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NonbondedForce.h
1 #ifndef OPENMM_NONBONDEDFORCE_H_
2 #define OPENMM_NONBONDEDFORCE_H_
3
4 /* -------------------------------------------------------------------------- *
5 * OpenMM *
6 * -------------------------------------------------------------------------- *
7 * This is part of the OpenMM molecular simulation toolkit originating from *
8 * Simbios, the NIH National Center for Physics-Based Simulation of *
9 * Biological Structures at Stanford, funded under the NIH Roadmap for *
10 * Medical Research, grant U54 GM072970. See https://simtk.org. *
11 * *
12 * Portions copyright (c) 2008-2014 Stanford University and the Authors. *
13 * Authors: Peter Eastman *
14 * Contributors: *
15 * *
16 * Permission is hereby granted, free of charge, to any person obtaining a *
17 * copy of this software and associated documentation files (the "Software"), *
18 * to deal in the Software without restriction, including without limitation *
19 * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
20 * and/or sell copies of the Software, and to permit persons to whom the *
21 * Software is furnished to do so, subject to the following conditions: *
22 * *
23 * The above copyright notice and this permission notice shall be included in *
24 * all copies or substantial portions of the Software. *
25 * *
26 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
27 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
28 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
29 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
30 * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
31 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
32 * USE OR OTHER DEALINGS IN THE SOFTWARE. *
33 * -------------------------------------------------------------------------- */
34
35 #include "Context.h"
36 #include "Force.h"
37 #include <map>
38 #include <set>
39 #include <utility>
40 #include <vector>
41 #include "internal/windowsExport.h"
42
43 namespace OpenMM {
44
81 class OPENMM_EXPORT NonbondedForce : public Force {
82 public:
86 enum NonbondedMethod {
91 NoCutoff = 0,
96 CutoffNonPeriodic = 1,
102 CutoffPeriodic = 2,
107 Ewald = 3,
112 PME = 4
113 };
117 NonbondedForce();
121 int getNumParticles() const {
122 return particles.size();
123 }
127 int getNumExceptions() const {
128 return exceptions.size();
129 }
133 NonbondedMethod getNonbondedMethod() const;
137 void setNonbondedMethod(NonbondedMethod method);
144 double getCutoffDistance() const;
151 void setCutoffDistance(double distance);
156 bool getUseSwitchingFunction() const;
161 void setUseSwitchingFunction(bool use);
166 double getSwitchingDistance() const;
171 void setSwitchingDistance(double distance);
175 double getReactionFieldDielectric() const;
179 void setReactionFieldDielectric(double dielectric);
189 double getEwaldErrorTolerance() const;
199 void setEwaldErrorTolerance(double tol);
209 void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
219 void setPMEParameters(double alpha, int nx, int ny, int nz);
232 int addParticle(double charge, double sigma, double epsilon);
241 void getParticleParameters(int index, double& charge, double& sigma, double& epsilon) const;
252 void setParticleParameters(int index, double charge, double sigma, double epsilon);
269 int addException(int particle1, int particle2, double chargeProd, double sigma, double epsilon, bool replace = false);
280 void getExceptionParameters(int index, int& particle1, int& particle2, double& chargeProd, double& sigma, double& epsilon) const;
293 void setExceptionParameters(int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon);
306 void createExceptionsFromBonds(const std::vector<std::pair<int, int> >& bonds, double coulomb14Scale, double lj14Scale);
313 bool getUseDispersionCorrection() const {
314 return useDispersionCorrection;
315 }
322 void setUseDispersionCorrection(bool useCorrection) {
323 useDispersionCorrection = useCorrection;
324 }
331 int getReciprocalSpaceForceGroup() const;
341 void setReciprocalSpaceForceGroup(int group);
354 void updateParametersInContext(Context& context);
361 bool usesPeriodicBoundaryConditions() const {
362 return nonbondedMethod == NonbondedForce::CutoffPeriodic ||
363 nonbondedMethod == NonbondedForce::Ewald ||
364 nonbondedMethod == NonbondedForce::PME;
365 }
366 protected:
367 ForceImpl* createImpl() const;
368 private:
369 class ParticleInfo;
370 class ExceptionInfo;
371 NonbondedMethod nonbondedMethod;
372 double cutoffDistance, switchingDistance, rfDielectric, ewaldErrorTol, alpha;
373 bool useSwitchingFunction, useDispersionCorrection;
374 int recipForceGroup, nx, ny, nz;
375 void addExclusionsToSet(const std::vector<std::set<int> >& bonded12, std::set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const;
376 std::vector<ParticleInfo> particles;
377 std::vector<ExceptionInfo> exceptions;
378 std::map<std::pair<int, int>, int> exceptionMap;
379 };
380
385 class NonbondedForce::ParticleInfo {
386 public:
387 double charge, sigma, epsilon;
388 ParticleInfo() {
389 charge = sigma = epsilon = 0.0;
390 }
391 ParticleInfo(double charge, double sigma, double epsilon) :
392 charge(charge), sigma(sigma), epsilon(epsilon) {
393 }
394 };
395
400 class NonbondedForce::ExceptionInfo {
401 public:
402 int particle1, particle2;
403 double chargeProd, sigma, epsilon;
404 ExceptionInfo() {
405 particle1 = particle2 = -1;
406 chargeProd = sigma = epsilon = 0.0;
407 }
408 ExceptionInfo(int particle1, int particle2, double chargeProd, double sigma, double epsilon) :
409 particle1(particle1), particle2(particle2), chargeProd(chargeProd), sigma(sigma), epsilon(epsilon) {
410 }
411 };
412
413 } // namespace OpenMM
414
415 #endif /*OPENMM_NONBONDEDFORCE_H_*/
OpenMM::Context
A Context stores the complete state of a simulation.
Definition: Context.h:67
OpenMM::NonbondedForce::CutoffPeriodic
Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic...
Definition: NonbondedForce.h:102
OpenMM::NonbondedForce::Ewald
Periodic boundary conditions are used, and Ewald summation is used to compute the interaction of each...
Definition: NonbondedForce.h:107
OpenMM::NonbondedForce::PME
Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the...
Definition: NonbondedForce.h:112
OpenMM::NonbondedForce::getUseDispersionCorrection
bool getUseDispersionCorrection() const
Get whether to add a contribution to the energy that approximately represents the effect of Lennard-J...
Definition: NonbondedForce.h:313
OpenMM::Force
Force objects apply forces to the particles in a System, or alter their behavior in other ways...
Definition: Force.h:65
OpenMM::NonbondedForce::setUseDispersionCorrection
void setUseDispersionCorrection(bool useCorrection)
Set whether to add a contribution to the energy that approximately represents the effect of Lennard-J...
Definition: NonbondedForce.h:322
OpenMM::NonbondedForce::getNumExceptions
int getNumExceptions() const
Get the number of special interactions that should be calculated differently from other interactions...
Definition: NonbondedForce.h:127
OpenMM::NonbondedForce::getNumParticles
int getNumParticles() const
Get the number of particles for which force field parameters have been defined.
Definition: NonbondedForce.h:121
OpenMM::NonbondedForce::usesPeriodicBoundaryConditions
bool usesPeriodicBoundaryConditions() const
Returns whether or not this force makes use of periodic boundary conditions.
Definition: NonbondedForce.h:361
OpenMM::NonbondedForce::NonbondedMethod
NonbondedMethod
This is an enumeration of the different methods that may be used for handling long range nonbonded fo...
Definition: NonbondedForce.h:86
OpenMM::NonbondedForce
This class implements nonbonded interactions between particles, including a Coulomb force to represen...
Definition: NonbondedForce.h:81
OpenMM
Definition: AndersenThermostat.h:40