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62 typedef struct gmx_ga2la
{
68 int start_space_search
;
71 /* Clear all the entries in the ga2la list */
72 static void ga2la_clear(gmx_ga2la_t ga2la
)
78 for(i
=0; i
<ga2la
->nalloc
; i
++)
80 ga2la
->laa
[i
].cell
= -1;
85 for(i
=0; i
<ga2la
->nalloc
; i
++)
87 ga2la
->lal
[i
].ga
= -1;
88 ga2la
->lal
[i
].next
= -1;
90 ga2la
->start_space_search
= ga2la
->mod
;
94 static gmx_ga2la_t
ga2la_init(int nat_tot
,int nat_loc
)
100 /* There are two methods implemented for finding the local atom number
101 * belonging to a global atom number:
102 * 1) a simple, direct array
103 * 2) a list of linked lists indexed with the global number modulo mod.
104 * Memory requirements:
106 * 2) nat_loc*(2+1-2(1-e^-1/2))*4 ints
107 * where nat_loc is the number of atoms in the home + communicated zones.
108 * Method 1 is faster for low parallelization, 2 for high parallelization.
109 * We switch to method 2 when it uses less than half the memory method 1.
111 ga2la
->bAll
= (nat_tot
< 1024 || 9*nat_loc
>= nat_tot
);
114 ga2la
->nalloc
= nat_tot
;
115 snew(ga2la
->laa
,ga2la
->nalloc
);
119 /* Make the direct list twice as long as the number of local atoms.
120 * The fraction of entries in the list with:
121 * 0 size lists: e^-1/f
122 * >=1 size lists: 1 - e^-1/f
123 * where f is: the direct list length / #local atoms
124 * The fraction of atoms not in the direct list is: 1-f(1-e^-1/f).
126 ga2la
->mod
= 2*nat_loc
;
127 ga2la
->nalloc
= over_alloc_dd(ga2la
->mod
);
128 snew(ga2la
->lal
,ga2la
->nalloc
);
136 /* Set the ga2la entry for global atom a_gl to local atom a_loc and cell. */
137 static void ga2la_set(gmx_ga2la_t ga2la
,int a_gl
,int a_loc
,int cell
)
143 ga2la
->laa
[a_gl
].la
= a_loc
;
144 ga2la
->laa
[a_gl
].cell
= cell
;
149 ind
= a_gl
% ga2la
->mod
;
151 if (ga2la
->lal
[ind
].ga
>= 0)
153 /* Search the last entry in the linked list for this index */
155 while(ga2la
->lal
[ind_prev
].next
>= 0)
157 ind_prev
= ga2la
->lal
[ind_prev
].next
;
159 /* Search for space in the array */
160 ind
= ga2la
->start_space_search
;
161 while (ind
< ga2la
->nalloc
&& ga2la
->lal
[ind
].ga
>= 0)
165 /* If we are at the end of the list we need to increase the size */
166 if (ind
== ga2la
->nalloc
)
168 ga2la
->nalloc
= over_alloc_dd(ind
+1);
169 srenew(ga2la
->lal
,ga2la
->nalloc
);
170 for(i
=ind
; i
<ga2la
->nalloc
; i
++)
172 ga2la
->lal
[i
].ga
= -1;
173 ga2la
->lal
[i
].next
= -1;
176 ga2la
->lal
[ind_prev
].next
= ind
;
178 ga2la
->start_space_search
= ind
+ 1;
180 ga2la
->lal
[ind
].ga
= a_gl
;
181 ga2la
->lal
[ind
].la
= a_loc
;
182 ga2la
->lal
[ind
].cell
= cell
;
185 /* Delete the ga2la entry for global atom a_gl */
186 static void ga2la_del(gmx_ga2la_t ga2la
,int a_gl
)
192 ga2la
->laa
[a_gl
].cell
= -1;
198 ind
= a_gl
% ga2la
->mod
;
201 if (ga2la
->lal
[ind
].ga
== a_gl
)
205 ga2la
->lal
[ind_prev
].next
= ga2la
->lal
[ind
].next
;
207 /* This index is a linked entry, so we free an entry.
208 * Check if we are creating the first empty space.
210 if (ind
< ga2la
->start_space_search
)
212 ga2la
->start_space_search
= ind
;
215 ga2la
->lal
[ind
].ga
= -1;
216 ga2la
->lal
[ind
].cell
= -1;
217 ga2la
->lal
[ind
].next
= -1;
222 ind
= ga2la
->lal
[ind
].next
;
229 /* Change the local atom for present ga2la entry for global atom a_gl */
230 static void ga2la_change_la(gmx_ga2la_t ga2la
,int a_gl
,int a_loc
)
236 ga2la
->laa
[a_gl
].la
= a_loc
;
241 ind
= a_gl
% ga2la
->mod
;
244 if (ga2la
->lal
[ind
].ga
== a_gl
)
246 ga2la
->lal
[ind
].la
= a_loc
;
250 ind
= ga2la
->lal
[ind
].next
;
257 /* Returns if the global atom a_gl available locally.
258 * Sets the local atom and cell,
259 * cell can be larger than the number of zones,
260 * in which case it indicates that it is more than one cell away
261 * in zone cell - #zones.
263 static bool ga2la_get(const gmx_ga2la_t ga2la
,int a_gl
,int *a_loc
,int *cell
)
269 *a_loc
= ga2la
->laa
[a_gl
].la
;
270 *cell
= ga2la
->laa
[a_gl
].cell
;
272 return (ga2la
->laa
[a_gl
].cell
>= 0);
275 ind
= a_gl
% ga2la
->mod
;
278 if (ga2la
->lal
[ind
].ga
== a_gl
)
280 *a_loc
= ga2la
->lal
[ind
].la
;
281 *cell
= ga2la
->lal
[ind
].cell
;
285 ind
= ga2la
->lal
[ind
].next
;
292 /* Returns if the global atom a_gl is a home atom.
293 * Sets the local atom.
295 static bool ga2la_get_home(const gmx_ga2la_t ga2la
,int a_gl
,int *a_loc
)
301 *a_loc
= ga2la
->laa
[a_gl
].la
;
303 return (ga2la
->laa
[a_gl
].cell
== 0);
306 ind
= a_gl
% ga2la
->mod
;
309 if (ga2la
->lal
[ind
].ga
== a_gl
)
311 if (ga2la
->lal
[ind
].cell
== 0)
313 *a_loc
= ga2la
->lal
[ind
].la
;
322 ind
= ga2la
->lal
[ind
].next
;
329 /* Returns if the global atom a_gl is a home atom.
331 static bool ga2la_is_home(const gmx_ga2la_t ga2la
,int a_gl
)
337 return (ga2la
->laa
[a_gl
].cell
== 0);
340 ind
= a_gl
% ga2la
->mod
;
343 if (ga2la
->lal
[ind
].ga
== a_gl
)
345 return (ga2la
->lal
[ind
].cell
== 0);
347 ind
= ga2la
->lal
[ind
].next
;
358 #endif /* _gmx_ga2la_h */