/*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
* GROMACS is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with GROMACS; if not, see
* http://www.gnu.org/licenses, or write to the Free Software Foundation,
* Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
* If you want to redistribute modifications to GROMACS, please
* consider that scientific software is very special. Version
* control is crucial - bugs must be traceable. We will be happy to
* consider code for inclusion in the official distribution, but
* derived work must not be called official GROMACS. Details are found
* in the README & COPYING files - if they are missing, get the
* official version at http://www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef _state_h_
#define _state_h_
#include "simple.h"
#include "../../swap/enums.h"
#ifdef __cplusplus
extern "C" {
#endif
/*
* The t_state struct should contain all the (possibly) non-static
* information required to define the state of the system.
* Currently the random seeds for SD and BD are missing.
*/
/* These enums are used in flags as (1<= estLAMBDA && (e) <= estTC_INT) || ((e) >= estSVIR_PREV && (e) <= estMC_RNGI)))
/* The names of the state entries, defined in src/gmxlib/checkpoint.c */
extern const char *est_names[estNR];
typedef struct
{
real disre_initf; /* The scaling factor for initializing the time av. */
int ndisrepairs; /* The number of distance restraints */
real *disre_rm3tav; /* The r^-3 time averaged pair distances */
real orire_initf; /* The scaling factor for initializing the time av. */
int norire_Dtav; /* The number of matrix element in dtav (npair*5) */
real *orire_Dtav; /* The time averaged orientation tensors */
} history_t;
/* Struct used for checkpointing only.
* This struct would not be required with unlimited precision.
* But because of limited precision, the COM motion removal implementation
* can cause the kinetic energy in the MD loop to differ by a few bits from
* the kinetic energy one would determine from state.v.
*/
typedef struct
{
gmx_bool bUpToDate;
int ekin_n;
tensor *ekinh;
tensor *ekinf;
tensor *ekinh_old;
tensor ekin_total;
double *ekinscalef_nhc;
double *ekinscaleh_nhc;
double *vscale_nhc;
real dekindl;
real mvcos;
} ekinstate_t;
/* energy history for delta_h histograms */
typedef struct
{
int nndh; /* the number of energy difference lists */
int *ndh; /* the number in each energy difference list */
real **dh; /* the energy difference lists */
double start_time; /* the start time of these energy diff blocks */
double start_lambda; /* lambda at start time */
gmx_bool start_lambda_set; /* whether the lambda value is set. Here
For backward-compatibility. */
} delta_h_history_t;
typedef struct
{
int nlambda; /* total number of lambda states - for history*/
gmx_bool bEquil; /* Have we reached equilibration */
int *n_at_lam; /* number of points observed at each lambda */
real *wl_histo; /* histogram for WL flatness determination */
real wl_delta; /* current wang-landau delta */
real *dfavg; /* used to update the free energy estimate for AIM */
real *sum_dvdl; /* used to update the sum of the derivative of the potential energy term at lambda */
real *store_fepot; /* store the potential energy at lambda */
int *aim_at_lam; /* number of points observed at each lambda after chosen*/
int *laccept; /* track lambda acceptance */
real *sum_weights; /* weights of the states */
real *sum_dg; /* free energies of the states -- not actually used for weighting, but informational */
real *sum_minvar; /* corrections to weights for minimum variance */
real *sum_variance; /* variances of the states */
real **accum_p; /* accumulated bennett weights for n+1 */
real **accum_m; /* accumulated bennett weights for n-1 */
real **accum_p2; /* accumulated squared bennett weights for n+1 */
real **accum_m2; /* accumulated squared bennett weights for n-1 */
real **Tij; /* transition matrix */
real **Tij_empirical; /* Empirical transition matrix */
} df_history_t;
typedef struct
{
gmx_int64_t nsteps; /* The number of steps in the history */
gmx_int64_t nsum; /* The nr. of steps in the ener_ave and ener_sum */
double * ener_ave; /* Energy term history sum to get fluctuations */
double * ener_sum; /* Energy term history sum to get fluctuations */
int nener; /* Number of energy terms in two previous arrays */
gmx_int64_t nsteps_sim; /* The number of steps in ener_sum_sim */
gmx_int64_t nsum_sim; /* The number of frames in ener_sum_sim */
double * ener_sum_sim; /* Energy term history sum of the whole sim */
delta_h_history_t *dht; /* The BAR energy differences */
}
energyhistory_t;
typedef struct
{
/* If one uses essential dynamics or flooding on a group of atoms from
* more than one molecule, we cannot make this group whole with
* do_pbc_first_mtop(). We assume that the ED group has the correct PBC
* representation at the beginning of the simulation and keep track
* of the shifts to always get it into that representation.
* For proper restarts from a checkpoint we store the positions of the
* reference group at the time of checkpoint writing */
gmx_bool bFromCpt; /* Did we start from a checkpoint file? */
int nED; /* No. of ED/Flooding data sets, if <1 no ED */
int *nref; /* No. of atoms in i'th reference structure */
int *nav; /* Same for average structure */
rvec **old_sref; /* Positions of the reference atoms
at the last time step (with correct PBC
representation) */
rvec **old_sref_p; /* Pointer to these positions */
rvec **old_sav; /* Same for the average positions */
rvec **old_sav_p;
}
edsamstate_t;
typedef struct
{
int eSwapCoords; /* Swapping along x, y, or z-direction? */
int nat_req[eCompNR][eIonNR]; /* Requested ion numbers per type an comp. */
int *nat_req_p[eCompNR][eIonNR]; /* Pointer to this data (for .cpt writing) */
int nAverage; /* Use average over this many swap attempt
steps when determining the ion counts */
int inflow_netto[eCompNR][eIonNR]; /* Flux determined from the # of swaps */
int *inflow_netto_p[eCompNR][eIonNR]; /* Pointer to this data */
int *nat_past[eCompNR][eIonNR]; /* Array with nAverage entries for history */
int *nat_past_p[eCompNR][eIonNR]; /* Pointer points to the first entry only */
/* Channel flux detection, this is counting only and has no influence on whether swaps
* are performed or not: */
int fluxfromAtoB[eCompNR][eIonNR]; /* Flux determined from the split cylinders */
int *fluxfromAtoB_p[eCompNR][eIonNR]; /* Pointer to this data */
int *fluxleak; /* Flux not going through any channel */
int nions; /* Size of the following arrays */
unsigned char *comp_from; /* Ion came from which compartment? */
unsigned char *channel_label; /* Through which channel did this ion pass? */
/* To also make multimeric channel proteins whole, we save the last whole configuration of
* the channels in the checkpoint file. If we have no checkpoint file, we assume that the
* starting configuration hast the correct PBC representation after making the individual
* molecules whole */
gmx_bool bFromCpt; /* Did we started from a checkpoint file? */
int nat[eChanNR]; /* Size of xc_old_whole, i.e. the number of
atoms in each channel */
rvec *xc_old_whole[eChanNR]; /* Last known whole positions of the two
channels (important for multimeric ch.!) */
rvec **xc_old_whole_p[eChanNR]; /* Pointer to these positions */
}
swapstate_t;
typedef struct
{
int natoms;
int ngtc;
int nnhpres;
int nhchainlength; /* number of nose-hoover chains */
int flags; /* Flags telling which entries are present */
int fep_state; /* indicates which of the alchemical states we are in */
real *lambda; /* lambda vector */
matrix box; /* box vector coordinates */
matrix box_rel; /* Relitaive box vectors to preserve shape */
matrix boxv; /* box velocitites for Parrinello-Rahman pcoupl */
matrix pres_prev; /* Pressure of the previous step for pcoupl */
matrix svir_prev; /* Shake virial for previous step for pcoupl */
matrix fvir_prev; /* Force virial of the previous step for pcoupl */
double *nosehoover_xi; /* for Nose-Hoover tcoupl (ngtc) */
double *nosehoover_vxi; /* for N-H tcoupl (ngtc) */
double *nhpres_xi; /* for Nose-Hoover pcoupl for barostat */
double *nhpres_vxi; /* for Nose-Hoover pcoupl for barostat */
double *therm_integral; /* for N-H/V-rescale tcoupl (ngtc) */
real veta; /* trotter based isotropic P-coupling */
real vol0; /* initial volume,required for computing NPT conserverd quantity */
int nalloc; /* Allocation size for x, v and sd_x when !=NULL*/
rvec *x; /* the coordinates (natoms) */
rvec *v; /* the velocities (natoms) */
rvec *sd_X; /* random part of the x update for stoch. dyn. */
rvec *cg_p; /* p vector for conjugate gradient minimization */
history_t hist; /* Time history for restraints */
ekinstate_t ekinstate; /* The state of the kinetic energy data */
energyhistory_t enerhist; /* Energy history for statistics */
swapstate_t swapstate; /* Position swapping */
df_history_t dfhist; /*Free energy history for free energy analysis */
edsamstate_t edsamstate; /* Essential dynamics / flooding history */
int ddp_count; /* The DD partitioning count for this state */
int ddp_count_cg_gl; /* The DD part. count for index_gl */
int ncg_gl; /* The number of local charge groups */
int *cg_gl; /* The global cg number of the local cgs */
int cg_gl_nalloc; /* Allocation size of cg_gl; */
} t_state;
typedef struct
{
double *Qinv; /* inverse mass of thermostat -- computed from inputs, but a good place to store */
double *QPinv; /* inverse mass of thermostat for barostat -- computed from inputs, but a good place to store */
double Winv; /* Pressure mass inverse -- computed, not input, but a good place to store. Need to make a matrix later */
tensor Winvm; /* inverse pressure mass tensor, computed */
} t_extmass;
typedef struct
{
real veta;
double rscale;
double vscale;
double rvscale;
double alpha;
double *vscale_nhc;
} t_vetavars;
#ifdef __cplusplus
}
#endif
#endif /* _state_h_ */