Apps on a Mac for a computational research scientist

This note documents steps to make a newly fresh Mac OS machine a computing environment for computational mechanicians.

First, install some applications, after a *system update*. All these apps are just dmg files, and thus installation is easy. Essential apps

1. Monolingual (remove unused languages), Onyx (utility)

2. Pages, Keynote

3. Dropbox, Slack

4. Atext (speed up writing)

5. Gmsh, Paraview (FE mesh generator, scientific visualisation), Matlab, Adobe Illustrator (commercial)

6. Iterm2 (terminal) :

7. mactex (latex backend), Texpad (latex editor, commercial), detexify (Mac app): to get latex for any symbols, better than the web version. Mtpro2 font (alerady purchased it, just install): if encountering this error Bbbk command already defined, then modify this: /usr/local/texlive/texmf-local/tex/latex/mtpro2/mtpro2.sty, comment line with Bbbk

8. gif brewery (to make GIFs)

9. Install Safari extensions ([20+ Best Safari Extensions (2018) | TechWiser](https://techwiser.com/20-best-safari-extensions-2018/))

10. * Amphetamine: (similar to Caffein) or use terminal: caffeinate -u -t 7200

11. Alfred (30 AUD), Dropzone 3 (7 AUD), Default Folder X (50 AUD), Better touch tool (30 AUD), Batender (if your menu bar is crowded), Ring Menu (8 aud)

12. Sublime Text, amazing text editor

13. TotalSpace2, virtual desktop manager ()

14. Spotify, music, (Youtube too many ads) (free)

15. Be focused (free)

16. Fleeter [https://freeter.io/user-guide/getting-started/freeter-basics](https://freeter.io/user-guide/getting-started/freeter-basics)

17. Spotify, LyricsX,Toothfairy (particularly using AirPods)

18. Slack

19. Check this https://github.com/serhii-londar/open-source-mac-os-apps

defaults write com.apple.mail AddressesIncludeNameOnPasteboard -bool false

defaults write com.apple.finder _FXShowPosixPathInTitle -bool true; killall Finder (Show full path in Finder’s title bar)

Next, we will *install compilers* and make our terminals better. I learned from these useful links. [https://coderwall.com/p/yiot4q/setup-vim-powerline-and-iterm2-on-mac-os-x](https://coderwall.com/p/yiot4q/setup-vim-powerline-and-iterm2-on-mac-os-x) [https://github.com/nicolashery/mac-dev-setup](https://github.com/nicolashery/mac-dev-setup)

1. Xcode, ( command line tools automatically installed)

2. Cmake (dmg), then do: sudo “/Applications/CMake.app/Contents/bin/cmake-gui” —install

3. VTK library, from source

— download VTK from its webpage

— ccmake ~/Downloads/VTK-7.0.0

— press ‘c’ for a couple of times, then ‘g’

— make -j#

— sudo make install

—> VTK will be installed at /usr/local/include/vtk-7.0/ and /usr/local/lib

4. home-brew:

— ruby -e “$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)”

— brew doctor

— brew update

— brew install boost (seems that on mac os Mojave, this is no need)

One thing we need to do is tell the system to use programs installed by Hombrew (in /usr/local/bin) rather than the OS default if it exists. We do this by adding /usr/local/bin to your $PATH environment variable:

$ echo ‘export PATH=“/usr/local/bin:$PATH”’ >> ~/.bash_profile

5. Open MPI: brew-install open-mpi or from source (the former is easy)

6. Change caps lock key to escape (System preferences, keyboard, modifiers…

7. oh my zsh (this is a very good bash)

sh -c “$(curl -fsSL https://raw.github.com/robbyrussell/oh-my-zsh/master/tools/install.sh)”

8. set up vim:

— install pathogen (vim plugin install manager):

mkdir -p ~/.vim/autoload ~/.vim/bundle && \

curl -LSso ~/.vim/autoload/pathogen.vim

https://tpo.pe/pathogen.vim

— use vimrc in dropbox/

— [https://danielmiessler.com/blog/enhancements-to-shell-and-vim-productivity/](https://danielmiessler.com/blog/enhancements-to-shell-and-vim-productivity/)

— use Ctrl r to search for command history in Iterm2

9. Set up iterm2:

— *iTerm2 Preferences*, under *Profiles* and *Colors*, select Solarized Dark

— use Solarized dark color scheme, prefs -> Profiles -> Text -> Draw bold text in bright colors. Deselect it.

— Under **Keys** tab, in **Hotkey** section, enable *“Show/hide iTerm2 with a system-wide hotkey”* and input your hotkey combination, e.g. I use Ctrl + Shift + L.

— Under **Pointer**, in **Miscellaneous Settings** section, enable *“Focus follows mouse”*.

— copy Dropbox/zshrc to ~/.zshrc

— copy Dropbox/vimrc to ~/.vimrc

— Download Microsoft *consolas font:* [Install Consolas font on Mac · GitHub](https://gist.github.com/nmcc/4e8ead6c380d8331fedd04e1aa41d351), then change iterm2 font to consolas

-- NORMAL --