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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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#include <iostream> |
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using namespace std; |
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double mass; |
31 |
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double lattice_constant; |
32 |
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double eam_drho; // The distance between each of the points indexed by rho. |
33 |
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double eam_rcut; // The cutoff radius for eam. |
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double eam_dr; // The distance between each of the rho points. |
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int eam_nrho; // Number of points indexed by rho |
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int eam_nr; // The number of points based on r (Both Phi(r) and Rho(r)). |
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double eam_rcut; // The cutoff radius for eam. |
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int eam_ident; // Atomic number |
38 |
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int ident; |
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int last; // 0 -> default |
76 |
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void add( atomStruct &info, double *the_eam_rvals, |
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double *the_eam_rhovals,double *the_eam_Frhovals ){ |
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|
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int i; |
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|
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// check for duplicates |
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|
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if( !strcmp( info.name, name ) ){ |
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char* ffPath_env = "FORCE_PARAM_PATH"; |
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char* ffPath; |
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char temp[200]; |
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char errMsg[1000]; |
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|
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headAtomType = NULL; |
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currentAtomType = NULL; |
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|
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// Set eamRcut to 0.0 |
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eamRcut = 0.0; |
171 |
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|
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// do the funtion wrapping |
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wrapMeFF( this ); |
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// Init the atomStruct mpi type |
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atomStruct atomProto; // mpiPrototype |
182 |
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int atomBC[3] = {15,4,6}; // block counts |
182 |
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int atomBC[3] = {15,5,5}; // block counts |
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MPI_Aint atomDspls[3]; // displacements |
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MPI_Datatype atomMbrTypes[3]; // member mpi types |
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#endif // is_mpi |
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} |
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void EAM_FF::initForceField( int ljMixRule ){ |
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void EAM_FF::calcRcut( void ){ |
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|
270 |
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#ifdef IS_MPI |
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double tempEamRcut = eamRcut; |
272 |
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MPI_Allreduce( &tempEamRcut, &eamRcut, 1, MPI_DOUBLE, MPI_MAX, |
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MPI_COMM_WORLD); |
274 |
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#endif //is_mpi |
275 |
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entry_plug->setDefaultRcut(eamRcut); |
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} |
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|
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|
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void EAM_FF::initForceField( int ljMixRule ){ |
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initFortran( ljMixRule, 0 ); |
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} |
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#endif // is_mpi |
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} |
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|
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void EAM_FF::readParams( void ){ |
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info.last = 1; // initialize last to have the last set. |
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// if things go well, last will be set to 0 |
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|
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int i; |
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int identNum; |
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double *eam_rvals; // Z of r values |
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double *eam_rhovals; // rho of r values |
481 |
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} |
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|
483 |
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entry_plug->useLJ = 0; |
484 |
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484 |
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entry_plug->useEAM = 1; |
485 |
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// Walk down again and send out EAM type |
486 |
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currentAtomType = headAtomType->next; |
487 |
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while( currentAtomType != NULL ){ |
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|
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if( currentAtomType->name[0] != '\0' ){ |
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isError = 0; |
491 |
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|
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newEAMtype( &(currentAtomType->lattice_constant), |
493 |
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&(currentAtomType->eam_nrho), |
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&(currentAtomType->eam_drho), |
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currentAtomType->eam_Frhovals, |
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&(currentAtomType->eam_ident), |
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&isError); |
503 |
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|
504 |
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if( isError ){ |
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sprintf( painCave.errMsg, |
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"Error initializing the \"%s\" atom type in fortran EAM\n", |
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MPIcheckPoint(); |
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#endif // is_mpi |
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|
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} |
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void EAM_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
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int i; |
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|
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// initialize the atoms |
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|
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Atom* thisAtom; |
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for( i=0; i<nAtoms; i++ ){ |
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currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
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the_atoms[i]->setMass( currentAtomType->mass ); |
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the_atoms[i]->setIdent( currentAtomType->ident ); |
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the_atoms[i]->setEAM(); |
548 |
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the_atoms[i]->setEamRcut( currentAtomType->eam_rcut); |
549 |
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|
550 |
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if (eamRcut < currentAtomType->eam_rcut) eamRcut = currentAtomType->eam_rcut; |
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|
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} |
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} |
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double **eam_rvals, |
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double **eam_rhovals, |
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double **eam_Frhovals){ |
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|
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double* myEam_rvals; |
680 |
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double* myEam_rhovals; |
681 |
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double* myEam_Frhovals; |
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|
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char* ffPath_env = "FORCE_PARAM_PATH"; |
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char* ffPath; |
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char* the_token; |
686 |
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char* eam_eof_test; |
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FILE *eamFile; |
688 |
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const int BUFFERSIZE = 2000; |
688 |
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const int BUFFERSIZE = 3000; |
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|
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char temp[200]; |
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int linenumber; |
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int nReadLines; |
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char eam_read_buffer[BUFFERSIZE]; |
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|
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int i,j; |
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linenumber = 0; |
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info.eam_rcut = atof( the_token); |
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837 |
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|
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// Ok now we have to allocate point arrays and read in number of points |
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// Index the arrays for fortran, starting at 1 |
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*eam_Frhovals = new double[info.eam_nrho]; |
842 |
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*eam_rvals = new double[info.eam_nr]; |
843 |
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*eam_rhovals = new double[info.eam_nr]; |
841 |
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myEam_Frhovals = new double[info.eam_nrho]; |
842 |
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myEam_rvals = new double[info.eam_nr]; |
843 |
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myEam_rhovals = new double[info.eam_nr]; |
844 |
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|
845 |
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// Parse F of rho vals. |
846 |
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// Assume for now that we have a complete number of lines |
848 |
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nReadLines = int(info.eam_nrho/5); |
849 |
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851 |
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|
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for (i=0;i<nReadLines;i++){ |
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j = i*5; |
854 |
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854 |
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|
855 |
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// Read next line |
856 |
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eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
857 |
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linenumber++; |
871 |
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painCave.isFatal = 1; |
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simError(); |
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} |
874 |
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|
875 |
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myEam_Frhovals[j+0] = atof( the_token ); |
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|
851 |
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*eam_Frhovals[j+0] = atof( the_token ); |
852 |
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|
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// Value 2 |
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if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
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sprintf( painCave.errMsg, |
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painCave.isFatal = 1; |
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simError(); |
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} |
884 |
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|
885 |
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*eam_Frhovals[j+1] = atof( the_token ); |
884 |
> |
|
885 |
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myEam_Frhovals[j+1] = atof( the_token ); |
886 |
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|
887 |
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// Value 3 |
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if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
891 |
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painCave.isFatal = 1; |
892 |
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simError(); |
893 |
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} |
894 |
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|
895 |
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myEam_Frhovals[j+2] = atof( the_token ); |
896 |
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|
871 |
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*eam_Frhovals[j+2] = atof( the_token ); |
872 |
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|
897 |
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// Value 4 |
898 |
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if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
899 |
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sprintf( painCave.errMsg, |
901 |
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painCave.isFatal = 1; |
902 |
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simError(); |
903 |
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} |
880 |
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|
881 |
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*eam_Frhovals[j+3] = atof( the_token ); |
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905 |
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myEam_Frhovals[j+3] = atof( the_token ); |
906 |
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|
907 |
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// Value 5 |
908 |
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if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
909 |
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sprintf( painCave.errMsg, |
911 |
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painCave.isFatal = 1; |
912 |
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simError(); |
913 |
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} |
914 |
+ |
|
915 |
+ |
myEam_Frhovals[j+4] = atof( the_token ); |
916 |
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|
891 |
– |
*eam_Frhovals[j+4] = atof( the_token ); |
892 |
– |
|
917 |
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} |
918 |
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// Parse Z of r vals |
919 |
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|
943 |
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simError(); |
944 |
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} |
945 |
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|
946 |
< |
*eam_rvals[j+0] = atof( the_token ); |
946 |
> |
myEam_rvals[j+0] = atof( the_token ); |
947 |
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|
948 |
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// Value 2 |
949 |
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if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
953 |
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simError(); |
954 |
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} |
955 |
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|
956 |
< |
*eam_rvals[j+1] = atof( the_token ); |
956 |
> |
myEam_rvals[j+1] = atof( the_token ); |
957 |
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|
958 |
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// Value 3 |
959 |
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if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
963 |
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simError(); |
964 |
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} |
965 |
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|
966 |
< |
*eam_rvals[j+2] = atof( the_token ); |
966 |
> |
myEam_rvals[j+2] = atof( the_token ); |
967 |
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|
968 |
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// Value 4 |
969 |
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if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
973 |
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simError(); |
974 |
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} |
975 |
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|
976 |
< |
*eam_rvals[j+3] = atof( the_token ); |
976 |
> |
myEam_rvals[j+3] = atof( the_token ); |
977 |
|
|
978 |
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// Value 5 |
979 |
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if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
983 |
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simError(); |
984 |
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} |
985 |
|
|
986 |
< |
*eam_rvals[j+4] = atof( the_token ); |
986 |
> |
myEam_rvals[j+4] = atof( the_token ); |
987 |
|
|
988 |
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} |
989 |
|
// Parse rho of r vals |
1013 |
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simError(); |
1014 |
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} |
1015 |
|
|
1016 |
< |
*eam_rhovals[j+0] = atof( the_token ); |
1016 |
> |
myEam_rhovals[j+0] = atof( the_token ); |
1017 |
|
|
1018 |
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// Value 2 |
1019 |
< |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
1019 |
> |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
1020 |
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sprintf( painCave.errMsg, |
1021 |
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"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
1022 |
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painCave.isFatal = 1; |
1023 |
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simError(); |
1024 |
|
} |
1025 |
|
|
1026 |
< |
*eam_rhovals[j+1] = atof( the_token ); |
1026 |
> |
myEam_rhovals[j+1] = atof( the_token ); |
1027 |
|
|
1028 |
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// Value 3 |
1029 |
< |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
1029 |
> |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
1030 |
|
sprintf( painCave.errMsg, |
1031 |
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"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
1032 |
|
painCave.isFatal = 1; |
1033 |
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simError(); |
1034 |
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} |
1035 |
|
|
1036 |
< |
*eam_rhovals[j+2] = atof( the_token ); |
1036 |
> |
myEam_rhovals[j+2] = atof( the_token ); |
1037 |
|
|
1038 |
|
// Value 4 |
1039 |
< |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
1039 |
> |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
1040 |
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sprintf( painCave.errMsg, |
1041 |
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"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
1042 |
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painCave.isFatal = 1; |
1043 |
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simError(); |
1044 |
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} |
1045 |
|
|
1046 |
< |
*eam_rhovals[j+3] = atof( the_token ); |
1046 |
> |
myEam_rhovals[j+3] = atof( the_token ); |
1047 |
|
|
1048 |
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// Value 5 |
1049 |
< |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
1049 |
> |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
1050 |
|
sprintf( painCave.errMsg, |
1051 |
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
1052 |
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painCave.isFatal = 1; |
1053 |
|
simError(); |
1054 |
|
} |
1055 |
|
|
1056 |
< |
*eam_rhovals[j+4] = atof( the_token ); |
1057 |
< |
|
1056 |
> |
myEam_rhovals[j+4] = atof( the_token ); |
1057 |
> |
|
1058 |
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} |
1059 |
+ |
*eam_rvals = myEam_rvals; |
1060 |
+ |
*eam_rhovals = myEam_rhovals; |
1061 |
+ |
*eam_Frhovals = myEam_Frhovals; |
1062 |
|
|
1063 |
|
fclose(eamFile); |
1064 |
|
return 0; |