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Commit 3b6925ae authored by Andy Simmonett's avatar Andy Simmonett Committed by GitHub
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Merge pull request #1 from peastman/ljpme 

Cleanup to LJ PME code
parents 5a8a8aa9 f7a102fb
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Showing with 2199 additions and 193 deletions
serialization/tests/TestSerializeIntegrator.cpp
View file @ 3b6925ae
...@@ -137,12 +137,20 @@ void testSerializeCustomIntegrator() { ...@@ -137,12 +137,20 @@ void testSerializeCustomIntegrator() {
intg->addGlobalVariable("oute", 0); intg->addGlobalVariable("oute", 0);
intg->addGlobalVariable("oute1", 0); intg->addGlobalVariable("oute1", 0);
intg->addGlobalVariable("oute2", 0); intg->addGlobalVariable("oute2", 0);
intg->addGlobalVariable("oute3_conditional_v1", 0);// HACK: need addGlobals to be alphabetical to work around bug
intg->addGlobalVariable("oute3_conditional_v2", 0);
intg->addComputePerDof("outf", "f"); intg->addComputePerDof("outf", "f");
intg->addComputePerDof("outf1", "f1"); intg->addComputePerDof("outf1", "f1");
intg->addComputePerDof("outf2", "f2"); intg->addComputePerDof("outf2", "f2");
intg->addComputeGlobal("oute", "energy"); intg->addComputeGlobal("oute", "energy");
intg->addComputeGlobal("oute1", "energy1"); intg->addComputeGlobal("oute1", "energy1");
intg->addComputeGlobal("oute2", "energy2"); intg->addComputeGlobal("oute2", "energy2");
intg->beginIfBlock("1 > 0");
intg->addComputeGlobal("oute3_conditional_v1", "energy");
intg->endBlock();
intg->beginWhileBlock("0 > 1");
intg->addComputeGlobal("oute3_conditional_v2", "energy");
intg->endBlock();
intg->addUpdateContextState(); intg->addUpdateContextState();
intg->addConstrainVelocities(); intg->addConstrainVelocities();
intg->addComputeSum("summand2", "v*v+f*f"); intg->addComputeSum("summand2", "v*v+f*f");
...@@ -216,13 +224,13 @@ int main() { ...@@ -216,13 +224,13 @@ int main() {
testSerializeVerletIntegrator(); testSerializeVerletIntegrator();
testSerializeVariableLangevinIntegrator(); testSerializeVariableLangevinIntegrator();
testSerializeVariableVerletIntegrator(); testSerializeVariableVerletIntegrator();
testSerializeLangevinIntegrator(); testSerializeLangevinIntegrator();
testSerializeCompoundIntegrator(); testSerializeCompoundIntegrator();
} }
catch(const exception& e) { catch(const exception& e) {
return 1; cout << "exception: " << e.what() << endl;
return 1;
} }
cout << "Done" << endl;
return 0; return 0;
} }
tests/TestCustomIntegrator.h
View file @ 3b6925ae
...@@ -858,6 +858,43 @@ void testEnergyParameterDerivatives() { ...@@ -858,6 +858,43 @@ void testEnergyParameterDerivatives() {
ASSERT_EQUAL_TOL(dEdtheta0, values[2][1], 1e-5); ASSERT_EQUAL_TOL(dEdtheta0, values[2][1], 1e-5);
} }
/**
* Test an integrator that modifies the step size.
*/
void testChangeDT() {
System system;
system.addParticle(1.0);
CustomIntegrator integrator(0.5);
integrator.addGlobalVariable("dt_global", 0.0);
integrator.addPerDofVariable("dt_dof", 0.0);
integrator.addComputeGlobal("dt", "dt+1");
integrator.addComputePerDof("dt_dof", "dt");
integrator.addComputeGlobal("dt_global", "dt");
Context context(system, integrator, platform);
vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0);
context.setPositions(positions);
for (int i = 0; i < 5; i++) {
integrator.step(1);
double dt = 1.5+i;
ASSERT_EQUAL_TOL(dt, integrator.getStepSize(), 1e-5);
ASSERT_EQUAL_TOL(dt, integrator.getGlobalVariable(0), 1e-5);
vector<Vec3> values;
integrator.getPerDofVariable(0, values);
ASSERT_EQUAL_VEC(Vec3(dt, dt, dt), values[0], 1e-5);
}
integrator.setStepSize(1.0);
for (int i = 0; i < 5; i++) {
integrator.step(1);
double dt = 2.0+i;
ASSERT_EQUAL_TOL(dt, integrator.getStepSize(), 1e-5);
ASSERT_EQUAL_TOL(dt, integrator.getGlobalVariable(0), 1e-5);
vector<Vec3> values;
integrator.getPerDofVariable(0, values);
ASSERT_EQUAL_VEC(Vec3(dt, dt, dt), values[0], 1e-5);
}
}
void runPlatformTests(); void runPlatformTests();
int main(int argc, char* argv[]) { int main(int argc, char* argv[]) {
...@@ -879,6 +916,7 @@ int main(int argc, char* argv[]) { ...@@ -879,6 +916,7 @@ int main(int argc, char* argv[]) {
testWhileBlock(); testWhileBlock();
testChangingGlobal(); testChangingGlobal();
testEnergyParameterDerivatives(); testEnergyParameterDerivatives();
testChangeDT();
runPlatformTests(); runPlatformTests();
} }
catch(const exception& e) { catch(const exception& e) {
......
tests/TestCustomNonbondedForce.h
View file @ 3b6925ae
...@@ -878,6 +878,16 @@ void testLargeInteractionGroup() { ...@@ -878,6 +878,16 @@ void testLargeInteractionGroup() {
State state3 = context.getState(State::Forces); State state3 = context.getState(State::Forces);
for (int i = 0; i < numParticles; i++) for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state3.getForces()[i], 1e-4); ASSERT_EQUAL_VEC(state1.getForces()[i], state3.getForces()[i], 1e-4);
// Now make the interaction group empty. The energy should then be zero.
set1.clear();
set2.clear();
nonbonded->setInteractionGroupParameters(0, set1, set2);
context.reinitialize();
context.setPositions(positions);
State state4 = context.getState(State::Energy);
ASSERT_EQUAL(0.0, state4.getPotentialEnergy());
} }
void testInteractionGroupLongRangeCorrection() { void testInteractionGroupLongRangeCorrection() {
...@@ -1024,6 +1034,65 @@ void testMultipleCutoffs() { ...@@ -1024,6 +1034,65 @@ void testMultipleCutoffs() {
} }
} }
void testMultipleSwitches() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
// Add multiple CustomNonbondedForces, one with a switching function and one without.
CustomNonbondedForce* nonbonded1 = new CustomNonbondedForce("2*r");
nonbonded1->addParticle(vector<double>());
nonbonded1->addParticle(vector<double>());
nonbonded1->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
nonbonded1->setCutoffDistance(1.0);
system.addForce(nonbonded1);
CustomNonbondedForce* nonbonded2 = new CustomNonbondedForce("3*r");
nonbonded2->addParticle(vector<double>());
nonbonded2->addParticle(vector<double>());
nonbonded2->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
nonbonded2->setCutoffDistance(1.0);
nonbonded2->setSwitchingDistance(0.5);
nonbonded2->setUseSwitchingFunction(true);
nonbonded2->setForceGroup(1);
system.addForce(nonbonded2);
Context context(system, integrator, platform);
double r = 0.8;
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, r, 0);
context.setPositions(positions);
double t = (r-0.5)/(1.0-0.5);
double switchValue = 1+t*t*t*(-10+t*(15-t*6));
double switchDeriv = t*t*(-30+t*(60-t*30))/(1.0-0.5);
double e1 = 2.0*r;
double e2 = 3.0*r*switchValue;
double f1 = 2.0;
double f2 = 3.0*switchValue + 3.0*switchDeriv*r;
// Check the first force.
State state = context.getState(State::Forces | State::Energy, false, 1);
ASSERT_EQUAL_VEC(Vec3(0, f1, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -f1, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_TOL(e1, state.getPotentialEnergy(), TOL);
// Check the second force.
state = context.getState(State::Forces | State::Energy, false, 2);
ASSERT_EQUAL_VEC(Vec3(0, f2, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -f2, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_TOL(e2, state.getPotentialEnergy(), TOL);
// Check the sum of both forces.
state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_VEC(Vec3(0, f1+f2, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -f1-f2, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_TOL(e1+e2, state.getPotentialEnergy(), TOL);
}
void testIllegalVariable() { void testIllegalVariable() {
System system; System system;
system.addParticle(1.0); system.addParticle(1.0);
...@@ -1144,6 +1213,7 @@ int main(int argc, char* argv[]) { ...@@ -1144,6 +1213,7 @@ int main(int argc, char* argv[]) {
testInteractionGroupLongRangeCorrection(); testInteractionGroupLongRangeCorrection();
testInteractionGroupTabulatedFunction(); testInteractionGroupTabulatedFunction();
testMultipleCutoffs(); testMultipleCutoffs();
testMultipleSwitches();
testIllegalVariable(); testIllegalVariable();
testEnergyParameterDerivatives(); testEnergyParameterDerivatives();
testEnergyParameterDerivatives2(); testEnergyParameterDerivatives2();
......
tests/TestEwald.h
View file @ 3b6925ae
...@@ -365,7 +365,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) { ...@@ -365,7 +365,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
double expectedAlpha, actualAlpha; double expectedAlpha, actualAlpha;
int expectedSize[3], actualSize[3]; int expectedSize[3], actualSize[3];
NonbondedForceImpl::calcPMEParameters(system, *force, expectedAlpha, expectedSize[0], expectedSize[1], expectedSize[2]); NonbondedForceImpl::calcPMEParameters(system, *force, expectedAlpha, expectedSize[0], expectedSize[1], expectedSize[2], false);
force->getPMEParametersInContext(context, actualAlpha, actualSize[0], actualSize[1], actualSize[2]); force->getPMEParametersInContext(context, actualAlpha, actualSize[0], actualSize[1], actualSize[2]);
ASSERT_EQUAL_TOL(expectedAlpha, actualAlpha, 1e-5); ASSERT_EQUAL_TOL(expectedAlpha, actualAlpha, 1e-5);
for (int i = 0; i < 3; i++) { for (int i = 0; i < 3; i++) {
......
tests/TestGayBerneForce.h
View file @ 3b6925ae
...@@ -78,7 +78,7 @@ void testPointParticles() { ...@@ -78,7 +78,7 @@ void testPointParticles() {
State state2 = context.getState(State::Forces | State::Energy, false, 2); State state2 = context.getState(State::Forces | State::Energy, false, 2);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5); ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
for (int i = 0; i < numParticles; i++) for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5); ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
} }
void testEnergyScales() { void testEnergyScales() {
......
tests/TestLangevinIntegrator.h
View file @ 3b6925ae
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -74,9 +74,9 @@ void testSingleBond() { ...@@ -74,9 +74,9 @@ void testSingleBond() {
integrator.step(1); integrator.step(1);
} }
// Not set the friction to a tiny value and see if it conserves energy. // Now set the friction to 0 and see if it conserves energy.
integrator.setFriction(5e-5); integrator.setFriction(0.0);
context.setPositions(positions); context.setPositions(positions);
State state = context.getState(State::Energy); State state = context.getState(State::Energy);
double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy(); double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
......
tests/TestMonteCarloAnisotropicBarostat.h
View file @ 3b6925ae
...@@ -31,6 +31,7 @@ ...@@ -31,6 +31,7 @@
#include "openmm/internal/AssertionUtilities.h" #include "openmm/internal/AssertionUtilities.h"
#include "openmm/CustomExternalForce.h" #include "openmm/CustomExternalForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/MonteCarloBarostat.h" #include "openmm/MonteCarloBarostat.h"
#include "openmm/MonteCarloAnisotropicBarostat.h" #include "openmm/MonteCarloAnisotropicBarostat.h"
#include "openmm/Context.h" #include "openmm/Context.h"
...@@ -69,8 +70,9 @@ void testIdealGas() { ...@@ -69,8 +70,9 @@ void testIdealGas() {
} }
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], true, true, true, frequency); MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], true, true, true, frequency);
system.addForce(barostat); system.addForce(barostat);
ASSERT(barostat->usesPeriodicBoundaryConditions()); HarmonicBondForce* bonds = new HarmonicBondForce();
ASSERT(system.usesPeriodicBoundaryConditions()); bonds->setUsesPeriodicBoundaryConditions(true);
system.addForce(bonds); // So it won't complain the system is non-periodic.
// Test it for three different temperatures. // Test it for three different temperatures.
...@@ -129,8 +131,9 @@ void testIdealGasAxis(int axis) { ...@@ -129,8 +131,9 @@ void testIdealGasAxis(int axis) {
} }
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], scaleX, scaleY, scaleZ, frequency); MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], scaleX, scaleY, scaleZ, frequency);
system.addForce(barostat); system.addForce(barostat);
ASSERT(barostat->usesPeriodicBoundaryConditions()); HarmonicBondForce* bonds = new HarmonicBondForce();
ASSERT(system.usesPeriodicBoundaryConditions()); bonds->setUsesPeriodicBoundaryConditions(true);
system.addForce(bonds); // So it won't complain the system is non-periodic.
// Test it for three different temperatures. // Test it for three different temperatures.
...@@ -187,8 +190,6 @@ void testRandomSeed() { ...@@ -187,8 +190,6 @@ void testRandomSeed() {
system.addForce(forceField); system.addForce(forceField);
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, true, true, true, 1); MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, true, true, true, 1);
system.addForce(barostat); system.addForce(barostat);
ASSERT(barostat->usesPeriodicBoundaryConditions());
ASSERT(system.usesPeriodicBoundaryConditions());
vector<Vec3> positions(numParticles); vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles); vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
...@@ -262,6 +263,9 @@ void testTriclinic() { ...@@ -262,6 +263,9 @@ void testTriclinic() {
} }
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temperature, true, true, true, frequency); MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temperature, true, true, true, frequency);
system.addForce(barostat); system.addForce(barostat);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->setUsesPeriodicBoundaryConditions(true);
system.addForce(bonds); // So it won't complain the system is non-periodic.
// Run a simulation // Run a simulation
......
tests/TestMonteCarloBarostat.h
View file @ 3b6925ae
...@@ -32,6 +32,7 @@ ...@@ -32,6 +32,7 @@
#include "openmm/internal/AssertionUtilities.h" #include "openmm/internal/AssertionUtilities.h"
#include "openmm/MonteCarloBarostat.h" #include "openmm/MonteCarloBarostat.h"
#include "openmm/Context.h" #include "openmm/Context.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h" #include "openmm/NonbondedForce.h"
#include "openmm/System.h" #include "openmm/System.h"
#include "openmm/LangevinIntegrator.h" #include "openmm/LangevinIntegrator.h"
...@@ -105,8 +106,9 @@ void testIdealGas() { ...@@ -105,8 +106,9 @@ void testIdealGas() {
} }
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency); MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency);
system.addForce(barostat); system.addForce(barostat);
ASSERT(barostat->usesPeriodicBoundaryConditions()); HarmonicBondForce* bonds = new HarmonicBondForce();
ASSERT(system.usesPeriodicBoundaryConditions()); bonds->setUsesPeriodicBoundaryConditions(true);
system.addForce(bonds); // So it won't complain the system is non-periodic.
// Test it for three different temperatures. // Test it for three different temperatures.
...@@ -153,8 +155,6 @@ void testRandomSeed() { ...@@ -153,8 +155,6 @@ void testRandomSeed() {
system.addForce(forceField); system.addForce(forceField);
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, 1); MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, 1);
system.addForce(barostat); system.addForce(barostat);
ASSERT(barostat->usesPeriodicBoundaryConditions());
ASSERT(system.usesPeriodicBoundaryConditions());
vector<Vec3> positions(numParticles); vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles); vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
......
tests/TestNonbondedForce.h
View file @ 3b6925ae
...@@ -35,10 +35,12 @@ ...@@ -35,10 +35,12 @@
#include "openmm/HarmonicBondForce.h" #include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h" #include "openmm/NonbondedForce.h"
#include "openmm/System.h" #include "openmm/System.h"
#include "openmm/Units.h"
#include "openmm/VerletIntegrator.h" #include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h" #include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h" #include "sfmt/SFMT.h"
#include <iostream> #include <iostream>
#include <iomanip>
#include <vector> #include <vector>
using namespace OpenMM; using namespace OpenMM;
...@@ -46,6 +48,1661 @@ using namespace std; ...@@ -46,6 +48,1661 @@ using namespace std;
const double TOL = 1e-5; const double TOL = 1e-5;
void make_waterbox(int natoms, double boxEdgeLength, NonbondedForce *forceField, vector<Vec3> &positions, vector<double>& eps, vector<double>& sig,
vector<pair<int, int> >& bonds, System &system, bool do_electrostatics) {
const int RESSIZE = 3;
const double masses[RESSIZE] = { 8.0, 1.0, 1.0 };
const double charges[RESSIZE] = { -0.834, 0.417, 0.417 };
// Values from the CHARMM force field, in AKMA units
const double epsilons[RESSIZE] = { -0.1521, -0.046, -0.046 };
const double halfrmins[RESSIZE] = { 1.7682, 0.2245, 0.2245 };
positions.clear();
if(natoms == 6){
const double coords[6][3] = {
{ 2.000000, 2.000000, 2.000000},
{ 2.500000, 2.000000, 3.000000},
{ 1.500000, 2.000000, 3.000000},
{ 0.000000, 0.000000, 0.000000},
{ 0.500000, 0.000000, 1.000000},
{ -0.500000, 0.000000, 1.000000}
};
for(int atom = 0; atom < natoms; ++atom)
positions.push_back(Vec3(coords[atom][0], coords[atom][1], coords[atom][2])*OpenMM::NmPerAngstrom);
}else if(natoms == 375){
const double coords[375][3] = {
{ -6.22, -6.25, -6.24 },
{ -5.32, -6.03, -6.00 },
{ -6.75, -5.56, -5.84 },
{ -3.04, -6.23, -6.19 },
{ -3.52, -5.55, -5.71 },
{ -3.59, -6.43, -6.94 },
{ 0.02, -6.23, -6.14 },
{ -0.87, -5.97, -6.37 },
{ 0.53, -6.03, -6.93 },
{ 3.10, -6.20, -6.27 },
{ 3.87, -6.35, -5.72 },
{ 2.37, -6.11, -5.64 },
{ 6.18, -6.14, -6.20 },
{ 6.46, -6.66, -5.44 },
{ 6.26, -6.74, -6.94 },
{ -6.21, -3.15, -6.24 },
{ -6.23, -3.07, -5.28 },
{ -6.02, -2.26, -6.55 },
{ -3.14, -3.07, -6.16 },
{ -3.38, -3.63, -6.90 },
{ -2.18, -3.05, -6.17 },
{ -0.00, -3.16, -6.23 },
{ -0.03, -2.30, -6.67 },
{ 0.05, -2.95, -5.29 },
{ 3.08, -3.11, -6.14 },
{ 2.65, -2.55, -6.79 },
{ 3.80, -3.53, -6.62 },
{ 6.16, -3.14, -6.16 },
{ 7.04, -3.32, -6.51 },
{ 5.95, -2.27, -6.51 },
{ -6.20, -0.04, -6.15 },
{ -5.43, 0.32, -6.59 },
{ -6.95, 0.33, -6.62 },
{ -3.10, -0.06, -6.19 },
{ -3.75, 0.42, -6.69 },
{ -2.46, 0.60, -5.93 },
{ 0.05, -0.01, -6.17 },
{ -0.10, 0.02, -7.12 },
{ -0.79, 0.16, -5.77 },
{ 3.03, 0.00, -6.19 },
{ 3.54, 0.08, -7.01 },
{ 3.69, -0.22, -5.53 },
{ 6.17, 0.05, -6.19 },
{ 5.78, -0.73, -6.57 },
{ 7.09, -0.17, -6.04 },
{ -6.20, 3.15, -6.25 },
{ -6.59, 3.18, -5.37 },
{ -5.87, 2.25, -6.33 },
{ -3.09, 3.04, -6.17 },
{ -3.88, 3.58, -6.26 },
{ -2.41, 3.54, -6.63 },
{ 0.00, 3.06, -6.26 },
{ -0.71, 3.64, -6.00 },
{ 0.65, 3.15, -5.55 },
{ 3.14, 3.06, -6.23 },
{ 3.11, 3.31, -5.30 },
{ 2.38, 3.49, -6.63 },
{ 6.19, 3.14, -6.25 },
{ 6.82, 3.25, -5.54 },
{ 5.76, 2.30, -6.07 },
{ -6.22, 6.26, -6.19 },
{ -6.22, 5.74, -7.00 },
{ -5.89, 5.67, -5.52 },
{ -3.04, 6.24, -6.20 },
{ -3.08, 5.28, -6.17 },
{ -3.96, 6.52, -6.25 },
{ -0.05, 6.21, -6.16 },
{ 0.82, 6.58, -6.06 },
{ 0.01, 5.64, -6.93 },
{ 3.10, 6.25, -6.15 },
{ 3.64, 5.47, -6.31 },
{ 2.46, 6.24, -6.87 },
{ 6.22, 6.20, -6.27 },
{ 5.37, 6.42, -5.88 },
{ 6.80, 6.07, -5.51 },
{ -6.19, -6.15, -3.13 },
{ -6.37, -7.01, -3.51 },
{ -6.25, -6.29, -2.18 },
{ -3.10, -6.27, -3.11 },
{ -2.29, -5.77, -2.99 },
{ -3.80, -5.62, -2.98 },
{ -0.03, -6.18, -3.15 },
{ -0.07, -7.05, -2.75 },
{ 0.68, -5.74, -2.70 },
{ 3.10, -6.14, -3.07 },
{ 2.35, -6.72, -3.23 },
{ 3.86, -6.65, -3.37 },
{ 6.22, -6.20, -3.16 },
{ 6.82, -6.36, -2.43 },
{ 5.35, -6.13, -2.75 },
{ -6.26, -3.13, -3.12 },
{ -6.16, -2.27, -2.70 },
{ -5.36, -3.47, -3.18 },
{ -3.11, -3.05, -3.14 },
{ -3.31, -3.96, -3.34 },
{ -2.77, -3.06, -2.24 },
{ 0.00, -3.13, -3.16 },
{ 0.48, -2.37, -2.81 },
{ -0.57, -3.40, -2.44 },
{ 3.09, -3.09, -3.16 },
{ 2.41, -3.19, -2.49 },
{ 3.91, -3.07, -2.67 },
{ 6.19, -3.04, -3.08 },
{ 5.64, -3.61, -3.61 },
{ 6.93, -3.58, -2.82 },
{ -6.18, -0.00, -3.04 },
{ -6.00, -0.59, -3.78 },
{ -6.79, 0.64, -3.39 },
{ -3.05, -0.03, -3.07 },
{ -2.95, 0.80, -3.52 },
{ -4.00, -0.20, -3.07 },
{ -0.03, 0.03, -3.06 },
{ -0.33, -0.37, -3.87 },
{ 0.89, -0.21, -2.99 },
{ 3.13, -0.05, -3.10 },
{ 3.44, 0.81, -3.34 },
{ 2.21, 0.07, -2.86 },
{ 6.20, -0.05, -3.13 },
{ 6.89, 0.60, -3.20 },
{ 5.58, 0.30, -2.49 },
{ -6.23, 3.09, -3.16 },
{ -5.62, 3.79, -2.94 },
{ -6.33, 2.60, -2.33 },
{ -3.10, 3.08, -3.04 },
{ -3.84, 3.47, -3.51 },
{ -2.40, 3.01, -3.69 },
{ 0.01, 3.04, -3.11 },
{ -0.56, 3.59, -3.64 },
{ 0.28, 3.60, -2.38 },
{ 3.04, 3.11, -3.09 },
{ 3.49, 2.30, -2.87 },
{ 3.70, 3.66, -3.51 },
{ 6.15, 3.14, -3.11 },
{ 6.52, 2.52, -3.74 },
{ 6.72, 3.06, -2.34 },
{ -6.22, 6.15, -3.13 },
{ -5.49, 6.21, -2.51 },
{ -6.56, 7.04, -3.18 },
{ -3.11, 6.24, -3.05 },
{ -3.76, 5.83, -3.62 },
{ -2.26, 5.92, -3.37 },
{ 0.03, 6.25, -3.07 },
{ 0.34, 5.63, -3.73 },
{ -0.87, 6.00, -2.91 },
{ 3.07, 6.15, -3.08 },
{ 3.29, 6.92, -2.56 },
{ 3.39, 6.35, -3.96 },
{ 6.22, 6.14, -3.12 },
{ 5.79, 6.38, -2.29 },
{ 6.25, 6.96, -3.62 },
{ -6.21, -6.20, -0.06 },
{ -5.79, -6.87, 0.48 },
{ -6.43, -5.50, 0.54 },
{ -3.16, -6.21, -0.02 },
{ -2.50, -6.87, 0.20 },
{ -2.77, -5.37, 0.23 },
{ -0.00, -6.14, -0.00 },
{ 0.68, -6.72, -0.33 },
{ -0.64, -6.73, 0.38 },
{ 3.03, -6.20, -0.01 },
{ 3.77, -6.56, -0.51 },
{ 3.43, -5.85, 0.78 },
{ 6.25, -6.16, -0.00 },
{ 5.36, -6.09, -0.36 },
{ 6.24, -6.97, 0.49 },
{ -6.24, -3.05, -0.01 },
{ -6.35, -3.64, 0.73 },
{ -5.42, -3.33, -0.42 },
{ -3.09, -3.06, 0.05 },
{ -2.44, -3.62, -0.38 },
{ -3.90, -3.21, -0.43 },
{ 0.05, -3.10, 0.02 },
{ -0.31, -2.35, -0.43 },
{ -0.63, -3.77, 0.01 },
{ 3.05, -3.09, -0.04 },
{ 3.28, -3.90, 0.41 },
{ 3.65, -2.43, 0.30 },
{ 6.20, -3.04, -0.03 },
{ 5.66, -3.31, 0.71 },
{ 6.78, -3.79, -0.19 },
{ -6.18, 0.04, -0.04 },
{ -6.73, -0.73, -0.15 },
{ -5.98, 0.06, 0.89 },
{ -3.11, -0.04, -0.04 },
{ -3.36, -0.08, 0.87 },
{ -2.70, 0.81, -0.14 },
{ -0.02, -0.02, -0.05 },
{ -0.45, 0.28, 0.75 },
{ 0.90, 0.15, 0.07 },
{ 3.04, 0.02, -0.01 },
{ 3.26, -0.82, 0.38 },
{ 3.89, 0.45, -0.13 },
{ 6.19, 0.05, -0.03 },
{ 5.52, -0.56, 0.25 },
{ 7.01, -0.29, 0.32 },
{ -6.14, 3.08, 0.00 },
{ -6.83, 2.82, 0.61 },
{ -6.59, 3.64, -0.64 },
{ -3.05, 3.09, -0.04 },
{ -3.79, 2.50, 0.09 },
{ -3.18, 3.80, 0.59 },
{ 0.02, 3.14, 0.04 },
{ -0.89, 3.04, -0.19 },
{ 0.49, 2.57, -0.57 },
{ 3.14, 3.15, 0.00 },
{ 3.28, 2.28, 0.37 },
{ 2.30, 3.08, -0.45 },
{ 6.27, 3.08, -0.00 },
{ 5.55, 2.54, -0.33 },
{ 5.83, 3.87, 0.34 },
{ -6.18, 6.15, -0.03 },
{ -6.45, 6.21, 0.88 },
{ -6.26, 7.05, -0.36 },
{ -3.06, 6.19, -0.05 },
{ -2.84, 6.64, 0.76 },
{ -3.99, 5.96, 0.03 },
{ -0.00, 6.20, 0.06 },
{ -0.67, 5.99, -0.59 },
{ 0.76, 6.46, -0.44 },
{ 3.10, 6.26, -0.03 },
{ 3.57, 6.09, 0.78 },
{ 2.57, 5.47, -0.18 },
{ 6.26, 6.18, 0.02 },
{ 5.53, 5.64, -0.29 },
{ 5.95, 7.08, -0.06 },
{ -6.26, -6.21, 3.07 },
{ -5.98, -6.38, 3.97 },
{ -5.46, -5.94, 2.62 },
{ -3.10, -6.24, 3.04 },
{ -2.69, -6.51, 3.87 },
{ -3.43, -5.35, 3.21 },
{ -0.03, -6.16, 3.06 },
{ 0.83, -6.00, 3.42 },
{ -0.30, -6.99, 3.45 },
{ 3.15, -6.25, 3.11 },
{ 2.77, -5.60, 3.72 },
{ 2.68, -6.10, 2.28 },
{ 6.20, -6.21, 3.16 },
{ 5.75, -6.73, 2.50 },
{ 6.69, -5.56, 2.66 },
{ -6.17, -3.10, 3.04 },
{ -6.82, -2.44, 3.28 },
{ -6.12, -3.69, 3.80 },
{ -3.08, -3.04, 3.11 },
{ -3.59, -3.56, 3.72 },
{ -2.97, -3.61, 2.34 },
{ 0.01, -3.04, 3.11 },
{ -0.86, -3.41, 3.20 },
{ 0.56, -3.78, 2.86 },
{ 3.07, -3.07, 3.15 },
{ 3.81, -3.68, 3.13 },
{ 2.80, -2.98, 2.23 },
{ 6.20, -3.04, 3.13 },
{ 5.48, -3.64, 2.92 },
{ 6.98, -3.49, 2.81 },
{ -6.18, -0.05, 3.12 },
{ -6.41, 0.66, 3.69 },
{ -6.33, 0.28, 2.23 },
{ -3.05, 0.03, 3.10 },
{ -3.46, -0.42, 3.83 },
{ -3.57, -0.19, 2.33 },
{ 0.03, -0.02, 3.15 },
{ 0.23, -0.08, 2.21 },
{ -0.81, 0.41, 3.18 },
{ 3.09, 0.00, 3.03 },
{ 2.48, -0.29, 3.71 },
{ 3.91, 0.16, 3.51 },
{ 6.19, -0.06, 3.11 },
{ 6.05, 0.47, 2.33 },
{ 6.59, 0.52, 3.74 },
{ -6.20, 3.05, 3.05 },
{ -6.87, 3.73, 3.17 },
{ -5.55, 3.24, 3.73 },
{ -3.11, 3.06, 3.15 },
{ -3.64, 3.74, 2.71 },
{ -2.32, 3.00, 2.62 },
{ 0.02, 3.05, 3.06 },
{ -0.87, 3.14, 3.38 },
{ 0.48, 3.82, 3.42 },
{ 3.07, 3.10, 3.16 },
{ 3.95, 3.44, 2.97 },
{ 2.76, 2.73, 2.32 },
{ 6.19, 3.07, 3.16 },
{ 7.02, 3.30, 2.72 },
{ 5.52, 3.27, 2.51 },
{ -6.19, 6.24, 3.15 },
{ -5.56, 5.88, 2.52 },
{ -7.05, 5.96, 2.83 },
{ -3.10, 6.14, 3.08 },
{ -2.34, 6.69, 3.27 },
{ -3.86, 6.69, 3.29 },
{ -0.04, 6.24, 3.13 },
{ 0.63, 6.54, 2.53 },
{ 0.08, 5.29, 3.18 },
{ 3.12, 6.24, 3.14 },
{ 3.57, 5.82, 2.40 },
{ 2.23, 5.90, 3.12 },
{ 6.25, 6.19, 3.06 },
{ 5.55, 5.59, 3.32 },
{ 6.08, 6.99, 3.55 },
{ -6.20, -6.16, 6.15 },
{ -6.29, -5.99, 7.09 },
{ -6.09, -7.11, 6.09 },
{ -3.09, -6.19, 6.27 },
{ -2.56, -5.90, 5.52 },
{ -3.80, -6.69, 5.87 },
{ 0.02, -6.25, 6.24 },
{ -0.70, -5.70, 6.51 },
{ 0.25, -5.93, 5.36 },
{ 3.11, -6.18, 6.14 },
{ 3.76, -6.54, 6.74 },
{ 2.29, -6.20, 6.64 },
{ 6.22, -6.17, 6.15 },
{ 6.61, -6.98, 6.47 },
{ 5.56, -5.94, 6.81 },
{ -6.21, -3.10, 6.14 },
{ -6.76, -2.66, 6.78 },
{ -5.51, -3.50, 6.65 },
{ -3.13, -3.05, 6.18 },
{ -2.19, -3.14, 6.34 },
{ -3.50, -3.89, 6.43 },
{ 0.01, -3.06, 6.15 },
{ -0.06, -2.81, 7.07 },
{ -0.25, -3.98, 6.13 },
{ 3.04, -3.09, 6.17 },
{ 3.84, -3.51, 5.84 },
{ 3.25, -2.85, 7.08 },
{ 6.26, -3.13, 6.19 },
{ 6.01, -2.20, 6.09 },
{ 5.47, -3.55, 6.54 },
{ -6.20, 0.01, 6.27 },
{ -5.79, -0.70, 5.78 },
{ -6.67, 0.51, 5.60 },
{ -3.13, 0.01, 6.14 },
{ -3.53, -0.35, 6.94 },
{ -2.21, 0.17, 6.39 },
{ -0.04, -0.04, 6.20 },
{ 0.26, 0.47, 5.46 },
{ 0.51, 0.22, 6.93 },
{ 3.10, -0.05, 6.23 },
{ 2.33, 0.44, 5.95 },
{ 3.85, 0.45, 5.92 },
{ 6.19, -0.01, 6.26 },
{ 7.05, 0.16, 5.88 },
{ 5.58, 0.02, 5.52 },
{ -6.22, 3.04, 6.17 },
{ -5.45, 3.57, 5.95 },
{ -6.62, 3.50, 6.92 },
{ -3.09, 3.16, 6.21 },
{ -3.71, 2.75, 5.61 },
{ -2.60, 2.43, 6.59 },
{ -0.02, 3.10, 6.26 },
{ 0.89, 3.27, 6.05 },
{ -0.44, 2.94, 5.41 },
{ 3.12, 3.04, 6.23 },
{ 2.31, 3.53, 6.43 },
{ 3.59, 3.60, 5.60 },
{ 6.23, 3.05, 6.24 },
{ 5.92, 3.91, 6.54 },
{ 6.02, 3.03, 5.30 },
{ -6.15, 6.21, 6.24 },
{ -6.27, 6.46, 5.32 },
{ -7.00, 5.85, 6.51 },
{ -3.07, 6.15, 6.22 },
{ -3.98, 6.27, 5.94 },
{ -2.66, 7.01, 6.10 },
{ 0.04, 6.20, 6.25 },
{ -0.38, 5.50, 5.75 },
{ -0.36, 7.00, 5.93 },
{ 3.12, 6.15, 6.24 },
{ 3.66, 6.88, 5.93 },
{ 2.25, 6.33, 5.86 },
{ 6.20, 6.27, 6.19 },
{ 5.46, 5.65, 6.19 },
{ 6.97, 5.73, 6.39 }
};
for(int atom = 0; atom < natoms; ++atom)
positions.push_back(Vec3(coords[atom][0], coords[atom][1], coords[atom][2])*OpenMM::NmPerAngstrom);
}else{
throw exception();
}
system.setDefaultPeriodicBoxVectors(Vec3(boxEdgeLength, 0, 0),
Vec3(0, boxEdgeLength, 0),
Vec3(0, 0, boxEdgeLength));
sig.clear();
eps.clear();
bonds.clear();
for(int atom = 0; atom < natoms; ++atom){
system.addParticle(masses[atom%RESSIZE]);
double sigma = 2.0*pow(2.0, -1.0/6.0)*halfrmins[atom%RESSIZE]*OpenMM::NmPerAngstrom;
double epsilon = fabs(epsilons[atom%RESSIZE])*OpenMM::KJPerKcal;
sig.push_back(0.5*sigma);
eps.push_back(2.0*sqrt(epsilon));
if(atom%RESSIZE == 0){
bonds.push_back(pair<int, int>(atom, atom+1));
bonds.push_back(pair<int, int>(atom, atom+2));
}
double charge = do_electrostatics ? charges[atom] : 0;
forceField->addParticle(charge, sigma, epsilon);
}
}
void print_forces(const vector<Vec3>& forces){
// Print the forces in AKMA units, to compare against other codes.
std::cout << "Forces:" << std::endl;
for(int n = 0; n < forces.size(); ++ n){
std::cout << setw(3)<< n+1
<< setw(16) << setprecision(10) << -forces[n][0]*OpenMM::NmPerAngstrom*OpenMM::KcalPerKJ
<< setw(16) << setprecision(10) << -forces[n][1]*OpenMM::NmPerAngstrom*OpenMM::KcalPerKJ
<< setw(16) << setprecision(10) << -forces[n][2]*OpenMM::NmPerAngstrom*OpenMM::KcalPerKJ << std::endl;
}
}
void test_water2_dpme_energies_forces_no_exclusions() {
const double cutoff = 7.0*OpenMM::NmPerAngstrom;
const double alpha = 4.0124063605;
const double dalpha = 4.0124063605;
const int grid = 32;
NonbondedForce* forceField = new NonbondedForce();
vector<Vec3> positions;
vector<double> epsvals;
vector<double> sigvals;
vector<pair<int, int> > bonds;
System system;
const int NATOMS = 6;
double boxEdgeLength = 25*OpenMM::NmPerAngstrom;
make_waterbox(NATOMS, boxEdgeLength, forceField, positions, epsvals, sigvals, bonds, system, false);
forceField->setNonbondedMethod(OpenMM::NonbondedForce::LJPME);
forceField->setPMEParameters(alpha, grid, grid, grid);
forceField->setLJPMEParameters(dalpha, grid, grid, grid);
forceField->setCutoffDistance(cutoff);
forceField->setReactionFieldDielectric(1.0);
system.addForce(forceField);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
/**
* Gromacs reference values from the following inputs
*
------------------------------------------------
water2.gro
------------------------------------------------
MD of 2 waters, t= 0.0
6
1SOL OW1 1 0.200 0.200 0.200
1SOL HW1 2 0.250 0.200 0.300
1SOL HW2 3 0.150 0.200 0.300
2SOL OW1 4 0.000 0.000 0.000
2SOL HW1 5 0.050 0.000 0.100
2SOL HW2 6 -0.050 0.000 0.100
2.50000 2.50000 2.50000
------------------------------------------------
------------------------------------------------
water2.gro
------------------------------------------------
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 no 1.0 1.0
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
OW OW 8 15.99940 -0.834 A 3.15057e-01 6.36386e-01
HW HW 1 1.00800 0.417 A 4.00014e-02 1.92464e-01
#ifdef NOEXCLUDE
[ moleculetype ]
; molname nrexcl
SOL 0
#else
[ moleculetype ]
; molname nrexcl
SOL 3
#endif
#ifdef NOCHARGE
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 OW 1 SOL OW1 1 0.000
2 HW 1 SOL HW1 1 0.000
3 HW 1 SOL HW2 1 0.000
#else
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 OW 1 SOL OW1 1 -0.834
2 HW 1 SOL HW1 1 0.417
3 HW 1 SOL HW2 1 0.417
#endif
[ settles ]
; i j funct length
1 1 0.09572 0.15139
#ifndef NOEXCLUDE
[ exclusions ]
1 2 3
2 1 3
3 1 2
#endif
------------------------------------------------
------------------------------------------------
water2.top
------------------------------------------------
#include "tip3p.tpi"
[ system ]
Water dimer
[ molecules ]
SOL 2
------------------------------------------------
------------------------------------------------
water2.mdp
------------------------------------------------
define = -DNOCHARGE -DNOEXCLUDE
;define = -DNOCHARGE
rvdw = 0.7
vdw-modifier = Potential-Shift
;vdw-modifier = None
rlist = 0.9
rcoulomb = 0.7
nstfout = 1
fourierspacing = 0.08
pme-order = 5
ewald-rtol = 1.5E-2
ewald-rtol-lj = 1.5E-2
vdwtype = PME
lj-pme-comb-rule = geometric
continuation = yes
------------------------------------------------
run commands:-
gmx grompp -c water2.gro -p water2.top -f water2.mdp -o run.tpr
gmx mdrun -s run.tpr -o traj.trr -pforce 1E-16
gmx dump -f traj.trr
*/
double refenergy = 1.34804e+03;
vector<Vec3> refforces(6);
refforces[0] = Vec3( 3.15301e-01, -3.91114e-03, -6.68965e+04);
refforces[1] = Vec3( 1.67241e+04, -3.79846e-02, 3.34487e+04);
refforces[2] = Vec3(-1.67243e+04, -9.55931e-02, 3.34486e+04);
refforces[3] = Vec3(-1.71643e+00, -1.76696e+00, -6.68993e+04);
refforces[4] = Vec3( 1.67254e+04, 1.59080e+00, 3.34495e+04);
refforces[5] = Vec3(-1.67239e+04, 3.13897e-01, 3.34491e+04);
State state = context.getState(State::Forces | State::Energy);
double energy = state.getPotentialEnergy();
// std::cout << "Energy " << energy << std::endl;
const vector<Vec3>& forces = state.getForces();
// print_forces(forces);
ASSERT_EQUAL_TOL(refenergy, energy, 1E-4);
for(int n = 0; n < NATOMS; ++n)
ASSERT_EQUAL_VEC(refforces[n], forces[n], 1E-4);
}
void test_water2_dpme_energies_forces_with_exclusions() {
const double cutoff = 7.0*OpenMM::NmPerAngstrom;
const double alpha = 4.0124063605;
const double dalpha = 4.0124063605;
const int grid = 32;
NonbondedForce* forceField = new NonbondedForce();
vector<Vec3> positions;
vector<double> epsvals;
vector<double> sigvals;
vector<pair<int, int> > bonds;
System system;
const int NATOMS = 6;
double boxEdgeLength = 25*OpenMM::NmPerAngstrom;
make_waterbox(NATOMS, boxEdgeLength, forceField, positions, epsvals, sigvals, bonds, system, false);
forceField->setNonbondedMethod(OpenMM::NonbondedForce::LJPME);
forceField->createExceptionsFromBonds(bonds, 1.0, 1.0);
forceField->setPMEParameters(alpha, grid, grid, grid);
forceField->setLJPMEParameters(dalpha, grid, grid, grid);
forceField->setCutoffDistance(cutoff);
forceField->setUseSwitchingFunction(false);
forceField->setUseDispersionCorrection(false);
forceField->setReactionFieldDielectric(1.0);
system.addForce(forceField);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
double refenergy = -7.78060e-01;
vector<Vec3> refforces(6);
// Gromacs reference values. See comments in test_water2_dpme_energies_forces_no_exclusions() for details.
refforces[0] = Vec3( 3.15301e-01, -3.91114e-03, 9.48373e-01);
refforces[1] = Vec3(-4.74745e-02, -3.79846e-02, -5.69616e-02);
refforces[2] = Vec3(-7.16866e-02, -9.55931e-02, -1.43348e-01);
refforces[3] = Vec3(-1.78136e+00, -1.76696e+00, -1.70022e+00);
refforces[4] = Vec3( 1.19309e+00, 1.59080e+00, 7.95443e-01);
refforces[5] = Vec3( 3.92366e-01, 3.13897e-01, 1.56962e-01);
State state = context.getState(State::Forces | State::Energy);
double energy = state.getPotentialEnergy();
// std::cout << "Energy " << energy << std::endl;
const vector<Vec3>& forces = state.getForces();
// print_forces(forces);
ASSERT_EQUAL_TOL(refenergy, energy, 1E-4);
for(int n = 0; n < NATOMS; ++n)
ASSERT_EQUAL_VEC(refforces[n], forces[n], 5E-4);
}
void test_water125_dpme_vs_long_cutoff_no_exclusions() {
const double cutoff = 8.5*OpenMM::NmPerAngstrom;
const double alpha = 0.45*OpenMM::AngstromsPerNm;
const double dalpha = 0.45*OpenMM::AngstromsPerNm;
const int grid = 32;
NonbondedForce* forceField = new NonbondedForce();
vector<Vec3> positions;
vector<double> epsvals;
vector<double> sigvals;
vector<pair<int, int> > bonds;
System system;
const int NATOMS = 375;
double boxEdgeLength = 17.01*OpenMM::NmPerAngstrom;
make_waterbox(NATOMS, boxEdgeLength, forceField, positions, epsvals, sigvals, bonds, system, false);
forceField->setNonbondedMethod(OpenMM::NonbondedForce::LJPME);
forceField->setPMEParameters(alpha, grid, grid, grid);
forceField->setLJPMEParameters(dalpha, grid, grid, grid);
forceField->setCutoffDistance(cutoff);
forceField->setReactionFieldDielectric(1.0);
system.addForce(forceField);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
double energy = state.getPotentialEnergy();
/*
* Gromacs reference values. See comments in test_water2_dpme_energies_forces_no_exclusions() for details.
* Coordinates are from make_waterbox, and the .gro file looks like
*
;define = -DNOCHARGE -DNOEXCLUDE
define = -DNOCHARGE
vdw-modifier = Potential-Shift
rvdw = 1.15
rlist = 1.15
rcoulomb = 1.15
fourierspacing = 0.04
nstfout = 1
pme-order = 5
ewald-rtol = 1E-8
ewald-rtol-lj = 1E-8
vdwtype = PME
lj-pme-comb-rule = geometric
continuation = yes
*/
double gromacs_energy = 5.63157e+05;
// std::cout << "Energy " << energy << std::endl;
const vector<Vec3>& forces = state.getForces();
// print_forces(forces);
vector<Vec3> refforces(NATOMS);
refforces[ 0] = Vec3(-1.12446e+05, -2.71952e+05, -1.91471e+05);
refforces[ 1] = Vec3( 2.70479e+05, 6.61172e+04, 7.21277e+04);
refforces[ 2] = Vec3(-1.58058e+05, 2.05779e+05, 1.19292e+05);
refforces[ 3] = Vec3( 3.16438e+05, -1.27994e+05, 1.08811e+05);
refforces[ 4] = Vec3(-1.36520e+05, 1.93405e+05, 1.36521e+05);
refforces[ 5] = Vec3(-1.79957e+05, -6.54374e+04, -2.45393e+05);
refforces[ 6] = Vec3( 1.30626e+05, -1.36728e+05, 2.93833e+05);
refforces[ 7] = Vec3(-2.74564e+05, 8.02095e+04, -7.09524e+04);
refforces[ 8] = Vec3( 1.43952e+05, 5.64523e+04, -2.22980e+05);
refforces[ 9] = Vec3(-4.22852e+04, 2.14660e+04, -3.23254e+05);
refforces[ 10] = Vec3( 2.28059e+05, -4.44251e+04, 1.62898e+05);
refforces[ 11] = Vec3(-1.85776e+05, 2.29044e+04, 1.60326e+05);
refforces[ 12] = Vec3(-1.02075e+05, 3.27346e+05, 1.47993e+04);
refforces[ 13] = Vec3( 7.77195e+04, -1.44336e+05, 2.10959e+05);
refforces[ 14] = Vec3( 2.44142e+04, -1.83111e+05, -2.25837e+05);
refforces[ 15] = Vec3(-4.81843e+04, -2.72889e+05, -1.75068e+05);
refforces[ 16] = Vec3(-5.46666e+03, 2.18711e+04, 2.62456e+05);
refforces[ 17] = Vec3( 5.35890e+04, 2.51021e+05, -8.74311e+04);
refforces[ 18] = Vec3(-2.04721e+05, 1.58918e+05, 2.20448e+05);
refforces[ 19] = Vec3(-7.05932e+04, -1.64717e+05, -2.17659e+05);
refforces[ 20] = Vec3( 2.75339e+05, 5.73611e+03, -2.86718e+03);
refforces[ 21] = Vec3(-5.65480e+03, -2.81809e+05, -1.38358e+05);
refforces[ 22] = Vec3(-7.85576e+03, 2.25204e+05, -1.15217e+05);
refforces[ 23] = Vec3( 1.34846e+04, 5.66345e+04, 2.53512e+05);
refforces[ 24] = Vec3(-7.73167e+04, -4.43114e+04, 3.22354e+05);
refforces[ 25] = Vec3(-1.24372e+05, 1.61973e+05, -1.88001e+05);
refforces[ 26] = Vec3( 2.01689e+05, -1.17651e+05, -1.34455e+05);
refforces[ 27] = Vec3(-1.79300e+05, -1.97922e+05, 1.94294e+05);
refforces[ 28] = Vec3( 2.38945e+05, -4.88761e+04, -9.50350e+04);
refforces[ 29] = Vec3(-5.95911e+04, 2.46878e+05, -9.93159e+04);
refforces[ 30] = Vec3(-1.31892e+04, -2.15675e+05, 2.68757e+05);
refforces[ 31] = Vec3( 2.31232e+05, 1.08107e+05, -1.32129e+05);
refforces[ 32] = Vec3(-2.18089e+05, 1.07592e+05, -1.36669e+05);
refforces[ 33] = Vec3( 1.90632e+04, -3.62889e+05, 8.61608e+04);
refforces[ 34] = Vec3(-2.16178e+05, 1.59639e+05, -1.66288e+05);
refforces[ 35] = Vec3( 1.97134e+05, 2.03295e+05, 8.00862e+04);
refforces[ 36] = Vec3( 3.40071e+05, -6.87734e+04, 1.22584e+05);
refforces[ 37] = Vec3(-4.17943e+04, 8.35901e+03, -2.64693e+05);
refforces[ 38] = Vec3(-2.98358e+05, 6.03813e+04, 1.42075e+05);
refforces[ 39] = Vec3(-3.21693e+05, 4.40885e+04, 1.41154e+04);
refforces[ 40] = Vec3( 1.28817e+05, 2.02067e+04, -2.07114e+05);
refforces[ 41] = Vec3( 1.92948e+05, -6.43160e+04, 1.92949e+05);
refforces[ 42] = Vec3(-1.46001e+05, 3.20840e+05, 7.97305e+04);
refforces[ 43] = Vec3(-1.27705e+05, -2.55411e+05, -1.24428e+05);
refforces[ 44] = Vec3( 2.73737e+05, -6.54594e+04, 4.46323e+04);
refforces[ 45] = Vec3( 1.50212e+04, 2.43629e+05, -2.20084e+05);
refforces[ 46] = Vec3(-1.07432e+05, 8.26408e+03, 2.42419e+05);
refforces[ 47] = Vec3( 9.23685e+04, -2.51915e+05, -2.23909e+04);
refforces[ 48] = Vec3( 3.14327e+04, -2.94199e+05, 1.55484e+05);
refforces[ 49] = Vec3(-2.23665e+05, 1.52883e+05, -2.54793e+04);
refforces[ 50] = Vec3( 1.92227e+05, 1.41342e+05, -1.30033e+05);
refforces[ 51] = Vec3( 5.73542e+04, -2.08689e+05, -2.68170e+05);
refforces[ 52] = Vec3(-2.26784e+05, 1.85259e+05, 8.30474e+04);
refforces[ 53] = Vec3( 1.69446e+05, 2.34613e+04, 1.85087e+05);
refforces[ 54] = Vec3( 2.25490e+05, -1.91311e+05, -1.40103e+05);
refforces[ 55] = Vec3(-8.20802e+03, 6.83988e+04, 2.54448e+05);
refforces[ 56] = Vec3(-2.17315e+05, 1.22953e+05, -1.14373e+05);
refforces[ 57] = Vec3(-7.09510e+04, 2.05639e+05, -2.69540e+05);
refforces[ 58] = Vec3( 1.93603e+05, 3.38041e+04, 2.18192e+05);
refforces[ 59] = Vec3(-1.22579e+05, -2.39458e+05, 5.13124e+04);
refforces[ 60] = Vec3(-1.07250e+05, 3.35982e+05, 6.89600e+03);
refforces[ 61] = Vec3( 6.90672e-01, -1.44228e+05, -2.24659e+05);
refforces[ 62] = Vec3( 1.07222e+05, -1.91701e+05, 2.17695e+05);
refforces[ 63] = Vec3( 2.64846e+05, 1.94002e+05, 5.27262e+03);
refforces[ 64] = Vec3(-1.12985e+04, -2.71176e+05, 8.47510e+03);
refforces[ 65] = Vec3(-2.53630e+05, 7.71894e+04, -1.37831e+04);
refforces[ 66] = Vec3(-3.04551e+05, 4.21918e+04, 1.88948e+05);
refforces[ 67] = Vec3( 2.87326e+05, 1.22193e+05, 3.30263e+04);
refforces[ 68] = Vec3( 1.73006e+04, -1.64358e+05, -2.22023e+05);
refforces[ 69] = Vec3( 2.45556e+04, 2.20596e+05, 2.41913e+05);
refforces[ 70] = Vec3( 1.50804e+05, -2.17829e+05, -4.46813e+04);
refforces[ 71] = Vec3(-1.75369e+05, -2.74087e+03, -1.97287e+05);
refforces[ 72] = Vec3( 8.65787e+04, -2.77188e+04, -3.15014e+05);
refforces[ 73] = Vec3(-2.42127e+05, 6.26659e+04, 1.11092e+05);
refforces[ 74] = Vec3( 1.55591e+05, -3.48752e+04, 2.03883e+05);
refforces[ 75] = Vec3( 7.06224e+04, 2.96642e+05, -1.51267e+05);
refforces[ 76] = Vec3(-5.39280e+04, -2.57657e+05, -1.13850e+05);
refforces[ 77] = Vec3(-1.67422e+04, -3.90659e+04, 2.65102e+05);
refforces[ 78] = Vec3(-4.52577e+04, -3.21552e+05, -7.01075e+04);
refforces[ 79] = Vec3( 2.35182e+05, 1.45173e+05, 3.48411e+04);
refforces[ 80] = Vec3(-1.89931e+05, 1.76363e+05, 3.52722e+04);
refforces[ 81] = Vec3(-2.29347e+05, 1.06977e+05, -2.70703e+05);
refforces[ 82] = Vec3(-1.17929e+04, -2.56493e+05, 1.17929e+05);
refforces[ 83] = Vec3( 2.41161e+05, 1.49452e+05, 1.52847e+05);
refforces[ 84] = Vec3( 2.32633e+03, 3.03443e+05, 1.27473e+05);
refforces[ 85] = Vec3(-2.11215e+05, -1.63335e+05, -4.50583e+04);
refforces[ 86] = Vec3( 2.08887e+05, -1.40170e+05, -8.24544e+04);
refforces[ 87] = Vec3( 5.83172e+04, 2.82133e+04, -3.26001e+05);
refforces[ 88] = Vec3( 1.76890e+05, -4.71698e+04, 2.15220e+05);
refforces[ 89] = Vec3(-2.35168e+05, 1.89225e+04, 1.10825e+05);
refforces[ 90] = Vec3(-2.72444e+05, -1.46998e+05, -1.00637e+05);
refforces[ 91] = Vec3( 2.78426e+04, 2.39442e+05, 1.16936e+05);
refforces[ 92] = Vec3( 2.44570e+05, -9.23920e+04, -1.63042e+04);
refforces[ 93] = Vec3(-3.10100e+04, 2.93390e+05, -1.87196e+05);
refforces[ 94] = Vec3(-6.38830e+04, -2.90671e+05, -6.38833e+04);
refforces[ 95] = Vec3( 9.48775e+04, -2.79002e+03, 2.51149e+05);
refforces[ 96] = Vec3( 4.18753e+04, -1.23438e+05, -3.10188e+05);
refforces[ 97] = Vec3( 1.29157e+05, 2.04500e+05, 9.41770e+04);
refforces[ 98] = Vec3(-1.71038e+05, -8.10180e+04, 2.16049e+05);
refforces[ 99] = Vec3(-5.61490e+04, 2.26993e+04, -3.44090e+05);
refforces[100] = Vec3(-1.96230e+05, -2.88572e+04, 1.93344e+05);
refforces[101] = Vec3( 2.52383e+05, 6.15570e+03, 1.50813e+05);
refforces[102] = Vec3(-6.33126e+04, 3.55941e+05, 8.51300e+04);
refforces[103] = Vec3(-1.75405e+05, -1.81783e+05, -1.69027e+05);
refforces[104] = Vec3( 2.38759e+05, -1.74232e+05, 8.38891e+04);
refforces[105] = Vec3( 1.51480e+05, -4.90606e+04, 3.17956e+05);
refforces[106] = Vec3( 4.93229e+04, -1.61668e+05, -2.02771e+05);
refforces[107] = Vec3(-2.00831e+05, 2.10712e+05, -1.15233e+05);
refforces[108] = Vec3( 2.20204e+05, -2.33820e+05, 1.51386e+05);
refforces[109] = Vec3( 3.36498e+04, 2.79296e+05, -1.51424e+05);
refforces[110] = Vec3(-2.53896e+05, -4.54334e+04, 2.10242e-01);
refforces[111] = Vec3(-1.94665e+05, 2.05890e+05, 2.40510e+05);
refforces[112] = Vec3(-9.73233e+04, -1.29764e+05, -2.62775e+05);
refforces[113] = Vec3( 2.92049e+05, -7.61856e+04, 2.22208e+04);
refforces[114] = Vec3( 1.60261e+05, -3.43716e+05, 1.52456e+04);
refforces[115] = Vec3( 1.11151e+05, 3.08358e+05, -8.60527e+04);
refforces[116] = Vec3(-2.71443e+05, 3.54056e+04, 7.08103e+04);
refforces[117] = Vec3(-4.27331e+04, -3.19871e+05, -1.68415e+05);
refforces[118] = Vec3( 2.28408e+05, 2.15171e+05, -2.31720e+04);
refforces[119] = Vec3(-1.85616e+05, 1.04782e+05, 1.91602e+05);
refforces[120] = Vec3(-1.66057e+05, -9.58191e+04, -2.78448e+05);
refforces[121] = Vec3( 1.91258e+05, 2.19476e+05, 6.89779e+04);
refforces[122] = Vec3(-2.52379e+04, -1.23674e+05, 2.09489e+05);
refforces[123] = Vec3( 6.55172e+03, -9.23173e+04, 3.29554e+05);
refforces[124] = Vec3(-2.14685e+05, 1.13143e+05, -1.36353e+05);
refforces[125] = Vec3( 2.08124e+05, -2.08124e+04, -1.93257e+05);
refforces[126] = Vec3( 1.02696e+05, -3.39299e+05, -4.47114e+04);
refforces[127] = Vec3(-1.81786e+05, 1.75407e+05, -1.69029e+05);
refforces[128] = Vec3( 7.90534e+04, 1.63962e+05, 2.13738e+05);
refforces[129] = Vec3(-3.45588e+05, 9.36838e+04, 5.67939e+04);
refforces[130] = Vec3( 1.44967e+05, -2.60943e+05, 7.08730e+04);
refforces[131] = Vec3( 2.00649e+05, 1.67207e+05, -1.27685e+05);
refforces[132] = Vec3(-2.70181e+05, 2.05707e+05, -3.11852e+04);
refforces[133] = Vec3( 1.09331e+05, -1.83207e+05, -1.86162e+05);
refforces[134] = Vec3( 1.60883e+05, -2.25804e+04, 2.17340e+05);
refforces[135] = Vec3(-1.04496e+05, -2.97000e+05, -1.63733e+05);
refforces[136] = Vec3( 2.11303e+05, 1.73661e+04, 1.79462e+05);
refforces[137] = Vec3(-1.06849e+05, 2.79694e+05, -1.57134e+04);
refforces[138] = Vec3(-3.82271e+04, 2.11942e+05, 2.60118e+05);
refforces[139] = Vec3(-1.96098e+05, -1.23692e+05, -1.71962e+05);
refforces[140] = Vec3( 2.34334e+05, -8.82195e+04, -8.82188e+04);
refforces[141] = Vec3( 2.17634e+05, 2.72527e+05, 1.42967e+05);
refforces[142] = Vec3( 9.30924e+04, -1.86185e+05, -1.98197e+05);
refforces[143] = Vec3(-3.10770e+05, -8.63246e+04, 5.52480e+04);
refforces[144] = Vec3(-1.63880e+05, -2.98869e+05, 1.01299e+05);
refforces[145] = Vec3( 6.83424e+04, 2.39196e+05, 1.61538e+05);
refforces[146] = Vec3( 9.55787e+04, 5.97354e+04, -2.62846e+05);
refforces[147] = Vec3( 1.06430e+05, -2.97083e+05, -7.97261e+04);
refforces[148] = Vec3(-1.14920e+05, 6.41394e+04, 2.21823e+05);
refforces[149] = Vec3( 8.52531e+03, 2.33043e+05, -1.42101e+05);
refforces[150] = Vec3(-4.96390e+04, -4.12076e+04, -3.67834e+05);
refforces[151] = Vec3( 1.25352e+05, -1.99962e+05, 1.61166e+05);
refforces[152] = Vec3(-7.57841e+04, 2.41138e+05, 2.06689e+05);
refforces[153] = Vec3(-3.06397e+05, -5.15222e+04, -1.37080e+05);
refforces[154] = Vec3( 1.92949e+05, -1.92945e+05, 6.43163e+04);
refforces[155] = Vec3( 1.13490e+05, 2.44443e+05, 7.27504e+04);
refforces[156] = Vec3(-3.74471e+03, 3.83223e+05, -2.14754e+04);
refforces[157] = Vec3( 2.17881e+05, -1.85835e+05, -1.05735e+05);
refforces[158] = Vec3(-2.14191e+05, -1.97454e+05, 1.27176e+05);
refforces[159] = Vec3(-3.33357e+05, -1.38307e+04, -1.17320e+05);
refforces[160] = Vec3( 2.04157e+05, -9.93173e+04, -1.37945e+05);
refforces[161] = Vec3( 1.29262e+05, 1.13105e+05, 2.55294e+05);
refforces[162] = Vec3( 2.50185e+05, 2.64217e+05, -7.18219e+04);
refforces[163] = Vec3(-2.46668e+05, 1.94013e+04, -9.97745e+04);
refforces[164] = Vec3(-3.50266e+03, -2.83658e+05, 1.71598e+05);
refforces[165] = Vec3(-2.05824e+05, 2.71177e+05, -1.16442e+05);
refforces[166] = Vec3(-3.52163e+04, -1.88897e+05, 2.36923e+05);
refforces[167] = Vec3( 2.41012e+05, -8.22954e+04, -1.20505e+05);
refforces[168] = Vec3( 6.89329e+04, 2.09489e+05, 2.76583e+05);
refforces[169] = Vec3( 1.87999e+05, -1.61968e+05, -1.24368e+05);
refforces[170] = Vec3(-2.56932e+05, -4.75793e+04, -1.52255e+05);
refforces[171] = Vec3( 3.39431e+05, -5.75509e+04, 1.62795e+05);
refforces[172] = Vec3(-1.27767e+05, 2.66184e+05, -1.59709e+05);
refforces[173] = Vec3(-2.11726e+05, -2.08613e+05, -3.11349e+03);
refforces[174] = Vec3(-2.58601e+05, 4.61975e+04, -2.46016e+05);
refforces[175] = Vec3( 7.15587e+04, -2.52015e+05, 1.40007e+05);
refforces[176] = Vec3( 1.87109e+05, 2.05820e+05, 1.06028e+05);
refforces[177] = Vec3( 3.92176e+03, 2.94819e+05, -1.84065e+05);
refforces[178] = Vec3(-1.67230e+05, -8.36141e+04, 2.29167e+05);
refforces[179] = Vec3( 1.63334e+05, -2.11213e+05, -4.50586e+04);
refforces[180] = Vec3( 1.11151e+05, 2.40551e+05, -2.68210e+05);
refforces[181] = Vec3(-1.76495e+05, -2.47099e+05, -3.53002e+04);
refforces[182] = Vec3( 6.52872e+04, 6.52855e+03, 3.03586e+05);
refforces[183] = Vec3(-4.84049e+04, -2.73305e+05, -2.95224e+05);
refforces[184] = Vec3(-9.04206e+04, -1.44672e+04, 3.29135e+05);
refforces[185] = Vec3( 1.38830e+05, 2.87820e+05, -3.38610e+04);
refforces[186] = Vec3(-2.09072e+05, -1.53610e+05, -2.86654e+05);
refforces[187] = Vec3(-1.30322e+05, 9.09223e+04, 2.42461e+05);
refforces[188] = Vec3( 3.39380e+05, 6.27113e+04, 4.42669e+04);
refforces[189] = Vec3(-3.15692e+05, 1.48900e+05, -9.20420e+04);
refforces[190] = Vec3( 7.13687e+04, -2.72503e+05, 1.26518e+05);
refforces[191] = Vec3( 2.44351e+05, 1.23612e+05, -3.44964e+04);
refforces[192] = Vec3(-2.80727e+04, 3.15077e+05, -2.05427e+05);
refforces[193] = Vec3(-2.29004e+05, -2.08496e+05, 9.57028e+04);
refforces[194] = Vec3( 2.57096e+05, -1.06603e+05, 1.09738e+05);
refforces[195] = Vec3( 3.33213e+05, -7.80040e+04, -5.04749e+03);
refforces[196] = Vec3(-2.07680e+05, -7.82574e+04, 1.83605e+05);
refforces[197] = Vec3(-1.25574e+05, 1.56274e+05, -1.78599e+05);
refforces[198] = Vec3( 2.66795e+05, -2.82879e+04, -2.26620e+05);
refforces[199] = Vec3(-2.28291e+05, -1.82015e+05, 4.01046e+04);
refforces[200] = Vec3(-3.85027e+04, 2.10288e+05, 1.86592e+05);
refforces[201] = Vec3( 1.93076e+05, 2.05300e+05, 2.64591e+05);
refforces[202] = Vec3(-3.32259e+05, -3.65117e+04, -8.39768e+04);
refforces[203] = Vec3( 1.39204e+05, -1.68822e+05, -1.80669e+05);
refforces[204] = Vec3( 2.15422e+05, 2.88264e+05, 2.49786e+04);
refforces[205] = Vec3( 4.29235e+04, -2.66744e+05, 1.13441e+05);
refforces[206] = Vec3(-2.58339e+05, -2.15280e+04, -1.38395e+05);
refforces[207] = Vec3( 3.27580e+05, -4.93781e+04, 7.43625e+03);
refforces[208] = Vec3(-2.11622e+05, -1.58716e+05, -9.69925e+04);
refforces[209] = Vec3(-1.15917e+05, 2.08125e+05, 8.95715e+04);
refforces[210] = Vec3( 1.10967e+05, -2.71544e+05, -2.06279e+05);
refforces[211] = Vec3(-8.86155e+04, 1.96918e+04, 2.98676e+05);
refforces[212] = Vec3(-2.23913e+04, 2.51912e+05, -9.23690e+04);
refforces[213] = Vec3( 1.91611e+05, -7.99998e+04, -2.83463e+05);
refforces[214] = Vec3( 7.08725e+04, 1.44963e+05, 2.60941e+05);
refforces[215] = Vec3(-2.62503e+05, -6.49202e+04, 2.25808e+04);
refforces[216] = Vec3(-6.63168e+04, -2.84265e+04, 3.72700e+05);
refforces[217] = Vec3(-2.02131e+05, -6.33547e+04, -1.96097e+05);
refforces[218] = Vec3( 2.68466e+05, 9.18414e+04, -1.76621e+05);
refforces[219] = Vec3(-6.80052e+03, 2.72744e+05, -2.21849e+05);
refforces[220] = Vec3( 1.52709e+05, -5.52356e+04, 2.63181e+05);
refforces[221] = Vec3(-1.45890e+05, -2.17461e+05, -4.12893e+04);
refforces[222] = Vec3( 3.07522e+05, -1.21146e+05, 1.14593e+05);
refforces[223] = Vec3(-2.11787e+05, -1.56664e+05, -8.99363e+04);
refforces[224] = Vec3(-9.57076e+04, 2.77857e+05, -2.46987e+04);
refforces[225] = Vec3(-3.24882e+05, -3.09840e+04, -1.31947e+05);
refforces[226] = Vec3( 8.33124e+04, -5.05809e+04, 2.67793e+05);
refforces[227] = Vec3( 2.41536e+05, 8.15185e+04, -1.35863e+05);
refforces[228] = Vec3(-2.16561e+04, -1.67607e+05, -2.70252e+05);
refforces[229] = Vec3( 1.10825e+05, -7.29802e+04, 2.24354e+05);
refforces[230] = Vec3(-8.91995e+04, 2.40572e+05, 4.59512e+04);
refforces[231] = Vec3(-2.22246e+05, 1.96766e+05, -2.46638e+05);
refforces[232] = Vec3( 3.04748e+05, 5.66971e+04, 1.27568e+05);
refforces[233] = Vec3(-8.24632e+04, -2.53495e+05, 1.19113e+05);
refforces[234] = Vec3( 2.20621e+05, -2.03896e+05, 6.63128e+04);
refforces[235] = Vec3(-9.59082e+04, 1.64055e+05, 1.53960e+05);
refforces[236] = Vec3(-1.24758e+05, 3.98170e+04, -2.20320e+05);
refforces[237] = Vec3(-7.79583e+03, -3.49688e+04, 3.64330e+05);
refforces[238] = Vec3(-1.43293e+05, -1.65580e+05, -2.10163e+05);
refforces[239] = Vec3( 1.51159e+05, 2.00522e+05, -1.54247e+05);
refforces[240] = Vec3( 1.82058e+05, -3.72909e+04, -2.80373e+05);
refforces[241] = Vec3(-1.95792e+05, 1.98809e+05, 7.22936e+04);
refforces[242] = Vec3( 1.36910e+04, -1.61546e+05, 2.08094e+05);
refforces[243] = Vec3( 1.40288e+05, 3.27379e+05, 4.78569e+03);
refforces[244] = Vec3(-1.70016e+05, -1.73349e+05, 2.03353e+05);
refforces[245] = Vec3( 2.97331e+04, -1.54072e+05, -2.08134e+05);
refforces[246] = Vec3( 1.21932e+05, 3.52267e+05, 4.69291e+04);
refforces[247] = Vec3(-2.91621e+05, -1.24021e+05, 3.01674e+04);
refforces[248] = Vec3( 1.69673e+05, -2.28288e+05, -7.71238e+04);
refforces[249] = Vec3(-1.41105e+05, 1.52818e+05, 2.59197e+05);
refforces[250] = Vec3( 2.15511e+05, -1.77650e+05, -5.82442e+03);
refforces[251] = Vec3(-7.43779e+04, 2.47926e+04, -2.53438e+05);
refforces[252] = Vec3(-3.34214e+04, 3.09554e+05, 1.58194e+05);
refforces[253] = Vec3(-2.05877e+05, -1.71563e+05, -6.00467e+04);
refforces[254] = Vec3( 2.39329e+05, -1.38076e+05, -9.81875e+04);
refforces[255] = Vec3( 1.32793e+05, -3.72271e+05, 2.88491e+04);
refforces[256] = Vec3(-9.02633e+04, 2.78646e+05, 2.23700e+05);
refforces[257] = Vec3(-4.25632e+04, 9.36427e+04, -2.52553e+05);
refforces[258] = Vec3( 2.97252e+05, 2.17294e+05, -2.50945e+03);
refforces[259] = Vec3(-1.35724e+05, -1.48966e+05, 2.41658e+05);
refforces[260] = Vec3(-1.61536e+05, -6.83423e+04, -2.39199e+05);
refforces[261] = Vec3( 2.50550e+05, -1.39926e+05, 2.48375e+05);
refforces[262] = Vec3( 5.51783e+04, -1.65530e+04, -2.59341e+05);
refforces[263] = Vec3(-3.05734e+05, 1.56505e+05, 1.09189e+04);
refforces[264] = Vec3(-4.44616e+04, 4.17040e+04, -3.31507e+05);
refforces[265] = Vec3(-1.79702e+05, -8.54319e+04, 2.00323e+05);
refforces[266] = Vec3( 2.24182e+05, 4.37421e+04, 1.31227e+05);
refforces[267] = Vec3(-9.89367e+04, -3.76136e+05, 2.17157e+04);
refforces[268] = Vec3(-4.44424e+04, 1.68244e+05, -2.47606e+05);
refforces[269] = Vec3( 1.43421e+05, 2.07965e+05, 2.25893e+05);
refforces[270] = Vec3(-1.09030e+03, -2.44686e+05, -2.30145e+05);
refforces[271] = Vec3(-1.86963e+05, 1.89757e+05, 3.34863e+04);
refforces[272] = Vec3( 1.88003e+05, 5.49541e+04, 1.96680e+05);
refforces[273] = Vec3(-1.15452e+05, -1.55243e+05, 2.81412e+05);
refforces[274] = Vec3(-1.35893e+05, 1.74355e+05, -1.12817e+05);
refforces[275] = Vec3( 2.51361e+05, -1.90905e+04, -1.68633e+05);
refforces[276] = Vec3( 1.76202e+05, -2.31601e+05, -2.00886e+05);
refforces[277] = Vec3(-2.96697e+05, 3.00025e+04, 1.06676e+05);
refforces[278] = Vec3( 1.20457e+05, 2.01635e+05, 9.42700e+04);
refforces[279] = Vec3(-1.66320e+05, -9.08355e+02, 2.65478e+05);
refforces[280] = Vec3( 2.44823e+05, 9.45895e+04, -5.28589e+04);
refforces[281] = Vec3(-7.84765e+04, -9.36654e+04, -2.12648e+05);
refforces[282] = Vec3(-6.58002e+03, -1.21918e+05, 3.16459e+05);
refforces[283] = Vec3( 2.15225e+05, 5.96416e+04, -1.14097e+05);
refforces[284] = Vec3(-2.08615e+05, 6.22725e+04, -2.02387e+05);
refforces[285] = Vec3( 7.09186e+04, 1.83619e+05, 2.71862e+05);
refforces[286] = Vec3( 1.78911e+05, -1.02234e+05, -1.78910e+05);
refforces[287] = Vec3(-2.49882e+05, -8.13582e+04, -9.29803e+04);
refforces[288] = Vec3(-1.35529e+04, -3.20226e+05, -1.16293e+05);
refforces[289] = Vec3( 2.28053e+05, 1.65034e+05, 5.70125e+04);
refforces[290] = Vec3(-2.14515e+05, 1.55237e+05, 5.92732e+04);
refforces[291] = Vec3(-2.65006e+05, 1.75233e+05, 1.91268e+05);
refforces[292] = Vec3( 2.29905e+05, 1.02940e+05, -2.05886e+05);
refforces[293] = Vec3( 3.51345e+04, -2.78156e+05, 1.46393e+04);
refforces[294] = Vec3( 1.59458e+05, 2.25128e+05, 2.11611e+05);
refforces[295] = Vec3( 1.24813e+05, -1.16492e+05, -2.05249e+05);
refforces[296] = Vec3(-2.84281e+05, -1.08601e+05, -6.38824e+03);
refforces[297] = Vec3( 2.61767e+05, -7.55993e+04, -2.32576e+05);
refforces[298] = Vec3(-2.07803e+05, -1.78116e+05, 7.71831e+04);
refforces[299] = Vec3(-5.39242e+04, 2.53755e+05, 1.55427e+05);
refforces[300] = Vec3(-6.44117e+03, 2.31328e+05, -2.54922e+05);
refforces[301] = Vec3(-2.61097e+04, 4.93208e+04, 2.72709e+05);
refforces[302] = Vec3( 3.25053e+04, -2.80718e+05, -1.77304e+04);
refforces[303] = Vec3( 7.06280e+04, 7.26140e+04, 3.28446e+05);
refforces[304] = Vec3( 1.45890e+05, 7.98271e+04, -2.06449e+05);
refforces[305] = Vec3(-2.16516e+05, -1.52473e+05, -1.21980e+05);
refforces[306] = Vec3( 1.94879e+05, -2.83084e+05, 1.41824e+05);
refforces[307] = Vec3(-2.57149e+05, 1.96432e+05, 9.64284e+04);
refforces[308] = Vec3( 6.22633e+04, 8.66280e+04, -2.38228e+05);
refforces[309] = Vec3( 3.26456e+04, 1.17141e+05, -3.28374e+05);
refforces[310] = Vec3( 2.01298e+05, -1.11486e+05, 1.85810e+05);
refforces[311] = Vec3(-2.33937e+05, -5.70482e+03, 1.42641e+05);
refforces[312] = Vec3( 6.42964e+04, 1.88719e+05, -2.86572e+05);
refforces[313] = Vec3( 1.22184e+05, -2.53768e+05, 1.00254e+05);
refforces[314] = Vec3(-1.86433e+05, 6.49694e+04, 1.86429e+05);
refforces[315] = Vec3(-4.12317e+04, -1.73607e+04, -3.68620e+05);
refforces[316] = Vec3(-1.78981e+05, 1.43186e+05, 2.08269e+05);
refforces[317] = Vec3( 2.20155e+05, -1.25802e+05, 1.60395e+05);
refforces[318] = Vec3(-1.58613e+05, 3.01594e+05, -1.29345e+05);
refforces[319] = Vec3( 2.79698e+05, -2.67790e+04, 4.76063e+04);
refforces[320] = Vec3(-1.21063e+05, -2.74847e+05, 8.17976e+04);
refforces[321] = Vec3( 1.00451e+05, 2.03427e+05, -2.75044e+05);
refforces[322] = Vec3(-2.13956e+04, 7.64144e+04, 2.81199e+05);
refforces[323] = Vec3(-7.91039e+04, -2.79910e+05, -6.08590e+03);
refforces[324] = Vec3(-2.80664e+05, 5.26142e+04, -1.53706e+05);
refforces[325] = Vec3( 2.23923e+05, -1.17559e+05, -9.23685e+04);
refforces[326] = Vec3( 5.68062e+04, 6.49218e+04, 2.46158e+05);
refforces[327] = Vec3( 2.88911e+05, -1.17893e+05, -7.40828e+04);
refforces[328] = Vec3(-6.38612e+04, 2.37565e+05, -2.55450e+04);
refforces[329] = Vec3(-2.25033e+05, -1.19637e+05, 9.96952e+04);
refforces[330] = Vec3( 1.03510e+04, 7.35559e+04, 3.47129e+05);
refforces[331] = Vec3( 1.26778e+05, -2.19542e+05, -1.51515e+05);
refforces[332] = Vec3(-1.37190e+05, 1.45950e+05, -1.95573e+05);
refforces[333] = Vec3(-1.31816e+05, 5.57951e+04, -2.81935e+05);
refforces[334] = Vec3(-1.08367e+05, -9.75306e+04, 2.16731e+05);
refforces[335] = Vec3( 2.40191e+05, 4.17715e+04, 6.52667e+04);
refforces[336] = Vec3(-2.86680e+05, -2.63007e+05, 1.37964e+04);
refforces[337] = Vec3( 1.03914e+05, 1.76653e+05, -2.56324e+05);
refforces[338] = Vec3( 1.82779e+05, 8.64040e+04, 2.42594e+05);
refforces[339] = Vec3( 1.09800e+03, -3.11636e+05, 1.85833e+05);
refforces[340] = Vec3(-2.39750e+05, 1.52568e+05, -8.71817e+04);
refforces[341] = Vec3( 2.38635e+05, 1.59089e+05, -9.86351e+04);
refforces[342] = Vec3(-8.76706e+04, -6.10520e+04, 3.31680e+05);
refforces[343] = Vec3( 2.64692e+05, 5.23233e+04, -1.16959e+05);
refforces[344] = Vec3(-1.76973e+05, 8.70353e+03, -2.14689e+05);
refforces[345] = Vec3(-1.15976e+05, -2.72303e+05, -1.33307e+05);
refforces[346] = Vec3( 2.20682e+05, 1.51896e+05, -6.30516e+04);
refforces[347] = Vec3(-1.04744e+05, 1.20457e+05, 1.96395e+05);
refforces[348] = Vec3( 4.57064e+04, 3.43550e+05, 7.23245e+04);
refforces[349] = Vec3(-1.91414e+05, -1.26580e+05, -1.85241e+05);
refforces[350] = Vec3( 1.45684e+05, -2.17040e+05, 1.12977e+05);
refforces[351] = Vec3(-1.88623e+05, -1.22936e+04, 3.10223e+05);
refforces[352] = Vec3( 3.06931e+05, 5.73380e+04, -7.08300e+04);
refforces[353] = Vec3(-1.18279e+05, -4.50586e+04, -2.39376e+05);
refforces[354] = Vec3( 8.31603e+04, -2.75958e+05, 1.16877e+05);
refforces[355] = Vec3(-2.08784e+05, 1.26300e+05, 5.15494e+04);
refforces[356] = Vec3( 1.25608e+05, 1.49661e+05, -1.68370e+05);
refforces[357] = Vec3( 1.44100e+05, -2.34453e+05, 1.73916e+05);
refforces[358] = Vec3(-8.65072e+04, 2.39988e+05, 8.37141e+04);
refforces[359] = Vec3(-5.75432e+04, -5.48037e+03, -2.57574e+05);
refforces[360] = Vec3( 2.72504e+05, 2.99781e+04, 1.85778e+05);
refforces[361] = Vec3(-3.41026e+04, 7.10483e+04, -2.61466e+05);
refforces[362] = Vec3(-2.38458e+05, -1.00996e+05, 7.57451e+04);
refforces[363] = Vec3( 1.45826e+05, -2.81284e+05, 1.15502e+05);
refforces[364] = Vec3(-2.63407e+05, 3.47332e+04, -8.10477e+04);
refforces[365] = Vec3( 1.17594e+05, 2.46657e+05, -3.44181e+04);
refforces[366] = Vec3( 2.59381e+05, -5.73297e+04, 2.56690e+05);
refforces[367] = Vec3(-1.25834e+05, -2.09725e+05, -1.49803e+05);
refforces[368] = Vec3(-1.33554e+05, 2.67105e+05, -1.06844e+05);
refforces[369] = Vec3( 7.18473e+04, -2.59021e+05, 1.89797e+05);
refforces[370] = Vec3( 1.56664e+05, 2.11783e+05, -8.99369e+04);
refforces[371] = Vec3(-2.28511e+05, 4.72761e+04, -9.98083e+04);
refforces[372] = Vec3(-1.99083e+04, 3.17042e+05, -5.62792e+04);
refforces[373] = Vec3(-1.96875e+05, -1.64948e+05, -7.96758e-01);
refforces[374] = Vec3( 2.16840e+05, -1.52072e+05, 5.63215e+04);
const double longcutoff = 30.0*OpenMM::NmPerAngstrom;
const double longcutoff2 = longcutoff*longcutoff;
const double cutoff2 = cutoff*cutoff;
const double cutoff6inv = 1.0 / (cutoff2*cutoff2*cutoff2);
const int nboxes = ceil(longcutoff/boxEdgeLength);
double refenergy = 0.0;
// Loop over home box first...
for(int i = 0; i < NATOMS; ++ i){
for(int j = i+1; j < NATOMS; ++j){
Vec3 dR = positions[i] - positions[j];
double R2 = dR[0]*dR[0] + dR[1]*dR[1] + dR[2]*dR[2];
double sig2 = (sigvals[i] + sigvals[j])*(sigvals[i] + sigvals[j]) / R2;
double sig6 = sig2*sig2*sig2;
double eps = epsvals[i]*epsvals[j];
refenergy += 2.0*eps*(sig6-1.0)*sig6;
if(R2 < cutoff2){
// Add a shift term for direct space parts withing t
refenergy += 2.0*eps*(pow(sigvals[i]+sigvals[j], 6) - 64.0*pow(sigvals[i]*sigvals[j], 3))*cutoff6inv;
}
}
}
// ... and now add in the image box terms
for(int bx = -nboxes; bx <= nboxes; ++bx){
for(int by = -nboxes; by <= nboxes; ++by){
for(int bz = -nboxes; bz <= nboxes; ++bz){
if(bx==0 && by==0 && bz==0) continue;
Vec3 offset(bx*boxEdgeLength, by*boxEdgeLength, bz*boxEdgeLength);
for(int i = 0; i < NATOMS; ++ i){
for(int j = 0; j < NATOMS; ++j){
Vec3 dR = positions[i] - positions[j] + offset;
double R2 = dR[0]*dR[0] + dR[1]*dR[1] + dR[2]*dR[2];
if(R2 > longcutoff2) continue;
double sig2 = (sigvals[i] + sigvals[j])*(sigvals[i] + sigvals[j]) / R2;
double sig6 = sig2*sig2*sig2;
double eps = epsvals[i]*epsvals[j];
refenergy += eps*(sig6-1.0)*sig6;
if(R2 < cutoff2){
// Add a shift term for direct space parts withing teh
refenergy += eps*(pow(sigvals[i]+sigvals[j], 6) - 64.0*pow(sigvals[i]*sigvals[j], 3))*cutoff6inv;
}
}
}
}
}
}
refenergy *= 0.5;
// For this test the reference energy is 545636 kJ/mol, while the difference between DPME and 30A cutoffs
// is just 1.062 kJ/mol. The difference is due to the fact that arithmetic mean combination rules are used
// up to the cutoff, while the reciprocal space uses the geometric mean. See DOI: 10.1021/acs.jctc.5b00726
ASSERT_EQUAL_TOL(refenergy, energy, 5E-6);
ASSERT_EQUAL_TOL(gromacs_energy, energy, 5E-4);
for(int n = 0; n < NATOMS; ++n)
ASSERT_EQUAL_VEC(refforces[n], forces[n], 5E-4);
}
void test_water125_dpme_vs_long_cutoff_with_exclusions() {
const double cutoff = 11.5*OpenMM::NmPerAngstrom;
const double alpha = 0.45*OpenMM::AngstromsPerNm;
const double dalpha = 4.2760443169;
const int grid = 60;
NonbondedForce* forceField = new NonbondedForce();
vector<Vec3> positions;
vector<double> epsvals;
vector<double> sigvals;
vector<pair<int, int> > bonds;
System system;
const int NATOMS = 375;
double boxEdgeLength = 23.01*OpenMM::NmPerAngstrom;
make_waterbox(NATOMS, boxEdgeLength, forceField, positions, epsvals, sigvals, bonds, system, false);
forceField->setNonbondedMethod(OpenMM::NonbondedForce::LJPME);
forceField->createExceptionsFromBonds(bonds, 1.0, 1.0);
forceField->setPMEParameters(alpha, grid, grid, grid);
forceField->setLJPMEParameters(dalpha, grid, grid, grid);
forceField->setCutoffDistance(cutoff);
forceField->setReactionFieldDielectric(1.0);
system.addForce(forceField);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
double energy = state.getPotentialEnergy();
// std::cout << "Energy " << energy << std::endl;
const vector<Vec3>& forces = state.getForces();
// print_forces(forces);
// Gromacs reference values. See comments in test_water2_dpme_energies_forces_no_exclusions() for details.
double gromacs_energy = -2.17481e+02;
vector<Vec3> refforces(NATOMS);
refforces[ 0] = Vec3(-3.10130e+01, -6.01219e+01, -5.31302e+01);
refforces[ 1] = Vec3( 4.21376e+00, 9.13811e-01, 9.61319e-01);
refforces[ 2] = Vec3( 1.42363e+00, 2.97219e+00, 1.27185e+00);
refforces[ 3] = Vec3(-3.70172e+01, -2.95228e+01, -6.27987e+01);
refforces[ 4] = Vec3(-6.57386e-01, 2.39279e+00, 1.53243e+00);
refforces[ 5] = Vec3(-1.61426e+00, 7.11728e-01, 9.99752e-01);
refforces[ 6] = Vec3( 1.60813e+01, -6.77979e+01, -1.01302e+02);
refforces[ 7] = Vec3(-4.23118e+00, 9.25550e-01, 1.28003e+00);
refforces[ 8] = Vec3( 1.81589e+00, 1.10083e+00, 1.28615e+00);
refforces[ 9] = Vec3(-2.24427e+00, -5.71071e+01, -3.18064e+01);
refforces[ 10] = Vec3( 3.41715e+00, 1.32918e+00, 1.27908e+00);
refforces[ 11] = Vec3(-3.09930e+00, 9.91868e-01, 1.69245e+00);
refforces[ 12] = Vec3( 6.08033e+01, -1.02990e+02, -8.26733e+01);
refforces[ 13] = Vec3(-1.01346e+00, 1.35475e+00, 4.13725e+00);
refforces[ 14] = Vec3(-6.71645e-01, 4.69536e-01, 4.64774e-01);
refforces[ 15] = Vec3(-6.39056e+01, -9.85756e-01, -4.97837e+01);
refforces[ 16] = Vec3( 9.97113e-01, 1.13195e-01, 4.49387e+00);
refforces[ 17] = Vec3( 9.48864e-01, 4.22217e+00, 1.56364e+00);
refforces[ 18] = Vec3( 2.18124e+01, -6.14078e+01, -8.10129e+01);
refforces[ 19] = Vec3(-5.59701e-01, -1.47528e+00, 1.40157e+00);
refforces[ 20] = Vec3( 4.29539e+00, 4.27738e-02, 1.03009e+00);
refforces[ 21] = Vec3(-2.62377e+01, 2.55532e+01, -6.89576e+01);
refforces[ 22] = Vec3( 1.17222e-01, 3.81618e+00, 1.74502e+00);
refforces[ 23] = Vec3( 1.46448e-01, 1.06214e-01, 4.27946e+00);
refforces[ 24] = Vec3(-1.90819e+00, 9.86513e+00, -1.05364e+02);
refforces[ 25] = Vec3(-1.18537e+00, 1.75021e+00, 1.54448e+00);
refforces[ 26] = Vec3( 2.96182e+00, -9.48323e-01, 1.61299e+00);
refforces[ 27] = Vec3( 5.61257e+01, 7.69427e+01, -5.84534e+01);
refforces[ 28] = Vec3(-8.11821e-01, -7.15455e-01, 6.60049e-01);
refforces[ 29] = Vec3(-9.20901e-01, 3.76217e+00, 1.35685e+00);
refforces[ 30] = Vec3(-5.03791e+01, 2.24324e+01, -4.31606e+01);
refforces[ 31] = Vec3( 3.72530e+00, 3.48275e-01, 1.40060e+00);
refforces[ 32] = Vec3( 7.61265e-01, 8.56416e-01, 6.23359e-01);
refforces[ 33] = Vec3( 1.95683e+01, 4.16950e+01, -4.33266e+01);
refforces[ 34] = Vec3(-2.19677e+00, 1.06287e+00, 1.58260e+00);
refforces[ 35] = Vec3( 1.70923e+00, 2.09511e+00, 9.84492e-01);
refforces[ 36] = Vec3(-7.84273e+01, -3.34396e+01, -3.66486e+01);
refforces[ 37] = Vec3(-1.53567e-01, 1.74934e-01, 1.15266e+00);
refforces[ 38] = Vec3(-3.45548e+00, 1.68633e-01, 1.15923e+00);
refforces[ 39] = Vec3( 6.90725e+01, -2.09426e+01, -5.31532e+01);
refforces[ 40] = Vec3( 1.33274e+00, 3.09504e-01, 1.40065e+00);
refforces[ 41] = Vec3( 1.65828e+00, -1.96378e-01, 2.68350e+00);
refforces[ 42] = Vec3( 3.39954e+01, -2.65418e+01, -6.81184e+01);
refforces[ 43] = Vec3(-1.17491e+00, -2.88793e+00, 1.40541e+00);
refforces[ 44] = Vec3(-9.63132e-01, -3.78178e-01, 1.06756e+00);
refforces[ 45] = Vec3(-4.44610e+01, -1.81736e+01, -6.19409e+01);
refforces[ 46] = Vec3( 1.48529e+00, 8.95548e-06, 4.60732e+00);
refforces[ 47] = Vec3( 1.00451e+00, -3.88830e+00, 1.27726e+00);
refforces[ 48] = Vec3(-4.23022e+00, 2.52963e+01, -3.04756e+01);
refforces[ 49] = Vec3(-3.45228e+00, 7.61191e-01, 9.40731e-01);
refforces[ 50] = Vec3( 2.78622e+00, 8.32081e-01, 1.37588e+00);
refforces[ 51] = Vec3( 1.63360e+01, 3.02230e+01, -3.91446e+01);
refforces[ 52] = Vec3(-2.64761e+00, 1.18509e+00, 9.81393e-01);
refforces[ 53] = Vec3( 1.74883e+00, -1.51958e-01, 2.56504e+00);
refforces[ 54] = Vec3(-3.01111e+01, 4.08021e+01, -3.45058e+01);
refforces[ 55] = Vec3(-1.17129e-01, 9.74282e-02, 4.56402e+00);
refforces[ 56] = Vec3(-3.03696e+00, 4.44012e-01, 1.44269e+00);
refforces[ 57] = Vec3( 7.57956e+01, -1.12043e+01, -3.92084e+01);
refforces[ 58] = Vec3(-1.55617e+00, 2.26444e-01, 2.88234e+00);
refforces[ 59] = Vec3(-1.37287e+00, -3.79045e+00, 8.55326e-01);
refforces[ 60] = Vec3(-2.88831e+01, 5.72484e+01, -7.17030e+01);
refforces[ 61] = Vec3( 6.88458e-01, -2.06343e+00, 1.03552e+00);
refforces[ 62] = Vec3( 6.94194e-01, -1.83673e+00, 2.90979e+00);
refforces[ 63] = Vec3(-7.87489e+01, 2.17729e+01, -3.72371e+01);
refforces[ 64] = Vec3( 1.39267e-01, -4.55150e+00, 9.53893e-01);
refforces[ 65] = Vec3(-4.27928e+00, -1.14139e+00, 9.25405e-01);
refforces[ 66] = Vec3( 7.13947e+01, 3.02722e+01, -5.16551e+01);
refforces[ 67] = Vec3( 4.07933e+00, -1.28199e+00, 9.34707e-01);
refforces[ 68] = Vec3(-7.53668e-02, -2.14888e+00, 1.27713e+00);
refforces[ 69] = Vec3(-9.36762e+00, 2.98321e+01, -5.70761e+01);
refforces[ 70] = Vec3( 1.35989e+00, -3.09988e+00, 9.89945e-01);
refforces[ 71] = Vec3(-2.20314e+00, -7.81892e-01, 1.21781e+00);
refforces[ 72] = Vec3( 4.89194e+01, 7.40749e+01, -4.22017e+01);
refforces[ 73] = Vec3(-4.25696e+00, -1.18954e+00, 1.04383e+00);
refforces[ 74] = Vec3(-1.40510e+00, -9.87719e-01, 3.30559e+00);
refforces[ 75] = Vec3(-4.95912e+01, -8.24838e+01, -1.82510e+01);
refforces[ 76] = Vec3( 7.39933e-01, 9.29483e-01, -1.09883e+00);
refforces[ 77] = Vec3( 9.70359e-01, 1.03012e+00, 4.01759e+00);
refforces[ 78] = Vec3(-7.87499e+00, -1.87981e+01, 5.77017e+00);
refforces[ 79] = Vec3( 3.82847e+00, 1.01191e+00, -7.30715e-02);
refforces[ 80] = Vec3(-2.64831e+00, 1.68402e+00, 1.06474e-01);
refforces[ 81] = Vec3( 1.81335e+01, -6.72766e+01, 7.21397e+01);
refforces[ 82] = Vec3(-1.89188e-01, 1.27803e+00, 8.45103e-01);
refforces[ 83] = Vec3( 2.47584e+00, 1.54044e+00, 6.55440e-01);
refforces[ 84] = Vec3(-1.05824e+00, -6.50833e+01, -3.88413e+01);
refforces[ 85] = Vec3(-3.21762e+00, 1.58809e+00, -1.32879e-01);
refforces[ 86] = Vec3( 3.30285e+00, 1.52154e+00, -3.56471e-01);
refforces[ 87] = Vec3( 4.41972e+01, -3.58815e+01, 4.01227e+01);
refforces[ 88] = Vec3(-1.22923e+00, 8.91826e-01, 2.84505e+00);
refforces[ 89] = Vec3(-4.31649e+00, 1.00895e+00, 4.43366e-01);
refforces[ 90] = Vec3(-3.65176e+01, 4.86616e+01, -6.44163e+00);
refforces[ 91] = Vec3( 1.03989e+00, 3.91910e+00, 7.93373e-01);
refforces[ 92] = Vec3( 4.11089e+00, -4.60733e-01, -7.78461e-02);
refforces[ 93] = Vec3(-1.58332e+01, -6.82045e+01, 6.62934e+01);
refforces[ 94] = Vec3(-7.75645e-02, -3.66897e+00, -3.55044e-01);
refforces[ 95] = Vec3( 4.08399e-01, 2.84950e-01, 3.80641e+00);
refforces[ 96] = Vec3(-5.05975e+00, 4.20346e+01, 3.49518e+01);
refforces[ 97] = Vec3( 9.82673e-01, 2.64451e+00, 4.02971e-01);
refforces[ 98] = Vec3(-1.24992e+00, -3.34479e-01, 1.95012e+00);
refforces[ 99] = Vec3( 2.31815e+00, -2.30056e+00, 6.49918e+01);
refforces[100] = Vec3(-2.16986e+00, -1.05184e-01, 1.89395e+00);
refforces[101] = Vec3( 3.51302e+00, 1.83706e-01, 7.08534e-01);
refforces[102] = Vec3( 4.46929e+01, -7.11604e+01, -6.62201e+00);
refforces[103] = Vec3(-1.87730e+00, -1.10206e+00, -1.47504e+00);
refforces[104] = Vec3(-1.41639e+00, -1.36347e+00, 6.10811e-01);
refforces[105] = Vec3(-3.12256e+01, -1.73923e+01, -4.47428e+01);
refforces[106] = Vec3( 7.92004e-01, -1.39066e+00, -2.68309e+00);
refforces[107] = Vec3( 1.54891e+00, 2.50018e+00, -6.21395e-01);
refforces[108] = Vec3(-3.83585e+01, 3.90231e+01, -3.68876e+01);
refforces[109] = Vec3( 1.86446e-01, 3.49120e+00, -4.00101e-01);
refforces[110] = Vec3(-4.05592e+00, -2.21609e-01, 2.13257e-01);
refforces[111] = Vec3( 5.70991e+01, -5.95502e+01, -4.08285e+01);
refforces[112] = Vec3(-4.25039e-01, -3.96206e-01, -3.23550e+00);
refforces[113] = Vec3( 4.14811e+00, -1.47859e-01, 1.11071e-01);
refforces[114] = Vec3(-2.74979e+01, 4.40260e+01, 3.06766e+00);
refforces[115] = Vec3( 2.22804e-01, 3.48934e+00, -1.96162e-01);
refforces[116] = Vec3(-4.21754e+00, 1.18655e-01, 3.36974e-01);
refforces[117] = Vec3( 6.32783e+01, 8.02719e+01, 1.38219e+01);
refforces[118] = Vec3(-1.49058e+00, 1.87045e+00, -1.32164e-01);
refforces[119] = Vec3(-2.30776e+00, 1.73240e-01, 1.92445e+00);
refforces[120] = Vec3(-4.04272e+01, -1.77143e+01, 1.57461e+01);
refforces[121] = Vec3( 1.82378e+00, 2.60376e+00, 2.33866e-01);
refforces[122] = Vec3( 1.33379e+00, -1.16675e+00, 3.34265e+00);
refforces[123] = Vec3(-8.78170e+00, 1.35313e+01, -5.40700e+01);
refforces[124] = Vec3(-2.72817e+00, 3.27413e-01, -6.95012e-01);
refforces[125] = Vec3( 2.41935e+00, -2.66049e-01, -1.62940e+00);
refforces[126] = Vec3(-3.63273e+01, 6.91610e+01, -3.72663e+00);
refforces[127] = Vec3(-1.40546e+00, 7.48503e-01, -9.73230e-01);
refforces[128] = Vec3( 5.39530e-01, 8.56302e-01, 2.57617e+00);
refforces[129] = Vec3( 2.54426e+01, -5.04169e+01, -1.76229e+01);
refforces[130] = Vec3( 6.82595e-01, -3.17362e+00, 2.20610e-01);
refforces[131] = Vec3( 1.94539e+00, 1.53325e+00, -4.24624e-01);
refforces[132] = Vec3( 3.61678e+01, -7.89030e+01, -9.61808e+00);
refforces[133] = Vec3(-1.29295e+00, -1.55223e+00, -1.88241e+00);
refforces[134] = Vec3(-1.51438e+00, 3.14594e-02, 3.60043e+00);
refforces[135] = Vec3(-4.60860e+01, 6.18971e+01, 1.38188e+01);
refforces[136] = Vec3( 3.07506e+00, -9.60659e-01, 1.81485e+00);
refforces[137] = Vec3( 6.46515e-01, -7.30203e-01, -2.17471e-01);
refforces[138] = Vec3( 7.76539e+00, 3.18751e+01, -6.18739e+01);
refforces[139] = Vec3(-2.12790e+00, -1.06577e+00, -1.03098e+00);
refforces[140] = Vec3( 3.70469e+00, -7.70591e-01, -2.00619e-01);
refforces[141] = Vec3(-4.02748e+01, 1.93804e+01, 1.92911e+01);
refforces[142] = Vec3( 5.74429e-01, -1.58840e+00, -2.07083e+00);
refforces[143] = Vec3(-4.21689e+00, -7.25280e-01, 1.61839e-01);
refforces[144] = Vec3( 4.10890e+01, 6.50772e+01, -6.64661e+00);
refforces[145] = Vec3( 2.02022e-01, -1.46124e+00, 1.99785e+00);
refforces[146] = Vec3( 1.91733e-01, -1.14906e+00, -4.18291e+00);
refforces[147] = Vec3( 3.77785e+01, 1.01191e+02, -6.07436e+00);
refforces[148] = Vec3(-1.03030e+00, -1.26650e+00, 3.57188e+00);
refforces[149] = Vec3(-7.42295e-01, -1.05437e+00, -1.47491e+00);
refforces[150] = Vec3(-7.40150e+01, -3.53477e+01, 1.81946e+01);
refforces[151] = Vec3( 1.65267e+00, 1.39873e+00, 1.46780e+00);
refforces[152] = Vec3( 1.18632e+00, 2.66165e+00, 1.61236e+00);
refforces[153] = Vec3( 3.89536e+01, -2.96071e+01, -1.38610e+01);
refforces[154] = Vec3( 2.05061e+00, 1.54050e+00, 5.35476e-01);
refforces[155] = Vec3( 4.98336e-01, 3.85036e+00, 4.21301e-01);
refforces[156] = Vec3(-5.53456e+01, -6.87157e+01, -3.55693e+01);
refforces[157] = Vec3( 3.17070e+00, 1.65800e+00, -3.99476e-01);
refforces[158] = Vec3(-2.02395e+00, 1.48143e+00, 1.00879e+00);
refforces[159] = Vec3( 5.94087e+01, -4.57694e+01, 2.77585e+01);
refforces[160] = Vec3( 2.05570e+00, 1.46552e+00, -1.41447e+00);
refforces[161] = Vec3( 2.97741e-01, 9.12876e-01, 3.27902e+00);
refforces[162] = Vec3( 1.93442e+01, -4.16391e+01, 3.34803e-01);
refforces[163] = Vec3(-3.93865e+00, 8.46322e-01, -4.47285e-01);
refforces[164] = Vec3(-7.34898e-01, 9.82679e-01, 1.44017e+00);
refforces[165] = Vec3(-3.34824e+01, -1.38834e+01, -2.62952e+01);
refforces[166] = Vec3( 1.26693e+00, -1.10171e+00, 3.22806e+00);
refforces[167] = Vec3( 3.49758e+00, -1.84534e-01, -4.62412e-01);
refforces[168] = Vec3( 1.82122e+00, -5.69776e+01, -3.86605e+01);
refforces[169] = Vec3( 1.92404e+00, -1.05303e+00, -4.52186e-01);
refforces[170] = Vec3(-3.25172e+00, 9.44050e-02, -5.87318e-01);
refforces[171] = Vec3(-5.98475e+01, 1.85708e+01, -2.67060e+01);
refforces[172] = Vec3(-3.77230e-01, 3.29609e+00, -4.81590e-01);
refforces[173] = Vec3(-1.66002e+00, -2.41098e+00, 1.03425e-01);
refforces[174] = Vec3( 6.47852e+01, 4.38661e+00, 1.77482e+01);
refforces[175] = Vec3(-1.29162e-01, -3.40031e+00, 3.91521e-01);
refforces[176] = Vec3( 1.28253e+00, 2.14633e+00, 2.64792e-01);
refforces[177] = Vec3( 2.95010e+01, -5.60376e+00, 4.16733e+01);
refforces[178] = Vec3(-1.43378e+00, -1.96178e-01, 2.40594e+00);
refforces[179] = Vec3(-1.56255e+00, -3.08967e+00, -3.14335e-01);
refforces[180] = Vec3(-6.02384e+01, -1.59585e+01, 7.16798e+01);
refforces[181] = Vec3( 1.68669e+00, -3.54228e+00, -2.98122e-01);
refforces[182] = Vec3( 9.46412e-01, -8.03852e-02, 4.17305e+00);
refforces[183] = Vec3( 3.87313e+00, 4.46632e+01, 4.59130e+01);
refforces[184] = Vec3(-9.83299e-02, -8.11669e-02, 4.04515e+00);
refforces[185] = Vec3( 6.64172e-01, 3.66814e+00, -2.58278e-01);
refforces[186] = Vec3(-1.65450e+01, 2.35336e+01, 7.09485e+01);
refforces[187] = Vec3(-6.98821e-01, 2.45516e-01, 2.69560e+00);
refforces[188] = Vec3( 4.04145e+00, 5.46258e-02, -1.82210e-02);
refforces[189] = Vec3( 2.39311e+01, 1.22785e+01, -2.13260e+01);
refforces[190] = Vec3(-3.33802e-02, -3.60205e+00, 6.21747e-01);
refforces[191] = Vec3( 3.50616e+00, 6.09623e-01, -7.40284e-02);
refforces[192] = Vec3( 2.32693e+01, -1.88836e+01, 1.24193e+01);
refforces[193] = Vec3(-2.25948e+00, -1.74718e+00, 2.65705e-01);
refforces[194] = Vec3(-1.32949e+00, -8.67446e-01, 7.75386e-01);
refforces[195] = Vec3(-4.40626e+01, 1.17032e+01, -4.18284e+01);
refforces[196] = Vec3( 1.61723e+00, -6.18309e-01, 2.45312e+00);
refforces[197] = Vec3( 1.42535e+00, 1.71801e+00, -1.86477e+00);
refforces[198] = Vec3( 3.37157e+00, -1.65818e+01, 7.59773e+01);
refforces[199] = Vec3(-2.81989e+00, -1.37877e+00, -9.60015e-02);
refforces[200] = Vec3(-8.77602e-02, 2.44299e+00, 1.17362e+00);
refforces[201] = Vec3( 2.44644e+01, -3.26831e+01, -5.34506e+01);
refforces[202] = Vec3(-4.14853e+00, -9.48873e-02, -2.18126e-01);
refforces[203] = Vec3( 8.13810e-01, -1.30429e+00, -1.62539e+00);
refforces[204] = Vec3( 1.03414e+01, -4.14898e+00, 2.56841e+01);
refforces[205] = Vec3(-1.50990e-01, -3.90514e+00, 2.98649e-01);
refforces[206] = Vec3(-3.60035e+00, -7.83546e-02, -7.95300e-01);
refforces[207] = Vec3( 4.49059e+01, 2.88959e+01, 1.53626e+01);
refforces[208] = Vec3(-2.55855e+00, -1.55231e+00, -3.96734e-01);
refforces[209] = Vec3(-1.14072e+00, 3.25255e+00, 2.39860e-01);
refforces[210] = Vec3(-4.12850e+01, 6.11654e+01, 2.43179e+01);
refforces[211] = Vec3( 1.20781e+00, -8.28196e-01, 4.26212e+00);
refforces[212] = Vec3( 7.30387e-01, -9.26965e-01, -9.32605e-01);
refforces[213] = Vec3(-1.64972e+01, 4.58667e+01, 5.58154e+01);
refforces[214] = Vec3( 4.43484e-01, -1.67205e+00, 3.42164e+00);
refforces[215] = Vec3(-4.14170e+00, -9.68400e-01, -9.21231e-02);
refforces[216] = Vec3( 1.79252e+01, 6.24205e+01, -1.47777e+01);
refforces[217] = Vec3(-2.53437e+00, -9.16373e-01, -1.63636e+00);
refforces[218] = Vec3( 3.32247e+00, -1.29776e+00, -1.07427e+00);
refforces[219] = Vec3( 1.79752e+01, 5.16430e+01, 3.90249e+01);
refforces[220] = Vec3( 7.14180e-01, -1.00018e+00, 3.14118e+00);
refforces[221] = Vec3(-1.07965e+00, -3.41285e+00, -2.24161e-01);
refforces[222] = Vec3( 3.16317e+01, 4.98025e+01, -4.17518e+01);
refforces[223] = Vec3(-2.55899e+00, -1.63433e+00, -3.76149e-01);
refforces[224] = Vec3(-1.19443e+00, -1.02227e+00, -5.37349e-02);
refforces[225] = Vec3(-3.77249e+01, -4.85845e+01, -2.11073e+01);
refforces[226] = Vec3( 7.98995e-01, 1.26056e+00, 4.28442e+00);
refforces[227] = Vec3( 3.35648e+00, 9.11653e-01, -8.07025e-01);
refforces[228] = Vec3(-3.16004e+01, -2.04156e+01, 5.01542e+01);
refforces[229] = Vec3( 8.97766e-01, 1.34997e+00, 2.86585e+00);
refforces[230] = Vec3(-2.09603e-01, 4.05651e+00, -1.91043e-02);
refforces[231] = Vec3( 3.61582e+01, -3.35593e+01, 4.19940e+01);
refforces[232] = Vec3( 3.66075e+00, 7.71021e-01, 3.45598e-01);
refforces[233] = Vec3(-7.50361e-01, 1.22549e+00, 7.98677e-01);
refforces[234] = Vec3(-4.42511e+01, -2.71049e+01, -4.56576e+01);
refforces[235] = Vec3(-3.30181e-01, 1.98824e+00, 2.21005e+00);
refforces[236] = Vec3(-7.68719e-01, 9.09063e-01, -3.77633e+00);
refforces[237] = Vec3( 7.33817e+01, -3.03886e+01, -7.59758e+01);
refforces[238] = Vec3(-1.71701e+00, 1.41048e+00, -1.84182e+00);
refforces[239] = Vec3(-1.35491e+00, 2.27816e+00, -1.08799e+00);
refforces[240] = Vec3(-4.58218e+01, -2.91931e+01, 1.12369e+01);
refforces[241] = Vec3( 1.68546e+00, 2.81258e+00, 3.93755e-01);
refforces[242] = Vec3( 8.28917e-01, -1.32237e+00, 2.91182e+00);
refforces[243] = Vec3( 5.44446e+00, -3.99466e+01, 6.77923e+00);
refforces[244] = Vec3(-1.09231e+00, -5.21927e-01, 1.83581e+00);
refforces[245] = Vec3( 5.24849e-02, -7.21832e-01, -3.35896e+00);
refforces[246] = Vec3(-1.29863e+01, -3.94851e+01, -2.70347e+01);
refforces[247] = Vec3(-3.94725e+00, -2.01688e-01, 5.93703e-02);
refforces[248] = Vec3( 1.30447e+00, -2.35362e+00, -2.94278e-01);
refforces[249] = Vec3( 2.56542e+01, -3.79434e+01, -6.19782e+01);
refforces[250] = Vec3( 2.48025e+00, -1.19994e+00, 1.41640e-01);
refforces[251] = Vec3(-5.01379e-01, 2.48607e-01, -3.97535e+00);
refforces[252] = Vec3( 3.46461e+01, -8.37214e+01, -3.92225e+01);
refforces[253] = Vec3(-2.80216e+00, -1.13524e+00, 1.85582e-02);
refforces[254] = Vec3(-1.28421e+00, -9.50174e-01, -5.56828e-01);
refforces[255] = Vec3(-3.56755e+01, 1.44176e+01, -7.63345e-01);
refforces[256] = Vec3( 1.25547e+00, 2.64846e+00, 1.29226e+00);
refforces[257] = Vec3( 1.22691e+00, 5.72301e-01, -4.09853e+00);
refforces[258] = Vec3(-6.02997e+00, -1.31579e+01, -5.03304e+01);
refforces[259] = Vec3(-4.59947e-01, -8.09031e-01, 3.08383e+00);
refforces[260] = Vec3(-8.93872e-01, -3.70797e-01, -2.89773e+00);
refforces[261] = Vec3(-1.92458e+00, 2.50787e+01, -4.30937e+01);
refforces[262] = Vec3( 2.10381e-01, -1.24125e-01, -4.01554e+00);
refforces[263] = Vec3(-3.85853e+00, 6.72311e-01, 4.06873e-02);
refforces[264] = Vec3( 1.66952e+01, 1.47383e+01, 4.13458e+01);
refforces[265] = Vec3(-2.12261e+00, -5.40916e-01, 1.54532e+00);
refforces[266] = Vec3( 3.54041e+00, -4.73740e-02, 4.73489e-01);
refforces[267] = Vec3( 4.43789e+01, 6.96271e+01, 4.06335e+00);
refforces[268] = Vec3(-9.59563e-01, 9.94730e-01, -3.12464e+00);
refforces[269] = Vec3(-1.42363e+00, 1.62107e+00, 1.87365e+00);
refforces[270] = Vec3(-5.38380e+01, 2.27365e+01, 1.95666e+01);
refforces[271] = Vec3( 1.47405e+00, 2.11523e+00, 1.97777e-01);
refforces[272] = Vec3( 2.54377e+00, -4.04439e-02, 1.97927e+00);
refforces[273] = Vec3( 1.33568e+01, 1.88750e+01, -3.59233e+01);
refforces[274] = Vec3(-1.09293e+00, 2.25841e+00, -4.61222e-01);
refforces[275] = Vec3( 3.27762e+00, -1.71208e-01, -8.67824e-01);
refforces[276] = Vec3(-3.41864e+01, 3.38579e+01, 5.95219e+01);
refforces[277] = Vec3(-4.18249e+00, -8.81154e-02, 1.97498e-01);
refforces[278] = Vec3( 1.06177e+00, 2.34089e+00, 2.42037e-01);
refforces[279] = Vec3( 2.35073e+01, 1.61625e+01, -2.58858e+01);
refforces[280] = Vec3( 3.87903e+00, 1.67313e-01, -4.03473e-02);
refforces[281] = Vec3(-5.12341e-01, -5.62857e-01, -3.19237e+00);
refforces[282] = Vec3( 3.39154e+01, -5.09470e+00, -2.29146e+01);
refforces[283] = Vec3(-1.24992e+00, 5.24960e-01, -1.16022e+00);
refforces[284] = Vec3(-2.39537e+00, 1.82818e-01, -1.53421e+00);
refforces[285] = Vec3(-5.56195e+01, 2.89266e+01, -2.61137e+01);
refforces[286] = Vec3( 2.49596e+00, -1.03213e+00, -1.51258e+00);
refforces[287] = Vec3( 1.02471e+00, -1.05342e+00, -6.79809e-01);
refforces[288] = Vec3(-1.52895e+01, 4.83734e+01, -7.33233e+00);
refforces[289] = Vec3( 3.77837e+00, -1.59224e+00, 2.02675e-01);
refforces[290] = Vec3(-3.51854e+00, -1.54234e+00, 2.89348e-01);
refforces[291] = Vec3( 3.22262e+01, 2.32542e+01, 2.37269e+01);
refforces[292] = Vec3( 1.88520e+00, -1.38396e+00, -1.98750e+00);
refforces[293] = Vec3( 4.99036e-02, -4.53129e+00, -2.13859e-01);
refforces[294] = Vec3(-7.48274e+00, 3.71318e+01, -2.35667e+01);
refforces[295] = Vec3( 7.81671e-01, -1.07371e+00, -2.37009e+00);
refforces[296] = Vec3(-3.98896e+00, -9.36146e-01, 2.62843e-02);
refforces[297] = Vec3( 4.33081e+01, 4.24806e+01, 3.21190e+01);
refforces[298] = Vec3(-2.52531e+00, -1.90285e+00, 2.72091e-01);
refforces[299] = Vec3(-9.70927e-01, -1.13219e+00, 1.47351e+00);
refforces[300] = Vec3(-4.71070e+01, -7.19253e+01, 5.82986e+01);
refforces[301] = Vec3( 6.82929e-01, 1.00679e+00, -6.94522e-01);
refforces[302] = Vec3( 8.31359e-01, 7.09804e-01, -8.12652e-01);
refforces[303] = Vec3( 3.62309e+00, -3.42931e+01, 1.98231e+01);
refforces[304] = Vec3( 1.23138e+00, 8.49297e-01, -2.39283e+00);
refforces[305] = Vec3(-2.87428e+00, 1.41050e+00, -1.03948e+00);
refforces[306] = Vec3(-3.83149e+00, -2.61638e+01, 2.98550e+01);
refforces[307] = Vec3(-2.90010e+00, 1.38356e+00, -1.22906e+00);
refforces[308] = Vec3( 2.62337e-01, 9.72795e-01, -4.02660e+00);
refforces[309] = Vec3( 7.84655e+00, -5.09531e+01, 7.96762e+01);
refforces[310] = Vec3( 2.46967e+00, 9.48901e-01, -1.17317e+00);
refforces[311] = Vec3(-4.11596e+00, 7.95633e-01, -1.39335e+00);
refforces[312] = Vec3( 5.03705e+01, -8.09993e+01, 1.13172e+02);
refforces[313] = Vec3(-4.48925e-01, 4.29309e-01, -5.50572e-01);
refforces[314] = Vec3(-2.66201e+00, 1.05662e+00, -1.44247e+00);
refforces[315] = Vec3(-6.12660e+01, 2.31218e+01, 4.57287e+01);
refforces[316] = Vec3( 8.42017e-01, 1.41042e+00, -7.78795e-01);
refforces[317] = Vec3( 3.11298e+00, -8.04273e-01, -1.51273e+00);
refforces[318] = Vec3( 1.83823e+01, -2.83588e+01, 6.13597e+01);
refforces[319] = Vec3( 4.37781e+00, 8.12091e-02, -1.33992e+00);
refforces[320] = Vec3(-5.81396e-01, -3.61991e+00, -1.22489e+00);
refforces[321] = Vec3(-4.85270e+01, -6.50314e+01, 7.16441e+01);
refforces[322] = Vec3(-3.40093e-02, 9.01514e-01, -1.26573e+00);
refforces[323] = Vec3(-8.67193e-02, -3.94828e+00, -8.97127e-01);
refforces[324] = Vec3( 6.25833e+01, -2.31957e+01, 8.66089e+01);
refforces[325] = Vec3( 2.49809e+00, -7.64197e-01, -1.27775e+00);
refforces[326] = Vec3( 2.11019e-01, 7.81764e-01, -1.23664e+00);
refforces[327] = Vec3( 2.04801e+01, 3.14002e+01, 6.96727e+01);
refforces[328] = Vec3(-7.99932e-01, 4.35586e+00, -8.77957e-01);
refforces[329] = Vec3(-2.87129e+00, -1.02321e+00, -1.42702e+00);
refforces[330] = Vec3(-6.36347e+01, -3.58428e+01, 4.52682e+01);
refforces[331] = Vec3( 1.32210e+00, -2.58500e+00, -1.43327e+00);
refforces[332] = Vec3( 1.52218e+00, 1.63513e+00, -2.29784e+00);
refforces[333] = Vec3( 4.36105e+00, 3.70776e+01, 6.46133e+01);
refforces[334] = Vec3(-1.19452e+00, -1.01252e+00, -1.43172e+00);
refforces[335] = Vec3( 4.34983e+00, -6.52342e-02, -1.33662e+00);
refforces[336] = Vec3( 1.13050e+01, 4.99187e+01, 7.16119e+01);
refforces[337] = Vec3( 2.29221e-01, 6.35843e-01, -3.59259e+00);
refforces[338] = Vec3( 1.65239e+00, 4.20995e-01, -1.42878e+00);
refforces[339] = Vec3(-1.79210e+01, 1.92423e+01, 1.77516e+01);
refforces[340] = Vec3(-2.91278e+00, 9.22214e-01, -8.41281e-01);
refforces[341] = Vec3( 2.96465e+00, 1.05962e+00, -6.85280e-01);
refforces[342] = Vec3( 5.19378e+01, -2.55266e+01, 3.63518e+01);
refforces[343] = Vec3(-1.13088e+00, 4.54600e-01, -1.30862e+00);
refforces[344] = Vec3(-2.05369e+00, -9.69459e-03, -2.69351e+00);
refforces[345] = Vec3(-4.22214e+01, 4.88282e+01, 3.76741e+01);
refforces[346] = Vec3( 3.46996e+00, 9.57280e-01, -7.60128e-01);
refforces[347] = Vec3( 7.62585e-01, 1.14548e+00, -8.06697e-01);
refforces[348] = Vec3(-2.35024e+01, -6.73585e+01, 6.49050e+01);
refforces[349] = Vec3(-1.58984e+00, -6.44551e-01, -2.37758e+00);
refforces[350] = Vec3( 1.32604e+00, -2.37576e+00, -1.54939e+00);
refforces[351] = Vec3( 2.57776e+01, -1.40743e+01, 2.06580e+01);
refforces[352] = Vec3( 4.24916e+00, 6.10665e-02, -8.19360e-01);
refforces[353] = Vec3(-7.94423e-01, -1.75764e-01, -3.51414e+00);
refforces[354] = Vec3(-1.24260e+01, 6.96334e-01, 5.97705e+01);
refforces[355] = Vec3(-3.38899e+00, 9.44919e-01, -1.25780e+00);
refforces[356] = Vec3( 6.81664e-01, 1.16965e+00, -2.34256e+00);
refforces[357] = Vec3( 5.15292e+01, 5.13086e+01, 6.16724e+01);
refforces[358] = Vec3(-1.04216e+00, 3.34685e+00, -1.33787e+00);
refforces[359] = Vec3(-9.57017e-01, -1.59610e-01, -4.31963e+00);
refforces[360] = Vec3(-5.88173e+01, 3.30524e+01, 6.23031e+01);
refforces[361] = Vec3( 9.35413e-01, -1.09829e+00, -4.65202e+00);
refforces[362] = Vec3( 6.95250e-01, -1.24375e+00, -6.50832e-01);
refforces[363] = Vec3( 1.64454e+01, 1.08071e+02, 3.76968e+01);
refforces[364] = Vec3(-4.25249e+00, -1.10053e+00, -7.56357e-01);
refforces[365] = Vec3( 1.17898e+00, -1.10215e+00, -8.21366e-01);
refforces[366] = Vec3(-5.20527e+00, 5.49522e+01, 4.55303e+01);
refforces[367] = Vec3(-7.98794e-01, -2.78246e+00, -1.27815e+00);
refforces[368] = Vec3(-1.02109e+00, -1.21921e+00, -1.26706e+00);
refforces[369] = Vec3( 3.05185e+00, 3.99846e+01, 5.39902e+01);
refforces[370] = Vec3( 1.93675e+00, -1.28986e+00, -1.21655e+00);
refforces[371] = Vec3(-4.14952e+00, -1.06509e+00, -9.52154e-01);
refforces[372] = Vec3( 6.06000e+01, 2.50872e+01, 4.29623e+01);
refforces[373] = Vec3(-3.50284e+00, -1.47848e+00, -7.98049e-01);
refforces[374] = Vec3(-8.66087e-01, -1.73056e+00, -6.59554e-01);
// Find the exclusion information
vector<set<int> > exclusions(NATOMS);
for (int i = 0; i < forceField->getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
forceField->getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
exclusions[particle1].insert(particle2);
exclusions[particle2].insert(particle1);
}
const double longcutoff = 35.0*OpenMM::NmPerAngstrom;
const double longcutoff2 = longcutoff*longcutoff;
const double cutoff2 = cutoff*cutoff;
const double cutoff6inv = 1.0 / (cutoff2*cutoff2*cutoff2);
const int nboxes = ceil(longcutoff/boxEdgeLength);
double refenergy = 0.0;
// Loop over home box first...
for(int i = 0; i < NATOMS; ++ i){
for(int j = i+1; j < NATOMS; ++j){
Vec3 dR = positions[i] - positions[j];
double R2 = dR[0]*dR[0] + dR[1]*dR[1] + dR[2]*dR[2];
double sig2 = (sigvals[i] + sigvals[j])*(sigvals[i] + sigvals[j]) / R2;
double sig6 = sig2*sig2*sig2;
double eps = epsvals[i]*epsvals[j];
refenergy += 2.0*eps*(sig6-1.0)*sig6;
if(R2 < cutoff2){
// Add a shift term for direct space parts withing t
refenergy += 2.0*eps*(pow(sigvals[i]+sigvals[j], 6) - 64.0*pow(sigvals[i]*sigvals[j], 3))*cutoff6inv;
}
}
}
// ... back out exclusions
for (int ii = 0; ii < NATOMS; ii++){
for (set<int>::const_iterator iter = exclusions[ii].begin(); iter != exclusions[ii].end(); ++iter) {
if (*iter > ii) {
int i = ii;
int j = *iter;
Vec3 dR = positions[i] - positions[j];
double R2 = dR[0]*dR[0] + dR[1]*dR[1] + dR[2]*dR[2];
double sig2 = (sigvals[i] + sigvals[j])*(sigvals[i] + sigvals[j]) / R2;
double sig6 = sig2*sig2*sig2;
double eps = epsvals[i]*epsvals[j];
refenergy -= 2.0*eps*(sig6-1.0)*sig6;
if(R2 < cutoff2){
// Add a shift term for direct space parts withing t
refenergy -= 2.0*eps*(pow(sigvals[i]+sigvals[j], 6) - 64.0*pow(sigvals[i]*sigvals[j], 3))*cutoff6inv;
}
}
}
}
// ... and now add in the image box terms
for(int bx = -nboxes; bx <= nboxes; ++bx){
for(int by = -nboxes; by <= nboxes; ++by){
for(int bz = -nboxes; bz <= nboxes; ++bz){
if(bx==0 && by==0 && bz==0) continue;
Vec3 offset(bx*boxEdgeLength, by*boxEdgeLength, bz*boxEdgeLength);
for(int i = 0; i < NATOMS; ++ i){
for(int j = 0; j < NATOMS; ++j){
Vec3 dR = positions[i] - positions[j] + offset;
double R2 = dR[0]*dR[0] + dR[1]*dR[1] + dR[2]*dR[2];
if(R2 > longcutoff2) continue;
double sig2 = (sigvals[i] + sigvals[j])*(sigvals[i] + sigvals[j]) / R2;
double sig6 = sig2*sig2*sig2;
double eps = epsvals[i]*epsvals[j];
refenergy += eps*(sig6-1.0)*sig6;
if(R2 < cutoff2){
// Add a shift term for direct space parts withing teh
refenergy += eps*(pow(sigvals[i]+sigvals[j], 6) - 64.0*pow(sigvals[i]*sigvals[j], 3))*cutoff6inv;
}
}
}
}
}
}
refenergy *= 0.5;
// For this test the reference energy is -294.078 kJ/mol, while the difference between DPME and 30A cutoffs
// is just 0.064 kJ/mol. The difference is due to the fact that arithmetic mean combination rules are used
// up to the cutoff, while the reciprocal space uses the geometric mean. See DOI: 10.1021/acs.jctc.5b00726
ASSERT_EQUAL_TOL(refenergy, energy, 5E-4);
ASSERT_EQUAL_TOL(gromacs_energy, energy, 5E-5);
// Forces accumulated in single precision are tested to a more permissive criterion; the double
// precision platform can match to 5E-5.
for(int n = 0; n < NATOMS; ++n)
ASSERT_EQUAL_VEC(refforces[n], forces[n], 1E-4);
}
void testCoulomb() { void testCoulomb() {
System system; System system;
system.addParticle(1.0); system.addParticle(1.0);
...@@ -689,6 +2346,10 @@ void runPlatformTests(); ...@@ -689,6 +2346,10 @@ void runPlatformTests();
int main(int argc, char* argv[]) { int main(int argc, char* argv[]) {
try { try {
initializeTests(argc, argv); initializeTests(argc, argv);
test_water2_dpme_energies_forces_no_exclusions();
test_water2_dpme_energies_forces_with_exclusions();
test_water125_dpme_vs_long_cutoff_no_exclusions();
test_water125_dpme_vs_long_cutoff_with_exclusions();
testCoulomb(); testCoulomb();
testLJ(); testLJ();
testExclusionsAnd14(); testExclusionsAnd14();
......
tests/TestParser.cpp
View file @ 3b6925ae
#include "../libraries/lepton/include/Lepton.h" #include "../libraries/lepton/include/Lepton.h"
#include "openmm/internal/AssertionUtilities.h"
#include <iostream> #include <iostream>
#include <limits> #include <limits>
#include <map> #include <map>
using namespace Lepton; using namespace Lepton;
using namespace OpenMM;
using namespace std; using namespace std;
#define ASSERT_EQUAL_TOL(expected, found, tol) {double _scale_ = std::fabs(expected) > 1.0 ? std::fabs(expected) : 1.0; if (!(std::fabs((expected)-(found))/_scale_ <= (tol))) throw exception();};
/** /**
* This is a custom function equal to f(x,y) = 2*x*y. * This is a custom function equal to f(x,y) = 2*x*y.
*/ */
...@@ -101,6 +101,18 @@ void verifyEvaluation(const string& expression, double x, double y, double expec ...@@ -101,6 +101,18 @@ void verifyEvaluation(const string& expression, double x, double y, double expec
compiled.getVariableReference("y") = y; compiled.getVariableReference("y") = y;
value = compiled.evaluate(); value = compiled.evaluate();
ASSERT_EQUAL_TOL(expectedValue, value, 1e-10); ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
// Try specifying memory locations for the compiled expression.
map<string, double*> variablePointers;
variablePointers["x"] = &x;
variablePointers["y"] = &y;
CompiledExpression compiled2 = parsed.createCompiledExpression();
compiled2.setVariableLocations(variablePointers);
value = compiled2.evaluate();
ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
ASSERT_EQUAL(&x, &compiled2.getVariableReference("x"));
ASSERT_EQUAL(&y, &compiled2.getVariableReference("y"));
// Make sure that variable renaming works. // Make sure that variable renaming works.
......
tests/TestVariableLangevinIntegrator.h
View file @ 3b6925ae
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -74,9 +74,9 @@ void testSingleBond() { ...@@ -74,9 +74,9 @@ void testSingleBond() {
integrator.step(1); integrator.step(1);
} }
// Now set the friction to a tiny value and see if it conserves energy. // Now set the friction to 0 and see if it conserves energy.
integrator.setFriction(5e-5); integrator.setFriction(0.0);
context.setPositions(positions); context.setPositions(positions);
State state = context.getState(State::Energy); State state = context.getState(State::Energy);
double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy(); double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
......
wrappers/python/CMakeLists.txt
View file @ 3b6925ae
...@@ -274,7 +274,7 @@ add_custom_target(PythonSdist ...@@ -274,7 +274,7 @@ add_custom_target(PythonSdist
) )
# Install binary module (to system location) # Install binary module (to system location)
set(PYTHON_SETUP_COMMAND "install") set(PYTHON_SETUP_COMMAND "install --root=\$ENV{DESTDIR}/")
configure_file(pysetup.cmake.in configure_file(pysetup.cmake.in
"${CMAKE_CURRENT_BINARY_DIR}/pysetupinstall.cmake" @ONLY) "${CMAKE_CURRENT_BINARY_DIR}/pysetupinstall.cmake" @ONLY)
add_custom_target(PythonInstall add_custom_target(PythonInstall
......
wrappers/python/setup.py
View file @ 3b6925ae
...@@ -229,8 +229,8 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM, ...@@ -229,8 +229,8 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
def main(): def main():
if sys.version_info < (2, 6): if sys.version_info < (2, 7):
reportError("OpenMM requires Python 2.6 or better.") reportError("OpenMM requires Python 2.7 or better.")
if platform.system() == 'Darwin': if platform.system() == 'Darwin':
macVersion = [int(x) for x in platform.mac_ver()[0].split('.')] macVersion = [int(x) for x in platform.mac_ver()[0].split('.')]
if tuple(macVersion) < (10, 5): if tuple(macVersion) < (10, 5):
......
wrappers/python/simtk/openmm/app/__init__.py
View file @ 3b6925ae
...@@ -6,7 +6,7 @@ from __future__ import absolute_import ...@@ -6,7 +6,7 @@ from __future__ import absolute_import
__docformat__ = "epytext en" __docformat__ = "epytext en"
__author__ = "Peter Eastman" __author__ = "Peter Eastman"
__copyright__ = "Copyright 2015, Stanford University and Peter Eastman" __copyright__ = "Copyright 2016, Stanford University and Peter Eastman"
__credits__ = [] __credits__ = []
__license__ = "MIT" __license__ = "MIT"
__maintainer__ = "Peter Eastman" __maintainer__ = "Peter Eastman"
...@@ -44,3 +44,10 @@ PME = forcefield.PME ...@@ -44,3 +44,10 @@ PME = forcefield.PME
HBonds = forcefield.HBonds HBonds = forcefield.HBonds
AllBonds = forcefield.AllBonds AllBonds = forcefield.AllBonds
HAngles = forcefield.HAngles HAngles = forcefield.HAngles
Single = topology.Single
Double = topology.Double
Triple = topology.Triple
Aromatic = topology.Aromatic
Amide = topology.Amide
wrappers/python/simtk/openmm/app/amberprmtopfile.py
View file @ 3b6925ae
...@@ -36,6 +36,7 @@ from math import sqrt ...@@ -36,6 +36,7 @@ from math import sqrt
from simtk.openmm.app import Topology from simtk.openmm.app import Topology
from simtk.openmm.app import PDBFile from simtk.openmm.app import PDBFile
from simtk.openmm.app.internal import amber_file_parser from simtk.openmm.app.internal import amber_file_parser
from simtk.openmm.app.internal.singleton import Singleton
from . import forcefield as ff from . import forcefield as ff
from . import element as elem from . import element as elem
import simtk.unit as u import simtk.unit as u
...@@ -44,27 +45,27 @@ from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors ...@@ -44,27 +45,27 @@ from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
# Enumerated values for implicit solvent model # Enumerated values for implicit solvent model
class HCT(object): class HCT(Singleton):
def __repr__(self): def __repr__(self):
return 'HCT' return 'HCT'
HCT = HCT() HCT = HCT()
class OBC1(object): class OBC1(Singleton):
def __repr__(self): def __repr__(self):
return 'OBC1' return 'OBC1'
OBC1 = OBC1() OBC1 = OBC1()
class OBC2(object): class OBC2(Singleton):
def __repr__(self): def __repr__(self):
return 'OBC2' return 'OBC2'
OBC2 = OBC2() OBC2 = OBC2()
class GBn(object): class GBn(Singleton):
def __repr__(self): def __repr__(self):
return 'GBn' return 'GBn'
GBn = GBn() GBn = GBn()
class GBn2(object): class GBn2(Singleton):
def __repr__(self): def __repr__(self):
return 'GBn2' return 'GBn2'
GBn2 = GBn2() GBn2 = GBn2()
......
wrappers/python/simtk/openmm/app/checkpointreporter.py
View file @ 3b6925ae
...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of ...@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org. Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2014 Stanford University and the Authors. Portions copyright (c) 2014-2016 Stanford University and the Authors.
Authors: Robert McGibbon Authors: Robert McGibbon
Contributors: Contributors:
...@@ -33,6 +33,9 @@ __author__ = "Robert McGibbon" ...@@ -33,6 +33,9 @@ __author__ = "Robert McGibbon"
__version__ = "1.0" __version__ = "1.0"
import simtk.openmm as mm import simtk.openmm as mm
import os
import os.path
__all__ = ['CheckpointReporter'] __all__ = ['CheckpointReporter']
...@@ -80,12 +83,7 @@ class CheckpointReporter(object): ...@@ -80,12 +83,7 @@ class CheckpointReporter(object):
""" """
self._reportInterval = reportInterval self._reportInterval = reportInterval
if isinstance(file, str): self._file = file
self._own_handle = True
self._out = open(file, 'w+b', 0)
else:
self._out = file
self._own_handle = False
def describeNextReport(self, simulation): def describeNextReport(self, simulation):
"""Get information about the next report this object will generate. """Get information about the next report this object will generate.
...@@ -116,13 +114,24 @@ class CheckpointReporter(object): ...@@ -116,13 +114,24 @@ class CheckpointReporter(object):
state : State state : State
The current state of the simulation The current state of the simulation
""" """
self._out.seek(0) if isinstance(self._file, str):
chk = simulation.context.createCheckpoint() # Do a safe save.
self._out.write(chk)
self._out.truncate() tempFilename1 = self._file+".backup1"
self._out.flush() tempFilename2 = self._file+".backup2"
with open(tempFilename1, 'w+b', 0) as out:
def __del__(self): out.write(simulation.context.createCheckpoint())
if self._own_handle: exists = os.path.exists(self._file)
self._out.close() if exists:
os.rename(self._file, tempFilename2)
os.rename(tempFilename1, self._file)
if exists:
os.remove(tempFilename2)
else:
# Replace the contents of the file.
self._file.seek(0)
chk = simulation.context.createCheckpoint()
self._file.write(chk)
self._file.truncate()
self._file.flush()
wrappers/python/simtk/openmm/app/dcdfile.py
View file @ 3b6925ae
...@@ -77,6 +77,7 @@ class DCDFile(object): ...@@ -77,6 +77,7 @@ class DCDFile(object):
if is_quantity(dt): if is_quantity(dt):
dt = dt.value_in_unit(picoseconds) dt = dt.value_in_unit(picoseconds)
dt /= 0.04888821 dt /= 0.04888821
self._dt = dt
boxFlag = 0 boxFlag = 0
if topology.getUnitCellDimensions() is not None: if topology.getUnitCellDimensions() is not None:
boxFlag = 1 boxFlag = 1
...@@ -116,9 +117,19 @@ class DCDFile(object): ...@@ -116,9 +117,19 @@ class DCDFile(object):
raise ValueError('Particle position is infinite') raise ValueError('Particle position is infinite')
file = self._file file = self._file
self._modelCount += 1
if self._interval > 1 and self._firstStep+self._modelCount*self._interval > 1<<31:
# This will exceed the range of a 32 bit integer. To avoid crashing or producing a corrupt file,
# update the header to say the trajectory consisted of a smaller number of larger steps (so the
# total trajectory length remains correct).
self._firstStep //= self._interval
self._dt *= self._interval
self._interval = 1
file.seek(0, os.SEEK_SET)
file.write(struct.pack('<i4c9if', 84, b'C', b'O', b'R', b'D', 0, self._firstStep, self._interval, 0, 0, 0, 0, 0, 0, self._dt))
# Update the header. # Update the header.
self._modelCount += 1
file.seek(8, os.SEEK_SET) file.seek(8, os.SEEK_SET)
file.write(struct.pack('<i', self._modelCount)) file.write(struct.pack('<i', self._modelCount))
file.seek(20, os.SEEK_SET) file.seek(20, os.SEEK_SET)
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 3b6925ae
...@@ -40,10 +40,12 @@ import math ...@@ -40,10 +40,12 @@ import math
from math import sqrt, cos from math import sqrt, cos
from copy import deepcopy from copy import deepcopy
from heapq import heappush, heappop from heapq import heappush, heappop
from collections import defaultdict
import simtk.openmm as mm import simtk.openmm as mm
import simtk.unit as unit import simtk.unit as unit
from . import element as elem from . import element as elem
from simtk.openmm.app import Topology from simtk.openmm.app import Topology
from simtk.openmm.app.internal.singleton import Singleton
def _convertParameterToNumber(param): def _convertParameterToNumber(param):
if unit.is_quantity(param): if unit.is_quantity(param):
...@@ -52,46 +54,80 @@ def _convertParameterToNumber(param): ...@@ -52,46 +54,80 @@ def _convertParameterToNumber(param):
return param.value_in_unit_system(unit.md_unit_system) return param.value_in_unit_system(unit.md_unit_system)
return float(param) return float(param)
def _parseFunctions(element):
"""Parse the attributes on an XML tag to find any tabulated functions it defines."""
functions = []
for function in element.findall('Function'):
values = [float(x) for x in function.text.split()]
if 'type' in function.attrib:
functionType = function.attrib['type']
else:
functionType = 'Continuous1D'
params = {}
for key in function.attrib:
if key.endswith('size'):
params[key] = int(function.attrib[key])
elif key.endswith('min') or key.endswith('max'):
params[key] = float(function.attrib[key])
functions.append((function.attrib['name'], functionType, values, params))
return functions
def _createFunctions(force, functions):
"""Add TabulatedFunctions to a Force based on the information that was recorded by _parseFunctions()."""
for (name, type, values, params) in functions:
if type == 'Continuous1D':
force.addTabulatedFunction(name, mm.Continuous1DFunction(values, params['min'], params['max']))
elif type == 'Continuous2D':
force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax']))
elif type == 'Continuous3D':
force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], params['zsize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax'], params['zmin'], params['zmax']))
elif type == 'Discrete1D':
force.addTabulatedFunction(name, mm.Discrete1DFunction(values))
elif type == 'Discrete2D':
force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], values))
elif type == 'Discrete3D':
force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
# Enumerated values for nonbonded method # Enumerated values for nonbonded method
class NoCutoff(object): class NoCutoff(Singleton):
def __repr__(self): def __repr__(self):
return 'NoCutoff' return 'NoCutoff'
NoCutoff = NoCutoff() NoCutoff = NoCutoff()
class CutoffNonPeriodic(object): class CutoffNonPeriodic(Singleton):
def __repr__(self): def __repr__(self):
return 'CutoffNonPeriodic' return 'CutoffNonPeriodic'
CutoffNonPeriodic = CutoffNonPeriodic() CutoffNonPeriodic = CutoffNonPeriodic()
class CutoffPeriodic(object): class CutoffPeriodic(Singleton):
def __repr__(self): def __repr__(self):
return 'CutoffPeriodic' return 'CutoffPeriodic'
CutoffPeriodic = CutoffPeriodic() CutoffPeriodic = CutoffPeriodic()
class Ewald(object): class Ewald(Singleton):
def __repr__(self): def __repr__(self):
return 'Ewald' return 'Ewald'
Ewald = Ewald() Ewald = Ewald()
class PME(object): class PME(Singleton):
def __repr__(self): def __repr__(self):
return 'PME' return 'PME'
PME = PME() PME = PME()
# Enumerated values for constraint type # Enumerated values for constraint type
class HBonds(object): class HBonds(Singleton):
def __repr__(self): def __repr__(self):
return 'HBonds' return 'HBonds'
HBonds = HBonds() HBonds = HBonds()
class AllBonds(object): class AllBonds(Singleton):
def __repr__(self): def __repr__(self):
return 'AllBonds' return 'AllBonds'
AllBonds = AllBonds() AllBonds = AllBonds()
class HAngles(object): class HAngles(Singleton):
def __repr__(self): def __repr__(self):
return 'HAngles' return 'HAngles'
HAngles = HAngles() HAngles = HAngles()
...@@ -326,7 +362,7 @@ class ForceField(object): ...@@ -326,7 +362,7 @@ class ForceField(object):
"""Register a new residue template.""" """Register a new residue template."""
if template.name in self._templates: if template.name in self._templates:
# There is already a template with this name, so check the override levels. # There is already a template with this name, so check the override levels.
existingTemplate = self._templates[template.name] existingTemplate = self._templates[template.name]
if template.overrideLevel < existingTemplate.overrideLevel: if template.overrideLevel < existingTemplate.overrideLevel:
# The existing one takes precedence, so just return. # The existing one takes precedence, so just return.
...@@ -338,9 +374,9 @@ class ForceField(object): ...@@ -338,9 +374,9 @@ class ForceField(object):
self._templateSignatures[existingSignature].remove(existingTemplate) self._templateSignatures[existingSignature].remove(existingTemplate)
else: else:
raise ValueError('Residue template %s with the same override level %d already exists.' % (template.name, template.overrideLevel)) raise ValueError('Residue template %s with the same override level %d already exists.' % (template.name, template.overrideLevel))
# Register the template. # Register the template.
self._templates[template.name] = template self._templates[template.name] = template
signature = _createResidueSignature([atom.element for atom in template.atoms]) signature = _createResidueSignature([atom.element for atom in template.atoms])
if signature in self._templateSignatures: if signature in self._templateSignatures:
...@@ -351,7 +387,7 @@ class ForceField(object): ...@@ -351,7 +387,7 @@ class ForceField(object):
def registerPatch(self, patch): def registerPatch(self, patch):
"""Register a new patch that can be applied to templates.""" """Register a new patch that can be applied to templates."""
self._patches[patch.name] = patch self._patches[patch.name] = patch
def registerTemplatePatch(self, residue, patch, patchResidueIndex): def registerTemplatePatch(self, residue, patch, patchResidueIndex):
"""Register that a particular patch can be used with a particular residue.""" """Register that a particular patch can be used with a particular residue."""
if residue not in self._templatePatches: if residue not in self._templatePatches:
...@@ -487,7 +523,7 @@ class ForceField(object): ...@@ -487,7 +523,7 @@ class ForceField(object):
else: else:
self.constraints[key] = distance self.constraints[key] = distance
system.addConstraint(atom1, atom2, distance) system.addConstraint(atom1, atom2, distance)
def recordMatchedAtomParameters(self, residue, template, matches): def recordMatchedAtomParameters(self, residue, template, matches):
"""Record parameters for atoms based on having matched a residue to a template.""" """Record parameters for atoms based on having matched a residue to a template."""
matchAtoms = dict(zip(matches, residue.atoms())) matchAtoms = dict(zip(matches, residue.atoms()))
...@@ -604,21 +640,21 @@ class ForceField(object): ...@@ -604,21 +640,21 @@ class ForceField(object):
self.deletedBonds = [] self.deletedBonds = []
self.addedExternalBonds = [] self.addedExternalBonds = []
self.deletedExternalBonds = [] self.deletedExternalBonds = []
def createPatchedTemplates(self, templates): def createPatchedTemplates(self, templates):
"""Apply this patch to a set of templates, creating new modified ones.""" """Apply this patch to a set of templates, creating new modified ones."""
if len(templates) != self.numResidues: if len(templates) != self.numResidues:
raise ValueError("Patch '%s' expected %d templates, received %d", (self.name, self.numResidues, len(templates))) raise ValueError("Patch '%s' expected %d templates, received %d", (self.name, self.numResidues, len(templates)))
# Construct a new version of each template. # Construct a new version of each template.
newTemplates = [] newTemplates = []
for index, template in enumerate(templates): for index, template in enumerate(templates):
newTemplate = ForceField._TemplateData("%s-%s" % (template.name, self.name)) newTemplate = ForceField._TemplateData("%s-%s" % (template.name, self.name))
newTemplates.append(newTemplate) newTemplates.append(newTemplate)
# Build the list of atoms in it. # Build the list of atoms in it.
for atom in template.atoms: for atom in template.atoms:
if not any(deleted.name == atom.name and deleted.residue == index for deleted in self.deletedAtoms): if not any(deleted.name == atom.name and deleted.residue == index for deleted in self.deletedAtoms):
newTemplate.atoms.append(ForceField._TemplateAtomData(atom.name, atom.type, atom.element, atom.parameters)) newTemplate.atoms.append(ForceField._TemplateAtomData(atom.name, atom.type, atom.element, atom.parameters))
...@@ -632,9 +668,9 @@ class ForceField(object): ...@@ -632,9 +668,9 @@ class ForceField(object):
if atom.name not in newAtomIndex: if atom.name not in newAtomIndex:
raise ValueError("Patch '%s' modifies nonexistent atom '%s' in template '%s'" % (self.name, atom.name, template.name)) raise ValueError("Patch '%s' modifies nonexistent atom '%s' in template '%s'" % (self.name, atom.name, template.name))
newTemplate.atoms[newAtomIndex[atom.name]] = ForceField._TemplateAtomData(atom.name, atom.type, atom.element, atom.parameters) newTemplate.atoms[newAtomIndex[atom.name]] = ForceField._TemplateAtomData(atom.name, atom.type, atom.element, atom.parameters)
# Copy over the virtual sites, translating the atom indices. # Copy over the virtual sites, translating the atom indices.
indexMap = dict([(oldAtomIndex[name], newAtomIndex[name]) for name in newAtomIndex if name in oldAtomIndex]) indexMap = dict([(oldAtomIndex[name], newAtomIndex[name]) for name in newAtomIndex if name in oldAtomIndex])
for site in template.virtualSites: for site in template.virtualSites:
if site.index in indexMap and all(i in indexMap for i in site.atoms): if site.index in indexMap and all(i in indexMap for i in site.atoms):
...@@ -642,9 +678,9 @@ class ForceField(object): ...@@ -642,9 +678,9 @@ class ForceField(object):
newSite.index = indexMap[site.index] newSite.index = indexMap[site.index]
newSite.atoms = [indexMap[i] for i in site.atoms] newSite.atoms = [indexMap[i] for i in site.atoms]
newTemplate.virtualSites.append(newSite) newTemplate.virtualSites.append(newSite)
# Build the lists of bonds and external bonds. # Build the lists of bonds and external bonds.
atomMap = dict([(template.atoms[i], indexMap[i]) for i in indexMap]) atomMap = dict([(template.atoms[i], indexMap[i]) for i in indexMap])
deletedBonds = [(atom1.name, atom2.name) for atom1, atom2 in self.deletedBonds if atom1.residue == index and atom2.residue == index] deletedBonds = [(atom1.name, atom2.name) for atom1, atom2 in self.deletedBonds if atom1.residue == index and atom2.residue == index]
for atom1, atom2 in template.bonds: for atom1, atom2 in template.bonds:
...@@ -666,7 +702,7 @@ class ForceField(object): ...@@ -666,7 +702,7 @@ class ForceField(object):
for atom in self.addedExternalBonds: for atom in self.addedExternalBonds:
newTemplate.addExternalBondByName(atom.name) newTemplate.addExternalBondByName(atom.name)
return newTemplates return newTemplates
class _PatchAtomData(object): class _PatchAtomData(object):
"""Inner class used to encapsulate data about an atom in a patch definition.""" """Inner class used to encapsulate data about an atom in a patch definition."""
def __init__(self, description): def __init__(self, description):
...@@ -757,7 +793,7 @@ class ForceField(object): ...@@ -757,7 +793,7 @@ class ForceField(object):
raise ValueError('%s: No parameters defined for atom type %s' % (self.forceName, t)) raise ValueError('%s: No parameters defined for atom type %s' % (self.forceName, t))
def _getResidueTemplateMatches(self, res, bondedToAtom, templateSignatures=None): def _getResidueTemplateMatches(self, res, bondedToAtom, templateSignatures=None, ignoreExternalBonds=False):
"""Return the residue template matches, or None if none are found. """Return the residue template matches, or None if none are found.
Parameters Parameters
...@@ -784,14 +820,14 @@ class ForceField(object): ...@@ -784,14 +820,14 @@ class ForceField(object):
if signature in templateSignatures: if signature in templateSignatures:
allMatches = [] allMatches = []
for t in templateSignatures[signature]: for t in templateSignatures[signature]:
match = _matchResidue(res, t, bondedToAtom) match = _matchResidue(res, t, bondedToAtom, ignoreExternalBonds)
if match is not None: if match is not None:
allMatches.append((t, match)) allMatches.append((t, match))
if len(allMatches) == 1: if len(allMatches) == 1:
template = allMatches[0][0] template = allMatches[0][0]
matches = allMatches[0][1] matches = allMatches[0][1]
elif len(allMatches) > 1: elif len(allMatches) > 1:
raise Exception('Multiple matching templates found for residue %d (%s).' % (res.index+1, res.name)) raise Exception('Multiple matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches)))
return [template, matches] return [template, matches]
def _buildBondedToAtomList(self, topology): def _buildBondedToAtomList(self, topology):
...@@ -846,7 +882,7 @@ class ForceField(object): ...@@ -846,7 +882,7 @@ class ForceField(object):
return unmatched_residues return unmatched_residues
def getMatchingTemplates(self, topology): def getMatchingTemplates(self, topology, ignoreExternalBonds=False):
"""Return a list of forcefield residue templates matching residues in the specified topology. """Return a list of forcefield residue templates matching residues in the specified topology.
.. CAUTION:: This method is experimental, and its API is subject to change. .. CAUTION:: This method is experimental, and its API is subject to change.
...@@ -855,7 +891,8 @@ class ForceField(object): ...@@ -855,7 +891,8 @@ class ForceField(object):
---------- ----------
topology : Topology topology : Topology
The Topology whose residues are to be checked against the forcefield residue templates. The Topology whose residues are to be checked against the forcefield residue templates.
ignoreExternalBonds : bool=False
If true, ignore external bonds when matching residues to templates.
Returns Returns
------- -------
templates : list of _TemplateData templates : list of _TemplateData
...@@ -869,7 +906,7 @@ class ForceField(object): ...@@ -869,7 +906,7 @@ class ForceField(object):
templates = list() # list of templates matching the corresponding residues templates = list() # list of templates matching the corresponding residues
for res in topology.residues(): for res in topology.residues():
# Attempt to match one of the existing templates. # Attempt to match one of the existing templates.
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom) [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom, ignoreExternalBonds=ignoreExternalBonds)
# Raise an exception if we have found no templates that match. # Raise an exception if we have found no templates that match.
if matches is None: if matches is None:
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1, res.name, _findMatchErrors(self, res))) raise ValueError('No template found for residue %d (%s). %s' % (res.index+1, res.name, _findMatchErrors(self, res)))
...@@ -912,7 +949,7 @@ class ForceField(object): ...@@ -912,7 +949,7 @@ class ForceField(object):
if signature in signatures: if signature in signatures:
# Signature is the same as an existing residue; check connectivity. # Signature is the same as an existing residue; check connectivity.
for check_residue in unique_unmatched_residues: for check_residue in unique_unmatched_residues:
matches = _matchResidue(check_residue, template, bondedToAtom) matches = _matchResidue(check_residue, template, bondedToAtom, False)
if matches is not None: if matches is not None:
is_unique = False is_unique = False
if is_unique: if is_unique:
...@@ -924,7 +961,8 @@ class ForceField(object): ...@@ -924,7 +961,8 @@ class ForceField(object):
return [templates, unique_unmatched_residues] return [templates, unique_unmatched_residues]
def createSystem(self, topology, nonbondedMethod=NoCutoff, nonbondedCutoff=1.0*unit.nanometer, def createSystem(self, topology, nonbondedMethod=NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
constraints=None, rigidWater=True, removeCMMotion=True, hydrogenMass=None, residueTemplates=dict(), **args): constraints=None, rigidWater=True, removeCMMotion=True, hydrogenMass=None, residueTemplates=dict(),
ignoreExternalBonds=False, **args):
"""Construct an OpenMM System representing a Topology with this force field. """Construct an OpenMM System representing a Topology with this force field.
Parameters Parameters
...@@ -949,16 +987,21 @@ class ForceField(object): ...@@ -949,16 +987,21 @@ class ForceField(object):
added to a hydrogen is subtracted from the heavy atom to keep added to a hydrogen is subtracted from the heavy atom to keep
their total mass the same. their total mass the same.
residueTemplates : dict=dict() residueTemplates : dict=dict()
Key: Topology Residue object Key: Topology Residue object
Value: string, name of _TemplateData residue template object to use for Value: string, name of _TemplateData residue template object to use for (Key) residue.
(Key) residue This allows user to specify which template to apply to particular Residues
This allows user to specify which template to apply to particular Residues in the event that multiple matching templates are available (e.g Fe2+ and Fe3+
in the event that multiple matching templates are available (e.g Fe2+ and Fe3+ templates in the ForceField for a monoatomic iron ion in the topology).
templates in the ForceField for a monoatomic iron ion in the topology). ignoreExternalBonds : boolean=False
If true, ignore external bonds when matching residues to templates. This is
useful when the Topology represents one piece of a larger molecule, so chains are
not terminated properly. This option can create ambiguities where multiple
templates match the same residue. If that happens, use the residueTemplates
argument to specify which one to use.
args args
Arbitrary additional keyword arguments may also be specified. Arbitrary additional keyword arguments may also be specified.
This allows extra parameters to be specified that are specific to This allows extra parameters to be specified that are specific to
particular force fields. particular force fields.
Returns Returns
------- -------
...@@ -996,34 +1039,34 @@ class ForceField(object): ...@@ -996,34 +1039,34 @@ class ForceField(object):
if res in residueTemplates: if res in residueTemplates:
tname = residueTemplates[res] tname = residueTemplates[res]
template = self._templates[tname] template = self._templates[tname]
matches = _matchResidue(res, template, bondedToAtom) matches = _matchResidue(res, template, bondedToAtom, ignoreExternalBonds)
if matches is None: if matches is None:
raise Exception('User-supplied template %s does not match the residue %d (%s)' % (tname, res.index+1, res.name)) raise Exception('User-supplied template %s does not match the residue %d (%s)' % (tname, res.index+1, res.name))
else: else:
# Attempt to match one of the existing templates. # Attempt to match one of the existing templates.
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom) [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom, ignoreExternalBonds=ignoreExternalBonds)
if matches is None: if matches is None:
unmatchedResidues.append(res) unmatchedResidues.append(res)
else: else:
data.recordMatchedAtomParameters(res, template, matches) data.recordMatchedAtomParameters(res, template, matches)
# Try to apply patches to find matches for any unmatched residues. # Try to apply patches to find matches for any unmatched residues.
if len(unmatchedResidues) > 0: if len(unmatchedResidues) > 0:
unmatchedResidues = _applyPatchesToMatchResidues(self, data, unmatchedResidues, bondedToAtom) unmatchedResidues = _applyPatchesToMatchResidues(self, data, unmatchedResidues, bondedToAtom, ignoreExternalBonds)
# If we still haven't found a match for a residue, attempt to use residue template generators to create # If we still haven't found a match for a residue, attempt to use residue template generators to create
# new templates (and potentially atom types/parameters). # new templates (and potentially atom types/parameters).
for res in unmatchedResidues: for res in unmatchedResidues:
# A template might have been generated on an earlier iteration of this loop. # A template might have been generated on an earlier iteration of this loop.
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom) [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom, ignoreExternalBonds=ignoreExternalBonds)
if matches is None: if matches is None:
# Try all generators. # Try all generators.
for generator in self._templateGenerators: for generator in self._templateGenerators:
if generator(self, res): if generator(self, res):
# This generator has registered a new residue template that should match. # This generator has registered a new residue template that should match.
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom) [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom, ignoreExternalBonds=ignoreExternalBonds)
if matches is None: if matches is None:
# Something went wrong because the generated template does not match the residue signature. # Something went wrong because the generated template does not match the residue signature.
raise Exception('The residue handler %s indicated it had correctly parameterized residue %s, but the generated template did not match the residue signature.' % (generator.__class__.__name__, str(res))) raise Exception('The residue handler %s indicated it had correctly parameterized residue %s, but the generated template did not match the residue signature.' % (generator.__class__.__name__, str(res)))
...@@ -1252,7 +1295,7 @@ def _createResidueSignature(elements): ...@@ -1252,7 +1295,7 @@ def _createResidueSignature(elements):
s += element.symbol+str(count) s += element.symbol+str(count)
return s return s
def _matchResidue(res, template, bondedToAtom): def _matchResidue(res, template, bondedToAtom, ignoreExternalBonds=False):
"""Determine whether a residue matches a template and return a list of corresponding atoms. """Determine whether a residue matches a template and return a list of corresponding atoms.
Parameters Parameters
...@@ -1263,6 +1306,8 @@ def _matchResidue(res, template, bondedToAtom): ...@@ -1263,6 +1306,8 @@ def _matchResidue(res, template, bondedToAtom):
The template to compare it to The template to compare it to
bondedToAtom : list bondedToAtom : list
Enumerates which other atoms each atom is bonded to Enumerates which other atoms each atom is bonded to
ignoreExternalBonds : bool
If true, ignore external bonds when matching templates
Returns Returns
------- -------
...@@ -1285,7 +1330,7 @@ def _matchResidue(res, template, bondedToAtom): ...@@ -1285,7 +1330,7 @@ def _matchResidue(res, template, bondedToAtom):
for atom in atoms: for atom in atoms:
bonds = [renumberAtoms[x] for x in bondedToAtom[atom.index] if x in renumberAtoms] bonds = [renumberAtoms[x] for x in bondedToAtom[atom.index] if x in renumberAtoms]
bondedTo.append(bonds) bondedTo.append(bonds)
externalBonds.append(len([x for x in bondedToAtom[atom.index] if x not in renumberAtoms])) externalBonds.append(0 if ignoreExternalBonds else len([x for x in bondedToAtom[atom.index] if x not in renumberAtoms]))
# For each unique combination of element and number of bonds, make sure the residue and # For each unique combination of element and number of bonds, make sure the residue and
# template have the same number of atoms. # template have the same number of atoms.
...@@ -1298,15 +1343,15 @@ def _matchResidue(res, template, bondedToAtom): ...@@ -1298,15 +1343,15 @@ def _matchResidue(res, template, bondedToAtom):
residueTypeCount[key] += 1 residueTypeCount[key] += 1
templateTypeCount = {} templateTypeCount = {}
for i, atom in enumerate(template.atoms): for i, atom in enumerate(template.atoms):
key = (atom.element, len(atom.bondedTo), atom.externalBonds) key = (atom.element, len(atom.bondedTo), 0 if ignoreExternalBonds else atom.externalBonds)
if key not in templateTypeCount: if key not in templateTypeCount:
templateTypeCount[key] = 1 templateTypeCount[key] = 1
templateTypeCount[key] += 1 templateTypeCount[key] += 1
if residueTypeCount != templateTypeCount: if residueTypeCount != templateTypeCount:
return None return None
# Identify template atoms that could potentially be matches for each atom. # Identify template atoms that could potentially be matches for each atom.
candidates = [[] for i in range(numAtoms)] candidates = [[] for i in range(numAtoms)]
for i in range(numAtoms): for i in range(numAtoms):
for j, atom in enumerate(template.atoms): for j, atom in enumerate(template.atoms):
...@@ -1314,13 +1359,13 @@ def _matchResidue(res, template, bondedToAtom): ...@@ -1314,13 +1359,13 @@ def _matchResidue(res, template, bondedToAtom):
continue continue
if len(atom.bondedTo) != len(bondedTo[i]): if len(atom.bondedTo) != len(bondedTo[i]):
continue continue
if atom.externalBonds != externalBonds[i]: if not ignoreExternalBonds and atom.externalBonds != externalBonds[i]:
continue continue
candidates[i].append(j) candidates[i].append(j)
# Find an optimal ordering for matching atoms. This means 1) start with the one that has the fewest options, # Find an optimal ordering for matching atoms. This means 1) start with the one that has the fewest options,
# and 2) follow with ones that are bonded to an already matched atom. # and 2) follow with ones that are bonded to an already matched atom.
searchOrder = [] searchOrder = []
atomsToOrder = set(range(numAtoms)) atomsToOrder = set(range(numAtoms))
efficientAtomSet = set() efficientAtomSet = set()
...@@ -1388,12 +1433,12 @@ def _findAtomMatches(template, bondedTo, matches, hasMatch, candidates, position ...@@ -1388,12 +1433,12 @@ def _findAtomMatches(template, bondedTo, matches, hasMatch, candidates, position
return False return False
def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom): def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom, ignoreExternalBonds):
"""Try to apply patches to find matches for residues.""" """Try to apply patches to find matches for residues."""
# Start by creating all templates than can be created by applying a combination of one-residue patches # Start by creating all templates than can be created by applying a combination of one-residue patches
# to a single template. The number of these is usually not too large, and they often cover a large fraction # to a single template. The number of these is usually not too large, and they often cover a large fraction
# of residues. # of residues.
patchedTemplateSignatures = {} patchedTemplateSignatures = {}
patchedTemplates = {} patchedTemplates = {}
for name, template in forcefield._templates.items(): for name, template in forcefield._templates.items():
...@@ -1409,23 +1454,23 @@ def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom): ...@@ -1409,23 +1454,23 @@ def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom):
patchedTemplateSignatures[signature].append(patchedTemplate) patchedTemplateSignatures[signature].append(patchedTemplate)
else: else:
patchedTemplateSignatures[signature] = [patchedTemplate] patchedTemplateSignatures[signature] = [patchedTemplate]
# Now see if any of those templates matches any of the residues. # Now see if any of those templates matches any of the residues.
unmatchedResidues = [] unmatchedResidues = []
for res in residues: for res in residues:
[template, matches] = forcefield._getResidueTemplateMatches(res, bondedToAtom, patchedTemplateSignatures) [template, matches] = forcefield._getResidueTemplateMatches(res, bondedToAtom, patchedTemplateSignatures, ignoreExternalBonds)
if matches is None: if matches is None:
unmatchedResidues.append(res) unmatchedResidues.append(res)
else: else:
data.recordMatchedAtomParameters(res, template, matches) data.recordMatchedAtomParameters(res, template, matches)
if len(unmatchedResidues) == 0: if len(unmatchedResidues) == 0:
return [] return []
# We need to consider multi-residue patches. This can easily lead to a combinatorial explosion, so we make a simplifying # We need to consider multi-residue patches. This can easily lead to a combinatorial explosion, so we make a simplifying
# assumption: that no residue is affected by more than one multi-residue patch (in addition to any number of single-residue # assumption: that no residue is affected by more than one multi-residue patch (in addition to any number of single-residue
# patches). Record all multi-residue patches, and the templates they can be applied to. # patches). Record all multi-residue patches, and the templates they can be applied to.
patches = {} patches = {}
maxPatchSize = 0 maxPatchSize = 0
for patch in forcefield._patches.values(): for patch in forcefield._patches.values():
...@@ -1441,9 +1486,9 @@ def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom): ...@@ -1441,9 +1486,9 @@ def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom):
patches[patchName][patchResidueIndex].append(forcefield._templates[templateName]) patches[patchName][patchResidueIndex].append(forcefield._templates[templateName])
if templateName in patchedTemplates: if templateName in patchedTemplates:
patches[patchName][patchResidueIndex] += patchedTemplates[templateName] patches[patchName][patchResidueIndex] += patchedTemplates[templateName]
# Record which unmatched residues are bonded to each other. # Record which unmatched residues are bonded to each other.
bonds = set() bonds = set()
topology = residues[0].chain.topology topology = residues[0].chain.topology
for atom1, atom2 in topology.bonds(): for atom1, atom2 in topology.bonds():
...@@ -1454,26 +1499,26 @@ def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom): ...@@ -1454,26 +1499,26 @@ def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom):
bond = tuple(sorted((res1, res2), key=lambda x: x.index)) bond = tuple(sorted((res1, res2), key=lambda x: x.index))
if bond not in bonds: if bond not in bonds:
bonds.add(bond) bonds.add(bond)
# Identify clusters of unmatched residues that are all bonded to each other. These are the ones we'll # Identify clusters of unmatched residues that are all bonded to each other. These are the ones we'll
# try to apply multi-residue patches to. # try to apply multi-residue patches to.
clusterSize = 2 clusterSize = 2
clusters = bonds clusters = bonds
while clusterSize <= maxPatchSize: while clusterSize <= maxPatchSize:
# Try to apply patches to clusters of this size. # Try to apply patches to clusters of this size.
for patchName in patches: for patchName in patches:
patch = forcefield._patches[patchName] patch = forcefield._patches[patchName]
if patch.numResidues == clusterSize: if patch.numResidues == clusterSize:
matchedClusters = _matchToMultiResiduePatchedTemplates(data, clusters, patch, patches[patchName], bondedToAtom) matchedClusters = _matchToMultiResiduePatchedTemplates(data, clusters, patch, patches[patchName], bondedToAtom, ignoreExternalBonds)
for cluster in matchedClusters: for cluster in matchedClusters:
for residue in cluster: for residue in cluster:
unmatchedResidues.remove(residue) unmatchedResidues.remove(residue)
bonds = set(bond for bond in bonds if bond[0] in unmatchedResidues and bond[1] in unmatchedResidues) bonds = set(bond for bond in bonds if bond[0] in unmatchedResidues and bond[1] in unmatchedResidues)
# Now extend the clusters to find ones of the next size up. # Now extend the clusters to find ones of the next size up.
largerClusters = set() largerClusters = set()
for cluster in clusters: for cluster in clusters:
for bond in bonds: for bond in bonds:
...@@ -1501,34 +1546,34 @@ def _generatePatchedSingleResidueTemplates(template, patches, index, newTemplate ...@@ -1501,34 +1546,34 @@ def _generatePatchedSingleResidueTemplates(template, patches, index, newTemplate
# This probably means the patch is inconsistent with another one that has already been applied, # This probably means the patch is inconsistent with another one that has already been applied,
# so just ignore it. # so just ignore it.
patchedTemplate = None patchedTemplate = None
# Call this function recursively to generate combinations of patches. # Call this function recursively to generate combinations of patches.
if index+1 < len(patches): if index+1 < len(patches):
_generatePatchedSingleResidueTemplates(template, patches, index+1, newTemplates) _generatePatchedSingleResidueTemplates(template, patches, index+1, newTemplates)
if patchedTemplate is not None: if patchedTemplate is not None:
_generatePatchedSingleResidueTemplates(patchedTemplate, patches, index+1, newTemplates) _generatePatchedSingleResidueTemplates(patchedTemplate, patches, index+1, newTemplates)
def _matchToMultiResiduePatchedTemplates(data, clusters, patch, residueTemplates, bondedToAtom): def _matchToMultiResiduePatchedTemplates(data, clusters, patch, residueTemplates, bondedToAtom, ignoreExternalBonds):
"""Apply a multi-residue patch to templates, then try to match them against clusters of residues.""" """Apply a multi-residue patch to templates, then try to match them against clusters of residues."""
matchedClusters = [] matchedClusters = []
selectedTemplates = [None]*patch.numResidues selectedTemplates = [None]*patch.numResidues
_applyMultiResiduePatch(data, clusters, patch, residueTemplates, selectedTemplates, 0, matchedClusters, bondedToAtom) _applyMultiResiduePatch(data, clusters, patch, residueTemplates, selectedTemplates, 0, matchedClusters, bondedToAtom, ignoreExternalBonds)
return matchedClusters return matchedClusters
def _applyMultiResiduePatch(data, clusters, patch, candidateTemplates, selectedTemplates, index, matchedClusters, bondedToAtom): def _applyMultiResiduePatch(data, clusters, patch, candidateTemplates, selectedTemplates, index, matchedClusters, bondedToAtom, ignoreExternalBonds):
"""This is called recursively to apply a multi-residue patch to all possible combinations of templates.""" """This is called recursively to apply a multi-residue patch to all possible combinations of templates."""
if index < patch.numResidues: if index < patch.numResidues:
for template in candidateTemplates[index]: for template in candidateTemplates[index]:
selectedTemplates[index] = template selectedTemplates[index] = template
_applyMultiResiduePatch(data, clusters, patch, candidateTemplates, selectedTemplates, index+1, matchedClusters, bondedToAtom) _applyMultiResiduePatch(data, clusters, patch, candidateTemplates, selectedTemplates, index+1, matchedClusters, bondedToAtom, ignoreExternalBonds)
else: else:
# We're at the deepest level of the recursion. We've selected a template for each residue, so apply the patch, # We're at the deepest level of the recursion. We've selected a template for each residue, so apply the patch,
# then try to match it against clusters. # then try to match it against clusters.
try: try:
patchedTemplates = patch.createPatchedTemplates(selectedTemplates) patchedTemplates = patch.createPatchedTemplates(selectedTemplates)
except: except:
...@@ -1541,7 +1586,7 @@ def _applyMultiResiduePatch(data, clusters, patch, candidateTemplates, selectedT ...@@ -1541,7 +1586,7 @@ def _applyMultiResiduePatch(data, clusters, patch, candidateTemplates, selectedT
for residues in itertools.permutations(cluster): for residues in itertools.permutations(cluster):
residueMatches = [] residueMatches = []
for residue, template in zip(residues, patchedTemplates): for residue, template in zip(residues, patchedTemplates):
matches = _matchResidue(residue, template, bondedToAtom) matches = _matchResidue(residue, template, bondedToAtom, ignoreExternalBonds)
if matches is None: if matches is None:
residueMatches = None residueMatches = None
break break
...@@ -1549,18 +1594,18 @@ def _applyMultiResiduePatch(data, clusters, patch, candidateTemplates, selectedT ...@@ -1549,18 +1594,18 @@ def _applyMultiResiduePatch(data, clusters, patch, candidateTemplates, selectedT
residueMatches.append(matches) residueMatches.append(matches)
if residueMatches is not None: if residueMatches is not None:
# We successfully matched the template to the residues. Record the parameters. # We successfully matched the template to the residues. Record the parameters.
for i in range(patch.numResidues): for i in range(patch.numResidues):
data.recordMatchedAtomParameters(residues[i], patchedTemplates[i], residueMatches[i]) data.recordMatchedAtomParameters(residues[i], patchedTemplates[i], residueMatches[i])
newlyMatchedClusters.append(cluster) newlyMatchedClusters.append(cluster)
break break
# Record which clusters were successfully matched. # Record which clusters were successfully matched.
matchedClusters += newlyMatchedClusters matchedClusters += newlyMatchedClusters
for cluster in newlyMatchedClusters: for cluster in newlyMatchedClusters:
clusters.remove(cluster) clusters.remove(cluster)
def _findMatchErrors(forcefield, res): def _findMatchErrors(forcefield, res):
"""Try to guess why a residue failed to match any template and return an error message.""" """Try to guess why a residue failed to match any template and return an error message."""
...@@ -1662,6 +1707,7 @@ class HarmonicBondGenerator(object): ...@@ -1662,6 +1707,7 @@ class HarmonicBondGenerator(object):
def __init__(self, forcefield): def __init__(self, forcefield):
self.ff = forcefield self.ff = forcefield
self.bondsForAtomType = defaultdict(set)
self.types1 = [] self.types1 = []
self.types2 = [] self.types2 = []
self.length = [] self.length = []
...@@ -1670,8 +1716,13 @@ class HarmonicBondGenerator(object): ...@@ -1670,8 +1716,13 @@ class HarmonicBondGenerator(object):
def registerBond(self, parameters): def registerBond(self, parameters):
types = self.ff._findAtomTypes(parameters, 2) types = self.ff._findAtomTypes(parameters, 2)
if None not in types: if None not in types:
index = len(self.types1)
self.types1.append(types[0]) self.types1.append(types[0])
self.types2.append(types[1]) self.types2.append(types[1])
for t in types[0]:
self.bondsForAtomType[t].add(index)
for t in types[1]:
self.bondsForAtomType[t].add(index)
self.length.append(_convertParameterToNumber(parameters['length'])) self.length.append(_convertParameterToNumber(parameters['length']))
self.k.append(_convertParameterToNumber(parameters['k'])) self.k.append(_convertParameterToNumber(parameters['k']))
...@@ -1697,7 +1748,7 @@ class HarmonicBondGenerator(object): ...@@ -1697,7 +1748,7 @@ class HarmonicBondGenerator(object):
for bond in data.bonds: for bond in data.bonds:
type1 = data.atomType[data.atoms[bond.atom1]] type1 = data.atomType[data.atoms[bond.atom1]]
type2 = data.atomType[data.atoms[bond.atom2]] type2 = data.atomType[data.atoms[bond.atom2]]
for i in range(len(self.types1)): for i in self.bondsForAtomType[type1]:
types1 = self.types1[i] types1 = self.types1[i]
types2 = self.types2[i] types2 = self.types2[i]
if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1): if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1):
...@@ -1717,6 +1768,7 @@ class HarmonicAngleGenerator(object): ...@@ -1717,6 +1768,7 @@ class HarmonicAngleGenerator(object):
def __init__(self, forcefield): def __init__(self, forcefield):
self.ff = forcefield self.ff = forcefield
self.anglesForAtom2Type = defaultdict(list)
self.types1 = [] self.types1 = []
self.types2 = [] self.types2 = []
self.types3 = [] self.types3 = []
...@@ -1726,9 +1778,12 @@ class HarmonicAngleGenerator(object): ...@@ -1726,9 +1778,12 @@ class HarmonicAngleGenerator(object):
def registerAngle(self, parameters): def registerAngle(self, parameters):
types = self.ff._findAtomTypes(parameters, 3) types = self.ff._findAtomTypes(parameters, 3)
if None not in types: if None not in types:
index = len(self.types1)
self.types1.append(types[0]) self.types1.append(types[0])
self.types2.append(types[1]) self.types2.append(types[1])
self.types3.append(types[2]) self.types3.append(types[2])
for t in types[1]:
self.anglesForAtom2Type[t].append(index)
self.angle.append(_convertParameterToNumber(parameters['angle'])) self.angle.append(_convertParameterToNumber(parameters['angle']))
self.k.append(_convertParameterToNumber(parameters['k'])) self.k.append(_convertParameterToNumber(parameters['k']))
...@@ -1755,7 +1810,7 @@ class HarmonicAngleGenerator(object): ...@@ -1755,7 +1810,7 @@ class HarmonicAngleGenerator(object):
type1 = data.atomType[data.atoms[angle[0]]] type1 = data.atomType[data.atoms[angle[0]]]
type2 = data.atomType[data.atoms[angle[1]]] type2 = data.atomType[data.atoms[angle[1]]]
type3 = data.atomType[data.atoms[angle[2]]] type3 = data.atomType[data.atoms[angle[2]]]
for i in range(len(self.types1)): for i in self.anglesForAtom2Type[type2]:
types1 = self.types1[i] types1 = self.types1[i]
types2 = self.types2[i] types2 = self.types2[i]
types3 = self.types3[i] types3 = self.types3[i]
...@@ -2228,7 +2283,7 @@ class LennardJonesGenerator(object): ...@@ -2228,7 +2283,7 @@ class LennardJonesGenerator(object):
reverseMap[typeMap[typeValue]] = typeValue reverseMap[typeMap[typeValue]] = typeValue
# Now everything is assigned. Create the A- and B-coefficient arrays # Now everything is assigned. Create the A- and B-coefficient arrays
acoef = [0]*(numLjTypes*numLjTypes) acoef = [0]*(numLjTypes*numLjTypes)
bcoef = acoef[:] bcoef = acoef[:]
for m in range(numLjTypes): for m in range(numLjTypes):
...@@ -2271,11 +2326,11 @@ class LennardJonesGenerator(object): ...@@ -2271,11 +2326,11 @@ class LennardJonesGenerator(object):
def postprocessSystem(self, sys, data, args): def postprocessSystem(self, sys, data, args):
# Create the exceptions. # Create the exceptions.
bondIndices = _findBondsForExclusions(data, sys) bondIndices = _findBondsForExclusions(data, sys)
if self.lj14scale == 1: if self.lj14scale == 1:
# Just exclude the 1-2 and 1-3 interactions. # Just exclude the 1-2 and 1-3 interactions.
self.force.createExclusionsFromBonds(bondIndices, 2) self.force.createExclusionsFromBonds(bondIndices, 2)
else: else:
forceCopy = deepcopy(self.force) forceCopy = deepcopy(self.force)
...@@ -2283,7 +2338,7 @@ class LennardJonesGenerator(object): ...@@ -2283,7 +2338,7 @@ class LennardJonesGenerator(object):
self.force.createExclusionsFromBonds(bondIndices, 3) self.force.createExclusionsFromBonds(bondIndices, 3)
if self.force.getNumExclusions() > forceCopy.getNumExclusions() and self.lj14scale != 0: if self.force.getNumExclusions() > forceCopy.getNumExclusions() and self.lj14scale != 0:
# We need to create a CustomBondForce and use it to implement the scaled 1-4 interactions. # We need to create a CustomBondForce and use it to implement the scaled 1-4 interactions.
bonded = mm.CustomBondForce('%g*epsilon*((sigma/r)^12-(sigma/r)^6)' % (4*self.lj14scale)) bonded = mm.CustomBondForce('%g*epsilon*((sigma/r)^12-(sigma/r)^6)' % (4*self.lj14scale))
bonded.addPerBondParameter('sigma') bonded.addPerBondParameter('sigma')
bonded.addPerBondParameter('epsilon') bonded.addPerBondParameter('epsilon')
...@@ -2589,6 +2644,7 @@ class CustomNonbondedGenerator(object): ...@@ -2589,6 +2644,7 @@ class CustomNonbondedGenerator(object):
generator.perParticleParams.append(param.attrib['name']) generator.perParticleParams.append(param.attrib['name'])
generator.params = ForceField._AtomTypeParameters(ff, 'CustomNonbondedForce', 'Atom', generator.perParticleParams) generator.params = ForceField._AtomTypeParameters(ff, 'CustomNonbondedForce', 'Atom', generator.perParticleParams)
generator.params.parseDefinitions(element) generator.params.parseDefinitions(element)
generator.functions += _parseFunctions(element)
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.CustomNonbondedForce.NoCutoff, methodMap = {NoCutoff:mm.CustomNonbondedForce.NoCutoff,
...@@ -2601,19 +2657,7 @@ class CustomNonbondedGenerator(object): ...@@ -2601,19 +2657,7 @@ class CustomNonbondedGenerator(object):
force.addGlobalParameter(param, self.globalParams[param]) force.addGlobalParameter(param, self.globalParams[param])
for param in self.perParticleParams: for param in self.perParticleParams:
force.addPerParticleParameter(param) force.addPerParticleParameter(param)
for (name, type, values, params) in self.functions: _createFunctions(force, self.functions)
if type == 'Continuous1D':
force.addTabulatedFunction(name, mm.Continuous1DFunction(values, params['min'], params['max']))
elif type == 'Continuous2D':
force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax']))
elif type == 'Continuous3D':
force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], params['zsize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax'], params['zmin'], params['zmax']))
elif type == 'Discrete1D':
force.addTabulatedFunction(name, mm.Discrete1DFunction(values))
elif type == 'Discrete2D':
force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], values))
elif type == 'Discrete3D':
force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
for atom in data.atoms: for atom in data.atoms:
values = self.params.getAtomParameters(atom, data) values = self.params.getAtomParameters(atom, data)
force.addParticle(values) force.addParticle(values)
...@@ -2660,19 +2704,7 @@ class CustomGBGenerator(object): ...@@ -2660,19 +2704,7 @@ class CustomGBGenerator(object):
generator.computedValues.append((value.attrib['name'], value.text, computationMap[value.attrib['type']])) generator.computedValues.append((value.attrib['name'], value.text, computationMap[value.attrib['type']]))
for term in element.findall('EnergyTerm'): for term in element.findall('EnergyTerm'):
generator.energyTerms.append((term.text, computationMap[term.attrib['type']])) generator.energyTerms.append((term.text, computationMap[term.attrib['type']]))
for function in element.findall("Function"): generator.functions += _parseFunctions(element)
values = [float(x) for x in function.text.split()]
if 'type' in function.attrib:
type = function.attrib['type']
else:
type = 'Continuous1D'
params = {}
for key in function.attrib:
if key.endswith('size'):
params[key] = int(function.attrib[key])
elif key.endswith('min') or key.endswith('max'):
params[key] = float(function.attrib[key])
generator.functions.append((function.attrib['name'], type, values, params))
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.CustomGBForce.NoCutoff, methodMap = {NoCutoff:mm.CustomGBForce.NoCutoff,
...@@ -2689,19 +2721,7 @@ class CustomGBGenerator(object): ...@@ -2689,19 +2721,7 @@ class CustomGBGenerator(object):
force.addComputedValue(value[0], value[1], value[2]) force.addComputedValue(value[0], value[1], value[2])
for term in self.energyTerms: for term in self.energyTerms:
force.addEnergyTerm(term[0], term[1]) force.addEnergyTerm(term[0], term[1])
for (name, type, values, params) in self.functions: _createFunctions(force, self.functions)
if type == 'Continuous1D':
force.addTabulatedFunction(name, mm.Continuous1DFunction(values, params['min'], params['max']))
elif type == 'Continuous2D':
force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax']))
elif type == 'Continuous3D':
force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], params['zsize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax'], params['zmin'], params['zmax']))
elif type == 'Discrete1D':
force.addTabulatedFunction(name, mm.Discrete1DFunction(values))
elif type == 'Discrete2D':
force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], values))
elif type == 'Discrete3D':
force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
for atom in data.atoms: for atom in data.atoms:
values = self.params.getAtomParameters(atom, data) values = self.params.getAtomParameters(atom, data)
force.addParticle(values) force.addParticle(values)
...@@ -2712,6 +2732,171 @@ class CustomGBGenerator(object): ...@@ -2712,6 +2732,171 @@ class CustomGBGenerator(object):
parsers["CustomGBForce"] = CustomGBGenerator.parseElement parsers["CustomGBForce"] = CustomGBGenerator.parseElement
## @private
class CustomHbondGenerator(object):
"""A CustomHbondGenerator constructs a CustomHbondForce."""
def __init__(self, forcefield):
self.ff = forcefield
self.donorTypes1 = []
self.donorTypes2 = []
self.donorTypes3 = []
self.acceptorTypes1 = []
self.acceptorTypes2 = []
self.acceptorTypes3 = []
self.globalParams = {}
self.perDonorParams = []
self.perAcceptorParams = []
self.donorParamValues = []
self.acceptorParamValues = []
self.functions = []
@staticmethod
def parseElement(element, ff):
generator = CustomHbondGenerator(ff)
ff.registerGenerator(generator)
generator.energy = element.attrib['energy']
generator.bondCutoff = int(element.attrib['bondCutoff'])
generator.particlesPerDonor = int(element.attrib['particlesPerDonor'])
generator.particlesPerAcceptor = int(element.attrib['particlesPerAcceptor'])
if generator.particlesPerDonor < 1 or generator.particlesPerDonor > 3:
raise ValueError('Illegal value for particlesPerDonor for CustomHbondForce')
if generator.particlesPerAcceptor < 1 or generator.particlesPerAcceptor > 3:
raise ValueError('Illegal value for particlesPerAcceptor for CustomHbondForce')
for param in element.findall('GlobalParameter'):
generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
for param in element.findall('PerDonorParameter'):
generator.perDonorParams.append(param.attrib['name'])
for param in element.findall('PerAcceptorParameter'):
generator.perAcceptorParams.append(param.attrib['name'])
for donor in element.findall('Donor'):
types = ff._findAtomTypes(donor.attrib, 3)[:generator.particlesPerDonor]
if None not in types:
generator.donorTypes1.append(types[0])
if len(types) > 1:
generator.donorTypes2.append(types[1])
if len(types) > 2:
generator.donorTypes3.append(types[2])
generator.donorParamValues.append([float(donor.attrib[param]) for param in generator.perDonorParams])
for acceptor in element.findall('Acceptor'):
types = ff._findAtomTypes(acceptor.attrib, 3)[:generator.particlesPerAcceptor]
if None not in types:
generator.acceptorTypes1.append(types[0])
if len(types) > 1:
generator.acceptorTypes2.append(types[1])
if len(types) > 2:
generator.acceptorTypes3.append(types[2])
generator.acceptorParamValues.append([float(acceptor.attrib[param]) for param in generator.perAcceptorParams])
generator.functions += _parseFunctions(element)
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.CustomHbondForce.NoCutoff,
CutoffNonPeriodic:mm.CustomHbondForce.CutoffNonPeriodic,
CutoffPeriodic:mm.CustomHbondForce.CutoffPeriodic}
if nonbondedMethod not in methodMap:
raise ValueError('Illegal nonbonded method for CustomNonbondedForce')
force = mm.CustomHbondForce(self.energy)
sys.addForce(force)
for param in self.globalParams:
force.addGlobalParameter(param, self.globalParams[param])
for param in self.perDonorParams:
force.addPerDonorParameter(param)
for param in self.perAcceptorParams:
force.addPerAcceptorParameter(param)
_createFunctions(force, self.functions)
force.setNonbondedMethod(methodMap[nonbondedMethod])
force.setCutoffDistance(nonbondedCutoff)
# Add donors.
if self.particlesPerDonor == 1:
for atom in data.atoms:
type1 = data.atomType[atom]
for i in range(len(self.donorTypes1)):
types1 = self.donorTypes1[i]
if type1 in self.donorTypes1[i]:
force.addDonor(atom.index, -1, -1, self.donorParamValues[i])
elif self.particlesPerDonor == 2:
for bond in data.bonds:
type1 = data.atomType[data.atoms[bond.atom1]]
type2 = data.atomType[data.atoms[bond.atom2]]
for i in range(len(self.donorTypes1)):
types1 = self.donorTypes1[i]
types2 = self.donorTypes2[i]
if type1 in types1 and type2 in types2:
force.addDonor(bond.atom1, bond.atom2, -1, self.donorParamValues[i])
elif type1 in types2 and type2 in types1:
force.addDonor(bond.atom2, bond.atom1, -1, self.donorParamValues[i])
else:
for angle in data.angles:
type1 = data.atomType[data.atoms[angle[0]]]
type2 = data.atomType[data.atoms[angle[1]]]
type3 = data.atomType[data.atoms[angle[2]]]
for i in range(len(self.donorTypes1)):
types1 = self.donorTypes1[i]
types2 = self.donorTypes2[i]
types3 = self.donorTypes3[i]
if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1):
force.addDonor(angle[0], angle[1], angle[2], self.donorParamValues[i])
# Add acceptors.
if self.particlesPerAcceptor == 1:
for atom in data.atoms:
type1 = data.atomType[atom]
for i in range(len(self.acceptorTypes1)):
types1 = self.acceptorTypes1[i]
if type1 in self.acceptorTypes1[i]:
force.addAcceptor(atom.index, -1, -1, self.acceptorParamValues[i])
elif self.particlesPerAcceptor == 2:
for bond in data.bonds:
type1 = data.atomType[data.atoms[bond.atom1]]
type2 = data.atomType[data.atoms[bond.atom2]]
for i in range(len(self.acceptorTypes1)):
types1 = self.acceptorTypes1[i]
types2 = self.acceptorTypes2[i]
if type1 in types1 and type2 in types2:
force.addAcceptor(bond.atom1, bond.atom2, -1, self.acceptorParamValues[i])
elif type1 in types2 and type2 in types1:
force.addAcceptor(bond.atom2, bond.atom1, -1, self.acceptorParamValues[i])
else:
for angle in data.angles:
type1 = data.atomType[data.atoms[angle[0]]]
type2 = data.atomType[data.atoms[angle[1]]]
type3 = data.atomType[data.atoms[angle[2]]]
for i in range(len(self.acceptorTypes1)):
types1 = self.acceptorTypes1[i]
types2 = self.acceptorTypes2[i]
types3 = self.acceptorTypes3[i]
if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1):
force.addAcceptor(angle[0], angle[1], angle[2], self.acceptorParamValues[i])
# Add exclusions.
for donor in range(force.getNumDonors()):
(d1, d2, d3, params) = force.getDonorParameters(donor)
outerAtoms = set((d1, d2, d3))
if -1 in outerAtoms:
outerAtoms.remove(-1)
excludedAtoms = set(outerAtoms)
for i in range(self.bondCutoff):
newOuterAtoms = set()
for atom in outerAtoms:
for bond in data.atomBonds[atom]:
b = data.bonds[bond]
bondedAtom = (b.atom2 if b.atom1 == atom else b.atom1)
if bondedAtom not in excludedAtoms:
newOuterAtoms.add(bondedAtom)
excludedAtoms.add(bondedAtom)
outerAtoms = newOuterAtoms
for acceptor in range(force.getNumAcceptors()):
(a1, a2, a3, params) = force.getAcceptorParameters(acceptor)
if a1 in excludedAtoms or a2 in excludedAtoms or a3 in excludedAtoms:
force.addExclusion(donor, acceptor)
parsers["CustomHbondForce"] = CustomHbondGenerator.parseElement
## @private ## @private
class CustomManyParticleGenerator(object): class CustomManyParticleGenerator(object):
"""A CustomManyParticleGenerator constructs a CustomManyParticleForce.""" """A CustomManyParticleGenerator constructs a CustomManyParticleForce."""
...@@ -4732,7 +4917,7 @@ class AmoebaMultipoleGenerator(object): ...@@ -4732,7 +4917,7 @@ class AmoebaMultipoleGenerator(object):
bondedAtomZ = data.atoms[bondedAtomZIndex] bondedAtomZ = data.atoms[bondedAtomZIndex]
if (kx == 0 and kz == bondedAtomZType): if (kx == 0 and kz == bondedAtomZType):
kz = bondedAtomZIndex zaxis = bondedAtomZIndex
savedMultipoleDict = multipoleDict savedMultipoleDict = multipoleDict
hit = 5 hit = 5
......
wrappers/python/simtk/openmm/app/gromacstopfile.py
View file @ 3b6925ae
...@@ -772,7 +772,7 @@ class GromacsTopFile(object): ...@@ -772,7 +772,7 @@ class GromacsTopFile(object):
if periodic is None: if periodic is None:
periodic = mm.PeriodicTorsionForce() periodic = mm.PeriodicTorsionForce()
sys.addForce(periodic) sys.addForce(periodic)
periodic.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], int(params[7]), float(params[5])*degToRad, k) periodic.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], int(float(params[7])), float(params[5])*degToRad, k)
elif dihedralType == '2': elif dihedralType == '2':
# Harmonic torsion # Harmonic torsion
k = float(params[6]) k = float(params[6])
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 3b6925ae
...@@ -353,13 +353,13 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k ...@@ -353,13 +353,13 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
if cutoff is not None: if cutoff is not None:
params += "; cutoff=%.16g" % cutoff params += "; cutoff=%.16g" % cutoff
if kappa > 0: if kappa > 0:
force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-exp(-kappa*B)/solventDielectric)*q^2/B"+params, force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-exp(-kappa*B)/solventDielectric)*charge^2/B"+params,
CustomGBForce.SingleParticle) CustomGBForce.SingleParticle)
elif kappa < 0: elif kappa < 0:
# Do kappa check here to avoid repeating code everywhere # Do kappa check here to avoid repeating code everywhere
raise ValueError('kappa/ionic strength must be >= 0') raise ValueError('kappa/ionic strength must be >= 0')
else: else:
force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B"+params, force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*charge^2/B"+params,
CustomGBForce.SingleParticle) CustomGBForce.SingleParticle)
if SA=='ACE': if SA=='ACE':
force.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6; radius=or+offset"+params, CustomGBForce.SingleParticle) force.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6; radius=or+offset"+params, CustomGBForce.SingleParticle)
...@@ -367,17 +367,17 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k ...@@ -367,17 +367,17 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
raise ValueError('Unknown surface area method: '+SA) raise ValueError('Unknown surface area method: '+SA)
if cutoff is None: if cutoff is None:
if kappa > 0: if kappa > 0:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-exp(-kappa*f)/solventDielectric)*q1*q2/f;" force.addEnergyTerm("-138.935485*(1/soluteDielectric-exp(-kappa*f)/solventDielectric)*charge1*charge2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions) "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
else: else:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;" force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*charge1*charge2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions) "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
else: else:
if kappa > 0: if kappa > 0:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-exp(-kappa*f)/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");" force.addEnergyTerm("-138.935485*(1/soluteDielectric-exp(-kappa*f)/solventDielectric)*charge1*charge2*(1/f-"+str(1/cutoff)+");"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions) "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
else: else:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");" force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*charge1*charge2*(1/f-"+str(1/cutoff)+");"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions) "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
...@@ -476,7 +476,7 @@ class CustomAmberGBForceBase(CustomGBForce): ...@@ -476,7 +476,7 @@ class CustomAmberGBForceBase(CustomGBForce):
class GBSAHCTForce(CustomAmberGBForceBase): class GBSAHCTForce(CustomAmberGBForceBase):
"""This class is equivalent to Amber ``igb=1`` """This class is equivalent to Amber ``igb=1``
The list of parameters to ``addParticle`` is: ``[q, or, sr]``. The list of parameters to ``addParticle`` is: ``[charge, or, sr]``.
Parameters Parameters
---------- ----------
...@@ -499,7 +499,7 @@ class GBSAHCTForce(CustomAmberGBForceBase): ...@@ -499,7 +499,7 @@ class GBSAHCTForce(CustomAmberGBForceBase):
cutoff=None, kappa=0.0): cutoff=None, kappa=0.0):
CustomAmberGBForceBase.__init__(self) CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" self.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
...@@ -537,7 +537,7 @@ class GBSAHCTForce(CustomAmberGBForceBase): ...@@ -537,7 +537,7 @@ class GBSAHCTForce(CustomAmberGBForceBase):
class GBSAOBC1Force(CustomAmberGBForceBase): class GBSAOBC1Force(CustomAmberGBForceBase):
"""This class is equivalent to Amber ``igb=2`` """This class is equivalent to Amber ``igb=2``
The list of parameters to ``addParticle`` is: ``[q, or, sr]``. The list of parameters to ``addParticle`` is: ``[charge, or, sr]``.
Parameters Parameters
---------- ----------
...@@ -561,7 +561,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase): ...@@ -561,7 +561,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase):
CustomAmberGBForceBase.__init__(self) CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" self.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
...@@ -599,7 +599,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase): ...@@ -599,7 +599,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase):
class GBSAOBC2Force(GBSAOBC1Force): class GBSAOBC2Force(GBSAOBC1Force):
"""This class is equivalent to Amber ``igb=5`` """This class is equivalent to Amber ``igb=5``
The list of parameters to ``addParticle`` is: ``[q, or, sr]``. The list of parameters to ``addParticle`` is: ``[charge, or, sr]``.
Parameters Parameters
---------- ----------
...@@ -625,7 +625,7 @@ class GBSAOBC2Force(GBSAOBC1Force): ...@@ -625,7 +625,7 @@ class GBSAOBC2Force(GBSAOBC1Force):
# is different. We inherit for getStandardParameters. # is different. We inherit for getStandardParameters.
CustomAmberGBForceBase.__init__(self) CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" self.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
...@@ -641,7 +641,7 @@ class GBSAOBC2Force(GBSAOBC1Force): ...@@ -641,7 +641,7 @@ class GBSAOBC2Force(GBSAOBC1Force):
class GBSAGBnForce(CustomAmberGBForceBase): class GBSAGBnForce(CustomAmberGBForceBase):
"""This class is equivalent to Amber ``igb=7`` """This class is equivalent to Amber ``igb=7``
The list of parameters to ``addParticle`` is: ``[q, or, sr]``. The list of parameters to ``addParticle`` is: ``[charge, or, sr]``.
Parameters Parameters
---------- ----------
...@@ -746,7 +746,7 @@ class GBSAGBnForce(CustomAmberGBForceBase): ...@@ -746,7 +746,7 @@ class GBSAGBnForce(CustomAmberGBForceBase):
CustomGBForce.addParticle(self, p + [radIndex]) CustomGBForce.addParticle(self, p + [radIndex])
def _addEnergyTerms(self): def _addEnergyTerms(self):
self.addPerParticleParameter("q") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.addPerParticleParameter("radindex") self.addPerParticleParameter("radindex")
...@@ -834,7 +834,7 @@ class GBSAGBn2Force(GBSAGBnForce): ...@@ -834,7 +834,7 @@ class GBSAGBn2Force(GBSAGBnForce):
return radii return radii
def _addEnergyTerms(self): def _addEnergyTerms(self):
self.addPerParticleParameter("q") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.addPerParticleParameter("alpha") self.addPerParticleParameter("alpha")
......
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