Advanced topics

Climate surface coefficient files

The climate surface coefficient files used by ANUCLIM need to be created using ANUSPLIN, a suite of programs developed by Hutchinson (1989, 1991, 1999). ANUSPLIN is distributed by the Centre for Resource and Environmental Studies. See http://cres.anu.edu.au for details. The ANUSPLIN technique of thin­plate smoothing splines is used for the spatial interpolation of meteorological variables from irregular networks. Some general rules apply when creating the climate surface coefficient files for use by the ANUCLIM package. They are:

• The input data for each meteorological variable must be the twelve monthly values.
• The units for the meteorological variable must be as stated in the surflist file.
• At least two and not more than three independent variables must be used
• The first two independent variables must be longitude and latitude in that order
• The third independent variable must be one of the following:
  • elevation
  • distance from coast (ESOCLIM only)
  • rainfall
  The units must be those specified in Units of data in your input files

There can be more than one climate surface coefficient file per meteorological variable per country, for instance, Australia currently has seven rainfall surfaces,

The surflist file

The surflist file is a text file that describes the surfaces that ANUCLIM can use. ANUCLIM is supplied with a standard surflist file that describes the Australian climate surfaces. This file is called surflist and is found in the surf directory of the ANUCLIM installation. A copy of this file can also be found in doc/standard-surflist.txt in the ANUCLIM installation directory in case your installation does not include the Australian climate surfaces. If you need to add or change surfaces, add countries or build a surflist file from scratch, see the supplied surflist file for details. Comments in the surflist file describe its structure in detail. Filenames in the surflist file are interpreted relative to the directory containing the surflist file. This means that if your surfaces and surflist file are all in the same directory, you don't have to specify a directory path in front of the surface filenames in the surflist file.

Making the .bcp file available to other people

In most cases, only a single .bcp file need be generated for each DEM of interest, and this file can be shared by all users on your system. In order to do this...

• Generate the .bcp file with BIOCLIM.
• Check to see if a directory called bcp exists in the ANUCLIM installation root directory. The full pathname of this directory can be determined by clicking Find files on the main BIOMAP window (it should be listed in the search patterns at the top of the Modify search path dialog).
• If the bcp directory doesn't exist, create it. You may need root or superuser privileges to do this. Make sure that you create it with permissions that allow all interested users to access files in it.
• Copy your .bcp file into the bcp directory. Make sure that the copied file has permissions that allow all interested users to read it.

Once you have done this, all ANUCLIM users on your system should see the .bcp file in the file list in the BIOMAP main window.

Running the programs from a command file.

ANUCLIM normally processes your input files when you click the Run button, but there are times when this may not be desired behaviour. You can use ANUCLIM to generate a command file which can then be used to run the bioclim, esoclim, groclim or biomap back end programs at a later stage.

There are two ways of generating command files with ANUCLIM:

• Use the generate command file option on the options panel of the BIOCLIM, ESOCLIM or GROCLIM windows.
• Process your input data in the usual interactive fashion by clicking the Run button. Once the command has completed (i.e. the Run button becomes active again), the command file used in that run will be saved in the ANUCLIM settings directory. Under unix, the files are saved as ~/.anuclim/last-*.cmd. Under Microsoft windows they are saved as ~/Anuclim-config/last-*.cmd. (~ is shorthand for your home directory. On Microsoft Windows this is usually C:/). Note that this method will work even if you click the stop button while the process is running, or if the back end process is killed by some other means.

You can also use anuclimc to generate command files.

The back end programs do not create any windows of their own, so they can be submitted as batch jobs or incorporated in a shell script. This is useful if the processing takes a long time (e.g. processing a large DEM), or if you want to run a series of jobs in sequence. In most unix shells and at the MS-DOS command line prompt you can use the syntax
program_name < command_file > log_file
to achieve this. For example
bioclim < bioclim_species1.cmd > bioclim_species1.log
Note that on both unix and Microsoft Windows you will have to ensure that the PATH environment variable is set to include the directory where the back end programs are located. This is usually the bin directory in the ANUCLIM installation directory.

The command files are plain text files, and can be viewed or edited with a text editor. The command files generated by ANUCLIM contain comments that describe the meaning of each directive in the file. If you edit a command file you must take care to preserve the exact formatting of the original file. See Manual pages for command-line programs for more information.

Command line version of ANUCLIM

The ANUCLIM package is supplied with a supplementary program called anuclimc . This program provides a way to generate command files from a command line prompt, and does not use the window system of your computer. It is identical to the anuclim front-end program supplied on the ANUCLIM 1.8 CD. anuclimc can be found in the bin directory of the ANUCLIM distribution, The user manual for anuclimc is distributed as a PostScript file and can be found in anuclimc.ps in the doc directory of the ANUCLIM installation.

Radiation ratio tables

The estimated values of radiation obtained from the radiation surface can in some cases be modified by slope and aspect. In order to use this feature, you need slope/aspect ratio tables (flat surface to inclined plane) for the area of interest and a slope value and an aspect value for each location in your input data. The programs are currently structured so that to modify radiation estimates across a country, a corresponding ratio file is needed for each rainfall surface coefficient file. You must also select the rainfall surface in order for the radiation modification to take effect.

The values in this ratio file are currently obtained by running the program CLOUDY (Fleming, 1971; Austin, Cunningham, Fleming, 1984 and Fleming, 1987), and requires actual meteorological data for a representative station which is located within the limits of the rainfall area. Ratio values in the tables are needed for

• 13 slopes, ranging from 0 ­ 60 degrees in steps of 5 degrees.
• 37 aspects, ranging from 0 ­ 360 degrees in steps of 10 degrees
• 12 months
• diffuse and direct radiation

The units for the radiation values are Mj/m²/day for the total radiation received on a surface. These values are split into two component parts, diffuse radiation and direct radiation in order to use the ratio tables. The package uses the relationship relating diffuse and total radiation developed by Kalma and Fleming (1972) given by the following equation
kdf=ktt(1-e^{0.8(1-0.9/ktt)})
where
kdf= diffuse radiation divided by extraterrestrial radiation ktt= total radiation divided by extraterrestrial radiation (extraterrestrial radiation is calculated from latitude)

The surflist file contains lines that specify which tables are available and the rainfall surface patch they correspond to. The supplied surflist file specifies just 2 radiation ratio tables. The lines concerned look like this:

  PART 4
#
   1  1 nqlratio.dat
   1  5 tasratio.dat

Each line lists the country number, rainfall patch number and ratio table filename (relative to the directory containing the surflist file). The rainfall patch number is derived from the sequence of rainfall surface files listed in part 3 of the surflist file. The first rainfall surface is patch 1, the 2nd rainfall surface is patch 2 and so on. If you add or change the ratio table lines in the surflist file, you must take care to preserve the formatting exactly. These lines have the fortran format

(1x,2i3,1x,a)

Each ratio-table file consists of 12 sets of diffuse radiation values, followed by 12 sets of direct radiation values (one set for each month). Each set of radiation values consists of 37 lines of aspect values, and on each line are the 13 slope values. Each line has the fortran format

(11x,13f5.2)

The first line of aspect data refers to -5<=aspect<5, the next line refers to 5<=aspect<15, and so on up to line 37, which refers to 355<=aspect<365. The first slope value on a line refers to -2.5<=slope<2.5, the next one to 2.5<=slope<7.5 and so on up to the 13th field which refers to 57.5<=slope<62.5.

The table values are used to modify the radiation using the following algorithm:

• rdif is the ratio table diffuse value for the slope, aspect and month concerned.
• rdir is the ratio table direct value for the slope, aspect and month concerned.
• qext is the theoretical radiation received by a point on the ground during the month concerned based on its latitude alone (i.e. doesn't take into account atmospheric effects).
• qest is the radiation value from the climate surface for a given location in a given month.
• qmod is the final modified radiation value

ktt = qest/qext
kdf=ktt(1-e^{0.8(1-0.9/ktt)})
kdf = kdf * qext
kdr = qest - kdf
kdf = kdf * rdif
kdr = kdr * rdir
qmod= = kdf + kdr

Customising fonts, colours etc.

You can change the fonts, colours and other properties of the ANUCLIM windows by creating or editing a text file containing option and value settings.

• On Microsoft windows, the file must be called ~/Anuclim-config/app-defaults.txt. (~ is shorthand for your home directory. On Microsoft Windows this is usually C:/, unless overridden by the HOME environment variable.
• On unix, you can either edit the .Xdefaults file in your home directory, create a file called ~/.anuclim/app-defaults, or use the xrdb -merge filename command. If you edit the .Xdefaults file, the changes you make won't take effect until you restart the X server (usually by logging out and logging in again).

The file should contain lines in the form

option: value

You can have blank lines in the file. Any line beginning with an exclamation mark(!) is treated as a comment. An app-defaults file containing all the configurable settings for ANUCLIM can be found in doc/app-defaults.txt in the ANUCLIM installation directory. The values shown in this file are those that give the default appearance. Copy any of the lines from this file into your own app-defaults file and change the values to suit your taste.

Directory for temporary files

ANUCLIM uses various temporary files in its operation. Usually these files are quite small, so the default directory settings are OK. However, if you are generating grid output from BIOMAP, these files can be quite large. If you run out of space in the standard temporary file directories, you can set environment variables to specify the name of your temporary file directory. On unix, set CRESEXECTEMP . On Microsoft Windows, set TEMP. The standard temporary file directories are usually /tmp on unix and c:\windows\temp on Microsoft Windows, but are determined at run time by looking in a number of standard places to see what is available and writable. If you set an environment variable, you must restart ANUCLIM from a shell that has inherited the new value.

Files in the surf directory

The file naming conventions for files in the surf directory are as follows:

Filename pattern	Contents
surflist*	Surface file catalog used by ANUCLIM to find surface files
*.?s?	Surface coefficient files. The digits before and after the "s" in the extension are the major and minor surface version numbers respectively.