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Unverified Commit add2bbee authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Attempt at fixing errors with barostat (#4106) 

* Attempt at fixing errors with barostat

* Missing ContextSelector
parent 3b3def0e
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Showing with 88 additions and 34 deletions
olla/include/openmm/kernels.h
View file @ add2bbee
......@@ -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) 2008-2022 Stanford University and the Authors. *
* Portions copyright (c) 2008-2023 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -1458,6 +1458,13 @@ public:
* @param rigidMolecules whether molecules should be kept rigid while scaling coordinates
*/
virtual void initialize(const System& system, const Force& barostat, bool rigidMolecules=true) = 0;
/**
* Save the coordinates before attempting a Monte Carlo step. This allows us to restore them
* if the step is rejected.
*
* @param context the context in which to execute this kernel
*/
virtual void saveCoordinates(ContextImpl& context) = 0;
/**
* Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
* This version scales the x, y, and z positions independently.
......@@ -1472,8 +1479,8 @@ public:
*/
virtual void scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ) = 0;
/**
* Reject the most recent Monte Carlo step, restoring the particle positions to where they were before
* scaleCoordinates() was last called.
* Reject the most recent Monte Carlo step, restoring the particle positions to where they were when
* saveCoordinates() was last called.
*
* @param context the context in which to execute this kernel
*/
......
openmmapi/src/MonteCarloAnisotropicBarostatImpl.cpp
View file @ add2bbee
......@@ -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) 2010-2020 Stanford University and the Authors. *
* Portions copyright (c) 2010-2023 Stanford University and the Authors. *
* Authors: Peter Eastman, Lee-Ping Wang *
* Contributors: *
* *
......@@ -107,10 +107,11 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context,
double newVolume = volume+deltaVolume;
Vec3 lengthScale(1.0, 1.0, 1.0);
lengthScale[axis] = newVolume/volume;
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale[0], lengthScale[1], lengthScale[2]);
kernel.getAs<ApplyMonteCarloBarostatKernel>().saveCoordinates(context);
context.getOwner().setPeriodicBoxVectors(Vec3(box[0][0]*lengthScale[0], box[0][1]*lengthScale[1], box[0][2]*lengthScale[2]),
Vec3(box[1][0]*lengthScale[0], box[1][1]*lengthScale[1], box[1][2]*lengthScale[2]),
Vec3(box[2][0]*lengthScale[0], box[2][1]*lengthScale[1], box[2][2]*lengthScale[2]));
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale[0], lengthScale[1], lengthScale[2]);
// Compute the energy of the modified system.
......
openmmapi/src/MonteCarloBarostatImpl.cpp
View file @ add2bbee
......@@ -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) 2010-2020 Stanford University and the Authors. *
* Portions copyright (c) 2010-2023 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -78,8 +78,9 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context, bool& forc
double deltaVolume = volumeScale*2*(SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber()-0.5);
double newVolume = volume+deltaVolume;
double lengthScale = pow(newVolume/volume, 1.0/3.0);
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale, lengthScale, lengthScale);
kernel.getAs<ApplyMonteCarloBarostatKernel>().saveCoordinates(context);
context.getOwner().setPeriodicBoxVectors(box[0]*lengthScale, box[1]*lengthScale, box[2]*lengthScale);
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale, lengthScale, lengthScale);
// Compute the energy of the modified system.
......
openmmapi/src/MonteCarloFlexibleBarostatImpl.cpp
View file @ add2bbee
......@@ -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) 2010-2021 Stanford University and the Authors. *
* Portions copyright (c) 2010-2023 Stanford University and the Authors. *
* Authors: Peter Eastman, Sander Vandenhaute *
* Contributors: *
* *
......@@ -95,8 +95,9 @@ void MonteCarloFlexibleBarostatImpl::updateContextState(ContextImpl& context, bo
// Scale particle coordinates and update box vectors in context.
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, trial[0][0]/box[0][0], trial[1][1]/box[1][1], trial[2][2]/box[2][2]);
kernel.getAs<ApplyMonteCarloBarostatKernel>().saveCoordinates(context);
context.getOwner().setPeriodicBoxVectors(trial[0], trial[1], trial[2]);
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, trial[0][0]/box[0][0], trial[1][1]/box[1][1], trial[2][2]/box[2][2]);
// Compute the energy of the modified system.
......
openmmapi/src/MonteCarloMembraneBarostatImpl.cpp
View file @ add2bbee
......@@ -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) 2010-2020 Stanford University and the Authors. *
* Portions copyright (c) 2010-2023 Stanford University and the Authors. *
* Authors: Peter Eastman, Lee-Ping Wang *
* Contributors: *
* *
......@@ -108,10 +108,11 @@ void MonteCarloMembraneBarostatImpl::updateContextState(ContextImpl& context, bo
deltaVolume = 0;
}
double deltaArea = box[0][0]*lengthScale[0]*box[1][1]*lengthScale[1] - box[0][0]*box[1][1];
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale[0], lengthScale[1], lengthScale[2]);
kernel.getAs<ApplyMonteCarloBarostatKernel>().saveCoordinates(context);
context.getOwner().setPeriodicBoxVectors(Vec3(box[0][0]*lengthScale[0], box[0][1]*lengthScale[1], box[0][2]*lengthScale[2]),
Vec3(box[1][0]*lengthScale[0], box[1][1]*lengthScale[1], box[1][2]*lengthScale[2]),
Vec3(box[2][0]*lengthScale[0], box[2][1]*lengthScale[1], box[2][2]*lengthScale[2]));
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale[0], lengthScale[1], lengthScale[2]);
// Compute the energy of the modified system.
......
platforms/common/include/openmm/common/CommonKernels.h
View file @ add2bbee
......@@ -1547,6 +1547,13 @@ public:
* @param rigidMolecules whether molecules should be kept rigid while scaling coordinates
*/
void initialize(const System& system, const Force& barostat, bool rigidMolecules=true);
/**
* Save the coordinates before attempting a Monte Carlo step. This allows us to restore them
* if the step is rejected.
*
* @param context the context in which to execute this kernel
*/
void saveCoordinates(ContextImpl& context);
/**
* Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
* This version scales the x, y, and z positions independently.
......@@ -1561,8 +1568,8 @@ public:
*/
void scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ);
/**
* Reject the most recent Monte Carlo step, restoring the particle positions to where they were before
* scaleCoordinates() was last called.
* Reject the most recent Monte Carlo step, restoring the particle positions to where they were when
* saveCoordinates() was last called.
*
* @param context the context in which to execute this kernel
*/
......
platforms/common/src/CommonKernels.cpp
View file @ add2bbee
......@@ -7713,6 +7713,15 @@ void CommonApplyMonteCarloBarostatKernel::initialize(const System& system, const
kernel = program->createKernel("scalePositions");
}
void CommonApplyMonteCarloBarostatKernel::saveCoordinates(ContextImpl& context) {
ContextSelector selector(cc);
cc.getPosq().copyTo(savedPositions);
cc.getLongForceBuffer().copyTo(savedLongForces);
if (savedFloatForces.isInitialized())
cc.getFloatForceBuffer().copyTo(savedFloatForces);
lastPosCellOffsets = cc.getPosCellOffsets();
}
void CommonApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ) {
ContextSelector selector(cc);
if (!hasInitializedKernels) {
......@@ -7755,11 +7764,6 @@ void CommonApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context,
kernel->addArg(moleculeAtoms);
kernel->addArg(moleculeStartIndex);
}
cc.getPosq().copyTo(savedPositions);
cc.getLongForceBuffer().copyTo(savedLongForces);
if (savedFloatForces.isInitialized())
cc.getFloatForceBuffer().copyTo(savedFloatForces);
lastPosCellOffsets = cc.getPosCellOffsets();
kernel->setArg(0, (float) scaleX);
kernel->setArg(1, (float) scaleY);
kernel->setArg(2, (float) scaleZ);
......
platforms/reference/include/ReferenceKernels.h
View file @ add2bbee
......@@ -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) 2008-2022 Stanford University and the Authors. *
* Portions copyright (c) 2008-2023 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -1575,6 +1575,13 @@ public:
* @param rigidMolecules whether molecules should be kept rigid while scaling coordinates
*/
void initialize(const System& system, const Force& barostat, bool rigidMolecules=true);
/**
* Save the coordinates before attempting a Monte Carlo step. This allows us to restore them
* if the step is rejected.
*
* @param context the context in which to execute this kernel
*/
void saveCoordinates(ContextImpl& context);
/**
* Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
* This version scales the x, y, and z positions independently.
......@@ -1589,8 +1596,8 @@ public:
*/
void scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ);
/**
* Reject the most recent Monte Carlo step, restoring the particle positions to where they were before
* scaleCoordinates() was last called.
* Reject the most recent Monte Carlo step, restoring the particle positions to where they were when
* saveCoordinates() was last called.
*
* @param context the context in which to execute this kernel
*/
......
platforms/reference/include/ReferenceMonteCarloBarostat.h
View file @ add2bbee
......@@ -56,6 +56,16 @@ class ReferenceMonteCarloBarostat {
~ReferenceMonteCarloBarostat();
/**---------------------------------------------------------------------------------------
Save the positions before applying the barostat.
@param atomPositions atom positions
--------------------------------------------------------------------------------------- */
void savePositions(std::vector<OpenMM::Vec3>& atomPositions);
/**---------------------------------------------------------------------------------------
Apply the barostat at the start of a time step, scaling x, y, and z coordinates independently.
......
platforms/reference/src/ReferenceKernels.cpp
View file @ add2bbee
......@@ -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) 2008-2022 Stanford University and the Authors. *
* Portions copyright (c) 2008-2023 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -35,7 +35,6 @@
#include "ReferenceAngleBondIxn.h"
#include "ReferenceBondForce.h"
#include "ReferenceBrownianDynamics.h"
#include "ReferenceCCMAAlgorithm.h"
#include "ReferenceCMAPTorsionIxn.h"
#include "ReferenceConstraints.h"
#include "ReferenceCustomAngleIxn.h"
......@@ -2897,7 +2896,7 @@ void ReferenceApplyMonteCarloBarostatKernel::initialize(const System& system, co
this->rigidMolecules = rigidMolecules;
}
void ReferenceApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ) {
void ReferenceApplyMonteCarloBarostatKernel::saveCoordinates(ContextImpl& context) {
if (barostat == NULL) {
if (rigidMolecules)
barostat = new ReferenceMonteCarloBarostat(context.getSystem().getNumParticles(), context.getMolecules());
......@@ -2908,6 +2907,11 @@ void ReferenceApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& conte
barostat = new ReferenceMonteCarloBarostat(context.getSystem().getNumParticles(), molecules);
}
}
vector<Vec3>& posData = extractPositions(context);
barostat->savePositions(posData);
}
void ReferenceApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ) {
vector<Vec3>& posData = extractPositions(context);
Vec3* boxVectors = extractBoxVectors(context);
barostat->applyBarostat(posData, boxVectors, scaleX, scaleY, scaleZ);
......
platforms/reference/src/SimTKReference/ReferenceMonteCarloBarostat.cpp
View file @ add2bbee
......@@ -52,6 +52,21 @@ ReferenceMonteCarloBarostat::ReferenceMonteCarloBarostat(int numAtoms, const vec
ReferenceMonteCarloBarostat::~ReferenceMonteCarloBarostat() {
}
/**---------------------------------------------------------------------------------------
Save the positions before applying the barostat.
@param atomPositions atom positions
--------------------------------------------------------------------------------------- */
void ReferenceMonteCarloBarostat::savePositions(vector<Vec3>& atomPositions) {
int numAtoms = savedAtomPositions[0].size();
for (int i = 0; i < numAtoms; i++)
for (int j = 0; j < 3; j++)
savedAtomPositions[j][i] = atomPositions[i][j];
}
/**---------------------------------------------------------------------------------------
Apply the barostat at the start of a time step.
......@@ -65,11 +80,6 @@ ReferenceMonteCarloBarostat::~ReferenceMonteCarloBarostat() {
--------------------------------------------------------------------------------------- */
void ReferenceMonteCarloBarostat::applyBarostat(vector<Vec3>& atomPositions, const Vec3* boxVectors, double scaleX, double scaleY, double scaleZ) {
int numAtoms = savedAtomPositions[0].size();
for (int i = 0; i < numAtoms; i++)
for (int j = 0; j < 3; j++)
savedAtomPositions[j][i] = atomPositions[i][j];
// Loop over molecules.
for (auto& molecule : molecules) {
......@@ -98,7 +108,7 @@ void ReferenceMonteCarloBarostat::applyBarostat(vector<Vec3>& atomPositions, con
/**---------------------------------------------------------------------------------------
Restore atom positions to what they were before applyBarostat() was called.
Restore atom positions to what they were before savePositions() was called.
@param atomPositions atom positions
......
plugins/rpmd/openmmapi/src/RPMDMonteCarloBarostatImpl.cpp
View file @ add2bbee
......@@ -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) 2010-2015 Stanford University and the Authors. *
* Portions copyright (c) 2010-2023 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -107,8 +107,9 @@ void RPMDMonteCarloBarostatImpl::updateRPMDState(ContextImpl& context) {
double newVolume = volume+deltaVolume;
double lengthScale = std::pow(newVolume/volume, 1.0/3.0);
context.setPositions(centroid);
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale, lengthScale, lengthScale);
kernel.getAs<ApplyMonteCarloBarostatKernel>().saveCoordinates(context);
context.getOwner().setPeriodicBoxVectors(box[0]*lengthScale, box[1]*lengthScale, box[2]*lengthScale);
kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale, lengthScale, lengthScale);
State scaledState = context.getOwner().getState(State::Positions);
// Now apply the same offset to all the copies.
......
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