├── .gitattributes ├── .gitignore ├── .gitlab-ci.yml ├── AUTHORS.rst ├── CHANGELOG.rst ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── aux ├── cadishi.bash ├── json2yaml.py ├── md_to_cadishi.py └── yaml2json.py ├── cadishi ├── __init__.py ├── base.py ├── data │ └── histograms_template.yaml ├── dict_util.py ├── dictfs.py ├── exe │ ├── __init__.py │ ├── check_parameter_file.py │ ├── cli.py │ ├── histograms.py │ ├── histograms_example.py │ ├── histograms_legacy.py │ ├── merge.py │ ├── random_trajectory.py │ └── unpack.py ├── h5pickle.py ├── io │ ├── __init__.py │ ├── ascii.py │ ├── dummy.py │ ├── hdf5.py │ ├── md.py │ └── pickel.py ├── kernel │ ├── Makefile │ ├── README │ ├── __init__.py │ ├── c_cudh.pyx │ ├── c_cudh_functions.cu │ ├── c_dist.pyx │ ├── c_pydh.pyx │ ├── c_pydh_functions.cc │ ├── common.py │ ├── cudh.py │ ├── dist.py │ ├── include │ │ ├── c_cudh.h │ │ ├── c_pydh.h │ │ ├── common.h │ │ ├── common.hpp │ │ ├── config.h │ │ ├── config.hpp │ │ ├── cuda_exceptions.hpp │ │ ├── cudh.h │ │ ├── exceptions.hpp │ │ └── pydh.h │ ├── pydh.py │ └── unit_tests.cc ├── pbc.py ├── tests │ ├── __init__.py │ ├── data │ │ └── trajectory.h5 │ ├── minimal_driver.py │ ├── perf_kernel.py │ ├── run_tests.sh │ ├── test_base_container.py │ ├── test_dict_util.py │ ├── test_dictfs.py │ ├── test_h5pickle.py │ ├── test_pydh_cudh.py │ ├── test_pydh_dist.py │ └── test_util_generate_random.py ├── util.py ├── version.py └── worker.py ├── conda ├── README ├── conda_build.sh └── recipe │ ├── build.sh │ └── meta.yaml ├── doc ├── Makefile ├── README ├── _static │ └── __empty__ ├── _templates │ └── __empty__ ├── conf.py ├── executables.rst ├── html │ ├── .buildinfo │ ├── _downloads │ │ ├── input_example.py │ │ └── plot_hdf5_data.py │ ├── _images │ │ └── cadishi.png │ ├── _modules │ │ ├── cadishi │ │ │ ├── base.html │ │ │ ├── dict_util.html │ │ │ ├── dictfs.html │ │ │ ├── exe │ │ │ │ ├── cli.html │ │ │ │ ├── histograms.html │ │ │ │ ├── json2yaml.html │ │ │ │ ├── unpack.html │ │ │ │ └── yaml2json.html │ │ │ ├── h5pickle.html │ │ │ ├── io │ │ │ │ ├── ascii.html │ │ │ │ ├── dummy.html │ │ │ │ ├── hdf5.html │ │ │ │ └── pickel.html │ │ │ ├── kernel │ │ │ │ ├── common.html │ │ │ │ ├── cudh.html │ │ │ │ ├── dist.html │ │ │ │ └── pydh.html │ │ │ ├── util.html │ │ │ └── version.html │ │ └── index.html │ ├── _sources │ │ ├── executables.rst.txt │ │ ├── index.rst.txt │ │ ├── kernel.rst.txt │ │ └── modules.rst.txt │ ├── _static │ │ ├── __empty__ │ │ ├── ajax-loader.gif │ │ ├── basic.css │ │ ├── classic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── contents.png │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── jquery-3.1.0.js │ │ ├── jquery.js │ │ ├── minus.png │ │ ├── navigation.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── sidebar.js │ │ ├── sphinxdoc.css │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ ├── 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