ReferenceKernels.h 50.2 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
#ifndef OPENMM_REFERENCEKERNELS_H_
#define OPENMM_REFERENCEKERNELS_H_

/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
 * -------------------------------------------------------------------------- *
 * This is part of the OpenMM molecular simulation toolkit originating from   *
 * Simbios, the NIH National Center for Physics-Based Simulation of           *
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
 *                                                                            *
12
 * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
 * Permission is hereby granted, free of charge, to any person obtaining a    *
 * copy of this software and associated documentation files (the "Software"), *
 * to deal in the Software without restriction, including without limitation  *
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
 * and/or sell copies of the Software, and to permit persons to whom the      *
 * Software is furnished to do so, subject to the following conditions:       *
 *                                                                            *
 * The above copyright notice and this permission notice shall be included in *
 * all copies or substantial portions of the Software.                        *
 *                                                                            *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
 * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
 * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
 * -------------------------------------------------------------------------- */

35
#include "ReferencePlatform.h"
36
#include "openmm/kernels.h"
37
38
#include "SimTKOpenMMRealType.h"
#include "ReferenceNeighborList.h"
39
#include "lepton/CompiledExpression.h"
40
#include "lepton/ExpressionProgram.h"
41

42
class CpuObc;
Mark Friedrichs's avatar
Mark Friedrichs committed
43
class CpuGBVI;
44
class ReferenceAndersenThermostat;
45
class ReferenceCustomCompoundBondIxn;
46
class ReferenceCustomHbondIxn;
47
class ReferenceBrownianDynamics;
48
class ReferenceStochasticDynamics;
49
class ReferenceConstraintAlgorithm;
50
class ReferenceMonteCarloBarostat;
51
class ReferenceVariableStochasticDynamics;
52
class ReferenceVariableVerletDynamics;
53
class ReferenceVerletDynamics;
54
class ReferenceCustomDynamics;
55

56
57
namespace OpenMM {

58
/**
59
60
61
 * This kernel is invoked at the beginning and end of force and energy computations.  It gives the
 * Platform a chance to clear buffers and do other initialization at the beginning, and to do any
 * necessary work at the end to determine the final results.
62
 */
63
class ReferenceCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
64
public:
65
    ReferenceCalcForcesAndEnergyKernel(std::string name, const Platform& platform) : CalcForcesAndEnergyKernel(name, platform) {
66
67
68
69
70
71
72
73
    }
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     */
    void initialize(const System& system);
    /**
74
     * This is called at the beginning of each force/energy computation, before calcForcesAndEnergy() has been called on
75
76
     * any ForceImpl.
     *
77
78
79
     * @param context       the context in which to execute this kernel
     * @param includeForce  true if forces should be computed
     * @param includeEnergy true if potential energy should be computed
80
     * @param groups        a set of bit flags for which force groups to include
81
     */
82
    void beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups);
83
    /**
84
     * This is called at the end of each force/energy computation, after calcForcesAndEnergy() has been called on
85
86
     * every ForceImpl.
     *
87
88
89
     * @param context       the context in which to execute this kernel
     * @param includeForce  true if forces should be computed
     * @param includeEnergy true if potential energy should be computed
90
     * @param groups        a set of bit flags for which force groups to include
91
     * @return the potential energy of the system.  This value is added to all values returned by ForceImpls'
92
     * calcForcesAndEnergy() methods.  That is, each force kernel may <i>either</i> return its contribution to the
93
     * energy directly, <i>or</i> add it to an internal buffer so that it will be included here.
94
     */
95
    double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups);
96
97
private:
    std::vector<RealVec> savedForces;
98
99
};

100
/**
101
102
 * This kernel provides methods for setting and retrieving various state data: time, positions,
 * velocities, and forces.
103
 */
104
class ReferenceUpdateStateDataKernel : public UpdateStateDataKernel {
105
public:
106
    ReferenceUpdateStateDataKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : UpdateStateDataKernel(name, platform), data(data) {
107
108
109
110
111
112
113
114
115
116
117
118
    }
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     */
    void initialize(const System& system);
    /**
     * Get the current time (in picoseconds).
     *
     * @param context    the context in which to execute this kernel
     */
119
    double getTime(const ContextImpl& context) const;
120
121
122
123
124
    /**
     * Set the current time (in picoseconds).
     *
     * @param context    the context in which to execute this kernel
     */
125
    void setTime(ContextImpl& context, double time);
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
    /**
     * Get the positions of all particles.
     *
     * @param positions  on exit, this contains the particle positions
     */
    void getPositions(ContextImpl& context, std::vector<Vec3>& positions);
    /**
     * Set the positions of all particles.
     *
     * @param positions  a vector containg the particle positions
     */
    void setPositions(ContextImpl& context, const std::vector<Vec3>& positions);
    /**
     * Get the velocities of all particles.
     *
     * @param velocities  on exit, this contains the particle velocities
     */
    void getVelocities(ContextImpl& context, std::vector<Vec3>& velocities);
    /**
     * Set the velocities of all particles.
     *
     * @param velocities  a vector containg the particle velocities
     */
    void setVelocities(ContextImpl& context, const std::vector<Vec3>& velocities);
    /**
     * Get the current forces on all particles.
     *
     * @param forces  on exit, this contains the forces
     */
    void getForces(ContextImpl& context, std::vector<Vec3>& forces);
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
    /**
     * Get the current periodic box vectors.
     *
     * @param a      on exit, this contains the vector defining the first edge of the periodic box
     * @param b      on exit, this contains the vector defining the second edge of the periodic box
     * @param c      on exit, this contains the vector defining the third edge of the periodic box
     */
    void getPeriodicBoxVectors(ContextImpl& context, Vec3& a, Vec3& b, Vec3& c) const;
    /**
     * Set the current periodic box vectors.
     *
     * @param a      the vector defining the first edge of the periodic box
     * @param b      the vector defining the second edge of the periodic box
     * @param c      the vector defining the third edge of the periodic box
     */
    void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const;
Peter Eastman's avatar
Peter Eastman committed
172
173
174
175
176
177
178
179
180
181
182
183
    /**
     * Create a checkpoint recording the current state of the Context.
     * 
     * @param stream    an output stream the checkpoint data should be written to
     */
    void createCheckpoint(ContextImpl& context, std::ostream& stream);
    /**
     * Load a checkpoint that was written by createCheckpoint().
     * 
     * @param stream    an input stream the checkpoint data should be read from
     */
    void loadCheckpoint(ContextImpl& context, std::istream& stream);
184
185
186
187
private:
    ReferencePlatform::PlatformData& data;
};

188
189
190
191
192
193
/**
 * This kernel modifies the positions of particles to enforce distance constraints.
 */
class ReferenceApplyConstraintsKernel : public ApplyConstraintsKernel {
public:
    ReferenceApplyConstraintsKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) :
194
            ApplyConstraintsKernel(name, platform), data(data) {
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
    }
    ~ReferenceApplyConstraintsKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     */
    void initialize(const System& system);
    /**
     * Update particle positions to enforce constraints.
     *
     * @param context    the context in which to execute this kernel
     * @param tol        the distance tolerance within which constraints must be satisfied.
     */
    void apply(ContextImpl& context, double tol);
210
211
212
213
214
215
216
    /**
     * Update particle velocities to enforce constraints.
     *
     * @param context    the context in which to execute this kernel
     * @param tol        the velocity tolerance within which constraints must be satisfied.
     */
    void applyToVelocities(ContextImpl& context, double tol);
217
218
private:
    ReferencePlatform::PlatformData& data;
219
220
    std::vector<RealOpenMM> masses;
    std::vector<RealOpenMM> inverseMasses;
221
222
};

223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
/**
 * This kernel recomputes the positions of virtual sites.
 */
class ReferenceVirtualSitesKernel : public VirtualSitesKernel {
public:
    ReferenceVirtualSitesKernel(std::string name, const Platform& platform) : VirtualSitesKernel(name, platform) {
    }
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     */
    void initialize(const System& system);
    /**
     * Compute the virtual site locations.
     *
     * @param context    the context in which to execute this kernel
     */
    void computePositions(ContextImpl& context);
};

244
/**
245
 * This kernel is invoked by HarmonicBondForce to calculate the forces acting on the system and the energy of the system.
246
 */
247
class ReferenceCalcHarmonicBondForceKernel : public CalcHarmonicBondForceKernel {
248
public:
249
    ReferenceCalcHarmonicBondForceKernel(std::string name, const Platform& platform) : CalcHarmonicBondForceKernel(name, platform) {
250
    }
251
    ~ReferenceCalcHarmonicBondForceKernel();
252
    /**
253
     * Initialize the kernel.
254
     * 
255
     * @param system     the System this kernel will be applied to
256
257
258
259
     * @param force      the HarmonicBondForce this kernel will be used for
     */
    void initialize(const System& system, const HarmonicBondForce& force);
    /**
260
261
262
263
264
265
     * Execute the kernel to calculate the forces and/or energy.
     *
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
266
     */
267
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
268
269
270
271
272
273
274
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the HarmonicBondForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const HarmonicBondForce& force);
275
276
277
278
279
280
private:
    int numBonds;
    int **bondIndexArray;
    RealOpenMM **bondParamArray;
};

281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
/**
 * This kernel is invoked by CustomBondForce to calculate the forces acting on the system and the energy of the system.
 */
class ReferenceCalcCustomBondForceKernel : public CalcCustomBondForceKernel {
public:
    ReferenceCalcCustomBondForceKernel(std::string name, const Platform& platform) : CalcCustomBondForceKernel(name, platform) {
    }
    ~ReferenceCalcCustomBondForceKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CustomBondForce this kernel will be used for
     */
    void initialize(const System& system, const CustomBondForce& force);
    /**
297
     * Execute the kernel to calculate the forces and/or energy.
298
     *
299
300
301
302
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
303
     */
304
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
305
306
307
308
309
310
311
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CustomBondForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CustomBondForce& force);
312
313
314
315
private:
    int numBonds;
    int **bondIndexArray;
    RealOpenMM **bondParamArray;
316
    Lepton::CompiledExpression energyExpression, forceExpression;
317
318
319
    std::vector<std::string> parameterNames, globalParameterNames;
};

320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
/**
 * This kernel is invoked by HarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
 */
class ReferenceCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
public:
    ReferenceCalcHarmonicAngleForceKernel(std::string name, const Platform& platform) : CalcHarmonicAngleForceKernel(name, platform) {
    }
    ~ReferenceCalcHarmonicAngleForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the HarmonicAngleForce this kernel will be used for
     */
    void initialize(const System& system, const HarmonicAngleForce& force);
    /**
336
337
338
339
340
341
     * Execute the kernel to calculate the forces and/or energy.
     *
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
342
     */
343
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
344
345
346
347
348
349
350
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the HarmonicAngleForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force);
351
352
353
354
355
356
private:
    int numAngles;
    int **angleIndexArray;
    RealOpenMM **angleParamArray;
};

357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
/**
 * This kernel is invoked by CustomAngleForce to calculate the forces acting on the system and the energy of the system.
 */
class ReferenceCalcCustomAngleForceKernel : public CalcCustomAngleForceKernel {
public:
    ReferenceCalcCustomAngleForceKernel(std::string name, const Platform& platform) : CalcCustomAngleForceKernel(name, platform) {
    }
    ~ReferenceCalcCustomAngleForceKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CustomAngleForce this kernel will be used for
     */
    void initialize(const System& system, const CustomAngleForce& force);
    /**
373
     * Execute the kernel to calculate the forces and/or energy.
374
     *
375
376
377
378
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
379
     */
380
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
381
382
383
384
385
386
387
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CustomAngleForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CustomAngleForce& force);
388
389
390
391
private:
    int numAngles;
    int **angleIndexArray;
    RealOpenMM **angleParamArray;
392
    Lepton::CompiledExpression energyExpression, forceExpression;
393
394
395
    std::vector<std::string> parameterNames, globalParameterNames;
};

396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
/**
 * This kernel is invoked by PeriodicTorsionForce to calculate the forces acting on the system and the energy of the system.
 */
class ReferenceCalcPeriodicTorsionForceKernel : public CalcPeriodicTorsionForceKernel {
public:
    ReferenceCalcPeriodicTorsionForceKernel(std::string name, const Platform& platform) : CalcPeriodicTorsionForceKernel(name, platform) {
    }
    ~ReferenceCalcPeriodicTorsionForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the PeriodicTorsionForce this kernel will be used for
     */
    void initialize(const System& system, const PeriodicTorsionForce& force);
    /**
412
413
414
415
416
417
     * Execute the kernel to calculate the forces and/or energy.
     *
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
418
     */
419
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
420
421
422
423
424
425
426
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the PeriodicTorsionForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force);
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
private:
    int numTorsions;
    int **torsionIndexArray;
    RealOpenMM **torsionParamArray;
};

/**
 * This kernel is invoked by RBTorsionForce to calculate the forces acting on the system and the energy of the system.
 */
class ReferenceCalcRBTorsionForceKernel : public CalcRBTorsionForceKernel {
public:
    ReferenceCalcRBTorsionForceKernel(std::string name, const Platform& platform) : CalcRBTorsionForceKernel(name, platform) {
    }
    ~ReferenceCalcRBTorsionForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the RBTorsionForce this kernel will be used for
     */
    void initialize(const System& system, const RBTorsionForce& force);
    /**
449
450
451
452
453
454
     * Execute the kernel to calculate the forces and/or energy.
     *
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
455
     */
456
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
457
458
459
460
461
462
463
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the RBTorsionForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const RBTorsionForce& force);
464
465
466
467
468
469
private:
    int numTorsions;
    int **torsionIndexArray;
    RealOpenMM **torsionParamArray;
};

470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
/**
 * This kernel is invoked by CMAPTorsionForce to calculate the forces acting on the system and the energy of the system.
 */
class ReferenceCalcCMAPTorsionForceKernel : public CalcCMAPTorsionForceKernel {
public:
    ReferenceCalcCMAPTorsionForceKernel(std::string name, const Platform& platform) : CalcCMAPTorsionForceKernel(name, platform) {
    }
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CMAPTorsionForce this kernel will be used for
     */
    void initialize(const System& system, const CMAPTorsionForce& force);
    /**
485
     * Execute the kernel to calculate the forces and/or energy.
486
     *
487
488
489
490
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
491
     */
492
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
493
494
495
496
497
498
private:
    std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
    std::vector<int> torsionMaps;
    std::vector<std::vector<int> > torsionIndices;
};

499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
/**
 * This kernel is invoked by CustomTorsionForce to calculate the forces acting on the system and the energy of the system.
 */
class ReferenceCalcCustomTorsionForceKernel : public CalcCustomTorsionForceKernel {
public:
    ReferenceCalcCustomTorsionForceKernel(std::string name, const Platform& platform) : CalcCustomTorsionForceKernel(name, platform) {
    }
    ~ReferenceCalcCustomTorsionForceKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CustomTorsionForce this kernel will be used for
     */
    void initialize(const System& system, const CustomTorsionForce& force);
    /**
515
     * Execute the kernel to calculate the forces and/or energy.
516
     *
517
518
519
520
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
521
     */
522
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
523
524
525
526
527
528
529
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CustomTorsionForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CustomTorsionForce& force);
530
531
532
533
private:
    int numTorsions;
    int **torsionIndexArray;
    RealOpenMM **torsionParamArray;
534
    Lepton::CompiledExpression energyExpression, forceExpression;
535
536
537
    std::vector<std::string> parameterNames, globalParameterNames;
};

538
539
540
541
542
543
544
545
546
547
548
549
550
/**
 * This kernel is invoked by NonbondedForce to calculate the forces acting on the system.
 */
class ReferenceCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
    ReferenceCalcNonbondedForceKernel(std::string name, const Platform& platform) : CalcNonbondedForceKernel(name, platform) {
    }
    ~ReferenceCalcNonbondedForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the NonbondedForce this kernel will be used for
551
     */
552
    void initialize(const System& system, const NonbondedForce& force);
553
    /**
554
555
556
557
558
     * Execute the kernel to calculate the forces and/or energy.
     *
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
559
     * @param includeReciprocal  true if reciprocal space interactions should be included
560
     * @return the potential energy due to the force
561
     */
562
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal);
563
564
565
566
567
568
569
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the NonbondedForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const NonbondedForce& force);
570
private:
Peter Eastman's avatar
Peter Eastman committed
571
    int numParticles, num14;
572
    int **bonded14IndexArray;
Peter Eastman's avatar
Peter Eastman committed
573
    RealOpenMM **particleParamArray, **bonded14ParamArray;
574
    RealOpenMM nonbondedCutoff, switchingDistance, rfDielectric, ewaldAlpha, dispersionCoefficient;
575
    int kmax[3], gridSize[3];
576
    bool useSwitchingFunction;
577
578
579
    std::vector<std::set<int> > exclusions;
    NonbondedMethod nonbondedMethod;
    NeighborList* neighborList;
580
581
};

582
583
584
585
586
/**
 * This kernel is invoked by CustomNonbondedForce to calculate the forces acting on the system.
 */
class ReferenceCalcCustomNonbondedForceKernel : public CalcCustomNonbondedForceKernel {
public:
587
    ReferenceCalcCustomNonbondedForceKernel(std::string name, const Platform& platform) : CalcCustomNonbondedForceKernel(name, platform), forceCopy(NULL) {
588
589
590
591
592
593
594
595
596
597
    }
    ~ReferenceCalcCustomNonbondedForceKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CustomNonbondedForce this kernel will be used for
     */
    void initialize(const System& system, const CustomNonbondedForce& force);
    /**
598
     * Execute the kernel to calculate the forces and/or energy.
599
     *
600
601
602
603
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
604
     */
605
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
606
607
608
609
610
611
612
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CustomNonbondedForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
613
private:
614
615
    int numParticles;
    RealOpenMM **particleParamArray;
616
617
    RealOpenMM nonbondedCutoff, switchingDistance, periodicBoxSize[3], longRangeCoefficient;
    bool useSwitchingFunction, hasInitializedLongRangeCorrection;
618
619
    CustomNonbondedForce* forceCopy;
    std::map<std::string, double> globalParamValues;
620
    std::vector<std::set<int> > exclusions;
621
    Lepton::CompiledExpression energyExpression, forceExpression;
622
    std::vector<std::string> parameterNames, globalParameterNames;
623
    std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
624
625
626
627
    NonbondedMethod nonbondedMethod;
    NeighborList* neighborList;
};

628
/**
629
 * This kernel is invoked by GBSAOBCForce to calculate the forces acting on the system.
630
 */
631
class ReferenceCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
632
public:
633
    ReferenceCalcGBSAOBCForceKernel(std::string name, const Platform& platform) : CalcGBSAOBCForceKernel(name, platform) {
634
    }
635
    ~ReferenceCalcGBSAOBCForceKernel();
636
    /**
637
     * Initialize the kernel.
638
     * 
639
     * @param system     the System this kernel will be applied to
640
     * @param force      the GBSAOBCForce this kernel will be used for
641
     */
642
    void initialize(const System& system, const GBSAOBCForce& force);
643
    /**
644
645
646
647
648
649
     * Execute the kernel to calculate the forces and/or energy.
     *
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
650
     */
651
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
652
653
654
655
656
657
658
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the GBSAOBCForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force);
659
660
661
private:
    CpuObc* obc;
    std::vector<RealOpenMM> charges;
662
    bool isPeriodic;
663
664
};

Mark Friedrichs's avatar
Mark Friedrichs committed
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
/**
 * This kernel is invoked by GBVIForce to calculate the forces acting on the system.
 */
class ReferenceCalcGBVIForceKernel : public CalcGBVIForceKernel {
public:
    ReferenceCalcGBVIForceKernel(std::string name, const Platform& platform) : CalcGBVIForceKernel(name, platform) {
    }
    ~ReferenceCalcGBVIForceKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system       the System this kernel will be applied to
     * @param force        the GBVIForce this kernel will be used for
     * @param scaled radii the scaled radii (Eq. 5 of Labute paper)
     */
    void initialize(const System& system, const GBVIForce& force, const std::vector<double> & scaledRadii);
    /**
682
683
684
685
686
687
     * Execute the kernel to calculate the forces and/or energy.
     *
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
Mark Friedrichs's avatar
Mark Friedrichs committed
688
     */
689
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
Mark Friedrichs's avatar
Mark Friedrichs committed
690
691
692
private:
    CpuGBVI * gbvi;
    std::vector<RealOpenMM> charges;
693
    bool isPeriodic;
Mark Friedrichs's avatar
Mark Friedrichs committed
694
695
};

696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
/**
 * This kernel is invoked by CustomGBForce to calculate the forces acting on the system.
 */
class ReferenceCalcCustomGBForceKernel : public CalcCustomGBForceKernel {
public:
    ReferenceCalcCustomGBForceKernel(std::string name, const Platform& platform) : CalcCustomGBForceKernel(name, platform) {
    }
    ~ReferenceCalcCustomGBForceKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CustomGBForce this kernel will be used for
     */
    void initialize(const System& system, const CustomGBForce& force);
    /**
712
     * Execute the kernel to calculate the forces and/or energy.
713
     *
714
715
716
717
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
718
     */
719
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
720
721
722
723
724
725
726
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CustomGBForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CustomGBForce& force);
727
728
private:
    int numParticles;
729
    bool isPeriodic;
730
    RealOpenMM **particleParamArray;
731
    RealOpenMM nonbondedCutoff;
732
733
734
    std::vector<std::set<int> > exclusions;
    std::vector<std::string> particleParameterNames, globalParameterNames, valueNames;
    std::vector<Lepton::ExpressionProgram> valueExpressions;
735
    std::vector<std::vector<Lepton::ExpressionProgram> > valueDerivExpressions;
736
    std::vector<std::vector<Lepton::ExpressionProgram> > valueGradientExpressions;
737
738
739
    std::vector<OpenMM::CustomGBForce::ComputationType> valueTypes;
    std::vector<Lepton::ExpressionProgram> energyExpressions;
    std::vector<std::vector<Lepton::ExpressionProgram> > energyDerivExpressions;
740
    std::vector<std::vector<Lepton::ExpressionProgram> > energyGradientExpressions;
741
742
743
744
745
    std::vector<OpenMM::CustomGBForce::ComputationType> energyTypes;
    NonbondedMethod nonbondedMethod;
    NeighborList* neighborList;
};

746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
/**
 * This kernel is invoked by CustomExternalForce to calculate the forces acting on the system and the energy of the system.
 */
class ReferenceCalcCustomExternalForceKernel : public CalcCustomExternalForceKernel {
public:
    ReferenceCalcCustomExternalForceKernel(std::string name, const Platform& platform) : CalcCustomExternalForceKernel(name, platform) {
    }
    ~ReferenceCalcCustomExternalForceKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CustomExternalForce this kernel will be used for
     */
    void initialize(const System& system, const CustomExternalForce& force);
    /**
762
     * Execute the kernel to calculate the forces and/or energy.
763
     *
764
765
766
767
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
768
     */
769
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
770
771
772
773
774
775
776
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CustomExternalForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force);
777
778
779
780
private:
    int numParticles;
    std::vector<int> particles;
    RealOpenMM **particleParamArray;
781
    Lepton::CompiledExpression energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
782
783
784
    std::vector<std::string> parameterNames, globalParameterNames;
};

785
786
787
788
789
/**
 * This kernel is invoked by CustomHbondForce to calculate the forces acting on the system.
 */
class ReferenceCalcCustomHbondForceKernel : public CalcCustomHbondForceKernel {
public:
790
    ReferenceCalcCustomHbondForceKernel(std::string name, const Platform& platform) : CalcCustomHbondForceKernel(name, platform), ixn(NULL) {
791
792
793
794
795
796
797
798
799
800
    }
    ~ReferenceCalcCustomHbondForceKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CustomHbondForce this kernel will be used for
     */
    void initialize(const System& system, const CustomHbondForce& force);
    /**
801
     * Execute the kernel to calculate the forces and/or energy.
802
     *
803
804
805
806
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
807
     */
808
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
809
810
811
812
813
814
815
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CustomHbondForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CustomHbondForce& force);
816
817
private:
    int numDonors, numAcceptors, numParticles;
818
    bool isPeriodic;
819
    RealOpenMM **donorParamArray, **acceptorParamArray;
820
    RealOpenMM nonbondedCutoff;
821
    ReferenceCustomHbondIxn* ixn;
822
    std::vector<std::set<int> > exclusions;
823
    std::vector<std::string> globalParameterNames;
824
825
};

826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
/**
 * This kernel is invoked by CustomCompoundBondForce to calculate the forces acting on the system.
 */
class ReferenceCalcCustomCompoundBondForceKernel : public CalcCustomCompoundBondForceKernel {
public:
    ReferenceCalcCustomCompoundBondForceKernel(std::string name, const Platform& platform) : CalcCustomCompoundBondForceKernel(name, platform), ixn(NULL) {
    }
    ~ReferenceCalcCustomCompoundBondForceKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CustomCompoundBondForce this kernel will be used for
     */
    void initialize(const System& system, const CustomCompoundBondForce& force);
    /**
     * Execute the kernel to calculate the forces and/or energy.
     *
     * @param context        the context in which to execute this kernel
     * @param includeForces  true if forces should be calculated
     * @param includeEnergy  true if the energy should be calculated
     * @return the potential energy due to the force
     */
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
850
851
852
853
854
855
856
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CustomCompoundBondForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force);
857
858
859
860
861
862
863
private:
    int numBonds, numParticles;
    RealOpenMM **bondParamArray;
    ReferenceCustomCompoundBondIxn* ixn;
    std::vector<std::string> globalParameterNames;
};

864
865
866
867
868
/**
 * This kernel is invoked by VerletIntegrator to take one time step.
 */
class ReferenceIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
public:
869
    ReferenceIntegrateVerletStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVerletStepKernel(name, platform),
870
        data(data), dynamics(0) {
871
    }
872
    ~ReferenceIntegrateVerletStepKernel();
873
    /**
874
     * Initialize the kernel.
875
     * 
876
877
     * @param system     the System this kernel will be applied to
     * @param integrator the VerletIntegrator this kernel will be used for
878
     */
879
    void initialize(const System& system, const VerletIntegrator& integrator);
880
881
882
    /**
     * Execute the kernel.
     * 
883
884
     * @param context    the context in which to execute this kernel
     * @param integrator the VerletIntegrator this kernel is being used for
885
     */
886
    void execute(ContextImpl& context, const VerletIntegrator& integrator);
887
888
889
890
891
892
893
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the VerletIntegrator this kernel is being used for
     */
    double computeKineticEnergy(ContextImpl& context, const VerletIntegrator& integrator);
894
private:
895
    ReferencePlatform::PlatformData& data;
896
    ReferenceVerletDynamics* dynamics;
897
    std::vector<RealOpenMM> masses;
898
    double prevStepSize;
899
900
901
902
903
904
905
};

/**
 * This kernel is invoked by LangevinIntegrator to take one time step.
 */
class ReferenceIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
public:
906
    ReferenceIntegrateLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateLangevinStepKernel(name, platform),
907
        data(data), dynamics(0) {
908
    }
909
    ~ReferenceIntegrateLangevinStepKernel();
910
    /**
Peter Eastman's avatar
Peter Eastman committed
911
     * Initialize the kernel, setting up the particle masses.
912
     * 
913
914
     * @param system     the System this kernel will be applied to
     * @param integrator the LangevinIntegrator this kernel will be used for
915
     */
916
    void initialize(const System& system, const LangevinIntegrator& integrator);
917
918
919
    /**
     * Execute the kernel.
     * 
920
921
     * @param context    the context in which to execute this kernel
     * @param integrator the LangevinIntegrator this kernel is being used for
922
     */
923
    void execute(ContextImpl& context, const LangevinIntegrator& integrator);
924
925
926
927
928
929
930
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the LangevinIntegrator this kernel is being used for
     */
    double computeKineticEnergy(ContextImpl& context, const LangevinIntegrator& integrator);
931
private:
932
    ReferencePlatform::PlatformData& data;
933
    ReferenceStochasticDynamics* dynamics;
934
    std::vector<RealOpenMM> masses;
935
    double prevTemp, prevFriction, prevStepSize;
936
937
938
939
940
941
942
};

/**
 * This kernel is invoked by BrownianIntegrator to take one time step.
 */
class ReferenceIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
public:
943
    ReferenceIntegrateBrownianStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateBrownianStepKernel(name, platform),
944
        data(data), dynamics(0) {
945
    }
946
    ~ReferenceIntegrateBrownianStepKernel();
947
    /**
948
     * Initialize the kernel.
949
     * 
950
951
     * @param system     the System this kernel will be applied to
     * @param integrator the BrownianIntegrator this kernel will be used for
952
     */
953
    void initialize(const System& system, const BrownianIntegrator& integrator);
954
955
956
    /**
     * Execute the kernel.
     * 
957
958
     * @param context    the context in which to execute this kernel
     * @param integrator the BrownianIntegrator this kernel is being used for
959
     */
960
    void execute(ContextImpl& context, const BrownianIntegrator& integrator);
961
962
963
964
965
966
967
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the BrownianIntegrator this kernel is being used for
     */
    double computeKineticEnergy(ContextImpl& context, const BrownianIntegrator& integrator);
968
private:
969
    ReferencePlatform::PlatformData& data;
970
    ReferenceBrownianDynamics* dynamics;
971
    std::vector<RealOpenMM> masses;
972
    double prevTemp, prevFriction, prevStepSize;
973
974
};

975
976
977
978
979
980
/**
 * This kernel is invoked by VariableLangevinIntegrator to take one time step.
 */
class ReferenceIntegrateVariableLangevinStepKernel : public IntegrateVariableLangevinStepKernel {
public:
    ReferenceIntegrateVariableLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVariableLangevinStepKernel(name, platform),
981
        data(data), dynamics(0) {
982
983
984
985
986
987
    }
    ~ReferenceIntegrateVariableLangevinStepKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
988
     * @param integrator the VariableLangevinIntegrator this kernel will be used for
989
990
991
992
993
994
     */
    void initialize(const System& system, const VariableLangevinIntegrator& integrator);
    /**
     * Execute the kernel.
     *
     * @param context    the context in which to execute this kernel
995
     * @param integrator the VariableLangevinIntegrator this kernel is being used for
996
     * @param maxTime    the maximum time beyond which the simulation should not be advanced
997
     * @return the size of the step that was taken
998
     */
999
    double execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime);
1000
1001
1002
1003
1004
1005
1006
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the VariableLangevinIntegrator this kernel is being used for
     */
    double computeKineticEnergy(ContextImpl& context, const VariableLangevinIntegrator& integrator);
1007
1008
1009
private:
    ReferencePlatform::PlatformData& data;
    ReferenceVariableStochasticDynamics* dynamics;
1010
    std::vector<RealOpenMM> masses;
1011
1012
1013
    double prevTemp, prevFriction, prevErrorTol;
};

1014
1015
1016
1017
1018
1019
/**
 * This kernel is invoked by VariableVerletIntegrator to take one time step.
 */
class ReferenceIntegrateVariableVerletStepKernel : public IntegrateVariableVerletStepKernel {
public:
    ReferenceIntegrateVariableVerletStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVariableVerletStepKernel(name, platform),
1020
        data(data), dynamics(0) {
1021
1022
1023
1024
1025
1026
    }
    ~ReferenceIntegrateVariableVerletStepKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
1027
     * @param integrator the VariableVerletIntegrator this kernel will be used for
1028
1029
1030
1031
1032
1033
     */
    void initialize(const System& system, const VariableVerletIntegrator& integrator);
    /**
     * Execute the kernel.
     *
     * @param context    the context in which to execute this kernel
1034
     * @param integrator the VariableVerletIntegrator this kernel is being used for
1035
     * @param maxTime    the maximum time beyond which the simulation should not be advanced
1036
     * @return the size of the step that was taken
1037
     */
1038
    double execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime);
1039
1040
1041
1042
1043
1044
1045
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the VariableVerletIntegrator this kernel is being used for
     */
    double computeKineticEnergy(ContextImpl& context, const VariableVerletIntegrator& integrator);
1046
1047
1048
private:
    ReferencePlatform::PlatformData& data;
    ReferenceVariableVerletDynamics* dynamics;
1049
    std::vector<RealOpenMM> masses;
1050
    double prevErrorTol;
1051
1052
};

1053
1054
1055
1056
1057
1058
/**
 * This kernel is invoked by CustomIntegrator to take one time step.
 */
class ReferenceIntegrateCustomStepKernel : public IntegrateCustomStepKernel {
public:
    ReferenceIntegrateCustomStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateCustomStepKernel(name, platform),
1059
        data(data), dynamics(0) {
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
    }
    ~ReferenceIntegrateCustomStepKernel();
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     * @param integrator the CustomIntegrator this kernel will be used for
     */
    void initialize(const System& system, const CustomIntegrator& integrator);
    /**
     * Execute the kernel.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the CustomIntegrator this kernel is being used for
     * @param forcesAreValid if the context has been modified since the last time step, this will be
     *                       false to show that cached forces are invalid and must be recalculated.
     *                       On exit, this should specify whether the cached forces are valid at the
     *                       end of the step.
     */
    void execute(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
    /**
     * Compute the kinetic energy.
     * 
     * @param context    the context in which to execute this kernel
     * @param integrator the CustomIntegrator this kernel is being used for
     * @param forcesAreValid if the context has been modified since the last time step, this will be
     *                       false to show that cached forces are invalid and must be recalculated.
     *                       On exit, this should specify whether the cached forces are valid at the
     *                       end of the step.
     */
    double computeKineticEnergy(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
    /**
     * Get the values of all global variables.
     *
     * @param context   the context in which to execute this kernel
     * @param values    on exit, this contains the values
     */
    void getGlobalVariables(ContextImpl& context, std::vector<double>& values) const;
    /**
     * Set the values of all global variables.
     *
     * @param context   the context in which to execute this kernel
     * @param values    a vector containing the values
     */
    void setGlobalVariables(ContextImpl& context, const std::vector<double>& values);
    /**
     * Get the values of a per-DOF variable.
     *
     * @param context   the context in which to execute this kernel
     * @param variable  the index of the variable to get
     * @param values    on exit, this contains the values
     */
    void getPerDofVariable(ContextImpl& context, int variable, std::vector<Vec3>& values) const;
    /**
     * Set the values of a per-DOF variable.
     *
     * @param context   the context in which to execute this kernel
     * @param variable  the index of the variable to get
     * @param values    a vector containing the values
     */
    void setPerDofVariable(ContextImpl& context, int variable, const std::vector<Vec3>& values);
private:
    ReferencePlatform::PlatformData& data;
    ReferenceCustomDynamics* dynamics;
    std::vector<RealOpenMM> masses, globalValues;
    std::vector<std::vector<OpenMM::RealVec> > perDofValues; 
};

1128
/**
Peter Eastman's avatar
Peter Eastman committed
1129
 * This kernel is invoked by AndersenThermostat at the start of each time step to adjust the particle velocities.
1130
1131
1132
 */
class ReferenceApplyAndersenThermostatKernel : public ApplyAndersenThermostatKernel {
public:
1133
    ReferenceApplyAndersenThermostatKernel(std::string name, const Platform& platform) : ApplyAndersenThermostatKernel(name, platform), thermostat(0) {
1134
    }
1135
    ~ReferenceApplyAndersenThermostatKernel();
1136
    /**
1137
     * Initialize the kernel.
1138
     * 
1139
1140
     * @param system     the System this kernel will be applied to
     * @param thermostat the AndersenThermostat this kernel will be used for
1141
     */
1142
    void initialize(const System& system, const AndersenThermostat& thermostat);
1143
1144
1145
    /**
     * Execute the kernel.
     * 
1146
     * @param context    the context in which to execute this kernel
1147
     */
1148
    void execute(ContextImpl& context);
1149
1150
private:
    ReferenceAndersenThermostat* thermostat;
1151
    std::vector<std::vector<int> > particleGroups;
1152
    std::vector<RealOpenMM> masses;
1153
1154
};

1155
1156
1157
1158
1159
/**
 * This kernel is invoked by MonteCarloBarostat to adjust the periodic box volume
 */
class ReferenceApplyMonteCarloBarostatKernel : public ApplyMonteCarloBarostatKernel {
public:
1160
    ReferenceApplyMonteCarloBarostatKernel(std::string name, const Platform& platform) : ApplyMonteCarloBarostatKernel(name, platform), barostat(NULL) {
1161
1162
1163
1164
1165
1166
1167
1168
    }
    ~ReferenceApplyMonteCarloBarostatKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param barostat   the MonteCarloBarostat this kernel will be used for
     */
1169
    void initialize(const System& system, const Force& barostat);
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
    /**
     * Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
     * This version scales the x, y, and z positions independently.
     * This is called BEFORE the periodic box size is modified.  It should begin by translating each particle
     * or cluster into the first periodic box, so that coordinates will still be correct after the box size
     * is changed.
     *
     * @param context    the context in which to execute this kernel
     * @param scaleX     the scale factor by which to multiply particle x-coordinate
     * @param scaleY     the scale factor by which to multiply particle y-coordinate
     * @param scaleZ     the scale factor by which to multiply particle z-coordinate
     */
1182
    void scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ);
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
    /**
     * Reject the most recent Monte Carlo step, restoring the particle positions to where they were before
     * scaleCoordinates() was last called.
     *
     * @param context    the context in which to execute this kernel
     */
    void restoreCoordinates(ContextImpl& context);
private:
    ReferenceMonteCarloBarostat* barostat;
};

1194
1195
1196
1197
1198
/**
 * This kernel is invoked to remove center of mass motion from the system.
 */
class ReferenceRemoveCMMotionKernel : public RemoveCMMotionKernel {
public:
1199
    ReferenceRemoveCMMotionKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : RemoveCMMotionKernel(name, platform), data(data) {
1200
1201
    }
    /**
Peter Eastman's avatar
Peter Eastman committed
1202
     * Initialize the kernel, setting up the particle masses.
1203
     * 
1204
1205
     * @param system     the System this kernel will be applied to
     * @param force      the CMMotionRemover this kernel will be used for
1206
     */
1207
    void initialize(const System& system, const CMMotionRemover& force);
1208
1209
1210
    /**
     * Execute the kernel.
     * 
1211
     * @param context    the context in which to execute this kernel
1212
     */
1213
    void execute(ContextImpl& context);
1214
private:
1215
    ReferencePlatform::PlatformData& data;
1216
    std::vector<double> masses;
1217
    int frequency;
1218
1219
};

1220
1221
1222
} // namespace OpenMM

#endif /*OPENMM_REFERENCEKERNELS_H_*/