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Commit 511f3c3b authored by Lee-Ping Wang's avatar Lee-Ping Wang
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Implemented unit tests for MonteCarloAnisotropicBarostat

parent a4cfb127
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openmmapi/src/MonteCarloAnisotropicBarostatImpl.cpp
View file @ 511f3c3b
......@@ -91,6 +91,7 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureZ())*(AVOGADRO*1e-25);
break;
}
rnd = genrand_real2(random)*3.0;
}
// Modify the periodic box size.
......
platforms/cuda/tests/TestCudaMonteCarloAnisotropicBarostat.cpp
View file @ 511f3c3b
......@@ -30,11 +30,10 @@
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of MonteCarloBarostat.
* This tests the CUDA implementation of MonteCarloAnisotropicBarostat.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/MonteCarloAnisotropicBarostat.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
......@@ -90,7 +89,7 @@ void testChangingBoxSize() {
ASSERT(ok);
}
void testIdealGas(int aniso) {
void testIdealGas() {
const int numParticles = 64;
const int frequency = 10;
const int steps = 1000;
......@@ -111,8 +110,6 @@ void testIdealGas(int aniso) {
system.addParticle(1.0);
positions[i] = Vec3(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
}
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency);
if (aniso)
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
system.addForce(barostat);
......@@ -135,15 +132,81 @@ void testIdealGas(int aniso) {
Vec3 box[3];
context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
volume += box[0][0]*box[1][1]*box[2][2];
if (!aniso) {
ASSERT_EQUAL_TOL(0.5*box[0][0], box[1][1], 1e-5);
ASSERT_EQUAL_TOL(2*box[0][0], box[2][2], 1e-5);
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], frequency, scaleX, scaleY, scaleZ);
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);
}
}
}
......@@ -161,7 +224,7 @@ void testRandomSeed() {
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, 1);
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, 1);
system.addForce(barostat);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
......@@ -209,31 +272,23 @@ void testRandomSeed() {
}
}
void testWater(int aniso) {
const int gridSize = 8;
const int numMolecules = gridSize*gridSize*gridSize;
void testIce() {
const int numMolecules = 432;
const int frequency = 10;
const int steps = 400;
const double temp = 273.15;
const double pressure = 3;
const double spacing = 0.32;
const double angle = 109.47*M_PI/180;
const double dOH = 0.1;
const double dHH = dOH*2*std::sin(0.5*angle);
// Create a box of SPC water molecules.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(gridSize*spacing, 0, 0), Vec3(0, gridSize*spacing, 0), Vec3(0, 0, gridSize*spacing));
system.setDefaultPeriodicBoxVectors(Vec3(2.7042, 0, 0), Vec3(0, 2.3419, 0), Vec3(0, 0, 2.2080));
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
nonbonded->setUseDispersionCorrection(true);
vector<Vec3> positions;
Vec3 offset1(dOH, 0, 0);
Vec3 offset2(dOH*std::cos(angle), dOH*std::sin(angle), 0);
for (int i = 0; i < gridSize; ++i) {
for (int j = 0; j < gridSize; ++j) {
for (int k = 0; k < gridSize; ++k) {
for (int i = 0; i < numMolecules; ++i) {
int firstParticle = system.getNumParticles();
system.addParticle(16.0);
system.addParticle(1.0);
......@@ -241,10 +296,6 @@ void testWater(int aniso) {
nonbonded->addParticle(-0.82, 0.316557, 0.650194);
nonbonded->addParticle(0.41, 1, 0);
nonbonded->addParticle(0.41, 1, 0);
Vec3 pos = Vec3(spacing*i, spacing*j, spacing*k);
positions.push_back(pos);
positions.push_back(pos+offset1);
positions.push_back(pos+offset2);
system.addConstraint(firstParticle, firstParticle+1, dOH);
system.addConstraint(firstParticle, firstParticle+2, dOH);
system.addConstraint(firstParticle+1, firstParticle+2, dHH);
......@@ -252,11 +303,9 @@ void testWater(int aniso) {
nonbonded->addException(firstParticle, firstParticle+2, 0, 1, 0);
nonbonded->addException(firstParticle+1, firstParticle+2, 0, 1, 0);
}
}
}
vector<Vec3> positions(system.getNumParticles());
#include "ice_ih.dat"
system.addForce(nonbonded);
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, frequency);
if (aniso)
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, frequency);
system.addForce(barostat);
......@@ -275,7 +324,7 @@ void testWater(int aniso) {
}
volume /= steps;
double density = numMolecules*18/(AVOGADRO*volume*1e-21);
ASSERT_USUALLY_EQUAL_TOL(1.0, density, 0.02);
ASSERT_USUALLY_EQUAL_TOL(0.913, density, 0.02);
}
int main(int argc, char* argv[]) {
......@@ -283,11 +332,12 @@ int main(int argc, char* argv[]) {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testChangingBoxSize();
testIdealGas(0);
testIdealGas(1);
testIdealGas();
testIdealGasAxis(0);
testIdealGasAxis(1);
testIdealGasAxis(2);
testRandomSeed();
testWater(0);
testWater(1);
testIce();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/cuda/tests/ice_ih.dat 0 → 100644
View file @ 511f3c3b
This diff is collapsed.
platforms/opencl/tests/TestOpenCLMonteCarloAnisotropicBarostat.cpp
View file @ 511f3c3b
......@@ -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) 2008-2010 Stanford University and the Authors. *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -30,11 +30,10 @@
* -------------------------------------------------------------------------- */
/**
* This tests the OpenCL implementation of MonteCarloBarostat.
* This tests the OpenCL implementation of MonteCarloAnisotropicBarostat.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/MonteCarloAnisotropicBarostat.h"
#include "openmm/Context.h"
#include "OpenCLPlatform.h"
......@@ -90,7 +89,7 @@ void testChangingBoxSize() {
ASSERT(ok);
}
void testIdealGas(int aniso) {
void testIdealGas() {
const int numParticles = 64;
const int frequency = 10;
const int steps = 1000;
......@@ -111,8 +110,6 @@ void testIdealGas(int aniso) {
system.addParticle(1.0);
positions[i] = Vec3(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
}
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency);
if (aniso)
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
system.addForce(barostat);
......@@ -135,18 +132,81 @@ void testIdealGas(int aniso) {
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));
}
}
// Ratios will only be correct if box deformations are isotropic.
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;
if (!aniso) {
ASSERT_EQUAL_TOL(0.5*box[0][0], box[1][1], 1e-5);
ASSERT_EQUAL_TOL(2*box[0][0], box[2][2], 1e-5);
// 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], frequency, scaleX, scaleY, scaleZ);
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);
}
}
}
......@@ -164,7 +224,7 @@ void testRandomSeed() {
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, 1);
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, 1);
system.addForce(barostat);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
......@@ -212,31 +272,23 @@ void testRandomSeed() {
}
}
void testWater(int aniso) {
const int gridSize = 8;
const int numMolecules = gridSize*gridSize*gridSize;
void testIce() {
const int numMolecules = 432;
const int frequency = 10;
const int steps = 400;
const double temp = 273.15;
const double pressure = 3;
const double spacing = 0.32;
const double angle = 109.47*M_PI/180;
const double dOH = 0.1;
const double dHH = dOH*2*std::sin(0.5*angle);
// Create a box of SPC water molecules.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(gridSize*spacing, 0, 0), Vec3(0, gridSize*spacing, 0), Vec3(0, 0, gridSize*spacing));
system.setDefaultPeriodicBoxVectors(Vec3(2.7042, 0, 0), Vec3(0, 2.3419, 0), Vec3(0, 0, 2.2080));
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
nonbonded->setUseDispersionCorrection(true);
vector<Vec3> positions;
Vec3 offset1(dOH, 0, 0);
Vec3 offset2(dOH*std::cos(angle), dOH*std::sin(angle), 0);
for (int i = 0; i < gridSize; ++i) {
for (int j = 0; j < gridSize; ++j) {
for (int k = 0; k < gridSize; ++k) {
for (int i = 0; i < numMolecules; ++i) {
int firstParticle = system.getNumParticles();
system.addParticle(16.0);
system.addParticle(1.0);
......@@ -244,10 +296,6 @@ void testWater(int aniso) {
nonbonded->addParticle(-0.82, 0.316557, 0.650194);
nonbonded->addParticle(0.41, 1, 0);
nonbonded->addParticle(0.41, 1, 0);
Vec3 pos = Vec3(spacing*i, spacing*j, spacing*k);
positions.push_back(pos);
positions.push_back(pos+offset1);
positions.push_back(pos+offset2);
system.addConstraint(firstParticle, firstParticle+1, dOH);
system.addConstraint(firstParticle, firstParticle+2, dOH);
system.addConstraint(firstParticle+1, firstParticle+2, dHH);
......@@ -255,11 +303,9 @@ void testWater(int aniso) {
nonbonded->addException(firstParticle, firstParticle+2, 0, 1, 0);
nonbonded->addException(firstParticle+1, firstParticle+2, 0, 1, 0);
}
}
}
vector<Vec3> positions(system.getNumParticles());
#include "ice_ih.dat"
system.addForce(nonbonded);
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, frequency);
if (aniso)
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, frequency);
system.addForce(barostat);
......@@ -278,7 +324,7 @@ void testWater(int aniso) {
}
volume /= steps;
double density = numMolecules*18/(AVOGADRO*volume*1e-21);
ASSERT_USUALLY_EQUAL_TOL(1.0, density, 0.02);
ASSERT_USUALLY_EQUAL_TOL(0.913, density, 0.02);
}
int main(int argc, char* argv[]) {
......@@ -286,11 +332,12 @@ int main(int argc, char* argv[]) {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testChangingBoxSize();
testIdealGas(0);
testIdealGas(1);
testIdealGas();
testIdealGasAxis(0);
testIdealGasAxis(1);
testIdealGasAxis(2);
testRandomSeed();
testWater(0);
testWater(1);
testIce();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......@@ -299,5 +346,3 @@ int main(int argc, char* argv[]) {
cout << "Done" << endl;
return 0;
}
platforms/opencl/tests/ice_ih.dat 0 → 100644
View file @ 511f3c3b
This diff is collapsed.
platforms/reference/tests/TestReferenceMonteCarloAnisotropicBarostat.cpp
View file @ 511f3c3b
......@@ -110,7 +110,7 @@ void testIdealGas() {
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(pressure, pressure, pressure, temp[0], frequency);
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
system.addForce(barostat);
// Test it for three different temperatures.
......@@ -140,6 +140,77 @@ void testIdealGas() {
}
}
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.
ReferencePlatform platform;
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], frequency, scaleX, scaleY, scaleZ);
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;
......@@ -155,7 +226,7 @@ void testRandomSeed() {
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(pressure, temp, 1);
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, 1);
system.addForce(barostat);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
......@@ -206,6 +277,9 @@ void testRandomSeed() {
int main() {
try {
testIdealGas();
testIdealGasAxis(0);
testIdealGasAxis(1);
testIdealGasAxis(2);
testRandomSeed();
}
catch(const exception& e) {
......
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