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Unverified Commit bb3073d4 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Virtual site for symmetric molecules (#4185) 

* Reference implementation of SymmetrySite

* Common implementation of SymmetrySite

* Removed duplicated code

* Serialization for SymmetrySite

* Fixed compilation error building C wrapper

* Added SymmetrySite to user guide

* Bug fix

* Added P21 test case
parent b6196754
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serialization/tests/TestSerializeSystem.cpp
View file @ bb3073d4
......@@ -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) 2010-2017 Stanford University and the Authors. *
* Portions copyright (c) 2010-2023 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -99,6 +99,17 @@ void compareSystems(System& system, System& system2) {
ASSERT_EQUAL_CONTAINERS(woExpected, wo);
ASSERT_EQUAL_CONTAINERS(wxExpected, wx);
ASSERT_EQUAL_CONTAINERS(wyExpected, wy);
const SymmetrySite& site9 = dynamic_cast<const SymmetrySite&>(system2.getVirtualSite(9));
ASSERT_EQUAL(3, site9.getParticle(0));
Vec3 Rx, Ry, Rz;
site9.getRotationMatrix(Rx, Ry, Rz);
double ct = cos(1.1);
double st = sin(1.1);
ASSERT_EQUAL_VEC(Vec3(ct, 0, -st), Rx, 0);
ASSERT_EQUAL_VEC(Vec3(0, 1, 0), Ry, 0);
ASSERT_EQUAL_VEC(Vec3(st, 0, ct), Rz, 0);
ASSERT_EQUAL_VEC(Vec3(1, 2, 3), site9.getOffsetVector(), 0);
ASSERT(site9.getUseBoxVectors());
ASSERT_EQUAL(system.getNumForces(), system2.getNumForces());
for (int i = 0; i < system.getNumForces(); i++)
ASSERT(typeid(system.getForce(i)) == typeid(system2.getForce(i)))
......@@ -120,6 +131,10 @@ void testSerialization() {
system.setVirtualSite(6, new ThreeParticleAverageSite(2, 4, 3, 0.5, 0.2, 0.3));
system.setVirtualSite(7, new OutOfPlaneSite(0, 3, 1, 0.1, 0.2, 0.5));
system.setVirtualSite(8, new LocalCoordinatesSite({4, 3, 2, 1}, {0.1, 0.2, 0.3, 0.4}, {-1.0, 0.4, 0.4, 0.2}, {0.3, 0.7, 0.0, -1.0}, Vec3(-0.5, 1.0, 1.5)));
double ct = cos(1.1);
double st = sin(1.1);
Vec3 Rx(ct, 0, -st), Ry(0, 1, 0), Rz(st, 0, ct), v(1, 2, 3);
system.setVirtualSite(9, new SymmetrySite(3, Rx, Ry, Rz, v, true));
system.addForce(new HarmonicBondForce());
// Serialize and then deserialize it, then make sure the systems are identical.
......
tests/TestVirtualSites.h
View file @ bb3073d4
......@@ -306,6 +306,170 @@ void testLocalCoordinates(int numSiteParticles) {
}
}
/**
* Test a SymmetrySite virtual site.
*/
void testSymmetry(bool useBoxVectors) {
System system;
system.setDefaultPeriodicBoxVectors(Vec3(5, 0, 0), Vec3(0, 10, 0), Vec3(0, 0, 15));
system.addParticle(1.0);
system.addParticle(0.0);
double ct = cos(1.1);
double st = sin(1.1);
Vec3 Rx(ct, -st, 0), Ry(st, ct, 0), Rz(0, 0, 1), v(1, 2, 3);
system.setVirtualSite(1, new SymmetrySite(0, Rx, Ry, Rz, v, useBoxVectors));
CustomExternalForce* forceField = new CustomExternalForce("2*x^2+3*y^2+4*z^2");
system.addForce(forceField);
forceField->addParticle(0);
forceField->addParticle(1);
LangevinIntegrator integrator(300.0, 0.1, 0.002);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0.5, 1.2, -2.3);
context.setPositions(positions);
context.applyConstraints(0.0001);
for (int i = 0; i < 1000; i++) {
State state = context.getState(State::Positions | State::Forces);
const vector<Vec3>& pos = state.getPositions();
Vec3 expectedPos;
if (useBoxVectors) {
Vec3 p(pos[0][0]/5, pos[0][1]/10, pos[0][2]/15);
expectedPos = Vec3(Rx.dot(p), Ry.dot(p), Rz.dot(p))+v;
expectedPos = Vec3(5*expectedPos[0], 10*expectedPos[1], 15*expectedPos[2]);
}
else
expectedPos = Vec3(Rx.dot(pos[0]), Ry.dot(pos[0]), Rz.dot(pos[0]))+v;
ASSERT_EQUAL_VEC(expectedPos, pos[1], 1e-5);
Vec3 f1(-4*pos[0][0], -6*pos[0][1], -8*pos[0][2]);
Vec3 f2(-4*pos[1][0], -6*pos[1][1], -8*pos[1][2]);
if (useBoxVectors)
f2 = Vec3(f2[0]*5, f2[1]*10, f2[2]*15);
f2 = Vec3(Rx[0]*f2[0] + Ry[0]*f2[1] + Rz[0]*f2[2],
Rx[1]*f2[0] + Ry[1]*f2[1] + Rz[1]*f2[2],
Rx[2]*f2[0] + Ry[2]*f2[1] + Rz[2]*f2[2]);
if (useBoxVectors)
f2 = Vec3(f2[0]/5, f2[1]/10, f2[2]/15);
ASSERT_EQUAL_VEC(f1+f2, state.getForces()[0], 1e-4);
integrator.step(1);
}
// Test the force against a finite difference approximation.
context.setPositions(positions);
context.applyConstraints(0.0001);
State state = context.getState(State::Forces);
Vec3 f0 = state.getForces()[0];
double norm = std::sqrt(f0.dot(f0));
const double delta = 1e-2;
double step = 0.5*delta/norm;
vector<Vec3> positions2 = positions;
vector<Vec3> positions3 = positions;
positions2[0] -= f0*step;
positions3[0] += f0*step;
context.setPositions(positions2);
context.applyConstraints(0.0001);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
context.applyConstraints(0.0001);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/delta, 1e-3)
}
/**
* Test a SymmetrySite virtual site within a P21 space group and non-orthogonal unit cell axes.
*/
void testSymmetryP21NonOrthogonal() {
// Roy P21 (CCDC ID QAXMEH31)
Vec3 Rx(-1.0, 0, 0), Ry(0, 1, 0), Rz(0, 0, -1), v(0, 0.5, 0);
Vec3 a = Vec3(10.771, 0, 0);
Vec3 b = Vec3(0, 11.019, 0);
Vec3 c = Vec3(-5.320, 0, 10.117);
Vec3 boxVectors[3];
boxVectors[0] = a;
boxVectors[1] = b;
boxVectors[2] = c;
Vec3 recipBoxVectors[3];
double determinant = boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2];
double scale = 1.0/determinant;
recipBoxVectors[0] = Vec3(boxVectors[1][1]*boxVectors[2][2], 0, 0)*scale;
recipBoxVectors[1] = Vec3(-boxVectors[1][0]*boxVectors[2][2], boxVectors[0][0]*boxVectors[2][2], 0)*scale;
recipBoxVectors[2] = Vec3(boxVectors[1][0]*boxVectors[2][1]-boxVectors[1][1]*boxVectors[2][0], -boxVectors[0][0]*boxVectors[2][1], boxVectors[0][0]*boxVectors[1][1])*scale;
System system;
system.setDefaultPeriodicBoxVectors(a, b, c);
system.addParticle(1.0);
system.addParticle(0.0);
bool useBoxVectors = true;
system.setVirtualSite(1, new SymmetrySite(0, Rx, Ry, Rz, v, useBoxVectors));
CustomExternalForce* forceField = new CustomExternalForce("2*x^2+3*y^2+4*z^2");
system.addForce(forceField);
forceField->addParticle(0);
forceField->addParticle(1);
LangevinIntegrator integrator(300.0, 0.1, 0.002);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
// Initial sulfur position: 1.92556489 4.05148760 1.84034785
// P21 SymOp symmetry location: -1.92556489 9.56098760 -1.84034785
positions[0] = Vec3(1.92556489,4.05148760,1.84034785);
Vec3 p21 = Vec3(-1.92556489,9.56098760,-1.84034785);
context.setPositions(positions);
context.applyConstraints(0.0001);
for (int i = 0; i < 1000; i++) {
State state = context.getState(State::Positions | State::Forces);
const vector<Vec3> &pos = state.getPositions();
if (i == 0) {
ASSERT_EQUAL_VEC(p21, pos[1], 1e-5)
}
else {
Vec3 expectedPos;
Vec3 r = pos[0];
r = Vec3(r[0] * recipBoxVectors[0][0] + r[1] * recipBoxVectors[1][0] + r[2] * recipBoxVectors[2][0],
r[1] * recipBoxVectors[1][1] + r[2] * recipBoxVectors[2][1],
r[2] * recipBoxVectors[2][2]);
expectedPos = Vec3(Rx.dot(r), Ry.dot(r), Rz.dot(r)) + v;
expectedPos = Vec3(expectedPos[0] * boxVectors[0][0] + expectedPos[1] * boxVectors[1][0] +
expectedPos[2] * boxVectors[2][0],
expectedPos[1] * boxVectors[1][1] + expectedPos[2] * boxVectors[2][1],
expectedPos[2] * boxVectors[2][2]);
ASSERT_EQUAL_VEC(expectedPos, pos[1], 1e-5)
}
Vec3 f1(-4*pos[0][0], -6*pos[0][1], -8*pos[0][2]);
Vec3 f2(-4*pos[1][0], -6*pos[1][1], -8*pos[1][2]);
f2 = Vec3(f2[0]*boxVectors[0][0] + f2[1]*boxVectors[1][0] + f2[2]*boxVectors[2][0],
f2[1]*boxVectors[1][1] + f2[2]*boxVectors[2][1],
f2[2]*boxVectors[2][2]);
f2 = Vec3(Rx[0]*f2[0] + Ry[0]*f2[1] + Rz[0]*f2[2],
Rx[1]*f2[0] + Ry[1]*f2[1] + Rz[1]*f2[2],
Rx[2]*f2[0] + Ry[2]*f2[1] + Rz[2]*f2[2]);
f2 = Vec3(f2[0]*recipBoxVectors[0][0] + f2[1]*recipBoxVectors[1][0] + f2[2]*recipBoxVectors[2][0],
f2[1]*recipBoxVectors[1][1] + f2[2]*recipBoxVectors[2][1],
f2[2]*recipBoxVectors[2][2]);
ASSERT_EQUAL_VEC(f1+f2, state.getForces()[0], 1e-4)
integrator.step(1);
}
// Test the force against a finite difference approximation.
context.setPositions(positions);
context.applyConstraints(0.0001);
State state = context.getState(State::Forces);
Vec3 f0 = state.getForces()[0];
double norm = std::sqrt(f0.dot(f0));
const double delta = 1e-2;
double step = 0.5*delta/norm;
vector<Vec3> positions2 = positions;
vector<Vec3> positions3 = positions;
positions2[0] -= f0*step;
positions3[0] += f0*step;
context.setPositions(positions2);
context.applyConstraints(0.0001);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
context.applyConstraints(0.0001);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/delta, 1e-3)
}
/**
* Make sure that energy, linear momentum, and angular momentum are all conserved
* when using virtual sites.
......@@ -630,10 +794,13 @@ int main(int argc, char* argv[]) {
testLocalCoordinates(2);
testLocalCoordinates(3);
testLocalCoordinates(4);
testSymmetry(false);
testSymmetry(true);
testConservationLaws();
testOverlappingSites();
testNestedSites();
testReordering();
testSymmetryP21NonOrthogonal();
runPlatformTests();
}
catch(const exception& e) {
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ bb3073d4
......@@ -226,6 +226,7 @@ UNITS = {
("LocalCoordinatesSite", "getXWeights") : (None, ()),
("LocalCoordinatesSite", "getYWeights") : (None, ()),
("LocalCoordinatesSite", "getLocalPosition") : ("unit.nanometer", ()),
("SymmetrySite", "getOffsetVector") : (None, ()),
("SerializationNode", "getChildren") : (None, ()),
("SerializationNode", "getChildNode") : (None, ()),
("SerializationNode", "getProperties") : (None, ()),
......
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