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 */
 183