strainjedi 1.0.0__tar.gz

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  1. strainjedi-1.0.0/LICENSE +21 -0
  2. strainjedi-1.0.0/LICENSE_old +21 -0
  3. strainjedi-1.0.0/PKG-INFO +18 -0
  4. strainjedi-1.0.0/README.rst +34 -0
  5. strainjedi-1.0.0/setup.cfg +4 -0
  6. strainjedi-1.0.0/setup.py +25 -0
  7. strainjedi-1.0.0/strainjedi/__init__.py +9 -0
  8. strainjedi-1.0.0/strainjedi/colors.py +111 -0
  9. strainjedi-1.0.0/strainjedi/io/__init__.py +0 -0
  10. strainjedi-1.0.0/strainjedi/io/gaussian.py +438 -0
  11. strainjedi-1.0.0/strainjedi/io/orca.py +370 -0
  12. strainjedi-1.0.0/strainjedi/io/qchem.py +434 -0
  13. strainjedi-1.0.0/strainjedi/jedi.py +1965 -0
  14. strainjedi-1.0.0/strainjedi/quotes.py +9 -0
  15. strainjedi-1.0.0/strainjedi.egg-info/PKG-INFO +18 -0
  16. strainjedi-1.0.0/strainjedi.egg-info/SOURCES.txt +18 -0
  17. strainjedi-1.0.0/strainjedi.egg-info/dependency_links.txt +1 -0
  18. strainjedi-1.0.0/strainjedi.egg-info/requires.txt +4 -0
  19. strainjedi-1.0.0/strainjedi.egg-info/top_level.txt +2 -0
  20. strainjedi-1.0.0/tests/test_Jedi.py +39 -0
strainjedi-1.0.0/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2023 Henry Wang, Sanna Benter, Wilke Dononelli, Tim Neudecker
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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.
strainjedi-1.0.0/LICENSE_old ADDED
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+ MIT License
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+
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+ Copyright (c) 2023 Henry Wang
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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.
strainjedi-1.0.0/PKG-INFO ADDED
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+ Metadata-Version: 2.1
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+ Name: strainjedi
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+ Version: 1.0.0
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+ Summary: The python distribution for the JEDI analysis
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+ Home-page: https://github.com/neudecker-group/jedi
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+ Author: Tim Neudecker, Sanna Benter, Henry Wang, Wilke Dononelli
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+ Author-email: neudecker@uni-bremen.de
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+ License: MIT
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+ Classifier: Development Status :: 5 - Production/Stable
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: Operating System :: POSIX :: Linux
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+ Classifier: Programming Language :: Python :: 3.8
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+ License-File: LICENSE
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+ License-File: LICENSE_old
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+ Requires-Dist: mpi4py>=2.0
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+ Requires-Dist: numpy
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+ Requires-Dist: ase
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+ Requires-Dist: pytest
strainjedi-1.0.0/README.rst ADDED
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+ Judgement of Energy DIstribution
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+ =============================
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+
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+ JEDI is a quantum chemical strain analysis tool working with the Atomic Simulation Environment (ASE).
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+
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+
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+
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+ Requirements
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+ ------------
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+
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+ * Python_ 3.8 or later
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+ * NumPy_ (base N-dimensional array package)
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+ * ase_ 3.23 (functions to determine atomic structures' geometries and quantum chemical calculators)
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+
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+
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+
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+
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+ Installation
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+ ------------
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+
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+ Add ``~/jedi`` to your $PYTHONPATH environment variable
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+
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+
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+
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+ Tutorial
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+ ------------
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+
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+ A tutorial is available here: https://neudecker-group.github.io/jedi/
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+
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+
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+
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+ .. _Python: http://www.python.org/
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+ .. _NumPy: http://docs.scipy.org/doc/numpy/reference/
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+ .. _ase: https://wiki.fysik.dtu.dk/ase/
strainjedi-1.0.0/setup.cfg ADDED
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+ [egg_info]
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+ tag_build =
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+ tag_date = 0
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+
strainjedi-1.0.0/setup.py ADDED
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+ from setuptools import setup
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+
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+ setup(
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+ name='strainjedi',
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+ version='1.0.0',
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+ description='The python distribution for the JEDI analysis',
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+ url='https://github.com/neudecker-group/jedi',
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+ author='Tim Neudecker, Sanna Benter, Henry Wang, Wilke Dononelli',
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+ author_email='neudecker@uni-bremen.de',
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+ license='MIT',
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+ packages=['strainjedi','strainjedi/io'],
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+ install_requires=['mpi4py>=2.0',
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+ 'numpy',
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+ 'ase',
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+ 'pytest'
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+ ],
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+
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+ classifiers=[
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+ 'Development Status :: 5 - Production/Stable',
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+ 'Intended Audience :: Science/Research',
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+
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+ 'Operating System :: POSIX :: Linux',
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+ 'Programming Language :: Python :: 3.8',
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+ ],
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+ )
strainjedi-1.0.0/strainjedi/__init__.py ADDED
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+ """
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+ strainjedi.
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+
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+ The JEDI analysis python library.
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+ """
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+
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+ __version__ = "1.0.0"
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+ __author__ = 'Tim Neudecker, Sanna Benter, Henry Wang, Wilke Dononelli'
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+ __credits__ = 'Neudecker Group'
strainjedi-1.0.0/strainjedi/colors.py ADDED
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+ #####color code from Jmol https://jmol.sourceforge.net/jscolors/ #########
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+ colors={
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+ 'H': [1.0, 1.0, 1.0],
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+ 'He': [0.8509803921568627, 1.0, 1.0],
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+ 'Li': [0.8, 0.5019607843137255, 1.0],
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+ 'Be': [0.7607843137254902, 1.0, 0.0],
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+ 'B': [1.0, 0.7098039215686275, 0.7098039215686275],
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+ 'C': [0.5647058823529412, 0.5647058823529412, 0.5647058823529412],
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+ 'N': [0.18823529411764706, 0.3137254901960784, 0.9725490196078431],
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+ 'O': [1.0, 0.050980392156862744, 0.050980392156862744],
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+ 'F': [0.5647058823529412, 0.8784313725490196, 0.3137254901960784],
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+ 'Ne': [0.7019607843137254, 0.8901960784313725, 0.9607843137254902],
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+ 'Na': [0.6705882352941176, 0.3607843137254902, 0.9490196078431372],
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+ 'Mg': [0.5411764705882353, 1.0, 0.0],
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+ 'Al': [0.7490196078431373, 0.6509803921568628, 0.6509803921568628],
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+ 'Si': [0.9411764705882353, 0.7843137254901961, 0.6274509803921569],
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+ 'P': [1.0, 0.5019607843137255, 0.0],
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+ 'S': [1.0, 1.0, 0.18823529411764706],
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+ 'Cl': [0.12156862745098039, 0.9411764705882353, 0.12156862745098039],
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+ 'Ar': [0.5019607843137255, 0.8196078431372549, 0.8901960784313725],
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+ 'K': [0.5607843137254902, 0.25098039215686274, 0.8313725490196079],
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+ 'Ca': [0.23921568627450981, 1.0, 0.0],
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+ 'Sc': [0.9019607843137255, 0.9019607843137255, 0.9019607843137255],
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+ 'Ti': [0.7490196078431373, 0.7607843137254902, 0.7803921568627451],
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+ 'V': [0.6509803921568628, 0.6509803921568628, 0.6705882352941176],
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+ 'Cr': [0.5411764705882353, 0.6, 0.7803921568627451],
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+ 'Mn': [0.611764705882353, 0.47843137254901963, 0.7803921568627451],
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+ 'Fe': [0.8784313725490196, 0.4, 0.2],
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+ 'Co': [0.9411764705882353, 0.5647058823529412, 0.6274509803921569],
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+ 'Ni': [0.3137254901960784, 0.8156862745098039, 0.3137254901960784],
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+ 'Cu': [0.7843137254901961, 0.5019607843137255, 0.2],
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+ 'Zn': [0.49019607843137253, 0.5019607843137255, 0.6901960784313725],
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+ 'Ga': [0.7607843137254902, 0.5607843137254902, 0.5607843137254902],
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+ 'Ge': [0.4, 0.5607843137254902, 0.5607843137254902],
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+ 'As': [0.7411764705882353, 0.5019607843137255, 0.8901960784313725],
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+ 'Se': [1.0, 0.6313725490196078, 0.0],
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+ 'Br': [0.6509803921568628, 0.1607843137254902, 0.1607843137254902],
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+ 'Kr': [0.3607843137254902, 0.7215686274509804, 0.8196078431372549],
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+ 'Rb': [0.4392156862745098, 0.1803921568627451, 0.6901960784313725],
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+ 'Sr': [0.0, 1.0, 0.0],
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+ 'Y': [0.5803921568627451, 1.0, 1.0],
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+ 'Zr': [0.5803921568627451, 0.8784313725490196, 0.8784313725490196],
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+ 'Nb': [0.45098039215686275, 0.7607843137254902, 0.788235294117647],
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+ 'Mo': [0.32941176470588235, 0.7098039215686275, 0.7098039215686275],
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+ 'Tc': [0.23137254901960785, 0.6196078431372549, 0.6196078431372549],
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+ 'Ru': [0.1411764705882353, 0.5607843137254902, 0.5607843137254902],
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+ 'Rh': [0.0392156862745098, 0.49019607843137253, 0.5490196078431373],
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+ 'Pd': [0.0, 0.4117647058823529, 0.5215686274509804],
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+ 'Ag': [0.7529411764705882, 0.7529411764705882, 0.7529411764705882],
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+ 'Cd': [1.0, 0.8509803921568627, 0.5607843137254902],
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+ 'In': [0.6509803921568628, 0.4588235294117647, 0.45098039215686275],
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+ 'Sn': [0.4, 0.5019607843137255, 0.5019607843137255],
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+ 'Sb': [0.6196078431372549, 0.38823529411764707, 0.7098039215686275],
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+ 'Te': [0.8313725490196079, 0.47843137254901963, 0.0],
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+ 'I': [0.5803921568627451, 0.0, 0.5803921568627451],
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+ 'Xe': [0.25882352941176473, 0.6196078431372549, 0.6901960784313725],
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+ 'Cs': [0.3411764705882353, 0.09019607843137255, 0.5607843137254902],
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+ 'Ba': [0.0, 0.788235294117647, 0.0],
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+ 'La': [0.4392156862745098, 0.8313725490196079, 1.0],
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+ 'Ce': [1.0, 1.0, 0.7803921568627451],
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+ 'Pr': [0.8509803921568627, 1.0, 0.7803921568627451],
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+ 'Nd': [0.7803921568627451, 1.0, 0.7803921568627451],
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+ 'Pm': [0.6392156862745098, 1.0, 0.7803921568627451],
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+ 'Sm': [0.5607843137254902, 1.0, 0.7803921568627451],
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+ 'Eu': [0.3803921568627451, 1.0, 0.7803921568627451],
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+ 'Gd': [0.27058823529411763, 1.0, 0.7803921568627451],
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+ 'Tb': [0.18823529411764706, 1.0, 0.7803921568627451],
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+ 'Dy': [0.12156862745098039, 1.0, 0.7803921568627451],
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+ 'Ho': [0.0, 1.0, 0.611764705882353],
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+ 'Er': [0.0, 0.9019607843137255, 0.4588235294117647],
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+ 'Tm': [0.0, 0.8313725490196079, 0.3215686274509804],
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+ 'Yb': [0.0, 0.7490196078431373, 0.2196078431372549],
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+ 'Lu': [0.0, 0.6705882352941176, 0.1411764705882353],
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+ 'Hf': [0.30196078431372547, 0.7607843137254902, 1.0],
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+ 'Ta': [0.30196078431372547, 0.6509803921568628, 1.0],
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+ 'W': [0.12941176470588237, 0.5803921568627451, 0.8392156862745098],
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+ 'Re': [0.14901960784313725, 0.49019607843137253, 0.6705882352941176],
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+ 'Os': [0.14901960784313725, 0.4, 0.5882352941176471],
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+ 'Ir': [0.09019607843137255, 0.32941176470588235, 0.5294117647058824],
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+ 'Pt': [0.8156862745098039, 0.8156862745098039, 0.8784313725490196],
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+ 'Au': [1.0, 0.8196078431372549, 0.13725490196078433],
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+ 'Hg': [0.7215686274509804, 0.7215686274509804, 0.8156862745098039],
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+ 'Tl': [0.6509803921568628, 0.32941176470588235, 0.30196078431372547],
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+ 'Pb': [0.3411764705882353, 0.34901960784313724, 0.3803921568627451],
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+ 'Bi': [0.6196078431372549, 0.30980392156862746, 0.7098039215686275],
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+ 'Po': [0.6705882352941176, 0.3607843137254902, 0.0],
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+ 'At': [0.4588235294117647, 0.30980392156862746, 0.27058823529411763],
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+ 'Rn': [0.25882352941176473, 0.5098039215686274, 0.5882352941176471],
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+ 'Fr': [0.25882352941176473, 0.0, 0.4],
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+ 'Ra': [0.0, 0.49019607843137253, 0.0],
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+ 'Ac': [0.4392156862745098, 0.6705882352941176, 0.9803921568627451],
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+ 'Th': [0.0, 0.7294117647058823, 1.0],
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+ 'Pa': [0.0, 0.6313725490196078, 1.0],
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+ 'U': [0.0, 0.5607843137254902, 1.0],
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+ 'Np': [0.0, 0.5019607843137255, 1.0],
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+ 'Pu': [0.0, 0.4196078431372549, 1.0],
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+ 'Am': [0.32941176470588235, 0.3607843137254902, 0.9490196078431372],
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+ 'Cm': [0.47058823529411764, 0.3607843137254902, 0.8901960784313725],
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+ 'Bk': [0.5411764705882353, 0.30980392156862746, 0.8901960784313725],
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+ 'Cf': [0.6313725490196078, 0.21176470588235294, 0.8313725490196079],
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+ 'Es': [0.7019607843137254, 0.12156862745098039, 0.8313725490196079],
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+ 'Fm': [0.7019607843137254, 0.12156862745098039, 0.7294117647058823],
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+ 'Md': [0.7019607843137254, 0.050980392156862744, 0.6509803921568628],
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+ 'No': [0.7411764705882353, 0.050980392156862744, 0.5294117647058824],
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+ 'Lr': [0.7803921568627451, 0.0, 0.4],
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+ 'Rf': [0.8, 0.0, 0.34901960784313724],
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+ 'Db': [0.8196078431372549, 0.0, 0.30980392156862746],
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+ 'Sg': [0.8509803921568627, 0.0, 0.27058823529411763],
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+ 'Bh': [0.8784313725490196, 0.0, 0.2196078431372549],
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+ 'Hs': [0.9019607843137255, 0.0, 0.1803921568627451],
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+ 'Mt': [0.9215686274509803, 0.0, 0.14901960784313725]}
strainjedi-1.0.0/strainjedi/io/__init__.py ADDED
File without changes