Move ifunc.* to topology/

This does not solve the main cyclic dependency that comes from
interaction_function definition depending on all the functions that
evaluate the interactions, but it does centralize this dependency to
topology: pbcutil -> gmxlib dependency is now removed.

Part of #1854.

Change-Id: Iaed05348cf663db7faeb7154a2838ea84d8bde1b

diff --git a/docs/doxygen/cycle-suppressions.txt b/docs/doxygen/cycle-suppressions.txt
index 0ab715c85231126efcb8b1bbf14a8a39cc2f1ee7..638d706ff5d67748ebbcf3fabd92d42ce63989c7 100644 (file)
--- a/docs/doxygen/cycle-suppressions.txt
+++ b/docs/doxygen/cycle-suppressions.txt
@@ -13,8 +13,8 @@ mdlib -> imd
 mdlib -> ewald
 mdlib -> pulling
 topology -> gmxlib
+topology -> listed-forces
 pbcutil -> fileio
-pbcutil -> gmxlib
 pbcutil -> mdtypes
 listed-forces -> mdlib
 utility -> math

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index c4374500672fdc00c442c047e32cd45db801f279..e87a9b9481146c4e02b9e6b63d916ddd135b121d 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -55,7 +55,6 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
@@ -91,6 +90,7 @@
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/idef.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/basedefinitions.h"

diff --git a/src/gromacs/fileio/pdbio.cpp b/src/gromacs/fileio/pdbio.cpp
index 947debefeae52b3a1008006b5deec747880e5920..e99a9a6f44fedd520c4bf2e0cf8959c6875b054b 100644 (file)
--- a/src/gromacs/fileio/pdbio.cpp
+++ b/src/gromacs/fileio/pdbio.cpp
@@ -46,11 +46,11 @@
 #include <string>
 
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"

diff --git a/src/gromacs/fileio/tngio.cpp b/src/gromacs/fileio/tngio.cpp
index cf21019a55d318a46853852a53b83ffbba2be56b..5981310ff6a3e6322456af398a536a8bd46ee438 100644 (file)
--- a/src/gromacs/fileio/tngio.cpp
+++ b/src/gromacs/fileio/tngio.cpp
@@ -42,9 +42,9 @@
 #include "tng/tng_io.h"
 #endif
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/baseversion.h"

diff --git a/src/gromacs/fileio/tpxio.cpp b/src/gromacs/fileio/tpxio.cpp
index 03faed6ebc185a251ff6c3fd804889ae23bf61f9..98878555672756b035f610ebc0a1d9b35828c166 100644 (file)
--- a/src/gromacs/fileio/tpxio.cpp
+++ b/src/gromacs/fileio/tpxio.cpp
@@ -50,7 +50,6 @@
 #include "gromacs/fileio/filetypes.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/gmxfio-xdr.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
@@ -59,6 +58,7 @@
 #include "gromacs/pbcutil/boxutilities.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"

diff --git a/src/gromacs/gmxana/edittop.cpp b/src/gromacs/gmxana/edittop.cpp
index cf1d8a89dfa8afaf290449f0e09a8b298d09057f..3e69165cb76d2e13b63e826b66011ced485ef83d 100644 (file)
--- a/src/gromacs/gmxana/edittop.cpp
+++ b/src/gromacs/gmxana/edittop.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/gmxlib/ifunc.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxana/gmx_energy.cpp b/src/gromacs/gmxana/gmx_energy.cpp
index 84b85696df4c3dcf594e7db85f21b2d921b2aa3d..24231af1cb18cce87253a746b32010e54991e6fc 100644 (file)
--- a/src/gromacs/gmxana/gmx_energy.cpp
+++ b/src/gromacs/gmxana/gmx_energy.cpp
@@ -52,11 +52,11 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/mdebin.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/arraysize.h"

diff --git a/src/gromacs/gmxana/gmx_hbond.cpp b/src/gromacs/gmxana/gmx_hbond.cpp
index 2af41a655771798f627e497c250388ff33ae78de..4e0e0a6a6e24f7509f94458fc2d475ad579a7c0a 100644 (file)
--- a/src/gromacs/gmxana/gmx_hbond.cpp
+++ b/src/gromacs/gmxana/gmx_hbond.cpp
@@ -56,10 +56,10 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/arraysize.h"

diff --git a/src/gromacs/gmxana/gmx_lie.cpp b/src/gromacs/gmxana/gmx_lie.cpp
index 5f5c2ac33622eec47c3e86deb3000a0fd4a33a02..95720fa9511ca1d3cb9b170ceabb275209e81c49 100644 (file)
--- a/src/gromacs/gmxana/gmx_lie.cpp
+++ b/src/gromacs/gmxana/gmx_lie.cpp
@@ -48,8 +48,8 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/arraysize.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxana/gmx_mk_angndx.cpp b/src/gromacs/gmxana/gmx_mk_angndx.cpp
index 0d51def408e9a65fa0b13aa8316663976fcfa93d..1125d15c53d20084f3155f5f9c23df664ea131f8 100644 (file)
--- a/src/gromacs/gmxana/gmx_mk_angndx.cpp
+++ b/src/gromacs/gmxana/gmx_mk_angndx.cpp
@@ -41,7 +41,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/gmxlib/ifunc.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/arraysize.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/gmxana/gmx_nmeig.cpp b/src/gromacs/gmxana/gmx_nmeig.cpp
index 40b96458e20a73cb8398696f9a3a7f81e58fc73a..0e677b227031e0b2970730ae4f3fd277fc9b4f83 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmeig.cpp
+++ b/src/gromacs/gmxana/gmx_nmeig.cpp
@@ -46,11 +46,11 @@
 #include "gromacs/gmxana/eigio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/linearalgebra/eigensolver.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/arraysize.h"

diff --git a/src/gromacs/gmxana/gmx_rms.cpp b/src/gromacs/gmxana/gmx_rms.cpp
index 5a0a73886211bd26ef83b8843bdcc29e045075cf..4d07961f3e0f559f50111e42387631b609c9d7ee 100644 (file)
--- a/src/gromacs/gmxana/gmx_rms.cpp
+++ b/src/gromacs/gmxana/gmx_rms.cpp
@@ -50,10 +50,10 @@
 #include "gromacs/gmxana/cmat.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/princ.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/arraysize.h"

diff --git a/src/gromacs/gmxlib/disre.h b/src/gromacs/gmxlib/disre.h
index 56fbb54bc2c7668ef59ff95f0cccb8a873c0dfa3..4b462b3a98c4ccdcd1860d72331b1c3ba4d241e3 100644 (file)
--- a/src/gromacs/gmxlib/disre.h
+++ b/src/gromacs/gmxlib/disre.h
@@ -39,7 +39,7 @@
 
 #include <stdio.h>
 
-#include "gromacs/gmxlib/ifunc.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/basedefinitions.h"
 
 struct gmx_mtop_t;

diff --git a/src/gromacs/gmxlib/orires.cpp b/src/gromacs/gmxlib/orires.cpp
index 9ecf47c348c9761e991fab6ab202267b423e3e4b..8bac1ae7890cf9b7675d89433538077457f50b7a 100644 (file)
--- a/src/gromacs/gmxlib/orires.cpp
+++ b/src/gromacs/gmxlib/orires.cpp
@@ -40,7 +40,6 @@
 
 #include <cmath>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/linearalgebra/nrjac.h"
@@ -53,6 +52,7 @@
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxlib/orires.h b/src/gromacs/gmxlib/orires.h
index 4fa2859a50f1f1a353d68aec6c6e3b0c320fc474..c982256254b3299efd711d9f93088327840e5c7d 100644 (file)
--- a/src/gromacs/gmxlib/orires.h
+++ b/src/gromacs/gmxlib/orires.h
@@ -39,7 +39,7 @@
 
 #include <stdio.h>
 
-#include "gromacs/gmxlib/ifunc.h"
+#include "gromacs/topology/ifunc.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxpreprocess/convparm.cpp b/src/gromacs/gmxpreprocess/convparm.cpp
index 1cdc235bc10d212b06a53d53f9807e9bfb7a61fc..2b437ebfb2bbd242844dde6ceb2bc74c52fffbc6 100644 (file)
--- a/src/gromacs/gmxpreprocess/convparm.cpp
+++ b/src/gromacs/gmxpreprocess/convparm.cpp
@@ -43,7 +43,6 @@
 
 #include <cmath>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/topio.h"
 #include "gromacs/gmxpreprocess/toputil.h"
@@ -51,6 +50,7 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxpreprocess/gen_ad.cpp b/src/gromacs/gmxpreprocess/gen_ad.cpp
index 8b8efdd102729af7fa040e46bc8ad95cc21f2834..ee7bf4cc3847401da96937dbf00b0187c6371e92 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_ad.cpp
+++ b/src/gromacs/gmxpreprocess/gen_ad.cpp
@@ -48,7 +48,6 @@
 #include <algorithm>
 
 #include "gromacs/fileio/confio.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/pgutil.h"
@@ -56,6 +55,7 @@
 #include "gromacs/gmxpreprocess/topio.h"
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxpreprocess/gen_vsite.cpp b/src/gromacs/gmxpreprocess/gen_vsite.cpp
index 792f888ece739923ba4739d8d634d8dc5e9d7355..f0a47dd5acced09036f0dafddf52a8c01bfb7dda 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_vsite.cpp
+++ b/src/gromacs/gmxpreprocess/gen_vsite.cpp
@@ -45,7 +45,6 @@
 #include <cmath>
 
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxpreprocess/add_par.h"
 #include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
@@ -55,6 +54,7 @@
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/basedefinitions.h"

diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.cpp b/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
index 24df7d03be03e8f7b244c138f34d6487512664cf..858e36d7b04443f9394721836eab3af47703f4f8 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
+++ b/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
@@ -43,11 +43,11 @@
 #include <climits>
 #include <cmath>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/topdirs.h"
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/math/vecdump.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxpreprocess/gpp_nextnb.cpp b/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
index c35bb27b1c6013485de30e0f0272df003d4cf620..704ff8a894ee0d8c7d98ee530073d9022a05f12c 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
+++ b/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
@@ -41,8 +41,8 @@
 
 #include <stdlib.h>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index 53aa3136c42d9e8b1347e85088072e7cd3c7ead8..8b3ffeb8296f48b10b96a4183b6e3c0bc8825d42 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -55,7 +55,6 @@
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxlib/calcgrid.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxlib/splitter.h"
 #include "gromacs/gmxlib/warninp.h"
 #include "gromacs/gmxpreprocess/add_par.h"
@@ -82,6 +81,7 @@
 #include "gromacs/pbcutil/boxutilities.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"

diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index ac56e798b81b8f06cc2283c88b317233532ac4c1..081eeaf9dc9a58e6fc40f6dd784de9f61dd81d4b 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -47,7 +47,6 @@
 #include <algorithm>
 
 #include "gromacs/gmxlib/chargegroup.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/readinp.h"
 #include "gromacs/gmxlib/warninp.h"
@@ -60,6 +59,7 @@
 #include "gromacs/mdtypes/pull-params.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/symtab.h"

diff --git a/src/gromacs/gmxpreprocess/tomorse.cpp b/src/gromacs/gmxpreprocess/tomorse.cpp
index 47689fb5bb7c8c1424b5aeb9c40e38e9402c01ea..c2e1ebe4b41eb6ccccb47e1e5fbd5448148e37dc 100644 (file)
--- a/src/gromacs/gmxpreprocess/tomorse.cpp
+++ b/src/gromacs/gmxpreprocess/tomorse.cpp
@@ -45,10 +45,10 @@
 
 #include <cmath>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/grompp-impl.h"
 #include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"

diff --git a/src/gromacs/gmxpreprocess/topio.cpp b/src/gromacs/gmxpreprocess/topio.cpp
index c9c4e9877e88d67ba6692b580664f952a5a61c4d..6aa7e98545260f2c27832e90eeda8f79451dc51a 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.cpp
+++ b/src/gromacs/gmxpreprocess/topio.cpp
@@ -49,7 +49,6 @@
 #include <sys/types.h>
 
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxlib/warninp.h"
 #include "gromacs/gmxpreprocess/gmxcpp.h"
 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
@@ -66,6 +65,7 @@
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/gmxpreprocess/toppush.cpp b/src/gromacs/gmxpreprocess/toppush.cpp
index 04f9be821a22bea0fd67d2a3581e944b14de4e41..18942f8b30fca0ef2edfcceb9143634d2f98cb23 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.cpp
+++ b/src/gromacs/gmxpreprocess/toppush.cpp
@@ -45,7 +45,6 @@
 
 #include <algorithm>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxlib/warninp.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
@@ -54,6 +53,7 @@
 #include "gromacs/gmxpreprocess/topdirs.h"
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxpreprocess/topshake.cpp b/src/gromacs/gmxpreprocess/topshake.cpp
index a616f83a19238c633c01502a5d28533cca09671a..bf0537ddaf7d1dfe658d87cbc3bd2997986e8f51 100644 (file)
--- a/src/gromacs/gmxpreprocess/topshake.cpp
+++ b/src/gromacs/gmxpreprocess/topshake.cpp
@@ -43,13 +43,13 @@
 
 #include <cmath>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/gmxpreprocess/topdirs.h"
 #include "gromacs/gmxpreprocess/toppush.h"
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/math/units.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxpreprocess/toputil.cpp b/src/gromacs/gmxpreprocess/toputil.cpp
index e1c03f47379616df9f124e21f396b1b624ff2bb1..ddd2bd95d80545df1878439bac4947369c02459d 100644 (file)
--- a/src/gromacs/gmxpreprocess/toputil.cpp
+++ b/src/gromacs/gmxpreprocess/toputil.cpp
@@ -45,11 +45,11 @@
 
 #include <algorithm>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/topdirs.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxassert.h"

diff --git a/src/gromacs/gmxpreprocess/vsite_parm.cpp b/src/gromacs/gmxpreprocess/vsite_parm.cpp
index 98de2cf9ab2317c36f756f40c23af21d52642e83..5a6332d1785109d2f6fd4f0465a080cbbafeb220 100644 (file)
--- a/src/gromacs/gmxpreprocess/vsite_parm.cpp
+++ b/src/gromacs/gmxpreprocess/vsite_parm.cpp
@@ -45,7 +45,6 @@
 
 #include <algorithm>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxpreprocess/add_par.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/resall.h"
@@ -53,6 +52,7 @@
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/listed-forces/bonded.h b/src/gromacs/listed-forces/bonded.h
index 04a909116a29cd2387788a7849b0f35c74e2daf5..c58dc96ba5cb979c98cd130d75ad0c39413dbe42 100644 (file)
--- a/src/gromacs/listed-forces/bonded.h
+++ b/src/gromacs/listed-forces/bonded.h
@@ -49,7 +49,6 @@
 
 #include <stdio.h>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/fcdata.h"
@@ -59,6 +58,7 @@
 #include "gromacs/pbcutil/pbc-simd.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/topology/idef.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus

diff --git a/src/gromacs/listed-forces/manage-threading.cpp b/src/gromacs/listed-forces/manage-threading.cpp
index aeb4e308ea9c71d5f7016ef4f1cac090c0980413..b4438d406a8a2ab69679e0ea04ebfede5f992340 100644 (file)
--- a/src/gromacs/listed-forces/manage-threading.cpp
+++ b/src/gromacs/listed-forces/manage-threading.cpp
@@ -52,9 +52,9 @@
 #include <algorithm>
 
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/listed-forces/listed-forces.h"
 #include "gromacs/pbcutil/ishift.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/calc_verletbuf.cpp b/src/gromacs/mdlib/calc_verletbuf.cpp
index cb3c7c249a726c56194ce2e4463485feaeb3e876..3e8d74f81d7134347dd3491ad211403ebb9fcd33 100644 (file)
--- a/src/gromacs/mdlib/calc_verletbuf.cpp
+++ b/src/gromacs/mdlib/calc_verletbuf.cpp
@@ -43,7 +43,6 @@
 
 #include <algorithm>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/calculate-ewald-splitting-coefficient.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
@@ -52,6 +51,7 @@
 #include "gromacs/mdlib/nbnxn_util.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/constr.h b/src/gromacs/mdlib/constr.h
index 4c660be35baf4236e265bb2d0647559544a8b847..85079c3f1d1ef89d20de23fc254af73ec4747c69 100644 (file)
--- a/src/gromacs/mdlib/constr.h
+++ b/src/gromacs/mdlib/constr.h
@@ -39,10 +39,10 @@
 #define GMX_MBLIB_CONSTR_H
 
 #include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/topology/idef.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/real.h"
 

diff --git a/src/gromacs/mdlib/ebin.cpp b/src/gromacs/mdlib/ebin.cpp
index 3c9b9e157fc0dc4a479e0048b66a719cafaa9c44..9777c3e14241177f0c044d96a22de4a99fcb390e 100644 (file)
--- a/src/gromacs/mdlib/ebin.cpp
+++ b/src/gromacs/mdlib/ebin.cpp
@@ -42,10 +42,10 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/perf_est.cpp b/src/gromacs/mdlib/perf_est.cpp
index 330964933c26bd440dcdbb77813e5093d9db6378..9c855a7c083f231e8e4648652b2804b8d9843f9a 100644 (file)
--- a/src/gromacs/mdlib/perf_est.cpp
+++ b/src/gromacs/mdlib/perf_est.cpp
@@ -40,12 +40,12 @@
 
 #include <cmath>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
 

diff --git a/src/gromacs/pbcutil/mshift.cpp b/src/gromacs/pbcutil/mshift.cpp
index 91c5b89fe76b6b3bd99ef2308a85e7fe735ebd37..92bbdd7b7ae480c0fcc160cf5264088662ac4245 100644 (file)
--- a/src/gromacs/pbcutil/mshift.cpp
+++ b/src/gromacs/pbcutil/mshift.cpp
@@ -42,10 +42,10 @@
 
 #include <algorithm>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/idef.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/tools/check.cpp b/src/gromacs/tools/check.cpp
index 14d1f3ebc79fd44cc4c728a29a7dca23c335143e..0b5d58e02338b0e1dc0cb2989e91b4a65b93d038 100644 (file)
--- a/src/gromacs/tools/check.cpp
+++ b/src/gromacs/tools/check.cpp
@@ -48,7 +48,6 @@
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xtcio.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/md_enums.h"
@@ -56,6 +55,7 @@
 #include "gromacs/tools/compare.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"

diff --git a/src/gromacs/tools/compare.cpp b/src/gromacs/tools/compare.cpp
index 5c7bf3491f1c3fffae142ca8d345486aa68c56c9..f696e724a524e4b26c61f357e786b541e7f4647b 100644 (file)
--- a/src/gromacs/tools/compare.cpp
+++ b/src/gromacs/tools/compare.cpp
@@ -48,9 +48,9 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/tools/convert_tpr.cpp b/src/gromacs/tools/convert_tpr.cpp
index 9c1d5b12293fb77e73098573bf2032c36165f561..0cd03ff7fe1b19a95041202054bd02b847db7d0d 100644 (file)
--- a/src/gromacs/tools/convert_tpr.cpp
+++ b/src/gromacs/tools/convert_tpr.cpp
@@ -43,13 +43,13 @@
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trrio.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/random/random.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"

diff --git a/src/gromacs/topology/idef.cpp b/src/gromacs/topology/idef.cpp
index 879459f63071268dd9935ccedf7d7f2b1fc1c17d..0ad6cbba67d47f31e0997c5fef4da5a079bf6dfb 100644 (file)
--- a/src/gromacs/topology/idef.cpp
+++ b/src/gromacs/topology/idef.cpp
@@ -40,7 +40,7 @@
 
 #include <cstdio>
 
-#include "gromacs/gmxlib/ifunc.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/txtdump.h"
 

diff --git a/src/gromacs/gmxlib/ifunc.cpp b/src/gromacs/topology/ifunc.cpp
similarity index 100%
rename from src/gromacs/gmxlib/ifunc.cpp
rename to src/gromacs/topology/ifunc.cpp

diff --git a/src/gromacs/gmxlib/ifunc.h b/src/gromacs/topology/ifunc.h
similarity index 98%
rename from src/gromacs/gmxlib/ifunc.h
rename to src/gromacs/topology/ifunc.h
index 2d33d68ee0a81eae7da299861c83ad89b4da9e28..3ce1a22858b7bf54c7c332036f0140025af9a298 100644 (file)
--- a/src/gromacs/gmxlib/ifunc.h
+++ b/src/gromacs/topology/ifunc.h
@@ -34,8 +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.
  */
-#ifndef GMX_GMXLIB_IFUNC_H
-#define GMX_GMXLIB_IFUNC_H
+#ifndef GMX_TOPOLOGY_IFUNC_H
+#define GMX_TOPOLOGY_IFUNC_H
 
 #include "gromacs/topology/idef.h"
 

diff --git a/src/gromacs/topology/mtop_util.cpp b/src/gromacs/topology/mtop_util.cpp
index 7c2fcf8880f9fe961bca6fabc600905f84597211..63414604a43d332eeefef66f8961a64345da7022 100644 (file)
--- a/src/gromacs/topology/mtop_util.cpp
+++ b/src/gromacs/topology/mtop_util.cpp
@@ -42,11 +42,11 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/idef.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/topology/topsort.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/topology/topology.cpp b/src/gromacs/topology/topology.cpp
index 23e9e87d4700cba3f19358fba371e293003b608b..c2d0f602ccce840000bd45c4c8113cf067deebca 100644 (file)
--- a/src/gromacs/topology/topology.cpp
+++ b/src/gromacs/topology/topology.cpp
@@ -42,8 +42,8 @@
 
 #include <algorithm>
 
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/vecdump.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"

diff --git a/src/gromacs/topology/topsort.cpp b/src/gromacs/topology/topsort.cpp
index 3357679cadf76c478731d972c54ef4b2a3331fd3..de8e9850a072b1697f3b4625bfb38b508ff08872 100644 (file)
--- a/src/gromacs/topology/topsort.cpp
+++ b/src/gromacs/topology/topsort.cpp
@@ -40,7 +40,7 @@
 
 #include <stdio.h>
 
-#include "gromacs/gmxlib/ifunc.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/programs/view/manager.cpp b/src/programs/view/manager.cpp
index 7758267f3c27ebc06e5e189a43f0a35ba58d61a1..64b5fb2e083289024b8a05c078ece76748041b99 100644 (file)
--- a/src/programs/view/manager.cpp
+++ b/src/programs/view/manager.cpp
@@ -52,12 +52,12 @@
 #endif
 
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/gmxlib/ifunc.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/coolstuff.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"