-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * 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.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * 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.
+ *
+ * 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.
*
- * If you want to redistribute modifications, 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 www.gromacs.org.
+ * 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.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * 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.
*
- * For more info, check our website at http://www.gromacs.org
+ * 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:
- * Gromacs Runs On Most of All Computer Systems
+ * 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 _mdebin_bar_h
#define _mdebin_bar_h
+#include "gromacs/legacyheaders/mdebin.h"
+
#ifdef __cplusplus
extern "C" {
#endif
+
/* The functions & data structures here describe writing
energy differences (or their histogram )for use with g_bar */
/* Data for one foreign lambda, or derivative. */
typedef struct
{
- real *dh; /* the raw energy difference data -- actually, store more in here. */
- float *dhf; /* raw difference data -- in floats, for storage. */
- unsigned int ndh; /* number of data points */
- unsigned int ndhmax; /* the maximum number of points */
-
- int nhist; /* the number of histograms. There can either be
- 0 (for no histograms)
- 1 (for 'foreign lambda' histograms)
- 2 (for derivative histograms: there's
- a 'forward' and 'backward' histogram
- containing the minimum and maximum
- values, respectively). */
- int *bin[2]; /* the histogram(s) */
- double dx; /* the histogram spacing in kJ/mol. This is the
- same for the two histograms? */
- unsigned int nbins; /* the number of bins in the histograms*/
- gmx_large_int_t x0[2]; /* the starting point in units of spacing
- of the histogram */
- unsigned int maxbin[2]; /* highest bin number with data */
-
- gmx_bool derivative; /* whether this delta_h contains derivatives */
- double lambda; /* current lambda */
- gmx_bool written; /* whether this data has already been written out */
-
- double subblock_d[4]; /* data for an mdebin subblock for I/O. */
- gmx_large_int_t subblock_l[4]; /* data for an mdebin subblock for I/O. */
- int subblock_i[4]; /* data for an mdebin subblock for I/O. */
+ real *dh; /* the raw energy data. */
+ float *dhf; /* raw difference data -- in floats, for storage. */
+ unsigned int ndh; /* number of data points */
+ unsigned int ndhmax; /* the maximum number of points */
+
+ int nhist; /* the number of histograms. There can either be
+ 0 (for no histograms)
+ 1 (for 'foreign lambda' histograms)
+ 2 (for derivative histograms: there's
+ a 'forward' and 'backward' histogram
+ containing the minimum and maximum
+ values, respectively). */
+ int *bin[2]; /* the histogram(s) */
+ double dx; /* the histogram spacing in kJ/mol. This is the
+ same for the two histograms? */
+ unsigned int nbins; /* the number of bins in the histograms*/
+ gmx_int64_t x0[2]; /* the starting point in units of spacing
+ of the histogram */
+ unsigned int maxbin[2]; /* highest bin number with data */
+
+ int type; /* the block type according to dhbtDH, etc. */
+ int derivative; /* The derivative direction (as an index in the lambda
+ vector) if this delta_h contains derivatives */
+ double *lambda; /* lambda vector (or NULL if not applicable) */
+ int nlambda; /* length of the lambda vector */
+ gmx_bool written; /* whether this data has already been written out */
+
+ gmx_int64_t subblock_meta_l[5]; /* metadata for an mdebin subblock for
+ I/O: for histogram counts, etc.*/
+ double *subblock_meta_d; /* metadata subblock for I/O, used for
+ communicating doubles (i.e. the lambda
+ vector) */
+ int subblock_meta_i[4]; /* metadata subblock for I/O, used for
+ communicating ints (i.e. derivative indices,
+ etc.) */
} t_mde_delta_h;
/* the type definition is in mdebin_bar.h */
struct t_mde_delta_h_coll
{
- t_mde_delta_h *dh; /* the delta h data */
- int ndh; /* the number of delta_h structures */
- double start_time; /* start time of the current dh collection */
- double delta_time; /* time difference between samples */
- gmx_bool start_time_set; /* whether the start time has been set */
- double start_lambda; /* starting lambda for continuous motion of state*/
- double delta_lambda; /* delta lambda, for continuous motion of state */
- double temperature; /* the temperature of the samples*/
- double subblock_d[5]; /* data for writing an mdebin subblock for I/O */
+ t_mde_delta_h *dh; /* the delta h data */
+ int ndh; /* the number of delta_h structures */
+
+ int nlambda; /* number of bar dU delta_h structures */
+ t_mde_delta_h *dh_du; /* the delta h data (pointer into dh) */
+
+ int ndhdl; /* number of bar dU delta_h structures */
+ t_mde_delta_h *dh_dhdl; /* the dhdl data (pointer into dh) */
+
+ t_mde_delta_h *dh_energy; /* energy output block (pointer into dh) */
+ t_mde_delta_h *dh_pv; /* pV output block (pointer into dh) */
+ t_mde_delta_h *dh_expanded; /* expanded ensemble output block (pointer
+ into dh) */
+
+ double start_time; /* start time of the current dh collection */
+ double delta_time; /* time difference between samples */
+ gmx_bool start_time_set; /* whether the start time has been set */
+ double start_lambda; /* starting lambda for continuous motion of state*/
+ double delta_lambda; /* delta lambda, for continuous motion of state */
+ double temperature; /* the temperature of the samples*/
+
+ double *native_lambda_vec; /* The lambda vector describing the current
+ lambda state if it is set (NULL otherwise) */
+ int n_lambda_vec; /* the size of the native lambda vector */
+ int *native_lambda_components; /* the native lambda (and by extension,
+ foreign lambda) components in terms
+ of efptFEP, efptMASS, etc. */
+ int lambda_index; /* the lambda_fep_state */
+
+ double *subblock_d; /* for writing a metadata mdebin subblock for I/O */
+ int *subblock_i; /* for writing a metadata mdebin subblock for I/O */
+
+ double *lambda_vec_subblock; /* native lambda vector data subblock for
+ I/O */
+ int *lambda_index_subblock; /* lambda vector index data subblock for I/O */
};
ir = the input record */
void mde_delta_h_coll_init(t_mde_delta_h_coll *dhc,
- const t_inputrec *ir);
+ const t_inputrec *ir);
/* add a bunch of samples to the delta_h collection
dhc = the collection
/* add a bunch of samples - note fep_state is double to allow for better data storage */
void mde_delta_h_coll_add_dh(t_mde_delta_h_coll *dhc,
- double fep_state,
- double energy,
- double pV,
- int bExpanded,
- int bPrintEnergy,
- int bPressure,
- int ndhdl,
- int nlambda,
- double *dhdl,
- double *foreign_dU,
- double time);
+ double fep_state,
+ double energy,
+ double pV,
+ double *dhdl,
+ double *foreign_dU,
+ double time);
/* write the data associated with the du blocks collection as a collection
of mdebin blocks.
/* set the energyhistory variables to save state */
void mde_delta_h_coll_update_energyhistory(t_mde_delta_h_coll *dhc,
- energyhistory_t *enerhist);
+ energyhistory_t *enerhist);
/* restore the variables from an energyhistory */
void mde_delta_h_coll_restore_energyhistory(t_mde_delta_h_coll *dhc,
- energyhistory_t *enerhist);
+ energyhistory_t *enerhist);
#ifdef __cplusplus
}
#endif
-#endif /* _mdebin_bar_h */
-
+#endif /* _mdebin_bar_h */