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Unverified Commit d12f9f89 authored by Andy Simmonett's avatar Andy Simmonett
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Clean up implementation of NHC, add propagator test

parent c692624f
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Showing with 386 additions and 164 deletions
olla/include/openmm/kernels.h
View file @ d12f9f89
......@@ -1328,26 +1328,51 @@ public:
* This kernel is invoked by NoseHooverChainThermostat at the beginning and end of each time step
* to update the Nose-Hoover chain.
*/
class PropagateNoseHooverChainKernel : public KernelImpl {
class NoseHooverChainKernel : public KernelImpl {
public:
static std::string Name() {
return "PropagateNoseHooverChain";
return "NoseHooverChain";
}
PropagateNoseHooverChainKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
NoseHooverChainKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*/
virtual void initialize() = 0;
/**
* Execute the kernel that propagates the Nose Hoover chain and determines the velocity scale factor.
*
* @param system the System this kernel will be applied to
* @param noseHooverChain the NoseHooverChain this kernel will be used for
* @param context the context in which to execute this kernel
* @param noseHooverChain the object describing the chain to be propagated.
* @param kineticEnergy the kineticEnergy of the particles being thermostated by this chain.
* @param timeStep the time step used by the integrator.
* @return the velocity scale factor to apply to the particles associated with this heat bath.
*/
virtual void initialize(const System& system, const NoseHooverChain& noseHooverChain) = 0;
virtual double propagateChain(ContextImpl& context, const NoseHooverChain &noseHooverChain, double kineticEnergy, double timeStep) = 0;
/**
* Execute the kernel.
* Execute the kernal that computes the total (kinetic + potential) heat bath energy.
*
* @param context the context in which to execute this kernel
* @param noseHooverChain the chain whose energy is to be determined.
* @return the total heat bath energy.
*/
virtual double computeHeatBathEnergy(ContextImpl& context, const NoseHooverChain &noseHooverChain) = 0;
/**
* Execute the kernel that computes the kinetic energy for a subset of atoms,
* or the relative kinetic energy of Drude particles with respect to their parent atoms
*
* @param context the context in which to execute this kernel
* @param noseHooverChain the chain whose energy is to be determined.
*/
virtual double computeMaskedKineticEnergy(ContextImpl& context, const NoseHooverChain &noseHooverChain) = 0;
/**
* Execute the kernel that scales the velocities of particles associated with a nose hoover chain
*
* @param context the context in which to execute this kernel
* @param noseHooverChain the chain whose energy is to be determined.
* @param scaleFactor the multiplicative factor by which velocities are scaled.
*/
virtual void execute(ContextImpl& context, const NoseHooverChain &noseHooverChain, double kineticEnergy, double timeStep) = 0;
virtual void scaleVelocities(ContextImpl& context, const NoseHooverChain &noseHooverChain, double scaleFactor) = 0;
};
/**
......
openmmapi/include/openmm/NoseHooverChain.h
View file @ d12f9f89
......@@ -35,6 +35,7 @@
#include "Force.h"
#include <string>
#include <vector>
#include "openmm/OpenMMException.h"
#include "internal/windowsExport.h"
namespace OpenMM {
......@@ -89,18 +90,6 @@ public:
std::string NumYoshidaSuzukiTimeSteps() const {
return defaultLabel + "NoseHooverChainNumYoshidaSuzukiTimeSteps";
}
/**
* This is the name of the parameter that stores the force acting on the ith bead
*/
std::string Force(int i) const {
return defaultLabel + "NoseHooverChainForce" + std::to_string(i);
}
/**
* This is the name of the parameter that stores the mass of the ith bead
*/
std::string Mass(int i) const {
return defaultLabel + "NoseHooverChainMass" + std::to_string(i);
}
/**
* This is the name of the parameter that stores the position of the ith bead
*/
......@@ -125,9 +114,12 @@ public:
* @param defaultNumYoshidaSuzuki the default number of Yoshida Suzuki steps used to propagate this chain (1, 3, or 5).
* @param defaultLabel the default label used to distinguish this Nose-Hoover chain from others that may
* be used to control a different set of particles, e.g. for Drude oscillators
* @param thermostatedAtoms the list of atoms to be handled by this thermostat
* @param parentAtoms the list of parent atoms, if this thermostat handles Drude particles. Empty vector otherwise.
*/
NoseHooverChain(double defaultTemperature, double defaultCollisionFrequency, int defaultNumDOFs, int defaultChainLength,
int defaultNumMTS, int defaultNumYoshidaSuzuki, const std::string &defaultLabel);
int defaultNumMTS, int defaultNumYoshidaSuzuki, const std::string &defaultLabel,
const std::vector<int>& thermostatedAtoms, const std::vector<int>& parentAtoms);
/**
* Get the default temperature of the heat bath (in Kelvin).
*
......@@ -249,6 +241,44 @@ public:
void setDefaultLabel(const std::string& label) {
defaultLabel = label;
}
/**
* Get the atom ids of all atoms that are thermostated
*
* @returns ids of all atoms that are being handled by this thermostat
*/
const std::vector<int>& getThermostatedAtoms() const {
return thermostatedAtoms;
}
/**
* Set list of atoms that are handled by this thermostat
*
* @param atomIDs
*/
void setThermostatedAtoms(const std::vector<int>& atomIDs){
thermostatedAtoms = atomIDs;
}
/**
* In case this thermostat handles the kinetic energy of Drude particles relative to the
* atoms that they are attached to, get the atom ids of all parent atoms.
* If this is a regular thermostat, returns an empty vector.
*
* @returns ids of all parent atoms
*/
const std::vector<int>& getParentAtoms() const {
return parentAtoms;
}
/**
* In case this thermostat handles the kinetic energy of Drude particles
* set the atom IDs of all parent atoms.
*
* @param parentIDs
*/
void setParentAtoms(const std::vector<int>& parentIDs){
if (not parentIDs.size() == thermostatedAtoms.size()){
throw OpenMMException("The number of parent atoms has to be the same as the number of thermostated atoms, or zero.");
}
parentAtoms = parentIDs;
}
/**
* Get the default weights used in the Yoshida Suzuki multi time step decomposition (dimensionless)
*
......@@ -271,6 +301,7 @@ private:
int defaultNumDOFs, defaultChainLength, defaultNumMTS, defaultNumYS;
// The suffix used to distinguish NH chains, e.g. for Drude particles vs. regular particles.
std::string defaultLabel;
std::vector<int> thermostatedAtoms, parentAtoms;
};
} // namespace OpenMM
......
openmmapi/include/openmm/VelocityVerletIntegrator.h
View file @ d12f9f89
......@@ -67,8 +67,26 @@ public:
* @param chainID id of the Nose-Hoover-Chain
*/
double propagateChain(double kineticEnergy, int chainID=0);
/**
* Add a Nose-Hoover Chain thermostat to control the temperature of the systeml
*
* @param system the system to be thermostated. Note: this must be setup, i.e. all
* particles should have been added, before calling this function.
* @param temperature the target temperature for the system.
* @param collisionFrequency the frequency of the interaction with the heat bath (in 1/ps).
* @param chainLength the number of beads in the Nose-Hoover chain.
* @param numMTS the number of step in the multiple time step chain propagation algorithm.
* @param numYoshidaSuzuki the number of terms in the Yoshida-Suzuki multi time step decomposition
* used in the chain propagation algorithm (must be 1, 3, or 5).
*/
int addNoseHooverChainThermostat(System& system, double temperature, double collisionFrequency,
int chainLength, int numMTS, int numYoshidaSuzuki);
/**
* Compute the total (potential + kinetic) heat bath energy for all heat baths
* associated with this integrator, at the current time.
*/
double computeHeatBathEnergy();
protected:
/**
* This will be called by the Context when it is created. It informs the Integrator
......@@ -90,9 +108,8 @@ protected:
*/
double computeKineticEnergy();
private:
Kernel vvKernel;
Kernel vvKernel, nhcKernel;
std::vector<NoseHooverChain*> noseHooverChains;
std::vector<Kernel> nhcKernels;
};
} // namespace OpenMM
......
openmmapi/include/openmm/internal/NoseHooverChainImpl.h
View file @ d12f9f89
......@@ -58,7 +58,6 @@ public:
std::vector<std::string> getKernelNames();
private:
const NoseHooverChain& owner;
Kernel kernel;
};
} // namespace OpenMM
......
openmmapi/src/ContextImpl.cpp
View file @ d12f9f89
......@@ -52,6 +52,11 @@ using namespace OpenMM;
using namespace std;
const static char CHECKPOINT_MAGIC_BYTES[] = "OpenMM Binary Checkpoint\n";
void printvars(std::map<std::string, double> & map) {
for(auto & v: map) {
std::cout << v.first << " " << v.second << std::endl;
}
}
ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integrator, Platform* platform, const map<string, string>& properties, ContextImpl* originalContext) :
owner(owner), system(system), integrator(integrator), hasInitializedForces(false), hasSetPositions(false), integratorIsDeleted(false),
......
openmmapi/src/NoseHooverChain.cpp
View file @ d12f9f89
......@@ -37,10 +37,12 @@ using namespace OpenMM;
NoseHooverChain::NoseHooverChain(double defaultTemperature, double defaultCollisionFrequency,
int defaultNumDOFs, int defaultChainLength, int defaultNumMTS,
int defaultNumYoshidaSuzuki, const std::string &defaultLabel) :
int defaultNumYoshidaSuzuki, const std::string &defaultLabel,
const std::vector<int>& thermostatedAtoms, const std::vector<int>& parentAtoms):
defaultTemp(defaultTemperature), defaultFreq(defaultCollisionFrequency), defaultNumDOFs(defaultNumDOFs),
defaultChainLength(defaultChainLength), defaultNumMTS(defaultNumMTS), defaultNumYS(defaultNumYS),
defaultLabel(defaultLabel) {}
defaultChainLength(defaultChainLength), defaultNumMTS(defaultNumMTS), defaultNumYS(defaultNumYoshidaSuzuki),
defaultLabel(defaultLabel), thermostatedAtoms(thermostatedAtoms), parentAtoms(parentAtoms)
{}
ForceImpl* NoseHooverChain::createImpl() const {
return new NoseHooverChainImpl(*this);
......
openmmapi/src/NoseHooverChainImpl.cpp
View file @ d12f9f89
......@@ -38,6 +38,7 @@
#include "sfmt/SFMT.h"
#include <string>
#include <vector>
#include <iostream>
using namespace OpenMM;
using std::vector;
......@@ -46,76 +47,26 @@ NoseHooverChainImpl::NoseHooverChainImpl(const NoseHooverChain& owner) : owner(o
}
void NoseHooverChainImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(PropagateNoseHooverChainKernel::Name(), context);
kernel.getAs<PropagateNoseHooverChainKernel>().initialize(context.getSystem(), owner);
}
void NoseHooverChainImpl::updateContextState(ContextImpl& context, bool& forcesInvalid) {
// This kernel updates the Nose-Hoover particles when invoked explicitly
// via its propagate(), which is called from the integrator.
}
double NoseHooverChainImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
// This kernel doesn't compute an energy or force. Instead it is invoked
// directly by the integrator via it's propagate() method.
return 0;
}
std::map<std::string, double> NoseHooverChainImpl::getDefaultParameters() {
std::map<std::string, double> parameters;
const auto &owner = getOwner();
double frequency = owner.getDefaultCollisionFrequency();
int chainLength = owner.getDefaultChainLength();
double T = owner.getDefaultTemperature();
double kT = BOLTZ * T;
int DOFs = owner.getDefaultNumDegreesOfFreedom();
parameters[owner.Temperature()] = T;
parameters[owner.CollisionFrequency()] = frequency;
parameters[owner.ChainLength()] = chainLength;
parameters[owner.NumYoshidaSuzukiTimeSteps()] = owner.getDefaultNumYoshidaSuzukiTimeSteps();
parameters[owner.NumMultiTimeSteps()] = owner.getDefaultNumMultiTimeSteps();
parameters[owner.NumDegreesOfFreedom()] = DOFs;
for(int i = 0; i < chainLength; ++i) {
parameters[owner.Force(i)] = 0;
parameters[owner.Position(i)] = 0;
parameters[owner.Mass(i)] = kT / (frequency * frequency);
parameters[owner.Velocity(i)] = 0;
}
parameters[owner.Mass(0)] *= DOFs;
// Set the velocities to the appropriate Boltzmann distribution;
// this is copied from Context::setVelocitiesToTemperature()
OpenMM_SFMT::SFMT sfmt;
int randomSeed = 0; //TODO figure out where / how this should be handled
init_gen_rand(randomSeed, sfmt);
vector<double> randoms;
while (randoms.size() < chainLength) {
double x, y, r2;
do {
x = 2.0*genrand_real2(sfmt)-1.0;
y = 2.0*genrand_real2(sfmt)-1.0;
r2 = x*x + y*y;
} while (r2 >= 1.0 || r2 == 0.0);
double multiplier = sqrt((-2.0*log(r2))/r2);
randoms.push_back(x*multiplier);
randoms.push_back(y*multiplier);
}
int nextRandom = 0;
for (int i = 0; i < chainLength; i++) {
double velocityScale = 1 / frequency; // = sqrt(kT / Q) = sqrt(kT / [ kT frequency^-2])
parameters[owner.Velocity(i)] = velocityScale * randoms[nextRandom++];
}
// N.B. the zeroth entry is computed as a function of the instantaneous KE at the start of propagate
for(int i = 1; i < chainLength-1; ++i) {
const double & v = parameters[owner.Velocity(i)];
parameters[owner.Force(i+1)] = (parameters[owner.Mass(i)] * v * v - kT) / parameters[owner.Mass(i+1)];
}
return parameters;
}
std::vector<std::string> NoseHooverChainImpl::getKernelNames() {
std::vector<std::string> names;
names.push_back(PropagateNoseHooverChainKernel::Name());
return names;
return std::vector<std::string>();
}
openmmapi/src/VelocityVerletIntegrator.cpp
View file @ d12f9f89
......@@ -39,6 +39,7 @@
#include "openmm/internal/ContextImpl.h"
#include "openmm/kernels.h"
#include <string>
#include <iostream>
using namespace OpenMM;
using std::string;
......@@ -50,6 +51,7 @@ VelocityVerletIntegrator::VelocityVerletIntegrator(double stepSize) {
}
double VelocityVerletIntegrator::propagateChain(double kineticEnergy, int chainID) {
return nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, *noseHooverChains[chainID], kineticEnergy, getStepSize());
}
/*int VelocityVerletIntegrator::addMaskedNoseHooverChain(System& system, std::vector<int> mask, std::vector<int> parents, double temperature,
......@@ -62,8 +64,13 @@ int VelocityVerletIntegrator::addNoseHooverChainThermostat(System& system, doubl
std::vector<int> mask, parents;
int nDOF = 0;
int numForces = system.getNumForces();
vector<int> thermostatedParticles;
vector<int> parentParticles;
for(int particle = 0; particle < system.getNumParticles(); ++particle) {
if(system.getParticleMass(particle) > 0) nDOF += 3;
if(system.getParticleMass(particle) > 0) {
nDOF += 3;
thermostatedParticles.push_back(particle);
}
}
nDOF -= system.getNumConstraints();
for (int forceNum = 0; forceNum < numForces; ++forceNum) {
......@@ -71,15 +78,25 @@ int VelocityVerletIntegrator::addNoseHooverChainThermostat(System& system, doubl
}
auto nhcForce = new NoseHooverChain(temperature, collisionFrequency, nDOF, chainLength,
numMTS, numYoshidaSuzuki, std::to_string(noseHooverChains.size()));
numMTS, numYoshidaSuzuki, std::to_string(noseHooverChains.size()),
thermostatedParticles, parentParticles);
system.addForce(nhcForce);
noseHooverChains.push_back(nhcForce);
return noseHooverChains.size() - 1;
}
double VelocityVerletIntegrator::computeKineticEnergy() {
return vvKernel.getAs<IntegrateVelocityVerletStepKernel>().computeKineticEnergy(*context, *this);
}
double VelocityVerletIntegrator::computeHeatBathEnergy() {
double energy = 0;
for(auto &nhc : noseHooverChains) {
energy += nhcKernel.getAs<NoseHooverChainKernel>().computeHeatBathEnergy(*context, *nhc);
}
return energy;
}
void VelocityVerletIntegrator::initialize(ContextImpl& contextRef) {
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
......@@ -87,20 +104,18 @@ void VelocityVerletIntegrator::initialize(ContextImpl& contextRef) {
owner = &contextRef.getOwner();
vvKernel = context->getPlatform().createKernel(IntegrateVelocityVerletStepKernel::Name(), contextRef);
vvKernel.getAs<IntegrateVelocityVerletStepKernel>().initialize(contextRef.getSystem(), *this);
for (auto * nhc: noseHooverChains){
nhcKernels.push_back(context->getPlatform().createKernel(PropagateNoseHooverChainKernel::Name(), contextRef));
nhcKernels.back().getAs<PropagateNoseHooverChainKernel>().initialize(contextRef.getSystem(), *nhc);
}
nhcKernel = context->getPlatform().createKernel(NoseHooverChainKernel::Name(), contextRef);
nhcKernel.getAs<NoseHooverChainKernel>().initialize();
}
void VelocityVerletIntegrator::cleanup() {
vvKernel = Kernel();
nhcKernels.clear();
nhcKernel = Kernel();
}
vector<string> VelocityVerletIntegrator::getKernelNames() {
std::vector<std::string> names;
names.push_back(PropagateNoseHooverChainKernel::Name());
names.push_back(NoseHooverChainKernel::Name());
names.push_back(IntegrateVelocityVerletStepKernel::Name());
return names;
}
......@@ -108,8 +123,23 @@ vector<string> VelocityVerletIntegrator::getKernelNames() {
void VelocityVerletIntegrator::step(int steps) {
if (context == NULL)
throw OpenMMException("This Integrator is not bound to a context!");
double scale, kineticEnergy;
for (int i = 0; i < steps; ++i) {
context->updateContextState();
for(auto &nhc : noseHooverChains) {
kineticEnergy = nhcKernel.getAs<NoseHooverChainKernel>().computeMaskedKineticEnergy(*context, *nhc);
//std::cout << "ke " << kineticEnergy << std::endl;
scale = nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, *nhc, kineticEnergy, getStepSize());
//std::cout << "scl " << scale << std::endl;
nhcKernel.getAs<NoseHooverChainKernel>().scaleVelocities(*context, *nhc, scale);
}
vvKernel.getAs<IntegrateVelocityVerletStepKernel>().execute(*context, *this);
for(auto &nhc : noseHooverChains) {
kineticEnergy = nhcKernel.getAs<NoseHooverChainKernel>().computeMaskedKineticEnergy(*context, *nhc);
scale = nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, *nhc, kineticEnergy, getStepSize());
//std::cout << "ke " << kineticEnergy << " scale " << scale << std::endl;
nhcKernel.getAs<NoseHooverChainKernel>().scaleVelocities(*context, *nhc, scale);
}
}
}
platforms/reference/include/ReferenceKernels.h
View file @ d12f9f89
......@@ -1430,24 +1430,52 @@ private:
* This kernel is invoked by NoseHooverChain at the start of each time step to adjust the thermostat
* and update the associated particle velocities.
*/
class ReferencePropagateNoseHooverChainKernel : public PropagateNoseHooverChainKernel {
class ReferenceNoseHooverChainKernel : public NoseHooverChainKernel {
public:
ReferencePropagateNoseHooverChainKernel(std::string name, const Platform& platform) : PropagateNoseHooverChainKernel(name, platform), chainPropagator(0) {
ReferenceNoseHooverChainKernel(std::string name, const Platform& platform) : NoseHooverChainKernel(name, platform), chainPropagator(0) {
}
~ReferencePropagateNoseHooverChainKernel();
~ReferenceNoseHooverChainKernel();
/**
* Initialize the kernel.
*/
virtual void initialize();
/**
* Execute the kernel that propagates the Nose Hoover chain and determines the velocity scale factor.
*
* @param system the System this kernel will be applied to
* @param thermostat the NoseHooverChain this kernel will be used for
* @param context the context in which to execute this kernel
* @param noseHooverChain the object describing the chain to be propagated.
* @param kineticEnergy the kineticEnergy of the particles being thermostated by this chain.
* @param timeStep the time step used by the integrator.
* @return the velocity scale factor to apply to the particles associated with this heat bath.
*/
void initialize(const System& system, const NoseHooverChain& chain);
virtual double propagateChain(ContextImpl& context, const NoseHooverChain &nhc, double kineticEnergy, double timeStep);
/**
* Execute the kernel.
* Execute the kernal that computes the total (kinetic + potential) heat bath energy.
*
* @param context the context in which to execute this kernel
* @param noseHooverChain the chain whose energy is to be determined.
* @return the total heat bath energy.
*/
virtual double computeHeatBathEnergy(ContextImpl& context, const NoseHooverChain &nhc);
/**
* Execute the kernel that computes the kinetic energy for a subset of atoms,
* or the relative kinetic energy of Drude particles with respect to their parent atoms
*
* @param context the context in which to execute this kernel
* @param noseHooverChain the chain whose energy is to be determined.
*/
virtual double computeMaskedKineticEnergy(ContextImpl& context, const NoseHooverChain &noseHooverChain);
/**
* Execute the kernel that scales the velocities of particles associated with a nose hoover chain
*
* @param context the context in which to execute this kernel
* @param noseHooverChain the chain whose energy is to be determined.
* @param scaleFactor the multiplicative factor by which velocities are scaled.
*/
void execute(ContextImpl& context, const NoseHooverChain &nhc, double kineticEnergy, double timeStep);
virtual void scaleVelocities(ContextImpl& context, const NoseHooverChain &noseHooverChain, double scaleFactor);
private:
ReferenceNoseHooverChain* chainPropagator;
};
......
platforms/reference/include/ReferenceNoseHooverChain.h
View file @ d12f9f89
......@@ -59,10 +59,8 @@ class ReferenceNoseHooverChain {
Propagate the Nose-Hoover chain a half timestep and find the appropriate velocity scaling
@param kineticEnergy the instantaneous kinetic energy of the particles being thermostated
@param chainMasses the "masses" assigned to each thermostat bead in ps^2 kJ / mol
@param chainVelocities the velocities of the chain's beads in nm / ps
@param chainPositions the positions of the chains's beads in nm
@param chainForces the forces on each bead in the chain
@param numDOFs the number of degrees of freedom in the system that this chain thermostats
@param temperature thermostat temperature in Kelvin
@param collisionFrequency collision frequency for each atom in ps^-1
......@@ -70,9 +68,8 @@ class ReferenceNoseHooverChain {
@param numMTS number of multi timestep increments used in the Trotter expansion
@param YSWeights vector of weights used in the Yoshida-Suzuki multi-timestepping.
--------------------------------------------------------------------------------------- */
double propagate(double kineticEnergy, const vector<double>& chainMasses,
vector<double>& chainVelocities, vector<double>& chainPositions,
vector<double>& chainForces, int numDOFs,
double propagate(double kineticEnergy, vector<double>& chainVelocities,
vector<double>& chainPositions, int numDOFs,
double temperature, double collisionFrequency, double timeStep,
int numMTS, const vector<double>& YSWeights) const;
};
......
platforms/reference/src/ReferenceKernelFactory.cpp
View file @ d12f9f89
......@@ -90,8 +90,8 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
return new ReferenceIntegrateVerletStepKernel(name, platform, data);
if (name == IntegrateVelocityVerletStepKernel::Name())
return new ReferenceIntegrateVelocityVerletStepKernel(name, platform, data);
if (name == PropagateNoseHooverChainKernel::Name())
return new ReferencePropagateNoseHooverChainKernel(name, platform);
if (name == NoseHooverChainKernel::Name())
return new ReferenceNoseHooverChainKernel(name, platform);
if (name == IntegrateLangevinStepKernel::Name())
return new ReferenceIntegrateLangevinStepKernel(name, platform, data);
if (name == IntegrateBrownianStepKernel::Name())
......
platforms/reference/src/ReferenceKernels.cpp
View file @ d12f9f89
......@@ -2422,39 +2422,118 @@ void ReferenceApplyAndersenThermostatKernel::execute(ContextImpl& context) {
context.getIntegrator().getStepSize());
}
ReferencePropagateNoseHooverChainKernel::~ReferencePropagateNoseHooverChainKernel() {
ReferenceNoseHooverChainKernel::~ReferenceNoseHooverChainKernel() {
if (chainPropagator)
delete chainPropagator;
}
void ReferencePropagateNoseHooverChainKernel::initialize(const System& system, const NoseHooverChain& nhc) {
void ReferenceNoseHooverChainKernel::initialize() {
this->chainPropagator = new ReferenceNoseHooverChain();
//SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) thermostat.getRandomNumberSeed());
}
void ReferencePropagateNoseHooverChainKernel::execute(ContextImpl& context, const NoseHooverChain &nhc, double kineticEnergy, double timeStep) {
int chainLength = context.getParameter(nhc.ChainLength());
std::vector<double> chainPositions(chainLength), chainVelocities(chainLength), chainForces(chainLength),
chainMasses(chainLength);
double temperature = context.getParameter(nhc.Temperature());
double collisionFrequency = context.getParameter(nhc.CollisionFrequency());
int numDOFs = context.getParameter(nhc.NumDegreesOfFreedom());
int numMTS = context.getParameter(nhc.NumMultiTimeSteps());
double ReferenceNoseHooverChainKernel::propagateChain(ContextImpl& context, const NoseHooverChain &nhc, double kineticEnergy, double timeStep) {
// Get the variables describing the NHC
int chainLength = nhc.getDefaultChainLength();
double temperature = nhc.getDefaultTemperature();
double collisionFrequency = nhc.getDefaultCollisionFrequency();
int numDOFs = nhc.getDefaultNumDegreesOfFreedom();
int numMTS = nhc.getDefaultNumMultiTimeSteps();
// Get the state of the NHC from the context
std::vector<double> chainPositions(chainLength), chainVelocities(chainLength);
for(int i = 0; i < chainLength; ++i) {
chainPositions[i] = context.getParameter(nhc.Position(i));
chainVelocities[i] = context.getParameter(nhc.Velocity(i));
chainMasses[i] = context.getParameter(nhc.Mass(i));
chainForces[i] = context.getParameter(nhc.Force(i));
}
chainPropagator->propagate(kineticEnergy, chainMasses, chainVelocities, chainPositions, chainForces, numDOFs,
temperature, collisionFrequency, timeStep, numMTS, nhc.getDefaultYoshidaSuzukiWeights());
//chain->applyThermostat(particleGroups, velData, masses,
// context.getParameter(AndersenThermostat::Temperature()),
// context.getParameter(AndersenThermostat::CollisionFrequency()),
// context.getIntegrator().getStepSize());
double scale = chainPropagator->propagate(kineticEnergy, chainVelocities, chainPositions, numDOFs,
temperature, collisionFrequency, timeStep,
numMTS, nhc.getDefaultYoshidaSuzukiWeights());
// Update the state of the NHC in the context
for(int i = 0; i < chainLength; ++i) {
context.setParameter(nhc.Position(i), chainPositions[i]);
context.setParameter(nhc.Velocity(i), chainVelocities[i]);
}
return scale;
}
double ReferenceNoseHooverChainKernel::computeHeatBathEnergy(ContextImpl& context, const NoseHooverChain &nhc) {
double energy = 0;
int chainLength = nhc.getDefaultChainLength();
double temperature = nhc.getDefaultTemperature();
double collisionFrequency = nhc.getDefaultCollisionFrequency();
double kT = temperature * BOLTZ;
int numDOFs = nhc.getDefaultNumDegreesOfFreedom();
for(int i = 0; i < chainLength; ++i) {
double mass = kT / (collisionFrequency * collisionFrequency);
mass *= i ? 1 : numDOFs;
double velocity = context.getParameter(nhc.Velocity(i));
// The kinetic energy of this bead
energy += 0.5 * mass * velocity * velocity;
// The potential energy of this bead
double position = context.getParameter(nhc.Position(i));
energy += numDOFs * kT * position;
}
return energy;
}
double ReferenceNoseHooverChainKernel::computeMaskedKineticEnergy(ContextImpl& context, const NoseHooverChain &noseHooverChain) {
const std::vector<int>& mask = noseHooverChain.getThermostatedAtoms();
const std::vector<int>& parents = noseHooverChain.getParentAtoms();
std::vector<Vec3>& velocities = extractVelocities(context);
// TODO move these bad boys into the class
const System& system = context.getSystem();
int numParticles = system.getNumParticles();
std::vector<double> masses(numParticles);
for (int i = 0; i < numParticles; ++i)
masses[i] = system.getParticleMass(i);
double ke = 0;
if (parents.size() == 0){
// scale absolute velocities
for (auto m: mask){
ke += 0.5 * masses[m] * velocities[m].dot(velocities[m]);
}
} else {
// scale velocities relative to parent
assert(parents.size() == mask.size());
Vec3 velocity;
double mass;
for (int i=0; i < mask.size(); i++){
velocity = velocities[mask[i]] - velocities[parents[i]];
mass = masses[mask[i]] * masses[parents[i]] / (masses[mask[i]] + masses[parents[i]]);
ke += 0.5 * mass * velocity.dot(velocity);
}
}
return ke;
}
void ReferenceNoseHooverChainKernel::scaleVelocities(ContextImpl& context, const NoseHooverChain &noseHooverChain, double scaleFactor) {
const std::vector<int>& mask = noseHooverChain.getThermostatedAtoms();
const std::vector<int>& parents = noseHooverChain.getParentAtoms();
std::vector<Vec3>& velocities = extractVelocities(context);
if (parents.size() == 0){
// scale absolute velocities
for (auto m: mask){
//std::cout << m << " " << velocities[m] << " " << scaleFactor << std::endl;
velocities[m] *= scaleFactor;
}
} else {
std::cout << "OUCHH" << std::endl;
// scale velocities relative to parent
assert(parents.size() == mask.size());
for (int i=0; i < mask.size(); i++){
velocities[mask[i]] = velocities[parents[i]] + scaleFactor * (velocities[mask[i]] - velocities[parents[i]]);
}
}
}
ReferenceApplyMonteCarloBarostatKernel::~ReferenceApplyMonteCarloBarostatKernel() {
if (barostat)
delete barostat;
......
platforms/reference/src/ReferencePlatform.cpp
View file @ d12f9f89
......@@ -67,7 +67,7 @@ ReferencePlatform::ReferencePlatform() {
registerKernelFactory(CalcGayBerneForceKernel::Name(), factory);
registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateVelocityVerletStepKernel::Name(), factory);
registerKernelFactory(PropagateNoseHooverChainKernel::Name(), factory);
registerKernelFactory(NoseHooverChainKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableLangevinStepKernel::Name(), factory);
......
platforms/reference/src/SimTKReference/ReferenceNoseHooverChain.cpp
View file @ d12f9f89
......@@ -25,7 +25,9 @@
#include <cmath>
#include <string.h>
#include <sstream>
#include <exception>
#include <iostream>
#include <fenv.h>
#include "SimTKOpenMMUtilities.h"
#include "ReferenceNoseHooverChain.h"
......@@ -50,16 +52,22 @@ using namespace OpenMM;
ReferenceNoseHooverChain::~ReferenceNoseHooverChain() {
}
double ReferenceNoseHooverChain::propagate(double kineticEnergy, const vector<double>& chainMasses,
vector<double>& chainVelocities, vector<double>& chainPositions,
vector<double>& chainForces, int numDOFs,
double ReferenceNoseHooverChain::propagate(double kineticEnergy, vector<double>& chainVelocities,
vector<double>& chainPositions, int numDOFs,
double temperature, double collisionFrequency, double timeStep,
int numMTS, const vector<double>& YSWeights) const {
double scale = 1;
double KE2 = 2 * kineticEnergy;
const double kT = BOLTZ * temperature;
const size_t chainLength = chainMasses.size();
const size_t chainLength = chainPositions.size();
std::vector<double> chainForces(chainLength, 0);
std::vector<double> chainMasses(chainLength, kT/(collisionFrequency*collisionFrequency));
chainMasses[0] *= numDOFs;
feenableexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW);
double KE2 = 2 * kineticEnergy;
chainForces[0] = (KE2 - numDOFs * kT) / chainMasses[0];
for (int bead = 0; bead < chainLength - 1; ++bead) {
chainForces[bead + 1] = (chainMasses[bead] * chainVelocities[bead] * chainVelocities[bead] - kT) / chainMasses[bead + 1];
}
for (int mts = 0; mts < numMTS; ++mts) {
for (const auto &ys : YSWeights) {
double wdt = ys * timeStep / numMTS;
......@@ -83,7 +91,10 @@ double ReferenceNoseHooverChain::propagate(double kineticEnergy, const vector<do
chainVelocities[bead] = aa * (aa * chainVelocities[bead] + 0.25 * wdt * chainForces[bead]);
chainForces[bead + 1] = (chainMasses[bead] * chainVelocities[bead] * chainVelocities[bead] - kT) / chainMasses[bead + 1];
}
chainVelocities.back() += 0.25 * wdt * chainForces.back();
chainVelocities[chainLength-1] += 0.25 * wdt * chainForces.back();
// std::cout << "P " << chainPositions.back() << std::endl;
// std::cout << "V " << chainVelocities.back() << std::endl;
// std::cout << "F " << chainForces.back() << std::endl;
} // YS loop
} // MTS loop
return scale;
......
tests/TestNoseHooverThermostat.h
View file @ d12f9f89
......@@ -39,16 +39,26 @@
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <iomanip>
#include <vector>
using namespace OpenMM;
using namespace std;
void testSingleBond() {
// Check conservation of system + bath energy for a harmonic oscillator
System system;
system.addParticle(2.0);
system.addParticle(2.0);
VelocityVerletIntegrator integrator(0.01);
VelocityVerletIntegrator integrator(0.001);
double temperature = 300; // kelvin
double collisionFrequency = 0.1; // 1/ps
int numMTS = 3;
int numYS = 3;
int chainLength = 5;
int numDOF = 6;
integrator.addNoseHooverChainThermostat(system, temperature, collisionFrequency,
chainLength, numMTS, numYS);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
......@@ -58,25 +68,24 @@ void testSingleBond() {
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// This is simply a harmonic oscillator, so compare it to the analytical solution.
integrator.step(10000);
const double freq = 1.0;
double mean_temp = 0.0;
for (int i = 0; i < 10000000; ++i) {
State state = context.getState(State::Energy);
const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
for (int i = 0; i < 1000; ++i) {
state = context.getState(State::Positions | State::Velocities | State::Energy);
double KE = state.getKineticEnergy();
double PE = state.getPotentialEnergy();
double time = state.getTime();
double expectedDist = 1.5+0.5*std::cos(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
double expectedSpeed = -0.5*freq*std::sin(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
double temperature = 2 * KE / (BOLTZ * numDOF);
mean_temp = (i*mean_temp + temperature)/(i+1);
double energy = KE + PE + integrator.computeHeatBathEnergy();
if(i % 100 == 0)
std::cout << " Time: " << std::setw(4) << time
<< " Temperature: " << std::setw(8) << std::setprecision(3) << temperature
<< " Mean Temperature: " << std::setw(8) << std::setprecision(3) << mean_temp
<< " Total Energy: " << std::setw(12) << std::setprecision(8) << energy << std::endl;
integrator.step(1);
}
ASSERT_EQUAL_TOL(10.0, context.getState(0).getTime(), 1e-5);
}
void testConstraints() {
......@@ -132,15 +141,49 @@ void testConstraints() {
}
}
void testNHCPropagation() {
// test if the velocity scale factor goes to one for a single particle
// with no forces in the system
for (int numMTS = 1; numMTS < 5; numMTS++){
for (int numYS = 1; numYS <=5; numYS+=2){
for (int chainLength = 2; chainLength < 6; chainLength += 2){
double temperature = 300; // kelvin
double collisionFrequency = 20; // 1/ps
int numDOFs = 1;
int chainLength = 4;
int numMTS = 3;
int numYS = 1;
std::string label;
NoseHooverChain nhc(temperature, collisionFrequency, numDOFs, chainLength, numMTS, numYS, label);
double collisionFrequency = 0.01; // 1/ps
VelocityVerletIntegrator integrator(0.001);
// make system
System system;
double mass = 1;
system.addParticle(mass);
std::vector<int> particleList {0};
int chainID = integrator.addNoseHooverChainThermostat(system, temperature, collisionFrequency,
chainLength, numMTS, numYS);
Context context(system, integrator, platform);
// propagate the chain
double velocity = 0.1;
double scale, kineticEnergy;
for(int i = 0; i < 100; ++i) {
kineticEnergy = 3 * 0.5 * mass * velocity * velocity;
scale = integrator.propagateChain(kineticEnergy, chainID);
velocity *= scale;
}
ASSERT_EQUAL_TOL(1, scale, 1e-3);
}
}
}
}
void testPropagateChainConsistentWithPythonReference() {
VelocityVerletIntegrator integrator(0.001);
System system;
double mass = 1;
system.addParticle(mass);
double kineticEnergy = 1e6;
double temperature=300, collisionFrequency=1, chainLength=3, numMTS=3, numYS=3;
int chainID = integrator.addNoseHooverChainThermostat(system, temperature, collisionFrequency,
chainLength, numMTS, numYS);
Context context(system, integrator, platform);
double scale = integrator.propagateChain(kineticEnergy, chainID);
std::cout << std::setw(12) << std::setprecision(10) << scale << std::endl;
ASSERT_EQUAL_TOL(0.9674732261005896, scale, 1e-5)
}
void runPlatformTests();
......@@ -148,9 +191,11 @@ void runPlatformTests();
int main(int argc, char* argv[]) {
try {
initializeTests(argc, argv);
testSingleBond();
testConstraints();
runPlatformTests();
//testNHCPropagation();
testPropagateChainConsistentWithPythonReference();
//testSingleBond();
//testConstraints();
//runPlatformTests();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ d12f9f89
......@@ -67,7 +67,7 @@ SKIP_METHODS = [('State', 'getPositions'),
('IntegrateVariableVerletStepKernel',),
('IntegrateVerletStepKernel',),
('IntegrateVelocityVerletStepKernel',),
('PropagateNoseHooverChainKernel',),
('NoseHooverChainKernel',),
('IntegrateCustomStepKernel',),
('Kernel',),
('KernelFactory',),
......@@ -468,7 +468,9 @@ UNITS = {
("MonteCarloMembraneBarostat", "getXYMode") : (None, ()),
("MonteCarloMembraneBarostat", "getZMode") : (None, ()),
("DrudeLangevinIntegrator", "getDrudeFriction") : ("1/unit.picosecond", ()),
("NoseHooverChain", "getDefaultYoshidaSuzukiWeights") : ("unit.dimensionless", ()),
("NoseHooverChain", "getParentAtoms") : (None, ()),
("NoseHooverChain", "getThermostatedAtoms") : (None, ()),
("NoseHooverChain", "getDefaultYoshidaSuzukiWeights") : (None, ()),
("DrudeSCFIntegrator", "getMinimizationErrorTolerance") : ("unit.kilojoules_per_mole/unit.nanometer", ()),
("RPMDIntegrator", "getContractions") : (None, ()),
("RPMDIntegrator", "getTotalEnergy") : ("unit.kilojoules_per_mole", ()),
......
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