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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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#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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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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169 |
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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} |
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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" ); |
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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 ); |
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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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} |
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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 ); |
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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,;" ); |
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if( the_token != NULL ){ |
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strcpy( currentAtomType->name, the_token ); |
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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 ); |
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exit(8); |
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} |
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sscanf( the_token, "%d", ¤tAtomType->isDipole ); |
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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 ); |
300 |
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exit(8); |
301 |
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} |
302 |
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sscanf( the_token, "%lf", ¤tAtomType->mass ); |
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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 ); |
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exit(8); |
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} |
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sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
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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 ); |
314 |
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exit(8); |
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} |
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sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
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if( currentAtomType->isDipole ){ |
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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 ); |
322 |
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exit(8); |
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} |
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sscanf( the_token, "%lf", ¤tAtomType->dipole ); |
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} |
327 |
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} |
328 |
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} |
329 |
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tempAtomType = new LinkedType; |
331 |
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currentAtomType->next = tempAtomType; |
332 |
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currentAtomType = tempAtomType; |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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} |
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// initialize the atoms |
340 |
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341 |
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DirectionalAtom* dAtom; |
342 |
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343 |
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for( i=0; i<nAtoms; i++ ){ |
344 |
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345 |
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currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
346 |
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if( currentAtomType == NULL ){ |
347 |
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fprintf( stderr, "AtomType error, %s not found in force file.\n", |
348 |
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the_atoms[i]->getType() ); |
349 |
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exit(8); |
350 |
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} |
351 |
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352 |
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the_atoms[i]->setMass( currentAtomType->mass ); |
353 |
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the_atoms[i]->setEpslon( currentAtomType->epslon ); |
354 |
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the_atoms[i]->setSigma( currentAtomType->sigma ); |
355 |
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the_atoms[i]->setLJ(); |
356 |
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357 |
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if( currentAtomType->isDipole ){ |
358 |
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if( the_atoms[i]->isDirectional() ){ |
359 |
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360 |
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dAtom = (DirectionalAtom *) the_atoms[i]; |
361 |
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dAtom->setMu( currentAtomType->dipole ); |
362 |
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dAtom->setHasDipole( 1 ); |
363 |
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dAtom->setJx( 0.0 ); |
364 |
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dAtom->setJy( 0.0 ); |
365 |
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dAtom->setJz( 0.0 ); |
366 |
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367 |
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if(!strcmp("SSD",the_atoms[i]->getType())){ |
368 |
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dAtom->setI( waterI ); |
369 |
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dAtom->setSSD( 1 ); |
370 |
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} |
371 |
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else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
372 |
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dAtom->setI( headI ); |
373 |
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dAtom->setSSD( 0 ); |
374 |
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} |
375 |
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else{ |
376 |
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fprintf(stderr, |
377 |
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"AtmType error, %s does not have a moment of inertia set.\n", |
378 |
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the_atoms[i]->getType() ); |
379 |
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exit(8); |
380 |
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} |
381 |
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entry_plug->n_dipoles++; |
382 |
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} |
383 |
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else{ |
384 |
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std::cerr |
385 |
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<< "TraPPE_ExFF error: Atom \"" |
386 |
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<< currentAtomType->name << "\" is a dipole, yet no standard" |
387 |
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<< " orientation was specifed in the BASS file.\n"; |
388 |
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exit(8); |
389 |
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} |
390 |
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} |
391 |
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else{ |
392 |
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if( the_atoms[i]->isDirectional() ){ |
393 |
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std::cerr |
394 |
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<< "TraPPE_ExFF error: Atom \"" |
395 |
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<< currentAtomType->name << "\" was given a standard orientation" |
396 |
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<< " in the BASS file, yet it is not a dipole.\n"; |
397 |
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exit(8); |
398 |
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} |
399 |
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} |
400 |
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} |
401 |
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402 |
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403 |
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// clean up the memory |
404 |
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405 |
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delete headAtomType; |
406 |
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|
} |
407 |
|
|
|
408 |
|
|
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
409 |
|
|
|
410 |
|
|
class LinkedType { |
411 |
|
|
public: |
412 |
|
|
LinkedType(){ |
413 |
|
|
next = NULL; |
414 |
|
|
nameA[0] = '\0'; |
415 |
|
|
nameB[0] = '\0'; |
416 |
|
|
type[0] = '\0'; |
417 |
|
|
} |
418 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
419 |
|
|
|
420 |
|
|
LinkedType* find(char* key1, char* key2){ |
421 |
|
|
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
422 |
|
|
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
423 |
|
|
if( next != NULL ) return next->find(key1, key2); |
424 |
|
|
return NULL; |
425 |
|
|
} |
426 |
|
|
|
427 |
|
|
char nameA[15]; |
428 |
|
|
char nameB[15]; |
429 |
|
|
char type[30]; |
430 |
|
|
double d0; |
431 |
|
|
|
432 |
|
|
LinkedType* next; |
433 |
|
|
}; |
434 |
|
|
|
435 |
|
|
|
436 |
|
|
|
437 |
|
|
LinkedType* headBondType; |
438 |
|
|
LinkedType* currentBondType; |
439 |
|
|
LinkedType* tempBondType; |
440 |
|
|
|
441 |
|
|
char readLine[500]; |
442 |
|
|
char* the_token; |
443 |
|
|
char* eof_test; |
444 |
|
|
int foundBond = 0; |
445 |
|
|
int lineNum = 0; |
446 |
|
|
int i, a, b; |
447 |
|
|
char* atomA; |
448 |
|
|
char* atomB; |
449 |
|
|
|
450 |
|
|
SRI **the_sris; |
451 |
|
|
Atom** the_atoms; |
452 |
|
|
int nBonds; |
453 |
|
|
the_sris = entry_plug->sr_interactions; |
454 |
|
|
the_atoms = entry_plug->atoms; |
455 |
|
|
nBonds = entry_plug->n_bonds; |
456 |
|
|
|
457 |
|
|
// read in the bond types. |
458 |
|
|
|
459 |
|
|
rewind( frcFile ); |
460 |
|
|
headBondType = new LinkedType; |
461 |
|
|
currentBondType = headBondType; |
462 |
|
|
|
463 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
464 |
|
|
lineNum++; |
465 |
|
|
if( eof_test == NULL ){ |
466 |
|
|
fprintf( stderr, "Error in reading Bonds from force file.\n" ); |
467 |
|
|
exit(8); |
468 |
|
|
} |
469 |
|
|
|
470 |
|
|
|
471 |
|
|
while( !foundBond ){ |
472 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
473 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
474 |
|
|
lineNum++; |
475 |
|
|
} |
476 |
|
|
if( eof_test == NULL ){ |
477 |
|
|
fprintf( stderr, |
478 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
479 |
|
|
lineNum ); |
480 |
|
|
exit(8); |
481 |
|
|
} |
482 |
|
|
|
483 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
484 |
|
|
foundBond = !strcmp( "BondTypes", the_token ); |
485 |
|
|
|
486 |
|
|
if( !foundBond ){ |
487 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
488 |
|
|
lineNum++; |
489 |
|
|
|
490 |
|
|
if( eof_test == NULL ){ |
491 |
|
|
fprintf( stderr, |
492 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
493 |
|
|
lineNum ); |
494 |
|
|
exit(8); |
495 |
|
|
} |
496 |
|
|
} |
497 |
|
|
} |
498 |
|
|
|
499 |
|
|
// we are now at the BondTypes section. |
500 |
|
|
|
501 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
502 |
|
|
lineNum++; |
503 |
|
|
|
504 |
|
|
if( eof_test == NULL ){ |
505 |
|
|
fprintf( stderr, |
506 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
507 |
|
|
lineNum ); |
508 |
|
|
exit(8); |
509 |
|
|
} |
510 |
|
|
|
511 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
512 |
|
|
|
513 |
|
|
if( readLine[0] != '!' ){ |
514 |
|
|
|
515 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
516 |
|
|
if( the_token != NULL ){ |
517 |
|
|
|
518 |
|
|
strcpy( currentBondType->nameA, the_token ); |
519 |
|
|
|
520 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
521 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
522 |
|
|
exit(8); |
523 |
|
|
} |
524 |
|
|
|
525 |
|
|
strcpy( currentBondType->nameB, the_token ); |
526 |
|
|
|
527 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
528 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
529 |
|
|
exit(8); |
530 |
|
|
} |
531 |
|
|
|
532 |
|
|
strcpy( currentBondType->type, the_token ); |
533 |
|
|
|
534 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
535 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
536 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
537 |
|
|
exit(8); |
538 |
|
|
} |
539 |
|
|
|
540 |
|
|
sscanf( the_token, "%lf", ¤tBondType->d0 ); |
541 |
|
|
} |
542 |
|
|
|
543 |
|
|
else{ |
544 |
|
|
fprintf(stderr, |
545 |
|
|
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
546 |
|
|
currentBondType->type, |
547 |
|
|
lineNum ); |
548 |
|
|
exit(8); |
549 |
|
|
} |
550 |
|
|
} |
551 |
|
|
} |
552 |
|
|
|
553 |
|
|
tempBondType = new LinkedType; |
554 |
|
|
currentBondType->next = tempBondType; |
555 |
|
|
currentBondType = tempBondType; |
556 |
|
|
|
557 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
558 |
|
|
lineNum++; |
559 |
|
|
} |
560 |
|
|
|
561 |
|
|
|
562 |
|
|
// initialize the Bonds |
563 |
|
|
|
564 |
|
|
|
565 |
|
|
for( i=0; i<nBonds; i++ ){ |
566 |
|
|
|
567 |
|
|
a = the_bonds[i].a; |
568 |
|
|
b = the_bonds[i].b; |
569 |
|
|
|
570 |
|
|
atomA = the_atoms[a]->getType(); |
571 |
|
|
atomB = the_atoms[b]->getType(); |
572 |
|
|
currentBondType = headBondType->find( atomA, atomB ); |
573 |
|
|
if( currentBondType == NULL ){ |
574 |
|
|
fprintf( stderr, "BondType error, %s - %s not found in force file.\n", |
575 |
|
|
atomA, atomB ); |
576 |
|
|
exit(8); |
577 |
|
|
} |
578 |
|
|
|
579 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
580 |
|
|
|
581 |
|
|
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
582 |
|
|
*the_atoms[b], |
583 |
|
|
currentBondType->d0 ); |
584 |
|
|
entry_plug->n_constraints++; |
585 |
|
|
} |
586 |
|
|
} |
587 |
|
|
|
588 |
|
|
|
589 |
|
|
// clean up the memory |
590 |
|
|
|
591 |
|
|
delete headBondType; |
592 |
|
|
|
593 |
|
|
} |
594 |
|
|
|
595 |
|
|
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
596 |
|
|
|
597 |
|
|
class LinkedType { |
598 |
|
|
public: |
599 |
|
|
LinkedType(){ |
600 |
|
|
next = NULL; |
601 |
|
|
nameA[0] = '\0'; |
602 |
|
|
nameB[0] = '\0'; |
603 |
|
|
nameC[0] = '\0'; |
604 |
|
|
type[0] = '\0'; |
605 |
|
|
} |
606 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
607 |
|
|
|
608 |
|
|
LinkedType* find( char* key1, char* key2, char* key3 ){ |
609 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
610 |
|
|
&& !strcmp( nameC, key3 ) ) return this; |
611 |
|
|
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
612 |
|
|
&& !strcmp( nameC, key1 ) ) return this; |
613 |
|
|
if( next != NULL ) return next->find(key1, key2, key3); |
614 |
|
|
return NULL; |
615 |
|
|
} |
616 |
|
|
|
617 |
|
|
char nameA[15]; |
618 |
|
|
char nameB[15]; |
619 |
|
|
char nameC[15]; |
620 |
|
|
char type[30]; |
621 |
|
|
double k1, k2, k3, t0; |
622 |
|
|
|
623 |
|
|
LinkedType* next; |
624 |
|
|
}; |
625 |
|
|
|
626 |
|
|
LinkedType* headBendType; |
627 |
|
|
LinkedType* currentBendType; |
628 |
|
|
LinkedType* tempBendType; |
629 |
|
|
|
630 |
|
|
char readLine[500]; |
631 |
|
|
char* the_token; |
632 |
|
|
char* eof_test; |
633 |
|
|
int foundBend = 0; |
634 |
|
|
int lineNum = 0; |
635 |
|
|
int i, a, b, c, index; |
636 |
|
|
char* atomA; |
637 |
|
|
char* atomB; |
638 |
|
|
char* atomC; |
639 |
|
|
QuadraticBend* qBend; |
640 |
|
|
|
641 |
|
|
SRI **the_sris; |
642 |
|
|
Atom** the_atoms; |
643 |
|
|
int nBends; |
644 |
|
|
the_sris = entry_plug->sr_interactions; |
645 |
|
|
the_atoms = entry_plug->atoms; |
646 |
|
|
nBends = entry_plug->n_bends; |
647 |
|
|
|
648 |
|
|
// read in the bend types. |
649 |
|
|
|
650 |
|
|
rewind( frcFile ); |
651 |
|
|
headBendType = new LinkedType; |
652 |
|
|
currentBendType = headBendType; |
653 |
|
|
|
654 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
655 |
|
|
lineNum++; |
656 |
|
|
if( eof_test == NULL ){ |
657 |
|
|
fprintf( stderr, "Error in reading Bends from force file.\n" ); |
658 |
|
|
exit(8); |
659 |
|
|
} |
660 |
|
|
|
661 |
|
|
|
662 |
|
|
while( !foundBend ){ |
663 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
664 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
665 |
|
|
lineNum++; |
666 |
|
|
} |
667 |
|
|
if( eof_test == NULL ){ |
668 |
|
|
fprintf( stderr, |
669 |
|
|
"Error in reading Bends from force file at line %d.\n", |
670 |
|
|
lineNum ); |
671 |
|
|
exit(8); |
672 |
|
|
} |
673 |
|
|
|
674 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
675 |
|
|
foundBend = !strcmp( "BendTypes", the_token ); |
676 |
|
|
|
677 |
|
|
if( !foundBend ){ |
678 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
679 |
|
|
lineNum++; |
680 |
|
|
|
681 |
|
|
if( eof_test == NULL ){ |
682 |
|
|
fprintf( stderr, |
683 |
|
|
"Error in reading Bends from force file at line %d.\n", |
684 |
|
|
lineNum ); |
685 |
|
|
exit(8); |
686 |
|
|
} |
687 |
|
|
} |
688 |
|
|
} |
689 |
|
|
|
690 |
|
|
// we are now at the BendTypes section. |
691 |
|
|
|
692 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
693 |
|
|
lineNum++; |
694 |
|
|
|
695 |
|
|
if( eof_test == NULL ){ |
696 |
|
|
fprintf( stderr, |
697 |
|
|
"Error in reading Bends from force file at line %d.\n", |
698 |
|
|
lineNum ); |
699 |
|
|
exit(8); |
700 |
|
|
} |
701 |
|
|
|
702 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
703 |
|
|
|
704 |
|
|
if( readLine[0] != '!' ){ |
705 |
|
|
|
706 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
707 |
|
|
if( the_token != NULL ){ |
708 |
|
|
|
709 |
|
|
strcpy( currentBendType->nameA, the_token ); |
710 |
|
|
|
711 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
712 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
713 |
|
|
exit(8); |
714 |
|
|
} |
715 |
|
|
|
716 |
|
|
strcpy( currentBendType->nameB, the_token ); |
717 |
|
|
|
718 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
719 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
720 |
|
|
exit(8); |
721 |
|
|
} |
722 |
|
|
|
723 |
|
|
strcpy( currentBendType->nameC, the_token ); |
724 |
|
|
|
725 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
726 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
727 |
|
|
exit(8); |
728 |
|
|
} |
729 |
|
|
|
730 |
|
|
strcpy( currentBendType->type, the_token ); |
731 |
|
|
|
732 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
733 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
734 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
735 |
|
|
exit(8); |
736 |
|
|
} |
737 |
|
|
|
738 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
739 |
|
|
|
740 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
741 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
742 |
|
|
exit(8); |
743 |
|
|
} |
744 |
|
|
|
745 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
746 |
|
|
|
747 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
748 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
749 |
|
|
exit(8); |
750 |
|
|
} |
751 |
|
|
|
752 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
753 |
|
|
|
754 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
755 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
756 |
|
|
exit(8); |
757 |
|
|
} |
758 |
|
|
|
759 |
|
|
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
760 |
|
|
} |
761 |
|
|
|
762 |
|
|
else{ |
763 |
|
|
fprintf(stderr, |
764 |
|
|
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
765 |
|
|
currentBendType->type, |
766 |
|
|
lineNum ); |
767 |
|
|
exit(8); |
768 |
|
|
} |
769 |
|
|
} |
770 |
|
|
} |
771 |
|
|
|
772 |
|
|
tempBendType = new LinkedType; |
773 |
|
|
currentBendType->next = tempBendType; |
774 |
|
|
currentBendType = tempBendType; |
775 |
|
|
|
776 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
777 |
|
|
lineNum++; |
778 |
|
|
} |
779 |
|
|
|
780 |
|
|
|
781 |
|
|
// initialize the Bends |
782 |
|
|
|
783 |
|
|
for( i=0; i<nBends; i++ ){ |
784 |
|
|
|
785 |
|
|
a = the_bends[i].a; |
786 |
|
|
b = the_bends[i].b; |
787 |
|
|
c = the_bends[i].c; |
788 |
|
|
|
789 |
|
|
atomA = the_atoms[a]->getType(); |
790 |
|
|
atomB = the_atoms[b]->getType(); |
791 |
|
|
atomC = the_atoms[c]->getType(); |
792 |
|
|
currentBendType = headBendType->find( atomA, atomB, atomC ); |
793 |
|
|
if( currentBendType == NULL ){ |
794 |
|
|
fprintf( stderr, "BendType error, %s - %s - %s not found" |
795 |
|
|
" in force file.\n", |
796 |
|
|
atomA, atomB, atomC ); |
797 |
|
|
exit(8); |
798 |
|
|
} |
799 |
|
|
|
800 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
801 |
|
|
|
802 |
|
|
index = i + entry_plug->n_bonds; |
803 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
804 |
|
|
*the_atoms[b], |
805 |
|
|
*the_atoms[c] ); |
806 |
|
|
qBend->setConstants( currentBendType->k1, |
807 |
|
|
currentBendType->k2, |
808 |
|
|
currentBendType->k3, |
809 |
|
|
currentBendType->t0 ); |
810 |
|
|
the_sris[index] = qBend; |
811 |
|
|
} |
812 |
|
|
} |
813 |
|
|
|
814 |
|
|
|
815 |
|
|
// clean up the memory |
816 |
|
|
|
817 |
|
|
delete headBendType; |
818 |
|
|
|
819 |
|
|
} |
820 |
|
|
|
821 |
|
|
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
822 |
|
|
|
823 |
|
|
class LinkedType { |
824 |
|
|
public: |
825 |
|
|
LinkedType(){ |
826 |
|
|
next = NULL; |
827 |
|
|
nameA[0] = '\0'; |
828 |
|
|
nameB[0] = '\0'; |
829 |
|
|
nameC[0] = '\0'; |
830 |
|
|
type[0] = '\0'; |
831 |
|
|
} |
832 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
833 |
|
|
|
834 |
|
|
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
835 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
836 |
|
|
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
837 |
|
|
|
838 |
|
|
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
839 |
|
|
!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this; |
840 |
|
|
|
841 |
|
|
if( next != NULL ) return next->find(key1, key2, key3, key4); |
842 |
|
|
return NULL; |
843 |
|
|
} |
844 |
|
|
|
845 |
|
|
char nameA[15]; |
846 |
|
|
char nameB[15]; |
847 |
|
|
char nameC[15]; |
848 |
|
|
char nameD[15]; |
849 |
|
|
char type[30]; |
850 |
|
|
double k1, k2, k3, k4; |
851 |
|
|
|
852 |
|
|
LinkedType* next; |
853 |
|
|
}; |
854 |
|
|
|
855 |
|
|
LinkedType* headTorsionType; |
856 |
|
|
LinkedType* currentTorsionType; |
857 |
|
|
LinkedType* tempTorsionType; |
858 |
|
|
|
859 |
|
|
char readLine[500]; |
860 |
|
|
char* the_token; |
861 |
|
|
char* eof_test; |
862 |
|
|
int foundTorsion = 0; |
863 |
|
|
int lineNum = 0; |
864 |
|
|
int i, a, b, c, d, index; |
865 |
|
|
char* atomA; |
866 |
|
|
char* atomB; |
867 |
|
|
char* atomC; |
868 |
|
|
char* atomD; |
869 |
|
|
CubicTorsion* cTors; |
870 |
|
|
|
871 |
|
|
SRI **the_sris; |
872 |
|
|
Atom** the_atoms; |
873 |
|
|
int nTorsions; |
874 |
|
|
the_sris = entry_plug->sr_interactions; |
875 |
|
|
the_atoms = entry_plug->atoms; |
876 |
|
|
nTorsions = entry_plug->n_torsions; |
877 |
|
|
|
878 |
|
|
// read in the torsion types. |
879 |
|
|
|
880 |
|
|
rewind( frcFile ); |
881 |
|
|
headTorsionType = new LinkedType; |
882 |
|
|
currentTorsionType = headTorsionType; |
883 |
|
|
|
884 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
885 |
|
|
lineNum++; |
886 |
|
|
if( eof_test == NULL ){ |
887 |
|
|
fprintf( stderr, "Error in reading Torsions from force file.\n" ); |
888 |
|
|
exit(8); |
889 |
|
|
} |
890 |
|
|
|
891 |
|
|
|
892 |
|
|
while( !foundTorsion ){ |
893 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
894 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
895 |
|
|
lineNum++; |
896 |
|
|
} |
897 |
|
|
if( eof_test == NULL ){ |
898 |
|
|
fprintf( stderr, |
899 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
900 |
|
|
lineNum ); |
901 |
|
|
exit(8); |
902 |
|
|
} |
903 |
|
|
|
904 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
905 |
|
|
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
906 |
|
|
|
907 |
|
|
if( !foundTorsion ){ |
908 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
909 |
|
|
lineNum++; |
910 |
|
|
|
911 |
|
|
if( eof_test == NULL ){ |
912 |
|
|
fprintf( stderr, |
913 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
914 |
|
|
lineNum ); |
915 |
|
|
exit(8); |
916 |
|
|
} |
917 |
|
|
} |
918 |
|
|
} |
919 |
|
|
|
920 |
|
|
// we are now at the TorsionTypes section. |
921 |
|
|
|
922 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
923 |
|
|
lineNum++; |
924 |
|
|
|
925 |
|
|
if( eof_test == NULL ){ |
926 |
|
|
fprintf( stderr, |
927 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
928 |
|
|
lineNum ); |
929 |
|
|
exit(8); |
930 |
|
|
} |
931 |
|
|
|
932 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
933 |
|
|
|
934 |
|
|
if( readLine[0] != '!' ){ |
935 |
|
|
|
936 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
937 |
|
|
if( the_token != NULL ){ |
938 |
|
|
|
939 |
|
|
strcpy( currentTorsionType->nameA, the_token ); |
940 |
|
|
|
941 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
942 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
943 |
|
|
exit(8); |
944 |
|
|
} |
945 |
|
|
|
946 |
|
|
strcpy( currentTorsionType->nameB, the_token ); |
947 |
|
|
|
948 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
949 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
950 |
|
|
exit(8); |
951 |
|
|
} |
952 |
|
|
|
953 |
|
|
strcpy( currentTorsionType->nameC, the_token ); |
954 |
|
|
|
955 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
956 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
957 |
|
|
exit(8); |
958 |
|
|
} |
959 |
|
|
|
960 |
|
|
strcpy( currentTorsionType->nameD, the_token ); |
961 |
|
|
|
962 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
963 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
964 |
|
|
exit(8); |
965 |
|
|
} |
966 |
|
|
|
967 |
|
|
strcpy( currentTorsionType->type, the_token ); |
968 |
|
|
|
969 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
970 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
971 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
972 |
|
|
exit(8); |
973 |
|
|
} |
974 |
|
|
|
975 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
976 |
|
|
|
977 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
978 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
979 |
|
|
exit(8); |
980 |
|
|
} |
981 |
|
|
|
982 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
983 |
|
|
|
984 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
985 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
986 |
|
|
exit(8); |
987 |
|
|
} |
988 |
|
|
|
989 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
990 |
|
|
|
991 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
992 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
993 |
|
|
exit(8); |
994 |
|
|
} |
995 |
|
|
|
996 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
997 |
|
|
} |
998 |
|
|
|
999 |
|
|
else{ |
1000 |
|
|
fprintf(stderr, |
1001 |
|
|
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1002 |
|
|
currentTorsionType->type, |
1003 |
|
|
lineNum ); |
1004 |
|
|
exit(8); |
1005 |
|
|
} |
1006 |
|
|
} |
1007 |
|
|
} |
1008 |
|
|
|
1009 |
|
|
tempTorsionType = new LinkedType; |
1010 |
|
|
currentTorsionType->next = tempTorsionType; |
1011 |
|
|
currentTorsionType = tempTorsionType; |
1012 |
|
|
|
1013 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1014 |
|
|
lineNum++; |
1015 |
|
|
} |
1016 |
|
|
|
1017 |
|
|
|
1018 |
|
|
// initialize the Torsions |
1019 |
|
|
|
1020 |
|
|
for( i=0; i<nTorsions; i++ ){ |
1021 |
|
|
|
1022 |
|
|
a = the_torsions[i].a; |
1023 |
|
|
b = the_torsions[i].b; |
1024 |
|
|
c = the_torsions[i].c; |
1025 |
|
|
d = the_torsions[i].d; |
1026 |
|
|
|
1027 |
|
|
atomA = the_atoms[a]->getType(); |
1028 |
|
|
atomB = the_atoms[b]->getType(); |
1029 |
|
|
atomC = the_atoms[c]->getType(); |
1030 |
|
|
atomD = the_atoms[d]->getType(); |
1031 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1032 |
|
|
if( currentTorsionType == NULL ){ |
1033 |
|
|
fprintf( stderr, "TorsionType error, %s - %s - %s - %s not found" |
1034 |
|
|
" in force file.\n", |
1035 |
|
|
atomA, atomB, atomC, atomD ); |
1036 |
|
|
exit(8); |
1037 |
|
|
} |
1038 |
|
|
|
1039 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1040 |
|
|
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
1041 |
|
|
|
1042 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1043 |
|
|
*the_atoms[c], *the_atoms[d] ); |
1044 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1045 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
1046 |
|
|
the_sris[index] = cTors; |
1047 |
|
|
} |
1048 |
|
|
} |
1049 |
|
|
|
1050 |
|
|
|
1051 |
|
|
// clean up the memory |
1052 |
|
|
|
1053 |
|
|
delete headTorsionType; |
1054 |
|
|
|
1055 |
|
|
} |