Skip to content

GitLab

Commit a5a368d0 authored by Peter Eastman's avatar Peter Eastman
Browse files

Bug fixes

parent b5eda392
Show whitespace changes
Inline Side-by-side
Showing with 15 additions and 17 deletions
openmmapi/src/NonbondedForceImpl.cpp
View file @ a5a368d0
......@@ -119,7 +119,7 @@ void NonbondedForceImpl::calcEwaldParameters(const System& system, const Nonbond
Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double tol = force.getEwaldErrorTolerance();
alpha = (1.0/force.getCutoffDistance())*std::sqrt(-log(0.5*tol));
alpha = (1.0/force.getCutoffDistance())*std::sqrt(-log(2.0*tol));
kmaxx = findZero(EwaldErrorFunction(boxVectors[0][0], alpha, tol), 10);
kmaxy = findZero(EwaldErrorFunction(boxVectors[1][1], alpha, tol), 10);
kmaxz = findZero(EwaldErrorFunction(boxVectors[2][2], alpha, tol), 10);
......
platforms/reference/tests/TestReferenceEwald.cpp
View file @ a5a368d0
......@@ -48,8 +48,8 @@
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
const double EWALD_TOL = 1e-5;
const double PME_TOL = 5e-5;
void testEwaldExact() {
......@@ -75,7 +75,7 @@ void testEwaldExact() {
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
nonbonded->setCutoffDistance(cutoff);
system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setEwaldErrorTolerance(TOL);
nonbonded->setEwaldErrorTolerance(EWALD_TOL);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......@@ -98,7 +98,7 @@ void testEwaldExact() {
double exactEnergy = - (1.7476 * 1.6022e-19 * 1.6022e-19 * 6.02214e+23 * numParticles) / (1.112e-10 * 0.282e-9 * 2 * 1000);
//cout << "exact\t\t: " << exactEnergy << endl;
//cout << "calc\t\t: " << state.getPotentialEnergy() << endl;
ASSERT_EQUAL_TOL(exactEnergy, state.getPotentialEnergy(), 100*TOL);
ASSERT_EQUAL_TOL(exactEnergy, state.getPotentialEnergy(), 100*EWALD_TOL);
}
......@@ -127,7 +127,7 @@ void testEwaldPME() {
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
nonbonded->setCutoffDistance(cutoff);
system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setEwaldErrorTolerance(TOL);
nonbonded->setEwaldErrorTolerance(EWALD_TOL);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......@@ -160,7 +160,7 @@ void testEwaldPME() {
norm = std::sqrt(norm);
const double delta = 1e-3;
const double delta = 1e-2;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
......@@ -171,13 +171,13 @@ void testEwaldPME() {
// See whether the potential energy changed by the expected amount.
tol = 1e-2;
State state2 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state1.getPotentialEnergy())/delta, tol)
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state1.getPotentialEnergy())/delta, fabs(EWALD_TOL*state2.getPotentialEnergy()/(state2.getPotentialEnergy()-state1.getPotentialEnergy())))
// (4) CHECK EXACT VALUE OF PME ENERGY
nonbonded->setNonbondedMethod(NonbondedForce::PME);
nonbonded->setEwaldErrorTolerance(PME_TOL);
context.reinitialize();
#include "nacl_amorph.dat"
context.setPositions(positions);
......@@ -213,9 +213,7 @@ void testEwaldPME() {
// See whether the potential energy changed by the expected amount.
State state4 = context.getState(State::Energy);
tol = 1e-2;
ASSERT_EQUAL_TOL(norm, (state4.getPotentialEnergy()-state3.getPotentialEnergy())/delta, tol)
ASSERT_EQUAL_TOL(norm, (state4.getPotentialEnergy()-state3.getPotentialEnergy())/delta, fabs(PME_TOL*state4.getPotentialEnergy()/(state4.getPotentialEnergy()-state3.getPotentialEnergy())))
}
void testEwald2Ions() {
......@@ -231,7 +229,7 @@ void testEwald2Ions() {
const double cutoff = 2.0;
nonbonded->setCutoffDistance(cutoff);
system.setPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
nonbonded->setEwaldErrorTolerance(TOL);
nonbonded->setEwaldErrorTolerance(EWALD_TOL);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -240,9 +238,9 @@ void testEwald2Ions() {
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(), 10*TOL);
ASSERT_EQUAL_VEC(Vec3(-123.711, 64.1877, -302.716), forces[0], 10*EWALD_TOL);
ASSERT_EQUAL_VEC(Vec3(123.711, -64.1877, 302.716), forces[1], 10*EWALD_TOL);
ASSERT_EQUAL_TOL(-217.276, state.getPotentialEnergy(), 10*EWALD_TOL);
}
void testWaterSystem() {
......@@ -267,7 +265,7 @@ void testWaterSystem() {
const double cutoff = 0.8;
nonbonded->setCutoffDistance(cutoff);
system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setEwaldErrorTolerance(TOL);
nonbonded->setEwaldErrorTolerance(EWALD_TOL);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment