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# Copyright 2001 Brad Chapman.
# Revisions copyright 2009-2010 by Peter Cock.
# Revisions copyright 2010 by Phillip Garland.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""D... | asherkhb/coge | bin/last_wrapper/Bio/Blast/Applications.py | Python | bsd-2-clause | 64,304 | [
"BLAST",
"Biopython"
] | d0f34cb171ca986ca0c1d93a5d0b207888614cd042924405dd3d182ffea82171 |
#
# Copyright (C) 2001-2017 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from collections import abc #... | ptosco/rdkit | rdkit/Chem/Descriptors.py | Python | bsd-3-clause | 7,814 | [
"RDKit"
] | 248e92414dd05ce3885e89a524018a64f42998ab621b035902d38cd2d0f6bb50 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import numpy as np
from pymatgen.analysis.local_env import LocalStructOrderParams, get_neighbors_of_site_with_index
from pymatgen.analysis.bond_vale... | nisse3000/pymatgen | pymatgen/analysis/magnetism/jahnteller.py | Python | mit | 16,436 | [
"CRYSTAL",
"pymatgen"
] | 51e2753d83ab6d8d4d2505b6db35c029e2a1764c6f0b0cd3cc2e41bb53be6709 |
"""Emojione autogen.
Generated from emojione source. Do not edit by hand.
MIT license.
Copyright (c) http://www.emojione.com
"""
from __future__ import unicode_literals
version = "3.1.3"
name = "emojione"
emoji = {
":100:": {
"category": "symbols",
"name": "hundred points",
"unicode": "1f... | archifix/settings | sublime/Packages/pymdownx/st3/pymdownx/emoji1_db.py | Python | mit | 480,981 | [
"CRYSTAL",
"FLEUR",
"Octopus"
] | 3d40470bd192b8480e4e5e7c10392095b8e9960f0bc454ca465e8971ebc316e9 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from .test_account_settings import AccountSettingsTestMixin
from ..ga_helpers import GaccoTestMixin, SUPER_USER_INFO
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.ga_django_admin import DjangoAdminPage
class GaAccountS... | nttks/edx-platform | common/test/acceptance/tests/lms/test_ga_account_settings.py | Python | agpl-3.0 | 4,833 | [
"VisIt"
] | 25c1bbafd7fbd1e78cdcc119ec35888800a7b70bd0e7826adb81b0779b6dd4d7 |
"""Algorithms for spectral clustering"""
# Author: Gael Varoquaux gael.varoquaux@normalesup.org
# Brian Cheung
# Wei LI <kuantkid@gmail.com>
# License: BSD
import warnings
import numpy as np
from ..base import BaseEstimator, ClusterMixin
from ..utils import check_random_state, as_float_array, depreca... | lucidfrontier45/scikit-learn | sklearn/cluster/spectral.py | Python | bsd-3-clause | 17,740 | [
"Brian",
"Gaussian"
] | 26ae77f1f1b8a540bf78259e9bc60f0fc92d331c1a5d1bee743e7c7bbb9ca66a |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | alejob/mdanalysis | package/MDAnalysis/coordinates/CRD.py | Python | gpl-2.0 | 9,335 | [
"CHARMM",
"MDAnalysis"
] | 4250b2dd98810d475d0e3dae44ac4e6361782d00f171e78e044b4d986c3cdb17 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# startexe - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of ... | heromod/migrid | mig/cgi-bin/startexe.py | Python | gpl-2.0 | 1,104 | [
"Brian"
] | 842f3c57ccf783f1e4a089bfd9c40f72fbc080b29ef7e805b008400e6d904e2d |
#!/usr/bin/env python3.2
"""
This evolved into a very specialized script that I'm only saving to tease apart
like Lego bits to make something more permanent later.
INPUT:
Three total inputs are required.
The first is a tab-delimited output file (-a) that is the product of parsing eukaryotic
annotation evidence. ... | jorvis/biocode | sandbox/jorvis/convert_euk_autoannotate_to_pathologic.py | Python | mit | 11,127 | [
"BLAST"
] | 76f1378abe96ea93e979720ab309f1c9c97627c5d53e1373c635702d23a72a51 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | aldian/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 217,245 | [
"Gaussian"
] | 8d2714c4644be0b9861853c54c1671b1118672ec9e52211fdc7ba8c621104a7b |
import os.path
import unittest
import shutil
from subprocess import check_output, check_call
from tempfile import NamedTemporaryFile
import pysam
from crumbs.utils.test_utils import TEST_DATA_DIR
from crumbs.utils.bin_utils import BIN_DIR
from crumbs.bam.bam_tools import (filter_bam, calmd_bam, realign_bam,
... | JoseBlanca/seq_crumbs | test/bam/test_bam_tools.py | Python | gpl-3.0 | 5,393 | [
"pysam"
] | 8c51562da5cdde7ac2ed820f0fdf48d870665038a54fc714b043a58d8169b8f3 |
# Storage filtering classes
#
# Copyright (C) 2013 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed... | cgwalters/anaconda | pyanaconda/ui/gui/spokes/filter.py | Python | gpl-2.0 | 26,312 | [
"VisIt"
] | 83d237ab3c6cae7ecaa494bc090d09fe98b0e0faf697569fb6ded71f1c158004 |
"""
A simple dynamic programming algorithm for the Travelling Salesman Problem.
This needs exponential time of course.
Author:
Christos Nitsas
(nitsas)
(chrisnitsas)
Language:
Python 3(.4)
Date:
August, 2014
"""
import collections
__all__ = ['Tour', 'TspSolverDynamicProgrammingWithMemoization', 'Solv... | nitsas/py3algs | py3algs/algorithms/tsp.py | Python | mit | 3,870 | [
"VisIt"
] | 196f4dc200f365a70cf4b2cbe0d3d358aada26e151e056a502019d19907c011f |
"""
Parser function parse() to parse the .nnkp output file of Wannier90 -pp.
"""
import inspect
import re
from collections import defaultdict
from . import show_output
# Match the lines in the nnkpts block
# Groups:
# 0: idx of first kpt
# 1: idx of second kpt
# 2,3,4: g1,g2,g3 (reciprocal lattice vector needed to b... | greschd/wannier90 | test-suite/tools/parsers/parse_nnkp.py | Python | gpl-2.0 | 2,639 | [
"Wannier90"
] | 12fcd20ef3662493b55d382e67b79495891de68314d0d879eb97db6dd16ef61c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
with open('README.rst') as readme_file:
readme = readme_file.read()
with open('HISTORY.rst') as history_file:
history = history_file.read()
# T... | benoistlaurent/dock2nc | setup.py | Python | gpl-3.0 | 2,116 | [
"NetCDF"
] | 6224e8b9b2c389f479613fc79a7e6caab4fbed93d62232b6cb4749b6dd209e82 |
from cardboard import types
from cardboard.ability import (
AbilityNotImplemented, spell, activated, triggered, static
)
from cardboard.cards import card, common, keywords, match
@card("Sage's Knowledge")
def sages_knowledge(card, abilities):
def sages_knowledge():
return AbilityNotImplemented
r... | Julian/cardboard | cardboard/cards/sets/portal_three_kingdoms.py | Python | mit | 24,574 | [
"VisIt"
] | 84ca968d99f8a51fbcc6836f2b1f491e6747638e1a054703f80f8fbabfbe5b7d |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | zjj2wry/kubernetes | cluster/juju/layers/kubernetes-master/reactive/kubernetes_master.py | Python | apache-2.0 | 43,359 | [
"CDK"
] | b6c0bad8735281e185bc9989adc882ac11316ec38737e04307bfa1700d85e181 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/test/bigdl/orca/ray/integration/test_yarn_reinit_raycontext.py | Python | apache-2.0 | 1,602 | [
"ORCA"
] | 096a6485f2b4fc6e07f34daa147fd62514d916ef1ac4fbf2c9766aa6a9dcaf7a |
#! /usr/bin/env python
"""
LLSG (Gomez Gonzalez et al. 2016)
"""
from __future__ import division
from __future__ import print_function
__author__ = 'C. Gomez @ ULg'
__all__ = ['llsg']
import numpy as np
from scipy.linalg import qr
import itertools as itt
from multiprocessing import Pool, cpu_count
from astropy.stats... | henry-ngo/VIP | vip_hci/llsg/llsg.py | Python | mit | 9,946 | [
"Gaussian"
] | 7545845a19a8bdf29a9a6371250f94300994d4106582b46bb1c7fa46817dc978 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | do/modeling/plot_correlations.py | Python | agpl-3.0 | 8,512 | [
"Galaxy"
] | 2e02f382d48aae1d25c91b81f93b3912c79438dcbfed4c1e3da2e7edb0ecda91 |
#
# Copyright 2014, 2021 Lars Pastewka (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software... | libAtoms/matscipy | scripts/fracture_mechanics/eval_J_integral.py | Python | lgpl-2.1 | 5,295 | [
"ASE",
"Matscipy"
] | a8674b2160cec90208619dcf04efaeed052a295ecd82a8c0f44cb5fffea02d84 |
# pmx Copyright Notice
# ============================
#
# The pmx source code is copyrighted, but you can freely use and
# copy it as long as you don't change or remove any of the copyright
# notices.
#
# ----------------------------------------------------------------------
# pmx is Copyright (C) 2006-2013 by Daniel ... | tectronics/pmx | pmx/forcefield2.py | Python | lgpl-3.0 | 51,968 | [
"Amber",
"CHARMM",
"Gromacs"
] | c956896a184f00bf05e2ec4ff33324ab6638b6417c81595c096ae46b974aa143 |
#! /usr/bin/env python
########################################################################
# File : dirac-admin-set-site-protocols
# Author : Stuart Paterson
########################################################################
"""
Defined protocols for each SE for a given site.
Example:
$ dirac-admin-se... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_set_site_protocols.py | Python | gpl-3.0 | 1,285 | [
"DIRAC"
] | 74ca1568efc2e517235c36c2b808f0c4a57ba4730aeb9931865d15f64f8e1bcb |
# Copyright (C) 2020
# Max Planck Institute for Polymer Research & JGU Mainz
# Copyright (C) 2012,2013,2015,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPR... | espressopp/espressopp | src/VerletList.py | Python | gpl-3.0 | 4,143 | [
"ESPResSo"
] | 90654abd5026afab2366917a571b5f34e49ea1f6ea12f48a7d5e1cfbe21b78c3 |
'''
=head1 NAME
STORIcontrol.py
=head1 SYNOPSIS
python ./STORIcontrol.py
STORI>start <run-name> <scratch/dir> <taxa file> <windowSize> <finalMaxFams>
STORI>start hemoglobin_eumetazoa_1x_STORI /home/ec2-user/STORI/Runfiles eumetazoa 4 20
STORI>start hemoglobin_euk_8x_STORI /home/ec2-user/STORI/Runfiles eukaryota ... | jgstern/STORI_singlenode | STORIcontrol.py | Python | gpl-2.0 | 25,102 | [
"BLAST"
] | ef0534ae4c3119de8ab723ed60681f306594c08b19d6feb2e8f430b3c4c89260 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | dhalperi/beam | sdks/python/apache_beam/runners/direct/direct_runner.py | Python | apache-2.0 | 6,718 | [
"VisIt"
] | 95847b88b694279584c7c825c50c7ae1cb295e46d6d58ab5d1aa655e242008d4 |
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be usefu... | scylladb/scylla-cluster-tests | sdcm/utils/data_validator.py | Python | agpl-3.0 | 32,352 | [
"VisIt"
] | b6aa5e83ac3bb90e4b66fd76b7997f33ac16702894d6f9f5dfef25811e1e20e4 |
#!/usr/bin/env python
###########################################################################
# #
# This Python script generates an input file to be used for #
# LAMMPS or ESPRESSO++ ... | espressopp/espressopp | bench/lennard_jones/gen_lennard_jones.py | Python | gpl-3.0 | 5,494 | [
"ESPResSo",
"Gaussian",
"Gromacs",
"LAMMPS"
] | 5a3edc5fae587871465bc83fe7cb1e96f4f0a404f398f8591a3c6b3d0c8e7dcf |
## -*- coding: utf-8 -*-
## Copyright (c) 2015-2022, Exa Analytics Development Team
## Distributed under the terms of the Apache License 2.0
#"""
#Parser for ADF's SCF Section
################################
#Parses the 'S C F' section of an ADF block output.
#"""
#from exatomic.exa import Parser, Matches, Match
#
#
#... | exa-analytics/exatomic | exatomic/adf/adf/scf.py | Python | apache-2.0 | 802 | [
"ADF"
] | caecbdfc0c39f67f9f59f018c4a27caf6b9fd714f7933236f2fa8ba3022e3257 |
""" core implementation of testing process: init, session, runtest loop. """
import argparse
import fnmatch
import functools
import importlib
import os
import sys
from typing import Callable
from typing import Dict
from typing import FrozenSet
from typing import Iterator
from typing import List
from typing import Optio... | JoelMarcey/buck | third-party/py/pytest/src/_pytest/main.py | Python | apache-2.0 | 28,359 | [
"VisIt"
] | 93bbc6ac3a1f90f24a43cf1a49b45ec233152b61712cac04e174fd5c06be51fa |
"""
DIRAC.ResourceStatusSystem package
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
| yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/__init__.py | Python | gpl-3.0 | 174 | [
"DIRAC"
] | 1bb5fbde5cfa13faa9a62eaf9c92e3ca2fb11167fb9eefc7f6dbd6846ed9f55c |
# -*- coding: utf-8 -*-
"""
jinja2.compiler
~~~~~~~~~~~~~~~
Compiles nodes into python code.
:copyright: Copyright 2008 by Armin Ronacher.
:license: BSD.
"""
from cStringIO import StringIO
from itertools import chain
from jinja2 import nodes
from jinja2.visitor import NodeVisitor, NodeTransformer
... | scyclops/Readable-Feeds | jinja2/compiler.py | Python | gpl-3.0 | 53,416 | [
"VisIt"
] | c9907b2ae6541db58f230be618899edc0d66d6854cdccafbb1d91a0a0748471a |
import ddapp.vtkAll as vtk
import ddapp.vtkNumpy as vnp
import drc as lcmdrc
import numpy as np
import time
class DepthImageProvider(object):
def __init__(self):
self.source = vtk.vtkMapServerSource()
self.source.Start()
def waitForSceneHeight(self):
viewId = lcmdrc.data_request_t.HE... | gizatt/director | src/python/ddapp/depthimageprovider.py | Python | bsd-3-clause | 1,182 | [
"VTK"
] | a67c7f679acbfca4282e72ccb6a4632ff50d87e96ec3abd1ac8aa74dc316db1c |
## \example rmf/link.py
# This example is like module/rmf/pdb.py except that instead of creating a
# new hierarchy from the rmf file, it simply links the existing hierarchy
# to the file. This mechanism can be used for loading multiple
# conformations for scoring or other analysis without having to set up
# restraints ... | shanot/imp | modules/rmf/examples/link.py | Python | gpl-3.0 | 1,236 | [
"exciting"
] | c7bbb49bb4d2c959aedecca19ed00ef35739e1961474573d24ffee741ea77ade |
import numpy
import subprocess
import math
from math import sqrt, exp
import matplotlib.pyplot as plt
import random
pi = 3.1415926
class CaliberationData:
# values are ordered in the N-E-W-S sequence
avgAmplitude = None # array containing average amplitude (gain)
# def CaliberateFromDataFile(filename):
def Loa... | ap1/PixeeBel | code/pysrc/caliberation.py | Python | mit | 5,246 | [
"Gaussian"
] | c0aa7d54efa3950a4e6e5ab8cfae5b2821fc009f72b5f9a6e2ec079425dab9a3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
python modules for plot utilities:
ImageViewer: main GUI framework for an universal image viewer
Author: Tong Zhang
Created: Feb. 3rd, 2015
"""
#import wxversion
#wxversion.ensureMinimal('2.8')
from __future__ import division
import wx
from wx.lib.agw import flo... | Archman/felapps | felapps/utils/pltutils.py | Python | mit | 138,511 | [
"Gaussian"
] | bb36bcab77c399a80d440a2266bfab1490b13ab9fdd97df8dd285e369665f184 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# liveio - communication with running jobs
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Lic... | heromod/migrid | mig/cgi-bin/liveio.py | Python | gpl-2.0 | 1,076 | [
"Brian"
] | 73d1006a2abb07b5467b9b80f0580bdb7bffac793a49f24bd6fa304eed545e18 |
#!/usr/bin/env python
# (C) Copyright IBM Corporation 2004, 2005
# All Rights Reserved.
#
# 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
# ... | execunix/vinos | xsrc/external/mit/MesaLib/dist/src/mapi/glapi/gen/gl_procs.py | Python | apache-2.0 | 6,852 | [
"Brian"
] | a37435d5aad563ffe02dd2524e944cfa373df219fc446e5d609f15893eb2cb68 |
import sqlite3
import time
import datetime
from contextlib import closing
from inject import assign_injectables
from getters import with_getters_for
def connect_database(database_file):
"""
Connect to a database
Args:
database_file the file containing the sqlite3 data.
"""
return sqlite3.connect(databas... | rahulraj/web_projects | assignment5/linkshort/databaseservice.py | Python | mit | 9,703 | [
"VisIt"
] | ecf33f10dc12bb0fac45448f0c422edf8f9dc9d15a973e6222e46b92b866dc8e |
"""
Methods for calculating Mutual Information in an embarrassingly parallel way.
Author: Daniel Homola <dani.homola@gmail.com>
License: BSD 3 clause
"""
import numpy as np
from scipy.special import gamma, psi
from sklearn.neighbors import NearestNeighbors
from joblib import Parallel, delayed
def get_mi_vector(MI_FS... | danielhomola/mifs | mifs/mi.py | Python | bsd-3-clause | 5,334 | [
"Brian"
] | 22bffcc74406f02d22e147de8f4957e07647997755c7b7ce74effd8423e5366e |
# Copyright (c) 2012 ARM Limited
# All rights reserved.
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implementation of the functionality ... | hoangt/gem5v | gem5v-diffs/vgem5/src/python/m5/SimObject.py | Python | bsd-3-clause | 42,548 | [
"VisIt"
] | 989b184612df23067bc1f70a8b4a3ce8f5ed5d757de6baf0c0be034991916431 |
# $Id$
#
# Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from __future__ import ... | jandom/rdkit | rdkit/Chem/Pharm3D/EmbedLib.py | Python | bsd-3-clause | 38,924 | [
"RDKit"
] | 2b7e4d2fd6f729b14c283251060ea228e4669c7cad03e73dd1c714950c04ef2d |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/domain/purchase.py | Python | gpl-2.0 | 31,865 | [
"VisIt"
] | e6e31e89075abb8eca59a50e71527fe7c4966282a11c21948aa69c3f4748c3aa |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2015, Heyo
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) a... | tszym/ansible | lib/ansible/modules/windows/win_nssm.py | Python | gpl-3.0 | 5,858 | [
"ADF"
] | 9b7c7929dcdea181e45a5c1de2a99f2ded96c4d73c1f9fabf9e00ce374da452e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Implementation of defect correction methods.
"""
import logging
import matplotlib.pyplot as plt
import numpy as np
import scipy
from scipy import stats
from pymatgen.analysis.defects.core import DefectCo... | gmatteo/pymatgen | pymatgen/analysis/defects/corrections.py | Python | mit | 38,851 | [
"VASP",
"pymatgen"
] | c8dd9145f27cf402fcc1c42fd2931423762bb2a10b3ec3105ddfec976d0783e4 |
##
# title: SensorInfoTable.py
# by: Brian Kim
# description: displays nxt sensor information
#
from InfoTable import InfoTable
class SensorInfoTable( InfoTable ):
pass
| briansan/rams | RAMS/gui/SensorInfoTable.py | Python | bsd-3-clause | 173 | [
"Brian"
] | e8fd68a7fa79da21b4779e40af5877b79ad29abc5751a1380af2e7689d6154fa |
"""
Copyright (c) 2015 Andreea Georgescu
Created on Sun Mar 1 19:51:42 2015
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
... | Andreea-G/Codds_DarkMatter | src/experiment_HaloIndep.py | Python | gpl-2.0 | 31,067 | [
"DIRAC",
"Gaussian"
] | a409b221c7c53d90bd9951de5ccdf023ad7c24e6358e5b363df9a970da68bf50 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement Table."""
from abc import ABCMeta, abstractmethod
import copy
from numbers import Integral
from math import log10
from sys import stdout
from hoom... | joaander/hoomd-blue | hoomd/write/table.py | Python | bsd-3-clause | 17,999 | [
"HOOMD-blue"
] | b86f77593d78eb4a014a788a5540f7ef564daec4a3d5831acf1129025b314582 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/removelocation.py | Python | gpl-2.0 | 5,225 | [
"VisIt"
] | 282867c0044a7185edb534d1fcaeff7412f87b733aa281c05fbac2a0235efc07 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | pkreissl/espresso | samples/dpd.py | Python | gpl-3.0 | 2,346 | [
"ESPResSo"
] | e84de12b6e0653f535cfc553f7b90d98a7aa524088ba6fec150dc373e30fad24 |
import time,math
from aiclasses import *
import aitools
#from aidatabase import *
class AICommander:
def __init__(self):
f = open("npcs/governments")
governments = []
for line in f:
governments.append(line.rstrip("\n"))
f.close()
print "GOVERNMENTS: " + str... | remremrem/EV-Tribute | world/aicommander.py | Python | mit | 807 | [
"Galaxy"
] | 0bdb4225e9783278d61d9f97fbca9cda0e6590042226f9a52c36192d0414a423 |
#!/usr/bin/env python
"""Sinusoidal grating in a gaussian mask"""
############################
# Import various modules #
############################
import VisionEgg
VisionEgg.start_default_logging(); VisionEgg.watch_exceptions()
from VisionEgg.Core import *
from VisionEgg.FlowControl import Presentation
from Vi... | visionegg/visionegg | demo/gabor.py | Python | lgpl-2.1 | 1,827 | [
"Gaussian"
] | 6b815e7e0657d7c948d2e8ffdd514192014a637172549ceaa0d289b41867eaf2 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | espressopp/espressopp | src/integrator/CapForce.py | Python | gpl-3.0 | 2,764 | [
"ESPResSo"
] | 25351b8b9dbb6bef686938bf419d2fb868039f3d2ee3c908ecc801743b5fb7c2 |
from rsf.proj import *
import math
#--------------------------#
#Basic Utils - Raanan Dafni#
#--------------------------#
#*************************************************************************************************#
#******************************************** VELOCITY *****************************************... | TobbeTripitaka/src | trip/admin/utilsRD.py | Python | gpl-2.0 | 8,710 | [
"Gaussian"
] | fb3118c9118a6a777d3fa9faf5c4763a9d39966b56b47244484966e957f65c3c |
#!/usr/bin/python2.7
# encoding: utf-8
#Libs import
from __future__ import division
#TR comment: 2 alternatives
import netCDF4 as nc
from scipy.io import netcdf
from pydap.client import open_url
import cPickle as pkl
import pickle as Pkl
import copy
from os.path import isfile
import gc
#Utility import
from pyseidon.u... | TheKingInYellow/PySeidon | pyseidon/fvcomClass/fvcomClass.py | Python | agpl-3.0 | 13,302 | [
"NetCDF"
] | a1d7e11f310a2825f74e6d236062c6e8b28353d64687d98853766d194db5bb21 |
#
# Author: Henrique Pereira Coutada Miranda
# Run a GW calculation using yambo
#
from __future__ import print_function
from yambopy import *
from qepy import *
import argparse
yambo = "yambo"
p2y = "p2y"
folder='bse'
def doublegrid():
global folder
folder = "%s_dbg"%folder
database()
#check if the n... | palful/yambopy | tutorial/mos2/bse_mos2.py | Python | bsd-3-clause | 4,048 | [
"Yambo"
] | 2ff755f75d5c335e447182159d8fa2e7d5407e01f879abca8b85455f6f856677 |
# shamelessly copied from pliExpertInfo (Vali, Mirakels, Littlesat)
from enigma import iServiceInformation, iPlayableService
from Components.Converter.Converter import Converter
from Components.Element import cached
from Components.config import config
from Tools.Transponder import ConvertToHumanReadable
from Tools.Ge... | opendroid-Team/enigma2-4.1 | lib/python/Components/Converter/PliExtraInfo.py | Python | gpl-2.0 | 24,777 | [
"Galaxy"
] | a02f6a897412a098aeb76d57ba2fcad9dd20c0939527392cbceb179ab9e20947 |
#!/usr/bin/env python
# Copyright 2017 Informatics Matters Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | InformaticsMatters/pipelines | src/python/pipelines/rdkit/o3dAlign.py | Python | apache-2.0 | 6,316 | [
"RDKit"
] | 1a817aed6c3141a49a13bcb5f9f791ea57fad4c29b109f360db25084bb9292c0 |
"""
Copyright (C) 2012 Alan J Lockett
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,... | hypernicon/pyec | pyec/optimize/__init__.py | Python | mit | 11,245 | [
"Gaussian"
] | bb8861f3c5c30b88de8be876f2bdf27ffb2dc162f9744c3954a9daebf76544ce |
###############################################################################
# ilastik: interactive learning and segmentation toolkit
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you can redistribute it and/or
# mod... | nielsbuwen/ilastik | ilastik/applets/thresholdTwoLevels/thresholdTwoLevelsGui.py | Python | gpl-3.0 | 18,390 | [
"Gaussian"
] | 6706358f232d34b887a3e7dac0fe3348bc847ae79aa861fab50cc3f6184b2e10 |
# vim: fdm=indent
'''
author: Fabio Zanini
date: 09/05/16
content: Utility functions
'''
# Functions
def mkdirs(newdir):
""" Create a directory and all parent folders.
Features:
- parent directories will be created
- if directory already exists, then do nothing
- if ther... | davidrglass/antidengue | src/util.py | Python | mit | 2,058 | [
"Biopython"
] | f88bdde91084a62ca3ab79e34b1fa716be1b529a888dc7815e3a401dd79dacf1 |
# AircraftParts.py
# Author: Ben Names
"""
This module contains a library of classes devoted to modeling aircraft parts.
The main purpose of this library is to model various types of aircraft parts.
Currently only wing objects are suported, however in the future it is possible
that fuselages as well as other parts wil... | bennames/AeroComBAT-Project | AeroComBAT/AircraftParts.py | Python | mit | 15,495 | [
"Mayavi"
] | 40dc883baa03f746bb94c7c0cc1fb8e628aee297c419d2264d8105e156a8b3d4 |
from external import wxPyPlot
import gen_utils
from module_base import ModuleBase
from module_mixins import IntrospectModuleMixin
import module_utils
try:
import Numeric
except:
import numarray as Numeric
import vtk
import wx
class histogram1D(IntrospectModuleMixin, ModuleBase):
"""Calculates and sh... | nagyistoce/devide | modules/viewers/histogram1D.py | Python | bsd-3-clause | 6,534 | [
"VTK"
] | 85ca047c15c8b56888b4f8876badbb75cfbca2f30a04a10aa0857737c787907f |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Removing unique constraint on 'SurveyQuestionResponse', fields ['phone', 'quest... | myvoice-nigeria/myvoice | myvoice/survey/migrations/0004_auto__del_field_surveyquestionresponse_phone__del_unique_surveyquestio.py | Python | bsd-2-clause | 14,491 | [
"VisIt"
] | 3c945471d7fafa73adc526741ed1d99a94cfd5e3f2b8f222ad16fe6d9a4ddaeb |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2017, Brian Coca <bcoca@ansible.com>
# (c) 2017, Adam Miller <admiller@redhat.com>
# (c) 2017 Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__m... | hryamzik/ansible | lib/ansible/modules/system/sysvinit.py | Python | gpl-3.0 | 13,402 | [
"Brian"
] | 7f621715b45f6fff0fbf9564b9e3a8beb9aaf719d60d9a6cb769865a14c62391 |
# Copyright 2004-2015 Tom Rothamel <pytom@bishoujo.us>
#
# 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, m... | joxer/Baka-No-Voltron | tmp/android.dist/private/renpy/display/imagemap.py | Python | gpl-2.0 | 6,404 | [
"VisIt"
] | dbcf13af9df25400d38ec6736fb2b353df2ed6a1e2e4595de78c6b1a1190132f |
#!/usr/bin/env python
#
# Copyright (C) 2014
# Brian Caswell <bmc@lungetech.com>
# Narf Industries <info@narfindustries.com>
#
# 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 res... | f0rki/cb-multios | original-challenges/LMS/poller/for-release/machine.py | Python | mit | 3,056 | [
"Brian"
] | a39cd1daa5c3a85e199a0540703efb175b941b15577597fd3e86f60342870e73 |
try: paraview.simple
except: from paraview.simple import *
from paraview import coprocessing
#--------------------------------------------------------------
# Code generated from cpstate.py to create the CoProcessor.
# ----------------------- CoProcessor definition -----------------------
def CreateCoProcessor()... | tfogal/freeprocessing | pvsim/pvpipeline.py | Python | lgpl-3.0 | 2,846 | [
"ParaView"
] | 193f968d5db1e2777e217fa67b3db78003152773e18a54692c676f1d867d0f72 |
# Standard Python packages
import math, cmath
import re
import itertools
import numbers
import random
import glob
import copy
# Special dependencies
import numpy, numpy.random # sudo apt-get install python-numpy
# import minuit # no package
# # Augustus dependencies
# try:
# from augustus.unitable.unitable import... | opendatagroup/cassius | trunk/cassius/containers.py | Python | apache-2.0 | 162,880 | [
"Gaussian"
] | 19054a75cfb6e906b99e78eb89ef5f3c42bdb3a48597c4cbbb6d16193ec1cb35 |
"""
========================================================
Gaussian process regression (GPR) on Mauna Loa CO2 data.
========================================================
This example is based on Section 5.4.3 of "Gaussian Processes for Machine
Learning" [RW2006]. It illustrates an example of complex kernel engine... | bnaul/scikit-learn | examples/gaussian_process/plot_gpr_co2.py | Python | bsd-3-clause | 6,357 | [
"Gaussian"
] | 8724566d06aa3ed4cb8f50efbdbeb762589bc736868d3f4332560783ef01416e |
#!/usr/bin/env python
#
# Copyright 2012 the V8 project authors. All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# noti... | victorzhao/miniblink49 | v8_4_5/tools/presubmit.py | Python | gpl-3.0 | 16,038 | [
"VisIt"
] | 4399103f2dd2618b1b5820f4e0702d112100e760dc652279c5e439fc5e191307 |
import os
from director import ioUtils
from director import objectmodel as om
from director import visualization as vis
from PythonQt import QtGui
class OpenDataHandler(object):
def __init__(self, mainWindowApp):
self.app = mainWindowApp
self.rootFolderName = 'data files'
self.openActio... | patmarion/director | src/python/director/opendatahandler.py | Python | bsd-3-clause | 2,361 | [
"VTK"
] | 65adce4c02d3e3e3bf536b6e59aff26fa4a03eb2daf5589c3b4d689231501337 |
#!/usr/bin/env python
# Copyright (c) 2017 Ryan Collins <rcollins@chgr.mgh.harvard.edu>
# Distributed under terms of the MIT license.
"""
Calculates non-duplicate primary-aligned binned coverage
of a chromosome from an input BAM file
"""
#Import libraries
import argparse
import sys
from subprocess import call
import... | RCollins13/WGD | bin/binCov.py | Python | mit | 8,336 | [
"pysam"
] | bf99ae1ea37db6b1718167b2f37bc2bb3d1f3d5ab42dfc822895bdd76c7c50fe |
#!/usr/bin/env python
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | intel-analytics/BigDL | python/chronos/src/setup.py | Python | apache-2.0 | 2,671 | [
"ORCA"
] | cb1feb6e17e2465e096bdbd21e6c8d750a0f3108038f7844c8c79caee13aee1a |
# ----------------------------------------------------------------------
# Copyright (c) 2016, The Regents of the University of California All
# rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# ... | drichmond/tinker | python/Description.py | Python | bsd-3-clause | 7,636 | [
"TINKER"
] | ebd43d6d0a923396aefaf7eb9230b0c0c7ecfbe904d45adcabd8a472aca7d345 |
# -*- coding: utf-8 -*-
# (c) 2016, Adrian Likins <alikins@redhat.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at you... | roadmapper/ansible | test/units/cli/test_galaxy.py | Python | gpl-3.0 | 51,815 | [
"Galaxy"
] | 1e4de7897cdf1d0d45290d503b556eada538710004290b35969a1635c7df6b62 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# grid_sftp - SFTP server providing access to MiG user homes
# Copyright (C) 2010-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU ... | heromod/migrid | mig/server/grid_sftp.py | Python | gpl-2.0 | 39,545 | [
"Brian"
] | 6d429402019f5cefe836ece75ee314eb3e3cb913dff7191635e65de1cd66d5ba |
#!/usr/bin/python -u
import os, subprocess
import collections
from argparse import Namespace
from gmx_lib import run_setup
from gmx_lib.run_setup import WorkdirStructure
from gmx_lib.gmx_engine import GmxEngine
from gmx_lib.gmx_params import GmxParameters
from modeling_lib.scwrl_engine import ScwrlEngine
from modeli... | ivanamihalek/smallmol | gmx09_protein_RNA_mutation_scan.py | Python | gpl-2.0 | 6,727 | [
"Gromacs"
] | cf811a7f5a6b90e5d1a325c872bc66d47fe9a2fd7d034e82b82d2fb47721bd62 |
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
#
# Maintainer: Jonathan Lange
from __future__ import division
import sys
import traceback
from zope.interface import implements
from twisted.python import reflect
from twisted.python.failure import Failure
from twisted.trial import util
from tw... | nlloyd/SubliminalCollaborator | libs/twisted/trial/test/test_pyunitcompat.py | Python | apache-2.0 | 6,690 | [
"VisIt"
] | 3c2ef62c3b01821aceffad49ba3847f164312960fe557d7fe803fb0ebe91e81f |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""ppcheckout
Usage:
ppcheckout [options] <projectid> [<projectname>]
ppcheckout -h | --help
ppcheckout --version
Automates the initial setup of a pgdp.net post processing project.
Examples:
ppcheckout projectID509579cf64be8
ppcheckout projectID509579cf64be8 ... | davem2/ppcheckout | ppcheckout/ppcheckout.py | Python | mit | 8,214 | [
"VisIt"
] | 4307841cffdea4c8ee860d0096a3017df2a507f543d89af66f65a3c9a3404e31 |
# If your project uses a database, you can set up database tests
# similar to what you see below. Be sure to set the db_uri to
# an appropriate uri for your testing database. sqlite is a good
# choice for testing, because you can use an in-memory database
# which is very fast.
from turbogears import testutil, database... | thehub/hubspace | hubspace/tests/save/test_model.py | Python | gpl-2.0 | 13,083 | [
"VisIt"
] | c24f9090130be6628e16e309d40a25e41c8cbfd5ccee34edfef22089bce41b16 |
import sys
sys.path.insert(1,"../../")
import h2o
from tests import pyunit_utils
def metric_accessors():
cars = h2o.import_file(path=pyunit_utils.locate("smalldata/junit/cars_20mpg.csv"))
r = cars[0].runif()
train = cars[r > .2]
valid = cars[r <= .2]
# regression
response_col = "economy"
... | nilbody/h2o-3 | h2o-py/tests/testdir_misc/pyunit_metric_accessors.py | Python | apache-2.0 | 43,296 | [
"Gaussian"
] | 475f7f086a72c098d11f04354b2f24fdf629cc19335eaaa4f9ad3b004c526961 |
#!/usr/bin/env python
########################################################################
# File : dirac-executor
# Author : Adria Casajus
########################################################################
"""
This is a script to launch DIRAC executors
"""
from __future__ import absolute_import
from __futu... | ic-hep/DIRAC | src/DIRAC/Core/scripts/dirac_executor.py | Python | gpl-3.0 | 1,973 | [
"DIRAC"
] | 58a32ea1e20b4aefee2581fc90650922c5837fd95ac66a0121a6c5253511bfd0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.entries.computed_entries import ComputedEntry, \
ComputedStructureEntry
test_dir = os.path.join(os.path.dirname(__file... | gVallverdu/pymatgen | pymatgen/entries/tests/test_computed_entries.py | Python | mit | 3,936 | [
"VASP",
"pymatgen"
] | 0a38b49ded8f8e19247481f073247c424adb1f80f532eff46139320c08dea208 |
'''
The settings for OSMC are handled by the OSMC Settings Addon (OSA).
In order to more easily accomodate future changes and enhancements, each OSMC settings bundle (module) is a separate addon.
The module can take the form of an xbmc service, an xbmc script, or an xbmc module, but it must be installed into the u... | mega-force/osmc | package/mediacenter-addon-osmc/src/script.module.osmcsetting.pioverclock/resources/osmc/OSMCSetting.py | Python | gpl-2.0 | 9,541 | [
"VisIt"
] | d81f050a4f90c9209997ab98a0d41139d708a49e78afb4a53eccbdf76c527182 |
# -*- mode: python; coding: utf-8 -*-
# This work is dedicated to the public domain.
"""unicode_to_latex - what it says
Provides ``unicode_to_latex(u)``, ``unicode_to_latex_bytes(u)``, and
``unicode_to_latex_string(u)``.
``unicode_to_latex_bytes`` returns ASCII bytes that can be fed to LaTeX to
reproduce the Unicode... | pkgw/pwkit | pwkit/unicode_to_latex.py | Python | mit | 81,062 | [
"Bowtie"
] | d52d1c1b99b42a8506b1081a82ca45083c3502620886c106230c9131b270a448 |
#!/usr/bin/env python
################################################################################
# GIPS: Geospatial Image Processing System
#
# AUTHOR: Matthew Hanson
# EMAIL: matt.a.hanson@gmail.com
#
# Copyright (C) 2014-2018 Applied Geosolutions
#
# This program is free software; you can redist... | Applied-GeoSolutions/gips | gips/data/core.py | Python | gpl-3.0 | 72,387 | [
"VisIt"
] | 18be44c8f968fe2830e95d34b846fba410fae0c7f8edbc3066a286e254c2e11d |
"""Molecular Dynamics."""
import warnings
import numpy as np
from ase.optimize.optimize import Dynamics
from ase.data import atomic_masses
from ase.md.logger import MDLogger
class MolecularDynamics(Dynamics):
"""Base-class for all MD classes."""
def __init__(self, atoms, timestep, trajectory, logfile=None,
... | suttond/MODOI | ase/md/md.py | Python | lgpl-3.0 | 1,299 | [
"ASE"
] | d5bada0110f9579b4401489a3783c53c753dcbfd266e02866ad03562d909fea3 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Views tests for the OSF."""
from __future__ import absolute_import
import datetime as dt
from rest_framework import status as http_status
import json
import time
import unittest
from future.moves.urllib.parse import quote
from flask import request
import mock
import ... | mfraezz/osf.io | tests/test_views.py | Python | apache-2.0 | 220,173 | [
"Brian",
"VisIt"
] | e4d6121c18676d29c521fecf0ba9251d0192fd80bf24d6029f6161c38dd66c0b |
"""
Views for the verification flow
"""
import json
import logging
import decimal
import datetime
from collections import namedtuple
from pytz import UTC
from ipware.ip import get_ip
from django.conf import settings
from django.core.urlresolvers import reverse
from django.http import (
HttpResponse, HttpResponseB... | eestay/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 41,196 | [
"VisIt"
] | 37cae14afa9b9ac727f636be0688492a7e8868507e712b4095c1c981705ab3b2 |
#==============================================================================
# Photon Diffusion
# Calculates the diffusion of photons in a non-absorbing medium (lanex phosphor) using Fick's laws of diffusion.
#==============================================================================
#Imports
from numpy import ... | drakero/Electron_Spectrometer | Photon_Diffusion/Photon_Diffusion.py | Python | mit | 8,606 | [
"DIRAC"
] | 7e7dad12982019116278be83de7bd7054402c5fbbdd8d851a2f11572acd83e2a |
from __future__ import (absolute_import, division, print_function)
import unittest
from mantid.simpleapi import logger
import numpy as np
import json
from AbinsModules import AbinsTestHelpers, CalculateSingleCrystal, LoadCASTEP
class AbinsCalculateSingleCrystalTest(unittest.TestCase):
_temperature = 10 # 10 K, ... | dymkowsk/mantid | scripts/test/AbinsCalculateSingleCrystalTest.py | Python | gpl-3.0 | 3,809 | [
"CRYSTAL"
] | 4e9ee7c527a5c693f486b7c898a05bbc10095acb55911a20a5137930830d5ae2 |
'''
Optimize function which does not change (too much)
with its every new evaluation
Initialization: with bounds. These can be real/integer interval or category
@author: iaroslav
'''
import random
import numpy as np
from scipy.spatial.distance import pdist, squareform
from scipy.optimize import minimize
import heap... | iaroslav-ai/black-box-optimization | backend.py | Python | mit | 8,169 | [
"Gaussian"
] | 1bbae48871d074e89a5b4123449e8d3f27a13b5c1b20226769f8363ad6e8190b |
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | nburn42/tensorflow | tensorflow/contrib/eager/python/examples/l2hmc/l2hmc_test.py | Python | apache-2.0 | 5,712 | [
"Gaussian"
] | 3b247682e93d3f7bfcaa51cdc79b9f852fee94a9cfe4acaebfb9317d18dbc7f5 |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2016 Francois Beaune, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any ... | docwhite/appleseed | scripts/updatetestsuiterefimages.py | Python | mit | 3,476 | [
"VisIt"
] | f887f6c266f40f4656e10fc3d85c2d78c2222d8873529ed73f6248937e00a423 |
__author__ = 'max'
import theano
from lasagne.random import get_rng
from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
from lasagne.layers import Layer
__all__ = [
"GaussianDropoutLayer",
]
class GaussianDropoutLayer(Layer):
"""Gaussian Dropout layer
Multiply values by gaussian varia... | XuezheMax/LasagneNLP | lasagne_nlp/networks/dropout.py | Python | apache-2.0 | 1,635 | [
"Gaussian"
] | 0544832f3188cef0a37f4a9b7f08a1b4d567929c559a5ff2fd7a2e2e23d07128 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either vers... | gph82/PyEMMA | pyemma/coordinates/data/util/reader_utils.py | Python | lgpl-3.0 | 9,522 | [
"MDTraj"
] | 6e43fc93be9ce0fd09c19fa7fa57238c09fe21f7ec95647f30548e3e791be14f |
import os
import unittest
from pymatgen.entries.correction_calculator import CorrectionCalculator
from pymatgen.util.testing import PymatgenTest
class CorrectionCalculatorTest(unittest.TestCase):
def setUp(self):
self.exclude_polyanions = [
"SO4",
"CO3",
"NO3",
... | vorwerkc/pymatgen | pymatgen/entries/tests/test_correction_calculator.py | Python | mit | 5,359 | [
"pymatgen"
] | cb23f7de4add3d41fbae330c8348dd372ed0566ce2c3e8bd39c2137bfc7036f4 |
# Copyright 2017 The Forseti Security Authors. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | forseti-security/forseti-security | google/cloud/forseti/services/inventory/base/crawler.py | Python | apache-2.0 | 2,029 | [
"VisIt"
] | 88ca210b4a37b752fc96e189d5da3ea6fe40fb5de1bc70c7f40badd2aac6af9f |
#
# Copyright (C) 2017-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | testsuite/python/time_series.py | Python | gpl-3.0 | 1,902 | [
"ESPResSo"
] | 400b863e00b81e1a4c30ee9d0fdc5e98414d6ed088a5b4bf62879087610fba8a |
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