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49 * The t_state struct should contain all the (possibly) non-static
50 * information required to define the state of the system.
51 * Currently the random seeds for SD and BD are missing.
54 /* for now, define the length of the NH chains here */
55 #define NHCHAINLENGTH 10
56 #define MAXLAMBDAS 1024
58 /* These enums are used in flags as (1<<est...).
59 * The order of these enums should not be changed,
60 * since that affects the checkpoint (.cpt) file format.
63 estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI, estTC_INT,
64 estX, estV, estSDX, estCGP, estLD_RNG, estLD_RNGI,
65 estDISRE_INITF, estDISRE_RM3TAV,
66 estORIRE_INITF, estORIRE_DTAV,
67 estSVIR_PREV, estNH_VXI, estVETA, estVOL0, estNHPRES_XI, estNHPRES_VXI, estFVIR_PREV,
68 estFEPSTATE, estMC_RNG, estMC_RNGI,
71 #define EST_DISTR(e) (!(((e) >= estLAMBDA && (e) <= estTC_INT) || ((e) >= estSVIR_PREV && (e) <= estMC_RNGI)))
73 /* The names of the state entries, defined in src/gmxlib/checkpoint.c */
74 extern const char *est_names[estNR];
78 real disre_initf; /* The scaling factor for initializing the time av. */
79 int ndisrepairs; /* The number of distance restraints */
80 real *disre_rm3tav; /* The r^-3 time averaged pair distances */
81 real orire_initf; /* The scaling factor for initializing the time av. */
82 int norire_Dtav; /* The number of matrix element in dtav (npair*5) */
83 real *orire_Dtav; /* The time averaged orientation tensors */
86 /* Struct used for checkpointing only.
87 * This struct would not be required with unlimited precision.
88 * But because of limited precision, the COM motion removal implementation
89 * can cause the kinetic energy in the MD loop to differ by a few bits from
90 * the kinetic energy one would determine from state.v.
100 double *ekinscalef_nhc;
101 double *ekinscaleh_nhc;
107 /* energy history for delta_h histograms */
110 int nndh; /* the number of energy difference lists */
111 int *ndh; /* the number in each energy difference list */
112 real **dh; /* the energy difference lists */
114 double start_time; /* the start time of these energy diff blocks */
115 double start_lambda; /* lambda at start time */
117 gmx_bool start_lambda_set; /* whether the lambda value is set. Here
118 For backward-compatibility. */
123 int nlambda; /* total number of lambda states - for history*/
125 gmx_bool bEquil; /* reached equilibration */
126 int *n_at_lam; /* number of points observed at each lambda */
127 real *wl_histo; /* histogram for WL flatness determination */
128 real wl_delta; /* current wang-landau delta */
130 real *sum_weights; /* weights of the states */
131 real *sum_dg; /* free energies of the states -- not actually used for weighting, but informational */
132 real *sum_minvar; /* corrections to weights for minimum variance */
133 real *sum_variance; /* variances of the states */
135 real **accum_p; /* accumulated bennett weights for n+1 */
136 real **accum_m; /* accumulated bennett weights for n-1 */
137 real **accum_p2; /* accumulated squared bennett weights for n+1 */
138 real **accum_m2; /* accumulated squared bennett weights for n-1 */
140 real **Tij; /* transition matrix */
141 real **Tij_empirical; /* Empirical transition matrix */
146 gmx_large_int_t nsteps; /* The number of steps in the history */
147 gmx_large_int_t nsum; /* The nr. of steps in the ener_ave and ener_sum */
148 double * ener_ave; /* Energy term history sum to get fluctuations */
149 double * ener_sum; /* Energy term history sum to get fluctuations */
150 int nener; /* Number of energy terms in two previous arrays */
151 gmx_large_int_t nsteps_sim; /* The number of steps in ener_sum_sim */
152 gmx_large_int_t nsum_sim; /* The number of frames in ener_sum_sim */
153 double * ener_sum_sim; /* Energy term history sum of the whole sim */
155 delta_h_history_t *dht; /* The BAR energy differences */
164 int nhchainlength; /* number of nose-hoover chains */
167 int flags; /* Flags telling which entries are present */
168 int fep_state; /* indicates which of the alchemical states we are in */
169 real *lambda; /* lambda vector */
170 matrix box; /* box vector coordinates */
171 matrix box_rel; /* Relitaive box vectors to preserve shape */
172 matrix boxv; /* box velocitites for Parrinello-Rahman pcoupl */
173 matrix pres_prev; /* Pressure of the previous step for pcoupl */
174 matrix svir_prev; /* Shake virial for previous step for pcoupl */
175 matrix fvir_prev; /* Force virial of the previous step for pcoupl */
176 double *nosehoover_xi; /* for Nose-Hoover tcoupl (ngtc) */
177 double *nosehoover_vxi; /* for N-H tcoupl (ngtc) */
178 double *nhpres_xi; /* for Nose-Hoover pcoupl for barostat */
179 double *nhpres_vxi; /* for Nose-Hoover pcoupl for barostat */
180 double *therm_integral; /* for N-H/V-rescale tcoupl (ngtc) */
181 real veta; /* trotter based isotropic P-coupling */
182 real vol0; /* initial volume,required for computing NPT conserverd quantity */
183 int nalloc; /* Allocation size for x, v and sd_x when !=NULL*/
184 rvec *x; /* the coordinates (natoms) */
185 rvec *v; /* the velocities (natoms) */
186 rvec *sd_X; /* random part of the x update for stoch. dyn. */
187 rvec *cg_p; /* p vector for conjugate gradient minimization */
189 unsigned int *ld_rng; /* RNG random state */
190 int *ld_rngi; /* RNG index */
192 int nmcrng; /* number of RNG states */
193 unsigned int *mc_rng; /* lambda MC RNG random state */
194 int *mc_rngi; /* lambda MC RNG index */
196 history_t hist; /* Time history for restraints */
198 ekinstate_t ekinstate; /* The state of the kinetic energy data */
200 energyhistory_t enerhist; /* Energy history for statistics */
201 df_history_t dfhist; /*Free energy history for free energy analysis */
203 int ddp_count; /* The DD partitioning count for this state */
204 int ddp_count_cg_gl; /* The DD part. count for index_gl */
205 int ncg_gl; /* The number of local charge groups */
206 int *cg_gl; /* The global cg number of the local cgs */
207 int cg_gl_nalloc; /* Allocation size of cg_gl; */
212 double *Qinv; /* inverse mass of thermostat -- computed from inputs, but a good place to store */
213 double *QPinv; /* inverse mass of thermostat for barostat -- computed from inputs, but a good place to store */
214 double Winv; /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */
215 tensor Winvm; /* inverse pressure mass tensor, computed */
234 #endif /* _state_h_ */