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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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mmeineke |
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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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mmeineke |
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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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mmeineke |
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mmeineke |
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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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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 parseAtomLJ( 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 LJfunctionWrapper( 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, 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 (*newLJtype)( int* ident, double* mass, double* epslon, double* sigma, |
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int* status ); |
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void (*initLJfortran) ( int *nLocal, int *identArray, int *isError ); |
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LJ_FF* currentLJwrap; |
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//**************************************************************** |
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// begins the actual forcefield stuff. |
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//**************************************************************** |
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LJ_FF::LJ_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] = {15,3,2}; // 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.ident, &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, "LJ_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, "LJ_FF file opened sucessfully." ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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LJ_FF::~LJ_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 LJ_FF::wrapMe( void ){ |
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char* currentFF = "LJ"; |
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int isError = 0; |
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forcefactory_( currentFF, &isError, LJfunctionWrapper, strlen(currentFF) ); |
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if( isError ){ |
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sprintf( painCave.errMsg, |
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"LJ_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, "LJ_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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newLJtype = p1; |
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initLJfortran = p2; |
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currentLJwrap->setLJfortran( p3 ); |
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} |
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void LJ_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 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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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->mass = info.mass; |
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next->epslon = info.epslon; |
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next->sigma = info.sigma; |
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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.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.last = 0; |
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} |
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#endif |
284 |
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285 |
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char name[15]; |
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double mass; |
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double epslon; |
288 |
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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 |
298 |
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299 |
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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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308 |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif |
311 |
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312 |
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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 |
339 |
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if( readLine[0] != '!' ){ |
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// the parser returns 0 if the line was blank |
342 |
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if( parseAtomLJ( readLine, lineNum, info ) ){ |
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info.ident = identNum; |
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headAtomType->add( info );; |
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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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} |
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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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"LJ_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. |
361 |
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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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368 |
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sprintf( checkPointMsg, |
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"successfully sent lJ force type: \"%s\"\n", |
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info.name ); |
371 |
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MPIcheckPoint(); |
372 |
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373 |
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currentAtomType = currentAtomType->next; |
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} |
375 |
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info.last = 1; |
376 |
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sendFrcStruct( &info, mpiAtomStructType ); |
377 |
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378 |
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} |
379 |
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380 |
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else{ |
381 |
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382 |
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// listen for node 0 to send out the force params |
383 |
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384 |
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MPIcheckPoint(); |
385 |
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386 |
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headAtomType = new LinkedType; |
387 |
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recieveFrcStruct( &info, mpiAtomStructType ); |
388 |
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389 |
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while( !info.last ){ |
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392 |
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headAtomType->add( info ); |
394 |
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395 |
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MPIcheckPoint(); |
396 |
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397 |
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recieveFrcStruct( &info, mpiAtomStructType ); |
398 |
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} |
399 |
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} |
400 |
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#endif // is_mpi |
401 |
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402 |
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// call new A_types in fortran |
403 |
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404 |
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int isError; |
405 |
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currentAtomType = headAtomType; |
406 |
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while( currentAtomType != NULL ){ |
407 |
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408 |
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if( currentAtomType->name[0] != '\0' ){ |
409 |
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isError = 0; |
410 |
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newLJtype( &(currentAtomType->ident), |
411 |
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&(currentAtomType->mass), |
412 |
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&(currentAtomType->epslon), |
413 |
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&(currentAtomType->sigma), |
414 |
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&isError ); |
415 |
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if( isError ){ |
416 |
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sprintf( painCave.errMsg, |
417 |
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"Error initializing the \"%s\" atom type in fortran\n", |
418 |
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currentAtomType->name ); |
419 |
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painCave.isFatal = 1; |
420 |
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simError(); |
421 |
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} |
422 |
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} |
423 |
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currentAtomType = currentAtomType->next; |
424 |
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} |
425 |
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426 |
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#ifdef IS_MPI |
427 |
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sprintf( checkPointMsg, |
428 |
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"LJ_FF atom structures successfully sent to fortran\n" ); |
429 |
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MPIcheckPoint(); |
430 |
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#endif // is_mpi |
431 |
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432 |
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433 |
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|
|
434 |
|
|
// initialize the atoms |
435 |
|
|
|
436 |
|
|
double bigSigma = 0.0; |
437 |
|
|
Atom* thisAtom; |
438 |
|
|
|
439 |
|
|
for( i=0; i<nAtoms; i++ ){ |
440 |
|
|
|
441 |
|
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
442 |
|
|
if( currentAtomType == NULL ){ |
443 |
|
|
sprintf( painCave.errMsg, |
444 |
|
|
"AtomType error, %s not found in force file.\n", |
445 |
|
|
the_atoms[i]->getType() ); |
446 |
|
|
painCave.isFatal = 1; |
447 |
|
|
simError(); |
448 |
|
|
} |
449 |
|
|
|
450 |
|
|
the_atoms[i]->setMass( currentAtomType->mass ); |
451 |
|
|
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
452 |
|
|
the_atoms[i]->setSigma( currentAtomType->sigma ); |
453 |
|
|
the_atoms[i]->setIdent( currentAtomType->ident ); |
454 |
|
|
the_atoms[i]->setLJ(); |
455 |
|
|
|
456 |
|
|
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
457 |
|
|
} |
458 |
|
|
|
459 |
|
|
|
460 |
|
|
#ifdef IS_MPI |
461 |
|
|
double tempBig = bigSigma; |
462 |
|
|
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
463 |
|
|
#endif //is_mpi |
464 |
|
|
|
465 |
|
|
//calc rCut and rList |
466 |
|
|
|
467 |
|
|
entry_plug->rCut = 2.5 * bigSigma; |
468 |
|
|
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0; |
469 |
|
|
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0; |
470 |
|
|
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0; |
471 |
|
|
|
472 |
|
|
entry_plug->rList = entry_plug->rCut + 1.0; |
473 |
|
|
|
474 |
|
|
// clean up the memory |
475 |
|
|
|
476 |
|
|
delete headAtomType; |
477 |
|
|
|
478 |
|
|
#ifdef IS_MPI |
479 |
|
|
sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" ); |
480 |
|
|
MPIcheckPoint(); |
481 |
|
|
#endif // is_mpi |
482 |
|
|
|
483 |
|
|
initFortran(); |
484 |
|
|
entry_plug->refreshSim(); |
485 |
|
|
|
486 |
|
|
} |
487 |
|
|
|
488 |
|
|
void LJ_FF::initializeBonds( bond_pair* the_bonds ){ |
489 |
|
|
|
490 |
|
|
if( entry_plug->n_bonds ){ |
491 |
|
|
sprintf( painCave.errMsg, |
492 |
|
|
"LJ_FF does not support bonds.\n" ); |
493 |
|
|
painCave.isFatal = 1; |
494 |
|
|
simError(); |
495 |
|
|
} |
496 |
|
|
#ifdef IS_MPI |
497 |
|
|
MPIcheckPoint(); |
498 |
|
|
#endif // is_mpi |
499 |
|
|
|
500 |
|
|
} |
501 |
|
|
|
502 |
|
|
void LJ_FF::initializeBends( bend_set* the_bends ){ |
503 |
|
|
|
504 |
|
|
if( entry_plug->n_bends ){ |
505 |
|
|
sprintf( painCave.errMsg, |
506 |
|
|
"LJ_FF does not support bends.\n" ); |
507 |
|
|
painCave.isFatal = 1; |
508 |
|
|
simError(); |
509 |
|
|
} |
510 |
|
|
#ifdef IS_MPI |
511 |
|
|
MPIcheckPoint(); |
512 |
|
|
#endif // is_mpi |
513 |
|
|
|
514 |
|
|
} |
515 |
|
|
|
516 |
|
|
void LJ_FF::initializeTorsions( torsion_set* the_torsions ){ |
517 |
|
|
|
518 |
|
|
if( entry_plug->n_torsions ){ |
519 |
|
|
sprintf( painCave.errMsg, |
520 |
|
|
"LJ_FF does not support torsions.\n" ); |
521 |
|
|
painCave.isFatal = 1; |
522 |
|
|
simError(); |
523 |
|
|
} |
524 |
|
|
#ifdef IS_MPI |
525 |
|
|
MPIcheckPoint(); |
526 |
|
|
#endif // is_mpi |
527 |
|
|
|
528 |
|
|
} |
529 |
|
|
|
530 |
|
|
|
531 |
|
|
void LJ_FF::fastForward( char* stopText, char* searchOwner ){ |
532 |
|
|
|
533 |
|
|
int foundText = 0; |
534 |
|
|
char* the_token; |
535 |
|
|
|
536 |
|
|
rewind( frcFile ); |
537 |
|
|
lineNum = 0; |
538 |
|
|
|
539 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
540 |
|
|
lineNum++; |
541 |
|
|
if( eof_test == NULL ){ |
542 |
|
|
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
543 |
|
|
" file is empty.\n", |
544 |
|
|
searchOwner ); |
545 |
|
|
painCave.isFatal = 1; |
546 |
|
|
simError(); |
547 |
|
|
} |
548 |
|
|
|
549 |
|
|
|
550 |
|
|
while( !foundText ){ |
551 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
552 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
553 |
|
|
lineNum++; |
554 |
|
|
} |
555 |
|
|
if( eof_test == NULL ){ |
556 |
|
|
sprintf( painCave.errMsg, |
557 |
|
|
"Error fast forwarding force file for %s at " |
558 |
|
|
"line %d: file ended unexpectedly.\n", |
559 |
|
|
searchOwner, |
560 |
|
|
lineNum ); |
561 |
|
|
painCave.isFatal = 1; |
562 |
|
|
simError(); |
563 |
|
|
} |
564 |
|
|
|
565 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
566 |
|
|
foundText = !strcmp( stopText, the_token ); |
567 |
|
|
|
568 |
|
|
if( !foundText ){ |
569 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
570 |
|
|
lineNum++; |
571 |
|
|
|
572 |
|
|
if( eof_test == NULL ){ |
573 |
|
|
sprintf( painCave.errMsg, |
574 |
|
|
"Error fast forwarding force file for %s at " |
575 |
|
|
"line %d: file ended unexpectedly.\n", |
576 |
|
|
searchOwner, |
577 |
|
|
lineNum ); |
578 |
|
|
painCave.isFatal = 1; |
579 |
|
|
simError(); |
580 |
|
|
} |
581 |
|
|
} |
582 |
|
|
} |
583 |
|
|
} |
584 |
|
|
|
585 |
|
|
|
586 |
|
|
|
587 |
|
|
int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ){ |
588 |
|
|
|
589 |
|
|
char* the_token; |
590 |
|
|
|
591 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
592 |
|
|
if( the_token != NULL ){ |
593 |
|
|
|
594 |
|
|
strcpy( info.name, the_token ); |
595 |
|
|
|
596 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
597 |
|
|
sprintf( painCave.errMsg, |
598 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
599 |
|
|
painCave.isFatal = 1; |
600 |
|
|
simError(); |
601 |
|
|
} |
602 |
|
|
|
603 |
|
|
info.mass = atof( the_token ); |
604 |
|
|
|
605 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
606 |
|
|
sprintf( painCave.errMsg, |
607 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
608 |
|
|
painCave.isFatal = 1; |
609 |
|
|
simError(); |
610 |
|
|
} |
611 |
|
|
|
612 |
|
|
info.epslon = atof( the_token ); |
613 |
|
|
|
614 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
615 |
|
|
sprintf( painCave.errMsg, |
616 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
617 |
|
|
painCave.isFatal = 1; |
618 |
|
|
simError(); |
619 |
|
|
} |
620 |
|
|
|
621 |
|
|
info.sigma = atof( the_token ); |
622 |
|
|
|
623 |
|
|
return 1; |
624 |
|
|
} |
625 |
|
|
else return 0; |
626 |
|
|
} |
627 |
|
|
|
628 |
|
|
|
629 |
|
|
void LJ_FF::doForces( int calcPot ){ |
630 |
|
|
|
631 |
|
|
int i; |
632 |
|
|
double* frc; |
633 |
|
|
double* pos; |
634 |
|
|
short int passedCalcPot = (short int)calcPot; |
635 |
|
|
|
636 |
|
|
// forces are zeroed here, before any are acumulated. |
637 |
|
|
// NOTE: do not rezero the forces in Fortran. |
638 |
|
|
|
639 |
|
|
for(i=0; i<entry_plug->n_atoms; i++){ |
640 |
|
|
entry_plug->atoms[i]->zeroForces(); |
641 |
|
|
} |
642 |
|
|
|
643 |
|
|
frc = Atom::getFrcArray(); |
644 |
|
|
pos = Atom::getPosArray(); |
645 |
|
|
|
646 |
|
|
// entry_plug->lrPot = -1; |
647 |
|
|
doLJfortran( pos, frc, &(entry_plug->lrPot), &passedCalcPot ); |
648 |
|
|
|
649 |
|
|
|
650 |
|
|
// fprintf( stderr, |
651 |
|
|
// "lrPot = %lf\n", entry_plug->lrPot ); |
652 |
|
|
|
653 |
|
|
} |
654 |
|
|
|
655 |
|
|
void LJ_FF::initFortran( void ){ |
656 |
|
|
|
657 |
|
|
int nLocal = entry_plug->n_atoms; |
658 |
|
|
int *ident; |
659 |
|
|
int isError; |
660 |
|
|
int i; |
661 |
|
|
|
662 |
|
|
ident = new int[nLocal]; |
663 |
|
|
|
664 |
|
|
for(i=0; i<nLocal; i++){ |
665 |
|
|
ident[i] = entry_plug->atoms[i]->getIdent(); |
666 |
|
|
} |
667 |
|
|
|
668 |
|
|
isError = 0; |
669 |
|
|
initLJfortran( &nLocal, ident, &isError ); |
670 |
|
|
|
671 |
|
|
if(isError){ |
672 |
|
|
sprintf( painCave.errMsg, |
673 |
|
|
"LJ_FF error: There was an error initializing the component list in fortran.\n" ); |
674 |
|
|
painCave.isFatal = 1; |
675 |
|
|
simError(); |
676 |
|
|
} |
677 |
|
|
|
678 |
|
|
|
679 |
|
|
#ifdef IS_MPI |
680 |
|
|
sprintf( checkPointMsg, "LJ_FF successfully initialized the fortran component list.\n" ); |
681 |
|
|
MPIcheckPoint(); |
682 |
|
|
#endif // is_mpi |
683 |
|
|
|
684 |
|
|
delete[] ident; |
685 |
|
|
|
686 |
|
|
} |
687 |
|
|
|