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35 /*! \libinternal \file
36 * \brief Declares the state for the modular simulator
38 * \author Pascal Merz <pascal.merz@me.com>
39 * \ingroup module_modularsimulator
42 #ifndef GMX_MODULARSIMULATOR_STATEPROPAGATORDATA_H
43 #define GMX_MODULARSIMULATOR_STATEPROPAGATORDATA_H
45 #include "gromacs/gpu_utils/hostallocator.h"
46 #include "gromacs/math/paddedvector.h"
47 #include "gromacs/math/vectypes.h"
49 #include "modularsimulatorinterfaces.h"
59 enum class ConstraintVariable;
60 class FreeEnergyPerturbationElement;
63 * \ingroup module_modularsimulator
64 * \brief StatePropagatorData and associated data
66 * The `StatePropagatorData` contains a little more than the pure
67 * statistical-physical micro state, namely the positions,
68 * velocities, forces, and box matrix, as well as a backup of
69 * the positions and box of the last time step. While it takes
70 * part in the simulator loop to be able to backup positions /
71 * boxes and save the current state if needed, it's main purpose
72 * is to offer access to its data via getter methods. All elements
73 * reading or writing to this data need a pointer to the
74 * `StatePropagatorData` and need to request their data explicitly. This
75 * will later simplify the understanding of data dependencies
78 * The `StatePropagatorData` takes part in the simulator run, as it might
79 * have to save a valid state at the right moment during the
80 * integration. Placing the StatePropagatorData correctly is for now the
81 * duty of the simulator builder - this might be automatized later
82 * if we have enough meta-data of the variables (i.e., if
83 * `StatePropagatorData` knows at which time the variables currently are,
84 * and can decide when a valid state (full-time step of all
85 * variables) is reached. The `StatePropagatorData` is also a client of
86 * both the trajectory signaller and writer - it will save a
87 * state for later writeout during the simulator step if it
88 * knows that trajectory writing will occur later in the step,
89 * and it knows how to write to file given a file pointer by
90 * the `TrajectoryElement`.
92 * Note that the `StatePropagatorData` can be converted to and from the
93 * legacy `t_state` object. This is useful when dealing with
94 * functionality which has not yet been adapted to use the new
95 * data approach - of the elements currently implemented, only
96 * domain decomposition, PME load balancing, and the initial
97 * constraining are using this.
99 class StatePropagatorData final :
100 public ISimulatorElement,
101 public ITrajectoryWriterClient,
102 public ITrajectorySignallerClient,
103 public ICheckpointHelperClient
107 StatePropagatorData(int numAtoms,
110 t_state* globalState,
114 int nstxout_compressed,
116 FreeEnergyPerturbationElement* freeEnergyPerturbationElement,
117 const t_inputrec* inputrec,
118 const t_mdatoms* mdatoms);
120 // Allow access to state
121 //! Get write access to position vector
122 ArrayRefWithPadding<RVec> positionsView();
123 //! Get read access to position vector
124 ArrayRefWithPadding<const RVec> constPositionsView() const;
125 //! Get write access to previous position vector
126 ArrayRefWithPadding<RVec> previousPositionsView();
127 //! Get read access to previous position vector
128 ArrayRefWithPadding<const RVec> constPreviousPositionsView() const;
129 //! Get write access to velocity vector
130 ArrayRefWithPadding<RVec> velocitiesView();
131 //! Get read access to velocity vector
132 ArrayRefWithPadding<const RVec> constVelocitiesView() const;
133 //! Get write access to force vector
134 ArrayRefWithPadding<RVec> forcesView();
135 //! Get read access to force vector
136 ArrayRefWithPadding<const RVec> constForcesView() const;
137 //! Get pointer to box
139 //! Get const pointer to box
140 const rvec* constBox();
141 //! Get pointer to previous box
143 //! Get const pointer to previous box
144 const rvec* constPreviousBox();
145 //! Get the local number of atoms
148 /*! \brief Register run function for step / time
150 * This needs to be called during the integration part of the simulator,
151 * at the moment at which the state is at a full time step. Positioning
152 * this element is the responsibility of the programmer writing the
153 * integration algorithm! If the current step is a trajectory writing
154 * step, StatePropagatorData will save a backup for later writeout.
156 * This is also the place at which the current state becomes the previous
159 * @param step The step number
160 * @param time The time
161 * @param registerRunFunction Function allowing to register a run function
163 void scheduleTask(Step step, Time time, const RegisterRunFunctionPtr& registerRunFunction) override;
165 /*! \brief Backup starting velocities
167 * This is only needed for vv, where the first (velocity) half step is only
168 * used to compute the constraint virial, but the velocities need to be reset
170 * TODO: There must be a more elegant solution to this!
172 void elementSetup() override;
174 //! No element teardown needed
175 void elementTeardown() override {}
178 // (doxygen doesn't like these)
179 // Classes which need access to legacy state
180 friend class DomDecHelper;
184 //! The total number of atoms in the system
186 //! The position writeout frequency
188 //! The velocity writeout frequency
190 //! The force writeout frequency
192 //! The compressed position writeout frequency
193 int nstxout_compressed_;
195 //! The local number of atoms
197 //! The position vector
198 PaddedHostVector<RVec> x_;
199 //! The position vector of the previous step
200 PaddedHostVector<RVec> previousX_;
201 //! The velocity vector
202 PaddedHostVector<RVec> v_;
204 PaddedHostVector<RVec> f_;
207 //! The box matrix of the previous step
209 //! The DD partitioning count for legacy t_state compatibility
212 //! Move x_ to previousX_
214 //! OMP helper to move x_ to previousX_
215 void copyPosition(int start, int end);
217 // Access to legacy state
218 //! Get a deep copy of the current state in legacy format
219 std::unique_ptr<t_state> localState();
220 //! Update the current state with a state in legacy format
221 void setLocalState(std::unique_ptr<t_state> state);
222 //! Get a pointer to the global state
223 t_state* globalState();
224 //! Get a force pointer
225 PaddedHostVector<gmx::RVec>* forcePointer();
227 //! Pointer to keep a backup of the state for later writeout
228 std::unique_ptr<t_state> localStateBackup_;
229 //! Step at which next writeout occurs
231 //! Backup current state
234 //! ITrajectorySignallerClient implementation
235 SignallerCallbackPtr registerTrajectorySignallerCallback(TrajectoryEvent event) override;
237 //! ITrajectoryWriterClient implementation
238 ITrajectoryWriterCallbackPtr registerTrajectoryWriterCallback(TrajectoryEvent event) override;
240 //! ICheckpointHelperClient implementation
241 void writeCheckpoint(t_state* localState, t_state* globalState) override;
243 //! Callback writing the state to file
244 void write(gmx_mdoutf* outf, Step step, Time time);
246 //! Whether we're doing VV and need to reset velocities after the first half step
247 bool vvResetVelocities_;
248 //! Velocities backup for VV
249 PaddedHostVector<RVec> velocityBackup_;
250 //! Function resetting the velocities
251 void resetVelocities();
253 //! Pointer to the free energy perturbation element (for trajectory writing only)
254 FreeEnergyPerturbationElement* freeEnergyPerturbationElement_;
256 // Access to ISimulator data
259 //! Handles communication.
260 const t_commrec* cr_;
261 //! Full simulation state (only non-nullptr on master rank).
262 t_state* globalState_;
264 //! No trajectory writer setup needed
265 void trajectoryWriterSetup(gmx_mdoutf gmx_unused* outf) override {}
266 //! No trajectory writer teardown needed
267 void trajectoryWriterTeardown(gmx_mdoutf gmx_unused* outf) override {}
272 #endif // GMX_MODULARSIMULATOR_STATEPROPAGATORDATA_H