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41 * This file contains the definition of the microstate of the simulated system
43 * History of observables that needs to be checkpointed should be stored
44 * in ObservablesHistory.
45 * The state of the mdrun machinery that needs to be checkpointed is also
51 * \ingroup module_mdtypes
54 #ifndef GMX_MDTYPES_STATE_H
55 #define GMX_MDTYPES_STATE_H
61 #include "gromacs/math/paddedvector.h"
62 #include "gromacs/math/vectypes.h"
63 #include "gromacs/mdtypes/md_enums.h"
64 #include "gromacs/utility/basedefinitions.h"
65 #include "gromacs/utility/real.h"
75 * The t_state struct should contain all the (possibly) non-static
76 * information required to define the state of the system.
77 * Currently the random seeds for SD and BD are missing.
80 /* \brief Enum for all entries in \p t_state
82 * These enums are used in flags as (1<<est...).
83 * The order of these enums should not be changed,
84 * since that affects the checkpoint (.cpt) file format.
88 estBOX
, estBOX_REL
, estBOXV
, estPRES_PREV
, estNH_XI
, estTHERM_INT
,
89 estX
, estV
, estSDX_NOTSUPPORTED
, estCGP
,
90 estLD_RNG_NOTSUPPORTED
, estLD_RNGI_NOTSUPPORTED
,
91 estDISRE_INITF
, estDISRE_RM3TAV
,
92 estORIRE_INITF
, estORIRE_DTAV
,
93 estSVIR_PREV
, estNH_VXI
, estVETA
, estVOL0
, estNHPRES_XI
, estNHPRES_VXI
, estFVIR_PREV
,
94 estFEPSTATE
, estMC_RNG_NOTSUPPORTED
, estMC_RNGI_NOTSUPPORTED
,
99 //! \brief The names of the state entries, defined in src/gmxlib/checkpoint.c
100 extern const char *est_names
[estNR
];
102 /*! \libinternal \brief History information for NMR distance and orientation restraints
104 * Often this is only used for reporting observables, and thus should not
105 * actually be part of the microstate. But with time-dependent restraining
106 * they are actually part of the (non-Markovian) microstate.
107 * \todo Rename this with a more descriptive name.
115 real disre_initf
; //!< The scaling factor for initializing the time av.
116 int ndisrepairs
; //!< The number of distance restraints
117 real
*disre_rm3tav
; //!< The r^-3 time averaged pair distances
118 real orire_initf
; //!< The scaling factor for initializing the time av.
119 int norire_Dtav
; //!< The number of matrix element in dtav (npair*5)
120 real
*orire_Dtav
; //!< The time averaged orientation tensors
123 /*! \libinternal \brief Struct used for checkpointing only
125 * This struct would not be required with unlimited precision.
126 * But because of limited precision, the COM motion removal implementation
127 * can cause the kinetic energy in the MD loop to differ by a few bits from
128 * the kinetic energy one would determine from state.v.
135 gmx_bool bUpToDate
; //!< Test if all data is up to date
136 int ekin_n
; //!< The number of tensors
137 tensor
*ekinh
; //!< Half step Ekin, size \p ekin_n
138 tensor
*ekinf
; //!< Full step Ekin, size \p ekin_n
139 tensor
*ekinh_old
; //!< Half step Ekin of the previous step, size \p ekin_n
140 tensor ekin_total
; //!< Total kinetic energy
141 std::vector
<double> ekinscalef_nhc
; //!< Nose-Hoover Ekin scaling factors for full step Ekin
142 std::vector
<double> ekinscaleh_nhc
; //!< Nose-Hoover Ekin scaling factors for half step Ekin
143 std::vector
<double> vscale_nhc
; //!< Nose-Hoover velocity scaling factors
144 real dekindl
; //!< dEkin/dlambda, with free-energy
145 real mvcos
; //!< Cosine(z) component of the momentum, for viscosity calculations
148 /*! \brief Free-energy sampling history struct
150 * \todo Split out into microstate and observables history.
152 typedef struct df_history_t
154 int nlambda
; //!< total number of lambda states - for history
156 gmx_bool bEquil
; //!< Have we reached equilibration
157 int *n_at_lam
; //!< number of points observed at each lambda
158 real
*wl_histo
; //!< histogram for WL flatness determination
159 real wl_delta
; //!< current wang-landau delta
161 real
*sum_weights
; //!< weights of the states
162 real
*sum_dg
; //!< free energies of the states -- not actually used for weighting, but informational
163 real
*sum_minvar
; //!< corrections to weights for minimum variance
164 real
*sum_variance
; //!< variances of the states
166 real
**accum_p
; //!< accumulated bennett weights for n+1
167 real
**accum_m
; //!< accumulated bennett weights for n-1
168 real
**accum_p2
; //!< accumulated squared bennett weights for n+1
169 real
**accum_m2
; //!< accumulated squared bennett weights for n-1
171 real
**Tij
; //!< transition matrix
172 real
**Tij_empirical
; //!< Empirical transition matrix
177 /*! \brief The microstate of the system
179 * The global state will contain complete data for all used entries.
180 * The local state with domain decomposition will have partial entries
181 * for which \p stateEntryIsAtomProperty() is true. Some entries that
182 * are used in the global state might not be present in the local state.
183 * \todo Move pure observables history to ObservablesHistory.
192 int natoms
; //!< Number of atoms, local + non-local; this is the size of \p x, \p v and \p cg_p, when used
193 int ngtc
; //!< The number of temperature coupling groups
194 int nnhpres
; //!< The NH-chain length for the MTTK barostat
195 int nhchainlength
; //!< The NH-chain length for temperature coupling
196 int flags
; //!< Set of bit-flags telling which entries are present, see enum at the top of the file
197 int fep_state
; //!< indicates which of the alchemical states we are in
198 std::array
<real
, efptNR
> lambda
; //!< Free-energy lambda vector
199 matrix box
; //!< Matrix of box vectors
200 matrix box_rel
; //!< Relative box vectors to preserve box shape
201 matrix boxv
; //!< Box velocities for Parrinello-Rahman P-coupling
202 matrix pres_prev
; //!< Pressure of the previous step for pcoupl
203 matrix svir_prev
; //!< Shake virial for previous step for pcoupl
204 matrix fvir_prev
; //!< Force virial of the previous step for pcoupl
205 std::vector
<double> nosehoover_xi
; //!< Nose-Hoover coordinates (ngtc)
206 std::vector
<double> nosehoover_vxi
; //!< Nose-Hoover velocities (ngtc)
207 std::vector
<double> nhpres_xi
; //!< Pressure Nose-Hoover coordinates
208 std::vector
<double> nhpres_vxi
; //!< Pressure Nose-Hoover velocities
209 std::vector
<double> therm_integral
; //!< Work exterted N-H/V-rescale T-coupling (ngtc)
210 double baros_integral
; //!< For Berendsen P-coupling conserved quantity
211 real veta
; //!< Trotter based isotropic P-coupling
212 real vol0
; //!< Initial volume,required for computing MTTK conserved quantity
213 PaddedRVecVector x
; //!< The coordinates (natoms)
214 PaddedRVecVector v
; //!< The velocities (natoms)
215 PaddedRVecVector cg_p
; //!< p vector for conjugate gradient minimization
217 ekinstate_t ekinstate
; //!< The state of the kinetic energy
219 /* History for special algorithms, should be moved to a history struct */
220 history_t hist
; //!< Time history for restraints
221 df_history_t
*dfhist
; //!< Free-energy history for free energy analysis
222 std::shared_ptr
<gmx::AwhHistory
> awhHistory
; //!< Accelerated weight histogram history
224 int ddp_count
; //!< The DD partitioning count for this state
225 int ddp_count_cg_gl
; //!< The DD partitioning count for index_gl
226 std::vector
<int> cg_gl
; //!< The global cg number of the local cgs
230 /* We don't document the structs below, as they don't belong here.
231 * TODO: Move the next two structs out of state.h.
234 typedef struct t_extmass
236 double *Qinv
; /* inverse mass of thermostat -- computed from inputs, but a good place to store */
237 double *QPinv
; /* inverse mass of thermostat for barostat -- computed from inputs, but a good place to store */
238 double Winv
; /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */
239 tensor Winvm
; /* inverse pressure mass tensor, computed */
255 //! Resizes the T- and P-coupling state variables
256 void init_gtc_state(t_state
*state
, int ngtc
, int nnhpres
, int nhchainlength
);
258 //! Change the number of atoms represented by this state, allocating memory as needed.
259 void state_change_natoms(t_state
*state
, int natoms
);
261 //! Allocates memory for free-energy history
262 void init_dfhist_state(t_state
*state
, int dfhistNumLambda
);
264 /*! \brief Compares two states, write the differences to stdout */
265 void comp_state(const t_state
*st1
, const t_state
*st2
, gmx_bool bRMSD
, real ftol
, real abstol
);
267 /*! \brief Allocates an rvec pointer and copy the contents of v to it */
268 rvec
*getRvecArrayFromPaddedRVecVector(const PaddedRVecVector
*v
,
271 /*! \brief Determine the relative box components
273 * Set box_rel e.g. used in mdrun state, used to preserve the box shape
274 * \param[in] ir Input record
275 * \param[inout] state State
277 void set_box_rel(const t_inputrec
*ir
, t_state
*state
);
279 /*! \brief Make sure the relative box shape remains the same
281 * This function ensures that the relative box dimensions are
282 * preserved, which otherwise might diffuse away due to rounding
283 * errors in pressure coupling or the deform option.
285 * \param[in] ir Input record
286 * \param[in] box_rel Relative box dimensions
287 * \param[inout] box The corrected actual box dimensions
289 void preserve_box_shape(const t_inputrec
*ir
, matrix box_rel
, matrix box
);