[Dart-dev] [6382] DART/trunk: update the rest of the html files which document namelists;
nancy at ucar.edu
nancy at ucar.edu
Wed Aug 7 14:45:16 MDT 2013
Revision: 6382
Author: nancy
Date: 2013-08-07 14:45:16 -0600 (Wed, 07 Aug 2013)
Log Message:
-----------
update the rest of the html files which document namelists;
make sure there .nml files match the code and documentation.
add the separator lines which have a link back to the top.
remove the paragraph found in many html files that indicates
the namelist is optional.
Modified Paths:
--------------
DART/trunk/assim_tools/assim_tools_mod.html
DART/trunk/cov_cutoff/cov_cutoff_mod.html
DART/trunk/diagnostics/oned/obs_diag.html
DART/trunk/diagnostics/threed_sphere/obs_diag.html
DART/trunk/doc/html/boilerplate/boilerplate.html
DART/trunk/ensemble_manager/ensemble_manager_mod.html
DART/trunk/location/channel/location_mod.html
DART/trunk/location/threed_cartesian/location_mod.html
DART/trunk/location/threed_sphere/location_mod.html
DART/trunk/models/9var/model_mod.html
DART/trunk/models/NCOMMAS/dart_to_ncommas.html
DART/trunk/models/NCOMMAS/ncommas_to_dart.html
DART/trunk/models/POP/dart_to_pop.html
DART/trunk/models/POP/pop_to_dart.html
DART/trunk/models/cam/cam_to_dart.html
DART/trunk/models/cam/dart_to_cam.html
DART/trunk/models/cam/model_mod.html
DART/trunk/models/clm/clm_to_dart.html
DART/trunk/models/clm/dart_to_clm.html
DART/trunk/models/coamps/model_mod.html
DART/trunk/models/forced_lorenz_96/model_mod.html
DART/trunk/models/ikeda/model_mod.html
DART/trunk/models/lorenz_04/model_mod.html
DART/trunk/models/lorenz_63/model_mod.html
DART/trunk/models/lorenz_84/model_mod.html
DART/trunk/models/lorenz_96/model_mod.html
DART/trunk/models/model_mod.html
DART/trunk/models/mpas_atm/model_to_dart.html
DART/trunk/models/mpas_ocn/model_to_dart.html
DART/trunk/models/noah/dart_to_noah.html
DART/trunk/models/noah/model_mod.html
DART/trunk/models/null_model/model_mod.html
DART/trunk/models/pe2lyr/model_mod.html
DART/trunk/models/simple_advection/model_mod.html
DART/trunk/models/wrf/WRF_DART_utilities/dart_to_wrf.html
DART/trunk/models/wrf/WRF_DART_utilities/replace_wrf_fields.html
DART/trunk/models/wrf/model_mod.html
DART/trunk/obs_sequence/obs_seq_to_netcdf.html
DART/trunk/obs_sequence/obs_sequence_mod.html
DART/trunk/observations/GTSPP/GTSPP.html
DART/trunk/observations/NCEP/ascii_to_obs/create_real_obs.html
DART/trunk/observations/NCEP/prep_bufr/prep_bufr.html
DART/trunk/observations/WOD/WOD.html
DART/trunk/observations/gps/gps.html
DART/trunk/observations/var/rad_3dvar_to_dart.html
DART/trunk/random_seq/random_seq_mod.html
DART/trunk/reg_factor/reg_factor_mod.html
DART/trunk/smoother/smoother_mod.html
DART/trunk/time_manager/time_manager_mod.html
DART/trunk/utilities/utilities_mod.html
Added Paths:
-----------
DART/trunk/models/clm/model_mod.html
-------------- next part --------------
Modified: DART/trunk/assim_tools/assim_tools_mod.html
===================================================================
--- DART/trunk/assim_tools/assim_tools_mod.html 2013-08-07 20:29:40 UTC (rev 6381)
+++ DART/trunk/assim_tools/assim_tools_mod.html 2013-08-07 20:45:16 UTC (rev 6382)
@@ -525,12 +525,6 @@
</TABLE>
<P>
-Optional namelist interface
-<A HREF="#Namelist"> <em class=code>&assim_tools_nml</em> </A>
-may be read from file <em class=file>input.nml</em>.
-</P>
-
-<P>
A note about documentation style.
Optional arguments are enclosed in brackets
<em class=optionalcode>[like this]</em>.
Modified: DART/trunk/cov_cutoff/cov_cutoff_mod.html
===================================================================
--- DART/trunk/cov_cutoff/cov_cutoff_mod.html 2013-08-07 20:29:40 UTC (rev 6381)
+++ DART/trunk/cov_cutoff/cov_cutoff_mod.html 2013-08-07 20:45:16 UTC (rev 6382)
@@ -122,12 +122,6 @@
</TABLE>
<P>
-Optional namelist interface
-<A HREF="#Namelist"> <em class=code>&cov_cutoff_nml</em> </A>
-may be read from file <em class=file>input.nml</em>.
-</P>
-
-<P>
A note about documentation style.
Optional arguments are enclosed in brackets
<em class=optionalcode>[like this]</em>.
Modified: DART/trunk/diagnostics/oned/obs_diag.html
===================================================================
--- DART/trunk/diagnostics/oned/obs_diag.html 2013-08-07 20:29:40 UTC (rev 6381)
+++ DART/trunk/diagnostics/oned/obs_diag.html 2013-08-07 20:45:16 UTC (rev 6382)
@@ -201,28 +201,43 @@
<!--==================================================================-->
<A NAME="Namelist"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>NAMELIST</H2>
-<P>We adhere to the F90 standard of starting a namelist with an ampersand
-'&' and terminating with a slash '/' for all our namelist input.
-Consider yourself forewarned that character strings that contain a '/' must be
-enclosed in quotes to prevent them from prematurely terminating the namelist.
-The namelist declaration (i.e. what follows) has a different syntax, naturally.
+<P>
+This namelist is read from the file <em class=file>input.nml</em>.
+Namelists start with an ampersand
+'&' and terminate with a slash '/'.
+Character strings that contain a '/' must be
+enclosed in quotes to prevent them from
+prematurely terminating the namelist.
</P>
+
<div class=namelist>
<pre>
-<em class=call>namelist / obs_diag_nml / </em> &
- obs_sequence_name, obs_sequence_list, bin_width_days, bin_width_seconds, &
- init_skip_days, init_skip_seconds, max_num_bins, Nregions, lonlim1, lonlim2, reg_names, &
- create_rank_histogram, outliers_in_histogram, trusted_obs, verbose
+&obs_diag_nml
+ obs_sequence_name = 'obs_seq.final',
+ obs_sequence_list = '',
+ bin_width_days = -1,
+ bin_width_seconds = -1,
+ init_skip_days = 0,
+ init_skip_seconds = 0,
+ max_num_bins = 9999,
+ trusted_obs = 'null',
+ Nregions = 3,
+ lonlim1 = 0.00, 0.00, 0.50, -1.0,
+ lonlim2 = 1.01, 0.50, 1.01, -1.0,
+ reg_names = 'whole', 'yin', 'yang', 'bogus',
+ create_rank_histogram = .true.,
+ outliers_in_histogram = .true.,
+ verbose = .false.
+ /
</pre>
</div>
-<div class=indent1>
-<!-- Description -->
+<br />
+<br />
<P>
-This namelist is read in a file called <em class=file>input.nml</em>.
The allowable ranges for the region boundaries are: lon [0.0, 1.0).
The 1D locations are conceived as the distance around a unit sphere.
An observation with a location exactly ON a region boundary cannot
@@ -239,135 +254,129 @@
One of them has to be an empty string ... i.e. <em class="code">''</em>.
</P>
-<TABLE border=0 cellpadding=3 width=100%>
-<TR><TH align=left>Contents </TH>
- <TH align=left>Type </TH>
- <TH align=left>Description </TH></TR>
+<div>
+<TABLE border=0 cellpadding=10 width=100% summary='namelist description'>
+<THEAD align=left>
+<TR><TH> Item </TH>
+ <TH> Type </TH>
+ <TH> Description </TH> </TR>
+</THEAD>
-<TR><!--contents--><TD valign=top> obs_sequence_name </TD>
- <!-- type --><TD valign=top> character </TD>
- <!--descript--><TD>Name of the observation sequence file(s). <br />
- This may be a relative or absolute filename. If the filename
- contains a '/', the filename is considered to be comprised of
- everything to the right, and a directory structure to the left.
- The directory structure is then queried to see if it can be
- incremented to handle a sequence of observation files.
- The default behavior of <em class="program">obs_diag</em>
- is to look for additional files to include until the files
- are exhausted or an <em class=file>obs_seq.final</em> file
- is found that contains observations beyond the timeframe of
- interest.<br />e.g. 'obsdir_001/obs_seq.final' will cause
- <em class="program">obs_diag</em> to look for
- 'obsdir_002/obs_seq.final', and so on.<br />
- If this is set, <em class=code>obs_sequence_list</em>
- must be set to a null string ('').<br />
- Default: 'obs_seq.final'</TD></TR>
+<TBODY valign=top>
-<TR><!--contents--><TD valign=top> obs_sequence_list </TD>
- <!-- type --><TD valign=top> character </TD>
- <!--descript--><TD>Name of an ascii text file which contains a list
- of one or more observation sequence files, one per line.
- If this is specified, <em class=code>obs_sequence_name</em>
- must be set to a null string (''). Can be created by any method,
- including sending the output of the 'ls' command to a file,
- a text editor, or another program. If this is set,
- <em class=code>obs_sequence_name</em>
- must be set to a null string ('').<br />
- Default: '' - an empty string.</TD></TR>
+<TR><TD> obs_sequence_name </TD>
+ <TD> character </TD>
+ <TD>Name of the observation sequence file(s). <br />
+This may be a relative or absolute filename. If the filename contains a '/',
+the filename is considered to be comprised of everything to the right, and a
+directory structure to the left. The directory structure is then queried to
+see if it can be incremented to handle a sequence of observation files. The
+default behavior of <em class="program">obs_diag</em> is to look for
+additional files to include until the files are exhausted or an
+<em class=file>obs_seq.final</em> file is found that contains observations beyond
+the timeframe of interest.<br />e.g. 'obsdir_001/obs_seq.final' will cause
+<em class="program">obs_diag</em> to look for 'obsdir_002/obs_seq.final', and so on.
+<br />
+If this is set, <em class=code>obs_sequence_list</em> must be set to a null string (' ').
+</TD></TR>
-<TR><!--contents--><TD valign=top>bin_width_days, bin_width_seconds</TD>
- <!-- type --><TD valign=top>integer </TD>
- <!--descript--><TD>Specifies the width of the analysis window. All
- observations within a window centered at the observation time
- +/- bin_width_[days,seconds] is used. If both values are 0 -
- half the separation between observation times as defined in
- the observation sequence file is used for the bin width
- (i.e. all observations used).<br />
- Default: 0, 0</TD></TR>
+<TR><TD> obs_sequence_list </TD>
+ <TD> character </TD>
+ <TD>Name of an ascii text file which contains a list of one or more
+observation sequence files, one per line. If this is specified,
+<em class=code>obs_sequence_name</em> must be set to a null string (' ').
+Can be created by any method, including sending the output of the 'ls'
+command to a file, a text editor, or another program. If this is set,
+<em class=code>obs_sequence_name</em> must be set to a null string (' ').
+</TD></TR>
-<TR><!--contents--><TD valign=top>init_skip_days, init_skip_seconds</TD>
- <!-- type --><TD valign=top>integer </TD>
- <!--descript--><TD>Ignore all observations before this time.
- This allows one to skip the 'spinup' or stabilization
- period of an assimilation.
- <br />
- Default: 0, 0</TD></TR>
+<TR><TD> bin_width_days, bin_width_seconds </TD>
+ <TD> integer </TD>
+ <TD>Specifies the width of the analysis window. All observations within a
+window centered at the observation time +/- bin_width_[days,seconds] is used.
+If both values are 0, half the separation between observation times as
+defined in the observation sequence file is used for the bin width (i.e. all
+observations used).
+</TD></TR>
-<TR><!--contents--><TD valign=top> max_num_bins </TD>
- <!-- type --><TD valign=top> integer </TD>
- <!--descript--><TD>This provides a way to restrict the number of
- temporal bins. If <em class=code>max_num_bins</em> is set
- to '10', only 10 timesteps will be output - provided
- there are that many.
- <br />
- Default: 9999</TD></TR>
+<TR><TD> init_skip_days, init_skip_seconds </TD>
+ <TD> integer </TD>
+ <TD>Ignore all observations before this time. This allows one to skip the
+'spinup' or stabilization period of an assimilation.
+</TD></TR>
-<TR><!--contents--><TD valign=top>Nregions </TD>
- <!-- type --><TD valign=top>integer </TD>
- <!--descript--><TD>The number of regions for the unit circle for which
- you'd like observation-space diagnostics. If 4 is not enough,
- increase <em class=code>MaxRegions</em> in
- <em class=file>obs_diag.f90</em> and recompile.
- <br />
- Default: 4</TD></TR>
+<TR><TD> max_num_bins </TD>
+ <TD> integer </TD>
+ <TD>This provides a way to restrict the number of temporal bins. If
+<em class=code>max_num_bins</em> is set to '10', only 10 timesteps will be output,
+provided there are that many.
+</TD></TR>
-<TR><!--contents--><TD valign=top>lonlim1 </TD>
- <!-- type --><TD valign=top>real(r8) array of length(4)</TD>
- <!--descript--><TD>starting value of coordinates defining 'regions'.
- A value of -1 indicates the start of 'no region'.<br />
- Default is (/ 0.00, 0.00, 0.50, -1.0/)</TD></TR>
+<TR><TD> Nregions </TD>
+ <TD> integer </TD>
+ <TD>The number of regions for the unit circle for which you'd like
+observation-space diagnostics. If 4 is not enough increase
+<em class=code>MaxRegions</em> in <em class=file>obs_diag.f90</em> and recompile.
+</TD></TR>
-<TR><!--contents--><TD valign=top>lonlim2 </TD>
- <!-- type --><TD valign=top>real(r8) array of length(4)</TD>
- <!--descript--><TD>ending value of coordinates defining 'regions'.
- A value of -1 indicates the end of 'no region'.<br />
- Default is (/ 1.01, 0.50, 1.01, -1.0/)</TD></TR>
+<TR><TD> lonlim1 </TD>
+ <TD> real(r8) array of length(Nregions) </TD>
+ <TD>starting value of coordinates defining 'regions'. A value of -1
+indicates the start of 'no region'.
+</TD></TR>
-<TR><!--contents--><TD valign=top>reg_names </TD>
- <!-- type --><TD valign=top>character(len=6), dimension(4)</TD>
- <!--descript--><TD>Array of names for each of the regions.
- The default example has the unit circle as a whole and divided
- into two equal parts, so there are only three regions.<br />
- Default: 'whole','yin','yang','bogus' </TD></TR>
+<TR><TD> lonlim2 </TD>
+ <TD> real(r8) array of length(Nregions) </TD>
+ <TD>ending value of coordinates defining 'regions'. A value of -1 indicates
+the end of 'no region'.
+</TD></TR>
-<TR><!--contents--><TD valign=top>create_rank_histogram</TD>
- <!-- type --><TD valign=top> logical </TD>
- <!--descript--><TD>Determines whether or not to create the rank histogram IFF
- the observation sequence file has individual ensemble members - as
- determined by <em class=file>input.nml</em>
- <em class=code>&filter_nml:num_output_obs_members</em><br />
- Default: .true. </TD></TR>
+<TR><TD> reg_names </TD>
+ <TD> character(len=6), dimension(Nregions) </TD>
+<TD>Array of names for each of the regions. The default example has the unit
+circle as a whole and divided into two equal parts, so there are only three
+regions.
+</TD></TR>
-<TR><!--contents--><TD valign=top>outliers_in_histogram</TD>
- <!-- type --><TD valign=top> logical </TD>
- <!--descript--><TD>Determines whether or not to use observations that
- have been rejected by the outlier threshhold mechanism in the
- calculation of the rank histogram.<br />
- Default: .true. </TD></TR>
+<TR><TD> create_rank_histogram </TD>
+ <TD> logical </TD>
+ <TD>Determines whether or not to create the rank histogram IFF the
+observation sequence file has individual ensemble members. Number of output
+observation values is set when running filter in the &filter_nml namelist
+item: <em class=code>&filter_nml:num_output_obs_members</em>
+</TD></TR>
-<TR><!--contents--><TD valign=top>trusted_obs </TD>
- <!-- type --><TD valign=top>character(len=32), dimension(5)</TD>
- <!--descript--><TD>Array of names for observation TYPES that will be included in
- the statistics if at all possible
- (i.e. the forward observation operator succeeds). For 1D observations
- (which are all fake ... ) the only choices are 'RAW_STATE_VARIABLE'
- and/or 'RAW_STATE_1D_INTEGRAL'<br />
- Default: 'null' </TD></TR>
+<TR><TD> outliers_in_histogram </TD>
+ <TD> logical </TD>
+ <TD>Determines whether or not to use observations that have been rejected by
+the outlier threshhold mechanism in the calculation of the rank histogram.
+</TD></TR>
-<TR><!--contents--><TD valign=top>verbose </TD>
- <!-- type --><TD valign=top>logical </TD>
- <!--descript--><TD>switch controlling amount of run-time output.<br />
- Default is .false. (suppress most output)</TD></TR>
+<TR><TD> trusted_obs </TD>
+ <TD> character(len=32), dimension(5) </TD>
+ <TD>Array of names for observation TYPES that will be included in the
+statistics if at all possible (i.e. the forward observation operator
+succeeds). For 1D observations the only choices in the code as distributed
+are 'RAW_STATE_VARIABLE' and/or 'RAW_STATE_1D_INTEGRAL'. (Additional 1D
+observation types can be added by the user.)
+</TD></TR>
+<TR><TD> verbose </TD>
+ <TD> logical </TD>
+ <TD>switch controlling amount of run-time output.
+</TD></TR>
+
+</TBODY>
</TABLE>
+</div>
-</div>
<br />
+<br />
<!--==================================================================-->
<A NAME="Modules"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>MODULES DIRECTLY USED</H2>
<PRE>
types_mod
@@ -394,7 +403,7 @@
<!--==================================================================-->
<A NAME="FilesUsed"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>FILES</H2>
<UL>
<LI>input namelist; <em class=file>input.nml</em>
@@ -476,7 +485,7 @@
<!--==================================================================-->
<A NAME="References"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>REFERENCES</H2>
<ol>
<li> none </li>
@@ -487,7 +496,7 @@
<!--==================================================================-->
<A NAME="Errors"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>ERROR CODES and CONDITIONS</H2>
<div class=errors>
<TABLE border=1 cellspacing=1 cellpadding=10 width=100%>
@@ -514,7 +523,7 @@
<!--==================================================================-->
<A NAME="FuturePlans"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>FUTURE PLANS</H2>
<P>
none.
@@ -525,7 +534,7 @@
<!--==================================================================-->
<A NAME="PrivateComponents"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>PRIVATE COMPONENTS</H2>
<P>
N/A
@@ -536,7 +545,7 @@
<!--==================================================================-->
<A NAME="Legalese"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>Terms of Use</H2>
<P>
Modified: DART/trunk/diagnostics/threed_sphere/obs_diag.html
===================================================================
--- DART/trunk/diagnostics/threed_sphere/obs_diag.html 2013-08-07 20:29:40 UTC (rev 6381)
+++ DART/trunk/diagnostics/threed_sphere/obs_diag.html 2013-08-07 20:45:16 UTC (rev 6382)
@@ -288,281 +288,251 @@
<tr><td>8+</td><td>reserved for future use</td></tr>
</table>
-<P>
- Optional namelist interface
- <A HREF="#Namelist"><em class=code>&obs_diag_nml</em></A>
- may be read from file <em class=file>input.nml</em>.
-</P>
-
<!--==================================================================-->
<!--=================== DESCRIPTION OF A NAMELIST ===================-->
<!--==================================================================-->
<A NAME="Namelist"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>NAMELIST</H2>
-<P>We adhere to the F90 standard of starting a namelist with an ampersand
-'&' and terminating with a slash '/' for all our namelist input.
-Consider yourself forewarned that filenames that contain a '/' must be
-enclosed in quotes to prevent them from prematurely terminating the namelist.
-The namelist declaration (i.e. what follows) has a different syntax, naturally.
+<P>
+This namelist is read from the file <em class=file>input.nml</em>.
+Namelists start with an ampersand
+'&' and terminate with a slash '/'.
+Character strings that contain a '/' must be
+enclosed in quotes to prevent them from
+prematurely terminating the namelist.
</P>
+
<div class=namelist>
<pre>
-<em class=call>namelist / obs_diag_nml / </em>
- obs_sequence_name, obs_sequence_list, first_bin_center, last_bin_center,
- bin_separation, bin_width, time_to_skip, max_num_bins,
- plevel, hlevel, mlevel,
- rat_cri, input_qc_threshold,
- Nregions, lonlim1, lonlim2, latlim1, latlim2,
- reg_names, print_mismatched_locs, <em class=removed>print_obs_locations,</em> verbose,
- outliers_in_histogram
+&obs_diag_nml
+ obs_sequence_name = 'obs_seq.final',
+ obs_sequence_list = '',
+ first_bin_center = 2003, 1, 1, 0, 0, 0 ,
+ last_bin_center = 2003, 1, 2, 0, 0, 0 ,
+ bin_separation = 0, 0, 0, 6, 0, 0 ,
+ bin_width = 0, 0, 0, 6, 0, 0 ,
+ time_to_skip = 0, 0, 0, 6, 0, 0 ,
+ max_num_bins = 1000,
+ rat_cri = 3.0,
+ input_qc_threshold = 3.0,
+ trusted_obs = 'null',
+ Nregions = 4,
+ lonlim1 = 0.0, 0.0, 0.0, 235.0,
+ lonlim2 = 360.0, 360.0, 360.0, 295.0,
+ latlim1 = 20.0, -80.0, -20.0, 25.0,
+ latlim2 = 80.0, -20.0, 20.0, 55.0,
+ reg_names = 'Northern Hemisphere', 'Southern Hemisphere', 'Tropics', 'North America',
+ print_mismatched_locs = .false.,
+ create_rank_histogram = .false.,
+ outliers_in_histogram = .false.,
+ verbose = .false.
+/
</pre>
</div>
-<div class=indent1>
-<!-- Description -->
-
-<P>This namelist is read in a file called <em class=file>input.nml</em>. <br />
- The date-time integer arrays in this namelist have the form
- (YYYY, MO, DA, HR, MIN, SEC). <br />
- The allowable ranges for the region boundaries are: latitude [-90.,90],
- longitude [0.,Inf.]
<br />
<br />
- You can only specify <strong>either</strong>
- <em class="code">obs_sequence_name</em>
- <strong>or</strong>
- <em class="code">obs_sequence_list</em> -- not both.
- One of them has to be an empty string ... i.e. <em class="code">''</em>.
+
+<P> The date-time integer arrays in this namelist have the form
+ (YYYY, MM, DE, HR, MIN, SEC). <br /> The allowable ranges for the region
+ boundaries are: latitude [-90.,90], longitude [0.,Inf.]
+</P><P>
+ You can only specify <strong>either</strong> <em
+ class="code">obs_sequence_name</em> <strong>or</strong> <em
+ class="code">obs_sequence_list</em> -- not both. One of them has to be an
+ empty string ... i.e. <em class="code">''</em>.
</P>
-<TABLE border=0 cellpadding=3 width=100%>
-<TR><TH align=left>Contents </TH>
- <TH align=left>Type </TH>
- <TH align=left>Description </TH></TR>
+<div>
+<TABLE border=0 cellpadding=10 width=100% summary='namelist description'>
+<THEAD align=left>
+<TR><TH> Item </TH>
+ <TH> Type </TH>
+ <TH> Description </TH> </TR>
+</THEAD>
-<TR><!--contents--><TD valign=top> obs_sequence_name </TD>
- <!-- type --><TD valign=top> character </TD>
- <!--descript--><TD>Name of the observation sequence file(s). <br />
- This may be a relative or absolute filename. If the filename
- contains a '/', the filename is considered to be comprised of
- everything to the right, and a directory structure to the left.
- The directory structure is then queried to see if it can be
- incremented to handle a sequence of observation files.
- The default behavior of <em class="program">obs_diag</em>
- is to look for additional files to include until the files
- are exhausted or an <em class=file>obs_seq.final</em> file
- is found that contains observations beyond the timeframe of
- interest.<br />e.g. 'obsdir_001/obs_seq.final' will cause
- <em class="program">obs_diag</em> to look for
- 'obsdir_002/obs_seq.final', and so on.<br />
- If this is set, <em class=code>obs_sequence_list</em> must be set to ''.
- <br />
- Default 'obs_seq.final'</TD></TR>
+<TBODY valign=top>
+<TR><TD> obs_sequence_name </TD>
+ <TD> character </TD>
+ <TD>Name of the observation sequence file(s). <br />
+This may be a relative or absolute filename. If the filename contains a '/'
+the filename is considered to be comprised of everything to the right, and a
+directory structure to the left. The directory structure is then queried to
+see if it can be incremented to handle a sequence of observation files. The
+default behavior of <em class="program">obs_diag</em> is to look for
+additional files to include until the files are exhausted or an
+<em class=file>obs_seq.final</em> file is found that contains observations beyond
+the timeframe of interest.<br />
+e.g. 'obsdir_001/obs_seq.final' will cause <em class="program">obs_diag</em> to
+look for 'obsdir_002/obs_seq.final', and so on.<br />
+If this is set, <em class=code>obs_sequence_list</em> must be set to ' '
+(empty string).
+</TD></TR>
-<TR><!--contents--><TD valign=top> obs_sequence_list </TD>
- <!-- type --><TD valign=top> character </TD>
- <!--descript--><TD>Name of an ascii text file which contains a list
- of one or more observation sequence files, one per line.
- If this is specified, <em class=code>obs_sequence_name</em> must be set to ''.
- Can be created by any method, including sending the output
- of the 'ls' command to a file, a text editor, or another program.
- If this is set, <em class=code>obs_sequence_name</em> must be set to ''.
- <br />
- Default '' - an empty string.</TD></TR>
+<TR><TD> obs_sequence_list </TD>
+ <TD> character </TD>
+ <TD>Name of an ascii text file which contains a list of one or more
+observation sequence files, one per line. If this is specified,
+<em class=code>obs_sequence_name</em> must be set to ' '. Can be created by any
+method, including sending the output of the 'ls' command to a file, a text
+editor, or another program. If this is set, <em class=code>obs_sequence_name</em>
+must be set to ' ' (empty string).
+</TD></TR>
-<TR><!--contents--><TD valign=top> first_bin_center </TD>
- <!-- type --><TD valign=top> integer, dimension(6) </TD>
- <!--descript--><TD>first timeslot of the first obs_seq.final file to process.
- The six integers are: year, month, day, hour, hour, minute,
- second -- in that order. <em class="program">obs_diag</em> has
- improved run-time output that reports the time and date of the
- first and last observations in every observation sequence file.
- Look for the string 'First observation date' in the logfile.
- If the <em class="code">verbose</em> is 'true', it is also
- written to the screen.<br />
- Default: 2003, 1, 1, 0, 0, 0</TD></TR>
+<TR><TD> first_bin_center </TD>
+ <TD> integer, dimension(6) </TD>
+ <TD>first timeslot of the first obs_seq.final file to process. The six
+integers are: year, month, day, hour, hour, minute, second, in that order.
+<em class="program">obs_diag</em> has improved run-time output that reports
+the time and date of the first and last observations in every observation
+sequence file. Look for the string 'First observation date' in the logfile.
+If the <em class="code">verbose</em> is 'true', it is also written to the
+screen.</TD></TR>
-<TR><!--contents--><TD valign=top> last_bin_center </TD>
- <!-- type --><TD valign=top> integer, dimension(6) </TD>
- <!--descript--><TD>last timeslot of interest.
- (reminder: the last timeslot of day 1 is hour 0 of day 2)
- The six integers are: year, month, day, hour, hour, minute,
- second -- in that order. This does not need to be exact,
- the values from <em class=code>first_bin_center</em> and
- <em class=code>bin_separation</em> are used to populate the time
- array and stop on or before the time defined by
- <em class=code>last_bin_center</em>.
- See also <em class=code>max_num_bins</em>.<br />
- Default: 2003, 1, 2, 0, 0, 0</TD></TR>
+<TR><TD> last_bin_center </TD>
+ <TD> integer, dimension(6) </TD>
+ <TD>last timeslot of interest. (reminder: the last timeslot of day 1 is hour
+0 of day 2) The six integers are: year, month, day, hour, hour, minute,
+second, in that order. This does not need to be exact, the values from
+<em class=code>first_bin_center</em> and <em class=code>bin_separation</em> are
+used to populate the time array and stop on or before the time defined by <em
+class=code>last_bin_center</em>. See also <em class=code>max_num_bins</em>.
+</TD></TR>
-<TR><!--contents--><TD valign=top> bin_separation </TD>
- <!-- type --><TD valign=top> integer, dimension(6) </TD>
- <!--descript--><TD>Time between bin centers.
- The year and month values <em>must</em> be zero.<br />
- Default: 0, 0, 0, 6, 0, 0</TD></TR>
+<TR><TD> bin_separation </TD>
+ <TD> integer, dimension(6) </TD>
+ <TD>Time between bin centers. The year and month values <em>must</em> be zero.
+</TD></TR>
-<TR><!--contents--><TD valign=top> bin_width </TD>
- <!-- type --><TD valign=top> integer, dimension(6) </TD>
- <!--descript--><TD>Time span around bin centers in which obs will be
- compared. The year and month values <em>must</em> be zero.
- Frequently, but not required to be, the same as the values
- for bin_separation.<br />
- Default: 0, 0, 0, 6, 0, 0</TD></TR>
+<TR><TD> bin_width </TD>
+ <TD> integer, dimension(6) </TD>
+ <TD>Time span around bin centers in which obs will be compared. The year and
+month values <em>must</em> be zero. Frequently, but not required to be, the
+same as the values for bin_separation.
+0</TD></TR>
-<TR><!--contents--><TD valign=top> time_to_skip </TD>
- <!-- type --><TD valign=top> integer, dimension(6) </TD>
- <!--descript--><TD>Time span at the beginning to skip when calculating
- vertical profiles of rms error and bias. The year and month
- values <em>must</em> be zero. Useful because it takes some
- time for the assimilation to settle down from the climatological
- spread at the start. <em class=code>time_to_skip</em> is an
- amount of time AFTER the first edge of the first bin.<br />
- Default: 0, 0, 1, 0, 0, 0</TD></TR>
+<TR><TD> time_to_skip </TD>
+ <TD> integer, dimension(6) </TD>
+ <TD>Time span at the beginning to skip when calculating vertical profiles of
+rms error and bias. The year and month values <em>must</em> be zero. Useful
+because it takes some time for the assimilation to settle down from the
+climatological spread at the start. <em class=code>time_to_skip</em> is an
+amount of time AFTER the first edge of the first bin.
+</TD></TR>
-<TR><!--contents--><TD valign=top> max_num_bins </TD>
- <!-- type --><TD valign=top> integer </TD>
- <!--descript--><TD>This provides an alternative way to declare the
- <em class=code>last_bin_center</em>.
- If <em class=code>max_num_bins</em> is set to '10', only
- 10 timesteps will be output - provided
- <em class=code>last_bin_center</em> is set to some later date.
- <br />
- Default: 1000000</TD></TR>
+<TR><TD> max_num_bins </TD>
+ <TD> integer </TD>
+ <TD>This provides an alternative way to declare the <em
+class=code>last_bin_center</em>. If <em class=code>max_num_bins</em> is set
+to '10', only 10 timesteps will be output - provided <em class=code>last_bin_center</em>
+is set to some later date.
+</TD></TR>
-<TR><!--contents--><TD valign=top> plevel </TD>
- <!-- type --><TD valign=top> integer, <em class="new">dimension(50)</em></TD>
- <!--descript--><TD>The midpoints defining the pressure levels for the
- vertical binning. There is no specification of bin width - a
- continuum is used. If a single midpoint value is entered, the
- bin edges are +/- 10% of the midpoint value. If you'd like to
- change that ... see the routine
- <em class="routine">Rmidpoints2edges()</em>.<br />
- Default: (1000, 925, 850, 700, 500, 400, 300,
- 250, 200, 150, 100)</TD></TR>
+<TR><TD> plevel </TD>
+ <TD> integer, <em class="new">dimension(50)</em> </TD>
+ <TD>The midpoints defining the pressure levels for the vertical binning.
+There is no specification of bin width - a continuum is used. If a single
+midpoint value is entered, the bin edges are +/- 10% of the midpoint value.
+If you'd like to change that see the routine <em class="routine">Rmidpoints2edges()</em>.
+</TD></TR>
-<TR><!--contents--><TD valign=top> hlevel </TD>
- <!-- type --><TD valign=top> integer, <em class="new">dimension(50)</em></TD>
- <!--descript--><TD>Same, but for observations that have height(m) as the
- vertical coordinate.<br />
- Default: (1000, 2000, 3000, 4000, 5000, 6000,
- 7000, 8000, 9000, 10000, 11000)</TD></TR>
+<TR><TD> hlevel </TD>
+ <TD> integer, <em class="new">dimension(50)</em> </TD>
+ <TD>Same, but for observations that have height(m) as the vertical coordinate.
+</TD></TR>
-<TR><!--contents--><TD valign=top> mlevel </TD>
- <!-- type --><TD valign=top> integer, <em class="new">dimension(50)</em></TD>
- <!--descript--><TD>Same, but for observations on model level
- (good luck getting them).<br />
- Default: (1, 2, 3, 4, 5, 6, 7, 8, 9, 10)</TD></TR>
+<TR><TD> mlevel </TD>
+ <TD> integer, <em class="new">dimension(50)</em> </TD>
+ <TD>Same, but for observations on model level
+</TD></TR>
-<TR><!--contents--><TD valign=top> rat_cri </TD>
- <!-- type --><TD valign=top> real </TD>
- <!--descript--><TD>Ratio of 'distance' of the ensemble mean to the observation
- in terms of the standard deviation of the ensemble and
- observational error.<br />
- <em class="code">abs(prior_mean-obsval) / sqrt(prior_spread+obs_error_variance)</em><br />
- Since we generally don't have all the ensemble members (in the
- <em class="file">obs_seq.final</em> file) we cannot
- calculate the covariance term that should be in the denominator,
- so it is not really the normalized distance. If this ratio is
- larger than <em class="code">rat_cri</em> then the observation
- <em class="removed">is suspect and will be ignored</em> will
- simply be counted in <b>NbadIZ</b>.
- A histogram of the ratios is saved in <em
- class="file">LargeInnov.txt</em>, as are individual observations
- that have a large ratio (i.e. the outliers)<br />
- Default: 5000.0</TD></TR>
+<TR><TD> <em class=removed>rat_cri</em> </TD>
+ <TD> <em class=removed>real</em </TD>
+ <TD>No longer supported.
+</TD></TR>
-<TR><!--contents--><TD valign=top> input_qc_threshold </TD>
- <!-- type --><TD valign=top> real </TD>
- <!--descript--><TD>Observations with quality control values greater than this
- <em class="removed">will be excluded from the diagnostics</em>
- will be counted in <b>NbadQC</b>.<br />
- Default: 4.0</TD></TR>
+<TR><TD> input_qc_threshold </TD>
+ <TD> real </TD>
+ <TD>Observations with quality control values greater than this
+<em class="removed">will be excluded from the diagnostics</em> will be counted in
+<b>NbadQC</b>.
+</TD></TR>
-<TR><!--contents--><TD valign=top> Nregions </TD>
- <!-- type --><TD valign=top> integer </TD>
- <!--descript--><TD>Number of regions of the globe for which you'd like
- obs space diagnostics. Must be between [1,50].<br />
- Default: 4</TD></TR>
+<TR><TD> Nregions </TD>
+ <TD> integer </TD>
+ <TD>Number of regions of the globe for which obs space diagnostics
+are computed separately. Must be between [1,50].
+</TD></TR>
-<TR><!--contents--><TD valign=top> lonlim1 </TD>
- <!-- type --><TD valign=top> real, <em class="new">dimension(50)</em></TD>
- <!--descript--><TD>Westernmost longitudes of each of the regions.<br />
- Default: 0.0, 0.0, 0.0, 235.0</TD></TR>
+<TR><TD> lonlim1 </TD>
+ <TD> real, <em class="new">dimension(50)</em> </TD>
+ <TD>Westernmost longitudes of each of the regions.
+</TD></TR>
-<TR><!--contents--><TD valign=top> lonlim2 </TD>
- <!-- type --><TD valign=top> real, <em class="new">dimension(50)</em></TD>
- <!--descript--><TD>Easternmost longitudes of each of the regions.
- <em class="new">If any of these values is <b>less than</b>
- the westernmost values, it defines a region that spans the
- prime meridian. No problem.</em> It is perfectly acceptable
- to specify lonlim1 = 330 , lonlim2 = 50 to identify a region
- like "Africa".<br />
- Default: 360.0, 360.0, 360.0, 295.0</TD></TR>
+<TR><TD> lonlim2 </TD>
+ <TD> real, <em class="new">dimension(50)</em> </TD>
+ <TD>Easternmost longitudes of each of the regions. <em class="new">If any of
+these values is <b>less than</b> the westernmost values, it defines a region
+that spans the prime meridian. </em> e.g. a specification of
+lonlim1 = 330 , lonlim2 = 50 would identify a region like "Africa".
+</TD></TR>
-<TR><!--contents--><TD valign=top> latlim1 </TD>
- <!-- type --><TD valign=top> real, <em class="new">dimension(50)</em></TD>
- <!--descript--><TD>Southernmost latitudes of the regions.<br />
- Default: 20.0, -80.0, -20.0, 25.0</TD></TR>
+<TR><TD> latlim1 </TD>
+ <TD> real, <em class="new">dimension(50)</em> </TD>
+ <TD>Southernmost latitudes of the regions.
+</TD></TR>
-<TR><!--contents--><TD valign=top> latlim2 </TD>
- <!-- type --><TD valign=top> real, <em class="new">dimension(50)</em></TD>
- <!--descript--><TD>Northernmost latitudes of the regions.<br />
- Default: 80.0, -20.0, 20.0, 55.0</TD></TR>
+<TR><TD> latlim2 </TD>
+ <TD> real, <em class="new">dimension(50)</em> </TD>
+ <TD>Northernmost latitudes of the regions.
+</TD></TR>
-<TR><!--contents--><TD valign=top> reg_names </TD>
- <!-- type --><TD valign=top> character(len=129), <em class="new">dimension(50)</em> </TD>
- <!--descript--><TD>Array of names for the regions to be analyzed.<br />
- Default: 'Northern Hemisphere','Southern Hemisphere',
- 'Tropics','North America'</TD></TR>
+<TR><TD> reg_names </TD>
+ <TD> character(len=129), <em class="new">dimension(50)</em> </TD>
+ <TD>Array of names for the regions to be analyzed. Will be used
+for plot titles.
+</TD></TR>
-<TR><!--contents--><TD valign=top> print_mismatched_locs </TD>
- <!-- type --><TD valign=top> logical </TD>
- <!--descript--><TD>Print instances where U and V "pairs" don't have the
- same location.<br />
- Default: .false. </TD></TR>
+<TR><TD> print_mismatched_locs </TD>
+ <TD> logical </TD>
+ <TD>Print instances where U and V "pairs" don't have the same location.
+</TD></TR>
-<TR><!--contents--><TD valign=top><em class=removed>print_obs_locations</em> </TD>
- <!-- type --><TD valign=top><em class=removed>logical </em> </TD>
- <!--descript--><TD><em class=removed>Create additional output files with the lat/lon
- location of each observation, obs type, and QC value. These
- files are named <em
- class="file">observation_locations.xxx.dat</em> and may be
- plotted with <em
- class="file">DART/diagnostics/matlab/plot_observation_locations.m</em>.
- There is one output file per temporal bin.
- For pathological reasons, these files cannot exist prior to execution.
- If they do, an error will result, and execution halts..
- <br />
- Default: .false.</em> <strong>To plot the locations of observations,</strong>
- please convert your observation sequence file to netCDF with
- <a href="../../obs_sequence/obs_seq_to_netcdf.html">obs_seq_to_netcdf</a> and then
- plot with
- <a href="../../diagnostics/matlab/plot_obs_netcdf.m">plot_obs_netcdf</a>
- </TD></TR>
+<TR><TD><em class=removed>print_obs_locations</em> </TD>
+ <TD><em class=removed>logical </em> </TD>
+ <TD>No longer supported.
+<strong>To plot the locations of observations,</strong> please convert
+your observation sequence file to netCDF with
+<a href="../../obs_sequence/obs_seq_to_netcdf.html">obs_seq_to_netcdf</a>
+and then plot with
+<a href="../../diagnostics/matlab/plot_obs_netcdf.m">plot_obs_netcdf</a>
+</TD></TR>
-<TR><!--contents--><TD valign=top> verbose </TD>
- <!-- type --><TD valign=top> logical </TD>
- <!--descript--><TD>Print extra info about the obs_diag run.<br />
- Default: .false. </TD></TR>
+<TR><TD> verbose </TD>
+ <TD> logical </TD>
+ <TD>Print extra info about the obs_diag run.
+</TD></TR>
-<TR><!--contents--><TD valign=top>outliers_in_histogram</TD>
- <!-- type --><TD valign=top> logical </TD>
- <!--descript--><TD>Determines whether or not to use observations that
- have been rejected by the outlier threshhold mechanism in the
- calculation of the rank histogram.<br />
- Default: .false. </TD></TR>
+<TR><TD> outliers_in_histogram </TD>
+ <TD> logical </TD>
+ <TD>Determines whether or not to use observations that have been rejected by
+the outlier threshhold mechanism in the calculation of the rank histogram.
+</TD></TR>
-</TABLE>
+</TBODY>
+</TABLE>
</div>
+
<br />
+<br />
<!--==================================================================-->
<A NAME="Modules"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>OTHER MODULES USED</H2>
<PRE>
obs_sequence_mod
@@ -584,7 +554,7 @@
<!--==================================================================-->
<A NAME="FilesUsed"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>FILES</H2>
<UL><LI><em class="file">input.nml</em> is used for
<em class="code">obs_diag_nml</em></LI>
@@ -755,7 +725,7 @@
<!--==================================================================-->
<A NAME="Usage"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>USAGE</H2>
<P>
@@ -919,7 +889,7 @@
<!--==================================================================-->
<A NAME="References"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>REFERENCES</H2>
<ol>
<li> none </li>
@@ -930,7 +900,7 @@
<!--==================================================================-->
<A NAME="Errors"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>ERROR CODES and CONDITIONS</H2>
<div class=errors>
@@ Diff output truncated at 40000 characters. @@
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