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AmoebaVdwForce.h
1 #ifndef OPENMM_AMOEBA_VDW_FORCE_H_
2 #define OPENMM_AMOEBA_VDW_FORCE_H_
3
4 /* -------------------------------------------------------------------------- *
5 * OpenMMAmoeba *
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) 2008-2012 Stanford University and the Authors. *
13 * Authors: Mark Friedrichs, 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 "openmm/Force.h"
36 #include "internal/windowsExportAmoeba.h"
37 #include <vector>
38
39 namespace OpenMM {
40
55 class OPENMM_EXPORT_AMOEBA AmoebaVdwForce : public Force {
56 public:
60 enum NonbondedMethod {
65 NoCutoff = 0,
70 CutoffPeriodic = 1,
71 };
72
76 AmoebaVdwForce();
77
81 int getNumParticles() const {
82 return parameters.size();
83 }
84
95 void setParticleParameters(int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor);
96
107 void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon, double& reductionFactor) const;
108
109
120 int addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor);
121
127 void setSigmaCombiningRule(const std::string& sigmaCombiningRule);
128
134 const std::string& getSigmaCombiningRule(void) const;
135
141 void setEpsilonCombiningRule(const std::string& epsilonCombiningRule);
142
148 const std::string& getEpsilonCombiningRule(void) const;
149
156 bool getUseDispersionCorrection() const {
157 return useDispersionCorrection;
158 }
159
166 void setUseDispersionCorrection(bool useCorrection) {
167 useDispersionCorrection = useCorrection;
168 }
169
176 void setParticleExclusions(int particleIndex, const std::vector<int>& exclusions);
177
184 void getParticleExclusions(int particleIndex, std::vector<int>& exclusions) const;
185
189 void setCutoff(double cutoff);
190
194 double getCutoff() const;
195
199 NonbondedMethod getNonbondedMethod() const;
200
204 void setNonbondedMethod(NonbondedMethod method);
214 void updateParametersInContext(Context& context);
221 bool usesPeriodicBoundaryConditions() const {
222 return nonbondedMethod == AmoebaVdwForce::CutoffPeriodic;
223 }
224 protected:
225 ForceImpl* createImpl() const;
226 private:
227
228 class VdwInfo;
229 NonbondedMethod nonbondedMethod;
230 double cutoff;
231 bool useDispersionCorrection;
232
233 std::string sigmaCombiningRule;
234 std::string epsilonCombiningRule;
235
236 std::vector< std::vector<int> > exclusions;
237 std::vector<VdwInfo> parameters;
238 std::vector< std::vector< std::vector<double> > > sigEpsTable;
239 };
240
245 class AmoebaVdwForce::VdwInfo {
246 public:
247 int parentIndex;
248 double reductionFactor, sigma, epsilon, cutoff;
249 VdwInfo() {
250 parentIndex = -1;
251 reductionFactor = 0.0;
252 sigma = 1.0;
253 epsilon = 0.0;
254 }
255 VdwInfo(int parentIndex, double sigma, double epsilon, double reductionFactor) :
256 parentIndex(parentIndex), sigma(sigma), epsilon(epsilon), reductionFactor(reductionFactor) {
257 }
258 };
259
260 } // namespace OpenMM
261
262 #endif /*OPENMM_AMOEBA_VDW_FORCE_H_*/
263
OpenMM::AmoebaVdwForce::getUseDispersionCorrection
bool getUseDispersionCorrection() const
Get whether to add a contribution to the energy that approximately represents the effect of VdW inter...
Definition: AmoebaVdwForce.h:156
OpenMM::AmoebaVdwForce
This class implements a buffered 14-7 potential used to model van der Waals forces.
Definition: AmoebaVdwForce.h:55
OpenMM::Context
A Context stores the complete state of a simulation.
Definition: Context.h:67
OpenMM::AmoebaVdwForce::CutoffPeriodic
Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic...
Definition: AmoebaVdwForce.h:70
OpenMM::Force
Force objects apply forces to the particles in a System, or alter their behavior in other ways...
Definition: Force.h:65
OpenMM::AmoebaVdwForce::usesPeriodicBoundaryConditions
bool usesPeriodicBoundaryConditions() const
Returns whether or not this force makes use of periodic boundary conditions.
Definition: AmoebaVdwForce.h:221
OpenMM::AmoebaVdwForce::getNumParticles
int getNumParticles() const
Get the number of particles.
Definition: AmoebaVdwForce.h:81
OpenMM::AmoebaVdwForce::setUseDispersionCorrection
void setUseDispersionCorrection(bool useCorrection)
Set whether to add a contribution to the energy that approximately represents the effect of VdW inter...
Definition: AmoebaVdwForce.h:166
OpenMM
Definition: AndersenThermostat.h:40
OpenMM::AmoebaVdwForce::NonbondedMethod
NonbondedMethod
This is an enumeration of the different methods that may be used for handling long range nonbonded fo...
Definition: AmoebaVdwForce.h:60