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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 __NonbondedEnergyDebug__ = false;
bool __NonbondedForceDebug__ = false;
bool __ShiftedNonbondedEnergyDebug__ = false;
bool __ShiftedNonbondedForceDebug__ = false;
bool __GRFNonbondedEnergyDebug__ = false;
bool __GRFNonbondedForceDebug__ = false;
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)
{
if(flag)
fprintf(stderr, "%-8s%-3s%-6d%-6d%-12.5lf%-12.5lf%-12.5lf%-12.5lf%-12.lf%-12.5lf\n",
cutType, ljType, a1, a2, ljA, ljB, charge, sep, estPot, ljPot);
}
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)
{
if(flag)
fprintf(stderr, "%-8s%-3s%-6d%-6d%-12.5lf%-12.5lf%-12.5lf%-12.5lf%-12.lf%-12.5lf%-12.5lf\n",
cutType, ljType, a1, a2, ljA, ljB, charge, sep, estPot, ljPot, force);
}
inline void AdCoulombAndLennardJonesAEnergy(ListElement* interaction,
double** coordinates,
double EPSILON_RP,
double cutoff,
double* vdw_pot,
double* est_pot)
{
int atom_one, atom_two;
double length_rec, vdw_hold, est_hold;
double lennardJonesA, lennardJonesB, chargeProduct;
Vector3D seperation_s;
atom_one = interaction->bond[0];
atom_two = interaction->bond[1];
lennardJonesA = interaction->params[0];
lennardJonesB = interaction->params[1];
chargeProduct = interaction->params[2];
//calculate seperation vector (r1 - r2)
*(seperation_s.vector + 0) = coordinates[atom_one][0] - coordinates[atom_two][0];
*(seperation_s.vector + 1) = coordinates[atom_one][1] - coordinates[atom_two][1];
*(seperation_s.vector + 2) = coordinates[atom_one][2] - coordinates[atom_two][2];
//calculate the interatomic distance
Ad3DVectorLength(&seperation_s);
if(seperation_s.length > cutoff)
return;
//add this length to the linked list element the bond belongs to
interaction->length = seperation_s.length;
//get reciprocal of seperation
length_rec = 1/seperation_s.length;
vdw_hold = pow(length_rec, 6);
est_hold = (EPSILON_RP*chargeProduct*length_rec);
lennardJonesA *= vdw_hold*vdw_hold;
lennardJonesB *= vdw_hold;
*est_pot += est_hold;
*vdw_pot += lennardJonesA - lennardJonesB;
#ifdef BASE_NONBONDED_DEBUG
AdNonbondedEnergyLog("Normal", "A", atomOne, atomTwo, lennardJonesA, lennardJonesB,
chargeProduct, separation_s.length, est_hold, (lennardJonesA - lennardJonesB),
__NonbondedEnergyDebug__);
#endif
}
inline void AdCoulombAndLennardJonesAForce(ListElement* interaction,
double** coordinates,
double** forces,
double EPSILON_RP,
double cutoff,
double* vdw_pot,
double* est_pot)
{
int atom_one, atom_two;
double force_mag;
double length_rec, vdw_hold, est_hold;
double lennardJonesA, lennardJonesB, chargeProduct;
Vector3D seperation_s;
atom_one = interaction->bond[0];
atom_two = interaction->bond[1];
lennardJonesA = interaction->params[0];
lennardJonesB = interaction->params[1];
chargeProduct = interaction->params[2];
//calculate seperation vector (r1 - r2)
*(seperation_s.vector + 0) = coordinates[atom_one][0] - coordinates[atom_two][0];
*(seperation_s.vector + 1) = coordinates[atom_one][1] - coordinates[atom_two][1];
*(seperation_s.vector + 2) = coordinates[atom_one][2] - coordinates[atom_two][2];
//calculate the interatomic distance
Ad3DVectorLength(&seperation_s);
if(seperation_s.length > cutoff)
return;
//add this length to the linked list wlement the bond belongs to
interaction->length = seperation_s.length;
//get reciprocal of seperation
length_rec = 1/seperation_s.length;
//calculate vdw holder
vdw_hold = pow(length_rec, 6);
//while this is being calculate
//calculate some non dependant variables
//est holder
est_hold = EPSILON_RP*chargeProduct*length_rec;
//vdw holder may be finished now so calculate vdw consts
lennardJonesA *= vdw_hold*vdw_hold;
lennardJonesB *= vdw_hold;
*est_pot += est_hold;
*vdw_pot += lennardJonesA - lennardJonesB;
force_mag = est_hold*length_rec;
//add the vdw force to the est force
force_mag += 6*length_rec*(2*lennardJonesA - lennardJonesB);
force_mag *= length_rec;
//calculate the force on atom one along the vector (r1 - r2)
//the force on atom two is the opposite of this force
*(seperation_s.vector + 0) *= force_mag;
*(seperation_s.vector + 1) *= force_mag;
*(seperation_s.vector + 2) *= force_mag;
forces[atom_one][0] += *(seperation_s.vector + 0);
forces[atom_one][1] += *(seperation_s.vector + 1);
forces[atom_one][2] += *(seperation_s.vector + 2);
forces[atom_two][0] -= *(seperation_s.vector + 0);
forces[atom_two][1] -= *(seperation_s.vector + 1);
forces[atom_two][2] -= *(seperation_s.vector + 2);
#ifdef BASE_NONBONDED_DEBUG
AdNonbondedForceLog("Normal", "A", atomOne, atomTwo, lennardJonesA, lennardJonesB,
chargeProduct, separation_s.length, est_hold,
(lennardJonesA - lennardJonesB), forceMag,
__NonbondedForceDebug__);
#endif
}
inline void AdCoulombAndLennardJonesAForceTest(ListElement* interaction,
Vector3D* seperation_s,
double** forces,
double EPSILON_RP,
double* vdw_pot,
double* est_pot)
{
int atom_one, atom_two;
double force_mag;
double length_rec, vdw_hold, est_hold;
double lennardJonesA, lennardJonesB, chargeProduct;
atom_one = interaction->bond[0];
atom_two = interaction->bond[1];
lennardJonesA = interaction->params[0];
lennardJonesB = interaction->params[1];
chargeProduct = interaction->params[2];
/*//calculate the interatomic distance
Ad3DVectorLength(&seperation_s);*/
//add this length to the linked list wlement the bond belongs to
interaction->length = seperation_s->length;
//get reciprocal of seperation
length_rec = 1/seperation_s->length;
//calculate vdw holder
vdw_hold = pow(length_rec, 6);
//while this is being calculate
//calculate some non dependant variables
//est holder
est_hold = EPSILON_RP*chargeProduct*length_rec;
//vdw holder may be finished now so calculate vdw consts
lennardJonesA *= vdw_hold*vdw_hold;
lennardJonesB *= vdw_hold;
*est_pot += est_hold;
*vdw_pot += lennardJonesA - lennardJonesB;
force_mag = est_hold*length_rec;
//add the vdw force to the est force
force_mag += 6*length_rec*(2*lennardJonesA - lennardJonesB);
force_mag *= length_rec;
//calculate the force on atom one along the vector (r1 - r2)
//the force on atom two is the opposite of this force
*(seperation_s->vector + 0) *= force_mag;
*(seperation_s->vector + 1) *= force_mag;
*(seperation_s->vector + 2) *= force_mag;
forces[atom_one][0] += *(seperation_s->vector + 0);
forces[atom_one][1] += *(seperation_s->vector + 1);
forces[atom_one][2] += *(seperation_s->vector + 2);
forces[atom_two][0] -= *(seperation_s->vector + 0);
forces[atom_two][1] -= *(seperation_s->vector + 1);
forces[atom_two][2] -= *(seperation_s->vector + 2);
}
inline void AdShiftedCoulombAndLennardJonesAForce(ListElement* interaction,
double** coordinates,
double** forces,
double EPSILON_RP,
double cut,
double r_cutoff2,
double* vdw_pot,
double* est_pot)
{
int atom_one, atom_two;
double force_mag;
double length_rec, vdw_hold, est_hold;
double shift_fac;
double lennardJonesA, lennardJonesB, chargeProduct;
Vector3D seperation_s;
atom_one = interaction->bond[0];
atom_two = interaction->bond[1];
lennardJonesA = interaction->params[0];
lennardJonesB = interaction->params[1];
chargeProduct = interaction->params[2];
*(seperation_s.vector + 0) = coordinates[atom_one][0] - coordinates[atom_two][0];
*(seperation_s.vector + 1) = coordinates[atom_one][1] - coordinates[atom_two][1];
*(seperation_s.vector + 2) = coordinates[atom_one][2] - coordinates[atom_two][2];
Ad3DVectorLength(&seperation_s);
if(seperation_s.length > cut)
return;
interaction->length = seperation_s.length;
length_rec = 1/seperation_s.length;
vdw_hold = pow(length_rec, 6);
est_hold = EPSILON_RP*chargeProduct*length_rec;
//est shift factor
shift_fac = (cut - seperation_s.length)*(cut - seperation_s.length)*r_cutoff2;
lennardJonesA *= vdw_hold*vdw_hold;
lennardJonesB *= vdw_hold;
//the shifted est force is EST_HOLD*(length_rec - r_cutoff2*length)
force_mag = (length_rec - r_cutoff2*seperation_s.length);
*est_pot += (est_hold*shift_fac);
*vdw_pot += lennardJonesA - lennardJonesB;
//apply the shift to the est force
force_mag *= est_hold;
//add the vdw force
force_mag += 6*length_rec*(2*lennardJonesA - lennardJonesB);
force_mag *= length_rec;
*(seperation_s.vector + 0) *= force_mag;
*(seperation_s.vector + 1) *= force_mag;
*(seperation_s.vector + 2) *= force_mag;
forces[atom_one][0] += *(seperation_s.vector + 0);
forces[atom_one][1] += *(seperation_s.vector + 1);
forces[atom_one][2] += *(seperation_s.vector + 2);
forces[atom_two][0] -= *(seperation_s.vector + 0);
forces[atom_two][1] -= *(seperation_s.vector + 1);
forces[atom_two][2] -= *(seperation_s.vector + 2);
#ifdef BASE_NONBONDED_DEBUG
AdNonbondedForceLog("Shifted", "A", atomOne, atomTwo, lennardJonesA, lennardJonesB,
chargeProduct, separation_s.length, est_hold,
(lennardJonesA - lennardJonesB), forceMag,
__ShiftedNonbondedForceDebug__);
#endif
}
inline void AdGRFCoulombAndLennardJonesAForce(ListElement* interaction,
double** coordinates,
double** forces,
double EPSILON_RP,
double cutoff,
double b0,
double b1,
double* vdw_pot,
double* est_pot)
{
int atom_one, atom_two;
double force_mag;
double length_rec, vdw_hold, est_hold;
double lennardJonesA, lennardJonesB, chargeProduct;
Vector3D seperation_s;
atom_one = interaction->bond[0];
atom_two = interaction->bond[1];
lennardJonesA = interaction->params[0];
lennardJonesB = interaction->params[1];
chargeProduct = interaction->params[2];
*(seperation_s.vector + 0) = coordinates[atom_one][0] - coordinates[atom_two][0];
*(seperation_s.vector + 1) = coordinates[atom_one][1] - coordinates[atom_two][1];
*(seperation_s.vector + 2) = coordinates[atom_one][2] - coordinates[atom_two][2];
Ad3DVectorLength(&seperation_s);
if(seperation_s.length > cutoff)
return;
interaction->length = seperation_s.length;
length_rec = 1/seperation_s.length;
vdw_hold = pow(length_rec, 6);
est_hold = EPSILON_RP*chargeProduct*length_rec;
lennardJonesA *= vdw_hold*vdw_hold;
lennardJonesB *= vdw_hold;
//GRF
*est_pot += est_hold + EPSILON_RP*chargeProduct*b0;
*vdw_pot += lennardJonesA - lennardJonesB;
force_mag = est_hold*length_rec + EPSILON_RP*chargeProduct*b1*seperation_s.length;
//add the vdw force to the est force
force_mag += 6*length_rec*(2*lennardJonesA - lennardJonesB);
//Since we have to divide the separation vector by this
force_mag *=length_rec;
*(seperation_s.vector + 0) *= force_mag;
*(seperation_s.vector + 1) *= force_mag;
*(seperation_s.vector + 2) *= force_mag;
forces[atom_one][0] += *(seperation_s.vector + 0);
forces[atom_one][1] += *(seperation_s.vector + 1);
forces[atom_one][2] += *(seperation_s.vector + 2);
forces[atom_two][0] -= *(seperation_s.vector + 0);
forces[atom_two][1] -= *(seperation_s.vector + 1);
forces[atom_two][2] -= *(seperation_s.vector + 2);
#ifdef BASE_NONBONDED_DEBUG
AdNonbondedForceLog("GRF", "A", atomOne, atomTwo, lennardJonesA, lennardJonesB,
chargeProduct, separation_s.length, est_hold,
(lennardJonesA - lennardJonesB), forceMag,
__GRFNonbondedForceDebug__);
#endif
}
inline void AdShiftedCoulombAndLennardJonesAEnergy(ListElement* interaction,
double** coordinates,
double EPSILON_RP,
double cut,
double r_cutoff2,
double* vdw_pot,
double* est_pot)
{
int atom_one, atom_two;
double length_rec, vdw_hold, est_hold;
double shift_fac;
double lennardJonesA, lennardJonesB, chargeProduct;
Vector3D seperation_s;
atom_one = interaction->bond[0];
atom_two = interaction->bond[1];
lennardJonesA = interaction->params[0];
lennardJonesB = interaction->params[1];
chargeProduct = interaction->params[2];
*(seperation_s.vector + 0) = coordinates[atom_one][0] - coordinates[atom_two][0];
*(seperation_s.vector + 1) = coordinates[atom_one][1] - coordinates[atom_two][1];
*(seperation_s.vector + 2) = coordinates[atom_one][2] - coordinates[atom_two][2];
Ad3DVectorLength(&seperation_s);
if(seperation_s.length > cut)
return;
interaction->length = seperation_s.length;
length_rec = 1/seperation_s.length;
vdw_hold = pow(length_rec, 6);
est_hold = (EPSILON_RP*chargeProduct*length_rec);
//est shift factor
shift_fac = (cut - seperation_s.length)*(cut - seperation_s.length)*r_cutoff2;
lennardJonesA *= vdw_hold*vdw_hold;
lennardJonesB *= vdw_hold;
//modify the potential by the shift function
*est_pot += (est_hold*shift_fac);
*vdw_pot += lennardJonesA - lennardJonesB;
#ifdef BASE_NONBONDED_DEBUG
AdNonbondedEnergyLog("Shifted", "A", atomOne, atomTwo, lennardJonesA, lennardJonesB,
chargeProduct, separation_s.length, est_hold, (lennardJonesA - lennardJonesB),
__ShiftedNonbondedEnergyDebug__);
#endif
}
inline void AdGRFCoulombAndLennardJonesAEnergy(ListElement* interaction,
double** coordinates,
double EPSILON_RP,
double cutoff,
double b0,
double b1,
double* vdw_pot,
double* est_pot)
{
int atom_one, atom_two;
double length_rec, vdw_hold, est_hold;
double lennardJonesA, lennardJonesB, chargeProduct;
Vector3D seperation_s;
atom_one = interaction->bond[0];
atom_two = interaction->bond[1];
lennardJonesA = interaction->params[0];
lennardJonesB = interaction->params[1];
chargeProduct = interaction->params[2];
*(seperation_s.vector + 0) = coordinates[atom_one][0] - coordinates[atom_two][0];
*(seperation_s.vector + 1) = coordinates[atom_one][1] - coordinates[atom_two][1];
*(seperation_s.vector + 2) = coordinates[atom_one][2] - coordinates[atom_two][2];
Ad3DVectorLength(&seperation_s);
if(seperation_s.length > cutoff)
return;
interaction->length = seperation_s.length;
length_rec = 1/seperation_s.length;
vdw_hold = pow(length_rec, 6);
est_hold = EPSILON_RP*chargeProduct*(length_rec + b0);
lennardJonesA *= vdw_hold*vdw_hold;
lennardJonesB *= vdw_hold;
*est_pot += est_hold;
*vdw_pot += lennardJonesA - lennardJonesB;
#ifdef BASE_NONBONDED_DEBUG
AdNonbondedEnergyLog("GRF", "A", atomOne, atomTwo, lennardJonesA, lennardJonesB,
chargeProduct, separation_s.length, est_hold, (lennardJonesA - lennardJonesB),
__GRFNonbondedEnergyDebug__);
#endif
}
/*
inline void AdCoulombAndLennardJonesAForce(ListElement* interaction,
double** coordinates,
double** forces,
double EPSILON_RP,
double* vdw_pot,
double* est_pot)
{
int atom_one, atom_two;
double force_mag;
double length_rec, vdw_hold, est_hold;
double lennardJonesA, lennardJonesB, chargeProduct;
Vector3D seperation_s;
atom_one = interaction->bond[0];
atom_two = interaction->bond[1];
lennardJonesA = interaction->params[0];
lennardJonesB = interaction->params[1];
chargeProduct = interaction->params[2];
//calculate seperation vector (r1 - r2)
*(seperation_s.vector + 0) = coordinates[atom_one][0] - coordinates[atom_two][0];
*(seperation_s.vector + 1) = coordinates[atom_one][1] - coordinates[atom_two][1];
*(seperation_s.vector + 2) = coordinates[atom_one][2] - coordinates[atom_two][2];
//calculate the interatomic distance
Ad3DVectorLength(&seperation_s);
//add this length to the linked list wlement the bond belongs to
interaction->length = seperation_s.length;
//get reciprocal of seperation
length_rec = 1/seperation_s.length;
//calculate vdw holder
e = _mm_mul(d,d);
f = _mm_mul(d,d);
g = __mm_mul(d,d);
e = __mm_mul(f,e);
g = __mm_mul(g,e)
//while this is being calculate
//calculate some non dependant variables
//est holder
est_hold = _mm_mul(EPSILON_RP, chargeProduct);
est_hold = __mm_mul(est_hold, length_rec);
//vdw holder may be finished now so calculate vdw consts
lennardJonesA *= __mm_mul(lennardJonesA, vdw_hold)
lennardJonesB *= __mm_mul(lennardJonesB, vdw_hold)
lennardJonesA *= __mm_mul(lennardJonesA, vdw_hold)
*est_pot += est_hold;
*vdw_pot += lennardJonesA - lennardJonesB;
force_mag = __mm_mul(est_hold, length_rec);
//add the vdw force to the est force
force_mag += 6*length_rec*(2*lennardJonesA - lennardJonesB);
force_mag *= length_rec;
//calculate the force on atom one along the vector (r1 - r2)
//the force on atom two is the opposite of this force
*(seperation_s.vector + 0) *= force_mag;
*(seperation_s.vector + 1) *= force_mag;
*(seperation_s.vector + 2) *= force_mag;
forces[atom_one][0] += *(seperation_s.vector + 0);
forces[atom_one][1] += *(seperation_s.vector + 1);
forces[atom_one][2] += *(seperation_s.vector + 2);
forces[atom_two][0] -= *(seperation_s.vector + 0);
forces[atom_two][1] -= *(seperation_s.vector + 1);
forces[atom_two][2] -= *(seperation_s.vector + 2);
}
*/
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