include/mdebin.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gromacs Runs On Most of All Computer Systems
  34  */
  35
  36 #ifndef _mdebin_h
  37 #define _mdebin_h
  38
  39 #include "typedefs.h"
  40 #include "sysstuff.h"
  41 #include "ebin.h"
  42 #include "enxio.h"
  43 #include "types/state.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 /* The functions & data structures here determine the content for outputting
  50    the .edr file; the file format and actual writing is done with functions
  51    defined in enxio.h */
  52
  53 /* forward declaration */
  54 typedef struct t_mde_delta_h_coll t_mde_delta_h_coll;
  55
  56 /* This is the collection of energy averages collected during mdrun, and to
  57    be written out to the .edr file. */
  58 typedef struct {
  59   double delta_t;
  60   t_ebin *ebin;
  61   int    ie,iconrmsd,ib,ivol,idens,ipv,ienthalpy;
  62   int    isvir,ifvir,ipres,ivir,isurft,ipc,itemp,itc,itcb,iu,imu;
  63   int    ivcos,ivisc;
  64   int    nE,nEg,nEc,nTC,nTCP,nU,nNHC;
  65   int    *igrp;
  66   char   **grpnms;
  67   int    mde_n,mdeb_n;
  68   real   *tmp_r;
  69   rvec   *tmp_v;
  70   gmx_bool   bConstr;
  71   gmx_bool   bConstrVir;
  72   gmx_bool   bTricl;
  73   gmx_bool   bDynBox;
  74   gmx_bool   bNHC_trotter;
  75   gmx_bool   bPrintNHChains;
  76   gmx_bool   bMTTK;
  77   gmx_bool   bMu; /* true if dipole is calculated */
  78   gmx_bool   bDiagPres;
  79   gmx_bool   bVir;
  80   gmx_bool   bPress;
  81   gmx_bool   bSurft;
  82   int    f_nre;
  83   int    epc;
  84   real   ref_p;
  85   int    etc;
  86   int    nCrmsd;
  87   gmx_bool   bEner[F_NRE];
  88   gmx_bool   bEInd[egNR];
  89   char   **print_grpnms;
  90
  91   FILE   *fp_dhdl; /* the dhdl.xvg output file */
  92   t_mde_delta_h_coll *dhc; /* the delta U components (raw data + histogram) */
  93   real *temperatures;
  94 } t_mdebin;
  95
  96 t_mdebin *init_mdebin(ener_file_t fp_ene,
  97                              const gmx_mtop_t *mtop,
  98                              const t_inputrec *ir,
  99                              FILE *fp_dhdl);
 100 /* Initiate MD energy bin and write header to energy file. */
 101
 102 FILE *open_dhdl(const char *filename,const t_inputrec *ir,
 103                        const output_env_t oenv);
 104 /* Open the dhdl file for output */
 105
 106 /* update the averaging structures. Called every time
 107    the energies are evaluated. */
 108 void upd_mdebin(t_mdebin *md,
 109         gmx_bool bDoDHDL,
 110         gmx_bool bSum,
 111         double time,
 112         real tmass,
 113         gmx_enerdata_t *enerd,
 114         t_state *state,
 115         t_lambda *fep,
 116         t_expanded *expand,
 117         matrix  lastbox,
 118         tensor svir,
 119         tensor fvir,
 120         tensor vir,
 121         tensor pres,
 122         gmx_ekindata_t *ekind,
 123         rvec mu_tot,
 124         gmx_constr_t constr);
 125
 126 void upd_mdebin_step(t_mdebin *md);
 127 /* Updates only the step count in md */
 128
 129 void print_ebin_header(FILE *log,gmx_large_int_t steps,double time,real lamb);
 130
 131 void print_ebin(ener_file_t fp_ene,gmx_bool bEne,gmx_bool bDR,gmx_bool bOR,
 132                        FILE *log,
 133                        gmx_large_int_t step,double time,
 134                        int mode,gmx_bool bCompact,
 135                        t_mdebin *md,t_fcdata *fcd,
 136                        gmx_groups_t *groups,t_grpopts *opts);
 137
 138
 139
 140 /* Between .edr writes, the averages are history dependent,
 141    and that history needs to be retained in checkpoints.
 142    These functions set/read the energyhistory_t structure
 143    that is written to checkpoints in checkpoint.c */
 144
 145 /* Set the energyhistory_t data structure from a mdebin structure */
 146 void update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin);
 147
 148 /* Read the energyhistory_t data structure to a mdebin structure*/
 149 void restore_energyhistory_from_state(t_mdebin * mdebin,
 150                                              energyhistory_t * enerhist);
 151
 152 #ifdef __cplusplus
 153 }
 154 #endif
 155
 156 #endif  /* _mdebin_h */
 157