Merge release-5-0 into master

[alexxy/gromacs.git] / src / gromacs / mdlib / nbnxn_kernels / nbnxn_kernel_ref.c

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
index 0be4be644d987e9eecf22b6a64f4457644cfe755..4cad2a2f5637ba5b410af8db8ca1225cc441d1a6 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
@@ -32,21 +32,24 @@
  * 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 <math.h>
 #include <assert.h>
+#include <math.h>
 
-#include "typedefs.h"
-#include "vec.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"
-#include "force.h"
-#include "gmx_omp_nthreads.h"
-#include "nbnxn_kernel_ref.h"
-#include "../nbnxn_consts.h"
-#include "nbnxn_kernel_common.h"
 
 /*! \brief Typedefs for declaring lookup tables of kernel functions.
  */
@@ -70,21 +73,21 @@ typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t     *nbl,
 /* Analytical reaction-field kernels */
 #define CALC_COUL_RF
 #define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_CUT
 #define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_FORCE_SWITCH
 #define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#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 "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_GEOM
 #define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_LB
 #undef LJ_CUT
 #undef LJ_EWALD
@@ -94,42 +97,42 @@ typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t     *nbl,
 /* Tabulated exclusion interaction electrostatics kernels */
 #define CALC_COUL_TAB
 #define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_CUT
 #define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_FORCE_SWITCH
 #define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#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 "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_GEOM
 #define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#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
 #define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_CUT
 #define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_FORCE_SWITCH
 #define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#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 "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_GEOM
 #define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_LB
 #undef LJ_CUT
 #undef LJ_EWALD
@@ -182,6 +185,7 @@ nbnxn_kernel_ref(const nbnxn_pairlist_set_t *nbl_list,
     int                coult;
     int                vdwt;
     int                nb;
+    int                nthreads gmx_unused;
 
     nnbl = nbl_list->nnbl;
     nbl  = nbl_list->nbl;
@@ -239,7 +243,8 @@ nbnxn_kernel_ref(const nbnxn_pairlist_set_t *nbl_list,
         gmx_incons("Unsupported vdwtype in nbnxn reference kernel");
     }
 
-#pragma omp parallel for schedule(static) num_threads(gmx_omp_nthreads_get(emntNonbonded))
+    nthreads = gmx_omp_nthreads_get(emntNonbonded);
+#pragma omp parallel for schedule(static) num_threads(nthreads)
     for (nb = 0; nb < nnbl; nb++)
     {
         nbnxn_atomdata_output_t *out;