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Commit f11bafd9 authored by peastman's avatar peastman
Browse files

Merge pull request #828 from peastman/cleanup 

Cleanup to AMOEBA code
parents 162d69a2 d95b90b9
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Showing with 3048 additions and 3061 deletions
plugins/amoeba/platforms/cuda/tests/TestCudaWcaDispersionForce.cpp
View file @ f11bafd9
......@@ -54,30 +54,18 @@ const double TOL = 1e-4;
extern "C" void registerAmoebaCudaKernelFactories();
void compareForcesEnergy( std::string& testName, double expectedEnergy, double energy,
void compareForcesEnergy(std::string& testName, double expectedEnergy, double energy,
const std::vector<Vec3>& expectedForces,
const std::vector<Vec3>& forces, double tolerance, FILE* log ) {
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "%s: expected energy=%14.7e %14.7e\n", testName.c_str(), expectedEnergy, energy );
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] );
const std::vector<Vec3>& forces, double tolerance) {
for (unsigned int ii = 0; ii < forces.size(); ii++) {
ASSERT_EQUAL_VEC_MOD(expectedForces[ii], forces[ii], tolerance, testName);
}
(void) fflush( log );
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC_MOD( expectedForces[ii], forces[ii], tolerance, testName );
}
ASSERT_EQUAL_TOL_MOD( expectedEnergy, energy, tolerance, testName );
ASSERT_EQUAL_TOL_MOD(expectedEnergy, energy, tolerance, testName);
}
// test Wca dispersion
void testWcaDispersionAmmonia( FILE* log ) {
void testWcaDispersionAmmonia() {
std::string testName = "testWcaDispersionAmmonia";
......@@ -88,48 +76,48 @@ void testWcaDispersionAmmonia( FILE* log ) {
System system;
AmoebaWcaDispersionForce* amoebaWcaDispersionForce = new AmoebaWcaDispersionForce();;
amoebaWcaDispersionForce->setEpso( 4.6024000e-01 );
amoebaWcaDispersionForce->setEpsh( 5.6484000e-02 );
amoebaWcaDispersionForce->setRmino( 1.7025000e-01 );
amoebaWcaDispersionForce->setRminh( 1.3275000e-01 );
amoebaWcaDispersionForce->setDispoff( 2.6000000e-02 );
amoebaWcaDispersionForce->setAwater( 3.3428000e+01 );
amoebaWcaDispersionForce->setSlevy( 1.0000000e+00 );
amoebaWcaDispersionForce->setShctd( 8.1000000e-01 );
amoebaWcaDispersionForce->setEpso( 4.6024000e-01);
amoebaWcaDispersionForce->setEpsh( 5.6484000e-02);
amoebaWcaDispersionForce->setRmino( 1.7025000e-01);
amoebaWcaDispersionForce->setRminh( 1.3275000e-01);
amoebaWcaDispersionForce->setDispoff(2.6000000e-02);
amoebaWcaDispersionForce->setAwater( 3.3428000e+01);
amoebaWcaDispersionForce->setSlevy( 1.0000000e+00);
amoebaWcaDispersionForce->setShctd( 8.1000000e-01);
// addParticle: radius, epsilon
for( unsigned int ii = 0; ii < 2; ii++ ){
system.addParticle( 1.4007000e+01 );
amoebaWcaDispersionForce->addParticle( 1.8550000e-01, 4.3932000e-01 );
for (unsigned int ii = 0; ii < 2; ii++) {
system.addParticle( 1.4007000e+01);
amoebaWcaDispersionForce->addParticle( 1.8550000e-01, 4.3932000e-01);
system.addParticle( 1.0080000e+00 );
amoebaWcaDispersionForce->addParticle( 1.3500000e-01, 8.3680000e-02 );
system.addParticle( 1.0080000e+00);
amoebaWcaDispersionForce->addParticle( 1.3500000e-01, 8.3680000e-02);
system.addParticle( 1.0080000e+00 );
amoebaWcaDispersionForce->addParticle( 1.3500000e-01, 8.3680000e-02 );
system.addParticle( 1.0080000e+00);
amoebaWcaDispersionForce->addParticle( 1.3500000e-01, 8.3680000e-02);
system.addParticle( 1.0080000e+00 );
amoebaWcaDispersionForce->addParticle( 1.3500000e-01, 8.3680000e-02 );
system.addParticle( 1.0080000e+00);
amoebaWcaDispersionForce->addParticle( 1.3500000e-01, 8.3680000e-02);
}
std::vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3( 1.5927280e-01, 1.7000000e-06, 1.6491000e-03 );
positions[1] = Vec3( 2.0805540e-01, -8.1258800e-02, 3.7282500e-02 );
positions[2] = Vec3( 2.0843610e-01, 8.0953200e-02, 3.7462200e-02 );
positions[3] = Vec3( 1.7280780e-01, 2.0730000e-04, -9.8741700e-02 );
positions[4] = Vec3( -1.6743680e-01, 1.5900000e-05, -6.6149000e-03 );
positions[5] = Vec3( -2.0428260e-01, 8.1071500e-02, 4.1343900e-02 );
positions[6] = Vec3( -6.7308300e-02, 1.2800000e-05, 1.0623300e-02 );
positions[7] = Vec3( -2.0426290e-01, -8.1231400e-02, 4.1033500e-02 );
positions[0] = Vec3( 1.5927280e-01, 1.7000000e-06, 1.6491000e-03);
positions[1] = Vec3( 2.0805540e-01, -8.1258800e-02, 3.7282500e-02);
positions[2] = Vec3( 2.0843610e-01, 8.0953200e-02, 3.7462200e-02);
positions[3] = Vec3( 1.7280780e-01, 2.0730000e-04, -9.8741700e-02);
positions[4] = Vec3( -1.6743680e-01, 1.5900000e-05, -6.6149000e-03);
positions[5] = Vec3( -2.0428260e-01, 8.1071500e-02, 4.1343900e-02);
positions[6] = Vec3( -6.7308300e-02, 1.2800000e-05, 1.0623300e-02);
positions[7] = Vec3( -2.0426290e-01, -8.1231400e-02, 4.1033500e-02);
system.addForce(amoebaWcaDispersionForce);
std::string platformName;
platformName = "CUDA";
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName( platformName ) );
Context context(system, integrator, Platform::getPlatformByName(platformName));
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
......@@ -141,17 +129,17 @@ void testWcaDispersionAmmonia( FILE* log ) {
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = -2.6981209e+01;
expectedForces[0] = Vec3( 4.7839388e+00, -7.3510133e-04, -5.0382764e-01 );
expectedForces[1] = Vec3( 1.4657758e+00, 1.2431003e+00, -6.7075886e-01 );
expectedForces[2] = Vec3( 1.4563936e+00, -1.2399917e+00, -6.7443841e-01 );
expectedForces[3] = Vec3( 2.1116744e+00, -2.7407512e-03, 1.3271245e+00 );
expectedForces[4] = Vec3( -4.7528440e+00, -1.5148066e-03, 1.2653813e+00 );
expectedForces[5] = Vec3( -1.1875619e+00, -1.2866678e+00, -3.9109060e-01 );
expectedForces[6] = Vec3( -2.6885679e+00, -4.3038639e-04, 3.3763583e-02 );
expectedForces[7] = Vec3( -1.1888087e+00, 1.2889802e+00, -3.8615387e-01 );
expectedForces[0] = Vec3( 4.7839388e+00, -7.3510133e-04, -5.0382764e-01);
expectedForces[1] = Vec3( 1.4657758e+00, 1.2431003e+00, -6.7075886e-01);
expectedForces[2] = Vec3( 1.4563936e+00, -1.2399917e+00, -6.7443841e-01);
expectedForces[3] = Vec3( 2.1116744e+00, -2.7407512e-03, 1.3271245e+00);
expectedForces[4] = Vec3( -4.7528440e+00, -1.5148066e-03, 1.2653813e+00);
expectedForces[5] = Vec3( -1.1875619e+00, -1.2866678e+00, -3.9109060e-01);
expectedForces[6] = Vec3( -2.6885679e+00, -4.3038639e-04, 3.3763583e-02);
expectedForces[7] = Vec3( -1.1888087e+00, 1.2889802e+00, -3.8615387e-01);
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy(testName, expectedEnergy, energy, expectedForces, forces, tolerance);
// Try changing the particle parameters and make sure it's still correct.
......@@ -168,7 +156,7 @@ void testWcaDispersionAmmonia( FILE* log ) {
bool exceptionThrown = false;
try {
// This should throw an exception.
compareForcesEnergy(testName, state1.getPotentialEnergy(), state2.getPotentialEnergy(), state1.getForces(), state2.getForces(), tolerance, log);
compareForcesEnergy(testName, state1.getPotentialEnergy(), state2.getPotentialEnergy(), state1.getForces(), state2.getForces(), tolerance);
}
catch (std::exception ex) {
exceptionThrown = true;
......@@ -176,7 +164,7 @@ void testWcaDispersionAmmonia( FILE* log ) {
ASSERT(exceptionThrown);
amoebaWcaDispersionForce->updateParametersInContext(context);
state1 = context.getState(State::Forces | State::Energy);
compareForcesEnergy(testName, state1.getPotentialEnergy(), state2.getPotentialEnergy(), state1.getForces(), state2.getForces(), tolerance, log);
compareForcesEnergy(testName, state1.getPotentialEnergy(), state2.getPotentialEnergy(), state1.getForces(), state2.getForces(), tolerance);
}
int main(int argc, char* argv[]) {
......@@ -185,11 +173,10 @@ int main(int argc, char* argv[]) {
registerAmoebaCudaKernelFactories();
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
FILE* log = NULL;
// test Wca dispersion force using two ammonia molecules
testWcaDispersionAmmonia( log );
testWcaDispersionAmmonia();
} catch(const std::exception& e) {
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ f11bafd9
......@@ -99,7 +99,7 @@ void ReferenceCalcAmoebaBondForceKernel::initialize(const System& system, const
particle1.push_back(particle1Index);
particle2.push_back(particle2Index);
length.push_back( static_cast<RealOpenMM>(lengthValue));
length.push_back(static_cast<RealOpenMM>(lengthValue));
kQuadratic.push_back(static_cast<RealOpenMM>(kValue));
}
globalBondCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalBondCubic());
......@@ -153,7 +153,7 @@ void ReferenceCalcAmoebaAngleForceKernel::initialize(const System& system, const
particle1.push_back(particle1Index);
particle2.push_back(particle2Index);
particle3.push_back(particle3Index);
angle.push_back( static_cast<RealOpenMM>(angleValue));
angle.push_back(static_cast<RealOpenMM>(angleValue));
kQuadratic.push_back(static_cast<RealOpenMM>(k));
}
globalAngleCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleCubic());
......@@ -206,8 +206,8 @@ void ReferenceCalcAmoebaInPlaneAngleForceKernel::initialize(const System& system
particle2.push_back(particle2Index);
particle3.push_back(particle3Index);
particle4.push_back(particle4Index);
angle.push_back( static_cast<RealOpenMM>(angleValue));
kQuadratic.push_back( static_cast<RealOpenMM>(k));
angle.push_back(static_cast<RealOpenMM>(angleValue));
kQuadratic.push_back(static_cast<RealOpenMM>(k));
}
globalInPlaneAngleCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleCubic());
globalInPlaneAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleQuartic());
......@@ -314,9 +314,9 @@ void ReferenceCalcAmoebaStretchBendForceKernel::initialize(const System& system,
particle3.push_back(particle3Index);
lengthABParameters.push_back(static_cast<RealOpenMM>(lengthAB));
lengthCBParameters.push_back(static_cast<RealOpenMM>(lengthCB));
angleParameters.push_back( static_cast<RealOpenMM>(angle));
k1Parameters.push_back( static_cast<RealOpenMM>(k1));
k2Parameters.push_back( static_cast<RealOpenMM>(k2));
angleParameters.push_back(static_cast<RealOpenMM>(angle));
k1Parameters.push_back(static_cast<RealOpenMM>(k1));
k2Parameters.push_back(static_cast<RealOpenMM>(k2));
}
}
......@@ -1043,14 +1043,14 @@ void ReferenceCalcAmoebaWcaDispersionForceKernel::initialize(const System& syste
totalMaximumDispersionEnergy = static_cast<RealOpenMM>(AmoebaWcaDispersionForceImpl::getTotalMaximumDispersionEnergy(force));
epso = static_cast<RealOpenMM>(force.getEpso() );
epsh = static_cast<RealOpenMM>(force.getEpsh() );
rmino = static_cast<RealOpenMM>(force.getRmino() );
rminh = static_cast<RealOpenMM>(force.getRminh() );
epso = static_cast<RealOpenMM>(force.getEpso());
epsh = static_cast<RealOpenMM>(force.getEpsh());
rmino = static_cast<RealOpenMM>(force.getRmino());
rminh = static_cast<RealOpenMM>(force.getRminh());
awater = static_cast<RealOpenMM>(force.getAwater());
shctd = static_cast<RealOpenMM>(force.getShctd() );
shctd = static_cast<RealOpenMM>(force.getShctd());
dispoff = static_cast<RealOpenMM>(force.getDispoff());
slevy = static_cast<RealOpenMM>(force.getSlevy() );
slevy = static_cast<RealOpenMM>(force.getSlevy());
}
double ReferenceCalcAmoebaWcaDispersionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceInPlaneAngleForce.cpp
View file @ f11bafd9
......@@ -210,9 +210,9 @@ RealOpenMM AmoebaReferenceInPlaneAngleForce::calculateAngleIxn(const RealVec& po
RealOpenMM delta2 = delta*two;
AmoebaReferenceForce::getCrossProduct(deltaR[BD], deltaR[CD], deltaR[BDxCD]);
AmoebaReferenceForce::getCrossProduct(deltaR[T], deltaR[CD], deltaR[TxCD] );
AmoebaReferenceForce::getCrossProduct(deltaR[T], deltaR[CD], deltaR[TxCD]);
AmoebaReferenceForce::getCrossProduct(deltaR[AD], deltaR[BD], deltaR[ADxBD]);
AmoebaReferenceForce::getCrossProduct(deltaR[AD], deltaR[T], deltaR[ADxT] );
AmoebaReferenceForce::getCrossProduct(deltaR[AD], deltaR[T], deltaR[ADxT]);
for (int ii = 0; ii < 3; ii++) {
RealOpenMM term = deltaR[BDxCD][ii] + delta2*deltaR[TxCD][ii];
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceOutOfPlaneBendForce.cpp
View file @ f11bafd9
......@@ -91,7 +91,7 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateOutOfPlaneBendIxn(const
std::vector<RealOpenMM> tempVector(3);
AmoebaReferenceForce::getCrossProduct(deltaR[CB], deltaR[DB], tempVector);
RealOpenMM eE = AmoebaReferenceForce::getDotProduct3(deltaR[AB], tempVector );
RealOpenMM eE = AmoebaReferenceForce::getDotProduct3(deltaR[AB], tempVector);
RealOpenMM dot = AmoebaReferenceForce::getDotProduct3(deltaR[AD], deltaR[CD]);
RealOpenMM cc = rAD2*rCD2 - dot*dot;
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferencePiTorsionForce.cpp
View file @ f11bafd9
......@@ -88,8 +88,8 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn(const RealVec& p
deltaR[P][ii] += positionAtomC[ii];
deltaR[Q][ii] += positionAtomD[ii];
}
AmoebaReferenceForce::getCrossProduct(deltaR[CP], deltaR[DC], deltaR[T] );
AmoebaReferenceForce::getCrossProduct(deltaR[DC], deltaR[QD], deltaR[U] );
AmoebaReferenceForce::getCrossProduct(deltaR[CP], deltaR[DC], deltaR[T]);
AmoebaReferenceForce::getCrossProduct(deltaR[DC], deltaR[QD], deltaR[U]);
AmoebaReferenceForce::getCrossProduct(deltaR[T], deltaR[U], deltaR[TU]);
RealOpenMM rT2 = AmoebaReferenceForce::getNormSquared3(deltaR[T]);
......@@ -123,8 +123,8 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn(const RealVec& p
RealOpenMM factorT = dedphi/(rDC*rT2);
RealOpenMM factorU = -dedphi/(rDC*rU2);
AmoebaReferenceForce::getCrossProduct(deltaR[T], deltaR[DC], deltaR[dT] );
AmoebaReferenceForce::getCrossProduct(deltaR[U], deltaR[DC], deltaR[dU] );
AmoebaReferenceForce::getCrossProduct(deltaR[T], deltaR[DC], deltaR[dT]);
AmoebaReferenceForce::getCrossProduct(deltaR[U], deltaR[DC], deltaR[dU]);
for (int ii = 0; ii < 3; ii++) {
deltaR[dT][ii] *= factorT;
deltaR[dU][ii] *= factorU;
......@@ -133,11 +133,11 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn(const RealVec& p
AmoebaReferenceForce::getCrossProduct(deltaR[dT], deltaR[DC], deltaR[dP] );
AmoebaReferenceForce::getCrossProduct(deltaR[dU], deltaR[DC], deltaR[dQ] );
AmoebaReferenceForce::getCrossProduct(deltaR[DP], deltaR[dT], deltaR[dC1] );
AmoebaReferenceForce::getCrossProduct(deltaR[dU], deltaR[QD], deltaR[dC2] );
AmoebaReferenceForce::getCrossProduct(deltaR[DP], deltaR[dT], deltaR[dC1]);
AmoebaReferenceForce::getCrossProduct(deltaR[dU], deltaR[QD], deltaR[dC2]);
AmoebaReferenceForce::getCrossProduct(deltaR[dT], deltaR[CP], deltaR[dD1] );
AmoebaReferenceForce::getCrossProduct(deltaR[QC], deltaR[dU], deltaR[dD2] );
AmoebaReferenceForce::getCrossProduct(deltaR[dT], deltaR[CP], deltaR[dD1]);
AmoebaReferenceForce::getCrossProduct(deltaR[QC], deltaR[dU], deltaR[dD2]);
AmoebaReferenceForce::getCrossProduct(deltaR[BD], deltaR[dP], d[A] );
AmoebaReferenceForce::getCrossProduct(deltaR[dP], deltaR[AD], d[B] );
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.cpp
View file @ f11bafd9
......@@ -478,7 +478,7 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn(const
AmoebaReferenceForce::getCrossProduct(deltaR[CA], deltaR[dT], d[B]);
AmoebaReferenceForce::getCrossProduct(deltaR[dU], deltaR[DC], tmp[0]);
AmoebaReferenceForce::getCrossProduct(deltaR[dT], deltaR[BA], d[C] );
AmoebaReferenceForce::getCrossProduct(deltaR[dT], deltaR[BA], d[C]);
AmoebaReferenceForce::getCrossProduct(deltaR[DB], deltaR[dU], tmp[1]);
d[B][0] += tmp[0][0];
......@@ -507,12 +507,12 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn(const
// dB2
AmoebaReferenceForce::getCrossProduct(deltaR[dU2], deltaR[DC], tmp[0] );
AmoebaReferenceForce::getCrossProduct(deltaR[dU2], deltaR[DC], tmp[0]);
// dC2
AmoebaReferenceForce::getCrossProduct(deltaR[DB], deltaR[dU2], tmp[1] );
AmoebaReferenceForce::getCrossProduct(deltaR[dV2], deltaR[ED], tmp[2] );
AmoebaReferenceForce::getCrossProduct(deltaR[DB], deltaR[dU2], tmp[1]);
AmoebaReferenceForce::getCrossProduct(deltaR[dV2], deltaR[ED], tmp[2]);
d[B][0] += tmp[0][0];
d[B][1] += tmp[0][1];
......@@ -524,8 +524,8 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn(const
// dD2
AmoebaReferenceForce::getCrossProduct(deltaR[dU2], deltaR[CB], tmp[0] );
AmoebaReferenceForce::getCrossProduct(deltaR[EC], deltaR[dV2], tmp[1] );
AmoebaReferenceForce::getCrossProduct(deltaR[dU2], deltaR[CB], tmp[0]);
AmoebaReferenceForce::getCrossProduct(deltaR[EC], deltaR[dV2], tmp[1]);
d[D][0] += tmp[0][0] + tmp[1][0];
d[D][1] += tmp[0][1] + tmp[1][1];
......@@ -533,7 +533,7 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn(const
// dE
AmoebaReferenceForce::getCrossProduct(deltaR[dV2], deltaR[DC], d[E] );
AmoebaReferenceForce::getCrossProduct(deltaR[dV2], deltaR[DC], d[E]);
// ---------------------------------------------------------------------------------------
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceVdwForce.h
View file @ f11bafd9
......@@ -252,7 +252,7 @@ private:
CombiningFunction _combineEpsilons;
RealOpenMM arithmeticEpsilonCombiningRule(RealOpenMM epsilonI, RealOpenMM epsilonJ) const;
RealOpenMM geometricEpsilonCombiningRule(RealOpenMM epsilonI, RealOpenMM epsilonJ) const;
RealOpenMM harmonicEpsilonCombiningRule( RealOpenMM epsilonI, RealOpenMM epsilonJ) const;
RealOpenMM harmonicEpsilonCombiningRule(RealOpenMM epsilonI, RealOpenMM epsilonJ) const;
RealOpenMM hhgEpsilonCombiningRule( RealOpenMM epsilonI, RealOpenMM epsilonJ) const;
/**---------------------------------------------------------------------------------------
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaGeneralizedKirkwoodForce.cpp
View file @ f11bafd9
......@@ -90,7 +90,7 @@ static void setupMultipoleAmmonia(System& system, AmoebaGeneralizedKirkwoodForce
// first N
 
system.addParticle(1.4007000e+01);
amoebaMultipoleForce->addMultipole( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 1, 2, 3, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03);
amoebaMultipoleForce->addMultipole(-5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 1, 2, 3, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03);
 
// 3 H attached to first N
 
......@@ -120,7 +120,7 @@ static void setupMultipoleAmmonia(System& system, AmoebaGeneralizedKirkwoodForce
// second N
 
system.addParticle( 1.4007000e+01);
amoebaMultipoleForce->addMultipole( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 5, 6, 7, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03);
amoebaMultipoleForce->addMultipole(-5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 5, 6, 7, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03);
 
// 3 H attached to second N
 
......@@ -267,7 +267,7 @@ static void setupMultipoleAmmonia(System& system, AmoebaGeneralizedKirkwoodForce
// addParticle: charge, radius, scalingFactor
 
for (unsigned int ii = 0; ii < 2; ii++) {
amoebaGeneralizedKirkwoodForce->addParticle( -5.7960000e-01, 1.5965000e-01, 6.9000000e-01);
amoebaGeneralizedKirkwoodForce->addParticle(-5.7960000e-01, 1.5965000e-01, 6.9000000e-01);
amoebaGeneralizedKirkwoodForce->addParticle( 1.9320000e-01, 1.2360000e-01, 6.9000000e-01);
amoebaGeneralizedKirkwoodForce->addParticle( 1.9320000e-01, 1.2360000e-01, 6.9000000e-01);
amoebaGeneralizedKirkwoodForce->addParticle( 1.9320000e-01, 1.2360000e-01, 6.9000000e-01);
......@@ -282,10 +282,10 @@ static void getForcesEnergyMultipoleAmmonia(Context& context, std::vector<Vec3>&
positions[1] = Vec3( 2.0805540e-01, -8.1258800e-02, 3.7282500e-02);
positions[2] = Vec3( 2.0843610e-01, 8.0953200e-02, 3.7462200e-02);
positions[3] = Vec3( 1.7280780e-01, 2.0730000e-04, -9.8741700e-02);
positions[4] = Vec3( -1.6743680e-01, 1.5900000e-05, -6.6149000e-03);
positions[5] = Vec3( -2.0428260e-01, 8.1071500e-02, 4.1343900e-02);
positions[6] = Vec3( -6.7308300e-02, 1.2800000e-05, 1.0623300e-02);
positions[7] = Vec3( -2.0426290e-01, -8.1231400e-02, 4.1033500e-02);
positions[4] = Vec3(-1.6743680e-01, 1.5900000e-05, -6.6149000e-03);
positions[5] = Vec3(-2.0428260e-01, 8.1071500e-02, 4.1343900e-02);
positions[6] = Vec3(-6.7308300e-02, 1.2800000e-05, 1.0623300e-02);
positions[7] = Vec3(-2.0426290e-01, -8.1231400e-02, 4.1033500e-02);
 
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
......@@ -5744,7 +5744,7 @@ static void setupAndGetForcesEnergyMultipoleVillin(AmoebaMultipoleForce::Polariz
// GK force
 
AmoebaGeneralizedKirkwoodForce* amoebaGeneralizedKirkwoodForce = new AmoebaGeneralizedKirkwoodForce();
amoebaGeneralizedKirkwoodForce->setSolventDielectric( 7.8300000e+01);
amoebaGeneralizedKirkwoodForce->setSolventDielectric(7.8300000e+01);
amoebaGeneralizedKirkwoodForce->setSoluteDielectric( 1.0000000e+00);
amoebaGeneralizedKirkwoodForce->setIncludeCavityTerm(includeCavityTerm);
 
......@@ -7039,11 +7039,11 @@ static void testGeneralizedKirkwoodAmmoniaDirectPolarization() {
 
double expectedEnergy = -7.6636680e+01;
 
expectedForces[0] = Vec3( -6.9252994e+02, -8.9085133e+00, 9.6489739e+01);
expectedForces[0] = Vec3(-6.9252994e+02, -8.9085133e+00, 9.6489739e+01);
expectedForces[1] = Vec3( 1.5593797e+02, -6.0331931e+01, 1.5104507e+01);
expectedForces[2] = Vec3( 1.5870088e+02, 6.1702809e+01, 6.7708985e+00);
expectedForces[3] = Vec3( 1.4089885e+02, 7.5870617e+00, -1.1362294e+02);
expectedForces[4] = Vec3( -1.8916205e+02, 2.1465549e-01, -4.3433152e+02);
expectedForces[4] = Vec3(-1.8916205e+02, 2.1465549e-01, -4.3433152e+02);
expectedForces[5] = Vec3( 1.0208290e+01, 6.2676753e+01, 1.4987953e+02);
expectedForces[6] = Vec3( 4.0621859e+02, 1.8962203e-01, 1.3021956e+02);
expectedForces[7] = Vec3( 9.7274235e+00, -6.3130458e+01, 1.4949024e+02);
......@@ -7072,11 +7072,11 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarization() {
 
double expectedEnergy = -7.8018875e+01;
 
expectedForces[0] = Vec3( -7.6820301e+02, -1.0102760e+01, 1.0094389e+02);
expectedForces[0] = Vec3(-7.6820301e+02, -1.0102760e+01, 1.0094389e+02);
expectedForces[1] = Vec3( 1.7037307e+02, -7.5621857e+01, 2.3320365e+01);
expectedForces[2] = Vec3( 1.7353828e+02, 7.7199741e+01, 1.3965379e+01);
expectedForces[3] = Vec3( 1.5045244e+02, 8.5784569e+00, -1.3377619e+02);
expectedForces[4] = Vec3( -2.1811615e+02, -1.6818022e-01, -4.6103163e+02);
expectedForces[4] = Vec3(-2.1811615e+02, -1.6818022e-01, -4.6103163e+02);
expectedForces[5] = Vec3( 6.2091942e+00, 7.6748687e+01, 1.5883463e+02);
expectedForces[6] = Vec3( 4.8035662e+02, 4.9704902e-01, 1.3948083e+02);
expectedForces[7] = Vec3( 5.3895456e+00, -7.7131137e+01, 1.5826273e+02);
......@@ -7108,11 +7108,11 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm() {
 
double expectedEnergy = -6.0434582e+01;
 
expectedForces[0] = Vec3( -7.8323218e+02, -1.0097644e+01, 1.0256890e+02);
expectedForces[0] = Vec3(-7.8323218e+02, -1.0097644e+01, 1.0256890e+02);
expectedForces[1] = Vec3( 1.7078480e+02, -7.1896701e+01, 2.0840172e+01);
expectedForces[2] = Vec3( 1.7394089e+02, 7.3488594e+01, 1.1484648e+01);
expectedForces[3] = Vec3( 1.5169364e+02, 8.5611299e+00, -1.2968050e+02);
expectedForces[4] = Vec3( -2.1669693e+02, -1.5926823e-01, -4.6636274e+02);
expectedForces[4] = Vec3(-2.1669693e+02, -1.5926823e-01, -4.6636274e+02);
expectedForces[5] = Vec3( 8.7397444e+00, 7.3330990e+01, 1.6016898e+02);
expectedForces[6] = Vec3( 4.8684950e+02, 4.8937161e-01, 1.4137061e+02);
expectedForces[7] = Vec3( 7.9205382e+00, -7.3716473e+01, 1.5960993e+02);
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaInPlaneAngleForce.cpp
View file @ f11bafd9
......@@ -215,9 +215,9 @@ static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& po
double delta2 = delta*2.0;
crossProductVector3(deltaR[BD], deltaR[CD], deltaR[BDxCD]);
crossProductVector3(deltaR[T], deltaR[CD], deltaR[TxCD] );
crossProductVector3(deltaR[T], deltaR[CD], deltaR[TxCD]);
crossProductVector3(deltaR[AD], deltaR[BD], deltaR[ADxBD]);
crossProductVector3(deltaR[AD], deltaR[T], deltaR[ADxT] );
crossProductVector3(deltaR[AD], deltaR[T], deltaR[ADxT]);
for (int ii = 0; ii < 3; ii++) {
double term = deltaR[BDxCD][ii] + delta2*deltaR[TxCD][ii];
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaOutOfPlaneBendForce.cpp
View file @ f11bafd9
......@@ -114,7 +114,7 @@ static void computeAmoebaOutOfPlaneBendForce(int bondIndex, std::vector<Vec3>&
double tempVector[3];
crossProductVector3(deltaR[CB], deltaR[DB], tempVector);
double eE = dotVector3(deltaR[AB], tempVector );
double eE = dotVector3(deltaR[AB], tempVector);
double dot = dotVector3(deltaR[AD], deltaR[CD]);
double cc = rAD2*rCD2 - dot*dot;
......@@ -278,8 +278,8 @@ void testOneOutOfPlaneBend() {
AmoebaOutOfPlaneBendForce* amoebaOutOfPlaneBendForce = new AmoebaOutOfPlaneBendForce();
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendCubic( -0.1400000E-01);
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendQuartic( 0.5600000E-04);
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendPentic( -0.7000000E-06);
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendQuartic(0.5600000E-04);
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendPentic(-0.7000000E-06);
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendSextic( 0.2200000E-07);
double kOutOfPlaneBend = 0.328682196E-01;
......@@ -330,8 +330,8 @@ void testOneOutOfPlaneBend2(int setId) {
AmoebaOutOfPlaneBendForce* amoebaOutOfPlaneBendForce = new AmoebaOutOfPlaneBendForce();
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendCubic( -0.1400000E-01);
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendQuartic( 0.5600000E-04);
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendPentic( -0.7000000E-06);
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendQuartic(0.5600000E-04);
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendPentic(-0.7000000E-06);
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendSextic( 0.2200000E-07);
/*
285 441 442 443 444 0.328682196E-01
......@@ -352,15 +352,15 @@ void testOneOutOfPlaneBend2(int setId) {
*/
std::map<int,Vec3> coordinates;
coordinates[440] = Vec3( 0.893800000E+01, 0.439800000E+01, 0.343100000E+01);
coordinates[441] = Vec3( 0.779100000E+01, 0.614600000E+01, 0.390100000E+01);
coordinates[442] = Vec3( 0.915400000E+01, 0.683900000E+01, 0.389400000E+01);
coordinates[443] = Vec3( 0.101770000E+02, 0.619000000E+01, 0.379900000E+01);
coordinates[444] = Vec3( 0.921000000E+01, 0.813800000E+01, 0.398600000E+01);
coordinates[445] = Vec3( 0.708500000E+01, 0.672900000E+01, 0.332700000E+01);
coordinates[446] = Vec3( 0.744300000E+01, 0.605200000E+01, 0.491900000E+01);
coordinates[447] = Vec3( 0.100820000E+02, 0.859300000E+01, 0.398200000E+01);
coordinates[448] = Vec3( 0.838000000E+01, 0.866100000E+01, 0.406000000E+01);
coordinates[440] = Vec3(0.893800000E+01, 0.439800000E+01, 0.343100000E+01);
coordinates[441] = Vec3(0.779100000E+01, 0.614600000E+01, 0.390100000E+01);
coordinates[442] = Vec3(0.915400000E+01, 0.683900000E+01, 0.389400000E+01);
coordinates[443] = Vec3(0.101770000E+02, 0.619000000E+01, 0.379900000E+01);
coordinates[444] = Vec3(0.921000000E+01, 0.813800000E+01, 0.398600000E+01);
coordinates[445] = Vec3(0.708500000E+01, 0.672900000E+01, 0.332700000E+01);
coordinates[446] = Vec3(0.744300000E+01, 0.605200000E+01, 0.491900000E+01);
coordinates[447] = Vec3(0.100820000E+02, 0.859300000E+01, 0.398200000E+01);
coordinates[448] = Vec3(0.838000000E+01, 0.866100000E+01, 0.406000000E+01);
double kOutOfPlaneBend = 0.328682196E-01;
std::vector<int> particleIndices;
......@@ -435,15 +435,15 @@ void testOneOutOfPlaneBend2(int setId) {
static double totalEnergy;
if (iter == 0) {
totalForces[441] = Vec3( 0.0, 0.0, 0.0);
totalForces[442] = Vec3( 0.0, 0.0, 0.0);
totalForces[443] = Vec3( 0.0, 0.0, 0.0);
totalForces[444] = Vec3( 0.0, 0.0, 0.0);
totalForces[445] = Vec3( 0.0, 0.0, 0.0);
totalForces[446] = Vec3( 0.0, 0.0, 0.0);
totalForces[447] = Vec3( 0.0, 0.0, 0.0);
totalForces[448] = Vec3( 0.0, 0.0, 0.0);
totalForces[449] = Vec3( 0.0, 0.0, 0.0);
totalForces[441] = Vec3(0.0, 0.0, 0.0);
totalForces[442] = Vec3(0.0, 0.0, 0.0);
totalForces[443] = Vec3(0.0, 0.0, 0.0);
totalForces[444] = Vec3(0.0, 0.0, 0.0);
totalForces[445] = Vec3(0.0, 0.0, 0.0);
totalForces[446] = Vec3(0.0, 0.0, 0.0);
totalForces[447] = Vec3(0.0, 0.0, 0.0);
totalForces[448] = Vec3(0.0, 0.0, 0.0);
totalForces[449] = Vec3(0.0, 0.0, 0.0);
totalEnergy = 0.0;
}
iter++;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaPiTorsionForce.cpp
View file @ f11bafd9
......@@ -108,8 +108,8 @@ static void computeAmoebaPiTorsionForce(int bondIndex, std::vector<Vec3>& posit
deltaR[P][ii] += positions[particle3][ii];
deltaR[Q][ii] += positions[particle4][ii];
}
crossProductVector3(deltaR[CP], deltaR[DC], deltaR[T] );
crossProductVector3(deltaR[DC], deltaR[QD], deltaR[U] );
crossProductVector3(deltaR[CP], deltaR[DC], deltaR[T]);
crossProductVector3(deltaR[DC], deltaR[QD], deltaR[U]);
crossProductVector3(deltaR[T], deltaR[U], deltaR[TU]);
double rT2 = dotVector3(deltaR[T], deltaR[T]);
......@@ -144,8 +144,8 @@ static void computeAmoebaPiTorsionForce(int bondIndex, std::vector<Vec3>& posit
double factorT = dedphi/(rDC*rT2);
double factorU = -dedphi/(rDC*rU2);
crossProductVector3(deltaR[T], deltaR[DC], deltaR[dT] );
crossProductVector3(deltaR[U], deltaR[DC], deltaR[dU] );
crossProductVector3(deltaR[T], deltaR[DC], deltaR[dT]);
crossProductVector3(deltaR[U], deltaR[DC], deltaR[dU]);
for (int ii = 0; ii < 3; ii++) {
deltaR[dT][ii] *= factorT;
deltaR[dU][ii] *= factorU;
......@@ -154,11 +154,11 @@ static void computeAmoebaPiTorsionForce(int bondIndex, std::vector<Vec3>& posit
crossProductVector3(deltaR[dT], deltaR[DC], deltaR[dP] );
crossProductVector3(deltaR[dU], deltaR[DC], deltaR[dQ] );
crossProductVector3(deltaR[DP], deltaR[dT], deltaR[dC1] );
crossProductVector3(deltaR[dU], deltaR[QD], deltaR[dC2] );
crossProductVector3(deltaR[DP], deltaR[dT], deltaR[dC1]);
crossProductVector3(deltaR[dU], deltaR[QD], deltaR[dC2]);
crossProductVector3(deltaR[dT], deltaR[CP], deltaR[dD1] );
crossProductVector3(deltaR[QC], deltaR[dU], deltaR[dD2] );
crossProductVector3(deltaR[dT], deltaR[CP], deltaR[dD1]);
crossProductVector3(deltaR[QC], deltaR[dU], deltaR[dD2]);
crossProductVector3(deltaR[BD], deltaR[dP], d[A] );
crossProductVector3(deltaR[dP], deltaR[AD], d[B] );
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaTorsionTorsionForce.cpp
View file @ f11bafd9
......@@ -2611,12 +2611,12 @@ void testTorsionTorsion(int systemId, bool includeDerivs) {
positions[4] = Vec3(-0.760612300E+01, -0.992590200E+01, -0.275088400E+01);
positions[5] = Vec3(-0.516893900E+01, -0.788347000E+01, -0.316943000E+01);
expectedForces[0] = Vec3( 0.906091624E+00, -0.529814945E-01, 0.690384140E+00);
expectedForces[0] = Vec3(0.906091624E+00, -0.529814945E-01, 0.690384140E+00);
expectedForces[1] = Vec3(-0.124550232E+01, -0.999341692E+00, -0.590867130E+00);
expectedForces[2] = Vec3( 0.534419689E+00, 0.612404926E-01, 0.547380310E-01);
expectedForces[2] = Vec3(0.534419689E+00, 0.612404926E-01, 0.547380310E-01);
expectedForces[3] = Vec3(-5.732010432E-01, 2.645718463E+00, -1.585204274E-01);
expectedForces[4] = Vec3( 3.781920539E-01, -1.654635768E+00, 4.265386268E-03);
expectedForces[5] = Vec3( 0.0, 0.0, 0.0);
expectedForces[4] = Vec3(3.781920539E-01, -1.654635768E+00, 4.265386268E-03);
expectedForces[5] = Vec3(0.0, 0.0, 0.0);
expectedEnergy = -2.699654759E+00;
......@@ -2632,14 +2632,14 @@ void testTorsionTorsion(int systemId, bool includeDerivs) {
positions[2] = Vec3(-0.128314660E+02, -0.876338000E+00, 0.942959800E+01);
positions[3] = Vec3(-0.130879850E+02, -0.760280000E-01, 0.814732200E+01);
positions[4] = Vec3(-0.120888080E+02, 0.112050000E-01, 0.722704500E+01);
positions[5] = Vec3( 0.0, 0.0, 0.0);
positions[5] = Vec3(0.0, 0.0, 0.0);
expectedForces[0] = Vec3( 4.165851130E-01, 6.608242922E-01, -8.082168261E-01);
expectedForces[0] = Vec3(4.165851130E-01, 6.608242922E-01, -8.082168261E-01);
expectedForces[1] = Vec3(-6.024659721E-01, -8.878744406E-01, 1.322274444E+00);
expectedForces[2] = Vec3( 3.196925118E-02, -3.137497848E-01, -8.207984001E-01);
expectedForces[3] = Vec3( 3.842205941E-02, 2.602732089E-01, 1.547586195E-01);
expectedForces[4] = Vec3( 1.154895485E-01, 2.805267242E-01, 1.519821623E-01);
expectedForces[5] = Vec3( 0.0, 0.0, 0.0);
expectedForces[2] = Vec3(3.196925118E-02, -3.137497848E-01, -8.207984001E-01);
expectedForces[3] = Vec3(3.842205941E-02, 2.602732089E-01, 1.547586195E-01);
expectedForces[4] = Vec3(1.154895485E-01, 2.805267242E-01, 1.519821623E-01);
expectedForces[5] = Vec3(0.0, 0.0, 0.0);
expectedEnergy = -3.372536909E+00;
}
......
plugins/amoeba/platforms/reference/tests/TestReferenceWcaDispersionForce.cpp
View file @ f11bafd9
......@@ -84,7 +84,7 @@ void testWcaDispersionAmmonia(FILE* log) {
amoebaWcaDispersionForce->setRmino( 1.7025000e-01);
amoebaWcaDispersionForce->setRminh( 1.3275000e-01);
amoebaWcaDispersionForce->setDispoff(2.6000000e-02);
amoebaWcaDispersionForce->setAwater( 3.3428000e+01);
amoebaWcaDispersionForce->setAwater(3.3428000e+01);
amoebaWcaDispersionForce->setSlevy( 1.0000000e+00);
amoebaWcaDispersionForce->setShctd( 8.1000000e-01);
......@@ -110,10 +110,10 @@ void testWcaDispersionAmmonia(FILE* log) {
positions[1] = Vec3( 2.0805540e-01, -8.1258800e-02, 3.7282500e-02);
positions[2] = Vec3( 2.0843610e-01, 8.0953200e-02, 3.7462200e-02);
positions[3] = Vec3( 1.7280780e-01, 2.0730000e-04, -9.8741700e-02);
positions[4] = Vec3( -1.6743680e-01, 1.5900000e-05, -6.6149000e-03);
positions[5] = Vec3( -2.0428260e-01, 8.1071500e-02, 4.1343900e-02);
positions[6] = Vec3( -6.7308300e-02, 1.2800000e-05, 1.0623300e-02);
positions[7] = Vec3( -2.0426290e-01, -8.1231400e-02, 4.1033500e-02);
positions[4] = Vec3(-1.6743680e-01, 1.5900000e-05, -6.6149000e-03);
positions[5] = Vec3(-2.0428260e-01, 8.1071500e-02, 4.1343900e-02);
positions[6] = Vec3(-6.7308300e-02, 1.2800000e-05, 1.0623300e-02);
positions[7] = Vec3(-2.0426290e-01, -8.1231400e-02, 4.1033500e-02);
system.addForce(amoebaWcaDispersionForce);
ASSERT(!amoebaWcaDispersionForce->usesPeriodicBoundaryConditions());
......@@ -138,10 +138,10 @@ void testWcaDispersionAmmonia(FILE* log) {
expectedForces[1] = Vec3( 1.4657758e+00, 1.2431003e+00, -6.7075886e-01);
expectedForces[2] = Vec3( 1.4563936e+00, -1.2399917e+00, -6.7443841e-01);
expectedForces[3] = Vec3( 2.1116744e+00, -2.7407512e-03, 1.3271245e+00);
expectedForces[4] = Vec3( -4.7528440e+00, -1.5148066e-03, 1.2653813e+00);
expectedForces[5] = Vec3( -1.1875619e+00, -1.2866678e+00, -3.9109060e-01);
expectedForces[6] = Vec3( -2.6885679e+00, -4.3038639e-04, 3.3763583e-02);
expectedForces[7] = Vec3( -1.1888087e+00, 1.2889802e+00, -3.8615387e-01);
expectedForces[4] = Vec3(-4.7528440e+00, -1.5148066e-03, 1.2653813e+00);
expectedForces[5] = Vec3(-1.1875619e+00, -1.2866678e+00, -3.9109060e-01);
expectedForces[6] = Vec3(-2.6885679e+00, -4.3038639e-04, 3.3763583e-02);
expectedForces[7] = Vec3(-1.1888087e+00, 1.2889802e+00, -3.8615387e-01);
double tolerance = 1.0e-04;
compareForcesEnergy(testName, expectedEnergy, energy, expectedForces, forces, tolerance, log);
......
plugins/amoeba/serialization/src/AmoebaAngleForceProxy.cpp
View file @ f11bafd9
......@@ -66,13 +66,13 @@ void* AmoebaAngleForceProxy::deserialize(const SerializationNode& node) const {
AmoebaAngleForce* force = new AmoebaAngleForce();
try {
force->setAmoebaGlobalAngleCubic(node.getDoubleProperty( "cubic"));
force->setAmoebaGlobalAngleCubic(node.getDoubleProperty("cubic"));
force->setAmoebaGlobalAngleQuartic(node.getDoubleProperty("quartic"));
force->setAmoebaGlobalAnglePentic(node.getDoubleProperty( "pentic"));
force->setAmoebaGlobalAngleSextic(node.getDoubleProperty( "sextic"));
force->setAmoebaGlobalAnglePentic(node.getDoubleProperty("pentic"));
force->setAmoebaGlobalAngleSextic(node.getDoubleProperty("sextic"));
const SerializationNode& bonds = node.getChildNode("Angles");
for ( unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) {
for (unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) {
const SerializationNode& bond = bonds.getChildren()[ii];
force->addAngle(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getIntProperty("p3"), bond.getDoubleProperty("d"), bond.getDoubleProperty("k"));
}
......
plugins/amoeba/serialization/src/AmoebaBondForceProxy.cpp
View file @ f11bafd9
......@@ -65,7 +65,7 @@ void* AmoebaBondForceProxy::deserialize(const SerializationNode& node) const {
force->setAmoebaGlobalBondCubic(node.getDoubleProperty("cubic"));
force->setAmoebaGlobalBondQuartic(node.getDoubleProperty("quartic"));
const SerializationNode& bonds = node.getChildNode("Bonds");
for ( unsigned int ii = 0; ii < (int) bonds.getChildren().size(); ii++) {
for (unsigned int ii = 0; ii < (int) bonds.getChildren().size(); ii++) {
const SerializationNode& bond = bonds.getChildren()[ii];
force->addBond(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getDoubleProperty("d"), bond.getDoubleProperty("k"));
}
......
plugins/amoeba/serialization/src/AmoebaGeneralizedKirkwoodForceProxy.cpp
View file @ f11bafd9
......@@ -45,17 +45,17 @@ void AmoebaGeneralizedKirkwoodForceProxy::serialize(const void* object, Serializ
node.setIntProperty("version", 1);
const AmoebaGeneralizedKirkwoodForce& force = *reinterpret_cast<const AmoebaGeneralizedKirkwoodForce*>(object);
node.setDoubleProperty("GeneralizedKirkwoodSolventDielectric", force.getSolventDielectric() );
node.setDoubleProperty("GeneralizedKirkwoodSoluteDielectric", force.getSoluteDielectric() );
//node.setDoubleProperty("GeneralizedKirkwoodDielectricOffset", force.getDielectricOffset() );
node.setDoubleProperty("GeneralizedKirkwoodProbeRadius", force.getProbeRadius() );
node.setDoubleProperty("GeneralizedKirkwoodSurfaceAreaFactor", force.getSurfaceAreaFactor() );
node.setIntProperty( "GeneralizedKirkwoodIncludeCavityTerm", force.getIncludeCavityTerm() );
node.setDoubleProperty("GeneralizedKirkwoodSolventDielectric", force.getSolventDielectric());
node.setDoubleProperty("GeneralizedKirkwoodSoluteDielectric", force.getSoluteDielectric());
//node.setDoubleProperty("GeneralizedKirkwoodDielectricOffset", force.getDielectricOffset());
node.setDoubleProperty("GeneralizedKirkwoodProbeRadius", force.getProbeRadius());
node.setDoubleProperty("GeneralizedKirkwoodSurfaceAreaFactor", force.getSurfaceAreaFactor());
node.setIntProperty( "GeneralizedKirkwoodIncludeCavityTerm", force.getIncludeCavityTerm());
SerializationNode& particles = node.createChildNode("GeneralizedKirkwoodParticles");
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
double radius, charge, scalingFactor;
force.getParticleParameters( ii, charge, radius, scalingFactor );
force.getParticleParameters(ii, charge, radius, scalingFactor);
particles.createChildNode("Particle").setDoubleProperty("charge", charge).setDoubleProperty("radius", radius).setDoubleProperty("scaleFactor", scalingFactor);
}
......@@ -67,17 +67,17 @@ void* AmoebaGeneralizedKirkwoodForceProxy::deserialize(const SerializationNode&
AmoebaGeneralizedKirkwoodForce* force = new AmoebaGeneralizedKirkwoodForce();
try {
force->setSolventDielectric( node.getDoubleProperty( "GeneralizedKirkwoodSolventDielectric" ) );
force->setSoluteDielectric( node.getDoubleProperty( "GeneralizedKirkwoodSoluteDielectric" ) );
//force->setDielectricOffset( node.getDoubleProperty( "GeneralizedKirkwoodDielectricOffset" ) );
force->setProbeRadius( node.getDoubleProperty( "GeneralizedKirkwoodProbeRadius" ) );
force->setSurfaceAreaFactor( node.getDoubleProperty( "GeneralizedKirkwoodSurfaceAreaFactor" ) );
force->setIncludeCavityTerm( node.getIntProperty( "GeneralizedKirkwoodIncludeCavityTerm" ) );
force->setSolventDielectric( node.getDoubleProperty("GeneralizedKirkwoodSolventDielectric"));
force->setSoluteDielectric( node.getDoubleProperty("GeneralizedKirkwoodSoluteDielectric"));
//force->setDielectricOffset( node.getDoubleProperty("GeneralizedKirkwoodDielectricOffset"));
force->setProbeRadius( node.getDoubleProperty("GeneralizedKirkwoodProbeRadius"));
force->setSurfaceAreaFactor( node.getDoubleProperty("GeneralizedKirkwoodSurfaceAreaFactor"));
force->setIncludeCavityTerm( node.getIntProperty( "GeneralizedKirkwoodIncludeCavityTerm"));
const SerializationNode& particles = node.getChildNode("GeneralizedKirkwoodParticles");
for (unsigned int ii = 0; ii < particles.getChildren().size(); ii++) {
const SerializationNode& particle = particles.getChildren()[ii];
force->addParticle( particle.getDoubleProperty("charge"), particle.getDoubleProperty("radius"), particle.getDoubleProperty("scaleFactor"));
force->addParticle(particle.getDoubleProperty("charge"), particle.getDoubleProperty("radius"), particle.getDoubleProperty("scaleFactor"));
}
}
catch (...) {
......
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