include/mdebin.h

   1 /*
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  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   bMTTK;
  76   gmx_bool   bDiagPres;
  77   gmx_bool   bVir;
  78   gmx_bool   bPress;
  79   gmx_bool   bSurft;
  80   gmx_bool   bMu;
  81   int    f_nre;
  82   int    epc;
  83   real   ref_p;
  84   int    etc;
  85   int    nCrmsd;
  86   gmx_bool   bEner[F_NRE];
  87   gmx_bool   bEInd[egNR];
  88   char   **print_grpnms;
  89
  90   FILE   *fp_dhdl; /* the dhdl.xvg output file */
  91   gmx_bool dhdl_derivatives; /* whether to write the derivatives to dhdl.xvg */
  92   t_mde_delta_h_coll *dhc; /* the BAR delta U (raw data + histogram) */
  93 } t_mdebin;
  94
  95 t_mdebin *init_mdebin(ener_file_t fp_ene,
  96                              const gmx_mtop_t *mtop,
  97                              const t_inputrec *ir,
  98                              FILE *fp_dhdl);
  99 /* Initiate MD energy bin and write header to energy file. */
 100
 101 FILE *open_dhdl(const char *filename,const t_inputrec *ir,
 102                        const output_env_t oenv);
 103 /* Open the dhdl file for output */
 104
 105 /* update the averaging structures. Called every time
 106    the energies are evaluated. */
 107 void upd_mdebin(t_mdebin *md,
 108                        gmx_bool write_dhdl,
 109                        gmx_bool bSum,
 110                        double time,
 111                        real tmass,
 112                        gmx_enerdata_t *enerd,
 113                        t_state *state,
 114                        matrix  lastbox,
 115                        tensor svir,
 116                        tensor fvir,
 117                        tensor vir,
 118                        tensor pres,
 119                        gmx_ekindata_t *ekind,
 120                        rvec mu_tot,
 121                        gmx_constr_t constr);
 122
 123 void upd_mdebin_step(t_mdebin *md);
 124 /* Updates only the step count in md */
 125
 126 void print_ebin_header(FILE *log,gmx_large_int_t steps,double time,real lamb);
 127
 128 void print_ebin(ener_file_t fp_ene,gmx_bool bEne,gmx_bool bDR,gmx_bool bOR,
 129                        FILE *log,
 130                        gmx_large_int_t step,double time,
 131                        int mode,gmx_bool bCompact,
 132                        t_mdebin *md,t_fcdata *fcd,
 133                        gmx_groups_t *groups,t_grpopts *opts);
 134
 135
 136
 137 /* Between .edr writes, the averages are history dependent,
 138    and that history needs to be retained in checkpoints.
 139    These functions set/read the energyhistory_t structure
 140    that is written to checkpoints in checkpoint.c */
 141
 142 /* Set the energyhistory_t data structure from a mdebin structure */
 143 void update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin);
 144
 145 /* Read the energyhistory_t data structure to a mdebin structure*/
 146 void restore_energyhistory_from_state(t_mdebin * mdebin,
 147                                              energyhistory_t * enerhist);
 148
 149 #ifdef __cplusplus
 150 }
 151 #endif
 152
 153 #endif  /* _mdebin_h */
 154