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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() {
intg->addGlobalVariable("oute", 0);
intg->addGlobalVariable("oute1", 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("outf1", "f1");
intg->addComputePerDof("outf2", "f2");
intg->addComputeGlobal("oute", "energy");
intg->addComputeGlobal("oute1", "energy1");
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->addConstrainVelocities();
intg->addComputeSum("summand2", "v*v+f*f");
......@@ -220,9 +228,9 @@ int main() {
testSerializeCompoundIntegrator();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
tests/TestCustomIntegrator.h
View file @ 3b6925ae
......@@ -858,6 +858,43 @@ void testEnergyParameterDerivatives() {
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();
int main(int argc, char* argv[]) {
......@@ -879,6 +916,7 @@ int main(int argc, char* argv[]) {
testWhileBlock();
testChangingGlobal();
testEnergyParameterDerivatives();
testChangeDT();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomNonbondedForce.h
View file @ 3b6925ae
......@@ -878,6 +878,16 @@ void testLargeInteractionGroup() {
State state3 = context.getState(State::Forces);
for (int i = 0; i < numParticles; i++)
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() {
......@@ -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() {
System system;
system.addParticle(1.0);
......@@ -1144,6 +1213,7 @@ int main(int argc, char* argv[]) {
testInteractionGroupLongRangeCorrection();
testInteractionGroupTabulatedFunction();
testMultipleCutoffs();
testMultipleSwitches();
testIllegalVariable();
testEnergyParameterDerivatives();
testEnergyParameterDerivatives2();
......
tests/TestEwald.h
View file @ 3b6925ae
......@@ -365,7 +365,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
double expectedAlpha, actualAlpha;
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]);
ASSERT_EQUAL_TOL(expectedAlpha, actualAlpha, 1e-5);
for (int i = 0; i < 3; i++) {
......
tests/TestGayBerneForce.h
View file @ 3b6925ae
......@@ -78,7 +78,7 @@ void testPointParticles() {
State state2 = context.getState(State::Forces | State::Energy, false, 2);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
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() {
......
tests/TestLangevinIntegrator.h
View file @ 3b6925ae
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -74,9 +74,9 @@ void testSingleBond() {
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);
State state = context.getState(State::Energy);
double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
......
tests/TestMonteCarloAnisotropicBarostat.h
View file @ 3b6925ae
......@@ -31,6 +31,7 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/MonteCarloAnisotropicBarostat.h"
#include "openmm/Context.h"
......@@ -69,8 +70,9 @@ void testIdealGas() {
}
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], true, true, true, frequency);
system.addForce(barostat);
ASSERT(barostat->usesPeriodicBoundaryConditions());
ASSERT(system.usesPeriodicBoundaryConditions());
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->setUsesPeriodicBoundaryConditions(true);
system.addForce(bonds); // So it won't complain the system is non-periodic.
// Test it for three different temperatures.
......@@ -129,8 +131,9 @@ void testIdealGasAxis(int axis) {
}
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], scaleX, scaleY, scaleZ, frequency);
system.addForce(barostat);
ASSERT(barostat->usesPeriodicBoundaryConditions());
ASSERT(system.usesPeriodicBoundaryConditions());
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->setUsesPeriodicBoundaryConditions(true);
system.addForce(bonds); // So it won't complain the system is non-periodic.
// Test it for three different temperatures.
......@@ -187,8 +190,6 @@ void testRandomSeed() {
system.addForce(forceField);
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, true, true, true, 1);
system.addForce(barostat);
ASSERT(barostat->usesPeriodicBoundaryConditions());
ASSERT(system.usesPeriodicBoundaryConditions());
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) {
......@@ -262,6 +263,9 @@ void testTriclinic() {
}
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temperature, true, true, true, frequency);
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
......
tests/TestMonteCarloBarostat.h
View file @ 3b6925ae
......@@ -32,6 +32,7 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/Context.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
......@@ -105,8 +106,9 @@ void testIdealGas() {
}
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency);
system.addForce(barostat);
ASSERT(barostat->usesPeriodicBoundaryConditions());
ASSERT(system.usesPeriodicBoundaryConditions());
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->setUsesPeriodicBoundaryConditions(true);
system.addForce(bonds); // So it won't complain the system is non-periodic.
// Test it for three different temperatures.
......@@ -153,8 +155,6 @@ void testRandomSeed() {
system.addForce(forceField);
MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, 1);
system.addForce(barostat);
ASSERT(barostat->usesPeriodicBoundaryConditions());
ASSERT(system.usesPeriodicBoundaryConditions());
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) {
......
tests/TestNonbondedForce.h
View file @ 3b6925ae
......@@ -35,10 +35,12 @@
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/Units.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <iomanip>
#include <vector>
using namespace OpenMM;
......@@ -46,6 +48,1661 @@ using namespace std;
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() {
System system;
system.addParticle(1.0);
......@@ -689,6 +2346,10 @@ void runPlatformTests();
int main(int argc, char* argv[]) {
try {
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();
testLJ();
testExclusionsAnd14();
......
tests/TestParser.cpp
View file @ 3b6925ae
#include "../libraries/lepton/include/Lepton.h"
#include "openmm/internal/AssertionUtilities.h"
#include <iostream>
#include <limits>
#include <map>
using namespace Lepton;
using namespace OpenMM;
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.
*/
......@@ -102,6 +102,18 @@ void verifyEvaluation(const string& expression, double x, double y, double expec
value = compiled.evaluate();
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.
variables.clear();
......
tests/TestVariableLangevinIntegrator.h
View file @ 3b6925ae
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -74,9 +74,9 @@ void testSingleBond() {
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);
State state = context.getState(State::Energy);
double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
......
wrappers/python/CMakeLists.txt
View file @ 3b6925ae
......@@ -274,7 +274,7 @@ add_custom_target(PythonSdist
)
# Install binary module (to system location)
set(PYTHON_SETUP_COMMAND "install")
set(PYTHON_SETUP_COMMAND "install --root=\$ENV{DESTDIR}/")
configure_file(pysetup.cmake.in
"${CMAKE_CURRENT_BINARY_DIR}/pysetupinstall.cmake" @ONLY)
add_custom_target(PythonInstall
......
wrappers/python/setup.py
View file @ 3b6925ae
......@@ -229,8 +229,8 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
def main():
if sys.version_info < (2, 6):
reportError("OpenMM requires Python 2.6 or better.")
if sys.version_info < (2, 7):
reportError("OpenMM requires Python 2.7 or better.")
if platform.system() == 'Darwin':
macVersion = [int(x) for x in platform.mac_ver()[0].split('.')]
if tuple(macVersion) < (10, 5):
......
wrappers/python/simtk/openmm/app/__init__.py
View file @ 3b6925ae
......@@ -6,7 +6,7 @@ from __future__ import absolute_import
__docformat__ = "epytext en"
__author__ = "Peter Eastman"
__copyright__ = "Copyright 2015, Stanford University and Peter Eastman"
__copyright__ = "Copyright 2016, Stanford University and Peter Eastman"
__credits__ = []
__license__ = "MIT"
__maintainer__ = "Peter Eastman"
......@@ -44,3 +44,10 @@ PME = forcefield.PME
HBonds = forcefield.HBonds
AllBonds = forcefield.AllBonds
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
from simtk.openmm.app import Topology
from simtk.openmm.app import PDBFile
from simtk.openmm.app.internal import amber_file_parser
from simtk.openmm.app.internal.singleton import Singleton
from . import forcefield as ff
from . import element as elem
import simtk.unit as u
......@@ -44,27 +45,27 @@ from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
# Enumerated values for implicit solvent model
class HCT(object):
class HCT(Singleton):
def __repr__(self):
return 'HCT'
HCT = HCT()
class OBC1(object):
class OBC1(Singleton):
def __repr__(self):
return 'OBC1'
OBC1 = OBC1()
class OBC2(object):
class OBC2(Singleton):
def __repr__(self):
return 'OBC2'
OBC2 = OBC2()
class GBn(object):
class GBn(Singleton):
def __repr__(self):
return 'GBn'
GBn = GBn()
class GBn2(object):
class GBn2(Singleton):
def __repr__(self):
return '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
Biological Structures at Stanford, funded under the NIH Roadmap for
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
Contributors:
......@@ -33,6 +33,9 @@ __author__ = "Robert McGibbon"
__version__ = "1.0"
import simtk.openmm as mm
import os
import os.path
__all__ = ['CheckpointReporter']
......@@ -80,12 +83,7 @@ class CheckpointReporter(object):
"""
self._reportInterval = reportInterval
if isinstance(file, str):
self._own_handle = True
self._out = open(file, 'w+b', 0)
else:
self._out = file
self._own_handle = False
self._file = file
def describeNextReport(self, simulation):
"""Get information about the next report this object will generate.
......@@ -116,13 +114,24 @@ class CheckpointReporter(object):
state : State
The current state of the simulation
"""
self._out.seek(0)
chk = simulation.context.createCheckpoint()
self._out.write(chk)
self._out.truncate()
self._out.flush()
def __del__(self):
if self._own_handle:
self._out.close()
if isinstance(self._file, str):
# Do a safe save.
tempFilename1 = self._file+".backup1"
tempFilename2 = self._file+".backup2"
with open(tempFilename1, 'w+b', 0) as out:
out.write(simulation.context.createCheckpoint())
exists = os.path.exists(self._file)
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):
if is_quantity(dt):
dt = dt.value_in_unit(picoseconds)
dt /= 0.04888821
self._dt = dt
boxFlag = 0
if topology.getUnitCellDimensions() is not None:
boxFlag = 1
......@@ -116,9 +117,19 @@ class DCDFile(object):
raise ValueError('Particle position is infinite')
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.
self._modelCount += 1
file.seek(8, os.SEEK_SET)
file.write(struct.pack('<i', self._modelCount))
file.seek(20, os.SEEK_SET)
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 3b6925ae
......@@ -40,10 +40,12 @@ import math
from math import sqrt, cos
from copy import deepcopy
from heapq import heappush, heappop
from collections import defaultdict
import simtk.openmm as mm
import simtk.unit as unit
from . import element as elem
from simtk.openmm.app import Topology
from simtk.openmm.app.internal.singleton import Singleton
def _convertParameterToNumber(param):
if unit.is_quantity(param):
......@@ -52,46 +54,80 @@ def _convertParameterToNumber(param):
return param.value_in_unit_system(unit.md_unit_system)
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
class NoCutoff(object):
class NoCutoff(Singleton):
def __repr__(self):
return 'NoCutoff'
NoCutoff = NoCutoff()
class CutoffNonPeriodic(object):
class CutoffNonPeriodic(Singleton):
def __repr__(self):
return 'CutoffNonPeriodic'
CutoffNonPeriodic = CutoffNonPeriodic()
class CutoffPeriodic(object):
class CutoffPeriodic(Singleton):
def __repr__(self):
return 'CutoffPeriodic'
CutoffPeriodic = CutoffPeriodic()
class Ewald(object):
class Ewald(Singleton):
def __repr__(self):
return 'Ewald'
Ewald = Ewald()
class PME(object):
class PME(Singleton):
def __repr__(self):
return 'PME'
PME = PME()
# Enumerated values for constraint type
class HBonds(object):
class HBonds(Singleton):
def __repr__(self):
return 'HBonds'
HBonds = HBonds()
class AllBonds(object):
class AllBonds(Singleton):
def __repr__(self):
return 'AllBonds'
AllBonds = AllBonds()
class HAngles(object):
class HAngles(Singleton):
def __repr__(self):
return 'HAngles'
HAngles = HAngles()
......@@ -757,7 +793,7 @@ class ForceField(object):
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.
Parameters
......@@ -784,14 +820,14 @@ class ForceField(object):
if signature in templateSignatures:
allMatches = []
for t in templateSignatures[signature]:
match = _matchResidue(res, t, bondedToAtom)
match = _matchResidue(res, t, bondedToAtom, ignoreExternalBonds)
if match is not None:
allMatches.append((t, match))
if len(allMatches) == 1:
template = allMatches[0][0]
matches = allMatches[0][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]
def _buildBondedToAtomList(self, topology):
......@@ -846,7 +882,7 @@ class ForceField(object):
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.
.. CAUTION:: This method is experimental, and its API is subject to change.
......@@ -855,7 +891,8 @@ class ForceField(object):
----------
topology : Topology
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
-------
templates : list of _TemplateData
......@@ -869,7 +906,7 @@ class ForceField(object):
templates = list() # list of templates matching the corresponding residues
for res in topology.residues():
# 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.
if matches is None:
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):
if signature in signatures:
# Signature is the same as an existing residue; check connectivity.
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:
is_unique = False
if is_unique:
......@@ -924,7 +961,8 @@ class ForceField(object):
return [templates, unique_unmatched_residues]
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.
Parameters
......@@ -950,11 +988,16 @@ class ForceField(object):
their total mass the same.
residueTemplates : dict=dict()
Key: Topology Residue object
Value: string, name of _TemplateData residue template object to use for
(Key) residue
Value: string, name of _TemplateData residue template object to use for (Key) residue.
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+
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
Arbitrary additional keyword arguments may also be specified.
This allows extra parameters to be specified that are specific to
......@@ -996,12 +1039,12 @@ class ForceField(object):
if res in residueTemplates:
tname = residueTemplates[res]
template = self._templates[tname]
matches = _matchResidue(res, template, bondedToAtom)
matches = _matchResidue(res, template, bondedToAtom, ignoreExternalBonds)
if matches is None:
raise Exception('User-supplied template %s does not match the residue %d (%s)' % (tname, res.index+1, res.name))
else:
# 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:
unmatchedResidues.append(res)
else:
......@@ -1010,20 +1053,20 @@ class ForceField(object):
# Try to apply patches to find matches for any unmatched residues.
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
# new templates (and potentially atom types/parameters).
for res in unmatchedResidues:
# 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:
# Try all generators.
for generator in self._templateGenerators:
if generator(self, res):
# 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:
# 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)))
......@@ -1252,7 +1295,7 @@ def _createResidueSignature(elements):
s += element.symbol+str(count)
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.
Parameters
......@@ -1263,6 +1306,8 @@ def _matchResidue(res, template, bondedToAtom):
The template to compare it to
bondedToAtom : list
Enumerates which other atoms each atom is bonded to
ignoreExternalBonds : bool
If true, ignore external bonds when matching templates
Returns
-------
......@@ -1285,7 +1330,7 @@ def _matchResidue(res, template, bondedToAtom):
for atom in atoms:
bonds = [renumberAtoms[x] for x in bondedToAtom[atom.index] if x in renumberAtoms]
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
# template have the same number of atoms.
......@@ -1298,7 +1343,7 @@ def _matchResidue(res, template, bondedToAtom):
residueTypeCount[key] += 1
templateTypeCount = {}
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:
templateTypeCount[key] = 1
templateTypeCount[key] += 1
......@@ -1314,7 +1359,7 @@ def _matchResidue(res, template, bondedToAtom):
continue
if len(atom.bondedTo) != len(bondedTo[i]):
continue
if atom.externalBonds != externalBonds[i]:
if not ignoreExternalBonds and atom.externalBonds != externalBonds[i]:
continue
candidates[i].append(j)
......@@ -1388,7 +1433,7 @@ def _findAtomMatches(template, bondedTo, matches, hasMatch, candidates, position
return False
def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom):
def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom, ignoreExternalBonds):
"""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
# to a single template. The number of these is usually not too large, and they often cover a large fraction
......@@ -1414,7 +1459,7 @@ def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom):
unmatchedResidues = []
for res in residues:
[template, matches] = forcefield._getResidueTemplateMatches(res, bondedToAtom, patchedTemplateSignatures)
[template, matches] = forcefield._getResidueTemplateMatches(res, bondedToAtom, patchedTemplateSignatures, ignoreExternalBonds)
if matches is None:
unmatchedResidues.append(res)
else:
......@@ -1466,7 +1511,7 @@ def _applyPatchesToMatchResidues(forcefield, data, residues, bondedToAtom):
for patchName in patches:
patch = forcefield._patches[patchName]
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 residue in cluster:
unmatchedResidues.remove(residue)
......@@ -1510,21 +1555,21 @@ def _generatePatchedSingleResidueTemplates(template, patches, index, newTemplate
_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."""
matchedClusters = []
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
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."""
if index < patch.numResidues:
for template in candidateTemplates[index]:
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:
# 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.
......@@ -1541,7 +1586,7 @@ def _applyMultiResiduePatch(data, clusters, patch, candidateTemplates, selectedT
for residues in itertools.permutations(cluster):
residueMatches = []
for residue, template in zip(residues, patchedTemplates):
matches = _matchResidue(residue, template, bondedToAtom)
matches = _matchResidue(residue, template, bondedToAtom, ignoreExternalBonds)
if matches is None:
residueMatches = None
break
......@@ -1662,6 +1707,7 @@ class HarmonicBondGenerator(object):
def __init__(self, forcefield):
self.ff = forcefield
self.bondsForAtomType = defaultdict(set)
self.types1 = []
self.types2 = []
self.length = []
......@@ -1670,8 +1716,13 @@ class HarmonicBondGenerator(object):
def registerBond(self, parameters):
types = self.ff._findAtomTypes(parameters, 2)
if None not in types:
index = len(self.types1)
self.types1.append(types[0])
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.k.append(_convertParameterToNumber(parameters['k']))
......@@ -1697,7 +1748,7 @@ class HarmonicBondGenerator(object):
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.types1)):
for i in self.bondsForAtomType[type1]:
types1 = self.types1[i]
types2 = self.types2[i]
if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1):
......@@ -1717,6 +1768,7 @@ class HarmonicAngleGenerator(object):
def __init__(self, forcefield):
self.ff = forcefield
self.anglesForAtom2Type = defaultdict(list)
self.types1 = []
self.types2 = []
self.types3 = []
......@@ -1726,9 +1778,12 @@ class HarmonicAngleGenerator(object):
def registerAngle(self, parameters):
types = self.ff._findAtomTypes(parameters, 3)
if None not in types:
index = len(self.types1)
self.types1.append(types[0])
self.types2.append(types[1])
self.types3.append(types[2])
for t in types[1]:
self.anglesForAtom2Type[t].append(index)
self.angle.append(_convertParameterToNumber(parameters['angle']))
self.k.append(_convertParameterToNumber(parameters['k']))
......@@ -1755,7 +1810,7 @@ class HarmonicAngleGenerator(object):
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.types1)):
for i in self.anglesForAtom2Type[type2]:
types1 = self.types1[i]
types2 = self.types2[i]
types3 = self.types3[i]
......@@ -2589,6 +2644,7 @@ class CustomNonbondedGenerator(object):
generator.perParticleParams.append(param.attrib['name'])
generator.params = ForceField._AtomTypeParameters(ff, 'CustomNonbondedForce', 'Atom', generator.perParticleParams)
generator.params.parseDefinitions(element)
generator.functions += _parseFunctions(element)
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.CustomNonbondedForce.NoCutoff,
......@@ -2601,19 +2657,7 @@ class CustomNonbondedGenerator(object):
force.addGlobalParameter(param, self.globalParams[param])
for param in self.perParticleParams:
force.addPerParticleParameter(param)
for (name, type, values, params) in 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))
_createFunctions(force, self.functions)
for atom in data.atoms:
values = self.params.getAtomParameters(atom, data)
force.addParticle(values)
......@@ -2660,19 +2704,7 @@ class CustomGBGenerator(object):
generator.computedValues.append((value.attrib['name'], value.text, computationMap[value.attrib['type']]))
for term in element.findall('EnergyTerm'):
generator.energyTerms.append((term.text, computationMap[term.attrib['type']]))
for function in element.findall("Function"):
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))
generator.functions += _parseFunctions(element)
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.CustomGBForce.NoCutoff,
......@@ -2689,19 +2721,7 @@ class CustomGBGenerator(object):
force.addComputedValue(value[0], value[1], value[2])
for term in self.energyTerms:
force.addEnergyTerm(term[0], term[1])
for (name, type, values, params) in 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))
_createFunctions(force, self.functions)
for atom in data.atoms:
values = self.params.getAtomParameters(atom, data)
force.addParticle(values)
......@@ -2712,6 +2732,171 @@ class CustomGBGenerator(object):
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
class CustomManyParticleGenerator(object):
"""A CustomManyParticleGenerator constructs a CustomManyParticleForce."""
......@@ -4732,7 +4917,7 @@ class AmoebaMultipoleGenerator(object):
bondedAtomZ = data.atoms[bondedAtomZIndex]
if (kx == 0 and kz == bondedAtomZType):
kz = bondedAtomZIndex
zaxis = bondedAtomZIndex
savedMultipoleDict = multipoleDict
hit = 5
......
wrappers/python/simtk/openmm/app/gromacstopfile.py
View file @ 3b6925ae
......@@ -772,7 +772,7 @@ class GromacsTopFile(object):
if periodic is None:
periodic = mm.PeriodicTorsionForce()
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':
# Harmonic torsion
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
if cutoff is not None:
params += "; cutoff=%.16g" % cutoff
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)
elif kappa < 0:
# Do kappa check here to avoid repeating code everywhere
raise ValueError('kappa/ionic strength must be >= 0')
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)
if SA=='ACE':
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
raise ValueError('Unknown surface area method: '+SA)
if cutoff is None:
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)
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)
else:
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)
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)
......@@ -476,7 +476,7 @@ class CustomAmberGBForceBase(CustomGBForce):
class GBSAHCTForce(CustomAmberGBForceBase):
"""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
----------
......@@ -499,7 +499,7 @@ class GBSAHCTForce(CustomAmberGBForceBase):
cutoff=None, kappa=0.0):
CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q")
self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # 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);"
......@@ -537,7 +537,7 @@ class GBSAHCTForce(CustomAmberGBForceBase):
class GBSAOBC1Force(CustomAmberGBForceBase):
"""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
----------
......@@ -561,7 +561,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase):
CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q")
self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # 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);"
......@@ -599,7 +599,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase):
class GBSAOBC2Force(GBSAOBC1Force):
"""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
----------
......@@ -625,7 +625,7 @@ class GBSAOBC2Force(GBSAOBC1Force):
# is different. We inherit for getStandardParameters.
CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q")
self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # 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);"
......@@ -641,7 +641,7 @@ class GBSAOBC2Force(GBSAOBC1Force):
class GBSAGBnForce(CustomAmberGBForceBase):
"""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
----------
......@@ -746,7 +746,7 @@ class GBSAGBnForce(CustomAmberGBForceBase):
CustomGBForce.addParticle(self, p + [radIndex])
def _addEnergyTerms(self):
self.addPerParticleParameter("q")
self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius
self.addPerParticleParameter("radindex")
......@@ -834,7 +834,7 @@ class GBSAGBn2Force(GBSAGBnForce):
return radii
def _addEnergyTerms(self):
self.addPerParticleParameter("q")
self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius
self.addPerParticleParameter("alpha")
......
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