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RPMDIntegrator.h
1 #ifndef OPENMM_RPMDINTEGRATOR_H_
2 #define OPENMM_RPMDINTEGRATOR_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 "openmm/Integrator.h"
36 #include "openmm/Kernel.h"
37 #include "openmm/State.h"
38 #include "openmm/Vec3.h"
39 #include "openmm/internal/windowsExportRpmd.h"
40 #include <map>
41
42 namespace OpenMM {
43
69 class OPENMM_EXPORT_RPMD RPMDIntegrator : public Integrator {
70 public:
79 RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize);
92 RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize, const std::map<int, int>& contractions);
96 int getNumCopies() const {
97 return numCopies;
98 }
104 double getTemperature() const {
105 return temperature;
106 }
112 void setTemperature(double temp) {
113 temperature = temp;
114 }
121 double getFriction() const {
122 return friction;
123 }
130 void setFriction(double coeff) {
131 friction = coeff;
132 }
136 bool getApplyThermostat() const {
137 return applyThermostat;
138 }
142 void setApplyThermostat(bool apply) {
143 applyThermostat = apply;
144 }
148 int getRandomNumberSeed() const {
149 return randomNumberSeed;
150 }
163 void setRandomNumberSeed(int seed) {
164 randomNumberSeed = seed;
165 }
172 const std::map<int, int>& getContractions() const {
173 return contractions;
174 }
181 void setPositions(int copy, const std::vector<Vec3>& positions);
188 void setVelocities(int copy, const std::vector<Vec3>& velocities);
201 State getState(int copy, int types, bool enforcePeriodicBox=false, int groups=0xFFFFFFFF);
206 double getTotalEnergy();
212 void step(int steps);
213 protected:
219 void initialize(ContextImpl& context);
224 void cleanup();
228 void stateChanged(State::DataType changed);
232 std::vector<std::string> getKernelNames();
236 double computeKineticEnergy();
237 private:
238 double temperature, friction;
239 int numCopies, randomNumberSeed;
240 bool applyThermostat;
241 std::map<int, int> contractions;
242 bool forcesAreValid, hasSetPosition, hasSetVelocity, isFirstStep;
243 Kernel kernel;
244 };
245
246 } // namespace OpenMM
247
248 #endif /*OPENMM_RPMDINTEGRATOR_H_*/
OpenMM::RPMDIntegrator::getContractions
const std::map< int, int > & getContractions() const
Get the ring polymer contractions to use for evaluating different force groups.
Definition: RPMDIntegrator.h:172
OpenMM::RPMDIntegrator::setFriction
void setFriction(double coeff)
Set the friction coefficient which determines how strongly the system is coupled to the heat bath (in...
Definition: RPMDIntegrator.h:130
OpenMM::RPMDIntegrator::setTemperature
void setTemperature(double temp)
Set the temperature of the heat bath (in Kelvin).
Definition: RPMDIntegrator.h:112
OpenMM::RPMDIntegrator::getApplyThermostat
bool getApplyThermostat() const
Get whether a thermostat is applied to the system.
Definition: RPMDIntegrator.h:136
OpenMM::State
A State object records a snapshot of the current state of a simulation at a point in time...
Definition: State.h:54
OpenMM::RPMDIntegrator::getRandomNumberSeed
int getRandomNumberSeed() const
Get the random number seed.
Definition: RPMDIntegrator.h:148
OpenMM::RPMDIntegrator::getTemperature
double getTemperature() const
Get the temperature of the heat bath (in Kelvin).
Definition: RPMDIntegrator.h:104
OpenMM::RPMDIntegrator::getNumCopies
int getNumCopies() const
Get the number of copies of the system being simulated.
Definition: RPMDIntegrator.h:96
OpenMM::Integrator
An Integrator defines a method for simulating a System by integrating the equations of motion...
Definition: Integrator.h:54
OpenMM::RPMDIntegrator
This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD)...
Definition: RPMDIntegrator.h:69
OpenMM::State::DataType
DataType
This is an enumeration of the types of data which may be stored in a State.
Definition: State.h:61
OpenMM::Kernel
A Kernel encapsulates a particular implementation of a calculation that can be performed on the data ...
Definition: Kernel.h:58
OpenMM::RPMDIntegrator::getFriction
double getFriction() const
Get the friction coefficient which determines how strongly the system is coupled to the heat bath (in...
Definition: RPMDIntegrator.h:121
OpenMM
Definition: AndersenThermostat.h:40
OpenMM::RPMDIntegrator::setRandomNumberSeed
void setRandomNumberSeed(int seed)
Set the random number seed.
Definition: RPMDIntegrator.h:163
OpenMM::RPMDIntegrator::setApplyThermostat
void setApplyThermostat(bool apply)
Set whether a thermostat is applied to the system.
Definition: RPMDIntegrator.h:142