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Commit 0fa56f2e authored by peastman's avatar peastman
Browse files

Merge pull request #1461 from peastman/periodic 

Allow periodic boundary conditions for bonded forces
parents 4bd2f9d2 b458028f
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Showing with 372 additions and 8 deletions
tests/TestCustomAngleForce.h
View file @ 0fa56f2e
......@@ -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) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,6 +29,9 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/CustomAngleForce.h"
......@@ -145,6 +148,39 @@ void testIllegalVariable() {
ASSERT(threwException);
}
void testPeriodic() {
// Create a force that uses periodic boundary conditions.
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 1.5, 0), Vec3(0, 0, 3));
VerletIntegrator integrator(0.01);
CustomAngleForce* angles = new CustomAngleForce("0.5*k*(theta-theta0)^2");
angles->addPerAngleParameter("theta0");
angles->addPerAngleParameter("k");
vector<double> parameters(2);
parameters[0] = M_PI/3;
parameters[1] = 1.1;
angles->addAngle(0, 1, 2, parameters);
angles->setUsesPeriodicBoundaryConditions(true);
system.addForce(angles);
angles->setUsesPeriodicBoundaryConditions(true);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double torque = 1.1*M_PI/6;
ASSERT_EQUAL_VEC(Vec3(2*torque, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -torque, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*1.1*(M_PI/6)*(M_PI/6), state.getPotentialEnergy(), TOL);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -152,6 +188,7 @@ int main(int argc, char* argv[]) {
initializeTests(argc, argv);
testAngles();
testIllegalVariable();
testPeriodic();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomBondForce.h
View file @ 0fa56f2e
......@@ -148,6 +148,36 @@ void testIllegalVariable() {
ASSERT(threwException);
}
void testPeriodic() {
// Create a force that uses periodic boundary conditions.
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
VerletIntegrator integrator(0.01);
CustomBondForce* forceField = new CustomBondForce("scale*k*(r-r0)^2");
forceField->addPerBondParameter("r0");
forceField->addPerBondParameter("k");
forceField->addGlobalParameter("scale", 0.5);
vector<double> parameters(2);
parameters[0] = 1.9;
parameters[1] = 0.8;
forceField->addBond(0, 1, parameters);
forceField->setUsesPeriodicBoundaryConditions(true);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.9, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0.8*0.9, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.8*0.9*0.9, state.getPotentialEnergy(), TOL);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -156,6 +186,7 @@ int main(int argc, char* argv[]) {
testBonds();
testManyParameters();
testIllegalVariable();
testPeriodic();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomCentroidBondForce.h
View file @ 0fa56f2e
......@@ -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) 2015 Stanford University and the Authors. *
* Portions copyright (c) 2015-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -277,6 +277,62 @@ void testIllegalVariable() {
ASSERT(threwException);
}
void testPeriodic() {
// Create a force that uses periodic boundary conditions.
System system;
system.addParticle(1.0);
system.addParticle(2.0);
system.addParticle(3.0);
system.addParticle(4.0);
system.addParticle(5.0);
system.setDefaultPeriodicBoxVectors(Vec3(2, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "k*distance(g1,g2)^2");
force->addPerBondParameter("k");
vector<int> particles1;
particles1.push_back(0);
particles1.push_back(1);
vector<int> particles2;
particles2.push_back(2);
particles2.push_back(3);
particles2.push_back(4);
force->addGroup(particles1);
force->addGroup(particles2);
vector<int> groups;
groups.push_back(0);
groups.push_back(1);
vector<double> parameters;
parameters.push_back(1.0);
force->addBond(groups, parameters);
force->setUsesPeriodicBoundaryConditions(true);
system.addForce(force);
// The center of mass of group 0 is (1.5, 0, 0).
vector<Vec3> positions(5);
positions[0] = Vec3(2.5, 0, 0);
positions[1] = Vec3(1, 0, 0);
// The center of mass of group 1 is (-1, 0, 0).
positions[2] = Vec3(-6, 0, 0);
positions[3] = Vec3(-1, 0, 0);
positions[4] = Vec3(2, 0, 0);
// Check the forces and energy.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(0.5*0.5, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(Vec3(-2*0.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-2*0.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_VEC(Vec3(2*0.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(2*0.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
ASSERT_EQUAL_VEC(Vec3(2*0.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -286,6 +342,7 @@ int main(int argc, char* argv[]) {
testComplexFunction();
testCustomWeights();
testIllegalVariable();
testPeriodic();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomCompoundBondForce.h
View file @ 0fa56f2e
......@@ -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) 2012-2015 Stanford University and the Authors. *
* Portions copyright (c) 2012-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -330,6 +330,82 @@ void testIllegalVariable() {
ASSERT(threwException);
}
void testPeriodic() {
// Create a force that uses periodic boundary conditions.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
CustomCompoundBondForce* custom = new CustomCompoundBondForce(4, "0.5*kb*((distance(p1,p2)-b0)^2+(distance(p2,p3)-b0)^2)+0.5*ka*(angle(p2,p3,p4)-a0)^2+kt*(1+cos(dihedral(p1,p2,p3,p4)-t0))");
custom->addPerBondParameter("kb");
custom->addPerBondParameter("ka");
custom->addPerBondParameter("kt");
custom->addPerBondParameter("b0");
custom->addPerBondParameter("a0");
custom->addPerBondParameter("t0");
vector<int> particles(4);
particles[0] = 0;
particles[1] = 1;
particles[2] = 3;
particles[3] = 2;
vector<double> parameters(6);
parameters[0] = 1.5;
parameters[1] = 0.8;
parameters[2] = 0.6;
parameters[3] = 1.1;
parameters[4] = 2.9;
parameters[5] = 1.3;
custom->addBond(particles, parameters);
custom->setUsesPeriodicBoundaryConditions(true);
customSystem.addForce(custom);
// Create an identical system using standard forces.
System standardSystem;
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.1, 1.5);
bonds->addBond(1, 3, 1.1, 1.5);
bonds->setUsesPeriodicBoundaryConditions(true);
standardSystem.addForce(bonds);
HarmonicAngleForce* angles = new HarmonicAngleForce();
angles->addAngle(1, 3, 2, 2.9, 0.8);
angles->setUsesPeriodicBoundaryConditions(true);
standardSystem.addForce(angles);
PeriodicTorsionForce* torsions = new PeriodicTorsionForce();
torsions->addTorsion(0, 1, 3, 2, 1, 1.3, 0.6);
torsions->setUsesPeriodicBoundaryConditions(true);
standardSystem.addForce(torsions);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
vector<Vec3> positions(4);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -341,6 +417,7 @@ int main(int argc, char* argv[]) {
testContinuous3DFunction();
testMultipleBonds();
testIllegalVariable();
testPeriodic();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomTorsionForce.h
View file @ 0fa56f2e
......@@ -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) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -186,6 +186,42 @@ void testIllegalVariable() {
ASSERT(threwException);
}
void testPeriodic() {
// Create a force that uses periodic boundary conditions.
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
VerletIntegrator integrator(0.01);
CustomTorsionForce* torsions = new CustomTorsionForce("k*(1+cos(n*theta-theta0))");
torsions->addPerTorsionParameter("theta0");
torsions->addPerTorsionParameter("n");
torsions->addGlobalParameter("k", 1.1);
vector<double> parameters(2);
parameters[0] = M_PI/3;
parameters[1] = 2;
torsions->addTorsion(0, 1, 2, 3, parameters);
torsions->setUsesPeriodicBoundaryConditions(true);
system.addForce(torsions);
Context context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 2);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double torque = -2*1.1*std::sin(2*M_PI/3);
ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -torque, 0), forces[3], TOL);
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
ASSERT_EQUAL_TOL(1.1*(1+std::cos(2*M_PI/3)), state.getPotentialEnergy(), TOL);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -194,6 +230,7 @@ int main(int argc, char* argv[]) {
testTorsions();
testRange();
testIllegalVariable();
testPeriodic();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestHarmonicAngleForce.h
View file @ 0fa56f2e
......@@ -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) 2008-2015 Stanford University and the Authors.s *
* Portions copyright (c) 2008-2016 Stanford University and the Authors.s *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -93,12 +93,40 @@ void testAngles() {
}
}
void testPeriodic() {
// Create a force that uses periodic boundary conditions.
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 1.5, 0), Vec3(0, 0, 3));
VerletIntegrator integrator(0.01);
HarmonicAngleForce* angles = new HarmonicAngleForce();
angles->addAngle(0, 1, 2, PI_M/3, 1.1);
system.addForce(angles);
angles->setUsesPeriodicBoundaryConditions(true);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double torque = 1.1*PI_M/6;
ASSERT_EQUAL_VEC(Vec3(2*torque, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -torque, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*1.1*(PI_M/6)*(PI_M/6), state.getPotentialEnergy(), TOL);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
try {
initializeTests(argc, argv);
testAngles();
testPeriodic();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestHarmonicBondForce.h
View file @ 0fa56f2e
......@@ -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) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -82,12 +82,37 @@ void testBonds() {
}
}
void testPeriodic() {
// Create a force that uses periodic boundary conditions.
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
VerletIntegrator integrator(0.01);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.2, 0.8);
bonds->setUsesPeriodicBoundaryConditions(true);
system.addForce(bonds);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.2, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0.8*0.2, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.8*0.2*0.2, state.getPotentialEnergy(), TOL);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
try {
initializeTests(argc, argv);
testBonds();
testPeriodic();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestPeriodicTorsionForce.h
View file @ 0fa56f2e
......@@ -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) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -88,12 +88,43 @@ void testPeriodicTorsions() {
}
}
void testPeriodic() {
// Create a force that uses periodic boundary conditions.
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
VerletIntegrator integrator(0.01);
PeriodicTorsionForce* torsions = new PeriodicTorsionForce();
torsions->addTorsion(0, 1, 2, 3, 2, PI_M/3, 1.1);
torsions->setUsesPeriodicBoundaryConditions(true);
system.addForce(torsions);
Context context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 2);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double torque = -2*1.1*std::sin(2*PI_M/3);
ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -torque, 0), forces[3], TOL);
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
ASSERT_EQUAL_TOL(1.1*(1+std::cos(2*PI_M/3)), state.getPotentialEnergy(), TOL);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
try {
initializeTests(argc, argv);
testPeriodicTorsions();
testPeriodic();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestRBTorsionForce.h
View file @ 0fa56f2e
......@@ -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) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -107,12 +107,53 @@ void testRBTorsions() {
}
}
void testPeriodic() {
// Create a force that uses periodic boundary conditions.
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
VerletIntegrator integrator(0.01);
RBTorsionForce* torsions = new RBTorsionForce();
torsions->addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
torsions->setUsesPeriodicBoundaryConditions(true);
system.addForce(torsions);
Context context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(0, 0, 2);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double psi = 0.5*PI_M;
double torque = 0.0;
for (int i = 1; i < 6; ++i) {
double c = 0.1*(i+1);
torque += -c*i*std::pow(std::cos(psi), i-1)*std::sin(psi);
}
ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -torque, 0), forces[3], TOL);
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
double energy = 0.0;
for (int i = 0; i < 6; ++i) {
double c = 0.1*(i+1);
energy += c*std::pow(std::cos(psi), i);
}
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
try {
initializeTests(argc, argv);
testRBTorsions();
testPeriodic();
runPlatformTests();
}
catch(const exception& e) {
......
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