Merge libgmxana into libgromacs.

- Move contents of src/tools/ into src/gromacs/gmxana/, except for
  g_tune_pme.c and g_pme_error.c.
- Delete unused src/tools/g_membed.c.
- Adjust the build system accordingly, removing references to gmxana.
- Merge contents of libgmxana.pc into libgromacs.pc and remove the
  former.
- Move src/gromacs/legacyheaders/gmx_ana.h into src/gromacs/gmxana/ and
  adjust files that include it accordingly.  Removed a few unnecessary
  inclusions of this header.  Don't install it, as it doesn't do much
  good.
- Merge src/contrib/g_sdf.c into src/contrib/gmx_sdf.c to make it
  independent of gmx_ana.h.  Remove gmx_sdf() from gmx_ana.h.

Closes #1013.

Change-Id: I34ba52fc938823833103123c8ada06d169abf7de

diff --git a/src/contrib/g_sdf.c b/src/contrib/g_sdf.c
deleted file mode 100644 (file)
index 1e020c4..0000000
--- a/src/contrib/g_sdf.c
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * 
- *                This source code is part of
- * 
- *                 G   R   O   M   A   C   S
- * 
- *          GROningen MAchine for Chemical Simulations
- * 
- *                        VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- * 
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
- * 
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- * 
- * For more info, check our website at http://www.gromacs.org
- * 
- * And Hey:
- * Green Red Orange Magenta Azure Cyan Skyblue
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <gmx_ana.h>
-
-
-/* This is just a wrapper binary.
-* The code that used to be in g_sdf.c is now in gmx_sdf.c,
-* where the old main function is called gmx_sdf().
-*/
-int
-main(int argc, char *argv[])
-{
-  gmx_sdf(argc,argv);
-  return 0;
-}
-
-
-  

diff --git a/src/contrib/gmx_sdf.c b/src/contrib/gmx_sdf.c
index 0a44beb2e3c862ba9cda362293dc1095e0735e50..88d7fe761fdd712229436638a44f76641f73c8de 100644 (file)
--- a/src/contrib/gmx_sdf.c
+++ b/src/contrib/gmx_sdf.c
@@ -39,7 +39,6 @@
 #include "gstat.h"
 #include "matio.h"
 #include "gmx_fatal.h"
-#include "gmx_ana.h"
 
 
 #define G_REF1      0
@@ -768,3 +767,10 @@ int gmx_sdf(int argc,char *argv[])
   
   return 0;
 }
+
+int
+main(int argc, char *argv[])
+{
+  gmx_sdf(argc,argv);
+  return 0;
+}

diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
index e38eec6cd5acfd34db50803ed827d21c9812f7a4..9703ca9b67777a3f6ff04a1a1ca4da1984f502b6 100644 (file)
--- a/src/gromacs/CMakeLists.txt
+++ b/src/gromacs/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
 # David van der Spoel, Berk Hess, Erik Lindahl, and including many
 # others, as listed in the AUTHORS file in the top-level source
 # directory and at http://www.gromacs.org.
@@ -38,6 +38,7 @@ add_subdirectory(legacyheaders)
 add_subdirectory(gmxlib)
 add_subdirectory(mdlib)
 add_subdirectory(gmxpreprocess)
+add_subdirectory(gmxana)
 add_subdirectory(analysisdata)
 add_subdirectory(commandline)
 add_subdirectory(linearalgebra)
@@ -104,7 +105,8 @@ if(GMX_BUILD_OWN_FFTW)
 endif()
 
 target_link_libraries(libgromacs ${GMX_GPU_LIBRARIES}
-                      ${GMX_EXTRA_LIBRARIES} ${FFT_LIBRARIES} ${XML_LIBRARIES}
+                      ${GMX_EXTRA_LIBRARIES}
+                      ${FFT_LIBRARIES} ${XML_LIBRARIES} ${GSL_LIBRARIES}
                       ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS})
 set_target_properties(libgromacs PROPERTIES
                       OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"

diff --git a/src/gromacs/gmxana/CMakeLists.txt b/src/gromacs/gmxana/CMakeLists.txt
new file mode 100644 (file)
index 0000000..89a289c
--- /dev/null
+++ b/src/gromacs/gmxana/CMakeLists.txt
@@ -0,0 +1,37 @@
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2013, by the GROMACS development team, led by
+# David van der Spoel, Berk Hess, Erik Lindahl, and including many
+# others, as listed in the AUTHORS file in the top-level source
+# directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+file(GLOB GMXANA_SOURCES *.c *.cpp)
+
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${GMXANA_SOURCES} PARENT_SCOPE)

diff --git a/src/tools/addconf.c b/src/gromacs/gmxana/addconf.c
similarity index 100%
rename from src/tools/addconf.c
rename to src/gromacs/gmxana/addconf.c

diff --git a/src/tools/addconf.h b/src/gromacs/gmxana/addconf.h
similarity index 100%
rename from src/tools/addconf.h
rename to src/gromacs/gmxana/addconf.h

diff --git a/src/tools/anadih.c b/src/gromacs/gmxana/anadih.c
similarity index 100%
rename from src/tools/anadih.c
rename to src/gromacs/gmxana/anadih.c

diff --git a/src/tools/autocorr.c b/src/gromacs/gmxana/autocorr.c
similarity index 100%
rename from src/tools/autocorr.c
rename to src/gromacs/gmxana/autocorr.c

diff --git a/src/tools/binsearch.c b/src/gromacs/gmxana/binsearch.c
similarity index 100%
rename from src/tools/binsearch.c
rename to src/gromacs/gmxana/binsearch.c

diff --git a/src/tools/binsearch.h b/src/gromacs/gmxana/binsearch.h
similarity index 100%
rename from src/tools/binsearch.h
rename to src/gromacs/gmxana/binsearch.h

diff --git a/src/tools/calcpot.c b/src/gromacs/gmxana/calcpot.c
similarity index 100%
rename from src/tools/calcpot.c
rename to src/gromacs/gmxana/calcpot.c

diff --git a/src/tools/calcpot.h b/src/gromacs/gmxana/calcpot.h
similarity index 100%
rename from src/tools/calcpot.h
rename to src/gromacs/gmxana/calcpot.h

diff --git a/src/tools/cmat.c b/src/gromacs/gmxana/cmat.c
similarity index 100%
rename from src/tools/cmat.c
rename to src/gromacs/gmxana/cmat.c

diff --git a/src/tools/cmat.h b/src/gromacs/gmxana/cmat.h
similarity index 100%
rename from src/tools/cmat.h
rename to src/gromacs/gmxana/cmat.h

diff --git a/src/tools/correl.c b/src/gromacs/gmxana/correl.c
similarity index 100%
rename from src/tools/correl.c
rename to src/gromacs/gmxana/correl.c

diff --git a/src/tools/correl.h b/src/gromacs/gmxana/correl.h
similarity index 100%
rename from src/tools/correl.h
rename to src/gromacs/gmxana/correl.h

diff --git a/src/tools/dens_filter.c b/src/gromacs/gmxana/dens_filter.c
similarity index 100%
rename from src/tools/dens_filter.c
rename to src/gromacs/gmxana/dens_filter.c

diff --git a/src/tools/dens_filter.h b/src/gromacs/gmxana/dens_filter.h
similarity index 100%
rename from src/tools/dens_filter.h
rename to src/gromacs/gmxana/dens_filter.h

diff --git a/src/tools/dlist.c b/src/gromacs/gmxana/dlist.c
similarity index 100%
rename from src/tools/dlist.c
rename to src/gromacs/gmxana/dlist.c

diff --git a/src/tools/edittop.c b/src/gromacs/gmxana/edittop.c
similarity index 100%
rename from src/tools/edittop.c
rename to src/gromacs/gmxana/edittop.c

diff --git a/src/tools/eigio.c b/src/gromacs/gmxana/eigio.c
similarity index 100%
rename from src/tools/eigio.c
rename to src/gromacs/gmxana/eigio.c

diff --git a/src/tools/eigio.h b/src/gromacs/gmxana/eigio.h
similarity index 100%
rename from src/tools/eigio.h
rename to src/gromacs/gmxana/eigio.h

diff --git a/src/tools/expfit.c b/src/gromacs/gmxana/expfit.c
similarity index 100%
rename from src/tools/expfit.c
rename to src/gromacs/gmxana/expfit.c

diff --git a/src/tools/fitahx.c b/src/gromacs/gmxana/fitahx.c
similarity index 100%
rename from src/tools/fitahx.c
rename to src/gromacs/gmxana/fitahx.c

diff --git a/src/tools/fitahx.h b/src/gromacs/gmxana/fitahx.h
similarity index 100%
rename from src/tools/fitahx.h
rename to src/gromacs/gmxana/fitahx.h

diff --git a/src/tools/geminate.c b/src/gromacs/gmxana/geminate.c
similarity index 100%
rename from src/tools/geminate.c
rename to src/gromacs/gmxana/geminate.c

diff --git a/src/tools/geminate.h b/src/gromacs/gmxana/geminate.h
similarity index 100%
rename from src/tools/geminate.h
rename to src/gromacs/gmxana/geminate.h

diff --git a/src/gromacs/legacyheaders/gmx_ana.h b/src/gromacs/gmxana/gmx_ana.h
similarity index 99%
rename from src/gromacs/legacyheaders/gmx_ana.h
rename to src/gromacs/gmxana/gmx_ana.h
index 062fc9752703811ddec6835c31525b3dde183033..27f54d6b8efaa32ff72c587b4ac0565150133dba 100644 (file)
--- a/src/gromacs/legacyheaders/gmx_ana.h
+++ b/src/gromacs/gmxana/gmx_ana.h
@@ -225,9 +225,6 @@ gmx_saltbr(int argc, char *argv[]);
 int
 gmx_sas(int argc, char *argv[]);
 
-int
-gmx_sdf(int argc, char *argv[]);
-
 int
 gmx_select(int argc, char *argv[]);
 

diff --git a/src/tools/gmx_anadock.c b/src/gromacs/gmxana/gmx_anadock.c
similarity index 100%
rename from src/tools/gmx_anadock.c
rename to src/gromacs/gmxana/gmx_anadock.c

diff --git a/src/tools/gmx_anaeig.c b/src/gromacs/gmxana/gmx_anaeig.c
similarity index 100%
rename from src/tools/gmx_anaeig.c
rename to src/gromacs/gmxana/gmx_anaeig.c

diff --git a/src/tools/gmx_analyze.c b/src/gromacs/gmxana/gmx_analyze.c
similarity index 100%
rename from src/tools/gmx_analyze.c
rename to src/gromacs/gmxana/gmx_analyze.c

diff --git a/src/tools/gmx_angle.c b/src/gromacs/gmxana/gmx_angle.c
similarity index 100%
rename from src/tools/gmx_angle.c
rename to src/gromacs/gmxana/gmx_angle.c

diff --git a/src/tools/gmx_bar.c b/src/gromacs/gmxana/gmx_bar.c
similarity index 100%
rename from src/tools/gmx_bar.c
rename to src/gromacs/gmxana/gmx_bar.c

diff --git a/src/tools/gmx_bond.c b/src/gromacs/gmxana/gmx_bond.c
similarity index 100%
rename from src/tools/gmx_bond.c
rename to src/gromacs/gmxana/gmx_bond.c

diff --git a/src/tools/gmx_bundle.c b/src/gromacs/gmxana/gmx_bundle.c
similarity index 100%
rename from src/tools/gmx_bundle.c
rename to src/gromacs/gmxana/gmx_bundle.c

diff --git a/src/tools/gmx_chi.c b/src/gromacs/gmxana/gmx_chi.c
similarity index 100%
rename from src/tools/gmx_chi.c
rename to src/gromacs/gmxana/gmx_chi.c

diff --git a/src/tools/gmx_cluster.c b/src/gromacs/gmxana/gmx_cluster.c
similarity index 100%
rename from src/tools/gmx_cluster.c
rename to src/gromacs/gmxana/gmx_cluster.c

diff --git a/src/tools/gmx_clustsize.c b/src/gromacs/gmxana/gmx_clustsize.c
similarity index 100%
rename from src/tools/gmx_clustsize.c
rename to src/gromacs/gmxana/gmx_clustsize.c

diff --git a/src/tools/gmx_confrms.c b/src/gromacs/gmxana/gmx_confrms.c
similarity index 100%
rename from src/tools/gmx_confrms.c
rename to src/gromacs/gmxana/gmx_confrms.c

diff --git a/src/tools/gmx_covar.c b/src/gromacs/gmxana/gmx_covar.c
similarity index 100%
rename from src/tools/gmx_covar.c
rename to src/gromacs/gmxana/gmx_covar.c

diff --git a/src/tools/gmx_current.c b/src/gromacs/gmxana/gmx_current.c
similarity index 100%
rename from src/tools/gmx_current.c
rename to src/gromacs/gmxana/gmx_current.c

diff --git a/src/tools/gmx_density.c b/src/gromacs/gmxana/gmx_density.c
similarity index 100%
rename from src/tools/gmx_density.c
rename to src/gromacs/gmxana/gmx_density.c

diff --git a/src/tools/gmx_densmap.c b/src/gromacs/gmxana/gmx_densmap.c
similarity index 100%
rename from src/tools/gmx_densmap.c
rename to src/gromacs/gmxana/gmx_densmap.c

diff --git a/src/tools/gmx_densorder.c b/src/gromacs/gmxana/gmx_densorder.c
similarity index 100%
rename from src/tools/gmx_densorder.c
rename to src/gromacs/gmxana/gmx_densorder.c

diff --git a/src/tools/gmx_dielectric.c b/src/gromacs/gmxana/gmx_dielectric.c
similarity index 100%
rename from src/tools/gmx_dielectric.c
rename to src/gromacs/gmxana/gmx_dielectric.c

diff --git a/src/tools/gmx_dipoles.c b/src/gromacs/gmxana/gmx_dipoles.c
similarity index 100%
rename from src/tools/gmx_dipoles.c
rename to src/gromacs/gmxana/gmx_dipoles.c

diff --git a/src/tools/gmx_disre.c b/src/gromacs/gmxana/gmx_disre.c
similarity index 100%
rename from src/tools/gmx_disre.c
rename to src/gromacs/gmxana/gmx_disre.c

diff --git a/src/tools/gmx_dist.c b/src/gromacs/gmxana/gmx_dist.c
similarity index 100%
rename from src/tools/gmx_dist.c
rename to src/gromacs/gmxana/gmx_dist.c

diff --git a/src/tools/gmx_do_dssp.c b/src/gromacs/gmxana/gmx_do_dssp.c
similarity index 100%
rename from src/tools/gmx_do_dssp.c
rename to src/gromacs/gmxana/gmx_do_dssp.c

diff --git a/src/tools/gmx_dos.c b/src/gromacs/gmxana/gmx_dos.c
similarity index 100%
rename from src/tools/gmx_dos.c
rename to src/gromacs/gmxana/gmx_dos.c

diff --git a/src/tools/gmx_dyecoupl.c b/src/gromacs/gmxana/gmx_dyecoupl.c
similarity index 100%
rename from src/tools/gmx_dyecoupl.c
rename to src/gromacs/gmxana/gmx_dyecoupl.c

diff --git a/src/tools/gmx_dyndom.c b/src/gromacs/gmxana/gmx_dyndom.c
similarity index 100%
rename from src/tools/gmx_dyndom.c
rename to src/gromacs/gmxana/gmx_dyndom.c

diff --git a/src/tools/gmx_editconf.c b/src/gromacs/gmxana/gmx_editconf.c
similarity index 100%
rename from src/tools/gmx_editconf.c
rename to src/gromacs/gmxana/gmx_editconf.c

diff --git a/src/tools/gmx_eneconv.c b/src/gromacs/gmxana/gmx_eneconv.c
similarity index 100%
rename from src/tools/gmx_eneconv.c
rename to src/gromacs/gmxana/gmx_eneconv.c

diff --git a/src/tools/gmx_enemat.c b/src/gromacs/gmxana/gmx_enemat.c
similarity index 100%
rename from src/tools/gmx_enemat.c
rename to src/gromacs/gmxana/gmx_enemat.c

diff --git a/src/tools/gmx_energy.c b/src/gromacs/gmxana/gmx_energy.c
similarity index 100%
rename from src/tools/gmx_energy.c
rename to src/gromacs/gmxana/gmx_energy.c

diff --git a/src/tools/gmx_filter.c b/src/gromacs/gmxana/gmx_filter.c
similarity index 100%
rename from src/tools/gmx_filter.c
rename to src/gromacs/gmxana/gmx_filter.c

diff --git a/src/tools/gmx_genbox.cpp b/src/gromacs/gmxana/gmx_genbox.cpp
similarity index 100%
rename from src/tools/gmx_genbox.cpp
rename to src/gromacs/gmxana/gmx_genbox.cpp

diff --git a/src/tools/gmx_genconf.c b/src/gromacs/gmxana/gmx_genconf.c
similarity index 100%
rename from src/tools/gmx_genconf.c
rename to src/gromacs/gmxana/gmx_genconf.c

diff --git a/src/tools/gmx_genion.c b/src/gromacs/gmxana/gmx_genion.c
similarity index 100%
rename from src/tools/gmx_genion.c
rename to src/gromacs/gmxana/gmx_genion.c

diff --git a/src/tools/gmx_genpr.c b/src/gromacs/gmxana/gmx_genpr.c
similarity index 100%
rename from src/tools/gmx_genpr.c
rename to src/gromacs/gmxana/gmx_genpr.c

diff --git a/src/tools/gmx_gyrate.c b/src/gromacs/gmxana/gmx_gyrate.c
similarity index 100%
rename from src/tools/gmx_gyrate.c
rename to src/gromacs/gmxana/gmx_gyrate.c

diff --git a/src/tools/gmx_h2order.c b/src/gromacs/gmxana/gmx_h2order.c
similarity index 100%
rename from src/tools/gmx_h2order.c
rename to src/gromacs/gmxana/gmx_h2order.c

diff --git a/src/tools/gmx_hbond.c b/src/gromacs/gmxana/gmx_hbond.c
similarity index 100%
rename from src/tools/gmx_hbond.c
rename to src/gromacs/gmxana/gmx_hbond.c

diff --git a/src/tools/gmx_helix.c b/src/gromacs/gmxana/gmx_helix.c
similarity index 100%
rename from src/tools/gmx_helix.c
rename to src/gromacs/gmxana/gmx_helix.c

diff --git a/src/tools/gmx_helixorient.c b/src/gromacs/gmxana/gmx_helixorient.c
similarity index 100%
rename from src/tools/gmx_helixorient.c
rename to src/gromacs/gmxana/gmx_helixorient.c

diff --git a/src/tools/gmx_hydorder.c b/src/gromacs/gmxana/gmx_hydorder.c
similarity index 100%
rename from src/tools/gmx_hydorder.c
rename to src/gromacs/gmxana/gmx_hydorder.c

diff --git a/src/tools/gmx_kinetics.c b/src/gromacs/gmxana/gmx_kinetics.c
similarity index 100%
rename from src/tools/gmx_kinetics.c
rename to src/gromacs/gmxana/gmx_kinetics.c

diff --git a/src/tools/gmx_lie.c b/src/gromacs/gmxana/gmx_lie.c
similarity index 100%
rename from src/tools/gmx_lie.c
rename to src/gromacs/gmxana/gmx_lie.c

diff --git a/src/tools/gmx_make_edi.c b/src/gromacs/gmxana/gmx_make_edi.c
similarity index 100%
rename from src/tools/gmx_make_edi.c
rename to src/gromacs/gmxana/gmx_make_edi.c

diff --git a/src/tools/gmx_make_ndx.c b/src/gromacs/gmxana/gmx_make_ndx.c
similarity index 100%
rename from src/tools/gmx_make_ndx.c
rename to src/gromacs/gmxana/gmx_make_ndx.c

diff --git a/src/tools/gmx_mdmat.c b/src/gromacs/gmxana/gmx_mdmat.c
similarity index 100%
rename from src/tools/gmx_mdmat.c
rename to src/gromacs/gmxana/gmx_mdmat.c

diff --git a/src/tools/gmx_membed.c b/src/gromacs/gmxana/gmx_membed.c
similarity index 100%
rename from src/tools/gmx_membed.c
rename to src/gromacs/gmxana/gmx_membed.c

diff --git a/src/tools/gmx_mindist.c b/src/gromacs/gmxana/gmx_mindist.c
similarity index 100%
rename from src/tools/gmx_mindist.c
rename to src/gromacs/gmxana/gmx_mindist.c

diff --git a/src/tools/gmx_mk_angndx.c b/src/gromacs/gmxana/gmx_mk_angndx.c
similarity index 100%
rename from src/tools/gmx_mk_angndx.c
rename to src/gromacs/gmxana/gmx_mk_angndx.c

diff --git a/src/tools/gmx_morph.c b/src/gromacs/gmxana/gmx_morph.c
similarity index 100%
rename from src/tools/gmx_morph.c
rename to src/gromacs/gmxana/gmx_morph.c

diff --git a/src/tools/gmx_msd.c b/src/gromacs/gmxana/gmx_msd.c
similarity index 100%
rename from src/tools/gmx_msd.c
rename to src/gromacs/gmxana/gmx_msd.c

diff --git a/src/tools/gmx_nmeig.c b/src/gromacs/gmxana/gmx_nmeig.c
similarity index 100%
rename from src/tools/gmx_nmeig.c
rename to src/gromacs/gmxana/gmx_nmeig.c

diff --git a/src/tools/gmx_nmens.c b/src/gromacs/gmxana/gmx_nmens.c
similarity index 100%
rename from src/tools/gmx_nmens.c
rename to src/gromacs/gmxana/gmx_nmens.c

diff --git a/src/tools/gmx_nmtraj.c b/src/gromacs/gmxana/gmx_nmtraj.c
similarity index 100%
rename from src/tools/gmx_nmtraj.c
rename to src/gromacs/gmxana/gmx_nmtraj.c

diff --git a/src/tools/gmx_options.c b/src/gromacs/gmxana/gmx_options.c
similarity index 100%
rename from src/tools/gmx_options.c
rename to src/gromacs/gmxana/gmx_options.c

diff --git a/src/tools/gmx_order.c b/src/gromacs/gmxana/gmx_order.c
similarity index 100%
rename from src/tools/gmx_order.c
rename to src/gromacs/gmxana/gmx_order.c

diff --git a/src/tools/gmx_pme_error.c b/src/gromacs/gmxana/gmx_pme_error.c
similarity index 100%
rename from src/tools/gmx_pme_error.c
rename to src/gromacs/gmxana/gmx_pme_error.c

diff --git a/src/tools/gmx_polystat.c b/src/gromacs/gmxana/gmx_polystat.c
similarity index 100%
rename from src/tools/gmx_polystat.c
rename to src/gromacs/gmxana/gmx_polystat.c

diff --git a/src/tools/gmx_potential.c b/src/gromacs/gmxana/gmx_potential.c
similarity index 100%
rename from src/tools/gmx_potential.c
rename to src/gromacs/gmxana/gmx_potential.c

diff --git a/src/tools/gmx_principal.c b/src/gromacs/gmxana/gmx_principal.c
similarity index 100%
rename from src/tools/gmx_principal.c
rename to src/gromacs/gmxana/gmx_principal.c

diff --git a/src/tools/gmx_rama.c b/src/gromacs/gmxana/gmx_rama.c
similarity index 100%
rename from src/tools/gmx_rama.c
rename to src/gromacs/gmxana/gmx_rama.c

diff --git a/src/tools/gmx_rdf.c b/src/gromacs/gmxana/gmx_rdf.c
similarity index 100%
rename from src/tools/gmx_rdf.c
rename to src/gromacs/gmxana/gmx_rdf.c

diff --git a/src/tools/gmx_rms.c b/src/gromacs/gmxana/gmx_rms.c
similarity index 100%
rename from src/tools/gmx_rms.c
rename to src/gromacs/gmxana/gmx_rms.c

diff --git a/src/tools/gmx_rmsdist.c b/src/gromacs/gmxana/gmx_rmsdist.c
similarity index 100%
rename from src/tools/gmx_rmsdist.c
rename to src/gromacs/gmxana/gmx_rmsdist.c

diff --git a/src/tools/gmx_rmsf.c b/src/gromacs/gmxana/gmx_rmsf.c
similarity index 100%
rename from src/tools/gmx_rmsf.c
rename to src/gromacs/gmxana/gmx_rmsf.c

diff --git a/src/tools/gmx_rotacf.c b/src/gromacs/gmxana/gmx_rotacf.c
similarity index 100%
rename from src/tools/gmx_rotacf.c
rename to src/gromacs/gmxana/gmx_rotacf.c

diff --git a/src/tools/gmx_rotmat.c b/src/gromacs/gmxana/gmx_rotmat.c
similarity index 100%
rename from src/tools/gmx_rotmat.c
rename to src/gromacs/gmxana/gmx_rotmat.c

diff --git a/src/tools/gmx_saltbr.c b/src/gromacs/gmxana/gmx_saltbr.c
similarity index 100%
rename from src/tools/gmx_saltbr.c
rename to src/gromacs/gmxana/gmx_saltbr.c

diff --git a/src/tools/gmx_sans.c b/src/gromacs/gmxana/gmx_sans.c
similarity index 100%
rename from src/tools/gmx_sans.c
rename to src/gromacs/gmxana/gmx_sans.c

diff --git a/src/tools/gmx_sas.c b/src/gromacs/gmxana/gmx_sas.c
similarity index 100%
rename from src/tools/gmx_sas.c
rename to src/gromacs/gmxana/gmx_sas.c

diff --git a/src/tools/gmx_saxs.c b/src/gromacs/gmxana/gmx_saxs.c
similarity index 100%
rename from src/tools/gmx_saxs.c
rename to src/gromacs/gmxana/gmx_saxs.c

diff --git a/src/tools/gmx_sgangle.c b/src/gromacs/gmxana/gmx_sgangle.c
similarity index 100%
rename from src/tools/gmx_sgangle.c
rename to src/gromacs/gmxana/gmx_sgangle.c

diff --git a/src/tools/gmx_sham.c b/src/gromacs/gmxana/gmx_sham.c
similarity index 100%
rename from src/tools/gmx_sham.c
rename to src/gromacs/gmxana/gmx_sham.c

diff --git a/src/tools/gmx_sigeps.c b/src/gromacs/gmxana/gmx_sigeps.c
similarity index 100%
rename from src/tools/gmx_sigeps.c
rename to src/gromacs/gmxana/gmx_sigeps.c

diff --git a/src/tools/gmx_sorient.c b/src/gromacs/gmxana/gmx_sorient.c
similarity index 100%
rename from src/tools/gmx_sorient.c
rename to src/gromacs/gmxana/gmx_sorient.c

diff --git a/src/tools/gmx_spatial.c b/src/gromacs/gmxana/gmx_spatial.c
similarity index 100%
rename from src/tools/gmx_spatial.c
rename to src/gromacs/gmxana/gmx_spatial.c

diff --git a/src/tools/gmx_spol.c b/src/gromacs/gmxana/gmx_spol.c
similarity index 100%
rename from src/tools/gmx_spol.c
rename to src/gromacs/gmxana/gmx_spol.c

diff --git a/src/tools/gmx_tcaf.c b/src/gromacs/gmxana/gmx_tcaf.c
similarity index 100%
rename from src/tools/gmx_tcaf.c
rename to src/gromacs/gmxana/gmx_tcaf.c

diff --git a/src/tools/gmx_traj.c b/src/gromacs/gmxana/gmx_traj.c
similarity index 100%
rename from src/tools/gmx_traj.c
rename to src/gromacs/gmxana/gmx_traj.c

diff --git a/src/tools/gmx_trjcat.c b/src/gromacs/gmxana/gmx_trjcat.c
similarity index 100%
rename from src/tools/gmx_trjcat.c
rename to src/gromacs/gmxana/gmx_trjcat.c

diff --git a/src/tools/gmx_trjconv.c b/src/gromacs/gmxana/gmx_trjconv.c
similarity index 100%
rename from src/tools/gmx_trjconv.c
rename to src/gromacs/gmxana/gmx_trjconv.c

diff --git a/src/tools/gmx_trjorder.c b/src/gromacs/gmxana/gmx_trjorder.c
similarity index 100%
rename from src/tools/gmx_trjorder.c
rename to src/gromacs/gmxana/gmx_trjorder.c

diff --git a/src/tools/gmx_tune_pme.c b/src/gromacs/gmxana/gmx_tune_pme.c
similarity index 100%
rename from src/tools/gmx_tune_pme.c
rename to src/gromacs/gmxana/gmx_tune_pme.c

diff --git a/src/tools/gmx_vanhove.c b/src/gromacs/gmxana/gmx_vanhove.c
similarity index 100%
rename from src/tools/gmx_vanhove.c
rename to src/gromacs/gmxana/gmx_vanhove.c

diff --git a/src/tools/gmx_velacc.c b/src/gromacs/gmxana/gmx_velacc.c
similarity index 100%
rename from src/tools/gmx_velacc.c
rename to src/gromacs/gmxana/gmx_velacc.c

diff --git a/src/tools/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp
similarity index 100%
rename from src/tools/gmx_wham.cpp
rename to src/gromacs/gmxana/gmx_wham.cpp

diff --git a/src/tools/gmx_wheel.c b/src/gromacs/gmxana/gmx_wheel.c
similarity index 100%
rename from src/tools/gmx_wheel.c
rename to src/gromacs/gmxana/gmx_wheel.c

diff --git a/src/tools/gmx_xpm2ps.c b/src/gromacs/gmxana/gmx_xpm2ps.c
similarity index 100%
rename from src/tools/gmx_xpm2ps.c
rename to src/gromacs/gmxana/gmx_xpm2ps.c

diff --git a/src/tools/hxprops.c b/src/gromacs/gmxana/hxprops.c
similarity index 100%
rename from src/tools/hxprops.c
rename to src/gromacs/gmxana/hxprops.c

diff --git a/src/tools/hxprops.h b/src/gromacs/gmxana/hxprops.h
similarity index 100%
rename from src/tools/hxprops.h
rename to src/gromacs/gmxana/hxprops.h

diff --git a/src/tools/interf.h b/src/gromacs/gmxana/interf.h
similarity index 100%
rename from src/tools/interf.h
rename to src/gromacs/gmxana/interf.h

diff --git a/src/tools/levenmar.c b/src/gromacs/gmxana/levenmar.c
similarity index 100%
rename from src/tools/levenmar.c
rename to src/gromacs/gmxana/levenmar.c

diff --git a/src/tools/nsc.c b/src/gromacs/gmxana/nsc.c
similarity index 100%
rename from src/tools/nsc.c
rename to src/gromacs/gmxana/nsc.c

diff --git a/src/tools/nsc.h b/src/gromacs/gmxana/nsc.h
similarity index 100%
rename from src/tools/nsc.h
rename to src/gromacs/gmxana/nsc.h

diff --git a/src/tools/nsfactor.c b/src/gromacs/gmxana/nsfactor.c
similarity index 100%
rename from src/tools/nsfactor.c
rename to src/gromacs/gmxana/nsfactor.c

diff --git a/src/tools/nsfactor.h b/src/gromacs/gmxana/nsfactor.h
similarity index 100%
rename from src/tools/nsfactor.h
rename to src/gromacs/gmxana/nsfactor.h

diff --git a/src/tools/polynomials.c b/src/gromacs/gmxana/polynomials.c
similarity index 100%
rename from src/tools/polynomials.c
rename to src/gromacs/gmxana/polynomials.c

diff --git a/src/tools/powerspect.c b/src/gromacs/gmxana/powerspect.c
similarity index 100%
rename from src/tools/powerspect.c
rename to src/gromacs/gmxana/powerspect.c

diff --git a/src/tools/powerspect.h b/src/gromacs/gmxana/powerspect.h
similarity index 100%
rename from src/tools/powerspect.h
rename to src/gromacs/gmxana/powerspect.h

diff --git a/src/tools/pp2shift.c b/src/gromacs/gmxana/pp2shift.c
similarity index 100%
rename from src/tools/pp2shift.c
rename to src/gromacs/gmxana/pp2shift.c

diff --git a/src/tools/pp2shift.h b/src/gromacs/gmxana/pp2shift.h
similarity index 100%
rename from src/tools/pp2shift.h
rename to src/gromacs/gmxana/pp2shift.h

diff --git a/src/gromacs/gmxlib/sfactor.c b/src/gromacs/gmxlib/sfactor.c
index 5ec013c64fa44d1aee051a0ed879f365a17332ad..7d7b1636bf2c938eb8c2a569fe396507f17e8f7d 100644 (file)
--- a/src/gromacs/gmxlib/sfactor.c
+++ b/src/gromacs/gmxlib/sfactor.c
@@ -55,7 +55,6 @@
 #include "gmxfio.h"
 #include "xvgr.h"
 #include "matio.h"
-#include "gmx_ana.h"
 #include "names.h"
 #include "sfactor.h"
 

diff --git a/src/gromacs/libgromacs.pc.cmakein b/src/gromacs/libgromacs.pc.cmakein
index d059a34767e004920a3d2a799b1a20f22863dfd9..5cc1da7b318dbab3381d50a4178d99e02d4fc012 100644 (file)
--- a/src/gromacs/libgromacs.pc.cmakein
+++ b/src/gromacs/libgromacs.pc.cmakein
@@ -5,7 +5,7 @@ Name: libgromacs
 Description: Gromacs library
 URL: http://www.gromacs.org
 Version: @PROJECT_VERSION@
-Requires: @PKG_FFT@ @PKG_XML@
+Requires: @PKG_FFT@ @PKG_XML@ @PKG_GSL@
 Libs.private: @CMAKE_THREAD_LIBS_INIT@ @PKG_DL_LIBS@ @OpenMP_LINKER_FLAGS@
 Libs: -L${libdir} -lgromacs@GMX_LIBS_SUFFIX@ @PKG_FFT_LIBS@ -lm
 Cflags: -I${includedir} @PKG_CFLAGS@

diff --git a/src/programs/gmx/CMakeLists.txt b/src/programs/gmx/CMakeLists.txt
index be3c495e758a76ac68810cda45660192c221ed3c..edaaef66bf73ff177c3f60c38765ca302c147865 100644 (file)
--- a/src/programs/gmx/CMakeLists.txt
+++ b/src/programs/gmx/CMakeLists.txt
@@ -33,7 +33,7 @@
 # the research papers on the package. Check out http://www.gromacs.org.
 
 add_executable(gmx gmx.cpp legacymodules.cpp)
-target_link_libraries(gmx libgromacs gmxana ${GMX_EXE_LINKER_FLAGS})
+target_link_libraries(gmx libgromacs ${GMX_EXE_LINKER_FLAGS})
 set_target_properties(gmx PROPERTIES OUTPUT_NAME "gmx${GMX_BINARY_SUFFIX}")
 
 configure_file(CreateLinks.cmake.cmakein CreateLinks.cmake @ONLY)

diff --git a/src/programs/gmx/legacymodules.cpp b/src/programs/gmx/legacymodules.cpp
index cf20a6494db46933cc55cbd29a523c107fa1729e..0a3c2b694aed4b51b31bb6e4f364cc8473d8fdbd 100644 (file)
--- a/src/programs/gmx/legacymodules.cpp
+++ b/src/programs/gmx/legacymodules.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
  * others, as listed in the AUTHORS file in the top-level source
  * directory and at http://www.gromacs.org.
@@ -44,7 +44,7 @@
 #include "gromacs/onlinehelp/helpwritercontext.h"
 #include "gromacs/utility/exceptions.h"
 
-#include "gromacs/legacyheaders/gmx_ana.h"
+#include "gromacs/gmxana/gmx_ana.h"
 
 namespace
 {

diff --git a/src/tools/CMakeLists.txt b/src/tools/CMakeLists.txt
index 578c640bb4f7a4ba0e621150bd28e909f3e52c77..106e88ad0343cf13be5fce83beb57facace7092a 100644 (file)
--- a/src/tools/CMakeLists.txt
+++ b/src/tools/CMakeLists.txt
@@ -1,44 +1,3 @@
-add_library(gmxana 
-            autocorr.c      expfit.c        polynomials.c   levenmar.c      
-            anadih.c        pp2shift.c      dlist.c         
-            eigio.c         cmat.c          nsc.c
-            hxprops.c       fitahx.c        
-            geminate.c      nsfactor.c
-            gmx_analyze.c   gmx_anaeig.c    gmx_angle.c     gmx_bond.c      
-            gmx_bundle.c    gmx_chi.c       gmx_cluster.c   gmx_confrms.c   
-            gmx_covar.c     gmx_current.c   
-            gmx_density.c   gmx_densmap.c       
-            gmx_dielectric.c        
-            gmx_kinetics.c  gmx_spatial.c   gmx_tune_pme.c
-            gmx_dipoles.c   gmx_disre.c     gmx_dist.c      gmx_dyndom.c    
-            gmx_enemat.c    gmx_energy.c    gmx_lie.c       gmx_filter.c    
-            gmx_gyrate.c    gmx_h2order.c   gmx_hbond.c     gmx_helix.c     
-            gmx_mindist.c   gmx_msd.c       gmx_morph.c     gmx_nmeig.c     
-            gmx_nmens.c     gmx_order.c     gmx_principal.c 
-            gmx_polystat.c  gmx_potential.c gmx_rama.c      
-            gmx_rdf.c       gmx_rms.c       gmx_rmsf.c      
-            gmx_rotacf.c    gmx_saltbr.c    gmx_sas.c       gmx_sans.c
-            gmx_rmsdist.c   gmx_rotmat.c
-            gmx_sgangle.c   gmx_sorient.c   gmx_spol.c      gmx_tcaf.c      
-            gmx_traj.c      gmx_velacc.c    gmx_helixorient.c 
-            gmx_clustsize.c gmx_mdmat.c     gmx_wham.cpp
-            correl.c        gmx_sham.c      gmx_nmtraj.c    
-            gmx_trjconv.c   gmx_trjcat.c    gmx_trjorder.c  gmx_xpm2ps.c    
-            gmx_editconf.c  gmx_genbox.cpp    gmx_genion.c    gmx_genconf.c
-            gmx_genpr.c     gmx_eneconv.c   gmx_vanhove.c   gmx_wheel.c     
-            addconf.c       calcpot.c       edittop.c       gmx_bar.c
-            gmx_pme_error.c gmx_options.c   gmx_dos.c
-            gmx_hydorder.c  gmx_densorder.c powerspect.c    dens_filter.c
-            binsearch.c     gmx_dyecoupl.c  gmx_make_edi.c  gmx_sigeps.c
-            gmx_do_dssp.c   gmx_anadock.c   gmx_make_ndx.c  gmx_mk_angndx.c
-           gmx_saxs.c
-            )
-
-
-target_link_libraries(gmxana libgromacs ${GSL_LIBRARIES} ${GMX_SHARED_LINKER_FLAGS})
-set_target_properties(gmxana PROPERTIES OUTPUT_NAME "gmxana${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION}
-    COMPILE_FLAGS "${OpenMP_C_FLAGS}")
-
 # List of programs with single corresponding .c source file,
 # used to create build rules automatically.
 #
@@ -46,26 +5,13 @@ set(GMX_TOOLS_PROGRAMS
     g_tune_pme g_pme_error
     )
 
-set(GMX_TOOLS_PROGRAMS_NOT_FOR_INSTALLATION
-  # names of any executables that should be built but not installed can go here
-    )
-
-
-foreach(TOOL ${GMX_TOOLS_PROGRAMS} ${GMX_TOOLS_PROGRAMS_NOT_FOR_INSTALLATION})
+foreach(TOOL ${GMX_TOOLS_PROGRAMS})
     add_executable(${TOOL} ${TOOL}.c)
     gmx_add_man_page(${TOOL})
-    target_link_libraries(${TOOL} gmxana ${GMX_EXE_LINKER_FLAGS})
+    target_link_libraries(${TOOL} libgromacs ${GMX_EXE_LINKER_FLAGS})
     set_target_properties(${TOOL} PROPERTIES OUTPUT_NAME "${TOOL}${GMX_BINARY_SUFFIX}")
-endforeach(TOOL ${GMX_TOOLS_PROGRAMS}) 
+endforeach(TOOL ${GMX_TOOLS_PROGRAMS})
 
-
-install(TARGETS gmxana DESTINATION ${LIB_INSTALL_DIR} COMPONENT runtime)
 install(TARGETS ${GMX_TOOLS_PROGRAMS}
         DESTINATION ${BIN_INSTALL_DIR}
         COMPONENT runtime)
-
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgmxana.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libgmxana.pc @ONLY)
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmxana.pc
-        DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
-        RENAME "libgmxana${GMX_LIBS_SUFFIX}.pc"
-        COMPONENT development)

diff --git a/src/tools/g_membed.c b/src/tools/g_membed.c
deleted file mode 100644 (file)
index d9bd19e..0000000
--- a/src/tools/g_membed.c
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- *
- *                This source code is part of
- *
- *                 G   R   O   M   A   C   S
- *
- *          GROningen MAchine for Chemical Simulations
- *
- *                        VERSION 4.0.3
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * Green Red Orange Magenta Azure Cyan Skyblue
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <gmx_ana.h>
-
-
-/* This is just a wrapper binary.
- * The code that used to be in g_anaeig.c is now in gmx_anaeig.c,
- * where the old main function is called gmx_anaeig().
- */
-int
-main(int argc, char *argv[])
-{
-    gmx_membed(argc, argv);
-    return 0;
-}

diff --git a/src/tools/g_pme_error.c b/src/tools/g_pme_error.c
index 48c12a3661137297638ba8698438718ce4c3fefc..6249737ed2f95402faa81f3008b88cc5ceabf14f 100644 (file)
--- a/src/tools/g_pme_error.c
+++ b/src/tools/g_pme_error.c
@@ -31,13 +31,7 @@
  * And Hey:
  * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <gmx_ana.h>
-
+#include "gromacs/gmxana/gmx_ana.h"
 
 /* This is just a wrapper binary.
  */

diff --git a/src/tools/g_tune_pme.c b/src/tools/g_tune_pme.c
index 2fc4e012a8db006ef37935d2e8539214d0b2634d..ab68d58791fe214026dcc067bab0c06b38e3d294 100644 (file)
--- a/src/tools/g_tune_pme.c
+++ b/src/tools/g_tune_pme.c
@@ -31,13 +31,7 @@
  * And Hey:
  * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <gmx_ana.h>
-
+#include "gromacs/gmxana/gmx_ana.h"
 
 /* This is just a wrapper binary.
  */

diff --git a/src/tools/libgmxana.pc.cmakein b/src/tools/libgmxana.pc.cmakein
deleted file mode 100644 (file)
index 16b8850..0000000
--- a/src/tools/libgmxana.pc.cmakein
+++ /dev/null
@@ -1,12 +0,0 @@
-libdir=@LIB_INSTALL_DIR@
-includedir=@INCL_INSTALL_DIR@
-
-Name: libgmxana
-Description: Gromacs analysis lib
-URL: http://www.gromacs.org
-Version: @PROJECT_VERSION@
-Requires: @PKG_GSL@ libgromacs@GMX_LIBS_SUFFIX@
-Libs.private: -lm @CMAKE_THREAD_LIBS_INIT@
-Libs: -L${libdir} -lgmxana@GMX_LIBS_SUFFIX@
-Cflags: -I${includedir} @PKG_CFLAGS@
-