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Update test_1.py Update setup.py
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-49
lines changed

‎.gitignore

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*.venv
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*~
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*.pyc
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*.cpython*.so
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__pycache__
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.venv
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../build
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dist
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*egg-info
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*.pyc

‎AUTHORS

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W. Beck Andrews <[email protected]>
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Xander Mensah <[email protected]>
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Katsuyo Thornton <[email protected]>

‎BinaryTests.py

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This file was deleted.

‎LICENSE.md

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MIT License
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎BinarySystems.py ‎ammber/BinarySystems.py

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from scipy.interpolate import CubicSpline
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import numpy as np
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from pycalphad import calculate
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import PRISMS_PF_fileGen
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from PRISMS_PF_fileGen import write_binary_isothermal_parabolic_parameters
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class BinaryIsothermalDiscretePhase:
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"Class representing a single phase at one temperature described by a set of points in composition-Gibbs free energy space"
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def __init__(self, xdata, Gdata):

‎PRISMS_PF_fileGen.py ‎ammber/PRISMS_PF_fileGen.py

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def binary_isothermal_write_parabolic_parameters(binaryIsothermalSys, output_file, template_file, phases=None, component="comp_1"):
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def write_binary_isothermal_parabolic_parameters(binaryIsothermalSys, output_file, template_file, phases=None, component="comp_1"):
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"""
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Creates a parameters file from a BinaryIsothermal2ndOrderSystem
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Parameters
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----------
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binaryIsothermalSys : BinaryIsothermal2ndOrderSystem
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system to draw parameters from
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output_file : string
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path to file to create
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template_file : string

‎ammber/__init__.py

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"""
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ammber.
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A Python package for parametrizing gibbs free energy curves for phase-field modeling.
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"""
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__version__ = "0.1.0"
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__author__ = 'Xander or Beck or Katsuyo'
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__credits__ = 'University of Michigan'

‎maintenance/copyright.py

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#
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#
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import os
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import sys
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from collections import defaultdict
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from datetime import datetime
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from subprocess import Popen, PIPE
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root = os.path.dirname(sys.argv[0])
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def read_authors(fn):
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return {email.strip('<>'): name for name, email in
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[line.rsplit(maxsplit=1) for line in open(fn, 'r')]}
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def parse_git_log(log, authors):
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committers = defaultdict(set)
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author = None
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date = None
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for line in log.decode('utf-8').split('\n'):
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if line.startswith('commit'):
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if date is not None and author is not None:
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committers[author].add(date.year)
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elif line.startswith('Author:'):
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email = line.rsplit('<', maxsplit=1)[1][:-1]
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elif line.startswith('Date:'):
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date = datetime.strptime(line[5:].rsplit(maxsplit=1)[0].strip(),
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'%a %b %d %H:%M:%S %Y')
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try:
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author = authors[email]
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except KeyError:
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author = email
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elif 'copyright' in line.lower() or 'license' in line.lower():
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date = None
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if date is not None:
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committers[author].add(date.year)
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return committers
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def pretty_years(years):
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years = sorted(years)
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prev_year = prev_out = years[0]
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s = '{}'.format(prev_year)
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for year in years[1:]:
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if year - prev_year > 1:
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if year - prev_out > 1:
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if prev_year == prev_out:
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s = '{}, {}'.format(s, year)
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else:
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s = '{}-{}, {}'.format(s, prev_year, year)
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else:
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s = '{}, {}'.format(s, prev_year)
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prev_out = year
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prev_year = year
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if prev_year - prev_out == 1:
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s = '{}-{}'.format(s, prev_year)
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elif prev_year - prev_out > 1:
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s = '{}, {}'.format(s, prev_year)
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return s
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authors = read_authors('{}/../AUTHORS'.format(root))
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process = Popen(['git', 'log', '--follow', sys.argv[1]], stdout=PIPE,
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stderr=PIPE)
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stdout, stderr = process.communicate()
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committers = parse_git_log(stdout, authors)
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prefix = 'Copyright'
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for name, years in committers.items():
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print('{} {} {}'.format(prefix, pretty_years(years), name))
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prefix = ' ' * len(prefix)
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print()

‎maintenance/replace_header.py

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#
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#
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import sys
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file_lines = open(sys.argv[1], 'r').readlines()
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header_lines = sys.stdin.readlines()
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while file_lines[0].startswith('#'):
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file_lines = file_lines[1:]
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file_lines.insert(0, '#\n')
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for header_line in header_lines[::-1]:
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file_lines.insert(0, '# {}'.format(header_line).strip() + '\n')
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file_lines.insert(0, '#\n')
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open(sys.argv[1], 'w').writelines(file_lines)

‎maintenance/update_license_headers.sh

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#! /bin/sh
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# Updates all Python files with license taken from README.md and copyright information obtained from the git log.
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for fn in setup.py `find ammber test -name "*.py"`; do
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echo $fn
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python3 maintenance/copyright.py $fn | cat - LICENSE.md | python3 maintenance/replace_header.py $fn
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done

‎setup.py

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#
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# Copyright 2024 William Beck Andrews
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#
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# MIT License
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#
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# Permission is hereby granted, free of charge, to any person obtaining a copy
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# of this software and associated documentation files (the "Software"), to deal
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# in the Software without restriction, including without limitation the rights
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# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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# copies of the Software, and to permit persons to whom the Software is
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# furnished to do so, subject to the following conditions:
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#
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# The above copyright notice and this permission notice shall be included in all
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# copies or substantial portions of the Software.
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#
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# SOFTWARE.
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#
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from setuptools import setup
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setup(
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name='ammber',
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version='0.1.0',
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description='A Python package for parametrizing gibbs free energy curves for phase-field modeling',
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url='https://github.com/UMThorntongroup/',
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author='W. Beck Andrews',
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author_email='[email protected]',
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license='MIT',
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test_suite='tests',
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packages=['ammber'],
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install_requires=['numpy<2.0',
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'scipy',
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'pycalphad'
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],
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classifiers=[
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'Development Status :: 1 - Planning',
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'Intended Audience :: Science/Research',
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'License :: OSI Approved :: MIT License',
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'Programming Language :: Python :: 2',
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'Programming Language :: Python :: 2.7',
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'Programming Language :: Python :: 3',
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'Programming Language :: Python :: 3.4',
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'Programming Language :: Python :: 3.5',
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],
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)

‎test/test_1.py

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"""
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Tests functions
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"""
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import ammber.BinarySystems as BS
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def test_01():
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phase1 = BS.BinaryIsothermal2ndOrderPhase(fmin = 0, kwell= 1, cmin= 0.5)
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assert (phase1.free_energy(0.5) == 0)

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