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Commit 14e78600 authored by Peter Eastman's avatar Peter Eastman
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Deleted GBVIForce

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platforms/reference/tests/TestReferenceGBVIForce.cpp deleted 100644 → 0
View file @ b20c20fe
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the reference implementation of GBVIForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "ReferencePlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/GBVIForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/NonbondedForce.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
ReferencePlatform platform;
const double TOL = 1e-5;
void testSingleParticle() {
System system;
system.addParticle(2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBVIForce* forceField = new GBVIForce();
double charge = -1.0;
double radius = 0.15;
double gamma = 1.0;
forceField->addParticle(charge, radius, gamma);
system.addForce(forceField);
ASSERT(!forceField->usesPeriodicBoundaryConditions());
ASSERT(!system.usesPeriodicBoundaryConditions());
Context context(system, integrator, platform);
vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Energy);
double bornRadius = radius;
double eps0 = EPSILON0;
double tau = (1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric());
double bornEnergy = (-charge*charge/(8*PI_M*eps0))*tau/bornRadius;
double nonpolarEnergy = -gamma*tau*std::pow(radius/bornRadius, 3.0);
double expectedE = (bornEnergy+nonpolarEnergy);
double obtainedE = state.getPotentialEnergy();
double diff = fabs((obtainedE - expectedE)/expectedE);
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
}
void testEnergyEthane(int applyBornRadiiScaling) {
const int numParticles = 8;
System system;
LangevinIntegrator integrator(0, 0.1, 0.01);
// harmonic bond
double C_HBondDistance = 0.1097;
double C_CBondDistance = 0.1504;
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, C_HBondDistance, 0.0);
bonds->addBond(2, 1, C_HBondDistance, 0.0);
bonds->addBond(3, 1, C_HBondDistance, 0.0);
bonds->addBond(1, 4, C_CBondDistance, 0.0);
bonds->addBond(5, 4, C_HBondDistance, 0.0);
bonds->addBond(6, 4, C_HBondDistance, 0.0);
bonds->addBond(7, 4, C_HBondDistance, 0.0);
system.addForce(bonds);
double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
int AM1_BCC = 1;
H_charge = -0.053;
C_charge = -3.0*H_charge;
if (AM1_BCC) {
C_radius = 0.180;
C_gamma = -0.2863;
H_radius = 0.125;
H_gamma = 0.2437;
}
else {
C_radius = 0.215;
C_gamma = -1.1087;
H_radius = 0.150;
H_gamma = 0.1237;
}
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
GBVIForce* forceField = new GBVIForce();
if (applyBornRadiiScaling) {
forceField->setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
}
else {
forceField->setBornRadiusScalingMethod(GBVIForce::NoScaling);
}
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
forceField->addParticle(H_charge, H_radius, H_gamma);
nonbonded->addParticle( H_charge, H_radius, 0.0);
}
forceField->setParticleParameters(1, C_charge, C_radius, C_gamma);
forceField->setParticleParameters(4, C_charge, C_radius, C_gamma);
nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
forceField->addBond(0, 1, C_HBondDistance);
forceField->addBond(2, 1, C_HBondDistance);
forceField->addBond(3, 1, C_HBondDistance);
forceField->addBond(1, 4, C_CBondDistance);
forceField->addBond(5, 4, C_HBondDistance);
forceField->addBond(6, 4, C_HBondDistance);
forceField->addBond(7, 4, C_HBondDistance);
std::vector<pair<int, int> > bondExceptions;
std::vector<double> bondDistances;
bondExceptions.push_back(pair<int, int>(0, 1));
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(2, 1));
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(3, 1));
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(1, 4));
bondDistances.push_back(C_CBondDistance);
bondExceptions.push_back(pair<int, int>(5, 4));
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(6, 4));
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(7, 4));
bondDistances.push_back(C_HBondDistance);
nonbonded->createExceptionsFromBonds(bondExceptions, 0.0, 0.0);
system.addForce(forceField);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
positions[0] = Vec3(0.5480, 1.7661, 0.0000);
positions[1] = Vec3(0.7286, 0.8978, 0.6468);
positions[2] = Vec3(0.4974, 0.0000, 0.0588);
positions[3] = Vec3(0.0000, 0.9459, 1.4666);
positions[4] = Vec3(2.1421, 0.8746, 1.1615);
positions[5] = Vec3(2.3239, 0.0050, 1.8065);
positions[6] = Vec3(2.8705, 0.8295, 0.3416);
positions[7] = Vec3(2.3722, 1.7711, 1.7518);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
// Take a small step in the direction of the energy gradient.
double norm = 0.0;
double forceSum[3] = { 0.0, 0.0, 0.0 };
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
forceSum[0] += f[0];
forceSum[1] += f[1];
forceSum[2] += f[2];
}
norm = std::sqrt(norm);
const double delta = 1e-4;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
// See whether the potential energy changed by the expected amount.
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
}
int main() {
try {
testSingleParticle();
testEnergyEthane(0);
testEnergyEthane(1);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
serialization/include/openmm/serialization/GBVIForceProxy.h deleted 100644 → 0
View file @ b20c20fe
#ifndef OPENMM_GBVIFORCE_PROXY_H_
#define OPENMM_GBVIFORCE_PROXY_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/windowsExport.h"
#include "openmm/serialization/SerializationProxy.h"
namespace OpenMM {
/**
* This is a proxy for serializing GBVIForce objects.
*/
class OPENMM_EXPORT GBVIForceProxy : public SerializationProxy {
public:
GBVIForceProxy();
void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const;
};
} // namespace OpenMM
#endif /*OPENMM_GBVIFORCE_PROXY_H_*/
serialization/src/GBVIForceProxy.cpp deleted 100644 → 0
View file @ b20c20fe
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/GBVIForceProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h"
#include "openmm/GBVIForce.h"
#include <sstream>
using namespace OpenMM;
using namespace std;
GBVIForceProxy::GBVIForceProxy() : SerializationProxy("GBVIForce") {
}
void GBVIForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 2);
const GBVIForce& force = *reinterpret_cast<const GBVIForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setIntProperty("method", (int) force.getNonbondedMethod());
node.setIntProperty("scalingMethod", (int) force.getBornRadiusScalingMethod());
node.setDoubleProperty("quinticLowerLimitFactor", force.getQuinticLowerLimitFactor());
node.setDoubleProperty("quinticUpperBornRadiusLimit", force.getQuinticUpperBornRadiusLimit());
node.setDoubleProperty("cutoff", force.getCutoffDistance());
node.setDoubleProperty("soluteDielectric", force.getSoluteDielectric());
node.setDoubleProperty("solventDielectric", force.getSolventDielectric());
SerializationNode& particles = node.createChildNode("Particles");
for (int i = 0; i < force.getNumParticles(); i++) {
double charge, radius, gamma;
force.getParticleParameters(i, charge, radius, gamma);
particles.createChildNode("Particle").setDoubleProperty("q", charge).setDoubleProperty("r", radius).setDoubleProperty("gamma", gamma);
}
SerializationNode& bonds = node.createChildNode("Bonds");
for (int i = 0; i < force.getNumBonds(); i++) {
int particle1, particle2;
double distance;
force.getBondParameters(i, particle1, particle2, distance);
bonds.createChildNode("Bond").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setDoubleProperty("d", distance);
}
}
void* GBVIForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
throw OpenMMException("Unsupported version number");
GBVIForce* force = new GBVIForce();
try {
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setNonbondedMethod((GBVIForce::NonbondedMethod) node.getIntProperty("method"));
force->setCutoffDistance(node.getDoubleProperty("cutoff"));
force->setSoluteDielectric(node.getDoubleProperty("soluteDielectric"));
force->setSolventDielectric(node.getDoubleProperty("solventDielectric"));
if( node.getIntProperty("version") >= 2 ){
force->setBornRadiusScalingMethod( (GBVIForce::BornRadiusScalingMethod) node.getIntProperty( "scalingMethod"));
force->setQuinticLowerLimitFactor(node.getDoubleProperty("quinticLowerLimitFactor"));
force->setQuinticUpperBornRadiusLimit(node.getDoubleProperty("quinticUpperBornRadiusLimit"));
}
const SerializationNode& particles = node.getChildNode("Particles");
for (int i = 0; i < (int) particles.getChildren().size(); i++) {
const SerializationNode& particle = particles.getChildren()[i];
force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("r"), particle.getDoubleProperty("gamma"));
}
const SerializationNode& bonds = node.getChildNode("Bonds");
for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
const SerializationNode& bond = bonds.getChildren()[i];
force->addBond(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getDoubleProperty("d"));
}
}
catch (...) {
delete force;
throw;
}
return force;
}
serialization/src/SerializationProxyRegistration.cpp
View file @ 14e78600
......@@ -45,7 +45,6 @@
#include "openmm/CustomNonbondedForce.h"
#include "openmm/CustomTorsionForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/GBVIForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/LangevinIntegrator.h"
......@@ -78,7 +77,6 @@
#include "openmm/serialization/CustomNonbondedForceProxy.h"
#include "openmm/serialization/CustomTorsionForceProxy.h"
#include "openmm/serialization/GBSAOBCForceProxy.h"
#include "openmm/serialization/GBVIForceProxy.h"
#include "openmm/serialization/HarmonicAngleForceProxy.h"
#include "openmm/serialization/HarmonicBondForceProxy.h"
#include "openmm/serialization/LangevinIntegratorProxy.h"
......@@ -132,7 +130,6 @@ extern "C" void registerSerializationProxies() {
SerializationProxy::registerProxy(typeid(Discrete2DFunction), new Discrete2DFunctionProxy());
SerializationProxy::registerProxy(typeid(Discrete3DFunction), new Discrete3DFunctionProxy());
SerializationProxy::registerProxy(typeid(GBSAOBCForce), new GBSAOBCForceProxy());
SerializationProxy::registerProxy(typeid(GBVIForce), new GBVIForceProxy());
SerializationProxy::registerProxy(typeid(HarmonicAngleForce), new HarmonicAngleForceProxy());
SerializationProxy::registerProxy(typeid(HarmonicBondForce), new HarmonicBondForceProxy());
SerializationProxy::registerProxy(typeid(LangevinIntegrator), new LangevinIntegratorProxy());
......
serialization/tests/TestSerializeGBVIForce.cpp deleted 100644 → 0
View file @ b20c20fe
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/GBVIForce.h"
#include "openmm/serialization/XmlSerializer.h"
#include <iostream>
#include <sstream>
using namespace OpenMM;
using namespace std;
void testSerialization() {
// Create a Force.
GBVIForce force;
force.setForceGroup(3);
force.setNonbondedMethod(GBVIForce::CutoffPeriodic);
force.setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
force.setQuinticLowerLimitFactor(0.123);
force.setQuinticUpperBornRadiusLimit(5.123);
force.setCutoffDistance(2.0);
force.setSoluteDielectric(5.1);
force.setSolventDielectric(50.0);
force.addParticle(1, 0.1, 0.01);
force.addParticle(0.5, 0.2, 0.02);
force.addParticle(-0.5, 0.3, 0.03);
force.addBond(0, 1, 2.0);
force.addBond(3, 5, 1.2);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<GBVIForce>(&force, "Force", buffer);
GBVIForce* copy = XmlSerializer::deserialize<GBVIForce>(buffer);
// Compare the two forces to see if they are identical.
GBVIForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getSoluteDielectric(), force2.getSoluteDielectric());
ASSERT_EQUAL(force.getSolventDielectric(), force2.getSolventDielectric());
ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
ASSERT_EQUAL(force.getQuinticUpperBornRadiusLimit(), force2.getQuinticUpperBornRadiusLimit());
ASSERT_EQUAL(force.getQuinticLowerLimitFactor(), force2.getQuinticLowerLimitFactor());
ASSERT_EQUAL(force.getBornRadiusScalingMethod(), force2.getBornRadiusScalingMethod());
for (int i = 0; i < force.getNumParticles(); i++) {
double charge1, radius1, scale1;
double charge2, radius2, scale2;
force.getParticleParameters(i, charge1, radius1, scale1);
force2.getParticleParameters(i, charge2, radius2, scale2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(radius1, radius2);
ASSERT_EQUAL(scale1, scale2);
}
ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
for (int i = 0; i < force.getNumBonds(); i++) {
int a1, a2, b1, b2;
double da, db;
force.getBondParameters(i, a1, a2, da);
force2.getBondParameters(i, b1, b2, db);
ASSERT_EQUAL(a1, b1);
ASSERT_EQUAL(a2, b2);
ASSERT_EQUAL(da, db);
}
}
int main() {
try {
testSerialization();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
wrappers/python/simtk/openmm/app/data/amber03_gbvi.xml deleted 100644 → 0
View file @ b20c20fe
<ForceField>
<GBVIForce soluteDielectric="1.0" >
<Atom type="0" charge="0.07601" radius="0.125" gamma="1.0196408" />
<Atom type="1" charge="-0.190263" radius="0.18" gamma="-1.1978792" />
<Atom type="2" charge="0.07601" radius="0.125" gamma="1.0196408" />
<Atom type="3" charge="0.07601" radius="0.125" gamma="1.0196408" />
<Atom type="4" charge="0.512403" radius="0.2" gamma="-0.5016616" />
<Atom type="5" charge="-0.55017" radius="0.14" gamma="21.2158088" />
<Atom type="6" charge="-0.404773" radius="0.165" gamma="-2.6204392" />
<Atom type="7" charge="0.294276" radius="0.125" gamma="4.3768824" />
<Atom type="8" charge="-0.027733" radius="0.18" gamma="-1.1978792" />
<Atom type="9" charge="0.120802" radius="0.125" gamma="1.0196408" />
<Atom type="10" charge="-0.229951" radius="0.18" gamma="-1.1978792" />
<Atom type="11" charge="0.077428" radius="0.125" gamma="1.0196408" />
<Atom type="12" charge="0.570224" radius="0.2" gamma="-0.5016616" />
<Atom type="13" charge="-0.555129" radius="0.14" gamma="21.2158088" />
<Atom type="14" charge="-0.300879" radius="0.165" gamma="-2.6204392" />
<Atom type="15" charge="0.233693" radius="0.125" gamma="4.3768824" />
<Atom type="16" charge="-0.131381" radius="0.18" gamma="-1.1978792" />
<Atom type="17" charge="0.053266" radius="0.125" gamma="1.0196408" />
<Atom type="18" charge="0.036707" radius="0.18" gamma="-1.1978792" />
<Atom type="19" charge="0.028012" radius="0.125" gamma="1.0196408" />
<Atom type="20" charge="0.012454" radius="0.18" gamma="-1.1978792" />
<Atom type="21" charge="0.002964" radius="0.125" gamma="1.0196408" />
<Atom type="22" charge="0.126329" radius="0.18" gamma="-1.1978792" />
<Atom type="23" charge="0.068148" radius="0.125" gamma="1.0196408" />
<Atom type="24" charge="-0.46489" radius="0.165" gamma="-2.6204392" />
<Atom type="25" charge="0.326274" radius="0.125" gamma="4.3768824" />
<Atom type="26" charge="0.565543" radius="0.2" gamma="-0.5016616" />
<Atom type="27" charge="-0.685774" radius="0.165" gamma="-2.6204392" />
<Atom type="28" charge="0.391052" radius="0.125" gamma="4.3768824" />
<Atom type="29" charge="-0.685774" radius="0.165" gamma="-2.6204392" />
<Atom type="30" charge="0.391052" radius="0.125" gamma="4.3768824" />
<Atom type="31" charge="0.730308" radius="0.2" gamma="-0.5016616" />
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wrappers/python/simtk/openmm/app/data/amber10_gbvi.xml deleted 100644 → 0
View file @ b20c20fe
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wrappers/python/simtk/openmm/app/data/amber96_gbvi.xml deleted 100644 → 0
View file @ b20c20fe
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wrappers/python/simtk/openmm/app/data/amber99_gbvi.xml deleted 100644 → 0
View file @ b20c20fe
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</GBVIForce>
</ForceField>
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 14e78600
......@@ -1393,92 +1393,6 @@ class GBSAOBCGenerator:
parsers["GBSAOBCForce"] = GBSAOBCGenerator.parseElement
## @private
class GBVIGenerator:
"""A GBVIGenerator constructs a GBVIForce."""
def __init__(self,ff):
self.ff = ff
self.fixedParameters = {}
self.fixedParameters['soluteDielectric'] = 1.0
self.fixedParameters['solventDielectric'] = 78.3
self.fixedParameters['scalingMethod'] = 1
self.fixedParameters['quinticUpperBornRadiusLimit'] = 5.0
self.fixedParameters['quinticLowerLimitFactor'] = 0.8
self.typeMap = {}
@staticmethod
def parseElement(element, ff):
generator = GBVIGenerator(ff)
for key in generator.fixedParameters.iterkeys():
if (key in element.attrib):
generator.fixedParameters[key] = float(element.attrib[key])
ff.registerGenerator(generator)
for atom in element.findall('Atom'):
types = ff._findAtomTypes(atom.attrib, 1)
if None not in types:
values = (float(atom.attrib['charge']), float(atom.attrib['radius']), float(atom.attrib['gamma']))
for t in types[0]:
generator.typeMap[t] = values
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.NonbondedForce.NoCutoff,
CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic}
if nonbondedMethod not in methodMap:
raise ValueError('Illegal nonbonded method for GB/VI Force')
# add particles
force = mm.GBVIForce()
for atom in data.atoms:
t = data.atomType[atom]
if t in self.typeMap:
values = self.typeMap[t]
force.addParticle(values[0], values[1], values[2])
else:
raise ValueError('No GB/VI parameters defined for atom type '+t)
# get HarmonicBond generator -- exit if not found
hbGenerator = 0
for generator in self.ff._forces:
if (generator.__class__.__name__ == 'HarmonicBondGenerator'):
hbGenerator = generator
break
if (hbGenerator == 0):
raise ValueError('HarmonicBondGenerator not found.')
# add bonds
for bond in data.bonds:
type1 = data.atomType[data.atoms[bond.atom1]]
type2 = data.atomType[data.atoms[bond.atom2]]
for i in range(len(hbGenerator.types1)):
types1 = hbGenerator.types1[i]
types2 = hbGenerator.types2[i]
if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1):
#bond.length = hbGenerator.length[i]
force.addBond(bond.atom1, bond.atom2, hbGenerator.length[i])
force.setNonbondedMethod(methodMap[nonbondedMethod])
force.setCutoffDistance(nonbondedCutoff)
force.setSolventDielectric(self.fixedParameters['solventDielectric'])
force.setSoluteDielectric(self.fixedParameters['soluteDielectric'])
force.setBornRadiusScalingMethod(self.fixedParameters['scalingMethod'])
force.setQuinticLowerLimitFactor(self.fixedParameters['quinticLowerLimitFactor'])
force.setQuinticUpperBornRadiusLimit(self.fixedParameters['quinticUpperBornRadiusLimit'])
sys.addForce(force)
parsers["GBVIForce"] = GBVIGenerator.parseElement
## @private
class CustomBondGenerator:
"""A CustomBondGenerator constructs a CustomBondForce."""
......
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ 14e78600
......@@ -674,7 +674,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
OPTIONAL ARGUMENTS
shake (String) - if 'h-bonds', will SHAKE all bonds to hydrogen and water; if 'all-bonds', will SHAKE all bonds and water (default: None)
gbmodel (String) - if 'OBC', OBC GBSA will be used; if 'GBVI', GB/VI will be used (default: None)
gbmodel (String) - if 'OBC', OBC GBSA will be used (default: None)
soluteDielectric (float) - The solute dielectric constant to use in the implicit solvent model (default: 1.0)
solventDielectric (float) - The solvent dielectric constant to use in the implicit solvent model (default: 78.5)
implicitSolventKappa (float) - The Debye screening parameter corresponding to implicit solvent ionic strength
......@@ -1097,8 +1097,6 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
# created above. Do not bind force to another name before this!
force.setReactionFieldDielectric(1.0)
# TODO: Add GBVI terms?
return system
#=============================================================================================
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ 14e78600
......@@ -43,7 +43,6 @@ SKIP_METHODS = [('State',),
('CalcCustomTorsionForceKernel',),
('CalcForcesAndEnergyKernel',),
('CalcGBSAOBCForceKernel',),
('CalcGBVIForceKernel',),
('CalcHarmonicAngleForceKernel',),
('CalcHarmonicBondForceKernel',),
('CalcKineticEnergyKernel',),
......@@ -393,14 +392,6 @@ UNITS = {
: (None, ('unit.elementary_charge',
'unit.nanometer', None)),
("GBSAOBCForce", "getSurfaceAreaEnergy") : ('unit.kilojoule_per_mole/unit.nanometer/unit.nanometer', ()),
("GBVIForce", "getBornRadiusScalingMethod") : (None, ()),
("GBVIForce", "getQuinticLowerLimitFactor") : (None, ()),
("GBVIForce", "getQuinticUpperBornRadiusLimit") : ('unit.nanometer', ()),
("GBVIForce", "getBondParameters")
: (None, (None, None, 'unit.nanometer')),
("GBVIForce", "getParticleParameters")
: (None, ('unit.elementary_charge',
'unit.nanometer', 'unit.kilojoule_per_mole')),
("HarmonicAngleForce", "getAngleParameters")
: (None, (None, None, None, 'unit.radian',
'unit.kilojoule_per_mole/(unit.radian*unit.radian)')),
......
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