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Commit a9c75e52 authored by peastman's avatar peastman
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Merge pull request #776 from peastman/bug 

Fixed bug in reference CustomCompoundBondForce
parents c66e086e 5ae844b2
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platforms/cuda/tests/TestCudaCustomCompoundBondForce.cpp
View file @ a9c75e52
......@@ -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 Stanford University and the Authors. *
* Portions copyright (c) 2012-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -152,21 +152,21 @@ void testPositionDependence() {
custom->addGlobalParameter("scale1", 0.3);
custom->addGlobalParameter("scale2", 0.2);
vector<int> particles(2);
particles[0] = 0;
particles[1] = 1;
particles[0] = 1;
particles[1] = 0;
vector<double> parameters;
custom->addBond(particles, parameters);
customSystem.addForce(custom);
vector<Vec3> positions(2);
positions[0] = Vec3(0.5, 1, 0);
positions[1] = Vec3(1.5, 1, 0);
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(0.3-0.2, 0, 0), state.getForces()[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(-0.3, -2, 0), state.getForces()[1], 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);
}
void testParallelComputation() {
......
platforms/opencl/tests/TestOpenCLCustomCompoundBondForce.cpp
View file @ a9c75e52
......@@ -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 Stanford University and the Authors. *
* Portions copyright (c) 2012-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -152,21 +152,21 @@ void testPositionDependence() {
custom->addGlobalParameter("scale1", 0.3);
custom->addGlobalParameter("scale2", 0.2);
vector<int> particles(2);
particles[0] = 0;
particles[1] = 1;
particles[0] = 1;
particles[1] = 0;
vector<double> parameters;
custom->addBond(particles, parameters);
customSystem.addForce(custom);
vector<Vec3> positions(2);
positions[0] = Vec3(0.5, 1, 0);
positions[1] = Vec3(1.5, 1, 0);
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(0.3-0.2, 0, 0), state.getForces()[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(-0.3, -2, 0), state.getForces()[1], 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);
}
void testParallelComputation() {
......
platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp
View file @ a9c75e52
/* Portions copyright (c) 2009-2010 Stanford University and Simbios.
/* Portions copyright (c) 2009-2015 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -127,7 +127,7 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
const vector<int>& atoms = bondAtoms[bond];
for (int i = 0; i < (int) particleTerms.size(); i++) {
const ParticleTermInfo& term = particleTerms[i];
variables[term.name] = atomCoordinates[term.atom][term.component];
variables[term.name] = atomCoordinates[atoms[term.atom]][term.component];
}
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
......
platforms/reference/tests/TestReferenceCustomCompoundBondForce.cpp
View file @ a9c75e52
......@@ -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 Stanford University and the Authors. *
* Portions copyright (c) 2012-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -155,21 +155,21 @@ void testPositionDependence() {
custom->addGlobalParameter("scale1", 0.3);
custom->addGlobalParameter("scale2", 0.2);
vector<int> particles(2);
particles[0] = 0;
particles[1] = 1;
particles[0] = 1;
particles[1] = 0;
vector<double> parameters;
custom->addBond(particles, parameters);
customSystem.addForce(custom);
vector<Vec3> positions(2);
positions[0] = Vec3(0.5, 1, 0);
positions[1] = Vec3(1.5, 1, 0);
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(0.3-0.2, 0, 0), state.getForces()[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(-0.3, -2, 0), state.getForces()[1], 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);
}
void testContinuous2DFunction() {
......
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