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Commit 73183c61 authored by ChayaSt's avatar ChayaSt
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resolved conflict

parents 0e218233 32e08b87
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Showing with 549 additions and 38 deletions
serialization/tests/TestSerializeMonteCarloMembraneBarostat.cpp
View file @ 73183c61
......@@ -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) 2010-2014 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -57,7 +57,7 @@ void testSerialization() {
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getDefaultPressure(), force2.getDefaultPressure());
ASSERT_EQUAL(force.getDefaultSurfaceTension(), force2.getDefaultSurfaceTension());
ASSERT_EQUAL(force.getTemperature(), force2.getTemperature());
ASSERT_EQUAL(force.getDefaultTemperature(), force2.getDefaultTemperature());
ASSERT_EQUAL(force.getXYMode(), force2.getXYMode());
ASSERT_EQUAL(force.getZMode(), force2.getZMode());
ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());
......
serialization/tests/TestSerializePeriodicTorsionForce.cpp
View file @ 73183c61
......@@ -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) 2010-2014 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -47,6 +47,7 @@ void testSerialization() {
force.addTorsion(0, 2, 3, 4, 2, 2.0, 2.1);
force.addTorsion(2, 3, 4, 7, 1, 3.0, 2.2);
force.addTorsion(5, 1, 2, 3, 3, 4.0, 2.3);
force.setUsesPeriodicBoundaryConditions(true);
// Serialize and then deserialize it.
......@@ -58,6 +59,7 @@ void testSerialization() {
PeriodicTorsionForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
for (int i = 0; i < force.getNumTorsions(); i++) {
int a1, a2, a3, a4, b1, b2, b3, b4, perioda, periodb;
......
serialization/tests/TestSerializeRBTorsionForce.cpp
View file @ 73183c61
......@@ -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) 2010-2014 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -46,6 +46,7 @@ void testSerialization() {
force.addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
force.addTorsion(0, 2, 3, 4, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7);
force.addTorsion(2, 3, 4, 7, -1, -2, -3, 1.1, 2.2, 3.3);
force.setUsesPeriodicBoundaryConditions(true);
// Serialize and then deserialize it.
......@@ -57,6 +58,7 @@ void testSerialization() {
RBTorsionForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
for (int i = 0; i < force.getNumTorsions(); i++) {
int a1, a2, a3, a4, b1, b2, b3, b4;
......
tests/TestCMAPTorsionForce.h
View file @ 73183c61
......@@ -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) 2010-2015 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -158,6 +158,61 @@ void testChangingParameters() {
ASSERT_EQUAL_TOL(2-20*sin(M_PI/4), energy, 1e-5);
}
void testPeriodic() {
const int mapSize = 36;
// Create two systems that use periodic boundary conditions: one with a pair
// of periodic torsions, and one with a CMAP torsion that approximates the same force.
System system1;
for (int i = 0; i < 5; i++)
system1.addParticle(1.0);
PeriodicTorsionForce* periodic = new PeriodicTorsionForce();
periodic->addTorsion(0, 1, 2, 3, 2, M_PI/4, 1.5);
periodic->addTorsion(1, 2, 3, 4, 3, M_PI/3, 2.0);
periodic->setUsesPeriodicBoundaryConditions(true);
system1.addForce(periodic);
System system2;
for (int i = 0; i < 5; i++)
system2.addParticle(1.0);
CMAPTorsionForce* cmap = new CMAPTorsionForce();
vector<double> mapEnergy(mapSize*mapSize);
for (int i = 0; i < mapSize; i++) {
double angle1 = i*2*M_PI/mapSize;
double energy1 = 1.5*(1+cos(2*angle1-M_PI/4));
for (int j = 0; j < mapSize; j++) {
double angle2 = j*2*M_PI/mapSize;
double energy2 = 2.0*(1+cos(3*angle2-M_PI/3));
mapEnergy[i+j*mapSize] = energy1+energy2;
}
}
cmap->addMap(mapSize, mapEnergy);
cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4);
cmap->setUsesPeriodicBoundaryConditions(true);
system2.addForce(cmap);
// Set the atoms in various positions, and verify that both systems give equal forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(5);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(system1, integrator1, platform);
Context c2(system2, integrator2, platform);
for (int i = 0; i < 50; 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 < system1.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 0.05);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-3);
}
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -165,6 +220,7 @@ int main(int argc, char* argv[]) {
initializeTests(argc, argv);
testCMAPTorsions();
testChangingParameters();
testPeriodic();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomAngleForce.h
View file @ 73183c61
......@@ -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 @ 73183c61
......@@ -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 @ 73183c61
......@@ -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 @ 73183c61
......@@ -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: *
* *
......@@ -171,7 +171,7 @@ void testContinuous2DFunction() {
const double xmin = 0.4;
const double xmax = 1.1;
const double ymin = 0.0;
const double ymax = 0.9;
const double ymax = 0.95;
System system;
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
......@@ -215,10 +215,10 @@ void testContinuous3DFunction() {
const int zsize = 12;
const double xmin = 0.4;
const double xmax = 1.1;
const double ymin = 0.0;
const double ymax = 0.9;
const double ymin = 2.0;
const double ymax = 2.9;
const double zmin = 0.2;
const double zmax = 1.3;
const double zmax = 1.35;
System system;
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
......@@ -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/TestCustomNonbondedForce.h
View file @ 73183c61
......@@ -937,6 +937,37 @@ void testInteractionGroupLongRangeCorrection() {
ASSERT_EQUAL_TOL(expected, energy2-energy1, 1e-4);
}
void testInteractionGroupTabulatedFunction() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r-1)+1");
set<int> set1, set2;
set1.insert(0);
set2.insert(1);
forceField->addInteractionGroup(set1, set2);
forceField->addParticle(vector<double>());
forceField->addParticle(vector<double>());
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(sin(0.25*i));
forceField->addTabulatedFunction("fn", new Discrete1DFunction(table));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
for (int i = 0; i < (int) table.size(); i++) {
positions[1] = Vec3(i+1, 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, 0), forces[0], 1e-6);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
}
}
void testMultipleCutoffs() {
System system;
system.addParticle(1.0);
......@@ -1033,6 +1064,7 @@ int main(int argc, char* argv[]) {
testInteractionGroups();
testLargeInteractionGroup();
testInteractionGroupLongRangeCorrection();
testInteractionGroupTabulatedFunction();
testMultipleCutoffs();
testIllegalVariable();
runPlatformTests();
......
tests/TestCustomTorsionForce.h
View file @ 73183c61
......@@ -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/TestEwald.h
View file @ 73183c61
......@@ -270,6 +270,49 @@ void testTriclinic() {
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-4);
}
void testTriclinic2() {
// Create a triclinic box containing a large molecule made up of randomly positioned particles and make sure the
// results match the reference platform.
if (platform.getName() == "Reference")
return;
const int numParticles = 1000;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(3.2, 0, 0), Vec3(-1.1, 3.1, 0), Vec3(-1.1, -1.5, 2.7));
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
NonbondedForce* force = new NonbondedForce();
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
force->addParticle(i%2 == 0 ? -1.0 : 1.0, 1.0, 0.0);
positions[i] = Vec3(10*genrand_real2(sfmt)-2, 10*genrand_real2(sfmt)-2, 10*genrand_real2(sfmt)-2);
if (i > 0) {
Vec3 delta = positions[i-1]-positions[i];
system.addConstraint(i-1, i, sqrt(delta.dot(delta)));
}
}
system.addForce(force);
force->setNonbondedMethod(NonbondedForce::PME);
force->setCutoffDistance(1.0);
force->setReciprocalSpaceForceGroup(1);
force->setPMEParameters(2.62826, 27, 25, 24);
// Compute the forces and energy.
VerletIntegrator integ1(0.001);
Context context1(system, integ1, platform);
context1.setPositions(positions);
VerletIntegrator integ2(0.001);
Context context2(system, integ2, Platform::getPlatformByName("Reference"));
context2.setPositions(positions);
State state1 = context1.getState(State::Forces | State::Energy, false, 2);
State state2 = context2.getState(State::Forces | State::Energy, false, 2);
ASSERT_EQUAL_TOL(state2.getPotentialEnergy(), state1.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state2.getForces()[i], state1.getForces()[i], 1e-4);
}
void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
// Create a cloud of random point charges.
......@@ -391,6 +434,7 @@ int main(int argc, char* argv[]) {
testEwaldPME(false);
testEwaldPME(true);
testTriclinic();
testTriclinic2();
testErrorTolerance(NonbondedForce::Ewald);
testErrorTolerance(NonbondedForce::PME);
testPMEParameters();
......
tests/TestHarmonicAngleForce.h
View file @ 73183c61
......@@ -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 @ 73183c61
......@@ -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/TestMonteCarloAnisotropicBarostat.h
View file @ 73183c61
......@@ -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, Lee-Ping Wang *
* Contributors: *
* *
......@@ -75,7 +75,7 @@ void testIdealGas() {
// Test it for three different temperatures.
for (int i = 0; i < 3; i++) {
barostat->setTemperature(temp[i]);
barostat->setDefaultTemperature(temp[i]);
LangevinIntegrator integrator(temp[i], 0.1, 0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
......@@ -135,7 +135,7 @@ void testIdealGasAxis(int axis) {
// Test it for three different temperatures.
for (int i = 0; i < 3; i++) {
barostat->setTemperature(temp[i]);
barostat->setDefaultTemperature(temp[i]);
LangevinIntegrator integrator(temp[i], 0.1, 0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
......@@ -371,7 +371,7 @@ void testEinsteinCrystal() {
// Create the barostat.
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pres3[p], pres3[p], pres3[p]), temp, (a==0||a==3), (a==1||a==3), (a==2||a==3), frequency);
system.addForce(barostat);
barostat->setTemperature(temp);
barostat->setDefaultTemperature(temp);
LangevinIntegrator integrator(temp, 0.1, 0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
......@@ -417,7 +417,7 @@ void testEinsteinCrystal() {
// Create the barostat.
MonteCarloBarostat* barostat = new MonteCarloBarostat(pres3[p], temp, frequency);
system.addForce(barostat);
barostat->setTemperature(temp);
barostat->setDefaultTemperature(temp);
LangevinIntegrator integrator(temp, 0.1, 0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
......
tests/TestMonteCarloBarostat.h
View file @ 73183c61
......@@ -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: *
* *
......@@ -111,7 +111,7 @@ void testIdealGas() {
// Test it for three different temperatures.
for (int i = 0; i < 3; i++) {
barostat->setTemperature(temp[i]);
barostat->setDefaultTemperature(temp[i]);
LangevinIntegrator integrator(temp[i], 0.1, 0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
......
tests/TestPeriodicTorsionForce.h
View file @ 73183c61
......@@ -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 @ 73183c61
......@@ -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) {
......
wrappers/generateWrappers.py
View file @ 73183c61
......@@ -397,6 +397,7 @@ extern OPENMM_EXPORT void %(name)s_insert(%(name)s* set, %(type)s value);""" % v
/* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
extern OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState(const OpenMM_Context* target, int types, int enforcePeriodicBox);
extern OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState_2(const OpenMM_Context* target, int types, int enforcePeriodicBox, int groups);
extern OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_loadPluginsFromDirectory(const char* directory);
extern OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_getPluginLoadFailures();
extern OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeSystem(const OpenMM_System* system);
......@@ -801,6 +802,10 @@ OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState(const OpenMM_Context* target
State result = reinterpret_cast<const Context*>(target)->getState(types, enforcePeriodicBox);
return reinterpret_cast<OpenMM_State*>(new State(result));
}
OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState_2(const OpenMM_Context* target, int types, int enforcePeriodicBox, int groups) {
State result = reinterpret_cast<const Context*>(target)->getState(types, enforcePeriodicBox, groups);
return reinterpret_cast<OpenMM_State*>(new State(result));
}
OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_loadPluginsFromDirectory(const char* directory) {
vector<string> result = Platform::loadPluginsFromDirectory(string(directory));
return reinterpret_cast<OpenMM_StringArray*>(new vector<string>(result));
......@@ -1314,6 +1319,14 @@ MODULE OpenMM
integer*4 enforcePeriodicBox
type(OpenMM_State) result
end subroutine
subroutine OpenMM_Context_getState_2(target, types, enforcePeriodicBox, groups, result)
use OpenMM_Types; implicit none
type (OpenMM_Context) target
integer*4 types
integer*4 enforcePeriodicBox
integer*4 groups
type(OpenMM_State) result
end subroutine
subroutine OpenMM_Platform_loadPluginsFromDirectory(directory, result)
use OpenMM_Types; implicit none
character(*) directory
......@@ -1991,6 +2004,12 @@ OPENMM_EXPORT void openmm_context_getstate_(const OpenMM_Context*& target, int c
OPENMM_EXPORT void OPENMM_CONTEXT_GETSTATE(const OpenMM_Context*& target, int const& types, int const& enforcePeriodicBox, OpenMM_State*& result) {
result = OpenMM_Context_getState(target, types, enforcePeriodicBox);
}
OPENMM_EXPORT void openmm_context_getstate_2_(const OpenMM_Context*& target, int const& types, int const& enforcePeriodicBox, int const& groups, OpenMM_State*& result) {
result = OpenMM_Context_getState_2(target, types, enforcePeriodicBox, groups);
}
OPENMM_EXPORT void OPENMM_CONTEXT_GETSTATE_2(const OpenMM_Context*& target, int const& types, int const& enforcePeriodicBox, int const& groups, OpenMM_State*& result) {
result = OpenMM_Context_getState_2(target, types, enforcePeriodicBox, groups);
}
OPENMM_EXPORT void openmm_platform_loadpluginsfromdirectory_(const char* directory, OpenMM_StringArray*& result, int length) {
result = OpenMM_Platform_loadPluginsFromDirectory(makeString(directory, length).c_str());
}
......
wrappers/python/CMakeLists.txt
View file @ 73183c61
......@@ -108,17 +108,10 @@ else(SWIG_EXECUTABLE)
set(SWIG_VERSION "0.0.0" CACHE STRING "Swig version" FORCE)
endif(SWIG_EXECUTABLE)
# Enforce swig version
if (PYTHON_VERSION_MAJOR EQUAL 3)
string(COMPARE LESS "${SWIG_VERSION}" "2.0.4" SWIG_VERSION_ERROR)
if(SWIG_VERSION_ERROR)
message("Swig version must be 2.0.4 or greater for Python 3! (You have ${SWIG_VERSION})")
endif(SWIG_VERSION_ERROR)
else(PYTHON_VERSION_MAJOR EQUAL 3)
string(COMPARE LESS "${SWIG_VERSION}" "1.3.39" SWIG_VERSION_ERROR)
if(SWIG_VERSION_ERROR)
message("Swig version must be 1.3.39 or greater for Python 2! (You have ${SWIG_VERSION})")
endif(SWIG_VERSION_ERROR)
endif(PYTHON_VERSION_MAJOR EQUAL 3)
string(COMPARE LESS "${SWIG_VERSION}" "3.0.5" SWIG_VERSION_ERROR)
if(SWIG_VERSION_ERROR)
message("Swig version must be 3.0.5 or greater! (You have ${SWIG_VERSION})")
endif(SWIG_VERSION_ERROR)
find_package(Doxygen REQUIRED)
mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
......
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 73183c61
......@@ -8,11 +8,10 @@ Structures at Stanford, funded under the NIH Roadmap for Medical Research,
grant U54 GM072970. See https://simtk.org. This code was originally part of
the ParmEd program and was ported for use with OpenMM.
Copyright (c) 2014-2015 the Authors
Copyright (c) 2014-2016 the Authors
Author: Jason M. Swails
Contributors:
Date: August 19, 2014
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
......@@ -111,7 +110,7 @@ def _strip_optunit(thing, unit):
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_resre = re.compile(r'(\d+)([a-zA-Z]*)')
_resre = re.compile(r'(-?\d+)([a-zA-Z]*)')
class CharmmPsfFile(object):
"""A chemical structure instantiated from CHARMM files.
......
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