1 |
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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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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// generate the force file name |
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chuckv |
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mmeineke |
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strcpy( fileName, "TraPPE_Ex.frc" ); |
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chuckv |
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fprintf( stderr,"Trying to open %s\n", fileName ); |
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mmeineke |
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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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chuckv |
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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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mmeineke |
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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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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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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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} |
168 |
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the_token = strtok( readLine, " ,;\t#\n" ); |
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foundAtom = !strcmp( "AtomTypes", the_token ); |
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172 |
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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. |
186 |
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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 ); |
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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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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 ); |
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exit(8); |
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} |
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sscanf( the_token, "%lf", ¤tAtomType->dipole ); |
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} |
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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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DirectionalAtom* dAtom; |
257 |
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for( i=0; i<nAtoms; i++ ){ |
259 |
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currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
261 |
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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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} |
266 |
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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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272 |
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if( currentAtomType->isDipole ){ |
273 |
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if( the_atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *) the_atoms[i]; |
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dAtom->setMu( currentAtomType->dipole ); |
277 |
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dAtom->setHasDipole( 1 ); |
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dAtom->setJx( 0.0 ); |
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dAtom->setJy( 0.0 ); |
280 |
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dAtom->setJz( 0.0 ); |
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282 |
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if(!strcmp("SSD",the_atoms[i]->getType())){ |
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dAtom->setI( waterI ); |
284 |
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dAtom->setSSD( 1 ); |
285 |
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} |
286 |
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else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
287 |
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dAtom->setI( headI ); |
288 |
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dAtom->setSSD( 0 ); |
289 |
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} |
290 |
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else{ |
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fprintf(stderr, |
292 |
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"AtmType error, %s does not have a moment of inertia set.\n", |
293 |
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the_atoms[i]->getType() ); |
294 |
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exit(8); |
295 |
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} |
296 |
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entry_plug->n_dipoles++; |
297 |
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} |
298 |
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else{ |
299 |
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std::cerr |
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<< "TraPPE_ExFF error: Atom \"" |
301 |
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<< currentAtomType->name << "\" is a dipole, yet no standard" |
302 |
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<< " orientation was specifed in the BASS file.\n"; |
303 |
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exit(8); |
304 |
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} |
305 |
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} |
306 |
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else{ |
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if( the_atoms[i]->isDirectional() ){ |
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std::cerr |
309 |
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<< "TraPPE_ExFF error: Atom \"" |
310 |
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<< currentAtomType->name << "\" was given a standard orientation" |
311 |
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<< " in the BASS file, yet it is not a dipole.\n"; |
312 |
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exit(8); |
313 |
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} |
314 |
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} |
315 |
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} |
316 |
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317 |
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318 |
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// clean up the memory |
319 |
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320 |
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delete headAtomType; |
321 |
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} |
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323 |
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void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
324 |
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325 |
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class LinkedType { |
326 |
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public: |
327 |
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LinkedType(){ |
328 |
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next = NULL; |
329 |
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nameA[0] = '\0'; |
330 |
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nameB[0] = '\0'; |
331 |
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type[0] = '\0'; |
332 |
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} |
333 |
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~LinkedType(){ if( next != NULL ) delete next; } |
334 |
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335 |
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LinkedType* find(char* key1, char* key2){ |
336 |
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if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
337 |
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if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
338 |
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if( next != NULL ) return next->find(key1, key2); |
339 |
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return NULL; |
340 |
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} |
341 |
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342 |
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char nameA[15]; |
343 |
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char nameB[15]; |
344 |
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char type[30]; |
345 |
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double d0; |
346 |
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347 |
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LinkedType* next; |
348 |
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}; |
349 |
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350 |
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351 |
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352 |
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LinkedType* headBondType; |
353 |
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LinkedType* currentBondType; |
354 |
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LinkedType* tempBondType; |
355 |
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356 |
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char readLine[500]; |
357 |
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char* the_token; |
358 |
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char* eof_test; |
359 |
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int foundBond = 0; |
360 |
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int lineNum = 0; |
361 |
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int i, a, b; |
362 |
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char* atomA; |
363 |
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char* atomB; |
364 |
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365 |
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SRI **the_sris; |
366 |
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Atom** the_atoms; |
367 |
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int nBonds; |
368 |
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the_sris = entry_plug->sr_interactions; |
369 |
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the_atoms = entry_plug->atoms; |
370 |
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nBonds = entry_plug->n_bonds; |
371 |
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372 |
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// read in the bond types. |
373 |
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374 |
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rewind( frcFile ); |
375 |
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headBondType = new LinkedType; |
376 |
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currentBondType = headBondType; |
377 |
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378 |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
379 |
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lineNum++; |
380 |
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if( eof_test == NULL ){ |
381 |
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fprintf( stderr, "Error in reading Bonds from force file.\n" ); |
382 |
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exit(8); |
383 |
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} |
384 |
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385 |
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386 |
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while( !foundBond ){ |
387 |
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while( eof_test != NULL && readLine[0] != '#' ){ |
388 |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
389 |
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lineNum++; |
390 |
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} |
391 |
|
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if( eof_test == NULL ){ |
392 |
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fprintf( stderr, |
393 |
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"Error in reading Bonds from force file at line %d.\n", |
394 |
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lineNum ); |
395 |
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exit(8); |
396 |
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} |
397 |
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|
398 |
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the_token = strtok( readLine, " ,;\t#\n" ); |
399 |
|
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foundBond = !strcmp( "BondTypes", the_token ); |
400 |
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|
401 |
|
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if( !foundBond ){ |
402 |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
403 |
|
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lineNum++; |
404 |
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|
405 |
|
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if( eof_test == NULL ){ |
406 |
|
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fprintf( stderr, |
407 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
408 |
|
|
lineNum ); |
409 |
|
|
exit(8); |
410 |
|
|
} |
411 |
|
|
} |
412 |
|
|
} |
413 |
|
|
|
414 |
|
|
// we are now at the BondTypes section. |
415 |
|
|
|
416 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
417 |
|
|
lineNum++; |
418 |
|
|
|
419 |
|
|
if( eof_test == NULL ){ |
420 |
|
|
fprintf( stderr, |
421 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
422 |
|
|
lineNum ); |
423 |
|
|
exit(8); |
424 |
|
|
} |
425 |
|
|
|
426 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
427 |
|
|
|
428 |
|
|
if( readLine[0] != '!' ){ |
429 |
|
|
|
430 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
431 |
|
|
if( the_token != NULL ){ |
432 |
|
|
|
433 |
|
|
strcpy( currentBondType->nameA, the_token ); |
434 |
|
|
|
435 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
436 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
437 |
|
|
exit(8); |
438 |
|
|
} |
439 |
|
|
|
440 |
|
|
strcpy( currentBondType->nameB, the_token ); |
441 |
|
|
|
442 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
443 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
444 |
|
|
exit(8); |
445 |
|
|
} |
446 |
|
|
|
447 |
|
|
strcpy( currentBondType->type, the_token ); |
448 |
|
|
|
449 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
450 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
451 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
452 |
|
|
exit(8); |
453 |
|
|
} |
454 |
|
|
|
455 |
|
|
sscanf( the_token, "%lf", ¤tBondType->d0 ); |
456 |
|
|
} |
457 |
|
|
|
458 |
|
|
else{ |
459 |
|
|
fprintf(stderr, |
460 |
|
|
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
461 |
|
|
currentBondType->type, |
462 |
|
|
lineNum ); |
463 |
|
|
exit(8); |
464 |
|
|
} |
465 |
|
|
} |
466 |
|
|
} |
467 |
|
|
|
468 |
|
|
tempBondType = new LinkedType; |
469 |
|
|
currentBondType->next = tempBondType; |
470 |
|
|
currentBondType = tempBondType; |
471 |
|
|
|
472 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
473 |
|
|
lineNum++; |
474 |
|
|
} |
475 |
|
|
|
476 |
|
|
|
477 |
|
|
// initialize the Bonds |
478 |
|
|
|
479 |
|
|
|
480 |
|
|
for( i=0; i<nBonds; i++ ){ |
481 |
|
|
|
482 |
|
|
a = the_bonds[i].a; |
483 |
|
|
b = the_bonds[i].b; |
484 |
|
|
|
485 |
|
|
atomA = the_atoms[a]->getType(); |
486 |
|
|
atomB = the_atoms[b]->getType(); |
487 |
|
|
currentBondType = headBondType->find( atomA, atomB ); |
488 |
|
|
if( currentBondType == NULL ){ |
489 |
|
|
fprintf( stderr, "BondType error, %s - %s not found in force file.\n", |
490 |
|
|
atomA, atomB ); |
491 |
|
|
exit(8); |
492 |
|
|
} |
493 |
|
|
|
494 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
495 |
|
|
|
496 |
|
|
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
497 |
|
|
*the_atoms[b], |
498 |
|
|
currentBondType->d0 ); |
499 |
|
|
entry_plug->n_constraints++; |
500 |
|
|
} |
501 |
|
|
} |
502 |
|
|
|
503 |
|
|
|
504 |
|
|
// clean up the memory |
505 |
|
|
|
506 |
|
|
delete headBondType; |
507 |
|
|
|
508 |
|
|
} |
509 |
|
|
|
510 |
|
|
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
511 |
|
|
|
512 |
|
|
class LinkedType { |
513 |
|
|
public: |
514 |
|
|
LinkedType(){ |
515 |
|
|
next = NULL; |
516 |
|
|
nameA[0] = '\0'; |
517 |
|
|
nameB[0] = '\0'; |
518 |
|
|
nameC[0] = '\0'; |
519 |
|
|
type[0] = '\0'; |
520 |
|
|
} |
521 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
522 |
|
|
|
523 |
|
|
LinkedType* find( char* key1, char* key2, char* key3 ){ |
524 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
525 |
|
|
&& !strcmp( nameC, key3 ) ) return this; |
526 |
|
|
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
527 |
|
|
&& !strcmp( nameC, key1 ) ) return this; |
528 |
|
|
if( next != NULL ) return next->find(key1, key2, key3); |
529 |
|
|
return NULL; |
530 |
|
|
} |
531 |
|
|
|
532 |
|
|
char nameA[15]; |
533 |
|
|
char nameB[15]; |
534 |
|
|
char nameC[15]; |
535 |
|
|
char type[30]; |
536 |
|
|
double k1, k2, k3, t0; |
537 |
|
|
|
538 |
|
|
LinkedType* next; |
539 |
|
|
}; |
540 |
|
|
|
541 |
|
|
LinkedType* headBendType; |
542 |
|
|
LinkedType* currentBendType; |
543 |
|
|
LinkedType* tempBendType; |
544 |
|
|
|
545 |
|
|
char readLine[500]; |
546 |
|
|
char* the_token; |
547 |
|
|
char* eof_test; |
548 |
|
|
int foundBend = 0; |
549 |
|
|
int lineNum = 0; |
550 |
|
|
int i, a, b, c, index; |
551 |
|
|
char* atomA; |
552 |
|
|
char* atomB; |
553 |
|
|
char* atomC; |
554 |
|
|
QuadraticBend* qBend; |
555 |
|
|
|
556 |
|
|
SRI **the_sris; |
557 |
|
|
Atom** the_atoms; |
558 |
|
|
int nBends; |
559 |
|
|
the_sris = entry_plug->sr_interactions; |
560 |
|
|
the_atoms = entry_plug->atoms; |
561 |
|
|
nBends = entry_plug->n_bends; |
562 |
|
|
|
563 |
|
|
// read in the bend types. |
564 |
|
|
|
565 |
|
|
rewind( frcFile ); |
566 |
|
|
headBendType = new LinkedType; |
567 |
|
|
currentBendType = headBendType; |
568 |
|
|
|
569 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
570 |
|
|
lineNum++; |
571 |
|
|
if( eof_test == NULL ){ |
572 |
|
|
fprintf( stderr, "Error in reading Bends from force file.\n" ); |
573 |
|
|
exit(8); |
574 |
|
|
} |
575 |
|
|
|
576 |
|
|
|
577 |
|
|
while( !foundBend ){ |
578 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
579 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
580 |
|
|
lineNum++; |
581 |
|
|
} |
582 |
|
|
if( eof_test == NULL ){ |
583 |
|
|
fprintf( stderr, |
584 |
|
|
"Error in reading Bends from force file at line %d.\n", |
585 |
|
|
lineNum ); |
586 |
|
|
exit(8); |
587 |
|
|
} |
588 |
|
|
|
589 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
590 |
|
|
foundBend = !strcmp( "BendTypes", the_token ); |
591 |
|
|
|
592 |
|
|
if( !foundBend ){ |
593 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
594 |
|
|
lineNum++; |
595 |
|
|
|
596 |
|
|
if( eof_test == NULL ){ |
597 |
|
|
fprintf( stderr, |
598 |
|
|
"Error in reading Bends from force file at line %d.\n", |
599 |
|
|
lineNum ); |
600 |
|
|
exit(8); |
601 |
|
|
} |
602 |
|
|
} |
603 |
|
|
} |
604 |
|
|
|
605 |
|
|
// we are now at the BendTypes section. |
606 |
|
|
|
607 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
608 |
|
|
lineNum++; |
609 |
|
|
|
610 |
|
|
if( eof_test == NULL ){ |
611 |
|
|
fprintf( stderr, |
612 |
|
|
"Error in reading Bends from force file at line %d.\n", |
613 |
|
|
lineNum ); |
614 |
|
|
exit(8); |
615 |
|
|
} |
616 |
|
|
|
617 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
618 |
|
|
|
619 |
|
|
if( readLine[0] != '!' ){ |
620 |
|
|
|
621 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
622 |
|
|
if( the_token != NULL ){ |
623 |
|
|
|
624 |
|
|
strcpy( currentBendType->nameA, the_token ); |
625 |
|
|
|
626 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
627 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
628 |
|
|
exit(8); |
629 |
|
|
} |
630 |
|
|
|
631 |
|
|
strcpy( currentBendType->nameB, the_token ); |
632 |
|
|
|
633 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
634 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
635 |
|
|
exit(8); |
636 |
|
|
} |
637 |
|
|
|
638 |
|
|
strcpy( currentBendType->nameC, the_token ); |
639 |
|
|
|
640 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
641 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
642 |
|
|
exit(8); |
643 |
|
|
} |
644 |
|
|
|
645 |
|
|
strcpy( currentBendType->type, the_token ); |
646 |
|
|
|
647 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
648 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
649 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
650 |
|
|
exit(8); |
651 |
|
|
} |
652 |
|
|
|
653 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
654 |
|
|
|
655 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
656 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
657 |
|
|
exit(8); |
658 |
|
|
} |
659 |
|
|
|
660 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
661 |
|
|
|
662 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
663 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
664 |
|
|
exit(8); |
665 |
|
|
} |
666 |
|
|
|
667 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
668 |
|
|
|
669 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
670 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
671 |
|
|
exit(8); |
672 |
|
|
} |
673 |
|
|
|
674 |
|
|
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
675 |
|
|
} |
676 |
|
|
|
677 |
|
|
else{ |
678 |
|
|
fprintf(stderr, |
679 |
|
|
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
680 |
|
|
currentBendType->type, |
681 |
|
|
lineNum ); |
682 |
|
|
exit(8); |
683 |
|
|
} |
684 |
|
|
} |
685 |
|
|
} |
686 |
|
|
|
687 |
|
|
tempBendType = new LinkedType; |
688 |
|
|
currentBendType->next = tempBendType; |
689 |
|
|
currentBendType = tempBendType; |
690 |
|
|
|
691 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
692 |
|
|
lineNum++; |
693 |
|
|
} |
694 |
|
|
|
695 |
|
|
|
696 |
|
|
// initialize the Bends |
697 |
|
|
|
698 |
|
|
for( i=0; i<nBends; i++ ){ |
699 |
|
|
|
700 |
|
|
a = the_bends[i].a; |
701 |
|
|
b = the_bends[i].b; |
702 |
|
|
c = the_bends[i].c; |
703 |
|
|
|
704 |
|
|
atomA = the_atoms[a]->getType(); |
705 |
|
|
atomB = the_atoms[b]->getType(); |
706 |
|
|
atomC = the_atoms[c]->getType(); |
707 |
|
|
currentBendType = headBendType->find( atomA, atomB, atomC ); |
708 |
|
|
if( currentBendType == NULL ){ |
709 |
|
|
fprintf( stderr, "BendType error, %s - %s - %s not found" |
710 |
|
|
" in force file.\n", |
711 |
|
|
atomA, atomB, atomC ); |
712 |
|
|
exit(8); |
713 |
|
|
} |
714 |
|
|
|
715 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
716 |
|
|
|
717 |
|
|
index = i + entry_plug->n_bonds; |
718 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
719 |
|
|
*the_atoms[b], |
720 |
|
|
*the_atoms[c] ); |
721 |
|
|
qBend->setConstants( currentBendType->k1, |
722 |
|
|
currentBendType->k2, |
723 |
|
|
currentBendType->k3, |
724 |
|
|
currentBendType->t0 ); |
725 |
|
|
the_sris[index] = qBend; |
726 |
|
|
} |
727 |
|
|
} |
728 |
|
|
|
729 |
|
|
|
730 |
|
|
// clean up the memory |
731 |
|
|
|
732 |
|
|
delete headBendType; |
733 |
|
|
|
734 |
|
|
} |
735 |
|
|
|
736 |
|
|
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
737 |
|
|
|
738 |
|
|
class LinkedType { |
739 |
|
|
public: |
740 |
|
|
LinkedType(){ |
741 |
|
|
next = NULL; |
742 |
|
|
nameA[0] = '\0'; |
743 |
|
|
nameB[0] = '\0'; |
744 |
|
|
nameC[0] = '\0'; |
745 |
|
|
type[0] = '\0'; |
746 |
|
|
} |
747 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
748 |
|
|
|
749 |
|
|
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
750 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
751 |
|
|
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
752 |
|
|
|
753 |
|
|
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
754 |
|
|
!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this; |
755 |
|
|
|
756 |
|
|
if( next != NULL ) return next->find(key1, key2, key3, key4); |
757 |
|
|
return NULL; |
758 |
|
|
} |
759 |
|
|
|
760 |
|
|
char nameA[15]; |
761 |
|
|
char nameB[15]; |
762 |
|
|
char nameC[15]; |
763 |
|
|
char nameD[15]; |
764 |
|
|
char type[30]; |
765 |
|
|
double k1, k2, k3, k4; |
766 |
|
|
|
767 |
|
|
LinkedType* next; |
768 |
|
|
}; |
769 |
|
|
|
770 |
|
|
LinkedType* headTorsionType; |
771 |
|
|
LinkedType* currentTorsionType; |
772 |
|
|
LinkedType* tempTorsionType; |
773 |
|
|
|
774 |
|
|
char readLine[500]; |
775 |
|
|
char* the_token; |
776 |
|
|
char* eof_test; |
777 |
|
|
int foundTorsion = 0; |
778 |
|
|
int lineNum = 0; |
779 |
|
|
int i, a, b, c, d, index; |
780 |
|
|
char* atomA; |
781 |
|
|
char* atomB; |
782 |
|
|
char* atomC; |
783 |
|
|
char* atomD; |
784 |
|
|
CubicTorsion* cTors; |
785 |
|
|
|
786 |
|
|
SRI **the_sris; |
787 |
|
|
Atom** the_atoms; |
788 |
|
|
int nTorsions; |
789 |
|
|
the_sris = entry_plug->sr_interactions; |
790 |
|
|
the_atoms = entry_plug->atoms; |
791 |
|
|
nTorsions = entry_plug->n_torsions; |
792 |
|
|
|
793 |
|
|
// read in the torsion types. |
794 |
|
|
|
795 |
|
|
rewind( frcFile ); |
796 |
|
|
headTorsionType = new LinkedType; |
797 |
|
|
currentTorsionType = headTorsionType; |
798 |
|
|
|
799 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
800 |
|
|
lineNum++; |
801 |
|
|
if( eof_test == NULL ){ |
802 |
|
|
fprintf( stderr, "Error in reading Torsions from force file.\n" ); |
803 |
|
|
exit(8); |
804 |
|
|
} |
805 |
|
|
|
806 |
|
|
|
807 |
|
|
while( !foundTorsion ){ |
808 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
809 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
810 |
|
|
lineNum++; |
811 |
|
|
} |
812 |
|
|
if( eof_test == NULL ){ |
813 |
|
|
fprintf( stderr, |
814 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
815 |
|
|
lineNum ); |
816 |
|
|
exit(8); |
817 |
|
|
} |
818 |
|
|
|
819 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
820 |
|
|
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
821 |
|
|
|
822 |
|
|
if( !foundTorsion ){ |
823 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
824 |
|
|
lineNum++; |
825 |
|
|
|
826 |
|
|
if( eof_test == NULL ){ |
827 |
|
|
fprintf( stderr, |
828 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
829 |
|
|
lineNum ); |
830 |
|
|
exit(8); |
831 |
|
|
} |
832 |
|
|
} |
833 |
|
|
} |
834 |
|
|
|
835 |
|
|
// we are now at the TorsionTypes section. |
836 |
|
|
|
837 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
838 |
|
|
lineNum++; |
839 |
|
|
|
840 |
|
|
if( eof_test == NULL ){ |
841 |
|
|
fprintf( stderr, |
842 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
843 |
|
|
lineNum ); |
844 |
|
|
exit(8); |
845 |
|
|
} |
846 |
|
|
|
847 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
848 |
|
|
|
849 |
|
|
if( readLine[0] != '!' ){ |
850 |
|
|
|
851 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
852 |
|
|
if( the_token != NULL ){ |
853 |
|
|
|
854 |
|
|
strcpy( currentTorsionType->nameA, the_token ); |
855 |
|
|
|
856 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
857 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
858 |
|
|
exit(8); |
859 |
|
|
} |
860 |
|
|
|
861 |
|
|
strcpy( currentTorsionType->nameB, the_token ); |
862 |
|
|
|
863 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
864 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
865 |
|
|
exit(8); |
866 |
|
|
} |
867 |
|
|
|
868 |
|
|
strcpy( currentTorsionType->nameC, the_token ); |
869 |
|
|
|
870 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
871 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
872 |
|
|
exit(8); |
873 |
|
|
} |
874 |
|
|
|
875 |
|
|
strcpy( currentTorsionType->nameD, the_token ); |
876 |
|
|
|
877 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
878 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
879 |
|
|
exit(8); |
880 |
|
|
} |
881 |
|
|
|
882 |
|
|
strcpy( currentTorsionType->type, the_token ); |
883 |
|
|
|
884 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
885 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
886 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
887 |
|
|
exit(8); |
888 |
|
|
} |
889 |
|
|
|
890 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
891 |
|
|
|
892 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
893 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
894 |
|
|
exit(8); |
895 |
|
|
} |
896 |
|
|
|
897 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
898 |
|
|
|
899 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
900 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
901 |
|
|
exit(8); |
902 |
|
|
} |
903 |
|
|
|
904 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
905 |
|
|
|
906 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
907 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
908 |
|
|
exit(8); |
909 |
|
|
} |
910 |
|
|
|
911 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
912 |
|
|
} |
913 |
|
|
|
914 |
|
|
else{ |
915 |
|
|
fprintf(stderr, |
916 |
|
|
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
917 |
|
|
currentTorsionType->type, |
918 |
|
|
lineNum ); |
919 |
|
|
exit(8); |
920 |
|
|
} |
921 |
|
|
} |
922 |
|
|
} |
923 |
|
|
|
924 |
|
|
tempTorsionType = new LinkedType; |
925 |
|
|
currentTorsionType->next = tempTorsionType; |
926 |
|
|
currentTorsionType = tempTorsionType; |
927 |
|
|
|
928 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
929 |
|
|
lineNum++; |
930 |
|
|
} |
931 |
|
|
|
932 |
|
|
|
933 |
|
|
// initialize the Torsions |
934 |
|
|
|
935 |
|
|
for( i=0; i<nTorsions; i++ ){ |
936 |
|
|
|
937 |
|
|
a = the_torsions[i].a; |
938 |
|
|
b = the_torsions[i].b; |
939 |
|
|
c = the_torsions[i].c; |
940 |
|
|
d = the_torsions[i].d; |
941 |
|
|
|
942 |
|
|
atomA = the_atoms[a]->getType(); |
943 |
|
|
atomB = the_atoms[b]->getType(); |
944 |
|
|
atomC = the_atoms[c]->getType(); |
945 |
|
|
atomD = the_atoms[d]->getType(); |
946 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
947 |
|
|
if( currentTorsionType == NULL ){ |
948 |
|
|
fprintf( stderr, "TorsionType error, %s - %s - %s - %s not found" |
949 |
|
|
" in force file.\n", |
950 |
|
|
atomA, atomB, atomC, atomD ); |
951 |
|
|
exit(8); |
952 |
|
|
} |
953 |
|
|
|
954 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
955 |
|
|
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
956 |
|
|
|
957 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
958 |
|
|
*the_atoms[c], *the_atoms[d] ); |
959 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
960 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
961 |
|
|
the_sris[index] = cTors; |
962 |
|
|
} |
963 |
|
|
} |
964 |
|
|
|
965 |
|
|
|
966 |
|
|
// clean up the memory |
967 |
|
|
|
968 |
|
|
delete headTorsionType; |
969 |
|
|
|
970 |
|
|
} |