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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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#include "ForceFields.hpp" |
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#include "SRI.hpp" |
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#include "simError.h" |
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#include <fortranWrappers.hpp> |
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#ifdef IS_MPI |
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#include "mpiForceField.h" |
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#endif // is_mpi |
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mmeineke |
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mmeineke |
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namespace TPE { // restrict the access of the folowing to this file only. |
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// Declare the structures that will be passed by 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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double w0; |
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double v0; |
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int isSSD; |
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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 -> tells nodes to stop listening |
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} atomStruct; |
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typedef struct{ |
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char nameA[15]; |
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char nameB[15]; |
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char type[30]; |
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double d0; |
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int last; // 0 -> default |
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// 1 -> tells nodes to stop listening |
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} bondStruct; |
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typedef struct{ |
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char nameA[15]; |
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char nameB[15]; |
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char nameC[15]; |
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char type[30]; |
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double k1, k2, k3, t0; |
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int last; // 0 -> default |
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// 1 -> tells nodes to stop listening |
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} bendStruct; |
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typedef struct{ |
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char nameA[15]; |
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char nameB[15]; |
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char nameC[15]; |
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char nameD[15]; |
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char type[30]; |
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double k1, k2, k3, k4; |
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int last; // 0 -> default |
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// 1 -> tells nodes to stop listening |
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} torsionStruct; |
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int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
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int parseBond( char *lineBuffer, int lineNum, bondStruct &info ); |
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int parseBend( char *lineBuffer, int lineNum, bendStruct &info ); |
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int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ); |
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#ifdef IS_MPI |
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MPI_Datatype mpiAtomStructType; |
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MPI_Datatype mpiBondStructType; |
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MPI_Datatype mpiBendStructType; |
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MPI_Datatype mpiTorsionStructType; |
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mmeineke |
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#endif |
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} // namespace |
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using namespace TPE; |
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//**************************************************************** |
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// begins the actual forcefield stuff. |
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//**************************************************************** |
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mmeineke |
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TraPPE_ExFF::TraPPE_ExFF(){ |
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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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mmeineke |
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// do the funtion wrapping |
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mmeineke |
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wrapMeFF( this ); |
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#ifdef IS_MPI |
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int i; |
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// ********************************************************************** |
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// Init the atomStruct mpi type |
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atomStruct atomProto; // mpiPrototype |
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int atomBC[3] = {15,6,4}; // 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.isSSD, &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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// Init the bondStruct mpi type |
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bondStruct bondProto; // mpiPrototype |
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int bondBC[3] = {60,1,1}; // block counts |
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MPI_Aint bondDspls[3]; // displacements |
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MPI_Datatype bondMbrTypes[3]; // member mpi types |
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MPI_Address(&bondProto.nameA, &bondDspls[0]); |
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MPI_Address(&bondProto.d0, &bondDspls[1]); |
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MPI_Address(&bondProto.last, &bondDspls[2]); |
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bondMbrTypes[0] = MPI_CHAR; |
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bondMbrTypes[1] = MPI_DOUBLE; |
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bondMbrTypes[2] = MPI_INT; |
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for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
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MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
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MPI_Type_commit(&mpiBondStructType); |
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// ********************************************************************** |
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// Init the bendStruct mpi type |
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bendStruct bendProto; // mpiPrototype |
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int bendBC[3] = {75,4,1}; // block counts |
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MPI_Aint bendDspls[3]; // displacements |
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MPI_Datatype bendMbrTypes[3]; // member mpi types |
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MPI_Address(&bendProto.nameA, &bendDspls[0]); |
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MPI_Address(&bendProto.k1, &bendDspls[1]); |
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MPI_Address(&bendProto.last, &bendDspls[2]); |
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bendMbrTypes[0] = MPI_CHAR; |
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bendMbrTypes[1] = MPI_DOUBLE; |
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bendMbrTypes[2] = MPI_INT; |
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for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
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MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
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MPI_Type_commit(&mpiBendStructType); |
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// ********************************************************************** |
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// Init the torsionStruct mpi type |
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torsionStruct torsionProto; // mpiPrototype |
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int torsionBC[3] = {90,4,1}; // block counts |
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MPI_Aint torsionDspls[3]; // displacements |
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MPI_Datatype torsionMbrTypes[3]; // member mpi types |
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MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
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MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
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MPI_Address(&torsionProto.last, &torsionDspls[2]); |
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torsionMbrTypes[0] = MPI_CHAR; |
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torsionMbrTypes[1] = MPI_DOUBLE; |
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torsionMbrTypes[2] = MPI_INT; |
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for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
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MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
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&mpiTorsionStructType); |
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MPI_Type_commit(&mpiTorsionStructType); |
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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, "TraPPE_Ex.frc" ); |
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// fprintf( stderr,"Trying to open %s\n", fileName ); |
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// attempt to open the file in the current directory first. |
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frcFile = fopen( fileName, "r" ); |
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if( frcFile == NULL ){ |
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// next see if the force path enviorment variable is set |
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ffPath = getenv( ffPath_env ); |
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if( ffPath == NULL ) { |
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STR_DEFINE(ffPath, FRC_PATH ); |
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} |
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strcpy( temp, ffPath ); |
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strcat( temp, "/" ); |
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strcat( temp, fileName ); |
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strcpy( fileName, temp ); |
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frcFile = fopen( fileName, "r" ); |
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if( frcFile == NULL ){ |
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sprintf( painCave.errMsg, |
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"Error opening the force field parameter file: %s\n" |
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"Have you tried setting the FORCE_PARAM_PATH environment " |
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"vairable?\n", |
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fileName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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#ifdef IS_MPI |
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} |
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sprintf( checkPointMsg, "TraPPE_ExFF file opened sucessfully." ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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TraPPE_ExFF::~TraPPE_ExFF(){ |
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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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mmeineke |
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void TraPPE_ExFF::doForces( int calcPot ){ |
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mmeineke |
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mmeineke |
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int i, isError; |
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double* frc; |
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double* pos; |
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double* tau; |
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short int passedCalcPot = (short int)calcPot; |
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// forces are zeroed here, before any are acumulated. |
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// NOTE: do not rezero the forces in Fortran. |
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for(i=0; i<entry_plug->n_atoms; i++){ |
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entry_plug->atoms[i]->zeroForces(); |
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} |
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frc = Atom::getFrcArray(); |
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pos = Atom::getPosArray(); |
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tau = entry_plug->tau; |
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isError = 0; |
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fortranForceLoop( pos, frc, &(entry_plug->lrPot), tau, |
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&passedCalcPot, &isError ); |
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if( isError ){ |
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sprintf( painCave.errMsg, |
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"Error returned from the fortran force calculation.\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, |
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"successfully returned from the force calculation.\n" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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void TraPPE_ExFF::initFortran( void ){ |
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int nLocal = entry_plug->n_atoms; |
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int *ident; |
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int isError; |
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int i; |
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ident = new int[nLocal]; |
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for(i=0; i<nLocal; i++){ |
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ident[i] = entry_plug->atoms[i]->getIdent(); |
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} |
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isError = 0; |
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initfortran( &nLocal, ident, &isError ); |
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if(isError){ |
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sprintf( painCave.errMsg, |
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"TraPPE_ExFF error: There was an error initializing the component list in fortran.\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, "TraPPE_ExFF successfully initialized the fortran component list.\n" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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delete[] ident; |
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} |
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mmeineke |
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void TraPPE_ExFF::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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mmeineke |
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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 TraPPE_Ex atom type \"%s\" found in " |
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"the TraPPE_ExFF 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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mmeineke |
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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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mmeineke |
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next->isDipole = info.isDipole; |
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next->isSSD = info.isSSD; |
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mmeineke |
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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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mmeineke |
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next->w0 = info.w0; |
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next->v0 = info.v0; |
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next->ident = info.ident; |
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mmeineke |
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} |
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} |
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mmeineke |
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#ifdef IS_MPI |
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mmeineke |
270 |
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void duplicate( atomStruct &info ){ |
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strcpy(info.name, name); |
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mmeineke |
291 |
info.isDipole = isDipole; |
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info.isSSD = isSSD; |
392 |
mmeineke |
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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.dipole = dipole; |
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mmeineke |
291 |
info.w0 = w0; |
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info.v0 = v0; |
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mmeineke |
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info.last = 0; |
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} |
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#endif |
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|
char name[15]; |
405 |
|
|
int isDipole; |
406 |
mmeineke |
291 |
int isSSD; |
407 |
mmeineke |
270 |
double mass; |
408 |
|
|
double epslon; |
409 |
|
|
double sigma; |
410 |
|
|
double dipole; |
411 |
mmeineke |
291 |
double w0; |
412 |
|
|
double v0; |
413 |
|
|
int ident; |
414 |
mmeineke |
270 |
LinkedType* next; |
415 |
|
|
}; |
416 |
|
|
|
417 |
|
|
LinkedType* headAtomType; |
418 |
|
|
LinkedType* currentAtomType; |
419 |
|
|
atomStruct info; |
420 |
|
|
info.last = 1; // initialize last to have the last set. |
421 |
|
|
// if things go well, last will be set to 0 |
422 |
mmeineke |
291 |
|
423 |
mmeineke |
270 |
|
424 |
|
|
|
425 |
|
|
int i; |
426 |
mmeineke |
291 |
int identNum; |
427 |
mmeineke |
270 |
|
428 |
mmeineke |
291 |
Atom** the_atoms; |
429 |
|
|
int nAtoms; |
430 |
|
|
the_atoms = entry_plug->atoms; |
431 |
|
|
nAtoms = entry_plug->n_atoms; |
432 |
|
|
|
433 |
|
|
|
434 |
mmeineke |
270 |
////////////////////////////////////////////////// |
435 |
|
|
// a quick water fix |
436 |
|
|
|
437 |
|
|
double waterI[3][3]; |
438 |
|
|
waterI[0][0] = 1.76958347772500; |
439 |
|
|
waterI[0][1] = 0.0; |
440 |
|
|
waterI[0][2] = 0.0; |
441 |
|
|
|
442 |
|
|
waterI[1][0] = 0.0; |
443 |
|
|
waterI[1][1] = 0.614537057924513; |
444 |
|
|
waterI[1][2] = 0.0; |
445 |
|
|
|
446 |
|
|
waterI[2][0] = 0.0; |
447 |
|
|
waterI[2][1] = 0.0; |
448 |
|
|
waterI[2][2] = 1.15504641980049; |
449 |
|
|
|
450 |
|
|
|
451 |
|
|
double headI[3][3]; |
452 |
|
|
headI[0][0] = 1125; |
453 |
|
|
headI[0][1] = 0.0; |
454 |
|
|
headI[0][2] = 0.0; |
455 |
|
|
|
456 |
|
|
headI[1][0] = 0.0; |
457 |
|
|
headI[1][1] = 1125; |
458 |
|
|
headI[1][2] = 0.0; |
459 |
|
|
|
460 |
|
|
headI[2][0] = 0.0; |
461 |
|
|
headI[2][1] = 0.0; |
462 |
|
|
headI[2][2] = 250; |
463 |
|
|
|
464 |
|
|
|
465 |
|
|
|
466 |
|
|
////////////////////////////////////////////////// |
467 |
|
|
|
468 |
mmeineke |
291 |
|
469 |
mmeineke |
270 |
#ifdef IS_MPI |
470 |
|
|
if( worldRank == 0 ){ |
471 |
|
|
#endif |
472 |
|
|
|
473 |
|
|
// read in the atom types. |
474 |
mmeineke |
291 |
|
475 |
mmeineke |
270 |
headAtomType = new LinkedType; |
476 |
|
|
|
477 |
mmeineke |
291 |
fastForward( "AtomTypes", "initializeAtoms" ); |
478 |
|
|
|
479 |
mmeineke |
270 |
// we are now at the AtomTypes section. |
480 |
|
|
|
481 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
482 |
|
|
lineNum++; |
483 |
|
|
|
484 |
mmeineke |
291 |
|
485 |
|
|
// read a line, and start parseing out the atom types |
486 |
|
|
|
487 |
mmeineke |
270 |
if( eof_test == NULL ){ |
488 |
|
|
sprintf( painCave.errMsg, |
489 |
|
|
"Error in reading Atoms from force file at line %d.\n", |
490 |
|
|
lineNum ); |
491 |
|
|
painCave.isFatal = 1; |
492 |
|
|
simError(); |
493 |
|
|
} |
494 |
|
|
|
495 |
mmeineke |
291 |
identNum = 1; |
496 |
|
|
// stop reading at end of file, or at next section |
497 |
mmeineke |
270 |
while( readLine[0] != '#' && eof_test != NULL ){ |
498 |
mmeineke |
291 |
|
499 |
|
|
// toss comment lines |
500 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
501 |
|
|
|
502 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
503 |
|
|
if( parseAtom( readLine, lineNum, info ) ){ |
504 |
|
|
info.ident = identNum; |
505 |
|
|
headAtomType->add( info );; |
506 |
|
|
identNum++; |
507 |
mmeineke |
270 |
} |
508 |
|
|
} |
509 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
510 |
|
|
lineNum++; |
511 |
|
|
} |
512 |
|
|
|
513 |
|
|
#ifdef IS_MPI |
514 |
|
|
|
515 |
|
|
// send out the linked list to all the other processes |
516 |
|
|
|
517 |
|
|
sprintf( checkPointMsg, |
518 |
mmeineke |
291 |
"TraPPE_ExFF atom structures read successfully." ); |
519 |
mmeineke |
270 |
MPIcheckPoint(); |
520 |
|
|
|
521 |
mmeineke |
291 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
522 |
mmeineke |
270 |
while( currentAtomType != NULL ){ |
523 |
|
|
currentAtomType->duplicate( info ); |
524 |
mmeineke |
291 |
|
525 |
|
|
|
526 |
|
|
|
527 |
mmeineke |
270 |
sendFrcStruct( &info, mpiAtomStructType ); |
528 |
mmeineke |
291 |
|
529 |
|
|
sprintf( checkPointMsg, |
530 |
|
|
"successfully sent TraPPE_Ex force type: \"%s\"\n", |
531 |
|
|
info.name ); |
532 |
|
|
MPIcheckPoint(); |
533 |
|
|
|
534 |
mmeineke |
270 |
currentAtomType = currentAtomType->next; |
535 |
|
|
} |
536 |
|
|
info.last = 1; |
537 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
538 |
|
|
|
539 |
|
|
} |
540 |
|
|
|
541 |
|
|
else{ |
542 |
|
|
|
543 |
|
|
// listen for node 0 to send out the force params |
544 |
|
|
|
545 |
|
|
MPIcheckPoint(); |
546 |
|
|
|
547 |
|
|
headAtomType = new LinkedType; |
548 |
|
|
recieveFrcStruct( &info, mpiAtomStructType ); |
549 |
mmeineke |
291 |
|
550 |
mmeineke |
270 |
while( !info.last ){ |
551 |
|
|
|
552 |
mmeineke |
291 |
|
553 |
|
|
|
554 |
mmeineke |
270 |
headAtomType->add( info ); |
555 |
mmeineke |
291 |
|
556 |
|
|
MPIcheckPoint(); |
557 |
|
|
|
558 |
mmeineke |
270 |
recieveFrcStruct( &info, mpiAtomStructType ); |
559 |
|
|
} |
560 |
|
|
} |
561 |
|
|
#endif // is_mpi |
562 |
|
|
|
563 |
mmeineke |
291 |
// call new A_types in fortran |
564 |
mmeineke |
270 |
|
565 |
mmeineke |
291 |
int isError; |
566 |
mmeineke |
296 |
|
567 |
|
|
// dummy variables |
568 |
|
|
|
569 |
|
|
int isGB = 0; |
570 |
|
|
int isLJ = 1; |
571 |
|
|
|
572 |
|
|
|
573 |
mmeineke |
291 |
currentAtomType = headAtomType; |
574 |
|
|
while( currentAtomType != NULL ){ |
575 |
|
|
|
576 |
|
|
if( currentAtomType->name[0] != '\0' ){ |
577 |
|
|
isError = 0; |
578 |
|
|
newTPEtype( &(currentAtomType->ident), |
579 |
|
|
&(currentAtomType->mass), |
580 |
|
|
&(currentAtomType->epslon), |
581 |
|
|
&(currentAtomType->sigma), |
582 |
mmeineke |
296 |
&isLJ, |
583 |
|
|
&(currentAtomType->isSSD), |
584 |
mmeineke |
291 |
&(currentAtomType->isDipole), |
585 |
mmeineke |
296 |
&isGB, |
586 |
mmeineke |
291 |
&(currentAtomType->w0), |
587 |
|
|
&(currentAtomType->v0), |
588 |
mmeineke |
296 |
&(currentAtomType->dipole), |
589 |
mmeineke |
291 |
&isError ); |
590 |
|
|
if( isError ){ |
591 |
|
|
sprintf( painCave.errMsg, |
592 |
|
|
"Error initializing the \"%s\" atom type in fortran\n", |
593 |
|
|
currentAtomType->name ); |
594 |
|
|
painCave.isFatal = 1; |
595 |
|
|
simError(); |
596 |
|
|
} |
597 |
|
|
} |
598 |
|
|
currentAtomType = currentAtomType->next; |
599 |
|
|
} |
600 |
|
|
|
601 |
|
|
#ifdef IS_MPI |
602 |
|
|
sprintf( checkPointMsg, |
603 |
|
|
"TraPPE_ExFF atom structures successfully sent to fortran\n" ); |
604 |
|
|
MPIcheckPoint(); |
605 |
|
|
#endif // is_mpi |
606 |
|
|
|
607 |
|
|
|
608 |
mmeineke |
270 |
// initialize the atoms |
609 |
|
|
|
610 |
mmeineke |
291 |
double bigSigma = 0.0; |
611 |
mmeineke |
270 |
DirectionalAtom* dAtom; |
612 |
|
|
|
613 |
|
|
for( i=0; i<nAtoms; i++ ){ |
614 |
|
|
|
615 |
|
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
616 |
|
|
if( currentAtomType == NULL ){ |
617 |
|
|
sprintf( painCave.errMsg, |
618 |
|
|
"AtomType error, %s not found in force file.\n", |
619 |
|
|
the_atoms[i]->getType() ); |
620 |
|
|
painCave.isFatal = 1; |
621 |
|
|
simError(); |
622 |
|
|
} |
623 |
|
|
|
624 |
|
|
the_atoms[i]->setMass( currentAtomType->mass ); |
625 |
|
|
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
626 |
|
|
the_atoms[i]->setSigma( currentAtomType->sigma ); |
627 |
|
|
the_atoms[i]->setLJ(); |
628 |
|
|
|
629 |
mmeineke |
291 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
630 |
|
|
|
631 |
mmeineke |
270 |
if( currentAtomType->isDipole ){ |
632 |
|
|
if( the_atoms[i]->isDirectional() ){ |
633 |
|
|
|
634 |
|
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
635 |
|
|
dAtom->setMu( currentAtomType->dipole ); |
636 |
|
|
dAtom->setHasDipole( 1 ); |
637 |
|
|
dAtom->setJx( 0.0 ); |
638 |
|
|
dAtom->setJy( 0.0 ); |
639 |
|
|
dAtom->setJz( 0.0 ); |
640 |
|
|
|
641 |
|
|
if(!strcmp("SSD",the_atoms[i]->getType())){ |
642 |
|
|
dAtom->setI( waterI ); |
643 |
|
|
dAtom->setSSD( 1 ); |
644 |
|
|
} |
645 |
|
|
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
646 |
|
|
dAtom->setI( headI ); |
647 |
|
|
dAtom->setSSD( 0 ); |
648 |
|
|
} |
649 |
|
|
else{ |
650 |
|
|
sprintf(painCave.errMsg, |
651 |
|
|
"AtmType error, %s does not have a moment of inertia set.\n", |
652 |
|
|
the_atoms[i]->getType() ); |
653 |
|
|
painCave.isFatal = 1; |
654 |
|
|
simError(); |
655 |
|
|
} |
656 |
|
|
entry_plug->n_dipoles++; |
657 |
|
|
} |
658 |
|
|
else{ |
659 |
|
|
|
660 |
|
|
sprintf( painCave.errMsg, |
661 |
|
|
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
662 |
|
|
" orientation was specifed in the BASS file.\n", |
663 |
|
|
currentAtomType->name ); |
664 |
|
|
painCave.isFatal = 1; |
665 |
|
|
simError(); |
666 |
|
|
} |
667 |
|
|
} |
668 |
|
|
else{ |
669 |
|
|
if( the_atoms[i]->isDirectional() ){ |
670 |
|
|
sprintf( painCave.errMsg, |
671 |
|
|
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
672 |
|
|
"orientation in the BASS file, yet it is not a dipole.\n", |
673 |
|
|
currentAtomType->name); |
674 |
|
|
painCave.isFatal = 1; |
675 |
|
|
simError(); |
676 |
|
|
} |
677 |
|
|
} |
678 |
|
|
} |
679 |
|
|
|
680 |
mmeineke |
291 |
#ifdef IS_MPI |
681 |
|
|
double tempBig = bigSigma; |
682 |
|
|
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
683 |
|
|
#endif //is_mpi |
684 |
mmeineke |
270 |
|
685 |
mmeineke |
291 |
//calc rCut and rList |
686 |
|
|
|
687 |
|
|
entry_plug->rCut = 2.5 * bigSigma; |
688 |
|
|
|
689 |
|
|
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) |
690 |
|
|
entry_plug->rCut = entry_plug->box_x / 2.0; |
691 |
|
|
|
692 |
|
|
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) |
693 |
|
|
entry_plug->rCut = entry_plug->box_y / 2.0; |
694 |
|
|
|
695 |
|
|
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) |
696 |
|
|
entry_plug->rCut = entry_plug->box_z / 2.0; |
697 |
|
|
|
698 |
|
|
entry_plug->rList = entry_plug->rCut + 1.0; |
699 |
|
|
|
700 |
|
|
|
701 |
mmeineke |
270 |
// clean up the memory |
702 |
|
|
|
703 |
|
|
delete headAtomType; |
704 |
|
|
|
705 |
|
|
#ifdef IS_MPI |
706 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" ); |
707 |
|
|
MPIcheckPoint(); |
708 |
|
|
#endif // is_mpi |
709 |
|
|
|
710 |
mmeineke |
296 |
initFortran(); |
711 |
|
|
entry_plug->refreshSim(); |
712 |
|
|
|
713 |
mmeineke |
270 |
} |
714 |
|
|
|
715 |
|
|
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
716 |
|
|
|
717 |
|
|
class LinkedType { |
718 |
|
|
public: |
719 |
|
|
LinkedType(){ |
720 |
|
|
next = NULL; |
721 |
|
|
nameA[0] = '\0'; |
722 |
|
|
nameB[0] = '\0'; |
723 |
|
|
type[0] = '\0'; |
724 |
|
|
} |
725 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
726 |
|
|
|
727 |
|
|
LinkedType* find(char* key1, char* key2){ |
728 |
|
|
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
729 |
|
|
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
730 |
|
|
if( next != NULL ) return next->find(key1, key2); |
731 |
|
|
return NULL; |
732 |
|
|
} |
733 |
|
|
|
734 |
mmeineke |
291 |
|
735 |
mmeineke |
270 |
void add( bondStruct &info ){ |
736 |
mmeineke |
291 |
|
737 |
|
|
// check for duplicates |
738 |
|
|
int dup = 0; |
739 |
|
|
|
740 |
|
|
if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
741 |
|
|
if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
742 |
|
|
|
743 |
|
|
if(dup){ |
744 |
|
|
sprintf( painCave.errMsg, |
745 |
|
|
"Duplicate TraPPE_Ex bond type \"%s - %s\" found in " |
746 |
|
|
"the TraPPE_ExFF param file./n", |
747 |
|
|
nameA, nameB ); |
748 |
|
|
painCave.isFatal = 1; |
749 |
|
|
simError(); |
750 |
|
|
} |
751 |
|
|
|
752 |
|
|
|
753 |
mmeineke |
270 |
if( next != NULL ) next->add(info); |
754 |
|
|
else{ |
755 |
|
|
next = new LinkedType(); |
756 |
|
|
strcpy(next->nameA, info.nameA); |
757 |
|
|
strcpy(next->nameB, info.nameB); |
758 |
|
|
strcpy(next->type, info.type); |
759 |
|
|
next->d0 = info.d0; |
760 |
|
|
} |
761 |
|
|
} |
762 |
|
|
|
763 |
mmeineke |
291 |
#ifdef IS_MPI |
764 |
mmeineke |
270 |
void duplicate( bondStruct &info ){ |
765 |
|
|
strcpy(info.nameA, nameA); |
766 |
|
|
strcpy(info.nameB, nameB); |
767 |
|
|
strcpy(info.type, type); |
768 |
|
|
info.d0 = d0; |
769 |
|
|
info.last = 0; |
770 |
|
|
} |
771 |
|
|
|
772 |
|
|
|
773 |
|
|
#endif |
774 |
|
|
|
775 |
|
|
char nameA[15]; |
776 |
|
|
char nameB[15]; |
777 |
|
|
char type[30]; |
778 |
|
|
double d0; |
779 |
|
|
|
780 |
|
|
LinkedType* next; |
781 |
|
|
}; |
782 |
|
|
|
783 |
|
|
|
784 |
|
|
|
785 |
|
|
LinkedType* headBondType; |
786 |
|
|
LinkedType* currentBondType; |
787 |
|
|
bondStruct info; |
788 |
|
|
info.last = 1; // initialize last to have the last set. |
789 |
|
|
// if things go well, last will be set to 0 |
790 |
|
|
|
791 |
|
|
SRI **the_sris; |
792 |
|
|
Atom** the_atoms; |
793 |
|
|
int nBonds; |
794 |
|
|
the_sris = entry_plug->sr_interactions; |
795 |
|
|
the_atoms = entry_plug->atoms; |
796 |
|
|
nBonds = entry_plug->n_bonds; |
797 |
|
|
|
798 |
mmeineke |
291 |
int i, a, b; |
799 |
|
|
char* atomA; |
800 |
|
|
char* atomB; |
801 |
mmeineke |
270 |
|
802 |
|
|
#ifdef IS_MPI |
803 |
|
|
if( worldRank == 0 ){ |
804 |
|
|
#endif |
805 |
|
|
|
806 |
|
|
// read in the bond types. |
807 |
|
|
|
808 |
|
|
headBondType = new LinkedType; |
809 |
|
|
|
810 |
mmeineke |
291 |
fastForward( "BondTypes", "initializeBonds" ); |
811 |
|
|
|
812 |
|
|
// we are now at the bondTypes section |
813 |
|
|
|
814 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
815 |
mmeineke |
270 |
lineNum++; |
816 |
|
|
|
817 |
|
|
|
818 |
mmeineke |
291 |
// read a line, and start parseing out the atom types |
819 |
|
|
|
820 |
mmeineke |
270 |
if( eof_test == NULL ){ |
821 |
|
|
sprintf( painCave.errMsg, |
822 |
mmeineke |
291 |
"Error in reading bonds from force file at line %d.\n", |
823 |
mmeineke |
270 |
lineNum ); |
824 |
|
|
painCave.isFatal = 1; |
825 |
|
|
simError(); |
826 |
|
|
} |
827 |
|
|
|
828 |
mmeineke |
291 |
// stop reading at end of file, or at next section |
829 |
mmeineke |
270 |
while( readLine[0] != '#' && eof_test != NULL ){ |
830 |
mmeineke |
291 |
|
831 |
|
|
// toss comment lines |
832 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
833 |
|
|
|
834 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
835 |
|
|
if( parseBond( readLine, lineNum, info ) ){ |
836 |
|
|
headBondType->add( info ); |
837 |
mmeineke |
270 |
} |
838 |
|
|
} |
839 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
840 |
|
|
lineNum++; |
841 |
|
|
} |
842 |
mmeineke |
291 |
|
843 |
mmeineke |
270 |
#ifdef IS_MPI |
844 |
|
|
|
845 |
|
|
// send out the linked list to all the other processes |
846 |
|
|
|
847 |
|
|
sprintf( checkPointMsg, |
848 |
|
|
"TraPPE_Ex bond structures read successfully." ); |
849 |
|
|
MPIcheckPoint(); |
850 |
|
|
|
851 |
|
|
currentBondType = headBondType; |
852 |
|
|
while( currentBondType != NULL ){ |
853 |
|
|
currentBondType->duplicate( info ); |
854 |
|
|
sendFrcStruct( &info, mpiBondStructType ); |
855 |
|
|
currentBondType = currentBondType->next; |
856 |
|
|
} |
857 |
|
|
info.last = 1; |
858 |
|
|
sendFrcStruct( &info, mpiBondStructType ); |
859 |
|
|
|
860 |
|
|
} |
861 |
|
|
|
862 |
|
|
else{ |
863 |
|
|
|
864 |
|
|
// listen for node 0 to send out the force params |
865 |
|
|
|
866 |
|
|
MPIcheckPoint(); |
867 |
|
|
|
868 |
|
|
headBondType = new LinkedType; |
869 |
|
|
recieveFrcStruct( &info, mpiBondStructType ); |
870 |
|
|
while( !info.last ){ |
871 |
|
|
|
872 |
|
|
headBondType->add( info ); |
873 |
|
|
recieveFrcStruct( &info, mpiBondStructType ); |
874 |
|
|
} |
875 |
|
|
} |
876 |
|
|
#endif // is_mpi |
877 |
|
|
|
878 |
|
|
|
879 |
|
|
// initialize the Bonds |
880 |
|
|
|
881 |
|
|
|
882 |
|
|
for( i=0; i<nBonds; i++ ){ |
883 |
|
|
|
884 |
|
|
a = the_bonds[i].a; |
885 |
|
|
b = the_bonds[i].b; |
886 |
|
|
|
887 |
|
|
atomA = the_atoms[a]->getType(); |
888 |
|
|
atomB = the_atoms[b]->getType(); |
889 |
|
|
currentBondType = headBondType->find( atomA, atomB ); |
890 |
|
|
if( currentBondType == NULL ){ |
891 |
|
|
sprintf( painCave.errMsg, |
892 |
|
|
"BondType error, %s - %s not found in force file.\n", |
893 |
|
|
atomA, atomB ); |
894 |
|
|
painCave.isFatal = 1; |
895 |
|
|
simError(); |
896 |
|
|
} |
897 |
|
|
|
898 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
899 |
|
|
|
900 |
|
|
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
901 |
|
|
*the_atoms[b], |
902 |
|
|
currentBondType->d0 ); |
903 |
|
|
entry_plug->n_constraints++; |
904 |
|
|
} |
905 |
|
|
} |
906 |
|
|
|
907 |
|
|
|
908 |
|
|
// clean up the memory |
909 |
|
|
|
910 |
|
|
delete headBondType; |
911 |
|
|
|
912 |
|
|
#ifdef IS_MPI |
913 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" ); |
914 |
|
|
MPIcheckPoint(); |
915 |
|
|
#endif // is_mpi |
916 |
|
|
|
917 |
|
|
} |
918 |
|
|
|
919 |
|
|
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
920 |
|
|
|
921 |
|
|
class LinkedType { |
922 |
|
|
public: |
923 |
|
|
LinkedType(){ |
924 |
|
|
next = NULL; |
925 |
|
|
nameA[0] = '\0'; |
926 |
|
|
nameB[0] = '\0'; |
927 |
|
|
nameC[0] = '\0'; |
928 |
|
|
type[0] = '\0'; |
929 |
|
|
} |
930 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
931 |
|
|
|
932 |
|
|
LinkedType* find( char* key1, char* key2, char* key3 ){ |
933 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
934 |
|
|
&& !strcmp( nameC, key3 ) ) return this; |
935 |
|
|
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
936 |
|
|
&& !strcmp( nameC, key1 ) ) return this; |
937 |
|
|
if( next != NULL ) return next->find(key1, key2, key3); |
938 |
|
|
return NULL; |
939 |
|
|
} |
940 |
|
|
|
941 |
mmeineke |
291 |
void add( bendStruct &info ){ |
942 |
mmeineke |
270 |
|
943 |
mmeineke |
291 |
// check for duplicates |
944 |
|
|
int dup = 0; |
945 |
|
|
|
946 |
|
|
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
947 |
|
|
&& !strcmp( nameC, info.nameC ) ) dup = 1; |
948 |
|
|
if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
949 |
|
|
&& !strcmp( nameC, info.nameA ) ) dup = 1; |
950 |
|
|
|
951 |
|
|
if(dup){ |
952 |
|
|
sprintf( painCave.errMsg, |
953 |
|
|
"Duplicate TraPPE_Ex bend type \"%s - %s - %s\" found in " |
954 |
|
|
"the TraPPE_ExFF param file./n", |
955 |
|
|
nameA, nameB, nameC ); |
956 |
|
|
painCave.isFatal = 1; |
957 |
|
|
simError(); |
958 |
|
|
} |
959 |
|
|
|
960 |
mmeineke |
270 |
if( next != NULL ) next->add(info); |
961 |
|
|
else{ |
962 |
|
|
next = new LinkedType(); |
963 |
|
|
strcpy(next->nameA, info.nameA); |
964 |
|
|
strcpy(next->nameB, info.nameB); |
965 |
|
|
strcpy(next->nameC, info.nameC); |
966 |
|
|
strcpy(next->type, info.type); |
967 |
|
|
next->k1 = info.k1; |
968 |
|
|
next->k2 = info.k2; |
969 |
|
|
next->k3 = info.k3; |
970 |
|
|
next->t0 = info.t0; |
971 |
|
|
} |
972 |
|
|
} |
973 |
mmeineke |
291 |
|
974 |
|
|
#ifdef IS_MPI |
975 |
|
|
|
976 |
mmeineke |
270 |
void duplicate( bendStruct &info ){ |
977 |
|
|
strcpy(info.nameA, nameA); |
978 |
|
|
strcpy(info.nameB, nameB); |
979 |
|
|
strcpy(info.nameC, nameC); |
980 |
|
|
strcpy(info.type, type); |
981 |
|
|
info.k1 = k1; |
982 |
|
|
info.k2 = k2; |
983 |
|
|
info.k3 = k3; |
984 |
|
|
info.t0 = t0; |
985 |
|
|
info.last = 0; |
986 |
|
|
} |
987 |
|
|
|
988 |
|
|
#endif // is_mpi |
989 |
|
|
|
990 |
|
|
char nameA[15]; |
991 |
|
|
char nameB[15]; |
992 |
|
|
char nameC[15]; |
993 |
|
|
char type[30]; |
994 |
|
|
double k1, k2, k3, t0; |
995 |
|
|
|
996 |
|
|
LinkedType* next; |
997 |
|
|
}; |
998 |
|
|
|
999 |
|
|
LinkedType* headBendType; |
1000 |
|
|
LinkedType* currentBendType; |
1001 |
|
|
bendStruct info; |
1002 |
|
|
info.last = 1; // initialize last to have the last set. |
1003 |
|
|
// if things go well, last will be set to 0 |
1004 |
|
|
|
1005 |
|
|
QuadraticBend* qBend; |
1006 |
mmeineke |
311 |
GhostBend* gBend; |
1007 |
mmeineke |
270 |
SRI **the_sris; |
1008 |
|
|
Atom** the_atoms; |
1009 |
|
|
int nBends; |
1010 |
|
|
the_sris = entry_plug->sr_interactions; |
1011 |
|
|
the_atoms = entry_plug->atoms; |
1012 |
|
|
nBends = entry_plug->n_bends; |
1013 |
|
|
|
1014 |
mmeineke |
291 |
int i, a, b, c; |
1015 |
|
|
char* atomA; |
1016 |
|
|
char* atomB; |
1017 |
|
|
char* atomC; |
1018 |
mmeineke |
270 |
|
1019 |
mmeineke |
291 |
|
1020 |
mmeineke |
270 |
#ifdef IS_MPI |
1021 |
|
|
if( worldRank == 0 ){ |
1022 |
|
|
#endif |
1023 |
|
|
|
1024 |
|
|
// read in the bend types. |
1025 |
|
|
|
1026 |
|
|
headBendType = new LinkedType; |
1027 |
|
|
|
1028 |
mmeineke |
291 |
fastForward( "BendTypes", "initializeBends" ); |
1029 |
mmeineke |
270 |
|
1030 |
mmeineke |
291 |
// we are now at the bendTypes section |
1031 |
mmeineke |
270 |
|
1032 |
mmeineke |
291 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1033 |
|
|
lineNum++; |
1034 |
|
|
|
1035 |
|
|
// read a line, and start parseing out the bend types |
1036 |
mmeineke |
270 |
|
1037 |
|
|
if( eof_test == NULL ){ |
1038 |
|
|
sprintf( painCave.errMsg, |
1039 |
mmeineke |
291 |
"Error in reading bends from force file at line %d.\n", |
1040 |
mmeineke |
270 |
lineNum ); |
1041 |
|
|
painCave.isFatal = 1; |
1042 |
|
|
simError(); |
1043 |
|
|
} |
1044 |
mmeineke |
291 |
|
1045 |
|
|
// stop reading at end of file, or at next section |
1046 |
mmeineke |
270 |
while( readLine[0] != '#' && eof_test != NULL ){ |
1047 |
mmeineke |
291 |
|
1048 |
|
|
// toss comment lines |
1049 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
1050 |
|
|
|
1051 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
1052 |
|
|
if( parseBend( readLine, lineNum, info ) ){ |
1053 |
|
|
headBendType->add( info ); |
1054 |
mmeineke |
270 |
} |
1055 |
|
|
} |
1056 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1057 |
|
|
lineNum++; |
1058 |
|
|
} |
1059 |
mmeineke |
291 |
|
1060 |
mmeineke |
270 |
#ifdef IS_MPI |
1061 |
|
|
|
1062 |
|
|
// send out the linked list to all the other processes |
1063 |
|
|
|
1064 |
|
|
sprintf( checkPointMsg, |
1065 |
|
|
"TraPPE_Ex bend structures read successfully." ); |
1066 |
|
|
MPIcheckPoint(); |
1067 |
|
|
|
1068 |
|
|
currentBendType = headBendType; |
1069 |
|
|
while( currentBendType != NULL ){ |
1070 |
|
|
currentBendType->duplicate( info ); |
1071 |
|
|
sendFrcStruct( &info, mpiBendStructType ); |
1072 |
|
|
currentBendType = currentBendType->next; |
1073 |
|
|
} |
1074 |
|
|
info.last = 1; |
1075 |
|
|
sendFrcStruct( &info, mpiBendStructType ); |
1076 |
|
|
|
1077 |
|
|
} |
1078 |
|
|
|
1079 |
|
|
else{ |
1080 |
|
|
|
1081 |
|
|
// listen for node 0 to send out the force params |
1082 |
|
|
|
1083 |
|
|
MPIcheckPoint(); |
1084 |
|
|
|
1085 |
|
|
headBendType = new LinkedType; |
1086 |
|
|
recieveFrcStruct( &info, mpiBendStructType ); |
1087 |
|
|
while( !info.last ){ |
1088 |
|
|
|
1089 |
|
|
headBendType->add( info ); |
1090 |
|
|
recieveFrcStruct( &info, mpiBendStructType ); |
1091 |
|
|
} |
1092 |
|
|
} |
1093 |
|
|
#endif // is_mpi |
1094 |
|
|
|
1095 |
|
|
// initialize the Bends |
1096 |
mmeineke |
291 |
|
1097 |
|
|
int index; |
1098 |
mmeineke |
270 |
|
1099 |
|
|
for( i=0; i<nBends; i++ ){ |
1100 |
|
|
|
1101 |
|
|
a = the_bends[i].a; |
1102 |
|
|
b = the_bends[i].b; |
1103 |
|
|
c = the_bends[i].c; |
1104 |
|
|
|
1105 |
|
|
atomA = the_atoms[a]->getType(); |
1106 |
|
|
atomB = the_atoms[b]->getType(); |
1107 |
mmeineke |
311 |
|
1108 |
|
|
if( the_bends[i].isGhost ) atomC = "GHOST"; |
1109 |
|
|
else atomC = the_atoms[c]->getType(); |
1110 |
|
|
|
1111 |
mmeineke |
270 |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1112 |
|
|
if( currentBendType == NULL ){ |
1113 |
|
|
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1114 |
|
|
" in force file.\n", |
1115 |
|
|
atomA, atomB, atomC ); |
1116 |
|
|
painCave.isFatal = 1; |
1117 |
|
|
simError(); |
1118 |
|
|
} |
1119 |
|
|
|
1120 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1121 |
|
|
|
1122 |
|
|
index = i + entry_plug->n_bonds; |
1123 |
mmeineke |
311 |
|
1124 |
|
|
if( the_bends[i].isGhost){ |
1125 |
|
|
|
1126 |
|
|
if( the_bends[i].ghost == b ){ |
1127 |
|
|
// do nothing |
1128 |
|
|
} |
1129 |
|
|
else if( the_bends[i].ghost == a ){ |
1130 |
|
|
c = a; |
1131 |
|
|
a = b; |
1132 |
|
|
b = a; |
1133 |
|
|
} |
1134 |
|
|
else{ |
1135 |
|
|
sprintf( painCave.errMsg, |
1136 |
|
|
"BendType error, %s - %s - %s,\n" |
1137 |
|
|
" --> central atom is not " |
1138 |
|
|
"correctly identified with the " |
1139 |
|
|
"\"ghostVectorSource = \" tag.\n", |
1140 |
|
|
atomA, atomB, atomC ); |
1141 |
|
|
painCave.isFatal = 1; |
1142 |
|
|
simError(); |
1143 |
|
|
} |
1144 |
|
|
|
1145 |
|
|
gBend = new GhostBend( *the_atoms[a], |
1146 |
|
|
*the_atoms[b] ); |
1147 |
|
|
gBend->setConstants( currentBendType->k1, |
1148 |
|
|
currentBendType->k2, |
1149 |
|
|
currentBendType->k3, |
1150 |
|
|
currentBendType->t0 ); |
1151 |
|
|
the_sris[index] = gBend; |
1152 |
|
|
} |
1153 |
|
|
else{ |
1154 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
1155 |
|
|
*the_atoms[b], |
1156 |
|
|
*the_atoms[c] ); |
1157 |
|
|
qBend->setConstants( currentBendType->k1, |
1158 |
|
|
currentBendType->k2, |
1159 |
|
|
currentBendType->k3, |
1160 |
|
|
currentBendType->t0 ); |
1161 |
|
|
the_sris[index] = qBend; |
1162 |
|
|
} |
1163 |
mmeineke |
270 |
} |
1164 |
|
|
} |
1165 |
|
|
|
1166 |
|
|
|
1167 |
|
|
// clean up the memory |
1168 |
|
|
|
1169 |
|
|
delete headBendType; |
1170 |
|
|
|
1171 |
|
|
#ifdef IS_MPI |
1172 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" ); |
1173 |
|
|
MPIcheckPoint(); |
1174 |
|
|
#endif // is_mpi |
1175 |
|
|
|
1176 |
|
|
} |
1177 |
|
|
|
1178 |
|
|
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
1179 |
|
|
|
1180 |
|
|
class LinkedType { |
1181 |
|
|
public: |
1182 |
|
|
LinkedType(){ |
1183 |
|
|
next = NULL; |
1184 |
|
|
nameA[0] = '\0'; |
1185 |
|
|
nameB[0] = '\0'; |
1186 |
|
|
nameC[0] = '\0'; |
1187 |
|
|
type[0] = '\0'; |
1188 |
|
|
} |
1189 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
1190 |
|
|
|
1191 |
|
|
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
1192 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
1193 |
|
|
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
1194 |
|
|
|
1195 |
|
|
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
1196 |
mmeineke |
291 |
!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
1197 |
mmeineke |
270 |
|
1198 |
|
|
if( next != NULL ) return next->find(key1, key2, key3, key4); |
1199 |
|
|
return NULL; |
1200 |
|
|
} |
1201 |
|
|
|
1202 |
|
|
void add( torsionStruct &info ){ |
1203 |
mmeineke |
291 |
|
1204 |
|
|
// check for duplicates |
1205 |
|
|
int dup = 0; |
1206 |
|
|
|
1207 |
|
|
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
1208 |
|
|
!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
1209 |
|
|
|
1210 |
|
|
if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
1211 |
|
|
!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
1212 |
|
|
|
1213 |
|
|
if(dup){ |
1214 |
|
|
sprintf( painCave.errMsg, |
1215 |
|
|
"Duplicate TraPPE_Ex torsion type \"%s - %s - %s - %s\" found in " |
1216 |
|
|
"the TraPPE_ExFF param file./n", nameA, nameB, nameC, nameD ); |
1217 |
|
|
painCave.isFatal = 1; |
1218 |
|
|
simError(); |
1219 |
|
|
} |
1220 |
|
|
|
1221 |
mmeineke |
270 |
if( next != NULL ) next->add(info); |
1222 |
|
|
else{ |
1223 |
|
|
next = new LinkedType(); |
1224 |
|
|
strcpy(next->nameA, info.nameA); |
1225 |
|
|
strcpy(next->nameB, info.nameB); |
1226 |
|
|
strcpy(next->nameC, info.nameC); |
1227 |
|
|
strcpy(next->type, info.type); |
1228 |
|
|
next->k1 = info.k1; |
1229 |
|
|
next->k2 = info.k2; |
1230 |
|
|
next->k3 = info.k3; |
1231 |
|
|
next->k4 = info.k4; |
1232 |
|
|
} |
1233 |
|
|
} |
1234 |
mmeineke |
291 |
|
1235 |
|
|
#ifdef IS_MPI |
1236 |
mmeineke |
270 |
|
1237 |
|
|
void duplicate( torsionStruct &info ){ |
1238 |
|
|
strcpy(info.nameA, nameA); |
1239 |
|
|
strcpy(info.nameB, nameB); |
1240 |
|
|
strcpy(info.nameC, nameC); |
1241 |
|
|
strcpy(info.nameD, nameD); |
1242 |
|
|
strcpy(info.type, type); |
1243 |
|
|
info.k1 = k1; |
1244 |
|
|
info.k2 = k2; |
1245 |
|
|
info.k3 = k3; |
1246 |
|
|
info.k4 = k4; |
1247 |
|
|
info.last = 0; |
1248 |
|
|
} |
1249 |
|
|
|
1250 |
|
|
#endif |
1251 |
|
|
|
1252 |
|
|
char nameA[15]; |
1253 |
|
|
char nameB[15]; |
1254 |
|
|
char nameC[15]; |
1255 |
|
|
char nameD[15]; |
1256 |
|
|
char type[30]; |
1257 |
|
|
double k1, k2, k3, k4; |
1258 |
|
|
|
1259 |
|
|
LinkedType* next; |
1260 |
|
|
}; |
1261 |
|
|
|
1262 |
|
|
LinkedType* headTorsionType; |
1263 |
|
|
LinkedType* currentTorsionType; |
1264 |
|
|
torsionStruct info; |
1265 |
|
|
info.last = 1; // initialize last to have the last set. |
1266 |
|
|
// if things go well, last will be set to 0 |
1267 |
|
|
|
1268 |
|
|
int i, a, b, c, d, index; |
1269 |
|
|
char* atomA; |
1270 |
|
|
char* atomB; |
1271 |
|
|
char* atomC; |
1272 |
|
|
char* atomD; |
1273 |
|
|
CubicTorsion* cTors; |
1274 |
|
|
|
1275 |
|
|
SRI **the_sris; |
1276 |
|
|
Atom** the_atoms; |
1277 |
|
|
int nTorsions; |
1278 |
|
|
the_sris = entry_plug->sr_interactions; |
1279 |
|
|
the_atoms = entry_plug->atoms; |
1280 |
|
|
nTorsions = entry_plug->n_torsions; |
1281 |
|
|
|
1282 |
|
|
#ifdef IS_MPI |
1283 |
|
|
if( worldRank == 0 ){ |
1284 |
|
|
#endif |
1285 |
|
|
|
1286 |
|
|
// read in the torsion types. |
1287 |
|
|
|
1288 |
|
|
headTorsionType = new LinkedType; |
1289 |
mmeineke |
291 |
|
1290 |
|
|
fastForward( "TorsionTypes", "initializeTorsions" ); |
1291 |
mmeineke |
270 |
|
1292 |
mmeineke |
291 |
// we are now at the torsionTypes section |
1293 |
mmeineke |
270 |
|
1294 |
mmeineke |
291 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1295 |
|
|
lineNum++; |
1296 |
mmeineke |
270 |
|
1297 |
mmeineke |
291 |
|
1298 |
|
|
// read a line, and start parseing out the atom types |
1299 |
mmeineke |
270 |
|
1300 |
|
|
if( eof_test == NULL ){ |
1301 |
|
|
sprintf( painCave.errMsg, |
1302 |
mmeineke |
291 |
"Error in reading torsions from force file at line %d.\n", |
1303 |
mmeineke |
270 |
lineNum ); |
1304 |
|
|
painCave.isFatal = 1; |
1305 |
|
|
simError(); |
1306 |
|
|
} |
1307 |
mmeineke |
291 |
|
1308 |
|
|
// stop reading at end of file, or at next section |
1309 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
1310 |
mmeineke |
270 |
|
1311 |
mmeineke |
291 |
// toss comment lines |
1312 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
1313 |
|
|
|
1314 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
1315 |
|
|
if( parseTorsion( readLine, lineNum, info ) ){ |
1316 |
|
|
headTorsionType->add( info ); |
1317 |
mmeineke |
270 |
} |
1318 |
|
|
} |
1319 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1320 |
|
|
lineNum++; |
1321 |
|
|
} |
1322 |
|
|
|
1323 |
|
|
#ifdef IS_MPI |
1324 |
|
|
|
1325 |
|
|
// send out the linked list to all the other processes |
1326 |
|
|
|
1327 |
|
|
sprintf( checkPointMsg, |
1328 |
|
|
"TraPPE_Ex torsion structures read successfully." ); |
1329 |
|
|
MPIcheckPoint(); |
1330 |
|
|
|
1331 |
|
|
currentTorsionType = headTorsionType; |
1332 |
|
|
while( currentTorsionType != NULL ){ |
1333 |
|
|
currentTorsionType->duplicate( info ); |
1334 |
|
|
sendFrcStruct( &info, mpiTorsionStructType ); |
1335 |
|
|
currentTorsionType = currentTorsionType->next; |
1336 |
|
|
} |
1337 |
|
|
info.last = 1; |
1338 |
|
|
sendFrcStruct( &info, mpiTorsionStructType ); |
1339 |
|
|
|
1340 |
|
|
} |
1341 |
|
|
|
1342 |
|
|
else{ |
1343 |
|
|
|
1344 |
|
|
// listen for node 0 to send out the force params |
1345 |
|
|
|
1346 |
|
|
MPIcheckPoint(); |
1347 |
|
|
|
1348 |
|
|
headTorsionType = new LinkedType; |
1349 |
|
|
recieveFrcStruct( &info, mpiTorsionStructType ); |
1350 |
|
|
while( !info.last ){ |
1351 |
|
|
|
1352 |
|
|
headTorsionType->add( info ); |
1353 |
|
|
recieveFrcStruct( &info, mpiTorsionStructType ); |
1354 |
|
|
} |
1355 |
|
|
} |
1356 |
|
|
#endif // is_mpi |
1357 |
|
|
|
1358 |
|
|
// initialize the Torsions |
1359 |
|
|
|
1360 |
|
|
for( i=0; i<nTorsions; i++ ){ |
1361 |
|
|
|
1362 |
|
|
a = the_torsions[i].a; |
1363 |
|
|
b = the_torsions[i].b; |
1364 |
|
|
c = the_torsions[i].c; |
1365 |
|
|
d = the_torsions[i].d; |
1366 |
|
|
|
1367 |
|
|
atomA = the_atoms[a]->getType(); |
1368 |
|
|
atomB = the_atoms[b]->getType(); |
1369 |
|
|
atomC = the_atoms[c]->getType(); |
1370 |
|
|
atomD = the_atoms[d]->getType(); |
1371 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1372 |
|
|
if( currentTorsionType == NULL ){ |
1373 |
|
|
sprintf( painCave.errMsg, |
1374 |
|
|
"TorsionType error, %s - %s - %s - %s not found" |
1375 |
|
|
" in force file.\n", |
1376 |
|
|
atomA, atomB, atomC, atomD ); |
1377 |
|
|
painCave.isFatal = 1; |
1378 |
|
|
simError(); |
1379 |
|
|
} |
1380 |
|
|
|
1381 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1382 |
|
|
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
1383 |
|
|
|
1384 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1385 |
|
|
*the_atoms[c], *the_atoms[d] ); |
1386 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1387 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
1388 |
|
|
the_sris[index] = cTors; |
1389 |
|
|
} |
1390 |
|
|
} |
1391 |
|
|
|
1392 |
|
|
|
1393 |
|
|
// clean up the memory |
1394 |
|
|
|
1395 |
|
|
delete headTorsionType; |
1396 |
|
|
|
1397 |
|
|
#ifdef IS_MPI |
1398 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" ); |
1399 |
|
|
MPIcheckPoint(); |
1400 |
|
|
#endif // is_mpi |
1401 |
|
|
|
1402 |
|
|
} |
1403 |
mmeineke |
291 |
|
1404 |
|
|
void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){ |
1405 |
|
|
|
1406 |
|
|
int foundText = 0; |
1407 |
|
|
char* the_token; |
1408 |
|
|
|
1409 |
|
|
rewind( frcFile ); |
1410 |
|
|
lineNum = 0; |
1411 |
|
|
|
1412 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1413 |
|
|
lineNum++; |
1414 |
|
|
if( eof_test == NULL ){ |
1415 |
|
|
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
1416 |
|
|
" file is empty.\n", |
1417 |
|
|
searchOwner ); |
1418 |
|
|
painCave.isFatal = 1; |
1419 |
|
|
simError(); |
1420 |
|
|
} |
1421 |
|
|
|
1422 |
|
|
|
1423 |
|
|
while( !foundText ){ |
1424 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
1425 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1426 |
|
|
lineNum++; |
1427 |
|
|
} |
1428 |
|
|
if( eof_test == NULL ){ |
1429 |
|
|
sprintf( painCave.errMsg, |
1430 |
|
|
"Error fast forwarding force file for %s at " |
1431 |
|
|
"line %d: file ended unexpectedly.\n", |
1432 |
|
|
searchOwner, |
1433 |
|
|
lineNum ); |
1434 |
|
|
painCave.isFatal = 1; |
1435 |
|
|
simError(); |
1436 |
|
|
} |
1437 |
|
|
|
1438 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
1439 |
|
|
foundText = !strcmp( stopText, the_token ); |
1440 |
|
|
|
1441 |
|
|
if( !foundText ){ |
1442 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1443 |
|
|
lineNum++; |
1444 |
|
|
|
1445 |
|
|
if( eof_test == NULL ){ |
1446 |
|
|
sprintf( painCave.errMsg, |
1447 |
|
|
"Error fast forwarding force file for %s at " |
1448 |
|
|
"line %d: file ended unexpectedly.\n", |
1449 |
|
|
searchOwner, |
1450 |
|
|
lineNum ); |
1451 |
|
|
painCave.isFatal = 1; |
1452 |
|
|
simError(); |
1453 |
|
|
} |
1454 |
|
|
} |
1455 |
|
|
} |
1456 |
|
|
} |
1457 |
|
|
|
1458 |
|
|
|
1459 |
|
|
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1460 |
|
|
|
1461 |
|
|
char* the_token; |
1462 |
|
|
|
1463 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1464 |
|
|
if( the_token != NULL ){ |
1465 |
|
|
|
1466 |
|
|
strcpy( info.name, the_token ); |
1467 |
|
|
|
1468 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1469 |
|
|
sprintf( painCave.errMsg, |
1470 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1471 |
|
|
painCave.isFatal = 1; |
1472 |
|
|
simError(); |
1473 |
|
|
} |
1474 |
|
|
|
1475 |
|
|
info.isDipole = atoi( the_token ); |
1476 |
|
|
|
1477 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1478 |
|
|
sprintf( painCave.errMsg, |
1479 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1480 |
|
|
painCave.isFatal = 1; |
1481 |
|
|
simError(); |
1482 |
|
|
} |
1483 |
|
|
|
1484 |
|
|
info.isSSD = atoi( the_token ); |
1485 |
|
|
|
1486 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1487 |
|
|
sprintf( painCave.errMsg, |
1488 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1489 |
|
|
painCave.isFatal = 1; |
1490 |
|
|
simError(); |
1491 |
|
|
} |
1492 |
|
|
|
1493 |
|
|
info.mass = atof( the_token ); |
1494 |
|
|
|
1495 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1496 |
|
|
sprintf( painCave.errMsg, |
1497 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1498 |
|
|
painCave.isFatal = 1; |
1499 |
|
|
simError(); |
1500 |
|
|
} |
1501 |
|
|
|
1502 |
|
|
info.epslon = atof( the_token ); |
1503 |
|
|
|
1504 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1505 |
|
|
sprintf( painCave.errMsg, |
1506 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1507 |
|
|
painCave.isFatal = 1; |
1508 |
|
|
simError(); |
1509 |
|
|
} |
1510 |
|
|
|
1511 |
|
|
info.sigma = atof( the_token ); |
1512 |
|
|
|
1513 |
|
|
if( info.isDipole ){ |
1514 |
|
|
|
1515 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1516 |
|
|
sprintf( painCave.errMsg, |
1517 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1518 |
|
|
painCave.isFatal = 1; |
1519 |
|
|
simError(); |
1520 |
|
|
} |
1521 |
|
|
|
1522 |
|
|
info.dipole = atof( the_token ); |
1523 |
|
|
} |
1524 |
|
|
else info.dipole = 0.0; |
1525 |
|
|
|
1526 |
|
|
if( info.isSSD ){ |
1527 |
|
|
|
1528 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1529 |
|
|
sprintf( painCave.errMsg, |
1530 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1531 |
|
|
painCave.isFatal = 1; |
1532 |
|
|
simError(); |
1533 |
|
|
} |
1534 |
|
|
|
1535 |
|
|
info.w0 = atof( the_token ); |
1536 |
|
|
|
1537 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1538 |
|
|
sprintf( painCave.errMsg, |
1539 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1540 |
|
|
painCave.isFatal = 1; |
1541 |
|
|
simError(); |
1542 |
|
|
} |
1543 |
|
|
|
1544 |
|
|
info.v0 = atof( the_token ); |
1545 |
|
|
} |
1546 |
|
|
else info.v0 = info.w0 = 0.0; |
1547 |
|
|
|
1548 |
|
|
return 1; |
1549 |
|
|
} |
1550 |
|
|
else return 0; |
1551 |
|
|
} |
1552 |
|
|
|
1553 |
|
|
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1554 |
|
|
|
1555 |
|
|
char* the_token; |
1556 |
|
|
|
1557 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1558 |
|
|
if( the_token != NULL ){ |
1559 |
|
|
|
1560 |
|
|
strcpy( info.nameA, the_token ); |
1561 |
|
|
|
1562 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1563 |
|
|
sprintf( painCave.errMsg, |
1564 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1565 |
|
|
painCave.isFatal = 1; |
1566 |
|
|
simError(); |
1567 |
|
|
} |
1568 |
|
|
|
1569 |
|
|
strcpy( info.nameB, the_token ); |
1570 |
|
|
|
1571 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1572 |
|
|
sprintf( painCave.errMsg, |
1573 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1574 |
|
|
painCave.isFatal = 1; |
1575 |
|
|
simError(); |
1576 |
|
|
} |
1577 |
|
|
|
1578 |
|
|
strcpy( info.type, the_token ); |
1579 |
|
|
|
1580 |
|
|
if( !strcmp( info.type, "fixed" ) ){ |
1581 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1582 |
|
|
sprintf( painCave.errMsg, |
1583 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1584 |
|
|
painCave.isFatal = 1; |
1585 |
|
|
simError(); |
1586 |
|
|
} |
1587 |
|
|
|
1588 |
|
|
info.d0 = atof( the_token ); |
1589 |
|
|
} |
1590 |
|
|
else{ |
1591 |
|
|
sprintf( painCave.errMsg, |
1592 |
|
|
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
1593 |
|
|
info.type, |
1594 |
|
|
lineNum ); |
1595 |
|
|
painCave.isFatal = 1; |
1596 |
|
|
simError(); |
1597 |
|
|
} |
1598 |
|
|
|
1599 |
|
|
return 1; |
1600 |
|
|
} |
1601 |
|
|
else return 0; |
1602 |
|
|
} |
1603 |
|
|
|
1604 |
|
|
|
1605 |
|
|
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1606 |
|
|
|
1607 |
|
|
char* the_token; |
1608 |
|
|
|
1609 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1610 |
|
|
if( the_token != NULL ){ |
1611 |
|
|
|
1612 |
|
|
strcpy( info.nameA, the_token ); |
1613 |
|
|
|
1614 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1615 |
|
|
sprintf( painCave.errMsg, |
1616 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1617 |
|
|
painCave.isFatal = 1; |
1618 |
|
|
simError(); |
1619 |
|
|
} |
1620 |
|
|
|
1621 |
|
|
strcpy( info.nameB, the_token ); |
1622 |
|
|
|
1623 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1624 |
|
|
sprintf( painCave.errMsg, |
1625 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1626 |
|
|
painCave.isFatal = 1; |
1627 |
|
|
simError(); |
1628 |
|
|
} |
1629 |
|
|
|
1630 |
|
|
strcpy( info.nameC, the_token ); |
1631 |
|
|
|
1632 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1633 |
|
|
sprintf( painCave.errMsg, |
1634 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1635 |
|
|
painCave.isFatal = 1; |
1636 |
|
|
simError(); |
1637 |
|
|
} |
1638 |
|
|
|
1639 |
|
|
strcpy( info.type, the_token ); |
1640 |
|
|
|
1641 |
|
|
if( !strcmp( info.type, "quadratic" ) ){ |
1642 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1643 |
|
|
sprintf( painCave.errMsg, |
1644 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1645 |
|
|
painCave.isFatal = 1; |
1646 |
|
|
simError(); |
1647 |
|
|
} |
1648 |
|
|
|
1649 |
|
|
info.k1 = atof( the_token ); |
1650 |
|
|
|
1651 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1652 |
|
|
sprintf( painCave.errMsg, |
1653 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1654 |
|
|
painCave.isFatal = 1; |
1655 |
|
|
simError(); |
1656 |
|
|
} |
1657 |
|
|
|
1658 |
|
|
info.k2 = atof( the_token ); |
1659 |
|
|
|
1660 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1661 |
|
|
sprintf( painCave.errMsg, |
1662 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1663 |
|
|
painCave.isFatal = 1; |
1664 |
|
|
simError(); |
1665 |
|
|
} |
1666 |
|
|
|
1667 |
|
|
info.k3 = atof( the_token ); |
1668 |
|
|
|
1669 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1670 |
|
|
sprintf( painCave.errMsg, |
1671 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1672 |
|
|
painCave.isFatal = 1; |
1673 |
|
|
simError(); |
1674 |
|
|
} |
1675 |
|
|
|
1676 |
|
|
info.t0 = atof( the_token ); |
1677 |
|
|
} |
1678 |
|
|
|
1679 |
|
|
else{ |
1680 |
|
|
sprintf( painCave.errMsg, |
1681 |
|
|
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
1682 |
|
|
info.type, |
1683 |
|
|
lineNum ); |
1684 |
|
|
painCave.isFatal = 1; |
1685 |
|
|
simError(); |
1686 |
|
|
} |
1687 |
|
|
|
1688 |
|
|
return 1; |
1689 |
|
|
} |
1690 |
|
|
else return 0; |
1691 |
|
|
} |
1692 |
|
|
|
1693 |
|
|
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1694 |
|
|
|
1695 |
|
|
char* the_token; |
1696 |
|
|
|
1697 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1698 |
|
|
if( the_token != NULL ){ |
1699 |
|
|
|
1700 |
|
|
strcpy( info.nameA, the_token ); |
1701 |
|
|
|
1702 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1703 |
|
|
sprintf( painCave.errMsg, |
1704 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1705 |
|
|
painCave.isFatal = 1; |
1706 |
|
|
simError(); |
1707 |
|
|
} |
1708 |
|
|
|
1709 |
|
|
strcpy( info.nameB, the_token ); |
1710 |
|
|
|
1711 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1712 |
|
|
sprintf( painCave.errMsg, |
1713 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1714 |
|
|
painCave.isFatal = 1; |
1715 |
|
|
simError(); |
1716 |
|
|
} |
1717 |
|
|
|
1718 |
|
|
strcpy( info.nameC, the_token ); |
1719 |
|
|
|
1720 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1721 |
|
|
sprintf( painCave.errMsg, |
1722 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1723 |
|
|
painCave.isFatal = 1; |
1724 |
|
|
simError(); |
1725 |
|
|
} |
1726 |
|
|
|
1727 |
|
|
strcpy( info.nameD, the_token ); |
1728 |
|
|
|
1729 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1730 |
|
|
sprintf( painCave.errMsg, |
1731 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1732 |
|
|
painCave.isFatal = 1; |
1733 |
|
|
simError(); |
1734 |
|
|
} |
1735 |
|
|
|
1736 |
|
|
strcpy( info.type, the_token ); |
1737 |
|
|
|
1738 |
|
|
if( !strcmp( info.type, "cubic" ) ){ |
1739 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1740 |
|
|
sprintf( painCave.errMsg, |
1741 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1742 |
|
|
painCave.isFatal = 1; |
1743 |
|
|
simError(); |
1744 |
|
|
} |
1745 |
|
|
|
1746 |
|
|
info.k1 = atof( the_token ); |
1747 |
|
|
|
1748 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1749 |
|
|
sprintf( painCave.errMsg, |
1750 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1751 |
|
|
painCave.isFatal = 1; |
1752 |
|
|
simError(); |
1753 |
|
|
} |
1754 |
|
|
|
1755 |
|
|
info.k2 = atof( the_token ); |
1756 |
|
|
|
1757 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1758 |
|
|
sprintf( painCave.errMsg, |
1759 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1760 |
|
|
painCave.isFatal = 1; |
1761 |
|
|
simError(); |
1762 |
|
|
} |
1763 |
|
|
|
1764 |
|
|
info.k3 = atof( the_token ); |
1765 |
|
|
|
1766 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1767 |
|
|
sprintf( painCave.errMsg, |
1768 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1769 |
|
|
painCave.isFatal = 1; |
1770 |
|
|
simError(); |
1771 |
|
|
} |
1772 |
|
|
|
1773 |
|
|
info.k4 = atof( the_token ); |
1774 |
|
|
|
1775 |
|
|
} |
1776 |
|
|
|
1777 |
|
|
else{ |
1778 |
|
|
sprintf( painCave.errMsg, |
1779 |
|
|
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1780 |
|
|
info.type, |
1781 |
|
|
lineNum ); |
1782 |
|
|
painCave.isFatal = 1; |
1783 |
|
|
simError(); |
1784 |
|
|
} |
1785 |
|
|
|
1786 |
|
|
return 1; |
1787 |
|
|
} |
1788 |
|
|
|
1789 |
|
|
else return 0; |
1790 |
|
|
} |