Atmospheric Mac OS

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Dark Mode is a dramatic new look that's easy on your eyes and helps you focus on your work. Dark Mode uses a dark color scheme that works system wide, including with the apps that come with your Mac. And third-party apps can adopt it, too.

Turn on Dark Mode

Choose Apple menu  > System Preferences, click General, then select one of the Appearance options at the top of the window:

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• Light: Use the light appearance.
• Dark: Use the dark appearance.
• Auto: Automatically use the light appearance during the day, and the dark appearance at night.

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How Dark Mode works with some apps and features

Some apps and features have special Dark Mode settings or behaviors.

Mail. To use a light background for email messages while Dark Mode is turned on, open Mail and choose Mail > Preferences, then click the Viewing tab and deselect “Use dark backgrounds for messages.”

Maps. To use a light background for maps while Dark Mode is turned on, open Maps and choose Maps > Preferences, then select ”Always use light map appearance.” In earlier versions of macOS, click View in the menu bar in Maps, then deselect Use Dark Map.

Notes. To use a light background for notes while Dark Mode is turned on, open Notes and choose Notes > Preferences, then deselect “Use dark backgrounds for note content.”

Safari. When you use Dark Mode, Safari automatically shows a website in Dark Mode if the website has been designed to support it. If the website doesn't support Dark Mode, you can use Safari Reader to read articles in Dark Mode.

TextEdit.To use a light background for documents while Dark Mode is turned on, click View in the menu bar in TextEdit, then deselect Use Dark Background for Windows. (Requires macOS Mojave 10.14.2 or later.)

Dynamic Desktop. If you turn on Dark Mode while using Dynamic Desktop, the desktop may change to the dark still image. You can change this setting in Desktop & Screen Saver preferences.

After upgrading to Yosemite (10.10), many things were broken, so I had to make a fairly clean start. These seem to be the essentials that I'm using now.

• For a terminal, iTerm 2 integrates nicely between linux and Mac OS X.
• As an emacs editor, Aguamacs Emacs works well for me. It's integrated into Mac OS, allowing you to use standard mac key combinations (say, command v to paste), but also has all the emacs key bindings, too.
• For laTex, there's a nice distribution MacTex.
• For genuine linux/unix applications, I'm using MacPorts.. It is nice in that when you request something (say, the CDO utlities, as discussed below), it will automatically get all the dependencies. (These libraries can cause quite a headache otherwise!)
• To get work done with netcdf files, these applications are helpful.
  • The CDO utilities. Not to be confused with Collateral Debt Obligations (a crafty way for bankers to fleece the rest of us), these are utilities for manipulating netcdf files, developed at MPI Hamburg. Get them with macports.
  • The NCO utilities are another suite of operators for workign with netcdf files. They are less customized to meteorological output as CDO, but great for raw calculations. Get them with macports. (Note that I had to get get the developer version of Java to make this work, JDK.)
  • Alas, Matlab is not free, but if you have it, I wrote this script to open netcdf files in matlab more easily. Comments/concerns are appreciated.
  • For quickly viewing netcdf files, ncview is helpful. You can get it with macports.
  • Another, more powerful option for visualizing netcdf files is panoply, developed by NASA GISS. You can get it from the link.
• If you have a tablet, I recommend iAnnotate for viewing and commenting on PDFs. It integrates nicely with DrobBox and Box, and has allowed me to go almost paperless!

I'll do my best to keep this page more up-to-date. Please emailme with suggestions and comments!

WARNING: Most of the notes below have fallen way out-of-date with theadvances in OS. (Aaack, this makes me feel old.) I've kept them in case something might be useful.

• 10.08
Note that there is *finally* a pdf viewer for Firefox (version 3) on the Intel Mac! Get it here: PDF plugin for Firefox on Intel Mac!!!!

•
Install x11 and all the developers tools. You need them for fink.
for x11 you need a .bashrc
I initially put my preferences and aliasing in .profile, but realized that
it wasn't loading. It worked when I had the .bashrc source .profile.
But it's best just to put all the information in .bashrc to begin with.

•
To get scroll bars,
Look in your .xinitrc file (or make it). Add:
xterm -sb -sl 1000 &
The -sb gets you the scroll bar, -sl makes it 1000 lines.
This doesn't seem to work. But you can make it automatic by updating
the x11 preferences. Under the Applications heading, go to
Customized Menu. Here you can make the Terminal command:
xterm -sb -sl 1000
I made this the terminal that launches when you press [apple key]n
make your terminal even nicer and easier to read!!!!
xterm -sb -sl 1000 -fa Monaco -fs 12 -bg linen
Monaco's the only font I've been able to use. You can change the size with
-fs. -bg sets the background color
the color 'seashell2' is also decent, and 'cornsilk2'
(I changed to this default when I hooked my computer up to a higher
resolution monitor.)
See my .bashrc file for the most up-to-date terminal commands

•
Multiple desktops - a must! I got the Codetex version ($40) that is
quite nice. But there are some decent open souce versions to that you
can get for free. See:
http://tazman.princeton.edu/osx/
This website is amazing!
A friend is using the desk top manager version, and quite happy:
http://desktopmanager.berlios.de/

•
Get fink to get all the useful unix/linux codes you're used to using. Make
sure to install the mac developers tools before installing fink. This
will give you compilers, etc. that you need.
Using fink, I got:
-imagemagick (convert and other programs, great for changing from
eps to jpg, etc.)
-gv
-gimp (image processing)
-tetex (the full latex packages)
-ispell (a spell checker)
-gnome terminal [DOESN'T WORK!]
In search of a better terminal I tried downloading gnome-terminal.
But it doesn't work.

•
I found these applications to be quite handy. Not from fink.
(Just google them to find them.)
- quicksilver (a launcher)
- firefox (a browser) [also get the pdf viewer plugin:
'PDF Browser Plugin,' so it doesn't have to use
preview to look at pdfs. This way it doesn't have to
automatically save the pdf to your desktop.
http://www.schubert-it.com/pluginpdf/ ]
- aquamacs emacs (a text editor)
- texniscope (a pdf viewer, good with pdflatex)
- adium (an IM client)

•
To make a backup on my external hard drive, named squall:
cd /Users/
rsync -EaH epg /Volumes/squall/
The -E option saves source forks, a mac way of storing certain data
The -a option puts it in archive mode. It will search recursively,
copying links, permissions, times, groups, owners, and devices.
The -H option preserves hard links.
Another possible command is: rsync -aH --delete [source] [destination]
With this option, if rsync sees that a file exist in the destination drive
that is not in the source drive, it will delete it. So, your backup is
cleaned up like your home system. HOWEVER - this can sting you if you
accidently deleted a file in your home system.

•
To find your IP address (while working remotely), type
ifconfig
Look for en1: ...
This will contain your inet address 128. . . .
This is the one to use!
I assume you can get your hardwired address this way too.

•
I downloaded openoffice.org 1.1.2 - the stable release for mac os-x
If the start up program doesn't work, the manual start is:
setenv DISPLAY localhost:0
setenv DYLD_LIBRARY_PATH /Applications/OpenOffice.org1.1.2/program:/Applications/OpenOffice.org1.1.2/program
sh soffice
(But the start up program worked for me!
Their is now a better version, 2.0.? - I downloaded it, and won't use this
older one anymore.

•
A nice IM client: adium (google it - you just grab the executable)
It runs AOL IM, and a few others. The AOL client, AIM, isn't as stable
isn't as nice!

•
To make vi a little nicer, with syntax highlighting, you need a
'.vimrc' file in your home directory. Here's the one I've got so far.
I should be able to add colorschemes to get color highlighting (nice for
programing), but my efforts so far have proved futile.
GFDL:
syntax on
colorscheme delek
set tabstop=2
set autoindent
syntax enable
I must comment out the colorscheme request, as it can't find it. You
comment with a '
The math vimrc is much nicer. I'll use it, but with a few necessary
tweaks:
----
set nocompatible ' Use Vim defaults (much better!)
set bs=2 ' allow backspacing over everything in insert mode
'set ai ' always set autoindenting on
'set backup ' keep a backup file
set viminfo='20,'50 ' read/write a .viminfo file, don't store more
' than 50 lines of registers
set history=50 ' keep 50 lines of command line history
set ruler ' show the cursor position all the time
' Only do this part when compiled with support for autocommands
if has('autocmd')
' In text files, always limit the width of text to 78 characters
autocmd BufRead *.txt set tw=78
' When editing a file, always jump to the last cursor position
autocmd BufReadPost *
if line('') > 0 && line ('') <= line('$')
exe 'normal! g''
endif
endif
if has('cscope')
set csprg=/usr/bin/cscope
set csto=0
set cst
set nocsverb
' add any database in current directory
if filereadable('cscope.out')
cs add cscope.out
' else add database pointed to by environment
elseif $CSCOPE_DB != '
cs add $CSCOPE_DB
endif
set csverb
endif
' Switch syntax highlighting on, when the terminal has colors
' Also switch on highlighting the last used search pattern.
if &t_Co > 2 has('gui_running')
syntax on
set hlsearch
endif
if &term'xterm'
set t_Co=8
set t_Sb=m
set t_Sf=m
endif
---
The tweaks were to comment out the if &t_Co line above, so that syntax
highlighting is always turned on. Then, I had to comment out
the final if statement, if &term'xterm' because it was trying add
colors unsuccessfully.

•
I needed to download Stuffit 10.0 to decompress a .sit file.

•
With keynote, use latex equation editor for equations. See the latex stuff
file for details!

•
to set up my computer as an ssh server:
as root, first set up keys (these are not pass phrase protected,
because of the -N ' option)
(to become root, type su, or if that doesn't work, try sudo su)
ssh-keygen -b 1024 -t rsa -f /etc/ssh_host_rsa_key -N '
ssh-keygen -b 1024 -t dsa -f /etc/ssh_host_dsa_key -N '
ssh-keygen -d -b 1024 -f /etc/ssh_host_key -N ' -C '$(hostname)'
Then, I mades some important changes to this configuration file:
/etc/sshd_config
36c36
< #PermitRootLogin yes <-------- this was in the old file
---
> PermitRootLogin no <-------- this is what I changed it to
55c55
< #PermitEmptyPasswords no
---
> PermitEmptyPasswords no <-- make sure you don't get yourself in trouble
80c80
< #X11Forwarding no
---
> X11Forwarding yes <- allows you to tunnel windows, etc.
lastly, to run the server, type (must be root)
/usr/sbin/sshd
Note: you'll get an error message:
Disabling protocol version 1. Could not load host key
I was told that this is an earlier version of ssh. So you shouldn't have
a problem, unless the other computer you are using doesn't have the current
ssh version.
there's a way to make this start up automatically when you start the
computer, but I'd don't use it enough at this point

•
password stuff:
I'm not sure what root password was to begin with - my user account had
the same pa
to change root password,
as root: passwd
to change epg password, use either mac standard stuff, or, as root,
passwd epg
or you might, not as root, be able to say,
passwd

•
added ferret, fallowing andy jacobsen's web page
http://tazman.princeton.edu/osx/ferret.html
I got the ferret.tgz file, put it in my desktop, and did this to load it:
sudo tcsh
cd /usr/local
tar zxvf ~/Desktop/ferret.tgz
I had to fix the paths for bash, but the template
/usr/local/ferret/bin/ferret_paths_bash_template
seemed to work. I just copied it over to replace the tcsh ferret_paths file,
and tried to modify the call for the data - I'm not sure if I have it right.
But so far, so good.

•
Got ncview
http://meteora.ucsd.edu/~pierce/ncview_home_page.html
Now you can get it from fink! See Andy Jacobson's page, listed at the top.
Obsolete advice: first use fink to get the netcdf package. This is necessary to
get the right libraries for ncview.
Put it in my Applications directory. Followed the instructions in the
included README file. Seems to work fine, after I aliased it properly.
Don't try to load the ulibunits (?) package - it won't work on the mac!

•
I've got a pretty sweet .bashrc file, with sophisticated completions and
shortcuts to avoid typing & all the time to make applications that launch
new windows run in the background. I've got a copy of it in this directory,
as of today, 9/22/06. Check my most current version for the best fixes.

•
valuable program: screen
This allows you to run things on a shell, close it, go away, come back,
and reconnect from some other location, etc.
To start:
screen
ctrl-A tells screen that you're entering a screen command
ctrl-A A let's you rename a shell
ctrl-A c creates a new shell (you can rename it as above)
ctrl-A ' list all your shells, and allows you select the one you want
to work with
ctrl-A K kill the current screen
ctrl-A d detach from all screen sessions (after this, you can go
away from all sessions)
To reconnect:
screen -R
This lets you go back to your sessions!
To stop annoying flashing when you try to use the tab button to make
complete file names, etc., make a .screenrc file in your home directory
that has this line,
vbell off
More information is available here:
http://gentoo-wiki.com/TIP_Using_screen

Atmospheric Mac OS