCave.isEventLoop = 1;
168 >
169 >  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
170 >  int haveError;
171 >  
172 >  MPI_Status istatus;
173    int *AtomToProcMap = mpiSim->getAtomToProcMap();
174  
175 +  
176 +  haveError = 0;
177    if (worldRank == 0) {
178 +
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);
183 <      painCave.isFatal = 1;
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      
156 –    Atom **atoms = entry_plug->atoms;
157 –    DirectionalAtom* dAtom;
158 –
189      // Check to see that the number of atoms in the intial configuration file is the
190      // same as declared in simBass.
191      
# Line 163 | Line 193 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
193        sprintf( painCave.errMsg,
194                 "Initialize from File error. %s n_atoms, %d, "
195                 "does not match the BASS file's n_atoms, %d.\n",
196 <               c_in_name, n_atoms, entry_plug->n_atoms );
197 <      painCave.isFatal = 1;
196 >               c_in_name, n_atoms, simnfo->n_atoms );
197 >      haveError= 1;
198        simError();
199      }
200      
201 <    //read and toss the comment line
201 >    //read the boxMat from the comment line
202      
203      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
204      if(eof_test == NULL){
205        sprintf( painCave.errMsg,
206                 "error in reading commment in %s\n", c_in_name);
207 <      painCave.isFatal = 1;
207 >      haveError = 1;
208 >      simError();
209 >    }
210 >    
211 >    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
212 >    if( parseErr != NULL ){
213 >      strcpy( painCave.errMsg, parseErr );
214 >      haveError = 1;
215        simError();
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  
223      for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
224        
# Line 188 | Line 229 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
229                  "natoms  = %d; index = %d\n"
230                  "error reading the line from the file.\n",
231                  c_in_name, n_atoms, i );
232 <        painCave.isFatal = 1;
232 >        haveError= 1;
233          simError();
234        }
235      
236 +      if(haveError) nodeZeroError();
237 +
238        // Get the Node number which wants this atom:
239        which_node = AtomToProcMap[i];    
240 <      if (which_node == mpiSim->getMyNode()) {
240 >      if (which_node == 0) {
241          parseErr = parseDumpLine( read_buffer, i );
242          if( parseErr != NULL ){
243            strcpy( painCave.errMsg, parseErr );
244 <          painCave.isFatal = 1;
244 >          haveError = 1;
245            simError();
246          }    
247 <      } else {
248 <        MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
249 <                             TAKE_THIS_TAG);
250 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
247 >        if(haveError) nodeZeroError();
248 >      }
249 >      
250 >      else {
251 >      
252 >        myStatus = 1;
253 >        MPI_Send(&myStatus, 1, MPI_INT, which_node,
254 >                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
255 >        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
256 >                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
257 >        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
258 >                 MPI_COMM_WORLD);
259 >        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
260 >                 MPI_COMM_WORLD, &istatus);
261 >        
262 >        if(!myStatus) nodeZeroError();
263        }
264      }
265 <    sprintf(read_buffer, "GAMEOVER");
265 >    myStatus = -1;
266      for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
267 <      MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j,
268 <                           TAKE_THIS_TAG);
267 >      MPI_Send( &myStatus, 1, MPI_INT, j,
268 >                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
269      }
270      
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) {
278 <      MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
279 <                           TAKE_THIS_TAG, istatus);
280 <      if (strcmp(read_buffer, "GAMEOVER")) {
281 <        done = 1;
282 <        continue;
283 <      } else {
284 <        MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
285 <                             TAKE_THIS_TAG, istatus);
286 <        
287 <        parseErr = parseDumpLine( read_buffer, which_atom );
288 <        if( parseErr != NULL ){
289 <          strcpy( painCave.errMsg, parseErr );
290 <          painCave.isFatal = 1;
291 <          simError();
292 <        }
278 >
279 >      MPI_Recv(&myStatus, 1, MPI_INT, 0,
280 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
281 >      
282 >      if(!myStatus) anonymousNodeDie();
283 >      
284 >      if(myStatus < 0) break;
285 >
286 >      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
287 >               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
288 >      MPI_Recv(&which_atom, 1, MPI_INT, 0,
289 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
290 >      
291 >      myStatus = 1;
292 >      parseErr = parseDumpLine( read_buffer, which_atom );
293 >      if( parseErr != NULL ){
294 >        strcpy( painCave.errMsg, parseErr );
295 >        myStatus = 0;;
296 >        simError();
297        }
298 +      
299 +      MPI_Send( &myStatus, 1, MPI_INT, 0,
300 +                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
301 +      
302      }
303    }
304 <        
304 >    
305 > // last  thing last, enable  fatalities.
306 >  painCave.isEventLoop = 0;
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
316   }
317  
# Line 243 | 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.
327    
328 <  Atom **atoms = entry_plug->atoms;
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 268 | Line 346 | char* InitializeFromFile::parseDumpLine(char* readLine
346      return strdup( painCave.errMsg );
347    }  
348   #else
349 <  n_atoms = entry_plug->n_atoms;
349 >  n_atoms = simnfo->n_atoms;
350    atomIndex = globalIndex;
351   #endif // is_mpi
352  
# Line 297 | 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 307 | 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 317 | 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 330 | 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 340 | 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 350 | 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 452 | 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 );
457 <  atoms[atomIndex]->setZ( rz );
458 <    
459 <  atoms[atomIndex]->set_vx( vx );
460 <  atoms[atomIndex]->set_vy( vy );
461 <  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],
541 +                                       double &time ){
542 +
543 +  char *foo; // the pointer to the current string token
544 +
545 +  // set the string tokenizer
546 +  
547 +  foo = strtok(readLine, " ,;\t");
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 +
560 +  foo = strtok(NULL, " ,;\t");
561 +  if(foo == NULL){
562 +    sprintf( painCave.errMsg,
563 +             "error in reading Hx[0] from %s\n",
564 +             c_in_name );
565 +    return strdup( painCave.errMsg );
566 +  }
567 +  boxMat[0] = atof( foo );
568 +  
569 +  foo = strtok(NULL, " ,;\t");
570 +  if(foo == NULL){
571 +    sprintf( painCave.errMsg,
572 +             "error in reading Hx[1] from %s\n",
573 +             c_in_name );
574 +    return strdup( painCave.errMsg );
575 +  }
576 +  boxMat[1] = atof( foo );
577 +    
578 +  foo = strtok(NULL, " ,;\t");
579 +  if(foo == NULL){
580 +    sprintf( painCave.errMsg,
581 +             "error in reading Hx[2] from %s\n",
582 +             c_in_name );
583 +    return strdup( painCave.errMsg );
584 +  }
585 +  boxMat[2] = atof( foo );    
586 +
587 +  // get the Hy vector
588 +
589 +  foo = strtok(NULL, " ,;\t");
590 +  if(foo == NULL){
591 +    sprintf( painCave.errMsg,
592 +             "error in reading Hy[0] from %s\n",
593 +             c_in_name );
594 +    return strdup( painCave.errMsg );
595 +  }
596 +  boxMat[3] = atof( foo );
597 +  
598 +  foo = strtok(NULL, " ,;\t");
599 +  if(foo == NULL){
600 +    sprintf( painCave.errMsg,
601 +             "error in reading Hy[1] from %s\n",
602 +             c_in_name );
603 +    return strdup( painCave.errMsg );
604 +  }
605 +  boxMat[4] = atof( foo );
606 +    
607 +  foo = strtok(NULL, " ,;\t");
608 +  if(foo == NULL){
609 +    sprintf( painCave.errMsg,
610 +             "error in reading Hy[2] from %s\n",
611 +             c_in_name );
612 +    return strdup( painCave.errMsg );
613 +  }
614 +  boxMat[5] = atof( foo );    
615 +
616 +  // get the Hz vector
617 +
618 +  foo = strtok(NULL, " ,;\t");
619 +  if(foo == NULL){
620 +    sprintf( painCave.errMsg,
621 +             "error in reading Hz[0] from %s\n",
622 +             c_in_name );
623 +    return strdup( painCave.errMsg );
624 +  }
625 +  boxMat[6] = atof( foo );
626 +  
627 +  foo = strtok(NULL, " ,;\t");
628 +  if(foo == NULL){
629 +    sprintf( painCave.errMsg,
630 +             "error in reading Hz[1] from %s\n",
631 +             c_in_name );
632 +    return strdup( painCave.errMsg );
633 +  }
634 +  boxMat[7] = atof( foo );
635 +    
636 +  foo = strtok(NULL, " ,;\t");
637 +  if(foo == NULL){
638 +    sprintf( painCave.errMsg,
639 +             "error in reading Hz[2] from %s\n",
640 +             c_in_name );
641 +    return strdup( painCave.errMsg );
642 +  }
643 +  boxMat[8] = atof( foo );    
644 +
645 +  return NULL;
646 + }
647 +
648 +
649 + #ifdef IS_MPI
650 +
651 + // a couple of functions to let us escape the read loop
652 +
653 + void initFile::nodeZeroError( void ){
654 +  int j, myStatus;
655 +  
656 +  myStatus = 0;
657 +  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
658 +    MPI_Send( &myStatus, 1, MPI_INT, j,
659 +              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
660 +  }  
661 +  
662 +
663 +  MPI_Finalize();
664 +  exit (0);
665 +  
666 + }
667 +
668 + void initFile::anonymousNodeDie( void ){
669 +
670 +  MPI_Finalize();
671 +  exit (0);
672 + }
673 +
674 + #endif //is_mpi

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