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root/group/trunk/mdtools/interface_implementation/LJ_FF.cpp
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Comparing trunk/mdtools/interface_implementation/LJ_FF.cpp (file contents):
Revision 230 by chuckv, Thu Jan 9 19:40:38 2003 UTC vs.
Revision 263 by chuckv, Tue Feb 4 20:15:48 2003 UTC

# Line 9 | Line 9 | using namespace std;
9   #include "SRI.hpp"
10   #include "simError.h"
11  
12 –
12   // Declare the structures that will be passed by the parser and  MPI
13  
14   typedef struct{
# Line 25 | Line 24 | int parseAtomLJ( char *lineBuffer, int lineNum, atomSt
24   int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info );
25  
26   #ifdef IS_MPI
28 –
27   #include "mpiForceField.h"
28  
29   MPI_Datatype mpiAtomStructType;
# Line 33 | Line 31 | LJ_FF::LJ_FF(){
31   #endif
32  
33  
34 + // declaration of functions needed to wrap the fortran module
35 +
36 + extern "C" {
37 +  void forcefactory_( char* forceName,
38 +                      int* status,
39 +                      void (*wrapFunction)( void (*p1)( int* ident,
40 +                                                        double* mass,
41 +                                                        double* epslon,
42 +                                                        double* sigma,
43 +                                                        int* status ),
44 +                                            void (*p2)( int *nLocal,
45 +                                                        int *identArray,
46 +                                                        int *isError ),
47 +                                            void (*p3)( double* positionArray,
48 +                                                        double* forceArray,
49 +                                                        double* potentialEnergy,
50 +                                                        short int* doPotentialCalc )),
51 +                      int forceNameLength );
52 + }
53 +
54 +
55 + void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon,
56 +                                   double* sigma, int* status ),
57 +                        void (*p2)( int *nLocal, int *identArray, int *isError ),
58 +                        void (*p3)( double* positionArray,double* forceArray,
59 +                                    double* potentialEnergy,
60 +                                    short int* doPotentialCalc ) );
61 +
62 + void (*newLJtype)( int* ident, double* mass, double* epslon, double* sigma,
63 +                   int* status );
64 +
65 + void (*initLJfortran) ( int *nLocal, int *identArray, int *isError );
66 +
67 + LJ_FF* currentLJwrap;
68 +
69 +
70 + //****************************************************************
71 + // begins the actual forcefield stuff.  
72 + //****************************************************************
73 +
74 +
75   LJ_FF::LJ_FF(){
76  
77    char fileName[200];
# Line 41 | Line 80 | LJ_FF::LJ_FF(){
80    char temp[200];
81    char errMsg[1000];
82  
83 +  // do the funtion wrapping
84 +  currentLJwrap = this;
85 +  wrapMe();
86 +
87   #ifdef IS_MPI
88    int i;
89    
# Line 133 | Line 176 | LJ_FF::~LJ_FF(){
176      fclose( frcFile );
177      
178   #ifdef IS_MPI
179 +  }
180 + #endif // is_mpi
181 + }
182 +
183 +
184 + void LJ_FF::wrapMe( void ){
185 +  
186 +  char* currentFF = "LJ";
187 +  int isError = 0;
188 +  
189 +  forcefactory_( currentFF, &isError, LJfunctionWrapper, strlen(currentFF) );
190 +
191 +  if( isError ){
192 +    
193 +    sprintf( painCave.errMsg,
194 +             "LJ_FF error: an error was returned from fortran when the "
195 +             "the functions were being wrapped.\n" );
196 +    painCave.isFatal = 1;
197 +    simError();
198    }
199 +
200 + #ifdef IS_MPI
201 +  sprintf( checkPointMsg, "LJ_FF functions succesfully wrapped." );
202 +  MPIcheckPoint();
203   #endif // is_mpi
204   }
205 +  
206  
207 + void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon,
208 +                                   double* sigma, int* status ),
209 +                        void (*p2)( int*, int*, int* ),
210 +                        void (*p3)( double* positionArray,double* forceArray,
211 +                                    double* potentialEnergy,
212 +                                    short int* doPotentialCalc ) ){
213 +  
214 +  
215 +  newLJtype = p1;
216 +  initLJfortran = p2;
217 +  currentLJwrap->setLJfortran( p3 );
218 + }
219 +
220 +
221 +
222   void LJ_FF::initializeAtoms( void ){
223    
224    class LinkedType {
# Line 159 | Line 241 | void LJ_FF::initializeAtoms( void ){
241        // check for duplicates
242        
243        if( !strcmp( info.name, name ) ){
244 <        sprintf( simError.painCave,
244 >        sprintf( painCave.errMsg,
245                   "Duplicate LJ atom type \"%s\" found in "
246                   "the LJ_FF param file./n",
247                   name );
# Line 224 | Line 306 | void LJ_FF::initializeAtoms( void ){
306  
307      headAtomType = new LinkedType;
308      
309 <    fastFoward( "AtomTypes", "initializeAtoms" );
309 >    fastForward( "AtomTypes", "initializeAtoms" );
310  
311      // we are now at the AtomTypes section.
312      
# Line 268 | Line 350 | void LJ_FF::initializeAtoms( void ){
350               "LJ_FF atom structures read successfully." );
351      MPIcheckPoint();
352  
353 <    currentAtomType = headAtomType;
353 >    currentAtomType = headAtomType->next; //skip the first element who is a place holder.
354      while( currentAtomType != NULL ){
355        currentAtomType->duplicate( info );
356 +
357 +
358 +
359        sendFrcStruct( &info, mpiAtomStructType );
360 +
361 +      sprintf( checkPointMsg,
362 +               "successfully sent lJ force type: \"%s\"\n",
363 +               info.name );
364 +      MPIcheckPoint();
365 +
366        currentAtomType = currentAtomType->next;
367      }
368      info.last = 1;
# Line 287 | Line 378 | void LJ_FF::initializeAtoms( void ){
378  
379      headAtomType = new LinkedType;
380      recieveFrcStruct( &info, mpiAtomStructType );
381 +    
382      while( !info.last ){
383  
384 +
385 +
386        headAtomType->add( info );
387 +      
388 +      MPIcheckPoint();
389 +
390        recieveFrcStruct( &info, mpiAtomStructType );
391      }
392    }
393   #endif // is_mpi
394  
395    // call new A_types in fortran
396 +  
397 +  int isError;
398 +  currentAtomType = headAtomType;
399 +  while( currentAtomType != NULL ){
400 +    
401 +    if( currentAtomType->name[0] != '\0' ){
402 +      isError = 0;
403 +          newLJtype( &(currentAtomType->ident),
404 +                 &(currentAtomType->mass),
405 +                 &(currentAtomType->epslon),
406 +                 &(currentAtomType->sigma),
407 +                 &isError );
408 +      if( isError ){
409 +        sprintf( painCave.errMsg,
410 +                 "Error initializing the \"%s\" atom type in fortran\n",
411 +                 currentAtomType->name );
412 +        painCave.isFatal = 1;
413 +        simError();
414 +      }
415 +    }
416 +    currentAtomType = currentAtomType->next;
417 +  }
418 +      
419 + #ifdef IS_MPI
420 +  sprintf( checkPointMsg,
421 +           "LJ_FF atom structures successfully sent to fortran\n" );
422 +  MPIcheckPoint();
423 + #endif // is_mpi
424  
425 +  
426  
427    // initialize the atoms
428    
429 +  double bigSigma = 0.0;
430    Atom* thisAtom;
431  
432    for( i=0; i<nAtoms; i++ ){
# Line 318 | Line 445 | void LJ_FF::initializeAtoms( void ){
445      the_atoms[i]->setSigma( currentAtomType->sigma );
446      the_atoms[i]->setIdent( currentAtomType->ident );
447      the_atoms[i]->setLJ();
448 +
449 +    if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
450    }
451  
452 +  
453 + #ifdef IS_MPI
454 +  double tempBig = bigSigma;
455 +  MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX );
456 + #endif  //is_mpi
457  
458 +  //calc rCut and rList
459 +
460 +  entry_plug->rCut = 2.5 * bigSigma;
461 +  if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0;
462 +  if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0;
463 +  if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0;
464 +
465 +  entry_plug->rList = entry_plug->rCut + 1.0;
466 +
467    // clean up the memory
468    
469    delete headAtomType;
# Line 330 | Line 473 | void LJ_FF::initializeAtoms( void ){
473    MPIcheckPoint();
474   #endif // is_mpi
475  
476 +  initFortran();
477 +  entry_plug->refreshSim();
478 +
479   }
480  
481   void LJ_FF::initializeBonds( bond_pair* the_bonds ){
# Line 471 | Line 617 | int parseAtomLJ( char *lineBuffer, int lineNum,  atomS
617    }
618    else return 0;
619   }
620 +
621 +
622 + void LJ_FF::doForces( int calcPot ){
623 +
624 +  int i;
625 +  double* frc;
626 +  double* pos;
627 +  short int passedCalcPot = (short int)calcPot;
628 +
629 +  // forces are zeroed here, before any are acumulated.
630 +  // NOTE: do not rezero the forces in Fortran.
631 +
632 +  for(i=0; i<entry_plug->n_atoms; i++){
633 +    entry_plug->atoms[i]->zeroForces();
634 +  }
635 +
636 +  frc = Atom::getFrcArray();
637 +  pos = Atom::getPosArray();
638 +
639 + //   entry_plug->lrPot = -1;
640 +  doLJfortran( pos, frc, &(entry_plug->lrPot), &passedCalcPot );
641 +
642 +
643 +  //   fprintf( stderr,
644 +  //   "lrPot =  %lf\n", entry_plug->lrPot );
645 +  
646 + }
647 +  
648 + void LJ_FF::initFortran( void ){
649 +  
650 +  int nLocal = entry_plug->n_atoms;
651 +  int *ident;
652 +  int isError;
653 +  int i;
654 +
655 +  ident = new int[nLocal];
656 +
657 +  for(i=0; i<nLocal; i++){
658 +    ident[i] = entry_plug->atoms[i]->getIdent();
659 +  }
660 +
661 +  isError = 0;
662 +  initLJfortran( &nLocal, ident, &isError );
663 +  
664 +  if(isError){
665 +    sprintf( painCave.errMsg,
666 +             "LJ_FF error: There was an error initializing the component list in fortran.\n" );
667 +    painCave.isFatal = 1;
668 +    simError();
669 +  }
670 +
671 +  
672 + #ifdef IS_MPI
673 +  sprintf( checkPointMsg, "LJ_FF successfully initialized the fortran component list.\n" );
674 +  MPIcheckPoint();
675 + #endif // is_mpi
676 +  
677 +  delete[] ident;
678 +
679 + }
680 +  

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