rwest

- simple
- public over private
- personal vanity
- internet is global
- permalinks
- one important item per page
- don't break the browser
- don't wanker in technology
- a medium is not a grande
- break convention for your users

rwest

#!/usr/bin/env python
# encoding: utf-8
"""Extract cartesian geometries from gaussian log files using openbabel.

Reads all files that end '.log' in the current working directory.
Puts corresponding .mol files in the 'Geometries' subdirectory.

Created by Richard West on 2009-10-15.
Copyright (c) 2009 MIT. All rights reserved.
"""

rwest

import pybel
output = file('smiles.txt','w')
for inchi in file('inchis.txt'):
	molecule = pybel.readstring("inchi",inchi)
	output.write( molecule.write('smiles') )

rwest

#! /usr/bin/env python
# Recursively search folders for '.log' files and scan them for a certain regular expression.
import re # regular expressions
import fileinput, sys, os

# precompile the search into a RegularExpression object to make it faster when we do it lots of times
searchExpression=re.compile("Sum\ of\ electronic\ and\ zero-point\ Energies=\s*([\-0-9.]+)")

def process_folder(folderpath):
	#print "searching",folderpath

rwest

% for paragraph summaries
\newcommand{\parsum}[1]{
	\marginpar{
		\raggedright{} 
		\footnotesize{
			{\sffamily \setlength{\baselineskip}{0.6\baselineskip}\textcolor{grey}{#1} \par}
		}
	}
}

rwest

	# Stop wasting my time compiling PowerPC-compatible C extensions on my intel Mac
	import distutils.sysconfig
	config = distutils.sysconfig.get_config_vars()
	for key,value in config.iteritems():
		location = str(value).find('-arch ppc')
		if location>=0:
			print "removing '-arch ppc' from %s"%(key)
			config[key] = value.replace('-arch ppc ','')

# Tip from Lisandro Dalcin:

rwest

;; sort out backspace in .emacs on monch
(keyboard-translate ?\C-h ?\C-?)
(keyboard-translate ?\C-? ?\C-h)
(global-set-key "\C-h" 'delete-backward-char)

rwest

# set up git author details for commits and merges
export GIT_AUTHOR_NAME="Richard West"
export GIT_AUTHOR_EMAIL=rwest@mit.edu
export GIT_COMMITTER_NAME="Richard West"
export GIT_COMMITTER_EMAIL=rwest@mit.edu
# change the default editor from vi to emacs
export GIT_EDITOR=emacs  # doesn't work with the old version of git on monch
export VISUAL=emacs # a more generic system-wide editor command that does the trick

rwest

TemperatureModel: Constant (K) 800 1000 1500
PressureModel: Constant (atm) 1 5 10


SpectroscopicDataEstimator: FrequencyGroups
PressureDependence: ReservoirState
PDepKineticsModel: Chebyshev
TRange: (K) 800 2000 7 4
PRange: (bar) 1 10 3 3

rwest

!#/bin/sh
echo "Which version of chemkin?"
echo "   Chemkin Regular (21 seats)"
echo "   Chemkin Pro (1 seat)"
OPTIONS="standard pro"
select opt in $OPTIONS; do
    if [ "$opt" = "standard" ]; then
     xterm -ls -title 'Chemkin Regular - do not close before chemkin!' -bg grey -e ksh "
     source /home/reaction/chemkin15101_linuxx8664/bin/chemkin_setup.ksh
     echo 'QUIT CHEMKIN BEFORE CLOSING THIS WINDOW OR YOU MAY NOT CHECK IN THE LICENCE';