/* #define DEBUG_NNB */
-typedef struct {
+typedef struct
+{
int ai, aj;
} sortable;
-static int
-bond_sort (const void *a, const void *b)
+static int bond_sort(const void* a, const void* b)
{
const sortable *sa, *sb;
if (sa->ai == sb->ai)
{
- return (sa->aj-sb->aj);
+ return (sa->aj - sb->aj);
}
else
{
- return (sa->ai-sb->ai);
+ return (sa->ai - sb->ai);
}
}
-static int
-compare_int (const void * a, const void * b)
+static int compare_int(const void* a, const void* b)
{
- return ( *reinterpret_cast<const int*>(a) - *reinterpret_cast<const int*>(b) );
+ return (*reinterpret_cast<const int*>(a) - *reinterpret_cast<const int*>(b));
}
#ifdef DEBUG
-#define prints(str, n, s) __prints(str, n, s)
-static void __prints(char *str, int n, sortable *s)
+# define prints(str, n, s) __prints(str, n, s)
+static void __prints(char* str, int n, sortable* s)
{
int i;
}
}
#else
-#define prints(str, n, s)
+# define prints(str, n, s)
#endif
-void init_nnb(t_nextnb *nnb, int nr, int nrex)
+void init_nnb(t_nextnb* nnb, int nr, int nrex)
{
int i;
snew(nnb->nrexcl, nr);
for (i = 0; (i < nr); i++)
{
- snew(nnb->a[i], nrex+1);
- snew(nnb->nrexcl[i], nrex+1);
+ snew(nnb->a[i], nrex + 1);
+ snew(nnb->nrexcl[i], nrex + 1);
}
}
-static void add_nnb (t_nextnb *nnb, int nre, int i, int j)
+static void add_nnb(t_nextnb* nnb, int nre, int i, int j)
{
- srenew(nnb->a[i][nre], nnb->nrexcl[i][nre]+1);
+ srenew(nnb->a[i][nre], nnb->nrexcl[i][nre] + 1);
nnb->a[i][nre][nnb->nrexcl[i][nre]] = j;
nnb->nrexcl[i][nre]++;
}
-void done_nnb (t_nextnb *nnb)
+void done_nnb(t_nextnb* nnb)
{
int i, nre;
{
if (nnb->nrexcl[i][nre] > 0)
{
- sfree (nnb->a[i][nre]);
+ sfree(nnb->a[i][nre]);
}
}
- sfree (nnb->nrexcl[i]);
- sfree (nnb->a[i]);
+ sfree(nnb->nrexcl[i]);
+ sfree(nnb->a[i]);
}
- sfree (nnb->a);
- sfree (nnb->nrexcl);
+ sfree(nnb->a);
+ sfree(nnb->nrexcl);
nnb->nr = 0;
nnb->nrex = 0;
}
#ifdef DEBUG_NNB
-void __print_nnb(t_nextnb *nnb, char *s)
+void __print_nnb(t_nextnb* nnb, char* s)
{
int i, j, k;
}
#endif
-static void nnb2excl(t_nextnb *nnb, t_blocka *excl)
+static void nnb2excl(t_nextnb* nnb, t_blocka* excl)
{
int i, j, j_index;
int nre, nrx, nrs, nr_of_sortables;
- sortable *s;
+ sortable* s;
- srenew(excl->index, nnb->nr+1);
+ srenew(excl->index, nnb->nr + 1);
excl->index[0] = 0;
for (i = 0; (i < nnb->nr); i++)
{
prints("nnb2excl before qsort", nr_of_sortables, s);
if (nr_of_sortables > 1)
{
- qsort (s, nr_of_sortables, static_cast<size_t>(sizeof(s[0])), bond_sort);
+ qsort(s, nr_of_sortables, static_cast<size_t>(sizeof(s[0])), bond_sort);
prints("nnb2excl after qsort", nr_of_sortables, s);
}
{
for (j = 1; (j < nr_of_sortables); j++)
{
- if ((s[j].ai != s[j-1].ai) || (s[j].aj != s[j-1].aj))
+ if ((s[j].ai != s[j - 1].ai) || (s[j].aj != s[j - 1].aj))
{
- s[j_index++] = s[j-1];
+ s[j_index++] = s[j - 1];
}
}
- s[j_index++] = s[j-1];
+ s[j_index++] = s[j - 1];
}
nr_of_sortables = j_index;
prints("after rm-double", j_index, s);
/* make space for arrays */
- srenew(excl->a, excl->nra+nr_of_sortables);
+ srenew(excl->a, excl->nra + nr_of_sortables);
/* put the sorted exclusions in the target list */
for (nrs = 0; (nrs < nr_of_sortables); nrs++)
{
- excl->a[excl->nra+nrs] = s[nrs].aj;
+ excl->a[excl->nra + nrs] = s[nrs].aj;
}
- excl->nra += nr_of_sortables;
- excl->index[i+1] = excl->nra;
+ excl->nra += nr_of_sortables;
+ excl->index[i + 1] = excl->nra;
/* cleanup temporary space */
- sfree (s);
+ sfree(s);
}
}
* the routine will return true if the query atom is already listed as
* first or second neighbor (exclusion) in nnb.
*/
-static bool
-atom_is_present_in_nnb(const t_nextnb * nnb,
- int atom,
- int highest_order,
- int query)
+static bool atom_is_present_in_nnb(const t_nextnb* nnb, int atom, int highest_order, int query)
{
GMX_RELEASE_ASSERT(highest_order < nnb->nrex, "Inconsistent nnb seach parameters");
}
static void do_gen(int nrbonds, /* total number of bonds in s */
- sortable *s, /* bidirectional list of bonds */
- t_nextnb *nnb) /* the tmp storage for excl */
+ sortable* s, /* bidirectional list of bonds */
+ t_nextnb* nnb) /* the tmp storage for excl */
/* Assume excl is initalised and s[] contains all bonds bidirectional */
{
int i, j, k, n, nb;
// with high exclusion order
if (!atom_is_present_in_nnb(nnb, i, n, nnb->a[nb][n][k]))
{
- add_nnb(nnb, n+1, i, nnb->a[nb][n][k]);
+ add_nnb(nnb, n + 1, i, nnb->a[nb][n][k]);
}
}
}
}
}
print_nnb(nnb, "After exclude rest");
-
}
-static void add_b(InteractionsOfType *bonds, int *nrf, sortable *s)
+static void add_b(InteractionsOfType* bonds, int* nrf, sortable* s)
{
int i = 0;
- for (const auto &bond : bonds->interactionTypes)
+ for (const auto& bond : bonds->interactionTypes)
{
int ai = bond.ai();
int aj = bond.aj();
if ((ai < 0) || (aj < 0))
{
- gmx_fatal(FARGS, "Impossible atom numbers in bond %d: ai=%d, aj=%d",
- i, ai, aj);
+ gmx_fatal(FARGS, "Impossible atom numbers in bond %d: ai=%d, aj=%d", i, ai, aj);
}
/* Add every bond twice */
s[(*nrf)].ai = ai;
}
}
-void gen_nnb(t_nextnb *nnb, gmx::ArrayRef<InteractionsOfType> plist)
+void gen_nnb(t_nextnb* nnb, gmx::ArrayRef<InteractionsOfType> plist)
{
- sortable *s;
+ sortable* s;
int nrbonds, nrf;
nrbonds = 0;
if (IS_CHEMBOND(i))
{
/* we need every bond twice (bidirectional) */
- nrbonds += 2*plist[i].size();
+ nrbonds += 2 * plist[i].size();
}
}
sfree(s);
}
-static void
-sort_and_purge_nnb(t_nextnb *nnb)
+static void sort_and_purge_nnb(t_nextnb* nnb)
{
int i, j, k, m, n, cnt, prev, idx;
bool found;
}
-void generate_excl (int nrexcl,
- int nratoms,
- gmx::ArrayRef<InteractionsOfType> plist,
- t_blocka *excl)
+void generate_excl(int nrexcl, int nratoms, gmx::ArrayRef<InteractionsOfType> plist, t_blocka* excl)
{
t_nextnb nnb;
if (nrexcl < 0)
gen_nnb(&nnb, plist);
excl->nr = nratoms;
sort_and_purge_nnb(&nnb);
- nnb2excl (&nnb, excl);
+ nnb2excl(&nnb, excl);
done_nnb(&nnb);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff