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42 * This file contains the definition of the microstate of the simulated system
44 * History of observables that needs to be checkpointed should be stored
45 * in ObservablesHistory.
46 * The state of the mdrun machinery that needs to be checkpointed is also
52 * \ingroup module_mdtypes
55 #ifndef GMX_MDTYPES_STATE_H
56 #define GMX_MDTYPES_STATE_H
62 #include "gromacs/gpu_utils/hostallocator.h"
63 #include "gromacs/math/paddedvector.h"
64 #include "gromacs/math/vectypes.h"
65 #include "gromacs/mdtypes/md_enums.h"
66 #include "gromacs/utility/arrayref.h"
67 #include "gromacs/utility/basedefinitions.h"
68 #include "gromacs/utility/enumerationhelpers.h"
69 #include "gromacs/utility/real.h"
76 enum class CheckpointDataOperation;
77 template<CheckpointDataOperation operation>
81 //! Convenience alias for until all is moved in the gmx namespace
83 using PaddedHostVector = gmx::PaddedHostVector<T>;
86 * The t_state struct should contain all the (possibly) non-static
87 * information required to define the state of the system.
88 * Currently the random seeds for SD and BD are missing.
91 /* \brief Enum for all entries in \p t_state
93 * These enums are used in flags as (1<<est...).
94 * The order of these enums should not be changed,
95 * since that affects the checkpoint (.cpt) file format.
110 estLD_RNG_NOTSUPPORTED,
111 estLD_RNGI_NOTSUPPORTED,
124 estMC_RNG_NOTSUPPORTED,
125 estMC_RNGI_NOTSUPPORTED,
131 //! \brief The names of the state entries, defined in src/gmxlib/checkpoint.c
132 extern const char* est_names[estNR];
134 /*! \libinternal \brief History information for NMR distance and orientation restraints
136 * Often this is only used for reporting observables, and thus should not
137 * actually be part of the microstate. But with time-dependent restraining
138 * they are actually part of the (non-Markovian) microstate.
139 * \todo Rename this with a more descriptive name.
146 real disre_initf; //!< The scaling factor for initializing the time av.
147 int ndisrepairs; //!< The number of distance restraints
148 real* disre_rm3tav; //!< The r^-3 time averaged pair distances
149 real orire_initf; //!< The scaling factor for initializing the time av.
150 int norire_Dtav; //!< The number of matrix element in dtav (npair*5)
151 real* orire_Dtav; //!< The time averaged orientation tensors
154 /*! \libinternal \brief Struct used for checkpointing only
156 * This struct would not be required with unlimited precision.
157 * But because of limited precision, the COM motion removal implementation
158 * can cause the kinetic energy in the MD loop to differ by a few bits from
159 * the kinetic energy one would determine from state.v.
166 gmx_bool bUpToDate; //!< Test if all data is up to date
167 int ekin_n; //!< The number of tensors
168 tensor* ekinh; //!< Half step Ekin, size \p ekin_n
169 tensor* ekinf; //!< Full step Ekin, size \p ekin_n
170 tensor* ekinh_old; //!< Half step Ekin of the previous step, size \p ekin_n
171 tensor ekin_total; //!< Total kinetic energy
172 std::vector<double> ekinscalef_nhc; //!< Nose-Hoover Ekin scaling factors for full step Ekin
173 std::vector<double> ekinscaleh_nhc; //!< Nose-Hoover Ekin scaling factors for half step Ekin
174 std::vector<double> vscale_nhc; //!< Nose-Hoover velocity scaling factors
175 real dekindl; //!< dEkin/dlambda, with free-energy
176 real mvcos; //!< Cosine(z) component of the momentum, for viscosity calculations
177 /*! \brief Whether KE terms have been read from the checkpoint.
179 * Only used for managing whether the call to compute_globals
180 * before we enter the MD loop should compute these quantities
182 bool hasReadEkinState;
185 * \brief Allows to read and write checkpoint within modular simulator
186 * \tparam operation Whether we're reading or writing
187 * \param checkpointData The CheckpointData object
189 template<gmx::CheckpointDataOperation operation>
190 void doCheckpoint(gmx::CheckpointData<operation> checkpointData);
193 /*! \brief Free-energy sampling history struct
195 * \todo Split out into microstate and observables history.
197 typedef struct df_history_t
199 int nlambda; //!< total number of lambda states - for history
201 gmx_bool bEquil; //!< Have we reached equilibration
202 int* n_at_lam; //!< number of points observed at each lambda
203 real* wl_histo; //!< histogram for WL flatness determination
204 real wl_delta; //!< current wang-landau delta
206 real* sum_weights; //!< weights of the states
207 real* sum_dg; //!< free energies of the states -- not actually used for weighting, but informational
208 real* sum_minvar; //!< corrections to weights for minimum variance
209 real* sum_variance; //!< variances of the states
211 real** accum_p; //!< accumulated bennett weights for n+1
212 real** accum_m; //!< accumulated bennett weights for n-1
213 real** accum_p2; //!< accumulated squared bennett weights for n+1
214 real** accum_m2; //!< accumulated squared bennett weights for n-1
216 real** Tij; //!< transition matrix
217 real** Tij_empirical; //!< Empirical transition matrix
222 /*! \brief The microstate of the system
224 * The global state will contain complete data for all used entries.
225 * The local state with domain decomposition will have partial entries
226 * for which \p stateEntryIsAtomProperty() is true. Some entries that
227 * are used in the global state might not be present in the local state.
228 * \todo Move pure observables history to ObservablesHistory.
236 int natoms; //!< Number of atoms, local + non-local; this is the size of \p x, \p v and \p cg_p, when used
237 int ngtc; //!< The number of temperature coupling groups
238 int nnhpres; //!< The number of NH-chains for the MTTK barostat (always 1 or 0)
239 int nhchainlength; //!< The NH-chain length for temperature coupling and MTTK barostat
240 int flags; //!< Set of bit-flags telling which entries are present, see enum at the top of the file
241 int fep_state; //!< indicates which of the alchemical states we are in
242 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real> lambda; //!< Free-energy lambda vector
243 matrix box; //!< Matrix of box vectors
244 matrix box_rel; //!< Relative box vectors to preserve box shape
245 matrix boxv; //!< Box velocities for Parrinello-Rahman P-coupling
246 matrix pres_prev; //!< Pressure of the previous step for pcoupl
247 matrix svir_prev; //!< Shake virial for previous step for pcoupl
248 matrix fvir_prev; //!< Force virial of the previous step for pcoupl
249 std::vector<double> nosehoover_xi; //!< Nose-Hoover coordinates (ngtc)
250 std::vector<double> nosehoover_vxi; //!< Nose-Hoover velocities (ngtc)
251 std::vector<double> nhpres_xi; //!< Pressure Nose-Hoover coordinates
252 std::vector<double> nhpres_vxi; //!< Pressure Nose-Hoover velocities
253 std::vector<double> therm_integral; //!< Work exterted N-H/V-rescale T-coupling (ngtc)
254 double baros_integral; //!< For Berendsen P-coupling conserved quantity
255 real veta; //!< Trotter based isotropic P-coupling
256 real vol0; //!< Initial volume,required for computing MTTK conserved quantity
257 PaddedHostVector<gmx::RVec> x; //!< The coordinates (natoms)
258 PaddedHostVector<gmx::RVec> v; //!< The velocities (natoms)
259 PaddedHostVector<gmx::RVec> cg_p; //!< p vector for conjugate gradient minimization
261 ekinstate_t ekinstate; //!< The state of the kinetic energy
263 /* History for special algorithms, should be moved to a history struct */
264 history_t hist; //!< Time history for restraints
265 df_history_t* dfhist; //!< Free-energy history for free energy analysis
266 std::shared_ptr<gmx::AwhHistory> awhHistory; //!< Accelerated weight histogram history
268 int ddp_count; //!< The DD partitioning count for this state
269 int ddp_count_cg_gl; //!< The DD partitioning count for index_gl
270 std::vector<int> cg_gl; //!< The global cg number of the local cgs
272 std::vector<double> pull_com_prev_step; //!< The COM of the previous step of each pull group
276 /* We don't document the structs below, as they don't belong here.
277 * TODO: Move the next two structs out of state.h.
282 std::vector<double> Qinv; /* inverse mass of thermostat -- computed from inputs, but a good place to store */
283 std::vector<double> QPinv; /* inverse mass of thermostat for barostat -- computed from inputs, but a good place to store */
284 double Winv; /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */
285 tensor Winvm; /* inverse pressure mass tensor, computed */
301 //! Resizes the T- and P-coupling state variables
302 void init_gtc_state(t_state* state, int ngtc, int nnhpres, int nhchainlength);
304 //! Change the number of atoms represented by this state, allocating memory as needed.
305 void state_change_natoms(t_state* state, int natoms);
307 //! Allocates memory for free-energy history
308 void init_dfhist_state(t_state* state, int dfhistNumLambda);
310 /*! \brief Compares two states, write the differences to stdout */
311 void comp_state(const t_state* st1, const t_state* st2, gmx_bool bRMSD, real ftol, real abstol);
313 /*! \brief Allocates an rvec pointer and copy the contents of v to it */
314 rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n);
316 /*! \brief Determine the relative box components
318 * Set box_rel e.g. used in mdrun state, used to preserve the box shape
319 * \param[in] ir Input record
320 * \param[inout] state State
322 void set_box_rel(const t_inputrec* ir, t_state* state);
324 /*! \brief Make sure the relative box shape remains the same
326 * This function ensures that the relative box dimensions are
327 * preserved, which otherwise might diffuse away due to rounding
328 * errors in pressure coupling or the deform option.
330 * \param[in] ir Input record
331 * \param[in] box_rel Relative box dimensions
332 * \param[inout] box The corrected actual box dimensions
334 void preserve_box_shape(const t_inputrec* ir, matrix box_rel, matrix box);
336 /*! \brief Returns an arrayRef to the positions in \p state when \p state!=null
338 * When \p state=nullptr, returns an empty arrayRef.
340 * \note The size returned is the number of atoms, without padding.
342 * \param[in] state The state, can be nullptr
344 static inline gmx::ArrayRef<const gmx::RVec> positionsFromStatePointer(const t_state* state)
348 return gmx::makeConstArrayRef(state->x).subArray(0, state->natoms);
356 /*! \brief Prints the current lambda state to the log file.
358 * \param[in] fplog The log file. If fplog == nullptr there will be no output.
359 * \param[in] lambda The array of lambda values.
360 * \param[in] isInitialOutput Whether this output is the initial lambda state or not.
362 void printLambdaStateToLog(FILE* fplog, gmx::ArrayRef<const real> lambda, bool isInitialOutput);
365 /*! \brief Fills fep_state and lambda if needed
367 * If FEP or simulated tempering is in use, fills fep_state
368 * and lambda on master rank.
370 * Reports the initial lambda state to the log file. */
371 void initialize_lambdas(FILE* fplog, const t_inputrec& ir, bool isMaster, int* fep_state, gmx::ArrayRef<real> lambda);