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Commit fd473eea authored by Peter Eastman's avatar Peter Eastman
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platforms/cuda/tests/TestCudaCMMotionRemover.cpp
View file @ fd473eea
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,94 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of AndersenThermostat.
*/
#include "CudaTests.h"
#include "TestCMMotionRemover.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
Vec3 calcCM(const vector<Vec3>& values, System& system) {
Vec3 cm;
for (int j = 0; j < system.getNumParticles(); ++j) {
cm[0] += values[j][0]*system.getParticleMass(j);
cm[1] += values[j][1]*system.getParticleMass(j);
cm[2] += values[j][2]*system.getParticleMass(j);
}
return cm;
}
void testMotionRemoval(Integrator& integrator) {
const int numParticles = 8;
System system;
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(2, 3, 2.0, 0.5);
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i+1);
nonbonded->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(nonbonded);
CMMotionRemover* remover = new CMMotionRemover();
system.addForce(remover);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Now run it for a while and see if the center of mass remains fixed.
Vec3 cmPos = calcCM(context.getState(State::Positions).getPositions(), system);
for (int i = 0; i < 1000; ++i) {
integrator.step(1);
State state = context.getState(State::Positions | State::Velocities);
Vec3 pos = calcCM(state.getPositions(), system);
ASSERT_EQUAL_VEC(cmPos, pos, 1e-2);
Vec3 vel = calcCM(state.getVelocities(), system);
if (i > 0) {
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), vel, 1e-2);
}
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
LangevinIntegrator langevin(0.0, 1e-5, 0.01);
testMotionRemoval(langevin);
VerletIntegrator verlet(0.01);
testMotionRemoval(verlet);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaCheckpoints.cpp
View file @ fd473eea
......@@ -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) 2012-2013 Stanford University and the Authors. *
* Portions copyright (c) 2012-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,45 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests creating and loading checkpoints with the CUDA platform.
*/
#include "CudaPlatform.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/Context.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <sstream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void compareStates(State& s1, State& s2) {
ASSERT_EQUAL_TOL(s1.getTime(), s2.getTime(), TOL);
int numParticles = s1.getPositions().size();
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(s1.getPositions()[i], s2.getPositions()[i], TOL);
ASSERT_EQUAL_VEC(s1.getVelocities()[i], s2.getVelocities()[i], TOL);
Vec3 a1, b1, c1, a2, b2, c2;
s1.getPeriodicBoxVectors(a1, b1, c1);
s2.getPeriodicBoxVectors(a2, b2, c2);
ASSERT_EQUAL_VEC(a1, a2, TOL);
ASSERT_EQUAL_VEC(b1, b2, TOL);
ASSERT_EQUAL_VEC(c1, c2, TOL);
for (map<string, double>::const_iterator iter = s1.getParameters().begin(); iter != s1.getParameters().end(); ++iter)
ASSERT_EQUAL(iter->second, (*s2.getParameters().find(iter->first)).second);
}
}
#include "CudaTests.h"
#include "TestCheckpoints.h"
void testCheckpoint() {
const int numParticles = 100;
......@@ -159,71 +122,6 @@ void testCheckpoint() {
compareStates(s6, s8);
}
void testSetState() {
const int numParticles = 10;
const double boxSize = 3.0;
const double temperature = 200.0;
System system;
system.addForce(new AndersenThermostat(0.0, 100.0));
NonbondedForce* nonbonded = new NonbondedForce();
system.addForce(nonbonded);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
nonbonded->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.2, 0.1);
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
}
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
context.setParameter(AndersenThermostat::Temperature(), temperature);
// Run for a little while.
integrator.step(100);
// Record the current state.
State s1 = context.getState(State::Positions | State::Velocities | State::Parameters);
// Continue the simulation for a few more steps and record a partial state.
integrator.step(10);
State s2 = context.getState(State::Positions);
// Restore the original state and see if everything gets restored correctly.
context.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
context.setParameter(AndersenThermostat::Temperature(), temperature+10);
context.setState(s1);
State s3 = context.getState(State::Positions | State::Velocities | State::Parameters);
compareStates(s1, s3);
// Set the partial state and see if the correct things were set.
context.setState(s2);
State s4 = context.getState(State::Positions | State::Velocities | State::Parameters);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(s2.getPositions()[i], s4.getPositions()[i], TOL);
ASSERT_EQUAL_VEC(s1.getVelocities()[i], s4.getVelocities()[i], TOL);
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testCheckpoint();
testSetState();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testCheckpoint();
}
platforms/cuda/tests/TestCudaCustomAngleForce.cpp
View file @ fd473eea
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,107 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CustomAngleForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomAngleForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void testAngles() {
// Create a system using a CustomAngleForce.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomAngleForce* custom = new CustomAngleForce("scale*k*(theta-theta0)^2");
custom->addPerAngleParameter("theta0");
custom->addPerAngleParameter("k");
custom->addGlobalParameter("scale", 0.5);
vector<double> parameters(2);
parameters[0] = 1.5;
parameters[1] = 0.8;
custom->addAngle(0, 1, 2, parameters);
parameters[0] = 2.0;
parameters[1] = 0.5;
custom->addAngle(1, 2, 3, parameters);
customSystem.addForce(custom);
// Create an identical system using a HarmonicAngleForce.
System harmonicSystem;
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
HarmonicAngleForce* harmonic = new HarmonicAngleForce();
harmonic->addAngle(0, 1, 2, 1.5, 0.8);
harmonic->addAngle(1, 2, 3, 2.0, 0.5);
harmonicSystem.addForce(harmonic);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(4);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(harmonicSystem, integrator2, platform);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
// Try changing the angle parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[1] = 0.9;
custom->setAngleParameters(0, 0, 1, 2, parameters);
parameters[0] = 2.1;
parameters[1] = 0.6;
custom->setAngleParameters(1, 1, 2, 3, parameters);
custom->updateParametersInContext(c1);
harmonic->setAngleParameters(0, 0, 1, 2, 1.6, 0.9);
harmonic->setAngleParameters(1, 1, 2, 3, 2.1, 0.6);
harmonic->updateParametersInContext(c2);
{
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
}
#include "CudaTests.h"
#include "TestCustomAngleForce.h"
void testParallelComputation() {
System system;
......@@ -160,17 +61,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testAngles();
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/cuda/tests/TestCudaCustomBondForce.cpp
View file @ fd473eea
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,111 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CustomBondForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomBondForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void testBonds() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomBondForce* forceField = new CustomBondForce("scale*k*(r-r0)^2");
forceField->addPerBondParameter("r0");
forceField->addPerBondParameter("k");
forceField->addGlobalParameter("scale", 0.5);
vector<double> parameters(2);
parameters[0] = 1.5;
parameters[1] = 0.8;
forceField->addBond(0, 1, parameters);
parameters[0] = 1.2;
parameters[1] = 0.7;
forceField->addBond(1, 2, parameters);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.7*0.2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.8*0.5*0.5 + 0.5*0.7*0.2*0.2, state.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[1] = 0.9;
forceField->setBondParameters(0, 0, 1, parameters);
parameters[0] = 1.3;
parameters[1] = 0.8;
forceField->setBondParameters(1, 1, 2, parameters);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.9*0.4, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.8*0.3, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.9*0.4*0.4 + 0.5*0.8*0.3*0.3, state.getPotentialEnergy(), TOL);
}
}
void testManyParameters() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomBondForce* forceField = new CustomBondForce("(a+b+c+d+e+f+g+h+i)*r");
forceField->addPerBondParameter("a");
forceField->addPerBondParameter("b");
forceField->addPerBondParameter("c");
forceField->addPerBondParameter("d");
forceField->addPerBondParameter("e");
forceField->addPerBondParameter("f");
forceField->addPerBondParameter("g");
forceField->addPerBondParameter("h");
forceField->addPerBondParameter("i");
vector<double> parameters(forceField->getNumPerBondParameters());
for (int i = 0; i < parameters.size(); i++)
parameters[i] = i;
forceField->addBond(0, 1, parameters);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2.5, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double f = 1+2+3+4+5+6+7+8;
ASSERT_EQUAL_VEC(Vec3(0, f, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -f, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(f*2.5, state.getPotentialEnergy(), TOL);
}
#include "CudaTests.h"
#include "TestCustomBondForce.h"
void testParallelComputation() {
System system;
......@@ -164,18 +61,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testBonds();
testManyParameters();
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/cuda/tests/TestCudaCustomCentroidBondForce.cpp 0 → 100644
View file @ fd473eea
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2015 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. *
* -------------------------------------------------------------------------- */
#include "CudaTests.h"
#include "TestCustomCentroidBondForce.h"
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaCustomCompoundBondForce.cpp
View file @ fd473eea
......@@ -29,145 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CustomCompoundBondForce.
*/
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomCompoundBondForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void testBond() {
// Create a system using a CustomCompoundBondForce.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomCompoundBondForce* custom = new CustomCompoundBondForce(4, "0.5*kb*((distance(p1,p2)-b0)^2+(distance(p2,p3)-b0)^2)+0.5*ka*(angle(p2,p3,p4)-a0)^2+kt*(1+cos(dihedral(p1,p2,p3,p4)-t0))");
custom->addPerBondParameter("kb");
custom->addPerBondParameter("ka");
custom->addPerBondParameter("kt");
custom->addPerBondParameter("b0");
custom->addPerBondParameter("a0");
custom->addPerBondParameter("t0");
vector<int> particles(4);
particles[0] = 0;
particles[1] = 1;
particles[2] = 3;
particles[3] = 2;
vector<double> parameters(6);
parameters[0] = 1.5;
parameters[1] = 0.8;
parameters[2] = 0.6;
parameters[3] = 1.1;
parameters[4] = 2.9;
parameters[5] = 1.3;
custom->addBond(particles, parameters);
customSystem.addForce(custom);
// Create an identical system using standard forces.
System standardSystem;
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.1, 1.5);
bonds->addBond(1, 3, 1.1, 1.5);
standardSystem.addForce(bonds);
HarmonicAngleForce* angles = new HarmonicAngleForce();
angles->addAngle(1, 3, 2, 2.9, 0.8);
standardSystem.addForce(angles);
PeriodicTorsionForce* torsions = new PeriodicTorsionForce();
torsions->addTorsion(0, 1, 3, 2, 1, 1.3, 0.6);
standardSystem.addForce(torsions);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
vector<Vec3> positions(4);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[3] = 1.3;
custom->setBondParameters(0, particles, parameters);
custom->updateParametersInContext(c1);
bonds->setBondParameters(0, 0, 1, 1.3, 1.6);
bonds->setBondParameters(1, 1, 3, 1.3, 1.6);
bonds->updateParametersInContext(c2);
{
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = s1.getForces();
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
}
void testPositionDependence() {
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomCompoundBondForce* custom = new CustomCompoundBondForce(2, "scale1*distance(p1,p2)+scale2*x1+2*y2");
custom->addGlobalParameter("scale1", 0.3);
custom->addGlobalParameter("scale2", 0.2);
vector<int> particles(2);
particles[0] = 1;
particles[1] = 0;
vector<double> parameters;
custom->addBond(particles, parameters);
customSystem.addForce(custom);
vector<Vec3> positions(2);
positions[0] = Vec3(1.5, 1, 0);
positions[1] = Vec3(0.5, 1, 0);
VerletIntegrator integrator(0.01);
Context context(customSystem, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(0.3*1.0+0.2*0.5+2*1, state.getPotentialEnergy(), 1e-5);
ASSERT_EQUAL_VEC(Vec3(-0.3, -2, 0), state.getForces()[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(0.3-0.2, 0, 0), state.getForces()[1], 1e-5);
}
#include "CudaTests.h"
#include "TestCustomCompoundBondForce.h"
void testParallelComputation() {
System system;
......@@ -202,165 +65,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
void testContinuous2DFunction() {
const int xsize = 10;
const int ysize = 11;
const double xmin = 0.4;
const double xmax = 1.1;
const double ymin = 0.0;
const double ymax = 0.9;
System system;
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1)+1");
vector<int> particles(1, 0);
forceField->addBond(particles, vector<double>());
vector<double> table(xsize*ysize);
for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++) {
double x = xmin + i*(xmax-xmin)/xsize;
double y = ymin + j*(ymax-ymin)/ysize;
table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
}
}
forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
positions[0] = Vec3(x, y, 1.5);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double energy = 1;
Vec3 force(0, 0, 0);
if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
energy = sin(0.25*x)*cos(0.33*y)+1;
force[0] = -0.25*cos(0.25*x)*cos(0.33*y);
force[1] = 0.3*sin(0.25*x)*sin(0.33*y);
}
ASSERT_EQUAL_VEC(force, forces[0], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
}
}
}
void testContinuous3DFunction() {
const int xsize = 10;
const int ysize = 11;
const int zsize = 12;
const double xmin = 0.4;
const double xmax = 1.1;
const double ymin = 0.0;
const double ymax = 0.9;
const double zmin = 0.2;
const double zmax = 1.3;
System system;
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1,z1)+1");
vector<int> particles(1, 0);
forceField->addBond(particles, vector<double>());
vector<double> table(xsize*ysize*zsize);
for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++) {
for (int k = 0; k < zsize; k++) {
double x = xmin + i*(xmax-xmin)/xsize;
double y = ymin + j*(ymax-ymin)/ysize;
double z = zmin + k*(zmax-zmin)/zsize;
table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
}
}
}
forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
positions[0] = Vec3(x, y, z);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double energy = 1;
Vec3 force(0, 0, 0);
if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1;
force[0] = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
force[1] = 0.3*sin(0.25*x)*sin(0.33*y)*(1.0+z);
force[2] = -sin(0.25*x)*cos(0.33*y);
}
ASSERT_EQUAL_VEC(force, forces[0], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
}
}
}
}
void testMultipleBonds() {
// Two compound bonds using Urey-Bradley example from API doc
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomCompoundBondForce* custom = new CustomCompoundBondForce(3,
"0.5*(kangle*(angle(p1,p2,p3)-theta0)^2+kbond*(distance(p1,p3)-r0)^2)");
custom->addPerBondParameter("kangle");
custom->addPerBondParameter("kbond");
custom->addPerBondParameter("theta0");
custom->addPerBondParameter("r0");
vector<double> parameters(4);
parameters[0] = 1.0;
parameters[1] = 1.0;
parameters[2] = 2 * M_PI / 3;
parameters[3] = sqrt(3.0) / 2;
vector<int> particles0(3);
particles0[0] = 0;
particles0[1] = 1;
particles0[2] = 2;
vector<int> particles1(3);
particles1[0] = 1;
particles1[1] = 2;
particles1[2] = 3;
custom->addBond(particles0, parameters);
custom->addBond(particles1, parameters);
customSystem.addForce(custom);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 0.5, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(0.5, 0, 0);
positions[3] = Vec3(0.6, 0, 0.4);
VerletIntegrator integrator(0.01);
Context context(customSystem, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(0.199, state.getPotentialEnergy(), 1e-3);
vector<Vec3> forces(state.getForces());
ASSERT_EQUAL_VEC(Vec3(-1.160, 0.112, 0.0), forces[0], 1e-3);
ASSERT_EQUAL_VEC(Vec3(0.927, 1.047, -0.638), forces[1], 1e-3);
ASSERT_EQUAL_VEC(Vec3(-0.543, -1.160, 0.721), forces[2], 1e-3);
ASSERT_EQUAL_VEC(Vec3(0.776, 0.0, -0.084), forces[3], 1e-3);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testBond();
testPositionDependence();
testParallelComputation();
testContinuous2DFunction();
testContinuous3DFunction();
testMultipleBonds();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/cuda/tests/TestCudaCustomExternalForce.cpp
View file @ fd473eea
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,106 +29,9 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CustomExternalForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "CudaTests.h"
#include "TestCustomExternalForce.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void testForce() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomExternalForce* forceField = new CustomExternalForce("scale*(x+yscale*(y-y0)^2)");
forceField->addPerParticleParameter("y0");
forceField->addPerParticleParameter("yscale");
forceField->addGlobalParameter("scale", 0.5);
vector<double> parameters(2);
parameters[0] = 0.5;
parameters[1] = 2.0;
forceField->addParticle(0, parameters);
parameters[0] = 1.5;
parameters[1] = 3.0;
forceField->addParticle(2, parameters);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 1);
positions[2] = Vec3(1, 0, 1);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.0*2.0*1.5, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.0*1.5*1.5), state.getPotentialEnergy(), TOL);
}
// Try changing the parameters and make sure it's still correct.
parameters[0] = 1.4;
parameters[1] = 3.5;
forceField->setParticleParameters(1, 2, parameters);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.5*2.0*1.4, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.5*1.4*1.4), state.getPotentialEnergy(), TOL);
}
}
void testManyParameters() {
System system;
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomExternalForce* forceField = new CustomExternalForce("xscale*(x-x0)^2+yscale*(y-y0)^2+zscale*(z-z0)^2");
forceField->addPerParticleParameter("x0");
forceField->addPerParticleParameter("y0");
forceField->addPerParticleParameter("z0");
forceField->addPerParticleParameter("xscale");
forceField->addPerParticleParameter("yscale");
forceField->addPerParticleParameter("zscale");
vector<double> parameters(6);
parameters[0] = 1.0;
parameters[1] = 2.0;
parameters[2] = 3.0;
parameters[3] = 0.1;
parameters[4] = 0.2;
parameters[5] = 0.3;
forceField->addParticle(0, parameters);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
positions[0] = Vec3(0, -1, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(2*0.1*1.0, 2*0.2*3.0, 2*0.3*3.0), forces[0], TOL);
ASSERT_EQUAL_TOL(0.1*1*1 + 0.2*3*3 + 0.3*3*3, state.getPotentialEnergy(), TOL);
}
void testParallelComputation() {
System system;
......@@ -161,18 +64,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testForce();
testManyParameters();
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/cuda/tests/TestCudaCustomGBForce.cpp
View file @ fd473eea
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
......@@ -7,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -30,453 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CustomGBForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "sfmt/SFMT.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomGBForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMethod customMethod) {
const int numMolecules = 70;
const int numParticles = numMolecules*2;
const double boxSize = 10.0;
const double cutoff = 2.0;
// Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
System standardSystem;
System customSystem;
for (int i = 0; i < numParticles; i++) {
standardSystem.addParticle(1.0);
customSystem.addParticle(1.0);
}
standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
customSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
GBSAOBCForce* obc = new GBSAOBCForce();
CustomGBForce* custom = new CustomGBForce();
obc->setCutoffDistance(cutoff);
custom->setCutoffDistance(cutoff);
custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale");
custom->addGlobalParameter("solventDielectric", obc->getSolventDielectric());
custom->addGlobalParameter("soluteDielectric", obc->getSoluteDielectric());
custom->addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
"U=r+sr2;"
"C=2*(1/or1-1/L)*step(sr2-r-or1);"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
string invCutoffString = "";
if (obcMethod != GBSAOBCForce::NoCutoff) {
stringstream s;
s<<(1.0/cutoff);
invCutoffString = s.str();
}
custom->addEnergyTerm("138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*("+invCutoffString+"-1/f);"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
obc->addParticle(1.0, 0.2, 0.5);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.5;
custom->addParticle(params);
obc->addParticle(-1.0, 0.1, 0.5);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
else {
obc->addParticle(1.0, 0.2, 0.8);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.8;
custom->addParticle(params);
obc->addParticle(-1.0, 0.1, 0.8);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
}
obc->setNonbondedMethod(obcMethod);
custom->setNonbondedMethod(customMethod);
standardSystem.addForce(obc);
customSystem.addForce(custom);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context context1(standardSystem, integrator1, platform);
context1.setPositions(positions);
context1.setVelocities(velocities);
State state1 = context1.getState(State::Forces | State::Energy);
Context context2(customSystem, integrator2, platform);
context2.setPositions(positions);
context2.setVelocities(velocities);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
// Try changing the particle parameters and make sure it's still correct.
for (int i = 0; i < numMolecules/2; i++) {
obc->setParticleParameters(2*i, 1.1, 0.3, 0.6);
params[0] = 1.1;
params[1] = 0.3;
params[2] = 0.6;
custom->setParticleParameters(2*i, params);
obc->setParticleParameters(2*i+1, -1.1, 0.2, 0.4);
params[0] = -1.1;
params[1] = 0.2;
params[2] = 0.4;
custom->setParticleParameters(2*i+1, params);
}
obc->updateParametersInContext(context1);
custom->updateParametersInContext(context2);
state1 = context1.getState(State::Forces | State::Energy);
state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
}
void testMembrane() {
const int numMolecules = 70;
const int numParticles = numMolecules*2;
const double boxSize = 10.0;
// Create a system with an implicit membrane.
System system;
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
}
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
CustomGBForce* custom = new CustomGBForce();
custom->setCutoffDistance(2.0);
custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale");
custom->addGlobalParameter("thickness", 3);
custom->addGlobalParameter("solventDielectric", 78.3);
custom->addGlobalParameter("soluteDielectric", 1);
custom->addComputedValue("Imol", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
"U=r+sr2;"
"C=2*(1/or1-1/L)*step(sr2-r-or1);"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
custom->addComputedValue("Imem", "(1/radius+2*log(2)/thickness)/(1+exp(7.2*(abs(z)+radius-0.5*thickness)))", CustomGBForce::SingleParticle);
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=max(Imol,Imem)*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.5;
custom->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
else {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.8;
custom->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
custom->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
}
system.addForce(custom);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-2;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
}
void testTabulatedFunction() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "0", CustomGBForce::ParticlePair);
force->addEnergyTerm("fn(r)+1", CustomGBForce::ParticlePair);
force->addParticle(vector<double>());
force->addParticle(vector<double>());
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(std::sin(0.25*i));
force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (int i = 1; i < 30; i++) {
double x = (7.0/30.0)*i;
positions[1] = Vec3(x, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double force = (x < 1.0 || x > 6.0 ? 0.0 : -std::cos(x-1.0));
double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
}
for (int i = 1; i < 20; i++) {
double x = 0.25*i+1.0;
positions[1] = Vec3(x, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Energy);
double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
}
}
void testMultipleChainRules() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "2*r", CustomGBForce::ParticlePair);
force->addComputedValue("b", "a+1", CustomGBForce::SingleParticle);
force->addComputedValue("c", "2*b+a", CustomGBForce::SingleParticle);
force->addEnergyTerm("0.1*a+1*b+10*c", CustomGBForce::SingleParticle); // 0.1*(2*r) + 2*r+1 + 10*(3*a+2) = 0.2*r + 2*r+1 + 40*r+20+20*r = 62.2*r+21
force->addParticle(vector<double>());
force->addParticle(vector<double>());
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (int i = 1; i < 5; i++) {
positions[1] = Vec3(i, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(124.4, 0, 0), forces[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(-124.4, 0, 0), forces[1], 1e-4);
ASSERT_EQUAL_TOL(2*(62.2*i+21), state.getPotentialEnergy(), 0.02);
}
}
void testPositionDependence() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "r", CustomGBForce::ParticlePair);
force->addComputedValue("b", "a+x*y", CustomGBForce::SingleParticle);
force->addEnergyTerm("b*z", CustomGBForce::SingleParticle);
force->addEnergyTerm("b1+b2", CustomGBForce::ParticlePair); // = 2*r+x1*y1+x2*y2
force->addParticle(vector<double>());
force->addParticle(vector<double>());
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
vector<Vec3> forces(2);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < 5; i++) {
positions[0] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
positions[1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
Vec3 delta = positions[0]-positions[1];
double r = sqrt(delta.dot(delta));
double energy = 2*r+positions[0][0]*positions[0][1]+positions[1][0]*positions[1][1];
for (int j = 0; j < 2; j++)
energy += positions[j][2]*(r+positions[j][0]*positions[j][1]);
Vec3 force1(-(1+positions[0][2])*delta[0]/r-(1+positions[0][2])*positions[0][1]-(1+positions[1][2])*delta[0]/r,
-(1+positions[0][2])*delta[1]/r-(1+positions[0][2])*positions[0][0]-(1+positions[1][2])*delta[1]/r,
-(1+positions[0][2])*delta[2]/r-(r+positions[0][0]*positions[0][1])-(1+positions[1][2])*delta[2]/r);
Vec3 force2((1+positions[0][2])*delta[0]/r+(1+positions[1][2])*delta[0]/r-(1+positions[1][2])*positions[1][1],
(1+positions[0][2])*delta[1]/r+(1+positions[1][2])*delta[1]/r-(1+positions[1][2])*positions[1][0],
(1+positions[0][2])*delta[2]/r+(1+positions[1][2])*delta[2]/r-(r+positions[1][0]*positions[1][1]));
ASSERT_EQUAL_VEC(force1, forces[0], 1e-4);
ASSERT_EQUAL_VEC(force2, forces[1], 1e-4);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(2), positions3(2);
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
}
}
void testExclusions() {
for (int i = 0; i < 4; i++) {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "r", i < 2 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
force->addEnergyTerm("a", CustomGBForce::SingleParticle);
force->addEnergyTerm("(1+a1+a2)*r", i%2 == 0 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
force->addParticle(vector<double>());
force->addParticle(vector<double>());
force->addExclusion(0, 1);
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double f, energy;
switch (i)
{
case 0: // e = 0
f = 0;
energy = 0;
break;
case 1: // e = r
f = 1;
energy = 1;
break;
case 2: // e = 2r
f = 2;
energy = 2;
break;
case 3: // e = 3r + 2r^2
f = 7;
energy = 5;
break;
default:
ASSERT(false);
}
ASSERT_EQUAL_VEC(Vec3(f, 0, 0), forces[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(-f, 0, 0), forces[1], 1e-4);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = stepSize/norm;
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/stepSize, 1e-3*abs(state.getPotentialEnergy()));
}
}
#include "CudaTests.h"
#include "TestCustomGBForce.h"
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testOBC(GBSAOBCForce::NoCutoff, CustomGBForce::NoCutoff);
testOBC(GBSAOBCForce::CutoffNonPeriodic, CustomGBForce::CutoffNonPeriodic);
testOBC(GBSAOBCForce::CutoffPeriodic, CustomGBForce::CutoffPeriodic);
testMembrane();
testTabulatedFunction();
testMultipleChainRules();
testPositionDependence();
testExclusions();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaCustomHbondForce.cpp
View file @ fd473eea
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,220 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CustomHbondForce.
*/
#include "CudaTests.h"
#include "TestCustomHbondForce.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomHbondForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void testHbond() {
// Create a system using a CustomHbondForce.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomHbondForce* custom = new CustomHbondForce("0.5*kr*(distance(d1,a1)-r0)^2 + 0.5*ktheta*(angle(a1,d1,d2)-theta0)^2 + 0.5*kpsi*(angle(d1,a1,a2)-psi0)^2 + kchi*(1+cos(n*dihedral(a3,a2,a1,d1)-chi0))");
custom->addPerDonorParameter("r0");
custom->addPerDonorParameter("theta0");
custom->addPerDonorParameter("psi0");
custom->addPerAcceptorParameter("chi0");
custom->addPerAcceptorParameter("n");
custom->addGlobalParameter("kr", 0.4);
custom->addGlobalParameter("ktheta", 0.5);
custom->addGlobalParameter("kpsi", 0.6);
custom->addGlobalParameter("kchi", 0.7);
vector<double> parameters(3);
parameters[0] = 1.5;
parameters[1] = 1.7;
parameters[2] = 1.9;
custom->addDonor(1, 0, -1, parameters);
parameters.resize(2);
parameters[0] = 2.1;
parameters[1] = 2;
custom->addAcceptor(2, 3, 4, parameters);
custom->setCutoffDistance(10.0);
customSystem.addForce(custom);
// Create an identical system using HarmonicBondForce, HarmonicAngleForce, and PeriodicTorsionForce.
System standardSystem;
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
HarmonicBondForce* bond = new HarmonicBondForce();
bond->addBond(1, 2, 1.5, 0.4);
standardSystem.addForce(bond);
HarmonicAngleForce* angle = new HarmonicAngleForce();
angle->addAngle(0, 1, 2, 1.7, 0.5);
angle->addAngle(1, 2, 3, 1.9, 0.6);
standardSystem.addForce(angle);
PeriodicTorsionForce* torsion = new PeriodicTorsionForce();
torsion->addTorsion(1, 2, 3, 4, 2, 2.1, 0.7);
standardSystem.addForce(torsion);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(5);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
}
// Try changing the parameters and make sure it's still correct.
parameters.resize(3);
parameters[0] = 1.4;
parameters[1] = 1.7;
parameters[2] = 1.9;
custom->setDonorParameters(0, 1, 0, -1, parameters);
parameters.resize(2);
parameters[0] = 2.2;
parameters[1] = 2;
custom->setAcceptorParameters(0, 2, 3, 4, parameters);
bond->setBondParameters(0, 1, 2, 1.4, 0.4);
torsion->setTorsionParameters(0, 1, 2, 3, 4, 2, 2.2, 0.7);
custom->updateParametersInContext(c1);
bond->updateParametersInContext(c2);
torsion->updateParametersInContext(c2);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
}
void testExclusions() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomHbondForce* custom = new CustomHbondForce("(distance(d1,a1)-1)^2");
custom->addDonor(0, 1, -1, vector<double>());
custom->addDonor(1, 0, -1, vector<double>());
custom->addAcceptor(2, 0, -1, vector<double>());
custom->addExclusion(1, 0);
system.addForce(custom);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2, 0);
positions[2] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(2, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(1.0, state.getPotentialEnergy(), TOL);
}
void testCutoff() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomHbondForce* custom = new CustomHbondForce("(distance(d1,a1)-1)^2");
custom->addDonor(0, 1, -1, vector<double>());
custom->addDonor(1, 0, -1, vector<double>());
custom->addAcceptor(2, 0, -1, vector<double>());
custom->setNonbondedMethod(CustomHbondForce::CutoffNonPeriodic);
custom->setCutoffDistance(2.5);
system.addForce(custom);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 3, 0);
positions[2] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(2, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(1.0, state.getPotentialEnergy(), TOL);
}
void testCustomFunctions() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomHbondForce* custom = new CustomHbondForce("foo(distance(d1,a1))");
custom->addDonor(1, 0, -1, vector<double>());
custom->addDonor(2, 0, -1, vector<double>());
custom->addAcceptor(0, 1, -1, vector<double>());
vector<double> function(2);
function[0] = 0;
function[1] = 1;
custom->addTabulatedFunction("foo", new Continuous1DFunction(function, 0, 10));
system.addForce(custom);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2, 0);
positions[2] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0.1, 0.1, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -0.1, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.1, 0, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.1*2+0.1*2, state.getPotentialEnergy(), TOL);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testHbond();
testExclusions();
testCutoff();
testCustomFunctions();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaCustomIntegrator.cpp
View file @ fd473eea
......@@ -29,666 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CustomIntegrator.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/CustomIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
const double TOL = 1e-5;
/**
* Test a simple leapfrog integrator on a single bond.
*/
void testSingleBond() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
const double dt = 0.01;
CustomIntegrator integrator(dt);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.setKineticEnergyExpression("m*v1*v1/2; v1=v+0.5*dt*f/m");
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
vector<Vec3> velocities(2);
velocities[0] = Vec3(-0.5*dt*0.5*0.5, 0, 0);
velocities[1] = Vec3(0.5*dt*0.5*0.5, 0, 0);
context.setVelocities(velocities);
// This is simply a harmonic oscillator, so compare it to the analytical solution.
const double freq = 1.0;;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Velocities | State::Energy);
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], 1e-4);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 1e-4);
double expectedSpeed = -0.5*freq*std::sin(freq*(time-dt/2));
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 1e-4);
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
ASSERT_EQUAL_TOL(0.5*0.5*0.5, energy, 1e-4);
integrator.step(1);
}
}
/**
* Test an integrator that enforces constraints.
*/
void testConstraints() {
const int numParticles = 8;
System system;
CustomIntegrator integrator(0.002);
integrator.addPerDofVariable("oldx", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("oldx", "x");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "(x-oldx)/dt");
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i%2 == 0 ? 5.0 : 10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
for (int i = 0; i < numParticles-1; ++i)
system.addConstraint(i, i+1, 1.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy);
for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5);
}
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
if (i == 1)
initialEnergy = energy;
else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1);
}
}
/**
* Test an integrator that applies constraints directly to velocities.
*/
void testVelocityConstraints() {
const int numParticles = 10;
System system;
CustomIntegrator integrator(0.002);
integrator.addPerDofVariable("x1", 0);
integrator.addComputePerDof("v", "v+0.5*dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("x1", "x");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "v+0.5*dt*f/m+(x-x1)/dt");
integrator.addConstrainVelocities();
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i%2 == 0 ? 5.0 : 10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
// Constrain the first three particles with SHAKE.
system.addConstraint(0, 1, 1.0);
system.addConstraint(1, 2, 1.0);
// Constrain the next three with SETTLE.
system.addConstraint(3, 4, 1.0);
system.addConstraint(5, 4, 1.0);
system.addConstraint(3, 5, sqrt(2.0));
// Constraint the rest with CCMA.
for (int i = 6; i < numParticles-1; ++i)
system.addConstraint(i, i+1, 1.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) {
integrator.step(2);
State state = context.getState(State::Positions | State::Velocities | State::Energy);
for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5);
if (i > 0) {
Vec3 v1 = state.getVelocities()[particle1];
Vec3 v2 = state.getVelocities()[particle2];
double vel = (v1-v2).dot(p1-p2);
ASSERT_EQUAL_TOL(0.0, vel, 2e-5);
}
}
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
if (i == 0)
initialEnergy = energy;
else if (i > 0)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
CustomIntegrator integrator(0.002);
integrator.addPerDofVariable("oldx", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("oldx", "x");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "(x-oldx)/dt");
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities | State::Positions);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
/**
* Test an integrator with an AndersenThermostat to see if updateContextState()
* is being handled correctly.
*/
void testWithThermostat() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 20.0;
const int numSteps = 5000;
System system;
CustomIntegrator integrator(0.003);
integrator.addUpdateContextState();
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
AndersenThermostat* thermostat = new AndersenThermostat(temp, collisionFreq);
system.addForce(thermostat);
integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
context.setPositions(positions);
context.setVelocitiesToTemperature(temp);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double ke = 0.0;
for (int i = 0; i < numSteps; ++i) {
State state = context.getState(State::Energy);
ke += state.getKineticEnergy();
integrator.step(10);
}
ke /= numSteps;
double expected = 0.5*numParticles*3*BOLTZ*temp;
ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.1);
}
/**
* Test a Monte Carlo integrator that uses global variables and depends on energy.
*/
void testMonteCarlo() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
CustomIntegrator integrator(0.1);
const double kT = BOLTZ*300.0;
integrator.addGlobalVariable("kT", kT);
integrator.addGlobalVariable("oldE", 0);
integrator.addGlobalVariable("accept", 0);
integrator.addPerDofVariable("oldx", 0);
integrator.addComputeGlobal("oldE", "energy");
integrator.addComputePerDof("oldx", "x");
integrator.addComputePerDof("x", "x+dt*gaussian");
integrator.addComputeGlobal("accept", "step(exp((oldE-energy)/kT)-uniform)");
integrator.addComputePerDof("x", "select(accept, x, oldx)");
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 2.0, 10.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// Compute the histogram of distances and see if it satisfies a Boltzmann distribution.
const int numBins = 100;
const double maxDist = 4.0;
const int numIterations = 5000;
vector<int> counts(numBins, 0);
for (int i = 0; i < numIterations; ++i) {
integrator.step(10);
State state = context.getState(State::Positions);
Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
double dist = sqrt(delta.dot(delta));
if (dist < maxDist)
counts[(int) (numBins*dist/maxDist)]++;
}
vector<double> expected(numBins, 0);
double sum = 0;
for (int i = 0; i < numBins; i++) {
double dist = (i+0.5)*maxDist/numBins;
expected[i] = dist*dist*exp(-5.0*(dist-2)*(dist-2)/kT);
sum += expected[i];
}
for (int i = 0; i < numBins; i++)
ASSERT_USUALLY_EQUAL_TOL((double) counts[i]/numIterations, expected[i]/sum, 0.01);
}
/**
* Test the ComputeSum operation.
*/
void testSum() {
const int numParticles = 200;
const double boxSize = 10;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedForce* nb = new NonbondedForce();
system.addForce(nb);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(i%10 == 0 ? 0.0 : 1.5);
nb->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.1, 1);
bool close = true;
while (close) {
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
close = false;
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 1)
close = true;
}
}
}
CustomIntegrator integrator(0.005);
integrator.addGlobalVariable("ke", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputeSum("ke", "m*v*v/2");
Context context(system, integrator, platform);
context.setPositions(positions);
// See if the sum is being computed correctly.
for (int i = 0; i < 100; ++i) {
State state = context.getState(State::Energy);
ASSERT_EQUAL_TOL(state.getKineticEnergy(), integrator.getGlobalVariable(0), 1e-5);
integrator.step(1);
}
}
/**
* Test an integrator that both uses and modifies a context parameter.
*/
void testParameter() {
System system;
system.addParticle(1.0);
AndersenThermostat* thermostat = new AndersenThermostat(0.1, 0.1);
system.addForce(thermostat);
CustomIntegrator integrator(0.1);
integrator.addGlobalVariable("temp", 0);
integrator.addComputeGlobal("temp", "AndersenTemperature");
integrator.addComputeGlobal("AndersenTemperature", "temp*2");
integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
Context context(system, integrator, platform);
// See if the parameter is being used correctly.
for (int i = 0; i < 10; i++) {
integrator.step(1);
ASSERT_EQUAL_TOL(context.getParameter("AndersenTemperature"), 0.1*(1<<(i+1)), 1e-5);
}
}
/**
* Test random number distributions.
*/
void testRandomDistributions() {
const int numParticles = 100;
const int numBins = 20;
const int numSteps = 100;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
CustomIntegrator integrator(0.1);
integrator.addPerDofVariable("a", 0);
integrator.addPerDofVariable("b", 0);
integrator.addComputePerDof("a", "uniform");
integrator.addComputePerDof("b", "gaussian");
Context context(system, integrator, platform);
// See if the random numbers are distributed correctly.
vector<int> bins(numBins);
double mean = 0.0;
double var = 0.0;
double skew = 0.0;
double kurtosis = 0.0;
vector<Vec3> values;
for (int i = 0; i < numSteps; i++) {
integrator.step(1);
integrator.getPerDofVariable(0, values);
for (int i = 0; i < numParticles; i++)
for (int j = 0; j < 3; j++) {
double v = values[i][j];
ASSERT(v >= 0 && v < 1);
bins[(int) (v*numBins)]++;
}
integrator.getPerDofVariable(1, values);
for (int i = 0; i < numParticles; i++)
for (int j = 0; j < 3; j++) {
double v = values[i][j];
mean += v;
var += v*v;
skew += v*v*v;
kurtosis += v*v*v*v;
}
}
// Check the distribution of uniform randoms.
int numValues = numParticles*numSteps*3;
double expected = numValues/(double) numBins;
double tol = 4*sqrt(expected);
for (int i = 0; i < numBins; i++)
ASSERT(bins[i] >= expected-tol && bins[i] <= expected+tol);
// Check the distribution of gaussian randoms.
mean /= numValues;
var /= numValues;
skew /= numValues;
kurtosis /= numValues;
double c2 = var-mean*mean;
double c3 = skew-3*var*mean+2*mean*mean*mean;
double c4 = kurtosis-4*skew*mean-3*var*var+12*var*mean*mean-6*mean*mean*mean*mean;
ASSERT_EQUAL_TOL(0.0, mean, 3.0/sqrt((double) numValues));
ASSERT_EQUAL_TOL(1.0, c2, 3.0/pow(numValues, 1.0/3.0));
ASSERT_EQUAL_TOL(0.0, c3, 3.0/pow(numValues, 1.0/4.0));
ASSERT_EQUAL_TOL(0.0, c4, 3.0/pow(numValues, 1.0/4.0));
}
/**
* Test getting and setting per-DOF variables.
*/
void testPerDofVariables() {
const int numParticles = 200;
const double boxSize = 10;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedForce* nb = new NonbondedForce();
system.addForce(nb);
nb->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.5);
nb->addParticle(i%2 == 0 ? 1 : -1, 0.1, 1);
bool close = true;
while (close) {
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
close = false;
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 0.1)
close = true;
}
}
}
CustomIntegrator integrator(0.01);
integrator.addPerDofVariable("temp", 0);
integrator.addPerDofVariable("pos", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputePerDof("pos", "x");
Context context(system, integrator, platform);
context.setPositions(positions);
vector<Vec3> initialValues(numParticles);
for (int i = 0; i < numParticles; i++)
initialValues[i] = Vec3(i+0.1, i+0.2, i+0.3);
integrator.setPerDofVariable(0, initialValues);
// Run a simulation, then query per-DOF values and see if they are correct.
vector<Vec3> values;
context.getState(State::Forces); // Cause atom reordering to happen before the first step
for (int i = 0; i < 200; ++i) {
integrator.step(1);
State state = context.getState(State::Positions);
integrator.getPerDofVariable(0, values);
for (int j = 0; j < numParticles; j++)
ASSERT_EQUAL_VEC(initialValues[j], values[j], 1e-5);
integrator.getPerDofVariable(1, values);
for (int j = 0; j < numParticles; j++)
ASSERT_EQUAL_VEC(state.getPositions()[j], values[j], 1e-5);
}
}
/**
* Test evaluating force groups separately.
*/
void testForceGroups() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
CustomIntegrator integrator(0.01);
integrator.addPerDofVariable("outf", 0);
integrator.addPerDofVariable("outf1", 0);
integrator.addPerDofVariable("outf2", 0);
integrator.addGlobalVariable("oute", 0);
integrator.addGlobalVariable("oute1", 0);
integrator.addGlobalVariable("oute2", 0);
integrator.addComputePerDof("outf", "f");
integrator.addComputePerDof("outf1", "f1");
integrator.addComputePerDof("outf2", "f2");
integrator.addComputeGlobal("oute", "energy");
integrator.addComputeGlobal("oute1", "energy1");
integrator.addComputeGlobal("oute2", "energy2");
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.5, 1.1);
bonds->setForceGroup(1);
system.addForce(bonds);
NonbondedForce* nb = new NonbondedForce();
nb->addParticle(0.2, 1, 0);
nb->addParticle(0.2, 1, 0);
nb->setForceGroup(2);
system.addForce(nb);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// See if the various forces are computed correctly.
integrator.step(1);
vector<Vec3> f, f1, f2;
double e1 = 0.5*1.1*0.5*0.5;
double e2 = 138.935456*0.2*0.2/2.0;
integrator.getPerDofVariable(0, f);
integrator.getPerDofVariable(1, f1);
integrator.getPerDofVariable(2, f2);
ASSERT_EQUAL_VEC(Vec3(1.1*0.5, 0, 0), f1[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(-1.1*0.5, 0, 0), f1[1], 1e-5);
ASSERT_EQUAL_VEC(Vec3(-138.935456*0.2*0.2/4.0, 0, 0), f2[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(138.935456*0.2*0.2/4.0, 0, 0), f2[1], 1e-5);
ASSERT_EQUAL_VEC(f1[0]+f2[0], f[0], 1e-5);
ASSERT_EQUAL_VEC(f1[1]+f2[1], f[1], 1e-5);
ASSERT_EQUAL_TOL(e1, integrator.getGlobalVariable(1), 1e-5);
ASSERT_EQUAL_TOL(e2, integrator.getGlobalVariable(2), 1e-5);
ASSERT_EQUAL_TOL(e1+e2, integrator.getGlobalVariable(0), 1e-5);
// Make sure they also match the values returned by the Context.
State s = context.getState(State::Forces | State::Energy, false);
State s1 = context.getState(State::Forces | State::Energy, false, 2);
State s2 = context.getState(State::Forces | State::Energy, false, 4);
vector<Vec3> c, c1, c2;
c = context.getState(State::Forces, false).getForces();
c1 = context.getState(State::Forces, false, 2).getForces();
c2 = context.getState(State::Forces, false, 4).getForces();
ASSERT_EQUAL_VEC(f[0], c[0], 1e-5);
ASSERT_EQUAL_VEC(f[1], c[1], 1e-5);
ASSERT_EQUAL_VEC(f1[0], c1[0], 1e-5);
ASSERT_EQUAL_VEC(f1[1], c1[1], 1e-5);
ASSERT_EQUAL_VEC(f2[0], c2[0], 1e-5);
ASSERT_EQUAL_VEC(f2[1], c2[1], 1e-5);
ASSERT_EQUAL_TOL(s.getPotentialEnergy(), integrator.getGlobalVariable(0), 1e-5);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), integrator.getGlobalVariable(1), 1e-5);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), integrator.getGlobalVariable(2), 1e-5);
}
/**
* Test a multiple time step r-RESPA integrator.
*/
void testRespa() {
const int numParticles = 8;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
CustomIntegrator integrator(0.002);
integrator.addComputePerDof("v", "v+0.5*dt*f1/m");
for (int i = 0; i < 2; i++) {
integrator.addComputePerDof("v", "v+0.5*(dt/2)*f0/m");
integrator.addComputePerDof("x", "x+(dt/2)*v");
integrator.addComputePerDof("v", "v+0.5*(dt/2)*f0/m");
}
integrator.addComputePerDof("v", "v+0.5*dt*f1/m");
HarmonicBondForce* bonds = new HarmonicBondForce();
for (int i = 0; i < numParticles-2; i++)
bonds->addBond(i, i+1, 1.0, 0.5);
system.addForce(bonds);
NonbondedForce* nb = new NonbondedForce();
nb->setCutoffDistance(2.0);
nb->setNonbondedMethod(NonbondedForce::Ewald);
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i%2 == 0 ? 5.0 : 10.0);
nb->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
nb->setForceGroup(1);
nb->setReciprocalSpaceForceGroup(0);
system.addForce(nb);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and monitor energy conservations.
double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Energy);
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
if (i == 1)
initialEnergy = energy;
else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05);
integrator.step(2);
}
}
#include "CudaTests.h"
#include "TestCustomIntegrator.h"
/**
* Make sure random numbers are computed correctly when steps get merged.
......@@ -756,117 +98,6 @@ void testMergedRandoms() {
}
}
void testIfBlock() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
const double dt = 0.01;
CustomIntegrator integrator(dt);
integrator.addGlobalVariable("a", 0);
integrator.addGlobalVariable("b", 0);
integrator.addComputeGlobal("b", "1");
integrator.beginIfBlock("a < 3.5");
integrator.addComputeGlobal("b", "a+1");
integrator.endBlock();
Context context(system, integrator, platform);
// Set "a" to 1.7 and verify that "b" gets set to a+1.
integrator.setGlobalVariable(0, 1.7);
integrator.step(1);
ASSERT_EQUAL_TOL(2.7, integrator.getGlobalVariable(1), 1e-6);
// Now set it to a value that should cause the block to be skipped.
integrator.setGlobalVariable(0, 4.1);
integrator.step(1);
ASSERT_EQUAL_TOL(1.0, integrator.getGlobalVariable(1), 1e-6);
}
void testWhileBlock() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
const double dt = 0.01;
CustomIntegrator integrator(dt);
integrator.addGlobalVariable("a", 0);
integrator.addGlobalVariable("b", 0);
integrator.addComputeGlobal("b", "1");
integrator.beginWhileBlock("b <= a");
integrator.addComputeGlobal("b", "b+1");
integrator.endBlock();
Context context(system, integrator, platform);
// Try a case where the loop should be skipped.
integrator.setGlobalVariable(0, -3.3);
integrator.step(1);
ASSERT_EQUAL_TOL(1.0, integrator.getGlobalVariable(1), 1e-6);
// In this case it should be executed exactly once.
integrator.setGlobalVariable(0, 1.2);
integrator.step(1);
ASSERT_EQUAL_TOL(2.0, integrator.getGlobalVariable(1), 1e-6);
// In this case, it should be executed several times.
integrator.setGlobalVariable(0, 5.3);
integrator.step(1);
ASSERT_EQUAL_TOL(6.0, integrator.getGlobalVariable(1), 1e-6);
}
/**
* Test modifying a global variable, then using it in a per-DOF computation.
*/
void testChangingGlobal() {
System system;
system.addParticle(1.0);
CustomIntegrator integrator(0.1);
integrator.addGlobalVariable("g", 0);
integrator.addPerDofVariable("a", 0);
integrator.addPerDofVariable("b", 0);
integrator.addComputeGlobal("g", "g+1");
integrator.addComputePerDof("a", "0.5");
integrator.addComputePerDof("b", "a+g");
Context context(system, integrator, platform);
// See if everything is being calculated correctly..
for (int i = 0; i < 10; i++) {
integrator.step(1);
ASSERT_EQUAL_TOL(i+1.0, integrator.getGlobalVariable(0), 1e-5);
vector<Vec3> values;
integrator.getPerDofVariable(1, values);
ASSERT_EQUAL_VEC(Vec3(i+1.5, i+1.5, i+1.5), values[0], 1e-5);
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testSingleBond();
testConstraints();
testVelocityConstraints();
testConstrainedMasslessParticles();
testWithThermostat();
testMonteCarlo();
testSum();
testParameter();
testRandomDistributions();
testPerDofVariables();
testForceGroups();
testRespa();
testMergedRandoms();
testIfBlock();
testWhileBlock();
testChangingGlobal();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testMergedRandoms();
}
platforms/cuda/tests/TestCudaCustomManyParticleForce.cpp
View file @ fd473eea
......@@ -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) 2014 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,705 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CustomManyParticleForce.
*/
#include "CudaTests.h"
#include "TestCustomManyParticleForce.h"
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomCompoundBondForce.h"
#include "openmm/CustomManyParticleForce.h"
#include "openmm/System.h"
#include "openmm/TabulatedFunction.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
Vec3 computeDelta(const Vec3& pos1, const Vec3& pos2, bool periodic, const Vec3* periodicBoxVectors) {
Vec3 diff = pos1-pos2;
if (periodic) {
diff -= periodicBoxVectors[2]*floor(diff[2]/periodicBoxVectors[2][2]+0.5);
diff -= periodicBoxVectors[1]*floor(diff[1]/periodicBoxVectors[1][1]+0.5);
diff -= periodicBoxVectors[0]*floor(diff[0]/periodicBoxVectors[0][0]+0.5);
}
return diff;
}
void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize, bool triclinic) {
// Create a System and Context.
int numParticles = force->getNumParticles();
CustomManyParticleForce::NonbondedMethod nonbondedMethod = force->getNonbondedMethod();
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
Vec3 boxVectors[3];
if (triclinic) {
boxVectors[0] = Vec3(boxSize, 0, 0);
boxVectors[1] = Vec3(0.2*boxSize, boxSize, 0);
boxVectors[2] = Vec3(-0.3*boxSize, -0.1*boxSize, boxSize);
}
else {
boxVectors[0] = Vec3(boxSize, 0, 0);
boxVectors[1] = Vec3(0, boxSize, 0);
boxVectors[2] = Vec3(0, 0, boxSize);
}
system.setDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
system.addForce(force);
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy);
double c = context.getParameter("C");
// See if the energy matches the expected value.
double expectedEnergy = 0;
bool periodic = (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic);
for (int i = 0; i < (int) expectedSets.size(); i++) {
int p1 = expectedSets[i][0];
int p2 = expectedSets[i][1];
int p3 = expectedSets[i][2];
Vec3 d12 = computeDelta(positions[p2], positions[p1], periodic, boxVectors);
Vec3 d13 = computeDelta(positions[p3], positions[p1], periodic, boxVectors);
Vec3 d23 = computeDelta(positions[p3], positions[p2], periodic, boxVectors);
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
double ctheta1 = d12.dot(d13)/(r12*r13);
double ctheta2 = -d12.dot(d23)/(r12*r23);
double ctheta3 = d13.dot(d23)/(r13*r23);
double rprod = r12*r13*r23;
expectedEnergy += c*(1+3*ctheta1*ctheta2*ctheta3)/(rprod*rprod*rprod);
}
ASSERT_EQUAL_TOL(expectedEnergy, state1.getPotentialEnergy(), 1e-5);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
const vector<Vec3>& forces = state1.getForces();
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4);
}
void validateStillingerWeber(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize) {
// Create a System and Context.
int numParticles = force->getNumParticles();
CustomManyParticleForce::NonbondedMethod nonbondedMethod = force->getNonbondedMethod();
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(force);
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy);
double L = context.getParameter("L");
double eps = context.getParameter("eps");
double a = context.getParameter("a");
double gamma = context.getParameter("gamma");
double sigma = context.getParameter("sigma");
// See if the energy matches the expected value.
double expectedEnergy = 0;
for (int i = 0; i < (int) expectedSets.size(); i++) {
int p1 = expectedSets[i][0];
int p2 = expectedSets[i][1];
int p3 = expectedSets[i][2];
Vec3 d12 = positions[p2]-positions[p1];
Vec3 d13 = positions[p3]-positions[p1];
Vec3 d23 = positions[p3]-positions[p2];
if (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic) {
for (int j = 0; j < 3; j++) {
d12[j] -= floor(d12[j]/boxSize+0.5f)*boxSize;
d13[j] -= floor(d13[j]/boxSize+0.5f)*boxSize;
d23[j] -= floor(d23[j]/boxSize+0.5f)*boxSize;
}
}
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
double ctheta1 = d12.dot(d13)/(r12*r13);
double ctheta2 = -d12.dot(d23)/(r12*r23);
double ctheta3 = d13.dot(d23)/(r13*r23);
expectedEnergy += L*eps*(ctheta1+1.0/3.0)*(ctheta1+1.0/3.0)*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));
}
ASSERT_EQUAL_TOL(expectedEnergy, state1.getPotentialEnergy(), 1e-5);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
const vector<Vec3>& forces = state1.getForces();
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4);
}
void testNoCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
int sets[4][3] = {{0,1,2}, {1,2,3}, {2,3,0}, {3,0,1}};
vector<const int*> expectedSets(&sets[0], &sets[4]);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
force->setNonbondedMethod(CustomManyParticleForce::CutoffNonPeriodic);
force->setCutoffDistance(1.55);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
positions.push_back(Vec3(0.2, 0.5, -0.1));
int sets[7][3] = {{0,1,2}, {0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,2,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[7]);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testPeriodic() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
force->setCutoffDistance(1.05);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
positions.push_back(Vec3(0.2, 0.5, -0.1));
double boxSize = 2.1;
int sets[5][3] = {{0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[5]);
validateAxilrodTeller(force, positions, expectedSets, boxSize, false);
}
void testTriclinic() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
force->setCutoffDistance(1.05);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
positions.push_back(Vec3(0.2, 0.5, -0.1));
double boxSize = 2.1;
int sets[4][3] = {{0,1,3}, {0,1,4}, {0,3,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[4]);
validateAxilrodTeller(force, positions, expectedSets, boxSize, true);
}
void testExclusions() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
positions.push_back(Vec3(0.2, 0.5, -0.1));
force->addExclusion(0, 2);
force->addExclusion(0, 3);
int sets[5][3] = {{0,1,4}, {1,2,3}, {1,2,4}, {1,3,4}, {2,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[5]);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testAllTerms() {
int numParticles = 4;
// Create a system with a CustomManyParticleForce.
System system1;
CustomManyParticleForce* force1 = new CustomManyParticleForce(4,
"distance(p1,p2)+angle(p1,p4,p3)+dihedral(p1,p3,p2,p4)+x1+y4+z3");
system1.addForce(force1);
vector<double> params;
for (int i = 0; i < numParticles; i++) {
system1.addParticle(1.0);
force1->addParticle(params, i);
}
set<int> filter;
filter.insert(0);
force1->setTypeFilter(0, filter);
filter.clear();
filter.insert(1);
force1->setTypeFilter(1, filter);
filter.clear();
filter.insert(3);
force1->setTypeFilter(2, filter);
filter.clear();
filter.insert(2);
force1->setTypeFilter(3, filter);
// Create a system that use a CustomCompoundBondForce to compute exactly the same interactions.
System system2;
CustomCompoundBondForce* force2 = new CustomCompoundBondForce(4,
"distance(p1,p2)+angle(p1,p3,p4)+dihedral(p1,p4,p2,p3)+x1+y3+z4");
system2.addForce(force2);
vector<int> particles;
particles.push_back(0);
particles.push_back(1);
particles.push_back(2);
particles.push_back(3);
force2->addBond(particles, params);
for (int i = 0; i < numParticles; i++)
system2.addParticle(1.0);
// Create contexts for both of them.
vector<Vec3> positions;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++)
positions.push_back(Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt)));
VerletIntegrator integrator1(0.001);
VerletIntegrator integrator2(0.001);
Context context1(system1, integrator1, platform);
Context context2(system2, integrator2, platform);
context1.setPositions(positions);
context2.setPositions(positions);
// See if they produce identical forces and energies.
State state1 = context1.getState(State::Forces | State::Energy);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state2.getPotentialEnergy(), state1.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state2.getForces()[i], state1.getForces()[i], 1e-4);
}
void testParameters() {
// Create a system.
int numParticles = 5;
System system;
CustomManyParticleForce* force = new CustomManyParticleForce(3, "C*scale1*scale2*scale3*(distance(p1,p2)+distance(p2,p3)+distance(p1,p3))");
force->addGlobalParameter("C", 2.0);
force->addPerParticleParameter("scale");
vector<double> params(1);
vector<Vec3> positions;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
params[0] = i+1;
force->addParticle(params);
positions.push_back(Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt)));
system.addParticle(1.0);
}
system.addForce(force);
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
// See if the energy is correct.
State state = context.getState(State::Energy);
double expectedEnergy = 0;
for (int i = 0; i < numParticles; i++)
for (int j = i+1; j < numParticles; j++)
for (int k = j+1; k < numParticles; k++) {
Vec3 d12 = positions[j]-positions[i];
Vec3 d13 = positions[k]-positions[i];
Vec3 d23 = positions[k]-positions[j];
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
expectedEnergy += 2.0*(i+1)*(j+1)*(k+1)*(r12+r13+r23);
}
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
// Modify the parameters.
context.setParameter("C", 3.5);
for (int i = 0; i < numParticles; i++) {
params[0] = 0.5*i-0.1;
force->setParticleParameters(i, params, 0);
}
force->updateParametersInContext(context);
// See if the energy is still correct.
state = context.getState(State::Energy);
expectedEnergy = 0;
for (int i = 0; i < numParticles; i++)
for (int j = i+1; j < numParticles; j++)
for (int k = j+1; k < numParticles; k++) {
Vec3 d12 = positions[j]-positions[i];
Vec3 d13 = positions[k]-positions[i];
Vec3 d23 = positions[k]-positions[j];
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
expectedEnergy += 3.5*(0.5*i-0.1)*(0.5*j-0.1)*(0.5*k-0.1)*(r12+r13+r23);
}
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
}
void testTabulatedFunctions() {
int numParticles = 5;
// Create two tabulated functions.
vector<double> values;
values.push_back(0.0);
values.push_back(50.0);
Continuous1DFunction* f1 = new Continuous1DFunction(values, 0, 100);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> c(numParticles);
for (int i = 0; i < numParticles; i++)
c[i] = genrand_real2(sfmt);
values.resize(numParticles*numParticles*numParticles);
for (int i = 0; i < numParticles; i++)
for (int j = 0; j < numParticles; j++)
for (int k = 0; k < numParticles; k++)
values[i+numParticles*j+numParticles*numParticles*k] = c[i]+c[j]+c[k];
Discrete3DFunction* f2 = new Discrete3DFunction(numParticles, numParticles, numParticles, values);
// Create a system.
System system;
CustomManyParticleForce* force = new CustomManyParticleForce(3, "f1(distance(p1,p2)+distance(p2,p3)+distance(p1,p3))*f2(atom1, atom2, atom3)");
force->addPerParticleParameter("atom");
force->addTabulatedFunction("f1", f1);
force->addTabulatedFunction("f2", f2);
vector<double> params(1);
vector<Vec3> positions;
for (int i = 0; i < numParticles; i++) {
params[0] = i;
force->addParticle(params);
positions.push_back(Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt)));
system.addParticle(1.0);
}
system.addForce(force);
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
// See if the energy is correct.
State state = context.getState(State::Energy);
double expectedEnergy = 0;
for (int i = 0; i < numParticles; i++)
for (int j = i+1; j < numParticles; j++)
for (int k = j+1; k < numParticles; k++) {
Vec3 d12 = positions[j]-positions[i];
Vec3 d13 = positions[k]-positions[i];
Vec3 d23 = positions[k]-positions[j];
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
expectedEnergy += 0.5*(r12+r13+r23)*(c[i]+c[j]+c[k]);
}
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
}
void testTypeFilters() {
// Create a system.
System system;
for (int i = 0; i < 5; i++)
system.addParticle(1.0);
CustomManyParticleForce* force = new CustomManyParticleForce(3, "c1*(distance(p1,p2)+distance(p1,p3))");
force->addPerParticleParameter("c");
double c[] = {1.0, 2.0, 1.3, 1.5, -2.1};
int type[] = {0, 1, 0, 1, 5};
vector<double> params(1);
for (int i = 0; i < 5; i++) {
params[0] = c[i];
force->addParticle(params, type[i]);
}
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
positions.push_back(Vec3(0.2, 0.5, -0.1));
set<int> f1, f2;
f1.insert(0);
f2.insert(1);
f2.insert(5);
force->setTypeFilter(0, f1);
force->setTypeFilter(1, f2);
force->setTypeFilter(2, f2);
system.addForce(force);
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
// See if the energy is correct.
State state = context.getState(State::Energy);
double expectedEnergy = 0;
int sets[6][3] = {{0,1,3}, {0,1,4}, {0,3,4}, {2,1,3}, {2,1,4}, {2,3,4}};
for (int i = 0; i < 6; i++) {
int p1 = sets[i][0];
int p2 = sets[i][1];
int p3 = sets[i][2];
Vec3 d12 = positions[p2]-positions[p1];
Vec3 d13 = positions[p3]-positions[p1];
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
expectedEnergy += c[p1]*(r12+r13);
}
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
}
void testLargeSystem() {
int gridSize = 8;
int numParticles = gridSize*gridSize*gridSize;
double boxSize = 3.0;
double spacing = boxSize/gridSize;
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
force->setCutoffDistance(0.6);
vector<double> params;
vector<Vec3> positions;
System system;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
force->addParticle(params);
positions.push_back(Vec3((i+0.4*genrand_real2(sfmt))*spacing, (j+0.4*genrand_real2(sfmt))*spacing, (k+0.4*genrand_real2(sfmt))*spacing));
system.addParticle(1.0);
}
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(force);
VerletIntegrator integrator1(0.001);
VerletIntegrator integrator2(0.001);
Context context1(system, integrator1, Platform::getPlatformByName("Reference"));
Context context2(system, integrator2, platform);
context1.setPositions(positions);
context2.setPositions(positions);
State state1 = context1.getState(State::Forces | State::Energy);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
void testCentralParticleModeNoCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
"r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
force->addGlobalParameter("L", 23.13);
force->addGlobalParameter("eps", 25.894776);
force->addGlobalParameter("a", 1.8);
force->addGlobalParameter("sigma", 0.23925);
force->addGlobalParameter("gamma", 1.2);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(0.1, 0, 0));
positions.push_back(Vec3(0, 0.11, 0.03));
positions.push_back(Vec3(0.04, 0, -0.08));
int sets[12][3] = {{0,1,2}, {0,1,3}, {0,2,3}, {1,0,2}, {1,0,3}, {1, 2, 3}, {2,0,1}, {2,0,3}, {2, 1, 3}, {3,0,1}, {3,0,2}, {3,1,2}};
vector<const int*> expectedSets(&sets[0], &sets[12]);
validateStillingerWeber(force, positions, expectedSets, 2.0);
}
void testCentralParticleModeCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
"r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
force->addGlobalParameter("L", 23.13);
force->addGlobalParameter("eps", 25.894776);
force->addGlobalParameter("a", 1.8);
force->addGlobalParameter("sigma", 0.23925);
force->addGlobalParameter("gamma", 1.2);
force->setNonbondedMethod(CustomManyParticleForce::CutoffNonPeriodic);
force->setCutoffDistance(0.155);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(0.1, 0, 0));
positions.push_back(Vec3(0, 0.11, 0.03));
positions.push_back(Vec3(0.04, 0, -0.08));
int sets[8][3] = {{0,1,2}, {0,1,3}, {0,2,3}, {1,0,2}, {1,0,3}, {1, 2, 3}, {2,0,1}, {3,0,1}};
vector<const int*> expectedSets(&sets[0], &sets[8]);
validateStillingerWeber(force, positions, expectedSets, 2.0);
}
void testCentralParticleModeLargeSystem() {
int gridSize = 8;
int numParticles = gridSize*gridSize*gridSize;
double boxSize = 2.0;
double spacing = boxSize/gridSize;
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
"r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
force->addGlobalParameter("L", 23.13);
force->addGlobalParameter("eps", 25.894776);
force->addGlobalParameter("a", 1.8);
force->addGlobalParameter("sigma", 0.23925);
force->addGlobalParameter("gamma", 1.2);
force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
force->setCutoffDistance(1.8*0.23925);
vector<double> params;
vector<Vec3> positions;
System system;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
force->addParticle(params);
positions.push_back(Vec3((i+0.4*genrand_real2(sfmt))*spacing, (j+0.4*genrand_real2(sfmt))*spacing, (k+0.4*genrand_real2(sfmt))*spacing));
system.addParticle(1.0);
}
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(force);
VerletIntegrator integrator1(0.001);
VerletIntegrator integrator2(0.001);
Context context1(system, integrator1, Platform::getPlatformByName("Reference"));
Context context2(system, integrator2, platform);
context1.setPositions(positions);
context2.setPositions(positions);
State state1 = context1.getState(State::Forces | State::Energy);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testNoCutoff();
testCutoff();
testPeriodic();
testTriclinic();
testExclusions();
testAllTerms();
testParameters();
testTabulatedFunctions();
testTypeFilters();
testLargeSystem();
testCentralParticleModeNoCutoff();
testCentralParticleModeCutoff();
testCentralParticleModeLargeSystem();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaCustomNonbondedForce.cpp
View file @ fd473eea
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
......@@ -30,608 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests all the different force terms in the CUDA implementation of CustomNonbondedForce.
*/
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/internal/AssertionUtilities.h"
#include "sfmt/SFMT.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include <cmath>
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
const double TOL = 1e-5;
void testSimpleExpression() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("-0.1*r^3");
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double force = 0.1*3*(2*2);
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(-0.1*(2*2*2), state.getPotentialEnergy(), TOL);
}
void testParameters() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("scale*a*(r*b)^3; a=a1*a2; b=c+b1+b2");
forceField->addPerParticleParameter("a");
forceField->addPerParticleParameter("b");
forceField->addGlobalParameter("scale", 3.0);
forceField->addGlobalParameter("c", -1.0);
vector<double> params(2);
params[0] = 1.5;
params[1] = 2.0;
forceField->addParticle(params);
params[0] = 2.0;
params[1] = 3.0;
forceField->addParticle(params);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
context.setPositions(positions);
context.setParameter("scale", 1.0);
context.setParameter("c", 0.0);
State state = context.getState(State::Forces | State::Energy);
vector<Vec3> forces = state.getForces();
double force = -3.0*3*5.0*(10*10);
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(3.0*(10*10*10), state.getPotentialEnergy(), TOL);
// Try changing the global parameters and make sure it's still correct.
context.setParameter("scale", 1.5);
context.setParameter("c", 1.0);
state = context.getState(State::Forces | State::Energy);
forces = state.getForces();
force = -1.5*3.0*3*6.0*(12*12);
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(1.5*3.0*(12*12*12), state.getPotentialEnergy(), TOL);
// Try changing the per-particle parameters and make sure it's still correct.
params[0] = 1.6;
params[1] = 2.1;
forceField->setParticleParameters(0, params);
params[0] = 1.9;
params[1] = 2.8;
forceField->setParticleParameters(1, params);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
forces = state.getForces();
force = -1.5*1.6*1.9*3*5.9*(11.8*11.8);
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(1.5*1.6*1.9*(11.8*11.8*11.8), state.getPotentialEnergy(), TOL);
}
void testManyParameters() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("(a1*a2+b1*b2+c1*c2+d1*d2+e1*e2)*r");
forceField->addPerParticleParameter("a");
forceField->addPerParticleParameter("b");
forceField->addPerParticleParameter("c");
forceField->addPerParticleParameter("d");
forceField->addPerParticleParameter("e");
vector<double> params(5);
params[0] = 1.0;
params[1] = 2.0;
params[2] = 3.0;
params[3] = 4.0;
params[4] = 5.0;
forceField->addParticle(params);
params[0] = 1.1;
params[1] = 1.2;
params[2] = 1.3;
params[3] = 1.4;
params[4] = 1.5;
forceField->addParticle(params);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
vector<Vec3> forces = state.getForces();
double force = 1*1.1 + 2*1.2 + 3*1.3 + 4*1.4 + 5*1.5;
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(2*force, state.getPotentialEnergy(), TOL);
}
void testExclusions() {
System system;
VerletIntegrator integrator(0.01);
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("a*r; a=a1+a2");
nonbonded->addPerParticleParameter("a");
vector<double> params(1);
vector<Vec3> positions(4);
for (int i = 0; i < 4; i++) {
system.addParticle(1.0);
params[0] = i+1;
nonbonded->addParticle(params);
positions[i] = Vec3(i, 0, 0);
}
nonbonded->addExclusion(0, 1);
nonbonded->addExclusion(1, 2);
nonbonded->addExclusion(2, 3);
nonbonded->addExclusion(0, 2);
nonbonded->addExclusion(1, 3);
system.addForce(nonbonded);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(1+4, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-(1+4), 0, 0), forces[3], TOL);
ASSERT_EQUAL_TOL((1+4)*3.0, state.getPotentialEnergy(), TOL);
}
void testCutoff() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("r");
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
forceField->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
forceField->setCutoffDistance(2.5);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2, 0);
positions[2] = Vec3(0, 3, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, 1, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -1, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(2.0+1.0, state.getPotentialEnergy(), TOL);
}
void testPeriodic() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("r");
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
forceField->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
forceField->setCutoffDistance(2.0);
system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2.1, 0);
positions[2] = Vec3(0, 3, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -2, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 2, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(1.9+1+0.9, state.getPotentialEnergy(), TOL);
}
void testTriclinic() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
Vec3 a(3.1, 0, 0);
Vec3 b(0.4, 3.5, 0);
Vec3 c(-0.1, -0.5, 4.0);
system.setDefaultPeriodicBoxVectors(a, b, c);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("r");
nonbonded->addParticle(vector<double>());
nonbonded->addParticle(vector<double>());
nonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
const double cutoff = 1.5;
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int iteration = 0; iteration < 50; iteration++) {
// Generate random positions for the two particles.
positions[0] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
positions[1] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
context.setPositions(positions);
// Loop over all possible periodic copies and find the nearest one.
Vec3 delta;
double distance2 = 100.0;
for (int i = -1; i < 2; i++)
for (int j = -1; j < 2; j++)
for (int k = -1; k < 2; k++) {
Vec3 d = positions[1]-positions[0]+a*i+b*j+c*k;
if (d.dot(d) < distance2) {
delta = d;
distance2 = d.dot(d);
}
}
double distance = sqrt(distance2);
// See if the force and energy are correct.
State state = context.getState(State::Forces | State::Energy);
if (distance >= cutoff) {
ASSERT_EQUAL(0.0, state.getPotentialEnergy());
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[0], 0);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[1], 0);
}
else {
const Vec3 force = delta/sqrt(delta.dot(delta));
ASSERT_EQUAL_TOL(distance, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(force, state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(-force, state.getForces()[1], TOL);
}
}
}
void testContinuous1DFunction() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r)+1");
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(sin(0.25*i));
forceField->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (int i = 1; i < 30; i++) {
double x = (7.0/30.0)*i;
positions[1] = Vec3(x, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double force = (x < 1.0 || x > 6.0 ? 0.0 : -cos(x-1.0));
double energy = (x < 1.0 || x > 6.0 ? 0.0 : sin(x-1.0))+1.0;
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
}
for (int i = 1; i < 20; i++) {
double x = 0.25*i+1.0;
positions[1] = Vec3(x, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Energy);
double energy = (x < 1.0 || x > 6.0 ? 0.0 : sin(x-1.0))+1.0;
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
}
}
void testContinuous2DFunction() {
const int xsize = 20;
const int ysize = 21;
const double xmin = 0.4;
const double xmax = 1.5;
const double ymin = 0.0;
const double ymax = 2.1;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a)+1");
forceField->addGlobalParameter("a", 0.0);
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
vector<double> table(xsize*ysize);
for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++) {
double x = xmin + i*(xmax-xmin)/xsize;
double y = ymin + j*(ymax-ymin)/ysize;
table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
}
}
forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
positions[1] = Vec3(x, 0, 0);
context.setParameter("a", y);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double energy = 1;
double force = 0;
if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
energy = sin(0.25*x)*cos(0.33*y)+1.0;
force = -0.25*cos(0.25*x)*cos(0.33*y);
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
}
}
}
void testContinuous3DFunction() {
const int xsize = 10;
const int ysize = 11;
const int zsize = 12;
const double xmin = 0.4;
const double xmax = 1.1;
const double ymin = 0.0;
const double ymax = 0.9;
const double zmin = 0.2;
const double zmax = 1.3;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a,b)+1");
forceField->addGlobalParameter("a", 0.0);
forceField->addGlobalParameter("b", 0.0);
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
vector<double> table(xsize*ysize*zsize);
for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++) {
for (int k = 0; k < zsize; k++) {
double x = xmin + i*(xmax-xmin)/xsize;
double y = ymin + j*(ymax-ymin)/ysize;
double z = zmin + k*(zmax-zmin)/zsize;
table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
}
}
}
forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
positions[1] = Vec3(x, 0, 0);
context.setParameter("a", y);
context.setParameter("b", z);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double energy = 1;
double force = 0;
if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1.0;
force = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
}
}
}
}
void testDiscrete1DFunction() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r-1)+1");
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(sin(0.25*i));
forceField->addTabulatedFunction("fn", new Discrete1DFunction(table));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (int i = 0; i < (int) table.size(); i++) {
positions[1] = Vec3(i+1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
}
}
void testDiscrete2DFunction() {
const int xsize = 10;
const int ysize = 5;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r-1,a)+1");
forceField->addGlobalParameter("a", 0.0);
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
vector<double> table;
for (int i = 0; i < xsize; i++)
for (int j = 0; j < ysize; j++)
table.push_back(sin(0.25*i)+cos(0.33*j));
forceField->addTabulatedFunction("fn", new Discrete2DFunction(xsize, ysize, table));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (int i = 0; i < (int) table.size(); i++) {
positions[1] = Vec3((i%xsize)+1, 0, 0);
context.setPositions(positions);
context.setParameter("a", i/xsize);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
}
}
void testDiscrete3DFunction() {
const int xsize = 8;
const int ysize = 5;
const int zsize = 6;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r-1,a,b)+1");
forceField->addGlobalParameter("a", 0.0);
forceField->addGlobalParameter("b", 0.0);
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
vector<double> table;
for (int i = 0; i < xsize; i++)
for (int j = 0; j < ysize; j++)
for (int k = 0; k < zsize; k++)
table.push_back(sin(0.25*i)+cos(0.33*j)+0.12345*k);
forceField->addTabulatedFunction("fn", new Discrete3DFunction(xsize, ysize, zsize, table));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (int i = 0; i < (int) table.size(); i++) {
positions[1] = Vec3((i%xsize)+1, 0, 0);
context.setPositions(positions);
context.setParameter("a", (i/xsize)%ysize);
context.setParameter("b", i/(xsize*ysize));
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
}
}
void testCoulombLennardJones() {
const int numMolecules = 300;
const int numParticles = numMolecules*2;
const double boxSize = 20.0;
// Create two systems: one with a NonbondedForce, and one using a CustomNonbondedForce to implement the same interaction.
System standardSystem;
System customSystem;
for (int i = 0; i < numParticles; i++) {
standardSystem.addParticle(1.0);
customSystem.addParticle(1.0);
}
NonbondedForce* standardNonbonded = new NonbondedForce();
CustomNonbondedForce* customNonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6)+138.935456*q/r; q=q1*q2; sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
customNonbonded->addPerParticleParameter("q");
customNonbonded->addPerParticleParameter("sigma");
customNonbonded->addPerParticleParameter("eps");
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
standardNonbonded->addParticle(1.0, 0.2, 0.1);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.1;
customNonbonded->addParticle(params);
standardNonbonded->addParticle(-1.0, 0.1, 0.1);
params[0] = -1.0;
params[1] = 0.1;
customNonbonded->addParticle(params);
}
else {
standardNonbonded->addParticle(1.0, 0.2, 0.2);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.2;
customNonbonded->addParticle(params);
standardNonbonded->addParticle(-1.0, 0.1, 0.2);
params[0] = -1.0;
params[1] = 0.1;
customNonbonded->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
standardNonbonded->addException(2*i, 2*i+1, 0.0, 1.0, 0.0);
customNonbonded->addExclusion(2*i, 2*i+1);
}
standardNonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
customNonbonded->setNonbondedMethod(CustomNonbondedForce::NoCutoff);
standardSystem.addForce(standardNonbonded);
customSystem.addForce(customNonbonded);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context context1(standardSystem, integrator1, platform);
Context context2(customSystem, integrator2, platform);
context1.setPositions(positions);
context2.setPositions(positions);
context1.setVelocities(velocities);
context2.setVelocities(velocities);
State state1 = context1.getState(State::Forces | State::Energy);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
}
#include "CudaTests.h"
#include "TestCustomNonbondedForce.h"
void testParallelComputation() {
System system;
......@@ -670,396 +69,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
void testSwitchingFunction() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("10/r^2");
vector<double> params;
nonbonded->addParticle(params);
nonbonded->addParticle(params);
nonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
nonbonded->setCutoffDistance(2.0);
nonbonded->setUseSwitchingFunction(true);
nonbonded->setSwitchingDistance(1.5);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
// Compute the interaction at various distances.
for (double r = 1.0; r < 2.5; r += 0.1) {
positions[1] = Vec3(r, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
// See if the energy is correct.
double expectedEnergy = 10/(r*r);
double switchValue;
if (r <= 1.5)
switchValue = 1;
else if (r >= 2.0)
switchValue = 0;
else {
double t = (r-1.5)/0.5;
switchValue = 1+t*t*t*(-10+t*(15-t*6));
}
ASSERT_EQUAL_TOL(switchValue*expectedEnergy, state.getPotentialEnergy(), TOL);
// See if the force is the gradient of the energy.
double delta = 1e-3;
positions[1] = Vec3(r-delta, 0, 0);
context.setPositions(positions);
double e1 = context.getState(State::Energy).getPotentialEnergy();
positions[1] = Vec3(r+delta, 0, 0);
context.setPositions(positions);
double e2 = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL((e2-e1)/(2*delta), state.getForces()[0][0], 1e-3);
}
}
void testLongRangeCorrection() {
// Create a box of particles.
int gridSize = 5;
int numParticles = gridSize*gridSize*gridSize;
double boxSize = gridSize*0.7;
double cutoff = boxSize/3;
System standardSystem;
System customSystem;
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
NonbondedForce* standardNonbonded = new NonbondedForce();
CustomNonbondedForce* customNonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6); sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
customNonbonded->addPerParticleParameter("sigma");
customNonbonded->addPerParticleParameter("eps");
vector<Vec3> positions(numParticles);
int index = 0;
vector<double> params1(2);
params1[0] = 1.1;
params1[1] = 0.5;
vector<double> params2(2);
params2[0] = 1;
params2[1] = 1;
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
standardSystem.addParticle(1.0);
customSystem.addParticle(1.0);
if (index%2 == 0) {
standardNonbonded->addParticle(0, params1[0], params1[1]);
customNonbonded->addParticle(params1);
}
else {
standardNonbonded->addParticle(0, params2[0], params2[1]);
customNonbonded->addParticle(params2);
}
positions[index] = Vec3(i*boxSize/gridSize, j*boxSize/gridSize, k*boxSize/gridSize);
index++;
}
standardNonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
customNonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
standardNonbonded->setCutoffDistance(cutoff);
customNonbonded->setCutoffDistance(cutoff);
standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
customSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
standardNonbonded->setUseDispersionCorrection(true);
customNonbonded->setUseLongRangeCorrection(true);
standardNonbonded->setUseSwitchingFunction(true);
customNonbonded->setUseSwitchingFunction(true);
standardNonbonded->setSwitchingDistance(0.8*cutoff);
customNonbonded->setSwitchingDistance(0.8*cutoff);
standardSystem.addForce(standardNonbonded);
customSystem.addForce(customNonbonded);
// Compute the correction for the standard force.
Context context1(standardSystem, integrator1, platform);
context1.setPositions(positions);
double standardEnergy1 = context1.getState(State::Energy).getPotentialEnergy();
standardNonbonded->setUseDispersionCorrection(false);
context1.reinitialize();
context1.setPositions(positions);
double standardEnergy2 = context1.getState(State::Energy).getPotentialEnergy();
// Compute the correction for the custom force.
Context context2(customSystem, integrator2, platform);
context2.setPositions(positions);
double customEnergy1 = context2.getState(State::Energy).getPotentialEnergy();
customNonbonded->setUseLongRangeCorrection(false);
context2.reinitialize();
context2.setPositions(positions);
double customEnergy2 = context2.getState(State::Energy).getPotentialEnergy();
// See if they agree.
ASSERT_EQUAL_TOL(standardEnergy1-standardEnergy2, customEnergy1-customEnergy2, 1e-4);
}
void testInteractionGroups() {
const int numParticles = 6;
System system;
VerletIntegrator integrator(0.01);
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("v1+v2");
nonbonded->addPerParticleParameter("v");
vector<double> params(1, 0.001);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
nonbonded->addParticle(params);
params[0] *= 10;
}
set<int> set1, set2, set3, set4;
set1.insert(2);
set2.insert(0);
set2.insert(1);
set2.insert(2);
set2.insert(3);
set2.insert(4);
set2.insert(5);
nonbonded->addInteractionGroup(set1, set2); // Particle 2 interacts with every other particle.
set3.insert(0);
set3.insert(1);
set4.insert(4);
set4.insert(5);
nonbonded->addInteractionGroup(set3, set4); // Particles 0 and 1 interact with 4 and 5.
nonbonded->addExclusion(1, 2); // Add an exclusion to make sure it gets skipped.
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
context.setPositions(positions);
State state = context.getState(State::Energy);
double expectedEnergy = 331.423; // Each digit is the number of interactions a particle particle is involved in.
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), TOL);
}
void testLargeInteractionGroup() {
const int numMolecules = 300;
const int numParticles = numMolecules*2;
const double boxSize = 20.0;
// Create a large system.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6)+138.935456*q/r; q=q1*q2; sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
nonbonded->addPerParticleParameter("q");
nonbonded->addPerParticleParameter("sigma");
nonbonded->addPerParticleParameter("eps");
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.1;
nonbonded->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
nonbonded->addParticle(params);
}
else {
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.2;
nonbonded->addParticle(params);
params[0] = -1.0;
params[1] = 0.1;
nonbonded->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
nonbonded->addExclusion(2*i, 2*i+1);
}
nonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
system.addForce(nonbonded);
// Compute the forces.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state1 = context.getState(State::Forces);
// Modify the force so only one particle interacts with everything else.
set<int> set1, set2;
set1.insert(151);
for (int i = 0; i < numParticles; i++)
set2.insert(i);
nonbonded->addInteractionGroup(set1, set2);
context.reinitialize();
context.setPositions(positions);
State state2 = context.getState(State::Forces);
// The force on that one particle should be the same.
ASSERT_EQUAL_VEC(state1.getForces()[151], state2.getForces()[151], 1e-4);
// Modify the interaction group so it includes all interactions. This should now reproduce the original forces
// on all atoms.
for (int i = 0; i < numParticles; i++)
set1.insert(i);
nonbonded->setInteractionGroupParameters(0, set1, set2);
context.reinitialize();
context.setPositions(positions);
State state3 = context.getState(State::Forces);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state3.getForces()[i], 1e-4);
}
void testInteractionGroupLongRangeCorrection() {
const int numParticles = 10;
const double boxSize = 10.0;
const double cutoff = 0.5;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("c1*c2*r^-4");
nonbonded->addPerParticleParameter("c");
vector<Vec3> positions(numParticles);
vector<double> params(1);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
params[0] = (i%2 == 0 ? 1.1 : 2.0);
nonbonded->addParticle(params);
positions[i] = Vec3(0.5*i, 0, 0);
}
nonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
// Setup nonbonded groups. They involve 1 interaction of type AA,
// 2 of type BB, and 5 of type AB.
set<int> set1, set2, set3, set4, set5;
set1.insert(0);
set1.insert(1);
set1.insert(2);
nonbonded->addInteractionGroup(set1, set1);
set2.insert(3);
set3.insert(4);
set3.insert(6);
set3.insert(8);
nonbonded->addInteractionGroup(set2, set3);
set4.insert(5);
set5.insert(7);
set5.insert(9);
nonbonded->addInteractionGroup(set4, set5);
// Compute energy with and without the correction.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
double energy1 = context.getState(State::Energy).getPotentialEnergy();
nonbonded->setUseLongRangeCorrection(true);
context.reinitialize();
context.setPositions(positions);
double energy2 = context.getState(State::Energy).getPotentialEnergy();
// Check the result.
double sum = (1.1*1.1 + 2*2.0*2.0 + 5*1.1*2.0)*2.0;
int numPairs = (numParticles*(numParticles+1))/2;
double expected = 2*M_PI*numParticles*numParticles*sum/(numPairs*boxSize*boxSize*boxSize);
ASSERT_EQUAL_TOL(expected, energy2-energy1, 1e-4);
}
void testMultipleCutoffs() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
// Add multiple nonbonded forces that have different cutoffs.
CustomNonbondedForce* nonbonded1 = new CustomNonbondedForce("2*r");
nonbonded1->addParticle(vector<double>());
nonbonded1->addParticle(vector<double>());
nonbonded1->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
nonbonded1->setCutoffDistance(2.5);
system.addForce(nonbonded1);
CustomNonbondedForce* nonbonded2 = new CustomNonbondedForce("3*r");
nonbonded2->addParticle(vector<double>());
nonbonded2->addParticle(vector<double>());
nonbonded2->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
nonbonded2->setCutoffDistance(2.9);
nonbonded2->setForceGroup(1);
system.addForce(nonbonded2);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 0, 0);
for (double r = 2.4; r < 3.2; r += 0.2) {
positions[1][1] = r;
context.setPositions(positions);
double e1 = (r < 2.5 ? 2.0*r : 0.0);
double e2 = (r < 2.9 ? 3.0*r : 0.0);
double f1 = (r < 2.5 ? 2.0 : 0.0);
double f2 = (r < 2.9 ? 3.0 : 0.0);
// Check the first force.
State state = context.getState(State::Forces | State::Energy, false, 1);
ASSERT_EQUAL_VEC(Vec3(0, f1, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -f1, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_TOL(e1, state.getPotentialEnergy(), TOL);
// Check the second force.
state = context.getState(State::Forces | State::Energy, false, 2);
ASSERT_EQUAL_VEC(Vec3(0, f2, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -f2, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_TOL(e2, state.getPotentialEnergy(), TOL);
// Check the sum of both forces.
state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_VEC(Vec3(0, f1+f2, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -f1-f2, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_TOL(e1+e2, state.getPotentialEnergy(), TOL);
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testSimpleExpression();
testParameters();
testManyParameters();
testExclusions();
testCutoff();
testPeriodic();
testTriclinic();
testContinuous1DFunction();
testContinuous2DFunction();
testContinuous3DFunction();
testDiscrete1DFunction();
testDiscrete2DFunction();
testDiscrete3DFunction();
testCoulombLennardJones();
testParallelComputation();
testSwitchingFunction();
testLongRangeCorrection();
testInteractionGroups();
testLargeInteractionGroup();
testInteractionGroupLongRangeCorrection();
testMultipleCutoffs();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/cuda/tests/TestCudaCustomTorsionForce.cpp
View file @ fd473eea
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,146 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CustomTorsionForce.
*/
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomTorsionForce.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
const double TOL = 1e-5;
void testTorsions() {
// Create a system using a CustomTorsionForce.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomTorsionForce* custom = new CustomTorsionForce("k*(1+cos(n*theta-theta0))");
custom->addPerTorsionParameter("theta0");
custom->addPerTorsionParameter("n");
custom->addGlobalParameter("k", 0.5);
vector<double> parameters(2);
parameters[0] = 1.5;
parameters[1] = 1;
custom->addTorsion(0, 1, 2, 3, parameters);
parameters[0] = 2.0;
parameters[1] = 2;
custom->addTorsion(1, 2, 3, 4, parameters);
customSystem.addForce(custom);
// Create an identical system using a PeriodicTorsionForce.
System harmonicSystem;
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
VerletIntegrator integrator(0.01);
PeriodicTorsionForce* periodic = new PeriodicTorsionForce();
periodic->addTorsion(0, 1, 2, 3, 1, 1.5, 0.5);
periodic->addTorsion(1, 2, 3, 4, 2, 2.0, 0.5);
harmonicSystem.addForce(periodic);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(5);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(harmonicSystem, integrator2, platform);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
// Try changing the torsion parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[1] = 2;
custom->setTorsionParameters(0, 0, 1, 2, 3, parameters);
parameters[0] = 2.1;
parameters[1] = 3;
custom->setTorsionParameters(1, 1, 2, 3, 4, parameters);
custom->updateParametersInContext(c1);
periodic->setTorsionParameters(0, 0, 1, 2, 3, 2, 1.6, 0.5);
periodic->setTorsionParameters(1, 1, 2, 3, 4, 3, 2.1, 0.5);
periodic->updateParametersInContext(c2);
{
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
}
void testRange() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
CustomTorsionForce* custom = new CustomTorsionForce("theta");
custom->addTorsion(0, 1, 2, 3, vector<double>());
system.addForce(custom);
// Set the atoms in various positions, and verify that the angle is always in the expected range.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(4);
VerletIntegrator integrator(0.01);
double minAngle = 1000;
double maxAngle = -1000;
Context context(system, integrator, platform);
for (int i = 0; i < 100; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
context.setPositions(positions);
double angle = context.getState(State::Energy).getPotentialEnergy();
if (angle < minAngle)
minAngle = angle;
if (angle > maxAngle)
maxAngle = angle;
}
ASSERT(minAngle >= -M_PI);
ASSERT(maxAngle <= M_PI);
}
#include "CudaTests.h"
#include "TestCustomTorsionForce.h"
void testParallelComputation() {
System system;
......@@ -199,18 +61,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testTorsions();
testRange();
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/cuda/tests/TestCudaEwald.cpp
View file @ fd473eea
......@@ -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) 2008-2014 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,344 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the Ewald summation method CUDA implementation of NonbondedForce.
*/
#include "CudaTests.h"
#include "TestEwald.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "ReferencePlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/internal/ContextImpl.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
const double TOL = 1e-5;
void testEwaldPME(bool includeExceptions) {
// Use amorphous NaCl system for the tests
const int numParticles = 894;
const double cutoff = 1.2;
const double boxSize = 3.00646;
double tol = 1e-5;
ReferencePlatform reference;
System system;
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
nonbonded->setCutoffDistance(cutoff);
nonbonded->setEwaldErrorTolerance(tol);
for (int i = 0; i < numParticles/2; i++)
system.addParticle(22.99);
for (int i = 0; i < numParticles/2; i++)
system.addParticle(35.45);
for (int i = 0; i < numParticles/2; i++)
nonbonded->addParticle(1.0, 1.0,0.0);
for (int i = 0; i < numParticles/2; i++)
nonbonded->addParticle(-1.0, 1.0,0.0);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(nonbonded);
vector<Vec3> positions(numParticles);
#include "nacl_amorph.dat"
if (includeExceptions) {
// Add some exclusions.
for (int i = 0; i < numParticles-1; i++) {
Vec3 delta = positions[i]-positions[i+1];
if (sqrt(delta.dot(delta)) < 0.5*cutoff)
nonbonded->addException(i, i+1, i%2 == 0 ? 0.0 : 0.5, 1.0, 0.0);
}
}
// (1) Check whether the Reference and CUDA platforms agree when using Ewald Method
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context cuContext(system, integrator1, platform);
Context referenceContext(system, integrator2, reference);
cuContext.setPositions(positions);
referenceContext.setPositions(positions);
State cuState = cuContext.getState(State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Forces | State::Energy);
tol = 1e-2;
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(referenceState.getForces()[i], cuState.getForces()[i], tol);
}
tol = 1e-5;
ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cuState.getPotentialEnergy(), tol);
// (2) Check whether Ewald method in CUDA is self-consistent
double norm = 0.0;
for (int i = 0; i < numParticles; ++i) {
Vec3 f = cuState.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
}
norm = std::sqrt(norm);
const double delta = 5e-3;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = cuState.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
VerletIntegrator integrator3(0.01);
Context cuContext2(system, integrator3, platform);
cuContext2.setPositions(positions);
tol = 1e-2;
State cuState2 = cuContext2.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (cuState2.getPotentialEnergy()-cuState.getPotentialEnergy())/delta, tol)
// (3) Check whether the Reference and CUDA platforms agree when using PME
nonbonded->setNonbondedMethod(NonbondedForce::PME);
cuContext.reinitialize();
referenceContext.reinitialize();
cuContext.setPositions(positions);
referenceContext.setPositions(positions);
cuState = cuContext.getState(State::Forces | State::Energy);
referenceState = referenceContext.getState(State::Forces | State::Energy);
tol = 1e-2;
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(referenceState.getForces()[i], cuState.getForces()[i], tol);
}
tol = 1e-5;
ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cuState.getPotentialEnergy(), tol);
// (4) Check whether PME method in CUDA is self-consistent
norm = 0.0;
for (int i = 0; i < numParticles; ++i) {
Vec3 f = cuState.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
}
norm = std::sqrt(norm);
step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = cuState.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
VerletIntegrator integrator4(0.01);
Context cuContext3(system, integrator4, platform);
cuContext3.setPositions(positions);
tol = 1e-2;
State cuState3 = cuContext3.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (cuState3.getPotentialEnergy()-cuState.getPotentialEnergy())/delta, tol)
}
void testEwald2Ions() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(-1.0, 1, 0);
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
const double cutoff = 2.0;
nonbonded->setCutoffDistance(cutoff);
nonbonded->setEwaldErrorTolerance(TOL);
system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(3.048000,2.764000,3.156000);
positions[1] = Vec3(2.809000,2.888000,2.571000);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-123.711, 64.1877, -302.716), forces[0], 10*TOL);
ASSERT_EQUAL_VEC(Vec3( 123.711, -64.1877, 302.716), forces[1], 10*TOL);
ASSERT_EQUAL_TOL(-217.276, state.getPotentialEnergy(), 0.01/*10*TOL*/);
}
void testTriclinic() {
// Create a triclinic box containing eight particles.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(2.5, 0, 0), Vec3(0.5, 3.0, 0), Vec3(0.7, 0.9, 3.5));
for (int i = 0; i < 8; i++)
system.addParticle(1.0);
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
force->setNonbondedMethod(NonbondedForce::PME);
force->setCutoffDistance(1.0);
force->setPMEParameters(3.45891, 32, 40, 48);
for (int i = 0; i < 4; i++)
force->addParticle(-1, 0.440104, 0.4184); // Cl parameters
for (int i = 0; i < 4; i++)
force->addParticle(1, 0.332840, 0.0115897); // Na parameters
vector<Vec3> positions(8);
positions[0] = Vec3(1.744, 2.788, 3.162);
positions[1] = Vec3(1.048, 0.762, 2.340);
positions[2] = Vec3(2.489, 1.570, 2.817);
positions[3] = Vec3(1.027, 1.893, 3.271);
positions[4] = Vec3(0.937, 0.825, 0.009);
positions[5] = Vec3(2.290, 1.887, 3.352);
positions[6] = Vec3(1.266, 1.111, 2.894);
positions[7] = Vec3(0.933, 1.862, 3.490);
// Compute the forces and energy.
VerletIntegrator integ(0.001);
Context context(system, integ, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
// Compare them to values computed by Gromacs.
double expectedEnergy = -963.370;
vector<Vec3> expectedForce(8);
expectedForce[0] = Vec3(4.25253e+01, -1.23503e+02, 1.22139e+02);
expectedForce[1] = Vec3(9.74752e+01, 1.68213e+02, 1.93169e+02);
expectedForce[2] = Vec3(-1.50348e+02, 1.29165e+02, 3.70435e+02);
expectedForce[3] = Vec3(9.18644e+02, -3.52571e+00, -1.34772e+03);
expectedForce[4] = Vec3(-1.61193e+02, 9.01528e+01, -7.12904e+01);
expectedForce[5] = Vec3(2.82630e+02, 2.78029e+01, -3.72864e+02);
expectedForce[6] = Vec3(-1.47454e+02, -2.14448e+02, -3.55789e+02);
expectedForce[7] = Vec3(-8.82195e+02, -7.39132e+01, 1.46202e+03);
for (int i = 0; i < 8; i++) {
ASSERT_EQUAL_VEC(expectedForce[i], state.getForces()[i], 1e-4);
}
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-4);
}
void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
// Create a cloud of random point charges.
const int numParticles = 51;
const double boxWidth = 5.0;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
force->addParticle(-1.0+i*2.0/(numParticles-1), 1.0, 0.0);
positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
}
force->setNonbondedMethod(method);
// For various values of the cutoff and error tolerance, see if the actual error is reasonable.
for (double cutoff = 1.0; cutoff < boxWidth/2; cutoff *= 1.2) {
force->setCutoffDistance(cutoff);
vector<Vec3> refForces;
double norm = 0.0;
for (double tol = 5e-5; tol < 1e-3; tol *= 2.0) {
force->setEwaldErrorTolerance(tol);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces);
if (refForces.size() == 0) {
refForces = state.getForces();
for (int i = 0; i < numParticles; i++)
norm += refForces[i].dot(refForces[i]);
norm = sqrt(norm);
}
else {
double diff = 0.0;
for (int i = 0; i < numParticles; i++) {
Vec3 delta = refForces[i]-state.getForces()[i];
diff += delta.dot(delta);
}
diff = sqrt(diff)/norm;
ASSERT(diff < 2*tol);
}
}
}
}
void testPMEParameters() {
// Create a cloud of random point charges.
const int numParticles = 51;
const double boxWidth = 4.7;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
force->addParticle(-1.0+i*2.0/(numParticles-1), 1.0, 0.0);
positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
}
force->setNonbondedMethod(NonbondedForce::PME);
// Compute the energy with an error tolerance of 1e-3.
force->setEwaldErrorTolerance(1e-3);
VerletIntegrator integrator1(0.01);
Context context1(system, integrator1, platform);
context1.setPositions(positions);
double energy1 = context1.getState(State::Energy).getPotentialEnergy();
// Try again with an error tolerance of 1e-4.
force->setEwaldErrorTolerance(1e-4);
VerletIntegrator integrator2(0.01);
Context context2(system, integrator2, platform);
context2.setPositions(positions);
double energy2 = context2.getState(State::Energy).getPotentialEnergy();
// Now explicitly set the parameters. These should match the values that were
// used for tolerance 1e-3.
force->setPMEParameters(2.49291157051793, 32, 32, 32);
VerletIntegrator integrator3(0.01);
Context context3(system, integrator3, platform);
context3.setPositions(positions);
double energy3 = context3.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(energy1, energy3, 1e-6);
ASSERT(fabs((energy1-energy2)/energy1) > 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testEwaldPME(false);
testEwaldPME(true);
// testEwald2Ions();
testTriclinic();
testErrorTolerance(NonbondedForce::Ewald);
testErrorTolerance(NonbondedForce::PME);
testPMEParameters();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaGBSAOBCForce.cpp
View file @ fd473eea
......@@ -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) 2008-2014 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,245 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of GBSAOBCForce.
*/
#include "CudaTests.h"
#include "TestGBSAOBCForce.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "ReferencePlatform.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include "openmm/NonbondedForce.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
const double TOL = 1e-5;
void testSingleParticle() {
System system;
system.addParticle(2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* gbsa = new GBSAOBCForce();
NonbondedForce* nonbonded = new NonbondedForce();
gbsa->addParticle(0.5, 0.15, 1);
nonbonded->addParticle(0.5, 1, 0);
system.addForce(gbsa);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Energy);
double bornRadius = 0.15-0.009; // dielectric offset
double eps0 = EPSILON0;
double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/gbsa->getSoluteDielectric()-1.0/gbsa->getSolventDielectric())/bornRadius;
double extendedRadius = 0.15+0.14; // probe radius
double nonpolarEnergy = 4*PI_M*2.25936*extendedRadius*extendedRadius*std::pow(0.15/bornRadius, 6.0);
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
// Change the parameters and see if it is still correct.
gbsa->setParticleParameters(0, 0.4, 0.25, 1);
gbsa->updateParametersInContext(context);
state = context.getState(State::Energy);
bornRadius = 0.25-0.009; // dielectric offset
bornEnergy = (-0.4*0.4/(8*PI_M*eps0))*(1.0/gbsa->getSoluteDielectric()-1.0/gbsa->getSolventDielectric())/bornRadius;
extendedRadius = 0.25+0.14;
nonpolarEnergy = 4*PI_M*2.25936*extendedRadius*extendedRadius*std::pow(0.25/bornRadius, 6.0);
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
}
void testGlobalSettings() {
System system;
system.addParticle(2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* forceField = new GBSAOBCForce();
forceField->addParticle(0.5, 0.15, 1);
const double soluteDielectric = 2.1;
const double solventDielectric = 35.0;
const double surfaceAreaEnergy = 0.75;
forceField->setSoluteDielectric(soluteDielectric);
forceField->setSolventDielectric(solventDielectric);
forceField->setSurfaceAreaEnergy(surfaceAreaEnergy);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Energy);
double bornRadius = 0.15-0.009; // dielectric offset
double eps0 = EPSILON0;
double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/soluteDielectric-1.0/solventDielectric)/bornRadius;
double extendedRadius = 0.15+0.14; // probe radius
double nonpolarEnergy = 4*PI_M*surfaceAreaEnergy*extendedRadius*extendedRadius*std::pow(0.15/bornRadius, 6.0);
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
}
void testCutoffAndPeriodic() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* gbsa = new GBSAOBCForce();
NonbondedForce* nonbonded = new NonbondedForce();
gbsa->addParticle(-1, 0.15, 1);
nonbonded->addParticle(-1, 1, 0);
gbsa->addParticle(1, 0.15, 1);
nonbonded->addParticle(1, 1, 0);
const double cutoffDistance = 3.0;
const double boxSize = 10.0;
nonbonded->setCutoffDistance(cutoffDistance);
gbsa->setCutoffDistance(cutoffDistance);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(gbsa);
system.addForce(nonbonded);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
// Calculate the forces for both cutoff and periodic with two different atom positions.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
gbsa->setNonbondedMethod(GBSAOBCForce::CutoffNonPeriodic);
Context context(system, integrator, platform);
context.setPositions(positions);
State state1 = context.getState(State::Forces);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
gbsa->setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
context.reinitialize();
context.setPositions(positions);
State state2 = context.getState(State::Forces);
positions[1][0]+= boxSize;
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
gbsa->setNonbondedMethod(GBSAOBCForce::CutoffNonPeriodic);
context.reinitialize();
context.setPositions(positions);
State state3 = context.getState(State::Forces);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
gbsa->setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
context.reinitialize();
context.setPositions(positions);
State state4 = context.getState(State::Forces);
// All forces should be identical, exception state3 which should be zero.
ASSERT_EQUAL_VEC(state1.getForces()[0], state2.getForces()[0], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[1], state2.getForces()[1], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[0], state4.getForces()[0], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[1], state4.getForces()[1], 0.01);
ASSERT_EQUAL_VEC(state3.getForces()[0], Vec3(0, 0, 0), 0.01);
ASSERT_EQUAL_VEC(state3.getForces()[1], Vec3(0, 0, 0), 0.01);
void runPlatformTests() {
}
void testForce(int numParticles, NonbondedForce::NonbondedMethod method, GBSAOBCForce::NonbondedMethod method2) {
ReferencePlatform reference;
System system;
GBSAOBCForce* gbsa = new GBSAOBCForce();
NonbondedForce* nonbonded = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(1.0);
double charge = i%2 == 0 ? -1 : 1;
gbsa->addParticle(charge, 0.15, 1);
nonbonded->addParticle(charge, 1, 0);
}
nonbonded->setNonbondedMethod(method);
gbsa->setNonbondedMethod(method2);
nonbonded->setCutoffDistance(3.0);
gbsa->setCutoffDistance(3.0);
int grid = (int) floor(0.5+pow(numParticles, 1.0/3.0));
if (method == NonbondedForce::CutoffPeriodic) {
double boxSize = (grid+1)*1.1;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
}
system.addForce(gbsa);
system.addForce(nonbonded);
LangevinIntegrator integrator1(0, 0.1, 0.01);
LangevinIntegrator integrator2(0, 0.1, 0.01);
Context context(system, integrator1, platform);
Context refContext(system, integrator2, reference);
// Set random (but uniformly distributed) positions for all the particles.
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < grid; i++)
for (int j = 0; j < grid; j++)
for (int k = 0; k < grid; k++)
positions[i*grid*grid+j*grid+k] = Vec3(i*1.1, j*1.1, k*1.1);
for (int i = 0; i < numParticles; ++i)
positions[i] = positions[i] + Vec3(0.5*genrand_real2(sfmt), 0.5*genrand_real2(sfmt), 0.5*genrand_real2(sfmt));
context.setPositions(positions);
refContext.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
State refState = refContext.getState(State::Forces | State::Energy);
// Make sure the CUDA and Reference platforms agree.
double norm = 0.0;
double diff = 0.0;
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
Vec3 delta = f-refState.getForces()[i];
diff += delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2];
}
norm = std::sqrt(norm);
diff = std::sqrt(diff);
ASSERT_EQUAL_TOL(0.0, diff, 0.001*norm);
ASSERT_EQUAL_TOL(state.getPotentialEnergy(), refState.getPotentialEnergy(), 1e-3);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
// (This doesn't work with cutoffs, since the energy changes discontinuously at the cutoff distance.)
if (method == NonbondedForce::NoCutoff)
{
const double delta = 0.3;
double step = 0.5*delta/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/delta, 1e-2)
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testSingleParticle();
testGlobalSettings();
testCutoffAndPeriodic();
for (int i = 5; i < 11; i++) {
testForce(i*i*i, NonbondedForce::NoCutoff, GBSAOBCForce::NoCutoff);
testForce(i*i*i, NonbondedForce::CutoffNonPeriodic, GBSAOBCForce::CutoffNonPeriodic);
testForce(i*i*i, NonbondedForce::CutoffPeriodic, GBSAOBCForce::CutoffPeriodic);
}
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cuda/tests/TestCudaHarmonicAngleForce.cpp
View file @ fd473eea
......@@ -7,7 +7,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -30,74 +30,9 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of HarmonicAngleForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
const double TOL = 1e-5;
void testAngles() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
HarmonicAngleForce* forceField = new HarmonicAngleForce();
forceField->addAngle(0, 1, 2, PI_M/3, 1.1);
forceField->addAngle(1, 2, 3, PI_M/2, 1.2);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(2, 1, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
double torque1 = 1.1*PI_M/6;
double torque2 = 1.2*PI_M/4;
ASSERT_EQUAL_VEC(Vec3(torque1, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5*torque2, 0.5*torque2, 0), forces[3], TOL); // reduced by sqrt(2) due to the bond length, another sqrt(2) due to the angle
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
ASSERT_EQUAL_TOL(0.5*1.1*(PI_M/6)*(PI_M/6) + 0.5*1.2*(PI_M/4)*(PI_M/4), state.getPotentialEnergy(), TOL);
}
// Try changing the angle parameters and make sure it's still correct.
forceField->setAngleParameters(0, 0, 1, 2, PI_M/3.1, 1.3);
forceField->setAngleParameters(1, 1, 2, 3, PI_M/2.1, 1.4);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
double dtheta1 = (PI_M/2)-(PI_M/3.1);
double dtheta2 = (3*PI_M/4)-(PI_M/2.1);
double torque1 = 1.3*dtheta1;
double torque2 = 1.4*dtheta2;
ASSERT_EQUAL_VEC(Vec3(torque1, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5*torque2, 0.5*torque2, 0), forces[3], TOL); // reduced by sqrt(2) due to the bond length, another sqrt(2) due to the angle
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
ASSERT_EQUAL_TOL(0.5*1.3*dtheta1*dtheta1 + 0.5*1.4*dtheta2*dtheta2, state.getPotentialEnergy(), TOL);
}
}
#include "CudaTests.h"
#include "TestHarmonicAngleForce.h"
#include <map>
void testParallelComputation() {
System system;
......@@ -127,17 +62,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testAngles();
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/cuda/tests/TestCudaHarmonicBondForce.cpp
View file @ fd473eea
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,66 +29,9 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of HarmonicBondForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include <iostream>
#include "CudaTests.h"
#include "TestHarmonicBondForce.h"
#include <map>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
const double TOL = 1e-5;
void testBonds() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 0.8);
forceField->addBond(1, 2, 1.2, 0.7);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.7*0.2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.8*0.5*0.5 + 0.5*0.7*0.2*0.2, state.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
forceField->setBondParameters(0, 0, 1, 1.6, 0.9);
forceField->setBondParameters(1, 1, 2, 1.3, 0.8);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.9*0.4, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.8*0.3, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.9*0.4*0.4 + 0.5*0.8*0.3*0.3, state.getPotentialEnergy(), TOL);
}
}
void testParallelComputation() {
System system;
......@@ -118,18 +61,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testBonds();
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
testParallelComputation();
}
platforms/cuda/tests/TestCudaLangevinIntegrator.cpp
View file @ fd473eea
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,256 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of LangevinIntegrator.
*/
#include "CudaTests.h"
#include "TestLangevinIntegrator.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
const double TOL = 1e-5;
void testSingleBond() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// This is simply a damped harmonic oscillator, so compare it to the analytical solution.
double freq = std::sqrt(1-0.05*0.05);
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Velocities);
double time = state.getTime();
double expectedDist = 1.5+0.5*std::exp(-0.05*time)*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*std::exp(-0.05*time)*(0.05*std::cos(freq*time)+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);
integrator.step(1);
}
// Not set the friction to a tiny value and see if it conserves energy.
integrator.setFriction(5e-5);
context.setPositions(positions);
State state = context.getState(State::Energy);
double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
for (int i = 0; i < 1000; ++i) {
state = context.getState(State::Energy);
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1);
}
}
void testTemperature() {
const int numParticles = 8;
const double temp = 100.0;
System system;
LangevinIntegrator integrator(temp, 2.0, 0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
context.setPositions(positions);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double ke = 0.0;
for (int i = 0; i < 10000; ++i) {
State state = context.getState(State::Energy);
ke += state.getKineticEnergy();
integrator.step(1);
}
ke /= 10000;
double expected = 0.5*numParticles*3*BOLTZ*temp;
ASSERT_USUALLY_EQUAL_TOL(expected, ke, 6/std::sqrt(10000.0));
}
void testConstraints() {
const int numParticles = 8;
const int numConstraints = 5;
const double temp = 100.0;
System system;
LangevinIntegrator integrator(temp, 2.0, 0.01);
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
system.addConstraint(0, 1, 1.0);
system.addConstraint(1, 2, 1.0);
system.addConstraint(2, 3, 1.0);
system.addConstraint(4, 5, 1.0);
system.addConstraint(6, 7, 1.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions);
for (int j = 0; j < numConstraints; ++j) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 1e-4);
}
integrator.step(1);
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
LangevinIntegrator integrator(300.0, 2.0, 0.01);
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
System system;
LangevinIntegrator integrator(temp, 2.0, 0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(0, 0, 0);
}
// Try twice with the same random seed.
integrator.setRandomNumberSeed(5);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state1 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state2 = context.getState(State::Positions);
// Try twice with a different random seed.
integrator.setRandomNumberSeed(10);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state3 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state4 = context.getState(State::Positions);
// Compare the results.
for (int i = 0; i < numParticles; i++) {
for (int j = 0; j < 3; j++) {
ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
ASSERT(state3.getPositions()[i][j] == state4.getPositions()[i][j]);
ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
}
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testSingleBond();
testTemperature();
testConstraints();
testConstrainedMasslessParticles();
testRandomSeed();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaLocalEnergyMinimizer.cpp
View file @ fd473eea
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
......@@ -7,7 +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) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -30,187 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/AssertionUtilities.h"
#include "CudaPlatform.h"
#include "openmm/Context.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/LocalEnergyMinimizer.h"
#include "openmm/NonbondedForce.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/VirtualSite.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
void testHarmonicBonds() {
const int numParticles = 10;
System system;
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
// Create a chain of particles connected by harmonic bonds.
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
positions[i] = Vec3(i, 0, 0);
if (i > 0)
bonds->addBond(i-1, i, 1+0.1*i, 1);
}
// Minimize it and check that all bonds are at their equilibrium distances.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
LocalEnergyMinimizer::minimize(context, 1e-5);
State state = context.getState(State::Positions);
for (int i = 1; i < numParticles; i++) {
Vec3 delta = state.getPositions()[i]-state.getPositions()[i-1];
ASSERT_EQUAL_TOL(1+0.1*i, sqrt(delta.dot(delta)), 1e-4);
}
}
void testLargeSystem() {
const int numMolecules = 25;
const int numParticles = numMolecules*2;
const double cutoff = 2.0;
const double boxSize = 4.0;
const double tolerance = 10;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setCutoffDistance(cutoff);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
system.addForce(nonbonded);
// Create a cloud of molecules.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numMolecules; i++) {
system.addParticle(1.0);
system.addParticle(1.0);
nonbonded->addParticle(-1.0, 0.2, 0.2);
nonbonded->addParticle(1.0, 0.2, 0.2);
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
system.addConstraint(2*i, 2*i+1, 1.0);
}
// Minimize it and verify that the energy has decreased.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State initialState = context.getState(State::Forces | State::Energy);
LocalEnergyMinimizer::minimize(context, tolerance);
State finalState = context.getState(State::Forces | State::Energy | State::Positions);
ASSERT(finalState.getPotentialEnergy() < initialState.getPotentialEnergy());
// Compute the force magnitude, subtracting off any component parallel to a constraint, and
// check that it satisfies the requested tolerance.
double forceNorm = 0.0;
for (int i = 0; i < numParticles; i += 2) {
Vec3 dir = finalState.getPositions()[i+1]-finalState.getPositions()[i];
double distance = sqrt(dir.dot(dir));
dir *= 1.0/distance;
Vec3 f = finalState.getForces()[i];
f -= dir*dir.dot(f);
forceNorm += f.dot(f);
f = finalState.getForces()[i+1];
f -= dir*dir.dot(f);
forceNorm += f.dot(f);
}
forceNorm = sqrt(forceNorm/(5*numMolecules));
ASSERT(forceNorm < 2*tolerance);
}
void testVirtualSites() {
const int numMolecules = 25;
const int numParticles = numMolecules*3;
const double cutoff = 2.0;
const double boxSize = 4.0;
const double tolerance = 10;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setCutoffDistance(cutoff);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
system.addForce(nonbonded);
// Create a cloud of molecules.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numMolecules; i++) {
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
nonbonded->addParticle(-1.0, 0.2, 0.2);
nonbonded->addParticle(0.5, 0.2, 0.2);
nonbonded->addParticle(0.5, 0.2, 0.2);
positions[3*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[3*i+1] = Vec3(positions[3*i][0]+1.0, positions[3*i][1], positions[3*i][2]);
positions[3*i+2] = Vec3();
system.addConstraint(3*i, 3*i+1, 1.0);
system.setVirtualSite(3*i+2, new TwoParticleAverageSite(3*i, 3*i+1, 0.5, 0.5));
}
// Minimize it and verify that the energy has decreased.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
context.applyConstraints(1e-5);
State initialState = context.getState(State::Forces | State::Energy);
LocalEnergyMinimizer::minimize(context, tolerance);
State finalState = context.getState(State::Forces | State::Energy | State::Positions);
ASSERT(finalState.getPotentialEnergy() < initialState.getPotentialEnergy());
// Compute the force magnitude, subtracting off any component parallel to a constraint, and
// check that it satisfies the requested tolerance.
double forceNorm = 0.0;
for (int i = 0; i < numParticles; i += 3) {
Vec3 dir = finalState.getPositions()[i+1]-finalState.getPositions()[i];
double distance = sqrt(dir.dot(dir));
dir *= 1.0/distance;
Vec3 f = finalState.getForces()[i];
f -= dir*dir.dot(f);
forceNorm += f.dot(f);
f = finalState.getForces()[i+1];
f -= dir*dir.dot(f);
forceNorm += f.dot(f);
// Check the virtual site location.
ASSERT_EQUAL_VEC((finalState.getPositions()[i+1]+finalState.getPositions()[i])*0.5, finalState.getPositions()[i+2], 1e-5);
}
forceNorm = sqrt(forceNorm/(5*numMolecules));
ASSERT(forceNorm < 2*tolerance);
}
#include "CudaTests.h"
#include "TestLocalEnergyMinimizer.h"
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testHarmonicBonds();
testLargeSystem();
testVirtualSites();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaMonteCarloAnisotropicBarostat.cpp
View file @ fd473eea
......@@ -6,8 +6,8 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Authors: Peter Eastman, Lee-Ping Wang *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
......@@ -29,449 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of MonteCarloAnisotropicBarostat.
*/
#include "CudaTests.h"
#include "TestMonteCarloAnisotropicBarostat.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/MonteCarloAnisotropicBarostat.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include "SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
void testIdealGas() {
const int numParticles = 64;
const int frequency = 10;
const int steps = 1000;
const double pressure = 1.5;
const double pressureInMD = pressure*(AVOGADRO*1e-25);
const double temp[] = {300.0, 600.0, 1000.0};
const double initialVolume = numParticles*BOLTZ*temp[1]/pressureInMD;
const double initialLength = std::pow(initialVolume, 1.0/3.0);
// Create a gas of noninteracting particles.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(initialLength, 0, 0), Vec3(0, 0.5*initialLength, 0), Vec3(0, 0, 2*initialLength));
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
system.addParticle(1.0);
positions[i] = Vec3(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
}
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], true, true, true, frequency);
system.addForce(barostat);
// Test it for three different temperatures.
for (int i = 0; i < 3; i++) {
barostat->setTemperature(temp[i]);
LangevinIntegrator integrator(temp[i], 0.1, 0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the volume is correct.
double volume = 0.0;
for (int j = 0; j < steps; ++j) {
Vec3 box[3];
context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
volume += box[0][0]*box[1][1]*box[2][2];
integrator.step(frequency);
}
volume /= steps;
double expected = (numParticles+1)*BOLTZ*temp[i]/pressureInMD;
ASSERT_USUALLY_EQUAL_TOL(expected, volume, 3/std::sqrt((double) steps));
}
}
void testIdealGasAxis(int axis) {
// Test scaling just one axis.
const int numParticles = 64;
const int frequency = 10;
const int steps = 1000;
const double pressure = 1.5;
const double pressureInMD = pressure*(AVOGADRO*1e-25); // pressure in kJ/mol/nm^3
const double temp[] = {300.0, 600.0, 1000.0};
const double initialVolume = numParticles*BOLTZ*temp[1]/pressureInMD;
const double initialLength = std::pow(initialVolume, 1.0/3.0);
const bool scaleX = (axis == 0);
const bool scaleY = (axis == 1);
const bool scaleZ = (axis == 2);
double boxX;
double boxY;
double boxZ;
// Create a gas of noninteracting particles.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(initialLength, 0, 0), Vec3(0, 0.5*initialLength, 0), Vec3(0, 0, 2*initialLength));
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
system.addParticle(1.0);
positions[i] = Vec3(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
}
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], scaleX, scaleY, scaleZ, frequency);
system.addForce(barostat);
// Test it for three different temperatures.
for (int i = 0; i < 3; i++) {
barostat->setTemperature(temp[i]);
LangevinIntegrator integrator(temp[i], 0.1, 0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the volume is correct.
double volume = 0.0;
for (int j = 0; j < steps; ++j) {
Vec3 box[3];
context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
boxX = box[0][0];
boxY = box[1][1];
boxZ = box[2][2];
volume += box[0][0]*box[1][1]*box[2][2];
integrator.step(frequency);
}
volume /= steps;
double expected = (numParticles+1)*BOLTZ*temp[i]/pressureInMD;
ASSERT_USUALLY_EQUAL_TOL(expected, volume, 3/std::sqrt((double) steps));
if (!scaleX) {
ASSERT(boxX == initialLength);
}
if (!scaleY) {
ASSERT(boxY == 0.5*initialLength);
}
if (!scaleZ) {
ASSERT(boxZ == 2*initialLength);
}
}
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
const double pressure = 1.5;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(8, 0, 0), Vec3(0, 8, 0), Vec3(0, 0, 8));
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, true, true, true, 1);
system.addForce(barostat);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(0, 0, 0);
}
// Try twice with the same random seed.
barostat->setRandomNumberSeed(5);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state1 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state2 = context.getState(State::Positions);
// Try twice with a different random seed.
barostat->setRandomNumberSeed(10);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state3 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state4 = context.getState(State::Positions);
// Compare the results.
for (int i = 0; i < numParticles; i++) {
for (int j = 0; j < 3; j++) {
ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
ASSERT(state3.getPositions()[i][j] == state4.getPositions()[i][j]);
ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
}
}
}
void testTriclinic() {
const int numParticles = 64;
const int frequency = 10;
const int steps = 1000;
const double pressure = 1.5;
const double pressureInMD = pressure*(AVOGADRO*1e-25); // pressure in kJ/mol/nm^3
const double temperature = 300.0;
const double initialVolume = numParticles*BOLTZ*temperature/pressureInMD;
const double initialLength = std::pow(initialVolume, 1.0/3.0);
// Create a gas of noninteracting particles.
System system;
Vec3 initialBox[3];
initialBox[0] = Vec3(initialLength, 0, 0);
initialBox[1] = Vec3(0.2*initialLength, initialLength, 0);
initialBox[2] = Vec3(0.1*initialLength, 0.3*initialLength, initialLength);
system.setDefaultPeriodicBoxVectors(initialBox[0], initialBox[1], initialBox[2]);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
system.addParticle(1.0);
positions[i] = Vec3(initialLength*genrand_real2(sfmt), initialLength*genrand_real2(sfmt), initialLength*genrand_real2(sfmt));
}
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temperature, true, true, true, frequency);
system.addForce(barostat);
// Run a simulation
LangevinIntegrator integrator(temperature, 0.1, 0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the volume is correct.
double volume = 0.0;
for (int j = 0; j < steps; ++j) {
Vec3 box[3];
context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
volume += box[0][0]*box[1][1]*box[2][2];
integrator.step(frequency);
}
volume /= steps;
double expected = (numParticles+1)*BOLTZ*temperature/pressureInMD;
ASSERT_USUALLY_EQUAL_TOL(expected, volume, 3/std::sqrt((double) steps));
// Make sure the box vectors have been scaled consistently.
State state = context.getState(State::Positions);
Vec3 box[3];
state.getPeriodicBoxVectors(box[0], box[1], box[2]);
double xscale = box[2][0]/(0.1*initialLength);
double yscale = box[2][1]/(0.3*initialLength);
double zscale = box[2][2]/(1.0*initialLength);
for (int i = 0; i < 3; i++) {
ASSERT_EQUAL_VEC(Vec3(xscale*initialBox[i][0], yscale*initialBox[i][1], zscale*initialBox[i][2]), box[i], 1e-5);
}
// The barostat should have put all particles inside the first periodic box. One integration step
// has happened since then, so they may have moved slightly outside it.
for (int i = 0; i < numParticles; i++) {
Vec3 pos = state.getPositions()[i];
ASSERT(pos[2]/box[2][2] > -1 && pos[2]/box[2][2] < 2);
pos -= box[2]*floor(pos[2]/box[2][2]);
ASSERT(pos[1]/box[1][1] > -1 && pos[1]/box[1][1] < 2);
pos -= box[1]*floor(pos[1]/box[1][1]);
ASSERT(pos[0]/box[0][0] > -1 && pos[0]/box[0][0] < 2);
}
}
/**
* Run a constant pressure simulation on an anisotropic Einstein crystal
* using isotropic and anisotropic barostats. There are a total of 15 simulations:
*
* 1) 3 pressures: 9.0, 10.0, 11.0 bar, for each of the following groups:
* 2) 3 groups of simulations that scale just one axis: x, y, z
* 3) 1 group of simulations that scales all three axes in the anisotropic barostat
* 4) 1 group of simulations that scales all three axes in the isotropic barostat
*
* Results that we will check:
*
* a) In each group of simulations, the volume should decrease with increasing pressure
* b) In the three simulation groups that scale just one axis, the compressibility (i.e. incremental volume change
* with increasing pressure) should go like kx > ky > kz (because the spring constant is largest in the z-direction)
* c) The anisotropic barostat should produce the same result as the isotropic barostat when all three axes are scaled
*/
void testEinsteinCrystal() {
const int numParticles = 64;
const int frequency = 2;
const int equil = 10000;
const int steps = 5000;
const double pressure = 10.0;
const double pressureInMD = pressure*(AVOGADRO*1e-25); // pressure in kJ/mol/nm^3
const double temp = 300.0; // Only test one temperature since we're looking at three pressures.
const double pres3[] = {2.0, 8.0, 15.0};
const double initialVolume = numParticles*BOLTZ*temp/pressureInMD;
const double initialLength = std::pow(initialVolume, 1.0/3.0);
vector<double> initialPositions(3);
vector<double> results;
// Run four groups of anisotropic simulations; scaling just x, y, z, then all three.
for (int a = 0; a < 4; a++) {
// Test barostat for three different pressures.
for (int p = 0; p < 3; p++) {
// Create a system of noninteracting particles attached by harmonic springs to their initial positions.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(initialLength, 0, 0), Vec3(0, initialLength, 0), Vec3(0, 0, initialLength));
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
// Anisotropic force constants.
CustomExternalForce* force = new CustomExternalForce("0.005*(x-x0)^2 + 0.01*(y-y0)^2 + 0.02*(z-z0)^2");
force->addPerParticleParameter("x0");
force->addPerParticleParameter("y0");
force->addPerParticleParameter("z0");
NonbondedForce* nb = new NonbondedForce();
nb->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
for (int i = 0; i < numParticles; ++i) {
system.addParticle(1.0);
positions[i] = Vec3(((i/16)%4+0.5)*initialLength/4, ((i/4)%4+0.5)*initialLength/4, (i%4+0.5)*initialLength/4);
initialPositions[0] = positions[i][0];
initialPositions[1] = positions[i][1];
initialPositions[2] = positions[i][2];
force->addParticle(i, initialPositions);
nb->addParticle(0, initialLength/6, 0.1);
}
system.addForce(force);
system.addForce(nb);
// Create the barostat.
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pres3[p], pres3[p], pres3[p]), temp, (a==0||a==3), (a==1||a==3), (a==2||a==3), frequency);
system.addForce(barostat);
barostat->setTemperature(temp);
LangevinIntegrator integrator(temp, 0.1, 0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
// Let it equilibrate.
integrator.step(equil);
// Now run it for a while and see if the volume is correct.
double volume = 0.0;
for (int j = 0; j < steps; ++j) {
Vec3 box[3];
context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
volume += box[0][0]*box[1][1]*box[2][2];
integrator.step(frequency);
}
volume /= steps;
results.push_back(volume);
}
}
for (int p = 0; p < 3; p++) {
// Create a system of noninteracting particles attached by harmonic springs to their initial positions.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(initialLength, 0, 0), Vec3(0, initialLength, 0), Vec3(0, 0, initialLength));
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
// Anisotropic force constants.
CustomExternalForce* force = new CustomExternalForce("0.005*(x-x0)^2 + 0.01*(y-y0)^2 + 0.02*(z-z0)^2");
force->addPerParticleParameter("x0");
force->addPerParticleParameter("y0");
force->addPerParticleParameter("z0");
NonbondedForce* nb = new NonbondedForce();
nb->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
for (int i = 0; i < numParticles; ++i) {
system.addParticle(1.0);
positions[i] = Vec3(((i/16)%4+0.5)*initialLength/4, ((i/4)%4+0.5)*initialLength/4, (i%4+0.5)*initialLength/4);
initialPositions[0] = positions[i][0];
initialPositions[1] = positions[i][1];
initialPositions[2] = positions[i][2];
force->addParticle(i, initialPositions);
nb->addParticle(0, initialLength/6, 0.1);
}
system.addForce(force);
system.addForce(nb);
// Create the barostat.
MonteCarloBarostat* barostat = new MonteCarloBarostat(pres3[p], temp, frequency);
system.addForce(barostat);
barostat->setTemperature(temp);
LangevinIntegrator integrator(temp, 0.1, 0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
// Let it equilibrate.
integrator.step(equil);
// Now run it for a while and see if the volume is correct.
double volume = 0.0;
for (int j = 0; j < steps; ++j) {
Vec3 box[3];
context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
volume += box[0][0]*box[1][1]*box[2][2];
integrator.step(frequency);
}
volume /= steps;
results.push_back(volume);
}
// Check to see if volumes decrease with increasing pressure.
ASSERT_USUALLY_TRUE(results[0] > results[1]);
ASSERT_USUALLY_TRUE(results[1] > results[2]);
ASSERT_USUALLY_TRUE(results[3] > results[4]);
ASSERT_USUALLY_TRUE(results[4] > results[5]);
ASSERT_USUALLY_TRUE(results[6] > results[7]);
ASSERT_USUALLY_TRUE(results[7] > results[8]);
// Check to see if incremental volume changes with increasing pressure go like kx > ky > kz.
ASSERT_USUALLY_TRUE((results[0] - results[1]) > (results[3] - results[4]));
ASSERT_USUALLY_TRUE((results[1] - results[2]) > (results[4] - results[5]));
ASSERT_USUALLY_TRUE((results[3] - results[4]) > (results[6] - results[7]));
ASSERT_USUALLY_TRUE((results[4] - results[5]) > (results[7] - results[8]));
// Check to see if the volumes are equal for isotropic and anisotropic (all axis).
ASSERT_USUALLY_EQUAL_TOL(results[9], results[12], 3/std::sqrt((double) steps));
ASSERT_USUALLY_EQUAL_TOL(results[10], results[13], 3/std::sqrt((double) steps));
ASSERT_USUALLY_EQUAL_TOL(results[11], results[14], 3/std::sqrt((double) steps));
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testIdealGas();
testIdealGasAxis(0);
testIdealGasAxis(1);
testIdealGasAxis(2);
testRandomSeed();
testTriclinic();
//testEinsteinCrystal();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
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