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mhoffman/bashrc

Created April 30, 2016 21:46
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  1. mhoffman created this gist Apr 30, 2016.
    834 changes: 834 additions & 0 deletions bashrc
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1,834 @@
    # ~/.bashrc: executed by bash(1) for non-login shells.
    # .see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
    # for examples
    # If running non interactively, do nothing

    ########################################################
    #|# Preamble #
    ########################################################
    [ -z "$PS1" ] && return

    # Determine platform first
    export platform='unknown'
    uname=$(uname)
    if [[ "x${uname}" == "xDarwin" ]]; then
    export platform='mac'
    elif [[ "x${uname}" == "xLinux" ]]; then
    export platform='linux'
    fi

    export dnsdomainname='unknown'
    if which dnsdomainname >/dev/null; then
    export dnsdomainname=$(dnsdomainname)
    else
    export dnsdomainname='unknown'
    fi

    export domainname='unknown'
    if which domainname >/dev/null; then
    export domainname=$(domainname)
    else
    export domainname='unknown'
    fi

    export hostname='unknown'
    if which domainname >/dev/null; then
    export hostname=$(hostname)
    else
    export hostname='unknown'
    fi

    ########################################################
    #|# General #
    ########################################################

    alias dirbashrc="grep -nT '^#|' ~/.bashrc"
    alias bashrc="vim ~/.bashrc"



    ########################################################
    #|## Bash, PATH #
    ########################################################

    # put here for early evaluation
    alias rebash='source ~/.bashrc'
    alias=ipython

    parse_git_branch() {

    git branch 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/ (\1)/'

    }


    ########################################################
    #|## Extra git enhancements #
    ########################################################
    # enable programmable completion features (you don't need to enable
    # this, if it's already enabled in /etc/bash.bashrc).
    if [ -f /etc/bash_completion ]; then
    . /etc/bash_completion
    elif [ -f /opt/local/etc/profile.d/bash_completion.sh ]; then
    . /opt/local/etc/profile.d/bash_completion.sh
    elif [ -d ~/.bash_completion ]; then
    echo "Found user bash-completions"
    for fn in ~/.bash_completion/*sh; do
    echo ${fn}
    source ${fn}
    done
    fi


    # have to stay here before setting PS1
    export GIT_PS1_SHOWDIRTYSTATE=true
    export export GIT_PS1_SHOWSTASHSTATE=true



    # set a fancy prompt
    declare -F | grep __git_ps1 > /dev/null
    if [ "$?" -eq 0 ]
    then
    echo ${platform}
    export PS1='\[\033[01;32m\]\u@\h\[\033[01;34m\]:\w\[\033[31m\]$(__git_ps1 "(%s)")\[\033[01;34m\]$\[\033[00m\] '
    else
    if [[ ${platform} == 'mac' ]]; then
    export PS1='\[\033[01;32m\]\u@\h\[\033[01;34m\]:\w\[\033[31m\]$(parse_git_branch)\[\033[01;34m\]$\[\033[00m\] '
    else
    export PS1='\[\033[01;32m\]\u@\h\[\033[01;34m\]:\w\[\033[31m\]\[\033[01;34m\]$\[\033[00m\] '
    fi
    fi

    PATH="${HOME}/.local/bin":\
    "${HOME}/.scripts":\
    "/var/lib/gems/1.9.1/bin":\
    "/var/lib/gems/1.9/bin":\
    "/var/lib/gems/1.8/bin":\
    "${HOME}/.gem/ruby/1.9.1/bin":\
    "${HOME}/.gem/ruby/2.0.0/bin":\
    "${GOBIN}":\
    ${PATH};

    shopt -s cdspell
    shopt -s histappend
    shopt -s expand_aliases
    shopt -s lithist
    shopt -s extglob
    set show-all-if-ambiguous on

    # set bash to vi mode
    # (hit ESC for command mode/
    # hit i for insert mode)
    #set -o vi

    # don't put duplicate lines in the history. See bash(1) for more options
    export HISTCONTROL=ignoredups
    export HISTIGNORE="&:ls:[bf]g:[cb]d:b:exit:[ ]*"
    export HISTSIZE=99999


    # enable color support of ls and also add handy aliases
    export INPUTRC=~/.inputrc
    if [[ ${platform} == 'mac' ]]; then
    export CLICOLOR=YES
    eval `dircolors -b`
    export JAVA_HOME=$(/usr/libexec/java_home)
    else
    eval `dircolors -b`
    fi

    #key bindings

    bind '"\M-a"':"\"bd\""
    bind '"\M-k"':"\"ls -f\""
    # enable smart history search
    bind '"\e[A":history-search-backward'
    bind '"\e[B":history-search-forward'
    ########################################################
    #|## Environment #
    ########################################################

    export EDITOR=vim
    export FC="/usr/bin/gfortran"
    export F2PY_FCOMPILER='gfortran'
    export GDFONTPATH="/usr/share/fonts/truetype/latex-xft-fonts/"

    ########################################################
    #|## Aliases, Utiliites #
    ########################################################

    # bash sugar
    alias ls='ls --color=auto'
    alias cdreadlink='cd $(readlink -f .)' # cd to real absolute path
    alias ldir='ls -l --color=always | grep -e "^d"' # list only directories
    alias gr='grep'
    alias c='clear'
    alias ct='printf "\033c"' # clear terminal
    alias l='ls -lhtr --color=auto --time-style long-iso && pwd'
    alias ll='clear && ls -lhtr --color=auto --time-style long-iso && pwd'
    alias ltail='ls -rtlh | tail -n 20'
    alias j='jobs'
    alias g='gthumb'
    alias d='date'
    alias v='vim'
    alias rl='readlink -f'
    alias eb='vim ~/.bashrc'
    alias kk='kill %'


    alias dir='ls --color=auto --format=vertical'
    alias vdir='ls --color=auto --format=long'
    alias keyjnote='impressive -T 100 -t CrossFade '
    alias git-svn-pull='git svn fetch; git merge git-svn'
    alias gitsy='git pull; git push'
    alias gy='gitsy'
    alias gitst='git st'
    alias modularize='touch __init__.py'
    alias top='htop -d 1'
    alias ..="cd .."
    alias ...="cd ../.."
    alias ....="cd ../../.."
    alias .....="cd ../../../.."
    alias ......="cd ../../../../.."
    alias .......="cd ../../../../../.."
    alias ........="cd ../../../../../../.."
    alias .........="cd ../../../../../../../.."
    alias ..........="cd ../../../../../../../../.."
    alias ...........="cd ../../../../../../../../../.."
    alias ............="cd ../../../../../../../../../../.."
    alias .............="cd ../../../../../../../../../../../.."
    alias vb=vboxmanage
    alias vh=vboxheadless
    alias sd="sudo shutdown -fh now"
    alias hk=heroku

    # Make the bash feel smoother
    # correct common typos
    alias sl='ls'
    alias iv='vi'
    alias vi='vim'
    alias dc='cd'
    alias tpo='top'
    alias otp='top'
    alias mem="ps aux | awk '{print \$2, \$4, \$11}' | sort -k2rn | head -n 20"
    alias t='top'
    alias db='bd'
    alias b='bd'
    alias rs='./manage.py runserver &'
    alias ds='./manage.py shell'
    alias dt='./manage.py test'
    alias pr='./tools/update_from_git.sh'
    alias ks='kmos shell'
    alias be='bundle exec'
    alias bert='bundle exec rake test'
    alias berd='bundle exec rake db:migrate'
    alias q='echo "You are not on a queueing system, dummy. Stop checking for running jobs!!!!"'
    alias nose=nosetests

    # vim
    alias vi=vim
    alias vim="vim -O"



    alias unlock="python -c 'from ctypes import *; X11 = cdll.LoadLibrary(\"libX11.so.6\"); display = X11.XOpenDisplay(None); X11.XkbLockModifiers(display, c_uint(0x0100), c_uint(2), c_uint(0)); X11.XCloseDisplay(display)'"

    alias getmyip="curl http://ipecho.net/plain"

    function fqpn(){
    if [ "x${1}" == "x" ]
    then
    rel_path="."
    else
    rel_path="${1}"
    fi

    hn=$(hostname -f)
    pn=$(readlink -f ${rel_path} )
    echo ${hn}:${pn}
    }

    function loclink(){
    if [ "x${1}" == "x" ]
    then
    return
    else
    fn="${1}"
    fi
    cp --remove-destination $(readlink ${fn} ) ${fn}
    }

    function path(){
    old=$IFS
    IFS=:
    printf "%s\n" $PATH
    IFS=$old
    }
    pantex (){
    pandoc --csl=$(readlink -f ~/src/citation-styles/american-chemical-society.csl ) -sS --bibliography $(echo *.bib) ${1} -o $(basename ${1} .md).pdf
    }
    function n { seq 1 $1| { shift; xargs -i -- "$@"; } }
    function executify(){
    file=${1}
    if [ -f ${file} -a ! -x ${file} ]
    then
    chmod 755 ${file}
    fi
    ./${file}
    }
    function pdfbiblatex(){
    for command in pdflatex bibtex pdflatex pdflatex
    do
    ${command} ${1}
    done
    }
    function pdf_colorpages(){
    gs -o - -sDEVICE=inkcov ${1} | grep -v "^ 0.00000 0.00000 0.00000" | grep -B1 CMYK | grep Page
    echo -en "Total pages"
    pdfinfo ${1} | grep Pages
    }

    function pdf_prepress(){
    gs -sDEVICE=pdfwrite -dSAFER -dPDFSETTINGS=/prepress -dNOPAUSE -r150x150 -sOutputFile=$(basename ${1} .pdf)_prepress.pdf -dBATCH ${1}
    }
    function pdf_printer(){
    gs -sDEVICE=pdfwrite -dSAFER -dPDFSETTINGS=/printer -dUseCIEColor=true -dNOPAUSE -r150x150 -sOutputFile=$(basename ${1} .pdf)_printer.pdf -dBATCH ${1}
    }
    function pdf_ebook(){
    gs -sDEVICE=pdfwrite -dSAFER -dPDFSETTINGS=/ebook -dNOPAUSE -r150x150 -sOutputFile=$(basename ${1} .pdf)_ebook.pdf -dBATCH ${1}
    }
    function pdf_screen(){
    gs -sDEVICE=pdfwrite -dSAFER -dPDFSETTINGS=/screen -dNOPAUSE -r150x150 -sOutputFile=$(basename ${1} .pdf)_screen.pdf -dBATCH ${1}
    }

    function pdf_bw(){
    gs -sOutputFile=$(basename ${1} .pdf)_bw.pdf -sDEVICE=pdfwrite -sColorConversionStrategy=Gray -dNOPAUSE -dBATCH -dProcessColorModel=/DeviceGray -dCompatibilityLevel=1.4 $(basename ${1} .pdf).pdf < /dev/null
    }

    function pygraph(){
    TMP=$(mktemp -d)
    sfood -i ${1} > ${TMP}/SFOOD
    sfood-graph ${TMP}/SFOOD > ${TMP}/SFOOD.dot
    dot -Tpdf ${TMP}/SFOOD.dot > SFOOD.pdf
    xpdf SFOOD.pdf
    rm -rf ${TMP}
    }

    function note(){
    if [ "x${1}" == "x" ]
    then
    message='Hello World'
    else
    message=${1}
    fi
    notify-send -u normal -t 10 -i info 'hw' ${1}
    }

    function rsafevi() {
    link_name="${1}.$(date +"%Y%m%d-%H%M%S").$(sudo env | grep SUDO_USER | cut -d= -f 2)"
    sudo cp ${1} ${link_name}
    sudo vi ${1}
    #if [ ${link_name} -ef ${1} ]
    #then
    #sudo rm ${link_name}
    #fi
    }
    alias rvi=rsafevi
    function fname() { find . -name "*$@*"; }
    function fregex() { find . -regextype posix-egrep -regex "*$@*"; }
    function firegex() { find . -regextype posix-egrep -iregex "*$@*"; }
    function finame() { find . -iname "*$@*"; }

    function safevi() {
    cp ${1} ${1}.$(date +"%Y%m%d-%H%M%S")
    vi ${1}
    }
    # always use pushd/popd by default
    # and if directory turns out to be a file, we open it with vi :-)
    function cd() {
    if [ "$#" = "0" ]
    then
    pushd ${HOME} > /dev/null
    elif [ -f "${1}" ]
    then
    ${EDITOR} ${1}
    else
    pushd "$1" > /dev/null
    fi
    }

    # bd 5 goes 5 directories back in history
    function bd(){
    if [ "$#" = "0" ]
    then
    popd > /dev/null
    else
    for i in $(seq ${1})
    do
    popd > /dev/null
    done
    fi
    }

    function cdup(){
    if [ "$#" = "0" ]
    then
    cd ..
    else
    reldir=''
    for i in $(seq ${1})
    do
    reldir="${reldir}../"
    done
    cd ${reldir}
    fi
    }
    # bash bookmark manager, credit goes to getmizanur at Stackoverflow
    function bm() {
    bookmark_storage="${HOME}/.bookmarks"
    USAGE="Usage: cdb [-c|-g|-d|-l] [bookmark]
    cd -c <bookmark>
    Bookmark the current directory under <bookmark>
    cd -g <bookmark>
    Go to the directory saved under <boomark>
    cd -d <boomark>
    Delete directory under <bookmark>
    " ;
    if [ ! -e ${bookmark_storage} ] ; then
    mkdir ${bookmark_storage}
    fi

    case $1 in
    # create bookmark
    -c) shift
    if [ ! -f ${bookmark_storage}/$1 ] ; then
    echo "$(pwd)" > ${bookmark_storage}/"$1" ;
    else
    echo "Try again! Looks like there is already a bookmark '$1'"
    fi
    ;;
    # goto bookmark
    -g) shift
    if [ -f ${bookmark_storage}/${1} ] ; then
    cd $(cat ${bookmark_storage}/${1})
    else
    echo "Mmm...looks like your bookmark has spontaneously combusted. What I mean to say is that your bookmark does not exist." ;
    fi
    ;;
    # delete bookmark
    -d) shift
    if [ -f ${bookmark_storage}/$1 ] ; then
    rm ${bookmark_storage}/"$1" ;
    else
    echo "Oops, forgot to specify the bookmark" ;
    fi
    ;;
    # list bookmarks
    -l) shift
    for bookmark in ${bookmark_storage}/*
    do
    echo "$(basename ${bookmark}) -> $(cat ${bookmark})" ;
    done

    ;;
    *) echo "$USAGE" ;
    ;;
    esac
    }

    # call pdflatex on a tex file and open with xpdf
    function xpdflatex(){
    pdflatex ${1}
    xpdf $(basename ${1} .tex).pdf
    }
    # standard way to install python package in user space
    alias pyuserinstall='python setup.py install --user'

    alias line_profile="kernprof.py -lv"

    # shortcut for building standalone C program
    # from standalone Python script using Cython
    function cython-build(){
    echo -e $1
    cython --verbose --embed $1
    gcc -O3 -I/usr/include/python2.7 -o $(basename ${1} .py) $(basename ${1} .py).c -lpython2.7 -lphtread -lm -lutil -ldl
    }


    # miscellaneous
    alias cleanmake='make clean; make'
    alias cm='cleanmake'

    if [[ ${platform} == 'linux' ]]; then
    alias units='units -e'
    fi
    alias xmod='xmodmap ~/.xmodmap'

    alias pysh='ipython --profile=pysh'

    # copy a file to middle mouse-button
    alias clip='xclip -selection clipboard'
    alias xclip='xclip -selection clipboard'

    pman() { # view man pages the fancy way
    tmp=$(mktemp); man -t $1 | ps2pdf - ${tmp} && xpdf -z 'width' -g 1280x1000 ${tmp} && rm ${tmp};
    };


    alias fuck='$(thefuck $(fc -ln -1))'
    alias pysyntax="python -m 'py_compile' "
    alias is=inkscape
    isexport(){
    if [ "${2}x" = "x" ]
    then
    res=90
    else
    res=${2}
    fi
    seed=$(basename ${1} .svg)
    JPEG2PS_INSTALLED=true
    hash jpeg2ps 2>/dev/null || JPE2PS_INSTALLED=false
    if $JPEG2PS_INSTALLED
    then
    inkscape --export-area-snap -e ${seed}.png ${1} -d ${res} -b white
    convert ${seed}.{png,jpg}
    jpeg2ps ${seed}.jpg > ${seed}.eps
    epstopdf ${seed}.eps
    # touch up to make it more current than pdf, for paper buildout
    touch ${seed}.eps
    else
    inkscape --export-area-snap -E $(basename ${1} .svg).eps -A $(basename ${1} .svg).pdf -e $(basename ${1} .svg).png ${1} -d ${res}
    fi
    }

    ########################################################
    #|# Platform Specifics #
    ########################################################
    ########################################################
    #|## Mac OS X #
    ########################################################
    if [[ ${platform} == 'mac' ]]; then
    export PATH=~/.cabal/bin:/opt/local/libexec/gnubin:${PATH}:/Users/$(whoami)/Library/Python/2.7/bin/:/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin
    export DISPLAY="127.0.0.1:0.0"
    export CDPATH=.:~:~/src:~/stanford:~/phd:~/ssh_mounts
    export GOPATH=~/src/gocode
    export PATH=${PATH}:${GOPATH}/bin
    export PYTHONPATH="${HOME}/.local/lib/python2.7/site-packages/"
    export PATH=${PATH}:/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin
    alias xpdf=open
    alias o=open
    alias finder=open
    alias nautilus=open
    ########################################################
    #|## Linux #
    ########################################################
    elif [[ ${platform} == 'linux' ]]; then
    export PATH=${PATH}
    export CDPATH=.:~:~/src

    fi

    ########################################################
    #|# Host Specifics #
    ########################################################


    ########################################################
    #|## SLAC #
    ########################################################
    if [ "x${dnsdomainname}" == "xslac.stanford.edu" ]
    then
    if [ "x${STY}" == "x" ] # check if we are in screen
    then # we are not ...
    echo ${DISPLAY} > /scratch/.$(whoami).display # first store the current value of $DISPLAY in a throaway file
    screen -ADR # then attach to existing screen session or start new one
    export IGNOREEOF=1 # to make sure we don't accidentalu kill the screen session
    export DISPLAY=$(cat /scratch/.$(whoami).display) # load the $DISPLAY variable again from filesystem
    rm -f /scratch/.$(whoami).display # delete throwaway file
    fi


    unset SSH_ASKPASS # otherwise the default askpass program just waits forever without an X server
    alias q='bjobs -w'
    alias qdel=bkill
    alias py='ipython --gui=None --pylab=None'
    alias qdelall="bjobs | tail -n+2 | awk '{print \$1}' | xargs bkill -r"
    function qrun(){
    bjobs | head -n 1
    bjobs | grep RUN
    echo "You have $(bjobs | grep RUN | wc -l) running jobs."
    }

    alias qstat='bjobs -u all | grep suncat'
    alias pri='bqueues -r suncat'
    alias p='bqueues -r suncat'
    alias g='display -resize 1024x768 -size 1024x768'
    function esp(){
    python2.7 -m py_compile ${1}
    if [ $? -ne 0 ]
    then
    echo "Not compiling"
    return 1
    fi
    chmod -v 755 $1
    #esp-ver-bsub 17 -J "$(head -$((${RANDOM} % `wc -l < ~/.names` + 1)) ~/.names | tail -1)" $@
    esp-ver-bsub 20 $@
    }
    alias qsub=esp
    alias vmdt="vmd -dispdev text"

    #source /afs/slac/g/suncat/gpaw/setupenv
    export PATH=${PATH}:/afs/slac/g/suncat/bin:/usr/local/bin
    export CDPATH=.:~:~/src:/nfs/slac/g/suncatfs/maxjh
    export PYTHONPATH=/u/if/maxjh/.local/lib/python2.7/site-packages/:/nfs/slac/g/suncatfs/sw/espv17/lib/python2.7/site-packages/:${PYTHONPATH}
    #export PYTHONPATH=/nfs/slac/g/suncatfs/sw/espv17/lib/python2.7/site-packages/
    export LD_LIBRARY_PATH=/nfs/slac/g/suncatfs/sw/espv17/intellib:/nfs/slac/g/suncatfs/sw/external/openmpi/1.6.3/install/lib:/afs/slac/package/lsf/curr/lib:/nfs/slac/g/suncatfs/sw/python276/lib64:/nfs/slac/g/suncatfs/sw/python276/lib:/nfs/slac/g/suncatfs/sw/python276noafs/intellib:/nfs/slac/g/suncatfs/sw/espv17/intellib:/nfs/slac/g/suncatfs/sw/external/openmpi/1.6.3/install/lib
    alias slac="echo 'You are already at SLAC!'"
    else
    alias slac="ssh -Y [email protected]"
    alias slacmount='sshfs -o workaround=rename -o follow_symlinks -o transform_symlinks [email protected]: ~/ssh_mounts/slac'
    function fromslac(){
    scp -r "[email protected]:${1}" .
    }
    fi


    ########################################################
    #|## sherlock #
    ########################################################
    if [ "x$(hostname)" = "xsherlock-ln02.stanford.edu" -o "x$(hostname)" = "xsherlock-ln01.stanford.edu" ]
    then
    module load vmd/1.9.2
    module load intel/2016.u1
    module load QuantumEspresso/5.1.1/intel
    #module load python/2.7.5
    module load openmpi/1.8.7/intel
    module load tensorflow/0.5.0
    module load gcc/4.9.1
    unset SSH_ASKPASS # otherwise the default askpass program just waits forever without an X server
    #source ~/.local/bin/activate
    alias q="qstat -u $(whoami)"
    alias qdelall="scancel -u $(whoami)"
    alias vpy=/home/vossj/suncat/bin/python
    #export PATH=/home/vossj/suncat/bin:${PATH}
    export CDPATH=.:~:~/src
    export PATH=/home/maxjh/env/kmos/bin/:/home/maxjh/.local/bin:${PATH}
    #export PYTHONPATH=${PYTHONPATH}:/home/vossj/suncat/lib/python2.7/site-packages
    export PYTHONPATH=/home/maxjh/env/kmos/lib/python2.7/site-packages:${PYTHONPATH}
    export PYTHONPATH=/home/maxjh/env/kmos/lib64/python2.7/site-packages:${PYTHONPATH}
    export PYTHONPATH=/home/maxjh/.local/lib/python2.7/site-packages:${PYTHONPATH}

    if [ "x${STY}" == "x" ]
    then
    echo ${DISPLAY} > /scratch/users/$(whoami)/display
    screen -ADR -s /bin/bash
    export IGNOREEOF=1
    export DISPLAY=$(cat /scratch/users/$(whoami)/display)
    rm -f /scratch/users/$(whoami)/display
    fi
    else
    alias sherlock='kinit -R; ssh -KY sherlock.stanford.edu'
    function fromsherlock(){
    scp -r "[email protected]:${1}" .
    }
    fi



    if [ "x$(hostname)" = "xpeekbox64" -a "x${dnsdomainname}" = "xtheo.chemie.tu-muenchen.de" ]
    then
    alias barriers='echo Stupid!'
    alias barriersmount='echo Stupid!'
    alias q='echo " No queueing system here, you knuckle-head !"'
    export PATH_TO_ARXIV='/mnt/arxiv_s3/'
    export DJANGO_SETTINGS_MODULE='settings'
    [ -z "$PYTHONPATH" ] && export PYTHONPATH="/user/hoffmann/src/cmr_install"
    [ -n "$PYTHONPATH" ] && export PYTHONPATH="/user/hoffmann/src/cmr_install:$PYTHONPATH"
    [ -z "$PATH" ] && export PATH="/user/hoffmann/src/cmr_install/tools"
    [ -n "$PATH" ] && export PATH="/user/hoffmann/src/cmr_install/tools:$PATH"

    else
    alias barriers='ssh [email protected]'
    alias barriersmount='sshfs [email protected]: ~/ssh_mounts/barriers'

    fi

    if [ "x${dnsdomainname}" = "xbc.rzg.mpg.de" ]
    then
    module load git
    module load intel
    module load impi/4.0.0
    export CDPATH=.:~:~/src:~/calculations/2x2_thinslab/calc
    alias q="qstat | grep $(whoami)"
    export CASTEP_COMMAND='source /etc/profile.d/modules.sh; module load impi; mpiexec -n 64 /u/mhoffman/bin/castep'
    export CASTEP_PP_PATH='/u/mhoffman/CASTEP/PSPs'
    export PSPOT_DIR=${CASTEP_PP_PATH}
    alias py=ipython
    alias atop='tail $(ls -rt1 *.o* | tail -n 17)'
    else
    alias py='ipython --pylab=None --gui=None'
    alias ot=octave
    # aims cluster in garching
    alias heystunnel='ssh -N -f -l mhoffman -L 7778:heys.theo.chemie.tu-muenchen.de:22 server.theo.chemie.tu-muenchen.de'
    alias heys='ssh -l mhoffman -p 7778 localhost'

    alias aimstunnel='ssh -N -f -l mhoffman -L 7777:aims01.bc.rzg.mpg.de:22 gate.rzg.mpg.de'
    alias aims='ssh -l mhoffman -p 7777 localhost'

    alias aimsmount='sshfs -p 7777 mhoffman@localhost: ~/ssh_mounts/aimscluster -o workaround=rename'

    alias vip='ssh [email protected]'
    alias vipmount='sshfs [email protected]: ~/ssh_mounts/vip'
    alias vip='ssh [email protected]'
    alias vipmount='sshfs [email protected]: ~/ssh_mounts/vip'
    fi

    ########################################################
    #|## CHEMIE TU MUENCHEN #
    ########################################################
    if [ "x${dnsdomainname}" = "xtheo.chemie.tu-muenchen.de" -o "x$(hostname)" = "xheys" ]
    then
    if [ "x${hostname}" != "xserver" ]
    then
    source /user/hoffmann/.rvm/scripts/rvm # for using ruby
    fi
    export CDPATH=.:~:~/src:~/phd:~/ssh_mounts:/data/hoffmann
    #export http_proxy="http://proxy.theo.chemie.tu-muenchen.de:3128"
    export no_proxy=localhost,127.0.0.1
    #export https_proxy="${http_proxy}"
    #export HTTP_PROXY="${http_proxy}"
    #export HTTPS_PROXY="${http_proxy}"
    export CASTEP_COMMAND='mpirun.openmpi -np 4 castep'
    export CASTEP_PP_PATH='/user/hoffmann/src/PSPs'
    alias ldapvi='/usr/bin/ldapvi --ldap-conf --bind sasl --tls strict --starttls --sasl-mech GSSAPI'
    k(){
    if [ -n "$(tokens | grep afs)" ]
    then
    kinit -R
    else
    kinit --renewable --forwardable
    fi
    }
    else
    # server of theoretical chemistry in garching
    alias theochem='ssh [email protected] '
    alias theochemmount='sshfs -o workaround=rename -o follow_symlinks -o transform_symlinks [email protected]: ~/ssh_mounts/theochem'
    fi


    ########################################################
    #|## azetbur at FHI #
    ########################################################
    if [ ! "x$(domainname)" = "xppb" ] # azetbur in berlin
    then
    alias azetbur='ssh [email protected]'
    alias azetmount='sshfs [email protected]: ~/ssh_mounts/azetbur'
    fi

    if [ "x$(hostname)" = "xbutz" ]
    then
    alias q='echo " No queueing system here, you knuckle-head !"'
    fi


    ########################################################
    #|# Program Specifics #
    ########################################################

    #set ifort environment variables
    if [ -e /opt/intel/bin/compilervars.sh ]; then
    source /opt/intel/bin/compilervars.sh ia32
    fi
    if [ "x$(hostname)" = "xbutz" ]
    then
    export BLPAPI_ROOT=~/src/blpapi
    export GPGKEY=26067AA0
    export GOPATH=~/src/go
    export PATH=$PATH:$GOPATH/bin
    alias battery='acpi -V | grep Battery'
    #alias xpdf=evince
    # Go variables
    export CDPATH=.:~:~/src:~/stanford:~/phd:~/ssh_mounts
    export GOBIN=~/src/go/bin
    export PATH=$PATH:$GOBIN
    export PATH_TO_ARXIV='/home/mhoffman/src/arxiv_s3'
    export CASTEP_COMMAND='castep'
    export CASTEP_PP_PATH='/home/mhoffman/src/CASTEP/PSPs'
    #source /home/mhoffman/.rvm/scripts/rvm # for using ruby
    bright(){
    sudo -s "echo ${1} > /proc/acpi/video/OVGA/DD02/brightness"
    }
    # set environment variables for openFOAM
    #. /opt/openfoam201/etc/bashrc
    export PERL5LIB=~/.perl5/lib/perl5
    # start redshift if not running
    fi

    export GPAW_SETUP_PATH=${HOME}/src/gpaw/gpaw-setups-0.8.7929

    if ! which ag >/dev/null; then
    alias ag=ase-gui
    fi

    #if which hub &2>1 >/dev/null; then
    #alias git=hub
    #fi

    #PATH=$PATH:$HOME/.rvm/bin # Add RVM to PATH for scripting

    #if [[ ${platform} == 'linux' ]]; then
    ##which xmodmap && xmod
    #fi
    alias trm="echo 'your terminal is ' $TERM"

    ########################################################
    #|## Package-Managment APT/Macports #
    ########################################################
    # apt-get
    if [[ ${platform} == 'mac' ]]; then
    alias clean='sudo port clean'
    alias install='sudo port -v install'
    alias remove='sudo port uninstall'
    alias search='port -v search'
    alias show='port info'
    alias update='sudo port -v selfupdate'
    alias upgrade='sudo port upgrade outdated'
    alias vmd=' /Applications/VMD\ 1.9.2.app/Contents/MacOS/startup.command'
    else
    alias autoremove='sudo apt-get autoremove -y'
    alias build-dep='sudo apt-get build-dep'
    alias clean='sudo apt-get clean'
    alias dist-upgrade='sudo apt-get dist-upgrade'
    alias install='sudo apt-get install -y'
    alias purge='sudo apt-get remove --purge'
    alias reinstall='sudo apt-get install --reinstall'
    alias remove='sudo apt-get remove'
    alias search='apt-cache search'
    alias show='apt-cache show'
    alias update='sudo apt-get update'
    alias upgrade='sudo apt-get upgrade'
    fi


    ########################################################
    #|## Heroku #
    ########################################################
    if [ -d /usr/local/heroku/bin/ ]
    then
    export PATH="/usr/local/heroku/bin:$PATH"
    fi

    ########################################################
    #|## NVM #
    ########################################################
    if [ -d ${HOME}/.nvm ]
    then
    export NVM_DIR="${HOME}/.nvm"
    [ -s "$NVM_DIR/nvm.sh" ] && . "$NVM_DIR/nvm.sh" # This loads nvm
    fi
    67 changes: 67 additions & 0 deletions gitconfig
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    [user]
    name = hoffmannm
    email = [email protected]
    [color]
    ui = auto
    [color "branch"]
    current = yellow reverse
    local = yellow
    remote = green
    [color "diff"]
    meta = yellow bold
    frag = magenta bold
    old = red bold
    new = green bold
    [color "status"]
    added = yellow
    changed = green
    untracked = cyan


    [alias]
    st = status
    ci = commit
    br = branch
    co = checkout
    df = diff
    lg = log -p
    ps = push
    pl = pull
    sync = !"git pl; git ps"
    sy = !"git pl; git ps"
    gr = log --color --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr)%C(bold blue)<%an>%Creset' --abbrev-commit
    nicelog = log --graph --full-history --all --color --pretty=format:"%x1b[31m%h%x09%x1b[32m%d%x1b[0m%x20%s"
    top = rev-parse --show-toplevel
    mt = mergetool
    man = help
    bad = bisect bad
    good = bisect good
    ar = !( git archive HEAD --prefix $(basename $(readlink -f .))-$($(basename $(readlink -f .)) version)/ --format tar | gzip > $(basename $(readlink -f .))-$($(basename $(readlink -f .)) version).tar.gz)
    root = rev-parse --show-toplevel
    vdiff = difftool -d -t opendiff
    contributors = !git log --format='%aN' | sort -u

    # use git like a feed reader
    ribbon = tag --force _ribbon origin/master
    catchup = log --reverse --topo-order _ribbon..origin/master
    d = difftool

    [sendemail]
    smtpserver = smtp.gmail.com
    smtpserverport = 587
    smtpencryption = tls
    smtpuser = [email protected]
    [github]
    user = mhoffman
    [remote "aims"]
    uploadpack = /afs/rzg/.cs/git/@sys/1.8.4/bin/git-upload-pack
    receivepack = /afs/rzg/.cs/git/@sys/1.8.4/bin/git-receive-pack

    [push]
    default = matching
    [diff]
    tool = vimdiff
    [difftool]
    prompt = false
    [merge]
    tool = vimdiff
    78 changes: 78 additions & 0 deletions install_dotfiles
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    #!/bin/bash -eu

    SCRIPTS_FOLDER=~/.scripts # Change this to wherever you keep custom scripts, this should be in you $PATH variable
    VIM_ROOT=~/.vim # The user vim directory for bundle managed plugins
    IPYTHON_ROOT=~/.ipython # full IPython customizations needs it own directory ...


    # Above the fold
    ######################################################################################################################
    # below the fold

    # Determine platform first
    export platform='unknown'
    uname=$(uname)
    if [[ "x${uname}" == "xDarwin" ]]; then
    export platform='mac'
    elif [[ "x${uname}" == "xLinux" ]]; then
    export platform='linux'
    fi


    # install main config files
    for dotfile in bashrc #vimrc gitconfig xmodmap inputrc hgrc curlrc tmux.conf plan caffrc pypirc sblrc screenrc
    do
    if [ -L ~/.${dotfile} ]
    then
    rm ~/.${dotfile}
    fi
    ln -sv $(pwd)/${dotfile} ~/.${dotfile}
    done

    # install .vim/vim for vim vundle
    if [ -L ${VIM_ROOT}/vim ]
    then
    rm ${VIM_ROOT}/vim
    fi
    ln -sv $(pwd)/vim ${VIM_ROOT}

    mkdir -p ${IPYTHON_ROOT}/profile_default

    # install ipython config dir
    if [ -L ${IPYTHON_ROOT}/profile_default/ipython_config.py ]
    then
    rm ${IPYTHON_ROOT}/profile_default/ipython_config.py
    fi
    ln -sv $(pwd)/ipython_config.py ${IPYTHON_ROOT}/profile_default/ipython_config.py

    # install scripts folder
    if [ ! -d ${SCRIPTS_FOLDER} ]
    then
    mkdir -p ${SCRIPTS_FOLDER}
    fi

    # put scripts in scripts folder
    for script in scripts/*
    do
    if [ ! -e ${SCRIPTS_FOLDER}/$(basename ${script}) ]
    then
    if [[ ${platform} == 'mac' ]]; then
    ln -sv $(greadlink -f ${script}) ${SCRIPTS_FOLDER}/$(basename ${script})
    else
    ln -sv $(readlink -f ${script}) ${SCRIPTS_FOLDER}/$(basename ${script})
    fi
    fi
    done

    echo -e "\n\nIf vim shows attitude, run:"
    echo -e "git clone https://github.com/gmarik/Vundle.vim.git ${VIM_ROOT}/bundle/Vundle.vim"
    echo -e "vim +PluginInstall +qall"

    if [ ! -d ${VIM_ROOT}/bundle ]
    then
    echo "Ok, ok, I am already trying to do that"
    git clone https://github.com/gmarik/Vundle.vim.git ${VIM_ROOT}/bundle/Vundle.vim
    echo "And now let's try to install all those pesky plugins ..."
    vim +PluginInstall +qall
    echo "Done!"
    fi
    299 changes: 299 additions & 0 deletions vimrc
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    set nocompatible " be iMproved
    filetype off " required!

    set rtp+=~/.vim/bundle/Vundle.vim
    call vundle#begin()

    Plugin 'gmarik/Vundle.vim'
    Plugin 'closetag.vim'
    Plugin 'godlygeek/tabular'
    Plugin 'plasticboy/vim-markdown'
    Plugin 'scrooloose/nerdtree'
    Plugin 'comments.vim'
    Plugin 'browsereload-mac.vim'
    Plugin 'coffee.vim'
    Plugin 'vim-coffee-script'
    Plugin 'WebAPI.vim'
    Plugin 'Gist.vim'

    call vundle#end()
    " let Vundle manage Vundle
    " and don't put the comment on the same line

    """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
    " General behavior
    """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
    set autowrite " Speichert bei jedem :make, ;next, :rewind etc.
    set autoread

    if match($TERM, "screen")!=-1
    set term=xterm
    endif

    set title " Set buffer name as terminal name

    " Schaltet syntax-highlighting und korrektes Einrücken an
    " und filetype spezifisches ein
    syntax on
    filetype plugin indent on

    " Vermeidet Probleme beim pasten aus dem Browser
    set paste

    " Stellt die Dateinamenerweiterung wie unter bash ein
    set wildmode=longest,list

    " Der Zeiger springt kurz zur öffnenden Klammer, wenn die schließende
    " eingegeben wird
    set showmatch
    set matchtime=1 " In diesem Fall 1/10 sek.


    set autoindent " automatic and smart indentation
    set smartindent
    set copyindent

    " Die Einrückweite pro Level
    set shiftwidth=4

    " Ein Tab wird wie 2 Leerzeichen angezeigt und dank expandtab werden tabs
    " gleich als Leerzeichen eingefügt.
    set tabstop=4
    set expandtab
    set softtabstop=4
    set smarttab

    " Setzt die maximale Textbreite von Fließtext
    set linebreak
    set textwidth=66

    " highlight lines that are to long
    " highlight OverLength ctermbg=red ctermfg=white guibg=#592929
    " match OverLength /\%79v.\+/

    " Wenn mit /suchwort gesucht wird, springt der Zeiger schon beim Eintippen
    set incsearch

    "Sucht standardmäßig ohne Groß- und Kleinschreibung zu unterscheiden
    set ignorecase

    "Blendet Zeileninformation ein
    set ruler

    "Blendet Formatierungszeichen ein
    set lcs=tab:>-,trail:-,nbsp:~
    set nolist

    "Faltet automatisch neue Dateien nach Einrückung ein
    set foldmethod=indent
    "set foldcolumn=8
    set foldlevel=8
    set showcmd " Display an incomplete command in the lower right corner of the Vim window

    set mouse-=a " Disable mouse
    set mousehide " Hide mouse after chars typed
    """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
    " Keyboard short cuts
    """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
    " change the mapleader from \ to ,
    let mapleader=","
    "let mapleader=" "

    " Show trailing characters and such
    map <leader>st :set list<CR>
    " Quickly edit/reload the vimrc file
    nmap <silent> <leader>oc :e $MYVIMRC<CR>
    nmap <silent> <leader>rc :so $MYVIMRC<CR>
    " Shortcut for hypergit
    nmap <leader>g :ToggleGitMenu<CR>
    " Save files, close vim
    map <leader>w :w<CR>
    map <leader>x :x<CR>
    map <leader>q :q!<CR>
    " Shortcuts for NERD tree
    map <leader>n :NERDTree .<CR>
    " Simplify saving and closing of files
    "map <F5> :silent execute "!pdflatex % > /dev/null && xpdf -remote paper -reload > /dev/null &"<CR>ggG<C-o><C-o>
    map <F5> :!%<CR>
    map <F8> :w<CR>
    map <F10> :x<CR>
    " Spellcheck, ignore tex comments
    map <F9> :set spell<CR>
    let g:tex_comment_nospell=1

    " Shortcuts for ConqueTerm shell
    map <leader>sh :ConqueTermSplit bash<CR>
    map <leader>vsh :ConqueTermVSplit bash<CR>
    map <leader>py :ConqueTermSplit ipython<CR>
    map <leader>vpy :ConqueTermVSplit ipython<CR>
    " open MRU menu
    nnoremap <leader>m :MRU<CR>
    " NERDtree on <leader>t
    nnoremap <leader>t :NERDTree<CR>
    " remove trailing whitespace
    map <leader>rt :%s/\s\+$//<CR>
    map <leader>sp :set paste<CR>
    map <leader>fl a.format(**locals())<ESC>
    map <leader>up i#!/usr/bin/env python<CR><CR>if __name__ == '__main__':<CR>
    map <leader>um i#!/usr/bin/env python<CR><CR>def main():<CR> pass<CR><CR>if __name__ == '__main__':<CR> main()<ESC>
    map <leader>in iif __name__ == '__main__':<CR>
    " open FuzzyFinder
    map <leader>ff :FufFile<CR>
    " Have NERDTree alway open in the current folder
    set autochdir
    let NERDTreeChDirMode=2


    " Setzt die Ergebnisse einer Stringsuche immer in die Mitte des Bildschirms
    nmap n nzzzv
    nmap N Nzzzv
    nmap * *zzzv
    nmap # #zzzv
    nmap g* g*zzzv
    nmap g# g#zzzv
    " Change windows size next to each other using <, >
    "nmap <C-<> <C-w><
    "nmap <C->> <C-w>>

    " Einrücken der ganzen Datei mit --
    fun! BenIndent()
    let oldLine=line('.')
    normal(gg=G)
    execute ':' . oldLine
    endfun
    map -- :call BenIndent()<cr>
    let g:AutoPairsFlyMode=1
    let g:AutoPairsShortCutBackInsert='<M-b>'

    """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
    " Language specific behavior
    """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

    " Fortran
    " Fixes 'bug' in wrong form recognition
    let fortran_free_source=1
    let fortran_fold=1
    "autocmd FileType fortran compiler ifort


    " Java Spezifisches
    let java_highlight_all=1
    let java_highlight_functions="style"
    let java_allow_cpp_keywords=1


    " LaTeX Spezifisches
    set iskeyword+=:
    "let g:Tex_Env_theorem "\\pspicture(0,0)(,)(,)\<CR>\<CR>\\endpspicture"
    let g:Tex_DefaultTargetFormat='pdf'
    let g:Tex_CompileRule='latex --interaction=nonstopmode $*'
    let g:Tex_CompileRule_ps='dvips -q -Ppdf -o $*.ps $*.dvi'
    let g:Tex_CompileRule_pdf='ps2pdf $*.ps'
    let g:Tex_FormatDependency_pdf = 'dvi,ps,pdf'
    let g:Tex_IgnoredWarnings=' \"Underfull\n".
    \"Overfull\n".
    \"specifier changed to\n".
    \"You have requested\n".
    \"Missing number, treated as zero.\n".
    \"There were undefined references\n".
    \"Citation %.%# undefined\n"
    \"Unused global option"'


    autocmd Filetype html,xml,xsl source ~/.vim/scripts/closetag.vim
    ""Enables OmniComplete Toggeling with only Ctrl-n
    "set complete-=k complete+=k

    let NERDTreeIgnore=['\~$', '\.pyc$', '\.pyo$', '\.class$', 'pip-log\.txt$', '\.o$']

    nnoremap <tab> <c-p>
    " Function to automagically increase number of marked column
    fun! Incr()
    let l = line(".")
    let c = virtcol("'<")
    let l1 = line("'<")
    let l2 = line("'>")
    if l1 > l2
    let a = l - l2
    else
    let a = l - l1
    endif
    if a != 0
    exe 'normal '.c.'|'
    exe 'normal '.a."\<c-a>"
    endif
    normal `<
    endfunction
    vnoremap <c-a> :call Incr()<CR>
    "jump to last position when reopen
    autocmd BufReadPost *
    \ if line("'\"") > 0 && line("'\"") <= line("$") |
    \ exe "normal! g`\"" |
    \ endif

    """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
    " Plugin specific behavior
    """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
    " OmniCompletion
    "Omni Completion für alle möglichen sprachen einschalten
    autocmd FileType python set omnifunc=pythoncomplete#Complete
    autocmd FileType javascript set omnifunc=javascriptcomplete#CompleteJS
    "autocmd FileType html set omnifunc=htmlcomplete#CompleteTags
    autocmd FileType css set omnifunc=csscomplete#CompleteCSS
    "autocmd FileType xml set omnifunc=xmlcomplete#CompleteTags
    "autocmd FileType php set omnifunc=phpcomplete#CompletePHP
    "autocmd FileType c set omnifunc=ccomplete#Complete

    let g:SuperTabDefaultCompletionType = "context"
    set completeopt=menuone,longest,preview

    " for Goerz' sendToScreen gimmick
    autocmd BufNewFile,BufRead *.py let b:sendToProgramMode="ipython"
    let b:sendToProgramName="~/.vim/scripts/send2screen.py -S ipy1 "


    " settings for pydiction (Python tab completion) plugin)
    let g:pydiction_location="~/.vim/ftplugin/pydiction/complete-dict"
    let g:pydiction_menu_height=20

    let g:tex_flavor='latex'


    "" for Go
    "filetype off
    "filetype plugin indent off
    "set runtimepath += "/usr/local/go/misc/vim"
    "filetype plugin indent on
    "syntax on

    let g:instant_markdown_slow = 1

    " allow for better search and replace
    vnoremap <silent> s //e<C-r>=&selection=='exclusive'?'+1':''<CR><CR>
    \:<C-u>call histdel('search',-1)<Bar>let @/=histget('search',-1)<CR>gv
    omap s :normal vs<CR>
    function! NumberToggle()
    if(&relativenumber == 1)
    set number
    else
    set relativenumber
    endif
    endfunc

    nnoremap <C-n> :call NumberToggle()<cr>