/
cljshiftfunction.cpp
7033 lines (5783 loc) · 293 KB
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cljshiftfunction.cpp
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/********************************************\
*
* Sire - Molecular Simulation Framework
*
* Copyright (C) 2014 Christopher Woods
*
* This program 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 program 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
* For full details of the license please see the COPYING file
* that should have come with this distribution.
*
* You can contact the authors via the developer's mailing list
* at http://siremol.org
*
\*********************************************/
#include "cljshiftfunction.h"
#include "SireMaths/multifloat.h"
#include "SireMaths/multidouble.h"
#include "SireMaths/multiint.h"
#include "SireUnits/units.h"
#include "SireError/errors.h"
#include "SireStream/datastream.h"
#include "SireStream/shareddatastream.h"
#include "SireVol/gridinfo.h"
#include <QElapsedTimer>
#include <QDebug>
using namespace SireMM;
using namespace SireMaths;
using namespace SireVol;
using namespace SireBase;
using namespace SireUnits;
using namespace SireStream;
/////////
///////// Implementation of CLJShiftFunction
/////////
static const RegisterMetaType<CLJShiftFunction> r_shift;
QDataStream &operator<<(QDataStream &ds, const CLJShiftFunction &func)
{
writeHeader(ds, r_shift, 1);
ds << static_cast<const CLJCutoffFunction&>(func);
return ds;
}
QDataStream &operator>>(QDataStream &ds, CLJShiftFunction &func)
{
VersionID v = readHeader(ds, r_shift);
if (v == 1)
{
ds >> static_cast<CLJCutoffFunction&>(func);
}
else
throw version_error(v, "1", r_shift, CODELOC);
return ds;
}
CLJShiftFunction::CLJShiftFunction()
: ConcreteProperty<CLJShiftFunction,CLJCutoffFunction>()
{}
CLJFunctionPtr CLJShiftFunction::defaultShiftFunction()
{
static CLJFunctionPtr ptr( new CLJShiftFunction() );
return ptr;
}
CLJShiftFunction::CLJShiftFunction(Length cutoff)
: ConcreteProperty<CLJShiftFunction,CLJCutoffFunction>(cutoff)
{}
CLJShiftFunction::CLJShiftFunction(Length coul_cutoff, Length lj_cutoff)
: ConcreteProperty<CLJShiftFunction,CLJCutoffFunction>(coul_cutoff, lj_cutoff)
{}
CLJShiftFunction::CLJShiftFunction(const Space &space, Length cutoff)
: ConcreteProperty<CLJShiftFunction,CLJCutoffFunction>(space, cutoff)
{}
CLJShiftFunction::CLJShiftFunction(const Space &space, Length coul_cutoff, Length lj_cutoff)
: ConcreteProperty<CLJShiftFunction,CLJCutoffFunction>(space, coul_cutoff,
lj_cutoff)
{}
CLJShiftFunction::CLJShiftFunction(Length cutoff, COMBINING_RULES combining_rules)
: ConcreteProperty<CLJShiftFunction,CLJCutoffFunction>(cutoff, combining_rules)
{}
CLJShiftFunction::CLJShiftFunction(Length coul_cutoff, Length lj_cutoff,
COMBINING_RULES combining_rules)
: ConcreteProperty<CLJShiftFunction,CLJCutoffFunction>(
coul_cutoff, lj_cutoff, combining_rules)
{}
CLJShiftFunction::CLJShiftFunction(const Space &space, COMBINING_RULES combining_rules)
: ConcreteProperty<CLJShiftFunction,CLJCutoffFunction>(space, combining_rules)
{}
CLJShiftFunction::CLJShiftFunction(const Space &space, Length cutoff,
COMBINING_RULES combining_rules)
: ConcreteProperty<CLJShiftFunction,CLJCutoffFunction>(
space, cutoff, combining_rules)
{}
CLJShiftFunction::CLJShiftFunction(const Space &space, Length coul_cutoff, Length lj_cutoff,
COMBINING_RULES combining_rules)
: ConcreteProperty<CLJShiftFunction,CLJCutoffFunction>(
space, coul_cutoff, lj_cutoff, combining_rules)
{}
/** Copy constructor */
CLJShiftFunction::CLJShiftFunction(const CLJShiftFunction &other)
: ConcreteProperty<CLJShiftFunction,CLJCutoffFunction>(other)
{}
/** Destructor */
CLJShiftFunction::~CLJShiftFunction()
{}
/** Copy assignment operator */
CLJShiftFunction& CLJShiftFunction::operator=(const CLJShiftFunction &other)
{
CLJCutoffFunction::operator=(other);
return *this;
}
/** Comparison operator */
bool CLJShiftFunction::operator==(const CLJShiftFunction &other) const
{
return CLJCutoffFunction::operator==(other);
}
/** Comparison operator */
bool CLJShiftFunction::operator!=(const CLJShiftFunction &other) const
{
return not operator==(other);
}
const char* CLJShiftFunction::typeName()
{
return QMetaType::typeName( qMetaTypeId<CLJShiftFunction>() );
}
const char* CLJShiftFunction::what() const
{
return CLJShiftFunction::typeName();
}
CLJShiftFunction* CLJShiftFunction::clone() const
{
return new CLJShiftFunction(*this);
}
QString CLJShiftFunction::toString() const
{
if (this->hasCutoff())
return QObject::tr("CLJShiftFunction( coulombCutoff() == %1 A, "
"ljCutoff() == %2 A, space() == %3 )")
.arg(coulombCutoff().to(angstrom))
.arg(ljCutoff().to(angstrom))
.arg(space().toString());
else
return QObject::tr("CLJShiftFunction( no cutoff, space() == %1 )")
.arg(space().toString());
}
/** Calculate the coulomb and LJ intermolecular energy of all of the atoms in 'atoms',
returning the results in the arguments 'cnrg' and 'ljnrg' */
void CLJShiftFunction::calcVacEnergyGeo(const CLJAtoms &atoms,
double &cnrg, double &ljnrg) const
{
const MultiFloat *xa = atoms.x().constData();
const MultiFloat *ya = atoms.y().constData();
const MultiFloat *za = atoms.z().constData();
const MultiFloat *qa = atoms.q().constData();
const MultiFloat *siga = atoms.sigma().constData();
const MultiFloat *epsa = atoms.epsilon().constData();
const MultiInt *ida = atoms.ID().constData();
const MultiFloat Rc(coul_cutoff);
const MultiFloat Rlj(lj_cutoff);
const MultiFloat one_over_Rc( 1.0 / coul_cutoff );
const MultiFloat one_over_Rc2( 1.0 / (coul_cutoff*coul_cutoff) );
const MultiFloat half(0.5);
const MultiInt dummy_id = CLJAtoms::idOfDummy();
const qint32 dummy_int = dummy_id[0];
MultiFloat tmp, r, one_over_r, sig2_over_r2, sig6_over_r6;
MultiDouble icnrg(0), iljnrg(0);
MultiInt itmp;
int n = atoms.x().count();
for (int i=0; i<n; ++i)
{
for (int ii=0; ii<MultiFloat::size(); ++ii)
{
if (ida[i][ii] != dummy_int)
{
const MultiInt id( ida[i][ii] );
const MultiFloat x( xa[i][ii] );
const MultiFloat y( ya[i][ii] );
const MultiFloat z( za[i][ii] );
if (qa[i][ii] != 0)
{
const MultiFloat q( qa[i][ii] );
if (epsa[i][ii] == 0)
{
//coulomb calculation only
for (int j=i; j<n; ++j)
{
// if i == j then we double-calculate the energies, so must
// scale them by 0.5
const MultiFloat scale( i == j ? 0.5 : 1.0 );
//calculate the distance between the fixed and mobile atoms
tmp = xa[j] - x;
r = tmp * tmp;
tmp = ya[j] - y;
r.multiplyAdd(tmp, tmp);
tmp = za[j] - z;
r.multiplyAdd(tmp, tmp);
r = r.sqrt();
one_over_r = r.reciprocal();
//calculate the coulomb energy using shift-electrostatics
// energy = q0q1 * { 1/r - 1/Rc + 1/Rc^2 [r - Rc] }
tmp = r - Rc;
tmp *= one_over_Rc2;
tmp -= one_over_Rc;
tmp += one_over_r;
tmp *= q * qa[j];
//apply the cutoff - compare r against Rc. This will
//return 1 if r is less than Rc, or 0 otherwise. Logical
//and will then remove all energies where r >= Rc
tmp &= r.compareLess(Rc);
//make sure that the ID of atoms1 is not zero, and is
//also not the same as the atoms0.
itmp = ida[j].compareEqual(dummy_id);
itmp |= ida[j].compareEqual(id);
icnrg += scale * tmp.logicalAndNot(itmp);
}
}
else
{
//calculate both coulomb and LJ
const MultiFloat sig( siga[i][ii] );
const MultiFloat eps( epsa[i][ii] );
for (int j=i; j<n; ++j)
{
// if i == j then we double-calculate the energies, so must
// scale them by 0.5
const MultiFloat scale( i == j ? 0.5 : 1.0 );
//calculate the distance between the fixed and mobile atoms
tmp = xa[j] - x;
r = tmp * tmp;
tmp = ya[j] - y;
r.multiplyAdd(tmp, tmp);
tmp = za[j] - z;
r.multiplyAdd(tmp, tmp);
r = r.sqrt();
one_over_r = r.reciprocal();
//calculate the coulomb energy using shift-electrostatics
// energy = q0q1 * { 1/r - 1/Rc + 1/Rc^2 [r - Rc] }
tmp = r - Rc;
tmp *= one_over_Rc2;
tmp -= one_over_Rc;
tmp += one_over_r;
tmp *= q * qa[j];
//apply the cutoff - compare r against Rc. This will
//return 1 if r is less than Rc, or 0 otherwise. Logical
//and will then remove all energies where r >= Rc
tmp &= r.compareLess(Rc);
//make sure that the ID of atoms1 is not zero, and is
//also not the same as the atoms0.
itmp = ida[j].compareEqual(dummy_id);
itmp |= ida[j].compareEqual(id);
icnrg += scale * tmp.logicalAndNot(itmp);
//now the LJ energy
sig2_over_r2 = sig * siga[j] * one_over_r;
sig2_over_r2 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig6_over_r6*sig2_over_r2;
tmp = sig6_over_r6 * sig6_over_r6;
tmp -= sig6_over_r6;
tmp *= eps;
tmp *= epsa[j];
//apply the cutoff - compare r against Rlj. This will
//return 1 if r is less than Rlj, or 0 otherwise. Logical
//and will then remove all energies where r >= Rlj
tmp &= r.compareLess(Rlj);
iljnrg += scale * tmp.logicalAndNot(itmp);
}
}
}
else
{
//LJ calculation only
const MultiFloat sig( siga[i][ii] );
const MultiFloat eps( epsa[i][ii] );
for (int j=i; j<n; ++j)
{
// if i == j then we double-calculate the energies, so must
// scale them by 0.5
const MultiFloat scale( i == j ? 0.5 : 1.0 );
//calculate the distance between the fixed and mobile atoms
tmp = xa[j] - x;
r = tmp * tmp;
tmp = ya[j] - y;
r.multiplyAdd(tmp, tmp);
tmp = za[j] - z;
r.multiplyAdd(tmp, tmp);
r = r.sqrt();
one_over_r = r.reciprocal();
sig2_over_r2 = sig * siga[j] * one_over_r;
sig2_over_r2 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig6_over_r6*sig2_over_r2;
tmp = sig6_over_r6 * sig6_over_r6;
tmp -= sig6_over_r6;
tmp *= eps;
tmp *= epsa[j];
//apply the cutoff - compare r against Rlj. This will
//return 1 if r is less than Rlj, or 0 otherwise. Logical
//and will then remove all energies where r >= Rlj
tmp &= r.compareLess(Rlj);
iljnrg += scale * tmp.logicalAndNot(itmp);
}
}
}
}
}
cnrg = icnrg.sum();
ljnrg = iljnrg.sum();
}
/** Calculate the intermolecular energy between all atoms in 'atoms0' and all
atoms in 'atoms1', returning the result in the arguments 'cnrg' and 'ljnrg' */
void CLJShiftFunction::calcVacEnergyGeo(const CLJAtoms &atoms0, const CLJAtoms &atoms1,
double &cnrg, double &ljnrg, float min_distance) const
{
const MultiFloat *x0 = atoms0.x().constData();
const MultiFloat *y0 = atoms0.y().constData();
const MultiFloat *z0 = atoms0.z().constData();
const MultiFloat *q0 = atoms0.q().constData();
const MultiFloat *sig0 = atoms0.sigma().constData();
const MultiFloat *eps0 = atoms0.epsilon().constData();
const MultiInt *id0 = atoms0.ID().constData();
const MultiFloat *x1 = atoms1.x().constData();
const MultiFloat *y1 = atoms1.y().constData();
const MultiFloat *z1 = atoms1.z().constData();
const MultiFloat *q1 = atoms1.q().constData();
const MultiFloat *sig1 = atoms1.sigma().constData();
const MultiFloat *eps1 = atoms1.epsilon().constData();
const MultiInt *id1 = atoms1.ID().constData();
const MultiFloat Rc(coul_cutoff);
const MultiFloat Rlj(lj_cutoff);
const MultiFloat one_over_Rc( 1.0 / coul_cutoff );
const MultiFloat one_over_Rc2( 1.0 / (coul_cutoff*coul_cutoff) );
const MultiFloat half(0.5);
const MultiInt dummy_id = CLJAtoms::idOfDummy();
const qint32 dummy_int = dummy_id[0];
MultiFloat tmp, r, one_over_r, sig2_over_r2, sig6_over_r6;
MultiDouble icnrg(0), iljnrg(0);
MultiInt itmp;
const int n0 = atoms0.x().count();
const int n1 = atoms1.x().count();
for (int i=0; i<n0; ++i)
{
for (int ii=0; ii<MultiFloat::count(); ++ii)
{
if (id0[i][ii] != dummy_int)
{
const MultiInt id(id0[i][ii]);
if (q0[i][ii] != 0)
{
const MultiFloat x(x0[i][ii]);
const MultiFloat y(y0[i][ii]);
const MultiFloat z(z0[i][ii]);
const MultiFloat q(q0[i][ii]);
if (eps0[i][ii] == 0)
{
//coulomb energy only
for (int j=0; j<n1; ++j)
{
//calculate the distance between the fixed and mobile atoms
tmp = x1[j] - x;
r = tmp * tmp;
tmp = y1[j] - y;
r.multiplyAdd(tmp, tmp);
tmp = z1[j] - z;
r.multiplyAdd(tmp, tmp);
r = r.sqrt();
one_over_r = r.reciprocal();
//calculate the coulomb energy using shift-electrostatics
// energy = q0q1 * { 1/r - 1/Rc + 1/Rc^2 [r - Rc] }
tmp = r - Rc;
tmp *= one_over_Rc2;
tmp -= one_over_Rc;
tmp += one_over_r;
tmp *= q * q1[j];
//apply the cutoff - compare r against Rc. This will
//return 1 if r is less than Rc, or 0 otherwise. Logical
//and will then remove all energies where r >= Rc
tmp &= r.compareLess(Rc);
//make sure that the ID of atoms1 is not zero, and is
//also not the same as the atoms0.
itmp = id1[j].compareEqual(dummy_id);
itmp |= id1[j].compareEqual(id);
icnrg += tmp.logicalAndNot(itmp);
}
}
else
{
const MultiFloat sig(sig0[i][ii]);
const MultiFloat eps(eps0[i][ii]);
for (int j=0; j<n1; ++j)
{
//calculate the distance between the fixed and mobile atoms
tmp = x1[j] - x;
r = tmp * tmp;
tmp = y1[j] - y;
r.multiplyAdd(tmp, tmp);
tmp = z1[j] - z;
r.multiplyAdd(tmp, tmp);
r = r.sqrt();
one_over_r = r.reciprocal();
//calculate the coulomb energy using shift-electrostatics
// energy = q0q1 * { 1/r - 1/Rc + 1/Rc^2 [r - Rc] }
tmp = r - Rc;
tmp *= one_over_Rc2;
tmp -= one_over_Rc;
tmp += one_over_r;
tmp *= q * q1[j];
//apply the cutoff - compare r against Rc. This will
//return 1 if r is less than Rc, or 0 otherwise. Logical
//and will then remove all energies where r >= Rc
tmp &= r.compareLess(Rc);
//make sure that the ID of atoms1 is not zero, and is
//also not the same as the atoms0.
//logical and will remove all energies where id1 == 0 or id0 == id1
itmp = id1[j].compareEqual(dummy_id);
itmp |= id1[j].compareEqual(id);
icnrg += tmp.logicalAndNot(itmp);
//Now do the LJ energy
//arithmetic combining rules
sig2_over_r2 = sig * sig1[j] * one_over_r;
sig2_over_r2 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig6_over_r6*sig2_over_r2;
tmp = sig6_over_r6 * sig6_over_r6;
tmp -= sig6_over_r6;
tmp *= eps;
tmp *= eps1[j];
//apply the cutoff - compare r against Rlj. This will
//return 1 if r is less than Rlj, or 0 otherwise. Logical
//and will then remove all energies where r >= Rlj
tmp &= r.compareLess(Rlj);
iljnrg += tmp.logicalAndNot(itmp);
}
}
}
else if (eps0[i][ii] != 0)
{
//LJ energy only
const MultiFloat x(x0[i][ii]);
const MultiFloat y(y0[i][ii]);
const MultiFloat z(z0[i][ii]);
const MultiFloat sig(sig0[i][ii]);
const MultiFloat eps(eps0[i][ii]);
for (int j=0; j<n1; ++j)
{
//calculate the distance between the fixed and mobile atoms
tmp = x1[j] - x;
r = tmp * tmp;
tmp = y1[j] - y;
r.multiplyAdd(tmp, tmp);
tmp = z1[j] - z;
r.multiplyAdd(tmp, tmp);
r = r.sqrt();
one_over_r = r.reciprocal();
//arithmetic combining rules
sig2_over_r2 = sig * sig1[j] * one_over_r;
sig2_over_r2 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig6_over_r6*sig2_over_r2;
tmp = sig6_over_r6 * sig6_over_r6;
tmp -= sig6_over_r6;
tmp *= eps;
tmp *= eps1[j];
//apply the cutoff - compare r against Rlj. This will
//return 1 if r is less than Rlj, or 0 otherwise. Logical
//and will then remove all energies where r >= Rlj
tmp &= r.compareLess(Rlj);
itmp = id1[j].compareEqual(dummy_id);
itmp |= id1[j].compareEqual(id);
iljnrg += tmp.logicalAndNot(itmp);
}
}
}
}
}
cnrg = icnrg.sum();
ljnrg = iljnrg.sum();
}
/** Calculate the coulomb and LJ intermolecular energy of all of the atoms in 'atoms',
assuming periodic boundary conditions in a cubic box of size 'box_dimensions',
returning the results in 'cnrg' and 'ljnrg' */
void CLJShiftFunction::calcBoxEnergyGeo(const CLJAtoms &atoms, const Vector &box_dimensions,
double &cnrg, double &ljnrg) const
{
const MultiFloat *xa = atoms.x().constData();
const MultiFloat *ya = atoms.y().constData();
const MultiFloat *za = atoms.z().constData();
const MultiFloat *qa = atoms.q().constData();
const MultiFloat *siga = atoms.sigma().constData();
const MultiFloat *epsa = atoms.epsilon().constData();
const MultiInt *ida = atoms.ID().constData();
const MultiFloat Rc(coul_cutoff);
const MultiFloat Rlj(lj_cutoff);
const MultiFloat one_over_Rc( 1.0 / coul_cutoff );
const MultiFloat one_over_Rc2( 1.0 / (coul_cutoff*coul_cutoff) );
const MultiFloat half(0.5);
const MultiInt dummy_id = CLJAtoms::idOfDummy();
const qint32 dummy_int = dummy_id[0];
MultiFloat tmp, r, one_over_r, sig2_over_r2, sig6_over_r6;
MultiDouble icnrg(0), iljnrg(0);
MultiInt itmp;
const MultiFloat box_x( box_dimensions.x() );
const MultiFloat box_y( box_dimensions.y() );
const MultiFloat box_z( box_dimensions.z() );
const MultiFloat half_box_x( 0.5 * box_dimensions.x() );
const MultiFloat half_box_y( 0.5 * box_dimensions.y() );
const MultiFloat half_box_z( 0.5 * box_dimensions.z() );
int n = atoms.x().count();
for (int i=0; i<n; ++i)
{
for (int ii=0; ii<MultiFloat::size(); ++ii)
{
if (ida[i][ii] != dummy_int)
{
const MultiInt id( ida[i][ii] );
const MultiFloat x( xa[i][ii] );
const MultiFloat y( ya[i][ii] );
const MultiFloat z( za[i][ii] );
const MultiFloat q( qa[i][ii] );
const MultiFloat sig( siga[i][ii] );
const MultiFloat eps( epsa[i][ii] );
for (int j=i; j<n; ++j)
{
// if i == j then we double-calculate the energies, so must
// scale them by 0.5
const MultiFloat scale( i == j ? 0.5 : 1.0 );
tmp = xa[j] - x;
tmp &= MULTIFLOAT_POS_MASK; // this creates the absolute value :-)
tmp -= box_x.logicalAnd( half_box_x.compareLess(tmp) );
r = tmp * tmp;
tmp = ya[j] - y;
tmp &= MULTIFLOAT_POS_MASK; // this creates the absolute value :-)
tmp -= box_y.logicalAnd( half_box_y.compareLess(tmp) );
r.multiplyAdd(tmp, tmp);
tmp = za[j] - z;
tmp &= MULTIFLOAT_POS_MASK; // this creates the absolute value :-)
tmp -= box_z.logicalAnd( half_box_z.compareLess(tmp) );
r.multiplyAdd(tmp, tmp);
r = r.sqrt();
one_over_r = r.reciprocal();
//calculate the coulomb energy using shift-electrostatics
// energy = q0q1 * { 1/r - 1/Rc + 1/Rc^2 [r - Rc] }
tmp = r - Rc;
tmp *= one_over_Rc2;
tmp -= one_over_Rc;
tmp += one_over_r;
tmp *= q * qa[j];
//apply the cutoff - compare r against Rc. This will
//return 1 if r is less than Rc, or 0 otherwise. Logical
//and will then remove all energies where r >= Rc
tmp &= r.compareLess(Rc);
//make sure that the ID of atoms1 is not zero, and is
//also not the same as the atoms0.
itmp = ida[j].compareEqual(dummy_id);
itmp |= ida[j].compareEqual(id);
icnrg += scale * tmp.logicalAndNot(itmp);
//now the LJ energy
sig2_over_r2 = sig * siga[j] * one_over_r;
sig2_over_r2 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig6_over_r6*sig2_over_r2;
tmp = sig6_over_r6 * sig6_over_r6;
tmp -= sig6_over_r6;
tmp *= eps;
tmp *= epsa[j];
//apply the cutoff - compare r against Rlj. This will
//return 1 if r is less than Rlj, or 0 otherwise. Logical
//and will then remove all energies where r >= Rlj
tmp &= r.compareLess(Rlj);
iljnrg += scale * tmp.logicalAndNot(itmp);
}
}
}
}
cnrg = icnrg.sum();
ljnrg = iljnrg.sum();
}
/** Calculate the intermolecular energy between all atoms in 'atoms0' and all
atoms in 'atoms1', assuming periodic boundary conditions in a cubic box
of size 'box_dimensions, returning the result in the arguments 'cnrg' and 'ljnrg' */
void CLJShiftFunction::calcBoxEnergyGeo(const CLJAtoms &atoms0, const CLJAtoms &atoms1,
const Vector &box_dimensions,
double &cnrg, double &ljnrg, float min_distance) const
{
const MultiFloat *x0 = atoms0.x().constData();
const MultiFloat *y0 = atoms0.y().constData();
const MultiFloat *z0 = atoms0.z().constData();
const MultiFloat *q0 = atoms0.q().constData();
const MultiFloat *sig0 = atoms0.sigma().constData();
const MultiFloat *eps0 = atoms0.epsilon().constData();
const MultiInt *id0 = atoms0.ID().constData();
const MultiFloat *x1 = atoms1.x().constData();
const MultiFloat *y1 = atoms1.y().constData();
const MultiFloat *z1 = atoms1.z().constData();
const MultiFloat *q1 = atoms1.q().constData();
const MultiFloat *sig1 = atoms1.sigma().constData();
const MultiFloat *eps1 = atoms1.epsilon().constData();
const MultiInt *id1 = atoms1.ID().constData();
const MultiFloat Rc(coul_cutoff);
const MultiFloat Rlj(lj_cutoff);
const MultiFloat one_over_Rc( 1.0 / coul_cutoff );
const MultiFloat one_over_Rc2( 1.0 / (coul_cutoff*coul_cutoff) );
const MultiFloat half(0.5);
const MultiInt dummy_id = CLJAtoms::idOfDummy();
const qint32 dummy_int = dummy_id[0];
MultiFloat tmp, r, one_over_r, sig2_over_r2, sig6_over_r6;
MultiDouble icnrg(0), iljnrg(0);
MultiInt itmp;
const MultiFloat box_x( box_dimensions.x() );
const MultiFloat box_y( box_dimensions.y() );
const MultiFloat box_z( box_dimensions.z() );
const MultiFloat half_box_x( 0.5 * box_dimensions.x() );
const MultiFloat half_box_y( 0.5 * box_dimensions.y() );
const MultiFloat half_box_z( 0.5 * box_dimensions.z() );
const int n0 = atoms0.x().count();
const int n1 = atoms1.x().count();
for (int i=0; i<n0; ++i)
{
for (int ii=0; ii<MultiFloat::count(); ++ii)
{
if (id0[i][ii] != dummy_int)
{
const MultiInt id(id0[i][ii]);
const MultiFloat x(x0[i][ii]);
const MultiFloat y(y0[i][ii]);
const MultiFloat z(z0[i][ii]);
const MultiFloat q(q0[i][ii]);
const MultiFloat sig(sig0[i][ii]);
const MultiFloat eps(eps0[i][ii]);
for (int j=0; j<n1; ++j)
{
tmp = x1[j] - x;
tmp &= MULTIFLOAT_POS_MASK; // this creates the absolute value :-)
tmp -= box_x.logicalAnd( half_box_x.compareLess(tmp) );
r = tmp * tmp;
tmp = y1[j] - y;
tmp &= MULTIFLOAT_POS_MASK; // this creates the absolute value :-)
tmp -= box_y.logicalAnd( half_box_y.compareLess(tmp) );
r.multiplyAdd(tmp, tmp);
tmp = z1[j] - z;
tmp &= MULTIFLOAT_POS_MASK; // this creates the absolute value :-)
tmp -= box_z.logicalAnd( half_box_z.compareLess(tmp) );
r.multiplyAdd(tmp, tmp);
r = r.sqrt();
one_over_r = r.reciprocal();
//calculate the coulomb energy using shift-electrostatics
// energy = q0q1 * { 1/r - 1/Rc + 1/Rc^2 [r - Rc] }
tmp = r - Rc;
tmp *= one_over_Rc2;
tmp -= one_over_Rc;
tmp += one_over_r;
tmp *= q * q1[j];
//apply the cutoff - compare r against Rc. This will
//return 1 if r is less than Rc, or 0 otherwise. Logical
//and will then remove all energies where r >= Rc
tmp &= r.compareLess(Rc);
//make sure that the ID of atoms1 is not zero, and is
//also not the same as the atoms0.
//logical and will remove all energies where id1 == 0 or id0 == id1
itmp = id1[j].compareEqual(dummy_id);
itmp |= id1[j].compareEqual(id);
icnrg += tmp.logicalAndNot(itmp);
//Now do the LJ energy
//arithmetic combining rules
sig2_over_r2 = sig * sig1[j] * one_over_r;
sig2_over_r2 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig6_over_r6*sig2_over_r2;
tmp = sig6_over_r6 * sig6_over_r6;
tmp -= sig6_over_r6;
tmp *= eps;
tmp *= eps1[j];
//apply the cutoff - compare r against Rlj. This will
//return 1 if r is less than Rlj, or 0 otherwise. Logical
//and will then remove all energies where r >= Rlj
tmp &= r.compareLess(Rlj);
iljnrg += tmp.logicalAndNot(itmp);
}
}
}
}
cnrg = icnrg.sum();
ljnrg = iljnrg.sum();
}
/** Calculate the coulomb and LJ intermolecular energy of all of the atoms in 'atoms',
returning the results in the arguments 'cnrg' and 'ljnrg' */
void CLJShiftFunction::calcVacEnergyAri(const CLJAtoms &atoms,
double &cnrg, double &ljnrg) const
{
const MultiFloat *xa = atoms.x().constData();
const MultiFloat *ya = atoms.y().constData();
const MultiFloat *za = atoms.z().constData();
const MultiFloat *qa = atoms.q().constData();
const MultiFloat *siga = atoms.sigma().constData();
const MultiFloat *epsa = atoms.epsilon().constData();
const MultiInt *ida = atoms.ID().constData();
const MultiFloat Rc(coul_cutoff);
const MultiFloat Rlj(lj_cutoff);
const MultiFloat one_over_Rc( 1.0 / coul_cutoff );
const MultiFloat one_over_Rc2( 1.0 / (coul_cutoff*coul_cutoff) );
const MultiFloat half(0.5);
const MultiInt dummy_id = CLJAtoms::idOfDummy();
const qint32 dummy_int = dummy_id[0];
MultiFloat tmp, r, one_over_r, sig2_over_r2, sig6_over_r6;
MultiDouble icnrg(0), iljnrg(0);
MultiInt itmp;
int n = atoms.x().count();
for (int i=0; i<n; ++i)
{
for (int ii=0; ii<MultiFloat::size(); ++ii)
{
if (ida[i][ii] != dummy_int)
{
const MultiInt id( ida[i][ii] );
const MultiFloat x( xa[i][ii] );
const MultiFloat y( ya[i][ii] );
const MultiFloat z( za[i][ii] );
if (qa[i][ii] != 0)
{
const MultiFloat q( qa[i][ii] );
if (epsa[i][ii] == 0)
{
//coulomb calculation only
for (int j=i; j<n; ++j)
{
// if i == j then we double-calculate the energies, so must
// scale them by 0.5
const MultiFloat scale( i == j ? 0.5 : 1.0 );
//calculate the distance between the fixed and mobile atoms
tmp = xa[j] - x;
r = tmp * tmp;
tmp = ya[j] - y;
r.multiplyAdd(tmp, tmp);
tmp = za[j] - z;
r.multiplyAdd(tmp, tmp);
r = r.sqrt();
one_over_r = r.reciprocal();
//calculate the coulomb energy using shift-electrostatics
// energy = q0q1 * { 1/r - 1/Rc + 1/Rc^2 [r - Rc] }
tmp = r - Rc;
tmp *= one_over_Rc2;
tmp -= one_over_Rc;
tmp += one_over_r;
tmp *= q * qa[j];
//apply the cutoff - compare r against Rc. This will
//return 1 if r is less than Rc, or 0 otherwise. Logical
//and will then remove all energies where r >= Rc
tmp &= r.compareLess(Rc);
//make sure that the ID of atoms1 is not zero, and is
//also not the same as the atoms0.
itmp = ida[j].compareEqual(dummy_id);
itmp |= ida[j].compareEqual(id);
icnrg += scale * tmp.logicalAndNot(itmp);
}
}
else
{
//calculate both coulomb and LJ
const MultiFloat sig( siga[i][ii] * siga[i][ii] );
const MultiFloat eps( epsa[i][ii] );
for (int j=i; j<n; ++j)
{
// if i == j then we double-calculate the energies, so must
// scale them by 0.5
const MultiFloat scale( i == j ? 0.5 : 1.0 );
//calculate the distance between the fixed and mobile atoms
tmp = xa[j] - x;
r = tmp * tmp;
tmp = ya[j] - y;
r.multiplyAdd(tmp, tmp);
tmp = za[j] - z;
r.multiplyAdd(tmp, tmp);
r = r.sqrt();
one_over_r = r.reciprocal();
//calculate the coulomb energy using shift-electrostatics
// energy = q0q1 * { 1/r - 1/Rc + 1/Rc^2 [r - Rc] }
tmp = r - Rc;
tmp *= one_over_Rc2;
tmp -= one_over_Rc;
tmp += one_over_r;
tmp *= q * qa[j];
//apply the cutoff - compare r against Rc. This will
//return 1 if r is less than Rc, or 0 otherwise. Logical
//and will then remove all energies where r >= Rc
tmp &= r.compareLess(Rc);
//make sure that the ID of atoms1 is not zero, and is
//also not the same as the atoms0.
itmp = ida[j].compareEqual(dummy_id);
itmp |= ida[j].compareEqual(id);
icnrg += scale * tmp.logicalAndNot(itmp);
//now the LJ energy
tmp = sig + (siga[j]*siga[j]);
tmp *= half;
sig2_over_r2 = tmp * one_over_r;
sig2_over_r2 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig2_over_r2*sig2_over_r2;
sig6_over_r6 = sig6_over_r6*sig2_over_r2;
tmp = sig6_over_r6 * sig6_over_r6;
tmp -= sig6_over_r6;
tmp *= eps;
tmp *= epsa[j];
//apply the cutoff - compare r against Rlj. This will
//return 1 if r is less than Rlj, or 0 otherwise. Logical
//and will then remove all energies where r >= Rlj
tmp &= r.compareLess(Rlj);
iljnrg += scale * tmp.logicalAndNot(itmp);
}
}
}
else
{
//LJ calculation only
const MultiFloat sig( siga[i][ii] * siga[i][ii] );
const MultiFloat eps( epsa[i][ii] );
for (int j=i; j<n; ++j)
{
// if i == j then we double-calculate the energies, so must
// scale them by 0.5
const MultiFloat scale( i == j ? 0.5 : 1.0 );
//calculate the distance between the fixed and mobile atoms
tmp = xa[j] - x;
r = tmp * tmp;
tmp = ya[j] - y;