2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
36 * \brief Declares the global reduction element for the modular simulator
38 * \author Pascal Merz <pascal.merz@me.com>
39 * \ingroup module_modularsimulator
41 * This header is only used within the modular simulator module
44 #ifndef GMX_MODULARSIMULATOR_COMPUTEGLOBALSELEMENT_H
45 #define GMX_MODULARSIMULATOR_COMPUTEGLOBALSELEMENT_H
47 #include "gromacs/mdlib/simulationsignal.h"
48 #include "gromacs/mdlib/vcm.h"
50 #include "energydata.h"
51 #include "modularsimulatorinterfaces.h"
52 #include "statepropagatordata.h"
53 #include "topologyholder.h"
55 struct gmx_global_stat;
61 class FreeEnergyPerturbationData;
62 class LegacySimulatorData;
66 //! \addtogroup module_modularsimulator
69 //! The different global reduction schemes we know about
70 enum class ComputeGlobalsAlgorithm
76 //! The function type allowing to request a check of the number of bonded interactions
77 typedef std::function<void()> CheckBondedInteractionsCallback;
80 * \brief Encapsulate the calls to `compute_globals`
82 * This element aims at offering an interface to the legacy
83 * implementation which is compatible with the new simulator approach.
85 * The element comes in 3 (templated) flavors: the leap-frog case, the first
86 * call during a velocity-verlet integrator, and the second call during a
87 * velocity-verlet integrator. In velocity verlet, the state at the beginning
88 * of the step corresponds to
90 * velocities at time t - dt/2
91 * The first velocity propagation (+dt/2) therefore actually corresponds to the
92 * previous step, bringing the state to the full timestep at time t. Most global
93 * reductions are made at this point. The second call is needed to correct the
94 * constraint virial after the second propagation of velocities (+dt/2) and of
95 * the positions (+dt).
97 * \tparam algorithm The global reduction scheme
99 template<ComputeGlobalsAlgorithm algorithm>
100 class ComputeGlobalsElement final :
101 public ISimulatorElement,
102 public IEnergySignallerClient,
103 public ITrajectorySignallerClient,
104 public ITopologyHolderClient
108 ComputeGlobalsElement(StatePropagatorData* statePropagatorData,
109 EnergyData* energyData,
110 FreeEnergyPerturbationData* freeEnergyPerturbationData,
111 SimulationSignals* signals,
114 const MDLogger& mdlog,
116 const t_inputrec* inputrec,
117 const MDAtoms* mdAtoms,
119 gmx_wallcycle* wcycle,
121 const gmx_mtop_t& global_top,
122 Constraints* constr);
125 ~ComputeGlobalsElement() override;
127 /*! \brief Element setup - first call to compute_globals
130 void elementSetup() override;
132 /*! \brief Register run function for step / time
134 * This registers the call to compute_globals when needed.
136 * \param step The step number
137 * \param time The time
138 * \param registerRunFunction Function allowing to register a run function
140 void scheduleTask(Step step, Time time, const RegisterRunFunction& registerRunFunction) override;
142 //! Get callback to request checking of bonded interactions
143 CheckBondedInteractionsCallback getCheckNumberOfBondedInteractionsCallback();
145 //! No element teardown needed
146 void elementTeardown() override {}
148 /*! \brief Factory method implementation
150 * \param legacySimulatorData Pointer allowing access to simulator level data
151 * \param builderHelper ModularSimulatorAlgorithmBuilder helper object
152 * \param statePropagatorData Pointer to the \c StatePropagatorData object
153 * \param energyData Pointer to the \c EnergyData object
154 * \param freeEnergyPerturbationData Pointer to the \c FreeEnergyPerturbationData object
155 * \param globalCommunicationHelper Pointer to the \c GlobalCommunicationHelper object
157 * \throws std::bad_any_cast on internal error in VelocityVerlet algorithm builder.
158 * \throws std::bad_alloc when out of memory.
160 * \return Pointer to the element to be added. Element needs to have been stored using \c storeElement
162 static ISimulatorElement* getElementPointerImpl(LegacySimulatorData* legacySimulatorData,
163 ModularSimulatorAlgorithmBuilderHelper* builderHelper,
164 StatePropagatorData* statePropagatorData,
165 EnergyData* energyData,
166 FreeEnergyPerturbationData* freeEnergyPerturbationData,
167 GlobalCommunicationHelper* globalCommunicationHelper);
170 //! ITopologyClient implementation
171 void setTopology(const gmx_localtop_t* top) override;
172 //! IEnergySignallerClient implementation
173 std::optional<SignallerCallback> registerEnergyCallback(EnergySignallerEvent event) override;
174 //! ITrajectorySignallerClient implementation
175 std::optional<SignallerCallback> registerTrajectorySignallerCallback(TrajectoryEvent event) override;
176 //! The compute_globals call
177 void compute(Step step, unsigned int flags, SimulationSignaller* signaller, bool useLastBox, bool isInit = false);
179 //! Next step at which energy needs to be reduced
180 Step energyReductionStep_;
181 //! Next step at which virial needs to be reduced
182 Step virialReductionStep_;
184 //! For VV only, we need to schedule twice per step. This keeps track of the scheduling stage.
185 Step vvSchedulingStep_;
187 //! Whether center of mass motion stopping is enabled
188 const bool doStopCM_;
189 //! Number of steps after which center of mass motion is removed
191 //! Compute globals communication period
193 //! The last (planned) step (only used for LF)
194 const Step lastStep_;
195 //! The initial step (only used for VV)
196 const Step initStep_;
197 //! A dummy signaller (used for setup and VV)
198 std::unique_ptr<SimulationSignaller> nullSignaller_;
200 /*! \brief Check that DD doesn't miss bonded interactions
202 * Domain decomposition could incorrectly miss a bonded
203 * interaction, but checking for that requires a global
204 * communication stage, which does not otherwise happen in DD
205 * code. So we do that alongside the first global energy reduction
206 * after a new DD is made. These variables handle whether the
207 * check happens, and the result it returns.
210 int totalNumberOfBondedInteractions_;
211 bool shouldCheckNumberOfBondedInteractions_;
214 /*! \brief Signal to ComputeGlobalsElement that it should check for DD errors
216 * Note that this should really be the responsibility of the DD element.
217 * MDLogger, global and local topology are only needed due to the call to
218 * checkNumberOfBondedInteractions(...).
220 * The DD element should have a single variable which gets reduced, and then
221 * be responsible for the checking after a global reduction has happened.
222 * This would, however, require a new approach for the compute_globals calls,
223 * which is not yet implemented. So for now, we're leaving this here.
225 void needToCheckNumberOfBondedInteractions();
227 //! Global reduction struct
228 gmx_global_stat* gstat_;
230 // TODO: Clarify relationship to data objects and find a more robust alternative to raw pointers (#3583)
231 //! Pointer to the microstate
232 StatePropagatorData* statePropagatorData_;
233 //! Pointer to the energy data (needed for the tensors and mu_tot)
234 EnergyData* energyData_;
235 //! Pointer to the local topology (only needed for checkNumberOfBondedInteractions)
236 const gmx_localtop_t* localTopology_;
237 //! Pointer to the free energy perturbation data
238 FreeEnergyPerturbationData* freeEnergyPerturbationData_;
240 //! Center of mass motion removal
243 SimulationSignals* signals_;
245 // Access to ISimulator data
249 const MDLogger& mdlog_;
250 //! Handles communication.
252 //! Contains user input mdp options.
253 const t_inputrec* inputrec_;
254 //! Full system topology - only needed for checkNumberOfBondedInteractions.
255 const gmx_mtop_t& top_global_;
256 //! Atom parameters for this domain.
257 const MDAtoms* mdAtoms_;
258 //! Handles constraints.
259 Constraints* constr_;
260 //! Manages flop accounting.
262 //! Manages wall cycle accounting.
263 gmx_wallcycle* wcycle_;
264 //! Parameters for force calculations.
271 #endif // GMX_MODULARSIMULATOR_COMPUTEGLOBALSELEMENT_H