[Dart-dev] [5907] DART/branches/development: The COSMOS work has been reviewed and is ready for use by the general public .
nancy at ucar.edu
nancy at ucar.edu
Tue Oct 30 13:12:51 MDT 2012
Revision: 5907
Author: thoar
Date: 2012-10-30 13:12:50 -0600 (Tue, 30 Oct 2012)
Log Message:
-----------
The COSMOS work has been reviewed and is ready for use by the general public.
Modified Paths:
--------------
DART/branches/development/obs_def/obs_def_COSMOS_mod.f90
DART/branches/development/observations/COSMOS/COSMOS_level2_to_obs.f90
DART/branches/development/observations/COSMOS/work/input.nml
Added Paths:
-----------
DART/branches/development/observations/COSMOS/COSMOS_level2_to_obs.html
DART/branches/development/observations/COSMOS/data/COSMIC_parlist.nc
-------------- next part --------------
Modified: DART/branches/development/obs_def/obs_def_COSMOS_mod.f90
===================================================================
--- DART/branches/development/obs_def/obs_def_COSMOS_mod.f90 2012-10-29 20:01:07 UTC (rev 5906)
+++ DART/branches/development/obs_def/obs_def_COSMOS_mod.f90 2012-10-30 19:12:50 UTC (rev 5907)
@@ -96,8 +96,6 @@
interactive_cosmos_metadata, &
get_expected_neutron_intensity
-integer :: num_neutron_intensity = 0 ! observation counter ... useful length of metadata arrays
-
! version controlled file description for error handling, do not edit
character(len=128), parameter :: &
source = "$URL$", &
@@ -113,11 +111,6 @@
type site_metadata
private
-! character(len=metadatalength) :: sitename
-! type(location_type) :: location
-! real(r8) :: latitude
-! real(r8) :: longitude
-! real(r8) :: elevation
real(r8) :: bd ! Dry Soil Bulk Density [ g / cm^3]
real(r8) :: lattwat ! Lattice Water Content [M^3 / M^3]
real(r8) :: N ! High Energy Neutron Intensity
@@ -129,18 +122,18 @@
end type site_metadata
type(site_metadata), allocatable, dimension(:) :: observation_metadata
+type(site_metadata) :: missing_metadata
character(len=6), parameter :: COSMOSSTRING = 'cosmic'
logical :: debug = .FALSE.
integer :: MAXcosmoskey = 24*366 ! one year of hourly data - to start
-integer :: cosmoskey = 0
+integer :: cosmoskey = 0 ! useful length of metadata arrays
!----------------------------------------------------------------------------
contains
!----------------------------------------------------------------------------
-
subroutine initialize_module
!----------------------------------------------------------------------------
! subroutine initialize_module
@@ -152,19 +145,18 @@
module_initialized = .true.
+missing_metadata%bd = MISSING_R8
+missing_metadata%lattwat = MISSING_R8
+missing_metadata%N = MISSING_R8
+missing_metadata%alpha = MISSING_R8
+missing_metadata%L1 = MISSING_R8
+missing_metadata%L2 = MISSING_R8
+missing_metadata%L3 = MISSING_R8
+missing_metadata%L4 = MISSING_R8
+
allocate(observation_metadata(MAXcosmoskey))
-do i = 1,MAXcosmoskey
- observation_metadata(i)%bd = MISSING_R8
- observation_metadata(i)%lattwat = MISSING_R8
- observation_metadata(i)%N = MISSING_R8
- observation_metadata(i)%alpha = MISSING_R8
- observation_metadata(i)%L1 = MISSING_R8
- observation_metadata(i)%L2 = MISSING_R8
- observation_metadata(i)%L3 = MISSING_R8
- observation_metadata(i)%L4 = MISSING_R8
-! observation_metadata(i)%location = set_location_missing()
-enddo
+observation_metadata(:) = missing_metadata
end subroutine initialize_module
@@ -184,7 +176,7 @@
cosmoskey = cosmoskey + 1 ! increase module storage used counter
! Make sure the new key is within the length of the metadata arrays.
-call key_out_of_range(cosmoskey,'set_cosmos_metadata')
+call grow_metadata(cosmoskey,'set_cosmos_metadata')
key = cosmoskey ! now that we know its legal
@@ -214,7 +206,7 @@
if ( .not. module_initialized ) call initialize_module
! Make sure the desired key is within the length of the metadata arrays.
-call key_out_of_range(key,'get_cosmos_metadata')
+call key_within_range(key,'get_cosmos_metadata')
bd = observation_metadata(key)%bd
lattwat = observation_metadata(key)%lattwat
@@ -407,8 +399,7 @@
subroutine get_expected_neutron_intensity(state, location, key, val, istatus)
!----------------------------------------------------------------------
-!subroutine get_expected_neutron_intensity(state, location, key, val, istatus)
-! uses a weighting function calculated by COSMIC (COsmic-ray Soil
+! Uses a weighting function calculated by COSMIC (COsmic-ray Soil
! Moisture Interaction Code)
real(r8), intent(in) :: state(:) ! state vector
@@ -484,7 +475,7 @@
integer :: angle, angledz, maxangle ! loop indices for an integration interval
integer :: i, zi, nlevels, iunit
real(r8) :: loc_array(3)
-real(r8) :: loc_lon, loc_lat, obs_val
+real(r8) :: loc_lon, loc_lat, loc_value
type(location_type) :: loc
!=================================================================================
@@ -498,7 +489,7 @@
!=================================================================================
! Make sure the desired key is within the length of the metadata arrays.
-call key_out_of_range(key,'get_expected_neutron_intensity')
+call key_within_range(key,'get_expected_neutron_intensity')
bd = observation_metadata(key)%bd
vwclat = observation_metadata(key)%lattwat
@@ -509,11 +500,6 @@
L3 = observation_metadata(key)%L3
L4 = observation_metadata(key)%L4
-write(*,*)'TJH debug '
-write(*,*)bd, vwclat, N, alpha
-write(*,*)L1,L2,L3,L4
-write(*,*)
-
!=================================================================================
! Determine the number of soil layers and their depths
! using only the standard DART interfaces to model
@@ -527,7 +513,7 @@
nlevels = 0
COUNTLEVELS : do i = 1,maxlayers
loc = set_location(loc_lon, loc_lat, real(i,r8), VERTISLEVEL)
- call model_interpolate(state,loc,KIND_GEOPOTENTIAL_HEIGHT,obs_val,istatus)
+ call model_interpolate(state,loc,KIND_GEOPOTENTIAL_HEIGHT,loc_value,istatus)
if (istatus /= 0) exit COUNTLEVELS
nlevels = nlevels + 1
enddo COUNTLEVELS
@@ -553,7 +539,7 @@
! not checking this error code because it worked just a few lines earlier
loc = set_location(loc_lon, loc_lat, layerz(i), VERTISHEIGHT)
- call model_interpolate(state,loc,KIND_SOIL_MOISTURE,obs_val,istatus)
+ call model_interpolate(state,loc,KIND_SOIL_MOISTURE,loc_value,istatus)
if (istatus /= 0) then
write(string1,*) 'FAILED to determine soil moisture for layer',i
@@ -563,7 +549,7 @@
return
endif
- soil_moisture(i) = obs_val
+ soil_moisture(i) = loc_value
enddo FINDLEVELS
@@ -636,14 +622,6 @@
zthick(i) = dz(i) - dz(i-1) ! Remaining layers
enddo
-if ( 2 == 1 ) then ! TJH DEBUG OUTPUT BLOCK
- iunit = open_file('cosmos_layers.txt',form='formatted',action='write')
- do i = 1,nlyr
- write(iunit,*)dz(i),vwc(i),zthick(i)
- enddo
- call close_file(iunit)
-endif
-
! Angle distribution parameters (HARDWIRED)
!rr: Using 0.5 deg angle intervals appears to be sufficient
!rr: (smaller angles increase the computing time for COSMIC)
@@ -736,27 +714,71 @@
-subroutine key_out_of_range(key, routine)
+subroutine key_within_range(key, routine)
!----------------------------------------------------------------------
-! Make sure we are addrssing within the metadata arrays
+! Make sure we are addressing within the metadata arrays
integer, intent(in) :: key
character(len=*), intent(in) :: routine
! fine -- no problem.
-if (key <= MAXcosmoskey) return
+if ((key > 0) .and. (key <= cosmoskey)) return
-! Bad news. Tell the user.
-write(string1, *) 'key (',key,') exceeds Nmax_neutron_intensity (', MAXcosmoskey,')'
-write(string2, *) 'Increase MAXcosmoskey in namelist and rerun.'
-call error_handler(E_ERR,routine,string1,source,revision,revdate,text2=string2)
+! Bad news. Tell the user.
+write(string1, *) 'key (',key,') not within known range ( 1,', cosmoskey,')'
+call error_handler(E_ERR,routine,string1,source,revision,revdate)
-! FIXME ... reallocate and get on with it.
+end subroutine key_within_range
-end subroutine key_out_of_range
+subroutine grow_metadata(key, routine)
+!----------------------------------------------------------------------
+! If the allocatable metadata arrays are not big enough ... try again
+integer, intent(in) :: key
+character(len=*), intent(in) :: routine
+
+integer :: i, orglength
+type(site_metadata), allocatable, dimension(:) :: safe_metadata
+
+! fine -- no problem.
+if ((key > 0) .and. (key <= MAXcosmoskey)) return
+
+orglength = MAXcosmoskey
+MAXcosmoskey = 2 * orglength
+
+! Check for some error conditions.
+if (key < 1) then
+ write(string1, *) 'key (',key,') must be >= 1'
+ call error_handler(E_ERR,routine,string1,source,revision,revdate)
+elseif (key >= 2*MAXcosmoskey) then
+ write(string1, *) 'key (',key,') really unexpected.'
+ write(string2, *) 'doubling storage will not help.'
+ call error_handler(E_ERR,routine,string1,source,revision,revdate, &
+ text2=string2)
+endif
+
+! News. Tell the user we are increasing storage.
+write(string1, *) 'key (',key,') exceeds Nmax_neutron_intensity (',orglength,')'
+write(string2, *) 'Increasing Nmax_neutron_intensity to ',MAXcosmoskey
+call error_handler(E_MSG,routine,string1,source,revision,revdate,text2=string2)
+
+allocate(safe_metadata(orglength))
+safe_metadata(:) = observation_metadata(:)
+
+deallocate(observation_metadata)
+ allocate(observation_metadata(MAXcosmoskey))
+
+observation_metadata(1:orglength) = safe_metadata(:)
+observation_metadata(orglength+1:MAXcosmoskey) = missing_metadata
+
+deallocate(safe_metadata)
+
+end subroutine grow_metadata
+
+
+
end module obs_def_COSMOS_mod
! END DART PREPROCESS MODULE CODE
Modified: DART/branches/development/observations/COSMOS/COSMOS_level2_to_obs.f90
===================================================================
--- DART/branches/development/observations/COSMOS/COSMOS_level2_to_obs.f90 2012-10-29 20:01:07 UTC (rev 5906)
+++ DART/branches/development/observations/COSMOS/COSMOS_level2_to_obs.f90 2012-10-30 19:12:50 UTC (rev 5907)
@@ -83,12 +83,11 @@
character(len=128) :: text_input_file = 'corcounts.txt'
character(len=128) :: obs_out_file = 'obs_seq.out'
character(len=128) :: sitename = 'missing'
-integer :: year
real(r8) :: maxgoodqc = 3
logical :: verbose = .false.
namelist /COSMOS_to_obs_nml/ site_metadata_file, text_input_file, &
- obs_out_file, sitename, year, maxgoodqc, verbose
+ obs_out_file, sitename, maxgoodqc, verbose
!-----------------------------------------------------------------------
! globally-scoped variables
@@ -179,7 +178,7 @@
! Read the COSMOS metadata/parameters for each site.
! These will be added to the metadata for neutron intensity observations.
-nSites = read_cosmos_metadata(site_metadata_file)
+nSites = read_site_metadata(site_metadata_file)
siteIndx = find_site_index(sitename)
bd = cosmos_metadata(siteIndx)%bd
lattwat = cosmos_metadata(siteIndx)%lattwat
@@ -204,6 +203,14 @@
call find_textfile_dims(text_input_file, max_obs)
+if (max_obs < 0) then
+ write (string1,*) '<'//trim(text_input_file)//'> does not exist.'
+ call error_handler(E_ERR,'main', string1, source, revision, revdate)
+elseif (max_obs < 2) then
+ write (string1,*) trim(text_input_file)//' has no observation values in it.'
+ call error_handler(E_ERR,'main', string1, source, revision, revdate)
+endif
+
iunit = open_file(text_input_file, 'formatted', 'read')
if (verbose) print *, 'opened input file ' // trim(text_input_file)
@@ -413,14 +420,14 @@
- function read_cosmos_metadata(site_metadata_file)
+ function read_site_metadata(site_metadata_file)
!----------------------------------------------------------------------------
-! nsites = read_cosmos_metadata(site_metadata_file)
+! nsites = read_site_metadata(site_metadata_file)
!
! Read the list of parameters for every site we know about and
! return the number of sites we know about.
-integer :: read_cosmos_metadata
+integer :: read_site_metadata
character(len=*), intent(in) :: site_metadata_file
integer :: strlength
@@ -432,34 +439,34 @@
if ( .not. file_exist(site_metadata_file) ) then
write(string1,*) 'COSMIC parameter file [', trim(site_metadata_file),'] does not exist.'
- call error_handler(E_ERR,'read_cosmos_metadata',string1,source,revision,revdate)
+ call error_handler(E_ERR,'read_site_metadata',string1,source,revision,revdate)
endif
call nc_check(nf90_open(site_metadata_file, NF90_NOWRITE, ncid), &
- 'read_cosmos_metadata', 'open '//trim(site_metadata_file))
+ 'read_site_metadata', 'open '//trim(site_metadata_file))
call nc_check(nf90_inq_dimid(ncid, 'nsites', dimIDs(1)), &
- 'read_cosmos_metadata','inq_dimid nsites '//trim(site_metadata_file))
-call nc_check(nf90_inquire_dimension(ncid, dimIDs(1), len=read_cosmos_metadata), &
- 'read_cosmos_metadata','inquire_dimension nsites '//trim(site_metadata_file))
+ 'read_site_metadata','inq_dimid nsites '//trim(site_metadata_file))
+call nc_check(nf90_inquire_dimension(ncid, dimIDs(1), len=read_site_metadata), &
+ 'read_site_metadata','inquire_dimension nsites '//trim(site_metadata_file))
call nc_check(nf90_inq_dimid(ncid, 'strlength', dimIDs(2)), &
- 'read_cosmos_metadata','inq_dimid strlength '//trim(site_metadata_file))
+ 'read_site_metadata','inq_dimid strlength '//trim(site_metadata_file))
call nc_check(nf90_inquire_dimension(ncid, dimIDs(2), len=strlength), &
- 'read_cosmos_metadata','inquire_dimension strlength '//trim(site_metadata_file))
+ 'read_site_metadata','inquire_dimension strlength '//trim(site_metadata_file))
call nc_check(nf90_inq_varid(ncid, 'sitenames', VarID), &
- 'read_cosmos_metadata','inq_varid sitenames '//trim(site_metadata_file))
+ 'read_site_metadata','inq_varid sitenames '//trim(site_metadata_file))
-allocate(cosmos_metadata(read_cosmos_metadata))
+allocate(cosmos_metadata(read_site_metadata))
-do isite = 1,read_cosmos_metadata
+do isite = 1,read_site_metadata
sitename = ''
write(string1,*)'get_var sitename site ',isite,' '//trim(site_metadata_file)
call nc_check(nf90_get_var(ncid, VarID, sitename(1:strlength), &
- start=(/1, isite/), count=(/strlength,1/)), 'read_cosmos_metadata', string1)
+ start=(/1, isite/), count=(/strlength,1/)), 'read_site_metadata', string1)
cosmos_metadata(isite)%sitename = trim(sitename(1:strlength))
@@ -467,10 +474,10 @@
enddo
-call nc_check(nf90_close(ncid), 'read_cosmos_metadata', 'close '//trim(site_metadata_file))
+call nc_check(nf90_close(ncid), 'read_site_metadata', 'close '//trim(site_metadata_file))
if (verbose) then
-do isite = 1,read_cosmos_metadata
+do isite = 1,read_site_metadata
write(*,*)
write(*,*)'site name ',cosmos_metadata(isite)%sitename
write(*,*)'longitude ',cosmos_metadata(isite)%longitude
@@ -488,7 +495,7 @@
enddo
endif
-end function read_cosmos_metadata
+end function read_site_metadata
@@ -534,9 +541,9 @@
start(1) = siteindx
count(1) = 1
-call nc_check(nf90_inq_varid(ncid, varname, VarID), 'read_cosmos_metadata', 'inq_varid '//trim(varname))
+call nc_check(nf90_inq_varid(ncid, varname, VarID), 'read_site_metadata', 'inq_varid '//trim(varname))
call nc_check(nf90_get_var(ncid, VarID, tempspace, start=start, count=count ), &
- 'read_cosmos_metadata', 'get_var '//trim(varname))
+ 'read_site_metadata', 'get_var '//trim(varname))
slot = tempspace(1)
end subroutine get_var
Added: DART/branches/development/observations/COSMOS/COSMOS_level2_to_obs.html
===================================================================
--- DART/branches/development/observations/COSMOS/COSMOS_level2_to_obs.html (rev 0)
+++ DART/branches/development/observations/COSMOS/COSMOS_level2_to_obs.html 2012-10-30 19:12:50 UTC (rev 5907)
@@ -0,0 +1,475 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
+ "http://www.w3.org/TR/html4/strict.dtd">
+<HTML>
+<HEAD>
+<TITLE>program COSMOS_level2_to_obs</TITLE>
+<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+<link href="../../doc/html/dart.ico" rel="shortcut icon" />
+</HEAD>
+<BODY>
+<A NAME="TOP"></A>
+
+<H1>PROGRAM <em class=program>COSMOS_level2_to_obs</em></H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+ <td valign=middle>
+ <img src="../../doc/html/Dartboard7.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="#DataSources">DATA SOURCES</A> /
+<A HREF="#Programs">PROGRAMS</A> /
+<A HREF="#Namelist">NAMELIST</A> /
+<A HREF="#References">REFERENCES</A> /
+<A HREF="#Errors">ERRORS</A> /
+<A HREF="#FuturePlans">PLANS</A> /
+<A HREF="#Legalese">TERMS OF USE</A>
+
+<H1>Overview</H1>
+
+<H4>COSMOS "Level 2" Text File to DART Converter</H4>
+
+<P>
+<a href="http://cosmos.hwr.arizona.edu/">COSMOS</a> is an NSF supported
+project to measure soil moisture on the horizontal scale of hectometers
+and depths of decimeters using cosmic-ray neutrons.
+The data for each station is available from the COSMOS data portal with
+several levels of processing. The metadata for each station
+(location, height, etc) is also available from the data portal.
+The <b>Level 2 Data</b> is most suited for use with DART.
+<br />
+<br />
+Since each site has a separate input data file, and the metadata for
+each site must essentially be hand-input to the converter program, it is
+generally easiest to convert the observations for each site separately
+and then use the <a href="../../obs_sequence/obs_sequence_tool.html">
+obs_sequence_tool.f90</a> to combine the observations from multiple sites
+and restrict the DART observation sequence file to contain just the
+observations of the timeframe of interest.
+<br />
+<br />
+FYI - in DART, the soil moisture profile is converted to expected neutron counts using
+the <b>CO</b>smic-ray <b>S</b>oil <b>M</b>oisture <b>I</b>nteraction <b>C</b>ode (COSMIC),
+developed at the University of Arizona by Rafael Rosolem and Jim Shuttleworth.
+<br />
+<br />
+The workflow is usually:
+</P>
+<ol>
+<li><a href="http://cosmos.hwr.arizona.edu/Probes/probemap.php">get the site metadata</a>
+ and enter it in the <em class=file>input.nml</em>
+ <em class=input>&COSMOS_to_obs_nml</em></li>
+
+<li>download the Level 2 Data and prefix the filename with the station name (or else they
+ all get named <em class=file>corcounts.txt</em>)
+ and enter the filename into <em class=input>&COSMOS_to_obs_nml</em></li>
+
+<li>make sure the station soil parameters and COSMIC parameters are contained in the
+ <em class=file>observations/COSMOS/data/COSMIC_parlist.nc</em>
+ (more on this in <a href="#COSMICparameters">the section on COSMIC parameters</a>)</li>
+
+<li>run <em class=program>COSMOS_level2_to_obs</em> to generate a DART observation sequence
+ file for the station and rename the output file if necessary
+ (you can explicity name the output file via the namelist).</li>
+
+<li>repeat steps 1-4 for this converter to generate a DART observation sequence
+ file for each station.</li>
+
+<li>use the <a href="../../obs_sequence/obs_sequence_tool.html">obs_sequence_tool.f90</a>
+ to combine the observations from multiple sites</li>
+</ol>
+
+
+<!--==================================================================-->
+
+<A NAME="DataSources"></A>
+<div class="top">[<a href="#">top</a>]</div><hr />
+<H2>DATA SOURCES</H2>
+
+<P>
+The COSMOS data portal can be found at:
+<a href="http://cosmos.hwr.arizona.edu/Probes/probemap.php">
+http://cosmos.hwr.arizona.edu/Probes/probemap.php</a>
+The data for each station is available from the data portal with several
+levels of processing. The metadata for each station (location, height, etc) is also
+available from the data portal. The <b>Level 2 Data</b> is most suited for use with DART.
+An example of the Level 2 Data follows:
+</P>
+<pre>
+YYYY-MM-DD HH:MM MOD PROBE PRESS SCALE SANPE INTEN OTHER CORR ERR
+2009-10-23 18:34 5996 0.800 1.087 06.901 2.486 1.062 1.000 1768 022
+2009-10-23 19:34 5885 0.800 1.080 06.901 2.486 1.059 1.000 1729 022
+2009-10-23 20:34 6085 0.800 1.072 06.901 2.486 1.059 1.000 1774 022
+2009-10-23 21:34 6339 0.800 1.068 06.901 2.486 1.059 1.000 1843 023
+...
+</pre>
+
+<!--==================================================================-->
+
+<A NAME="Programs"></A>
+<div class="top">[<a href="#">top</a>]</div><hr />
+<H2>PROGRAMS</H2>
+<P>
+The <em class=file>COSMOS_level2_to_obs.f90</em> file is the source code
+for the main converter program.
+At present there is an uncomfortable assumption that the order of the columns
+in the Level 2 data is fixed. I hope to relax that requirement in the near future.
+<em class=program>COSMOS_level2_to_obs</em>
+reads each text line into a character buffer
+and then reads from that buffer to parse up the data items.
+The items are then combined with the COSMIC parameters for that site
+and written to a DART-format observation sequence file. The DART format
+allows for the additional COSMIC parameters to be contained as metadata for
+each observation.
+</P>
+<P>
+To compile and test, go into the <em class=file>COSMOS/work</em> subdirectory and
+run the <em class=program>quickbuild.csh</em>
+script to build the converter and a couple of general purpose utilities.
+The <a href="../../obs_sequence/obs_sequence_tool.html">obs_sequence_tool</a>
+manipulates (i.e. combines, subsets) DART observation files once they have been created.
+The default observations supported are those defined in
+<a href="../../obs_def/obs_def_tower_mod.f90">DART/obs_def/obs_def_tower_mod.f90</a> and
+<a href="../../obs_def/obs_def_COSMOS_mod.f90">DART/obs_def/obs_def_COSMOS_mod.f90</a>.
+If you need additional observation types, you will have to add the
+appropriate <em class=file>obs_def_XXX_mod.f90</em> file to the
+<em class=file>input.nml</em> <em class=code>&preprocess_nml:input_files</em>
+variable and run <em class=program>quickbuild.csh</em> again.
+It rebuilds the table of supported observation types before
+compiling the source code.
+</P>
+
+<A NAME="COSMICparameters"></A>
+<div class=indent1>
+<H3>COSMIC parameters</H3>
+<P>
+Additional information is needed by DART to convert soil moisture profiles
+to neutron counts. Each COSMOS instrument has site-specific parameters
+describing soil properties etc. Those parameters have been inserted into
+the observation file as metadata for each observation to simplify the
+DART observation operator.
+It is a bit redundant as currently implemented, but it is convenient.
+<br />
+<br />
+<em class=program>COSMOS_level2_to_obs</em> reads the site name from
+the input namelist and the known station information from
+<em class=file>COSMIC_parlist.nc</em>. The simplest way to add a new station to
+<em class=file>COSMIC_parlist.nc</em> is probably to:
+</P>
+<ol><li>manually enter the information into the "data" section of
+ <em class=file>COSMIC_parlist_station.txt</em></li>
+ <li>then use <em class=program>ncgen</em> to convert
+ <em class=file>COSMIC_parlist_station.txt</em> to a netCDF file.</li>
+ <li>That netCDF file can be concatenated onto <em class=file>COSMIC_parlist.nc</em>
+ with a simple <em class=program>ncrcat</em> command.</li>
+</ol>
+<P>
+Listing the sites already supported is easy:
+</P>
+<div class=unix>
+<pre>
+observations/COSMOS/data % <em class=input>ncdump -v sitenames COSMIC_parlist.nc</em>
+netcdf COSMIC_parlist {
+dimensions:
+ nsites = UNLIMITED ; // (42 currently)
+ strlength = 21 ;
+variables:
+ char sitenames(nsites, strlength) ;
+ sitenames:long_name = "COSMOS Site Names" ;
+ double longitude(nsites) ;
+ longitude:long_name = "Longitude" ;
+ longitude:units = "degrees" ;
+ double latitude(nsites) ;
+ latitude:long_name = "Latitude" ;
+ latitude:units = "degrees" ;
+ double elevation(nsites) ;
+ elevation:long_name = "Elevation" ;
+ elevation:units = "m" ;
+ double bd(nsites) ;
+ bd:long_name = "Dry Soil Bulk Density" ;
+ bd:units = "g cm{-3}" ;
+ double lattwat(nsites) ;
+ lattwat:long_name = "Lattice Water Content" ;
+ lattwat:units = "m{3} m{-3}" ;
+ double N(nsites) ;
+ N:long_name = "High Energy Neutron Intensity" ;
+ N:units = "relative counts" ;
+ double alpha(nsites) ;
+ alpha:long_name = "Ratio of Fast Neutron Creation Factor (Soil to Water)" ;
+ alpha:units = "-" ;
+ double L1(nsites) ;
+ L1:long_name = "High Energy Soil Attenuation Length" ;
+ L1:units = "g cm{-2}" ;
+ double L2(nsites) ;
+ L2:long_name = "High Energy Water Attenuation Length" ;
+ L2:units = "g cm{-2}" ;
+ double L3(nsites) ;
+ L3:long_name = "Fast Neutron Soil Attenuation Length" ;
+ L3:units = "g cm{-2}" ;
+ double L4(nsites) ;
+ L4:long_name = "Fast Neutron Water Attenuation Length" ;
+ L4:units = "g cm{-2}" ;
+
+// global attributes:
+ :website = "COsmic-ray Soil Moisture Observing System (COSMOS) -
+ http://cosmos.hwr.arizona.edu" ;
+data:
+
+ sitenames =
+ "ARM-1 ",
+ "Austin_Cary ",
+ "Bondville ",
+ "Brookings ",
+ "Chestnut_Ridge_NOAA ",
+ "Coastal_Sage_UCI ",
+ "Daniel_Forest ",
+ "Desert_Chaparral_UCI ",
+ "Fort_Peck ",
+ "Harvard_Forest ",
+ "Hauser_Farm_North ",
+ "Hauser_Farm_South ",
+ "Howland ",
+ "Iowa_Validation_Site ",
+ "Island_Dairy ",
+ "JERC ",
+ "Kendall ",
+ "KLEE ",
+ "Manitou_Forest_Ground",
+ "Metolius ",
+ "Morgan_Monroe ",
+ "Mozark ",
+ "Mpala_North ",
+ "Neb_Field_3 ",
+ "P301 ",
+ "Park_Falls ",
+ "Pe-de-Gigante ",
+ "Rancho_No_Tengo ",
+ "Reynolds_Creek ",
+ "Rietholzbach ",
+ "Rosemount ",
+ "San_Pedro_2 ",
+ "Santa_Rita_Creosote ",
+ "Savannah_River ",
+ "Silver_Sword ",
+ "SMAP-OK ",
+ "Soaproot ",
+ "Sterling ",
+ "Tonzi_Ranch ",
+ "UMBS ",
+ "UVA ",
+ "Wind_River " ;
+}
+</pre>
+</div>
+
+<P>The observation sequence files will look something like the following,
+the attributes in yellow are the information from <em class=file>COSMIC_parlist.nc</em>:
+</P>
+
+<div class=unix>
+<pre>
+ obs_sequence
+obs_kind_definitions
+ 1
+ 20 COSMOS_NEUTRON_INTENSITY
+ num_copies: 1 num_qc: 1
+ num_obs: 3840 max_num_obs: 3840
+observation
+COSMOS QC
+ first: 1 last: 3840
+ OBS 1
+ 1048.0000000000000
+ 1.0000000000000000
+ -1 2 -1
+obdef
+loc3d
+ 4.154723123116714 0.7997185899100618 0.000000000000000 -1
+kind
+ 20
+<div style="color: yellow"> cosmic
+ 0.88500000000000001 5.84099999999999966E-002 336.95696938999998 0.31918025877000000
+ 161.98621864285701 129.14558984999999 55.311849408000000 3.8086191933000002
+ 1</div>
+ 77340 150034
+ 1225.0000000000000
+ ...
+</pre>
+</div>
+</div><!-- end of block indent -->
+<P></P><!-- needed to make 'top' align correctly -->
+
+<!--==================================================================-->
+<!--=================== DESCRIPTION OF A NAMELIST ===================-->
+<!--==================================================================-->
+
+<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>
+<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
+</pre>
+</div>
+
+<div class=indent1>
+<!-- Description -->
+
+<P>This namelist is read in a file called <em class=file>input.nml</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>
+
+<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><!--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><!--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><!--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><!--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><!--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>
+
+</TABLE>
+
+<H3 class=indent1>Example</H3>
+
+<pre>
+&COSMOS_to_obs_nml
+ site_metadata_file = '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 -->
+
+<!--==================================================================-->
+<!-- References. -->
+<!--==================================================================-->
+
+<A NAME="References"></A>
+<div class="top">[<a href="#">top</a>]</div><hr />
+<H2>References</H2>
+<ul>
+<li><a href="http://cosmos.hwr.arizona.edu">The COSMOS web page.</a></li>
+
+<li>Franz, T.E, M. Zreda, T.P.A. Ferre, R. Rosolem, C. Zweck, S. Stillman,
+ X. Zeng and W.J. Shuttleworth, 2012: Measurement depth of the cosmic-ray
+ soil moisture probe affected by hydrogen from various sources.
+ <span style="font-style: italic;"> Water Resources Research</span>
+ <span style="font-weight: bold;">48</span>, W08515,
+ <a href="http://dx.doi.org/10.1029/2012WR011871">doi:10.1029/2012WR011871</a>
+ </li>
+
+<li>Franz, T.E, M. Zreda, R. Rosolem, T.P.A. Ferre, 2012:
+ Field validation of cosmic-ray soil moisture probe using a distributed sensor network.
+ <span style="font-style: italic;">Vadose Zone Journal</span> (in press),
+ <a href="http://dx.doi.org/10.2136/vzj2012.0046">doi:10.2136/vzj2012.0046</a>
+ </li>
+</ul>
+
+<!--==================================================================-->
+<!-- Describe the bugs. -->
+<!--==================================================================-->
+
+<A NAME="KnownBugs"></A>
+<div class="top">[<a href="#">top</a>]</div><hr />
+<H2>KNOWN BUGS</H2>
+<P>
+none
+</P>
+
+<!--==================================================================-->
+<!-- Describe Future Plans. -->
+<!--==================================================================-->
+
+<A NAME="FuturePlans"></A>
+<div class="top">[<a href="#">top</a>]</div><hr />
+<H2>FUTURE PLANS</H2>
+<ul>
+<li>Implement a routine to automatically determine the column indices of
+the columns of interest.</li>
+<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 -->
+<!--==================================================================-->
+
+<A NAME="Legalese"></A>
+<div class="top">[<a href="#">top</a>]</div><hr />
+<H2>Terms of Use</H2>
+
+<P>
+DART software - Copyright 2004 - 2011 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> Tim Hoar </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 history: </TD><TD> try "svn log" or "svn diff" </TD></TR>
+</TABLE>
+
+<!--==================================================================-->
+
+</BODY>
+</HTML>
Property changes on: DART/branches/development/observations/COSMOS/COSMOS_level2_to_obs.html
___________________________________________________________________
Added: svn:mime-type
+ text/html
Added: svn:keywords
+ Date Rev Author HeadURL Id
Added: svn:eol-style
+ native
Added: DART/branches/development/observations/COSMOS/data/COSMIC_parlist.nc
===================================================================
(Binary files differ)
Property changes on: DART/branches/development/observations/COSMOS/data/COSMIC_parlist.nc
___________________________________________________________________
Added: svn:mime-type
+ application/x-netcdf
Modified: DART/branches/development/observations/COSMOS/work/input.nml
===================================================================
--- DART/branches/development/observations/COSMOS/work/input.nml 2012-10-29 20:01:07 UTC (rev 5906)
+++ DART/branches/development/observations/COSMOS/work/input.nml 2012-10-30 19:12:50 UTC (rev 5907)
@@ -3,7 +3,7 @@
output_obs_kind_mod_file = '../../../obs_kind/obs_kind_mod.f90',
input_obs_def_mod_file = '../../../obs_def/DEFAULT_obs_def_mod.F90',
output_obs_def_mod_file = '../../../obs_def/obs_def_mod.f90',
- input_files = '../../../obs_def/obs_def_tower_mod.f90'
+ input_files = '../../../obs_def/obs_def_tower_mod.f90',
'../../../obs_def/obs_def_COSMOS_mod.f90'
/
@@ -25,12 +25,24 @@
&COSMOS_to_obs_nml
site_metadata_file = '../data/COSMIC_parlist.nc',
- text_input_file = '../data/corcounts.txt',
- obs_out_file = 'obs_seq.out',
- sitename = 'wind_river',
+ text_input_file = '../data/SantaRita.corcounts.txt',
+ obs_out_file = 'SantaRita.obs_seq.out',
+ sitename = 'Santa_Rita_Creosote',
maxgoodqc = 1,
verbose = .TRUE.
/
# For COSMOS_level2_to_obs, the filename is data/corcounts.txt
# For COSMOS_to_obs, the filename is data/COSMOS_SantaRita_2011.dat
+
+&obs_sequence_tool_nml
+ filename_seq = 'Austin_Cary.obs_seq.out', 'SantaRita.obs_seq.out',
+ filename_out = 'obs_seq.combined',
+ filename_seq_list = '',
+ num_input_files = 2,
+ first_obs_days = -1,
+ first_obs_seconds = -1,
+ last_obs_days = -1,
+ last_obs_seconds = -1
+ /
+
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