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Unverified Commit 8ac9cc44 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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DrudeForce supports periodic boundary conditions (#4523) 

* DrudeForce supports periodic boundary conditions

* Fixed uninitialized memory
parent 3cb6f8d7
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Showing with 69 additions and 20 deletions
plugins/drude/openmmapi/include/openmm/DrudeForce.h
View file @ 8ac9cc44
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -134,7 +134,7 @@ public:
*/
int addScreenedPair(int particle1, int particle2, double thole);
/**
* Get the force field parameters for screened pair.
* Get the force field parameters for a screened pair.
*
* @param index the index of the pair for which to get parameters
* @param[out] particle1 the index within this Force of the first particle involved in the interaction
......@@ -143,7 +143,7 @@ public:
*/
void getScreenedPairParameters(int index, int& particle1, int& particle2, double& thole) const;
/**
* Set the force field parameters for screened pair.
* Set the force field parameters for a screened pair.
*
* @param index the index of the pair for which to get parameters
* @param particle1 the index within this Force of the first particle involved in the interaction
......@@ -162,15 +162,19 @@ public:
* be used to add new particles or screenedPairs, only to change the parameters of existing ones.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*
* Periodic boundary conditions are only applied to screened pairs. They are never used for the
* force between a Drude particle and its parent particle, regardless of this setting.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if nonbondedMethod uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
......@@ -178,6 +182,7 @@ private:
class ScreenedPairInfo;
std::vector<ParticleInfo> particles;
std::vector<ScreenedPairInfo> screenedPairs;
bool usePeriodic;
};
/**
......
plugins/drude/openmmapi/src/DrudeForce.cpp
View file @ 8ac9cc44
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013-2021 Stanford University and the Authors. *
* Portions copyright (c) 2013-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -38,7 +38,7 @@
using namespace OpenMM;
using namespace std;
DrudeForce::DrudeForce() {
DrudeForce::DrudeForce() : usePeriodic(false) {
}
int DrudeForce::addParticle(int particle, int particle1, int particle2, int particle3, int particle4, double charge, double polarizability, double aniso12, double aniso34) {
......@@ -105,3 +105,11 @@ ForceImpl* DrudeForce::createImpl() const {
void DrudeForce::updateParametersInContext(Context& context) {
dynamic_cast<DrudeForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void DrudeForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool DrudeForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/drude/platforms/common/src/CommonDrudeKernels.cpp
View file @ 8ac9cc44
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013-2023 Stanford University and the Authors. *
* Portions copyright (c) 2013-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -158,6 +158,7 @@ void CommonCalcDrudeForceKernel::initialize(const System& system, const DrudeFor
}
pairParams.upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["PARAMS"] = cc.getBondedUtilities().addArgument(pairParams, "float2");
cc.getBondedUtilities().addInteraction(atoms, cc.replaceStrings(CommonDrudeKernelSources::drudePairForce, replacements), force.getForceGroup());
}
......
plugins/drude/platforms/common/src/kernels/drudePairForce.cc
View file @ 8ac9cc44
......@@ -7,6 +7,9 @@ real3 force4 = make_real3(0);
// First pair.
real3 delta = make_real3(pos1.x-pos3.x, pos1.y-pos3.y, pos1.z-pos3.z);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real rInv = RSQRT(dot(delta, delta));
real r = RECIP(rInv);
real u = drudeParams.x*r;
......@@ -20,6 +23,9 @@ force3 -= f;
// Second pair.
delta = make_real3(pos1.x-pos4.x, pos1.y-pos4.y, pos1.z-pos4.z);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(delta)
#endif
rInv = RSQRT(dot(delta, delta));
r = RECIP(rInv);
u = drudeParams.x*r;
......@@ -33,6 +39,9 @@ force4 -= f;
// Third pair.
delta = make_real3(pos2.x-pos3.x, pos2.y-pos3.y, pos2.z-pos3.z);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(delta)
#endif
rInv = RSQRT(dot(delta, delta));
r = RECIP(rInv);
u = drudeParams.x*r;
......@@ -46,6 +55,9 @@ force3 -= f;
// Fourth pair.
delta = make_real3(pos2.x-pos4.x, pos2.y-pos4.y, pos2.z-pos4.z);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(delta)
#endif
rInv = RSQRT(dot(delta, delta));
r = RECIP(rInv);
u = drudeParams.x*r;
......
plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp
View file @ 8ac9cc44
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2011-2023 Stanford University and the Authors. *
* Portions copyright (c) 2011-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -36,6 +36,7 @@
#include "SimTKOpenMMUtilities.h"
#include "ReferenceConstraints.h"
#include "ReferenceVirtualSites.h"
#include "ReferenceForce.h"
#include <set>
using namespace OpenMM;
......@@ -56,6 +57,11 @@ static vector<Vec3>& extractForces(ContextImpl& context) {
return *data->forces;
}
static Vec3* extractBoxVectors(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return data->periodicBoxVectors;
}
static ReferenceConstraints& extractConstraints(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *data->constraints;
......@@ -103,6 +109,7 @@ void ReferenceCalcDrudeForceKernel::initialize(const System& system, const Drude
pairThole.resize(numPairs);
for (int i = 0; i < numPairs; i++)
force.getScreenedPairParameters(i, pair1[i], pair2[i], pairThole[i]);
periodic = force.usesPeriodicBoundaryConditions();
}
double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -170,6 +177,7 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include
// Compute the screened interaction between bonded dipoles.
int numPairs = pair1.size();
Vec3* boxVectors = extractBoxVectors(context);
for (int i = 0; i < numPairs; i++) {
int dipole1 = pair1[i];
int dipole2 = pair2[i];
......@@ -181,8 +189,13 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include
int p1 = dipole1Particles[j];
int p2 = dipole2Particles[k];
double chargeProduct = charge[dipole1]*charge[dipole2]*(j == k ? 1 : -1);
Vec3 delta = pos[p1]-pos[p2];
double r = sqrt(delta.dot(delta));
double deltaR[ReferenceForce::LastDeltaRIndex];
if (periodic)
ReferenceForce::getDeltaRPeriodic(pos[p2], pos[p1], boxVectors, deltaR);
else
ReferenceForce::getDeltaR(pos[p2], pos[p1], deltaR);
Vec3 delta(deltaR[ReferenceForce::XIndex], deltaR[ReferenceForce::YIndex], deltaR[ReferenceForce::ZIndex]);
double r = deltaR[ReferenceForce::RIndex];
double u = r*uscale;
double screening = 1.0 - (1.0+0.5*u)*exp(-u);
energy += ONE_4PI_EPS0*chargeProduct*screening/r;
......
plugins/drude/platforms/reference/src/ReferenceDrudeKernels.h
View file @ 8ac9cc44
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013-2023 Stanford University and the Authors. *
* Portions copyright (c) 2013-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -77,6 +77,7 @@ private:
std::vector<double> charge, polarizability, aniso12, aniso34;
std::vector<int> pair1, pair2;
std::vector<double> pairThole;
bool periodic;
};
/**
......
plugins/drude/tests/TestDrudeForce.h
View file @ 8ac9cc44
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -127,26 +127,29 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) {
return 1.0-(1.0+u/2)*exp(-u);
}
void testThole() {
void testThole(bool periodic) {
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double thole = 2.5;
const double box = 2.0;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(box, 0, 0), Vec3(0, box, 0), Vec3(0, 0, box));
DrudeForce* drude = new DrudeForce();
drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
drude->addParticle(3, 2, -1, -1, -1, charge, alpha, 1, 1);
drude->addScreenedPair(0, 1, thole);
drude->setUsesPeriodicBoundaryConditions(periodic);
system.addForce(drude);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, -0.5, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 0.3);
positions[2] = Vec3(1.1, 0, 0);
positions[3] = Vec3(1.1, 0, 0.3);
double energySpring1 = 0.5*k*0.5*0.5;
double energySpring2 = 0.5*k*0.3*0.3;
double energyDipole = 0.0;
......@@ -154,6 +157,11 @@ void testThole() {
for (int i = 0; i < 2; i++)
for (int j = 2; j < 4; j++) {
Vec3 delta = positions[i]-positions[j];
if (periodic) {
delta[0] -= box*floor(delta[0]/box+0.5);
delta[1] -= box*floor(delta[1]/box+0.5);
delta[2] -= box*floor(delta[2]/box+0.5);
}
double r = sqrt(delta.dot(delta));
energyDipole += ONE_4PI_EPS0*q[i]*q[j]*computeScreening(r, thole, alpha, alpha)/r;
}
......@@ -204,7 +212,8 @@ int main(int argc, char* argv[]) {
setupKernels(argc, argv);
testSingleParticle();
testAnisotropicParticle();
testThole();
testThole(false);
testThole(true);
testChangingParameters();
runPlatformTests();
}
......
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