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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.
*/
#include <Base/AdForceFieldFunctions.h>
bool __HarmonicAngleEnergyDebug__ = false;
bool __HarmonicAngleForceDebug__ = false;
inline void AdHarmonicAngleForce(double *interaction, double **coordinates, double **forces, double *ang_pot)
{
register int i;
int atom_one, atom_two, atom_three;
double coff_A, ang_cnst, eq_ang;
double cosine_ang, angle, d_theta, forceMag;
double forceOne, forceThree;
double numerator, denominator, dtheta_du;
Vector3D ba_v, bc_v;
//decode interaction
atom_one = (int)interaction[0];
atom_two = (int)interaction[1];
atom_three = (int)interaction[2];
ang_cnst = interaction[3];
eq_ang = interaction[4];
//find the two vectors ba_v, bc_v
for(i=0; i<3; i++)
{
ba_v.vector[i] = coordinates[atom_one][i] - coordinates[atom_two][i];
bc_v.vector[i] = coordinates[atom_three][i] - coordinates[atom_two][i];
}
//ba.bc/|ba||bc| = cos(theta)
//therefore calculate ba.bc
numerator = Ad3DDotProduct(&ba_v, &bc_v);
//now find the length of ba and bc
Ad3DVectorLength(&ba_v);
Ad3DVectorLength(&bc_v);
//find |ba|*|bc|
denominator = ba_v.length*bc_v.length;
//now calculate cosine of theta
cosine_ang = numerator/denominator;
#ifdef SAFE_ANGLE
//check if the cosin_ang has slipped beyond
//the valid range due to numerical imprecision.
if(cosine_ang > 1)
cosine_ang = 1;
else if(cosine_ang < -1)
cosine_ang = -1;
#endif
//find the associated angle
angle = acos(cosine_ang);
//calculate d_theta and hence the potential and the angular acceleration
d_theta = angle - eq_ang;
forceMag = -ang_cnst*d_theta;
*ang_pot -= forceMag*d_theta*0.5;
//find dtheta_du
dtheta_du = (1 - cosine_ang*cosine_ang);
dtheta_du = -1/sqrt(dtheta_du);
//calculate coff_A
coff_A = (forceMag*dtheta_du);
//find the nine partial derivatives needed
for(i=0; i<3;i++)
{
forceOne = (coff_A/denominator)*( bc_v.vector[i] - (bc_v.length/ba_v.length)*cosine_ang*ba_v.vector[i]);
forceThree = (coff_A/denominator)*( ba_v.vector[i] - (ba_v.length/bc_v.length)*cosine_ang*bc_v.vector[i]);
forces[atom_two][i] -= (forceOne + forceThree);
forces[atom_one][i] += forceOne;
forces[atom_three][i] += forceThree;
}
#ifdef BASE_BONDED_DEBUG
if(__HarmonicAngleForceDebug__)
{
fprintf(stderr, "%-6d%-6d%-6d%-12.5lf%-12.5lf%-12.5lf%-12.5lf%-12.5lf\n",
atom_one,
atom_two,
atom_three,
ang_cnst,
eq_ang,
angle,
*ang_pot,
forceMag);
}
#endif
}
inline void AdHarmonicAngleEnergy(double* interaction, double** coordinates, double* ang_pot)
{
register int i;
int atom_one, atom_two, atom_three;
double ang_cnst, eq_ang;
double cosine_ang, angle, d_theta, forceMag;
double numerator, denominator;
Vector3D ba_v, bc_v;
//decode interaction
atom_one = (int)interaction[0];
atom_two = (int)interaction[1];
atom_three = (int)interaction[2];
ang_cnst = interaction[3];
eq_ang = interaction[4];
//find the two vectors ba_v, bc_v
for(i=0; i<3; i++)
{
ba_v.vector[i] = coordinates[atom_one][i] - coordinates[atom_two][i];
bc_v.vector[i] = coordinates[atom_three][i] - coordinates[atom_two][i];
}
//ba.bc/|ba||bc| = cos(theta)
//therefore calculate ba.bc
numerator = Ad3DDotProduct(&ba_v, &bc_v);
//now find the length of ba and bc
Ad3DVectorLength(&ba_v);
Ad3DVectorLength(&bc_v);
//find |ba|*|bc|
denominator = ba_v.length*bc_v.length;
//now calculate cosine of theta
cosine_ang = numerator/denominator;
#ifdef SAFE_ANGLE
//check if the cosin_ang has slipped beyond
//the valid range due to numerical imprecision.
if(cosine_ang > 1)
cosine_ang = 1;
else if(cosine_ang < -1)
cosine_ang = -1;
#endif
//find the associated angle
angle = acos(cosine_ang);
//calculate d_theta and hence the potential and the angular acceleration
d_theta = angle - eq_ang;
forceMag = -ang_cnst*d_theta;
*ang_pot -= forceMag*d_theta*0.5;
#ifdef BASE_BONDED_DEBUG
if(__HarmonicAngleEnergyDebug__)
{
fprintf(stderr, "%-6d%-6d%-6d%-12.5lf%-12.5lf%-12.5lf%-12.5lf%-12.5lf%\n",
atom_one,
atom_two,
atom_three,
ang_cnst,
eq_ang,
cosine_ang,
angle,
*ang_pot);
}
#endif
}
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