include/mdebin.h

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  38
  39 #ifndef _mdebin_h
  40 #define _mdebin_h
  41 #include "visibility.h"
  42 #include "typedefs.h"
  43 #include "sysstuff.h"
  44 #include "ebin.h"
  45 #include "enxio.h"
  46 #include "types/state.h"
  47
  48 #ifdef __cplusplus
  49 extern "C" {
  50 #endif
  51
  52 /* The functions & data structures here determine the content for outputting
  53    the .edr file; the file format and actual writing is done with functions
  54    defined in enxio.h */
  55
  56 /* forward declaration */
  57 typedef struct t_mde_delta_h_coll t_mde_delta_h_coll;
  58
  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     gmx_bool            bConstr;
  75     gmx_bool            bConstrVir;
  76     gmx_bool            bTricl;
  77     gmx_bool            bDynBox;
  78     gmx_bool            bNHC_trotter;
  79     gmx_bool            bPrintNHChains;
  80     gmx_bool            bMTTK;
  81     gmx_bool            bMu; /* true if dipole is calculated */
  82     gmx_bool            bDiagPres;
  83     gmx_bool            bVir;
  84     gmx_bool            bPress;
  85     gmx_bool            bSurft;
  86     int                 f_nre;
  87     int                 epc;
  88     real                ref_p;
  89     int                 etc;
  90     int                 nCrmsd;
  91     gmx_bool            bEner[F_NRE];
  92     gmx_bool            bEInd[egNR];
  93     char              **print_grpnms;
  94
  95     FILE               *fp_dhdl; /* the dhdl.xvg output file */
  96     double             *dE;      /* energy components for dhdl.xvg output */
  97     t_mde_delta_h_coll *dhc;     /* the delta U components (raw data + histogram) */
  98     real               *temperatures;
  99 } t_mdebin;
 100
 101
 102 /* delta_h block type enum: the kinds of energies written out. */
 103 enum
 104 {
 105     dhbtDH   = 0, /* delta H BAR energy difference*/
 106     dhbtDHDL = 1, /* dH/dlambda derivative */
 107     dhbtEN,       /* System energy */
 108     dhbtPV,       /* pV term */
 109     dhbtEXPANDED, /* expanded ensemble statistics */
 110     dhbtNR
 111 };
 112
 113
 114
 115 t_mdebin *init_mdebin(ener_file_t       fp_ene,
 116                       const gmx_mtop_t *mtop,
 117                       const t_inputrec *ir,
 118                       FILE             *fp_dhdl);
 119 /* Initiate MD energy bin and write header to energy file. */
 120
 121 GMX_LIBMD_EXPORT
 122 FILE *open_dhdl(const char *filename, const t_inputrec *ir,
 123                 const 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 GMX_LIBMD_EXPORT
 129 void upd_mdebin(t_mdebin       *md,
 130                 gmx_bool        bDoDHDL,
 131                 gmx_bool        bSum,
 132                 double          time,
 133                 real            tmass,
 134                 gmx_enerdata_t *enerd,
 135                 t_state        *state,
 136                 t_lambda       *fep,
 137                 t_expanded     *expand,
 138                 matrix          lastbox,
 139                 tensor          svir,
 140                 tensor          fvir,
 141                 tensor          vir,
 142                 tensor          pres,
 143                 gmx_ekindata_t *ekind,
 144                 rvec            mu_tot,
 145                 gmx_constr_t    constr);
 146
 147 GMX_LIBMD_EXPORT
 148 void upd_mdebin_step(t_mdebin *md);
 149 /* Updates only the step count in md */
 150
 151 GMX_LIBMD_EXPORT
 152 void print_ebin_header(FILE *log, gmx_large_int_t steps, double time, real lamb);
 153
 154 GMX_LIBMD_EXPORT
 155 void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
 156                 FILE *log,
 157                 gmx_large_int_t step, double time,
 158                 int mode, gmx_bool bCompact,
 159                 t_mdebin *md, t_fcdata *fcd,
 160                 gmx_groups_t *groups, t_grpopts *opts);
 161
 162
 163
 164 /* Between .edr writes, the averages are history dependent,
 165    and that history needs to be retained in checkpoints.
 166    These functions set/read the energyhistory_t structure
 167    that is written to checkpoints in checkpoint.c */
 168
 169 /* Set the energyhistory_t data structure from a mdebin structure */
 170 GMX_LIBMD_EXPORT
 171 void update_energyhistory(energyhistory_t * enerhist, t_mdebin * mdebin);
 172
 173 /* Read the energyhistory_t data structure to a mdebin structure*/
 174 GMX_LIBMD_EXPORT
 175 void restore_energyhistory_from_state(t_mdebin        * mdebin,
 176                                       energyhistory_t * enerhist);
 177
 178 #ifdef __cplusplus
 179 }
 180 #endif
 181
 182 #endif  /* _mdebin_h */