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Commit 5d9fc98b authored by peastman's avatar peastman
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Finished CUDA version of CustomCentroidBondForce

parent 4d823b0a
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Showing with 83 additions and 14 deletions
platforms/cuda/src/CudaKernels.cpp
View file @ 5d9fc98b
......@@ -4252,16 +4252,34 @@ public:
}
void getParticlesInGroup(int index, vector<int>& particles) {
vector<double> parameters;
force.getBondParameters(index, particles, parameters);
vector<int> groups;
force.getBondParameters(index, groups, parameters);
for (int i = 0; i < groups.size(); i++) {
vector<int> groupParticles;
vector<double> weights;
force.getGroupParameters(groups[i], groupParticles, weights);
particles.insert(particles.end(), groupParticles.begin(), groupParticles.end());
}
}
bool areGroupsIdentical(int group1, int group2) {
vector<int> particles;
vector<int> groups1, groups2;
vector<double> parameters1, parameters2;
force.getBondParameters(group1, particles, parameters1);
force.getBondParameters(group2, particles, parameters2);
force.getBondParameters(group1, groups1, parameters1);
force.getBondParameters(group2, groups2, parameters2);
for (int i = 0; i < (int) parameters1.size(); i++)
if (parameters1[i] != parameters2[i])
return false;
for (int i = 0; i < groups1.size(); i++) {
vector<int> groupParticles;
vector<double> weights1, weights2;
force.getGroupParameters(groups1[i], groupParticles, weights1);
force.getGroupParameters(groups2[i], groupParticles, weights2);
if (weights1.size() != weights2.size())
return false;
for (int j = 0; j < weights1.size(); j++)
if (weights1[j] != weights2[j])
return false;
}
return true;
}
private:
......
platforms/cuda/tests/TestCudaCustomCentroidBondForce.cpp
View file @ 5d9fc98b
......@@ -115,21 +115,34 @@ void testHarmonicBond() {
ASSERT_EQUAL_VEC(Vec3(4*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
// All the particles should be treated as a single molecule.
vector<std::vector<int> > molecules = context.getMolecules();
ASSERT_EQUAL(1, molecules.size());
ASSERT_EQUAL(5, molecules[0].size());
}
void testComplexFunction() {
int numParticles = 4;
int numParticles = 5;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(2.0);
vector<double> table(20);
for (int i = 0; i < 20; i++)
table[i] = sin(0.11*i);
// When every group contains only one particle, a CustomCentroidBondForce is identical to a
// CustomCompoundBondForce. Use that to test a complicated energy function with lots of terms.
CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+distance(p1,p2)*angle(p3,p2,p4)+0.5*dihedral(p2,p1,p4,p3)");
CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+distance(g1,g2)*angle(g3,g2,g4)+0.5*dihedral(g2,g1,g4,g3)");
CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+fn(distance(p1,p2))*angle(p3,p2,p4)+scale*dihedral(p2,p1,p4,p3)");
CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+fn(distance(g1,g2))*angle(g3,g2,g4)+scale*dihedral(g2,g1,g4,g3)");
compound->addGlobalParameter("scale", 0.5);
centroid->addGlobalParameter("scale", 0.5);
compound->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
centroid->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
// Add a single bond to the CustomCompoundBondForce.
// Add two bonds to the CustomCompoundBondForce.
vector<int> particles(4);
vector<double> parameters;
......@@ -138,8 +151,13 @@ void testComplexFunction() {
particles[2] = 2;
particles[3] = 3;
compound->addBond(particles, parameters);
particles[0] = 2;
particles[1] = 4;
particles[2] = 3;
particles[3] = 1;
compound->addBond(particles, parameters);
// Add an identical bond to the CustomCentroidBondForce. As a stronger test, make sure that
// Add identical bonds to the CustomCentroidBondForce. As a stronger test, make sure that
// group number is different from particle number.
vector<int> groupMembers(1);
......@@ -151,12 +169,19 @@ void testComplexFunction() {
centroid->addGroup(groupMembers);
groupMembers[0] = 2;
centroid->addGroup(groupMembers);
groupMembers[0] = 4;
centroid->addGroup(groupMembers);
vector<int> groups(4);
groups[0] = 1;
groups[1] = 2;
groups[2] = 3;
groups[3] = 0;
centroid->addBond(groups, parameters);
groups[0] = 3;
groups[1] = 4;
groups[2] = 0;
groups[3] = 2;
centroid->addBond(groups, parameters);
// Add both forces as different force groups, and create a context.
......
platforms/reference/tests/TestReferenceCustomCentroidBondForce.cpp
View file @ 5d9fc98b
......@@ -39,6 +39,7 @@
#include "openmm/CustomCentroidBondForce.h"
#include "openmm/CustomCompoundBondForce.h"
#include "openmm/System.h"
#include "openmm/TabulatedFunction.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
......@@ -115,21 +116,34 @@ void testHarmonicBond() {
ASSERT_EQUAL_VEC(Vec3(4*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
// All the particles should be treated as a single molecule.
vector<std::vector<int> > molecules = context.getMolecules();
ASSERT_EQUAL(1, molecules.size());
ASSERT_EQUAL(5, molecules[0].size());
}
void testComplexFunction() {
int numParticles = 4;
int numParticles = 5;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(2.0);
vector<double> table(20);
for (int i = 0; i < 20; i++)
table[i] = sin(0.11*i);
// When every group contains only one particle, a CustomCentroidBondForce is identical to a
// CustomCompoundBondForce. Use that to test a complicated energy function with lots of terms.
CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+distance(p1,p2)*angle(p3,p2,p4)+0.5*dihedral(p2,p1,p4,p3)");
CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+distance(g1,g2)*angle(g3,g2,g4)+0.5*dihedral(g2,g1,g4,g3)");
CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+fn(distance(p1,p2))*angle(p3,p2,p4)+scale*dihedral(p2,p1,p4,p3)");
CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+fn(distance(g1,g2))*angle(g3,g2,g4)+scale*dihedral(g2,g1,g4,g3)");
compound->addGlobalParameter("scale", 0.5);
centroid->addGlobalParameter("scale", 0.5);
compound->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
centroid->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
// Add a single bond to the CustomCompoundBondForce.
// Add two bonds to the CustomCompoundBondForce.
vector<int> particles(4);
vector<double> parameters;
......@@ -138,8 +152,13 @@ void testComplexFunction() {
particles[2] = 2;
particles[3] = 3;
compound->addBond(particles, parameters);
particles[0] = 2;
particles[1] = 4;
particles[2] = 3;
particles[3] = 1;
compound->addBond(particles, parameters);
// Add an identical bond to the CustomCentroidBondForce. As a stronger test, make sure that
// Add identical bonds to the CustomCentroidBondForce. As a stronger test, make sure that
// group number is different from particle number.
vector<int> groupMembers(1);
......@@ -151,12 +170,19 @@ void testComplexFunction() {
centroid->addGroup(groupMembers);
groupMembers[0] = 2;
centroid->addGroup(groupMembers);
groupMembers[0] = 4;
centroid->addGroup(groupMembers);
vector<int> groups(4);
groups[0] = 1;
groups[1] = 2;
groups[2] = 3;
groups[3] = 0;
centroid->addBond(groups, parameters);
groups[0] = 3;
groups[1] = 4;
groups[2] = 0;
groups[3] = 2;
centroid->addBond(groups, parameters);
// Add both forces as different force groups, and create a context.
......
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