OpenCLKernels.cpp 378 KB
Newer Older
1
2
3
4
5
6
7
8
/* -------------------------------------------------------------------------- *
 *                                   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.               *
 *                                                                            *
9
 * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
 * This program is free software: you can redistribute it and/or modify       *
 * it under the terms of the GNU Lesser General Public License as published   *
 * by the Free Software Foundation, either version 3 of the License, or       *
 * (at your option) any later version.                                        *
 *                                                                            *
 * This program is distributed in the hope that it will be useful,            *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
 * GNU Lesser General Public License for more details.                        *
 *                                                                            *
 * You should have received a copy of the GNU Lesser General Public License   *
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
 * -------------------------------------------------------------------------- */

#include "OpenCLKernels.h"
28
#include "OpenCLForceInfo.h"
29
30
#include "openmm/LangevinIntegrator.h"
#include "openmm/Context.h"
31
#include "openmm/internal/AndersenThermostatImpl.h"
32
#include "openmm/internal/CMAPTorsionForceImpl.h"
33
#include "openmm/internal/ContextImpl.h"
34
#include "openmm/internal/CustomCentroidBondForceImpl.h"
35
#include "openmm/internal/CustomCompoundBondForceImpl.h"
36
#include "openmm/internal/CustomHbondForceImpl.h"
37
#include "openmm/internal/CustomManyParticleForceImpl.h"
38
#include "openmm/internal/CustomNonbondedForceImpl.h"
39
#include "openmm/internal/NonbondedForceImpl.h"
40
#include "openmm/internal/OSRngSeed.h"
Peter Eastman's avatar
Peter Eastman committed
41
#include "OpenCLBondedUtilities.h"
42
#include "OpenCLExpressionUtilities.h"
43
#include "OpenCLIntegrationUtilities.h"
44
#include "OpenCLNonbondedUtilities.h"
45
#include "OpenCLKernelSources.h"
46
#include "lepton/ExpressionTreeNode.h"
47
#include "lepton/Operation.h"
48
49
#include "lepton/Parser.h"
#include "lepton/ParsedExpression.h"
50
51
#include "SimTKOpenMMRealType.h"
#include "SimTKOpenMMUtilities.h"
52
#include <algorithm>
53
#include <cmath>
54
#include <set>
55
56
57

using namespace OpenMM;
using namespace std;
58
59
using Lepton::ExpressionTreeNode;
using Lepton::Operation;
60

61
62
63
64
65
66
67
static void setPosqCorrectionArg(OpenCLContext& cl, cl::Kernel& kernel, int index) {
    if (cl.getUseMixedPrecision())
        kernel.setArg<cl::Buffer>(index, cl.getPosqCorrection().getDeviceBuffer());
    else
        kernel.setArg<void*>(index, NULL);
}

68
69
70
71
72
73
74
static void setPeriodicBoxSizeArg(OpenCLContext& cl, cl::Kernel& kernel, int index) {
    if (cl.getUseDoublePrecision())
        kernel.setArg<mm_double4>(index, cl.getPeriodicBoxSizeDouble());
    else
        kernel.setArg<mm_float4>(index, cl.getPeriodicBoxSize());
}

75
static void setPeriodicBoxArgs(OpenCLContext& cl, cl::Kernel& kernel, int index) {
76
    if (cl.getUseDoublePrecision()) {
77
78
        kernel.setArg<mm_double4>(index++, cl.getPeriodicBoxSizeDouble());
        kernel.setArg<mm_double4>(index++, cl.getInvPeriodicBoxSizeDouble());
79
80
81
82
83
        kernel.setArg<mm_double4>(index++, cl.getPeriodicBoxVecXDouble());
        kernel.setArg<mm_double4>(index++, cl.getPeriodicBoxVecYDouble());
        kernel.setArg<mm_double4>(index, cl.getPeriodicBoxVecZDouble());
    }
    else {
84
85
        kernel.setArg<mm_float4>(index++, cl.getPeriodicBoxSize());
        kernel.setArg<mm_float4>(index++, cl.getInvPeriodicBoxSize());
86
87
88
89
        kernel.setArg<mm_float4>(index++, cl.getPeriodicBoxVecX());
        kernel.setArg<mm_float4>(index++, cl.getPeriodicBoxVecY());
        kernel.setArg<mm_float4>(index, cl.getPeriodicBoxVecZ());
    }
90
91
}

92
93
94
95
96
97
98
static bool isZeroExpression(const Lepton::ParsedExpression& expression) {
    const Lepton::Operation& op = expression.getRootNode().getOperation();
    if (op.getId() != Lepton::Operation::CONSTANT)
        return false;
    return (dynamic_cast<const Lepton::Operation::Constant&>(op).getValue() == 0.0);
}

99
100
101
102
103
104
105
106
107
108
109
110
111
112
static bool usesVariable(const Lepton::ExpressionTreeNode& node, const string& variable) {
    const Lepton::Operation& op = node.getOperation();
    if (op.getId() == Lepton::Operation::VARIABLE && op.getName() == variable)
        return true;
    for (int i = 0; i < (int) node.getChildren().size(); i++)
        if (usesVariable(node.getChildren()[i], variable))
            return true;
    return false;
}

static bool usesVariable(const Lepton::ParsedExpression& expression, const string& variable) {
    return usesVariable(expression.getRootNode(), variable);
}

113
114
115
116
static pair<ExpressionTreeNode, string> makeVariable(const string& name, const string& value) {
    return make_pair(ExpressionTreeNode(new Operation::Variable(name)), value);
}

117
void OpenCLCalcForcesAndEnergyKernel::initialize(const System& system) {
118
119
}

120
void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
121
    cl.setForcesValid(true);
122
123
124
    cl.clearAutoclearBuffers();
    for (vector<OpenCLContext::ForcePreComputation*>::iterator iter = cl.getPreComputations().begin(); iter != cl.getPreComputations().end(); ++iter)
        (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
125
    OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
126
    cl.setComputeForceCount(cl.getComputeForceCount()+1);
127
    nb.prepareInteractions(groups);
128
129
130
    map<string, double>& derivs = cl.getEnergyParamDerivWorkspace();
    for (map<string, double>::const_iterator iter = context.getParameters().begin(); iter != context.getParameters().end(); ++iter)
        derivs[iter->first] = 0;
131
132
}

133
double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups, bool& valid) {
134
    cl.getBondedUtilities().computeInteractions(groups);
135
    cl.getNonbondedUtilities().computeInteractions(groups, includeForces, includeEnergy);
136
137
138
    double sum = 0.0;
    for (vector<OpenCLContext::ForcePostComputation*>::iterator iter = cl.getPostComputations().begin(); iter != cl.getPostComputations().end(); ++iter)
        sum += (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
139
    cl.reduceForces();
140
    cl.getIntegrationUtilities().distributeForcesFromVirtualSites();
141
    if (includeEnergy) {
142
        OpenCLArray& energyArray = cl.getEnergyBuffer();
143
        if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
144
145
146
147
148
149
150
151
152
153
154
            double* energy = (double*) cl.getPinnedBuffer();
            energyArray.download(energy);
            for (int i = 0; i < energyArray.getSize(); i++)
                sum += energy[i];
        }
        else {
            float* energy = (float*) cl.getPinnedBuffer();
            energyArray.download(energy);
            for (int i = 0; i < energyArray.getSize(); i++)
                sum += energy[i];
        }
155
    }
156
157
    if (!cl.getForcesValid())
        valid = false;
158
    return sum;
159
160
}

161
void OpenCLUpdateStateDataKernel::initialize(const System& system) {
162
163
}

164
double OpenCLUpdateStateDataKernel::getTime(const ContextImpl& context) const {
165
    return cl.getTime();
166
167
}

168
void OpenCLUpdateStateDataKernel::setTime(ContextImpl& context, double time) {
169
170
171
    vector<OpenCLContext*>& contexts = cl.getPlatformData().contexts;
    for (int i = 0; i < (int) contexts.size(); i++)
        contexts[i]->setTime(time);
172
173
}

174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
class OpenCLUpdateStateDataKernel::GetPositionsTask : public ThreadPool::Task {
public:
    GetPositionsTask(OpenCLContext& cl, vector<Vec3>& positions, vector<mm_float4>& posCorrection) : cl(cl), positions(positions), posCorrection(posCorrection) {
    }
    void execute(ThreadPool& threads, int threadIndex) {
        // Compute the position of each particle to return to the user.  This is done in parallel for speed.
        
        const vector<int>& order = cl.getAtomIndex();
        int numParticles = cl.getNumAtoms();
        Vec3 boxVectors[3];
        cl.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
        int numThreads = threads.getNumThreads();
        int start = threadIndex*numParticles/numThreads;
        int end = (threadIndex+1)*numParticles/numThreads;
        if (cl.getUseDoublePrecision()) {
            mm_double4* posq = (mm_double4*) cl.getPinnedBuffer();
            for (int i = start; i < end; ++i) {
                mm_double4 pos = posq[i];
                mm_int4 offset = cl.getPosCellOffsets()[i];
                positions[order[i]] = Vec3(pos.x, pos.y, pos.z)-boxVectors[0]*offset.x-boxVectors[1]*offset.y-boxVectors[2]*offset.z;
            }
        }
        else if (cl.getUseMixedPrecision()) {
            mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
            for (int i = start; i < end; ++i) {
                mm_float4 pos1 = posq[i];
                mm_float4 pos2 = posCorrection[i];
                mm_int4 offset = cl.getPosCellOffsets()[i];
                positions[order[i]] = Vec3((double)pos1.x+(double)pos2.x, (double)pos1.y+(double)pos2.y, (double)pos1.z+(double)pos2.z)-boxVectors[0]*offset.x-boxVectors[1]*offset.y-boxVectors[2]*offset.z;
            }
        }
        else {
            mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
            for (int i = start; i < end; ++i) {
                mm_float4 pos = posq[i];
                mm_int4 offset = cl.getPosCellOffsets()[i];
                positions[order[i]] = Vec3(pos.x, pos.y, pos.z)-boxVectors[0]*offset.x-boxVectors[1]*offset.y-boxVectors[2]*offset.z;
            }
        }
    }
    OpenCLContext& cl;
    vector<Vec3>& positions;
    vector<mm_float4>& posCorrection;
};

Peter Eastman's avatar
Peter Eastman committed
219
void OpenCLUpdateStateDataKernel::getPositions(ContextImpl& context, vector<Vec3>& positions) {
220
221
    int numParticles = context.getSystem().getNumParticles();
    positions.resize(numParticles);
222
    vector<mm_float4> posCorrection;
223
224
225
226
227
228
    if (cl.getUseDoublePrecision()) {
        mm_double4* posq = (mm_double4*) cl.getPinnedBuffer();
        cl.getPosq().download(posq);
    }
    else if (cl.getUseMixedPrecision()) {
        mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
229
230
        cl.getPosq().download(posq, false);
        posCorrection.resize(numParticles);
231
232
233
234
235
        cl.getPosqCorrection().download(posCorrection);
    }
    else {
        mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
        cl.getPosq().download(posq);
236
    }
237
238
239
240
241
242
    
    // Filling in the output array is done in parallel for speed.
    
    GetPositionsTask task(cl, positions, posCorrection);
    cl.getPlatformData().threads.execute(task);
    cl.getPlatformData().threads.waitForThreads();
243
244
}

Peter Eastman's avatar
Peter Eastman committed
245
void OpenCLUpdateStateDataKernel::setPositions(ContextImpl& context, const vector<Vec3>& positions) {
246
    const vector<cl_int>& order = cl.getAtomIndex();
247
    int numParticles = context.getSystem().getNumParticles();
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
    if (cl.getUseDoublePrecision()) {
        mm_double4* posq = (mm_double4*) cl.getPinnedBuffer();
        cl.getPosq().download(posq);
        for (int i = 0; i < numParticles; ++i) {
            mm_double4& pos = posq[i];
            const Vec3& p = positions[order[i]];
            pos.x = p[0];
            pos.y = p[1];
            pos.z = p[2];
        }
        for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
            posq[i] = mm_double4(0.0, 0.0, 0.0, 0.0);
        cl.getPosq().upload(posq);
    }
    else {
        mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
        cl.getPosq().download(posq);
        for (int i = 0; i < numParticles; ++i) {
            mm_float4& pos = posq[i];
            const Vec3& p = positions[order[i]];
            pos.x = (cl_float) p[0];
            pos.y = (cl_float) p[1];
            pos.z = (cl_float) p[2];
        }
        for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
            posq[i] = mm_float4(0.0f, 0.0f, 0.0f, 0.0f);
        cl.getPosq().upload(posq);
    }
    if (cl.getUseMixedPrecision()) {
        mm_float4* posCorrection = (mm_float4*) cl.getPinnedBuffer();
        for (int i = 0; i < numParticles; ++i) {
            mm_float4& c = posCorrection[i];
            const Vec3& p = positions[order[i]];
            c.x = (cl_float) (p[0]-(cl_float)p[0]);
            c.y = (cl_float) (p[1]-(cl_float)p[1]);
            c.z = (cl_float) (p[2]-(cl_float)p[2]);
            c.w = 0;
        }
        for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
            posCorrection[i] = mm_float4(0.0f, 0.0f, 0.0f, 0.0f);
        cl.getPosqCorrection().upload(posCorrection);
    }
290
    for (int i = 0; i < (int) cl.getPosCellOffsets().size(); i++)
291
        cl.getPosCellOffsets()[i] = mm_int4(0, 0, 0, 0);
292
    cl.reorderAtoms();
293
294
}

Peter Eastman's avatar
Peter Eastman committed
295
void OpenCLUpdateStateDataKernel::getVelocities(ContextImpl& context, vector<Vec3>& velocities) {
296
    const vector<cl_int>& order = cl.getAtomIndex();
297
298
    int numParticles = context.getSystem().getNumParticles();
    velocities.resize(numParticles);
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        mm_double4* velm = (mm_double4*) cl.getPinnedBuffer();
        cl.getVelm().download(velm);
        for (int i = 0; i < numParticles; ++i) {
            mm_double4 vel = velm[i];
            mm_int4 offset = cl.getPosCellOffsets()[i];
            velocities[order[i]] = Vec3(vel.x, vel.y, vel.z);
        }
    }
    else {
        mm_float4* velm = (mm_float4*) cl.getPinnedBuffer();
        cl.getVelm().download(velm);
        for (int i = 0; i < numParticles; ++i) {
            mm_float4 vel = velm[i];
            mm_int4 offset = cl.getPosCellOffsets()[i];
            velocities[order[i]] = Vec3(vel.x, vel.y, vel.z);
        }
316
317
318
    }
}

Peter Eastman's avatar
Peter Eastman committed
319
void OpenCLUpdateStateDataKernel::setVelocities(ContextImpl& context, const vector<Vec3>& velocities) {
320
    const vector<cl_int>& order = cl.getAtomIndex();
321
    int numParticles = context.getSystem().getNumParticles();
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        mm_double4* velm = (mm_double4*) cl.getPinnedBuffer();
        cl.getVelm().download(velm);
        for (int i = 0; i < numParticles; ++i) {
            mm_double4& vel = velm[i];
            const Vec3& p = velocities[order[i]];
            vel.x = p[0];
            vel.y = p[1];
            vel.z = p[2];
        }
        for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
            velm[i] = mm_double4(0.0, 0.0, 0.0, 0.0);
        cl.getVelm().upload(velm);
    }
    else {
        mm_float4* velm = (mm_float4*) cl.getPinnedBuffer();
        cl.getVelm().download(velm);
        for (int i = 0; i < numParticles; ++i) {
            mm_float4& vel = velm[i];
            const Vec3& p = velocities[order[i]];
            vel.x = p[0];
            vel.y = p[1];
            vel.z = p[2];
        }
        for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
            velm[i] = mm_float4(0.0f, 0.0f, 0.0f, 0.0f);
        cl.getVelm().upload(velm);
    }
350
351
}

Peter Eastman's avatar
Peter Eastman committed
352
void OpenCLUpdateStateDataKernel::getForces(ContextImpl& context, vector<Vec3>& forces) {
353
    const vector<cl_int>& order = cl.getAtomIndex();
354
355
    int numParticles = context.getSystem().getNumParticles();
    forces.resize(numParticles);
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
    if (cl.getUseDoublePrecision()) {
        mm_double4* force = (mm_double4*) cl.getPinnedBuffer();
        cl.getForce().download(force);
        for (int i = 0; i < numParticles; ++i) {
            mm_double4 f = force[i];
            forces[order[i]] = Vec3(f.x, f.y, f.z);
        }
    }
    else {
        mm_float4* force = (mm_float4*) cl.getPinnedBuffer();
        cl.getForce().download(force);
        for (int i = 0; i < numParticles; ++i) {
            mm_float4 f = force[i];
            forces[order[i]] = Vec3(f.x, f.y, f.z);
        }
371
372
373
    }
}

374
void OpenCLUpdateStateDataKernel::getEnergyParameterDerivatives(ContextImpl& context, map<string, double>& derivs) {
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
    const vector<string>& paramDerivNames = cl.getEnergyParamDerivNames();
    int numDerivs = paramDerivNames.size();
    if (numDerivs == 0)
        return;
    derivs = cl.getEnergyParamDerivWorkspace();
    OpenCLArray& derivArray = cl.getEnergyParamDerivBuffer();
    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        vector<double> derivBuffers;
        derivArray.download(derivBuffers);
        for (int i = numDerivs; i < derivArray.getSize(); i += numDerivs)
            for (int j = 0; j < numDerivs; j++)
                derivBuffers[j] += derivBuffers[i+j];
        for (int i = 0; i < numDerivs; i++)
            derivs[paramDerivNames[i]] += derivBuffers[i];
    }
    else {
        vector<float> derivBuffers;
        derivArray.download(derivBuffers);
        for (int i = numDerivs; i < derivArray.getSize(); i += numDerivs)
            for (int j = 0; j < numDerivs; j++)
                derivBuffers[j] += derivBuffers[i+j];
        for (int i = 0; i < numDerivs; i++)
            derivs[paramDerivNames[i]] += derivBuffers[i];
    }
399
400
}

401
void OpenCLUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Vec3& a, Vec3& b, Vec3& c) const {
402
    cl.getPeriodicBoxVectors(a, b, c);
403
404
}

405
void OpenCLUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) {
406
    vector<OpenCLContext*>& contexts = cl.getPlatformData().contexts;
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421

    // If any particles have been wrapped to the first periodic box, we need to unwrap them
    // to avoid changing their positions.

    vector<Vec3> positions;
    for (int i = 0; i < (int) cl.getPosCellOffsets().size(); i++) {
        mm_int4& offset = cl.getPosCellOffsets()[i];
        if (offset.x != 0 || offset.y != 0 || offset.z != 0) {
            getPositions(context, positions);
            break;
        }
    }
    
    // Update the vectors.

422
    for (int i = 0; i < (int) contexts.size(); i++)
423
        contexts[i]->setPeriodicBoxVectors(a, b, c);
424
425
    if (positions.size() > 0)
        setPositions(context, positions);
426
427
}

Peter Eastman's avatar
Peter Eastman committed
428
void OpenCLUpdateStateDataKernel::createCheckpoint(ContextImpl& context, ostream& stream) {
429
    int version = 2;
Peter Eastman's avatar
Peter Eastman committed
430
    stream.write((char*) &version, sizeof(int));
431
432
    int precision = (cl.getUseDoublePrecision() ? 2 : cl.getUseMixedPrecision() ? 1 : 0);
    stream.write((char*) &precision, sizeof(int));
Peter Eastman's avatar
Peter Eastman committed
433
434
    double time = cl.getTime();
    stream.write((char*) &time, sizeof(double));
Peter Eastman's avatar
Peter Eastman committed
435
436
    int stepCount = cl.getStepCount();
    stream.write((char*) &stepCount, sizeof(int));
437
438
    int stepsSinceReorder = cl.getStepsSinceReorder();
    stream.write((char*) &stepsSinceReorder, sizeof(int));
439
    char* buffer = (char*) cl.getPinnedBuffer();
440
441
442
443
444
445
446
447
    cl.getPosq().download(buffer);
    stream.write(buffer, cl.getPosq().getSize()*cl.getPosq().getElementSize());
    if (cl.getUseMixedPrecision()) {
        cl.getPosqCorrection().download(buffer);
        stream.write(buffer, cl.getPosqCorrection().getSize()*cl.getPosqCorrection().getElementSize());
    }
    cl.getVelm().download(buffer);
    stream.write(buffer, cl.getVelm().getSize()*cl.getVelm().getElementSize());
448
    stream.write((char*) &cl.getAtomIndex()[0], sizeof(cl_int)*cl.getAtomIndex().size());
Peter Eastman's avatar
Peter Eastman committed
449
    stream.write((char*) &cl.getPosCellOffsets()[0], sizeof(mm_int4)*cl.getPosCellOffsets().size());
450
451
452
    Vec3 boxVectors[3];
    cl.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
    stream.write((char*) boxVectors, 3*sizeof(Vec3));
Peter Eastman's avatar
Peter Eastman committed
453
    cl.getIntegrationUtilities().createCheckpoint(stream);
Peter Eastman's avatar
Peter Eastman committed
454
    SimTKOpenMMUtilities::createCheckpoint(stream);
Peter Eastman's avatar
Peter Eastman committed
455
456
457
458
459
}

void OpenCLUpdateStateDataKernel::loadCheckpoint(ContextImpl& context, istream& stream) {
    int version;
    stream.read((char*) &version, sizeof(int));
460
    if (version != 2)
Peter Eastman's avatar
Peter Eastman committed
461
        throw OpenMMException("Checkpoint was created with a different version of OpenMM");
462
463
464
465
466
    int precision;
    stream.read((char*) &precision, sizeof(int));
    int expectedPrecision = (cl.getUseDoublePrecision() ? 2 : cl.getUseMixedPrecision() ? 1 : 0);
    if (precision != expectedPrecision)
        throw OpenMMException("Checkpoint was created with a different numeric precision");
Peter Eastman's avatar
Peter Eastman committed
467
468
    double time;
    stream.read((char*) &time, sizeof(double));
469
    int stepCount, stepsSinceReorder;
Peter Eastman's avatar
Peter Eastman committed
470
    stream.read((char*) &stepCount, sizeof(int));
471
    stream.read((char*) &stepsSinceReorder, sizeof(int));
Peter Eastman's avatar
Peter Eastman committed
472
    vector<OpenCLContext*>& contexts = cl.getPlatformData().contexts;
Peter Eastman's avatar
Peter Eastman committed
473
    for (int i = 0; i < (int) contexts.size(); i++) {
Peter Eastman's avatar
Peter Eastman committed
474
        contexts[i]->setTime(time);
Peter Eastman's avatar
Peter Eastman committed
475
        contexts[i]->setStepCount(stepCount);
476
        contexts[i]->setStepsSinceReorder(stepsSinceReorder);
Peter Eastman's avatar
Peter Eastman committed
477
    }
478
    char* buffer = (char*) cl.getPinnedBuffer();
479
    stream.read(buffer, cl.getPosq().getSize()*cl.getPosq().getElementSize());
480
    cl.getPosq().upload(buffer);
481
482
483
484
485
    if (cl.getUseMixedPrecision()) {
        stream.read(buffer, cl.getPosqCorrection().getSize()*cl.getPosqCorrection().getElementSize());
        cl.getPosqCorrection().upload(buffer);
    }
    stream.read(buffer, cl.getVelm().getSize()*cl.getVelm().getElementSize());
486
487
488
    cl.getVelm().upload(buffer);
    stream.read((char*) &cl.getAtomIndex()[0], sizeof(cl_int)*cl.getAtomIndex().size());
    cl.getAtomIndexArray().upload(cl.getAtomIndex());
Peter Eastman's avatar
Peter Eastman committed
489
    stream.read((char*) &cl.getPosCellOffsets()[0], sizeof(mm_int4)*cl.getPosCellOffsets().size());
490
491
    Vec3 boxVectors[3];
    stream.read((char*) &boxVectors, 3*sizeof(Vec3));
Peter Eastman's avatar
Peter Eastman committed
492
    for (int i = 0; i < (int) contexts.size(); i++)
493
        contexts[i]->setPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
Peter Eastman's avatar
Peter Eastman committed
494
    cl.getIntegrationUtilities().loadCheckpoint(stream);
Peter Eastman's avatar
Peter Eastman committed
495
    SimTKOpenMMUtilities::loadCheckpoint(stream);
496
    for (int i = 0; i < (int) cl.getReorderListeners().size(); i++)
Peter Eastman's avatar
Peter Eastman committed
497
        cl.getReorderListeners()[i]->execute();
Peter Eastman's avatar
Peter Eastman committed
498
499
}

500
501
502
503
void OpenCLApplyConstraintsKernel::initialize(const System& system) {
}

void OpenCLApplyConstraintsKernel::apply(ContextImpl& context, double tol) {
504
505
506
    if (!hasInitializedKernel) {
        hasInitializedKernel = true;
        map<string, string> defines;
507
        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
508
509
510
        cl::Program program = cl.createProgram(OpenCLKernelSources::constraints, defines);
        applyDeltasKernel = cl::Kernel(program, "applyPositionDeltas");
        applyDeltasKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
511
512
        setPosqCorrectionArg(cl, applyDeltasKernel, 1);
        applyDeltasKernel.setArg<cl::Buffer>(2, cl.getIntegrationUtilities().getPosDelta().getDeviceBuffer());
513
514
515
516
517
518
    }
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
    cl.clearBuffer(integration.getPosDelta());
    integration.applyConstraints(tol);
    cl.executeKernel(applyDeltasKernel, cl.getNumAtoms());
    integration.computeVirtualSites();
519
520
}

521
522
523
524
void OpenCLApplyConstraintsKernel::applyToVelocities(ContextImpl& context, double tol) {
    cl.getIntegrationUtilities().applyVelocityConstraints(tol);
}

525
526
527
528
529
530
531
void OpenCLVirtualSitesKernel::initialize(const System& system) {
}

void OpenCLVirtualSitesKernel::computePositions(ContextImpl& context) {
    cl.getIntegrationUtilities().computeVirtualSites();
}

532
class OpenCLHarmonicBondForceInfo : public OpenCLForceInfo {
533
public:
534
    OpenCLHarmonicBondForceInfo(const HarmonicBondForce& force) : OpenCLForceInfo(0), force(force) {
535
536
537
538
    }
    int getNumParticleGroups() {
        return force.getNumBonds();
    }
Peter Eastman's avatar
Peter Eastman committed
539
    void getParticlesInGroup(int index, vector<int>& particles) {
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
        int particle1, particle2;
        double length, k;
        force.getBondParameters(index, particle1, particle2, length, k);
        particles.resize(2);
        particles[0] = particle1;
        particles[1] = particle2;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2;
        double length1, length2, k1, k2;
        force.getBondParameters(group1, particle1, particle2, length1, k1);
        force.getBondParameters(group2, particle1, particle2, length2, k2);
        return (length1 == length2 && k1 == k2);
    }
private:
    const HarmonicBondForce& force;
};

558
559
560
561
562
OpenCLCalcHarmonicBondForceKernel::~OpenCLCalcHarmonicBondForceKernel() {
    if (params != NULL)
        delete params;
}

563
void OpenCLCalcHarmonicBondForceKernel::initialize(const System& system, const HarmonicBondForce& force) {
564
565
566
567
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    numBonds = endIndex-startIndex;
568
569
    if (numBonds == 0)
        return;
Peter Eastman's avatar
Peter Eastman committed
570
    vector<vector<int> > atoms(numBonds, vector<int>(2));
571
    params = OpenCLArray::create<mm_float2>(cl, numBonds, "bondParams");
572
573
574
    vector<mm_float2> paramVector(numBonds);
    for (int i = 0; i < numBonds; i++) {
        double length, k;
Peter Eastman's avatar
Peter Eastman committed
575
        force.getBondParameters(startIndex+i, atoms[i][0], atoms[i][1], length, k);
576
        paramVector[i] = mm_float2((cl_float) length, (cl_float) k);
577
578
    }
    params->upload(paramVector);
Peter Eastman's avatar
Peter Eastman committed
579
    map<string, string> replacements;
580
    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
581
    replacements["COMPUTE_FORCE"] = OpenCLKernelSources::harmonicBondForce;
Peter Eastman's avatar
Peter Eastman committed
582
    replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
583
584
    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::bondForce, replacements), force.getForceGroup());
    cl.addForce(new OpenCLHarmonicBondForceInfo(force));
585
586
}

587
double OpenCLCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
588
589
    return 0.0;
}
590

591
592
593
594
595
596
void OpenCLCalcHarmonicBondForceKernel::copyParametersToContext(ContextImpl& context, const HarmonicBondForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    if (numBonds != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of bonds has changed");
597
598
    if (numBonds == 0)
        return;
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
    
    // Record the per-bond parameters.
    
    vector<mm_float2> paramVector(numBonds);
    for (int i = 0; i < numBonds; i++) {
        int atom1, atom2;
        double length, k;
        force.getBondParameters(startIndex+i, atom1, atom2, length, k);
        paramVector[i] = mm_float2((cl_float) length, (cl_float) k);
    }
    params->upload(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

616
617
class OpenCLCustomBondForceInfo : public OpenCLForceInfo {
public:
Peter Eastman's avatar
Peter Eastman committed
618
    OpenCLCustomBondForceInfo(const CustomBondForce& force) : OpenCLForceInfo(0), force(force) {
619
620
621
622
    }
    int getNumParticleGroups() {
        return force.getNumBonds();
    }
Peter Eastman's avatar
Peter Eastman committed
623
    void getParticlesInGroup(int index, vector<int>& particles) {
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
        int particle1, particle2;
        vector<double> parameters;
        force.getBondParameters(index, particle1, particle2, parameters);
        particles.resize(2);
        particles[0] = particle1;
        particles[1] = particle2;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2;
        vector<double> parameters1, parameters2;
        force.getBondParameters(group1, particle1, particle2, parameters1);
        force.getBondParameters(group2, particle1, particle2, parameters2);
        for (int i = 0; i < (int) parameters1.size(); i++)
            if (parameters1[i] != parameters2[i])
                return false;
        return true;
    }
private:
    const CustomBondForce& force;
};

OpenCLCalcCustomBondForceKernel::~OpenCLCalcCustomBondForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
}

void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const CustomBondForce& force) {
653
654
655
656
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    numBonds = endIndex-startIndex;
657
658
    if (numBonds == 0)
        return;
659
    vector<vector<int> > atoms(numBonds, vector<int>(2));
660
661
    params = new OpenCLParameterSet(cl, force.getNumPerBondParameters(), numBonds, "customBondParams");
    vector<vector<cl_float> > paramVector(numBonds);
662
663
    for (int i = 0; i < numBonds; i++) {
        vector<double> parameters;
664
        force.getBondParameters(startIndex+i, atoms[i][0], atoms[i][1], parameters);
665
        paramVector[i].resize(parameters.size());
666
        for (int j = 0; j < (int) parameters.size(); j++)
667
            paramVector[i][j] = (cl_float) parameters[j];
668
    }
669
    params->setParameterValues(paramVector);
Peter Eastman's avatar
Peter Eastman committed
670
    cl.addForce(new OpenCLCustomBondForceInfo(force));
671
672
673
674
675
676
677
678
679
680
681
682
683

    // Record information for the expressions.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
    Lepton::ParsedExpression forceExpression = energyExpression.differentiate("r").optimize();
    map<string, Lepton::ParsedExpression> expressions;
    expressions["energy += "] = energyExpression;
684
    expressions["real dEdR = "] = forceExpression;
685
686
687
688
689
690
691

    // Create the kernels.

    map<string, string> variables;
    variables["r"] = "r";
    for (int i = 0; i < force.getNumPerBondParameters(); i++) {
        const string& name = force.getPerBondParameterName(i);
692
        variables[name] = "bondParams"+params->getParameterSuffix(i);
693
    }
694
    if (force.getNumGlobalParameters() > 0) {
695
        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customBondGlobals", CL_MEM_READ_ONLY);
696
697
698
699
        globals->upload(globalParamValues);
        string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
700
            string value = argName+"["+cl.intToString(i)+"]";
701
702
            variables[name] = value;
        }
703
    }
704
705
706
707
708
709
    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
        string paramName = force.getEnergyParameterDerivativeName(i);
        string derivVariable = cl.getBondedUtilities().addEnergyParameterDerivative(paramName);
        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
        expressions[derivVariable+" += "] = derivExpression;
    }
710
    stringstream compute;
711
712
    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
713
714
        string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
        compute<<buffer.getType()<<" bondParams"<<(i+1)<<" = "<<argName<<"[index];\n";
715
    }
peastman's avatar
peastman committed
716
717
    vector<const TabulatedFunction*> functions;
    vector<pair<string, string> > functionNames;
718
    compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
719
    map<string, string> replacements;
720
    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
721
    replacements["COMPUTE_FORCE"] = compute.str();
722
    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::bondForce, replacements), force.getForceGroup());
723
724
}

725
double OpenCLCalcCustomBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
726
727
    if (globals != NULL) {
        bool changed = false;
728
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
729
730
731
732
733
734
735
736
737
738
739
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    return 0.0;
}

740
741
742
743
744
745
void OpenCLCalcCustomBondForceKernel::copyParametersToContext(ContextImpl& context, const CustomBondForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    if (numBonds != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of bonds has changed");
746
747
    if (numBonds == 0)
        return;
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
    
    // Record the per-bond parameters.
    
    vector<vector<cl_float> > paramVector(numBonds);
    vector<double> parameters;
    for (int i = 0; i < numBonds; i++) {
        int atom1, atom2;
        force.getBondParameters(startIndex+i, atom1, atom2, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

767
class OpenCLHarmonicAngleForceInfo : public OpenCLForceInfo {
768
public:
769
    OpenCLHarmonicAngleForceInfo(const HarmonicAngleForce& force) : OpenCLForceInfo(0), force(force) {
770
771
772
773
    }
    int getNumParticleGroups() {
        return force.getNumAngles();
    }
Peter Eastman's avatar
Peter Eastman committed
774
    void getParticlesInGroup(int index, vector<int>& particles) {
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
        int particle1, particle2, particle3;
        double angle, k;
        force.getAngleParameters(index, particle1, particle2, particle3, angle, k);
        particles.resize(3);
        particles[0] = particle1;
        particles[1] = particle2;
        particles[2] = particle3;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2, particle3;
        double angle1, angle2, k1, k2;
        force.getAngleParameters(group1, particle1, particle2, particle3, angle1, k1);
        force.getAngleParameters(group2, particle1, particle2, particle3, angle2, k2);
        return (angle1 == angle2 && k1 == k2);
    }
private:
    const HarmonicAngleForce& force;
};

OpenCLCalcHarmonicAngleForceKernel::~OpenCLCalcHarmonicAngleForceKernel() {
    if (params != NULL)
        delete params;
}

void OpenCLCalcHarmonicAngleForceKernel::initialize(const System& system, const HarmonicAngleForce& force) {
800
801
802
803
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumAngles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumAngles()/numContexts;
    numAngles = endIndex-startIndex;
804
805
    if (numAngles == 0)
        return;
Peter Eastman's avatar
Peter Eastman committed
806
    vector<vector<int> > atoms(numAngles, vector<int>(3));
807
    params = OpenCLArray::create<mm_float2>(cl, numAngles, "angleParams");
808
809
810
    vector<mm_float2> paramVector(numAngles);
    for (int i = 0; i < numAngles; i++) {
        double angle, k;
Peter Eastman's avatar
Peter Eastman committed
811
        force.getAngleParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], angle, k);
812
        paramVector[i] = mm_float2((cl_float) angle, (cl_float) k);
813
814
815

    }
    params->upload(paramVector);
Peter Eastman's avatar
Peter Eastman committed
816
    map<string, string> replacements;
817
    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
818
    replacements["COMPUTE_FORCE"] = OpenCLKernelSources::harmonicAngleForce;
Peter Eastman's avatar
Peter Eastman committed
819
    replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
820
821
    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::angleForce, replacements), force.getForceGroup());
    cl.addForce(new OpenCLHarmonicAngleForceInfo(force));
822
823
}

824
double OpenCLCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
825
826
827
    return 0.0;
}

828
829
830
831
832
833
void OpenCLCalcHarmonicAngleForceKernel::copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumAngles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumAngles()/numContexts;
    if (numAngles != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of angles has changed");
834
835
    if (numAngles == 0)
        return;
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
    
    // Record the per-angle parameters.
    
    vector<mm_float2> paramVector(numAngles);
    for (int i = 0; i < numAngles; i++) {
        int atom1, atom2, atom3;
        double angle, k;
        force.getAngleParameters(startIndex+i, atom1, atom2, atom3, angle, k);
        paramVector[i] = mm_float2((cl_float) angle, (cl_float) k);
    }
    params->upload(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

853
854
class OpenCLCustomAngleForceInfo : public OpenCLForceInfo {
public:
Peter Eastman's avatar
Peter Eastman committed
855
    OpenCLCustomAngleForceInfo(const CustomAngleForce& force) : OpenCLForceInfo(0), force(force) {
856
857
858
859
    }
    int getNumParticleGroups() {
        return force.getNumAngles();
    }
Peter Eastman's avatar
Peter Eastman committed
860
    void getParticlesInGroup(int index, vector<int>& particles) {
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
        int particle1, particle2, particle3;
        vector<double> parameters;
        force.getAngleParameters(index, particle1, particle2, particle3, parameters);
        particles.resize(3);
        particles[0] = particle1;
        particles[1] = particle2;
        particles[2] = particle3;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2, particle3;
        vector<double> parameters1, parameters2;
        force.getAngleParameters(group1, particle1, particle2, particle3, parameters1);
        force.getAngleParameters(group2, particle1, particle2, particle3, parameters2);
        for (int i = 0; i < (int) parameters1.size(); i++)
            if (parameters1[i] != parameters2[i])
                return false;
        return true;
    }
private:
    const CustomAngleForce& force;
};

OpenCLCalcCustomAngleForceKernel::~OpenCLCalcCustomAngleForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
}

void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const CustomAngleForce& force) {
891
892
893
894
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumAngles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumAngles()/numContexts;
    numAngles = endIndex-startIndex;
895
896
    if (numAngles == 0)
        return;
897
    vector<vector<int> > atoms(numAngles, vector<int>(3));
898
899
900
901
    params = new OpenCLParameterSet(cl, force.getNumPerAngleParameters(), numAngles, "customAngleParams");
    vector<vector<cl_float> > paramVector(numAngles);
    for (int i = 0; i < numAngles; i++) {
        vector<double> parameters;
902
        force.getAngleParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], parameters);
903
904
905
906
907
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
Peter Eastman's avatar
Peter Eastman committed
908
    cl.addForce(new OpenCLCustomAngleForceInfo(force));
909
910
911
912
913
914
915
916
917
918
919
920
921

    // Record information for the expressions.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
    Lepton::ParsedExpression forceExpression = energyExpression.differentiate("theta").optimize();
    map<string, Lepton::ParsedExpression> expressions;
    expressions["energy += "] = energyExpression;
922
    expressions["real dEdAngle = "] = forceExpression;
923
924
925
926
927
928
929
930
931

    // Create the kernels.

    map<string, string> variables;
    variables["theta"] = "theta";
    for (int i = 0; i < force.getNumPerAngleParameters(); i++) {
        const string& name = force.getPerAngleParameterName(i);
        variables[name] = "angleParams"+params->getParameterSuffix(i);
    }
932
    if (force.getNumGlobalParameters() > 0) {
933
        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customAngleGlobals", CL_MEM_READ_ONLY);
934
935
936
937
        globals->upload(globalParamValues);
        string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
938
            string value = argName+"["+cl.intToString(i)+"]";
939
940
            variables[name] = value;
        }
941
    }
942
943
944
945
946
947
    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
        string paramName = force.getEnergyParameterDerivativeName(i);
        string derivVariable = cl.getBondedUtilities().addEnergyParameterDerivative(paramName);
        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
        expressions[derivVariable+" += "] = derivExpression;
    }
948
949
950
    stringstream compute;
    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
951
952
        string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
        compute<<buffer.getType()<<" angleParams"<<(i+1)<<" = "<<argName<<"[index];\n";
953
    }
peastman's avatar
peastman committed
954
955
    vector<const TabulatedFunction*> functions;
    vector<pair<string, string> > functionNames;
956
    compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
957
    map<string, string> replacements;
958
    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
959
    replacements["COMPUTE_FORCE"] = compute.str();
960
    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::angleForce, replacements), force.getForceGroup());
961
962
}

963
double OpenCLCalcCustomAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
964
965
966
967
968
969
970
971
972
973
974
975
976
977
    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    return 0.0;
}

978
979
980
981
982
983
void OpenCLCalcCustomAngleForceKernel::copyParametersToContext(ContextImpl& context, const CustomAngleForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumAngles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumAngles()/numContexts;
    if (numAngles != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of angles has changed");
984
985
    if (numAngles == 0)
        return;
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
    
    // Record the per-angle parameters.
    
    vector<vector<cl_float> > paramVector(numAngles);
    vector<double> parameters;
    for (int i = 0; i < numAngles; i++) {
        int atom1, atom2, atom3;
        force.getAngleParameters(startIndex+i, atom1, atom2, atom3, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

1005
1006
class OpenCLPeriodicTorsionForceInfo : public OpenCLForceInfo {
public:
Peter Eastman's avatar
Peter Eastman committed
1007
    OpenCLPeriodicTorsionForceInfo(const PeriodicTorsionForce& force) : OpenCLForceInfo(0), force(force) {
1008
1009
1010
1011
    }
    int getNumParticleGroups() {
        return force.getNumTorsions();
    }
Peter Eastman's avatar
Peter Eastman committed
1012
    void getParticlesInGroup(int index, vector<int>& particles) {
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
        int particle1, particle2, particle3, particle4, periodicity;
        double phase, k;
        force.getTorsionParameters(index, particle1, particle2, particle3, particle4, periodicity, phase, k);
        particles.resize(4);
        particles[0] = particle1;
        particles[1] = particle2;
        particles[2] = particle3;
        particles[3] = particle4;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2, particle3, particle4, periodicity1, periodicity2;
        double phase1, phase2, k1, k2;
        force.getTorsionParameters(group1, particle1, particle2, particle3, particle4, periodicity1, phase1, k1);
1026
        force.getTorsionParameters(group2, particle1, particle2, particle3, particle4, periodicity2, phase2, k2);
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
        return (periodicity1 == periodicity2 && phase1 == phase2 && k1 == k2);
    }
private:
    const PeriodicTorsionForce& force;
};

OpenCLCalcPeriodicTorsionForceKernel::~OpenCLCalcPeriodicTorsionForceKernel() {
    if (params != NULL)
        delete params;
}

void OpenCLCalcPeriodicTorsionForceKernel::initialize(const System& system, const PeriodicTorsionForce& force) {
1039
1040
1041
1042
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    numTorsions = endIndex-startIndex;
1043
1044
    if (numTorsions == 0)
        return;
Peter Eastman's avatar
Peter Eastman committed
1045
    vector<vector<int> > atoms(numTorsions, vector<int>(4));
1046
    params = OpenCLArray::create<mm_float4>(cl, numTorsions, "periodicTorsionParams");
1047
1048
    vector<mm_float4> paramVector(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
Peter Eastman's avatar
Peter Eastman committed
1049
        int periodicity;
1050
        double phase, k;
Peter Eastman's avatar
Peter Eastman committed
1051
        force.getTorsionParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], periodicity, phase, k);
1052
        paramVector[i] = mm_float4((cl_float) k, (cl_float) phase, (cl_float) periodicity, 0.0f);
1053
1054
    }
    params->upload(paramVector);
Peter Eastman's avatar
Peter Eastman committed
1055
    map<string, string> replacements;
1056
    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
1057
    replacements["COMPUTE_FORCE"] = OpenCLKernelSources::periodicTorsionForce;
Peter Eastman's avatar
Peter Eastman committed
1058
    replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float4");
1059
    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
Peter Eastman's avatar
Peter Eastman committed
1060
    cl.addForce(new OpenCLPeriodicTorsionForceInfo(force));
1061
1062
}

1063
double OpenCLCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
1064
1065
1066
    return 0.0;
}

1067
1068
1069
1070
1071
1072
void OpenCLCalcPeriodicTorsionForceKernel::copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    if (numTorsions != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of torsions has changed");
1073
1074
    if (numTorsions == 0)
        return;
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
    
    // Record the per-torsion parameters.
    
    vector<mm_float4> paramVector(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        int atom1, atom2, atom3, atom4, periodicity;
        double phase, k;
        force.getTorsionParameters(startIndex+i, atom1, atom2, atom3, atom4, periodicity, phase, k);
        paramVector[i] = mm_float4((cl_float) k, (cl_float) phase, (cl_float) periodicity, 0.0f);
    }
    params->upload(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

1092
1093
class OpenCLRBTorsionForceInfo : public OpenCLForceInfo {
public:
Peter Eastman's avatar
Peter Eastman committed
1094
    OpenCLRBTorsionForceInfo(const RBTorsionForce& force) : OpenCLForceInfo(0), force(force) {
1095
1096
1097
1098
    }
    int getNumParticleGroups() {
        return force.getNumTorsions();
    }
Peter Eastman's avatar
Peter Eastman committed
1099
    void getParticlesInGroup(int index, vector<int>& particles) {
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
        int particle1, particle2, particle3, particle4;
        double c0, c1, c2, c3, c4, c5;
        force.getTorsionParameters(index, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5);
        particles.resize(4);
        particles[0] = particle1;
        particles[1] = particle2;
        particles[2] = particle3;
        particles[3] = particle4;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2, particle3, particle4;
        double c0a, c0b, c1a, c1b, c2a, c2b, c3a, c3b, c4a, c4b, c5a, c5b;
        force.getTorsionParameters(group1, particle1, particle2, particle3, particle4, c0a, c1a, c2a, c3a, c4a, c5a);
1113
        force.getTorsionParameters(group2, particle1, particle2, particle3, particle4, c0b, c1b, c2b, c3b, c4b, c5b);
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
        return (c0a == c0b && c1a == c1b && c2a == c2b && c3a == c3b && c4a == c4b && c5a == c5b);
    }
private:
    const RBTorsionForce& force;
};

OpenCLCalcRBTorsionForceKernel::~OpenCLCalcRBTorsionForceKernel() {
    if (params != NULL)
        delete params;
}

void OpenCLCalcRBTorsionForceKernel::initialize(const System& system, const RBTorsionForce& force) {
1126
1127
1128
1129
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    numTorsions = endIndex-startIndex;
1130
1131
    if (numTorsions == 0)
        return;
Peter Eastman's avatar
Peter Eastman committed
1132
    vector<vector<int> > atoms(numTorsions, vector<int>(4));
1133
    params = OpenCLArray::create<mm_float8>(cl, numTorsions, "rbTorsionParams");
1134
1135
1136
    vector<mm_float8> paramVector(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        double c0, c1, c2, c3, c4, c5;
Peter Eastman's avatar
Peter Eastman committed
1137
        force.getTorsionParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], c0, c1, c2, c3, c4, c5);
1138
        paramVector[i] = mm_float8((cl_float) c0, (cl_float) c1, (cl_float) c2, (cl_float) c3, (cl_float) c4, (cl_float) c5, 0.0f, 0.0f);
1139
1140
1141

    }
    params->upload(paramVector);
Peter Eastman's avatar
Peter Eastman committed
1142
    map<string, string> replacements;
1143
    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
1144
    replacements["COMPUTE_FORCE"] = OpenCLKernelSources::rbTorsionForce;
Peter Eastman's avatar
Peter Eastman committed
1145
    replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float8");
1146
    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
Peter Eastman's avatar
Peter Eastman committed
1147
    cl.addForce(new OpenCLRBTorsionForceInfo(force));
1148
1149
}

1150
double OpenCLCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
1151
1152
1153
    return 0.0;
}

1154
1155
1156
1157
1158
1159
void OpenCLCalcRBTorsionForceKernel::copyParametersToContext(ContextImpl& context, const RBTorsionForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    if (numTorsions != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of torsions has changed");
1160
1161
    if (numTorsions == 0)
        return;
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
    
    // Record the per-torsion parameters.
    
    vector<mm_float8> paramVector(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        int atom1, atom2, atom3, atom4;
        double c0, c1, c2, c3, c4, c5;
        force.getTorsionParameters(startIndex+i, atom1, atom2, atom3, atom4, c0, c1, c2, c3, c4, c5);
        paramVector[i] = mm_float8((cl_float) c0, (cl_float) c1, (cl_float) c2, (cl_float) c3, (cl_float) c4, (cl_float) c5, 0.0f, 0.0f);
    }
    params->upload(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

1179
1180
class OpenCLCMAPTorsionForceInfo : public OpenCLForceInfo {
public:
Peter Eastman's avatar
Peter Eastman committed
1181
    OpenCLCMAPTorsionForceInfo(const CMAPTorsionForce& force) : OpenCLForceInfo(0), force(force) {
1182
1183
1184
1185
    }
    int getNumParticleGroups() {
        return force.getNumTorsions();
    }
Peter Eastman's avatar
Peter Eastman committed
1186
    void getParticlesInGroup(int index, vector<int>& particles) {
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
        int map, a1, a2, a3, a4, b1, b2, b3, b4;
        force.getTorsionParameters(index, map, a1, a2, a3, a4, b1, b2, b3, b4);
        particles.resize(8);
        particles[0] = a1;
        particles[1] = a2;
        particles[2] = a3;
        particles[3] = a4;
        particles[4] = b1;
        particles[5] = b2;
        particles[6] = b3;
        particles[7] = b4;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int map1, map2, a1, a2, a3, a4, b1, b2, b3, b4;
        force.getTorsionParameters(group1, map1, a1, a2, a3, a4, b1, b2, b3, b4);
        force.getTorsionParameters(group2, map2, a1, a2, a3, a4, b1, b2, b3, b4);
        return (map1 == map2);
    }
private:
    const CMAPTorsionForce& force;
};

OpenCLCalcCMAPTorsionForceKernel::~OpenCLCalcCMAPTorsionForceKernel() {
    if (coefficients != NULL)
        delete coefficients;
    if (mapPositions != NULL)
        delete mapPositions;
    if (torsionMaps != NULL)
        delete torsionMaps;
}

void OpenCLCalcCMAPTorsionForceKernel::initialize(const System& system, const CMAPTorsionForce& force) {
1219
1220
1221
1222
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    numTorsions = endIndex-startIndex;
1223
1224
1225
1226
    if (numTorsions == 0)
        return;
    int numMaps = force.getNumMaps();
    vector<mm_float4> coeffVec;
1227
    mapPositionsVec.resize(numMaps);
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
    vector<double> energy;
    vector<vector<double> > c;
    int currentPosition = 0;
    for (int i = 0; i < numMaps; i++) {
        int size;
        force.getMapParameters(i, size, energy);
        CMAPTorsionForceImpl::calcMapDerivatives(size, energy, c);
        mapPositionsVec[i] = mm_int2(currentPosition, size);
        currentPosition += 4*size*size;
        for (int j = 0; j < size*size; j++) {
1238
1239
1240
1241
            coeffVec.push_back(mm_float4((float) c[j][0], (float) c[j][1], (float) c[j][2], (float) c[j][3]));
            coeffVec.push_back(mm_float4((float) c[j][4], (float) c[j][5], (float) c[j][6], (float) c[j][7]));
            coeffVec.push_back(mm_float4((float) c[j][8], (float) c[j][9], (float) c[j][10], (float) c[j][11]));
            coeffVec.push_back(mm_float4((float) c[j][12], (float) c[j][13], (float) c[j][14], (float) c[j][15]));
1242
1243
        }
    }
1244
    vector<vector<int> > atoms(numTorsions, vector<int>(8));
1245
    vector<cl_int> torsionMapsVec(numTorsions);
1246
1247
    for (int i = 0; i < numTorsions; i++)
        force.getTorsionParameters(startIndex+i, torsionMapsVec[i], atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], atoms[i][4], atoms[i][5], atoms[i][6], atoms[i][7]);
1248
1249
1250
    coefficients = OpenCLArray::create<mm_float4>(cl, coeffVec.size(), "cmapTorsionCoefficients");
    mapPositions = OpenCLArray::create<mm_int2>(cl, numMaps, "cmapTorsionMapPositions");
    torsionMaps = OpenCLArray::create<cl_int>(cl, numTorsions, "cmapTorsionMaps");
1251
1252
1253
    coefficients->upload(coeffVec);
    mapPositions->upload(mapPositionsVec);
    torsionMaps->upload(torsionMapsVec);
1254
    map<string, string> replacements;
1255
    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
1256
1257
1258
    replacements["COEFF"] = cl.getBondedUtilities().addArgument(coefficients->getDeviceBuffer(), "float4");
    replacements["MAP_POS"] = cl.getBondedUtilities().addArgument(mapPositions->getDeviceBuffer(), "int2");
    replacements["MAPS"] = cl.getBondedUtilities().addArgument(torsionMaps->getDeviceBuffer(), "int");
1259
    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::cmapTorsionForce, replacements), force.getForceGroup());
Peter Eastman's avatar
Peter Eastman committed
1260
    cl.addForce(new OpenCLCMAPTorsionForceInfo(force));
1261
1262
}

1263
double OpenCLCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
1264
1265
1266
    return 0.0;
}

1267
void OpenCLCalcCMAPTorsionForceKernel::copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force) {
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
    int numMaps = force.getNumMaps();
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    numTorsions = endIndex-startIndex;
    if (mapPositions->getSize() != numMaps)
        throw OpenMMException("updateParametersInContext: The number of maps has changed");
    if (torsionMaps->getSize() != numTorsions)
        throw OpenMMException("updateParametersInContext: The number of CMAP torsions has changed");

    // Update the maps.

    vector<mm_float4> coeffVec;
    vector<double> energy;
    vector<vector<double> > c;
    int currentPosition = 0;
    for (int i = 0; i < numMaps; i++) {
        int size;
        force.getMapParameters(i, size, energy);
        if (size != mapPositionsVec[i].y)
            throw OpenMMException("updateParametersInContext: The size of a map has changed");
        CMAPTorsionForceImpl::calcMapDerivatives(size, energy, c);
        currentPosition += 4*size*size;
        for (int j = 0; j < size*size; j++) {
            coeffVec.push_back(mm_float4((float) c[j][0], (float) c[j][1], (float) c[j][2], (float) c[j][3]));
            coeffVec.push_back(mm_float4((float) c[j][4], (float) c[j][5], (float) c[j][6], (float) c[j][7]));
            coeffVec.push_back(mm_float4((float) c[j][8], (float) c[j][9], (float) c[j][10], (float) c[j][11]));
            coeffVec.push_back(mm_float4((float) c[j][12], (float) c[j][13], (float) c[j][14], (float) c[j][15]));
        }
    }
    coefficients->upload(coeffVec);

    // Update the indices.

    vector<int> torsionMapsVec(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        int index[8];
        force.getTorsionParameters(i, torsionMapsVec[i], index[0], index[1], index[2], index[3], index[4], index[5], index[6], index[7]);
    }
    torsionMaps->upload(torsionMapsVec);
1308
1309
}

1310
1311
class OpenCLCustomTorsionForceInfo : public OpenCLForceInfo {
public:
Peter Eastman's avatar
Peter Eastman committed
1312
    OpenCLCustomTorsionForceInfo(const CustomTorsionForce& force) : OpenCLForceInfo(0), force(force) {
1313
1314
1315
1316
    }
    int getNumParticleGroups() {
        return force.getNumTorsions();
    }
Peter Eastman's avatar
Peter Eastman committed
1317
    void getParticlesInGroup(int index, vector<int>& particles) {
1318
1319
1320
        int particle1, particle2, particle3, particle4;
        vector<double> parameters;
        force.getTorsionParameters(index, particle1, particle2, particle3, particle4, parameters);
Peter Eastman's avatar
Bug fix  
Peter Eastman committed
1321
        particles.resize(4);
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
        particles[0] = particle1;
        particles[1] = particle2;
        particles[2] = particle3;
        particles[3] = particle4;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2, particle3, particle4;
        vector<double> parameters1, parameters2;
        force.getTorsionParameters(group1, particle1, particle2, particle3, particle4, parameters1);
        force.getTorsionParameters(group2, particle1, particle2, particle3, particle4, parameters2);
        for (int i = 0; i < (int) parameters1.size(); i++)
            if (parameters1[i] != parameters2[i])
                return false;
        return true;
    }
private:
    const CustomTorsionForce& force;
};

OpenCLCalcCustomTorsionForceKernel::~OpenCLCalcCustomTorsionForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
}

void OpenCLCalcCustomTorsionForceKernel::initialize(const System& system, const CustomTorsionForce& force) {
1349
1350
1351
1352
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    numTorsions = endIndex-startIndex;
1353
1354
    if (numTorsions == 0)
        return;
1355
    vector<vector<int> > atoms(numTorsions, vector<int>(4));
1356
1357
1358
1359
    params = new OpenCLParameterSet(cl, force.getNumPerTorsionParameters(), numTorsions, "customTorsionParams");
    vector<vector<cl_float> > paramVector(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        vector<double> parameters;
1360
        force.getTorsionParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], parameters);
1361
1362
1363
1364
1365
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
Peter Eastman's avatar
Peter Eastman committed
1366
    cl.addForce(new OpenCLCustomTorsionForceInfo(force));
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379

    // Record information for the expressions.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
    Lepton::ParsedExpression forceExpression = energyExpression.differentiate("theta").optimize();
    map<string, Lepton::ParsedExpression> expressions;
    expressions["energy += "] = energyExpression;
1380
    expressions["real dEdAngle = "] = forceExpression;
1381
1382
1383
1384
1385
1386
1387
1388
1389

    // Create the kernels.

    map<string, string> variables;
    variables["theta"] = "theta";
    for (int i = 0; i < force.getNumPerTorsionParameters(); i++) {
        const string& name = force.getPerTorsionParameterName(i);
        variables[name] = "torsionParams"+params->getParameterSuffix(i);
    }
1390
    if (force.getNumGlobalParameters() > 0) {
1391
        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customTorsionGlobals", CL_MEM_READ_ONLY);
1392
1393
1394
1395
        globals->upload(globalParamValues);
        string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
1396
            string value = argName+"["+cl.intToString(i)+"]";
1397
1398
            variables[name] = value;
        }
1399
    }
1400
1401
1402
1403
1404
1405
    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
        string paramName = force.getEnergyParameterDerivativeName(i);
        string derivVariable = cl.getBondedUtilities().addEnergyParameterDerivative(paramName);
        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
        expressions[derivVariable+" += "] = derivExpression;
    }
1406
1407
1408
    stringstream compute;
    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
1409
1410
        string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
        compute<<buffer.getType()<<" torsionParams"<<(i+1)<<" = "<<argName<<"[index];\n";
1411
    }
peastman's avatar
peastman committed
1412
1413
    vector<const TabulatedFunction*> functions;
    vector<pair<string, string> > functionNames;
1414
    compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
1415
    map<string, string> replacements;
1416
    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
1417
    replacements["COMPUTE_FORCE"] = compute.str();
1418
    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
1419
1420
}

1421
double OpenCLCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    return 0.0;
}

1436
1437
1438
1439
1440
1441
void OpenCLCalcCustomTorsionForceKernel::copyParametersToContext(ContextImpl& context, const CustomTorsionForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    if (numTorsions != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of torsions has changed");
1442
1443
    if (numTorsions == 0)
        return;
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
    
    // Record the per-torsion parameters.
    
    vector<vector<cl_float> > paramVector(numTorsions);
    vector<double> parameters;
    for (int i = 0; i < numTorsions; i++) {
        int atom1, atom2, atom3, atom4;
        force.getTorsionParameters(startIndex+i, atom1, atom2, atom3, atom4, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
class OpenCLNonbondedForceInfo : public OpenCLForceInfo {
public:
    OpenCLNonbondedForceInfo(int requiredBuffers, const NonbondedForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
    }
    bool areParticlesIdentical(int particle1, int particle2) {
        double charge1, charge2, sigma1, sigma2, epsilon1, epsilon2;
        force.getParticleParameters(particle1, charge1, sigma1, epsilon1);
        force.getParticleParameters(particle2, charge2, sigma2, epsilon2);
        return (charge1 == charge2 && sigma1 == sigma2 && epsilon1 == epsilon2);
    }
    int getNumParticleGroups() {
        return force.getNumExceptions();
    }
Peter Eastman's avatar
Peter Eastman committed
1476
    void getParticlesInGroup(int index, vector<int>& particles) {
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
        int particle1, particle2;
        double chargeProd, sigma, epsilon;
        force.getExceptionParameters(index, particle1, particle2, chargeProd, sigma, epsilon);
        particles.resize(2);
        particles[0] = particle1;
        particles[1] = particle2;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2;
        double chargeProd1, chargeProd2, sigma1, sigma2, epsilon1, epsilon2;
        force.getExceptionParameters(group1, particle1, particle2, chargeProd1, sigma1, epsilon1);
        force.getExceptionParameters(group2, particle1, particle2, chargeProd2, sigma2, epsilon2);
        return (chargeProd1 == chargeProd2 && sigma1 == sigma2 && epsilon1 == epsilon2);
    }
private:
    const NonbondedForce& force;
};

1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
class OpenCLCalcNonbondedForceKernel::PmeIO : public CalcPmeReciprocalForceKernel::IO {
public:
    PmeIO(OpenCLContext& cl, cl::Kernel addForcesKernel) : cl(cl), addForcesKernel(addForcesKernel), forceTemp(NULL) {
        forceTemp = OpenCLArray::create<mm_float4>(cl, cl.getNumAtoms(), "PmeForce");
        addForcesKernel.setArg<cl::Buffer>(0, forceTemp->getDeviceBuffer());
    }
    ~PmeIO() {
        if (forceTemp != NULL)
            delete forceTemp;
    }
    float* getPosq() {
        cl.getPosq().download(posq);
        return (float*) &posq[0];
    }
    void setForce(float* force) {
        forceTemp->upload(force);
        addForcesKernel.setArg<cl::Buffer>(1, cl.getForce().getDeviceBuffer());
        cl.executeKernel(addForcesKernel, cl.getNumAtoms());
    }
private:
    OpenCLContext& cl;
    vector<mm_float4> posq;
    OpenCLArray* forceTemp;
    cl::Kernel addForcesKernel;
};

class OpenCLCalcNonbondedForceKernel::PmePreComputation : public OpenCLContext::ForcePreComputation {
public:
    PmePreComputation(OpenCLContext& cl, Kernel& pme, CalcPmeReciprocalForceKernel::IO& io) : cl(cl), pme(pme), io(io) {
    }
    void computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
peastman's avatar
peastman committed
1526
1527
        Vec3 boxVectors[3] = {Vec3(cl.getPeriodicBoxSize().x, 0, 0), Vec3(0, cl.getPeriodicBoxSize().y, 0), Vec3(0, 0, cl.getPeriodicBoxSize().z)};
        pme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, boxVectors, includeEnergy);
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
    }
private:
    OpenCLContext& cl;
    Kernel pme;
    CalcPmeReciprocalForceKernel::IO& io;
};

class OpenCLCalcNonbondedForceKernel::PmePostComputation : public OpenCLContext::ForcePostComputation {
public:
    PmePostComputation(Kernel& pme, CalcPmeReciprocalForceKernel::IO& io) : pme(pme), io(io) {
    }
    double computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
        return pme.getAs<CalcPmeReciprocalForceKernel>().finishComputation(io);
    }
private:
    Kernel pme;
    CalcPmeReciprocalForceKernel::IO& io;
};

1547
1548
class OpenCLCalcNonbondedForceKernel::SyncQueuePreComputation : public OpenCLContext::ForcePreComputation {
public:
1549
    SyncQueuePreComputation(OpenCLContext& cl, cl::CommandQueue queue, int forceGroup) : cl(cl), queue(queue), forceGroup(forceGroup) {
1550
1551
    }
    void computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
peastman's avatar
Bug fix  
peastman committed
1552
        if ((groups&(1<<forceGroup)) != 0) {
1553
            vector<cl::Event> events(1);
peastman's avatar
Bug fix  
peastman committed
1554
1555
1556
            cl.getQueue().enqueueMarker(&events[0]);
            queue.enqueueWaitForEvents(events);
        }
1557
1558
1559
1560
    }
private:
    OpenCLContext& cl;
    cl::CommandQueue queue;
peastman's avatar
Bug fix  
peastman committed
1561
    int forceGroup;
1562
1563
1564
1565
};

class OpenCLCalcNonbondedForceKernel::SyncQueuePostComputation : public OpenCLContext::ForcePostComputation {
public:
1566
1567
1568
1569
1570
1571
1572
1573
    SyncQueuePostComputation(OpenCLContext& cl, cl::Event& event, OpenCLArray& pmeEnergyBuffer, int forceGroup) : cl(cl), event(event),
            pmeEnergyBuffer(pmeEnergyBuffer), forceGroup(forceGroup) {
    }
    void setKernel(cl::Kernel kernel) {
        addEnergyKernel = kernel;
        addEnergyKernel.setArg<cl::Buffer>(0, pmeEnergyBuffer.getDeviceBuffer());
        addEnergyKernel.setArg<cl::Buffer>(1, cl.getEnergyBuffer().getDeviceBuffer());
        addEnergyKernel.setArg<cl_int>(2, pmeEnergyBuffer.getSize());
1574
1575
    }
    double computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
peastman's avatar
Bug fix  
peastman committed
1576
        if ((groups&(1<<forceGroup)) != 0) {
1577
            vector<cl::Event> events(1);
peastman's avatar
Bug fix  
peastman committed
1578
            events[0] = event;
1579
            event = cl::Event();
peastman's avatar
Bug fix  
peastman committed
1580
            cl.getQueue().enqueueWaitForEvents(events);
1581
1582
            if (includeEnergy)
                cl.executeKernel(addEnergyKernel, pmeEnergyBuffer.getSize());
peastman's avatar
Bug fix  
peastman committed
1583
        }
1584
1585
1586
1587
1588
        return 0.0;
    }
private:
    OpenCLContext& cl;
    cl::Event& event;
1589
1590
    cl::Kernel addEnergyKernel;
    OpenCLArray& pmeEnergyBuffer;
peastman's avatar
Bug fix  
peastman committed
1591
    int forceGroup;
1592
1593
};

1594
1595
1596
OpenCLCalcNonbondedForceKernel::~OpenCLCalcNonbondedForceKernel() {
    if (sigmaEpsilon != NULL)
        delete sigmaEpsilon;
1597
1598
    if (exceptionParams != NULL)
        delete exceptionParams;
1599
1600
1601
1602
    if (cosSinSums != NULL)
        delete cosSinSums;
    if (pmeGrid != NULL)
        delete pmeGrid;
Peter Eastman's avatar
Peter Eastman committed
1603
1604
    if (pmeGrid2 != NULL)
        delete pmeGrid2;
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
    if (pmeBsplineModuliX != NULL)
        delete pmeBsplineModuliX;
    if (pmeBsplineModuliY != NULL)
        delete pmeBsplineModuliY;
    if (pmeBsplineModuliZ != NULL)
        delete pmeBsplineModuliZ;
    if (pmeBsplineTheta != NULL)
        delete pmeBsplineTheta;
    if (pmeAtomRange != NULL)
        delete pmeAtomRange;
    if (pmeAtomGridIndex != NULL)
        delete pmeAtomGridIndex;
1617
1618
    if (pmeEnergyBuffer != NULL)
        delete pmeEnergyBuffer;
1619
1620
1621
1622
    if (sort != NULL)
        delete sort;
    if (fft != NULL)
        delete fft;
1623
1624
    if (pmeio != NULL)
        delete pmeio;
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
1640
1641
1642
1643
1644
}

void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const NonbondedForce& force) {

    // Identify which exceptions are 1-4 interactions.

    vector<pair<int, int> > exclusions;
    vector<int> exceptions;
    for (int i = 0; i < force.getNumExceptions(); i++) {
        int particle1, particle2;
        double chargeProd, sigma, epsilon;
        force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
        exclusions.push_back(pair<int, int>(particle1, particle2));
        if (chargeProd != 0.0 || epsilon != 0.0)
            exceptions.push_back(i);
    }

    // Initialize nonbonded interactions.

    int numParticles = force.getNumParticles();
1645
    sigmaEpsilon = OpenCLArray::create<mm_float2>(cl, cl.getPaddedNumAtoms(), "sigmaEpsilon");
1646
1647
1648
    vector<mm_float4> posqf(cl.getPaddedNumAtoms(), mm_float4(0,0,0,0));
    vector<mm_double4> posqd(cl.getPaddedNumAtoms(), mm_double4(0,0,0,0));
    vector<mm_float2> sigmaEpsilonVector(cl.getPaddedNumAtoms(), mm_float2(0,0));
1649
    vector<vector<int> > exclusionList(numParticles);
1650
    double sumSquaredCharges = 0.0;
1651
1652
    hasCoulomb = false;
    hasLJ = false;
1653
1654
1655
    for (int i = 0; i < numParticles; i++) {
        double charge, sigma, epsilon;
        force.getParticleParameters(i, charge, sigma, epsilon);
1656
1657
1658
1659
        if (cl.getUseDoublePrecision())
            posqd[i] = mm_double4(0, 0, 0, charge);
        else
            posqf[i] = mm_float4(0, 0, 0, (float) charge);
1660
        sigmaEpsilonVector[i] = mm_float2((float) (0.5*sigma), (float) (2.0*sqrt(epsilon)));
1661
        exclusionList[i].push_back(i);
1662
        sumSquaredCharges += charge*charge;
1663
1664
1665
1666
        if (charge != 0.0)
            hasCoulomb = true;
        if (epsilon != 0.0)
            hasLJ = true;
1667
1668
1669
1670
1671
    }
    for (int i = 0; i < (int) exclusions.size(); i++) {
        exclusionList[exclusions[i].first].push_back(exclusions[i].second);
        exclusionList[exclusions[i].second].push_back(exclusions[i].first);
    }
1672
1673
1674
1675
    if (cl.getUseDoublePrecision())
        cl.getPosq().upload(posqd);
    else
        cl.getPosq().upload(posqf);
1676
    sigmaEpsilon->upload(sigmaEpsilonVector);
1677
1678
1679
    nonbondedMethod = CalcNonbondedForceKernel::NonbondedMethod(force.getNonbondedMethod());
    bool useCutoff = (nonbondedMethod != NoCutoff);
    bool usePeriodic = (nonbondedMethod != NoCutoff && nonbondedMethod != CutoffNonPeriodic);
1680
    map<string, string> defines;
1681
1682
    defines["HAS_COULOMB"] = (hasCoulomb ? "1" : "0");
    defines["HAS_LENNARD_JONES"] = (hasLJ ? "1" : "0");
1683
    defines["USE_LJ_SWITCH"] = (useCutoff && force.getUseSwitchingFunction() ? "1" : "0");
1684
    if (useCutoff) {
1685
1686
        // Compute the reaction field constants.

1687
1688
        double reactionFieldK = pow(force.getCutoffDistance(), -3.0)*(force.getReactionFieldDielectric()-1.0)/(2.0*force.getReactionFieldDielectric()+1.0);
        double reactionFieldC = (1.0 / force.getCutoffDistance())*(3.0*force.getReactionFieldDielectric())/(2.0*force.getReactionFieldDielectric()+1.0);
1689
1690
        defines["REACTION_FIELD_K"] = cl.doubleToString(reactionFieldK);
        defines["REACTION_FIELD_C"] = cl.doubleToString(reactionFieldC);
1691
1692
1693
1694
1695
1696
1697
1698
1699
        
        // Compute the switching coefficients.
        
        if (force.getUseSwitchingFunction()) {
            defines["LJ_SWITCH_CUTOFF"] = cl.doubleToString(force.getSwitchingDistance());
            defines["LJ_SWITCH_C3"] = cl.doubleToString(10/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 3.0));
            defines["LJ_SWITCH_C4"] = cl.doubleToString(15/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 4.0));
            defines["LJ_SWITCH_C5"] = cl.doubleToString(6/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 5.0));
        }
1700
    }
1701
    if (force.getUseDispersionCorrection() && cl.getContextIndex() == 0)
1702
1703
1704
        dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(system, force);
    else
        dispersionCoefficient = 0.0;
1705
    alpha = 0;
1706
    ewaldSelfEnergy = 0.0;
1707
    if (nonbondedMethod == Ewald) {
1708
1709
1710
1711
        // Compute the Ewald parameters.

        int kmaxx, kmaxy, kmaxz;
        NonbondedForceImpl::calcEwaldParameters(system, force, alpha, kmaxx, kmaxy, kmaxz);
1712
1713
        defines["EWALD_ALPHA"] = cl.doubleToString(alpha);
        defines["TWO_OVER_SQRT_PI"] = cl.doubleToString(2.0/sqrt(M_PI));
1714
        defines["USE_EWALD"] = "1";
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
1728
1729
1730
1731
1732
        if (cl.getContextIndex() == 0) {
            ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);

            // Create the reciprocal space kernels.

            map<string, string> replacements;
            replacements["NUM_ATOMS"] = cl.intToString(numParticles);
            replacements["KMAX_X"] = cl.intToString(kmaxx);
            replacements["KMAX_Y"] = cl.intToString(kmaxy);
            replacements["KMAX_Z"] = cl.intToString(kmaxz);
            replacements["EXP_COEFFICIENT"] = cl.doubleToString(-1.0/(4.0*alpha*alpha));
            cl::Program program = cl.createProgram(OpenCLKernelSources::ewald, replacements);
            ewaldSumsKernel = cl::Kernel(program, "calculateEwaldCosSinSums");
            ewaldForcesKernel = cl::Kernel(program, "calculateEwaldForces");
            int elementSize = (cl.getUseDoublePrecision() ? sizeof(mm_double2) : sizeof(mm_float2));
            cosSinSums = new OpenCLArray(cl, (2*kmaxx-1)*(2*kmaxy-1)*(2*kmaxz-1), elementSize, "cosSinSums");
        }
    }
1733
    else if (nonbondedMethod == PME) {
1734
1735
1736
1737
1738
1739
        // Compute the PME parameters.

        NonbondedForceImpl::calcPMEParameters(system, force, alpha, gridSizeX, gridSizeY, gridSizeZ);
        gridSizeX = OpenCLFFT3D::findLegalDimension(gridSizeX);
        gridSizeY = OpenCLFFT3D::findLegalDimension(gridSizeY);
        gridSizeZ = OpenCLFFT3D::findLegalDimension(gridSizeZ);
1740
1741
        defines["EWALD_ALPHA"] = cl.doubleToString(alpha);
        defines["TWO_OVER_SQRT_PI"] = cl.doubleToString(2.0/sqrt(M_PI));
1742
        defines["USE_EWALD"] = "1";
1743
1744
1745
1746
1747
1748
1749
1750
1751
        if (cl.getContextIndex() == 0) {
            ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
            pmeDefines["PME_ORDER"] = cl.intToString(PmeOrder);
            pmeDefines["NUM_ATOMS"] = cl.intToString(numParticles);
            pmeDefines["RECIP_EXP_FACTOR"] = cl.doubleToString(M_PI*M_PI/(alpha*alpha));
            pmeDefines["GRID_SIZE_X"] = cl.intToString(gridSizeX);
            pmeDefines["GRID_SIZE_Y"] = cl.intToString(gridSizeY);
            pmeDefines["GRID_SIZE_Z"] = cl.intToString(gridSizeZ);
            pmeDefines["EPSILON_FACTOR"] = cl.doubleToString(sqrt(ONE_4PI_EPS0));
1752
            pmeDefines["M_PI"] = cl.doubleToString(M_PI);
1753
1754
1755
1756
1757
1758
1759
1760
1761
1762
1763
1764
1765
1766
            bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
            if (deviceIsCpu)
                pmeDefines["DEVICE_IS_CPU"] = "1";
            if (cl.getPlatformData().useCpuPme) {
                // Create the CPU PME kernel.

                try {
                    cpuPme = getPlatform().createKernel(CalcPmeReciprocalForceKernel::Name(), *cl.getPlatformData().context);
                    cpuPme.getAs<CalcPmeReciprocalForceKernel>().initialize(gridSizeX, gridSizeY, gridSizeZ, numParticles, alpha);
                    cl::Program program = cl.createProgram(OpenCLKernelSources::pme, pmeDefines);
                    cl::Kernel addForcesKernel = cl::Kernel(program, "addForces");
                    pmeio = new PmeIO(cl, addForcesKernel);
                    cl.addPreComputation(new PmePreComputation(cl, cpuPme, *pmeio));
                    cl.addPostComputation(new PmePostComputation(cpuPme, *pmeio));
1767
                }
1768
1769
                catch (OpenMMException& ex) {
                    // The CPU PME plugin isn't available.
1770
                }
1771
1772
1773
1774
1775
1776
1777
            }
            if (pmeio == NULL) {
                // Create required data structures.

                int elementSize = (cl.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
                pmeGrid = new OpenCLArray(cl, gridSizeX*gridSizeY*gridSizeZ, 2*elementSize, "pmeGrid");
                pmeGrid2 = new OpenCLArray(cl, gridSizeX*gridSizeY*gridSizeZ, 2*elementSize, "pmeGrid2");
peastman's avatar
peastman committed
1778
1779
1780
1781
                if (cl.getSupports64BitGlobalAtomics())
                    cl.addAutoclearBuffer(*pmeGrid2);
                else
                    cl.addAutoclearBuffer(*pmeGrid);
1782
1783
1784
1785
1786
1787
                pmeBsplineModuliX = new OpenCLArray(cl, gridSizeX, elementSize, "pmeBsplineModuliX");
                pmeBsplineModuliY = new OpenCLArray(cl, gridSizeY, elementSize, "pmeBsplineModuliY");
                pmeBsplineModuliZ = new OpenCLArray(cl, gridSizeZ, elementSize, "pmeBsplineModuliZ");
                pmeBsplineTheta = new OpenCLArray(cl, PmeOrder*numParticles, 4*elementSize, "pmeBsplineTheta");
                pmeAtomRange = OpenCLArray::create<cl_int>(cl, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
                pmeAtomGridIndex = OpenCLArray::create<mm_int2>(cl, numParticles, "pmeAtomGridIndex");
1788
1789
1790
                int energyElementSize = (cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
                pmeEnergyBuffer = new OpenCLArray(cl, cl.getNumThreadBlocks()*OpenCLContext::ThreadBlockSize, energyElementSize, "pmeEnergyBuffer");
                cl.clearBuffer(*pmeEnergyBuffer);
1791
                sort = new OpenCLSort(cl, new SortTrait(), cl.getNumAtoms());
1792
                fft = new OpenCLFFT3D(cl, gridSizeX, gridSizeY, gridSizeZ, true);
1793
                string vendor = cl.getDevice().getInfo<CL_DEVICE_VENDOR>();
Peter Eastman's avatar
Peter Eastman committed
1794
1795
1796
                bool isNvidia = (vendor.size() >= 6 && vendor.substr(0, 6) == "NVIDIA");
                if (isNvidia)
                    pmeDefines["USE_ALTERNATE_MEMORY_ACCESS_PATTERN"] = "1";
1797
                usePmeQueue = (!cl.getPlatformData().disablePmeStream && isNvidia);
1798
                if (usePmeQueue) {
peastman's avatar
peastman committed
1799
                    pmeDefines["USE_PME_STREAM"] = "1";
1800
1801
1802
1803
1804
                    pmeQueue = cl::CommandQueue(cl.getContext(), cl.getDevice());
                    int recipForceGroup = force.getReciprocalSpaceForceGroup();
                    if (recipForceGroup < 0)
                        recipForceGroup = force.getForceGroup();
                    cl.addPreComputation(new SyncQueuePreComputation(cl, pmeQueue, recipForceGroup));
1805
                    cl.addPostComputation(syncQueue = new SyncQueuePostComputation(cl, pmeSyncEvent, *pmeEnergyBuffer, recipForceGroup));
1806
                }
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
1819
1820
1821
1822

                // Initialize the b-spline moduli.

                int maxSize = max(max(gridSizeX, gridSizeY), gridSizeZ);
                vector<double> data(PmeOrder);
                vector<double> ddata(PmeOrder);
                vector<double> bsplines_data(maxSize);
                data[PmeOrder-1] = 0.0;
                data[1] = 0.0;
                data[0] = 1.0;
                for (int i = 3; i < PmeOrder; i++) {
                    double div = 1.0/(i-1.0);
                    data[i-1] = 0.0;
                    for (int j = 1; j < (i-1); j++)
                        data[i-j-1] = div*(j*data[i-j-2]+(i-j)*data[i-j-1]);
                    data[0] = div*data[0];
1823
                }
1824
1825
1826
1827
1828
1829
1830
1831
1832
1833
1834
1835
1836
1837
1838
1839
1840
1841
1842
1843
1844
1845
1846
1847
1848
1849
1850
1851
1852
1853
1854

                // Differentiate.

                ddata[0] = -data[0];
                for (int i = 1; i < PmeOrder; i++)
                    ddata[i] = data[i-1]-data[i];
                double div = 1.0/(PmeOrder-1);
                data[PmeOrder-1] = 0.0;
                for (int i = 1; i < (PmeOrder-1); i++)
                    data[PmeOrder-i-1] = div*(i*data[PmeOrder-i-2]+(PmeOrder-i)*data[PmeOrder-i-1]);
                data[0] = div*data[0];
                for (int i = 0; i < maxSize; i++)
                    bsplines_data[i] = 0.0;
                for (int i = 1; i <= PmeOrder; i++)
                    bsplines_data[i] = data[i-1];

                // Evaluate the actual bspline moduli for X/Y/Z.

                for(int dim = 0; dim < 3; dim++) {
                    int ndata = (dim == 0 ? gridSizeX : dim == 1 ? gridSizeY : gridSizeZ);
                    vector<cl_double> moduli(ndata);
                    for (int i = 0; i < ndata; i++) {
                        double sc = 0.0;
                        double ss = 0.0;
                        for (int j = 0; j < ndata; j++) {
                            double arg = (2.0*M_PI*i*j)/ndata;
                            sc += bsplines_data[j]*cos(arg);
                            ss += bsplines_data[j]*sin(arg);
                        }
                        moduli[i] = (float) (sc*sc+ss*ss);
                    }
1855
                    for (int i = 0; i < ndata; i++)
1856
1857
1858
1859
1860
1861
1862
1863
1864
1865
1866
1867
1868
1869
1870
1871
1872
1873
1874
1875
1876
1877
1878
                    {
                        if (moduli[i] < 1.0e-7)
                            moduli[i] = (moduli[i-1]+moduli[i+1])*0.5f;
                    }
                    if (cl.getUseDoublePrecision()) {
                        if (dim == 0)
                            pmeBsplineModuliX->upload(moduli);
                        else if (dim == 1)
                            pmeBsplineModuliY->upload(moduli);
                        else
                            pmeBsplineModuliZ->upload(moduli);
                    }
                    else {
                        vector<float> modulif(ndata);
                        for (int i = 0; i < ndata; i++)
                            modulif[i] = (float) moduli[i];
                        if (dim == 0)
                            pmeBsplineModuliX->upload(modulif);
                        else if (dim == 1)
                            pmeBsplineModuliY->upload(modulif);
                        else
                            pmeBsplineModuliZ->upload(modulif);
                    }
1879
                }
1880
            }
1881
1882
        }
    }
1883
1884
1885

    // Add the interaction to the default nonbonded kernel.
    
1886
    string source = cl.replaceStrings(OpenCLKernelSources::coulombLennardJones, defines);
1887
    cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup());
Peter Eastman's avatar
Peter Eastman committed
1888
    if (hasLJ)
1889
        cl.getNonbondedUtilities().addParameter(OpenCLNonbondedUtilities::ParameterInfo("sigmaEpsilon", "float", 2, sizeof(cl_float2), sigmaEpsilon->getDeviceBuffer()));
1890

1891
    // Initialize the exceptions.
1892

1893
1894
1895
1896
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*exceptions.size()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*exceptions.size()/numContexts;
    int numExceptions = endIndex-startIndex;
1897
    if (numExceptions > 0) {
1898
        exceptionAtoms.resize(numExceptions);
Peter Eastman's avatar
Peter Eastman committed
1899
        vector<vector<int> > atoms(numExceptions, vector<int>(2));
1900
        exceptionParams = OpenCLArray::create<mm_float4>(cl, numExceptions, "exceptionParams");
1901
        vector<mm_float4> exceptionParamsVector(numExceptions);
1902
        for (int i = 0; i < numExceptions; i++) {
1903
            double chargeProd, sigma, epsilon;
Peter Eastman's avatar
Peter Eastman committed
1904
            force.getExceptionParameters(exceptions[startIndex+i], atoms[i][0], atoms[i][1], chargeProd, sigma, epsilon);
1905
            exceptionParamsVector[i] = mm_float4((float) (ONE_4PI_EPS0*chargeProd), (float) sigma, (float) (4.0*epsilon), 0.0f);
1906
            exceptionAtoms[i] = make_pair(atoms[i][0], atoms[i][1]);
1907
        }
1908
        exceptionParams->upload(exceptionParamsVector);
Peter Eastman's avatar
Peter Eastman committed
1909
1910
        map<string, string> replacements;
        replacements["PARAMS"] = cl.getBondedUtilities().addArgument(exceptionParams->getDeviceBuffer(), "float4");
1911
        cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::nonbondedExceptions, replacements), force.getForceGroup());
Peter Eastman's avatar
Peter Eastman committed
1912
1913
    }
    cl.addForce(new OpenCLNonbondedForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
1914
1915
}

1916
double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal) {
1917
    bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
1918
1919
1920
1921
1922
1923
1924
1925
1926
1927
    if (!hasInitializedKernel) {
        hasInitializedKernel = true;
        if (cosSinSums != NULL) {
            ewaldSumsKernel.setArg<cl::Buffer>(0, cl.getEnergyBuffer().getDeviceBuffer());
            ewaldSumsKernel.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
            ewaldSumsKernel.setArg<cl::Buffer>(2, cosSinSums->getDeviceBuffer());
            ewaldForcesKernel.setArg<cl::Buffer>(0, cl.getForceBuffers().getDeviceBuffer());
            ewaldForcesKernel.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
            ewaldForcesKernel.setArg<cl::Buffer>(2, cosSinSums->getDeviceBuffer());
        }
1928
        if (pmeGrid != NULL) {
1929
            cl::Program program = cl.createProgram(OpenCLKernelSources::pme, pmeDefines);
1930
            pmeUpdateBsplinesKernel = cl::Kernel(program, "updateBsplines");
1931
            pmeAtomRangeKernel = cl::Kernel(program, "findAtomRangeForGrid");
1932
            pmeZIndexKernel = cl::Kernel(program, "recordZIndex");
1933
1934
            pmeSpreadChargeKernel = cl::Kernel(program, "gridSpreadCharge");
            pmeConvolutionKernel = cl::Kernel(program, "reciprocalConvolution");
1935
            pmeEvalEnergyKernel = cl::Kernel(program, "gridEvaluateEnergy");
1936
            pmeInterpolateForceKernel = cl::Kernel(program, "gridInterpolateForce");
1937
            int elementSize = (cl.getUseDoublePrecision() ? sizeof(mm_double4) : sizeof(mm_float4));
1938
1939
            pmeUpdateBsplinesKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
            pmeUpdateBsplinesKernel.setArg<cl::Buffer>(1, pmeBsplineTheta->getDeviceBuffer());
1940
            pmeUpdateBsplinesKernel.setArg(2, OpenCLContext::ThreadBlockSize*PmeOrder*elementSize, NULL);
1941
            pmeUpdateBsplinesKernel.setArg<cl::Buffer>(3, pmeAtomGridIndex->getDeviceBuffer());
1942
1943
1944
            pmeAtomRangeKernel.setArg<cl::Buffer>(0, pmeAtomGridIndex->getDeviceBuffer());
            pmeAtomRangeKernel.setArg<cl::Buffer>(1, pmeAtomRange->getDeviceBuffer());
            pmeAtomRangeKernel.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
1945
1946
            pmeZIndexKernel.setArg<cl::Buffer>(0, pmeAtomGridIndex->getDeviceBuffer());
            pmeZIndexKernel.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
1947
1948
1949
            pmeSpreadChargeKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
            pmeSpreadChargeKernel.setArg<cl::Buffer>(1, pmeAtomGridIndex->getDeviceBuffer());
            pmeSpreadChargeKernel.setArg<cl::Buffer>(2, pmeAtomRange->getDeviceBuffer());
peastman's avatar
peastman committed
1950
1951
1952
1953
            if (cl.getSupports64BitGlobalAtomics())
                pmeSpreadChargeKernel.setArg<cl::Buffer>(3, pmeGrid2->getDeviceBuffer());
            else
                pmeSpreadChargeKernel.setArg<cl::Buffer>(3, pmeGrid->getDeviceBuffer());
1954
            pmeSpreadChargeKernel.setArg<cl::Buffer>(4, pmeBsplineTheta->getDeviceBuffer());
Peter Eastman's avatar
Peter Eastman committed
1955
            pmeConvolutionKernel.setArg<cl::Buffer>(0, pmeGrid2->getDeviceBuffer());
1956
1957
1958
1959
            pmeConvolutionKernel.setArg<cl::Buffer>(1, pmeBsplineModuliX->getDeviceBuffer());
            pmeConvolutionKernel.setArg<cl::Buffer>(2, pmeBsplineModuliY->getDeviceBuffer());
            pmeConvolutionKernel.setArg<cl::Buffer>(3, pmeBsplineModuliZ->getDeviceBuffer());
            pmeEvalEnergyKernel.setArg<cl::Buffer>(0, pmeGrid2->getDeviceBuffer());
1960
            pmeEvalEnergyKernel.setArg<cl::Buffer>(1, usePmeQueue ? pmeEnergyBuffer->getDeviceBuffer() : cl.getEnergyBuffer().getDeviceBuffer());
1961
1962
1963
            pmeEvalEnergyKernel.setArg<cl::Buffer>(2, pmeBsplineModuliX->getDeviceBuffer());
            pmeEvalEnergyKernel.setArg<cl::Buffer>(3, pmeBsplineModuliY->getDeviceBuffer());
            pmeEvalEnergyKernel.setArg<cl::Buffer>(4, pmeBsplineModuliZ->getDeviceBuffer());
1964
1965
            pmeInterpolateForceKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
            pmeInterpolateForceKernel.setArg<cl::Buffer>(1, cl.getForceBuffers().getDeviceBuffer());
1966
            pmeInterpolateForceKernel.setArg<cl::Buffer>(2, pmeGrid->getDeviceBuffer());
1967
            pmeInterpolateForceKernel.setArg<cl::Buffer>(11, pmeAtomGridIndex->getDeviceBuffer());
1968
1969
            if (cl.getSupports64BitGlobalAtomics()) {
                pmeFinishSpreadChargeKernel = cl::Kernel(program, "finishSpreadCharge");
peastman's avatar
peastman committed
1970
1971
                pmeFinishSpreadChargeKernel.setArg<cl::Buffer>(0, pmeGrid2->getDeviceBuffer());
                pmeFinishSpreadChargeKernel.setArg<cl::Buffer>(1, pmeGrid->getDeviceBuffer());
1972
            }
1973
1974
            if (usePmeQueue)
                syncQueue->setKernel(cl::Kernel(program, "addEnergy"));
1975
       }
1976
    }
1977
    if (cosSinSums != NULL && includeReciprocal) {
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
        mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
        mm_double4 recipBoxSize = mm_double4(2*M_PI/boxSize.x, 2*M_PI/boxSize.y, 2*M_PI/boxSize.z, 0.0);
        double recipCoefficient = ONE_4PI_EPS0*4*M_PI/(boxSize.x*boxSize.y*boxSize.z);
        if (cl.getUseDoublePrecision()) {
            ewaldSumsKernel.setArg<mm_double4>(3, recipBoxSize);
            ewaldSumsKernel.setArg<cl_double>(4, recipCoefficient);
            ewaldForcesKernel.setArg<mm_double4>(3, recipBoxSize);
            ewaldForcesKernel.setArg<cl_double>(4, recipCoefficient);
        }
        else {
            ewaldSumsKernel.setArg<mm_float4>(3, mm_float4((float) recipBoxSize.x, (float) recipBoxSize.y, (float) recipBoxSize.z, 0));
            ewaldSumsKernel.setArg<cl_float>(4, (cl_float) recipCoefficient);
            ewaldForcesKernel.setArg<mm_float4>(3, mm_float4((float) recipBoxSize.x, (float) recipBoxSize.y, (float) recipBoxSize.z, 0));
            ewaldForcesKernel.setArg<cl_float>(4, (cl_float) recipCoefficient);
        }
1993
1994
1995
        cl.executeKernel(ewaldSumsKernel, cosSinSums->getSize());
        cl.executeKernel(ewaldForcesKernel, cl.getNumAtoms());
    }
1996
    if (pmeGrid != NULL && includeReciprocal) {
1997
        if (usePmeQueue && !includeEnergy)
1998
            cl.setQueue(pmeQueue);
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
        
        // Invert the periodic box vectors.
        
        Vec3 boxVectors[3];
        cl.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
        double determinant = boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2];
        double scale = 1.0/determinant;
        mm_double4 recipBoxVectors[3];
        recipBoxVectors[0] = mm_double4(boxVectors[1][1]*boxVectors[2][2]*scale, 0, 0, 0);
        recipBoxVectors[1] = mm_double4(-boxVectors[1][0]*boxVectors[2][2]*scale, boxVectors[0][0]*boxVectors[2][2]*scale, 0, 0);
        recipBoxVectors[2] = mm_double4((boxVectors[1][0]*boxVectors[2][1]-boxVectors[1][1]*boxVectors[2][0])*scale, -boxVectors[0][0]*boxVectors[2][1]*scale, boxVectors[0][0]*boxVectors[1][1]*scale, 0);
        mm_float4 recipBoxVectorsFloat[3];
        for (int i = 0; i < 3; i++)
            recipBoxVectorsFloat[i] = mm_float4((float) recipBoxVectors[i].x, (float) recipBoxVectors[i].y, (float) recipBoxVectors[i].z, 0);
        
        // Execute the reciprocal space kernels.

2016
        setPeriodicBoxArgs(cl, pmeUpdateBsplinesKernel, 4);
2017
        if (cl.getUseDoublePrecision()) {
2018
2019
2020
            pmeUpdateBsplinesKernel.setArg<mm_double4>(9, recipBoxVectors[0]);
            pmeUpdateBsplinesKernel.setArg<mm_double4>(10, recipBoxVectors[1]);
            pmeUpdateBsplinesKernel.setArg<mm_double4>(11, recipBoxVectors[2]);
2021
2022
        }
        else {
2023
2024
2025
            pmeUpdateBsplinesKernel.setArg<mm_float4>(9, recipBoxVectorsFloat[0]);
            pmeUpdateBsplinesKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[1]);
            pmeUpdateBsplinesKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[2]);
2026
        }
2027
        cl.executeKernel(pmeUpdateBsplinesKernel, cl.getNumAtoms());
2028
        if (deviceIsCpu && !cl.getSupports64BitGlobalAtomics()) {
2029
            setPeriodicBoxArgs(cl, pmeSpreadChargeKernel, 5);
2030
            if (cl.getUseDoublePrecision()) {
2031
2032
2033
                pmeSpreadChargeKernel.setArg<mm_double4>(10, recipBoxVectors[0]);
                pmeSpreadChargeKernel.setArg<mm_double4>(11, recipBoxVectors[1]);
                pmeSpreadChargeKernel.setArg<mm_double4>(12, recipBoxVectors[2]);
2034
2035
            }
            else {
2036
2037
2038
                pmeSpreadChargeKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[0]);
                pmeSpreadChargeKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[1]);
                pmeSpreadChargeKernel.setArg<mm_float4>(12, recipBoxVectorsFloat[2]);
2039
            }
2040
2041
2042
2043
            cl.executeKernel(pmeSpreadChargeKernel, 2*cl.getDevice().getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>(), 1);
        }
        else {
            sort->sort(*pmeAtomGridIndex);
2044
            if (cl.getSupports64BitGlobalAtomics()) {
2045
            setPeriodicBoxArgs(cl, pmeSpreadChargeKernel, 5);
2046
                if (cl.getUseDoublePrecision()) {
2047
2048
2049
                    pmeSpreadChargeKernel.setArg<mm_double4>(10, recipBoxVectors[0]);
                    pmeSpreadChargeKernel.setArg<mm_double4>(11, recipBoxVectors[1]);
                    pmeSpreadChargeKernel.setArg<mm_double4>(12, recipBoxVectors[2]);
2050
2051
                }
                else {
2052
2053
2054
                    pmeSpreadChargeKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[0]);
                    pmeSpreadChargeKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[1]);
                    pmeSpreadChargeKernel.setArg<mm_float4>(12, recipBoxVectorsFloat[2]);
2055
                }
2056
                cl.executeKernel(pmeSpreadChargeKernel, cl.getNumAtoms());
2057
2058
                cl.executeKernel(pmeFinishSpreadChargeKernel, pmeGrid->getSize());
            }
2059
            else {
2060
                cl.executeKernel(pmeAtomRangeKernel, cl.getNumAtoms());
2061
                setPeriodicBoxSizeArg(cl, pmeZIndexKernel, 2);
2062
2063
2064
2065
                if (cl.getUseDoublePrecision())
                    pmeZIndexKernel.setArg<mm_double4>(3, recipBoxVectors[2]);
                else
                    pmeZIndexKernel.setArg<mm_float4>(3, recipBoxVectorsFloat[2]);
2066
                cl.executeKernel(pmeZIndexKernel, cl.getNumAtoms());
2067
                cl.executeKernel(pmeSpreadChargeKernel, cl.getNumAtoms());
2068
            }
2069
        }
Peter Eastman's avatar
Peter Eastman committed
2070
        fft->execFFT(*pmeGrid, *pmeGrid2, true);
2071
        mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
2072
        if (cl.getUseDoublePrecision()) {
2073
2074
2075
2076
2077
2078
            pmeConvolutionKernel.setArg<mm_double4>(4, recipBoxVectors[0]);
            pmeConvolutionKernel.setArg<mm_double4>(5, recipBoxVectors[1]);
            pmeConvolutionKernel.setArg<mm_double4>(6, recipBoxVectors[2]);
            pmeEvalEnergyKernel.setArg<mm_double4>(5, recipBoxVectors[0]);
            pmeEvalEnergyKernel.setArg<mm_double4>(6, recipBoxVectors[1]);
            pmeEvalEnergyKernel.setArg<mm_double4>(7, recipBoxVectors[2]);
2079
2080
        }
        else {
2081
2082
2083
2084
2085
2086
            pmeConvolutionKernel.setArg<mm_float4>(4, recipBoxVectorsFloat[0]);
            pmeConvolutionKernel.setArg<mm_float4>(5, recipBoxVectorsFloat[1]);
            pmeConvolutionKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[2]);
            pmeEvalEnergyKernel.setArg<mm_float4>(5, recipBoxVectorsFloat[0]);
            pmeEvalEnergyKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[1]);
            pmeEvalEnergyKernel.setArg<mm_float4>(7, recipBoxVectorsFloat[2]);
2087
        }
2088
2089
        if (includeEnergy)
            cl.executeKernel(pmeEvalEnergyKernel, cl.getNumAtoms());
2090
        cl.executeKernel(pmeConvolutionKernel, cl.getNumAtoms());
Peter Eastman's avatar
Peter Eastman committed
2091
        fft->execFFT(*pmeGrid2, *pmeGrid, false);
2092
        setPeriodicBoxArgs(cl, pmeInterpolateForceKernel, 3);
2093
        if (cl.getUseDoublePrecision()) {
2094
2095
2096
            pmeInterpolateForceKernel.setArg<mm_double4>(8, recipBoxVectors[0]);
            pmeInterpolateForceKernel.setArg<mm_double4>(9, recipBoxVectors[1]);
            pmeInterpolateForceKernel.setArg<mm_double4>(10, recipBoxVectors[2]);
2097
2098
        }
        else {
2099
2100
2101
            pmeInterpolateForceKernel.setArg<mm_float4>(8, recipBoxVectorsFloat[0]);
            pmeInterpolateForceKernel.setArg<mm_float4>(9, recipBoxVectorsFloat[1]);
            pmeInterpolateForceKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[2]);
2102
        }
2103
2104
2105
2106
        if (deviceIsCpu)
            cl.executeKernel(pmeInterpolateForceKernel, 2*cl.getDevice().getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>(), 1);
        else
            cl.executeKernel(pmeInterpolateForceKernel, cl.getNumAtoms());
2107
2108
2109
2110
        if (usePmeQueue) {
            pmeQueue.enqueueMarker(&pmeSyncEvent);
            cl.restoreDefaultQueue();
        }
2111
    }
2112
2113
    double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
    if (dispersionCoefficient != 0.0 && includeDirect) {
2114
        mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
2115
2116
2117
        energy += dispersionCoefficient/(boxSize.x*boxSize.y*boxSize.z);
    }
    return energy;
2118
2119
}

2120
2121
2122
2123
2124
2125
2126
2127
2128
2129
2130
2131
2132
2133
2134
2135
2136
2137
2138
2139
void OpenCLCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const NonbondedForce& force) {
    // Make sure the new parameters are acceptable.
    
    if (force.getNumParticles() != cl.getNumAtoms())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
    if (!hasCoulomb || !hasLJ) {
        for (int i = 0; i < force.getNumParticles(); i++) {
            double charge, sigma, epsilon;
            force.getParticleParameters(i, charge, sigma, epsilon);
            if (!hasCoulomb && charge != 0.0)
                throw OpenMMException("updateParametersInContext: The nonbonded force kernel does not include Coulomb interactions, because all charges were originally 0");
            if (!hasLJ && epsilon != 0.0)
                throw OpenMMException("updateParametersInContext: The nonbonded force kernel does not include Lennard-Jones interactions, because all epsilons were originally 0");
        }
    }
    vector<int> exceptions;
    for (int i = 0; i < force.getNumExceptions(); i++) {
        int particle1, particle2;
        double chargeProd, sigma, epsilon;
        force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
2140
        if (exceptionAtoms.size() > exceptions.size() && make_pair(particle1, particle2) == exceptionAtoms[exceptions.size()])
2141
            exceptions.push_back(i);
2142
2143
        else if (chargeProd != 0.0 || epsilon != 0.0)
            throw OpenMMException("updateParametersInContext: The set of non-excluded exceptions has changed");
2144
2145
2146
2147
2148
2149
2150
2151
    }
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*exceptions.size()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*exceptions.size()/numContexts;
    int numExceptions = endIndex-startIndex;
    
    // Record the per-particle parameters.
    
2152
    OpenCLArray& posq = cl.getPosq();
2153
    posq.download(cl.getPinnedBuffer());
2154
    mm_float4* posqf = (mm_float4*) cl.getPinnedBuffer();
2155
    mm_double4* posqd = (mm_double4*) cl.getPinnedBuffer();
2156
    vector<mm_float2> sigmaEpsilonVector(cl.getPaddedNumAtoms(), mm_float2(0,0));
2157
    double sumSquaredCharges = 0.0;
2158
    const vector<cl_int>& order = cl.getAtomIndex();
2159
2160
2161
2162
    for (int i = 0; i < force.getNumParticles(); i++) {
        int index = order[i];
        double charge, sigma, epsilon;
        force.getParticleParameters(index, charge, sigma, epsilon);
2163
2164
2165
2166
        if (cl.getUseDoublePrecision())
            posqd[i].w = charge;
        else
            posqf[i].w = (float) charge;
2167
2168
2169
        sigmaEpsilonVector[index] = mm_float2((float) (0.5*sigma), (float) (2.0*sqrt(epsilon)));
        sumSquaredCharges += charge*charge;
    }
2170
    posq.upload(cl.getPinnedBuffer());
2171
2172
2173
2174
2175
2176
2177
2178
2179
2180
2181
2182
2183
2184
2185
2186
2187
    sigmaEpsilon->upload(sigmaEpsilonVector);
    
    // Record the exceptions.
    
    if (numExceptions > 0) {
        vector<vector<int> > atoms(numExceptions, vector<int>(2));
        vector<mm_float4> exceptionParamsVector(numExceptions);
        for (int i = 0; i < numExceptions; i++) {
            double chargeProd, sigma, epsilon;
            force.getExceptionParameters(exceptions[startIndex+i], atoms[i][0], atoms[i][1], chargeProd, sigma, epsilon);
            exceptionParamsVector[i] = mm_float4((float) (ONE_4PI_EPS0*chargeProd), (float) sigma, (float) (4.0*epsilon), 0.0f);
        }
        exceptionParams->upload(exceptionParamsVector);
    }
    
    // Compute other values.
    
2188
    if (nonbondedMethod == Ewald || nonbondedMethod == PME)
2189
        ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI) : 0.0);
2190
    if (force.getUseDispersionCorrection() && cl.getContextIndex() == 0 && (nonbondedMethod == CutoffPeriodic || nonbondedMethod == Ewald || nonbondedMethod == PME))
2191
2192
2193
2194
        dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(context.getSystem(), force);
    cl.invalidateMolecules();
}

2195
2196
2197
2198
2199
2200
2201
2202
2203
2204
2205
2206
2207
void OpenCLCalcNonbondedForceKernel::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
    if (nonbondedMethod != PME)
        throw OpenMMException("getPMEParametersInContext: This Context is not using PME");
    if (cl.getPlatformData().useCpuPme)
        cpuPme.getAs<CalcPmeReciprocalForceKernel>().getPMEParameters(alpha, nx, ny, nz);
    else {
        alpha = this->alpha;
        nx = gridSizeX;
        ny = gridSizeY;
        nz = gridSizeZ;
    }
}

2208
2209
2210
class OpenCLCustomNonbondedForceInfo : public OpenCLForceInfo {
public:
    OpenCLCustomNonbondedForceInfo(int requiredBuffers, const CustomNonbondedForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
2211
2212
2213
2214
2215
2216
2217
2218
2219
2220
2221
        if (force.getNumInteractionGroups() > 0) {
            groupsForParticle.resize(force.getNumParticles());
            for (int i = 0; i < force.getNumInteractionGroups(); i++) {
                set<int> set1, set2;
                force.getInteractionGroupParameters(i, set1, set2);
                for (set<int>::const_iterator iter = set1.begin(); iter != set1.end(); ++iter)
                    groupsForParticle[*iter].insert(2*i);
                for (set<int>::const_iterator iter = set2.begin(); iter != set2.end(); ++iter)
                    groupsForParticle[*iter].insert(2*i+1);
            }
        }
2222
2223
2224
2225
2226
2227
    }
    bool areParticlesIdentical(int particle1, int particle2) {
        vector<double> params1;
        vector<double> params2;
        force.getParticleParameters(particle1, params1);
        force.getParticleParameters(particle2, params2);
2228
        for (int i = 0; i < (int) params1.size(); i++)
2229
2230
            if (params1[i] != params2[i])
                return false;
2231
2232
        if (groupsForParticle.size() > 0 && groupsForParticle[particle1] != groupsForParticle[particle2])
            return false;
2233
2234
2235
        return true;
    }
    int getNumParticleGroups() {
2236
        return force.getNumExclusions();
2237
    }
Peter Eastman's avatar
Peter Eastman committed
2238
    void getParticlesInGroup(int index, vector<int>& particles) {
2239
        int particle1, particle2;
2240
        force.getExclusionParticles(index, particle1, particle2);
2241
2242
2243
2244
2245
2246
2247
2248
2249
        particles.resize(2);
        particles[0] = particle1;
        particles[1] = particle2;
    }
    bool areGroupsIdentical(int group1, int group2) {
        return true;
    }
private:
    const CustomNonbondedForce& force;
2250
    vector<set<int> > groupsForParticle;
2251
2252
2253
2254
2255
2256
2257
};

OpenCLCalcCustomNonbondedForceKernel::~OpenCLCalcCustomNonbondedForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
2258
2259
    if (interactionGroupData != NULL)
        delete interactionGroupData;
2260
2261
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
2262
2263
    if (forceCopy != NULL)
        delete forceCopy;
2264
2265
2266
2267
2268
2269
}

void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, const CustomNonbondedForce& force) {
    int forceIndex;
    for (forceIndex = 0; forceIndex < system.getNumForces() && &system.getForce(forceIndex) != &force; ++forceIndex)
        ;
2270
    string prefix = (force.getNumInteractionGroups() == 0 ? "custom"+cl.intToString(forceIndex)+"_" : "");
2271
2272
2273
2274

    // Record parameters and exclusions.

    int numParticles = force.getNumParticles();
2275
    params = new OpenCLParameterSet(cl, force.getNumPerParticleParameters(), numParticles, "customNonbondedParameters");
2276
    if (force.getNumGlobalParameters() > 0)
2277
        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customNonbondedGlobals", CL_MEM_READ_ONLY);
2278
    vector<vector<cl_float> > paramVector(numParticles);
2279
2280
2281
2282
    vector<vector<int> > exclusionList(numParticles);
    for (int i = 0; i < numParticles; i++) {
        vector<double> parameters;
        force.getParticleParameters(i, parameters);
2283
        paramVector[i].resize(parameters.size());
2284
        for (int j = 0; j < (int) parameters.size(); j++)
2285
            paramVector[i][j] = (cl_float) parameters[j];
2286
2287
        exclusionList[i].push_back(i);
    }
2288
2289
2290
2291
2292
    for (int i = 0; i < force.getNumExclusions(); i++) {
        int particle1, particle2;
        force.getExclusionParticles(i, particle1, particle2);
        exclusionList[particle1].push_back(particle2);
        exclusionList[particle2].push_back(particle1);
2293
    }
2294
    params->setParameterValues(paramVector);
2295
2296
2297

    // Record the tabulated functions.

2298
2299
    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
2300
    vector<const TabulatedFunction*> functionList;
2301
    vector<string> tableTypes;
2302
    for (int i = 0; i < force.getNumFunctions(); i++) {
2303
2304
        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
2305
        string arrayName = prefix+"table"+cl.intToString(i);
2306
        functionDefinitions.push_back(make_pair(name, arrayName));
2307
        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
peastman's avatar
peastman committed
2308
        int width;
2309
        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
2310
        tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
2311
        tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
peastman's avatar
peastman committed
2312
        cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(arrayName, "float", width, width*sizeof(float), tabulatedFunctions[tabulatedFunctions.size()-1]->getDeviceBuffer()));
2313
2314
2315
2316
        if (width == 1)
            tableTypes.push_back("float");
        else
            tableTypes.push_back("float"+cl.intToString(width));
2317
2318
2319
2320
2321
2322
2323
2324
2325
2326
2327
2328
2329
2330
    }

    // Record information for the expressions.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    if (globals != NULL)
        globals->upload(globalParamValues);
    bool useCutoff = (force.getNonbondedMethod() != CustomNonbondedForce::NoCutoff);
    bool usePeriodic = (force.getNonbondedMethod() != CustomNonbondedForce::NoCutoff && force.getNonbondedMethod() != CustomNonbondedForce::CutoffNonPeriodic);
2331
    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction(), functions).optimize();
2332
    Lepton::ParsedExpression forceExpression = energyExpression.differentiate("r").optimize();
2333
2334
2335
    map<string, Lepton::ParsedExpression> forceExpressions;
    forceExpressions["tempEnergy += "] = energyExpression;
    forceExpressions["tempForce -= "] = forceExpression;
2336
2337
2338

    // Create the kernels.

2339
2340
2341
2342
2343
    vector<pair<ExpressionTreeNode, string> > variables;
    ExpressionTreeNode rnode(new Operation::Variable("r"));
    variables.push_back(make_pair(rnode, "r"));
    variables.push_back(make_pair(ExpressionTreeNode(new Operation::Square(), rnode), "r2"));
    variables.push_back(make_pair(ExpressionTreeNode(new Operation::Reciprocal(), rnode), "invR"));
2344
2345
    for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
        const string& name = force.getPerParticleParameterName(i);
2346
2347
        variables.push_back(makeVariable(name+"1", prefix+"params"+params->getParameterSuffix(i, "1")));
        variables.push_back(makeVariable(name+"2", prefix+"params"+params->getParameterSuffix(i, "2")));
2348
2349
2350
    }
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        const string& name = force.getGlobalParameterName(i);
2351
        string value = "globals["+cl.intToString(i)+"]";
2352
        variables.push_back(makeVariable(name, prefix+value));
2353
    }
2354
2355
2356
2357
2358
2359
    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
        string paramName = force.getEnergyParameterDerivativeName(i);
        string derivVariable = cl.getNonbondedUtilities().addEnergyParameterDerivative(paramName);
        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
        forceExpressions[derivVariable+" += interactionScale*switchValue*"] = derivExpression;
    }
2360
    stringstream compute;
2361
    compute << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, prefix+"temp");
2362
2363
    map<string, string> replacements;
    replacements["COMPUTE_FORCE"] = compute.str();
2364
2365
2366
2367
2368
2369
2370
2371
2372
    replacements["USE_SWITCH"] = (useCutoff && force.getUseSwitchingFunction() ? "1" : "0");
    if (force.getUseSwitchingFunction()) {
        // Compute the switching coefficients.
        
        replacements["SWITCH_CUTOFF"] = cl.doubleToString(force.getSwitchingDistance());
        replacements["SWITCH_C3"] = cl.doubleToString(10/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 3.0));
        replacements["SWITCH_C4"] = cl.doubleToString(15/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 4.0));
        replacements["SWITCH_C5"] = cl.doubleToString(6/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 5.0));
    }
2373
    string source = cl.replaceStrings(OpenCLKernelSources::customNonbonded, replacements);
2374
    if (force.getNumInteractionGroups() > 0)
2375
        initInteractionGroups(force, source, tableTypes);
2376
2377
2378
2379
2380
2381
2382
2383
2384
2385
    else {
        cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup());
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
            cl.getNonbondedUtilities().addParameter(OpenCLNonbondedUtilities::ParameterInfo(prefix+"params"+cl.intToString(i+1), buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
        }
        if (globals != NULL) {
            globals->upload(globalParamValues);
            cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(prefix+"globals", "float", 1, sizeof(cl_float), globals->getDeviceBuffer()));
        }
2386
    }
2387
    cl.addForce(new OpenCLCustomNonbondedForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
2388
2389
2390
2391
2392
2393
2394
2395
2396
2397
2398
    
    // Record information for the long range correction.
    
    if (force.getNonbondedMethod() == CustomNonbondedForce::CutoffPeriodic && force.getUseLongRangeCorrection() && cl.getContextIndex() == 0) {
        forceCopy = new CustomNonbondedForce(force);
        hasInitializedLongRangeCorrection = false;
    }
    else {
        longRangeCoefficient = 0.0;
        hasInitializedLongRangeCorrection = true;
    }
2399
2400
}

2401
void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbondedForce& force, const string& interactionSource, const vector<string>& tableTypes) {
2402
2403
2404
2405
    // Process groups to form tiles.
    
    vector<vector<int> > atomLists;
    vector<pair<int, int> > tiles;
peastman's avatar
peastman committed
2406
    map<pair<int, int>, int> duplicateInteractions;
2407
2408
2409
2410
2411
2412
2413
2414
2415
2416
2417
2418
2419
2420
    for (int group = 0; group < force.getNumInteractionGroups(); group++) {
        // Get the list of atoms in this group and sort them.
        
        set<int> set1, set2;
        force.getInteractionGroupParameters(group, set1, set2);
        vector<int> atoms1, atoms2;
        atoms1.insert(atoms1.begin(), set1.begin(), set1.end());
        atoms2.insert(atoms2.begin(), set2.begin(), set2.end());
        sort(atoms1.begin(), atoms1.end());
        sort(atoms2.begin(), atoms2.end());
        
        // Find how many tiles we will create for this group.
        
        int tileWidth = min(min(32, (int) atoms1.size()), (int) atoms2.size());
2421
2422
        if (tileWidth == 0)
            continue;
2423
2424
2425
2426
2427
2428
2429
2430
2431
2432
2433
2434
2435
2436
2437
2438
2439
2440
2441
2442
2443
2444
2445
2446
2447
2448
2449
        int numBlocks1 = (atoms1.size()+tileWidth-1)/tileWidth;
        int numBlocks2 = (atoms2.size()+tileWidth-1)/tileWidth;
        
        // Add the tiles.
        
        for (int i = 0; i < numBlocks1; i++)
            for (int j = 0; j < numBlocks2; j++)
                tiles.push_back(make_pair(atomLists.size()+i, atomLists.size()+numBlocks1+j));
        
        // Add the atom lists.
        
        for (int i = 0; i < numBlocks1; i++) {
            vector<int> atoms;
            int first = i*tileWidth;
            int last = min((i+1)*tileWidth, (int) atoms1.size());
            for (int j = first; j < last; j++)
                atoms.push_back(atoms1[j]);
            atomLists.push_back(atoms);
        }
        for (int i = 0; i < numBlocks2; i++) {
            vector<int> atoms;
            int first = i*tileWidth;
            int last = min((i+1)*tileWidth, (int) atoms2.size());
            for (int j = first; j < last; j++)
                atoms.push_back(atoms2[j]);
            atomLists.push_back(atoms);
        }
peastman's avatar
peastman committed
2450
2451
2452
2453
2454
2455
2456
2457
2458
2459
2460
2461
2462
2463
2464
2465
2466
        
        // If this group contains duplicate interactions, record that we need to skip them once.
        
        for (int i = 0; i < (int) atoms1.size(); i++) {
            int a1 = atoms1[i];
            if (set2.find(a1) == set2.end())
                continue;
            for (int j = 0; j < (int) atoms2.size() && atoms2[j] < a1; j++) {
                int a2 = atoms2[j];
                if (set1.find(a2) != set1.end()) {
                    pair<int, int> key = make_pair(a2, a1);
                    if (duplicateInteractions.find(key) == duplicateInteractions.end())
                        duplicateInteractions[key] = 0;
                    duplicateInteractions[key]++;
                }
            }
        }
2467
2468
2469
2470
2471
2472
2473
2474
    }
    
    // Build a lookup table for quickly identifying excluded interactions.
    
    set<pair<int, int> > exclusions;
    for (int i = 0; i < force.getNumExclusions(); i++) {
        int p1, p2;
        force.getExclusionParticles(i, p1, p2);
peastman's avatar
peastman committed
2475
        exclusions.insert(make_pair(min(p1, p2), max(p1, p2)));
2476
2477
2478
2479
2480
2481
2482
2483
2484
2485
2486
2487
2488
2489
2490
2491
2492
    }
    
    // Build the exclusion flags for each tile.  While we're at it, filter out tiles
    // where all interactions are excluded, and sort the tiles by size.

    vector<vector<int> > exclusionFlags(tiles.size());
    vector<pair<int, int> > tileOrder;
    for (int tile = 0; tile < tiles.size(); tile++) {
        if (atomLists[tiles[tile].first].size() < atomLists[tiles[tile].second].size()) {
            // For efficiency, we want the first axis to be the larger one.
            
            int swap = tiles[tile].first;
            tiles[tile].first = tiles[tile].second;
            tiles[tile].second = swap;
        }
        vector<int>& atoms1 = atomLists[tiles[tile].first];
        vector<int>& atoms2 = atomLists[tiles[tile].second];
peastman's avatar
peastman committed
2493
        vector<int> flags(atoms1.size(), (int) (1LL<<atoms2.size())-1);
2494
2495
2496
2497
2498
        int numExcluded = 0;
        for (int i = 0; i < (int) atoms1.size(); i++)
            for (int j = 0; j < (int) atoms2.size(); j++) {
                int a1 = atoms1[i];
                int a2 = atoms2[j];
peastman's avatar
peastman committed
2499
2500
2501
2502
2503
2504
2505
2506
2507
2508
2509
                bool isExcluded = false;
                pair<int, int> key = make_pair(min(a1, a2), max(a1, a2));
                if (a1 == a2 || exclusions.find(key) != exclusions.end())
                    isExcluded = true; // This is an excluded interaction.
                else if (duplicateInteractions.find(key) != duplicateInteractions.end() && duplicateInteractions[key] > 0) {
                    // Both atoms are in both sets, so skip duplicate interactions.
                    
                    isExcluded = true;
                    duplicateInteractions[key]--;
                }
                if (isExcluded) {
2510
2511
2512
2513
2514
2515
2516
                    flags[i] &= -1-(1<<j);
                    numExcluded++;
                }
            }
        if (numExcluded == atoms1.size()*atoms2.size())
            continue; // All interactions are excluded.
        tileOrder.push_back(make_pair((int) -atoms2.size(), tile));
peastman's avatar
peastman committed
2517
        exclusionFlags[tile] = flags;
2518
2519
2520
2521
2522
2523
2524
2525
2526
2527
2528
2529
2530
2531
2532
2533
2534
2535
2536
2537
2538
2539
2540
2541
2542
    }
    sort(tileOrder.begin(), tileOrder.end());
    
    // Merge tiles to get as close as possible to 32 along the first axis of each one.
    
    vector<int> tileSetStart;
    tileSetStart.push_back(0);
    int tileSetSize = 0;
    for (int i = 0; i < tileOrder.size(); i++) {
        int tile = tileOrder[i].second;
        int size = atomLists[tiles[tile].first].size();
        if (tileSetSize+size > 32) {
            tileSetStart.push_back(i);
            tileSetSize = 0;
        }
        tileSetSize += size;
    }
    tileSetStart.push_back(tileOrder.size());
    
    // Build the data structures.
    
    int numTileSets = tileSetStart.size()-1;
    vector<mm_int4> groupData;
    for (int tileSet = 0; tileSet < numTileSets; tileSet++) {
        int indexInTileSet = 0;
2543
2544
2545
2546
2547
2548
2549
2550
        int minSize = 0;
        if (cl.getSIMDWidth() < 32) {
            // We need to include a barrier inside the inner loop, so ensure that all
            // threads will loop the same number of times.
            
            for (int i = tileSetStart[tileSet]; i < tileSetStart[tileSet+1]; i++)
                minSize = max(minSize, (int) atomLists[tiles[tileOrder[i].second].first].size());
        }
2551
2552
2553
2554
        for (int i = tileSetStart[tileSet]; i < tileSetStart[tileSet+1]; i++) {
            int tile = tileOrder[i].second;
            vector<int>& atoms1 = atomLists[tiles[tile].first];
            vector<int>& atoms2 = atomLists[tiles[tile].second];
2555
            int range = indexInTileSet + ((indexInTileSet+max(minSize, (int) atoms1.size()))<<16);
2556
2557
2558
2559
2560
2561
2562
2563
2564
2565
            int allFlags = (1<<atoms2.size())-1;
            for (int j = 0; j < (int) atoms1.size(); j++) {
                int a1 = atoms1[j];
                int a2 = (j < atoms2.size() ? atoms2[j] : 0);
                int flags = (exclusionFlags[tile].size() > 0 ? exclusionFlags[tile][j] : allFlags);
                groupData.push_back(mm_int4(a1, a2, range, flags<<indexInTileSet));
            }
            indexInTileSet += atoms1.size();
        }
        for (; indexInTileSet < 32; indexInTileSet++)
2566
            groupData.push_back(mm_int4(0, 0, minSize<<16, 0));
2567
2568
2569
2570
2571
2572
2573
2574
2575
2576
2577
2578
2579
2580
2581
2582
2583
2584
2585
2586
2587
2588
2589
2590
2591
    }
    interactionGroupData = OpenCLArray::create<mm_int4>(cl, groupData.size(), "interactionGroupData");
    interactionGroupData->upload(groupData);
    
    // Create the kernel.
    
    map<string, string> replacements;
    replacements["COMPUTE_INTERACTION"] = interactionSource;
    const string suffixes[] = {"x", "y", "z", "w"};
    stringstream localData;
    int localDataSize = 0;
    vector<OpenCLNonbondedUtilities::ParameterInfo>& buffers = params->getBuffers(); 
    for (int i = 0; i < (int) buffers.size(); i++) {
        if (buffers[i].getNumComponents() == 1)
            localData<<buffers[i].getComponentType()<<" params"<<(i+1)<<";\n";
        else {
            for (int j = 0; j < buffers[i].getNumComponents(); ++j)
                localData<<buffers[i].getComponentType()<<" params"<<(i+1)<<"_"<<suffixes[j]<<";\n";
        }
        localDataSize += buffers[i].getSize();
    }
    replacements["ATOM_PARAMETER_DATA"] = localData.str();
    stringstream args;
    for (int i = 0; i < (int) buffers.size(); i++)
        args<<", __global const "<<buffers[i].getType()<<"* restrict global_params"<<(i+1);
2592
2593
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        args << ", __global const " << tableTypes[i]<< "* restrict table" << i;
2594
2595
    if (globals != NULL)
        args<<", __global const float* restrict globals";
2596
2597
2598
2599
2600
2601
2602
2603
2604
2605
2606
2607
2608
2609
2610
2611
2612
2613
2614
2615
2616
    replacements["PARAMETER_ARGUMENTS"] = args.str();
    stringstream load1;
    for (int i = 0; i < (int) buffers.size(); i++)
        load1<<buffers[i].getType()<<" params"<<(i+1)<<"1 = global_params"<<(i+1)<<"[atom1];\n";
    replacements["LOAD_ATOM1_PARAMETERS"] = load1.str();
    stringstream loadLocal2;
    for (int i = 0; i < (int) buffers.size(); i++) {
        if (buffers[i].getNumComponents() == 1)
            loadLocal2<<"localData[get_local_id(0)].params"<<(i+1)<<" = global_params"<<(i+1)<<"[atom2];\n";
        else {
            loadLocal2<<buffers[i].getType()<<" temp_params"<<(i+1)<<" = global_params"<<(i+1)<<"[atom2];\n";
            for (int j = 0; j < buffers[i].getNumComponents(); ++j)
                loadLocal2<<"localData[get_local_id(0)].params"<<(i+1)<<"_"<<suffixes[j]<<" = temp_params"<<(i+1)<<"."<<suffixes[j]<<";\n";
        }
    }
    replacements["LOAD_LOCAL_PARAMETERS"] = loadLocal2.str();
    stringstream load2;
    for (int i = 0; i < (int) buffers.size(); i++) {
        if (buffers[i].getNumComponents() == 1)
            load2<<buffers[i].getType()<<" params"<<(i+1)<<"2 = localData[localIndex].params"<<(i+1)<<";\n";
        else {
2617
            load2<<buffers[i].getType()<<" params"<<(i+1)<<"2 = ("<<buffers[i].getType()<<") (";
2618
2619
2620
2621
2622
2623
2624
2625
2626
2627
2628
2629
2630
2631
            for (int j = 0; j < buffers[i].getNumComponents(); ++j) {
                if (j > 0)
                    load2<<", ";
                load2<<"localData[localIndex].params"<<(i+1)<<"_"<<suffixes[j];
            }
            load2<<");\n";
        }
    }
    replacements["LOAD_ATOM2_PARAMETERS"] = load2.str();
    map<string, string> defines;
    if (force.getNonbondedMethod() != CustomNonbondedForce::NoCutoff)
        defines["USE_CUTOFF"] = "1";
    if (force.getNonbondedMethod() == CustomNonbondedForce::CutoffPeriodic)
        defines["USE_PERIODIC"] = "1";
2632
    defines["LOCAL_MEMORY_SIZE"] = cl.intToString(max(32, cl.getNonbondedUtilities().getForceThreadBlockSize()));
2633
2634
2635
2636
2637
2638
2639
2640
2641
2642
2643
2644
2645
2646
2647
2648
    double cutoff = force.getCutoffDistance();
    defines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
    defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
    defines["TILE_SIZE"] = "32";
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*numTileSets/numContexts;
    int endIndex = (cl.getContextIndex()+1)*numTileSets/numContexts;
    defines["FIRST_TILE"] = cl.intToString(startIndex);
    defines["LAST_TILE"] = cl.intToString(endIndex);
    if ((localDataSize/4)%2 == 0 && !cl.getUseDoublePrecision())
        defines["PARAMETER_SIZE_IS_EVEN"] = "1";
    cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customNonbondedGroups, replacements), defines);
    interactionGroupKernel = cl::Kernel(program, "computeInteractionGroups");
    numGroupThreadBlocks = cl.getNonbondedUtilities().getNumForceThreadBlocks();
}

2649
double OpenCLCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
2650
2651
    if (globals != NULL) {
        bool changed = false;
2652
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
2653
2654
2655
2656
2657
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
2658
        if (changed) {
2659
            globals->upload(globalParamValues);
2660
            if (forceCopy != NULL) {
2661
                CustomNonbondedForceImpl::calcLongRangeCorrection(*forceCopy, context.getOwner(), longRangeCoefficient, longRangeCoefficientDerivs);
2662
2663
2664
                hasInitializedLongRangeCorrection = true;
            }
        }
2665
    }
2666
    if (!hasInitializedLongRangeCorrection) {
2667
        CustomNonbondedForceImpl::calcLongRangeCorrection(*forceCopy, context.getOwner(), longRangeCoefficient, longRangeCoefficientDerivs);
2668
2669
        hasInitializedLongRangeCorrection = true;
    }
2670
2671
2672
2673
    if (interactionGroupData != NULL) {
        if (!hasInitializedKernel) {
            hasInitializedKernel = true;
            int index = 0;
2674
2675
            bool useLong = cl.getSupports64BitGlobalAtomics();
            interactionGroupKernel.setArg<cl::Buffer>(index++, (useLong ? cl.getLongForceBuffer() : cl.getForceBuffers()).getDeviceBuffer());
2676
2677
2678
            interactionGroupKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
            interactionGroupKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
            interactionGroupKernel.setArg<cl::Buffer>(index++, interactionGroupData->getDeviceBuffer());
2679
2680
            setPeriodicBoxArgs(cl, interactionGroupKernel, index);
            index += 5;
2681
2682
            for (int i = 0; i < (int) params->getBuffers().size(); i++)
                interactionGroupKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
2683
2684
            for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
                interactionGroupKernel.setArg<cl::Memory>(index++, tabulatedFunctions[i]->getDeviceBuffer());
2685
2686
2687
            if (globals != NULL)
                interactionGroupKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        }
2688
        int forceThreadBlockSize = max(32, cl.getNonbondedUtilities().getForceThreadBlockSize());
2689
2690
        cl.executeKernel(interactionGroupKernel, numGroupThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
    }
2691
    mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
2692
2693
2694
2695
2696
    double volume = boxSize.x*boxSize.y*boxSize.z;
    map<string, double>& derivs = cl.getEnergyParamDerivWorkspace();
    for (int i = 0; i < longRangeCoefficientDerivs.size(); i++)
        derivs[forceCopy->getEnergyParameterDerivativeName(i)] += longRangeCoefficientDerivs[i]/volume;
    return longRangeCoefficient/volume;
2697
}
Peter Eastman's avatar
Peter Eastman committed
2698

2699
2700
2701
2702
2703
2704
2705
2706
2707
2708
2709
2710
2711
2712
2713
2714
2715
void OpenCLCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force) {
    int numParticles = force.getNumParticles();
    if (numParticles != cl.getNumAtoms())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
    
    // Record the per-particle parameters.
    
    vector<vector<cl_float> > paramVector(numParticles);
    vector<double> parameters;
    for (int i = 0; i < numParticles; i++) {
        force.getParticleParameters(i, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
2716
2717
2718
    // If necessary, recompute the long range correction.
    
    if (forceCopy != NULL) {
2719
        CustomNonbondedForceImpl::calcLongRangeCorrection(force, context.getOwner(), longRangeCoefficient, longRangeCoefficientDerivs);
2720
2721
2722
2723
        hasInitializedLongRangeCorrection = true;
        *forceCopy = force;
    }
    
2724
2725
2726
2727
2728
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

Peter Eastman's avatar
Peter Eastman committed
2729
2730
2731
2732
2733
2734
2735
2736
2737
2738
2739
2740
2741
2742
class OpenCLGBSAOBCForceInfo : public OpenCLForceInfo {
public:
    OpenCLGBSAOBCForceInfo(int requiredBuffers, const GBSAOBCForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
    }
    bool areParticlesIdentical(int particle1, int particle2) {
        double charge1, charge2, radius1, radius2, scale1, scale2;
        force.getParticleParameters(particle1, charge1, radius1, scale1);
        force.getParticleParameters(particle2, charge2, radius2, scale2);
        return (charge1 == charge2 && radius1 == radius2 && scale1 == scale2);
    }
private:
    const GBSAOBCForce& force;
};

2743
2744
2745
2746
2747
OpenCLCalcGBSAOBCForceKernel::~OpenCLCalcGBSAOBCForceKernel() {
    if (params != NULL)
        delete params;
    if (bornSum != NULL)
        delete bornSum;
2748
2749
    if (longBornSum != NULL)
        delete longBornSum;
2750
2751
2752
2753
    if (bornRadii != NULL)
        delete bornRadii;
    if (bornForce != NULL)
        delete bornForce;
2754
2755
    if (longBornForce != NULL)
        delete longBornForce;
2756
2757
2758
2759
2760
    if (obcChain != NULL)
        delete obcChain;
}

void OpenCLCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCForce& force) {
2761
2762
    if (cl.getPlatformData().contexts.size() > 1)
        throw OpenMMException("GBSAOBCForce does not support using multiple OpenCL devices");
2763
    OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
2764
    params = OpenCLArray::create<mm_float2>(cl, cl.getPaddedNumAtoms(), "gbsaObcParams");
2765
2766
2767
    int elementSize = (cl.getUseDoublePrecision() ? sizeof(cl_double) : sizeof(cl_float));
    bornRadii = new OpenCLArray(cl, cl.getPaddedNumAtoms(), elementSize, "bornRadii");
    obcChain = new OpenCLArray(cl, cl.getPaddedNumAtoms(), elementSize, "obcChain");
2768
    if (cl.getSupports64BitGlobalAtomics()) {
2769
2770
        longBornSum = OpenCLArray::create<cl_long>(cl, cl.getPaddedNumAtoms(), "longBornSum");
        longBornForce = OpenCLArray::create<cl_long>(cl, cl.getPaddedNumAtoms(), "longBornForce");
2771
        bornForce = new OpenCLArray(cl, cl.getPaddedNumAtoms(), elementSize, "bornForce");
2772
2773
        cl.addAutoclearBuffer(*longBornSum);
        cl.addAutoclearBuffer(*longBornForce);
2774
2775
    }
    else {
2776
2777
        bornSum = new OpenCLArray(cl, cl.getPaddedNumAtoms()*nb.getNumForceBuffers(), elementSize, "bornSum");
        bornForce = new OpenCLArray(cl, cl.getPaddedNumAtoms()*nb.getNumForceBuffers(), elementSize, "bornForce");
2778
2779
        cl.addAutoclearBuffer(*bornSum);
        cl.addAutoclearBuffer(*bornForce);
2780
    }
2781
2782
    vector<mm_float4> posqf(cl.getPaddedNumAtoms());
    vector<mm_double4> posqd(cl.getPaddedNumAtoms());
2783
    vector<mm_float2> paramsVector(cl.getPaddedNumAtoms(), mm_float2(1,1));
2784
    const double dielectricOffset = 0.009;
2785
    for (int i = 0; i < force.getNumParticles(); i++) {
2786
2787
2788
        double charge, radius, scalingFactor;
        force.getParticleParameters(i, charge, radius, scalingFactor);
        radius -= dielectricOffset;
2789
        paramsVector[i] = mm_float2((float) radius, (float) (scalingFactor*radius));
2790
2791
2792
2793
        if (cl.getUseDoublePrecision())
            posqd[i] = mm_double4(0, 0, 0, charge);
        else
            posqf[i] = mm_float4(0, 0, 0, (float) charge);
2794
    }
2795
2796
2797
2798
    if (cl.getUseDoublePrecision())
        cl.getPosq().upload(posqd);
    else
        cl.getPosq().upload(posqf);
2799
    params->upload(paramsVector);
2800
    prefactor = -ONE_4PI_EPS0*((1.0/force.getSoluteDielectric())-(1.0/force.getSolventDielectric()));
2801
    surfaceAreaFactor = -6.0*4*M_PI*force.getSurfaceAreaEnergy();
2802
2803
    bool useCutoff = (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff);
    bool usePeriodic = (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff && force.getNonbondedMethod() != GBSAOBCForce::CutoffNonPeriodic);
2804
    cutoff = force.getCutoffDistance();
2805
    string source = OpenCLKernelSources::gbsaObc2;
2806
    nb.addInteraction(useCutoff, usePeriodic, false, cutoff, vector<vector<int> >(), source, force.getForceGroup());
2807
    nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("obcParams", "float", 2, sizeof(cl_float2), params->getDeviceBuffer()));;
2808
    nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("bornForce", "real", 1, elementSize, bornForce->getDeviceBuffer()));;
Peter Eastman's avatar
Peter Eastman committed
2809
    cl.addForce(new OpenCLGBSAOBCForceInfo(nb.getNumForceBuffers(), force));
2810
2811
}

2812
double OpenCLCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
2813
    OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
2814
    bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
2815
2816
2817
2818
    if (!hasCreatedKernels) {
        // These Kernels cannot be created in initialize(), because the OpenCLNonbondedUtilities has not been initialized yet then.

        hasCreatedKernels = true;
2819
        maxTiles = (nb.getUseCutoff() ? nb.getInteractingTiles().getSize() : 0);
2820
2821
2822
2823
2824
        map<string, string> defines;
        if (nb.getUseCutoff())
            defines["USE_CUTOFF"] = "1";
        if (nb.getUsePeriodic())
            defines["USE_PERIODIC"] = "1";
2825
2826
        defines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
        defines["CUTOFF"] = cl.doubleToString(cutoff);
2827
        defines["PREFACTOR"] = cl.doubleToString(prefactor);
2828
        defines["SURFACE_AREA_FACTOR"] = cl.doubleToString(surfaceAreaFactor);
2829
2830
2831
2832
        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
        defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
        defines["NUM_BLOCKS"] = cl.intToString(cl.getNumAtomBlocks());
        defines["FORCE_WORK_GROUP_SIZE"] = cl.intToString(nb.getForceThreadBlockSize());
2833
2834
2835
2836
2837
2838
2839
2840
        defines["TILE_SIZE"] = cl.intToString(OpenCLContext::TileSize);
        int numExclusionTiles = nb.getExclusionTiles().getSize();
        defines["NUM_TILES_WITH_EXCLUSIONS"] = cl.intToString(numExclusionTiles);
        int numContexts = cl.getPlatformData().contexts.size();
        int startExclusionIndex = cl.getContextIndex()*numExclusionTiles/numContexts;
        int endExclusionIndex = (cl.getContextIndex()+1)*numExclusionTiles/numContexts;
        defines["FIRST_EXCLUSION_TILE"] = cl.intToString(startExclusionIndex);
        defines["LAST_EXCLUSION_TILE"] = cl.intToString(endExclusionIndex);
2841
2842
2843
        string platformVendor = cl::Platform(cl.getDevice().getInfo<CL_DEVICE_PLATFORM>()).getInfo<CL_PLATFORM_VENDOR>();
        if (platformVendor == "Apple")
            defines["USE_APPLE_WORKAROUND"] = "1";
2844
2845
2846
2847
        string file;
        if (deviceIsCpu)
            file = OpenCLKernelSources::gbsaObc_cpu;
        else
2848
            file = OpenCLKernelSources::gbsaObc;
2849
        cl::Program program = cl.createProgram(file, defines);
2850
        bool useLong = cl.getSupports64BitGlobalAtomics();
2851
        int index = 0;
2852
        computeBornSumKernel = cl::Kernel(program, "computeBornSum");
2853
        computeBornSumKernel.setArg<cl::Buffer>(index++, (useLong ? longBornSum->getDeviceBuffer() : bornSum->getDeviceBuffer()));
2854
2855
        computeBornSumKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
        computeBornSumKernel.setArg<cl::Buffer>(index++, params->getDeviceBuffer());
2856
        if (nb.getUseCutoff()) {
2857
2858
            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
2859
            index += 5; // The periodic box size arguments are set when the kernel is executed.
2860
            computeBornSumKernel.setArg<cl_uint>(index++, maxTiles);
2861
            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getBlockCenters().getDeviceBuffer());
2862
            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getBlockBoundingBoxes().getDeviceBuffer());
2863
            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getInteractingAtoms().getDeviceBuffer());
2864
        }
2865
2866
        else
            computeBornSumKernel.setArg<cl_uint>(index++, cl.getNumAtomBlocks()*(cl.getNumAtomBlocks()+1)/2);
2867
        computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getExclusionTiles().getDeviceBuffer());
2868
        force1Kernel = cl::Kernel(program, "computeGBSAForce1");
2869
        index = 0;
2870
2871
        force1Kernel.setArg<cl::Buffer>(index++, (useLong ? cl.getLongForceBuffer().getDeviceBuffer() : cl.getForceBuffers().getDeviceBuffer()));
        force1Kernel.setArg<cl::Buffer>(index++, (useLong ? longBornForce->getDeviceBuffer() : bornForce->getDeviceBuffer()));
2872
2873
2874
        force1Kernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        force1Kernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
        force1Kernel.setArg<cl::Buffer>(index++, bornRadii->getDeviceBuffer());
2875
        if (nb.getUseCutoff()) {
2876
2877
            force1Kernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
            force1Kernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
2878
            index += 5; // The periodic box size arguments are set when the kernel is executed.
2879
            force1Kernel.setArg<cl_uint>(index++, maxTiles);
2880
            force1Kernel.setArg<cl::Buffer>(index++, nb.getBlockCenters().getDeviceBuffer());
2881
            force1Kernel.setArg<cl::Buffer>(index++, nb.getBlockBoundingBoxes().getDeviceBuffer());
2882
            force1Kernel.setArg<cl::Buffer>(index++, nb.getInteractingAtoms().getDeviceBuffer());
2883
        }
2884
2885
        else
            force1Kernel.setArg<cl_uint>(index++, cl.getNumAtomBlocks()*(cl.getNumAtomBlocks()+1)/2);
2886
        force1Kernel.setArg<cl::Buffer>(index++, nb.getExclusionTiles().getDeviceBuffer());
2887
        program = cl.createProgram(OpenCLKernelSources::gbsaObcReductions, defines);
2888
2889
        reduceBornSumKernel = cl::Kernel(program, "reduceBornSum");
        reduceBornSumKernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
Peter Eastman's avatar
Peter Eastman committed
2890
        reduceBornSumKernel.setArg<cl_int>(1, nb.getNumForceBuffers());
2891
2892
2893
        reduceBornSumKernel.setArg<cl_float>(2, 1.0f);
        reduceBornSumKernel.setArg<cl_float>(3, 0.8f);
        reduceBornSumKernel.setArg<cl_float>(4, 4.85f);
2894
        reduceBornSumKernel.setArg<cl::Buffer>(5, (useLong ? longBornSum->getDeviceBuffer() : bornSum->getDeviceBuffer()));
2895
2896
2897
        reduceBornSumKernel.setArg<cl::Buffer>(6, params->getDeviceBuffer());
        reduceBornSumKernel.setArg<cl::Buffer>(7, bornRadii->getDeviceBuffer());
        reduceBornSumKernel.setArg<cl::Buffer>(8, obcChain->getDeviceBuffer());
2898
        reduceBornForceKernel = cl::Kernel(program, "reduceBornForce");
2899
2900
2901
2902
2903
2904
2905
2906
2907
2908
        index = 0;
        reduceBornForceKernel.setArg<cl_int>(index++, cl.getPaddedNumAtoms());
        reduceBornForceKernel.setArg<cl_int>(index++, nb.getNumForceBuffers());
        reduceBornForceKernel.setArg<cl::Buffer>(index++, bornForce->getDeviceBuffer());
        if (useLong)
            reduceBornForceKernel.setArg<cl::Buffer>(index++, longBornForce->getDeviceBuffer());
        reduceBornForceKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        reduceBornForceKernel.setArg<cl::Buffer>(index++, params->getDeviceBuffer());
        reduceBornForceKernel.setArg<cl::Buffer>(index++, bornRadii->getDeviceBuffer());
        reduceBornForceKernel.setArg<cl::Buffer>(index++, obcChain->getDeviceBuffer());
2909
    }
2910
    if (nb.getUseCutoff()) {
2911
2912
        setPeriodicBoxArgs(cl, computeBornSumKernel, 5);
        setPeriodicBoxArgs(cl, force1Kernel, 7);
2913
2914
        if (maxTiles < nb.getInteractingTiles().getSize()) {
            maxTiles = nb.getInteractingTiles().getSize();
2915
            computeBornSumKernel.setArg<cl::Buffer>(3, nb.getInteractingTiles().getDeviceBuffer());
2916
2917
            computeBornSumKernel.setArg<cl_uint>(10, maxTiles);
            computeBornSumKernel.setArg<cl::Buffer>(13, nb.getInteractingAtoms().getDeviceBuffer());
2918
            force1Kernel.setArg<cl::Buffer>(5, nb.getInteractingTiles().getDeviceBuffer());
2919
2920
            force1Kernel.setArg<cl_uint>(12, maxTiles);
            force1Kernel.setArg<cl::Buffer>(15, nb.getInteractingAtoms().getDeviceBuffer());
2921
        }
2922
    }
2923
    cl.executeKernel(computeBornSumKernel, nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());
2924
    cl.executeKernel(reduceBornSumKernel, cl.getPaddedNumAtoms());
2925
    cl.executeKernel(force1Kernel, nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());
2926
    cl.executeKernel(reduceBornForceKernel, cl.getPaddedNumAtoms());
2927
    return 0.0;
2928
}
2929

2930
2931
2932
2933
2934
2935
2936
2937
2938
void OpenCLCalcGBSAOBCForceKernel::copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force) {
    // Make sure the new parameters are acceptable.
    
    int numParticles = force.getNumParticles();
    if (numParticles != cl.getNumAtoms())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
    
    // Record the per-particle parameters.
    
2939
2940
    OpenCLArray& posq = cl.getPosq();
    mm_float4* posqf = (mm_float4*) cl.getPinnedBuffer();
2941
2942
    mm_double4* posqd = (mm_double4*) cl.getPinnedBuffer();
    posq.download(cl.getPinnedBuffer());
2943
    vector<mm_float2> paramsVector(cl.getPaddedNumAtoms(), mm_float2(1,1));
2944
2945
2946
2947
2948
2949
    const double dielectricOffset = 0.009;
    for (int i = 0; i < numParticles; i++) {
        double charge, radius, scalingFactor;
        force.getParticleParameters(i, charge, radius, scalingFactor);
        radius -= dielectricOffset;
        paramsVector[i] = mm_float2((float) radius, (float) (scalingFactor*radius));
2950
2951
2952
2953
        if (cl.getUseDoublePrecision())
            posqd[i].w = charge;
        else
            posqf[i].w = (float) charge;
2954
    }
2955
    posq.upload(cl.getPinnedBuffer());
2956
2957
2958
2959
2960
2961
2962
    params->upload(paramsVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

2963
2964
2965
2966
2967
2968
2969
2970
2971
class OpenCLCustomGBForceInfo : public OpenCLForceInfo {
public:
    OpenCLCustomGBForceInfo(int requiredBuffers, const CustomGBForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
    }
    bool areParticlesIdentical(int particle1, int particle2) {
        vector<double> params1;
        vector<double> params2;
        force.getParticleParameters(particle1, params1);
        force.getParticleParameters(particle2, params2);
2972
        for (int i = 0; i < (int) params1.size(); i++)
2973
2974
2975
2976
2977
2978
2979
            if (params1[i] != params2[i])
                return false;
        return true;
    }
    int getNumParticleGroups() {
        return force.getNumExclusions();
    }
Peter Eastman's avatar
Peter Eastman committed
2980
    void getParticlesInGroup(int index, vector<int>& particles) {
2981
2982
2983
2984
2985
2986
2987
2988
2989
2990
2991
2992
2993
2994
2995
2996
2997
2998
        int particle1, particle2;
        force.getExclusionParticles(index, particle1, particle2);
        particles.resize(2);
        particles[0] = particle1;
        particles[1] = particle2;
    }
    bool areGroupsIdentical(int group1, int group2) {
        return true;
    }
private:
    const CustomGBForce& force;
};

OpenCLCalcCustomGBForceKernel::~OpenCLCalcCustomGBForceKernel() {
    if (params != NULL)
        delete params;
    if (computedValues != NULL)
        delete computedValues;
2999
3000
    if (energyDerivs != NULL)
        delete energyDerivs;
3001
3002
    if (energyDerivChain != NULL)
        delete energyDerivChain;
3003
3004
    if (longEnergyDerivs != NULL)
        delete longEnergyDerivs;
3005
3006
    if (globals != NULL)
        delete globals;
3007
3008
    if (valueBuffers != NULL)
        delete valueBuffers;
3009
3010
    if (longValueBuffers != NULL)
        delete longValueBuffers;
3011
3012
3013
3014
3015
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
}

void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const CustomGBForce& force) {
3016
3017
    if (cl.getPlatformData().contexts.size() > 1)
        throw OpenMMException("CustomGBForce does not support using multiple OpenCL devices");
3018
    cutoff = force.getCutoffDistance();
3019
    bool useExclusionsForValue = false;
3020
    numComputedValues = force.getNumComputedValues();
3021
3022
    vector<string> computedValueNames(force.getNumComputedValues());
    vector<string> computedValueExpressions(force.getNumComputedValues());
3023
3024
    if (force.getNumComputedValues() > 0) {
        CustomGBForce::ComputationType type;
3025
        force.getComputedValueParameters(0, computedValueNames[0], computedValueExpressions[0], type);
3026
3027
3028
3029
        if (type == CustomGBForce::SingleParticle)
            throw OpenMMException("OpenCLPlatform requires that the first computed value for a CustomGBForce be of type ParticlePair or ParticlePairNoExclusions.");
        useExclusionsForValue = (type == CustomGBForce::ParticlePair);
        for (int i = 1; i < force.getNumComputedValues(); i++) {
3030
            force.getComputedValueParameters(i, computedValueNames[i], computedValueExpressions[i], type);
3031
3032
3033
3034
3035
3036
3037
            if (type != CustomGBForce::SingleParticle)
                throw OpenMMException("OpenCLPlatform requires that a CustomGBForce only have one computed value of type ParticlePair or ParticlePairNoExclusions.");
        }
    }
    int forceIndex;
    for (forceIndex = 0; forceIndex < system.getNumForces() && &system.getForce(forceIndex) != &force; ++forceIndex)
        ;
3038
    string prefix = "custom"+cl.intToString(forceIndex)+"_";
3039
3040
3041
3042

    // Record parameters and exclusions.

    int numParticles = force.getNumParticles();
3043
3044
3045
3046
    int paddedNumParticles = cl.getPaddedNumAtoms();
    int numParams = force.getNumPerParticleParameters();
    params = new OpenCLParameterSet(cl, force.getNumPerParticleParameters(), paddedNumParticles, "customGBParameters", true);
    computedValues = new OpenCLParameterSet(cl, force.getNumComputedValues(), paddedNumParticles, "customGBComputedValues", true, cl.getUseDoublePrecision());
3047
    if (force.getNumGlobalParameters() > 0)
3048
        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customGBGlobals", CL_MEM_READ_ONLY);
3049
    vector<vector<cl_float> > paramVector(paddedNumParticles, vector<cl_float>(numParams, 0));
3050
3051
3052
3053
    vector<vector<int> > exclusionList(numParticles);
    for (int i = 0; i < numParticles; i++) {
        vector<double> parameters;
        force.getParticleParameters(i, parameters);
3054
        for (int j = 0; j < (int) parameters.size(); j++)
3055
3056
3057
3058
3059
3060
3061
3062
3063
3064
3065
3066
3067
3068
3069
            paramVector[i][j] = (cl_float) parameters[j];
        exclusionList[i].push_back(i);
    }
    for (int i = 0; i < force.getNumExclusions(); i++) {
        int particle1, particle2;
        force.getExclusionParticles(i, particle1, particle2);
        exclusionList[particle1].push_back(particle2);
        exclusionList[particle2].push_back(particle1);
    }
    params->setParameterValues(paramVector);

    // Record the tabulated functions.

    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
3070
    vector<const TabulatedFunction*> functionList;
3071
    stringstream tableArgs;
3072
3073
3074
    for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
3075
        string arrayName = prefix+"table"+cl.intToString(i);
3076
        functionDefinitions.push_back(make_pair(name, arrayName));
3077
        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
peastman's avatar
peastman committed
3078
        int width;
3079
        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
3080
        tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
3081
        tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
peastman's avatar
peastman committed
3082
        cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(arrayName, "float", width, width*sizeof(float), tabulatedFunctions[tabulatedFunctions.size()-1]->getDeviceBuffer()));
3083
3084
3085
3086
        tableArgs << ", __global const float";
        if (width > 1)
            tableArgs << width;
        tableArgs << "* restrict " << arrayName;
3087
3088
    }

3089
    // Record the global parameters.
3090
3091
3092
3093
3094
3095
3096
3097
3098

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    if (globals != NULL)
        globals->upload(globalParamValues);
3099
3100
3101

    // Record derivatives of expressions needed for the chain rule terms.

3102
    vector<vector<Lepton::ParsedExpression> > valueGradientExpressions(force.getNumComputedValues());
3103
    vector<vector<Lepton::ParsedExpression> > valueDerivExpressions(force.getNumComputedValues());
Peter Eastman's avatar
Peter Eastman committed
3104
    needParameterGradient = false;
3105
3106
3107
3108
3109
3110
3111
    for (int i = 1; i < force.getNumComputedValues(); i++) {
        Lepton::ParsedExpression ex = Lepton::Parser::parse(computedValueExpressions[i], functions).optimize();
        valueGradientExpressions[i].push_back(ex.differentiate("x").optimize());
        valueGradientExpressions[i].push_back(ex.differentiate("y").optimize());
        valueGradientExpressions[i].push_back(ex.differentiate("z").optimize());
        if (!isZeroExpression(valueGradientExpressions[i][0]) || !isZeroExpression(valueGradientExpressions[i][1]) || !isZeroExpression(valueGradientExpressions[i][2]))
            needParameterGradient = true;
3112
3113
         for (int j = 0; j < i; j++)
            valueDerivExpressions[i].push_back(ex.differentiate(computedValueNames[j]).optimize());
3114
    }
3115
    vector<vector<Lepton::ParsedExpression> > energyDerivExpressions(force.getNumEnergyTerms());
Peter Eastman's avatar
Peter Eastman committed
3116
    vector<bool> needChainForValue(force.getNumComputedValues(), false);
3117
3118
3119
3120
3121
3122
    for (int i = 0; i < force.getNumEnergyTerms(); i++) {
        string expression;
        CustomGBForce::ComputationType type;
        force.getEnergyTermParameters(i, expression, type);
        Lepton::ParsedExpression ex = Lepton::Parser::parse(expression, functions).optimize();
        for (int j = 0; j < force.getNumComputedValues(); j++) {
Peter Eastman's avatar
Peter Eastman committed
3123
            if (type == CustomGBForce::SingleParticle) {
3124
                energyDerivExpressions[i].push_back(ex.differentiate(computedValueNames[j]).optimize());
Peter Eastman's avatar
Peter Eastman committed
3125
3126
3127
                if (!isZeroExpression(energyDerivExpressions[i].back()))
                    needChainForValue[j] = true;
            }
3128
3129
            else {
                energyDerivExpressions[i].push_back(ex.differentiate(computedValueNames[j]+"1").optimize());
Peter Eastman's avatar
Peter Eastman committed
3130
3131
                if (!isZeroExpression(energyDerivExpressions[i].back()))
                    needChainForValue[j] = true;
3132
                energyDerivExpressions[i].push_back(ex.differentiate(computedValueNames[j]+"2").optimize());
Peter Eastman's avatar
Peter Eastman committed
3133
3134
                if (!isZeroExpression(energyDerivExpressions[i].back()))
                    needChainForValue[j] = true;
3135
3136
3137
            }
        }
    }
3138
    bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
3139
    bool useLong = cl.getSupports64BitGlobalAtomics();
3140
    if (useLong) {
3141
        longEnergyDerivs = OpenCLArray::create<cl_long>(cl, force.getNumComputedValues()*cl.getPaddedNumAtoms(), "customGBLongEnergyDerivatives");
Peter Eastman's avatar
Peter Eastman committed
3142
        energyDerivs = new OpenCLParameterSet(cl, force.getNumComputedValues(), cl.getPaddedNumAtoms(), "customGBEnergyDerivatives", true);
3143
3144
    }
    else
Peter Eastman's avatar
Peter Eastman committed
3145
        energyDerivs = new OpenCLParameterSet(cl, force.getNumComputedValues(), cl.getPaddedNumAtoms()*cl.getNonbondedUtilities().getNumForceBuffers(), "customGBEnergyDerivatives", true);
3146
3147
    energyDerivChain = new OpenCLParameterSet(cl, force.getNumComputedValues(), cl.getPaddedNumAtoms(), "customGBEnergyDerivativeChain", true);

3148
3149
    // Create the kernels.

3150
3151
    bool useCutoff = (force.getNonbondedMethod() != CustomGBForce::NoCutoff);
    bool usePeriodic = (force.getNonbondedMethod() != CustomGBForce::NoCutoff && force.getNonbondedMethod() != CustomGBForce::CutoffNonPeriodic);
3152
3153
3154
    {
        // Create the N2 value kernel.

3155
        vector<pair<ExpressionTreeNode, string> > variables;
3156
        map<string, string> rename;
3157
3158
3159
3160
        ExpressionTreeNode rnode(new Operation::Variable("r"));
        variables.push_back(make_pair(rnode, "r"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Square(), rnode), "r2"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Reciprocal(), rnode), "invR"));
3161
3162
        for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
            const string& name = force.getPerParticleParameterName(i);
3163
3164
            variables.push_back(makeVariable(name+"1", "params"+params->getParameterSuffix(i, "1")));
            variables.push_back(makeVariable(name+"2", "params"+params->getParameterSuffix(i, "2")));
3165
3166
            rename[name+"1"] = name+"2";
            rename[name+"2"] = name+"1";
3167
3168
3169
        }
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
3170
            string value = "globals["+cl.intToString(i)+"]";
3171
            variables.push_back(makeVariable(name, value));
3172
        }
3173
3174
        map<string, Lepton::ParsedExpression> n2ValueExpressions;
        stringstream n2ValueSource;
3175
3176
3177
        Lepton::ParsedExpression ex = Lepton::Parser::parse(computedValueExpressions[0], functions).optimize();
        n2ValueExpressions["tempValue1 = "] = ex;
        n2ValueExpressions["tempValue2 = "] = ex.renameVariables(rename);
3178
        n2ValueSource << cl.getExpressionUtilities().createExpressions(n2ValueExpressions, variables, functionList, functionDefinitions, "temp");
3179
        map<string, string> replacements;
Peter Eastman's avatar
Peter Eastman committed
3180
3181
        string n2ValueStr = n2ValueSource.str();
        replacements["COMPUTE_VALUE"] = n2ValueStr;
3182
3183
        stringstream extraArgs, loadLocal1, loadLocal2, load1, load2;
        if (force.getNumGlobalParameters() > 0)
Peter Eastman's avatar
Peter Eastman committed
3184
            extraArgs << ", __global const float* globals";
Peter Eastman's avatar
Peter Eastman committed
3185
        pairValueUsesParam.resize(params->getBuffers().size(), false);
3186
3187
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
3188
            string paramName = "params"+cl.intToString(i+1);
Peter Eastman's avatar
Peter Eastman committed
3189
3190
3191
3192
3193
3194
3195
3196
            if (n2ValueStr.find(paramName+"1") != n2ValueStr.npos || n2ValueStr.find(paramName+"2") != n2ValueStr.npos) {
                extraArgs << ", __global const " << buffer.getType() << "* restrict global_" << paramName << ", __local " << buffer.getType() << "* restrict local_" << paramName;
                loadLocal1 << "local_" << paramName << "[localAtomIndex] = " << paramName << "1;\n";
                loadLocal2 << "local_" << paramName << "[localAtomIndex] = global_" << paramName << "[j];\n";
                load1 << buffer.getType() << " " << paramName << "1 = global_" << paramName << "[atom1];\n";
                load2 << buffer.getType() << " " << paramName << "2 = local_" << paramName << "[atom2];\n";
                pairValueUsesParam[i] = true;
            }
3197
        }
3198
        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
3199
3200
3201
3202
3203
        replacements["LOAD_LOCAL_PARAMETERS_FROM_1"] = loadLocal1.str();
        replacements["LOAD_LOCAL_PARAMETERS_FROM_GLOBAL"] = loadLocal2.str();
        replacements["LOAD_ATOM1_PARAMETERS"] = load1.str();
        replacements["LOAD_ATOM2_PARAMETERS"] = load2.str();
        if (useCutoff)
3204
            pairValueDefines["USE_CUTOFF"] = "1";
3205
        if (usePeriodic)
3206
            pairValueDefines["USE_PERIODIC"] = "1";
3207
        if (useExclusionsForValue)
3208
3209
            pairValueDefines["USE_EXCLUSIONS"] = "1";
        pairValueDefines["FORCE_WORK_GROUP_SIZE"] = cl.intToString(cl.getNonbondedUtilities().getForceThreadBlockSize());
3210
        pairValueDefines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
3211
3212
3213
3214
        pairValueDefines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
        pairValueDefines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
        pairValueDefines["NUM_BLOCKS"] = cl.intToString(cl.getNumAtomBlocks());
        pairValueDefines["TILE_SIZE"] = cl.intToString(OpenCLContext::TileSize);
3215
3216
3217
3218
        string file;
        if (deviceIsCpu)
            file = OpenCLKernelSources::customGBValueN2_cpu;
        else
3219
3220
            file = OpenCLKernelSources::customGBValueN2;
        pairValueSrc = cl.replaceStrings(file, replacements);
3221
3222
        if (useExclusionsForValue)
            cl.getNonbondedUtilities().requestExclusions(exclusionList);
3223
3224
3225
3226
3227
3228
    }
    {
        // Create the kernel to reduce the N2 value and calculate other values.

        stringstream reductionSource, extraArgs;
        if (force.getNumGlobalParameters() > 0)
Peter Eastman's avatar
Peter Eastman committed
3229
            extraArgs << ", __global const float* globals";
3230
3231
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
3232
            string paramName = "params"+cl.intToString(i+1);
3233
            extraArgs << ", __global const " << buffer.getType() << "* restrict " << paramName;
3234
3235
3236
        }
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
3237
            string valueName = "values"+cl.intToString(i+1);
3238
            extraArgs << ", __global " << buffer.getType() << "* restrict global_" << valueName;
3239
3240
3241
            reductionSource << buffer.getType() << " local_" << valueName << ";\n";
        }
        reductionSource << "local_values" << computedValues->getParameterSuffix(0) << " = sum;\n";
3242
        map<string, string> variables;
3243
3244
3245
        variables["x"] = "pos.x";
        variables["y"] = "pos.y";
        variables["z"] = "pos.z";
3246
3247
3248
        for (int i = 0; i < force.getNumPerParticleParameters(); i++)
            variables[force.getPerParticleParameterName(i)] = "params"+params->getParameterSuffix(i, "[index]");
        for (int i = 0; i < force.getNumGlobalParameters(); i++)
3249
            variables[force.getGlobalParameterName(i)] = "globals["+cl.intToString(i)+"]";
3250
3251
3252
3253
        for (int i = 1; i < force.getNumComputedValues(); i++) {
            variables[computedValueNames[i-1]] = "local_values"+computedValues->getParameterSuffix(i-1);
            map<string, Lepton::ParsedExpression> valueExpressions;
            valueExpressions["local_values"+computedValues->getParameterSuffix(i)+" = "] = Lepton::Parser::parse(computedValueExpressions[i], functions).optimize();
3254
            reductionSource << cl.getExpressionUtilities().createExpressions(valueExpressions, variables, functionList, functionDefinitions, "value"+cl.intToString(i)+"_temp");
3255
        }
3256
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
3257
            string valueName = "values"+cl.intToString(i+1);
3258
3259
3260
            reductionSource << "global_" << valueName << "[index] = local_" << valueName << ";\n";
        }
        map<string, string> replacements;
3261
        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
3262
3263
        replacements["COMPUTE_VALUES"] = reductionSource.str();
        map<string, string> defines;
3264
        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
3265
        cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customGBValuePerParticle, replacements), defines);
3266
3267
3268
3269
3270
        perParticleValueKernel = cl::Kernel(program, "computePerParticleValues");
    }
    {
        // Create the N2 energy kernel.

3271
3272
3273
3274
3275
        vector<pair<ExpressionTreeNode, string> > variables;
        ExpressionTreeNode rnode(new Operation::Variable("r"));
        variables.push_back(make_pair(rnode, "r"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Square(), rnode), "r2"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Reciprocal(), rnode), "invR"));
3276
3277
        for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
            const string& name = force.getPerParticleParameterName(i);
3278
3279
            variables.push_back(makeVariable(name+"1", "params"+params->getParameterSuffix(i, "1")));
            variables.push_back(makeVariable(name+"2", "params"+params->getParameterSuffix(i, "2")));
3280
3281
        }
        for (int i = 0; i < force.getNumComputedValues(); i++) {
3282
3283
            variables.push_back(makeVariable(computedValueNames[i]+"1", "values"+computedValues->getParameterSuffix(i, "1")));
            variables.push_back(makeVariable(computedValueNames[i]+"2", "values"+computedValues->getParameterSuffix(i, "2")));
3284
3285
        }
        for (int i = 0; i < force.getNumGlobalParameters(); i++)
3286
            variables.push_back(makeVariable(force.getGlobalParameterName(i), "globals["+cl.intToString(i)+"]"));
3287
        stringstream n2EnergySource;
3288
        bool anyExclusions = (force.getNumExclusions() > 0);
3289
3290
3291
3292
3293
3294
        for (int i = 0; i < force.getNumEnergyTerms(); i++) {
            string expression;
            CustomGBForce::ComputationType type;
            force.getEnergyTermParameters(i, expression, type);
            if (type == CustomGBForce::SingleParticle)
                continue;
3295
            bool exclude = (anyExclusions && type == CustomGBForce::ParticlePair);
3296
            map<string, Lepton::ParsedExpression> n2EnergyExpressions;
3297
3298
            n2EnergyExpressions["tempEnergy += "] = Lepton::Parser::parse(expression, functions).optimize();
            n2EnergyExpressions["dEdR += "] = Lepton::Parser::parse(expression, functions).differentiate("r").optimize();
3299
3300
            if (useLong) {
                for (int j = 0; j < force.getNumComputedValues(); j++) {
Peter Eastman's avatar
Peter Eastman committed
3301
                    if (needChainForValue[j]) {
3302
3303
3304
                        string index = cl.intToString(j+1);
                        n2EnergyExpressions["/*"+cl.intToString(i+1)+"*/ deriv"+index+"_1 += "] = energyDerivExpressions[i][2*j];
                        n2EnergyExpressions["/*"+cl.intToString(i+1)+"*/ deriv"+index+"_2 += "] = energyDerivExpressions[i][2*j+1];
Peter Eastman's avatar
Peter Eastman committed
3305
                    }
3306
3307
3308
3309
                }
            }
            else {
                for (int j = 0; j < force.getNumComputedValues(); j++) {
Peter Eastman's avatar
Peter Eastman committed
3310
                    if (needChainForValue[j]) {
3311
3312
                        n2EnergyExpressions["/*"+cl.intToString(i+1)+"*/ deriv"+energyDerivs->getParameterSuffix(j, "_1")+" += "] = energyDerivExpressions[i][2*j];
                        n2EnergyExpressions["/*"+cl.intToString(i+1)+"*/ deriv"+energyDerivs->getParameterSuffix(j, "_2")+" += "] = energyDerivExpressions[i][2*j+1];
Peter Eastman's avatar
Peter Eastman committed
3313
                    }
3314
                }
3315
3316
3317
            }
            if (exclude)
                n2EnergySource << "if (!isExcluded) {\n";
3318
            n2EnergySource << cl.getExpressionUtilities().createExpressions(n2EnergyExpressions, variables, functionList, functionDefinitions, "temp");
3319
3320
            if (exclude)
                n2EnergySource << "}\n";
3321
3322
        }
        map<string, string> replacements;
Peter Eastman's avatar
Peter Eastman committed
3323
3324
        string n2EnergyStr = n2EnergySource.str();
        replacements["COMPUTE_INTERACTION"] = n2EnergyStr;
3325
        stringstream extraArgs, loadLocal1, loadLocal2, clearLocal, load1, load2, declare1, recordDeriv, storeDerivs1, storeDerivs2, declareTemps, setTemps;
3326
        if (force.getNumGlobalParameters() > 0)
Peter Eastman's avatar
Peter Eastman committed
3327
            extraArgs << ", __global const float* globals";
Peter Eastman's avatar
Peter Eastman committed
3328
        pairEnergyUsesParam.resize(params->getBuffers().size(), false);
3329
3330
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
3331
            string paramName = "params"+cl.intToString(i+1);
Peter Eastman's avatar
Peter Eastman committed
3332
3333
3334
3335
3336
3337
3338
3339
            if (n2EnergyStr.find(paramName+"1") != n2EnergyStr.npos || n2EnergyStr.find(paramName+"2") != n2EnergyStr.npos) {
                extraArgs << ", __global const " << buffer.getType() << "* restrict global_" << paramName << ", __local " << buffer.getType() << "* restrict local_" << paramName;
                loadLocal1 << "local_" << paramName << "[localAtomIndex] = " << paramName << "1;\n";
                loadLocal2 << "local_" << paramName << "[localAtomIndex] = global_" << paramName << "[j];\n";
                load1 << buffer.getType() << " " << paramName << "1 = global_" << paramName << "[atom1];\n";
                load2 << buffer.getType() << " " << paramName << "2 = local_" << paramName << "[atom2];\n";
                pairEnergyUsesParam[i] = true;
            }
3340
        }
Peter Eastman's avatar
Peter Eastman committed
3341
        pairEnergyUsesValue.resize(computedValues->getBuffers().size(), false);
3342
3343
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
3344
            string valueName = "values"+cl.intToString(i+1);
Peter Eastman's avatar
Peter Eastman committed
3345
3346
3347
3348
3349
3350
3351
3352
            if (n2EnergyStr.find(valueName+"1") != n2EnergyStr.npos || n2EnergyStr.find(valueName+"2") != n2EnergyStr.npos) {
                extraArgs << ", __global const " << buffer.getType() << "* restrict global_" << valueName << ", __local " << buffer.getType() << "* restrict local_" << valueName;
                loadLocal1 << "local_" << valueName << "[localAtomIndex] = " << valueName << "1;\n";
                loadLocal2 << "local_" << valueName << "[localAtomIndex] = global_" << valueName << "[j];\n";
                load1 << buffer.getType() << " " << valueName << "1 = global_" << valueName << "[atom1];\n";
                load2 << buffer.getType() << " " << valueName << "2 = local_" << valueName << "[atom2];\n";
                pairEnergyUsesValue[i] = true;
            }
3353
        }
3354
        if (useLong) {
3355
            extraArgs << ", __global long* restrict derivBuffers";
3356
            for (int i = 0; i < force.getNumComputedValues(); i++) {
3357
                string index = cl.intToString(i+1);
3358
                extraArgs << ", __local real* restrict local_deriv" << index;
3359
                clearLocal << "local_deriv" << index << "[localAtomIndex] = 0.0f;\n";
3360
3361
                declare1 << "real deriv" << index << "_1 = 0;\n";
                load2 << "real deriv" << index << "_2 = 0;\n";
3362
3363
3364
                recordDeriv << "local_deriv" << index << "[atom2] += deriv" << index << "_2;\n";
                storeDerivs1 << "STORE_DERIVATIVE_1(" << index << ")\n";
                storeDerivs2 << "STORE_DERIVATIVE_2(" << index << ")\n";
3365
                declareTemps << "__local real tempDerivBuffer" << index << "[64];\n";
3366
3367
3368
3369
3370
3371
                setTemps << "tempDerivBuffer" << index << "[get_local_id(0)] = deriv" << index << "_1;\n";
            }
        }
        else {
            for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
3372
                string index = cl.intToString(i+1);
3373
                extraArgs << ", __global " << buffer.getType() << "* restrict derivBuffers" << index << ", __local " << buffer.getType() << "* restrict local_deriv" << index;
3374
3375
3376
3377
3378
3379
3380
3381
3382
                clearLocal << "local_deriv" << index << "[localAtomIndex] = 0.0f;\n";
                declare1 << buffer.getType() << " deriv" << index << "_1 = 0.0f;\n";
                load2 << buffer.getType() << " deriv" << index << "_2 = 0.0f;\n";
                recordDeriv << "local_deriv" << index << "[atom2] += deriv" << index << "_2;\n";
                storeDerivs1 << "STORE_DERIVATIVE_1(" << index << ")\n";
                storeDerivs2 << "STORE_DERIVATIVE_2(" << index << ")\n";
                declareTemps << "__local " << buffer.getType() << " tempDerivBuffer" << index << "[64];\n";
                setTemps << "tempDerivBuffer" << index << "[get_local_id(0)] = deriv" << index << "_1;\n";
            }
3383
        }
3384
3385
3386
        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
        replacements["LOAD_LOCAL_PARAMETERS_FROM_1"] = loadLocal1.str();
        replacements["LOAD_LOCAL_PARAMETERS_FROM_GLOBAL"] = loadLocal2.str();
3387
        replacements["CLEAR_LOCAL_DERIVATIVES"] = clearLocal.str();
3388
3389
        replacements["LOAD_ATOM1_PARAMETERS"] = load1.str();
        replacements["LOAD_ATOM2_PARAMETERS"] = load2.str();
3390
        replacements["DECLARE_ATOM1_DERIVATIVES"] = declare1.str();
3391
3392
3393
        replacements["RECORD_DERIVATIVE_2"] = recordDeriv.str();
        replacements["STORE_DERIVATIVES_1"] = storeDerivs1.str();
        replacements["STORE_DERIVATIVES_2"] = storeDerivs2.str();
3394
3395
        replacements["DECLARE_TEMP_BUFFERS"] = declareTemps.str();
        replacements["SET_TEMP_BUFFERS"] = setTemps.str();
3396
        if (useCutoff)
3397
            pairEnergyDefines["USE_CUTOFF"] = "1";
3398
        if (usePeriodic)
3399
            pairEnergyDefines["USE_PERIODIC"] = "1";
3400
        if (anyExclusions)
3401
3402
            pairEnergyDefines["USE_EXCLUSIONS"] = "1";
        pairEnergyDefines["FORCE_WORK_GROUP_SIZE"] = cl.intToString(cl.getNonbondedUtilities().getForceThreadBlockSize());
3403
        pairEnergyDefines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
3404
3405
3406
3407
        pairEnergyDefines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
        pairEnergyDefines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
        pairEnergyDefines["NUM_BLOCKS"] = cl.intToString(cl.getNumAtomBlocks());
        pairEnergyDefines["TILE_SIZE"] = cl.intToString(OpenCLContext::TileSize);
3408
3409
3410
3411
        string file;
        if (deviceIsCpu)
            file = OpenCLKernelSources::customGBEnergyN2_cpu;
        else
3412
3413
            file = OpenCLKernelSources::customGBEnergyN2;
        pairEnergySrc = cl.replaceStrings(file, replacements);
3414
3415
3416
3417
    }
    {
        // Create the kernel to reduce the derivatives and calculate per-particle energy terms.

3418
        stringstream compute, extraArgs, reduce;
3419
        if (force.getNumGlobalParameters() > 0)
Peter Eastman's avatar
Peter Eastman committed
3420
            extraArgs << ", __global const float* globals";
3421
3422
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
3423
            string paramName = "params"+cl.intToString(i+1);
3424
            extraArgs << ", __global const " << buffer.getType() << "* restrict " << paramName;
3425
3426
3427
        }
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
3428
            string valueName = "values"+cl.intToString(i+1);
3429
            extraArgs << ", __global const " << buffer.getType() << "* restrict " << valueName;
3430
        }
3431
3432
        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
3433
            string index = cl.intToString(i+1);
3434
            extraArgs << ", __global " << buffer.getType() << "* restrict derivBuffers" << index;
3435
3436
            compute << buffer.getType() << " deriv" << index << " = derivBuffers" << index << "[index];\n";
        }
3437
3438
3439
3440
3441
        for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivChain->getBuffers()[i];
            string index = cl.intToString(i+1);
            extraArgs << ", __global " << buffer.getType() << "* restrict derivChain" << index;
        }
3442
        if (useLong) {
3443
            extraArgs << ", __global const long* restrict derivBuffersIn";
3444
3445
            for (int i = 0; i < energyDerivs->getNumParameters(); ++i)
                reduce << "derivBuffers" << energyDerivs->getParameterSuffix(i, "[index]") <<
3446
                        " = (1.0f/0x100000000)*derivBuffersIn[index+PADDED_NUM_ATOMS*" << cl.intToString(i) << "];\n";
3447
3448
3449
        }
        else {
            for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++)
3450
                reduce << "REDUCE_VALUE(derivBuffers" << cl.intToString(i+1) << ", " << energyDerivs->getBuffers()[i].getType() << ")\n";
3451
        }
Peter Eastman's avatar
Peter Eastman committed
3452
3453
3454
        
        // Compute the various expressions.
        
3455
        map<string, string> variables;
3456
3457
3458
        variables["x"] = "pos.x";
        variables["y"] = "pos.y";
        variables["z"] = "pos.z";
3459
3460
3461
        for (int i = 0; i < force.getNumPerParticleParameters(); i++)
            variables[force.getPerParticleParameterName(i)] = "params"+params->getParameterSuffix(i, "[index]");
        for (int i = 0; i < force.getNumGlobalParameters(); i++)
3462
            variables[force.getGlobalParameterName(i)] = "globals["+cl.intToString(i)+"]";
3463
3464
        for (int i = 0; i < force.getNumComputedValues(); i++)
            variables[computedValueNames[i]] = "values"+computedValues->getParameterSuffix(i, "[index]");
Peter Eastman's avatar
Peter Eastman committed
3465
        map<string, Lepton::ParsedExpression> expressions;
3466
3467
3468
3469
3470
3471
        for (int i = 0; i < force.getNumEnergyTerms(); i++) {
            string expression;
            CustomGBForce::ComputationType type;
            force.getEnergyTermParameters(i, expression, type);
            if (type != CustomGBForce::SingleParticle)
                continue;
3472
            Lepton::ParsedExpression parsed = Lepton::Parser::parse(expression, functions).optimize();
3473
            expressions["/*"+cl.intToString(i+1)+"*/ energy += "] = parsed;
3474
            for (int j = 0; j < force.getNumComputedValues(); j++)
3475
                expressions["/*"+cl.intToString(i+1)+"*/ deriv"+energyDerivs->getParameterSuffix(j)+" += "] = energyDerivExpressions[i][j];
3476
3477
3478
3479
            Lepton::ParsedExpression gradx = parsed.differentiate("x").optimize();
            Lepton::ParsedExpression grady = parsed.differentiate("y").optimize();
            Lepton::ParsedExpression gradz = parsed.differentiate("z").optimize();
            if (!isZeroExpression(gradx))
3480
                expressions["/*"+cl.intToString(i+1)+"*/ force.x -= "] = gradx;
3481
            if (!isZeroExpression(grady))
3482
                expressions["/*"+cl.intToString(i+1)+"*/ force.y -= "] = grady;
3483
            if (!isZeroExpression(gradz))
3484
                expressions["/*"+cl.intToString(i+1)+"*/ force.z -= "] = gradz;
Peter Eastman's avatar
Peter Eastman committed
3485
3486
3487
        }
        for (int i = 1; i < force.getNumComputedValues(); i++)
            for (int j = 0; j < i; j++)
3488
                expressions["real dV"+cl.intToString(i)+"dV"+cl.intToString(j)+" = "] = valueDerivExpressions[i][j];
3489
        compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functionList, functionDefinitions, "temp");
Peter Eastman's avatar
Peter Eastman committed
3490
3491
3492
        
        // Record values.
        
3493
3494
3495
3496
        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
            string index = cl.intToString(i+1);
            compute << "derivBuffers" << index << "[index] = deriv" << index << ";\n";
        }
Peter Eastman's avatar
Peter Eastman committed
3497
3498
        compute << "forceBuffers[index] = forceBuffers[index]+force;\n";
        for (int i = 1; i < force.getNumComputedValues(); i++) {
3499
            compute << "real totalDeriv"<<i<<" = dV"<<i<<"dV0";
Peter Eastman's avatar
Peter Eastman committed
3500
3501
3502
3503
            for (int j = 1; j < i; j++)
                compute << " + totalDeriv"<<j<<"*dV"<<i<<"dV"<<j;
            compute << ";\n";
            compute << "deriv"<<(i+1)<<" *= totalDeriv"<<i<<";\n";
3504
3505
        }
        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
3506
            string index = cl.intToString(i+1);
3507
            compute << "derivChain" << index << "[index] = deriv" << index << ";\n";
3508
3509
3510
        }
        map<string, string> replacements;
        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
3511
3512
        replacements["REDUCE_DERIVATIVES"] = reduce.str();
        replacements["COMPUTE_ENERGY"] = compute.str();
3513
        map<string, string> defines;
3514
3515
        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
        defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
3516
        cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customGBEnergyPerParticle, replacements), defines);
3517
        perParticleEnergyKernel = cl::Kernel(program, "computePerParticleEnergy");
3518
    }
Peter Eastman's avatar
Peter Eastman committed
3519
3520
3521
3522
3523
    if (needParameterGradient) {
        // Create the kernel to compute chain rule terms for computed values that depend explicitly on particle coordinates.

        stringstream compute, extraArgs;
        if (force.getNumGlobalParameters() > 0)
Peter Eastman's avatar
Peter Eastman committed
3524
            extraArgs << ", __global const float* globals";
Peter Eastman's avatar
Peter Eastman committed
3525
3526
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
3527
            string paramName = "params"+cl.intToString(i+1);
3528
            extraArgs << ", __global const " << buffer.getType() << "* restrict " << paramName;
Peter Eastman's avatar
Peter Eastman committed
3529
3530
3531
        }
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
3532
            string valueName = "values"+cl.intToString(i+1);
3533
            extraArgs << ", __global const " << buffer.getType() << "* restrict " << valueName;
Peter Eastman's avatar
Peter Eastman committed
3534
3535
3536
        }
        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
3537
            string index = cl.intToString(i+1);
3538
            extraArgs << ", __global " << buffer.getType() << "* restrict derivBuffers" << index;
Peter Eastman's avatar
Peter Eastman committed
3539
3540
3541
3542
3543
3544
3545
3546
3547
            compute << buffer.getType() << " deriv" << index << " = derivBuffers" << index << "[index];\n";
        }
        map<string, string> variables;
        variables["x"] = "pos.x";
        variables["y"] = "pos.y";
        variables["z"] = "pos.z";
        for (int i = 0; i < force.getNumPerParticleParameters(); i++)
            variables[force.getPerParticleParameterName(i)] = "params"+params->getParameterSuffix(i, "[index]");
        for (int i = 0; i < force.getNumGlobalParameters(); i++)
3548
            variables[force.getGlobalParameterName(i)] = "globals["+cl.intToString(i)+"]";
Peter Eastman's avatar
Peter Eastman committed
3549
3550
3551
        for (int i = 0; i < force.getNumComputedValues(); i++)
            variables[computedValueNames[i]] = "values"+computedValues->getParameterSuffix(i, "[index]");
        for (int i = 1; i < force.getNumComputedValues(); i++) {
3552
            string is = cl.intToString(i);
3553
            compute << "real4 dV"<<is<<"dR = (real4) 0;\n";
3554
3555
3556
            for (int j = 1; j < i; j++) {
                if (!isZeroExpression(valueDerivExpressions[i][j])) {
                    map<string, Lepton::ParsedExpression> derivExpressions;
3557
                    string js = cl.intToString(j);
3558
                    derivExpressions["real dV"+is+"dV"+js+" = "] = valueDerivExpressions[i][j];
3559
                    compute << cl.getExpressionUtilities().createExpressions(derivExpressions, variables, functionList, functionDefinitions, "temp_"+is+"_"+js);
3560
3561
3562
3563
                    compute << "dV"<<is<<"dR += dV"<<is<<"dV"<<js<<"*dV"<<js<<"dR;\n";
                }
            }
            map<string, Lepton::ParsedExpression> gradientExpressions;
Peter Eastman's avatar
Peter Eastman committed
3564
            if (!isZeroExpression(valueGradientExpressions[i][0]))
3565
                gradientExpressions["dV"+is+"dR.x += "] = valueGradientExpressions[i][0];
Peter Eastman's avatar
Peter Eastman committed
3566
            if (!isZeroExpression(valueGradientExpressions[i][1]))
3567
                gradientExpressions["dV"+is+"dR.y += "] = valueGradientExpressions[i][1];
Peter Eastman's avatar
Peter Eastman committed
3568
            if (!isZeroExpression(valueGradientExpressions[i][2]))
3569
                gradientExpressions["dV"+is+"dR.z += "] = valueGradientExpressions[i][2];
3570
            compute << cl.getExpressionUtilities().createExpressions(gradientExpressions, variables, functionList, functionDefinitions, "temp");
3571
3572
        }
        for (int i = 1; i < force.getNumComputedValues(); i++) {
3573
            string is = cl.intToString(i);
3574
            compute << "force -= deriv"<<energyDerivs->getParameterSuffix(i)<<"*dV"<<is<<"dR;\n";
Peter Eastman's avatar
Peter Eastman committed
3575
3576
3577
3578
3579
        }
        map<string, string> replacements;
        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
        replacements["COMPUTE_FORCES"] = compute.str();
        map<string, string> defines;
3580
        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
Peter Eastman's avatar
Peter Eastman committed
3581
3582
3583
        cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customGBGradientChainRule, replacements), defines);
        gradientChainRuleKernel = cl::Kernel(program, "computeGradientChainRuleTerms");
    }
3584
    {
Peter Eastman's avatar
Peter Eastman committed
3585
        // Create the code to calculate chain rules terms as part of the default nonbonded kernel.
3586

3587
        vector<pair<ExpressionTreeNode, string> > globalVariables;
3588
3589
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
3590
            string value = "globals["+cl.intToString(i)+"]";
3591
            globalVariables.push_back(makeVariable(name, prefix+value));
3592
        }
3593
        vector<pair<ExpressionTreeNode, string> > variables = globalVariables;
3594
        map<string, string> rename;
3595
3596
3597
3598
        ExpressionTreeNode rnode(new Operation::Variable("r"));
        variables.push_back(make_pair(rnode, "r"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Square(), rnode), "r2"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Reciprocal(), rnode), "invR"));
3599
3600
        for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
            const string& name = force.getPerParticleParameterName(i);
3601
3602
            variables.push_back(makeVariable(name+"1", prefix+"params"+params->getParameterSuffix(i, "1")));
            variables.push_back(makeVariable(name+"2", prefix+"params"+params->getParameterSuffix(i, "2")));
Peter Eastman's avatar
Peter Eastman committed
3603
3604
            rename[name+"1"] = name+"2";
            rename[name+"2"] = name+"1";
3605
3606
3607
3608
        }
        map<string, Lepton::ParsedExpression> derivExpressions;
        stringstream chainSource;
        Lepton::ParsedExpression dVdR = Lepton::Parser::parse(computedValueExpressions[0], functions).differentiate("r").optimize();
3609
3610
        derivExpressions["real dV0dR1 = "] = dVdR;
        derivExpressions["real dV0dR2 = "] = dVdR.renameVariables(rename);
3611
        chainSource << cl.getExpressionUtilities().createExpressions(derivExpressions, variables, functionList, functionDefinitions, prefix+"temp0_");
Peter Eastman's avatar
Peter Eastman committed
3612
3613
3614
3615
3616
3617
3618
        if (needChainForValue[0]) {
            if (useExclusionsForValue)
                chainSource << "if (!isExcluded) {\n";
            chainSource << "tempForce -= dV0dR1*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "1") << ";\n";
            chainSource << "tempForce -= dV0dR2*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "2") << ";\n";
            if (useExclusionsForValue)
                chainSource << "}\n";
3619
        }
Peter Eastman's avatar
Peter Eastman committed
3620
3621
3622
3623
        for (int i = 1; i < force.getNumComputedValues(); i++) {
            if (needChainForValue[i]) {
                chainSource << "tempForce -= dV0dR1*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(i, "1") << ";\n";
                chainSource << "tempForce -= dV0dR2*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(i, "2") << ";\n";
3624
            }
3625
3626
        }
        map<string, string> replacements;
Peter Eastman's avatar
Peter Eastman committed
3627
3628
        string chainStr = chainSource.str();
        replacements["COMPUTE_FORCE"] = chainStr;
3629
        string source = cl.replaceStrings(OpenCLKernelSources::customGBChainRule, replacements);
3630
3631
        vector<OpenCLNonbondedUtilities::ParameterInfo> parameters;
        vector<OpenCLNonbondedUtilities::ParameterInfo> arguments;
3632
3633
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
3634
            string paramName = prefix+"params"+cl.intToString(i+1);
Peter Eastman's avatar
Peter Eastman committed
3635
3636
            if (chainStr.find(paramName+"1") != chainStr.npos || chainStr.find(paramName+"2") != chainStr.npos)
                parameters.push_back(OpenCLNonbondedUtilities::ParameterInfo(paramName, buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
3637
3638
3639
        }
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
3640
            string paramName = prefix+"values"+cl.intToString(i+1);
Peter Eastman's avatar
Peter Eastman committed
3641
3642
            if (chainStr.find(paramName+"1") != chainStr.npos || chainStr.find(paramName+"2") != chainStr.npos)
                parameters.push_back(OpenCLNonbondedUtilities::ParameterInfo(paramName, buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
3643
        }
3644
        for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++) {
Peter Eastman's avatar
Peter Eastman committed
3645
            if (needChainForValue[i]) { 
3646
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivChain->getBuffers()[i];
3647
                string paramName = prefix+"dEdV"+cl.intToString(i+1);
Peter Eastman's avatar
Peter Eastman committed
3648
3649
                parameters.push_back(OpenCLNonbondedUtilities::ParameterInfo(paramName, buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
            }
3650
3651
3652
        }
        if (globals != NULL) {
            globals->upload(globalParamValues);
3653
3654
            arguments.push_back(OpenCLNonbondedUtilities::ParameterInfo(prefix+"globals", "float", 1, sizeof(cl_float), globals->getDeviceBuffer()));
        }
3655
        cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, force.getNumExclusions() > 0, cutoff, exclusionList, source, force.getForceGroup());
Peter Eastman's avatar
Peter Eastman committed
3656
3657
3658
3659
        for (int i = 0; i < (int) parameters.size(); i++)
            cl.getNonbondedUtilities().addParameter(parameters[i]);
        for (int i = 0; i < (int) arguments.size(); i++)
            cl.getNonbondedUtilities().addArgument(arguments[i]);
3660
3661
    }
    cl.addForce(new OpenCLCustomGBForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
3662
    if (useLong)
3663
        cl.addAutoclearBuffer(*longEnergyDerivs);
Peter Eastman's avatar
Peter Eastman committed
3664
3665
3666
    else {
        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
3667
            cl.addAutoclearBuffer(buffer.getMemory(), buffer.getSize()*energyDerivs->getNumObjects());
Peter Eastman's avatar
Peter Eastman committed
3668
3669
        }
    }
3670
3671
}

3672
double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
3673
    bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
3674
    OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
3675
    int elementSize = (cl.getUseDoublePrecision() ? sizeof(cl_double) : sizeof(cl_float));
3676
3677
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
3678
3679
3680
3681
3682
3683
3684
3685
3686
3687
3688
3689
        
        // These two kernels can't be compiled in initialize(), because the nonbonded utilities object
        // has not yet been initialized then.

        {
            int numExclusionTiles = nb.getExclusionTiles().getSize();
            pairValueDefines["NUM_TILES_WITH_EXCLUSIONS"] = cl.intToString(numExclusionTiles);
            int numContexts = cl.getPlatformData().contexts.size();
            int startExclusionIndex = cl.getContextIndex()*numExclusionTiles/numContexts;
            int endExclusionIndex = (cl.getContextIndex()+1)*numExclusionTiles/numContexts;
            pairValueDefines["FIRST_EXCLUSION_TILE"] = cl.intToString(startExclusionIndex);
            pairValueDefines["LAST_EXCLUSION_TILE"] = cl.intToString(endExclusionIndex);
3690
            pairValueDefines["CUTOFF"] = cl.doubleToString(cutoff);
3691
3692
3693
3694
3695
3696
3697
3698
3699
3700
3701
3702
3703
            cl::Program program = cl.createProgram(pairValueSrc, pairValueDefines);
            pairValueKernel = cl::Kernel(program, "computeN2Value");
            pairValueSrc = "";
            pairValueDefines.clear();
        }
        {
            int numExclusionTiles = nb.getExclusionTiles().getSize();
            pairEnergyDefines["NUM_TILES_WITH_EXCLUSIONS"] = cl.intToString(numExclusionTiles);
            int numContexts = cl.getPlatformData().contexts.size();
            int startExclusionIndex = cl.getContextIndex()*numExclusionTiles/numContexts;
            int endExclusionIndex = (cl.getContextIndex()+1)*numExclusionTiles/numContexts;
            pairEnergyDefines["FIRST_EXCLUSION_TILE"] = cl.intToString(startExclusionIndex);
            pairEnergyDefines["LAST_EXCLUSION_TILE"] = cl.intToString(endExclusionIndex);
3704
            pairEnergyDefines["CUTOFF"] = cl.doubleToString(cutoff);
3705
3706
3707
3708
3709
3710
3711
3712
            cl::Program program = cl.createProgram(pairEnergySrc, pairEnergyDefines);
            pairEnergyKernel = cl::Kernel(program, "computeN2Energy");
            pairEnergySrc = "";
            pairEnergyDefines.clear();
        }

        // Set arguments for kernels.
        
3713
        maxTiles = (nb.getUseCutoff() ? nb.getInteractingTiles().getSize() : 0);
3714
        bool useLong = cl.getSupports64BitGlobalAtomics();
3715
        if (useLong) {
3716
            longValueBuffers = OpenCLArray::create<cl_long>(cl, cl.getPaddedNumAtoms(), "customGBLongValueBuffers");
3717
3718
            cl.addAutoclearBuffer(*longValueBuffers);
            cl.clearBuffer(*longValueBuffers);
3719
3720
        }
        else {
3721
            valueBuffers = new OpenCLArray(cl, cl.getPaddedNumAtoms()*nb.getNumForceBuffers(), elementSize, "customGBValueBuffers");
3722
            cl.addAutoclearBuffer(*valueBuffers);
3723
3724
            cl.clearBuffer(*valueBuffers);
        }
3725
3726
        int index = 0;
        pairValueKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
3727
        pairValueKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*4*elementSize, NULL);
3728
        pairValueKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusions().getDeviceBuffer());
3729
        pairValueKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionTiles().getDeviceBuffer());
3730
        pairValueKernel.setArg<cl::Buffer>(index++, useLong ? longValueBuffers->getDeviceBuffer() : valueBuffers->getDeviceBuffer());
3731
        pairValueKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*elementSize, NULL);
3732
3733
3734
        if (nb.getUseCutoff()) {
            pairValueKernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
            pairValueKernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
3735
            index += 5; // Periodic box size arguments are set when the kernel is executed.
3736
            pairValueKernel.setArg<cl_uint>(index++, maxTiles);
3737
            pairValueKernel.setArg<cl::Buffer>(index++, nb.getBlockCenters().getDeviceBuffer());
3738
            pairValueKernel.setArg<cl::Buffer>(index++, nb.getBlockBoundingBoxes().getDeviceBuffer());
3739
            pairValueKernel.setArg<cl::Buffer>(index++, nb.getInteractingAtoms().getDeviceBuffer());
3740
        }
3741
3742
        else
            pairValueKernel.setArg<cl_uint>(index++, cl.getNumAtomBlocks()*(cl.getNumAtomBlocks()+1)/2);
3743
3744
3745
        if (globals != NULL)
            pairValueKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
Peter Eastman's avatar
Peter Eastman committed
3746
3747
3748
3749
3750
            if (pairValueUsesParam[i]) {
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
                pairValueKernel.setArg<cl::Memory>(index++, buffer.getMemory());
                pairValueKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*buffer.getSize(), NULL);
            }
3751
        }
3752
3753
        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            pairValueKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
3754
        index = 0;
3755
3756
        perParticleValueKernel.setArg<cl_int>(index++, cl.getPaddedNumAtoms());
        perParticleValueKernel.setArg<cl_int>(index++, nb.getNumForceBuffers());
3757
        perParticleValueKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
3758
        perParticleValueKernel.setArg<cl::Buffer>(index++, useLong ? longValueBuffers->getDeviceBuffer() : valueBuffers->getDeviceBuffer());
3759
        if (globals != NULL)
3760
            perParticleValueKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
3761
        for (int i = 0; i < (int) params->getBuffers().size(); i++)
3762
            perParticleValueKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
3763
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++)
3764
            perParticleValueKernel.setArg<cl::Memory>(index++, computedValues->getBuffers()[i].getMemory());
3765
3766
        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            perParticleValueKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
3767
        index = 0;
3768
        pairEnergyKernel.setArg<cl::Buffer>(index++, useLong ? cl.getLongForceBuffer().getDeviceBuffer() : cl.getForceBuffers().getDeviceBuffer());
3769
        pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
3770
        pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*4*elementSize, NULL);
3771
        pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
3772
        pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*4*elementSize, NULL);
3773
        pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusions().getDeviceBuffer());
3774
        pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionTiles().getDeviceBuffer());
3775
3776
3777
        if (nb.getUseCutoff()) {
            pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
            pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
3778
            index += 5; // Periodic box size arguments are set when the kernel is executed.
3779
            pairEnergyKernel.setArg<cl_uint>(index++, maxTiles);
3780
            pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getBlockCenters().getDeviceBuffer());
3781
            pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getBlockBoundingBoxes().getDeviceBuffer());
3782
            pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractingAtoms().getDeviceBuffer());
3783
        }
3784
3785
        else
            pairEnergyKernel.setArg<cl_uint>(index++, cl.getNumAtomBlocks()*(cl.getNumAtomBlocks()+1)/2);
3786
3787
3788
        if (globals != NULL)
            pairEnergyKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
Peter Eastman's avatar
Peter Eastman committed
3789
3790
3791
3792
3793
            if (pairEnergyUsesParam[i]) {
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
                pairEnergyKernel.setArg<cl::Memory>(index++, buffer.getMemory());
                pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*buffer.getSize(), NULL);
            }
3794
3795
        }
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
Peter Eastman's avatar
Peter Eastman committed
3796
3797
3798
3799
3800
            if (pairEnergyUsesValue[i]) {
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
                pairEnergyKernel.setArg<cl::Memory>(index++, buffer.getMemory());
                pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*buffer.getSize(), NULL);
            }
3801
        }
3802
3803
3804
        if (useLong) {
            pairEnergyKernel.setArg<cl::Memory>(index++, longEnergyDerivs->getDeviceBuffer());
            for (int i = 0; i < numComputedValues; ++i)
3805
                pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*elementSize, NULL);
3806
3807
3808
3809
3810
3811
3812
        }
        else {
            for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
                pairEnergyKernel.setArg<cl::Memory>(index++, buffer.getMemory());
                pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*buffer.getSize(), NULL);
            }
3813
        }
3814
3815
        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            pairEnergyKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
3816
3817
3818
        index = 0;
        perParticleEnergyKernel.setArg<cl_int>(index++, cl.getPaddedNumAtoms());
        perParticleEnergyKernel.setArg<cl_int>(index++, nb.getNumForceBuffers());
3819
        perParticleEnergyKernel.setArg<cl::Buffer>(index++, cl.getForceBuffers().getDeviceBuffer());
3820
        perParticleEnergyKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
3821
        perParticleEnergyKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
3822
3823
3824
        if (globals != NULL)
            perParticleEnergyKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        for (int i = 0; i < (int) params->getBuffers().size(); i++)
3825
            perParticleEnergyKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
3826
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++)
3827
            perParticleEnergyKernel.setArg<cl::Memory>(index++, computedValues->getBuffers()[i].getMemory());
3828
        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++)
3829
            perParticleEnergyKernel.setArg<cl::Memory>(index++, energyDerivs->getBuffers()[i].getMemory());
3830
3831
        for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++)
            perParticleEnergyKernel.setArg<cl::Memory>(index++, energyDerivChain->getBuffers()[i].getMemory());
3832
3833
        if (useLong)
            perParticleEnergyKernel.setArg<cl::Memory>(index++, longEnergyDerivs->getDeviceBuffer());
3834
3835
        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            perParticleEnergyKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
Peter Eastman's avatar
Peter Eastman committed
3836
3837
3838
3839
3840
3841
3842
3843
3844
3845
3846
3847
3848
        if (needParameterGradient) {
            index = 0;
            gradientChainRuleKernel.setArg<cl::Buffer>(index++, cl.getForceBuffers().getDeviceBuffer());
            gradientChainRuleKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
            if (globals != NULL)
                gradientChainRuleKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
            for (int i = 0; i < (int) params->getBuffers().size(); i++)
                gradientChainRuleKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
            for (int i = 0; i < (int) computedValues->getBuffers().size(); i++)
                gradientChainRuleKernel.setArg<cl::Memory>(index++, computedValues->getBuffers()[i].getMemory());
            for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++)
                gradientChainRuleKernel.setArg<cl::Memory>(index++, energyDerivs->getBuffers()[i].getMemory());
        }
3849
3850
3851
    }
    if (globals != NULL) {
        bool changed = false;
3852
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
3853
3854
3855
3856
3857
3858
3859
3860
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
3861
    if (nb.getUseCutoff()) {
3862
3863
        setPeriodicBoxArgs(cl, pairValueKernel, 8);
        setPeriodicBoxArgs(cl, pairEnergyKernel, 9);
3864
3865
        if (maxTiles < nb.getInteractingTiles().getSize()) {
            maxTiles = nb.getInteractingTiles().getSize();
3866
            pairValueKernel.setArg<cl::Buffer>(6, nb.getInteractingTiles().getDeviceBuffer());
3867
3868
            pairValueKernel.setArg<cl_uint>(13, maxTiles);
            pairValueKernel.setArg<cl::Buffer>(16, nb.getInteractingAtoms().getDeviceBuffer());
3869
            pairEnergyKernel.setArg<cl::Buffer>(7, nb.getInteractingTiles().getDeviceBuffer());
3870
3871
            pairEnergyKernel.setArg<cl_uint>(14, maxTiles);
            pairEnergyKernel.setArg<cl::Buffer>(17, nb.getInteractingAtoms().getDeviceBuffer());
3872
        }
3873
    }
3874
    cl.executeKernel(pairValueKernel, nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());
3875
    cl.executeKernel(perParticleValueKernel, cl.getPaddedNumAtoms());
3876
    cl.executeKernel(pairEnergyKernel, nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());
3877
    cl.executeKernel(perParticleEnergyKernel, cl.getPaddedNumAtoms());
Peter Eastman's avatar
Peter Eastman committed
3878
3879
    if (needParameterGradient)
        cl.executeKernel(gradientChainRuleKernel, cl.getPaddedNumAtoms());
3880
3881
3882
    return 0.0;
}

3883
3884
3885
3886
3887
3888
3889
void OpenCLCalcCustomGBForceKernel::copyParametersToContext(ContextImpl& context, const CustomGBForce& force) {
    int numParticles = force.getNumParticles();
    if (numParticles != cl.getNumAtoms())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
    
    // Record the per-particle parameters.
    
3890
    vector<vector<cl_float> > paramVector(cl.getPaddedNumAtoms(), vector<cl_float>(force.getNumPerParticleParameters(), 0));
3891
3892
3893
3894
3895
3896
3897
3898
3899
3900
3901
3902
3903
    vector<double> parameters;
    for (int i = 0; i < numParticles; i++) {
        force.getParticleParameters(i, parameters);
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

3904
3905
class OpenCLCustomExternalForceInfo : public OpenCLForceInfo {
public:
Peter Eastman's avatar
Peter Eastman committed
3906
    OpenCLCustomExternalForceInfo(const CustomExternalForce& force, int numParticles) : OpenCLForceInfo(0), force(force), indices(numParticles, -1) {
3907
3908
3909
3910
3911
3912
3913
3914
3915
3916
3917
3918
3919
3920
3921
3922
3923
3924
3925
        vector<double> params;
        for (int i = 0; i < force.getNumParticles(); i++) {
            int particle;
            force.getParticleParameters(i, particle, params);
            indices[particle] = i;
        }
    }
    bool areParticlesIdentical(int particle1, int particle2) {
        particle1 = indices[particle1];
        particle2 = indices[particle2];
        if (particle1 == -1 && particle2 == -1)
            return true;
        if (particle1 == -1 || particle2 == -1)
            return false;
        int temp;
        vector<double> params1;
        vector<double> params2;
        force.getParticleParameters(particle1, temp, params1);
        force.getParticleParameters(particle2, temp, params2);
3926
        for (int i = 0; i < (int) params1.size(); i++)
3927
3928
3929
3930
3931
3932
3933
3934
3935
3936
3937
3938
3939
3940
3941
3942
3943
            if (params1[i] != params2[i])
                return false;
        return true;
    }
private:
    const CustomExternalForce& force;
    vector<int> indices;
};

OpenCLCalcCustomExternalForceKernel::~OpenCLCalcCustomExternalForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
}

void OpenCLCalcCustomExternalForceKernel::initialize(const System& system, const CustomExternalForce& force) {
3944
3945
3946
3947
3948
3949
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumParticles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumParticles()/numContexts;
    numParticles = endIndex-startIndex;
    if (numParticles == 0)
        return;
3950
    vector<vector<int> > atoms(numParticles, vector<int>(1));
3951
3952
    params = new OpenCLParameterSet(cl, force.getNumPerParticleParameters(), numParticles, "customExternalParams");
    vector<vector<cl_float> > paramVector(numParticles);
3953
3954
    for (int i = 0; i < numParticles; i++) {
        vector<double> parameters;
3955
        force.getParticleParameters(startIndex+i, atoms[i][0], parameters);
3956
        paramVector[i].resize(parameters.size());
3957
        for (int j = 0; j < (int) parameters.size(); j++)
3958
            paramVector[i][j] = (cl_float) parameters[j];
3959
    }
3960
    params->setParameterValues(paramVector);
3961
3962
3963
3964
3965
3966
3967
3968
3969
3970
    cl.addForce(new OpenCLCustomExternalForceInfo(force, system.getNumParticles()));

    // Record information for the expressions.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
3971
3972
3973
    map<string, Lepton::CustomFunction*> customFunctions;
    customFunctions["periodicdistance"] = cl.getExpressionUtilities().getPeriodicDistancePlaceholder();
    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction(), customFunctions).optimize();
3974
3975
3976
3977
3978
    Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x").optimize();
    Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y").optimize();
    Lepton::ParsedExpression forceExpressionZ = energyExpression.differentiate("z").optimize();
    map<string, Lepton::ParsedExpression> expressions;
    expressions["energy += "] = energyExpression;
3979
3980
3981
    expressions["real dEdX = "] = forceExpressionX;
    expressions["real dEdY = "] = forceExpressionY;
    expressions["real dEdZ = "] = forceExpressionZ;
3982
3983
3984
3985

    // Create the kernels.

    map<string, string> variables;
3986
3987
3988
    variables["x"] = "pos1.x";
    variables["y"] = "pos1.y";
    variables["z"] = "pos1.z";
3989
3990
    for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
        const string& name = force.getPerParticleParameterName(i);
3991
        variables[name] = "particleParams"+params->getParameterSuffix(i);
3992
    }
3993
    if (force.getNumGlobalParameters() > 0) {
3994
        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customExternalGlobals", CL_MEM_READ_ONLY);
3995
3996
3997
3998
        globals->upload(globalParamValues);
        string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
3999
            string value = argName+"["+cl.intToString(i)+"]";
4000
4001
            variables[name] = value;
        }
4002
4003
    }
    stringstream compute;
4004
4005
    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
4006
4007
        string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
        compute<<buffer.getType()<<" particleParams"<<(i+1)<<" = "<<argName<<"[index];\n";
4008
    }
peastman's avatar
peastman committed
4009
4010
    vector<const TabulatedFunction*> functions;
    vector<pair<string, string> > functionNames;
4011
    compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
4012
    map<string, string> replacements;
4013
    replacements["COMPUTE_FORCE"] = compute.str();
4014
    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::customExternalForce, replacements), force.getForceGroup());
4015
4016
}

4017
double OpenCLCalcCustomExternalForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
4018
4019
    if (globals != NULL) {
        bool changed = false;
4020
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
4021
4022
4023
4024
4025
4026
4027
4028
4029
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    return 0.0;
4030
}
4031

4032
4033
4034
4035
4036
4037
void OpenCLCalcCustomExternalForceKernel::copyParametersToContext(ContextImpl& context, const CustomExternalForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumParticles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumParticles()/numContexts;
    if (numParticles != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
4038
4039
    if (numParticles == 0)
        return;
4040
4041
4042
4043
4044
4045
4046
4047
4048
4049
4050
4051
4052
4053
4054
4055
4056
4057
4058
    
    // Record the per-particle parameters.
    
    vector<vector<cl_float> > paramVector(numParticles);
    vector<double> parameters;
    for (int i = 0; i < numParticles; i++) {
        int particle;
        force.getParticleParameters(startIndex+i, particle, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

4059
4060
4061
4062
4063
4064
4065
4066
4067
4068
class OpenCLCustomHbondForceInfo : public OpenCLForceInfo {
public:
    OpenCLCustomHbondForceInfo(int requiredBuffers, const CustomHbondForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
    }
    bool areParticlesIdentical(int particle1, int particle2) {
        return true;
    }
    int getNumParticleGroups() {
        return force.getNumDonors()+force.getNumAcceptors()+force.getNumExclusions();
    }
Peter Eastman's avatar
Peter Eastman committed
4069
    void getParticlesInGroup(int index, vector<int>& particles) {
4070
4071
4072
4073
        int p1, p2, p3;
        vector<double> parameters;
        if (index < force.getNumDonors()) {
            force.getDonorParameters(index, p1, p2, p3, parameters);
4074
4075
4076
4077
4078
4079
            particles.clear();
            particles.push_back(p1);
            if (p2 > -1)
                particles.push_back(p2);
            if (p3 > -1)
                particles.push_back(p3);
4080
4081
4082
4083
4084
            return;
        }
        index -= force.getNumDonors();
        if (index < force.getNumAcceptors()) {
            force.getAcceptorParameters(index, p1, p2, p3, parameters);
4085
4086
4087
4088
4089
4090
            particles.clear();
            particles.push_back(p1);
            if (p2 > -1)
                particles.push_back(p2);
            if (p3 > -1)
                particles.push_back(p3);
4091
4092
4093
4094
4095
            return;
        }
        index -= force.getNumAcceptors();
        int donor, acceptor;
        force.getExclusionParticles(index, donor, acceptor);
4096
        particles.clear();
4097
        force.getDonorParameters(donor, p1, p2, p3, parameters);
4098
4099
4100
4101
4102
        particles.push_back(p1);
        if (p2 > -1)
            particles.push_back(p2);
        if (p3 > -1)
            particles.push_back(p3);
4103
        force.getAcceptorParameters(acceptor, p1, p2, p3, parameters);
4104
4105
4106
4107
4108
        particles.push_back(p1);
        if (p2 > -1)
            particles.push_back(p2);
        if (p3 > -1)
            particles.push_back(p3);
4109
4110
4111
4112
4113
4114
4115
4116
4117
4118
4119
4120
4121
4122
4123
4124
4125
4126
4127
4128
4129
4130
4131
4132
4133
4134
4135
4136
4137
4138
4139
4140
4141
4142
4143
4144
4145
4146
4147
4148
4149
    }
    bool areGroupsIdentical(int group1, int group2) {
        int p1, p2, p3;
        vector<double> params1, params2;
        if (group1 < force.getNumDonors() && group2 < force.getNumDonors()) {
            force.getDonorParameters(group1, p1, p2, p3, params1);
            force.getDonorParameters(group2, p1, p2, p3, params2);
            return (params1 == params2 && params1 == params2);
        }
        if (group1 < force.getNumDonors() || group2 < force.getNumDonors())
            return false;
        group1 -= force.getNumDonors();
        group2 -= force.getNumDonors();
        if (group1 < force.getNumAcceptors() && group2 < force.getNumAcceptors()) {
            force.getAcceptorParameters(group1, p1, p2, p3, params1);
            force.getAcceptorParameters(group2, p1, p2, p3, params2);
            return (params1 == params2 && params1 == params2);
        }
        if (group1 < force.getNumAcceptors() || group2 < force.getNumAcceptors())
            return false;
        return true;
    }
private:
    const CustomHbondForce& force;
};

OpenCLCalcCustomHbondForceKernel::~OpenCLCalcCustomHbondForceKernel() {
    if (donorParams != NULL)
        delete donorParams;
    if (acceptorParams != NULL)
        delete acceptorParams;
    if (donors != NULL)
        delete donors;
    if (acceptors != NULL)
        delete acceptors;
    if (donorBufferIndices != NULL)
        delete donorBufferIndices;
    if (acceptorBufferIndices != NULL)
        delete acceptorBufferIndices;
    if (globals != NULL)
        delete globals;
4150
4151
4152
4153
    if (donorExclusions != NULL)
        delete donorExclusions;
    if (acceptorExclusions != NULL)
        delete acceptorExclusions;
4154
4155
4156
4157
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
}

4158
4159
4160
4161
4162
4163
4164
4165
4166
4167
4168
4169
static void addDonorAndAcceptorCode(stringstream& computeDonor, stringstream& computeAcceptor, const string& value) {
    computeDonor << value;
    computeAcceptor << value;
}

static void applyDonorAndAcceptorForces(stringstream& applyToDonor, stringstream& applyToAcceptor, int atom, const string& value) {
    string forceNames[] = {"f1", "f2", "f3"};
    if (atom < 3)
        applyToAcceptor << forceNames[atom]<<".xyz += "<<value<<";\n";
    else
        applyToDonor << forceNames[atom-3]<<".xyz += "<<value<<";\n";
}
4170

4171
void OpenCLCalcCustomHbondForceKernel::initialize(const System& system, const CustomHbondForce& force) {
4172
4173
    // Record the lists of donors and acceptors, and the parameters for each one.

4174
4175
4176
4177
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumDonors()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumDonors()/numContexts;
    numDonors = endIndex-startIndex;
4178
    numAcceptors = force.getNumAcceptors();
4179
4180
    if (numDonors == 0 || numAcceptors == 0)
        return;
4181
    int numParticles = system.getNumParticles();
4182
4183
    donors = OpenCLArray::create<mm_int4>(cl, numDonors, "customHbondDonors");
    acceptors = OpenCLArray::create<mm_int4>(cl, numAcceptors, "customHbondAcceptors");
4184
4185
4186
    donorParams = new OpenCLParameterSet(cl, force.getNumPerDonorParameters(), numDonors, "customHbondDonorParameters");
    acceptorParams = new OpenCLParameterSet(cl, force.getNumPerAcceptorParameters(), numAcceptors, "customHbondAcceptorParameters");
    if (force.getNumGlobalParameters() > 0)
4187
        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customHbondGlobals", CL_MEM_READ_ONLY);
4188
4189
4190
4191
    vector<vector<cl_float> > donorParamVector(numDonors);
    vector<mm_int4> donorVector(numDonors);
    for (int i = 0; i < numDonors; i++) {
        vector<double> parameters;
4192
        force.getDonorParameters(startIndex+i, donorVector[i].x, donorVector[i].y, donorVector[i].z, parameters);
4193
4194
4195
4196
4197
4198
4199
4200
4201
4202
4203
4204
4205
4206
4207
4208
4209
4210
        donorParamVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            donorParamVector[i][j] = (cl_float) parameters[j];
    }
    donors->upload(donorVector);
    donorParams->setParameterValues(donorParamVector);
    vector<vector<cl_float> > acceptorParamVector(numAcceptors);
    vector<mm_int4> acceptorVector(numAcceptors);
    for (int i = 0; i < numAcceptors; i++) {
        vector<double> parameters;
        force.getAcceptorParameters(i, acceptorVector[i].x, acceptorVector[i].y, acceptorVector[i].z, parameters);
        acceptorParamVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            acceptorParamVector[i][j] = (cl_float) parameters[j];
    }
    acceptors->upload(acceptorVector);
    acceptorParams->setParameterValues(acceptorParamVector);

4211
    // Select an output buffer index for each donor and acceptor.
4212

4213
4214
    donorBufferIndices = OpenCLArray::create<mm_int4>(cl, numDonors, "customHbondDonorBuffers");
    acceptorBufferIndices = OpenCLArray::create<mm_int4>(cl, numAcceptors, "customHbondAcceptorBuffers");
4215
4216
    vector<mm_int4> donorBufferVector(numDonors);
    vector<mm_int4> acceptorBufferVector(numAcceptors);
4217
    vector<int> donorBufferCounter(numParticles, 0);
4218
    for (int i = 0; i < numDonors; i++)
4219
4220
4221
        donorBufferVector[i] = mm_int4(donorVector[i].x > -1 ? donorBufferCounter[donorVector[i].x]++ : 0,
                                       donorVector[i].y > -1 ? donorBufferCounter[donorVector[i].y]++ : 0,
                                       donorVector[i].z > -1 ? donorBufferCounter[donorVector[i].z]++ : 0, 0);
4222
    vector<int> acceptorBufferCounter(numParticles, 0);
4223
    for (int i = 0; i < numAcceptors; i++)
4224
4225
4226
        acceptorBufferVector[i] = mm_int4(acceptorVector[i].x > -1 ? acceptorBufferCounter[acceptorVector[i].x]++ : 0,
                                       acceptorVector[i].y > -1 ? acceptorBufferCounter[acceptorVector[i].y]++ : 0,
                                       acceptorVector[i].z > -1 ? acceptorBufferCounter[acceptorVector[i].z]++ : 0, 0);
4227
4228
    donorBufferIndices->upload(donorBufferVector);
    acceptorBufferIndices->upload(acceptorBufferVector);
4229
4230
4231
4232
4233
4234
    int maxBuffers = 1;
    for (int i = 0; i < (int) donorBufferCounter.size(); i++)
        maxBuffers = max(maxBuffers, donorBufferCounter[i]);
    for (int i = 0; i < (int) acceptorBufferCounter.size(); i++)
        maxBuffers = max(maxBuffers, acceptorBufferCounter[i]);
    cl.addForce(new OpenCLCustomHbondForceInfo(maxBuffers, force));
4235
4236
4237

    // Record exclusions.

4238
4239
    vector<mm_int4> donorExclusionVector(numDonors, mm_int4(-1, -1, -1, -1));
    vector<mm_int4> acceptorExclusionVector(numAcceptors, mm_int4(-1, -1, -1, -1));
4240
4241
4242
    for (int i = 0; i < force.getNumExclusions(); i++) {
        int donor, acceptor;
        force.getExclusionParticles(i, donor, acceptor);
4243
4244
4245
        if (donor < startIndex || donor >= endIndex)
            continue;
        donor -= startIndex;
4246
4247
4248
4249
4250
4251
4252
4253
4254
4255
4256
4257
4258
4259
4260
4261
4262
4263
4264
4265
        if (donorExclusionVector[donor].x == -1)
            donorExclusionVector[donor].x = acceptor;
        else if (donorExclusionVector[donor].y == -1)
            donorExclusionVector[donor].y = acceptor;
        else if (donorExclusionVector[donor].z == -1)
            donorExclusionVector[donor].z = acceptor;
        else if (donorExclusionVector[donor].w == -1)
            donorExclusionVector[donor].w = acceptor;
        else
            throw OpenMMException("CustomHbondForce: OpenCLPlatform does not support more than four exclusions per donor");
        if (acceptorExclusionVector[acceptor].x == -1)
            acceptorExclusionVector[acceptor].x = donor;
        else if (acceptorExclusionVector[acceptor].y == -1)
            acceptorExclusionVector[acceptor].y = donor;
        else if (acceptorExclusionVector[acceptor].z == -1)
            acceptorExclusionVector[acceptor].z = donor;
        else if (acceptorExclusionVector[acceptor].w == -1)
            acceptorExclusionVector[acceptor].w = donor;
        else
            throw OpenMMException("CustomHbondForce: OpenCLPlatform does not support more than four exclusions per acceptor");
4266
    }
4267
4268
    donorExclusions = OpenCLArray::create<mm_int4>(cl, numDonors, "customHbondDonorExclusions");
    acceptorExclusions = OpenCLArray::create<mm_int4>(cl, numAcceptors, "customHbondAcceptorExclusions");
4269
4270
    donorExclusions->upload(donorExclusionVector);
    acceptorExclusions->upload(acceptorExclusionVector);
4271
4272
4273
4274
4275

    // Record the tabulated functions.

    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
4276
    vector<const TabulatedFunction*> functionList;
4277
4278
    stringstream tableArgs;
    for (int i = 0; i < force.getNumFunctions(); i++) {
4279
4280
        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
4281
        string arrayName = "table"+cl.intToString(i);
4282
        functionDefinitions.push_back(make_pair(name, arrayName));
4283
        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
peastman's avatar
peastman committed
4284
        int width;
4285
        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
4286
        tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
4287
        tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
peastman's avatar
peastman committed
4288
4289
4290
4291
        tableArgs << ", __global const float";
        if (width > 1)
            tableArgs << width;
        tableArgs << "* restrict " << arrayName;
4292
4293
    }

4294
    // Record information about parameters.
4295
4296
4297
4298
4299
4300
4301
4302
4303
4304
4305
4306
4307
4308
4309
4310
4311
4312
4313
4314

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    if (globals != NULL)
        globals->upload(globalParamValues);
    map<string, string> variables;
    for (int i = 0; i < force.getNumPerDonorParameters(); i++) {
        const string& name = force.getPerDonorParameterName(i);
        variables[name] = "donorParams"+donorParams->getParameterSuffix(i);
    }
    for (int i = 0; i < force.getNumPerAcceptorParameters(); i++) {
        const string& name = force.getPerAcceptorParameterName(i);
        variables[name] = "acceptorParams"+acceptorParams->getParameterSuffix(i);
    }
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        const string& name = force.getGlobalParameterName(i);
4315
        variables[name] = "globals["+cl.intToString(i)+"]";
4316
    }
4317
4318
4319
4320
4321
4322
4323
4324
4325
4326
4327
4328
4329
4330
4331
4332
4333
4334
4335

    // Now to generate the kernel.  First, it needs to calculate all distances, angles,
    // and dihedrals the expression depends on.

    map<string, vector<int> > distances;
    map<string, vector<int> > angles;
    map<string, vector<int> > dihedrals;
    Lepton::ParsedExpression energyExpression = CustomHbondForceImpl::prepareExpression(force, functions, distances, angles, dihedrals);
    map<string, Lepton::ParsedExpression> forceExpressions;
    set<string> computedDeltas;
    computedDeltas.insert("D1A1");
    string atomNames[] = {"A1", "A2", "A3", "D1", "D2", "D3"};
    string atomNamesLower[] = {"a1", "a2", "a3", "d1", "d2", "d3"};
    stringstream computeDonor, computeAcceptor, extraArgs;
    int index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
        if (computedDeltas.count(deltaName) == 0) {
4336
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName+" = delta("+atomNamesLower[atoms[0]]+", "+atomNamesLower[atoms[1]]+");\n");
4337
4338
            computedDeltas.insert(deltaName);
        }
4339
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real r_"+deltaName+" = SQRT(delta"+deltaName+".w);\n");
4340
        variables[iter->first] = "r_"+deltaName;
4341
        forceExpressions["real dEdDistance"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
4342
4343
4344
4345
4346
4347
4348
4349
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        string angleName = "angle_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]];
        if (computedDeltas.count(deltaName1) == 0) {
4350
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName1+" = delta("+atomNamesLower[atoms[1]]+", "+atomNamesLower[atoms[0]]+");\n");
4351
4352
4353
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
4354
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName2+" = delta("+atomNamesLower[atoms[1]]+", "+atomNamesLower[atoms[2]]+");\n");
4355
4356
            computedDeltas.insert(deltaName2);
        }
4357
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real "+angleName+" = computeAngle(delta"+deltaName1+", delta"+deltaName2+");\n");
4358
        variables[iter->first] = angleName;
4359
        forceExpressions["real dEdAngle"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
4360
4361
4362
4363
4364
4365
4366
4367
4368
4369
4370
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        string dihedralName = "dihedral_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]]+atomNames[atoms[3]];
        if (computedDeltas.count(deltaName1) == 0) {
4371
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName1+" = delta("+atomNamesLower[atoms[0]]+", "+atomNamesLower[atoms[1]]+");\n");
4372
4373
4374
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
4375
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName2+" = delta("+atomNamesLower[atoms[2]]+", "+atomNamesLower[atoms[1]]+");\n");
4376
4377
4378
            computedDeltas.insert(deltaName2);
        }
        if (computedDeltas.count(deltaName3) == 0) {
4379
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName3+" = delta("+atomNamesLower[atoms[2]]+", "+atomNamesLower[atoms[3]]+");\n");
4380
4381
            computedDeltas.insert(deltaName3);
        }
4382
4383
4384
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 "+crossName1+" = computeCross(delta"+deltaName1+", delta"+deltaName2+");\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 "+crossName2+" = computeCross(delta"+deltaName2+", delta"+deltaName3+");\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real "+dihedralName+" = computeAngle("+crossName1+", "+crossName2+");\n");
4385
4386
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, dihedralName+" *= (delta"+deltaName1+".x*"+crossName2+".x + delta"+deltaName1+".y*"+crossName2+".y + delta"+deltaName1+".z*"+crossName2+".z < 0 ? -1 : 1);\n");
        variables[iter->first] = dihedralName;
4387
        forceExpressions["real dEdDihedral"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
4388
4389
4390
4391
    }

    // Next it needs to load parameters from global memory.

4392
    if (force.getNumGlobalParameters() > 0)
4393
        extraArgs << ", __global const float* restrict globals";
4394
4395
    for (int i = 0; i < (int) donorParams->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = donorParams->getBuffers()[i];
4396
        extraArgs << ", __global const "+buffer.getType()+"* restrict donor"+buffer.getName();
4397
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, buffer.getType()+" donorParams"+cl.intToString(i+1)+" = donor"+buffer.getName()+"[index];\n");
4398
4399
4400
    }
    for (int i = 0; i < (int) acceptorParams->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = acceptorParams->getBuffers()[i];
4401
        extraArgs << ", __global const "+buffer.getType()+"* restrict acceptor"+buffer.getName();
4402
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, buffer.getType()+" acceptorParams"+cl.intToString(i+1)+" = acceptor"+buffer.getName()+"[index];\n");
4403
    }
4404
4405
4406

    // Now evaluate the expressions.

4407
    computeAcceptor << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, "temp");
4408
    forceExpressions["energy += "] = energyExpression;
4409
    computeDonor << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, "temp");
4410
4411
4412
4413
4414
4415
4416

    // Finally, apply forces to atoms.

    index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
4417
        string value = "(dEdDistance"+cl.intToString(index)+"/r_"+deltaName+")*delta"+deltaName+".xyz";
4418
4419
4420
4421
4422
4423
4424
4425
4426
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[0], "-"+value);
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[1], value);
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "{\n");
4427
4428
4429
4430
4431
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 crossProd = cross(delta"+deltaName2+", delta"+deltaName1+");\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real lengthCross = max(length(crossProd), (real) 1e-6f);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 deltaCross0 = -cross(delta"+deltaName1+", crossProd)*dEdAngle"+cl.intToString(index)+"/(delta"+deltaName1+".w*lengthCross);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 deltaCross2 = cross(delta"+deltaName2+", crossProd)*dEdAngle"+cl.intToString(index)+"/(delta"+deltaName2+".w*lengthCross);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 deltaCross1 = -(deltaCross0+deltaCross2);\n");
4432
4433
4434
4435
4436
4437
4438
4439
4440
4441
4442
4443
4444
4445
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[0], "deltaCross0.xyz");
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[1], "deltaCross1.xyz");
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[2], "deltaCross2.xyz");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "}\n");
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "{\n");
4446
4447
4448
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real r = SQRT(delta"+deltaName2+".w);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 ff;\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "ff.x = (-dEdDihedral"+cl.intToString(index)+"*r)/"+crossName1+".w;\n");
4449
4450
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "ff.y = (delta"+deltaName1+".x*delta"+deltaName2+".x + delta"+deltaName1+".y*delta"+deltaName2+".y + delta"+deltaName1+".z*delta"+deltaName2+".z)/delta"+deltaName2+".w;\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "ff.z = (delta"+deltaName3+".x*delta"+deltaName2+".x + delta"+deltaName3+".y*delta"+deltaName2+".y + delta"+deltaName3+".z*delta"+deltaName2+".z)/delta"+deltaName2+".w;\n");
4451
4452
4453
4454
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "ff.w = (dEdDihedral"+cl.intToString(index)+"*r)/"+crossName2+".w;\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 internalF0 = ff.x*"+crossName1+";\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 internalF3 = ff.w*"+crossName2+";\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 s = ff.y*internalF0 - ff.z*internalF3;\n");
4455
4456
4457
4458
4459
4460
4461
4462
4463
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[0], "internalF0.xyz");
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[1], "s.xyz-internalF0.xyz");
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[2], "-s.xyz-internalF3.xyz");
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[3], "internalF3.xyz");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "}\n");
    }

    // Generate the kernels.

4464
    map<string, string> replacements;
4465
4466
    replacements["COMPUTE_DONOR_FORCE"] = computeDonor.str();
    replacements["COMPUTE_ACCEPTOR_FORCE"] = computeAcceptor.str();
4467
4468
    replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
    map<string, string> defines;
4469
4470
4471
4472
    defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
    defines["NUM_DONORS"] = cl.intToString(numDonors);
    defines["NUM_ACCEPTORS"] = cl.intToString(numAcceptors);
    defines["PI"] = cl.doubleToString(M_PI);
4473
4474
    if (force.getNonbondedMethod() != CustomHbondForce::NoCutoff) {
        defines["USE_CUTOFF"] = "1";
4475
        defines["CUTOFF_SQUARED"] = cl.doubleToString(force.getCutoffDistance()*force.getCutoffDistance());
4476
4477
4478
    }
    if (force.getNonbondedMethod() != CustomHbondForce::NoCutoff && force.getNonbondedMethod() != CustomHbondForce::CutoffNonPeriodic)
        defines["USE_PERIODIC"] = "1";
4479
4480
    if (force.getNumExclusions() > 0)
        defines["USE_EXCLUSIONS"] = "1";
4481
    cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customHbondForce, replacements), defines);
4482
4483
    donorKernel = cl::Kernel(program, "computeDonorForces");
    acceptorKernel = cl::Kernel(program, "computeAcceptorForces");
4484
4485
}

4486
double OpenCLCalcCustomHbondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
4487
4488
    if (numDonors == 0 || numAcceptors == 0)
        return 0.0;
4489
4490
4491
4492
4493
4494
4495
4496
4497
4498
4499
4500
4501
4502
    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    if (!hasInitializedKernel) {
        hasInitializedKernel = true;
        int index = 0;
4503
4504
4505
        donorKernel.setArg<cl::Buffer>(index++, cl.getForceBuffers().getDeviceBuffer());
        donorKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        donorKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
4506
        donorKernel.setArg<cl::Buffer>(index++, donorExclusions->getDeviceBuffer());
4507
4508
4509
4510
        donorKernel.setArg<cl::Buffer>(index++, donors->getDeviceBuffer());
        donorKernel.setArg<cl::Buffer>(index++, acceptors->getDeviceBuffer());
        donorKernel.setArg<cl::Buffer>(index++, donorBufferIndices->getDeviceBuffer());
        donorKernel.setArg(index++, 3*OpenCLContext::ThreadBlockSize*sizeof(mm_float4), NULL);
4511
        index += 5; // Periodic box size arguments are set when the kernel is executed.
4512
        if (globals != NULL)
4513
            donorKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
4514
4515
        for (int i = 0; i < (int) donorParams->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = donorParams->getBuffers()[i];
4516
            donorKernel.setArg<cl::Memory>(index++, buffer.getMemory());
4517
4518
4519
        }
        for (int i = 0; i < (int) acceptorParams->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = acceptorParams->getBuffers()[i];
4520
            donorKernel.setArg<cl::Memory>(index++, buffer.getMemory());
4521
        }
4522
4523
        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            donorKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
4524
4525
4526
4527
        index = 0;
        acceptorKernel.setArg<cl::Buffer>(index++, cl.getForceBuffers().getDeviceBuffer());
        acceptorKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        acceptorKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
4528
        acceptorKernel.setArg<cl::Buffer>(index++, acceptorExclusions->getDeviceBuffer());
4529
4530
4531
4532
        acceptorKernel.setArg<cl::Buffer>(index++, donors->getDeviceBuffer());
        acceptorKernel.setArg<cl::Buffer>(index++, acceptors->getDeviceBuffer());
        acceptorKernel.setArg<cl::Buffer>(index++, acceptorBufferIndices->getDeviceBuffer());
        acceptorKernel.setArg(index++, 3*OpenCLContext::ThreadBlockSize*sizeof(mm_float4), NULL);
4533
        index += 5; // Periodic box size arguments are set when the kernel is executed.
4534
4535
4536
4537
        if (globals != NULL)
            acceptorKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        for (int i = 0; i < (int) donorParams->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = donorParams->getBuffers()[i];
4538
            acceptorKernel.setArg<cl::Memory>(index++, buffer.getMemory());
4539
4540
4541
        }
        for (int i = 0; i < (int) acceptorParams->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = acceptorParams->getBuffers()[i];
4542
            acceptorKernel.setArg<cl::Memory>(index++, buffer.getMemory());
4543
        }
4544
4545
        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            acceptorKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
4546
    }
4547
    setPeriodicBoxArgs(cl, donorKernel, 8);
Peter Eastman's avatar
Peter Eastman committed
4548
    cl.executeKernel(donorKernel, max(numDonors, numAcceptors));
4549
    setPeriodicBoxArgs(cl, acceptorKernel, 8);
Peter Eastman's avatar
Peter Eastman committed
4550
    cl.executeKernel(acceptorKernel, max(numDonors, numAcceptors));
4551
4552
4553
    return 0.0;
}

4554
4555
4556
4557
4558
4559
4560
4561
4562
4563
4564
void OpenCLCalcCustomHbondForceKernel::copyParametersToContext(ContextImpl& context, const CustomHbondForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumDonors()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumDonors()/numContexts;
    if (numDonors != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of donors has changed");
    if (numAcceptors != force.getNumAcceptors())
        throw OpenMMException("updateParametersInContext: The number of acceptors has changed");
    
    // Record the per-donor parameters.
    
4565
4566
4567
4568
4569
4570
4571
4572
4573
4574
4575
    if (numDonors > 0) {
        vector<vector<cl_float> > donorParamVector(numDonors);
        vector<double> parameters;
        for (int i = 0; i < numDonors; i++) {
            int d1, d2, d3;
            force.getDonorParameters(startIndex+i, d1, d2, d3, parameters);
            donorParamVector[i].resize(parameters.size());
            for (int j = 0; j < (int) parameters.size(); j++)
                donorParamVector[i][j] = (cl_float) parameters[j];
        }
        donorParams->setParameterValues(donorParamVector);
4576
4577
4578
4579
    }
    
    // Record the per-acceptor parameters.
    
4580
4581
4582
4583
4584
4585
4586
4587
4588
4589
4590
    if (numAcceptors > 0) {
        vector<vector<cl_float> > acceptorParamVector(numAcceptors);
        vector<double> parameters;
        for (int i = 0; i < numAcceptors; i++) {
            int a1, a2, a3;
            force.getAcceptorParameters(i, a1, a2, a3, parameters);
            acceptorParamVector[i].resize(parameters.size());
            for (int j = 0; j < (int) parameters.size(); j++)
                acceptorParamVector[i][j] = (cl_float) parameters[j];
        }
        acceptorParams->setParameterValues(acceptorParamVector);
4591
4592
4593
4594
4595
4596
4597
    }
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

4598
4599
4600
4601
4602
4603
4604
4605
4606
4607
4608
4609
4610
4611
4612
4613
4614
4615
4616
4617
4618
4619
4620
4621
4622
4623
4624
4625
4626
4627
4628
4629
4630
4631
4632
4633
4634
4635
4636
4637
4638
4639
4640
4641
4642
4643
4644
4645
4646
4647
4648
4649
4650
4651
4652
4653
4654
4655
4656
4657
4658
4659
4660
4661
4662
4663
4664
4665
4666
4667
4668
4669
4670
4671
4672
4673
4674
4675
4676
4677
4678
4679
4680
4681
4682
4683
4684
4685
4686
4687
4688
4689
4690
4691
4692
4693
4694
4695
4696
4697
4698
4699
4700
4701
4702
4703
4704
4705
4706
4707
4708
4709
4710
4711
4712
4713
4714
4715
4716
4717
4718
4719
4720
4721
4722
4723
4724
4725
4726
4727
4728
4729
4730
4731
4732
4733
4734
4735
4736
4737
4738
4739
4740
4741
4742
4743
4744
4745
4746
4747
4748
4749
4750
4751
4752
4753
4754
4755
4756
4757
4758
4759
4760
4761
4762
4763
4764
4765
4766
4767
4768
4769
4770
4771
4772
4773
4774
4775
4776
4777
4778
4779
4780
4781
4782
4783
4784
4785
4786
4787
4788
4789
4790
4791
4792
4793
4794
4795
4796
4797
4798
4799
4800
4801
4802
4803
4804
4805
4806
4807
4808
4809
class OpenCLCustomCentroidBondForceInfo : public OpenCLForceInfo {
public:
    OpenCLCustomCentroidBondForceInfo(const CustomCentroidBondForce& force) : OpenCLForceInfo(0), force(force) {
    }
    int getNumParticleGroups() {
        return force.getNumBonds();
    }
    void getParticlesInGroup(int index, vector<int>& particles) {
        vector<double> parameters;
        vector<int> groups;
        force.getBondParameters(index, groups, parameters);
        for (int i = 0; i < groups.size(); i++) {
            vector<int> groupParticles;
            vector<double> weights;
            force.getGroupParameters(groups[i], groupParticles, weights);
            particles.insert(particles.end(), groupParticles.begin(), groupParticles.end());
        }
    }
    bool areGroupsIdentical(int group1, int group2) {
        vector<int> groups1, groups2;
        vector<double> parameters1, parameters2;
        force.getBondParameters(group1, groups1, parameters1);
        force.getBondParameters(group2, groups2, parameters2);
        for (int i = 0; i < (int) parameters1.size(); i++)
            if (parameters1[i] != parameters2[i])
                return false;
        for (int i = 0; i < groups1.size(); i++) {
            vector<int> groupParticles;
            vector<double> weights1, weights2;
            force.getGroupParameters(groups1[i], groupParticles, weights1);
            force.getGroupParameters(groups2[i], groupParticles, weights2);
            if (weights1.size() != weights2.size())
                return false;
            for (int j = 0; j < weights1.size(); j++)
                if (weights1[j] != weights2[j])
                    return false;
        }
        return true;
    }
private:
    const CustomCentroidBondForce& force;
};

OpenCLCalcCustomCentroidBondForceKernel::~OpenCLCalcCustomCentroidBondForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
    if (groupParticles != NULL)
        delete groupParticles;
    if (groupWeights != NULL)
        delete groupWeights;
    if (groupOffsets != NULL)
        delete groupOffsets;
    if (groupForces != NULL)
        delete groupForces;
    if (bondGroups != NULL)
        delete bondGroups;
    if (centerPositions != NULL)
        delete centerPositions;
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
}

void OpenCLCalcCustomCentroidBondForceKernel::initialize(const System& system, const CustomCentroidBondForce& force) {
    numBonds = force.getNumBonds();
    if (numBonds == 0)
        return;
    if (!cl.getSupports64BitGlobalAtomics())
        throw OpenMMException("CustomCentroidBondForce requires a device that supports 64 bit atomic operations");
    cl.addForce(new OpenCLCustomCentroidBondForceInfo(force));
    
    // Record the groups.
    
    numGroups = force.getNumGroups();
    vector<cl_int> groupParticleVec;
    vector<cl_float> groupWeightVecFloat;
    vector<cl_double> groupWeightVecDouble;
    vector<cl_int> groupOffsetVec;
    groupOffsetVec.push_back(0);
    for (int i = 0; i < numGroups; i++) {
        vector<int> particles;
        vector<double> weights;
        force.getGroupParameters(i, particles, weights);
        groupParticleVec.insert(groupParticleVec.end(), particles.begin(), particles.end());
        groupOffsetVec.push_back(groupParticleVec.size());
    }
    vector<vector<double> > normalizedWeights;
    CustomCentroidBondForceImpl::computeNormalizedWeights(force, system, normalizedWeights);
    if (cl.getUseDoublePrecision()) {
        for (int i = 0; i < numGroups; i++)
            groupWeightVecDouble.insert(groupWeightVecDouble.end(), normalizedWeights[i].begin(), normalizedWeights[i].end());
    }
    else {
        for (int i = 0; i < numGroups; i++)
            for (int j = 0; j < normalizedWeights[i].size(); j++)
                groupWeightVecFloat.push_back((float) normalizedWeights[i][j]);
    }
    groupParticles = OpenCLArray::create<int>(cl, groupParticleVec.size(), "groupParticles");
    groupParticles->upload(groupParticleVec);
    if (cl.getUseDoublePrecision()) {
        groupWeights = OpenCLArray::create<double>(cl, groupParticleVec.size(), "groupWeights");
        groupWeights->upload(groupWeightVecDouble);
        centerPositions = OpenCLArray::create<mm_double4>(cl, numGroups, "centerPositions");
    }
    else {
        groupWeights = OpenCLArray::create<float>(cl, groupParticleVec.size(), "groupWeights");
        groupWeights->upload(groupWeightVecFloat);
        centerPositions = OpenCLArray::create<mm_float4>(cl, numGroups, "centerPositions");
    }
    groupOffsets = OpenCLArray::create<int>(cl, groupOffsetVec.size(), "groupOffsets");
    groupOffsets->upload(groupOffsetVec);
    groupForces = OpenCLArray::create<long long>(cl, numGroups*3, "groupForces");
    cl.addAutoclearBuffer(*groupForces);
    
    // Record the bonds.
    
    int groupsPerBond = force.getNumGroupsPerBond();
    vector<cl_int> bondGroupVec(numBonds*groupsPerBond);
    params = new OpenCLParameterSet(cl, force.getNumPerBondParameters(), numBonds, "customCentroidBondParams");
    vector<vector<float> > paramVector(numBonds);
    for (int i = 0; i < numBonds; i++) {
        vector<int> groups;
        vector<double> parameters;
        force.getBondParameters(i, groups, parameters);
        for (int j = 0; j < groups.size(); j++)
            bondGroupVec[i+j*numBonds] = groups[j];
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (float) parameters[j];
    }
    params->setParameterValues(paramVector);
    bondGroups = OpenCLArray::create<int>(cl, bondGroupVec.size(), "bondGroups");
    bondGroups->upload(bondGroupVec);

    // Record the tabulated functions.

    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
    vector<const TabulatedFunction*> functionList;
    stringstream extraArgs;
    for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
        string arrayName = "table"+cl.intToString(i);
        functionDefinitions.push_back(make_pair(name, arrayName));
        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
        int width;
        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
        tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
        tabulatedFunctions.back()->upload(f);
        extraArgs << ", __global const float";
        if (width > 1)
            extraArgs << width;
        extraArgs << "* restrict " << arrayName;
    }
    
    // Record information about parameters.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (float) force.getGlobalParameterDefaultValue(i);
    }
    map<string, string> variables;
    for (int i = 0; i < groupsPerBond; i++) {
        string index = cl.intToString(i+1);
        variables["x"+index] = "pos"+index+".x";
        variables["y"+index] = "pos"+index+".y";
        variables["z"+index] = "pos"+index+".z";
    }
    for (int i = 0; i < force.getNumPerBondParameters(); i++) {
        const string& name = force.getPerBondParameterName(i);
        variables[name] = "bondParams"+params->getParameterSuffix(i);
    }
    if (force.getNumGlobalParameters() > 0) {
        globals = OpenCLArray::create<float>(cl, force.getNumGlobalParameters(), "customCentroidBondGlobals");
        globals->upload(globalParamValues);
        extraArgs << ", __global const float* restrict globals";
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
            string value = "globals["+cl.intToString(i)+"]";
            variables[name] = value;
        }
    }

    // Now to generate the kernel.  First, it needs to calculate all distances, angles,
    // and dihedrals the expression depends on.

    map<string, vector<int> > distances;
    map<string, vector<int> > angles;
    map<string, vector<int> > dihedrals;
    Lepton::ParsedExpression energyExpression = CustomCentroidBondForceImpl::prepareExpression(force, functions, distances, angles, dihedrals);
    map<string, Lepton::ParsedExpression> forceExpressions;
    set<string> computedDeltas;
    vector<string> atomNames, posNames;
    for (int i = 0; i < groupsPerBond; i++) {
        string index = cl.intToString(i+1);
        atomNames.push_back("P"+index);
        posNames.push_back("pos"+index);
    }
    stringstream compute;
    for (int i = 0; i < groupsPerBond; i++) {
        compute<<"int group"<<(i+1)<<" = bondGroups[index+"<<(i*numBonds)<<"];\n";
        compute<<"real4 pos"<<(i+1)<<" = centerPositions[group"<<(i+1)<<"];\n";
    }
    int index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName = atomNames[groups[0]]+atomNames[groups[1]];
        if (computedDeltas.count(deltaName) == 0) {
4810
            compute<<"real4 delta"<<deltaName<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
4811
4812
4813
4814
4815
4816
4817
4818
4819
4820
4821
4822
4823
            computedDeltas.insert(deltaName);
        }
        compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
        variables[iter->first] = "r_"+deltaName;
        forceExpressions["real dEdDistance"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName1 = atomNames[groups[1]]+atomNames[groups[0]];
        string deltaName2 = atomNames[groups[1]]+atomNames[groups[2]];
        string angleName = "angle_"+atomNames[groups[0]]+atomNames[groups[1]]+atomNames[groups[2]];
        if (computedDeltas.count(deltaName1) == 0) {
4824
            compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[0]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
4825
4826
4827
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
4828
            compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[2]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
4829
4830
4831
4832
4833
4834
4835
4836
4837
4838
4839
4840
4841
4842
4843
4844
            computedDeltas.insert(deltaName2);
        }
        compute<<"real "<<angleName<<" = computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        variables[iter->first] = angleName;
        forceExpressions["real dEdAngle"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName1 = atomNames[groups[0]]+atomNames[groups[1]];
        string deltaName2 = atomNames[groups[2]]+atomNames[groups[1]];
        string deltaName3 = atomNames[groups[2]]+atomNames[groups[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        string dihedralName = "dihedral_"+atomNames[groups[0]]+atomNames[groups[1]]+atomNames[groups[2]]+atomNames[groups[3]];
        if (computedDeltas.count(deltaName1) == 0) {
4845
            compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
4846
4847
4848
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
4849
            compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
4850
4851
4852
            computedDeltas.insert(deltaName2);
        }
        if (computedDeltas.count(deltaName3) == 0) {
4853
            compute<<"real4 delta"<<deltaName3<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[3]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
4854
4855
4856
4857
4858
4859
4860
4861
4862
4863
4864
4865
4866
4867
4868
4869
4870
4871
4872
4873
4874
4875
4876
4877
4878
4879
4880
4881
4882
4883
4884
4885
4886
4887
4888
4889
4890
4891
4892
4893
4894
4895
4896
4897
4898
4899
4900
4901
4902
4903
4904
4905
4906
4907
4908
4909
4910
4911
4912
4913
4914
4915
4916
4917
4918
4919
4920
4921
4922
4923
4924
4925
4926
4927
4928
4929
4930
4931
4932
4933
4934
4935
4936
4937
4938
4939
4940
4941
4942
4943
4944
4945
4946
4947
4948
4949
4950
4951
4952
4953
4954
4955
4956
4957
4958
4959
4960
4961
4962
4963
4964
4965
4966
4967
4968
4969
4970
4971
4972
4973
            computedDeltas.insert(deltaName3);
        }
        compute<<"real4 "<<crossName1<<" = computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        compute<<"real4 "<<crossName2<<" = computeCross(delta"<<deltaName2<<", delta"<<deltaName3<<");\n";
        compute<<"real "<<dihedralName<<" = computeAngle("<<crossName1<<", "<<crossName2<<");\n";
        compute<<dihedralName<<" *= (delta"<<deltaName1<<".x*"<<crossName2<<".x + delta"<<deltaName1<<".y*"<<crossName2<<".y + delta"<<deltaName1<<".z*"<<crossName2<<".z < 0 ? -1 : 1);\n";
        variables[iter->first] = dihedralName;
        forceExpressions["real dEdDihedral"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }

    // Now evaluate the expressions.

    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
        extraArgs<<", __global const "<<buffer.getType()<<"* restrict globalParams"<<i;
        compute<<buffer.getType()<<" bondParams"<<(i+1)<<" = globalParams"<<i<<"[index];\n";
    }
    forceExpressions["energy += "] = energyExpression;
    compute << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, "temp");

    // Finally, apply forces to groups.

    vector<string> forceNames;
    for (int i = 0; i < groupsPerBond; i++) {
        string istr = cl.intToString(i+1);
        string forceName = "force"+istr;
        forceNames.push_back(forceName);
        compute<<"real3 "<<forceName<<" = (real3) 0;\n";
        compute<<"{\n";
        Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x"+istr).optimize();
        Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y"+istr).optimize();
        Lepton::ParsedExpression forceExpressionZ = energyExpression.differentiate("z"+istr).optimize();
        map<string, Lepton::ParsedExpression> expressions;
        if (!isZeroExpression(forceExpressionX))
            expressions[forceName+".x -= "] = forceExpressionX;
        if (!isZeroExpression(forceExpressionY))
            expressions[forceName+".y -= "] = forceExpressionY;
        if (!isZeroExpression(forceExpressionZ))
            expressions[forceName+".z -= "] = forceExpressionZ;
        if (expressions.size() > 0)
            compute<<cl.getExpressionUtilities().createExpressions(expressions, variables, functionList, functionDefinitions, "coordtemp");
        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName = atomNames[groups[0]]+atomNames[groups[1]];
        string value = "(dEdDistance"+cl.intToString(index)+"/r_"+deltaName+")*delta"+deltaName+".xyz";
        compute<<forceNames[groups[0]]<<" += "<<"-"<<value<<";\n";
        compute<<forceNames[groups[1]]<<" += "<<value<<";\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName1 = atomNames[groups[1]]+atomNames[groups[0]];
        string deltaName2 = atomNames[groups[1]]+atomNames[groups[2]];
        compute<<"{\n";
        compute<<"real4 crossProd = cross(delta"<<deltaName2<<", delta"<<deltaName1<<");\n";
        compute<<"real lengthCross = max(length(crossProd), (real) 1e-6f);\n";
        compute<<"real4 deltaCross0 = -cross(delta"<<deltaName1<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName1<<".w*lengthCross);\n";
        compute<<"real4 deltaCross2 = cross(delta"<<deltaName2<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName2<<".w*lengthCross);\n";
        compute<<"real4 deltaCross1 = -(deltaCross0+deltaCross2);\n";
        compute<<forceNames[groups[0]]<<".xyz += deltaCross0.xyz;\n";
        compute<<forceNames[groups[1]]<<".xyz += deltaCross1.xyz;\n";
        compute<<forceNames[groups[2]]<<".xyz += deltaCross2.xyz;\n";
        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName1 = atomNames[groups[0]]+atomNames[groups[1]];
        string deltaName2 = atomNames[groups[2]]+atomNames[groups[1]];
        string deltaName3 = atomNames[groups[2]]+atomNames[groups[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        compute<<"{\n";
        compute<<"real r = sqrt(delta"<<deltaName2<<".w);\n";
        compute<<"real4 ff;\n";
        compute<<"ff.x = (-dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName1<<".w;\n";
        compute<<"ff.y = (delta"<<deltaName1<<".x*delta"<<deltaName2<<".x + delta"<<deltaName1<<".y*delta"<<deltaName2<<".y + delta"<<deltaName1<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
        compute<<"ff.z = (delta"<<deltaName3<<".x*delta"<<deltaName2<<".x + delta"<<deltaName3<<".y*delta"<<deltaName2<<".y + delta"<<deltaName3<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
        compute<<"ff.w = (dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName2<<".w;\n";
        compute<<"real4 internalF0 = ff.x*"<<crossName1<<";\n";
        compute<<"real4 internalF3 = ff.w*"<<crossName2<<";\n";
        compute<<"real4 s = ff.y*internalF0 - ff.z*internalF3;\n";
        compute<<forceNames[groups[0]]<<".xyz += internalF0.xyz;\n";
        compute<<forceNames[groups[1]]<<".xyz += s.xyz-internalF0.xyz;\n";
        compute<<forceNames[groups[2]]<<".xyz += -s.xyz-internalF3.xyz;\n";
        compute<<forceNames[groups[3]]<<".xyz += internalF3.xyz;\n";
        compute<<"}\n";
    }
    
    // Save the forces to global memory.
    
    for (int i = 0; i < groupsPerBond; i++) {
        compute<<"atom_add(&groupForce[group"<<(i+1)<<"], (long) (force"<<(i+1)<<".x*0x100000000));\n";
        compute<<"atom_add(&groupForce[group"<<(i+1)<<"+NUM_GROUPS], (long) (force"<<(i+1)<<".y*0x100000000));\n";
        compute<<"atom_add(&groupForce[group"<<(i+1)<<"+NUM_GROUPS*2], (long) (force"<<(i+1)<<".z*0x100000000));\n";
    }
    map<string, string> replacements;
    replacements["M_PI"] = cl.doubleToString(M_PI);
    replacements["NUM_GROUPS"] = cl.intToString(numGroups);
    replacements["NUM_BONDS"] = cl.intToString(numBonds);
    replacements["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
    replacements["EXTRA_ARGS"] = extraArgs.str();
    replacements["COMPUTE_FORCE"] = compute.str();
    cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customCentroidBond, replacements));
    index = 0;
    computeCentersKernel = cl::Kernel(program, "computeGroupCenters");
    computeCentersKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
    computeCentersKernel.setArg<cl::Buffer>(index++, groupParticles->getDeviceBuffer());
    computeCentersKernel.setArg<cl::Buffer>(index++, groupWeights->getDeviceBuffer());
    computeCentersKernel.setArg<cl::Buffer>(index++, groupOffsets->getDeviceBuffer());
    computeCentersKernel.setArg<cl::Buffer>(index++, centerPositions->getDeviceBuffer());
    index = 0;
    groupForcesKernel = cl::Kernel(program, "computeGroupForces");
    groupForcesKernel.setArg<cl::Buffer>(index++, groupForces->getDeviceBuffer());
    index++; // Energy buffer hasn't been created yet
    groupForcesKernel.setArg<cl::Buffer>(index++, centerPositions->getDeviceBuffer());
    groupForcesKernel.setArg<cl::Buffer>(index++, bondGroups->getDeviceBuffer());
4974
    index += 5; // Periodic box information
4975
4976
4977
4978
4979
4980
4981
4982
4983
4984
4985
4986
4987
4988
4989
    for (int i = 0; i < tabulatedFunctions.size(); i++)
        groupForcesKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
    if (globals != NULL)
        groupForcesKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
    for (int i = 0; i < (int) params->getBuffers().size(); i++)
        groupForcesKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
    index = 0;
    applyForcesKernel = cl::Kernel(program, "applyForcesToAtoms");
    applyForcesKernel.setArg<cl::Buffer>(index++, groupParticles->getDeviceBuffer());
    applyForcesKernel.setArg<cl::Buffer>(index++, groupWeights->getDeviceBuffer());
    applyForcesKernel.setArg<cl::Buffer>(index++, groupOffsets->getDeviceBuffer());
    applyForcesKernel.setArg<cl::Buffer>(index++, groupForces->getDeviceBuffer());
}

double OpenCLCalcCustomCentroidBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
4990
4991
    if (numBonds == 0)
        return 0.0;
4992
4993
4994
4995
4996
4997
4998
4999
5000
5001
5002
5003
5004
    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            float value = (float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    cl.executeKernel(computeCentersKernel, OpenCLContext::TileSize*numGroups);
    groupForcesKernel.setArg<cl::Buffer>(1, cl.getEnergyBuffer().getDeviceBuffer());
5005
    setPeriodicBoxArgs(cl, groupForcesKernel, 4);
5006
5007
5008
5009
5010
5011
5012
    cl.executeKernel(groupForcesKernel, numBonds);
    applyForcesKernel.setArg<cl::Buffer>(4, cl.getLongForceBuffer().getDeviceBuffer());
    cl.executeKernel(applyForcesKernel, OpenCLContext::TileSize*numGroups);
    return 0.0;
}

void OpenCLCalcCustomCentroidBondForceKernel::copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force) {
5013
    if (numBonds != force.getNumBonds())
5014
5015
5016
5017
5018
5019
5020
5021
5022
5023
        throw OpenMMException("updateParametersInContext: The number of bonds has changed");
    if (numBonds == 0)
        return;
    
    // Record the per-bond parameters.
    
    vector<vector<float> > paramVector(numBonds);
    vector<int> particles;
    vector<double> parameters;
    for (int i = 0; i < numBonds; i++) {
5024
        force.getBondParameters(i, particles, parameters);
5025
5026
5027
5028
5029
5030
5031
5032
5033
5034
5035
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

5036
5037
class OpenCLCustomCompoundBondForceInfo : public OpenCLForceInfo {
public:
Peter Eastman's avatar
Peter Eastman committed
5038
    OpenCLCustomCompoundBondForceInfo(const CustomCompoundBondForce& force) : OpenCLForceInfo(0), force(force) {
5039
5040
5041
5042
5043
5044
5045
5046
5047
5048
5049
5050
5051
5052
5053
5054
5055
5056
5057
5058
5059
5060
5061
5062
5063
5064
5065
5066
5067
5068
5069
5070
5071
5072
5073
5074
5075
5076
5077
5078
5079
5080
5081
5082
5083
5084
5085
5086
5087
5088
5089
5090
5091
5092
5093
5094
    }
    int getNumParticleGroups() {
        return force.getNumBonds();
    }
    void getParticlesInGroup(int index, vector<int>& particles) {
        vector<double> parameters;
        force.getBondParameters(index, particles, parameters);
    }
    bool areGroupsIdentical(int group1, int group2) {
        vector<int> particles;
        vector<double> parameters1, parameters2;
        force.getBondParameters(group1, particles, parameters1);
        force.getBondParameters(group2, particles, parameters2);
        for (int i = 0; i < (int) parameters1.size(); i++)
            if (parameters1[i] != parameters2[i])
                return false;
        return true;
    }
private:
    const CustomCompoundBondForce& force;
};

OpenCLCalcCustomCompoundBondForceKernel::~OpenCLCalcCustomCompoundBondForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
}

void OpenCLCalcCustomCompoundBondForceKernel::initialize(const System& system, const CustomCompoundBondForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    numBonds = endIndex-startIndex;
    if (numBonds == 0)
        return;
    int particlesPerBond = force.getNumParticlesPerBond();
    vector<vector<int> > atoms(numBonds, vector<int>(particlesPerBond));
    params = new OpenCLParameterSet(cl, force.getNumPerBondParameters(), numBonds, "customCompoundBondParams");
    vector<vector<cl_float> > paramVector(numBonds);
    for (int i = 0; i < numBonds; i++) {
        vector<double> parameters;
        force.getBondParameters(startIndex+i, atoms[i], parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    cl.addForce(new OpenCLCustomCompoundBondForceInfo(force));

    // Record the tabulated functions.

    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
5095
    vector<const TabulatedFunction*> functionList;
5096
5097
    stringstream tableArgs;
    for (int i = 0; i < force.getNumFunctions(); i++) {
5098
5099
5100
        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
peastman's avatar
peastman committed
5101
        int width;
5102
        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
5103
        OpenCLArray* array = OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction");
5104
5105
        tabulatedFunctions.push_back(array);
        array->upload(f);
peastman's avatar
peastman committed
5106
        string arrayName = cl.getBondedUtilities().addArgument(array->getDeviceBuffer(), width == 1 ? "float" : "float"+cl.intToString(width));
5107
5108
5109
5110
5111
5112
5113
5114
5115
5116
5117
5118
5119
        functionDefinitions.push_back(make_pair(name, arrayName));
    }
    
    // Record information about parameters.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    map<string, string> variables;
    for (int i = 0; i < particlesPerBond; i++) {
5120
        string index = cl.intToString(i+1);
5121
5122
5123
5124
5125
5126
5127
5128
5129
        variables["x"+index] = "pos"+index+".x";
        variables["y"+index] = "pos"+index+".y";
        variables["z"+index] = "pos"+index+".z";
    }
    for (int i = 0; i < force.getNumPerBondParameters(); i++) {
        const string& name = force.getPerBondParameterName(i);
        variables[name] = "bondParams"+params->getParameterSuffix(i);
    }
    if (force.getNumGlobalParameters() > 0) {
5130
        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customCompoundBondGlobals", CL_MEM_READ_ONLY);
5131
5132
5133
5134
        globals->upload(globalParamValues);
        string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
5135
            string value = argName+"["+cl.intToString(i)+"]";
5136
5137
5138
5139
5140
5141
5142
5143
5144
5145
5146
5147
5148
5149
5150
            variables[name] = value;
        }
    }

    // Now to generate the kernel.  First, it needs to calculate all distances, angles,
    // and dihedrals the expression depends on.

    map<string, vector<int> > distances;
    map<string, vector<int> > angles;
    map<string, vector<int> > dihedrals;
    Lepton::ParsedExpression energyExpression = CustomCompoundBondForceImpl::prepareExpression(force, functions, distances, angles, dihedrals);
    map<string, Lepton::ParsedExpression> forceExpressions;
    set<string> computedDeltas;
    vector<string> atomNames, posNames;
    for (int i = 0; i < particlesPerBond; i++) {
5151
        string index = cl.intToString(i+1);
5152
5153
5154
5155
5156
5157
5158
5159
5160
        atomNames.push_back("P"+index);
        posNames.push_back("pos"+index);
    }
    stringstream compute;
    int index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
        if (computedDeltas.count(deltaName) == 0) {
5161
            compute<<"real4 delta"<<deltaName<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5162
5163
            computedDeltas.insert(deltaName);
        }
5164
        compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
5165
        variables[iter->first] = "r_"+deltaName;
5166
        forceExpressions["real dEdDistance"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
5167
5168
5169
5170
5171
5172
5173
5174
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        string angleName = "angle_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]];
        if (computedDeltas.count(deltaName1) == 0) {
5175
            compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[0]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5176
5177
5178
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
5179
            compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[2]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5180
5181
            computedDeltas.insert(deltaName2);
        }
5182
        compute<<"real "<<angleName<<" = ccb_computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
5183
        variables[iter->first] = angleName;
5184
        forceExpressions["real dEdAngle"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
5185
5186
5187
5188
5189
5190
5191
5192
5193
5194
5195
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        string dihedralName = "dihedral_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]]+atomNames[atoms[3]];
        if (computedDeltas.count(deltaName1) == 0) {
5196
            compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5197
5198
5199
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
5200
            compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5201
5202
5203
            computedDeltas.insert(deltaName2);
        }
        if (computedDeltas.count(deltaName3) == 0) {
5204
            compute<<"real4 delta"<<deltaName3<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[3]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5205
5206
            computedDeltas.insert(deltaName3);
        }
5207
5208
5209
        compute<<"real4 "<<crossName1<<" = ccb_computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        compute<<"real4 "<<crossName2<<" = ccb_computeCross(delta"<<deltaName2<<", delta"<<deltaName3<<");\n";
        compute<<"real "<<dihedralName<<" = ccb_computeAngle("<<crossName1<<", "<<crossName2<<");\n";
5210
5211
        compute<<dihedralName<<" *= (delta"<<deltaName1<<".x*"<<crossName2<<".x + delta"<<deltaName1<<".y*"<<crossName2<<".y + delta"<<deltaName1<<".z*"<<crossName2<<".z < 0 ? -1 : 1);\n";
        variables[iter->first] = dihedralName;
5212
        forceExpressions["real dEdDihedral"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
5213
5214
5215
5216
5217
5218
5219
5220
5221
5222
    }

    // Now evaluate the expressions.

    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
        string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
        compute<<buffer.getType()<<" bondParams"<<(i+1)<<" = "<<argName<<"[index];\n";
    }
    forceExpressions["energy += "] = energyExpression;
5223
5224
5225
5226
5227
5228
    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
        string paramName = force.getEnergyParameterDerivativeName(i);
        string derivVariable = cl.getBondedUtilities().addEnergyParameterDerivative(paramName);
        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
        forceExpressions[derivVariable+" += "] = derivExpression;
    }
5229
    compute << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, "temp");
5230
5231
5232
5233
5234

    // Finally, apply forces to atoms.

    vector<string> forceNames;
    for (int i = 0; i < particlesPerBond; i++) {
5235
        string istr = cl.intToString(i+1);
5236
5237
        string forceName = "force"+istr;
        forceNames.push_back(forceName);
5238
        compute<<"real4 "<<forceName<<" = (real4) 0;\n";
5239
5240
5241
5242
5243
5244
5245
5246
5247
5248
5249
5250
        compute<<"{\n";
        Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x"+istr).optimize();
        Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y"+istr).optimize();
        Lepton::ParsedExpression forceExpressionZ = energyExpression.differentiate("z"+istr).optimize();
        map<string, Lepton::ParsedExpression> expressions;
        if (!isZeroExpression(forceExpressionX))
            expressions[forceName+".x -= "] = forceExpressionX;
        if (!isZeroExpression(forceExpressionY))
            expressions[forceName+".y -= "] = forceExpressionY;
        if (!isZeroExpression(forceExpressionZ))
            expressions[forceName+".z -= "] = forceExpressionZ;
        if (expressions.size() > 0)
5251
            compute<<cl.getExpressionUtilities().createExpressions(expressions, variables, functionList, functionDefinitions, "coordtemp");
5252
5253
5254
5255
5256
5257
        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
5258
        string value = "(dEdDistance"+cl.intToString(index)+"/r_"+deltaName+")*delta"+deltaName+".xyz";
5259
5260
5261
5262
5263
5264
5265
5266
5267
        compute<<forceNames[atoms[0]]<<".xyz += "<<"-"<<value<<";\n";
        compute<<forceNames[atoms[1]]<<".xyz += "<<value<<";\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        compute<<"{\n";
5268
5269
5270
5271
5272
        compute<<"real4 crossProd = cross(delta"<<deltaName2<<", delta"<<deltaName1<<");\n";
        compute<<"real lengthCross = max(length(crossProd), (real) 1e-6f);\n";
        compute<<"real4 deltaCross0 = -cross(delta"<<deltaName1<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName1<<".w*lengthCross);\n";
        compute<<"real4 deltaCross2 = cross(delta"<<deltaName2<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName2<<".w*lengthCross);\n";
        compute<<"real4 deltaCross1 = -(deltaCross0+deltaCross2);\n";
5273
5274
5275
5276
5277
5278
5279
5280
5281
5282
5283
5284
5285
5286
        compute<<forceNames[atoms[0]]<<".xyz += deltaCross0.xyz;\n";
        compute<<forceNames[atoms[1]]<<".xyz += deltaCross1.xyz;\n";
        compute<<forceNames[atoms[2]]<<".xyz += deltaCross2.xyz;\n";
        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        compute<<"{\n";
5287
5288
5289
        compute<<"real r = SQRT(delta"<<deltaName2<<".w);\n";
        compute<<"real4 ff;\n";
        compute<<"ff.x = (-dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName1<<".w;\n";
5290
5291
        compute<<"ff.y = (delta"<<deltaName1<<".x*delta"<<deltaName2<<".x + delta"<<deltaName1<<".y*delta"<<deltaName2<<".y + delta"<<deltaName1<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
        compute<<"ff.z = (delta"<<deltaName3<<".x*delta"<<deltaName2<<".x + delta"<<deltaName3<<".y*delta"<<deltaName2<<".y + delta"<<deltaName3<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
5292
5293
5294
5295
        compute<<"ff.w = (dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName2<<".w;\n";
        compute<<"real4 internalF0 = ff.x*"<<crossName1<<";\n";
        compute<<"real4 internalF3 = ff.w*"<<crossName2<<";\n";
        compute<<"real4 s = ff.y*internalF0 - ff.z*internalF3;\n";
5296
5297
5298
5299
5300
5301
5302
5303
        compute<<forceNames[atoms[0]]<<".xyz += internalF0.xyz;\n";
        compute<<forceNames[atoms[1]]<<".xyz += s.xyz-internalF0.xyz;\n";
        compute<<forceNames[atoms[2]]<<".xyz += -s.xyz-internalF3.xyz;\n";
        compute<<forceNames[atoms[3]]<<".xyz += internalF3.xyz;\n";
        compute<<"}\n";
    }
    cl.getBondedUtilities().addInteraction(atoms, compute.str(), force.getForceGroup());
    map<string, string> replacements;
5304
    replacements["M_PI"] = cl.doubleToString(M_PI);
5305
5306
5307
5308
5309
5310
5311
5312
5313
5314
5315
5316
5317
5318
5319
5320
5321
5322
    cl.getBondedUtilities().addPrefixCode(cl.replaceStrings(OpenCLKernelSources::customCompoundBond, replacements));;
}

double OpenCLCalcCustomCompoundBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    return 0.0;
}

5323
5324
5325
5326
5327
5328
void OpenCLCalcCustomCompoundBondForceKernel::copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    if (numBonds != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of bonds has changed");
5329
5330
    if (numBonds == 0)
        return;
5331
5332
5333
5334
5335
5336
5337
5338
5339
5340
5341
5342
5343
5344
5345
5346
5347
5348
5349
    
    // Record the per-bond parameters.
    
    vector<vector<cl_float> > paramVector(numBonds);
    vector<int> particles;
    vector<double> parameters;
    for (int i = 0; i < numBonds; i++) {
        force.getBondParameters(startIndex+i, particles, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

5350
5351
5352
5353
5354
5355
5356
5357
5358
5359
5360
5361
5362
5363
5364
5365
5366
5367
5368
5369
5370
5371
5372
5373
5374
5375
5376
5377
5378
5379
5380
5381
5382
5383
5384
5385
5386
5387
5388
5389
5390
5391
5392
5393
5394
5395
5396
5397
5398
5399
5400
5401
5402
5403
5404
5405
5406
5407
5408
5409
5410
5411
5412
5413
5414
5415
5416
5417
5418
5419
5420
5421
5422
5423
5424
5425
5426
5427
5428
5429
5430
5431
5432
5433
5434
5435
5436
5437
5438
5439
5440
5441
5442
5443
5444
5445
5446
5447
5448
5449
5450
5451
5452
5453
5454
5455
5456
5457
5458
5459
5460
5461
5462
5463
5464
5465
5466
5467
5468
5469
5470
5471
5472
5473
5474
5475
5476
5477
5478
5479
5480
5481
5482
5483
5484
5485
5486
5487
5488
5489
5490
5491
5492
5493
5494
5495
5496
5497
5498
5499
5500
5501
5502
5503
5504
5505
5506
5507
5508
5509
5510
5511
5512
5513
5514
5515
5516
5517
5518
5519
5520
5521
5522
5523
5524
5525
5526
5527
5528
5529
5530
5531
5532
5533
5534
5535
5536
5537
5538
5539
5540
5541
5542
5543
5544
5545
5546
5547
5548
5549
5550
5551
5552
5553
5554
5555
5556
5557
5558
5559
5560
5561
5562
5563
5564
5565
5566
5567
5568
5569
5570
5571
5572
5573
5574
5575
5576
5577
5578
5579
class OpenCLCustomManyParticleForceInfo : public OpenCLForceInfo {
public:
    OpenCLCustomManyParticleForceInfo(const CustomManyParticleForce& force) : OpenCLForceInfo(0), force(force) {
    }
    bool areParticlesIdentical(int particle1, int particle2) {
        vector<double> params1, params2;
        int type1, type2;
        force.getParticleParameters(particle1, params1, type1);
        force.getParticleParameters(particle2, params2, type2);
        if (type1 != type2)
            return false;
        for (int i = 0; i < (int) params1.size(); i++)
            if (params1[i] != params2[i])
                return false;
        return true;
    }
    int getNumParticleGroups() {
        return force.getNumExclusions();
    }
    void getParticlesInGroup(int index, vector<int>& particles) {
        int particle1, particle2;
        force.getExclusionParticles(index, particle1, particle2);
        particles.resize(2);
        particles[0] = particle1;
        particles[1] = particle2;
    }
    bool areGroupsIdentical(int group1, int group2) {
        return true;
    }
private:
    const CustomManyParticleForce& force;
};

OpenCLCalcCustomManyParticleForceKernel::~OpenCLCalcCustomManyParticleForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
    if (orderIndex != NULL)
        delete orderIndex;
    if (particleOrder != NULL)
        delete particleOrder;
    if (particleTypes != NULL)
        delete particleTypes;
    if (exclusions != NULL)
        delete exclusions;
    if (exclusionStartIndex != NULL)
        delete exclusionStartIndex;
    if (blockCenter != NULL)
        delete blockCenter;
    if (blockBoundingBox != NULL)
        delete blockBoundingBox;
    if (neighborPairs != NULL)
        delete neighborPairs;
    if (numNeighborPairs != NULL)
        delete numNeighborPairs;
    if (neighborStartIndex != NULL)
        delete neighborStartIndex;
    if (neighbors != NULL)
        delete neighbors;
    if (numNeighborsForAtom != NULL)
        delete numNeighborsForAtom;
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
}

void OpenCLCalcCustomManyParticleForceKernel::initialize(const System& system, const CustomManyParticleForce& force) {
    if (!cl.getSupports64BitGlobalAtomics())
        throw OpenMMException("CustomManyParticleForce requires a device that supports 64 bit atomic operations");
    int numParticles = force.getNumParticles();
    int particlesPerSet = force.getNumParticlesPerSet();
    bool centralParticleMode = (force.getPermutationMode() == CustomManyParticleForce::UniqueCentralParticle);
    nonbondedMethod = CalcCustomManyParticleForceKernel::NonbondedMethod(force.getNonbondedMethod());
    forceWorkgroupSize = 128;
    findNeighborsWorkgroupSize = (cl.getSIMDWidth() >= 32 ? 128 : 32);
    
    // Record parameter values.
    
    params = new OpenCLParameterSet(cl, force.getNumPerParticleParameters(), numParticles, "customManyParticleParameters");
    vector<vector<float> > paramVector(numParticles);
    for (int i = 0; i < numParticles; i++) {
        vector<double> parameters;
        int type;
        force.getParticleParameters(i, parameters, type);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (float) parameters[j];
    }
    params->setParameterValues(paramVector);
    cl.addForce(new OpenCLCustomManyParticleForceInfo(force));

    // Record the tabulated functions.

    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
    vector<const TabulatedFunction*> functionList;
    stringstream tableArgs;
    for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
        string arrayName = "table"+cl.intToString(i);
        functionDefinitions.push_back(make_pair(name, arrayName));
        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
        int width;
        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
        tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
        tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
        tableArgs << ", __global const float";
        if (width > 1)
            tableArgs << width;
        tableArgs << "* restrict " << arrayName;
    }
    
    // Record information about parameters.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (float) force.getGlobalParameterDefaultValue(i);
    }
    vector<pair<ExpressionTreeNode, string> > variables;
    for (int i = 0; i < particlesPerSet; i++) {
        string index = cl.intToString(i+1);
        variables.push_back(makeVariable("x"+index, "pos"+index+".x"));
        variables.push_back(makeVariable("y"+index, "pos"+index+".y"));
        variables.push_back(makeVariable("z"+index, "pos"+index+".z"));
    }
    for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
        const string& name = force.getPerParticleParameterName(i);
        for (int j = 0; j < particlesPerSet; j++) {
            string index = cl.intToString(j+1);
            variables.push_back(makeVariable(name+index, "params"+params->getParameterSuffix(i, index)));
        }
    }
    if (force.getNumGlobalParameters() > 0) {
        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customManyParticleGlobals", CL_MEM_READ_ONLY);
        globals->upload(globalParamValues);
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
            string value = "globals["+cl.intToString(i)+"]";
            variables.push_back(makeVariable(name, value));
        }
    }
    
    // Build data structures for type filters.
    
    vector<int> particleTypesVec;
    vector<int> orderIndexVec;
    vector<std::vector<int> > particleOrderVec;
    int numTypes;
    CustomManyParticleForceImpl::buildFilterArrays(force, numTypes, particleTypesVec, orderIndexVec, particleOrderVec);
    bool hasTypeFilters = (particleOrderVec.size() > 1);
    if (hasTypeFilters) {
        particleTypes = OpenCLArray::create<int>(cl, particleTypesVec.size(), "customManyParticleTypes");
        orderIndex = OpenCLArray::create<int>(cl, orderIndexVec.size(), "customManyParticleOrderIndex");
        particleOrder = OpenCLArray::create<int>(cl, particleOrderVec.size()*particlesPerSet, "customManyParticleOrder");
        particleTypes->upload(particleTypesVec);
        orderIndex->upload(orderIndexVec);
        vector<int> flattenedOrder(particleOrder->getSize());
        for (int i = 0; i < (int) particleOrderVec.size(); i++)
            for (int j = 0; j < particlesPerSet; j++)
                flattenedOrder[i*particlesPerSet+j] = particleOrderVec[i][j];
        particleOrder->upload(flattenedOrder);
    }
    
    // Build data structures for exclusions.
    
    if (force.getNumExclusions() > 0) {
        vector<vector<int> > particleExclusions(numParticles);
        for (int i = 0; i < force.getNumExclusions(); i++) {
            int p1, p2;
            force.getExclusionParticles(i, p1, p2);
            particleExclusions[p1].push_back(p2);
            particleExclusions[p2].push_back(p1);
        }
        vector<int> exclusionsVec;
        vector<int> exclusionStartIndexVec(numParticles+1);
        exclusionStartIndexVec[0] = 0;
        for (int i = 0; i < numParticles; i++) {
            sort(particleExclusions[i].begin(), particleExclusions[i].end());
            exclusionsVec.insert(exclusionsVec.end(), particleExclusions[i].begin(), particleExclusions[i].end());
            exclusionStartIndexVec[i+1] = exclusionsVec.size();
        }
        exclusions = OpenCLArray::create<int>(cl, exclusionsVec.size(), "customManyParticleExclusions");
        exclusionStartIndex = OpenCLArray::create<int>(cl, exclusionStartIndexVec.size(), "customManyParticleExclusionStart");
        exclusions->upload(exclusionsVec);
        exclusionStartIndex->upload(exclusionStartIndexVec);
    }
    
    // Build data structures for the neighbor list.
    
    if (nonbondedMethod != NoCutoff) {
        int numAtomBlocks = cl.getNumAtomBlocks();
        int elementSize = (cl.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
        blockCenter = new OpenCLArray(cl, numAtomBlocks, 4*elementSize, "blockCenter");
        blockBoundingBox = new OpenCLArray(cl, numAtomBlocks, 4*elementSize, "blockBoundingBox");
        numNeighborPairs = OpenCLArray::create<int>(cl, 1, "customManyParticleNumNeighborPairs");
        neighborStartIndex = OpenCLArray::create<int>(cl, numParticles+1, "customManyParticleNeighborStartIndex");
        numNeighborsForAtom = OpenCLArray::create<int>(cl, numParticles, "customManyParticleNumNeighborsForAtom");

        // Select a size for the array that holds the neighbor list.  We have to make a fairly
        // arbitrary guess, but if this turns out to be too small we'll increase it later.

        maxNeighborPairs = 150*numParticles;
        neighborPairs = OpenCLArray::create<mm_int2>(cl, maxNeighborPairs, "customManyParticleNeighborPairs");
        neighbors = OpenCLArray::create<int>(cl, maxNeighborPairs, "customManyParticleNeighbors");
    }

    // Now to generate the kernel.  First, it needs to calculate all distances, angles,
    // and dihedrals the expression depends on.

    map<string, vector<int> > distances;
    map<string, vector<int> > angles;
    map<string, vector<int> > dihedrals;
    Lepton::ParsedExpression energyExpression = CustomManyParticleForceImpl::prepareExpression(force, functions, distances, angles, dihedrals);
    map<string, Lepton::ParsedExpression> forceExpressions;
    set<string> computedDeltas;
    vector<string> atomNames, posNames;
    for (int i = 0; i < particlesPerSet; i++) {
        string index = cl.intToString(i+1);
        atomNames.push_back("P"+index);
        posNames.push_back("pos"+index);
    }
    stringstream compute;
    int index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
        if (computedDeltas.count(deltaName) == 0) {
5580
            compute<<"real4 delta"<<deltaName<<" = delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5581
5582
5583
5584
5585
5586
5587
5588
5589
5590
5591
5592
5593
            computedDeltas.insert(deltaName);
        }
        compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
        variables.push_back(makeVariable(iter->first, "r_"+deltaName));
        forceExpressions["real dEdDistance"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        string angleName = "angle_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]];
        if (computedDeltas.count(deltaName1) == 0) {
5594
            compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[0]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5595
5596
5597
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
5598
            compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[2]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5599
5600
5601
5602
5603
5604
5605
5606
5607
5608
5609
5610
5611
5612
5613
5614
            computedDeltas.insert(deltaName2);
        }
        compute<<"real "<<angleName<<" = computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        variables.push_back(makeVariable(iter->first, angleName));
        forceExpressions["real dEdAngle"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        string dihedralName = "dihedral_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]]+atomNames[atoms[3]];
        if (computedDeltas.count(deltaName1) == 0) {
5615
            compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5616
5617
5618
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
5619
            compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[1]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5620
5621
5622
            computedDeltas.insert(deltaName2);
        }
        if (computedDeltas.count(deltaName3) == 0) {
5623
            compute<<"real4 delta"<<deltaName3<<" = delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[3]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
5624
5625
5626
5627
5628
5629
5630
5631
5632
5633
5634
5635
5636
5637
5638
5639
5640
5641
5642
5643
5644
5645
5646
5647
5648
5649
5650
5651
5652
5653
5654
5655
5656
5657
5658
5659
5660
5661
5662
5663
5664
5665
5666
5667
5668
5669
5670
5671
5672
5673
5674
5675
5676
5677
5678
5679
5680
            computedDeltas.insert(deltaName3);
        }
        compute<<"real4 "<<crossName1<<" = computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        compute<<"real4 "<<crossName2<<" = computeCross(delta"<<deltaName2<<", delta"<<deltaName3<<");\n";
        compute<<"real "<<dihedralName<<" = computeAngle("<<crossName1<<", "<<crossName2<<");\n";
        compute<<dihedralName<<" *= (delta"<<deltaName1<<".x*"<<crossName2<<".x + delta"<<deltaName1<<".y*"<<crossName2<<".y + delta"<<deltaName1<<".z*"<<crossName2<<".z < 0 ? -1 : 1);\n";
        variables.push_back(makeVariable(iter->first, dihedralName));
        forceExpressions["real dEdDihedral"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }

    // Now evaluate the expressions.

    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
        compute<<buffer.getType()<<" params"<<(i+1)<<" = global_params"<<(i+1)<<"[index];\n";
    }
    forceExpressions["energy += "] = energyExpression;
    compute << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, "temp");

    // Apply forces to atoms.

    vector<string> forceNames;
    for (int i = 0; i < particlesPerSet; i++) {
        string istr = cl.intToString(i+1);
        string forceName = "force"+istr;
        forceNames.push_back(forceName);
        compute<<"real4 "<<forceName<<" = (real4) 0;\n";
        compute<<"{\n";
        Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x"+istr).optimize();
        Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y"+istr).optimize();
        Lepton::ParsedExpression forceExpressionZ = energyExpression.differentiate("z"+istr).optimize();
        map<string, Lepton::ParsedExpression> expressions;
        if (!isZeroExpression(forceExpressionX))
            expressions[forceName+".x -= "] = forceExpressionX;
        if (!isZeroExpression(forceExpressionY))
            expressions[forceName+".y -= "] = forceExpressionY;
        if (!isZeroExpression(forceExpressionZ))
            expressions[forceName+".z -= "] = forceExpressionZ;
        if (expressions.size() > 0)
            compute<<cl.getExpressionUtilities().createExpressions(expressions, variables, functionList, functionDefinitions, "coordtemp");
        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
        string value = "(dEdDistance"+cl.intToString(index)+"/r_"+deltaName+")*delta"+deltaName+".xyz";
        compute<<forceNames[atoms[0]]<<".xyz += "<<"-"<<value<<";\n";
        compute<<forceNames[atoms[1]]<<".xyz += "<<value<<";\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        compute<<"{\n";
        compute<<"real4 crossProd = cross(delta"<<deltaName2<<", delta"<<deltaName1<<");\n";
5681
        compute<<"real lengthCross = max(SQRT(dot(crossProd, crossProd)), (real) 1e-6f);\n";
5682
5683
5684
5685
5686
5687
5688
5689
5690
5691
5692
5693
5694
5695
5696
5697
5698
5699
5700
5701
5702
5703
5704
5705
5706
5707
5708
5709
5710
5711
5712
5713
5714
5715
5716
5717
5718
5719
5720
5721
5722
5723
5724
5725
5726
5727
5728
5729
5730
5731
5732
5733
        compute<<"real4 deltaCross0 = -cross(delta"<<deltaName1<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName1<<".w*lengthCross);\n";
        compute<<"real4 deltaCross2 = cross(delta"<<deltaName2<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName2<<".w*lengthCross);\n";
        compute<<"real4 deltaCross1 = -(deltaCross0+deltaCross2);\n";
        compute<<forceNames[atoms[0]]<<".xyz += deltaCross0.xyz;\n";
        compute<<forceNames[atoms[1]]<<".xyz += deltaCross1.xyz;\n";
        compute<<forceNames[atoms[2]]<<".xyz += deltaCross2.xyz;\n";
        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        compute<<"{\n";
        compute<<"real r = sqrt(delta"<<deltaName2<<".w);\n";
        compute<<"real4 ff;\n";
        compute<<"ff.x = (-dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName1<<".w;\n";
        compute<<"ff.y = (delta"<<deltaName1<<".x*delta"<<deltaName2<<".x + delta"<<deltaName1<<".y*delta"<<deltaName2<<".y + delta"<<deltaName1<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
        compute<<"ff.z = (delta"<<deltaName3<<".x*delta"<<deltaName2<<".x + delta"<<deltaName3<<".y*delta"<<deltaName2<<".y + delta"<<deltaName3<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
        compute<<"ff.w = (dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName2<<".w;\n";
        compute<<"real4 internalF0 = ff.x*"<<crossName1<<";\n";
        compute<<"real4 internalF3 = ff.w*"<<crossName2<<";\n";
        compute<<"real4 s = ff.y*internalF0 - ff.z*internalF3;\n";
        compute<<forceNames[atoms[0]]<<".xyz += internalF0.xyz;\n";
        compute<<forceNames[atoms[1]]<<".xyz += s.xyz-internalF0.xyz;\n";
        compute<<forceNames[atoms[2]]<<".xyz += -s.xyz-internalF3.xyz;\n";
        compute<<forceNames[atoms[3]]<<".xyz += internalF3.xyz;\n";
        compute<<"}\n";
    }
    
    // Store forces to global memory.
    
    for (int i = 0; i < particlesPerSet; i++)
        compute<<"storeForce(atom"<<(i+1)<<", "<<forceNames[i]<<", forceBuffers);\n";
    
    // Create other replacements that depend on the number of particles per set.
    
    stringstream numCombinations, atomsForCombination, isValidCombination, permute, loadData, verifyCutoff, verifyExclusions;
    if (hasTypeFilters) {
        permute<<"int particleSet[] = {";
        for (int i = 0; i < particlesPerSet; i++) {
            permute<<"p"<<(i+1);
            if (i < particlesPerSet-1)
                permute<<", ";
        }
        permute<<"};\n";
    }
    for (int i = 0; i < particlesPerSet; i++) {
        if (hasTypeFilters)
peastman's avatar
Bug fix  
peastman committed
5734
            permute<<"int atom"<<(i+1)<<" = particleSet[particleOrder["<<particlesPerSet<<"*order+"<<i<<"]];\n";
5735
5736
5737
5738
5739
5740
5741
5742
5743
5744
5745
5746
5747
5748
5749
5750
5751
5752
5753
5754
5755
5756
5757
5758
5759
5760
5761
5762
5763
5764
5765
5766
5767
5768
5769
5770
5771
5772
5773
5774
5775
5776
5777
5778
5779
5780
5781
5782
5783
5784
5785
5786
5787
5788
5789
5790
5791
5792
        else
            permute<<"int atom"<<(i+1)<<" = p"<<(i+1)<<";\n";
        loadData<<"real4 pos"<<(i+1)<<" = posq[atom"<<(i+1)<<"];\n";
        for (int j = 0; j < (int) params->getBuffers().size(); j++)
            loadData<<params->getBuffers()[j].getType()<<" params"<<(j+1)<<(i+1)<<" = global_params"<<(j+1)<<"[atom"<<(i+1)<<"];\n";
    }
    if (centralParticleMode) {
        for (int i = 1; i < particlesPerSet; i++) {
            if (i > 1)
                isValidCombination<<" && p"<<(i+1)<<">p"<<i<<" && ";
            isValidCombination<<"p"<<(i+1)<<"!=p1";
        }
    }
    else {
        for (int i = 2; i < particlesPerSet; i++) {
            if (i > 2)
                isValidCombination<<" && ";
            isValidCombination<<"a"<<(i+1)<<">a"<<i;
        }
    }
    atomsForCombination<<"int tempIndex = index;\n";
    for (int i = 1; i < particlesPerSet; i++) {
        if (i > 1)
            numCombinations<<"*";
        numCombinations<<"numNeighbors";
        if (centralParticleMode)
            atomsForCombination<<"int a"<<(i+1)<<" = tempIndex%numNeighbors;\n";
        else
            atomsForCombination<<"int a"<<(i+1)<<" = 1+tempIndex%numNeighbors;\n";
        if (i < particlesPerSet-1)
            atomsForCombination<<"tempIndex /= numNeighbors;\n";
    }
    if (particlesPerSet > 2) {
        if (centralParticleMode)
            atomsForCombination<<"a2 = (a3%2 == 0 ? a2 : numNeighbors-a2-1);\n";
        else
            atomsForCombination<<"a2 = (a3%2 == 0 ? a2 : numNeighbors-a2+1);\n";
    }
    for (int i = 1; i < particlesPerSet; i++) {
        if (nonbondedMethod == NoCutoff) {
            if (centralParticleMode)
                atomsForCombination<<"int p"<<(i+1)<<" = a"<<(i+1)<<";\n";
            else
                atomsForCombination<<"int p"<<(i+1)<<" = p1+a"<<(i+1)<<";\n";
        }
        else {
            if (centralParticleMode)
                atomsForCombination<<"int p"<<(i+1)<<" = neighbors[firstNeighbor+a"<<(i+1)<<"];\n";
            else
                atomsForCombination<<"int p"<<(i+1)<<" = neighbors[firstNeighbor-1+a"<<(i+1)<<"];\n";
        }
    }
    if (nonbondedMethod != NoCutoff) {
        for (int i = 1; i < particlesPerSet; i++)
            verifyCutoff<<"real4 pos"<<(i+1)<<" = posq[p"<<(i+1)<<"];\n";
        if (!centralParticleMode) {
            for (int i = 1; i < particlesPerSet; i++) {
                for (int j = i+1; j < particlesPerSet; j++)
5793
                    verifyCutoff<<"includeInteraction &= (delta(pos"<<(i+1)<<", pos"<<(j+1)<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ).w < CUTOFF_SQUARED);\n";
5794
5795
5796
5797
5798
5799
5800
5801
5802
5803
5804
5805
5806
5807
5808
5809
5810
5811
5812
5813
5814
5815
5816
5817
5818
5819
5820
5821
5822
5823
5824
5825
5826
5827
5828
5829
5830
5831
5832
5833
5834
5835
5836
5837
5838
5839
5840
5841
5842
5843
5844
5845
5846
5847
5848
5849
5850
5851
5852
5853
5854
5855
5856
5857
5858
5859
5860
5861
5862
            }
        }
    }
    if (force.getNumExclusions() > 0) {
        int startCheckFrom = (nonbondedMethod == NoCutoff ? 0 : 1);
        for (int i = startCheckFrom; i < particlesPerSet; i++)
            for (int j = i+1; j < particlesPerSet; j++)
                verifyExclusions<<"includeInteraction &= !isInteractionExcluded(p"<<(i+1)<<", p"<<(j+1)<<", exclusions, exclusionStartIndex);\n";
    }
    string computeTypeIndex = "particleTypes[p"+cl.intToString(particlesPerSet)+"]";
    for (int i = particlesPerSet-2; i >= 0; i--)
        computeTypeIndex = "particleTypes[p"+cl.intToString(i+1)+"]+"+cl.intToString(numTypes)+"*("+computeTypeIndex+")";
    
    // Create replacements for extra arguments.
    
    stringstream extraArgs;
    if (force.getNumGlobalParameters() > 0)
        extraArgs << ", __global const float* globals";
    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
        extraArgs<<", __global const "<<buffer.getType()<<"* restrict global_params"<<(i+1);
    }

    // Create the kernels.

    map<string, string> replacements;
    replacements["COMPUTE_INTERACTION"] = compute.str();
    replacements["NUM_CANDIDATE_COMBINATIONS"] = numCombinations.str();
    replacements["FIND_ATOMS_FOR_COMBINATION_INDEX"] = atomsForCombination.str();
    replacements["IS_VALID_COMBINATION"] = isValidCombination.str();
    replacements["VERIFY_CUTOFF"] = verifyCutoff.str();
    replacements["VERIFY_EXCLUSIONS"] = verifyExclusions.str();
    replacements["PERMUTE_ATOMS"] = permute.str();
    replacements["LOAD_PARTICLE_DATA"] = loadData.str();
    replacements["COMPUTE_TYPE_INDEX"] = computeTypeIndex;
    replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
    map<string, string> defines;
    if (nonbondedMethod != NoCutoff)
        defines["USE_CUTOFF"] = "1";
    if (nonbondedMethod == CutoffPeriodic)
        defines["USE_PERIODIC"] = "1";
    if (centralParticleMode)
        defines["USE_CENTRAL_PARTICLE"] = "1";
    if (hasTypeFilters)
        defines["USE_FILTERS"] = "1";
    if (force.getNumExclusions() > 0)
        defines["USE_EXCLUSIONS"] = "1";
    defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
    defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
    defines["M_PI"] = cl.doubleToString(M_PI);
    defines["CUTOFF_SQUARED"] = cl.doubleToString(force.getCutoffDistance()*force.getCutoffDistance());
    defines["TILE_SIZE"] = cl.intToString(OpenCLContext::TileSize);
    defines["NUM_BLOCKS"] = cl.intToString(cl.getNumAtomBlocks());
    defines["FIND_NEIGHBORS_WORKGROUP_SIZE"] = cl.intToString(findNeighborsWorkgroupSize);
    cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customManyParticle, replacements), defines);
    forceKernel = cl::Kernel(program, "computeInteraction");
    blockBoundsKernel = cl::Kernel(program, "findBlockBounds");
    neighborsKernel = cl::Kernel(program, "findNeighbors");
    startIndicesKernel = cl::Kernel(program, "computeNeighborStartIndices");
    copyPairsKernel = cl::Kernel(program, "copyPairsToNeighborList");
}

double OpenCLCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
    if (!hasInitializedKernel) {
        hasInitializedKernel = true;
        
        // Set arguments for the force kernel.
        
        int index = 0;
5863
        forceKernel.setArg<cl::Buffer>(index++, cl.getLongForceBuffer().getDeviceBuffer());
5864
5865
        forceKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
5866
5867
        setPeriodicBoxArgs(cl, forceKernel, index);
        index += 5;
5868
5869
5870
5871
5872
5873
5874
5875
5876
5877
5878
5879
5880
5881
5882
5883
5884
5885
5886
5887
5888
5889
5890
5891
5892
5893
        if (nonbondedMethod != NoCutoff) {
            forceKernel.setArg<cl::Buffer>(index++, neighbors->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(index++, neighborStartIndex->getDeviceBuffer());
        }
        if (particleTypes != NULL) {
            forceKernel.setArg<cl::Buffer>(index++, particleTypes->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(index++, orderIndex->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(index++, particleOrder->getDeviceBuffer());
        }
        if (exclusions != NULL) {
            forceKernel.setArg<cl::Buffer>(index++, exclusions->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(index++, exclusionStartIndex->getDeviceBuffer());
        }
        if (globals != NULL)
            forceKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
            forceKernel.setArg<cl::Memory>(index++, buffer.getMemory());
        }
        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            forceKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
        
        if (nonbondedMethod != NoCutoff) {
            // Set arguments for the block bounds kernel.

            index = 0;
5894
5895
            setPeriodicBoxArgs(cl, blockBoundsKernel, index);
            index += 5;
5896
5897
5898
5899
5900
5901
5902
5903
            blockBoundsKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
            blockBoundsKernel.setArg<cl::Buffer>(index++, blockCenter->getDeviceBuffer());
            blockBoundsKernel.setArg<cl::Buffer>(index++, blockBoundingBox->getDeviceBuffer());
            blockBoundsKernel.setArg<cl::Buffer>(index++, numNeighborPairs->getDeviceBuffer());

            // Set arguments for the neighbor list kernel.

            index = 0;
5904
5905
            setPeriodicBoxArgs(cl, neighborsKernel, index);
            index += 5;
5906
5907
5908
5909
5910
5911
5912
5913
5914
5915
5916
5917
5918
5919
5920
5921
5922
5923
5924
5925
5926
5927
5928
5929
5930
5931
5932
5933
5934
5935
5936
5937
5938
5939
5940
5941
5942
5943
5944
5945
5946
5947
5948
5949
5950
            neighborsKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
            neighborsKernel.setArg<cl::Buffer>(index++, blockCenter->getDeviceBuffer());
            neighborsKernel.setArg<cl::Buffer>(index++, blockBoundingBox->getDeviceBuffer());
            neighborsKernel.setArg<cl::Buffer>(index++, neighborPairs->getDeviceBuffer());
            neighborsKernel.setArg<cl::Buffer>(index++, numNeighborPairs->getDeviceBuffer());
            neighborsKernel.setArg<cl::Buffer>(index++, numNeighborsForAtom->getDeviceBuffer());
            index++;
            if (exclusions != NULL) {
                neighborsKernel.setArg<cl::Buffer>(index++, exclusions->getDeviceBuffer());
                neighborsKernel.setArg<cl::Buffer>(index++, exclusionStartIndex->getDeviceBuffer());
            }
            
            // Set arguments for the kernel to find neighbor list start indices.
            
            index = 0;
            startIndicesKernel.setArg<cl::Buffer>(index++, numNeighborsForAtom->getDeviceBuffer());
            startIndicesKernel.setArg<cl::Buffer>(index++, neighborStartIndex->getDeviceBuffer());
            startIndicesKernel.setArg<cl::Buffer>(index++, numNeighborPairs->getDeviceBuffer());

            // Set arguments for the kernel to assemble the final neighbor list.
            
            index = 0;
            copyPairsKernel.setArg<cl::Buffer>(index++, neighborPairs->getDeviceBuffer());
            copyPairsKernel.setArg<cl::Buffer>(index++, neighbors->getDeviceBuffer());
            copyPairsKernel.setArg<cl::Buffer>(index++, numNeighborPairs->getDeviceBuffer());
            index++;
            copyPairsKernel.setArg<cl::Buffer>(index++, numNeighborsForAtom->getDeviceBuffer());
            copyPairsKernel.setArg<cl::Buffer>(index++, neighborStartIndex->getDeviceBuffer());
       }
    }
    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    while (true) {
        int* numPairs = (int*) cl.getPinnedBuffer();
        cl::Event event;
        if (nonbondedMethod != NoCutoff) {
5951
            neighborsKernel.setArg<int>(11, maxNeighborPairs);
5952
5953
5954
5955
5956
5957
5958
5959
5960
5961
5962
5963
5964
            startIndicesKernel.setArg<int>(3, maxNeighborPairs);
            copyPairsKernel.setArg<int>(3, maxNeighborPairs);
            cl.executeKernel(blockBoundsKernel, cl.getNumAtomBlocks());
            cl.executeKernel(neighborsKernel, cl.getNumAtoms(), findNeighborsWorkgroupSize);

            // We need to make sure there was enough memory for the neighbor list.  Download the
            // information asynchronously so kernels can be running at the same time.

            numNeighborPairs->download(numPairs, false);
            cl.getQueue().enqueueMarker(&event);
            cl.executeKernel(startIndicesKernel, 256, 256);
            cl.executeKernel(copyPairsKernel, maxNeighborPairs);
        }
5965
5966
        int maxThreads = min(cl.getNumAtoms()*forceWorkgroupSize, cl.getEnergyBuffer().getSize());
        cl.executeKernel(forceKernel, maxThreads, forceWorkgroupSize);
5967
5968
5969
5970
5971
5972
5973
5974
5975
5976
5977
5978
5979
5980
        if (nonbondedMethod != NoCutoff) {
            // Make sure there was enough memory for the neighbor list.

            event.wait();
            if (*numPairs > maxNeighborPairs) {
                // Resize the arrays and run the calculation again.

                delete neighborPairs;
                neighborPairs = NULL;
                delete neighbors;
                neighbors = NULL;
                maxNeighborPairs = (int) (1.1*(*numPairs));
                neighborPairs = OpenCLArray::create<mm_int2>(cl, maxNeighborPairs, "customManyParticleNeighborPairs");
                neighbors = OpenCLArray::create<int>(cl, maxNeighborPairs, "customManyParticleNeighbors");
5981
5982
                forceKernel.setArg<cl::Buffer>(8, neighbors->getDeviceBuffer());
                neighborsKernel.setArg<cl::Buffer>(8, neighborPairs->getDeviceBuffer());
5983
5984
                copyPairsKernel.setArg<cl::Buffer>(0, neighborPairs->getDeviceBuffer());
                copyPairsKernel.setArg<cl::Buffer>(1, neighbors->getDeviceBuffer());
5985
5986
5987
5988
5989
5990
5991
5992
5993
5994
5995
5996
5997
5998
5999
6000
6001
6002
6003
6004
6005
6006
6007
6008
6009
6010
6011
6012
6013
6014
6015
                continue;
            }
        }
        break;
    }
    return 0.0;
}

void OpenCLCalcCustomManyParticleForceKernel::copyParametersToContext(ContextImpl& context, const CustomManyParticleForce& force) {
    int numParticles = force.getNumParticles();
    if (numParticles != cl.getNumAtoms())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
    
    // Record the per-particle parameters.
    
    vector<vector<float> > paramVector(numParticles);
    vector<double> parameters;
    int type;
    for (int i = 0; i < numParticles; i++) {
        force.getParticleParameters(i, parameters, type);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

6016
6017
6018
6019
OpenCLIntegrateVerletStepKernel::~OpenCLIntegrateVerletStepKernel() {
}

void OpenCLIntegrateVerletStepKernel::initialize(const System& system, const VerletIntegrator& integrator) {
6020
    cl.getPlatformData().initializeContexts(system);
6021
    cl::Program program = cl.createProgram(OpenCLKernelSources::verlet, "");
6022
6023
    kernel1 = cl::Kernel(program, "integrateVerletPart1");
    kernel2 = cl::Kernel(program, "integrateVerletPart2");
6024
6025
6026
}

void OpenCLIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIntegrator& integrator) {
6027
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
6028
6029
    int numAtoms = cl.getNumAtoms();
    double dt = integrator.getStepSize();
6030
6031
6032
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
        kernel1.setArg<cl_int>(0, numAtoms);
6033
        kernel1.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
6034
        kernel1.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
6035
6036
6037
6038
        setPosqCorrectionArg(cl, kernel1, 3);
        kernel1.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(6, integration.getPosDelta().getDeviceBuffer());
6039
        kernel2.setArg<cl_int>(0, numAtoms);
6040
        kernel2.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
6041
        kernel2.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
6042
6043
6044
        setPosqCorrectionArg(cl, kernel2, 3);
        kernel2.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(5, integration.getPosDelta().getDeviceBuffer());
6045
    }
6046
    cl.getIntegrationUtilities().setNextStepSize(dt);
6047
6048
6049
6050
6051
6052
6053

    // Call the first integration kernel.

    cl.executeKernel(kernel1, numAtoms);

    // Apply constraints.

6054
    integration.applyConstraints(integrator.getConstraintTolerance());
6055
6056
6057
6058

    // Call the second integration kernel.

    cl.executeKernel(kernel2, numAtoms);
6059
    integration.computeVirtualSites();
6060
6061
6062
6063
6064

    // Update the time and step count.

    cl.setTime(cl.getTime()+dt);
    cl.setStepCount(cl.getStepCount()+1);
6065
    cl.reorderAtoms();
6066
6067
6068
6069
6070
6071
    
    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
6072
6073
}

6074
6075
6076
6077
double OpenCLIntegrateVerletStepKernel::computeKineticEnergy(ContextImpl& context, const VerletIntegrator& integrator) {
    return cl.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}

6078
6079
6080
6081
6082
6083
OpenCLIntegrateLangevinStepKernel::~OpenCLIntegrateLangevinStepKernel() {
    if (params != NULL)
        delete params;
}

void OpenCLIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) {
6084
    cl.getPlatformData().initializeContexts(system);
6085
6086
    cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
    map<string, string> defines;
6087
6088
    defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
    defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
6089
    cl::Program program = cl.createProgram(OpenCLKernelSources::langevin, defines, "");
6090
6091
    kernel1 = cl::Kernel(program, "integrateLangevinPart1");
    kernel2 = cl::Kernel(program, "integrateLangevinPart2");
6092
    params = new OpenCLArray(cl, 3, cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(cl_double) : sizeof(cl_float), "langevinParams");
6093
6094
6095
6096
    prevStepSize = -1.0;
}

void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const LangevinIntegrator& integrator) {
6097
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
6098
    int numAtoms = cl.getNumAtoms();
6099
6100
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
6101
6102
6103
6104
        kernel1.setArg<cl::Buffer>(0, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(1, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(3, params->getDeviceBuffer());
6105
6106
6107
        kernel1.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, integration.getRandom().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
6108
6109
6110
6111
        setPosqCorrectionArg(cl, kernel2, 1);
        kernel2.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
6112
    }
6113
6114
6115
    double temperature = integrator.getTemperature();
    double friction = integrator.getFriction();
    double stepSize = integrator.getStepSize();
6116
    cl.getIntegrationUtilities().setNextStepSize(stepSize);
6117
6118
6119
6120
6121
    if (temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
        // Calculate the integration parameters.

        double tau = (friction == 0.0 ? 0.0 : 1.0/friction);
        double kT = BOLTZ*temperature;
Peter Eastman's avatar
Peter Eastman committed
6122
        double vscale = exp(-stepSize/tau);
6123
        double fscale = (1-vscale)*tau;
Peter Eastman's avatar
Peter Eastman committed
6124
        double noisescale = sqrt(2*kT/tau)*sqrt(0.5*(1-vscale*vscale)*tau);
6125
6126
6127
6128
6129
6130
6131
6132
6133
6134
6135
6136
6137
6138
        if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
            vector<cl_double> p(params->getSize());
            p[0] = vscale;
            p[1] = fscale;
            p[2] = noisescale;
            params->upload(p);
        }
        else {
            vector<cl_float> p(params->getSize());
            p[0] = (cl_float) vscale;
            p[1] = (cl_float) fscale;
            p[2] = (cl_float) noisescale;
            params->upload(p);
        }
6139
6140
6141
6142
6143
6144
6145
        prevTemp = temperature;
        prevFriction = friction;
        prevStepSize = stepSize;
    }

    // Call the first integration kernel.

6146
    kernel1.setArg<cl_uint>(6, integration.prepareRandomNumbers(cl.getPaddedNumAtoms()));
6147
6148
6149
6150
    cl.executeKernel(kernel1, numAtoms);

    // Apply constraints.

6151
    integration.applyConstraints(integrator.getConstraintTolerance());
6152
6153
6154
6155

    // Call the second integration kernel.

    cl.executeKernel(kernel2, numAtoms);
6156
    integration.computeVirtualSites();
6157
6158
6159
6160
6161

    // Update the time and step count.

    cl.setTime(cl.getTime()+stepSize);
    cl.setStepCount(cl.getStepCount()+1);
6162
    cl.reorderAtoms();
6163
6164
6165
6166
6167
6168
    
    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
6169
}
6170

6171
6172
6173
6174
double OpenCLIntegrateLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const LangevinIntegrator& integrator) {
    return cl.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}

6175
6176
6177
6178
OpenCLIntegrateBrownianStepKernel::~OpenCLIntegrateBrownianStepKernel() {
}

void OpenCLIntegrateBrownianStepKernel::initialize(const System& system, const BrownianIntegrator& integrator) {
6179
    cl.getPlatformData().initializeContexts(system);
6180
6181
    cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
    map<string, string> defines;
6182
    defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
6183
    cl::Program program = cl.createProgram(OpenCLKernelSources::brownian, defines, "");
6184
6185
6186
6187
6188
6189
6190
6191
6192
6193
6194
6195
    kernel1 = cl::Kernel(program, "integrateBrownianPart1");
    kernel2 = cl::Kernel(program, "integrateBrownianPart2");
    prevStepSize = -1.0;
}

void OpenCLIntegrateBrownianStepKernel::execute(ContextImpl& context, const BrownianIntegrator& integrator) {
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
    int numAtoms = cl.getNumAtoms();
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
        kernel1.setArg<cl::Buffer>(2, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(3, integration.getPosDelta().getDeviceBuffer());
6196
6197
        kernel1.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, integration.getRandom().getDeviceBuffer());
6198
        kernel2.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
6199
6200
6201
        setPosqCorrectionArg(cl, kernel2, 2);
        kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(4, integration.getPosDelta().getDeviceBuffer());
6202
6203
6204
6205
6206
6207
    }
    double temperature = integrator.getTemperature();
    double friction = integrator.getFriction();
    double stepSize = integrator.getStepSize();
    if (temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
        double tau = (friction == 0.0 ? 0.0 : 1.0/friction);
6208
6209
6210
6211
6212
6213
6214
6215
6216
6217
        if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
            kernel1.setArg<cl_double>(0, tau*stepSize);
            kernel1.setArg<cl_double>(1, sqrt(2.0f*BOLTZ*temperature*stepSize*tau));
            kernel2.setArg<cl_double>(0, 1.0/stepSize);
        }
        else {
            kernel1.setArg<cl_float>(0, (cl_float) (tau*stepSize));
            kernel1.setArg<cl_float>(1, (cl_float) (sqrt(2.0f*BOLTZ*temperature*stepSize*tau)));
            kernel2.setArg<cl_float>(0, (cl_float) (1.0/stepSize));
        }
6218
6219
6220
6221
6222
6223
6224
        prevTemp = temperature;
        prevFriction = friction;
        prevStepSize = stepSize;
    }

    // Call the first integration kernel.

6225
    kernel1.setArg<cl_uint>(6, integration.prepareRandomNumbers(cl.getPaddedNumAtoms()));
6226
6227
6228
6229
6230
6231
6232
6233
6234
    cl.executeKernel(kernel1, numAtoms);

    // Apply constraints.

    integration.applyConstraints(integrator.getConstraintTolerance());

    // Call the second integration kernel.

    cl.executeKernel(kernel2, numAtoms);
6235
    integration.computeVirtualSites();
6236
6237
6238
6239
6240

    // Update the time and step count.

    cl.setTime(cl.getTime()+stepSize);
    cl.setStepCount(cl.getStepCount()+1);
6241
    cl.reorderAtoms();
6242
6243
6244
6245
6246
6247
    
    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
6248
}
6249

6250
6251
6252
6253
double OpenCLIntegrateBrownianStepKernel::computeKineticEnergy(ContextImpl& context, const BrownianIntegrator& integrator) {
    return cl.getIntegrationUtilities().computeKineticEnergy(0);
}

6254
6255
6256
6257
OpenCLIntegrateVariableVerletStepKernel::~OpenCLIntegrateVariableVerletStepKernel() {
}

void OpenCLIntegrateVariableVerletStepKernel::initialize(const System& system, const VariableVerletIntegrator& integrator) {
6258
    cl.getPlatformData().initializeContexts(system);
6259
    cl::Program program = cl.createProgram(OpenCLKernelSources::verlet, "");
6260
6261
6262
    kernel1 = cl::Kernel(program, "integrateVerletPart1");
    kernel2 = cl::Kernel(program, "integrateVerletPart2");
    selectSizeKernel = cl::Kernel(program, "selectVerletStepSize");
6263
    blockSize = min(min(256, system.getNumParticles()), (int) selectSizeKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(cl.getDevice()));
6264
6265
}

6266
double OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
6267
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
6268
    int numAtoms = cl.getNumAtoms();
6269
    bool useDouble = cl.getUseDoublePrecision() || cl.getUseMixedPrecision();
6270
6271
6272
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
        kernel1.setArg<cl_int>(0, numAtoms);
6273
        kernel1.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
6274
        kernel1.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
6275
6276
6277
6278
        setPosqCorrectionArg(cl, kernel1, 3);
        kernel1.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(6, integration.getPosDelta().getDeviceBuffer());
6279
        kernel2.setArg<cl_int>(0, numAtoms);
6280
        kernel2.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
6281
        kernel2.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
6282
6283
6284
        setPosqCorrectionArg(cl, kernel2, 3);
        kernel2.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(5, integration.getPosDelta().getDeviceBuffer());
6285
        selectSizeKernel.setArg<cl_int>(0, numAtoms);
6286
        selectSizeKernel.setArg<cl::Buffer>(3, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
6287
6288
        selectSizeKernel.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        selectSizeKernel.setArg<cl::Buffer>(5, cl.getForce().getDeviceBuffer());
6289
6290
        int elementSize = (useDouble ? sizeof(cl_double) : sizeof(cl_float));
        selectSizeKernel.setArg(6, blockSize*elementSize, NULL);
6291
6292
6293
6294
    }

    // Select the step size to use.

6295
6296
6297
6298
6299
6300
6301
6302
6303
6304
    double maxStepSize = maxTime-cl.getTime();
    float maxStepSizeFloat = (float) maxStepSize;
    if (useDouble) {
        selectSizeKernel.setArg<cl_double>(1, maxStepSize);
        selectSizeKernel.setArg<cl_double>(2, integrator.getErrorTolerance());
    }
    else {
        selectSizeKernel.setArg<cl_float>(1, maxStepSizeFloat);
        selectSizeKernel.setArg<cl_float>(2, (cl_float) integrator.getErrorTolerance());
    }
6305
6306
6307
6308
6309
6310
6311
6312
6313
6314
6315
6316
6317
    cl.executeKernel(selectSizeKernel, blockSize, blockSize);

    // Call the first integration kernel.

    cl.executeKernel(kernel1, numAtoms);

    // Apply constraints.

    integration.applyConstraints(integrator.getConstraintTolerance());

    // Call the second integration kernel.

    cl.executeKernel(kernel2, numAtoms);
6318
    integration.computeVirtualSites();
6319
6320
6321
6322
6323
6324
    
    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
6325
6326
6327

    // Update the time and step count.

6328
6329
    double dt = cl.getIntegrationUtilities().getLastStepSize();
    double time = cl.getTime()+dt;
6330
6331
6332
6333
6334
6335
6336
6337
    if (useDouble) {
        if (dt == maxStepSize)
            time = maxTime; // Avoid round-off error
    }
    else {
        if (dt == maxStepSizeFloat)
            time = maxTime; // Avoid round-off error
    }
6338
6339
    cl.setTime(time);
    cl.setStepCount(cl.getStepCount()+1);
6340
    cl.reorderAtoms();
6341
    return dt;
6342
6343
}

6344
6345
6346
6347
double OpenCLIntegrateVariableVerletStepKernel::computeKineticEnergy(ContextImpl& context, const VariableVerletIntegrator& integrator) {
    return cl.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}

6348
6349
6350
6351
6352
6353
OpenCLIntegrateVariableLangevinStepKernel::~OpenCLIntegrateVariableLangevinStepKernel() {
    if (params != NULL)
        delete params;
}

void OpenCLIntegrateVariableLangevinStepKernel::initialize(const System& system, const VariableLangevinIntegrator& integrator) {
6354
    cl.getPlatformData().initializeContexts(system);
6355
6356
    cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
    map<string, string> defines;
6357
6358
    defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
    defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
6359
    cl::Program program = cl.createProgram(OpenCLKernelSources::langevin, defines, "");
6360
6361
6362
    kernel1 = cl::Kernel(program, "integrateLangevinPart1");
    kernel2 = cl::Kernel(program, "integrateLangevinPart2");
    selectSizeKernel = cl::Kernel(program, "selectLangevinStepSize");
6363
    params = new OpenCLArray(cl, 3, cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(cl_double) : sizeof(cl_float), "langevinParams");
Peter Eastman's avatar
Peter Eastman committed
6364
6365
    blockSize = min(256, system.getNumParticles());
    blockSize = max(blockSize, params->getSize());
6366
    blockSize = min(blockSize, (int) selectSizeKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(cl.getDevice()));
6367
6368
}

6369
double OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {
6370
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
6371
    int numAtoms = cl.getNumAtoms();
6372
    bool useDouble = cl.getUseDoublePrecision() || cl.getUseMixedPrecision();
6373
6374
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
6375
6376
6377
6378
        kernel1.setArg<cl::Buffer>(0, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(1, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(3, params->getDeviceBuffer());
6379
6380
6381
        kernel1.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, integration.getRandom().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
6382
6383
6384
6385
        setPosqCorrectionArg(cl, kernel2, 1);
        kernel2.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
6386
        selectSizeKernel.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
6387
6388
6389
        selectSizeKernel.setArg<cl::Buffer>(5, cl.getVelm().getDeviceBuffer());
        selectSizeKernel.setArg<cl::Buffer>(6, cl.getForce().getDeviceBuffer());
        selectSizeKernel.setArg<cl::Buffer>(7, params->getDeviceBuffer());
6390
        int elementSize = (useDouble ? sizeof(cl_double) : sizeof(cl_float));
6391
6392
        selectSizeKernel.setArg(8, params->getSize()*elementSize, NULL);
        selectSizeKernel.setArg(9, blockSize*elementSize, NULL);
6393
6394
6395
6396
    }

    // Select the step size to use.

6397
6398
6399
6400
6401
6402
6403
6404
6405
6406
6407
6408
6409
6410
    double maxStepSize = maxTime-cl.getTime();
    float maxStepSizeFloat = (float) maxStepSize;
    if (useDouble) {
        selectSizeKernel.setArg<cl_double>(0, maxStepSize);
        selectSizeKernel.setArg<cl_double>(1, integrator.getErrorTolerance());
        selectSizeKernel.setArg<cl_double>(2, integrator.getFriction() == 0.0 ? 0.0 : 1.0/integrator.getFriction());
        selectSizeKernel.setArg<cl_double>(3, BOLTZ*integrator.getTemperature());
    }
    else {
        selectSizeKernel.setArg<cl_float>(0, maxStepSizeFloat);
        selectSizeKernel.setArg<cl_float>(1, (cl_float) integrator.getErrorTolerance());
        selectSizeKernel.setArg<cl_float>(2, (cl_float) (integrator.getFriction() == 0.0 ? 0.0 : 1.0/integrator.getFriction()));
        selectSizeKernel.setArg<cl_float>(3, (cl_float) (BOLTZ*integrator.getTemperature()));
    }
6411
6412
6413
6414
    cl.executeKernel(selectSizeKernel, blockSize, blockSize);

    // Call the first integration kernel.

6415
    kernel1.setArg<cl_uint>(6, integration.prepareRandomNumbers(cl.getPaddedNumAtoms()));
6416
6417
6418
6419
6420
6421
6422
6423
6424
    cl.executeKernel(kernel1, numAtoms);

    // Apply constraints.

    integration.applyConstraints(integrator.getConstraintTolerance());

    // Call the second integration kernel.

    cl.executeKernel(kernel2, numAtoms);
6425
    integration.computeVirtualSites();
6426
6427
6428
6429
6430
6431
    
    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
6432
6433
6434

    // Update the time and step count.

6435
6436
    double dt = cl.getIntegrationUtilities().getLastStepSize();
    double time = cl.getTime()+dt;
6437
6438
6439
6440
6441
6442
6443
6444
    if (useDouble) {
        if (dt == maxStepSize)
            time = maxTime; // Avoid round-off error
    }
    else {
        if (dt == maxStepSizeFloat)
            time = maxTime; // Avoid round-off error
    }
6445
6446
    cl.setTime(time);
    cl.setStepCount(cl.getStepCount()+1);
6447
    cl.reorderAtoms();
6448
    return dt;
6449
6450
}

6451
6452
6453
6454
double OpenCLIntegrateVariableLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const VariableLangevinIntegrator& integrator) {
    return cl.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}

6455
6456
class OpenCLIntegrateCustomStepKernel::ReorderListener : public OpenCLContext::ReorderListener {
public:
6457
6458
    ReorderListener(OpenCLContext& cl, OpenCLParameterSet& perDofValues, vector<vector<cl_float> >& localPerDofValuesFloat, vector<vector<cl_double> >& localPerDofValuesDouble, bool& deviceValuesAreCurrent) :
            cl(cl), perDofValues(perDofValues), localPerDofValuesFloat(localPerDofValuesFloat), localPerDofValuesDouble(localPerDofValuesDouble), deviceValuesAreCurrent(deviceValuesAreCurrent) {
6459
6460
6461
6462
6463
6464
6465
6466
        int numAtoms = cl.getNumAtoms();
        lastAtomOrder.resize(numAtoms);
        for (int i = 0; i < numAtoms; i++)
            lastAtomOrder[i] = cl.getAtomIndex()[i];
    }
    void execute() {
        // Reorder the per-DOF variables to reflect the new atom order.

6467
6468
        if (perDofValues.getNumParameters() == 0)
            return;
6469
        int numAtoms = cl.getNumAtoms();
6470
6471
6472
6473
6474
6475
6476
6477
6478
6479
6480
6481
6482
6483
6484
6485
6486
6487
6488
6489
6490
6491
6492
6493
6494
6495
6496
6497
6498
6499
6500
6501
6502
        const vector<int>& order = cl.getAtomIndex();
        if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
            if (deviceValuesAreCurrent)
                perDofValues.getParameterValues(localPerDofValuesDouble);
            vector<vector<cl_double> > swap(3*numAtoms);
            for (int i = 0; i < numAtoms; i++) {
                swap[3*lastAtomOrder[i]] = localPerDofValuesDouble[3*i];
                swap[3*lastAtomOrder[i]+1] = localPerDofValuesDouble[3*i+1];
                swap[3*lastAtomOrder[i]+2] = localPerDofValuesDouble[3*i+2];
            }
            for (int i = 0; i < numAtoms; i++) {
                localPerDofValuesDouble[3*i] = swap[3*order[i]];
                localPerDofValuesDouble[3*i+1] = swap[3*order[i]+1];
                localPerDofValuesDouble[3*i+2] = swap[3*order[i]+2];
            }
            perDofValues.setParameterValues(localPerDofValuesDouble);
        }
        else {
            if (deviceValuesAreCurrent)
                perDofValues.getParameterValues(localPerDofValuesFloat);
            vector<vector<cl_float> > swap(3*numAtoms);
            for (int i = 0; i < numAtoms; i++) {
                swap[3*lastAtomOrder[i]] = localPerDofValuesFloat[3*i];
                swap[3*lastAtomOrder[i]+1] = localPerDofValuesFloat[3*i+1];
                swap[3*lastAtomOrder[i]+2] = localPerDofValuesFloat[3*i+2];
            }
            for (int i = 0; i < numAtoms; i++) {
                localPerDofValuesFloat[3*i] = swap[3*order[i]];
                localPerDofValuesFloat[3*i+1] = swap[3*order[i]+1];
                localPerDofValuesFloat[3*i+2] = swap[3*order[i]+2];
            }
            perDofValues.setParameterValues(localPerDofValuesFloat);
        }
6503
6504
        for (int i = 0; i < numAtoms; i++)
            lastAtomOrder[i] = order[i];
Peter Eastman's avatar
Peter Eastman committed
6505
        deviceValuesAreCurrent = true;
6506
6507
6508
6509
    }
private:
    OpenCLContext& cl;
    OpenCLParameterSet& perDofValues;
6510
6511
    vector<vector<cl_float> >& localPerDofValuesFloat;
    vector<vector<cl_double> >& localPerDofValuesDouble;
Peter Eastman's avatar
Peter Eastman committed
6512
    bool& deviceValuesAreCurrent;
Peter Eastman's avatar
Peter Eastman committed
6513
    vector<int> lastAtomOrder;
6514
6515
};

6516
6517
6518
OpenCLIntegrateCustomStepKernel::~OpenCLIntegrateCustomStepKernel() {
    if (globalValues != NULL)
        delete globalValues;
6519
6520
    if (sumBuffer != NULL)
        delete sumBuffer;
6521
6522
    if (summedValue != NULL)
        delete summedValue;
6523
6524
6525
6526
    if (uniformRandoms != NULL)
        delete uniformRandoms;
    if (randomSeed != NULL)
        delete randomSeed;
6527
6528
    if (perDofValues != NULL)
        delete perDofValues;
6529
6530
    for (map<int, OpenCLArray*>::iterator iter = savedForces.begin(); iter != savedForces.end(); ++iter)
        delete iter->second;
6531
6532
6533
6534
6535
6536
}

void OpenCLIntegrateCustomStepKernel::initialize(const System& system, const CustomIntegrator& integrator) {
    cl.getPlatformData().initializeContexts(system);
    cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
    numGlobalVariables = integrator.getNumGlobalVariables();
6537
    int elementSize = (cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
6538
    sumBuffer = new OpenCLArray(cl, ((3*system.getNumParticles()+3)/4)*4, elementSize, "sumBuffer");
6539
    summedValue = new OpenCLArray(cl, 1, elementSize, "summedValue");
6540
6541
    perDofValues = new OpenCLParameterSet(cl, integrator.getNumPerDofVariables(), 3*system.getNumParticles(), "perDofVariables", false, cl.getUseDoublePrecision() || cl.getUseMixedPrecision());
    cl.addReorderListener(new ReorderListener(cl, *perDofValues, localPerDofValuesFloat, localPerDofValuesDouble, deviceValuesAreCurrent));
6542
6543
6544
    SimTKOpenMMUtilities::setRandomNumberSeed(integrator.getRandomNumberSeed());
}

6545
string OpenCLIntegrateCustomStepKernel::createPerDofComputation(const string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator, const string& forceName, const string& energyName) {
6546
6547
6548
6549
6550
6551
6552
    const string suffixes[] = {".x", ".y", ".z"};
    string suffix = suffixes[component];
    map<string, Lepton::ParsedExpression> expressions;
    if (variable == "x")
        expressions["position"+suffix+" = "] = expr;
    else if (variable == "v")
        expressions["velocity"+suffix+" = "] = expr;
6553
    else if (variable == "")
6554
        expressions["sum[3*index+"+cl.intToString(component)+"] = "] = expr;
6555
6556
6557
6558
6559
    else {
        for (int i = 0; i < integrator.getNumPerDofVariables(); i++)
            if (variable == integrator.getPerDofVariableName(i))
                expressions["perDof"+suffix.substr(1)+perDofValues->getParameterSuffix(i)+" = "] = expr;
    }
6560
6561
    if (expressions.size() == 0)
        throw OpenMMException("Unknown per-DOF variable: "+variable);
6562
6563
6564
    map<string, string> variables;
    variables["x"] = "position"+suffix;
    variables["v"] = "velocity"+suffix;
6565
    variables[forceName] = "f"+suffix;
6566
    variables["gaussian"] = "gaussian"+suffix;
6567
    variables["uniform"] = "uniform"+suffix;
6568
6569
    variables["m"] = "mass";
    variables["dt"] = "stepSize";
6570
    if (energyName != "")
Peter Eastman's avatar
Peter Eastman committed
6571
        variables[energyName] = "energy";
6572
    for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
6573
        variables[integrator.getGlobalVariableName(i)] = "globals["+cl.intToString(globalVariableIndex[i])+"]";
6574
6575
    for (int i = 0; i < integrator.getNumPerDofVariables(); i++)
        variables[integrator.getPerDofVariableName(i)] = "perDof"+suffix.substr(1)+perDofValues->getParameterSuffix(i);
6576
    for (int i = 0; i < (int) parameterNames.size(); i++)
6577
        variables[parameterNames[i]] = "globals["+cl.intToString(parameterVariableIndex[i])+"]";
peastman's avatar
peastman committed
6578
6579
    vector<const TabulatedFunction*> functions;
    vector<pair<string, string> > functionNames;
6580
    string tempType = (cl.getSupportsDoublePrecision() ? "double" : "float");
6581
    return cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp"+cl.intToString(component)+"_", tempType);
6582
6583
}

6584
void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid) {
6585
6586
6587
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
    int numAtoms = cl.getNumAtoms();
    int numSteps = integrator.getNumComputations();
6588
    bool useDouble = cl.getUseDoublePrecision() || cl.getUseMixedPrecision();
6589
6590
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
6591
6592
6593
6594
        
        // Initialize various data structures.
        
        const map<string, double>& params = context.getParameters();
6595
6596
        for (map<string, double>::const_iterator iter = params.begin(); iter != params.end(); ++iter)
            parameterNames.push_back(iter->first);
6597
        kernels.resize(integrator.getNumComputations());
6598
6599
        requiredGaussian.resize(integrator.getNumComputations(), 0);
        requiredUniform.resize(integrator.getNumComputations(), 0);
6600
6601
6602
6603
        needsGlobals.resize(numSteps, false);
        globalExpressions.resize(numSteps);
        stepType.resize(numSteps);
        stepTarget.resize(numSteps);
6604
        merged.resize(numSteps, false);
6605
        modifiesParameters = false;
6606
        map<string, string> defines;
6607
6608
        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
        defines["WORK_GROUP_SIZE"] = cl.intToString(OpenCLContext::ThreadBlockSize);
6609
        
6610
6611
6612
6613
6614
6615
6616
6617
6618
        // Record information about all the computation steps.

        vector<string> variable(numSteps);
        vector<int> forceGroup;
        vector<vector<Lepton::ParsedExpression> > expression;
        CustomIntegratorUtilities::analyzeComputations(context, integrator, expression, comparisons, blockEnd, invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy, forceGroup);
        for (int step = 0; step < numSteps; step++) {
            string expr;
            integrator.getComputationStep(step, stepType[step], variable[step], expr);
6619
            if (stepType[step] == CustomIntegrator::WhileBlockStart)
6620
                blockEnd[blockEnd[step]] = step; // Record where to branch back to.
6621
            if (stepType[step] == CustomIntegrator::ComputeGlobal || stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart)
6622
6623
6624
6625
6626
6627
                for (int i = 0; i < (int) expression[step].size(); i++)
                    globalExpressions[step].push_back(expression[step][i].createCompiledExpression());
        }
        for (int step = 0; step < numSteps; step++) {
            for (int i = 0; i < (int) globalExpressions[step].size(); i++)
                expressionSet.registerExpression(globalExpressions[step][i]);
6628
6629
        }
        
6630
        // Record the indices for variables in the CompiledExpressionSet.
6631
        
6632
6633
6634
6635
6636
6637
6638
6639
6640
6641
6642
        gaussianVariableIndex = expressionSet.getVariableIndex("gaussian");
        uniformVariableIndex = expressionSet.getVariableIndex("uniform");
        dtVariableIndex = expressionSet.getVariableIndex("dt");
        for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
            globalVariableIndex.push_back(expressionSet.getVariableIndex(integrator.getGlobalVariableName(i)));
        for (int i = 0; i < (int) parameterNames.size(); i++)
            parameterVariableIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));

        // Record the variable names and flags for the force and energy in each step.

        forceGroupFlags.resize(numSteps, -1);
6643
        vector<string> forceGroupName;
6644
        vector<string> energyGroupName;
6645
        for (int i = 0; i < 32; i++) {
6646
6647
6648
6649
6650
6651
            stringstream fname;
            fname << "f" << i;
            forceGroupName.push_back(fname.str());
            stringstream ename;
            ename << "energy" << i;
            energyGroupName.push_back(ename.str());
6652
6653
        }
        vector<string> forceName(numSteps, "f");
6654
        vector<string> energyName(numSteps, "energy");
6655
        stepEnergyVariableIndex.resize(numSteps, expressionSet.getVariableIndex("energy"));
6656
        for (int step = 0; step < numSteps; step++) {
6657
6658
6659
6660
6661
6662
6663
6664
6665
6666
6667
6668
6669
6670
6671
6672
6673
6674
6675
6676
6677
6678
6679
6680
6681
6682
6683
6684
6685
6686
6687
6688
6689
6690
6691
6692
6693
6694
6695
6696
6697
6698
6699
            if (needsForces[step] && forceGroup[step] > -1)
                forceName[step] = forceGroupName[forceGroup[step]];
            if (needsEnergy[step] && forceGroup[step] > -1) {
                energyName[step] = energyGroupName[forceGroup[step]];
                stepEnergyVariableIndex[step] = expressionSet.getVariableIndex(energyName[step]);
            }
            if (forceGroup[step] > -1)
                forceGroupFlags[step] = 1<<forceGroup[step];
            if (forceGroupFlags[step] == -2 && step > 0)
                forceGroupFlags[step] = forceGroupFlags[step-1];
            if (forceGroupFlags[step] != -2 && savedForces.find(forceGroupFlags[step]) == savedForces.end())
                savedForces[forceGroupFlags[step]] = new OpenCLArray(cl, cl.getForce().getSize(), cl.getForce().getElementSize(), "savedForces");
        }
        
        // Allocate space for storing global values, both on the host and the device.
        
        globalValuesFloat.resize(expressionSet.getNumVariables());
        globalValuesDouble.resize(expressionSet.getNumVariables());
        int elementSize = (cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
        globalValues = new OpenCLArray(cl, expressionSet.getNumVariables(), elementSize, "globalValues");
        for (int i = 0; i < integrator.getNumGlobalVariables(); i++) {
            globalValuesDouble[globalVariableIndex[i]] = initialGlobalVariables[i];
            expressionSet.setVariable(globalVariableIndex[i], initialGlobalVariables[i]);
        }
        for (int i = 0; i < (int) parameterVariableIndex.size(); i++) {
            double value = context.getParameter(parameterNames[i]);
            globalValuesDouble[parameterVariableIndex[i]] = value;
            expressionSet.setVariable(parameterVariableIndex[i], value);
        }
        
        // Record information about the targets of steps that will be stored in global variables.
        
        for (int step = 0; step < numSteps; step++) {
            if (stepType[step] == CustomIntegrator::ComputeGlobal || stepType[step] == CustomIntegrator::ComputeSum) {
                if (variable[step] == "dt")
                    stepTarget[step].type = DT;
                for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
                    if (variable[step] == integrator.getGlobalVariableName(i))
                        stepTarget[step].type = VARIABLE;
                for (int i = 0; i < (int) parameterNames.size(); i++)
                    if (variable[step] == parameterNames[i]) {
                        stepTarget[step].type = PARAMETER;
                        modifiesParameters = true;
6700
                    }
6701
6702
6703
6704
6705
6706
6707
6708
6709
6710
6711
6712
6713
6714
                stepTarget[step].variableIndex = expressionSet.getVariableIndex(variable[step]);
            }
        }

        // Identify which per-DOF steps are going to require global variables or context parameters.

        for (int step = 0; step < numSteps; step++) {
            if (stepType[step] == CustomIntegrator::ComputePerDof || stepType[step] == CustomIntegrator::ComputeSum) {
                for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
                    if (usesVariable(expression[step][0], integrator.getGlobalVariableName(i)))
                        needsGlobals[step] = true;
                for (int i = 0; i < (int) parameterNames.size(); i++)
                    if (usesVariable(expression[step][0], parameterNames[i]))
                        needsGlobals[step] = true;
6715
            }
6716
6717
6718
6719
        }
        
        // Determine how each step will represent the position (as just a value, or a value plus a delta).
        
peastman's avatar
peastman committed
6720
        hasAnyConstraints = (context.getSystem().getNumConstraints() > 0);
6721
6722
        vector<bool> storePosAsDelta(numSteps, false);
        vector<bool> loadPosAsDelta(numSteps, false);
peastman's avatar
peastman committed
6723
6724
6725
6726
6727
6728
6729
6730
6731
6732
6733
6734
6735
6736
6737
6738
        if (hasAnyConstraints) {
            bool beforeConstrain = false;
            for (int step = numSteps-1; step >= 0; step--) {
                if (stepType[step] == CustomIntegrator::ConstrainPositions)
                    beforeConstrain = true;
                else if (stepType[step] == CustomIntegrator::ComputePerDof && variable[step] == "x" && beforeConstrain)
                    storePosAsDelta[step] = true;
            }
            bool storedAsDelta = false;
            for (int step = 0; step < numSteps; step++) {
                loadPosAsDelta[step] = storedAsDelta;
                if (storePosAsDelta[step] == true)
                    storedAsDelta = true;
                if (stepType[step] == CustomIntegrator::ConstrainPositions)
                    storedAsDelta = false;
            }
6739
6740
        }
        
6741
6742
6743
        // Identify steps that can be merged into a single kernel.
        
        for (int step = 1; step < numSteps; step++) {
peastman's avatar
peastman committed
6744
            if ((needsForces[step] || needsEnergy[step]) && (invalidatesForces[step-1] || forceGroupFlags[step] != forceGroupFlags[step-1]))
6745
                continue;
6746
            if (stepType[step-1] == CustomIntegrator::ComputePerDof && stepType[step] == CustomIntegrator::ComputePerDof)
6747
6748
                merged[step] = true;
        }
6749
6750
6751
6752
6753
6754
        for (int step = numSteps-1; step > 0; step--)
            if (merged[step]) {
                needsForces[step-1] = (needsForces[step] || needsForces[step-1]);
                needsEnergy[step-1] = (needsEnergy[step] || needsEnergy[step-1]);
                needsGlobals[step-1] = (needsGlobals[step] || needsGlobals[step-1]);
            }
6755
        
6756
6757
6758
        // Loop over all steps and create the kernels for them.
        
        for (int step = 0; step < numSteps; step++) {
6759
            if ((stepType[step] == CustomIntegrator::ComputePerDof || stepType[step] == CustomIntegrator::ComputeSum) && !merged[step]) {
6760
6761
6762
6763
6764
                // Compute a per-DOF value.
                
                stringstream compute;
                for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
                    const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
6765
6766
6767
                    compute << buffer.getType()<<" perDofx"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index];\n";
                    compute << buffer.getType()<<" perDofy"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index+1];\n";
                    compute << buffer.getType()<<" perDofz"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index+2];\n";
6768
                }
6769
                int numGaussian = 0, numUniform = 0;
6770
                for (int j = step; j < numSteps && (j == step || merged[j]); j++) {
6771
6772
                    numGaussian += numAtoms*usesVariable(expression[j][0], "gaussian");
                    numUniform += numAtoms*usesVariable(expression[j][0], "uniform");
6773
                    compute << "{\n";
6774
                    if (numGaussian > 0)
6775
                        compute << "float4 gaussian = gaussianValues[gaussianIndex+index];\n";
6776
                    if (numUniform > 0)
6777
                        compute << "float4 uniform = uniformValues[uniformIndex+index];\n";
6778
                    for (int i = 0; i < 3; i++)
6779
                        compute << createPerDofComputation(stepType[j] == CustomIntegrator::ComputePerDof ? variable[j] : "", expression[j][0], i, integrator, forceName[j], energyName[j]);
6780
6781
6782
                    if (variable[j] == "x") {
                        if (storePosAsDelta[j]) {
                            if (cl.getSupportsDoublePrecision())
6783
                                compute << "posDelta[index] = convert_mixed4(convert_double4(position)-convert_double4(loadPos(posq, posqCorrection, index)));\n";
6784
6785
6786
                            else
                                compute << "posDelta[index] = position-posq[index];\n";
                        }
6787
                        else
6788
                            compute << "storePos(posq, posqCorrection, index, position);\n";
6789
                    }
6790
                    else if (variable[j] == "v")
6791
                        compute << "velm[index] = convert_mixed4(velocity);\n";
6792
6793
6794
                    else {
                        for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
                            const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
6795
6796
6797
                            compute << "perDofValues"<<cl.intToString(i+1)<<"[3*index] = perDofx"<<cl.intToString(i+1)<<";\n";
                            compute << "perDofValues"<<cl.intToString(i+1)<<"[3*index+1] = perDofy"<<cl.intToString(i+1)<<";\n";
                            compute << "perDofValues"<<cl.intToString(i+1)<<"[3*index+2] = perDofz"<<cl.intToString(i+1)<<";\n";
6798
                        }
6799
                    }
6800
                    if (numGaussian > 0)
6801
                        compute << "gaussianIndex += NUM_ATOMS;\n";
6802
                    if (numUniform > 0)
6803
                        compute << "uniformIndex += NUM_ATOMS;\n";
6804
                    compute << "}\n";
6805
6806
6807
6808
6809
6810
                }
                map<string, string> replacements;
                replacements["COMPUTE_STEP"] = compute.str();
                stringstream args;
                for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
                    const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
6811
                    string valueName = "perDofValues"+cl.intToString(i+1);
6812
6813
6814
                    args << ", __global " << buffer.getType() << "* restrict " << valueName;
                }
                replacements["PARAMETER_ARGUMENTS"] = args.str();
6815
6816
6817
6818
                if (loadPosAsDelta[step])
                    defines["LOAD_POS_AS_DELTA"] = "1";
                else if (defines.find("LOAD_POS_AS_DELTA") != defines.end())
                    defines.erase("LOAD_POS_AS_DELTA");
6819
6820
6821
                cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customIntegratorPerDof, replacements), defines);
                cl::Kernel kernel = cl::Kernel(program, "computePerDof");
                kernels[step].push_back(kernel);
6822
6823
                requiredGaussian[step] = numGaussian;
                requiredUniform[step] = numUniform;
6824
6825
                int index = 0;
                kernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
6826
                setPosqCorrectionArg(cl, kernel, index++);
6827
6828
6829
6830
6831
                kernel.setArg<cl::Buffer>(index++, integration.getPosDelta().getDeviceBuffer());
                kernel.setArg<cl::Buffer>(index++, cl.getVelm().getDeviceBuffer());
                kernel.setArg<cl::Buffer>(index++, cl.getForce().getDeviceBuffer());
                kernel.setArg<cl::Buffer>(index++, integration.getStepSize().getDeviceBuffer());
                kernel.setArg<cl::Buffer>(index++, globalValues->getDeviceBuffer());
6832
                kernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
Peter Eastman's avatar
Peter Eastman committed
6833
                index += 4;
6834
6835
                for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
                    kernel.setArg<cl::Memory>(index++, perDofValues->getBuffers()[i].getMemory());
6836
                if (stepType[step] == CustomIntegrator::ComputeSum) {
6837
6838
                    // Create a second kernel for this step that sums the values.

6839
                    program = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
6840
                    kernel = cl::Kernel(program, useDouble ? "computeDoubleSum" : "computeFloatSum");
6841
6842
6843
                    kernels[step].push_back(kernel);
                    index = 0;
                    kernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
6844
                    kernel.setArg<cl::Buffer>(index++, summedValue->getDeviceBuffer());
6845
                    kernel.setArg<cl_int>(index++, 3*numAtoms);
6846
                }
6847
            }
6848
6849
6850
6851
6852
6853
6854
6855
            else if (stepType[step] == CustomIntegrator::ConstrainPositions) {
                // Apply position constraints.

                cl::Program program = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
                cl::Kernel kernel = cl::Kernel(program, "applyPositionDeltas");
                kernels[step].push_back(kernel);
                int index = 0;
                kernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
6856
                setPosqCorrectionArg(cl, kernel, index++);
6857
6858
                kernel.setArg<cl::Buffer>(index++, integration.getPosDelta().getDeviceBuffer());
            }
6859
        }
6860
        
6861
6862
6863
6864
6865
6866
6867
6868
        // Initialize the random number generator.
        
        int maxUniformRandoms = 1;
        for (int i = 0; i < (int) requiredUniform.size(); i++)
            maxUniformRandoms = max(maxUniformRandoms, requiredUniform[i]);
        uniformRandoms = OpenCLArray::create<mm_float4>(cl, maxUniformRandoms, "uniformRandoms");
        randomSeed = OpenCLArray::create<mm_int4>(cl, cl.getNumThreadBlocks()*OpenCLContext::ThreadBlockSize, "randomSeed");
        vector<mm_int4> seed(randomSeed->getSize());
6869
        int rseed = integrator.getRandomNumberSeed();
6870
        // A random seed of 0 means use a unique one
6871
6872
6873
        if (rseed == 0)
            rseed = osrngseed();
        unsigned int r = (unsigned int) (rseed+1);
6874
6875
6876
6877
6878
6879
6880
6881
6882
        for (int i = 0; i < randomSeed->getSize(); i++) {
            seed[i].x = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
            seed[i].y = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
            seed[i].z = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
            seed[i].w = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
        }
        randomSeed->upload(seed);
        cl::Program randomProgram = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
        randomKernel = cl::Kernel(randomProgram, "generateRandomNumbers");
6883
6884
6885
        randomKernel.setArg<cl_int>(0, maxUniformRandoms);
        randomKernel.setArg<cl::Buffer>(1, uniformRandoms->getDeviceBuffer());
        randomKernel.setArg<cl::Buffer>(2, randomSeed->getDeviceBuffer());
6886
        
6887
6888
6889
6890
6891
6892
6893
6894
6895
6896
6897
6898
6899
6900
6901
6902
6903
6904
6905
6906
6907
6908
6909
        // Create the kernel for computing kinetic energy.

        stringstream computeKE;
        for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
            computeKE << buffer.getType()<<" perDofx"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index];\n";
            computeKE << buffer.getType()<<" perDofy"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index+1];\n";
            computeKE << buffer.getType()<<" perDofz"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index+2];\n";
        }
        Lepton::ParsedExpression keExpression = Lepton::Parser::parse(integrator.getKineticEnergyExpression()).optimize();
        for (int i = 0; i < 3; i++)
            computeKE << createPerDofComputation("", keExpression, i, integrator, "f", "");
        map<string, string> replacements;
        replacements["COMPUTE_STEP"] = computeKE.str();
        stringstream args;
        for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
            string valueName = "perDofValues"+cl.intToString(i+1);
            args << ", __global " << buffer.getType() << "* restrict " << valueName;
        }
        replacements["PARAMETER_ARGUMENTS"] = args.str();
        if (defines.find("LOAD_POS_AS_DELTA") != defines.end())
            defines.erase("LOAD_POS_AS_DELTA");
Peter Eastman's avatar
Peter Eastman committed
6910
        cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customIntegratorPerDof, replacements), defines);
6911
        kineticEnergyKernel = cl::Kernel(program, "computePerDof");
Peter Eastman's avatar
Peter Eastman committed
6912
        int index = 0;
6913
6914
6915
6916
6917
6918
6919
6920
        kineticEnergyKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
        setPosqCorrectionArg(cl, kineticEnergyKernel, index++);
        kineticEnergyKernel.setArg<cl::Buffer>(index++, integration.getPosDelta().getDeviceBuffer());
        kineticEnergyKernel.setArg<cl::Buffer>(index++, cl.getVelm().getDeviceBuffer());
        kineticEnergyKernel.setArg<cl::Buffer>(index++, cl.getForce().getDeviceBuffer());
        kineticEnergyKernel.setArg<cl::Buffer>(index++, integration.getStepSize().getDeviceBuffer());
        kineticEnergyKernel.setArg<cl::Buffer>(index++, globalValues->getDeviceBuffer());
        kineticEnergyKernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
6921
        index += 2;
6922
        kineticEnergyKernel.setArg<cl::Buffer>(index++, uniformRandoms->getDeviceBuffer());
Peter Eastman's avatar
Peter Eastman committed
6923
6924
6925
6926
        if (cl.getUseDoublePrecision())
            kineticEnergyKernel.setArg<cl_double>(index++, 0.0);
        else
            kineticEnergyKernel.setArg<cl_float>(index++, 0.0f);
6927
6928
6929
6930
6931
6932
6933
6934
6935
6936
        for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
            kineticEnergyKernel.setArg<cl::Memory>(index++, perDofValues->getBuffers()[i].getMemory());
        keNeedsForce = usesVariable(keExpression, "f");

        // Create a second kernel to sum the values.

        program = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
        sumKineticEnergyKernel = cl::Kernel(program, useDouble ? "computeDoubleSum" : "computeFloatSum");
        index = 0;
        sumKineticEnergyKernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
6937
        sumKineticEnergyKernel.setArg<cl::Buffer>(index++, summedValue->getDeviceBuffer());
6938
        sumKineticEnergyKernel.setArg<cl_int>(index++, 3*numAtoms);
6939
    }
6940
    
6941
    // Make sure all values (variables, parameters, etc.) are up to date.
6942
    
6943
    if (!deviceValuesAreCurrent) {
6944
6945
6946
6947
        if (useDouble)
            perDofValues->setParameterValues(localPerDofValuesDouble);
        else
            perDofValues->setParameterValues(localPerDofValuesFloat);
6948
6949
6950
6951
        deviceValuesAreCurrent = true;
    }
    localValuesAreCurrent = false;
    double stepSize = integrator.getStepSize();
6952
    recordGlobalValue(stepSize, GlobalTarget(DT, dtVariableIndex));
6953
6954
6955
6956
6957
    for (int i = 0; i < (int) parameterNames.size(); i++) {
        double value = context.getParameter(parameterNames[i]);
        if (value != globalValuesDouble[parameterVariableIndex[i]]) {
            globalValuesDouble[parameterVariableIndex[i]] = value;
            deviceGlobalsAreCurrent = false;
6958
6959
        }
    }
6960
}
6961

6962
6963
6964
6965
6966
6967
void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid) {
    prepareForComputation(context, integrator, forcesAreValid);
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
    int numAtoms = cl.getNumAtoms();
    int numSteps = integrator.getNumComputations();
    
6968
6969
    // Loop over computation steps in the integrator and execute them.

6970
6971
    for (int step = 0; step < numSteps; ) {
        int nextStep = step+1;
6972
        int lastForceGroups = context.getLastForceGroups();
6973
        if ((needsForces[step] || needsEnergy[step]) && (!forcesAreValid || lastForceGroups != forceGroupFlags[step])) {
6974
6975
6976
6977
6978
6979
6980
6981
6982
6983
            if (forcesAreValid && savedForces.find(lastForceGroups) != savedForces.end()) {
                // The forces are still valid.  We just need a different force group right now.  Save the old
                // forces in case we need them again.
                
                cl.getForce().copyTo(*savedForces[lastForceGroups]);
                validSavedForces.insert(lastForceGroups);
            }
            else
                validSavedForces.clear();
            
6984
6985
6986
            // Recompute forces and/or energy.  Figure out what is actually needed
            // between now and the next time they get invalidated again.
            
6987
6988
6989
            bool computeForce = (needsForces[step] || computeBothForceAndEnergy[step]);
            bool computeEnergy = (needsEnergy[step] || computeBothForceAndEnergy[step]);
            if (!computeEnergy && validSavedForces.find(forceGroupFlags[step]) != validSavedForces.end()) {
6990
6991
                // We can just restore the forces we saved earlier.
                
6992
                savedForces[forceGroupFlags[step]]->copyTo(cl.getForce());
6993
6994
6995
            }
            else {
                recordChangedParameters(context);
6996
                energy = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
6997
            forcesAreValid = true;
6998
            }
6999
        }
7000
7001
7002
7003
7004
7005
7006
7007
7008
7009
        if (needsGlobals[step] && !deviceGlobalsAreCurrent) {
            // Upload the global values to the device.
            
            if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision())
                globalValues->upload(globalValuesDouble);
            else {
                for (int j = 0; j < (int) globalValuesDouble.size(); j++)
                    globalValuesFloat[j] = (float) globalValuesDouble[j];
                globalValues->upload(globalValuesFloat);
            }
7010
        }
7011
7012
7013
7014
        if (stepType[step] == CustomIntegrator::ComputePerDof && !merged[step]) {
            kernels[step][0].setArg<cl_uint>(9, integration.prepareRandomNumbers(requiredGaussian[step]));
            kernels[step][0].setArg<cl::Buffer>(8, integration.getRandom().getDeviceBuffer());
            kernels[step][0].setArg<cl::Buffer>(10, uniformRandoms->getDeviceBuffer());
Peter Eastman's avatar
Peter Eastman committed
7015
            if (cl.getUseDoublePrecision())
7016
                kernels[step][0].setArg<cl_double>(11, energy);
Peter Eastman's avatar
Peter Eastman committed
7017
            else
7018
7019
7020
                kernels[step][0].setArg<cl_float>(11, (cl_float) energy);
            if (requiredUniform[step] > 0)
                cl.executeKernel(randomKernel, numAtoms);
peastman's avatar
peastman committed
7021
            cl.executeKernel(kernels[step][0], numAtoms, 128);
7022
7023
7024
7025
7026
7027
7028
7029
7030
7031
7032
        }
        else if (stepType[step] == CustomIntegrator::ComputeGlobal) {
            expressionSet.setVariable(uniformVariableIndex, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
            expressionSet.setVariable(gaussianVariableIndex, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
            expressionSet.setVariable(stepEnergyVariableIndex[step], energy);
            recordGlobalValue(globalExpressions[step][0].evaluate(), stepTarget[step]);
        }
        else if (stepType[step] == CustomIntegrator::ComputeSum) {
            kernels[step][0].setArg<cl_uint>(9, integration.prepareRandomNumbers(requiredGaussian[step]));
            kernels[step][0].setArg<cl::Buffer>(8, integration.getRandom().getDeviceBuffer());
            kernels[step][0].setArg<cl::Buffer>(10, uniformRandoms->getDeviceBuffer());
Peter Eastman's avatar
Peter Eastman committed
7033
            if (cl.getUseDoublePrecision())
7034
                kernels[step][0].setArg<cl_double>(11, energy);
Peter Eastman's avatar
Peter Eastman committed
7035
            else
7036
7037
                kernels[step][0].setArg<cl_float>(11, (cl_float) energy);
            if (requiredUniform[step] > 0)
7038
                cl.executeKernel(randomKernel, numAtoms);
7039
            cl.clearBuffer(*sumBuffer);
peastman's avatar
peastman committed
7040
            cl.executeKernel(kernels[step][0], numAtoms, 128);
7041
7042
7043
7044
            cl.executeKernel(kernels[step][1], OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
            if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
                double value;
                summedValue->download(&value);
7045
                recordGlobalValue(value, stepTarget[step]);
7046
7047
7048
7049
            }
            else {
                float value;
                summedValue->download(&value);
7050
                recordGlobalValue(value, stepTarget[step]);
7051
            }
7052
        }
7053
        else if (stepType[step] == CustomIntegrator::UpdateContextState) {
7054
            recordChangedParameters(context);
7055
            context.updateContextState();
7056
        }
7057
        else if (stepType[step] == CustomIntegrator::ConstrainPositions) {
peastman's avatar
peastman committed
7058
7059
7060
7061
            if (hasAnyConstraints) {
                cl.getIntegrationUtilities().applyConstraints(integrator.getConstraintTolerance());
                cl.executeKernel(kernels[step][0], numAtoms);
            }
7062
            cl.getIntegrationUtilities().computeVirtualSites();
7063
        }
7064
        else if (stepType[step] == CustomIntegrator::ConstrainVelocities) {
7065
7066
            cl.getIntegrationUtilities().applyVelocityConstraints(integrator.getConstraintTolerance());
        }
7067
        else if (stepType[step] == CustomIntegrator::IfBlockStart) {
7068
7069
7070
            if (!evaluateCondition(step))
                nextStep = blockEnd[step]+1;
        }
7071
        else if (stepType[step] == CustomIntegrator::WhileBlockStart) {
7072
7073
7074
            if (!evaluateCondition(step))
                nextStep = blockEnd[step]+1;
        }
7075
        else if (stepType[step] == CustomIntegrator::BlockEnd) {
7076
7077
7078
7079
            if (blockEnd[step] != -1)
                nextStep = blockEnd[step]; // Return to the start of a while block.
        }
        if (invalidatesForces[step])
7080
            forcesAreValid = false;
7081
        step = nextStep;
7082
    }
7083
    recordChangedParameters(context);
7084
7085
7086

    // Update the time and step count.

7087
    cl.setTime(cl.getTime()+integrator.getStepSize());
7088
    cl.setStepCount(cl.getStepCount()+1);
7089
    cl.reorderAtoms();
7090
7091
7092
7093
    if (cl.getAtomsWereReordered()) {
        forcesAreValid = false;
        validSavedForces.clear();
    }
7094
7095
7096
7097
7098
7099
    
    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
7100
7101
}

7102
7103
7104
7105
7106
7107
7108
7109
7110
7111
7112
7113
7114
7115
7116
7117
7118
7119
7120
7121
7122
7123
7124
bool OpenCLIntegrateCustomStepKernel::evaluateCondition(int step) {
    expressionSet.setVariable(uniformVariableIndex, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
    expressionSet.setVariable(gaussianVariableIndex, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
    expressionSet.setVariable(stepEnergyVariableIndex[step], energy);
    double lhs = globalExpressions[step][0].evaluate();
    double rhs = globalExpressions[step][1].evaluate();
    switch (comparisons[step]) {
        case CustomIntegratorUtilities::EQUAL:
            return (lhs == rhs);
        case CustomIntegratorUtilities::LESS_THAN:
            return (lhs < rhs);
        case CustomIntegratorUtilities::GREATER_THAN:
            return (lhs > rhs);
        case CustomIntegratorUtilities::NOT_EQUAL:
            return (lhs != rhs);
        case CustomIntegratorUtilities::LESS_THAN_OR_EQUAL:
            return (lhs <= rhs);
        case CustomIntegratorUtilities::GREATER_THAN_OR_EQUAL:
            return (lhs >= rhs);
    }
    throw OpenMMException("Invalid comparison operator");
}

7125
7126
7127
7128
7129
7130
7131
7132
7133
double OpenCLIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid) {
    prepareForComputation(context, integrator, forcesAreValid);
    if (keNeedsForce && !forcesAreValid) {
        // Compute the force.  We want to then mark that forces are valid, which means also computing
        // potential energy if any steps will expect it to be valid too.
        
        bool willNeedEnergy = false;
        for (int i = 0; i < integrator.getNumComputations(); i++)
            willNeedEnergy |= needsEnergy[i];
Peter Eastman's avatar
Peter Eastman committed
7134
        energy = context.calcForcesAndEnergy(true, willNeedEnergy, -1);
7135
7136
        forcesAreValid = true;
    }
7137
    cl.clearBuffer(*sumBuffer);
7138
7139
    kineticEnergyKernel.setArg<cl::Buffer>(8, cl.getIntegrationUtilities().getRandom().getDeviceBuffer());
    kineticEnergyKernel.setArg<cl_uint>(9, 0);
7140
7141
7142
7143
    cl.executeKernel(kineticEnergyKernel, cl.getNumAtoms());
    cl.executeKernel(sumKineticEnergyKernel, OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        double ke;
7144
        summedValue->download(&ke);
7145
7146
7147
7148
        return ke;
    }
    else {
        float ke;
7149
        summedValue->download(&ke);
7150
7151
7152
7153
        return ke;
    }
}

7154
7155
7156
void OpenCLIntegrateCustomStepKernel::recordGlobalValue(double value, GlobalTarget target) {
    switch (target.type) {
        case DT:
7157
7158
            if (value != globalValuesDouble[dtVariableIndex])
                deviceGlobalsAreCurrent = false;
7159
            expressionSet.setVariable(dtVariableIndex, value);
7160
            globalValuesDouble[dtVariableIndex] = value;
7161
            cl.getIntegrationUtilities().setNextStepSize(value);
7162
7163
7164
7165
7166
7167
7168
7169
7170
7171
            break;
        case VARIABLE:
        case PARAMETER:
            expressionSet.setVariable(target.variableIndex, value);
            globalValuesDouble[target.variableIndex] = value;
            deviceGlobalsAreCurrent = false;
            break;
    }
}

7172
7173
7174
void OpenCLIntegrateCustomStepKernel::recordChangedParameters(ContextImpl& context) {
    if (!modifiesParameters)
        return;
7175
7176
7177
7178
    for (int i = 0; i < (int) parameterNames.size(); i++) {
        double value = context.getParameter(parameterNames[i]);
        if (value != globalValuesDouble[parameterVariableIndex[i]])
            context.setParameter(parameterNames[i], globalValuesDouble[parameterVariableIndex[i]]);
7179
7180
7181
    }
}

7182
void OpenCLIntegrateCustomStepKernel::getGlobalVariables(ContextImpl& context, vector<double>& values) const {
7183
7184
7185
7186
    if (globalValues == NULL) {
        // The data structures haven't been created yet, so just return the list of values that was given earlier.
        
        values = initialGlobalVariables;
7187
    }
7188
7189
7190
    values.resize(numGlobalVariables);
    for (int i = 0; i < numGlobalVariables; i++)
        values[i] = globalValuesDouble[globalVariableIndex[i]];
7191
7192
7193
}

void OpenCLIntegrateCustomStepKernel::setGlobalVariables(ContextImpl& context, const vector<double>& values) {
7194
7195
    if (numGlobalVariables == 0)
        return;
7196
7197
7198
7199
7200
7201
7202
7203
7204
    if (globalValues == NULL) {
        // The data structures haven't been created yet, so just store the list of values.
        
        initialGlobalVariables = values;
        return;
    }
    for (int i = 0; i < numGlobalVariables; i++) {
        globalValuesDouble[globalVariableIndex[i]] = values[i];
        expressionSet.setVariable(globalVariableIndex[i], values[i]);
7205
    }
7206
    deviceGlobalsAreCurrent = false;
7207
7208
7209
7210
}

void OpenCLIntegrateCustomStepKernel::getPerDofVariable(ContextImpl& context, int variable, vector<Vec3>& values) const {
    values.resize(perDofValues->getNumObjects()/3);
7211
7212
7213
7214
7215
7216
7217
7218
7219
7220
7221
7222
7223
7224
7225
7226
7227
7228
7229
    const vector<int>& order = cl.getAtomIndex();
    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        if (!localValuesAreCurrent) {
            perDofValues->getParameterValues(localPerDofValuesDouble);
            localValuesAreCurrent = true;
        }
        for (int i = 0; i < (int) values.size(); i++)
            for (int j = 0; j < 3; j++)
                values[order[i]][j] = localPerDofValuesDouble[3*i+j][variable];
    }
    else {
        if (!localValuesAreCurrent) {
            perDofValues->getParameterValues(localPerDofValuesFloat);
            localValuesAreCurrent = true;
        }
        for (int i = 0; i < (int) values.size(); i++)
            for (int j = 0; j < 3; j++)
                values[order[i]][j] = localPerDofValuesFloat[3*i+j][variable];
    }
7230
7231
7232
}

void OpenCLIntegrateCustomStepKernel::setPerDofVariable(ContextImpl& context, int variable, const vector<Vec3>& values) {
7233
7234
7235
7236
7237
7238
7239
7240
7241
7242
7243
7244
7245
7246
7247
7248
7249
7250
    const vector<int>& order = cl.getAtomIndex();
    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        if (!localValuesAreCurrent) {
            perDofValues->getParameterValues(localPerDofValuesDouble);
            localValuesAreCurrent = true;
        }
        for (int i = 0; i < (int) values.size(); i++)
            for (int j = 0; j < 3; j++)
                localPerDofValuesDouble[3*i+j][variable] = values[order[i]][j];
    }
    else {
        if (!localValuesAreCurrent) {
            perDofValues->getParameterValues(localPerDofValuesFloat);
            localValuesAreCurrent = true;
        }
        for (int i = 0; i < (int) values.size(); i++)
            for (int j = 0; j < 3; j++)
                localPerDofValuesFloat[3*i+j][variable] = (float) values[order[i]][j];
7251
7252
7253
7254
    }
    deviceValuesAreCurrent = false;
}

7255
OpenCLApplyAndersenThermostatKernel::~OpenCLApplyAndersenThermostatKernel() {
7256
7257
    if (atomGroups != NULL)
        delete atomGroups;
7258
7259
7260
7261
7262
}

void OpenCLApplyAndersenThermostatKernel::initialize(const System& system, const AndersenThermostat& thermostat) {
    randomSeed = thermostat.getRandomNumberSeed();
    map<string, string> defines;
7263
    defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
7264
    cl::Program program = cl.createProgram(OpenCLKernelSources::andersenThermostat, defines);
7265
    kernel = cl::Kernel(program, "applyAndersenThermostat");
Peter Eastman's avatar
Peter Eastman committed
7266
    cl.getIntegrationUtilities().initRandomNumberGenerator(randomSeed);
7267
7268
7269
7270

    // Create the arrays with the group definitions.

    vector<vector<int> > groups = AndersenThermostatImpl::calcParticleGroups(system);
7271
    atomGroups = OpenCLArray::create<int>(cl, cl.getNumAtoms(), "atomGroups");
7272
7273
7274
7275
7276
7277
    vector<int> atoms(atomGroups->getSize());
    for (int i = 0; i < (int) groups.size(); i++) {
        for (int j = 0; j < (int) groups[i].size(); j++)
            atoms[groups[i][j]] = i;
    }
    atomGroups->upload(atoms);
7278
7279
7280
7281
7282
7283
7284
7285
}

void OpenCLApplyAndersenThermostatKernel::execute(ContextImpl& context) {
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
        kernel.setArg<cl::Buffer>(2, cl.getVelm().getDeviceBuffer());
        kernel.setArg<cl::Buffer>(3, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
        kernel.setArg<cl::Buffer>(4, cl.getIntegrationUtilities().getRandom().getDeviceBuffer());
7286
        kernel.setArg<cl::Buffer>(6, atomGroups->getDeviceBuffer());
7287
7288
7289
7290
7291
7292
7293
    }
    kernel.setArg<cl_float>(0, (cl_float) context.getParameter(AndersenThermostat::CollisionFrequency()));
    kernel.setArg<cl_float>(1, (cl_float) (BOLTZ*context.getParameter(AndersenThermostat::Temperature())));
    kernel.setArg<cl_uint>(5, cl.getIntegrationUtilities().prepareRandomNumbers(cl.getPaddedNumAtoms()));
    cl.executeKernel(kernel, cl.getNumAtoms());
}

7294
7295
7296
7297
7298
7299
7300
7301
7302
OpenCLApplyMonteCarloBarostatKernel::~OpenCLApplyMonteCarloBarostatKernel() {
    if (savedPositions != NULL)
        delete savedPositions;
    if (moleculeAtoms != NULL)
        delete moleculeAtoms;
    if (moleculeStartIndex != NULL)
        delete moleculeStartIndex;
}

7303
void OpenCLApplyMonteCarloBarostatKernel::initialize(const System& system, const Force& thermostat) {
7304
    savedPositions = new OpenCLArray(cl, cl.getPaddedNumAtoms(), cl.getUseDoublePrecision() ? sizeof(mm_double4) : sizeof(mm_float4), "savedPositions");
7305
    cl::Program program = cl.createProgram(OpenCLKernelSources::monteCarloBarostat);
7306
    kernel = cl::Kernel(program, "scalePositions");
7307
7308
}

7309
void OpenCLApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ) {
7310
7311
7312
7313
7314
7315
7316
7317
7318
7319
7320
7321
7322
7323
7324
7325
7326
7327
7328
7329
7330
7331
7332
7333
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;

        // Create the arrays with the molecule definitions.

        vector<vector<int> > molecules = context.getMolecules();
        numMolecules = molecules.size();
        moleculeAtoms = OpenCLArray::create<int>(cl, cl.getNumAtoms(), "moleculeAtoms");
        moleculeStartIndex = OpenCLArray::create<int>(cl, numMolecules+1, "moleculeStartIndex");
        vector<int> atoms(moleculeAtoms->getSize());
        vector<int> startIndex(moleculeStartIndex->getSize());
        int index = 0;
        for (int i = 0; i < numMolecules; i++) {
            startIndex[i] = index;
            for (int j = 0; j < (int) molecules[i].size(); j++)
                atoms[index++] = molecules[i][j];
        }
        startIndex[numMolecules] = index;
        moleculeAtoms->upload(atoms);
        moleculeStartIndex->upload(startIndex);

        // Initialize the kernel arguments.
        
        kernel.setArg<cl_int>(3, numMolecules);
7334
7335
7336
        kernel.setArg<cl::Buffer>(9, cl.getPosq().getDeviceBuffer());
        kernel.setArg<cl::Buffer>(10, moleculeAtoms->getDeviceBuffer());
        kernel.setArg<cl::Buffer>(11, moleculeStartIndex->getDeviceBuffer());
7337
    }
7338
7339
    int bytesToCopy = cl.getPosq().getSize()*(cl.getUseDoublePrecision() ? sizeof(mm_double4) : sizeof(mm_float4));
    cl.getQueue().enqueueCopyBuffer(cl.getPosq().getDeviceBuffer(), savedPositions->getDeviceBuffer(), 0, 0, bytesToCopy);
7340
7341
7342
    kernel.setArg<cl_float>(0, (cl_float) scaleX);
    kernel.setArg<cl_float>(1, (cl_float) scaleY);
    kernel.setArg<cl_float>(2, (cl_float) scaleZ);
7343
    setPeriodicBoxArgs(cl, kernel, 4);
7344
    cl.executeKernel(kernel, cl.getNumAtoms());
7345
7346
    for (int i = 0; i < (int) cl.getPosCellOffsets().size(); i++)
        cl.getPosCellOffsets()[i] = mm_int4(0, 0, 0, 0);
7347
    lastAtomOrder = cl.getAtomIndex();
7348
7349
7350
}

void OpenCLApplyMonteCarloBarostatKernel::restoreCoordinates(ContextImpl& context) {
7351
7352
    int bytesToCopy = cl.getPosq().getSize()*(cl.getUseDoublePrecision() ? sizeof(mm_double4) : sizeof(mm_float4));
    cl.getQueue().enqueueCopyBuffer(savedPositions->getDeviceBuffer(), cl.getPosq().getDeviceBuffer(), 0, 0, bytesToCopy);
7353
7354
}

7355
7356
7357
7358
7359
7360
7361
7362
OpenCLRemoveCMMotionKernel::~OpenCLRemoveCMMotionKernel() {
    if (cmMomentum != NULL)
        delete cmMomentum;
}

void OpenCLRemoveCMMotionKernel::initialize(const System& system, const CMMotionRemover& force) {
    frequency = force.getFrequency();
    int numAtoms = cl.getNumAtoms();
7363
    cmMomentum = OpenCLArray::create<mm_float4>(cl, (numAtoms+OpenCLContext::ThreadBlockSize-1)/OpenCLContext::ThreadBlockSize, "cmMomentum");
7364
7365
7366
7367
    double totalMass = 0.0;
    for (int i = 0; i < numAtoms; i++)
        totalMass += system.getParticleMass(i);
    map<string, string> defines;
7368
    defines["INVERSE_TOTAL_MASS"] = cl.doubleToString(totalMass == 0 ? 0.0 : 1.0/totalMass);
7369
    cl::Program program = cl.createProgram(OpenCLKernelSources::removeCM, defines);
7370
7371
7372
7373
7374
7375
7376
7377
7378
7379
7380
7381
7382
7383
7384
7385
    kernel1 = cl::Kernel(program, "calcCenterOfMassMomentum");
    kernel1.setArg<cl_int>(0, numAtoms);
    kernel1.setArg<cl::Buffer>(1, cl.getVelm().getDeviceBuffer());
    kernel1.setArg<cl::Buffer>(2, cmMomentum->getDeviceBuffer());
    kernel1.setArg(3, OpenCLContext::ThreadBlockSize*sizeof(mm_float4), NULL);
    kernel2 = cl::Kernel(program, "removeCenterOfMassMomentum");
    kernel2.setArg<cl_int>(0, numAtoms);
    kernel2.setArg<cl::Buffer>(1, cl.getVelm().getDeviceBuffer());
    kernel2.setArg<cl::Buffer>(2, cmMomentum->getDeviceBuffer());
    kernel2.setArg(3, OpenCLContext::ThreadBlockSize*sizeof(mm_float4), NULL);
}

void OpenCLRemoveCMMotionKernel::execute(ContextImpl& context) {
    cl.executeKernel(kernel1, cl.getNumAtoms());
    cl.executeKernel(kernel2, cl.getNumAtoms());
}