src/gromacs/mdlib/compute_io.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "compute_io.h"
  40
  41 #include <signal.h>
  42 #include <stdlib.h>
  43
  44 #include "gromacs/mdtypes/inputrec.h"
  45 #include "gromacs/mdtypes/md_enums.h"
  46 #include "gromacs/mdtypes/pull-params.h"
  47 #include "gromacs/topology/topology.h"
  48
  49 static int div_nsteps(int nsteps, int nst)
  50 {
  51     if (nst > 0)
  52     {
  53         return (1 + nsteps + nst - 1)/nst;
  54     }
  55     else
  56     {
  57         return 0;
  58     }
  59 }
  60
  61 double compute_io(t_inputrec *ir, int natoms, gmx_groups_t *groups,
  62                   int nrener, int nrepl)
  63 {
  64
  65     int    nsteps = ir->nsteps;
  66     int    i, nxtcatoms = 0;
  67     int    nstx, nstv, nstf, nste, nstlog, nstxtc;
  68     double cio;
  69
  70     nstx   = div_nsteps(nsteps, ir->nstxout);
  71     nstv   = div_nsteps(nsteps, ir->nstvout);
  72     nstf   = div_nsteps(nsteps, ir->nstfout);
  73     nstxtc = div_nsteps(nsteps, ir->nstxout_compressed);
  74     if (ir->nstxout_compressed > 0)
  75     {
  76         for (i = 0; i < natoms; i++)
  77         {
  78             if (groups->grpnr[egcCompressedX] == nullptr || groups->grpnr[egcCompressedX][i] == 0)
  79             {
  80                 nxtcatoms++;
  81             }
  82         }
  83     }
  84     nstlog = div_nsteps(nsteps, ir->nstlog);
  85     /* We add 2 for the header */
  86     nste   = div_nsteps(2+nsteps, ir->nstenergy);
  87
  88     cio  = 80*natoms;
  89     cio += (nstx+nstf+nstv)*sizeof(real)*(3.0*natoms);
  90     cio += nstxtc*(14*4 + nxtcatoms*5.0); /* roughly 5 bytes per atom */
  91     cio += nstlog*(nrener*16*2.0);        /* 16 bytes per energy term plus header */
  92     /* t_energy contains doubles, but real is written to edr */
  93     cio += (1.0*nste)*nrener*3*sizeof(real);
  94
  95     if ((ir->efep != efepNO || ir->bSimTemp) && (ir->fepvals->nstdhdl > 0))
  96     {
  97         int ndh    = ir->fepvals->n_lambda;
  98         int ndhdl  = 0;
  99         int nchars = 0;
 100
 101         for (i = 0; i < efptNR; i++)
 102         {
 103             if (ir->fepvals->separate_dvdl[i])
 104             {
 105                 ndhdl += 1;
 106             }
 107         }
 108
 109         if (ir->fepvals->separate_dhdl_file == esepdhdlfileYES)
 110         {
 111             nchars = 8 + ndhdl*8 + ndh*10; /* time data ~8 chars/entry, dH data ~10 chars/entry */
 112             if (ir->expandedvals->elmcmove > elmcmoveNO)
 113             {
 114                 nchars += 5;   /* alchemical state */
 115             }
 116
 117             if (ir->fepvals->edHdLPrintEnergy != edHdLPrintEnergyNO)
 118             {
 119                 nchars += 12; /* energy for dhdl */
 120             }
 121             cio += div_nsteps(nsteps, ir->fepvals->nstdhdl)*nchars;
 122         }
 123         else
 124         {
 125             /* dH output to ener.edr: */
 126             if (ir->fepvals->dh_hist_size <= 0)
 127             {
 128                 int ndh_tot = ndh+ndhdl;
 129                 if (ir->expandedvals->elmcmove > elmcmoveNO)
 130                 {
 131                     ndh_tot += 1;
 132                 }
 133                 if (ir->fepvals->edHdLPrintEnergy != edHdLPrintEnergyNO)
 134                 {
 135                     ndh_tot += 1;
 136                 }
 137                 /* as data blocks: 1 real per dH point */
 138                 cio += div_nsteps(nsteps, ir->fepvals->nstdhdl)*ndh_tot*sizeof(real);
 139             }
 140             else
 141             {
 142                 /* as histograms: dh_hist_size ints per histogram */
 143                 cio += div_nsteps(nsteps, ir->nstenergy)*
 144                     sizeof(int)*ir->fepvals->dh_hist_size*ndh;
 145             }
 146         }
 147     }
 148     if (ir->pull != nullptr)
 149     {
 150         cio += div_nsteps(nsteps, ir->pull->nstxout)*20; /* roughly 20 chars per line */
 151         cio += div_nsteps(nsteps, ir->pull->nstfout)*20; /* roughly 20 chars per line */
 152     }
 153
 154     return cio*nrepl/(1024*1024);
 155 }