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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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|
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#include <iostream> |
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using namespace std; |
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|
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#include "ForceFields.hpp" |
| 9 |
#include "SRI.hpp" |
| 10 |
#include "simError.h" |
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|
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|
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#ifdef IS_MPI |
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|
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#include "mpiForceField.h" |
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|
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|
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// Declare the structures that will be passed by MPI |
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|
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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 last; // 0 -> default |
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// 1 -> tells nodes to stop listening |
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} atomStruct; |
| 28 |
MPI_Datatype mpiAtomStructType; |
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|
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#endif |
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|
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|
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|
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LJ_FF::LJ_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]; |
| 40 |
char errMsg[1000]; |
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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] = {15,3,1}; // 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.last, &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, "LJ_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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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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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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LJ_FF::~LJ_FF(){ |
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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 LJ_FF::initializeAtoms( void ){ |
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|
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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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|
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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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|
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#ifdef IS_MPI |
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void add( atomStruct &info ){ |
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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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} |
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} |
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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.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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LinkedType* next; |
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}; |
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|
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LinkedType* headAtomType; |
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LinkedType* currentAtomType; |
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LinkedType* tempAtomType; |
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|
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#ifdef IS_MPI |
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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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#endif |
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|
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|
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char readLine[500]; |
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char* the_token; |
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char* eof_test; |
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int foundAtom = 0; |
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int lineNum = 0; |
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int i; |
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|
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|
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////////////////////////////////////////////////// |
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// a quick water fix |
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|
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double waterI[3][3]; |
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waterI[0][0] = 1.76958347772500; |
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waterI[0][1] = 0.0; |
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waterI[0][2] = 0.0; |
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|
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waterI[1][0] = 0.0; |
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waterI[1][1] = 0.614537057924513; |
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waterI[1][2] = 0.0; |
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|
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waterI[2][0] = 0.0; |
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waterI[2][1] = 0.0; |
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waterI[2][2] = 1.15504641980049; |
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|
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|
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double headI[3][3]; |
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headI[0][0] = 1125; |
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headI[0][1] = 0.0; |
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headI[0][2] = 0.0; |
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|
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headI[1][0] = 0.0; |
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headI[1][1] = 1125; |
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headI[1][2] = 0.0; |
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|
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headI[2][0] = 0.0; |
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headI[2][1] = 0.0; |
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headI[2][2] = 250; |
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|
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|
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|
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////////////////////////////////////////////////// |
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|
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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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|
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|
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif |
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|
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// read in the atom types. |
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|
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rewind( frcFile ); |
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headAtomType = new LinkedType; |
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currentAtomType = headAtomType; |
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|
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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if( eof_test == NULL ){ |
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sprintf( painCave.errMsg, "Error in reading Atoms from force file.\n" ); |
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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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while( !foundAtom ){ |
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while( eof_test != NULL && readLine[0] != '#' ){ |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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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; |
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simError(); |
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} |
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|
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the_token = strtok( readLine, " ,;\t#\n" ); |
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foundAtom = !strcmp( "AtomTypes", the_token ); |
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|
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if( !foundAtom ){ |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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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; |
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simError(); |
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} |
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} |
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} |
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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 ); |
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lineNum++; |
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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; |
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simError(); |
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} |
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|
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while( readLine[0] != '#' && eof_test != NULL ){ |
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|
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if( readLine[0] != '!' ){ |
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|
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the_token = strtok( readLine, " \n\t,;" ); |
| 310 |
if( the_token != NULL ){ |
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|
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strcpy( currentAtomType->name, the_token ); |
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|
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
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sprintf( painCave.errMsg, |
| 316 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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sscanf( the_token, "%lf", ¤tAtomType->mass ); |
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|
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
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sprintf( painCave.errMsg, |
| 325 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
| 331 |
|
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
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sprintf( painCave.errMsg, |
| 334 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 335 |
painCave.isFatal = 1; |
| 336 |
simError(); |
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} |
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|
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sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
| 340 |
} |
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} |
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|
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tempAtomType = new LinkedType; |
| 344 |
currentAtomType->next = tempAtomType; |
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currentAtomType = tempAtomType; |
| 346 |
|
| 347 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 348 |
lineNum++; |
| 349 |
} |
| 350 |
|
| 351 |
#ifdef IS_MPI |
| 352 |
|
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// send out the linked list to all the other processes |
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|
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sprintf( checkPointMsg, |
| 356 |
"LJ_FF atom structures read successfully." ); |
| 357 |
MPIcheckPoint(); |
| 358 |
|
| 359 |
currentAtomType = headAtomType; |
| 360 |
while( currentAtomType != NULL ){ |
| 361 |
currentAtomType->duplicate( info ); |
| 362 |
sendFrcStruct( &info, mpiAtomStructType ); |
| 363 |
currentAtomType = currentAtomType->next; |
| 364 |
} |
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info.last = 1; |
| 366 |
sendFrcStruct( &info, mpiAtomStructType ); |
| 367 |
|
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} |
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|
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else{ |
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|
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// listen for node 0 to send out the force params |
| 373 |
|
| 374 |
MPIcheckPoint(); |
| 375 |
|
| 376 |
headAtomType = new LinkedType; |
| 377 |
recieveFrcStruct( &info, mpiAtomStructType ); |
| 378 |
while( !info.last ){ |
| 379 |
|
| 380 |
headAtomType->add( info ); |
| 381 |
recieveFrcStruct( &info, mpiAtomStructType ); |
| 382 |
} |
| 383 |
} |
| 384 |
#endif // is_mpi |
| 385 |
|
| 386 |
|
| 387 |
// initialize the atoms |
| 388 |
|
| 389 |
Atom* thisAtom; |
| 390 |
|
| 391 |
for( i=0; i<nAtoms; i++ ){ |
| 392 |
|
| 393 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
| 394 |
if( currentAtomType == NULL ){ |
| 395 |
sprintf( painCave.errMsg, |
| 396 |
"AtomType error, %s not found in force file.\n", |
| 397 |
the_atoms[i]->getType() ); |
| 398 |
painCave.isFatal = 1; |
| 399 |
simError(); |
| 400 |
} |
| 401 |
|
| 402 |
the_atoms[i]->setMass( currentAtomType->mass ); |
| 403 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
| 404 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
| 405 |
the_atoms[i]->setLJ(); |
| 406 |
} |
| 407 |
|
| 408 |
|
| 409 |
// clean up the memory |
| 410 |
|
| 411 |
delete headAtomType; |
| 412 |
|
| 413 |
#ifdef IS_MPI |
| 414 |
sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" ); |
| 415 |
MPIcheckPoint(); |
| 416 |
#endif // is_mpi |
| 417 |
|
| 418 |
} |
| 419 |
|
| 420 |
void LJ_FF::initializeBonds( bond_pair* the_bonds ){ |
| 421 |
|
| 422 |
if( entry_plug->n_bonds ){ |
| 423 |
sprintf( painCave.errMsg, |
| 424 |
"LJ_FF does not support bonds.\n" ); |
| 425 |
painCave.isFatal = 1; |
| 426 |
simError(); |
| 427 |
} |
| 428 |
#ifdef IS_MPI |
| 429 |
MPIcheckPoint(); |
| 430 |
#endif // is_mpi |
| 431 |
|
| 432 |
} |
| 433 |
|
| 434 |
void LJ_FF::initializeBends( bend_set* the_bends ){ |
| 435 |
|
| 436 |
if( entry_plug->n_bends ){ |
| 437 |
sprintf( painCave.errMsg, |
| 438 |
"LJ_FF does not support bends.\n" ); |
| 439 |
painCave.isFatal = 1; |
| 440 |
simError(); |
| 441 |
} |
| 442 |
#ifdef IS_MPI |
| 443 |
MPIcheckPoint(); |
| 444 |
#endif // is_mpi |
| 445 |
|
| 446 |
} |
| 447 |
|
| 448 |
void LJ_FF::initializeTorsions( torsion_set* the_torsions ){ |
| 449 |
|
| 450 |
if( entry_plug->n_torsions ){ |
| 451 |
sprintf( painCave.errMsg, |
| 452 |
"LJ_FF does not support torsions.\n" ); |
| 453 |
painCave.isFatal = 1; |
| 454 |
simError(); |
| 455 |
} |
| 456 |
#ifdef IS_MPI |
| 457 |
MPIcheckPoint(); |
| 458 |
#endif // is_mpi |
| 459 |
|
| 460 |
} |
