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 #ifdef __cplusplus
  44 extern "C" {
  45 #endif
  46
  47 typedef struct {
  48     int  la;
  49     int  cell;
  50 } gmx_laa_t;
  51
  52 typedef struct {
  53     int  ga;
  54     int  la;
  55     int  cell;
  56     int  next;
  57 } gmx_lal_t;
  58
  59 typedef struct gmx_ga2la {
  60     bool      bAll;
  61     int       mod;
  62     int       nalloc;
  63     gmx_laa_t *laa;
  64     gmx_lal_t *lal;
  65     int       start_space_search;
  66 } t_gmx_ga2la;
  67
  68 /* Clear all the entries in the ga2la list */
  69 static void ga2la_clear(gmx_ga2la_t ga2la)
  70 {
  71     int i;
  72
  73     if (ga2la->bAll)
  74     {
  75         for(i=0; i<ga2la->nalloc; i++)
  76         {
  77             ga2la->laa[i].cell = -1;
  78         }
  79     }
  80     else
  81     {
  82         for(i=0; i<ga2la->nalloc; i++)
  83         {
  84             ga2la->lal[i].ga   = -1;
  85             ga2la->lal[i].next = -1;
  86         }
  87         ga2la->start_space_search = ga2la->mod;
  88     }
  89 }
  90
  91 static gmx_ga2la_t ga2la_init(int nat_tot,int nat_loc)
  92 {
  93     gmx_ga2la_t ga2la;
  94
  95     snew(ga2la,1);
  96
  97     /* There are two methods implemented for finding the local atom number
  98      * belonging to a global atom number:
  99      * 1) a simple, direct array
 100      * 2) a list of linked lists indexed with the global number modulo mod.
 101      * Memory requirements:
 102      * 1) nat_tot*2 ints
 103      * 2) nat_loc*(2+1-2(1-e^-1/2))*4 ints
 104      * where nat_loc is the number of atoms in the home + communicated zones.
 105      * Method 1 is faster for low parallelization, 2 for high parallelization.
 106      * We switch to method 2 when it uses less than half the memory method 1.
 107      */
 108     ga2la->bAll = (nat_tot < 1024 || 9*nat_loc >= nat_tot);
 109     if (ga2la->bAll)
 110     {
 111         ga2la->nalloc = nat_tot;
 112         snew(ga2la->laa,ga2la->nalloc);
 113     }
 114     else
 115     {
 116         /* Make the direct list twice as long as the number of local atoms.
 117          * The fraction of entries in the list with:
 118          * 0   size lists: e^-1/f
 119          * >=1 size lists: 1 - e^-1/f
 120          * where f is: the direct list length / #local atoms
 121          * The fraction of atoms not in the direct list is: 1-f(1-e^-1/f).
 122          */
 123         ga2la->mod = 2*nat_loc;
 124         ga2la->nalloc = over_alloc_dd(ga2la->mod);
 125         snew(ga2la->lal,ga2la->nalloc);
 126     }
 127
 128     ga2la_clear(ga2la);
 129
 130     return ga2la;
 131 }
 132
 133 /* Set the ga2la entry for global atom a_gl to local atom a_loc and cell. */
 134 static void ga2la_set(gmx_ga2la_t ga2la,int a_gl,int a_loc,int cell)
 135 {
 136     int ind,ind_prev,i;
 137
 138     if (ga2la->bAll)
 139     {
 140         ga2la->laa[a_gl].la   = a_loc;
 141         ga2la->laa[a_gl].cell = cell;
 142
 143         return;
 144     }
 145
 146     ind = a_gl % ga2la->mod;
 147
 148     if (ga2la->lal[ind].ga >= 0)
 149     {
 150         /* Search the last entry in the linked list for this index */
 151         ind_prev = ind;
 152         while(ga2la->lal[ind_prev].next >= 0)
 153         {
 154             ind_prev = ga2la->lal[ind_prev].next;
 155         }
 156         /* Search for space in the array */
 157         ind = ga2la->start_space_search;
 158         while (ind < ga2la->nalloc && ga2la->lal[ind].ga >= 0)
 159         {
 160             ind++;
 161         }
 162         /* If we are at the end of the list we need to increase the size */
 163         if (ind == ga2la->nalloc)
 164         {
 165             ga2la->nalloc = over_alloc_dd(ind+1);
 166             srenew(ga2la->lal,ga2la->nalloc);
 167             for(i=ind; i<ga2la->nalloc; i++)
 168             {
 169                 ga2la->lal[i].ga   = -1;
 170                 ga2la->lal[i].next = -1;
 171             }
 172         }
 173         ga2la->lal[ind_prev].next = ind;
 174
 175         ga2la->start_space_search = ind + 1;
 176     }
 177     ga2la->lal[ind].ga   = a_gl;
 178     ga2la->lal[ind].la   = a_loc;
 179     ga2la->lal[ind].cell = cell;
 180 }
 181
 182 /* Delete the ga2la entry for global atom a_gl */
 183 static void ga2la_del(gmx_ga2la_t ga2la,int a_gl)
 184 {
 185     int ind,ind_prev;
 186
 187     if (ga2la->bAll)
 188     {
 189         ga2la->laa[a_gl].cell = -1;
 190
 191         return;
 192     }
 193
 194     ind_prev = -1;
 195     ind = a_gl % ga2la->mod;
 196     do
 197     {
 198         if (ga2la->lal[ind].ga == a_gl)
 199         {
 200             if (ind_prev >= 0)
 201             {
 202                 ga2la->lal[ind_prev].next = ga2la->lal[ind].next;
 203
 204                 /* This index is a linked entry, so we free an entry.
 205                  * Check if we are creating the first empty space.
 206                  */
 207                 if (ind < ga2la->start_space_search)
 208                 {
 209                     ga2la->start_space_search = ind;
 210                 }
 211             }
 212             ga2la->lal[ind].ga   = -1;
 213             ga2la->lal[ind].cell = -1;
 214             ga2la->lal[ind].next = -1;
 215
 216             return;
 217         }
 218         ind_prev = ind;
 219         ind = ga2la->lal[ind].next;
 220     }
 221     while (ind >= 0);
 222
 223     return;
 224 }
 225
 226 /* Change the local atom for present ga2la entry for global atom a_gl */
 227 static void ga2la_change_la(gmx_ga2la_t ga2la,int a_gl,int a_loc)
 228 {
 229     int ind;
 230
 231     if (ga2la->bAll)
 232     {
 233         ga2la->laa[a_gl].la = a_loc;
 234
 235         return;
 236     }
 237
 238     ind = a_gl % ga2la->mod;
 239     do
 240     {
 241         if (ga2la->lal[ind].ga == a_gl)
 242         {
 243             ga2la->lal[ind].la = a_loc;
 244
 245             return;
 246         }
 247         ind = ga2la->lal[ind].next;
 248     }
 249     while (ind >= 0);
 250
 251     return;
 252 }
 253
 254 /* Returns if the global atom a_gl available locally.
 255  * Sets the local atom and cell,
 256  * cell can be larger than the number of zones,
 257  * in which case it indicates that it is more than one cell away
 258  * in zone cell - #zones.
 259  */
 260 static bool ga2la_get(const gmx_ga2la_t ga2la,int a_gl,int *a_loc,int *cell)
 261 {
 262     int ind;
 263
 264     if (ga2la->bAll)
 265     {
 266         *a_loc = ga2la->laa[a_gl].la;
 267         *cell  = ga2la->laa[a_gl].cell;
 268
 269         return (ga2la->laa[a_gl].cell >= 0);
 270     }
 271
 272     ind = a_gl % ga2la->mod;
 273     do
 274     {
 275         if (ga2la->lal[ind].ga == a_gl)
 276         {
 277             *a_loc = ga2la->lal[ind].la;
 278             *cell  = ga2la->lal[ind].cell;
 279
 280             return TRUE;
 281         }
 282         ind = ga2la->lal[ind].next;
 283     }
 284     while (ind >= 0);
 285
 286     return FALSE;
 287 }
 288
 289 /* Returns if the global atom a_gl is a home atom.
 290  * Sets the local atom.
 291  */
 292 static bool ga2la_get_home(const gmx_ga2la_t ga2la,int a_gl,int *a_loc)
 293 {
 294     int ind;
 295
 296     if (ga2la->bAll)
 297     {
 298         *a_loc = ga2la->laa[a_gl].la;
 299
 300         return (ga2la->laa[a_gl].cell == 0);
 301     }
 302
 303     ind = a_gl % ga2la->mod;
 304     do
 305     {
 306         if (ga2la->lal[ind].ga == a_gl)
 307         {
 308             if (ga2la->lal[ind].cell == 0)
 309             {
 310                 *a_loc = ga2la->lal[ind].la;
 311
 312                 return TRUE;
 313             }
 314             else
 315             {
 316                 return FALSE;
 317             }
 318         }
 319         ind = ga2la->lal[ind].next;
 320     }
 321     while (ind >= 0);
 322
 323     return FALSE;
 324 }
 325
 326 /* Returns if the global atom a_gl is a home atom.
 327  */
 328 static bool ga2la_is_home(const gmx_ga2la_t ga2la,int a_gl)
 329 {
 330     int ind;
 331
 332     if (ga2la->bAll)
 333     {
 334         return (ga2la->laa[a_gl].cell == 0);
 335     }
 336
 337     ind = a_gl % ga2la->mod;
 338     do
 339     {
 340         if (ga2la->lal[ind].ga == a_gl)
 341         {
 342             return (ga2la->lal[ind].cell == 0);
 343         }
 344         ind = ga2la->lal[ind].next;
 345     }
 346     while (ind >= 0);
 347
 348     return FALSE;
 349 }
 350
 351 #ifdef __cplusplus
 352 }
 353 #endif
 354
 355 #endif /* _gmx_ga2la_h */