Move types/ishift.h to pbcutil/

- Remove the include from typedefs.h, and add it to files that are using
  it.

Change-Id: I752648c73ba767eff30c113c84aabd5c7d7494ac

diff --git a/src/gromacs/gmxana/gmx_disre.c b/src/gromacs/gmxana/gmx_disre.c
index 44cb518879282a340ec33a8f96dffbd17a7da2ee..1b06a6aba4402f425f360a988172a8f51e2d847c 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.c
+++ b/src/gromacs/gmxana/gmx_disre.c
@@ -67,6 +67,7 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxlib/bondfree.c b/src/gromacs/gmxlib/bondfree.c
index 9cd603913d9d5362970a832a93ef0f413e6d58f6..d4834aa3acf0cf1829c56ad7dd0496f38d80488f 100644 (file)
--- a/src/gromacs/gmxlib/bondfree.c
+++ b/src/gromacs/gmxlib/bondfree.c
@@ -38,29 +38,31 @@
 #include <config.h>
 #endif
 
-#include <math.h>
 #include <assert.h>
+#include <math.h>
+
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/utilities.h"
 #include "txtdump.h"
 #include "bondf.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "ns.h"
 #include "macros.h"
 #include "names.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/pbcutil/mshift.h"
 #include "disre.h"
 #include "orires.h"
 #include "force.h"
 #include "nonbonded.h"
 #include "restcbt.h"
 
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
 #include "gromacs/simd/vector_operations.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Find a better place for this? */
 const int cmap_coeff_matrix[] = {

diff --git a/src/gromacs/gmxlib/disre.c b/src/gromacs/gmxlib/disre.c
index df70ce0fbbc3d2223edb2d8e5c75afb637cdf45f..695719b230a59f2434824cc8ac177c6236ab2912 100644 (file)
--- a/src/gromacs/gmxlib/disre.c
+++ b/src/gromacs/gmxlib/disre.c
@@ -53,6 +53,7 @@
 #include "mtop_util.h"
 
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.c b/src/gromacs/gmxlib/nonbonded/nonbonded.c
index 946c01cebf939fee171b75b01b36197f4f0117f7..eefd0e992a60fd1cabeab2d28f42cc0fc620bbd2 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nonbonded.c
+++ b/src/gromacs/gmxlib/nonbonded/nonbonded.c
@@ -49,7 +49,6 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/math/utilities.h"
 #include "macros.h"
-#include "gromacs/utility/cstringutil.h"
 #include "force.h"
 #include "names.h"
 #include "force.h"
@@ -58,8 +57,10 @@
 #include "nonbonded.h"
 #include "gromacs/simd/simd.h"
 
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxlib/orires.c b/src/gromacs/gmxlib/orires.c
index e8b0b5c0d3bbfae853284c31a79ba83d03585737..4e0c70f08647b300943e374866b466273b84f2a6 100644 (file)
--- a/src/gromacs/gmxlib/orires.c
+++ b/src/gromacs/gmxlib/orires.c
@@ -50,6 +50,7 @@
 #include "gromacs/linearalgebra/nrjac.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxpreprocess/insert-molecules.cpp b/src/gromacs/gmxpreprocess/insert-molecules.cpp
index d444521fd551c7e96a68a1afe37c17cd7da45446..a69ad76497f8dcd4823b9cd9c2b9c47f63e9941c 100644 (file)
--- a/src/gromacs/gmxpreprocess/insert-molecules.cpp
+++ b/src/gromacs/gmxpreprocess/insert-molecules.cpp
@@ -40,26 +40,26 @@
 #include <config.h>
 #endif
 
-
 #include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/fileio/confio.h"
 #include "macros.h"
-#include "gromacs/random/random.h"
-#include "gromacs/utility/futil.h"
 #include "atomprop.h"
 #include "names.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
 #include "addconf.h"
 #include "read-conformation.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/fileio/xvgr.h"
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/random/random.h"
 #include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static gmx_bool in_box(t_pbc *pbc, rvec x)
 {

diff --git a/src/gromacs/legacyheaders/typedefs.h b/src/gromacs/legacyheaders/typedefs.h
index b7566f13b2e7f39634adb8b22316c4f291fcf060..3579427edb9d585dfe7c1830071442c3a15a74b1 100644 (file)
--- a/src/gromacs/legacyheaders/typedefs.h
+++ b/src/gromacs/legacyheaders/typedefs.h
@@ -52,7 +52,6 @@
 #include "types/topology.h"
 #include "types/energy.h"
 #include "types/inputrec.h"
-#include "types/ishift.h"
 #include "types/nrnb.h"
 #include "types/nblist.h"
 #include "types/nbnxn_pairlist.h"

diff --git a/src/gromacs/legacyheaders/vsite.h b/src/gromacs/legacyheaders/vsite.h
index a30ec2b734dabbb9e86b4361d9dc541c6d28c77b..f507f8bd0440f3da04625b919b21f0872abfc5e5 100644 (file)
--- a/src/gromacs/legacyheaders/vsite.h
+++ b/src/gromacs/legacyheaders/vsite.h
@@ -39,7 +39,9 @@
 #define _vsite_h
 
 #include <stdio.h>
+
 #include "typedefs.h"
+#include "../pbcutil/ishift.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/mdlib/calcvir.c b/src/gromacs/mdlib/calcvir.c
index ebbb8b2940c3682f5602bf93dc320c28ea2baba0..35254d587c84a40396230748e090ed9627a78934 100644 (file)
--- a/src/gromacs/mdlib/calcvir.c
+++ b/src/gromacs/mdlib/calcvir.c
@@ -43,6 +43,7 @@
 #include "macros.h"
 
 #include "gromacs/math/vectypes.h"
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 

diff --git a/src/gromacs/mdlib/csettle.c b/src/gromacs/mdlib/csettle.c
index 85011ff6d2273d0d942560527f3ece8d80aea2d2..396cd93cfa0fda64c37dde9a7cac00e62ed7509e 100644 (file)
--- a/src/gromacs/mdlib/csettle.c
+++ b/src/gromacs/mdlib/csettle.c
@@ -40,11 +40,14 @@
 
 #include <math.h>
 #include <stdio.h>
-#include "gromacs/math/vec.h"
+
 #include "constr.h"
+
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/pbcutil/pbc.h"
 
 typedef struct
 {

diff --git a/src/gromacs/mdlib/domdec.c b/src/gromacs/mdlib/domdec.c
index 4cbaecda08e622ec46dadb823627448fa3f205ba..369257f9d1ed5a6d99a1b83c002af6a3fe3bc7f1 100644 (file)
--- a/src/gromacs/mdlib/domdec.c
+++ b/src/gromacs/mdlib/domdec.c
@@ -45,14 +45,11 @@
 #include <assert.h>
 
 #include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/fatalerror.h"
 #include "network.h"
 #include "gromacs/math/vec.h"
 #include "domdec.h"
 #include "domdec_network.h"
 #include "nrnb.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "chargegroup.h"
 #include "constr.h"
 #include "mdatoms.h"
@@ -74,13 +71,17 @@
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/imd/imd.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/pulling/pull_rotation.h"
 #include "gromacs/swap/swapcoords.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/qsort_threadsafe.h"
+#include "gromacs/utility/smalloc.h"
 
 #define DDRANK(dd, rank)    (rank)
 #define DDMASTERRANK(dd)   (dd->masterrank)

diff --git a/src/gromacs/mdlib/domdec_con.c b/src/gromacs/mdlib/domdec_con.c
index 288ea8de3f030a1f161e072aac02faf264afc090..78015c90888ce3802d4b81feb5d6bb672006add3 100644 (file)
--- a/src/gromacs/mdlib/domdec_con.c
+++ b/src/gromacs/mdlib/domdec_con.c
@@ -38,7 +38,6 @@
 #endif
 #include <assert.h>
 
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
 #include "constr.h"
 #include "types/commrec.h"
@@ -50,7 +49,9 @@
 #include "gmx_omp_nthreads.h"
 #include "macros.h"
 
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     int  nsend;

diff --git a/src/gromacs/mdlib/force.c b/src/gromacs/mdlib/force.c
index 48e0be45d40017e93cf36f3627328707ccbd4635..61d69484493efe5bda0d41e069887b0c63fd6912 100644 (file)
--- a/src/gromacs/mdlib/force.c
+++ b/src/gromacs/mdlib/force.c
@@ -48,11 +48,9 @@
 #include "nonbonded.h"
 #include "names.h"
 #include "network.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "ns.h"
 #include "nrnb.h"
 #include "bondf.h"
-#include "gromacs/pbcutil/mshift.h"
 #include "txtdump.h"
 #include "coulomb.h"
 #include "pme.h"
@@ -63,6 +61,9 @@
 
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/forcerec.c b/src/gromacs/mdlib/forcerec.c
index b05d7a970eddd43b1c5e5aedc02cef8fb8469d79..c999e409144979472660e9954fed3ef6eae50806 100644 (file)
--- a/src/gromacs/mdlib/forcerec.c
+++ b/src/gromacs/mdlib/forcerec.c
@@ -38,24 +38,22 @@
 #include <config.h>
 #endif
 
+#include <assert.h>
 #include <math.h>
 #include <string.h>
-#include <assert.h>
+
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/utilities.h"
 #include "macros.h"
-#include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "gromacs/utility/fatalerror.h"
 #include "gromacs/math/units.h"
 #include "force.h"
 #include "tables.h"
 #include "nonbonded.h"
 #include "names.h"
 #include "network.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "ns.h"
 #include "txtdump.h"
 #include "coulomb.h"
@@ -73,6 +71,11 @@
 #include "gmx_detect_hardware.h"
 #include "inputrec.h"
 
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
 #include "types/nbnxn_cuda_types_ext.h"
 #include "gpu_utils.h"
 #include "nbnxn_cuda_data_mgmt.h"

diff --git a/src/gromacs/mdlib/genborn.c b/src/gromacs/mdlib/genborn.c
index a5eaa86a80457bbfbf56a03a721c46224c2fe2a9..4aa032448bbcd4d6800f28cc2aaf5c5c94ae2da2 100644 (file)
--- a/src/gromacs/mdlib/genborn.c
+++ b/src/gromacs/mdlib/genborn.c
@@ -51,12 +51,13 @@
 #include "domdec.h"
 #include "network.h"
 #include "mtop_util.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "nrnb.h"
 #include "bondf.h"
 
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/nbnxn_atomdata.c b/src/gromacs/mdlib/nbnxn_atomdata.c
index dc632c5fbfd50e9f66875abf9a5380c9010d90f4..f80ab2ea6315342dcea6aafafca94e8e329b6abd 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_atomdata.c
+++ b/src/gromacs/mdlib/nbnxn_atomdata.c
@@ -51,6 +51,7 @@
 #include "gmx_omp_nthreads.h"
 #include "thread_mpi/atomic.h"
 
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/gmxomp.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
index fe19707ddd80376d3ad14521eff25d2bd194894d..6bb1e3ad8de06631ca7e7ce5ce298ed692dd2586 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
@@ -48,7 +48,6 @@
 #include "types/simple.h"
 #include "types/nbnxn_pairlist.h"
 #include "types/nb_verlet.h"
-#include "types/ishift.h"
 #include "types/force_flags.h"
 #include "../nbnxn_consts.h"
 
@@ -61,6 +60,7 @@
 #include "nbnxn_cuda.h"
 #include "nbnxn_cuda_data_mgmt.h"
 
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/cstringutil.h"
 
 #if defined TEXOBJ_SUPPORTED && __CUDA_ARCH__ >= 300

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
index f2886e625fc9366001be40a29a221e7c6a806d5c..119079675f591828af937b1857cb3c3a6668d382 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
@@ -58,6 +58,7 @@
 #include "pmalloc_cuda.h"
 #include "gpu_utils.h"
 
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh
index 84634d5e7e4b0ad033452c0e8a4263830fc8a000..43ebddb034d2abe8861f307d693874a521f6e55e 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh
@@ -34,6 +34,7 @@
  */
 
 #include "gromacs/math/utilities.h"
+#include "gromacs/pbcutil/ishift.h"
 /* Note that floating-point constants in CUDA code should be suffixed
  * with f (e.g. 0.5f), to stop the compiler producing intermediate
  * code that is in double precision.

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c
index 7ce061ff2140722826220812b50b1ebaa9e42e6c..43a1da735d387d24a57e13ffad4a37d88e552095 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c
@@ -1,7 +1,7 @@
 /*
  * 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.
@@ -36,6 +36,8 @@
 #include <config.h>
 #endif
 
+#include "gromacs/pbcutil/ishift.h"
+
 #include "nbnxn_kernel_common.h"
 
 static void

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c
index f0b7df70be4f2b1d2ab72ad6e97041680af848fa..451c0f40ea35b1ad7acf826efd782283c0bbdc58 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c
@@ -39,10 +39,13 @@
 #include <math.h>
 
 #include "types/simple.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/vec.h"
 #include "typedefs.h"
 #include "force.h"
+
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+
 #include "nbnxn_kernel_gpu_ref.h"
 #include "../nbnxn_consts.h"
 #include "nbnxn_kernel_common.h"

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
index 14c620c9b1351120c1a4d02e31795692b32316a9..2fe3dc93f9e077b673fd1d64eac364aa93ce5077 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
@@ -40,10 +40,13 @@
 #include <assert.h>
 
 #include "typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
 #include "force.h"
 #include "gmx_omp_nthreads.h"
+
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/smalloc.h"
+
 #include "nbnxn_kernel_ref.h"
 #include "../nbnxn_consts.h"
 #include "nbnxn_kernel_common.h"

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
index 01d8090765b2c4eb0d01772b05310f1b21c8b81f..89310bd7dceafd9733995bad573ebdda8f2e64fd 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
@@ -32,6 +32,7 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
 #include "gromacs/simd/vector_operations.h"

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
index 4f9626f4bafdc7274a04a88b255f4947f755db33..1bf915712b6335d47c728aa40d20108a3423f581 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
@@ -32,6 +32,7 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
 #include "gromacs/simd/vector_operations.h"

diff --git a/src/gromacs/mdlib/nbnxn_search.c b/src/gromacs/mdlib/nbnxn_search.c
index 0da2f8c225443f95c2366bda02c8343a05aa1837..cc70013ba06654b8dacdbc670323aa6369dc2885 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.c
+++ b/src/gromacs/mdlib/nbnxn_search.c
@@ -41,12 +41,10 @@
 #include <string.h>
 #include <assert.h>
 
-#include "gromacs/utility/smalloc.h"
 #include "types/commrec.h"
 #include "macros.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "nbnxn_consts.h"
 /* nbnxn_internal.h included gromacs/simd/macros.h */
 #include "nbnxn_internal.h"
@@ -59,7 +57,9 @@
 #include "nrnb.h"
 #include "ns.h"
 
-#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/smalloc.h"
 
 #ifdef NBNXN_SEARCH_BB_SIMD4
 /* Always use 4-wide SIMD for bounding box calculations */

diff --git a/src/gromacs/mdlib/ns.c b/src/gromacs/mdlib/ns.c
index 22aa90c4bbdeca3311f2c38eca4015fd8eee9cfc..141989b0fce57954fa2f6cf6cc61710b2b858e14 100644 (file)
--- a/src/gromacs/mdlib/ns.c
+++ b/src/gromacs/mdlib/ns.c
@@ -42,7 +42,6 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
@@ -52,9 +51,7 @@
 #include "force.h"
 #include "nonbonded.h"
 #include "ns.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "names.h"
-#include "gromacs/utility/fatalerror.h"
 #include "nrnb.h"
 #include "txtdump.h"
 #include "mtop_util.h"
@@ -62,6 +59,10 @@
 #include "domdec.h"
 #include "adress.h"
 
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 /*
  *    E X C L U S I O N   H A N D L I N G

diff --git a/src/gromacs/mdlib/qmmm.c b/src/gromacs/mdlib/qmmm.c
index d19a7154032b2d87bbc37dbfe96fd0e212bbf9e7..04218383856ea78070405e61baed5ac77fdc7e64 100644 (file)
--- a/src/gromacs/mdlib/qmmm.c
+++ b/src/gromacs/mdlib/qmmm.c
@@ -39,10 +39,13 @@
 #endif
 
 #include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "macros.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/units.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
@@ -50,19 +53,18 @@
 #include "gromacs/fileio/confio.h"
 #include "names.h"
 #include "network.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "ns.h"
 #include "nrnb.h"
 #include "bondf.h"
 #include "txtdump.h"
 #include "qmmm.h"
-#include <stdio.h>
-#include <string.h>
-#include "gromacs/utility/fatalerror.h"
 #include "typedefs.h"
-#include <stdlib.h>
 #include "mtop_util.h"
 
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 /* declarations of the interfaces to the QM packages. The _SH indicate
  * the QM interfaces can be used for Surface Hopping simulations

diff --git a/src/gromacs/mdlib/rf_util.c b/src/gromacs/mdlib/rf_util.c
index 3e7037febcf9343f56c1e9e1edd2b2f8c5c51b14..6b92694a15d302b5dfdbeaaa67e5a5e9ffb67897 100644 (file)
--- a/src/gromacs/mdlib/rf_util.c
+++ b/src/gromacs/mdlib/rf_util.c
@@ -42,9 +42,10 @@
 #include "force.h"
 #include "names.h"
 #include "copyrite.h"
-#include "gromacs/pbcutil/pbc.h"
 
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 

diff --git a/src/gromacs/mdlib/sim_util.c b/src/gromacs/mdlib/sim_util.c
index e2e3b08302efc43e3791bc1ed3e0ee91a509d3c4..9fa881613d27c246a2a09a3a2fe9c8f74bf2d7e5 100644 (file)
--- a/src/gromacs/mdlib/sim_util.c
+++ b/src/gromacs/mdlib/sim_util.c
@@ -48,14 +48,12 @@
 
 #include "typedefs.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
 #include "names.h"
 #include "txtdump.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "chargegroup.h"
 #include "gromacs/math/vec.h"
 #include "nrnb.h"
-#include "gromacs/pbcutil/mshift.h"
 #include "mdrun.h"
 #include "sim_util.h"
 #include "update.h"
@@ -83,9 +81,12 @@
 #include "../gmxlib/nonbonded/nb_free_energy.h"
 
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
 #include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/pulling/pull_rotation.h"

diff --git a/src/gromacs/mdlib/vsite.c b/src/gromacs/mdlib/vsite.c
index bf3d2e0ec47d1ae64bdce2cb2e324cd3adedb5f7..5f66b0c77257dc8ce6b8092e23af11162780c6f8 100644 (file)
--- a/src/gromacs/mdlib/vsite.c
+++ b/src/gromacs/mdlib/vsite.c
@@ -44,17 +44,18 @@
 #include "types/commrec.h"
 #include "vsite.h"
 #include "macros.h"
-#include "gromacs/utility/smalloc.h"
 #include "nrnb.h"
 #include "gromacs/math/vec.h"
 #include "network.h"
-#include "gromacs/pbcutil/mshift.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "domdec.h"
 #include "mtop_util.h"
 #include "gmx_omp_nthreads.h"
 
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Routines to send/recieve coordinates and force
  * of constructing atoms.

diff --git a/src/gromacs/pbcutil/CMakeLists.txt b/src/gromacs/pbcutil/CMakeLists.txt
index 1df0b1064c0c68434953fdcf772a5397a24174f2..0366753a1b6b1890a0dcdd388fadd06077fa6ef5 100644 (file)
--- a/src/gromacs/pbcutil/CMakeLists.txt
+++ b/src/gromacs/pbcutil/CMakeLists.txt
@@ -36,6 +36,7 @@ file(GLOB PBCUTIL_SOURCES *.cpp *.c)
 set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${PBCUTIL_SOURCES} PARENT_SCOPE)
 
 set(PBCUTIL_PUBLIC_HEADERS
+    ishift.h
     pbc.h
     rmpbc.h)
 

diff --git a/src/gromacs/legacyheaders/types/ishift.h b/src/gromacs/pbcutil/ishift.h
similarity index 93%
rename from src/gromacs/legacyheaders/types/ishift.h
rename to src/gromacs/pbcutil/ishift.h
index 4c44dfe92e4ac073537d207dd28fb534527c79ac..464f3c0139069ac9d85d4f83a7465165aa736a7d 100644 (file)
--- a/src/gromacs/legacyheaders/types/ishift.h
+++ b/src/gromacs/pbcutil/ishift.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, 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.
@@ -34,13 +34,8 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-
-
-/* not really neccesary, right now: */
-#ifdef __cplusplus
-extern "C" {
-#endif
-
+#ifndef GMX_PBCUTIL_ISHIFT_H
+#define GMX_PBCUTIL_ISHIFT_H
 
 #define D_BOX_Z 1
 #define D_BOX_Y 1
@@ -58,7 +53,4 @@ extern "C" {
 #define IS2Y(iv)      ((((iv) / N_BOX_X) % N_BOX_Y) - D_BOX_Y)
 #define IS2Z(iv)      ((iv) / (N_BOX_X*N_BOX_Y) - D_BOX_Z)
 
-
-#ifdef __cplusplus
-}
 #endif

diff --git a/src/gromacs/pbcutil/pbc.c b/src/gromacs/pbcutil/pbc.c
index 68381ae102958a08baa8540e7ba87f4b0e70d903..d2ebf4f8f89c6dd83178b64c5d9ade06571805bc 100644 (file)
--- a/src/gromacs/pbcutil/pbc.c
+++ b/src/gromacs/pbcutil/pbc.c
@@ -52,6 +52,7 @@
 
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"