[Dart-dev] [4856] DART/trunk/models/cam: Moved the trans_*html codes to be 'next to' the

nancy at ucar.edu nancy at ucar.edu
Thu Apr 14 16:24:50 MDT 2011


Revision: 4856
Author:   thoar
Date:     2011-04-14 16:24:49 -0600 (Thu, 14 Apr 2011)
Log Message:
-----------
Moved the trans_*html codes to be 'next to' the
corresponding/matching Fortran codes.
Changed the references that I could find so as not to
break the links. Added the snappy new DART documentation header
and moved the namelist to be 'first'.

Modified Paths:
--------------
    DART/trunk/models/cam/doc/cam_guidelines.html
    DART/trunk/models/cam/model_mod.html

Added Paths:
-----------
    DART/trunk/models/cam/trans_date_to_dart.html
    DART/trunk/models/cam/trans_pv_sv_time0.html

Removed Paths:
-------------
    DART/trunk/models/cam/doc/trans_date_to_dart_instr.html
    DART/trunk/models/cam/doc/trans_pv_sv_time0_instr.html

-------------- next part --------------
Modified: DART/trunk/models/cam/doc/cam_guidelines.html
===================================================================
--- DART/trunk/models/cam/doc/cam_guidelines.html	2011-04-14 22:04:06 UTC (rev 4855)
+++ DART/trunk/models/cam/doc/cam_guidelines.html	2011-04-14 22:24:49 UTC (rev 4856)
@@ -262,7 +262,7 @@
               <LI>find and link to the obs_seq.out files</LI>
 	      <LI>find and link to filter_ic[.#] files.
 		     Such an ensemble can be created from CAM initial files using
-		     <A HREF="./trans_pv_sv_time0_instr.html">
+		     <A HREF="../trans_pv_sv_time0.html">
 		     .../DART/models/cam/trans_pv_sv_time0.f90</A>. </LI>
               <LI>define which CAM and CLM initial files to use.  
                      Some initial and filter_ic files are available from 
@@ -281,7 +281,7 @@
                      .false. otherwise.</LI>
               <LI>init_time_days is the first Gregorian day of your assimilation.
 		 This can be obtained from the program 
-		 <A HREF="./trans_date_to_dart_instr.html">
+		 <A HREF="../trans_date_to_dart.html">
 		 ...DART/models/cam/trans_date_to_dart.f90 </A> </LI>
               <LI>init_time_seconds is the first second of your assimilation (usually 0).</LI>
           </UL>

Deleted: DART/trunk/models/cam/doc/trans_date_to_dart_instr.html
===================================================================
--- DART/trunk/models/cam/doc/trans_date_to_dart_instr.html	2011-04-14 22:04:06 UTC (rev 4855)
+++ DART/trunk/models/cam/doc/trans_date_to_dart_instr.html	2011-04-14 22:24:49 UTC (rev 4856)
@@ -1,60 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
-          "http://www.w3.org/TR/html4/strict.dtd">
-<HTML>
-<HEAD>
-<TITLE>trans_date_to_dart</TITLE>
-<link rel="stylesheet" type="text/css" href="../../../doc/html/doc.css">
-</HEAD>
-<BODY>
-<A NAME="TOP"></A>
-
-<center>
-<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-
-<H1>Program <em class=program>trans_date_to_dart</em></H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
-
-<P>
-<em class=program>trans_date_to_dart</em> translates a standard date and time into Gregorian and DART date/time pairs.
-It will be compiled automatically by .../DART/models/cam/work/workshop_setup.csh.
-It opens a pre-existing file called 'date_greg' which must be in the run directory
-and which must contain a date and time on the first line, in the form
-</P>
-<PRE>
-yyyy/mm/dd hh:mm:ss
-</PRE>
-<P>
-It will write out the gregorian day and time onto line 2 of the same file.
-It will also write out the date in the format the CAM wants to see onto the 3rd line.
-It does not require any namelist input from input.nml.
-</P>
-
-<!--==================================================================-->
-<!-- Legalese & Metadata                                              -->
-<!--==================================================================-->
-
-<A NAME="Legalese"></A>
-<HR>
-<H2>Terms of Use</H2>
-
-<P>
-DART software - Copyright &#169; 2004 - 2010 UCAR.<br>
-This open source software is provided by UCAR, "as is",<br>
-without charge, subject to all terms of use at<br>
-<a href="http://www.image.ucar.edu/DAReS/DART/DART_download">
-http://www.image.ucar.edu/DAReS/DART/DART_download</a>
-</P>
-
-<TABLE border=0 cellpadding=0 width=100% summary="">
-<TR><TD valign=top>Contact:       </TD><TD> Kevin Raeder </TD></TR>
-<TR><TD valign=top>Revision:      </TD><TD> $Revision$ </TD></TR>
-<TR><TD valign=top>Source:        </TD><TD> $URL$ </TD></TR>
-<TR><TD valign=top>Change Date:   </TD><TD> $Date$ </TD></TR>
-<TR><TD valign=top>Change&nbsp;history:&nbsp;</TD><TD> try "svn&nbsp;log" or "svn&nbsp;diff" </TD></TR>
-</TABLE>
-
-<!--==================================================================-->
-
-</BODY>
-</HTML>

Deleted: DART/trunk/models/cam/doc/trans_pv_sv_time0_instr.html
===================================================================
--- DART/trunk/models/cam/doc/trans_pv_sv_time0_instr.html	2011-04-14 22:04:06 UTC (rev 4855)
+++ DART/trunk/models/cam/doc/trans_pv_sv_time0_instr.html	2011-04-14 22:24:49 UTC (rev 4856)
@@ -1,153 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
-          "http://www.w3.org/TR/html4/strict.dtd">
-<HTML>
-<HEAD>
-<TITLE>trans_pv_sv_time0 </TITLE>
-<link rel="stylesheet" type="text/css" href="../../../doc/html/doc.css">
-</HEAD>
-<BODY>
-<A NAME="TOP"></A>
-
-<center>
-<A HREF="#Namelist">NAMELIST</A> /
-<A HREF="#FilesUsed">FILES</A> /
-<A HREF="#References">REFERENCES</A> /
-<A HREF="#Errors">ERRORS</A> /
-<A HREF="#FuturePlans">PLANS</A> /
-<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-
-<H1>Program <em class=program>trans_pv_sv_time0</em></H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
-
-<P>
-You can make filter_ic files from caminput_#.nc files using the program
-.../DART/models/cam/trans_pv_sv_time0.f90.
-This is compiled in .../DART/models/cam/work by default if you use workshop_setup.csh.
-<em class=program>trans_pv_sv_time0</em> needs to be run for each caminput file. 
-So far there is not a robust script for running trans_pv_sv_time0, 
-but you can write your own. 
-<br><br>
-You'll need to have several files in the directory where trans_pv_sv_time0 is run:
-</P>
-
-<UL>
-   <LI> input.nml containing perfect_model_nml, which provides the Gregorian 
-        timestamp for the filter_ic file in variables
-        <PRE>
-           init_time_days    = 146827,
-           init_time_seconds = 0,
-        </PRE>
-        This date can be generated using 
-	<A HREF="./trans_date_to_dart_instr.html"> 
-	.../DART/models/cam/trans_date_to_dart.f90</A>.  
-   </LI>
-   <LI> 'topog_file.nc' for your resolution. 
-        A copy of this should be in with the rest of the CAM
-	input files that are listed in the CAM "namelistin" in variable bnd_topo.  
-	It will be named similarly to 
-        .../something/else/more/topo-from-cami_0000-09-01_64x128_L26_c030918.nc 
-   </LI>
-   <LI> link or copy your CAM initial file caminput_#.nc to 'caminput.nc',
-        which is the name trans_pv_sv_time0 wants to see.
-   </LI>
-</UL>
-
-<P>
-Each run of trans_pv_sv_time0 will create a 'temp_ud' file, 
-which should be renamed <em class=file>filter_ic.####</em>, 
-where ####&nbsp;=&nbsp;1,...,num_ens (padded with 0s)
-is taken from the caminput_#.nc used as input.
-You might want to put these new filter_ic files in a directory that has MPI
-in the name, so that you know whether they work with Jamaica (new state vector order)
-or Iceland (old).
-</P>
-
-<!--==================================================================-->
-<!--=================== DESCRIPTION OF A NAMELIST  ===================-->
-<!--==================================================================-->
-
-<A NAME="Namelist"></A>
-<HR>
-<H2>NAMELIST</H2>
-<P>
-There is no namelist unique to this program. 
-</P>
-
-<!--==================================================================-->
-<!-- Describe the Files Used by this module.                          -->
-<!--==================================================================-->
-
-<A NAME="FilesUsed"></A>
-<HR>
-<H2>FILES</H2>
-<P>
-still working on this part
-</P>
-
-<!--==================================================================-->
-<!-- Cite references, if need be.                                     -->
-<!--==================================================================-->
-
-<A NAME="References"></A>
-<HR>
-<H2>REFERENCES</H2>
-<ul>
-<li> none </li>
-</ul>
-
-<!--==================================================================-->
-<!-- Describe all the error conditions and codes.                     -->
-<!--==================================================================-->
-
-<A NAME="Errors"></A>
-<HR>
-<H2>ERROR CODES and CONDITIONS</H2>
-<P>
-still working on this part
-</P>
-
-<H2>KNOWN BUGS</H2>
-<P>
-none at this time
-</P>
-
-<!--==================================================================-->
-<!-- Describe Future Plans.                                           -->
-<!--==================================================================-->
-
-<A NAME="FuturePlans"></A>
-<HR>
-<H2>FUTURE PLANS</H2>
-<P>
-none at this time
-</P>
-
-<!--==================================================================-->
-<!-- Legalese & Metadata                                              -->
-<!--==================================================================-->
-
-<A NAME="Legalese"></A>
-<HR>
-<H2>Terms of Use</H2>
-
-<P>
-DART software - Copyright &#169; 2004 - 2010 UCAR.<br>
-This open source software is provided by UCAR, "as is",<br>
-without charge, subject to all terms of use at<br>
-<a href="http://www.image.ucar.edu/DAReS/DART/DART_download">
-http://www.image.ucar.edu/DAReS/DART/DART_download</a>
-</P>
-
-<TABLE border=0 cellpadding=0 width=100% summary="">
-<TR><TD valign=top>Contact:       </TD><TD> Kevin Raeder </TD></TR>
-<TR><TD valign=top>Revision:      </TD><TD> $Revision$ </TD></TR>
-<TR><TD valign=top>Source:        </TD><TD> $URL$ </TD></TR>
-<TR><TD valign=top>Change Date:   </TD><TD> $Date$ </TD></TR>
-<TR><TD valign=top>Change&nbsp;history:&nbsp;</TD><TD> try "svn&nbsp;log" or "svn&nbsp;diff" </TD></TR>
-</TABLE>
-
-<!--==================================================================-->
-
-</BODY>
-</HTML>

Modified: DART/trunk/models/cam/model_mod.html
===================================================================
--- DART/trunk/models/cam/model_mod.html	2011-04-14 22:04:06 UTC (rev 4855)
+++ DART/trunk/models/cam/model_mod.html	2011-04-14 22:24:49 UTC (rev 4856)
@@ -3,24 +3,37 @@
 <HTML>
 <HEAD>
 <TITLE>module model_mod (CAM)</TITLE>
-<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css" />
 </HEAD>
 <BODY>
 <A NAME="TOP"></A>
 
-<center>
+<H1>MODULE model_mod (CAM)</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+    <td valign=middle>
+    <img src="../../doc/html/Dartboard9.png" alt="DART project logo" height=70 />
+    </td>
+    <td>
+       <P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
+          <small><small>version information for this file: <br />
+          <!-- version tag follows, do not edit -->
+          $Id$</small></small>
+       </P></td>
+</tr>
+</table>
+
+<A HREF="#Namelist">NAMELIST</A> /
 <A HREF="#Interface">INTERFACES</A> /
-<A HREF="#Namelist">NAMELIST</A> /
 <A HREF="#FilesUsed">FILES</A> /
 <A HREF="#References">REFERENCES</A> /
 <A HREF="#Errors">ERRORS</A> /
 <A HREF="#FuturePlans">PLANS</A> /
 <A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
 <A HREF="#Legalese">TERMS OF USE</A>
-</center>
 
-<H1>MODULE model_mod (CAM)</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
 
 <P>
 The 17 public interfaces in model_mod
@@ -88,7 +101,161 @@
 </UL> 
 
 <!--==================================================================-->
+<!--=================== DESCRIPTION OF A NAMELIST ====================-->
+<!--==================================================================-->
 
+<A NAME="Namelist"></A>
+<HR>
+<H2>NAMELIST</H2>
+<P>We adhere to the F90 standard of starting a namelist with an ampersand
+'&amp;' and terminating with a slash '/' for all our namelist input.
+The declarations have a different syntax, naturally.
+</P>
+<div class=namelist>
+<pre>
+<em class=call>namelist / model_nml / </em> &amp;
+     output_state_vector,  model_version,  model_config_file,          &amp;  
+       state_num_0d,   state_num_1d,   state_num_2d,   state_num_3d,   &amp;  
+     state_names_0d, state_names_1d, state_names_2d, state_names_3d,   &amp;
+                      which_vert_1d,  which_vert_2d,  which_vert_3d,   &amp;
+     pert_names, pert_sd, pert_base_vals,                              &amp;
+     highest_obs_pressure_mb, highest_state_pressure_mb,               &amp;
+     max_obs_lat_degree, Time_step_seconds, Time_step_days
+</pre>
+</div>
+
+<div class=indent1>
+<!-- Description -->
+
+<P>
+This namelist is read in a file called <em class=file>input.nml</em>
+The specification of lists of names and numbers for the various dimensions 
+enables the very flexible definition of the state vector.  It can be
+done via the namelist, instead of recompiling DART for each different set.
+One hurdle that still remains is that distinct filter_ics are
+necessary for each separate set of fields which compose the state vector.
+</P>
+
+<P>
+The dimension of these lists is currently hardwired to size 100. 
+If more variables types need to be assimilated (e.g. many chemical species),
+look for the integer parameter MAX_STATE_NAMES in the source code
+and change it to a long enough value and recompile DART.
+Longer term we intend to investigate using 2 different nameslists
+inside model_mod; one for setting the length of the lists and another
+to actually read in the data which fills the lists.
+</P>
+
+<P>
+The values for which_vert_#d is described in 
+DART/location/threed_sphere/location_mod.html.
+</P>
+
+<P>
+The names of the fields to put into the state vector come from the CAM initial
+file field names.
+</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>output_state_vector  </TD>
+    <!--  type  --><TD valign=top>logical              </TD>
+    <!--descript--><TD>Controls the output to netCDF files. 
+     If .true., output the raw dart state vector. If .false.,
+     output the prognostic flavor (gridded data) for easier 
+     plotting (recommended).  Defaults to .false.</TD></TR>
+<TR><!--contents--><TD valign=top>model_version        </TD>
+    <!--  type  --><TD valign=top>character(len=128)   </TD>
+    <!--descript--><TD>The number of the CAM version being 
+       used, i.e. '3.0.7'.  (no letters allowed, so rename cam3_0_p1)
+                     Default = '3.0' .</TD></TR>
+<TR><!--contents--><TD valign=top>model_config_file    </TD>
+    <!--  type  --><TD valign=top>character(len=128)   </TD>
+    <!--descript--><TD>CAM initial file used to provide 
+       configuration information.  Default 'caminput.nc'.</TD></TR>
+<TR><!--contents--><TD valign=top>state_num_#d, #=0,1,2,3   </TD>
+    <!--  type  --><TD valign=top>integer                   </TD>
+    <!--descript--><TD>Numbers of fields of various dimensions to put 
+                     into the state vector.
+                     Defaults state_num_0d=0, _1d=0, _2d=1, _3d=4 .</TD></TR>
+<TR><!--contents--><TD valign=top>state_names_#d, #=0,1,2,3        </TD>
+    <!--  type  --><TD valign=top>character(len=8), dimension(100)  </TD>
+    <!--descript--><TD>Names of fields of various dimensions to put 
+                      into the state vector.  Defaults
+<PRE>state_names_0d='        ', state_names_1d='        ',
+state_names_2d='PS      '
+state_names_3d='T       ','U       ','V       ','Q       '</PRE>
+     </TD></TR>
+<TR><!--contents--><TD valign=top>which_vert_#d, #=1,2,3           </TD>
+    <!--  type  --><TD valign=top>integer, dimension(100)           </TD>
+    <!--descript--><TD>Vertical location types of fields in 
+                 state_names_#d.  Defaults 
+                       <UL><LI> which_vert_1d = state_num_1d*-2, 
+                           <LI> which_vert_2d = state_num_2d*-1, 
+                           <LI> which_vert_3d = state_num_3d* 1 </UL> </TD></TR>
+<TR><!--contents--><TD valign=top>pert_names                         </TD>
+    <!--  type  --><TD valign=top>character(len=8), dimension(100)    </TD>
+    <!--descript--><TD>List of field(s) whose values need to be changed at or before 
+                       the beginning of an assimilation.  To make filter generate
+                       an ensemble from a single model state by randomly perturbing it,
+                       list the fields to be perturbed here.  To make trans_pv_sv_pert0
+                       reset a single field to a constant value, list that field here.
+                       Trans_pv_sv_pert0 would be run as many times as there are ensemble
+                       members (see pert_base_vals), in order to provide spread to that 
+                       variable. 
+                       Defaults <BR>
+                      <PRE>pert_names='        ' </PRE></TD></TR>
+<TR><!--contents--><TD valign=top>pert_sd                            </TD>
+    <!--  type  --><TD valign=top>real(r8), dimension(100)    </TD>
+    <!--descript--><TD>If positive, it's the standard deviation of the 
+     perturbation for each field in the pert_names list (filter).  
+     If negative, then pert_names can contain only one entry, and that field 
+     will be set to a different constant value for each ensemble member 
+     (trans_pv_sv_pert0).  Those values come from pert_base_vals.
+                       Defaults to a MISSING real value and
+                       unused unless pert_names is set.  </TD></TR>
+<TR><!--contents--><TD valign=top>pert_base_vals              </TD>
+    <!--  type  --><TD valign=top>real(r8), dimension(100)    </TD>
+    <!--descript--><TD>If pert_sd (yes, 'sd') is negative, this is the list of 
+       values to use for each ensemble member when perturbing the single 
+       field named in pert_names.
+       Otherwise, it's the list of values to which the fieldS listed in
+       pert_names will be reset if filter is told to create an ensemble from
+       a single state vector.
+       Defaults to a MISSING real value and unused unless pert_names 
+       is set and pert_base_vals is /= this missing value (-888888.0d0).  </TD></TR>
+<TR><!--contents--><TD valign=top>max_obs_lat_degree             </TD>
+    <!--  type  --><TD valign=top>real(r8)                       </TD>
+    <!--descript--><TD>Observations closer to the poles than this 
+                       latitude will be ignored.
+                       Default 90 degrees </TD></TR>
+<TR><!--contents--><TD valign=top>highest_obs_pressure_mb       </TD>
+    <!--  type  --><TD valign=top>real(r8)                      </TD>
+    <!--descript--><TD>Observations higher than this pressure are ignored.
+                       Default  150.0 hPa </TD></TR>
+<TR><!--contents--><TD valign=top>highest_state_pressure_mb     </TD>
+    <!--  type  --><TD valign=top>real(r8)                      </TD>
+    <!--descript--><TD>Influence of all obs on model points higher than 
+                       this is reduced.
+                       Default  150.0 hPa </TD></TR>
+<TR><!--contents--><TD valign=top>Time_step_seconds          </TD>
+    <!--  type  --><TD valign=top>real(r8)                   </TD>
+    <!--descript--><TD>Forecast duration (the part &#60; 1 day)
+                       Default  21600 sec </TD></TR>
+<TR><!--contents--><TD valign=top>Time_step_days             </TD>
+    <!--  type  --><TD valign=top>real(r8)                   </TD>
+    <!--descript--><TD>Forecast duration (the part &#62; 24*3600 sec)
+                       Default  0 days </TD></TR>
+</TABLE>
+
+</div>
+<br>
+
+<!--==================================================================-->
+<!--==================================================================-->
+
 <A NAME="OtherModulesUsed"></A>
 <HR>
 <H2>OTHER MODULES USED</H2>
@@ -608,10 +775,10 @@
 </P>
 
 <P>
-This subroutine is also used by trans_pv_sv_pert0 for the off-line
+This subroutine is also used by <em class=program>trans_pv_sv_pert0</em> for the off-line
 perturbation of fields the model considers to be parameters.  In this use a
 new random sequence seed must be provided via an input file ("ens_member")
-for each ensemble member, since trans_pv_sv_pert0 is executed once for each
+for each ensemble member, since <em class=program>trans_pv_sv_pert0</em> is executed once for each
 member and can't keep a series of different seeds intact.  
 </P>
 
@@ -743,157 +910,6 @@
 </div>
 <br>
 
-<!--===================== DESCRIPTION OF A NAMELIST =====================-->
-
-<A NAME="Namelist"></A>
-<HR>
-<H2>NAMELIST</H2>
-<P>We adhere to the F90 standard of starting a namelist with an ampersand
-'&amp;' and terminating with a slash '/' for all our namelist input.
-The declarations have a different syntax, naturally.
-</P>
-<div class=namelist>
-<pre>
-<em class=call>namelist / model_nml / </em> &amp;
-     output_state_vector,  model_version,  model_config_file,          &amp;  
-       state_num_0d,   state_num_1d,   state_num_2d,   state_num_3d,   &amp;  
-     state_names_0d, state_names_1d, state_names_2d, state_names_3d,   &amp;
-                      which_vert_1d,  which_vert_2d,  which_vert_3d,   &amp;
-     pert_names, pert_sd, pert_base_vals,                              &amp;
-     highest_obs_pressure_mb, highest_state_pressure_mb,               &amp;
-     max_obs_lat_degree, Time_step_seconds, Time_step_days
-</pre>
-</div>
-
-<div class=indent1>
-<!-- Description -->
-
-<P>
-This namelist is read in a file called <em class=file>input.nml</em>
-The specification of lists of names and numbers for the various dimensions 
-enables the very flexible definition of the state vector.  It can be
-done via the namelist, instead of recompiling DART for each different set.
-One hurdle that still remains is that distinct filter_ics are
-necessary for each separate set of fields which compose the state vector.
-</P>
-
-<P>
-The dimension of these lists is currently hardwired to size 100. 
-If more variables types need to be assimilated (e.g. many chemical species),
-look for the integer parameter MAX_STATE_NAMES in the source code
-and change it to a long enough value and recompile DART.
-Longer term we intend to investigate using 2 different nameslists
-inside model_mod; one for setting the length of the lists and another
-to actually read in the data which fills the lists.
-</P>
-
-<P>
-The values for which_vert_#d is described in 
-DART/location/threed_sphere/location_mod.html.
-</P>
-
-<P>
-The names of the fields to put into the state vector come from the CAM initial
-file field names.
-</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>output_state_vector  </TD>
-    <!--  type  --><TD valign=top>logical              </TD>
-    <!--descript--><TD>Controls the output to netCDF files. 
-     If .true., output the raw dart state vector. If .false.,
-     output the prognostic flavor (gridded data) for easier 
-     plotting (recommended).  Defaults to .false.</TD></TR>
-<TR><!--contents--><TD valign=top>model_version        </TD>
-    <!--  type  --><TD valign=top>character(len=128)   </TD>
-    <!--descript--><TD>The number of the CAM version being 
-       used, i.e. '3.0.7'.  (no letters allowed, so rename cam3_0_p1)
-                     Default = '3.0' .</TD></TR>
-<TR><!--contents--><TD valign=top>model_config_file    </TD>
-    <!--  type  --><TD valign=top>character(len=128)   </TD>
-    <!--descript--><TD>CAM initial file used to provide 
-       configuration information.  Default 'caminput.nc'.</TD></TR>
-<TR><!--contents--><TD valign=top>state_num_#d, #=0,1,2,3   </TD>
-    <!--  type  --><TD valign=top>integer                   </TD>
-    <!--descript--><TD>Numbers of fields of various dimensions to put 
-                     into the state vector.
-                     Defaults state_num_0d=0, _1d=0, _2d=1, _3d=4 .</TD></TR>
-<TR><!--contents--><TD valign=top>state_names_#d, #=0,1,2,3        </TD>
-    <!--  type  --><TD valign=top>character(len=8), dimension(100)  </TD>
-    <!--descript--><TD>Names of fields of various dimensions to put 
-                      into the state vector.  Defaults
-<PRE>state_names_0d='        ', state_names_1d='        ',
-state_names_2d='PS      '
-state_names_3d='T       ','U       ','V       ','Q       '</PRE>
-     </TD></TR>
-<TR><!--contents--><TD valign=top>which_vert_#d, #=1,2,3           </TD>
-    <!--  type  --><TD valign=top>integer, dimension(100)           </TD>
-    <!--descript--><TD>Vertical location types of fields in 
-                 state_names_#d.  Defaults 
-                       <UL><LI> which_vert_1d = state_num_1d*-2, 
-                           <LI> which_vert_2d = state_num_2d*-1, 
-                           <LI> which_vert_3d = state_num_3d* 1 </UL> </TD></TR>
-<TR><!--contents--><TD valign=top>pert_names                         </TD>
-    <!--  type  --><TD valign=top>character(len=8), dimension(100)    </TD>
-    <!--descript--><TD>List of field(s) whose values need to be changed at or before 
-                       the beginning of an assimilation.  To make filter generate
-                       an ensemble from a single model state by randomly perturbing it,
-                       list the fields to be perturbed here.  To make trans_pv_sv_pert0
-                       reset a single field to a constant value, list that field here.
-                       Trans_pv_sv_pert0 would be run as many times as there are ensemble
-                       members (see pert_base_vals), in order to provide spread to that 
-                       variable. 
-                       Defaults <BR>
-                      <PRE>pert_names='        ' </PRE></TD></TR>
-<TR><!--contents--><TD valign=top>pert_sd                            </TD>
-    <!--  type  --><TD valign=top>real(r8), dimension(100)    </TD>
-    <!--descript--><TD>If positive, it's the standard deviation of the 
-     perturbation for each field in the pert_names list (filter).  
-     If negative, then pert_names can contain only one entry, and that field 
-     will be set to a different constant value for each ensemble member 
-     (trans_pv_sv_pert0).  Those values come from pert_base_vals.
-                       Defaults to a MISSING real value and
-                       unused unless pert_names is set.  </TD></TR>
-<TR><!--contents--><TD valign=top>pert_base_vals              </TD>
-    <!--  type  --><TD valign=top>real(r8), dimension(100)    </TD>
-    <!--descript--><TD>If pert_sd (yes, 'sd') is negative, this is the list of 
-       values to use for each ensemble member when perturbing the single 
-       field named in pert_names.
-       Otherwise, it's the list of values to which the fieldS listed in
-       pert_names will be reset if filter is told to create an ensemble from
-       a single state vector.
-       Defaults to a MISSING real value and unused unless pert_names 
-       is set and pert_base_vals is /= this missing value (-888888.0d0).  </TD></TR>
-<TR><!--contents--><TD valign=top>max_obs_lat_degree             </TD>
-    <!--  type  --><TD valign=top>real(r8)                       </TD>
-    <!--descript--><TD>Observations closer to the poles than this 
-                       latitude will be ignored.
-                       Default 90 degrees </TD></TR>
-<TR><!--contents--><TD valign=top>highest_obs_pressure_mb       </TD>
-    <!--  type  --><TD valign=top>real(r8)                      </TD>
-    <!--descript--><TD>Observations higher than this pressure are ignored.
-                       Default  150.0 hPa </TD></TR>
-<TR><!--contents--><TD valign=top>highest_state_pressure_mb     </TD>
-    <!--  type  --><TD valign=top>real(r8)                      </TD>
-    <!--descript--><TD>Influence of all obs on model points higher than 
-                       this is reduced.
-                       Default  150.0 hPa </TD></TR>
-<TR><!--contents--><TD valign=top>Time_step_seconds          </TD>
-    <!--  type  --><TD valign=top>real(r8)                   </TD>
-    <!--descript--><TD>Forecast duration (the part &#60; 1 day)
-                       Default  21600 sec </TD></TR>
-<TR><!--contents--><TD valign=top>Time_step_days             </TD>
-    <!--  type  --><TD valign=top>real(r8)                   </TD>
-    <!--descript--><TD>Forecast duration (the part &#62; 24*3600 sec)
-                       Default  0 days </TD></TR>
-</TABLE>
-
-</div>
-<br>
-
 <!--==================================================================-->
 <!-- Describe the Files Used by this module.                          -->
 <!--==================================================================-->

Copied: DART/trunk/models/cam/trans_date_to_dart.html (from rev 4851, DART/trunk/models/cam/doc/trans_date_to_dart_instr.html)
===================================================================
--- DART/trunk/models/cam/trans_date_to_dart.html	                        (rev 0)
+++ DART/trunk/models/cam/trans_date_to_dart.html	2011-04-14 22:24:49 UTC (rev 4856)
@@ -0,0 +1,60 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
+          "http://www.w3.org/TR/html4/strict.dtd">
+<HTML>
+<HEAD>
+<TITLE>trans_date_to_dart</TITLE>
+<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+</HEAD>
+<BODY>
+<A NAME="TOP"></A>
+
+<center>
+<A HREF="#Legalese">TERMS OF USE</A>
+</center>
+
+<H1>Program <em class=program>trans_date_to_dart</em></H1>
+<!-- version tag follows, do not edit --><P>$Id$</P>
+
+<P>
+<em class=program>trans_date_to_dart</em> translates a standard date and time into Gregorian and DART date/time pairs.
+It will be compiled automatically by .../DART/models/cam/work/workshop_setup.csh.
+It opens a pre-existing file called 'date_greg' which must be in the run directory
+and which must contain a date and time on the first line, in the form
+</P>
+<PRE>
+yyyy/mm/dd hh:mm:ss
+</PRE>
+<P>
+It will write out the gregorian day and time onto line 2 of the same file.
+It will also write out the date in the format the CAM wants to see onto the 3rd line.
+It does not require any namelist input from input.nml.
+</P>
+
+<!--==================================================================-->
+<!-- Legalese & Metadata                                              -->
+<!--==================================================================-->
+
+<A NAME="Legalese"></A>
+<HR>
+<H2>Terms of Use</H2>
+
+<P>
+DART software - Copyright &#169; 2004 - 2010 UCAR.<br>
+This open source software is provided by UCAR, "as is",<br>
+without charge, subject to all terms of use at<br>
+<a href="http://www.image.ucar.edu/DAReS/DART/DART_download">
+http://www.image.ucar.edu/DAReS/DART/DART_download</a>
+</P>
+
+<TABLE border=0 cellpadding=0 width=100% summary="">
+<TR><TD valign=top>Contact:       </TD><TD> Kevin Raeder </TD></TR>
+<TR><TD valign=top>Revision:      </TD><TD> $Revision$ </TD></TR>
+<TR><TD valign=top>Source:        </TD><TD> $URL$ </TD></TR>
+<TR><TD valign=top>Change Date:   </TD><TD> $Date$ </TD></TR>
+<TR><TD valign=top>Change&nbsp;history:&nbsp;</TD><TD> try "svn&nbsp;log" or "svn&nbsp;diff" </TD></TR>
+</TABLE>
+
+<!--==================================================================-->
+
+</BODY>
+</HTML>

Copied: DART/trunk/models/cam/trans_pv_sv_time0.html (from rev 4851, DART/trunk/models/cam/doc/trans_pv_sv_time0_instr.html)
===================================================================
--- DART/trunk/models/cam/trans_pv_sv_time0.html	                        (rev 0)
+++ DART/trunk/models/cam/trans_pv_sv_time0.html	2011-04-14 22:24:49 UTC (rev 4856)
@@ -0,0 +1,153 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
+          "http://www.w3.org/TR/html4/strict.dtd">
+<HTML>
+<HEAD>
+<TITLE>trans_pv_sv_time0 </TITLE>
+<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+</HEAD>
+<BODY>
+<A NAME="TOP"></A>
+
+<center>
+<A HREF="#Namelist">NAMELIST</A> /
+<A HREF="#FilesUsed">FILES</A> /
+<A HREF="#References">REFERENCES</A> /
+<A HREF="#Errors">ERRORS</A> /
+<A HREF="#FuturePlans">PLANS</A> /
+<A HREF="#Legalese">TERMS OF USE</A>
+</center>
+
+<H1>Program <em class=program>trans_pv_sv_time0</em></H1>
+<!-- version tag follows, do not edit --><P>$Id$</P>
+
+<P>
+You can make filter_ic files from caminput_#.nc files using the program
+.../DART/models/cam/trans_pv_sv_time0.f90.
+This is compiled in .../DART/models/cam/work by default if you use workshop_setup.csh.
+<em class=program>trans_pv_sv_time0</em> needs to be run for each caminput file. 
+So far there is not a robust script for running trans_pv_sv_time0, 
+but you can write your own. 
+<br><br>
+You'll need to have several files in the directory where trans_pv_sv_time0 is run:
+</P>
+
+<UL>
+   <LI> input.nml containing perfect_model_nml, which provides the Gregorian 
+        timestamp for the filter_ic file in variables
+        <PRE>
+           init_time_days    = 146827,
+           init_time_seconds = 0,
+        </PRE>
+        This date can be generated using 
+	<A HREF="./trans_date_to_dart_instr.html"> 
+	.../DART/models/cam/trans_date_to_dart.f90</A>.  
+   </LI>
+   <LI> 'topog_file.nc' for your resolution. 
+        A copy of this should be in with the rest of the CAM
+	input files that are listed in the CAM "namelistin" in variable bnd_topo.  
+	It will be named similarly to 
+        .../something/else/more/topo-from-cami_0000-09-01_64x128_L26_c030918.nc 
+   </LI>
+   <LI> link or copy your CAM initial file caminput_#.nc to 'caminput.nc',
+        which is the name trans_pv_sv_time0 wants to see.
+   </LI>
+</UL>
+
+<P>
+Each run of trans_pv_sv_time0 will create a 'temp_ud' file, 
+which should be renamed <em class=file>filter_ic.####</em>, 
+where ####&nbsp;=&nbsp;1,...,num_ens (padded with 0s)
+is taken from the caminput_#.nc used as input.
+You might want to put these new filter_ic files in a directory that has MPI
+in the name, so that you know whether they work with Jamaica (new state vector order)
+or Iceland (old).
+</P>
+
+<!--==================================================================-->
+<!--=================== DESCRIPTION OF A NAMELIST  ===================-->
+<!--==================================================================-->
+
+<A NAME="Namelist"></A>
+<HR>
+<H2>NAMELIST</H2>
+<P>
+There is no namelist unique to this program. 
+</P>
+
+<!--==================================================================-->
+<!-- Describe the Files Used by this module.                          -->
+<!--==================================================================-->
+
+<A NAME="FilesUsed"></A>
+<HR>
+<H2>FILES</H2>
+<P>
+still working on this part
+</P>
+
+<!--==================================================================-->
+<!-- Cite references, if need be.                                     -->
+<!--==================================================================-->
+
+<A NAME="References"></A>
+<HR>
+<H2>REFERENCES</H2>
+<ul>
+<li> none </li>
+</ul>
+
+<!--==================================================================-->
+<!-- Describe all the error conditions and codes.                     -->
+<!--==================================================================-->
+
+<A NAME="Errors"></A>
+<HR>
+<H2>ERROR CODES and CONDITIONS</H2>
+<P>
+still working on this part
+</P>
+
+<H2>KNOWN BUGS</H2>
+<P>
+none at this time
+</P>
+
+<!--==================================================================-->
+<!-- Describe Future Plans.                                           -->
+<!--==================================================================-->
+
+<A NAME="FuturePlans"></A>
+<HR>
+<H2>FUTURE PLANS</H2>
+<P>
+none at this time
+</P>
+
+<!--==================================================================-->
+<!-- Legalese & Metadata                                              -->
+<!--==================================================================-->
+
+<A NAME="Legalese"></A>
+<HR>
+<H2>Terms of Use</H2>
+
+<P>
+DART software - Copyright &#169; 2004 - 2010 UCAR.<br>
+This open source software is provided by UCAR, "as is",<br>
+without charge, subject to all terms of use at<br>
+<a href="http://www.image.ucar.edu/DAReS/DART/DART_download">
+http://www.image.ucar.edu/DAReS/DART/DART_download</a>
+</P>
+
+<TABLE border=0 cellpadding=0 width=100% summary="">
+<TR><TD valign=top>Contact:       </TD><TD> Kevin Raeder </TD></TR>
+<TR><TD valign=top>Revision:      </TD><TD> $Revision$ </TD></TR>
+<TR><TD valign=top>Source:        </TD><TD> $URL$ </TD></TR>
+<TR><TD valign=top>Change Date:   </TD><TD> $Date$ </TD></TR>
+<TR><TD valign=top>Change&nbsp;history:&nbsp;</TD><TD> try "svn&nbsp;log" or "svn&nbsp;diff" </TD></TR>
+</TABLE>
+
+<!--==================================================================-->
+
+</BODY>
+</HTML>


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