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mmeineke |
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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <iostream> |
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using namespace std; |
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#include "ForceFields.hpp" |
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#include "SRI.hpp" |
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chuckv |
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#ifdef IS_MPI |
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mmeineke |
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#include "mpiForceField.h" |
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chuckv |
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int myNode; |
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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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int isDipole; |
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int last; // 0 -> default |
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// 1 -> tells nodes to stop listening |
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// -1 -> an error has occured. (handled in mpiForceField) |
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} atomStruct; |
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MPI_Datatype mpiAtomStructType; |
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mmeineke |
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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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// -1 -> an error has occured. (handled in mpiForceField) |
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} bondStruct; |
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MPI_Datatype mpiBondStructType; |
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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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// -1 -> an error has occured. (handled in mpiForceField) |
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} bendStruct; |
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MPI_Datatype mpiBendStructType; |
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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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// -1 -> an error has occured. (handled in mpiForceField) |
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} TorsionStruct; |
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MPI_Datatype mpiTorsionStructType; |
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chuckv |
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#endif |
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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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mmeineke |
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char errMsg[1000]; |
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mmeineke |
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|
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chuckv |
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#ifdef IS_MPI |
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int i; |
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int mpiError; |
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mmeineke |
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int cleanOpen = 0; |
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mmeineke |
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|
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chuckv |
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mpiError = MPI_Comm_rank(MPI_COMM_WORLD,&myNode); |
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mmeineke |
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|
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// ********************************************************************** |
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// Init the atomStruct mpi type |
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chuckv |
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atomStruct atomProto; // mpiPrototype |
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int atomBC[3] = {15,4,2}; // block counts |
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MPI_Aint atomDspls[3]; // displacements |
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MPI_Datatype atomMbrTypes[3]; // member mpi types |
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chuckv |
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chuckv |
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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.isDipole, &atomDspls[2]); |
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mmeineke |
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chuckv |
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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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mmeineke |
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chuckv |
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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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mmeineke |
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chuckv |
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mmeineke |
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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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chuckv |
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mmeineke |
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mmeineke |
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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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chuckv |
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if( myNode == 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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mmeineke |
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// fprintf( stderr,"Trying to open %s\n", fileName ); |
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chuckv |
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// attempt to open the file in the current directory first. |
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mmeineke |
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frcFile = fopen( fileName, "r" ); |
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if( frcFile == NULL ){ |
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chuckv |
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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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mmeineke |
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sprintf( errMsg, |
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chuckv |
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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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mmeineke |
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#ifdef IS_MPI |
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cleanOpen = 0; |
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mpiError = MPI_Bcast(cleanOpen,1,MPI_INT,0,MPI_COMM_WORLD); |
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#endif |
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ffError( errMsg ); |
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chuckv |
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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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mmeineke |
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sprintf( errMsg, |
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chuckv |
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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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mmeineke |
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#ifdef IS_MPI |
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cleanOpen = 0; |
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mpiError = MPI_Bcast(cleanOpen,1,MPI_INT,0,MPI_COMM_WORLD); |
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#endif |
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ffError( errMsg ); |
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chuckv |
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} |
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mmeineke |
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} |
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mmeineke |
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cleanOpen = 1; |
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chuckv |
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#ifdef IS_MPI |
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mmeineke |
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} |
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mmeineke |
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mpiError = MPI_Bcast(cleanOpen,1,MPI_INT,0,MPI_COMM_WORLD); |
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if( !cleanOpen ) fferror( NULL ); |
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chuckv |
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#endif |
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mmeineke |
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} |
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chuckv |
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mmeineke |
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TraPPE_ExFF::~TraPPE_ExFF(){ |
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fclose( frcFile ); |
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} |
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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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chuckv |
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#ifdef IS_MPI |
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void add( atomStruct &info ){ |
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if( next != NULL ) next->add(info); |
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else{ |
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next = new LinkedType(); |
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strcpy(next->name, info.name); |
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next->isDipole = info.dipole; |
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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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} |
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} |
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void duplicate( atomStruct &info ){ |
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strcpy(info.name, name); |
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info.isDipole = dipole; |
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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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info.last = 0; |
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} |
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#endif |
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mmeineke |
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char name[15]; |
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int isDipole; |
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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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LinkedType* next; |
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}; |
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LinkedType* headAtomType; |
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LinkedType* currentAtomType; |
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LinkedType* tempAtomType; |
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mmeineke |
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#ifdef IS_MPI |
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atomStruct info; |
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info.last = -1; // initialize last to have the error set. |
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// if things go well, last will be set to 0 |
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#endif |
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mmeineke |
10 |
char readLine[500]; |
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char* the_token; |
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char* eof_test; |
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int foundAtom = 0; |
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int lineNum = 0; |
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int i; |
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mmeineke |
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char errMsg[1000]; |
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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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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 |
147 |
#ifdef IS_MPI |
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if( myNode == 0 ){ |
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#endif |
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// read in the atom types. |
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rewind( frcFile ); |
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headAtomType = new LinkedType; |
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currentAtomType = headAtomType; |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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mmeineke |
10 |
if( eof_test == NULL ){ |
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mmeineke |
152 |
sprintf( errMsg, "Error in reading Atoms from force file.\n" ); |
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#ifdef IS_MPI |
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sendFrcStruct( &info, mpiAtomStructType ); |
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#endif |
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ffError(errMsg); |
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mmeineke |
10 |
} |
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mmeineke |
147 |
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while( !foundAtom ){ |
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while( eof_test != NULL && readLine[0] != '#' ){ |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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} |
385 |
mmeineke |
10 |
if( eof_test == NULL ){ |
386 |
mmeineke |
152 |
sprintf( errMsg, |
387 |
mmeineke |
10 |
"Error in reading Atoms from force file at line %d.\n", |
388 |
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lineNum ); |
389 |
mmeineke |
152 |
#ifdef IS_MPI |
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|
|
sendFrcStruct( &info, mpiAtomStructType ); |
391 |
|
|
#endif |
392 |
|
|
ffError(errMsg); |
393 |
mmeineke |
147 |
} |
394 |
|
|
|
395 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
396 |
|
|
foundAtom = !strcmp( "AtomTypes", the_token ); |
397 |
|
|
|
398 |
|
|
if( !foundAtom ){ |
399 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
400 |
|
|
lineNum++; |
401 |
|
|
|
402 |
|
|
if( eof_test == NULL ){ |
403 |
mmeineke |
152 |
sprintf( errMsg, |
404 |
mmeineke |
147 |
"Error in reading Atoms from force file at line %d.\n", |
405 |
|
|
lineNum ); |
406 |
mmeineke |
152 |
#ifdef IS_MPI |
407 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
408 |
|
|
#endif |
409 |
|
|
ffError(errMsg); |
410 |
mmeineke |
147 |
} |
411 |
|
|
} |
412 |
mmeineke |
10 |
} |
413 |
|
|
|
414 |
mmeineke |
147 |
// we are now at the AtomTypes section. |
415 |
|
|
|
416 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
417 |
|
|
lineNum++; |
418 |
|
|
|
419 |
|
|
if( eof_test == NULL ){ |
420 |
mmeineke |
152 |
sprintf( errMsg, |
421 |
mmeineke |
147 |
"Error in reading Atoms from force file at line %d.\n", |
422 |
|
|
lineNum ); |
423 |
mmeineke |
152 |
#ifdef IS_MPI |
424 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
425 |
|
|
#endif |
426 |
|
|
ffError(errMsg); |
427 |
mmeineke |
147 |
} |
428 |
|
|
|
429 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
430 |
mmeineke |
10 |
|
431 |
mmeineke |
147 |
if( readLine[0] != '!' ){ |
432 |
mmeineke |
10 |
|
433 |
mmeineke |
147 |
the_token = strtok( readLine, " \n\t,;" ); |
434 |
|
|
if( the_token != NULL ){ |
435 |
|
|
|
436 |
|
|
strcpy( currentAtomType->name, the_token ); |
437 |
|
|
|
438 |
mmeineke |
10 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
439 |
mmeineke |
152 |
sprintf( errMsg, "Error parseing AtomTypes: line %d\n", lineNum ); |
440 |
|
|
#ifdef IS_MPI |
441 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
442 |
|
|
#endif |
443 |
|
|
ffError(errMsg); |
444 |
mmeineke |
10 |
} |
445 |
|
|
|
446 |
mmeineke |
147 |
sscanf( the_token, "%d", ¤tAtomType->isDipole ); |
447 |
|
|
|
448 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
449 |
mmeineke |
152 |
sprintf( errMsg, "Error parseing AtomTypes: line %d\n", lineNum ); |
450 |
|
|
#ifdef IS_MPI |
451 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
452 |
|
|
#endif |
453 |
|
|
ffError(errMsg); |
454 |
mmeineke |
147 |
} |
455 |
|
|
|
456 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->mass ); |
457 |
|
|
|
458 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
459 |
mmeineke |
152 |
sprintf( errMsg, "Error parseing AtomTypes: line %d\n", lineNum ); |
460 |
|
|
#ifdef IS_MPI |
461 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
462 |
|
|
#endif |
463 |
|
|
ffError(errMsg); |
464 |
mmeineke |
147 |
} |
465 |
|
|
|
466 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
467 |
|
|
|
468 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
469 |
mmeineke |
152 |
sprintf( errMsg, "Error parseing AtomTypes: line %d\n", lineNum ); |
470 |
|
|
#ifdef IS_MPI |
471 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
472 |
|
|
#endif |
473 |
|
|
ffError(errMsg); |
474 |
mmeineke |
147 |
} |
475 |
|
|
|
476 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
477 |
|
|
|
478 |
|
|
if( currentAtomType->isDipole ){ |
479 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
480 |
mmeineke |
152 |
sprintf( errMsg, "Error parseing AtomTypes: line %d\n", |
481 |
|
|
lineNum ); |
482 |
|
|
#ifdef IS_MPI |
483 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
484 |
|
|
#endif |
485 |
|
|
ffError(errMsg); |
486 |
mmeineke |
147 |
} |
487 |
|
|
|
488 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->dipole ); |
489 |
|
|
} |
490 |
mmeineke |
10 |
} |
491 |
|
|
} |
492 |
mmeineke |
147 |
|
493 |
|
|
tempAtomType = new LinkedType; |
494 |
|
|
currentAtomType->next = tempAtomType; |
495 |
|
|
currentAtomType = tempAtomType; |
496 |
|
|
|
497 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
498 |
|
|
lineNum++; |
499 |
mmeineke |
10 |
} |
500 |
mmeineke |
147 |
|
501 |
|
|
#ifdef IS_MPI |
502 |
mmeineke |
152 |
|
503 |
|
|
// send out the linked list to all the other processes |
504 |
|
|
|
505 |
|
|
currentAtomType = headAtomType; |
506 |
|
|
while( currentAtomType != NULL ){ |
507 |
|
|
currentAtomType->duplicate( info ); |
508 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
509 |
|
|
currentAtomType = currentAtomType->next; |
510 |
|
|
} |
511 |
|
|
info.last = 1; |
512 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
513 |
|
|
|
514 |
mmeineke |
147 |
} |
515 |
|
|
|
516 |
|
|
else{ |
517 |
mmeineke |
10 |
|
518 |
mmeineke |
152 |
// listen for node 0 to send out the force params |
519 |
|
|
|
520 |
|
|
headAtomType = new LinkedType; |
521 |
|
|
recieveFrcStruct( &info, mpiAtomStructType ); |
522 |
|
|
while( !info.last ){ |
523 |
|
|
|
524 |
|
|
headAtomType->add( info ); |
525 |
|
|
recieveFrcStruct( &info, mpiAtomStructType ); |
526 |
|
|
} |
527 |
|
|
|
528 |
|
|
if( info.last < 0 ) ffError( NULL ); // an error has occured, exit quietly. |
529 |
|
|
|
530 |
mmeineke |
10 |
|
531 |
|
|
} |
532 |
mmeineke |
147 |
#endif |
533 |
mmeineke |
10 |
|
534 |
|
|
|
535 |
|
|
// initialize the atoms |
536 |
|
|
|
537 |
|
|
DirectionalAtom* dAtom; |
538 |
|
|
|
539 |
|
|
for( i=0; i<nAtoms; i++ ){ |
540 |
|
|
|
541 |
|
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
542 |
|
|
if( currentAtomType == NULL ){ |
543 |
mmeineke |
152 |
sprintf( errMsg, "AtomType error, %s not found in force file.\n", |
544 |
mmeineke |
10 |
the_atoms[i]->getType() ); |
545 |
mmeineke |
152 |
ffError(errMsg); |
546 |
mmeineke |
10 |
} |
547 |
|
|
|
548 |
|
|
the_atoms[i]->setMass( currentAtomType->mass ); |
549 |
|
|
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
550 |
|
|
the_atoms[i]->setSigma( currentAtomType->sigma ); |
551 |
|
|
the_atoms[i]->setLJ(); |
552 |
|
|
|
553 |
|
|
if( currentAtomType->isDipole ){ |
554 |
|
|
if( the_atoms[i]->isDirectional() ){ |
555 |
|
|
|
556 |
|
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
557 |
|
|
dAtom->setMu( currentAtomType->dipole ); |
558 |
|
|
dAtom->setHasDipole( 1 ); |
559 |
|
|
dAtom->setJx( 0.0 ); |
560 |
|
|
dAtom->setJy( 0.0 ); |
561 |
|
|
dAtom->setJz( 0.0 ); |
562 |
|
|
|
563 |
|
|
if(!strcmp("SSD",the_atoms[i]->getType())){ |
564 |
|
|
dAtom->setI( waterI ); |
565 |
|
|
dAtom->setSSD( 1 ); |
566 |
|
|
} |
567 |
|
|
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
568 |
|
|
dAtom->setI( headI ); |
569 |
|
|
dAtom->setSSD( 0 ); |
570 |
|
|
} |
571 |
|
|
else{ |
572 |
mmeineke |
152 |
sprintf(errMsg, |
573 |
mmeineke |
10 |
"AtmType error, %s does not have a moment of inertia set.\n", |
574 |
|
|
the_atoms[i]->getType() ); |
575 |
mmeineke |
152 |
ffError(errMsg); |
576 |
mmeineke |
10 |
} |
577 |
|
|
entry_plug->n_dipoles++; |
578 |
|
|
} |
579 |
|
|
else{ |
580 |
mmeineke |
152 |
|
581 |
|
|
sprintf( errMsg, |
582 |
|
|
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
583 |
|
|
" orientation was specifed in the BASS file.\n", |
584 |
|
|
currentAtomType->name ); |
585 |
|
|
|
586 |
|
|
ffError(errMsg); |
587 |
mmeineke |
10 |
} |
588 |
|
|
} |
589 |
|
|
else{ |
590 |
|
|
if( the_atoms[i]->isDirectional() ){ |
591 |
mmeineke |
152 |
sprintf( errMsg, |
592 |
|
|
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
593 |
|
|
"orientation in the BASS file, yet it is not a dipole.\n", |
594 |
|
|
currentAtomType->name); |
595 |
|
|
ffError(errMsg); |
596 |
mmeineke |
10 |
} |
597 |
|
|
} |
598 |
|
|
} |
599 |
|
|
|
600 |
|
|
|
601 |
|
|
// clean up the memory |
602 |
|
|
|
603 |
|
|
delete headAtomType; |
604 |
|
|
} |
605 |
|
|
|
606 |
|
|
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
607 |
|
|
|
608 |
|
|
class LinkedType { |
609 |
|
|
public: |
610 |
|
|
LinkedType(){ |
611 |
|
|
next = NULL; |
612 |
|
|
nameA[0] = '\0'; |
613 |
|
|
nameB[0] = '\0'; |
614 |
|
|
type[0] = '\0'; |
615 |
|
|
} |
616 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
617 |
|
|
|
618 |
|
|
LinkedType* find(char* key1, char* key2){ |
619 |
|
|
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
620 |
|
|
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
621 |
|
|
if( next != NULL ) return next->find(key1, key2); |
622 |
|
|
return NULL; |
623 |
|
|
} |
624 |
|
|
|
625 |
mmeineke |
146 |
#ifdef IS_MPI |
626 |
|
|
void add( bondStruct &info ){ |
627 |
|
|
if( next != NULL ) next->add(info); |
628 |
|
|
else{ |
629 |
|
|
next = new LinkedType(); |
630 |
|
|
strcpy(next->nameA, info.nameA); |
631 |
|
|
strcpy(next->nameB, info.nameB); |
632 |
|
|
strcpy(next->type, info.type); |
633 |
|
|
next->d0 = info.d0; |
634 |
|
|
} |
635 |
|
|
} |
636 |
|
|
|
637 |
|
|
void duplicate( bondStruct &info ){ |
638 |
|
|
strcpy(info.nameA, nameA); |
639 |
|
|
strcpy(info.nameB, nameB); |
640 |
|
|
strcpy(info.type, type); |
641 |
|
|
info.d0 = d0; |
642 |
|
|
info.last = 0; |
643 |
|
|
} |
644 |
|
|
|
645 |
|
|
|
646 |
|
|
#endif |
647 |
|
|
|
648 |
mmeineke |
10 |
char nameA[15]; |
649 |
|
|
char nameB[15]; |
650 |
|
|
char type[30]; |
651 |
|
|
double d0; |
652 |
|
|
|
653 |
|
|
LinkedType* next; |
654 |
|
|
}; |
655 |
|
|
|
656 |
|
|
|
657 |
|
|
|
658 |
|
|
LinkedType* headBondType; |
659 |
|
|
LinkedType* currentBondType; |
660 |
|
|
LinkedType* tempBondType; |
661 |
|
|
|
662 |
|
|
char readLine[500]; |
663 |
|
|
char* the_token; |
664 |
|
|
char* eof_test; |
665 |
|
|
int foundBond = 0; |
666 |
|
|
int lineNum = 0; |
667 |
|
|
int i, a, b; |
668 |
|
|
char* atomA; |
669 |
|
|
char* atomB; |
670 |
|
|
|
671 |
|
|
SRI **the_sris; |
672 |
|
|
Atom** the_atoms; |
673 |
|
|
int nBonds; |
674 |
|
|
the_sris = entry_plug->sr_interactions; |
675 |
|
|
the_atoms = entry_plug->atoms; |
676 |
|
|
nBonds = entry_plug->n_bonds; |
677 |
|
|
|
678 |
|
|
// read in the bond types. |
679 |
|
|
|
680 |
|
|
rewind( frcFile ); |
681 |
|
|
headBondType = new LinkedType; |
682 |
|
|
currentBondType = headBondType; |
683 |
|
|
|
684 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
685 |
|
|
lineNum++; |
686 |
|
|
if( eof_test == NULL ){ |
687 |
|
|
fprintf( stderr, "Error in reading Bonds from force file.\n" ); |
688 |
|
|
exit(8); |
689 |
|
|
} |
690 |
|
|
|
691 |
|
|
|
692 |
|
|
while( !foundBond ){ |
693 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
694 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
695 |
|
|
lineNum++; |
696 |
|
|
} |
697 |
|
|
if( eof_test == NULL ){ |
698 |
|
|
fprintf( stderr, |
699 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
700 |
|
|
lineNum ); |
701 |
|
|
exit(8); |
702 |
|
|
} |
703 |
|
|
|
704 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
705 |
|
|
foundBond = !strcmp( "BondTypes", the_token ); |
706 |
|
|
|
707 |
|
|
if( !foundBond ){ |
708 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
709 |
|
|
lineNum++; |
710 |
|
|
|
711 |
|
|
if( eof_test == NULL ){ |
712 |
|
|
fprintf( stderr, |
713 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
714 |
|
|
lineNum ); |
715 |
|
|
exit(8); |
716 |
|
|
} |
717 |
|
|
} |
718 |
|
|
} |
719 |
|
|
|
720 |
|
|
// we are now at the BondTypes section. |
721 |
|
|
|
722 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
723 |
|
|
lineNum++; |
724 |
|
|
|
725 |
|
|
if( eof_test == NULL ){ |
726 |
|
|
fprintf( stderr, |
727 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
728 |
|
|
lineNum ); |
729 |
|
|
exit(8); |
730 |
|
|
} |
731 |
|
|
|
732 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
733 |
|
|
|
734 |
|
|
if( readLine[0] != '!' ){ |
735 |
|
|
|
736 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
737 |
|
|
if( the_token != NULL ){ |
738 |
|
|
|
739 |
|
|
strcpy( currentBondType->nameA, the_token ); |
740 |
|
|
|
741 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
742 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
743 |
|
|
exit(8); |
744 |
|
|
} |
745 |
|
|
|
746 |
|
|
strcpy( currentBondType->nameB, the_token ); |
747 |
|
|
|
748 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
749 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
750 |
|
|
exit(8); |
751 |
|
|
} |
752 |
|
|
|
753 |
|
|
strcpy( currentBondType->type, the_token ); |
754 |
|
|
|
755 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
756 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
757 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
758 |
|
|
exit(8); |
759 |
|
|
} |
760 |
|
|
|
761 |
|
|
sscanf( the_token, "%lf", ¤tBondType->d0 ); |
762 |
|
|
} |
763 |
|
|
|
764 |
|
|
else{ |
765 |
|
|
fprintf(stderr, |
766 |
|
|
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
767 |
|
|
currentBondType->type, |
768 |
|
|
lineNum ); |
769 |
|
|
exit(8); |
770 |
|
|
} |
771 |
|
|
} |
772 |
|
|
} |
773 |
|
|
|
774 |
|
|
tempBondType = new LinkedType; |
775 |
|
|
currentBondType->next = tempBondType; |
776 |
|
|
currentBondType = tempBondType; |
777 |
|
|
|
778 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
779 |
|
|
lineNum++; |
780 |
|
|
} |
781 |
|
|
|
782 |
|
|
|
783 |
|
|
// initialize the Bonds |
784 |
|
|
|
785 |
|
|
|
786 |
|
|
for( i=0; i<nBonds; i++ ){ |
787 |
|
|
|
788 |
|
|
a = the_bonds[i].a; |
789 |
|
|
b = the_bonds[i].b; |
790 |
|
|
|
791 |
|
|
atomA = the_atoms[a]->getType(); |
792 |
|
|
atomB = the_atoms[b]->getType(); |
793 |
|
|
currentBondType = headBondType->find( atomA, atomB ); |
794 |
|
|
if( currentBondType == NULL ){ |
795 |
|
|
fprintf( stderr, "BondType error, %s - %s not found in force file.\n", |
796 |
|
|
atomA, atomB ); |
797 |
|
|
exit(8); |
798 |
|
|
} |
799 |
|
|
|
800 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
801 |
|
|
|
802 |
|
|
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
803 |
|
|
*the_atoms[b], |
804 |
|
|
currentBondType->d0 ); |
805 |
|
|
entry_plug->n_constraints++; |
806 |
|
|
} |
807 |
|
|
} |
808 |
|
|
|
809 |
|
|
|
810 |
|
|
// clean up the memory |
811 |
|
|
|
812 |
|
|
delete headBondType; |
813 |
|
|
|
814 |
|
|
} |
815 |
|
|
|
816 |
|
|
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
817 |
|
|
|
818 |
|
|
class LinkedType { |
819 |
|
|
public: |
820 |
|
|
LinkedType(){ |
821 |
|
|
next = NULL; |
822 |
|
|
nameA[0] = '\0'; |
823 |
|
|
nameB[0] = '\0'; |
824 |
|
|
nameC[0] = '\0'; |
825 |
|
|
type[0] = '\0'; |
826 |
|
|
} |
827 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
828 |
|
|
|
829 |
|
|
LinkedType* find( char* key1, char* key2, char* key3 ){ |
830 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
831 |
|
|
&& !strcmp( nameC, key3 ) ) return this; |
832 |
|
|
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
833 |
|
|
&& !strcmp( nameC, key1 ) ) return this; |
834 |
|
|
if( next != NULL ) return next->find(key1, key2, key3); |
835 |
|
|
return NULL; |
836 |
|
|
} |
837 |
|
|
|
838 |
mmeineke |
146 |
#ifdef IS_MPI |
839 |
|
|
|
840 |
|
|
void add( bendStruct &info ){ |
841 |
|
|
if( next != NULL ) next->add(info); |
842 |
|
|
else{ |
843 |
|
|
next = new LinkedType(); |
844 |
|
|
strcpy(next->nameA, info.nameA); |
845 |
|
|
strcpy(next->nameB, info.nameB); |
846 |
|
|
strcpy(next->nameC, info.nameC); |
847 |
|
|
strcpy(next->type, info.type); |
848 |
|
|
next->k1 = info.k1; |
849 |
|
|
next->k2 = info.k2; |
850 |
|
|
next->k3 = info.k3; |
851 |
|
|
next->t0 = info.t0; |
852 |
|
|
} |
853 |
|
|
} |
854 |
|
|
|
855 |
|
|
void duplicate( bendStruct &info ){ |
856 |
|
|
strcpy(info.nameA, nameA); |
857 |
|
|
strcpy(info.nameB, nameB); |
858 |
|
|
strcpy(info.nameC, nameC); |
859 |
|
|
strcpy(info.type, type); |
860 |
|
|
info.k1 = k1; |
861 |
|
|
info.k2 = k2; |
862 |
|
|
info.k3 = k3; |
863 |
|
|
info.t0 = t0; |
864 |
|
|
info.last = 0; |
865 |
|
|
} |
866 |
|
|
|
867 |
|
|
#endif |
868 |
|
|
|
869 |
mmeineke |
10 |
char nameA[15]; |
870 |
|
|
char nameB[15]; |
871 |
|
|
char nameC[15]; |
872 |
|
|
char type[30]; |
873 |
|
|
double k1, k2, k3, t0; |
874 |
|
|
|
875 |
|
|
LinkedType* next; |
876 |
|
|
}; |
877 |
|
|
|
878 |
|
|
LinkedType* headBendType; |
879 |
|
|
LinkedType* currentBendType; |
880 |
|
|
LinkedType* tempBendType; |
881 |
|
|
|
882 |
|
|
char readLine[500]; |
883 |
|
|
char* the_token; |
884 |
|
|
char* eof_test; |
885 |
|
|
int foundBend = 0; |
886 |
|
|
int lineNum = 0; |
887 |
|
|
int i, a, b, c, index; |
888 |
|
|
char* atomA; |
889 |
|
|
char* atomB; |
890 |
|
|
char* atomC; |
891 |
|
|
QuadraticBend* qBend; |
892 |
|
|
|
893 |
|
|
SRI **the_sris; |
894 |
|
|
Atom** the_atoms; |
895 |
|
|
int nBends; |
896 |
|
|
the_sris = entry_plug->sr_interactions; |
897 |
|
|
the_atoms = entry_plug->atoms; |
898 |
|
|
nBends = entry_plug->n_bends; |
899 |
|
|
|
900 |
|
|
// read in the bend types. |
901 |
|
|
|
902 |
|
|
rewind( frcFile ); |
903 |
|
|
headBendType = new LinkedType; |
904 |
|
|
currentBendType = headBendType; |
905 |
|
|
|
906 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
907 |
|
|
lineNum++; |
908 |
|
|
if( eof_test == NULL ){ |
909 |
|
|
fprintf( stderr, "Error in reading Bends from force file.\n" ); |
910 |
|
|
exit(8); |
911 |
|
|
} |
912 |
|
|
|
913 |
|
|
|
914 |
|
|
while( !foundBend ){ |
915 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
916 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
917 |
|
|
lineNum++; |
918 |
|
|
} |
919 |
|
|
if( eof_test == NULL ){ |
920 |
|
|
fprintf( stderr, |
921 |
|
|
"Error in reading Bends from force file at line %d.\n", |
922 |
|
|
lineNum ); |
923 |
|
|
exit(8); |
924 |
|
|
} |
925 |
|
|
|
926 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
927 |
|
|
foundBend = !strcmp( "BendTypes", the_token ); |
928 |
|
|
|
929 |
|
|
if( !foundBend ){ |
930 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
931 |
|
|
lineNum++; |
932 |
|
|
|
933 |
|
|
if( eof_test == NULL ){ |
934 |
|
|
fprintf( stderr, |
935 |
|
|
"Error in reading Bends from force file at line %d.\n", |
936 |
|
|
lineNum ); |
937 |
|
|
exit(8); |
938 |
|
|
} |
939 |
|
|
} |
940 |
|
|
} |
941 |
|
|
|
942 |
|
|
// we are now at the BendTypes section. |
943 |
|
|
|
944 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
945 |
|
|
lineNum++; |
946 |
|
|
|
947 |
|
|
if( eof_test == NULL ){ |
948 |
|
|
fprintf( stderr, |
949 |
|
|
"Error in reading Bends from force file at line %d.\n", |
950 |
|
|
lineNum ); |
951 |
|
|
exit(8); |
952 |
|
|
} |
953 |
|
|
|
954 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
955 |
|
|
|
956 |
|
|
if( readLine[0] != '!' ){ |
957 |
|
|
|
958 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
959 |
|
|
if( the_token != NULL ){ |
960 |
|
|
|
961 |
|
|
strcpy( currentBendType->nameA, the_token ); |
962 |
|
|
|
963 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
964 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
965 |
|
|
exit(8); |
966 |
|
|
} |
967 |
|
|
|
968 |
|
|
strcpy( currentBendType->nameB, the_token ); |
969 |
|
|
|
970 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
971 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
972 |
|
|
exit(8); |
973 |
|
|
} |
974 |
|
|
|
975 |
|
|
strcpy( currentBendType->nameC, the_token ); |
976 |
|
|
|
977 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
978 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
979 |
|
|
exit(8); |
980 |
|
|
} |
981 |
|
|
|
982 |
|
|
strcpy( currentBendType->type, the_token ); |
983 |
|
|
|
984 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
985 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
986 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
987 |
|
|
exit(8); |
988 |
|
|
} |
989 |
|
|
|
990 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
991 |
|
|
|
992 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
993 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
994 |
|
|
exit(8); |
995 |
|
|
} |
996 |
|
|
|
997 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
998 |
|
|
|
999 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1000 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
1001 |
|
|
exit(8); |
1002 |
|
|
} |
1003 |
|
|
|
1004 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
1005 |
|
|
|
1006 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1007 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
1008 |
|
|
exit(8); |
1009 |
|
|
} |
1010 |
|
|
|
1011 |
|
|
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
1012 |
|
|
} |
1013 |
|
|
|
1014 |
|
|
else{ |
1015 |
|
|
fprintf(stderr, |
1016 |
|
|
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
1017 |
|
|
currentBendType->type, |
1018 |
|
|
lineNum ); |
1019 |
|
|
exit(8); |
1020 |
|
|
} |
1021 |
|
|
} |
1022 |
|
|
} |
1023 |
|
|
|
1024 |
|
|
tempBendType = new LinkedType; |
1025 |
|
|
currentBendType->next = tempBendType; |
1026 |
|
|
currentBendType = tempBendType; |
1027 |
|
|
|
1028 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1029 |
|
|
lineNum++; |
1030 |
|
|
} |
1031 |
|
|
|
1032 |
|
|
|
1033 |
|
|
// initialize the Bends |
1034 |
|
|
|
1035 |
|
|
for( i=0; i<nBends; i++ ){ |
1036 |
|
|
|
1037 |
|
|
a = the_bends[i].a; |
1038 |
|
|
b = the_bends[i].b; |
1039 |
|
|
c = the_bends[i].c; |
1040 |
|
|
|
1041 |
|
|
atomA = the_atoms[a]->getType(); |
1042 |
|
|
atomB = the_atoms[b]->getType(); |
1043 |
|
|
atomC = the_atoms[c]->getType(); |
1044 |
|
|
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1045 |
|
|
if( currentBendType == NULL ){ |
1046 |
|
|
fprintf( stderr, "BendType error, %s - %s - %s not found" |
1047 |
|
|
" in force file.\n", |
1048 |
|
|
atomA, atomB, atomC ); |
1049 |
|
|
exit(8); |
1050 |
|
|
} |
1051 |
|
|
|
1052 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1053 |
|
|
|
1054 |
|
|
index = i + entry_plug->n_bonds; |
1055 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
1056 |
|
|
*the_atoms[b], |
1057 |
|
|
*the_atoms[c] ); |
1058 |
|
|
qBend->setConstants( currentBendType->k1, |
1059 |
|
|
currentBendType->k2, |
1060 |
|
|
currentBendType->k3, |
1061 |
|
|
currentBendType->t0 ); |
1062 |
|
|
the_sris[index] = qBend; |
1063 |
|
|
} |
1064 |
|
|
} |
1065 |
|
|
|
1066 |
|
|
|
1067 |
|
|
// clean up the memory |
1068 |
|
|
|
1069 |
|
|
delete headBendType; |
1070 |
|
|
|
1071 |
|
|
} |
1072 |
|
|
|
1073 |
|
|
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
1074 |
|
|
|
1075 |
|
|
class LinkedType { |
1076 |
|
|
public: |
1077 |
|
|
LinkedType(){ |
1078 |
|
|
next = NULL; |
1079 |
|
|
nameA[0] = '\0'; |
1080 |
|
|
nameB[0] = '\0'; |
1081 |
|
|
nameC[0] = '\0'; |
1082 |
|
|
type[0] = '\0'; |
1083 |
|
|
} |
1084 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
1085 |
|
|
|
1086 |
|
|
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
1087 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
1088 |
|
|
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
1089 |
|
|
|
1090 |
|
|
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
1091 |
|
|
!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this; |
1092 |
|
|
|
1093 |
|
|
if( next != NULL ) return next->find(key1, key2, key3, key4); |
1094 |
|
|
return NULL; |
1095 |
|
|
} |
1096 |
|
|
|
1097 |
mmeineke |
146 |
#ifdef IS_MPI |
1098 |
|
|
|
1099 |
|
|
void add( torsionStruct &info ){ |
1100 |
|
|
if( next != NULL ) next->add(info); |
1101 |
|
|
else{ |
1102 |
|
|
next = new LinkedType(); |
1103 |
|
|
strcpy(next->nameA, info.nameA); |
1104 |
|
|
strcpy(next->nameB, info.nameB); |
1105 |
|
|
strcpy(next->nameC, info.nameC); |
1106 |
|
|
strcpy(next->type, info.type); |
1107 |
|
|
next->k1 = info.k1; |
1108 |
|
|
next->k2 = info.k2; |
1109 |
|
|
next->k3 = info.k3; |
1110 |
|
|
next->k4 = info.k4; |
1111 |
|
|
} |
1112 |
|
|
} |
1113 |
|
|
|
1114 |
|
|
void duplicate( torsionStruct &info ){ |
1115 |
|
|
strcpy(info.nameA, nameA); |
1116 |
|
|
strcpy(info.nameB, nameB); |
1117 |
|
|
strcpy(info.nameC, nameC); |
1118 |
|
|
strcpy(info.nameD, nameD); |
1119 |
|
|
strcpy(info.type, type); |
1120 |
|
|
info.k1 = k1; |
1121 |
|
|
info.k2 = k2; |
1122 |
|
|
info.k3 = k3; |
1123 |
|
|
info.k4 = k4; |
1124 |
|
|
info.last = 0; |
1125 |
|
|
} |
1126 |
|
|
|
1127 |
|
|
#endif |
1128 |
|
|
|
1129 |
mmeineke |
10 |
char nameA[15]; |
1130 |
|
|
char nameB[15]; |
1131 |
|
|
char nameC[15]; |
1132 |
|
|
char nameD[15]; |
1133 |
|
|
char type[30]; |
1134 |
|
|
double k1, k2, k3, k4; |
1135 |
|
|
|
1136 |
|
|
LinkedType* next; |
1137 |
|
|
}; |
1138 |
|
|
|
1139 |
|
|
LinkedType* headTorsionType; |
1140 |
|
|
LinkedType* currentTorsionType; |
1141 |
|
|
LinkedType* tempTorsionType; |
1142 |
|
|
|
1143 |
|
|
char readLine[500]; |
1144 |
|
|
char* the_token; |
1145 |
|
|
char* eof_test; |
1146 |
|
|
int foundTorsion = 0; |
1147 |
|
|
int lineNum = 0; |
1148 |
|
|
int i, a, b, c, d, index; |
1149 |
|
|
char* atomA; |
1150 |
|
|
char* atomB; |
1151 |
|
|
char* atomC; |
1152 |
|
|
char* atomD; |
1153 |
|
|
CubicTorsion* cTors; |
1154 |
|
|
|
1155 |
|
|
SRI **the_sris; |
1156 |
|
|
Atom** the_atoms; |
1157 |
|
|
int nTorsions; |
1158 |
|
|
the_sris = entry_plug->sr_interactions; |
1159 |
|
|
the_atoms = entry_plug->atoms; |
1160 |
|
|
nTorsions = entry_plug->n_torsions; |
1161 |
|
|
|
1162 |
|
|
// read in the torsion types. |
1163 |
|
|
|
1164 |
|
|
rewind( frcFile ); |
1165 |
|
|
headTorsionType = new LinkedType; |
1166 |
|
|
currentTorsionType = headTorsionType; |
1167 |
|
|
|
1168 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1169 |
|
|
lineNum++; |
1170 |
|
|
if( eof_test == NULL ){ |
1171 |
|
|
fprintf( stderr, "Error in reading Torsions from force file.\n" ); |
1172 |
|
|
exit(8); |
1173 |
|
|
} |
1174 |
|
|
|
1175 |
|
|
|
1176 |
|
|
while( !foundTorsion ){ |
1177 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
1178 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1179 |
|
|
lineNum++; |
1180 |
|
|
} |
1181 |
|
|
if( eof_test == NULL ){ |
1182 |
|
|
fprintf( stderr, |
1183 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
1184 |
|
|
lineNum ); |
1185 |
|
|
exit(8); |
1186 |
|
|
} |
1187 |
|
|
|
1188 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
1189 |
|
|
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
1190 |
|
|
|
1191 |
|
|
if( !foundTorsion ){ |
1192 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1193 |
|
|
lineNum++; |
1194 |
|
|
|
1195 |
|
|
if( eof_test == NULL ){ |
1196 |
|
|
fprintf( stderr, |
1197 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
1198 |
|
|
lineNum ); |
1199 |
|
|
exit(8); |
1200 |
|
|
} |
1201 |
|
|
} |
1202 |
|
|
} |
1203 |
|
|
|
1204 |
|
|
// we are now at the TorsionTypes section. |
1205 |
|
|
|
1206 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1207 |
|
|
lineNum++; |
1208 |
|
|
|
1209 |
|
|
if( eof_test == NULL ){ |
1210 |
|
|
fprintf( stderr, |
1211 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
1212 |
|
|
lineNum ); |
1213 |
|
|
exit(8); |
1214 |
|
|
} |
1215 |
|
|
|
1216 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
1217 |
|
|
|
1218 |
|
|
if( readLine[0] != '!' ){ |
1219 |
|
|
|
1220 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
1221 |
|
|
if( the_token != NULL ){ |
1222 |
|
|
|
1223 |
|
|
strcpy( currentTorsionType->nameA, the_token ); |
1224 |
|
|
|
1225 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1226 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1227 |
|
|
exit(8); |
1228 |
|
|
} |
1229 |
|
|
|
1230 |
|
|
strcpy( currentTorsionType->nameB, the_token ); |
1231 |
|
|
|
1232 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1233 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1234 |
|
|
exit(8); |
1235 |
|
|
} |
1236 |
|
|
|
1237 |
|
|
strcpy( currentTorsionType->nameC, the_token ); |
1238 |
|
|
|
1239 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1240 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1241 |
|
|
exit(8); |
1242 |
|
|
} |
1243 |
|
|
|
1244 |
|
|
strcpy( currentTorsionType->nameD, the_token ); |
1245 |
|
|
|
1246 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1247 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1248 |
|
|
exit(8); |
1249 |
|
|
} |
1250 |
|
|
|
1251 |
|
|
strcpy( currentTorsionType->type, the_token ); |
1252 |
|
|
|
1253 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1254 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1255 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1256 |
|
|
exit(8); |
1257 |
|
|
} |
1258 |
|
|
|
1259 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
1260 |
|
|
|
1261 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1262 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1263 |
|
|
exit(8); |
1264 |
|
|
} |
1265 |
|
|
|
1266 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
1267 |
|
|
|
1268 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1269 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1270 |
|
|
exit(8); |
1271 |
|
|
} |
1272 |
|
|
|
1273 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
1274 |
|
|
|
1275 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1276 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1277 |
|
|
exit(8); |
1278 |
|
|
} |
1279 |
|
|
|
1280 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
1281 |
|
|
} |
1282 |
|
|
|
1283 |
|
|
else{ |
1284 |
|
|
fprintf(stderr, |
1285 |
|
|
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1286 |
|
|
currentTorsionType->type, |
1287 |
|
|
lineNum ); |
1288 |
|
|
exit(8); |
1289 |
|
|
} |
1290 |
|
|
} |
1291 |
|
|
} |
1292 |
|
|
|
1293 |
|
|
tempTorsionType = new LinkedType; |
1294 |
|
|
currentTorsionType->next = tempTorsionType; |
1295 |
|
|
currentTorsionType = tempTorsionType; |
1296 |
|
|
|
1297 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1298 |
|
|
lineNum++; |
1299 |
|
|
} |
1300 |
|
|
|
1301 |
|
|
|
1302 |
|
|
// initialize the Torsions |
1303 |
|
|
|
1304 |
|
|
for( i=0; i<nTorsions; i++ ){ |
1305 |
|
|
|
1306 |
|
|
a = the_torsions[i].a; |
1307 |
|
|
b = the_torsions[i].b; |
1308 |
|
|
c = the_torsions[i].c; |
1309 |
|
|
d = the_torsions[i].d; |
1310 |
|
|
|
1311 |
|
|
atomA = the_atoms[a]->getType(); |
1312 |
|
|
atomB = the_atoms[b]->getType(); |
1313 |
|
|
atomC = the_atoms[c]->getType(); |
1314 |
|
|
atomD = the_atoms[d]->getType(); |
1315 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1316 |
|
|
if( currentTorsionType == NULL ){ |
1317 |
|
|
fprintf( stderr, "TorsionType error, %s - %s - %s - %s not found" |
1318 |
|
|
" in force file.\n", |
1319 |
|
|
atomA, atomB, atomC, atomD ); |
1320 |
|
|
exit(8); |
1321 |
|
|
} |
1322 |
|
|
|
1323 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1324 |
|
|
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
1325 |
|
|
|
1326 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1327 |
|
|
*the_atoms[c], *the_atoms[d] ); |
1328 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1329 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
1330 |
|
|
the_sris[index] = cTors; |
1331 |
|
|
} |
1332 |
|
|
} |
1333 |
|
|
|
1334 |
|
|
|
1335 |
|
|
// clean up the memory |
1336 |
|
|
|
1337 |
|
|
delete headTorsionType; |
1338 |
|
|
|
1339 |
|
|
} |