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@rmcgibbo
rmcgibbo / pull-peterson.py
Created Jun 2, 2017
Automate downloading some basis sets from Kirk Peterson's website
View pull-peterson.py
from __future__ import print_function
import requests
import bs4
import re
headers = {
'Referer': 'http://tyr0.chem.wsu.edu/~kipeters/basissets/alkal-nr.html',
'Origin': 'http://tyr0.chem.wsu.edu',
'Upgrade-Insecure-Requests': '1',
'User-Agent': 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/56.0.2924.87 Safari/537.36',
'Content-Type': 'application/x-www-form-urlencoded',
View hartree-fock.ipynb
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View conda-system-libraries.json
{"linux-vdso.so.1": ["_license-1.1-py27_0", "_license-1.1-py27_1", "_license-1.1-py34_0", "_license-1.1-py34_1", "_license-1.1-py35_1", "abstract-rendering-0.1.0-np18py27_0", "abstract-rendering-0.3.1-np18py26_0", "abstract-rendering-0.3.1-np18py27_0", "abstract-rendering-0.4.0-np18py26_0", "abstract-rendering-0.4.0-np18py27_0", "abstract-rendering-0.5.0-np18py26_0", "abstract-rendering-0.5.0-np18py27_0", "abstract-rendering-0.5.0-np19py26_0", "abstract-rendering-0.5.0-np19py27_0", "abstract-rendering-0.5.1-np110py27_0", "abstract-rendering-0.5.1-np110py34_0", "abstract-rendering-0.5.1-np110py35_0", "abstract-rendering-0.5.1-np19py26_0", "abstract-rendering-0.5.1-np19py27_0", "abstract-rendering-0.5.1-np19py33_0", "abstract-rendering-0.5.1-np19py34_0", "abstract-rendering-0.5.1-np19py35_0", "astropy-0.2-np15py26_0", "astropy-0.2-np15py27_0", "astropy-0.2-np16py26_0", "astropy-0.2-np16py27_0", "astropy-0.2-np17py26_0", "astropy-0.2-np17py27_0", "astropy-0.2-np17py33_0", "astropy-0.2.1-np15py26_0", "astropy-0.2
View conda-base-env.json
{
"linux-vdso.so.1": [
"_license-1.1-py27_0",
"_license-1.1-py27_1",
"_license-1.1-py34_0",
"_license-1.1-py34_1",
"_license-1.1-py35_1",
"abstract-rendering-0.1.0-np18py27_0",
"abstract-rendering-0.3.1-np18py26_0",
"abstract-rendering-0.3.1-np18py27_0",
@rmcgibbo
rmcgibbo / testcase.cc
Last active Dec 29, 2015
Test of different LAPACK functions for computing eigenvalues of a symmetric matrix (corresponding to the routines used by numpy.linalg.eigh and scipy.linalg.eigh, and numpy.linalg.eig)
View testcase.cc
// Compile with: `clang++ -o test testcase.cc -framework Accelerate`
// run with ./test <N> <seed>
// Copyright [2015] Robert T. McGibbon
// Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
// The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
View gist:1d0f5d166ca48253b5a9
$ python -c "import pprint, pip.pep425tags; pprint.pprint(pip.pep425tags.get_supported())"
[('cp35', 'cp35m', 'macosx_10_0_x86_64'),
('cp35', 'cp35m', 'macosx_10_0_intel'),
('cp35', 'cp35m', 'macosx_10_0_fat3'),
('cp35', 'cp35m', 'macosx_10_0_fat64'),
('cp35', 'cp35m', 'macosx_10_0_universal'),
('cp35', 'cp35m', 'macosx_10_1_x86_64'),
('cp35', 'cp35m', 'macosx_10_1_intel'),
('cp35', 'cp35m', 'macosx_10_1_fat3'),
('cp35', 'cp35m', 'macosx_10_1_fat64'),
View minimize.py.log
Loading the system and PDB file...
Creating the Simulation...
Minimizing...
OpenMM L-BFGS Minimizer
At iterate 0 f= -2.400392e+05 |g|=8.113642e+04
At iterate 1 f= 1.839185e+04 |g|=2.585253e+06
At iterate 2 f= -2.142435e+05 |g|=3.565821e+05
At iterate 3 f= -2.435828e+05 |g|=1.209668e+05
At iterate 4 f= -2.503961e+05 |g|=5.927351e+04
At iterate 5 f= -2.557794e+05 |g|=4.352573e+04
View gist:c6b4257b34accf6ea688
$ doccheck simtk.openmm.openmm
simtk.openmm.openmm.AmoebaAngleForce.addAngle ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
Undocumented arguments: {'quadraticK'}
Documented non-arguments: {'quadratic'}
simtk.openmm.openmm.AmoebaAngleForce.getAngleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
Documented non-arguments: {'particle1', 'particle3', 'length', 'quadratic', 'particle2'}
simtk.openmm.openmm.AmoebaAngleForce.setAngleParameters ( /home/rmcgibbo/miniconda/envs/openmm/lib/python3.4/site-packages/simtk/openmm/openmm.py )
Undocumented arguments: {'quadraticK'}
View gromacs-xstream (1).ipynb
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View xstream-md-benchmarks.ipynb
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