ChangeLog

2012-03-06 Magnus Hagdorn
 * PyGC/progs/Makefile.am: add new file
 * PyGC/progs/animate: add script to generate animations
 * PyGC/progs/plotGCvar: fix some bugs

2011-11-07 Magnus Hagdorn
 * m4macros/netcdf.m4: the netCDF4 package of SL6 stores the module files in
   a new location so we need to look for them in various places

2011-10-04 Magnus Hagdorn
 * PyGC/PyGC/IO/GC_profile.py: deal with litho temperature profiles

2011-09-28 Magnus Hagdorn
 * PyGC/progs/cf2GC: need to flip coordinates before computing lon/lats
   if necessary

2011-09-27 Magnus Hagdorn
 * PyGC/progs/cf2GC: fix bug computing x0,y0. flip coordinate axes if
   necessary

2011-09-26 Magnus Hagdorn
 * PyGC/PyGC/IO/GC_netcdf.py: move netCDF module selection to its own file
 * PyGC/PyGC/IO/GC_proj.py: add method to store CF mapping variable
 * PyGC/PyGC/IO/Makefile.am: add new file
 * PyGC/PyGC/IO/__init__.py: load various modules
 * PyGC/PyGC/IO/netcdf.py: find a suitable netCDF module
 * PyGC/progs/Makefile.am: add new program
 * PyGC/progs/cf2GC: new program to convert a CF compliant file into a GC input
   file. Currently, the data has to be projected to a suitable geographic
   coord system

2011-06-01 Magnus Hagdorn
 * PyGC/PyGC/IO/GC_loadfile.py: fix index ordering

2011-05-31 Magnus Hagdorn
 * PyGC/progs/plotGCProfile: add option to limit the yrange
 * extensions/erosion/scripts/plotGCSedsProfile: ditto

2011-05-24 Magnus Hagdorn
 * doc/Makefile.am: remake docs if any tex or eps file has changed

2011-03-16 Magnus Hagdorn
 * libglimmer/glimmer_searchcircle.F90: simplify search circle computations

2011-03-07 Magnus Hagdorn
 * example-drivers/eis/Makefile.am: decent into test directories for various
   test run related rules
 * extensions/erosion/src/Makefile.am: make sure erosion lib is static only

2011-03-04 Magnus Hagdorn
 * tests/EISMINT/EISMINT-1/*.config: add output file with 1000a output freq
 * tests/EISMINT/EISMINT-2/*.config: ditto

2011-02-09 Magnus Hagdorn
 * PyGC/PyGC/GC_options.py: make var method public
 * PyGC/progs/Makefile.am: add new program
 * PyGC/progs/compareGCvar: new program to display difference in a variable
   between two files
 
2011-01-12 Magnus Hagdorn
 * Makefile.am: remove gold standard distribution directory once tar-balled
 * configure.in: make sure path to gold standard is absolute
 * extra_rules.am: report missing files; make sure data to be compared has been
   computed; only create directory if files are to be copied, use hard links
   rather than copy the files
 * example-drivers/Makefile.am: add a check-data target
 * example-drivers/EISMINT-3/Makefile.am: ditto
 * tests/EISMINT/EISMINT-1/Makefile.am: specify which data files are required
   for gold standard
 * tests/EISMINT/EISMINT-2/Makefile.am: ditto
 * tests/exact-isothermal/Makefile.am: add a check-data and dist-gold-standard
   target
 * tests/exact-isothermal/tests/Makefile.am: include extra_rules.am

2010-12-03 Sarah Shannon
 * extra_rules.am: add dist-gold-standard rule to create a tar file of test data	
 * Makefile.am: ditto
	
2010-11-25 Sarah Shannon
 * extra_rules.am: add check-data rule to compare tests to gold standards

2010-11-24 Magnus Hagdorn
 * extra_rules.am: add macro to find relative builddir path; use it to find
   gold standard files

2010-09-01 Magnus Hagdorn
 * PyGC/progs/plotEISMINT2stats: print legend if more than one file is
   specified on command line

2010-07-30 Magnus Hagdorn
 * extra_rules.am: pass all dependencies to glide launcher
 * PyGC/data/Makefile.am: add new file
 * PyGC/data/eismint.prof: add file containing profile for EISMINT plots
 * example-drivers/EISMINT-3/EISMINT-3/Makefile.am: remove jid files
 * example-drivers/eis/fenscan/Makefile.am: ditto
 * tests/EISMINT/EISMINT-1/Makefile.am: ditto
 * tests/EISMINT/EISMINT-2/Makefile.am: ditto
 * tests/EISMINT/benchmarks/Makefile.am: ditto
 * /tests/EISMINT/erosion/Makefile.am: ditto
 * tests/EISMINT/isos/Makefile.am: remove jid files; add some plotting
 * tests/EISMINT/lin-non_lin/Makefile.am: ditto
 * tests/exact-isothermal/tests/Makefile.am: ditto
 * scripts/glide_launch.py: use subprocess module to start glide; when
   submitting jobs to SGE figure out if job depends on completion of
   another and store job ID in file

2010-07-19 Magnus Hagdorn
 * PyGC/PyGC/GC_options.py: add new option
 * progs/plotGCvar: add option to overlay plot with ice thickness mask

2010-07-19 Magnus Hagdorn
 * extra_rules.am: add rules to do some more plotting
 * PyGC/PyGC/IO/GC_loadfile.py: fix bug with temperature profile in lithosphere
 * PyGC/progs/plotGCSpot: add program to plot vertical profiles at a particular
   location
 * PyGC/progs/Makefile.am: distribute new program
 * example-drivers/eis/fenscan/Makefile.am: do some more plotting

2010-07-19 Magnus Hagdorn
 * extra_rules.am: add rules to do some more plotting
 * PyGC/progs/plotGCSpotTS: add program to plot variable at one location through
   time
 * PyGC/progs/Makefile.am: distribute new program
 * extensions/erosion/scripts/Makefile.am: ditto
 * example-drivers/eis/fenscan/Makefile.am: do some more plotting
 
2010-07-13 Magnus Hagdorn
 * extra_rules.am: add rules to do some more plotting
 * PyGC/PyGC/GC_colourmap.py: fix path to colourmaps when run from source dir
 * example-drivers/eis/fenscan/Makefile.am: do some more plotting
 * extensions/erosion/scripts/plotGCSedsProfile: new program to plot a
   sediment profile
 
2010-07-09 Magnus Hagdorn
 * extra_rules.am: add macro to plot sediments
 * example-drivers/eis/fenscan/Makefile.am: plot final sediment thickness
 * extensions/erosion/scripts/plotGCseds: use CLI option to specify colourmap

2010-07-09 Magnus Hagdorn
 * rename make.rules.in to extra_rules.am
 * Makefile.am: remove rule to build make.rules
 * doc/ext/Makefile.am: distribute missing files
 * doc/ext/erosion/Makefile.am: ditto
 * doc/ext/erosion/figs/Makefile.am: ditto
 * doc/ext/libphaml/Makefile.am: ditto
 * example-drivers/EISMINT-3/EISMINT-3/Makefile.am: include automake fragment
   extra_rules.am directly
 * example-drivers/eis/fenscan/Makefile.am: ditto
 * example-drivers/eis/src/Makefile.am: ditto
 * extensions/erosion/src/Makefile.am: ditto 
 * extensions/libphaml/Makefile.am: ditto
 * src/gc2-dist/libglide/Makefile.am: ditto
 * libglimmer/Makefile.am: ditto
 * libglimmer-solve/Makefile.am: ditto
 * libglint/Makefile.am: ditto
 * tests/EISMINT/EISMINT-1/Makefile.am: ditto
 * tests/EISMINT/EISMINT-2/Makefile.am: ditto
 * tests/EISMINT/benchmarks/Makefile.am: ditto
 * tests/EISMINT/erosion/Makefile.am: ditto
 * tests/EISMINT/isos/Makefile.am: ditto
 * tests/EISMINT/lin-non_lin/Makefile.am: ditto
 * tests/EISMINT/src/Makefile.am: ditto
 * tests/exact-isothermal/src/Makefile.am: ditto

2010-07-09 Magnus Hagdorn
 * ./doc/*/Makefile.am: do not distribute built graphics

2010-07-08 Magnus Hagdorn
 * Makefile.am: change order of sub-directories
 * configure.in: remove one directory, add another
 * example-drivers/eis/fenscan/fenscan-erosion.config: moved from erosion
   directory, adjusted to use the same forcing as the other Fennoscandian 
   examples
 * example-drivers/eis/src/eis_erosion.F90: added sediment cover
 * example-drivers/eis/src/eis_erosion.F90: moved from erosion directory
 * example-drivers/eis/src/Makefile.am: optionally build eis_erosion driver
 * extensions/erosion/Makefile.am: remove tests directory
 * extensions/erosion/src/Makefile.am: only build library
 * tests/EISMINT/Makefile.am: add new directory
 * tests/EISMINT/erosion: moved tests from erosion directory
 * tests/EISMINT/src/simple_erosion.F90: moved from erosion directory
 * tests/EISMINT/src/Makefile.am: optionally build erosion EISMINT driver

2010-07-08 Magnus Hagdorn
 * example-drivers/eis/src/eis_ela.F90: fix bug in mass balance computation

2010-07-07 Magnus Hagdorn
 * doc/ext/libphaml/libphaml-app.tex: including the various files for appendices

2010-07-07 Magnus Hagdorn
 * configure.in: generate Makfile for building phaml documentation
 * doc/glimmer.bib: add phaml references
 * doc/glimmer.tex: add Time Wylie to list of authors
 * doc/make_doc.rules: add rules to turn pdf and png files to eps
 * doc/common/definitions.tex: define booleans controlling extensions here
 * doc/common/packages.tex: add fancybox
 * doc/ext/selected_ext.tex.in: only handle setting of booleans
 * doc/ext/libphaml: copied from extensions/libphaml/doc/src
 * doc/ext/Makefile.am: handle new directory
 * doc/ext/ext-app.tex: add file containing extensions appendices
 * doc/ext/ext.tex: add file including various extensions
 * extensions/libphaml/doc: removed

2010-07-07 Magnus Hagdorn
 * doc/glimmer.tex: rearrange documentation, introduce parts
 * doc/ext/ext.tex.in: turn chapter into a part
 * doc/ext/erosion/erosion.tex: move headings up one level
 * doc/ext/erosion/theory.tex: ditto
 * doc/ext/erosion/transport.tex: ditto
 * doc/ext/erosion/ug.tex: ditto

2010-07-06 Magnus Hagdorn
 * Makefile.am: removed optional compilation of libphaml
 * configure.in: move code for enabling libphaml next to other extensions;
   and tidy it up a bit; not sure if the graphics bit still works since I
   didn't get the dependencies to work
 * extensions/Makefile.am: optionally decend into libphaml subdirectory
 * libphaml moved to extensions/libphaml
 * extensions/libphaml/Makefile.am: use new macros to figure out how to
   compile it

2010-07-06 Magnus Hagdorn
 * make.rules.in: add rule to figure out dependencies
 * */Makfile.am: remove module files, use rule in make.rules to build file
   containing dependencies; only apply static flag to our own libraries and
   link program dynamically
 * scripts/f90_dependencies.py: fix bug

2010-07-06 Magnus Hagdorn
 * libphaml/Makefile.am: build only a single phaml library
 * libphaml/phaml_support.F90: make it work with intel compiler

2010-07-05 Magnus Hagdorn
 * update copyright notices

2010-07-05 Magnus Hagdorn
 * merged 1661:1812 of glimmer-cism-extensions branch
 
2010-07-05 Magnus Hagdorn
 * configure.in: always generate libphaml/Makefile so sources get distributed;
   bump version to 1.7.1
 * libphaml/Makefile.am: do not distribute external files

2010-07-02 William Lipscomb
  * Moved glimmer_restart_gcm.F90 from libglimmer to libglide.
    Required because of dependency on glide_types
     	
2010-07-02 William Lipscomb
  * Various changes to make the Glimmer-CISM source code consistent with the latest 
    version of CESM:
  * Removed ifdefs and replaced them with 'if (GLC_DEBUG)' since ifdefs are highly
    discouraged in CESM code.  May remove some of these later.
  * Added new module glimmer_restart_gcm	
  * Modified the procedure for reading and writing restarts such that there are
    no gcm dependencies in the Glimmer-CISM source code.
 	    
2010-06-21 Magnus Hagdorn
 * scripts/qsub_glide.sh: undo last change which broke it

2010-06-17 Magnus Hagdorn
 * configure.in: set F77 to FC if not set; fix generation of files
 * tests/exact-isothermal/src/Makefile.am: minor change

2010-06-16 William Lipscomb
  * I had previously changed the name of glimmer_writestats_module to glimmer_writestats
    to satisfy the CESM convention that module and file names should agree.
    I had also changed subroutine glimmer_writestats to glimmer_write_stats so that it
    would not conflict with the new module name.
    With this commit I changed use statements and subroutine calls in various modules accordingly.
  * Commented out references to CESM restart code in glint_initialise.F90.
    Will find a more flexible solution later.
  * Changed Makefile.am in libglint and example_drivers/glint/src, to reflect that
    glint_example_clim.F90 has been moved to libglint
	
2010-06-16 William Lipscomb
  * Remove use of CESM shared code in glimmer_config.F90.
    (This code was used to specify a fileunit for reading config files.)
    Instead, pass the desired fileunit in argument lists.
	
2010-06-16 Magnus Hagdorn
 * update copyright years to the years where the files were modified according
   to svn log

2010-06-16 Magnus Hagdorn
 * Makefile.am: conditionally add libphaml directory
 * configure.in: always generate libphaml/Makefile

2010-06-15 William Lipscomb
 * Checked in the contents of the CESM source_glimmer-cism directory.
 * These include most of the *F90 and *vars_def files in the libglimmer,
   libglimmer-solve, libglide, and libglint directories (but not the 
   files that are programs, since these will not compile in CESM).
 * I updated the copyright notice in all the files I checked in.
   The dates are listed as "2004, 2005, 2006, 2007, 2008, 2009, 2010".
   Magnus has offered to go through each file and include only years
   during which the files changed.
 * I also implemented several changes suggested by Rupert Gladstone to
   make the GCM interfaces cleaner and more generic.  A more extensive
   redesign of the Glint/GCM interfaces will likely follow this summer.	 
 * I removed the old restart code, which Magnus had already commented out.
   The current code restarts exactly using hotstart files.	
 * I made various other minor changes too numerous to mention.
 * Remaining tasks are commented 'TO DO'.  The most important task is to
   correctly upscale the fields passed back to the coupler.	 	 	 
 * I have not yet checked that the modified code will build.  To do this,
   I first need to get the code to configure and build with the changes
   Magnus made a few weeks ago.
   	
2010-06-15 William Lipscomb
 * moved glint_example_clim.F90 from example_drivers/glint/src to libglint
  (This module is not a driver, and it is needed for the CESM build.)

2010-05-11 Magnus Hagdorn
 * m4macros/glimmer.m4: fix macro to look for new config script

2010-05-10 Magnus Hagdorn
 * configure.in: create new file
 * make.rules.in: configure now generates make.rules with correct SGE options
 * example-drivers/eis/fenscan/fenscan.config: hot file should store variables
   in double precision
 * example-drivers/eis/fenscan/fenscan-gthf.config: ditto
 * tests/EISMINT/EISMINT-2/e2.[afik].config: ditto
 * example-drivers/eis/fenscan/Makefile.am: include correct make rules
 * example-drivers/EISMINT-3/EISMINT-3/Makefile.am: ditto
 * tests/EISMINT/benchmarks/Makefile.am: ditto
 * tests/EISMINT/EISMINT-1/Makefile.am: ditto
 * tests/EISMINT/EISMINT-2/Makefile.am: ditto
 * tests/EISMINT/isos/Makefile.am: ditto
 * tests/EISMINT/lin-non_lin/Makefile.am: ditto

2010-05-10 Magnus Hagdorn
 * merged glimmer-cism-gcm r1460:HEAD

2010-05-09 William Lipscomb
 More code cleanup:  Removed most '!lipscomb' comments, and put ifdefs around
	debugging write statements.  The remaining comments indicate where I have
	questions or where there is still work to do.  At this point the code is
	ready to be merged into the glimmer-cism2 trunk.
 * libglide/glide.F90
 * libglide/glide_setup.F90
 * libglide/glimmer_ncio.F90
 * libglide/glide_types.F90
 * libglide/glide_temp.F90
 * libglide/glide_diagnostics.F90
 * libglimmer/glimmer_paramets.F90
 * libglimmer/glimmer_log.F90
 * libglimmer/nc2config.F90
 * libglint/glint_timestep.F90
 * libglint/glint_initialise.F90
 * libglint/glint_interp.F90
 * libglint/glint_global_grid.F90
 * libglint/glint_mbal.F90
 * libglint/glint_mbal_coupling.F90
 * libglint/glint_climate.F90
 * libglint/glint_global_interp.F90
 * libglint/glint_type.F90
 * libglint/glint_main.F90

2010-05-07 Magnus Hagdorn
 * libglide/glide_lithot_vars.def: swap around definitions to reduce diff with
   trunk
 * libglide/glide_vars.def: ditto

2010-05-06 William Lipscomb
 General code cleanup, plus the following specific changes:
 * libglint/glint_main.F90: added subroutines glint_allocate_arrays_ccsm,
	accumulate_averages_ccsm, calculate_averages_ccsm
 * libglint/glint_timestep.F90: added ccsm_smb flag and related logic
 * libglint/glint_interp.F90: added local mask (lmask) for type downscale
 * libglint/glint_climate.F90: added subroutine glint_downscaling_ccsm
 * libglint/glint_mbal_coupling.F90: added subroutine glint_accumulate_ccsm
 * libglint/glint_type.F90: added subroutine glint_i_upscaled_fields_ccsm
 * libglint/glint_global_interp.F90: moved the new CCSM upscaling and downscaling
	subroutines to modules containing similar non-CCSM subroutines
 * libglint/glint_initialise.F90: minor changes
 * libglint/glint_vars.def: changed 'mask' to 'outmask', added 'inmask';
	inmask is true where global input data are valid
 * libglint/glint.F90: deleted (was previously renamed to glint_main.F90)
 * libglide/glide_vars.def: removed duplicate 'hot' variables
 * libglide/glide_lithot_vars.def: removed duplicate 'hot' variables
	
2010-05-03 William Lipscomb
 * Changed the list of output fields returned to CCSM: removed ice thickness (gthck),
   split runoff into ice and liquid components (grofi and grofl).  These files are
   affected:
 * libglint/glint_global_interp.F90
 * libglint/glint_main.F90
 * libglint/glint_timestep.F90

2010-05-03 William Lipscomb
 Many changes required for coupling with CCSM:
 * libglimmer/glimmer_log.F90: new subroutine set_glimmer_unit
 * libglimmer/nc2config.F90: changed stdout to l_stdout to avoid conflict with CCSM
 * libglimmer/glimmer_paramets.F90: added variables for debugging
 * libglide/glide.F90: added a comment
 * libglide/glide_setup.F90: set there=.false. before inquire
 * libglide/glimmer_ncio.F90: set model%numerics%tstart to value in hotstart file
 * libglint/glint_main.F90: many changes associated with passing CCSM fields to
	and from Glimmer
 * libglint/glint_initialise.F90: minor stuff for debugging
 * libglint/glint_global_grid.F90: added global mask for type global_grid
 * libglint/glint_interp.F90: added local mask (lmask) for type downscale
 * libglint/glint_mbal.F90: Added case(0) for whichacab (sfc mass balance from GCM)
 * libglint/glint_mbal_coupling.F90: mods associated with getting SMB from GCM
 * libglint/glint_timestep.F90: many changes associated with passing CCSM fields
	to and from Glimmer
 * libglint/glint_type.F90: added option whichacab = 0 (sfc mass balance from GCM)
 * libglint/glint_global_interp.F90: added routines for upscaling and downscaling
	CCSM fields between global and local grids
	
2010-03-23 Magnus Hagdorn
 * scripts/generate_ncvars.py: write to log when input variables are scaled
 * utils/compare.cpp: attempt to apply scales to netCDF files when present
   before comparing variables

2010-03-19 Magnus Hagdorn
 * scripts/generate_ncvars.py: fix bug with scaling factors

2010-02-26 Magnus Hagdorn
 * libglimmer/ncdf_template.F90.in: load modules containing scales, declare
   variable for scales
 * scripts/generate_ncvars.py: store scaleing factors in netCDF attribute, 
   only apply scaling factors if they are not attached to the variable

2010-02-25 Magnus Hagdorn
 * doc/ug/glide.tex: document new option
 * libglide/glimmer_ncio.F90: use default float type for time variable
 * libglide/glimmer_ncparams.F90: add option to change default float type
 * libglimmer/glimmer_ncdf.F90: define default float type for netCDF variables
 * libglimmer/ncdf_template.F90.in: add function which applies default float
   type where required
 * scripts/generate_ncvars.py: use default float type for all FP variables

2010-05-03 Magnus Hagdorn
 * Makefile.am: install glimmer-cism-config

2010-03-29 Magnus Hagdorn
 * configure.in: change version to 1.5.1

2010-03-22 Magnus Hagdorn
 * doc/doclets/figs/gc-branches.svg: updated to reflect latest plans
 * doc/doclets/gc-branches.tex: ditto

2010-03-12 Magnus Hagdorn
 * configure.in: look for inkscape, add new Makefiles
 * doc/Makefile.am: add new subdirectory
 * doc/dg_pdf.tex: use macro to define where common directory is
 * doc/dg_ps.tex: ditto
 * doc/glimmer_pdf.tex: ditto
 * doc/glimmer_ps.tex: ditto
 * doc/num_pdf.tex: ditto
 * doc/num_ps.tex: ditto
 * doc/tut_pdf.tex: ditto
 * doc/tut_ps.tex: ditto
 * doc/ug_pdf.tex: ditto
 * doc/ug_ps.tex: ditto
 * doc/common/definitions.tex: ditto
 * doc/make_doc.rules: add rule for generating eps from svg file
 * doc/doclets: add document describing glimmer-cism branches for 2010

2010-01-27 Magnus Hagdorn
 * configure.in: use new macro to figure out how to disable free form line length limit
 * m4macros/ax_f90_no_line_limit_flag.m4: new macro to find flag to disable free form
   line length limit

2009-11-10 Magnus Hagdorn
 * Makefile.am: add new subdirectory
 * configure.in: check for C++ compiler and C++ bindings to netCDF
 * m4macros/netcdf.m4: implemented check for C++ netCDF bindings
 * utils/Makefile.am: compile new program
 * utils/compare.cpp: add new utility which tests if two netCDF files
   are reasonably identical

2009-10-16 Magnus Hagdorn
 * example-drivers/eis/src/eis_ela.F90: use parameter for internal message
   buffer size
 * example-drivers/eis/src/eis_slc.F90: ditto
 * example-drivers/eis/src/eis_temp.F90: ditto
 * libglide/glimmer_ncio.F90: ditto

2009-10-16 Magnus Hagdorn
 * libglide/glide.F90: use derivative module
 * libglide/glide_thck.F90: ditto, remove old code

2009-10-16 Magnus Hagdorn
 * libglimmer/glimmer_deriv.F90: slight clean up, reformat comments to 
   doxygen
 * libglimmer/unittest_glimmer_deriv.F90: updated copyright notice
 * libglimmer/xls.F90: ditto

2009-10-16 Magnus Hagdorn
 * libglimmer/unittest_glimmer_deriv.F90: fix indentation
 * libglimmer/glimmer_deriv.F90: ditto
 * libglimmer/xls.F90: ditto

2009-10-16 Magnus Hagdorn
 * libglimmer/unittest_glimmer_deriv.F90: copied from lanl branch, renamed 
   name space
 * libglimmer/glimmer_deriv.F90: ditto
 * libglimmer/xls.F90: copied from lanl
 * libglimmer/Makefile.am: add glimmer_deriv.F90 to libglimmer

2009-10-15 Magnus Hagdorn
 * libglide/Makefile.am: fix out-of-dir build bugs

2009-10-15 Magnus Hagdorn
 * example-drivers/EISMINT-3/EISMINT-3/EISMINT3GL.input.nc: make CF compliant
 * example-drivers/eis/fenscan/europe.20km.nc: ditto
 * tests/EISMINT/EISMINT-2/mound.nc: ditto
 * tests/EISMINT/EISMINT-2/trough.nc: ditto

2009-10-14 Magnus Hagdorn
 * libglide/glide_lithot_vars.def: new variable definition file for lithot
   variables
 * libglide/Makefile.am: add new file
 * libglide/glide.F90: optionally handle lithot I/O
 * libglide/glide_stop.F90: ditto
 * libglide/glide_vars.def: take out lithot variables, fix standard name of
   of wvel variable
 * libglide/glimmer_ncio.F90: bump convention to 1.4
 * scripts/generate_ncvars.py: only output coordinate attribute if mapping
   is available

2009-10-14 Magnus Hagdorn
 * libglide/glide_nc_custom.F90: handle coordinate values
 * libglide/glide_types.F90: add arrays for storing coordinate values
 * libglide/glide_vars.def: improve CF standard compliance
 * libglide/glimmer_ncio.F90: check if the number of vertical levels is as
   expected, bump CF version number to 1.3
 * scripts/generate_ncvars.py: load some dimension variables

2009-10-14 Magnus Hagdorn
 * libglimmer/glimmer_paramets.F90: rename module
 * scripts/generate_ncvars.py, lots of .F90: rename module

2009-10-13 Magnus Hagdorn
 * tests/exact-isothermal/scripts/plot_diff.py: reimplemented using matplotlib
   and numpy
 * tests/exact-isothermal/scripts/plot_errors.py: ditto
 * tests/exact-isothermal/scripts/plot_time.py: ditto
 * tests/exact-isothermal/scripts/plot_vol.py: ditto
 * tests/exact-isothermal/scripts/process_verif.py: ditto
 * tests/exact-isothermal/tests/Makefile.am: call new visualisation programs

2009-10-07 Magnus Hagdorn
 * libglint/Makefile.am: forgot to add module directory
 * m4macros/hdf5.m4: improved hdf5 detector, it's similar to the netcdf one
 * m4macros/netcdf.m4: change how HDF5 libraries are handled
 * scripts/glide_launch.py: fix location of SGE submission script
 * tests/exact-isothermal/scripts/run_verif.py: ditto
 * tests/exact-isothermal/tests/Makefile.am: add SGE options

2009-09-30 Magnus Hagdorn
 * configure.in: export fortran compiler flag which sets the module search
   path
 * example-drivers/EISMINT-3/src/Makefile.am: use new variable containing
   fortran compiler flag for module search path and use correct variable
   for fortran netcdf module search path
 * example-drivers/eis/src/Makefile.am: ditto
 * example-drivers/glint/src/Makefile.am: ditto
 * libglide/Makefile.am: ditto
 * libglimmer/Makefile.am: ditto
 * libglimmer-solve/Makefile.am: ditto
 * libglint/Makefile.am: ditto
 * tests/EISMINT/src/Makefile.am: ditto
 * tests/exact-isothermal/src/Makefile.am: ditto

2009-09-30 Magnus Hagdorn
 * m4macros/netcdf.m4: bah, introduced bug when no particular directory is
   specified - fixed now 

2009-09-30 Magnus Hagdorn
 * m4macros/netcdf.m4: fix bug when location of netCDF lib is specified
   manually

2009-09-29 Magnus Hagdorn
 * libglimmer/glimmer_commandline.F90: add doxygen strings
 * libglimmer/glimmer_config.F90: ditto
 * libglimmer/glimmer_ts.F90: minor fix

2009-09-28 Ian Rutt
 * libglide/glide.F90: Fixed bug with basal heat flux - field read from
   file was being overridden with constant value. Reordered code, but
   still not ideal, as overriding will happen the other way round now.
 * doc/num/temp_solve.tex: Added a file with the beginnings of a new, more
   detailed description of the temperature solver (something I was
   working on last year, but didn't finish). Not integrated into the main
   docs yet.
	
2009-09-28 Magnus Hagdorn
 * example-drivers/EISMINT-3/src/eismint3_glide.F90: setup config file directory
 * example-drivers/eis/src/eis_glide.F90: ditto
 * tests/EISMINT/src/simple_glide.F90: ditto
 * example-drivers/eis/src/eis_ela.F90: prepend config file directory to input
   file name
 * example-drivers/eis/src/eis_slc.F90: ditto
 * example-drivers/eis/src/eis_temp.F90: ditto
 * libglide/glide_setup.F90: ditto
 * libglide/glimmer_ncparams.F90: ditto
 * libglimmer/glimmer_anomcouple.F90: ditto
 * libglide/glide_thck.F90: change open mode of error file
 * libglimmer/Makefile.am: add new test
 * libglimmer/glimmer_config.F90: use parameter to specify maximum message length
 * libglimmer/glimmer_coordinates.F90: ditto
 * libglimmer/glimmer_log.F90: ditto
 * libglimmer/glimmer_map_init.F90: ditto
 * libglimmer/glimmer_map_types.F90: ditto
 * libglimmer/glimmer_ts.F90: ditto
 * libglimmer/glimmer_filenames.F90: add procedures to extract path to config
   file and to prepend config file path to a file name
 * libglimmer/glimmer_global.F90: add parameter specifying maximum message
   length
 * libglimmer/test_filenames.F90: test new functionality in glimmer_filenames

2009-09-17 Magnus Hagdorn
 * tests/exact-isothermal/scripts/run_verif.py: handle commandline similarly
   to glide_lauch.py
 * tests/exact-isothermal/tests/Makefile.am: specify what binary to use

2009-09-17 Magnus Hagdorn
 * configure.in: add new Makefile
 * example-drivers/Makefile.am: add a data target
 * example-drivers/EISMINT-3/Makefile.am: ditto
 * example-drivers/eis/Makefile.am: ditto
 * example-drivers/EISMINT-3/EISMINT-3/Makefile.am: new - run example
 * example-drivers/EISMINT-3/EISMINT-3/e3gl_steady.config: rename output file
   so make can figure out if it needs to do something
 * example-drivers/eis/fenscan/Makefile.am: specify binary to run

2009-09-16 Magnus Hagdorn
 * tests/Makefile.am: decent into subdirs when generating data
 * tests/exact-isothermal/Makefile.am: decent into subdirs
 * tests/exact-isothermal/scripts/run_verif.py: updated script to be analogous
   to glide_launch.py
 * tests/exact-isothermal/src/verif_glide.F90: use glimmer commandline parser
   and glimmer timer
 * tests/exact-isothermal/tests/Makefile.am: fix Makefile

2009-09-16 Magnus Hagdorn
 * configure.in: user can specify if they want to use the SGE to submit jobs
   when running tests/examples
 * make.rules: find the correct model to run
 * scripts/glide_launch.py: simplify selection of model
 * scripts/qsub_glide.sh: pass environment to SGE job
 * tests/EISMINT/EISMINT-1/Makefile.am: select simple_glide binary
 * tests/EISMINT/EISMINT-2/Makefile.am: ditto
 * tests/EISMINT/benchmarks/Makefile.am: ditto
 * tests/EISMINT/isos/Makefile.am: ditto
 * tests/EISMINT/lin-non_lin/Makefile.am: ditto

2009-09-15 Magnus Hagdorn
 * convert some more comments in another bunch of files to doxygen strings
 * libglimmer/glimmer_ncdf.F90: move second module to glimmer_scales.F90

2009-09-15 Magnus Hagdorn
 * convert comments in a bunch of files to doxygen strings

2009-09-14 Magnus Hagdorn
 * README: document new make target to build tar-ball of html docs
 * doc/Makefile.am: new target to build tar-ball of html docs which
   can be uploaded to berliOS (or elsewhere)

2009-09-10 Magnus Hagdorn
 * libglimmer/glimmer_ts.F90: change documentation strings to doxygen

2009-09-10 Magnus Hagdorn
 * README: document documentation build
 * bootstrap: don't warn about possible incompatibilities in Makefiles
 * configure.in: find doxygen
 * doc/Makefile.am: add targets for doxygen 
 * doc/glimmer-cism.cfg.in: added template doxygen configuration
 * m4macros/amdoxygen.am: makefile snippet for doxygen
 * m4macros/ax_prog_doxygen.m4: autoconf macro for handling doxygen

2009-09-08 Magnus Hagdorn
 * libglimmer/glimmer_vers.F90.in.in: fix fortran error

2009-09-07 Magnus Hagdorn
 * libglimmer/glimmer_vers.F90.in.in: version numbers are no longer stored in
   a module, but accessed through accessors to avoid unnessary recompilations
 * libglide/glide.F90: call new accessor to get version
 * libglide/glimmer_ncparams.F90: ditto
 * libglimmer/Makefile.am: pass top source directory to version script
 * libglimmer/createSVNVersion.sh: run svnversion on top source dir
 * libglimmer/glimmer_global.F90: do not load version numbers

2009-09-07 Magnus Hagdorn
 * doc/common/Makefile.am: forgot to distribute file
 * doc/num/figs/Makefile.am: ditto
 * doc/ug/varlist.tex: include list of variables

2009-09-07 Magnus Hagdorn
 * Makefile.am: forgot sub directory
 * configure.in: rename package to glimmer-cism
 * doc/Makefile.am: do not distribute generated docs
 * doc/dg/figures/Makefile.am: do not distribute images
 * doc/num/figs/Makefile.am: ditto
 * doc/num/gnu/Makefile.am: ditto
 * doc/ug/figs/Makefile.am: ditto
 * doc/ug/Makefile.am: fix paths
 * example-drivers/glint/src/Makefile.am: fix bug
 * tests/exact-isothermal/src/Makefile.am:  rename installation directory

2009-09-04 Magnus Hagdorn
 * Makefile.am: add new subdirectory
 * configure.in: handle new directories
 * libglint/Makefile.am: forgot a file
 * add glint examples

2009-09-04 Magnus Hagdorn
 * Makefile.am: add new subdirectory
 * configure.in: handle new directories
 * EISMINT-3/src/Makefile.am: link to the correct libs
 * add libglint and EISMINT3 examples

2009-09-04 Magnus Hagdorn
 * added EISMINT-3 greenland example

2009-09-04 Magnus Hagdorn
 * Makefile.am: add new subdirectory
 * configure.in: handle new directories
 * libglimmer/Makefile.am: forgot a file
 * add eis driver and example setups

2009-09-04 Magnus Hagdorn
 * Makefile.am: distribute new file
 * configure.in: handle new directories
 * tests/Makefile.am: ditto
 * add EISMINT 1 and 2 tests

2009-09-04 Magnus Hagdorn
 * Makefile.am: add new subdirectory
 * configure.in: create new Makefiles

2009-09-04 Magnus Hagdorn
 * configure.in: move internal blas around to libglimmer-solve
 * libglide/Makefile.am: undo rearrangement since dep tracker is fixed
 * libglimmer/Makefile.am: blas directory is removed
 * libglimmer-solve/Makefile.am: optionally build internal blas and link to
   libglimmer-solve.a
 * libglimmer-solve/SLAP/Makefile.am: fix bug
 * move libglimmer/blas to libglimmer-solve/blas

2009-09-04 Magnus Hagdorn
 * libglide/Makefile.am: tell the f90 dependency tracker to use libtool
 * libglimmer/Makefile.am: fix bugs
 * libglimmer-solve/Makefile.am: add dependency tracker
 * scripts/f90_dependencies.py: add option to produce output for libtool

2009-09-04 Magnus Hagdorn
 * Makefile.am: add new directory
 * bootstrap: look for libtool
 * configure.in: use libtool to build libraries
 * libglide/Makefile.am: use libtool
 * libglimmer/Makefile.am: ditto
 * move libglimmer/solve to libglimmer-solve

2009-09-04 Magnus Hagdorn
 * Makefile.am: add new subdirectory
 * configure.in: create new Makefile
 * libglide: populate libglide

2009-09-04 Magnus Hagdorn
 * doc/Makefile.am: only build figures if documentation is built
 * libglimmer/Makefile.am: forgot to the ncdf template
 * libglimmer/solve/Makefile.am: add sparse matrix handler

2009-09-03 Magnus Hagdorn
 * libglimmer/Makefile.am: add targets for libglimmer-IO.a

2009-09-03 Magnus Hagdorn
 * configure.in: add new subdirectory
 * libglimmer/Makefile.am: handle new subdirectory
 * libglimmer/solve/SLAP/Makefile.am: handle dependencies, run SLAP test
 * libglimmer/blas: added reference implementation of BLAS required for
   SLAP from netlib

2009-09-03 Magnus Hagdorn
 * configure.in: add new directories
 * libglimmer/Makefile.am: decent into new subdirectory
 * add vanilla SLAP library

2009-09-03 Magnus Hagdorn
 * Makefile.am: add new sub-directories
 * configure.in: uncomment restart facility, handle new directories
 * add scripts
 * add files for libglimmer

2009-09-02 Magnus Hagdorn
 * Makefile.am: decent into documentation directory
 * configure.in: make documentation builds configure option
 * doc/glimmer.tex: no longer autogenerated
 
2009-09-02 Magnus Hagdorn
 * copy documentation and get it to compile

2009-09-02 Magnus Hagdorn
 * populate project with basic files to get autotools to work