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/*
Project: Adun
Copyright (C) 2005 Michael Johnston & Jordi Villa-Freixa
Author: Michael Johnston
This application is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This application is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Library General Public License for more details.
You should have received a copy of the GNU General Public
License along with this library; if not, write to the Free
Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111 USA.
*/
#ifndef AD_FORCEFIELD_FUNCTIONS
#define AD_FORCEFIELD_FUNCTIONS
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <stdbool.h>
#include <float.h>
#include <fenv.h>
#include "Base/AdVector.h"
#include "Base/AdLinkedList.h"
/**
Debugging
*/
//If BASE_DEBUG is defined, define
//BASE_BONDED_DEBUG & BASE_NONBONDED_DEBUG if they're not
//already defined.
#ifdef BASE_DEBUG
#ifndef BASE_BONDED_DEBUG
#define BASE_BONDED_DEBUG
#endif
#ifndef BASE_NONBONDED_DEBUG
#define BASE_NONBONDED_DEBUG
#endif
#endif
extern bool __HarmonicBondEnergyDebug__;
extern bool __HarmonicBondForceDebug__;
extern bool __HarmonicAngleEnergyDebug__;
extern bool __HarmonicAngleForceDebug__;
extern bool __FourierTorsionEnergyDebug__;
extern bool __FourierTorsionForceDebug__;
extern bool __HarmonicImproperTorsionEnergyDebug__;
extern bool __HarmonicImproperTorsionForceDebug__;
extern bool __NonbondedEnergyDebug__;
extern bool __NonbondedForceDebug__;
extern bool __ShiftedNonbondedEnergyDebug__;
extern bool __ShiftedNonbondedForceDebug__;
extern bool __GRFNonbondedEnergyDebug__;
extern bool __GRFNonbondedForceDebug__;
inline void AdNonbondedEnergyLog(char* cutType, char* ljType, int a1, int a2, double ljA,
double ljB, double charge, double sep, double estPot, double ljPot,
bool flag);
inline void AdNonbondedForceLog(char* cutType, char* ljType, int a1, int a2, double ljA,
double ljB, double charge, double sep, double estPot, double ljPot, double force,
bool flag);
/**
\defgroup Functions Functions
\ingroup Base
*/
/**
\defgroup Types Types
\ingroup Base
*/
/**
These are the primitive functions used to calculate the energy and force
terms of a force field.
\defgroup ForceFieldFunctions Force Field
\ingroup Functions
@{
*/
/*
* Harmonic Bond
*/
/** Calculates the energy of a bond using a harmonic bond function */
inline void AdHarmonicBondEnergy(double *bond, double **coordinates, double *bnd_pot);
/** Calculates the energy and force of a bond using a harmonic bond function */
inline void AdHarmonicBondForce(double* bond, double **coordinates, double **forces, double* bnd_pot);
/**
Enzymix force field uses k*(x-x0)² instead of k/2*(x-xo)² like other force fields
*/
inline void AdEnzymixBondEnergy(double* bond, double **coordinates, double* bnd_pot);
/**
As harmonic force except force magnitude is 2k*(x-x0) instead of k*(x-xo) like other force fields
*/
inline void AdEnzymixBondForce(double* bond, double **coordinates, double **forces, double* bnd_pot);
/*
* Harmonic Angle
*/
/** Calculates the energy of an angle using a harmonic angle function */
inline void AdHarmonicAngleEnergy(double *interaction, double **coordinates, double *ang_pot);
inline void AdHarmonicAngleForce(double *interaction, double **coordinates, double **forces, double *ang_pot);
/**
Enzymix force field uses k*(x-x0)² instead of k/2*(x-xo)² like other force fields
Where x is the angle.
*/
inline void AdEnzymixAngleEnergy(double *interaction, double** coordinates, double *ang_pot);
inline void AdEnzymixAngleForce(double *interaction, double **coordinates, double **forces, double *ang_pot);
/*
* fourier torsion
*/
/** calculates the energy of a proper torsion using a fourier torsion function */
inline void AdFourierTorsionEnergy(double *interaction, double **coordinates, double *tor_pot);
inline void AdFourierTorsionForce(double *interaction, double **coordinates, double **forces, double *tor_pot);
/*
Calculate the torsion angle for four atoms. Torsion 4 element array each element an atom index. The
atoms position must be given by the corresponding row in coordinates.
*/
inline double AdCalculateTorsionAngle(int* torsion, double** coordinates);
/*
* harmonic improper torsion
*/
/** calculates the energy of an improper torsion using a harmonic function */
inline void AdHarmonicImproperTorsionEnergy(double *interaction, double **coordinates , double *itor_pot);
inline void AdHarmonicImproperTorsionForce(double *interaction, double **coordinates, double **forces, double *itor_pot);
/** Calculates the combined energy of a coloumb electrostatic and lennard jones A term.
Lennard Jones A uses parameters A and B. These functions are optimised for use in
Adun AdForceField obects.
\todo Possibly move the separation and cutoff rejection code to AdunKernel classes */
inline void AdCoulombAndLennardJonesAEnergy(ListElement* interaction,
double** coordinates,
double EPSILON_RP,
double cutoff,
double* vdw_pot,
double* est_pot);
inline void AdCoulombAndLennardJonesAForce(ListElement* interaction,
double** coordinates,
double** forces,
double EPSILON_RP,
double cutoff,
double* vdw_pot,
double* est_pot);
inline void AdShiftedCoulombAndLennardJonesAEnergy(ListElement* interaction,
double** coordinates,
double EPSILON_RP,
double cut,
double r_cutoff2,
double* vdw_pot,
double* est_pot);
inline void AdShiftedCoulombAndLennardJonesAForce(ListElement* interaction,
double** coordinates,
double** forces,
double EPSILON_RP,
double cut,
double r_cutoff2,
double* vdw_pot,
double* est_pot);
inline void AdGRFCoulombAndLennardJonesAEnergy(ListElement* interaction,
double** coordinates,
double EPSILON_RP,
double cutoff,
double b0,
double b1,
double* vdw_pot,
double* est_pot);
inline void AdGRFCoulombAndLennardJonesAForce(ListElement* interaction,
double** coordinates,
double** forces,
double EPSILON_RP,
double cutoff,
double b0,
double b1,
double* vdw_pot,
double* est_pot);
/** Calculates the combined energy of a coloumb electrostatic and lennard jones B term.
Lennard Jones A uses parameters well depth and equilibrium separation.
These functions are optimised for use in Adun AdForceField obects.*/
inline void AdCoulombAndLennardJonesBEnergy(ListElement* interaction,
double** coordinates,
double EPSILON_RP,
double cutoff,
double* vdw_pot,
double* est_pot);
inline void AdCoulombAndLennardJonesBForce(ListElement* interaction,
double** coordinates,
double** forces,
double EPSILON_RP,
double cutoff,
double* vdw_pot,
double* est_pot);
inline void AdShiftedCoulombAndLennardJonesBForce(ListElement* interaction,
double** coordinates,
double** forces,
double EPSILON_RP,
double cut,
double r_cutoff2,
double* vdw_pot,
double* est_pot);
inline void AdShiftedCoulombAndLennardJonesBEnergy(ListElement* interaction,
double** coordinates,
double EPSILON_RP,
double cut,
double r_cutoff2,
double* vdw_pot,
double* est_pot);
inline void AdGRFCoulombAndLennardJonesBEnergy(ListElement* interaction,
double** coordinates,
double EPSILON_RP,
double cutoff,
double b0,
double b1,
double* vdw_pot,
double* est_pot);
inline void AdGRFCoulombAndLennardJonesBForce(ListElement* interaction,
double** coordinates,
double** forces,
double EPSILON_RP,
double cutoff,
double b0,
double b1,
double* vdw_pot,
double* est_pot);
//test
inline void AdCoulombAndLennardJonesAForceTest(ListElement* interaction,
Vector3D* seperation_s,
double** forces,
double EPSILON_RP,
double* vdw_pot,
double* est_pot);
/** \@}**/
#endif
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