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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 417 by gezelter, Thu Mar 27 01:49:45 2003 UTC vs.
Revision 689 by tim, Tue Aug 12 19:56:49 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 >  std::cerr << "Hello from Initialize from file.\n";
32 >
33   #ifdef IS_MPI
34    if (worldRank == 0) {
35   #endif
# Line 40 | 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 61 | Line 72 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
72   }
73  
74  
75 < void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
75 > void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
76  
77    int i, j, done, which_node, which_atom; // loop counter
78  
# Line 75 | Line 86 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
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  
93 <  entry_plug = the_entry_plug;
93 >  simnfo = the_simnfo;
94  
95  
96   #ifndef IS_MPI
# Line 91 | Line 105 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
105  
106    n_atoms = atoi( read_buffer );
107  
108 <  Atom **atoms = entry_plug->atoms;
108 >  Atom **atoms = simnfo->atoms;
109    DirectionalAtom* dAtom;
110  
111 <  if( n_atoms != entry_plug->n_atoms ){
111 >  if( n_atoms != simnfo->n_atoms ){
112      sprintf( painCave.errMsg,
113               "Initialize from File error. %s n_atoms, %d, "
114               "does not match the BASS file's n_atoms, %d.\n",
115 <             c_in_name, n_atoms, entry_plug->n_atoms );
115 >             c_in_name, n_atoms, simnfo->n_atoms );
116      painCave.isFatal = 1;
117      simError();
118    }
119    
120 <  //read and toss the comment line
120 >  //read the box mat from the comment line
121    
122    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
123    if(eof_test == NULL){
# Line 113 | Line 127 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
127      simError();
128    }
129  
130 +  parseErr = parseBoxLine( read_buffer, boxMat, currTime );
131 +  if( parseErr != NULL ){
132 +    strcpy( painCave.errMsg, parseErr );
133 +    painCave.isFatal = 1;
134 +    simError();
135 +  }
136 +
137 +  for(i=0;i<3;i++)
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++){
145      
146      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
# Line 132 | Line 160 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
160        strcpy( painCave.errMsg, parseErr );
161        painCave.isFatal = 1;
162        simError();
163 <    }    
163 >    }
164    }
165  
166  
167    // MPI Section of code..........
168   #else //IS_MPI
169  
170 <  MPI::Status istatus;
170 >  // first thing first, suspend fatalities.
171 >  painCave.isEventLoop = 1;
172 >
173 >  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
174 >  int haveError;
175 >  
176 >  MPI_Status istatus;
177    int *AtomToProcMap = mpiSim->getAtomToProcMap();
178  
179 +  
180 +  haveError = 0;
181    if (worldRank == 0) {
182 +
183      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
184      if( eof_test == NULL ){
185        sprintf( painCave.errMsg,
186                 "Error reading 1st line of %d \n ",c_in_name);
187 <      painCave.isFatal = 1;
187 >      haveError = 1;
188        simError();
189      }
190      
191      n_atoms = atoi( read_buffer );
192      
193 <    Atom **atoms = entry_plug->atoms;
193 >    Atom **atoms = simnfo->atoms;
194      DirectionalAtom* dAtom;
195  
196      // Check to see that the number of atoms in the intial configuration file is the
# Line 163 | Line 200 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
200        sprintf( painCave.errMsg,
201                 "Initialize from File error. %s n_atoms, %d, "
202                 "does not match the BASS file's n_atoms, %d.\n",
203 <               c_in_name, n_atoms, entry_plug->n_atoms );
204 <      painCave.isFatal = 1;
203 >               c_in_name, n_atoms, simnfo->n_atoms );
204 >      haveError= 1;
205        simError();
206      }
207      
208 <    //read and toss the comment line
208 >    //read the boxMat from the comment line
209      
210      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
211      if(eof_test == NULL){
212        sprintf( painCave.errMsg,
213                 "error in reading commment in %s\n", c_in_name);
214 <      painCave.isFatal = 1;
214 >      haveError = 1;
215        simError();
216      }
217 +    
218 +    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
219 +    if( parseErr != NULL ){
220 +      strcpy( painCave.errMsg, parseErr );
221 +      haveError = 1;
222 +      simError();
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  
230      for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
231        
# Line 188 | Line 236 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
236                  "natoms  = %d; index = %d\n"
237                  "error reading the line from the file.\n",
238                  c_in_name, n_atoms, i );
239 <        painCave.isFatal = 1;
239 >        haveError= 1;
240          simError();
241        }
242      
243 +      if(haveError) nodeZeroError();
244 +
245        // Get the Node number which wants this atom:
246        which_node = AtomToProcMap[i];    
247 <      if (which_node == mpiSim->getMyNode()) {
247 >      if (which_node == 0) {
248          parseErr = parseDumpLine( read_buffer, i );
249          if( parseErr != NULL ){
250            strcpy( painCave.errMsg, parseErr );
251 <          painCave.isFatal = 1;
251 >          haveError = 1;
252            simError();
253          }    
254 <      } else {
255 <        MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
256 <                             TAKE_THIS_TAG);
257 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
254 >        if(haveError) nodeZeroError();
255 >      }
256 >      
257 >      else {
258 >      
259 >        myStatus = 1;
260 >        MPI_Send(&myStatus, 1, MPI_INT, which_node,
261 >                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
262 >        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
263 >                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
264 >        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
265 >                 MPI_COMM_WORLD);
266 >        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
267 >                 MPI_COMM_WORLD, &istatus);
268 >        
269 >        if(!myStatus) nodeZeroError();
270        }
271      }
272 <    sprintf(read_buffer, "GAMEOVER");
272 >    myStatus = -1;
273      for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
274 <      MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j,
275 <                           TAKE_THIS_TAG);
274 >      MPI_Send( &myStatus, 1, MPI_INT, j,
275 >                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
276      }
277 <
277 >    
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) {
285 <      MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
286 <                           TAKE_THIS_TAG, istatus);
287 <      if (strcmp(read_buffer, "GAMEOVER")) {
288 <        done = 1;
289 <        continue;
290 <      } else {
291 <        MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
292 <                             TAKE_THIS_TAG, istatus);
293 <        parseErr = parseDumpLine( read_buffer, which_atom );
294 <        if( parseErr != NULL ){
295 <          strcpy( painCave.errMsg, parseErr );
296 <          painCave.isFatal = 1;
297 <          simError();
298 <        }
285 >
286 >      MPI_Recv(&myStatus, 1, MPI_INT, 0,
287 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
288 >      
289 >      if(!myStatus) anonymousNodeDie();
290 >      
291 >      if(myStatus < 0) break;
292 >
293 >      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
294 >               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
295 >      MPI_Recv(&which_atom, 1, MPI_INT, 0,
296 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
297 >      
298 >      myStatus = 1;
299 >      parseErr = parseDumpLine( read_buffer, which_atom );
300 >      if( parseErr != NULL ){
301 >        strcpy( painCave.errMsg, parseErr );
302 >        myStatus = 0;;
303 >        simError();
304        }
305 +      
306 +      MPI_Send( &myStatus, 1, MPI_INT, 0,
307 +                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
308 +      
309      }
310    }
311 <        
311 >    
312 > // last  thing last, enable  fatalities.
313 >  painCave.isEventLoop = 0;
314 >
315 >  for(i=0;i<3;i++)
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
323   }
324  
325 < char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
325 > char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
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.
334    
335 <  Atom **atoms = entry_plug->atoms;
335 >  Atom **atoms = simnfo->atoms;
336    DirectionalAtom* dAtom;
337    
338 <  int n_atoms;
338 >  int j, n_atoms, atomIndex;
339  
340   #ifdef IS_MPI
341    n_atoms = mpiSim->getTotAtoms();
342 +  atomIndex=-1;        
343 +  for (j=0; j < mpiSim->getMyNlocal(); j++) {
344 +    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
345 +  }
346 +  if (atomIndex == -1) {
347 +    sprintf( painCave.errMsg,
348 +             "Initialize from file error. Atom at index %d "
349 +             "in file %s does not exist on processor %d .\n",
350 +             globalIndex, c_in_name, mpiSim->getMyNode() );
351 +    return strdup( painCave.errMsg );
352 +  }  
353   #else
354 <  n_atoms = entry_plug->n_atoms;
354 >  n_atoms = simnfo->n_atoms;
355 >  atomIndex = globalIndex;
356   #endif // is_mpi
357  
262 –
358    // set the string tokenizer
359    
360    foo = strtok(readLine, " ,;\t");
# Line 285 | 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 295 | 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 305 | 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 318 | 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 328 | 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 338 | 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 440 | 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 );
540 <  atoms[atomIndex]->setZ( rz );
541 <    
542 <  atoms[atomIndex]->set_vx( vx );
543 <  atoms[atomIndex]->set_vy( vy );
544 <  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],
546 >                                       double &time ){
547 >
548 >  char *foo; // the pointer to the current string token
549 >  int j;
550 >
551 >  // set the string tokenizer
552 >  
553 >  foo = strtok(readLine, " ,;\t");
554 >  // set the timeToken.
555 >
556 >  if(foo == NULL){
557 >    sprintf( painCave.errMsg,
558 >             "error in reading Time from %s\n",
559 >             c_in_name );
560 >    return strdup( painCave.errMsg );
561 >  }
562 >  time = atof( foo );
563 >
564 >  // get the Hx vector
565 >
566 >  foo = strtok(NULL, " ,;\t");
567 >  if(foo == NULL){
568 >    sprintf( painCave.errMsg,
569 >             "error in reading Hx[0] from %s\n",
570 >             c_in_name );
571 >    return strdup( painCave.errMsg );
572 >  }
573 >  boxMat[0] = atof( foo );
574 >  
575 >  foo = strtok(NULL, " ,;\t");
576 >  if(foo == NULL){
577 >    sprintf( painCave.errMsg,
578 >             "error in reading Hx[1] from %s\n",
579 >             c_in_name );
580 >    return strdup( painCave.errMsg );
581 >  }
582 >  boxMat[1] = atof( foo );
583 >    
584 >  foo = strtok(NULL, " ,;\t");
585 >  if(foo == NULL){
586 >    sprintf( painCave.errMsg,
587 >             "error in reading Hx[2] from %s\n",
588 >             c_in_name );
589 >    return strdup( painCave.errMsg );
590 >  }
591 >  boxMat[2] = atof( foo );    
592  
593 +  // get the Hy vector
594 +
595 +  foo = strtok(NULL, " ,;\t");
596 +  if(foo == NULL){
597 +    sprintf( painCave.errMsg,
598 +             "error in reading Hy[0] from %s\n",
599 +             c_in_name );
600 +    return strdup( painCave.errMsg );
601 +  }
602 +  boxMat[3] = atof( foo );
603 +  
604 +  foo = strtok(NULL, " ,;\t");
605 +  if(foo == NULL){
606 +    sprintf( painCave.errMsg,
607 +             "error in reading Hy[1] from %s\n",
608 +             c_in_name );
609 +    return strdup( painCave.errMsg );
610 +  }
611 +  boxMat[4] = atof( foo );
612 +    
613 +  foo = strtok(NULL, " ,;\t");
614 +  if(foo == NULL){
615 +    sprintf( painCave.errMsg,
616 +             "error in reading Hy[2] from %s\n",
617 +             c_in_name );
618 +    return strdup( painCave.errMsg );
619 +  }
620 +  boxMat[5] = atof( foo );    
621 +
622 +  // get the Hz vector
623 +
624 +  foo = strtok(NULL, " ,;\t");
625 +  if(foo == NULL){
626 +    sprintf( painCave.errMsg,
627 +             "error in reading Hz[0] from %s\n",
628 +             c_in_name );
629 +    return strdup( painCave.errMsg );
630 +  }
631 +  boxMat[6] = atof( foo );
632 +  
633 +  foo = strtok(NULL, " ,;\t");
634 +  if(foo == NULL){
635 +    sprintf( painCave.errMsg,
636 +             "error in reading Hz[1] from %s\n",
637 +             c_in_name );
638 +    return strdup( painCave.errMsg );
639 +  }
640 +  boxMat[7] = atof( foo );
641 +    
642 +  foo = strtok(NULL, " ,;\t");
643 +  if(foo == NULL){
644 +    sprintf( painCave.errMsg,
645 +             "error in reading Hz[2] from %s\n",
646 +             c_in_name );
647 +    return strdup( painCave.errMsg );
648 +  }
649 +  boxMat[8] = atof( foo );    
650 +
651    return NULL;
652   }
653 +
654 +
655 + #ifdef IS_MPI
656 +
657 + // a couple of functions to let us escape the read loop
658 +
659 + void initFile::nodeZeroError( void ){
660 +  int j, myStatus;
661 +  
662 +  myStatus = 0;
663 +  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
664 +    MPI_Send( &myStatus, 1, MPI_INT, j,
665 +              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
666 +  }  
667 +  
668 +
669 +  MPI_Finalize();
670 +  exit (0);
671 +  
672 + }
673 +
674 + void initFile::anonymousNodeDie( void ){
675 +
676 +  MPI_Finalize();
677 +  exit (0);
678 + }
679 +
680 + #endif //is_mpi

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