Jarvist Moore Frost jarvist

Computational Physicist, searching for Electronic Structure nirvana.

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 / 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 / keybase.md

Created December 6, 2016 16:46

I hereby claim:

To claim this, I am signing this object:

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 / 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 / Julia Recombi Example

Created June 18, 2015 23:24

Stat Mech Recombination from various (Boltzmann, FD) kernels

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	"worksheets": [
	{

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 / 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 / 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 / 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)