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mmeineke |
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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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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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#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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// 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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double epslon; |
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double sigma; |
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double dipole; |
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int isDipole; |
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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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int parseAtomSSD( char *lineBuffer, int lineNum, atomStruct &info ); |
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#ifdef IS_MPI |
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#include "mpiForceField.h" |
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MPI_Datatype mpiAtomStructType; |
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#endif |
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// declaration of functions needed to wrap the fortran module |
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extern "C" { |
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void forcefactory_( char* forceName, |
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int* status, |
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void (*wrapFunction)( void (*p1)( int* ident, |
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double* mass, |
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double* epslon, |
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double* sigma, |
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int* status ), |
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void (*p2)( int *nLocal, |
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int *identArray, |
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int *isError ), |
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void (*p3)( double* positionArray, |
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double* forceArray, |
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double* potentialEnergy, |
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short int* doPotentialCalc )), |
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int forceNameLength ); |
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} |
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void SSDfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, |
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double* sigma, int* status ), |
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void (*p2)( int *nLocal, int *identArray, |
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int *isError ), |
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void (*p3)( double* positionArray,double* forceArray, |
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double* potentialEnergy, |
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short int* doPotentialCalc ) ); |
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void (*newSSDtype)( int* ident, double* mass, double* epslon, double* sigma, |
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int* status ); |
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void (*initSSDfortran) ( int *nLocal, int *identArray, int *isError ); |
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mmeineke |
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SSD_FF* currentSSDwrap; |
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mmeineke |
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//**************************************************************** |
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// begins the actual forcefield stuff. |
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//**************************************************************** |
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SSD_FF::SSD_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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char errMsg[1000]; |
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// do the funtion wrapping |
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currentLJwrap = this; |
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wrapMe(); |
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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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int atomBC[3] = {15,4,3}; // 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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MPI_Address(&atomProto.name, &atomDspls[0]); |
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MPI_Address(&atomProto.mass, &atomDspls[1]); |
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MPI_Address(&atomProto.isDipole, &atomDspls[2]); |
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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, "SSD_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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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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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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sprintf( checkPointMsg, "SSD_FF file opened sucessfully." ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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SSD_FF::~SSD_FF(){ |
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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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void SSD_FF::wrapMe( void ){ |
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char* currentFF = "SSD"; |
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int isError = 0; |
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forcefactory_( currentFF, &isError, SSDfunctionWrapper, strlen(currentFF) ); |
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if( isError ){ |
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sprintf( painCave.errMsg, |
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"SSD_FF error: an error was returned from fortran when the " |
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"the functions were being wrapped.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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#ifdef IS_MPI |
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sprintf( checkPointMsg, "SSD_FF functions succesfully wrapped." ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, |
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double* sigma, int* status ), |
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void (*p2)( int*, int*, int* ), |
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void (*p3)( double* positionArray,double* forceArray, |
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double* potentialEnergy, |
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short int* doPotentialCalc ) ){ |
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newSSDtype = p1; |
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initSSDfortran = p2; |
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currentLJwrap->setSSDfortran( p3 ); |
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} |
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void SSD_FF::initializeAtoms( void ){ |
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class LinkedType { |
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public: |
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LinkedType(){ |
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next = NULL; |
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name[0] = '\0'; |
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} |
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~LinkedType(){ if( next != NULL ) delete next; } |
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LinkedType* 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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void add( atomStruct &info ){ |
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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 SSD_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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if( next != NULL ) next->add(info); |
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else{ |
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next = new LinkedType(); |
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strcpy(next->name, info.name); |
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next->isDipole = info.isDipole; |
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next->mass = info.mass; |
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next->epslon = info.epslon; |
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next->sigma = info.sigma; |
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next->dipole = info.dipole; |
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next->ident = info.ident; |
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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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info.isDipole = isDipole; |
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info.mass = mass; |
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info.epslon = epslon; |
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info.sigma = sigma; |
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info.ident = ident; |
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info.dipole = dipole; |
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info.last = 0; |
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} |
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#endif |
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char name[15]; |
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int isDipole; |
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double dipole; |
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double mass; |
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double epslon; |
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double sigma; |
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int ident; |
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LinkedType* next; |
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}; |
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LinkedType* headAtomType; |
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LinkedType* currentAtomType; |
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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 i; |
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int identNum; |
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Atom** the_atoms; |
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int nAtoms; |
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the_atoms = entry_plug->atoms; |
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nAtoms = entry_plug->n_atoms; |
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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 LinkedType; |
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fastForward( "AtomTypes", "initializeAtoms" ); |
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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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while( readLine[0] != '#' && eof_test != NULL ){ |
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// toss comment lines |
| 348 |
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if( readLine[0] != '!' ){ |
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// the parser returns 0 if the line was blank |
| 351 |
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if( parseAtomLJ( readLine, lineNum, info ) ){ |
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info.ident = identNum; |
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headAtomType->add( info );; |
| 354 |
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identNum++; |
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} |
| 356 |
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} |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 358 |
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lineNum++; |
| 359 |
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} |
| 360 |
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#ifdef IS_MPI |
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// send out the linked list to all the other processes |
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sprintf( checkPointMsg, |
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"SSD_FF atom structures read successfully." ); |
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MPIcheckPoint(); |
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currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
| 370 |
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while( currentAtomType != NULL ){ |
| 371 |
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currentAtomType->duplicate( info ); |
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sendFrcStruct( &info, mpiAtomStructType ); |
| 376 |
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| 377 |
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sprintf( checkPointMsg, |
| 378 |
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"successfully sent ssd force type: \"%s\"\n", |
| 379 |
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info.name ); |
| 380 |
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MPIcheckPoint(); |
| 381 |
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| 382 |
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currentAtomType = currentAtomType->next; |
| 383 |
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} |
| 384 |
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info.last = 1; |
| 385 |
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sendFrcStruct( &info, mpiAtomStructType ); |
| 386 |
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| 387 |
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} |
| 388 |
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else{ |
| 390 |
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| 391 |
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// listen for node 0 to send out the force params |
| 392 |
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| 393 |
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MPIcheckPoint(); |
| 394 |
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| 395 |
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headAtomType = new LinkedType; |
| 396 |
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recieveFrcStruct( &info, mpiAtomStructType ); |
| 397 |
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| 398 |
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while( !info.last ){ |
| 399 |
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headAtomType->add( info ); |
| 403 |
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| 404 |
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MPIcheckPoint(); |
| 405 |
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| 406 |
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recieveFrcStruct( &info, mpiAtomStructType ); |
| 407 |
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} |
| 408 |
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} |
| 409 |
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#endif // is_mpi |
| 410 |
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| 411 |
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// call new A_types in fortran |
| 412 |
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| 413 |
|
|
int isError; |
| 414 |
|
|
currentAtomType = headAtomType; |
| 415 |
|
|
while( currentAtomType != NULL ){ |
| 416 |
|
|
|
| 417 |
|
|
if( currentAtomType->name[0] != '\0' ){ |
| 418 |
|
|
isError = 0; |
| 419 |
|
|
newSSDtype( &(currentAtomType->ident), |
| 420 |
|
|
&(currentAtomType->mass), |
| 421 |
|
|
&(currentAtomType->epslon), |
| 422 |
|
|
&(currentAtomType->sigma), |
| 423 |
|
|
&isError ); |
| 424 |
|
|
if( isError ){ |
| 425 |
|
|
sprintf( painCave.errMsg, |
| 426 |
|
|
"Error initializing the \"%s\" atom type in fortran\n", |
| 427 |
|
|
currentAtomType->name ); |
| 428 |
|
|
painCave.isFatal = 1; |
| 429 |
|
|
simError(); |
| 430 |
|
|
} |
| 431 |
|
|
} |
| 432 |
|
|
currentAtomType = currentAtomType->next; |
| 433 |
|
|
} |
| 434 |
|
|
|
| 435 |
|
|
#ifdef IS_MPI |
| 436 |
|
|
sprintf( checkPointMsg, |
| 437 |
|
|
"SSD_FF atom structures successfully sent to fortran\n" ); |
| 438 |
|
|
MPIcheckPoint(); |
| 439 |
|
|
#endif // is_mpi |
| 440 |
|
|
|
| 441 |
|
|
|
| 442 |
|
|
|
| 443 |
|
|
// initialize the atoms |
| 444 |
|
|
|
| 445 |
|
|
////////////////////////////////////////////////// |
| 446 |
|
|
// a quick water fix |
| 447 |
|
|
|
| 448 |
|
|
double waterI[3][3]; |
| 449 |
|
|
waterI[0][0] = 1.76958347772500; |
| 450 |
|
|
waterI[0][1] = 0.0; |
| 451 |
|
|
waterI[0][2] = 0.0; |
| 452 |
|
|
|
| 453 |
|
|
waterI[1][0] = 0.0; |
| 454 |
|
|
waterI[1][1] = 0.614537057924513; |
| 455 |
|
|
waterI[1][2] = 0.0; |
| 456 |
|
|
|
| 457 |
|
|
waterI[2][0] = 0.0; |
| 458 |
|
|
waterI[2][1] = 0.0; |
| 459 |
|
|
waterI[2][2] = 1.15504641980049; |
| 460 |
|
|
|
| 461 |
|
|
double bigSigma = 0.0; |
| 462 |
|
|
Atom* thisAtom; |
| 463 |
|
|
DirectionalAtom* dAtom; |
| 464 |
|
|
|
| 465 |
|
|
for( i=0; i<nAtoms; i++ ){ |
| 466 |
|
|
|
| 467 |
|
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
| 468 |
|
|
if( currentAtomType == NULL ){ |
| 469 |
|
|
sprintf( painCave.errMsg, |
| 470 |
|
|
"AtomType error, %s not found in force file.\n", |
| 471 |
|
|
the_atoms[i]->getType() ); |
| 472 |
|
|
painCave.isFatal = 1; |
| 473 |
|
|
simError(); |
| 474 |
|
|
} |
| 475 |
|
|
|
| 476 |
|
|
the_atoms[i]->setMass( currentAtomType->mass ); |
| 477 |
|
|
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
| 478 |
|
|
the_atoms[i]->setSigma( currentAtomType->sigma ); |
| 479 |
|
|
the_atoms[i]->setIdent( currentAtomType->ident ); |
| 480 |
|
|
the_atoms[i]->setLJ(); |
| 481 |
|
|
|
| 482 |
|
|
if( currentAtomType->isDipole ){ |
| 483 |
|
|
if( the_atoms[i]->isDirectional() ){ |
| 484 |
|
|
|
| 485 |
|
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
| 486 |
|
|
dAtom->setMu( currentAtomType->dipole ); |
| 487 |
|
|
dAtom->setHasDipole( 1 ); |
| 488 |
|
|
dAtom->setJx( 0.0 ); |
| 489 |
|
|
dAtom->setJy( 0.0 ); |
| 490 |
|
|
dAtom->setJz( 0.0 ); |
| 491 |
|
|
|
| 492 |
|
|
if(!strcmp("SSD",the_atoms[i]->getType())){ |
| 493 |
|
|
dAtom->setI( waterI ); |
| 494 |
|
|
dAtom->setSSD( 1 ); |
| 495 |
|
|
} |
| 496 |
|
|
else{ |
| 497 |
|
|
sprintf(painCave.errMsg, |
| 498 |
|
|
"AtmType error, %s does not have a moment of inertia set.\n", |
| 499 |
|
|
the_atoms[i]->getType() ); |
| 500 |
|
|
painCave.isFatal = 1; |
| 501 |
|
|
simError(); |
| 502 |
|
|
} |
| 503 |
|
|
entry_plug->n_dipoles++; |
| 504 |
|
|
} |
| 505 |
|
|
else{ |
| 506 |
|
|
|
| 507 |
|
|
sprintf( painCave.errMsg, |
| 508 |
|
|
"SSD_FF error: Atom \"%s\" is a dipole, yet no standard" |
| 509 |
|
|
" orientation was specifed in the BASS file.\n", |
| 510 |
|
|
currentAtomType->name ); |
| 511 |
|
|
painCave.isFatal = 1; |
| 512 |
|
|
simError(); |
| 513 |
|
|
} |
| 514 |
|
|
} |
| 515 |
|
|
else{ |
| 516 |
|
|
if( the_atoms[i]->isDirectional() ){ |
| 517 |
|
|
sprintf( painCave.errMsg, |
| 518 |
|
|
"SSD_FF error: Atom \"%s\" was given a standard" |
| 519 |
|
|
"orientation in the BASS file, yet it is not a dipole.\n", |
| 520 |
|
|
currentAtomType->name); |
| 521 |
|
|
painCave.isFatal = 1; |
| 522 |
|
|
simError(); |
| 523 |
|
|
} |
| 524 |
|
|
} |
| 525 |
|
|
|
| 526 |
|
|
|
| 527 |
|
|
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
| 528 |
|
|
} |
| 529 |
|
|
|
| 530 |
|
|
|
| 531 |
|
|
#ifdef IS_MPI |
| 532 |
|
|
double tempBig = bigSigma; |
| 533 |
|
|
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
| 534 |
|
|
#endif //is_mpi |
| 535 |
|
|
|
| 536 |
|
|
//calc rCut and rList |
| 537 |
|
|
|
| 538 |
|
|
entry_plug->rCut = 2.5 * bigSigma; |
| 539 |
|
|
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0; |
| 540 |
|
|
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0; |
| 541 |
|
|
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0; |
| 542 |
|
|
|
| 543 |
|
|
entry_plug->rList = entry_plug->rCut + 1.0; |
| 544 |
|
|
|
| 545 |
|
|
// clean up the memory |
| 546 |
|
|
|
| 547 |
|
|
delete headAtomType; |
| 548 |
|
|
|
| 549 |
|
|
#ifdef IS_MPI |
| 550 |
|
|
sprintf( checkPointMsg, "SSD_FF atoms initialized succesfully" ); |
| 551 |
|
|
MPIcheckPoint(); |
| 552 |
|
|
#endif // is_mpi |
| 553 |
|
|
|
| 554 |
|
|
initFortran(); |
| 555 |
|
|
entry_plug->refreshSim(); |
| 556 |
|
|
|
| 557 |
|
|
} |
| 558 |
|
|
|
| 559 |
|
|
void SSD_FF::initializeBonds( bond_pair* the_bonds ){ |
| 560 |
|
|
|
| 561 |
|
|
if( entry_plug->n_bonds ){ |
| 562 |
|
|
sprintf( painCave.errMsg, |
| 563 |
|
|
"SSD_FF does not support bonds.\n" ); |
| 564 |
|
|
painCave.isFatal = 1; |
| 565 |
|
|
simError(); |
| 566 |
|
|
} |
| 567 |
|
|
#ifdef IS_MPI |
| 568 |
|
|
MPIcheckPoint(); |
| 569 |
|
|
#endif // is_mpi |
| 570 |
|
|
|
| 571 |
|
|
} |
| 572 |
|
|
|
| 573 |
|
|
void SSD_FF::initializeBends( bend_set* the_bends ){ |
| 574 |
|
|
|
| 575 |
|
|
if( entry_plug->n_bends ){ |
| 576 |
|
|
sprintf( painCave.errMsg, |
| 577 |
|
|
"SSD_FF does not support bends.\n" ); |
| 578 |
|
|
painCave.isFatal = 1; |
| 579 |
|
|
simError(); |
| 580 |
|
|
} |
| 581 |
|
|
#ifdef IS_MPI |
| 582 |
|
|
MPIcheckPoint(); |
| 583 |
|
|
#endif // is_mpi |
| 584 |
|
|
|
| 585 |
|
|
} |
| 586 |
|
|
|
| 587 |
|
|
void SSD_FF::initializeTorsions( torsion_set* the_torsions ){ |
| 588 |
|
|
|
| 589 |
|
|
if( entry_plug->n_torsions ){ |
| 590 |
|
|
sprintf( painCave.errMsg, |
| 591 |
|
|
"SSD_FF does not support torsions.\n" ); |
| 592 |
|
|
painCave.isFatal = 1; |
| 593 |
|
|
simError(); |
| 594 |
|
|
} |
| 595 |
|
|
#ifdef IS_MPI |
| 596 |
|
|
MPIcheckPoint(); |
| 597 |
|
|
#endif // is_mpi |
| 598 |
|
|
|
| 599 |
|
|
} |
| 600 |
|
|
|
| 601 |
|
|
|
| 602 |
|
|
void SSD_FF::fastForward( char* stopText, char* searchOwner ){ |
| 603 |
|
|
|
| 604 |
|
|
int foundText = 0; |
| 605 |
|
|
char* the_token; |
| 606 |
|
|
|
| 607 |
|
|
rewind( frcFile ); |
| 608 |
|
|
lineNum = 0; |
| 609 |
|
|
|
| 610 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 611 |
|
|
lineNum++; |
| 612 |
|
|
if( eof_test == NULL ){ |
| 613 |
|
|
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
| 614 |
|
|
" file is empty.\n", |
| 615 |
|
|
searchOwner ); |
| 616 |
|
|
painCave.isFatal = 1; |
| 617 |
|
|
simError(); |
| 618 |
|
|
} |
| 619 |
|
|
|
| 620 |
|
|
|
| 621 |
|
|
while( !foundText ){ |
| 622 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
| 623 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 624 |
|
|
lineNum++; |
| 625 |
|
|
} |
| 626 |
|
|
if( eof_test == NULL ){ |
| 627 |
|
|
sprintf( painCave.errMsg, |
| 628 |
|
|
"Error fast forwarding force file for %s at " |
| 629 |
|
|
"line %d: file ended unexpectedly.\n", |
| 630 |
|
|
searchOwner, |
| 631 |
|
|
lineNum ); |
| 632 |
|
|
painCave.isFatal = 1; |
| 633 |
|
|
simError(); |
| 634 |
|
|
} |
| 635 |
|
|
|
| 636 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
| 637 |
|
|
foundText = !strcmp( stopText, the_token ); |
| 638 |
|
|
|
| 639 |
|
|
if( !foundText ){ |
| 640 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 641 |
|
|
lineNum++; |
| 642 |
|
|
|
| 643 |
|
|
if( eof_test == NULL ){ |
| 644 |
|
|
sprintf( painCave.errMsg, |
| 645 |
|
|
"Error fast forwarding force file for %s at " |
| 646 |
|
|
"line %d: file ended unexpectedly.\n", |
| 647 |
|
|
searchOwner, |
| 648 |
|
|
lineNum ); |
| 649 |
|
|
painCave.isFatal = 1; |
| 650 |
|
|
simError(); |
| 651 |
|
|
} |
| 652 |
|
|
} |
| 653 |
|
|
} |
| 654 |
|
|
} |
| 655 |
|
|
|
| 656 |
|
|
|
| 657 |
|
|
|
| 658 |
|
|
int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ){ |
| 659 |
|
|
|
| 660 |
|
|
char* the_token; |
| 661 |
|
|
|
| 662 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
| 663 |
|
|
if( the_token != NULL ){ |
| 664 |
|
|
|
| 665 |
|
|
strcpy( info.name, the_token ); |
| 666 |
|
|
|
| 667 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 668 |
|
|
sprintf( painCave.errMsg, |
| 669 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 670 |
|
|
painCave.isFatal = 1; |
| 671 |
|
|
simError(); |
| 672 |
|
|
} |
| 673 |
|
|
|
| 674 |
|
|
info.isDipole = atoi( the_token ); |
| 675 |
|
|
|
| 676 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 677 |
|
|
sprintf( painCave.errMsg, |
| 678 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 679 |
|
|
painCave.isFatal = 1; |
| 680 |
|
|
simError(); |
| 681 |
|
|
} |
| 682 |
|
|
|
| 683 |
|
|
info.mass = atof( the_token ); |
| 684 |
|
|
|
| 685 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 686 |
|
|
sprintf( painCave.errMsg, |
| 687 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 688 |
|
|
painCave.isFatal = 1; |
| 689 |
|
|
simError(); |
| 690 |
|
|
} |
| 691 |
|
|
|
| 692 |
|
|
info.epslon = atof( the_token ); |
| 693 |
|
|
|
| 694 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 695 |
|
|
sprintf( painCave.errMsg, |
| 696 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 697 |
|
|
painCave.isFatal = 1; |
| 698 |
|
|
simError(); |
| 699 |
|
|
} |
| 700 |
|
|
|
| 701 |
|
|
info.sigma = atof( the_token ); |
| 702 |
|
|
|
| 703 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 704 |
|
|
sprintf( painCave.errMsg, |
| 705 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 706 |
|
|
painCave.isFatal = 1; |
| 707 |
|
|
simError(); |
| 708 |
|
|
} |
| 709 |
|
|
|
| 710 |
|
|
info.dipole = atof( the_token ); |
| 711 |
|
|
|
| 712 |
|
|
return 1; |
| 713 |
|
|
} |
| 714 |
|
|
else return 0; |
| 715 |
|
|
} |
| 716 |
|
|
|
| 717 |
|
|
|
| 718 |
|
|
void SSD_FF::doForces( int calcPot ){ |
| 719 |
|
|
|
| 720 |
|
|
int i; |
| 721 |
|
|
double* frc; |
| 722 |
|
|
double* pos; |
| 723 |
|
|
short int passedCalcPot = (short int)calcPot; |
| 724 |
|
|
|
| 725 |
|
|
// forces are zeroed here, before any are acumulated. |
| 726 |
|
|
// NOTE: do not rezero the forces in Fortran. |
| 727 |
|
|
|
| 728 |
|
|
for(i=0; i<entry_plug->n_atoms; i++){ |
| 729 |
|
|
entry_plug->atoms[i]->zeroForces(); |
| 730 |
|
|
} |
| 731 |
|
|
|
| 732 |
|
|
frc = Atom::getFrcArray(); |
| 733 |
|
|
pos = Atom::getPosArray(); |
| 734 |
|
|
|
| 735 |
|
|
// entry_plug->lrPot = -1; |
| 736 |
|
|
doSSDfortran( pos, frc, &(entry_plug->lrPot), &passedCalcPot ); |
| 737 |
|
|
|
| 738 |
|
|
|
| 739 |
|
|
// fprintf( stderr, |
| 740 |
|
|
// "lrPot = %lf\n", entry_plug->lrPot ); |
| 741 |
|
|
|
| 742 |
|
|
} |
| 743 |
|
|
|
| 744 |
|
|
void SSD_FF::initFortran( void ){ |
| 745 |
|
|
|
| 746 |
|
|
int nLocal = entry_plug->n_atoms; |
| 747 |
|
|
int *ident; |
| 748 |
|
|
int isError; |
| 749 |
|
|
int i; |
| 750 |
|
|
|
| 751 |
|
|
ident = new int[nLocal]; |
| 752 |
|
|
|
| 753 |
|
|
for(i=0; i<nLocal; i++){ |
| 754 |
|
|
ident[i] = entry_plug->atoms[i]->getIdent(); |
| 755 |
|
|
} |
| 756 |
|
|
|
| 757 |
|
|
isError = 0; |
| 758 |
|
|
initSSDfortran( &nLocal, ident, &isError ); |
| 759 |
|
|
|
| 760 |
|
|
if(isError){ |
| 761 |
|
|
sprintf( painCave.errMsg, |
| 762 |
|
|
"SSD_FF error: There was an error initializing the component list in fortran.\n" ); |
| 763 |
|
|
painCave.isFatal = 1; |
| 764 |
|
|
simError(); |
| 765 |
|
|
} |
| 766 |
|
|
|
| 767 |
|
|
|
| 768 |
|
|
#ifdef IS_MPI |
| 769 |
|
|
sprintf( checkPointMsg, "SSD_FF successfully initialized the fortran component list.\n" ); |
| 770 |
|
|
MPIcheckPoint(); |
| 771 |
|
|
#endif // is_mpi |
| 772 |
|
|
|
| 773 |
|
|
delete[] ident; |
| 774 |
|
|
|
| 775 |
|
|
} |
