/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * 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,
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- * as published by the Free Software Foundation; either version 2
+ * 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.
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* To help us fund GROMACS development, we humbly ask that you cite
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*/
#ifndef _state_h_
#define _state_h_
-#include "simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/swap/enums.h"
#ifdef __cplusplus
extern "C" {
* Currently the random seeds for SD and BD are missing.
*/
-/* for now, define the length of the NH chains here */
-#define NHCHAINLENGTH 10
-#define MAXLAMBDAS 1024
-
/* These enums are used in flags as (1<<est...).
* The order of these enums should not be changed,
* since that affects the checkpoint (.cpt) file format.
*/
- enum { estLAMBDA,
- estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI, estTC_INT,
- estX, estV, estSDX, estCGP, estLD_RNG, estLD_RNGI,
- estDISRE_INITF, estDISRE_RM3TAV,
- estORIRE_INITF, estORIRE_DTAV,
- estSVIR_PREV, estNH_VXI, estVETA, estVOL0, estNHPRES_XI, estNHPRES_VXI, estFVIR_PREV,
- estFEPSTATE, estMC_RNG, estMC_RNGI,
- estNR };
+enum {
+ estLAMBDA,
+ estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI, estTC_INT,
+ estX, estV, estSDX, estCGP, estLD_RNG, estLD_RNGI,
+ estDISRE_INITF, estDISRE_RM3TAV,
+ estORIRE_INITF, estORIRE_DTAV,
+ estSVIR_PREV, estNH_VXI, estVETA, estVOL0, estNHPRES_XI, estNHPRES_VXI, estFVIR_PREV,
+ estFEPSTATE, estMC_RNG, estMC_RNGI,
+ estNR
+};
#define EST_DISTR(e) (!(((e) >= estLAMBDA && (e) <= estTC_INT) || ((e) >= estSVIR_PREV && (e) <= estMC_RNGI)))
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 */
+ 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.
*/
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;
+ 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 */
+ 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 */
+ 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;
+} delta_h_history_t;
typedef struct
{
- int nlambda; /* total number of lambda states - for history*/
+ int nlambda; /* total number of lambda states - for history*/
- gmx_bool bEquil; /* 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 */
+ 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 *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 *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 **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 */
- real **Tij; /* transition matrix */
- real **Tij_empirical; /* Empirical transition matrix */
} df_history_t;
typedef struct
{
- gmx_large_int_t nsteps; /* The number of steps in the history */
- gmx_large_int_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_large_int_t nsteps_sim; /* The number of steps in ener_sum_sim */
- gmx_large_int_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 */
+ 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
{
- int natoms;
- int ngtc;
- int nnhpres;
- int nhchainlength; /* number of nose-hoover chains */
- int nrng;
- int nrngi;
- 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 */
-
- unsigned int *ld_rng; /* RNG random state */
- int *ld_rngi; /* RNG index */
-
- int nmcrng; /* number of RNG states */
- unsigned int *mc_rng; /* lambda MC RNG random state */
- int *mc_rngi; /* lambda MC RNG index */
-
- history_t hist; /* Time history for restraints */
-
- ekinstate_t ekinstate; /* The state of the kinetic energy data */
-
- energyhistory_t enerhist; /* Energy history for statistics */
- df_history_t dfhist; /*Free energy history for free energy analysis */
-
- 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; */
+ /* 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 */
+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;
+{
+ real veta;
+ double rscale;
+ double vscale;
+ double rvscale;
+ double alpha;
+ double *vscale_nhc;
} t_vetavars;
#ifdef __cplusplus
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff