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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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|
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#include <iostream> |
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using namespace std; |
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|
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#include "ForceFields.hpp" |
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#include "SRI.hpp" |
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|
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|
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DipoleTestFF::DipoleTestFF(){ |
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|
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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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|
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// generate the force file name |
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|
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strcpy( fileName, "DipoleTest.frc" ); |
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|
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// attempt to open the file in the current directory first. |
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|
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frcFile = fopen( fileName, "r" ); |
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|
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if( frcFile == NULL ){ |
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|
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// next see if the force path enviorment variable is set |
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|
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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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|
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frcFile = fopen( fileName, "r" ); |
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|
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if( frcFile == NULL ){ |
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|
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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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|
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DipoleTestFF::~DipoleTestFF(){ |
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|
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fclose( frcFile ); |
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} |
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|
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void DipoleTestFF::initializeAtoms( void ){ |
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|
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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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|
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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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|
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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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|
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LinkedType* headAtomType; |
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LinkedType* currentAtomType; |
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LinkedType* tempAtomType; |
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|
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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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////////////////////////////////////////////////// |
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// a quick water fix |
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|
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double testI[3][3]; |
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testI[0][0] = 1.76958347772500; |
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testI[0][1] = 0.0; |
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testI[0][2] = 0.0; |
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|
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testI[1][0] = 0.0; |
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testI[1][1] = 0.614537057924513; |
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testI[1][2] = 0.0; |
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|
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testI[2][0] = 0.0; |
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testI[2][1] = 0.0; |
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testI[2][2] = 1.15504641980049; |
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|
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////////////////////////////////////////////////// |
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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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|
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// read in the atom types. |
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|
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rewind( frcFile ); |
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headAtomType = new LinkedType; |
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currentAtomType = headAtomType; |
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|
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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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|
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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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|
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the_token = strtok( readLine, " ,;\t#\n" ); |
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foundAtom = !strcmp( "AtomTypes", the_token ); |
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|
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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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|
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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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|
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// we are now at the AtomTypes section. |
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|
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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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|
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while( readLine[0] != '#' && eof_test != NULL ){ |
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|
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if( readLine[0] != '!' ){ |
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|
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the_token = strtok( readLine, " \n\t,;" ); |
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if( the_token != NULL ){ |
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|
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strcpy( currentAtomType->name, the_token ); |
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|
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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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|
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sscanf( the_token, "%d", ¤tAtomType->isDipole ); |
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|
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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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|
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sscanf( the_token, "%lf", ¤tAtomType->mass ); |
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|
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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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|
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sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
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|
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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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|
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sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
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|
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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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|
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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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|
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tempAtomType = new LinkedType; |
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currentAtomType->next = tempAtomType; |
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currentAtomType = tempAtomType; |
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|
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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} |
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|
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|
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// initialize the atoms |
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|
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DirectionalAtom* dAtom; |
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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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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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|
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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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if( currentAtomType->isDipole ){ |
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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 ); |
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dAtom->setHasDipole( 1 ); |
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dAtom->setSSD( 1 ); |
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dAtom->setJx( 0.0 ); |
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dAtom->setJy( 0.0 ); |
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dAtom->setJz( 0.0 ); |
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|
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dAtom->setI( testI ); |
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|
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entry_plug->n_dipoles++; |
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} |
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else{ |
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std::cerr |
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<< "DipoleTestFF error: Atom \"" |
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<< currentAtomType->name << "\" is a dipole, yet no standard" |
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<< " orientation was specifed in the BASS file.\n"; |
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exit(8); |
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} |
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} |
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else{ |
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if( the_atoms[i]->isDirectional() ){ |
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std::cerr |
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<< "DipoleTestFF error: Atom \"" |
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<< currentAtomType->name << "\" was given a standard orientation" |
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<< " in the BASS file, yet it is not a dipole.\n"; |
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exit(8); |
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} |
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} |
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} |
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|
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|
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// clean up the memory |
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|
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delete headAtomType; |
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} |
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|
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void DipoleTestFF::initializeBonds( bond_pair* the_bonds ){ |
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|
| 285 |
if( entry_plug->n_bonds ){ |
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std::cerr << "DipoleTest does not support bonds!\n"; |
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exit(8); |
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} |
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} |
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|
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void DipoleTestFF::initializeBends( bend_set* the_bends ){ |
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|
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if( entry_plug->n_bends ){ |
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std::cerr << "DipoleTest does not support bends!\n"; |
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exit(8); |
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} |
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} |
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|
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void DipoleTestFF::initializeTorsions( torsion_set* the_torsions ){ |
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|
| 301 |
if( entry_plug->n_torsions ){ |
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std::cerr << "DipoleTest does not support torsions!\n"; |
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exit(8); |
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} |
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} |
