/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* 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 "nbnxn_kernel_ref.h"
+
+#include "config.h"
+
+#include <assert.h>
#include <math.h>
-#include "typedefs.h"
-#include "vec.h"
-#include "smalloc.h"
-#include "force.h"
-#include "gmx_omp_nthreads.h"
-#include "nbnxn_kernel_ref.h"
-#include "../nbnxn_consts.h"
-#include "nbnxn_kernel_common.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/smalloc.h"
/*! \brief Typedefs for declaring lookup tables of kernel functions.
*/
+
+typedef void (*p_nbk_func_noener)(const nbnxn_pairlist_t *nbl,
+ const nbnxn_atomdata_t *nbat,
+ const interaction_const_t *ic,
+ rvec *shift_vec,
+ real *f,
+ real *fshift);
+
typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t *nbl,
const nbnxn_atomdata_t *nbat,
const interaction_const_t *ic,
real *Vvdw,
real *Vc);
-typedef void (*p_nbk_func_noener)(const nbnxn_pairlist_t *nbl,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- real *f,
- real *fshift);
-
/* Analytical reaction-field kernels */
#define CALC_COUL_RF
-
-/* Include the force+energy kernels */
-#define CALC_ENERGIES
-#include "nbnxn_kernel_ref_outer.h"
-#undef CALC_ENERGIES
-
-/* Include the force+energygroups kernels */
-#define CALC_ENERGIES
-#define ENERGY_GROUPS
-#include "nbnxn_kernel_ref_outer.h"
-#undef ENERGY_GROUPS
-#undef CALC_ENERGIES
-
-/* Include the force only kernels */
-#include "nbnxn_kernel_ref_outer.h"
-
+#define LJ_CUT
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_CUT
+#define LJ_FORCE_SWITCH
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_FORCE_SWITCH
+#define LJ_POT_SWITCH
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_POT_SWITCH
+#define LJ_EWALD
+#define LJ_CUT
+#define LJ_EWALD_COMB_GEOM
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_EWALD_COMB_GEOM
+#define LJ_EWALD_COMB_LB
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_EWALD_COMB_LB
+#undef LJ_CUT
+#undef LJ_EWALD
#undef CALC_COUL_RF
/* Tabulated exclusion interaction electrostatics kernels */
#define CALC_COUL_TAB
-
-/* Include the force+energy kernels */
-#define CALC_ENERGIES
-#include "nbnxn_kernel_ref_outer.h"
-#undef CALC_ENERGIES
-
-/* Include the force+energygroups kernels */
-#define CALC_ENERGIES
-#define ENERGY_GROUPS
-#include "nbnxn_kernel_ref_outer.h"
-#undef ENERGY_GROUPS
-#undef CALC_ENERGIES
-
-/* Include the force only kernels */
-#include "nbnxn_kernel_ref_outer.h"
-
+#define LJ_CUT
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_CUT
+#define LJ_FORCE_SWITCH
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_FORCE_SWITCH
+#define LJ_POT_SWITCH
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_POT_SWITCH
+#define LJ_EWALD
+#define LJ_CUT
+#define LJ_EWALD_COMB_GEOM
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_EWALD_COMB_GEOM
+#define LJ_EWALD_COMB_LB
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_EWALD_COMB_LB
+#undef LJ_CUT
+#undef LJ_EWALD
/* Twin-range cut-off kernels */
#define VDW_CUTOFF_CHECK
-
-/* Include the force+energy kernels */
-#define CALC_ENERGIES
-#include "nbnxn_kernel_ref_outer.h"
-#undef CALC_ENERGIES
-
-/* Include the force+energygroups kernels */
-#define CALC_ENERGIES
-#define ENERGY_GROUPS
-#include "nbnxn_kernel_ref_outer.h"
-#undef ENERGY_GROUPS
-#undef CALC_ENERGIES
-
-/* Include the force only kernels */
-#include "nbnxn_kernel_ref_outer.h"
-
+#define LJ_CUT
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_CUT
+#define LJ_FORCE_SWITCH
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_FORCE_SWITCH
+#define LJ_POT_SWITCH
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_POT_SWITCH
+#define LJ_EWALD
+#define LJ_CUT
+#define LJ_EWALD_COMB_GEOM
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_EWALD_COMB_GEOM
+#define LJ_EWALD_COMB_LB
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
+#undef LJ_EWALD_COMB_LB
+#undef LJ_CUT
+#undef LJ_EWALD
#undef VDW_CUTOFF_CHECK
-
#undef CALC_COUL_TAB
coultRF, coultTAB, coultTAB_TWIN, coultNR
};
-p_nbk_func_ener p_nbk_c_ener[coultNR] =
+enum {
+ vdwtCUT, vdwtFSWITCH, vdwtPSWITCH, vdwtEWALDGEOM, vdwtEWALDLB, vdwtNR
+};
+
+p_nbk_func_noener p_nbk_c_noener[coultNR][vdwtNR] =
{
- nbnxn_kernel_ref_rf_ener,
- nbnxn_kernel_ref_tab_ener,
- nbnxn_kernel_ref_tab_twin_ener
+ { nbnxn_kernel_ElecRF_VdwLJ_F_ref, nbnxn_kernel_ElecRF_VdwLJFsw_F_ref, nbnxn_kernel_ElecRF_VdwLJPsw_F_ref, nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_ref, nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_ref },
+ { nbnxn_kernel_ElecQSTab_VdwLJ_F_ref, nbnxn_kernel_ElecQSTab_VdwLJFsw_F_ref, nbnxn_kernel_ElecQSTab_VdwLJPsw_F_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_F_ref },
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref }
};
-p_nbk_func_ener p_nbk_c_energrp[coultNR] =
+p_nbk_func_ener p_nbk_c_ener[coultNR][vdwtNR] =
{
- nbnxn_kernel_ref_rf_energrp,
- nbnxn_kernel_ref_tab_energrp,
- nbnxn_kernel_ref_tab_twin_energrp
+ { nbnxn_kernel_ElecRF_VdwLJ_VF_ref, nbnxn_kernel_ElecRF_VdwLJFsw_VF_ref, nbnxn_kernel_ElecRF_VdwLJPsw_VF_ref, nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_ref, nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_ref },
+ { nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTab_VdwLJFsw_VF_ref, nbnxn_kernel_ElecQSTab_VdwLJPsw_VF_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VF_ref },
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref }
};
-p_nbk_func_noener p_nbk_c_noener[coultNR] =
+p_nbk_func_ener p_nbk_c_energrp[coultNR][vdwtNR] =
{
- nbnxn_kernel_ref_rf_noener,
- nbnxn_kernel_ref_tab_noener,
- nbnxn_kernel_ref_tab_twin_noener
+ { nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecRF_VdwLJFsw_VgrpF_ref, nbnxn_kernel_ElecRF_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_ref, nbnxn_kernel_ElecRF_VdwLJEwCombLB_VgrpF_ref },
+ { nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTab_VdwLJFsw_VgrpF_ref, nbnxn_kernel_ElecQSTab_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VgrpF_ref },
+ { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref }
};
void
int nnbl;
nbnxn_pairlist_t **nbl;
int coult;
+ int vdwt;
int nb;
nnbl = nbl_list->nnbl;
}
}
+ if (ic->vdwtype == evdwCUT)
+ {
+ switch (ic->vdw_modifier)
+ {
+ case eintmodPOTSHIFT:
+ case eintmodNONE:
+ vdwt = vdwtCUT;
+ break;
+ case eintmodFORCESWITCH:
+ vdwt = vdwtFSWITCH;
+ break;
+ case eintmodPOTSWITCH:
+ vdwt = vdwtPSWITCH;
+ break;
+ default:
+ gmx_incons("Unsupported VdW modifier");
+ break;
+ }
+ }
+ else if (ic->vdwtype == evdwPME)
+ {
+ if (ic->ljpme_comb_rule == ljcrGEOM)
+ {
+ assert(nbat->comb_rule == ljcrGEOM);
+ vdwt = vdwtEWALDGEOM;
+ }
+ else
+ {
+ assert(nbat->comb_rule == ljcrLB);
+ vdwt = vdwtEWALDLB;
+ }
+ }
+ else
+ {
+ gmx_incons("Unsupported vdwtype in nbnxn reference kernel");
+ }
+
#pragma omp parallel for schedule(static) num_threads(gmx_omp_nthreads_get(emntNonbonded))
for (nb = 0; nb < nnbl; nb++)
{
if (!(force_flags & GMX_FORCE_ENERGY))
{
/* Don't calculate energies */
- p_nbk_c_noener[coult](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p);
+ p_nbk_c_noener[coult][vdwt](nbl[nb], nbat,
+ ic,
+ shift_vec,
+ out->f,
+ fshift_p);
}
else if (out->nV == 1)
{
out->Vvdw[0] = 0;
out->Vc[0] = 0;
- p_nbk_c_ener[coult](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p,
- out->Vvdw,
- out->Vc);
+ p_nbk_c_ener[coult][vdwt](nbl[nb], nbat,
+ ic,
+ shift_vec,
+ out->f,
+ fshift_p,
+ out->Vvdw,
+ out->Vc);
}
else
{
out->Vc[i] = 0;
}
- p_nbk_c_energrp[coult](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p,
- out->Vvdw,
- out->Vc);
+ p_nbk_c_energrp[coult][vdwt](nbl[nb], nbat,
+ ic,
+ shift_vec,
+ out->f,
+ fshift_p,
+ out->Vvdw,
+ out->Vc);
}
}
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