├── .codecov.yml ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ └── gh-ci.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .pylintrc ├── AUTHORS.md ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── devtools └── conda-envs │ └── test_env.yaml ├── docs ├── Makefile ├── README.md ├── make.bat ├── requirements.yaml ├── source │ ├── _static │ │ └── README.md │ ├── _templates │ │ └── README.md │ ├── api.rst │ ├── api │ │ ├── velocityautocorr.rst │ │ └── viscosity.rst │ ├── conf.py │ ├── getting_started.ipynb │ └── index.rst └── tutorials │ ├── helfand_dev_toy_system.ipynb │ ├── vacf_doc_example.ipynb │ ├── vacf_testing_examples.ipynb │ └── viscosity_early_demo.ipynb ├── pyproject.toml ├── readthedocs.yaml ├── setup.cfg ├── setup.py ├── transport_analysis ├── __init__.py ├── _version.py ├── data │ ├── README.md │ ├── __init__.py │ ├── ethylene_carbonate │ │ ├── topology.pdb │ │ └── trajectory.trr │ ├── files.py │ └── mda.txt ├── due.py ├── tests │ ├── __init__.py │ ├── conftest.py │ ├── test_transport_analysis.py │ ├── test_velocityautocorr.py │ ├── test_viscosity.py │ └── utils.py ├── velocityautocorr.py └── viscosity.py └── versioneer.py /.codecov.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/.codecov.yml -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | transport_analysis/_version.py export-subst 2 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/.github/ISSUE_TEMPLATE/bug_report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/.github/ISSUE_TEMPLATE/feature_request.md -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/.github/PULL_REQUEST_TEMPLATE.md -------------------------------------------------------------------------------- /.github/workflows/gh-ci.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/.github/workflows/gh-ci.yaml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /.pylintrc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/.pylintrc -------------------------------------------------------------------------------- /AUTHORS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/AUTHORS.md -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/README.md -------------------------------------------------------------------------------- /devtools/conda-envs/test_env.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/devtools/conda-envs/test_env.yaml -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/README.md -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/requirements.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/requirements.yaml -------------------------------------------------------------------------------- /docs/source/_static/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/source/_static/README.md -------------------------------------------------------------------------------- /docs/source/_templates/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/source/_templates/README.md -------------------------------------------------------------------------------- /docs/source/api.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/source/api.rst -------------------------------------------------------------------------------- /docs/source/api/velocityautocorr.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/source/api/velocityautocorr.rst -------------------------------------------------------------------------------- /docs/source/api/viscosity.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/source/api/viscosity.rst -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/getting_started.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/source/getting_started.ipynb -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/tutorials/helfand_dev_toy_system.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/tutorials/helfand_dev_toy_system.ipynb -------------------------------------------------------------------------------- /docs/tutorials/vacf_doc_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/tutorials/vacf_doc_example.ipynb -------------------------------------------------------------------------------- /docs/tutorials/vacf_testing_examples.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/tutorials/vacf_testing_examples.ipynb -------------------------------------------------------------------------------- /docs/tutorials/viscosity_early_demo.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/docs/tutorials/viscosity_early_demo.ipynb -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/pyproject.toml -------------------------------------------------------------------------------- /readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/readthedocs.yaml -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/setup.cfg -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/setup.py -------------------------------------------------------------------------------- /transport_analysis/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/__init__.py -------------------------------------------------------------------------------- /transport_analysis/_version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/_version.py -------------------------------------------------------------------------------- /transport_analysis/data/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/data/README.md -------------------------------------------------------------------------------- /transport_analysis/data/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /transport_analysis/data/ethylene_carbonate/topology.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/data/ethylene_carbonate/topology.pdb -------------------------------------------------------------------------------- /transport_analysis/data/ethylene_carbonate/trajectory.trr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/data/ethylene_carbonate/trajectory.trr -------------------------------------------------------------------------------- /transport_analysis/data/files.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/data/files.py -------------------------------------------------------------------------------- /transport_analysis/data/mda.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/data/mda.txt -------------------------------------------------------------------------------- /transport_analysis/due.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/due.py -------------------------------------------------------------------------------- /transport_analysis/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /transport_analysis/tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/tests/conftest.py -------------------------------------------------------------------------------- /transport_analysis/tests/test_transport_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/tests/test_transport_analysis.py -------------------------------------------------------------------------------- /transport_analysis/tests/test_velocityautocorr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/tests/test_velocityautocorr.py -------------------------------------------------------------------------------- /transport_analysis/tests/test_viscosity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/tests/test_viscosity.py -------------------------------------------------------------------------------- /transport_analysis/tests/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/tests/utils.py -------------------------------------------------------------------------------- /transport_analysis/velocityautocorr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/velocityautocorr.py -------------------------------------------------------------------------------- /transport_analysis/viscosity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/transport_analysis/viscosity.py -------------------------------------------------------------------------------- /versioneer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MDAnalysis/transport-analysis/HEAD/versioneer.py --------------------------------------------------------------------------------