src/gromacs/legacyheaders/mdebin.h

   1 /*
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  37
  38 #ifndef _mdebin_h
  39 #define _mdebin_h
  40
  41 #include <stdio.h>
  42
  43 #include "gromacs/fileio/enxio.h"
  44 #include "gromacs/legacyheaders/ebin.h"
  45 #include "gromacs/legacyheaders/typedefs.h"
  46 #include "gromacs/legacyheaders/types/state.h"
  47
  48 struct gmx_constr;
  49 struct gmx_ekindata_t;
  50 struct gmx_output_env_t;
  51
  52 #ifdef __cplusplus
  53 extern "C" {
  54 #endif
  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 {
  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     gmx_bool            bVir;
  88     gmx_bool            bPress;
  89     gmx_bool            bSurft;
  90     int                 f_nre;
  91     int                 epc;
  92     real                ref_p;
  93     int                 etc;
  94     int                 nCrmsd;
  95     gmx_bool            bEner[F_NRE];
  96     gmx_bool            bEInd[egNR];
  97     char              **print_grpnms;
  98
  99     FILE               *fp_dhdl; /* the dhdl.xvg output file */
 100     double             *dE;      /* energy components for dhdl.xvg output */
 101     t_mde_delta_h_coll *dhc;     /* the delta U components (raw data + histogram) */
 102     real               *temperatures;
 103 } t_mdebin;
 104
 105
 106 /* delta_h block type enum: the kinds of energies written out. */
 107 enum
 108 {
 109     dhbtDH   = 0, /* delta H BAR energy difference*/
 110     dhbtDHDL = 1, /* dH/dlambda derivative */
 111     dhbtEN,       /* System energy */
 112     dhbtPV,       /* pV term */
 113     dhbtEXPANDED, /* expanded ensemble statistics */
 114     dhbtNR
 115 };
 116
 117
 118
 119 t_mdebin *init_mdebin(ener_file_t       fp_ene,
 120                       const gmx_mtop_t *mtop,
 121                       const t_inputrec *ir,
 122                       FILE             *fp_dhdl);
 123 /* Initiate MD energy bin and write header to energy file. */
 124
 125 FILE *open_dhdl(const char *filename, const t_inputrec *ir,
 126                 const gmx_output_env_t *oenv);
 127 /* Open the dhdl file for output */
 128
 129 /* update the averaging structures. Called every time
 130    the energies are evaluated. */
 131 void upd_mdebin(t_mdebin                 *md,
 132                 gmx_bool                  bDoDHDL,
 133                 gmx_bool                  bSum,
 134                 double                    time,
 135                 real                      tmass,
 136                 gmx_enerdata_t           *enerd,
 137                 t_state                  *state,
 138                 t_lambda                 *fep,
 139                 t_expanded               *expand,
 140                 matrix                    lastbox,
 141                 tensor                    svir,
 142                 tensor                    fvir,
 143                 tensor                    vir,
 144                 tensor                    pres,
 145                 struct gmx_ekindata_t    *ekind,
 146                 rvec                      mu_tot,
 147                 struct gmx_constr        *constr);
 148
 149 void upd_mdebin_step(t_mdebin *md);
 150 /* Updates only the step count in md */
 151
 152 void print_ebin_header(FILE *log, gmx_int64_t steps, double time, real lamb);
 153
 154 void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
 155                 FILE *log,
 156                 gmx_int64_t step, double time,
 157                 int mode, gmx_bool bCompact,
 158                 t_mdebin *md, t_fcdata *fcd,
 159                 gmx_groups_t *groups, t_grpopts *opts);
 160
 161
 162
 163 /* Between .edr writes, the averages are history dependent,
 164    and that history needs to be retained in checkpoints.
 165    These functions set/read the energyhistory_t structure
 166    that is written to checkpoints in checkpoint.c */
 167
 168 /* Set the energyhistory_t data structure from a mdebin structure */
 169 void update_energyhistory(energyhistory_t * enerhist, t_mdebin * mdebin);
 170
 171 /* Read the energyhistory_t data structure to a mdebin structure*/
 172 void restore_energyhistory_from_state(t_mdebin        * mdebin,
 173                                       energyhistory_t * enerhist);
 174
 175 #ifdef __cplusplus
 176 }
 177 #endif
 178
 179 #endif  /* _mdebin_h */