src/gromacs/mdlib/mdebin.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   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, 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.
  10  *
  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.
  15  *
  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.
  20  *
  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.
  25  *
  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.
  33  *
  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.
  36  */
  37 #ifndef GMX_MDLIB_MDEBIN_H
  38 #define GMX_MDLIB_MDEBIN_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/fileio/enxio.h"
  43 #include "gromacs/mdlib/ebin.h"
  44 #include "gromacs/mdtypes/forcerec.h"
  45 #include "gromacs/mdtypes/state.h"
  46
  47 struct gmx_constr;
  48 struct gmx_ekindata_t;
  49 struct gmx_mtop_t;
  50 struct gmx_output_env_t;
  51 struct t_expanded;
  52 struct t_fcdata;
  53 struct t_grpopts;
  54 struct t_lambda;
  55
  56 /* The functions & data structures here determine the content for outputting
  57    the .edr file; the file format and actual writing is done with functions
  58    defined in enxio.h */
  59
  60 /* forward declaration */
  61 typedef struct t_mde_delta_h_coll t_mde_delta_h_coll;
  62
  63
  64 /* This is the collection of energy averages collected during mdrun, and to
  65    be written out to the .edr file. */
  66 typedef struct t_mdebin {
  67     double              delta_t;
  68     t_ebin             *ebin;
  69     int                 ie, iconrmsd, ib, ivol, idens, ipv, ienthalpy;
  70     int                 isvir, ifvir, ipres, ivir, isurft, ipc, itemp, itc, itcb, iu, imu;
  71     int                 ivcos, ivisc;
  72     int                 nE, nEg, nEc, nTC, nTCP, nU, nNHC;
  73     int                *igrp;
  74     char              **grpnms;
  75     int                 mde_n, mdeb_n;
  76     real               *tmp_r;
  77     rvec               *tmp_v;
  78     gmx_bool            bConstr;
  79     gmx_bool            bConstrVir;
  80     gmx_bool            bTricl;
  81     gmx_bool            bDynBox;
  82     gmx_bool            bNHC_trotter;
  83     gmx_bool            bPrintNHChains;
  84     gmx_bool            bMTTK;
  85     gmx_bool            bMu; /* true if dipole is calculated */
  86     gmx_bool            bDiagPres;
  87     int                 f_nre;
  88     int                 epc;
  89     real                ref_p;
  90     int                 etc;
  91     int                 nCrmsd;
  92     gmx_bool            bEner[F_NRE];
  93     gmx_bool            bEInd[egNR];
  94     char              **print_grpnms;
  95
  96     FILE               *fp_dhdl; /* the dhdl.xvg output file */
  97     double             *dE;      /* energy components for dhdl.xvg output */
  98     t_mde_delta_h_coll *dhc;     /* the delta U components (raw data + histogram) */
  99     real               *temperatures;
 100 } t_mdebin;
 101
 102
 103 /* delta_h block type enum: the kinds of energies written out. */
 104 enum
 105 {
 106     dhbtDH   = 0, /* delta H BAR energy difference*/
 107     dhbtDHDL = 1, /* dH/dlambda derivative */
 108     dhbtEN,       /* System energy */
 109     dhbtPV,       /* pV term */
 110     dhbtEXPANDED, /* expanded ensemble statistics */
 111     dhbtNR
 112 };
 113
 114
 115
 116 t_mdebin *init_mdebin(ener_file_t       fp_ene,
 117                       const gmx_mtop_t *mtop,
 118                       const t_inputrec *ir,
 119                       FILE             *fp_dhdl);
 120 /* Initiate MD energy bin and write header to energy file. */
 121
 122 FILE *open_dhdl(const char *filename, const t_inputrec *ir,
 123                 const gmx_output_env_t *oenv);
 124 /* Open the dhdl file for output */
 125
 126 /* update the averaging structures. Called every time
 127    the energies are evaluated. */
 128 void upd_mdebin(t_mdebin                 *md,
 129                 gmx_bool                  bDoDHDL,
 130                 gmx_bool                  bSum,
 131                 double                    time,
 132                 real                      tmass,
 133                 gmx_enerdata_t           *enerd,
 134                 t_state                  *state,
 135                 t_lambda                 *fep,
 136                 t_expanded               *expand,
 137                 matrix                    lastbox,
 138                 tensor                    svir,
 139                 tensor                    fvir,
 140                 tensor                    vir,
 141                 tensor                    pres,
 142                 gmx_ekindata_t           *ekind,
 143                 rvec                      mu_tot,
 144                 gmx_constr               *constr);
 145
 146 void upd_mdebin_step(t_mdebin *md);
 147 /* Updates only the step count in md */
 148
 149 void print_ebin_header(FILE *log, gmx_int64_t steps, double time);
 150
 151 void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
 152                 FILE *log,
 153                 gmx_int64_t step, double time,
 154                 int mode,
 155                 t_mdebin *md, t_fcdata *fcd,
 156                 gmx_groups_t *groups, t_grpopts *opts);
 157
 158
 159
 160 /* Between .edr writes, the averages are history dependent,
 161    and that history needs to be retained in checkpoints.
 162    These functions set/read the energyhistory_t structure
 163    that is written to checkpoints in checkpoint.c */
 164
 165 /* Set the energyhistory_t data structure from a mdebin structure */
 166 void update_energyhistory(energyhistory_t * enerhist, t_mdebin * mdebin);
 167
 168 /* Read the energyhistory_t data structure to a mdebin structure*/
 169 void restore_energyhistory_from_state(t_mdebin        * mdebin,
 170                                       energyhistory_t * enerhist);
 171
 172 #endif