[Dart-dev] [7959] DART/trunk: Mostly formatting tweaks in the html files to make sure the 'top'
nancy at ucar.edu
nancy at ucar.edu
Wed May 6 16:18:27 MDT 2015
Revision: 7959
Author: thoar
Date: 2015-05-06 16:18:27 -0600 (Wed, 06 May 2015)
Log Message:
-----------
Mostly formatting tweaks in the html files to make sure the 'top'
link is inline with the horizontal rule. Real important - not.
Added some bulletproofing to the matlab scripts to prevent Matlab
from making 1D (character) arrays into column-major when character
arrays should be row-major.
Added some useful options to the gfortran compiler template.
Added support for an upper atmosphere observation that allows the
SSUSI observation converter to compile (sheesh!) the converter is already
in the trunk and is in use on the tiegcm branch.
The changes to assim_model_mod.f90 are improved commenting - nothing executable.
obs_utilities_mod.f90 has a new routine getvarshape() to return the array
of sizes for any netCDF variable.
Added tutorial/index.html and listed it in the DART/index.html
Modified Paths:
--------------
DART/trunk/assim_model/assim_model_mod.f90
DART/trunk/filter/filter.html
DART/trunk/index.html
DART/trunk/matlab/GetBgridInfo.m
DART/trunk/matlab/GetWRFInfo.m
DART/trunk/matlab/plot_phase_space.m
DART/trunk/mkmf/mkmf.template
DART/trunk/mkmf/mkmf.template.gfortran
DART/trunk/models/lorenz_63/work/input.nml
DART/trunk/models/noah/dart_to_noah.html
DART/trunk/models/noah/noah_to_dart.html
DART/trunk/mpi_utilities/tests/Makefile
DART/trunk/obs_def/obs_def_upper_atm_mod.f90
DART/trunk/observations/utilities/obs_utilities_mod.f90
DART/trunk/utilities/utilities_mod.f90
Added Paths:
-----------
DART/trunk/tutorial/index.html
-------------- next part --------------
Modified: DART/trunk/assim_model/assim_model_mod.f90
===================================================================
--- DART/trunk/assim_model/assim_model_mod.f90 2015-05-06 17:13:30 UTC (rev 7958)
+++ DART/trunk/assim_model/assim_model_mod.f90 2015-05-06 22:18:27 UTC (rev 7959)
@@ -1285,8 +1285,12 @@
call nc_check(NF90_Inquire_Dimension(ncid, unlimitedDimID, varname, lngth ), &
'nc_append_time', 'inquire_dimension unlimited')
-if (lngth /= ncFileId%Ntimes) call error_handler(E_ERR,'nc_append_time', &
- 'time mirror and netcdf file time dimension out-of-sync',source,revision,revdate)
+if (lngth /= ncFileId%Ntimes) then
+ write(msgstring,*)'netCDF file has length ',lngth,' /= mirror has length of ',ncFileId%Ntimes
+ call error_handler(E_ERR,'nc_append_time', &
+ 'time mirror and netcdf file time dimension out-of-sync', &
+ source,revision,revdate,text2=msgstring)
+endif
! make sure the time mirror can handle another entry.
if ( lngth == ncFileID%NtimesMAX ) then
Modified: DART/trunk/filter/filter.html
===================================================================
--- DART/trunk/filter/filter.html 2015-05-06 17:13:30 UTC (rev 7958)
+++ DART/trunk/filter/filter.html 2015-05-06 22:18:27 UTC (rev 7959)
@@ -680,8 +680,7 @@
<li>Release memory for state vector and observation ensemble members. </li>
</ul>
-<br />
-<br />
+<P><!-- make sure the 'top' is aligned correctly --></P>
<!--==================================================================-->
<!--=================== DESCRIPTION OF A NAMELIST ====================-->
@@ -1118,8 +1117,7 @@
</div>
-<br />
-<br />
+<P><!-- make sure the 'top' is aligned correctly --></P>
<!--==================================================================-->
<!-- Describe the modules used by this program. -->
@@ -1143,8 +1141,7 @@
smoother_mod
</PRE>
-<br />
-<br />
+<P><!-- make sure the 'top' is aligned correctly --></P>
<!--==================================================================-->
<!-- Describe the Files Used by this module. -->
@@ -1165,8 +1162,7 @@
<LI>input.nml, to read &filter_nml</LI>
</UL>
-<br />
-<br />
+<P><!-- make sure the 'top' is aligned correctly --></P>
<!--==================================================================-->
<!-- Cite references, if need be. -->
@@ -1258,8 +1254,7 @@
</ul>
-<br />
-<br />
+<P><!-- make sure the 'top' is aligned correctly --></P>
<!--==================================================================-->
<!-- Describe all the error conditions and codes. -->
@@ -1312,8 +1307,7 @@
none
</P>
-<br />
-<br />
+<P><!-- make sure the 'top' is aligned correctly --></P>
<!--==================================================================-->
<!-- Describe Future Plans. -->
@@ -1330,8 +1324,7 @@
interested in additional functionality in DART.
</P>
-<br />
-<br />
+<P><!-- make sure the 'top' is aligned correctly --></P>
<!--==================================================================-->
<!-- Legalese & Metadata -->
Modified: DART/trunk/index.html
===================================================================
--- DART/trunk/index.html 2015-05-06 17:13:30 UTC (rev 7958)
+++ DART/trunk/index.html 2015-05-06 22:18:27 UTC (rev 7959)
@@ -81,8 +81,8 @@
<P>
The best way to get to know the DART software is to follow along while
-reading the tutorial documents in the <em class="file">DART_LAB</em>
-and then the <em class="file">DART/tutorial</em> directory.
+reading the tutorial documents in the <a href="DART_LAB/DART_LAB.html">DART_LAB</a>
+and then the <a href="tutorial/index.html">DART/tutorial</a> directory.
</P>
<P>
The latest official release is named "Lanai".
@@ -113,6 +113,8 @@
contains links to all the documentation for this DART release.
</P>
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<A NAME="UserDocs"></A>
@@ -149,10 +151,8 @@
<A HREF="doc/html/tut1.pdf">PDF document</A> which
covers much of the background for how and why
the algorithms in DART work.
-The final tutorial is again more of a workshop format,
-with a <A HREF="tutorial/index.pdf">PDF index</A>
-which lists the
-multiple separate sections covering various parts of
+The <a href="tutorial/index.html">full-fledged DART Tutorial</a> is more
+of a workshop format, with multiple sections covering various parts of
DART with suggested exercises at the end of most sections.
</P>
@@ -163,6 +163,8 @@
part of DART. For introductory materials, see the links above.
<P>
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<A NAME="Programs"></A>
@@ -193,7 +195,7 @@
<LI><A href="preprocess/preprocess.html">preprocess</A> - used during compiling</LI>
<LI><A href="mkmf/mkmf.html">mkmf</A> - used to generate makefiles during compiling</LI>
<LI><A href="filter/wakeup_filter.html">wakeup_filter</A> - used when filter runs a parallel model advance</LI>
-<LI><A href="system_simulation/system_simulation.html">system_simulation </A> (sampling error correction) - generate the files used for Sampling Error Correction option</LI>
+<LI><A href="system_simulation/system_simulation.html">system_simulation</A> (sampling error correction) - generate the files used for Sampling Error Correction option</LI>
</UL>
<A NAME="Diagnostics"></A>
@@ -226,23 +228,23 @@
<LI> </LI>
<LI><A href="observations/AIRS/AIRS.html">AIRS data</A></LI>
<LI><A href="observations/Ameriflux/level4_to_obs.html">Ameriflux tower data</A></LI>
-<LI><A href="observations/COSMOS/COSMOS_development.html">COSMOS groundwater data </A> (development format)</LI>
+<LI><A href="observations/COSMOS/COSMOS_development.html">COSMOS groundwater data</A> (development format)</LI>
<LI><A href="observations/COSMOS/COSMOS_to_obs.html">COSMOS groundwater data</A></LI>
<LI><A href="observations/gps/gps.html">GPS Radio Occultation data</A></LI>
<LI><A href="observations/GTSPP/GTSPP.html">GTSPP data</A></LI>
<LI><A href="observations/MADIS/MADIS.html">MADIS data</A></LI>
-<LI><A href="observations/MIDAS/MIDAS_to_obs.html">MIDAS TEC data </A> (netcdf intermediate files)</LI>
+<LI><A href="observations/MIDAS/MIDAS_to_obs.html">MIDAS TEC data</A> (netcdf intermediate files)</LI>
<LI><A href="observations/NCEP/prep_bufr/prep_bufr.html">NCEP prepbufr to ascii</A></LI>
<LI><A href="observations/NCEP/ascii_to_obs/create_real_obs.html">NCEP ascii to obs_seq</A></LI>
<LI><A href="observations/quikscat/QuikSCAT.html">QuikSCAT data</A></LI>
<LI><A href="observations/radar/radar.html">Radar data</A></LI>
-<LI><A href="observations/snow/snow_to_obs.html">MODIS Snow data </A> (ascii)</LI>
-<LI><A href="observations/MODIS/MODIS_README.html">MODIS data </A> (ORNL DAAC)</LI>
+<LI><A href="observations/snow/snow_to_obs.html">MODIS Snow data</A> (ascii)</LI>
+<LI><A href="observations/MODIS/MODIS_README.html">MODIS data</A> (ORNL DAAC)</LI>
<LI><A href="observations/SSEC/SSEC.html">SSEC data</A></LI>
<LI><A href="observations/text/text_to_obs.html">ascii/text data</A></LI>
-<LI><A href="observations/tropical_cyclone/tc_to_obs.html">Tropical Cyclone ATCF reports </A> (ascii)</LI>
-<LI><A href="observations/tpw/tpw.html">Total Precipitable Water obs </A> (ascii)</LI>
-<LI><A href="observations/var/littler_tf_dart.html">little-r data </A></LI>
+<LI><A href="observations/tropical_cyclone/tc_to_obs.html">Tropical Cyclone ATCF reports</A> (ascii)</LI>
+<LI><A href="observations/tpw/tpw.html">Total Precipitable Water obs</A> (ascii)</LI>
+<LI><A href="observations/var/littler_tf_dart.html">little-r data</A></LI>
<LI><A href="observations/var/rad_3dvar_to_dart.html">3DVAR radar data</A></LI>
<LI><A href="observations/var/var.html">var obs data</A></LI>
<LI><A href="observations/WOD/WOD.html">World Ocean Database data</A></LI>
@@ -279,6 +281,8 @@
<LI>wrf <A href="models/wrf/WRF_DART_utilities/wrf_dart_obs_preprocess.html">wrf_dart_obs_preprocess</A> - preprocess observations intended to be assimilated into WRF. Program has understanding of the WRF domain information.</LI>
</UL>
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<A NAME="Models"></A>
@@ -299,43 +303,45 @@
<UL style="list-style: none;">
<LI><A HREF="models/model_mod.html">Overview for all models</A></LI>
-<LI><A HREF="models/template/model_mod.f90">template </A> (source)</LI>
+<LI><A HREF="models/template/model_mod.f90">template</A> (source)</LI>
<LI> </LI>
-<LI><A HREF="models/9var/model_mod.html">9var </A> (html)</LI>
-<LI><A HREF="models/am2/model_mod.f90">AM2 </A> (source)</LI>
-<LI><A HREF="models/bgrid_solo/model_mod.f90">bgrid_solo </A> (source)</LI>
-<LI><A HREF="models/cam/model_mod.html">CAM </A> (html)</LI>
-<LI><A HREF="models/CESM/model_mod.html">CESM </A> (html)</LI>
-<LI><A HREF="models/clm/model_mod.html">CLM </A> (html)</LI>
-<LI><A HREF="models/coamps/model_mod.html">COAMPS </A> (html)</LI>
-<LI><A HREF="models/coamps_nest/model_mod.f90">COAMPS_nest </A> (source)</LI>
-<LI><A HREF="models/dynamo/model_mod.f90">dynamo </A> (source)</LI>
-<LI><A HREF="models/forced_barot/model_mod.f90">forced_barot </A> (source)</LI>
-<LI><A HREF="models/forced_lorenz_96/model_mod.html">forced_lorenz_96 </A> (html)</LI>
-<LI><A HREF="models/gitm/model_mod.html">GITM </A> (html)</LI>
-<LI><A HREF="models/ikeda/model_mod.html">ikeda </A> (html)</LI>
-<LI><A HREF="models/lorenz_04/model_mod.html">Lorenz_04 </A> (html)</LI>
-<LI><A HREF="models/lorenz_63/model_mod.html">Lorenz_63 </A> (html)</LI>
-<LI><A HREF="models/lorenz_84/model_mod.html">Lorenz_84 </A> (html)</LI>
-<LI><A HREF="models/lorenz_96/model_mod.html">Lorenz_96 </A> (html)</LI>
-<LI><A HREF="models/lorenz_96_2scale/model_mod.f90">Lorenz_96_2scale </A> (source)</LI>
-<LI><A HREF="models/MITgcm_annulus/model_mod.f90">MITgcm_annulus </A> (source)</LI>
-<LI><A HREF="models/MITgcm_ocean/model_mod.html">MITgcm_ocean </A> (html)</LI>
-<LI><A HREF="models/mpas_atm/model_mod.html">MPAS_atm </A> (html)</LI>
-<LI><A HREF="models/mpas_ocn/model_mod.html">MPAS_ocn </A> (html)</LI>
-<LI><A HREF="models/NAAPS/model_mod.f90">NAAPS </A> (source)</LI>
-<LI><A HREF="models/NCOMMAS/model_mod.html">NCOMMAS </A> (html)</LI>
-<LI><A HREF="models/noah/model_mod.html">NOAH </A> (html)</LI>
-<LI><A HREF="models/null_model/model_mod.html">null_model </A> (html)</LI>
-<LI><A HREF="models/pe2lyr/model_mod.html">pe2lyr </A> (html)</LI>
-<LI><A HREF="models/POP/model_mod.html">POP </A> (html)</LI>
-<LI><A HREF="models/rose/model_mod.f90">Rose </A> (source)</LI>
-<LI><A HREF="models/simple_advection/model_mod.html">simple_advection </A> (html)</LI>
-<LI><A HREF="models/sqg/model_mod.html">SQG </A> (html)</LI>
-<LI><A HREF="models/tiegcm/model_mod.f90">TIEgcm </A> (source)</LI>
-<LI><A HREF="models/wrf/model_mod.html">WRF </A> (html)</LI>
+<LI><A HREF="models/9var/model_mod.html">9var</A> (html)</LI>
+<LI><A HREF="models/am2/model_mod.f90">AM2</A> (source)</LI>
+<LI><A HREF="models/bgrid_solo/model_mod.f90">bgrid_solo</A> (source)</LI>
+<LI><A HREF="models/cam/model_mod.html">CAM</A> (html)</LI>
+<LI><A HREF="models/CESM/model_mod.html">CESM</A> (html)</LI>
+<LI><A HREF="models/clm/model_mod.html">CLM</A> (html)</LI>
+<LI><A HREF="models/coamps/model_mod.html">COAMPS</A> (html)</LI>
+<LI><A HREF="models/coamps_nest/model_mod.f90">COAMPS_nest</A> (source)</LI>
+<LI><A HREF="models/dynamo/model_mod.f90">dynamo</A> (source)</LI>
+<LI><A HREF="models/forced_barot/model_mod.f90">forced_barot</A> (source)</LI>
+<LI><A HREF="models/forced_lorenz_96/model_mod.html">forced_lorenz_96</A> (html)</LI>
+<LI><A HREF="models/gitm/model_mod.html">GITM</A> (html)</LI>
+<LI><A HREF="models/ikeda/model_mod.html">ikeda</A> (html)</LI>
+<LI><A HREF="models/lorenz_04/model_mod.html">Lorenz_04</A> (html)</LI>
+<LI><A HREF="models/lorenz_63/model_mod.html">Lorenz_63</A> (html)</LI>
+<LI><A HREF="models/lorenz_84/model_mod.html">Lorenz_84</A> (html)</LI>
+<LI><A HREF="models/lorenz_96/model_mod.html">Lorenz_96</A> (html)</LI>
+<LI><A HREF="models/lorenz_96_2scale/model_mod.f90">Lorenz_96_2scale</A> (source)</LI>
+<LI><A HREF="models/MITgcm_annulus/model_mod.f90">MITgcm_annulus</A> (source)</LI>
+<LI><A HREF="models/MITgcm_ocean/model_mod.html">MITgcm_ocean</A> (html)</LI>
+<LI><A HREF="models/mpas_atm/model_mod.html">MPAS_atm</A> (html)</LI>
+<LI><A HREF="models/mpas_ocn/model_mod.html">MPAS_ocn</A> (html)</LI>
+<LI><A HREF="models/NAAPS/model_mod.f90">NAAPS</A> (source)</LI>
+<LI><A HREF="models/NCOMMAS/model_mod.html">NCOMMAS</A> (html)</LI>
+<LI><A HREF="models/noah/model_mod.html">NOAH</A> (html)</LI>
+<LI><A HREF="models/null_model/model_mod.html">null_model</A> (html)</LI>
+<LI><A HREF="models/pe2lyr/model_mod.html">pe2lyr</A> (html)</LI>
+<LI><A HREF="models/POP/model_mod.html">POP</A> (html)</LI>
+<LI><A HREF="models/rose/model_mod.f90">Rose</A> (source)</LI>
+<LI><A HREF="models/simple_advection/model_mod.html">simple_advection</A> (html)</LI>
+<LI><A HREF="models/sqg/model_mod.html">SQG</A> (html)</LI>
+<LI><A HREF="models/tiegcm/model_mod.f90">TIEgcm</A> (source)</LI>
+<LI><A HREF="models/wrf/model_mod.html">WRF</A> (html)</LI>
</UL>
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<A NAME="Namelists"></A>
@@ -468,6 +474,8 @@
<LI>wrf <A HREF="models/wrf/WRF_DART_utilities/wrf_to_dart.nml#Namelist">&wrf_to_dart_nml</A></LI>
</UL>
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<A NAME="Modules"></A>
@@ -509,6 +517,7 @@
<LI><A href="utilities/utilities_mod.html">utilities/utilities_mod</A></LI>
</UL>
+<P><!-- make sure the 'top' is aligned correctly --></P>
<!--==================================================================-->
@@ -529,9 +538,11 @@
<LI><A HREF='doc/html/history/ASP_DART_exercise.html'>ASP DART exercises</A></LI>
<LI><A HREF='doc/html/history/DART_ASP_Summer2003.html'>DART ASP Summer 2003 Workshop</A></LI>
<LI><A HREF='mkmf/mkmf.html'>mkmf</A></LI>
+<LI><A HREF='tutorial/index.html'>DART Tutorial</A></LI>
<LI><A HREF='DART_LAB/DART_LAB.html'>DART_LAB</A></LI>
</UL>
+<P><!-- make sure the 'top' is aligned correctly --></P>
<!--==================================================================-->
<!--==================================================================-->
@@ -573,82 +584,82 @@
<LI><A href="location/threed_cartesian/location_mod.html">location/threed_cartesian/location_mod</A></LI>
<LI><A href="location/threed_sphere/location_mod.html">location/threed_sphere/location_mod</A></LI>
<LI><A href="mkmf/mkmf.html">mkmf/mkmf</A></LI>
-<LI><A href="models/9var/model_mod.f90">models/9var/model_mod </A> (source)</LI>
-<LI><A href="models/9var/model_mod.html">models/9var/model_mod </A> (html)</LI>
+<LI><A href="models/9var/model_mod.f90">models/9var/model_mod</A> (source)</LI>
+<LI><A href="models/9var/model_mod.html">models/9var/model_mod</A> (html)</LI>
<LI><A href="models/CESM/cesm_to_dart.html">models/CESM/cesm_to_dart</A></LI>
<LI><A href="models/CESM/dart_to_cesm.html">models/CESM/dart_to_cesm</A></LI>
-<LI><A href="models/CESM/model_mod.f90">models/CESM/model_mod </A> (source)</LI>
-<LI><A href="models/CESM/model_mod.html">models/CESM/model_mod </A> (html)</LI>
-<LI><A href="models/MITgcm_annulus/model_mod.f90">models/MITgcm_annulus/model_mod </A> (source)</LI>
+<LI><A href="models/CESM/model_mod.f90">models/CESM/model_mod</A> (source)</LI>
+<LI><A href="models/CESM/model_mod.html">models/CESM/model_mod</A> (html)</LI>
+<LI><A href="models/MITgcm_annulus/model_mod.f90">models/MITgcm_annulus/model_mod</A> (source)</LI>
<LI><A href="models/MITgcm_ocean/create_ocean_obs.html">models/MITgcm_ocean/create_ocean_obs</A></LI>
-<LI><A href="models/MITgcm_ocean/model_mod.f90">models/MITgcm_ocean/model_mod </A> (source)</LI>
-<LI><A href="models/MITgcm_ocean/model_mod.html">models/MITgcm_ocean/model_mod </A> (html)</LI>
+<LI><A href="models/MITgcm_ocean/model_mod.f90">models/MITgcm_ocean/model_mod</A> (source)</LI>
+<LI><A href="models/MITgcm_ocean/model_mod.html">models/MITgcm_ocean/model_mod</A> (html)</LI>
<LI><A href="models/MITgcm_ocean/trans_pv_sv.html">models/MITgcm_ocean/trans_pv_sv</A></LI>
<LI><A href="models/MITgcm_ocean/trans_sv_pv.html">models/MITgcm_ocean/trans_sv_pv</A></LI>
-<LI><A href="models/NAAPS/model_mod.f90">models/NAAPS/model_mod </A> (source)</LI>
+<LI><A href="models/NAAPS/model_mod.f90">models/NAAPS/model_mod</A> (source)</LI>
<LI><A href="models/NCOMMAS/dart_to_ncommas.html">models/NCOMMAS/dart_to_ncommas</A></LI>
-<LI><A href="models/NCOMMAS/model_mod.f90">models/NCOMMAS/model_mod </A> (source)</LI>
-<LI><A href="models/NCOMMAS/model_mod.html">models/NCOMMAS/model_mod </A> (html)</LI>
+<LI><A href="models/NCOMMAS/model_mod.f90">models/NCOMMAS/model_mod</A> (source)</LI>
+<LI><A href="models/NCOMMAS/model_mod.html">models/NCOMMAS/model_mod</A> (html)</LI>
<LI><A href="models/NCOMMAS/ncommas_to_dart.html">models/NCOMMAS/ncommas_to_dart</A></LI>
-<LI><A href="models/POP/dart_pop_mod.html">models/POP/dart_pop_mod </A> (html)</LI>
+<LI><A href="models/POP/dart_pop_mod.html">models/POP/dart_pop_mod</A> (html)</LI>
<LI><A href="models/POP/dart_to_pop.html">models/POP/dart_to_pop</A></LI>
-<LI><A href="models/POP/model_mod.f90">models/POP/model_mod </A> (source)</LI>
-<LI><A href="models/POP/model_mod.html">models/POP/model_mod </A> (html)</LI>
+<LI><A href="models/POP/model_mod.f90">models/POP/model_mod</A> (source)</LI>
+<LI><A href="models/POP/model_mod.html">models/POP/model_mod</A> (html)</LI>
<LI><A href="models/POP/pop_to_dart.html">models/POP/pop_to_dart</A></LI>
-<LI><A href="models/am2/model_mod.f90">models/am2/model_mod </A> (source)</LI>
-<LI><A href="models/bgrid_solo/model_mod.f90">models/bgrid_solo/model_mod </A> (source)</LI>
+<LI><A href="models/am2/model_mod.f90">models/am2/model_mod</A> (source)</LI>
+<LI><A href="models/bgrid_solo/model_mod.f90">models/bgrid_solo/model_mod</A> (source)</LI>
<LI><A href="models/cam/cam_to_dart.html">models/cam/cam_to_dart</A></LI>
<LI><A href="models/cam/dart_to_cam.html">models/cam/dart_to_cam</A></LI>
<LI><A href="models/cam/doc/cam_guidelines.html">models/cam/doc/cam_guidelines</A></LI>
<LI><A href="models/cam/doc/script_doc.html">models/cam/doc/script_doc</A></LI>
-<LI><A href="models/cam/model_mod.f90">models/cam/model_mod </A> (source)</LI>
-<LI><A href="models/cam/model_mod.html">models/cam/model_mod </A> (html)</LI>
+<LI><A href="models/cam/model_mod.f90">models/cam/model_mod</A> (source)</LI>
+<LI><A href="models/cam/model_mod.html">models/cam/model_mod</A> (html)</LI>
<LI><A href="models/clm/clm_to_dart.html">models/clm/clm_to_dart</A></LI>
<LI><A href="models/clm/dart_to_clm.html">models/clm/dart_to_clm</A></LI>
-<LI><A href="models/clm/model_mod.f90">models/clm/model_mod </A> (source)</LI>
-<LI><A href="models/coamps/model_mod.f90">models/coamps/model_mod </A> (source)</LI>
-<LI><A href="models/coamps/model_mod.html">models/coamps/model_mod </A> (html)</LI>
-<LI><A href="models/coamps_nest/model_mod.f90">models/coamps_nest/model_mod </A> (source)</LI>
-<LI><A href="models/dynamo/model_mod.f90">models/dynamo/model_mod </A> (source)</LI>
-<LI><A href="models/forced_barot/model_mod.f90">models/forced_barot/model_mod </A> (source)</LI>
-<LI><A href="models/forced_lorenz_96/model_mod.f90">models/forced_lorenz_96/model_mod </A> (source)</LI>
-<LI><A href="models/forced_lorenz_96/model_mod.html">models/forced_lorenz_96/model_mod </A> (html)</LI>
-<LI><A href="models/gitm/model_mod.f90">models/gitm/model_mod </A> (source)</LI>
-<LI><A href="models/gitm/model_mod.html">models/gitm/model_mod </A> (html)</LI>
-<LI><A href="models/ikeda/model_mod.f90">models/ikeda/model_mod </A> (source)</LI>
-<LI><A href="models/ikeda/model_mod.html">models/ikeda/model_mod </A> (html)</LI>
-<LI><A href="models/lorenz_04/model_mod.f90">models/lorenz_04/model_mod </A> (source)</LI>
-<LI><A href="models/lorenz_04/model_mod.html">models/lorenz_04/model_mod </A> (html)</LI>
-<LI><A href="models/lorenz_63/model_mod.f90">models/lorenz_63/model_mod </A> (source)</LI>
-<LI><A href="models/lorenz_63/model_mod.html">models/lorenz_63/model_mod </A> (html)</LI>
-<LI><A href="models/lorenz_84/model_mod.f90">models/lorenz_84/model_mod </A> (source)</LI>
-<LI><A href="models/lorenz_84/model_mod.html">models/lorenz_84/model_mod </A> (html)</LI>
-<LI><A href="models/lorenz_96/model_mod.f90">models/lorenz_96/model_mod </A> (source)</LI>
-<LI><A href="models/lorenz_96/model_mod.html">models/lorenz_96/model_mod </A> (html)</LI>
-<LI><A href="models/lorenz_96_2scale/model_mod.f90">models/lorenz_96_2scale/model_mod </A> (source)</LI>
-<LI><A href="models/model_mod.html">models/model_mod </A> (html)</LI>
-<LI><A href="models/mpas_atm/model_mod.f90">models/mpas_atm/model_mod </A> (source)</LI>
-<LI><A href="models/mpas_atm/model_mod.html">models/mpas_atm/model_mod </A> (html)</LI>
+<LI><A href="models/clm/model_mod.f90">models/clm/model_mod</A> (source)</LI>
+<LI><A href="models/coamps/model_mod.f90">models/coamps/model_mod</A> (source)</LI>
+<LI><A href="models/coamps/model_mod.html">models/coamps/model_mod</A> (html)</LI>
+<LI><A href="models/coamps_nest/model_mod.f90">models/coamps_nest/model_mod</A> (source)</LI>
+<LI><A href="models/dynamo/model_mod.f90">models/dynamo/model_mod</A> (source)</LI>
+<LI><A href="models/forced_barot/model_mod.f90">models/forced_barot/model_mod</A> (source)</LI>
+<LI><A href="models/forced_lorenz_96/model_mod.f90">models/forced_lorenz_96/model_mod</A> (source)</LI>
+<LI><A href="models/forced_lorenz_96/model_mod.html">models/forced_lorenz_96/model_mod</A> (html)</LI>
+<LI><A href="models/gitm/model_mod.f90">models/gitm/model_mod</A> (source)</LI>
+<LI><A href="models/gitm/model_mod.html">models/gitm/model_mod</A> (html)</LI>
+<LI><A href="models/ikeda/model_mod.f90">models/ikeda/model_mod</A> (source)</LI>
+<LI><A href="models/ikeda/model_mod.html">models/ikeda/model_mod</A> (html)</LI>
+<LI><A href="models/lorenz_04/model_mod.f90">models/lorenz_04/model_mod</A> (source)</LI>
+<LI><A href="models/lorenz_04/model_mod.html">models/lorenz_04/model_mod</A> (html)</LI>
+<LI><A href="models/lorenz_63/model_mod.f90">models/lorenz_63/model_mod</A> (source)</LI>
+<LI><A href="models/lorenz_63/model_mod.html">models/lorenz_63/model_mod</A> (html)</LI>
+<LI><A href="models/lorenz_84/model_mod.f90">models/lorenz_84/model_mod</A> (source)</LI>
+<LI><A href="models/lorenz_84/model_mod.html">models/lorenz_84/model_mod</A> (html)</LI>
+<LI><A href="models/lorenz_96/model_mod.f90">models/lorenz_96/model_mod</A> (source)</LI>
+<LI><A href="models/lorenz_96/model_mod.html">models/lorenz_96/model_mod</A> (html)</LI>
+<LI><A href="models/lorenz_96_2scale/model_mod.f90">models/lorenz_96_2scale/model_mod</A> (source)</LI>
+<LI><A href="models/model_mod.html">models/model_mod</A> (html)</LI>
+<LI><A href="models/mpas_atm/model_mod.f90">models/mpas_atm/model_mod</A> (source)</LI>
+<LI><A href="models/mpas_atm/model_mod.html">models/mpas_atm/model_mod</A> (html)</LI>
<LI><A href="models/mpas_atm/model_to_dart.html">models/mpas_atm/model_to_dart</A></LI>
-<LI><A href="models/mpas_ocn/model_mod.f90">models/mpas_ocn/model_mod </A> (source)</LI>
-<LI><A href="models/mpas_ocn/model_mod.html">models/mpas_ocn/model_mod </A> (html)</LI>
+<LI><A href="models/mpas_ocn/model_mod.f90">models/mpas_ocn/model_mod</A> (source)</LI>
+<LI><A href="models/mpas_ocn/model_mod.html">models/mpas_ocn/model_mod</A> (html)</LI>
<LI><A href="models/mpas_ocn/model_to_dart.html">models/mpas_ocn/model_to_dart</A></LI>
<LI><A href="models/noah/dart_to_noah.html">models/noah/dart_to_noah</A></LI>
-<LI><A href="models/noah/model_mod.f90">models/noah/model_mod </A> (source)</LI>
-<LI><A href="models/noah/model_mod.html">models/noah/model_mod </A> (html)</LI>
+<LI><A href="models/noah/model_mod.f90">models/noah/model_mod</A> (source)</LI>
+<LI><A href="models/noah/model_mod.html">models/noah/model_mod</A> (html)</LI>
<LI><A href="models/noah/noah_to_dart.html">models/noah/noah_to_dart</A></LI>
-<LI><A href="models/null_model/model_mod.f90">models/null_model/model_mod </A> (source)</LI>
-<LI><A href="models/null_model/model_mod.html">models/null_model/model_mod </A> (html)</LI>
-<LI><A href="models/pe2lyr/model_mod.f90">models/pe2lyr/model_mod </A> (source)</LI>
-<LI><A href="models/pe2lyr/model_mod.html">models/pe2lyr/model_mod </A> (html)</LI>
-<LI><A href="models/rose/model_mod.f90">models/rose/model_mod </A> (source)</LI>
-<LI><A href="models/simple_advection/model_mod.f90">models/simple_advection/model_mod </A> (source)</LI>
-<LI><A href="models/simple_advection/model_mod.html">models/simple_advection/model_mod </A> (html)</LI>
-<LI><A href="models/sqg/model_mod.f90">models/sqg/model_mod </A> (source)</LI>
-<LI><A href="models/template/model_mod.f90">models/template/model_mod </A> (source)</LI>
-<LI><A href="models/tiegcm/model_mod.f90">models/tiegcm/model_mod </A> (source)</LI>
-<LI><A href="models/wrf/model_mod.f90">models/wrf/model_mod </A> (source)</LI>
-<LI><A href="models/wrf/model_mod.html">models/wrf/model_mod </A> (html)</LI>
+<LI><A href="models/null_model/model_mod.f90">models/null_model/model_mod</A> (source)</LI>
+<LI><A href="models/null_model/model_mod.html">models/null_model/model_mod</A> (html)</LI>
+<LI><A href="models/pe2lyr/model_mod.f90">models/pe2lyr/model_mod</A> (source)</LI>
+<LI><A href="models/pe2lyr/model_mod.html">models/pe2lyr/model_mod</A> (html)</LI>
+<LI><A href="models/rose/model_mod.f90">models/rose/model_mod</A> (source)</LI>
+<LI><A href="models/simple_advection/model_mod.f90">models/simple_advection/model_mod</A> (source)</LI>
+<LI><A href="models/simple_advection/model_mod.html">models/simple_advection/model_mod</A> (html)</LI>
+<LI><A href="models/sqg/model_mod.f90">models/sqg/model_mod</A> (source)</LI>
+<LI><A href="models/template/model_mod.f90">models/template/model_mod</A> (source)</LI>
+<LI><A href="models/tiegcm/model_mod.f90">models/tiegcm/model_mod</A> (source)</LI>
+<LI><A href="models/wrf/model_mod.f90">models/wrf/model_mod</A> (source)</LI>
+<LI><A href="models/wrf/model_mod.html">models/wrf/model_mod</A> (html)</LI>
<LI><A href="models/wrf/shell_scripts/advance_model.html">models/wrf/shell_scripts/advance_model</A></LI>
<LI><A href="models/wrf/WRF_DART_utilities/dart_to_wrf.html">models/wrf/WRF_DART_utilities/dart_to_wrf</A></LI>
<LI><A href="models/wrf/WRF_DART_utilities/replace_wrf_fields.html">models/wrf/WRF_DART_utilities/replace_wrf_fields</A></LI>
@@ -700,10 +711,11 @@
<LI><A href="random_seq/random_seq_mod.html">random_seq/random_seq_mod</A></LI>
<LI><A href="reg_factor/reg_factor_mod.html">reg_factor/reg_factor_mod</A></LI>
<LI><A href="smoother/smoother_mod.html">smoother/smoother_mod</A></LI>
-<LI><A href="system_simulation/system_simulation.html">system_simulation/system_simulation </A> (sampling error correction)</LI>
+<LI><A href="system_simulation/system_simulation.html">system_simulation/system_simulation</A> (sampling error correction)</LI>
<LI><A href="time_manager/advance_time.html">time_manager/advance_time</A></LI>
<LI><A href="time_manager/schedule_mod.html">time_manager/schedule_mod</A></LI>
<LI><A href="time_manager/time_manager_mod.html">time_manager/time_manager_mod</A></LI>
+<LI><A HREF='tutorial/index.html'>DART Tutorial</A></LI>
<LI><A href="utilities/closest_member_tool.html">utilities/closest_member_tool</A></LI>
<LI><A href="utilities/compare_states.html">utilities/compare_states</A></LI>
<LI><A href="utilities/model_mod_check.html">utilities/model_mod_check</A></LI>
@@ -713,6 +725,8 @@
</UL>
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<!-- Legalese & Metadata -->
<!--==================================================================-->
Modified: DART/trunk/matlab/GetBgridInfo.m
===================================================================
--- DART/trunk/matlab/GetBgridInfo.m 2015-05-06 17:13:30 UTC (rev 7958)
+++ DART/trunk/matlab/GetBgridInfo.m 2015-05-06 22:18:27 UTC (rev 7959)
@@ -150,11 +150,11 @@
% If there is only one copy, the string needs to be transposed.
metadata = nc_varget(fname,'CopyMetaData');
[N,M] = size(metadata);
- if (M == 1)
- metadata = metadata';
- [N,M] = size(metadata);
+ if M == 1
+ cell_array{1} = metadata';
+ else
+ cell_array = mat2cell(metadata, ones(1,N), M);
end
- cell_array = mat2cell(metadata, ones(1,N), M);
ens_mem = strtrim(cell_array{1});
str1 = sprintf('Input ensemble member metadata STRING. <cr> for ''%s'' ',ens_mem);
s1 = input(str1,'s');
Modified: DART/trunk/matlab/GetWRFInfo.m
===================================================================
--- DART/trunk/matlab/GetWRFInfo.m 2015-05-06 17:13:30 UTC (rev 7958)
+++ DART/trunk/matlab/GetWRFInfo.m 2015-05-06 22:18:27 UTC (rev 7959)
@@ -199,7 +199,11 @@
% query for ensemble member string
metadata = nc_varget(fname,'CopyMetaData');
[N,M] = size(metadata);
- cell_array = mat2cell(metadata, ones(1,N), M);
+ if M == 1
+ cell_array{1} = metadata';
+ else
+ cell_array = mat2cell(metadata, ones(1,N), M);
+ end
ens_mem = strtrim(cell_array{1});
str1 = sprintf('Input ensemble member metadata STRING. <cr> for ''%s'' ',ens_mem);
s1 = input(str1,'s');
Modified: DART/trunk/matlab/plot_phase_space.m
===================================================================
--- DART/trunk/matlab/plot_phase_space.m 2015-05-06 17:13:30 UTC (rev 7958)
+++ DART/trunk/matlab/plot_phase_space.m 2015-05-06 22:18:27 UTC (rev 7959)
@@ -74,11 +74,15 @@
% Set a viable default ensemble member string
metadata = nc_varget(fname,'CopyMetaData');
[N,M] = size(metadata);
- cell_array = mat2cell(metadata, ones(1,N), M);
+ if M == 1
+ cell_array{1} = metadata';
+ else
+ cell_array = mat2cell(metadata, ones(1,N), M);
+ end
ens_mem = strtrim(cell_array{1});
disp('It is necessary to pick an ensemble member to plot.')
disp('Since we pick it based on the metadata string, it could be:')
- disp('''true_state'', ''ensemble mean'', ''ensemble member10'' ... you get it.')
+ disp('''true state'', ''ensemble mean'', ''ensemble member10'' ... you get it.')
str1 = sprintf('Input ensemble member metadata STRING. <cr> for ''%s''\n',ens_mem);
s1 = input(str1,'s');
if ~ isempty(s1), ens_mem = s1; end
@@ -119,11 +123,15 @@
% Set a viable default ensemble member string
metadata = nc_varget(fname,'CopyMetaData');
[N,M] = size(metadata);
- cell_array = mat2cell(metadata, ones(1,N), M);
+ if M == 1
+ cell_array{1} = metadata';
+ else
+ cell_array = mat2cell(metadata, ones(1,N), M);
+ end
ens_mem = strtrim(cell_array{1});
disp('It is necessary to pick an ensemble member to plot.')
disp('Since we pick it based on the metadata string, it could be:')
- disp('''true_state'', ''ensemble mean'', ''ensemble member10'' ... you get it.')
+ disp('''true state'', ''ensemble mean'', ''ensemble member10'' ... you get it.')
str1 = sprintf('Input ensemble member metadata STRING. <cr> for ''%s''\n',ens_mem);
s1 = input(str1,'s');
if ~ isempty(s1), ens_mem = s1; end
@@ -186,11 +194,15 @@
% Set a viable default ensemble member string
metadata = nc_varget(fname,'CopyMetaData');
[N,M] = size(metadata);
- cell_array = mat2cell(metadata, ones(1,N), M);
+ if M == 1
+ cell_array{1} = metadata';
+ else
+ cell_array = mat2cell(metadata, ones(1,N), M);
+ end
ens_mem = strtrim(cell_array{1});
disp('It is necessary to pick an ensemble member to plot.')
disp('Since we pick it based on the metadata string, it could be:')
- disp('''true_state'', ''ensemble mean'', ''ensemble member10'' ... you get it.')
+ disp('''true state'', ''ensemble mean'', ''ensemble member10'' ... you get it.')
str1 = sprintf('Input ensemble member metadata STRING. <cr> for ''%s''\n',ens_mem);
s1 = input(str1,'s');
if ~ isempty(s1), ens_mem = s1; end
@@ -257,11 +269,15 @@
% Set a viable default ensemble member string
metadata = nc_varget(fname,'CopyMetaData');
[N,M] = size(metadata);
- cell_array = mat2cell(metadata, ones(1,N), M);
+ if M == 1
+ cell_array{1} = metadata';
+ else
+ cell_array = mat2cell(metadata, ones(1,N), M);
+ end
ens_mem = strtrim(cell_array{1});
disp('It is necessary to pick an ensemble member to plot.')
disp('Since we pick it based on the metadata string, it could be:')
- disp('''true_state'', ''ensemble mean'', ''ensemble member10'' ... you get it.')
+ disp('''true state'', ''ensemble mean'', ''ensemble member10'' ... you get it.')
str1 = sprintf('Input ensemble member metadata STRING. <cr> for ''%s''\n',ens_mem);
s1 = input(str1,'s');
if ~ isempty(s1), ens_mem = s1; end
Modified: DART/trunk/mkmf/mkmf.template
===================================================================
--- DART/trunk/mkmf/mkmf.template 2015-05-06 17:13:30 UTC (rev 7958)
+++ DART/trunk/mkmf/mkmf.template 2015-05-06 22:18:27 UTC (rev 7959)
@@ -9,9 +9,13 @@
# typical use with mkmf
# mkmf -t mkmf.template.xxxx ...
#
+# Suggested (perhaps required) flags:
+# -ffree-line-length-none handles "long" lines - i.e. longer than 72 chars
#
# Suggested debugging flags:
# -g add debugging information to executable
+# -Wuninitialized catch uninitialized variables
+# -Wunused issue warning for unused variables - keeps code clean
# -fbacktrace runtime errors try to print out a stack backtrace
# -fbounds-check add runtime-checking for out-of-range array indices
# -ffpe-trap=invalid,zero,overflow
@@ -83,7 +87,8 @@
FFLAGS = -O2 -ffree-line-length-none $(INCS)
LDFLAGS = $(FFLAGS) $(LIBS)
-#FFLAGS = -g -ffree-line-length-none -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow $(INCS)
+# FFLAGS = -g -Wuninitialized -Wunused -ffree-line-length-none -fbounds-check \
+# -fbacktrace -ffpe-trap=invalid,zero,overflow $(INCS)
# <next few lines under version control, do not edit>
# $URL$
Modified: DART/trunk/mkmf/mkmf.template.gfortran
===================================================================
--- DART/trunk/mkmf/mkmf.template.gfortran 2015-05-06 17:13:30 UTC (rev 7958)
+++ DART/trunk/mkmf/mkmf.template.gfortran 2015-05-06 22:18:27 UTC (rev 7959)
@@ -9,9 +9,13 @@
# typical use with mkmf
# mkmf -t mkmf.template.xxxx ...
#
+# Suggested (perhaps required) flags:
+# -ffree-line-length-none handles "long" lines - i.e. longer than 72 chars
#
# Suggested debugging flags:
# -g add debugging information to executable
+# -Wuninitialized catch uninitialized variables
+# -Wunused issue warning for unused variables - keeps code clean
# -fbacktrace runtime errors try to print out a stack backtrace
# -fbounds-check add runtime-checking for out-of-range array indices
# -ffpe-trap=invalid,zero,overflow
@@ -83,7 +87,8 @@
FFLAGS = -O2 -ffree-line-length-none $(INCS)
LDFLAGS = $(FFLAGS) $(LIBS)
-#FFLAGS = -g -Wunused -ffree-line-length-none -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow $(INCS)
+# FFLAGS = -g -Wuninitialized -Wunused -ffree-line-length-none -fbounds-check \
+# -fbacktrace -ffpe-trap=invalid,zero,overflow $(INCS)
# <next few lines under version control, do not edit>
# $URL$
Modified: DART/trunk/models/lorenz_63/work/input.nml
===================================================================
--- DART/trunk/models/lorenz_63/work/input.nml 2015-05-06 17:13:30 UTC (rev 7958)
+++ DART/trunk/models/lorenz_63/work/input.nml 2015-05-06 22:18:27 UTC (rev 7959)
@@ -210,3 +210,24 @@
verbose = .false.
/
+
+&schedule_nml
+ calendar = 'Gregorian',
+ first_bin_start = 1601, 1, 1, 0, 0, 0,
+ first_bin_end = 2999, 1, 1, 0, 0, 0,
+ last_bin_end = 2999, 1, 1, 0, 0, 0,
+ bin_interval_days = 1000000,
+ bin_interval_seconds = 0,
+ max_num_bins = 1000,
+ print_table = .true.
+ /
+
+&obs_seq_to_netcdf_nml
+ obs_sequence_name = 'obs_seq.out.xyz'
+ obs_sequence_list = ''
+ append_to_netcdf = .false.
+ lonlim1 = 0.0
+ lonlim2 = 1.0
+ verbose = .false.
+ /
+
Modified: DART/trunk/models/noah/dart_to_noah.html
===================================================================
--- DART/trunk/models/noah/dart_to_noah.html 2015-05-06 17:13:30 UTC (rev 7958)
+++ DART/trunk/models/noah/dart_to_noah.html 2015-05-06 22:18:27 UTC (rev 7959)
@@ -115,6 +115,8 @@
thing is true for the NOAH restart files (<em class=file>noah_restart.nc</em>).
</P>
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<!--=================== DESCRIPTION OF A NAMELIST ====================-->
<!--==================================================================-->
@@ -286,7 +288,7 @@
Change these at your own risk!
</P>
-<br />
+<P><!-- make sure the 'top' is aligned correctly --></P>
<!--==================================================================-->
@@ -304,8 +306,9 @@
types_mod
utilities_mod
</PRE>
-<br />
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<!-- Describe the Files Used by this module. -->
<!--==================================================================-->
@@ -324,8 +327,9 @@
<LI><em class=file>noah_advance_information.txt</em> - which contains a
list of "LDASIN" files needed to advance the model.</LI>
</UL>
-<br />
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<!-- Cite references, if need be. -->
<!--==================================================================-->
@@ -339,6 +343,8 @@
http://www.ral.ucar.edu/research/land/technology/lsm.php</a>
</ul>
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<!-- Describe all the error conditions and codes. -->
<!--==================================================================-->
@@ -355,6 +361,8 @@
none
</P>
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<!-- Describe Future Plans. -->
<!--==================================================================-->
@@ -366,6 +374,8 @@
None.
</P>
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
<!-- Legalese & Metadata -->
<!--==================================================================-->
Modified: DART/trunk/models/noah/noah_to_dart.html
===================================================================
--- DART/trunk/models/noah/noah_to_dart.html 2015-05-06 17:13:30 UTC (rev 7958)
+++ DART/trunk/models/noah/noah_to_dart.html 2015-05-06 22:18:27 UTC (rev 7959)
@@ -66,6 +66,8 @@
linking the appropriate files to these static filenames.
</P>
+<P><!-- make sure the 'top' is aligned correctly --></P>
+
<!--==================================================================-->
@@ Diff output truncated at 40000 characters. @@
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