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/enerdata.h"
  45
  46 class energyhistory_t;
  47 struct gmx_ekindata_t;
  48 struct gmx_enerdata_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 namespace gmx
  58 {
  59 class Awh;
  60 class Constraints;
  61 }
  62
  63 extern const char *egrp_nm[egNR+1];
  64
  65 /* The functions & data structures here determine the content for outputting
  66    the .edr file; the file format and actual writing is done with functions
  67    defined in enxio.h */
  68
  69 /* forward declaration */
  70 typedef struct t_mde_delta_h_coll t_mde_delta_h_coll;
  71
  72
  73 /* This is the collection of energy averages collected during mdrun, and to
  74    be written out to the .edr file. */
  75 typedef struct t_mdebin {
  76     double              delta_t;
  77     t_ebin             *ebin;
  78     int                 ie, iconrmsd, ib, ivol, idens, ipv, ienthalpy;
  79     int                 isvir, ifvir, ipres, ivir, isurft, ipc, itemp, itc, itcb, iu, imu;
  80     int                 ivcos, ivisc;
  81     int                 nE, nEg, nEc, nTC, nTCP, nU, nNHC;
  82     int                *igrp;
  83     int                 mde_n, mdeb_n;
  84     real               *tmp_r;
  85     rvec               *tmp_v;
  86     gmx_bool            bConstr;
  87     gmx_bool            bConstrVir;
  88     gmx_bool            bTricl;
  89     gmx_bool            bDynBox;
  90     gmx_bool            bNHC_trotter;
  91     gmx_bool            bPrintNHChains;
  92     gmx_bool            bMTTK;
  93     gmx_bool            bMu; /* true if dipole is calculated */
  94     gmx_bool            bDiagPres;
  95     gmx_bool            bPres;
  96     int                 f_nre;
  97     int                 epc;
  98     real                ref_p;
  99     int                 etc;
 100     int                 nCrmsd;
 101     gmx_bool            bEner[F_NRE];
 102     gmx_bool            bEInd[egNR];
 103     char              **print_grpnms;
 104
 105     FILE               *fp_dhdl; /* the dhdl.xvg output file */
 106     double             *dE;      /* energy components for dhdl.xvg output */
 107     t_mde_delta_h_coll *dhc;     /* the delta U components (raw data + histogram) */
 108     real               *temperatures;
 109 } t_mdebin;
 110
 111
 112 /* delta_h block type enum: the kinds of energies written out. */
 113 enum
 114 {
 115     dhbtDH   = 0, /* delta H BAR energy difference*/
 116     dhbtDHDL = 1, /* dH/dlambda derivative */
 117     dhbtEN,       /* System energy */
 118     dhbtPV,       /* pV term */
 119     dhbtEXPANDED, /* expanded ensemble statistics */
 120     dhbtNR
 121 };
 122
 123
 124
 125 t_mdebin *init_mdebin(ener_file_t       fp_ene,
 126                       const gmx_mtop_t *mtop,
 127                       const t_inputrec *ir,
 128                       FILE             *fp_dhdl,
 129                       bool              isRerun = false);
 130 /* Initiate MD energy bin and write header to energy file. */
 131
 132 //! Destroy mdebin
 133 void done_mdebin(t_mdebin *mdebin);
 134
 135 FILE *open_dhdl(const char *filename, const t_inputrec *ir,
 136                 const gmx_output_env_t *oenv);
 137 /* Open the dhdl file for output */
 138
 139 /* update the averaging structures. Called every time
 140    the energies are evaluated. */
 141 void upd_mdebin(t_mdebin                 *md,
 142                 gmx_bool                  bDoDHDL,
 143                 gmx_bool                  bSum,
 144                 double                    time,
 145                 real                      tmass,
 146                 gmx_enerdata_t           *enerd,
 147                 t_state                  *state,
 148                 t_lambda                 *fep,
 149                 t_expanded               *expand,
 150                 matrix                    lastbox,
 151                 tensor                    svir,
 152                 tensor                    fvir,
 153                 tensor                    vir,
 154                 tensor                    pres,
 155                 gmx_ekindata_t           *ekind,
 156                 rvec                      mu_tot,
 157                 const gmx::Constraints   *constr);
 158
 159 void upd_mdebin_step(t_mdebin *md);
 160 /* Updates only the step count in md */
 161
 162 void print_ebin_header(FILE *log, int64_t steps, double time);
 163
 164 void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
 165                 FILE *log,
 166                 int64_t step, double time,
 167                 int mode,
 168                 t_mdebin *md, t_fcdata *fcd,
 169                 gmx_groups_t *groups, t_grpopts *opts,
 170                 gmx::Awh *awh);
 171
 172
 173
 174 /* Between .edr writes, the averages are history dependent,
 175    and that history needs to be retained in checkpoints.
 176    These functions set/read the energyhistory_t class
 177    that is written to checkpoints in checkpoint.c */
 178
 179 /* Set the energyhistory_t data from a mdebin structure */
 180 void update_energyhistory(energyhistory_t * enerhist, const t_mdebin * mdebin);
 181
 182 /* Read the energyhistory_t data to a mdebin structure*/
 183 void restore_energyhistory_from_state(t_mdebin              * mdebin,
 184                                       const energyhistory_t * enerhist);
 185
 186 #endif