diff --git a/NOTES.org b/NOTES.org deleted file mode 100644 index e8d3f632..00000000 --- a/NOTES.org +++ /dev/null @@ -1,46 +0,0 @@ -* Install for development - #+begin_src sh - pip install --no-deps -e . - #+end_src - -* creating enviroments for development - - create the base runtime enviroment with - #+begin_src sh - conda env create -n 'env name' -f environment.yml - #+end_src - - To add development stuff do - #+begin_src sh - conda env update -n 'env name' -f environment-dev.yml -f 'optional-recipes' - #+end_src - - -* Using pre-commit - see https://pre-commit.com/ - - pre-commit adds hooks to autocheck - - #+begin_src sh - # install - conda install -n env-name pre-commit - - # init - pre-commit install - - # run on all files - pre-commit run --all-files - - # run on staged - pre-commit run - #+end_src - -* Testing - #+begin_src sh - # run all tests - pytest -x -v --runslow - - # omit slow tests - pytest -x -v - - #+end_src diff --git a/README-1.md b/README-1.md deleted file mode 100644 index 234eed32..00000000 --- a/README-1.md +++ /dev/null @@ -1,81 +0,0 @@ -# `thermoextrap`: Thermodynamic Extrapolation/Interpolation Library -This repository contains code used and described in: - -Monroe, J. I.; Hatch, H. W.; Mahynski, N. A.; Shell, M. S.; Shen, V. K. Extrapolation and Interpolation Strategies for Efficiently Estimating Structural Observables as a Function of Temperature and Density. J. Chem. Phys. 2020, 153 (14), 144101. https://doi.org/10.1063/5.0014282. - -Monroe, J. I.; Krekelberg, W. P.; McDannald, A.; Shen, V. K. Leveraging Uncertainty Estiamtes and Derivative Information in Gaussian Process Regression for Expediated Data Collection in Molecular Simulations. In preparation. - -# Overview - -If you find this code useful in producing published works, please provide an appropriate citation. -Note that the second citation is focused on adding features that make use of GPR models based on derivative information produced by the core code base. -For now, the GPR code, along with more information, may be found under docs/notebooks/gpr. -In a future release, we expect this to be fully integrated into the code base rather than a standalone module. - -Code included here can be used to perform thermodynamic extrapolation and -interpolation of observables calculated from molecular simulations. This allows -for more efficient use of simulation data for calculating how observables change -with simulation conditions, including temperature, density, pressure, chemical -potential, or force field parameters. Users are highly encourage to work through -the Jupyter Notebook tutorial (Ideal_Gas_Example.ipynb) presenting examples for -a variety of different observable functional forms. We only guarantee that this -code is functional for the test cases we present here or for which it has -previously been applied Additionally, the code may be in continuous development -at any time. Use at your own risk and always check to make sure the produced -results make sense. If bugs are found, please report them. If specific features -would be helpful just let us know and we will be happy to work with you to come -up with a solution. - - -# Status - -This package is actively used by the author. Please feel free to create a pull request for wanted features and suggestions! - - -# Installation - -`thermoextrap` may be installed with either (recommended) -```bash -conda install -c wpk-nist thermoextrap -``` -or -```bash -pip install thermoextrap -``` - -If you use pip, then you can include additional dependencies using -```bash -pip install thermoextrap[all] -``` - -If you install `thermoextrap` with conda, there are additional optional dependencies that take some care for installation. We recommend installing the following via `pip`, as the versions on the conda/conda-forge channels are often a bit old. -```bash -pip install tensorflow tensorflow-probability gpflow -``` - -# Contact -Questions may be addressed to Bill Krekelberg at william.krekelberg@nist.gov or Jacob Monroe at jacob.monroe@uark.edu. - - -# Documentation - -Documentation can be found at -For a deeper dive, look at the [documentation](https://pages.nist.gov/thermo-extrap/) - - -## License - -This is free software. See [LICENSE](LICENSE). - -## Related work - -This package extensively uses the ``cmomy`` package to handle central comoments. See [here](https://github.com/usnistgov/cmomy). - - -## Credits - -This package was created with -[Cookiecutter](https://github.com/audreyr/cookiecutter) and the -[wpk-nist-gov/cookiecutter-pypackage](https://github.com/wpk-nist-gov/cookiecutter-pypackage) -Project template forked from -[audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage).