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CustomBondForce.h
1 #ifndef OPENMM_CUSTOMBONDEDFORCE_H_
2 #define OPENMM_CUSTOMBONDEDFORCE_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) 2008-2012 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 "Force.h"
36 #include "Vec3.h"
37 #include <vector>
38 #include "internal/windowsExport.h"
39
40 namespace OpenMM {
41
73 class OPENMM_EXPORT CustomBondForce : public Force {
74 public:
81 explicit CustomBondForce(const std::string& energy);
85 int getNumBonds() const {
86 return bonds.size();
87 }
91 int getNumPerBondParameters() const {
92 return parameters.size();
93 }
97 int getNumGlobalParameters() const {
98 return globalParameters.size();
99 }
103 const std::string& getEnergyFunction() const;
107 void setEnergyFunction(const std::string& energy);
114 int addPerBondParameter(const std::string& name);
121 const std::string& getPerBondParameterName(int index) const;
128 void setPerBondParameterName(int index, const std::string& name);
136 int addGlobalParameter(const std::string& name, double defaultValue);
143 const std::string& getGlobalParameterName(int index) const;
150 void setGlobalParameterName(int index, const std::string& name);
157 double getGlobalParameterDefaultValue(int index) const;
164 void setGlobalParameterDefaultValue(int index, double defaultValue);
173 int addBond(int particle1, int particle2, const std::vector<double>& parameters);
182 void getBondParameters(int index, int& particle1, int& particle2, std::vector<double>& parameters) const;
191 void setBondParameters(int index, int particle1, int particle2, const std::vector<double>& parameters);
202 void updateParametersInContext(Context& context);
209 bool usesPeriodicBoundaryConditions() const {
210 return false;
211 }
212 protected:
213 ForceImpl* createImpl() const;
214 private:
215 class BondInfo;
216 class BondParameterInfo;
217 class GlobalParameterInfo;
218 std::string energyExpression;
219 std::vector<BondParameterInfo> parameters;
220 std::vector<GlobalParameterInfo> globalParameters;
221 std::vector<BondInfo> bonds;
222 };
223
228 class CustomBondForce::BondInfo {
229 public:
230 int particle1, particle2;
231 std::vector<double> parameters;
232 BondInfo() : particle1(-1), particle2(-1) {
233 }
234 BondInfo(int particle1, int particle2, const std::vector<double>& parameters) :
235 particle1(particle1), particle2(particle2), parameters(parameters) {
236 }
237 };
238
243 class CustomBondForce::BondParameterInfo {
244 public:
245 std::string name;
246 BondParameterInfo() {
247 }
248 BondParameterInfo(const std::string& name) : name(name) {
249 }
250 };
251
256 class CustomBondForce::GlobalParameterInfo {
257 public:
258 std::string name;
259 double defaultValue;
260 GlobalParameterInfo() {
261 }
262 GlobalParameterInfo(const std::string& name, double defaultValue) : name(name), defaultValue(defaultValue) {
263 }
264 };
265
266 } // namespace OpenMM
267
268 #endif /*OPENMM_CUSTOMBONDEDFORCE_H_*/
OpenMM::Context
A Context stores the complete state of a simulation.
Definition: Context.h:67
OpenMM::CustomBondForce
This class implements bonded interactions between pairs of particles.
Definition: CustomBondForce.h:73
OpenMM::CustomBondForce::getNumGlobalParameters
int getNumGlobalParameters() const
Get the number of global parameters that the interaction depends on.
Definition: CustomBondForce.h:97
OpenMM::Force
Force objects apply forces to the particles in a System, or alter their behavior in other ways...
Definition: Force.h:65
OpenMM::CustomBondForce::getNumBonds
int getNumBonds() const
Get the number of bonds for which force field parameters have been defined.
Definition: CustomBondForce.h:85
OpenMM::CustomBondForce::usesPeriodicBoundaryConditions
bool usesPeriodicBoundaryConditions() const
Returns whether or not this force makes use of periodic boundary conditions.
Definition: CustomBondForce.h:209
OpenMM::CustomBondForce::getNumPerBondParameters
int getNumPerBondParameters() const
Get the number of per-bond parameters that the interaction depends on.
Definition: CustomBondForce.h:91
OpenMM
Definition: AndersenThermostat.h:40