1 |
mmeineke |
377 |
#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <iostream> |
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using namespace std; |
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#include "ForceFields.hpp" |
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#include "SRI.hpp" |
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#include "simError.h" |
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TraPPEFF::TraPPEFF(){ |
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#ifdef IS_MPI |
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sprintf( painCave.errMsg, |
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"TraPPE ForceField does not currently support mpi" ); |
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painCave.isFatal = 1; |
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simError(); |
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#endif // is_mpi |
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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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// generate the force file name |
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strcpy( fileName, "TraPPE.frc" ); |
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// attempt to open the file in the current directory first. |
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frcFile = fopen( fileName, "r" ); |
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if( frcFile == NULL ){ |
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// next see if the force path enviorment variable is set |
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ffPath = getenv( ffPath_env ); |
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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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} |
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} |
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TraPPEFF::~TraPPEFF(){ |
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fclose( frcFile ); |
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} |
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void TraPPEFF::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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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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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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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, "%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 ); |
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exit(8); |
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} |
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sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
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} |
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} |
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tempAtomType = new LinkedType; |
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currentAtomType->next = tempAtomType; |
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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 |
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for( i=0; i<nAtoms; i++ ){ |
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currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
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if( currentAtomType == NULL ){ |
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fprintf( stderr, "AtomType error, %s not found in force file.\n", |
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the_atoms[i]->getType() ); |
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exit(8); |
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} |
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the_atoms[i]->setMass( currentAtomType->mass ); |
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the_atoms[i]->setEpslon( currentAtomType->epslon ); |
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the_atoms[i]->setSigma( currentAtomType->sigma ); |
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the_atoms[i]->setLJ(); |
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} |
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// clean up the memory |
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delete headAtomType; |
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} |
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void TraPPEFF::initializeBonds( bond_pair* the_bonds ){ |
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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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nameA[0] = '\0'; |
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nameB[0] = '\0'; |
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type[0] = '\0'; |
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} |
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~LinkedType(){ if( next != NULL ) delete next; } |
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LinkedType* find(char* key1, char* key2){ |
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if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
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if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
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if( next != NULL ) return next->find(key1, key2); |
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return NULL; |
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} |
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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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LinkedType* next; |
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}; |
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LinkedType* headBondType; |
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LinkedType* currentBondType; |
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LinkedType* tempBondType; |
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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 foundBond = 0; |
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int lineNum = 0; |
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int i, a, b; |
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char* atomA; |
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char* atomB; |
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SRI **the_sris; |
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Atom** the_atoms; |
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int nBonds; |
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the_sris = entry_plug->sr_interactions; |
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the_atoms = entry_plug->atoms; |
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nBonds = entry_plug->n_bonds; |
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// read in the bond types. |
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rewind( frcFile ); |
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headBondType = new LinkedType; |
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currentBondType = headBondType; |
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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 Bonds from force file.\n" ); |
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exit(8); |
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} |
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283 |
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while( !foundBond ){ |
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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 Bonds 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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foundBond = !strcmp( "BondTypes", the_token ); |
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299 |
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if( !foundBond ){ |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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303 |
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if( eof_test == NULL ){ |
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fprintf( stderr, |
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"Error in reading Bonds 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 BondTypes section. |
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314 |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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317 |
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if( eof_test == NULL ){ |
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fprintf( stderr, |
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"Error in reading Bonds 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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324 |
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while( readLine[0] != '#' && eof_test != NULL ){ |
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326 |
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if( readLine[0] != '!' ){ |
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328 |
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the_token = strtok( readLine, " \n\t,;" ); |
329 |
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if( the_token != NULL ){ |
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strcpy( currentBondType->nameA, the_token ); |
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333 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
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fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
335 |
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exit(8); |
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} |
337 |
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strcpy( currentBondType->nameB, the_token ); |
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340 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
341 |
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fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
342 |
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exit(8); |
343 |
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} |
344 |
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345 |
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strcpy( currentBondType->type, the_token ); |
346 |
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347 |
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if( !strcmp( currentBondType->type, "fixed" ) ){ |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
349 |
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fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
350 |
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exit(8); |
351 |
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} |
352 |
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353 |
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sscanf( the_token, "%lf", ¤tBondType->d0 ); |
354 |
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} |
355 |
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356 |
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else{ |
357 |
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fprintf(stderr, |
358 |
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"Unknown TraPPE bond type \"%s\" at line %d\n", |
359 |
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currentBondType->type, |
360 |
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lineNum ); |
361 |
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exit(8); |
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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tempBondType = new LinkedType; |
367 |
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currentBondType->next = tempBondType; |
368 |
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currentBondType = tempBondType; |
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 Bonds |
376 |
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377 |
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378 |
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for( i=0; i<nBonds; i++ ){ |
379 |
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380 |
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a = the_bonds[i].a; |
381 |
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b = the_bonds[i].b; |
382 |
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383 |
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atomA = the_atoms[a]->getType(); |
384 |
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atomB = the_atoms[b]->getType(); |
385 |
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currentBondType = headBondType->find( atomA, atomB ); |
386 |
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if( currentBondType == NULL ){ |
387 |
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fprintf( stderr, "BondType error, %s - %s not found in force file.\n", |
388 |
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atomA, atomB ); |
389 |
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exit(8); |
390 |
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} |
391 |
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392 |
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if( !strcmp( currentBondType->type, "fixed" ) ){ |
393 |
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394 |
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the_sris[i] = new ConstrainedBond( *the_atoms[a], |
395 |
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*the_atoms[b], |
396 |
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currentBondType->d0 ); |
397 |
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entry_plug->n_constraints++; |
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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// clean up the memory |
403 |
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404 |
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delete headBondType; |
405 |
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} |
406 |
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407 |
|
|
void TraPPEFF::initializeBends( bend_set* the_bends ){ |
408 |
|
|
|
409 |
|
|
class LinkedType { |
410 |
|
|
public: |
411 |
|
|
LinkedType(){ |
412 |
|
|
next = NULL; |
413 |
|
|
nameA[0] = '\0'; |
414 |
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nameB[0] = '\0'; |
415 |
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nameC[0] = '\0'; |
416 |
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type[0] = '\0'; |
417 |
|
|
} |
418 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
419 |
|
|
|
420 |
|
|
LinkedType* find( char* key1, char* key2, char* key3 ){ |
421 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
422 |
|
|
&& !strcmp( nameC, key3 ) ) return this; |
423 |
|
|
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
424 |
|
|
&& !strcmp( nameC, key1 ) ) return this; |
425 |
|
|
if( next != NULL ) return next->find(key1, key2, key3); |
426 |
|
|
return NULL; |
427 |
|
|
} |
428 |
|
|
|
429 |
|
|
char nameA[15]; |
430 |
|
|
char nameB[15]; |
431 |
|
|
char nameC[15]; |
432 |
|
|
char type[30]; |
433 |
|
|
double k1, k2, k3, t0; |
434 |
|
|
|
435 |
|
|
LinkedType* next; |
436 |
|
|
}; |
437 |
|
|
|
438 |
|
|
LinkedType* headBendType; |
439 |
|
|
LinkedType* currentBendType; |
440 |
|
|
LinkedType* tempBendType; |
441 |
|
|
|
442 |
|
|
char readLine[500]; |
443 |
|
|
char* the_token; |
444 |
|
|
char* eof_test; |
445 |
|
|
int foundBend = 0; |
446 |
|
|
int lineNum = 0; |
447 |
|
|
int i, a, b, c, index; |
448 |
|
|
char* atomA; |
449 |
|
|
char* atomB; |
450 |
|
|
char* atomC; |
451 |
|
|
QuadraticBend* qBend; |
452 |
|
|
|
453 |
|
|
SRI **the_sris; |
454 |
|
|
Atom** the_atoms; |
455 |
|
|
int nBends; |
456 |
|
|
the_sris = entry_plug->sr_interactions; |
457 |
|
|
the_atoms = entry_plug->atoms; |
458 |
|
|
nBends = entry_plug->n_bends; |
459 |
|
|
|
460 |
|
|
// read in the bend types. |
461 |
|
|
|
462 |
|
|
rewind( frcFile ); |
463 |
|
|
headBendType = new LinkedType; |
464 |
|
|
currentBendType = headBendType; |
465 |
|
|
|
466 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
467 |
|
|
lineNum++; |
468 |
|
|
if( eof_test == NULL ){ |
469 |
|
|
fprintf( stderr, "Error in reading Bends from force file.\n" ); |
470 |
|
|
exit(8); |
471 |
|
|
} |
472 |
|
|
|
473 |
|
|
|
474 |
|
|
while( !foundBend ){ |
475 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
476 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
477 |
|
|
lineNum++; |
478 |
|
|
} |
479 |
|
|
if( eof_test == NULL ){ |
480 |
|
|
fprintf( stderr, |
481 |
|
|
"Error in reading Bends from force file at line %d.\n", |
482 |
|
|
lineNum ); |
483 |
|
|
exit(8); |
484 |
|
|
} |
485 |
|
|
|
486 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
487 |
|
|
foundBend = !strcmp( "BendTypes", the_token ); |
488 |
|
|
|
489 |
|
|
if( !foundBend ){ |
490 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
491 |
|
|
lineNum++; |
492 |
|
|
|
493 |
|
|
if( eof_test == NULL ){ |
494 |
|
|
fprintf( stderr, |
495 |
|
|
"Error in reading Bends from force file at line %d.\n", |
496 |
|
|
lineNum ); |
497 |
|
|
exit(8); |
498 |
|
|
} |
499 |
|
|
} |
500 |
|
|
} |
501 |
|
|
|
502 |
|
|
// we are now at the BendTypes section. |
503 |
|
|
|
504 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
505 |
|
|
lineNum++; |
506 |
|
|
|
507 |
|
|
if( eof_test == NULL ){ |
508 |
|
|
fprintf( stderr, |
509 |
|
|
"Error in reading Bends from force file at line %d.\n", |
510 |
|
|
lineNum ); |
511 |
|
|
exit(8); |
512 |
|
|
} |
513 |
|
|
|
514 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
515 |
|
|
|
516 |
|
|
if( readLine[0] != '!' ){ |
517 |
|
|
|
518 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
519 |
|
|
if( the_token != NULL ){ |
520 |
|
|
|
521 |
|
|
strcpy( currentBendType->nameA, the_token ); |
522 |
|
|
|
523 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
524 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
525 |
|
|
exit(8); |
526 |
|
|
} |
527 |
|
|
|
528 |
|
|
strcpy( currentBendType->nameB, the_token ); |
529 |
|
|
|
530 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
531 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
532 |
|
|
exit(8); |
533 |
|
|
} |
534 |
|
|
|
535 |
|
|
strcpy( currentBendType->nameC, the_token ); |
536 |
|
|
|
537 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
538 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
539 |
|
|
exit(8); |
540 |
|
|
} |
541 |
|
|
|
542 |
|
|
strcpy( currentBendType->type, the_token ); |
543 |
|
|
|
544 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
545 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
546 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
547 |
|
|
exit(8); |
548 |
|
|
} |
549 |
|
|
|
550 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
551 |
|
|
|
552 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
553 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
554 |
|
|
exit(8); |
555 |
|
|
} |
556 |
|
|
|
557 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
558 |
|
|
|
559 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
560 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
561 |
|
|
exit(8); |
562 |
|
|
} |
563 |
|
|
|
564 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
565 |
|
|
|
566 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
567 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
568 |
|
|
exit(8); |
569 |
|
|
} |
570 |
|
|
|
571 |
|
|
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
572 |
|
|
} |
573 |
|
|
|
574 |
|
|
else{ |
575 |
|
|
fprintf(stderr, |
576 |
|
|
"Unknown TraPPE bend type \"%s\" at line %d\n", |
577 |
|
|
currentBendType->type, |
578 |
|
|
lineNum ); |
579 |
|
|
exit(8); |
580 |
|
|
} |
581 |
|
|
} |
582 |
|
|
} |
583 |
|
|
|
584 |
|
|
tempBendType = new LinkedType; |
585 |
|
|
currentBendType->next = tempBendType; |
586 |
|
|
currentBendType = tempBendType; |
587 |
|
|
|
588 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
589 |
|
|
lineNum++; |
590 |
|
|
} |
591 |
|
|
|
592 |
|
|
|
593 |
|
|
// initialize the Bends |
594 |
|
|
|
595 |
|
|
for( i=0; i<nBends; i++ ){ |
596 |
|
|
|
597 |
|
|
a = the_bends[i].a; |
598 |
|
|
b = the_bends[i].b; |
599 |
|
|
c = the_bends[i].c; |
600 |
|
|
|
601 |
|
|
atomA = the_atoms[a]->getType(); |
602 |
|
|
atomB = the_atoms[b]->getType(); |
603 |
|
|
atomC = the_atoms[c]->getType(); |
604 |
|
|
currentBendType = headBendType->find( atomA, atomB, atomC ); |
605 |
|
|
if( currentBendType == NULL ){ |
606 |
|
|
fprintf( stderr, "BendType error, %s - %s - %s not found" |
607 |
|
|
" in force file.\n", |
608 |
|
|
atomA, atomB, atomC ); |
609 |
|
|
exit(8); |
610 |
|
|
} |
611 |
|
|
|
612 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
613 |
|
|
|
614 |
|
|
index = i + entry_plug->n_bonds; |
615 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
616 |
|
|
*the_atoms[b], |
617 |
|
|
*the_atoms[c] ); |
618 |
|
|
qBend->setConstants( currentBendType->k1, |
619 |
|
|
currentBendType->k2, |
620 |
|
|
currentBendType->k3, |
621 |
|
|
currentBendType->t0 ); |
622 |
|
|
the_sris[index] = qBend; |
623 |
|
|
} |
624 |
|
|
} |
625 |
|
|
|
626 |
|
|
|
627 |
|
|
// clean up the memory |
628 |
|
|
|
629 |
|
|
delete headBendType; |
630 |
|
|
} |
631 |
|
|
|
632 |
|
|
void TraPPEFF::initializeTorsions( torsion_set* the_torsions ){ |
633 |
|
|
|
634 |
|
|
class LinkedType { |
635 |
|
|
public: |
636 |
|
|
LinkedType(){ |
637 |
|
|
next = NULL; |
638 |
|
|
nameA[0] = '\0'; |
639 |
|
|
nameB[0] = '\0'; |
640 |
|
|
nameC[0] = '\0'; |
641 |
|
|
type[0] = '\0'; |
642 |
|
|
} |
643 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
644 |
|
|
|
645 |
|
|
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
646 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
647 |
|
|
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
648 |
|
|
|
649 |
|
|
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
650 |
|
|
!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this; |
651 |
|
|
|
652 |
|
|
if( next != NULL ) return next->find(key1, key2, key3, key4); |
653 |
|
|
return NULL; |
654 |
|
|
} |
655 |
|
|
|
656 |
|
|
char nameA[15]; |
657 |
|
|
char nameB[15]; |
658 |
|
|
char nameC[15]; |
659 |
|
|
char nameD[15]; |
660 |
|
|
char type[30]; |
661 |
|
|
double k1, k2, k3, k4; |
662 |
|
|
|
663 |
|
|
LinkedType* next; |
664 |
|
|
}; |
665 |
|
|
|
666 |
|
|
LinkedType* headTorsionType; |
667 |
|
|
LinkedType* currentTorsionType; |
668 |
|
|
LinkedType* tempTorsionType; |
669 |
|
|
|
670 |
|
|
char readLine[500]; |
671 |
|
|
char* the_token; |
672 |
|
|
char* eof_test; |
673 |
|
|
int foundTorsion = 0; |
674 |
|
|
int lineNum = 0; |
675 |
|
|
int i, a, b, c, d, index; |
676 |
|
|
char* atomA; |
677 |
|
|
char* atomB; |
678 |
|
|
char* atomC; |
679 |
|
|
char* atomD; |
680 |
|
|
CubicTorsion* cTors; |
681 |
|
|
|
682 |
|
|
SRI **the_sris; |
683 |
|
|
Atom** the_atoms; |
684 |
|
|
int nTorsions; |
685 |
|
|
the_sris = entry_plug->sr_interactions; |
686 |
|
|
the_atoms = entry_plug->atoms; |
687 |
|
|
nTorsions = entry_plug->n_torsions; |
688 |
|
|
|
689 |
|
|
// read in the torsion types. |
690 |
|
|
|
691 |
|
|
rewind( frcFile ); |
692 |
|
|
headTorsionType = new LinkedType; |
693 |
|
|
currentTorsionType = headTorsionType; |
694 |
|
|
|
695 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
696 |
|
|
lineNum++; |
697 |
|
|
if( eof_test == NULL ){ |
698 |
|
|
fprintf( stderr, "Error in reading Torsions from force file.\n" ); |
699 |
|
|
exit(8); |
700 |
|
|
} |
701 |
|
|
|
702 |
|
|
|
703 |
|
|
while( !foundTorsion ){ |
704 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
705 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
706 |
|
|
lineNum++; |
707 |
|
|
} |
708 |
|
|
if( eof_test == NULL ){ |
709 |
|
|
fprintf( stderr, |
710 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
711 |
|
|
lineNum ); |
712 |
|
|
exit(8); |
713 |
|
|
} |
714 |
|
|
|
715 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
716 |
|
|
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
717 |
|
|
|
718 |
|
|
if( !foundTorsion ){ |
719 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
720 |
|
|
lineNum++; |
721 |
|
|
|
722 |
|
|
if( eof_test == NULL ){ |
723 |
|
|
fprintf( stderr, |
724 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
725 |
|
|
lineNum ); |
726 |
|
|
exit(8); |
727 |
|
|
} |
728 |
|
|
} |
729 |
|
|
} |
730 |
|
|
|
731 |
|
|
// we are now at the TorsionTypes section. |
732 |
|
|
|
733 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
734 |
|
|
lineNum++; |
735 |
|
|
|
736 |
|
|
if( eof_test == NULL ){ |
737 |
|
|
fprintf( stderr, |
738 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
739 |
|
|
lineNum ); |
740 |
|
|
exit(8); |
741 |
|
|
} |
742 |
|
|
|
743 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
744 |
|
|
|
745 |
|
|
if( readLine[0] != '!' ){ |
746 |
|
|
|
747 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
748 |
|
|
if( the_token != NULL ){ |
749 |
|
|
|
750 |
|
|
strcpy( currentTorsionType->nameA, the_token ); |
751 |
|
|
|
752 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
753 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
754 |
|
|
exit(8); |
755 |
|
|
} |
756 |
|
|
|
757 |
|
|
strcpy( currentTorsionType->nameB, the_token ); |
758 |
|
|
|
759 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
760 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
761 |
|
|
exit(8); |
762 |
|
|
} |
763 |
|
|
|
764 |
|
|
strcpy( currentTorsionType->nameC, the_token ); |
765 |
|
|
|
766 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
767 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
768 |
|
|
exit(8); |
769 |
|
|
} |
770 |
|
|
|
771 |
|
|
strcpy( currentTorsionType->nameD, the_token ); |
772 |
|
|
|
773 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
774 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
775 |
|
|
exit(8); |
776 |
|
|
} |
777 |
|
|
|
778 |
|
|
strcpy( currentTorsionType->type, the_token ); |
779 |
|
|
|
780 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
781 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
782 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
783 |
|
|
exit(8); |
784 |
|
|
} |
785 |
|
|
|
786 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
787 |
|
|
|
788 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
789 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
790 |
|
|
exit(8); |
791 |
|
|
} |
792 |
|
|
|
793 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
794 |
|
|
|
795 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
796 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
797 |
|
|
exit(8); |
798 |
|
|
} |
799 |
|
|
|
800 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
801 |
|
|
|
802 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
803 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
804 |
|
|
exit(8); |
805 |
|
|
} |
806 |
|
|
|
807 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
808 |
|
|
} |
809 |
|
|
|
810 |
|
|
else{ |
811 |
|
|
fprintf(stderr, |
812 |
|
|
"Unknown TraPPE torsion type \"%s\" at line %d\n", |
813 |
|
|
currentTorsionType->type, |
814 |
|
|
lineNum ); |
815 |
|
|
exit(8); |
816 |
|
|
} |
817 |
|
|
} |
818 |
|
|
} |
819 |
|
|
|
820 |
|
|
tempTorsionType = new LinkedType; |
821 |
|
|
currentTorsionType->next = tempTorsionType; |
822 |
|
|
currentTorsionType = tempTorsionType; |
823 |
|
|
|
824 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
825 |
|
|
lineNum++; |
826 |
|
|
} |
827 |
|
|
|
828 |
|
|
|
829 |
|
|
// initialize the Torsions |
830 |
|
|
|
831 |
|
|
for( i=0; i<nTorsions; i++ ){ |
832 |
|
|
|
833 |
|
|
a = the_torsions[i].a; |
834 |
|
|
b = the_torsions[i].b; |
835 |
|
|
c = the_torsions[i].c; |
836 |
|
|
d = the_torsions[i].d; |
837 |
|
|
|
838 |
|
|
atomA = the_atoms[a]->getType(); |
839 |
|
|
atomB = the_atoms[b]->getType(); |
840 |
|
|
atomC = the_atoms[c]->getType(); |
841 |
|
|
atomD = the_atoms[d]->getType(); |
842 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
843 |
|
|
if( currentTorsionType == NULL ){ |
844 |
|
|
fprintf( stderr, "TorsionType error, %s - %s - %s - %s not found" |
845 |
|
|
" in force file.\n", |
846 |
|
|
atomA, atomB, atomC, atomD ); |
847 |
|
|
exit(8); |
848 |
|
|
} |
849 |
|
|
|
850 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
851 |
|
|
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
852 |
|
|
|
853 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
854 |
|
|
*the_atoms[c], *the_atoms[d] ); |
855 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
856 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
857 |
|
|
the_sris[index] = cTors; |
858 |
|
|
} |
859 |
|
|
} |
860 |
|
|
|
861 |
|
|
|
862 |
|
|
// clean up the memory |
863 |
|
|
|
864 |
|
|
delete headTorsionType; |
865 |
|
|
} |