From: Teemu Murtola Date: Mon, 20 Jul 2015 07:00:01 +0000 (+0300) Subject: Rename trnio.* to trrio.* X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=ee8d2805e8a1510b37cdeab4df06daca196bfb01;hp=64a6716f5a93af9cd89db4e62142a871a95a27b7;p=alexxy%2Fgromacs.git Rename trnio.* to trrio.* These routines write .trr files, and the old name was really confusing, as there is also an efTRN, which means something different... The routines will be renamed in a separate commit. Removed unnecessary includes of trnio.h. Change-Id: If02f561ad51c73eb2080195587795d0c8ae1b082 --- diff --git a/src/contrib/anaf.c b/src/contrib/anaf.c index 044d987048..df4d1f8681 100644 --- a/src/contrib/anaf.c +++ b/src/contrib/anaf.c @@ -51,7 +51,7 @@ #include "gromacs/utility/smalloc.h" #include "gromacs/fileio/gmxfio.h" #include "gromacs/fileio/tpxio.h" -#include "gromacs/fileio/trnio.h" +#include "gromacs/fileio/trrio.h" #include "txtdump.h" #include "gromacs/math/vec.h" diff --git a/src/contrib/mkice.c b/src/contrib/mkice.c index a60b847cdd..389a20386b 100644 --- a/src/contrib/mkice.c +++ b/src/contrib/mkice.c @@ -50,7 +50,7 @@ #include "gromacs/math/units.h" #include "names.h" #include "txtdump.h" -#include "gromacs/fileio/trnio.h" +#include "gromacs/fileio/trrio.h" #include "gromacs/topology/symtab.h" #include "gromacs/fileio/strdb.h" #include "gromacs/fileio/confio.h" diff --git a/src/contrib/test.c b/src/contrib/test.c index 865f4b8b47..888ae65950 100644 --- a/src/contrib/test.c +++ b/src/contrib/test.c @@ -51,7 +51,6 @@ #include "gromacs/math/units.h" #include "names.h" #include "txtdump.h" -#include "gromacs/fileio/trnio.h" #include "gromacs/fileio/confio.h" real pot(real x,real qq,real c6,real c12) diff --git a/src/gromacs/fileio/CMakeLists.txt b/src/gromacs/fileio/CMakeLists.txt index 0c638a78a8..c3a4552954 100644 --- a/src/gromacs/fileio/CMakeLists.txt +++ b/src/gromacs/fileio/CMakeLists.txt @@ -1,7 +1,7 @@ # # This file is part of the GROMACS molecular simulation package. # -# Copyright (c) 2013,2014, by the GROMACS development team, led by +# Copyright (c) 2013,2014,2015, 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. @@ -53,7 +53,7 @@ gmx_install_headers( pdbio.h tpxio.h trajectory_writing.h - trnio.h + trrio.h trx.h trxio.h xdr_datatype.h diff --git a/src/gromacs/fileio/mdoutf.cpp b/src/gromacs/fileio/mdoutf.cpp index db89c8ea6a..b6140640ff 100644 --- a/src/gromacs/fileio/mdoutf.cpp +++ b/src/gromacs/fileio/mdoutf.cpp @@ -40,7 +40,7 @@ #include "gromacs/fileio/gmxfio.h" #include "gromacs/fileio/tngio.h" #include "gromacs/fileio/trajectory_writing.h" -#include "gromacs/fileio/trnio.h" +#include "gromacs/fileio/trrio.h" #include "gromacs/fileio/xtcio.h" #include "gromacs/fileio/xvgr.h" #include "gromacs/legacyheaders/checkpoint.h" diff --git a/src/gromacs/fileio/trnio.cpp b/src/gromacs/fileio/trrio.cpp similarity index 99% rename from src/gromacs/fileio/trnio.cpp rename to src/gromacs/fileio/trrio.cpp index b843db3317..9951fba746 100644 --- a/src/gromacs/fileio/trnio.cpp +++ b/src/gromacs/fileio/trrio.cpp @@ -36,7 +36,7 @@ */ #include "gmxpre.h" -#include "trnio.h" +#include "trrio.h" #include diff --git a/src/gromacs/fileio/trnio.h b/src/gromacs/fileio/trrio.h similarity index 96% rename from src/gromacs/fileio/trnio.h rename to src/gromacs/fileio/trrio.h index 3550790f91..cb45bb6c19 100644 --- a/src/gromacs/fileio/trnio.h +++ b/src/gromacs/fileio/trrio.h @@ -34,9 +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_FILEIO_TRNIO_H -#define GMX_FILEIO_TRNIO_H +#ifndef GMX_FILEIO_TRRIO_H +#define GMX_FILEIO_TRRIO_H #include "gromacs/math/vectypes.h" #include "gromacs/utility/basedefinitions.h" @@ -50,9 +49,9 @@ * The files are backward compatible, therefore the header holds * some unused variables. * - * The routines in the corresponding c-file trnio.c - * are based on the lower level routines in gmxfio.c - * The integer file pointer returned from open_trn + * The routines in the corresponding c-file trrio.cpp + * are based on the lower level routines in gmxfio.cpp + * The file handle returned from open_trn * can also be used with the routines in gmxfio.h * **************************************************************/ diff --git a/src/gromacs/fileio/trxio.cpp b/src/gromacs/fileio/trxio.cpp index 116dc4c2a8..50bd6d5e32 100644 --- a/src/gromacs/fileio/trxio.cpp +++ b/src/gromacs/fileio/trxio.cpp @@ -53,7 +53,7 @@ #include "gromacs/fileio/tngio.h" #include "gromacs/fileio/tngio_for_tools.h" #include "gromacs/fileio/tpxio.h" -#include "gromacs/fileio/trnio.h" +#include "gromacs/fileio/trrio.h" #include "gromacs/fileio/trx.h" #include "gromacs/fileio/xdrf.h" #include "gromacs/fileio/xtcio.h" diff --git a/src/gromacs/gmxana/eigio.c b/src/gromacs/gmxana/eigio.c index 1561d5a446..1d421e51f5 100644 --- a/src/gromacs/gmxana/eigio.c +++ b/src/gromacs/gmxana/eigio.c @@ -38,7 +38,8 @@ #include "eigio.h" -#include "gromacs/fileio/trnio.h" +#include "gromacs/fileio/tpxio.h" +#include "gromacs/fileio/trrio.h" #include "gromacs/math/vec.h" #include "gromacs/utility/futil.h" #include "gromacs/utility/smalloc.h" diff --git a/src/gromacs/gmxana/gmx_angle.c b/src/gromacs/gmxana/gmx_angle.c index 88304ed029..67208e0f89 100644 --- a/src/gromacs/gmxana/gmx_angle.c +++ b/src/gromacs/gmxana/gmx_angle.c @@ -41,7 +41,7 @@ #include "gromacs/commandline/pargs.h" #include "gromacs/correlationfunctions/autocorr.h" -#include "gromacs/fileio/trnio.h" +#include "gromacs/fileio/trrio.h" #include "gromacs/fileio/xvgr.h" #include "gromacs/gmxana/gmx_ana.h" #include "gromacs/gmxana/gstat.h" diff --git a/src/gromacs/gmxana/gmx_cluster.c b/src/gromacs/gmxana/gmx_cluster.c index 3a746b6eb3..011fe580e2 100644 --- a/src/gromacs/gmxana/gmx_cluster.c +++ b/src/gromacs/gmxana/gmx_cluster.c @@ -43,7 +43,6 @@ #include "gromacs/commandline/pargs.h" #include "gromacs/fileio/confio.h" #include "gromacs/fileio/matio.h" -#include "gromacs/fileio/trnio.h" #include "gromacs/fileio/trxio.h" #include "gromacs/fileio/xvgr.h" #include "gromacs/gmxana/cmat.h" diff --git a/src/gromacs/gmxana/gmx_covar.c b/src/gromacs/gmxana/gmx_covar.c index bad3518aba..779326f0b5 100644 --- a/src/gromacs/gmxana/gmx_covar.c +++ b/src/gromacs/gmxana/gmx_covar.c @@ -42,7 +42,6 @@ #include "gromacs/commandline/pargs.h" #include "gromacs/fileio/confio.h" #include "gromacs/fileio/matio.h" -#include "gromacs/fileio/trnio.h" #include "gromacs/fileio/trxio.h" #include "gromacs/fileio/xvgr.h" #include "gromacs/gmxana/eigio.h" diff --git a/src/gromacs/gmxana/gmx_sigeps.c b/src/gromacs/gmxana/gmx_sigeps.c index f426fe4e51..3866506b28 100644 --- a/src/gromacs/gmxana/gmx_sigeps.c +++ b/src/gromacs/gmxana/gmx_sigeps.c @@ -40,9 +40,6 @@ #include #include "gromacs/commandline/pargs.h" -#include "gromacs/fileio/confio.h" -#include "gromacs/fileio/pdbio.h" -#include "gromacs/fileio/trnio.h" #include "gromacs/fileio/xvgr.h" #include "gromacs/legacyheaders/macros.h" #include "gromacs/legacyheaders/names.h" diff --git a/src/gromacs/gmxana/gmx_trjcat.c b/src/gromacs/gmxana/gmx_trjcat.c index 6f8463f63e..d6c2335650 100644 --- a/src/gromacs/gmxana/gmx_trjcat.c +++ b/src/gromacs/gmxana/gmx_trjcat.c @@ -46,7 +46,6 @@ #include "gromacs/fileio/pdbio.h" #include "gromacs/fileio/tngio.h" #include "gromacs/fileio/tngio_for_tools.h" -#include "gromacs/fileio/trnio.h" #include "gromacs/fileio/trxio.h" #include "gromacs/fileio/xtcio.h" #include "gromacs/fileio/xvgr.h" diff --git a/src/gromacs/gmxana/gmx_trjconv.c b/src/gromacs/gmxana/gmx_trjconv.c index 9db84bee50..f0e64ed790 100644 --- a/src/gromacs/gmxana/gmx_trjconv.c +++ b/src/gromacs/gmxana/gmx_trjconv.c @@ -48,7 +48,7 @@ #include "gromacs/fileio/pdbio.h" #include "gromacs/fileio/tngio_for_tools.h" #include "gromacs/fileio/tpxio.h" -#include "gromacs/fileio/trnio.h" +#include "gromacs/fileio/trrio.h" #include "gromacs/fileio/trxio.h" #include "gromacs/fileio/xtcio.h" #include "gromacs/fileio/xvgr.h" diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp index 304e68c20b..8a6e43c666 100644 --- a/src/gromacs/gmxpreprocess/grompp.cpp +++ b/src/gromacs/gmxpreprocess/grompp.cpp @@ -52,7 +52,6 @@ #include "gromacs/fileio/confio.h" #include "gromacs/fileio/enxio.h" #include "gromacs/fileio/tpxio.h" -#include "gromacs/fileio/trnio.h" #include "gromacs/fileio/trxio.h" #include "gromacs/gmxpreprocess/add_par.h" #include "gromacs/gmxpreprocess/convparm.h" diff --git a/src/gromacs/gmxpreprocess/readrot.cpp b/src/gromacs/gmxpreprocess/readrot.cpp index 6968670a27..4615d2faf3 100644 --- a/src/gromacs/gmxpreprocess/readrot.cpp +++ b/src/gromacs/gmxpreprocess/readrot.cpp @@ -36,7 +36,7 @@ */ #include "gmxpre.h" -#include "gromacs/fileio/trnio.h" +#include "gromacs/fileio/trrio.h" #include "gromacs/gmxpreprocess/readir.h" #include "gromacs/legacyheaders/names.h" #include "gromacs/legacyheaders/txtdump.h" diff --git a/src/gromacs/mdlib/expanded.c b/src/gromacs/mdlib/expanded.c index f1a1bce5e8..402662de4c 100644 --- a/src/gromacs/mdlib/expanded.c +++ b/src/gromacs/mdlib/expanded.c @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by + * Copyright (c) 2012,2013,2014,2015, 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. @@ -40,7 +40,6 @@ #include "gromacs/domdec/domdec.h" #include "gromacs/fileio/confio.h" #include "gromacs/fileio/gmxfio.h" -#include "gromacs/fileio/trnio.h" #include "gromacs/fileio/xtcio.h" #include "gromacs/legacyheaders/calcmu.h" #include "gromacs/legacyheaders/chargegroup.h" diff --git a/src/gromacs/mdlib/stat.cpp b/src/gromacs/mdlib/stat.cpp index 08ae193dff..fc906209eb 100644 --- a/src/gromacs/mdlib/stat.cpp +++ b/src/gromacs/mdlib/stat.cpp @@ -40,7 +40,6 @@ #include #include "gromacs/domdec/domdec.h" -#include "gromacs/fileio/trnio.h" #include "gromacs/fileio/xtcio.h" #include "gromacs/legacyheaders/checkpoint.h" #include "gromacs/legacyheaders/constr.h" diff --git a/src/gromacs/pulling/pull_rotation.cpp b/src/gromacs/pulling/pull_rotation.cpp index 187fef017f..a44e84a477 100644 --- a/src/gromacs/pulling/pull_rotation.cpp +++ b/src/gromacs/pulling/pull_rotation.cpp @@ -48,7 +48,6 @@ #include "gromacs/domdec/domdec.h" #include "gromacs/fileio/gmxfio.h" -#include "gromacs/fileio/trnio.h" #include "gromacs/fileio/xvgr.h" #include "gromacs/legacyheaders/copyrite.h" #include "gromacs/legacyheaders/gmx_ga2la.h" diff --git a/src/gromacs/tools/check.cpp b/src/gromacs/tools/check.cpp index cc19905b07..0c34c66cb1 100644 --- a/src/gromacs/tools/check.cpp +++ b/src/gromacs/tools/check.cpp @@ -45,7 +45,6 @@ #include "gromacs/fileio/enxio.h" #include "gromacs/fileio/gmxfio.h" #include "gromacs/fileio/tpxio.h" -#include "gromacs/fileio/trnio.h" #include "gromacs/fileio/trxio.h" #include "gromacs/fileio/xtcio.h" #include "gromacs/legacyheaders/macros.h" diff --git a/src/gromacs/tools/convert_tpr.cpp b/src/gromacs/tools/convert_tpr.cpp index 696f61c202..a222ef578f 100644 --- a/src/gromacs/tools/convert_tpr.cpp +++ b/src/gromacs/tools/convert_tpr.cpp @@ -41,7 +41,7 @@ #include "gromacs/commandline/pargs.h" #include "gromacs/fileio/enxio.h" #include "gromacs/fileio/tpxio.h" -#include "gromacs/fileio/trnio.h" +#include "gromacs/fileio/trrio.h" #include "gromacs/gmxpreprocess/readir.h" #include "gromacs/legacyheaders/checkpoint.h" #include "gromacs/legacyheaders/macros.h" diff --git a/src/gromacs/tools/dump.cpp b/src/gromacs/tools/dump.cpp index d9b20863d9..65a028ced8 100644 --- a/src/gromacs/tools/dump.cpp +++ b/src/gromacs/tools/dump.cpp @@ -50,7 +50,7 @@ #include "gromacs/fileio/tngio.h" #include "gromacs/fileio/tngio_for_tools.h" #include "gromacs/fileio/tpxio.h" -#include "gromacs/fileio/trnio.h" +#include "gromacs/fileio/trrio.h" #include "gromacs/fileio/xtcio.h" #include "gromacs/gmxpreprocess/gmxcpp.h" #include "gromacs/legacyheaders/checkpoint.h"