ReferenceKernels.h 55.2 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) 2008-2016 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/CustomFunction.h"
41
#include "lepton/ExpressionProgram.h"
42

43
44
namespace OpenMM {

45
class ReferenceObc;
46
class ReferenceAndersenThermostat;
47
class ReferenceCustomCentroidBondIxn;
48
class ReferenceCustomCompoundBondIxn;
49
class ReferenceCustomHbondIxn;
50
class ReferenceCustomManyParticleIxn;
51
class ReferenceGayBerneForce;
52
class ReferenceBrownianDynamics;
53
class ReferenceStochasticDynamics;
54
class ReferenceConstraintAlgorithm;
55
class ReferenceMonteCarloBarostat;
56
class ReferenceVariableStochasticDynamics;
57
class ReferenceVariableVerletDynamics;
58
class ReferenceVerletDynamics;
59
class ReferenceCustomDynamics;
60

61
/**
62
63
64
 * 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.
65
 */
66
class ReferenceCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
67
public:
68
    ReferenceCalcForcesAndEnergyKernel(std::string name, const Platform& platform) : CalcForcesAndEnergyKernel(name, platform) {
69
70
71
72
73
74
75
76
    }
    /**
     * Initialize the kernel.
     * 
     * @param system     the System this kernel will be applied to
     */
    void initialize(const System& system);
    /**
77
     * This is called at the beginning of each force/energy computation, before calcForcesAndEnergy() has been called on
78
79
     * any ForceImpl.
     *
80
81
82
     * @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
83
     * @param groups        a set of bit flags for which force groups to include
84
     */
85
    void beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups);
86
    /**
87
     * This is called at the end of each force/energy computation, after calcForcesAndEnergy() has been called on
88
89
     * every ForceImpl.
     *
90
91
92
     * @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
93
     * @param groups        a set of bit flags for which force groups to include
94
95
     * @param valid         the method may set this to false to indicate the results are invalid and the force/energy
     *                      calculation should be repeated
96
     * @return the potential energy of the system.  This value is added to all values returned by ForceImpls'
97
     * calcForcesAndEnergy() methods.  That is, each force kernel may <i>either</i> return its contribution to the
98
     * energy directly, <i>or</i> add it to an internal buffer so that it will be included here.
99
     */
100
    double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups, bool& valid);
101
102
private:
    std::vector<RealVec> savedForces;
103
104
};

105
/**
106
107
 * This kernel provides methods for setting and retrieving various state data: time, positions,
 * velocities, and forces.
108
 */
109
class ReferenceUpdateStateDataKernel : public UpdateStateDataKernel {
110
public:
111
    ReferenceUpdateStateDataKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : UpdateStateDataKernel(name, platform), data(data) {
112
113
114
115
116
117
118
119
120
121
122
123
    }
    /**
     * 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
     */
124
    double getTime(const ContextImpl& context) const;
125
126
127
128
129
    /**
     * Set the current time (in picoseconds).
     *
     * @param context    the context in which to execute this kernel
     */
130
    void setTime(ContextImpl& context, double time);
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
156
157
158
159
160
    /**
     * 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);
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
    /**
     * 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
     */
176
    void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c);
Peter Eastman's avatar
Peter Eastman committed
177
178
179
180
181
182
183
184
185
186
187
188
    /**
     * 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);
189
190
191
192
private:
    ReferencePlatform::PlatformData& data;
};

193
194
195
196
197
198
/**
 * 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) :
199
            ApplyConstraintsKernel(name, platform), data(data) {
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
    }
    ~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);
215
216
217
218
219
220
221
    /**
     * 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);
222
223
private:
    ReferencePlatform::PlatformData& data;
224
225
    std::vector<RealOpenMM> masses;
    std::vector<RealOpenMM> inverseMasses;
226
227
};

228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
/**
 * 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);
};

249
/**
250
 * This kernel is invoked by HarmonicBondForce to calculate the forces acting on the system and the energy of the system.
251
 */
252
class ReferenceCalcHarmonicBondForceKernel : public CalcHarmonicBondForceKernel {
253
public:
254
    ReferenceCalcHarmonicBondForceKernel(std::string name, const Platform& platform) : CalcHarmonicBondForceKernel(name, platform) {
255
    }
256
    ~ReferenceCalcHarmonicBondForceKernel();
257
    /**
258
     * Initialize the kernel.
259
     * 
260
     * @param system     the System this kernel will be applied to
261
262
263
264
     * @param force      the HarmonicBondForce this kernel will be used for
     */
    void initialize(const System& system, const HarmonicBondForce& force);
    /**
265
266
267
268
269
270
     * 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
271
     */
272
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
273
274
275
276
277
278
279
    /**
     * 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);
280
281
282
283
private:
    int numBonds;
    int **bondIndexArray;
    RealOpenMM **bondParamArray;
284
    bool usePeriodic;
285
286
};

287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
/**
 * 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);
    /**
303
     * Execute the kernel to calculate the forces and/or energy.
304
     *
305
306
307
308
     * @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
309
     */
310
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
311
312
313
314
315
316
317
    /**
     * 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);
318
319
320
321
private:
    int numBonds;
    int **bondIndexArray;
    RealOpenMM **bondParamArray;
322
    Lepton::CompiledExpression energyExpression, forceExpression;
323
    std::vector<std::string> parameterNames, globalParameterNames;
324
    bool usePeriodic;
325
326
};

327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
/**
 * 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);
    /**
343
344
345
346
347
348
     * 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
349
     */
350
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
351
352
353
354
355
356
357
    /**
     * 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);
358
359
360
361
private:
    int numAngles;
    int **angleIndexArray;
    RealOpenMM **angleParamArray;
362
    bool usePeriodic;
363
364
};

365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
/**
 * 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);
    /**
381
     * Execute the kernel to calculate the forces and/or energy.
382
     *
383
384
385
386
     * @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
387
     */
388
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
389
390
391
392
393
394
395
    /**
     * 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);
396
397
398
399
private:
    int numAngles;
    int **angleIndexArray;
    RealOpenMM **angleParamArray;
400
    Lepton::CompiledExpression energyExpression, forceExpression;
401
    std::vector<std::string> parameterNames, globalParameterNames;
402
    bool usePeriodic;
403
404
};

405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
/**
 * 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);
    /**
421
422
423
424
425
426
     * 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
427
     */
428
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
429
430
431
432
433
434
435
    /**
     * 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);
436
437
438
439
private:
    int numTorsions;
    int **torsionIndexArray;
    RealOpenMM **torsionParamArray;
440
    bool usePeriodic;
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
};

/**
 * 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);
    /**
459
460
461
462
463
464
     * 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
465
     */
466
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
467
468
469
470
471
472
473
    /**
     * 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);
474
475
476
477
private:
    int numTorsions;
    int **torsionIndexArray;
    RealOpenMM **torsionParamArray;
478
    bool usePeriodic;
479
480
};

481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
/**
 * 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);
    /**
496
     * Execute the kernel to calculate the forces and/or energy.
497
     *
498
499
500
501
     * @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
502
     */
503
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
504
505
506
507
508
509
510
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CMAPTorsionForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
511
512
513
514
private:
    std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
    std::vector<int> torsionMaps;
    std::vector<std::vector<int> > torsionIndices;
515
    bool usePeriodic;
516
517
};

518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
/**
 * 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);
    /**
534
     * Execute the kernel to calculate the forces and/or energy.
535
     *
536
537
538
539
     * @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
540
     */
541
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
542
543
544
545
546
547
548
    /**
     * 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);
549
550
551
552
private:
    int numTorsions;
    int **torsionIndexArray;
    RealOpenMM **torsionParamArray;
553
    Lepton::CompiledExpression energyExpression, forceExpression;
554
    std::vector<std::string> parameterNames, globalParameterNames;
555
    bool usePeriodic;
556
557
};

558
559
560
561
562
563
564
565
566
567
568
569
570
/**
 * 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
571
     */
572
    void initialize(const System& system, const NonbondedForce& force);
573
    /**
574
575
576
577
578
     * 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
579
     * @param includeReciprocal  true if reciprocal space interactions should be included
580
     * @return the potential energy due to the force
581
     */
582
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal);
583
584
585
586
587
588
589
    /**
     * 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);
590
591
592
593
594
595
596
597
598
    /**
     * Get the parameters being used for PME.
     * 
     * @param alpha   the separation parameter
     * @param nx      the number of grid points along the X axis
     * @param ny      the number of grid points along the Y axis
     * @param nz      the number of grid points along the Z axis
     */
    void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
599
private:
Peter Eastman's avatar
Peter Eastman committed
600
    int numParticles, num14;
601
    int **bonded14IndexArray;
Peter Eastman's avatar
Peter Eastman committed
602
    RealOpenMM **particleParamArray, **bonded14ParamArray;
603
    RealOpenMM nonbondedCutoff, switchingDistance, rfDielectric, ewaldAlpha, dispersionCoefficient;
604
    int kmax[3], gridSize[3];
605
    bool useSwitchingFunction;
606
607
608
    std::vector<std::set<int> > exclusions;
    NonbondedMethod nonbondedMethod;
    NeighborList* neighborList;
609
610
};

611
612
613
614
615
/**
 * This kernel is invoked by CustomNonbondedForce to calculate the forces acting on the system.
 */
class ReferenceCalcCustomNonbondedForceKernel : public CalcCustomNonbondedForceKernel {
public:
616
    ReferenceCalcCustomNonbondedForceKernel(std::string name, const Platform& platform) : CalcCustomNonbondedForceKernel(name, platform), forceCopy(NULL) {
617
618
619
620
621
622
623
624
625
626
    }
    ~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);
    /**
627
     * Execute the kernel to calculate the forces and/or energy.
628
     *
629
630
631
632
     * @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
633
     */
634
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
635
636
637
638
639
640
641
    /**
     * 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);
642
private:
643
644
    int numParticles;
    RealOpenMM **particleParamArray;
645
646
    RealOpenMM nonbondedCutoff, switchingDistance, periodicBoxSize[3], longRangeCoefficient;
    bool useSwitchingFunction, hasInitializedLongRangeCorrection;
647
648
    CustomNonbondedForce* forceCopy;
    std::map<std::string, double> globalParamValues;
649
    std::vector<std::set<int> > exclusions;
650
    Lepton::CompiledExpression energyExpression, forceExpression;
651
    std::vector<std::string> parameterNames, globalParameterNames;
652
    std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
653
654
655
656
    NonbondedMethod nonbondedMethod;
    NeighborList* neighborList;
};

657
/**
658
 * This kernel is invoked by GBSAOBCForce to calculate the forces acting on the system.
659
 */
660
class ReferenceCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
661
public:
662
    ReferenceCalcGBSAOBCForceKernel(std::string name, const Platform& platform) : CalcGBSAOBCForceKernel(name, platform) {
663
    }
664
    ~ReferenceCalcGBSAOBCForceKernel();
665
    /**
666
     * Initialize the kernel.
667
     * 
668
     * @param system     the System this kernel will be applied to
669
     * @param force      the GBSAOBCForce this kernel will be used for
670
     */
671
    void initialize(const System& system, const GBSAOBCForce& force);
672
    /**
673
674
675
676
677
678
     * 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
679
     */
680
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
681
682
683
684
685
686
687
    /**
     * 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);
688
private:
689
    ReferenceObc* obc;
690
    std::vector<RealOpenMM> charges;
691
    bool isPeriodic;
692
693
};

694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
/**
 * 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);
    /**
710
     * Execute the kernel to calculate the forces and/or energy.
711
     *
712
713
714
715
     * @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
716
     */
717
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
718
719
720
721
722
723
724
    /**
     * 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);
725
726
private:
    int numParticles;
727
    bool isPeriodic;
728
    RealOpenMM **particleParamArray;
729
    RealOpenMM nonbondedCutoff;
730
731
732
    std::vector<std::set<int> > exclusions;
    std::vector<std::string> particleParameterNames, globalParameterNames, valueNames;
    std::vector<Lepton::ExpressionProgram> valueExpressions;
733
    std::vector<std::vector<Lepton::ExpressionProgram> > valueDerivExpressions;
734
    std::vector<std::vector<Lepton::ExpressionProgram> > valueGradientExpressions;
735
736
737
    std::vector<OpenMM::CustomGBForce::ComputationType> valueTypes;
    std::vector<Lepton::ExpressionProgram> energyExpressions;
    std::vector<std::vector<Lepton::ExpressionProgram> > energyDerivExpressions;
738
    std::vector<std::vector<Lepton::ExpressionProgram> > energyGradientExpressions;
739
740
741
742
743
    std::vector<OpenMM::CustomGBForce::ComputationType> energyTypes;
    NonbondedMethod nonbondedMethod;
    NeighborList* neighborList;
};

744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
/**
 * 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);
    /**
760
     * Execute the kernel to calculate the forces and/or energy.
761
     *
762
763
764
765
     * @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
766
     */
767
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
768
769
770
771
772
773
774
    /**
     * 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);
775
private:
776
    class PeriodicDistanceFunction;
777
778
779
    int numParticles;
    std::vector<int> particles;
    RealOpenMM **particleParamArray;
780
    Lepton::CompiledExpression energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
781
    std::vector<std::string> parameterNames, globalParameterNames;
782
783
784
785
786
787
788
789
790
791
792
    RealVec* boxVectors;
};

class ReferenceCalcCustomExternalForceKernel::PeriodicDistanceFunction : public Lepton::CustomFunction {
public:
    RealVec** boxVectorHandle;
    PeriodicDistanceFunction(RealVec** boxVectorHandle);
    int getNumArguments() const;
    double evaluate(const double* arguments) const;
    double evaluateDerivative(const double* arguments, const int* derivOrder) const;
    Lepton::CustomFunction* clone() const;
793
794
};

795
796
797
798
799
/**
 * This kernel is invoked by CustomHbondForce to calculate the forces acting on the system.
 */
class ReferenceCalcCustomHbondForceKernel : public CalcCustomHbondForceKernel {
public:
800
    ReferenceCalcCustomHbondForceKernel(std::string name, const Platform& platform) : CalcCustomHbondForceKernel(name, platform), ixn(NULL) {
801
802
803
804
805
806
807
808
809
810
    }
    ~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);
    /**
811
     * Execute the kernel to calculate the forces and/or energy.
812
     *
813
814
815
816
     * @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
817
     */
818
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
819
820
821
822
823
824
825
    /**
     * 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);
826
827
private:
    int numDonors, numAcceptors, numParticles;
828
    bool isPeriodic;
829
    RealOpenMM **donorParamArray, **acceptorParamArray;
830
    RealOpenMM nonbondedCutoff;
831
    ReferenceCustomHbondIxn* ixn;
832
    std::vector<std::set<int> > exclusions;
833
    std::vector<std::string> globalParameterNames;
834
835
};

836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
/**
 * This kernel is invoked by CustomCentroidBondForce to calculate the forces acting on the system.
 */
class ReferenceCalcCustomCentroidBondForceKernel : public CalcCustomCentroidBondForceKernel {
public:
    ReferenceCalcCustomCentroidBondForceKernel(std::string name, const Platform& platform) : CalcCustomCentroidBondForceKernel(name, platform), ixn(NULL) {
    }
    ~ReferenceCalcCustomCentroidBondForceKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CustomCentroidBondForce this kernel will be used for
     */
    void initialize(const System& system, const CustomCentroidBondForce& 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);
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CustomCentroidBondForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force);
private:
    int numBonds, numParticles;
    RealOpenMM **bondParamArray;
    ReferenceCustomCentroidBondIxn* ixn;
    std::vector<std::string> globalParameterNames;
872
    bool usePeriodic;
873
874
};

875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
/**
 * 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);
899
900
901
902
903
904
905
    /**
     * 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);
906
private:
907
    int numBonds;
908
909
910
    RealOpenMM **bondParamArray;
    ReferenceCustomCompoundBondIxn* ixn;
    std::vector<std::string> globalParameterNames;
911
    bool usePeriodic;
912
913
};

914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
/**
 * This kernel is invoked by CustomManyParticleForce to calculate the forces acting on the system and the energy of the system.
 */
class ReferenceCalcCustomManyParticleForceKernel : public CalcCustomManyParticleForceKernel {
public:
    ReferenceCalcCustomManyParticleForceKernel(std::string name, const Platform& platform) : CalcCustomManyParticleForceKernel(name, platform), ixn(NULL) {
    }
    ~ReferenceCalcCustomManyParticleForceKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the CustomManyParticleForce this kernel will be used for
     */
    void initialize(const System& system, const CustomManyParticleForce& 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);
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the CustomManyParticleForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const CustomManyParticleForce& force);
private:
    int numParticles;
    RealOpenMM cutoffDistance;
    RealOpenMM **particleParamArray;
    ReferenceCustomManyParticleIxn* ixn;
    std::vector<std::string> globalParameterNames;
    NonbondedMethod nonbondedMethod;
};

954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
/**
 * This kernel is invoked by GayBerneForce to calculate the forces acting on the system.
 */
class ReferenceCalcGayBerneForceKernel : public CalcGayBerneForceKernel {
public:
    ReferenceCalcGayBerneForceKernel(std::string name, const Platform& platform) : CalcGayBerneForceKernel(name, platform), ixn(NULL) {
    }
    ~ReferenceCalcGayBerneForceKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param force      the GayBerneForce this kernel will be used for
     */
    void initialize(const System& system, const GayBerneForce& 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
     * @return the potential energy due to the force
     */
    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
    /**
     * Copy changed parameters over to a context.
     *
     * @param context    the context to copy parameters to
     * @param force      the GayBerneForce to copy the parameters from
     */
    void copyParametersToContext(ContextImpl& context, const GayBerneForce& force);
private:
    ReferenceGayBerneForce* ixn;
};

988
989
990
991
992
/**
 * This kernel is invoked by VerletIntegrator to take one time step.
 */
class ReferenceIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
public:
993
    ReferenceIntegrateVerletStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVerletStepKernel(name, platform),
994
        data(data), dynamics(0) {
995
    }
996
    ~ReferenceIntegrateVerletStepKernel();
997
    /**
998
     * Initialize the kernel.
999
     * 
1000
1001
     * @param system     the System this kernel will be applied to
     * @param integrator the VerletIntegrator this kernel will be used for
1002
     */
1003
    void initialize(const System& system, const VerletIntegrator& integrator);
1004
1005
1006
    /**
     * Execute the kernel.
     * 
1007
1008
     * @param context    the context in which to execute this kernel
     * @param integrator the VerletIntegrator this kernel is being used for
1009
     */
1010
    void execute(ContextImpl& context, const VerletIntegrator& integrator);
1011
1012
1013
1014
1015
1016
1017
    /**
     * 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);
1018
private:
1019
    ReferencePlatform::PlatformData& data;
1020
    ReferenceVerletDynamics* dynamics;
1021
    std::vector<RealOpenMM> masses;
1022
    double prevStepSize;
1023
1024
1025
1026
1027
1028
1029
};

/**
 * This kernel is invoked by LangevinIntegrator to take one time step.
 */
class ReferenceIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
public:
1030
    ReferenceIntegrateLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateLangevinStepKernel(name, platform),
1031
        data(data), dynamics(0) {
1032
    }
1033
    ~ReferenceIntegrateLangevinStepKernel();
1034
    /**
Peter Eastman's avatar
Peter Eastman committed
1035
     * Initialize the kernel, setting up the particle masses.
1036
     * 
1037
1038
     * @param system     the System this kernel will be applied to
     * @param integrator the LangevinIntegrator this kernel will be used for
1039
     */
1040
    void initialize(const System& system, const LangevinIntegrator& integrator);
1041
1042
1043
    /**
     * Execute the kernel.
     * 
1044
1045
     * @param context    the context in which to execute this kernel
     * @param integrator the LangevinIntegrator this kernel is being used for
1046
     */
1047
    void execute(ContextImpl& context, const LangevinIntegrator& integrator);
1048
1049
1050
1051
1052
1053
1054
    /**
     * 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);
1055
private:
1056
    ReferencePlatform::PlatformData& data;
1057
    ReferenceStochasticDynamics* dynamics;
1058
    std::vector<RealOpenMM> masses;
1059
    double prevTemp, prevFriction, prevStepSize;
1060
1061
1062
1063
1064
1065
1066
};

/**
 * This kernel is invoked by BrownianIntegrator to take one time step.
 */
class ReferenceIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
public:
1067
    ReferenceIntegrateBrownianStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateBrownianStepKernel(name, platform),
1068
        data(data), dynamics(0) {
1069
    }
1070
    ~ReferenceIntegrateBrownianStepKernel();
1071
    /**
1072
     * Initialize the kernel.
1073
     * 
1074
1075
     * @param system     the System this kernel will be applied to
     * @param integrator the BrownianIntegrator this kernel will be used for
1076
     */
1077
    void initialize(const System& system, const BrownianIntegrator& integrator);
1078
1079
1080
    /**
     * Execute the kernel.
     * 
1081
1082
     * @param context    the context in which to execute this kernel
     * @param integrator the BrownianIntegrator this kernel is being used for
1083
     */
1084
    void execute(ContextImpl& context, const BrownianIntegrator& integrator);
1085
1086
1087
1088
1089
1090
1091
    /**
     * 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);
1092
private:
1093
    ReferencePlatform::PlatformData& data;
1094
    ReferenceBrownianDynamics* dynamics;
1095
    std::vector<RealOpenMM> masses;
1096
    double prevTemp, prevFriction, prevStepSize;
1097
1098
};

1099
1100
1101
1102
1103
1104
/**
 * 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),
1105
        data(data), dynamics(0) {
1106
1107
1108
1109
1110
1111
    }
    ~ReferenceIntegrateVariableLangevinStepKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
1112
     * @param integrator the VariableLangevinIntegrator this kernel will be used for
1113
1114
1115
1116
1117
1118
     */
    void initialize(const System& system, const VariableLangevinIntegrator& integrator);
    /**
     * Execute the kernel.
     *
     * @param context    the context in which to execute this kernel
1119
     * @param integrator the VariableLangevinIntegrator this kernel is being used for
1120
     * @param maxTime    the maximum time beyond which the simulation should not be advanced
1121
     * @return the size of the step that was taken
1122
     */
1123
    double execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime);
1124
1125
1126
1127
1128
1129
1130
    /**
     * 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);
1131
1132
1133
private:
    ReferencePlatform::PlatformData& data;
    ReferenceVariableStochasticDynamics* dynamics;
1134
    std::vector<RealOpenMM> masses;
1135
1136
1137
    double prevTemp, prevFriction, prevErrorTol;
};

1138
1139
1140
1141
1142
1143
/**
 * 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),
1144
        data(data), dynamics(0) {
1145
1146
1147
1148
1149
1150
    }
    ~ReferenceIntegrateVariableVerletStepKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
1151
     * @param integrator the VariableVerletIntegrator this kernel will be used for
1152
1153
1154
1155
1156
1157
     */
    void initialize(const System& system, const VariableVerletIntegrator& integrator);
    /**
     * Execute the kernel.
     *
     * @param context    the context in which to execute this kernel
1158
     * @param integrator the VariableVerletIntegrator this kernel is being used for
1159
     * @param maxTime    the maximum time beyond which the simulation should not be advanced
1160
     * @return the size of the step that was taken
1161
     */
1162
    double execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime);
1163
1164
1165
1166
1167
1168
1169
    /**
     * 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);
1170
1171
1172
private:
    ReferencePlatform::PlatformData& data;
    ReferenceVariableVerletDynamics* dynamics;
1173
    std::vector<RealOpenMM> masses;
1174
    double prevErrorTol;
1175
1176
};

1177
1178
1179
1180
1181
1182
/**
 * 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),
1183
        data(data), dynamics(0) {
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
    }
    ~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);
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
    /**
     * 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);
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
    /**
     * 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; 
};

1252
/**
Peter Eastman's avatar
Peter Eastman committed
1253
 * This kernel is invoked by AndersenThermostat at the start of each time step to adjust the particle velocities.
1254
1255
1256
 */
class ReferenceApplyAndersenThermostatKernel : public ApplyAndersenThermostatKernel {
public:
1257
    ReferenceApplyAndersenThermostatKernel(std::string name, const Platform& platform) : ApplyAndersenThermostatKernel(name, platform), thermostat(0) {
1258
    }
1259
    ~ReferenceApplyAndersenThermostatKernel();
1260
    /**
1261
     * Initialize the kernel.
1262
     * 
1263
1264
     * @param system     the System this kernel will be applied to
     * @param thermostat the AndersenThermostat this kernel will be used for
1265
     */
1266
    void initialize(const System& system, const AndersenThermostat& thermostat);
1267
1268
1269
    /**
     * Execute the kernel.
     * 
1270
     * @param context    the context in which to execute this kernel
1271
     */
1272
    void execute(ContextImpl& context);
1273
1274
private:
    ReferenceAndersenThermostat* thermostat;
1275
    std::vector<std::vector<int> > particleGroups;
1276
    std::vector<RealOpenMM> masses;
1277
1278
};

1279
1280
1281
1282
1283
/**
 * This kernel is invoked by MonteCarloBarostat to adjust the periodic box volume
 */
class ReferenceApplyMonteCarloBarostatKernel : public ApplyMonteCarloBarostatKernel {
public:
1284
    ReferenceApplyMonteCarloBarostatKernel(std::string name, const Platform& platform) : ApplyMonteCarloBarostatKernel(name, platform), barostat(NULL) {
1285
1286
1287
1288
1289
1290
1291
1292
    }
    ~ReferenceApplyMonteCarloBarostatKernel();
    /**
     * Initialize the kernel.
     *
     * @param system     the System this kernel will be applied to
     * @param barostat   the MonteCarloBarostat this kernel will be used for
     */
1293
    void initialize(const System& system, const Force& barostat);
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
    /**
     * 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
     */
1306
    void scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ);
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
    /**
     * 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;
};

1318
1319
1320
1321
1322
/**
 * This kernel is invoked to remove center of mass motion from the system.
 */
class ReferenceRemoveCMMotionKernel : public RemoveCMMotionKernel {
public:
1323
    ReferenceRemoveCMMotionKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : RemoveCMMotionKernel(name, platform), data(data) {
1324
1325
    }
    /**
Peter Eastman's avatar
Peter Eastman committed
1326
     * Initialize the kernel, setting up the particle masses.
1327
     * 
1328
1329
     * @param system     the System this kernel will be applied to
     * @param force      the CMMotionRemover this kernel will be used for
1330
     */
1331
    void initialize(const System& system, const CMMotionRemover& force);
1332
1333
1334
    /**
     * Execute the kernel.
     * 
1335
     * @param context    the context in which to execute this kernel
1336
     */
1337
    void execute(ContextImpl& context);
1338
private:
1339
    ReferencePlatform::PlatformData& data;
1340
    std::vector<double> masses;
1341
    int frequency;
1342
1343
};

1344
1345
1346
} // namespace OpenMM

#endif /*OPENMM_REFERENCEKERNELS_H_*/