src/gromacs/mdlib/compute_io.cpp

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