ContextImpl.cpp 15.6 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) 2008-2012 Stanford University and the Authors.      *
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
 * Permission is hereby granted, free of charge, to any person obtaining a    *
 * copy of this software and associated documentation files (the "Software"), *
 * to deal in the Software without restriction, including without limitation  *
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
 * and/or sell copies of the Software, and to permit persons to whom the      *
 * Software is furnished to do so, subject to the following conditions:       *
 *                                                                            *
 * The above copyright notice and this permission notice shall be included in *
 * all copies or substantial portions of the Software.                        *
 *                                                                            *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
 * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
 * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
 * -------------------------------------------------------------------------- */

32
33
34
35
36
37
#include "openmm/Force.h"
#include "openmm/Integrator.h"
#include "openmm/OpenMMException.h"
#include "openmm/System.h"
#include "openmm/kernels.h"
#include "openmm/internal/ForceImpl.h"
38
#include "openmm/internal/ContextImpl.h"
39
#include "openmm/State.h"
40
#include "openmm/VirtualSite.h"
Peter Eastman's avatar
Peter Eastman committed
41
42
#include "openmm/Context.h"
#include <iostream>
43
#include <map>
44
#include <utility>
45
46
47
#include <vector>

using namespace OpenMM;
Peter Eastman's avatar
Peter Eastman committed
48
using namespace std;
49

50
ContextImpl::ContextImpl(Context& owner, System& system, Integrator& integrator, Platform* platform, const map<string, string>& properties) :
51
         owner(owner), system(system), integrator(integrator), hasInitializedForces(false), hasSetPositions(false), lastForceGroups(-1), platform(platform), platformData(NULL) {
52
53
    if (system.getNumParticles() == 0)
        throw OpenMMException("Cannot create a Context for a System with no particles");
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
    
    // Check for errors in virtual sites and massless particles.
    
    for (int i = 0; i < system.getNumParticles(); i++) {
        if (system.isVirtualSite(i)) {
            if (system.getParticleMass(i) != 0.0)
                throw OpenMMException("Virtual site has nonzero mass");
            const VirtualSite& site = system.getVirtualSite(i);
            for (int j = 0; j < site.getNumParticles(); j++)
                if (system.isVirtualSite(site.getParticle(j)))
                    throw OpenMMException("A virtual site cannot depend on another virtual site");
        }
    }
    for (int i = 0; i < system.getNumConstraints(); i++) {
        int particle1, particle2;
        double distance;
        system.getConstraintParameters(i, particle1, particle2, distance);
        if (system.getParticleMass(particle1) == 0.0 || system.getParticleMass(particle2) == 0.0)
            throw OpenMMException("A constraint cannot involve a massless particle");
    }
    
    // Find the list of kernels required.
    
77
78
    vector<string> kernelNames;
    kernelNames.push_back(CalcKineticEnergyKernel::Name());
79
    kernelNames.push_back(CalcForcesAndEnergyKernel::Name());
80
    kernelNames.push_back(UpdateStateDataKernel::Name());
81
    for (int i = 0; i < system.getNumForces(); ++i) {
82
        forceImpls.push_back(system.getForce(i).createImpl());
83
84
        map<string, double> forceParameters = forceImpls[forceImpls.size()-1]->getDefaultParameters();
        parameters.insert(forceParameters.begin(), forceParameters.end());
85
86
87
        vector<string> forceKernels = forceImpls[forceImpls.size()-1]->getKernelNames();
        kernelNames.insert(kernelNames.begin(), forceKernels.begin(), forceKernels.end());
    }
88
    hasInitializedForces = true;
89
90
    vector<string> integratorKernels = integrator.getKernelNames();
    kernelNames.insert(kernelNames.begin(), integratorKernels.begin(), integratorKernels.end());
91
    if (platform == 0)
92
        this->platform = platform = &Platform::findPlatform(kernelNames);
93
    else if (!platform->supportsKernels(kernelNames))
94
        throw OpenMMException("Specified a Platform for a Context which does not support all required kernels");
95
96
97
    
    // Create and initialize kernels and other objects.
    
98
    platform->contextCreated(*this, properties);
99
    initializeForcesKernel = platform->createKernel(CalcForcesAndEnergyKernel::Name(), *this);
100
    initializeForcesKernel.getAs<CalcForcesAndEnergyKernel>().initialize(system);
101
    kineticEnergyKernel = platform->createKernel(CalcKineticEnergyKernel::Name(), *this);
102
    kineticEnergyKernel.getAs<CalcKineticEnergyKernel>().initialize(system);
103
    updateStateDataKernel = platform->createKernel(UpdateStateDataKernel::Name(), *this);
104
    updateStateDataKernel.getAs<UpdateStateDataKernel>().initialize(system);
105
    applyConstraintsKernel = platform->createKernel(ApplyConstraintsKernel::Name(), *this);
106
    applyConstraintsKernel.getAs<ApplyConstraintsKernel>().initialize(system);
107
    virtualSitesKernel = platform->createKernel(VirtualSitesKernel::Name(), *this);
108
    virtualSitesKernel.getAs<VirtualSitesKernel>().initialize(system);
109
110
    Vec3 periodicBoxVectors[3];
    system.getDefaultPeriodicBoxVectors(periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
111
    updateStateDataKernel.getAs<UpdateStateDataKernel>().setPeriodicBoxVectors(*this, periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
112
    for (size_t i = 0; i < forceImpls.size(); ++i)
113
        forceImpls[i]->initialize(*this);
114
    integrator.initialize(*this);
115
    updateStateDataKernel.getAs<UpdateStateDataKernel>().setVelocities(*this, vector<Vec3>(system.getNumParticles()));
116
117
}

118
ContextImpl::~ContextImpl() {
119
120
    for (int i = 0; i < (int) forceImpls.size(); ++i)
        delete forceImpls[i];
121
122
123
124
125
126
127
128
    
    // Make sure all kernels get properly deleted before contextDestroyed() is called.
    
    initializeForcesKernel = Kernel();
    kineticEnergyKernel = Kernel();
    updateStateDataKernel = Kernel();
    applyConstraintsKernel = Kernel();
    virtualSitesKernel = Kernel();
129
    integrator.cleanup();
130
    platform->contextDestroyed(*this);
131
132
}

133
double ContextImpl::getTime() const {
134
    return updateStateDataKernel.getAs<const UpdateStateDataKernel>().getTime(*this);
135
136
}

137
void ContextImpl::setTime(double t) {
138
    updateStateDataKernel.getAs<UpdateStateDataKernel>().setTime(*this, t);
139
140
141
}

void ContextImpl::getPositions(std::vector<Vec3>& positions) {
142
    updateStateDataKernel.getAs<UpdateStateDataKernel>().getPositions(*this, positions);
143
144
145
}

void ContextImpl::setPositions(const std::vector<Vec3>& positions) {
146
    hasSetPositions = true;
147
    updateStateDataKernel.getAs<UpdateStateDataKernel>().setPositions(*this, positions);
148
    integrator.stateChanged(State::Positions);
149
150
151
}

void ContextImpl::getVelocities(std::vector<Vec3>& velocities) {
152
    updateStateDataKernel.getAs<UpdateStateDataKernel>().getVelocities(*this, velocities);
153
154
155
}

void ContextImpl::setVelocities(const std::vector<Vec3>& velocities) {
156
    updateStateDataKernel.getAs<UpdateStateDataKernel>().setVelocities(*this, velocities);
157
    integrator.stateChanged(State::Velocities);
158
159
160
}

void ContextImpl::getForces(std::vector<Vec3>& forces) {
161
    updateStateDataKernel.getAs<UpdateStateDataKernel>().getForces(*this, forces);
162
163
}

164
165
166
167
const std::map<std::string, double>& ContextImpl::getParameters() const {
    return parameters;
}

168
double ContextImpl::getParameter(std::string name) {
169
170
171
172
173
    if (parameters.find(name) == parameters.end())
        throw OpenMMException("Called getParameter() with invalid parameter name");
    return parameters[name];
}

174
void ContextImpl::setParameter(std::string name, double value) {
175
176
177
    if (parameters.find(name) == parameters.end())
        throw OpenMMException("Called setParameter() with invalid parameter name");
    parameters[name] = value;
178
    integrator.stateChanged(State::Parameters);
179
180
}

181
void ContextImpl::getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) {
182
    updateStateDataKernel.getAs<UpdateStateDataKernel>().getPeriodicBoxVectors(*this, a, b, c);
183
184
185
186
187
188
189
190
191
}

void ContextImpl::setPeriodicBoxVectors(const Vec3& a, const Vec3& b, const Vec3& c) {
    if (a[1] != 0.0 || a[2] != 0.0)
        throw OpenMMException("First periodic box vector must be parallel to x.");
    if (b[0] != 0.0 || b[2] != 0.0)
        throw OpenMMException("Second periodic box vector must be parallel to y.");
    if (c[0] != 0.0 || c[1] != 0.0)
        throw OpenMMException("Third periodic box vector must be parallel to z.");
192
    updateStateDataKernel.getAs<UpdateStateDataKernel>().setPeriodicBoxVectors(*this, a, b, c);
193
194
}

195
void ContextImpl::applyConstraints(double tol) {
196
    applyConstraintsKernel.getAs<ApplyConstraintsKernel>().apply(*this, tol);
197
198
}

199
void ContextImpl::computeVirtualSites() {
200
    virtualSitesKernel.getAs<VirtualSitesKernel>().computePositions(*this);
201
202
}

203
double ContextImpl::calcForcesAndEnergy(bool includeForces, bool includeEnergy, int groups) {
204
205
    if (!hasSetPositions)
        throw OpenMMException("Particle positions have not been set");
206
    lastForceGroups = groups;
207
    CalcForcesAndEnergyKernel& kernel = initializeForcesKernel.getAs<CalcForcesAndEnergyKernel>();
208
    double energy = 0.0;
209
    kernel.beginComputation(*this, includeForces, includeEnergy, groups);
210
    for (int i = 0; i < (int) forceImpls.size(); ++i)
211
212
        energy += forceImpls[i]->calcForcesAndEnergy(*this, includeForces, includeEnergy, groups);
    energy += kernel.finishComputation(*this, includeForces, includeEnergy, groups);
213
    return energy;
214
215
}

216
217
218
219
int ContextImpl::getLastForceGroups() const {
    return lastForceGroups;
}

220
double ContextImpl::calcKineticEnergy() {
221
    return kineticEnergyKernel.getAs<CalcKineticEnergyKernel>().execute(*this);
222
223
}

224
void ContextImpl::updateContextState() {
225
226
227
228
    for (int i = 0; i < (int) forceImpls.size(); ++i)
        forceImpls[i]->updateContextState(*this);
}

229
230
231
232
const vector<ForceImpl*>& ContextImpl::getForceImpls() const {
    return forceImpls;
}

233
234
235
236
vector<ForceImpl*>& ContextImpl::getForceImpls() {
    return forceImpls;
}

237
void* ContextImpl::getPlatformData() {
238
239
240
    return platformData;
}

241
242
243
244
const void* ContextImpl::getPlatformData() const {
    return platformData;
}

245
void ContextImpl::setPlatformData(void* data) {
246
247
    platformData = data;
}
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267

const vector<vector<int> >& ContextImpl::getMolecules() const {
    if (!hasInitializedForces)
        throw OpenMMException("ContextImpl: getMolecules() cannot be called until all ForceImpls have been initialized");
    if (molecules.size() > 0 || system.getNumParticles() == 0)
        return molecules;

    // First make a list of bonds and constraints.

    vector<pair<int, int> > bonds;
    for (int i = 0; i < system.getNumConstraints(); i++) {
        int particle1, particle2;
        double distance;
        system.getConstraintParameters(i, particle1, particle2, distance);
        bonds.push_back(std::make_pair(particle1, particle2));
    }
    for (int i = 0; i < (int) forceImpls.size(); i++) {
        vector<pair<int, int> > forceBonds = forceImpls[i]->getBondedParticles();
        bonds.insert(bonds.end(), forceBonds.begin(), forceBonds.end());
    }
268
269
270
271
272
273
274
    for (int i = 0; i < system.getNumParticles(); i++) {
        if (system.isVirtualSite(i)) {
            const VirtualSite& site = system.getVirtualSite(i);
            for (int j = 0; j < site.getNumParticles(); j++)
                bonds.push_back(std::make_pair(i, site.getParticle(j)));
        }
    }
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305

    // Make a list of every other particle to which each particle is connected

    int numParticles = system.getNumParticles();
    vector<vector<int> > particleBonds(numParticles);
    for (int i = 0; i < (int) bonds.size(); i++) {
        particleBonds[bonds[i].first].push_back(bonds[i].second);
        particleBonds[bonds[i].second].push_back(bonds[i].first);
    }

    // Now tag particles by which molecule they belong to.

    vector<int> particleMolecule(numParticles, -1);
    int numMolecules = 0;
    for (int i = 0; i < numParticles; i++)
        if (particleMolecule[i] == -1)
            tagParticlesInMolecule(i, numMolecules++, particleMolecule, particleBonds);
    molecules.resize(numMolecules);
    for (int i = 0; i < numParticles; i++)
        molecules[particleMolecule[i]].push_back(i);
    return molecules;
}

void ContextImpl::tagParticlesInMolecule(int particle, int molecule, vector<int>& particleMolecule, vector<vector<int> >& particleBonds) {
    // Recursively tag particles as belonging to a particular molecule.

    particleMolecule[particle] = molecule;
    for (int i = 0; i < (int) particleBonds[particle].size(); i++)
        if (particleMolecule[particleBonds[particle][i]] == -1)
            tagParticlesInMolecule(particleBonds[particle][i], molecule, particleMolecule, particleBonds);
}
Peter Eastman's avatar
Peter Eastman committed
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330

static void writeString(ostream& stream, string str) {
    int length = str.size();
    stream.write((char*) &length, sizeof(int));
    stream.write((char*) &str[0], length);
}

static string readString(istream& stream) {
    int length;
    stream.read((char*) &length, sizeof(int));
    string str(length, ' ');
    stream.read((char*) &str[0], length);
    return str;
}

void ContextImpl::createCheckpoint(ostream& stream) {
    writeString(stream, getPlatform().getName());
    int numParticles = getSystem().getNumParticles();
    stream.write((char*) &numParticles, sizeof(int));
    int numParameters = parameters.size();
    stream.write((char*) &numParameters, sizeof(int));
    for (map<string, double>::const_iterator iter = parameters.begin(); iter != parameters.end(); ++iter) {
        writeString(stream, iter->first);
        stream.write((char*) &iter->second, sizeof(double));
    }
331
    updateStateDataKernel.getAs<UpdateStateDataKernel>().createCheckpoint(*this, stream);
Peter Eastman's avatar
Peter Eastman committed
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
    stream.flush();
}

void ContextImpl::loadCheckpoint(istream& stream) {
    string platformName = readString(stream);
    if (platformName != getPlatform().getName())
        throw OpenMMException("loadCheckpoint: Checkpoint was created with a different Platform: "+platformName);
    int numParticles;
    stream.read((char*) &numParticles, sizeof(int));
    if (numParticles != getSystem().getNumParticles())
        throw OpenMMException("loadCheckpoint: Checkpoint contains the wrong number of particles");
    int numParameters;
    stream.read((char*) &numParameters, sizeof(int));
    for (int i = 0; i < numParameters; i++) {
        string name = readString(stream);
        double value;
        stream.read((char*) &value, sizeof(double));
        parameters[name] = value;
    }
351
    updateStateDataKernel.getAs<UpdateStateDataKernel>().loadCheckpoint(*this, stream);
Peter Eastman's avatar
Peter Eastman committed
352
}