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Commit e1e1e12d authored by peastman's avatar peastman
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Changed definition of polarizability to match CHARMM

parent 1aa2ccb7
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Showing with 40 additions and 40 deletions
plugins/drude/platforms/cuda/src/CudaDrudeKernels.cpp
View file @ e1e1e12d
......@@ -126,9 +126,9 @@ void CudaCalcDrudeForceKernel::initialize(const System& system, const DrudeForce
double a1 = (atoms[i][2] == -1 ? 1 : aniso12);
double a2 = (atoms[i][3] == -1 || atoms[i][4] == -1 ? 1 : aniso34);
double a3 = 3-a1-a2;
double k3 = charge*charge/(polarizability*a3);
double k1 = charge*charge/(polarizability*a1) - k3;
double k2 = charge*charge/(polarizability*a2) - k3;
double k3 = ONE_4PI_EPS0*charge*charge/(polarizability*a3);
double k1 = ONE_4PI_EPS0*charge*charge/(polarizability*a1) - k3;
double k2 = ONE_4PI_EPS0*charge*charge/(polarizability*a2) - k3;
if (atoms[i][2] == -1) {
atoms[i][2] = 0;
k1 = 0;
......
plugins/drude/platforms/cuda/tests/TestCudaDrudeForce.cpp
View file @ e1e1e12d
......@@ -76,9 +76,9 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg
}
void testSingleParticle() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
......@@ -92,9 +92,9 @@ void testSingleParticle() {
}
void testAnisotropicParticle() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double a1 = 0.8;
const double a2 = 1.1;
const double k1 = k/a1;
......@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) {
}
void testThole() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double thole = 2.5;
System system;
system.addParticle(1.0);
......@@ -157,9 +157,9 @@ void testThole() {
}
void testChangingParameters() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
Platform& platform = Platform::getPlatformByName("CUDA");
// Create the system.
......@@ -184,9 +184,9 @@ void testChangingParameters() {
// Modify the parameters.
const double k2 = 2.2;
const double k2 = ONE_4PI_EPS0*2.2;
const double charge2 = 0.3;
const double alpha2 = charge2*charge2/k2;
const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
drude->updateParametersInContext(context);
state = context.getState(State::Energy);
......
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.cpp
View file @ e1e1e12d
......@@ -131,9 +131,9 @@ void OpenCLCalcDrudeForceKernel::initialize(const System& system, const DrudeFor
double a1 = (atoms[i][2] == -1 ? 1 : aniso12);
double a2 = (atoms[i][3] == -1 || atoms[i][4] == -1 ? 1 : aniso34);
double a3 = 3-a1-a2;
double k3 = charge*charge/(polarizability*a3);
double k1 = charge*charge/(polarizability*a1) - k3;
double k2 = charge*charge/(polarizability*a2) - k3;
double k3 = ONE_4PI_EPS0*charge*charge/(polarizability*a3);
double k1 = ONE_4PI_EPS0*charge*charge/(polarizability*a1) - k3;
double k2 = ONE_4PI_EPS0*charge*charge/(polarizability*a2) - k3;
if (atoms[i][2] == -1) {
atoms[i][2] = 0;
k1 = 0;
......
plugins/drude/platforms/opencl/tests/TestOpenCLDrudeForce.cpp
View file @ e1e1e12d
......@@ -76,9 +76,9 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg
}
void testSingleParticle() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
......@@ -92,9 +92,9 @@ void testSingleParticle() {
}
void testAnisotropicParticle() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double a1 = 0.8;
const double a2 = 1.1;
const double k1 = k/a1;
......@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) {
}
void testThole() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double thole = 2.5;
System system;
system.addParticle(1.0);
......@@ -157,9 +157,9 @@ void testThole() {
}
void testChangingParameters() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
Platform& platform = Platform::getPlatformByName("OpenCL");
// Create the system.
......@@ -184,9 +184,9 @@ void testChangingParameters() {
// Modify the parameters.
const double k2 = 2.2;
const double k2 = ONE_4PI_EPS0*2.2;
const double charge2 = 0.3;
const double alpha2 = charge2*charge2/k2;
const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
drude->updateParametersInContext(context);
state = context.getState(State::Energy);
......
plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp
View file @ e1e1e12d
......@@ -136,9 +136,9 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include
RealOpenMM a1 = (p2 == -1 ? 1 : aniso12[i]);
RealOpenMM a2 = (p3 == -1 || p4 == -1 ? 1 : aniso34[i]);
RealOpenMM a3 = 3-a1-a2;
RealOpenMM k3 = charge[i]*charge[i]/(polarizability[i]*a3);
RealOpenMM k1 = charge[i]*charge[i]/(polarizability[i]*a1) - k3;
RealOpenMM k2 = charge[i]*charge[i]/(polarizability[i]*a2) - k3;
RealOpenMM k3 = ONE_4PI_EPS0*charge[i]*charge[i]/(polarizability[i]*a3);
RealOpenMM k1 = ONE_4PI_EPS0*charge[i]*charge[i]/(polarizability[i]*a1) - k3;
RealOpenMM k2 = ONE_4PI_EPS0*charge[i]*charge[i]/(polarizability[i]*a2) - k3;
// Compute the isotropic force.
......
plugins/drude/platforms/reference/tests/TestReferenceDrudeForce.cpp
View file @ e1e1e12d
......@@ -76,9 +76,9 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg
}
void testSingleParticle() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
......@@ -92,9 +92,9 @@ void testSingleParticle() {
}
void testAnisotropicParticle() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double a1 = 0.8;
const double a2 = 1.1;
const double k1 = k/a1;
......@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) {
}
void testThole() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double thole = 2.5;
System system;
system.addParticle(1.0);
......@@ -157,9 +157,9 @@ void testThole() {
}
void testChangingParameters() {
const double k = 1.5;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = charge*charge/k;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
Platform& platform = Platform::getPlatformByName("Reference");
// Create the system.
......@@ -184,9 +184,9 @@ void testChangingParameters() {
// Modify the parameters.
const double k2 = 2.2;
const double k2 = ONE_4PI_EPS0*2.2;
const double charge2 = 0.3;
const double alpha2 = charge2*charge2/k2;
const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
drude->updateParametersInContext(context);
state = context.getState(State::Energy);
......
wrappers/python/simtk/openmm/app/data/swm4ndp.xml
View file @ e1e1e12d
......@@ -30,7 +30,7 @@
<Atom type="swm4ndp-OD" charge="-1.71636" sigma="1" epsilon="0"/>
</NonbondedForce>
<DrudeForce>
<Particle type1="swm4ndp-OD" type2="swm4ndp-O" charge="-1.71636" polarizability="7.040850e-6" thole="1.3"/>
<Particle type1="swm4ndp-OD" type2="swm4ndp-O" charge="-1.71636" polarizability="0.000978253" thole="1.3"/>
</DrudeForce>
</ForceField>
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