src/gromacs/mdlib/ebin.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "ebin.h"
  41
  42 #include <cmath>
  43 #include <cstring>
  44
  45 #include "gromacs/math/units.h"
  46 #include "gromacs/math/utilities.h"
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/topology/ifunc.h"
  49 #include "gromacs/trajectory/energyframe.h"
  50 #include "gromacs/utility/cstringutil.h"
  51 #include "gromacs/utility/fatalerror.h"
  52 #include "gromacs/utility/smalloc.h"
  53
  54 t_ebin *mk_ebin()
  55 {
  56     t_ebin *eb;
  57
  58     snew(eb, 1);
  59
  60     return eb;
  61 }
  62
  63 void done_ebin(t_ebin *eb)
  64 {
  65     for (int i = 0; i < eb->nener; i++)
  66     {
  67         sfree(eb->enm[i].name);
  68         sfree(eb->enm[i].unit);
  69     }
  70     sfree(eb->e);
  71     sfree(eb->e_sim);
  72     sfree(eb->enm);
  73 }
  74
  75 int get_ebin_space(t_ebin *eb, int nener, const char *const enm[], const char *unit)
  76 {
  77     int         index;
  78     int         i, f;
  79     const char *u;
  80
  81     index      = eb->nener;
  82     eb->nener += nener;
  83     srenew(eb->e, eb->nener);
  84     srenew(eb->e_sim, eb->nener);
  85     srenew(eb->enm, eb->nener);
  86     for (i = index; (i < eb->nener); i++)
  87     {
  88         eb->e[i].e        = 0;
  89         eb->e[i].eav      = 0;
  90         eb->e[i].esum     = 0;
  91         eb->e_sim[i].e    = 0;
  92         eb->e_sim[i].eav  = 0;
  93         eb->e_sim[i].esum = 0;
  94         eb->enm[i].name   = gmx_strdup(enm[i-index]);
  95         if (unit != nullptr)
  96         {
  97             eb->enm[i].unit = gmx_strdup(unit);
  98         }
  99         else
 100         {
 101             /* Determine the unit from the longname.
 102              * These units should have been defined in ifunc.c
 103              * But even better would be if all interactions functions
 104              * return energies and all non-interaction function
 105              * entries would be removed from the ifunc array.
 106              */
 107             u = unit_energy;
 108             for (f = 0; f < F_NRE; f++)
 109             {
 110                 if (strcmp(eb->enm[i].name,
 111                            interaction_function[f].longname) == 0)
 112                 {
 113                     /* Only the terms in this list are not energies */
 114                     switch (f)
 115                     {
 116                         case F_DISRESVIOL: u = unit_length;   break;
 117                         case F_ORIRESDEV:  u = "obs";         break;
 118                         case F_TEMP:       u = unit_temp_K;   break;
 119                         case F_PDISPCORR:
 120                         case F_PRES:       u = unit_pres_bar; break;
 121                     }
 122                 }
 123             }
 124             eb->enm[i].unit = gmx_strdup(u);
 125         }
 126     }
 127
 128     return index;
 129 }
 130
 131 void add_ebin(t_ebin *eb, int index, int nener, const real ener[], gmx_bool bSum)
 132 {
 133     int       i, m;
 134     double    e, invmm, diff;
 135     t_energy *eg, *egs;
 136
 137     if ((index+nener > eb->nener) || (index < 0))
 138     {
 139         gmx_fatal(FARGS, "%s-%d: Energies out of range: index=%d nener=%d maxener=%d",
 140                   __FILE__, __LINE__, index, nener, eb->nener);
 141     }
 142
 143     eg = &(eb->e[index]);
 144
 145     for (i = 0; (i < nener); i++)
 146     {
 147         eg[i].e      = ener[i];
 148     }
 149
 150     if (bSum)
 151     {
 152         egs = &(eb->e_sim[index]);
 153
 154         m = eb->nsum;
 155
 156         if (m == 0)
 157         {
 158             for (i = 0; (i < nener); i++)
 159             {
 160                 eg[i].eav    = 0;
 161                 eg[i].esum   = ener[i];
 162                 egs[i].esum += ener[i];
 163             }
 164         }
 165         else
 166         {
 167             invmm = (1.0/m)/(m+1.0);
 168
 169             for (i = 0; (i < nener); i++)
 170             {
 171                 /* Value for this component */
 172                 e = ener[i];
 173
 174                 /* first update sigma, then sum */
 175                 diff         = eg[i].esum - m*e;
 176                 eg[i].eav   += diff*diff*invmm;
 177                 eg[i].esum  += e;
 178                 egs[i].esum += e;
 179             }
 180         }
 181     }
 182 }
 183
 184 void ebin_increase_count(t_ebin *eb, gmx_bool bSum)
 185 {
 186     eb->nsteps++;
 187     eb->nsteps_sim++;
 188
 189     if (bSum)
 190     {
 191         eb->nsum++;
 192         eb->nsum_sim++;
 193     }
 194 }
 195
 196 void reset_ebin_sums(t_ebin *eb)
 197 {
 198     eb->nsteps = 0;
 199     eb->nsum   = 0;
 200     /* The actual sums are cleared when the next frame is stored */
 201 }
 202
 203 void pr_ebin(FILE *fp, t_ebin *eb, int index, int nener, int nperline,
 204              int prmode, gmx_bool bPrHead)
 205 {
 206     int  i, j, i0;
 207     int  rc;
 208     char buf[30];
 209
 210     rc = 0;
 211
 212     if (index < 0 || index > eb->nener)
 213     {
 214         gmx_fatal(FARGS, "Invalid index in pr_ebin: %d", index);
 215     }
 216     int start = index;
 217     if (nener > eb->nener)
 218     {
 219         gmx_fatal(FARGS, "Invalid nener in pr_ebin: %d", nener);
 220     }
 221     int end = eb->nener;
 222     if (nener != -1)
 223     {
 224         end = index + nener;
 225     }
 226     for (i = start; (i < end) && rc >= 0; )
 227     {
 228         if (bPrHead)
 229         {
 230             i0 = i;
 231             for (j = 0; (j < nperline) && (i < end) && rc >= 0; j++, i++)
 232             {
 233                 if (strncmp(eb->enm[i].name, "Pres", 4) == 0)
 234                 {
 235                     /* Print the pressure unit to avoid confusion */
 236                     sprintf(buf, "%s (%s)", eb->enm[i].name, unit_pres_bar);
 237                     rc = fprintf(fp, "%15s", buf);
 238                 }
 239                 else
 240                 {
 241                     rc = fprintf(fp, "%15s", eb->enm[i].name);
 242                 }
 243             }
 244
 245             if (rc >= 0)
 246             {
 247                 rc = fprintf(fp, "\n");
 248             }
 249
 250             i = i0;
 251         }
 252         for (j = 0; (j < nperline) && (i < end) && rc >= 0; j++, i++)
 253         {
 254             switch (prmode)
 255             {
 256                 case eprNORMAL:
 257                     rc = fprintf(fp, "   %12.5e", eb->e[i].e);
 258                     break;
 259                 case eprAVER:
 260                     if (eb->nsum_sim > 0)
 261                     {
 262                         rc = fprintf(fp, "   %12.5e", eb->e_sim[i].esum/eb->nsum_sim);
 263                     }
 264                     else
 265                     {
 266                         rc = fprintf(fp, "    %-12s", "N/A");
 267                     }
 268                     break;
 269                 default: gmx_fatal(FARGS, "Invalid print mode %d in pr_ebin",
 270                                    prmode);
 271             }
 272
 273         }
 274         if (rc >= 0)
 275         {
 276             rc = fprintf(fp, "\n");
 277         }
 278     }
 279     if (rc < 0)
 280     {
 281         gmx_fatal(FARGS, "Cannot write to logfile; maybe you are out of disk space?");
 282     }
 283 }