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root/group/trunk/OOPSE/libmdtools/EAM_FF.cpp
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Comparing trunk/OOPSE/libmdtools/EAM_FF.cpp (file contents):
Revision 631 by chuckv, Thu Jul 17 19:25:51 2003 UTC vs.
Revision 976 by chrisfen, Thu Jan 22 17:34:20 2004 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstdio>
3 < #include <cstring>
1 > #include <stdlib.h>
2 > #include <stdio.h>
3 > #include <string.h>
4  
5   #include <iostream>
6   using namespace std;
# Line 30 | Line 30 | namespace EAM_NS{
30      double mass;
31      double lattice_constant;
32      double eam_drho;  // The distance between each of the points indexed by rho.
33 +    double eam_rcut;  // The cutoff radius for eam.
34      double eam_dr;    // The distance between each of the rho points.    
35      int eam_nrho;  // Number of points indexed by rho
36      int eam_nr;    // The number of points based on r (Both Phi(r) and Rho(r)).
36 –    double eam_rcut;  // The cutoff radius for eam.
37      int eam_ident; // Atomic number
38      int ident;
39      int last;      //  0  -> default
# Line 76 | Line 76 | namespace EAM_NS{
76      void add( atomStruct &info, double *the_eam_rvals,
77                double *the_eam_rhovals,double *the_eam_Frhovals ){
78  
79 –      int i;
80 –
79        // check for duplicates
80        
81        if( !strcmp( info.name, name ) ){
# Line 164 | Line 162 | EAM_FF::EAM_FF(){
162    char* ffPath_env = "FORCE_PARAM_PATH";
163    char* ffPath;
164    char temp[200];
167 –  char errMsg[1000];
165  
166    headAtomType = NULL;
167    currentAtomType = NULL;
168  
169 +  // Set eamRcut to 0.0
170 +  eamRcut = 0.0;
171 +
172    // do the funtion wrapping
173    wrapMeFF( this );
174  
# Line 179 | Line 179 | EAM_FF::EAM_FF(){
179    // Init the atomStruct mpi type
180  
181    atomStruct atomProto; // mpiPrototype
182 <  int atomBC[3] = {15,4,6};  // block counts
182 >  int atomBC[3] = {15,5,5};  // block counts
183    MPI_Aint atomDspls[3];           // displacements
184    MPI_Datatype atomMbrTypes[3];    // member mpi types
185  
# Line 264 | Line 264 | EAM_FF::~EAM_FF(){
264   #endif // is_mpi
265   }
266  
267 < void EAM_FF::initForceField( int ljMixRule ){
267 >
268 > void EAM_FF::calcRcut( void ){
269    
270 + #ifdef IS_MPI
271 +  double tempEamRcut = eamRcut;
272 +  MPI_Allreduce( &tempEamRcut, &eamRcut, 1, MPI_DOUBLE, MPI_MAX,
273 +                 MPI_COMM_WORLD);
274 + #endif  //is_mpi
275 +  entry_plug->setDefaultRcut(eamRcut);
276 + }
277 +
278 +
279 + void EAM_FF::initForceField( int ljMixRule ){
280    initFortran( ljMixRule, 0 );
281   }
282  
# Line 284 | Line 295 | void EAM_FF::cleanMe( void ){
295   #endif // is_mpi
296   }
297  
298 +
299   void EAM_FF::readParams( void ){
300  
301    atomStruct info;
302    info.last = 1; // initialize last to have the last set.
303                   // if things go well, last will be set to 0
304  
293 –  int i;
305    int identNum;
306    double *eam_rvals;    // Z of r values
307    double *eam_rhovals;  // rho of r values
# Line 396 | Line 407 | void EAM_FF::readParams( void ){
407      MPIcheckPoint();
408  
409      headAtomType = new LinkedAtomType;
410 <    recieveFrcStruct( &info, mpiAtomStructType );
410 >    receiveFrcStruct( &info, mpiAtomStructType );
411  
412      while( !info.last ){
413        
# Line 422 | Line 433 | void EAM_FF::readParams( void ){
433        
434        MPIcheckPoint();
435  
436 <      recieveFrcStruct( &info, mpiAtomStructType );
436 >      receiveFrcStruct( &info, mpiAtomStructType );
437  
438  
439      }
# Line 438 | Line 449 | void EAM_FF::readParams( void ){
449    int isDipole = 0;
450    int isSSD = 0;
451    int isGB = 0;
452 <  int isEAM= 1;
452 >  int isEAM = 1;
453 >  int isCharge = 0;
454    double dipole = 0.0;
455 +  double charge = 0.0;
456    double eamSigma = 0.0;
457    double eamEpslon = 0.0;
458    
# Line 454 | Line 467 | void EAM_FF::readParams( void ){
467                   &isDipole,
468                   &isGB,
469                   &isEAM,
470 +                 &isCharge,
471                   &eamEpslon,
472                   &eamSigma,
473 +                 &charge,
474                   &dipole,
475                   &isError );
476        if( isError ){
# Line 470 | Line 485 | void EAM_FF::readParams( void ){
485    }
486        
487    entry_plug->useLJ = 0;
488 <
488 >  entry_plug->useEAM = 1;
489    // Walk down again and send out EAM type
490    currentAtomType = headAtomType->next;
491    while( currentAtomType != NULL ){
492      
493      if( currentAtomType->name[0] != '\0' ){
494        isError = 0;
495 +
496        newEAMtype( &(currentAtomType->lattice_constant),
497                    &(currentAtomType->eam_nrho),
498                    &(currentAtomType->eam_drho),
# Line 488 | Line 504 | void EAM_FF::readParams( void ){
504                    currentAtomType->eam_Frhovals,
505                    &(currentAtomType->eam_ident),
506                    &isError);
507 +
508        if( isError ){
509          sprintf( painCave.errMsg,
510                   "Error initializing the \"%s\" atom type in fortran EAM\n",
# Line 507 | Line 524 | void EAM_FF::readParams( void ){
524    MPIcheckPoint();
525   #endif // is_mpi
526  
527 +
528 +
529   }
530  
531  
532   void EAM_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){
533    
534    int i;
535 <
535 >  
536    // initialize the atoms
537    
519 –
520 –  Atom* thisAtom;
521 –
538    for( i=0; i<nAtoms; i++ ){
539      
540      currentAtomType = headAtomType->find( the_atoms[i]->getType() );
# Line 533 | Line 549 | void EAM_FF::initializeAtoms( int nAtoms, Atom** the_a
549      the_atoms[i]->setMass( currentAtomType->mass );
550      the_atoms[i]->setIdent( currentAtomType->ident );
551      the_atoms[i]->setEAM();
552 +    the_atoms[i]->setEamRcut( currentAtomType->eam_rcut);
553  
554 +    if (eamRcut < currentAtomType->eam_rcut) eamRcut = currentAtomType->eam_rcut;
555 +
556    }
557   }
558  
# Line 661 | Line 680 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
680                       double **eam_rvals,
681                       double **eam_rhovals,
682                       double **eam_Frhovals){
683 <  
683 >  double* myEam_rvals;
684 >  double* myEam_rhovals;
685 >  double* myEam_Frhovals;
686 >
687    char* ffPath_env = "FORCE_PARAM_PATH";
688    char* ffPath;
689    char* the_token;
690    char* eam_eof_test;
691    FILE *eamFile;
692 <  const int BUFFERSIZE = 2000;
692 >  const int BUFFERSIZE = 3000;
693  
694    char temp[200];
695    int linenumber;
696    int nReadLines;
697    char eam_read_buffer[BUFFERSIZE];
698  
699 +
700    int i,j;
701  
702    linenumber = 0;
# Line 814 | Line 837 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
837    info.eam_rcut = atof( the_token);
838  
839  
840 +
841 +
842 +
843    // Ok now we have to allocate point arrays and read in number of points
844    // Index the arrays for fortran, starting at 1
845 <  *eam_Frhovals = new double[info.eam_nrho];
846 <  *eam_rvals    = new double[info.eam_nr];
847 <  *eam_rhovals  = new double[info.eam_nr];
845 >  myEam_Frhovals = new double[info.eam_nrho];
846 >  myEam_rvals    = new double[info.eam_nr];
847 >  myEam_rhovals  = new double[info.eam_nr];
848  
849    // Parse F of rho vals.
850  
851    // Assume for now that we have a complete number of lines
852    nReadLines = int(info.eam_nrho/5);
853 +  
854  
855 +
856    for (i=0;i<nReadLines;i++){
857      j = i*5;
858 <    
858 >
859      // Read next line
860      eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
861      linenumber++;
# Line 847 | Line 875 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
875        painCave.isFatal = 1;
876        simError();
877      }
878 +
879 +    myEam_Frhovals[j+0] = atof( the_token );
880      
851 –    *eam_Frhovals[j+0] = atof( the_token );
852 –    
881      // Value 2
882      if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
883        sprintf( painCave.errMsg,
# Line 857 | Line 885 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
885        painCave.isFatal = 1;
886        simError();
887      }
888 <  
889 <    *eam_Frhovals[j+1] = atof( the_token );
888 >
889 >    myEam_Frhovals[j+1] = atof( the_token );
890      
891      // Value 3
892      if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
# Line 867 | Line 895 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
895        painCave.isFatal = 1;
896        simError();
897      }
898 +
899 +    myEam_Frhovals[j+2] = atof( the_token );
900      
871 –    *eam_Frhovals[j+2] = atof( the_token );
872 –    
901      // Value 4
902      if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
903        sprintf( painCave.errMsg,
# Line 877 | Line 905 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
905        painCave.isFatal = 1;
906        simError();
907      }
880 –    
881 –    *eam_Frhovals[j+3] = atof( the_token );
908  
909 +    myEam_Frhovals[j+3] = atof( the_token );
910 +
911      // Value 5
912      if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
913        sprintf( painCave.errMsg,
# Line 887 | Line 915 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
915        painCave.isFatal = 1;
916        simError();
917      }
918 +
919 +    myEam_Frhovals[j+4] = atof( the_token );
920      
891 –    *eam_Frhovals[j+4] = atof( the_token );
892 –    
921    }
922    // Parse Z of r vals
923    
# Line 919 | Line 947 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
947        simError();
948      }
949      
950 <    *eam_rvals[j+0] = atof( the_token );
950 >    myEam_rvals[j+0] = atof( the_token );
951  
952      // Value 2
953      if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
# Line 929 | Line 957 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
957        simError();
958      }
959    
960 <    *eam_rvals[j+1] = atof( the_token );
960 >    myEam_rvals[j+1] = atof( the_token );
961  
962      // Value 3
963      if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
# Line 939 | Line 967 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
967        simError();
968      }
969    
970 <    *eam_rvals[j+2] = atof( the_token );
970 >    myEam_rvals[j+2] = atof( the_token );
971  
972      // Value 4
973      if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
# Line 949 | Line 977 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
977        simError();
978      }
979    
980 <    *eam_rvals[j+3] = atof( the_token );
980 >    myEam_rvals[j+3] = atof( the_token );
981  
982      // Value 5
983      if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
# Line 959 | Line 987 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
987        simError();
988      }
989    
990 <    *eam_rvals[j+4] = atof( the_token );
990 >    myEam_rvals[j+4] = atof( the_token );
991  
992    }
993    // Parse rho of r vals
# Line 989 | Line 1017 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
1017        simError();
1018      }
1019    
1020 <    *eam_rhovals[j+0] = atof( the_token );
1020 >    myEam_rhovals[j+0] = atof( the_token );
1021  
1022      // Value 2
1023 <    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
1023 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1024        sprintf( painCave.errMsg,
1025                 "Error parseing EAM nrho: line in %s\n", eamPotFile );
1026        painCave.isFatal = 1;
1027        simError();
1028      }
1029    
1030 <    *eam_rhovals[j+1] = atof( the_token );
1030 >    myEam_rhovals[j+1] = atof( the_token );
1031  
1032      // Value 3
1033 <    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
1033 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1034        sprintf( painCave.errMsg,
1035                 "Error parseing EAM nrho: line in %s\n", eamPotFile );
1036        painCave.isFatal = 1;
1037        simError();
1038      }
1039    
1040 <    *eam_rhovals[j+2] = atof( the_token );
1040 >    myEam_rhovals[j+2] = atof( the_token );
1041  
1042      // Value 4
1043 <    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
1043 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1044        sprintf( painCave.errMsg,
1045                 "Error parseing EAM nrho: line in %s\n", eamPotFile );
1046        painCave.isFatal = 1;
1047        simError();
1048      }
1049    
1050 <    *eam_rhovals[j+3] = atof( the_token );
1050 >    myEam_rhovals[j+3] = atof( the_token );
1051  
1052      // Value 5
1053 <    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
1053 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1054        sprintf( painCave.errMsg,
1055                 "Error parseing EAM nrho: line in %s\n", eamPotFile );
1056        painCave.isFatal = 1;
1057        simError();
1058      }
1059    
1060 <    *eam_rhovals[j+4] = atof( the_token );
1061 <
1060 >    myEam_rhovals[j+4] = atof( the_token );
1061 >
1062    }
1063 +  *eam_rvals = myEam_rvals;
1064 +  *eam_rhovals = myEam_rhovals;
1065 +  *eam_Frhovals = myEam_Frhovals;
1066  
1067    fclose(eamFile);
1068    return 0;

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