src/gromacs/mdlib/ebin.cpp

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  38 /* This file is completely threadsafe - keep it that way! */
  39 #include "gmxpre.h"
  40
  41 #include "ebin.h"
  42
  43 #include <cmath>
  44 #include <cstring>
  45
  46 #include <algorithm>
  47
  48 #include "gromacs/math/units.h"
  49 #include "gromacs/math/utilities.h"
  50 #include "gromacs/math/vec.h"
  51 #include "gromacs/topology/ifunc.h"
  52 #include "gromacs/trajectory/energyframe.h"
  53 #include "gromacs/utility/arrayref.h"
  54 #include "gromacs/utility/basedefinitions.h"
  55 #include "gromacs/utility/cstringutil.h"
  56 #include "gromacs/utility/fatalerror.h"
  57 #include "gromacs/utility/smalloc.h"
  58 #include "gromacs/utility/stringutil.h"
  59
  60 t_ebin* mk_ebin()
  61 {
  62     t_ebin* eb;
  63
  64     snew(eb, 1);
  65
  66     return eb;
  67 }
  68
  69 void done_ebin(t_ebin* eb)
  70 {
  71     for (int i = 0; i < eb->nener; i++)
  72     {
  73         sfree(eb->enm[i].name);
  74         sfree(eb->enm[i].unit);
  75     }
  76     sfree(eb->e);
  77     sfree(eb->e_sim);
  78     sfree(eb->enm);
  79     sfree(eb);
  80 }
  81
  82 int get_ebin_space(t_ebin* eb, int nener, const char* const enm[], const char* unit)
  83 {
  84     int         index;
  85     int         i, f;
  86     const char* u;
  87
  88     index = eb->nener;
  89     eb->nener += nener;
  90     srenew(eb->e, eb->nener);
  91     srenew(eb->e_sim, eb->nener);
  92     srenew(eb->enm, eb->nener);
  93     for (i = index; (i < eb->nener); i++)
  94     {
  95         eb->e[i].e        = 0;
  96         eb->e[i].eav      = 0;
  97         eb->e[i].esum     = 0;
  98         eb->e_sim[i].e    = 0;
  99         eb->e_sim[i].eav  = 0;
 100         eb->e_sim[i].esum = 0;
 101         eb->enm[i].name   = gmx_strdup(enm[i - index]);
 102         if (unit != nullptr)
 103         {
 104             eb->enm[i].unit = gmx_strdup(unit);
 105         }
 106         else
 107         {
 108             /* Determine the unit from the longname.
 109              * These units should have been defined in ifunc.c
 110              * But even better would be if all interactions functions
 111              * return energies and all non-interaction function
 112              * entries would be removed from the ifunc array.
 113              */
 114             u = unit_energy;
 115             for (f = 0; f < F_NRE; f++)
 116             {
 117                 if (strcmp(eb->enm[i].name, interaction_function[f].longname) == 0)
 118                 {
 119                     /* Only the terms in this list are not energies */
 120                     switch (f)
 121                     {
 122                         case F_DISRESVIOL: u = unit_length; break;
 123                         case F_ORIRESDEV: u = "obs"; break;
 124                         case F_TEMP: u = unit_temp_K; break;
 125                         case F_PDISPCORR:
 126                         case F_PRES: u = unit_pres_bar; break;
 127                     }
 128                 }
 129             }
 130             eb->enm[i].unit = gmx_strdup(u);
 131         }
 132     }
 133
 134     return index;
 135 }
 136
 137 // ICC 19 -O3 -msse2 generates wrong code. Lower optimization levels
 138 // and other SIMD levels seem fine, however.
 139 #if defined __ICC
 140 #    pragma intel optimization_level 2
 141 #endif
 142 void add_ebin(t_ebin* eb, int entryIndex, int nener, const real ener[], gmx_bool bSum)
 143 {
 144     int       i, m;
 145     double    e, invmm, diff;
 146     t_energy *eg, *egs;
 147
 148     if ((entryIndex + nener > eb->nener) || (entryIndex < 0))
 149     {
 150         gmx_fatal(FARGS, "%s-%d: Energies out of range: entryIndex=%d nener=%d maxener=%d",
 151                   __FILE__, __LINE__, entryIndex, nener, eb->nener);
 152     }
 153
 154     eg = &(eb->e[entryIndex]);
 155
 156     for (i = 0; (i < nener); i++)
 157     {
 158         eg[i].e = ener[i];
 159     }
 160
 161     if (bSum)
 162     {
 163         egs = &(eb->e_sim[entryIndex]);
 164
 165         m = eb->nsum;
 166
 167         if (m == 0)
 168         {
 169             for (i = 0; (i < nener); i++)
 170             {
 171                 eg[i].eav  = 0;
 172                 eg[i].esum = ener[i];
 173                 egs[i].esum += ener[i];
 174             }
 175         }
 176         else
 177         {
 178             invmm = (1.0 / m) / (m + 1.0);
 179
 180             for (i = 0; (i < nener); i++)
 181             {
 182                 /* Value for this component */
 183                 e = ener[i];
 184
 185                 /* first update sigma, then sum */
 186                 diff = eg[i].esum - m * e;
 187                 eg[i].eav += diff * diff * invmm;
 188                 eg[i].esum += e;
 189                 egs[i].esum += e;
 190             }
 191         }
 192     }
 193 }
 194
 195 // TODO It would be faster if this function was templated on both bSum
 196 // and whether eb->nsum was zero, to lift the branches out of the loop
 197 // over all possible energy terms, but that is true for a lot of the
 198 // ebin and mdebin functionality, so we should do it all or nothing.
 199 void add_ebin_indexed(t_ebin*                   eb,
 200                       int                       entryIndex,
 201                       gmx::ArrayRef<bool>       shouldUse,
 202                       gmx::ArrayRef<const real> ener,
 203                       gmx_bool                  bSum)
 204 {
 205
 206     GMX_ASSERT(shouldUse.size() == ener.size(), "View sizes must match");
 207     GMX_ASSERT(entryIndex + std::count(shouldUse.begin(), shouldUse.end(), true) <= eb->nener,
 208                gmx::formatString("Energies out of range: entryIndex=%d nener=%td maxener=%d", entryIndex,
 209                                  std::count(shouldUse.begin(), shouldUse.end(), true), eb->nener)
 210                        .c_str());
 211     GMX_ASSERT(entryIndex >= 0, "Must have non-negative entry");
 212
 213     const int    m              = eb->nsum;
 214     const double invmm          = (m == 0) ? 0 : (1.0 / m) / (m + 1.0);
 215     t_energy*    energyEntry    = &(eb->e[entryIndex]);
 216     t_energy*    simEnergyEntry = &(eb->e_sim[entryIndex]);
 217     auto         shouldUseIter  = shouldUse.begin();
 218     for (const auto& theEnergy : ener)
 219     {
 220         if (*shouldUseIter)
 221         {
 222             energyEntry->e = theEnergy;
 223             if (bSum)
 224             {
 225                 if (m == 0)
 226                 {
 227                     energyEntry->eav  = 0;
 228                     energyEntry->esum = theEnergy;
 229                     simEnergyEntry->esum += theEnergy;
 230                 }
 231                 else
 232                 {
 233                     /* first update sigma, then sum */
 234                     double diff = energyEntry->esum - m * theEnergy;
 235                     energyEntry->eav += diff * diff * invmm;
 236                     energyEntry->esum += theEnergy;
 237                     simEnergyEntry->esum += theEnergy;
 238                 }
 239                 ++simEnergyEntry;
 240             }
 241             ++energyEntry;
 242         }
 243         ++shouldUseIter;
 244     }
 245 }
 246
 247 void ebin_increase_count(int increment, t_ebin* eb, gmx_bool bSum)
 248 {
 249     eb->nsteps += increment;
 250     eb->nsteps_sim += increment;
 251
 252     if (bSum)
 253     {
 254         eb->nsum += increment;
 255         eb->nsum_sim += increment;
 256     }
 257 }
 258
 259 void reset_ebin_sums(t_ebin* eb)
 260 {
 261     eb->nsteps = 0;
 262     eb->nsum   = 0;
 263     /* The actual sums are cleared when the next frame is stored */
 264 }
 265
 266 void pr_ebin(FILE* fp, t_ebin* eb, int entryIndex, int nener, int nperline, int prmode, gmx_bool bPrHead)
 267 {
 268     int  i, j, i0;
 269     int  rc;
 270     char buf[30];
 271
 272     rc = 0;
 273
 274     if (entryIndex < 0 || entryIndex > eb->nener)
 275     {
 276         gmx_fatal(FARGS, "Invalid entryIndex in pr_ebin: %d", entryIndex);
 277     }
 278     int start = entryIndex;
 279     if (nener > eb->nener)
 280     {
 281         gmx_fatal(FARGS, "Invalid nener in pr_ebin: %d", nener);
 282     }
 283     int end = eb->nener;
 284     if (nener != -1)
 285     {
 286         end = entryIndex + nener;
 287     }
 288     for (i = start; (i < end) && rc >= 0;)
 289     {
 290         if (bPrHead)
 291         {
 292             i0 = i;
 293             for (j = 0; (j < nperline) && (i < end) && rc >= 0; j++, i++)
 294             {
 295                 if (strncmp(eb->enm[i].name, "Pres", 4) == 0)
 296                 {
 297                     /* Print the pressure unit to avoid confusion */
 298                     sprintf(buf, "%s (%s)", eb->enm[i].name, unit_pres_bar);
 299                     rc = fprintf(fp, "%15s", buf);
 300                 }
 301                 else
 302                 {
 303                     rc = fprintf(fp, "%15s", eb->enm[i].name);
 304                 }
 305             }
 306
 307             if (rc >= 0)
 308             {
 309                 rc = fprintf(fp, "\n");
 310             }
 311
 312             i = i0;
 313         }
 314         for (j = 0; (j < nperline) && (i < end) && rc >= 0; j++, i++)
 315         {
 316             switch (prmode)
 317             {
 318                 case eprNORMAL: rc = fprintf(fp, "   %12.5e", eb->e[i].e); break;
 319                 case eprAVER:
 320                     if (eb->nsum_sim > 0)
 321                     {
 322                         rc = fprintf(fp, "   %12.5e", eb->e_sim[i].esum / eb->nsum_sim);
 323                     }
 324                     else
 325                     {
 326                         rc = fprintf(fp, "    %-12s", "N/A");
 327                     }
 328                     break;
 329                 default: gmx_fatal(FARGS, "Invalid print mode %d in pr_ebin", prmode);
 330             }
 331         }
 332         if (rc >= 0)
 333         {
 334             rc = fprintf(fp, "\n");
 335         }
 336     }
 337     if (rc < 0)
 338     {
 339         gmx_fatal(FARGS, "Cannot write to logfile; maybe you are out of disk space?");
 340     }
 341 }