* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/ns.h"
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "macros.h"
+
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/math/utilities.h"
-#include "vec.h"
-#include "network.h"
-#include "nsgrid.h"
-#include "force.h"
-#include "nonbonded.h"
-#include "ns.h"
-#include "pbc.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "nrnb.h"
-#include "txtdump.h"
-#include "mtop_util.h"
-
-#include "domdec.h"
-#include "adress.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+#include "adress.h"
/*
* E X C L U S I O N H A N D L I N G
*
************************************************/
-static void reallocate_nblist(t_nblist *nl)
+void reallocate_nblist(t_nblist *nl)
{
if (gmx_debug_at)
{
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.
*/
nl->maxnri = homenr*4;
nl->maxnrj = 0;
- nl->maxlen = 0;
nl->nri = -1;
nl->nrj = 0;
nl->iinr = NULL;
nl->gid = NULL;
nl->shift = NULL;
nl->jindex = NULL;
+ nl->jjnr = NULL;
+ nl->excl_fep = NULL;
reallocate_nblist(nl);
nl->jindex[0] = 0;
* 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
|| nbl->nlist_sr[eNL_QQ_WATER].kernelptr_vf == NULL
-#ifndef DISABLE_WATERWATER_NLIST
|| nbl->nlist_sr[eNL_VDWQQ_WATERWATER].kernelptr_vf == NULL
- || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == NULL
-#endif
- )
+ || nbl->nlist_sr[eNL_QQ_WATERWATER].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)
{
nl->nri = -1;
nl->nrj = 0;
- nl->maxlen = 0;
if (nl->jindex)
{
nl->jindex[0] = 0;
-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];
-
- /* nlist length for water i molecules is treated statically
- * in the innerloops
- */
- if (len > nlist->maxlen)
- {
- nlist->maxlen = len;
- }
}
}
-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;
if (iwater != esolNO)
{
- vdwc = &nlist[eNL_VDWQQ_WATER];
- vdw = &nlist[eNL_VDW];
- coul = &nlist[eNL_QQ_WATER];
-#ifndef DISABLE_WATERWATER_NLIST
+ vdwc = &nlist[eNL_VDWQQ_WATER];
+ vdw = &nlist[eNL_VDW];
+ coul = &nlist[eNL_QQ_WATER];
vdwc_ww = &nlist[eNL_VDWQQ_WATERWATER];
coul_ww = &nlist[eNL_QQ_WATERWATER];
-#endif
}
else
{
if (bDoCoul && bDoVdW)
{
new_i_nblist(vdwc, i_atom, shift, gid);
-#ifndef DISABLE_WATERWATER_NLIST
new_i_nblist(vdwc_ww, i_atom, shift, gid);
-#endif
}
if (bDoVdW)
{
if (bDoCoul)
{
new_i_nblist(coul, i_atom, shift, gid);
-#ifndef DISABLE_WATERWATER_NLIST
new_i_nblist(coul_ww, i_atom, shift, gid);
-#endif
}
/* Loop over the j charge groups */
for (j = 0; (j < nj); j++)
}
else
{
-#ifdef DISABLE_WATERWATER_NLIST
- /* Add entries for the three atoms - only do VdW if we need to */
- if (!bDoVdW)
- {
- add_j_to_nblist(coul, jj0, bLR);
- }
- else
- {
- add_j_to_nblist(vdwc, jj0, bLR);
- }
- add_j_to_nblist(coul, jj0+1, bLR);
- add_j_to_nblist(coul, jj0+2, bLR);
-#else
/* One entry for the entire water-water interaction */
if (!bDoVdW)
{
{
add_j_to_nblist(vdwc_ww, jj0, bLR);
}
-#endif
}
}
else if (iwater == esolTIP4P && jwater == esolTIP4P)
}
else
{
-#ifdef DISABLE_WATERWATER_NLIST
- /* Add entries for the four atoms - only do VdW if we need to */
- if (bDoVdW)
- {
- add_j_to_nblist(vdw, jj0, bLR);
- }
- add_j_to_nblist(coul, jj0+1, bLR);
- add_j_to_nblist(coul, jj0+2, bLR);
- add_j_to_nblist(coul, jj0+3, bLR);
-#else
/* One entry for the entire water-water interaction */
if (!bDoVdW)
{
{
add_j_to_nblist(vdwc_ww, jj0, bLR);
}
-#endif
}
}
else
close_i_nblist(vdw);
close_i_nblist(coul);
close_i_nblist(vdwc);
-#ifndef DISABLE_WATERWATER_NLIST
close_i_nblist(coul_ww);
close_i_nblist(vdwc_ww);
-#endif
}
else
{
*
************************************************/
-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;
gmx_ns_t *ns;
atom_id **nl_lr_ljc, **nl_lr_one, **nl_sr;
int *nlr_ljc, *nlr_one, *nsr;
- gmx_domdec_t *dd = NULL;
+ gmx_domdec_t *dd;
t_block *cgs = &(top->cgs);
int *cginfo = fr->cginfo;
/* atom_id *i_atoms,*cgsindex=cgs->index; */
ns = &fr->ns;
bDomDec = DOMAINDECOMP(cr);
- if (bDomDec)
- {
- dd = cr->dd;
- }
+ dd = cr->dd;
bTriclinicX = ((YY < grid->npbcdim &&
(!bDomDec || dd->nc[YY] == 1) && box[YY][XX] != 0) ||
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff