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Running Autobk

The AUTOBK Input File

To begin editing an AUTOBK input file, type C-x C-f or select Open File from the Files menu. You will be asked for the name of a file in the `feff' subdirectory. Before responding with a name, delete the characters `feff/' so that you will open a file in the `Cu' subdirectory. Then type out `autobk.inp'. You will be presented with a blank window. Notice that you are now in Autobk minor mode, the menu bar has the Autobk label, and there is an Autobk menu in the menu bar.

Before writing a template, let's set several variables that will be useful in the next few steps of the tutorial. In the Input menu you will notice options for Set path to input data, Set path to feff files, and Set output path. The key sequences for these are C-c C-d followed by d, f, and o respectively. These are used to tell @fuse{} where to find different sorts of files. Run each of these functions using `data/' as the data path, `feff/' as the feff path, and `data/' as the output path.

Now insert a template by typing C-c C-t t, selecting `Autobk template' from the `Autobk' menu, or clicking mouse-1 on the top-most toolbar icon. Note that the information about file paths that you just entered has appeared in appropriate places in the template. Note that, just as with the ATOMS template, hotspot markings have been placed in the template as a visual cue for where keyword values must be inserted. If you enter reasonable data at each hotspot, it is quite likely that your input file will run to completion.

Now fill in appropriate values at each hotpot. Use values of 1, 1, and 4 for kmin, rmin, and rmax respectively. Write `cu10k.dat' after `data/' for the data keyword and `chi.dat' after `feff/' for the theory keyword. Pick a good basename for the output files, `cu10k' should do just fine. You can delete the line with e0 as we will let AUTOBK find it. Now place the screen cursor on one of the keywords, kmin for example. Hit M-?. This command causes @fuse{} to display a description of the keyword under the screen cursor in the echo area. Now hit M-ret. If you put a number in as the value for kmin, you will see a message in the echo area saying that this value is ok. Try changing the value of kmin to q and hitting M-ret again. Don't forget to change it back! Now place the screen cursor on the data keyword and try M-? and M-ret again. Notice that the keyword checking facility knows about and checks for readable files. If you like the help given by M-?, you can have it happen automatically by hiting C-c C-b t or selecting Fuse-doc mode from the top of the Input menu. With fuse-doc mode turned on, a keyword description will automatically be displayed in the echo area whenever the screen cursor comes to rest on a keyword. This works in any program minor mode. The messages displayed are the same as those displayed by C-c C-b k or the question mark icon in the toolbar.

Now finish filling in the template and save it. It should look like Figure 6.

Several interesting things happened when you saved this file. The Local Variables list was written to this files just as it was to `atoms.inp' and `feff.inp'. Notice that the values for file paths that you entered earlier were written to the list. The next time that you edit this file, it will not be necessary to re-enter that information. @fuse{} will read it from the Local Variables list. Also note that a time stamp was placed after the Local Variables list. This is updated every time you save the file so you will always know when you last edited the file. Now move the mouse cursor so it is over the line that specifies the data file. See how the background flashes orange as soon as the cursor is over either the keyword data or the filename? This orange flashing is a visual cue in @fuse{} that the mouse cursor is in a position where hitting S-mouse-3 will do something. That something depends on the kind of input file you are editing and on the location of the mouse cursor. In this case, hitting S-MOUSE-3 will open and display the file under the cursor. These orange areas are set when the input file is first visited and whenever it is saved. You can turn off the orange flashing for a given buffer in the Input - Miscellaneous submenu.

Figure 6: Completed AUTOBK input file

**image file autobk-inp.jpg**

Running and Plotting in AUTOBK Mode

Now run AUTOBK. Note that the run-time messages from AUTOBK will be added to those already in the run-time messages buffer. Also note that the elapsed time of the run is written to the buffer in the run-time frame. This is printed out in the form of your computers `time' shell command. On my Linux system using bash, it looks like this:

193.560u 0.160s 0:09.25 97.2%	0+0k 0+0io 171pf+0w

The relevant number is the third one. This says that that particular AUTOBK run took 0 minutes and 9.25 seconds. Check the man pages for your shell for complete details about the `time' command.

Once the run is finished (it should not take long), there are several things that can be plotted. In the Autobk menu there are several entries under the heading Plotting. The things that can be displayed automatically from this input file are the @greek{mu,E} data along with the background (C-c C-p b and shown in Figure 7), @greek{chi,k} (C-c C-p k), and @greek{chi,k} along with the theoretical @greek{chi,k} from the FEFF run (C-c C-p t). The @greek{mu,E} and @greek{chi,k} plots are also bound to toolbar icons.

Although we will not be using this feature of AUTOBK during this tutorial, it has the ability to batch process @greek{mu,E} data into @greek{chi,k}. The instructions then look the same for each data set and are separated in the input file by lines of dashes. In @fuse{}, a line-of-dashes separated set of instructions is called a stanza. AUTOBK mode in @fuse{} has several functions for operating on stanzas. In the Autobk menu there are options for running AUTOBK on the entire file or on the stanza currently occupied by the screen cursor. The plotting functions described in the last paragraph all work on the current stanza. Additionally there is a plotting function for displaying all @greek{chi,k} from the input file (C-c C-p a and bound to the toolbar).

@ifnotinfo

Figure 7: Plotting the data and background

**image file autobk-plot.jpg**

Examining the output of AUTOBK

Plotting the output files from AUTOBK is an important part of evaluating and understanding the result, but there is more to the interpretation of data than making pretty pictures. For example, from an AUTOBK run, it is important to know where @ezero{} is. Hit C-c C-s e. A line with e0f = 8976.886 is inserted in the stanza. Cool! Where did that come from?

Now hit C-c C-f l, select Look at log file from either the Autobk or Input - Visit files menu, or hit the third toolbar icon (the one with the thumbtack). Doing so displays the log file from your autobk run. Somewhere around line 15 in the log file is the final value of @ezero{} found by AUTOBK. The C-c C-f l key sequence and its related menu and toolbar bindings are the common way of examining log files in @fuse{}. That key sequence and the thumbtack icon will always display the log file appropriate to the current input file.(3) You can easily return to the input file by hitting M-C-`.

@fuse{} is clever enough to search the log file for the final value of @ezero{} and insert it into the input file. The e0f keyword tells AUTOBK to fix @ezero{} to that value. If you want to play around with other background removal parameter while keeping @ezero{} fixed, e0f is the right keyword. In the next chapter you will learn of other ways that @fuse{} is able to glean information from log and other files for use in input files.


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