From: Teemu Murtola Date: Sat, 31 May 2014 04:18:31 +0000 (+0300) Subject: Move mtop_util.* and topsort.* to topology/ X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=60c02f12abc001b4ce8c2e5ff2486396c921e4b7;p=alexxy%2Fgromacs.git 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 886621af3f..c27576c02f 100644 --- 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 8f3495b052..30d248e539 100644 --- 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 d7fc7a4982..7dc48935a6 100644 --- 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 990dd923f4..b3f770b86c 100644 --- 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 1b06a6aba4..1efdfb4170 100644 --- 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 4d3c9a3713..bf7d66f924 100644 --- 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 e13aa0c8ae..909e855554 100644 --- 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 0bf58ea1f3..5497dfd098 100644 --- 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 b0c5e9c104..20cd09df7e 100644 --- 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 695719b230..1723063664 100644 --- 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 4e0c70f086..4905338314 100644 --- 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 e89b0bbb31..e5ac010016 100644 --- 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 3e5f7ecd35..03b8a70be6 100644 --- 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 44a592d68c..1cfeba8e7b 100644 --- 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 8bd07dfd78..3d560b9330 100644 --- 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 1d6b2a72f3..edb0ac519e 100644 --- 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 92b684cc2b..cf70978d15 100644 --- 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 3dd544e604..dcf8bd47b5 100644 --- 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 369257f9d1..3e66c89633 100644 --- 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 78015c9088..728d2afd90 100644 --- 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 8ed2977144..e2f9f6d703 100644 --- 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 836b23d8fb..e3fe4cbd9a 100644 --- 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 4aa032448b..6085462cf8 100644 --- 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 3e98b33881..790c479327 100644 --- 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 f0cb36106e..85c1ca3a9d 100644 --- 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 9b443e5653..0fbb30f4d9 100644 --- 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 4f90b61347..ed5ad0ea41 100644 --- 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 ca5a52e2a9..07e068ada9 100644 --- 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 35e2e1b2b4..178bd265b5 100644 --- 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 141989b0fc..fef3331506 100644 --- 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 d74148f047..92d049ae20 100644 --- a/src/gromacs/mdlib/perf_est.c +++ b/src/gromacs/mdlib/perf_est.c @@ -40,14 +40,15 @@ #include -#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 0421838385..1858d4903a 100644 --- 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 409c045336..8ddbc94859 100644 --- 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 ba882e50ca..74e8950737 100644 --- 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 d6e4bd4593..83b4665e25 100644 --- 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 5f66b0c772..3f4c11a182 100644 --- 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 3ab4fa5d2f..265749eeee 100644 --- 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 1df31d6402..f9054e85d0 100644 --- 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 66824597a6..edcb14520c 100644 --- 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 59f5ff21e9..91ecdded11 100644 --- 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 d44c2d9197..c375c169c7 100644 --- 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 524d6d6f55..16becfb6c3 100644 --- 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 248e2d5e2a..28aa6da558 100644 --- 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 dc207a7321..a6ffdfb009 100644 --- 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 04daeb5d19..9c04dc2e2c 100644 --- 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 @@ -40,12 +41,13 @@ #include #include -#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 a9b913f521..a0cfef1aff 100644 --- 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 0fe9719a7c..3cae133ac7 100644 --- 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 #endif -#include "typedefs.h" -#include "topsort.h" -#include "gromacs/utility/smalloc.h" +#include + +#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 74c287838b..53505a40c3 100644 --- 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 f9b12a6559..bad0af3ab3 100644 --- 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 e34bfaf9e6..04ebc2a94d 100644 --- 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 d023c6b026..b6777c6506 100644 --- 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"