Renamed bonded module as 'listed-forces'

[alexxy/gromacs.git] / src / gromacs / gmxlib / nonbonded / nonbonded.c

diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.c b/src/gromacs/gmxlib/nonbonded/nonbonded.c
index 40244b7be6cc74673687dac51aedda3885cf7490..c21e3201b28283e39faf42cb7707d573db1fdb4b 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nonbonded.c
+++ b/src/gromacs/gmxlib/nonbonded/nonbonded.c
@@ -34,71 +34,69 @@
  * 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/nonbonded.h"
+
+#include "config.h"
 
 #include <stdio.h>
 #include <stdlib.h>
 
 #include "thread_mpi/threads.h"
 
-#include "typedefs.h"
-#include "txtdump.h"
-#include "ns.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic_adress.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic_cg.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/listed-forces/bonded.h"
 #include "gromacs/math/utilities.h"
-#include "macros.h"
-#include "force.h"
-#include "names.h"
-#include "force.h"
-#include "bondf.h"
-#include "nrnb.h"
-#include "nonbonded.h"
-#include "gromacs/simd/simd.h"
-
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/simd/simd.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "nb_kernel.h"
-#include "nb_free_energy.h"
-#include "nb_generic.h"
-#include "nb_generic_cg.h"
-#include "nb_generic_adress.h"
-
 /* Different default (c) and SIMD instructions interaction-specific kernels */
-#include "nb_kernel_c/nb_kernel_c.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h"
 
 #if (defined GMX_SIMD_X86_SSE2) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_sse2_single/nb_kernel_sse2_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h"
 #endif
 #if (defined GMX_SIMD_X86_SSE4_1) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_avx_256_single/nb_kernel_avx_256_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h"
 #endif
 #if (defined GMX_SIMD_X86_SSE2 && defined GMX_DOUBLE)
-#    include "nb_kernel_sse2_double/nb_kernel_sse2_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h"
 #endif
 #if (defined GMX_SIMD_X86_SSE4_1 && defined GMX_DOUBLE)
-#    include "nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_128_FMA && defined GMX_DOUBLE)
-#    include "nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER && defined GMX_DOUBLE)
-#    include "nb_kernel_avx_256_double/nb_kernel_avx_256_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h"
 #endif
 #if (defined GMX_SIMD_SPARC64_HPC_ACE && defined GMX_DOUBLE)
-#    include "nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h"
 #endif
 
 
@@ -658,6 +656,8 @@ do_nonbonded_listed(int ftype, int nbonds,
 
         if (r2 >= fr->tab14.r*fr->tab14.r)
         {
+            /* This check isn't race free. But it doesn't matter because if a race occurs the only
+             * disadvantage is that the warning is printed twice */
             if (warned_rlimit == FALSE)
             {
                 nb_listed_warning_rlimit(x, ai, aj, global_atom_index, sqrt(r2), fr->tab14.r);