src/gromacs/mdlib/mdebin.h

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  37 #ifndef GMX_MDLIB_MDEBIN_H
  38 #define GMX_MDLIB_MDEBIN_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/fileio/enxio.h"
  43 #include "gromacs/mdlib/ebin.h"
  44 #include "gromacs/mdtypes/forcerec.h"
  45
  46 class energyhistory_t;
  47 struct gmx_constr;
  48 struct gmx_ekindata_t;
  49 struct gmx_mtop_t;
  50 struct gmx_output_env_t;
  51 struct t_expanded;
  52 struct t_fcdata;
  53 struct t_grpopts;
  54 struct t_lambda;
  55 class t_state;
  56
  57 /* The functions & data structures here determine the content for outputting
  58    the .edr file; the file format and actual writing is done with functions
  59    defined in enxio.h */
  60
  61 /* forward declaration */
  62 typedef struct t_mde_delta_h_coll t_mde_delta_h_coll;
  63
  64
  65 /* This is the collection of energy averages collected during mdrun, and to
  66    be written out to the .edr file. */
  67 typedef struct t_mdebin {
  68     double              delta_t;
  69     t_ebin             *ebin;
  70     int                 ie, iconrmsd, ib, ivol, idens, ipv, ienthalpy;
  71     int                 isvir, ifvir, ipres, ivir, isurft, ipc, itemp, itc, itcb, iu, imu;
  72     int                 ivcos, ivisc;
  73     int                 nE, nEg, nEc, nTC, nTCP, nU, nNHC;
  74     int                *igrp;
  75     char              **grpnms;
  76     int                 mde_n, mdeb_n;
  77     real               *tmp_r;
  78     rvec               *tmp_v;
  79     gmx_bool            bConstr;
  80     gmx_bool            bConstrVir;
  81     gmx_bool            bTricl;
  82     gmx_bool            bDynBox;
  83     gmx_bool            bNHC_trotter;
  84     gmx_bool            bPrintNHChains;
  85     gmx_bool            bMTTK;
  86     gmx_bool            bMu; /* true if dipole is calculated */
  87     gmx_bool            bDiagPres;
  88     int                 f_nre;
  89     int                 epc;
  90     real                ref_p;
  91     int                 etc;
  92     int                 nCrmsd;
  93     gmx_bool            bEner[F_NRE];
  94     gmx_bool            bEInd[egNR];
  95     char              **print_grpnms;
  96
  97     FILE               *fp_dhdl; /* the dhdl.xvg output file */
  98     double             *dE;      /* energy components for dhdl.xvg output */
  99     t_mde_delta_h_coll *dhc;     /* the delta U components (raw data + histogram) */
 100     real               *temperatures;
 101 } t_mdebin;
 102
 103
 104 /* delta_h block type enum: the kinds of energies written out. */
 105 enum
 106 {
 107     dhbtDH   = 0, /* delta H BAR energy difference*/
 108     dhbtDHDL = 1, /* dH/dlambda derivative */
 109     dhbtEN,       /* System energy */
 110     dhbtPV,       /* pV term */
 111     dhbtEXPANDED, /* expanded ensemble statistics */
 112     dhbtNR
 113 };
 114
 115
 116
 117 t_mdebin *init_mdebin(ener_file_t       fp_ene,
 118                       const gmx_mtop_t *mtop,
 119                       const t_inputrec *ir,
 120                       FILE             *fp_dhdl);
 121 /* Initiate MD energy bin and write header to energy file. */
 122
 123 FILE *open_dhdl(const char *filename, const t_inputrec *ir,
 124                 const gmx_output_env_t *oenv);
 125 /* Open the dhdl file for output */
 126
 127 /* update the averaging structures. Called every time
 128    the energies are evaluated. */
 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               *constr);
 146
 147 void upd_mdebin_step(t_mdebin *md);
 148 /* Updates only the step count in md */
 149
 150 void print_ebin_header(FILE *log, gmx_int64_t steps, double time);
 151
 152 void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
 153                 FILE *log,
 154                 gmx_int64_t step, double time,
 155                 int mode,
 156                 t_mdebin *md, t_fcdata *fcd,
 157                 gmx_groups_t *groups, t_grpopts *opts);
 158
 159
 160
 161 /* Between .edr writes, the averages are history dependent,
 162    and that history needs to be retained in checkpoints.
 163    These functions set/read the energyhistory_t class
 164    that is written to checkpoints in checkpoint.c */
 165
 166 /* Set the energyhistory_t data from a mdebin structure */
 167 void update_energyhistory(energyhistory_t * enerhist, const t_mdebin * mdebin);
 168
 169 /* Read the energyhistory_t data to a mdebin structure*/
 170 void restore_energyhistory_from_state(t_mdebin              * mdebin,
 171                                       const energyhistory_t * enerhist);
 172
 173 #endif