/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * 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.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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-
- * This program is free software; you can redistribute it and/or
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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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+ * 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.
*
- * And Hey:
- * GRoups of Organic Molecules in ACtion for Science
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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.
}
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 nrng;
- int nrngi;
+ 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 */
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 */
+ swapstate_t swapstate; /* Position swapping */
df_history_t dfhist; /*Free energy history for free energy analysis */
edsamstate_t edsamstate; /* Essential dynamics / flooding history */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff