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Commit 82e118fb authored by Peter Eastman's avatar Peter Eastman
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Bug fixes to triclinic boxes for reference AmoebaMultipoleForce

parent 5e3a0a05
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Showing with 157 additions and 84 deletions
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 82e118fb
/* Portions copyright (c) 2006-2014 Stanford University and Simbios.
/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -5036,7 +5036,7 @@ void AmoebaReferencePmeMultipoleForce::computeAmoebaBsplines(const vector<Multip
RealOpenMM w = position[0]*_recipBoxVectors[0][jj]+position[1]*_recipBoxVectors[1][jj]+position[2]*_recipBoxVectors[2][jj];
RealOpenMM fr = _pmeGridDimensions[jj]*(w-(int)(w+0.5)+0.5);
int ifr = static_cast<int>(fr);
int ifr = static_cast<int>(floor(fr));
w = fr - ifr;
igrid[jj] = ifr - AMOEBA_PME_ORDER + 1;
igrid[jj] += igrid[jj] < 0 ? _pmeGridDimensions[jj] : 0;
......@@ -5197,14 +5197,14 @@ void AmoebaReferencePmeMultipoleForce::transformPotentialToCartesianCoordinates(
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 6; j++) {
b[i][j] = a[index1[i]][index1[j]]*a[index2[i]][index2[j]];
if (index1[i] != index2[i])
if (index1[j] != index2[j])
b[i][j] *= 2;
}
}
for (int i = 3; i < 6; i++) {
for (int j = 0; j < 6; j++) {
b[i][j] = a[index1[i]][index1[j]]*a[index2[i]][index2[j]];
if (index1[i] != index2[i])
if (index1[j] != index2[j])
b[i][j] += a[index1[i]][index2[j]]*a[index2[i]][index1[j]];
}
}
......@@ -5410,7 +5410,7 @@ void AmoebaReferencePmeMultipoleForce::computeFixedPotentialFromGrid()
}
}
t_complex AmoebaReferencePmeMultipoleForce::computeInducedDipoleGridValue(const int2& particleGridIndices, const RealVec* fracToCart, int ix, int iy,
t_complex AmoebaReferencePmeMultipoleForce::computeInducedDipoleGridValue(const int2& particleGridIndices, const RealVec* cartToFrac, int ix, int iy,
const IntVec& gridPoint,
const vector<RealVec>& inputInducedDipole,
const vector<RealVec>& inputInducedDipolePolar) const
......@@ -5430,16 +5430,12 @@ t_complex AmoebaReferencePmeMultipoleForce::computeInducedDipoleGridValue(const
if (iz >= _pmeGridDimensions[2]) {
iz -= _pmeGridDimensions[2];
}
RealVec inducedDipole = RealVec(inputInducedDipole[atomIndex][0]*fracToCart[0][0] + inputInducedDipole[atomIndex][1]*fracToCart[0][1] + inputInducedDipole[atomIndex][2]*fracToCart[0][2],
inputInducedDipole[atomIndex][0]*fracToCart[1][0] + inputInducedDipole[atomIndex][1]*fracToCart[1][1] + inputInducedDipole[atomIndex][2]*fracToCart[1][2],
inputInducedDipole[atomIndex][0]*fracToCart[2][0] + inputInducedDipole[atomIndex][1]*fracToCart[2][1] + inputInducedDipole[atomIndex][2]*fracToCart[2][2]);
RealVec inducedDipolePolar = RealVec(inputInducedDipolePolar[atomIndex][0]*fracToCart[0][0] + inputInducedDipolePolar[atomIndex][1]*fracToCart[0][1] + inputInducedDipolePolar[atomIndex][2]*fracToCart[0][2],
inputInducedDipolePolar[atomIndex][0]*fracToCart[1][0] + inputInducedDipolePolar[atomIndex][1]*fracToCart[1][1] + inputInducedDipolePolar[atomIndex][2]*fracToCart[1][2],
inputInducedDipolePolar[atomIndex][0]*fracToCart[2][0] + inputInducedDipolePolar[atomIndex][1]*fracToCart[2][1] + inputInducedDipolePolar[atomIndex][2]*fracToCart[2][2]);
// RealVec inducedDipolePolar = RealVec(scale[0]*inputInducedDipolePolar[atomIndex][0],
// scale[1]*inputInducedDipolePolar[atomIndex][1],
// scale[2]*inputInducedDipolePolar[atomIndex][2]);
RealVec inducedDipole = RealVec(inputInducedDipole[atomIndex][0]*cartToFrac[0][0] + inputInducedDipole[atomIndex][1]*cartToFrac[0][1] + inputInducedDipole[atomIndex][2]*cartToFrac[0][2],
inputInducedDipole[atomIndex][0]*cartToFrac[1][0] + inputInducedDipole[atomIndex][1]*cartToFrac[1][1] + inputInducedDipole[atomIndex][2]*cartToFrac[1][2],
inputInducedDipole[atomIndex][0]*cartToFrac[2][0] + inputInducedDipole[atomIndex][1]*cartToFrac[2][1] + inputInducedDipole[atomIndex][2]*cartToFrac[2][2]);
RealVec inducedDipolePolar = RealVec(inputInducedDipolePolar[atomIndex][0]*cartToFrac[0][0] + inputInducedDipolePolar[atomIndex][1]*cartToFrac[0][1] + inputInducedDipolePolar[atomIndex][2]*cartToFrac[0][2],
inputInducedDipolePolar[atomIndex][0]*cartToFrac[1][0] + inputInducedDipolePolar[atomIndex][1]*cartToFrac[1][1] + inputInducedDipolePolar[atomIndex][2]*cartToFrac[1][2],
inputInducedDipolePolar[atomIndex][0]*cartToFrac[2][0] + inputInducedDipolePolar[atomIndex][1]*cartToFrac[2][1] + inputInducedDipolePolar[atomIndex][2]*cartToFrac[2][2]);
RealOpenMM4 t = _thetai[0][atomIndex*AMOEBA_PME_ORDER+ix];
RealOpenMM4 u = _thetai[1][atomIndex*AMOEBA_PME_ORDER+iy];
......@@ -5460,10 +5456,10 @@ t_complex AmoebaReferencePmeMultipoleForce::computeInducedDipoleGridValue(const
void AmoebaReferencePmeMultipoleForce::spreadInducedDipolesOnGrid(const vector<RealVec>& inputInducedDipole,
const vector<RealVec>& inputInducedDipolePolar)
{
RealVec fracToCart[3];
RealVec cartToFrac[3];
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
fracToCart[i][j] = _pmeGridDimensions[j]*_recipBoxVectors[i][j];
cartToFrac[j][i] = _pmeGridDimensions[j]*_recipBoxVectors[i][j];
for (int gridIndex = 0; gridIndex < _totalGridSize; gridIndex++)
{
......@@ -5486,13 +5482,13 @@ void AmoebaReferencePmeMultipoleForce::spreadInducedDipolesOnGrid(const vector<R
int2 particleGridIndices;
particleGridIndices[0] = x*_pmeGridDimensions[1]*_pmeGridDimensions[2]+y*_pmeGridDimensions[2]+z1;
particleGridIndices[1] = x*_pmeGridDimensions[1]*_pmeGridDimensions[2]+y*_pmeGridDimensions[2]+z2;
gridValue += computeInducedDipoleGridValue(particleGridIndices, fracToCart, ix, iy, gridPoint, inputInducedDipole, inputInducedDipolePolar);
gridValue += computeInducedDipoleGridValue(particleGridIndices, cartToFrac, ix, iy, gridPoint, inputInducedDipole, inputInducedDipolePolar);
if (z1 > gridPoint[2])
{
particleGridIndices[0] = x*_pmeGridDimensions[1]*_pmeGridDimensions[2]+y*_pmeGridDimensions[2];
particleGridIndices[1] = x*_pmeGridDimensions[1]*_pmeGridDimensions[2]+y*_pmeGridDimensions[2]+gridPoint[2];
gridValue += computeInducedDipoleGridValue(particleGridIndices, fracToCart, ix, iy, gridPoint, inputInducedDipole, inputInducedDipolePolar);
gridValue += computeInducedDipoleGridValue(particleGridIndices, cartToFrac, ix, iy, gridPoint, inputInducedDipole, inputInducedDipolePolar);
}
}
}
......@@ -5714,8 +5710,6 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceFixedMultipol
const int deriv3[] = {3, 8, 9, 6, 14, 16, 12, 19, 17, 18};
vector<RealOpenMM> cphi(10*_numParticles);
transformPotentialToCartesianCoordinates(_phi, cphi);
// RealVec scale;
// getPmeScale(scale);
RealVec fracToCart[3];
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
......@@ -5739,22 +5733,6 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceFixedMultipol
multipole[8] = particleData[i].quadrupole[QXZ]*2.0;
multipole[9] = particleData[i].quadrupole[QYZ]*2.0;
// const RealOpenMM* phi = &_phi[20*i];
// torques[i][0] += _electric*(multipole[3]*scale[1]*phi[2] - multipole[2]*scale[2]*phi[3]
// + 2.0*(multipole[6]-multipole[5])*scale[1]*scale[2]*phi[9]
// + multipole[8]*scale[0]*scale[1]*phi[7] + multipole[9]*scale[1]*scale[1]*phi[5]
// - multipole[7]*scale[0]*scale[2]*phi[8] - multipole[9]*scale[2]*scale[2]*phi[6]);
//
// torques[i][1] += _electric*(multipole[1]*scale[2]*phi[3] - multipole[3]*scale[0]*phi[1]
// + 2.0*(multipole[4]-multipole[6])*scale[0]*scale[2]*phi[8]
// + multipole[7]*scale[1]*scale[2]*phi[9] + multipole[8]*scale[2]*scale[2]*phi[6]
// - multipole[8]*scale[0]*scale[0]*phi[4] - multipole[9]*scale[0]*scale[1]*phi[7]);
//
// torques[i][2] += _electric*(multipole[2]*scale[0]*phi[1] - multipole[1]*scale[1]*phi[2]
// + 2.0*(multipole[5]-multipole[4])*scale[0]*scale[1]*phi[7]
// + multipole[7]*scale[0]*scale[0]*phi[4] + multipole[9]*scale[0]*scale[2]*phi[8]
// - multipole[7]*scale[1]*scale[1]*phi[5] - multipole[8]*scale[1]*scale[2]*phi[9]);
const RealOpenMM* phi = &cphi[10*i];
torques[i][0] += _electric*(multipole[3]*phi[2] - multipole[2]*phi[3]
+ 2.0*(multipole[6]-multipole[5])*phi[9]
......@@ -5782,15 +5760,6 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceFixedMultipol
multipole[7] = _transformed[i].quadrupole[QXY];
multipole[8] = _transformed[i].quadrupole[QXZ];
multipole[9] = _transformed[i].quadrupole[QYZ];
// multipole[1] *= scale[0];
// multipole[2] *= scale[1];
// multipole[3] *= scale[2];
// multipole[4] *= scale[0]*scale[0];
// multipole[5] *= scale[1]*scale[1];
// multipole[6] *= scale[2]*scale[2];
// multipole[7] *= scale[0]*scale[1];
// multipole[8] *= scale[0]*scale[2];
// multipole[9] *= scale[1]*scale[2];
RealVec f = RealVec(0.0, 0.0, 0.0);
for (int k = 0; k < 10; k++) {
......@@ -5799,9 +5768,6 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceFixedMultipol
f[1] += multipole[k]*_phi[20*i+deriv2[k]];
f[2] += multipole[k]*_phi[20*i+deriv3[k]];
}
// f[0] *= scale[0];
// f[1] *= scale[1];
// f[2] *= scale[2];
f *= (_electric);
forces[i] -= RealVec(f[0]*fracToCart[0][0] + f[1]*fracToCart[0][1] + f[2]*fracToCart[0][2],
f[0]*fracToCart[1][0] + f[1]*fracToCart[1][1] + f[2]*fracToCart[1][2],
......@@ -5832,8 +5798,6 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceInducedDipole
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
cartToFrac[j][i] = fracToCart[i][j] = _pmeGridDimensions[j]*_recipBoxVectors[i][j];
// RealVec scale;
// getPmeScale(scale);
RealOpenMM energy = 0.0;
for (int i = 0; i < _numParticles; i++) {
......@@ -5881,16 +5845,6 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceInducedDipole
multipole[7] = _transformed[i].quadrupole[QXY];
multipole[8] = _transformed[i].quadrupole[QXZ];
multipole[9] = _transformed[i].quadrupole[QYZ];
// multipole[1] *= scale[0];
// multipole[2] *= scale[1];
// multipole[3] *= scale[2];
//
// multipole[4] *= scale[0]*scale[0];
// multipole[5] *= scale[1]*scale[1];
// multipole[6] *= scale[2]*scale[2];
// multipole[7] *= scale[0]*scale[1];
// multipole[8] *= scale[0]*scale[2];
// multipole[9] *= scale[1]*scale[2];
inducedDipole[0] = _inducedDipole[i][0]*cartToFrac[0][0] + _inducedDipole[i][1]*cartToFrac[0][1] + _inducedDipole[i][2]*cartToFrac[0][2];
inducedDipole[1] = _inducedDipole[i][0]*cartToFrac[1][0] + _inducedDipole[i][1]*cartToFrac[1][1] + _inducedDipole[i][2]*cartToFrac[1][2];
......@@ -5930,9 +5884,6 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceInducedDipole
f[2] += multipole[k]*_phidp[20*i+deriv3[k]];
}
// f[0] *= scale[0];
// f[1] *= scale[1];
// f[2] *= scale[2];
f *= (0.5*_electric);
forces[iIndex] -= RealVec(f[0]*fracToCart[0][0] + f[1]*fracToCart[0][1] + f[2]*fracToCart[0][2],
f[0]*fracToCart[1][0] + f[1]*fracToCart[1][1] + f[2]*fracToCart[1][2],
......@@ -5943,9 +5894,6 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::computeReciprocalSpaceInducedDipole
void AmoebaReferencePmeMultipoleForce::recordFixedMultipoleField()
{
// RealVec scale;
// getPmeScale(scale);
// scale *= -1.0;
RealVec fracToCart[3];
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
......@@ -5968,9 +5916,6 @@ void AmoebaReferencePmeMultipoleForce::initializeInducedDipoles(vector<UpdateInd
void AmoebaReferencePmeMultipoleForce::recordInducedDipoleField(vector<RealVec>& field, vector<RealVec>& fieldPolar)
{
// RealVec scale;
// getPmeScale(scale);
// scale *= -1.0;
RealVec fracToCart[3];
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
......@@ -6152,7 +6097,6 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeSelfEnergy(const vector
RealOpenMM term = 2.0*_alphaEwald*_alphaEwald;
RealOpenMM energy = (cii + term*(dii/3.0 + 2.0*term*qii/5.0));
energy *= -(_electric*_alphaEwald/(_dielectric*SQRT_PI));
return energy;
}
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 82e118fb
/* Portions copyright (c) 2006-2014 Stanford University and Simbios.
/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -973,7 +973,7 @@ protected:
* @param particleK positions and parameters (charge, labFrame dipoles, quadrupoles, ...) for particle K
* @param scalingFactors scaling factors for interaction
* @param forces vector of particle forces to be updated
* @param torques vector of particle torques to be updated
* @param torque vector of particle torques to be updated
*/
RealOpenMM calculateElectrostaticPairIxn(const MultipoleParticleData& particleI, const MultipoleParticleData& particleK,
const std::vector<RealOpenMM>& scalingFactors, std::vector<OpenMM::RealVec>& forces, std::vector<RealVec>& torque) const;
......@@ -987,6 +987,7 @@ protected:
* @param particleW particle3 of lab frame for particleI
* @param axisType axis type (Bisector/Z-then-X, ...)
* @param torque torque on particle I
* @param forces vector of particle forces to be updated
*/
void mapTorqueToForceForParticle(const MultipoleParticleData& particleI,
const MultipoleParticleData& particleU,
......@@ -1004,8 +1005,6 @@ protected:
* @param axisType vector of axis types (Bisector/Z-then-X, ...) for particles
* @param torques output torques
* @param forces output forces
*
* @return energy
*/
void mapTorqueToForce(std::vector<MultipoleParticleData>& particleData,
const std::vector<int>& multipoleAtomXs,
......@@ -1388,7 +1387,7 @@ private:
/**
* Modify input vector of differences in particle positions for periodic boundary conditions.
*
* @param delta input vector of difference in particle positios; on output adjusted for
* @param delta input vector of difference in particle positions; on output adjusted for
* periodic boundary conditions
*/
void getPeriodicDelta(RealVec& deltaR) const;
......@@ -1466,12 +1465,9 @@ private:
* Compute induced dipole grid value.
*
* @param particleGridIndices particle grid indices
* @param scale integer grid dimension/box size for each dimension
* @param ix x-dimension offset value
* @param iy y-dimension offset value
* @param gridPoint grid point for which value is to be computed
* @param inputInducedDipole induced dipole value
* @param inputInducedDipolePolar induced dipole value
*/
RealOpenMM computeFixedMultipolesGridValue(const int2& particleGridIndices, int ix, int iy, const IntVec& gridPoint) const;
......@@ -1542,7 +1538,7 @@ private:
* @param jIndex particle J index
* @param preFactor1 first factor used in calculating field
* @param preFactor2 second factor used in calculating field
* @param deltaR delta in particle positions after adjusting for periodic boundary conditions
* @param delta delta in particle positions after adjusting for periodic boundary conditions
* @param inducedDipole vector of induced dipoles
* @param field vector of field at each particle due induced dipole of other particles
*/
......@@ -1574,14 +1570,14 @@ private:
* Compute induced dipole grid value.
*
* @param atomIndices indices of first and last atom contiputing to grid point value
* @param scale integer grid dimension/box size for each dimension
* @param cartToFrac transformation matrix from Cartesian to fractional coordinates
* @param ix x-dimension offset value
* @param iy y-dimension offset value
* @param gridPoint grid point for which value is to be computed
* @param inputInducedDipole induced dipole value
* @param inputInducedDipolePolar induced dipole polar value
*/
t_complex computeInducedDipoleGridValue(const int2& atomIndices, const RealVec* fracToCart, int ix, int iy, const IntVec& gridPoint,
t_complex computeInducedDipoleGridValue(const int2& atomIndices, const RealVec* cartToFrac, int ix, int iy, const IntVec& gridPoint,
const std::vector<RealVec>& inputInducedDipole,
const std::vector<RealVec>& inputInducedDipolePolar) const;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaMultipoleForce.cpp
View file @ 82e118fb
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -39,6 +39,7 @@
#include "openmm/System.h"
#include "openmm/AmoebaMultipoleForce.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/Vec3.h"
#include <iostream>
#include <vector>
#include <stdlib.h>
......@@ -50,6 +51,7 @@
using namespace OpenMM;
using namespace std;
extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
......@@ -2802,6 +2804,133 @@ static void testMultipoleGridPotential( FILE* log ) {
}
void testTriclinic() {
// Create a triclinic box containing eight particles.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(1.8643, 0, 0), Vec3(-0.16248445120445926, 1.8572057756524414, 0), Vec3(0.16248445120445906, -0.14832299817478897, 1.8512735025730875));
for (int i = 0; i < 24; i++)
system.addParticle(1.0);
AmoebaMultipoleForce* force = new AmoebaMultipoleForce();
system.addForce(force);
force->setNonbondedMethod(AmoebaMultipoleForce::PME);
force->setCutoffDistance(0.7);
force->setMutualInducedTargetEpsilon(1e-6);
vector<int> grid(3);
grid[0] = grid[1] = grid[2] = 24;
force->setPmeGridDimensions(grid);
force->setAEwald(5.4459051633620055);
double o_charge = -0.42616, h_charge = 0.21308;
vector<double> o_dipole(3), h_dipole(3), o_quadrupole(9, 0.0), h_quadrupole(9, 0.0);
o_dipole[0] = 0;
o_dipole[1] = 0;
o_dipole[2] = 0.0033078867454609203;
h_dipole[0] = -0.0053536858428776405;
h_dipole[1] = 0;
h_dipole[2] = -0.014378273997907321;
o_quadrupole[0] = 0.00016405937591036892;
o_quadrupole[4] = -0.00021618201787005826;
o_quadrupole[8] = 5.212264195968935e-05;
h_quadrupole[0] = 0.00011465301060008312;
h_quadrupole[4] = 8.354184196619263e-05;
h_quadrupole[8] = -0.00019819485256627578;
h_quadrupole[2] = h_quadrupole[6] = -6.523731100577879e-05;
for (int i = 0; i < 8; i++) {
int atom1 = 3*i, atom2 = 3*i+1, atom3 = 3*i+2;
force->addMultipole(o_charge, o_dipole, o_quadrupole, 1, atom2, atom3, -1, 0.39, pow(0.001*0.92, 1.0/6.0), 0.001*0.92);
force->addMultipole(h_charge, h_dipole, h_quadrupole, 0, atom1, atom3, -1, 0.39, pow(0.001*0.539, 1.0/6.0), 0.001*0.539);
force->addMultipole(h_charge, h_dipole, h_quadrupole, 0, atom1, atom2, -1, 0.39, pow(0.001*0.539, 1.0/6.0), 0.001*0.539);
vector<int> coval1_12(2);
coval1_12[0] = atom2;
coval1_12[1] = atom3;
force->setCovalentMap(atom1, AmoebaMultipoleForce::Covalent12, coval1_12);
vector<int> coval2_12(1);
coval2_12[0] = atom1;
force->setCovalentMap(atom2, AmoebaMultipoleForce::Covalent12, coval2_12);
force->setCovalentMap(atom3, AmoebaMultipoleForce::Covalent12, coval2_12);
vector<int> coval2_13(1);
coval2_13[0] = atom3;
force->setCovalentMap(atom2, AmoebaMultipoleForce::Covalent13, coval2_13);
vector<int> coval3_13(1);
coval3_13[0] = atom2;
force->setCovalentMap(atom3, AmoebaMultipoleForce::Covalent13, coval3_13);
vector<int> polar(3);
polar[0] = atom1;
polar[1] = atom2;
polar[2] = atom3;
force->setCovalentMap(atom1, AmoebaMultipoleForce::PolarizationCovalent11, polar);
force->setCovalentMap(atom2, AmoebaMultipoleForce::PolarizationCovalent11, polar);
force->setCovalentMap(atom3, AmoebaMultipoleForce::PolarizationCovalent11, polar);
}
vector<Vec3> positions(24);
positions[0] = Vec3(0.867966, 0.708769, -0.0696862);
positions[1] = Vec3(0.780946, 0.675579, -0.0382259);
positions[2] = Vec3(0.872223, 0.681424, -0.161756);
positions[3] = Vec3(-0.0117313, 0.824445, 0.683762);
positions[4] = Vec3(0.0216892, 0.789544, 0.605003);
positions[5] = Vec3(0.0444268, 0.782601, 0.75302);
positions[6] = Vec3(0.837906, -0.0092611, 0.681463);
positions[7] = Vec3(0.934042, 0.0098069, 0.673406);
positions[8] = Vec3(0.793962, 0.0573676, 0.626984);
positions[9] = Vec3(0.658995, 0.184432, -0.692317);
positions[10] = Vec3(0.588543, 0.240231, -0.671793);
positions[11] = Vec3(0.618153, 0.106275, -0.727368);
positions[12] = Vec3(0.71466, 0.575358, 0.233152);
positions[13] = Vec3(0.636812, 0.612604, 0.286268);
positions[14] = Vec3(0.702502, 0.629465, 0.15182);
positions[15] = Vec3(-0.242658, -0.850419, -0.250483);
positions[16] = Vec3(-0.169206, -0.836825, -0.305829);
positions[17] = Vec3(-0.279321, -0.760247, -0.24031);
positions[18] = Vec3(-0.803838, -0.360559, 0.230369);
positions[19] = Vec3(-0.811375, -0.424813, 0.301849);
positions[20] = Vec3(-0.761939, -0.2863, 0.270962);
positions[21] = Vec3(-0.148063, 0.824409, -0.827221);
positions[22] = Vec3(-0.20902, 0.868798, -0.7677);
positions[23] = Vec3(-0.0700878, 0.882333, -0.832221);
// Compute the forces and energy.
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("Reference"));
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
// Compare them to values computed by Gromacs.
double expectedEnergy = 6.8278696;
vector<Vec3> expectedForce(24);
expectedForce[0] = Vec3(-104.755, 14.0833, 34.359);
expectedForce[1] = Vec3(97.324, -1.41419, -142.976);
expectedForce[2] = Vec3(29.3968, -6.31784, -3.8702);
expectedForce[3] = Vec3(39.1915, 66.852, -28.5767);
expectedForce[4] = Vec3(-8.17554, -6.71532, 7.63162);
expectedForce[5] = Vec3(-87.3745, -91.8639, 35.4761);
expectedForce[6] = Vec3(-19.7568, -40.8693, 5.60238);
expectedForce[7] = Vec3(0.840984, 26.878, 10.7822);
expectedForce[8] = Vec3(14.3469, 12.0583, -12.075);
expectedForce[9] = Vec3(13.757, 16.9954, 46.9403);
expectedForce[10] = Vec3(-5.04172, -14.008, -15.3804);
expectedForce[11] = Vec3(-2.1715, 3.7405, -37.2209);
expectedForce[12] = Vec3(-70.2284, -9.10438, -40.1287);
expectedForce[13] = Vec3(4.46014, 3.89949, 4.64842);
expectedForce[14] = Vec3(43.045, -4.79905, 151.879);
expectedForce[15] = Vec3(20.2129, -0.895376, -27.2086);
expectedForce[16] = Vec3(-5.10448, 3.57732, 17.0498);
expectedForce[17] = Vec3(-13.7695, -1.03345, 12.3093);
expectedForce[18] = Vec3(2.94972, 0.338904, -10.9914);
expectedForce[19] = Vec3(0.69036, 1.22591, 4.50198);
expectedForce[20] = Vec3(-4.61495, -2.76981, 3.57732);
expectedForce[21] = Vec3(73.1489, 16.167, -99.5834);
expectedForce[22] = Vec3(-31.8235, 6.11282, -21.125);
expectedForce[23] = Vec3(13.167, 7.42242, 103.102);
for (int i = 0; i < 24; i++) {
ASSERT_EQUAL_VEC(expectedForce[i], state.getForces()[i], 1e-2);
}
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-2);
}
int main( int numberOfArguments, char* argv[] ) {
try {
......@@ -2850,6 +2979,10 @@ int main( int numberOfArguments, char* argv[] ) {
testPMEMutualPolarizationLargeWater( log );
// triclinic box of water
testTriclinic();
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
......
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