hiPhive - npm Package Compare versions

Comparing version 1.4 to 1.5

hiPhive.egg-info/dependency_links.txt

+

hiPhive.egg-info/PKG-INFO

+Metadata-Version: 2.4
+Name: hiPhive
+Version: 1.5
+Summary: High-order force constants for the masses
+Author: Fredrik Eriksson, Erik Fransson, Paul Erhart
+Maintainer-email: The hiPhive developers team <[e-mail]>
+License: MIT License
+        
+        Copyright (c) 2018 materials-modeling
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Documentation, https://hiphive.materialsmodeling.org
+Project-URL: Repository, https://gitlab.com/materials-modeling/hiphive/
+Keywords: chemistry,physics,scientific
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: ase
+Requires-Dist: h5py
+Requires-Dist: numba>=0.55
+Requires-Dist: numpy>=1.18
+Requires-Dist: pandas
+Requires-Dist: scipy>=1.0.0
+Requires-Dist: spglib>=2.5
+Requires-Dist: sympy>=1.1
+Requires-Dist: trainstation>=0.2
+Dynamic: license-file
+
+hiPhive
+=======
+
+**hiPhive** is a tool for efficiently extracting high-order force constants from atomistic simulations, most commonly density functional theory calculations.
+A detailed description of the functionality provided as well as an extensive tutorial can be found in the `user guide <https://hiphive.materialsmodeling.org/>`_.
+Complete examples of using **hiphive** for force constants extraction can be found in the `hiphive-examples repository <https://gitlab.com/materials-modeling/hiphive-examples/>`_.
+
+**hiPhive** is written in Python, which allows easy integration with countless first-principles codes and analysis tools accessible in Python, and allows for a simple and intuitive user interface.
+For example using the following snippet one can train a force constant potential:
+
+.. code-block:: python
+
+   cs = ClusterSpace(primitive_cell, cutoffs)
+   sc = StructureContainer(cs, list_of_training_structure)
+   opt = Optimizer(sc.get_fit_data())
+   opt.train()
+   fcp = ForceConstantPotential(cs, opt.parameters)
+
+after which it can be used in various ways, e.g., for generating phonon dispersions, computing phonon lifetimes, or running molecular dynamics simulations.
+
+For questions and help please use the `hiphive discussion forum on matsci.org <https://matsci.org/hiphive>`_.
+**hiPhive** and its development are hosted on `gitlab <https://gitlab.com/materials-modeling/hiphive>`_.
+
+
+Installation
+------------
+
+**hiPhive** can be installed via `pip`::
+
+    pip3 install hiphive
+
+or via `conda <https://anaconda.org/conda-forge/hiphive>`_::
+
+    conda install -c conda-forge hiphive
+
+**hiPhive** requires Python3 and invokes functionality from several external libraries including the
+`atomic simulation environment <https://wiki.fysik.dtu.dk/ase>`_,
+`scikit-learn <http://scikit-learn.org/>`_,
+`spglib <https://phonopy.github.io/spglib/>`_,
+`SymPy <http://www.sympy.org/en/index.html>`_, and
+`trainstation <https://trainstation.materialsmodeling.org/>`_.
+Please consult the `installation section of the user guide <https://hiphive.materialsmodeling.org/installation.html>`_ for details.
+
+
+Credits
+-------
+
+**hiPhive** has been developed at the `Department of Physics <https://www.chalmers.se/en/departments/physics/Pages/default.aspx>`_ of `Chalmers University of Technology <https://www.chalmers.se/>`_ (Gothenburg, Sweden) in the `Condensed Matter and Materials Theory division <http://www.materialsmodeling.org>`_.
+
+When using **hiPhive** in your research please cite the following paper:
+
+| Fredrik Eriksson, Erik Fransson, and Paul Erhart
+| *The Hiphive Package for the Extraction of High‐Order Force Constants by Machine Learning*
+| Adv. Theory. Sim., 1800184 (2019)
+| `doi: 10.1002/adts.201800184 <https://doi.org/10.1002/adts.201800184>`_
+
+Please consult the `Credits <https://hiphive.materialsmodeling.org/credits>`_ page of the documentation for additional references.

hiPhive.egg-info/requires.txt

+ase
+h5py
+numba>=0.55
+numpy>=1.18
+pandas
+scipy>=1.0.0
+spglib>=2.5
+sympy>=1.1
+trainstation>=0.2

hiPhive.egg-info/SOURCES.txt

+LICENSE
+README.rst
+pyproject.toml
+hiPhive.egg-info/PKG-INFO
+hiPhive.egg-info/SOURCES.txt
+hiPhive.egg-info/dependency_links.txt
+hiPhive.egg-info/requires.txt
+hiPhive.egg-info/top_level.txt
+hiphive/__init__.py
+hiphive/cluster_space.py
+hiphive/cluster_space_data.py
+hiphive/config.py
+hiphive/cutoffs.py
+hiphive/force_constant_model.py
+hiphive/force_constant_potential.py
+hiphive/force_constants.py
+hiphive/structure_container.py
+hiphive/utilities.py
+hiphive/calculators/__init__.py
+hiphive/calculators/ase_calculator.py
+hiphive/calculators/numba_calc.py
+hiphive/calculators/zbl.py
+hiphive/core/__init__.py
+hiphive/core/atoms.py
+hiphive/core/cluster_space_builder.py
+hiphive/core/clusters.py
+hiphive/core/config.py
+hiphive/core/debug.py
+hiphive/core/eigentensors.py
+hiphive/core/orbits.py
+hiphive/core/rotational_constraints.py
+hiphive/core/structure_alignment.py
+hiphive/core/structures.py
+hiphive/core/tensors.py
+hiphive/core/translational_constraints.py
+hiphive/core/utilities.py
+hiphive/input_output/__init__.py
+hiphive/input_output/gpumd.py
+hiphive/input_output/logging_tools.py
+hiphive/input_output/phonopy.py
+hiphive/input_output/pretty_table_prints.py
+hiphive/input_output/read_write_files.py
+hiphive/input_output/shengBTE.py
+hiphive/md_tools/__init__.py
+hiphive/md_tools/spectral_energy_density.py
+hiphive/self_consistent_phonons/__init__.py
+hiphive/self_consistent_phonons/self_consistent_harmonic_model.py
+hiphive/structure_generation/__init__.py
+hiphive/structure_generation/phonon.py
+hiphive/structure_generation/rattle.py

hiPhive.egg-info/top_level.txt

+hiphive

pyproject.toml

+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "hiPhive"
+description = "High-order force constants for the masses"
+dynamic = ["version"]
+dependencies = [
+    "ase",
+    "h5py",
+    "numba>=0.55",
+    "numpy>=1.18",  # imposed by numba
+    "pandas",
+    "scipy>=1.0.0",  # imposed by numba
+    "spglib>=2.5",
+    "sympy>=1.1",
+    "trainstation>=0.2",
+]
+requires-python = ">=3.9"
+authors = [
+  {name = "Fredrik Eriksson"},
+  {name = "Erik Fransson"},
+  {name = "Paul Erhart"}
+]
+maintainers = [
+  {name = "The hiPhive developers team", email = "[e-mail]"}
+]
+readme = "README.rst"
+keywords = ["chemistry", "physics", "scientific"]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Intended Audience :: Science/Research",
+]
+
+[project.license]
+file = "LICENSE"
+
+[project.urls]
+Documentation = "https://hiphive.materialsmodeling.org"
+Repository = "https://gitlab.com/materials-modeling/hiphive/"
+
+[tool.setuptools.dynamic]
+version = {attr = "hiphive.__version__"}
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["hiphive*"]

hiphive/__init__.py

@@ -12,13 +12,3 @@ """
 
-__project__ = 'hiPhive'
-__description__ = 'High-order force constants for the masses'
-__authors__ = ['Fredrik Eriksson',
-               'Erik Fransson',
-               'Paul Erhart']
-__copyright__ = '2024'
-__license__ = 'MIT License'
-__credits__ = ['Fredrik Eriksson',
-               'Erik Fransson',
-               'Paul Erhart']
-__version__ = '1.4'
+__version__ = '1.5'
 __all__ = ['ClusterSpace',
@@ -30,5 +20,1 @@ 'StructureContainer',
            'enforce_rotational_sum_rules']
-__maintainer__ = 'The hiPhive developers team'
-__maintainer_email__ = '[e-mail]'
-__status__ = 'Stable'
-__url__ = 'http://hiphive.materialsmodeling.org/'

hiphive/cluster_space.py

@@ -53,3 +53,3 @@ """
         parameter will be forwarded to
-        `spglib <https://atztogo.github.io/spglib/>`_)
+        `spglib <https://phonopy.github.io/spglib/>`_)
     length_scale : float
@@ -56,0 +56,0 @@ This will be used as a normalization constant for the eigentensors

PKG-INFO

@@ -1,9 +0,32 @@
-Metadata-Version: 2.1
-Name: hiphive
-Version: 1.4
+Metadata-Version: 2.4
+Name: hiPhive
+Version: 1.5
 Summary: High-order force constants for the masses
-Home-page: http://hiphive.materialsmodeling.org/
-Maintainer: The hiPhive developers team
-Maintainer-email: [e-mail]
-Platform: unix
+Author: Fredrik Eriksson, Erik Fransson, Paul Erhart
+Maintainer-email: The hiPhive developers team <[e-mail]>
+License: MIT License
+        
+        Copyright (c) 2018 materials-modeling
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Documentation, https://hiphive.materialsmodeling.org
+Project-URL: Repository, https://gitlab.com/materials-modeling/hiphive/
+Keywords: chemistry,physics,scientific
 Classifier: Development Status :: 5 - Production/Stable
@@ -19,4 +42,4 @@ Classifier: Operating System :: OS Independent
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
 License-File: LICENSE
@@ -29,6 +52,6 @@ Requires-Dist: ase
 Requires-Dist: scipy>=1.0.0
-Requires-Dist: scikit-learn
 Requires-Dist: spglib>=2.5
 Requires-Dist: sympy>=1.1
 Requires-Dist: trainstation>=0.2
+Dynamic: license-file
 
@@ -73,3 +96,3 @@ hiPhive
 `scikit-learn <http://scikit-learn.org/>`_,
-`spglib <https://atztogo.github.io/spglib/>`_,
+`spglib <https://phonopy.github.io/spglib/>`_,
 `SymPy <http://www.sympy.org/en/index.html>`_, and
@@ -76,0 +99,0 @@ `trainstation <https://trainstation.materialsmodeling.org/>`_.

README.rst

@@ -39,3 +39,3 @@ hiPhive
 `scikit-learn <http://scikit-learn.org/>`_,
-`spglib <https://atztogo.github.io/spglib/>`_,
+`spglib <https://phonopy.github.io/spglib/>`_,
 `SymPy <http://www.sympy.org/en/index.html>`_, and
@@ -42,0 +42,0 @@ `trainstation <https://trainstation.materialsmodeling.org/>`_.

CONTRIBUTING.md

-Contribution guidelines
-=======================
-
-Some general guidelines:
-
-* **Read the contribution guidelines**.<br>
-  You have done well so far but keep on reading all the way to the **bottom of
-  this page**.
-
-* **Remember and apply the contribution guidelines!**<br>
-  [(random user guideline quizzing can occur at any
-  time)](http://www.ohsinc.com/services/employee-drug-testing/)
-
-* Use [expressive function and variable names](https://xkcd.com/910/), e.g.,
-  * Good: `get_number_of_structures` (Python), `getNumberOfStructures` (C++)
-  * Avoid: `get_nbr_struct` or any variation thereof
-  * Good: `get_number_of_allowed_elements` (Python),
-    `getNumberOfAllowedElements` (C++)
-  * Avoid: `get_Mi` or any variation thereof
-  * Avoid anything remotely resembling `int mytmp = 13`
-
-* Document and comment, document and comment, document and comment, document
-  and comment, document and comment ... (it cannot be said too often).<br>
-  Language specific guide lines are given below.
-
-* Always imagine someone else has to be able to read your code. Hence do your
-  best at writing [*clean and structured* code](https://www.xkcd.com/1513/).
-  * Avoid commenting out blocks of code for "later use/reference" in commits.
-  * When writing C++ code, separate declaration and definition in `*.hpp` and
-    `*.cpp` files. This is not just a matter of good coding style but
-    [compilation time during development](https://xkcd.com/303/).
-
-
-C++
----
-
-This project adopts a more concise [style](https://www.xkcd.com/1695/) when
-writing C++ code that is in the spirit of
-[K&R](https://en.wikipedia.org/wiki/Indent_style) and
-[pep7](https://www.python.org/dev/peps/pep-0007/) (yes, that's a thing).
-
-Any functions/functionality *must* be properly documented. The API documentation
-is generated using [doxygen](http://www.stack.nl/~dimitri/doxygen/). You should
-therefore include comment blocks that document your code and are formatted to
-comply with the doxygen markup style.
-
-For most functions, class members, etc. that can be comprehensively described
-using a single line one can use the triple-slash form, e.g.,
-```
-private:
-   /// Space group number according to ITCA.
-   int _spacegroup;
-
-public:
-   /// Returns the space group number.
-   int getSpacegroup() { return _spacegroup; }
-```
-
-For more substantial functions, classes, or other elements (such as ``enum``-s)
-adopt the extended documentation form
-```
-/**
-  @brief Write a structure to file.
-  @details This function writes an atomic structure to file using different formats.
-  @param struct   The atomic configuration
-  @param filename The name of the output file.
-  @param format   The output file format; possible values: 'vasp', 'xyz'\
-*/
-void writeStructureToFile(AtomicStructure *struct, string::string filename, string::string format) {
-    ...
-}
-```
-Usually, declaration and definition are split between `*.hpp` and `*.cpp` files.
-In that case, the following variation is preferred. In the `*.hpp` file:
-```
-/// Write a structure to file.
-void writeStructureToFile(AtomicStructure *, string::string, string::string);
-```
-In the `*.cpp` file:
-```
-/**
-  @details This function writes an atomic structure to file using different formats.
-  @param struct   The atomic configuration
-  @param filename The name of the output file.
-  @param format   The output file format; possible values: 'vasp', 'xyz'
-*/
-void writeStructureToFile(AtomicStructure *struct, string::string filename, string::string format) {
-    ...
-}
-```
-More examples can of course be found in the code.
-
-Please use [CamelCase](https://en.wikipedia.org/wiki/Camel_case) and [expressive
-names](https://xkcd.com/302/) for functions, classes, and members (avoiding
-unnecessary and non-standard abbreviations). Good examples are
-``writeStructureToFile``, ``AtomicStructure``. Private and
-protected class members should be preceded by an underscore as in
-``_myPrivateVariable``.
-
-Please ensure [const
-correctness](https://isocpp.org/wiki/faq/const-correctness).
-
-
-Python
-------
-
-Code should be [pep8](https://www.Python.org/dev/peps/pep-0008/) compliant and
-pass [pyflakes](https://pypi.Python.org/pypi/pyflakes). (Eventually,
-pep8/pyflakes will be added to the CI, at which point code *must* be
-compliant.)
-
-Any functions/functionality *must* be properly documented. This includes
-[docstrings](https://en.wikipedia.org/wiki/Docstring) for functions, classes,
-and modules that clearly describe the task performed, the interface (where
-necessary), the output, and if possible an example. This code uses [NumPy Style
-Python Docstrings](http://sphinxcontrib-
-napoleon.readthedocs.io/en/latest/example_numpy.html).
-
-When in doubt ask the main developers. Also [the coding conventions from
-ASE](https://wiki.fysik.dtu.dk/ase/development/Python_codingstandard.html)
-provide useful guidelines.
-
-Good job, you are still reading! [Will you make it to the
-end?](https://xkcd.com/169/)
-
-
-Please use spaces
------------------
-
-While you are entitled to [your own
-opinion](http://lea.verou.me/2012/01/why-tabs-are-clearly-superior/) this
-project uses spaces instead of tabs. Even if you are geeky enough to care and
-like [Silicon Valley](https://www.youtube.com/watch?v=SsoOG6ZeyUI) you should
-know that [developers who use spaces make more
-money](https://stackoverflow.blog/2017/06/15/developers-use-spaces-make-money-use-tabs/).
-Also the use of spaces is strongly recommended by our beloved
-[pep8](https://www.Python.org/dev/peps/pep-0008/) standard.
-
-
-Commits/issues/merge requests
------------------------------
-
-### General guidelines
-
-Bug reports, features suggestions, code review etc must be handled via gitlab.
-The following [workflow](https://xkcd.com/1172/) is *strongly* encouraged:
-
-__Preparation phase:__
-
-As an issue reporter:
-* Create an issue in the Backlog.
-   * When creating an issue for a __feature request__, it is good practise to
-     describe who the issue is to be developed for, what should be achieved,
-     and ensure that implementation of the feature result in user value.
-     Good practise is to write a
-     [user story](https://www.mountaingoatsoftware.com/agile/user-stories),
-     e.g.:
-         1. _As a user at a neutron source, I would like to be able to compare_
-            _my acquired powder diffraction data with `icet` simulations, so that_
-            _I can explain my temperature dependent observations._
-         2. _As a developer, I would like to easily figure out how to best_
-            _contribute to the `icet` project._
-
-         For a discussion of good user stories, see
-     [discussion on Mountain Goat's homepage](https://www.mountaingoatsoftware.com/agile/user-stories)
-     It is also a good idea to describe how a succesful implementation can be
-     demonstrated. For example for the above user stories we can write:
-         1. DEMO: Demonstrate that a user via Python can;
-             1. Import neutron powder diffraction data
-             2. Carry out an `icet`/`mchammer` simulation at finite temperature
-             3. Calculate the scattering curves from the ensemble obtained from
-                the `icet`/`mchammer` simulation
-             4. Plot experimental data and simulation data in the same widget
-         2. DEMO: A potential developer, rather than an actual developer, can
-            1. find the contribution guidelines when pointed to the `icet`
-               homepage
-            2. Contribute successfully to the code (i.e. pass a review) after
-               having read the guidelines.
-
-   * When creating a __bug report__, it is important to describe how the bug can
-     be reproduced.
-* Invite comments from users, developers, and the [product
-  owner](https://en.wikipedia.org/wiki/Scrum_(software_development)#Product_owner)
-  and other stakeholders via the GitLab interface (e.g., use `@username` to
-  address specific team members in issue descriptions, messages, or discussions)
-* Review the input and make adjustments according to input. If the issue is
-  considered to take more than five days to complete, try to split it into
-  smaller ones, each with their own user story.
-* Once the issue is ready for development, the product owner and *only* the
-  product owner (or a person appointed by the product owner) can move the issue
-  to the `To Do` column. The product owner may choose to assign the issue to a
-  developer or let it be up for grasp for anyone interested.
-
-__Development phase:__
-
-As a developer:
-* If the issue is not already assigned to you, assign it to yourself. Move the
-  issue to the `Doing` column.
-* Create a branch from the issue via the GitLab interface. Ensure that other
-  people can see from the issue which branch you are working on.
-* Once the work on the issue has been completed *first* clean up your code and
-  review the [items that will be covered during review (see
-  below)](http://commadot.com/wtf-per-minute/). Make sure that the described
-  demonstration can be done, that there are unit tests (or regression tests in
-  case of bug fixes), and developer and user documentation.
-* Move the issue to the column `Review`. Reassign the issue to [*another*
-  developer](https://www.xkcd.com/1833/) or leave the issue unassigned and thus
-  up for grasp by *another* developer
-
-__Review phase:__
-
-As a reviewer:
-* If the issue up for review is not already assigned to you, assign it to
-  yourself.
-
-* The development related to the issue must be reviewed for
-  * sufficient test coverage.
-  * code passes all existing tests
-  * functionality
-  * performance
-  * code quality
-  * compliance to style guide
-  * addition of new unit tests
-  * demonstration is fulfilled
-
-* If the code review is successful the code is merged into master by the
-  reviewer. If the review is unsuccesful, the reviewer's comments are added as a
-  comment to the issue. Reviewer moves the issue back to the `To Do` column and
-  reassigns the issue to the developer.
-  The responsibility for making the code compliant resides with
-  the developer *not* the reviewer.
-For almost all issues, the time from creating a branch to merging into master
-should not exceed two weeks (one week is preferable).
-
-
-### Commit messages
-
-When writing commit messages, generating issues, or submitting merge requests,
-[write meaningful and concise commit messages](https://xkcd.com/1296/). Also
-please use the following prefixes to identify the category of your
-commit/issue/merge request.
-
-* BLD: change related to building
-* BUG: bug fix
-* DATA: general data
-* DOC: documentation
-* ENH: enhancement
-* MAINT: maintenance commit (refactoring, typos, etc.)
-* STY: style fix (whitespace, PEP8)
-* TST: addition or modification of tests
-
-The first line should not exceed 78 characters. If you require more
-space, insert an empty line after the "title" and add a longer message
-below. In this message, you should again limit yourself to 78
-characters *per* line.
-
-Hint: If you are using emacs you can use ``Meta``+``q``
-[shortcut](https://shortcutworld.com/en/Emacs/23.2.1/linux/all) to
-"reflow the text". In sublime you can achieve a similar effect by using
-``Alt``+``q`` (on Linux)/ ``Alt``+``Cmd``+``q`` (on MacOSX). In VIM, the command
-is gq.

hiphive.egg-info/dependency_links.txt

-

hiphive.egg-info/PKG-INFO

-Metadata-Version: 2.1
-Name: hiphive
-Version: 1.4
-Summary: High-order force constants for the masses
-Home-page: http://hiphive.materialsmodeling.org/
-Maintainer: The hiPhive developers team
-Maintainer-email: [e-mail]
-Platform: unix
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Topic :: Scientific/Engineering :: Physics
-License-File: LICENSE
-Requires-Dist: ase
-Requires-Dist: h5py
-Requires-Dist: numba>=0.55
-Requires-Dist: numpy>=1.18
-Requires-Dist: pandas
-Requires-Dist: scipy>=1.0.0
-Requires-Dist: scikit-learn
-Requires-Dist: spglib>=2.5
-Requires-Dist: sympy>=1.1
-Requires-Dist: trainstation>=0.2
-
-hiPhive
-=======
-
-**hiPhive** is a tool for efficiently extracting high-order force constants from atomistic simulations, most commonly density functional theory calculations.
-A detailed description of the functionality provided as well as an extensive tutorial can be found in the `user guide <https://hiphive.materialsmodeling.org/>`_.
-Complete examples of using **hiphive** for force constants extraction can be found in the `hiphive-examples repository <https://gitlab.com/materials-modeling/hiphive-examples/>`_.
-
-**hiPhive** is written in Python, which allows easy integration with countless first-principles codes and analysis tools accessible in Python, and allows for a simple and intuitive user interface.
-For example using the following snippet one can train a force constant potential:
-
-.. code-block:: python
-
-   cs = ClusterSpace(primitive_cell, cutoffs)
-   sc = StructureContainer(cs, list_of_training_structure)
-   opt = Optimizer(sc.get_fit_data())
-   opt.train()
-   fcp = ForceConstantPotential(cs, opt.parameters)
-
-after which it can be used in various ways, e.g., for generating phonon dispersions, computing phonon lifetimes, or running molecular dynamics simulations.
-
-For questions and help please use the `hiphive discussion forum on matsci.org <https://matsci.org/hiphive>`_.
-**hiPhive** and its development are hosted on `gitlab <https://gitlab.com/materials-modeling/hiphive>`_.
-
-
-Installation
-------------
-
-**hiPhive** can be installed via `pip`::
-
-    pip3 install hiphive
-
-or via `conda <https://anaconda.org/conda-forge/hiphive>`_::
-
-    conda install -c conda-forge hiphive
-
-**hiPhive** requires Python3 and invokes functionality from several external libraries including the
-`atomic simulation environment <https://wiki.fysik.dtu.dk/ase>`_,
-`scikit-learn <http://scikit-learn.org/>`_,
-`spglib <https://atztogo.github.io/spglib/>`_,
-`SymPy <http://www.sympy.org/en/index.html>`_, and
-`trainstation <https://trainstation.materialsmodeling.org/>`_.
-Please consult the `installation section of the user guide <https://hiphive.materialsmodeling.org/installation.html>`_ for details.
-
-
-Credits
--------
-
-**hiPhive** has been developed at the `Department of Physics <https://www.chalmers.se/en/departments/physics/Pages/default.aspx>`_ of `Chalmers University of Technology <https://www.chalmers.se/>`_ (Gothenburg, Sweden) in the `Condensed Matter and Materials Theory division <http://www.materialsmodeling.org>`_.
-
-When using **hiPhive** in your research please cite the following paper:
-
-| Fredrik Eriksson, Erik Fransson, and Paul Erhart
-| *The Hiphive Package for the Extraction of High‐Order Force Constants by Machine Learning*
-| Adv. Theory. Sim., 1800184 (2019)
-| `doi: 10.1002/adts.201800184 <https://doi.org/10.1002/adts.201800184>`_
-
-Please consult the `Credits <https://hiphive.materialsmodeling.org/credits>`_ page of the documentation for additional references.

hiphive.egg-info/requires.txt

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-numpy>=1.18
-pandas
-scipy>=1.0.0
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hiphive.egg-info/SOURCES.txt

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hiphive/calculators/.mypy_cache/3.6/abc.meta.json

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hiphive/calculators/.mypy_cache/3.6/builtins.meta.json

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hiphive/calculators/.mypy_cache/3.6/codecs.meta.json

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hiphive/calculator...ache/3.6/collections/__init__.meta.json

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hiphive/calculator...ypy_cache/3.6/collections/abc.data.json

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hiphive/calculator...ypy_cache/3.6/collections/abc.meta.json

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hiphive/calculators/.mypy_cache/3.6/copy.data.json

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hiphive/calculators/.mypy_cache/3.6/copy.meta.json

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hiphive/calculator..._cache/3.6/distutils/__init__.data.json

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hiphive/calculator..._cache/3.6/distutils/__init__.meta.json

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hiphive/calculator...y_cache/3.6/distutils/version.data.json

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hiphive/calculator...y_cache/3.6/distutils/version.meta.json

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hiphive/calculator...py_cache/3.6/hiphive/__init__.data.json

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hiphive/calculator...py_cache/3.6/hiphive/__init__.meta.json

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hiphive/calculator.../hiphive/calculators/__init__.data.json

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hiphive/calculator.../hiphive/calculators/__init__.meta.json

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hiphive/calculator...ve/calculators/ase_calculator.data.json

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hiphive/calculator...ve/calculators/ase_calculator.meta.json

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hiphive/calculator...iphive/calculators/numba_calc.data.json

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hiphive/calculator...iphive/calculators/numba_calc.meta.json

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hiphive/calculator...che/3.6/hiphive/cluster_space.data.json

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hiphive/calculator...che/3.6/hiphive/cluster_space.meta.json

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hiphive/calculators/.mypy_cache/3.6/hiphive/config.data.json

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hiphive/calculators/.mypy_cache/3.6/hiphive/config.meta.json

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hiphive/calculator...che/3.6/hiphive/core/__init__.data.json

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hiphive/calculator...che/3.6/hiphive/core/__init__.meta.json

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hiphive/calculator..._cache/3.6/hiphive/core/atoms.data.json

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hiphive/calculator..._cache/3.6/hiphive/core/atoms.meta.json

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hiphive/calculator...ve/core/cluster_space_builder.data.json

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hiphive/calculator...ve/core/cluster_space_builder.meta.json

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hiphive/calculator.../3.6/hiphive/core/constraints.data.json

-{".class": "MypyFile", "_fullname": "hiphive.core.constraints", "_name": null, "is_stub": false, "names": {".class": "SymbolTable", "SparseMatrix": {".class": "SymbolTableNode", "cross_ref": "hiphive.core.utilities.SparseMatrix", "kind": "Gdef"}, "__doc__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.constraints.__doc__", "name": "__doc__", "type": "builtins.str"}}, "__file__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.constraints.__file__", "name": "__file__", "type": "builtins.str"}}, "__name__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.constraints.__name__", "name": "__name__", "type": "builtins.str"}}, "__package__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.constraints.__package__", "name": "__package__", "type": "builtins.str"}}, "coo_matrix": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready", "is_suppressed_import"], "fullname": "hiphive.core.constraints.coo_matrix", "name": "coo_matrix", "type": {".class": "AnyType"}}}, "create_constraint_map": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "FuncDef", "arg_kinds": [0], "arg_names": ["cs"], "flags": [], "fullname": "hiphive.core.constraints.create_constraint_map", "name": "create_constraint_map", "type": null}}, "logger": {".class": "SymbolTableNode", "cross_ref": "hiphive.io.logging.logger", "kind": "Gdef"}, "np": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready", "is_suppressed_import"], "fullname": "hiphive.core.constraints.np", "name": "np", "type": {".class": "AnyType"}}}, "sympy": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready", "is_suppressed_import"], "fullname": "hiphive.core.constraints.sympy", "name": "sympy", "type": {".class": "AnyType"}}}}, "path": "/home/erhart/progs/hiphive/hiphive/core/constraints.py"}

hiphive/calculator.../3.6/hiphive/core/constraints.meta.json

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hiphive/calculator.../3.6/hiphive/core/core_config.data.json

-{".class": "MypyFile", "_fullname": "hiphive.core.core_config", "_name": null, "is_stub": false, "names": {".class": "SymbolTable", "__doc__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.core_config.__doc__", "name": "__doc__", "type": "builtins.str"}}, "__file__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.core_config.__file__", "name": "__file__", "type": "builtins.str"}}, "__name__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.core_config.__name__", "name": "__name__", "type": "builtins.str"}}, "__package__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.core_config.__package__", "name": "__package__", "type": "builtins.str"}}, "constraint_vectors_compress_mode": {".class": 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hiphive/calculator.../3.6/hiphive/core/core_config.meta.json

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hiphive/calculator...3.6/hiphive/core/eigentensors.data.json

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hiphive/calculator...3.6/hiphive/core/eigentensors.meta.json

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hiphive/calculator...3.6/hiphive/core/get_clusters.data.json

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hiphive/calculator...3.6/hiphive/core/get_clusters.meta.json

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hiphive/calculator...e/3.6/hiphive/core/get_orbits.data.json

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hiphive/calculator...e/3.6/hiphive/core/get_orbits.meta.json

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hiphive/calculator..._cache/3.6/hiphive/core/orbit.data.json

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hiphive/calculator..._cache/3.6/hiphive/core/orbit.meta.json

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hiphive/calculator...phive/core/orientation_family.data.json

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hiphive/calculator...phive/core/orientation_family.meta.json

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hiphive/calculator...iphive/core/relate_structures.data.json

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hiphive/calculator...iphive/core/relate_structures.meta.json

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hiphive/calculator...e/core/rotational_constraints.data.json

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hiphive/calculator...e/core/rotational_constraints.meta.json

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hiphive/calculator...ache/3.6/hiphive/core/tensors.data.json

-{".class": "MypyFile", "_fullname": "hiphive.core.tensors", "_name": null, "is_stub": false, "names": {".class": "SymbolTable", "__doc__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.tensors.__doc__", "name": "__doc__", "type": "builtins.str"}}, "__file__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.tensors.__file__", "name": "__file__", "type": "builtins.str"}}, "__name__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.tensors.__name__", "name": "__name__", "type": "builtins.str"}}, "__package__": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready"], "fullname": "hiphive.core.tensors.__package__", "name": "__package__", "type": "builtins.str"}}, "_paths": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": [], "fullname": "hiphive.core.tensors._paths", "name": "_paths", "type": {".class": "Instance", "args": [{".class": "AnyType"}, {".class": "AnyType"}], "type_ref": "builtins.dict"}}}, "np": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "Var", "flags": ["is_ready", "is_suppressed_import"], "fullname": "hiphive.core.tensors.np", "name": "np", "type": {".class": "AnyType"}}}, "rotate_tensor": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "FuncDef", "arg_kinds": [0, 0, 1], "arg_names": ["T", "R", "path"], "flags": [], "fullname": "hiphive.core.tensors.rotate_tensor", "name": "rotate_tensor", "type": null}}, "rotation_to_cart_coord": {".class": "SymbolTableNode", "kind": "Gdef", "node": {".class": "FuncDef", "arg_kinds": [0, 0], "arg_names": ["R", "cell"], "flags": [], "fullname": "hiphive.core.tensors.rotation_to_cart_coord", "name": "rotation_to_cart_coord", "type": null}}}, "path": "/home/erhart/progs/hiphive/hiphive/core/tensors.py"}

hiphive/calculator...ache/3.6/hiphive/core/tensors.meta.json

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hiphive/calculator...he/3.6/hiphive/core/utilities.data.json

-{".class": "MypyFile", "_fullname": "hiphive.core.utilities", "_name": null, "is_stub": false, "names": {".class": "SymbolTable", "BiMap": {".class": "SymbolTableNode", "kind": "Gdef", "module_public": false, "node": {".class": "TypeInfo", "_promote": null, "abstract_attributes": [], "bases": ["builtins.object"], "declared_metaclass": null, "defn": {".class": "ClassDef", "fullname": "hiphive.core.utilities.BiMap", "name": "BiMap", "type_vars": []}, "flags": [], "fullname": "hiphive.core.utilities.BiMap", "metaclass_type": null, "module_name": "hiphive.core.utilities", "names": {".class": "SymbolTable", "__contains__": {".class": "SymbolTableNode", "kind": "Mdef", "node": {".class": "FuncDef", "arg_kinds": [0, 0], "arg_names": ["self", "value"], "flags": [], "fullname": "hiphive.core.utilities.BiMap.__contains__", "name": "__contains__", "type": null}}, "__getitem__": {".class": "SymbolTableNode", "kind": "Mdef", "node": {".class": "FuncDef", "arg_kinds": [0, 0], "arg_names": ["self", 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hiphive/calculator...he/3.6/hiphive/core/utilities.meta.json

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hiphive/calculator...ypy_cache/3.6/hiphive/cutoffs.data.json

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hiphive/calculator...ypy_cache/3.6/hiphive/cutoffs.meta.json

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hiphive/calculator.../hiphive/force_constant_model.data.json

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hiphive/calculator.../hiphive/force_constant_model.meta.json

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hiphive/calculator...hive/force_constant_potential.data.json

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hiphive/calculator..._cache/3.6/hiphive/io/logging.data.json

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hiphive/calculator..._cache/3.6/hiphive/io/logging.meta.json

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hiphive/calculator..._cache/3.6/hiphive/io/phonopy.data.json

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hiphive/calculator..._cache/3.6/hiphive/io/phonopy.meta.json

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hiphive/calculator...iphive/io/pretty_table_prints.data.json

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hiphive/calculator...iphive/io/pretty_table_prints.meta.json

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hiphive/calculator...6/hiphive/io/read_write_files.data.json

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hiphive/calculator...6/hiphive/io/read_write_files.meta.json

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hiphive/calculator...cache/3.6/hiphive/io/shengBTE.data.json

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hiphive/calculator...cache/3.6/hiphive/io/shengBTE.meta.json

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hiphive/calculator...6/hiphive/structure_container.data.json

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hiphive/calculators/.mypy_cache/3.6/string.meta.json

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hiphive/calculators/.mypy_cache/3.6/sys.data.json

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hiphive/calculators/.mypy_cache/3.6/tarfile.meta.json

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hiphive/fitting/.m...ache/3.6/collections/__init__.meta.json

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hiphive/fitting/.mypy_cache/3.6/collections/abc.data.json

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hiphive/fitting/.mypy_cache/3.6/copy.data.json

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hiphive/fitting/.mypy_cache/3.6/hiphive/__init__.data.json

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hiphive/fitting/.m...iphive/calculators/numba_calc.meta.json

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hiphive/fitting/.m...ve/core/cluster_space_builder.data.json

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hiphive/fitting/.m...ve/core/cluster_space_builder.meta.json

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hiphive/fitting/.m.../3.6/hiphive/core/constraints.data.json

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hiphive/fitting/.m.../3.6/hiphive/core/constraints.meta.json

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hiphive/fitting/.m.../3.6/hiphive/core/core_config.data.json

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hiphive/fitting/.m.../3.6/hiphive/core/core_config.meta.json

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hiphive/fitting/.m...3.6/hiphive/core/eigentensors.data.json

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hiphive/fitting/.m...3.6/hiphive/core/eigentensors.meta.json

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hiphive/fitting/.m...3.6/hiphive/core/get_clusters.data.json

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hiphive/fitting/.m...3.6/hiphive/core/get_clusters.meta.json

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hiphive/fitting/.m...e/3.6/hiphive/core/get_orbits.data.json

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hiphive/fitting/.m...e/3.6/hiphive/core/get_orbits.meta.json

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hiphive/fitting/.mypy_cache/3.6/hiphive/core/orbit.data.json

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hiphive/fitting/.m...6/hiphive/io/read_write_files.meta.json

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hiphive/fitting/.mypy_cache/3.6/math.meta.json

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hiphive/fitting/.mypy_cache/3.6/mypy_extensions.data.json

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hiphive/fitting/.mypy_cache/3.6/mypy_extensions.meta.json

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hiphive/fitting/.mypy_cache/3.6/os/__init__.meta.json

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hiphive/fitting/.mypy_cache/3.6/os/path.data.json

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hiphive/fitting/.mypy_cache/3.6/warnings.meta.json

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MANIFEST.in

-recursive-include hiphive *
-
-include CONTRIBUTING.md
-include LICENSE
-include MANIFEST.in
-include README.rst
-include setup.py
-
-prune tests
-prune **/__pycache__ 
-prune **/*ipynb_checkpoints

setup.py

-#!/usr/bin/env python3
-
-import re
-import sys
-from setuptools import setup, find_packages
-
-if sys.version_info < (3, 8, 0, 'final', 0):
-    raise SystemExit('Python 3.8 or later is required!')
-
-with open('README.rst', encoding='utf-8') as fd:
-    long_description = fd.read()
-
-with open('hiphive/__init__.py') as fd:
-    lines = '\n'.join(fd.readlines())
-
-version = re.search("__version__ = '(.*)'", lines).group(1)
-maintainer = re.search("__maintainer__ = '(.*)'", lines).group(1)
-maintainer_email = re.search("__maintainer_email__ = '(.*)'", lines).group(1)
-url = re.search("__url__ = '(.*)'", lines).group(1)
-license = re.search("__license__ = '(.*)'", lines).group(1)
-description = re.search("__description__ = '(.*)'", lines).group(1)
-
-# PyPI name
-name = 'hiphive'
-
-setup(name=name,
-      version=version,
-      description=description,
-      long_description=long_description,
-      url=url,
-      maintainer=maintainer,
-      maintainer_email=maintainer_email,
-      platforms=['unix'],
-      install_requires=['ase',
-                        'h5py',
-                        'numba>=0.55',
-                        'numpy>=1.18',  # imposed by numba
-                        'pandas',
-                        'scipy>=1.0.0',  # imposed by numba
-                        'scikit-learn',
-                        'spglib>=2.5',
-                        'sympy>=1.1',
-                        'trainstation>=0.2'],
-      packages=find_packages(),
-      classifiers=[
-          'Development Status :: 5 - Production/Stable',
-          'Operating System :: OS Independent',
-          'Programming Language :: Python :: 3 :: Only',
-          'Programming Language :: Python :: 3',
-          'Programming Language :: Python :: 3.8',
-          'Programming Language :: Python :: 3.9',
-          'Programming Language :: Python :: 3.10',
-          'Programming Language :: Python :: 3.11',
-          'Programming Language :: Python :: 3.12',
-          'Intended Audience :: Science/Research',
-          f'License :: OSI Approved :: {license}',
-          'Topic :: Scientific/Engineering :: Physics'])

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Worsened metrics

Total package byte prevSize

283021

-94.6%

Number of package files

52

-82.78%

Lines of code

6359

-73.56%