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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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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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#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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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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// do the funtion wrapping |
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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::initForceField( int ljMixRule ){ |
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initFortran( ljMixRule, entry_plug->useReactionField ); |
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} |
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mmeineke |
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mmeineke |
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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 |
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void duplicate( atomStruct &info ){ |
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strcpy(info.name, name); |
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mmeineke |
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info.isDipole = isDipole; |
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info.isSSD = isSSD; |
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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 |
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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]; |
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int isDipole; |
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mmeineke |
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int isSSD; |
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mmeineke |
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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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mmeineke |
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double w0; |
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double v0; |
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int ident; |
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mmeineke |
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LinkedType* next; |
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}; |
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LinkedType* headAtomType; |
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LinkedType* currentAtomType; |
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atomStruct info; |
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info.last = 1; // initialize last to have the last set. |
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// if things go well, last will be set to 0 |
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mmeineke |
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mmeineke |
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int i; |
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mmeineke |
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int identNum; |
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mmeineke |
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mmeineke |
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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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mmeineke |
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////////////////////////////////////////////////// |
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// a quick water fix |
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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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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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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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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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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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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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mmeineke |
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|
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mmeineke |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
401 |
|
|
#endif |
402 |
|
|
|
403 |
|
|
// read in the atom types. |
404 |
mmeineke |
291 |
|
405 |
mmeineke |
270 |
headAtomType = new LinkedType; |
406 |
|
|
|
407 |
mmeineke |
291 |
fastForward( "AtomTypes", "initializeAtoms" ); |
408 |
|
|
|
409 |
mmeineke |
270 |
// we are now at the AtomTypes section. |
410 |
|
|
|
411 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
412 |
|
|
lineNum++; |
413 |
|
|
|
414 |
mmeineke |
291 |
|
415 |
|
|
// read a line, and start parseing out the atom types |
416 |
|
|
|
417 |
mmeineke |
270 |
if( eof_test == NULL ){ |
418 |
|
|
sprintf( painCave.errMsg, |
419 |
|
|
"Error in reading Atoms from force file at line %d.\n", |
420 |
|
|
lineNum ); |
421 |
|
|
painCave.isFatal = 1; |
422 |
|
|
simError(); |
423 |
|
|
} |
424 |
|
|
|
425 |
mmeineke |
291 |
identNum = 1; |
426 |
|
|
// stop reading at end of file, or at next section |
427 |
mmeineke |
270 |
while( readLine[0] != '#' && eof_test != NULL ){ |
428 |
mmeineke |
291 |
|
429 |
|
|
// toss comment lines |
430 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
431 |
|
|
|
432 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
433 |
|
|
if( parseAtom( readLine, lineNum, info ) ){ |
434 |
|
|
info.ident = identNum; |
435 |
|
|
headAtomType->add( info );; |
436 |
|
|
identNum++; |
437 |
mmeineke |
270 |
} |
438 |
|
|
} |
439 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
440 |
|
|
lineNum++; |
441 |
|
|
} |
442 |
|
|
|
443 |
|
|
#ifdef IS_MPI |
444 |
|
|
|
445 |
|
|
// send out the linked list to all the other processes |
446 |
|
|
|
447 |
|
|
sprintf( checkPointMsg, |
448 |
mmeineke |
291 |
"TraPPE_ExFF atom structures read successfully." ); |
449 |
mmeineke |
270 |
MPIcheckPoint(); |
450 |
|
|
|
451 |
mmeineke |
291 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
452 |
mmeineke |
270 |
while( currentAtomType != NULL ){ |
453 |
|
|
currentAtomType->duplicate( info ); |
454 |
mmeineke |
291 |
|
455 |
|
|
|
456 |
|
|
|
457 |
mmeineke |
270 |
sendFrcStruct( &info, mpiAtomStructType ); |
458 |
mmeineke |
291 |
|
459 |
|
|
sprintf( checkPointMsg, |
460 |
|
|
"successfully sent TraPPE_Ex force type: \"%s\"\n", |
461 |
|
|
info.name ); |
462 |
|
|
MPIcheckPoint(); |
463 |
|
|
|
464 |
mmeineke |
270 |
currentAtomType = currentAtomType->next; |
465 |
|
|
} |
466 |
|
|
info.last = 1; |
467 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
468 |
|
|
|
469 |
|
|
} |
470 |
|
|
|
471 |
|
|
else{ |
472 |
|
|
|
473 |
|
|
// listen for node 0 to send out the force params |
474 |
|
|
|
475 |
|
|
MPIcheckPoint(); |
476 |
|
|
|
477 |
|
|
headAtomType = new LinkedType; |
478 |
|
|
recieveFrcStruct( &info, mpiAtomStructType ); |
479 |
mmeineke |
291 |
|
480 |
mmeineke |
270 |
while( !info.last ){ |
481 |
|
|
|
482 |
mmeineke |
291 |
|
483 |
|
|
|
484 |
mmeineke |
270 |
headAtomType->add( info ); |
485 |
mmeineke |
291 |
|
486 |
|
|
MPIcheckPoint(); |
487 |
|
|
|
488 |
mmeineke |
270 |
recieveFrcStruct( &info, mpiAtomStructType ); |
489 |
|
|
} |
490 |
|
|
} |
491 |
|
|
#endif // is_mpi |
492 |
|
|
|
493 |
mmeineke |
291 |
// call new A_types in fortran |
494 |
mmeineke |
270 |
|
495 |
mmeineke |
291 |
int isError; |
496 |
mmeineke |
296 |
|
497 |
|
|
// dummy variables |
498 |
|
|
|
499 |
|
|
int isGB = 0; |
500 |
|
|
int isLJ = 1; |
501 |
mmeineke |
362 |
double GB_dummy = 0.0; |
502 |
mmeineke |
296 |
|
503 |
|
|
|
504 |
mmeineke |
291 |
currentAtomType = headAtomType; |
505 |
|
|
while( currentAtomType != NULL ){ |
506 |
|
|
|
507 |
mmeineke |
362 |
if(currentAtomType->isDipole) entry_plug->useReactionField = 1; |
508 |
|
|
if(currentAtomType->isDipole) entry_plug->useDipole = 1; |
509 |
|
|
if(currentAtomType->isSSD) entry_plug->useSticky = 1; |
510 |
|
|
|
511 |
mmeineke |
291 |
if( currentAtomType->name[0] != '\0' ){ |
512 |
|
|
isError = 0; |
513 |
mmeineke |
362 |
makeAtype( &(currentAtomType->ident), |
514 |
|
|
&isLJ, |
515 |
|
|
&(currentAtomType->isSSD), |
516 |
|
|
&(currentAtomType->isDipole), |
517 |
|
|
&isGB, |
518 |
|
|
&(currentAtomType->epslon), |
519 |
|
|
&(currentAtomType->sigma), |
520 |
|
|
&(currentAtomType->dipole), |
521 |
|
|
&(currentAtomType->w0), |
522 |
|
|
&(currentAtomType->v0), |
523 |
|
|
&GB_dummy, |
524 |
|
|
&GB_dummy, |
525 |
|
|
&GB_dummy, |
526 |
|
|
&GB_dummy, |
527 |
|
|
&GB_dummy, |
528 |
|
|
&GB_dummy, |
529 |
|
|
&isError ); |
530 |
mmeineke |
291 |
if( isError ){ |
531 |
|
|
sprintf( painCave.errMsg, |
532 |
|
|
"Error initializing the \"%s\" atom type in fortran\n", |
533 |
|
|
currentAtomType->name ); |
534 |
|
|
painCave.isFatal = 1; |
535 |
|
|
simError(); |
536 |
|
|
} |
537 |
|
|
} |
538 |
|
|
currentAtomType = currentAtomType->next; |
539 |
|
|
} |
540 |
|
|
|
541 |
|
|
#ifdef IS_MPI |
542 |
|
|
sprintf( checkPointMsg, |
543 |
|
|
"TraPPE_ExFF atom structures successfully sent to fortran\n" ); |
544 |
|
|
MPIcheckPoint(); |
545 |
|
|
#endif // is_mpi |
546 |
|
|
|
547 |
|
|
|
548 |
mmeineke |
270 |
// initialize the atoms |
549 |
|
|
|
550 |
mmeineke |
291 |
double bigSigma = 0.0; |
551 |
mmeineke |
270 |
DirectionalAtom* dAtom; |
552 |
|
|
|
553 |
|
|
for( i=0; i<nAtoms; i++ ){ |
554 |
|
|
|
555 |
|
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
556 |
|
|
if( currentAtomType == NULL ){ |
557 |
|
|
sprintf( painCave.errMsg, |
558 |
|
|
"AtomType error, %s not found in force file.\n", |
559 |
|
|
the_atoms[i]->getType() ); |
560 |
|
|
painCave.isFatal = 1; |
561 |
|
|
simError(); |
562 |
|
|
} |
563 |
|
|
|
564 |
|
|
the_atoms[i]->setMass( currentAtomType->mass ); |
565 |
|
|
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
566 |
|
|
the_atoms[i]->setSigma( currentAtomType->sigma ); |
567 |
|
|
the_atoms[i]->setLJ(); |
568 |
|
|
|
569 |
mmeineke |
291 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
570 |
|
|
|
571 |
mmeineke |
270 |
if( currentAtomType->isDipole ){ |
572 |
|
|
if( the_atoms[i]->isDirectional() ){ |
573 |
|
|
|
574 |
|
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
575 |
|
|
dAtom->setMu( currentAtomType->dipole ); |
576 |
|
|
dAtom->setHasDipole( 1 ); |
577 |
|
|
dAtom->setJx( 0.0 ); |
578 |
|
|
dAtom->setJy( 0.0 ); |
579 |
|
|
dAtom->setJz( 0.0 ); |
580 |
|
|
|
581 |
|
|
if(!strcmp("SSD",the_atoms[i]->getType())){ |
582 |
|
|
dAtom->setI( waterI ); |
583 |
|
|
dAtom->setSSD( 1 ); |
584 |
|
|
} |
585 |
|
|
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
586 |
|
|
dAtom->setI( headI ); |
587 |
|
|
dAtom->setSSD( 0 ); |
588 |
|
|
} |
589 |
|
|
else{ |
590 |
|
|
sprintf(painCave.errMsg, |
591 |
|
|
"AtmType error, %s does not have a moment of inertia set.\n", |
592 |
|
|
the_atoms[i]->getType() ); |
593 |
|
|
painCave.isFatal = 1; |
594 |
|
|
simError(); |
595 |
|
|
} |
596 |
|
|
entry_plug->n_dipoles++; |
597 |
|
|
} |
598 |
|
|
else{ |
599 |
|
|
|
600 |
|
|
sprintf( painCave.errMsg, |
601 |
|
|
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
602 |
|
|
" orientation was specifed in the BASS file.\n", |
603 |
|
|
currentAtomType->name ); |
604 |
|
|
painCave.isFatal = 1; |
605 |
|
|
simError(); |
606 |
|
|
} |
607 |
|
|
} |
608 |
|
|
else{ |
609 |
|
|
if( the_atoms[i]->isDirectional() ){ |
610 |
|
|
sprintf( painCave.errMsg, |
611 |
|
|
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
612 |
|
|
"orientation in the BASS file, yet it is not a dipole.\n", |
613 |
|
|
currentAtomType->name); |
614 |
|
|
painCave.isFatal = 1; |
615 |
|
|
simError(); |
616 |
|
|
} |
617 |
|
|
} |
618 |
|
|
} |
619 |
|
|
|
620 |
mmeineke |
291 |
#ifdef IS_MPI |
621 |
|
|
double tempBig = bigSigma; |
622 |
|
|
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
623 |
|
|
#endif //is_mpi |
624 |
mmeineke |
270 |
|
625 |
mmeineke |
291 |
//calc rCut and rList |
626 |
|
|
|
627 |
|
|
entry_plug->rCut = 2.5 * bigSigma; |
628 |
|
|
|
629 |
|
|
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) |
630 |
|
|
entry_plug->rCut = entry_plug->box_x / 2.0; |
631 |
|
|
|
632 |
|
|
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) |
633 |
|
|
entry_plug->rCut = entry_plug->box_y / 2.0; |
634 |
|
|
|
635 |
|
|
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) |
636 |
|
|
entry_plug->rCut = entry_plug->box_z / 2.0; |
637 |
|
|
|
638 |
|
|
entry_plug->rList = entry_plug->rCut + 1.0; |
639 |
|
|
|
640 |
mmeineke |
362 |
entry_plug->useLJ = 1; // use Lennard Jones is on by default |
641 |
mmeineke |
291 |
|
642 |
mmeineke |
270 |
// clean up the memory |
643 |
|
|
|
644 |
|
|
delete headAtomType; |
645 |
|
|
|
646 |
|
|
#ifdef IS_MPI |
647 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" ); |
648 |
|
|
MPIcheckPoint(); |
649 |
|
|
#endif // is_mpi |
650 |
|
|
|
651 |
|
|
} |
652 |
|
|
|
653 |
|
|
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
654 |
|
|
|
655 |
|
|
class LinkedType { |
656 |
|
|
public: |
657 |
|
|
LinkedType(){ |
658 |
|
|
next = NULL; |
659 |
|
|
nameA[0] = '\0'; |
660 |
|
|
nameB[0] = '\0'; |
661 |
|
|
type[0] = '\0'; |
662 |
|
|
} |
663 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
664 |
|
|
|
665 |
|
|
LinkedType* find(char* key1, char* key2){ |
666 |
|
|
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
667 |
|
|
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
668 |
|
|
if( next != NULL ) return next->find(key1, key2); |
669 |
|
|
return NULL; |
670 |
|
|
} |
671 |
|
|
|
672 |
mmeineke |
291 |
|
673 |
mmeineke |
270 |
void add( bondStruct &info ){ |
674 |
mmeineke |
291 |
|
675 |
|
|
// check for duplicates |
676 |
|
|
int dup = 0; |
677 |
|
|
|
678 |
|
|
if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
679 |
|
|
if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
680 |
|
|
|
681 |
|
|
if(dup){ |
682 |
|
|
sprintf( painCave.errMsg, |
683 |
|
|
"Duplicate TraPPE_Ex bond type \"%s - %s\" found in " |
684 |
|
|
"the TraPPE_ExFF param file./n", |
685 |
|
|
nameA, nameB ); |
686 |
|
|
painCave.isFatal = 1; |
687 |
|
|
simError(); |
688 |
|
|
} |
689 |
|
|
|
690 |
|
|
|
691 |
mmeineke |
270 |
if( next != NULL ) next->add(info); |
692 |
|
|
else{ |
693 |
|
|
next = new LinkedType(); |
694 |
|
|
strcpy(next->nameA, info.nameA); |
695 |
|
|
strcpy(next->nameB, info.nameB); |
696 |
|
|
strcpy(next->type, info.type); |
697 |
|
|
next->d0 = info.d0; |
698 |
|
|
} |
699 |
|
|
} |
700 |
|
|
|
701 |
mmeineke |
291 |
#ifdef IS_MPI |
702 |
mmeineke |
270 |
void duplicate( bondStruct &info ){ |
703 |
|
|
strcpy(info.nameA, nameA); |
704 |
|
|
strcpy(info.nameB, nameB); |
705 |
|
|
strcpy(info.type, type); |
706 |
|
|
info.d0 = d0; |
707 |
|
|
info.last = 0; |
708 |
|
|
} |
709 |
|
|
|
710 |
|
|
|
711 |
|
|
#endif |
712 |
|
|
|
713 |
|
|
char nameA[15]; |
714 |
|
|
char nameB[15]; |
715 |
|
|
char type[30]; |
716 |
|
|
double d0; |
717 |
|
|
|
718 |
|
|
LinkedType* next; |
719 |
|
|
}; |
720 |
|
|
|
721 |
|
|
|
722 |
|
|
|
723 |
|
|
LinkedType* headBondType; |
724 |
|
|
LinkedType* currentBondType; |
725 |
|
|
bondStruct info; |
726 |
|
|
info.last = 1; // initialize last to have the last set. |
727 |
|
|
// if things go well, last will be set to 0 |
728 |
|
|
|
729 |
|
|
SRI **the_sris; |
730 |
|
|
Atom** the_atoms; |
731 |
|
|
int nBonds; |
732 |
|
|
the_sris = entry_plug->sr_interactions; |
733 |
|
|
the_atoms = entry_plug->atoms; |
734 |
|
|
nBonds = entry_plug->n_bonds; |
735 |
|
|
|
736 |
mmeineke |
291 |
int i, a, b; |
737 |
|
|
char* atomA; |
738 |
|
|
char* atomB; |
739 |
mmeineke |
270 |
|
740 |
|
|
#ifdef IS_MPI |
741 |
|
|
if( worldRank == 0 ){ |
742 |
|
|
#endif |
743 |
|
|
|
744 |
|
|
// read in the bond types. |
745 |
|
|
|
746 |
|
|
headBondType = new LinkedType; |
747 |
|
|
|
748 |
mmeineke |
291 |
fastForward( "BondTypes", "initializeBonds" ); |
749 |
|
|
|
750 |
|
|
// we are now at the bondTypes section |
751 |
|
|
|
752 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
753 |
mmeineke |
270 |
lineNum++; |
754 |
|
|
|
755 |
|
|
|
756 |
mmeineke |
291 |
// read a line, and start parseing out the atom types |
757 |
|
|
|
758 |
mmeineke |
270 |
if( eof_test == NULL ){ |
759 |
|
|
sprintf( painCave.errMsg, |
760 |
mmeineke |
291 |
"Error in reading bonds from force file at line %d.\n", |
761 |
mmeineke |
270 |
lineNum ); |
762 |
|
|
painCave.isFatal = 1; |
763 |
|
|
simError(); |
764 |
|
|
} |
765 |
|
|
|
766 |
mmeineke |
291 |
// stop reading at end of file, or at next section |
767 |
mmeineke |
270 |
while( readLine[0] != '#' && eof_test != NULL ){ |
768 |
mmeineke |
291 |
|
769 |
|
|
// toss comment lines |
770 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
771 |
|
|
|
772 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
773 |
|
|
if( parseBond( readLine, lineNum, info ) ){ |
774 |
|
|
headBondType->add( info ); |
775 |
mmeineke |
270 |
} |
776 |
|
|
} |
777 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
778 |
|
|
lineNum++; |
779 |
|
|
} |
780 |
mmeineke |
291 |
|
781 |
mmeineke |
270 |
#ifdef IS_MPI |
782 |
|
|
|
783 |
|
|
// send out the linked list to all the other processes |
784 |
|
|
|
785 |
|
|
sprintf( checkPointMsg, |
786 |
|
|
"TraPPE_Ex bond structures read successfully." ); |
787 |
|
|
MPIcheckPoint(); |
788 |
|
|
|
789 |
|
|
currentBondType = headBondType; |
790 |
|
|
while( currentBondType != NULL ){ |
791 |
|
|
currentBondType->duplicate( info ); |
792 |
|
|
sendFrcStruct( &info, mpiBondStructType ); |
793 |
|
|
currentBondType = currentBondType->next; |
794 |
|
|
} |
795 |
|
|
info.last = 1; |
796 |
|
|
sendFrcStruct( &info, mpiBondStructType ); |
797 |
|
|
|
798 |
|
|
} |
799 |
|
|
|
800 |
|
|
else{ |
801 |
|
|
|
802 |
|
|
// listen for node 0 to send out the force params |
803 |
|
|
|
804 |
|
|
MPIcheckPoint(); |
805 |
|
|
|
806 |
|
|
headBondType = new LinkedType; |
807 |
|
|
recieveFrcStruct( &info, mpiBondStructType ); |
808 |
|
|
while( !info.last ){ |
809 |
|
|
|
810 |
|
|
headBondType->add( info ); |
811 |
|
|
recieveFrcStruct( &info, mpiBondStructType ); |
812 |
|
|
} |
813 |
|
|
} |
814 |
|
|
#endif // is_mpi |
815 |
|
|
|
816 |
|
|
|
817 |
|
|
// initialize the Bonds |
818 |
|
|
|
819 |
|
|
|
820 |
|
|
for( i=0; i<nBonds; i++ ){ |
821 |
|
|
|
822 |
|
|
a = the_bonds[i].a; |
823 |
|
|
b = the_bonds[i].b; |
824 |
|
|
|
825 |
|
|
atomA = the_atoms[a]->getType(); |
826 |
|
|
atomB = the_atoms[b]->getType(); |
827 |
|
|
currentBondType = headBondType->find( atomA, atomB ); |
828 |
|
|
if( currentBondType == NULL ){ |
829 |
|
|
sprintf( painCave.errMsg, |
830 |
|
|
"BondType error, %s - %s not found in force file.\n", |
831 |
|
|
atomA, atomB ); |
832 |
|
|
painCave.isFatal = 1; |
833 |
|
|
simError(); |
834 |
|
|
} |
835 |
|
|
|
836 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
837 |
|
|
|
838 |
|
|
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
839 |
|
|
*the_atoms[b], |
840 |
|
|
currentBondType->d0 ); |
841 |
|
|
entry_plug->n_constraints++; |
842 |
|
|
} |
843 |
|
|
} |
844 |
|
|
|
845 |
|
|
|
846 |
|
|
// clean up the memory |
847 |
|
|
|
848 |
|
|
delete headBondType; |
849 |
|
|
|
850 |
|
|
#ifdef IS_MPI |
851 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" ); |
852 |
|
|
MPIcheckPoint(); |
853 |
|
|
#endif // is_mpi |
854 |
|
|
|
855 |
|
|
} |
856 |
|
|
|
857 |
|
|
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
858 |
|
|
|
859 |
|
|
class LinkedType { |
860 |
|
|
public: |
861 |
|
|
LinkedType(){ |
862 |
|
|
next = NULL; |
863 |
|
|
nameA[0] = '\0'; |
864 |
|
|
nameB[0] = '\0'; |
865 |
|
|
nameC[0] = '\0'; |
866 |
|
|
type[0] = '\0'; |
867 |
|
|
} |
868 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
869 |
|
|
|
870 |
|
|
LinkedType* find( char* key1, char* key2, char* key3 ){ |
871 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
872 |
|
|
&& !strcmp( nameC, key3 ) ) return this; |
873 |
|
|
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
874 |
|
|
&& !strcmp( nameC, key1 ) ) return this; |
875 |
|
|
if( next != NULL ) return next->find(key1, key2, key3); |
876 |
|
|
return NULL; |
877 |
|
|
} |
878 |
|
|
|
879 |
mmeineke |
291 |
void add( bendStruct &info ){ |
880 |
mmeineke |
270 |
|
881 |
mmeineke |
291 |
// check for duplicates |
882 |
|
|
int dup = 0; |
883 |
|
|
|
884 |
|
|
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
885 |
|
|
&& !strcmp( nameC, info.nameC ) ) dup = 1; |
886 |
|
|
if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
887 |
|
|
&& !strcmp( nameC, info.nameA ) ) dup = 1; |
888 |
|
|
|
889 |
|
|
if(dup){ |
890 |
|
|
sprintf( painCave.errMsg, |
891 |
|
|
"Duplicate TraPPE_Ex bend type \"%s - %s - %s\" found in " |
892 |
|
|
"the TraPPE_ExFF param file./n", |
893 |
|
|
nameA, nameB, nameC ); |
894 |
|
|
painCave.isFatal = 1; |
895 |
|
|
simError(); |
896 |
|
|
} |
897 |
|
|
|
898 |
mmeineke |
270 |
if( next != NULL ) next->add(info); |
899 |
|
|
else{ |
900 |
|
|
next = new LinkedType(); |
901 |
|
|
strcpy(next->nameA, info.nameA); |
902 |
|
|
strcpy(next->nameB, info.nameB); |
903 |
|
|
strcpy(next->nameC, info.nameC); |
904 |
|
|
strcpy(next->type, info.type); |
905 |
|
|
next->k1 = info.k1; |
906 |
|
|
next->k2 = info.k2; |
907 |
|
|
next->k3 = info.k3; |
908 |
|
|
next->t0 = info.t0; |
909 |
|
|
} |
910 |
|
|
} |
911 |
mmeineke |
291 |
|
912 |
|
|
#ifdef IS_MPI |
913 |
|
|
|
914 |
mmeineke |
270 |
void duplicate( bendStruct &info ){ |
915 |
|
|
strcpy(info.nameA, nameA); |
916 |
|
|
strcpy(info.nameB, nameB); |
917 |
|
|
strcpy(info.nameC, nameC); |
918 |
|
|
strcpy(info.type, type); |
919 |
|
|
info.k1 = k1; |
920 |
|
|
info.k2 = k2; |
921 |
|
|
info.k3 = k3; |
922 |
|
|
info.t0 = t0; |
923 |
|
|
info.last = 0; |
924 |
|
|
} |
925 |
|
|
|
926 |
|
|
#endif // is_mpi |
927 |
|
|
|
928 |
|
|
char nameA[15]; |
929 |
|
|
char nameB[15]; |
930 |
|
|
char nameC[15]; |
931 |
|
|
char type[30]; |
932 |
|
|
double k1, k2, k3, t0; |
933 |
|
|
|
934 |
|
|
LinkedType* next; |
935 |
|
|
}; |
936 |
|
|
|
937 |
|
|
LinkedType* headBendType; |
938 |
|
|
LinkedType* currentBendType; |
939 |
|
|
bendStruct info; |
940 |
|
|
info.last = 1; // initialize last to have the last set. |
941 |
|
|
// if things go well, last will be set to 0 |
942 |
|
|
|
943 |
|
|
QuadraticBend* qBend; |
944 |
mmeineke |
311 |
GhostBend* gBend; |
945 |
mmeineke |
270 |
SRI **the_sris; |
946 |
|
|
Atom** the_atoms; |
947 |
|
|
int nBends; |
948 |
|
|
the_sris = entry_plug->sr_interactions; |
949 |
|
|
the_atoms = entry_plug->atoms; |
950 |
|
|
nBends = entry_plug->n_bends; |
951 |
|
|
|
952 |
mmeineke |
291 |
int i, a, b, c; |
953 |
|
|
char* atomA; |
954 |
|
|
char* atomB; |
955 |
|
|
char* atomC; |
956 |
mmeineke |
270 |
|
957 |
mmeineke |
291 |
|
958 |
mmeineke |
270 |
#ifdef IS_MPI |
959 |
|
|
if( worldRank == 0 ){ |
960 |
|
|
#endif |
961 |
|
|
|
962 |
|
|
// read in the bend types. |
963 |
|
|
|
964 |
|
|
headBendType = new LinkedType; |
965 |
|
|
|
966 |
mmeineke |
291 |
fastForward( "BendTypes", "initializeBends" ); |
967 |
mmeineke |
270 |
|
968 |
mmeineke |
291 |
// we are now at the bendTypes section |
969 |
mmeineke |
270 |
|
970 |
mmeineke |
291 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
971 |
|
|
lineNum++; |
972 |
|
|
|
973 |
|
|
// read a line, and start parseing out the bend types |
974 |
mmeineke |
270 |
|
975 |
|
|
if( eof_test == NULL ){ |
976 |
|
|
sprintf( painCave.errMsg, |
977 |
mmeineke |
291 |
"Error in reading bends from force file at line %d.\n", |
978 |
mmeineke |
270 |
lineNum ); |
979 |
|
|
painCave.isFatal = 1; |
980 |
|
|
simError(); |
981 |
|
|
} |
982 |
mmeineke |
291 |
|
983 |
|
|
// stop reading at end of file, or at next section |
984 |
mmeineke |
270 |
while( readLine[0] != '#' && eof_test != NULL ){ |
985 |
mmeineke |
291 |
|
986 |
|
|
// toss comment lines |
987 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
988 |
|
|
|
989 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
990 |
|
|
if( parseBend( readLine, lineNum, info ) ){ |
991 |
|
|
headBendType->add( info ); |
992 |
mmeineke |
270 |
} |
993 |
|
|
} |
994 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
995 |
|
|
lineNum++; |
996 |
|
|
} |
997 |
mmeineke |
291 |
|
998 |
mmeineke |
270 |
#ifdef IS_MPI |
999 |
|
|
|
1000 |
|
|
// send out the linked list to all the other processes |
1001 |
|
|
|
1002 |
|
|
sprintf( checkPointMsg, |
1003 |
|
|
"TraPPE_Ex bend structures read successfully." ); |
1004 |
|
|
MPIcheckPoint(); |
1005 |
|
|
|
1006 |
|
|
currentBendType = headBendType; |
1007 |
|
|
while( currentBendType != NULL ){ |
1008 |
|
|
currentBendType->duplicate( info ); |
1009 |
|
|
sendFrcStruct( &info, mpiBendStructType ); |
1010 |
|
|
currentBendType = currentBendType->next; |
1011 |
|
|
} |
1012 |
|
|
info.last = 1; |
1013 |
|
|
sendFrcStruct( &info, mpiBendStructType ); |
1014 |
|
|
|
1015 |
|
|
} |
1016 |
|
|
|
1017 |
|
|
else{ |
1018 |
|
|
|
1019 |
|
|
// listen for node 0 to send out the force params |
1020 |
|
|
|
1021 |
|
|
MPIcheckPoint(); |
1022 |
|
|
|
1023 |
|
|
headBendType = new LinkedType; |
1024 |
|
|
recieveFrcStruct( &info, mpiBendStructType ); |
1025 |
|
|
while( !info.last ){ |
1026 |
|
|
|
1027 |
|
|
headBendType->add( info ); |
1028 |
|
|
recieveFrcStruct( &info, mpiBendStructType ); |
1029 |
|
|
} |
1030 |
|
|
} |
1031 |
|
|
#endif // is_mpi |
1032 |
|
|
|
1033 |
|
|
// initialize the Bends |
1034 |
mmeineke |
291 |
|
1035 |
|
|
int index; |
1036 |
mmeineke |
270 |
|
1037 |
|
|
for( i=0; i<nBends; i++ ){ |
1038 |
|
|
|
1039 |
|
|
a = the_bends[i].a; |
1040 |
|
|
b = the_bends[i].b; |
1041 |
|
|
c = the_bends[i].c; |
1042 |
|
|
|
1043 |
|
|
atomA = the_atoms[a]->getType(); |
1044 |
|
|
atomB = the_atoms[b]->getType(); |
1045 |
mmeineke |
311 |
|
1046 |
|
|
if( the_bends[i].isGhost ) atomC = "GHOST"; |
1047 |
|
|
else atomC = the_atoms[c]->getType(); |
1048 |
|
|
|
1049 |
mmeineke |
270 |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1050 |
|
|
if( currentBendType == NULL ){ |
1051 |
|
|
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1052 |
|
|
" in force file.\n", |
1053 |
|
|
atomA, atomB, atomC ); |
1054 |
|
|
painCave.isFatal = 1; |
1055 |
|
|
simError(); |
1056 |
|
|
} |
1057 |
|
|
|
1058 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1059 |
|
|
|
1060 |
|
|
index = i + entry_plug->n_bonds; |
1061 |
mmeineke |
311 |
|
1062 |
|
|
if( the_bends[i].isGhost){ |
1063 |
|
|
|
1064 |
|
|
if( the_bends[i].ghost == b ){ |
1065 |
|
|
// do nothing |
1066 |
|
|
} |
1067 |
|
|
else if( the_bends[i].ghost == a ){ |
1068 |
|
|
c = a; |
1069 |
|
|
a = b; |
1070 |
|
|
b = a; |
1071 |
|
|
} |
1072 |
|
|
else{ |
1073 |
|
|
sprintf( painCave.errMsg, |
1074 |
|
|
"BendType error, %s - %s - %s,\n" |
1075 |
|
|
" --> central atom is not " |
1076 |
|
|
"correctly identified with the " |
1077 |
|
|
"\"ghostVectorSource = \" tag.\n", |
1078 |
|
|
atomA, atomB, atomC ); |
1079 |
|
|
painCave.isFatal = 1; |
1080 |
|
|
simError(); |
1081 |
|
|
} |
1082 |
|
|
|
1083 |
|
|
gBend = new GhostBend( *the_atoms[a], |
1084 |
|
|
*the_atoms[b] ); |
1085 |
|
|
gBend->setConstants( currentBendType->k1, |
1086 |
|
|
currentBendType->k2, |
1087 |
|
|
currentBendType->k3, |
1088 |
|
|
currentBendType->t0 ); |
1089 |
|
|
the_sris[index] = gBend; |
1090 |
|
|
} |
1091 |
|
|
else{ |
1092 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
1093 |
|
|
*the_atoms[b], |
1094 |
|
|
*the_atoms[c] ); |
1095 |
|
|
qBend->setConstants( currentBendType->k1, |
1096 |
|
|
currentBendType->k2, |
1097 |
|
|
currentBendType->k3, |
1098 |
|
|
currentBendType->t0 ); |
1099 |
|
|
the_sris[index] = qBend; |
1100 |
|
|
} |
1101 |
mmeineke |
270 |
} |
1102 |
|
|
} |
1103 |
|
|
|
1104 |
|
|
|
1105 |
|
|
// clean up the memory |
1106 |
|
|
|
1107 |
|
|
delete headBendType; |
1108 |
|
|
|
1109 |
|
|
#ifdef IS_MPI |
1110 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" ); |
1111 |
|
|
MPIcheckPoint(); |
1112 |
|
|
#endif // is_mpi |
1113 |
|
|
|
1114 |
|
|
} |
1115 |
|
|
|
1116 |
|
|
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
1117 |
|
|
|
1118 |
|
|
class LinkedType { |
1119 |
|
|
public: |
1120 |
|
|
LinkedType(){ |
1121 |
|
|
next = NULL; |
1122 |
|
|
nameA[0] = '\0'; |
1123 |
|
|
nameB[0] = '\0'; |
1124 |
|
|
nameC[0] = '\0'; |
1125 |
|
|
type[0] = '\0'; |
1126 |
|
|
} |
1127 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
1128 |
|
|
|
1129 |
|
|
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
1130 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
1131 |
|
|
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
1132 |
|
|
|
1133 |
|
|
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
1134 |
mmeineke |
291 |
!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
1135 |
mmeineke |
270 |
|
1136 |
|
|
if( next != NULL ) return next->find(key1, key2, key3, key4); |
1137 |
|
|
return NULL; |
1138 |
|
|
} |
1139 |
|
|
|
1140 |
|
|
void add( torsionStruct &info ){ |
1141 |
mmeineke |
291 |
|
1142 |
|
|
// check for duplicates |
1143 |
|
|
int dup = 0; |
1144 |
|
|
|
1145 |
|
|
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
1146 |
|
|
!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
1147 |
|
|
|
1148 |
|
|
if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
1149 |
|
|
!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
1150 |
|
|
|
1151 |
|
|
if(dup){ |
1152 |
|
|
sprintf( painCave.errMsg, |
1153 |
|
|
"Duplicate TraPPE_Ex torsion type \"%s - %s - %s - %s\" found in " |
1154 |
|
|
"the TraPPE_ExFF param file./n", nameA, nameB, nameC, nameD ); |
1155 |
|
|
painCave.isFatal = 1; |
1156 |
|
|
simError(); |
1157 |
|
|
} |
1158 |
|
|
|
1159 |
mmeineke |
270 |
if( next != NULL ) next->add(info); |
1160 |
|
|
else{ |
1161 |
|
|
next = new LinkedType(); |
1162 |
|
|
strcpy(next->nameA, info.nameA); |
1163 |
|
|
strcpy(next->nameB, info.nameB); |
1164 |
|
|
strcpy(next->nameC, info.nameC); |
1165 |
|
|
strcpy(next->type, info.type); |
1166 |
|
|
next->k1 = info.k1; |
1167 |
|
|
next->k2 = info.k2; |
1168 |
|
|
next->k3 = info.k3; |
1169 |
|
|
next->k4 = info.k4; |
1170 |
|
|
} |
1171 |
|
|
} |
1172 |
mmeineke |
291 |
|
1173 |
|
|
#ifdef IS_MPI |
1174 |
mmeineke |
270 |
|
1175 |
|
|
void duplicate( torsionStruct &info ){ |
1176 |
|
|
strcpy(info.nameA, nameA); |
1177 |
|
|
strcpy(info.nameB, nameB); |
1178 |
|
|
strcpy(info.nameC, nameC); |
1179 |
|
|
strcpy(info.nameD, nameD); |
1180 |
|
|
strcpy(info.type, type); |
1181 |
|
|
info.k1 = k1; |
1182 |
|
|
info.k2 = k2; |
1183 |
|
|
info.k3 = k3; |
1184 |
|
|
info.k4 = k4; |
1185 |
|
|
info.last = 0; |
1186 |
|
|
} |
1187 |
|
|
|
1188 |
|
|
#endif |
1189 |
|
|
|
1190 |
|
|
char nameA[15]; |
1191 |
|
|
char nameB[15]; |
1192 |
|
|
char nameC[15]; |
1193 |
|
|
char nameD[15]; |
1194 |
|
|
char type[30]; |
1195 |
|
|
double k1, k2, k3, k4; |
1196 |
|
|
|
1197 |
|
|
LinkedType* next; |
1198 |
|
|
}; |
1199 |
|
|
|
1200 |
|
|
LinkedType* headTorsionType; |
1201 |
|
|
LinkedType* currentTorsionType; |
1202 |
|
|
torsionStruct info; |
1203 |
|
|
info.last = 1; // initialize last to have the last set. |
1204 |
|
|
// if things go well, last will be set to 0 |
1205 |
|
|
|
1206 |
|
|
int i, a, b, c, d, index; |
1207 |
|
|
char* atomA; |
1208 |
|
|
char* atomB; |
1209 |
|
|
char* atomC; |
1210 |
|
|
char* atomD; |
1211 |
|
|
CubicTorsion* cTors; |
1212 |
|
|
|
1213 |
|
|
SRI **the_sris; |
1214 |
|
|
Atom** the_atoms; |
1215 |
|
|
int nTorsions; |
1216 |
|
|
the_sris = entry_plug->sr_interactions; |
1217 |
|
|
the_atoms = entry_plug->atoms; |
1218 |
|
|
nTorsions = entry_plug->n_torsions; |
1219 |
|
|
|
1220 |
|
|
#ifdef IS_MPI |
1221 |
|
|
if( worldRank == 0 ){ |
1222 |
|
|
#endif |
1223 |
|
|
|
1224 |
|
|
// read in the torsion types. |
1225 |
|
|
|
1226 |
|
|
headTorsionType = new LinkedType; |
1227 |
mmeineke |
291 |
|
1228 |
|
|
fastForward( "TorsionTypes", "initializeTorsions" ); |
1229 |
mmeineke |
270 |
|
1230 |
mmeineke |
291 |
// we are now at the torsionTypes section |
1231 |
mmeineke |
270 |
|
1232 |
mmeineke |
291 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1233 |
|
|
lineNum++; |
1234 |
mmeineke |
270 |
|
1235 |
mmeineke |
291 |
|
1236 |
|
|
// read a line, and start parseing out the atom types |
1237 |
mmeineke |
270 |
|
1238 |
|
|
if( eof_test == NULL ){ |
1239 |
|
|
sprintf( painCave.errMsg, |
1240 |
mmeineke |
291 |
"Error in reading torsions from force file at line %d.\n", |
1241 |
mmeineke |
270 |
lineNum ); |
1242 |
|
|
painCave.isFatal = 1; |
1243 |
|
|
simError(); |
1244 |
|
|
} |
1245 |
mmeineke |
291 |
|
1246 |
|
|
// stop reading at end of file, or at next section |
1247 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
1248 |
mmeineke |
270 |
|
1249 |
mmeineke |
291 |
// toss comment lines |
1250 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
1251 |
|
|
|
1252 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
1253 |
|
|
if( parseTorsion( readLine, lineNum, info ) ){ |
1254 |
|
|
headTorsionType->add( info ); |
1255 |
mmeineke |
270 |
} |
1256 |
|
|
} |
1257 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1258 |
|
|
lineNum++; |
1259 |
|
|
} |
1260 |
|
|
|
1261 |
|
|
#ifdef IS_MPI |
1262 |
|
|
|
1263 |
|
|
// send out the linked list to all the other processes |
1264 |
|
|
|
1265 |
|
|
sprintf( checkPointMsg, |
1266 |
|
|
"TraPPE_Ex torsion structures read successfully." ); |
1267 |
|
|
MPIcheckPoint(); |
1268 |
|
|
|
1269 |
|
|
currentTorsionType = headTorsionType; |
1270 |
|
|
while( currentTorsionType != NULL ){ |
1271 |
|
|
currentTorsionType->duplicate( info ); |
1272 |
|
|
sendFrcStruct( &info, mpiTorsionStructType ); |
1273 |
|
|
currentTorsionType = currentTorsionType->next; |
1274 |
|
|
} |
1275 |
|
|
info.last = 1; |
1276 |
|
|
sendFrcStruct( &info, mpiTorsionStructType ); |
1277 |
|
|
|
1278 |
|
|
} |
1279 |
|
|
|
1280 |
|
|
else{ |
1281 |
|
|
|
1282 |
|
|
// listen for node 0 to send out the force params |
1283 |
|
|
|
1284 |
|
|
MPIcheckPoint(); |
1285 |
|
|
|
1286 |
|
|
headTorsionType = new LinkedType; |
1287 |
|
|
recieveFrcStruct( &info, mpiTorsionStructType ); |
1288 |
|
|
while( !info.last ){ |
1289 |
|
|
|
1290 |
|
|
headTorsionType->add( info ); |
1291 |
|
|
recieveFrcStruct( &info, mpiTorsionStructType ); |
1292 |
|
|
} |
1293 |
|
|
} |
1294 |
|
|
#endif // is_mpi |
1295 |
|
|
|
1296 |
|
|
// initialize the Torsions |
1297 |
|
|
|
1298 |
|
|
for( i=0; i<nTorsions; i++ ){ |
1299 |
|
|
|
1300 |
|
|
a = the_torsions[i].a; |
1301 |
|
|
b = the_torsions[i].b; |
1302 |
|
|
c = the_torsions[i].c; |
1303 |
|
|
d = the_torsions[i].d; |
1304 |
|
|
|
1305 |
|
|
atomA = the_atoms[a]->getType(); |
1306 |
|
|
atomB = the_atoms[b]->getType(); |
1307 |
|
|
atomC = the_atoms[c]->getType(); |
1308 |
|
|
atomD = the_atoms[d]->getType(); |
1309 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1310 |
|
|
if( currentTorsionType == NULL ){ |
1311 |
|
|
sprintf( painCave.errMsg, |
1312 |
|
|
"TorsionType error, %s - %s - %s - %s not found" |
1313 |
|
|
" in force file.\n", |
1314 |
|
|
atomA, atomB, atomC, atomD ); |
1315 |
|
|
painCave.isFatal = 1; |
1316 |
|
|
simError(); |
1317 |
|
|
} |
1318 |
|
|
|
1319 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1320 |
|
|
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
1321 |
|
|
|
1322 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1323 |
|
|
*the_atoms[c], *the_atoms[d] ); |
1324 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1325 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
1326 |
|
|
the_sris[index] = cTors; |
1327 |
|
|
} |
1328 |
|
|
} |
1329 |
|
|
|
1330 |
|
|
|
1331 |
|
|
// clean up the memory |
1332 |
|
|
|
1333 |
|
|
delete headTorsionType; |
1334 |
|
|
|
1335 |
|
|
#ifdef IS_MPI |
1336 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" ); |
1337 |
|
|
MPIcheckPoint(); |
1338 |
|
|
#endif // is_mpi |
1339 |
|
|
|
1340 |
|
|
} |
1341 |
mmeineke |
291 |
|
1342 |
|
|
void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){ |
1343 |
|
|
|
1344 |
|
|
int foundText = 0; |
1345 |
|
|
char* the_token; |
1346 |
|
|
|
1347 |
|
|
rewind( frcFile ); |
1348 |
|
|
lineNum = 0; |
1349 |
|
|
|
1350 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1351 |
|
|
lineNum++; |
1352 |
|
|
if( eof_test == NULL ){ |
1353 |
|
|
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
1354 |
|
|
" file is empty.\n", |
1355 |
|
|
searchOwner ); |
1356 |
|
|
painCave.isFatal = 1; |
1357 |
|
|
simError(); |
1358 |
|
|
} |
1359 |
|
|
|
1360 |
|
|
|
1361 |
|
|
while( !foundText ){ |
1362 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
1363 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1364 |
|
|
lineNum++; |
1365 |
|
|
} |
1366 |
|
|
if( eof_test == NULL ){ |
1367 |
|
|
sprintf( painCave.errMsg, |
1368 |
|
|
"Error fast forwarding force file for %s at " |
1369 |
|
|
"line %d: file ended unexpectedly.\n", |
1370 |
|
|
searchOwner, |
1371 |
|
|
lineNum ); |
1372 |
|
|
painCave.isFatal = 1; |
1373 |
|
|
simError(); |
1374 |
|
|
} |
1375 |
|
|
|
1376 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
1377 |
|
|
foundText = !strcmp( stopText, the_token ); |
1378 |
|
|
|
1379 |
|
|
if( !foundText ){ |
1380 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1381 |
|
|
lineNum++; |
1382 |
|
|
|
1383 |
|
|
if( eof_test == NULL ){ |
1384 |
|
|
sprintf( painCave.errMsg, |
1385 |
|
|
"Error fast forwarding force file for %s at " |
1386 |
|
|
"line %d: file ended unexpectedly.\n", |
1387 |
|
|
searchOwner, |
1388 |
|
|
lineNum ); |
1389 |
|
|
painCave.isFatal = 1; |
1390 |
|
|
simError(); |
1391 |
|
|
} |
1392 |
|
|
} |
1393 |
|
|
} |
1394 |
|
|
} |
1395 |
|
|
|
1396 |
|
|
|
1397 |
|
|
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1398 |
|
|
|
1399 |
|
|
char* the_token; |
1400 |
|
|
|
1401 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1402 |
|
|
if( the_token != NULL ){ |
1403 |
|
|
|
1404 |
|
|
strcpy( info.name, the_token ); |
1405 |
|
|
|
1406 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1407 |
|
|
sprintf( painCave.errMsg, |
1408 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1409 |
|
|
painCave.isFatal = 1; |
1410 |
|
|
simError(); |
1411 |
|
|
} |
1412 |
|
|
|
1413 |
|
|
info.isDipole = atoi( the_token ); |
1414 |
|
|
|
1415 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1416 |
|
|
sprintf( painCave.errMsg, |
1417 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1418 |
|
|
painCave.isFatal = 1; |
1419 |
|
|
simError(); |
1420 |
|
|
} |
1421 |
|
|
|
1422 |
|
|
info.isSSD = atoi( the_token ); |
1423 |
|
|
|
1424 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1425 |
|
|
sprintf( painCave.errMsg, |
1426 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1427 |
|
|
painCave.isFatal = 1; |
1428 |
|
|
simError(); |
1429 |
|
|
} |
1430 |
|
|
|
1431 |
|
|
info.mass = atof( the_token ); |
1432 |
|
|
|
1433 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1434 |
|
|
sprintf( painCave.errMsg, |
1435 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1436 |
|
|
painCave.isFatal = 1; |
1437 |
|
|
simError(); |
1438 |
|
|
} |
1439 |
|
|
|
1440 |
|
|
info.epslon = atof( the_token ); |
1441 |
|
|
|
1442 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1443 |
|
|
sprintf( painCave.errMsg, |
1444 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1445 |
|
|
painCave.isFatal = 1; |
1446 |
|
|
simError(); |
1447 |
|
|
} |
1448 |
|
|
|
1449 |
|
|
info.sigma = atof( the_token ); |
1450 |
|
|
|
1451 |
|
|
if( info.isDipole ){ |
1452 |
|
|
|
1453 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1454 |
|
|
sprintf( painCave.errMsg, |
1455 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1456 |
|
|
painCave.isFatal = 1; |
1457 |
|
|
simError(); |
1458 |
|
|
} |
1459 |
|
|
|
1460 |
|
|
info.dipole = atof( the_token ); |
1461 |
|
|
} |
1462 |
|
|
else info.dipole = 0.0; |
1463 |
|
|
|
1464 |
|
|
if( info.isSSD ){ |
1465 |
|
|
|
1466 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1467 |
|
|
sprintf( painCave.errMsg, |
1468 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1469 |
|
|
painCave.isFatal = 1; |
1470 |
|
|
simError(); |
1471 |
|
|
} |
1472 |
|
|
|
1473 |
|
|
info.w0 = atof( the_token ); |
1474 |
|
|
|
1475 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1476 |
|
|
sprintf( painCave.errMsg, |
1477 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1478 |
|
|
painCave.isFatal = 1; |
1479 |
|
|
simError(); |
1480 |
|
|
} |
1481 |
|
|
|
1482 |
|
|
info.v0 = atof( the_token ); |
1483 |
|
|
} |
1484 |
|
|
else info.v0 = info.w0 = 0.0; |
1485 |
|
|
|
1486 |
|
|
return 1; |
1487 |
|
|
} |
1488 |
|
|
else return 0; |
1489 |
|
|
} |
1490 |
|
|
|
1491 |
|
|
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1492 |
|
|
|
1493 |
|
|
char* the_token; |
1494 |
|
|
|
1495 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1496 |
|
|
if( the_token != NULL ){ |
1497 |
|
|
|
1498 |
|
|
strcpy( info.nameA, the_token ); |
1499 |
|
|
|
1500 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1501 |
|
|
sprintf( painCave.errMsg, |
1502 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1503 |
|
|
painCave.isFatal = 1; |
1504 |
|
|
simError(); |
1505 |
|
|
} |
1506 |
|
|
|
1507 |
|
|
strcpy( info.nameB, the_token ); |
1508 |
|
|
|
1509 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1510 |
|
|
sprintf( painCave.errMsg, |
1511 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1512 |
|
|
painCave.isFatal = 1; |
1513 |
|
|
simError(); |
1514 |
|
|
} |
1515 |
|
|
|
1516 |
|
|
strcpy( info.type, the_token ); |
1517 |
|
|
|
1518 |
|
|
if( !strcmp( info.type, "fixed" ) ){ |
1519 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1520 |
|
|
sprintf( painCave.errMsg, |
1521 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1522 |
|
|
painCave.isFatal = 1; |
1523 |
|
|
simError(); |
1524 |
|
|
} |
1525 |
|
|
|
1526 |
|
|
info.d0 = atof( the_token ); |
1527 |
|
|
} |
1528 |
|
|
else{ |
1529 |
|
|
sprintf( painCave.errMsg, |
1530 |
|
|
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
1531 |
|
|
info.type, |
1532 |
|
|
lineNum ); |
1533 |
|
|
painCave.isFatal = 1; |
1534 |
|
|
simError(); |
1535 |
|
|
} |
1536 |
|
|
|
1537 |
|
|
return 1; |
1538 |
|
|
} |
1539 |
|
|
else return 0; |
1540 |
|
|
} |
1541 |
|
|
|
1542 |
|
|
|
1543 |
|
|
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1544 |
|
|
|
1545 |
|
|
char* the_token; |
1546 |
|
|
|
1547 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1548 |
|
|
if( the_token != NULL ){ |
1549 |
|
|
|
1550 |
|
|
strcpy( info.nameA, the_token ); |
1551 |
|
|
|
1552 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1553 |
|
|
sprintf( painCave.errMsg, |
1554 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1555 |
|
|
painCave.isFatal = 1; |
1556 |
|
|
simError(); |
1557 |
|
|
} |
1558 |
|
|
|
1559 |
|
|
strcpy( info.nameB, the_token ); |
1560 |
|
|
|
1561 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1562 |
|
|
sprintf( painCave.errMsg, |
1563 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1564 |
|
|
painCave.isFatal = 1; |
1565 |
|
|
simError(); |
1566 |
|
|
} |
1567 |
|
|
|
1568 |
|
|
strcpy( info.nameC, the_token ); |
1569 |
|
|
|
1570 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1571 |
|
|
sprintf( painCave.errMsg, |
1572 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1573 |
|
|
painCave.isFatal = 1; |
1574 |
|
|
simError(); |
1575 |
|
|
} |
1576 |
|
|
|
1577 |
|
|
strcpy( info.type, the_token ); |
1578 |
|
|
|
1579 |
|
|
if( !strcmp( info.type, "quadratic" ) ){ |
1580 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1581 |
|
|
sprintf( painCave.errMsg, |
1582 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1583 |
|
|
painCave.isFatal = 1; |
1584 |
|
|
simError(); |
1585 |
|
|
} |
1586 |
|
|
|
1587 |
|
|
info.k1 = atof( the_token ); |
1588 |
|
|
|
1589 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1590 |
|
|
sprintf( painCave.errMsg, |
1591 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1592 |
|
|
painCave.isFatal = 1; |
1593 |
|
|
simError(); |
1594 |
|
|
} |
1595 |
|
|
|
1596 |
|
|
info.k2 = atof( the_token ); |
1597 |
|
|
|
1598 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1599 |
|
|
sprintf( painCave.errMsg, |
1600 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1601 |
|
|
painCave.isFatal = 1; |
1602 |
|
|
simError(); |
1603 |
|
|
} |
1604 |
|
|
|
1605 |
|
|
info.k3 = atof( the_token ); |
1606 |
|
|
|
1607 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1608 |
|
|
sprintf( painCave.errMsg, |
1609 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1610 |
|
|
painCave.isFatal = 1; |
1611 |
|
|
simError(); |
1612 |
|
|
} |
1613 |
|
|
|
1614 |
|
|
info.t0 = atof( the_token ); |
1615 |
|
|
} |
1616 |
|
|
|
1617 |
|
|
else{ |
1618 |
|
|
sprintf( painCave.errMsg, |
1619 |
|
|
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
1620 |
|
|
info.type, |
1621 |
|
|
lineNum ); |
1622 |
|
|
painCave.isFatal = 1; |
1623 |
|
|
simError(); |
1624 |
|
|
} |
1625 |
|
|
|
1626 |
|
|
return 1; |
1627 |
|
|
} |
1628 |
|
|
else return 0; |
1629 |
|
|
} |
1630 |
|
|
|
1631 |
|
|
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1632 |
|
|
|
1633 |
|
|
char* the_token; |
1634 |
|
|
|
1635 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1636 |
|
|
if( the_token != NULL ){ |
1637 |
|
|
|
1638 |
|
|
strcpy( info.nameA, the_token ); |
1639 |
|
|
|
1640 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1641 |
|
|
sprintf( painCave.errMsg, |
1642 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1643 |
|
|
painCave.isFatal = 1; |
1644 |
|
|
simError(); |
1645 |
|
|
} |
1646 |
|
|
|
1647 |
|
|
strcpy( info.nameB, the_token ); |
1648 |
|
|
|
1649 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1650 |
|
|
sprintf( painCave.errMsg, |
1651 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1652 |
|
|
painCave.isFatal = 1; |
1653 |
|
|
simError(); |
1654 |
|
|
} |
1655 |
|
|
|
1656 |
|
|
strcpy( info.nameC, the_token ); |
1657 |
|
|
|
1658 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1659 |
|
|
sprintf( painCave.errMsg, |
1660 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1661 |
|
|
painCave.isFatal = 1; |
1662 |
|
|
simError(); |
1663 |
|
|
} |
1664 |
|
|
|
1665 |
|
|
strcpy( info.nameD, the_token ); |
1666 |
|
|
|
1667 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1668 |
|
|
sprintf( painCave.errMsg, |
1669 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1670 |
|
|
painCave.isFatal = 1; |
1671 |
|
|
simError(); |
1672 |
|
|
} |
1673 |
|
|
|
1674 |
|
|
strcpy( info.type, the_token ); |
1675 |
|
|
|
1676 |
|
|
if( !strcmp( info.type, "cubic" ) ){ |
1677 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1678 |
|
|
sprintf( painCave.errMsg, |
1679 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1680 |
|
|
painCave.isFatal = 1; |
1681 |
|
|
simError(); |
1682 |
|
|
} |
1683 |
|
|
|
1684 |
|
|
info.k1 = atof( the_token ); |
1685 |
|
|
|
1686 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1687 |
|
|
sprintf( painCave.errMsg, |
1688 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1689 |
|
|
painCave.isFatal = 1; |
1690 |
|
|
simError(); |
1691 |
|
|
} |
1692 |
|
|
|
1693 |
|
|
info.k2 = atof( the_token ); |
1694 |
|
|
|
1695 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1696 |
|
|
sprintf( painCave.errMsg, |
1697 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1698 |
|
|
painCave.isFatal = 1; |
1699 |
|
|
simError(); |
1700 |
|
|
} |
1701 |
|
|
|
1702 |
|
|
info.k3 = atof( the_token ); |
1703 |
|
|
|
1704 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1705 |
|
|
sprintf( painCave.errMsg, |
1706 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1707 |
|
|
painCave.isFatal = 1; |
1708 |
|
|
simError(); |
1709 |
|
|
} |
1710 |
|
|
|
1711 |
|
|
info.k4 = atof( the_token ); |
1712 |
|
|
|
1713 |
|
|
} |
1714 |
|
|
|
1715 |
|
|
else{ |
1716 |
|
|
sprintf( painCave.errMsg, |
1717 |
|
|
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1718 |
|
|
info.type, |
1719 |
|
|
lineNum ); |
1720 |
|
|
painCave.isFatal = 1; |
1721 |
|
|
simError(); |
1722 |
|
|
} |
1723 |
|
|
|
1724 |
|
|
return 1; |
1725 |
|
|
} |
1726 |
|
|
|
1727 |
|
|
else return 0; |
1728 |
|
|
} |