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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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mmeineke |
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#include "simError.h" |
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mmeineke |
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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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// 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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} 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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} 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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} 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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mmeineke |
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} torsionStruct; |
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mmeineke |
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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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chuckv |
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#ifdef IS_MPI |
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int i; |
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mmeineke |
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mmeineke |
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// ********************************************************************** |
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mmeineke |
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// Init the atomStruct mpi type |
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chuckv |
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|
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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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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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mmeineke |
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if( worldRank == 0 ){ |
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chuckv |
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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( painCave.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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painCave.isFatal = 1; |
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simError(); |
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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( painCave.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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painCave.isFatal = 1; |
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simError(); |
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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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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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sprintf( checkPointMsg, "TraPPE_ExFF file opened sucessfully." ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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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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mmeineke |
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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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mmeineke |
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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 |
10 |
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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mmeineke |
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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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#endif |
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mmeineke |
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char readLine[500]; |
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char* the_token; |
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char* eof_test; |
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int foundAtom = 0; |
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int lineNum = 0; |
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int i; |
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mmeineke |
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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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mmeineke |
176 |
if( worldRank == 0 ){ |
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mmeineke |
147 |
#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++; |
363 |
mmeineke |
10 |
if( eof_test == NULL ){ |
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mmeineke |
176 |
sprintf( painCave.errMsg, "Error in reading Atoms from force file.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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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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} |
375 |
mmeineke |
10 |
if( eof_test == NULL ){ |
376 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
377 |
mmeineke |
10 |
"Error in reading Atoms from force file at line %d.\n", |
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lineNum ); |
379 |
mmeineke |
176 |
painCave.isFatal = 1; |
380 |
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simError(); |
381 |
mmeineke |
147 |
} |
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the_token = strtok( readLine, " ,;\t#\n" ); |
384 |
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foundAtom = !strcmp( "AtomTypes", the_token ); |
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if( !foundAtom ){ |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
388 |
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lineNum++; |
389 |
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390 |
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if( eof_test == NULL ){ |
391 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
392 |
mmeineke |
147 |
"Error in reading Atoms from force file at line %d.\n", |
393 |
|
|
lineNum ); |
394 |
mmeineke |
176 |
painCave.isFatal = 1; |
395 |
|
|
simError(); |
396 |
mmeineke |
147 |
} |
397 |
|
|
} |
398 |
mmeineke |
10 |
} |
399 |
|
|
|
400 |
mmeineke |
147 |
// we are now at the AtomTypes section. |
401 |
|
|
|
402 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
403 |
|
|
lineNum++; |
404 |
|
|
|
405 |
|
|
if( eof_test == NULL ){ |
406 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
407 |
mmeineke |
147 |
"Error in reading Atoms from force file at line %d.\n", |
408 |
|
|
lineNum ); |
409 |
mmeineke |
176 |
painCave.isFatal = 1; |
410 |
|
|
simError(); |
411 |
mmeineke |
147 |
} |
412 |
|
|
|
413 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
414 |
mmeineke |
10 |
|
415 |
mmeineke |
147 |
if( readLine[0] != '!' ){ |
416 |
mmeineke |
10 |
|
417 |
mmeineke |
147 |
the_token = strtok( readLine, " \n\t,;" ); |
418 |
|
|
if( the_token != NULL ){ |
419 |
|
|
|
420 |
|
|
strcpy( currentAtomType->name, the_token ); |
421 |
|
|
|
422 |
mmeineke |
10 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
423 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
424 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
425 |
|
|
painCave.isFatal = 1; |
426 |
|
|
simError(); |
427 |
mmeineke |
10 |
} |
428 |
|
|
|
429 |
mmeineke |
147 |
sscanf( the_token, "%d", ¤tAtomType->isDipole ); |
430 |
|
|
|
431 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
432 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
433 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
434 |
|
|
painCave.isFatal = 1; |
435 |
|
|
simError(); |
436 |
mmeineke |
147 |
} |
437 |
|
|
|
438 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->mass ); |
439 |
|
|
|
440 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
441 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
442 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
443 |
|
|
painCave.isFatal = 1; |
444 |
|
|
simError(); |
445 |
mmeineke |
147 |
} |
446 |
|
|
|
447 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
448 |
|
|
|
449 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
450 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
451 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
452 |
|
|
painCave.isFatal = 1; |
453 |
|
|
simError(); |
454 |
mmeineke |
147 |
} |
455 |
|
|
|
456 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
457 |
|
|
|
458 |
|
|
if( currentAtomType->isDipole ){ |
459 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
460 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
461 |
|
|
"Error parseing AtomTypes: line %d\n", |
462 |
mmeineke |
152 |
lineNum ); |
463 |
mmeineke |
176 |
painCave.isFatal = 1; |
464 |
|
|
simError(); |
465 |
mmeineke |
147 |
} |
466 |
|
|
|
467 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->dipole ); |
468 |
|
|
} |
469 |
mmeineke |
10 |
} |
470 |
|
|
} |
471 |
mmeineke |
147 |
|
472 |
|
|
tempAtomType = new LinkedType; |
473 |
|
|
currentAtomType->next = tempAtomType; |
474 |
|
|
currentAtomType = tempAtomType; |
475 |
|
|
|
476 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
477 |
|
|
lineNum++; |
478 |
mmeineke |
10 |
} |
479 |
mmeineke |
147 |
|
480 |
|
|
#ifdef IS_MPI |
481 |
mmeineke |
152 |
|
482 |
|
|
// send out the linked list to all the other processes |
483 |
mmeineke |
176 |
|
484 |
|
|
sprintf( checkPointMsg, |
485 |
|
|
"TraPPE_Ex atom structures read successfully." ); |
486 |
|
|
MPIcheckPoint(); |
487 |
|
|
|
488 |
mmeineke |
152 |
currentAtomType = headAtomType; |
489 |
|
|
while( currentAtomType != NULL ){ |
490 |
|
|
currentAtomType->duplicate( info ); |
491 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
492 |
|
|
currentAtomType = currentAtomType->next; |
493 |
|
|
} |
494 |
|
|
info.last = 1; |
495 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
496 |
|
|
|
497 |
mmeineke |
147 |
} |
498 |
|
|
|
499 |
|
|
else{ |
500 |
mmeineke |
10 |
|
501 |
mmeineke |
152 |
// listen for node 0 to send out the force params |
502 |
mmeineke |
176 |
|
503 |
|
|
MPIcheckPoint(); |
504 |
mmeineke |
152 |
|
505 |
|
|
headAtomType = new LinkedType; |
506 |
|
|
recieveFrcStruct( &info, mpiAtomStructType ); |
507 |
|
|
while( !info.last ){ |
508 |
|
|
|
509 |
|
|
headAtomType->add( info ); |
510 |
|
|
recieveFrcStruct( &info, mpiAtomStructType ); |
511 |
|
|
} |
512 |
mmeineke |
10 |
} |
513 |
mmeineke |
176 |
#endif // is_mpi |
514 |
mmeineke |
10 |
|
515 |
|
|
|
516 |
|
|
// initialize the atoms |
517 |
|
|
|
518 |
|
|
DirectionalAtom* dAtom; |
519 |
|
|
|
520 |
|
|
for( i=0; i<nAtoms; i++ ){ |
521 |
|
|
|
522 |
|
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
523 |
|
|
if( currentAtomType == NULL ){ |
524 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
525 |
|
|
"AtomType error, %s not found in force file.\n", |
526 |
mmeineke |
10 |
the_atoms[i]->getType() ); |
527 |
mmeineke |
176 |
painCave.isFatal = 1; |
528 |
|
|
simError(); |
529 |
mmeineke |
10 |
} |
530 |
|
|
|
531 |
|
|
the_atoms[i]->setMass( currentAtomType->mass ); |
532 |
|
|
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
533 |
|
|
the_atoms[i]->setSigma( currentAtomType->sigma ); |
534 |
|
|
the_atoms[i]->setLJ(); |
535 |
|
|
|
536 |
|
|
if( currentAtomType->isDipole ){ |
537 |
|
|
if( the_atoms[i]->isDirectional() ){ |
538 |
|
|
|
539 |
|
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
540 |
|
|
dAtom->setMu( currentAtomType->dipole ); |
541 |
|
|
dAtom->setHasDipole( 1 ); |
542 |
|
|
dAtom->setJx( 0.0 ); |
543 |
|
|
dAtom->setJy( 0.0 ); |
544 |
|
|
dAtom->setJz( 0.0 ); |
545 |
|
|
|
546 |
|
|
if(!strcmp("SSD",the_atoms[i]->getType())){ |
547 |
|
|
dAtom->setI( waterI ); |
548 |
|
|
dAtom->setSSD( 1 ); |
549 |
|
|
} |
550 |
|
|
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
551 |
|
|
dAtom->setI( headI ); |
552 |
|
|
dAtom->setSSD( 0 ); |
553 |
|
|
} |
554 |
|
|
else{ |
555 |
mmeineke |
176 |
sprintf(painCave.errMsg, |
556 |
mmeineke |
10 |
"AtmType error, %s does not have a moment of inertia set.\n", |
557 |
|
|
the_atoms[i]->getType() ); |
558 |
mmeineke |
176 |
painCave.isFatal = 1; |
559 |
|
|
simError(); |
560 |
mmeineke |
10 |
} |
561 |
|
|
entry_plug->n_dipoles++; |
562 |
|
|
} |
563 |
|
|
else{ |
564 |
mmeineke |
152 |
|
565 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
566 |
mmeineke |
152 |
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
567 |
|
|
" orientation was specifed in the BASS file.\n", |
568 |
|
|
currentAtomType->name ); |
569 |
mmeineke |
176 |
painCave.isFatal = 1; |
570 |
|
|
simError(); |
571 |
mmeineke |
10 |
} |
572 |
|
|
} |
573 |
|
|
else{ |
574 |
|
|
if( the_atoms[i]->isDirectional() ){ |
575 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
576 |
mmeineke |
152 |
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
577 |
|
|
"orientation in the BASS file, yet it is not a dipole.\n", |
578 |
|
|
currentAtomType->name); |
579 |
mmeineke |
176 |
painCave.isFatal = 1; |
580 |
|
|
simError(); |
581 |
mmeineke |
10 |
} |
582 |
|
|
} |
583 |
|
|
} |
584 |
|
|
|
585 |
|
|
|
586 |
|
|
// clean up the memory |
587 |
|
|
|
588 |
|
|
delete headAtomType; |
589 |
mmeineke |
176 |
|
590 |
|
|
#ifdef IS_MPI |
591 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" ); |
592 |
|
|
MPIcheckPoint(); |
593 |
|
|
#endif // is_mpi |
594 |
|
|
|
595 |
mmeineke |
10 |
} |
596 |
|
|
|
597 |
|
|
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
598 |
|
|
|
599 |
|
|
class LinkedType { |
600 |
|
|
public: |
601 |
|
|
LinkedType(){ |
602 |
|
|
next = NULL; |
603 |
|
|
nameA[0] = '\0'; |
604 |
|
|
nameB[0] = '\0'; |
605 |
|
|
type[0] = '\0'; |
606 |
|
|
} |
607 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
608 |
|
|
|
609 |
|
|
LinkedType* find(char* key1, char* key2){ |
610 |
|
|
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
611 |
|
|
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
612 |
|
|
if( next != NULL ) return next->find(key1, key2); |
613 |
|
|
return NULL; |
614 |
|
|
} |
615 |
|
|
|
616 |
mmeineke |
146 |
#ifdef IS_MPI |
617 |
|
|
void add( bondStruct &info ){ |
618 |
|
|
if( next != NULL ) next->add(info); |
619 |
|
|
else{ |
620 |
|
|
next = new LinkedType(); |
621 |
|
|
strcpy(next->nameA, info.nameA); |
622 |
|
|
strcpy(next->nameB, info.nameB); |
623 |
|
|
strcpy(next->type, info.type); |
624 |
|
|
next->d0 = info.d0; |
625 |
|
|
} |
626 |
|
|
} |
627 |
|
|
|
628 |
|
|
void duplicate( bondStruct &info ){ |
629 |
|
|
strcpy(info.nameA, nameA); |
630 |
|
|
strcpy(info.nameB, nameB); |
631 |
|
|
strcpy(info.type, type); |
632 |
|
|
info.d0 = d0; |
633 |
|
|
info.last = 0; |
634 |
|
|
} |
635 |
|
|
|
636 |
|
|
|
637 |
|
|
#endif |
638 |
|
|
|
639 |
mmeineke |
10 |
char nameA[15]; |
640 |
|
|
char nameB[15]; |
641 |
|
|
char type[30]; |
642 |
|
|
double d0; |
643 |
|
|
|
644 |
|
|
LinkedType* next; |
645 |
|
|
}; |
646 |
|
|
|
647 |
|
|
|
648 |
|
|
|
649 |
|
|
LinkedType* headBondType; |
650 |
|
|
LinkedType* currentBondType; |
651 |
|
|
LinkedType* tempBondType; |
652 |
|
|
|
653 |
mmeineke |
176 |
#ifdef IS_MPI |
654 |
|
|
bondStruct info; |
655 |
|
|
info.last = 1; // initialize last to have the last set. |
656 |
|
|
// if things go well, last will be set to 0 |
657 |
|
|
#endif |
658 |
|
|
|
659 |
mmeineke |
10 |
char readLine[500]; |
660 |
|
|
char* the_token; |
661 |
|
|
char* eof_test; |
662 |
|
|
int foundBond = 0; |
663 |
|
|
int lineNum = 0; |
664 |
|
|
int i, a, b; |
665 |
|
|
char* atomA; |
666 |
|
|
char* atomB; |
667 |
|
|
|
668 |
|
|
SRI **the_sris; |
669 |
|
|
Atom** the_atoms; |
670 |
|
|
int nBonds; |
671 |
|
|
the_sris = entry_plug->sr_interactions; |
672 |
|
|
the_atoms = entry_plug->atoms; |
673 |
|
|
nBonds = entry_plug->n_bonds; |
674 |
|
|
|
675 |
|
|
|
676 |
mmeineke |
176 |
#ifdef IS_MPI |
677 |
|
|
if( worldRank == 0 ){ |
678 |
|
|
#endif |
679 |
|
|
|
680 |
|
|
// read in the bond types. |
681 |
|
|
|
682 |
|
|
rewind( frcFile ); |
683 |
|
|
headBondType = new LinkedType; |
684 |
|
|
currentBondType = headBondType; |
685 |
|
|
|
686 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
687 |
|
|
lineNum++; |
688 |
mmeineke |
10 |
if( eof_test == NULL ){ |
689 |
mmeineke |
176 |
sprintf( painCave.errMsg, "Error in reading Bonds from force file.\n" ); |
690 |
|
|
painCave.isFatal = 1; |
691 |
|
|
simError(); |
692 |
mmeineke |
10 |
} |
693 |
|
|
|
694 |
mmeineke |
176 |
|
695 |
|
|
while( !foundBond ){ |
696 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
697 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
698 |
|
|
lineNum++; |
699 |
|
|
} |
700 |
mmeineke |
10 |
if( eof_test == NULL ){ |
701 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
702 |
mmeineke |
10 |
"Error in reading Bonds from force file at line %d.\n", |
703 |
|
|
lineNum ); |
704 |
mmeineke |
176 |
painCave.isFatal = 1; |
705 |
|
|
simError(); |
706 |
|
|
} |
707 |
|
|
|
708 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
709 |
|
|
foundBond = !strcmp( "BondTypes", the_token ); |
710 |
|
|
|
711 |
|
|
if( !foundBond ){ |
712 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
713 |
|
|
lineNum++; |
714 |
|
|
|
715 |
|
|
if( eof_test == NULL ){ |
716 |
|
|
sprintf( painCave.errMsg, |
717 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
718 |
|
|
lineNum ); |
719 |
|
|
painCave.isFatal = 1; |
720 |
|
|
simError(); |
721 |
|
|
} |
722 |
|
|
} |
723 |
mmeineke |
10 |
} |
724 |
|
|
|
725 |
mmeineke |
176 |
// we are now at the BondTypes section. |
726 |
|
|
|
727 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
728 |
|
|
lineNum++; |
729 |
|
|
|
730 |
|
|
if( eof_test == NULL ){ |
731 |
|
|
sprintf( painCave.errMsg, |
732 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
733 |
|
|
lineNum ); |
734 |
|
|
painCave.isFatal = 1; |
735 |
|
|
simError(); |
736 |
|
|
} |
737 |
|
|
|
738 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
739 |
mmeineke |
10 |
|
740 |
mmeineke |
176 |
if( readLine[0] != '!' ){ |
741 |
mmeineke |
10 |
|
742 |
mmeineke |
176 |
the_token = strtok( readLine, " \n\t,;" ); |
743 |
|
|
if( the_token != NULL ){ |
744 |
|
|
|
745 |
|
|
strcpy( currentBondType->nameA, the_token ); |
746 |
|
|
|
747 |
mmeineke |
10 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
748 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
749 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
750 |
|
|
painCave.isFatal = 1; |
751 |
|
|
simError(); |
752 |
mmeineke |
10 |
} |
753 |
|
|
|
754 |
mmeineke |
176 |
strcpy( currentBondType->nameB, the_token ); |
755 |
|
|
|
756 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
757 |
|
|
sprintf( painCave.errMsg, |
758 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
759 |
|
|
painCave.isFatal = 1; |
760 |
|
|
simError(); |
761 |
|
|
} |
762 |
|
|
|
763 |
|
|
strcpy( currentBondType->type, the_token ); |
764 |
|
|
|
765 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
766 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
767 |
|
|
sprintf( painCave.errMsg, |
768 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
769 |
|
|
painCave.isFatal = 1; |
770 |
|
|
simError(); |
771 |
|
|
} |
772 |
|
|
|
773 |
|
|
sscanf( the_token, "%lf", ¤tBondType->d0 ); |
774 |
|
|
} |
775 |
|
|
|
776 |
|
|
else{ |
777 |
|
|
sprintf( painCave.errMsg, |
778 |
|
|
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
779 |
|
|
currentBondType->type, |
780 |
|
|
lineNum ); |
781 |
|
|
painCave.isFatal = 1; |
782 |
|
|
simError(); |
783 |
|
|
} |
784 |
mmeineke |
10 |
} |
785 |
|
|
} |
786 |
mmeineke |
176 |
|
787 |
|
|
tempBondType = new LinkedType; |
788 |
|
|
currentBondType->next = tempBondType; |
789 |
|
|
currentBondType = tempBondType; |
790 |
|
|
|
791 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
792 |
|
|
lineNum++; |
793 |
mmeineke |
10 |
} |
794 |
|
|
|
795 |
mmeineke |
176 |
#ifdef IS_MPI |
796 |
mmeineke |
10 |
|
797 |
mmeineke |
176 |
// send out the linked list to all the other processes |
798 |
|
|
|
799 |
|
|
sprintf( checkPointMsg, |
800 |
|
|
"TraPPE_Ex bond structures read successfully." ); |
801 |
|
|
MPIcheckPoint(); |
802 |
|
|
|
803 |
|
|
currentBondType = headBondType; |
804 |
|
|
while( currentBondType != NULL ){ |
805 |
|
|
currentBondType->duplicate( info ); |
806 |
|
|
sendFrcStruct( &info, mpiBondStructType ); |
807 |
|
|
currentBondType = currentBondType->next; |
808 |
|
|
} |
809 |
|
|
info.last = 1; |
810 |
|
|
sendFrcStruct( &info, mpiBondStructType ); |
811 |
|
|
|
812 |
mmeineke |
10 |
} |
813 |
|
|
|
814 |
mmeineke |
176 |
else{ |
815 |
|
|
|
816 |
|
|
// listen for node 0 to send out the force params |
817 |
|
|
|
818 |
|
|
MPIcheckPoint(); |
819 |
|
|
|
820 |
|
|
headBondType = new LinkedType; |
821 |
|
|
recieveFrcStruct( &info, mpiBondStructType ); |
822 |
|
|
while( !info.last ){ |
823 |
|
|
|
824 |
|
|
headBondType->add( info ); |
825 |
|
|
recieveFrcStruct( &info, mpiBondStructType ); |
826 |
|
|
} |
827 |
|
|
} |
828 |
|
|
#endif // is_mpi |
829 |
mmeineke |
10 |
|
830 |
mmeineke |
176 |
|
831 |
mmeineke |
10 |
// initialize the Bonds |
832 |
|
|
|
833 |
|
|
|
834 |
|
|
for( i=0; i<nBonds; i++ ){ |
835 |
|
|
|
836 |
|
|
a = the_bonds[i].a; |
837 |
|
|
b = the_bonds[i].b; |
838 |
|
|
|
839 |
|
|
atomA = the_atoms[a]->getType(); |
840 |
|
|
atomB = the_atoms[b]->getType(); |
841 |
|
|
currentBondType = headBondType->find( atomA, atomB ); |
842 |
|
|
if( currentBondType == NULL ){ |
843 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
844 |
|
|
"BondType error, %s - %s not found in force file.\n", |
845 |
mmeineke |
10 |
atomA, atomB ); |
846 |
mmeineke |
176 |
painCave.isFatal = 1; |
847 |
|
|
simError(); |
848 |
mmeineke |
10 |
} |
849 |
|
|
|
850 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
851 |
|
|
|
852 |
|
|
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
853 |
|
|
*the_atoms[b], |
854 |
|
|
currentBondType->d0 ); |
855 |
|
|
entry_plug->n_constraints++; |
856 |
|
|
} |
857 |
|
|
} |
858 |
|
|
|
859 |
|
|
|
860 |
|
|
// clean up the memory |
861 |
|
|
|
862 |
|
|
delete headBondType; |
863 |
|
|
|
864 |
mmeineke |
176 |
#ifdef IS_MPI |
865 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" ); |
866 |
|
|
MPIcheckPoint(); |
867 |
|
|
#endif // is_mpi |
868 |
|
|
|
869 |
mmeineke |
10 |
} |
870 |
|
|
|
871 |
|
|
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
872 |
|
|
|
873 |
|
|
class LinkedType { |
874 |
|
|
public: |
875 |
|
|
LinkedType(){ |
876 |
|
|
next = NULL; |
877 |
|
|
nameA[0] = '\0'; |
878 |
|
|
nameB[0] = '\0'; |
879 |
|
|
nameC[0] = '\0'; |
880 |
|
|
type[0] = '\0'; |
881 |
|
|
} |
882 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
883 |
|
|
|
884 |
|
|
LinkedType* find( char* key1, char* key2, char* key3 ){ |
885 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
886 |
|
|
&& !strcmp( nameC, key3 ) ) return this; |
887 |
|
|
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
888 |
|
|
&& !strcmp( nameC, key1 ) ) return this; |
889 |
|
|
if( next != NULL ) return next->find(key1, key2, key3); |
890 |
|
|
return NULL; |
891 |
|
|
} |
892 |
|
|
|
893 |
mmeineke |
146 |
#ifdef IS_MPI |
894 |
|
|
|
895 |
|
|
void add( bendStruct &info ){ |
896 |
|
|
if( next != NULL ) next->add(info); |
897 |
|
|
else{ |
898 |
|
|
next = new LinkedType(); |
899 |
|
|
strcpy(next->nameA, info.nameA); |
900 |
|
|
strcpy(next->nameB, info.nameB); |
901 |
|
|
strcpy(next->nameC, info.nameC); |
902 |
|
|
strcpy(next->type, info.type); |
903 |
|
|
next->k1 = info.k1; |
904 |
|
|
next->k2 = info.k2; |
905 |
|
|
next->k3 = info.k3; |
906 |
|
|
next->t0 = info.t0; |
907 |
|
|
} |
908 |
|
|
} |
909 |
|
|
|
910 |
|
|
void duplicate( bendStruct &info ){ |
911 |
|
|
strcpy(info.nameA, nameA); |
912 |
|
|
strcpy(info.nameB, nameB); |
913 |
|
|
strcpy(info.nameC, nameC); |
914 |
|
|
strcpy(info.type, type); |
915 |
|
|
info.k1 = k1; |
916 |
|
|
info.k2 = k2; |
917 |
|
|
info.k3 = k3; |
918 |
|
|
info.t0 = t0; |
919 |
|
|
info.last = 0; |
920 |
|
|
} |
921 |
|
|
|
922 |
mmeineke |
176 |
#endif // is_mpi |
923 |
mmeineke |
146 |
|
924 |
mmeineke |
10 |
char nameA[15]; |
925 |
|
|
char nameB[15]; |
926 |
|
|
char nameC[15]; |
927 |
|
|
char type[30]; |
928 |
|
|
double k1, k2, k3, t0; |
929 |
|
|
|
930 |
|
|
LinkedType* next; |
931 |
|
|
}; |
932 |
|
|
|
933 |
|
|
LinkedType* headBendType; |
934 |
|
|
LinkedType* currentBendType; |
935 |
|
|
LinkedType* tempBendType; |
936 |
|
|
|
937 |
mmeineke |
176 |
#ifdef IS_MPI |
938 |
|
|
bendStruct info; |
939 |
|
|
info.last = 1; // initialize last to have the last set. |
940 |
|
|
// if things go well, last will be set to 0 |
941 |
|
|
#endif |
942 |
|
|
|
943 |
mmeineke |
10 |
char readLine[500]; |
944 |
|
|
char* the_token; |
945 |
|
|
char* eof_test; |
946 |
|
|
int foundBend = 0; |
947 |
|
|
int lineNum = 0; |
948 |
|
|
int i, a, b, c, index; |
949 |
|
|
char* atomA; |
950 |
|
|
char* atomB; |
951 |
|
|
char* atomC; |
952 |
|
|
QuadraticBend* qBend; |
953 |
|
|
|
954 |
|
|
SRI **the_sris; |
955 |
|
|
Atom** the_atoms; |
956 |
|
|
int nBends; |
957 |
|
|
the_sris = entry_plug->sr_interactions; |
958 |
|
|
the_atoms = entry_plug->atoms; |
959 |
|
|
nBends = entry_plug->n_bends; |
960 |
|
|
|
961 |
|
|
|
962 |
mmeineke |
176 |
#ifdef IS_MPI |
963 |
|
|
if( worldRank == 0 ){ |
964 |
|
|
#endif |
965 |
mmeineke |
10 |
|
966 |
mmeineke |
176 |
// read in the bend types. |
967 |
|
|
|
968 |
|
|
rewind( frcFile ); |
969 |
|
|
headBendType = new LinkedType; |
970 |
|
|
currentBendType = headBendType; |
971 |
mmeineke |
10 |
|
972 |
mmeineke |
176 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
973 |
|
|
lineNum++; |
974 |
mmeineke |
10 |
if( eof_test == NULL ){ |
975 |
mmeineke |
176 |
sprintf( painCave.errMsg, "Error in reading Bends from force file.\n" ); |
976 |
|
|
painCave.isFatal = 1; |
977 |
|
|
simError(); |
978 |
mmeineke |
10 |
} |
979 |
|
|
|
980 |
mmeineke |
176 |
|
981 |
|
|
while( !foundBend ){ |
982 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
983 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
984 |
|
|
lineNum++; |
985 |
|
|
} |
986 |
mmeineke |
10 |
if( eof_test == NULL ){ |
987 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
988 |
mmeineke |
10 |
"Error in reading Bends from force file at line %d.\n", |
989 |
|
|
lineNum ); |
990 |
mmeineke |
176 |
painCave.isFatal = 1; |
991 |
|
|
simError(); |
992 |
|
|
} |
993 |
|
|
|
994 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
995 |
|
|
foundBend = !strcmp( "BendTypes", the_token ); |
996 |
|
|
|
997 |
|
|
if( !foundBend ){ |
998 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
999 |
|
|
lineNum++; |
1000 |
|
|
|
1001 |
|
|
if( eof_test == NULL ){ |
1002 |
|
|
sprintf( painCave.errMsg, |
1003 |
|
|
"Error in reading Bends from force file at line %d.\n", |
1004 |
|
|
lineNum ); |
1005 |
|
|
painCave.isFatal = 1; |
1006 |
|
|
simError(); |
1007 |
|
|
} |
1008 |
|
|
} |
1009 |
mmeineke |
10 |
} |
1010 |
|
|
|
1011 |
mmeineke |
176 |
// we are now at the BendTypes section. |
1012 |
mmeineke |
10 |
|
1013 |
mmeineke |
176 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1014 |
|
|
lineNum++; |
1015 |
mmeineke |
10 |
|
1016 |
mmeineke |
176 |
if( eof_test == NULL ){ |
1017 |
|
|
sprintf( painCave.errMsg, |
1018 |
|
|
"Error in reading Bends from force file at line %d.\n", |
1019 |
|
|
lineNum ); |
1020 |
|
|
painCave.isFatal = 1; |
1021 |
|
|
simError(); |
1022 |
|
|
} |
1023 |
mmeineke |
10 |
|
1024 |
mmeineke |
176 |
while( readLine[0] != '#' && eof_test != NULL ){ |
1025 |
mmeineke |
10 |
|
1026 |
mmeineke |
176 |
if( readLine[0] != '!' ){ |
1027 |
mmeineke |
10 |
|
1028 |
mmeineke |
176 |
the_token = strtok( readLine, " \n\t,;" ); |
1029 |
|
|
if( the_token != NULL ){ |
1030 |
mmeineke |
10 |
|
1031 |
mmeineke |
176 |
strcpy( currentBendType->nameA, the_token ); |
1032 |
mmeineke |
10 |
|
1033 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1034 |
|
|
sprintf( painCave.errMsg, |
1035 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1036 |
|
|
painCave.isFatal = 1; |
1037 |
|
|
simError(); |
1038 |
|
|
} |
1039 |
mmeineke |
10 |
|
1040 |
mmeineke |
176 |
strcpy( currentBendType->nameB, the_token ); |
1041 |
mmeineke |
10 |
|
1042 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1043 |
|
|
sprintf( painCave.errMsg, |
1044 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1045 |
|
|
painCave.isFatal = 1; |
1046 |
|
|
simError(); |
1047 |
|
|
} |
1048 |
mmeineke |
10 |
|
1049 |
mmeineke |
176 |
strcpy( currentBendType->nameC, the_token ); |
1050 |
mmeineke |
10 |
|
1051 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1052 |
|
|
sprintf( painCave.errMsg, |
1053 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1054 |
|
|
painCave.isFatal = 1; |
1055 |
|
|
simError(); |
1056 |
|
|
} |
1057 |
mmeineke |
10 |
|
1058 |
mmeineke |
176 |
strcpy( currentBendType->type, the_token ); |
1059 |
mmeineke |
10 |
|
1060 |
mmeineke |
176 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1061 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1062 |
|
|
sprintf( painCave.errMsg, |
1063 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1064 |
|
|
painCave.isFatal = 1; |
1065 |
|
|
simError(); |
1066 |
|
|
} |
1067 |
mmeineke |
10 |
|
1068 |
mmeineke |
176 |
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
1069 |
mmeineke |
10 |
|
1070 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1071 |
|
|
sprintf( painCave.errMsg, |
1072 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1073 |
|
|
painCave.isFatal = 1; |
1074 |
|
|
simError(); |
1075 |
|
|
} |
1076 |
mmeineke |
10 |
|
1077 |
mmeineke |
176 |
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
1078 |
mmeineke |
10 |
|
1079 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1080 |
|
|
sprintf( painCave.errMsg, |
1081 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1082 |
|
|
painCave.isFatal = 1; |
1083 |
|
|
simError(); |
1084 |
|
|
} |
1085 |
mmeineke |
10 |
|
1086 |
mmeineke |
176 |
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
1087 |
mmeineke |
10 |
|
1088 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1089 |
|
|
sprintf( painCave.errMsg, |
1090 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1091 |
|
|
painCave.isFatal = 1; |
1092 |
|
|
simError(); |
1093 |
|
|
} |
1094 |
|
|
|
1095 |
|
|
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
1096 |
mmeineke |
10 |
} |
1097 |
mmeineke |
176 |
|
1098 |
|
|
else{ |
1099 |
|
|
sprintf( painCave.errMsg, |
1100 |
|
|
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
1101 |
|
|
currentBendType->type, |
1102 |
|
|
lineNum ); |
1103 |
|
|
painCave.isFatal = 1; |
1104 |
|
|
simError(); |
1105 |
|
|
} |
1106 |
mmeineke |
10 |
} |
1107 |
|
|
} |
1108 |
mmeineke |
176 |
|
1109 |
|
|
tempBendType = new LinkedType; |
1110 |
|
|
currentBendType->next = tempBendType; |
1111 |
|
|
currentBendType = tempBendType; |
1112 |
|
|
|
1113 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1114 |
|
|
lineNum++; |
1115 |
mmeineke |
10 |
} |
1116 |
mmeineke |
176 |
|
1117 |
|
|
#ifdef IS_MPI |
1118 |
mmeineke |
10 |
|
1119 |
mmeineke |
176 |
// send out the linked list to all the other processes |
1120 |
|
|
|
1121 |
|
|
sprintf( checkPointMsg, |
1122 |
|
|
"TraPPE_Ex bend structures read successfully." ); |
1123 |
|
|
MPIcheckPoint(); |
1124 |
|
|
|
1125 |
|
|
currentBendType = headBendType; |
1126 |
|
|
while( currentBendType != NULL ){ |
1127 |
|
|
currentBendType->duplicate( info ); |
1128 |
|
|
sendFrcStruct( &info, mpiBendStructType ); |
1129 |
|
|
currentBendType = currentBendType->next; |
1130 |
|
|
} |
1131 |
|
|
info.last = 1; |
1132 |
|
|
sendFrcStruct( &info, mpiBendStructType ); |
1133 |
mmeineke |
10 |
|
1134 |
|
|
} |
1135 |
|
|
|
1136 |
mmeineke |
176 |
else{ |
1137 |
|
|
|
1138 |
|
|
// listen for node 0 to send out the force params |
1139 |
|
|
|
1140 |
|
|
MPIcheckPoint(); |
1141 |
|
|
|
1142 |
|
|
headBendType = new LinkedType; |
1143 |
|
|
recieveFrcStruct( &info, mpiBendStructType ); |
1144 |
|
|
while( !info.last ){ |
1145 |
|
|
|
1146 |
|
|
headBendType->add( info ); |
1147 |
|
|
recieveFrcStruct( &info, mpiBendStructType ); |
1148 |
|
|
} |
1149 |
|
|
} |
1150 |
|
|
#endif // is_mpi |
1151 |
mmeineke |
10 |
|
1152 |
|
|
// initialize the Bends |
1153 |
|
|
|
1154 |
|
|
for( i=0; i<nBends; i++ ){ |
1155 |
|
|
|
1156 |
|
|
a = the_bends[i].a; |
1157 |
|
|
b = the_bends[i].b; |
1158 |
|
|
c = the_bends[i].c; |
1159 |
|
|
|
1160 |
|
|
atomA = the_atoms[a]->getType(); |
1161 |
|
|
atomB = the_atoms[b]->getType(); |
1162 |
|
|
atomC = the_atoms[c]->getType(); |
1163 |
|
|
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1164 |
|
|
if( currentBendType == NULL ){ |
1165 |
mmeineke |
176 |
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1166 |
mmeineke |
10 |
" in force file.\n", |
1167 |
|
|
atomA, atomB, atomC ); |
1168 |
mmeineke |
176 |
painCave.isFatal = 1; |
1169 |
|
|
simError(); |
1170 |
mmeineke |
10 |
} |
1171 |
|
|
|
1172 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1173 |
|
|
|
1174 |
|
|
index = i + entry_plug->n_bonds; |
1175 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
1176 |
|
|
*the_atoms[b], |
1177 |
|
|
*the_atoms[c] ); |
1178 |
|
|
qBend->setConstants( currentBendType->k1, |
1179 |
|
|
currentBendType->k2, |
1180 |
|
|
currentBendType->k3, |
1181 |
|
|
currentBendType->t0 ); |
1182 |
|
|
the_sris[index] = qBend; |
1183 |
|
|
} |
1184 |
|
|
} |
1185 |
|
|
|
1186 |
|
|
|
1187 |
|
|
// clean up the memory |
1188 |
|
|
|
1189 |
|
|
delete headBendType; |
1190 |
|
|
|
1191 |
mmeineke |
176 |
#ifdef IS_MPI |
1192 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" ); |
1193 |
|
|
MPIcheckPoint(); |
1194 |
|
|
#endif // is_mpi |
1195 |
|
|
|
1196 |
mmeineke |
10 |
} |
1197 |
|
|
|
1198 |
|
|
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
1199 |
|
|
|
1200 |
|
|
class LinkedType { |
1201 |
|
|
public: |
1202 |
|
|
LinkedType(){ |
1203 |
|
|
next = NULL; |
1204 |
|
|
nameA[0] = '\0'; |
1205 |
|
|
nameB[0] = '\0'; |
1206 |
|
|
nameC[0] = '\0'; |
1207 |
|
|
type[0] = '\0'; |
1208 |
|
|
} |
1209 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
1210 |
|
|
|
1211 |
|
|
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
1212 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
1213 |
|
|
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
1214 |
|
|
|
1215 |
|
|
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
1216 |
|
|
!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this; |
1217 |
|
|
|
1218 |
|
|
if( next != NULL ) return next->find(key1, key2, key3, key4); |
1219 |
|
|
return NULL; |
1220 |
|
|
} |
1221 |
|
|
|
1222 |
mmeineke |
146 |
#ifdef IS_MPI |
1223 |
|
|
|
1224 |
|
|
void add( torsionStruct &info ){ |
1225 |
|
|
if( next != NULL ) next->add(info); |
1226 |
|
|
else{ |
1227 |
|
|
next = new LinkedType(); |
1228 |
|
|
strcpy(next->nameA, info.nameA); |
1229 |
|
|
strcpy(next->nameB, info.nameB); |
1230 |
|
|
strcpy(next->nameC, info.nameC); |
1231 |
|
|
strcpy(next->type, info.type); |
1232 |
|
|
next->k1 = info.k1; |
1233 |
|
|
next->k2 = info.k2; |
1234 |
|
|
next->k3 = info.k3; |
1235 |
|
|
next->k4 = info.k4; |
1236 |
|
|
} |
1237 |
|
|
} |
1238 |
|
|
|
1239 |
|
|
void duplicate( torsionStruct &info ){ |
1240 |
|
|
strcpy(info.nameA, nameA); |
1241 |
|
|
strcpy(info.nameB, nameB); |
1242 |
|
|
strcpy(info.nameC, nameC); |
1243 |
|
|
strcpy(info.nameD, nameD); |
1244 |
|
|
strcpy(info.type, type); |
1245 |
|
|
info.k1 = k1; |
1246 |
|
|
info.k2 = k2; |
1247 |
|
|
info.k3 = k3; |
1248 |
|
|
info.k4 = k4; |
1249 |
|
|
info.last = 0; |
1250 |
|
|
} |
1251 |
|
|
|
1252 |
|
|
#endif |
1253 |
|
|
|
1254 |
mmeineke |
10 |
char nameA[15]; |
1255 |
|
|
char nameB[15]; |
1256 |
|
|
char nameC[15]; |
1257 |
|
|
char nameD[15]; |
1258 |
|
|
char type[30]; |
1259 |
|
|
double k1, k2, k3, k4; |
1260 |
|
|
|
1261 |
|
|
LinkedType* next; |
1262 |
|
|
}; |
1263 |
|
|
|
1264 |
|
|
LinkedType* headTorsionType; |
1265 |
|
|
LinkedType* currentTorsionType; |
1266 |
|
|
LinkedType* tempTorsionType; |
1267 |
|
|
|
1268 |
mmeineke |
176 |
#ifdef IS_MPI |
1269 |
|
|
torsionStruct info; |
1270 |
|
|
info.last = 1; // initialize last to have the last set. |
1271 |
|
|
// if things go well, last will be set to 0 |
1272 |
|
|
#endif |
1273 |
|
|
|
1274 |
mmeineke |
10 |
char readLine[500]; |
1275 |
|
|
char* the_token; |
1276 |
|
|
char* eof_test; |
1277 |
|
|
int foundTorsion = 0; |
1278 |
|
|
int lineNum = 0; |
1279 |
|
|
int i, a, b, c, d, index; |
1280 |
|
|
char* atomA; |
1281 |
|
|
char* atomB; |
1282 |
|
|
char* atomC; |
1283 |
|
|
char* atomD; |
1284 |
|
|
CubicTorsion* cTors; |
1285 |
|
|
|
1286 |
|
|
SRI **the_sris; |
1287 |
|
|
Atom** the_atoms; |
1288 |
|
|
int nTorsions; |
1289 |
|
|
the_sris = entry_plug->sr_interactions; |
1290 |
|
|
the_atoms = entry_plug->atoms; |
1291 |
|
|
nTorsions = entry_plug->n_torsions; |
1292 |
|
|
|
1293 |
mmeineke |
176 |
#ifdef IS_MPI |
1294 |
|
|
if( worldRank == 0 ){ |
1295 |
|
|
#endif |
1296 |
mmeineke |
10 |
|
1297 |
mmeineke |
176 |
// read in the torsion types. |
1298 |
mmeineke |
10 |
|
1299 |
mmeineke |
176 |
rewind( frcFile ); |
1300 |
|
|
headTorsionType = new LinkedType; |
1301 |
|
|
currentTorsionType = headTorsionType; |
1302 |
mmeineke |
10 |
|
1303 |
mmeineke |
176 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1304 |
|
|
lineNum++; |
1305 |
mmeineke |
10 |
if( eof_test == NULL ){ |
1306 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
1307 |
|
|
"Error in reading Torsions from force file.\n" ); |
1308 |
|
|
painCave.isFatal = 1; |
1309 |
|
|
simError(); |
1310 |
mmeineke |
10 |
} |
1311 |
|
|
|
1312 |
mmeineke |
176 |
|
1313 |
|
|
while( !foundTorsion ){ |
1314 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
1315 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1316 |
|
|
lineNum++; |
1317 |
|
|
} |
1318 |
mmeineke |
10 |
if( eof_test == NULL ){ |
1319 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
1320 |
mmeineke |
10 |
"Error in reading Torsions from force file at line %d.\n", |
1321 |
|
|
lineNum ); |
1322 |
mmeineke |
176 |
painCave.isFatal = 1; |
1323 |
|
|
simError(); |
1324 |
|
|
} |
1325 |
|
|
|
1326 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
1327 |
|
|
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
1328 |
|
|
|
1329 |
|
|
if( !foundTorsion ){ |
1330 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1331 |
|
|
lineNum++; |
1332 |
|
|
|
1333 |
|
|
if( eof_test == NULL ){ |
1334 |
|
|
sprintf( painCave.errMsg, |
1335 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
1336 |
|
|
lineNum ); |
1337 |
|
|
painCave.isFatal = 1; |
1338 |
|
|
simError(); |
1339 |
|
|
} |
1340 |
|
|
} |
1341 |
mmeineke |
10 |
} |
1342 |
|
|
|
1343 |
mmeineke |
176 |
// we are now at the TorsionTypes section. |
1344 |
mmeineke |
10 |
|
1345 |
mmeineke |
176 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1346 |
|
|
lineNum++; |
1347 |
mmeineke |
10 |
|
1348 |
mmeineke |
176 |
if( eof_test == NULL ){ |
1349 |
|
|
sprintf( painCave.errMsg, |
1350 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
1351 |
|
|
lineNum ); |
1352 |
|
|
painCave.isFatal = 1; |
1353 |
|
|
simError(); |
1354 |
|
|
} |
1355 |
mmeineke |
10 |
|
1356 |
mmeineke |
176 |
while( readLine[0] != '#' && eof_test != NULL ){ |
1357 |
mmeineke |
10 |
|
1358 |
mmeineke |
176 |
if( readLine[0] != '!' ){ |
1359 |
mmeineke |
10 |
|
1360 |
mmeineke |
176 |
the_token = strtok( readLine, " \n\t,;" ); |
1361 |
|
|
if( the_token != NULL ){ |
1362 |
mmeineke |
10 |
|
1363 |
mmeineke |
176 |
strcpy( currentTorsionType->nameA, the_token ); |
1364 |
mmeineke |
10 |
|
1365 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1366 |
|
|
sprintf( painCave.errMsg, |
1367 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1368 |
|
|
painCave.isFatal = 1; |
1369 |
|
|
simError(); |
1370 |
|
|
} |
1371 |
mmeineke |
10 |
|
1372 |
mmeineke |
176 |
strcpy( currentTorsionType->nameB, the_token ); |
1373 |
mmeineke |
10 |
|
1374 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1375 |
|
|
sprintf( painCave.errMsg, |
1376 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1377 |
|
|
painCave.isFatal = 1; |
1378 |
|
|
simError(); |
1379 |
|
|
} |
1380 |
mmeineke |
10 |
|
1381 |
mmeineke |
176 |
strcpy( currentTorsionType->nameC, the_token ); |
1382 |
mmeineke |
10 |
|
1383 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1384 |
|
|
sprintf( painCave.errMsg, |
1385 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1386 |
|
|
painCave.isFatal = 1; |
1387 |
|
|
simError(); |
1388 |
|
|
} |
1389 |
mmeineke |
10 |
|
1390 |
mmeineke |
176 |
strcpy( currentTorsionType->nameD, the_token ); |
1391 |
mmeineke |
10 |
|
1392 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1393 |
|
|
sprintf( painCave.errMsg, |
1394 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1395 |
|
|
painCave.isFatal = 1; |
1396 |
|
|
simError(); |
1397 |
|
|
} |
1398 |
mmeineke |
10 |
|
1399 |
mmeineke |
176 |
strcpy( currentTorsionType->type, the_token ); |
1400 |
mmeineke |
10 |
|
1401 |
mmeineke |
176 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1402 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1403 |
|
|
sprintf( painCave.errMsg, |
1404 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1405 |
|
|
painCave.isFatal = 1; |
1406 |
|
|
simError(); |
1407 |
|
|
} |
1408 |
mmeineke |
10 |
|
1409 |
mmeineke |
176 |
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
1410 |
mmeineke |
10 |
|
1411 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1412 |
|
|
sprintf( painCave.errMsg, |
1413 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1414 |
|
|
painCave.isFatal = 1; |
1415 |
|
|
simError(); |
1416 |
|
|
} |
1417 |
mmeineke |
10 |
|
1418 |
mmeineke |
176 |
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
1419 |
mmeineke |
10 |
|
1420 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1421 |
|
|
sprintf( painCave.errMsg, |
1422 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1423 |
|
|
painCave.isFatal = 1; |
1424 |
|
|
simError(); |
1425 |
|
|
} |
1426 |
mmeineke |
10 |
|
1427 |
mmeineke |
176 |
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
1428 |
mmeineke |
10 |
|
1429 |
mmeineke |
176 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1430 |
|
|
sprintf( painCave.errMsg, |
1431 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1432 |
|
|
painCave.isFatal = 1; |
1433 |
|
|
simError(); |
1434 |
|
|
} |
1435 |
|
|
|
1436 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
1437 |
mmeineke |
10 |
} |
1438 |
mmeineke |
176 |
|
1439 |
|
|
else{ |
1440 |
|
|
sprintf( painCave.errMsg, |
1441 |
|
|
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1442 |
|
|
currentTorsionType->type, |
1443 |
|
|
lineNum ); |
1444 |
|
|
painCave.isFatal = 1; |
1445 |
|
|
simError(); |
1446 |
|
|
} |
1447 |
mmeineke |
10 |
} |
1448 |
|
|
} |
1449 |
mmeineke |
176 |
|
1450 |
|
|
tempTorsionType = new LinkedType; |
1451 |
|
|
currentTorsionType->next = tempTorsionType; |
1452 |
|
|
currentTorsionType = tempTorsionType; |
1453 |
|
|
|
1454 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1455 |
|
|
lineNum++; |
1456 |
mmeineke |
10 |
} |
1457 |
mmeineke |
176 |
|
1458 |
|
|
#ifdef IS_MPI |
1459 |
mmeineke |
10 |
|
1460 |
mmeineke |
176 |
// send out the linked list to all the other processes |
1461 |
mmeineke |
10 |
|
1462 |
mmeineke |
176 |
sprintf( checkPointMsg, |
1463 |
|
|
"TraPPE_Ex torsion structures read successfully." ); |
1464 |
|
|
MPIcheckPoint(); |
1465 |
|
|
|
1466 |
|
|
currentTorsionType = headTorsionType; |
1467 |
|
|
while( currentTorsionType != NULL ){ |
1468 |
|
|
currentTorsionType->duplicate( info ); |
1469 |
|
|
sendFrcStruct( &info, mpiTorsionStructType ); |
1470 |
|
|
currentTorsionType = currentTorsionType->next; |
1471 |
|
|
} |
1472 |
|
|
info.last = 1; |
1473 |
|
|
sendFrcStruct( &info, mpiTorsionStructType ); |
1474 |
|
|
|
1475 |
mmeineke |
10 |
} |
1476 |
|
|
|
1477 |
mmeineke |
176 |
else{ |
1478 |
|
|
|
1479 |
|
|
// listen for node 0 to send out the force params |
1480 |
|
|
|
1481 |
|
|
MPIcheckPoint(); |
1482 |
|
|
|
1483 |
|
|
headTorsionType = new LinkedType; |
1484 |
|
|
recieveFrcStruct( &info, mpiTorsionStructType ); |
1485 |
|
|
while( !info.last ){ |
1486 |
|
|
|
1487 |
|
|
headTorsionType->add( info ); |
1488 |
|
|
recieveFrcStruct( &info, mpiTorsionStructType ); |
1489 |
|
|
} |
1490 |
|
|
} |
1491 |
|
|
#endif // is_mpi |
1492 |
mmeineke |
10 |
|
1493 |
|
|
// initialize the Torsions |
1494 |
|
|
|
1495 |
|
|
for( i=0; i<nTorsions; i++ ){ |
1496 |
|
|
|
1497 |
|
|
a = the_torsions[i].a; |
1498 |
|
|
b = the_torsions[i].b; |
1499 |
|
|
c = the_torsions[i].c; |
1500 |
|
|
d = the_torsions[i].d; |
1501 |
|
|
|
1502 |
|
|
atomA = the_atoms[a]->getType(); |
1503 |
|
|
atomB = the_atoms[b]->getType(); |
1504 |
|
|
atomC = the_atoms[c]->getType(); |
1505 |
|
|
atomD = the_atoms[d]->getType(); |
1506 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1507 |
|
|
if( currentTorsionType == NULL ){ |
1508 |
mmeineke |
176 |
sprintf( painCave.errMsg, |
1509 |
|
|
"TorsionType error, %s - %s - %s - %s not found" |
1510 |
mmeineke |
10 |
" in force file.\n", |
1511 |
|
|
atomA, atomB, atomC, atomD ); |
1512 |
mmeineke |
176 |
painCave.isFatal = 1; |
1513 |
|
|
simError(); |
1514 |
mmeineke |
10 |
} |
1515 |
|
|
|
1516 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1517 |
|
|
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
1518 |
|
|
|
1519 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1520 |
|
|
*the_atoms[c], *the_atoms[d] ); |
1521 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1522 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
1523 |
|
|
the_sris[index] = cTors; |
1524 |
|
|
} |
1525 |
|
|
} |
1526 |
|
|
|
1527 |
|
|
|
1528 |
|
|
// clean up the memory |
1529 |
|
|
|
1530 |
|
|
delete headTorsionType; |
1531 |
|
|
|
1532 |
mmeineke |
176 |
#ifdef IS_MPI |
1533 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" ); |
1534 |
|
|
MPIcheckPoint(); |
1535 |
|
|
#endif // is_mpi |
1536 |
|
|
|
1537 |
mmeineke |
10 |
} |