* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nbnxn_atomdata.h"
+
+#include "config.h"
+#include <assert.h>
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include <assert.h>
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "nbnxn_consts.h"
-#include "nbnxn_internal.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "gromacs/utility/gmxomp.h"
-#include "gmx_omp_nthreads.h"
+
#include "thread_mpi/atomic.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_internal.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
/* Default nbnxn allocation routine, allocates NBNXN_MEM_ALIGN byte aligned */
void nbnxn_alloc_aligned(void **ptr, size_t nbytes)
{
}
}
-/* Sets the atom type and LJ data in nbnxn_atomdata_t */
+/* Sets the atom type in nbnxn_atomdata_t */
static void nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t *nbat,
int ngrid,
const nbnxn_search_t nbs,
copy_int_to_nbat_int(nbs->a+ash, grid->cxy_na[i], ncz*grid->na_sc,
type, nbat->ntype-1, nbat->type+ash);
+ }
+ }
+}
+
+/* Sets the LJ combination rule parameters in nbnxn_atomdata_t */
+static void nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t *nbat,
+ int ngrid,
+ const nbnxn_search_t nbs)
+{
+ int g, i, ncz, ash;
+ const nbnxn_grid_t *grid;
- if (nbat->comb_rule != ljcrNONE)
+ if (nbat->comb_rule != ljcrNONE)
+ {
+ for (g = 0; g < ngrid; g++)
+ {
+ grid = &nbs->grid[g];
+
+ /* Loop over all columns and copy and fill */
+ for (i = 0; i < grid->ncx*grid->ncy; i++)
{
+ ncz = grid->cxy_ind[i+1] - grid->cxy_ind[i];
+ ash = (grid->cell0 + grid->cxy_ind[i])*grid->na_sc;
+
if (nbat->XFormat == nbatX4)
{
copy_lj_to_nbat_lj_comb_x4(nbat->nbfp_comb,
nbnxn_atomdata_mask_fep(nbat, ngrid, nbs);
}
+ /* This must be done after masking types for FEP */
+ nbnxn_atomdata_set_ljcombparams(nbat, ngrid, nbs);
+
nbnxn_atomdata_set_energygroups(nbat, ngrid, nbs, atinfo);
}