#include <math.h>
#include <string.h>
#include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gromacs/math/utilities.h"
#include "vec.h"
+#include "types/commrec.h"
#include "network.h"
#include "nsgrid.h"
#include "force.h"
int maxsr, int maxlr,
int ivdw, int ivdwmod,
int ielec, int ielecmod,
- int igeometry, int type)
+ int igeometry, int type,
+ gmx_bool bElecAndVdwSwitchDiffers)
{
t_nblist *nl;
int homenr;
}
/* This will also set the simd_padding_width field */
- gmx_nonbonded_set_kernel_pointers( (i == 0) ? log : NULL, nl);
+ gmx_nonbonded_set_kernel_pointers( (i == 0) ? log : NULL, nl, bElecAndVdwSwitchDiffers);
/* maxnri is influenced by the number of shifts (maximum is 8)
* and the number of energy groups.
* cache trashing.
*/
int maxsr, maxsr_wat, maxlr, maxlr_wat;
- int ielec, ielecf, ivdw, ielecmod, ielecmodf, ivdwmod, type;
+ int ielec, ivdw, ielecmod, ivdwmod, type;
int solvent;
int igeometry_def, igeometry_w, igeometry_ww;
int i;
+ gmx_bool bElecAndVdwSwitchDiffers;
t_nblists *nbl;
/* maxsr = homenr-fr->nWatMol*3; */
}
/* Determine the values for ielec/ivdw. */
- ielec = fr->nbkernel_elec_interaction;
- ivdw = fr->nbkernel_vdw_interaction;
- ielecmod = fr->nbkernel_elec_modifier;
- ivdwmod = fr->nbkernel_vdw_modifier;
- type = GMX_NBLIST_INTERACTION_STANDARD;
+ ielec = fr->nbkernel_elec_interaction;
+ ivdw = fr->nbkernel_vdw_interaction;
+ ielecmod = fr->nbkernel_elec_modifier;
+ ivdwmod = fr->nbkernel_vdw_modifier;
+ type = GMX_NBLIST_INTERACTION_STANDARD;
+ bElecAndVdwSwitchDiffers = ( (fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw));
fr->ns.bCGlist = (getenv("GMX_NBLISTCG") != 0);
if (!fr->ns.bCGlist)
type = GMX_NBLIST_INTERACTION_ADRESS;
}
init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ], &nbl->nlist_lr[eNL_VDWQQ],
- maxsr, maxlr, ivdw, ivdwmod, ielec, ielecmod, igeometry_def, type);
+ maxsr, maxlr, ivdw, ivdwmod, ielec, ielecmod, igeometry_def, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_VDW], &nbl->nlist_lr[eNL_VDW],
- maxsr, maxlr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, igeometry_def, type);
+ maxsr, maxlr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, igeometry_def, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_QQ], &nbl->nlist_lr[eNL_QQ],
- maxsr, maxlr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_def, type);
+ maxsr, maxlr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_def, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_WATER], &nbl->nlist_lr[eNL_VDWQQ_WATER],
- maxsr_wat, maxlr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_w, type);
+ maxsr_wat, maxlr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_w, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_QQ_WATER], &nbl->nlist_lr[eNL_QQ_WATER],
- maxsr_wat, maxlr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_w, type);
+ maxsr_wat, maxlr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_w, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_WATERWATER], &nbl->nlist_lr[eNL_VDWQQ_WATERWATER],
- maxsr_wat, maxlr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_ww, type);
+ maxsr_wat, maxlr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_ww, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_QQ_WATERWATER], &nbl->nlist_lr[eNL_QQ_WATERWATER],
- maxsr_wat, maxlr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_ww, type);
+ maxsr_wat, maxlr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_ww, type, bElecAndVdwSwitchDiffers);
/* Did we get the solvent loops so we can use optimized water kernels? */
if (nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf == NULL
)
{
fr->solvent_opt = esolNO;
- fprintf(log, "Note: The available nonbonded kernels do not support water optimization - disabling.\n");
+ if (log != NULL)
+ {
+ fprintf(log, "Note: The available nonbonded kernels do not support water optimization - disabling.\n");
+ }
}
if (fr->efep != efepNO)
{
- if ((fr->bEwald) && (fr->sc_alphacoul > 0)) /* need to handle long range differently if using softcore */
- {
- ielecf = GMX_NBKERNEL_ELEC_EWALD;
- ielecmodf = eintmodNONE;
- }
- else
- {
- ielecf = ielec;
- ielecmodf = ielecmod;
- }
-
init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_FREE], &nbl->nlist_lr[eNL_VDWQQ_FREE],
- maxsr, maxlr, ivdw, ivdwmod, ielecf, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
+ maxsr, maxlr, ivdw, ivdwmod, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_VDW_FREE], &nbl->nlist_lr[eNL_VDW_FREE],
- maxsr, maxlr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
+ maxsr, maxlr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_QQ_FREE], &nbl->nlist_lr[eNL_QQ_FREE],
- maxsr, maxlr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielecf, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
+ maxsr, maxlr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
}
}
/* QMMM MM list */
if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
{
init_nblist(log, &fr->QMMMlist, NULL,
- maxsr, maxlr, 0, 0, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_STANDARD);
+ maxsr, maxlr, 0, 0, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_STANDARD, bElecAndVdwSwitchDiffers);
}
if (log != NULL)
-static inline void new_i_nblist(t_nblist *nlist, atom_id i_atom, int shift, int gid)
+static gmx_inline void new_i_nblist(t_nblist *nlist, atom_id i_atom, int shift, int gid)
{
int i, k, nri, nshift;
}
}
-static inline void close_i_nblist(t_nblist *nlist)
+static gmx_inline void close_i_nblist(t_nblist *nlist)
{
int nri = nlist->nri;
int len;
nlist->jindex[nri+1] = nlist->nrj;
len = nlist->nrj - nlist->jindex[nri];
+ /* If there are no j-particles we have to reduce the
+ * number of i-particles again, to prevent errors in the
+ * kernel functions.
+ */
+ if ((len == 0) && (nlist->nri > 0))
+ {
+ nlist->nri--;
+ }
}
}
-static inline void close_nblist(t_nblist *nlist)
+static gmx_inline void close_nblist(t_nblist *nlist)
{
/* Only close this nblist when it has been initialized.
* Avoid the creation of i-lists with no j-particles.
}
}
-static inline void close_neighbor_lists(t_forcerec *fr, gmx_bool bMakeQMMMnblist)
+static gmx_inline void close_neighbor_lists(t_forcerec *fr, gmx_bool bMakeQMMMnblist)
{
int n, i;
}
-static inline void add_j_to_nblist(t_nblist *nlist, atom_id j_atom, gmx_bool bLR)
+static gmx_inline void add_j_to_nblist(t_nblist *nlist, atom_id j_atom, gmx_bool bLR)
{
int nrj = nlist->nrj;
nlist->nrj++;
}
-static inline void add_j_to_nblist_cg(t_nblist *nlist,
- atom_id j_start, int j_end,
- t_excl *bexcl, gmx_bool i_is_j,
- gmx_bool bLR)
+static gmx_inline void add_j_to_nblist_cg(t_nblist *nlist,
+ atom_id j_start, int j_end,
+ t_excl *bexcl, gmx_bool i_is_j,
+ gmx_bool bLR)
{
int nrj = nlist->nrj;
int j;
*
************************************************/
-static inline void get_dx(int Nx, real gridx, real rc2, int xgi, real x,
- int *dx0, int *dx1, real *dcx2)
+static gmx_inline void get_dx(int Nx, real gridx, real rc2, int xgi, real x,
+ int *dx0, int *dx1, real *dcx2)
{
real dcx, tmp;
int xgi0, xgi1, i;
}
}
-static inline void get_dx_dd(int Nx, real gridx, real rc2, int xgi, real x,
- int ncpddc, int shift_min, int shift_max,
- int *g0, int *g1, real *dcx2)
+static gmx_inline void get_dx_dd(int Nx, real gridx, real rc2, int xgi, real x,
+ int ncpddc, int shift_min, int shift_max,
+ int *g0, int *g1, real *dcx2)
{
real dcx, tmp;
int g_min, g_max, shift_home;