include/mdebin.h

   1 /*
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   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
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  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
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  15  * This program is free software; you can redistribute it and/or
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  35
  36 #ifndef _mdebin_h
  37 #define _mdebin_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include "typedefs.h"
  44 #include "sysstuff.h"
  45 #include "ebin.h"
  46 #include "enxio.h"
  47 #include "types/state.h"
  48
  49 #ifdef __cplusplus
  50 extern "C" {
  51 #endif
  52
  53 /* The functions & data structures here determine the content for outputting
  54    the .edr file; the file format and actual writing is done with functions
  55    defined in enxio.h */
  56
  57 /* forward declaration */
  58 typedef struct t_mde_delta_h_coll t_mde_delta_h_coll;
  59
  60 /* This is the collection of energy averages collected during mdrun, and to
  61    be written out to the .edr file. */
  62 typedef struct {
  63   double delta_t;
  64   t_ebin *ebin;
  65   int    ie,iconrmsd,ib,ivol,idens,ipv,ienthalpy;
  66   int    isvir,ifvir,ipres,ivir,isurft,ipc,itemp,itc,itcb,iu,imu;
  67   int    ivcos,ivisc;
  68   int    nE,nEg,nEc,nTC,nTCP,nU,nNHC;
  69   int    *igrp;
  70   char   **grpnms;
  71   int    mde_n,mdeb_n;
  72   real   *tmp_r;
  73   rvec   *tmp_v;
  74   bool   bConstr;
  75   bool   bConstrVir;
  76   bool   bTricl;
  77   bool   bDynBox;
  78   bool   bNHC_trotter;
  79   bool   bMTTK;
  80   int    f_nre;
  81   int    epc;
  82   tensor ref_p;
  83   int    etc;
  84   int    nCrmsd;
  85   bool   bEner[F_NRE];
  86   bool   bEInd[egNR];
  87   char   **print_grpnms;
  88
  89   FILE   *fp_dhdl; /* the dhdl.xvg output file */
  90   t_mde_delta_h_coll *dhc; /* the BAR delta U (raw data + histogram) */
  91 } t_mdebin;
  92
  93 extern t_mdebin *init_mdebin(ener_file_t fp_ene,
  94                              const gmx_mtop_t *mtop,
  95                              const t_inputrec *ir,
  96                              FILE *fp_dhdl);
  97 /* Initiate MD energy bin and write header to energy file. */
  98
  99 extern FILE *open_dhdl(const char *filename,const t_inputrec *ir,
 100                        const output_env_t oenv);
 101 /* Open the dhdl file for output */
 102
 103 /* update the averaging structures. Called every time
 104    the energies are evaluated. */
 105 extern void upd_mdebin(t_mdebin *md,
 106                        bool write_dhdl,
 107                        bool bSum,
 108                        double time,
 109                        real tmass,
 110                        gmx_enerdata_t *enerd,
 111                        t_state *state,
 112                        matrix  lastbox,
 113                        tensor svir,
 114                        tensor fvir,
 115                        tensor vir,
 116                        tensor pres,
 117                        gmx_ekindata_t *ekind,
 118                        rvec mu_tot,
 119                        gmx_constr_t constr);
 120
 121 extern void upd_mdebin_step(t_mdebin *md);
 122 /* Updates only the step count in md */
 123
 124 extern void print_ebin_header(FILE *log,gmx_large_int_t steps,double time,real lamb);
 125
 126 extern void print_ebin(ener_file_t fp_ene,bool bEne,bool bDR,bool bOR,
 127                        FILE *log,
 128                        gmx_large_int_t step,double time,
 129                        int mode,bool bCompact,
 130                        t_mdebin *md,t_fcdata *fcd,
 131                        gmx_groups_t *groups,t_grpopts *opts);
 132
 133
 134
 135 /* Between .edr writes, the averages are history dependent,
 136    and that history needs to be retained in checkpoints.
 137    These functions set/read the energyhistory_t structure
 138    that is written to checkpoints in checkpoint.c */
 139
 140 /* initialize the energyhistory_t data structure */
 141 extern void init_energyhistory(energyhistory_t * enerhist);
 142
 143 /* Set the energyhistory_t data structure from a mdebin structure */
 144 extern void update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin);
 145
 146 /* Read the energyhistory_t data structure to a mdebin structure*/
 147 extern void restore_energyhistory_from_state(t_mdebin * mdebin,
 148                                              energyhistory_t * enerhist);
 149
 150 #ifdef __cplusplus
 151 }
 152 #endif
 153
 154 #endif  /* _mdebin_h */
 155