-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * 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.
*
- * This source code is part of
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
*
- * G R O M A C S
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
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+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
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*
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
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- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
+ * 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 <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"
-/* Analytical reaction-field kernels */
-#define CALC_COUL_RF
+#include "config.h"
-/* Include the force+energy kernels */
-#define CALC_ENERGIES
-#include "nbnxn_kernel_ref_outer.h"
-#undef CALC_ENERGIES
+#include <assert.h>
+#include <math.h>
-/* Include the force+energygroups kernels */
-#define CALC_ENERGIES
-#define ENERGY_GROUPS
-#include "nbnxn_kernel_ref_outer.h"
-#undef ENERGY_GROUPS
-#undef CALC_ENERGIES
+#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.
+ */
-/* Include the force only kernels */
-#include "nbnxn_kernel_ref_outer.h"
+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,
+ rvec *shift_vec,
+ real *f,
+ real *fshift,
+ real *Vvdw,
+ real *Vc);
+/* Analytical reaction-field kernels */
+#define CALC_COUL_RF
+#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
-typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t *nbl,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- real *f,
- real *fshift,
- real *Vvdw,
- real *Vc);
+enum {
+ coultRF, coultTAB, coultTAB_TWIN, coultNR
+};
-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);
-
-enum { coultRF, coultTAB, coultTAB_TWIN, coultNR };
+enum {
+ vdwtCUT, vdwtFSWITCH, vdwtPSWITCH, vdwtEWALDGEOM, vdwtEWALDLB, vdwtNR
+};
-p_nbk_func_ener p_nbk_c_ener[coultNR] =
-{ nbnxn_kernel_ref_rf_ener,
- nbnxn_kernel_ref_tab_ener,
- nbnxn_kernel_ref_tab_twin_ener };
+p_nbk_func_noener p_nbk_c_noener[coultNR][vdwtNR] =
+{
+ { 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] =
-{ nbnxn_kernel_ref_rf_energrp,
- nbnxn_kernel_ref_tab_energrp,
- nbnxn_kernel_ref_tab_twin_energrp};
+p_nbk_func_ener p_nbk_c_ener[coultNR][vdwtNR] =
+{
+ { 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] =
-{ nbnxn_kernel_ref_rf_noener,
- nbnxn_kernel_ref_tab_noener,
- nbnxn_kernel_ref_tab_twin_noener };
+p_nbk_func_ener p_nbk_c_energrp[coultNR][vdwtNR] =
+{
+ { 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
nbnxn_kernel_ref(const nbnxn_pairlist_set_t *nbl_list,
const nbnxn_atomdata_t *nbat,
const interaction_const_t *ic,
rvec *shift_vec,
- int force_flags,
- int clearF,
+ int force_flags,
+ int clearF,
real *fshift,
real *Vc,
real *Vvdw)
{
- int nnbl;
+ int nnbl;
nbnxn_pairlist_t **nbl;
- int coult;
- int nb;
+ int coult;
+ int vdwt;
+ int nb;
nnbl = nbl_list->nnbl;
nbl = nbl_list->nbl;
}
}
+ 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++)
+ for (nb = 0; nb < nnbl; nb++)
{
nbnxn_atomdata_output_t *out;
- real *fshift_p;
+ real *fshift_p;
out = &nbat->out[nb];
if (clearF == enbvClearFYes)
{
- clear_f(nbat,nb,out->f);
+ clear_f(nbat, nb, out->f);
}
if ((force_flags & GMX_FORCE_VIRIAL) && nnbl == 1)
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
{
/* Calculate energy group contributions */
int i;
- for(i=0; i<out->nV; i++)
+ for (i = 0; i < out->nV; i++)
{
out->Vvdw[i] = 0;
}
- for(i=0; i<out->nV; i++)
+ for (i = 0; i < out->nV; i++)
{
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);
}
}
if (force_flags & GMX_FORCE_ENERGY)
{
- reduce_energies_over_lists(nbat,nnbl,Vvdw,Vc);
+ reduce_energies_over_lists(nbat, nnbl, Vvdw, Vc);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff