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Eric Berquist berquist

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@berquist
berquist / gist:9062967
Created February 18, 2014 01:41
ChemAxon CNMR Prediction
[espeon@osmium]$ cat ~/Desktop/indole.inchi /home/espeon/opt/apps/ChemAxon/MarvinBeans/bin
InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H
[espeon@osmium]$ obabel -iinchi ~/Desktop/indole.inchi -omol -O ~/Desktop/indole.mol --gen3d
1 molecule converted
[espeon@osmium]$ cat ~/Desktop/indole.mol /home/espeon/opt/apps/ChemAxon/MarvinBeans/bin
OpenBabel02171420403D
16 17 0 0 0 0 0 0 0 0999 V2000
2.1639 -0.6827 -0.0733 C 0 0 0 0 0 0 0 0 0 0 0 0
@berquist
berquist / gold.gjf
Created May 23, 2014 16:16
#p hf/gen
gold external basis test (ADZP)
0 2
Au 0.000000 0.000000 0.000000
Au 0
S 8 1.00
14703222.86676416 0.0000848
@berquist
berquist / wB97X.in
Created June 13, 2014 01:04
$comment
Test of wB97X functional (long-range corrected hybrid functional)
Geometry optimization of N2, followed by freqency calculations
(using finite difference methods).
Ref: J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008).
$end
$molecule
0 1
N1
@berquist
berquist / cclib_writer_example.py
Created December 23, 2014 17:47
from cclib.parser import ccopen
from cclib.writer import ccwrite
job = ccopen('phenol.out')
data = job.parse()
# file is None by default, but can take either a filename as a string or a file handle object,
phenol_cjson_string = ccwrite(data, 'cjson', file=None)
ccwrite(data, 'cjson', file='phenol.cjson')
with open('phenol.cjson', 'w') as phenol_cjsonfile:
@berquist
berquist / main.cpp
Last active August 29, 2015 14:19 — forked from alberto-santini/accumulate-sequential-vs-parallel.cpp
#include <algorithm>
#include <chrono>
#include <functional>
#include <future>
#include <iomanip>
#include <iostream>
#include <random>
#include "pcg_random.hpp" // Random number generator
@berquist
berquist / workflows_and_plans.md
Created April 29, 2015 02:12
EMSL BSEL examples

Database foundation

  • Download the EMSL BSE database. How is is stored remotely?
  • Save the contents locally. By default, it should use sqlite3 (I think it does already) but optionally try:
    • JSON
    • HDF5
  • The contents save locally must be in a sensible format and layout for calling from Python, so that formatting basis sets can be done on-the-fly by calling the "database". There shouldn't be any additional databases, like the ones currently present (one for each format).

Working with the database

@berquist
berquist / pyquante1_cookbook.ipynb
Created June 1, 2015 03:31
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@berquist
berquist / spherical_harmonics.py
Created June 16, 2015 23:05
#!/usr/bin/env python3
from sympy import conjugate, integrate, pi, sin, symbols
from sympy.functions.special.spherical_harmonics import Ynm
theta, phi = symbols("theta, phi", real=True)
l_max = 1
for l in range(l_max + 1):
@berquist
berquist / PKGBUILD
Created June 18, 2015 13:40
# $Id: PKGBUILD 238190 2015-04-28 11:41:49Z bpiotrowski $
# Maintainer:
# Contributor: Andrea Scarpino <andrea@archlinux.org>
# Contributor: Nick B <Shirakawasuna at gmail _dot_com>
pkgname=avogadro
pkgver=1.1.1
pkgrel=5
pkgdesc="An advanced molecular editor based on Qt"
arch=('i686' 'x86_64')
@berquist
berquist / mp2_tzvp_opt.xyz
Created July 15, 2015 14:27
9
C 0.4623340000 -0.7339750000 0.0000000000
C -0.8668080000 -0.0334060000 -0.0000010000
C 0.4044730000 0.7673810000 0.0000000000
H -1.4484130000 -0.0558210000 0.9098070000
H -1.4484160000 -0.0558190000 -0.9098070000
H 0.7725540000 -1.2264490000 -0.9098070000
H 0.7725470000 -1.2264510000 0.9098090000
H 0.6758640000 1.2822730000 0.9098080000