Move mtop_util.* and topsort.* to topology/

- Remove unnecessary includes of these headers.
- Some minor cleanup in the moved files.

Change-Id: I7ad70f4c1870307713db35b8b243bed1dc9cbdd2

diff --git a/src/gromacs/essentialdynamics/edsam.c b/src/gromacs/essentialdynamics/edsam.c
index 886621af3f0fcd8a161cc8e96dc448725ec045c6..c27576c02f5b854c1a4a0d6b9c24dceb44a41ee1 100644 (file)
--- a/src/gromacs/essentialdynamics/edsam.c
+++ b/src/gromacs/essentialdynamics/edsam.c
@@ -52,7 +52,7 @@
 #include "nrnb.h"
 #include "mdrun.h"
 #include "update.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"

diff --git a/src/gromacs/fileio/confio.c b/src/gromacs/fileio/confio.c
index 8f3495b052ed681574bf4da53572ce8bbadf6e5b..30d248e5394433250dd355e43fb8e04db5f34942 100644 (file)
--- a/src/gromacs/fileio/confio.c
+++ b/src/gromacs/fileio/confio.c
@@ -53,7 +53,7 @@
 #include "tpxio.h"
 #include "trxio.h"
 #include "copyrite.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmxfio.h"
 
 #include "gromacs/fileio/trx.h"

diff --git a/src/gromacs/fileio/tpxio.c b/src/gromacs/fileio/tpxio.c
index d7fc7a4982a3bd46d860ff99684a78ffc8f24b50..7dc48935a65326f15b37a7bb26221f2c422b872e 100644 (file)
--- a/src/gromacs/fileio/tpxio.c
+++ b/src/gromacs/fileio/tpxio.c
@@ -53,7 +53,7 @@
 #include "confio.h"
 #include "atomprop.h"
 #include "copyrite.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/block.h"

diff --git a/src/gromacs/gmxana/gmx_clustsize.c b/src/gromacs/gmxana/gmx_clustsize.c
index 990dd923f49e230647f561b3d344c8a816180a6a..b3f770b86ca31f3c0ebe3209c9f3d0230e58587a 100644 (file)
--- a/src/gromacs/gmxana/gmx_clustsize.c
+++ b/src/gromacs/gmxana/gmx_clustsize.c
@@ -57,7 +57,7 @@
 #include "pme.h"
 #include "gstat.h"
 #include "gromacs/fileio/matio.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmx_ana.h"
 
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxana/gmx_disre.c b/src/gromacs/gmxana/gmx_disre.c
index 1b06a6aba4402f425f360a988172a8f51e2d847c..1efdfb4170132a5591c837e6c6fdff9c69a2fef3 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.c
+++ b/src/gromacs/gmxana/gmx_disre.c
@@ -59,7 +59,7 @@
 #include "gromacs/fileio/trxio.h"
 #include "mdrun.h"
 #include "names.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmx_ana.h"
 
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_energy.c b/src/gromacs/gmxana/gmx_energy.c
index 4d3c9a3713598bf0103633f18b3846b863465511..bf7d66f924d8ed05ce4038995812e57e361ed6c4 100644 (file)
--- a/src/gromacs/gmxana/gmx_energy.c
+++ b/src/gromacs/gmxana/gmx_energy.c
@@ -58,7 +58,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "viewit.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmx_ana.h"
 #include "mdebin.h"
 

diff --git a/src/gromacs/gmxana/gmx_genion.c b/src/gromacs/gmxana/gmx_genion.c
index e13aa0c8ae06e6660166f2712a480c27a3b6767b..909e855554da4f569b58c1643c15cc0e62e7916b 100644 (file)
--- a/src/gromacs/gmxana/gmx_genion.c
+++ b/src/gromacs/gmxana/gmx_genion.c
@@ -57,7 +57,6 @@
 #include "mdrun.h"
 #include "gromacs/random/random.h"
 #include "index.h"
-#include "mtop_util.h"
 #include "gmx_ana.h"
 
 static void insert_ion(int nsa, int *nwater,

diff --git a/src/gromacs/gmxana/gmx_nmeig.c b/src/gromacs/gmxana/gmx_nmeig.c
index 0bf58ea1f385f1c3931500b01ab851661ddee2ee..5497dfd0985bf0478332cf84830c7dc637ca1532 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmeig.c
+++ b/src/gromacs/gmxana/gmx_nmeig.c
@@ -49,7 +49,7 @@
 #include "gstat.h"
 #include "txtdump.h"
 #include "eigio.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/math/units.h"
 #include "gmx_ana.h"
 

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index b0c5e9c10478f02162842a4bee316ed1361941f8..20cd09df7e77d494e42dd2a8623ae09933c56330 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -49,7 +49,7 @@
 #include "gromacs/math/units.h"
 #include "mdatoms.h"
 #include "coulomb.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "network.h"
 #include "main.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxlib/disre.c b/src/gromacs/gmxlib/disre.c
index 695719b230a59f2434824cc8ac177c6236ab2912..1723063664b24ace9abe4e9bfe54ad3379156899 100644 (file)
--- a/src/gromacs/gmxlib/disre.c
+++ b/src/gromacs/gmxlib/disre.c
@@ -50,7 +50,7 @@
 #include "copyrite.h"
 #include "disre.h"
 #include "main.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"

diff --git a/src/gromacs/gmxlib/orires.c b/src/gromacs/gmxlib/orires.c
index 4e0c70f08647b300943e374866b466273b84f2a6..490533831459ed02e082dde512797b83ce1eee0c 100644 (file)
--- a/src/gromacs/gmxlib/orires.c
+++ b/src/gromacs/gmxlib/orires.c
@@ -45,7 +45,7 @@
 #include "main.h"
 #include "copyrite.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 
 #include "gromacs/linearalgebra/nrjac.h"
 #include "gromacs/math/do_fit.h"

diff --git a/src/gromacs/gmxpreprocess/addconf.c b/src/gromacs/gmxpreprocess/addconf.c
index e89b0bbb311123e7d7679bc96645a48575f4e184..e5ac010016c89f260bb96ef36cd7feb0fdaf885c 100644 (file)
--- a/src/gromacs/gmxpreprocess/addconf.c
+++ b/src/gromacs/gmxpreprocess/addconf.c
@@ -52,7 +52,7 @@
 #include "mdatoms.h"
 #include "nrnb.h"
 #include "ns.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "chargegroup.h"
 
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
index 3e5f7ecd357b059c5dc51723cbd8f3a14ebe666a..03b8a70be6099bfdf541bc4e6a370f4c641e1719 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
+++ b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
@@ -45,7 +45,7 @@
 #include "typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gen_maxwell_velocities.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 
 static void low_mspeed(real tempi,
                        gmx_mtop_t *mtop, rvec v[], gmx_rng_t rng)

diff --git a/src/gromacs/gmxpreprocess/grompp.c b/src/gromacs/gmxpreprocess/grompp.c
index 44a592d68cf42423d0e9c5b017582d8c3443c908..1cfeba8e7b2f82e448b3fed82f0d519dc01fd4c3 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.c
+++ b/src/gromacs/gmxpreprocess/grompp.c
@@ -75,7 +75,7 @@
 #include "perf_est.h"
 #include "compute_io.h"
 #include "gpp_atomtype.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "genborn.h"
 #include "calc_verletbuf.h"
 #include "tomorse.h"

diff --git a/src/gromacs/gmxpreprocess/readir.c b/src/gromacs/gmxpreprocess/readir.c
index 8bd07dfd7853a2f8d6b43f05093ed09c620149ec..3d560b9330f5e02c7cedfe6bb9532652fc915ae2 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.c
+++ b/src/gromacs/gmxpreprocess/readir.c
@@ -56,7 +56,7 @@
 #include "network.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "chargegroup.h"
 #include "inputrec.h"
 #include "calc_verletbuf.h"

diff --git a/src/gromacs/imd/imd.c b/src/gromacs/imd/imd.c
index 1d6b2a72f3442720163bbbb6340e775851d0b015..edb0ac519e55911a97acf2f12c65dde9fde3bd94 100644 (file)
--- a/src/gromacs/imd/imd.c
+++ b/src/gromacs/imd/imd.c
@@ -67,7 +67,7 @@
 #include "gmx_ga2la.h"
 #include "gromacs/mdlib/groupcoord.h"
 #include "gromacs/fileio/confio.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "names.h"
 #include "gromacs/timing/wallcycle.h"
 

diff --git a/src/gromacs/mdlib/clincs.c b/src/gromacs/mdlib/clincs.c
index 92b684cc2bd998895cfc70d37cd1efcd9ff94ccf..cf70978d155d287e36832905280c5794e759e4ce 100644 (file)
--- a/src/gromacs/mdlib/clincs.c
+++ b/src/gromacs/mdlib/clincs.c
@@ -51,7 +51,7 @@
 #include "mdrun.h"
 #include "nrnb.h"
 #include "domdec.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmx_omp_nthreads.h"
 
 #include "gromacs/fileio/gmxfio.h"

diff --git a/src/gromacs/mdlib/constr.c b/src/gromacs/mdlib/constr.c
index 3dd544e604d2f13f7593223a3b48fa0cd1b11dd9..dcf8bd47b5fceb0cab93753fba5d985fc4aa0ad2 100644 (file)
--- a/src/gromacs/mdlib/constr.c
+++ b/src/gromacs/mdlib/constr.c
@@ -52,7 +52,7 @@
 #include "domdec.h"
 #include "gromacs/fileio/pdbio.h"
 #include "splitter.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "macros.h"
 #include "gmx_omp_nthreads.h"

diff --git a/src/gromacs/mdlib/domdec.c b/src/gromacs/mdlib/domdec.c
index 369257f9d1ed5a6d99a1b83c002af6a3fe3bc7f1..3e66c896339094c3b395ff4eb072b5f7ad0834a3 100644 (file)
--- a/src/gromacs/mdlib/domdec.c
+++ b/src/gromacs/mdlib/domdec.c
@@ -59,7 +59,7 @@
 #include "mdrun.h"
 #include "nsgrid.h"
 #include "shellfc.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmx_ga2la.h"
 #include "macros.h"
 #include "nbnxn_search.h"

diff --git a/src/gromacs/mdlib/domdec_con.c b/src/gromacs/mdlib/domdec_con.c
index 78015c90888ce3802d4b81feb5d6bb672006add3..728d2afd90bc5c35c436d7f496bec4a805f99ba2 100644 (file)
--- a/src/gromacs/mdlib/domdec_con.c
+++ b/src/gromacs/mdlib/domdec_con.c
@@ -43,7 +43,7 @@
 #include "types/commrec.h"
 #include "domdec.h"
 #include "domdec_network.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmx_ga2la.h"
 #include "gmx_hash.h"
 #include "gmx_omp_nthreads.h"

diff --git a/src/gromacs/mdlib/domdec_top.c b/src/gromacs/mdlib/domdec_top.c
index 8ed297714430db524e4179554ca7ea8b59c58510..e2f9f6d70317f7f19cf4134a3f713eb6851d340a 100644 (file)
--- a/src/gromacs/mdlib/domdec_top.c
+++ b/src/gromacs/mdlib/domdec_top.c
@@ -45,17 +45,17 @@
 #include "domdec_network.h"
 #include "names.h"
 #include "network.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "chargegroup.h"
-#include "gromacs/gmxlib/topsort.h"
-#include "mtop_util.h"
-#include "gromacs/pbcutil/mshift.h"
 #include "vsite.h"
 #include "gmx_ga2la.h"
 #include "force.h"
 #include "gmx_omp_nthreads.h"
 
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topsort.h"
 #include "gromacs/utility/cstringutil.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 836b23d8fbb85319074248d00c165665e5d563a5..e3fe4cbd9a637bc861775fa54d83dbf20b015eb2 100644 (file)
--- a/src/gromacs/mdlib/forcerec.c
+++ b/src/gromacs/mdlib/forcerec.c
@@ -62,7 +62,7 @@
 #include "domdec.h"
 #include "qmmm.h"
 #include "copyrite.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "nbnxn_simd.h"
 #include "nbnxn_search.h"
 #include "nbnxn_atomdata.h"

diff --git a/src/gromacs/mdlib/genborn.c b/src/gromacs/mdlib/genborn.c
index 4aa032448bbcd4d6800f28cc2aaf5c5c94ae2da2..6085462cf82b590f4591015c4b38e280c28f5700 100644 (file)
--- a/src/gromacs/mdlib/genborn.c
+++ b/src/gromacs/mdlib/genborn.c
@@ -50,7 +50,7 @@
 #include "gromacs/math/units.h"
 #include "domdec.h"
 #include "network.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "nrnb.h"
 #include "bondf.h"
 

diff --git a/src/gromacs/mdlib/genborn_sse2_double.c b/src/gromacs/mdlib/genborn_sse2_double.c
index 3e98b33881fc4272b1b25ac3b30ee6b3203bba9c..790c4793278eb46b52554b140053198ed76a1041 100644 (file)
--- a/src/gromacs/mdlib/genborn_sse2_double.c
+++ b/src/gromacs/mdlib/genborn_sse2_double.c
@@ -51,7 +51,6 @@
 #include "domdec.h"
 #include "network.h"
 #include "gromacs/utility/fatalerror.h"
-#include "mtop_util.h"
 #include "genborn.h"
 
 #include "gromacs/utility/gmxmpi.h"

diff --git a/src/gromacs/mdlib/genborn_sse2_single.c b/src/gromacs/mdlib/genborn_sse2_single.c
index f0cb36106e984cd8b675a2ab4e685f6c3f07f940..85c1ca3a9d79f54cff5e1d55431ebf8f0e446619 100644 (file)
--- a/src/gromacs/mdlib/genborn_sse2_single.c
+++ b/src/gromacs/mdlib/genborn_sse2_single.c
@@ -51,7 +51,6 @@
 #include "domdec.h"
 #include "network.h"
 #include "gromacs/utility/fatalerror.h"
-#include "mtop_util.h"
 #include "genborn.h"
 
 #include "gromacs/utility/gmxmpi.h"

diff --git a/src/gromacs/mdlib/md_support.c b/src/gromacs/mdlib/md_support.c
index 9b443e565314cc42005e70bc01d648e233eabffb..0fbb30f4d92780521a7817eaffd16cd191e5ee37 100644 (file)
--- a/src/gromacs/mdlib/md_support.c
+++ b/src/gromacs/mdlib/md_support.c
@@ -41,7 +41,7 @@
 #include "typedefs.h"
 #include "mdrun.h"
 #include "domdec.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "vcm.h"
 #include "nrnb.h"
 #include "macros.h"

diff --git a/src/gromacs/mdlib/mdatom.c b/src/gromacs/mdlib/mdatom.c
index 4f90b613478202d2bd136950ef101264aa74448f..ed5ad0ea412e610614aa0e65af34662916cf3a7d 100644 (file)
--- a/src/gromacs/mdlib/mdatom.c
+++ b/src/gromacs/mdlib/mdatom.c
@@ -44,7 +44,7 @@
 #include "mdatoms.h"
 #include "gromacs/utility/smalloc.h"
 #include "qmmm.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmx_omp_nthreads.h"
 
 #define ALMOST_ZERO 1e-30

diff --git a/src/gromacs/mdlib/mdebin.c b/src/gromacs/mdlib/mdebin.c
index ca5a52e2a9d72f5a0efec6fe0ecfd30096a8fd84..07e068ada9acd6206fc9caae61fe14e95560b01e 100644 (file)
--- a/src/gromacs/mdlib/mdebin.c
+++ b/src/gromacs/mdlib/mdebin.c
@@ -52,7 +52,7 @@
 #include "names.h"
 #include "orires.h"
 #include "constr.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "macros.h"

diff --git a/src/gromacs/mdlib/minimize.c b/src/gromacs/mdlib/minimize.c
index 35e2e1b2b4ac51b191602beacf752b23d224925c..178bd265b5820ed4abaf976c896c713278f44910 100644 (file)
--- a/src/gromacs/mdlib/minimize.c
+++ b/src/gromacs/mdlib/minimize.c
@@ -61,7 +61,7 @@
 #include "domdec.h"
 #include "mdatoms.h"
 #include "ns.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "pme.h"
 #include "bondf.h"
 #include "gmx_omp_nthreads.h"

diff --git a/src/gromacs/mdlib/ns.c b/src/gromacs/mdlib/ns.c
index 141989b0fce57954fa2f6cf6cc61710b2b858e14..fef3331506dd03f5b221af9e1059567b845b45c3 100644 (file)
--- a/src/gromacs/mdlib/ns.c
+++ b/src/gromacs/mdlib/ns.c
@@ -54,7 +54,7 @@
 #include "names.h"
 #include "nrnb.h"
 #include "txtdump.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 
 #include "domdec.h"
 #include "adress.h"

diff --git a/src/gromacs/mdlib/perf_est.c b/src/gromacs/mdlib/perf_est.c
index d74148f047c7472aa51bce03a86b33143932d46a..92d049ae20202e7d31fb21a663a392708ffd9787 100644 (file)
--- a/src/gromacs/mdlib/perf_est.c
+++ b/src/gromacs/mdlib/perf_est.c
@@ -40,14 +40,15 @@
 
 #include <math.h>
 
-#include "perf_est.h"
 #include "gromacs/math/vec.h"
-#include "mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
+
+#include "perf_est.h"
 #include "types/commrec.h"
 #include "nbnxn_search.h"
 #include "nbnxn_consts.h"
 
-
 /* Computational cost of bonded, non-bonded and PME calculations.
  * This will be machine dependent.
  * The numbers here are accurate for Intel Core2 and AMD Athlon 64

diff --git a/src/gromacs/mdlib/qmmm.c b/src/gromacs/mdlib/qmmm.c
index 04218383856ea78070405e61baed5ac77fdc7e64..1858d4903a47e24e65bff775d84124157b6453b5 100644 (file)
--- a/src/gromacs/mdlib/qmmm.c
+++ b/src/gromacs/mdlib/qmmm.c
@@ -59,7 +59,7 @@
 #include "txtdump.h"
 #include "qmmm.h"
 #include "typedefs.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/mdlib/shellfc.c b/src/gromacs/mdlib/shellfc.c
index 409c045336cb3f2c8909dcfd4d3eb65dcb472240..8ddbc94859f6c3b1150e41d49a5398d89a422c78 100644 (file)
--- a/src/gromacs/mdlib/shellfc.c
+++ b/src/gromacs/mdlib/shellfc.c
@@ -54,7 +54,7 @@
 #include "domdec.h"
 #include "gromacs/math/units.h"
 #include "shellfc.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "chargegroup.h"
 #include "macros.h"
 

diff --git a/src/gromacs/mdlib/tgroup.c b/src/gromacs/mdlib/tgroup.c
index ba882e50ca21eb3fa90484eafe3ff3f36d059551..74e89507375e32d2273a255eb3e23182870d1eb6 100644 (file)
--- a/src/gromacs/mdlib/tgroup.c
+++ b/src/gromacs/mdlib/tgroup.c
@@ -49,7 +49,7 @@
 #include "network.h"
 #include "update.h"
 #include "rbin.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmx_omp_nthreads.h"
 
 static void init_grptcstat(int ngtc, t_grp_tcstat tcstat[])

diff --git a/src/gromacs/mdlib/tpi.c b/src/gromacs/mdlib/tpi.c
index d6e4bd4593c7da9d90192145d3d3c939a4206586..83b4665e25e015ebe07eacbc3be3725f05a09c19 100644 (file)
--- a/src/gromacs/mdlib/tpi.c
+++ b/src/gromacs/mdlib/tpi.c
@@ -67,7 +67,7 @@
 #include "gromacs/fileio/xvgr.h"
 #include "mdatoms.h"
 #include "ns.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "pme.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
 

diff --git a/src/gromacs/mdlib/vsite.c b/src/gromacs/mdlib/vsite.c
index 5f66b0c77257dc8ce6b8092e23af11162780c6f8..3f4c11a1826279a582937ed687228497dadaedb2 100644 (file)
--- a/src/gromacs/mdlib/vsite.c
+++ b/src/gromacs/mdlib/vsite.c
@@ -48,7 +48,7 @@
 #include "gromacs/math/vec.h"
 #include "network.h"
 #include "domdec.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmx_omp_nthreads.h"
 
 #include "gromacs/pbcutil/ishift.h"

diff --git a/src/gromacs/pulling/pull.c b/src/gromacs/pulling/pull.c
index 3ab4fa5d2fbb04cfb34fc20ac41b34e33c2ecaba..265749eeee20aab14b3bcee408136f9898d319fd 100644 (file)
--- a/src/gromacs/pulling/pull.c
+++ b/src/gromacs/pulling/pull.c
@@ -51,7 +51,7 @@
 #include "pull.h"
 #include "names.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "mdrun.h"
 #include "gmx_ga2la.h"
 #include "copyrite.h"

diff --git a/src/gromacs/pulling/pull_rotation.c b/src/gromacs/pulling/pull_rotation.c
index 1df31d640276adc432149a4824b6b6fd4c6bf348..f9054e85d05db1cd772c0aef59d0443e02486f95 100644 (file)
--- a/src/gromacs/pulling/pull_rotation.c
+++ b/src/gromacs/pulling/pull_rotation.c
@@ -49,7 +49,7 @@
 #include "mdrun.h"
 #include "txtdump.h"
 #include "names.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "names.h"
 #include "gromacs/math/vec.h"
 #include "gmx_ga2la.h"

diff --git a/src/gromacs/swap/swapcoords.c b/src/gromacs/swap/swapcoords.c
index 66824597a665e6b3960dc3a92ab2dbfa968ed2de..edcb14520ca16177e883a16fa6d2ce187688c6a0 100644 (file)
--- a/src/gromacs/swap/swapcoords.c
+++ b/src/gromacs/swap/swapcoords.c
@@ -52,7 +52,7 @@
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/mdlib/groupcoord.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "names.h"

diff --git a/src/gromacs/tools/check.c b/src/gromacs/tools/check.c
index 59f5ff21e9d4f47d62ca654f42ed0dfc89738e45..91ecdded11fd6d7df41001ef30f93f64180a9985 100644 (file)
--- a/src/gromacs/tools/check.c
+++ b/src/gromacs/tools/check.c
@@ -53,7 +53,7 @@
 #include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "names.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/trnio.h"

diff --git a/src/gromacs/tools/compare.c b/src/gromacs/tools/compare.c
index d44c2d9197158a876308af7c6b80f177f6c0e956..c375c169c7b05c0a41330606aa1f63ecfb9b1296 100644 (file)
--- a/src/gromacs/tools/compare.c
+++ b/src/gromacs/tools/compare.c
@@ -51,7 +51,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/enxio.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/cstringutil.h"
 
 static void cmp_int(FILE *fp, const char *s, int index, int i1, int i2)

diff --git a/src/gromacs/tools/convert_tpr.c b/src/gromacs/tools/convert_tpr.c
index 524d6d6f551fefa10f9e17c879918f92b167f60e..16becfb6c381144253113f9ad16ebcbd4c72b5e1 100644 (file)
--- a/src/gromacs/tools/convert_tpr.c
+++ b/src/gromacs/tools/convert_tpr.c
@@ -47,7 +47,7 @@
 #include "macros.h"
 #include "names.h"
 #include "gromacs/gmxpreprocess/readir.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "checkpoint.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trnio.h"

diff --git a/src/gromacs/tools/dump.c b/src/gromacs/tools/dump.c
index 248e2d5e2aed6ea4c2fad1d9117a521f53a8e3f2..28aa6da5580a676ff649e136d23911154e01d3b2 100644 (file)
--- a/src/gromacs/tools/dump.c
+++ b/src/gromacs/tools/dump.c
@@ -48,7 +48,7 @@
 #include "names.h"
 #include "txtdump.h"
 #include "checkpoint.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/gmxfio.h"

diff --git a/src/gromacs/topology/CMakeLists.txt b/src/gromacs/topology/CMakeLists.txt
index dc207a7321d0e61601f22f23ea4f4cc59f4845e3..a6ffdfb009f8e1c7a6801089681703bc82a240ff 100644 (file)
--- a/src/gromacs/topology/CMakeLists.txt
+++ b/src/gromacs/topology/CMakeLists.txt
@@ -39,6 +39,7 @@ set(TOPOLOGY_PUBLIC_HEADERS
     atoms.h
     block.h
     idef.h
+    mtop_util.h
     symtab.h
     topology.h)
 

diff --git a/src/gromacs/gmxlib/mtop_util.c b/src/gromacs/topology/mtop_util.c
similarity index 99%
rename from src/gromacs/gmxlib/mtop_util.c
rename to src/gromacs/topology/mtop_util.c
index 04daeb5d19ef34233dc403584bab323f7496de86..9c04dc2e2c7c43aa948fcfac140cf01f0f8aa1e9 100644 (file)
--- a/src/gromacs/gmxlib/mtop_util.c
+++ b/src/gromacs/topology/mtop_util.c
@@ -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/topology/mtop_util.h"
 
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -40,12 +41,13 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "typedefs.h"
-#include "mtop_util.h"
-#include "topsort.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
 
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/topology/topsort.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/legacyheaders/mtop_util.h b/src/gromacs/topology/mtop_util.h
similarity index 98%
rename from src/gromacs/legacyheaders/mtop_util.h
rename to src/gromacs/topology/mtop_util.h
index a9b913f5216be0c928505416c63f337c9e760e63..a0cfef1aff277f1ea6e09ea8a5dc174a636ced67 100644 (file)
--- a/src/gromacs/legacyheaders/mtop_util.h
+++ b/src/gromacs/topology/mtop_util.h
@@ -34,10 +34,10 @@
  * 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_LEGACYHEADERS_MTOP_UTIL_H
-#define GMX_LEGACYHEADERS_MTOP_UTIL_H
+#ifndef GMX_TOPOLOGY_MTOP_UTIL_H
+#define GMX_TOPOLOGY_MTOP_UTIL_H
 
-#include "types/inputrec.h"
+#include "../legacyheaders/types/inputrec.h"
 #include "../utility/basedefinitions.h"
 
 #ifdef __cplusplus

diff --git a/src/gromacs/gmxlib/topsort.c b/src/gromacs/topology/topsort.c
similarity index 98%
rename from src/gromacs/gmxlib/topsort.c
rename to src/gromacs/topology/topsort.c
index 0fe9719a7cc6238c0bd189f522c1e6d120d0c06c..3cae133ac7786778c3d33f5d1903b16f7e666f7c 100644 (file)
--- a/src/gromacs/gmxlib/topsort.c
+++ b/src/gromacs/topology/topsort.c
@@ -34,15 +34,19 @@
  * 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/topology/topsort.h"
 
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
 
-#include "typedefs.h"
-#include "topsort.h"
-#include "gromacs/utility/smalloc.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/ifunc.h"
+
+#include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static gmx_bool ip_pert(int ftype, const t_iparams *ip)
 {

diff --git a/src/gromacs/gmxlib/topsort.h b/src/gromacs/topology/topsort.h
similarity index 93%
rename from src/gromacs/gmxlib/topsort.h
rename to src/gromacs/topology/topsort.h
index 74c287838bf86f366822244047115f406ff8585a..53505a40c3f3f6f437c4a21c12eaa1f9760809c1 100644 (file)
--- a/src/gromacs/gmxlib/topsort.h
+++ b/src/gromacs/topology/topsort.h
@@ -32,11 +32,11 @@
  * 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 _topsort_h
-#define _topsort_h
+#ifndef GMX_TOPOLOGY_TOPSORT_H
+#define GMX_TOPOLOGY_TOPSORT_H
 
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/programs/mdrun/md.c b/src/programs/mdrun/md.c
index f9b12a6559cb7f55af49453f7f1caf4e5b1f5c83..bad0af3ab333fe6f6ca01af19d1f53ea1a5c0753 100644 (file)
--- a/src/programs/mdrun/md.c
+++ b/src/programs/mdrun/md.c
@@ -65,13 +65,12 @@
 #include "qmmm.h"
 #include "domdec.h"
 #include "domdec_network.h"
-#include "gromacs/gmxlib/topsort.h"
 #include "coulomb.h"
 #include "constr.h"
 #include "shellfc.h"
 #include "gromacs/gmxpreprocess/compute_io.h"
 #include "checkpoint.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "sighandler.h"
 #include "txtdump.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/programs/mdrun/membed.c b/src/programs/mdrun/membed.c
index e34bfaf9e60d6576c4a45f04ae663b7833ce05da..04ebc2a94d1b69c1b8c0266592c37fd9793ee495 100644 (file)
--- a/src/programs/mdrun/membed.c
+++ b/src/programs/mdrun/membed.c
@@ -47,7 +47,7 @@
 #include "gromacs/essentialdynamics/edsam.h"
 #include "index.h"
 #include "names.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/utility/cstringutil.h"
 #include "membed.h"

diff --git a/src/programs/mdrun/runner.c b/src/programs/mdrun/runner.c
index d023c6b026ca523a9a98d8a16a159e2a062e3a00..b6777c65069c77d8a1c0bf4b6697ddf5d6e5e6be 100644 (file)
--- a/src/programs/mdrun/runner.c
+++ b/src/programs/mdrun/runner.c
@@ -66,7 +66,7 @@
 #include "constr.h"
 #include "mvdata.h"
 #include "checkpoint.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "sighandler.h"
 #include "txtdump.h"
 #include "gmx_detect_hardware.h"