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# coding=utf-8
# Copyright 2022 The Google Research 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... | google-research/google-research | smu/parser/smu_parser_lib.py | Python | apache-2.0 | 47,286 | [
"Gaussian",
"ORCA"
] | ef20a906b67a50a90d21b279be4cff3799f14878372fd514385d9c58a0fc2004 |
"""
This is a comment
"""
#try: # this part to import as part of the DIRAC framework
import xml.sax
from xml.sax.handler import ContentHandler
from DIRAC.Core.Workflow.Parameter import *
from DIRAC.Core.Workflow.Module import *
from DIRAC.Core.Workflow.Step import *
from DIRAC.Core.Workflow.Workflow import Workf... | andresailer/DIRAC | Core/Workflow/WorkflowReader.py | Python | gpl-3.0 | 4,858 | [
"DIRAC"
] | 5cef9076db8361dd0acbd0a9fc48fc24607621d31da158f758b53b27f8b2132c |
"""
Featurizes proposed binding pockets.
"""
import numpy as np
import logging
from deepchem.feat import Featurizer
from deepchem.utils.rdkit_utils import load_molecule
logger = logging.getLogger(__name__)
def boxes_to_atoms(coords, boxes):
"""Maps each box to a list of atoms in that box.
Given the coordinates... | miaecle/deepchem | deepchem/feat/binding_pocket_features.py | Python | mit | 3,434 | [
"MDTraj"
] | 5515446f2e4a2bba3a8ca261180820667d81d9a6ef887b474152bcf8ccff3c81 |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core.sparse_gp_mpi import SparseGP_MPI
from .. import kern
from ..likelihoods import Gaussian
from ..core.parameterization.variational import SpikeAndSlabPrior, SpikeAndSlabPoster... | gusmaogabriels/GPy | GPy/models/ss_gplvm.py | Python | bsd-3-clause | 4,601 | [
"Gaussian"
] | 054e461e5f0cc679a20bfcaca68c2238c4a1c397a32f8c4a0d906a14ae0e79f0 |
# Orca
#
# Copyright 2010 Consorcio Fernando de los Rios.
# Author: Javier Hernandez Antunez <jhernandez@emergya.es>
# Author: Alejandro Leiva <aleiva@emergya.es>
#
# This library 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 ... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/settings_manager.py | Python | gpl-3.0 | 20,476 | [
"ORCA"
] | ceb61e9c7b23c7a1988a986189b6a0de7457c3d07f3d5db55b2b811f5de5305a |
import numpy as np
import numba as nb
from numpy.random import PCG64
from timeit import timeit
bit_gen = PCG64()
next_d = bit_gen.cffi.next_double
state_addr = bit_gen.cffi.state_address
def normals(n, state):
out = np.empty(n)
for i in range((n + 1) // 2):
x1 = 2.0 * next_d(state) - 1.0
x2 =... | grlee77/numpy | numpy/random/_examples/numba/extending.py | Python | bsd-3-clause | 1,958 | [
"Gaussian"
] | 175370b7cd6220554db3f774f579bc851f5b321d24b0e7bc1c8a8878c0661724 |
"""QM/MM interface with QM=FHI-aims, MM=gromacs
QM could be something else, but you need to read in qm-atom charges
from the qm program (in method 'get_qm_charges')
One can have many QM regions, each with a different calculator.
There can be only one MM calculator, which is calculating the whole
system.
Non-bond... | grhawk/ASE | tools/ase/calculators/ase_qmmm_manyqm.py | Python | gpl-2.0 | 60,409 | [
"ASE",
"FHI-aims",
"GROMOS",
"Gromacs"
] | fcc2b73a7ef104bc86b97372b1a667fe976150aadaed018b99adccbea8931362 |
#!/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... | pli3/e2-openwbif | plugin/controllers/views/web/epgservicenow.py | Python | gpl-2.0 | 7,517 | [
"VisIt"
] | 5df81316aa681ea343d4b96de730a8dd474a36208014d46f4c160ad7bfffa463 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. 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
#
# U... | sunqm/pyscf | pyscf/mcscf/test/test_casci.py | Python | apache-2.0 | 9,067 | [
"PySCF"
] | 629eb6820b3493defb0271a5bd738579ec99e9bba33afcfeb4cffdd2e5bff14a |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# 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... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_serverautoscalepolicy.py | Python | gpl-3.0 | 7,975 | [
"VisIt"
] | 0506066562f3f6cd5ffdaf5dc7dfd49836de80be7044b48e5c20ce2c0ba9bcd6 |
#!/usr/bin/env python
# This example demonstrates the conversion of point data to cell data.
# The conversion is necessary because we want to threshold data based
# on cell scalar values.
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Read some data with point data attributes.... | VisTrails/VisTrails | examples/vtk_examples/DataManipulation/pointToCellData.py | Python | bsd-3-clause | 3,452 | [
"VTK"
] | b680352b5680ffef0b4a829b7f5e0385e43db5136a70c11d1c52e7ac7fa851ce |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'PresentMedicalHistory.tuberculosis'
db.add_column(u'patient_presentmedicalhistory', 'tubercu... | aazhbd/medical_info01 | patient/migrations/0004_auto__add_field_presentmedicalhistory_tuberculosis__add_field_presentm.py | Python | bsd-3-clause | 35,674 | [
"VisIt"
] | 887867219345feaa057c5f3f6998ecfce35aff0caebc946407521461990a7b44 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/gdal/package.py | Python | lgpl-2.1 | 3,990 | [
"NetCDF"
] | 770eaaf0bcb2eada909f2903ced7c9c560b4e1203f0f3a25b54d6da7bcae4650 |
#!/usr/bin/env python
'''
Created on 4 Feb 2010
@author: tcezard
'''
import os, sys, logging
from optparse import OptionParser
import utils
from utils import utils_param, utils_logging, compare_version_number,\
get_bwa_version, longest_common_substr_from_start, utils_commands
import command_runner
from utils.Genom... | tcezard/RADmapper | bin/RAD_assign_reads_to_consensus.py | Python | mit | 23,962 | [
"BWA"
] | 2ab713e8fca78ce1c5817e5b9a43a3cee27872b640be0a2891e6e3e41e422c55 |
# ======================================================================
# USER-GFMD - Elastic half-space methods for LAMMPS
# https://github.com/Atomistica/user-gfmd
#
# Copyright (2011-2016,2021)
# Lars Pastewka <lars.pastewka@imtek.uni-freiburg>,
# Tristan A. Sharp and others.
# See the AUTHORS file in the top... | Atomistica/user-gfmd | tests/TEST_error_convergence_ft_two_layers_lj_cut/eval.py | Python | gpl-2.0 | 9,609 | [
"LAMMPS"
] | 108dce556788d2c81f1e3ce482c59115728f9cd868340a9734b5290b4bdfd246 |
"""
The weather-helper script sets the weather data used (``inputs/weather.epw``) for simulations.
"""
import os
import cea.config
import cea.inputlocator
__author__ = "Daren Thomas"
__copyright__ = "Copyright 2019, Architecture and Building Systems - ETH Zurich"
__credits__ = ["Daren Thomas"]
__license__ = "MIT"
... | architecture-building-systems/CEAforArcGIS | cea/datamanagement/weather_helper.py | Python | mit | 1,672 | [
"EPW"
] | 6ae378bcd3f7d1923d0cbe6e6fea837820b523f261eb4c7b30c0e53fd7f3c6ff |
import numpy as np
import pybinding as pb
from pybinding.constants import pi, phi0, hbar
__all__ = ['mass_term', 'coulomb_potential', 'constant_magnetic_field',
'triaxial_strain', 'gaussian_bump']
def mass_term(delta):
"""Break sublattice symmetry, make massive Dirac electrons, open a band gap
On... | dean0x7d/pybinding | pybinding/repository/graphene/modifiers.py | Python | bsd-2-clause | 3,680 | [
"DIRAC",
"Gaussian"
] | 32735bebd21d50c3336fd4f4f697e91c800f909df738ebc5eca5960132090ca0 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkXMLPolyDataReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkXMLPolyDataReader.py | Python | bsd-3-clause | 496 | [
"VTK"
] | 9bff384fb1d264cd3c872480fffee6914ea7a2edf8eb0599412ac9ffcc43e5ce |
"""1-D Gaussian Processes for Regression and Bayesian Optimization"""
# Author: Charles Franzen
# License: MIT
from functools import partial
import numpy as np
import numpy.linalg as LA
import pandas as pd
import matplotlib.pyplot as plt
from scipy import stats
import dillinger.kernel_functions as kern
# main Gaus... | chipfranzen/dillinger | dillinger/gaussian_process.py | Python | mit | 8,314 | [
"Gaussian"
] | c1168d4643434715f81a7380d41dbf9b4c070ca76c004711fc0b842eca8e0df9 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
#
# 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 ... | sam-m888/gprime | gprime/filters/rules/person/_hasgallery.py | Python | gpl-2.0 | 2,032 | [
"Brian"
] | 0052ece7462d804aba7340f440ea2c901b7ffb81506950c0a230989d834796cf |
# -*- coding: utf-8 -*-
"""Release data for the IPython project."""
#-----------------------------------------------------------------------------
# Copyright (c) 2008, IPython Development Team.
# Copyright (c) 2001, Fernando Perez <fernando.perez@colorado.edu>
# Copyright (c) 2001, Janko Hauser <jhauser@zscout.de>... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/core/release.py | Python | apache-2.0 | 5,583 | [
"Brian"
] | a936f43e6d95e4d8c312693a8e8b7ab64bbe87d60d3278b945ed7d8ef31beada |
# -*- Mode: Python; 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 General Public License as published by
## the Free Sof... | andrebellafronte/stoq | stoq/gui/services.py | Python | gpl-2.0 | 32,977 | [
"VisIt"
] | 5906046d7df0c403d1bffd0547cdad287cd5c5644d59e85f62270c0ef41f7979 |
"""Contains the logic for handling read model invocation and read creation"""
import time
from multiprocessing import Process, Queue
import pysam
import numpy as np
import mitty.lib.vcfio as vio
from mitty.lib.sanitizeseq import sanitize
import mitty.simulation.rpc as rpc
from mitty.simulation.sequencing.writefastq i... | sbg/Mitty | mitty/simulation/readgenerate.py | Python | apache-2.0 | 8,916 | [
"pysam"
] | f77300c547b144d72c1471c4ad0ba5d2db53d0786526ac47d063fd188d3d66cc |
# Authors: Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Lorenzo De Santis <lorenzo.de-santis@u-psud.fr>
#
# License: BSD (3-clause)
# The computations in this code were primarily derived from Matti Häm... | Teekuningas/mne-python | mne/bem.py | Python | bsd-3-clause | 72,313 | [
"Mayavi"
] | bafb9561023b018f2e937c042513c4f1a6f5bde79c4fef0f8829da6f7eafdc20 |
# $Id$
#
# Copyright (C) 2003-2006 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.
#
""" Calculation of topo... | strets123/rdkit | rdkit/Chem/GraphDescriptors.py | Python | bsd-3-clause | 19,941 | [
"RDKit"
] | c39d1b65332392fd4996cf34112b67778b8d4d92abc7dda1a772b23116f4a94c |
# 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... | KaiSzuttor/espresso | src/python/espressomd/virtual_sites.py | Python | gpl-3.0 | 2,198 | [
"ESPResSo"
] | 6aa58789d0a8b62bfd73906a81d77f47a0d95b63a0272c9e56b51fc18dccf64a |
# vim: ts=4 sw=4 expandtab
""" This is an abstract module for visiting specific nodes. This is useed to
traverse the tree to generate warnings.
"""
def visit(event, *args):
""" This decorator is used to indicate which nodes the function should
examine. The function should accept (self, node) and return the rel... | hackathon-2014/laserspacecats-repo | toot-node/node_modules/restify/node_modules/verror/node_modules/extsprintf/deps/javascriptlint/javascriptlint/visitation.py | Python | gpl-2.0 | 1,893 | [
"VisIt"
] | 2ec0f972a5ed86c45da856e6e346a887e304d8a32ad988b38d25c45ab9f838fd |
""" Utility functions for processing point clouds.
Author: Charles R. Qi, Hao Su
Date: November 2016
"""
import os
import sys
import warnings
BASE_DIR = os.path.dirname(os.path.abspath(__file__))
sys.path.append(BASE_DIR)
# Draw point cloud
from eulerangles import euler2mat
# Point cloud IO
import numpy as np
from ... | googleinterns/deep-3d-reconstruction | scannet/utils/pc_utils.py | Python | apache-2.0 | 16,335 | [
"Gaussian"
] | 6e209d8eabb2f2d489116c0d133a8d12a021139385710c5fc362f6689f8219e4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import collections
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.units import (Energy, Time, Length, unitized, Mass, Memory,
EnergyArray, TimeArray, Length... | fraricci/pymatgen | pymatgen/core/tests/test_units.py | Python | mit | 8,589 | [
"pymatgen"
] | 6dd5615e01f888af086919b2eedc26a791ab398f93e7289fa4ed32bd724831f6 |
"""
CrystFEL stream format 2.2
Reflections measured after indexing
h k l I sigma(I) peak background fs/px ss/px
-18 38 -15 -77.63 50.81 50.00 22.12 248.3 861.5
= CrystFEL stream format 2.3 =
----- Begin chunk -----
Image filename: /lfs01/iwata/nureki/2015-Apr-KEK... | keitaroyam/yamtbx | yamtbx/dataproc/crystfel/stream.py | Python | bsd-3-clause | 14,891 | [
"CRYSTAL"
] | 19b0f55ab410aacbd3ca840ac8f5a146f5358b3dce2691c2c37464edfa946df2 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# vmbuilder - shared virtual machine builder functions and script
#
# Copyright (C) 2003-2012 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/shared/vmbuilder.py | Python | gpl-2.0 | 8,114 | [
"Brian"
] | e295b1bab32d6fc4de83870e4b0806d1034b5da5bfad52c5ca7c3d7381816d43 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
'''
freeseer - vga/presentation capture software
Copyright (C) 2013 Free and Open Source Software Learning Centre
http://fosslc.org
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 ... | Freeseer/freeseer | src/freeseer/plugins/output/videopreview/widget.py | Python | gpl-3.0 | 1,906 | [
"VisIt"
] | 99bae75197eadf4c029f6aac808f72db620aa31c0129eb6a2597d6c16269c686 |
# -*- coding: utf-8 -*-
# @Author: YangZhou
# @Date: 2016-12-24 18:47:10
# @Last Modified by: YangZhou
# @Last Modified time: 2017-06-19 12:36:00
from aces import config
import aces.tools as tl
from aces.runners.phonopy import runner as Runner
import time
class runner(Runner):
def force_constant(self):
... | vanceeasleaf/aces | aces/runners/phonopy_dfpt.py | Python | gpl-2.0 | 2,888 | [
"VASP",
"phonopy"
] | 16b819484bce89642120a348a8686f9577f9fe59241eb6c0c21c857a7a176ca7 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-core | tests/core/test_cylinder_diffusion_gsolve+dsolve.py | Python | gpl-3.0 | 5,170 | [
"MOOSE"
] | fd65973573a4a2724d953e34ba29b10ced2f7e00bb61b882f0964d69a2812c41 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# native-https - native https access
# Copyright (C) 2003-2014 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 License a... | heromod/migrid | mig/user/native-https.py | Python | gpl-2.0 | 2,281 | [
"Brian"
] | eec6901359d217b3f54053488a47a4438184695bdbd44df5637393bc79196798 |
import warnings
import json
import numpy as np
import menpo.io as mio
from menpo.shape import ColouredTriMesh, TexturedTriMesh, TriMesh, PointCloud
def _construct_shape_type(points, trilist, tcoords, texture, colour_per_vertex):
r"""
Construct the correct Shape subclass given the inputs. TexturedTriMesh
... | grigorisg9gr/menpo3d | menpo3d/io/input/mesh/base.py | Python | bsd-3-clause | 11,427 | [
"VTK"
] | d39656acf178cd81a17706b632e45e121665ca615c7ec2be55a06986312b30f3 |
"""
Functions for adding decorations (axes, colorbar, outlines..) to the
pipeline in a procedural way.
"""
# Author: Gael Varoquaux
# Copyright (c) 2007-2015 Enthought, Inc.
# License: BSD Style.
import numbers
import numpy as np
# Enthought library imports.
from traits.api import String, CFloat, Instance, HasTrait... | dmsurti/mayavi | mayavi/tools/decorations.py | Python | bsd-3-clause | 19,548 | [
"Mayavi",
"VTK"
] | 5dfcca96ed9763ca5efaf6a8d06f96a45533361bfd2d84c81e990d7793095857 |
""" Module with physical constants for use with ipython, profile
"physics".
Definition of Fundamental Physical Constants, CODATA Recommended Values
Source, Peter J. Mohr and Barry N. Taylor,
CODATA Recommended Values of the Fundamental
Physical Constants, 1998
... | alexdu/robot-sandbox | sim-files/dist/_ipython/ipy_constants.py | Python | gpl-3.0 | 19,500 | [
"Avogadro"
] | 94ac339631fcf703c695e39ed8454f25795bed0a32fcc20d211975a5c7f1570e |
#
# 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... | dasahcc/helix | helix-core/src/main/scripts/integration-test/script/driver_cmd_dict.py | Python | apache-2.0 | 17,093 | [
"ESPResSo"
] | fd68ddf6d1a439c52df6c1623e9e2779b4f55c320f453b2ed1ea3a1c4313006d |
import lmfit
import numpy
import scipy.optimize
import numbers
import copy
import suspect.basis
def complex_to_real(complex_fid):
"""
Standard optimization routines as used in lmfit require real data. This
function takes a complex FID and constructs a real version by concatenating
the imaginary part ... | bennyrowland/suspect | suspect/fitting/singlet.py | Python | mit | 14,306 | [
"Gaussian"
] | 81251b07f4a02618a502e413d5c8aa809603f94361916f11daad719502dc6a5e |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001-2007 Donald N. Allingham
# Copyright (C) 2008 Lukasz Rymarczyk
# Copyright (C) 2008 Raphael Ackermann
# Copyright (C) 2008-2011 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011-2013 Paul Franklin
#
# This pro... | pmghalvorsen/gramps_branch | gramps/cli/plug/__init__.py | Python | gpl-2.0 | 33,260 | [
"Brian"
] | dd1e587d1159d5745c8644941dc8c6a1e11cc63c58749f4077ef46a8b5048744 |
# 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 u... | mlperf/training_results_v0.7 | Fujitsu/benchmarks/resnet/implementations/implementation_open/mxnet/python/mxnet/numpy/random.py | Python | apache-2.0 | 12,205 | [
"Gaussian"
] | a0907c4301c25321264e81c0aea8755a919ffe305e64649634b6c820d91934f0 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/features/tests/test_sectionfunc.py | Python | bsd-3-clause | 6,602 | [
"NEURON"
] | e53e80eb47075729c6d444bbe76f849ff6c8680416b0ce2f638c043066aa592e |
from modeledcommandparameter import *
class Distribution(ModeledCommandParameter):
"""
A Distribution is a:
(1) bdistyp (I) beam distribution type {1:Gaussian 2:uniform circular segment}
(2-13) 12 Parameters for bdistyp
"""
begtag=''
endtag=''
models = {
'model_descripto... | jon2718/ipycool_2.0 | distribution.py | Python | mit | 3,019 | [
"Gaussian"
] | 2af8f5343f3b3a3cebbef6d6eb9c37fde8237981f2c1b6147ae4dcf9cd816526 |
#========= math
pi = 3.141592653589793
e = 2.718281828459045
#========= physics
lightSpeed = 299792458.0 # m/s
elementaryCharge = 1.60217657e-19 # coulombs
vacumPermeability = 4e-7*pi # Tesla . m/A
StefanBoltzmann = 5.67037321e-8 # W m^-2 K^-4
universalGas = 8.3144621... | ProkopHapala/SimpleSimulationEngine | python/pySimE/constants.py | Python | mit | 876 | [
"Avogadro"
] | 10bee8c87087df7f6dfb45c06e34458e7cd0b8976b7b021bc7925c90de5ab9af |
import collections as coll
import numpy as np
from scipy import ndimage as ndi
from ..util import img_as_float
from ..color import guess_spatial_dimensions
from .._shared.utils import warn, convert_to_float
__all__ = ['gaussian']
def _convert_input(image, preserve_range):
if preserve_range:
image = ima... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/skimage/filters/_gaussian.py | Python | gpl-3.0 | 4,655 | [
"Gaussian"
] | 12f45cf9c1e8a6d58c3260b4e849e557f19b211549aae041fb80bdd231bd519a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -*- Python -*-
"""
DoCoMoScenario.py
Service Server for DoCoMo Scenario API
The project is hosted on GitHub where your could fork the project or report
issues. Visit https://github.com/roboworks/
:copyright: (c) 2015 by Hiroyuki Okada, All rights re... | okadahiroyuki/trcp | trcp_chat/nodes/DoCoMoScenarioSrv.py | Python | mit | 3,839 | [
"VisIt"
] | bc742666dfef4392273c12c9828dbe6197a1cb6d4d81f864801cebcd8f612933 |
from __future__ import print_function
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
def link_incompatible_error():
print("Reading in original prostate data.")
prostate = h2o.import_file(path=pyunit_utils.locate("smalldata/prostate/prostate.csv.zip"))
pr... | nilbody/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_DEPRECATED_link_incompatible_errorGLM.py | Python | apache-2.0 | 1,102 | [
"Gaussian"
] | a73d9209b5132a50bcd1379146da443f7314b0c811a8808581b0941762dc3fd3 |
# module handling configuration and preferences for the BCMD GUI
import sys, os, os.path
import pprint, argparse
# environment and default settings
VERSION = 0.5
BCMD_HOME = os.path.dirname(os.path.abspath(os.path.join(__file__, '..')))
USER_HOME = os.path.expanduser('~')
PARSER = os.path.join(BCMD_HOME, 'bparser')
A... | bcmd/BCMD | bgui/Config.py | Python | gpl-2.0 | 9,214 | [
"Gaussian"
] | e7ce1a086fe4098f5b92d07cd158a0750cbd540fc344f8cc3dfe2fab2d09615f |
#!/usr/bin/env python
import pyscf
from benchmarking_utils import setup_logger, get_cpu_timings
log = setup_logger()
for n in (30, 50):
mol = pyscf.gto.M(atom=['H 0 0 %f' % i for i in range(n)],
basis='ccpvqz')
mf = mol.RHF().run()
mycc = mf.CCSD()
eris = mycc.ao2mo()
_, t1,... | sunqm/pyscf | examples/2-benchmark/ccsd_iteration.py | Python | apache-2.0 | 467 | [
"PySCF"
] | 2d1c0fefc92fb767cd1c531e5f21d361db53e5d6a5d4fd43e14762bee74bb486 |
import re
import numpy
import math
try:
# Python 3.x
import collections.abc as collections
except ImportError:
# Python 2.x
import collections
import PyQt5.QtCore
# Load dependencies
import ovito
import ovito.data
# Load the native code module
import Particles
# Inject selected classes into parent mo... | srinath-chakravarthy/ovito | src/plugins/particles/resources/python/ovito/data/particles/__init__.py | Python | gpl-3.0 | 46,733 | [
"OVITO"
] | 641502bf2fdce099009f21f848fa06b21d8b6e2df11061c744c6e982239bbef8 |
#!/usr/bin/python
#
# Copyright 2010 Brian Dolbec <brian.dolbec@gmail.com>
# Copyright(c) 2010, Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
#
"""Provides a breakdown list of USE flags or keywords used and by
what packages according to the Installed package database"""
from __f... | zmedico/gentoolkit | pym/gentoolkit/enalyze/analyze.py | Python | gpl-2.0 | 15,721 | [
"Brian"
] | 3a72a0a128cf1e4352879ec4a7ae3781297144c41bd3392b22b3f40e26c496d6 |
import os
import shutil
import sys
import glob
from setuptools import setup, find_packages
setup(
name='circlator',
version='1.5.5',
description='circlator: a tool to circularise genome assemblies',
packages = find_packages(),
package_data={'circlator': ['data/*']},
author='Martin Hunt, Nishad... | sanger-pathogens/circlator | setup.py | Python | gpl-3.0 | 1,005 | [
"pysam"
] | 8d6aa9233fc57ee20d683ea9dc788f903e0cfa0c3b6b321918c2bb622b4a2577 |
#load libs
from wx.lib.embeddedimage import PyEmbeddedImage
#----------------------------------------------------------------------
Icon16 = PyEmbeddedImage(
"iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAYAAAAf8/9hAAAD2UlEQVQ4jU1TC0yTVxS+pbWI"
"zARWCbgYrdINZ1egMCHDTf/BxAV84GiRBIabQlszLGQwNVKyOQVEoMACpQJFoFHDU7bVwBxD"
... | lukauskas/mMass-fork | gui/images_lib_gtk.py | Python | gpl-3.0 | 993,889 | [
"DFTB+"
] | 0fc1c8cc9a5342f4d068ad3439b62073ae8b397e236917d94d85824d4c236aec |
# -*- coding: utf-8 -*-
import sys
import textwrap
import pytest
from _pytest import fixtures
from _pytest.fixtures import FixtureLookupError
from _pytest.fixtures import FixtureRequest
from _pytest.pathlib import Path
from _pytest.pytester import get_public_names
from _pytest.warnings import SHOW_PYTEST_WARNINGS_ARG
... | txomon/pytest | testing/python/fixture.py | Python | mit | 124,651 | [
"VisIt"
] | 0edf0bfcbf02bb34607902c130e574afd2ebdd0f755d48a0616b4b35c5c874e5 |
# Copyright (C) 2010 Parker Phinney
# Copyright (C) 2009, 2010 OpenHatch, Inc.
# Copyright (C) 2010 Jessica McKellar
#
# 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 ... | ehashman/oh-mainline | mysite/account/tests.py | Python | agpl-3.0 | 21,272 | [
"VisIt"
] | a146da3f8085fd7c4028508b39efd4eec700f2f713e3e2d658f40531d84a6e4b |
"""
Tools for simulating the result of a cgi.FieldStorage()
call; useful for testing CGI scripts outside the Web
"""
class FieldMockup: # mocked-up input object
def __init__(self, str):
self.value = str
def formMockup(**kwargs): # pass ... | simontakite/sysadmin | pythonscripts/programmingpython/Internet/Web/cgi-bin/formMockup.py | Python | gpl-2.0 | 1,388 | [
"Brian"
] | ff6a050c0b21451aa385cb2b7e6bb9f76cb5b79fde3b8c9b36a37b95fdff5c97 |
""" pytest for WorkflowTasks
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=protected-access,missing-docstring,invalid-name
import json
import six
import sys
from mock import MagicMock
from pytest import mark
parametrize = mark.param... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/Client/test/Test_Client_RequestTasks.py | Python | gpl-3.0 | 11,381 | [
"DIRAC"
] | 7f86e3587bb85bfe1ae82abcea2838955107bddae53b96c2f6373764d446a391 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
"""
Check that all error messages are formatted the same way.
"""
from __future__ import print_function
import os
import sys
import glob
import re
import codecs
ROOT = os.path.join(os.path.dirname(__file__), "..", "..")
ERRORS = 0
# Path, line of messages that do not follo... | Luthaf/Chemharp | tests/lints/check-error-messages.py | Python | mpl-2.0 | 3,010 | [
"Chemfiles",
"LAMMPS"
] | e7f96cf3bb68fc240ace8f7d43218d38e89fa35d1f9399e5fc823ec8f34dec4d |
"""
Python module for creating, training and applying hidden
Markov models to discrete or continuous observations.
Author: Michael Hamilton, hamiltom@cs.colostate.edu
Theoretical concepts obtained from Rabiner, 1989.
"""
import numpy
import time, copy
import numpy.random
import numpy.linalg
import matplotlib.pyplot... | freinque/barbiturythme | barbiturythme/hmm.py | Python | gpl-2.0 | 24,648 | [
"CASINO"
] | 39b4f708d74441a193f2ed387e5de055454ed1f5dcb26f5828e2c416926d5ea8 |
#
# 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/src/bigdl/orca/learn/tf2/ray_estimator.py | Python | apache-2.0 | 19,777 | [
"ORCA"
] | 70e7070d0f57c88de1805c2abbce365b5f5ecde16a3cc2756445eeebbb8f9abf |
# Standard Library
import os
import shutil
import subprocess
from pathlib import Path
# BioPython
from Bio import SeqIO
from Bio.Align.Applications import ClustalOmegaCommandline
# OrthoEvol
from OrthoEvol.Tools.logit import LogIt
from OrthoEvol.utilities import FullUtilities
from OrthoEvol.Orthologs.GenBank import Gen... | datasnakes/Datasnakes-Scripts | OrthoEvol/Orthologs/Align/msa.py | Python | mit | 17,737 | [
"Biopython"
] | c950a3f13483002e89d82c24deac5a532fb345a196fcaa71b945aa1dd95bd09e |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Flask React SPA documentation build configuration file, created by
# sphinx-quickstart on Thu Sep 7 06:48:34 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in t... | briancappello/flask-react-spa | docs/conf.py | Python | mit | 5,584 | [
"Brian"
] | 0bc0e94775cbc3625eb99f15efd6da2bdab967baf66b09081f02d0505e90f41a |
# $Id$
#
# Copyright (C) 2002-2008 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.
#
""" command line util... | ptosco/rdkit | rdkit/ML/AnalyzeComposite.py | Python | bsd-3-clause | 9,361 | [
"RDKit"
] | 626a543933bcb1e2156128512c953943b479bdaa68bffe3ade5078e0b3034056 |
"""
chapter4.py
==========
Models from Chapter 4 of [G&L 2012].
- Model PC = Model with Portfolio Choice
Note that if using the book initial conditions, not all variables are being set at
present. This will affect some stock variable accounting.
[G&L 2012] "Monetary Economics: An Integrated Approach to credit, Mone... | brianr747/SFC_models | sfc_models/gl_book/chapter4.py | Python | apache-2.0 | 5,346 | [
"Brian"
] | 428c6a58f9ebe0cb6b29f52aeaeb656a61c0a12e2a731fb404c2be842363a093 |
model = """# Generated by PySCeS 0.7.0 (2010-10-07 19:43)
# Keywords
Description: Auto-regulatory network
Modelname: AutoRegulatoryNetwork
Output_In_Conc: True
Species_In_Conc: False
# GlobalUnitDefinitions
UnitVolume: litre, 1.0, 0, 1
UnitLength: metre, 1.0, 0, 1
UnitSubstance: item, 1.0, 0, 1
UnitArea: metre, 1.0... | SystemsBioinformatics/stochpy | stochpy/pscmodels/Autoreg.py | Python | gpl-3.0 | 7,624 | [
"PySCeS"
] | 8a8acf392c9314c75277679908b502946ec09c7987b5a9d5bd3dd55be3591c6d |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyCrispresso(PythonPackage):
"""Software pipeline for the analysis of CRISPR-Cas9 genome e... | LLNL/spack | var/spack/repos/builtin/packages/py-crispresso/package.py | Python | lgpl-2.1 | 1,135 | [
"Biopython"
] | fa90a7f89a6e1b6841e3fc1d976c0b2e37edc340ac59d9a80e84c4b60879b2f7 |
"""
=================
flask-geckoboard
=================
Geckoboard_ is a hosted, real-time status board serving up indicators
from web analytics, CRM, support, infrastructure, project management,
sales, etc. It can be connected to virtually any source of quantitative
data. This Flask_ plugin provides view decorator... | rossdeane/flask-geckoboard | flask_geckoboard/__init__.py | Python | mit | 12,681 | [
"Amber"
] | 809bf482e60b157d013baaf8acf63e9420f7a7d7bff7d6de0c0145a4bf66ffcf |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
from django.conf import settings
class Migration(migrations.Migration):
dependencies = [
migrations.swappable_dependency(settings.AUTH_USER_MODEL),
]
operations = [
migrations.Create... | ryanrborn/lds-leader-tool-suite-backend | llts/migrations/0001_initial.py | Python | mit | 6,883 | [
"VisIt"
] | 98b7aa1db8f997d58ad2f36cfe430b4680709721596fb62add286e6b6694b3f0 |
#!/usr/bin/env python3
"""bvc.py: Manages binary and integer variables for the MSA 2 QUBO problem"""
import math
import numpy as np
from matplotlib import pyplot as plt
try:
import gurobipy
except ImportError:
pass
__author__ = "Dan Mapleson, Luis Yanes, Katie Barr, Sophie Kirkwood and Tim Stitt"
__copyright__ = ... | maplesond/msa2qubo | bvc.py | Python | gpl-3.0 | 26,542 | [
"Biopython"
] | db14ff0182df5cae3b0f89985e59707cb44d6b4ba1b0b7a9a7b512f2209b3846 |
#
# co_co_only_spike_buffer_data_types.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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
... | kperun/nestml | pynestml/cocos/co_co_only_spike_buffer_data_types.py | Python | gpl-2.0 | 2,673 | [
"NEURON"
] | e0be948f2e3783e33677a5c55320ed8be16def42b25433ce9f6825e12807c7da |
import logging
import httplib2
import json
import os
import hashlib
# This module performs authentication based on the tokens
# issued by Globus Online's Nexus service, see this URL for
# details:
# http://globusonline.github.com/nexus-docs/api.html
#
# Import the Globus Online client libraries, originally
# sourced f... | kbase/auth_service | python-libs/oauth.py | Python | mit | 8,778 | [
"VisIt"
] | 89a721fbba3a6c15c97afd75c9546cd897a3354b3a6c6ee57f12796494b480f1 |
#!/usr/bin/env python
from sys import argv, stderr, exit
import subprocess
import numpy as np
from argparse import ArgumentParser
try:
from exactP import exactP_list
except:
stderr.write("Please build the exactP module by running 'make exactP'.\n")
exit(1)
try:
from PISMNC import PISMDataset
except:
subproc... | talbrecht/pism_pik06 | test/test_hydrology/runTestP.py | Python | gpl-3.0 | 8,902 | [
"NetCDF"
] | 0dc94603b177687e9836435b795c88bb402373b1b8e411aea56b1fef92422212 |
# 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 | testsuite/integrator/testVelocityVerlet.py | Python | gpl-3.0 | 4,313 | [
"ESPResSo"
] | d4e5b75a39478a6b97d7d748a9341037c35d92cf3299df4bbea5b73797e86352 |
import math
import numpy as np
from scipy import ndimage as ndi
from scipy.ndimage import filters as ndif
from collections import OrderedDict
from ..exposure import histogram
from .._shared.utils import assert_nD, warn
__all__ = ['try_all_threshold',
'threshold_adaptive',
'threshold_otsu',
... | ofgulban/scikit-image | skimage/filters/thresholding.py | Python | bsd-3-clause | 24,466 | [
"Gaussian"
] | 6633e17ab913a9dc4dad23a2c2b533dd1c69964eeb47cc0b256ff8cb806737d9 |
# -*- coding: utf-8 -*-
import re
import creoleparser
import creoleparser.elements
import genshi
import genshi.core
import pygments
import pygments.lexers
import pygments.formatters
from werkzeug import url_quote
from tipfy import local, escape, url_for
from tipfy.ext.i18n import _
from tipfy.ext.db import _slugif... | ac001/moe | project/app/moe/wiki/parser.py | Python | bsd-3-clause | 6,205 | [
"MOE"
] | 434d7bd3cbd554f2f7c53b076c56e864fcf75ea33488a9e8d08db4eb32c48e25 |
from __future__ import division
import os, sys, warnings
def fn_name(): return sys._getframe(1).f_code.co_name
try:
import gobject
import gtk; gdk = gtk.gdk
import pango
except ImportError:
raise ImportError("Gtk* backend requires pygtk to be installed.")
pygtk_version_required = (2,4,0)
if gtk.pygtk... | SpaceKatt/CSPLN | apps/scaffolding/mac/web2py/web2py.app/Contents/Resources/lib/python2.7/matplotlib/backends/backend_gtk.py | Python | gpl-3.0 | 43,329 | [
"FLEUR"
] | 4aeb004e80adbe2345355c0de322735e6d0a2a4fa0179b6b02c850c3f7f3af3a |
# (c) 2012, Michael DeHaan <michael.dehaan@gmail.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 your option) any lat... | mitodl/ansible | lib/ansible/utils/__init__.py | Python | gpl-3.0 | 39,074 | [
"VisIt"
] | 150be469b101d23e18095c83a88af0a1bfff44db5deddd76b77b880a483529d9 |
# coding=utf-8
# Copyright 2022 The Google Research 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... | google-research/google-research | eim/models/nis.py | Python | apache-2.0 | 8,872 | [
"Gaussian"
] | b3496574784d55c7a97975c2358ba605c1878a048e4472f6e69505e5219c6a79 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-list-users
# Author : Adrian Casajus
########################################################################
"""
Lists the users in the Configuration. If no group is specified return al... | avedaee/DIRAC | Interfaces/scripts/dirac-admin-list-users.py | Python | gpl-3.0 | 2,047 | [
"DIRAC"
] | be78da5da5e96e0c839d41d45696dcb035c420f3d539939b9da57c2dd390daa5 |
""" This file contains different utility functions that are not connected
in anyway to the networks presented in the tutorials, but rather help in
processing the outputs into a more understandable way.
For example ``tile_raster_images`` helps in generating a easy to grasp
image from a set of samples or weights.
Nois... | gdl-civestav-localization/cinvestav_location_fingerprinting | models/regression/deep_models/utils.py | Python | gpl-3.0 | 12,258 | [
"Gaussian"
] | 1a5aee97321f8b96e84fa156d5a53f6a4b06c316128dfa825938255020704e9d |
import numpy as np
from openpathsampling.netcdfplus import StorableObject
# The decorator @restores_ allows us to restore the object from a JSON
# string completely and can thus be stored automatically
class PES(StorableObject):
"""Abstract base class for toy potential energy surfaces.
"""
# For now, we... | choderalab/openpathsampling | openpathsampling/engines/toy/pes.py | Python | lgpl-2.1 | 9,856 | [
"Gaussian"
] | 8613b261b7a14f3801ee10550b3fc54370356a520d7b825984cec73004a5e15b |
########################################################################
# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015.
# It is licenced under the GPL 2.1 or higher.
# There is no warranty of any kind. You are welcome to make copies under
# the provisions of the GPL.
# This program builds a multiscale ... | BhallaLab/moose-examples | paper-2015/Fig4_ReacDiff/Fig4B.py | Python | gpl-2.0 | 7,167 | [
"MOOSE"
] | a2b886a2ddddc4643ae62488c5dc2971063d5030cccd017c5300877908cc2a86 |
#!/usr/bin/env python
#
# This code is part of the binding affinity prediction tools distribution
# and governed by its license. Please see the LICENSE file that should
# have been included as part of this package.
#
"""
Functions to read PDB/mmCIF files
"""
from __future__ import print_function, division
import os... | haddocking/binding_affinity | lib/parsers.py | Python | apache-2.0 | 4,255 | [
"Biopython"
] | b22f90cc88a07c53e5db8c182a39702fd392dcc3d52335a21595ddedc24dc05e |
#
# Copyright (C) 2013-2019 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... | fweik/espresso | samples/minimal-polymer.py | Python | gpl-3.0 | 2,972 | [
"ESPResSo"
] | fbb5c3d107a4bba612b8f3eb54c37a65fa18fb9bb1d4e87129294292dacfe276 |
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
import sys
sys.path.append("../")
from functions import *
from pylab import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import matplotlib.cm as cm
import os
####################################... | gviejo/ThalamusPhysio | python/figure_article/main_article_fig_2.py | Python | gpl-3.0 | 11,952 | [
"Gaussian"
] | 2c306c2bd1a32f7cf087c17d864859885fd4da97967c0d078549aea35db41a26 |
"""
[2016-01-06] Challenge #248 [Intermediate] A Measure of Edginess
https://www.reddit.com/r/dailyprogrammer/comments/3zqiiq/20160106_challenge_248_intermediate_a_measure_of/
Want to write a program that actually understands images it sees?
One of the mainstays of the computer vision toolkit is *[edge
detection](ht... | DayGitH/Python-Challenges | DailyProgrammer/DP20160106B.py | Python | mit | 5,425 | [
"exciting"
] | 3fad427ba8ab38b9ca02f7ff6300165077d0b3e582b9f7057f1038673bfb4a75 |
import ase
from ase.calculators.lj import LennardJones
from ase.constraints import FixBondLength
from ase.optimize import FIRE
for wrap in [False, True]:
a = ase.Atoms('CCC',
positions=[[1, 0, 5],
[0, 1, 5],
[-1, 0.5, 5]],
... | suttond/MODOI | ase/test/fix_bond_length_mic.py | Python | lgpl-3.0 | 753 | [
"ASE"
] | 10950dbaeef55b1cf662d9afa5405879f2305757e0d5ded7f4f2851db89b62f0 |
"""
Calculate spectroscopy limited maximum efficiency (SLME) given dielectric function data
Forked and adjusted from :
https://github.com/usnistgov/jarvis
References: 1) https://doi.org/10.1021/acs.chemmater.9b02166 &
2) http://dx.doi.org/10.1103/PhysRevLett.108.068701
"""
import os
from math import pi
... | davidwaroquiers/pymatgen | pymatgen/analysis/solar/slme.py | Python | mit | 9,539 | [
"VASP",
"pymatgen"
] | ff8d4e05d76d4d4e904bb115e70d5d6aa250f39d6aa2cfb97b2effd3b7ad2db4 |
import ast
from src.ast_pprint import parseprint
from types import *
import _ast
class PyUnitAssertionError(AssertionError):
pass
def assert_equal(a, b):
if a != b:
raise PyUnitAssertionError("{0} is not equal to {1}".format(a, b))
def assert_not_equal(a, b):
if a == b:
raise PyUnitAsse... | tcdl-utn/astmanipulation | src/testing_framework/astPyTest.py | Python | bsd-3-clause | 5,255 | [
"VisIt"
] | 69ed377d05ff10359a73227ff2f9bcc7318f1b186cfea169f0f1caa0a5bc5736 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
import copy as cp
from distutils.version import LooseVersion
import itertools as itt
from math import log
imp... | jniediek/mne-python | mne/cov.py | Python | bsd-3-clause | 76,115 | [
"Gaussian"
] | 8bdbba1339e341ca5c37cb64badfd99415aecd6b4d6d3c787aafc8e9e0e153af |
"""Module for calculating the electron-phonon coupling in an LCAO basis.
Electron-phonon coupling::
__
\ l + +
H = ) g c c ( a + a ),
el-ph /_ ij i j l l
l,ij
where ... | ajylee/gpaw-rtxs | gpaw/lcao/electronphonon.py | Python | gpl-3.0 | 29,004 | [
"ASE",
"GPAW"
] | b328655d5ecc96dd619867ad69e2ea24d893f9149d9641e1cf6d596538b628d0 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/ao2mo/_ao2mo.py | Python | apache-2.0 | 11,111 | [
"PySCF"
] | e30cdafc399e9a791f961e9866b6491788a22f0cfa874042f525d2dbaaedf3f3 |
'''
Script to extract auxiliary predictors and other raster-based variables for each station.
'''
from twx.db import StationSerialDataDb, CLIMDIV, MASK, TDI
from twx.infill import add_stn_raster_values
from twx.raster import RasterDataset
from twx.utils import TwxConfig
import numpy as np
import os
if __name__ == '__... | jaredwo/topowx | scripts/step19_add_raster_predictors.py | Python | gpl-3.0 | 3,951 | [
"NetCDF"
] | 9b6081b0b9f9a00de9d801a1472609ab70e23091d246503b5023e72bdee56aa7 |
import logging
import urllib
from functools import partial
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlresolvers import reverse
from django.contrib.auth.models import User
from django.contrib.auth.decorators i... | elimence/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 30,853 | [
"VisIt"
] | 8e53f2743e4865b0b706e41caf78c4bfe36414f07e9eaf60dd47e6c65ed69e28 |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
QAD Quantum Aided Design plugin
comando ROTATE per ruotare oggetti
-------------------
begin : 2013-09-27
copyright : iiiii
email ... | geosim/QAD | qad_rotate_cmd.py | Python | gpl-3.0 | 41,108 | [
"ESPResSo"
] | 7c4503973152d23a7a1cafeede5970fbacb9dd5da2db7e9ba939770710ac629b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Copyright (C) 2016 Sovrasov V. - All Rights Reserved
* You may use, distribute and modify this code under the
* terms of the MIT license.
* You should have received a copy of the MIT license with
* this file. If not visit https://opensource.org/licenses/MIT
'''
imp... | sovrasov/fuzzy-ml | src/crossValidation.py | Python | mit | 1,864 | [
"VisIt"
] | 48fdb579bd3864ce6f8341c0a26a73b611477dafd12e612b97b6169a8a374ebf |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'LegendOption'
db.create_table(u'profiles_legendoption', (
(u'id', self.gf('dja... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0056_auto__add_legendoption.py | Python | mit | 20,590 | [
"MOE"
] | 7e8be4624e082c70301f7a0b616bac04274279e835570c2ebd8d2da2c4e2f769 |
#
# Copyright (C) 2019 Greg Landrum
# 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 rdkit import Chem
from rdkit import Geometry
from rdki... | bp-kelley/rdkit | Code/GraphMol/Wrap/testSGroups.py | Python | bsd-3-clause | 17,783 | [
"RDKit"
] | ac3c4161d7634d2441e09b65e779ff61a740df650c2dc76a90d937384ddbc3b4 |
# ---
# jupyter:
# jupytext:
# formats: ipynb,.pct.py:percent
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.3'
# jupytext_version: 1.3.3
# kernelspec:
# display_name: Python 3
# language: python
# name: python3
# ---
# %% [markdown]
... | GPflow/GPflow | doc/source/notebooks/theory/Sanity_check.pct.py | Python | apache-2.0 | 5,239 | [
"Gaussian"
] | bfc30811e8a7d676e6700ce9f5b7f041715b7ab00941b190e66c5b3219346db8 |
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