[Dart-dev] [6281] DART/trunk: updates to the html files to fix syntax problems reported
nancy at ucar.edu
nancy at ucar.edu
Fri Jun 28 15:30:37 MDT 2013
Revision: 6281
Author: nancy
Date: 2013-06-28 15:30:36 -0600 (Fri, 28 Jun 2013)
Log Message:
-----------
updates to the html files to fix syntax problems reported
by the 'tidy' html syntax checker. also reformatted some
of the namelists and tables.
Modified Paths:
--------------
DART/trunk/assim_tools/assim_tools_mod.html
DART/trunk/diagnostics/oned/obs_diag.html
DART/trunk/ensemble_manager/ensemble_manager_mod.html
DART/trunk/location/oned/location_mod.html
DART/trunk/models/CESM/dart_to_cesm.html
DART/trunk/models/NCOMMAS/dart_to_ncommas.html
DART/trunk/models/NCOMMAS/model_mod.html
DART/trunk/models/NCOMMAS/ncommas_to_dart.html
DART/trunk/models/POP/dart_to_pop.html
DART/trunk/models/clm/clm_to_dart.html
DART/trunk/models/clm/dart_to_clm.html
DART/trunk/models/gitm/model_mod.html
DART/trunk/models/mpas_atm/model_mod.html
DART/trunk/models/mpas_ocn/model_mod.html
DART/trunk/obs_sequence/obs_seq_verify.html
DART/trunk/observations/AIRS/AIRS.html
DART/trunk/observations/Ameriflux/level4_to_obs.html
DART/trunk/observations/COSMOS/COSMOS_development.html
DART/trunk/observations/COSMOS/COSMOS_to_obs.html
DART/trunk/observations/MIDAS/MIDAS_to_obs.html
DART/trunk/observations/quikscat/QuikSCAT.html
DART/trunk/observations/snow/snow_to_obs.html
DART/trunk/observations/tpw/tpw.html
DART/trunk/random_seq/random_seq_mod.html
-------------- next part --------------
Modified: DART/trunk/assim_tools/assim_tools_mod.html
===================================================================
--- DART/trunk/assim_tools/assim_tools_mod.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/assim_tools/assim_tools_mod.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -312,7 +312,8 @@
<div>
-<TABLE border=0 cellpadding=10 width=100% summary='assim_tools namelist description'>
+<TABLE border=0 cellpadding=10 width=100%
+ summary='assim_tools namelist description'>
<THEAD align=left>
<TR><TH> Item </TH>
<TH> Type </TH>
@@ -518,7 +519,7 @@
<HR>
<H2>PUBLIC INTERFACES</H2>
-<TABLE>
+<TABLE summary='public interface list'>
<TR><TD><em class=call>use assim_tools_mod, only : </em></TD>
<TD><A HREF="#filter_assim">filter_assim</A></TD></TR>
</TABLE>
@@ -636,7 +637,7 @@
<A NAME="FilesUsed"></A>
<HR>
<H2>FILES</H2>
-<TABLE border=0>
+<TABLE border=0 summary='files used by this module'>
<TR><TH>filename</TH>
<TH>purpose</TH></TR>
<TR><TD>input.nml</TD>
@@ -703,7 +704,8 @@
<HR>
<H2>ERROR CODES and CONDITIONS</H2>
<div class=errors>
-<TABLE border=1 cellspacing=1 cellpadding=10 width=100%>
+<TABLE border=1 cellspacing=1 cellpadding=10 width=100%
+ summary='error codes and conditions'>
<TR><TH>Routine</TH><TH>Message</TH><TH>Comment</TH></TR>
<TR><!-- routine --><TD VALIGN=top>assim_tools_init</TD>
Modified: DART/trunk/diagnostics/oned/obs_diag.html
===================================================================
--- DART/trunk/diagnostics/oned/obs_diag.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/diagnostics/oned/obs_diag.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -226,8 +226,10 @@
The 1D locations are conceived as the distance around a unit sphere.
An observation with a location exactly ON a region boundary cannot
'count' for both regions. The logic used to resolve this is:
+</P>
<blockquote>if((lon ≥ lon1) .and. (lon < lon2)) keeper = .true.</blockquote>
<br />
+<P>
Consequently, if you want to include an observation precisely AT 1.0, (for example), you need to specify something a little larger than 1.0.<br /><br />
You can only specify <strong>either</strong>
<em class="code">obs_sequence_name</em>
Modified: DART/trunk/ensemble_manager/ensemble_manager_mod.html
===================================================================
--- DART/trunk/ensemble_manager/ensemble_manager_mod.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/ensemble_manager/ensemble_manager_mod.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -163,12 +163,10 @@
may improve performance.
</P>
-<P>
- <table width="100%"><tr>
- <td><a href="../doc/html/comm_pattern96.png"><img src="../doc/html/comm_pattern96.png" width="400"></a>
- <td><a href="../doc/html/comm_pattern512.png"><img src="../doc/html/comm_pattern512.png" width="400"></a>
- </table>
-</P>
+<table width="100%" summary='communication patterns'><tr>
+<td><a href="../doc/html/comm_pattern96.png"><img src="../doc/html/comm_pattern96.png" width="400"></a>
+<td><a href="../doc/html/comm_pattern512.png"><img src="../doc/html/comm_pattern512.png" width="400"></a>
+</table>
</div>
<br>
Modified: DART/trunk/location/oned/location_mod.html
===================================================================
--- DART/trunk/location/oned/location_mod.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/location/oned/location_mod.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -75,6 +75,7 @@
However, if the model interface code wants to intercept and alter
the default behavior of the get_close routines, they are able to.
The correct usage of the <em class=code>get_close</em> routines is as follows:
+</P>
<pre>
<em class=code>
call get_close_maxdist_init() ! must be called before get_close_obs_init()
@@ -85,6 +86,7 @@
call get_close_obs_destroy()
</em>
</pre>
+<P>
Regardless of the fact that the names include the string 'obs', they are
intended for use with any group of locations in the system, frequently
state vector items or observations, but any location is acceptable.
Modified: DART/trunk/models/CESM/dart_to_cesm.html
===================================================================
--- DART/trunk/models/CESM/dart_to_cesm.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/models/CESM/dart_to_cesm.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -2,13 +2,13 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<HTML>
<HEAD>
-<TITLE>program dart_to_pop</TITLE>
+<TITLE>program dart_to_CESM</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<H1>PROGRAM <em class=program>dart_to_pop</em></H1>
+<H1>PROGRAM <em class=program>dart_to_CESM</em></H1>
<table border=0 summary="" cellpadding=5>
<tr>
@@ -35,61 +35,23 @@
<H2>Overview</H2>
<P>
- <em class=program>dart_to_pop</em> is the program that updates a POP
- netCDF-format restart file (usually <em class=file>pop.r.nc</em>)
- with the state information contained in a DART output/restart file
- (e.g. <em class=file>perfect_ics, filter_ics, ... </em>).
- Only the CURRENT values in the POP restart file will be updated:
- specifically -
- <em class=code>SALT_CUR</em>,
- <em class=code>TEMP_CUR</em>,
- <em class=code>UVEL_CUR</em>,
- <em class=code>VVEL_CUR</em>, and
- <em class=code>PSURF_CUR</em>. It is <strong>necessary</strong> to
- perform a forward euler timestep since the '<em class=code>_OLD</em>'
- variables are untouched by DART. The DART model time is compared to the
- time in the POP restart file. If they are not identical, the program
- issues an error message and aborts.
- <br />
- <br />
- From the user perspective, most of the time
- <em class=program>dart_to_pop</em> will be used on DART files that
- have a header containing one time stamp followed by the model state.
- <br />
- <br />
- The <a href=#Namelist>dart_to_pop_nml</a> namelist allows
- <em class=program>dart_to_pop</em> to read the
- <em class=file>assim_model_state_ic</em> files that have
- <em class=italic>two</em> timestamps in the header. These files are
- temporarily generated when DART is used to advance the model.
- One timestamp is the 'advance_to' time, the other is the 'valid_time'
- of the model state. In this case, a namelist for POP (called
- <em class=file>pop_in.DART</em>) is written that contains the
- <em class=code>&time_manager_nml</em> settings appropriate to
- advance POP to the time requested by DART. The repository version
- of the <em class=program>advance_model.csh</em> script has a section
- to ensure the proper DART namelist settings for this case.
- <br />
- <br />
- Conditions required for successful execution of <em class=program>dart_to_pop</em>:
+<em class=program>dart_to_xxx</em> are a set of programs that
+convert from DART state vector format (a 1D fortran array) to the
+native file(s) a model needs to advance. See the documentation
+for each of the individual model pages for more information
+on the details of each converter:
</P>
-
<UL>
- <LI>a valid <em class=file>input.nml</em> namelist file for DART</LI>
- <LI>a DART file (typically <em class=file>filter_restart.xxxx</em> or
- <em class=file>filter_ics.xxxx</em>)</LI>
- <LI>a valid <em class=file>pop_in</em> namelist file for POP</LI>
- <LI>the POP geometry files mentioned in the <em class=file>pop_in</em> namelist file</LI>
- <LI>a POP restart file (typically <em class=file>pop.r.nc</em>).
- Keep in mind that the DART/POP interface requires the existence of
- a <em class=file>pop.r.nc</em> to harvest the geometry dimensions.</LI>
+<LI> <a href="../cam/dart_to_cam.html">dart_to_cam</a></LI>
+<LI> <a href="../POP/dart_to_pop.html">dart_to_pop</a></LI>
+<LI> <a href="../clm/dart_to_clm.html">dart_to_clm</a></LI>
</UL>
<P>
Since this program is called repeatedly for every ensemble member,
we have found it convenient to link the DART input file
-to the default input filename (<em class=file>dart.ic</em>). The same
-thing goes true for the POP output filename <em class=file>pop.r.nc</em>.
+to the default input filename, e.g. (<em class=file>dart.ic</em>).
+The same thing is true for the model output filenames.
</P>
<!--==================================================================-->
@@ -99,58 +61,39 @@
<A NAME="Namelist"></A>
<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.
+<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.
-The namelist declaration is:
+enclosed in quotes to prevent them from
+prematurely terminating the namelist.
</P>
+
<div class=namelist>
<pre>
-<em class=call>namelist / dart_to_pop_nml / </em> dart_to_pop_input_file, advance_time_present
+&dart_to_cam_nml
+ dart_to_cam_input_file = 'dart_ics',
+ dart_to_cam_output_file = 'caminput.nc',
+ advance_time_present = .true.,
+ /
+
+&dart_to_pop_nml
+ dart_to_pop_input_file = 'dart.ic',
+ advance_time_present = .false.
+ /
+
+&dart_to_clm_nml
+ dart_to_clm_output_file = 'dart_restart',
+ advance_time_present = .false.,
+ /
</pre>
</div>
-<div class=indent1>
-<!-- Description -->
-
-<P>
-This namelist is always read from a file called <em class=file>input.nml</em>.
+<P> See each of the model html pages for details on the
+namelist defaults and values.
</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>
-
-<TR><!--contents--><TD valign=top>dart_to_pop_input_file </TD>
- <!-- type --><TD valign=top>character(len=128) </TD>
- <!--descript--><TD>The name of the DART file containing the model state
- to insert into the POP restart file.
- <em class=units>[default: 'dart.ic']</em></TD></TR>
-
-<TR><!--contents--><TD valign=top>advance_time_present</TD>
- <!-- type --><TD valign=top>logical</TD>
- <!--descript--><TD>switch to control the ability to read a DART file
- containing TWO timestamps in the file header.
- If you are converting a DART initial conditions or
- restart file - this should be
- <em class=code>.false.</em> - these files have a
- single timestamp describing the valid time of the
- model state.
- <br />
- <br />
- If <em class=code>.true.</em>, TWO timestamps are
- expected to be the DART file header. In this case, a
- namelist for POP (called <em class=file>pop_in.DART</em>)
- is created that contains the
- <em class=code>&time_manager_nml</em> settings
- appropriate to advance POP to the time
- requested by DART.
- <em class=units>[default: .false.]</em></TD></TR>
-</TABLE>
-
-</div>
<br />
<!--==================================================================-->
@@ -181,14 +124,14 @@
<H2>FILES Read</H2>
<UL><LI>DART initial conditions/restart file; e.g. <em class=file>filter_ic</em></LI>
<LI>DART namelist file; <em class=file>input.nml</em></LI>
- <LI>POP namelist file; <em class=file>pop_in</em></LI>
- <LI>POP geometry files specified in <em class=file>pop_in</em></LI>
- <LI>POP restart file <em class=file>pop.r.nc</em> (to get grid values)</LI>
+ <LI>model namelist file</LI>
+ <LI>any model geometry files needed</LI>
+ <LI>possibly model restart file (to get grid values)</LI>
</UL>
<H2>FILES Written</H2>
-<UL><LI>POP restart file; <em class=file>pop.r.nc</em></LI>
- <LI>POP namelist file; <em class=file>pop_in.DART</em></LI>
+<UL><LI>model restart file</LI>
+ <LI>model namelist file</LI>
</UL>
@@ -206,7 +149,7 @@
The Data Assimilation Research Testbed: A Community Facility.
<span style="font-style: italic;">Bull. Amer. Meteor. Soc.</span>,
<span style="font-weight: bold;">90</span>, 1283-1296.<br />
- <a href="http://ams.allenpress.com/perlserv/?doi=10.1175%2F2009BAMS2618.1&request=get-abstract">DOI: 10.1175/2009BAMS2618.1</a></li>
+ <a href="http://ams.allenpress.com/perlserv/?doi=10.1175%2F2009BAMS2618.1&request=get-abstract">DOI: 10.1175/2009BAMS2618.1</a></li>
</ul>
<br />
Modified: DART/trunk/models/NCOMMAS/dart_to_ncommas.html
===================================================================
--- DART/trunk/models/NCOMMAS/dart_to_ncommas.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/models/NCOMMAS/dart_to_ncommas.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -167,7 +167,7 @@
dimension(160) </TD>
<!--descript--><TD>The list of variable names in the NCOMMAS restart file to use to
create the DART state vector and their corresponding DART kind.
- <em class=units>[default: <em>see example below</em>]</em></TD></TR>
+ <em class=units>[default: see example below]</em></TD></TR>
</TABLE>
<pre>
&ncommas_vars_nml
Modified: DART/trunk/models/NCOMMAS/model_mod.html
===================================================================
--- DART/trunk/models/NCOMMAS/model_mod.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/models/NCOMMAS/model_mod.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -42,7 +42,7 @@
make a namelist-controlled set of variables to be included in the DART state vector.
Each variable must also correspond to a DART "KIND"; required for the DART
interpolate routines. For example,
-<P>
+</P>
<pre>&ncommas_vars_nml
ncommas_state_variables = 'U', 'KIND_U_WIND_COMPONENT',
'V', 'KIND_V_WIND_COMPONENT',
Modified: DART/trunk/models/NCOMMAS/ncommas_to_dart.html
===================================================================
--- DART/trunk/models/NCOMMAS/ncommas_to_dart.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/models/NCOMMAS/ncommas_to_dart.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -126,7 +126,7 @@
dimension(160) </TD>
<!--descript--><TD>The list of variable names in the NCOMMAS restart file to use to
create the DART state vector and their corresponding DART kind.
- <em class=units>[default: <em>see example below</em>]</em></TD></TR>
+ <em class=units>[default: see example below]</em></TD></TR>
</TABLE>
<pre>
&ncommas_vars_nml
Modified: DART/trunk/models/POP/dart_to_pop.html
===================================================================
--- DART/trunk/models/POP/dart_to_pop.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/models/POP/dart_to_pop.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -206,7 +206,7 @@
The Data Assimilation Research Testbed: A Community Facility.
<span style="font-style: italic;">Bull. Amer. Meteor. Soc.</span>,
<span style="font-weight: bold;">90</span>, 1283-1296.<br />
- <a href="http://ams.allenpress.com/perlserv/?doi=10.1175%2F2009BAMS2618.1&request=get-abstract">DOI: 10.1175/2009BAMS2618.1</a></li>
+ <a href="http://ams.allenpress.com/perlserv/?doi=10.1175%2F2009BAMS2618.1&request=get-abstract">DOI: 10.1175/2009BAMS2618.1</a></li>
</ul>
<br />
Modified: DART/trunk/models/clm/clm_to_dart.html
===================================================================
--- DART/trunk/models/clm/clm_to_dart.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/models/clm/clm_to_dart.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -51,7 +51,6 @@
<UL>
<LI>a valid <em class=file>input.nml</em> namelist file for DART</LI>
<LI>the CLM history file mentioned in the <em class=file>input.nml</em> <em class=code>&model_nml:clm_history_filename</em> variable.</LI>
-</UL>
<LI>the CLM restart file mentioned in the <em class=file>input.nml</em> <em class=code>&model_nml:clm_restart_filename</em> variable.</LI>
</UL>
@@ -124,7 +123,7 @@
dimension(160) </TD>
<!--descript--><TD>The list of variable names in the CLM restart file to use to
create the DART state vector and their corresponding DART kind.
- <em class=units>[default: <em>see example below</em>]</em></TD></TR>
+ <em class=units>[default: see example below]</em></TD></TR>
</TABLE>
<pre>
&clm_vars_nml
Modified: DART/trunk/models/clm/dart_to_clm.html
===================================================================
--- DART/trunk/models/clm/dart_to_clm.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/models/clm/dart_to_clm.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -163,7 +163,7 @@
dimension(160) </TD>
<!--descript--><TD>The list of variable names in the CLM restart file to use to
create the DART state vector and their corresponding DART kind.
- <em class=units>[default: <em>see example below</em>]</em></TD></TR>
+ <em class=units>[default: see example below]</em></TD></TR>
</TABLE>
<pre>
&clm_vars_nml
Modified: DART/trunk/models/gitm/model_mod.html
===================================================================
--- DART/trunk/models/gitm/model_mod.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/models/gitm/model_mod.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -35,14 +35,18 @@
<H1>MODULE model_mod (GITM)</H1>
<P>The <strong>GITM </strong> interface for
- <strong>Data Assimilation Research Testbed (DART)</strong> is under development.
- <br />
- <br />
- Since GITM uses binary files for their restart mechanisms, it was really difficult to
- make a namelist-controlled set of variables to be included in the DART state vector.
- Each variable must also correspond to a DART "KIND"; required for the DART
- interpolate routines. For example, this is nowhere close to being correct:
+<strong>Data Assimilation Research Testbed (DART)</strong> is under development.
+</P>
+<br />
+<br />
<P>
+GITM uses binary files for their restart mechanisms, so no metadata is available
+to confirm the number and order of fields in the file. Care must be used
+to make sure the namelist-controlled set of variables to be included in the
+DART state vector is consistent with the restart files.
+Each variable must also correspond to a DART "KIND"; required for the DART
+interpolate routines. For example, this is nowhere close to being correct:
+</P>
<pre>&gitm_vars_nml
gitm_state_variables = 'Temperature', 'KIND_TEMPERATURE',
'eTemperature', 'KIND_TEMPERATURE',
@@ -59,8 +63,10 @@
Since DART is an ensemble algorithm, there are multiple restart files for a
single restart time: one for each ensemble member. Creating the initial ensemble
of states is an area of active research.
+</P>
<br />
<br />
+<P>
DART reads grid information for GITM from several sources. The <em class=file>UAM.in</em>
file specifies the number of latitudes/longitudes per block, and the number of blocks comes
from the <em class=file>GITM2/src/ModSize.f90</em> module.
@@ -113,12 +119,12 @@
<a name="conversions"></a>
<div class=indent1>
<h3>Converting between DART files and GITM restart files</h3>
- <P>is not quite straighforward. Given the namelist mechanism for
- determining the state variables and the fact that GITM netCDF
- files do not exist, - everything that is needed
- is not readily determined.
+ <P>The binary GITM files contain no metadata, so care is needed when
+ converting between DART state variables and GITM files.
+ </P>
<br />
<br />
+ <P>
There are two programs - both require the list of GITM variables to use in
the DART state vector: the
<em class="code">gitm_vars_nml</em> namelist in the
@@ -152,9 +158,9 @@
</div>
-<H1>Everything below here is complete fiction</H1>
-<H1>Everything below here is complete fiction</H1>
-<H1>Everything below here is complete fiction</H1>
+<H1>Everything below here has not been reviewed yet for GITM</H1>
+<H1>Everything below here has not been reviewed yet for GITM</H1>
+<H1>Everything below here has not been reviewed yet for GITM</H1>
<a name="InitialEnsemble"></a>
Modified: DART/trunk/models/mpas_atm/model_mod.html
===================================================================
--- DART/trunk/models/mpas_atm/model_mod.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/models/mpas_atm/model_mod.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -36,13 +36,15 @@
<P>The <strong>MPAS ATM </strong> interface for
<strong>Data Assimilation Research Testbed (DART)</strong> is under development.
+</P>
<br />
<br />
+<P>
Since MPAS ATM uses netcdf files for their restart mechanism,
a namelist-controlled set of variables is used to build the DART state vector.
Each variable must also correspond to a DART "KIND"; required for the DART
interpolate routines. For example:
-<P>
+</P>
<pre>&mpas_vars_nml
mpas_state_variables = 'uReconstructZonal', 'KIND_U_WIND_COMPONENT',
'uReconstructMeridional', 'KIND_V_WIND_COMPONENT',
@@ -153,7 +155,7 @@
<a name="conversions"></a>
<div class=indent1>
<h3>Converting between DART files and MPAS analysis files</h3>
- <P>is relatively straighforward. Given the namelist mechanism for
+ <P>is relatively straightforward. Given the namelist mechanism for
determining the state variables and the MPAS history netCDF
files exist, - everything that is needed is readily determined.
<br />
Modified: DART/trunk/models/mpas_ocn/model_mod.html
===================================================================
--- DART/trunk/models/mpas_ocn/model_mod.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/models/mpas_ocn/model_mod.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -42,7 +42,7 @@
a namelist-controlled set of variables is used to build the DART state vector.
Each variable must also correspond to a DART "KIND"; required for the DART
interpolate routines. For example:
-<P>
+</P>
<pre>&mpas_vars_nml
mpas_state_variables = 'uReconstructZonal', 'KIND_U_WIND_COMPONENT',
'uReconstructMeridional', 'KIND_V_WIND_COMPONENT',
Modified: DART/trunk/obs_sequence/obs_seq_verify.html
===================================================================
--- DART/trunk/obs_sequence/obs_seq_verify.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/obs_sequence/obs_seq_verify.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -309,7 +309,7 @@
called <em class=file>obs_seq.forecast.2008060818</em>.
<br />
<br />
-Just to reiterate the example, both namelists for <em class=program></em>
+Just to reiterate the example, both namelists for <em class=program>obs_seq_coverage</em>
and <em class=program>obs_seq_verify</em> are provided below.
</p>
<div class=routine>
Modified: DART/trunk/observations/AIRS/AIRS.html
===================================================================
--- DART/trunk/observations/AIRS/AIRS.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/observations/AIRS/AIRS.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -379,7 +379,7 @@
</pre>
</div>
-<P> </P>
+<br />
<div>
<TABLE border=0 cellpadding=3 width=100%>
Modified: DART/trunk/observations/Ameriflux/level4_to_obs.html
===================================================================
--- DART/trunk/observations/Ameriflux/level4_to_obs.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/observations/Ameriflux/level4_to_obs.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -50,7 +50,7 @@
The AmeriFlux Level 4 products are recorded using the local time.
DART observation sequence files use GMT. For more information about
AmeriFlux data products, go to
-<a href=" http://public.ornl.gov/ameriflux/dataproducts.shtml">
+<a href="http://public.ornl.gov/ameriflux/dataproducts.shtml">
http://public.ornl.gov/ameriflux/dataproducts.shtml</a>.
</P>
@@ -85,88 +85,96 @@
<A NAME="Namelist"></A>
<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.
+<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 /level4_to_obs_nml/ </em> text_input_file, obs_out_file, year, &
- timezoneoffset, latitude, longitude, elevation, inst_height, maxgoodqc, verbose
+&level4_to_obs_nml
+ text_input_file = 'textdata.input',
+ obs_out_file = 'obs_seq.out',
+ year = 2000,
+ timezoneoffset = 0,
+ latitude = 0,
+ longitude = 0,
+ elevation = 0,
+ flux_height = 0,
+ maxgoodqc = 3,
+ verbose = .false.
+ /
</pre>
</div>
-<H3 class=indent1>Discussion</H3>
+<div>
-<P>This namelist is read in a file called <em class=file>input.nml</em>.
-</P>
+<TABLE border=0 cellspacing=10 width=100% summary='level4_to_obs namelist description'>
+<THEAD align=left>
+<TR><TH>Contents </TH>
+ <TH>Type </TH>
+ <TH>Description </TH></TR>
+</THEAD>
-<TABLE border=0 cellspacing=10 width=100%>
-<TR><TH align=left>Contents </TH>
- <TH align=left>Type </TH>
- <TH align=left>Description </TH></TR>
-
-<TR><!--contents--><TD valign=top> text_input_file </TD>
- <!-- type --><TD valign=top> character(len=128) </TD>
+<TBODY valign=top>
+<TR><!--contents--><TD> text_input_file </TD>
+ <!-- type --><TD> character(len=128) </TD>
<!--descript--><TD>Name of the Level 4 ASCII file of comma-separated values.
- This may be a relative or absolute filename.<br />
- Default: 'textdata.input'</TD></TR>
+ This may be a relative or absolute filename. </TD></TR>
-<TR><!--contents--><TD valign=top> obs_out_file </TD>
- <!-- type --><TD valign=top> character(len=128) </TD>
- <!--descript--><TD>Name of the output observation sequence file.<br />
- Default: 'obs_seq.out'</TD></TR>
+<TR><!--contents--><TD> obs_out_file </TD>
+ <!-- type --><TD> character(len=128) </TD>
+ <!--descript--><TD>Name of the output observation sequence file.</TD></TR>
-<TR><!--contents--><TD valign=top> year </TD>
- <!-- type --><TD valign=top> integer </TD>
- <!--descript--><TD>The year of the observations in the Level 4 text file.<br />
- Default: none </TD></TR>
+<TR><!--contents--><TD> year </TD>
+ <!-- type --><TD> integer </TD>
+ <!--descript--><TD>The year of the observations in the Level 4 text file. </TD></TR>
-<TR><!--contents--><TD valign=top> timezoneoffset </TD>
- <!-- type --><TD valign=top> real </TD>
+<TR><!--contents--><TD> timezoneoffset </TD>
+ <!-- type --><TD> real </TD>
<!--descript--><TD>the time zone offset (in hours) of the station.
The tower observation times are local time, we need to convert them
- to GMT.<br />
- Default: none </TD></TR>
+ to GMT. </TD></TR>
-<TR><!--contents--><TD valign=top> latitude </TD>
- <!-- type --><TD valign=top> real </TD>
- <!--descript--><TD>Latitude (in degrees N) of the tower.<br />
- Default: none</TD></TR>
+<TR><!--contents--><TD> latitude </TD>
+ <!-- type --><TD> real </TD>
+ <!--descript--><TD>Latitude (in degrees N) of the tower. </TD></TR>
-<TR><!--contents--><TD valign=top> longitude </TD>
- <!-- type --><TD valign=top> real </TD>
+<TR><!--contents--><TD> longitude </TD>
+ <!-- type --><TD> real </TD>
<!--descript--><TD>Longitude (in degrees E) of the tower.
For internal consistency, DART uses longitudes in the range [0,360].
- An input value of -90 will be converted to 270, for example.<br />
- Default: none</TD></TR>
+ An input value of -90 will be converted to 270, for example. </TD></TR>
-<TR><!--contents--><TD valign=top> elevation </TD>
- <!-- type --><TD valign=top> real </TD>
- <!--descript--><TD>surface elevation (in meters) of the tower.<br />
- Default: none</TD></TR>
+<TR><!--contents--><TD> elevation </TD>
+ <!-- type --><TD> real </TD>
+ <!--descript--><TD>surface elevation (in meters) of the tower. </TD></TR>
-<TR><!--contents--><TD valign=top> flux_height </TD>
- <!-- type --><TD valign=top> real </TD>
- <!--descript--><TD>height (in meters) of the flux instrument on the tower.<br />
- Default: none</TD></TR>
+<TR><!--contents--><TD> flux_height </TD>
+ <!-- type --><TD> real </TD>
+ <!--descript--><TD>height (in meters) of the flux instrument on the tower.</TD></TR>
-<TR><!--contents--><TD valign=top> maxgoodqc </TD>
- <!-- type --><TD valign=top> real </TD>
+<TR><!--contents--><TD> maxgoodqc </TD>
+ <!-- type --><TD> real </TD>
<!--descript--><TD>maximum value of any observation quality control flag to
pass through to the output observation sequence. Keep in mind that
<em class=program>filter</em> has the ability to discriminate on the
value, so there is really little to be gained by rejecting them
- during the conversion.<br />
- Default: 3</TD></TR>
+ during the conversion. </TD></TR>
-<TR><!--contents--><TD valign=top> verbose </TD>
- <!-- type --><TD valign=top> logical </TD>
+<TR><!--contents--><TD> verbose </TD>
+ <!-- type --><TD> logical </TD>
<!--descript--><TD>Print extra information during the <em class=program>level4_to_obs</em>
- execution.<br />
- Default: .false. </TD></TR>
+ execution.</TD></TR>
+</TBODY>
</TABLE>
+</div>
<!--==================================================================-->
@@ -188,7 +196,7 @@
These values are mapped as follows:
</P>
-<table width=100% cellpadding=10>
+<table width=100% cellpadding=10 summary='data products summary'>
<tr><th align=left>Level 4 units </th>
<th align=left>Level 4 variable</th>
<th align=left>description </th>
@@ -242,14 +250,18 @@
<!-- >DART units <--><td> same </td></tr>
</table>
-<P>The <em class=code>LE_fqc</em>, <em class=code>H_fqc</em>, and <em class=code>NEE_or_fMDSqc</em> variables use the following convention:<br />
+<P>The <em class=code>LE_fqc</em>, <em class=code>H_fqc</em>, and <em class=code>NEE_or_fMDSqc</em> variables use the following convention:
+</P>
<blockquote>
0 = original, 1 = category A (most reliable), 2 = category B (medium), 3 = category C (least reliable). (Refer to Reichstein et al. 2005 Global Change Biology for more information)</blockquote>
<br />
-<br />
+<P>
I am repeating the AmeriFlux <a href="http://public.ornl.gov/ameriflux/data-fair-use.shtml">
Data Fair-Use Policy</a> because I believe it is important to be a good scientific citizen:
+</P>
+<br />
+
<blockquote>
The AmeriFlux data ... are freely available and were furnished by
individual AmeriFlux scientists who encourage their use. Please kindly inform in
@@ -268,7 +280,6 @@
those publishing papers using AmeriFlux data provide reprints to the PIs providing
the data and to the data archive at the Carbon Dioxide Information Analysis Center
(CDIAC).</blockquote>
-</P>
<!--==================================================================-->
Modified: DART/trunk/observations/COSMOS/COSMOS_development.html
===================================================================
--- DART/trunk/observations/COSMOS/COSMOS_development.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/observations/COSMOS/COSMOS_development.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -296,7 +296,7 @@
</pre>
</div>
</div><!-- end of block indent -->
-<P></P><!-- needed to make 'top' align correctly -->
+<P> </P><!-- needed to make 'top' align correctly -->
<!--==================================================================-->
<!--=================== DESCRIPTION OF A NAMELIST ===================-->
@@ -305,91 +305,101 @@
<A NAME="Namelist"></A>
<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.
+<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 /COSMOS_development_nml/ </em> site_metadata_file, &
- text_input_file, obs_out_file, sitename, year, maxgoodqc, verbose
+
+
+<div class=namelist>
+<pre>
+&COSMOS_development_nml
+ site_metadata_file = 'COSMIC_parlist.nc'
+ text_input_file = 'textdata.input',
+ obs_out_file = 'obs_seq.out',
+ sitename = 'missing',
+ year = -1
+ maxgoodqc = 3,
+ verbose = .false.
+ /
</pre>
</div>
-<div class=indent1>
-<!-- Description -->
+<div>
-<P>This namelist is read in a file called <em class=file>input.nml</em>.
-</P>
+<TABLE border=0 cellpadding=3 width=100% summary='Cosmos namelist description'>
+<THEAD align=left>
+<TR><TH>Contents </TH>
+ <TH>Type </TH>
+ <TH>Description </TH></TR>
+</THEAD>
-<TABLE border=0 cellpadding=3 width=100%>
-<TR><TH align=left>Contents </TH>
- <TH align=left>Type </TH>
- <TH align=left>Description </TH></TR>
+<TBODY valign=top>
+<TR>
+ <TD>site_metadata_file</TD>
+ <TD>character(len=256)</TD>
+ <TD>The netCDF file containing the parameter values for each site.
+</TD></TR>
-<TR><!--contents--><TD valign=top>site_metadata_file</TD>
- <!-- type --><TD valign=top>character(len=256)</TD>
- <!--descript--><TD valign=top>The netCDF file containing the
- parameter values for each site.<br \>
- <em class=units>[default: 'COSMIC_parlist.nc']</em>
- </TD></TR>
+<TR>
+ <TD>text_input_file</TD>
+ <TD>character(len=128)</TD>
+ <TD>The text file containing the raw observations for each site.
+</TD></TR>
-<TR><!--contents--><TD valign=top>text_input_file</TD>
- <!-- type --><TD valign=top>character(len=128)</TD>
- <!--descript--><TD valign=top>The text file containing the
- raw observations for each site.<br \>
- <em class=units>[default: 'corcounts.txt']</em>
- </TD></TR>
+<TR>
+ <TD>obs_out_file</TD>
+ <TD>character(len=128)</TD>
+ <TD>The output observation sequence file for DART.
+</TD></TR>
-<TR><!--contents--><TD valign=top>obs_out_file</TD>
- <!-- type --><TD valign=top>character(len=128)</TD>
- <!--descript--><TD valign=top>The observation sequence file
- for DART.<br \>
- <em class=units>[default: 'obs_seq.out']</em>
- </TD></TR>
+<TR>
+ <TD>sitename</TD>
+ <TD>character(len=128)</TD>
+ <TD>The name of the site. Must match one of the site names in
+the <em class=code>site_metadata_file</em>. Case-insensitive match,
+trailing blanks ignored.
+Use <em class=input>ncdump -v sitenames COSMIC_parlist.nc</em>
+</TD></TR>
-<TR><!--contents--><TD valign=top>sitename</TD>
- <!-- type --><TD valign=top>character(len=128)</TD>
- <!--descript--><TD valign=top>The name of the site. Must match one of the
- site names in <em class=code>site_metadata_file</em>.
- Case-insensitive match, trailing blanks ignored.<br />Use
- <em class=input>ncdump -v sitenames COSMIC_parlist.nc</em><br \>
- <em class=units>[default: 'missing']</em>
- </TD></TR>
+<TR>
+ <TD>year</TD>
+ <TD>integer</TD>
+ <TD>The year of the data.
+</TD></TR>
-<TR><!--contents--><TD valign=top>year</TD>
- <!-- type --><TD valign=top>integer</TD>
- <!--descript--><TD valign=top>The year of the observation input file.
- <em class=units>[default: none]</em>
- </TD></TR>
+<TR>
+ <TD>maxgoodqc</TD>
+ <TD>integer</TD>
+ <TD>left for future implementation.
+</TD></TR>
-<TR><!--contents--><TD valign=top>maxgoodqc</TD>
- <!-- type --><TD valign=top>integer</TD>
- <!--descript--><TD valign=top>left for future implementation.
- <em class=units>[default: 3]</em>
- </TD></TR>
+<TR>
+ <TD>verbose</TD>
+ <TD>logical</TD>
+ <TD>A switch to specify the amount of run-time output.
+<em class=code>.true.</em> the most amount of output.
+<em class=code>.false.</em> the least amount of output.
+</TD></TR>
-<TR><!--contents--><TD valign=top>verbose</TD>
- <!-- type --><TD valign=top>logical</TD>
- <!--descript--><TD valign=top>The switch to specify the run-time output.
- <em class=code>.true.</em> the most amount of output.
- <em class=code>.false.</em> the least amount of output.
- <em class=units>[default: .false.]</em>
- </TD></TR>
-
+</TBODY>
</TABLE>
<H3 class=indent1>Example</H3>
<pre>
&COSMOS_development_nml
- site_metadata_file = 'COSMIC_parlist.nc',
+ site_metadata_file = '../data/COSMIC_parlist.nc',
text_input_file = 'SantaRita_corcounts.txt',
obs_out_file = 'SantaRita_obs_seq.out',
sitename = 'Santa_Rita_Creosote',
</pre>
-</div><!-- end of indent1 -->
+</div>
<!--==================================================================-->
<!-- References. -->
@@ -440,8 +450,6 @@
<li>Implement a QC encoding that reflects the uncertainty of the measurement.
Presently, all Level 2 data have an incoming QC of 1.</li>
</ul>
-<P>
-</P>
<!--==================================================================-->
<!-- Legalese & Metadata -->
Modified: DART/trunk/observations/COSMOS/COSMOS_to_obs.html
===================================================================
--- DART/trunk/observations/COSMOS/COSMOS_to_obs.html 2013-06-27 23:03:27 UTC (rev 6280)
+++ DART/trunk/observations/COSMOS/COSMOS_to_obs.html 2013-06-28 21:30:36 UTC (rev 6281)
@@ -304,7 +304,7 @@
</pre>
</div>
</div><!-- end of block indent -->
-<P></P><!-- needed to make 'top' align correctly -->
+<P> </P><!-- needed to make 'top' align correctly -->
<!--==================================================================-->
<!--=================== DESCRIPTION OF A NAMELIST ===================-->
@@ -313,72 +313,81 @@
<A NAME="Namelist"></A>
<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.
+<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 /COSMOS_to_obs_nml/ </em> site_metadata_file, &
- text_input_file, obs_out_file, sitename, maxgoodqc, verbose
+
+
+<div class=namelist>
+<pre>
+&COSMOS_to_obs_nml
+ site_metadata_file = 'COSMIC_parlist.nc'
@@ Diff output truncated at 40000 characters. @@
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