
USEFUL/AMUSING MAC OSX APPS/FEATURES:
Sun Feb 29 13:05:27 MST 2004

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** VMD: view trajectory (also, view image);

finder->jar->Applications: run "VMD 1.8.2.app"-> 3 windows:

	terminal window (for info sent back from VMD; for cmd line control)
	display window (for display trajectory/model after loaded)
	VMD main window (for control of load, display, etc -- we use main win)

		File->new molecule->
			molecule file browser
				browse (to get parm file of atom types, etc)
					finder->...->
	~jar/words/585/display/bpti.a2/run.8k273.40_800_32_512/prmtop
					open
				file type
					parm
				load
				browse (to get trajectory data)
					finder->...->
	~jar/words/585/display/bpti.a2/run.8k273.40_800_32_512/_mdcrd.long
					open
				file type
					crd
				load

		[molecule displays - trajectory shown]

		Control within VMD main window:
			loop (default), step (skip frames), speed, stop/start

		Graphics->representation->
			coloring method
				name, resname, restype, charge, throb, ....
			drawing method
				lines, bonds, VDW, cartoon, surf, ribbons, ...

		Display->
			reset view
			stop rotation
			perspective
			stereo
				crossed eyes

		Mouse->
			rotate, translate, scale, center, query
			label, ...

		[keyboard shortcuts for some above, e.g.:
			r=rotate   t=translation,scale]
			

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** mddisplay: cf vmd

cd /Users/jar/Downloads/downloads-software-2/mddisplay

mddisplay -n ./examples/bpti.a2-1/mdcrd
	click on "help"


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** R: 

1) R demos - graphics, images, fonts, etc; 

R -or- (for better display?) Finder->StartR:2xclick

	demo(graphics)
	demo(persp)
	demo(image)
	demo(Japanese)
	help.search(".")

2) fit (local) data = calorimeter voltage time series
by use of **S** script, mod only slightly for R

cd ~/lib/R/exam1
R
	source("commands.s")	#run nonlinear lsq and exit R
cat commands.s			#view S/R script
cat commands.s|sed "s/#.*$//"|blone	#view script without comment clutter
vi scr results.fit		#compare S and R results
gv scr.ps & gv results.fit.ps &		#compare S and R plots of results
	

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** Xaos: tutorial/display Mandelbrot set + more

Xaos
	h = help (multi-multi-page)
	hh = choice of tutorials
		2 = intro to fractals
			1 = whole story
				repeated -> for speedup
				space to skip to next frame
				esc+1 to quit

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** ati radeon 9700 demos:
		`
1) screen savers:
Preferences->Display & Screen Saver: select ATI ????, test

2) chimp, debenvec:
Finder->Downloads->ATI SmartShader 2.0 Demos->DebenvecRNL->Sushi2_OSX:2xclick
	interactive=space bar; mesh=w; 2|3=split scrn; mouse=rotate image;
	[not all keys work with each demo]
	esc=reset; 
	esc+return=exit;

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xtoys:

cd ~/src/xtoys

1) xburn, xburn-jar: percolation on 2-d lattice
[vi xburn.txt]
xburn	     initial_fraction_trees		[block_size]
try:
	xburn	.50|.55|.57|.58|.59|.60|.61|.62|.65|.70	    4

2) xising: phase transition on 2-d lattice
[vi xising.txt]
xising 
	const. E	heat	   cool
	local algorithm		cluster algorithm
	periodic (normal)	antiperiodic	black	white
	...

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groff:
	gnu unix formatter ~= att unix formatter
	format eqns, tables;
	absolute control over typesetting;
	flat text files, std ascii;
	macros convert troff -> markup language;
	some (few) like troff better than tex, etc.
	troff remains a well-used pro-level formatter -
		(cf tex, framemaker, interleaf)

A) cf formatting under att-troff, gnu-troff

1) dn problem
cd /Users/jar/words/new/Port-from-dwbv3
gv -antialias -center -media letter letter*ps & gv -antialias -center -media letter test-letter*mm.ps &

2) zoning code
cd /Users/jar/words/new/Port-from-dwbv3
gv -antialias -center -media letter bbord*ps & gv -antialias -center -media letter test-bbord*mm.ps &

3) recipes = cookbook
cd /Users/jar/lib/recipes
gv -antialias -center -media letter Cookbook*ps & gv -antialias -center -media letter Cookbook.ps9908 &


B) control of typesetter

1) mailing wrapper
cd ~/words/new/EEEHA
vi address-file address-print.sh
	launch gv from address-print.sh
		exact center of banner header/footer
		exact center of address label, vertically
		rightmost position of address label, wrt longest address

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[kismac: if want to amuse - need another engenius]

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utils - mac proprietary:

	safari - 
		fast, clean, well-engineered (e.g. font size)

	finder/search - 
		fast search, easy navig thru tree

	sherlock - 
		enhanced google with commercial tinge
		search, airline info, dictionary, ...

	itunes -
		buy, listen, radio

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utils - non-proprietary:

tree displays of files/dirs/processes:
	
	pstree
		processes

	tree
		file hierarchy below . 

	dugraph = du|filter|dugraph
		file heirarchy below ., 
		one page only, with space on page allocated 
		by (cumsum) size of files

color: 
	ls

	cdiff = colordiff

	vim
		edit source file (.c, .sh, .awk, ...)
		turn on color with ":syntax enable"

system util: 

	bvi
		binary editor with vi commands

	hexcalc
		decimal/octal/hex calculator
		with added ops:
			e.g., >> << | & ~ ....
			help -> help screen

	whereis
		old version, that give max info:
			exec, srcs, man pages
			~/bin/whereis
		mac osx =? current gnu util
			minimal scope, detail
			/usr/bin/whereis

	fortune
		professes wisdom
		no unix system should lack it

	nc = netcat
echo -e "GET http://www.rupley.com HTTP/1.0\n\n" | nc www.rupley.com 80 | less
echo -e "GET http://10.0.0.6 HTTP/1.0\n\n" | nc 10.0.0.6 80 | less

	lsmac
		display macos special attributes


misc: 
	sunrise
		time sunrise/set, time moonrise/set, gmt, 
		moon phase, julian day, sidereal time, etc

	areacode
		fast search for/by areacode/city/state

	[recipes - see gnu groff cf att troff above]
		recipes: ~/lib/recipes/[Cookbook.ps|<recipe>]
		progs: ~/src/recipes or ~/bin/recipes/Rupley

	gperiodic
		periodic table, info each element

	menu meters
		mac menu bar: 
			net io, memory usage, disk activity, cpu activity,
			speakers, wireless, battery, date-time, palette, 
			bluetooth, login/logout

		pull down menus/info displays for each
	
	wmmk: wmWeather, wmMoonClock, wmSun, wmCalClock

		# all: for next mini-window -
			focus to parent window, enter any char, return

		# wmWeather: any key switch F<->C

		# wmMoonClock: click mini-win -> next mini-screen of info

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