2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
37 #ifndef GMX_MDLIB_MDEBIN_H
38 #define GMX_MDLIB_MDEBIN_H
42 #include "gromacs/fileio/enxio.h"
43 #include "gromacs/mdlib/ebin.h"
44 #include "gromacs/mdtypes/forcerec.h"
46 class energyhistory_t;
47 struct gmx_ekindata_t;
49 struct gmx_output_env_t;
62 /* The functions & data structures here determine the content for outputting
63 the .edr file; the file format and actual writing is done with functions
66 /* forward declaration */
67 typedef struct t_mde_delta_h_coll t_mde_delta_h_coll;
70 /* This is the collection of energy averages collected during mdrun, and to
71 be written out to the .edr file. */
72 typedef struct t_mdebin {
75 int ie, iconrmsd, ib, ivol, idens, ipv, ienthalpy;
76 int isvir, ifvir, ipres, ivir, isurft, ipc, itemp, itc, itcb, iu, imu;
78 int nE, nEg, nEc, nTC, nTCP, nU, nNHC;
87 gmx_bool bNHC_trotter;
88 gmx_bool bPrintNHChains;
90 gmx_bool bMu; /* true if dipole is calculated */
97 gmx_bool bEner[F_NRE];
101 FILE *fp_dhdl; /* the dhdl.xvg output file */
102 double *dE; /* energy components for dhdl.xvg output */
103 t_mde_delta_h_coll *dhc; /* the delta U components (raw data + histogram) */
108 /* delta_h block type enum: the kinds of energies written out. */
111 dhbtDH = 0, /* delta H BAR energy difference*/
112 dhbtDHDL = 1, /* dH/dlambda derivative */
113 dhbtEN, /* System energy */
114 dhbtPV, /* pV term */
115 dhbtEXPANDED, /* expanded ensemble statistics */
121 t_mdebin *init_mdebin(ener_file_t fp_ene,
122 const gmx_mtop_t *mtop,
123 const t_inputrec *ir,
125 /* Initiate MD energy bin and write header to energy file. */
128 void done_mdebin(t_mdebin *mdebin);
130 FILE *open_dhdl(const char *filename, const t_inputrec *ir,
131 const gmx_output_env_t *oenv);
132 /* Open the dhdl file for output */
134 /* update the averaging structures. Called every time
135 the energies are evaluated. */
136 void upd_mdebin(t_mdebin *md,
141 gmx_enerdata_t *enerd,
150 gmx_ekindata_t *ekind,
152 const gmx::Constraints *constr);
154 void upd_mdebin_step(t_mdebin *md);
155 /* Updates only the step count in md */
157 void print_ebin_header(FILE *log, gmx_int64_t steps, double time);
159 void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
161 gmx_int64_t step, double time,
163 t_mdebin *md, t_fcdata *fcd,
164 gmx_groups_t *groups, t_grpopts *opts,
169 /* Between .edr writes, the averages are history dependent,
170 and that history needs to be retained in checkpoints.
171 These functions set/read the energyhistory_t class
172 that is written to checkpoints in checkpoint.c */
174 /* Set the energyhistory_t data from a mdebin structure */
175 void update_energyhistory(energyhistory_t * enerhist, const t_mdebin * mdebin);
177 /* Read the energyhistory_t data to a mdebin structure*/
178 void restore_energyhistory_from_state(t_mdebin * mdebin,
179 const energyhistory_t * enerhist);