imdclient 0.1.2__py3-none-any.whl → 0.1.4__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- imdclient/{IMDREADER.py → IMD.py} +5 -4
- imdclient/IMDClient.py +118 -15
- imdclient/IMDProtocol.py +1 -0
- imdclient/data/gromacs/md/gromacs_v3_nst1.mdp +3 -3
- imdclient/data/gromacs/md/gromacs_v3_nst8.mdp +58 -0
- imdclient/data/lammps/md/{lammps_v3.in → lammps_v3_nst_1.in} +3 -3
- imdclient/data/lammps/md/lammps_v3_nst_8.in +71 -0
- imdclient/data/namd/md/{namd_v3.namd → namd_v3_nst_1.namd} +17 -5
- imdclient/data/namd/md/namd_v3_nst_8.namd +59 -0
- imdclient/tests/base.py +179 -45
- imdclient/tests/conftest.py +0 -39
- imdclient/tests/datafiles.py +33 -10
- imdclient/tests/docker_testing/docker.md +25 -0
- imdclient/tests/hpc_testing/gromacs/README.md +112 -0
- imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.mdp +58 -0
- imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.top +11764 -0
- imdclient/tests/hpc_testing/gromacs/struct.gro +21151 -0
- imdclient/tests/hpc_testing/gromacs/validate_gmx.sh +90 -0
- imdclient/tests/hpc_testing/lammps/README.md +62 -0
- imdclient/tests/hpc_testing/lammps/lammps_v3_nst_1.in +71 -0
- imdclient/tests/hpc_testing/lammps/topology_after_min.data +8022 -0
- imdclient/tests/hpc_testing/lammps/validate_lmp.sh +66 -0
- imdclient/tests/hpc_testing/namd/README.md +73 -0
- imdclient/tests/hpc_testing/namd/alanin.params +402 -0
- imdclient/tests/hpc_testing/namd/alanin.pdb +77 -0
- imdclient/tests/hpc_testing/namd/alanin.psf +206 -0
- imdclient/tests/hpc_testing/namd/namd_v3_nst_1.namd +59 -0
- imdclient/tests/hpc_testing/namd/validate_namd.sh +71 -0
- imdclient/tests/server.py +2 -11
- imdclient/tests/test_gromacs.py +32 -10
- imdclient/tests/test_imdclient.py +69 -0
- imdclient/tests/test_imdreader.py +74 -1
- imdclient/tests/test_lammps.py +57 -12
- imdclient/tests/test_manual.py +223 -65
- imdclient/tests/test_namd.py +101 -14
- imdclient/tests/test_stream_analysis.py +1 -1
- imdclient/tests/utils.py +0 -1
- imdclient-0.1.4.dist-info/LICENSE +5 -0
- imdclient-0.1.4.dist-info/METADATA +132 -0
- imdclient-0.1.4.dist-info/RECORD +57 -0
- {imdclient-0.1.2.dist-info → imdclient-0.1.4.dist-info}/WHEEL +1 -1
- imdclient/data/gromacs/md/gromacs_v3_nst1.tpr +0 -0
- imdclient/data/gromacs/md/gromacs_v3_nst1.trr +0 -0
- imdclient/data/lammps/md/lammps_trj.h5md +0 -0
- imdclient/data/namd/md/alanin.dcd +0 -0
- imdclient-0.1.2.dist-info/LICENSE +0 -674
- imdclient-0.1.2.dist-info/METADATA +0 -795
- imdclient-0.1.2.dist-info/RECORD +0 -42
- {imdclient-0.1.2.dist-info → imdclient-0.1.4.dist-info}/AUTHORS.md +0 -0
- {imdclient-0.1.2.dist-info → imdclient-0.1.4.dist-info}/top_level.txt +0 -0
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Metadata-Version: 2.1
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Name: imdclient
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Version: 0.1.4
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Summary: Receiver for IMD v2 and v3 data from simulation engines like Gromacs, LAMMPS, and NAMD
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Author-email: Lawson <ljwoods2@asu.edu>
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Maintainer-email: Lawson <ljwoods2@asu.edu>
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License: Copyright 2024 Lawson Woods
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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:
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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Keywords: molecular simulations
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Requires-Python: >=3.9
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Description-Content-Type: text/markdown
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License-File: LICENSE
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License-File: AUTHORS.md
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Requires-Dist: MDAnalysis>=2.7.0
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Provides-Extra: test
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Requires-Dist: pytest>=6.0; extra == "test"
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Requires-Dist: pytest-xdist>=2.5; extra == "test"
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Requires-Dist: pytest-cov>=3.0; extra == "test"
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Requires-Dist: MDAnalysisTests>=2.7.0; extra == "test"
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Requires-Dist: docker-py; extra == "test"
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Provides-Extra: doc
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Requires-Dist: sphinx; extra == "doc"
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Requires-Dist: sphinx_rtd_theme; extra == "doc"
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IMDClient
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==============================
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[//]: # (Badges)
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| **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since] [![Documentation Status][badge_docs]][url_docs]|
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| :----------------- | :------- |
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| **Status** | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov] |
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| **Community** | [![License: MIT][badge_license]][url_license] [![Powered by MDAnalysis][badge_mda]][url_mda]|
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[badge_actions]: https://github.com/becksteinlab/imdclient/actions/workflows/gh-ci.yaml/badge.svg
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[badge_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main/graph/badge.svg
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[badge_commits_since]: https://img.shields.io/github/commits-since/becksteinlab/imdclient/latest
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[badge_docs]: https://readthedocs.org/projects/imdclient/badge/?version=latest
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[badge_license]: https://img.shields.io/badge/License-MIT-blue.svg
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[badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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[badge_release]: https://img.shields.io/github/release-pre/becksteinlab/imdclient.svg
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[url_actions]: https://github.com/becksteinlab/imdclient/actions?query=branch%3Amain+workflow%3Agh-ci
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[url_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main
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[url_docs]: https://imdclient.readthedocs.io/en/latest/?badge=latest
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[url_latest_release]: https://github.com/becksteinlab/imdclient/releases
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[url_license]: https://opensource.org/license/mit
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[url_mda]: https://www.mdanalysis.org
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Receiver for [IMDv3 protocol](https://imdclient.readthedocs.io/en/latest/protocol_v3.html) from simulation engines like Gromacs, LAMMPS, and NAMD.
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IMDClient is bound by a [Code of Conduct](https://github.com/becksteinlab/imdreader/blob/main/CODE_OF_CONDUCT.md).
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### Installation
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IMDClient is available via PyPi and can be installed with pip:
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```bash
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pip install imdclient
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```
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To build IMDClient from source,
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we highly recommend using virtual environments.
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If possible, we strongly recommend that you use
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[Anaconda](https://docs.conda.io/en/latest/) as your package manager.
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Below we provide instructions both for `conda` and
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for `pip`.
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#### With conda
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Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
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Create a virtual environment and activate it:
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```
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conda create --name imdclient
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conda activate imdclient
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```
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<!-- Install the development and documentation dependencies:
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```
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conda env update --name imdreader --file devtools/conda-envs/test_env.yaml
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conda env update --name imdreader --file docs/requirements.yaml
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``` -->
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Build this package from source:
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```
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pip install -e .
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```
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If you want to update your dependencies (which can be risky!), run:
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```
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conda update --all
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```
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And when you are finished, you can exit the virtual environment with:
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```
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conda deactivate
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```
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#### With pip
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To build the package from source, run:
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```
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pip install .
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```
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If you want to create a development environment, install
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the dependencies required for tests and docs with:
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```
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pip install ".[test,doc]"
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```
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### Copyright
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The IMDClient source code is hosted at https://github.com/becksteinlab/imdclient
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and is available under the MIT license (see the file [LICENSE](https://github.com/becksteinlab/imdclient/blob/main/LICENSE)).
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Copyright (c) 2024, Lawson
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#### Acknowledgements
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Project based on the
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[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.
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<!-- Please cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using IMDReader in published work. -->
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imdclient/IMD.py,sha256=QkYU0OUxrrjKVxumeEju3Jcewkj46K7DBk_J3vO5m1E,3842
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imdclient/IMDClient.py,sha256=9AMKniQaCNDgWO2esF_SXEgdf3fp_4pcZ5fUNpzewcY,34349
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imdclient/IMDProtocol.py,sha256=wePIuFlKGIULWXHJPCmzRVWBGlBiyDOJXgjxyQb7ssY,4063
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imdclient/__init__.py,sha256=Pa5h6Fjyvyxf3ECzO43pcmLm3Vk-vOuEb5Gi6TDWhds,339
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imdclient/backends.py,sha256=QmHjwYbmvFVHz-uFgpSOA0UmZTZqiMGqWMO7B8wr1zs,10368
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imdclient/results.py,sha256=2MyjFdQMW7BfiHhG5X6wQwMVrF_0mKYFnv907lgLMas,9920
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imdclient/streamanalysis.py,sha256=Qq0h_WPO-wb0_lP8jTRHe0HX7UDZNgJFA6C4PZdUmK8,38385
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imdclient/streambase.py,sha256=rwhdyC2V3_9pSz_6rNwjSc4MNToI9S318OH7AH0arHA,6176
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imdclient/utils.py,sha256=VWxk4vQ6hzxoYRu-8Ge8fJG-EitJwgJR93wOWCvzY-0,3308
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imdclient/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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imdclient/data/gromacs/md/gromacs_struct.gro,sha256=kt4vE10iF_1RbeyTogmYmIY9yKJacofrzNT-hPHGyL8,1459301
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imdclient/data/gromacs/md/gromacs_v3.top,sha256=AXFEDjvz5Qqq-VECffimdeEvhD6L-H0SFPILW-6Sums,348329
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imdclient/data/gromacs/md/gromacs_v3_nst1.mdp,sha256=VFAS3uM0oifxuX5WLz85vvRlwmzR-BhQbMCzjweaJcU,3040
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imdclient/data/gromacs/md/gromacs_v3_nst8.mdp,sha256=CYz5gKFApeJMrJyCmd3kgPFzRjahgaLRNyIomuVyY0w,3053
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imdclient/data/lammps/md/lammps_topol.data,sha256=u4osSkn7yG9p2Egz9ovLW4eVmdaThPxeZ0L218J3-V0,172948
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imdclient/data/lammps/md/lammps_v3_nst_1.in,sha256=AcvkgNNDtTkB7RlFZwpUEKKp6W_7o_UFgrX_LwC3HXI,2586
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imdclient/data/lammps/md/lammps_v3_nst_8.in,sha256=gpdAp1dDhJbG06wZVDtBGUs6biJNz8EStV341S0uJ2s,2594
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imdclient/data/namd/md/alanin.params,sha256=zWw-UfqYD3-xpdA_8R8T-0OYBbUM6py7jKAq_uyu8HE,17389
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imdclient/data/namd/md/alanin.pdb,sha256=eccDD-ledUXjbB2s1fxY40lmAKWWDpxkxANbsOkqjHc,5615
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imdclient/data/namd/md/alanin.psf,sha256=VhCZeGFhpUa8yN5iEL19zlVjqIJg2JIdPzhazpRForY,12953
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imdclient/data/namd/md/namd_v3_nst_1.namd,sha256=EZU7PGyytZdGixrBnmpAcwonN0n_JTk9U-Q82FoqO7k,983
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imdclient/data/namd/md/namd_v3_nst_8.namd,sha256=WJmwj0E4nJVhYRr_ALBlTax6kyNkdRE1krPsmY-QFLM,984
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imdclient/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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imdclient/tests/base.py,sha256=gbu39CpII5mc9-rDSEZoQNv8JmNFwW1vviYkfOQmbD4,8043
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imdclient/tests/conftest.py,sha256=Xqz9ZjBXpnViSryR4CXjJdOyqZ1MOCAjuA0sRVwAVfk,31
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imdclient/tests/datafiles.py,sha256=0wAg1q5oB3Ve6XnSfnB6oGzbh7JvVpSGpj-ba0H2Z5w,1515
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imdclient/tests/server.py,sha256=x3IY5FDDS4z99_UyuuRe56CHd_XtfINJRolGbkNyOl8,6629
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imdclient/tests/test_gromacs.py,sha256=rXkabRB40xX7LRdF2_nrPgeNpfFF9J7m-5LeRNMA5TM,1454
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imdclient/tests/test_imdclient.py,sha256=FQwuNbJwOLgK33v5mFmbhaGaPSqXA8byTWFtYCpYyJo,7716
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imdclient/tests/test_imdreader.py,sha256=-DEFcwef87CZPXut45I2gpZPg_K3XXPFFreBqsW3ciE,25433
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imdclient/tests/test_lammps.py,sha256=hwZBVvhclN1mtPuYLyODUaWjlaZaAkhAFqX-mpQvWk4,2244
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imdclient/tests/test_manual.py,sha256=t5NeT1oPit9EMGxH4yG7hxnKQ24UEzZtR-vC1WOQAkc,8118
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imdclient/tests/test_stream_analysis.py,sha256=qqsm_Bv8qCXyNwgdSKZM8bLyiEO5nlpqJ-XtEn-YKew,1723
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imdclient/tests/utils.py,sha256=_x1gVQ3AmhaMurpcEPLKBG5BTGu4ZMy5EGUpr0P6D6g,854
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imdclient/tests/docker_testing/docker.md,sha256=SxHEpSA1mXAvzYzsxL0EesGqPCVC8qdRMbvxGz5R0Yo,840
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imdclient/tests/hpc_testing/gromacs/README.md,sha256=2SHVtIu5EyS8bwCMeWTZFgQoh1mmOwcBFjijzYDkj6k,2847
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imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.mdp,sha256=BZl554WoHVi0bQq-Eb8UeYrdfum2TBHhtWFj4DxReCY,3050
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imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.top,sha256=AXFEDjvz5Qqq-VECffimdeEvhD6L-H0SFPILW-6Sums,348329
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imdclient/tests/hpc_testing/gromacs/struct.gro,sha256=uT_Je8Jc37-o8gfkhFRH0PWcg3LOGkQj4ErSCkLMk00,1459301
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imdclient/tests/hpc_testing/gromacs/validate_gmx.sh,sha256=dszRgiWu-_9b4DxQP4u5x4Hi1liedjMG2YXQNURZQsQ,1938
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