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Commit 6b586f76 authored by Andy Simmonett's avatar Andy Simmonett Committed by GitHub
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Merge pull request #2 from peastman/ljpme 

More updates to dispersion PME
parents 3b6925ae e94e4d0a
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Showing with 2175 additions and 1754 deletions
docs-source/usersguide/application.rst
View file @ 6b586f76
......@@ -916,8 +916,9 @@ Value Meaning
:code:`NoCutoff` No cutoff is applied.
:code:`CutoffNonPeriodic` The reaction field method is used to eliminate all interactions beyond a cutoff distance. Not valid for AMOEBA.
:code:`CutoffPeriodic` The reaction field method is used to eliminate all interactions beyond a cutoff distance. Periodic boundary conditions are applied, so each atom interacts only with the nearest periodic copy of every other atom. Not valid for AMOEBA.
:code:`Ewald` Periodic boundary conditions are applied. Ewald summation is used to compute long range interactions. (This option is rarely used, since PME is much faster for all but the smallest systems.) Not valid for AMOEBA.
:code:`PME` Periodic boundary conditions are applied. The Particle Mesh Ewald method is used to compute long range interactions.
:code:`Ewald` Periodic boundary conditions are applied. Ewald summation is used to compute long range Coulomb interactions. (This option is rarely used, since PME is much faster for all but the smallest systems.) Not valid for AMOEBA.
:code:`PME` Periodic boundary conditions are applied. The Particle Mesh Ewald method is used to compute long range Coulomb interactions.
:code:`LJPME` Periodic boundary conditions are applied. The Particle Mesh Ewald method is used to compute long range interactions for both Coulomb and Lennard-Jones.
========================= ===========================================================================================================================================================================================================================================
......@@ -926,7 +927,7 @@ cutoff distance. Be sure to specify units, as shown in the examples above. For
example, :code:`nonbondedCutoff=1.5*nanometers` or
:code:`nonbondedCutoff=12*angstroms` are legal values.
When using :code:`Ewald` or :code:`PME`\ , you can optionally specify an
When using :code:`Ewald`, :code:`PME`, or :code:`LJPME`\ , you can optionally specify an
error tolerance for the force computation. For example:
::
......
docs-source/usersguide/references.bib
View file @ 6b586f76
......@@ -517,3 +517,15 @@
year = {2014},
type = {Journal Article}
}
@article{Wennberg2015
author = {Wennberg, Christian L. and Murtola, Teemu and Páll, Szilárd and Abraham, Mark J. and Hess, Berk and Lindahl, Erik},
title = {Direct-Space Corrections Enable Fast and Accurate {Lorentz–Berthelot} Combination Rule {Lennard-Jones} Lattice Summation},
journal = {Journal of Chemical Theory and Computation},
volume = {11},
number = {12},
pages = {5737-5746},
year = {2015},
type = {Journal Article}
}
docs-source/usersguide/theory.rst
View file @ 6b586f76
......@@ -412,7 +412,7 @@ and the number of nodes in the mesh along each dimension as
.. math::
n_\mathit{mesh}=\frac{2\alpha d}{{3d}^{1/5}}
n_\mathit{mesh}=\frac{2\alpha d}{{3\delta}^{1/5}}
where *d* is the width of the periodic box along that dimension. Alternatively,
......@@ -432,6 +432,38 @@ to numerical round-off error than Ewald summation. For Platforms that do
calculations in single precision, making :math:`\delta` too small (typically below about
5·10\ :sup:`-5`\ ) can actually cause the error to increase.
Lennard-Jones Interaction With Particle Mesh Ewald
==================================================
The PME algorithm can also be used for Lennard-Jones interactions. Usually this
is not necessary, since Lennard-Jones forces are short ranged, but there are
situations (such as membrane simulations) where neglecting interactions beyond
the cutoff can measurably affect results.
For computational efficiency, certain approximations are made\ :cite:`Wennberg2015`.
Interactions beyond the cutoff distance include only the attractive :math:`1/r^6`
term, not the repulsive :math:`1/r^{12}` term. Since the latter is much smaller
than the former at long distances, this usually has negligible effect. Also,
the interaction between particles farther apart than the cutoff distance is
computed using geometric combination rules:
.. math::
\sigma=\sqrt{\sigma_1 \sigma_2}
The effect of this approximation is also quite small, and it is still far more
accurate than ignoring the interactions altogether (which is what would happen
with PME).
The formula used to compute the number of nodes along each dimension of the mesh
is slightly different from the one used for Coulomb interactions:
.. math::
n_\mathit{mesh}=\frac{\alpha d}{{3\delta}^{1/20}}
As before, this is an empirical formula. It will usually produce an average
relative error in the forces less than or similar to :math:`\delta`\ , but that
is not guaranteed.
.. _gbsaobcforce:
GBSAOBCForce
......
openmmapi/include/openmm/NonbondedForce.h
View file @ 6b586f76
......@@ -101,18 +101,18 @@ public:
*/
CutoffPeriodic = 2,
/**
* Periodic boundary conditions are used, and Ewald summation is used to compute the interaction of each particle
* Periodic boundary conditions are used, and Ewald summation is used to compute the Coulomb interaction of each particle
* with all periodic copies of every other particle.
*/
Ewald = 3,
/**
* Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle
* Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the Coulomb interaction of each particle
* with all periodic copies of every other particle.
*/
PME = 4,
/**
* Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle
* with all periodic copies of every other particle for both electrostatics and dispersion. No switching is used for either interaction.
* with all periodic copies of every other particle for both Coulomb and Lennard-Jones. No switching is used for either interaction.
*/
LJPME = 5
};
......@@ -412,7 +412,8 @@ public:
bool usesPeriodicBoundaryConditions() const {
return nonbondedMethod == NonbondedForce::CutoffPeriodic ||
nonbondedMethod == NonbondedForce::Ewald ||
nonbondedMethod == NonbondedForce::PME;
nonbondedMethod == NonbondedForce::PME ||
nonbondedMethod == NonbondedForce::LJPME;
}
protected:
ForceImpl* createImpl() const;
......
openmmapi/src/NonbondedForce.cpp
View file @ 6b586f76
......@@ -48,7 +48,8 @@ using std::stringstream;
using std::vector;
NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), switchingDistance(-1.0), rfDielectric(78.3),
ewaldErrorTol(5e-4), alpha(0.0), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1), nx(0), ny(0), nz(0) {
ewaldErrorTol(5e-4), alpha(0.0), dalpha(0.0), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1),
nx(0), ny(0), nz(0), dnx(0), dny(0), dnz(0) {
}
NonbondedForce::NonbondedMethod NonbondedForce::getNonbondedMethod() const {
......
openmmapi/src/NonbondedForceImpl.cpp
View file @ 6b586f76
......@@ -90,9 +90,7 @@ void NonbondedForceImpl::initialize(ContextImpl& context) {
exceptions[particle1].insert(particle2);
exceptions[particle2].insert(particle1);
}
if (owner.getNonbondedMethod() == NonbondedForce::CutoffPeriodic ||
owner.getNonbondedMethod() == NonbondedForce::Ewald ||
owner.getNonbondedMethod() == NonbondedForce::PME) {
if (owner.getNonbondedMethod() != NonbondedForce::NoCutoff && owner.getNonbondedMethod() != NonbondedForce::CutoffNonPeriodic) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double cutoff = owner.getCutoffDistance();
......@@ -161,12 +159,19 @@ void NonbondedForceImpl::calcPMEParameters(const System& system, const Nonbonded
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double tol = force.getEwaldErrorTolerance();
alpha = (1.0/force.getCutoffDistance())*std::sqrt(-log(2.0*tol));
if (lj) {
xsize = (int) ceil(alpha*boxVectors[0][0]/(3*pow(tol, 0.05)));
ysize = (int) ceil(alpha*boxVectors[1][1]/(3*pow(tol, 0.05)));
zsize = (int) ceil(alpha*boxVectors[2][2]/(3*pow(tol, 0.05)));
}
else {
xsize = (int) ceil(2*alpha*boxVectors[0][0]/(3*pow(tol, 0.2)));
ysize = (int) ceil(2*alpha*boxVectors[1][1]/(3*pow(tol, 0.2)));
zsize = (int) ceil(2*alpha*boxVectors[2][2]/(3*pow(tol, 0.2)));
xsize = max(xsize, 5);
ysize = max(ysize, 5);
zsize = max(zsize, 5);
}
xsize = max(xsize, 6);
ysize = max(ysize, 6);
zsize = max(zsize, 6);
}
}
......
platforms/cpu/tests/TestCpuDispersionPME.cpp 0 → 100644
View file @ 6b586f76
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* 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) 2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "CpuTests.h"
#include "TestDispersionPME.h"
void runPlatformTests() {
}
platforms/cuda/include/CudaKernels.h
View file @ 6b586f76
......@@ -599,8 +599,8 @@ class CudaCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
CudaCalcNonbondedForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcNonbondedForceKernel(name, platform),
cu(cu), hasInitializedFFT(false), sigmaEpsilon(NULL), exceptionParams(NULL), cosSinSums(NULL), directPmeGrid(NULL), reciprocalPmeGrid(NULL),
pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeAtomRange(NULL), pmeAtomGridIndex(NULL),
pmeEnergyBuffer(NULL), sort(NULL), dispersionFft(NULL), fft(NULL), pmeio(NULL) {
pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeDispersionBsplineModuliX(NULL), pmeDispersionBsplineModuliY(NULL),
pmeDispersionBsplineModuliZ(NULL), pmeAtomRange(NULL), pmeAtomGridIndex(NULL), pmeEnergyBuffer(NULL), sort(NULL), dispersionFft(NULL), fft(NULL), pmeio(NULL) {
}
~CudaCalcNonbondedForceKernel();
/**
......@@ -672,6 +672,9 @@ private:
CudaArray* pmeBsplineModuliX;
CudaArray* pmeBsplineModuliY;
CudaArray* pmeBsplineModuliZ;
CudaArray* pmeDispersionBsplineModuliX;
CudaArray* pmeDispersionBsplineModuliY;
CudaArray* pmeDispersionBsplineModuliZ;
CudaArray* pmeAtomRange;
CudaArray* pmeAtomGridIndex;
CudaArray* pmeEnergyBuffer;
......
platforms/cuda/src/CudaKernels.cpp
View file @ 6b586f76
......@@ -1607,6 +1607,12 @@ CudaCalcNonbondedForceKernel::~CudaCalcNonbondedForceKernel() {
delete pmeBsplineModuliY;
if (pmeBsplineModuliZ != NULL)
delete pmeBsplineModuliZ;
if (pmeDispersionBsplineModuliX != NULL)
delete pmeDispersionBsplineModuliX;
if (pmeDispersionBsplineModuliY != NULL)
delete pmeDispersionBsplineModuliY;
if (pmeDispersionBsplineModuliZ != NULL)
delete pmeDispersionBsplineModuliZ;
if (pmeAtomRange != NULL)
delete pmeAtomRange;
if (pmeAtomGridIndex != NULL)
......@@ -1861,6 +1867,11 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
pmeBsplineModuliX = new CudaArray(cu, gridSizeX, elementSize, "pmeBsplineModuliX");
pmeBsplineModuliY = new CudaArray(cu, gridSizeY, elementSize, "pmeBsplineModuliY");
pmeBsplineModuliZ = new CudaArray(cu, gridSizeZ, elementSize, "pmeBsplineModuliZ");
if (doLJPME) {
pmeDispersionBsplineModuliX = new CudaArray(cu, dispersionGridSizeX, elementSize, "pmeDispersionBsplineModuliX");
pmeDispersionBsplineModuliY = new CudaArray(cu, dispersionGridSizeY, elementSize, "pmeDispersionBsplineModuliY");
pmeDispersionBsplineModuliZ = new CudaArray(cu, dispersionGridSizeZ, elementSize, "pmeDispersionBsplineModuliZ");
}
pmeAtomRange = CudaArray::create<int>(cu, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
pmeAtomGridIndex = CudaArray::create<int2>(cu, numParticles, "pmeAtomGridIndex");
int energyElementSize = (cu.getUseDoublePrecision() || cu.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
......@@ -1911,7 +1922,28 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
hasInitializedFFT = true;
// Initialize the b-spline moduli.
int maxSize = max(max(gridSizeX, gridSizeY), gridSizeZ);
for (int grid = 0; grid < 2; grid++) {
int xsize, ysize, zsize;
CudaArray *xmoduli, *ymoduli, *zmoduli;
if (grid == 0) {
xsize = gridSizeX;
ysize = gridSizeY;
zsize = gridSizeZ;
xmoduli = pmeBsplineModuliX;
ymoduli = pmeBsplineModuliY;
zmoduli = pmeBsplineModuliZ;
}
else {
if (!doLJPME)
continue;
xsize = dispersionGridSizeX;
ysize = dispersionGridSizeY;
zsize = dispersionGridSizeZ;
xmoduli = pmeDispersionBsplineModuliX;
ymoduli = pmeDispersionBsplineModuliY;
zmoduli = pmeDispersionBsplineModuliZ;
}
int maxSize = max(max(xsize, ysize), zsize);
vector<double> data(PmeOrder);
vector<double> ddata(PmeOrder);
vector<double> bsplines_data(maxSize);
......@@ -1944,7 +1976,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
// Evaluate the actual bspline moduli for X/Y/Z.
for(int dim = 0; dim < 3; dim++) {
int ndata = (dim == 0 ? gridSizeX : dim == 1 ? gridSizeY : gridSizeZ);
int ndata = (dim == 0 ? xsize : dim == 1 ? ysize : zsize);
vector<double> moduli(ndata);
for (int i = 0; i < ndata; i++) {
double sc = 0.0;
......@@ -1961,22 +1993,23 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
moduli[i] = (moduli[i-1]+moduli[i+1])*0.5;
if (cu.getUseDoublePrecision()) {
if (dim == 0)
pmeBsplineModuliX->upload(moduli);
xmoduli->upload(moduli);
else if (dim == 1)
pmeBsplineModuliY->upload(moduli);
ymoduli->upload(moduli);
else
pmeBsplineModuliZ->upload(moduli);
zmoduli->upload(moduli);
}
else {
vector<float> modulif(ndata);
for (int i = 0; i < ndata; i++)
modulif[i] = (float) moduli[i];
if (dim == 0)
pmeBsplineModuliX->upload(modulif);
xmoduli->upload(modulif);
else if (dim == 1)
pmeBsplineModuliY->upload(modulif);
ymoduli->upload(modulif);
else
pmeBsplineModuliZ->upload(modulif);
zmoduli->upload(modulif);
}
}
}
}
......
platforms/cuda/src/kernels/coulombLennardJones.cu
View file @ 6b586f76
......@@ -30,7 +30,7 @@
const real dar6 = dar4*dar2;
const real invR2 = invR*invR;
const real expDar2 = EXP(-dar2);
const real2 sigExpProd = sigmaEpsilon1*sigmaEpsilon2;
const float2 sigExpProd = sigmaEpsilon1*sigmaEpsilon2;
const real c6 = 64*sigExpProd.x*sigExpProd.x*sigExpProd.x*sigExpProd.y;
const real coef = invR2*invR2*invR2*c6;
const real eprefac = 1.0f + dar2 + 0.5f*dar4;
......
platforms/cuda/src/kernels/pme.cu
View file @ 6b586f76
......@@ -23,7 +23,7 @@ extern "C" __global__ void gridSpreadCharge(const real4* __restrict__ posq, real
real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ, const int2* __restrict__ pmeAtomGridIndex
#ifdef USE_LJPME
, const real2* __restrict__ sigmaEpsilon
, const float2* __restrict__ sigmaEpsilon
#endif
) {
real3 data[PME_ORDER];
......@@ -68,7 +68,7 @@ extern "C" __global__ void gridSpreadCharge(const real4* __restrict__ posq, real
// Spread the charge from this atom onto each grid point.
#ifdef USE_LJPME
const real2 sigEps = sigmaEpsilon[atom];
const float2 sigEps = sigmaEpsilon[atom];
const real charge = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y;
#else
const real charge = pos.w;
......@@ -250,7 +250,7 @@ void gridInterpolateForce(const real4* __restrict__ posq, unsigned long long* __
real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ, const int2* __restrict__ pmeAtomGridIndex
#ifdef USE_LJPME
, const real2* __restrict__ sigmaEpsilon
, const float2* __restrict__ sigmaEpsilon
#endif
) {
real3 data[PME_ORDER];
......@@ -325,7 +325,7 @@ void gridInterpolateForce(const real4* __restrict__ posq, unsigned long long* __
}
}
#ifdef USE_LJPME
const real2 sigEps = sigmaEpsilon[atom];
const float2 sigEps = sigmaEpsilon[atom];
real q = 8*sigEps.x*sigEps.x*sigEps.x*sigEps.y;
#else
real q = pos.w*EPSILON_FACTOR;
......
platforms/cuda/tests/TestCudaDispersionPME.cpp 0 → 100644
View file @ 6b586f76
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* 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) 2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "CudaTests.h"
#include "TestDispersionPME.h"
void runPlatformTests() {
}
platforms/opencl/tests/TestOpenCLDispersionPME.cpp 0 → 100644
View file @ 6b586f76
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* 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) 2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "OpenCLTests.h"
#include "TestDispersionPME.h"
void runPlatformTests() {
}
platforms/reference/tests/TestReferenceDispersionPME.cpp 0 → 100644
View file @ 6b586f76
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* 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) 2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "ReferenceTests.h"
#include "TestDispersionPME.h"
void runPlatformTests() {
}
serialization/src/NonbondedForceProxy.cpp
View file @ 6b586f76
......@@ -42,7 +42,7 @@ NonbondedForceProxy::NonbondedForceProxy() : SerializationProxy("NonbondedForce"
}
void NonbondedForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
node.setIntProperty("version", 2);
const NonbondedForce& force = *reinterpret_cast<const NonbondedForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setIntProperty("method", (int) force.getNonbondedMethod());
......@@ -59,6 +59,11 @@ void NonbondedForceProxy::serialize(const void* object, SerializationNode& node)
node.setIntProperty("nx", nx);
node.setIntProperty("ny", ny);
node.setIntProperty("nz", nz);
force.getLJPMEParameters(alpha, nx, ny, nz);
node.setDoubleProperty("ljAlpha", alpha);
node.setIntProperty("ljnx", nx);
node.setIntProperty("ljny", ny);
node.setIntProperty("ljnz", nz);
node.setIntProperty("recipForceGroup", force.getReciprocalSpaceForceGroup());
SerializationNode& particles = node.createChildNode("Particles");
for (int i = 0; i < force.getNumParticles(); i++) {
......@@ -76,7 +81,8 @@ void NonbondedForceProxy::serialize(const void* object, SerializationNode& node)
}
void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
throw OpenMMException("Unsupported version number");
NonbondedForce* force = new NonbondedForce();
try {
......@@ -93,6 +99,13 @@ void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
int ny = node.getIntProperty("ny", 0);
int nz = node.getIntProperty("nz", 0);
force->setPMEParameters(alpha, nx, ny, nz);
if (version >= 2) {
alpha = node.getDoubleProperty("ljAlpha", 0.0);
nx = node.getIntProperty("ljnx", 0);
ny = node.getIntProperty("ljny", 0);
nz = node.getIntProperty("ljnz", 0);
force->setLJPMEParameters(alpha, nx, ny, nz);
}
force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup", -1));
const SerializationNode& particles = node.getChildNode("Particles");
for (int i = 0; i < (int) particles.getChildren().size(); i++) {
......
serialization/tests/TestSerializeNonbondedForce.cpp
View file @ 6b586f76
......@@ -53,6 +53,9 @@ void testSerialization() {
double alpha = 0.5;
int nx = 3, ny = 5, nz = 7;
force.setPMEParameters(alpha, nx, ny, nz);
double dalpha = 0.8;
int dnx = 4, dny = 6, dnz = 7;
force.setLJPMEParameters(dalpha, dnx, dny, dnz);
force.addParticle(1, 0.1, 0.01);
force.addParticle(0.5, 0.2, 0.02);
force.addParticle(-0.5, 0.3, 0.03);
......@@ -84,6 +87,13 @@ void testSerialization() {
ASSERT_EQUAL(nx, nx2);
ASSERT_EQUAL(ny, ny2);
ASSERT_EQUAL(nz, nz2);
double dalpha2;
int dnx2, dny2, dnz2;
force2.getLJPMEParameters(dalpha2, dnx2, dny2, dnz2);
ASSERT_EQUAL(dalpha, dalpha2);
ASSERT_EQUAL(dnx, dnx2);
ASSERT_EQUAL(dny, dny2);
ASSERT_EQUAL(dnz, dnz2);
for (int i = 0; i < force.getNumParticles(); i++) {
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
......
tests/TestDispersionPME.h 0 → 100644
View file @ 6b586f76
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* 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) 2008-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/Units.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/internal/NonbondedForceImpl.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
void testErrorTolerance() {
// Create a cloud of random point charges.
const int numParticles = 200;
const double boxWidth = 5.0;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
force->addParticle(0.0, 0.1+0.2*genrand_real2(sfmt), genrand_real2(sfmt));
while (true) {
Vec3 pos = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
double minDist = boxWidth;
for (int j = 0; j < i; j++) {
Vec3 delta = pos-positions[j];
minDist = min(minDist, sqrt(delta.dot(delta)));
}
if (minDist > 0.1) {
positions[i] = pos;
break;
}
}
}
force->setNonbondedMethod(NonbondedForce::LJPME);
// For various values of the cutoff and error tolerance, see if the actual error is reasonable.
for (double cutoff = 0.8; cutoff < boxWidth/2; cutoff *= 1.3) {
force->setCutoffDistance(cutoff);
vector<Vec3> refForces;
double norm = 0.0;
for (double tol = 5e-5; tol < 1e-3; tol *= 2.0) {
force->setEwaldErrorTolerance(tol);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces);
if (refForces.size() == 0) {
refForces = state.getForces();
for (int i = 0; i < numParticles; i++)
norm += refForces[i].dot(refForces[i]);
norm = sqrt(norm);
}
else {
double diff = 0.0;
for (int i = 0; i < numParticles; i++) {
Vec3 delta = refForces[i]-state.getForces()[i];
diff += delta.dot(delta);
}
diff = sqrt(diff)/norm;
ASSERT(diff < 2*tol);
}
// See if the PME parameters were calculated correctly.
double expectedAlpha, actualAlpha;
int expectedSize[3], actualSize[3];
NonbondedForceImpl::calcPMEParameters(system, *force, expectedAlpha, expectedSize[0], expectedSize[1], expectedSize[2], true);
force->getLJPMEParametersInContext(context, actualAlpha, actualSize[0], actualSize[1], actualSize[2]);
ASSERT_EQUAL_TOL(expectedAlpha, actualAlpha, 1e-5);
for (int i = 0; i < 3; i++) {
ASSERT(actualSize[i] >= expectedSize[i]);
ASSERT(actualSize[i] < expectedSize[i]+10);
}
}
}
}
void testPMEParameters() {
// Create a cloud of random point charges.
const int numParticles = 51;
const double boxWidth = 4.7;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
force->addParticle(0.0, 0.1+0.2*genrand_real2(sfmt), genrand_real2(sfmt));
positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
}
force->setNonbondedMethod(NonbondedForce::LJPME);
// Compute the energy with an error tolerance of 1e-3.
force->setEwaldErrorTolerance(1e-3);
VerletIntegrator integrator1(0.01);
Context context1(system, integrator1, platform);
context1.setPositions(positions);
double energy1 = context1.getState(State::Energy).getPotentialEnergy();
double alpha;
int gridx, gridy, gridz;
force->getLJPMEParametersInContext(context1, alpha, gridx, gridy, gridz);
// Try again with an error tolerance of 1e-4.
force->setEwaldErrorTolerance(1e-4);
VerletIntegrator integrator2(0.01);
Context context2(system, integrator2, platform);
context2.setPositions(positions);
double energy2 = context2.getState(State::Energy).getPotentialEnergy();
// Now explicitly set the parameters. These should match the values that were
// used for tolerance 1e-3.
force->setLJPMEParameters(alpha, gridx, gridy, gridz);
VerletIntegrator integrator3(0.01);
Context context3(system, integrator3, platform);
context3.setPositions(positions);
double energy3 = context3.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(energy1, energy3, 1e-5);
ASSERT(fabs((energy1-energy2)/energy1) > 1e-5);
force->getLJPMEParametersInContext(context2, alpha, gridx, gridy, gridz);
}
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 testWater2DpmeEnergiesForcesNoExclusions() {
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 numAtoms = 6;
double boxEdgeLength = 25*OpenMM::NmPerAngstrom;
make_waterbox(numAtoms, 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();
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_TOL(refenergy, energy, 1E-4);
for (int n = 0; n < numAtoms; ++n)
ASSERT_EQUAL_VEC(refforces[n], forces[n], 1E-4);
}
void testWater2DpmeEnergiesForcesWithExclusions() {
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 numAtoms = 6;
double boxEdgeLength = 25*OpenMM::NmPerAngstrom;
make_waterbox(numAtoms, 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 testWater2DpmeEnergiesForcesNoExclusions() 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();
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_TOL(refenergy, energy, 1E-4);
for (int n = 0; n < numAtoms; ++n)
ASSERT_EQUAL_VEC(refforces[n], forces[n], 5E-4);
}
void testWater125DpmeVsLongCutoffNoExclusions() {
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 numAtoms = 375;
double boxEdgeLength = 17.01*OpenMM::NmPerAngstrom;
make_waterbox(numAtoms, 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 testWater2DpmeEnergiesForcesNoExclusions() 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;
const vector<Vec3>& forces = state.getForces();
vector<Vec3> refforces(numAtoms);
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 < numAtoms; ++ i) {
for (int j = i+1; j < numAtoms; ++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 < numAtoms; ++ i) {
for (int j = 0; j < numAtoms; ++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 < numAtoms; ++n)
ASSERT_EQUAL_VEC(refforces[n], forces[n], 5E-4);
}
void testWater125DpmeVsLongCutoffWithExclusions() {
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 numAtoms = 375;
double boxEdgeLength = 23.01*OpenMM::NmPerAngstrom;
make_waterbox(numAtoms, 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();
const vector<Vec3>& forces = state.getForces();
// Gromacs reference values. See comments in testWater2DpmeEnergiesForcesNoExclusions() for details.
double gromacs_energy = -2.17481e+02;
vector<Vec3> refforces(numAtoms);
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(numAtoms);
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 < numAtoms; ++ i) {
for (int j = i+1; j < numAtoms; ++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 < numAtoms; 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 < numAtoms; ++ i) {
for (int j = 0; j < numAtoms; ++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 < numAtoms; ++n)
ASSERT_EQUAL_VEC(refforces[n], forces[n], 1E-4);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
try {
initializeTests(argc, argv);
testErrorTolerance();
testPMEParameters();
testWater2DpmeEnergiesForcesNoExclusions();
testWater2DpmeEnergiesForcesWithExclusions();
testWater125DpmeVsLongCutoffNoExclusions();
testWater125DpmeVsLongCutoffWithExclusions();
runPlatformTests();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
tests/TestNonbondedForce.h
View file @ 6b586f76
......@@ -35,7 +35,6 @@
#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"
......@@ -48,1661 +47,6 @@ 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);
......@@ -2346,10 +690,6 @@ 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();
......
wrappers/python/simtk/openmm/app/__init__.py
View file @ 6b586f76
......@@ -40,6 +40,7 @@ CutoffNonPeriodic = forcefield.CutoffNonPeriodic
CutoffPeriodic = forcefield.CutoffPeriodic
Ewald = forcefield.Ewald
PME = forcefield.PME
LJPME = forcefield.LJPME
HBonds = forcefield.HBonds
AllBonds = forcefield.AllBonds
......
wrappers/python/simtk/openmm/app/amberprmtopfile.py
View file @ 6b586f76
......@@ -169,7 +169,7 @@ class AmberPrmtopFile(object):
----------
nonbondedMethod : object=NoCutoff
The method to use for nonbonded interactions. Allowed values are
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
nonbondedCutoff : distance=1*nanometer
The cutoff distance to use for nonbonded interactions
constraints : object=None
......@@ -202,7 +202,7 @@ class AmberPrmtopFile(object):
added to a hydrogen is subtracted from the heavy atom to keep their
total mass the same.
ewaldErrorTolerance : float=0.0005
The error tolerance to use if nonbondedMethod is Ewald or PME.
The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
switchDistance : float=0*nanometers
The distance at which the potential energy switching function is
turned on for Lennard-Jones interactions. If the switchDistance is 0
......@@ -222,10 +222,11 @@ class AmberPrmtopFile(object):
ff.CutoffNonPeriodic:'CutoffNonPeriodic',
ff.CutoffPeriodic:'CutoffPeriodic',
ff.Ewald:'Ewald',
ff.PME:'PME'}
ff.PME:'PME',
ff.LJPME:'LJPME'}
if nonbondedMethod not in methodMap:
raise ValueError('Illegal value for nonbonded method')
if not self._prmtop.getIfBox() and nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME):
if not self._prmtop.getIfBox() and nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME, ff.LJPME):
raise ValueError('Illegal nonbonded method for a non-periodic system')
constraintMap = {None:None,
ff.HBonds:'h-bonds',
......
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