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 <math.h>
  43 #include <string.h>
  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/utility/cstringutil.h"
  50 #include "gromacs/utility/fatalerror.h"
  51 #include "gromacs/utility/smalloc.h"
  52
  53 t_ebin *mk_ebin(void)
  54 {
  55     t_ebin *eb;
  56
  57     snew(eb, 1);
  58
  59     return eb;
  60 }
  61
  62 int get_ebin_space(t_ebin *eb, int nener, const char *enm[], const char *unit)
  63 {
  64     int         index;
  65     int         i, f;
  66     const char *u;
  67
  68     index      = eb->nener;
  69     eb->nener += nener;
  70     srenew(eb->e, eb->nener);
  71     srenew(eb->e_sim, eb->nener);
  72     srenew(eb->enm, eb->nener);
  73     for (i = index; (i < eb->nener); i++)
  74     {
  75         eb->e[i].e        = 0;
  76         eb->e[i].eav      = 0;
  77         eb->e[i].esum     = 0;
  78         eb->e_sim[i].e    = 0;
  79         eb->e_sim[i].eav  = 0;
  80         eb->e_sim[i].esum = 0;
  81         eb->enm[i].name   = gmx_strdup(enm[i-index]);
  82         if (unit != NULL)
  83         {
  84             eb->enm[i].unit = gmx_strdup(unit);
  85         }
  86         else
  87         {
  88             /* Determine the unit from the longname.
  89              * These units should have been defined in ifunc.c
  90              * But even better would be if all interactions functions
  91              * return energies and all non-interaction function
  92              * entries would be removed from the ifunc array.
  93              */
  94             u = unit_energy;
  95             for (f = 0; f < F_NRE; f++)
  96             {
  97                 if (strcmp(eb->enm[i].name,
  98                            interaction_function[f].longname) == 0)
  99                 {
 100                     /* Only the terms in this list are not energies */
 101                     switch (f)
 102                     {
 103                         case F_DISRESVIOL: u = unit_length;   break;
 104                         case F_ORIRESDEV:  u = "obs";         break;
 105                         case F_TEMP:       u = unit_temp_K;   break;
 106                         case F_PDISPCORR:
 107                         case F_PRES:       u = unit_pres_bar; break;
 108                     }
 109                 }
 110             }
 111             eb->enm[i].unit = gmx_strdup(u);
 112         }
 113     }
 114
 115     return index;
 116 }
 117
 118 void add_ebin(t_ebin *eb, int index, int nener, real ener[], gmx_bool bSum)
 119 {
 120     int       i, m;
 121     double    e, invmm, diff;
 122     t_energy *eg, *egs;
 123
 124     if ((index+nener > eb->nener) || (index < 0))
 125     {
 126         gmx_fatal(FARGS, "%s-%d: Energies out of range: index=%d nener=%d maxener=%d",
 127                   __FILE__, __LINE__, index, nener, eb->nener);
 128     }
 129
 130     eg = &(eb->e[index]);
 131
 132     for (i = 0; (i < nener); i++)
 133     {
 134         eg[i].e      = ener[i];
 135     }
 136
 137     if (bSum)
 138     {
 139         egs = &(eb->e_sim[index]);
 140
 141         m = eb->nsum;
 142
 143         if (m == 0)
 144         {
 145             for (i = 0; (i < nener); i++)
 146             {
 147                 eg[i].eav    = 0;
 148                 eg[i].esum   = ener[i];
 149                 egs[i].esum += ener[i];
 150             }
 151         }
 152         else
 153         {
 154             invmm = (1.0/(double)m)/((double)m+1.0);
 155
 156             for (i = 0; (i < nener); i++)
 157             {
 158                 /* Value for this component */
 159                 e = ener[i];
 160
 161                 /* first update sigma, then sum */
 162                 diff         = eg[i].esum - m*e;
 163                 eg[i].eav   += diff*diff*invmm;
 164                 eg[i].esum  += e;
 165                 egs[i].esum += e;
 166             }
 167         }
 168     }
 169 }
 170
 171 void ebin_increase_count(t_ebin *eb, gmx_bool bSum)
 172 {
 173     eb->nsteps++;
 174     eb->nsteps_sim++;
 175
 176     if (bSum)
 177     {
 178         eb->nsum++;
 179         eb->nsum_sim++;
 180     }
 181 }
 182
 183 void reset_ebin_sums(t_ebin *eb)
 184 {
 185     eb->nsteps = 0;
 186     eb->nsum   = 0;
 187     /* The actual sums are cleared when the next frame is stored */
 188 }
 189
 190 void pr_ebin(FILE *fp, t_ebin *eb, int index, int nener, int nperline,
 191              int prmode, gmx_bool bPrHead)
 192 {
 193     int  i, j, i0;
 194     real ee = 0;
 195     int  rc;
 196     char buf[30];
 197
 198     rc = 0;
 199
 200     if (index < 0)
 201     {
 202         gmx_fatal(FARGS, "Invalid index in pr_ebin: %d", index);
 203     }
 204     if (nener == -1)
 205     {
 206         nener = eb->nener;
 207     }
 208     else
 209     {
 210         nener = index + nener;
 211     }
 212     for (i = index; (i < nener) && rc >= 0; )
 213     {
 214         if (bPrHead)
 215         {
 216             i0 = i;
 217             for (j = 0; (j < nperline) && (i < nener) && rc >= 0; j++, i++)
 218             {
 219                 if (strncmp(eb->enm[i].name, "Pres", 4) == 0)
 220                 {
 221                     /* Print the pressure unit to avoid confusion */
 222                     sprintf(buf, "%s (%s)", eb->enm[i].name, unit_pres_bar);
 223                     rc = fprintf(fp, "%15s", buf);
 224                 }
 225                 else
 226                 {
 227                     rc = fprintf(fp, "%15s", eb->enm[i].name);
 228                 }
 229             }
 230
 231             if (rc >= 0)
 232             {
 233                 rc = fprintf(fp, "\n");
 234             }
 235
 236             i = i0;
 237         }
 238         for (j = 0; (j < nperline) && (i < nener) && rc >= 0; j++, i++)
 239         {
 240             switch (prmode)
 241             {
 242                 case eprNORMAL: ee = eb->e[i].e; break;
 243                 case eprAVER:   ee = eb->e_sim[i].esum/eb->nsum_sim; break;
 244                 default: gmx_fatal(FARGS, "Invalid print mode %d in pr_ebin",
 245                                    prmode);
 246             }
 247
 248             rc = fprintf(fp, "   %12.5e", ee);
 249         }
 250         if (rc >= 0)
 251         {
 252             rc = fprintf(fp, "\n");
 253         }
 254     }
 255     if (rc < 0)
 256     {
 257         gmx_fatal(FARGS, "Cannot write to logfile; maybe you are out of disk space?");
 258     }
 259 }
 260
 261 #ifdef DEBUGEBIN
 262 int main(int argc, char *argv[])
 263 {
 264 #define NE 12
 265 #define NT 7
 266 #define NS 5
 267
 268     t_ebin *eb;
 269     int     i;
 270     char    buf[25];
 271     char   *ce[NE], *ct[NT], *cs[NS];
 272     real    e[NE], t[NT], s[NS];
 273     int     ie, it, is;
 274
 275     eb = mk_ebin();
 276     for (i = 0; (i < NE); i++)
 277     {
 278         e[i] = i;
 279         sprintf(buf, "e%d", i);
 280         ce[i] = gmx_strdup(buf);
 281     }
 282     ie = get_ebin_space(eb, NE, ce);
 283     add_ebin(eb, ie, NE, e, 0);
 284     for (i = 0; (i < NS); i++)
 285     {
 286         s[i] = i;
 287         sprintf(buf, "s%d", i);
 288         cs[i] = gmx_strdup(buf);
 289     }
 290     is = get_ebin_space(eb, NS, cs);
 291     add_ebin(eb, is, NS, s, 0);
 292     for (i = 0; (i < NT); i++)
 293     {
 294         t[i] = i;
 295         sprintf(buf, "t%d", i);
 296         ct[i] = gmx_strdup(buf);
 297     }
 298     it = get_ebin_space(eb, NT, ct);
 299     add_ebin(eb, it, NT, t, 0);
 300
 301     printf("Normal:\n");
 302     pr_ebin(stdout, eb, 0, -1, 5, eprNORMAL, 1);
 303
 304     printf("Average:\n");
 305     pr_ebin(stdout, eb, ie, NE, 5, eprAVER, 1);
 306     pr_ebin(stdout, eb, is, NS, 3, eprAVER, 1);
 307     pr_ebin(stdout, eb, it, NT, 4, eprAVER, 1);
 308 }
 309 #endif