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Commit 41cd79a5 authored by peastman's avatar peastman
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Cleaned up formatting of AMOEBA reference code

parent 25a308e6
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Showing with 4541 additions and 4541 deletions
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.h
View file @ 41cd79a5
......@@ -40,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */
AmoebaReferenceTorsionTorsionForce( ){};
AmoebaReferenceTorsionTorsionForce() {};
/**---------------------------------------------------------------------------------------
......@@ -48,7 +48,7 @@ public:
--------------------------------------------------------------------------------------- */
~AmoebaReferenceTorsionTorsionForce( ){};
~AmoebaReferenceTorsionTorsionForce() {};
/**---------------------------------------------------------------------------------------
......@@ -71,16 +71,16 @@ public:
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numTorsionTorsions, std::vector<OpenMM::RealVec>& posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector<int>& particle5,
const std::vector<int>& chiralCheckAtom,
const std::vector<int>& gridIndices,
const std::vector< std::vector< std::vector< std::vector<RealOpenMM> > > >& torsionTorsionGrids,
std::vector<OpenMM::RealVec>& forceData ) const;
RealOpenMM calculateForceAndEnergy(int numTorsionTorsions, std::vector<OpenMM::RealVec>& posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
const std::vector<int>& particle4,
const std::vector<int>& particle5,
const std::vector<int>& chiralCheckAtom,
const std::vector<int>& gridIndices,
const std::vector< std::vector< std::vector< std::vector<RealOpenMM> > > >& torsionTorsionGrids,
std::vector<OpenMM::RealVec>& forceData) const;
private:
......@@ -105,7 +105,7 @@ private:
void loadGridValuesFromEnclosingRectangle(
const std::vector< std::vector< std::vector<RealOpenMM> > >& grid,
RealOpenMM angle1, RealOpenMM angle2, RealOpenMM corners[2][2],
RealOpenMM* fValues, RealOpenMM* fValues1, RealOpenMM* fValues2, RealOpenMM* fValues12 ) const;
RealOpenMM* fValues, RealOpenMM* fValues1, RealOpenMM* fValues2, RealOpenMM* fValues12) const;
/**---------------------------------------------------------------------------------------
......@@ -128,8 +128,8 @@ private:
--------------------------------------------------------------------------------------- */
void getBicubicCoefficientMatrix( const RealOpenMM* y, const RealOpenMM* y1, const RealOpenMM* y2, const RealOpenMM* y12,
const RealOpenMM d1, const RealOpenMM d2, RealOpenMM c[4][4] ) const;
void getBicubicCoefficientMatrix(const RealOpenMM* y, const RealOpenMM* y1, const RealOpenMM* y2, const RealOpenMM* y12,
const RealOpenMM d1, const RealOpenMM d2, RealOpenMM c[4][4]) const;
/**---------------------------------------------------------------------------------------
......@@ -167,7 +167,7 @@ private:
const RealOpenMM x1Lower, const RealOpenMM x1Upper,
const RealOpenMM x2Lower, const RealOpenMM x2Upper,
const RealOpenMM gridValue1, const RealOpenMM gridValue2,
RealOpenMM* functionValue, RealOpenMM* functionValue1, RealOpenMM* functionValue2 ) const;
RealOpenMM* functionValue, RealOpenMM* functionValue1, RealOpenMM* functionValue2) const;
/**---------------------------------------------------------------------------------------
......@@ -183,8 +183,8 @@ private:
--------------------------------------------------------------------------------------- */
int checkTorsionSign( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
const OpenMM::RealVec& positionAtomC, const OpenMM::RealVec& positionAtomD ) const;
int checkTorsionSign(const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
const OpenMM::RealVec& positionAtomC, const OpenMM::RealVec& positionAtomD) const;
/**---------------------------------------------------------------------------------------
......@@ -204,11 +204,11 @@ private:
--------------------------------------------------------------------------------------- */
RealOpenMM calculateTorsionTorsionIxn( const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
const OpenMM::RealVec& positionAtomC, const OpenMM::RealVec& positionAtomD,
const OpenMM::RealVec& positionAtomE, const OpenMM::RealVec* chiralCheckAtom,
const std::vector< std::vector< std::vector<RealOpenMM> > >& grid,
OpenMM::RealVec* forces ) const;
RealOpenMM calculateTorsionTorsionIxn(const OpenMM::RealVec& positionAtomA, const OpenMM::RealVec& positionAtomB,
const OpenMM::RealVec& positionAtomC, const OpenMM::RealVec& positionAtomD,
const OpenMM::RealVec& positionAtomE, const OpenMM::RealVec* chiralCheckAtom,
const std::vector< std::vector< std::vector<RealOpenMM> > >& grid,
OpenMM::RealVec* forces) const;
};
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceVdwForce.h
View file @ 41cd79a5
......@@ -34,7 +34,7 @@
namespace OpenMM {
class AmoebaReferenceVdwForce;
typedef RealOpenMM (AmoebaReferenceVdwForce::*CombiningFunction)( RealOpenMM x, RealOpenMM y) const;
typedef RealOpenMM (AmoebaReferenceVdwForce::*CombiningFunction)(RealOpenMM x, RealOpenMM y) const;
// ---------------------------------------------------------------------------------------
......@@ -71,7 +71,7 @@ public:
--------------------------------------------------------------------------------------- */
AmoebaReferenceVdwForce( );
AmoebaReferenceVdwForce();
/**---------------------------------------------------------------------------------------
......@@ -79,8 +79,8 @@ public:
--------------------------------------------------------------------------------------- */
AmoebaReferenceVdwForce( const std::string& sigmaCombiningRule,
const std::string& epsilonCombiningRule );
AmoebaReferenceVdwForce(const std::string& sigmaCombiningRule,
const std::string& epsilonCombiningRule);
/**---------------------------------------------------------------------------------------
......@@ -88,7 +88,7 @@ public:
--------------------------------------------------------------------------------------- */
~AmoebaReferenceVdwForce( ){};
~AmoebaReferenceVdwForce() {};
/**---------------------------------------------------------------------------------------
......@@ -98,7 +98,7 @@ public:
--------------------------------------------------------------------------------------- */
NonbondedMethod getNonbondedMethod( void ) const;
NonbondedMethod getNonbondedMethod() const;
/**---------------------------------------------------------------------------------------
......@@ -108,7 +108,7 @@ public:
--------------------------------------------------------------------------------------- */
void setNonbondedMethod( NonbondedMethod nonbondedMethod );
void setNonbondedMethod(NonbondedMethod nonbondedMethod);
/**---------------------------------------------------------------------------------------
......@@ -118,7 +118,7 @@ public:
--------------------------------------------------------------------------------------- */
double getCutoff( void ) const;
double getCutoff() const;
/**---------------------------------------------------------------------------------------
......@@ -128,7 +128,7 @@ public:
--------------------------------------------------------------------------------------- */
void setCutoff( double cutoff );
void setCutoff(double cutoff);
/**---------------------------------------------------------------------------------------
......@@ -138,7 +138,7 @@ public:
--------------------------------------------------------------------------------------- */
void setSigmaCombiningRule( const std::string& sigmaCombiningRule );
void setSigmaCombiningRule(const std::string& sigmaCombiningRule);
/**---------------------------------------------------------------------------------------
......@@ -148,7 +148,7 @@ public:
--------------------------------------------------------------------------------------- */
std::string getSigmaCombiningRule( void ) const;
std::string getSigmaCombiningRule() const;
/**---------------------------------------------------------------------------------------
......@@ -158,7 +158,7 @@ public:
--------------------------------------------------------------------------------------- */
void setEpsilonCombiningRule( const std::string& epsilonCombiningRule );
void setEpsilonCombiningRule(const std::string& epsilonCombiningRule);
/**---------------------------------------------------------------------------------------
......@@ -168,7 +168,7 @@ public:
--------------------------------------------------------------------------------------- */
std::string getEpsilonCombiningRule( void ) const;
std::string getEpsilonCombiningRule() const;
/**---------------------------------------------------------------------------------------
......@@ -197,12 +197,12 @@ public:
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numParticles, const std::vector<OpenMM::RealVec>& particlePositions,
const std::vector<int>& indexIVs,
const std::vector<RealOpenMM>& sigmas, const std::vector<RealOpenMM>& epsilons,
const std::vector<RealOpenMM>& reductions,
const std::vector< std::set<int> >& vdwExclusions,
std::vector<OpenMM::RealVec>& forces ) const;
RealOpenMM calculateForceAndEnergy(int numParticles, const std::vector<OpenMM::RealVec>& particlePositions,
const std::vector<int>& indexIVs,
const std::vector<RealOpenMM>& sigmas, const std::vector<RealOpenMM>& epsilons,
const std::vector<RealOpenMM>& reductions,
const std::vector< std::set<int> >& vdwExclusions,
std::vector<OpenMM::RealVec>& forces) const;
/**---------------------------------------------------------------------------------------
......@@ -221,12 +221,12 @@ public:
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numParticles, const std::vector<OpenMM::RealVec>& particlePositions,
const std::vector<int>& indexIVs,
const std::vector<RealOpenMM>& sigmas, const std::vector<RealOpenMM>& epsilons,
const std::vector<RealOpenMM>& reductions,
const NeighborList& neighborList,
std::vector<OpenMM::RealVec>& forces ) const;
RealOpenMM calculateForceAndEnergy(int numParticles, const std::vector<OpenMM::RealVec>& particlePositions,
const std::vector<int>& indexIVs,
const std::vector<RealOpenMM>& sigmas, const std::vector<RealOpenMM>& epsilons,
const std::vector<RealOpenMM>& reductions,
const NeighborList& neighborList,
std::vector<OpenMM::RealVec>& forces) const;
private:
......@@ -245,15 +245,15 @@ private:
RealOpenMM _taperCoefficients[3];
RealVec _periodicBoxVectors[3];
CombiningFunction _combineSigmas;
RealOpenMM arithmeticSigmaCombiningRule( RealOpenMM sigmaI, RealOpenMM sigmaJ ) const;
RealOpenMM geometricSigmaCombiningRule( RealOpenMM sigmaI, RealOpenMM sigmaJ ) const;
RealOpenMM cubicMeanSigmaCombiningRule( RealOpenMM sigmaI, RealOpenMM sigmaJ ) const;
RealOpenMM arithmeticSigmaCombiningRule(RealOpenMM sigmaI, RealOpenMM sigmaJ) const;
RealOpenMM geometricSigmaCombiningRule(RealOpenMM sigmaI, RealOpenMM sigmaJ) const;
RealOpenMM cubicMeanSigmaCombiningRule(RealOpenMM sigmaI, RealOpenMM sigmaJ) const;
CombiningFunction _combineEpsilons;
RealOpenMM arithmeticEpsilonCombiningRule( RealOpenMM epsilonI, RealOpenMM epsilonJ ) const;
RealOpenMM geometricEpsilonCombiningRule( RealOpenMM epsilonI, RealOpenMM epsilonJ ) const;
RealOpenMM harmonicEpsilonCombiningRule( RealOpenMM epsilonI, RealOpenMM epsilonJ ) const;
RealOpenMM hhgEpsilonCombiningRule( RealOpenMM epsilonI, RealOpenMM epsilonJ ) const;
RealOpenMM arithmeticEpsilonCombiningRule(RealOpenMM epsilonI, RealOpenMM epsilonJ) const;
RealOpenMM geometricEpsilonCombiningRule(RealOpenMM epsilonI, RealOpenMM epsilonJ) const;
RealOpenMM harmonicEpsilonCombiningRule( RealOpenMM epsilonI, RealOpenMM epsilonJ) const;
RealOpenMM hhgEpsilonCombiningRule( RealOpenMM epsilonI, RealOpenMM epsilonJ) const;
/**---------------------------------------------------------------------------------------
......@@ -272,9 +272,9 @@ private:
--------------------------------------------------------------------------------------- */
void setReducedPositions( int numParticles, const std::vector<RealVec>& particlePositions,
const std::vector<int>& indexIVs, const std::vector<RealOpenMM>& reductions,
std::vector<Vec3>& reducedPositions ) const;
void setReducedPositions(int numParticles, const std::vector<RealVec>& particlePositions,
const std::vector<int>& indexIVs, const std::vector<RealOpenMM>& reductions,
std::vector<Vec3>& reducedPositions) const;
/**---------------------------------------------------------------------------------------
......@@ -289,9 +289,9 @@ private:
--------------------------------------------------------------------------------------- */
void addReducedForce( unsigned int particleI, unsigned int particleIV,
RealOpenMM reduction, RealOpenMM sign,
Vec3& force, std::vector<OpenMM::RealVec>& forces ) const;
void addReducedForce(unsigned int particleI, unsigned int particleIV,
RealOpenMM reduction, RealOpenMM sign,
Vec3& force, std::vector<OpenMM::RealVec>& forces) const;
/**---------------------------------------------------------------------------------------
......@@ -301,7 +301,7 @@ private:
--------------------------------------------------------------------------------------- */
void setTaperCoefficients( double cutoff );
void setTaperCoefficients(double cutoff);
/**---------------------------------------------------------------------------------------
......@@ -317,9 +317,9 @@ private:
--------------------------------------------------------------------------------------- */
RealOpenMM calculatePairIxn( RealOpenMM combindedSigma, RealOpenMM combindedEpsilon,
const Vec3& particleIPosition, const Vec3& particleJPosition,
Vec3& force ) const;
RealOpenMM calculatePairIxn(RealOpenMM combindedSigma, RealOpenMM combindedEpsilon,
const Vec3& particleIPosition, const Vec3& particleJPosition,
Vec3& force) const;
};
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceWcaDispersionForce.cpp
View file @ 41cd79a5
......@@ -28,17 +28,17 @@
using std::vector;
using namespace OpenMM;
AmoebaReferenceWcaDispersionForce::AmoebaReferenceWcaDispersionForce( RealOpenMM epso, RealOpenMM epsh, RealOpenMM rmino, RealOpenMM rminh,
RealOpenMM awater, RealOpenMM shctd, RealOpenMM dispoff, RealOpenMM slevy ) :
AmoebaReferenceWcaDispersionForce::AmoebaReferenceWcaDispersionForce(RealOpenMM epso, RealOpenMM epsh, RealOpenMM rmino, RealOpenMM rminh,
RealOpenMM awater, RealOpenMM shctd, RealOpenMM dispoff, RealOpenMM slevy) :
_epso(epso), _epsh(epsh), _rmino(rmino), _rminh(rminh), _awater(awater), _shctd(shctd), _dispoff(dispoff), _slevy(slevy) {
}
RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiusI, RealOpenMM radiusK,
const RealVec& particleIPosition,
const RealVec& particleJPosition,
const RealOpenMM* const intermediateValues,
Vec3& force ) const {
RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn(RealOpenMM radiusI, RealOpenMM radiusK,
const RealVec& particleIPosition,
const RealVec& particleJPosition,
const RealOpenMM* const intermediateValues,
Vec3& force) const {
// ---------------------------------------------------------------------------------------
......@@ -62,7 +62,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
RealOpenMM zr = particleIPosition[2] - particleJPosition[2];
RealOpenMM r2 = xr*xr + yr*yr + zr*zr;
RealOpenMM r = SQRT( r2 );
RealOpenMM r = SQRT(r2);
RealOpenMM r3 = r2*r;
RealOpenMM sK = radiusK*_shctd;
......@@ -84,7 +84,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
RealOpenMM sum = zero;
RealOpenMM de = zero;
if( radiusI < (r + sK) ){
if (radiusI < (r + sK)) {
RealOpenMM rmax = (radiusI > (r - sK)) ? radiusI : (r - sK);
......@@ -93,7 +93,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
RealOpenMM lik3 = lik2*lik;
RealOpenMM lik4 = lik2*lik2;
if( lik < rmixo ){
if (lik < rmixo) {
RealOpenMM uik = (r + sK) < rmixo ? (r + sK) : rmixo;
RealOpenMM uik2 = uik*uik;
......@@ -103,7 +103,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
RealOpenMM term = four*PI/(fortyEight*r)* (three*(lik4-uik4) - eight*r*(lik3-uik3) + six*(r2-sK2)*(lik2-uik2));
RealOpenMM dl;
if( radiusI > (r - sK) ){
if (radiusI > (r - sK)) {
dl = -lik2 + two*(r2 + sK2);
dl *= lik2;
} else {
......@@ -112,7 +112,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
}
RealOpenMM du;
if( (r+sK) > rmixo ){
if ((r+sK) > rmixo) {
du = -uik2 + two*(r2 + sK2);
du *= -uik2;
} else {
......@@ -123,7 +123,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
sum += -emixo*term;
}
if( lik < rmixh ){
if (lik < rmixh) {
RealOpenMM uik = (r + sK) < rmixh ? (r + sK) : rmixh;
RealOpenMM uik2 = uik*uik;
......@@ -131,7 +131,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
RealOpenMM uik4 = uik2*uik2;
RealOpenMM term = four*PI / (fortyEight*r)*(three*(lik4-uik4) - eight*r*(lik3-uik3) + six*(r2-sK2)*(lik2-uik2));
RealOpenMM dl;
if( radiusI > (r-sK) ){
if (radiusI > (r-sK)) {
dl = -lik2 + two*(r2 + sK2);
dl *= lik2;
} else {
......@@ -140,7 +140,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
}
RealOpenMM du;
if (r+sK > rmixh){
if (r+sK > rmixh) {
du = -uik2 + two*(r2 + sK2);
du *= -uik2;
} else {
......@@ -162,7 +162,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
RealOpenMM uik12 = uik6 * uik6;
RealOpenMM uik13 = uik10 * uik3;
if( uik > rmixo ){
if (uik > rmixo) {
RealOpenMM lik = rmax > rmixo ? rmax : rmixo;
RealOpenMM lik2 = lik * lik;
......@@ -177,7 +177,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
RealOpenMM term = four*PI/(120.0*r*lik5*uik5)*(15.0*uik*lik*r*(uik4-lik4) - ten*uik2*lik2*(uik3-lik3) + six*(sK2-r2)*(uik5-lik5));
RealOpenMM dl;
if( radiusI > (r-sK) || rmax < rmixo ){
if (radiusI > (r-sK) || rmax < rmixo) {
dl = -five*lik2 + three*(r2 + sK2);
dl /= -lik5;
} else {
......@@ -189,7 +189,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
RealOpenMM idisp = -two*ao*term;
de -= two*ao*PI*(dl + du)/(15.0*r2);
term = four*PI/(2640.0*r*lik12*uik12) * (120.0*uik*lik*r*(uik11-lik11) - 66.0*uik2*lik2*(uik10-lik10) + 55.0*(sK2-r2)*(uik12-lik12));
if( radiusI > (r-sK) || rmax < rmixo ){
if (radiusI > (r-sK) || rmax < rmixo) {
dl = -six*lik2 + five*r2 + five*sK2;
dl /= -lik12;
} else {
......@@ -201,7 +201,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
de += ao*rmixo7*PI*(dl + du)/(60.0*r2);
sum += ao*rmixo7*term + idisp;
}
if (uik > rmixh){
if (uik > rmixh) {
lik = rmax > rmixh ? rmax : rmixh;
lik2 = lik * lik;
lik3 = lik2 * lik;
......@@ -215,7 +215,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
RealOpenMM term = four*PI / (120.0*r*lik5*uik5)*(15.0*uik*lik*r*(uik4-lik4) - ten*uik2*lik2*(uik3-lik3) + six*(sK2-r2)*(uik5-lik5));
RealOpenMM dl;
if( radiusI > (r-sK) || rmax < rmixh ){
if (radiusI > (r-sK) || rmax < rmixh) {
dl = -five*lik2 + three*(r2 + sK2);
dl /= -lik5;
} else {
......@@ -227,7 +227,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
RealOpenMM idisp = -four*ah*term;
de = de - four*ah*PI*(dl + du)/(15.0*r2);
term = four*PI / (2640.0*r*lik12*uik12)* (120.0*uik*lik*r*(uik11-lik11)- 66.0*uik2*lik2*(uik10-lik10)+ 55.0*(sK2-r2)*(uik12-lik12));
if( radiusI > (r-sK) || rmax < rmixh){
if (radiusI > (r-sK) || rmax < rmixh) {
dl = -six*lik2 + five*r2 + five*sK2;
dl = -dl / lik12;
} else {;
......@@ -254,12 +254,12 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculatePairIxn( RealOpenMM radiu
}
RealOpenMM AmoebaReferenceWcaDispersionForce::calculateForceAndEnergy( int numParticles,
const vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& radii,
const std::vector<RealOpenMM>& epsilons,
RealOpenMM totalMaximumDispersionEnergy,
vector<RealVec>& forces ) const {
RealOpenMM AmoebaReferenceWcaDispersionForce::calculateForceAndEnergy(int numParticles,
const vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& radii,
const std::vector<RealOpenMM>& epsilons,
RealOpenMM totalMaximumDispersionEnergy,
vector<RealVec>& forces) const {
// ---------------------------------------------------------------------------------------
......@@ -284,7 +284,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculateForceAndEnergy( int numPa
RealOpenMM intermediateValues[LastIntermediateValueIndex];
for( unsigned int ii = 0; ii < static_cast<unsigned int>(numParticles); ii++ ){
for (unsigned int ii = 0; ii < static_cast<unsigned int>(numParticles); ii++) {
RealOpenMM epsi = epsilons[ii];
RealOpenMM rmini = radii[ii];
......@@ -296,7 +296,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculateForceAndEnergy( int numPa
RealOpenMM rminI2 = rmini*rmini;
RealOpenMM rminI3 = rminI2*rmini;
RealOpenMM rmixo = two*(rmino3 + rminI3 ) / (rmino2 + rminI2);
RealOpenMM rmixo = two*(rmino3 + rminI3) / (rmino2 + rminI2);
intermediateValues[RMIXO] = rmixo;
RealOpenMM rmixo7 = rmixo*rmixo*rmixo;
......@@ -319,14 +319,14 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculateForceAndEnergy( int numPa
intermediateValues[AH] = emixh*rmixh7;
for( unsigned int jj = 0; jj < static_cast<unsigned int>(numParticles); jj++ ){
for (unsigned int jj = 0; jj < static_cast<unsigned int>(numParticles); jj++) {
if( ii == jj )continue;
if (ii == jj)continue;
Vec3 force;
energy += calculatePairIxn( rmini, radii[jj],
particlePositions[ii], particlePositions[jj],
intermediateValues, force );
energy += calculatePairIxn(rmini, radii[jj],
particlePositions[ii], particlePositions[jj],
intermediateValues, force);
forces[ii][0] += force[0];
forces[ii][1] += force[1];
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceWcaDispersionForce.h
View file @ 41cd79a5
......@@ -51,8 +51,8 @@ public:
--------------------------------------------------------------------------------------- */
AmoebaReferenceWcaDispersionForce( RealOpenMM epso, RealOpenMM epsh, RealOpenMM rmino, RealOpenMM rminh,
RealOpenMM awater, RealOpenMM shctd, RealOpenMM dispoff, RealOpenMM slevy );
AmoebaReferenceWcaDispersionForce(RealOpenMM epso, RealOpenMM epsh, RealOpenMM rmino, RealOpenMM rminh,
RealOpenMM awater, RealOpenMM shctd, RealOpenMM dispoff, RealOpenMM slevy);
/**---------------------------------------------------------------------------------------
......@@ -60,7 +60,7 @@ public:
--------------------------------------------------------------------------------------- */
~AmoebaReferenceWcaDispersionForce( ){};
~AmoebaReferenceWcaDispersionForce() {};
/**---------------------------------------------------------------------------------------
......@@ -77,10 +77,10 @@ public:
--------------------------------------------------------------------------------------- */
RealOpenMM calculateForceAndEnergy( int numParticles, const std::vector<OpenMM::RealVec>& particlePositions,
const std::vector<RealOpenMM>& radii,
const std::vector<RealOpenMM>& epsilons,
RealOpenMM totalMaximumDispersionEnergy, std::vector<OpenMM::RealVec>& forces ) const;
RealOpenMM calculateForceAndEnergy(int numParticles, const std::vector<OpenMM::RealVec>& particlePositions,
const std::vector<RealOpenMM>& radii,
const std::vector<RealOpenMM>& epsilons,
RealOpenMM totalMaximumDispersionEnergy, std::vector<OpenMM::RealVec>& forces) const;
private:
RealOpenMM _epso;
......@@ -109,10 +109,10 @@ private:
--------------------------------------------------------------------------------------- */
RealOpenMM calculatePairIxn( RealOpenMM radiusI, RealOpenMM radiusJ,
const OpenMM::RealVec& particleIPosition, const OpenMM::RealVec& particleJPosition,
const RealOpenMM* const intermediateValues,
Vec3& force ) const;
RealOpenMM calculatePairIxn(RealOpenMM radiusI, RealOpenMM radiusJ,
const OpenMM::RealVec& particleIPosition, const OpenMM::RealVec& particleJPosition,
const RealOpenMM* const intermediateValues,
Vec3& force) const;
};
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaAngleForce.cpp
View file @ 41cd79a5
......@@ -66,7 +66,7 @@ const double TOL = 1e-5;
--------------------------------------------------------------------------------------- */
static void crossProductVector3( double* vectorX, double* vectorY, double* vectorZ ){
static void crossProductVector3(double* vectorX, double* vectorY, double* vectorZ) {
vectorZ[0] = vectorX[1]*vectorY[2] - vectorX[2]*vectorY[1];
vectorZ[1] = vectorX[2]*vectorY[0] - vectorX[0]*vectorY[2];
......@@ -75,24 +75,24 @@ static void crossProductVector3( double* vectorX, double* vectorY, double* vecto
return;
}
static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, double quadraticK, double cubicK,
double quarticK, double penticK, double sexticK,
double* dEdR, double* energyTerm, FILE* log ) {
static void getPrefactorsGivenAngleCosine(double cosine, double idealAngle, double quadraticK, double cubicK,
double quarticK, double penticK, double sexticK,
double* dEdR, double* energyTerm, FILE* log) {
double angle;
if( cosine >= 1.0 ){
if (cosine >= 1.0) {
angle = 0.0f;
}
else if( cosine <= -1.0 ){
else if (cosine <= -1.0) {
angle = RADIAN*PI_M;
}
else {
angle = RADIAN*acos(cosine);
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "getPrefactorsGivenAngleCosine: cosine=%10.3e angle=%10.3e ideal=%10.3e\n", cosine, angle, idealAngle );
(void) fflush( log );
if (log) {
(void) fprintf(log, "getPrefactorsGivenAngleCosine: cosine=%10.3e angle=%10.3e ideal=%10.3e\n", cosine, angle, idealAngle);
(void) fflush(log);
}
#endif
......@@ -103,11 +103,11 @@ static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, dou
// deltaIdeal = r - r_0
*dEdR = ( 2.0 +
3.0*cubicK* deltaIdeal +
4.0*quarticK*deltaIdeal2 +
5.0*penticK* deltaIdeal3 +
6.0*sexticK* deltaIdeal4 );
*dEdR = (2.0 +
3.0*cubicK* deltaIdeal +
4.0*quarticK*deltaIdeal2 +
5.0*penticK* deltaIdeal3 +
6.0*sexticK* deltaIdeal4 );
*dEdR *= RADIAN*quadraticK*deltaIdeal;
......@@ -122,29 +122,29 @@ static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, dou
}
static void computeAmoebaAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaAngleForce& AmoebaAngleForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
std::vector<Vec3>& forces, double* energy, FILE* log) {
int particle1, particle2, particle3;
double idealAngle;
double quadraticK;
AmoebaAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, idealAngle, quadraticK );
AmoebaAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, idealAngle, quadraticK);
double cubicK = AmoebaAngleForce.getAmoebaGlobalAngleCubic();
double quarticK = AmoebaAngleForce.getAmoebaGlobalAngleQuartic();
double penticK = AmoebaAngleForce.getAmoebaGlobalAnglePentic();
double sexticK = AmoebaAngleForce.getAmoebaGlobalAngleSextic();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaAngleForce: bond %d [%d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, idealAngle, quadraticK, cubicK, quarticK, penticK, sexticK );
(void) fflush( log );
if (log) {
(void) fprintf(log, "computeAmoebaAngleForce: bond %d [%d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, idealAngle, quadraticK, cubicK, quarticK, penticK, sexticK);
(void) fflush(log);
}
#endif
double deltaR[2][3];
double r2_0 = 0.0;
double r2_1 = 0.0;
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
deltaR[0][ii] = positions[particle1][ii] - positions[particle2][ii];
r2_0 += deltaR[0][ii]*deltaR[0][ii];
......@@ -155,33 +155,33 @@ static void computeAmoebaAngleForce(int bondIndex, std::vector<Vec3>& positions
}
double pVector[3];
crossProductVector3( deltaR[0], deltaR[1], pVector );
double rp = sqrt( pVector[0]*pVector[0] + pVector[1]*pVector[1] + pVector[2]*pVector[2] );
if( rp < 1.0e-06 ){
crossProductVector3(deltaR[0], deltaR[1], pVector);
double rp = sqrt(pVector[0]*pVector[0] + pVector[1]*pVector[1] + pVector[2]*pVector[2]);
if (rp < 1.0e-06) {
rp = 1.0e-06;
}
double dot = deltaR[0][0]*deltaR[1][0] + deltaR[0][1]*deltaR[1][1] + deltaR[0][2]*deltaR[1][2];
double cosine = dot/sqrt(r2_0*r2_1);
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "dot=%10.3e r2_0=%10.3e r2_1=%10.3e\n", dot, r2_0, r2_1 );
(void) fflush( log );
if (log) {
(void) fprintf(log, "dot=%10.3e r2_0=%10.3e r2_1=%10.3e\n", dot, r2_0, r2_1);
(void) fflush(log);
}
#endif
double dEdR;
double energyTerm;
getPrefactorsGivenAngleCosine( cosine, idealAngle, quadraticK, cubicK,
quarticK, penticK, sexticK, &dEdR, &energyTerm, log );
getPrefactorsGivenAngleCosine(cosine, idealAngle, quadraticK, cubicK,
quarticK, penticK, sexticK, &dEdR, &energyTerm, log);
double termA = -dEdR/(r2_0*rp);
double termC = dEdR/(r2_1*rp);
double deltaCrossP[3][3];
crossProductVector3( deltaR[0], pVector, deltaCrossP[0] );
crossProductVector3( deltaR[1], pVector, deltaCrossP[2] );
for( int ii = 0; ii < 3; ii++ ){
crossProductVector3(deltaR[0], pVector, deltaCrossP[0]);
crossProductVector3(deltaR[1], pVector, deltaCrossP[2]);
for (int ii = 0; ii < 3; ii++) {
deltaCrossP[0][ii] *= termA;
deltaCrossP[2][ii] *= termC;
deltaCrossP[1][ii] = -1.0*(deltaCrossP[0][ii] + deltaCrossP[2][ii]);
......@@ -202,71 +202,71 @@ static void computeAmoebaAngleForce(int bondIndex, std::vector<Vec3>& positions
*energy += energyTerm;
}
static void computeAmoebaAngleForces( Context& context, AmoebaAngleForce& AmoebaAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
static void computeAmoebaAngleForces(Context& context, AmoebaAngleForce& AmoebaAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log) {
// get positions and zero forces
State state = context.getState(State::Positions);
std::vector<Vec3> positions = state.getPositions();
expectedForces.resize( positions.size() );
expectedForces.resize(positions.size());
for( unsigned int ii = 0; ii < expectedForces.size(); ii++ ){
for (unsigned int ii = 0; ii < expectedForces.size(); ii++) {
expectedForces[ii][0] = expectedForces[ii][1] = expectedForces[ii][2] = 0.0;
}
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < AmoebaAngleForce.getNumAngles(); ii++ ){
computeAmoebaAngleForce(ii, positions, AmoebaAngleForce, expectedForces, expectedEnergy, log );
for (int ii = 0; ii < AmoebaAngleForce.getNumAngles(); ii++) {
computeAmoebaAngleForce(ii, positions, AmoebaAngleForce, expectedForces, expectedEnergy, log);
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaAngleForces: expected energy=%14.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
if (log) {
(void) fprintf(log, "computeAmoebaAngleForces: expected energy=%14.7e\n", *expectedEnergy);
for (unsigned int ii = 0; ii < positions.size(); ii++) {
(void) fprintf(log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2]);
}
(void) fflush( log );
(void) fflush(log);
}
#endif
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaAngleForce& AmoebaAngleForce,
double tolerance, const std::string& idString, FILE* log) {
void compareWithExpectedForceAndEnergy(Context& context, AmoebaAngleForce& AmoebaAngleForce,
double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaAngleForces( context, AmoebaAngleForce, expectedForces, &expectedEnergy, log );
computeAmoebaAngleForces(context, AmoebaAngleForce, expectedForces, &expectedEnergy, log);
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
if (log) {
(void) fprintf(log, "computeAmoebaAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy());
for (unsigned int ii = 0; ii < forces.size(); ii++) {
(void) fprintf(log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2]);
}
(void) fflush( log );
(void) fflush(log);
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
for (unsigned int ii = 0; ii < forces.size(); ii++) {
ASSERT_EQUAL_VEC(expectedForces[ii], forces[ii], tolerance);
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), tolerance);
}
void testOneAngle( FILE* log ) {
void testOneAngle(FILE* log) {
System system;
int numberOfParticles = 3;
for( int ii = 0; ii < numberOfParticles; ii++ ){
for (int ii = 0; ii < numberOfParticles; ii++) {
system.addParticle(1.0);
}
......@@ -290,7 +290,7 @@ void testOneAngle( FILE* log ) {
system.addForce(amoebaAngleForce);
ASSERT(!amoebaAngleForce->usesPeriodicBoundaryConditions());
ASSERT(!system.usesPeriodicBoundaryConditions());
Context context(system, integrator, Platform::getPlatformByName( "Reference"));
Context context(system, integrator, Platform::getPlatformByName("Reference"));
std::vector<Vec3> positions(numberOfParticles);
......@@ -299,7 +299,7 @@ void testOneAngle( FILE* log ) {
positions[2] = Vec3(0, 0, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle", log );
compareWithExpectedForceAndEnergy(context, *amoebaAngleForce, TOL, "testOneAngle", log);
// Try changing the angle parameters and make sure it's still correct.
......@@ -307,29 +307,29 @@ void testOneAngle( FILE* log ) {
bool exceptionThrown = false;
try {
// This should throw an exception.
compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle", log );
compareWithExpectedForceAndEnergy(context, *amoebaAngleForce, TOL, "testOneAngle", log);
}
catch (std::exception ex) {
exceptionThrown = true;
}
ASSERT(exceptionThrown);
amoebaAngleForce->updateParametersInContext(context);
compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle", log );
compareWithExpectedForceAndEnergy(context, *amoebaAngleForce, TOL, "testOneAngle", log);
}
int main( int numberOfArguments, char* argv[] ) {
int main(int numberOfArguments, char* argv[]) {
try {
std::cout << "TestCudaAmoebaAngleForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
//FILE* log = fopen( "AmoebaAngleForce.log", "w" );;
//FILE* log = fopen("AmoebaAngleForce.log", "w");;
FILE* log = NULL;
//FILE* log = stderr;
testOneAngle( log );
testOneAngle(log);
#ifdef AMOEBA_DEBUG
if( log && log != stderr )
(void) fclose( log );
if (log && log != stderr)
(void) fclose(log);
#endif
}
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaBondForce.cpp
View file @ 41cd79a5
......@@ -49,22 +49,22 @@ extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
const double TOL = 1e-5;
static void computeAmoebaBondForce(int bondIndex, std::vector<Vec3>& positions, AmoebaBondForce& AmoebaBondForce,
std::vector<Vec3>& forces, double* energy ) {
std::vector<Vec3>& forces, double* energy) {
int particle1, particle2;
double bondLength;
double quadraticK;
double cubicK = AmoebaBondForce.getAmoebaGlobalBondCubic();
double quarticK = AmoebaBondForce.getAmoebaGlobalBondQuartic();
AmoebaBondForce.getBondParameters(bondIndex, particle1, particle2, bondLength, quadraticK );
AmoebaBondForce.getBondParameters(bondIndex, particle1, particle2, bondLength, quadraticK);
double deltaR[3];
double r2 = 0.0;
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
deltaR[ii] = positions[particle2][ii] - positions[particle1][ii];
r2 += deltaR[ii]*deltaR[ii];
}
double r = sqrt( r2 );
double r = sqrt(r2);
double bondDelta = (r - bondLength);
double bondDelta2 = bondDelta*bondDelta;
......@@ -84,64 +84,64 @@ static void computeAmoebaBondForce(int bondIndex, std::vector<Vec3>& positions,
}
static void computeAmoebaBondForces( Context& context, AmoebaBondForce& AmoebaBondForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
static void computeAmoebaBondForces(Context& context, AmoebaBondForce& AmoebaBondForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log) {
// get positions and zero forces
State state = context.getState(State::Positions);
std::vector<Vec3> positions = state.getPositions();
expectedForces.resize( positions.size() );
expectedForces.resize(positions.size());
for( unsigned int ii = 0; ii < expectedForces.size(); ii++ ){
for (unsigned int ii = 0; ii < expectedForces.size(); ii++) {
expectedForces[ii][0] = expectedForces[ii][1] = expectedForces[ii][2] = 0.0;
}
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < AmoebaBondForce.getNumBonds(); ii++ ){
computeAmoebaBondForce(ii, positions, AmoebaBondForce, expectedForces, expectedEnergy );
for (int ii = 0; ii < AmoebaBondForce.getNumBonds(); ii++) {
computeAmoebaBondForce(ii, positions, AmoebaBondForce, expectedForces, expectedEnergy);
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaBondForces: expected energy=%15.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%15.7e %15.7e %15.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
if (log) {
(void) fprintf(log, "computeAmoebaBondForces: expected energy=%15.7e\n", *expectedEnergy);
for (unsigned int ii = 0; ii < positions.size(); ii++) {
(void) fprintf(log, "%6u [%15.7e %15.7e %15.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2]);
}
(void) fflush( log );
(void) fflush(log);
}
#endif
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaBondForce& AmoebaBondForce, double tolerance, const std::string& idString, FILE* log) {
void compareWithExpectedForceAndEnergy(Context& context, AmoebaBondForce& AmoebaBondForce, double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaBondForces( context, AmoebaBondForce, expectedForces, &expectedEnergy, NULL );
computeAmoebaBondForces(context, AmoebaBondForce, expectedForces, &expectedEnergy, NULL);
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaBondForces: expected energy=%15.7e %15.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%15.7e %15.7e %15.7e] [%15.7e %15.7e %15.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
if (log) {
(void) fprintf(log, "computeAmoebaBondForces: expected energy=%15.7e %15.7e\n", expectedEnergy, state.getPotentialEnergy());
for (unsigned int ii = 0; ii < forces.size(); ii++) {
(void) fprintf(log, "%6u [%15.7e %15.7e %15.7e] [%15.7e %15.7e %15.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2]);
}
(void) fflush( log );
(void) fflush(log);
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
for (unsigned int ii = 0; ii < forces.size(); ii++) {
ASSERT_EQUAL_VEC(expectedForces[ii], forces[ii], tolerance);
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), tolerance);
}
void testOneBond( FILE* log ) {
void testOneBond(FILE* log) {
System system;
......@@ -156,22 +156,22 @@ void testOneBond( FILE* log ) {
double quadraticK = 1.0;
double cubicK = 2.0;
double quarticicK = 3.0;
amoebaBondForce->setAmoebaGlobalBondCubic( cubicK );
amoebaBondForce->setAmoebaGlobalBondQuartic( quarticicK );
amoebaBondForce->setAmoebaGlobalBondCubic(cubicK);
amoebaBondForce->setAmoebaGlobalBondQuartic(quarticicK);
amoebaBondForce->addBond(0, 1, bondLength, quadraticK);
system.addForce(amoebaBondForce);
Context context(system, integrator, Platform::getPlatformByName( "Reference"));
Context context(system, integrator, Platform::getPlatformByName("Reference"));
std::vector<Vec3> positions(2);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testOneBond", log );
compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testOneBond", log);
}
void testTwoBond( FILE* log ) {
void testTwoBond(FILE* log) {
System system;
......@@ -187,15 +187,15 @@ void testTwoBond( FILE* log ) {
double quadraticK = 1.0;
double cubicK = 2.0;
double quarticicK = 3.0;
amoebaBondForce->setAmoebaGlobalBondCubic( cubicK );
amoebaBondForce->setAmoebaGlobalBondQuartic( quarticicK );
amoebaBondForce->setAmoebaGlobalBondCubic(cubicK);
amoebaBondForce->setAmoebaGlobalBondQuartic(quarticicK);
amoebaBondForce->addBond(0, 1, bondLength, quadraticK);
amoebaBondForce->addBond(1, 2, bondLength, quadraticK);
system.addForce(amoebaBondForce);
ASSERT(!amoebaBondForce->usesPeriodicBoundaryConditions());
ASSERT(!system.usesPeriodicBoundaryConditions());
Context context(system, integrator, Platform::getPlatformByName( "Reference"));
Context context(system, integrator, Platform::getPlatformByName("Reference"));
std::vector<Vec3> positions(3);
positions[0] = Vec3(0, 1, 0);
......@@ -203,7 +203,7 @@ void testTwoBond( FILE* log ) {
positions[2] = Vec3(1, 0, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond", log );
compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testTwoBond", log);
// Try changing the bond parameters and make sure it's still correct.
......@@ -212,17 +212,17 @@ void testTwoBond( FILE* log ) {
bool exceptionThrown = false;
try {
// This should throw an exception.
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond", log );
compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testTwoBond", log);
}
catch (std::exception ex) {
exceptionThrown = true;
}
ASSERT(exceptionThrown);
amoebaBondForce->updateParametersInContext(context);
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond", log );
compareWithExpectedForceAndEnergy(context, *amoebaBondForce, TOL, "testTwoBond", log);
}
int main( int numberOfArguments, char* argv[] ) {
int main(int numberOfArguments, char* argv[]) {
try {
std::cout << "TestReferenceAmoebaBondForce running test..." << std::endl;
......@@ -230,11 +230,11 @@ int main( int numberOfArguments, char* argv[] ) {
FILE* log = NULL;
//FILE* log = stderr;
//testOneBond( log );
testTwoBond( log );
//testOneBond(log);
testTwoBond(log);
#ifdef AMOEBA_DEBUG
if( log && log != stderr )
(void) fclose( log );
if (log && log != stderr)
(void) fclose(log);
#endif
}
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaInPlaneAngleForce.cpp
View file @ 41cd79a5
......@@ -64,7 +64,7 @@ const double TOL = 1e-5;
--------------------------------------------------------------------------------------- */
static void crossProductVector3( double* vectorX, double* vectorY, double* vectorZ ){
static void crossProductVector3(double* vectorX, double* vectorY, double* vectorZ) {
vectorZ[0] = vectorX[1]*vectorY[2] - vectorX[2]*vectorY[1];
vectorZ[1] = vectorX[2]*vectorY[0] - vectorX[0]*vectorY[2];
......@@ -73,28 +73,28 @@ static void crossProductVector3( double* vectorX, double* vectorY, double* vecto
return;
}
static double dotVector3( double* vectorX, double* vectorY ){
static double dotVector3(double* vectorX, double* vectorY) {
return vectorX[0]*vectorY[0] + vectorX[1]*vectorY[1] + vectorX[2]*vectorY[2];
}
static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInPlaneAngle, double quadraticK, double cubicK,
double quarticK, double penticK, double sexticK,
double* dEdR, double* energyTerm, FILE* log ) {
static void getPrefactorsGivenInPlaneAngleCosine(double cosine, double idealInPlaneAngle, double quadraticK, double cubicK,
double quarticK, double penticK, double sexticK,
double* dEdR, double* energyTerm, FILE* log) {
double angle;
if( cosine >= 1.0 ){
if (cosine >= 1.0) {
angle = 0.0f;
}
else if( cosine <= -1.0 ){
else if (cosine <= -1.0) {
angle = RADIAN*PI_M;
}
else {
angle = RADIAN*acos(cosine);
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "getPrefactorsGivenInPlaneAngleCosine: cosine=%10.3e angle=%10.3e ideal=%10.3e\n", cosine, angle, idealInPlaneAngle );
(void) fflush( log );
if (log) {
(void) fprintf(log, "getPrefactorsGivenInPlaneAngleCosine: cosine=%10.3e angle=%10.3e ideal=%10.3e\n", cosine, angle, idealInPlaneAngle);
(void) fflush(log);
}
#endif
......@@ -105,11 +105,11 @@ static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInP
// deltaIdeal = r - r_0
*dEdR = ( 2.0 +
*dEdR = (2.0 +
3.0*cubicK* deltaIdeal +
4.0*quarticK*deltaIdeal2 +
5.0*penticK* deltaIdeal3 +
6.0*sexticK* deltaIdeal4 );
6.0*sexticK* deltaIdeal4 );
*dEdR *= RADIAN*quadraticK*deltaIdeal;
......@@ -124,22 +124,22 @@ static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInP
}
static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaInPlaneAngleForce& AmoebaInPlaneAngleForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
std::vector<Vec3>& forces, double* energy, FILE* log) {
int particle1, particle2, particle3, particle4;
double idealInPlaneAngle;
double quadraticK;
AmoebaInPlaneAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK );
AmoebaInPlaneAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK);
double cubicK = AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleCubic();
double quarticK = AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleQuartic();
double penticK = AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAnglePentic();
double sexticK = AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleSextic();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaInPlaneAngleForce: bond %d [%d %d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK, cubicK, quarticK, penticK, sexticK );
(void) fflush( log );
if (log) {
(void) fprintf(log, "computeAmoebaInPlaneAngleForce: bond %d [%d %d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK, cubicK, quarticK, penticK, sexticK);
(void) fflush(log);
}
#endif
......@@ -162,82 +162,82 @@ static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& po
// APxM, CPxM, ADxBD, BDxCD, TxCD, ADxT, dBxAD, CDxdB, LastDeltaAtomIndex
double deltaR[LastDeltaAtomIndex][3];
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
deltaR[AD][ii] = positions[particle1][ii] - positions[particle4][ii];
deltaR[BD][ii] = positions[particle2][ii] - positions[particle4][ii];
deltaR[CD][ii] = positions[particle3][ii] - positions[particle4][ii];
}
crossProductVector3( deltaR[AD], deltaR[CD], deltaR[T] );
crossProductVector3(deltaR[AD], deltaR[CD], deltaR[T]);
double rT2 = dotVector3( deltaR[T], deltaR[T] );
double delta = dotVector3( deltaR[T], deltaR[BD] );
double rT2 = dotVector3(deltaR[T], deltaR[T]);
double delta = dotVector3(deltaR[T], deltaR[BD]);
delta *= -1.0/rT2;
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
deltaR[P][ii] = positions[particle2][ii] + deltaR[T][ii]*delta;
deltaR[AP][ii] = positions[particle1][ii] - deltaR[P][ii];
deltaR[CP][ii] = positions[particle3][ii] - deltaR[P][ii];
}
double rAp2 = dotVector3( deltaR[AP], deltaR[AP] );
double rCp2 = dotVector3( deltaR[CP], deltaR[CP] );
if( rAp2 <= 0.0 && rCp2 <= 0.0 ){
double rAp2 = dotVector3(deltaR[AP], deltaR[AP]);
double rCp2 = dotVector3(deltaR[CP], deltaR[CP]);
if (rAp2 <= 0.0 && rCp2 <= 0.0) {
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaInPlaneAngleForce: rAp2 or rCp2 <= 0.0\n" );
(void) fflush( log );
if (log) {
(void) fprintf(log, "computeAmoebaInPlaneAngleForce: rAp2 or rCp2 <= 0.0\n");
(void) fflush(log);
}
#endif
return;
}
crossProductVector3( deltaR[CP], deltaR[AP], deltaR[M] );
crossProductVector3(deltaR[CP], deltaR[AP], deltaR[M]);
double rm = dotVector3( deltaR[M], deltaR[M] );
rm = sqrt( rm );
if( rm < 0.000001 ){
double rm = dotVector3(deltaR[M], deltaR[M]);
rm = sqrt(rm);
if (rm < 0.000001) {
rm = 0.000001;
}
double dot = dotVector3( deltaR[AP], deltaR[CP] );
double cosine = dot/sqrt( rAp2*rCp2 );
double dot = dotVector3(deltaR[AP], deltaR[CP]);
double cosine = dot/sqrt(rAp2*rCp2);
double dEdR;
double energyTerm;
getPrefactorsGivenInPlaneAngleCosine( cosine, idealInPlaneAngle, quadraticK, cubicK,
quarticK, penticK, sexticK, &dEdR, &energyTerm, log );
getPrefactorsGivenInPlaneAngleCosine(cosine, idealInPlaneAngle, quadraticK, cubicK,
quarticK, penticK, sexticK, &dEdR, &energyTerm, log);
double termA = -dEdR/(rAp2*rm);
double termC = dEdR/(rCp2*rm);
crossProductVector3( deltaR[AP], deltaR[M], deltaR[APxM] );
crossProductVector3( deltaR[CP], deltaR[M], deltaR[CPxM] );
crossProductVector3(deltaR[AP], deltaR[M], deltaR[APxM]);
crossProductVector3(deltaR[CP], deltaR[M], deltaR[CPxM]);
// forces will be gathered here
enum { dA, dB, dC, dD, LastDIndex };
double forceTerm[LastDIndex][3];
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
forceTerm[dA][ii] = deltaR[APxM][ii]*termA;
forceTerm[dC][ii] = deltaR[CPxM][ii]*termC;
forceTerm[dB][ii] = -1.0*( forceTerm[dA][ii] + forceTerm[dC][ii] );
forceTerm[dB][ii] = -1.0*(forceTerm[dA][ii] + forceTerm[dC][ii]);
}
double pTrT2 = dotVector3( forceTerm[dB], deltaR[T] );
double pTrT2 = dotVector3(forceTerm[dB], deltaR[T]);
pTrT2 /= rT2;
crossProductVector3( deltaR[CD], forceTerm[dB], deltaR[CDxdB] );
crossProductVector3( forceTerm[dB], deltaR[AD], deltaR[dBxAD] );
crossProductVector3(deltaR[CD], forceTerm[dB], deltaR[CDxdB]);
crossProductVector3(forceTerm[dB], deltaR[AD], deltaR[dBxAD]);
if( fabs( pTrT2 ) > 1.0e-08 ){
if (fabs(pTrT2) > 1.0e-08) {
double delta2 = delta*2.0;
crossProductVector3( deltaR[BD], deltaR[CD], deltaR[BDxCD] );
crossProductVector3( deltaR[T], deltaR[CD], deltaR[TxCD] );
crossProductVector3( deltaR[AD], deltaR[BD], deltaR[ADxBD] );
crossProductVector3( deltaR[AD], deltaR[T], deltaR[ADxT] );
for( int ii = 0; ii < 3; ii++ ){
crossProductVector3(deltaR[BD], deltaR[CD], deltaR[BDxCD]);
crossProductVector3(deltaR[T], deltaR[CD], deltaR[TxCD] );
crossProductVector3(deltaR[AD], deltaR[BD], deltaR[ADxBD]);
crossProductVector3(deltaR[AD], deltaR[T], deltaR[ADxT] );
for (int ii = 0; ii < 3; ii++) {
double term = deltaR[BDxCD][ii] + delta2*deltaR[TxCD][ii];
forceTerm[dA][ii] += delta*deltaR[CDxdB][ii] + term*pTrT2;
......@@ -245,16 +245,16 @@ static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& po
term = deltaR[ADxBD][ii] + delta2*deltaR[ADxT][ii];
forceTerm[dC][ii] += delta*deltaR[dBxAD][ii] + term*pTrT2;
forceTerm[dD][ii] = -( forceTerm[dA][ii] + forceTerm[dB][ii] + forceTerm[dC][ii] );
forceTerm[dD][ii] = -(forceTerm[dA][ii] + forceTerm[dB][ii] + forceTerm[dC][ii]);
}
}
else {
for( int ii = 0; ii < 3; ii++ ){
for (int ii = 0; ii < 3; ii++) {
forceTerm[dA][ii] += delta*deltaR[CDxdB][ii];
forceTerm[dC][ii] += delta*deltaR[dBxAD][ii];
forceTerm[dD][ii] = -( forceTerm[dA][ii] + forceTerm[dB][ii] + forceTerm[dC][ii] );
forceTerm[dD][ii] = -(forceTerm[dA][ii] + forceTerm[dB][ii] + forceTerm[dC][ii]);
}
}
......@@ -280,69 +280,69 @@ static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& po
}
static void computeAmoebaInPlaneAngleForces( Context& context, AmoebaInPlaneAngleForce& AmoebaInPlaneAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
static void computeAmoebaInPlaneAngleForces(Context& context, AmoebaInPlaneAngleForce& AmoebaInPlaneAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log) {
// get positions and zero forces
State state = context.getState(State::Positions);
std::vector<Vec3> positions = state.getPositions();
expectedForces.resize( positions.size() );
expectedForces.resize(positions.size());
for( unsigned int ii = 0; ii < expectedForces.size(); ii++ ){
for (unsigned int ii = 0; ii < expectedForces.size(); ii++) {
expectedForces[ii][0] = expectedForces[ii][1] = expectedForces[ii][2] = 0.0;
}
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < AmoebaInPlaneAngleForce.getNumAngles(); ii++ ){
computeAmoebaInPlaneAngleForce(ii, positions, AmoebaInPlaneAngleForce, expectedForces, expectedEnergy, log );
for (int ii = 0; ii < AmoebaInPlaneAngleForce.getNumAngles(); ii++) {
computeAmoebaInPlaneAngleForce(ii, positions, AmoebaInPlaneAngleForce, expectedForces, expectedEnergy, log);
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaInPlaneAngleForces: expected energy=%14.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
if (log) {
(void) fprintf(log, "computeAmoebaInPlaneAngleForces: expected energy=%14.7e\n", *expectedEnergy);
for (unsigned int ii = 0; ii < positions.size(); ii++) {
(void) fprintf(log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2]);
}
(void) fflush( log );
(void) fflush(log);
}
#endif
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaInPlaneAngleForce& AmoebaInPlaneAngleForce,
double tolerance, const std::string& idString, FILE* log) {
void compareWithExpectedForceAndEnergy(Context& context, AmoebaInPlaneAngleForce& AmoebaInPlaneAngleForce,
double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaInPlaneAngleForces( context, AmoebaInPlaneAngleForce, expectedForces, &expectedEnergy, log );
computeAmoebaInPlaneAngleForces(context, AmoebaInPlaneAngleForce, expectedForces, &expectedEnergy, log);
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaInPlaneAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
if (log) {
(void) fprintf(log, "computeAmoebaInPlaneAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy());
for (unsigned int ii = 0; ii < forces.size(); ii++) {
(void) fprintf(log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2]);
}
(void) fflush( log );
(void) fflush(log);
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
for (unsigned int ii = 0; ii < forces.size(); ii++) {
ASSERT_EQUAL_VEC(expectedForces[ii], forces[ii], tolerance);
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), tolerance);
}
void testOneAngle( FILE* log ) {
void testOneAngle(FILE* log) {
System system;
int numberOfParticles = 4;
for( int ii = 0; ii < numberOfParticles; ii++ ){
for (int ii = 0; ii < numberOfParticles; ii++) {
system.addParticle(1.0);
}
......@@ -366,7 +366,7 @@ void testOneAngle( FILE* log ) {
system.addForce(amoebaInPlaneAngleForce);
ASSERT(!amoebaInPlaneAngleForce->usesPeriodicBoundaryConditions());
ASSERT(!system.usesPeriodicBoundaryConditions());
Context context(system, integrator, Platform::getPlatformByName( "Reference"));
Context context(system, integrator, Platform::getPlatformByName("Reference"));
std::vector<Vec3> positions(numberOfParticles);
......@@ -376,7 +376,7 @@ void testOneAngle( FILE* log ) {
positions[3] = Vec3(1, 1, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
compareWithExpectedForceAndEnergy(context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log);
// Try changing the angle parameters and make sure it's still correct.
......@@ -384,29 +384,29 @@ void testOneAngle( FILE* log ) {
bool exceptionThrown = false;
try {
// This should throw an exception.
compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
compareWithExpectedForceAndEnergy(context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log);
}
catch (std::exception ex) {
exceptionThrown = true;
}
ASSERT(exceptionThrown);
amoebaInPlaneAngleForce->updateParametersInContext(context);
compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
compareWithExpectedForceAndEnergy(context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log);
}
int main( int numberOfArguments, char* argv[] ) {
int main(int numberOfArguments, char* argv[]) {
try {
std::cout << "TestReferenceAmoebaInPlaneAngleForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
FILE* log = NULL;
//FILE* log = stderr;
//FILE* log = fopen( "AmoebaInPlaneAngleForce.log", "w" );;
//FILE* log = fopen("AmoebaInPlaneAngleForce.log", "w");;
testOneAngle( NULL );
testOneAngle(NULL);
#ifdef AMOEBA_DEBUG
if( log && log != stderr )
(void) fclose( log );
if (log && log != stderr)
(void) fclose(log);
#endif
}
......
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