Notes Related With Softwares

Emacs has two types of search and replace functions: unconditional and queried. Unconditional search and replace To perform an unconditional search and replace, press; M-x . Then enter:

replace-string RET(Enter)

your_search_string RET

your_replace_string

Replace your_search_string with the existing text string you want to find and remove, and replace your_replace_string with the new text you want to add in its place.

Queried search and replace

To do a queried search and replace (with a prompt for replacing each occurrence of a text string),press M-% . You will then be prompted for your search and replace strings. Emacs will find and display each occurrence of the search string and ask you for further instructions. You can respond with any of the following options:

If you type any other character, Emacs will stop looking for occurrences and execute the character as a command. To restart the queried search and replace, type:

C-x M- M-RET

Emacs has commands for passing single command lines to inferior shell processes; it can also run a shell interactively with input and output to an Emacs buffer named shell or run a shell inside a terminal emulator window. There is a shell implemented entirely in Emacs, documented in a separate manual.

M-! RET

Run the shell command line cmd and display the output (shell-command).

M-x term

Run a subshell with input and output through an Emacs buffer. You can then give commands interactively. Full terminal emulation is available.

M-x eshell

Start the Emacs shell.

First, to list all packages;

M-x list-packages

this will automatically resfresh the archive contents. Then;

U

to mark all upgradable packages to be upgraded. Then;

x

to perform the new updates. (This information is adapted from here)

One can use several writing modes for Emacs. To view the documentation for the current major mode, including a list of its key bindings, type;

C-h m (describe mode)

For instance;

Html Mode

When you open .html file, it is automatically opened in html mode.However to change it manually;

M-x html-mode

Emacs have different key shortcuts for each different modes

*Some Keyboard Shortcuts for HTML Mode~

(This information is adapted from here)

How to write in Bold, Underline etc. as in Word in Emacs

Emacs has a “facemenu-*” command. See the menu 〖Edit ▸ Text Properties ▸ Face〗. Here are the hotkeys.

To be able to save and restore you need to save in enriched-mode . To open Emacs in enriched mode;

M-x enriched mode

Also to highlight some phrases or expressions one can use the followings;

M-x highlight-phrase

M-x highlight-regexp

M-x highlight-lines-matching-regexp

(This information is adapted from here.)

https://github.com/hsjunnesson/wolfram.el

Install package from melpa

M-x list-packages

Find wolfram-alpha then chhose the package to install via

I

Then to install the package

X

Then add this to your init file:

(require 'wolfram)

"Create an account at wolframalpha.com, then in your account select "My Apps (API)". Create a new AppID. In Emacs set that AppID as the custom variable wolfram-alpha-app-id."

I have AppID as : 3K4RRQ-3PQV87TE9X

M-x customize-save-variable wolfram-alpha-app-id 3K4RRQ-3PQV87TE9X

To make a query, run M-x wolfram-alpha then type your query. It will show the result in an org-mode buffer called WolframAlpha.

Wolfram mode needs to be installed for this purpose.

https://melpa.org/#/wolfram-mode

Things to do after installation:

This provides basic editing features for Wolfram Language " (http://reference.wolfram.com/language/), based on `math++.el'
(http://chasen.org/~daiti-m/dist/math++.el)."

You should add the followings to `~/.emacs.d/init.el'.

(autoload 'wolfram-mode "wolfram-mode" nil t)
(autoload 'run-wolfram "wolfram-mode" nil t)
(setq wolfram-program "/Applications/Mathematica.app/Contents/MacOS/MathKernel")
(add-to-list 'auto-mode-alist '("\\.m$" . wolfram-mode))

I usually work on files which are updated in the file system via version control. What's a quick way to reload a file without having to C-x C-f the file again and getting asked if I want to reload it?

M-x revert-buffer will do exactly what you want. It will still ask for confirmation.

Another option (my favorite) is the below function:

;; Source: http://www.emacswiki.org/emacs-en/download/misc-cmds.el
(defun revert-buffer-no-confirm ()
"Revert buffer without confirmation."
(interactive)
(revert-buffer :ignore-auto :noconfirm))

http://emacs.stackexchange.com/questions/169/how-do-i-reload-a-file-in-a-buffer

You can use the command load-file (M-x load-file, then press return twice to accept the default filename, which is the current file being edited).

You can also just move the point to the end of any sexp and press C-x C-e to execute just that sexp. Usually it's not necessary to reload the whole file if you're just changing a line or two.

Alternatively;

M-x eval-buffer

immediately evaluates all code in the buffer, its the quickest method, if your .emacs is idempotent.

http://stackoverflow.com/questions/2580650/how-can-i-reload-emacs-after-changing-it

Select th region first then;

M-x count-words-region

• Use C-x d to enter dired and choose the directory with the files in
• Use C-x C-q to turn dired into editing mode
• Use M-% to replace foo with bar in the dired buffer. This will change the file names
• Use C-c C-c to apply the changes or C-c ESC to cance

Also see; https://www.gnu.org/software/emacs/manual/html_node/emacs/Transforming-File-Names.html

C-x s (save-some-buffers)

One should use the command set-buffer-file-coding-system (C-x RET f), set the encoding, and then save the file.

Org provides useful ways of converting a region into a table. For this, select a region and press C-c |. For example, press C-c | on this:

some, comma, separated, values

will automagically produce this:

Usually, this command should be smart enough to guess what is the field separator for the region. If each line of the active region contains a TAB or a comma, it will assume this is the separator.

If you want to force the comma as a field separator, press C-u C-c |. If you want to force TAB as a field separator, press C-u C-u C-c |. If you want to force a specific number of spaces – say 3 – use C-u 3 C-c |.

http://orgmode.org/worg/org-tutorials/tables.html

Use \\ for new lines.

Or leave an empty line for new paragraphs.

(defun org-xor (a b)
   "Exclusive or."
   (if a (not b) b))

#+BEGIN_SRC emacs-lisp
(defun org-xor (a b)
"Exclusive or."
(if a (not b) b))
#+END_SRC

See http://orgmode.org/manual/Working-With-Source-Code.html

Lines starting with zero or more whitespace characters followed by one ‘#’ and a whitespace are treated as comments and, as such, are not exported.

Likewise, regions surrounded by ‘#+BEGIN_COMMENT’ ... ‘#+END_COMMENT’ are not exported.

Finally, a ‘COMMENT’ keyword at the beginning of an entry, but after any other keyword or priority cookie, comments out the entire subtree. In this case, the subtree is not exported and no code block within it is executed either1. The command below helps changing the comment status of a headline.

C-c ;

Toggle the ‘COMMENT’ keyword at the beginning of an entry.

This file is adapted from here.

With just a few keystrokes, Org's easy templates inserts empty pairs of structural elements, such as #+BEGIN_SRC and #+END_SRC. Easy templates use an expansion mechanism, which is native to Org, in a process similar to yasnippet and other Emacs template expansion packages.

<<> <s> <TAB> completes the ‘src’ code block.

< l <TAB>

expands to:

#+BEGIN_EXPORT latex

#+END_EXPORT

Org comes with these pre-defined easy templates:

More templates can added by customizing the variable org-structure-template-alist, whose docstring has additional details.

http://orgmode.org/manual/Easy-templates.html#Easy-templates

This can be done using pandoc. Install it via

brew install pandoc

Then;

pandoc -f markdown -t org -o newfile.org original-file.markdown

see here.

See here

You can make words bold, italic, underlined, verbatim and code, and, if you must, ‘+strike-through+’. Text in the code and verbatim string is not processed for Org mode specific syntax, it is exported verbatim.

(see https://orgmode.org/manual/Emphasis-and-monospace.html)

to be organized https://orgmode.org/manual/Working-with-source-code.html#Working-with-source-code

to be organized https://orgmode.org/manual/Previewing-LaTeX-fragments.html#Previewing-LaTeX-fragments

BBBABB BBBABB BBBABB When on A, I'd go in block visual mode

ctrl-v select the lines you want to modify,

press I (insert mode with capital i),

and apply any changes I want for the first line. Leaving visual mode esc will apply all changes on the first line to all lines. This information is adapted from here

• Type 'cmd' to search for the Shell.

Right click and launch as administrator.

• Enter without the quotes;

"bcdedit /set {bootmgr} path \EFI\opensuse\shim.efi"

This information is from http://opensuseadventures.blogspot.com.tr/2014/02/dual-booting-with-windows-8-not-as.html

• Open Yast
• Under the Systems section, click Boot Loader
• Click the Boot Loader Installation tab. Ensure that GRUB is displaying on the Boot Loader field and click Boot Loader Options.

lsb_release -a

https://help.ubuntu.com/community/CheckingYourUbuntuVersion

To install a downloaded Debian package (.deb)

sudo dpkg -i packagename.deb

To remove a Debian package (.deb)

sudo dpkg -r packagename

To Reconfigure/Repair an installed Debian Package

sudo dpkg-reconfigure packagename

http://askubuntu.com/questions/40779/how-do-i-install-a-deb-file-via-the-command-line

Edit the resolv.conf document;

sudo emacs /etc/resolv.conf>

http://www.cyberciti.biz/faq/ubuntu-linux-configure-dns-nameserver-ip-address/

First create the user with;

sudo adduser

Then add a user to the sudo group with the command

sudo adduser sudo

http://superuser.com/questions/196848/how-do-i-create-an-administrator-user-on-ubuntu

To create group in ubuntu;

sudo groupadd "group_name"

To add members to the group ;

sudo usermod -a -G "group_name" "user_to _be_added"

How to give Read and Write Access to Group and Folder

sudo chgrp -R "group_name" "/path_to_the_directory"

sudo chmod -R 777 "/path_to_the_directory"

Note '777' is for read,write and execute. One can use 'g+rwxs' also instead of 777. See the File permissons note here. For Instance, I want to create a group called my_group and add users "Ali" and "Veli" to the group and finally want to have permission of rwx to the folder /var/www Then;

sudo groupadd throne

sudo usermod -a -G throne Veli

sudo chgrp -R throne /var/www

sudo chmod -R g+rwxs /var/www

or

sudo chmod -R 777 /var/www

This information is adopted from https://gist.github.com/helger/3070258

Put the following code in ~/.bash_profile

function title {
    echo -ne "\033]0;"$*"\007"
}

Then in terminal write the name

title "Name of the tab"

https://superuser.com/questions/419775/with-bash-iterm2-how-to-name-tabs

From the Mac Terminal, you can immediately open whatever folder or directory you are working within into the Finder of OS X by simply typing the following command:

open .

http://osxdaily.com/2009/11/30/open-current-folder-in-finder-from-the-terminal/

This youtube link works fine.

If the link is broken see.

Also check the following link.

https://www.howtogeek.com/191323/how-to-share-printers-between-windows-mac-and-linux-pcs-on-a-network/

https://support.microsoft.com/en-us/help/2665700/how-to-print-to-a-windows-printer-from-a-mac

If Latexit does not render the command and even does not give any errors. Do the following.

Preferences -> Typesetting -> Ghostcript
alanina
/usr/local/bin/gs
girilmeli. Reset secenegi de otomatik olarak latex kurulumunun yerini bularak ayarlarinin yeniden yapmasini saglar.

In the "Tools menu", choose "show inspector". In the inspector, select "Annotations inspector".

Press CMD+A to select all annotations, then click backspace to delete them

https://apple.stackexchange.com/questions/52222/preview-remove-all-annotations

sudo pip install [package] --upgrade

For more info

pip freeze

or

yolk -l

for detailed package details.
Note that if the yolk is not installed; install it via

pip install yolk

For more info

pip install --upgrade pip

For more info

To learn the directory in Mathematica execute the following commands:
For global installation

$BaseDirectory

For user based installation;

$UserBaseDirectory

In general; Linux:

• system-wide installation (requires root priviledges):

  usr/share/Mathematica/Applications

• single-user installation:

  $HOME/.Mathematica/Applications/

Mac OS:

• system-wide installation (requires root priviledges):

  Library/Mathematica/Applications

• single-user installation:

  Users/<user>/Library/Mathematica/Applications

MSWindows:

• system-wide installation:

  C:\Documents and settings\All Users\Application data\Mathematica\Applications\

• single-user installation:

  C:\Documents and settings\<user>\Application Data\Mathematica\Applications\

Beware that in Windows these directories might be hidden!

First Way (From the Menu) In menu bar;
Cell->Delete All Output

Second Way (Command Line)

NotebookFind[SelectedNotebook[], "Output", All, CellStyle]; FrontEndExecute[FrontEndToken["Clear"]]

Third Way Alt + Click the one of the output line
This selects all output cells. Then
Delete all lines.

Also in order to select all input lines one can
Alt + Click the one of the input cell

opts = {PlotRange -> All, PlotStyle -> Red};
Plot[x^2, {x, 0, 1}, Evaluate[opts]]

http://stackoverflow.com/questions/22184011/save-plot-options-of-mathematica-into-a-single-variable

For instance I want to define a notebook file that contains constant values and then use that values for different .nb files.

• I have a long nb file. I want to subdivide different sections into separate smaller nb files and call and run them in a common nb file. How do I achieve this?
• If you want to keep it as a *.nb file then try using the following in your main notebook,

nb1 = NotebookOpen[filename];
SelectionMove[nb1, All, Notebook]
SelectionEvaluate[nb1]

This will open the notebook "filename", select all the elements of the notebook and then run them. You could also include an extra line,

NotebookClose[nb1]

at the very end of the notebook "filename.nb" so that it closes itself once it has finished running. Then you have all the expressions in your kernel and you can continue to do some calculations.

Another option is as follows:

• you can mark your cells as initilization cells (right click on the brackets -> initialization cell) and save it as a package (.m file).

  You can automatically save it as a package file by going into "Format -> Option Inspector", select "Selected Notebook" in "Show option values" goto "Notebook Options -> File Options" and set "AutoGeneratePackage" to "Automatic".

Import this .m file by the command Get["file"].

However this option has the disadvantage of reading code. But you see, the .m files are written in the standardform (I mean the way we write it in fortran). To me, the greatest advantage of .nb file is that we can write the expressions as printed in the book. So it is very easy to detect a mistake in .nb file. So I was wondering whether smaller .nb files can be called inside another .nb using Get.

(https://www.researchgate.net/post/Importing_and_running_nb_file_inside_another_in_mathematica2)

FourDivergence[exp, FourVector[p, mu]] calculates the partial derivative of exp w.r.t. p(mu). FourDivergence[exp, FourVector[p, mu], FourVector[p,nu], …]gives the multiple derivative.

Examples:
FourDivergence[FV[x, \[Beta]], FV[x, \[Delta]]]
Out: \(\bar{g}^{\beta \delta }\)

FourDivergence[FV[x, \[Beta]]/SP[x, x], FV[x, \[Delta]]] // FullSimplify

Out: \(\frac{\bar{x}^2 \bar{g}^{\beta \delta }-2 \bar{x}^{\beta +\delta }}{\bar{x}^4}\)

Since FeynCalc doesn't distinguish between upper and lower Lorentz indices, Kronecker delta and Minkowski metric are essentially represented by the same object.

Contract[MT[u, v] FV[x, v]]

returns the correct result instead of

Contract[KroneckerDelta[u,v] FV[x,v]]

http://mathematica.stackexchange.com/questions/80360/kronecker-delta-and-contraction-in-feyncalc

• First install the related package (Tracer.m) from the web page above. However, since it is an old package there are some errors you encounter when you use Mathematica 10 or latest versions. Hence, I advise you to download the package here.
• Open a Mathematica notebook
• First import the Tracer.m package to your notebook

Import["location of the file(Tracer.m)"] Then you can use the functions defined in that package. The manual is given here.

• Introduction to Tracer (Basic Examples)
• Electron-Electron Scattering
• Electron-Positron Scattering
• Compton Scattering
• Pair Annihilation

(Always check the installation instructions for new versions) Cadabra builds with the standard Apple compiler, but in order to build on OS X you need a number of packages from Homebrew (see http://brew.sh). Install these packages with::

brew install cmake boost pcre gmp python3
brew uninstall boost-python
brew install boost-python --with-python3
brew install pkgconfig
brew install gtkmm3 adwaita-icon-theme
sudo pip3 install sympy

The uninstall of boost-python in the 2nd line is to ensure that you have a version with python3 support. If the lines above prompt you to install XCode, go ahead and let it do that.

You also need a TeX installation such as MacTeX, http://tug.org/mactex/ . Any TeX will do, as long as 'latex' and 'dvipng' are available. Make sure to install TeX before attempting to build Cadabra, otherwise the Cadabra style files will not be installed in the appropriate place. Make sure 'latex' works from the terminal in which you will build Cadabra.

You need to clone the cadabra2 git repository (if you download the .zip file you will not have all data necessary to build). So do::

git clone https://github.com/kpeeters/cadabra2 After that you can build with the standard::

cd cadabra2
mkdir build
cd build
cmake ..
make
sudo make install

This will produce the command line app ``cadabra2`` and the Gtk notebook interface ``cadabra2-gtk``.

I am still planning a native OS X interface, but because building the Gtk interface is so easy and the result looks relatively decent, this has been put on hold for the time being.

Feedback from OS X users is very welcome because this is not my main development platform.

• lines ending in a semi-colon get their output printed, while those ending in a period do not.
• Cadabra often needs to know a bit more about properties of tensors or other symbols. Such properties are entered using the '::' symbol.

A simple example is the declaration of index sets, useful for automatic dummy index relabelling.

wget http://www.xact.es/download/xAct_1.1.2.tgz

Untar the folder via tar zxvf "name of the file".
Move the folder to tha basedirectory of mathematica which is for MacOS;
/Library/Mathematica

To learn the location of the base directory see Mathematica above.

The packages can be loaded using unix style

<<xAct/xTensor.m

or Mathematica style

<<xAct`xTensor`

Run the followings first

git config --global user.name 'sbilmis'
git config --global user.email 'sbilmis@metu.edu.tr'
git config --global color.ui 'auto'

Your settings will be seen in ~/.gitconfig file.

Help commands

git help <verb>
man git-<verb>
git <verb> -h #For a quick refresher
tldr git-<verb>

Go to the folder you want to initialize git and then run

git init

This will create a folder .git that contains all of your necessary repository files in the folder.

The main tool you use to determine which files are in which state is the git status command.

git status 
git status -s 
git status --short

git add my_file1 my_file2  

git clone https://..

#.gitignore file example

# ignore all .a files 
*.a

# but do track lib.a, even though you're ignoring .a files above 
!lib.a

# only ignore the TODO file in the current directory, not subdir/TODO 
/TODO

# ignore all files in the build/ directory 
build/

# ignore doc/notes.txt, but not doc/server/arch.txt 
doc/*.txt

# ignore all .pdf files in the doc/ directory and any of its subdirectories 
doc/**/*.pdf

See https://github.com/github/gitignore for gitignore templates.

git diff
gitt diff -cached
git diff --staged
git diftool
git difftool --staged
git difftool --tool-help

git rm –cached my_file1

git commit -m "My first comment"

git status

git diff my_file1

git add -u ; to add all the tracked files

git commit

git log

Start reading https://gitlab.com/help/ssh/README#locating-an-existing-ssh-key-pair

Create new ssh_key name and name as id_dsa

ssh-keygen -t rsa -C "selcukbilmis@gmail.com" -b 4096

Then copy the public SSH key as we will need it afterwards.

pbcopy < ~/.ssh/id_rsa.pub

The final step is to add your public SSH key to GitLab.

Navigate to the 'SSH Keys' tab in your 'Profile Settings'. Paste your key in the 'Key' section and give it a relevant 'Title'. Use an identifiable title like 'Work Laptop - Windows 7' or 'Home MacBook Pro 15'.

If you manually copied your public SSH key make sure you copied the entire key starting with ssh-rsa and ending with your email.

If you used a non-default file path for your GitLab SSH key pair, you must configure your SSH client to find your GitLab private SSH key for connections to your GitLab server (perhaps gitlab.com).

For your current terminal session you can do so using the following commands (replacing other_id_rsa with your private SSH key):

Git Bash on Windows / GNU/Linux / macOS:

eval $(ssh-agent -s)
ssh-add ~/.ssh/other_id_rsa

• From terminal type

touch .bash_profile

https://caskroom.github.io/

http://osxdaily.com/2013/02/05/improve-terminal-appearance-mac-os-x/

In .bash_profile add the following lines;

export PS1="\[\033[36m\]\u\[\033[m\]@\[\033[32m\]\h:\[\033[33;1m\]\w\[\033[m\]\$ " export CLICOLOR=1 export LSCOLORS=ExFxBxDxCxegedabagacad alias ls='ls -GFh'

The first line changes the bash prompt to be colorized, and rearranges the prompt to be “username@hostname:cwd $”

The next two lines enable command line colors, and define colors for the ‘ls’ command

Finally, we alias ls to include a few flags by default. -G colorizes output, -h makes sizes human readable, and -F throws a / after a directory, * after an executable, and a @ after a symlink, making it easier to quickly identify things in directory listings.

Another Documentation: https://www.cyberciti.biz/faq/apple-mac-osx-terminal-color-ls-output-option/

1. CLICOLOR – Use ANSI color sequences to distinguish file types.
2. LSCOLORS – The value of this variable describes what color to use for which attribute when colors are enabled with CLICOLOR

Understanding LSCOLORS values

You can define color for each attribute with the help of LSCOLORS, when colors are enabled with CLICOLOR. This string is a concatenation of pairs of the format fb, where f is the foreground color and b is the background color. The default value is:

exfxcxdxbxegedabagacad

Where, ls Attribute Foreground color Background color directory e x symbolic f x socket c x pipe d x executable b x block e g character e d executable a b executable a g directory a c directory a d

The color and their code values are as follows: Code Meaning (Color) a Black b Red c Green d Brown e Blue f Magenta g Cyan h Light grey A Bold black, usually shows up as dark grey B Bold red C Bold green D Bold brown, usually shows up as yellow E Bold blue F Bold magenta G Bold cyan H Bold light grey; looks like bright white x Default foreground or background

export CLICOLOR=1 export LSCOLORS=GxFxCxDxBxegedabagaced

http://osxdaily.com/2012/10/24/set-the-hostname-computer-name-and-bonjour-name-separately-in-os-x/

M-x list-packages Find org in the list I to choose the package to be installed X to execute the installation

https://melpa.org/#/getting-started Add following lines to .emacs file

;; To install marmalade packages (require 'package) (add-to-list 'package-archives '("melpa" . "http://melpa.org/packages/") t) (package-initialize) ;;;;;

M-x package-install RET zenburn-theme To activate it; M-x load-theme RET zenburn