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gezelter |
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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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chuckv |
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#include <iostream> |
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using namespace std; |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif //is_mpi |
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#include "ForceFields.hpp" |
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#include "SRI.hpp" |
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#include "simError.h" |
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#include "fortranWrappers.hpp" |
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#ifdef IS_MPI |
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#include "mpiForceField.h" |
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#endif // is_mpi |
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namespace EAM_NS{ |
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// Declare the structures that will be passed by the parser and MPI |
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typedef struct{ |
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char name[15]; |
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double mass; |
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chuckv |
627 |
double lattice_constant; |
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double eam_drho; // The distance between each of the points indexed by rho. |
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mmeineke |
814 |
double eam_rcut; // The cutoff radius for eam. |
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chuckv |
627 |
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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int eam_ident; // Atomic number |
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chuckv |
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int ident; |
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int last; // 0 -> default |
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// 1 -> in MPI: tells nodes to stop listening |
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} atomStruct; |
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chuckv |
627 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info, char *eamPotFile ); |
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chuckv |
631 |
int parseEAM( atomStruct &info, char *eamPotFile, double **eam_rvals, |
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double **eam_rhovals, double **eam_Frhovals); |
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chuckv |
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#ifdef IS_MPI |
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MPI_Datatype mpiAtomStructType; |
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#endif |
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class LinkedAtomType { |
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public: |
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LinkedAtomType(){ |
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next = NULL; |
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name[0] = '\0'; |
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chuckv |
627 |
eam_rvals = NULL; |
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eam_rhovals = NULL; |
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eam_Frhovals = NULL; |
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chuckv |
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} |
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chuckv |
627 |
~LinkedAtomType(){ |
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if( next != NULL ) delete next; |
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if( eam_rvals != NULL ) delete[] eam_rvals; |
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if( eam_rhovals != NULL ) delete[] eam_rhovals; |
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if( eam_Frhovals != NULL ) delete[] eam_Frhovals; |
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} |
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chuckv |
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LinkedAtomType* find(char* key){ |
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if( !strcmp(name, key) ) return this; |
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if( next != NULL ) return next->find(key); |
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return NULL; |
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} |
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chuckv |
627 |
void add( atomStruct &info, double *the_eam_rvals, |
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double *the_eam_rhovals,double *the_eam_Frhovals ){ |
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chuckv |
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// check for duplicates |
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if( !strcmp( info.name, name ) ){ |
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sprintf( painCave.errMsg, |
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"Duplicate LJ atom type \"%s\" found in " |
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"the LJ_FF param file./n", |
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name ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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chuckv |
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if( next != NULL ) next->add(info, the_eam_rvals, the_eam_rhovals, the_eam_Frhovals); |
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chuckv |
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else{ |
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next = new LinkedAtomType(); |
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strcpy(next->name, info.name); |
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chuckv |
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next->mass = info.mass; |
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next->lattice_constant = info.lattice_constant; |
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next->eam_nrho = info.eam_nrho; |
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next->eam_drho = info.eam_drho; |
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next->eam_nr = info.eam_nr; |
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next->eam_dr = info.eam_dr; |
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next->eam_rcut = info.eam_rcut; |
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next->eam_ident = info.eam_ident; |
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next->ident = info.ident; |
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next->eam_rvals = the_eam_rvals; |
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next->eam_rhovals = the_eam_rhovals; |
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next->eam_Frhovals = the_eam_Frhovals; |
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chuckv |
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} |
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} |
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#ifdef IS_MPI |
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void duplicate( atomStruct &info ){ |
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strcpy(info.name, name); |
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chuckv |
627 |
info.mass = mass; |
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info.lattice_constant = lattice_constant; |
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info.eam_nrho = eam_nrho; |
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info.eam_drho = eam_drho; |
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info.eam_nr = eam_nr; |
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info.eam_dr = eam_dr; |
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info.eam_rcut = eam_rcut; |
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info.eam_ident = eam_ident; |
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info.ident = ident; |
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info.last = 0; |
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chuckv |
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} |
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#endif |
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char name[15]; |
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double mass; |
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chuckv |
627 |
double lattice_constant; |
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int eam_nrho; // Number of points indexed by rho |
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double eam_drho; // The distance between each of the 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_dr; // The distance between each of the rho points. |
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chuckv |
631 |
double eam_rcut; // The cutoff radius for eam. |
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chuckv |
627 |
|
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double *eam_rvals; // Z of r values |
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double *eam_rhovals; // rho of r values |
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double *eam_Frhovals; // F of rho values |
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int eam_ident; // eam identity (atomic number) |
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chuckv |
499 |
int ident; |
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LinkedAtomType* next; |
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}; |
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LinkedAtomType* headAtomType; |
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LinkedAtomType* currentAtomType; |
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} |
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chuckv |
631 |
using namespace EAM_NS; |
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chuckv |
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//**************************************************************** |
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// begins the actual forcefield stuff. |
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//**************************************************************** |
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EAM_FF::EAM_FF(){ |
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char fileName[200]; |
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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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headAtomType = NULL; |
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currentAtomType = NULL; |
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chuckv |
669 |
// Set eamRcut to 0.0 |
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eamRcut = 0.0; |
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chuckv |
499 |
// do the funtion wrapping |
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wrapMeFF( this ); |
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#ifdef IS_MPI |
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int i; |
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// ********************************************************************** |
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// Init the atomStruct mpi type |
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atomStruct atomProto; // mpiPrototype |
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mmeineke |
814 |
int atomBC[3] = {15,5,5}; // block counts |
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chuckv |
499 |
MPI_Aint atomDspls[3]; // displacements |
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MPI_Datatype atomMbrTypes[3]; // member mpi types |
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MPI_Address(&atomProto.name, &atomDspls[0]); |
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MPI_Address(&atomProto.mass, &atomDspls[1]); |
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chuckv |
627 |
MPI_Address(&atomProto.eam_nrho, &atomDspls[2]); |
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chuckv |
499 |
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atomMbrTypes[0] = MPI_CHAR; |
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atomMbrTypes[1] = MPI_DOUBLE; |
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atomMbrTypes[2] = MPI_INT; |
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for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
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MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
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MPI_Type_commit(&mpiAtomStructType); |
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// *********************************************************************** |
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if( worldRank == 0 ){ |
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#endif |
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// generate the force file name |
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strcpy( fileName, "EAM_FF.frc" ); |
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// fprintf( stderr,"Trying to open %s\n", fileName ); |
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// attempt to open the file in the current directory first. |
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frcFile = fopen( fileName, "r" ); |
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if( frcFile == NULL ){ |
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// next see if the force path enviorment variable is set |
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ffPath = getenv( ffPath_env ); |
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if( ffPath == NULL ) { |
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STR_DEFINE(ffPath, FRC_PATH ); |
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} |
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strcpy( temp, ffPath ); |
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strcat( temp, "/" ); |
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strcat( temp, fileName ); |
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strcpy( fileName, temp ); |
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frcFile = fopen( fileName, "r" ); |
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if( frcFile == NULL ){ |
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sprintf( painCave.errMsg, |
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"Error opening the force field parameter file: %s\n" |
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"Have you tried setting the FORCE_PARAM_PATH environment " |
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"vairable?\n", |
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fileName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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#ifdef IS_MPI |
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} |
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chuckv |
627 |
sprintf( checkPointMsg, "EAM_FF file opened sucessfully." ); |
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chuckv |
499 |
MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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EAM_FF::~EAM_FF(){ |
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if( headAtomType != NULL ) delete headAtomType; |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif // is_mpi |
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fclose( frcFile ); |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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chuckv |
657 |
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void EAM_FF::calcRcut( void ){ |
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chuckv |
669 |
|
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#ifdef IS_MPI |
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double tempEamRcut = eamRcut; |
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MPI_Allreduce( &tempEamRcut, &eamRcut, 1, MPI_DOUBLE, MPI_MAX, |
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MPI_COMM_WORLD); |
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#endif //is_mpi |
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mmeineke |
859 |
entry_plug->setDefaultRcut(eamRcut); |
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chuckv |
657 |
} |
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chuckv |
499 |
void EAM_FF::initForceField( int ljMixRule ){ |
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initFortran( ljMixRule, 0 ); |
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} |
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void EAM_FF::cleanMe( void ){ |
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#ifdef IS_MPI |
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// keep the linked list in the mpi version |
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#else // is_mpi |
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// delete the linked list in the single processor version |
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if( headAtomType != NULL ) delete headAtomType; |
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#endif // is_mpi |
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} |
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chuckv |
657 |
|
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chuckv |
499 |
void EAM_FF::readParams( void ){ |
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atomStruct info; |
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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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int identNum; |
306 |
chuckv |
627 |
double *eam_rvals; // Z of r values |
307 |
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double *eam_rhovals; // rho of r values |
308 |
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double *eam_Frhovals; // F of rho values |
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char eamPotFile[1000]; |
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chuckv |
499 |
|
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bigSigma = 0.0; |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif |
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// read in the atom types. |
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headAtomType = new LinkedAtomType; |
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chuckv |
627 |
fastForward( "AtomTypes", "eam atom readParams" ); |
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chuckv |
499 |
|
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// we are now at the AtomTypes section. |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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// read a line, and start parseing out the atom types |
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if( eof_test == NULL ){ |
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sprintf( painCave.errMsg, |
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"Error in reading Atoms from force file at line %d.\n", |
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lineNum ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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identNum = 1; |
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// stop reading at end of file, or at next section |
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chuckv |
627 |
|
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chuckv |
499 |
while( readLine[0] != '#' && eof_test != NULL ){ |
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// toss comment lines |
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if( readLine[0] != '!' ){ |
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// the parser returns 0 if the line was blank |
348 |
chuckv |
627 |
if( parseAtom( readLine, lineNum, info, eamPotFile ) ){ |
349 |
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parseEAM(info,eamPotFile, &eam_rvals, |
350 |
chuckv |
631 |
&eam_rhovals, &eam_Frhovals); |
351 |
chuckv |
499 |
info.ident = identNum; |
352 |
chuckv |
627 |
headAtomType->add( info, eam_rvals, |
353 |
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eam_rhovals,eam_Frhovals ); |
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chuckv |
499 |
identNum++; |
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} |
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} |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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} |
360 |
chuckv |
627 |
|
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chuckv |
499 |
|
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#ifdef IS_MPI |
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chuckv |
627 |
|
365 |
chuckv |
499 |
|
366 |
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// send out the linked list to all the other processes |
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sprintf( checkPointMsg, |
369 |
chuckv |
627 |
"EAM_FF atom structures read successfully." ); |
370 |
chuckv |
499 |
MPIcheckPoint(); |
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currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
373 |
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while( currentAtomType != NULL ){ |
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currentAtomType->duplicate( info ); |
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sendFrcStruct( &info, mpiAtomStructType ); |
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380 |
chuckv |
627 |
// We have to now broadcast the Arrays |
381 |
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MPI_Bcast(currentAtomType->eam_rvals, |
382 |
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currentAtomType->eam_nr, |
383 |
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MPI_DOUBLE,0,MPI_COMM_WORLD); |
384 |
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MPI_Bcast(currentAtomType->eam_rhovals, |
385 |
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currentAtomType->eam_nr, |
386 |
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MPI_DOUBLE,0,MPI_COMM_WORLD); |
387 |
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MPI_Bcast(currentAtomType->eam_Frhovals, |
388 |
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currentAtomType->eam_nrho, |
389 |
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MPI_DOUBLE,0,MPI_COMM_WORLD); |
390 |
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391 |
chuckv |
499 |
sprintf( checkPointMsg, |
392 |
chuckv |
627 |
"successfully sent EAM force type: \"%s\"\n", |
393 |
chuckv |
499 |
info.name ); |
394 |
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MPIcheckPoint(); |
395 |
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|
|
currentAtomType = currentAtomType->next; |
397 |
|
|
} |
398 |
|
|
info.last = 1; |
399 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
400 |
|
|
|
401 |
|
|
} |
402 |
|
|
|
403 |
|
|
else{ |
404 |
|
|
|
405 |
|
|
// listen for node 0 to send out the force params |
406 |
|
|
|
407 |
|
|
MPIcheckPoint(); |
408 |
|
|
|
409 |
|
|
headAtomType = new LinkedAtomType; |
410 |
|
|
recieveFrcStruct( &info, mpiAtomStructType ); |
411 |
chuckv |
627 |
|
412 |
chuckv |
499 |
while( !info.last ){ |
413 |
chuckv |
627 |
|
414 |
|
|
// allocate the arrays |
415 |
chuckv |
499 |
|
416 |
chuckv |
627 |
eam_rvals = new double[info.eam_nr]; |
417 |
|
|
eam_rhovals = new double[info.eam_nr]; |
418 |
|
|
eam_Frhovals = new double[info.eam_nrho]; |
419 |
chuckv |
499 |
|
420 |
chuckv |
627 |
// We have to now broadcast the Arrays |
421 |
|
|
MPI_Bcast(eam_rvals, |
422 |
|
|
info.eam_nr, |
423 |
|
|
MPI_DOUBLE,0,MPI_COMM_WORLD); |
424 |
|
|
MPI_Bcast(eam_rhovals, |
425 |
|
|
info.eam_nr, |
426 |
|
|
MPI_DOUBLE,0,MPI_COMM_WORLD); |
427 |
|
|
MPI_Bcast(eam_Frhovals, |
428 |
|
|
info.eam_nrho, |
429 |
|
|
MPI_DOUBLE,0,MPI_COMM_WORLD); |
430 |
|
|
|
431 |
chuckv |
499 |
|
432 |
chuckv |
627 |
headAtomType->add( info, eam_rvals, eam_rhovals, eam_Frhovals ); |
433 |
chuckv |
499 |
|
434 |
|
|
MPIcheckPoint(); |
435 |
|
|
|
436 |
|
|
recieveFrcStruct( &info, mpiAtomStructType ); |
437 |
chuckv |
627 |
|
438 |
|
|
|
439 |
chuckv |
499 |
} |
440 |
|
|
} |
441 |
|
|
#endif // is_mpi |
442 |
|
|
|
443 |
|
|
// call new A_types in fortran |
444 |
|
|
|
445 |
|
|
int isError; |
446 |
|
|
|
447 |
|
|
// dummy variables |
448 |
chuckv |
627 |
int isLJ = 0; |
449 |
chuckv |
499 |
int isDipole = 0; |
450 |
|
|
int isSSD = 0; |
451 |
|
|
int isGB = 0; |
452 |
gezelter |
941 |
int isEAM = 1; |
453 |
|
|
int isCharge = 0; |
454 |
chuckv |
499 |
double dipole = 0.0; |
455 |
gezelter |
941 |
double charge = 0.0; |
456 |
chuckv |
631 |
double eamSigma = 0.0; |
457 |
|
|
double eamEpslon = 0.0; |
458 |
chuckv |
499 |
|
459 |
chuckv |
627 |
currentAtomType = headAtomType->next; |
460 |
chuckv |
499 |
while( currentAtomType != NULL ){ |
461 |
|
|
|
462 |
|
|
if( currentAtomType->name[0] != '\0' ){ |
463 |
|
|
isError = 0; |
464 |
|
|
makeAtype( &(currentAtomType->ident), |
465 |
|
|
&isLJ, |
466 |
|
|
&isSSD, |
467 |
|
|
&isDipole, |
468 |
|
|
&isGB, |
469 |
chuckv |
627 |
&isEAM, |
470 |
gezelter |
941 |
&isCharge, |
471 |
chuckv |
631 |
&eamEpslon, |
472 |
|
|
&eamSigma, |
473 |
gezelter |
941 |
&charge, |
474 |
chuckv |
499 |
&dipole, |
475 |
|
|
&isError ); |
476 |
|
|
if( isError ){ |
477 |
|
|
sprintf( painCave.errMsg, |
478 |
|
|
"Error initializing the \"%s\" atom type in fortran\n", |
479 |
|
|
currentAtomType->name ); |
480 |
|
|
painCave.isFatal = 1; |
481 |
|
|
simError(); |
482 |
|
|
} |
483 |
|
|
} |
484 |
|
|
currentAtomType = currentAtomType->next; |
485 |
|
|
} |
486 |
|
|
|
487 |
chuckv |
627 |
entry_plug->useLJ = 0; |
488 |
chuckv |
669 |
entry_plug->useEAM = 1; |
489 |
chuckv |
627 |
// 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 |
chuckv |
669 |
|
496 |
chuckv |
627 |
newEAMtype( &(currentAtomType->lattice_constant), |
497 |
|
|
&(currentAtomType->eam_nrho), |
498 |
|
|
&(currentAtomType->eam_drho), |
499 |
|
|
&(currentAtomType->eam_nr), |
500 |
|
|
&(currentAtomType->eam_dr), |
501 |
chuckv |
631 |
&(currentAtomType->eam_rcut), |
502 |
chuckv |
627 |
currentAtomType->eam_rvals, |
503 |
|
|
currentAtomType->eam_rhovals, |
504 |
|
|
currentAtomType->eam_Frhovals, |
505 |
|
|
&(currentAtomType->eam_ident), |
506 |
|
|
&isError); |
507 |
chuckv |
669 |
|
508 |
chuckv |
627 |
if( isError ){ |
509 |
|
|
sprintf( painCave.errMsg, |
510 |
|
|
"Error initializing the \"%s\" atom type in fortran EAM\n", |
511 |
|
|
currentAtomType->name ); |
512 |
|
|
painCave.isFatal = 1; |
513 |
|
|
simError(); |
514 |
|
|
} |
515 |
|
|
} |
516 |
|
|
currentAtomType = currentAtomType->next; |
517 |
|
|
} |
518 |
|
|
|
519 |
|
|
|
520 |
|
|
|
521 |
chuckv |
499 |
#ifdef IS_MPI |
522 |
|
|
sprintf( checkPointMsg, |
523 |
chuckv |
627 |
"EAM_FF atom structures successfully sent to fortran\n" ); |
524 |
chuckv |
499 |
MPIcheckPoint(); |
525 |
|
|
#endif // is_mpi |
526 |
|
|
|
527 |
chuckv |
657 |
|
528 |
chuckv |
669 |
|
529 |
chuckv |
499 |
} |
530 |
|
|
|
531 |
|
|
|
532 |
|
|
void EAM_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
533 |
|
|
|
534 |
|
|
int i; |
535 |
chuckv |
669 |
|
536 |
chuckv |
499 |
// initialize the atoms |
537 |
|
|
|
538 |
|
|
for( i=0; i<nAtoms; i++ ){ |
539 |
|
|
|
540 |
|
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
541 |
|
|
if( currentAtomType == NULL ){ |
542 |
|
|
sprintf( painCave.errMsg, |
543 |
|
|
"AtomType error, %s not found in force file.\n", |
544 |
|
|
the_atoms[i]->getType() ); |
545 |
|
|
painCave.isFatal = 1; |
546 |
|
|
simError(); |
547 |
|
|
} |
548 |
|
|
|
549 |
|
|
the_atoms[i]->setMass( currentAtomType->mass ); |
550 |
|
|
the_atoms[i]->setIdent( currentAtomType->ident ); |
551 |
chuckv |
627 |
the_atoms[i]->setEAM(); |
552 |
chuckv |
669 |
the_atoms[i]->setEamRcut( currentAtomType->eam_rcut); |
553 |
chuckv |
499 |
|
554 |
chuckv |
669 |
if (eamRcut < currentAtomType->eam_rcut) eamRcut = currentAtomType->eam_rcut; |
555 |
|
|
|
556 |
chuckv |
499 |
} |
557 |
|
|
} |
558 |
|
|
|
559 |
chuckv |
631 |
void EAM_FF::initializeBonds( int nBonds, Bond** BondArray, |
560 |
chuckv |
499 |
bond_pair* the_bonds ){ |
561 |
|
|
|
562 |
|
|
if( nBonds ){ |
563 |
|
|
sprintf( painCave.errMsg, |
564 |
|
|
"LJ_FF does not support bonds.\n" ); |
565 |
|
|
painCave.isFatal = 1; |
566 |
|
|
simError(); |
567 |
|
|
} |
568 |
|
|
} |
569 |
|
|
|
570 |
|
|
void EAM_FF::initializeBends( int nBends, Bend** bendArray, |
571 |
|
|
bend_set* the_bends ){ |
572 |
|
|
|
573 |
|
|
if( nBends ){ |
574 |
|
|
sprintf( painCave.errMsg, |
575 |
|
|
"LJ_FF does not support bends.\n" ); |
576 |
|
|
painCave.isFatal = 1; |
577 |
|
|
simError(); |
578 |
|
|
} |
579 |
|
|
} |
580 |
|
|
|
581 |
|
|
void EAM_FF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
582 |
|
|
torsion_set* the_torsions ){ |
583 |
|
|
|
584 |
|
|
if( nTorsions ){ |
585 |
|
|
sprintf( painCave.errMsg, |
586 |
|
|
"LJ_FF does not support torsions.\n" ); |
587 |
|
|
painCave.isFatal = 1; |
588 |
|
|
simError(); |
589 |
|
|
} |
590 |
|
|
} |
591 |
|
|
|
592 |
|
|
void EAM_FF::fastForward( char* stopText, char* searchOwner ){ |
593 |
|
|
|
594 |
|
|
int foundText = 0; |
595 |
|
|
char* the_token; |
596 |
|
|
|
597 |
|
|
rewind( frcFile ); |
598 |
|
|
lineNum = 0; |
599 |
|
|
|
600 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
601 |
|
|
lineNum++; |
602 |
|
|
if( eof_test == NULL ){ |
603 |
|
|
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
604 |
|
|
" file is empty.\n", |
605 |
|
|
searchOwner ); |
606 |
|
|
painCave.isFatal = 1; |
607 |
|
|
simError(); |
608 |
|
|
} |
609 |
|
|
|
610 |
|
|
|
611 |
|
|
while( !foundText ){ |
612 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
613 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
614 |
|
|
lineNum++; |
615 |
|
|
} |
616 |
|
|
if( eof_test == NULL ){ |
617 |
|
|
sprintf( painCave.errMsg, |
618 |
|
|
"Error fast forwarding force file for %s at " |
619 |
|
|
"line %d: file ended unexpectedly.\n", |
620 |
|
|
searchOwner, |
621 |
|
|
lineNum ); |
622 |
|
|
painCave.isFatal = 1; |
623 |
|
|
simError(); |
624 |
|
|
} |
625 |
|
|
|
626 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
627 |
|
|
foundText = !strcmp( stopText, the_token ); |
628 |
|
|
|
629 |
|
|
if( !foundText ){ |
630 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
631 |
|
|
lineNum++; |
632 |
|
|
|
633 |
|
|
if( eof_test == NULL ){ |
634 |
|
|
sprintf( painCave.errMsg, |
635 |
|
|
"Error fast forwarding force file for %s at " |
636 |
|
|
"line %d: file ended unexpectedly.\n", |
637 |
|
|
searchOwner, |
638 |
|
|
lineNum ); |
639 |
|
|
painCave.isFatal = 1; |
640 |
|
|
simError(); |
641 |
|
|
} |
642 |
|
|
} |
643 |
|
|
} |
644 |
|
|
} |
645 |
|
|
|
646 |
|
|
|
647 |
|
|
|
648 |
chuckv |
627 |
int EAM_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info, char *eamPotFile ){ |
649 |
chuckv |
499 |
|
650 |
|
|
char* the_token; |
651 |
|
|
|
652 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
653 |
|
|
if( the_token != NULL ){ |
654 |
|
|
|
655 |
|
|
strcpy( info.name, the_token ); |
656 |
|
|
|
657 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
658 |
|
|
sprintf( painCave.errMsg, |
659 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
660 |
|
|
painCave.isFatal = 1; |
661 |
|
|
simError(); |
662 |
|
|
} |
663 |
|
|
|
664 |
|
|
info.mass = atof( the_token ); |
665 |
|
|
|
666 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
667 |
|
|
sprintf( painCave.errMsg, |
668 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
669 |
|
|
painCave.isFatal = 1; |
670 |
|
|
simError(); |
671 |
|
|
} |
672 |
|
|
|
673 |
chuckv |
627 |
strcpy( eamPotFile, the_token ); |
674 |
|
|
return 1; |
675 |
|
|
} |
676 |
|
|
else return 0; |
677 |
|
|
} |
678 |
|
|
|
679 |
|
|
int EAM_NS::parseEAM(atomStruct &info, char *eamPotFile, |
680 |
|
|
double **eam_rvals, |
681 |
|
|
double **eam_rhovals, |
682 |
|
|
double **eam_Frhovals){ |
683 |
chuckv |
657 |
double* myEam_rvals; |
684 |
|
|
double* myEam_rhovals; |
685 |
|
|
double* myEam_Frhovals; |
686 |
|
|
|
687 |
chuckv |
627 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
688 |
|
|
char* ffPath; |
689 |
|
|
char* the_token; |
690 |
chuckv |
631 |
char* eam_eof_test; |
691 |
chuckv |
627 |
FILE *eamFile; |
692 |
chuckv |
657 |
const int BUFFERSIZE = 3000; |
693 |
chuckv |
631 |
|
694 |
chuckv |
627 |
char temp[200]; |
695 |
|
|
int linenumber; |
696 |
|
|
int nReadLines; |
697 |
chuckv |
631 |
char eam_read_buffer[BUFFERSIZE]; |
698 |
chuckv |
627 |
|
699 |
chuckv |
657 |
|
700 |
chuckv |
627 |
int i,j; |
701 |
|
|
|
702 |
|
|
linenumber = 0; |
703 |
|
|
|
704 |
|
|
// Open eam file |
705 |
|
|
eamFile = fopen( eamPotFile, "r" ); |
706 |
|
|
|
707 |
|
|
|
708 |
chuckv |
631 |
if( eamFile == NULL ){ |
709 |
chuckv |
627 |
|
710 |
|
|
// next see if the force path enviorment variable is set |
711 |
|
|
|
712 |
|
|
ffPath = getenv( ffPath_env ); |
713 |
|
|
if( ffPath == NULL ) { |
714 |
|
|
STR_DEFINE(ffPath, FRC_PATH ); |
715 |
|
|
} |
716 |
|
|
|
717 |
|
|
|
718 |
|
|
strcpy( temp, ffPath ); |
719 |
|
|
strcat( temp, "/" ); |
720 |
|
|
strcat( temp, eamPotFile ); |
721 |
|
|
strcpy( eamPotFile, temp ); |
722 |
|
|
|
723 |
|
|
eamFile = fopen( eamPotFile, "r" ); |
724 |
|
|
|
725 |
|
|
|
726 |
|
|
|
727 |
chuckv |
631 |
if( eamFile == NULL ){ |
728 |
chuckv |
627 |
|
729 |
|
|
sprintf( painCave.errMsg, |
730 |
|
|
"Error opening the EAM force parameter file: %s\n" |
731 |
|
|
"Have you tried setting the FORCE_PARAM_PATH environment " |
732 |
|
|
"vairable?\n", |
733 |
|
|
eamPotFile ); |
734 |
|
|
painCave.isFatal = 1; |
735 |
|
|
simError(); |
736 |
|
|
} |
737 |
|
|
} |
738 |
|
|
|
739 |
|
|
// First line is a comment line, read and toss it.... |
740 |
chuckv |
631 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
741 |
chuckv |
627 |
linenumber++; |
742 |
chuckv |
631 |
if(eam_eof_test == NULL){ |
743 |
chuckv |
627 |
sprintf( painCave.errMsg, |
744 |
|
|
"error in reading commment in %s\n", eamPotFile); |
745 |
|
|
painCave.isFatal = 1; |
746 |
|
|
simError(); |
747 |
|
|
} |
748 |
|
|
|
749 |
|
|
|
750 |
|
|
|
751 |
|
|
// The Second line contains atomic number, atomic mass and a lattice constant |
752 |
chuckv |
631 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
753 |
chuckv |
627 |
linenumber++; |
754 |
chuckv |
631 |
if(eam_eof_test == NULL){ |
755 |
chuckv |
627 |
sprintf( painCave.errMsg, |
756 |
|
|
"error in reading Identifier line in %s\n", eamPotFile); |
757 |
|
|
painCave.isFatal = 1; |
758 |
|
|
simError(); |
759 |
|
|
} |
760 |
|
|
|
761 |
|
|
|
762 |
|
|
|
763 |
|
|
|
764 |
chuckv |
631 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
765 |
chuckv |
627 |
sprintf( painCave.errMsg, |
766 |
|
|
"Error parseing EAM ident line in %s\n", eamPotFile ); |
767 |
|
|
painCave.isFatal = 1; |
768 |
|
|
simError(); |
769 |
|
|
} |
770 |
|
|
|
771 |
|
|
info.eam_ident = atoi( the_token ); |
772 |
|
|
|
773 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
774 |
|
|
sprintf( painCave.errMsg, |
775 |
|
|
"Error parseing EAM mass in %s\n", eamPotFile ); |
776 |
|
|
painCave.isFatal = 1; |
777 |
|
|
simError(); |
778 |
|
|
} |
779 |
|
|
info.mass = atof( the_token); |
780 |
|
|
|
781 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
782 |
|
|
sprintf( painCave.errMsg, |
783 |
|
|
"Error parseing EAM Lattice Constant %s\n", eamPotFile ); |
784 |
|
|
painCave.isFatal = 1; |
785 |
|
|
simError(); |
786 |
|
|
} |
787 |
|
|
info.lattice_constant = atof( the_token); |
788 |
|
|
|
789 |
|
|
// Next line is nrho, drho, nr, dr and rcut |
790 |
chuckv |
631 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
791 |
|
|
if(eam_eof_test == NULL){ |
792 |
chuckv |
627 |
sprintf( painCave.errMsg, |
793 |
|
|
"error in reading number of points line in %s\n", eamPotFile); |
794 |
|
|
painCave.isFatal = 1; |
795 |
|
|
simError(); |
796 |
|
|
} |
797 |
|
|
|
798 |
chuckv |
631 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
799 |
chuckv |
627 |
sprintf( painCave.errMsg, |
800 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
801 |
|
|
painCave.isFatal = 1; |
802 |
|
|
simError(); |
803 |
|
|
} |
804 |
|
|
|
805 |
|
|
info.eam_nrho = atoi( the_token ); |
806 |
|
|
|
807 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
808 |
|
|
sprintf( painCave.errMsg, |
809 |
|
|
"Error parseing EAM drho in %s\n", eamPotFile ); |
810 |
|
|
painCave.isFatal = 1; |
811 |
|
|
simError(); |
812 |
|
|
} |
813 |
|
|
info.eam_drho = atof( the_token); |
814 |
|
|
|
815 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
816 |
|
|
sprintf( painCave.errMsg, |
817 |
|
|
"Error parseing EAM # r in %s\n", eamPotFile ); |
818 |
|
|
painCave.isFatal = 1; |
819 |
|
|
simError(); |
820 |
|
|
} |
821 |
|
|
info.eam_nr = atoi( the_token); |
822 |
|
|
|
823 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
824 |
|
|
sprintf( painCave.errMsg, |
825 |
|
|
"Error parseing EAM dr in %s\n", eamPotFile ); |
826 |
|
|
painCave.isFatal = 1; |
827 |
|
|
simError(); |
828 |
|
|
} |
829 |
|
|
info.eam_dr = atof( the_token); |
830 |
|
|
|
831 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
832 |
|
|
sprintf( painCave.errMsg, |
833 |
|
|
"Error parseing EAM rcut in %s\n", eamPotFile ); |
834 |
|
|
painCave.isFatal = 1; |
835 |
|
|
simError(); |
836 |
|
|
} |
837 |
|
|
info.eam_rcut = atof( the_token); |
838 |
|
|
|
839 |
|
|
|
840 |
chuckv |
657 |
|
841 |
|
|
|
842 |
|
|
|
843 |
chuckv |
627 |
// Ok now we have to allocate point arrays and read in number of points |
844 |
|
|
// Index the arrays for fortran, starting at 1 |
845 |
chuckv |
657 |
myEam_Frhovals = new double[info.eam_nrho]; |
846 |
|
|
myEam_rvals = new double[info.eam_nr]; |
847 |
|
|
myEam_rhovals = new double[info.eam_nr]; |
848 |
chuckv |
627 |
|
849 |
|
|
// Parse F of rho vals. |
850 |
|
|
|
851 |
|
|
// Assume for now that we have a complete number of lines |
852 |
chuckv |
631 |
nReadLines = int(info.eam_nrho/5); |
853 |
chuckv |
657 |
|
854 |
chuckv |
627 |
|
855 |
chuckv |
657 |
|
856 |
chuckv |
627 |
for (i=0;i<nReadLines;i++){ |
857 |
|
|
j = i*5; |
858 |
chuckv |
657 |
|
859 |
chuckv |
627 |
// Read next line |
860 |
chuckv |
631 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
861 |
chuckv |
627 |
linenumber++; |
862 |
chuckv |
631 |
if(eam_eof_test == NULL){ |
863 |
chuckv |
627 |
sprintf( painCave.errMsg, |
864 |
|
|
"error in reading EAM file %s at line %d\n", |
865 |
|
|
eamPotFile,linenumber); |
866 |
|
|
painCave.isFatal = 1; |
867 |
|
|
simError(); |
868 |
|
|
} |
869 |
|
|
|
870 |
|
|
// Parse 5 values on each line into array |
871 |
|
|
// Value 1 |
872 |
chuckv |
631 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
873 |
chuckv |
499 |
sprintf( painCave.errMsg, |
874 |
chuckv |
627 |
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
875 |
chuckv |
499 |
painCave.isFatal = 1; |
876 |
|
|
simError(); |
877 |
|
|
} |
878 |
chuckv |
657 |
|
879 |
|
|
myEam_Frhovals[j+0] = atof( the_token ); |
880 |
chuckv |
499 |
|
881 |
chuckv |
627 |
// Value 2 |
882 |
|
|
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
883 |
|
|
sprintf( painCave.errMsg, |
884 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
885 |
|
|
painCave.isFatal = 1; |
886 |
|
|
simError(); |
887 |
|
|
} |
888 |
chuckv |
657 |
|
889 |
|
|
myEam_Frhovals[j+1] = atof( the_token ); |
890 |
chuckv |
627 |
|
891 |
|
|
// Value 3 |
892 |
|
|
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
893 |
|
|
sprintf( painCave.errMsg, |
894 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
895 |
|
|
painCave.isFatal = 1; |
896 |
|
|
simError(); |
897 |
|
|
} |
898 |
chuckv |
657 |
|
899 |
|
|
myEam_Frhovals[j+2] = atof( the_token ); |
900 |
chuckv |
627 |
|
901 |
|
|
// Value 4 |
902 |
|
|
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
903 |
|
|
sprintf( painCave.errMsg, |
904 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
905 |
|
|
painCave.isFatal = 1; |
906 |
|
|
simError(); |
907 |
|
|
} |
908 |
|
|
|
909 |
chuckv |
657 |
myEam_Frhovals[j+3] = atof( the_token ); |
910 |
|
|
|
911 |
chuckv |
627 |
// Value 5 |
912 |
|
|
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
913 |
|
|
sprintf( painCave.errMsg, |
914 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
915 |
|
|
painCave.isFatal = 1; |
916 |
|
|
simError(); |
917 |
|
|
} |
918 |
chuckv |
657 |
|
919 |
|
|
myEam_Frhovals[j+4] = atof( the_token ); |
920 |
chuckv |
627 |
|
921 |
chuckv |
499 |
} |
922 |
chuckv |
627 |
// Parse Z of r vals |
923 |
|
|
|
924 |
|
|
// Assume for now that we have a complete number of lines |
925 |
chuckv |
631 |
nReadLines = int(info.eam_nr/5); |
926 |
chuckv |
627 |
|
927 |
|
|
for (i=0;i<nReadLines;i++){ |
928 |
|
|
j = i*5; |
929 |
|
|
|
930 |
|
|
// Read next line |
931 |
chuckv |
631 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
932 |
chuckv |
627 |
linenumber++; |
933 |
chuckv |
631 |
if(eam_eof_test == NULL){ |
934 |
chuckv |
627 |
sprintf( painCave.errMsg, |
935 |
|
|
"error in reading EAM file %s at line %d\n", |
936 |
|
|
eamPotFile,linenumber); |
937 |
|
|
painCave.isFatal = 1; |
938 |
|
|
simError(); |
939 |
|
|
} |
940 |
|
|
|
941 |
|
|
// Parse 5 values on each line into array |
942 |
|
|
// Value 1 |
943 |
chuckv |
631 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
944 |
chuckv |
627 |
sprintf( painCave.errMsg, |
945 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
946 |
|
|
painCave.isFatal = 1; |
947 |
|
|
simError(); |
948 |
|
|
} |
949 |
|
|
|
950 |
chuckv |
657 |
myEam_rvals[j+0] = atof( the_token ); |
951 |
chuckv |
627 |
|
952 |
|
|
// Value 2 |
953 |
|
|
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
954 |
|
|
sprintf( painCave.errMsg, |
955 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
956 |
|
|
painCave.isFatal = 1; |
957 |
|
|
simError(); |
958 |
|
|
} |
959 |
|
|
|
960 |
chuckv |
657 |
myEam_rvals[j+1] = atof( the_token ); |
961 |
chuckv |
627 |
|
962 |
|
|
// Value 3 |
963 |
|
|
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
964 |
|
|
sprintf( painCave.errMsg, |
965 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
966 |
|
|
painCave.isFatal = 1; |
967 |
|
|
simError(); |
968 |
|
|
} |
969 |
|
|
|
970 |
chuckv |
657 |
myEam_rvals[j+2] = atof( the_token ); |
971 |
chuckv |
627 |
|
972 |
|
|
// Value 4 |
973 |
|
|
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
974 |
|
|
sprintf( painCave.errMsg, |
975 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
976 |
|
|
painCave.isFatal = 1; |
977 |
|
|
simError(); |
978 |
|
|
} |
979 |
|
|
|
980 |
chuckv |
657 |
myEam_rvals[j+3] = atof( the_token ); |
981 |
chuckv |
627 |
|
982 |
|
|
// Value 5 |
983 |
|
|
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
984 |
|
|
sprintf( painCave.errMsg, |
985 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
986 |
|
|
painCave.isFatal = 1; |
987 |
|
|
simError(); |
988 |
|
|
} |
989 |
|
|
|
990 |
chuckv |
657 |
myEam_rvals[j+4] = atof( the_token ); |
991 |
chuckv |
627 |
|
992 |
|
|
} |
993 |
|
|
// Parse rho of r vals |
994 |
|
|
|
995 |
|
|
// Assume for now that we have a complete number of lines |
996 |
|
|
|
997 |
|
|
for (i=0;i<nReadLines;i++){ |
998 |
|
|
j = i*5; |
999 |
|
|
|
1000 |
|
|
// Read next line |
1001 |
chuckv |
631 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
1002 |
chuckv |
627 |
linenumber++; |
1003 |
chuckv |
631 |
if(eam_eof_test == NULL){ |
1004 |
chuckv |
627 |
sprintf( painCave.errMsg, |
1005 |
|
|
"error in reading EAM file %s at line %d\n", |
1006 |
|
|
eamPotFile,linenumber); |
1007 |
|
|
painCave.isFatal = 1; |
1008 |
|
|
simError(); |
1009 |
|
|
} |
1010 |
|
|
|
1011 |
|
|
// Parse 5 values on each line into array |
1012 |
|
|
// Value 1 |
1013 |
chuckv |
631 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
1014 |
chuckv |
627 |
sprintf( painCave.errMsg, |
1015 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
1016 |
|
|
painCave.isFatal = 1; |
1017 |
|
|
simError(); |
1018 |
|
|
} |
1019 |
|
|
|
1020 |
chuckv |
657 |
myEam_rhovals[j+0] = atof( the_token ); |
1021 |
chuckv |
627 |
|
1022 |
|
|
// Value 2 |
1023 |
chuckv |
673 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
1024 |
chuckv |
627 |
sprintf( painCave.errMsg, |
1025 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
1026 |
|
|
painCave.isFatal = 1; |
1027 |
|
|
simError(); |
1028 |
|
|
} |
1029 |
|
|
|
1030 |
chuckv |
657 |
myEam_rhovals[j+1] = atof( the_token ); |
1031 |
chuckv |
627 |
|
1032 |
|
|
// Value 3 |
1033 |
chuckv |
673 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
1034 |
chuckv |
627 |
sprintf( painCave.errMsg, |
1035 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
1036 |
|
|
painCave.isFatal = 1; |
1037 |
|
|
simError(); |
1038 |
|
|
} |
1039 |
|
|
|
1040 |
chuckv |
657 |
myEam_rhovals[j+2] = atof( the_token ); |
1041 |
chuckv |
627 |
|
1042 |
|
|
// Value 4 |
1043 |
chuckv |
673 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
1044 |
chuckv |
627 |
sprintf( painCave.errMsg, |
1045 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
1046 |
|
|
painCave.isFatal = 1; |
1047 |
|
|
simError(); |
1048 |
|
|
} |
1049 |
|
|
|
1050 |
chuckv |
657 |
myEam_rhovals[j+3] = atof( the_token ); |
1051 |
chuckv |
627 |
|
1052 |
|
|
// Value 5 |
1053 |
chuckv |
673 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
1054 |
chuckv |
627 |
sprintf( painCave.errMsg, |
1055 |
|
|
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
1056 |
|
|
painCave.isFatal = 1; |
1057 |
|
|
simError(); |
1058 |
|
|
} |
1059 |
|
|
|
1060 |
chuckv |
657 |
myEam_rhovals[j+4] = atof( the_token ); |
1061 |
chuckv |
673 |
|
1062 |
chuckv |
627 |
} |
1063 |
chuckv |
657 |
*eam_rvals = myEam_rvals; |
1064 |
|
|
*eam_rhovals = myEam_rhovals; |
1065 |
|
|
*eam_Frhovals = myEam_Frhovals; |
1066 |
chuckv |
627 |
|
1067 |
|
|
fclose(eamFile); |
1068 |
|
|
return 0; |
1069 |
chuckv |
499 |
} |