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Commit 6b0b0a26 authored by Rossen Apostolov's avatar Rossen Apostolov
Browse files

New test systems for Ewald/PME methods.

parent 537221a0
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platforms/cuda/tests/TestCudaEwald.cpp
View file @ 6b0b0a26
......@@ -57,10 +57,10 @@ void testEwaldPME() {
// Use amorphous NaCl system for the tests
const int numParticles = 216;
const double cutoff = 0.8;
const double boxSize = 1.86206;
const double tol = 0.001;
const int numParticles = 894;
const double cutoff = 1.2;
const double boxSize = 3.00646;
double tol = 1e-5;
CudaPlatform cuda;
ReferencePlatform reference;
......@@ -93,10 +93,12 @@ void testEwaldPME() {
referenceContext.setPositions(positions);
State cudaState = cudaContext.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(cudaState.getForces()[i], referenceState.getForces()[i], tol);
ASSERT_EQUAL_VEC(referenceState.getForces()[i], cudaState.getForces()[i], tol);
}
ASSERT_EQUAL_TOL(cudaState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
tol = 1e-5;
ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cudaState.getPotentialEnergy(), tol);
// (2) Check whether Ewald method in Cuda is self-consistent
......@@ -117,6 +119,7 @@ void testEwaldPME() {
Context cudaContext2(system, integrator, cuda);
cudaContext2.setPositions(positions);
tol = 1e-4;
State cudaState2 = cudaContext2.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (cudaState2.getPotentialEnergy()-cudaState.getPotentialEnergy())/delta, tol)
......@@ -129,10 +132,12 @@ void testEwaldPME() {
referenceContext.setPositions(positions);
cudaState = cudaContext.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(cudaState.getForces()[i], referenceState.getForces()[i], tol);
ASSERT_EQUAL_VEC(referenceState.getForces()[i], cudaState.getForces()[i], tol);
}
ASSERT_EQUAL_TOL(cudaState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
tol = 1e-5;
ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cudaState.getPotentialEnergy(), tol);
// (4) Check whether PME method in Cuda is self-consistent
......@@ -152,6 +157,7 @@ void testEwaldPME() {
Context cudaContext3(system, integrator, cuda);
cudaContext3.setPositions(positions);
tol = 1e-4;
State cudaState3 = cudaContext3.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (cudaState3.getPotentialEnergy()-cudaState.getPotentialEnergy())/delta, tol)
......
platforms/cuda/tests/nacl_amorph.dat
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platforms/reference/tests/TestReferenceEwald.cpp
View file @ 6b0b0a26
......@@ -96,19 +96,20 @@ void testEwaldExact() {
// E has to be divided by 2 (per ion), multiplied by N(avogadro), multiplied by number of particles, and divided by 1000 for kJ
double exactEnergy = - (1.7476 * 1.6022e-19 * 1.6022e-19 * 6.02214e+23 * numParticles) / (1.112e-10 * 0.282e-9 * 2 * 1000);
ASSERT_EQUAL_TOL(exactEnergy, state.getPotentialEnergy(), 100*TOL);
// cout << "exactEnergy: " << exactEnergy << endl;
// cout << "PotentialEnergy: " << state.getPotentialEnergy() << endl;
}
void testEwaldPME() {
double tol = 1e-5;
const double boxSize = 3.00646;
const double cutoff = 1.2;
const int numParticles = 894;
// Use amorphous NaCl system
// The particles are simple charges, no VdW interactions
ReferencePlatform platform;
const int numParticles = 216;
System system;
for (int i = 0; i < numParticles/2; i++)
system.addParticle(22.99);
......@@ -121,9 +122,8 @@ void testEwaldPME() {
for (int i = 0; i < numParticles/2; i++)
nonbonded->addParticle(-1.0, 1.0,0.0);
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
const double cutoff = 0.8;
nonbonded->setCutoffDistance(cutoff);
system.setPeriodicBoxVectors(Vec3(1.86206, 0, 0), Vec3(0, 1.86206, 0), Vec3(0, 0, 1.86206));
system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setEwaldErrorTolerance(TOL);
system.addForce(nonbonded);
Context context(system, integrator, platform);
......@@ -134,21 +134,19 @@ void testEwaldPME() {
State state1 = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces1 = state1.getForces();
// for (int i = 0 ; i < numParticles ; i++)
// cout << "f [" << i << " : ]" << forces1[i] << endl;
// (1) CHECK EXACT VALUE OF EWALD ENERGY (Against Gromacs output)
tol = 1e-5;
ASSERT_EQUAL_TOL(-36687.5, state1.getPotentialEnergy(), tol);
ASSERT_EQUAL_TOL(-3.82047e+05, state1.getPotentialEnergy(), tol);
// (2) CHECK WHETHER THE EWALD FORCES ARE THE SAME AS THE GROMACS OUTPUT
tol = 1e-3;
tol = 1e-1;
#include "nacl_amorph_GromacsForcesEwald.dat"
// (3) CHECK SELF-CONSISTENCY
// Take a small step in the direction of the energy gradient.
// Take a small step in the direction of the energy gradient.
double norm = 0.0;
for (int i = 0; i < numParticles; ++i) {
......@@ -169,7 +167,7 @@ void testEwaldPME() {
// See whether the potential energy changed by the expected amount.
tol = 1e-4;
tol = 1e-2;
State state2 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state1.getPotentialEnergy())/delta, tol)
......@@ -180,21 +178,23 @@ void testEwaldPME() {
#include "nacl_amorph.dat"
context.setPositions(positions);
State state3 = context.getState(State::Forces | State::Energy);
tol = 1e-5;
// Gromacs PME energy for the same mesh
ASSERT_EQUAL_TOL(-36688.3, state3.getPotentialEnergy(), tol);
tol = 1e-5;
ASSERT_EQUAL_TOL(-3.82047e+05, state3.getPotentialEnergy(), tol);
// Gromacs Ewald energy
tol = 1e-4;
ASSERT_EQUAL_TOL(-36687.5, state3.getPotentialEnergy(), tol);
tol = 1e-5;
ASSERT_EQUAL_TOL(-3.82047e+05, state3.getPotentialEnergy(), tol);
// (5) CHECK WHETHER PME FORCES ARE THE SAME AS THE GROMACS OUTPUT
tol = 1e-3;
#include "nacl_amorph_GromacsForcesEwald.dat"
tol = 1e-1;
#include "nacl_amorph_GromacsForcesPME.dat"
// (6) CHECK PME FOR SELF-CONSISTENCY
// Take a small step in the direction of the energy gradient.
// Take a small step in the direction of the energy gradient.
norm = 0.0;
for (int i = 0; i < numParticles; ++i) {
......@@ -213,7 +213,7 @@ void testEwaldPME() {
// See whether the potential energy changed by the expected amount.
State state4 = context.getState(State::Energy);
tol = 1e-4;
tol = 1e-2;
ASSERT_EQUAL_TOL(norm, (state4.getPotentialEnergy()-state3.getPotentialEnergy())/delta, tol)
}
......@@ -248,8 +248,9 @@ void testEwald2Ions() {
void testWaterSystem() {
ReferencePlatform platform;
System system;
static int numParticles;
numParticles = 648;
static int numParticles = 648;
const double boxSize = 1.86206;
for (int i = 0 ; i < numParticles ; i++)
{
system.addParticle(1.0);
......@@ -265,7 +266,7 @@ void testWaterSystem() {
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
const double cutoff = 0.8;
nonbonded->setCutoffDistance(cutoff);
system.setPeriodicBoxVectors(Vec3(1.86206, 0, 0), Vec3(0, 1.86206, 0), Vec3(0, 0, 1.86206));
system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setEwaldErrorTolerance(TOL);
system.addForce(nonbonded);
Context context(system, integrator, platform);
......@@ -274,9 +275,6 @@ void testWaterSystem() {
context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state1.getForces();
// for (int i = 0 ; i < 42 ; i++)
// cout << "f [" << i << " : ]" << forces[i] << endl;
// cout << "PotentialEnergy: " << state1.getPotentialEnergy() << endl;
// Take a small step in the direction of the energy gradient.
......
platforms/reference/tests/nacl_amorph.dat
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platforms/reference/tests/nacl_amorph_GromacsForcesPME.dat 0 → 100644
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