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Commit 05ad28f2 authored by one's avatar one
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Merge OpenMM master into dtk26.04

parents 97239ca6 fc21fd19
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Showing with 842 additions and 211 deletions
plugins/drude/platforms/common/src/CommonDrudeKernels.cpp
View file @ 05ad28f2
......@@ -502,7 +502,10 @@ void CommonIntegrateDrudeSCFStepKernel::minimize(ContextImpl& context, double to
int numDrude = drudeParams.getSize();
int paddedNumAtoms = cc.getPaddedNumAtoms();
for (int iteration = 0; iteration < 50; iteration++) {
context.calcForcesAndEnergy(true, false, context.getIntegrator().getIntegrationForceGroups());
{
ContextDeselector deselector(cc);
context.calcForcesAndEnergy(true, false, context.getIntegrator().getIntegrationForceGroups());
}
minimizeKernel->execute(drudeParams.getSize());
cc.getLongForceBuffer().download(forces);
double totalForce = 0;
......
plugins/rpmd/platforms/common/src/CommonRpmdKernels.cpp
View file @ 05ad28f2
......@@ -297,7 +297,10 @@ void CommonIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
context.getPeriodicBoxVectors(finalBox[0], finalBox[1], finalBox[2]);
if (initialBox[0] != finalBox[0] || initialBox[1] != finalBox[1] || initialBox[2] != finalBox[2])
throw OpenMMException("Standard barostats cannot be used with RPMDIntegrator. Use RPMDMonteCarloBarostat instead.");
context.calcForcesAndEnergy(true, false, groupsNotContracted);
{
ContextDeselector deselector(cc);
context.calcForcesAndEnergy(true, false, groupsNotContracted);
}
copyFromContextKernel->setArg(7, i);
copyFromContextKernel->execute(cc.getNumAtoms());
}
......@@ -322,7 +325,10 @@ void CommonIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
copyToContextKernel->setArg(5, i);
copyToContextKernel->execute(cc.getNumAtoms());
context.computeVirtualSites();
context.calcForcesAndEnergy(true, false, groupFlags);
{
ContextDeselector deselector(cc);
context.calcForcesAndEnergy(true, false, groupFlags);
}
copyFromContextKernel->setArg(7, i);
copyFromContextKernel->execute(cc.getNumAtoms());
}
......
serialization/src/MonteCarloAnisotropicBarostatProxy.cpp
View file @ 05ad28f2
......@@ -4,7 +4,7 @@
* This is part of the OpenMM molecular simulation toolkit. *
* See https://openmm.org/development. *
* *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Portions copyright (c) 2010-2026 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -54,6 +54,7 @@ void MonteCarloAnisotropicBarostatProxy::serialize(const void* object, Serializa
node.setDoubleProperty("temperature", force.getDefaultTemperature());
node.setIntProperty("frequency", force.getFrequency());
node.setIntProperty("randomSeed", force.getRandomNumberSeed());
node.setBoolProperty("rigidScaling", force.getScaleMoleculesAsRigid());
}
void* MonteCarloAnisotropicBarostatProxy::deserialize(const SerializationNode& node) const {
......@@ -63,7 +64,7 @@ void* MonteCarloAnisotropicBarostatProxy::deserialize(const SerializationNode& n
try {
Vec3 pressure(node.getDoubleProperty("pressurex"), node.getDoubleProperty("pressurey"), node.getDoubleProperty("pressurez"));
force = new MonteCarloAnisotropicBarostat(pressure, node.getDoubleProperty("temperature"), node.getBoolProperty("scalex"),
node.getBoolProperty("scaley"), node.getBoolProperty("scalez"), node.getIntProperty("frequency"));
node.getBoolProperty("scaley"), node.getBoolProperty("scalez"), node.getIntProperty("frequency"), node.getBoolProperty("rigidScaling", true));
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setName(node.getStringProperty("name", force->getName()));
force->setRandomNumberSeed(node.getIntProperty("randomSeed"));
......
serialization/src/MonteCarloBarostatProxy.cpp
View file @ 05ad28f2
......@@ -4,7 +4,7 @@
* This is part of the OpenMM molecular simulation toolkit. *
* See https://openmm.org/development. *
* *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Portions copyright (c) 2010-2026 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -48,6 +48,7 @@ void MonteCarloBarostatProxy::serialize(const void* object, SerializationNode& n
node.setDoubleProperty("temperature", force.getDefaultTemperature());
node.setIntProperty("frequency", force.getFrequency());
node.setIntProperty("randomSeed", force.getRandomNumberSeed());
node.setBoolProperty("rigidScaling", force.getScaleMoleculesAsRigid());
}
void* MonteCarloBarostatProxy::deserialize(const SerializationNode& node) const {
......@@ -55,7 +56,8 @@ void* MonteCarloBarostatProxy::deserialize(const SerializationNode& node) const
throw OpenMMException("Unsupported version number");
MonteCarloBarostat* force = NULL;
try {
force = new MonteCarloBarostat(node.getDoubleProperty("pressure"), node.getDoubleProperty("temperature"), node.getIntProperty("frequency"));
force = new MonteCarloBarostat(node.getDoubleProperty("pressure"), node.getDoubleProperty("temperature"), node.getIntProperty("frequency"),
node.getBoolProperty("rigidScaling", true));
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setName(node.getStringProperty("name", force->getName()));
force->setRandomNumberSeed(node.getIntProperty("randomSeed"));
......
serialization/src/MonteCarloMembraneBarostatProxy.cpp
View file @ 05ad28f2
......@@ -4,7 +4,7 @@
* This is part of the OpenMM molecular simulation toolkit. *
* See https://openmm.org/development. *
* *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Portions copyright (c) 2010-2026 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -51,6 +51,7 @@ void MonteCarloMembraneBarostatProxy::serialize(const void* object, Serializatio
node.setIntProperty("zmode", force.getZMode());
node.setIntProperty("frequency", force.getFrequency());
node.setIntProperty("randomSeed", force.getRandomNumberSeed());
node.setBoolProperty("rigidScaling", force.getScaleMoleculesAsRigid());
}
void* MonteCarloMembraneBarostatProxy::deserialize(const SerializationNode& node) const {
......@@ -61,7 +62,7 @@ void* MonteCarloMembraneBarostatProxy::deserialize(const SerializationNode& node
MonteCarloMembraneBarostat::XYMode xymode = (MonteCarloMembraneBarostat::XYMode) node.getIntProperty("xymode");
MonteCarloMembraneBarostat::ZMode zmode = (MonteCarloMembraneBarostat::ZMode) node.getIntProperty("zmode");
force = new MonteCarloMembraneBarostat(node.getDoubleProperty("pressure"), node.getDoubleProperty("surfaceTension"),
node.getDoubleProperty("temperature"), xymode, zmode, node.getIntProperty("frequency"));
node.getDoubleProperty("temperature"), xymode, zmode, node.getIntProperty("frequency"), node.getBoolProperty("rigidScaling", true));
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setName(node.getStringProperty("name", force->getName()));
force->setRandomNumberSeed(node.getIntProperty("randomSeed"));
......
serialization/src/g_fmt.cpp
View file @ 05ad28f2
......@@ -33,10 +33,10 @@ extern "C" {
#endif
char *
g_fmt(register char *b, double x)
g_fmt(char *b, double x)
{
register int i, k;
register char *s;
int i, k;
char *s;
int decpt, j, sign;
char *b0, *s0, *se;
......
serialization/tests/TestSerializeMonteCarloAnisotropicBarostat.cpp
View file @ 05ad28f2
......@@ -4,7 +4,7 @@
* This is part of the OpenMM molecular simulation toolkit. *
* See https://openmm.org/development. *
* *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Portions copyright (c) 2010-2026 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -39,7 +39,7 @@ using namespace std;
void testSerialization() {
// Create a Force.
MonteCarloAnisotropicBarostat force(Vec3(15.1, 18.2, 19.3), 250.0, true, false, true, 14);
MonteCarloAnisotropicBarostat force(Vec3(15.1, 18.2, 19.3), 250.0, true, false, true, 14, false);
force.setForceGroup(3);
force.setName("custom name");
force.setRandomNumberSeed(3);
......@@ -62,6 +62,7 @@ void testSerialization() {
ASSERT_EQUAL(force.getScaleZ(), force2.getScaleZ());
ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());
ASSERT_EQUAL(force.getRandomNumberSeed(), force2.getRandomNumberSeed());
ASSERT_EQUAL(force.getScaleMoleculesAsRigid(), force2.getScaleMoleculesAsRigid());
}
int main() {
......
serialization/tests/TestSerializeMonteCarloBarostat.cpp
View file @ 05ad28f2
......@@ -4,7 +4,7 @@
* This is part of the OpenMM molecular simulation toolkit. *
* See https://openmm.org/development. *
* *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Portions copyright (c) 2010-2026 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -39,7 +39,7 @@ using namespace std;
void testSerialization() {
// Create a Force.
MonteCarloBarostat force(25.5, 250.0, 14);
MonteCarloBarostat force(25.5, 250.0, 14, false);
force.setForceGroup(3);
force.setName("custom name");
force.setRandomNumberSeed(3);
......@@ -59,6 +59,7 @@ void testSerialization() {
ASSERT_EQUAL(force.getDefaultTemperature(), force2.getDefaultTemperature());
ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());
ASSERT_EQUAL(force.getRandomNumberSeed(), force2.getRandomNumberSeed());
ASSERT_EQUAL(force.getScaleMoleculesAsRigid(), force2.getScaleMoleculesAsRigid());
}
int main() {
......
serialization/tests/TestSerializeMonteCarloMembraneBarostat.cpp
View file @ 05ad28f2
......@@ -4,7 +4,7 @@
* This is part of the OpenMM molecular simulation toolkit. *
* See https://openmm.org/development. *
* *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Portions copyright (c) 2010-2026 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -39,7 +39,7 @@ using namespace std;
void testSerialization() {
// Create a Force.
MonteCarloMembraneBarostat force(25.5, 11.2, 250.0, MonteCarloMembraneBarostat::XYAnisotropic, MonteCarloMembraneBarostat::ZFixed, 14);
MonteCarloMembraneBarostat force(25.5, 11.2, 250.0, MonteCarloMembraneBarostat::XYAnisotropic, MonteCarloMembraneBarostat::ZFixed, 14, false);
force.setForceGroup(3);
force.setName("custom name");
force.setRandomNumberSeed(3);
......@@ -62,6 +62,7 @@ void testSerialization() {
ASSERT_EQUAL(force.getZMode(), force2.getZMode());
ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());
ASSERT_EQUAL(force.getRandomNumberSeed(), force2.getRandomNumberSeed());
ASSERT_EQUAL(force.getScaleMoleculesAsRigid(), force2.getScaleMoleculesAsRigid());
}
int main() {
......
tests/TestMonteCarloAnisotropicBarostat.h
View file @ 05ad28f2
......@@ -4,7 +4,7 @@
* This is part of the OpenMM molecular simulation toolkit. *
* See https://openmm.org/development. *
* *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2026 Stanford University and the Authors. *
* Authors: Peter Eastman, Lee-Ping Wang *
* Contributors: *
* *
......@@ -29,6 +29,7 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/CustomIntegrator.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/MonteCarloAnisotropicBarostat.h"
......@@ -184,8 +185,75 @@ void testIdealGasAxis(int axis) {
}
}
void testMolecularGas() {
const int numMolecules = 64;
void testMoleculeScaling(bool rigid) {
int numMolecules = 10;
double initialWidth = 3.0;
// Create a system of diatomic molecules.
System system;
Vec3 initialBox[] = {Vec3(initialWidth, 0, 0), Vec3(0, initialWidth, 0), Vec3(0, 0, initialWidth)};
system.setDefaultPeriodicBoxVectors(initialBox[0], initialBox[1], initialBox[2]);
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
system.addForce(nonbonded);
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(1.0, 1.0, 1.0), 300.0, true, true, true, 1, rigid);
system.addForce(barostat);
vector<Vec3> positions;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numMolecules; i++) {
system.addParticle(1.0);
system.addParticle(1.0);
bonds->addBond(2*i, 2*i+1, 0.2, 1000.0);
nonbonded->addParticle(0.0, 0.1, 1.0);
nonbonded->addParticle(0.0, 0.1, 1.0);
Vec3 pos1(initialWidth*genrand_real2(sfmt), initialWidth*genrand_real2(sfmt), initialWidth*genrand_real2(sfmt));
Vec3 delta(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
delta /= sqrt(delta.dot(delta));
positions.push_back(pos1);
positions.push_back(pos1+delta);
}
// Use an integrator that applies the barostat but nothing else.
CustomIntegrator integrator(1.0);
integrator.addUpdateContextState();
// Let the barostat make some moves.
Context context(system, integrator, platform);
context.setPositions(positions);
integrator.step(100);
State state = context.getState(State::Positions);
// The box size should have changed.
Vec3 finalBox[3];
state.getPeriodicBoxVectors(finalBox[0], finalBox[1], finalBox[2]);
for (int i = 0; i < 3; i++)
ASSERT(finalBox[i][i] != initialBox[i][i]);
// See if the molecules were scaled correctly.
Vec3 boxScale(finalBox[0][0]/initialBox[0][0], finalBox[1][1]/initialBox[1][1], finalBox[2][2]/initialBox[2][2]);
for (int i = 0; i < numMolecules; i++) {
Vec3 delta1 = positions[2*i+1]-positions[2*i];
Vec3 delta2 = state.getPositions()[2*i+1]-state.getPositions()[2*i];
if (rigid) {
ASSERT_EQUAL_VEC(delta1, delta2, 1e-5);
}
else {
Vec3 expected(delta1[0]*boxScale[0], delta1[1]*boxScale[1], delta1[2]*boxScale[2]);
ASSERT_EQUAL_VEC(expected, delta2, 1e-5);
}
}
}
void testMolecularGas(bool rigid) {
const int numMolecules = 256;
const int frequency = 5;
const int steps = 5000;
const double pressure = 3.0;
......@@ -198,7 +266,7 @@ void testMolecularGas() {
System system;
system.setDefaultPeriodicBoxVectors(Vec3(initialLength, 0, 0), Vec3(0, 0.5*initialLength, 0), Vec3(0, 0, 2*initialLength));
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, true, true, true, frequency);
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, true, true, true, frequency, rigid);
system.addForce(barostat);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->setUsesPeriodicBoundaryConditions(true);
......@@ -211,8 +279,8 @@ void testMolecularGas() {
system.addParticle(1.0);
system.addParticle(1.0);
Vec3 pos(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
system.addConstraint(positions.size(), positions.size()+1, 0.1);
system.addConstraint(positions.size(), positions.size()+2, 0.1);
bonds->addBond(positions.size(), positions.size()+1, 0.1, 1.0);
bonds->addBond(positions.size(), positions.size()+2, 0.1, 1.0);
positions.push_back(pos);
positions.push_back(pos+Vec3(0.1, 0.0, 0.0));
positions.push_back(pos+Vec3(0.0, 0.1, 0.0));
......@@ -565,7 +633,10 @@ int main(int argc, char* argv[]) {
testIdealGasAxis(0);
testIdealGasAxis(1);
testIdealGasAxis(2);
testMolecularGas();
testMoleculeScaling(true);
testMoleculeScaling(false);
testMolecularGas(true);
testMolecularGas(false);
testRandomSeed();
testTriclinic();
//testEinsteinCrystal();
......
tests/TestMonteCarloBarostat.h
View file @ 05ad28f2
......@@ -4,7 +4,7 @@
* This is part of the OpenMM molecular simulation toolkit. *
* See https://openmm.org/development. *
* *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2026 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -30,6 +30,7 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/Context.h"
#include "openmm/CustomIntegrator.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
......@@ -141,9 +142,75 @@ void testIdealGas() {
}
}
void testMolecularGas() {
const int numMolecules = 64;
const int frequency = 10;
void testMoleculeScaling(bool rigid) {
int numMolecules = 10;
double initialWidth = 3.0;
// Create a system of diatomic molecules.
System system;
Vec3 initialBox[] = {Vec3(initialWidth, 0, 0), Vec3(0, initialWidth, 0), Vec3(0, 0, initialWidth)};
system.setDefaultPeriodicBoxVectors(initialBox[0], initialBox[1], initialBox[2]);
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
system.addForce(nonbonded);
MonteCarloBarostat* barostat = new MonteCarloBarostat(1.0, 300.0, 1, rigid);
system.addForce(barostat);
vector<Vec3> positions;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numMolecules; i++) {
system.addParticle(1.0);
system.addParticle(1.0);
bonds->addBond(2*i, 2*i+1, 0.2, 1000.0);
nonbonded->addParticle(0.0, 0.1, 1.0);
nonbonded->addParticle(0.0, 0.1, 1.0);
Vec3 pos1(initialWidth*genrand_real2(sfmt), initialWidth*genrand_real2(sfmt), initialWidth*genrand_real2(sfmt));
Vec3 delta(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
delta /= sqrt(delta.dot(delta));
positions.push_back(pos1);
positions.push_back(pos1+delta);
}
// Use an integrator that applies the barostat but nothing else.
CustomIntegrator integrator(1.0);
integrator.addUpdateContextState();
// Let the barostat make some moves.
Context context(system, integrator, platform);
context.setPositions(positions);
integrator.step(100);
State state = context.getState(State::Positions);
// The box size should have changed.
Vec3 finalBox[3];
state.getPeriodicBoxVectors(finalBox[0], finalBox[1], finalBox[2]);
ASSERT(finalBox[0][0] != initialBox[0][0]);
// See if the molecules were scaled correctly.
Vec3 boxScale(finalBox[0][0]/initialBox[0][0], finalBox[1][1]/initialBox[1][1], finalBox[2][2]/initialBox[2][2]);
for (int i = 0; i < numMolecules; i++) {
Vec3 delta1 = positions[2*i+1]-positions[2*i];
Vec3 delta2 = state.getPositions()[2*i+1]-state.getPositions()[2*i];
if (rigid) {
ASSERT_EQUAL_VEC(delta1, delta2, 1e-5);
}
else {
Vec3 expected(delta1[0]*boxScale[0], delta1[1]*boxScale[1], delta1[2]*boxScale[2]);
ASSERT_EQUAL_VEC(expected, delta2, 1e-5);
}
}
}
void testMolecularGas(bool rigid) {
const int numMolecules = 256;
const int frequency = 5;
const int steps = 1000;
const double pressure = 1.5;
const double pressureInMD = pressure*(AVOGADRO*1e-25); // pressure in kJ/mol/nm^3
......@@ -155,7 +222,7 @@ void testMolecularGas() {
System system;
system.setDefaultPeriodicBoxVectors(Vec3(initialLength, 0, 0), Vec3(0, 0.5*initialLength, 0), Vec3(0, 0, 2*initialLength));
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, frequency);
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, frequency, rigid);
system.addForce(barostat);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->setUsesPeriodicBoundaryConditions(true);
......@@ -177,8 +244,8 @@ void testMolecularGas() {
system.addParticle(3.0);
}
Vec3 pos(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
bonds->addBond(positions.size(), positions.size()+1, 0.1, 10.0);
system.addConstraint(positions.size(), positions.size()+2, 0.1);
bonds->addBond(positions.size(), positions.size()+1, 0.1, 1.0);
bonds->addBond(positions.size(), positions.size()+2, 0.1, 1.0);
positions.push_back(pos);
positions.push_back(pos+Vec3(0.1, 0.0, 0.0));
positions.push_back(pos+Vec3(0.0, 0.1, 0.0));
......@@ -381,7 +448,10 @@ int main(int argc, char* argv[]) {
initializeTests(argc, argv);
testChangingBoxSize();
testIdealGas();
testMolecularGas();
testMoleculeScaling(true);
testMoleculeScaling(false);
testMolecularGas(true);
testMolecularGas(false);
testRandomSeed();
// Don't run testWater() or testLJPressure() here, because they're very slow on
// Reference platform. Individual platforms can run them from runPlatformTests().
......
wrappers/python/openmm/app/__init__.py
View file @ 05ad28f2
......@@ -38,6 +38,8 @@ from .charmmpsffile import CharmmPsfFile, CharmmPSFWarning
from .simulatedtempering import SimulatedTempering
from .metadynamics import Metadynamics, BiasVariable
from .replicaexchangesampler import ReplicaExchangeSampler
from .replicaexchangereporter import ReplicaExchangeReporter
from .expandedensemblesampler import ExpandedEnsembleSampler
# Enumerated values
......
wrappers/python/openmm/app/expandedensemblesampler.py 0 → 100644
View file @ 05ad28f2
This diff is collapsed.
wrappers/python/openmm/app/forcefield.py
View file @ 05ad28f2
......@@ -1286,6 +1286,12 @@ class ForceField(object):
-------
system
the newly created System
Notes
-----
The constructed System contains one particle for each atom in the Topology,
and the particles are in the same order as the atoms. An atom's index in the
Topology is therefore also the index of its corresponding particle in the System.
"""
args['switchDistance'] = switchDistance
args['flexibleConstraints'] = flexibleConstraints
......
wrappers/python/openmm/app/internal/multistatesampler.py
View file @ 05ad28f2
......@@ -209,7 +209,7 @@ class MultistateSampler(object):
-------
an array containing the potential energies of all states in the order they appear in self.states
"""
energies = [0*kilojoules_per_mole for _ in self.states]
energies = [0 for _ in self.states]*kilojoules_per_mole
for i, subset in enumerate(self.subsets):
if self.groups is None:
# States don't depend on force groups, so we can just evaluate the energy of one state.
......@@ -241,6 +241,6 @@ class MultistateSampler(object):
an array containing the shifted potential energies of all states in the order they appear in self.states
"""
if len(self.subsets) == 1 and self.groups is None:
return [0*kilojoules_per_mole]*len(self.states)
return [0]*len(self.states)*kilojoules_per_mole
energies = self.computeAllEnergies()
return [e-energies[0] for e in energies]
\ No newline at end of file
wrappers/python/openmm/app/internal/safesave.py
View file @ 05ad28f2
......@@ -4,9 +4,9 @@ safesave.py: Helper module to ensure atomic overwrite/backup of existing files.
This is part of the OpenMM molecular simulation toolkit.
See https://openmm.org/development.
Portions copyright (c) 2025 Stanford University and the Authors.
Portions copyright (c) 2025-2026 Stanford University and the Authors.
Authors: Evan Pretti
Contributors:
Contributors: Peter Eastman
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
......@@ -51,11 +51,8 @@ def _getTempFilename(prefix):
for index in itertools.count():
name = f'{prefix}.{index}.tmp'
try:
with open(name, 'x'):
return name
except FileExistsError:
pass
if not os.path.exists(name):
return name
def save(data, filename):
"""
......
wrappers/python/openmm/app/replicaexchangereporter.py 0 → 100644
View file @ 05ad28f2
"""
replicaexchangereporter.py: Writes output for replica exchange simulations
This is part of the OpenMM molecular simulation toolkit.
See https://openmm.org/development.
Portions copyright (c) 2026 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.
"""
import openmm as mm
import openmm.app as app
import openmm.unit as unit
from openmm.app.internal import safesave
import os
class ReplicaExchangeReporter(object):
"""
This is a reporter for use with ReplicaExchangeSampler. It outputs the most important information required for
nearly all replica exchange simulations. It must be added to the sampler's list of reporters:
>>> sampler.reporters.append(ReplicaExchangeReporter(directory, interval, sampler))
As the simulation runs, it creates the following files in a user specified directory.
- A CSV file containing a log of what state each replica was in at each iteration.
- A set of XML files containing serialized State objects for each replica. These serve as checkpoints, allowing a
simulation to be resumed later.
- (optional) A trajectory file for each thermodynamic state. The coordinates in these files jump discontinuously
whenever an exchange happens.
- (optional) A trajectory file for each replica. The coordinates in these files are continuous, but the
thermodynamic states they explore change with time.
- (optional) A CSV file containing the reduced energy (potential energy divided by kT) of every replica in every
state at each iteration. This information is useful for calculating free energies.
The reduced energies are written as a matrix in flattened order for each iteration. You can load the file with
NumPy using the command
>>> energy = np.loadtxt('energy.csv', delimiter=',').reshape(-1, n_states, n_states)
`energy[i][j][k]` is the reduced energy of state k for replica j in iteration i.
To resume a simulation from the saved files, pass `resume=True` to the constructor. It will load all necessary
information and configure the ReplicaExchangeSampler correctly.
"""
def __init__(self, directory: str, reportInterval: int, sampler: "app.ReplicaExchangeSampler",
trajectoryPerState: bool = True, trajectoryPerReplica: bool = False, trajectoryFormat: str = 'xtc',
enforcePeriodicBox: bool | None = None, energy: bool = False, resume: bool = False):
"""
Create a ReplicaExchangeReporter.
Parameters
----------
directory: str
The path to the directory where the files will be written. The directory will be created if it does not
already exist. The directory must be empty unless resume is True, in which case it must contain the files
from an earlier simulation.
reportInterval: int
The frequency at which to write output, measured in iterations
sampler: openmm.app.ReplicaExchangeSampler
The sampler this reporter will be added to
trajectoryPerState: bool
If True, a trajectory file will be saved for each thermodynamic state.
trajectoryPerReplica: bool
If True, a trajectory file will be saved for each replica.
trajectoryFormat: str
The format in which to save trajectories. Supported options are 'xtc' and 'dcd'.
enforcePeriodicBox: bool
Specifies whether particle positions should be translated so the center of every molecule
lies in the same periodic box. If None (the default), it will automatically decide whether
to translate molecules based on whether the system being simulated uses periodic boundary
conditions.
energy: bool
If True, a CSV file will be saved containing reduced energies.
resume: bool
Specifies whether to resume an earlier simulation. If True, the checkpoint and log data will be loaded into
the ReplicaExchangeSampler, and future output will be appended to the existing files.
"""
trajectoryFormat = trajectoryFormat.lower()
self.directory = directory
self.reportInterval = reportInterval
self.trajectoryPerState = trajectoryPerState
self.trajectoryPerReplica = trajectoryPerReplica
self.format = format
self._log = None
self._energy = None
numStates = len(sampler.states)
# Validate the inputs and create the output directory if necessary.
if trajectoryFormat not in ('xtc', 'dcd'):
raise ValueError(f'Unsupported trajectory format: {trajectoryFormat}. Allowed values are "xtc" and "dcd".')
if resume:
if not os.path.isdir(directory):
raise ValueError(f'Cannot resume because the directory does not exist: {directory}')
def checkExists(filename):
if not os.path.isfile(os.path.join(directory, filename)):
raise ValueError(f'Cannot resume because the file {filename} does not exist.')
checkExists('log.csv')
if energy:
checkExists('energy.csv')
for i in range(numStates):
checkExists(f'checkpoint_{i}.xml')
if trajectoryPerState:
checkExists(f'state_{i}.{trajectoryFormat}')
if trajectoryPerReplica:
checkExists(f'replica_{i}.{trajectoryFormat}')
else:
if os.path.isdir(directory):
if len(os.listdir(directory)) > 0:
raise ValueError(f'The directory {directory} is not empty.')
else:
os.makedirs(directory)
# Load state assignments and checkpoints if resuming another simulation.
if resume:
for i in range(numStates):
with open(os.path.join(directory, f'checkpoint_{i}.xml')) as input:
sampler.replicaConformation[i] = mm.XmlSerializer.deserialize(input.read())
log = None
with open(os.path.join(directory, 'log.csv')) as input:
for line in input:
log = line
if log is None:
raise ValueError('Cannot resume because log file is empty.')
fields = log.split(',')
sampler.replicaStateIndex = [int(x) for x in fields[2:(numStates+2)]]
sampler._previousReplicaStateIndex = sampler.replicaStateIndex[:]
sampler.currentIteration = int(fields[0])
# Create reporters and open files for writing output.
def createReporter(filename):
path = os.path.join(directory, filename)
interval = reportInterval*sampler.stepsPerIteration
if trajectoryFormat == 'xtc':
return app.XTCReporter(path, reportInterval*sampler.stepsPerIteration, append=resume, enforcePeriodicBox=enforcePeriodicBox)
return app.DCDReporter(path, interval, append=resume, enforcePeriodicBox=enforcePeriodicBox)
self._stateReporters = []
self._replicaReporters = []
for i in range(numStates):
if trajectoryPerState:
self._stateReporters.append(createReporter(f'state_{i}.{trajectoryFormat}'))
if trajectoryPerReplica:
self._replicaReporters.append(createReporter(f'replica_{i}.{trajectoryFormat}'))
self._log = open(os.path.join(directory, 'log.csv'), 'a' if resume else 'w')
if not resume:
print(','.join(['Iteration', 'Step']+[f'Replica_{i}_State' for i in range(numStates)]), file=self._log)
self._log.flush()
if energy:
self._energy = open(os.path.join(directory, 'energy.csv'), 'a' if resume else 'w')
def __del__(self):
if self._log is not None:
self._log.close()
if self._energy is not None:
self._energy.close()
def __call__(self, sampler: "app.ReplicaExchangeSampler"):
"""This is invoked by the ReplicaExchangeSampler at the end of every iteration to generate output."""
if sampler.currentIteration % self.reportInterval != 0:
return
logData = [sampler.currentIteration, sampler.simulation.currentStep]+sampler.replicaStateIndex
print(','.join([str(x) for x in logData]), file=self._log)
self._log.flush()
if self._energy is not None:
import numpy as np
energy = np.array(sampler.replicaStateEnergy)
if sampler._kT is None:
energy /= unit.MOLAR_GAS_CONSTANT_R*sampler.simulation.integrator.getTemperature()
else:
energy /= sampler._kT
print(','.join([str(x) for x in energy.flatten()]), file=self._energy)
self._energy.flush()
for i, conf in enumerate(sampler.replicaConformation):
if len(self._stateReporters) > 0:
self._stateReporters[sampler.replicaStateIndex[i]].report(sampler.simulation, conf)
if len(self._replicaReporters) > 0:
self._replicaReporters[i].report(sampler.simulation, conf)
safesave.save(mm.XmlSerializer.serialize(conf), os.path.join(self.directory, f'checkpoint_{i}.xml'))
wrappers/python/openmm/app/replicaexchangesampler.py
View file @ 05ad28f2
......@@ -35,7 +35,7 @@ import random
class ReplicaExchangeSampler(object):
"""
ReplicaExchangeSampler uses replica exchange to simulate a system in a collection of different states. It supports
ReplicaExchangeSampler uses replica exchange to simulate a system in a collection of thermodynamic states. It supports
both temperature replica exchange, in which the states correspond to different temperatures, and Hamiltonian replica
exchange, in which they correspond to different potential functions. It also can combine them to vary temperature
and potential function at the same time.
......@@ -54,9 +54,9 @@ class ReplicaExchangeSampler(object):
- Hamiltonian replica exchange may be used to sample an alchemical transition between two endpoints. It produces
efficient sampling at every point along the transition pathway from which a free energy difference can be computed.
Each state (not to be confused with a State object) is represented by a dict containing property values. All states
must specify values for the same properties. They describe the ways in which the states differ from each other. The
following properties are supported.
Each thermodynamic state (not to be confused with a State object) is represented by a dict containing property
values. All states must specify values for the same properties. They describe the ways in which the states differ
from each other. The following properties are supported.
- 'temperature': the simulation temperature
- 'groups': a set containing the force groups to include when computing the energy, for example {0, 2}. It also may
......@@ -90,7 +90,16 @@ class ReplicaExchangeSampler(object):
Because replica exchange involves simulating many distinct replicas, the standard reporters used to generate output
from a simulation are often not appropriate. ReplicaExchangeSampler instead provides its own reporting mechanism.
Define a function that takes a ReplicaExchangeSampler as its only argument:
For most purposes, you can use the ReplicaExchangeReporter class. Create a reporter and add it to the sampler:
>>> sampler.reporters.append(ReplicaExchangeReporter(directory, interval, sampler))
It can write out a variety of types of information including a log of state assignments, trajectories for each
replica and/or state, reduced energies, and checkpoint files for resuming a simulation. See the documentation on
ReplicaExchangeReporter for details.
If you want to output other information, you can create your own reporters. Define a function that takes a
ReplicaExchangeSampler as its only argument:
>>> def report(sampler):
>>> # Generate whatever output you want here
......
wrappers/python/openmm/app/simulatedtempering.py
View file @ 05ad28f2
......@@ -6,7 +6,7 @@ simulatedtempering.py: Implements simulated tempering
This is part of the OpenMM molecular simulation toolkit.
See https://openmm.org/development.
Portions copyright (c) 2015 Stanford University and the Authors.
Portions copyright (c) 2015-2026 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
......@@ -32,28 +32,14 @@ __author__ = "Peter Eastman"
__version__ = "1.0"
import openmm.unit as unit
import math
import random
from sys import stdout
try:
import bz2
have_bz2 = True
except: have_bz2 = False
try:
import gzip
have_gzip = True
except: have_gzip = False
try:
import numpy
have_numpy = True
except: have_numpy = False
class SimulatedTempering(object):
"""SimulatedTempering implements the simulated tempering algorithm for accelerated sampling.
@deprecated This class exists mainly for historical reasons. It now is just a thin wrapper around ExpandedEnsembleSampler. It is still supported for backward compatibility, but using ExpandedEnsembleSampler directly is recommended since it is much more flexible.
It runs a simulation while allowing the temperature to vary. At high temperatures, it can more easily cross
energy barriers to explore a wider area of conformation space. At low temperatures, it can thoroughly
explore each local region. For details, see Marinari, E. and Parisi, G., Europhys. Lett. 19(6). pp. 451-458 (1992).
......@@ -106,160 +92,27 @@ class SimulatedTempering(object):
The interval (in time steps) at which to write information to the report file
reportFile: string or file
The file to write reporting information to, specified as a file name or file object
"""
self.simulation = simulation
"""
if temperatures is None:
if unit.is_quantity(minTemperature):
minTemperature = minTemperature.value_in_unit(unit.kelvin)
if unit.is_quantity(maxTemperature):
maxTemperature = maxTemperature.value_in_unit(unit.kelvin)
self.temperatures = [minTemperature*((float(maxTemperature)/minTemperature)**(i/float(numTemperatures-1))) for i in range(numTemperatures)]*unit.kelvin
else:
numTemperatures = len(temperatures)
self.temperatures = [(t.value_in_unit(unit.kelvin) if unit.is_quantity(t) else t)*unit.kelvin for t in temperatures]
if any(self.temperatures[i] >= self.temperatures[i+1] for i in range(numTemperatures-1)):
raise ValueError('The temperatures must be in strictly increasing order')
self.tempChangeInterval = tempChangeInterval
self.reportInterval = reportInterval
self.inverseTemperatures = [1.0/(unit.MOLAR_GAS_CONSTANT_R*t) for t in self.temperatures]
# If necessary, open the file we will write reports to.
self._openedFile = isinstance(reportFile, str)
if self._openedFile:
# Detect the desired compression scheme from the filename extension
# and open all files unbuffered
if reportFile.endswith('.gz'):
if not have_gzip:
raise RuntimeError("Cannot write .gz file because Python could not import gzip library")
self._out = gzip.GzipFile(fileobj=open(reportFile, 'wb', 0))
elif reportFile.endswith('.bz2'):
if not have_bz2:
raise RuntimeError("Cannot write .bz2 file because Python could not import bz2 library")
self._out = bz2.BZ2File(reportFile, 'w', 0)
else:
self._out = open(reportFile, 'w', 1)
else:
self._out = reportFile
# Initialize the weights.
if weights is None:
self._weights = [0.0]*numTemperatures
self._updateWeights = True
self._weightUpdateFactor = 1.0
self._histogram = [0]*numTemperatures
self._hasMadeTransition = False
else:
self._weights = weights
self._updateWeights = False
# Select the initial temperature.
self.currentTemperature = 0
self.simulation.integrator.setTemperature(self.temperatures[self.currentTemperature])
for param in self.simulation.context.getParameters():
if 'MonteCarloTemperature' in param:
self.simulation.context.setParameter(param, self.temperatures[self.currentTemperature])
# Add a reporter to the simulation which will handle the updates and reports.
class STReporter(object):
def __init__(self, st):
self.st = st
temperatures = [minTemperature*((float(maxTemperature)/minTemperature)**(i/float(numTemperatures-1))) for i in range(numTemperatures)]*unit.kelvin
self.temperatures = [(t.value_in_unit(unit.kelvin) if unit.is_quantity(t) else t)*unit.kelvin for t in temperatures]
states = [{'temperature':t} for t in temperatures]
from . import ExpandedEnsembleSampler
self._sampler = ExpandedEnsembleSampler(states, simulation, tempChangeInterval, weights=weights,
reportInterval=reportInterval, logFile=reportFile)
def describeNextReport(self, simulation):
st = self.st
steps1 = st.tempChangeInterval - simulation.currentStep%st.tempChangeInterval
steps2 = st.reportInterval - simulation.currentStep%st.reportInterval
steps = min(steps1, steps2)
isUpdateAttempt = (steps1 == steps)
if isUpdateAttempt:
return {'steps': steps, 'periodic':None, 'include':['velocities', 'energy']}
else:
return {'steps': steps, 'periodic':None, 'include':[]}
def report(self, simulation, state):
st = self.st
if simulation.currentStep%st.tempChangeInterval == 0:
st._attemptTemperatureChange(state)
if simulation.currentStep%st.reportInterval == 0:
st._writeReport()
simulation.reporters.append(STReporter(self))
# Write out the header line.
headers = ['Steps', 'Temperature (K)']
for t in self.temperatures:
headers.append('%gK Weight' % t.value_in_unit(unit.kelvin))
print('#"%s"' % ('"\t"').join(headers), file=self._out)
def __del__(self):
if self._openedFile:
self._out.close()
@property
def weights(self):
return [x-self._weights[0] for x in self._weights]
return self._sampler.weights
@property
def currentTemperature(self):
return self._sampler.currentStateIndex
def step(self, steps):
"""Advance the simulation by integrating a specified number of time steps."""
self.simulation.step(steps)
def _attemptTemperatureChange(self, state):
"""Attempt to move to a different temperature."""
# Compute the probability for each temperature. This is done in log space to avoid overflow.
logProbability = [(self._weights[i]-self.inverseTemperatures[i]*state.getPotentialEnergy()) for i in range(len(self._weights))]
maxLogProb = max(logProbability)
offset = maxLogProb + math.log(sum(math.exp(x-maxLogProb) for x in logProbability))
probability = [math.exp(x-offset) for x in logProbability]
r = random.random()
for j in range(len(probability)):
if r < probability[j]:
if j != self.currentTemperature:
# Rescale the velocities.
scale = math.sqrt(self.temperatures[j]/self.temperatures[self.currentTemperature])
if have_numpy:
velocities = scale*state.getVelocities(asNumpy=True).value_in_unit(unit.nanometers/unit.picoseconds)
else:
velocities = [v*scale for v in state.getVelocities().value_in_unit(unit.nanometers/unit.picoseconds)]
self.simulation.context.setVelocities(velocities)
# Select this temperature.
self._hasMadeTransition = True
self.currentTemperature = j
self.simulation.integrator.setTemperature(self.temperatures[j])
for param in self.simulation.context.getParameters():
if 'MonteCarloTemperature' in param:
self.simulation.context.setParameter(param, self.temperatures[self.currentTemperature])
if self._updateWeights:
# Update the weight factors.
self._weights[j] -= self._weightUpdateFactor
self._histogram[j] += 1
minCounts = min(self._histogram)
if minCounts > 20 and minCounts >= 0.2*sum(self._histogram)/len(self._histogram):
# Reduce the weight update factor and reset the histogram.
self._weightUpdateFactor *= 0.5
self._histogram = [0]*len(self.temperatures)
self._weights = [x-self._weights[0] for x in self._weights]
elif not self._hasMadeTransition and probability[self.currentTemperature] > 0.99:
# Rapidly increase the weight update factor at the start of the simulation to find
# a reasonable starting value.
self._weightUpdateFactor *= 2.0
self._histogram = [0]*len(self.temperatures)
return
r -= probability[j]
def _writeReport(self):
"""Write out a line to the report."""
temperature = self.temperatures[self.currentTemperature].value_in_unit(unit.kelvin)
values = [temperature]+self.weights
print(('%d\t' % self.simulation.currentStep) + '\t'.join('%g' % v for v in values), file=self._out)
self._sampler.step(steps)
wrappers/python/openmm/app/topology.py
View file @ 05ad28f2
......@@ -74,6 +74,10 @@ class Topology(object):
pairs are bonded to each other, and the dimensions of the crystallographic unit cell.
Atom and residue names should follow the PDB 3.0 nomenclature for all molecules for which one exists.
When a System is constructed from a Topology (for example with ForceField.createSystem()),
each atom is converted to a corresponding particle in the System. The particles are in the
same order as the atoms, so an atom's index in the Topology is also the index of its particle.
"""
_standardBonds = {}
......
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