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jarvist / SUMO test errors.stdout
Created July 6, 2018 11:37
[Fri06Jul-12:34]jarvist@nmscde005688:~/.local/lib/python3.5/site-packages/sumo/
> python3 -m unittest discover tests
............/home/jarvist/.local/lib/python3.5/site-packages/monty/dev.py:214: UserWarning: Cannot install excepthook, IPyhon.core.ultratb not available
"Cannot install excepthook, IPyhon.core.ultratb not available")
.................................................EEEEEEEEE.E...EEFF.Froot
+--sub1
+--sub2
| +--sub2sub1
+--sub3
+--sub3sub1
@jarvist
jarvist / poster_split.sh
Created July 6, 2018 11:29
# poster_split.sh
# Script to split (Google Docs 'Drawing') poster into 4 panels for printing @ A3
# mutool is part of mupdf-tools on debian
# Lovely fast built in poster command!
mutool poster -x2 -y2 "${1}" 2x2.pdf
# For tweeter.
# -background white -alpha remove - puts in white background, removes ugly black transparent regions
# -density 144 -resize 50% - super-sample @ 200% to add anti-aliasing (avoid jagged text)
@jarvist
jarvist / keybase.md
Created December 6, 2016 16:46

Keybase proof

I hereby claim:

  • I am jarvist on github.
  • I am jarvist (https://keybase.io/jarvist) on keybase.
  • I have a public key ASCjCstG9VXZQyQ-ZAyC71SKt-LDRCdDB7rDQ1ojV2y2SAo

To claim this, I am signing this object:

@jarvist
jarvist / Julia Physics Notebook Start.jl
Last active November 28, 2016 01:31
# Physics Constants for electronic structure + stat physics
# defined as const to help with type stability
# 2016-07 - Updated accuracy from https://github.com/DataWookie/PhysicalConstants.jl
const c = 2.99792458e8; # m / s # speed of light in this universe
#const G = 6.673e-11; # m^3 / kg s^2
const h= 6.62606896e-34; # kg m^2 / s
const hbar = const ħ = 1.05457162825e-34; # kg m^2 / s
const eV = const q = const ElectronVolt = 1.602176487e-19; # kg m^2 / s^2
const MassElectron = 9.10938188e-31; # kg
@jarvist
jarvist / delta_SCF_extract_values.sh
Created March 23, 2016 13:17
Shell scripts to generate Delta-SCF calculations with Gaussian & extract results; see http://jarvist.github.io/post/2016-03-17-delta-scf/
#!/bin/sh
# delta_SCF_extract_values.sh - extract values from Delta-SCF Gaussian calculations
for i in *neutral.log
do
# Kohn-Sham HOMO/LUMO from the 'neutral' Gaussian calculation
HOMO=` grep "occ" "${i}" | tail -n 1 | awk '{print $NF*27.2114}' `
LUMO=` grep "virt" "${i}" | head -n 1 | awk '{print $5*27.2114}' `
KSGAP=` echo "${LUMO} - ${HOMO}" | bc -l `
@jarvist
jarvist / Julia Recombi Example
Created June 18, 2015 23:24
Stat Mech Recombination from various (Boltzmann, FD) kernels
{
"metadata": {
"language": "Julia",
"name": "",
"signature": "sha256:1a9071938dba4bd8f1ff573acb818698bab505d669c6377b952b615085b22cb0"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
@jarvist
jarvist / bit_reverse_for_loop.c
Created September 18, 2014 18:38
Maximum coverage for loops; bit reversing integars http://jarvistmoorefrost.wordpress.com/2014/09/18/maximum-coverage-for-loops-bit-reversing-integars
for (i=0;i<256;i++)
{
// Alright, this is the plan
// First we take our variable
// Then we bit reverse it as binary
// Pretty confusing, but means it will fill in the temperature
// range with maximum coverage, rather than linear ramping
unsigned char r=i;
r=(r&0xF0)>>4 | (r&0x0F)<<4;
r=(r&0xCC)>>2 | (r&0x33)<<2;
@jarvist
jarvist / advancedmaterials.bst
Created March 31, 2014 14:06
Advanced Materials BibTex file... (from 2010)
%%
%% This is file `advancedmaterials.bst',
%% generated with the docstrip utility.
%%
%% The original source files were:
%%
%% merlin.mbs (with options: `seq-no,nm-init,ed-au,dt-jnl,xmth,dtbf,jtit-x,thtit-x,vol-it,vnum-cm,volp-blk,jpg-1,num-xser,jnm-x,bkpg-x,isbn,issn,ppx,xedn,xand,etal-xc,url,url-blk,nfss,')
%% ----------------------------------------
%% *** Advanced Materials - Jarvist Moore Frost May 2010 ***
%%
@jarvist
jarvist / flags.mk
Created March 20, 2014 13:43
Working (?) flags.mk file for compiling LMF March 2014 release (http://ccpforge.cse.rl.ac.uk/gf/project/lmf/frs/?action=FrsReleaseView&release_id=355) on Federoa / Xeon with GNU libraries (removed hard coded links to Intel MKL etc.)
# On Fedora, required sudo yum install libgomp lapack lapack-devel blas blas-devel tcsh
# LibXC compiled & installed by hand. There's also a version in the distribution repository.
#
# usage: flags.py [gcc|cray|intel] [dbg|opt] [mpi] [cuda] [elpa] [ls++] > flags.mk
#        scons -Y path/to/lm-x.xxy [-j nprocs] [build_target]
#
# default args: gcc opt
#
#
# the following is produced by:
@jarvist
jarvist / furthest.py
Created May 27, 2013 13:22
What are the distances to the furthest reaches of Draenen?
# Requires: https://github.com/speleo3/inkscape-speleo/blob/master/extensions/survex.py by Thomas Holder
from survex import Survex3D
#This is the Oxford Draenen data:
# http://www.oucc.org.uk/DraenenSurvey/
mig=Survex3D('OD2.3d')
for destination in 'wiggly2.1','luck3.19','rifleman.1','pow.44':
print "OD2 entrance.20 <> ",destination
length, path = mig.shortestpath('entrance.20',destination)