Introduction to Unix, DTDM, GrADS

1. Introduction to Unix, DTDM, GrADS http://www.atmos.ucla.edu/~fovell/AOSC115/

2. Some Unix basics(basis of Linux and Mac OS X) • The command prompt is $ (do not type it) • Unix commands presented in Courier font $ ls [lists your “visible” files] $ ls -a [lists all files, including invisible] $ ls -al [lists all files, includes size & other info] $ pwd [print working directory - shows your location]

3. Some Unix basics(continued) $ mkdir TEST [makes a directory called “TEST”] $ cd TEST [changes directory to “TEST”] $ cd .. [moves UP in directory hierarchy] $ cd TeST [command should FAIL… Unix is usually CASE SENSITIVE – though it isn’t on Mac]

4. Some Unix basics(continued) $ touch crap.txt [makes an empty file] $ gedit crap.txt [invoked Notepad-like text editor on Synoptic Lab machines] [add some text, save file and exit] $ ls -al crap.txt [see it’s there] $ cp crap.txt crap.txt.backup [make a copy with cp] $ rm crap.txt [the remove command. Asks for confirmation. Don’t type ‘y’] $ \rm crap.txt [remove without confirmation. Think before hitting ENTER!]

5. Some Unix basics(continued) $ mkdir BACKUP [makes a new directory] $ cp crap.txt.backup BACKUP/. [type exactly as written - there is NO space before the period] [the period means “keep the same name”] $ ls -al BACKUP/ [see a copy is in the new location] $ mkdir BACKUP/more_backup [a new subdirectory in a directory] $ cd BACKUP/more_backup [move to new subdirectory] $ cd $ pwd [cd by itself always takes you to your home directory]

6. Some Unix basics(continued) $ cp /home/fovell/part* . [asterisk is wild card character. There IS a space before the period] [copies all files matching text pattern to your directory] $ ls part* [lists files matching pattern] $ cat part1 part2 > both_parts [concatenates files] [greater-than sign is output redirect] $ more both_parts [more lists contents, one screen at a time] [hit space bar for next screenfull, type “q” to quit]

7. Your Unix PATH $ cp /home/fovell/execute_me . $ execute_me - if you receive execute_me: command not found your PATH needs changing - The PATH is an environment variable that tells Unix where to find stuff, and the order in which to look $ ./execute_me - this forces Unix to look in the current directory for the program to run

8. Fortran compiler • Try this command $ which ifort • If you get this… we definitely need to alter your Unix environment $ ifort: Command not found

9. Preparation for new users[for users with bash shell ONLY] $ cd $ mv .bash_profile .bash_profile_old [mv is move command] [.bash_profile is script file of commands, paths, etc., executed for every new terminal window] $ cat .bash_profile_old /home/fovell/addon2014.sh > .bash_profile [type exactly as shown] [greater-than sign is output redirect] $ source .bash_profile [changes to script file in present window do not take effect until “sourced”] $ which ifort [see: /opt/intel/composer_xe_2015.0.090/bin/intel64/ifort ] $ which grads [see /usr/bin/grads]

10. DTDM on our Synoptic Lab Linux computers • Synoptic Lab computers open during business hours ONLY and printing is difficult $ cp /home/fovell/DTDM_package_linux.tar .[note space and period!] $ tar –xvf DTDM_package_linux.tar $ cd DTDM $ make [makes the dtdm executable file]

11. Using DTDM $ dtdm < input_thermal.txt [runs model, makes output] [less-than sign provides contents of txt file to the dtdm executable] $ grads –l [starts up GrADS; ga-> is GrADS prompt] ga-> open thermal.anelastic ga-> query file

12. http://grads.iges.org/grads/gadoc/gadocindex.html Getting to know GrADS • Important commands open [file] open my_experiment q or query q file, q dims d or display d theta, d qvapor c or clear c set gxout contour, shaded, print, scatter d u;v [plots vectors set t 13 [sets to 13th time set cint 1.5 [contour interval set ccolor 4 [contour color blue printimout.gif gif [makes a GIF plot set display color white [makes white background** quit [quits GrADS **GrADS 2.1 and later ignores “color”, so ‘set display white’ suffices

13. Using DTDM (cont.) File 1 : DTDM demo simulation Descriptor: thermal.anelastic.ctl Binary: thermal.anelastic.dat Type = Gridded Xsize = 99 Ysize = 1 Zsize = 82 Tsize = 11 Number of Variables = 17 u 82 0 horizontal velocity up 82 0 pert horizontal velocity w 82 0 vertical velocity th 82 0 potential temperature thp 82 0 pert potential temperature pi 82 0 ndim pressure pip 82 0 pert ndim pressure ppmb 82 0 pert pressure in millibars pbyc 82 0 buoyancy pressure in millibars pdyn 82 0 dynamic pressure in millibars ptot 82 0 total pressure in millibars dudtd 82 0 U acceleration - dynamic dudtb 82 0 U acceleration - buoyancy dudtt 82 0 U acceleration - total dwdtd 82 0 W acceleration - dynamic dwdtb 82 0 W acceleration - buoyancy dwdtt 82 0 W acceleration - total • running dtdm model created two new GrADS files: thermal.anelastic.ctl thermal.anelastic.dat • contents of thermal.anelastic.ctl shown at left

14. ga-> set t 6ga-> start.gsga-> d thp

15. ga-> cga-> set black 0 0ga-> d thp

16. ga-> d ppmb [Note zero contour is back…]

17. ga-> cga-> set ccolor 1ga-> d pbyc

18. ga-> cga-> set ccolor 4ga-> d pdyn

19. GrADS default color sequence http://grads.iges.org/grads/gadoc/gadocindex.html

20. ga-> cga-> set ccolor 2ga-> d w*100

21. ga-> cga-> set gxout shadedga-> d wga-> scripts/cbarn.gsga-> set gxout contourga-> set ccolor 1ga-> d dwdtt dwdtt is Lagrangian dw/dt, not Eulerian ∂w/∂t

22. ga-> set t 9ga-> cga-> d u;w

23. Control vector length with set arrscl 0.5 20.0 [standard length set to 20 m/s] ga-> cga-> d skip(u,2,3);w

24. Zoom in ga-> cga-> q dimsga-> set x 30 70ga-> set xaxis 30 70 10ga-> d skip(u,2,3);w

25. ga-> draw xlab x (km)ga-> draw ylab height (km)ga-> draw title EXP01 uw t=9ga-> printim example01.gif gif Outside of GrADS, can display images using display

26. http://grads.iges.org/grads/gadoc/script.html#intro scripts/thermal.gs 'set mproj off' 'set display color white' 'clear' 'set grads off' 'scripts/rgbset.gs' * plot w 'set x 30 70' 'set gxout shaded' 'set clevs -12.5 -10 -7.5 -5 -2.5 0 2.5 5 7.5 10 12.5' 'set ccols 49 47 45 43 41 0 61 62 63 65 67 69' 'd w' 'scripts/cbarn.gs' 'set gxout contour'

27. ga-> set t 6ga-> scripts/thermal.gs

28. Three important commands ga-> reset • resets GrADS environment to starting conditions… Time dimension set to 1st time, gxout to contour, etc.. Does not close open files. ga-> reinit • resets AND closes all open files. “All but quit.” ga-> quit

29. Running another case $ gedit [edit input_thermal.txt] [change casename, ianelastic, csnd] &experiment casename = 'thermal.nonanelastic.30', $ &framework ipressure = 1, ianelastic = 0, csnd = 30., $ $ dtdm < input_thermal.txt

30. Multiple files with GrADS $ grads –l ga-> open thermal.anelastic ga-> open thermal.nonanelastic.30 When multiple files are open, append file number to variable name: e.g., d thp.2

31. ga-> start.gsga-> set t 11ga-> scripts/thermal.gsga-> set gxout contour ga-> set ccolor 1ga-> set cthick 8ga-> set cint 0.1ga-> d ppmb.1-ppmb.2

32. Animations made painlessga-> step.gs thp 1 11 1.0 Plots field thp …for steps through times 1 through 11, inclusive …with contour interval 1.0 …hit return to proceed to the next time

33. ga-> cga-> set x 50ga-> set z 1ga-> set t 1 11ga-> d max(w,z=1,z=82)ga-> set ccolor 4ga-> d max(w.2,z=1,z=82) Time series plots

34. ga-> cga-> set x 50ga-> set z 1 82ga-> set t 1 11ga-> d thp Hovmoller plots

35. More on GrADS image output ga-> printim image01.pngga-> printim image01.jpg jpg ga-> enable print image01.m ga-> print ga-> disable print GrADS 2.1 simplifies all of this… Once a *.m file is created, it can be converted (outside of GrADS) to a postscript or eps file $ gxps –c –i image01.m –o image01.ps $ gxeps –c –i image01.m –o image01.eps

36. Final cautions • Make backups • This command runs the model $ dtdm < input_thermal.txt • This command destroysthe input file! $ dtdm > input_thermal.txt

37. Advice • Don’t ask what’s the least you can do for me. Instead, ask what’s the most you can do for yourself.