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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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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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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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|
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chuckv |
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mpiError = MPI_Comm_rank(MPI_COMM_WORLD,&myNode); |
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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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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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fprintf( stderr,"Trying to open %s\n", fileName ); |
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// attempt to open the file in the current directory first. |
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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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fprintf( stderr, |
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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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exit( 8 ); |
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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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fprintf( stderr, |
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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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exit( 8 ); |
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} |
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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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mmeineke |
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} |
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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 |
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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char readLine[500]; |
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char* the_token; |
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char* eof_test; |
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int foundAtom = 0; |
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int lineNum = 0; |
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int i; |
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////////////////////////////////////////////////// |
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// 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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// 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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if( eof_test == NULL ){ |
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fprintf( stderr, "Error in reading Atoms from force file.\n" ); |
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exit(8); |
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} |
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while( !foundAtom ){ |
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while( eof_test != NULL && readLine[0] != '#' ){ |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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} |
283 |
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if( eof_test == NULL ){ |
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fprintf( stderr, |
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"Error in reading Atoms from force file at line %d.\n", |
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lineNum ); |
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exit(8); |
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} |
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the_token = strtok( readLine, " ,;\t#\n" ); |
291 |
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foundAtom = !strcmp( "AtomTypes", the_token ); |
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293 |
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if( !foundAtom ){ |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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297 |
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if( eof_test == NULL ){ |
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fprintf( stderr, |
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"Error in reading Atoms from force file at line %d.\n", |
300 |
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lineNum ); |
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exit(8); |
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} |
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} |
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} |
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// we are now at the AtomTypes section. |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
309 |
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lineNum++; |
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if( eof_test == NULL ){ |
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fprintf( stderr, |
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"Error in reading Atoms from force file at line %d.\n", |
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lineNum ); |
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exit(8); |
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} |
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while( readLine[0] != '#' && eof_test != NULL ){ |
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if( readLine[0] != '!' ){ |
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the_token = strtok( readLine, " \n\t,;" ); |
323 |
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if( the_token != NULL ){ |
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strcpy( currentAtomType->name, the_token ); |
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327 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
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fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
329 |
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exit(8); |
330 |
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} |
331 |
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sscanf( the_token, "%d", ¤tAtomType->isDipole ); |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
335 |
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fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
336 |
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exit(8); |
337 |
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} |
338 |
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339 |
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sscanf( the_token, "%lf", ¤tAtomType->mass ); |
340 |
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341 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
342 |
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fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
343 |
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exit(8); |
344 |
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} |
345 |
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sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
347 |
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348 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
349 |
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fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
350 |
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exit(8); |
351 |
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} |
352 |
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sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
354 |
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355 |
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if( currentAtomType->isDipole ){ |
356 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
357 |
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fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
358 |
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exit(8); |
359 |
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} |
360 |
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361 |
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sscanf( the_token, "%lf", ¤tAtomType->dipole ); |
362 |
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} |
363 |
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} |
364 |
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} |
365 |
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366 |
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tempAtomType = new LinkedType; |
367 |
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currentAtomType->next = tempAtomType; |
368 |
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currentAtomType = tempAtomType; |
369 |
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370 |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
371 |
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lineNum++; |
372 |
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} |
373 |
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374 |
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375 |
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// initialize the atoms |
376 |
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377 |
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DirectionalAtom* dAtom; |
378 |
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379 |
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for( i=0; i<nAtoms; i++ ){ |
380 |
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381 |
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currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
382 |
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if( currentAtomType == NULL ){ |
383 |
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fprintf( stderr, "AtomType error, %s not found in force file.\n", |
384 |
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the_atoms[i]->getType() ); |
385 |
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exit(8); |
386 |
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} |
387 |
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388 |
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the_atoms[i]->setMass( currentAtomType->mass ); |
389 |
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the_atoms[i]->setEpslon( currentAtomType->epslon ); |
390 |
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the_atoms[i]->setSigma( currentAtomType->sigma ); |
391 |
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the_atoms[i]->setLJ(); |
392 |
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393 |
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if( currentAtomType->isDipole ){ |
394 |
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if( the_atoms[i]->isDirectional() ){ |
395 |
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396 |
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dAtom = (DirectionalAtom *) the_atoms[i]; |
397 |
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dAtom->setMu( currentAtomType->dipole ); |
398 |
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dAtom->setHasDipole( 1 ); |
399 |
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dAtom->setJx( 0.0 ); |
400 |
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dAtom->setJy( 0.0 ); |
401 |
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dAtom->setJz( 0.0 ); |
402 |
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403 |
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if(!strcmp("SSD",the_atoms[i]->getType())){ |
404 |
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dAtom->setI( waterI ); |
405 |
|
|
dAtom->setSSD( 1 ); |
406 |
|
|
} |
407 |
|
|
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
408 |
|
|
dAtom->setI( headI ); |
409 |
|
|
dAtom->setSSD( 0 ); |
410 |
|
|
} |
411 |
|
|
else{ |
412 |
|
|
fprintf(stderr, |
413 |
|
|
"AtmType error, %s does not have a moment of inertia set.\n", |
414 |
|
|
the_atoms[i]->getType() ); |
415 |
|
|
exit(8); |
416 |
|
|
} |
417 |
|
|
entry_plug->n_dipoles++; |
418 |
|
|
} |
419 |
|
|
else{ |
420 |
|
|
std::cerr |
421 |
|
|
<< "TraPPE_ExFF error: Atom \"" |
422 |
|
|
<< currentAtomType->name << "\" is a dipole, yet no standard" |
423 |
|
|
<< " orientation was specifed in the BASS file.\n"; |
424 |
|
|
exit(8); |
425 |
|
|
} |
426 |
|
|
} |
427 |
|
|
else{ |
428 |
|
|
if( the_atoms[i]->isDirectional() ){ |
429 |
|
|
std::cerr |
430 |
|
|
<< "TraPPE_ExFF error: Atom \"" |
431 |
|
|
<< currentAtomType->name << "\" was given a standard orientation" |
432 |
|
|
<< " in the BASS file, yet it is not a dipole.\n"; |
433 |
|
|
exit(8); |
434 |
|
|
} |
435 |
|
|
} |
436 |
|
|
} |
437 |
|
|
|
438 |
|
|
|
439 |
|
|
// clean up the memory |
440 |
|
|
|
441 |
|
|
delete headAtomType; |
442 |
|
|
} |
443 |
|
|
|
444 |
|
|
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
445 |
|
|
|
446 |
|
|
class LinkedType { |
447 |
|
|
public: |
448 |
|
|
LinkedType(){ |
449 |
|
|
next = NULL; |
450 |
|
|
nameA[0] = '\0'; |
451 |
|
|
nameB[0] = '\0'; |
452 |
|
|
type[0] = '\0'; |
453 |
|
|
} |
454 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
455 |
|
|
|
456 |
|
|
LinkedType* find(char* key1, char* key2){ |
457 |
|
|
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
458 |
|
|
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
459 |
|
|
if( next != NULL ) return next->find(key1, key2); |
460 |
|
|
return NULL; |
461 |
|
|
} |
462 |
|
|
|
463 |
mmeineke |
146 |
#ifdef IS_MPI |
464 |
|
|
void add( bondStruct &info ){ |
465 |
|
|
if( next != NULL ) next->add(info); |
466 |
|
|
else{ |
467 |
|
|
next = new LinkedType(); |
468 |
|
|
strcpy(next->nameA, info.nameA); |
469 |
|
|
strcpy(next->nameB, info.nameB); |
470 |
|
|
strcpy(next->type, info.type); |
471 |
|
|
next->d0 = info.d0; |
472 |
|
|
} |
473 |
|
|
} |
474 |
|
|
|
475 |
|
|
void duplicate( bondStruct &info ){ |
476 |
|
|
strcpy(info.nameA, nameA); |
477 |
|
|
strcpy(info.nameB, nameB); |
478 |
|
|
strcpy(info.type, type); |
479 |
|
|
info.d0 = d0; |
480 |
|
|
info.last = 0; |
481 |
|
|
} |
482 |
|
|
|
483 |
|
|
|
484 |
|
|
#endif |
485 |
|
|
|
486 |
mmeineke |
10 |
char nameA[15]; |
487 |
|
|
char nameB[15]; |
488 |
|
|
char type[30]; |
489 |
|
|
double d0; |
490 |
|
|
|
491 |
|
|
LinkedType* next; |
492 |
|
|
}; |
493 |
|
|
|
494 |
|
|
|
495 |
|
|
|
496 |
|
|
LinkedType* headBondType; |
497 |
|
|
LinkedType* currentBondType; |
498 |
|
|
LinkedType* tempBondType; |
499 |
|
|
|
500 |
|
|
char readLine[500]; |
501 |
|
|
char* the_token; |
502 |
|
|
char* eof_test; |
503 |
|
|
int foundBond = 0; |
504 |
|
|
int lineNum = 0; |
505 |
|
|
int i, a, b; |
506 |
|
|
char* atomA; |
507 |
|
|
char* atomB; |
508 |
|
|
|
509 |
|
|
SRI **the_sris; |
510 |
|
|
Atom** the_atoms; |
511 |
|
|
int nBonds; |
512 |
|
|
the_sris = entry_plug->sr_interactions; |
513 |
|
|
the_atoms = entry_plug->atoms; |
514 |
|
|
nBonds = entry_plug->n_bonds; |
515 |
|
|
|
516 |
|
|
// read in the bond types. |
517 |
|
|
|
518 |
|
|
rewind( frcFile ); |
519 |
|
|
headBondType = new LinkedType; |
520 |
|
|
currentBondType = headBondType; |
521 |
|
|
|
522 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
523 |
|
|
lineNum++; |
524 |
|
|
if( eof_test == NULL ){ |
525 |
|
|
fprintf( stderr, "Error in reading Bonds from force file.\n" ); |
526 |
|
|
exit(8); |
527 |
|
|
} |
528 |
|
|
|
529 |
|
|
|
530 |
|
|
while( !foundBond ){ |
531 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
532 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
533 |
|
|
lineNum++; |
534 |
|
|
} |
535 |
|
|
if( eof_test == NULL ){ |
536 |
|
|
fprintf( stderr, |
537 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
538 |
|
|
lineNum ); |
539 |
|
|
exit(8); |
540 |
|
|
} |
541 |
|
|
|
542 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
543 |
|
|
foundBond = !strcmp( "BondTypes", the_token ); |
544 |
|
|
|
545 |
|
|
if( !foundBond ){ |
546 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
547 |
|
|
lineNum++; |
548 |
|
|
|
549 |
|
|
if( eof_test == NULL ){ |
550 |
|
|
fprintf( stderr, |
551 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
552 |
|
|
lineNum ); |
553 |
|
|
exit(8); |
554 |
|
|
} |
555 |
|
|
} |
556 |
|
|
} |
557 |
|
|
|
558 |
|
|
// we are now at the BondTypes section. |
559 |
|
|
|
560 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
561 |
|
|
lineNum++; |
562 |
|
|
|
563 |
|
|
if( eof_test == NULL ){ |
564 |
|
|
fprintf( stderr, |
565 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
566 |
|
|
lineNum ); |
567 |
|
|
exit(8); |
568 |
|
|
} |
569 |
|
|
|
570 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
571 |
|
|
|
572 |
|
|
if( readLine[0] != '!' ){ |
573 |
|
|
|
574 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
575 |
|
|
if( the_token != NULL ){ |
576 |
|
|
|
577 |
|
|
strcpy( currentBondType->nameA, the_token ); |
578 |
|
|
|
579 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
580 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
581 |
|
|
exit(8); |
582 |
|
|
} |
583 |
|
|
|
584 |
|
|
strcpy( currentBondType->nameB, the_token ); |
585 |
|
|
|
586 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
587 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
588 |
|
|
exit(8); |
589 |
|
|
} |
590 |
|
|
|
591 |
|
|
strcpy( currentBondType->type, the_token ); |
592 |
|
|
|
593 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
594 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
595 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
596 |
|
|
exit(8); |
597 |
|
|
} |
598 |
|
|
|
599 |
|
|
sscanf( the_token, "%lf", ¤tBondType->d0 ); |
600 |
|
|
} |
601 |
|
|
|
602 |
|
|
else{ |
603 |
|
|
fprintf(stderr, |
604 |
|
|
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
605 |
|
|
currentBondType->type, |
606 |
|
|
lineNum ); |
607 |
|
|
exit(8); |
608 |
|
|
} |
609 |
|
|
} |
610 |
|
|
} |
611 |
|
|
|
612 |
|
|
tempBondType = new LinkedType; |
613 |
|
|
currentBondType->next = tempBondType; |
614 |
|
|
currentBondType = tempBondType; |
615 |
|
|
|
616 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
617 |
|
|
lineNum++; |
618 |
|
|
} |
619 |
|
|
|
620 |
|
|
|
621 |
|
|
// initialize the Bonds |
622 |
|
|
|
623 |
|
|
|
624 |
|
|
for( i=0; i<nBonds; i++ ){ |
625 |
|
|
|
626 |
|
|
a = the_bonds[i].a; |
627 |
|
|
b = the_bonds[i].b; |
628 |
|
|
|
629 |
|
|
atomA = the_atoms[a]->getType(); |
630 |
|
|
atomB = the_atoms[b]->getType(); |
631 |
|
|
currentBondType = headBondType->find( atomA, atomB ); |
632 |
|
|
if( currentBondType == NULL ){ |
633 |
|
|
fprintf( stderr, "BondType error, %s - %s not found in force file.\n", |
634 |
|
|
atomA, atomB ); |
635 |
|
|
exit(8); |
636 |
|
|
} |
637 |
|
|
|
638 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
639 |
|
|
|
640 |
|
|
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
641 |
|
|
*the_atoms[b], |
642 |
|
|
currentBondType->d0 ); |
643 |
|
|
entry_plug->n_constraints++; |
644 |
|
|
} |
645 |
|
|
} |
646 |
|
|
|
647 |
|
|
|
648 |
|
|
// clean up the memory |
649 |
|
|
|
650 |
|
|
delete headBondType; |
651 |
|
|
|
652 |
|
|
} |
653 |
|
|
|
654 |
|
|
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
655 |
|
|
|
656 |
|
|
class LinkedType { |
657 |
|
|
public: |
658 |
|
|
LinkedType(){ |
659 |
|
|
next = NULL; |
660 |
|
|
nameA[0] = '\0'; |
661 |
|
|
nameB[0] = '\0'; |
662 |
|
|
nameC[0] = '\0'; |
663 |
|
|
type[0] = '\0'; |
664 |
|
|
} |
665 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
666 |
|
|
|
667 |
|
|
LinkedType* find( char* key1, char* key2, char* key3 ){ |
668 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
669 |
|
|
&& !strcmp( nameC, key3 ) ) return this; |
670 |
|
|
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
671 |
|
|
&& !strcmp( nameC, key1 ) ) return this; |
672 |
|
|
if( next != NULL ) return next->find(key1, key2, key3); |
673 |
|
|
return NULL; |
674 |
|
|
} |
675 |
|
|
|
676 |
mmeineke |
146 |
#ifdef IS_MPI |
677 |
|
|
|
678 |
|
|
void add( bendStruct &info ){ |
679 |
|
|
if( next != NULL ) next->add(info); |
680 |
|
|
else{ |
681 |
|
|
next = new LinkedType(); |
682 |
|
|
strcpy(next->nameA, info.nameA); |
683 |
|
|
strcpy(next->nameB, info.nameB); |
684 |
|
|
strcpy(next->nameC, info.nameC); |
685 |
|
|
strcpy(next->type, info.type); |
686 |
|
|
next->k1 = info.k1; |
687 |
|
|
next->k2 = info.k2; |
688 |
|
|
next->k3 = info.k3; |
689 |
|
|
next->t0 = info.t0; |
690 |
|
|
} |
691 |
|
|
} |
692 |
|
|
|
693 |
|
|
void duplicate( bendStruct &info ){ |
694 |
|
|
strcpy(info.nameA, nameA); |
695 |
|
|
strcpy(info.nameB, nameB); |
696 |
|
|
strcpy(info.nameC, nameC); |
697 |
|
|
strcpy(info.type, type); |
698 |
|
|
info.k1 = k1; |
699 |
|
|
info.k2 = k2; |
700 |
|
|
info.k3 = k3; |
701 |
|
|
info.t0 = t0; |
702 |
|
|
info.last = 0; |
703 |
|
|
} |
704 |
|
|
|
705 |
|
|
#endif |
706 |
|
|
|
707 |
mmeineke |
10 |
char nameA[15]; |
708 |
|
|
char nameB[15]; |
709 |
|
|
char nameC[15]; |
710 |
|
|
char type[30]; |
711 |
|
|
double k1, k2, k3, t0; |
712 |
|
|
|
713 |
|
|
LinkedType* next; |
714 |
|
|
}; |
715 |
|
|
|
716 |
|
|
LinkedType* headBendType; |
717 |
|
|
LinkedType* currentBendType; |
718 |
|
|
LinkedType* tempBendType; |
719 |
|
|
|
720 |
|
|
char readLine[500]; |
721 |
|
|
char* the_token; |
722 |
|
|
char* eof_test; |
723 |
|
|
int foundBend = 0; |
724 |
|
|
int lineNum = 0; |
725 |
|
|
int i, a, b, c, index; |
726 |
|
|
char* atomA; |
727 |
|
|
char* atomB; |
728 |
|
|
char* atomC; |
729 |
|
|
QuadraticBend* qBend; |
730 |
|
|
|
731 |
|
|
SRI **the_sris; |
732 |
|
|
Atom** the_atoms; |
733 |
|
|
int nBends; |
734 |
|
|
the_sris = entry_plug->sr_interactions; |
735 |
|
|
the_atoms = entry_plug->atoms; |
736 |
|
|
nBends = entry_plug->n_bends; |
737 |
|
|
|
738 |
|
|
// read in the bend types. |
739 |
|
|
|
740 |
|
|
rewind( frcFile ); |
741 |
|
|
headBendType = new LinkedType; |
742 |
|
|
currentBendType = headBendType; |
743 |
|
|
|
744 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
745 |
|
|
lineNum++; |
746 |
|
|
if( eof_test == NULL ){ |
747 |
|
|
fprintf( stderr, "Error in reading Bends from force file.\n" ); |
748 |
|
|
exit(8); |
749 |
|
|
} |
750 |
|
|
|
751 |
|
|
|
752 |
|
|
while( !foundBend ){ |
753 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
754 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
755 |
|
|
lineNum++; |
756 |
|
|
} |
757 |
|
|
if( eof_test == NULL ){ |
758 |
|
|
fprintf( stderr, |
759 |
|
|
"Error in reading Bends from force file at line %d.\n", |
760 |
|
|
lineNum ); |
761 |
|
|
exit(8); |
762 |
|
|
} |
763 |
|
|
|
764 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
765 |
|
|
foundBend = !strcmp( "BendTypes", the_token ); |
766 |
|
|
|
767 |
|
|
if( !foundBend ){ |
768 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
769 |
|
|
lineNum++; |
770 |
|
|
|
771 |
|
|
if( eof_test == NULL ){ |
772 |
|
|
fprintf( stderr, |
773 |
|
|
"Error in reading Bends from force file at line %d.\n", |
774 |
|
|
lineNum ); |
775 |
|
|
exit(8); |
776 |
|
|
} |
777 |
|
|
} |
778 |
|
|
} |
779 |
|
|
|
780 |
|
|
// we are now at the BendTypes section. |
781 |
|
|
|
782 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
783 |
|
|
lineNum++; |
784 |
|
|
|
785 |
|
|
if( eof_test == NULL ){ |
786 |
|
|
fprintf( stderr, |
787 |
|
|
"Error in reading Bends from force file at line %d.\n", |
788 |
|
|
lineNum ); |
789 |
|
|
exit(8); |
790 |
|
|
} |
791 |
|
|
|
792 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
793 |
|
|
|
794 |
|
|
if( readLine[0] != '!' ){ |
795 |
|
|
|
796 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
797 |
|
|
if( the_token != NULL ){ |
798 |
|
|
|
799 |
|
|
strcpy( currentBendType->nameA, the_token ); |
800 |
|
|
|
801 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
802 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
803 |
|
|
exit(8); |
804 |
|
|
} |
805 |
|
|
|
806 |
|
|
strcpy( currentBendType->nameB, the_token ); |
807 |
|
|
|
808 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
809 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
810 |
|
|
exit(8); |
811 |
|
|
} |
812 |
|
|
|
813 |
|
|
strcpy( currentBendType->nameC, the_token ); |
814 |
|
|
|
815 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
816 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
817 |
|
|
exit(8); |
818 |
|
|
} |
819 |
|
|
|
820 |
|
|
strcpy( currentBendType->type, the_token ); |
821 |
|
|
|
822 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
823 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
824 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
825 |
|
|
exit(8); |
826 |
|
|
} |
827 |
|
|
|
828 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
829 |
|
|
|
830 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
831 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
832 |
|
|
exit(8); |
833 |
|
|
} |
834 |
|
|
|
835 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
836 |
|
|
|
837 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
838 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
839 |
|
|
exit(8); |
840 |
|
|
} |
841 |
|
|
|
842 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
843 |
|
|
|
844 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
845 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
846 |
|
|
exit(8); |
847 |
|
|
} |
848 |
|
|
|
849 |
|
|
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
850 |
|
|
} |
851 |
|
|
|
852 |
|
|
else{ |
853 |
|
|
fprintf(stderr, |
854 |
|
|
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
855 |
|
|
currentBendType->type, |
856 |
|
|
lineNum ); |
857 |
|
|
exit(8); |
858 |
|
|
} |
859 |
|
|
} |
860 |
|
|
} |
861 |
|
|
|
862 |
|
|
tempBendType = new LinkedType; |
863 |
|
|
currentBendType->next = tempBendType; |
864 |
|
|
currentBendType = tempBendType; |
865 |
|
|
|
866 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
867 |
|
|
lineNum++; |
868 |
|
|
} |
869 |
|
|
|
870 |
|
|
|
871 |
|
|
// initialize the Bends |
872 |
|
|
|
873 |
|
|
for( i=0; i<nBends; i++ ){ |
874 |
|
|
|
875 |
|
|
a = the_bends[i].a; |
876 |
|
|
b = the_bends[i].b; |
877 |
|
|
c = the_bends[i].c; |
878 |
|
|
|
879 |
|
|
atomA = the_atoms[a]->getType(); |
880 |
|
|
atomB = the_atoms[b]->getType(); |
881 |
|
|
atomC = the_atoms[c]->getType(); |
882 |
|
|
currentBendType = headBendType->find( atomA, atomB, atomC ); |
883 |
|
|
if( currentBendType == NULL ){ |
884 |
|
|
fprintf( stderr, "BendType error, %s - %s - %s not found" |
885 |
|
|
" in force file.\n", |
886 |
|
|
atomA, atomB, atomC ); |
887 |
|
|
exit(8); |
888 |
|
|
} |
889 |
|
|
|
890 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
891 |
|
|
|
892 |
|
|
index = i + entry_plug->n_bonds; |
893 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
894 |
|
|
*the_atoms[b], |
895 |
|
|
*the_atoms[c] ); |
896 |
|
|
qBend->setConstants( currentBendType->k1, |
897 |
|
|
currentBendType->k2, |
898 |
|
|
currentBendType->k3, |
899 |
|
|
currentBendType->t0 ); |
900 |
|
|
the_sris[index] = qBend; |
901 |
|
|
} |
902 |
|
|
} |
903 |
|
|
|
904 |
|
|
|
905 |
|
|
// clean up the memory |
906 |
|
|
|
907 |
|
|
delete headBendType; |
908 |
|
|
|
909 |
|
|
} |
910 |
|
|
|
911 |
|
|
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
912 |
|
|
|
913 |
|
|
class LinkedType { |
914 |
|
|
public: |
915 |
|
|
LinkedType(){ |
916 |
|
|
next = NULL; |
917 |
|
|
nameA[0] = '\0'; |
918 |
|
|
nameB[0] = '\0'; |
919 |
|
|
nameC[0] = '\0'; |
920 |
|
|
type[0] = '\0'; |
921 |
|
|
} |
922 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
923 |
|
|
|
924 |
|
|
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
925 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
926 |
|
|
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
927 |
|
|
|
928 |
|
|
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
929 |
|
|
!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this; |
930 |
|
|
|
931 |
|
|
if( next != NULL ) return next->find(key1, key2, key3, key4); |
932 |
|
|
return NULL; |
933 |
|
|
} |
934 |
|
|
|
935 |
mmeineke |
146 |
#ifdef IS_MPI |
936 |
|
|
|
937 |
|
|
void add( torsionStruct &info ){ |
938 |
|
|
if( next != NULL ) next->add(info); |
939 |
|
|
else{ |
940 |
|
|
next = new LinkedType(); |
941 |
|
|
strcpy(next->nameA, info.nameA); |
942 |
|
|
strcpy(next->nameB, info.nameB); |
943 |
|
|
strcpy(next->nameC, info.nameC); |
944 |
|
|
strcpy(next->type, info.type); |
945 |
|
|
next->k1 = info.k1; |
946 |
|
|
next->k2 = info.k2; |
947 |
|
|
next->k3 = info.k3; |
948 |
|
|
next->k4 = info.k4; |
949 |
|
|
} |
950 |
|
|
} |
951 |
|
|
|
952 |
|
|
void duplicate( torsionStruct &info ){ |
953 |
|
|
strcpy(info.nameA, nameA); |
954 |
|
|
strcpy(info.nameB, nameB); |
955 |
|
|
strcpy(info.nameC, nameC); |
956 |
|
|
strcpy(info.nameD, nameD); |
957 |
|
|
strcpy(info.type, type); |
958 |
|
|
info.k1 = k1; |
959 |
|
|
info.k2 = k2; |
960 |
|
|
info.k3 = k3; |
961 |
|
|
info.k4 = k4; |
962 |
|
|
info.last = 0; |
963 |
|
|
} |
964 |
|
|
|
965 |
|
|
#endif |
966 |
|
|
|
967 |
mmeineke |
10 |
char nameA[15]; |
968 |
|
|
char nameB[15]; |
969 |
|
|
char nameC[15]; |
970 |
|
|
char nameD[15]; |
971 |
|
|
char type[30]; |
972 |
|
|
double k1, k2, k3, k4; |
973 |
|
|
|
974 |
|
|
LinkedType* next; |
975 |
|
|
}; |
976 |
|
|
|
977 |
|
|
LinkedType* headTorsionType; |
978 |
|
|
LinkedType* currentTorsionType; |
979 |
|
|
LinkedType* tempTorsionType; |
980 |
|
|
|
981 |
|
|
char readLine[500]; |
982 |
|
|
char* the_token; |
983 |
|
|
char* eof_test; |
984 |
|
|
int foundTorsion = 0; |
985 |
|
|
int lineNum = 0; |
986 |
|
|
int i, a, b, c, d, index; |
987 |
|
|
char* atomA; |
988 |
|
|
char* atomB; |
989 |
|
|
char* atomC; |
990 |
|
|
char* atomD; |
991 |
|
|
CubicTorsion* cTors; |
992 |
|
|
|
993 |
|
|
SRI **the_sris; |
994 |
|
|
Atom** the_atoms; |
995 |
|
|
int nTorsions; |
996 |
|
|
the_sris = entry_plug->sr_interactions; |
997 |
|
|
the_atoms = entry_plug->atoms; |
998 |
|
|
nTorsions = entry_plug->n_torsions; |
999 |
|
|
|
1000 |
|
|
// read in the torsion types. |
1001 |
|
|
|
1002 |
|
|
rewind( frcFile ); |
1003 |
|
|
headTorsionType = new LinkedType; |
1004 |
|
|
currentTorsionType = headTorsionType; |
1005 |
|
|
|
1006 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1007 |
|
|
lineNum++; |
1008 |
|
|
if( eof_test == NULL ){ |
1009 |
|
|
fprintf( stderr, "Error in reading Torsions from force file.\n" ); |
1010 |
|
|
exit(8); |
1011 |
|
|
} |
1012 |
|
|
|
1013 |
|
|
|
1014 |
|
|
while( !foundTorsion ){ |
1015 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
1016 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1017 |
|
|
lineNum++; |
1018 |
|
|
} |
1019 |
|
|
if( eof_test == NULL ){ |
1020 |
|
|
fprintf( stderr, |
1021 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
1022 |
|
|
lineNum ); |
1023 |
|
|
exit(8); |
1024 |
|
|
} |
1025 |
|
|
|
1026 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
1027 |
|
|
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
1028 |
|
|
|
1029 |
|
|
if( !foundTorsion ){ |
1030 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1031 |
|
|
lineNum++; |
1032 |
|
|
|
1033 |
|
|
if( eof_test == NULL ){ |
1034 |
|
|
fprintf( stderr, |
1035 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
1036 |
|
|
lineNum ); |
1037 |
|
|
exit(8); |
1038 |
|
|
} |
1039 |
|
|
} |
1040 |
|
|
} |
1041 |
|
|
|
1042 |
|
|
// we are now at the TorsionTypes section. |
1043 |
|
|
|
1044 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1045 |
|
|
lineNum++; |
1046 |
|
|
|
1047 |
|
|
if( eof_test == NULL ){ |
1048 |
|
|
fprintf( stderr, |
1049 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
1050 |
|
|
lineNum ); |
1051 |
|
|
exit(8); |
1052 |
|
|
} |
1053 |
|
|
|
1054 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
1055 |
|
|
|
1056 |
|
|
if( readLine[0] != '!' ){ |
1057 |
|
|
|
1058 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
1059 |
|
|
if( the_token != NULL ){ |
1060 |
|
|
|
1061 |
|
|
strcpy( currentTorsionType->nameA, the_token ); |
1062 |
|
|
|
1063 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1064 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1065 |
|
|
exit(8); |
1066 |
|
|
} |
1067 |
|
|
|
1068 |
|
|
strcpy( currentTorsionType->nameB, the_token ); |
1069 |
|
|
|
1070 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1071 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1072 |
|
|
exit(8); |
1073 |
|
|
} |
1074 |
|
|
|
1075 |
|
|
strcpy( currentTorsionType->nameC, the_token ); |
1076 |
|
|
|
1077 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1078 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1079 |
|
|
exit(8); |
1080 |
|
|
} |
1081 |
|
|
|
1082 |
|
|
strcpy( currentTorsionType->nameD, the_token ); |
1083 |
|
|
|
1084 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1085 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1086 |
|
|
exit(8); |
1087 |
|
|
} |
1088 |
|
|
|
1089 |
|
|
strcpy( currentTorsionType->type, the_token ); |
1090 |
|
|
|
1091 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1092 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1093 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1094 |
|
|
exit(8); |
1095 |
|
|
} |
1096 |
|
|
|
1097 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
1098 |
|
|
|
1099 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1100 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1101 |
|
|
exit(8); |
1102 |
|
|
} |
1103 |
|
|
|
1104 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
1105 |
|
|
|
1106 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1107 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1108 |
|
|
exit(8); |
1109 |
|
|
} |
1110 |
|
|
|
1111 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
1112 |
|
|
|
1113 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1114 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1115 |
|
|
exit(8); |
1116 |
|
|
} |
1117 |
|
|
|
1118 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
1119 |
|
|
} |
1120 |
|
|
|
1121 |
|
|
else{ |
1122 |
|
|
fprintf(stderr, |
1123 |
|
|
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1124 |
|
|
currentTorsionType->type, |
1125 |
|
|
lineNum ); |
1126 |
|
|
exit(8); |
1127 |
|
|
} |
1128 |
|
|
} |
1129 |
|
|
} |
1130 |
|
|
|
1131 |
|
|
tempTorsionType = new LinkedType; |
1132 |
|
|
currentTorsionType->next = tempTorsionType; |
1133 |
|
|
currentTorsionType = tempTorsionType; |
1134 |
|
|
|
1135 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1136 |
|
|
lineNum++; |
1137 |
|
|
} |
1138 |
|
|
|
1139 |
|
|
|
1140 |
|
|
// initialize the Torsions |
1141 |
|
|
|
1142 |
|
|
for( i=0; i<nTorsions; i++ ){ |
1143 |
|
|
|
1144 |
|
|
a = the_torsions[i].a; |
1145 |
|
|
b = the_torsions[i].b; |
1146 |
|
|
c = the_torsions[i].c; |
1147 |
|
|
d = the_torsions[i].d; |
1148 |
|
|
|
1149 |
|
|
atomA = the_atoms[a]->getType(); |
1150 |
|
|
atomB = the_atoms[b]->getType(); |
1151 |
|
|
atomC = the_atoms[c]->getType(); |
1152 |
|
|
atomD = the_atoms[d]->getType(); |
1153 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1154 |
|
|
if( currentTorsionType == NULL ){ |
1155 |
|
|
fprintf( stderr, "TorsionType error, %s - %s - %s - %s not found" |
1156 |
|
|
" in force file.\n", |
1157 |
|
|
atomA, atomB, atomC, atomD ); |
1158 |
|
|
exit(8); |
1159 |
|
|
} |
1160 |
|
|
|
1161 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1162 |
|
|
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
1163 |
|
|
|
1164 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1165 |
|
|
*the_atoms[c], *the_atoms[d] ); |
1166 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1167 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
1168 |
|
|
the_sris[index] = cTors; |
1169 |
|
|
} |
1170 |
|
|
} |
1171 |
|
|
|
1172 |
|
|
|
1173 |
|
|
// clean up the memory |
1174 |
|
|
|
1175 |
|
|
delete headTorsionType; |
1176 |
|
|
|
1177 |
|
|
} |