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AmoebaTorsionTorsionForce.h
1 #ifndef OPENMM_AMOEBA_TORSION_TORSION_FORCE_H_
2 #define OPENMM_AMOEBA_TORSION_TORSION_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
38 #include <vector>
39 #include <cmath>
40
41 namespace OpenMM {
42
43 typedef std::vector< std::vector< std::vector<double> > > TorsionTorsionGrid;
44 typedef std::vector< std::vector< std::vector<float> > > TorsionTorsionGridFloat;
45
53 class OPENMM_EXPORT_AMOEBA AmoebaTorsionTorsionForce : public Force {
54
55 public:
59 AmoebaTorsionTorsionForce(void);
60
64 int getNumTorsionTorsions(void) const {
65 return torsionTorsions.size();
66 }
67
71 int getNumTorsionTorsionGrids(void) const {
72 return torsionTorsionGrids.size();
73 }
74
87 int addTorsionTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex);
88
101 void getTorsionTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& chiralCheckAtomIndex, int& gridIndex) const;
102
115 void setTorsionTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex);
116
123 const std::vector<std::vector<std::vector<double> > >& getTorsionTorsionGrid(int index) const;
124
139 void setTorsionTorsionGrid(int index, const std::vector<std::vector<std::vector<double> > >& grid);
146 bool usesPeriodicBoundaryConditions() const {
147 return false;
148 }
149 protected:
150 ForceImpl* createImpl() const;
151 private:
152 class TorsionTorsionInfo;
153 class TorsionTorsionGridInfo;
154 std::vector<TorsionTorsionInfo> torsionTorsions;
155 std::vector<TorsionTorsionGridInfo> torsionTorsionGrids;
156 };
157
162 class AmoebaTorsionTorsionForce::TorsionTorsionInfo {
163
164 public:
165
166 int particle1, particle2, particle3, particle4, particle5;
167 int chiralCheckAtomIndex;
168 int gridIndex;
169 TorsionTorsionInfo() {
170 particle1 = particle2 = particle3 = particle4 = particle5 = chiralCheckAtomIndex = -1;
171 gridIndex = 0;
172 }
173 TorsionTorsionInfo(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) :
174 particle1(particle1), particle2(particle2), particle3(particle3),
175 particle4(particle4), particle5(particle5), gridIndex(gridIndex), chiralCheckAtomIndex(chiralCheckAtomIndex) {
176
177 }
178 };
179
184 class AmoebaTorsionTorsionForce::TorsionTorsionGridInfo {
185
186 public:
187
188 TorsionTorsionGridInfo() {
189 _size[0] = _size[1] = 0;
190 _startValues[0] = _startValues[1] = 0.0;
191 _spacing[0] = _spacing[1] = 1.0;
192 }
193
194 TorsionTorsionGridInfo(const TorsionTorsionGrid& grid);
195
196 const TorsionTorsionGrid& getTorsionTorsionGrid(void) const {
197 return _grid;
198 }
199 int getDimensionSize(int index) const {
200 return _size[index];
201 }
202 double getStartValue(int index) const {
203 return _startValues[index];
204 }
205 double getSpacing(int index) const {
206 return _spacing[index];
207 }
208
209 private:
210
211 TorsionTorsionGrid _grid;
212 int _size[2];
213 double _startValues[2];
214 double _spacing[2];
215 };
216
217 } // namespace OpenMM
218
219 #endif /*OPENMM_AMOEBA_TORSION_TORSION_FORCE_H_*/
OpenMM::TorsionTorsionGrid
std::vector< std::vector< std::vector< double > > > TorsionTorsionGrid
Definition: AmoebaTorsionTorsionForce.h:43
OpenMM::TorsionTorsionGridFloat
std::vector< std::vector< std::vector< float > > > TorsionTorsionGridFloat
Definition: AmoebaTorsionTorsionForce.h:44
OpenMM::AmoebaTorsionTorsionForce::getTorsionTorsionGrid
const std::vector< std::vector< std::vector< double > > > & getTorsionTorsionGrid(int index) const
Get the torsion-torsion grid at the specified index.
OpenMM::AmoebaTorsionTorsionForce
This class implements the Amoeba torsion-torsion interaction.
Definition: AmoebaTorsionTorsionForce.h:53
OpenMM::AmoebaTorsionTorsionForce::usesPeriodicBoundaryConditions
bool usesPeriodicBoundaryConditions() const
Returns whether or not this force makes use of periodic boundary conditions.
Definition: AmoebaTorsionTorsionForce.h:146
OpenMM::Force
Force objects apply forces to the particles in a System, or alter their behavior in other ways...
Definition: Force.h:65
OpenMM
Definition: AndersenThermostat.h:40
OpenMM::AmoebaTorsionTorsionForce::getNumTorsionTorsions
int getNumTorsionTorsions(void) const
Get the number of torsion-torsion terms in the potential function.
Definition: AmoebaTorsionTorsionForce.h:64
OpenMM::AmoebaTorsionTorsionForce::getNumTorsionTorsionGrids
int getNumTorsionTorsionGrids(void) const
Get the number of torsion-torsion grids.
Definition: AmoebaTorsionTorsionForce.h:71