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Commit 9dd055eb authored by Mark Friedrichs's avatar Mark Friedrichs
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Add unit test for NonbondedSoftcoreForce 

Cleanup code associated w/ NonbondedSoftcoreForce
parent ab60bff4
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plugins/freeEnergy/platforms/reference/src/ReferenceFreeEnergyKernels.cpp
View file @ 9dd055eb
...@@ -155,7 +155,6 @@ void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const Syste ...@@ -155,7 +155,6 @@ void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const Syste
nonbondedMethod = CalcNonbondedSoftcoreForceKernel::NonbondedSoftcoreMethod(force.getNonbondedMethod()); nonbondedMethod = CalcNonbondedSoftcoreForceKernel::NonbondedSoftcoreMethod(force.getNonbondedMethod());
nonbondedCutoff = (RealOpenMM) force.getCutoffDistance(); nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
//softCoreLJLambda = (RealOpenMM) force.getSoftCoreLJLambda();
Vec3 boxVectors[3]; Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]); system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
...@@ -168,42 +167,6 @@ void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const Syste ...@@ -168,42 +167,6 @@ void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const Syste
else else
neighborList = new NeighborList(); neighborList = new NeighborList();
#if 0
if (nonbondedMethod == Ewald || nonbondedMethod == PME) {
RealOpenMM ewaldErrorTol = (RealOpenMM) force.getEwaldErrorTolerance();
ewaldAlpha = (RealOpenMM) (std::sqrt(-std::log(ewaldErrorTol))/nonbondedCutoff);
RealOpenMM mx = periodicBoxSize[0]/nonbondedCutoff;
RealOpenMM my = periodicBoxSize[1]/nonbondedCutoff;
RealOpenMM mz = periodicBoxSize[2]/nonbondedCutoff;
RealOpenMM pi = (RealOpenMM) 3.1415926535897932385;
kmax[0] = (int)std::ceil(-(mx/pi)*std::log(ewaldErrorTol));
kmax[1] = (int)std::ceil(-(my/pi)*std::log(ewaldErrorTol));
kmax[2] = (int)std::ceil(-(mz/pi)*std::log(ewaldErrorTol));
if (kmax[0]%2 == 0)
kmax[0]++;
if (kmax[1]%2 == 0)
kmax[1]++;
if (kmax[2]%2 == 0)
kmax[2]++;
}
if (nonbondedMethod == Ewald || nonbondedMethod == PME) {
RealOpenMM ewaldErrorTol = (RealOpenMM) force.getEwaldErrorTolerance();
ewaldAlpha = (RealOpenMM) (std::sqrt(-std::log(ewaldErrorTol))/nonbondedCutoff);
RealOpenMM mx = periodicBoxSize[0]/nonbondedCutoff;
RealOpenMM my = periodicBoxSize[1]/nonbondedCutoff;
RealOpenMM mz = periodicBoxSize[2]/nonbondedCutoff;
RealOpenMM pi = (RealOpenMM) 3.1415926535897932385;
kmax[0] = (int)std::ceil(-(mx/pi)*std::log(ewaldErrorTol));
kmax[1] = (int)std::ceil(-(my/pi)*std::log(ewaldErrorTol));
kmax[2] = (int)std::ceil(-(mz/pi)*std::log(ewaldErrorTol));
if (kmax[0]%2 == 0)
kmax[0]++;
if (kmax[1]%2 == 0)
kmax[1]++;
if (kmax[2]%2 == 0)
kmax[2]++;
}
#endif
rfDielectric = (RealOpenMM)force.getReactionFieldDielectric(); rfDielectric = (RealOpenMM)force.getReactionFieldDielectric();
} }
...@@ -214,21 +177,18 @@ double ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::execute(ContextImpl& ...@@ -214,21 +177,18 @@ double ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::execute(ContextImpl&
RealOpenMM energy = 0; RealOpenMM energy = 0;
ReferenceFreeEnergyLJCoulombSoftcoreIxn clj; ReferenceFreeEnergyLJCoulombSoftcoreIxn clj;
// clj.setSoftCoreLJLambda( softCoreLJLambda );
bool periodic = (nonbondedMethod == CutoffPeriodic); bool periodic = (nonbondedMethod == CutoffPeriodic);
bool ewald = (nonbondedMethod == Ewald);
bool pme = (nonbondedMethod == PME);
if (nonbondedMethod != NoCutoff) { if (nonbondedMethod != NoCutoff) {
computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, periodicBoxSize, periodic || ewald || pme, nonbondedCutoff, 0.0); computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, periodicBoxSize, periodic, nonbondedCutoff, 0.0);
clj.setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric); clj.setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
} }
if (periodic || ewald || pme) if (periodic)
clj.setPeriodic(periodicBoxSize); clj.setPeriodic(periodicBoxSize);
if (ewald)
clj.setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]);
if (pme)
clj.setUsePME(ewaldAlpha);
clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, &energy); clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, &energy);
ReferenceBondForce refBondForce; ReferenceBondForce refBondForce;
ReferenceFreeEnergyLJCoulomb14Softcore nonbonded14; ReferenceFreeEnergyLJCoulomb14Softcore nonbonded14;
if (nonbondedMethod == CutoffNonPeriodic || nonbondedMethod == CutoffPeriodic) if (nonbondedMethod == CutoffNonPeriodic || nonbondedMethod == CutoffPeriodic)
......
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.cpp
View file @ 9dd055eb
...@@ -100,13 +100,11 @@ ReferenceFreeEnergyLJCoulomb14Softcore::~ReferenceFreeEnergyLJCoulomb14Softcore( ...@@ -100,13 +100,11 @@ ReferenceFreeEnergyLJCoulomb14Softcore::~ReferenceFreeEnergyLJCoulomb14Softcore(
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceFreeEnergyLJCoulomb14Softcore::getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1, void ReferenceFreeEnergyLJCoulomb14Softcore::getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1,
RealOpenMM q2, RealOpenMM epsfac, RealOpenMM q2, RealOpenMM epsfac,
RealOpenMM* parameters ) const { RealOpenMM* parameters ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceFreeEnergyLJCoulomb14Softcore::getDerivedParameters";
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
static const RealOpenMM six = 6.0; static const RealOpenMM six = 6.0;
...@@ -218,7 +216,7 @@ void ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices, ...@@ -218,7 +216,7 @@ void ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices,
*totalEnergy += energy; *totalEnergy += energy;
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate LJ pair ixn between two atoms Calculate LJ pair ixn between two atoms
...@@ -231,7 +229,7 @@ void ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices, ...@@ -231,7 +229,7 @@ void ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices,
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceFreeEnergyLJCoulomb14Softcore::calculateOneLJ14Ixn( RealOpenMM inverseR, RealOpenMM sig, RealOpenMM eps, void ReferenceFreeEnergyLJCoulomb14Softcore::calculateOneLJ14Ixn( RealOpenMM inverseR, RealOpenMM sig, RealOpenMM eps,
RealOpenMM* dEdR, RealOpenMM* energy ) const { RealOpenMM* dEdR, RealOpenMM* energy ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.h
View file @ 9dd055eb
...@@ -42,7 +42,6 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn { ...@@ -42,7 +42,6 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
RealOpenMM periodicBoxSize[3]; RealOpenMM periodicBoxSize[3];
RealOpenMM cutoffDistance; RealOpenMM cutoffDistance;
RealOpenMM krf, crf; RealOpenMM krf, crf;
RealOpenMM softCoreLJLambda;
int numRx, numRy, numRz; int numRx, numRy, numRz;
RealOpenMM alphaEwald; RealOpenMM alphaEwald;
...@@ -62,15 +61,13 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn { ...@@ -62,15 +61,13 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
@param atomCoordinates atom coordinates @param atomCoordinates atom coordinates
@param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex] @param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex]
@param forces force array (forces added) @param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy @param totalEnergy total energy
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const; RealOpenMM* totalEnergy ) const;
public: public:
...@@ -116,41 +113,7 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn { ...@@ -116,41 +113,7 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Set the force to use Ewald summation. Calculate parameters for ixn
@param alpha the Ewald separation parameter
@param kmaxx the largest wave vector in the x direction
@param kmaxy the largest wave vector in the y direction
@param kmaxz the largest wave vector in the z direction
--------------------------------------------------------------------------------------- */
void setUseEwald(RealOpenMM alpha, int kmaxx, int kmaxy, int kmaxz);
/**---------------------------------------------------------------------------------------
Set the force to use Particle-Mesh Ewald (PME) summation.
@param alpha the Ewald separation parameter
--------------------------------------------------------------------------------------- */
void setUsePME(RealOpenMM alpha);
/**---------------------------------------------------------------------------------------
Set the soft core LJ lambda
@param lambda the soft core LJ lambda
--------------------------------------------------------------------------------------- */
void setSoftCoreLJLambda(RealOpenMM lambda);
/**---------------------------------------------------------------------------------------
Calculate parameters for LJ 1-4 ixn
@param c6 c6 @param c6 c6
@param c12 c12 @param c12 c12
...@@ -164,8 +127,7 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn { ...@@ -164,8 +127,7 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1, void getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1,
RealOpenMM epsfacSqrt, RealOpenMM epsfacSqrt, RealOpenMM* parameters ) const;
RealOpenMM* parameters ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -180,62 +142,16 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn { ...@@ -180,62 +142,16 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
interacting w/ atom atomIndex interacting w/ atom atomIndex
@param fixedParameters non atom parameters (not currently used) @param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added) @param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy @param totalEnergy total energy
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculatePairIxn( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, void calculatePairIxn( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, int** exclusions, RealOpenMM** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const; RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
private: private:
/**---------------------------------------------------------------------------------------
Calculate Ewald ixn
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateEwaldIxn( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
/**---------------------------------------------------------------------------------------
Calculate PME ixn
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculatePMEIxn( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -250,7 +166,7 @@ private: ...@@ -250,7 +166,7 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOneLJIxn( RealOpenMM inverseR, RealOpenMM sig, RealOpenMM eps, void calculateOneLJIxn( RealOpenMM inverseR, RealOpenMM sig, RealOpenMM eps,
RealOpenMM* dEdR, RealOpenMM* energy ) const; RealOpenMM* dEdR, RealOpenMM* energy ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -266,7 +182,7 @@ private: ...@@ -266,7 +182,7 @@ private:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOneSoftCoreLJIxn( RealOpenMM r, RealOpenMM sig, RealOpenMM eps, void calculateOneSoftCoreLJIxn( RealOpenMM r, RealOpenMM sig, RealOpenMM eps,
RealOpenMM lambda, RealOpenMM* dEdR, RealOpenMM* energy ) const; RealOpenMM lambda, RealOpenMM* dEdR, RealOpenMM* energy ) const;
}; };
......
plugins/freeEnergy/platforms/reference/tests/TestReferenceLJSoftcoreForce.cpp 0 → 100644
View file @ 9dd055eb
/* -------------------------------------------------------------------------- *
* 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) 2008-2009 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. *
* -------------------------------------------------------------------------- */
/**
* This tests all the different force terms in the reference implementation of CustomGBForce.
*/
#include "../../../tests/AssertionUtilities.h"
#include "sfmt/SFMT.h"
#include "openmm/Context.h"
#include "openmm/CustomBondForce.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/NonbondedSoftcoreForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include <iostream>
#include <vector>
#include <algorithm>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
static const int NoCutoff = 0;
static const int CutoffNonPeriodic = 1;
static const int CutoffPeriodic = 2;
void testNonbondedSoftcore( double lambda1, double lambda2, int nonbondedMethod ){
const int numMolecules = 70;
const int numParticles = numMolecules*2;
const double boxSize = 10.0;
const double reactionFieldDielectric = 80.0;
const double cutoffDistance = 0.4*boxSize;
// Create two systems: one with a NonbondedSoftcoreForce, and one using a CustomNonbondedForce to implement the same interaction.
System standardSystem;
System customSystem;
for (int i = 0; i < numParticles; i++) {
standardSystem.addParticle(1.0);
customSystem.addParticle(1.0);
}
standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
customSystem.setDefaultPeriodicBoxVectors( Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedSoftcoreForce* nonbondedSoftcoreForce = new NonbondedSoftcoreForce();
CustomNonbondedForce* customNonbonded;
CustomBondForce* customBond;
if( nonbondedMethod == NoCutoff ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::NoCutoff );
customNonbonded = new CustomNonbondedForce("lambda*4*eps*(dem^2-dem)+138.935456*q/r;"
"q=q1*q2;"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda);"
"sigma=0.5*(sigma1+sigma2);"
"eps=sqrt(eps1*eps2);"
"lambda=min(lambda1,lambda2)");
customNonbonded->setNonbondedMethod( CustomNonbondedForce::NoCutoff );
customBond = new CustomBondForce("lambda*4*eps*(dem^2-dem)+138.935456*q/r;"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda)");
} else {
nonbondedSoftcoreForce->setCutoffDistance( cutoffDistance );
nonbondedSoftcoreForce->setReactionFieldDielectric( reactionFieldDielectric );
if( nonbondedMethod == CutoffNonPeriodic ){
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::CutoffNonPeriodic );
} else {
nonbondedSoftcoreForce->setNonbondedMethod( NonbondedSoftcoreForce::CutoffPeriodic );
}
customNonbonded = new CustomNonbondedForce("lambda*4*eps*(dem^2-dem)+138.935456*q*(1.0/r+(krf*r*r)-crf);"
"q=q1*q2;"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda);"
"sigma=0.5*(sigma1+sigma2);"
"eps=sqrt(eps1*eps2);"
"lambda=min(lambda1,lambda2)");
customBond = new CustomBondForce("withinCutoff*(lambda*4*eps*(dem^2-dem)+138.935456*q*(1.0/r+(krf*r*r)-crf));"
"withinCutoff=step(cutoff-r);"
"dem=1.0/(soft+rsig);"
"rsig=(r/sigma)^6;"
"soft=0.5*(1.0-lambda)");
customNonbonded->setCutoffDistance( cutoffDistance );
if( nonbondedMethod == CutoffNonPeriodic ){
customNonbonded->setNonbondedMethod( CustomNonbondedForce::CutoffNonPeriodic );
} else {
customNonbonded->setNonbondedMethod( CustomNonbondedForce::CutoffPeriodic );
}
double eps2 = (reactionFieldDielectric - 1.0)/(2.0*reactionFieldDielectric+1.0);
double kValue = eps2/(cutoffDistance*cutoffDistance*cutoffDistance);
customNonbonded->addGlobalParameter("krf", kValue );
customBond->addGlobalParameter("krf", kValue );
double cValue = (1.0/cutoffDistance)*(3.0*reactionFieldDielectric)/(2.0*reactionFieldDielectric + 1.0);
customNonbonded->addGlobalParameter("crf", cValue );
customBond->addGlobalParameter("crf", cValue );
customBond->addGlobalParameter("cutoff", cutoffDistance );
}
customNonbonded->addPerParticleParameter("q");
customNonbonded->addPerParticleParameter("sigma");
customNonbonded->addPerParticleParameter("eps");
customNonbonded->addPerParticleParameter("lambda");
customBond->addPerBondParameter("q");
customBond->addPerBondParameter("sigma");
customBond->addPerBondParameter("eps");
customBond->addPerBondParameter("lambda");
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(4);
// periodic boundary conditions not possible w/ CustomBond?
int includeExceptions = nonbondedMethod == CutoffPeriodic ? 0 : 1;
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
double charge = 1.0;
nonbondedSoftcoreForce->addParticle( charge, 0.2, 0.5, lambda1);
nonbondedSoftcoreForce->addParticle(-charge, 0.1, 0.5, lambda1);
params[0] = charge;
params[1] = 0.2;
params[2] = 0.5;
params[3] = lambda1;
customNonbonded->addParticle(params);
params[0] = -charge;
params[1] = 0.1;
customNonbonded->addParticle(params);
if( includeExceptions && i && ((i%4) == 0) ){
vector<double> bondParams(4);
nonbondedSoftcoreForce->addException(i-4, i, charge*charge, 0.2, 0.5, false, lambda1);
customNonbonded->addExclusion( i-4,i);
bondParams[0] = charge*charge;
bondParams[1] = 0.2;
bondParams[2] = 0.5;
bondParams[3] = lambda1;
customBond->addBond(i-4,i, bondParams );
}
} else {
double charge = 1.2;
nonbondedSoftcoreForce->addParticle( charge, 0.2, 0.8, lambda2);
nonbondedSoftcoreForce->addParticle(-charge, 0.1, 0.8, lambda2);
params[0] = charge;
params[1] = 0.2;
params[2] = 0.8;
params[3] = lambda2;
customNonbonded->addParticle(params);
params[0] = -charge;
params[1] = 0.1;
customNonbonded->addParticle(params);
if( includeExceptions && i && ((i%4) == 0) ){
vector<double> bondParams(4);
nonbondedSoftcoreForce->addException(i-4, i, charge*charge, 0.2, 0.5, false, lambda1);
customNonbonded->addExclusion( i-4,i);
bondParams[0] = charge*charge;
bondParams[1] = 0.2;
bondParams[2] = 0.5;
bondParams[3] = lambda2;
customBond->addBond(i-4,i, bondParams );
}
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
}
standardSystem.addForce(nonbondedSoftcoreForce);
customSystem.addForce(customNonbonded);
customSystem.addForce(customBond);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context context1(standardSystem, integrator1, Platform::getPlatformByName( "Reference"));
context1.setPositions(positions);
context1.setVelocities(velocities);
State state1 = context1.getState(State::Forces | State::Energy);
Context context2(customSystem, integrator2, Platform::getPlatformByName( "Reference"));
context2.setPositions(positions);
context2.setVelocities(velocities);
State state2 = context2.getState(State::Forces | State::Energy);
// (void) fprintf( stderr, "%10.1f %10.1f %15.7e %15.7e\n", lambda1, lambda2, state1.getPotentialEnergy(), state2.getPotentialEnergy());
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
}
int main() {
try {
// test various combinations of lambdas and boundary conditions/cutoffs
testNonbondedSoftcore( 1.0, 1.0 , NoCutoff );
testNonbondedSoftcore( 1.0, 0.0 , NoCutoff );
testNonbondedSoftcore( 1.0, 0.5 , NoCutoff );
testNonbondedSoftcore( 0.0, 0.0 , NoCutoff );
testNonbondedSoftcore( 1.0, 1.0 , CutoffNonPeriodic );
testNonbondedSoftcore( 1.0, 0.0 , CutoffNonPeriodic );
testNonbondedSoftcore( 1.0, 0.5 , CutoffNonPeriodic );
testNonbondedSoftcore( 0.0, 0.0 , CutoffNonPeriodic );
testNonbondedSoftcore( 1.0, 1.0 , CutoffPeriodic );
testNonbondedSoftcore( 1.0, 0.0 , CutoffPeriodic );
testNonbondedSoftcore( 1.0, 0.5 , CutoffPeriodic );
testNonbondedSoftcore( 0.0, 0.0 , CutoffPeriodic );
} catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
plugins/freeEnergy/platforms/reference/tests/TestReferenceOBCSoftcoreForce.cpp
View file @ 9dd055eb
...@@ -37,13 +37,12 @@ ...@@ -37,13 +37,12 @@
#include "sfmt/SFMT.h" #include "sfmt/SFMT.h"
#include "openmm/Context.h" #include "openmm/Context.h"
#include "ReferencePlatform.h"
#include "openmm/CustomGBForce.h" #include "openmm/CustomGBForce.h"
#include "openmm/GBSAOBCSoftcoreForce.h" #include "openmm/GBSAOBCSoftcoreForce.h"
#include "openmm/System.h" #include "openmm/System.h"
#include "openmm/VerletIntegrator.h" #include "openmm/VerletIntegrator.h"
#include <iostream> #include <iostream>
#include <vector> #include <vector>
#include <algorithm> #include <algorithm>
...@@ -53,7 +52,7 @@ using namespace std; ...@@ -53,7 +52,7 @@ using namespace std;
const double TOL = 1e-5; const double TOL = 1e-5;
void testSoftcoreOBC( double lambda1, double lambda2 ){ void testOBCSoftcore( double lambda1, double lambda2 ){
const int numMolecules = 70; const int numMolecules = 70;
const int numParticles = numMolecules*2; const int numParticles = numMolecules*2;
...@@ -168,9 +167,9 @@ int main() { ...@@ -168,9 +167,9 @@ int main() {
// test various combinations of lambdas // test various combinations of lambdas
testSoftcoreOBC( 1.0, 1.0 ); testOBCSoftcore( 1.0, 1.0 );
testSoftcoreOBC( 1.0, 0.0 ); testOBCSoftcore( 1.0, 0.0 );
testSoftcoreOBC( 1.0, 0.5 ); testOBCSoftcore( 1.0, 0.5 );
} catch(const exception& e) { } catch(const exception& e) {
cout << "exception: " << e.what() << endl; cout << "exception: " << e.what() << endl;
......
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