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Unverified Commit 86988b90 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Use LF-Middle for LangevinIntegrator and VariableLangevinIntegrator (#4440) 

* Made LangevinIntegrator identical to LangevinMiddleIntegrator

* Removed unused code

* VariableLangevinIntegrator uses LFMiddle
parent e62bdf6a
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Showing with 77 additions and 364 deletions
platforms/reference/include/ReferenceVariableStochasticDynamics.h
View file @ 86988b90
/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
/* Portions copyright (c) 2006-2024 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -33,7 +33,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
private:
std::vector<OpenMM::Vec3> xPrime;
std::vector<OpenMM::Vec3> xPrime, oldx;
std::vector<double> inverseMasses;
double friction, _accuracy;
......@@ -104,39 +104,31 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, double maxStepSize, double tolerance);
/**---------------------------------------------------------------------------------------
First update; based on code in update.c do_update_sd() Gromacs 3.1.4
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
@param inverseMasses inverse atom masses
@param xPrime xPrime
@param maxStepSize maximum time step
--------------------------------------------------------------------------------------- */
void updatePart1(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, std::vector<double>& inverseMasses,
std::vector<OpenMM::Vec3>& xPrime, double maxStepSize);
void updatePart1(int numberOfAtoms, std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses, double maxStepSize);
/**---------------------------------------------------------------------------------------
Second update
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
@param inverseMasses inverse atom masses
@param xPrime xPrime
--------------------------------------------------------------------------------------- */
void updatePart2(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses,
std::vector<OpenMM::Vec3>& xPrime);
std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
};
......
platforms/reference/src/ReferenceKernelFactory.cpp
View file @ 86988b90
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -94,8 +94,6 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
return new ReferenceIntegrateVerletStepKernel(name, platform, data);
if (name == IntegrateNoseHooverStepKernel::Name())
return new ReferenceIntegrateNoseHooverStepKernel(name, platform, data);
if (name == IntegrateLangevinStepKernel::Name())
return new ReferenceIntegrateLangevinStepKernel(name, platform, data);
if (name == IntegrateLangevinMiddleStepKernel::Name())
return new ReferenceIntegrateLangevinMiddleStepKernel(name, platform, data);
if (name == IntegrateBrownianStepKernel::Name())
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 86988b90
......@@ -61,7 +61,6 @@
#include "ReferenceProperDihedralBond.h"
#include "ReferenceRbDihedralBond.h"
#include "ReferenceRMSDForce.h"
#include "ReferenceStochasticDynamics.h"
#include "ReferenceTabulatedFunction.h"
#include "ReferenceVariableStochasticDynamics.h"
#include "ReferenceVariableVerletDynamics.h"
......@@ -2570,51 +2569,6 @@ void ReferenceIntegrateNoseHooverStepKernel::setChainStates(ContextImpl& context
chainVelocities = velocities;
}
ReferenceIntegrateLangevinStepKernel::~ReferenceIntegrateLangevinStepKernel() {
if (dynamics)
delete dynamics;
}
void ReferenceIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) {
int numParticles = system.getNumParticles();
masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i)
masses[i] = system.getParticleMass(i);
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
}
void ReferenceIntegrateLangevinStepKernel::execute(ContextImpl& context, const LangevinIntegrator& integrator) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
vector<Vec3>& posData = extractPositions(context);
vector<Vec3>& velData = extractVelocities(context);
vector<Vec3>& forceData = extractForces(context);
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters.
if (dynamics)
delete dynamics;
dynamics = new ReferenceStochasticDynamics(
context.getSystem().getNumParticles(),
stepSize,
friction,
temperature);
dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
dynamics->setVirtualSites(extractVirtualSites(context));
prevTemp = temperature;
prevFriction = friction;
prevStepSize = stepSize;
}
dynamics->update(context.getSystem(), posData, velData, forceData, masses, integrator.getConstraintTolerance());
data.time += stepSize;
data.stepCount++;
}
double ReferenceIntegrateLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const LangevinIntegrator& integrator) {
return computeShiftedKineticEnergy(context, masses, 0.5*integrator.getStepSize());
}
ReferenceIntegrateLangevinMiddleStepKernel::~ReferenceIntegrateLangevinMiddleStepKernel() {
if (dynamics)
delete dynamics;
......
platforms/reference/src/ReferencePlatform.cpp
View file @ 86988b90
......@@ -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) 2008-2023 Stanford University and the Authors. *
* Portions copyright (c) 2008-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -69,7 +69,6 @@ ReferencePlatform::ReferencePlatform() {
registerKernelFactory(CalcGayBerneForceKernel::Name(), factory);
registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateNoseHooverStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinMiddleStepKernel::Name(), factory);
registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableLangevinStepKernel::Name(), factory);
......
platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp deleted 100644 → 0
View file @ e62bdf6a
/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
* Contributors: Pande Group
*
* 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 <cstring>
#include <sstream>
#include "SimTKOpenMMUtilities.h"
#include "ReferenceStochasticDynamics.h"
#include "ReferenceVirtualSites.h"
#include "openmm/OpenMMException.h"
#include <cstdio>
using std::vector;
using namespace OpenMM;
/**---------------------------------------------------------------------------------------
ReferenceStochasticDynamics constructor
@param numberOfAtoms number of atoms
@param deltaT delta t for dynamics
@param friction friction coefficient
@param temperature temperature
--------------------------------------------------------------------------------------- */
ReferenceStochasticDynamics::ReferenceStochasticDynamics(int numberOfAtoms,
double deltaT, double friction,
double temperature) :
ReferenceDynamics(numberOfAtoms, deltaT, temperature), friction(friction) {
xPrime.resize(numberOfAtoms);
inverseMasses.resize(numberOfAtoms);
}
/**---------------------------------------------------------------------------------------
ReferenceStochasticDynamics destructor
--------------------------------------------------------------------------------------- */
ReferenceStochasticDynamics::~ReferenceStochasticDynamics() {
}
/**---------------------------------------------------------------------------------------
Get friction coefficient
--------------------------------------------------------------------------------------- */
double ReferenceStochasticDynamics::getFriction() const {
return friction;
}
/**---------------------------------------------------------------------------------------
First SD update; based on code in update.c do_update_sd() Gromacs 3.1.4
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param inverseMasses inverse atom masses
@param xPrime xPrime
--------------------------------------------------------------------------------------- */
void ReferenceStochasticDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities,
vector<Vec3>& forces, vector<double>& inverseMasses,
vector<Vec3>& xPrime) {
// perform first update
double dt = getDeltaT();
double friction = getFriction();
const double vscale = exp(-dt*friction);
const double fscale = (friction == 0 ? dt : (1-vscale)/friction);
const double kT = BOLTZ*getTemperature();
const double noisescale = sqrt(kT*(1-vscale*vscale));
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (inverseMasses[ii] != 0.0) {
double sqrtInvMass = sqrt(inverseMasses[ii]);
for (int jj = 0; jj < 3; jj++) {
velocities[ii][jj] = vscale*velocities[ii][jj] + fscale*inverseMasses[ii]*forces[ii][jj] + noisescale*sqrtInvMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
}
}
}
/**---------------------------------------------------------------------------------------
Second update; based on code in update.c do_update_sd() w/ bFirstHalf = false in Gromacs 3.1.4
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
--------------------------------------------------------------------------------------- */
void ReferenceStochasticDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities,
vector<Vec3>& forces, vector<double>& inverseMasses,
vector<Vec3>& xPrime) {
// perform second update
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (inverseMasses[ii] != 0.0)
xPrime[ii] = atomCoordinates[ii]+velocities[ii]*getDeltaT();
}
}
void ReferenceStochasticDynamics::updatePart3(int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<double>& inverseMasses,
vector<Vec3>& xPrime) {
double invStepSize = 1.0/getDeltaT();
for (int i = 0; i < numberOfAtoms; ++i)
if (inverseMasses[i] != 0) {
velocities[i] = (xPrime[i]-atomCoordinates[i])*invStepSize;
atomCoordinates[i] = xPrime[i];
}
}
/**---------------------------------------------------------------------------------------
Update -- driver routine for performing stochastic dynamics update of coordinates
and velocities
@param system the System to be integrated
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
--------------------------------------------------------------------------------------- */
void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& masses, double tolerance) {
// first-time-through initialization
int numberOfAtoms = system.getNumParticles();
if (getTimeStep() == 0) {
// invert masses
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == 0.0)
inverseMasses[ii] = 0.0;
else
inverseMasses[ii] = 1.0/masses[ii];
}
}
// 1st update
updatePart1(numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime);
// 2nd update
updatePart2(numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime);
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// copy xPrime -> atomCoordinates
updatePart3(numberOfAtoms, atomCoordinates, velocities, inverseMasses, xPrime);
getVirtualSites().computePositions(system, atomCoordinates);
incrementTimeStep();
}
platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp
View file @ 86988b90
/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
/* Portions copyright (c) 2006-2024 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -53,6 +53,7 @@ ReferenceVariableStochasticDynamics::ReferenceVariableStochasticDynamics(int num
double accuracy) :
ReferenceDynamics(numberOfAtoms, 0.0f, temperature), friction(friction), _accuracy(accuracy) {
xPrime.resize(numberOfAtoms);
oldx.resize(numberOfAtoms);
inverseMasses.resize(numberOfAtoms);
}
......@@ -97,38 +98,7 @@ double ReferenceVariableStochasticDynamics::getFriction() const {
return friction;
}
/**---------------------------------------------------------------------------------------
First SD update; based on code in update.c do_update_sd() Gromacs 3.1.4
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
@param inverseMasses inverse atom masses
@param xPrime xPrime
@param maxStepSize maximum time step
--------------------------------------------------------------------------------------- */
void ReferenceVariableStochasticDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities,
vector<Vec3>& forces, vector<double>& masses, vector<double>& inverseMasses,
vector<Vec3>& xPrime, double maxStepSize) {
// first-time-through initialization
if (getTimeStep() == 0) {
// invert masses
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == 0)
inverseMasses[ii] = 0;
else
inverseMasses[ii] = 1/masses[ii];
}
}
void ReferenceVariableStochasticDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses, double maxStepSize) {
// Select the step size to use
double error = 0;
for (int i = 0; i < numberOfAtoms; ++i) {
......@@ -138,59 +108,42 @@ void ReferenceVariableStochasticDynamics::updatePart1(int numberOfAtoms, vector<
}
}
error = sqrt(error/(numberOfAtoms*3));
double newStepSize = sqrt(getAccuracy()/error);
double dt = sqrt(getAccuracy()/error);
if (getDeltaT() > 0.0f)
newStepSize = std::min(newStepSize, getDeltaT()*2.0f); // For safety, limit how quickly dt can increase.
if (newStepSize > getDeltaT() && newStepSize < 1.2f*getDeltaT())
newStepSize = getDeltaT(); // Keeping dt constant between steps improves the behavior of the integrator.
if (newStepSize > maxStepSize)
newStepSize = maxStepSize;
setDeltaT(newStepSize);
dt = std::min(dt, getDeltaT()*2.0f); // For safety, limit how quickly dt can increase.
if (dt > getDeltaT() && dt < 1.2f*getDeltaT())
dt = getDeltaT(); // Keeping dt constant between steps improves the behavior of the integrator.
if (dt > maxStepSize)
dt = maxStepSize;
setDeltaT(dt);
// perform first update
double dt = getDeltaT();
double friction = getFriction();
const double vscale = exp(-dt*friction);
const double fscale = (friction == 0 ? dt : (1-vscale)/friction);
const double kT = BOLTZ*getTemperature();
const double noisescale = sqrt(kT*(1-vscale*vscale));
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] != 0) {
double sqrtInvMass = sqrt(inverseMasses[ii]);
for (int jj = 0; jj < 3; jj++) {
velocities[ii][jj] = vscale*velocities[ii][jj] + fscale*inverseMasses[ii]*forces[ii][jj] + noisescale*sqrtInvMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
}
}
for (int i = 0; i < numberOfAtoms; i++)
if (inverseMasses[i] != 0.0)
velocities[i] += (dt*inverseMasses[i])*forces[i];
}
/**---------------------------------------------------------------------------------------
Second update; based on code in update.c do_update_sd() w/ bFirstHalf = false in Gromacs 3.1.4
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
--------------------------------------------------------------------------------------- */
void ReferenceVariableStochasticDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities,
vector<Vec3>& forces, vector<double>& inverseMasses,
vector<Vec3>& xPrime) {
// perform second update
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (inverseMasses[ii] != 0.0)
for (int jj = 0; jj < 3; jj++)
xPrime[ii][jj] = atomCoordinates[ii][jj]+getDeltaT()*velocities[ii][jj];
}
vector<Vec3>& velocities, vector<double>& inverseMasses,
vector<Vec3>& xPrime) {
const double halfdt = 0.5*getDeltaT();
const double kT = BOLTZ*getTemperature();
const double friction = getFriction();
const double vscale = exp(-getDeltaT()*friction);
const double noisescale = sqrt(1-vscale*vscale);
for (int i = 0; i < numberOfAtoms; i++) {
if (inverseMasses[i] != 0.0) {
xPrime[i] = atomCoordinates[i] + velocities[i]*halfdt;
velocities[i] = vscale*velocities[i] + noisescale*sqrt(kT*inverseMasses[i])*Vec3(
SimTKOpenMMUtilities::getNormallyDistributedRandomNumber(),
SimTKOpenMMUtilities::getNormallyDistributedRandomNumber(),
SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
xPrime[i] = xPrime[i] + velocities[i]*halfdt;
oldx[i] = xPrime[i];
}
}
}
/**---------------------------------------------------------------------------------------
......@@ -209,30 +162,41 @@ void ReferenceVariableStochasticDynamics::updatePart2(int numberOfAtoms, vector<
void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities,
vector<Vec3>& forces, vector<double>& masses, double maxStepSize, double tolerance) {
int numberOfAtoms = system.getNumParticles();
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (getTimeStep() == 0) {
// Invert masses
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == 0.0)
inverseMasses[ii] = 0.0;
else
inverseMasses[ii] = 1/masses[ii];
}
}
// 1st update
int numberOfAtoms = system.getNumParticles();
updatePart1(numberOfAtoms, atomCoordinates, velocities, forces, masses, inverseMasses, xPrime, maxStepSize);
// 1st update
// 2nd update
updatePart1(numberOfAtoms, velocities, forces, inverseMasses, maxStepSize);
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
updatePart2(numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime);
// 2nd update
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
updatePart2(numberOfAtoms, atomCoordinates, velocities, inverseMasses, xPrime);
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// copy xPrime -> atomCoordinates
// copy xPrime -> atomCoordinates
double invStepSize = 1.0/getDeltaT();
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] != 0.0) {
velocities[ii] = (xPrime[ii]-atomCoordinates[ii])*invStepSize;
atomCoordinates[ii] = xPrime[ii];
}
}
double invStepSize = 1.0/getDeltaT();
for (int i = 0; i < numberOfAtoms; i++) {
if (masses[i] != 0.0) {
velocities[i] += (xPrime[i]-oldx[i])*invStepSize;
atomCoordinates[i] = xPrime[i];
}
}
getVirtualSites().computePositions(system, atomCoordinates);
incrementTimeStep();
getVirtualSites().computePositions(system, atomCoordinates);
incrementTimeStep();
}
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