include/gmx_ga2la.h

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  36 #ifndef _gmx_ga2la_h
  37 #define _gmx_ga2la_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 typedef struct {
  44     int  la;
  45     int  cell;
  46 } gmx_laa_t;
  47
  48 typedef struct {
  49     int  ga;
  50     int  la;
  51     int  cell;
  52     int  next;
  53 } gmx_lal_t;
  54
  55 typedef struct gmx_ga2la {
  56     bool      bAll;
  57     int       mod;
  58     int       nalloc;
  59     gmx_laa_t *laa;
  60     gmx_lal_t *lal;
  61     int       start_space_search;
  62 } t_gmx_ga2la;
  63
  64 /* Clear all the entries in the ga2la list */
  65 static void ga2la_clear(gmx_ga2la_t ga2la)
  66 {
  67     int i;
  68
  69     if (ga2la->bAll)
  70     {
  71         for(i=0; i<ga2la->nalloc; i++)
  72         {
  73             ga2la->laa[i].cell = -1;
  74         }
  75     }
  76     else
  77     {
  78         for(i=0; i<ga2la->nalloc; i++)
  79         {
  80             ga2la->lal[i].ga   = -1;
  81             ga2la->lal[i].next = -1;
  82         }
  83         ga2la->start_space_search = ga2la->mod;
  84     }
  85 }
  86
  87 static gmx_ga2la_t ga2la_init(int nat_tot,int nat_loc)
  88 {
  89     gmx_ga2la_t ga2la;
  90
  91     snew(ga2la,1);
  92
  93     /* There are two methods implemented for finding the local atom number
  94      * belonging to a global atom number:
  95      * 1) a simple, direct arrary
  96      * 2) a list of linked lists indexed with the global number modulo mod.
  97      * Memory requirements:
  98      * 1) nat_tot*2 ints
  99      * 2) nat_loc*(2+1-2(1-e^-1/2))*4 ints
 100      * where nat_loc is the number of atoms in the home + communicated zones.
 101      * Method 1 is faster for low parallelization, 2 for high parallelization.
 102      * We switch to method 2 when it uses less than half the memory method 1.
 103      */
 104     ga2la->bAll = (9*nat_loc >= nat_tot);
 105     if (ga2la->bAll)
 106     {
 107         ga2la->nalloc = nat_tot;
 108         snew(ga2la->laa,ga2la->nalloc);
 109     }
 110     else
 111     {
 112         /* Make the direct list twice as large as the number of local atoms.
 113          * The fraction of entries in the list with:
 114          * 0   size lists: e^-1/f
 115          * >=1 size lists: 1 - e^-1/f
 116          * where f is: the direct list length / #local atoms
 117          * The fraction of atoms not in the direct list is: 1-f(1-e^-1/f).
 118          */
 119         ga2la->mod = 2*nat_loc;
 120         ga2la->nalloc = over_alloc_dd(ga2la->mod);
 121         snew(ga2la->lal,ga2la->nalloc);
 122     }
 123
 124     ga2la_clear(ga2la);
 125
 126     return ga2la;
 127 }
 128
 129 /* Set the ga2la entry for global atom a_gl to local atom a_loc and cell. */
 130 static void ga2la_set(gmx_ga2la_t ga2la,int a_gl,int a_loc,int cell)
 131 {
 132     int ind,ind_prev,i;
 133
 134     if (ga2la->bAll)
 135     {
 136         ga2la->laa[a_gl].la   = a_loc;
 137         ga2la->laa[a_gl].cell = cell;
 138
 139         return;
 140     }
 141
 142     ind = a_gl % ga2la->mod;
 143
 144     if (ga2la->lal[ind].ga >= 0)
 145     {
 146         /* Search the last entry in the linked list for this index */
 147         ind_prev = ind;
 148         while(ga2la->lal[ind_prev].next >= 0)
 149         {
 150             ind_prev = ga2la->lal[ind_prev].next;
 151         }
 152         /* Search for space in the array */
 153         ind = ga2la->start_space_search;
 154         while (ind < ga2la->nalloc && ga2la->lal[ind].ga >= 0)
 155         {
 156             ind++;
 157         }
 158         /* If we are a the end of the list we need to increase the size */
 159         if (ind == ga2la->nalloc)
 160         {
 161             ga2la->nalloc = over_alloc_dd(ind+1);
 162             srenew(ga2la->lal,ga2la->nalloc);
 163             for(i=ind; i<ga2la->nalloc; i++)
 164             {
 165                 ga2la->lal[i].ga   = -1;
 166                 ga2la->lal[i].next = -1;
 167             }
 168         }
 169         ga2la->lal[ind_prev].next = ind;
 170
 171         ga2la->start_space_search = ind + 1;
 172     }
 173     ga2la->lal[ind].ga   = a_gl;
 174     ga2la->lal[ind].la   = a_loc;
 175     ga2la->lal[ind].cell = cell;
 176 }
 177
 178 /* Delete the ga2la entry for global atom a_gl */
 179 static void ga2la_del(gmx_ga2la_t ga2la,int a_gl)
 180 {
 181     int ind,ind_prev;
 182
 183     if (ga2la->bAll)
 184     {
 185         ga2la->laa[a_gl].cell = -1;
 186
 187         return;
 188     }
 189
 190     ind_prev = -1;
 191     ind = a_gl % ga2la->mod;
 192     do
 193     {
 194         if (ga2la->lal[ind].ga == a_gl)
 195         {
 196             if (ind_prev >= 0)
 197             {
 198                 ga2la->lal[ind_prev].next = ga2la->lal[ind].next;
 199
 200                 /* This index is a linked entry, so we free an entry.
 201                  * Check if we are creating the first empty space.
 202                  */
 203                 if (ind < ga2la->start_space_search)
 204                 {
 205                     ga2la->start_space_search = ind;
 206                 }
 207             }
 208             ga2la->lal[ind].ga   = -1;
 209             ga2la->lal[ind].cell = -1;
 210             ga2la->lal[ind].next = -1;
 211
 212             return;
 213         }
 214         ind_prev = ind;
 215         ind = ga2la->lal[ind].next;
 216     }
 217     while (ind >= 0);
 218
 219     return;
 220 }
 221
 222 /* Change the local atom for present ga2la entry for global atom a_gl */
 223 static void ga2la_change_la(gmx_ga2la_t ga2la,int a_gl,int a_loc)
 224 {
 225     int ind;
 226
 227     if (ga2la->bAll)
 228     {
 229         ga2la->laa[a_gl].la = a_loc;
 230
 231         return;
 232     }
 233
 234     ind = a_gl % ga2la->mod;
 235     do
 236     {
 237         if (ga2la->lal[ind].ga == a_gl)
 238         {
 239             ga2la->lal[ind].la = a_loc;
 240
 241             return;
 242         }
 243         ind = ga2la->lal[ind].next;
 244     }
 245     while (ind >= 0);
 246
 247     return;
 248 }
 249
 250 /* Returns if the global atom a_gl available locally.
 251  * Sets the local atom and cell,
 252  * cell can be larger than the number of zones,
 253  * in which case it indicates that it is more than one cell away
 254  * in zone cell - #zones.
 255  */
 256 static bool ga2la_get(const gmx_ga2la_t ga2la,int a_gl,int *a_loc,int *cell)
 257 {
 258     int ind;
 259
 260     if (ga2la->bAll)
 261     {
 262         *a_loc = ga2la->laa[a_gl].la;
 263         *cell  = ga2la->laa[a_gl].cell;
 264
 265         return (ga2la->laa[a_gl].cell >= 0);
 266     }
 267
 268     ind = a_gl % ga2la->mod;
 269     do
 270     {
 271         if (ga2la->lal[ind].ga == a_gl)
 272         {
 273             *a_loc = ga2la->lal[ind].la;
 274             *cell  = ga2la->lal[ind].cell;
 275
 276             return TRUE;
 277         }
 278         ind = ga2la->lal[ind].next;
 279     }
 280     while (ind >= 0);
 281
 282     return FALSE;
 283 }
 284
 285 /* Returns if the global atom a_gl is a home atom.
 286  * Sets the local atom.
 287  */
 288 static bool ga2la_home(const gmx_ga2la_t ga2la,int a_gl,int *a_loc)
 289 {
 290     int ind;
 291
 292     if (ga2la->bAll)
 293     {
 294         *a_loc = ga2la->laa[a_gl].la;
 295
 296         return (ga2la->laa[a_gl].cell == 0);
 297     }
 298
 299     ind = a_gl % ga2la->mod;
 300     do
 301     {
 302         if (ga2la->lal[ind].ga == a_gl)
 303         {
 304             if (ga2la->lal[ind].cell == 0)
 305             {
 306                 *a_loc = ga2la->lal[ind].la;
 307
 308                 return TRUE;
 309             }
 310             else
 311             {
 312                 return FALSE;
 313             }
 314         }
 315         ind = ga2la->lal[ind].next;
 316     }
 317     while (ind >= 0);
 318
 319     return FALSE;
 320 }
 321
 322 #endif /* _gmx_ga2la_h */