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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
4 |
|
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#include <iostream> |
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using namespace std; |
7 |
|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif //is_mpi |
11 |
|
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#include "ForceFields.hpp" |
13 |
#include "SRI.hpp" |
14 |
#include "simError.h" |
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|
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#include "fortranWrappers.hpp" |
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|
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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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|
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|
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|
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namespace EAM_NS{ |
25 |
|
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// Declare the structures that will be passed by the parser and MPI |
27 |
|
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typedef struct{ |
29 |
char name[15]; |
30 |
double mass; |
31 |
double epslon; |
32 |
double sigma; |
33 |
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; |
37 |
|
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int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
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|
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#ifdef IS_MPI |
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|
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MPI_Datatype mpiAtomStructType; |
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|
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#endif |
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|
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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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} |
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~LinkedAtomType(){ if( next != NULL ) delete next; } |
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|
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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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|
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|
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void add( atomStruct &info ){ |
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|
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// check for duplicates |
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|
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if( !strcmp( info.name, name ) ){ |
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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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|
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if( next != NULL ) next->add(info); |
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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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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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|
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|
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#ifdef IS_MPI |
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|
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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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|
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|
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#endif |
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|
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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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LinkedAtomType* next; |
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}; |
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|
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LinkedAtomType* headAtomType; |
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LinkedAtomType* currentAtomType; |
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|
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} |
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|
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using namespace LJ_NS; |
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|
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//**************************************************************** |
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// begins the actual forcefield stuff. |
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//**************************************************************** |
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|
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|
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EAM_FF::EAM_FF(){ |
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|
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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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|
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headAtomType = NULL; |
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currentAtomType = NULL; |
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|
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// do the funtion wrapping |
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wrapMeFF( this ); |
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|
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#ifdef IS_MPI |
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int i; |
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|
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// ********************************************************************** |
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// Init the atomStruct mpi type |
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|
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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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|
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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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|
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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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|
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for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
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|
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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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// *********************************************************************** |
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|
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if( worldRank == 0 ){ |
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#endif |
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|
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// generate the force file name |
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|
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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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|
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// attempt to open the file in the current directory first. |
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|
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frcFile = fopen( fileName, "r" ); |
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|
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if( frcFile == NULL ){ |
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|
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// next see if the force path enviorment variable is set |
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|
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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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|
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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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|
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frcFile = fopen( fileName, "r" ); |
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|
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if( frcFile == NULL ){ |
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|
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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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|
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#ifdef IS_MPI |
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} |
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|
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sprintf( checkPointMsg, "LJ_FF file opened sucessfully." ); |
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MPIcheckPoint(); |
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|
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#endif // is_mpi |
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} |
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|
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|
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EAM_FF::~EAM_FF(){ |
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|
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if( headAtomType != NULL ) delete headAtomType; |
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|
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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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|
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fclose( frcFile ); |
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|
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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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|
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void EAM_FF::initForceField( int ljMixRule ){ |
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|
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initFortran( ljMixRule, 0 ); |
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} |
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|
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void EAM_FF::cleanMe( void ){ |
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|
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#ifdef IS_MPI |
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|
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// keep the linked list in the mpi version |
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|
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#else // is_mpi |
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|
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// delete the linked list in the single processor version |
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|
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if( headAtomType != NULL ) delete headAtomType; |
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|
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#endif // is_mpi |
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} |
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|
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void EAM_FF::readParams( void ){ |
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|
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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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|
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int i; |
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int identNum; |
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|
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|
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bigSigma = 0.0; |
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#ifdef IS_MPI |
258 |
if( worldRank == 0 ){ |
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#endif |
260 |
|
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// read in the atom types. |
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|
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headAtomType = new LinkedAtomType; |
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|
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fastForward( "AtomTypes", "initializeAtoms" ); |
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|
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// we are now at the AtomTypes section. |
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|
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
270 |
lineNum++; |
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|
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|
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// read a line, and start parseing out the atom types |
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|
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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; |
280 |
simError(); |
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} |
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|
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identNum = 1; |
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// stop reading at end of file, or at next section |
285 |
while( readLine[0] != '#' && eof_test != NULL ){ |
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|
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// toss comment lines |
288 |
if( readLine[0] != '!' ){ |
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|
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// the parser returns 0 if the line was blank |
291 |
if( parseAtom( readLine, lineNum, info ) ){ |
292 |
info.ident = identNum; |
293 |
headAtomType->add( info );; |
294 |
identNum++; |
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} |
296 |
} |
297 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
298 |
lineNum++; |
299 |
} |
300 |
|
301 |
#ifdef IS_MPI |
302 |
|
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// send out the linked list to all the other processes |
304 |
|
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sprintf( checkPointMsg, |
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"LJ_FF atom structures read successfully." ); |
307 |
MPIcheckPoint(); |
308 |
|
309 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
310 |
while( currentAtomType != NULL ){ |
311 |
currentAtomType->duplicate( info ); |
312 |
|
313 |
|
314 |
|
315 |
sendFrcStruct( &info, mpiAtomStructType ); |
316 |
|
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sprintf( checkPointMsg, |
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"successfully sent lJ force type: \"%s\"\n", |
319 |
info.name ); |
320 |
MPIcheckPoint(); |
321 |
|
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currentAtomType = currentAtomType->next; |
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} |
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info.last = 1; |
325 |
sendFrcStruct( &info, mpiAtomStructType ); |
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|
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} |
328 |
|
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else{ |
330 |
|
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// listen for node 0 to send out the force params |
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|
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MPIcheckPoint(); |
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|
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headAtomType = new LinkedAtomType; |
336 |
recieveFrcStruct( &info, mpiAtomStructType ); |
337 |
|
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while( !info.last ){ |
339 |
|
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|
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|
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headAtomType->add( info ); |
343 |
|
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MPIcheckPoint(); |
345 |
|
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recieveFrcStruct( &info, mpiAtomStructType ); |
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} |
348 |
} |
349 |
#endif // is_mpi |
350 |
|
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// call new A_types in fortran |
352 |
|
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int isError; |
354 |
|
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// dummy variables |
356 |
int isLJ = 1; |
357 |
int isDipole = 0; |
358 |
int isSSD = 0; |
359 |
int isGB = 0; |
360 |
double dipole = 0.0; |
361 |
|
362 |
currentAtomType = headAtomType; |
363 |
while( currentAtomType != NULL ){ |
364 |
|
365 |
if( currentAtomType->name[0] != '\0' ){ |
366 |
isError = 0; |
367 |
makeAtype( &(currentAtomType->ident), |
368 |
&isLJ, |
369 |
&isSSD, |
370 |
&isDipole, |
371 |
&isGB, |
372 |
&(currentAtomType->epslon), |
373 |
&(currentAtomType->sigma), |
374 |
&dipole, |
375 |
&isError ); |
376 |
if( isError ){ |
377 |
sprintf( painCave.errMsg, |
378 |
"Error initializing the \"%s\" atom type in fortran\n", |
379 |
currentAtomType->name ); |
380 |
painCave.isFatal = 1; |
381 |
simError(); |
382 |
} |
383 |
} |
384 |
currentAtomType = currentAtomType->next; |
385 |
} |
386 |
|
387 |
entry_plug->useLJ = 1; |
388 |
|
389 |
#ifdef IS_MPI |
390 |
sprintf( checkPointMsg, |
391 |
"LJ_FF atom structures successfully sent to fortran\n" ); |
392 |
MPIcheckPoint(); |
393 |
#endif // is_mpi |
394 |
|
395 |
} |
396 |
|
397 |
|
398 |
void EAM_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
399 |
|
400 |
int i; |
401 |
|
402 |
// initialize the atoms |
403 |
|
404 |
|
405 |
Atom* thisAtom; |
406 |
|
407 |
for( i=0; i<nAtoms; i++ ){ |
408 |
|
409 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
410 |
if( currentAtomType == NULL ){ |
411 |
sprintf( painCave.errMsg, |
412 |
"AtomType error, %s not found in force file.\n", |
413 |
the_atoms[i]->getType() ); |
414 |
painCave.isFatal = 1; |
415 |
simError(); |
416 |
} |
417 |
|
418 |
the_atoms[i]->setMass( currentAtomType->mass ); |
419 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
420 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
421 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
422 |
the_atoms[i]->setLJ(); |
423 |
|
424 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
425 |
} |
426 |
} |
427 |
|
428 |
void LJ_FF::initializeBonds( int nBonds, Bond** BondArray, |
429 |
bond_pair* the_bonds ){ |
430 |
|
431 |
if( nBonds ){ |
432 |
sprintf( painCave.errMsg, |
433 |
"LJ_FF does not support bonds.\n" ); |
434 |
painCave.isFatal = 1; |
435 |
simError(); |
436 |
} |
437 |
} |
438 |
|
439 |
void EAM_FF::initializeBends( int nBends, Bend** bendArray, |
440 |
bend_set* the_bends ){ |
441 |
|
442 |
if( nBends ){ |
443 |
sprintf( painCave.errMsg, |
444 |
"LJ_FF does not support bends.\n" ); |
445 |
painCave.isFatal = 1; |
446 |
simError(); |
447 |
} |
448 |
} |
449 |
|
450 |
void EAM_FF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
451 |
torsion_set* the_torsions ){ |
452 |
|
453 |
if( nTorsions ){ |
454 |
sprintf( painCave.errMsg, |
455 |
"LJ_FF does not support torsions.\n" ); |
456 |
painCave.isFatal = 1; |
457 |
simError(); |
458 |
} |
459 |
} |
460 |
|
461 |
void EAM_FF::fastForward( char* stopText, char* searchOwner ){ |
462 |
|
463 |
int foundText = 0; |
464 |
char* the_token; |
465 |
|
466 |
rewind( frcFile ); |
467 |
lineNum = 0; |
468 |
|
469 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
470 |
lineNum++; |
471 |
if( eof_test == NULL ){ |
472 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
473 |
" file is empty.\n", |
474 |
searchOwner ); |
475 |
painCave.isFatal = 1; |
476 |
simError(); |
477 |
} |
478 |
|
479 |
|
480 |
while( !foundText ){ |
481 |
while( eof_test != NULL && readLine[0] != '#' ){ |
482 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
483 |
lineNum++; |
484 |
} |
485 |
if( eof_test == NULL ){ |
486 |
sprintf( painCave.errMsg, |
487 |
"Error fast forwarding force file for %s at " |
488 |
"line %d: file ended unexpectedly.\n", |
489 |
searchOwner, |
490 |
lineNum ); |
491 |
painCave.isFatal = 1; |
492 |
simError(); |
493 |
} |
494 |
|
495 |
the_token = strtok( readLine, " ,;\t#\n" ); |
496 |
foundText = !strcmp( stopText, the_token ); |
497 |
|
498 |
if( !foundText ){ |
499 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
500 |
lineNum++; |
501 |
|
502 |
if( eof_test == NULL ){ |
503 |
sprintf( painCave.errMsg, |
504 |
"Error fast forwarding force file for %s at " |
505 |
"line %d: file ended unexpectedly.\n", |
506 |
searchOwner, |
507 |
lineNum ); |
508 |
painCave.isFatal = 1; |
509 |
simError(); |
510 |
} |
511 |
} |
512 |
} |
513 |
} |
514 |
|
515 |
|
516 |
|
517 |
int EAM_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
518 |
|
519 |
char* the_token; |
520 |
|
521 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
522 |
if( the_token != NULL ){ |
523 |
|
524 |
strcpy( info.name, the_token ); |
525 |
|
526 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
527 |
sprintf( painCave.errMsg, |
528 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
529 |
painCave.isFatal = 1; |
530 |
simError(); |
531 |
} |
532 |
|
533 |
info.mass = atof( the_token ); |
534 |
|
535 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
536 |
sprintf( painCave.errMsg, |
537 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
538 |
painCave.isFatal = 1; |
539 |
simError(); |
540 |
} |
541 |
|
542 |
info.epslon = atof( the_token ); |
543 |
|
544 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
545 |
sprintf( painCave.errMsg, |
546 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
547 |
painCave.isFatal = 1; |
548 |
simError(); |
549 |
} |
550 |
|
551 |
info.sigma = atof( the_token ); |
552 |
|
553 |
return 1; |
554 |
} |
555 |
else return 0; |
556 |
} |