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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 669 by chuckv, Thu Aug 7 00:47:33 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 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;
# Line 182 | 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 270 | Line 267 | void EAM_FF::calcRcut( void ){
267  
268   void EAM_FF::calcRcut( void ){
269    
270 <  #ifdef IS_MPI
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->setRcut(eamRcut);
275 >  entry_plug->setDefaultRcut(eamRcut);
276   }
277  
278  
# Line 305 | Line 302 | void EAM_FF::readParams( void ){
302    info.last = 1; // initialize last to have the last set.
303                   // if things go well, last will be set to 0
304  
308 –  int i;
305    int identNum;
306    double *eam_rvals;    // Z of r values
307    double *eam_rhovals;  // rho of r values
# Line 411 | 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 437 | Line 433 | void EAM_FF::readParams( void ){
433        
434        MPIcheckPoint();
435  
436 <      recieveFrcStruct( &info, mpiAtomStructType );
436 >      receiveFrcStruct( &info, mpiAtomStructType );
437  
438  
439      }
# Line 453 | 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 469 | 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 535 | Line 535 | void EAM_FF::initializeAtoms( int nAtoms, Atom** the_a
535    
536    // initialize the atoms
537    
538 –
539 –  Atom* thisAtom;
540 –
538    for( i=0; i<nAtoms; i++ ){
539      
540      currentAtomType = headAtomType->find( the_atoms[i]->getType() );
# Line 551 | Line 548 | void EAM_FF::initializeAtoms( int nAtoms, Atom** the_a
548      
549      the_atoms[i]->setMass( currentAtomType->mass );
550      the_atoms[i]->setIdent( currentAtomType->ident );
554 –    the_atoms[i]->setEAM();
555 –    the_atoms[i]->setEamRcut( currentAtomType->eam_rcut);
551  
552      if (eamRcut < currentAtomType->eam_rcut) eamRcut = currentAtomType->eam_rcut;
553 <
553 >    
554    }
555   }
556  
# Line 1023 | Line 1018 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
1018      myEam_rhovals[j+0] = atof( the_token );
1019  
1020      // Value 2
1021 <    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
1021 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1022        sprintf( painCave.errMsg,
1023                 "Error parseing EAM nrho: line in %s\n", eamPotFile );
1024        painCave.isFatal = 1;
# Line 1033 | Line 1028 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
1028      myEam_rhovals[j+1] = atof( the_token );
1029  
1030      // Value 3
1031 <    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
1031 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1032        sprintf( painCave.errMsg,
1033                 "Error parseing EAM nrho: line in %s\n", eamPotFile );
1034        painCave.isFatal = 1;
# Line 1043 | Line 1038 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
1038      myEam_rhovals[j+2] = atof( the_token );
1039  
1040      // Value 4
1041 <    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
1041 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1042        sprintf( painCave.errMsg,
1043                 "Error parseing EAM nrho: line in %s\n", eamPotFile );
1044        painCave.isFatal = 1;
# Line 1053 | Line 1048 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
1048      myEam_rhovals[j+3] = atof( the_token );
1049  
1050      // Value 5
1051 <    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
1051 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1052        sprintf( painCave.errMsg,
1053                 "Error parseing EAM nrho: line in %s\n", eamPotFile );
1054        painCave.isFatal = 1;
# Line 1061 | Line 1056 | int EAM_NS::parseEAM(atomStruct &info, char *eamPotFil
1056      }
1057    
1058      myEam_rhovals[j+4] = atof( the_token );
1059 <
1059 >
1060    }
1061    *eam_rvals = myEam_rvals;
1062    *eam_rhovals = myEam_rhovals;

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