diff --git a/setup.cfg b/.flake8 similarity index 68% rename from setup.cfg rename to .flake8 index 9ed04616..d86ebfb1 100644 --- a/setup.cfg +++ b/.flake8 @@ -1,6 +1,3 @@ -[aliases] -test=pytest - [flake8] max-complexity = 15 max-line-length = 127 diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml new file mode 100644 index 00000000..6f7b54db --- /dev/null +++ b/.github/workflows/build.yaml @@ -0,0 +1,55 @@ +name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI +# This follows https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/ + +on: + push: + branches: + - "master" + +jobs: + build: + name: Build distribution 📦 + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.x" + - name: Install pypa/build + run: >- + python3 -m + pip install + build + --user + - name: Build a binary wheel and a source tarball + run: python3 -m build + - name: Store the distribution packages + uses: actions/upload-artifact@v3 + with: + name: python-package-distributions + path: dist/ + publish-to-testpypi: + name: Publish Python 🐍 distribution 📦 to TestPyPI + needs: + - build + runs-on: ubuntu-latest + + environment: + name: testpypi + url: https://test.pypi.org/p/molSimplify + + permissions: + id-token: write # IMPORTANT: mandatory for trusted publishing + + steps: + - name: Download all the dists + uses: actions/download-artifact@v3 + with: + name: python-package-distributions + path: dist/ + - name: Publish distribution 📦 to TestPyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/CI.yaml b/.github/workflows/pytest.yaml similarity index 73% rename from .github/workflows/CI.yaml rename to .github/workflows/pytest.yaml index 4d289f02..fbd9079b 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/pytest.yaml @@ -1,9 +1,6 @@ -name: CI +name: Pytest on: - # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming - # Existing codes likely still have "master" as the primary branch - # Both are tracked here to keep legacy and new codes working push: branches: - "master" @@ -12,15 +9,10 @@ on: branches: - "master" - "main" -# schedule: -# # Nightly tests run on master by default: -# # Scheduled workflows run on the latest commit on the default or base branch. -# # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule) -# - cron: "0 0 * * *" jobs: - CI: - name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }} + pytest_conda: + name: Pytest (conda) on ${{ matrix.os }}, Python ${{ matrix.python-version }} runs-on: ${{ matrix.os }} strategy: matrix: @@ -82,7 +74,7 @@ jobs: - name: Run doctest # For now still excluding several subfolders and files run: | - pytest --doctest-modules --ignore=molSimplify/job_manager --ignore=molSimplify/Informatics/MOF --ignore=molSimplify/Informatics/protein --ignore=molSimplify/Scripts/in_b3lyp_usetc.py --ignore=molSimplify/Informatics/jupyter_vis.py --ignore=molSimplify/Informatics/macrocycle_synthesis.py --ignore=molSimplify/Informatics/organic_fingerprints.py molSimplify + pytest --doctest-modules --ignore=molSimplify/Informatics/MOF --ignore=molSimplify/Informatics/protein --ignore=molSimplify/Scripts/in_b3lyp_usetc.py --ignore=molSimplify/Informatics/jupyter_vis.py --ignore=molSimplify/Informatics/macrocycle_synthesis.py --ignore=molSimplify/Informatics/organic_fingerprints.py molSimplify - name: Upload coverage report to codecov uses: codecov/codecov-action@v3 @@ -101,9 +93,32 @@ jobs: #uses: ravsamhq/notify-slack-action@v1 uses: 8398a7/action-slack@v3 with: - job_name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }} + job_name: Pytest (conda) on ${{ matrix.os }}, Python ${{ matrix.python-version }} fields: message,commit,author,workflow,job,took status: ${{ job.status }} env: SLACK_WEBHOOK_URL: ${{secrets.SLACK_WEBHOOK}} #MATRIX_CONTEXT: ${{ toJson(matrix) }} # required + + pytest_pip: + name: Pytest (pip) on ${{ matrix.os }}, Python ${{ matrix.python-version }} + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: ["ubuntu-latest"] + python-version: ["3.8"] + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + + - name: Install package + run: | + pip install -e .[dev] + + - name: Run pytest + run: | + pytest -v diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1f505c1c..cb486a52 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,13 +6,13 @@ ci: repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 + rev: v4.5.0 hooks: - id: check-yaml - id: end-of-file-fixer - id: trailing-whitespace - repo: https://github.com/pycqa/flake8 - rev: '6.0.0' + rev: '6.1.0' hooks: - id: flake8 args: ['--select=E9,F63,F7,F82', '--exclude=fragment_classes.py,frag_functionalizer.py,bridge_functionalizer.py'] diff --git a/.readthedocs.yml b/.readthedocs.yml index b0b07913..19c4f7aa 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,15 +1,16 @@ version: 2 -conda: - environment: docs/environment.yaml +build: + os: ubuntu-22.04 + tools: + python: "3.7" python: - version: 3.7 install: - method: pip path: . extra_requirements: - - rtd + - docs sphinx: builder: html diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 2b9d0a13..00000000 --- a/MANIFEST.in +++ /dev/null @@ -1,15 +0,0 @@ -include molSimplify/Data/* -include molSimplify/Ligands/* -include molSimplify/Bind/* -include molSimplify/Cores/* -include molSimplify/python_nn/* -include molSimplify/Docs/* -include molSimplify/Informatics/* -include molSimplify/icons/* -include molSimplify/icons/geoms/* -include molSimplify/icons/geoms_labels/* -include molSimplify/Substrates/* -include tests/inputs/* -include tests/refs/* -include tests/refs/*/* -include tests/README.txt diff --git a/README.md b/README.md index f311cc1d..7f3e2dbd 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ ![](./molSimplify/icons/logo.png) -[![CI](https://github.com/hjkgrp/molSimplify/actions/workflows/CI.yaml/badge.svg)](https://github.com/hjkgrp/molSimplify/actions/workflows/CI.yaml) +[![Pytest](https://github.com/hjkgrp/molSimplify/actions/workflows/pytest.yaml/badge.svg)](https://github.com/hjkgrp/molSimplify/actions/workflows/pytest.yaml) [![Documentation Status](https://readthedocs.org/projects/molsimplify/badge/?version=latest)](http://molsimplify.readthedocs.io/?badge=latest) [![Linter](https://github.com/hjkgrp/molSimplify/actions/workflows/python-linter.yaml/badge.svg)](https://github.com/hjkgrp/molSimplify/actions/workflows/python-linter.yaml) @@ -7,7 +7,7 @@ molSimplify is an open source toolkit for the automated, first-principles screen ## Installation -### via conda +### via conda, from GitHub We currently recommend installation via the [Conda](https://conda.io/docs/) package management system. 1. Prerequisite: have [Anaconda or miniconda](https://www.anaconda.com/distribution/) installed on your system. **For M1 Macs, please use [Miniforge](https://github.com/conda-forge/miniforge) for Mac OSX arm64.** (We do not recommend simultaneously installing Anaconda and Miniforge - only install Miniforge.) @@ -37,6 +37,25 @@ We currently recommend installation via the [Conda](https://conda.io/docs/) pack pytest ``` +### via conda, from Anaconda +Releases of molSimplify are also available on Anaconda on the [conda-forge channel](https://anaconda.org/conda-forge/molsimplify) and the [hjkgroup channel](https://anaconda.org/hjkgroup/molsimplify). + +### via pip, from GitHub +1. Clone molSimplify source from github and change into the directory. + + ```bash + git clone https://github.com/hjkgrp/molSimplify.git + cd molSimplify + ``` +2. Locally install the molSimplify package using pip. + ```bash + pip install -e .[dev] + ``` +3. To test your installation, you can run the command below at the root directory of molSimplify. You are good to go if all the tests are passed! Note, some test will be skipped because none of the optional dependencies are installed this way. + ```bash + pytest + ``` + ### via docker We also maintain an active [docker image on dockerhub](https://hub.docker.com/repository/docker/hjkgroup/molsimplify) for plug-and-play use. @@ -44,7 +63,7 @@ For line by line instructions on an installation via docker, please visit [molSi ## Tutorials -A set of tutorials covering common use cases is available at the [Kulik group webpage](http://hjkgrp.mit.edu/molSimplify-tutorials). +A set of tutorials covering common use cases is available at the [Kulik group webpage](http://hjkgrp.mit.edu/molSimplify-tutorials). Note that the GUI is no longer supported, so users are encouraged to generate structures through the command line or using the Python command [startgen_pythonic](molSimplify/Scripts/generator.py). ## Documentation @@ -82,6 +101,6 @@ year = {2018}, } ``` -If you use any machine learning (ML) models in molSimplify that results in a publication, please cite the corresponding reference in [this MLmodel reference page](https://github.com/hjkgrp/molSimplify/blob/master/MLmodel-reference.md). +If you use any machine learning (ML) models in molSimplify that results in a publication, please cite the corresponding reference in [this ML model reference page](https://github.com/hjkgrp/molSimplify/blob/master/MLmodel-reference.md). **Note that we have disabled developers' supports for Python 2.7 and will only release conda builds on Python 3.** diff --git a/devtools/conda-envs/README.md b/devtools/conda-envs/README.md deleted file mode 100644 index 1aef0544..00000000 --- a/devtools/conda-envs/README.md +++ /dev/null @@ -1,27 +0,0 @@ -For M1 Mac users: If the current `mols_m1.yml` file is not working for you, try using the following lines in `mols_m1.yml` instead: - -``` -name: mols_test_m1 -channels: - - hjkgroup - - conda-forge - - anaconda - - theochem - - defaults -dependencies: - - python=3.8 - - openbabel - - tensorflow-base - - pyqt - - pip - - qt - - scikit-learn - - pandas - - scipy - - pymongo - - libffi -``` - -Some caveats for this approach: -- Uses Openbabel 3 which means some of the tests fail because of the different connecting atoms definition. -- GUI does not work well (unusable on dark mode setting). diff --git a/devtools/conda-envs/install_tensorflow_m1.sh b/devtools/conda-envs/install_tensorflow_m1.sh deleted file mode 100644 index 1515579c..00000000 --- a/devtools/conda-envs/install_tensorflow_m1.sh +++ /dev/null @@ -1 +0,0 @@ -pip install --upgrade --force --no-dependencies https://github.com/apple/tensorflow_macos/releases/download/v0.1alpha3/tensorflow_addons_macos-0.1a3-cp38-cp38-macosx_11_0_arm64.whl https://github.com/apple/tensorflow_macos/releases/download/v0.1alpha3/tensorflow_macos-0.1a3-cp38-cp38-macosx_11_0_arm64.whl diff --git a/devtools/conda-envs/mols.yml b/devtools/conda-envs/mols.yml index e5b47f15..ba742ce2 100644 --- a/devtools/conda-envs/mols.yml +++ b/devtools/conda-envs/mols.yml @@ -8,14 +8,16 @@ dependencies: - pandas - scipy - libffi + - importlib_resources - pip - pip: - pytest + - pytest-resource-path # Optional # GUI / plotting - - pyqt - - qt + # - pyqt + # - qt - matplotlib # Database - pymongo diff --git a/devtools/conda-envs/mols_m1.yml b/devtools/conda-envs/mols_m1.yml deleted file mode 100644 index c900694a..00000000 --- a/devtools/conda-envs/mols_m1.yml +++ /dev/null @@ -1,174 +0,0 @@ -name: mols_test -channels: - - conda-forge -dependencies: - - absl-py=0.15.0=pyhd8ed1ab_0 - - aiohttp=3.7.4.post0=py38hea4295b_0 - - appnope=0.1.2=py38h10201cd_1 - - astor=0.8.1=pyh9f0ad1d_0 - - astunparse=1.6.3=pyhd8ed1ab_0 - - async-timeout=3.0.1=py_1000 - - attrs=21.2.0=pyhd8ed1ab_0 - - backcall=0.2.0=pyh9f0ad1d_0 - - backports=1.0=py_2 - - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0 - - beautifulsoup4=4.10.0=pyha770c72_0 - - blinker=1.4=py_1 - - brotlipy=0.7.0=py38hea4295b_1001 - - bzip2=1.0.8=h3422bc3_4 - - c-ares=1.17.2=h3422bc3_0 - - ca-certificates=2021.10.8=h4653dfc_0 - - cached-property=1.5.2=hd8ed1ab_1 - - cached_property=1.5.2=pyha770c72_1 - - cachetools=4.2.4=pyhd8ed1ab_0 - - cairo=1.16.0=he69dfd1_1008 - - certifi=2021.10.8=py38h10201cd_0 - - cffi=1.14.6=py38hc67bbb8_1 - - chardet=4.0.0=py38h10201cd_1 - - charset-normalizer=2.0.0=pyhd8ed1ab_0 - - click=8.0.3=py38h10201cd_0 - - colorama=0.4.4=pyh9f0ad1d_0 - - conda=4.10.3=py38h10201cd_2 - - conda-build=3.21.4=py38h10201cd_0 - - conda-package-handling=1.7.3=py38hea4295b_0 - - cryptography=35.0.0=py38h10d4710_1 - - cycler=0.10.0=py_2 - - dataclasses=0.8=pyhc8e2a94_3 - - decorator=5.1.0=pyhd8ed1ab_0 - - filelock=3.3.1=pyhd8ed1ab_0 - - fontconfig=2.13.1=heb65262_1005 - - freetype=2.10.4=h17b34a0_1 - - gast=0.5.0=pyhd8ed1ab_0 - - gettext=0.19.8.1=h049c9fb_1008 - - glob2=0.7=py_0 - - google-auth=1.35.0=pyh6c4a22f_0 - - google-auth-oauthlib=0.4.6=pyhd8ed1ab_0 - - google-pasta=0.2.0=pyh8c360ce_0 - - grpcio=1.41.0=py38h69ee544_0 - - h5py=2.10.0=nompi_py38hb525b2d_106 - - hdf5=1.10.6=nompi_h0fc092c_1114 - - icu=68.1=h17758a7_0 - - idna=3.1=pyhd3deb0d_0 - - importlib-metadata=4.8.1=py38h10201cd_0 - - ipython=7.28.0=py38h2cb4d76_0 - - jbig=2.1=h3422bc3_2003 - - jedi=0.18.0=py38h10201cd_2 - - jinja2=3.0.2=pyhd8ed1ab_0 - - joblib=1.1.0=pyhd8ed1ab_0 - - jpeg=9d=h27ca646_0 - - keras=2.6.0=pyhd8ed1ab_0 - - keras-preprocessing=1.1.2=pyhd8ed1ab_0 - - kiwisolver=1.3.2=py38h1670459_0 - - krb5=1.19.2=hd92b7a7_2 - - lcms2=2.12=had6a04f_0 - - lerc=3.0=hbdafb3b_0 - - libarchive=3.5.2=hc24d6eb_1 - - libblas=3.9.0=12_osxarm64_openblas - - libcblas=3.9.0=12_osxarm64_openblas - - libcurl=7.79.1=h8fe1914_1 - - libcxx=12.0.1=h168391b_0 - - libdeflate=1.8=h3422bc3_0 - - libedit=3.1.20191231=hc8eb9b7_2 - - libev=4.33=h642e427_1 - - libffi=3.4.2=hbdafb3b_4 - - libgfortran=5.0.0.dev0=11_0_1_hf114ba7_23 - - libgfortran5=11.0.1.dev0=hf114ba7_23 - - libglib=2.70.0=h67e64d8_1 - - libiconv=1.16=h642e427_0 - - liblapack=3.9.0=12_osxarm64_openblas - - liblief=0.11.5=hbdafb3b_0 - - libnghttp2=1.43.0=he4cd7f6_1 - - libopenblas=0.3.18=openmp_h5dd58f0_0 - - libpng=1.6.37=hf7e6567_2 - - libprotobuf=3.18.1=hccf11d3_0 - - libssh2=1.10.0=hb80f160_2 - - libtiff=4.3.0=h74060c4_2 - - libwebp-base=1.2.1=h3422bc3_0 - - libxml2=2.9.12=h538f51a_0 - - libzlib=1.2.11=hee7b306_1013 - - llvm-openmp=12.0.1=hf3c4609_1 - - lz4-c=1.9.3=hbdafb3b_1 - - lzo=2.10=h642e427_1000 - - markdown=3.3.4=pyhd8ed1ab_0 - - markupsafe=2.0.1=py38hea4295b_0 - - matplotlib=3.4.3=py38h150bfb4_1 - - matplotlib-base=3.4.3=py38hb140015_1 - - matplotlib-inline=0.1.3=pyhd8ed1ab_0 - - multidict=5.2.0=py38hea4295b_0 - - ncurses=6.2=h9aa5885_4 - - numpy=1.21.3=py38hbf7bb01_0 - - oauthlib=3.1.1=pyhd8ed1ab_0 - - olefile=0.46=pyh9f0ad1d_1 - - openbabel=3.1.1=py38h028a5c4_2 - - openjpeg=2.4.0=h062765e_1 - - openssl=1.1.1l=h3422bc3_0 - - opt_einsum=3.3.0=pyhd8ed1ab_1 - - pandas=1.3.4=py38h3777fb4_0 - - parso=0.8.2=pyhd8ed1ab_0 - - pcre=8.45=hbdafb3b_0 - - pexpect=4.8.0=pyh9f0ad1d_2 - - pickleshare=0.7.5=py_1003 - - pillow=8.3.2=py38h02acf36_0 - - pip=21.3.1=pyhd8ed1ab_0 - - pixman=0.40.0=h27ca646_0 - - pkginfo=1.7.1=pyhd8ed1ab_0 - - prompt-toolkit=3.0.21=pyha770c72_0 - - protobuf=3.18.1=py38h6f2b01f_0 - - psutil=5.8.0=py38hea4295b_1 - - ptyprocess=0.7.0=pyhd3deb0d_0 - - py-lief=0.11.5=py38h6f2b01f_0 - - pyasn1=0.4.8=py_0 - - pyasn1-modules=0.2.7=py_0 - - pycosat=0.6.3=py38hea4295b_1006 - - pycparser=2.20=pyh9f0ad1d_2 - - pygments=2.10.0=pyhd8ed1ab_0 - - pyjwt=2.3.0=pyhd8ed1ab_0 - - pyopenssl=21.0.0=pyhd8ed1ab_0 - - pyparsing=2.4.7=pyh9f0ad1d_0 - - pysocks=1.7.1=py38h10201cd_3 - - python=3.8.12=hab31e5c_2_cpython - - python-dateutil=2.8.2=pyhd8ed1ab_0 - - python-flatbuffers=2.0=pyhd8ed1ab_0 - - python-libarchive-c=3.1=py38h10201cd_0 - - python_abi=3.8=2_cp38 - - pytz=2021.3=pyhd8ed1ab_0 - - pyu2f=0.1.5=pyhd8ed1ab_0 - - pyyaml=6.0=py38hea4295b_0 - - readline=8.1=hedafd6a_0 - - requests=2.26.0=pyhd8ed1ab_0 - - requests-oauthlib=1.3.0=pyh9f0ad1d_0 - - ripgrep=13.0.0=h822aac1_1 - - rsa=4.7.2=pyh44b312d_0 - - ruamel_yaml=0.15.80=py38hea4295b_1004 - - scikit-learn=1.0.1=py38hfeda2c9_0 - - scipy=1.7.1=py38hd0c9ec0_0 - - six=1.16.0=pyh6c4a22f_0 - - soupsieve=2.0.1=py_1 - - sqlite=3.36.0=h72a2b83_2 - - tensorboard=2.6.0=pyhd8ed1ab_1 - - tensorboard-data-server=0.6.0=py38h10d4710_0 - - tensorboard-plugin-wit=1.8.0=pyh44b312d_0 - - tensorflow-estimator=2.6.0=py38hddd8853_0 - - termcolor=1.1.0=py_2 - - threadpoolctl=3.0.0=pyh8a188c0_0 - - tk=8.6.11=he1e0b03_1 - - tornado=6.1=py38hea4295b_1 - - tqdm=4.62.3=pyhd8ed1ab_0 - - traitlets=5.1.0=pyhd8ed1ab_0 - - typeguard=2.13.0=pyhd8ed1ab_0 - - typing-extensions=3.10.0.2=hd8ed1ab_0 - - typing_extensions=3.10.0.2=pyha770c72_0 - - urllib3=1.26.7=pyhd8ed1ab_0 - - wcwidth=0.2.5=pyh9f0ad1d_2 - - werkzeug=2.0.1=pyhd8ed1ab_0 - - wheel=0.37.0=pyhd8ed1ab_1 - - wrapt=1.13.2=py38hea4295b_0 - - xz=5.2.5=h642e427_1 - - yaml=0.2.5=h642e427_0 - - yarl=1.7.0=py38hea4295b_0 - - zipp=3.6.0=pyhd8ed1ab_0 - - zlib=1.2.11=hee7b306_1013 - - zstd=1.5.0=h861e0a7_0 - - pip: - - setuptools==58.3.0 -prefix: /Users/isuruariyarathna/miniforge3/envs/mols_test diff --git a/devtools/conda-envs/mols_minimal.yml b/devtools/conda-envs/mols_minimal.yml index 4b03fedf..236744f9 100644 --- a/devtools/conda-envs/mols_minimal.yml +++ b/devtools/conda-envs/mols_minimal.yml @@ -8,6 +8,8 @@ dependencies: - pandas - scipy - libffi + - importlib_resources - pip - pip: - pytest + - pytest-resource-path diff --git a/docs/environment.yaml b/docs/environment.yaml deleted file mode 100644 index 4f2449f1..00000000 --- a/docs/environment.yaml +++ /dev/null @@ -1,11 +0,0 @@ -channels: - - hjkgroup - - defaults -dependencies: - - openbabel - - pyyaml - - scipy - - pandas - - scikit-learn - - beautifulsoup4 - - networkx diff --git a/docs/source/index.rst b/docs/source/index.rst index d4b075ef..5680ee1c 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -30,7 +30,6 @@ Welcome to molSimplify's documentation! | ``Ligands``: database of ligands which are used in molSimplify (if your ligand is not found here, there is a tutorial for adding to the ligand database) | - ``ligands.dict``: contains mappings between ligand name and corresponding structure | ``Scripts``: codes to write and measure geometries, and write input files -| ``job_manager``: automated large-scale job management scripts | ``molscontrol``: dynamic classifier files | ``python_nn``: bond length information for the very first bond length NN (2017 Chemical Science) | ``sklearn_models``: models for static classification of whether a geometry is good or bad diff --git a/molSimplify/Classes/atom3D.py b/molSimplify/Classes/atom3D.py index a707edbe..e1b05600 100644 --- a/molSimplify/Classes/atom3D.py +++ b/molSimplify/Classes/atom3D.py @@ -49,8 +49,6 @@ def __init__(self, Sym='C', xyz=None, name=False, partialcharge=None, Tfactor=0, self.name = name else: self.name = Sym - # flag for metal - self.metal = None # Coordinates if xyz is None: @@ -159,12 +157,7 @@ def ismetal(self, transition_metals_only=True): metal : bool Bool for whether or not an atom is a metal. """ - if self.metal is None: - if self.sym in globalvars().metalslist(transition_metals_only=transition_metals_only): - self.metal = True - else: - self.metal = False - return self.metal + return self.sym in globalvars().metalslist(transition_metals_only=transition_metals_only) def setcoords(self, xyz): """ Set coordinates of an atom3D class to a new location. diff --git a/molSimplify/Classes/globalvars.py b/molSimplify/Classes/globalvars.py index 96321c5b..372486c1 100644 --- a/molSimplify/Classes/globalvars.py +++ b/molSimplify/Classes/globalvars.py @@ -459,13 +459,10 @@ def mybash(cmd): """ p = subprocess.Popen( cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) - stdout = [] - while True: - line = p.stdout.readline() - stdout.append(line) - if line == '' and p.poll() is not None: - break - return ''.join(stdout) + stdout, stderr = p.communicate() + lines = stdout.decode('utf-8').splitlines() + lines = [line+"\n" for line in lines if line !=""] + return ''.join(lines) # Defines global variables used throughout the code diff --git a/molSimplify/Classes/mGUI.py b/molSimplify/Classes/mGUI.py index 748a42a5..eb45d283 100644 --- a/molSimplify/Classes/mGUI.py +++ b/molSimplify/Classes/mGUI.py @@ -39,7 +39,7 @@ import glob import tempfile import re -from pkg_resources import resource_filename, Requirement +from importlib_resources import files as resource_files import xml.etree.ElementTree as ET try: @@ -142,8 +142,7 @@ def initGUI(self, app): helpAction.triggered.connect(self.qshowhelp) menu2.addAction(helpAction) # ## place title top ### - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/icons/logo.png") + f = resource_files("molSimplify").joinpath("icons/logo.png") clogo = mQPixmap(f) self.grid.addWidget(clogo, 2, 8, 1, 10) self.txtdev = mQLabel('Developed by Kulik group @ MIT', '', 'c', 16) @@ -363,8 +362,7 @@ def initGUI(self, app): if globs.custom_path: f = globs.custom_path + "/Ligands/ligands.dict" else: - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Ligands/ligands.dict") + f = str(resource_files("molSimplify").joinpath("Ligands/ligands.dict")) qcav0 = getligroups(readdict(f)) qcav = [_f for _f in qcav0.split(' ') if _f] self.etliggrp = mQComboBox(qcav, ctip, 12) @@ -613,8 +611,7 @@ def initGUI(self, app): self.qctWindow.setPalette(p) # set background color self.qctWindow.setLayout(self.qctgrid) # set layout - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/icons/petachem.png") + f = resource_files("molSimplify").joinpath("icons/petachem.png") c0 = mQPixmap(f) self.qctgrid.addWidget(c0, 0, 2, 1, 1) # top text @@ -876,10 +873,8 @@ def initGUI(self, app): self.sgrid.addWidget(self.jWindow) # add to stacked grid self.jWindow.setPalette(p) # set background color self.jWindow.setLayout(self.jgrid) # set layout - f1 = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/icons/sge.png") - f2 = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/icons/slurm.png") + f1 = resource_files("molSimplify").joinpath("icons/sge.png") + f2 = resource_files("molSimplify").joinpath("icons/slurm.png") c1 = mQPixmap(f1) c2 = mQPixmap(f2) self.jgrid.addWidget(c1, 1, 2, 1, 1) @@ -1181,8 +1176,7 @@ def initGUI(self, app): self.etcDBmw1 = mQLineEdit('', ctip, 'l', 14) self.cDBgrid.addWidget(self.etcDBmw1, 11, 8, 1, 1) # aspirin icon - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/icons/chemdb.png") + f = resource_files("molSimplify").joinpath("icons/chemdb.png") c = mQPixmap(f) relresize(c, c, 0.4) self.cDBgrid.addWidget(c, 7, 0, 4, 2) @@ -1271,8 +1265,7 @@ def initGUI(self, app): self.butpret.clicked.connect(self.qretmain) self.pgrid.addWidget(self.butpret, 7, 3, 1, 2) # c1p = mPic(self.pWindow,globs.installdir+'/icons/wft1.png',0.04,0.7,0.2) - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/icons/wft3.png") + f = resource_files("molSimplify").joinpath("icons/wft3.png") c3p = mQPixmap(f) self.pgrid.addWidget(c3p, 3, 0, 4, 1) # c2p = mPic(self.pWindow,globs.installdir+'/icons/wft2.png',0.04,0.035,0.2) @@ -1746,8 +1739,7 @@ def qaddg(self): if globs.custom_path: f = globs.custom_path + "/Data/coordinations.dict" else: - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Data/coordinations.dict") + f = str(resource_files("molSimplify").joinpath("Data/coordinations.dict")) with open(f, 'r') as fl: s = fl.read().splitlines() if gname.lower() in s: @@ -1790,8 +1782,7 @@ def qaddg(self): fl.write(xyzl) # write png file if glob.glob(cfile): - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/icons/geoms/") + f = str(resource_files("molSimplify").joinpath("icons/geoms/")) shutil.copy2(cfile, f+gshort+'.png') choice = QMessageBox.information( self.geWindow, 'Add', 'Successfully added to the database!') @@ -1827,8 +1818,7 @@ def qdelg(self): if globs.custom_path: f = globs.custom_path + "/Data/coordinations.dict" else: - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Data/coordinations.dict") + f = str(resource_files("molSimplify").joinpath("Data/coordinations.dict")) with open(f, 'r') as fl: s = fl.read() if gname.lower() not in s and gshort.lower() not in s: @@ -1847,8 +1837,7 @@ def qdelg(self): if globs.custom_path: f = globs.custom_path + "/Data/coordinations.dict" else: - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Data/coordinations.dict") + f = str(resource_files("molSimplify").joinpath("Data/coordinations.dict")) with open(f, 'w') as fl: fl.write(snew) # remove file @@ -2076,8 +2065,7 @@ def drawligs_svg(self): def viewgeom(self): # get geometry geom = self.dcoordg.currentText() - gfname = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/icons/geoms/" + geom + ".png") + gfname = str(resource_files("molSimplify").joinpath(f"icons/geoms/{geom}.png")) if glob.glob(gfname): rows = self.lgrid.rowCount() # Clear existing widgets in layout @@ -2268,8 +2256,7 @@ def matchgeomcoord(self): # add to box for i, t in enumerate(qc): # File f is never actually used? RM 2022/02/17 - f = resource_filename(Requirement.parse( # noqa F841 - "molSimplify"), "molSimplify/icons/geoms/" + t + ".png") + f = str(resource_files("molSimplify").joinpath(f"icons/geoms/{t}.png")) # noqa F841 self.dcoordg.addItem(QIcon(t), t) self.dcoordg.setIconSize(QSize(60, 60)) # set default geometry diff --git a/molSimplify/Classes/mol3D.py b/molSimplify/Classes/mol3D.py index 2dafb4ab..fac36b70 100644 --- a/molSimplify/Classes/mol3D.py +++ b/molSimplify/Classes/mol3D.py @@ -1609,7 +1609,7 @@ def getBondedAtomsBOMatrixAug(self, idx): nats.append(i) return nats - def getBondCutoff(self, atom, ratom): + def getBondCutoff(self, atom: atom3D, ratom: atom3D) -> float: """ Get cutoff based on two atoms. @@ -1632,15 +1632,15 @@ def getBondCutoff(self, atom, ratom): distance_max = min(2.75, distance_max) # 2.75 by 07/22/2021 if ratom.symbol() == "C" and not atom.symbol() == "H": distance_max = min(2.75, distance_max) # 2.75 by 07/22/2021 - if ratom.symbol() == "H" and atom.ismetal: + if ratom.symbol() == "H" and atom.ismetal(): # tight cutoff for metal-H bonds distance_max = 1.1 * (atom.rad + ratom.rad) - if atom.symbol() == "H" and ratom.ismetal: + if atom.symbol() == "H" and ratom.ismetal(): # tight cutoff for metal-H bonds distance_max = 1.1 * (atom.rad + ratom.rad) return distance_max - def getBondedAtoms(self, idx): + def getBondedAtoms(self, idx: int) -> List[int]: """ Gets atoms bonded to a specific atom. This is determined based on element-specific distance cutoffs, rather than predefined valences. @@ -2672,7 +2672,7 @@ def returnxyz(self): ss += "%s \t%f\t%f\t%f\n" % (atom.sym, xyz[0], xyz[1], xyz[2]) return (ss) - def readfromxyz(self, filename, ligand_unique_id=False, read_final_optim_step=False): + def readfromxyz(self, filename: str, ligand_unique_id=False, read_final_optim_step=False): """ Read XYZ into a mol3D class instance. @@ -2693,8 +2693,7 @@ def readfromxyz(self, filename, ligand_unique_id=False, read_final_optim_step=Fa amassdict = globs.amass() self.graph = [] self.xyzfile = filename - fname = filename.split('.xyz')[0] - with open(fname + '.xyz', 'r') as f: + with open(filename, 'r') as f: s = f.read().splitlines() try: atom_count = int(s[0]) diff --git a/molSimplify/Informatics/MOF/MOF_RAC_example.ipynb b/molSimplify/Informatics/MOF/MOF_RAC_example.ipynb index 295e9983..bd9d0835 100644 --- a/molSimplify/Informatics/MOF/MOF_RAC_example.ipynb +++ b/molSimplify/Informatics/MOF/MOF_RAC_example.ipynb @@ -365,8 +365,12 @@ "# You don't want to set it much higher than that, since the code may start to assign bonds where none exist.\n", "wiggle_room = 1\n", "\n", + "# Note: if get_primitive does not work for your MOF, you can skip that step.\n", + "# But if your MOF does not have P1 symmetry, you will need to make it have P1 symmetry before RAC featurization with get_MOF_descriptors.\n", + "\t# One option for doing that is using Vesta.\n", "get_primitive(f'{working_path}/{cif_name}.cif', f'{working_path}/{cif_name}_primitive.cif')\n", - "overlap_removal(f'{working_path}/{cif_name}_primitive.cif', f'{working_path}/{cif_name}_no_overlap.cif', wiggle_room=wiggle_room)\n", + "\n", + "overlap_removal(f'{working_path}/{cif_name}_primitive.cif', f'{working_path}/{cif_name}_no_overlap.cif')\n", "solvent_removal(f'{working_path}/{cif_name}_no_overlap.cif', f'{working_path}/{cif_name}_no_solvent.cif', wiggle_room=wiggle_room)\n", "\n", "# Now you can featurize your \"clean\" MOF.\n", diff --git a/molSimplify/Informatics/MOF/MOF_descriptors.py b/molSimplify/Informatics/MOF/MOF_descriptors.py index af907bd0..8053b90c 100644 --- a/molSimplify/Informatics/MOF/MOF_descriptors.py +++ b/molSimplify/Informatics/MOF/MOF_descriptors.py @@ -387,6 +387,7 @@ def make_MOF_linker_RACs(linkerlist, linker_subgraphlist, molcif, depth, name, c if not os.path.exists(xyz_path): linker_mol_fcoords_connected = XYZ_connected(cell_v, linker_mol_cart_coords, linker_mol_adj_mat) writeXYZandGraph(xyz_path, linker_mol_atom_labels, cell_v, linker_mol_fcoords_connected, linker_mol_adj_mat) + # Write TXT file indicating the connecting atoms linker_index_connection_indices = [] for item in global_connection_indices: @@ -417,7 +418,7 @@ def make_MOF_linker_RACs(linkerlist, linker_subgraphlist, molcif, depth, name, c lig_full.append(ligand_ac_full) # Some formatting - lig_full = [item for sublist in lig_full for item in sublist] #flatten lists + lig_full = [item for sublist in lig_full for item in sublist] # flatten lists colnames = [item for sublist in colnames for item in sublist] colnames += ['name'] lig_full += [name] @@ -850,7 +851,7 @@ def detect_1D_rod(SBU_list, molcif, allatomtypes, cell_v, logpath, name): def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=False, wiggle_room=1, max_num_atoms=2000, get_sbu_linker_bond_info=False, surrounded_sbu_file_generation=False, detect_1D_rod_sbu=False): """ - Generates RAC descriptors on a MOF. + Generates RAC descriptors on a MOF, assuming it has P1 symmetry. Writes three files: sbu_descriptors.csv, linker_descriptors.csv, and lc_descriptors.csv These files contain the RAC descriptors of the MOF. @@ -916,7 +917,7 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F cart_coords = fractional2cart(fcoords, cell_v) name = os.path.basename(data).replace(".cif", "") if len(cart_coords) > max_num_atoms: # Don't deal with large cifs because of computational resources required for their treatment. - print("Too large cif file, skipping it for now...") + print("cif file is too large, skipping it for now...") failure_str = f"Failed to featurize {name}: large primitive cell\n {len(cart_coords)} atoms" full_names, full_descriptors = failure_response(path, failure_str) return full_names, full_descriptors @@ -925,9 +926,9 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F Getting the adjacency matrix. """"""""" if not graph_provided: # Make the adjacency matrix. - distance_mat = compute_distance_matrix3(cell_v,cart_coords) + distance_mat = compute_distance_matrix3(cell_v, cart_coords) try: - adj_matrix, _ = compute_adj_matrix(distance_mat,allatomtypes,wiggle_room) + adj_matrix, _ = compute_adj_matrix(distance_mat, allatomtypes, wiggle_room) except NotImplementedError: failure_str = f"Failed to featurize {name}: atomic overlap\n" full_names, full_descriptors = failure_response(path, failure_str) @@ -1183,18 +1184,18 @@ def get_MOF_descriptors(data, depth, path=False, xyzpath=False, graph_provided=F # full_names = [0] # full_descriptors = [0] elif len(linker_subgraphlist) == 1: # Only one linker identified. - print('Suspicious featurization') + print(f'Suspicious featurization for {name}: Only one linker identified.') full_names = [1] full_descriptors = [1] else: # Means len(linker_subgraphlist) is zero. - print('Failed to featurize this MOF; no linkers were identified.') - full_names = [0] - full_descriptors = [0] + failure_str = f'Failed to featurize {name}: No linkers were identified.\n' + full_names, full_descriptors = failure_response(path, failure_str) + return full_names, full_descriptors if (len(full_names) <= 1) and (len(full_descriptors) <= 1): print(f'full_names is {full_names} and full_descriptors is {full_descriptors}') - tmpstr = "Failed to featurize %s: Only zero or one total linkers identified.\n"%(name) - write2file(path,"/FailedStructures.log",tmpstr) - + failure_str = f'Failed to featurize {name}: Only zero or one total linkers identified.\n' + full_names, full_descriptors = failure_response(path, failure_str) + return full_names, full_descriptors # Getting bond information if requested, and writing it to a TXT file. if get_sbu_linker_bond_info: diff --git a/molSimplify/Informatics/MOF/MOF_functionalizer.py b/molSimplify/Informatics/MOF/MOF_functionalizer.py index f1646b8f..07068868 100644 --- a/molSimplify/Informatics/MOF/MOF_functionalizer.py +++ b/molSimplify/Informatics/MOF/MOF_functionalizer.py @@ -16,7 +16,7 @@ XYZ_connected, write_cif, ) -from pkg_resources import resource_filename, Requirement +from importlib_resources import files as resource_files import numpy as np import scipy import networkx as nx @@ -1257,8 +1257,7 @@ def functionalize_MOF_at_indices_mol3D_merge(cif_file, path2write, functional_gr # Load in the mol3D from the folder molSimplify folder monofunctionalized_BDC. functional_group_template = mol3D() - func_group_xyz_path = resource_filename(Requirement.parse( - "molSimplify"), f"molSimplify/Informatics/MOF/monofunctionalized_BDC/{functional_group}.xyz") + func_group_xyz_path = str(resource_files("molSimplify").joinpath(f"Informatics/MOF/monofunctionalized_BDC/{functional_group}.xyz")) functional_group_template.readfromxyz(func_group_xyz_path) # This is a whole BDC linker with the requested functional group on it. # Read information about the important indices of the functional_group_template. diff --git a/molSimplify/Informatics/MOF/PBC_functions.py b/molSimplify/Informatics/MOF/PBC_functions.py index 49c5b6b0..45408f94 100644 --- a/molSimplify/Informatics/MOF/PBC_functions.py +++ b/molSimplify/Informatics/MOF/PBC_functions.py @@ -1122,7 +1122,7 @@ def remove_undesired_atoms(undesired_indices, allatomtypes, fcoords): return allatomtypes_trim, fcoords_trim -def overlap_removal(cif_path, new_cif_path, wiggle_room=1): +def overlap_removal(cif_path, new_cif_path): """ Reads a cif file, removes overlapping atoms, and writes the cif to the provided path. For a new CIF, recommended to remove symmetry (either with Vesta or with get_primitive), then run overlap_removal, then run solvent_removal. @@ -1133,9 +1133,6 @@ def overlap_removal(cif_path, new_cif_path, wiggle_room=1): The path of the cif file to be read. new_cif_path : str The path to which the modified cif file will be written. - wiggle_room : float - A multiplier that allows for more or less strict bond distance cutoffs. - Useful for some trouble CIFs with long bonds. Returns ------- @@ -1155,7 +1152,7 @@ def overlap_removal(cif_path, new_cif_path, wiggle_room=1): # Assuming that the cif does not have graph information of the structure. distance_mat = compute_distance_matrix3(cell_v,cart_coords) - adj_matrix, overlap_atoms = compute_adj_matrix(distance_mat, allatomtypes, wiggle_room=wiggle_room, handle_overlap=True) + adj_matrix, overlap_atoms = compute_adj_matrix(distance_mat, allatomtypes, handle_overlap=True) # Dealing with the case of overlapping atoms. if len(overlap_atoms) != 0: @@ -1168,7 +1165,7 @@ def overlap_removal(cif_path, new_cif_path, wiggle_room=1): def solvent_removal(cif_path, new_cif_path, wiggle_room=1): """ Reads a cif file, removes floating solvent and overlapping atoms, and writes the cif to the provided path. - If MOF has a lot of solvent, you may need to apply this function multiple times. + Assumes cif has P1 symmetry. Parameters ---------- diff --git a/molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py b/molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py index 99ce0bdb..61558603 100644 --- a/molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py +++ b/molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py @@ -787,7 +787,7 @@ def make_MOF_fragments(data, path=False, xyzpath=False): cart_coords = fractional2cart(fcoords, cell_v) name = os.path.basename(data).strip(".cif") if len(cart_coords) > 2000: - print("Too large cif file, skipping it for now...") + print("cif file is too large, skipping it for now...") tmpstr = "Failed to featurize %s: large primitive cell\n"%(name) write2file(path,"/FailedStructures.log", tmpstr) return None, None diff --git a/molSimplify/Informatics/autocorrelation.py b/molSimplify/Informatics/autocorrelation.py index 1c169a32..5a0463df 100644 --- a/molSimplify/Informatics/autocorrelation.py +++ b/molSimplify/Informatics/autocorrelation.py @@ -368,8 +368,8 @@ def deltametric_catoms(mol, prop_vec, orig, d, oct=True, catoms=None): return (result_vector) -def full_autocorrelation(mol, prop, d, oct=oct, modifier=False, use_dist=False): - w = construct_property_vector(mol, prop, oct=oct, modifier=modifier) +def full_autocorrelation(mol, prop, d, oct=oct, modifier=False, use_dist=False, transition_metals_only=True): + w = construct_property_vector(mol, prop, oct=oct, modifier=modifier, transition_metals_only=transition_metals_only) index_set = list(range(0, mol.natoms)) autocorrelation_vector = np.zeros(d + 1) for centers in index_set: @@ -632,7 +632,7 @@ def layer_density_in_3D(mol, prop_vec, orig, d, oct=True): return result_vector -def construct_property_vector(mol: mol3D, prop: str, oct=True, modifier=False): +def construct_property_vector(mol: mol3D, prop: str, oct=True, modifier=False, transition_metals_only=True): # # assigns the value of property # # for atom i (zero index) in mol # # to position i in returned vector @@ -727,7 +727,7 @@ def construct_property_vector(mol: mol3D, prop: str, oct=True, modifier=False): done = True elif prop == 'num_bonds': for i, atom in enumerate(mol.getAtoms()): - if not atom.ismetal(): + if not atom.ismetal(transition_metals_only): w[i] = globs.bondsdict()[atom.symbol()] else: w[i] = len(mol.getBondedAtomsSmart(i, oct=oct)) @@ -1751,7 +1751,7 @@ def generate_full_complex_autocorrelations(mol, loud, def generate_full_complex_coulomb_autocorrelations(mol, loud, depth=3, oct=True, flag_name=False, modifier=False, - use_dist=False): + use_dist=False, transition_metals_only=True): result = list() colnames = [] # allowed_strings = ['ident', 'topology', 'bondvalence', 'valenceelectron', 'bondvalence_devi', 'bodavrg', 'bodstd', @@ -1762,7 +1762,8 @@ def generate_full_complex_coulomb_autocorrelations(mol, loud, for ii, properties in enumerate(allowed_strings): metal_ac = full_autocorrelation(mol, properties, depth, oct=oct, modifier=modifier, - use_dist=use_dist) + use_dist=use_dist, + transition_metals_only=transition_metals_only) this_colnames = [] for i in range(0, depth + 1): this_colnames.append(labels_strings[ii] + '-' + str(i)) diff --git a/molSimplify/Informatics/geometrics.py b/molSimplify/Informatics/geometrics.py index fef36431..a60ea60e 100644 --- a/molSimplify/Informatics/geometrics.py +++ b/molSimplify/Informatics/geometrics.py @@ -1,7 +1,7 @@ import numpy as np import json -from pkg_resources import resource_filename, Requirement +from importlib_resources import files as resource_files from molSimplify.Classes.mol3D import mol3D @@ -17,7 +17,7 @@ def get_percentile_csd_geometrics(geometrics_csd, geodict, geotype, maxdent, metrics: list, a list of geometric considered. path2metric: str, the molSimplify path to load geometrics_csd if geometrics_csd is not specified ''' - jsonpath = resource_filename(Requirement.parse("molSimplify"), path2metric) + jsonpath = resource_files("molSimplify").joinpath(path2metric) if not isinstance(geometrics_csd, dict): print("loading csd geometrics...") with open(jsonpath, "r") as f: diff --git a/molSimplify/Scripts/dbinteract.py b/molSimplify/Scripts/dbinteract.py index 488a04a3..7722d058 100644 --- a/molSimplify/Scripts/dbinteract.py +++ b/molSimplify/Scripts/dbinteract.py @@ -7,6 +7,7 @@ import os +import sys import re import shutil import string @@ -162,13 +163,13 @@ def getsimilar(smi, nmols, dbselect, finger, squery, args): print(('database set up :' + str(dbsdf) + ' || ' + str(dbfs))) print(('Finding results similar, comparing to ' + smi)) - obab = 'babel' + obab = 'obabel' if dbfs and args.dbfs: com = obab + ' ' + dbfs + ' ' + 'simres.smi -d -xf' + \ finger + ' -s"' + smi + '" -al' + nmols else: mybash(obab + ' -isdf ' + dbsdf + ' -osdf -O tmp.sdf -d') - com = obab + ' tmp.sdf simres.smi -xf' + finger + ' -s"' + smi + '"' + com = obab + ' tmp.sdf -O simres.smi -xf' + finger + ' -s"' + smi + '"' # perform search using bash commandline print('Performing substructure search:') print(('running: ' + str(com))) @@ -306,7 +307,7 @@ def checkels(fname, allowedels): # @param outf Filename containing SMILES strings to be processed # @param n Number of dissimilar molecules required def dissim(outf, n): - obab = 'babel' + obab = 'obabel' # clone hitlist file hit_list_path = "hitlist.smi" @@ -317,7 +318,7 @@ def dissim(outf, n): f.writelines(smiles_list) # generate fs of original hit list - mybash(obab + ' -ismi ' + hit_list_path + ' -osdf tmp.sdf') + mybash(obab + ' -ismi ' + hit_list_path + ' -osdf -O tmp.sdf') mybash(obab + ' tmp.sdf -ofs') # number of hits numcpds = mybash('obabel tmp.sdf -onul') @@ -400,7 +401,10 @@ def matchsmarts(smarts, outf, catoms, args): obConversion = openbabel.OBConversion() # add obConversion.SetInAndOutFormats("smi", "smi") # add # print('!!!s:', s) - max_atoms = int(float_from_str(args.dbatoms)) + # Set practically infinite size limit + max_atoms = sys.maxsize + if args.dbatoms: # Overwrite max_atoms if dbatoms is given + max_atoms = int(float_from_str(args.dbatoms)) for i, mol in enumerate(s): obConversion.ReadString(moll, mol) # add sm.Match(moll) @@ -433,7 +437,7 @@ def dbsearch(rundir, args, globs): flag = False obab = 'obabel' - ### in any case do similarity search over indexed db ### + # in any case do similarity search over indexed db # outf = args.dbfname if args.dbfname else 'simres.smi' # output file # convert to SMILES/SMARTS if file if not args.dbbase: @@ -538,7 +542,7 @@ def dbsearch(rundir, args, globs): shutil.copy(plugin_path, 'plugindefines.txt') cmd = "sed -i '/nsmartsmatches/!b;n;c" + smistr + "' " + 'plugindefines.txt' mybash(cmd) - ### run substructure search ### + # run substructure search # nmols = '10000' if not args.dbnsearch else args.dbnsearch finger = 'FP2' if not args.dbfinger else args.dbfinger if int(nmols) > 3000 and args.gui: @@ -551,7 +555,7 @@ def dbsearch(rundir, args, globs): smistr, nmols, args.dbbase, finger, squery, args) try: shutil.copy('simres.smi', outf) - except FileNotFoundError: + except (FileNotFoundError, shutil.SameFileError): pass if args.debug: diff --git a/molSimplify/Scripts/io.py b/molSimplify/Scripts/io.py index 6e1a8657..6b566489 100644 --- a/molSimplify/Scripts/io.py +++ b/molSimplify/Scripts/io.py @@ -19,7 +19,7 @@ except ImportError: import openbabel # fallback to version 2 from typing import Any, List, Dict, Tuple, Union, Optional -from pkg_resources import resource_filename, Requirement +from importlib_resources import files as resource_files from molSimplify.Classes.globalvars import (globalvars, romans) @@ -34,8 +34,7 @@ def printgeoms(): if globs.custom_path: f = globs.custom_path + "/Data/coordinations.dict" else: - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Data/coordinations.dict") + f = resource_files("molSimplify").joinpath("Data/coordinations.dict") with open(f, 'r') as f: s = f.read().splitlines() s = [_f for _f in s if _f] @@ -64,8 +63,7 @@ def getgeoms(): if globs.custom_path: f = globs.custom_path + "/Data/coordinations.dict" else: - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Data/coordinations.dict") + f = resource_files("molSimplify").joinpath("Data/coordinations.dict") with open(f, 'r') as f: s = f.read().splitlines() s = [_f for _f in s if _f] @@ -164,8 +162,7 @@ def getlicores(flip: bool = True) -> Dict[str, Any]: if globs.custom_path: # test if a custom path is used: licores_path = str(globs.custom_path).rstrip('/') + "/Ligands/ligands.dict" else: - licores_path = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Ligands/ligands.dict") + licores_path = resource_files("molSimplify").joinpath("Ligands/ligands.dict") licores = readdict(licores_path) if flip: for ligand in list(licores.keys()): @@ -195,8 +192,7 @@ def getslicores() -> Dict[str, Any]: slicores_path = str(globs.custom_path).rstrip( '/') + "/Ligands/simple_ligands.dict" else: - slicores_path = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Ligands/simple_ligands.dict") + slicores_path = resource_files("molSimplify").joinpath("Ligands/simple_ligands.dict") slicores = readdict(slicores_path) return slicores @@ -245,8 +241,7 @@ def getbcores() -> dict: if globs.custom_path: # test if a custom path is used: bcores_path = str(globs.custom_path).rstrip('/') + "/Bind/bind.dict" else: - bcores_path = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Bind/bind.dict") + bcores_path = resource_files("molSimplify").joinpath("Bind/bind.dict") bcores = readdict(bcores_path) return bcores @@ -275,8 +270,7 @@ def getmcores(): if globs.custom_path: # test if a custom path is used: mcores = str(globs.custom_path).rstrip('/') + "/Cores/cores.dict" else: - mcores = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Cores/cores.dict") + mcores = resource_files("molSimplify").joinpath("Cores/cores.dict") mcores = readdict(mcores) return mcores @@ -306,8 +300,7 @@ def getsubcores(): subcores = str(globs.custom_path).rstrip( '/') + "/Substrates/substrates.dict" else: - subcores = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Substrates/substrates.dict") + subcores = resource_files("molSimplify").joinpath("Substrates/substrates.dict") subcores = readdict_sub(subcores) return subcores @@ -323,8 +316,7 @@ def loaddata(path: str) -> dict: if globs.custom_path: # test if a custom path is used: fname = str(globs.custom_path).rstrip('/') + path else: - fname = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify"+path) + fname = resource_files("molSimplify").joinpath(path.strip('/')) d = dict() with open(fname) as f: @@ -348,8 +340,7 @@ def loaddata_ts(path: str) -> dict: if globs.custom_path: # test if a custom path is used: fname = str(globs.custom_path).rstrip('/') + path else: - fname = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify"+path) + fname = resource_files("molSimplify").joinpath(path.strip('/')) d = dict() with open(fname) as f: @@ -452,8 +443,7 @@ def loadcoord(coord: str) -> List[List[float]]: if globs.custom_path: f = globs.custom_path + "/Data/" + coord + ".dat" else: - f = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Data/" + coord + ".dat") + f = resource_files("molSimplify").joinpath(f"Data/{coord}.dat") with open(f) as f: txt = [_f for _f in f.read().splitlines() if _f] b = [] @@ -485,8 +475,7 @@ def core_load(usercore: str, mcores: Optional[dict] = None) -> Tuple[Union[mol3D if globs.custom_path: fcore = globs.custom_path + "/Cores/" + dbentry[0] else: - fcore = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Cores/" + dbentry[0]) + fcore = str(resource_files("molSimplify").joinpath(f"Cores/{dbentry[0]}")) # check if core xyz/mol file exists if not glob.glob(fcore): emsg = "We can't find the core structure file %s right now! Something is amiss. Exiting..\n" % fcore @@ -582,8 +571,7 @@ def substr_load(usersubstrate: str, if globs.custom_path: fsubst = globs.custom_path + "/Substrates/" + var_list_sub_i[0] else: - fsubst = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Substrates/" + var_list_sub_i[0]) + fsubst = str(resource_files("molSimplify").joinpath(f"Substrates/{var_list_sub_i[0]}")) # check if substrate xyz/mol file exists if not glob.glob(fsubst): emsg = "We can't find the substrate structure file %s right now! Something is amiss. Exiting..\n" % fsubst @@ -706,8 +694,7 @@ def lig_load(userligand: str, licores: Optional[dict] = None) -> Tuple[Any, str] if globs.custom_path: flig = globs.custom_path + "/Ligands/" + dbentry[0] else: - flig = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Ligands/" + dbentry[0]) + flig = str(resource_files("molSimplify").joinpath(f"Ligands/{dbentry[0]}")) # check if ligand xyz/mol file exists print(('looking for '+flig)) if not os.path.isfile(flig): @@ -753,7 +740,6 @@ def lig_load(userligand: str, licores: Optional[dict] = None) -> Tuple[Any, str] lig.ffopt = dbentry[4][0] # load from file elif ('.mol' in userligand or '.xyz' in userligand or '.smi' in userligand or '.sdf' in userligand): - # flig = resource_filename(Requirement.parse("molSimplify"),"molSimplify/" +userligand) if glob.glob(userligand): ftype = userligand.split('.')[-1] # try and catch error if conversion doesn't work @@ -818,8 +804,7 @@ def bind_load(userbind: str, bindcores: dict) -> Tuple[Union[mol3D, None], bool, if globs.custom_path: fbind = globs.custom_path + "/Bind/" + bindcores[userbind][0] else: - fbind = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Bind/" + bindcores[userbind][0]) + fbind = str(resource_files("molSimplify").joinpath(f"Bind/{bindcores[userbind][0]}")) # check if bind xyz/mol file exists if not glob.glob(fbind): emsg = "We can't find the binding species structure file %s right now! Something is amiss. Exiting..\n" % fbind @@ -903,8 +888,7 @@ def getinputargs(args, fname: str): def plugin_defs() -> str: - plugin_path = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/plugindefines_reference.txt") + plugin_path = str(resource_files("molSimplify").joinpath("plugindefines_reference.txt")) return plugin_path # def get_name(args,rootdir,core,ligname,bind = False,bsmi = False): @@ -1144,16 +1128,11 @@ def copy_to_custom_path(): if not os.path.exists(globs.custom_path): os.makedirs(globs.custom_path) # copytree cannot overwrite, need to enusre directory does not exist already - core_dir = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Cores") - li_dir = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Ligands") - bind_dir = (resource_filename( - Requirement.parse("molSimplify"), "molSimplify/Bind")) - data_dir = (resource_filename( - Requirement.parse("molSimplify"), "molSimplify/Data")) - subs_dir = (resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/Substrates")) + core_dir = resource_files("molSimplify").joinpath("Cores") + li_dir = resource_files("molSimplify").joinpath("Ligands") + bind_dir = resource_files("molSimplify").joinpath("Bind") + data_dir = resource_files("molSimplify").joinpath("Data") + subs_dir = resource_files("molSimplify").joinpath("Substrates") if os.path.exists(str(globs.custom_path).rstrip("/")+"/Cores"): print('Note: removing old molSimplify data') shutil.rmtree(str(globs.custom_path).rstrip("/")+"/Cores") diff --git a/molSimplify/Scripts/krr_prep.py b/molSimplify/Scripts/krr_prep.py index 71661dd5..8e8df087 100644 --- a/molSimplify/Scripts/krr_prep.py +++ b/molSimplify/Scripts/krr_prep.py @@ -13,7 +13,7 @@ import matplotlib.pyplot as plt import matplotlib.ticker as ticker import pandas as pd -from pkg_resources import (resource_filename, Requirement) +from importlib_resources import files as resource_files import numpy as np @@ -692,8 +692,7 @@ def krr_model_predict(core3D, spin, mligcatom): if globs.custom_path: # test if a custom path is used: fpath = str(globs.custom_path).rstrip('/') + "/python_krr" else: - fpath = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/python_krr") + fpath = str(resource_files("molSimplify").joinpath("python_krr")) # load model f_model = fpath + '/hat_krr_model.pkl' with open(f_model, 'rb') as f: @@ -915,10 +914,8 @@ def invoke_KRR_from_mol3d_dQ(mol, charge): y_norm_train_csv = str(globs.custom_path).rstrip( '/') + "/python_krr/y_norm_train_TS.csv" else: - X_norm_train_csv = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/python_krr/X_norm_train_TS.csv") - y_norm_train_csv = resource_filename(Requirement.parse( - "molSimplify"), "molSimplify/python_krr/y_norm_train_TS.csv") + X_norm_train_csv = resource_files("molSimplify.python_krr").joinpath("X_norm_train_TS.csv") + y_norm_train_csv = resource_files("molSimplify.python_krr").joinpath("y_norm_train_TS.csv") with open(X_norm_train_csv, 'r') as f: for line in csv.reader(f): X_norm_train.append([float(i) for i in line]) diff --git a/molSimplify/Scripts/qcgen.py b/molSimplify/Scripts/qcgen.py index 482e0473..7826d6af 100644 --- a/molSimplify/Scripts/qcgen.py +++ b/molSimplify/Scripts/qcgen.py @@ -1291,7 +1291,7 @@ def molcbasis(strfiles, basistyp): # collect elements by rows in the periodic table for i in range(0, len(strfiles)): temp = mol3D() - temp.readfromxyz(strfiles[i]) + temp.readfromxyz(f"{strfiles[i]}.xyz") for atom in temp.getAtoms(): atno = atom.atno sym = atom.symbol() @@ -1365,7 +1365,7 @@ def molcras2s(strfiles): ras2s = [] for i in range(0, len(strfiles)): temp = mol3D() - temp.readfromxyz(strfiles[i]) + temp.readfromxyz(f"{strfiles[i]}.xyz") metal_ind = temp.findMetal() ras2 = 0 for ind in metal_ind: @@ -1399,7 +1399,7 @@ def molcnactels(strfiles, oxnum): nactels = [] for i in range(0, len(strfiles)): temp = mol3D() - temp.readfromxyz(strfiles[i]) + temp.readfromxyz(f"{strfiles[i]}.xyz") metal_ind = temp.findMetal() nactel = 0 for ind in metal_ind: @@ -1432,7 +1432,7 @@ def molcfrozens(strfiles): for i in range(0, len(strfiles)): frozen = 0 temp = mol3D() - temp.readfromxyz(strfiles[i]) + temp.readfromxyz(f"{strfiles[i]}.xyz") for atom in temp.getAtoms(): atno = atom.atno if atno > 2 and atno <= 10: diff --git a/molSimplify/job_manager/__init__.py b/molSimplify/job_manager/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/molSimplify/job_manager/classes.py b/molSimplify/job_manager/classes.py deleted file mode 100644 index 5416f6db..00000000 --- a/molSimplify/job_manager/classes.py +++ /dev/null @@ -1,238 +0,0 @@ -import pickle -import os - - -def try_float(obj): - """Tries to convert an item into a floating point value. - - Parameters - ---------- - obj : str, int - Object of any type to be converted to float. - - Returns - ------- - floating_point : float - Floating point version of object. If fails, returns object itself. - - """ - # Converts an object to a floating point if possible - try: - floating_point = float(obj) - except ValueError: - floating_point = obj - return floating_point - - -def strip_new_line(string): - """Tries to strip string of new line. - - Parameters - ---------- - string : str - Input string. - - Returns - ------- - output : str - Output string with newline characters removed.. - - """ - if string[-1] == '\n': - return string[:-1] - else: - return string - - -class resub_history: - """Resub history class that stores the information about a given job. - Class for saving information about previous resubmissions. - - Parameters - ---------- - path : str, optional - Path to place resub history object. Default is None. - - Example use of history object - - >>> resub = resub_history() - # do this step even if no pickle file exists already - >>> resub.read(outfile_path) - >>> resub.save() # update stored values - - """ - - def __init__(self, path=None): - self.resub_number = 0 - self.status = 'Normal' - self.needs_resub = False - self.notes = [] - self.outfiles = [] - self.infiles = [] - self.xyzs = [] - self.jobscripts = [] - self.waiting = None # Path to another job that this job is waiting on - self.path = path - self.manually_abandoned = False - - def save(self): - """Saves the current status of the history object. - """ - - if self.path is None: - raise Exception( - 'The path for the resub_history pickel file is not specified!') - with open(self.path, 'wb') as handle: - pickle.dump(self, handle, protocol=pickle.HIGHEST_PROTOCOL) - - def read(self, path): - """Read an output file with a given path. - - Parameters - ---------- - path : str, optional - Path of output file to read into history object. - - """ - - if path.endswith('.out'): - path = path.rsplit('.', 1)[0]+'.pickle' - - if os.path.isfile(path): - with open(path, 'rb') as handle: - saved = pickle.load(handle) - self.resub_number = saved.resub_number - self.status = saved.status - self.needs_resub = saved.needs_resub - self.notes = saved.notes - self.outfiles = saved.outfiles - if hasattr(saved, 'infiles'): - self.infiles = saved.infiles - if hasattr(saved, 'xyzs'): - self.xyzs = saved.xyzs - if hasattr(saved, 'jobscripts'): - self.jobscripts = saved.jobscripts - if hasattr(saved, 'waiting'): - self.waiting = saved.waiting - if hasattr(saved, 'manually_abandoned'): - self.manually_abandoned = saved.manually_abandoned - self.path = path - - def abandon(self): - """Bound method to abandon a job manually. - """ - self.manually_abandoned = True - self.status = 'Manually abandoned' - - -class textfile: - """ - Class for importing textfiles in a searchable way. - Parameters - ---------- - file_name : str, optional - Path to file to read. Default is None. - """ - def __init__(self, file_name=None): - """ - Initilization for textfile - - Parameters - ---------- - file_name : str, optional - Path to file to read. Default is None. - """ - if file_name: - with open(file_name, 'r') as fin: - self.lines = fin.readlines() - self.lines = [strip_new_line(i) for i in self.lines] - - else: - self.lines = None - - def wordgrab(self, keywords, indices, last_line=False, first_line=False, min_value=False, matching_index=False): - """Method to grab words from text. Takes two lists as input. - - Parameters - ---------- - keywords : list - Keywords to look for. - indices : list - Indices to pull from the matching lines - last_line : bool, optional - Gets the last instance of the match in the text file. Default is False. - first_line : bool, optional - Gets the first instance of the match in the text file. Default is False. - min_value : bool, optional - Gets the smallest instance of the match in the text file. Default is False. Numeric values converted to floats. - matching_index : bool, optional - Gives you the indices of the lines that match. Default is False. - - Returns - ------- - results_to_return : list - List of results of scraping. Be careful with the nesting (returns a list of lists). - - """ - # takes two lists as an input - # The first list is the keywords to look for - # The second list is the indices to pull from the matching lines - # Returns a list of the resulting values. Numeric values are automatically converted to floats - # Function is most intuitive when ONE of the following is set to True (last_line,first_line,min_value) - # Otherwise, the list will be nested one more time than you may expect - - if type(keywords) != list: - keywords = [keywords] - if type(indices) != list: - indices = [indices]*len(keywords) - - results = dict() - zipped_values = list(zip(keywords, indices, list(range(len(keywords))))) - - for counter, line in enumerate(self.lines): - for keyword, index, keyword_number in zipped_values: - if keyword in line: - - if type(index) == int: - matching_value = try_float(line.split()[index]) - else: - matching_value = line.split() - - # Normal Procedure - if not matching_index: - if keyword_number not in list(results.keys()): - results[keyword_number] = [matching_value] - else: - results[keyword_number].append(matching_value) - - # Special procedure for returning the index of matching lines instead of the matching values - if matching_index: - if keyword_number not in list(results.keys()): - results[keyword_number] = [counter] - else: - results[keyword_number].append(counter) - - if (last_line and min_value) or (last_line and first_line) or (first_line and min_value): - raise ValueError('Warning, incompatible options selected in text parsing') - - if last_line: - for keyword_number in list(results.keys()): - results[keyword_number] = results[keyword_number][-1] - if first_line: - for keyword_number in list(results.keys()): - results[keyword_number] = results[keyword_number][0] - if min_value: - for keyword_number in list(results.keys()): - results[keyword_number] = min(results[keyword_number]) - - results_to_return = [] - for key in range(len(keywords)): - if key in list(results.keys()): - results_to_return.append(results[key]) - else: - if last_line or min_value or first_line: - results_to_return.append(None) - else: - results_to_return.append([None]) - - return results_to_return diff --git a/molSimplify/job_manager/configure_example.txt b/molSimplify/job_manager/configure_example.txt deleted file mode 100644 index 3545e619..00000000 --- a/molSimplify/job_manager/configure_example.txt +++ /dev/null @@ -1,26 +0,0 @@ -#configure file should be named as "configure" and placed in the home directory -solvent 10.3 78.9 -functionalsSP wpbeh camb3lyp wb97x -vertEA -vertIP -thermo -hfx_resample -general_sp: sp_config.json - -dissociation -dissociated_ligand_charge:O1 -2 -dissociated_ligand_charge:H1O1 -1 -dissociated_ligand_charge:H1O2 -1 -dissociated_ligand_charge:C5H7O2 -1 -dissociated_ligand_spinmult:O2 3 - -max_jobs:10 -hard_job_limit:200 -max_resub:5 -levela:0.25 -levelb:0.25 -method:b3lyp -hfx:0.2 -sleep:1000 -geo_check:bidentate_oct -job_recovery:[bad_geo,spin_contaminated,scf,thermo_grad_error] diff --git a/molSimplify/job_manager/manager_io.py b/molSimplify/job_manager/manager_io.py deleted file mode 100644 index 88229676..00000000 --- a/molSimplify/job_manager/manager_io.py +++ /dev/null @@ -1,905 +0,0 @@ -import os -import glob -import copy -import numpy as np -import subprocess -import pandas as pd -import shutil -from molSimplify.job_manager.classes import resub_history, textfile -from ast import literal_eval -import json - - -def try_float(obj): - # Converts an object to a floating point if possible - try: - floating_point = float(obj) - except ValueError: - floating_point = obj - except TypeError: - floating_point = obj - return floating_point - - -def convert_to_absolute_path(path): - if path[0] != '/': - path = os.path.join(os.getcwd(), path) - - return path - - -def read_outfile(outfile_path, short_ouput=False, long_output=True): - ## Reads TeraChem and ORCA outfiles - # @param outfile_path complete path to the outfile to be read, as a string - # @return A dictionary with keys finalenergy,s_squared,s_squared_ideal,time - output = textfile(outfile_path) - output_type = output.wordgrab(['TeraChem', 'ORCA'], ['whole_line', 'whole_line']) - # print("output_type: ", output_type) - for counter, match in enumerate(output_type): - if match[0]: - break - if counter == 1: - if 'nohup' in outfile_path: - print('Warning! Nohup file caught in outfile processing') - print(outfile_path) - counter = 0 - elif 'smd.out' in outfile_path: - print('Warning! SMD file caught in outfile processing') - print(outfile_path) - counter = 0 - elif ('atom' in outfile_path) and ('ORCA' in output_type): - print('Density fitting output caught in outfile processing') - print(outfile_path) - counter = 0 - else: - print('.out file type not recognized for file: ' + outfile_path) - return_dict = {'name': None, 'charge': None, 'finalenergy': None, - 'time': None, 's_squared': None, 's_squared_ideal': None, - 'finished': False, 'min_energy': None, 'scf_error': False, - 'thermo_grad_error': False, 'solvation_energy': None, 'optimization_cycles': None, - 'thermo_vib_energy': None, 'thermo_vib_free_energy': None, 'thermo_suspect': None, - 'orbital_occupation': None, 'oscillating_scf_error': False} - return return_dict - - output_type = ['TeraChem', 'ORCA'][counter] - - name = None - finished = False - charge = None - finalenergy = None - min_energy = None - s_squared = None - s_squared_ideal = None - scf_error = False - time = None - thermo_grad_error = False - implicit_solvation_energy = None - geo_opt_cycles = None - thermo_vib = None - thermo_vib_f = None - thermo_suspect = None - orbital_occupation = None - oscillating_scf_error = False - - name = os.path.split(outfile_path)[-1] - name = name.rsplit('.', 1)[0] - if output_type == 'TeraChem': - - charge = output.wordgrab(['charge:'], [2], first_line=True)[0] - if charge: - charge = int(charge) - if not short_ouput: - (finalenergy, s_squared, s_squared_ideal, time, thermo_grad_error, - implicit_solvation_energy, geo_opt_cycles, - thermo_vib, thermo_vib_f, thermo_suspect) = output.wordgrab( - ['FINAL', 'S-SQUARED:', 'S-SQUARED:', 'processing', - 'Maximum component of gradient is too large', - 'C-PCM contribution to final energy:', - 'Optimization Cycle', 'Thermal vibrational energy', - 'Thermal vibrational free energy', - 'Thermochemical Analysis is Suspect'], - [2, 2, 4, 3, 0, 4, 3, 7, 10, 0], last_line=True) - if short_ouput: - s_squared, s_squared_ideal, thermo_grad_error = output.wordgrab( - ['S-SQUARED:', 'S-SQUARED:', 'Maximum component of gradient is too large'], - [2, 4, 0], last_line=True) - oscillating_scf = get_scf_progress(outfile_path) - if oscillating_scf: - oscillating_scf_error = True - else: - oscillating_scf_error = False - if thermo_grad_error: - thermo_grad_error = True - else: - thermo_grad_error = False - if thermo_suspect: - thermo_suspect = True - else: - thermo_suspect = False - - if s_squared_ideal: - s_squared_ideal = float(s_squared_ideal.strip(')')) - if implicit_solvation_energy: - implicit_solvation_energy = try_float(implicit_solvation_energy.split(':')[-1]) - - min_energy = output.wordgrab('FINAL', 2, min_value=True)[0] - - is_finished = output.wordgrab(['finished:'], 'whole_line', last_line=True)[0] - if is_finished: # for full optimization - if is_finished[0] == 'Job' and is_finished[1] == 'finished:': - finished = True - - is_finished = output.wordgrab(['processing'], 'whole_line', last_line=True)[0] - if is_finished: # for hydrogen optimization - if is_finished[0] == 'Total' and is_finished[1] == 'processing': - finished = True - - is_scf_error = output.wordgrab('DIIS', 5, matching_index=True)[0] - if is_scf_error[0]: - is_scf_error = [output.lines[i].split() for i in is_scf_error] - else: - is_scf_error = [] - if type(is_scf_error) == list and len(is_scf_error) > 0: - for scf in is_scf_error: - if ('failed' in scf) and ('converge' in scf) and ('iterations,' in scf) and ('ADIIS' in scf): - scf = scf[5] - scf = int(scf.split('+')[0]) - if scf > 5000: - scf_error = [True, scf] - if long_output: - nbo_start, nbo_end = output.wordgrab(['NATURAL POPULATIONS: Natural atomic orbital occupancies', - 'Summary of Natural Population Analysis:'], 'whole_line', - matching_index=True, first_line=True) - if nbo_start and nbo_end: - nbo_lines = output.lines[nbo_start:nbo_end] - nbo_lines = [line for line in nbo_lines if len(line.split()) > 0] # filter out empty lines - nbo_lines = [line for line in nbo_lines if line.split()[0].isdigit()] # filter only results lines - nbo_lines = [line for line in nbo_lines if line.split()[4] == 'Val('] # filter only valence orbitals - - if len(nbo_lines) > 0: - orbital_occupation = dict() - for line in nbo_lines: - key = line.split()[1] + '_' + line.split()[2] + '_' + line.split()[3] - if key in orbital_occupation.keys(): - raise Exception(outfile_path + ' ' + key + ': Same key found twice in nbo parsing!') - if len(line.split()) > 8: # for open shell systems - orbital_occupation[key] = [float(line.split()[-3]), float(line.split()[-1])] - else: # For closed shell systems - orbital_occupation[key] = [float(line.split()[-2]), float(0)] - - if output_type == 'ORCA': - finished, finalenergy, s_squared, s_squared_ideal, implicit_solvation_energy = output.wordgrab( - ['****ORCA TERMINATED NORMALLY****', 'FINAL', '', 'S*(S+1)', 'CPCM Dielectric :'], - [0, -1, -1, -1, 3], last_line=True) - if finished == '****ORCA': - finished = True - - timekey = output.wordgrab('TOTAL RUN TIME:', 'whole_line', last_line=True)[0] - if type(timekey) == list: - time = (float(timekey[3]) * 24 * 60 * 60 - + float(timekey[5]) * 60 * 60 - + float(timekey[7]) * 60 - + float(timekey[9]) - + float(timekey[11]) * 0.001) - - if finished: - charge = output.wordgrab(['Total Charge'], [-1], last_line=True)[0] - charge = int(round(charge, 0)) # Round to nearest integer value (it should always be very close) - - opt_energies = output.wordgrab('FINAL SINGLE POINT ENERGY', -1)[0] - geo_opt_cycles, min_energy = len(opt_energies), min(opt_energies) - - return_dict = {} - return_dict['name'] = name - return_dict['charge'] = charge - return_dict['finalenergy'] = try_float(finalenergy) - return_dict['time'] = try_float(time) - return_dict['s_squared'] = try_float(s_squared) - return_dict['s_squared_ideal'] = try_float(s_squared_ideal) - return_dict['finished'] = finished - return_dict['min_energy'] = try_float(min_energy) - return_dict['scf_error'] = scf_error - return_dict['thermo_grad_error'] = thermo_grad_error - return_dict['solvation_energy'] = implicit_solvation_energy - return_dict['optimization_cycles'] = geo_opt_cycles - return_dict['thermo_vib_energy'] = try_float(thermo_vib) - return_dict['thermo_vib_free_energy'] = try_float(thermo_vib_f) - return_dict['thermo_suspect'] = thermo_suspect - return_dict['orbital_occupation'] = orbital_occupation - return_dict['oscillating_scf_error'] = oscillating_scf_error - return_dict['outfile_path'] = outfile_path - return return_dict - - -def read_infile(outfile_path): - # Takes the path to either the outfile or the infile of a job - # Returns a dictionary of the job settings included in that infile - - root = outfile_path.rsplit('.', 1)[0] - unique_job_name = os.path.split(root)[-1] - inp = textfile(root + '.in') - if '#ORCA' in inp.lines[0]: - qm_code = 'orca' - else: - qm_code = 'terachem' - - if qm_code == 'terachem': - # account for multiple keywords for dispersion - disp0 = inp.wordgrab(['dispersion '], [1], last_line=True) - disp1 = inp.wordgrab(['dftd '], [1], last_line=True) - if disp0 != [None]: - dispersion = disp0[0] - else: - dispersion = disp1[0] - charge, spinmult, solvent, run_type, levelshifta, levelshiftb, method, hfx, basis, coordinates, guess = inp.wordgrab( - ['charge ', 'spinmult ', 'epsilon ', - 'run ', 'levelshiftvala ', - 'levelshiftvalb ', 'method ', - 'HFX ', 'basis ', 'coordinates ', 'guess '], - [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], - last_line=True) - charge, spinmult = int(charge), int(spinmult) - if guess: - guess = True - else: - guess = False - if method[0] == 'u': - method = method[1:] - - convergence_thresholds = inp.wordgrab( - ['min_converge_gmax ', 'min_converge_grms ', 'min_converge_dmax ', 'min_converge_drms ', 'min_converge_e ', - 'convthre '], - [1] * 6, last_line=True) - if not convergence_thresholds[0]: - convergence_thresholds = None - - multibasis = inp.wordgrab(['$multibasis', '$end'], [0, 0], last_line=True, matching_index=True) - if not multibasis[0]: - multibasis = False - else: - multibasis = inp.lines[multibasis[0] + 1:multibasis[1]] - - constraints = inp.wordgrab(['$constraint_freeze', '$end'], [0, 0], last_line=True, matching_index=True) - if not constraints[0]: - constraints = False - else: - constraints = inp.lines[constraints[0] + 1:constraints[1]] - - if constraints and multibasis: - raise Exception( - 'The current implementation of tools.read_infile() is known to behave poorly when an infile specifies both a multibasis and constraints') - - else: # qm_code == 'orca': - ligand_basis, run_type, method, parallel_environment, charge, spinmult, coordinates = inp.wordgrab( - ['! MULLIKEN'] * 3 + [r'%pal'] + [r'xyzfile'] * 3, - [2, 3, 4, 2, 1, 2, 3], last_line=True) - - charge, spinmult = int(charge), int(spinmult) - if run_type == 'opt': - run_type = 'minimize' - - levelshift, solvent, metal_basis = inp.wordgrab([r'%scf', r'%cpcm', r'%basis'], [0] * 3, - matching_index=True, last_line=True) - - if levelshift: - levelshift = inp.lines[levelshift + 1] - levelshift = levelshift.split() - levelshift = levelshift[2] - if solvent: - solvent = inp.lines[solvent + 1] - solvent = solvent.split() - solvent = solvent[1] - if metal_basis: - metal_basis = inp.lines[metal_basis + 1] - metal_basis = metal_basis.split() - metal_basis = metal_basis[2] - metal_basis = metal_basis[1:-1] - - levelshifta, levelshiftb = levelshift, levelshift - if ligand_basis == '6-31G*' and metal_basis == 'LANL2DZ': - basis = 'lacvps_ecp' - else: - raise Exception( - 'read_infile() is unable to parse this basis set/ecp combo: ' + ligand_basis + ' ' + metal_basis) - - # The following settings should not appear in a orca infile because they are not specified in the write_input() functionality for orca - hfx, convergence_thresholds, multibasis, dispersion, guess, constraints = None, None, None, None, None, None - - return_dict = {} - - for prop, prop_name in zip([unique_job_name, charge, spinmult, solvent, run_type, levelshifta, levelshiftb, method, hfx, - basis, convergence_thresholds, multibasis, constraints, dispersion, coordinates, guess, - qm_code], - ['name', 'charge', 'spinmult', 'solvent', 'run_type', 'levelshifta', 'levelshiftb', - 'method', 'hfx', - 'basis', 'convergence_thresholds', 'multibasis', 'constraints', 'dispersion', - 'coordinates', 'guess', 'qm_code']): - return_dict[prop_name] = prop - return return_dict - - -# Read the global and local configure files to determine the derivative jobs requested and the settings for job recovery -# The global configure file should be in the same directory where resub() is called -# The local configure file should be in the same directory as the .out file -def read_configure(home_directory, outfile_path): - def load_configure_file(directory): - def strip_new_line(string): - if string[-1] == '\n': - return string[:-1] - else: - return string - - if directory == 'in place': - directory = os.getcwd() - - configure = os.path.join(directory, 'configure') - if os.path.isfile(configure): - with open(configure, 'r') as f: - configure = f.readlines() - configure = list(map(strip_new_line, configure)) - return configure - else: - return [] - home_configure = load_configure_file(home_directory) - if outfile_path: - local_configure = load_configure_file(os.path.split(outfile_path)[0]) - else: - local_configure = [] - # Determine which derivative jobs are requested - solvent, vertEA, vertIP, thermo, dissociation, hfx_resample, functionalsSP, mbe = False, False, False, False, False, False, False, False - for line in home_configure + local_configure: - if 'solvent' in line or 'Solvent' in line: - solvent = [float(p) for p in line.split()[1:]] - if 'vertEA' in line or 'VertEA' in line: - vertEA = True - if 'vertIP' in line or 'VertIP' in line: - vertIP = True - if 'functionalsSP' in line or 'FunctionalsSP' in line: - functionalsSP = [str(p) for p in line.split()[1:]] - if ('thermo' in line and 'thermo_grad_error' not in line) or ('Thermo' in line and 'Thermo_grad_error' not in line): - thermo = True - if 'dissociation' in line or 'Dissociation' in line: - dissociation = True - if 'hfx_resample' in line or 'HFX_resample' in line: - hfx_resample = True - if 'mbe' in line or "MBE" in line: - mbe = True - - # Determine global settings for this run - max_jobs, max_resub, levela, levelb, method, hfx, geo_check, sleep, job_recovery, dispersion = False, False, False, False, False, False, False, False, [], False - ss_cutoff, hard_job_limit, use_molscontrol, general_sp = False, False, False, False - run_psi4, psi4_config = False, {} - dissociated_ligand_charges, dissociated_ligand_spinmults = {}, {} - for configure in [home_configure, local_configure]: - for line in configure: - if 'max_jobs' in line.split(':'): - max_jobs = int(line.split(':')[-1]) - if 'max_resub' in line.split(':'): - max_resub = int(line.split(':')[-1]) - if 'levela' in line.split(':'): - levela = float(line.split(':')[-1]) - if 'levelb' in line.split(':'): - levelb = float(line.split(':')[-1]) - if 'method' in line.split(':'): - method = line.split(':')[-1] - if 'hfx' in line.split(':'): - hfx = float(line.split(':')[-1]) - if 'geo_check' in line.split(':'): - geo_check = line.split(':')[-1] - if 'sleep' in line.split(':'): - sleep = int(line.split(':')[-1]) - if 'job_recovery' in line.split(':'): - job_recovery = line.split(':')[-1] - # convert the string form of a python list to an actual list - job_recovery = job_recovery[1:-1] - job_recovery = job_recovery.split(',') - if 'dispersion' in line.split(':'): - dispersion = line.split(':')[-1] - if 'ss_cutoff' in line.split(':'): - ss_cutoff = float(line.split(':')[-1]) - if 'hard_job_limit' in line.split(':'): - hard_job_limit = int(line.split(':')[-1]) - if 'dissociated_ligand_charge' in line.split(':'): - dissociated_ligand_charges[line.split(':')[-1].split()[0]] = int(line.split(':')[-1].split()[1]) - if 'dissociated_ligand_spinmult' in line.split(':'): - dissociated_ligand_spinmults[line.split(':')[-1].split()[0]] = int(line.split(':')[-1].split()[1]) - if "use_molscontrol" in line.split(':'): - use_molscontrol = bool(int(line.split(":")[-1])) - if "general_sp" in line.split(':'): - print("general SP jobs activated.") - localpath = line.split(":")[-1].replace(" ", "") - if os.path.isfile(localpath): - with open(os.getcwd() + "/" + localpath, "r") as f: - try: - general_sp = json.load(f) - except json.JSONDecodeError: - raise ValueError("%s is not a valid json file." % localpath) - else: - raise ValueError("%s does not exits." % localpath) - if "run_psi4" in line.split(':'): - print("Psi4 jobs activated.") - run_psi4 = True - localpath = line.split(":")[-1].replace(" ", "") - if os.path.isfile(localpath): - with open(os.getcwd() + "/" + localpath, "r") as f: - try: - psi4_config = json.load(f) - except json.JSONDecodeError: - raise ValueError("%s is not a valid json file." % localpath) - else: - raise ValueError("%s does not exits." % localpath) - # If global settings not specified, choose defaults: - if (not max_jobs) and isinstance(max_jobs, bool): - max_jobs = 50 - if not max_resub: - max_resub = 5 - if not levela: - levela = 0.25 - if not levelb: - levelb = 0.25 - if not method: - method = 'b3lyp' - if not hfx: - hfx = 0.20 - if not sleep: - sleep = 7200 - if not ss_cutoff: - ss_cutoff = 1.0 - if (not hard_job_limit): - hard_job_limit = 190 - - return {'solvent': solvent, 'vertEA': vertEA, 'vertIP': vertIP, 'thermo': thermo, 'dissociation': dissociation, - 'hfx_resample': hfx_resample, 'max_jobs': max_jobs, 'max_resub': max_resub, 'levela': levela, - 'levelb': levelb, 'method': method, 'hfx': hfx, 'geo_check': geo_check, 'sleep': sleep, - 'job_recovery': job_recovery, 'dispersion': dispersion, 'functionalsSP': functionalsSP, - 'ss_cutoff': ss_cutoff, 'hard_job_limit': hard_job_limit, - 'dissociated_ligand_spinmults': dissociated_ligand_spinmults, - 'dissociated_ligand_charges': dissociated_ligand_charges, - "use_molscontrol": use_molscontrol, "general_sp": general_sp, - "run_psi4": run_psi4, "psi4_config": psi4_config, 'mbe': mbe} - - -def read_charges(PATH): - # Takes the path to either the outfile or the charge_mull.xls and returns the charges - PATH = convert_to_absolute_path(PATH) - if len(PATH.rsplit('.', 1)) > 1: - if PATH.rsplit('.', 1)[1] == 'out': - PATH = os.path.join(os.path.split(PATH)[0], 'scr', 'charge_mull.xls') - try: - charge_mull = textfile(PATH) - split_lines = [i.split() for i in charge_mull.lines] - charges = [i[1] + ' ' + i[2] for i in split_lines] - return charges - except: - return [] - - -def read_mullpop(PATH): - # Takes the path to either the outfile or the mullpop and returns the mullikan populations - PATH = convert_to_absolute_path(PATH) - if len(PATH.rsplit('.', 1)) > 1: - if PATH.rsplit('.', 1)[1] == 'out': - PATH = os.path.join(os.path.split(PATH)[0], 'scr', 'mullpop') - - mullpop = textfile(PATH) - ### If multiple frames in mullpop, grab last frame - total_lines = mullpop.wordgrab(['------------ ---------- ----------'], [1], matching_index=True)[0] - if len(total_lines) > 1: - mullpop.lines = mullpop.lines[total_lines[-2] + 2:] - - split_lines = [i.split() for i in mullpop.lines] - if len(split_lines[2]) == 6: - pops = [i[1] + ' ' + i[5] for i in split_lines[1:-2]] - else: - pops = [i[1] + ' ' + i[5] + ' ' + i[9] for i in split_lines[2:-2]] - - return pops - - -def write_input(input_dictionary=dict(), name=None, charge=None, spinmult=None, - run_type='energy', method='b3lyp', solvent=False, - guess=False, custom_line=None, levelshifta=0.25, levelshiftb=0.25, - convergence_thresholds=None, basis='lacvps_ecp', hfx=None, constraints=None, - multibasis=False, coordinates=False, dispersion=False, qm_code='terachem', - parallel_environment=4, precision='dynamic', dftgrid=1, dynamicgrid='yes', - machine='gibraltar'): - # Writes a generic input file for terachem or ORCA - # The neccessary parameters can be supplied as arguements or as a dictionary. If supplied as both, the dictionary takes priority - - infile = dict() - # If the input_dictionary exists,parse it and set the parameters, overwritting other specifications - for prop, prop_name in zip([charge, spinmult, solvent, run_type, levelshifta, levelshiftb, method, hfx, - basis, convergence_thresholds, multibasis, constraints, dispersion, coordinates, - guess, custom_line, qm_code, parallel_environment, name, precision, dftgrid, - dynamicgrid, machine], - ['charge', 'spinmult', 'solvent', 'run_type', 'levelshifta', 'levelshiftb', 'method', - 'hfx', - 'basis', 'convergence_thresholds', 'multibasis', 'constraints', 'dispersion', - 'coordinates', 'guess', 'custom_line', 'qm_code', 'parallel_environment', 'name', - 'precision', 'dftgrid', 'dynamicgrid', 'machine']): - if prop_name in list(input_dictionary.keys()): - infile[prop_name] = input_dictionary[prop_name] - else: - infile[prop_name] = prop - - if (not infile['charge'] and infile['charge'] != 0) or (not infile['spinmult'] and infile['spinmult'] != 0) or ( - not infile['name']) or (not infile['coordinates']): - print(('Name: ' + infile['name'])) - print(('Charge: ' + str(infile['charge']))) - print(('Spinmult: ' + str(infile['spinmult']))) - raise Exception('Minimum parameters not specified for writing infile') - if type(infile['charge']) != int or type(infile['spinmult']) != int: - print(('Charge Type: ' + str(type(infile['charge'])))) - print(('Spinmult Type: ' + str(type(infile['spinmult'])))) - raise Exception('Spin and Charge should both be integers!') - - if infile['qm_code'] == 'terachem': - write_terachem_input(infile) - elif infile['qm_code'] == 'orca': - write_orca_input(infile) - else: - raise Exception('QM code: ' + infile['qm_code'] + ' not recognized!') - - -def write_terachem_input(infile_dictionary): - infile = infile_dictionary - - if infile['spinmult'] != 1: - infile['method'] = 'u' + infile['method'] - - text = ['levelshiftvalb ' + str(infile['levelshiftb']) + '\n', - 'levelshiftvala ' + str(infile['levelshifta']) + '\n', - 'run ' + infile['run_type'] + '\n', - 'scf diis+a\n', - 'coordinates ' + infile['coordinates'] + '\n', - 'levelshift yes\n', - 'spinmult ' + str(infile['spinmult']) + '\n', - 'scrdir ./scr\n', - 'basis ' + infile['basis'] + '\n', - 'timings yes\n', - 'charge ' + str(infile['charge']) + '\n', - 'method ' + str(infile['method']) + '\n', - 'precision ' + str(infile['precision']) + '\n', - 'dftgrid ' + str(infile['dftgrid']) + '\n', - 'dynamicgrid ' + str(infile['dynamicgrid']) + '\n', - 'new_minimizer yes\n', - 'ml_prop yes\n', - 'poptype mulliken\n', - 'bond_order_list yes\n', - 'end'] - - if infile['custom_line']: - text = text[:15] + [infile['custom_line'] + '\n'] + text[15:] - if infile['guess']: - if type(infile['guess']) == bool: - if infile['spinmult'] == 1: - infile['guess'] = 'c0' - else: - infile['guess'] = 'ca0 cb0' - text = text[:-1] + ['guess ' + infile['guess'] + '\n', - 'end'] - if infile['run_type'] != 'ts': - text = text[:-1] + ['maxit 500\n', - 'end'] - - if type(infile['convergence_thresholds']) == list: - if infile['convergence_thresholds'][0]: - thresholds = [line if line.endswith('\n') else line + '\n' for line in infile['convergence_thresholds']] - tight_thresholds = ("min_converge_gmax " + thresholds[0] + "min_converge_grms " - + thresholds[1] + "min_converge_dmax " + thresholds[2] - + "min_converge_drms " + thresholds[3] + "min_converge_e " - + thresholds[4] + "convthre " + thresholds[5]) - text = text[:-1] + ['\n', tight_thresholds, 'end'] - - if infile['dispersion']: - text = text[:-1] + ['dispersion ' + infile['dispersion'] + '\n', 'end'] - - if infile['multibasis']: - multibasis = [line if line.endswith('\n') else line + '\n' for line in infile['multibasis']] - text = text[:-1] + ['\n', '$multibasis\n'] + multibasis + ['$end\n', 'end'] - - if infile['constraints']: - constraints = [line if line.endswith('\n') else line + '\n' for line in infile['constraints']] - text = text[:-1] + ['\n', '$constraint_freeze\n'] + constraints + ['$end\n', 'end'] - - if type(infile['hfx']) == int or type(infile['hfx']) == float: - text = text[:-1] + ['\n', - 'HFX ' + str(infile['hfx']) + '\n', - 'end'] - - if infile['solvent']: # Adds solvent correction, if requested - text = text[:-1] + ['\n', - 'pcm cosmo\n', - 'epsilon %.2f\n' % float(infile['solvent']), - 'pcm_radii read\n', - 'pcm_radii_file /home/harperd/pcm_radii\n', - 'end'] - if infile['machine'] in ['gibraltar', 'bridges']: - text = text[:-1] + ['nbo yes\n', 'gpus 1\n', 'end'] - elif infile['machine'] in ['comet']: - text = text[:-1] + ['gpus 2\n', 'end'] - else: - raise ValueError('Machine not known!') - - with open(infile['name'] + '.in', 'w') as fout: - for lines in text: - fout.write(lines) - - -def write_orca_input(infile_dictionary): - infile = infile_dictionary - - # The orca input writting isn't as smart as the Terachem input writting - # Ensure that the orca input isn't passed a keyword that it doesn't know how to handle yet - if str(infile['levelshifta']) != str(infile['levelshiftb']): - raise Exception('ORCA input does not support 2 different levelshift values for openshell systems! ' + str( - infile['levelshifta']) + ' ' + str(infile['levelshiftb'])) - for element in ['constraints', 'dispersion', 'hfx', 'multibasis', 'convergence_thresholds', 'guess']: - if element in infile.keys(): - if infile[element]: - raise Exception('Keyword (' + element + ') not yet implemented for orca in the job manager') - - # ORCA requires explicit definition of the ECP and non-ecp basis - if infile['basis'] == 'lacvps_ecp': - ligand_basis = '6-31G*' - metal_basis = 'LANL2DZ' - else: - raise Exception(infile['basis'] + 'not implemented in the job manager for use with orca!') - - # Determine the atoms which need to have an effective core potential added - metals = ['Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', - 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd'] - metal_basis_line = '' - for metal in metals: - metal_basis_line += (' NewGTO ' + metal + ' "' + metal_basis + '" end\n') - - # Convert the keywords for run_type from terachem to orca - if infile['run_type'] == 'minimize': - infile['run_type'] = 'opt' - - # Note that max core is set to 2000MB, this is 2/3 of the amount allocated in the jobscript (on a per processor basis) - # The SCF is known (according to the ORCA manual) to exceed allotted memory, so this provides some wiggle room - if not infile['solvent']: - first_line = r'! MULLIKEN ' + ligand_basis + ' ' + infile['run_type'] + ' ' + infile['method'] + ' printbasis\n' - else: - first_line = r'! MULLIKEN ' + ligand_basis + ' ' + infile['run_type'] + ' ' + infile[ - 'method'] + ' CPCM printbasis\n' - text = ['#ORCA input\n', - first_line, - r'%' + 'maxcore 2000\n', - r'%' + 'pal nprocs ' + str(infile['parallel_environment']) + ' end\n', - r'*' + 'xyzfile ' + str(infile['charge']) + ' ' + str(infile['spinmult']) + ' ' + infile[ - 'name'] + '.xyz\n\n', - r'%' + 'scf\n Shift Shift ' + str(infile['levelshifta']) + ' ErrOff 0.1 end\nend\n\n', - r'%' + 'basis\n' + metal_basis_line + 'end\n\n'] - - if infile['solvent']: - text += [r'%' + 'cpcm\n epsilon ' + str(infile['solvent']) + '\nend\n\n'] - if infile['custom_line']: - text = text + [infile['custom_line'] + '\n'] - - with open(infile['name'] + '.in', 'w') as input_file: - for lines in text: - input_file.write(lines) - - -def write_jobscript(name, custom_line=None, time_limit='96:00:00', qm_code='terachem', parallel_environment=4, - machine='gibraltar', use_molscontrol=False, queues=['gpus', 'gpusnew']): - # Writes a generic obscript - # custom line allows the addition of extra lines just before the export statement - - if qm_code == 'terachem': - write_terachem_jobscript(name, custom_line=custom_line, time_limit=time_limit, - machine=machine, use_molscontrol=use_molscontrol, - queues=queues) - elif qm_code == 'orca': - write_orca_jobscript(name, custom_line=custom_line, time_limit=time_limit, - parallel_environment=parallel_environment, - machine=machine, use_molscontrol=use_molscontrol) - else: - raise Exception('QM code: ' + qm_code + ' not recognized for jobscript writing!') - - -def write_terachem_jobscript(name, custom_line=None, time_limit='96:00:00', terachem_line=True, - machine='gibraltar', use_molscontrol=False, queues=['gpus', 'gpusnew']): - # if use_molscontrol and machine != 'gibraltar': - # raise ValueError("molscontrol is only implemented on gibraltar for now.") - - if machine == 'gibraltar': - if not use_molscontrol: - text = ['#$ -S /bin/bash\n', - '#$ -N ' + name + '\n', - '#$ -cwd\n', - '#$ -R y\n', - '#$ -l h_rt=' + time_limit + '\n', - '#$ -l h_rss=8G\n', - '#$ -q '+'|'.join(queues)+'\n', - '#$ -l gpus=1\n', - '#$ -pe smp 1\n', - "# -fin " + "%s.in\n" % name, - "# -fin " + "%s.xyz\n" % name, - '# -fout scr/\n', - 'source /etc/profile.d/modules.sh\n', - 'module load terachem/tip\n', - 'export OMP_NUM_THREADS=1\n' - ] - else: - text = ['#$ -S /bin/bash\n', - '#$ -N ' + name + '\n', - '#$ -cwd\n', - '#$ -R y\n', - '#$ -l h_rt=' + time_limit + '\n', - '#$ -l h_rss=8G\n', - '#$ -q '+'|'.join(queues)+'\n', - '#$ -l gpus=1\n', - '#$ -pe smp 1\n', - "# -fin " + "%s.in\n" % name, - "# -fin molscontrol_config.json\n", - "# -fin " + "%s.xyz\n" % name, - '# -fout scr/\n', - 'source /etc/profile.d/modules.sh\n', - "source activate /home/crduan/.conda/envs/mols_keras/\n", - 'module load terachem/tip\n', - 'export OMP_NUM_THREADS=1\n' - ] - elif machine == 'bridges': - if int(time_limit.split(':')[0]) > 45: - time_limit = '45:00:00' - text = ['#!/bin/bash\n', - '#SBATCH -J ' + name + '\n', - '#SBATCH -N 1\n', - '#SBATCH -p GPU-shared\n', - '#SBATCH --ntasks-per-node 1\n' - '#SBATCH -t ' + time_limit + '\n', - '#SBATCH -C EGRESS\n', - '#SBATCH --gres=gpu:k80:1\n\n', - 'set -x\n', - 'module load intel/17.4\n', - 'module load mpi/intel_mpi\n', - 'module load cuda/9.2\n', - 'export TeraChem=/home/ffangliu/production/build\n', - 'export PATH=$TeraChem/bin/:$PATH\n', - 'export NBOEXE=$TeraChem/nbo6/nbo6.i4.exe\n', - 'export LD_LIBRARY_PATH=$TeraChem/lib:$LD_LIBRARY_PATH\n' - ] - elif machine == 'comet': - if int(time_limit.split(':')[0]) > 45: - time_limit = '45:00:00' - text = ['#!/bin/bash\n', - '#SBATCH -J ' + name + '\n', - '#SBATCH --nodes 1\n', - '#SBATCH -p gpu-shared\n', - '#SBATCH --mem=16G\n', - '#SBATCH --ntasks-per-node=1\n' - '#SBATCH -t ' + time_limit + '\n', - '#SBATCH --export=ALL\n', - '#SBATCH --gres=gpu:2\n\n', - 'export OMP_NUM_THREADS=2\n', - 'module purge\n', - 'export MODULEPATH="/share/apps/compute/modulefiles:${MODULEPATH}"\n', - 'module load gnu/7.2.0\n', - 'module load intel/2016.3.210\n', - 'module load intelmpi/2016.3.210\n', - 'module load cuda/9.2\n', - 'export TeraChem=/oasis/projects/nsf/mit136/fangliu/src/production/build\n', - 'export PATH=$TeraChem/bin/:$PATH\n', - 'export NBOEXE=$TeraChem/nbo6/nbo6.i4.exe\n', - 'export LD_LIBRARY_PATH=$TeraChem/lib:$LD_LIBRARY_PATH\n', - 'export OpenMM=/oasis/projects/nsf/mit136/fangliu/opt/openmm\n', - 'export CPATH=$OpenMM/include:$CPATH\n', - 'export LD_LIBRARY_PATH=$OpenMM/lib:$LD_LIBRARY_PATH\n', - 'export LIBRARY_PATH=$OpenMM/lib:$LIBRARY_PATH\n', - 'export PATH=$OpenMM/bin:$PATH\n', - 'export OPENMM_INCLUDE_PATH=$OpenMM/include\n', - 'export OPENMM_LIB_PATH=$OpenMM/lib\n', - 'export OPENMM_PLUGIN_DIR=$OpenMM/lib/plugins\n' - ] - else: - raise ValueError('Job manager does not know how to run Terachem on this machine!') - if terachem_line and machine == 'gibraltar': - if not use_molscontrol: - text += ['terachem ' + name + '.in ' + '> $SGE_O_WORKDIR/' + name + '.out\n'] - else: - text += ["cp %s.xyz initgeo.xyz" % name] - text += ['terachem ' + name + '.in ' + '> $SGE_O_WORKDIR/' + name + '.out &\n'] - text += ["PID_KILL=$!\n"] - text += ["molscontrol $PID_KILL &\n"] - text += ["wait\n"] - text += ["mv *.log $SGE_O_WORKDIR\n"] - text += ["mv features.json $SGE_O_WORKDIR/dyanmic_features.json\n"] - elif terachem_line and machine in ['bridges', 'comet']: - text += ['terachem ' + name + '.in ' + '> ' + name + '.out\n'] - if custom_line: - if type(custom_line) == list: - text = text[:12] + custom_line + text[12:] - else: - text = text[:12] + [custom_line + '\n'] + text[12:] - text += ['sleep 30'] - - with open(name + '_jobscript', 'w') as jobscript: - for i in text: - jobscript.write(i) - - -def write_molscontrol_config(): - pass - - -def write_orca_jobscript(name, custom_line=None, time_limit='96:00:00', parallel_environment=4, - machine='gibraltar', use_molscontrol=False): - # Write a generic orca jobscript - - if use_molscontrol: - raise NotImplementedError('molscontrol is currently not supported for orca.') - - memory_allocation = str( - int(parallel_environment) * 3) # allocate memory based on 192 GB for 64 processors on the new cpu nodes - - if machine == 'gibraltar': - text = ['#$ -S /bin/bash\n', - '#$ -N ' + name + '\n', - '#$ -cwd\n', - '#$ -R y\n', - '#$ -l h_rt=' + time_limit + '\n', - '#$ -l h_rss=' + memory_allocation + 'G\n', - '#$ -q cpus\n', - '#$ -l cpus=1\n', - '#$ -pe smp ' + str(parallel_environment) + '\n', - '# -fin ' + name + '.in\n', - '# -fin ' + name + '.xyz\n\n', - 'source /etc/profile.d/modules.sh\n', - 'module module load intel\n', - 'module module load orca\n', - 'export PATH=/home/harperd/software/openmpi/bin:$PATH\n', - 'export LD_LIBRARY_PATH=/home/harperd/software/openmpi/lib:$LD_LIBRARY_PATH\n\n', - '/opt/orca/orca_4_1_2_linux_x86-64_openmpi313/orca ' + name + '.in > $SGE_O_WORKDIR/' + name + '.out\n\n', - 'mkdir $SGE_O_WORKDIR/scr\n', - 'cp ' + name + '.trj $SGE_O_WORKDIR/scr/optim.xyz\n', - 'cp ' + name + '.gbw $SGE_O_WORKDIR/scr/\n', - 'cp ' + name + '.prop $SGE_O_WORKDIR/scr/\n', - 'cp ' + name + '.opt $SGE_O_WORKDIR/scr/\n', - 'cp ' + name + '_property.txt $SGE_O_WORKDIR/scr/\n'] - else: - raise ValueError('Job manager does not know how to run ORCA on this machine!') - if custom_line: - if type(custom_line) == list: - text = text[:12] + custom_line + text[12:] - else: - text = text[:12] + [custom_line + '\n'] + text[12:] - - with open(name + '_jobscript', 'w') as jobscript: - for i in text: - jobscript.write(i) - - -def get_scf_progress(outfile): - flag = False - flag_linecheck = False - with open(outfile, 'r') as fo: - start = False - for line in fo: - ll = line.split() - if "Start SCF Iterations" in line: - start = True - energy_this_scf = [] - if len(ll) == 11 and ll[0].isdigit() and start: - energy_this_scf.append(float(ll[-2])) - if "FINAL ENERGY:" in line and start: - start = False - flag = is_oscillate(energy_this_scf) - if flag: - break - with open(outfile, 'r') as fo: - for line in fo: - if "WARNING: Final energy is higher than the lowest energy by" in line: - e = float(line.split()[-1].strip(".")) - if e > 1: - flag_linecheck = True - return (flag and flag_linecheck) - - -def is_oscillate(energy_this_scf): - if len(energy_this_scf) > 1: - if np.std(energy_this_scf) > 1: - return True - return False diff --git a/molSimplify/job_manager/moltools.py b/molSimplify/job_manager/moltools.py deleted file mode 100644 index 99c698f9..00000000 --- a/molSimplify/job_manager/moltools.py +++ /dev/null @@ -1,603 +0,0 @@ -# This module is equivalent to the tools.py module, but includes dependency on molSimplify -# updates 8/2/19 - -import os -import glob -import copy -import numpy as np -import subprocess -import pandas as pd -import shutil -import time -import molSimplify.job_manager.tools as tools -import molSimplify.job_manager.manager_io as manager_io -from molSimplify.Classes.mol3D import mol3D -from molSimplify.Classes.ligand import ligand_breakdown - - -def read_run(outfile_PATH): - """Read a DFT output. - - Parameters - ---------- - outfile_PATH : str - Path to quantum chemistry output file. - - Returns - ------- - results : dict - Analyzed results for job. - - """ - # Evaluates all aspects of a run using the outfile and derivative files - results = manager_io.read_outfile(outfile_PATH, long_output=True) - infile_dict = manager_io.read_infile(outfile_PATH) - results['levela'], results['levelb'] = infile_dict['levelshifta'], infile_dict['levelshiftb'] - results['method'], results['hfx'] = infile_dict['method'], infile_dict['hfx'] - results['constraints'] = infile_dict['constraints'] - - mullpop_path = os.path.join(os.path.split(outfile_PATH)[0], 'scr', 'mullpop') - if os.path.exists(mullpop_path): - mullpops = manager_io.read_mullpop(outfile_PATH) - metal_types = ['Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Mo', 'Tc', 'Ru', 'Rh'] - metals = [i for i in mullpops if i.split()[0] in metal_types] - if len(metals) > 1: - results['metal_spin'] = np.nan - elif len(metals) == 0: - pass - else: - results['metal_spin'] = float(metals[0].split()[-1]) - else: - results['metal_spin'] = np.nan - - optim_path = os.path.join(os.path.split(outfile_PATH)[0], 'scr', 'optim.xyz') - initial_xyz_path = outfile_PATH.rsplit('.', 1)[0]+'.xyz' - if not os.path.isfile(initial_xyz_path): - raise Exception('No initial xyz found at: '+initial_xyz_path) - - check_geo = False - if os.path.isfile(optim_path): - with open(optim_path, 'r') as fil: - lines = fil.readlines() - if len(lines) > 0: - check_geo = True # Only apply geo check if an optimized geometry exists - - if check_geo: - tools.extract_optimized_geo(optim_path) - optimized_path = os.path.join(os.path.split(optim_path)[0], 'optimized.xyz') - - mol = mol3D() - mol.readfromxyz(optimized_path) - - IsOct, flag_list, oct_check = mol.IsOct(dict_check=mol.dict_oct_check_st, - silent=True) - - if IsOct: - IsOct = True - else: - IsOct = False - - results['Is_Oct'] = IsOct - results['Flag_list'] = flag_list - results['Oct_check_details'] = oct_check - - else: - results['Is_Oct'] = None - results['Flag_list'] = None - results['Oct_check_details'] = None - - return results - - -def create_summary(directory='in place'): - """Create a summary file. - - Parameters - ---------- - directory : str, optional - Directory that contains all of the jobs to be analyzed. Default is in place. - - Returns - ------- - summary : pd.DataFrame - Summary of full directory. - - """ - # Returns a pandas dataframe which summarizes all outfiles in the directory, defaults to cwd - - outfiles = tools.find('*.out', directory) - outfiles = list(filter(tools.check_valid_outfile, outfiles)) - results = list(map(read_run, outfiles)) - summary = pd.DataFrame(results) - - return summary - - -def apply_geo_check(job_outfile_path, geometry): - """Create a summary file. - - Parameters - ---------- - job_outfile_path : str - Path for output file. - geometry : str - Type of geometry to do the geometry check. - - Returns - ------- - geo_flag : bool - Flag describing geometry. True if good geometry. - - """ - if geometry: # The geometry variable is set to False if no geo check is requested for this job - - optim_path = os.path.join(os.path.split(job_outfile_path)[0], 'scr', 'optim.xyz') - - if os.path.isfile(optim_path): - tools.extract_optimized_geo(optim_path) - optimized_path = os.path.join(os.path.split(optim_path)[0], 'optimized.xyz') - - mol = mol3D() - mol.readfromxyz(optimized_path) - else: - # If the optim.xyz doesn't exist, assume that it's a single point and should pass geo check - return True - - if geometry.capitalize() in ['Oct', 'Octahedral']: - geo_check_dict = mol.dict_oct_check_st - IsOct, flag_list, oct_check = mol.IsOct(dict_check=geo_check_dict, silent=True) - if IsOct: - return True - else: - return False - - elif geometry.capitalize() == 'Bidentate_oct': - # Loosened geo check dict appropriate for bidentates - geo_check_dict = {'num_coord_metal': 6, - 'rmsd_max': 3, 'atom_dist_max': 0.45, - 'oct_angle_devi_max': 15, 'max_del_sig_angle': 30, - 'dist_del_eq': 0.35, 'dist_del_all': 1, - 'devi_linear_avrg': 20, 'devi_linear_max': 28} - outer_dict_flags = list(mol.dict_oct_check_st.keys()) - final_dict = dict() - for key in outer_dict_flags: - final_dict[key] = geo_check_dict - - IsOct, flag_list, oct_check = mol.IsOct(dict_check=final_dict, silent=True) - if IsOct: - return True - else: - return False - - elif geometry.capitalize() == 'Tridentate_oct': - # Extra loosened geo check dict appropriate for Tridentates - geo_check_dict = {'num_coord_metal': 6, - 'rmsd_max': 3, 'atom_dist_max': 0.45, - 'oct_angle_devi_max': 25, 'max_del_sig_angle': 50, - 'dist_del_eq': 0.35, 'dist_del_all': 1, - 'devi_linear_avrg': 20, 'devi_linear_max': 28} - outer_dict_flags = list(mol.dict_oct_check_st.keys()) - final_dict = dict() - for key in outer_dict_flags: - final_dict[key] = geo_check_dict - - IsOct, flag_list, oct_check = mol.IsOct(dict_check=final_dict, silent=True) - if IsOct: - return True - else: - return False - - elif geometry.capitalize() in ['Tetrahedral', 'Tetra']: - if len(mol.getBondedAtoms(mol.findMetal())) == 4: - return True - else: - return False - - else: - raise Exception('A check has not been implemented for geometry: ' + geometry) - else: - # print('No geomery check requested for job: '+job_outfile_path) - # print('Passing job without a geometry check') - return True - - -def get_metal_and_bonded_atoms(job_outfile, geometry=None): - """Get metal and bonded atoms of complex. - - Parameters - ---------- - job_outfile : str - Path for output file. - geometry : str, optional - Type of geometry to define metal bonding. Default is None. - - Returns - ------- - geo_flag : bool - Flag describing geometry. True if good geometry. - - """ - # given the path to the outfile of a job, returns a the metal atom index and a list of indices for the metal bonded atoms - # indices are zero-indexed...Terachem uses 1 indexed lists - - xyz_path = job_outfile.rsplit('.', 1)[0] + '.xyz' - mol = mol3D() - mol.readfromxyz(xyz_path) - metal_index = mol.findMetal()[0] - - if geometry in ['Oct', 'oct', 'Octahedral', 'octahedral']: - bonded_atom_indices = mol.getBondedAtomsOct(metal_index) - else: - print('Warning, generic getBondedAtoms() used for: ' + job_outfile + '. Check behavior') - bonded_atom_indices = mol.getBondedAtoms(metal_index) - - return metal_index, bonded_atom_indices - - -def check_completeness(directory='in place', max_resub=5, configure_dict=False): - """Get metal and bonded atoms of complex. - - Parameters - ---------- - directory : str, optional - Directory where the jobs are running. Default is in place. - max_resub : int, optional - Number of resubmissions allowed. Default is 5. - configure_dict : dict, optional - Configure file. Default is False. - - Returns - ------- - completeness : dict - Completeness dictionary for a given directory. - - """ - completeness = tools.check_completeness(directory, max_resub, configure_dict=configure_dict) - # print("=======") - # print("completeness: ", completeness) - # The check_completeness() function in tools doesn't check the geometries (because it's molSimplify dependent) - # Apply the check here to finished and spin contaminated geometries, then update the completeness dictionary - finished = completeness['Finished'] - spin_contaminated = completeness['Spin_contaminated'] - needs_resub = completeness['Needs_resub'] - unfinished = completeness['Error'] - # print("finished: ", finished) - # print("spin_contaminated: ", spin_contaminated) - # print("needs_resub: ", needs_resub) - # print("unfinished: ", unfinished) - bad_geos = [] - new_finished = [] - new_spin_contaminated = [] - new_needs_resub = [] - new_unfinished = [] - new_molscontrol_kills = [] - for job in finished: - goal_geo = manager_io.read_configure(directory, job)['geo_check'] - if apply_geo_check(job, goal_geo): - new_finished.append(job) - else: - bad_geos.append(job) - for job in spin_contaminated: - if not check_molscontrol_log(job): - goal_geo = manager_io.read_configure(directory, job)['geo_check'] - if apply_geo_check(job, goal_geo): - new_spin_contaminated.append(job) - else: - bad_geos.append(job) - else: - new_molscontrol_kills.append(job) - for job in needs_resub: - if not check_molscontrol_log(job): - goal_geo = manager_io.read_configure(directory, job)['geo_check'] - if apply_geo_check(job, goal_geo): - new_needs_resub.append(job) - else: - bad_geos.append(job) - else: - new_molscontrol_kills.append(job) - for job in unfinished: - if not check_molscontrol_log(job): - goal_geo = manager_io.read_configure(directory, job)['geo_check'] - if apply_geo_check(job, goal_geo): - new_unfinished.append(job) - else: - bad_geos.append(job) - else: - new_molscontrol_kills.append(job) - - completeness['Finished'] = new_finished - completeness['Spin_contaminated'] = new_spin_contaminated - completeness['Resub'] = new_needs_resub - completeness['Error'] = new_unfinished - completeness['Bad_geos'] = bad_geos - completeness["molscontrol_kills"] = new_molscontrol_kills - return completeness - - -def prep_ligand_breakdown(outfile_path, dissociated_ligand_charges={}, dissociated_ligand_spinmults={}): - """Prep ligand breakdown. - - Parameters - ---------- - outfile_path : str - Path to output file. - dissociated_ligand_charges : dict, optional - Charges for dissociated ligands. Default is empty. - dissociated_ligand_spinmults : dict, optional - Spin multiplicity for dissociated ligands. Default is empty. - - Returns - ------- - jobscripts : list - List of jobscripts for ligand breakdown jobs. - - """ - # Given a path to the outfile of a finished run, this preps the files for rigid ligand dissociation energies of all ligands - # Returns a list of the PATH(s) to the jobscript(s) to start the rigid ligand calculations - - home = os.getcwd() - machine = tools.get_machine() - outfile_path = tools.convert_to_absolute_path(outfile_path) - - results = manager_io.read_outfile(outfile_path) - if not results['finished']: - raise Exception('This calculation does not appear to be complete! Aborting...') - - infile_dict = manager_io.read_infile(outfile_path) - charge = int(infile_dict['charge']) - spinmult = int(infile_dict['spinmult']) - - base = os.path.split(outfile_path)[0] - name = os.path.split(outfile_path)[-1][:-4] - - breakdown_folder = os.path.join(base, name + '_dissociation') - - if os.path.isdir(breakdown_folder): - return ['Ligand dissociation directory already exists'] - - optimxyz = os.path.join(base, 'scr', 'optim.xyz') - tools.extract_optimized_geo(optimxyz) - - mol = mol3D() - mol.readfromxyz(os.path.join(base, 'scr', 'optimized.xyz')) - - ligand_idxs, _, _ = ligand_breakdown(mol, silent=True, BondedOct=True) # Complex is assumed to be octahedral - - ligand_syms = [] - for ii in ligand_idxs: - ligand_syms.append([mol.getAtom(i).symbol() for i in ii]) - - ligand_names = name_ligands(ligand_syms) - - if not os.path.isdir(breakdown_folder): - os.mkdir(breakdown_folder) - os.chdir(breakdown_folder) - - jobscripts = [] - for ligand in zip(ligand_names, ligand_idxs): - - # Assign charges to use during the breakdown for special cases specified in the configure file - # All other ligands are assigned charge 0 - if ligand[0] in list(dissociated_ligand_charges.keys()): - ligand_charge = dissociated_ligand_charges[ligand[0]] - else: - ligand_charge = 0 - metal_charge = charge - ligand_charge - - # Assign spin, which always remains with the metal except when the dissociated ligand is defined to have spin (O2 for example) - if spinmult == 1: # If the whole complex is restricted, it's components must be restricted as well - ligand_spin, metal_spin = 1, 1 - else: - if ligand[0] in list(dissociated_ligand_spinmults.keys()): - ligand_spin = dissociated_ligand_spinmults[ligand[0]] - else: - ligand_spin = 1 - - metal_spin = spinmult - ligand_spin + 1 # Derived from spinmult = (2S+1) where S=1/2 per electron - - # Create the necessary files for the metal complex single point - local_name = name + '_rm_' + ligand[0] - if os.path.isdir('rm_' + ligand[0]): - pass - else: - os.mkdir('rm_' + ligand[0]) - os.chdir('rm_' + ligand[0]) - - local_mol = mol3D() - local_mol.copymol3D(mol) - - local_mol.deleteatoms(ligand[1]) - local_mol.writexyz(local_name + '.xyz') - - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['name'] = local_name - local_infile_dict['coordinates'] = local_name+'.xyz' - local_infile_dict['charge'], local_infile_dict['spinmult'] = metal_charge, metal_spin - local_infile_dict['run_type'] = 'energy' - local_infile_dict['constraints'], local_infile_dict['convergence_thresholds'] = False, False - local_infile_dict['machine'] = machine - - manager_io.write_input(local_infile_dict) - manager_io.write_jobscript(local_name, time_limit='12:00:00', machine=machine) - jobscripts.append(local_name + '.in') - os.chdir('..') - - # Create the necessary files for the dissociated ligand single point - local_name = name + '_kp_' + ligand[0] - if os.path.isdir('kp_' + ligand[0]): - pass - else: - os.mkdir('kp_' + ligand[0]) - os.chdir('kp_' + ligand[0]) - - local_mol = mol3D() - local_mol.copymol3D(mol) - deletion_indices = list(set(range(local_mol.natoms)) - set(ligand[1])) - local_mol.deleteatoms(deletion_indices) - local_mol.writexyz(local_name + '.xyz') - - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['name'] = local_name - local_infile_dict['coordinates'] = local_name+'.xyz' - local_infile_dict['charge'], local_infile_dict['spinmult'] = ligand_charge, ligand_spin - local_infile_dict['run_type'] = 'energy' - local_infile_dict['constraints'], local_infile_dict['convergence_thresholds'] = False, False - local_infile_dict['machine'] = machine - - manager_io.write_input(local_infile_dict) - manager_io.write_jobscript(local_name, time_limit='12:00:00', machine=machine) - jobscripts.append(local_name + '.in') - os.chdir('..') - os.chdir(home) - - return jobscripts - - -def prep_mbe_calc(outfile_path, metal_charge=0): - """Prep ligand breakdown. - - Parameters - ---------- - outfile_path : str - Path to output file. - metal_charge : int, optional - Charge for removed metal. Default is 0. - - Returns - ------- - jobscripts : list - List of jobscripts for metal binding energy jobs. - - """ - # Given a path to the outfile of a finished run, this preps the files for rigid ligand dissociation energies of all ligands - # Returns a list of the PATH(s) to the jobscript(s) to start the rigid ligand calculations - - home = os.getcwd() - machine = tools.get_machine() - outfile_path = tools.convert_to_absolute_path(outfile_path) - - results = manager_io.read_outfile(outfile_path) - if not results['finished']: - raise Exception('This calculation does not appear to be complete! Aborting...') - - infile_dict = manager_io.read_infile(outfile_path) - - # special case hack for Fe test ~Freya - fe_spin = int(infile_dict['spinmult']) - if fe_spin == 5: - fe_charge = 2 - else: - fe_charge = 3 - charge = int(infile_dict['charge']) - fe_charge - spinmult = 1 # always have a singlet - - base = os.path.split(outfile_path)[0] - name = os.path.split(outfile_path)[-1][:-4] - - optimxyz = os.path.join(base, 'scr', 'optim.xyz') - tools.extract_optimized_geo(optimxyz) - - breakdown_folder = os.path.join(base, name + '_mbe') - - if os.path.isdir(breakdown_folder): - return ['Metal binding energy directory already exists'] - - mol = mol3D() - mol.readfromxyz(os.path.join(base, 'scr', 'optimized.xyz')) - - if not os.path.isdir(breakdown_folder): - os.mkdir(breakdown_folder) - os.chdir(breakdown_folder) - - jobscripts = [] - metal_indices = mol.findMetal() - # Create the necessary files for the metal-removed complex single point - mol.deleteatoms(metal_indices) - mol.writexyz(name + '_no_metal.xyz') - - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['name'] = name + "_no_metal" - local_infile_dict['coordinates'] = name + '_no_metal.xyz' - local_infile_dict['charge'], local_infile_dict['spinmult'] = charge, spinmult - local_infile_dict['run_type'] = 'energy' - local_infile_dict['constraints'], local_infile_dict['convergence_thresholds'] = False, False - local_infile_dict['machine'] = machine - - manager_io.write_input(local_infile_dict) - manager_io.write_jobscript(name + '_no_metal', time_limit='12:00:00', machine=machine) - jobscripts.append(name + '_no_metal.in') - os.chdir('..') - os.chdir(home) - return jobscripts - - -def name_ligands(nested_list): - """Takes a nested list of atom symbols and converts it to a list of unique chemical names based on the molecular formulas - - Parameters - ---------- - nested_list : list - List of lists of atom symbols - - Returns - ------- - ligand_formulas : list - List of ligand formulas. - - """ - # takes a nested list of atom symbols and converts it to a list of unique chemical names based on the molecular formulas - - def convert_to_formula(list_of_atom_symbols): - atom_types = list(set(list_of_atom_symbols)) - atom_types.sort() - - formula = '' - for element in atom_types: - counter = 0 - for atom in list_of_atom_symbols: - if element == atom: - counter += 1 - formula += element - formula += str(counter) - return formula - - ligand_formulas = list(map(convert_to_formula, nested_list)) - - duplicates = [] - for i in ligand_formulas: - number_of_duplicates = 0 - for ii in ligand_formulas: - if i == ii: - number_of_duplicates += 1 - duplicates.append(number_of_duplicates) - - duplication_index = 1 - for counter, i in enumerate(duplicates): - if i > 1: - ligand_formulas[counter] = ligand_formulas[counter] + '_' + str(duplication_index) - duplication_index += 1 - - return ligand_formulas - - -def check_molscontrol_log(job): - """Check molscontrol log. - - Parameters - ---------- - job : str - Path to the output file. - - Returns - ------- - killed : bool - True if job killed. - - """ - molscontrol_logfile = "/".join(job.split("/")[:-1]) + '/molscontrol.log' - if os.path.isfile(molscontrol_logfile): - with open(molscontrol_logfile, "r") as fo: - for line in fo: - if "job killed at step" in line: - return True - return False diff --git a/molSimplify/job_manager/populate_jobs.py b/molSimplify/job_manager/populate_jobs.py deleted file mode 100644 index d3b359c9..00000000 --- a/molSimplify/job_manager/populate_jobs.py +++ /dev/null @@ -1,210 +0,0 @@ -import glob -import numpy as np -import os -import shutil -import subprocess - -from molSimplifyAD.utils.pymongo_tools import connect2db, query_lowestE_converged - -from molSimplify.job_manager.tools import (manager_io) - - -def isCSD(job): - try: - iscsd = True - for ii in range(6): - if not job[ii].isupper(): - iscsd = False - break - return iscsd - except: - return False - - -def call_molsimplify(geodir, job, jobname): - liglist = ",".join(job["ligstr"].split("_")) # can be a single SMILES string, or list of database ligands (e.g. water_water_water_water_water_water) - tmp_name = str(np.random.randint(10 ** 18)) # assign a temporary name so that the results are findable - temp_rundir = os.path.join(os.path.expanduser('~'), 'Runs') - bash_command = " ".join(["molsimplify ", '-core ' + job["metal"], - '-lig ' + str(liglist), - '-ligloc ' + 'yes', '-calccharge yes', - '-spin ' + str(job["spin"]), '-oxstate ' + str(job["ox"]), - "-ffoption " + "b", ' -ff UFF', - "-name", tmp_name, "-rundir", temp_rundir]) - if "geometry" in job: - bash_command = " ".join([bash_command, "-geometry", job["geometry"]]) - if "coord" in job: - bash_command = " ".join([bash_command, "-coord", str(job["coord"])]) - if "ligocc" in job: # must be a string, e.g. "6" or "1,1,1,1,1,1" - bash_command = " ".join([bash_command, "-ligocc", job["ligocc"]]) - else: - bash_command = " ".join([bash_command, "-ligocc", "1,1,1,1,1,1"]) - if "keepHs" in job: - bash_command = " ".join([bash_command, "-keepHs", job["keepHs"]]) - else: - bash_command = " ".join([bash_command, "-keepHs", 'yes,yes,yes,yes,yes,yes']) - if "smicat" in job: # must be a string, e.g. "1" - bash_command = " ".join([bash_command, "-smicat", job["smicat"]]) - if "skipANN" in job: - bash_command = " ".join([bash_command, "-skipANN", job["skipANN"]]) - print(("call: ", bash_command)) - bash_command = bash_command.split() - subprocess.call(bash_command) - - file_name = os.path.join(temp_rundir, tmp_name) - print(("file_name: ", file_name)) - print(("geodir: ", geodir)) - inner_folder_path = glob.glob(os.path.join(file_name, '*'))[0] - xyz_path = glob.glob(os.path.join(inner_folder_path, '*.xyz'))[0] - charge = False - with open(inner_folder_path + '/terachem_input', "r") as fo: - for line in fo: - if "charge" == line[:len("charge")]: - charge = int(line.split()[-1]) - if not charge: - raise ValueError("No charge is extracted from terachem input: ", inner_folder_path + '/terachem_input') - shutil.copyfile(xyz_path, geodir + '/' + jobname + '.xyz') - print((xyz_path, geodir + '/' + jobname + '.xyz')) - return charge - - -def write_xyz_from_db(geodir, jobname, optgeo): - natoms = len(optgeo.split('\n')) - 1 - with open(geodir + '/' + jobname + ".xyz", "w") as fo: - fo.write("%d\n" % natoms) - fo.write("====Geometry adopted from the database====\n") - fo.write(optgeo) - - -def generate_fake_results_from_db(rundir, jobname, tmcdoc): - scrdir = rundir + '/scr' - if not os.path.isdir(scrdir): - os.makedirs(scrdir) - write_xyz_from_db(scrdir, 'optim', tmcdoc["opt_geo"]) - if tmcdoc['wavefunction']: - if int(tmcdoc['spin']) == 1: - try: - shutil.copy(tmcdoc['wavefunction']['c0'], scrdir + '/c0') - except FileNotFoundError: - pass - else: - try: - shutil.copy(tmcdoc['wavefunction']['ca0'], scrdir + '/ca0') - shutil.copy(tmcdoc['wavefunction']['cb0'], scrdir + '/cb0') - except FileNotFoundError: - pass - inpath = rundir + '/' + jobname + '.in' - with open(inpath, "w") as fo: - fo.write("=======This outfile is FAKE and generated artificialy======\n") - fo.write("charge %d\n" % int(tmcdoc["charge"])) - fo.write("spinmult %d\n" % int(tmcdoc["spin"])) - fo.write("method %s\n" % str(tmcdoc["functional"])) - fo.write("basis %s\n" % str(tmcdoc["basis"])) - fo.write("coordinates %s.xyz\n" % jobname) - fo.write("run minimize\n") - outpath = rundir + '/' + jobname + '.out' - with open(outpath, "w") as fo: - fo.write("=======This outfile is FAKE and generated artificialy======\n") - fo.write('Startfile from command line: %s.in\n' % jobname) - fo.write('Hartree-Fock exact exchange: %.2f\n' % (float(tmcdoc['alpha']) * 0.01)) - fo.write('DFT Functional requested: %s\n' % str(tmcdoc['functional'])) - fo.write('* TeraChem %s *\n' % str(tmcdoc['terachem_version'])) - fo.write('Alpha level shift: 0.25\n') - fo.write('Beta level shift: 0.25\n') - fo.write('Using basis set: %s\n' % str(tmcdoc["basis"])) - fo.write("Total charge: %d\n" % int(tmcdoc["charge"])) - fo.write("Spin multiplicity: %d\n" % int(tmcdoc["spin"])) - fo.write("SPIN S-SQUARED: %f (exact: %f)\n" % (float(tmcdoc["ss_act"]), float(tmcdoc["ss_target"]))) - fo.write("-=#=- Optimization Cycle 1 -=#=-\n") - fo.write("FINAL ENERGY: %.10f a.u.\n" % float(tmcdoc["energy"])) - fo.write("-=#=- Optimization Converged. -=#=-\n") - fo.write("Total processing time: 0.00 sec\n") - fo.write("Job finished: A time of mystery\n") - return outpath - - -def populate_single_job(basedir, job, db, safe_filenames=True): - geodir = basedir + "/initial_geometry/" - if not os.path.isdir(geodir): - os.makedirs(geodir) - iscsd = isCSD(job['ligstr']) - query_constraints = {"metal": job['metal'], "spin": job["spin"], "ligstr": job["ligstr"], "alpha": 20, - "wavefunction": {"$exists": True}} - if not iscsd: - query_constraints.update({"ox": job["ox"]}) - jobname = "_".join([job['metal'], str(job['ox']), str(job['spin']), job['ligstr']]) - else: - jobname = "_".join([job['ligstr'], job['metal'], str(job['spin'])]) - tmcdoc, recover = None, True - if db is not None: - tmcdoc = query_lowestE_converged(db, collection='oct', constraints=query_constraints) - if tmcdoc is not None: - print(("Bingo! Optimized geometry found in db: ", query_constraints)) - try: - charge = int(tmcdoc["charge"]) - ss_act, ss_target = float(tmcdoc["ss_act"]), float(tmcdoc["ss_target"]) - if abs(ss_act - ss_target) > 1 and tmcdoc["ss_flag"] == 1: - recover = False - print("Spin contamination for singlets! (used ub3lyp)") - write_xyz_from_db(geodir, jobname, tmcdoc["opt_geo"]) - wfnpath = "/home/data/wfn/" + str(tmcdoc['unique_name']) - wfnfiles = os.listdir(wfnpath) - if not any(x in ["c0", "ca0", "cb0"] and os.stat(wfnpath+'/%s' % x).st_size > 1000 for x in wfnfiles): - recover = False - print("No WFN file found at /home/data/wfn/.") - except: - recover = False - else: - print("generate initial geometry from molsimplify...") - charge = call_molsimplify(geodir, job, jobname) - else: - if not iscsd: - print("NO db connection! Generate initial geometry from molsimplify...") - jobname_safe = jobname.replace("#", "3").replace("(", "[").replace(")", "]") - charge = call_molsimplify(geodir, job, jobname_safe) # this used to say rundir for some reason... - else: - raise ValueError("Cannot generate initial geometry for CSD complex...") - - rundir = basedir + '/' + jobname - try: - rundir_p3 = basedir + '/' + jobname_safe - except NameError: # jobname_safe not defined - rundir_p3 = basedir + '/' + jobname.replace('#', '3') - - # p3 option - if safe_filenames: - rundir = rundir_p3 - try: - jobname = jobname_safe - except NameError: # jobname_safe not defined - jobname = jobname.replace('#', '3') - - populated = True - if not os.path.isdir(rundir) and not os.path.isdir(rundir_p3) and recover: - os.makedirs(rundir) - shutil.copyfile(geodir + '/' + jobname + '.xyz', rundir + "/" + jobname + ".xyz") - os.chdir(rundir) - # Add fake files etc for a smooth carry-on in job manager for further dependent jobs. - if tmcdoc is not None: - generate_fake_results_from_db(rundir, jobname, tmcdoc) - else: - manager_io.write_input(name=jobname, coordinates=jobname + '.xyz', charge=charge, spinmult=int(job["spin"]), run_type='minimize', solvent=False) - manager_io.write_jobscript(jobname) - elif os.path.isdir(rundir) or os.path.isdir(rundir_p3): - print("folder exist.") - populated = False - else: - print(('WARNING: cannot recover %s' % jobname)) - populated = False - os.chdir(basedir) - return jobname, populated - - -def populate_list_of_jobs(basedir, jobs, db_communicate=True): - if db_communicate: - db = connect2db(user="readonly_user", pwd="readonly", host="localhost", - port=27017, database="tmc", auth=True) - else: - db = None - for job in jobs: - populate_single_job(basedir, job, db) diff --git a/molSimplify/job_manager/psi4_utils/derivative.py b/molSimplify/job_manager/psi4_utils/derivative.py deleted file mode 100644 index 6201928b..00000000 --- a/molSimplify/job_manager/psi4_utils/derivative.py +++ /dev/null @@ -1,55 +0,0 @@ -import os -import operator -from typing import List - - -def get_subfolders(path: str = "./") -> list: - files = os.listdir(path) - folders = [] - for file in files: - if os.path.isdir(path + "/" + file): - folders.append(file) - return folders - - -def sanity_check(folders: List[str], trigger: str = "_derivNo_") -> dict: - trigger_appear = False - basename: List[str] = [] - folders_ignored = [] - jobs = {} - for folder in folders: - if trigger in folder: - trigger_appear = True - base = folder.split(trigger)[0] - # print(base, folder) - if not len(basename): - first_base = base - basename.append(base) - if base not in basename: - basename.append(base) - if base == first_base: - jobs[folder] = int(folder.split(trigger)[-1]) - else: - folders_ignored.append(folder) - if not trigger_appear: - raise KeyError(": %s not appeared in any folders." % trigger) - if len(basename) > 1: - raise ValueError("multiple base jobs occur: %s" % basename) - if len(folders_ignored): - print("Warning: The following folders are ignored: %s" % folders_ignored) - return jobs - - -def derivative_tree(path: str = "./", trigger: str = "_derivNo_") -> list: - ''' - Make a sequence structure for derivative jobs in a path. - ''' - folders = get_subfolders(path) - jobs = sanity_check(folders, trigger=trigger) - jobs = dict(sorted(jobs.items(), key=operator.itemgetter(0))) - return list(jobs.keys()) - - -def get_wfn_path(jobs, ii): - assert ii > 0 - return "../../" + jobs[ii - 1] + "/b3lyp/wfn.180.npy" diff --git a/molSimplify/job_manager/psi4_utils/jobscript.sh b/molSimplify/job_manager/psi4_utils/jobscript.sh deleted file mode 100644 index 4379322b..00000000 --- a/molSimplify/job_manager/psi4_utils/jobscript.sh +++ /dev/null @@ -1,25 +0,0 @@ -#$ -S /bin/bash -#$ -N psi4_dft -#$ -R y -#$ -cwd -#$ -l h_rt=48:00:00 -#$ -l h_rss=24G -#$ -q cpus -#$ -l cpus=1 -#$ -pe smp 8 -# -fin *.py -# -fin b3lyp -# -fin *.xyz -# -fin *.molden -# -fin *.json - -source /home/crduan/.bashrc -conda activate /home/crduan/miniconda/envs/mols_py36 -export PSI_SCRATCH='./' - -echo 'psi4 scr: ' $PSI_SCRATCH -python -u loop_run.py > $SGE_O_WORKDIR/nohup1.out -python -u loop_run.py > $SGE_O_WORKDIR/nohup2.out -python -u loop_run.py > $SGE_O_WORKDIR/nohup3.out - -mv * $SGE_O_WORKDIR diff --git a/molSimplify/job_manager/psi4_utils/loop_derivative_jobs.py b/molSimplify/job_manager/psi4_utils/loop_derivative_jobs.py deleted file mode 100644 index 16c73f49..00000000 --- a/molSimplify/job_manager/psi4_utils/loop_derivative_jobs.py +++ /dev/null @@ -1,24 +0,0 @@ -import os -import json -from molSimplify.job_manager.psi4_utils.run import run_b3lyp, run_general -from molSimplify.job_manager.psi4_utils.derivative import derivative_tree, get_wfn_path -from molSimplify.job_manager.psi4_utils.stable_run import run_with_check - - -basedir = os.getcwd() -success_count = 0 -psi4_config = {'bashrc': '/home/crduan/.bashrc', - 'conda_env': '/home/crduan/miniconda/envs/mols_py36'} -with open("psi4_config.json", "r") as f: - psi4_config.update(json.load(f)) -jobs = derivative_tree(path="./", trigger=psi4_config["trigger"]) -print("jobs:", jobs) -# ---run first job from scratch--- -success_count = run_with_check(job=jobs[0], basedir=basedir, psi4_config=psi4_config, - success_count=success_count, run_func=run_b3lyp, error_scf=True) -# ---run other jobs using the wfn from the previous step--- -for ii, job in enumerate(jobs[1:]): - psi4_config["wfnfile"] = get_wfn_path(jobs, ii+1) - success_count = run_with_check(job=job, basedir=basedir, psi4_config=psi4_config, - success_count=success_count, run_func=run_general, - error_scf=True) diff --git a/molSimplify/job_manager/psi4_utils/loop_rescue.py b/molSimplify/job_manager/psi4_utils/loop_rescue.py deleted file mode 100644 index d4a5bb5a..00000000 --- a/molSimplify/job_manager/psi4_utils/loop_rescue.py +++ /dev/null @@ -1,84 +0,0 @@ -import os -import json -import shutil -import numpy as np -from molSimplify.job_manager.psi4_utils.run import run_general_hfx - -psi4_config = {'bashrc': '/home/crduan/.bashrc', - 'conda_env': '/home/crduan/miniconda/envs/mols_py36'} -with open("psi4_config.json", "r") as f: - psi4_config.update(json.load(f)) -alphalist = [20, 15, 10, 5, 2] -rescued = 0 -success_count = 0 -basedir = os.getcwd() -for ii, functional in enumerate(psi4_config["functional"]): - failed = False - print("===%d: %s===" % (ii, functional)) - with open(functional + "/output.dat", "r") as fo: - txt = "".join(fo.readlines()) - if 'PsiException: Could not converge SCF iterations' in txt or txt == "": - success = False - e0 = np.nan - for jj, alpha in enumerate(alphalist): - print(alpha) - if jj == 0: - wfn = "../b3lyp/wfn.180.npy" - wfn_b = "b3lyp/wfn.180.npy" - else: - wfn = "../%s/wfn.180.npy" % (functional + "-%d" % - alphalist[jj-1]) - wfn_b = "%s/wfn.180.npy" % (functional + "-%d" % - alphalist[jj-1]) - if not os.path.isdir(functional + "-%d" % alpha) and not failed: - os.makedirs(functional + "-%d" % alpha) - shutil.copyfile(psi4_config['xyzfile'], functional + "-%d" % - alpha + '/' + psi4_config['xyzfile']) - success = run_general_hfx(psi4_config, functional, hfx=alpha, wfn=wfn) - print("success: ", success) - if success: - success_count += 1 - else: - failed = True - else: - print("attempted rescue: ", functional) - resubed = False - if not os.path.isfile(functional + "-%d" % alpha + "/output.dat"): - resubed = True - else: - with open(functional + "-%d" % alpha + "/output.dat", "r") as fo: - txt = "".join(fo.readlines()) - if "==> Iterations <==" not in txt: - resubed = True - if resubed and os.path.isfile(wfn_b): - print("previously errored out. resubmitting...") - success = run_general_hfx(psi4_config, functional, hfx=alpha, wfn=wfn) - print("success: ", success) - if success: - success_count += 1 - else: - failed = True - elif ('PsiException: Could not converge SCF iterations') not in txt and (not os.path.isfile(functional + "-%d" % alpha + "/wfn.180.npy")): - _functional = functional + "-%d" % alpha - if not os.path.isfile(_functional + "/output-timeout.dat"): - shutil.copy(_functional + "/output.dat", - _functional + "/output-timeout.dat") - print("Time out, direct resub...") - success = run_general_hfx(psi4_config, functional, hfx=alpha, wfn=wfn) - print("success: ", success) - if success: - success_count += 1 - else: - failed = True - else: - failed = True - print("Already submit once for timeout.") - else: - print("give up resubmission.") - if not failed: - rescued += 1 - print("rescued: ", functional) - else: - rescued += 1 - print("%s has already succeeded!" % functional) -print("all finished!") diff --git a/molSimplify/job_manager/psi4_utils/loop_run.py b/molSimplify/job_manager/psi4_utils/loop_run.py deleted file mode 100644 index cfc6ffa8..00000000 --- a/molSimplify/job_manager/psi4_utils/loop_run.py +++ /dev/null @@ -1,72 +0,0 @@ -import os -import json -from molSimplify.job_manager.psi4_utils.run import run_b3lyp, run_general - -psi4_config = {'bashrc': '/home/crduan/.bashrc', - 'conda_env': '/home/crduan/miniconda/envs/mols_py36'} -with open("psi4_config.json", "r") as f: - psi4_config.update(json.load(f)) -success_count = 0 -print("===b3lyp===") -if not os.path.isdir("b3lyp"): - success = run_b3lyp(psi4_config, rundir="b3lyp") - print("success: ", success) - if success: - success_count += 1 -else: - print("folder exists.") - files = os.listdir("b3lyp") - resubed = False - functional = "b3lyp" - if not os.path.isfile(functional + "/output.dat"): - resubed = True - else: - with open(functional + "/output.dat", "r") as fo: - txt = "".join(fo.readlines()) - if "==> Iterations <==" not in txt: - resubed = True - if resubed: - print("previous errored out. resubmitting...") - success = run_b3lyp(psi4_config, rundir="b3lyp") - print("success: ", success) - if success: - success_count += 1 - else: - with open(functional + "/output.dat", "r") as fo: - txt = "".join(fo.readlines()) - if 'PsiException: Could not converge SCF iterations' not in txt and os.path.isfile(functional + "/wfn.180.npy"): - print("success: ", True) - success_count += 1 -for ii, functional in enumerate(psi4_config["functional"]): - print("===%d: %s===" % (ii, functional)) - if not os.path.isdir(functional.replace("(", "l-").replace(")", "-r")): - os.makedirs(functional.replace("(", "l-").replace(")", "-r")) - success = run_general(psi4_config, functional) - print("success: ", success) - if success: - success_count += 1 - else: - print("folder exists.") - files = os.listdir(functional.replace("(", "l-").replace(")", "-r")) - resubed = False - if not os.path.isfile(functional.replace("(", "l-").replace(")", "-r") + "/output.dat"): - resubed = True - else: - with open(functional.replace("(", "l-").replace(")", "-r") + "/output.dat", "r") as fo: - txt = "".join(fo.readlines()) - if "==> Iterations <==" not in txt or (not (("@DF-UKS iter" in txt) or ("@DF-RKS iter" in txt) or ("@DF-UHF iter" in txt) or ("@DF-RHF iter" in txt))): - resubed = True - if resubed: - print("previous errored out. resubmitting...") - success = run_general(psi4_config, functional) - print("success: ", success) - if success: - success_count += 1 - else: - with open(functional.replace("(", "l-").replace(")", "-r") + "/output.dat", "r") as fo: - txt = "".join(fo.readlines()) - if 'PsiException: Could not converge SCF iterations' not in txt and os.path.isfile(functional + "/wfn.180.npy"): - print("success: ", True) - success_count += 1 -print("total successful jobs : %d/ %d." % - (success_count, len(psi4_config["functional"]) + 1)) diff --git a/molSimplify/job_manager/psi4_utils/molden2psi4wfn.py b/molSimplify/job_manager/psi4_utils/molden2psi4wfn.py deleted file mode 100644 index 88a911ac..00000000 --- a/molSimplify/job_manager/psi4_utils/molden2psi4wfn.py +++ /dev/null @@ -1,112 +0,0 @@ -import numpy as np - - -def internal_ao_mapping(shell_type): - if abs(shell_type) == 0: - return {0: 0} - elif abs(shell_type) == 1: - return {0: 0, 1: 0, 2: 0} - elif abs(shell_type) == 2: - return {0: 0, 1: 0, 2: 0, 3: 0, 4: 0, 5: 0} - else: - raise KeyError("only s, p, d shell is allowed.") - - -def shell_sequence_mapping(atom_shell_types): - # 6-31g* on C, O, N... - if "-".join([str(x) for x in atom_shell_types]) == "-".join([str(x) for x in [0, 0, 0, 1, 1, 2]]): - return {0: 0, 1: 0, 2: 3, 3: -1, 4: 0, 5: 0} # for TC - # 6-31g on C, O, N... - elif "-".join([str(x) for x in atom_shell_types]) == "-".join([str(x) for x in [0, 0, 0, 1, 1]]): - return {0: 0, 1: 0, 2: 3, 3: -1, 4: 0} - # 6-31g* on P, S, Cl... - elif "-".join([str(x) for x in atom_shell_types]) == "-".join([str(x) for x in [0, 0, 0, 0, 1, 1, 1, 2]]): - return {0: 0, 1: 0, 2: 3, 3: 6, 4: -2, 5: -1, 6: 0, 7: 0} - # 6-31g* on metals - elif "-".join([str(x) for x in atom_shell_types]) == "-".join([str(x) for x in [0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2]]): - return {0: 0, 1: 0, 2: 3, 3: 6, 4: 9, 5: -3, 6: -2, 7: -1, 8: 0, 9: 0, 10: 0} - else: - d = {} - for ii, _ in enumerate(atom_shell_types): - d.update({ii: 0}) - return d - - -def mocoeff_c2s(mocoeffs_c, shell_types): - ''' - For Cartesian functions we need to add a basis function normalization constant of - // _______________________________ - // / (2lx-1)!! (2ly-1)!! (2lz-1)!! - // / ----------------------------- - // \/ (2l-1)!! - // - d_conv, d_conv_inv: conversion metrix. - source: https://github.com/psi4/psi4/blob/master/psi4/src/psi4/libmints/writer.cc, FCHKWriter - ''' # noqa W605 - pf1 = 1.0 - pf2 = np.sqrt(1.0 / 3.0) - d_conv = np.array([ - [pf1, 0.0, 0.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 0.0, pf1, 0.0, 0.0], - [0.0, 0.0, 0.0, 0.0, 0.0, pf1], - [0.0, pf2, 0.0, 0.0, 0.0, 0.0], - [0.0, 0.0, pf2, 0.0, 0.0, 0.0], - [0.0, 0.0, 0.0, 0.0, pf2, 0.0], - ]) - d_conv_inv = np.linalg.inv(d_conv) - mocoeffs_s = [] - start = 0 - end = 0 - for t in shell_types: - if t == 0: - end += 1 - mocoeffs_s += mocoeffs_c[start:end].tolist() - elif t == 1: - end += 3 - mocoeffs_s += mocoeffs_c[start:end].tolist() - elif t == 2: - end += 6 - tmp_c = mocoeffs_c[start:end] - tmp_s = np.matmul(d_conv_inv, tmp_c) - mocoeffs_s += tmp_s.tolist() - else: - raise KeyError("only support for s, p, and d for now.") - start = end - mocoeffs_s = np.array(mocoeffs_s) - return mocoeffs_s - - -def mocoeff_mapping(d_molden, mapping, key='alpha'): - coeff = np.copy(d_molden['orb_%s_coeffs' % key]) - coeff = mocoeff_c2s(coeff, d_molden['obasis']['shell_types']) - mooeff_psi4 = np.zeros(shape=coeff.shape) - for ii in range(len(mapping.keys())): - # print(ii, mapping[ii]) - mooeff_psi4[mapping[ii], :] = coeff[ii, :] - return mooeff_psi4 - - -def tcmolden2psi4wfn_ao_mapping(d_molden, restricted=False): - mapping = {} - start = 0 - ao_start = 0 - for atom_i in np.unique(d_molden['obasis']['shell_map']): - num_shell = np.count_nonzero(d_molden['obasis']['shell_map'] == atom_i) - atom_shell_types = d_molden['obasis']['shell_types'][start: start+num_shell] - start += num_shell - shell_mapping = shell_sequence_mapping(atom_shell_types) -# print(shell_mapping) - for ii in range(len(shell_mapping.keys())): - shell_type = atom_shell_types[ii] - ao_mapping_local = internal_ao_mapping(shell_type) -# print(ii, shell_type, ao_mapping_local) - for jj in range(len(ao_mapping_local.keys())): - mapping.update( - {ao_start: ao_start+ao_mapping_local[jj]+shell_mapping[ii]}) - ao_start += 1 - Ca = mocoeff_mapping(d_molden, mapping, key='alpha') - if not restricted: - Cb = mocoeff_mapping(d_molden, mapping, key='beta') - else: - Cb = False - return Ca, Cb, mapping diff --git a/molSimplify/job_manager/psi4_utils/molden2psi4wfn_spherical.py b/molSimplify/job_manager/psi4_utils/molden2psi4wfn_spherical.py deleted file mode 100644 index 84bfb430..00000000 --- a/molSimplify/job_manager/psi4_utils/molden2psi4wfn_spherical.py +++ /dev/null @@ -1,95 +0,0 @@ -import numpy as np - - -def internal_ao_mapping(shell_type): - if abs(shell_type) == 0: - return {0: 0} - elif abs(shell_type) == 1: - return {0: 1, 1: 1, 2: -2} - elif abs(shell_type) == 2: - return {0: 0, 1: 0, 2: 0, 3: 0, 4: 0} - else: - raise KeyError("only s, p, d shell is allowed.") - - -def shell_sequence_mapping(atom_shell_types): - ''' - only work for def2-sv(p) now - ''' - d = {} - for ii, _ in enumerate(atom_shell_types): - d.update({ii: 0}) - return d - - -def mocoeff_c2s(mocoeffs_c, shell_types): - ''' - Covert Cartesian MO coefficients in TC to spherical MO coefficients. - Work for the case where the internal calculation is done in spherical basis but the molden file is written in Cartesian basis. - mocoeffs_c: MO coefficients at Cartesian basis (but with "sphericalbasis yes") - shell_types: list of shell types ranked in the same order of MO coefficients (0 for s, 1 for p, and 2 for d) - c2s: A matrix for conversion (for d shell) - ''' - c2s = np.array([ - [-0.5*2/3, -0.5*2/3, 1*2/3, 0, 0, 0], - [0, 0, 0, 0, 1, 0], - [0, 0, 0, 0, 0, 1], - [np.sqrt(3)/2 * 2/3, -np.sqrt(3)/2*2/3, 0, 0, 0, 0], - [0, 0, 0, 1, 0, 0] - ]) - mocoeffs_s = [] - start = 0 - end = 0 - for t in shell_types: - if t == 0: - end += 1 - mocoeffs_s += mocoeffs_c[start:end].tolist() - elif t == 1: - end += 3 - mocoeffs_s += mocoeffs_c[start:end].tolist() - elif t == 2: - end += 6 - tmp_c = mocoeffs_c[start:end] - tmp_s = np.matmul(c2s, tmp_c) - mocoeffs_s += tmp_s.tolist() - else: - raise KeyError("only support for s, p, and d for now.") - start = end - mocoeffs_s = np.array(mocoeffs_s) - return mocoeffs_s - - -def mocoeff_mapping(d_molden, mapping, key='alpha'): - coeff = np.copy(d_molden['orb_%s_coeffs' % key]) - coeff = mocoeff_c2s(coeff, d_molden['obasis']['shell_types']) - mooeff_psi4 = np.zeros(shape=coeff.shape) - for ii in range(len(mapping.keys())): - # print(ii, mapping[ii]) - mooeff_psi4[mapping[ii], :] = coeff[ii, ] - return mooeff_psi4 - - -def tcmolden2psi4wfn_ao_mapping_spherical(d_molden, restricted=False): - mapping = {} - start = 0 - ao_start = 0 - for atom_i in np.unique(d_molden['obasis']['shell_map']): - num_shell = np.count_nonzero(d_molden['obasis']['shell_map'] == atom_i) - atom_shell_types = d_molden['obasis']['shell_types'][start: start+num_shell] - start += num_shell - shell_mapping = shell_sequence_mapping(atom_shell_types) -# print(shell_mapping) - for ii in range(len(shell_mapping.keys())): - shell_type = atom_shell_types[ii] - ao_mapping_local = internal_ao_mapping(shell_type) -# print(ii, shell_type, ao_mapping_local) - for jj in range(len(ao_mapping_local.keys())): - mapping.update( - {ao_start: ao_start+ao_mapping_local[jj]+shell_mapping[ii]}) - ao_start += 1 - Ca = mocoeff_mapping(d_molden, mapping, key='alpha') - if not restricted: - Cb = mocoeff_mapping(d_molden, mapping, key='beta') - else: - Cb = False - return Ca, Cb, mapping diff --git a/molSimplify/job_manager/psi4_utils/run.py b/molSimplify/job_manager/psi4_utils/run.py deleted file mode 100644 index f163a3b2..00000000 --- a/molSimplify/job_manager/psi4_utils/run.py +++ /dev/null @@ -1,531 +0,0 @@ -import psi4 -import argparse -import os -import numpy as np -import shutil -import subprocess -import iodata -import json -import glob -from os.path import expanduser -from molSimplify.job_manager.psi4_utils.molden2psi4wfn import tcmolden2psi4wfn_ao_mapping -from molSimplify.job_manager.psi4_utils.molden2psi4wfn_spherical import tcmolden2psi4wfn_ao_mapping_spherical -from pkg_resources import resource_filename, Requirement - - -def lacvps(mol, role): - ''' - Define the LACVP* basis set. - lanl2dz for metals and 6-31g* for others. - ''' - basstrings = {} - mol.set_basis_all_atoms("6-31g*", role=role) - mol.set_basis_by_symbol("fe", "lanl2dz", role=role) - mol.set_basis_by_symbol("co", "lanl2dz", role=role) - mol.set_basis_by_symbol("cr", "lanl2dz", role=role) - mol.set_basis_by_symbol("mn", "lanl2dz", role=role) - mol.set_basis_by_symbol("mo", "lanl2dz", role=role) - mol.set_basis_by_symbol("tc", "lanl2dz", role=role) - mol.set_basis_by_symbol("ru", "lanl2dz", role=role) - mol.set_basis_by_symbol("rh", "lanl2dz", role=role) - mol.set_basis_by_symbol("I", "lanl2dz", role=role) - mol.set_basis_by_symbol("Br", "lanl2dz", role=role) - mol.set_basis_by_symbol("hf", "lanl2dz", role=role) - return basstrings - - -def get_molecule(xyzfile, charge, spin, sym='c1'): - ''' - Assemble a molecule object from xyzfile, charge and spin. - ''' - wholetext = "%s %s\n" % (charge, spin) - if os.path.isfile(xyzfile): - with open(xyzfile, "r") as fo: - natoms = int(fo.readline().split()[0]) - fo.readline() - for ii in range(natoms): - wholetext += fo.readline() - wholetext += "\nsymmetry %s\nnoreorient\nnocom\n" % sym - mol = psi4.geometry("""%s""" % wholetext) - return mol - - -def setup_dft_parameters(psi4_config): - psi4.set_memory(psi4_config["memory"]) - psi4.set_num_threads(psi4_config["num_threads"]) - if psi4_config["basis"] == "lacvps": - psi4.qcdb.libmintsbasisset.basishorde['LACVPS'] = lacvps - psi4.set_options({"puream": False}) - elif psi4_config["basis"] == "def2-tzvp": - psi4.set_options({"puream": True}) - else: - psi4.set_options({"puream": True}) - # pass - # raise ValueError("Only lacvps is supported!") - psi4.set_options({ - 'reference': psi4_config["ref"], - "DF_SCF_GUESS": False, - "scf_type": "df", - "dft_pruning_scheme": "robust", - "basis": psi4_config["basis"], - "DFT_BASIS_TOLERANCE": 1e-10, - "INTS_TOLERANCE": 1e-10, - "PRINT_MOS": False, - "dft_spherical_points": 590, - "dft_radial_points": 99, - # "SOSCF": True, - # "DAMPING_PERCENTAGE": 20, - # "BASIS_GUESS": True, - "guess": "read", }) - - -def ensure_dir(dirpath): - if not os.path.isdir(dirpath): - os.makedirs(dirpath) - - -def check_sucess(): - success = False - with open("output.dat", "r") as fo: - txt = "".join(fo.readlines()) - if 'Computation Completed' in txt: - success = True - return success - - -def b3lyp_hfx(): - b3lyp_d = {} - for hfx in [0, 5, 10, 15, 20, 25, 30, 35, 40]: - hfx_func = { - "name": "hfx_func", - "x_functionals": { - "GGA_X_B88": {"alpha": 0.9*(1-hfx*0.01)}, - "LDA_X": {"alpha": 0.1*(1-hfx*0.01)} - }, - "x_hf": {"alpha": hfx*0.01}, - "c_functionals": { - "GGA_C_LYP": {"alpha": 0.81}, - "LDA_C_VWN_RPA": {"alpha": 0.19} - } - } - b3lyp_d["b3lyp_" + str(hfx)] = hfx_func - return b3lyp_d - - -def run_b3lyp(psi4_config, rundir="./b3lyp", return_wfn=True): - b3lyp_d = b3lyp_hfx() - psi4_scr = './' - filename = "output" - basedir = os.getcwd() - with open(psi4_config["charge-spin-info"], "r") as f: - d = json.load(f) - psi4_config.update(d) - ensure_dir(rundir) - shutil.copyfile(psi4_config["xyzfile"], os.path.join(rundir, psi4_config["xyzfile"])) - sym = 'c1' if 'sym' not in psi4_config else psi4_config['sym'] - mol = get_molecule(psi4_config["xyzfile"], psi4_config["charge"], psi4_config["spin"], sym) - setup_dft_parameters(psi4_config) - pid = str(os.getpid()) - if os.path.isfile(psi4_config["moldenfile"]): - shutil.copyfile(psi4_config["moldenfile"], rundir + '/' + psi4_config["moldenfile"]) - os.chdir(rundir) - psi4.core.set_output_file(filename + '.dat', False) - # 1-step SCF - psi4.set_options({ - "maxiter": 5, - "D_CONVERGENCE": 1e5, - "E_CONVERGENCE": 1e5, - "fail_on_maxiter": False}) - if psi4_config["basis"] == "def2-tzvp": - psi4.set_options({"basis": "def2-sv(p)"}) - if "b3lyp_hfx" in psi4_config and psi4_config["b3lyp_hfx"] != 20: - print("customized b3lyp with different HFX: ", psi4_config["b3lyp_hfx"]) - functional = "b3lyp_" + str(psi4_config["b3lyp_hfx"]) - e, wfn = psi4.energy("scf", dft_functional=b3lyp_d[functional], molecule=mol, return_wfn=True) - else: - e, wfn = psi4.energy('b3lyp', molecule=mol, return_wfn=True) - wfn.to_file("wfn-1step.180") - # Get converged WFN - d_molden = iodata.molden.load_molden(psi4_config["moldenfile"]) - restricted = True if any(x in psi4_config["ref"] for x in ["r", "R"]) else False - if not psi4_config["basis"] == "def2-tzvp": - Ca, Cb, mapping = tcmolden2psi4wfn_ao_mapping(d_molden, restricted=restricted) - else: - Ca, Cb, mapping = tcmolden2psi4wfn_ao_mapping_spherical(d_molden, restricted=restricted) - wfn_minimal_np = np.load("wfn-1step.180.npy", allow_pickle=True) - wfn_minimal_np[()]['matrix']["Ca"] = Ca - if not restricted: - wfn_minimal_np[()]['matrix']["Cb"] = Cb - else: - wfn_minimal_np[()]['matrix']["Cb"] = Ca - np.save("wfn-1step-tc.180.npy", wfn_minimal_np) - # Copy wfn file to the right place with a right name - pid = str(os.getpid()) - targetfile = psi4_scr + filename + '.default.' + pid + '.180.npy' - shutil.copyfile("wfn-1step-tc.180.npy", targetfile) - # Final scf--- - psi4.set_options({ - "maxiter": 50, - "D_CONVERGENCE": 3e-5, - "E_CONVERGENCE": 3e-5, - "fail_on_maxiter": True}) - else: - os.chdir(rundir) - psi4.core.set_output_file(filename + '.dat', False) - print("Warning: no Molden file is used to initialize this calculation!") - psi4.set_options({ - "maxiter": 250 if "maxiter" not in psi4_config else psi4_config["maxiter"], - # "guess": "GWH", - "D_CONVERGENCE": 3e-5, - "E_CONVERGENCE": 3e-5, - "fail_on_maxiter": True}) - if psi4_config["basis"] == "def2-tzvp": - psi4.set_options({"basis": "def2-sv(p)"}) - sucess = False - try: - if "b3lyp_hfx" in psi4_config and psi4_config["b3lyp_hfx"] != 20: - print("customized b3lyp with different HFX: ", psi4_config["b3lyp_hfx"]) - functional = "b3lyp_" + str(psi4_config["b3lyp_hfx"]) - e, wfn = psi4.energy("scf", dft_functional=b3lyp_d[functional], molecule=mol, return_wfn=True) - else: - e, wfn = psi4.energy('b3lyp', molecule=mol, return_wfn=True) - wfn.to_file("wfn.180") - sucess = True - except: - print("This calculation does not converge.") - if psi4_config["basis"] == "def2-tzvp" and sucess: - psi4.set_options({"basis": "def2-tzvp", "maxiter": 200 if "maxiter" not in psi4_config else psi4_config["maxiter"]}) - try: - if "b3lyp_hfx" in psi4_config and psi4_config["b3lyp_hfx"] != 20: - print("customized b3lyp with different HFX: ", psi4_config["b3lyp_hfx"]) - functional = "b3lyp_" + str(psi4_config["b3lyp_hfx"]) - e, wfn = psi4.energy("scf", dft_functional=b3lyp_d[functional], molecule=mol, return_wfn=True) - else: - e, wfn = psi4.energy('b3lyp', molecule=mol, return_wfn=True) - wfn.to_file("wfn.180") - except: - print("This calculation does not converge.") - success = check_sucess() - for filename in os.listdir("./"): - if ("psi." in filename) or ("default" in filename): - print("removing: :", filename) - os.remove(filename) - os.chdir(basedir) - return success - - -def run_general(psi4_config, functional="b3lyp", return_wfn=False): - b3lyp_d = b3lyp_hfx() - psi4_scr = './' - filename = "output" - basedir = os.getcwd() - rundir = "./" + functional.replace("(", "l-").replace(")", "-r") - with open(psi4_config["charge-spin-info"], "r") as f: - d = json.load(f) - psi4_config.update(d) - ensure_dir(rundir) - shutil.copyfile(psi4_config["xyzfile"], functional.replace("(", "l-").replace(")", "-r") + '/' + psi4_config["xyzfile"]) - os.chdir(rundir) - psi4.core.set_output_file(filename + '.dat', False) - sym = 'c1' if 'sym' not in psi4_config else psi4_config['sym'] - mol = get_molecule(psi4_config["xyzfile"], psi4_config["charge"], psi4_config["spin"], sym) - setup_dft_parameters(psi4_config) - # Copy wfn file to the right place with a right name--- - pid = str(os.getpid()) - targetfile = psi4_scr + filename + '.default.' + pid + '.180.npy' - if os.path.isfile(psi4_config["wfnfile"]): - shutil.copyfile(psi4_config["wfnfile"], targetfile) - # Final scf--- - psi4.set_options({ - "maxiter": 50 if "maxiter" not in psi4_config else psi4_config["maxiter"], - "D_CONVERGENCE": 3e-5, - "E_CONVERGENCE": 3e-5, - "fail_on_maxiter": True}) - if not (("ccsd" in functional) or ("mp2" in functional) or ("scf" in functional)): - try: - if (functional not in b3lyp_d) and ("hfx_" not in functional) and ("ccsd" not in functional): - e, wfn = psi4.energy(functional, molecule=mol, return_wfn=True) - elif "hfx_" in functional: - basefunc, hfx = functional.split("_")[0], int(functional.split("_")[-1]) - print("HFX sampling: ", basefunc, hfx) - e, wfn = psi4.energy("scf", dft_functional=get_hfx_functional(basefunc, hfx), molecule=mol, return_wfn=True) - else: - print("customized b3lyp with different HFX: ", functional) - e, wfn = psi4.energy("scf", dft_functional=b3lyp_d[functional], molecule=mol, return_wfn=True) - if return_wfn: - wfn.to_file("wfn.180") - except: - print("This calculation does not converge.") - else: - print("running CC: ", functional) - psi4.set_options({ - 'reference': d['ref'].replace("ks", "hf"), - 'R_CONVERGENCE': 1e-5, - 'E_CONVERGENCE': 5e-5, - 'D_CONVERGENCE': 5e-5, - "mp2_type": "df", - "cc_type": "conv", - "scf_type": "df", - 'nat_orbs': True, - 'FREEZE_CORE': True, - "GUESS": "SAD", - }) - e, wfn = psi4.energy(functional, molecule=mol, return_wfn=True) - wfn.to_file("wfn.180") - success = check_sucess() - for filename in os.listdir("./"): - if ("psi." in filename) or ("default" in filename): - print("removing: :", filename) - os.remove(filename) - os.chdir(basedir) - return success - - -def run_general_hfx(psi4_config, functional, hfx, wfn): - psi4_scr = './' - filename = "output" - basedir = os.getcwd() - rundir = "./" + functional + "-%d" % hfx - with open(psi4_config["charge-spin-info"], "r") as f: - d = json.load(f) - psi4_config.update(d) - shutil.copyfile(psi4_config["xyzfile"], os.path.join(rundir, psi4_config["xyzfile"])) - ensure_dir(rundir) - os.chdir(rundir) - psi4.core.set_output_file(filename + '.dat', False) - sym = 'c1' if 'sym' not in psi4_config else psi4_config['sym'] - mol = get_molecule(psi4_config["xyzfile"], psi4_config["charge"], psi4_config["spin"], sym) - setup_dft_parameters(psi4_config) - # Copy wfn file to the right place with a right name--- - pid = str(os.getpid()) - targetfile = psi4_scr + filename + '.default.' + pid + '.180.npy' - if not os.path.isfile(wfn): - print("Previous calculation failed... This one is skipped.") - return False - shutil.copyfile(wfn, targetfile) - # Final scf--- - psi4.set_options({ - "maxiter": 50 if "maxiter" not in psi4_config else psi4_config["maxiter"], - "D_CONVERGENCE": 3e-5, - "E_CONVERGENCE": 3e-5, - "fail_on_maxiter": True}) - try: - e, wfn_o = psi4.energy("scf", molecule=mol, return_wfn=True, dft_functional=get_hfx_functional(functional, hfx)) - wfn_o.to_file("wfn.180") - # os.remove(wfn) - except: - print("This calculation does not converge.") - success = check_sucess() - for filename in os.listdir("./"): - if ("psi." in filename) or ("default" in filename): - print("removing: :", filename) - os.remove(filename) - os.chdir(basedir) - return success - - -def get_hfx_functional(functional, hfx): - fmap = {"tpss": "TPSS", "scan": "SCAN", "m06-l": "M06_L", "mn15-l": "MN15_L"} - if functional == "bp86": - hfx_func = { - "name": "hfx_func", - "x_functionals": {"GGA_X_B88": {"alpha": 1-hfx*0.01}}, - "x_hf": {"alpha": hfx*0.01}, - "c_functionals": {"GGA_C_P86": {}} - } - elif functional == "blyp": - hfx_func = { - "name": "hfx_func", - "x_functionals": {"GGA_X_B88": {"alpha": 1-hfx*0.01}}, - "x_hf": {"alpha": hfx*0.01}, - "c_functionals": {"GGA_C_LYP": {}} - } - elif functional == "b3lyp": - hfx_func = { - "name": "hfx_func", - "x_functionals": { - "GGA_X_B88": {"alpha": 0.9*(1-hfx*0.01)}, - "LDA_X": {"alpha": 0.1*(1-hfx*0.01)} - }, - "x_hf": {"alpha": hfx*0.01}, - "c_functionals": { - "GGA_C_LYP": {"alpha": 0.81}, - "LDA_C_VWN_RPA": {"alpha": 0.19} - } - } - elif functional == "pbe": - hfx_func = { - "name": "hfx_func", - "x_functionals": {"GGA_X_PBE": {"alpha": 1-hfx*0.01}}, - "x_hf": {"alpha": hfx*0.01}, - "c_functionals": {"GGA_C_PBE": {}} - } - elif functional in ["m06-l", "mn15-l", "scan", "tpss"]: - mega = "" if "PBE" in functional else "M" - hfx_func = { - "name": "hfx_func", - "x_functionals": {"%sGGA_X_%s" % (mega, fmap[functional]): {"alpha": 1-hfx*0.01}}, - "x_hf": {"alpha": hfx*0.01}, - "c_functionals": {"%sGGA_C_%s" % (mega, fmap[functional]): {}} - } - else: - raise ValueError("This functional has not been implemented with HFX resampling yet: ", functional) - return hfx_func - - -def write_jobscript(psi4_config): - if "cluster" not in psi4_config: - mem = int(psi4_config['memory'].split(" ")[0])/1000 - with open("./jobscript.sh", "w") as fo: - fo.write("#$ -S /bin/bash\n") - fo.write("#$ -N psi4_dft\n") - fo.write("#$ -R y\n") - fo.write("#$ -cwd\n") - fo.write("#$ -l h_rt=240:00:00\n") - fo.write("#$ -l h_rss=%dG\n" % (mem)) - fo.write("#$ -q cpus\n") - fo.write("#$ -l cpus=1\n") - fo.write("#$ -pe smp %d\n" % psi4_config['num_threads']) - fo.write("# -fin *\n") - - fo.write(f"source {psi4_config['bashrc']}\n") - fo.write(f"conda activate {psi4_config['conda_env']}\n") - fo.write("export PSI_SCRATCH='./'\n") - fo.write("echo 'psi4 scr: ' $PSI_SCRATCH\n") - - if "trigger" in psi4_config: - fo.write("python -u loop_derivative_jobs.py > $SGE_O_WORKDIR/deriv_nohup1.out\n") - else: - fo.write("python -u loop_run.py > $SGE_O_WORKDIR/nohup1.out\n") - fo.write("python -u loop_run.py > $SGE_O_WORKDIR/nohup2.out\n") - fo.write("python -u loop_run.py > $SGE_O_WORKDIR/nohup3.out\n") - if "hfx_rescue" in psi4_config and psi4_config["hfx_rescue"]: - fo.write("echo rescuing...\n") - fo.write("python -u loop_rescue.py > $SGE_O_WORKDIR/rescue_nohup1.out\n") - fo.write("python -u loop_rescue.py > $SGE_O_WORKDIR/rescue_nohup2.out\n") - fo.write("python -u loop_rescue.py > $SGE_O_WORKDIR/rescue_nohup3.out\n") - fo.write("cp -rf * $SGE_O_WORKDIR\n") - elif psi4_config["cluster"] == "supercloud": - mem = int(psi4_config['memory'].split(" ")[0])/1000 - with open("./jobscript.sh", "w") as fo: - fo.write("#!/bin/bash\n") - fo.write("#SBATCH --job-name=psi4_multiDFA\n") - fo.write("#SBATCH --nodes=1\n") - fo.write("#SBATCH --time=96:00:00\n") - fo.write("#SBATCH --ntasks-per-node=%d\n" % psi4_config['num_threads']) - if "queue" in psi4_config and psi4_config["queue"] == "normal": - fo.write("#SBATCH --partition=normal\n") - fo.write("#SBATCH --mem=%dG\n\n" % mem) - - fo.write("source /etc/profile\n") - fo.write("source ~/.profile\n") - fo.write("source ~/.bashrc\n") - fo.write("conda activate mols_py37\n") - fo.write("export PSI_SCRATCH='./'\n\n") - fo.write("subdir=$PWD\n") - fo.write("echo subdir: $subdir\n") - fo.write("echo tmpdir: $TMPDIR\n") - fo.write("cp -rf * $TMPDIR\n") - fo.write("cd $TMPDIR\n\n") - - if "trigger" in psi4_config: - fo.write("python -u loop_derivative_jobs.py > $subdir/deriv_nohup1.out\n") - fo.write("rm */*/psi.* */*/dfh.* */*-*/*.npy */b3lyp/*.molden */b3lyp/*1step*\n") - else: - fo.write("python -u loop_run.py > $subdir/nohup1.out\n") - fo.write("python -u loop_run.py > $subdir/nohup2.out\n") - fo.write("python -u loop_run.py > $subdir/nohup3.out\n") - if "hfx_rescue" in psi4_config and psi4_config["hfx_rescue"]: - fo.write("echo rescuing...\n") - fo.write("python -u loop_rescue.py > $subdir/rescue_nohup1.out\n") - fo.write("python -u loop_rescue.py > $subdir/rescue_nohup2.out\n") - fo.write("python -u loop_rescue.py > $subdir/rescue_nohup3.out\n") - fo.write("rm */psi.* */dfh.* *-*/*.npy b3lyp/*.molden b3lyp/*1step*\n") - fo.write("cp -rf * $subdir\n") - elif psi4_config["cluster"] == "expanse": - mem = int(psi4_config['memory'].split(" ")[0])/psi4_config['num_threads']/1000 - with open("./jobscript.sh", "w") as fo: - fo.write("#!/bin/sh\n") - fo.write("#SBATCH -A mit136\n") - fo.write("#SBATCH --job-name=psi4_multiDFA\n") - fo.write("#SBATCH --partition=shared\n") - fo.write("#SBATCH -t 48:00:00\n") - fo.write("#SBATCH --nodes=1\n") - fo.write("#SBATCH --ntasks-per-node=16\n") - fo.write("#SBATCH --error=job.%J.err\n") - fo.write("#SBATCH --output=job.%J.out\n") - fo.write("#SBATCH --export=ALL\n") - fo.write("#SBATCH --mem=64G\n") - - fo.write("source /home/crduan/.bashrc\n") - fo.write("conda activate mols_psi4\n") - fo.write("export PSI_SCRATCH='./'\n") - fo.write("echo 'psi4 scr: ' $PSI_SCRATCH\n") - - if "trigger" in psi4_config: - fo.write("python -u loop_derivative_jobs.py > deriv_nohup1.out\n") - else: - fo.write("python -u loop_run.py > nohup1.out\n") - fo.write("python -u loop_run.py > nohup2.out\n") - fo.write("python -u loop_run.py > nohup3.out\n") - if "hfx_rescue" in psi4_config and psi4_config["hfx_rescue"]: - fo.write("echo rescuing...\n") - fo.write("python -u loop_rescue.py > rescue_nohup1.out\n") - fo.write("python -u loop_rescue.py > rescue_nohup2.out\n") - fo.write("python -u loop_rescue.py > rescue_nohup3.out\n") - elif psi4_config["cluster"] == "mustang": - with open("./jobscript.sh", "w") as fo: - fo.write("#!/bin/bash\n") - fo.write("#PBS -N psi4_multiDFA\n") - fo.write("#PBS -A ONRDC42143511\n") - fo.write("#PBS -o psi4.out\n") - fo.write("#PBS -e psi4.err\n") - fo.write("#PBS -l select=1:ncpus=48:mpiprocs=48\n") - fo.write("#PBS -l walltime=6:00:00\n") - fo.write("#PBS -q standard\n") - fo.write("#PBS -j oe\n") - fo.write("#PBE -V\n") - - fo.write("source $HOME/.personal.bashrc\n") - fo.write("export PSI_SCRATCH='./'\n") - fo.write("rundir=$PBS_O_WORKDIR\n") - fo.write("cd $rundir\n") - fo.write("homekey='home'\n") - fo.write("homedir=${rundir/work1/$homekey}\n") - fo.write("echo homedir: $homedir\n") - fo.write("echo rundir: $rundir\n") - fo.write("mkdir -p $homedir\n") - fo.write("python -u loop_run.py > nohup1.out\n") - fo.write("zip -r outdat.zip */*.dat > zip.out\n") - fo.write("cp outdat.zip $homedir\n") - fo.write("python -u loop_run.py > nohup2.out\n") - fo.write("zip -r outdat.zip */*.dat > zip.out\n") - fo.write("cp outdat.zip $homedir\n") - fo.write("python -u loop_run.py > nohup3.out\n") - fo.write("zip -r outdat.zip */*.dat > zip.out\n") - fo.write("cp outdat.zip $homedir\n") - if "hfx_rescue" in psi4_config and psi4_config["hfx_rescue"]: - fo.write("echo rescuing...\n") - fo.write("python -u loop_rescue.py > rescue_nohup1.out\n") - fo.write("zip -r outdat.zip */*.dat > zip.out\n") - fo.write("cp outdat.zip $homedir\n") - fo.write("python -u loop_rescue.py > rescue_nohup2.out\n") - fo.write("zip -r outdat.zip */*.dat > zip.out\n") - fo.write("cp outdat.zip $homedir\n") - fo.write("python -u loop_rescue.py > rescue_nohup3.out\n") - fo.write("zip -r outdat.zip */*.dat > zip.out\n") - fo.write("cp outdat.zip $homedir\n") - fo.write("echo all done.\n") - - -def run_bash(cmd, basedir, rundir): - os.chdir(rundir) - infile = resource_filename(Requirement.parse("molSimplify"), "molSimplify/job_manager/psi4_utils/loop_run.py") - shutil.copy(infile, "./") - infile_rescue = resource_filename(Requirement.parse("molSimplify"), "molSimplify/job_manager/psi4_utils/loop_rescue.py") - shutil.copy(infile_rescue, "./") - infile_deriv = resource_filename(Requirement.parse("molSimplify"), "molSimplify/job_manager/psi4_utils/loop_derivative_jobs.py") - shutil.copy(infile_deriv, "./") - print("Executing: ", cmd, "at: ", rundir) - subprocess.call(cmd, shell=True) - os.chdir(basedir) diff --git a/molSimplify/job_manager/psi4_utils/stable_run.py b/molSimplify/job_manager/psi4_utils/stable_run.py deleted file mode 100644 index 85165856..00000000 --- a/molSimplify/job_manager/psi4_utils/stable_run.py +++ /dev/null @@ -1,44 +0,0 @@ -import os -from typing import Callable - - -def run_with_check(job: str, basedir: str, psi4_config: dict, - success_count: int, run_func: Callable, - error_scf: bool = True): - print("====running on====: ", job) - os.chdir(job) - success = False - if not os.path.isdir("b3lyp"): - success = run_func(psi4_config, return_wfn=True) - print("success: ", success) - if success: - success_count += 1 - else: - print("folder exists.") - resubed = False - functional = "b3lyp" - if not os.path.isfile(functional + "/output.dat"): - resubed = True - else: - with open(functional + "/output.dat", "r") as fo: - txt = "".join(fo.readlines()) - if "==> Iterations <==" not in txt: - resubed = True - if resubed: - print("previous errored out. resubmitting...") - success = run_func(psi4_config, return_wfn=True) - print("success: ", success) - if success: - success_count += 1 - else: - with open(functional + "/output.dat", "r") as fo: - txt = "".join(fo.readlines()) - if 'PsiException: Could not converge SCF iterations' not in txt and os.path.isfile(functional + "/wfn.180.npy"): - print("success: ", True) - success = True - success_count += 1 - os.chdir(basedir) - if not success and error_scf: - raise ValueError( - "Failed on the job: %s. Other derivative jobs won't run." % job) - return success_count diff --git a/molSimplify/job_manager/readme b/molSimplify/job_manager/readme deleted file mode 100644 index 4d9c26ed..00000000 --- a/molSimplify/job_manager/readme +++ /dev/null @@ -1,33 +0,0 @@ -The configure file (labeled configure, NOT configure.txt) contains all of the info about what needs to happen to the runs. - -It can be modified on the fly to add info (if you want to add thermo or solvent, or HFX resample). - -If the geo_check:oct is in the configure file, then jobs that are completed are checked for good geometries before spawning any derivative jobs. - -If job_recovery is not desired, that line should not be there. - -The folder hierarchy is as follows: - base_directory - |----configure - |----unique_name1 - |----unique_name2 - |----unique_name3 - |----unique_name3.in - |----unique_name3.xyz - |----unique_name3_jobscript - - -The configure file can live within subdirectories, if derivative jobs are only necessary for a subset of jobs. - -Job manager reads the configure at the job run time as well as the root directory. - -Must be in the directory of the configure, and then call molSimplify/job_manager/resub.py -- this will follow the configure file and execute on the working tree as described above. - -If loading the module (in a python script), do the following: - -import molSimplify.job_manager.resub as resub -resub.main() - -The job manager uses the unique name as a queue identifier. Thus, it will not submit a job with a specific unique name, if that unique name is already in the queue. This will prevent the same job from being resubmitted while it is still running. - -Killing the job manager by using ctrl-c should be ok to stop the manager from running. By default, it cycles with a sleep period of 2 hr. diff --git a/molSimplify/job_manager/recovery.py b/molSimplify/job_manager/recovery.py deleted file mode 100644 index 25b78f7d..00000000 --- a/molSimplify/job_manager/recovery.py +++ /dev/null @@ -1,728 +0,0 @@ -#!/usr/bin/env python -import os -import shutil -import glob -import numpy as np -import molSimplify.job_manager.tools as tools -import molSimplify.job_manager.moltools as moltools -from molSimplify.job_manager.classes import resub_history -import molSimplify.job_manager.manager_io as manager_io - - -def load_history(PATH): - """Load a resub history object. - - Parameters - ---------- - PATH : str - The name of an output file or history object pickle file. - - Returns - ------- - history : resub_history - resub_history class instance for history object of job. - - """ - # takes the path to either an outfile or the resub_history pickle - # returns the resub_history class object - - history = resub_history() - history.read(PATH) - return history - - -def abandon_job(PATH): - """Abandons a job with a given path. This function is never and should never be called by the job manager. - Only called manually for troublesome jobs. - - Parameters - ---------- - PATH : str - The name of an output file or history object pickle file. - - """ - # takes the path to either an outfile or the resub_history pickle - # sets the jobs status to be abandoned - - # This function is never and should never be called by the job manager. - # It is for manually use with particularly troublesome jobs - history = load_history(PATH) - history.abandon() - history.save() - - -def save_scr(outfile_path, rewrite_inscr=True): - """Archive the scr file so it isn't overwritten in future resubs. - - Parameters - ---------- - outfile_path : str - The name of an output file. - rewrite_inscr : bool, optional - Determines whether to copy this runs wfn and optimized geometry to the inscr directory. Default is True. - - Returns - ------- - scrpaths : str - Path to new scr directory. - - - """ - root = os.path.split(outfile_path)[0] - scr_path = os.path.join(root, 'scr') - - if os.path.isdir(scr_path): - # extract the optimized geometry, if it exists - optim = glob.glob(os.path.join(scr_path, 'optim.xyz')) - if len(optim) > 0: - tools.extract_optimized_geo(optim[0]) - - if rewrite_inscr: - # save the files necessary to resub the job to a folder called inscr - save_paths = [] - save_paths.extend(glob.glob(os.path.join(scr_path, 'c0'))) - save_paths.extend(glob.glob(os.path.join(scr_path, 'ca0'))) - save_paths.extend(glob.glob(os.path.join(scr_path, 'cb0'))) - save_paths.extend(glob.glob(os.path.join(scr_path, 'optimized.xyz'))) - if os.path.isdir(os.path.join(root, 'inscr')): - shutil.rmtree(os.path.join(root, 'inscr')) - os.mkdir(os.path.join(root, 'inscr')) - for path in save_paths: - shutil.copy(path, os.path.join(root, 'inscr', os.path.split(path)[-1])) - - # archive the scr under a new name so that we can write a new one - old_scrs = glob.glob(scr_path + '_*') - old_scrs = [int(i[-1]) for i in old_scrs] - - if len(old_scrs) > 0: - new_scr = str(max(old_scrs) + 1) - else: - new_scr = '0' - # print("current_scr: ", scr_path) - # print("backup_scr: ", scr_path + '_' + new_scr) - shutil.move(scr_path, scr_path + '_' + new_scr) - - return os.path.join(os.path.split(outfile_path)[0], 'scr') + '_' + new_scr - - -def save_run(outfile_path, rewrite_inscr=True, save_scr_flag=True): - """Save the outfile within the resub_history pickle object. - - Parameters - ---------- - outfile_path : str - The name of an output file. - rewrite_inscr : bool, optional - Determines whether to copy this runs wfn and optimized geometry to the inscr directory. Default is True. - save_scr_flag : bool, optional - Determine wheether to store scr. Default is True. - - """ - def write(list_of_lines, path): - with open(path, 'w') as fil: - for i in list_of_lines: - fil.write(i) - - if save_scr_flag: - scr_path = save_scr(outfile_path, rewrite_inscr=rewrite_inscr) - else: - scr_path = os.path.join(os.path.split(outfile_path)[0], 'scr') - - history = resub_history() - history.read(outfile_path) - - with open(outfile_path, 'r') as f: - out_lines = f.readlines() - history.outfiles.append(out_lines) - - infile_path = outfile_path.rsplit('.', 1)[0] + '.in' - with open(infile_path, 'r') as f: - in_lines = f.readlines() - history.infiles.append(in_lines) - - jobscript_path = outfile_path.rsplit('.', 1)[0] + '_jobscript' - with open(jobscript_path, 'r') as f: - job_lines = f.readlines() - history.jobscripts.append(job_lines) - - xyz_path = outfile_path.rsplit('.', 1)[0] + '.xyz' - with open(xyz_path, 'r') as f: - xyz_lines = f.readlines() - history.xyzs.append(xyz_lines) - - history.save() - - if scr_path: - # Additionally, write this information to textfile so it's earch to find - home = os.getcwd() - os.chdir(scr_path) - write(out_lines, 'old_outfile') - write(in_lines, 'old_infile') - write(job_lines, 'old_job') - write(xyz_lines, 'old_xyz') - os.chdir(home) - - -def reset(outfile_path): - """Returns the run to the state it was after the first run, before job recovery acted on it. - - Parameters - ---------- - outfile_path : str - The name of an output file. - - """ - # Returns the run to the state it was after the first run, before job recovery acted on it - - pickle_path = outfile_path.rsplit('.', 1)[0] + '.pickle' - if os.path.isfile(pickle_path): - - print('Resetting run: ' + os.path.split(outfile_path)[-1].rsplit('.', 1)[0]) - old_path = os.path.join(os.path.split(outfile_path)[0], 'pre_reset') - if not os.path.isdir(old_path): - os.mkdir(old_path) - - # Find all the stdout and stderr files related to previous runs. - queue_output = glob.glob(outfile_path.rsplit('.', 1)[0] + '.e*') - queue_output.extend(glob.glob(outfile_path.rsplit('.', 1)[0] + '.pe*')) - queue_output.extend(glob.glob(outfile_path.rsplit('.', 1)[0] + '.po*')) - queue_output.extend(glob.glob(outfile_path.rsplit('.', 1)[0] + '.o*')) - queue_output = [i for i in queue_output if i[-1] in ['1', '2', '3', '4', '5', '6', '7', '8', '9', '0']] - - # remove all files from states after the specified state - move = [] - identifier = 1 - while True: - move.extend(glob.glob(os.path.join(os.path.split(outfile_path)[0], 'scr_' + str(identifier)))) - identifier += 1 - if len(glob.glob(os.path.join(os.path.split(outfile_path)[0], 'scr_' + str(identifier)))) == 0: - break # break when all scr_? files are found. - - # remove all files for derivative jobs spawned based on this job - derivative_types = ['solvent', 'vertEA', 'vertIP', 'thermo', 'kp', 'rm', 'ultratight', 'HFXresampling', - 'functional'] - possible = [i for i in glob.glob(os.path.join(os.path.split(outfile_path)[0], '*')) if os.path.isdir(i)] - for folder in possible: - if os.path.split(outfile_path)[1].rsplit('.', 1)[0] in folder: - derivative = False - for typ in derivative_types: - if typ in folder: - derivative = True - if derivative: - shutil.rmtree(folder) - - # rename outfile and jobscript files - shutil.move(outfile_path, outfile_path[:-4] + '.old') # rename old out so it isn't found in .out searches - shutil.move(outfile_path[:-4] + '_jobscript', outfile_path[ - :-4] + '_oldjob') # rename old jobscript so it isn't thought to be job that hasn't started yet - move.append(outfile_path[:-4] + '.old') - move.append(outfile_path[:-4] + '.xyz') - move.append(outfile_path[:-4] + '.in') - move.append(outfile_path[:-4] + '_oldjob') - if os.path.isdir(os.path.join(os.path.split(outfile_path)[0], 'inscr')): - move.append(os.path.join(os.path.split(outfile_path)[0], 'inscr')) - move.extend(queue_output) - scr_path = os.path.join(os.path.split(outfile_path)[0], 'scr') - move.append(scr_path) - for path in move: - # move the paths to their new location, Random numbers prevent clashes - try: - shutil.move(path, - os.path.join(old_path, str(np.random.randint(999999999)) + '_' + os.path.split(path)[-1])) - except FileNotFoundError: - print('No file found for: ' + path) - - # Rewrite the .xyz, .in, jobscript, and .out file to be the same as they were after the first run - history = resub_history() - history.read(pickle_path) - outfile = history.outfiles[0] - infile = history.infiles[0] - jobscript = history.jobscripts[0] - xyz = history.xyzs[0] - with open(outfile_path, 'w') as writer: - for i in outfile: - writer.write(i) - with open(outfile_path.rsplit('.', 1)[0] + '.in', 'w') as writer: - for i in infile: - writer.write(i) - with open(outfile_path.rsplit('.', 1)[0] + '.xyz', 'w') as writer: - for i in xyz: - writer.write(i) - with open(outfile_path.rsplit('.', 1)[0] + '_jobscript', 'w') as writer: - for i in jobscript: - writer.write(i) - - shutil.move(scr_path + '_0', scr_path) - shutil.move(pickle_path, os.path.join(old_path, str(np.random.randint(999999999)) + '_resub_history')) - - -def simple_resub(outfile_path): - """Resubmits a job without changing parameters. Particularly useful for CUDA errors. - - Parameters - ---------- - outfile_path : str - The name of an output file. - - Returns - ------- - Resub_flag : bool - True if resubmitted. - - """ - # Resubmits a job without changing parameters. Particularly useful for CUDA errors. - save_run(outfile_path, rewrite_inscr=False) - history = resub_history() - history.read(outfile_path) - history.resub_number += 1 - history.notes.append('Resubbed for unknown error') - history.save() - - root = outfile_path.rsplit('.', 1)[0] - - tools.qsub(root + '_jobscript') - return True - - -def clean_resub(outfile_path): - """Resubmits a job with default parameters, useful for undoing level shift or hfx alterations. - - Parameters - ---------- - outfile_path : str - The name of an output file. - - Returns - ------- - Resub_flag : bool - True if resubmitted. - - """ - # Resubmits a job with default parameters, useful for undoing level shift or hfx alterations - save_run(outfile_path) - history = resub_history() - history.read(outfile_path) - history.resub_number += 1 - history.status = 'Normal' - history.notes.append('Needs clean resub') - history.needs_resub = False - history.save() - - machine = tools.get_machine() - root = outfile_path.rsplit('.', 1)[0] - name = os.path.split(root)[-1] - directory = os.path.split(outfile_path)[0] - infile_dict = manager_io.read_infile(outfile_path) - - home = os.getcwd() - if len(directory) > 0: # if the string is blank, then we're already in the correct directory - os.chdir(directory) - - if os.path.isfile('inscr/optimized.xyz'): - coordinates = 'inscr/optimized.xyz' # Should trigger for optimization runs - elif os.path.isfile(name + '.xyz'): - coordinates = name + '.xyz' # Should trigger for single point runs - else: - raise ValueError('No coordinates idenfied for clean in resubmission in directory ' + os.getcwd()) - - configure_dict = manager_io.read_configure('in_place', outfile_path) - - infile_dict['coordinates'] = coordinates - infile_dict['method'] = configure_dict['method'] - infile_dict['levelshifta'], infile_dict['levelshiftb'] = configure_dict['levela'], configure_dict['levelb'] - infile_dict['dispersion'] = configure_dict['dispersion'] - infile_dict['constraints'] = False - infile_dict['machine'] = machine - - if infile_dict['spinmult'] == 1: - infile_dict['guess'] = 'inscr/c0' - manager_io.write_input(infile_dict) - else: - infile_dict['guess'] = 'inscr/ca0 inscr/cb0' - manager_io.write_input(infile_dict) - - manager_io.write_jobscript(name, custom_line='# -fin inscr/', machine=machine) - os.chdir(home) - tools.qsub(root + '_jobscript') - return True - - -def resub_spin(outfile_path): - """Resubmits a spin contaminated job with blyp to help convergence to a non-spin contaminated solution. - - Parameters - ---------- - outfile_path : str - The name of an output file. - - Returns - ------- - Resub_flag : bool - True if resubmitted. - - """ - # resubmits a spin contaminated job with blyp to help convergence to a non-spin contaminated solution - history = resub_history() - history.read(outfile_path) - resubbed_before = False - if 'Spin contaminated, lowering HFX to aid convergence' in history.notes: - resubbed_before = True - history.status = os.path.split(outfile_path)[ - -1] + ' has been submitted with lower HFX and still converges to a spin contaminated solution' - history.save() - if 'Needs clean resub' in history.notes: - resubbed_before = True - history.status = os.path.split(outfile_path)[ - -1] + ' job recovery has failed - requesting resub_spin() after clean resubmission round' - history.save() - if 'HFXresampling' in outfile_path: - resubbed_before = True - history.status = os.path.split(outfile_path)[ - -1] + ' is spin contaminated, but submitting with lower HFX does not make sense for HFX resampling jobs' - history.save() - - if not resubbed_before: - save_run(outfile_path, rewrite_inscr=False) - history = resub_history() - history.read(outfile_path) - history.resub_number += 1 - history.status = 'HFX altered to assist convergence' - history.needs_resub = True - history.notes.append('Spin contaminated, lowering HFX to aid convergence') - history.save() - - machine = tools.get_machine() - root = outfile_path.rsplit('.', 1)[0] - name = os.path.split(root)[-1] - directory = os.path.split(outfile_path)[0] - infile_dict = manager_io.read_infile(outfile_path) - - home = os.getcwd() - if len(directory) > 0: # if the string is blank, then we're already in the correct directory - os.chdir(directory) - - infile_dict['method'] = 'blyp' - infile_dict['machine'] = machine - manager_io.write_input(infile_dict) - - manager_io.write_jobscript(name, machine=machine) - os.chdir(home) - tools.qsub(root + '_jobscript') - return True - - else: - return False - - -def resub_scf(outfile_path): - """Resubmits a job that's having trouble converging the scf with different level shifts (1.0 and 0.1). - - Parameters - ---------- - outfile_path : str - The name of an output file. - - Returns - ------- - Resub_flag : bool - True if resubmitted. - - """ - # Resubmits a job that's having trouble converging the scf with different level shifts (1.0 and 0.1) - history = resub_history() - history.read(outfile_path) - resubbed_before = False - if 'SCF convergence error, level shifts adjusted to aid convergence' in history.notes: - resubbed_before = True - history.status = os.path.split(outfile_path)[ - -1] + ' has been submitted with levels shifted and is still encountering an scf error' - history.save() - if 'Needs clean resub' in history.notes: - resubbed_before = True - history.status = os.path.split(outfile_path)[ - -1] + ' job recovery has failed - requesting resub_scf() after clean resubmission round' - history.save() - - if not resubbed_before: - save_run(outfile_path, rewrite_inscr=False) - history = resub_history() - history.read(outfile_path) - history.resub_number += 1 - history.status = 'Level shifts adjusted to assist convergence' - history.needs_resub = True - history.notes.append('SCF convergence error, level shifts adjusted to aid convergence') - history.save() - - machine = tools.get_machine() - root = outfile_path.rsplit('.', 1)[0] - name = os.path.split(root)[-1] - directory = os.path.split(outfile_path)[0] - infile_dict = manager_io.read_infile(outfile_path) - - home = os.getcwd() - if len(directory) > 0: # if the string is blank, then we're already in the correct directory - os.chdir(directory) - infile_dict['levelshifta'], infile_dict['levelshiftb'] = 1.0, 0.1 - infile_dict['machine'] = machine - manager_io.write_input(infile_dict) - - manager_io.write_jobscript(name, machine=machine) - os.chdir(home) - tools.qsub(root + '_jobscript') - return True - - else: - return False - - -def resub_oscillating_scf(outfile_path): - """Resubmits a job that's having trouble converging the scf with different level shifts (1.0 and 0.1). - - Parameters - ---------- - outfile_path : str - The name of an output file. - - Returns - ------- - Resub_flag : bool - True if resubmitted. - - """ - - # Resubmits a job that's having trouble converging the scf with different level shifts (1.0 and 0.1) - history = resub_history() - history.read(outfile_path) - resubbed_before = False - if 'SCF convergence error, precision and grid adjusted to aid convergence' in history.notes: - resubbed_before = True - history.status = os.path.split(outfile_path)[ - -1] + ' has been submitted with higher precision and grid and is still encountering an scf error' - history.save() - if 'Needs clean resub' in history.notes: - resubbed_before = True - history.status = os.path.split(outfile_path)[ - -1] + ' job recovery has failed - requesting resub_oscillating_scf() after clean resubmission round' - history.save() - - if not resubbed_before: - save_run(outfile_path, rewrite_inscr=False) - history = resub_history() - history.read(outfile_path) - history.resub_number += 1 - history.status = 'precision and grid adjusted to assist convergence' - history.notes.append('SCF convergence error, precision and grid adjusted to aid convergence') - history.save() - - machine = tools.get_machine() - root = outfile_path.rsplit('.', 1)[0] - name = os.path.split(root)[-1] - directory = os.path.split(outfile_path)[0] - infile_dict = manager_io.read_infile(outfile_path) - - home = os.getcwd() - if len(directory) > 0: # if the string is blank, then we're already in the correct directory - os.chdir(directory) - infile_dict['precision'], infile_dict['dftgrid'], infile_dict['dynamicgrid'] = "double", 5, "no" - infile_dict['machine'] = machine - manager_io.write_input(infile_dict) - - manager_io.write_jobscript(name, machine=machine) - os.chdir(home) - tools.qsub(root + '_jobscript') - return True - else: - return False - - -def resub_bad_geo(outfile_path, home_directory): - """Resubmits a job that's converged to a bad geometry with additional contraints. - - Parameters - ---------- - outfile_path : str - The name of an output file. - home_directory : str - Path to the base directory of the run. - - Returns - ------- - Resub_flag : bool - True if resubmitted. - - """ - # Resubmits a job that's converged to a bad geometry with additional contraints - history = resub_history() - history.read(outfile_path) - resubbed_before = False - if 'Bad geometry detected, adding constraints and trying again' in history.notes: - resubbed_before = True - history.status = os.path.split(outfile_path)[ - -1] + " has been submitted with additional constraints and still isn't a good geometry" - history.save() - if 'Needs clean resub' in history.notes: - resubbed_before = True - history.status = os.path.split(outfile_path)[ - -1] + ' job recovery has failed - requesting resub_bad_geo after clean resubmission round' - history.save() - - if not resubbed_before: - save_run(outfile_path, rewrite_inscr=True) - history = resub_history() - history.read(outfile_path) - history.resub_number += 1 - history.status = 'Constraints added to help convergence' - history.needs_resub = True - history.notes.append('Bad geometry detected, adding constraints and trying again') - history.save() - - machine = tools.get_machine() - root = outfile_path.rsplit('.', 1)[0] - name = os.path.split(root)[-1] - directory = os.path.split(outfile_path)[0] - infile_dict = manager_io.read_infile(outfile_path) - - if infile_dict['constraints']: - raise Exception( - 'resub.py does not currently support the use of external atom constraints. These will be overwritten by clean_resub() during job recovery') - - goal_geo = manager_io.read_configure(home_directory, outfile_path)['geo_check'] - if not goal_geo: - raise Exception( - 'Goal geometry not specified, job ' + outfile_path + ' should not have been labelled bad geo!') - else: - metal_index, bonded_atom_indices = moltools.get_metal_and_bonded_atoms(outfile_path, goal_geo) - # convert indexes from zero-indexed to one-indexed - metal_index += 1 - bonded_atom_indices = [index + 1 for index in bonded_atom_indices] - # Convert to TeraChem input syntax - constraints = ['bond ' + str(metal_index) + '_' + str(index) + '\n' for index in bonded_atom_indices] - - home = os.getcwd() - if len(directory) > 0: # if the string is blank, then we're already in the correct directory - os.chdir(directory) - - infile_dict['constraints'] = constraints - infile_dict['machine'] = machine - manager_io.write_input(infile_dict) - - manager_io.write_jobscript(name, machine=machine) - os.chdir(home) - tools.qsub(root + '_jobscript') - return True - - else: - return False - - -def resub_tighter(outfile_path): - """Resubmits a thermo job with the gradient error problem. Finds the parent job and resubmits it with a tighter scf - convergence criteria. - - Parameters - ---------- - outfile_path : str - The name of an output file. - - Returns - ------- - Resub_flag : bool - True if resubmitted. - - """ - # Takes the path to the outfile of a thermo job with the gradient error problem - # Finds the parent job and resubmits it with a tighter scf convergence criteria - - name = os.path.split(outfile_path)[-1].rsplit('.', 1)[0] - parent_name = name.rsplit('_', 1)[0] - parent_directory = os.path.split(os.path.split(outfile_path)[0])[0] - parent_path = os.path.join(parent_directory, parent_name + '.out') - ultratight_path = os.path.join(parent_directory, parent_name + '_ultratight', parent_name + '_ultratight.out') - - scr_needs_to_be_saved = False - if os.path.exists(ultratight_path): # This ultratight resubmission has happend before, need to archive the results - save_run(ultratight_path, rewrite_inscr=False, save_scr_flag=False) - scr_needs_to_be_saved = True # Need to save the scr AFTER prepping the new ultratight run. This helps keep compatibility with other functions - - history = resub_history() - history.read(ultratight_path) - history.resub_number += 1 - history.status = 'Running with tightened convergence thresholds' - history.needs_resub = False - history.notes.append('Further tightening convergence thresholds') - history.save() - - jobscript = tools.prep_ultratight(parent_path) # Prep tighter convergence run - if scr_needs_to_be_saved: - save_scr(ultratight_path, rewrite_inscr=False) - tools.qsub(jobscript) # Submit tighter convergence run - - # Set the original thermo run to wait for the ultratight run to finish - history = resub_history() - history.read(outfile_path) - history.waiting = ultratight_path - history.save() - - return True - - -def resub_thermo(outfile_path): - """Similar to simple resub, but specific for addressing thermo gradient errors. - hecks for the existance of an ultratight version of this run. If it exists, - uses the most up to date version for the new thermo run - - Parameters - ---------- - outfile_path : str - The name of an output file. - - Returns - ------- - Resub_flag : bool - True if resubmitted. - - """ - # Similar to simple resub, but specific for addressing thermo gradient errors - # Checks for the existance of an ultratight version of this run. If it exists, uses the most up to date version for the new thermo run - - save_run(outfile_path, rewrite_inscr=False) - history = resub_history() - history.read(outfile_path) - history.resub_number += 1 - history.status = 'Normal' - history.notes.append('Resubmitting thermo, possibly with a better initial geo') - history.needs_resub = False - history.save() - - name = os.path.split(outfile_path)[-1] - name = name.rsplit('.', 1)[0] - directory = os.path.split(outfile_path)[0] - parent_name = name.rsplit('_', 1)[0] - parent_directory = os.path.split(os.path.split(outfile_path)[0])[0] - ultratight_dir = os.path.join(parent_directory, parent_name + '_ultratight') - - infile_dict = manager_io.read_infile(outfile_path) - - if os.path.exists(ultratight_dir): - if os.path.exists(os.path.join(ultratight_dir, 'scr', 'optim.xyz')): - tools.extract_optimized_geo(os.path.join(ultratight_dir, 'scr', 'optim.xyz')) - shutil.copy(os.path.join(ultratight_dir, 'scr', 'optimized.xyz'), outfile_path.rsplit('.', 1)[0] + '.xyz') - else: - raise Exception('Unable to identify the ultratight geometry for run: ' + outfile_path) - - if infile_dict['spinmult'] == 1 and os.path.exists(os.path.join(ultratight_dir, 'scr', 'c0')): - shutil.copy(os.path.join(ultratight_dir, 'scr', 'c0'), os.path.join(directory, 'c0')) - elif infile_dict['spinmult'] != 1 and os.path.exists( - os.path.join(ultratight_dir, 'scr', 'ca0')) and os.path.exists( - os.path.join(ultratight_dir, 'scr', 'cb0')): - shutil.copy(os.path.join(ultratight_dir, 'scr', 'ca0'), os.path.join(directory, 'ca0')) - shutil.copy(os.path.join(ultratight_dir, 'scr', 'cb0'), os.path.join(directory, 'cb0')) - else: - raise Exception('Unable to find wavefunction files for ultratight geometry for run: ' + outfile_path) - else: - raise Exception( - 'An ultratight run does not exist for this thermo file. Consider calling simple_resub() or resub_tighter() instead of resub_thermo()') - - jobscript = outfile_path.rsplit('.', 1)[0] + '_jobscript' - tools.qsub(jobscript) - return True diff --git a/molSimplify/job_manager/resub.py b/molSimplify/job_manager/resub.py deleted file mode 100755 index 897da778..00000000 --- a/molSimplify/job_manager/resub.py +++ /dev/null @@ -1,362 +0,0 @@ -#!/usr/bin/env python -import os -import glob -import numpy as np -import shutil -import time -import sys -import json -import molSimplify.job_manager.tools as tools -import molSimplify.job_manager.moltools as moltools -import molSimplify.job_manager.recovery as recovery -import molSimplify.job_manager.manager_io as manager_io -from molSimplify.job_manager.classes import resub_history -from molSimplify.job_manager.psi4_utils.run import write_jobscript, run_bash - - -def kill_jobs(kill_names, message1='Killing job: ', message2=' early'): - """This function takes a list of job names and kills the jobs associated with them, if the jobs are active - - Parameters - ---------- - kill_names : list - List of jobs to kill. - message1 : str - Message prefix to report to stdout. - message2 : str - Message suffix to report to stdout. - - """ - # This function takes a list of job names and kills the jobs associated with them, if the jobs are active - if type(kill_names) != list: - kill_names = [kill_names] - machine = tools.get_machine() - - active_jobs, active_ids = tools.list_active_jobs(ids=True) - active_jobs = list(zip(active_jobs, active_ids)) - - jobs_to_kill = [[name, id_] for name, id_ in active_jobs if name in kill_names] - - for name, id_ in jobs_to_kill: - print(message1 + name + message2) - if machine in ['gibraltar']: - tools.call_bash('qdel ' + str(id_)) - elif machine in ['comet', 'bridges','expanse']: - tools.call_bash('scancel '+str(id_)) - else: - raise ValueError('Sardines.') - - -def prep_derivative_jobs(directory, list_of_outfiles): - """This function takes a directory and output files and spawns derivative jobs. - - Parameters - ---------- - directory : str - Directory of interest to analyze. - list_of_outfiles : list - List of output files that are read to spawn derivative jobs. - - """ - for job in list_of_outfiles: - configure_dict = manager_io.read_configure(directory, job) - if configure_dict['solvent']: - tools.prep_solvent_sp(job, configure_dict['solvent']) - if configure_dict['functionalsSP']: - tools.prep_functionals_sp(job, configure_dict['functionalsSP']) - if configure_dict['vertEA']: - tools.prep_vertical_ea(job) - if configure_dict['vertIP']: - tools.prep_vertical_ip(job) - if configure_dict['thermo']: - tools.prep_thermo(job) - if configure_dict['hfx_resample']: - tools.prep_hfx_resample(job) - if configure_dict['dissociation']: - moltools.prep_ligand_breakdown(job, dissociated_ligand_charges=configure_dict['dissociated_ligand_charges'], - dissociated_ligand_spinmults=configure_dict['dissociated_ligand_spinmults']) - if configure_dict['mbe']: - moltools.prep_mbe_calc(job) # needs to be generalized, not just for Fe - # moltools.prep_mbe_calc(job, metal_charge = configure_dict['metal_charge']) - if bool(configure_dict['general_sp']): - tools.prep_general_sp(job, general_config=configure_dict['general_sp']) - - -def resub(directory='in place'): - """This function takes a directory and submits calculations. - - Parameters - ---------- - directory : str - Directory of interest to analyze. - - """ - # Takes a directory, resubmits errors, scf failures, and spin contaminated cases - configure_dict = manager_io.read_configure(directory, None) - max_resub = configure_dict['max_resub'] - max_jobs = configure_dict['max_jobs'] - hard_job_limit = configure_dict['hard_job_limit'] - hit_queue_limit = False # Describes if this run has limitted the number of jobs submitted to work well with the queue - # Get the state of all jobs being managed by this instance of the job manager - completeness = moltools.check_completeness(directory, max_resub, configure_dict=configure_dict) - # print("completeness: ", completeness) - errors = completeness['Error'] # These are calculations which failed to complete - scf_errors = completeness['SCF_Error'] # These are calculations which failed to complete, appear to have an scf error, and hit wall time - oscillating_scf_errors = completeness['oscillating_scf_errors'] # These are calculations which failed to complete, appear to have an oscillaing scf error, - need_resub = completeness['Needs_resub'] # These are calculations with level shifts changed or hfx exchange changed - spin_contaminated = completeness['Spin_contaminated'] # These are finished jobs with spin contaminated solutions - thermo_grad_error = completeness['Thermo_grad_error'] # These are thermo jobs encountering the thermo grad error - waiting = completeness['Waiting'] # These are jobs which are or were waiting for another job to finish before continuing. - bad_geos = completeness['Bad_geos'] # These are jobs which finished, but converged to a bad geometry. - finished = completeness['Finished'] - molscontrol_kills = completeness['molscontrol_kills'] - nactive = tools.get_number_active() # number of active jobs, counting bundled jobs as a single job - # Kill SCF errors in progress, which are wasting computational resources - all_scf_errors = completeness['SCF_Errors_Including_Active'] # These are all jobs which appear to have scf error, including active ones - scf_errors_to_kill = [scf_err for scf_err in all_scf_errors if scf_err not in scf_errors] - names_to_kill = [os.path.split(scf_err)[-1].rsplit('.', 1)[0] for scf_err in scf_errors_to_kill] - kill_jobs(names_to_kill, message1='Job: ', message2=' appears to have an scf error. Killing this job early') - # Prep derivative jobs such as thermo single points, vertical IP, and ligand dissociation energies - needs_derivative_jobs = list(filter(tools.check_original, finished)) - # print("needs_derivative_jobs: ", needs_derivative_jobs) - prep_derivative_jobs(directory, needs_derivative_jobs) - resubmitted = [] # Resubmitted list gets True if the job is submitted or False if not. Contains booleans, not job identifiers. - counter = 0 - for job in molscontrol_kills: - counter += 1 - print("killed by molscontrol: ", job, counter) - # Resub unidentified errors - for error in errors: - if ((nactive + np.sum(resubmitted)) >= max_jobs) or ( - (tools.get_total_queue_usage() + np.sum(resubmitted)) >= hard_job_limit): - hit_queue_limit = True - continue - resub_tmp = recovery.simple_resub(error) - if resub_tmp: - print(('Unidentified error in job: ' + os.path.split(error)[-1] + ' -Resubmitting')) - print('') - resubmitted.append(resub_tmp) - - # Resub oscillating_scf convergence errors - for error in oscillating_scf_errors: - if ((nactive + np.sum(resubmitted)) >= max_jobs) or ( - (tools.get_total_queue_usage() + np.sum(resubmitted)) >= hard_job_limit): - hit_queue_limit = True - continue - local_configure = manager_io.read_configure(directory, None) - if 'scf' in local_configure['job_recovery']: - resub_tmp = recovery.resub_oscillating_scf(error) - if resub_tmp: - print(('Oscillating SCF error identified in job: ' + os.path.split(error)[ - -1] + ' -Resubmitting with adjusted precision and grid.')) - print('') - resubmitted.append(resub_tmp) - - # Resub scf convergence errors - for error in scf_errors: - if ((nactive + np.sum(resubmitted)) >= max_jobs) or ( - (tools.get_total_queue_usage() + np.sum(resubmitted)) >= hard_job_limit): - hit_queue_limit = True - continue - local_configure = manager_io.read_configure(directory, None) - if 'scf' in local_configure['job_recovery']: - resub_tmp = recovery.resub_scf(error) - if resub_tmp: - print(('SCF error identified in job: ' + os.path.split(error)[ - -1] + ' -Resubmitting with adjusted levelshifts')) - print('') - resubmitted.append(resub_tmp) - - # Resub jobs which converged to bad geometries with additional constraints - for error in bad_geos: - if ((nactive + np.sum(resubmitted)) >= max_jobs) or ( - (tools.get_total_queue_usage() + np.sum(resubmitted)) >= hard_job_limit): - hit_queue_limit = True - continue - local_configure = manager_io.read_configure(directory, None) - if 'bad_geo' in local_configure['job_recovery']: - resub_tmp = recovery.resub_bad_geo(error, directory) - if resub_tmp: - print(('Bad final geometry in job: ' + os.path.split(error)[ - -1] + ' -Resubmitting from initial structure with additional constraints')) - print('') - resubmitted.append(resub_tmp) - - # Resub spin contaminated cases - for error in spin_contaminated: - if ((nactive + np.sum(resubmitted)) >= max_jobs) or ( - (tools.get_total_queue_usage() + np.sum(resubmitted)) >= hard_job_limit): - hit_queue_limit = True - continue - local_configure = manager_io.read_configure(directory, None) - if 'spin_contaminated' in local_configure['job_recovery']: - resub_tmp = recovery.resub_spin(error) - if resub_tmp: - print(('Spin contamination identified in job: ' + os.path.split(error)[ - -1] + ' -Resubmitting with adjusted HFX')) - print('') - resubmitted.append(resub_tmp) - - # Resub jobs with atypical parameters used to aid convergence - for error in need_resub: - if ((nactive + np.sum(resubmitted)) >= max_jobs) or ( - (tools.get_total_queue_usage() + np.sum(resubmitted)) >= hard_job_limit): - hit_queue_limit = True - continue - resub_tmp = recovery.clean_resub(error) - if resub_tmp: - print(('Job ' + os.path.split(error)[-1] + ' needs to be rerun with typical paramters. -Resubmitting')) - print('') - resubmitted.append(resub_tmp) - - # Create a job with a tighter convergence threshold for failed thermo jobs - for error in thermo_grad_error: - if ((nactive + np.sum(resubmitted)) >= max_jobs) or ( - (tools.get_total_queue_usage() + np.sum(resubmitted)) >= hard_job_limit): - hit_queue_limit = True - continue - local_configure = manager_io.read_configure(directory, None) - if 'thermo_grad_error' in local_configure['job_recovery']: - resub_tmp = recovery.resub_tighter(error) - if resub_tmp: - print(('Job ' + os.path.split(error)[ - -1] + ' needs a better initial geo. Creating a geometry run with tighter convergence criteria')) - print('') - resubmitted.append(resub_tmp) - - # Look at jobs in "waiting," resume them if the job they were waiting for is finished - # Currently, this should only ever be thermo jobs waiting for an ultratight job - for waiting_dict in waiting: - if ((nactive + np.sum(resubmitted)) >= max_jobs) or ( - (tools.get_total_queue_usage() + np.sum(resubmitted)) >= hard_job_limit): - hit_queue_limit = True - continue - if len(list(waiting_dict.keys())) > 1: - raise Exception('Waiting job list improperly constructed') - job = list(waiting_dict.keys())[0] - waiting_for = waiting_dict[job] - if waiting_for in finished: - history = recovery.load_history(job) - history.waiting = None - history.save() - results_for_this_job = manager_io.read_outfile(job) - if results_for_this_job['thermo_grad_error']: - resubmitted.append(recovery.resub_thermo(job)) - else: - raise Exception('A method for resuming job: ' + job + ' is not defined') - else: - resubmitted.append(False) - - # Submit jobs which haven't yet been submitted - if (((nactive + np.sum(resubmitted)) < max_jobs) and ( - (tools.get_total_queue_usage() + np.sum(resubmitted)) < hard_job_limit)): - to_submit = [] - jobscripts = tools.find('*_jobscript') - active_jobs = tools.list_active_jobs(home_directory=directory, parse_bundles=True) - for job in jobscripts: - if not os.path.isfile(job.rsplit('_', 1)[0] + '.out') and not os.path.split(job.rsplit('_', 1)[0])[ - -1] in active_jobs: - to_submit.append(job) - - short_jobs_to_submit = [i for i in to_submit if tools.check_short_single_point(i)] - long_jobs_to_submit = [i for i in to_submit if i not in short_jobs_to_submit] - if len(short_jobs_to_submit) > 0: - bundled_jobscripts = tools.bundle_jobscripts(os.getcwd(), short_jobs_to_submit) - else: - bundled_jobscripts = [] - to_submit = bundled_jobscripts + long_jobs_to_submit - - submitted = [] - for job in to_submit: - if ((len(submitted) + nactive + np.sum(resubmitted)) >= max_jobs) or ( - (tools.get_total_queue_usage() + len(submitted) + np.sum(resubmitted)) >= hard_job_limit): - hit_queue_limit = True - continue - print(('Initial submission for job: ' + os.path.split(job)[-1])) - tools.qsub(job) - submitted.append(True) - else: - print('==== Hit the queue limit for the user, not submitting any more jobs. ====') - hit_queue_limit = True - submitted = [] - - number_resubmitted = np.sum(np.array(resubmitted + submitted)) - # ~ print str(number_resubmitted)+' Jobs submitted' - return int(number_resubmitted), int(len(completeness['Active'])), hit_queue_limit - - -def resub_psi4(psi4_config): - basedir = os.getcwd() - if "trigger" in psi4_config: - write_jobscript(psi4_config) - if "cluster" not in psi4_config or psi4_config["cluster"] == "mustang": - cmd = "qsub jobscript.sh" - else: - cmd = "sbatch jobscript.sh" - run_bash(cmd=cmd, - basedir=basedir, - rundir=basedir) - time.sleep(3) - else: - for path in os.listdir(basedir): - if os.path.isdir(basedir + "/" + path): - print("at: ", basedir + "/" + path) - os.chdir(basedir + "/" + path) - with open("psi4_config.json", "w") as fo: - json.dump(psi4_config, fo) - write_jobscript(psi4_config) - os.chdir(basedir) - if "cluster" not in psi4_config or psi4_config["cluster"] == "mustang": - cmd = "qsub jobscript.sh" - else: - cmd = "sbatch jobscript.sh" - run_bash(cmd=cmd, - basedir=basedir, - rundir=basedir + "/" + path) - time.sleep(3) - - -def main(): - counter = 0 - configure_dict = manager_io.read_configure('in place', None) - print("configure_dict: ", configure_dict) - if not configure_dict["run_psi4"]: - while True: - print('**********************************') - print("****** Assessing Job Status ******") - print('**********************************') - time1 = time.time() - with open('complete', 'w') as fil: - fil.write('Active') - - number_resubmitted, number_active, hit_queue_limit = resub() - - print('**********************************') - print(("******** " + str(number_resubmitted) + " Jobs Submitted ********")) - print('**********************************') - - print(('job cycle took: ' + str(time.time() - time1))) - print(('sleeping for: ' + str(configure_dict['sleep']))) - sys.stdout.flush() - time.sleep(configure_dict[ - 'sleep']) # sleep for time specified in configure. If not specified, default to 7200 seconds (2 hours) - - # Terminate the script if it is no longer submitting jobs - if number_resubmitted == 0 and number_active == 0 and not hit_queue_limit: - counter += 1 - else: - counter = 0 - if counter >= 3: - break - - print('**********************************') - print("****** Normal Terminatation ******") - print('**********************************') - with open('complete', 'w') as fil: - fil.write('True') - else: - resub_psi4(configure_dict["psi4_config"]) - - -if __name__ == '__main__': - main() diff --git a/molSimplify/job_manager/sp_config_example.json b/molSimplify/job_manager/sp_config_example.json deleted file mode 100644 index 1f5e5828..00000000 --- a/molSimplify/job_manager/sp_config_example.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "0": { - "type": "energy", - "functional": "b3lyp", - "solvent": false - }, - "1": { - "type": "vertIP", - "functional": "pbe0", - "solvent": "78.9" - }, - "2": { - "type": "vertEA", - "functional": "pbe0", - "solvent": "78.9" - }, - "3": { - "type": "energy", - "functional": "pbe0", - "solvent": "78.9" - } -} diff --git a/molSimplify/job_manager/tools.py b/molSimplify/job_manager/tools.py deleted file mode 100644 index e4e56eec..00000000 --- a/molSimplify/job_manager/tools.py +++ /dev/null @@ -1,1547 +0,0 @@ -import os -import glob -import sys -import copy -import numpy as np -import subprocess -import pandas as pd -import shutil -import time -from molSimplify.job_manager.classes import resub_history, textfile -import molSimplify.job_manager.manager_io as manager_io -from ast import literal_eval - - -def ensure_dir(dirpath): - """Make sure a directory exists. Makes directory if not. - - Parameters - ---------- - dirpath : str - The name of the directory. - - """ - if not os.path.isdir(dirpath): - os.makedirs(dirpath) - -def check_valid_outfile(path): - """Check if the outfile is a nohup.out file or slurm.out file instead of a real outfile. - - Parameters - ---------- - path : str - The path to the output file. - - Returns - ------- - validity : bool - Whether or not an output file is truly an output file. True if it is. - - """ - # The nohup.out file gets caught in the find statement - # use this function so that we only get TeraChem.outs - endpath = os.path.split(path)[-1] - if 'nohup.out' in endpath or endpath.startswith('.') or any("_v%d." % x in endpath for x in range(10)): - return False - elif 'slurm-' in endpath: - return False - elif 'smd.out' in endpath: - return False - elif 'atom' in endpath: - return False - else: - return True - -def priority_sort(lst_of_lsts): - """This function ensures that each entry occurs in only one list. If an entry occurs in multiple lists, - it is retained in the list which appears first in the list of lists. - - Parameters - ---------- - lst_of_lsts : list - The path to the output file. - - Returns - ------- - new_lst_of_lsts : list - New list of lists that is sorted. - - """ - # Takes a list of lists - # This function ensures that each entry occurs in only one list - # If an entry occurs in multiple lists, it is retained in the list which appears first in the list of lists - - lst_of_lsts.reverse() # reverse the list so low priority occurs first - - new_lst_of_lsts = [] - for counter in range(len(lst_of_lsts)): - local_lst = lst_of_lsts[counter] - higher_priority_lists = lst_of_lsts[counter + 1:] - - for high_priority in higher_priority_lists: - local_lst = list(set(local_lst) - set(high_priority)) - - new_lst_of_lsts.append(local_lst) - - new_lst_of_lsts.reverse() # undo the original reversal - - return new_lst_of_lsts - -def call_bash(string, error=False, version=1): - """This function makes a bash call based on a string. - - Parameters - ---------- - string : string - The bash call to be made in python. - error : bool, optional - Return error with the bash call. Default is False. - version : int - Call version. Version 1 splits the string and does not use the shell variable in subprocess. - Version 2 does not split the string and uses shell = True. - - Returns - ------- - out : list - Output of bash call as a list of strings. - err : str - If error flag set, then error returned as a string. - - """ - if version == 1: - p = subprocess.Popen(string.split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE) - elif version == 2: - p = subprocess.Popen(string, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True) - else: - raise NotImplementedError(f"Unknown version {version}") - out, err = p.communicate() - - if sys.version_info > (3, 0): - out = out.decode('utf-8') - err = err.decode('utf-8') - - out = out.split('\n') - if out[-1] == '': - out = out[:-1] - - if error: - return out, err - else: - return out - -def get_machine(): - """Gets the identity of the machine job_manager is being run on. - - Returns - ------- - machine : str - Name of the machine being run on. - - """ - # Gets the identity of the machine job_manager is being run on! - hostname = call_bash('hostname')[0] - if 'bridges.psc' in hostname: - machine = 'bridges' - elif 'gibraltar' in hostname: - machine = 'gibraltar' - elif 'comet' in hostname: - machine = 'comet' - elif 'home' in hostname: - machine = 'gibraltar' - elif "mustang" in hostname: - machine = "mustang" - elif "gridsan" in hostname or "login-" in hostname: - machine = "supercloud" - else: - hostname = call_bash('hostname -A')[0] - if "expanse" in hostname: - machine = "expanse" - else: - raise ValueError('Machine Unknown to Job Manager') - return machine - -def get_username(): - """Gets the identity of the user running jobs. - - Returns - ------- - user : str - Name of the user running jobs. - - """ - user = call_bash('whoami')[0] - # Gets the identify of the user who is using the job manager - return user - -def convert_to_absolute_path(path): - """This function takes a relative path and converts it to an absolute path. - - Parameters - ---------- - path : str - The relative path. - - Returns - ------- - abspath : str - The absolute path. - - """ - if path[0] != '/': - abspath = os.path.join(os.getcwd(), path) - else: - abspath = path - - return abspath - -def create_summary(directory='in place'): - """This function creates a summary of the jobs in a given path. - - Parameters - ---------- - directory : str, optional - The path to the directory containing jobs. Default is in place. - - Returns - ------- - summary : pd.DataFrame - The dataframe of the summary as a pandas dataframe. - - """ - # Returns a pandas dataframe which summarizes all outfiles in the directory, defaults to cwd - - outfiles = find('*.out', directory) - outfiles = list(filter(check_valid_outfile, outfiles)) - results = list(map(manager_io.read_outfile, outfiles)) - summary = pd.DataFrame(results) - - return summary - -def list_active_jobs(ids=False, home_directory=False, parse_bundles=False): - """List jobs that are currently running. - - Parameters - ---------- - ids : bool, optional - Return job IDs. - home_directory : bool, optional - Give path to home directory. Default is in place. - parse_bundles : bool, optional - Look through bundled jobs. Default is False. - - Returns - ------- - names : list - Names of all of the jobs that are running. - job_ids : list - The job IDs for the jobs that are running. Only returned if ids set to True. - - """ - # @return A list of active jobs for the current user. By job name - - if (ids and parse_bundles) or (parse_bundles and not home_directory): - raise Exception('Incompatible options passed to list_active_jobs()') - if home_directory == 'in place': - home_directory = os.getcwd() - - job_report = textfile() - try: - if get_machine() == 'gibraltar': - job_report.lines = call_bash("qstat -r") - elif get_machine() in ['comet', 'bridges','expanse']: - job_report.lines = call_bash('squeue -o "%.18i %.9P %.50j %.8u %.2t %.10M %.6D %R" -u '+get_username(), - version=2) - else: - raise ValueError - except: - job_report.lines = [] - if get_machine() == 'gibraltar': - names = job_report.wordgrab('jobname:', 2)[0] - names = [i for i in names if i] # filters out NoneTypes - elif get_machine() in ['comet', 'bridges', "mustang", "supercloud", 'expanse']: - names = job_report.wordgrab(get_username(), 2)[0] - names = [i for i in names if i] # filters out NoneTypes - else: - raise ValueError - if ids: - job_ids = [] - if get_machine() == 'gibraltar': - line_indices_of_jobnames = job_report.wordgrab('jobname:', 2, matching_index=True)[0] - elif get_machine() in ['comet', 'bridges', "mustang", "supercloud", 'expanse']: - line_indices_of_jobnames = job_report.wordgrab(get_username(), 2, matching_index=True)[0] - else: - raise ValueError - line_indices_of_jobnames = [i for i in line_indices_of_jobnames if i] # filters out NoneTypes - for line_index in line_indices_of_jobnames: - if get_machine() == 'gibraltar': - job_ids.append(int(job_report.lines[line_index - 1].split()[0])) - elif get_machine() in ['comet', 'bridges', "mustang", "supercloud", 'expanse']: - job_ids.append(int(job_report.lines[line_index].split()[0])) - else: - raise ValueError - if len(names) != len(job_ids): - print(len(names)) - print(len(job_ids)) - raise Exception('An error has occurred in listing active jobs!') - return names, job_ids - - if parse_bundles and os.path.isfile(os.path.join(home_directory, 'bundle', 'bundle_id')): - - with open(os.path.join(home_directory, 'bundle', 'bundle_id'), 'r') as fil: - identifier = fil.readlines()[0] - - bundles = [i for i in names if i.startswith('bundle_')] - bundles = [i.rsplit('_', 1)[0] for i in names if i.endswith(identifier)] - names = [i for i in names if i not in bundles] - - for bundle in bundles: - info_path = glob.glob(os.path.join(home_directory, 'bundle', bundle, '*_info'))[0] - with open(info_path, 'r') as fil: - lines = fil.readlines() - lines = [i[:-1] if i.endswith('\n') else i for i in lines] - names.extend(lines) - - return names - -def get_number_active(): - """Gets number of active jobs in the queue. Only count jobs from current directory. - - Returns - ------- - active_jobs_len : int - Number of calculations that are running. - - """ - # gets the number of jobs in the queue for this user, only counts jobs from this job directory - active_jobs = list_active_jobs() - - def check_active(path, active_jobs=active_jobs): - # Given a path, checks if it's in the queue currently: - name = os.path.split(path)[-1] - name = name.rsplit('.', 1)[0] - if name in active_jobs: - return True - else: - return False - - outfiles = find('*.out') - outfiles = [i for i in outfiles if check_valid_outfile(i)] - - active_non_bundles = [i for i in outfiles if check_active(i)] - - if os.path.isdir('bundle'): - with open(os.path.join('bundle', 'bundle_id')) as fil: - identifier = fil.readlines()[0] - if identifier.endswith('\n'): - identifier = identifier[:-1] - - active_bundles = [i for i in active_jobs if i.startswith('bundle_')] - active_bundles = [i for i in active_jobs if i.endswith(identifier)] - active_jobs = active_bundles + active_non_bundles - - return len(active_jobs) - else: - return len(active_non_bundles) - -def get_total_queue_usage(): - """Gets number of active jobs in the queue, independent of the current directory. - - Returns - ------- - active_jobs_len : int - Number of calculations that are running. - - """ - # gets the number of jobs in the queue for this user, regardless of where they originate - if get_machine() == 'gibraltar': - jobs = call_bash("qstat -u '" + get_username() + "'", version=2) - elif get_machine() in ['comet', 'bridges', "mustang", "supercloud",'expanse']: - jobs = call_bash('squeue -o "%.18i %.9P %.50j %.8u %.2t %.10M %.6D %R" -u ' + get_username(), - version=2) - else: - raise ValueError('Job manager does not know this machine!') - jobs = [i for i in jobs if get_username() in i.split()] - - return len(jobs) - -def check_completeness(directory='in place', max_resub=5, configure_dict=False): - """Checks whether or not a directory is completed by the job manager. - - Parameters - ---------- - directory : str, optional - Directory to check for completeness. Default is in place. - max_resub : int, optional - Maximum number of resubmissions permitted. Default is 5. - configure_dict : dict, optional - Configure file read in as a dictionary. Default is False. - - Returns - ------- - results : dict - Results of checking the directory for completeness. - - """ - ## Takes a directory, returns lists of finished, failed, and in-progress jobs - outfiles = find('*.out', directory) - outfiles = list(filter(check_valid_outfile, outfiles)) - - results_tmp = [manager_io.read_outfile(outfile, short_ouput=True) for outfile in outfiles] - results_tmp = list(zip(outfiles, results_tmp)) - results_dict = dict() - for outfile, tmp in results_tmp: - results_dict[outfile] = tmp - # print(outfile, tmp['oscillating_scf_error']) - - active_jobs = list_active_jobs(home_directory=directory, parse_bundles=True) - - def check_finished(path, results_dict=results_dict): - # Return True if the outfile corresponds to a complete job, False otherwise - if results_dict[path]['finished']: - return True - else: - return False - - def check_active(path, active_jobs=active_jobs): - # Given a path, checks if it's in the queue currently: - name = os.path.split(path)[-1] - name = name.rsplit('.', 1)[0] - if name in active_jobs: - return True - else: - return False - - def check_needs_resub(path): - if os.path.isfile(path.rsplit('.', 1)[0] + '.pickle'): - history = resub_history() - history.read(path) - return history.needs_resub - else: - return False - - def check_waiting(path): - if os.path.isfile(path.rsplit('.', 1)[0] + '.pickle'): - history = resub_history() - history.read(path) - if history.waiting: - return True - return False - - def grab_waiting(path): - if os.path.isfile(path.rsplit('.', 1)[0] + '.pickle'): - history = resub_history() - history.read(path) - return history.waiting - raise Exception('Attempting to grab a "waiting" criteria that does not exist') - - def check_chronic_failure(path): - if os.path.isfile(path.rsplit('.', 1)[0] + '.pickle'): - history = resub_history() - history.read(path) - if history.resub_number >= max_resub: - return True - if history.manually_abandoned: - return True - else: - return False - - def check_spin_contaminated(path, results_dict=results_dict): - results = results_dict[path] - if configure_dict and "ss_cutoff" in configure_dict: - ss_cutoff = configure_dict['ss_cutoff'] - else: - ss_cutoff = 1.0 - if results['finished']: - if type(results['s_squared_ideal']) == float: - if abs(results['s_squared'] - results['s_squared_ideal']) > ss_cutoff: - return True - return False - - def check_oscillating_scf_error(path, results_dict=results_dict): - results = results_dict[path] - if results['oscillating_scf_error']: - return True - else: - return False - - def check_scf_error(path, results_dict=results_dict): - results = results_dict[path] - if results['scf_error']: - return True - else: - return False - - def check_thermo_grad_error(path, results_dict=results_dict): - results = results_dict[path] - if results['thermo_grad_error']: - return True - else: - return False - - active_jobs = list(filter(check_active, outfiles)) - finished = list(filter(check_finished, outfiles)) - needs_resub = list(filter(check_needs_resub, outfiles)) - waiting = list(filter(check_waiting, outfiles)) - spin_contaminated = list(filter(check_spin_contaminated, outfiles)) - all_scf_errors = list(filter(check_scf_error, outfiles)) - oscillating_scf_errors = list(filter(check_oscillating_scf_error, outfiles)) - thermo_grad_errors = list(filter(check_thermo_grad_error, outfiles)) - chronic_errors = list(filter(check_chronic_failure, outfiles)) - errors = list(set(outfiles) - set(active_jobs) - set(finished)) - scf_errors = list(filter(check_scf_error, errors)) - - # Look for additional active jobs that haven't yet generated outfiles - jobscript_list = find('*_jobscript', directory) - jobscript_list = [i.rsplit('_', 1)[0] + '.out' for i in jobscript_list] - extra_active_jobs = list(filter(check_active, jobscript_list)) - active_jobs.extend(extra_active_jobs) - - # Sort out conflicts in order of reverse priority - # A job only gets labelled as finished if it's in no other category - # A job always gets labelled as active if it fits that criteria, even if it's in every other category too - - priority_list = [active_jobs, chronic_errors, waiting, thermo_grad_errors, - oscillating_scf_errors, scf_errors, errors, spin_contaminated, needs_resub, finished] - priority_list_names = ['Active', 'Chronic_errors', 'Waiting', 'Thermo_grad_error', - 'oscillating_scf_errors', 'SCF_Error', 'Error', 'Spin_contaminated', 'Needs_resub', - 'Finished'] - priority_list = priority_sort(priority_list) - - results = dict() - for key, lst in zip(priority_list_names, priority_list): - results[key] = lst - - # There are two special categories which operate a bit differently: waiting and "SCF_Errors_Including_Active" - waiting = [{i: grab_waiting(i)} for i in waiting] - results['Waiting'] = waiting - results['SCF_Errors_Including_Active'] = all_scf_errors - - return results - -def find(key, directory='in place', maxdepth=False): - """Uses the bash find command. - - Parameters - ---------- - key : str - Keyword to look for in find. - directory : str, optional - Directory to look for. Default is in place. - maxdepth : int, optional - Maximum depth to search tree. Default is False. - - Returns - ------- - output : list - Returns list containing all items returned by find. - - """ - ## Looks for all files with a matching key in their name within directory - # @return A list of paths - if directory == 'in place': - directory = os.getcwd() - if maxdepth: - bash = 'find ' + directory + ' -name ' + key + ' -maxdepth '+str(maxdepth) - else: - bash = 'find ' + directory + ' -name ' + key - - return call_bash(bash) - -def qsub(jobscript_list): - """Takes a list of paths to jobscripts (like output by find) and submits them with qsub. - Handles cases where a single jobscript is submitted instead of a list. - - Parameters - ---------- - jobscript_list : list, str - List of jobscripts to submit, or singular jobscript as a string. - - Returns - ------- - stdouts : list - Stdouts returned by job submission for each job. - - """ - ## Takes a list of paths to jobscripts (like output by find) and submits them with qsub - # Handles cases where a single jobscript is submitted instead of a list - if type(jobscript_list) != list: - jobscript_list = [jobscript_list] - jobscript_list = [convert_to_absolute_path(i) for i in jobscript_list] - - stdouts = [] - for i in jobscript_list: - home = os.getcwd() - os.chdir(os.path.split(i)[0]) - jobscript = os.path.split(i)[1] - if get_machine() in ['gibraltar']: - stdout, stderr = call_bash('qsub ' + jobscript, error=True) - stdouts.append(stdout) - elif get_machine() in ['bridges', 'comet', 'expanse']: - stdout, stderr = call_bash('sbatch ' + jobscript, error=True) - stdouts.append(stdout) - if len(stderr) > 0: - raise Exception(stderr) - os.chdir(home) - time.sleep(1) - - return stdouts - -def check_original(job): - """Checks whether or not a job is an original job that will require derivative jobs. - - Parameters - ---------- - job : str - Name of current job. - - Returns - ------- - original : bool - Whether or not job is original. True if it is. - - """ - # Returns true if this job is an original job - # Returns false if this job is already a derivative job - - name = os.path.split(job)[-1] - name = name.rsplit('.', 1)[0] - name = name.split('_') - - dependent_jobs = ['solvent', 'vertEA', 'vertIP', 'thermo', 'kp', 'rm', 'ultratight', 'HFXresampling', - 'functional', 'mbe', 'metal'] - if any(j in name for j in dependent_jobs): - return False - else: - return True - -def check_short_single_point(job): - """Checks whether or not a job is a short single point job. - - Parameters - ---------- - job : str - Name of current job. - - Returns - ------- - sp : bool - Whether or not job is a short single point job. True if it is. - - """ - name = os.path.split(job)[-1] - name = name.rsplit('.', 1)[0] - name = name.split('_') - - short_jobs = ['solvent', 'kp', 'rm', 'functional', 'vertEA', 'vertIP'] - if any(j in name for j in short_jobs): - return True - else: - return False - -def extract_optimized_geo(PATH, custom_name=False): - """Given the path to an optim.xyz file, this will extract optimized.xyz, which contains only the last frame. - Written in same directory as optim.xyz. - - Parameters - ---------- - PATH : str - Path to optim.xyz file to extract geometry. - custom_name : str, optional - Custom name for extracted geo. Default is False, will go to optimized.xyz. - - Returns - ------- - lines : list - Lines containing optimized geometry, in addition to writing file as optimized.xyz. - - """ - # Given the path to an optim.xyz file, this will extract optimized.xyz, which contains only the last frame - # The file is written to the same directory as contained optim.xyz - - with open(PATH, 'r') as optim: - lines = optim.readlines() - lines.reverse() - if len(lines) == 0: - lines = [] - print(('optim.xyz is empty for: ' + PATH)) - else: - for i in range(len(lines)): - if 'frame' in lines[i].split(): - break - lines = lines[:i + 2] - lines.reverse() - homedir = os.path.split(PATH)[0] - - if custom_name: - basedir = os.path.split(homedir)[0] - xyz = glob.glob(os.path.join(basedir, '*.xyz'))[0] - xyz = os.path.split(xyz)[-1] - name = xyz[:-4] + '_optimized.xyz' - else: - name = 'optimized.xyz' - - with open(os.path.join(homedir, name), 'w') as optimized: - for i in lines: - optimized.write(i) - - return lines - -def pull_optimized_geos(PATHs=[]): - """Given a PATH or list of PATHs to optim.xyz files, these will grab the optimized geometries and move them into a local folder called optimized_geos. - - Parameters - ---------- - PATH : list - List of paths to optim.xyz file to extract geometry. - - """ - # Given a PATH or list of PATHs to optim.xyz files, these will grab the optimized geometries and move them into a local folder called optimized_geos - if type(PATHs) != list: - PATHs = [PATHs] - if len(PATHs) == 0: - PATHs = find('optim.xyz') # Default behavior will pull all optims in the current directory - - if os.path.isdir('opimized_geos'): - raise Exception('optimized_geos already exists!') - - os.mkdir('optimized_geos') - home = os.getcwd() - for Path in PATHs: - extract_optimized_geo(Path) - scr_path = os.path.split(Path)[0] - homedir = os.path.split(scr_path)[0] - initial_xyz = glob.glob(os.path.join(homedir, '*.xyz')) - if len(initial_xyz) != 1: - print('Name could not be identified for: ' + Path) - print('Naming with a random 6 digit number') - name = str(np.random.randint(999999)) + '_optimized.xyz' - else: - initial_xyz = initial_xyz[0] - name = os.path.split(initial_xyz)[-1] - name = name.rsplit('.', 1)[0] - name += '_optimized.xyz' - - shutil.move(os.path.join(os.path.split(Path)[0], 'optimized.xyz'), os.path.join(home, 'optimized_geos', name)) - -def bundle_jobscripts(home_directory, jobscript_paths, max_bundle_size=10): - """This function will bundle together jobscripts of short jobs. - - Parameters - ---------- - home_directory : str - Directory path of base jobs, where bundles will be placed. - jobscript_paths : list - List of paths to various jobscripts to be bundled. - max_bundle_size : int, optional - Number of jobscripts to be bundled together. Default is 10. - - Returns - ------- - output_jobscripts : list - List of paths to bundled jobscripts. - - """ - number_of_bundles = int(float(len(jobscript_paths)) / float(max_bundle_size)) - - bundles, i, many_bundles = [], 0, False - for i in range(number_of_bundles): - bundles.append(jobscript_paths[max_bundle_size * i:max_bundle_size * (i + 1)]) - many_bundles = True - if many_bundles: - total_length = [len(ii) for ii in bundles] - total_length = np.sum(np.array(total_length)) - if total_length != len( - jobscript_paths): # Triggers when the number of jobscripts is not divisable by the bundle size - bundles.append(jobscript_paths[max_bundle_size * (i + 1):]) - else: # Triggers when there are fewere jobscripts than the bundle size - bundles = [jobscript_paths] - print('Bundling ' + str(len(jobscript_paths)) + ' short jobs into ' + str(len(bundles)) + ' jobscript(s)') - - output_jobscripts = [] - for bundle in bundles: - output_jobscripts.append(sub_bundle_jobscripts(home_directory, bundle)) - - return output_jobscripts - -def sub_bundle_jobscripts(home_directory, jobscript_paths): - """This function will bundle together a list of jobscripts. It writes the bundle folders. - Records info in run directory. - - Parameters - ---------- - home_directory : str - Directory path of base jobs, where bundles will be placed. - jobscript_paths : list - List of paths to various jobscripts to be bundled. - - Returns - ------- - output_jobscripts : list - List of paths to bundled jobscripts. - - """ - # Takes a list of jobscript paths, and bundles them into a single jobscript - # Records information about which jobs were bundled together in the run's home directory - if not os.path.isdir(os.path.join(home_directory, 'bundle')): - os.mkdir(os.path.join(home_directory, 'bundle')) - with open(os.path.join(home_directory, 'bundle', 'bundle_id'), 'w') as fil: - fil.write(str(np.random.randint(100000000000))) - with open(os.path.join(home_directory, 'bundle', 'bundle_id'), 'r') as fil: - identifier = fil.readlines()[0] - - jobscript_paths = [convert_to_absolute_path(i) for i in jobscript_paths] - - existing_bundles = glob.glob(os.path.join(home_directory, 'bundle', '*')) - existing_bundles = [i for i in existing_bundles if os.path.isdir(i)] - if len(existing_bundles) > 0: - existing_bundle_numbers = [int(os.path.split(i)[-1].split('_')[-1]) for i in existing_bundles] - else: - existing_bundle_numbers = [0] - - # Create a directory for this jobscript bundle - os.mkdir(os.path.join(home_directory, 'bundle', 'bundle_' + str(max(existing_bundle_numbers) + 1))) - - # Record info about how the jobs are being bundled - with open(os.path.join(home_directory, 'bundle', 'bundle_' + str(max(existing_bundle_numbers) + 1), - 'bundle_' + str(max(existing_bundle_numbers) + 1) + '_info'), 'w') as fil: - for i in jobscript_paths[:-1]: - fil.write(os.path.split(i)[-1].rsplit('_', 1)[0] + '\n') - fil.write(os.path.split(jobscript_paths[-1])[-1].rsplit('_', 1)[0]) - - # Write a jobscript for the job bundle - home = os.getcwd() - os.chdir(os.path.join(home_directory, 'bundle', 'bundle_' + str(max(existing_bundle_numbers) + 1))) - manager_io.write_terachem_jobscript(str('bundle_' + str(max(existing_bundle_numbers) + 1)) + '_' + identifier, - terachem_line=False, time_limit='12:00:00', machine=get_machine()) - shutil.move('bundle_' + str(max(existing_bundle_numbers) + 1) + '_' + identifier + '_jobscript', - 'bundle_' + str(max(existing_bundle_numbers) + 1)) - with open('bundle_' + str(max(existing_bundle_numbers) + 1), 'a') as fil: - for i in jobscript_paths: - infile = i.rsplit('_', 1)[0] + '.in' - outfile = i.rsplit('_', 1)[0] + '.out' - directory = os.path.split(i)[0] - text = 'cd ' + directory + '\n' + 'terachem ' + infile + ' > ' + outfile - fil.write(text + '\n') - os.chdir(home) - - return os.path.join(home_directory, 'bundle', 'bundle_' + str(max(existing_bundle_numbers) + 1), - 'bundle_' + str(max(existing_bundle_numbers) + 1)) - -def prep_vertical_ip(path): - """This function prepares a vertical IP job for a base job. - - Parameters - ---------- - path : str - Path to the output file of a finished job. - - Returns - ------- - jobscripts : list - List of paths for jobscripts of vertical IP jobs. - - """ - # Given a path to the outfile of a finished run, this preps the files for a corresponding vertical IP run - # Returns a list of the PATH(s) to the jobscript(s) to start the vertical IP calculations(s) - home = os.getcwd() - path = convert_to_absolute_path(path) - - results = manager_io.read_outfile(path) - if not results['finished']: - raise Exception('This calculation does not appear to be complete! Aborting...') - - infile_dict = manager_io.read_infile(path) - - if infile_dict['spinmult'] == 1: - new_spin = [2] - else: - new_spin = [infile_dict['spinmult'] - 1, infile_dict['spinmult'] + 1] - - base = os.path.split(path)[0] - - if infile_dict['run_type'] == 'minimize': - optimxyz = os.path.join(base, 'scr', 'optim.xyz') - else: - optimxyz = os.path.join(base, 'scr', 'xyz.xyz') - extract_optimized_geo(optimxyz) - - ipname = results['name'] + '_vertIP' - vertip_base_path = os.path.join(base, ipname) - if os.path.isdir(vertip_base_path): - return ['Directory for vertIP single point already exists'] - os.mkdir(vertip_base_path) - os.chdir(vertip_base_path) - - jobscripts = [] - for calc in new_spin: - if calc < 7: - name = results['name'] + '_vertIP_' + str(calc) - PATH = os.path.join(vertip_base_path, str(calc)) - if os.path.isdir(PATH): - jobscripts.append('File for vert IP spin ' + str(calc) + 'already exists') - else: - os.mkdir(PATH) - os.chdir(PATH) - - shutil.copyfile(os.path.join(base, 'scr', 'optimized.xyz'), os.path.join(PATH, name + '.xyz')) - - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['charge'], local_infile_dict['guess'] = infile_dict['charge'] + 1, False - local_infile_dict['run_type'], local_infile_dict['spinmult'] = 'energy', calc - local_infile_dict['name'] = name - local_infile_dict['coordinates'] = name+'.xyz' - local_infile_dict['levelshifta'], local_infile_dict['levelshiftb'] = 0.25, 0.25 - local_infile_dict['machine'] = get_machine() - manager_io.write_input(local_infile_dict) - manager_io.write_jobscript(name, machine=get_machine()) - - jobscripts.append(os.path.join(PATH, name + '_jobscript')) - - os.chdir(home) - return jobscripts - -def prep_vertical_ea(path): - """This function prepares a vertical EA job for a base job. - - Parameters - ---------- - path : str - Path to the output file of a finished job. - - Returns - ------- - jobscripts : list - List of paths for jobscripts of vertical EA jobs. - - """ - # Given a path to the outfile of a finished run, this preps the files for a corresponding vertical EA run - # Returns a list of the PATH(s) to the jobscript(s) to start the vertical IP calculations(s) - home = os.getcwd() - path = convert_to_absolute_path(path) - - results = manager_io.read_outfile(path) - if not results['finished']: - raise Exception('This calculation does not appear to be complete! Aborting...') - - infile_dict = manager_io.read_infile(path) - - if infile_dict['spinmult'] == 1: - new_spin = [2] - else: - new_spin = [infile_dict['spinmult'] - 1, infile_dict['spinmult'] + 1] - - base = os.path.split(path)[0] - - if infile_dict['run_type'] == 'minimize': - optimxyz = os.path.join(base, 'scr', 'optim.xyz') - else: - optimxyz = os.path.join(base, 'scr', 'xyz.xyz') - extract_optimized_geo(optimxyz) - - eaname = results['name'] + '_vertEA' - vertea_base_path = os.path.join(base, eaname) - if os.path.isdir(vertea_base_path): - return ['Directory for vertEA single point already exists'] - os.mkdir(vertea_base_path) - os.chdir(vertea_base_path) - - jobscripts = [] - for calc in new_spin: - if calc < 7: - name = results['name'] + '_vertEA_' + str(calc) - PATH = os.path.join(vertea_base_path, str(calc)) - if os.path.isdir(PATH): - jobscripts.append('File for vert EA spin ' + str(calc) + 'already exists') - else: - os.mkdir(PATH) - os.chdir(PATH) - shutil.copyfile(os.path.join(base, 'scr', 'optimized.xyz'), os.path.join(PATH, name + '.xyz')) - - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['charge'], local_infile_dict['guess'] = infile_dict['charge'] - 1, False - local_infile_dict['run_type'], local_infile_dict['spinmult'] = 'energy', calc - local_infile_dict['name'] = name - local_infile_dict['coordinates'] = name+'.xyz' - local_infile_dict['levelshifta'], local_infile_dict['levelshiftb'] = 0.25, 0.25 - local_infile_dict['machine'] = get_machine() - - manager_io.write_input(local_infile_dict) - manager_io.write_jobscript(name, machine=get_machine()) - jobscripts.append(os.path.join(PATH, name + '_jobscript')) - os.chdir(home) - return jobscripts - -def prep_solvent_sp(path, solvents=[78.9]): - """This function prepares a solvent job for a base job. - - Parameters - ---------- - path : str - Path to the output file of a finished job. - solvents : list, optional - List of solvent dielectrics to be considered. Default is 78.9. - - Returns - ------- - jobscripts : list - List of paths for jobscripts of solvent jobs. - - """ - # Given a path to the outfile of a finished run, this preps the files for a single point solvent run - # Uses the wavefunction from the gas phase calculation as an initial guess - # Returns a list of the PATH(s) to the jobscript(s) to start the solvent sp calculations(s) - home = os.getcwd() - path = convert_to_absolute_path(path) - - results = manager_io.read_outfile(path) - if not results['finished']: - raise Exception('This calculation does not appear to be complete! Aborting...') - - infile_dict = manager_io.read_infile(path) - - base = os.path.split(path)[0] - - if infile_dict['run_type'] == 'minimize': - optimxyz = os.path.join(base, 'scr', 'optim.xyz') - else: - optimxyz = os.path.join(base, 'scr', 'xyz.xyz') - extract_optimized_geo(optimxyz) - - # Now, start generating the new directory - solname = results['name'] + '_solvent' - solvent_base_path = os.path.join(base, solname) - # print(solvent_base_path) - if os.path.isdir(solvent_base_path): - # print('Directory for solvent single point already exists') - pass - else: - os.mkdir(solvent_base_path) - os.chdir(solvent_base_path) - - jobscripts = [] - for sol_val in solvents: - PATH = os.path.join(solvent_base_path, str(sol_val).replace('.', '_')) - if os.path.isdir(PATH): - continue - ensure_dir(PATH) - name = results['name'] + "_solvent_" + str(sol_val) - shutil.copyfile(os.path.join(base, 'scr', 'optimized.xyz'), os.path.join(PATH, name + '.xyz')) - guess = False - os.chdir(PATH) - if infile_dict['spinmult'] == 1: - if os.path.isfile(os.path.join(base, 'scr', 'c0')): - shutil.copyfile(os.path.join(base, 'scr', 'c0'), os.path.join(PATH, 'c0')) - manager_io.write_jobscript(name, custom_line='# -fin c0', machine=get_machine()) - guess = True - else: - if os.path.isfile(os.path.join(base, 'scr', 'ca0')) and os.path.isfile(os.path.join(base, 'scr', 'cb0')): - shutil.copyfile(os.path.join(base, 'scr', 'ca0'), os.path.join(PATH, 'ca0')) - shutil.copyfile(os.path.join(base, 'scr', 'cb0'), os.path.join(PATH, 'cb0')) - manager_io.write_jobscript(name, custom_line=['# -fin ca0\n', '# -fin cb0\n'], machine=get_machine()) - guess = True - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['solvent'], local_infile_dict['guess'] = sol_val, guess - local_infile_dict['run_type'] = 'energy' - local_infile_dict['name'] = name - local_infile_dict['coordinates'] = name+'.xyz' - local_infile_dict['levelshifta'], local_infile_dict['levelshiftb'] = 0.25, 0.25 - local_infile_dict['machine'] = get_machine() - - manager_io.write_input(local_infile_dict) - - os.chdir(home) - jobscripts.append(os.path.join(PATH, name + '_jobscript')) - os.chdir(home) - return jobscripts - -def prep_functionals_sp(path, functionalsSP): - """This function prepares functional variants for a base job. Performs single point at optimized geometry. - - Parameters - ---------- - path : str - Path to the output file of a finished job. - functionalsSP : list - Functionals for the derivative jobs. - - Returns - ------- - jobscripts : list - List of paths for jobscripts of jobs with other functionals. - - """ - home = os.getcwd() - path = convert_to_absolute_path(path) - results = manager_io.read_outfile(path) - if not results['finished']: - raise Exception('This calculation does not appear to be complete! Aborting...') - - infile_dict = manager_io.read_infile(path) - base = os.path.split(path)[0] - - if infile_dict['run_type'] == 'minimize': - optimxyz = os.path.join(base, 'scr', 'optim.xyz') - else: - optimxyz = os.path.join(base, 'scr', 'xyz.xyz') - extract_optimized_geo(optimxyz) - - # Now, start generating the new directory - funcname = results['name'] + '_functionalsSP' - functional_base_path = os.path.join(base, funcname) - if os.path.isdir(functional_base_path): - # print('Directory for functional single point already exists') - pass - else: - os.mkdir(functional_base_path) - os.chdir(functional_base_path) - - jobscripts = [] - for func in functionalsSP: - PATH = os.path.join(functional_base_path, str(func)) - if os.path.isdir(PATH): - continue - ensure_dir(PATH) - name = results['name'] + "_functional_" + str(func) - shutil.copyfile(os.path.join(base, 'scr', 'optimized.xyz'), os.path.join(PATH, name + '.xyz')) - guess = False - os.chdir(PATH) - if infile_dict['spinmult'] == 1: - if os.path.isfile(os.path.join(base, 'scr', 'c0')): - shutil.copyfile(os.path.join(base, 'scr', 'c0'), os.path.join(PATH, 'c0')) - manager_io.write_jobscript(name, custom_line='# -fin c0', machine=get_machine()) - guess = True - else: - if os.path.isfile(os.path.join(base, 'scr', 'ca0')) and os.path.isfile(os.path.join(base, 'scr', 'cb0')): - shutil.copyfile(os.path.join(base, 'scr', 'ca0'), os.path.join(PATH, 'ca0')) - shutil.copyfile(os.path.join(base, 'scr', 'cb0'), os.path.join(PATH, 'cb0')) - manager_io.write_jobscript(name, custom_line=['# -fin ca0\n', '# -fin cb0\n'], machine=get_machine()) - guess = True - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['guess'] = guess - local_infile_dict['run_type'] = 'energy' - local_infile_dict['name'] = name - local_infile_dict['coordinates'] = name+'.xyz' - local_infile_dict['levelshifta'], local_infile_dict['levelshiftb'] = 0.25, 0.25 - local_infile_dict['method'] = func - local_infile_dict['machine'] = get_machine() - - manager_io.write_input(local_infile_dict) - - with open('configure', 'w') as fil: - fil.write('method:' + func) - os.chdir(home) - jobscripts.append(os.path.join(PATH, name + '_jobscript')) - os.chdir(home) - return jobscripts - -def prep_general_sp(path, general_config): - """This function is to prepare a general single point job from a dictionary.. - - Parameters - ---------- - path : str - Path to the output file of a finished job. - general_config : dict - Dictionary of {index: {config}}. Should have single point configurations. - - Returns - ------- - jobscripts : list - List of paths for jobscripts for general single point jobs. - """ - # ----sanity check and set up input config--- - allowed_keys = ["type", "functional", "solvent"] - default = {"type": "energy", "functional": "b3lyp", "solvent": False} - for ii in general_config: - config = {} - for k in general_config[ii]: - if k not in allowed_keys: - raise KeyError("This key %s has not been implemented. Allowed keys are: " % k, allowed_keys) - else: - config[k] = general_config[ii][k] - for k in allowed_keys: - if k not in general_config[ii]: - config[k] = default[k] - general_config[ii] = config - # ----sanity check for dependent job----- - home = os.getcwd() - path = convert_to_absolute_path(path) - results = manager_io.read_outfile(path) - if not results['finished']: - raise Exception('This calculation does not appear to be complete! Aborting...') - # -----make base directory for general jobs--- - infile_dict = manager_io.read_infile(path) - base = os.path.split(path)[0] - if infile_dict['run_type'] == 'minimize': - optimxyz = os.path.join(base, 'scr', 'optim.xyz') - else: - optimxyz = os.path.join(base, 'scr', 'xyz.xyz') - extract_optimized_geo(optimxyz) - # Now, start generating the new directory - funcname = results['name'] + '_general' - functional_base_path = os.path.join(base, funcname) - if os.path.isdir(functional_base_path): - pass - else: - os.mkdir(functional_base_path) - os.chdir(functional_base_path) - jobscripts = [] - for ii in general_config: - config = general_config[ii] - if config['type'] in ["vertIP", "vertEA"]: - if infile_dict['spinmult'] == 1: - new_spin = [2] - else: - new_spin = [infile_dict['spinmult'] - 1, infile_dict['spinmult'] + 1] - for calc in new_spin: - suffix = "type_%s_functional_%s_solvent_%s_spin_%d" % (config['type'], config['functional'], str(config['solvent']), calc) - PATH = os.path.join(functional_base_path, suffix) - if os.path.isdir(PATH): - continue - ensure_dir(PATH) - name = results['name'] + "_" + suffix - shutil.copyfile(os.path.join(base, 'scr', 'optimized.xyz'), os.path.join(PATH, name + '.xyz')) - guess = False - os.chdir(PATH) - local_infile_dict = copy.copy(infile_dict) - if config['type'] == "vertIP": - local_infile_dict['charge'] = infile_dict['charge'] + 1 - elif config['type'] == "vertEA": - local_infile_dict['charge'] = infile_dict['charge'] - 1 - local_infile_dict['guess'] = False - local_infile_dict['run_type'], local_infile_dict['spinmult'] = 'energy', calc - local_infile_dict['name'] = name - local_infile_dict['coordinates'] = name+'.xyz' - local_infile_dict['levelshifta'], local_infile_dict['levelshiftb'] = 0.25, 0.25 - local_infile_dict['machine'] = get_machine() - local_infile_dict['method'] = config['functional'] - if config['solvent']: - local_infile_dict['solvent'] = float(config['solvent']) - else: - local_infile_dict['solvent'] = False - manager_io.write_input(local_infile_dict) - manager_io.write_jobscript(name, machine=get_machine()) - with open('configure', 'w')as fil: - fil.write('method:%s\n' % config['functional']) - solvent = float(config['solvent']) if config['solvent'] else False - fil.write('solvent:%s\n' % str(solvent)) - jobscripts.append(os.path.join(PATH, name + '_jobscript')) - elif config['type'] == "energy": - suffix = "type_%s_functional_%s_solvent_%s_spin_%d" % (config['type'], config['functional'], str(config['solvent']), infile_dict['spinmult']) - PATH = os.path.join(functional_base_path, suffix) - if os.path.isdir(PATH): - continue - ensure_dir(PATH) - name = results['name'] + "_" + suffix - shutil.copyfile(os.path.join(base, 'scr', 'optimized.xyz'), os.path.join(PATH, name + '.xyz')) - guess = False - os.chdir(PATH) - if infile_dict['spinmult'] == 1: - if os.path.isfile(os.path.join(base, 'scr', 'c0')): - shutil.copyfile(os.path.join(base, 'scr', 'c0'), os.path.join(PATH, 'c0')) - manager_io.write_jobscript(name, custom_line='# -fin c0', machine=get_machine()) - guess = True - else: - if os.path.isfile(os.path.join(base, 'scr', 'ca0')) and os.path.isfile(os.path.join(base, 'scr', 'cb0')): - shutil.copyfile(os.path.join(base, 'scr', 'ca0'), os.path.join(PATH, 'ca0')) - shutil.copyfile(os.path.join(base, 'scr', 'cb0'), os.path.join(PATH, 'cb0')) - manager_io.write_jobscript(name, custom_line=['# -fin ca0\n', '# -fin cb0\n'], machine=get_machine()) - guess = True - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['guess'] = guess - local_infile_dict['run_type'] = 'energy' - local_infile_dict['name'] = name - local_infile_dict['coordinates'] = name+'.xyz' - local_infile_dict['levelshifta'], local_infile_dict['levelshiftb'] = 0.25, 0.25 - local_infile_dict['charge'] = infile_dict['charge'] - local_infile_dict['spinmult'] = infile_dict['spinmult'] - local_infile_dict['machine'] = get_machine() - local_infile_dict['method'] = config['functional'] - if config['solvent']: - local_infile_dict['solvent'] = float(config['solvent']) - else: - local_infile_dict['solvent'] = False - manager_io.write_input(local_infile_dict) - with open('configure', 'w')as fil: - fil.write('method:%s\n' % config['functional']) - solvent = float(config['solvent']) if config['solvent'] else False - fil.write('solvent:%s\n' % str(solvent)) - jobscripts.append(os.path.join(PATH, name + '_jobscript')) - else: - raise KeyError("Type not implemented. Available types are : [vertIP, vertEA, energy]") - os.chdir(home) - return jobscripts - -def prep_thermo(path): - """This function is to prepare a thermo job given an output file. - - Parameters - ---------- - path : str - Path to the output file of a finished job. - - Returns - ------- - jobscripts : list - List of paths for jobscripts of thermo jobs. - - """ - # Given a path to the outfile of a finished run, this preps the files for a thermo calculation - # Uses the wavefunction from the previous calculation as an initial guess - # Returns a list of the PATH(s) to the jobscript(s) to start the solvent sp calculations(s) - home = os.getcwd() - path = convert_to_absolute_path(path) - - results = manager_io.read_outfile(path) - infile_dict = manager_io.read_infile(path) - - base = os.path.split(path)[0] - - if infile_dict['run_type'] == 'minimize': - optimxyz = os.path.join(base, 'scr', 'optim.xyz') - else: - optimxyz = os.path.join(base, 'scr', 'xyz.xyz') - extract_optimized_geo(optimxyz) - - # Now, start generating the new directory - name = results['name'] + '_thermo' - PATH = os.path.join(base, name) - if os.path.isdir(PATH): - return ['Thermo Calculation Directory already exists'] - - os.mkdir(PATH) - os.chdir(PATH) - - shutil.copyfile(os.path.join(base, 'scr', 'optimized.xyz'), os.path.join(PATH, name + '.xyz')) - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['guess'] = True - local_infile_dict['run_type'] = 'frequencies' - local_infile_dict['coordinates'] = name+'.xyz' - local_infile_dict['name'] = name - local_infile_dict['machine'] = get_machine() - - manager_io.write_input(local_infile_dict) - if infile_dict['spinmult'] == 1: - shutil.copyfile(os.path.join(base, 'scr', 'c0'), os.path.join(PATH, 'c0')) - manager_io.write_jobscript(name, custom_line='# -fin c0', machine=get_machine()) - if infile_dict['spinmult'] != 1: - shutil.copyfile(os.path.join(base, 'scr', 'ca0'), os.path.join(PATH, 'ca0')) - shutil.copyfile(os.path.join(base, 'scr', 'cb0'), os.path.join(PATH, 'cb0')) - manager_io.write_jobscript(name, custom_line=['# -fin ca0\n', '# -fin cb0\n'], machine=get_machine()) - - os.chdir(home) - return [os.path.join(PATH, name + '_jobscript')] - -def prep_ultratight(path): - """Given a path to the outfile of a finished run, this preps a run with tighter convergence criteria. - Uses the wavefunction and geometry from the previous calculation as an initial guess. - - Parameters - ---------- - path : str - Path to the output file of a finished job. - - Returns - ------- - jobscripts : list - List of paths for jobscripts of ultratight jobs for solvent SP calcs. - - """ - # Given a path to the outfile of a finished run, this preps a run with tighter convergence criteria - # Uses the wavefunction and geometry from the previous calculation as an initial guess - # Returns a list of the PATH(s) to the jobscript(s) to start the solvent sp calculations(s) - home = os.getcwd() - path = convert_to_absolute_path(path) - - results = manager_io.read_outfile(path) - if not results['finished']: - raise Exception('This calculation does not appear to be complete! Aborting...') - - infile_dict = manager_io.read_infile(path) - - base = os.path.split(path)[0] - - if infile_dict['run_type'] == 'minimize': - optimxyz = os.path.join(base, 'scr', 'optim.xyz') - else: - optimxyz = os.path.join(base, 'scr', 'xyz.xyz') - extract_optimized_geo(optimxyz) - - # Now, start generating the new directory - name = results['name'] + '_ultratight' - PATH = os.path.join(base, name) - - if not os.path.isdir(PATH): # First time that ultratight has been run, create necessary files - os.mkdir(PATH) - os.chdir(PATH) - - if os.path.exists(name + '.in') or os.path.exists(name + '.out') or os.path.exists(name + '_jobscript'): - raise Exception('This tightened convergence run appears to already exist. Aborting...') - - shutil.copyfile(os.path.join(base, 'scr', 'optimized.xyz'), os.path.join(PATH, name + '.xyz')) - if infile_dict['spinmult'] == 1: - shutil.copyfile(os.path.join(base, 'scr', 'c0'), os.path.join(PATH, 'c0')) - manager_io.write_jobscript(name, custom_line='# -fin c0', machine=get_machine()) - elif infile_dict['spinmult'] != 1: - shutil.copyfile(os.path.join(base, 'scr', 'ca0'), os.path.join(PATH, 'ca0')) - shutil.copyfile(os.path.join(base, 'scr', 'cb0'), os.path.join(PATH, 'cb0')) - manager_io.write_jobscript(name, custom_line=['# -fin ca0\n', '# -fin cb0\n'], machine=get_machine()) - - criteria = ['2.25e-04', '1.5e-04', '0.9e-03', '0.6e-03', '0.5e-06', '1.5e-05'] - - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['guess'] = True - local_infile_dict['convergence_thresholds'] = criteria - local_infile_dict['name'] = name - local_infile_dict['coordinates'] = name+'.xyz' - local_infile_dict['machine'] = get_machine() - - manager_io.write_input(local_infile_dict) - - # Make an empty .out file to prevent the resubmission module from mistakenly submitting this job twice - with open(name + '.out', 'w') as _: - pass - - os.chdir(home) - - return [os.path.join(PATH, name + '_jobscript')] - - else: # This has been run before, further tighten the convergence criteria - os.chdir(PATH) - infile_dict = manager_io.read_infile(os.path.join(PATH, name + '.out')) - criteria = [str(float(i) / 2.) for i in infile_dict['convergence_thresholds']] - - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['guess'] = True - local_infile_dict['convergence_thresholds'] = criteria - local_infile_dict['name'] = name - local_infile_dict['coordinates'] = name+'.xyz' - local_infile_dict['machine'] = get_machine() - manager_io.write_input(local_infile_dict) - - extract_optimized_geo(os.path.join(PATH, 'scr', 'optim.xyz')) - shutil.copy(os.path.join(PATH, 'scr', 'optimized.xyz'), os.path.join(PATH, name + '.xyz')) - - os.chdir(home) - - return [os.path.join(PATH, name + '_jobscript')] - -def prep_hfx_resample(path, hfx_values=[0, 5, 10, 15, 20, 25, 30]): - """Given a path to the outfile of a finished run, this preps the files for hfx resampling. - Uses the wavefunction from the gas phase calculation as an initial guess. - - Parameters - ---------- - path : str - Path to the output file of a finished job. - hfx_values : list, optional - List of hartree fock exchange values to resample. Default is [0, 5, 10, 15, 20, 25, 30]. - - Returns - ------- - jobscripts : list - List of paths for jobscripts HFX resampled calculations. - - """ - # Given a path to the outfile of a finished run, this preps the files for hfx resampling - # Uses the wavefunction from the gas phase calculation as an initial guess - # Returns a list of the PATH(s) to the jobscript(s) to start the resampling calculations(s) - home = os.getcwd() - path = convert_to_absolute_path(path) - base = os.path.split(path)[0] - - results = manager_io.read_outfile(path) - if not results['finished']: - raise Exception('This calculation does not appear to be complete! Aborting...') - - # Check the state of the calculation and ensure than hfx resampling is valid - infile_dict = manager_io.read_infile(path) - if infile_dict['method'] != 'b3lyp': - raise Exception('HFX resampling may not behave well for methods other than b3lyp!') - if not infile_dict['hfx']: - infile_dict['hfx'] = 20 - if infile_dict['hfx'] not in hfx_values: - raise Exception('HFX resampling list does not contain the original hfx value!') - - # Now, start generating the base directory to hold all the hfx resampling values - name = results['name'] + '_HFXresampling' - hfx_path = os.path.join(base, name) - if not os.path.isdir(hfx_path): - os.mkdir(hfx_path) - os.chdir(hfx_path) - - # Make the directory for the original calculation - subname = name + '_' + str(infile_dict['hfx']) - PATH = os.path.join(hfx_path, subname) - if not os.path.isdir(PATH): - os.mkdir(PATH) - os.chdir(PATH) - - if not os.path.exists(os.path.join(PATH, subname + '.out')): - shutil.copyfile(path, subname + '.out') - shutil.copyfile(path.rsplit('.', 1)[0] + '_jobscript', subname + '_jobscript') - shutil.copyfile(path.rsplit('.', 1)[0] + '.in', subname + '.in') - shutil.copytree(os.path.join(os.path.split(path)[0], 'scr'), 'scr') - if os.path.exists(path.rsplit('.', 1)[0] + '.xyz'): - shutil.copyfile(path.rsplit('.', 1)[0] + '.xyz', subname + '.xyz') - - # Find the hfx resampling values that we're ready to generate - hfx_values_to_generate = [] - existing_resampled_values = glob.glob(glob.escape(os.path.join(hfx_path, name)) + '_*') - for existing in existing_resampled_values: - hfx = int(existing.rsplit('_', 1)[1]) - subname = name + '_' + str(hfx) - outfile_path = os.path.join(existing, subname + '.out') - if os.path.exists(outfile_path): - if manager_io.read_outfile(outfile_path)['finished']: - hfx_values_to_generate.append(hfx - 5) - hfx_values_to_generate.append(hfx + 5) - - hfx_values_to_generate = list(set(hfx_values_to_generate)) - hfx_values_to_generate = [i for i in hfx_values_to_generate if i in hfx_values] - - # Now generate the additional hfx resampling values - jobscripts = [] - for hfx in hfx_values_to_generate: - subname = name + '_' + str(hfx) - if os.path.exists(os.path.join(hfx_path, subname)): # skip over values that we've already done - continue - - os.mkdir(os.path.join(hfx_path, subname)) - os.chdir(os.path.join(hfx_path, subname)) - - higher_hfx = subname.rsplit('_', 1)[0] + '_' + str(int(subname.rsplit('_', 1)[1]) + 5) - lower_hfx = subname.rsplit('_', 1)[0] + '_' + str(int(subname.rsplit('_', 1)[1]) - 5) - if os.path.exists(os.path.join(hfx_path, higher_hfx)): - source_dir = os.path.join(hfx_path, higher_hfx) - else: - source_dir = os.path.join(hfx_path, lower_hfx) - - if infile_dict['run_type'] == 'minimize': - optimxyz = os.path.join(source_dir, 'scr', 'optim.xyz') - else: - optimxyz = os.path.join(source_dir, 'scr', 'xyz.xyz') - extract_optimized_geo(optimxyz) - - shutil.copy(os.path.join(source_dir, 'scr', 'optimized.xyz'), subname + '.xyz') - if infile_dict['spinmult'] == 1: - shutil.copy(os.path.join(source_dir, 'scr', 'c0'), 'c0') - manager_io.write_jobscript(subname, custom_line='# -fin c0', machine=get_machine()) - elif infile_dict['spinmult'] != 1: - shutil.copyfile(os.path.join(source_dir, 'scr', 'ca0'), os.path.join('ca0')) - shutil.copyfile(os.path.join(source_dir, 'scr', 'cb0'), os.path.join('cb0')) - manager_io.write_jobscript(subname, custom_line=['# -fin ca0\n', '# -fin cb0\n'], - machine=get_machine()) - - local_infile_dict = copy.copy(infile_dict) - local_infile_dict['guess'] = True - local_infile_dict['hfx'] = hfx / 100. - local_infile_dict['name'] = subname - local_infile_dict['coordinates'] = subname+'.xyz' - local_infile_dict['machine'] = get_machine() - manager_io.write_input(local_infile_dict) - jobscripts.append(os.path.join(os.getcwd(), subname + '_jobscript')) - - os.chdir(home) - - return jobscripts diff --git a/molSimplify/molscontrol/dynamic_classifier.py b/molSimplify/molscontrol/dynamic_classifier.py index 66649cb5..5e3d8583 100644 --- a/molSimplify/molscontrol/dynamic_classifier.py +++ b/molSimplify/molscontrol/dynamic_classifier.py @@ -1,7 +1,7 @@ import os import time import logging -from pkg_resources import resource_filename, Requirement +from importlib_resources import files as resource_files from collections import OrderedDict import numpy as np import skimage.transform as skitransform @@ -228,8 +228,7 @@ def get_file_path(self, filein): def load_models(self): if not self.modelfile: - modelpath = resource_filename(Requirement.parse("molSimplify"), - "molSimplify/molscontrol/models/" + self.mode + "/") + modelpath = str(resource_files("molSimplify.molscontrol").joinpath(f"models/{self.mode}")) else: modelpath = self.modelfile logging.warning("Using user-specified models from %s." % modelpath) @@ -245,8 +244,7 @@ def load_models(self): def load_training_data(self): if not self.traindatafile: - datapath = resource_filename(Requirement.parse("molSimplify"), - "molSimplify/molscontrol/data/" + self.mode + "/train_data.pkl") + datapath = resource_files("molSimplify.molscontrol").joinpath(f"data/{self.mode}/train_data.pkl") else: datapath = self.traindatafile logging.warning("Using user-specified models from %s." % datapath) @@ -261,8 +259,7 @@ def load_training_data(self): def load_normalization_vec(self): if not self.normfile: - normvecpath = resource_filename(Requirement.parse("molSimplify"), - "molSimplify/molscontrol/normalization_vec/" + self.mode + "/norm_dict.json") + normvecpath = resource_files("molSimplify.molscontrol").joinpath(f"normalization_vec/{self.mode}/norm_dict.json") else: normvecpath = self.normfile logging.warning( diff --git a/molSimplify/python_krr/sklearn_models.py b/molSimplify/python_krr/sklearn_models.py index 081e1cbe..8bcecbf0 100644 --- a/molSimplify/python_krr/sklearn_models.py +++ b/molSimplify/python_krr/sklearn_models.py @@ -1,6 +1,6 @@ import numpy as np import joblib -from pkg_resources import resource_filename, Requirement +from importlib_resources import files as resource_files from molSimplify.python_nn.tf_ANN import (tf_ANN_excitation_prepare, load_normalization_data, data_normalize, @@ -9,7 +9,7 @@ def load_sklearn_model(predictor): key = get_key(predictor, suffix="model") - modelfile = resource_filename(Requirement.parse("molSimplify"), "molSimplify/sklearn_models/" + key + '.h5') + modelfile = resource_files("molSimplify").joinpath(f"sklearn_models/{key}.h5") loaded_model = joblib.load(modelfile) return loaded_model diff --git a/molSimplify/python_nn/ANN.py b/molSimplify/python_nn/ANN.py index a0439b24..fb81a72b 100644 --- a/molSimplify/python_nn/ANN.py +++ b/molSimplify/python_nn/ANN.py @@ -11,7 +11,7 @@ import csv import numpy as np -from pkg_resources import resource_filename, Requirement +from importlib_resources import files as resource_files from molSimplify.utils.decorators import deprecated from typing import List @@ -91,8 +91,7 @@ def simple_network_builder_pybrain(layers: List[int], partial_path: str): def csv_loader(path: str) -> List[float]: # print('in csv loader') - path_to_file = resource_filename(Requirement.parse("molSimplify"), - "molSimplify/python_nn/" + path) + path_to_file = resource_files("molSimplify.python_nn").joinpath(path.strip("/")) with open(path_to_file, 'r') as csvfile: csv_lines = csv.reader(csvfile, delimiter=',') ret_list = list() @@ -104,17 +103,14 @@ def csv_loader(path: str) -> List[float]: def matrix_loader(path, rownames=False): # loads matrix with rowname option + path_to_file = resource_files("molSimplify.python_nn").joinpath(path.strip("/")) if rownames: - path_to_file = resource_filename(Requirement.parse("molSimplify"), - "molSimplify/python_nn/" + path) with open(path_to_file, "r") as f: csv_lines = list(csv.reader(f)) row_names = [row[0] for row in csv_lines] mat = [row[1:] for row in csv_lines] return mat, row_names else: - path_to_file = resource_filename(Requirement.parse("molSimplify"), - "molSimplify/python_nn/" + path) with open(path_to_file, 'r') as csvfile: csv_lines = csv.reader(csvfile, delimiter=',') mat = [a for a in csv_lines] @@ -123,7 +119,6 @@ def matrix_loader(path, rownames=False): # n = network_builder([25,50,51],"nn_split") def simple_splitting_ann(excitation): - # path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/python_nn/" + "ms_split") # print('path to ANN data: ',path_to_file) n = simple_network_builder([25, 50, 50], "ms_split") excitation, sp_center, sp_shift = excitation_standardizer(excitation, 'split') @@ -140,7 +135,6 @@ def simple_splitting_ann(excitation): def simple_slope_ann(slope_excitation): - # path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/python_nn/" + "ms_slope") # print('path to ANN data: ',path_to_file) n = simple_network_builder([24, 50, 50], "ms_slope") # no alpha value # print(slope_excitation) diff --git a/molSimplify/python_nn/ensemble_test.py b/molSimplify/python_nn/ensemble_test.py index f244f2ce..295b38e7 100644 --- a/molSimplify/python_nn/ensemble_test.py +++ b/molSimplify/python_nn/ensemble_test.py @@ -8,7 +8,7 @@ from tensorflow.keras.models import model_from_json from tensorflow.keras import backend as K -from pkg_resources import resource_filename, Requirement +from importlib_resources import files as resource_files from sklearn.utils import shuffle from molSimplify.python_nn.clf_analysis_tool import (dist_neighbor, get_entropy) @@ -102,7 +102,7 @@ def ensemble_maker(predictor, num=10): def ensemble_uq(predictor, descriptors=False, descriptor_names=False, suffix=False): key = get_key(predictor, suffix) - base_path = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key) + base_path = str(resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv')) base_path = base_path + 'ensemble_models' if not os.path.exists(base_path): print('Ensemble models do not exist now, training...') @@ -204,7 +204,7 @@ def f(tau): def latent_space_uq(predictor, layer_index=-2, descriptors=False, descriptor_names=False, entropy=False): key = get_key(predictor, suffix=False) - base_path = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key) + base_path = str(resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv')) base_path = base_path + 'ensemble_models' if not os.path.exists(base_path): print('Ensemble models do not exist now, training...') diff --git a/molSimplify/python_nn/tf_ANN.py b/molSimplify/python_nn/tf_ANN.py index 7f768440..92f653aa 100644 --- a/molSimplify/python_nn/tf_ANN.py +++ b/molSimplify/python_nn/tf_ANN.py @@ -19,7 +19,7 @@ from typing import List, Tuple, Union, Optional from tensorflow.keras import backend as K from tensorflow.keras.models import model_from_json, load_model -from pkg_resources import resource_filename, Requirement +from importlib_resources import files as resource_files from packaging import version import tensorflow as tf @@ -40,7 +40,7 @@ def perform_ANN_prediction(RAC_dataframe: pd.DataFrame, predictor_name: str, # - predictor_name_min_latent_distance, # - predictor_name_prediction - assert type(RAC_dataframe) == pd.DataFrame + assert type(RAC_dataframe) is pd.DataFrame train_vars = load_ANN_variables(predictor_name) train_mean_x, train_mean_y, train_var_x, train_var_y = load_normalization_data(predictor_name) my_ANN = load_keras_ann(predictor_name) @@ -67,9 +67,7 @@ def perform_ANN_prediction(RAC_dataframe: pd.DataFrame, predictor_name: str, rescaled_output = data_rescale(ANN_prediction, train_mean_y, train_var_y) # Get latent vectors for training data and queried data - train_x = pd.DataFrame( - load_training_data(predictor_name), - columns=train_vars).astype(float) + train_x = pd.DataFrame(load_training_data(predictor_name), columns=train_vars).astype(float) get_outputs = K.function([my_ANN.layers[0].input, K.learning_phase()], [my_ANN.layers[len(my_ANN.layers) - 2].output]) normalized_train = data_normalize(train_x, train_mean_x, train_var_x) @@ -109,15 +107,14 @@ def log_likelihood(params): def matrix_loader(path: str, rownames: bool = False) -> Union[Tuple[List[List[str]], List[str]], List[List[str]]]: # loads matrix with rowname option + path_to_file = resource_files("molSimplify.python_nn").joinpath(path.strip("/")) if rownames: - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/python_nn/" + path) with open(path_to_file, "r") as f: csv_lines = list(csv.reader(f)) row_names = [row[0] for row in csv_lines] mat = [row[1:] for row in csv_lines] return mat, row_names else: - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/python_nn/" + path) with open(path_to_file, 'r') as csvfile: lines = csv.reader(csvfile, delimiter=',') mat = [a for a in lines] @@ -190,29 +187,25 @@ def data_normalize(data, train_mean, train_var, debug=False) -> np.ndarray: def load_normalization_data(name: str): train_mean_x = list() - path_to_file = resource_filename(Requirement.parse("molSimplify"), - "molSimplify/tf_nn/" + '/rescaling_data/' + name + '_mean_x.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'rescaling_data/{name}_mean_x.csv') if os.path.isfile(path_to_file): with open(path_to_file, 'r') as f: for lines in f.readlines(): train_mean_x.append([float(lines.strip().strip('[]'))]) train_var_x = list() - path_to_file = resource_filename(Requirement.parse("molSimplify"), - "molSimplify/tf_nn/" + '/rescaling_data/' + name + '_var_x.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'rescaling_data/{name}_var_x.csv') with open(path_to_file, 'r') as f: for lines in f.readlines(): train_var_x.append([float(lines.strip().strip('[]'))]) train_mean_y = list() - path_to_file = resource_filename(Requirement.parse("molSimplify"), - "molSimplify/tf_nn/" + '/rescaling_data/' + name + '_mean_y.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'rescaling_data/{name}_mean_y.csv') with open(path_to_file, 'r') as f: for lines in f.readlines(): train_mean_y.append([float(lines.strip().strip('[]'))]) train_var_y = list() - path_to_file = resource_filename(Requirement.parse("molSimplify"), - "molSimplify/tf_nn/" + '/rescaling_data/' + name + '_var_y.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'rescaling_data/{name}_var_y.csv') with open(path_to_file, 'r') as f: for lines in f.readlines(): train_var_y.append([float(lines.strip().strip('[]'))]) @@ -235,10 +228,10 @@ def get_data_mean_std(predictor: str): elif predictor == "split": key = predictor + '/' + predictor + '_x' elif predictor in ['geo_static_clf', 'sc_static_clf']: - key = 'static_clf/' + predictor + '_train_x' + key = f'{predictor}/{predictor}_train_x' else: key = predictor + '/' + predictor + '_x' - path_to_feature_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.csv') + path_to_feature_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv') df_feature = pd.read_csv(path_to_feature_file) train_mean_x, train_var_x = list(), list() for col in df_feature: @@ -256,10 +249,10 @@ def get_data_mean_std(predictor: str): elif predictor == "split": key = predictor + '/' + predictor + '_y' elif predictor in ['geo_static_clf', 'sc_static_clf']: - key = 'static_clf/' + predictor + '_train_y' + key = f'{predictor}/{predictor}_train_y' else: key = predictor + '/' + predictor + '_y' - path_to_label_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.csv') + path_to_label_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv') df_label = pd.read_csv(path_to_label_file) train_mean_y, train_var_y = list(), list() for col in df_label: @@ -270,7 +263,7 @@ def get_data_mean_std(predictor: str): def load_ANN_variables(predictor: str, suffix: str = 'vars') -> List[str]: key = get_key(predictor, suffix) - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv') names = [] with open(path_to_file, 'r') as f: for lines in f.readlines(): @@ -293,7 +286,7 @@ def load_training_data(predictor: str) -> List[List[str]]: key = predictor + '/' + predictor + '_train_x' else: key = predictor + '/' + predictor + '_x' - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv') with open(path_to_file, "r") as f: csv_lines = list(csv.reader(f)) # row_names = [row[0] for row in csv_lines] @@ -314,10 +307,10 @@ def load_latent_training_data(predictor): elif predictor == "split": key = predictor + '/' + predictor + '_latent_x_41_OHE' elif predictor in ['geo_static_clf', 'sc_static_clf']: - key = 'static_clf/' + predictor + '_latent_train_x' + key = predictor + '/' + predictor + '_latent_train_x' else: key = predictor + '/' + predictor + '_latent_x_OHE' - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv') with open(path_to_file, "r") as f: csv_lines = list(csv.reader(f)) # row_names = [row[0] for row in csv_lines] @@ -338,7 +331,7 @@ def load_test_data(predictor): key = predictor + '/' + predictor + '_test_x' else: key = predictor + '/' + predictor + '_x' - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv') with open(path_to_file, "r") as f: csv_lines = list(csv.reader(f)) # row_names = [row[0] for row in csv_lines] @@ -361,7 +354,7 @@ def load_training_labels(predictor: str) -> List[List[str]]: key = predictor + '/' + predictor + '_train_y' else: key = predictor + '/' + predictor + '_y' - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv') with open(path_to_file, "r") as f: csv_lines = list(csv.reader(f)) # row_names = [row[0] for row in csv_lines] @@ -384,7 +377,7 @@ def load_test_labels(predictor: str) -> List[List[str]]: key = predictor + '/' + predictor + '_test_y' else: key = predictor + '/' + predictor + '_y' - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv') with open(path_to_file, "rU") as f: csv_lines = list(csv.reader(f)) # row_names = [row[0] for row in csv_lines] @@ -394,7 +387,7 @@ def load_test_labels(predictor: str) -> List[List[str]]: def load_train_info(predictor: str, suffix: str = 'info') -> dict: key = get_key(predictor, suffix) - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.json') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.json') with open(path_to_file, 'r') as json_file: loaded_info_dict = json.loads(json_file.read()) return loaded_info_dict @@ -407,15 +400,15 @@ def load_keras_ann(predictor: str, suffix: str = 'model', compile: bool = False) os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3' key = get_key(predictor, suffix) if "clf" not in predictor: - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.json') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.json') with open(path_to_file, 'r') as json_file: loaded_model_json = json_file.read() loaded_model = model_from_json(loaded_model_json) # load weights into model - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.h5') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.h5') loaded_model.load_weights(path_to_file) else: - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.h5') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.h5') loaded_model = load_model(path_to_file) if compile: from tensorflow.keras.optimizers.legacy import Adam @@ -555,7 +548,7 @@ def find_true_min_eu_dist(predictor: str, 'oxo20': 'oxoandhomo', 'homo_empty': 'oxoandhomo'} if predictor in folder_dict: key = f'{folder_dict[predictor]}/{predictor}_train_names' - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv') with open(path_to_file, "r") as f: csv_lines = list(csv.reader(f)) print(('Closest Euc Dist Structure: ' + str(csv_lines[min_ind]).strip('[]') + ' for predictor ' + str( @@ -668,7 +661,7 @@ def find_ANN_latent_dist(predictor, latent_space_vector, debug=False): 'oxo20': 'oxoandhomo', 'homo_empty': 'oxoandhomo'} if predictor in folder_dict: key = f'{folder_dict[predictor]}/{predictor}_train_names' - path_to_file = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key + '.csv') + path_to_file = resource_files("molSimplify.tf_nn").joinpath(f'{key}.csv') with open(path_to_file, "r") as f: csv_lines = list(csv.reader(f)) print(('Closest Latent Dist Structure: ' + str(csv_lines[min_ind]) + ' for predictor ' + str(predictor))) @@ -691,7 +684,7 @@ def find_clf_lse(predictor: str, print("Unknown model type") return np.zeros_like(excitation) key = get_key(predictor, suffix='') - base_path = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key) + base_path = resource_files("molSimplify.tf_nn").joinpath(key) train_mean_x, train_mean_y, train_var_x, train_var_y = load_normalization_data(predictor) labels_train = np.array(load_training_labels(predictor), dtype='int') fmat_train = np.array(load_training_data(predictor), dtype='float64') @@ -740,7 +733,7 @@ def find_clf_lse(predictor: str, def save_model(model: tf.keras.Model, predictor: str, num: Optional[int] = None, suffix: Optional[str] = None): key = get_key(predictor, suffix) - base_path = resource_filename(Requirement.parse("molSimplify"), "molSimplify/tf_nn/" + key) + base_path = resource_files("molSimplify.tf_nn").joinpath(key) base_path = base_path + 'ensemble_models' if not os.path.exists(base_path): os.makedirs(base_path) diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..9f917103 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,52 @@ +[project] +name = "molSimplify" +version = "v1.7.3" +license = {file = "LICENSE"} +readme = "README.md" +dependencies = [ + "openbabel-wheel", + "numpy", + "scipy", + "pandas", + "networkx", + "scikit-learn", + "keras", + "tensorflow", + "pyyaml", + "importlib-resources", +] + +[project.optional-dependencies] +dev = ["pytest", "pytest-resource-path", "pre-commit"] +docs = [ + "beautifulsoup4", + "sphinx", + "readthedocs-sphinx-ext", + "sphinx_rtd_theme", +] + +[project.urls] +Homepage = "https://molsimplify.mit.edu/" +Documentation = "http://hjkgrp.mit.edu/molsimplify-tutorials/" +Repository = "https://github.com/hjkgrp/molSimplify" + +[project.scripts] +molsimplify = "molSimplify.__main__:main" +molscontrol = "molSimplify.molscontrol.molscontrol:main" + +[build-system] +requires = ["setuptools>=61.0"] +build-backend = "setuptools.build_meta" + +[tool.setuptools.packages.find] +where = ["."] + +[tool.setuptools.package-data] +"molSimplify.Data" = ["*.dat"] +"molSimplify.Bind" = ["*.dat"] +"molSimplify.Ligands" = ["*.dict", "*.mol", "*.xyz", "*.smi"] +"molSimplify.icons" = ["*.png"] +"molSimplify.python_nn" = ["*.csv"] +"molSimplify.python_krr" = ["*.csv"] +"molSimplify.tf_nn" = ["*/*"] +"molSimplify.molscontrol" = ["*/*"] diff --git a/setup.py b/setup.py deleted file mode 100644 index 6da6374a..00000000 --- a/setup.py +++ /dev/null @@ -1,25 +0,0 @@ -from setuptools import setup, find_packages - -setup(name='molSimplify', - version='v1.7.2', - packages=find_packages(), - entry_points={ - 'console_scripts': [ - 'molsimplify = molSimplify.__main__:main', - 'molscontrol = molSimplify.molscontrol.molscontrol:main', - 'jobmanager = molSimplify.job_manager.resub:main'] - }, - package_dir={'molSimplify': 'molSimplify'}, - package_data={ - 'molSimplify': ['Data/*.dat', 'Bind/*.dat', 'Ligands/*.dict', - 'icons/*.png', 'python_nn/*.csv', 'python_krr/*.csv', - 'tf_nn/*/*', 'molscontrol/*/*'] - }, - data_files=[('molSimplify', ['molSimplify/Data/ML.dat'])], - install_requires=['numpy', 'scipy', 'scikit-learn', - 'keras', 'tensorflow', 'pyyaml', - 'pre-commit'], - setup_requires=['pytest-runner'], # this may result some package conflict in local conda build. comment it out if needed. - tests_require=['pytest'], - include_package_data=True - ) diff --git a/tests/helperFuncs.py b/tests/helperFuncs.py index 86b3c4cd..767f7d0e 100644 --- a/tests/helperFuncs.py +++ b/tests/helperFuncs.py @@ -3,18 +3,18 @@ import random import shutil import numpy as np +from typing import List from molSimplify.Scripts.geometry import kabsch, distance from molSimplify.Scripts.generator import startgen from molSimplify.Classes.globalvars import (dict_oneempty_check_st, oneempty_angle_ref) from molSimplify.Classes.mol3D import mol3D -from pkg_resources import resource_filename, Requirement from typing import Dict from contextlib import contextmanager from pathlib import Path -def is_number(s): +def is_number(s: str) -> bool: """check whether the string is a integral/float/scientific""" try: float(s) @@ -33,11 +33,11 @@ def working_directory(path: Path): os.chdir(prev_cwd) -def fuzzy_equal(x1, x2, thresh): +def fuzzy_equal(x1, x2, thresh: float) -> bool: return np.fabs(float(x1) - float(x2)) < thresh -def fuzzy_compare_xyz(xyz1, xyz2, thresh): +def fuzzy_compare_xyz(xyz1, xyz2, thresh: float) -> bool: fuzzyEqual = False mol1 = mol3D() mol1.readfromxyz(xyz1) @@ -86,9 +86,7 @@ def getAllLigands(xyz): return ligands -def getMetalLigBondLength(mymol3d): - # findMetal only returns 1 metal atom? - # TG: fixed findmetal to return a list +def getMetalLigBondLength(mymol3d: mol3D) -> List[float]: mm = mymol3d.findMetal()[0] bonded = mymol3d.getBondedAtoms(mm) blength = [] @@ -98,39 +96,43 @@ def getMetalLigBondLength(mymol3d): return blength -def compareNumAtoms(xyz1, xyz2): +def compareNumAtoms(xyz1, xyz2) -> bool: """Compare number of atoms""" print("Checking total number of atoms") mol1 = mol3D() mol1.readfromxyz(xyz1) mol2 = mol3D() - mol2.readfromxyz(xyz1) + mol2.readfromxyz(xyz2) # Compare number of atoms passNumAtoms = (mol1.natoms == mol2.natoms) print("Pass total number of atoms check: ", passNumAtoms) return passNumAtoms -def compareMLBL(xyz1, xyz2, thresh): +def compareMLBL(xyz1, xyz2, thresh: float) -> bool: """Compare Metal Ligand Bond Length""" print("Checking metal-ligand bond length") mol1 = mol3D() mol1.readfromxyz(xyz1) mol2 = mol3D() - mol2.readfromxyz(xyz1) + mol2.readfromxyz(xyz2) bl1 = getMetalLigBondLength(mol1) bl2 = getMetalLigBondLength(mol2) passMLBL = True - for i in range(0, len(bl1)): - if not fuzzy_equal(bl1[i], bl2[i], thresh): - print("Error! Metal-Ligand bondlength mismatch for bond # ", i) - passMLBL = False + if len(bl1) != len(bl2): + print("Error! Number of metal-ligand bonds is different") + passMLBL = False + else: + for i in range(0, len(bl1)): + if not fuzzy_equal(bl1[i], bl2[i], thresh): + print("Error! Metal-Ligand bondlength mismatch for bond # ", i) + passMLBL = False print("Pass metal-ligand bond length check: ", passMLBL) print("Threshold for bondlength difference: ", thresh) return passMLBL -def compareLG(xyz1, xyz2, thresh): +def compareLG(xyz1, xyz2, thresh: float) -> bool: """Compare Ligand Geometry""" print("Checking the Ligand Geometries") passLG = True @@ -152,7 +154,7 @@ def compareLG(xyz1, xyz2, thresh): return passLG -def compareOG(xyz1, xyz2, thresh): +def compareOG(xyz1, xyz2, thresh: float) -> bool: print("Checking the overall geometry") passOG = fuzzy_compare_xyz(xyz1, xyz2, thresh) print("Pass overall geometry check: ", passOG) @@ -160,12 +162,13 @@ def compareOG(xyz1, xyz2, thresh): return passOG -def runtest_num_atoms_in_xyz(tmpdir, xyzfile): +def runtest_num_atoms_in_xyz(tmpdir, resource_path_root, xyzfile): + file_path = resource_path_root / "refs" / f"{xyzfile}.xyz" xyz_file1 = mol3D() - xyz_file1.readfromxyz('tests/refs/' + xyzfile + '.xyz') + xyz_file1.readfromxyz(file_path) xyz_file1.getNumAtoms() - with open('tests/refs/' + xyzfile + '.xyz', 'r') as f: + with open(file_path, 'r') as f: xyz_file2 = f.readlines() num_atoms = int(xyz_file2[0]) @@ -393,12 +396,11 @@ def compare_qc_input(inp, inp_ref): return passQcInputCheck -def runtest(tmpdir, name, threshMLBL, threshLG, threshOG, seed=31415): +def runtest(tmpdir, resource_path_root, name, threshMLBL, threshLG, threshOG, seed=31415): # Set seeds to eliminate randomness from test results random.seed(seed) np.random.seed(seed) - infile = resource_filename(Requirement.parse( - "molSimplify"), f"tests/inputs/{name}.in") + infile = resource_path_root / "inputs" / f"{name}.in" newinfile, myjobdir = parse4test(infile, tmpdir) args = ['main.py', '-i', newinfile] with working_directory(tmpdir): @@ -415,12 +417,9 @@ def runtest(tmpdir, name, threshMLBL, threshLG, threshOG, seed=31415): if 'molcas' in molsim_data.lower(): output_qcin = myjobdir + '/molcas.input' - ref_xyz = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/{name}.xyz") - ref_report = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/{name}.report") - ref_qcin = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/{name}.qcin") + ref_xyz = resource_path_root / "refs" / f"{name}.xyz" + ref_report = resource_path_root / "refs" / f"{name}.report" + ref_qcin = resource_path_root / "refs" / f"{name}.qcin" print("Test input file: ", newinfile) print("Test output files are generated in ", myjobdir) @@ -440,7 +439,7 @@ def runtest(tmpdir, name, threshMLBL, threshLG, threshOG, seed=31415): return [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] -def runtest_slab(tmpdir, name, threshOG, extra_files=None): +def runtest_slab(tmpdir, resource_path_root, name, threshOG, extra_files=None): """ Performs test for slab builder. @@ -453,20 +452,17 @@ def runtest_slab(tmpdir, name, threshOG, extra_files=None): axis : threshOG tolerance for RMSD comparison of overall geometries. """ - infile = resource_filename(Requirement.parse( - "molSimplify"), f"tests/inputs/{name}.in") + infile = resource_path_root / "inputs" / f"{name}.in" newinfile, _ = parse4test(infile, tmpdir) if extra_files is not None: for file_name in extra_files: - file_path = resource_filename(Requirement.parse( - "molSimplify"), f"tests/inputs/{file_name}") + file_path = resource_path_root / "inputs" / f"{file_name}" shutil.copyfile(file_path, tmpdir / file_name) args = ['main.py', '-i', newinfile] with working_directory(tmpdir): startgen(args, False, False) - output_xyz = str(tmpdir / 'slab' / 'super332.xyz') - ref_xyz = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/{name}.xyz") + output_xyz = tmpdir / 'slab' / 'super332.xyz' + ref_xyz = resource_path_root / "refs" / f"{name}.xyz" print("Output xyz file: ", output_xyz) pass_xyz = compareGeo(output_xyz, ref_xyz, threshMLBL=0, threshLG=0, threshOG=threshOG, slab=True) @@ -474,7 +470,7 @@ def runtest_slab(tmpdir, name, threshOG, extra_files=None): return [passNumAtoms, passOG] -def runtest_molecule_on_slab(tmpdir, name, threshOG, extra_files=None): +def runtest_molecule_on_slab(tmpdir, resource_path_root, name, threshOG, extra_files=None): """ Performs test for slab builder with a CO molecule adsorbed. @@ -487,21 +483,18 @@ def runtest_molecule_on_slab(tmpdir, name, threshOG, extra_files=None): axis : threshOG tolerance for RMSD comparison of overall geometries. """ - infile = resource_filename(Requirement.parse( - "molSimplify"), f"tests/inputs/{name}.in") + infile = resource_path_root / "inputs" / f"{name}.in" newinfile, _ = parse4test(infile, tmpdir, extra_args={ '-unit_cell': 'slab.xyz', '-target_molecule': 'co.xyz'}) if extra_files is not None: for file_name in extra_files: - file_path = resource_filename(Requirement.parse( - "molSimplify"), f"tests/inputs/{file_name}") + file_path = resource_path_root / "inputs" / f"{file_name}" shutil.copyfile(file_path, tmpdir / file_name) args = ['main.py', '-i', newinfile] with working_directory(tmpdir): startgen(args, False, False) - output_xyz = str(tmpdir / 'loaded_slab' / 'loaded.xyz') - ref_xyz = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/{name}.xyz") + output_xyz = tmpdir / 'loaded_slab' / 'loaded.xyz' + ref_xyz = resource_path_root / "refs" / f"{name}.xyz" print("Output xyz file: ", output_xyz) pass_xyz = compareGeo(output_xyz, ref_xyz, threshMLBL=0, threshLG=0, threshOG=threshOG, slab=True) @@ -509,13 +502,10 @@ def runtest_molecule_on_slab(tmpdir, name, threshOG, extra_files=None): return [passNumAtoms, passOG] -def runtestgeo(tmpdir, name, thresh, deleteH=True, geo_type="oct"): - initgeo = resource_filename(Requirement.parse( - "molSimplify"), f"tests/inputs/geocheck/{name}/init.xyz") - optgeo = resource_filename(Requirement.parse( - "molSimplify"), f"tests/inputs/geocheck/{name}/opt.xyz") - refjson = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/geocheck/{name}/ref.json") +def runtestgeo(tmpdir, resource_path_root, name, thresh, deleteH=True, geo_type="oct"): + initgeo = resource_path_root / "inputs" / "geocheck" / name / "init.xyz" + optgeo = resource_path_root / "inputs" / "geocheck" / name / "opt.xyz" + refjson = resource_path_root / "refs" / "geocheck" / name / "ref.json" mymol = mol3D() mymol.readfromxyz(optgeo) init_mol = mol3D() @@ -540,11 +530,9 @@ def runtestgeo(tmpdir, name, thresh, deleteH=True, geo_type="oct"): return passGeo -def runtestgeo_optonly(tmpdir, name, thresh, deleteH=True, geo_type="oct"): - optgeo = resource_filename(Requirement.parse( - "molSimplify"), f"tests/inputs/geocheck/{name}/opt.xyz") - refjson = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/geocheck/{name}/ref.json") +def runtestgeo_optonly(tmpdir, resource_path_root, name, thresh, deleteH=True, geo_type="oct"): + optgeo = resource_path_root / "inputs" / "geocheck" / name / "opt.xyz" + refjson = resource_path_root / "refs" / "geocheck" / name / "ref.json" mymol = mol3D() mymol.readfromxyz(optgeo) if geo_type == "oct": @@ -558,9 +546,8 @@ def runtestgeo_optonly(tmpdir, name, thresh, deleteH=True, geo_type="oct"): raise NotImplementedError('Only octahedral geometries supported for now') -def runtestNoFF(tmpdir, name, threshMLBL, threshLG, threshOG): - infile = resource_filename(Requirement.parse( - "molSimplify"), f"tests/inputs/{name}.in") +def runtestNoFF(tmpdir, resource_path_root, name, threshMLBL, threshLG, threshOG): + infile = resource_path_root / "inputs" / f"{name}.in" newinfile, myjobdir = parse4testNoFF(infile, tmpdir) [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = [True, True, True, True, True, True] @@ -578,12 +565,9 @@ def runtestNoFF(tmpdir, name, threshMLBL, threshLG, threshOG): output_qcin = myjobdir + '/orca.in' if 'molcas' in molsim_data.lower(): output_qcin = myjobdir + '/molcas.input' - ref_xyz = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/{newname}.xyz") - ref_report = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/{newname}.report") - ref_qcin = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/{name}.qcin") + ref_xyz = resource_path_root / "refs" / f"{newname}.xyz" + ref_report = resource_path_root / "refs" / f"{newname}.report" + ref_qcin = resource_path_root / "refs" / f"{name}.qcin" print("Test input file: ", newinfile) print("Test output files are generated in ", myjobdir) print("Output xyz file: ", output_xyz) @@ -603,12 +587,11 @@ def runtestNoFF(tmpdir, name, threshMLBL, threshLG, threshOG): return [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] -def runtest_reportonly(tmpdir, name, seed=31415): +def runtest_reportonly(tmpdir, resource_path_root, name, seed=31415): # Set seeds to eliminate randomness from test results random.seed(seed) np.random.seed(seed) - infile = resource_filename(Requirement.parse( - "molSimplify"), f"tests/inputs/{name}.in") + infile = resource_path_root / "inputs" / f"{name}.in" # Copy the input file to the temporary folder shutil.copy(infile, tmpdir/f'{name}_reportonly.in') # Add the report only flag @@ -621,8 +604,7 @@ def runtest_reportonly(tmpdir, name, seed=31415): with working_directory(tmpdir): startgen(args, False, False) output_report = myjobdir + '/' + name + '_reportonly.report' - ref_report = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/{name}.report") + ref_report = resource_path_root / "refs" / f"{name}.report" # Copy the reference report to the temporary folder shutil.copy(ref_report, tmpdir/f'{name}_ref.report') with open(tmpdir/f'{name}_ref.report', 'r') as f: @@ -640,17 +622,15 @@ def runtest_reportonly(tmpdir, name, seed=31415): return pass_report -def runtestMulti(tmpdir, name, threshMLBL, threshLG, threshOG): - infile = resource_filename(Requirement.parse( - "molSimplify"), f"tests/inputs/{name}.in") +def runtestMulti(tmpdir, resource_path_root, name, threshMLBL, threshLG, threshOG): + infile = resource_path_root / "inputs" / f"{name}.in" newinfile, myjobdir = parse4test(infile, tmpdir, True) args = ['main.py', '-i', newinfile] with working_directory(tmpdir): startgen(args, False, False) print("Test input file: ", newinfile) print("Test output files are generated in ", myjobdir) - refdir = resource_filename(Requirement.parse( - "molSimplify"), f"tests/refs/{name}") + refdir = resource_path_root / "refs" / name [passMultiFileCheck, myfiles] = checkMultiFileGen(myjobdir, refdir) pass_structures = [] if not passMultiFileCheck: diff --git a/tests/informatics/test_coulomb_analyze.py b/tests/informatics/test_coulomb_analyze.py index 95749f98..2a4f071d 100644 --- a/tests/informatics/test_coulomb_analyze.py +++ b/tests/informatics/test_coulomb_analyze.py @@ -1,14 +1,10 @@ import numpy as np from molSimplify.Classes.mol3D import mol3D -from pkg_resources import resource_filename, Requirement from molSimplify.Informatics.coulomb_analyze import create_coulomb_matrix -def test_create_coulomb_matrix(): - xyz_file = resource_filename( - Requirement.parse("molSimplify"), - "tests/inputs/cr3_f6_optimization.xyz" - ) +def test_create_coulomb_matrix(resource_path_root): + xyz_file = resource_path_root / "inputs" / "cr3_f6_optimization.xyz" mol = mol3D() mol.readfromxyz(xyz_file) cm = create_coulomb_matrix(mol) diff --git a/tests/inputs/geocheck/triplebond_linear_broken/opt.xyz b/tests/inputs/geocheck/triplebond_linear_broken/opt.xyz deleted file mode 100644 index 094fe7da..00000000 --- a/tests/inputs/geocheck/triplebond_linear_broken/opt.xyz +++ /dev/null @@ -1,48 +0,0 @@ -46 - -Cd 0.27940 6.13970 16.24340 -O 0.92180 7.25510 20.46480 -O -1.86240 6.98040 16.01340 -H -1.96780 7.62900 15.49890 -H -2.54610 6.51580 16.02940 -N 0.20910 5.36720 13.99150 -N -0.46460 3.95650 16.13730 -N -0.35170 5.51800 18.55470 -N 1.12060 8.19600 16.04450 -N 1.95300 8.55200 16.83540 -N 2.74700 8.92260 17.59560 -N 2.49990 5.29730 16.44810 -N 2.62139 4.32548 16.36395 -N 2.70900 2.94360 16.36490 -C 0.44580 6.12560 12.91640 -H 0.59490 7.05690 13.03630 -C 0.48130 5.60070 11.62540 -H 0.64320 6.16420 10.87820 -C 0.27770 4.25360 11.45720 -H 0.30400 3.87050 10.58880 -C 0.03180 3.45690 12.56820 -H -0.10330 2.52120 12.46970 -C -0.01260 4.04870 13.82660 -C -0.33230 3.26960 15.07090 -C -0.49440 1.78480 15.02270 -H -1.41930 1.54920 15.24570 -H 0.11440 1.36830 15.66770 -H -0.28400 1.46310 14.12140 -C -0.76340 3.32600 17.41560 -H 0.05530 2.91240 17.78670 -H -1.44320 2.61600 17.29230 -C -1.28880 4.38860 18.37170 -H -2.14830 4.73740 18.02480 -H -1.46500 3.97050 19.25160 -C 0.78520 5.08480 19.40860 -H 1.31990 4.40480 18.92600 -H 0.43700 4.67010 20.23720 -C 1.66450 6.25590 19.76490 -H 2.41480 5.94540 20.33060 -H 2.04540 6.64680 18.93810 -C -0.14350 7.73310 19.62620 -H 0.23790 8.13230 18.80550 -H -0.64800 8.43900 20.10460 -C -1.07970 6.60940 19.25250 -H -1.50650 6.25040 20.07140 -H -1.79450 6.95870 18.66380 diff --git a/tests/refs/geocheck/compact_bonding/ref.json b/tests/refs/geocheck/compact_bonding/ref.json deleted file mode 100644 index b1dfa32b..00000000 --- a/tests/refs/geocheck/compact_bonding/ref.json +++ /dev/null @@ -1 +0,0 @@ -{"oct_angle_devi_max": 12.509040337158584, "num_coord_metal": 6, "rmsd_max": -1, "max_del_sig_angle": 24.5649893674979, "dist_del_eq": 0, "devi_linear_max": 0.0, "atom_dist_max": "banned_by_user", "devi_linear_avrg": 0.0, "dist_del_all": 0.8729087434449587} diff --git a/tests/refs/geocheck/triplebond_linear_broken/ref.json b/tests/refs/geocheck/triplebond_linear_broken/ref.json deleted file mode 100644 index dacb6da5..00000000 --- a/tests/refs/geocheck/triplebond_linear_broken/ref.json +++ /dev/null @@ -1 +0,0 @@ -{"oct_angle_devi_max": 16.938430968598304, "num_coord_metal": 6, "rmsd_max": -1, "max_del_sig_angle": 37.4519818068396, "dist_del_eq": 0, "devi_linear_max": 62.79621100845071, "atom_dist_max": "banned_by_user", "devi_linear_avrg": 62.79621100845071, "dist_del_all": 0.24466501276101216} diff --git a/tests/refs/orca_ccsdt.report b/tests/refs/orca_ccsdt.report deleted file mode 100644 index 6e6c41f7..00000000 --- a/tests/refs/orca_ccsdt.report +++ /dev/null @@ -1,26 +0,0 @@ -Bad structure?, False -Min_dist (A), 1000 -Was ANN used?, True -geo_label, 1 -geo_prob, 0.9946129322052002 -geo_LSE, 0.6930601425111972 -geo_label_trust, very low -sc_label, 1 -sc_prob, 0.8634330630302429 -sc_LSE, 0.6931470250647405 -sc_label_trust, very low -split, 47.12842958921388 -split_dist, 18.91462055450386 -This spin, 5 -ANN_ground_state, 1 -homo, -15.494993125140807 -gap, 3.746240116650166 -homo_dist, 0.68992805 -gap_dist, 0.26609284 -ANN_bondl, [2.0098842331388456, 2.0098842331388456, 2.0098842331388456, 2.0098842331388456, 1.9381185776891228, 2.0859009557197328] -homo_trust, high -gap_trust, high -split_trust, very low -Was Catalytic ANN used?, False -Catalytic ANN reason, False -ML-bl (database, A), 1.62 diff --git a/tests/refs/orca_ccsdt.xyz b/tests/refs/orca_ccsdt.xyz deleted file mode 100644 index 49e49df8..00000000 --- a/tests/refs/orca_ccsdt.xyz +++ /dev/null @@ -1,63 +0,0 @@ -61 -02/06/2019 11:09, XYZ structure generated by mol3D Class, molSimplify -Fe 0.000000 0.000000 0.000000 -N -0.710450 0.905404 -0.942135 -C -2.086092 0.653124 -1.098946 -C -2.802413 1.781697 -0.781450 -C -1.872837 2.737795 -0.435990 -C -0.622386 2.158343 -0.552520 -H -0.116353 0.625454 -1.734749 -H -2.507151 -0.290452 -1.420309 -H -3.878665 1.886215 -0.806866 -H -2.070885 3.756987 -0.132677 -H 0.309869 2.668255 -0.351586 -N 3.091620 -2.646483 0.044745 -C 2.320645 -3.526091 0.708713 -C 2.134527 -3.096748 2.006446 -C 2.824190 -1.908414 2.130531 -C 3.402500 -1.658630 0.903315 -H 3.392803 -2.717926 -0.952191 -H 1.913992 -4.429877 0.274465 -H 1.560655 -3.594725 2.776285 -H 2.897089 -1.293143 3.017041 -H 4.015705 -0.803045 0.652473 -N -1.887583 -1.859670 1.175941 -C -3.119868 -2.362594 1.369665 -C -3.288409 -3.493150 0.597455 -C -2.107525 -3.678967 -0.091830 -C -1.265694 -2.654278 0.286712 -H -1.487948 -1.009458 1.629729 -H -3.856858 -1.932885 2.034989 -H -4.173470 -4.112736 0.542749 -H -1.885590 -4.472543 -0.792575 -H -0.256645 -2.498096 -0.068930 -N -3.181000 2.600173 2.667607 -C -2.324879 2.849241 3.674525 -C -2.028750 1.675379 4.335321 -C -2.734109 0.675756 3.698238 -C -3.434012 1.279099 2.674121 -H -3.576004 3.302370 2.003991 -H -1.937618 3.829895 3.917384 -H -1.372462 1.560786 5.186893 -H -2.737465 -0.375453 3.952795 -H -4.091380 0.780875 1.973868 -N 1.622876 1.431753 3.894954 -C 2.862443 1.953048 3.865710 -C 3.281754 2.085788 2.558545 -C 2.251046 1.625257 1.766302 -C 1.242300 1.230238 2.620626 -H 1.062017 1.222117 4.749491 -H 3.431885 2.221798 4.745590 -H 4.232929 2.474260 2.220314 -H 2.240260 1.582105 0.686917 -H 0.286199 0.817350 2.328196 -N 2.863843 -0.907697 -4.361222 -C 4.008098 -0.259645 -4.077501 -C 3.948790 0.253401 -2.798174 -C 2.716289 -0.100128 -2.289852 -C 2.072198 -0.815629 -3.277572 -H 2.633034 -1.392491 -5.256495 -H 4.840804 -0.164529 -4.761934 -H 4.717754 0.821569 -2.292262 -H 2.330956 0.135947 -1.308416 -H 1.081149 -1.244338 -3.207618 diff --git a/tests/refs/orca_dft.report b/tests/refs/orca_dft.report deleted file mode 100644 index 6e6c41f7..00000000 --- a/tests/refs/orca_dft.report +++ /dev/null @@ -1,26 +0,0 @@ -Bad structure?, False -Min_dist (A), 1000 -Was ANN used?, True -geo_label, 1 -geo_prob, 0.9946129322052002 -geo_LSE, 0.6930601425111972 -geo_label_trust, very low -sc_label, 1 -sc_prob, 0.8634330630302429 -sc_LSE, 0.6931470250647405 -sc_label_trust, very low -split, 47.12842958921388 -split_dist, 18.91462055450386 -This spin, 5 -ANN_ground_state, 1 -homo, -15.494993125140807 -gap, 3.746240116650166 -homo_dist, 0.68992805 -gap_dist, 0.26609284 -ANN_bondl, [2.0098842331388456, 2.0098842331388456, 2.0098842331388456, 2.0098842331388456, 1.9381185776891228, 2.0859009557197328] -homo_trust, high -gap_trust, high -split_trust, very low -Was Catalytic ANN used?, False -Catalytic ANN reason, False -ML-bl (database, A), 1.62 diff --git a/tests/refs/orca_dft.xyz b/tests/refs/orca_dft.xyz deleted file mode 100644 index 3c32a3b8..00000000 --- a/tests/refs/orca_dft.xyz +++ /dev/null @@ -1,63 +0,0 @@ -61 -02/06/2019 11:10, XYZ structure generated by mol3D Class, molSimplify -Fe 0.000000 0.000000 0.000000 -N -1.166850 0.976802 0.078706 -C -2.279176 0.556391 0.830527 -C -2.640263 1.527559 1.741466 -C -1.767410 2.587562 1.589974 -C -0.879099 2.256808 0.587144 -H -1.311705 0.950855 -0.939575 -H -2.777147 -0.395159 0.706385 -H -3.461297 1.459568 2.442347 -H -1.769717 3.513190 2.149537 -H -0.072764 2.887235 0.238150 -N 2.629963 -2.079560 1.178543 -C 2.383949 -3.388724 0.992782 -C 2.264234 -3.654026 -0.355964 -C 2.445005 -2.453179 -1.011083 -C 2.669209 -1.503663 -0.036305 -H 2.765764 -1.599987 2.095632 -H 2.295496 -4.111857 1.792657 -H 2.066063 -4.615145 -0.810833 -H 2.417002 -2.288617 -2.079864 -H 2.851262 -0.452372 -0.206404 -N -1.037819 -2.284226 2.153239 -C -2.117730 -2.620046 2.881638 -C -2.964290 -3.404612 2.125768 -C -2.369717 -3.546922 0.888731 -C -1.184540 -2.843468 0.938612 -H -0.236072 -1.696596 2.470875 -H -2.282879 -2.311959 3.905679 -H -3.909757 -3.825482 2.440845 -H -2.757499 -4.100746 0.044403 -H -0.472207 -2.744809 0.131599 -N -3.507195 0.722915 -2.689851 -C -2.821064 1.088934 -3.787421 -C -2.139128 0.002536 -4.294829 -C -2.425558 -1.063911 -3.467309 -C -3.272107 -0.586392 -2.488555 -H -4.109154 1.340913 -2.102093 -H -2.814753 2.090323 -4.197332 -H -1.502882 -0.010347 -5.169595 -H -2.058155 -2.076390 -3.566624 -H -3.690871 -1.163197 -1.674590 -N 2.294343 1.350732 3.793928 -C 3.387181 2.108941 3.592255 -C 3.503870 2.411816 2.251377 -C 2.436133 1.811021 1.618288 -C 1.710020 1.164919 2.597158 -H 1.961306 0.975967 4.709544 -H 4.062975 2.425133 4.375793 -H 4.280335 3.004531 1.786740 -H 2.212809 1.841008 0.561097 -H 0.806181 0.591504 2.443324 -N 2.477258 1.054750 -2.650100 -C 2.818083 2.319407 -2.344294 -C 1.694421 3.119410 -2.349712 -C 0.631115 2.302186 -2.673074 -C 1.147395 1.035081 -2.849768 -H 3.125194 0.239383 -2.718923 -H 3.827469 2.643659 -2.128553 -H 1.654410 4.180019 -2.141080 -H -0.404814 2.598360 -2.766745 -H 0.583817 0.149154 -3.109559 diff --git a/tests/refs/tetrahedral_1_noff.xyz b/tests/refs/tetrahedral_1_noff.xyz deleted file mode 100644 index 3cb57c9a..00000000 --- a/tests/refs/tetrahedral_1_noff.xyz +++ /dev/null @@ -1,15 +0,0 @@ -13 -10/26/2021 11:00, XYZ structure generated by mol3D Class, molSimplify -Fe 0.000000 0.000000 0.000000 -O -1.499066 1.499066 0.000000 -H -1.407541 2.447839 0.271333 -H -2.448453 1.415651 -0.271987 -O -1.499066 -1.499066 0.000000 -H -2.454076 -1.404888 0.247799 -H -1.406383 -2.454187 -0.247714 -O 1.499066 -1.499066 0.000000 -H 1.404994 -2.460620 0.221014 -H 2.459452 -1.394042 -0.221545 -O 1.499066 1.499066 0.000000 -H 1.650381 2.208810 0.674966 -H 2.208802 1.650476 -0.674918 diff --git a/tests/refs/tutorial_09_part_two.xyz b/tests/refs/tutorial_09_part_two.xyz deleted file mode 100644 index c1b6db63..00000000 --- a/tests/refs/tutorial_09_part_two.xyz +++ /dev/null @@ -1,27 +0,0 @@ -25 -08/10/2020 15:20, XYZ structure generated by mol3D Class, molSimplify -Zn -0.195653 0.009149 0.718395 -C 1.999458 0.703422 -0.072814 -C 2.009450 -0.747350 0.249742 -N 0.598980 -1.130704 0.168765 -N 0.777323 1.182827 0.567976 -H 1.908856 0.802519 -1.177335 -H 2.925443 1.229220 0.254221 -H 2.383933 -0.864488 1.282913 -H 2.703601 -1.325005 -0.417613 -H 0.512477 -2.016676 0.725321 -H 0.357850 -1.282602 -0.836877 -H 0.557452 2.035046 0.010565 -H 1.034243 1.618804 1.473307 -O 1.346503 0.222830 3.175583 -O -0.459095 0.099682 4.432868 -O -0.624669 -0.106588 2.053102 -C 0.128715 0.072808 3.215538 -H 0.064650 0.264819 5.242708 -N -1.459486 1.244963 -0.339476 -H -2.477855 1.022098 -0.263305 -H -1.490858 2.263016 -0.091141 -H -1.258170 1.212566 -1.367233 -O -1.745904 -1.266647 0.356920 -H -1.787800 -2.214173 0.651083 -H -2.606546 -1.168790 -0.125007 diff --git a/tests/runtest.py b/tests/runtest.py index 5032cc0c..982533d0 100644 --- a/tests/runtest.py +++ b/tests/runtest.py @@ -1,11 +1,10 @@ from molSimplify.Scripts.generator import startgen -from pkg_resources import resource_filename, Requirement -infile = resource_filename(Requirement.parse( - "molSimplify"), "tests/inputs/example_1_noff.in") -args = ['main.py', '-i', infile] -startgen(args, False, False) -infile = resource_filename(Requirement.parse( - "molSimplify"), "tests/inputs/example_1.in") -args = ['main.py', '-i', infile] -startgen(args, False, False) + +def runtest(resource_path_root): + infile = resource_path_root / "inputs" / "example_1_noff.in" + args = ['main.py', '-i', infile] + startgen(args, False, False) + infile = resource_path_root / "inputs" / "example_1.in" + args = ['main.py', '-i', infile] + startgen(args, False, False) diff --git a/tests/test_bidentate.py b/tests/test_bidentate.py index 2da281d8..42dc4359 100644 --- a/tests/test_bidentate.py +++ b/tests/test_bidentate.py @@ -1,7 +1,7 @@ import helperFuncs as hp -def test_bidentate(tmpdir): +def test_bidentate(tmpdir, resource_path_root): # There are two versions of this test depending on the openbabel version. # This is necessary because openbabel changed the numbering of atoms for v3. try: @@ -14,7 +14,7 @@ def test_bidentate(tmpdir): threshLG = 1.0 threshOG = 1.5 [passMultiFileCheck, pass_structures] = hp.runtestMulti( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passMultiFileCheck for f, passNumAtoms, passMLBL, passLG, passOG, pass_report in pass_structures: print(f) diff --git a/tests/test_example_1.py b/tests/test_example_1.py index ec7629e5..cd5023ec 100644 --- a/tests/test_example_1.py +++ b/tests/test_example_1.py @@ -1,28 +1,28 @@ import helperFuncs as hp -def test_example_1(tmpdir): +def test_example_1(tmpdir, resource_path_root): testName = "example_1" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG assert passOG assert pass_report - assert hp.runtest_reportonly(tmpdir, testName) + assert hp.runtest_reportonly(tmpdir, resource_path_root, testName) -def test_example_1_No_FF(tmpdir): +def test_example_1_No_FF(tmpdir, resource_path_root): testName = "example_1" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtestNoFF( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passMLBL assert passLG assert passOG diff --git a/tests/test_example_3.py b/tests/test_example_3.py index 04706b2e..86c67d1f 100644 --- a/tests/test_example_3.py +++ b/tests/test_example_3.py @@ -1,13 +1,16 @@ +import pytest import helperFuncs as hp -def test_example_3(tmpdir): +@pytest.mark.skip("Skipping example 3 + FF as it is unclear to me if the core " + "should be frozen during the final optimization. RM") +def test_example_3(tmpdir, resource_path_root): testName = "example_3" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG @@ -15,13 +18,13 @@ def test_example_3(tmpdir): assert pass_report, pass_qcin -def test_example_3_No_FF(tmpdir): +def test_example_3_No_FF(tmpdir, resource_path_root): testName = "example_3" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtestNoFF( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passMLBL assert passLG assert passOG diff --git a/tests/test_example_5.py b/tests/test_example_5.py index 57cc541e..9db5e10f 100644 --- a/tests/test_example_5.py +++ b/tests/test_example_5.py @@ -1,7 +1,7 @@ import helperFuncs as hp -def test_example_5(tmpdir): +def test_example_5(tmpdir, resource_path_root): # There are two versions of this test depending on the openbabel version. # This is necessary because openbabel changed the numbering of atoms for v3. try: @@ -14,7 +14,7 @@ def test_example_5(tmpdir): threshLG = 0.5 threshOG = 1.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG @@ -22,7 +22,7 @@ def test_example_5(tmpdir): assert pass_report, pass_qcin -def test_example_5_No_FF(tmpdir): +def test_example_5_No_FF(tmpdir, resource_path_root): # There are two versions of this test depending on the openbabel version. # This is necessary because openbabel changed the numbering of atoms for v3. try: @@ -35,7 +35,7 @@ def test_example_5_No_FF(tmpdir): threshLG = 0.5 threshOG = 1.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtestNoFF( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_example_7.py b/tests/test_example_7.py index cf3092bf..24cc6c66 100644 --- a/tests/test_example_7.py +++ b/tests/test_example_7.py @@ -1,13 +1,13 @@ import helperFuncs as hp -def test_example_7(tmpdir): +def test_example_7(tmpdir, resource_path_root): testName = "example_7" threshMLBL = 0.1 threshLG = 1.0 threshOG = 3.0 # Increased threshold from 2.0 to 3.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG @@ -15,13 +15,13 @@ def test_example_7(tmpdir): assert pass_report, pass_qcin -def test_example_7_No_FF(tmpdir): +def test_example_7_No_FF(tmpdir, resource_path_root): testName = "example_7" threshMLBL = 0.1 threshLG = 1.1 threshOG = 3.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtestNoFF( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passMLBL assert passLG assert passOG diff --git a/tests/test_example_8.py b/tests/test_example_8.py index 342995d6..7a3f22e2 100644 --- a/tests/test_example_8.py +++ b/tests/test_example_8.py @@ -1,13 +1,13 @@ import helperFuncs as hp -def test_example_8(tmpdir): +def test_example_8(tmpdir, resource_path_root): testName = "example_8" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_example_tbp.py b/tests/test_example_tbp.py index 7660277d..71ca729f 100644 --- a/tests/test_example_tbp.py +++ b/tests/test_example_tbp.py @@ -1,13 +1,13 @@ import helperFuncs as hp -def test_example_tbp(tmpdir): +def test_example_tbp(tmpdir, resource_path_root): testName = "example_tbp" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_ff_xtb.py b/tests/test_ff_xtb.py index 8eb57fbd..daee3148 100644 --- a/tests/test_ff_xtb.py +++ b/tests/test_ff_xtb.py @@ -9,14 +9,14 @@ @xtb_installed -def test_xtb_before(tmpdir): +def test_xtb_before(tmpdir, resource_path_root): testName = "xtb_H2O_before" threshMLBL = 0.01 threshLG = 0.01 threshOG = 2.0 (passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin) = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG, seed=31415) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG, seed=31415) assert passNumAtoms assert passMLBL assert passLG @@ -27,14 +27,14 @@ def test_xtb_before(tmpdir): @pytest.mark.skip(reason="TODO: figure out why this test started failing suddenly") @xtb_installed -def test_xtb_before_after(tmpdir): +def test_xtb_before_after(tmpdir, resource_path_root): testName = "xtb_imidazole_BA" threshMLBL = 0.01 threshLG = 0.01 threshOG = 0.05 (passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin) = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG, seed=31415) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG, seed=31415) assert passNumAtoms assert passMLBL assert passLG @@ -44,14 +44,14 @@ def test_xtb_before_after(tmpdir): @xtb_installed -def test_xtb_ANC_fail(tmpdir): +def test_xtb_ANC_fail(tmpdir, resource_path_root): testName = "xtb_ANC_fail" threshMLBL = 0.01 threshLG = 0.01 threshOG = 0.01 (passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin) = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG, seed=31415) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG, seed=31415) assert passNumAtoms assert passMLBL assert passLG @@ -61,14 +61,14 @@ def test_xtb_ANC_fail(tmpdir): @xtb_installed -def test_xtb_high_spin(tmpdir): +def test_xtb_high_spin(tmpdir, resource_path_root): testName = "xtb_bipy_spin5" threshMLBL = 0.01 threshLG = 0.05 threshOG = 0.5 (passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin) = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG, seed=31415) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG, seed=31415) assert passNumAtoms assert passMLBL assert passLG @@ -78,14 +78,14 @@ def test_xtb_high_spin(tmpdir): @xtb_installed -def test_xtb_final_opt(tmpdir): +def test_xtb_final_opt(tmpdir, resource_path_root): testName = "xtb_final_opt" threshMLBL = 0.01 threshLG = 0.01 threshOG = 0.05 (passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin) = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG, seed=31415) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG, seed=31415) assert passNumAtoms assert passMLBL assert passLG @@ -95,14 +95,14 @@ def test_xtb_final_opt(tmpdir): @xtb_installed -def test_gfnff(tmpdir): +def test_gfnff(tmpdir, resource_path_root): testName = "gfnff_NH3_BA" threshMLBL = 0.01 threshLG = 0.01 threshOG = 2.0 (passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin) = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG, seed=31415) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG, seed=31415) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_geocheck_oct.py b/tests/test_geocheck_oct.py index ce0abec2..0ad25e17 100644 --- a/tests/test_geocheck_oct.py +++ b/tests/test_geocheck_oct.py @@ -1,113 +1,26 @@ +import pytest import helperFuncs as hp -def test_example_1(tmpdir): - testName = "all_flying_away" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_2(tmpdir): - testName = "broken_ligands" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_3(tmpdir): - testName = "catom_change" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_4(tmpdir): - testName = "H_transfer" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_5(tmpdir): - testName = "ligand_assemble" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_6(tmpdir): - testName = "ligand_bent" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_7(tmpdir): - testName = "linear_broken" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_8(tmpdir): - testName = "methane_trans" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_9(tmpdir): - testName = "rotational_group" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_10(tmpdir): - testName = "switch_test" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh, deleteH=False) - assert passGeo - - -def test_example_11(tmpdir): - testName = "compact_bonding" - thresh = 0.01 - passGeo = hp.runtestgeo_optonly(tmpdir, testName, thresh) - assert passGeo - - -def test_example_12(tmpdir): - testName = "triplebond_linear_broken" - thresh = 0.01 - passGeo = hp.runtestgeo_optonly(tmpdir, testName, thresh) - assert passGeo - - -def test_example_13(tmpdir): - testName = "iodine_sulfur" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_14(tmpdir): - testName = "oct_comp_greedy" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_15(tmpdir): - testName = "atom_ordering_mismatch" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) - assert passGeo - - -def test_example_16(tmpdir): - testName = "iodide_radius" - thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh) +@pytest.mark.parametrize("testName", [ + "all_flying_away", + "broken_ligands", + "catom_change", + "H_transfer", + "ligand_assemble", + "ligand_bent", + "linear_broken", + "methane_trans", + "rotational_group", + "switch_test", + "compact_bonding", + "triplebond_linear_broken", + "iodine_sulfur", + "oct_comp_greedy", + "atom_ordering_mismatch", + "iodide_radius" +]) +def test_geocheck_oct(tmpdir, resource_path_root, testName): + thresh = 0.01 + passGeo = hp.runtestgeo(tmpdir, resource_path_root, testName, thresh) assert passGeo diff --git a/tests/test_geocheck_one_empty.py b/tests/test_geocheck_one_empty.py index 8ed604bf..81621cab 100644 --- a/tests/test_geocheck_one_empty.py +++ b/tests/test_geocheck_one_empty.py @@ -1,15 +1,15 @@ import helperFuncs as hp -def test_example_1(tmpdir): +def test_example_1(tmpdir, resource_path_root): testName = "one_empty_good" thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh, geo_type="one_empty") + passGeo = hp.runtestgeo(tmpdir, resource_path_root, testName, thresh, geo_type="one_empty") assert passGeo -def test_example_2(tmpdir): +def test_example_2(tmpdir, resource_path_root): testName = "one_empty_bad" thresh = 0.01 - passGeo = hp.runtestgeo(tmpdir, testName, thresh, geo_type="one_empty") + passGeo = hp.runtestgeo(tmpdir, resource_path_root, testName, thresh, geo_type="one_empty") assert passGeo diff --git a/tests/test_inparse.py b/tests/test_inparse.py index 7a4c9166..d3c29bb1 100644 --- a/tests/test_inparse.py +++ b/tests/test_inparse.py @@ -4,7 +4,6 @@ parseinputs_basic, parseinputs_advanced) from argparse import ArgumentParser, Namespace -from pkg_resources import resource_filename, Requirement def test_parseinputfile_empty(): @@ -59,11 +58,10 @@ def test_checkinput(monkeypatch): assert args.spin == '5' -def test_parseinputfile_inputfile_kwarg(): +def test_parseinputfile_inputfile_kwarg(resource_path_root): """Test that both methods of calling parseinputfile (with an args.i file or inputfile_str kwarg) yield the same result""" - infile = resource_filename(Requirement.parse( - "molSimplify"), "tests/inputs/example_1.in") + infile = resource_path_root / "inputs" / "example_1.in" args1 = Namespace(i=infile) parseinputfile(args1) diff --git a/tests/test_io.py b/tests/test_io.py index 1151f979..0ab41b46 100644 --- a/tests/test_io.py +++ b/tests/test_io.py @@ -1,12 +1,9 @@ import numpy as np from molSimplify.Scripts.io import lig_load -from pkg_resources import resource_filename, Requirement -def test_lig_load(): - lig_file = resource_filename( - Requirement.parse('molSimplify'), - 'tests/inputs/io/acac.mol2') +def test_lig_load(resource_path_root): + lig_file = str(resource_path_root / "inputs" / "io" / "acac.mol2") mol, emsg = lig_load(lig_file) # Assert that the error message is empty assert not emsg diff --git a/tests/test_joption_pythonic.py b/tests/test_joption_pythonic.py index 5b8b3b05..a9588284 100644 --- a/tests/test_joption_pythonic.py +++ b/tests/test_joption_pythonic.py @@ -1,9 +1,7 @@ - -from helperFuncs import jobname from molSimplify.Scripts.generator import startgen_pythonic -def test_joption_pythonic(tmpdir): +def test_joption_pythonic(tmpdir, resource_path_root): out_dir = "cr_thd_2_cl_4_s_1/cr_thd_2_cl_4_s_1_conf_1/jobscript" input_dict_homo = { '-core': "cr", @@ -23,9 +21,7 @@ def test_joption_pythonic(tmpdir): startgen_pythonic(input_dict_homo, write=1) with open(str(tmpdir) + "/" + out_dir, 'r') as f_in: data1 = f_in.readlines() - with open("tests/refs/joption_pythonic_jobscript", 'r') as f_in: + with open(resource_path_root / "refs" / "joption_pythonic_jobscript", 'r') as f_in: data2 = f_in.readlines() for i, j in zip(data1, data2): assert i == j - -#test_joption_pythonic("../Runs") diff --git a/tests/test_ligand_assign_consistent.py b/tests/test_ligand_assign_consistent.py index 8e3713e7..413e595f 100644 --- a/tests/test_ligand_assign_consistent.py +++ b/tests/test_ligand_assign_consistent.py @@ -1,14 +1,10 @@ from molSimplify.Classes.ligand import ligand_assign_consistent, ligand_breakdown from molSimplify.Classes.mol3D import mol3D -from pkg_resources import resource_filename, Requirement -def test_six_monodentate(): - xyz_file = resource_filename( - Requirement.parse("molSimplify"), - "tests/inputs/ligand_assign_consistent/" - "fe_water_ammonia_carbonyl_formaldehyde_hydrogensulfide_hydrocyanide.xyz" - ) +def test_six_monodentate(resource_path_root): + xyz_file = (resource_path_root / "inputs" / "ligand_assign_consistent" + / "fe_water_ammonia_carbonyl_formaldehyde_hydrogensulfide_hydrocyanide.xyz") mol = mol3D() mol.readfromxyz(xyz_file) @@ -36,11 +32,9 @@ def test_six_monodentate(): assert eq_con_list == [[14], [4], [18], [11]] -def test_triple_bidentate(): - xyz_file = resource_filename( - Requirement.parse("molSimplify"), - "tests/inputs/ligand_assign_consistent/fe_acac_bipy_bipy.xyz" - ) +def test_triple_bidentate(resource_path_root): + xyz_file = (resource_path_root / "inputs" / "ligand_assign_consistent" + / "fe_acac_bipy_bipy.xyz") mol = mol3D() mol.readfromxyz(xyz_file) diff --git a/tests/test_ligand_from_mol_file.py b/tests/test_ligand_from_mol_file.py index ada65713..78879af0 100644 --- a/tests/test_ligand_from_mol_file.py +++ b/tests/test_ligand_from_mol_file.py @@ -1,23 +1,18 @@ import pytest from molSimplify.Scripts.generator import startgen from helperFuncs import working_directory, compareGeo, compare_report_new -from pkg_resources import resource_filename, Requirement import shutil @pytest.mark.skip("Loading multidentate ligands from files is currently not supported") -def test_ligand_from_mol_file(tmpdir): - input_file = resource_filename(Requirement.parse( - "molSimplify"), "tests/inputs/ligand_from_mol_file.in") +def test_ligand_from_mol_file(tmpdir, resource_path_root): + input_file = resource_path_root / "inputs" / "ligand_from_mol_file.in" shutil.copyfile(input_file, tmpdir / "ligand_from_mol_file.in") - mol_file = resource_filename(Requirement.parse( - "molSimplify"), "tests/inputs/pdp.mol") + mol_file = resource_path_root / "inputs" / "pdp.mol" shutil.copyfile(mol_file, tmpdir / "pdp.mol") - ref_xyz = resource_filename(Requirement.parse( - "molSimplify"), "tests/refs/ligand_from_mol_file.xyz") - ref_report = resource_filename(Requirement.parse( - "molSimplify"), "tests/refs/ligand_from_mol_file.report") + ref_xyz = resource_path_root / "refs" / "ligand_from_mol_file.xyz" + ref_report = resource_path_root / "refs" / "ligand_from_mol_file.report" threshMLBL = 0.1 threshLG = 0.1 diff --git a/tests/test_ligands.py b/tests/test_ligands.py index f261fcb5..5cdf8234 100644 --- a/tests/test_ligands.py +++ b/tests/test_ligands.py @@ -1,17 +1,13 @@ import pytest from molSimplify.Classes.mol3D import mol3D from molSimplify.Scripts.io import readdict, lig_load -from pkg_resources import resource_filename, Requirement +from importlib_resources import files as resource_files from os import listdir from os.path import isfile, join -path_folder = resource_filename( - Requirement.parse("molSimplify"), "molSimplify/Ligands/" -) -path_dict = resource_filename( - Requirement.parse("molSimplify"), "molSimplify/Ligands/ligands.dict" -) +path_folder = resource_files("molSimplify").joinpath("Ligands") +path_dict = resource_files("molSimplify").joinpath("Ligands/ligands.dict") lig_dict = readdict(path_dict) @@ -21,7 +17,7 @@ def test_ligands_dict(lig_name): assert len(lig_dict[lig_name]) == 6 lig, emsg = lig_load(lig_name) # Assert that the ligand could be loaded - assert type(lig) == mol3D + assert type(lig) is mol3D assert emsg == '' # Assert that the charge of the loaded ligand equals the # charge noted in ligands.dict @@ -55,6 +51,7 @@ def test_ligands_dict(lig_name): # charge listed in ligands.dict assert sum([int(s) for s in sp[4::2]]) == charge + def test_no_repeats(): # This test ensures no key is used more than once in ligands.dict. listed_keys = [] diff --git a/tests/test_mol3D.py b/tests/test_mol3D.py index e074567c..32d98de8 100644 --- a/tests/test_mol3D.py +++ b/tests/test_mol3D.py @@ -2,7 +2,6 @@ import numpy as np from molSimplify.Classes.mol3D import mol3D from molSimplify.Classes.atom3D import atom3D -from pkg_resources import resource_filename, Requirement def test_adding_and_deleting_atoms(): @@ -122,11 +121,8 @@ def test_mutating_atoms(): ('trigonal_prismatic', 6, 'trigonal prismatic'), # ('pentagonal_bipyramidal', 7, 'pentagonal bipyramidal') ]) -def test_get_geometry_type(name, coordination_number, geometry_str): - xyz_file = resource_filename( - Requirement.parse("molSimplify"), - f"tests/inputs/geometry_type/{name}.xyz" - ) +def test_get_geometry_type(resource_path_root, name, coordination_number, geometry_str): + xyz_file = resource_path_root / "inputs" / "geometry_type" / f"{name}.xyz" mol = mol3D() mol.readfromxyz(xyz_file) @@ -137,11 +133,8 @@ def test_get_geometry_type(name, coordination_number, geometry_str): assert geo_report['aromatic'] is False -def test_get_geometry_type_catoms_arr(): - xyz_file = resource_filename( - Requirement.parse("molSimplify"), - "tests/inputs/geometry_type/octahedral.xyz" - ) +def test_get_geometry_type_catoms_arr(resource_path_root): + xyz_file = resource_path_root / "inputs" / "geometry_type" / "octahedral.xyz" mol = mol3D() mol.readfromxyz(xyz_file) @@ -155,11 +148,8 @@ def test_get_geometry_type_catoms_arr(): assert geo_report['aromatic'] is False -def test_readfromxyzfile(): - xyz_file = resource_filename( - Requirement.parse("molSimplify"), - "tests/inputs/cr3_f6_optimization.xyz" - ) +def test_readfromxyzfile(resource_path_root): + xyz_file = resource_path_root / "inputs" / "cr3_f6_optimization.xyz" mol = mol3D() mol.readfromxyz(xyz_file) diff --git a/tests/test_molcas_caspt2.py b/tests/test_molcas_caspt2.py index 72b910d1..d63557e7 100644 --- a/tests/test_molcas_caspt2.py +++ b/tests/test_molcas_caspt2.py @@ -1,13 +1,13 @@ import helperFuncs as hp -def test_molcas_caspt2(tmpdir): +def test_molcas_caspt2(tmpdir, resource_path_root): testName = "molcas_caspt2" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_molcas_casscf.py b/tests/test_molcas_casscf.py index e4401df9..ac43f26e 100644 --- a/tests/test_molcas_casscf.py +++ b/tests/test_molcas_casscf.py @@ -1,13 +1,13 @@ import helperFuncs as hp -def test_molcas_casscf(tmpdir): +def test_molcas_casscf(tmpdir, resource_path_root): testName = "molcas_casscf" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_old_ANNs.py b/tests/test_old_ANNs.py index 724c15ff..93455b0a 100644 --- a/tests/test_old_ANNs.py +++ b/tests/test_old_ANNs.py @@ -3,13 +3,13 @@ from molSimplify.python_nn.ANN import simple_network_builder -def test_old_ANN(tmpdir): +def test_old_ANN(tmpdir, resource_path_root): testName = "old_ANN" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, _] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_orca_ccsdt.py b/tests/test_orca_ccsdt.py index afebba29..d3bd8500 100644 --- a/tests/test_orca_ccsdt.py +++ b/tests/test_orca_ccsdt.py @@ -1,13 +1,13 @@ import helperFuncs as hp -def test_orca_ccsdt(tmpdir): +def test_orca_ccsdt(tmpdir, resource_path_root): testName = "orca_ccsdt" threshMLBL = 0.1 threshLG = 1.0 threshOG = 8.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_orca_dft.py b/tests/test_orca_dft.py index f3ef40ce..35ce4b4f 100644 --- a/tests/test_orca_dft.py +++ b/tests/test_orca_dft.py @@ -1,13 +1,13 @@ import helperFuncs as hp -def test_orca_dft(tmpdir): +def test_orca_dft(tmpdir, resource_path_root): testName = "orca_dft" threshMLBL = 0.1 threshLG = 1.0 threshOG = 8.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_qcgen.py b/tests/test_qcgen.py index afe457ba..69da5eee 100644 --- a/tests/test_qcgen.py +++ b/tests/test_qcgen.py @@ -1,7 +1,6 @@ import pytest import shutil from argparse import Namespace -from pkg_resources import resource_filename, Requirement from molSimplify.Scripts.qcgen import (tcgen, gamgen, qgen, mlpgen, ogen, molcgen) @@ -10,7 +9,7 @@ [(tcgen, 'terachem_input'), (gamgen, 'gam.inp'), (qgen, 'qch.inp'), (mlpgen, 'FeH2O6.mop'), (ogen, 'orca.in'), (molcgen, 'molcas.input')]) -def test_qcgen_defaults(gen_function, default_name, tmpdir): +def test_qcgen_defaults(resource_path_root, gen_function, default_name, tmpdir): """Calls the gen_function with as little parameters as possible to test the default input file generated.""" args = Namespace(jobdir=str(tmpdir), reportonly=None, spin=None, @@ -20,23 +19,21 @@ def test_qcgen_defaults(gen_function, default_name, tmpdir): correlation=None, unrestricted=None, bsep=None, ngauss=None, ndfunc=None, npfunc=None, sysoption=None, ctrloption=None, scfoption=None, statoption=None) - xyzfile = resource_filename(Requirement.parse( - 'molSimplify'), 'tests/inputs/qcgen/FeH2O6.xyz') + xyzfile = resource_path_root / "inputs" / "qcgen" / "FeH2O6.xyz" # Copy xyz file to tmpdir shutil.copy(xyzfile, tmpdir / 'FeH2O6.xyz') jobdirs = gen_function(args, [str(tmpdir / 'FeH2O6')], 'B3LYP') sub_dir = tmpdir - ref_dir = f'tests/refs/qcgen/{gen_function.__name__}' + ref_dir = resource_path_root / "refs" / "qcgen" / f"{gen_function.__name__}" # These two generate a different subfolder structure... if gen_function is gamgen or gen_function is qgen: sub_dir = tmpdir / 'FeH2O6/B3LYP' ref_dir = f'{ref_dir}/FeH2O6/B3LYP' assert jobdirs[0] == sub_dir - ref_file = resource_filename(Requirement.parse( - 'molSimplify'), f'{ref_dir}/{default_name}') + ref_file = resource_path_root / ref_dir / default_name with open(ref_file, 'r') as f: ref_lines = f.readlines() diff --git a/tests/test_racs.py b/tests/test_racs.py index 29232c07..531c3c3c 100644 --- a/tests/test_racs.py +++ b/tests/test_racs.py @@ -5,7 +5,6 @@ from molSimplify.Informatics.RACassemble import create_OHE from molSimplify.Informatics.lacRACAssemble import get_descriptor_vector from molSimplify.Scripts.io import lig_load -from pkg_resources import resource_filename, Requirement @pytest.mark.parametrize('xyz_path, ref_path', [ @@ -16,17 +15,13 @@ 'racs_Cr_acac_acac_bipy.pickle'), ('co_acac_en_water_hydrogensulfide.xyz', 'racs_Co_acac_en_water_hydrogensulfide.pickle')]) -def test_Mn_water2_ammonia_furan2_ammonia(xyz_path, ref_path): - xyz_path = resource_filename( - Requirement.parse('molSimplify'), - f'tests/refs/racs/{xyz_path}') +def test_Mn_water2_ammonia_furan2_ammonia(resource_path_root, xyz_path, ref_path): + xyz_path = resource_path_root / "refs" / "racs" / xyz_path mol = mol3D() mol.readfromxyz(xyz_path) features = mol.get_features() - ref_path = resource_filename( - Requirement.parse('molSimplify'), - f'tests/refs/racs/{ref_path}') + ref_path = resource_path_root / "refs" / "racs" / ref_path with open(ref_path, 'rb') as fin: ref_features = pickle.load(fin) @@ -35,15 +30,11 @@ def test_Mn_water2_ammonia_furan2_ammonia(xyz_path, ref_path): assert abs(val - ref_features[key]) < 1e-4 -def test_six_pyridine_vs_three_bipy(): +def test_six_pyridine_vs_three_bipy(resource_path_root): """Up to depth 2 the atom centered racs features for pyr_6 and bipy_3 should be the same""" - fe_pyr_6_path = resource_filename( - Requirement.parse('molSimplify'), - 'tests/refs/racs/fe_pyr_6.xyz') - fe_bipy_3_path = resource_filename( - Requirement.parse('molSimplify'), - 'tests/refs/racs/fe_bipy_3.xyz') + fe_pyr_6_path = resource_path_root / "refs" / "racs" / "fe_pyr_6.xyz" + fe_bipy_3_path = resource_path_root / "refs" / "racs" / "fe_bipy_3.xyz" fe_pyr_6 = mol3D() fe_pyr_6.readfromxyz(fe_pyr_6_path) fe_bipy_3 = mol3D() @@ -65,13 +56,9 @@ def test_six_pyridine_vs_three_bipy(): @pytest.mark.skip('Test fails because molSimplify averages the equatorial ' 'plane differently for bidentates') -def test_pyr_4_furan_2_vs_bipy_2_bifuran(): - fe_pyr_4_furan_2_path = resource_filename( - Requirement.parse('molSimplify'), - 'tests/refs/racs/fe_pyr_4_furan_2.xyz') - fe_bipy_2_bifuran_path = resource_filename( - Requirement.parse('molSimplify'), - 'tests/refs/racs/fe_bipy_2_bifuran.xyz') +def test_pyr_4_furan_2_vs_bipy_2_bifuran(resource_path_root): + fe_pyr_4_furan_2_path = resource_path_root / "refs" / "racs" / "fe_pyr_4_furan_2.xyz" + fe_bipy_2_bifuran_path = resource_path_root / "refs" / "racs" / "fe_bipy_2_bifuran.xyz" fe_pyr_4_furan_2 = mol3D() fe_pyr_4_furan_2.readfromxyz(fe_pyr_4_furan_2_path) fe_bipy_2_bifuran = mol3D() diff --git a/tests/test_rmsd.py b/tests/test_rmsd.py index c0f67958..bba5bd5e 100644 --- a/tests/test_rmsd.py +++ b/tests/test_rmsd.py @@ -1,31 +1,24 @@ import pytest from molSimplify.Classes.mol3D import mol3D from molSimplify.Scripts.rmsd import rigorous_rmsd -from pkg_resources import resource_filename, Requirement @pytest.mark.parametrize( 'path1,path2,ref_hungarian,ref_none', - [['example_1_noff.xyz', 'example_1.xyz', 0.3991, 0.7749], + [['example_1_noff', 'example_1', 0.3991, 0.7749], ['BUWGOQ', 'BUWGOQ_final', 2.43958, 0.49113], ['BUWGOQ_noH', 'BUWGOQ_noH_final', 1.74814, 0.11826], ['BUWGOQ', 'BUWGOQ_final_reordered', 2.43958, 3.02598]] ) -def test_rigorous_rmsd(path1, path2, ref_hungarian, ref_none, atol=1e-3): +def test_rigorous_rmsd(resource_path_root, path1, path2, ref_hungarian, ref_none, atol=1e-3): # Reference values calculated using https://pypi.org/project/rmsd/ # >>> calculate_rmsd --reorder path1.xyz path2.xyz # >>> calculate_rmsd path1.xyz path2.xyz - xyz_1 = resource_filename( - Requirement.parse("molSimplify"), - f"tests/inputs/rmsd/{path1}.xyz" - ) + xyz_1 = resource_path_root / "inputs" / "rmsd" / f"{path1}.xyz" mol1 = mol3D() mol1.readfromxyz(xyz_1) - xyz_2 = resource_filename( - Requirement.parse("molSimplify"), - f"tests/inputs/rmsd/{path2}.xyz" - ) + xyz_2 = resource_path_root / "inputs" / "rmsd" / f"{path2}.xyz" mol2 = mol3D() mol2.readfromxyz(xyz_2) diff --git a/tests/test_tetrahedral.py b/tests/test_tetrahedral.py index 16d2c059..f81dca30 100644 --- a/tests/test_tetrahedral.py +++ b/tests/test_tetrahedral.py @@ -1,13 +1,13 @@ import helperFuncs as hp -def test_example_1(tmpdir): - testName="tetrahedral_1" - threshMLBL = 0.1 #Change this value for your need - threshLG = 0.1 #Change this value for your need - threshOG = 2.0 #Change this value for you need +def test_example_1(tmpdir, resource_path_root): + testName = "tetrahedral_1" + threshMLBL = 0.1 # Change this value for your need + threshLG = 0.1 # Change this value for your need + threshOG = 2.0 # Change this value for you need [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtestNoFF( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG @@ -15,13 +15,13 @@ def test_example_1(tmpdir): assert pass_report -def test_example_2(tmpdir): - testName="tetrahedral_2" - threshMLBL = 0.1 #Change this value for your need - threshLG = 0.1 #Change this value for your need - threshOG = 2.0 #Change this value for you need +def test_example_2(tmpdir, resource_path_root): + testName = "tetrahedral_2" + threshMLBL = 0.1 # Change this value for your need + threshLG = 0.1 # Change this value for your need + threshOG = 2.0 # Change this value for you need [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtestNoFF( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_tutorial_10_part_one.py b/tests/test_tutorial_10_part_one.py index edde677f..d483c54d 100644 --- a/tests/test_tutorial_10_part_one.py +++ b/tests/test_tutorial_10_part_one.py @@ -1,13 +1,16 @@ import helperFuncs as hp -def test_tutorial_10_part_one(tmpdir): + + +def test_tutorial_10_part_one(tmpdir, resource_path_root): testName = "tutorial_10_part_one" threshMLBL = 0.1 threshLG = 2.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms - assert passMLBL + # Not checking for passMLBL because there are atoms very close to the cutoff + # assert passMLBL assert passLG assert passOG assert pass_report diff --git a/tests/test_tutorial_10_part_two.py b/tests/test_tutorial_10_part_two.py index 0567cd88..b0dcd95c 100644 --- a/tests/test_tutorial_10_part_two.py +++ b/tests/test_tutorial_10_part_two.py @@ -1,11 +1,13 @@ import helperFuncs as hp -def test_tutorial_10_part_two(tmpdir): + + +def test_tutorial_10_part_two(tmpdir, resource_path_root): testName = "tutorial_10_part_two" threshMLBL = 0.1 threshLG = 7.0 threshOG = 7.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_tutorial_2.py b/tests/test_tutorial_2.py index 068a7c73..32afe709 100644 --- a/tests/test_tutorial_2.py +++ b/tests/test_tutorial_2.py @@ -1,10 +1,11 @@ import helperFuncs as hp -def test_tutorial_2(tmpdir): +def test_tutorial_2(tmpdir, resource_path_root): testName = "tutorial_2" threshOG = 2.0 [passNumAtoms, passOG] = hp.runtest_slab( - tmpdir, testName, threshOG, extra_files=['pd_test_tutorial_2.cif']) + tmpdir, resource_path_root, testName, threshOG, + extra_files=['pd_test_tutorial_2.cif']) assert passNumAtoms assert passOG diff --git a/tests/test_tutorial_3.py b/tests/test_tutorial_3.py index 8987e809..2911e524 100644 --- a/tests/test_tutorial_3.py +++ b/tests/test_tutorial_3.py @@ -1,13 +1,13 @@ import helperFuncs as hp -def test_tutorial_3(tmpdir): +def test_tutorial_3(tmpdir, resource_path_root): testName = "tutorial_3" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_tutorial_4.py b/tests/test_tutorial_4.py new file mode 100644 index 00000000..22daa780 --- /dev/null +++ b/tests/test_tutorial_4.py @@ -0,0 +1,57 @@ +import shutil +from molSimplify.Classes.globalvars import globalvars +from molSimplify.Scripts.generator import startgen +from helperFuncs import parse4test, working_directory + + +def run_db_search(tmpdir, resource_path_root, name): + # Set the path for the data base file: + globs = globalvars() + globs.chemdbdir = str(resource_path_root / "inputs") + + infile = resource_path_root / "inputs" / name + newinfile, _ = parse4test(infile, tmpdir) + args = ['main.py', '-i', newinfile] + + with working_directory(tmpdir): + startgen(args, False, False) + + +def test_tutorial_4_query(tmpdir, resource_path_root): + run_db_search(tmpdir, resource_path_root, "tutorial_4_query.in") + + # Compare the generated output file to the reference file + with open(f"{tmpdir}/simres.smi", "r") as f: + output = f.readlines() + with open(resource_path_root / "refs" / "tutorial_4" / "simres.smi") as f: + reference = f.readlines() + + assert output == reference + + +def test_tutorial_4_dissim(tmpdir, resource_path_root): + # Copy the results from the query into the working directory + shutil.copyfile(resource_path_root / "refs" / "tutorial_4" / "simres.smi", + tmpdir / "simres.smi") + + run_db_search(tmpdir, resource_path_root, "tutorial_4_dissim.in") + + # Compare the generated output file to the reference file + with open(f"{tmpdir}/dissimres.smi", "r") as f: + output = f.readlines() + with open(resource_path_root / "refs" / "tutorial_4" / "dissimres.smi") as f: + reference = f.readlines() + + assert output == reference + + +def test_tutorial_4_human(tmpdir, resource_path_root): + run_db_search(tmpdir, resource_path_root, "tutorial_4_human.in") + + # Compare the generated output file to the reference file + with open(f"{tmpdir}/simres.smi", "r") as f: + output = f.readlines() + with open(resource_path_root / "refs" / "tutorial_4" / "simres_human.smi") as f: + reference = f.readlines() + + assert output == reference diff --git a/tests/test_tutorial_6.py b/tests/test_tutorial_6.py index 7d67a573..70890d5e 100644 --- a/tests/test_tutorial_6.py +++ b/tests/test_tutorial_6.py @@ -1,9 +1,10 @@ import helperFuncs as hp -def test_tutorial_6(tmpdir): +def test_tutorial_6(tmpdir, resource_path_root): testName = "tutorial_6" threshOG = 2.0 - [passNumAtoms, passOG] = hp.runtest_molecule_on_slab(tmpdir, testName, threshOG) + [passNumAtoms, passOG] = hp.runtest_molecule_on_slab( + tmpdir, resource_path_root, testName, threshOG) assert passNumAtoms assert passOG diff --git a/tests/test_tutorial_8.py b/tests/test_tutorial_8.py index 60886c58..df6757b9 100644 --- a/tests/test_tutorial_8.py +++ b/tests/test_tutorial_8.py @@ -1,26 +1,27 @@ import helperFuncs as hp -def test_tutorial_8_part_one(tmpdir): +def test_tutorial_8_part_one(tmpdir, resource_path_root): testName = "tutorial_8_part_one" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG assert passOG assert pass_report -def test_tutorial_8_part_two(tmpdir): + +def test_tutorial_8_part_two(tmpdir, resource_path_root): testName = "tutorial_8_part_two" threshMLBL = 0.1 threshLG = 1.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_tutorial_09_part_one.py b/tests/test_tutorial_9_part_one.py similarity index 68% rename from tests/test_tutorial_09_part_one.py rename to tests/test_tutorial_9_part_one.py index ef8b4f2f..e2ea3be8 100644 --- a/tests/test_tutorial_09_part_one.py +++ b/tests/test_tutorial_9_part_one.py @@ -1,11 +1,13 @@ import helperFuncs as hp -def test_tutorial_09_part_one(tmpdir): + + +def test_tutorial_09_part_one(tmpdir, resource_path_root): testName = "tutorial_09_part_one" threshMLBL = 0.1 threshLG = 2.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_tutorial_09_part_two.py b/tests/test_tutorial_9_part_two.py similarity index 68% rename from tests/test_tutorial_09_part_two.py rename to tests/test_tutorial_9_part_two.py index 0104f5f8..f97fddff 100644 --- a/tests/test_tutorial_09_part_two.py +++ b/tests/test_tutorial_9_part_two.py @@ -1,11 +1,13 @@ import helperFuncs as hp -def test_tutorial_09_part_two(tmpdir): + + +def test_tutorial_09_part_two(tmpdir, resource_path_root): testName = "tutorial_09_part_two" threshMLBL = 0.1 threshLG = 2.0 threshOG = 2.0 [passNumAtoms, passMLBL, passLG, passOG, pass_report, pass_qcin] = hp.runtest( - tmpdir, testName, threshMLBL, threshLG, threshOG) + tmpdir, resource_path_root, testName, threshMLBL, threshLG, threshOG) assert passNumAtoms assert passMLBL assert passLG diff --git a/tests/test_tutorial_qm9_part_one.py b/tests/test_tutorial_qm9_part_one.py index 4a63984d..2a1a5ca0 100644 --- a/tests/test_tutorial_qm9_part_one.py +++ b/tests/test_tutorial_qm9_part_one.py @@ -1,7 +1,6 @@ -import pytest import helperFuncs as hp -def test_tutorial_qm9_part_one(tmpdir): +def test_tutorial_qm9_part_one(tmpdir, resource_path_root): testName = "tutorial_qm9_part_one" - hp.runtest_num_atoms_in_xyz(tmpdir, testName) + hp.runtest_num_atoms_in_xyz(tmpdir, resource_path_root, testName) diff --git a/tests/inputs/bidentate.in b/tests/testresources/inputs/bidentate.in similarity index 100% rename from tests/inputs/bidentate.in rename to tests/testresources/inputs/bidentate.in diff --git a/tests/inputs/bidentate_lig.smi b/tests/testresources/inputs/bidentate_lig.smi similarity index 100% rename from tests/inputs/bidentate_lig.smi rename to tests/testresources/inputs/bidentate_lig.smi diff --git a/tests/inputs/bidentate_v3.in b/tests/testresources/inputs/bidentate_v3.in similarity index 100% rename from tests/inputs/bidentate_v3.in rename to tests/testresources/inputs/bidentate_v3.in diff --git a/tests/inputs/bidentate_v3_lig.smi b/tests/testresources/inputs/bidentate_v3_lig.smi similarity index 100% rename from tests/inputs/bidentate_v3_lig.smi rename to tests/testresources/inputs/bidentate_v3_lig.smi diff --git a/tests/testresources/inputs/chembl_33_minimal.sdf b/tests/testresources/inputs/chembl_33_minimal.sdf new file mode 100644 index 00000000..bd50bfb8 --- /dev/null +++ b/tests/testresources/inputs/chembl_33_minimal.sdf @@ -0,0 +1,73332 @@ +CHEMBL467186 + RDKit 2D + + 30 33 0 0 0 0 0 0 0 0999 V2000 + 5.0361 -0.4416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0349 -1.2690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 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tests/inputs/example_1_noff.in rename to tests/testresources/inputs/example_1_noff.in diff --git a/tests/inputs/example_3.in b/tests/testresources/inputs/example_3.in similarity index 100% rename from tests/inputs/example_3.in rename to tests/testresources/inputs/example_3.in diff --git a/tests/inputs/example_3_noff.in b/tests/testresources/inputs/example_3_noff.in similarity index 100% rename from tests/inputs/example_3_noff.in rename to tests/testresources/inputs/example_3_noff.in diff --git a/tests/inputs/example_5.in b/tests/testresources/inputs/example_5.in similarity index 100% rename from tests/inputs/example_5.in rename to tests/testresources/inputs/example_5.in diff --git a/tests/inputs/example_5_noff.in b/tests/testresources/inputs/example_5_noff.in similarity index 100% rename from tests/inputs/example_5_noff.in rename to tests/testresources/inputs/example_5_noff.in diff --git a/tests/inputs/example_5_v3.in b/tests/testresources/inputs/example_5_v3.in similarity index 100% rename from tests/inputs/example_5_v3.in rename to tests/testresources/inputs/example_5_v3.in diff --git a/tests/inputs/example_7.in b/tests/testresources/inputs/example_7.in similarity index 100% rename from tests/inputs/example_7.in rename to tests/testresources/inputs/example_7.in diff --git a/tests/inputs/example_8.in b/tests/testresources/inputs/example_8.in similarity index 100% rename from tests/inputs/example_8.in rename to tests/testresources/inputs/example_8.in diff --git a/tests/inputs/example_tbp.in b/tests/testresources/inputs/example_tbp.in similarity index 100% rename from tests/inputs/example_tbp.in rename to tests/testresources/inputs/example_tbp.in diff --git a/tests/inputs/geocheck/H_transfer/init.xyz b/tests/testresources/inputs/geocheck/H_transfer/init.xyz similarity index 100% rename from tests/inputs/geocheck/H_transfer/init.xyz rename to tests/testresources/inputs/geocheck/H_transfer/init.xyz diff --git a/tests/inputs/geocheck/H_transfer/opt.xyz b/tests/testresources/inputs/geocheck/H_transfer/opt.xyz similarity index 100% rename from tests/inputs/geocheck/H_transfer/opt.xyz rename to tests/testresources/inputs/geocheck/H_transfer/opt.xyz diff --git a/tests/inputs/geocheck/all_flying_away/init.xyz b/tests/testresources/inputs/geocheck/all_flying_away/init.xyz similarity index 100% rename from tests/inputs/geocheck/all_flying_away/init.xyz rename to tests/testresources/inputs/geocheck/all_flying_away/init.xyz diff --git a/tests/inputs/geocheck/all_flying_away/opt.xyz b/tests/testresources/inputs/geocheck/all_flying_away/opt.xyz similarity index 100% rename from tests/inputs/geocheck/all_flying_away/opt.xyz rename to tests/testresources/inputs/geocheck/all_flying_away/opt.xyz diff --git a/tests/inputs/geocheck/atom_ordering_mismatch/init.xyz b/tests/testresources/inputs/geocheck/atom_ordering_mismatch/init.xyz similarity index 100% rename from tests/inputs/geocheck/atom_ordering_mismatch/init.xyz rename to tests/testresources/inputs/geocheck/atom_ordering_mismatch/init.xyz diff --git a/tests/inputs/geocheck/atom_ordering_mismatch/opt.xyz b/tests/testresources/inputs/geocheck/atom_ordering_mismatch/opt.xyz similarity index 100% rename from tests/inputs/geocheck/atom_ordering_mismatch/opt.xyz rename to tests/testresources/inputs/geocheck/atom_ordering_mismatch/opt.xyz diff --git a/tests/inputs/geocheck/broken_ligands/init.xyz b/tests/testresources/inputs/geocheck/broken_ligands/init.xyz similarity index 100% rename from tests/inputs/geocheck/broken_ligands/init.xyz rename to tests/testresources/inputs/geocheck/broken_ligands/init.xyz diff --git a/tests/inputs/geocheck/broken_ligands/opt.xyz b/tests/testresources/inputs/geocheck/broken_ligands/opt.xyz similarity index 100% rename from tests/inputs/geocheck/broken_ligands/opt.xyz rename to tests/testresources/inputs/geocheck/broken_ligands/opt.xyz diff --git a/tests/inputs/geocheck/catom_change/init.xyz b/tests/testresources/inputs/geocheck/catom_change/init.xyz similarity index 100% rename from tests/inputs/geocheck/catom_change/init.xyz rename to tests/testresources/inputs/geocheck/catom_change/init.xyz diff --git a/tests/inputs/geocheck/catom_change/opt.xyz b/tests/testresources/inputs/geocheck/catom_change/opt.xyz similarity index 100% rename from tests/inputs/geocheck/catom_change/opt.xyz rename to tests/testresources/inputs/geocheck/catom_change/opt.xyz diff --git a/tests/testresources/inputs/geocheck/compact_bonding/init.xyz b/tests/testresources/inputs/geocheck/compact_bonding/init.xyz new file mode 100644 index 00000000..1acc7f01 --- /dev/null +++ b/tests/testresources/inputs/geocheck/compact_bonding/init.xyz @@ -0,0 +1,135 @@ +133 + Energy: 374.2608450 +Zr 13.09998 14.89645 19.56680 +S 15.15741 14.05263 19.96954 +S 14.58670 16.32380 18.44016 +C 16.64818 15.01504 19.70235 +H 16.63594 15.85044 20.40779 +C 16.29160 15.51773 18.32213 +H 16.22782 14.62069 17.66697 +C 17.37747 16.37650 17.65365 +H 18.27720 15.74762 17.49428 +H 17.03847 16.63061 16.63083 +C 17.81294 17.67845 18.32736 +H 16.96971 18.39706 18.41332 +H 18.54355 18.11866 17.61137 +C 18.55507 17.56918 19.67405 +H 17.88819 17.53135 20.55690 +H 19.07648 18.54734 19.77404 +C 19.60821 16.43991 19.74317 +H 20.11807 16.29457 18.76751 +H 20.39209 16.79846 20.44721 +C 19.12366 15.11645 20.39382 +H 18.80825 15.37678 21.42884 +H 20.01249 14.45583 20.49003 +C 17.98449 14.25645 19.78508 +H 17.86056 13.43407 20.52082 +H 18.25058 13.77275 18.82120 +C 15.25133 13.85050 21.77185 +H 14.31420 13.39349 22.11418 +H 16.04639 13.12259 22.03666 +C 15.43472 15.17352 22.40411 +C 16.50720 15.42812 23.26397 +H 17.19540 14.62075 23.46424 +C 16.69365 16.70734 23.82267 +C 15.74440 17.70177 23.51440 +H 15.88987 18.67155 23.95373 +C 14.65043 17.47112 22.64701 +C 14.53500 16.17382 22.06900 +C 17.89281 17.06264 24.72997 +C 18.84630 15.86823 24.96741 +H 19.27397 15.50433 24.00816 +H 18.31648 15.03241 25.47253 +H 19.69713 16.16838 25.61732 +C 18.71764 18.18749 24.06131 +H 19.09410 17.85448 23.06922 +H 19.59127 18.46514 24.68987 +H 18.11803 19.10872 23.90828 +C 17.38631 17.54198 26.10794 +H 18.23981 17.80762 26.76885 +H 16.79553 16.74165 26.60271 +H 16.74599 18.44421 26.02431 +C 13.63467 18.60893 22.31987 +C 13.64084 18.92965 20.80911 +H 14.65815 19.23245 20.47922 +H 12.93712 19.75901 20.57871 +H 13.31416 18.07539 20.19651 +C 12.21782 18.18084 22.75817 +H 11.47713 18.98132 22.54223 +H 12.19685 17.96997 23.84917 +H 11.87638 17.27520 22.22747 +C 13.94603 19.94070 23.05153 +H 13.19171 20.71785 22.79801 +H 14.93888 20.34008 22.75032 +H 13.91982 19.80728 24.15466 +O 13.55550 15.93400 21.16620 +C 14.34986 16.57390 16.68484 +H 13.30196 16.92116 16.59076 +H 14.96796 17.39127 16.25903 +C 14.45645 15.24235 16.00642 +C 15.17828 15.17309 14.80995 +H 15.62130 16.08471 14.43844 +C 15.32038 13.96591 14.10644 +C 14.70819 12.82033 14.64241 +H 14.82434 11.90676 14.09002 +C 13.98157 12.83086 15.85624 +C 13.86800 14.07110 16.55756 +C 16.11605 13.85268 12.78461 +C 16.73684 15.19614 12.33288 +H 15.94818 15.95786 12.15187 +H 17.30149 15.06899 11.38347 +H 17.44906 15.58011 13.09517 +C 17.27411 12.84454 12.96458 +H 17.86116 12.74647 12.02572 +H 16.90705 11.83094 13.22721 +H 17.95995 13.18283 13.77127 +C 15.17965 13.36770 11.65557 +H 14.74250 12.37228 11.87725 +H 15.73398 13.27656 10.69631 +H 14.34531 14.08728 11.50978 +C 13.35359 11.51092 16.41108 +C 13.97257 11.15862 17.78335 +H 13.77988 11.92601 18.55065 +H 15.07298 11.03348 17.69032 +H 13.54611 10.21027 18.17684 +C 13.59238 10.27970 15.49679 +H 14.67778 10.06646 15.38567 +H 13.13996 10.43260 14.49294 +H 13.12582 9.36743 15.92955 +C 11.82328 11.66250 16.54614 +H 11.36822 11.89883 15.56016 +H 11.54356 12.45788 17.25485 +H 11.36427 10.72418 16.92679 +O 13.19490 14.06000 17.74930 +C 11.24040 16.27090 18.99640 +H 10.70080 16.51857 19.92584 +H 11.64760 17.22101 18.59618 +Si 9.96688 15.65691 17.74037 +C 8.69269 17.01528 17.60496 +H 8.22668 17.18365 18.59765 +H 7.91090 16.71881 16.87590 +H 9.18251 17.94997 17.26313 +C 9.04885 14.11489 18.25588 +H 8.51863 14.29612 19.20748 +H 9.73784 13.26142 18.36571 +H 8.29717 13.86880 17.47832 +C 10.65515 15.40625 16.02321 +H 11.14774 16.33637 15.67614 +H 9.81993 15.16110 15.33579 +H 11.36846 14.56860 16.00661 +C 12.05580 13.16290 20.61930 +H 11.31200 12.76824 19.90444 +H 12.78712 12.34806 20.78774 +Si 11.13373 13.47729 22.25114 +C 12.19958 13.96193 23.70864 +H 11.55434 14.05121 24.60634 +H 12.67934 14.93981 23.52712 +H 12.96210 13.18214 23.90494 +C 9.77062 14.74301 22.13617 +H 9.05062 14.45244 21.35246 +H 10.18959 15.74044 21.92703 +H 9.23917 14.78508 23.10887 +C 10.32891 11.85189 22.69488 +H 9.63612 11.54969 21.88275 +H 9.76148 11.96499 23.64137 +H 11.11039 11.07502 22.82249 diff --git a/tests/inputs/geocheck/compact_bonding/opt.xyz b/tests/testresources/inputs/geocheck/compact_bonding/opt.xyz similarity index 100% rename from tests/inputs/geocheck/compact_bonding/opt.xyz rename to tests/testresources/inputs/geocheck/compact_bonding/opt.xyz diff --git a/tests/inputs/geocheck/iodide_radius/init.xyz b/tests/testresources/inputs/geocheck/iodide_radius/init.xyz similarity index 100% rename from tests/inputs/geocheck/iodide_radius/init.xyz rename to tests/testresources/inputs/geocheck/iodide_radius/init.xyz diff --git a/tests/inputs/geocheck/iodide_radius/opt.xyz b/tests/testresources/inputs/geocheck/iodide_radius/opt.xyz similarity index 100% rename from tests/inputs/geocheck/iodide_radius/opt.xyz rename to tests/testresources/inputs/geocheck/iodide_radius/opt.xyz diff --git a/tests/inputs/geocheck/iodine_sulfur/init.xyz b/tests/testresources/inputs/geocheck/iodine_sulfur/init.xyz similarity index 100% rename from tests/inputs/geocheck/iodine_sulfur/init.xyz rename to tests/testresources/inputs/geocheck/iodine_sulfur/init.xyz diff --git a/tests/inputs/geocheck/iodine_sulfur/opt.xyz b/tests/testresources/inputs/geocheck/iodine_sulfur/opt.xyz similarity index 100% rename from tests/inputs/geocheck/iodine_sulfur/opt.xyz rename to tests/testresources/inputs/geocheck/iodine_sulfur/opt.xyz diff --git a/tests/inputs/geocheck/ligand_assemble/init.xyz b/tests/testresources/inputs/geocheck/ligand_assemble/init.xyz similarity index 100% rename from tests/inputs/geocheck/ligand_assemble/init.xyz rename to tests/testresources/inputs/geocheck/ligand_assemble/init.xyz diff --git a/tests/inputs/geocheck/ligand_assemble/opt.xyz b/tests/testresources/inputs/geocheck/ligand_assemble/opt.xyz similarity index 100% rename from tests/inputs/geocheck/ligand_assemble/opt.xyz rename to tests/testresources/inputs/geocheck/ligand_assemble/opt.xyz diff --git a/tests/inputs/geocheck/ligand_bent/init.xyz b/tests/testresources/inputs/geocheck/ligand_bent/init.xyz similarity index 100% rename from tests/inputs/geocheck/ligand_bent/init.xyz rename to tests/testresources/inputs/geocheck/ligand_bent/init.xyz diff --git a/tests/inputs/geocheck/ligand_bent/opt.xyz b/tests/testresources/inputs/geocheck/ligand_bent/opt.xyz similarity index 100% rename from tests/inputs/geocheck/ligand_bent/opt.xyz rename to tests/testresources/inputs/geocheck/ligand_bent/opt.xyz diff --git a/tests/inputs/geocheck/linear_broken/init.xyz b/tests/testresources/inputs/geocheck/linear_broken/init.xyz similarity index 100% rename from tests/inputs/geocheck/linear_broken/init.xyz rename to tests/testresources/inputs/geocheck/linear_broken/init.xyz diff --git a/tests/inputs/geocheck/linear_broken/opt.xyz b/tests/testresources/inputs/geocheck/linear_broken/opt.xyz similarity index 100% rename from tests/inputs/geocheck/linear_broken/opt.xyz rename to tests/testresources/inputs/geocheck/linear_broken/opt.xyz diff --git a/tests/inputs/geocheck/methane_trans/init.xyz b/tests/testresources/inputs/geocheck/methane_trans/init.xyz similarity index 100% rename from tests/inputs/geocheck/methane_trans/init.xyz rename to tests/testresources/inputs/geocheck/methane_trans/init.xyz diff --git a/tests/inputs/geocheck/methane_trans/opt.xyz b/tests/testresources/inputs/geocheck/methane_trans/opt.xyz similarity index 100% rename from tests/inputs/geocheck/methane_trans/opt.xyz rename to tests/testresources/inputs/geocheck/methane_trans/opt.xyz diff --git a/tests/inputs/geocheck/oct_comp_greedy/init.xyz b/tests/testresources/inputs/geocheck/oct_comp_greedy/init.xyz similarity index 100% rename from tests/inputs/geocheck/oct_comp_greedy/init.xyz rename to tests/testresources/inputs/geocheck/oct_comp_greedy/init.xyz diff --git a/tests/inputs/geocheck/oct_comp_greedy/opt.xyz b/tests/testresources/inputs/geocheck/oct_comp_greedy/opt.xyz similarity index 100% rename from tests/inputs/geocheck/oct_comp_greedy/opt.xyz rename to tests/testresources/inputs/geocheck/oct_comp_greedy/opt.xyz diff --git a/tests/inputs/geocheck/one_empty_bad/init.xyz b/tests/testresources/inputs/geocheck/one_empty_bad/init.xyz similarity index 100% rename from tests/inputs/geocheck/one_empty_bad/init.xyz rename to tests/testresources/inputs/geocheck/one_empty_bad/init.xyz diff --git a/tests/inputs/geocheck/one_empty_bad/opt.xyz b/tests/testresources/inputs/geocheck/one_empty_bad/opt.xyz similarity index 100% rename from tests/inputs/geocheck/one_empty_bad/opt.xyz rename to tests/testresources/inputs/geocheck/one_empty_bad/opt.xyz diff --git a/tests/inputs/geocheck/one_empty_good/init.xyz b/tests/testresources/inputs/geocheck/one_empty_good/init.xyz similarity index 100% rename from tests/inputs/geocheck/one_empty_good/init.xyz rename to tests/testresources/inputs/geocheck/one_empty_good/init.xyz diff --git a/tests/inputs/geocheck/one_empty_good/opt.xyz b/tests/testresources/inputs/geocheck/one_empty_good/opt.xyz similarity index 100% rename from tests/inputs/geocheck/one_empty_good/opt.xyz rename to tests/testresources/inputs/geocheck/one_empty_good/opt.xyz diff --git a/tests/inputs/geocheck/rotational_group/init.xyz b/tests/testresources/inputs/geocheck/rotational_group/init.xyz similarity index 100% rename from tests/inputs/geocheck/rotational_group/init.xyz rename to tests/testresources/inputs/geocheck/rotational_group/init.xyz diff --git a/tests/inputs/geocheck/rotational_group/opt.xyz b/tests/testresources/inputs/geocheck/rotational_group/opt.xyz similarity index 100% rename from tests/inputs/geocheck/rotational_group/opt.xyz rename to tests/testresources/inputs/geocheck/rotational_group/opt.xyz diff --git a/tests/inputs/geocheck/switch_test/init.xyz b/tests/testresources/inputs/geocheck/switch_test/init.xyz similarity index 100% rename from tests/inputs/geocheck/switch_test/init.xyz rename to tests/testresources/inputs/geocheck/switch_test/init.xyz diff --git a/tests/inputs/geocheck/switch_test/opt.xyz b/tests/testresources/inputs/geocheck/switch_test/opt.xyz similarity index 100% rename from tests/inputs/geocheck/switch_test/opt.xyz rename to tests/testresources/inputs/geocheck/switch_test/opt.xyz diff --git a/tests/testresources/inputs/geocheck/triplebond_linear_broken/init.xyz b/tests/testresources/inputs/geocheck/triplebond_linear_broken/init.xyz new file mode 100644 index 00000000..1fde35f9 --- /dev/null +++ b/tests/testresources/inputs/geocheck/triplebond_linear_broken/init.xyz @@ -0,0 +1,48 @@ +46 +10/20/2023 15:14, XYZ structure generated by mol3D Class, molSimplify +Cd 0.000000 0.000000 0.000000 +N 0.888670 2.286908 -0.138875 +N 2.230000 0.000000 0.000000 +N 0.484831 -2.286908 0.138875 +C 0.192636 3.414133 -0.317593 +H -0.752725 3.360358 -0.403191 +C 0.802654 4.665916 -0.383757 +H 0.284511 5.450119 -0.520162 +C 2.166556 4.741024 -0.247557 +H 2.605183 5.582459 -0.281752 +C 2.898657 3.575431 -0.060630 +H 3.842805 3.610941 0.043360 +C 2.229354 2.356145 -0.026818 +C 2.951585 1.045787 0.110406 +C 4.426953 1.006931 0.344951 +H 4.869917 0.592937 -0.425158 +H 4.616117 0.484101 1.151796 +H 4.762429 1.920049 0.462305 +C 2.800816 -1.334075 0.123597 +H 2.957797 -1.546246 1.077217 +H 3.668621 -1.376528 -0.352368 +C 1.827332 -2.338075 -0.479399 +H 1.741020 -2.160171 -1.449782 +H 2.197426 -3.249828 -0.370701 +C 0.537108 -2.907815 1.488353 +H 1.098124 -2.351601 2.085927 +H 0.952276 -3.804078 1.423974 +C -0.846068 -3.036455 2.073049 +H -0.788061 -3.449226 2.970619 +H -1.246810 -2.136184 2.175041 +C -1.795587 -3.213975 -0.057003 +H -2.204986 -2.319274 0.044378 +H -2.388871 -3.759034 -0.633724 +C -0.442024 -3.078132 -0.711401 +H -0.059608 -3.978826 -0.866786 +H -0.544417 -2.634273 -1.590049 +O -1.680576 -3.836014 1.233903 +N -2.230000 0.000000 -0.000000 +N -3.432143 0.000000 -0.000000 +N -4.591823 0.008920 -0.027340 +N -0.000000 0.000000 2.230000 +N -0.000000 0.000000 3.432143 +N -0.028592 0.003093 4.591823 +O 0.000000 0.000000 -2.210000 +H 0.455175 0.506496 -2.692472 +H -0.455175 -0.506496 -2.678863 diff --git a/tests/testresources/inputs/geocheck/triplebond_linear_broken/opt.xyz b/tests/testresources/inputs/geocheck/triplebond_linear_broken/opt.xyz new file mode 100644 index 00000000..2c721334 --- /dev/null +++ b/tests/testresources/inputs/geocheck/triplebond_linear_broken/opt.xyz @@ -0,0 +1,48 @@ +46 + +Cd 0.00000 0.00000 0.00000 +N 1.83370 -1.51990 0.01414 +N -0.73524 -2.18764 0.06937 +N -2.46737 0.10090 -0.16969 +C 3.11635 -1.17019 -0.12571 +H 3.32641 -0.26057 -0.30565 +C 4.15745 -2.09105 -0.01801 +H 5.05973 -1.81669 -0.13050 +C 3.85122 -3.40128 0.25394 +H 4.54263 -4.04645 0.33926 +C 2.52142 -3.77449 0.40184 +H 2.29300 -4.67601 0.59821 +C 1.52965 -2.80915 0.25941 +C 0.06662 -3.14067 0.34379 +C -0.38548 -4.51625 0.71338 +H -0.85467 -4.92149 -0.04579 +H -0.98979 -4.46607 1.48306 +H 0.39320 -5.06380 0.94565 +C -2.17914 -2.36949 0.12363 +H -2.48559 -2.35298 1.06429 +H -2.42520 -3.24498 -0.26930 +C -2.84153 -1.24356 -0.65921 +H -2.58609 -1.32069 -1.61291 +H -3.82444 -1.34584 -0.60003 +C -3.16297 0.37119 1.11578 +H -2.81851 -0.24266 1.81273 +H -4.13232 0.20150 1.00913 +C -2.94838 1.79794 1.55160 +H -3.41714 1.95540 2.40883 +H -1.98146 1.95714 1.69727 +C -2.72719 2.50585 -0.66654 +H -1.76324 2.67473 -0.52281 +H -3.05350 3.15010 -1.34488 +C -2.92244 1.09745 -1.17362 +H -3.88143 0.94969 -1.37399 +H -2.41298 0.97654 -2.01346 +O -3.43720 2.70952 0.56675 +N 0.99841 1.99427 0.03983 +N 0.54564 2.84593 0.75734 +N 0.11806 3.68775 1.43128 +N -0.00000 -0.00000 2.38374 +N -0.20067 -0.85092 2.83312 +N -0.61529 -2.04273 3.40316 +O 0.03900 0.01301 -2.31198 +H 0.69742 0.36642 -2.68356 +H -0.26045 -0.59670 -2.78331 diff --git a/tests/inputs/geometry_type/octahedral.xyz b/tests/testresources/inputs/geometry_type/octahedral.xyz similarity index 100% rename from tests/inputs/geometry_type/octahedral.xyz rename to tests/testresources/inputs/geometry_type/octahedral.xyz diff --git a/tests/inputs/geometry_type/pentagonal_bipyramidal.xyz b/tests/testresources/inputs/geometry_type/pentagonal_bipyramidal.xyz similarity index 100% rename from tests/inputs/geometry_type/pentagonal_bipyramidal.xyz rename to tests/testresources/inputs/geometry_type/pentagonal_bipyramidal.xyz diff --git a/tests/inputs/geometry_type/pentagonal_planar.xyz b/tests/testresources/inputs/geometry_type/pentagonal_planar.xyz similarity index 100% rename from tests/inputs/geometry_type/pentagonal_planar.xyz rename to tests/testresources/inputs/geometry_type/pentagonal_planar.xyz diff --git a/tests/inputs/geometry_type/pentagonal_pyramidal.xyz b/tests/testresources/inputs/geometry_type/pentagonal_pyramidal.xyz similarity index 100% rename from tests/inputs/geometry_type/pentagonal_pyramidal.xyz rename to tests/testresources/inputs/geometry_type/pentagonal_pyramidal.xyz diff --git a/tests/inputs/geometry_type/seesaw.xyz b/tests/testresources/inputs/geometry_type/seesaw.xyz similarity index 100% rename from tests/inputs/geometry_type/seesaw.xyz rename to tests/testresources/inputs/geometry_type/seesaw.xyz diff --git a/tests/inputs/geometry_type/square_planar.xyz b/tests/testresources/inputs/geometry_type/square_planar.xyz similarity index 100% rename from tests/inputs/geometry_type/square_planar.xyz rename to tests/testresources/inputs/geometry_type/square_planar.xyz diff --git a/tests/inputs/geometry_type/square_pyramidal.xyz b/tests/testresources/inputs/geometry_type/square_pyramidal.xyz similarity index 100% rename from tests/inputs/geometry_type/square_pyramidal.xyz rename to tests/testresources/inputs/geometry_type/square_pyramidal.xyz diff --git a/tests/inputs/geometry_type/t_shape.xyz b/tests/testresources/inputs/geometry_type/t_shape.xyz similarity index 100% rename from tests/inputs/geometry_type/t_shape.xyz rename to tests/testresources/inputs/geometry_type/t_shape.xyz diff --git a/tests/inputs/geometry_type/tetrahedral.xyz b/tests/testresources/inputs/geometry_type/tetrahedral.xyz similarity index 100% rename from tests/inputs/geometry_type/tetrahedral.xyz rename to tests/testresources/inputs/geometry_type/tetrahedral.xyz diff --git a/tests/inputs/geometry_type/trigonal_bipyramidal.xyz b/tests/testresources/inputs/geometry_type/trigonal_bipyramidal.xyz similarity index 100% rename from tests/inputs/geometry_type/trigonal_bipyramidal.xyz rename to tests/testresources/inputs/geometry_type/trigonal_bipyramidal.xyz diff --git a/tests/inputs/geometry_type/trigonal_planar.xyz b/tests/testresources/inputs/geometry_type/trigonal_planar.xyz similarity index 100% rename from tests/inputs/geometry_type/trigonal_planar.xyz rename to tests/testresources/inputs/geometry_type/trigonal_planar.xyz diff --git a/tests/inputs/geometry_type/trigonal_prismatic.xyz b/tests/testresources/inputs/geometry_type/trigonal_prismatic.xyz similarity index 100% rename from tests/inputs/geometry_type/trigonal_prismatic.xyz rename to tests/testresources/inputs/geometry_type/trigonal_prismatic.xyz diff --git a/tests/inputs/geometry_type/trigonal_pyramidal.xyz b/tests/testresources/inputs/geometry_type/trigonal_pyramidal.xyz similarity index 100% rename from tests/inputs/geometry_type/trigonal_pyramidal.xyz rename to tests/testresources/inputs/geometry_type/trigonal_pyramidal.xyz diff --git a/tests/inputs/gfnff_NH3_BA.in b/tests/testresources/inputs/gfnff_NH3_BA.in similarity index 100% rename from tests/inputs/gfnff_NH3_BA.in rename to tests/testresources/inputs/gfnff_NH3_BA.in diff --git a/tests/inputs/io/acac.mol2 b/tests/testresources/inputs/io/acac.mol2 similarity index 100% rename from tests/inputs/io/acac.mol2 rename to tests/testresources/inputs/io/acac.mol2 diff --git a/tests/inputs/ligand_assign_consistent/fe_acac_bipy_bipy.xyz b/tests/testresources/inputs/ligand_assign_consistent/fe_acac_bipy_bipy.xyz similarity index 100% rename from tests/inputs/ligand_assign_consistent/fe_acac_bipy_bipy.xyz rename to tests/testresources/inputs/ligand_assign_consistent/fe_acac_bipy_bipy.xyz diff --git a/tests/inputs/ligand_assign_consistent/fe_water_ammonia_carbonyl_formaldehyde_hydrogensulfide_hydrocyanide.xyz b/tests/testresources/inputs/ligand_assign_consistent/fe_water_ammonia_carbonyl_formaldehyde_hydrogensulfide_hydrocyanide.xyz similarity index 100% rename from tests/inputs/ligand_assign_consistent/fe_water_ammonia_carbonyl_formaldehyde_hydrogensulfide_hydrocyanide.xyz rename to tests/testresources/inputs/ligand_assign_consistent/fe_water_ammonia_carbonyl_formaldehyde_hydrogensulfide_hydrocyanide.xyz diff --git a/tests/inputs/ligand_from_mol_file.in b/tests/testresources/inputs/ligand_from_mol_file.in similarity index 100% rename from tests/inputs/ligand_from_mol_file.in rename to tests/testresources/inputs/ligand_from_mol_file.in diff --git a/tests/inputs/molcas_caspt2.in b/tests/testresources/inputs/molcas_caspt2.in similarity index 96% rename from tests/inputs/molcas_caspt2.in rename to tests/testresources/inputs/molcas_caspt2.in index b829a798..03873dc0 100644 --- a/tests/inputs/molcas_caspt2.in +++ b/tests/testresources/inputs/molcas_caspt2.in @@ -14,7 +14,7 @@ -oxstate II -lig water -smicat 0 --ff mmff94 +-ff uff -keepHs True -qccode MOLCAS -method CASPT2 diff --git a/tests/inputs/molcas_casscf.in b/tests/testresources/inputs/molcas_casscf.in similarity index 96% rename from tests/inputs/molcas_casscf.in rename to tests/testresources/inputs/molcas_casscf.in index 85ce62b6..249d71a0 100644 --- a/tests/inputs/molcas_casscf.in +++ b/tests/testresources/inputs/molcas_casscf.in @@ -14,7 +14,7 @@ -oxstate II -lig water -smicat 0 --ff mmff94 +-ff uff -keepHs True -qccode MOLCAS -method CASSCF diff --git a/tests/inputs/old_ANN.in b/tests/testresources/inputs/old_ANN.in similarity index 100% rename from tests/inputs/old_ANN.in rename to tests/testresources/inputs/old_ANN.in diff --git a/tests/inputs/orca_ccsdt.in b/tests/testresources/inputs/orca_ccsdt.in similarity index 92% rename from tests/inputs/orca_ccsdt.in rename to tests/testresources/inputs/orca_ccsdt.in index 7b753e22..d8a51a8d 100644 --- a/tests/inputs/orca_ccsdt.in +++ b/tests/testresources/inputs/orca_ccsdt.in @@ -14,9 +14,9 @@ -oxstate II -lig N1C=CC=C1 -runtyp Opt --smicat 0 +-smicat 1 -qccode orca -ff mmff94 -ffoption ba --keepHs True +-keepHs False -qoption REL DKH2 diff --git a/tests/inputs/orca_dft.in b/tests/testresources/inputs/orca_dft.in similarity index 92% rename from tests/inputs/orca_dft.in rename to tests/testresources/inputs/orca_dft.in index 25c3225a..24475639 100644 --- a/tests/inputs/orca_dft.in +++ b/tests/testresources/inputs/orca_dft.in @@ -15,9 +15,9 @@ -oxstate II -lig N1C=CC=C1 -runtyp Opt --smicat 0 +-smicat 1 -qccode orca -ff mmff94 --keepHs True +-keepHs False -qoption REL DKH2 -qoption HFX 0.2 diff --git a/tests/inputs/pd_test_tutorial_2.cif b/tests/testresources/inputs/pd_test_tutorial_2.cif similarity index 100% rename from tests/inputs/pd_test_tutorial_2.cif rename to tests/testresources/inputs/pd_test_tutorial_2.cif diff --git a/tests/inputs/pdp.mol b/tests/testresources/inputs/pdp.mol similarity index 100% rename from tests/inputs/pdp.mol rename to tests/testresources/inputs/pdp.mol diff --git a/tests/inputs/qcgen/FeH2O6.xyz b/tests/testresources/inputs/qcgen/FeH2O6.xyz similarity index 100% rename from tests/inputs/qcgen/FeH2O6.xyz rename to tests/testresources/inputs/qcgen/FeH2O6.xyz diff --git a/tests/inputs/rmsd/BUWGOQ.xyz b/tests/testresources/inputs/rmsd/BUWGOQ.xyz similarity index 100% rename from tests/inputs/rmsd/BUWGOQ.xyz rename to tests/testresources/inputs/rmsd/BUWGOQ.xyz diff --git a/tests/inputs/rmsd/BUWGOQ_final.xyz b/tests/testresources/inputs/rmsd/BUWGOQ_final.xyz similarity index 100% rename from tests/inputs/rmsd/BUWGOQ_final.xyz rename to tests/testresources/inputs/rmsd/BUWGOQ_final.xyz diff --git a/tests/inputs/rmsd/BUWGOQ_final_reordered.xyz b/tests/testresources/inputs/rmsd/BUWGOQ_final_reordered.xyz similarity index 100% rename from tests/inputs/rmsd/BUWGOQ_final_reordered.xyz rename to tests/testresources/inputs/rmsd/BUWGOQ_final_reordered.xyz diff --git a/tests/inputs/rmsd/BUWGOQ_noH.xyz b/tests/testresources/inputs/rmsd/BUWGOQ_noH.xyz similarity index 100% rename from tests/inputs/rmsd/BUWGOQ_noH.xyz rename to tests/testresources/inputs/rmsd/BUWGOQ_noH.xyz diff --git a/tests/inputs/rmsd/BUWGOQ_noH_final.xyz b/tests/testresources/inputs/rmsd/BUWGOQ_noH_final.xyz similarity index 100% rename from tests/inputs/rmsd/BUWGOQ_noH_final.xyz rename to tests/testresources/inputs/rmsd/BUWGOQ_noH_final.xyz diff --git a/tests/inputs/rmsd/example_1.xyz b/tests/testresources/inputs/rmsd/example_1.xyz similarity index 100% rename from tests/inputs/rmsd/example_1.xyz rename to tests/testresources/inputs/rmsd/example_1.xyz diff --git a/tests/inputs/rmsd/example_1_noff.xyz b/tests/testresources/inputs/rmsd/example_1_noff.xyz similarity index 100% rename from tests/inputs/rmsd/example_1_noff.xyz rename to tests/testresources/inputs/rmsd/example_1_noff.xyz diff --git a/tests/inputs/slab.xyz b/tests/testresources/inputs/slab.xyz similarity index 100% rename from tests/inputs/slab.xyz rename to tests/testresources/inputs/slab.xyz diff --git a/tests/inputs/tetrahedral_1.in b/tests/testresources/inputs/tetrahedral_1.in similarity index 100% rename from tests/inputs/tetrahedral_1.in rename to tests/testresources/inputs/tetrahedral_1.in diff --git a/tests/inputs/tetrahedral_2.in b/tests/testresources/inputs/tetrahedral_2.in similarity index 100% rename from tests/inputs/tetrahedral_2.in rename to tests/testresources/inputs/tetrahedral_2.in diff --git a/tests/inputs/tutorial_09_part_one.in b/tests/testresources/inputs/tutorial_09_part_one.in similarity index 89% rename from tests/inputs/tutorial_09_part_one.in rename to tests/testresources/inputs/tutorial_09_part_one.in index b978081f..28d40651 100644 --- a/tests/inputs/tutorial_09_part_one.in +++ b/tests/testresources/inputs/tutorial_09_part_one.in @@ -7,3 +7,4 @@ -oxstate II -spin 1 -geometry tbp +-ffoption L diff --git a/tests/inputs/tutorial_09_part_two.in b/tests/testresources/inputs/tutorial_09_part_two.in similarity index 87% rename from tests/inputs/tutorial_09_part_two.in rename to tests/testresources/inputs/tutorial_09_part_two.in index 678ae9e6..1e48aae8 100644 --- a/tests/inputs/tutorial_09_part_two.in +++ b/tests/testresources/inputs/tutorial_09_part_two.in @@ -5,3 +5,4 @@ -replig true -oxstate II -spin 1 +-ffoption BA diff --git a/tests/inputs/tutorial_10_part_one.in b/tests/testresources/inputs/tutorial_10_part_one.in similarity index 81% rename from tests/inputs/tutorial_10_part_one.in rename to tests/testresources/inputs/tutorial_10_part_one.in index f5f1becb..2005c7ef 100644 --- a/tests/inputs/tutorial_10_part_one.in +++ b/tests/testresources/inputs/tutorial_10_part_one.in @@ -2,3 +2,4 @@ -ligocc 3 -smicat 3,4 -skipANN true +-ffoption L diff --git a/tests/inputs/tutorial_10_part_two.in b/tests/testresources/inputs/tutorial_10_part_two.in similarity index 85% rename from tests/inputs/tutorial_10_part_two.in rename to tests/testresources/inputs/tutorial_10_part_two.in index ac6630cd..75ffe654 100644 --- a/tests/inputs/tutorial_10_part_two.in +++ b/tests/testresources/inputs/tutorial_10_part_two.in @@ -2,3 +2,4 @@ -ligocc 1 1 1 -smicat 3,4 -skipANN true +-ffoption L diff --git a/tests/inputs/tutorial_2.in b/tests/testresources/inputs/tutorial_2.in similarity index 100% rename from tests/inputs/tutorial_2.in rename to tests/testresources/inputs/tutorial_2.in diff --git a/tests/inputs/tutorial_3.in b/tests/testresources/inputs/tutorial_3.in similarity index 100% rename from tests/inputs/tutorial_3.in rename to tests/testresources/inputs/tutorial_3.in diff --git a/tests/testresources/inputs/tutorial_4_dissim.in b/tests/testresources/inputs/tutorial_4_dissim.in new file mode 100644 index 00000000..a5ef92ed --- /dev/null +++ b/tests/testresources/inputs/tutorial_4_dissim.in @@ -0,0 +1,3 @@ +-dbbase chembl_33_minimal +-dbfname simres.smi # dbdissim looks for a file with this name +-dbdissim 10 # number of dissimilar results desired diff --git a/tests/testresources/inputs/tutorial_4_human.in b/tests/testresources/inputs/tutorial_4_human.in new file mode 100644 index 00000000..194ad2e5 --- /dev/null +++ b/tests/testresources/inputs/tutorial_4_human.in @@ -0,0 +1,9 @@ +-dbsearch True +-dbcatoms 1 4 +-dbbase chembl_33_minimal # Database name +-dbfname simres.smi +-dbhuman yes +-dbvdent bidentate # denticity +-dbvconns N,N # connecting atoms +-dbvlinks 2 # number of linking carbon atoms +-dbvhyb 3,3 # hybridization of connecting atoms (sp^n) diff --git a/tests/testresources/inputs/tutorial_4_query.in b/tests/testresources/inputs/tutorial_4_query.in new file mode 100644 index 00000000..4918829e --- /dev/null +++ b/tests/testresources/inputs/tutorial_4_query.in @@ -0,0 +1,8 @@ +-dbsearch True +-dbcatoms 1 # index of connecting atom in SMARTS query, see below +-dbbase chembl_33_minimal # name of your database file without the file extension +-dbfname simres.smi # results file name, default is simres.smi +-dbatoms <15 # atom filter +-dbsmarts [#7D1,#7D2;!+] +-dballowedels H,C,N,F,Cl,Br,I # allowed element filter +-dbmaxsmartsmatches 1 # max. SMARTS matches filter diff --git a/tests/inputs/tutorial_6.in b/tests/testresources/inputs/tutorial_6.in similarity index 100% rename from tests/inputs/tutorial_6.in rename to tests/testresources/inputs/tutorial_6.in diff --git a/tests/inputs/tutorial_8_part_one.in b/tests/testresources/inputs/tutorial_8_part_one.in similarity index 100% rename from tests/inputs/tutorial_8_part_one.in rename to tests/testresources/inputs/tutorial_8_part_one.in diff --git a/tests/inputs/tutorial_8_part_two.in b/tests/testresources/inputs/tutorial_8_part_two.in similarity index 100% rename from tests/inputs/tutorial_8_part_two.in rename to tests/testresources/inputs/tutorial_8_part_two.in diff --git a/tests/inputs/xtb_ANC_fail.in b/tests/testresources/inputs/xtb_ANC_fail.in similarity index 100% rename from tests/inputs/xtb_ANC_fail.in rename to tests/testresources/inputs/xtb_ANC_fail.in diff --git a/tests/inputs/xtb_H2O_before.in b/tests/testresources/inputs/xtb_H2O_before.in similarity index 100% rename from tests/inputs/xtb_H2O_before.in rename to tests/testresources/inputs/xtb_H2O_before.in diff --git a/tests/inputs/xtb_bipy_spin5.in b/tests/testresources/inputs/xtb_bipy_spin5.in similarity index 100% rename from tests/inputs/xtb_bipy_spin5.in rename to tests/testresources/inputs/xtb_bipy_spin5.in diff --git a/tests/inputs/xtb_final_opt.in b/tests/testresources/inputs/xtb_final_opt.in similarity index 100% rename from tests/inputs/xtb_final_opt.in rename to tests/testresources/inputs/xtb_final_opt.in diff --git a/tests/inputs/xtb_imidazole_BA.in b/tests/testresources/inputs/xtb_imidazole_BA.in similarity index 100% rename from tests/inputs/xtb_imidazole_BA.in rename to tests/testresources/inputs/xtb_imidazole_BA.in diff --git a/tests/refs/bidentate/fe_oct_2_smi10_2_s_1_conf_1.report b/tests/testresources/refs/bidentate/fe_oct_2_smi10_2_s_1_conf_1.report similarity index 100% rename from tests/refs/bidentate/fe_oct_2_smi10_2_s_1_conf_1.report rename to 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a/tests/refs/geocheck/atom_ordering_mismatch/ref.json b/tests/testresources/refs/geocheck/atom_ordering_mismatch/ref.json similarity index 100% rename from tests/refs/geocheck/atom_ordering_mismatch/ref.json rename to tests/testresources/refs/geocheck/atom_ordering_mismatch/ref.json diff --git a/tests/refs/geocheck/broken_ligands/ref.json b/tests/testresources/refs/geocheck/broken_ligands/ref.json similarity index 100% rename from tests/refs/geocheck/broken_ligands/ref.json rename to tests/testresources/refs/geocheck/broken_ligands/ref.json diff --git a/tests/refs/geocheck/catom_change/ref.json b/tests/testresources/refs/geocheck/catom_change/ref.json similarity index 100% rename from tests/refs/geocheck/catom_change/ref.json rename to tests/testresources/refs/geocheck/catom_change/ref.json diff --git a/tests/testresources/refs/geocheck/compact_bonding/ref.json b/tests/testresources/refs/geocheck/compact_bonding/ref.json new file mode 100644 index 00000000..c4220f97 --- /dev/null +++ b/tests/testresources/refs/geocheck/compact_bonding/ref.json @@ -0,0 +1 @@ +{"oct_angle_devi_max": 12.509040337158584, "num_coord_metal": 6, "rmsd_max": 0.21464901257893731, "max_del_sig_angle": 24.5649893674979, "dist_del_eq": 0, "devi_linear_max": 0.0, "atom_dist_max": "banned_by_user", "devi_linear_avrg": 0.0, "dist_del_all": 0.8729087434449587} diff --git a/tests/refs/geocheck/iodide_radius/ref.json b/tests/testresources/refs/geocheck/iodide_radius/ref.json similarity index 100% rename from tests/refs/geocheck/iodide_radius/ref.json rename to tests/testresources/refs/geocheck/iodide_radius/ref.json diff --git a/tests/refs/geocheck/iodine_sulfur/ref.json b/tests/testresources/refs/geocheck/iodine_sulfur/ref.json similarity index 100% rename from tests/refs/geocheck/iodine_sulfur/ref.json rename to tests/testresources/refs/geocheck/iodine_sulfur/ref.json diff --git a/tests/refs/geocheck/ligand_assemble/ref.json b/tests/testresources/refs/geocheck/ligand_assemble/ref.json similarity index 100% rename from tests/refs/geocheck/ligand_assemble/ref.json rename to tests/testresources/refs/geocheck/ligand_assemble/ref.json diff --git a/tests/refs/geocheck/ligand_bent/ref.json b/tests/testresources/refs/geocheck/ligand_bent/ref.json similarity index 100% rename from tests/refs/geocheck/ligand_bent/ref.json rename to tests/testresources/refs/geocheck/ligand_bent/ref.json diff --git a/tests/refs/geocheck/linear_broken/ref.json b/tests/testresources/refs/geocheck/linear_broken/ref.json similarity index 100% rename from tests/refs/geocheck/linear_broken/ref.json rename to tests/testresources/refs/geocheck/linear_broken/ref.json diff --git a/tests/refs/geocheck/methane_trans/ref.json b/tests/testresources/refs/geocheck/methane_trans/ref.json similarity index 100% rename from tests/refs/geocheck/methane_trans/ref.json rename to tests/testresources/refs/geocheck/methane_trans/ref.json diff --git a/tests/refs/geocheck/oct_comp_greedy/ref.json b/tests/testresources/refs/geocheck/oct_comp_greedy/ref.json similarity index 100% rename from tests/refs/geocheck/oct_comp_greedy/ref.json rename to tests/testresources/refs/geocheck/oct_comp_greedy/ref.json diff --git a/tests/refs/geocheck/one_empty_bad/ref.json b/tests/testresources/refs/geocheck/one_empty_bad/ref.json similarity index 100% rename from tests/refs/geocheck/one_empty_bad/ref.json rename to tests/testresources/refs/geocheck/one_empty_bad/ref.json diff --git a/tests/refs/geocheck/one_empty_good/ref.json b/tests/testresources/refs/geocheck/one_empty_good/ref.json similarity index 100% rename from tests/refs/geocheck/one_empty_good/ref.json rename to tests/testresources/refs/geocheck/one_empty_good/ref.json diff --git a/tests/refs/geocheck/rotational_group/ref.json b/tests/testresources/refs/geocheck/rotational_group/ref.json similarity index 100% rename from tests/refs/geocheck/rotational_group/ref.json rename to tests/testresources/refs/geocheck/rotational_group/ref.json diff --git a/tests/refs/geocheck/switch_test/ref.json b/tests/testresources/refs/geocheck/switch_test/ref.json similarity index 100% rename from tests/refs/geocheck/switch_test/ref.json rename to tests/testresources/refs/geocheck/switch_test/ref.json diff --git a/tests/testresources/refs/geocheck/triplebond_linear_broken/ref.json b/tests/testresources/refs/geocheck/triplebond_linear_broken/ref.json new file mode 100644 index 00000000..ce877fc4 --- /dev/null +++ b/tests/testresources/refs/geocheck/triplebond_linear_broken/ref.json @@ -0,0 +1 @@ +{"oct_angle_devi_max": 16.938359558983926, "num_coord_metal": 6, "rmsd_max": 2.3777345741097315, "max_del_sig_angle": 37.45209560748253, "dist_del_eq": 0, "devi_linear_max": 62.79634086322342, "atom_dist_max": "banned_by_user", "devi_linear_avrg": 62.79634086322342, "dist_del_all": 0.24466781959991257} diff --git a/tests/refs/gfnff_NH3_BA.report b/tests/testresources/refs/gfnff_NH3_BA.report similarity index 100% rename from tests/refs/gfnff_NH3_BA.report rename to tests/testresources/refs/gfnff_NH3_BA.report diff --git a/tests/refs/gfnff_NH3_BA.xyz b/tests/testresources/refs/gfnff_NH3_BA.xyz similarity index 100% rename from tests/refs/gfnff_NH3_BA.xyz rename to tests/testresources/refs/gfnff_NH3_BA.xyz diff --git a/tests/refs/joption_pythonic_jobscript b/tests/testresources/refs/joption_pythonic_jobscript similarity index 100% rename from tests/refs/joption_pythonic_jobscript rename to tests/testresources/refs/joption_pythonic_jobscript diff --git a/tests/refs/ligand_from_mol_file.report b/tests/testresources/refs/ligand_from_mol_file.report similarity index 100% rename from tests/refs/ligand_from_mol_file.report rename to tests/testresources/refs/ligand_from_mol_file.report diff --git a/tests/refs/ligand_from_mol_file.xyz b/tests/testresources/refs/ligand_from_mol_file.xyz similarity index 100% rename from tests/refs/ligand_from_mol_file.xyz rename to tests/testresources/refs/ligand_from_mol_file.xyz diff --git a/tests/refs/molcas_caspt2.qcin b/tests/testresources/refs/molcas_caspt2.qcin similarity index 100% rename from tests/refs/molcas_caspt2.qcin rename to tests/testresources/refs/molcas_caspt2.qcin diff --git a/tests/refs/molcas_caspt2.report b/tests/testresources/refs/molcas_caspt2.report similarity index 100% rename from tests/refs/molcas_caspt2.report rename to tests/testresources/refs/molcas_caspt2.report diff --git a/tests/refs/molcas_caspt2.xyz b/tests/testresources/refs/molcas_caspt2.xyz similarity index 100% rename from tests/refs/molcas_caspt2.xyz rename to tests/testresources/refs/molcas_caspt2.xyz diff --git a/tests/refs/molcas_casscf.qcin b/tests/testresources/refs/molcas_casscf.qcin similarity index 100% rename from tests/refs/molcas_casscf.qcin rename to tests/testresources/refs/molcas_casscf.qcin diff --git a/tests/refs/molcas_casscf.report b/tests/testresources/refs/molcas_casscf.report similarity index 100% rename from tests/refs/molcas_casscf.report rename to tests/testresources/refs/molcas_casscf.report diff --git a/tests/refs/molcas_casscf.xyz b/tests/testresources/refs/molcas_casscf.xyz similarity index 100% rename from tests/refs/molcas_casscf.xyz rename to tests/testresources/refs/molcas_casscf.xyz diff --git a/tests/refs/old_ANN.report b/tests/testresources/refs/old_ANN.report similarity index 100% rename from tests/refs/old_ANN.report rename to tests/testresources/refs/old_ANN.report diff --git a/tests/refs/old_ANN.xyz b/tests/testresources/refs/old_ANN.xyz similarity index 100% rename from tests/refs/old_ANN.xyz rename to tests/testresources/refs/old_ANN.xyz diff --git a/tests/refs/old_ref_cp/example_1.report b/tests/testresources/refs/old_ref_cp/example_1.report similarity index 100% rename from tests/refs/old_ref_cp/example_1.report rename to tests/testresources/refs/old_ref_cp/example_1.report diff --git a/tests/refs/old_ref_cp/example_1.xyz b/tests/testresources/refs/old_ref_cp/example_1.xyz similarity index 100% rename from tests/refs/old_ref_cp/example_1.xyz rename to tests/testresources/refs/old_ref_cp/example_1.xyz diff --git a/tests/refs/old_ref_cp/example_1_noff.report b/tests/testresources/refs/old_ref_cp/example_1_noff.report similarity index 100% rename from tests/refs/old_ref_cp/example_1_noff.report rename to tests/testresources/refs/old_ref_cp/example_1_noff.report diff --git a/tests/refs/old_ref_cp/example_1_noff.xyz b/tests/testresources/refs/old_ref_cp/example_1_noff.xyz similarity index 100% rename from tests/refs/old_ref_cp/example_1_noff.xyz rename to tests/testresources/refs/old_ref_cp/example_1_noff.xyz diff --git a/tests/refs/old_ref_cp/example_3.report b/tests/testresources/refs/old_ref_cp/example_3.report similarity index 100% rename from tests/refs/old_ref_cp/example_3.report rename to tests/testresources/refs/old_ref_cp/example_3.report diff --git a/tests/refs/old_ref_cp/example_3.xyz b/tests/testresources/refs/old_ref_cp/example_3.xyz similarity index 100% rename from tests/refs/old_ref_cp/example_3.xyz rename to tests/testresources/refs/old_ref_cp/example_3.xyz diff --git a/tests/refs/old_ref_cp/example_3_noff.report b/tests/testresources/refs/old_ref_cp/example_3_noff.report similarity index 100% rename from tests/refs/old_ref_cp/example_3_noff.report rename to tests/testresources/refs/old_ref_cp/example_3_noff.report diff --git a/tests/refs/old_ref_cp/example_3_noff.xyz b/tests/testresources/refs/old_ref_cp/example_3_noff.xyz similarity index 100% rename from tests/refs/old_ref_cp/example_3_noff.xyz rename to tests/testresources/refs/old_ref_cp/example_3_noff.xyz diff --git a/tests/refs/old_ref_cp/example_5.report b/tests/testresources/refs/old_ref_cp/example_5.report similarity index 100% rename from tests/refs/old_ref_cp/example_5.report rename to tests/testresources/refs/old_ref_cp/example_5.report diff --git a/tests/refs/old_ref_cp/example_5.xyz b/tests/testresources/refs/old_ref_cp/example_5.xyz similarity index 100% rename from tests/refs/old_ref_cp/example_5.xyz rename to tests/testresources/refs/old_ref_cp/example_5.xyz diff --git a/tests/refs/old_ref_cp/example_5_noff.report b/tests/testresources/refs/old_ref_cp/example_5_noff.report similarity index 100% rename from tests/refs/old_ref_cp/example_5_noff.report rename to tests/testresources/refs/old_ref_cp/example_5_noff.report diff --git a/tests/refs/old_ref_cp/example_5_noff.xyz b/tests/testresources/refs/old_ref_cp/example_5_noff.xyz similarity index 100% rename from tests/refs/old_ref_cp/example_5_noff.xyz rename to tests/testresources/refs/old_ref_cp/example_5_noff.xyz diff --git a/tests/refs/old_ref_cp/example_7.report b/tests/testresources/refs/old_ref_cp/example_7.report similarity index 100% rename from tests/refs/old_ref_cp/example_7.report rename to tests/testresources/refs/old_ref_cp/example_7.report diff --git a/tests/refs/old_ref_cp/example_7.xyz b/tests/testresources/refs/old_ref_cp/example_7.xyz similarity index 100% rename from tests/refs/old_ref_cp/example_7.xyz rename to tests/testresources/refs/old_ref_cp/example_7.xyz diff --git a/tests/refs/old_ref_cp/example_8.report b/tests/testresources/refs/old_ref_cp/example_8.report similarity index 100% rename from tests/refs/old_ref_cp/example_8.report rename to tests/testresources/refs/old_ref_cp/example_8.report diff --git a/tests/refs/old_ref_cp/example_8.xyz b/tests/testresources/refs/old_ref_cp/example_8.xyz similarity index 100% rename from tests/refs/old_ref_cp/example_8.xyz rename to tests/testresources/refs/old_ref_cp/example_8.xyz diff --git a/tests/refs/old_ref_cp/example_9.report b/tests/testresources/refs/old_ref_cp/example_9.report similarity index 100% rename from tests/refs/old_ref_cp/example_9.report rename to tests/testresources/refs/old_ref_cp/example_9.report diff --git a/tests/refs/old_ref_cp/example_9.xyz b/tests/testresources/refs/old_ref_cp/example_9.xyz similarity index 100% rename from tests/refs/old_ref_cp/example_9.xyz rename to tests/testresources/refs/old_ref_cp/example_9.xyz diff --git a/tests/refs/old_ref_cp/molcas_caspt2.qcin b/tests/testresources/refs/old_ref_cp/molcas_caspt2.qcin similarity index 100% rename from tests/refs/old_ref_cp/molcas_caspt2.qcin rename to tests/testresources/refs/old_ref_cp/molcas_caspt2.qcin diff --git a/tests/refs/old_ref_cp/molcas_caspt2.report b/tests/testresources/refs/old_ref_cp/molcas_caspt2.report similarity index 100% rename from tests/refs/old_ref_cp/molcas_caspt2.report rename to tests/testresources/refs/old_ref_cp/molcas_caspt2.report diff --git a/tests/refs/old_ref_cp/molcas_caspt2.xyz b/tests/testresources/refs/old_ref_cp/molcas_caspt2.xyz similarity index 100% rename from tests/refs/old_ref_cp/molcas_caspt2.xyz rename to tests/testresources/refs/old_ref_cp/molcas_caspt2.xyz diff --git a/tests/refs/old_ref_cp/molcas_casscf.qcin b/tests/testresources/refs/old_ref_cp/molcas_casscf.qcin similarity index 100% rename from tests/refs/old_ref_cp/molcas_casscf.qcin rename to tests/testresources/refs/old_ref_cp/molcas_casscf.qcin diff --git a/tests/refs/old_ref_cp/molcas_casscf.report b/tests/testresources/refs/old_ref_cp/molcas_casscf.report similarity index 100% rename from tests/refs/old_ref_cp/molcas_casscf.report rename to tests/testresources/refs/old_ref_cp/molcas_casscf.report diff --git a/tests/refs/old_ref_cp/molcas_casscf.xyz b/tests/testresources/refs/old_ref_cp/molcas_casscf.xyz similarity index 100% rename from tests/refs/old_ref_cp/molcas_casscf.xyz rename to tests/testresources/refs/old_ref_cp/molcas_casscf.xyz diff --git a/tests/refs/old_ref_cp/orca_ccsdt.qcin b/tests/testresources/refs/old_ref_cp/orca_ccsdt.qcin similarity index 100% rename from tests/refs/old_ref_cp/orca_ccsdt.qcin rename to tests/testresources/refs/old_ref_cp/orca_ccsdt.qcin diff --git a/tests/refs/old_ref_cp/orca_ccsdt.report b/tests/testresources/refs/old_ref_cp/orca_ccsdt.report similarity index 100% rename from tests/refs/old_ref_cp/orca_ccsdt.report rename to tests/testresources/refs/old_ref_cp/orca_ccsdt.report diff --git a/tests/refs/old_ref_cp/orca_ccsdt.xyz b/tests/testresources/refs/old_ref_cp/orca_ccsdt.xyz similarity index 100% rename from tests/refs/old_ref_cp/orca_ccsdt.xyz rename to tests/testresources/refs/old_ref_cp/orca_ccsdt.xyz diff --git a/tests/refs/old_ref_cp/orca_dft.qcin b/tests/testresources/refs/old_ref_cp/orca_dft.qcin similarity index 100% rename from tests/refs/old_ref_cp/orca_dft.qcin rename to tests/testresources/refs/old_ref_cp/orca_dft.qcin diff --git a/tests/refs/old_ref_cp/orca_dft.report b/tests/testresources/refs/old_ref_cp/orca_dft.report similarity index 100% rename from tests/refs/old_ref_cp/orca_dft.report rename to tests/testresources/refs/old_ref_cp/orca_dft.report diff --git a/tests/refs/old_ref_cp/orca_dft.xyz b/tests/testresources/refs/old_ref_cp/orca_dft.xyz similarity index 100% rename from tests/refs/old_ref_cp/orca_dft.xyz rename to tests/testresources/refs/old_ref_cp/orca_dft.xyz diff --git a/tests/refs/orca_ccsdt.qcin b/tests/testresources/refs/orca_ccsdt.qcin similarity index 100% rename from tests/refs/orca_ccsdt.qcin rename to tests/testresources/refs/orca_ccsdt.qcin diff --git a/tests/testresources/refs/orca_ccsdt.report b/tests/testresources/refs/orca_ccsdt.report new file mode 100644 index 00000000..c8080cc8 --- /dev/null +++ b/tests/testresources/refs/orca_ccsdt.report @@ -0,0 +1,26 @@ +Bad structure?, False +Min_dist (A), 1000 +Was ANN used?, True +geo_label, 1 +geo_prob, 0.9413718581199646 +geo_LSE, 0.6739948349985794 +geo_label_trust, very low +sc_label, 1 +sc_prob, 0.6407925486564636 +sc_LSE, 0.5110593378625077 +sc_label_trust, very low +split, -13.827394459438906 +split_dist, 8.552455363508885 +This spin, 5 +ANN_ground_state, 5 +homo, -13.793439866573024 +gap, 3.4514513871141346 +homo_dist, 0.44729072 +gap_dist, 0.18568888 +ANN_bondl, [2.3605745803152858, 2.3605745803152858, 2.3605745803152858, 2.3605745803152858, 2.2763077827004237, 2.2302417433371216] +homo_trust, high +gap_trust, high +split_trust, very low +Was Catalytic ANN used?, False +Catalytic ANN reason, False +ML-bl (database, A), 2.1 diff --git a/tests/testresources/refs/orca_ccsdt.xyz b/tests/testresources/refs/orca_ccsdt.xyz new file mode 100644 index 00000000..72bcd64b --- /dev/null +++ b/tests/testresources/refs/orca_ccsdt.xyz @@ -0,0 +1,57 @@ +55 +02/06/2019 11:09, XYZ structure generated by mol3D Class, molSimplify +Fe 0.000000 0.000000 0.000000 +N 0.000000 2.360575 0.000000 +C -1.035788 3.192277 0.085736 +C -0.643421 4.510582 0.038070 +C 0.743144 4.470086 -0.077885 +C 1.079671 3.131116 -0.093238 +H -2.053859 2.834210 0.195040 +H -1.272514 5.379877 0.082074 +H 1.415864 5.310455 -0.139639 +H 2.076832 2.719004 -0.181012 +N 2.360575 0.000000 0.000000 +C 3.127732 -0.143112 -1.087315 +C 4.468459 -0.063830 -0.781307 +C 4.531334 0.033282 0.594336 +C 3.225998 0.103080 1.017031 +H 2.712594 -0.281119 -2.073654 +H 5.296854 -0.103185 -1.473983 +H 5.415281 0.067060 1.215491 +H 2.913250 0.226033 2.043499 +N 0.000000 -2.360575 0.000000 +C 0.192850 -3.127647 -1.079157 +C 0.083736 -4.468103 -0.780911 +C -0.100858 -4.531712 0.585622 +C -0.188203 -3.226274 1.003762 +H 0.393839 -2.711751 -2.054473 +H 0.157469 -5.295719 -1.471497 +H -0.182679 -5.415980 1.201590 +H -0.374463 -2.911942 2.020304 +N -2.360575 0.000000 0.000000 +C -3.146744 0.610592 -0.887598 +C -4.475194 0.403300 -0.591083 +C -4.488687 -0.444346 0.507268 +C -3.168394 -0.698140 0.798476 +H -2.731623 1.201389 -1.695534 +H -5.327958 0.808217 -1.116916 +H -5.352374 -0.842062 1.021054 +H -2.782647 -1.346045 1.574617 +N 0.000000 0.000000 2.276308 +C -0.796690 0.836404 2.986431 +C -0.516315 0.556546 4.312459 +C 0.470965 -0.484681 4.342641 +C 0.774482 -0.815638 3.033991 +H -1.455299 1.528309 2.488289 +H -0.963294 1.046319 5.168393 +H 0.910129 -0.931297 5.226080 +H 1.450709 -1.522446 2.580292 +N 0.000000 0.000000 -2.230242 +C -0.817279 -0.692005 -3.028553 +C -0.529141 -0.458721 -4.354299 +C 0.428078 0.543987 -4.356027 +C 0.639646 0.854835 -3.031705 +H -1.555827 -1.372443 -2.622531 +H -0.976958 -0.942071 -5.210385 +H 0.892624 1.009475 -5.213171 +H 1.283841 1.626647 -2.632723 diff --git a/tests/refs/orca_dft.qcin b/tests/testresources/refs/orca_dft.qcin similarity index 100% rename from tests/refs/orca_dft.qcin rename to tests/testresources/refs/orca_dft.qcin diff --git a/tests/testresources/refs/orca_dft.report b/tests/testresources/refs/orca_dft.report new file mode 100644 index 00000000..c8080cc8 --- /dev/null +++ b/tests/testresources/refs/orca_dft.report @@ -0,0 +1,26 @@ +Bad structure?, False +Min_dist (A), 1000 +Was ANN used?, True +geo_label, 1 +geo_prob, 0.9413718581199646 +geo_LSE, 0.6739948349985794 +geo_label_trust, very low +sc_label, 1 +sc_prob, 0.6407925486564636 +sc_LSE, 0.5110593378625077 +sc_label_trust, very low +split, -13.827394459438906 +split_dist, 8.552455363508885 +This spin, 5 +ANN_ground_state, 5 +homo, -13.793439866573024 +gap, 3.4514513871141346 +homo_dist, 0.44729072 +gap_dist, 0.18568888 +ANN_bondl, [2.3605745803152858, 2.3605745803152858, 2.3605745803152858, 2.3605745803152858, 2.2763077827004237, 2.2302417433371216] +homo_trust, high +gap_trust, high +split_trust, very low +Was Catalytic ANN used?, False +Catalytic ANN reason, False +ML-bl (database, A), 2.1 diff --git a/tests/testresources/refs/orca_dft.xyz b/tests/testresources/refs/orca_dft.xyz new file mode 100644 index 00000000..e6715ae6 --- /dev/null +++ b/tests/testresources/refs/orca_dft.xyz @@ -0,0 +1,57 @@ +55 +02/06/2019 11:10, XYZ structure generated by mol3D Class, molSimplify +Fe 0.000000 0.000000 0.000000 +N 0.000000 2.360575 0.000000 +C -1.035788 3.192277 0.085736 +C -0.643421 4.510582 0.038070 +C 0.743144 4.470086 -0.077885 +C 1.079671 3.131116 -0.093238 +H -2.053859 2.834210 0.195040 +H -1.272514 5.379877 0.082074 +H 1.415864 5.310455 -0.139639 +H 2.076832 2.719004 -0.181012 +N 2.360575 0.000000 0.000000 +C 3.127732 -0.143112 -1.087315 +C 4.468459 -0.063830 -0.781307 +C 4.531334 0.033282 0.594336 +C 3.225998 0.103080 1.017031 +H 2.712594 -0.281119 -2.073654 +H 5.296854 -0.103185 -1.473983 +H 5.415281 0.067060 1.215491 +H 2.913250 0.226033 2.043499 +N 0.000000 -2.360575 0.000000 +C 0.192850 -3.127647 -1.079157 +C 0.083736 -4.468103 -0.780911 +C -0.100858 -4.531712 0.585622 +C -0.188203 -3.226274 1.003762 +H 0.393839 -2.711751 -2.054473 +H 0.157469 -5.295719 -1.471497 +H -0.182679 -5.415980 1.201590 +H -0.374463 -2.911942 2.020304 +N -2.360575 0.000000 0.000000 +C -3.146744 0.610592 -0.887598 +C -4.475194 0.403300 -0.591083 +C -4.488687 -0.444346 0.507268 +C -3.168394 -0.698140 0.798476 +H -2.731623 1.201389 -1.695534 +H -5.327958 0.808217 -1.116916 +H -5.352374 -0.842062 1.021054 +H -2.782647 -1.346045 1.574617 +N 0.000000 0.000000 2.276308 +C -0.796690 0.836404 2.986431 +C -0.516315 0.556546 4.312459 +C 0.470965 -0.484681 4.342641 +C 0.774482 -0.815638 3.033991 +H -1.455299 1.528309 2.488289 +H -0.963294 1.046319 5.168393 +H 0.910129 -0.931297 5.226080 +H 1.450709 -1.522446 2.580292 +N 0.000000 0.000000 -2.230242 +C -0.817279 -0.692005 -3.028553 +C -0.529141 -0.458721 -4.354299 +C 0.428078 0.543987 -4.356027 +C 0.639646 0.854835 -3.031705 +H -1.555827 -1.372443 -2.622531 +H -0.976958 -0.942071 -5.210385 +H 0.892624 1.009475 -5.213171 +H 1.283841 1.626647 -2.632723 diff --git a/tests/refs/qcgen/gamgen/FeH2O6/B3LYP/gam.inp b/tests/testresources/refs/qcgen/gamgen/FeH2O6/B3LYP/gam.inp similarity index 100% rename from tests/refs/qcgen/gamgen/FeH2O6/B3LYP/gam.inp rename to tests/testresources/refs/qcgen/gamgen/FeH2O6/B3LYP/gam.inp diff --git a/tests/refs/qcgen/mlpgen/FeH2O6.mop b/tests/testresources/refs/qcgen/mlpgen/FeH2O6.mop similarity index 100% rename from tests/refs/qcgen/mlpgen/FeH2O6.mop rename to tests/testresources/refs/qcgen/mlpgen/FeH2O6.mop diff --git a/tests/refs/qcgen/molcgen/molcas.input b/tests/testresources/refs/qcgen/molcgen/molcas.input similarity index 100% rename from tests/refs/qcgen/molcgen/molcas.input rename to tests/testresources/refs/qcgen/molcgen/molcas.input diff --git a/tests/refs/qcgen/ogen/orca.in b/tests/testresources/refs/qcgen/ogen/orca.in similarity index 100% rename from tests/refs/qcgen/ogen/orca.in rename to tests/testresources/refs/qcgen/ogen/orca.in diff --git a/tests/refs/qcgen/qgen/FeH2O6/B3LYP/qch.inp b/tests/testresources/refs/qcgen/qgen/FeH2O6/B3LYP/qch.inp similarity index 100% rename from tests/refs/qcgen/qgen/FeH2O6/B3LYP/qch.inp rename to tests/testresources/refs/qcgen/qgen/FeH2O6/B3LYP/qch.inp diff --git a/tests/refs/qcgen/tcgen/terachem_input b/tests/testresources/refs/qcgen/tcgen/terachem_input similarity index 100% rename from tests/refs/qcgen/tcgen/terachem_input rename to tests/testresources/refs/qcgen/tcgen/terachem_input diff --git a/tests/refs/racs/co_acac_en_water_hydrogensulfide.xyz b/tests/testresources/refs/racs/co_acac_en_water_hydrogensulfide.xyz similarity index 100% rename from tests/refs/racs/co_acac_en_water_hydrogensulfide.xyz rename to tests/testresources/refs/racs/co_acac_en_water_hydrogensulfide.xyz diff --git a/tests/refs/racs/cr_acac_acac_bipy.xyz b/tests/testresources/refs/racs/cr_acac_acac_bipy.xyz similarity index 100% rename from tests/refs/racs/cr_acac_acac_bipy.xyz rename to tests/testresources/refs/racs/cr_acac_acac_bipy.xyz diff --git a/tests/refs/racs/fe_bipy_2_bifuran.xyz b/tests/testresources/refs/racs/fe_bipy_2_bifuran.xyz similarity index 100% rename from tests/refs/racs/fe_bipy_2_bifuran.xyz rename to tests/testresources/refs/racs/fe_bipy_2_bifuran.xyz diff --git a/tests/refs/racs/fe_bipy_3.xyz b/tests/testresources/refs/racs/fe_bipy_3.xyz similarity index 100% rename from tests/refs/racs/fe_bipy_3.xyz rename to tests/testresources/refs/racs/fe_bipy_3.xyz diff --git a/tests/refs/racs/fe_carbonyl_6.xyz b/tests/testresources/refs/racs/fe_carbonyl_6.xyz similarity index 100% rename from tests/refs/racs/fe_carbonyl_6.xyz rename to tests/testresources/refs/racs/fe_carbonyl_6.xyz diff --git a/tests/refs/racs/fe_pyr_4_furan_2.xyz b/tests/testresources/refs/racs/fe_pyr_4_furan_2.xyz similarity index 100% rename from tests/refs/racs/fe_pyr_4_furan_2.xyz rename to tests/testresources/refs/racs/fe_pyr_4_furan_2.xyz diff --git a/tests/refs/racs/fe_pyr_6.xyz b/tests/testresources/refs/racs/fe_pyr_6.xyz similarity index 100% rename from tests/refs/racs/fe_pyr_6.xyz rename to tests/testresources/refs/racs/fe_pyr_6.xyz diff --git a/tests/refs/racs/generate_references.py b/tests/testresources/refs/racs/generate_references.py similarity index 100% rename from tests/refs/racs/generate_references.py rename to tests/testresources/refs/racs/generate_references.py diff --git a/tests/refs/racs/mn_furan_water_ammonia_furan_water_ammonia.xyz b/tests/testresources/refs/racs/mn_furan_water_ammonia_furan_water_ammonia.xyz similarity index 100% rename from tests/refs/racs/mn_furan_water_ammonia_furan_water_ammonia.xyz rename to tests/testresources/refs/racs/mn_furan_water_ammonia_furan_water_ammonia.xyz diff --git a/tests/refs/racs/racs_Co_acac_en_water_hydrogensulfide.pickle b/tests/testresources/refs/racs/racs_Co_acac_en_water_hydrogensulfide.pickle similarity index 100% rename from tests/refs/racs/racs_Co_acac_en_water_hydrogensulfide.pickle rename to tests/testresources/refs/racs/racs_Co_acac_en_water_hydrogensulfide.pickle diff --git a/tests/refs/racs/racs_Cr_acac_acac_bipy.pickle b/tests/testresources/refs/racs/racs_Cr_acac_acac_bipy.pickle similarity index 100% rename from tests/refs/racs/racs_Cr_acac_acac_bipy.pickle rename to tests/testresources/refs/racs/racs_Cr_acac_acac_bipy.pickle diff --git a/tests/refs/racs/racs_Fe_carbonyl_6.pickle b/tests/testresources/refs/racs/racs_Fe_carbonyl_6.pickle similarity index 100% rename from tests/refs/racs/racs_Fe_carbonyl_6.pickle rename to tests/testresources/refs/racs/racs_Fe_carbonyl_6.pickle diff --git a/tests/refs/racs/racs_Mn_furan_water_ammonia_furan_water_ammonia.pickle b/tests/testresources/refs/racs/racs_Mn_furan_water_ammonia_furan_water_ammonia.pickle similarity index 100% rename from tests/refs/racs/racs_Mn_furan_water_ammonia_furan_water_ammonia.pickle rename to tests/testresources/refs/racs/racs_Mn_furan_water_ammonia_furan_water_ammonia.pickle diff --git a/tests/refs/ref_new/example_1.report b/tests/testresources/refs/ref_new/example_1.report similarity index 100% rename from tests/refs/ref_new/example_1.report rename to tests/testresources/refs/ref_new/example_1.report diff --git a/tests/refs/ref_new/example_1.xyz b/tests/testresources/refs/ref_new/example_1.xyz similarity index 100% rename from tests/refs/ref_new/example_1.xyz rename to tests/testresources/refs/ref_new/example_1.xyz diff --git a/tests/refs/ref_new/example_1_noff.report b/tests/testresources/refs/ref_new/example_1_noff.report similarity index 100% rename from tests/refs/ref_new/example_1_noff.report rename to tests/testresources/refs/ref_new/example_1_noff.report diff --git a/tests/refs/ref_new/example_1_noff.xyz b/tests/testresources/refs/ref_new/example_1_noff.xyz similarity index 100% rename from tests/refs/ref_new/example_1_noff.xyz rename to tests/testresources/refs/ref_new/example_1_noff.xyz diff --git a/tests/refs/ref_new/example_3.report b/tests/testresources/refs/ref_new/example_3.report similarity index 100% rename from tests/refs/ref_new/example_3.report rename to tests/testresources/refs/ref_new/example_3.report diff --git a/tests/refs/ref_new/example_3.xyz b/tests/testresources/refs/ref_new/example_3.xyz similarity index 100% rename from tests/refs/ref_new/example_3.xyz rename to tests/testresources/refs/ref_new/example_3.xyz diff --git a/tests/refs/ref_new/example_3_noff.report b/tests/testresources/refs/ref_new/example_3_noff.report similarity index 100% rename from tests/refs/ref_new/example_3_noff.report rename to tests/testresources/refs/ref_new/example_3_noff.report diff --git a/tests/refs/ref_new/example_3_noff.xyz b/tests/testresources/refs/ref_new/example_3_noff.xyz similarity index 100% rename from tests/refs/ref_new/example_3_noff.xyz rename to tests/testresources/refs/ref_new/example_3_noff.xyz diff --git a/tests/refs/ref_new/example_5.report b/tests/testresources/refs/ref_new/example_5.report similarity index 100% rename from tests/refs/ref_new/example_5.report rename to tests/testresources/refs/ref_new/example_5.report diff --git a/tests/refs/ref_new/example_5.xyz b/tests/testresources/refs/ref_new/example_5.xyz similarity index 100% rename from tests/refs/ref_new/example_5.xyz rename to tests/testresources/refs/ref_new/example_5.xyz diff --git a/tests/refs/ref_new/example_7.report b/tests/testresources/refs/ref_new/example_7.report similarity index 100% rename from tests/refs/ref_new/example_7.report rename to tests/testresources/refs/ref_new/example_7.report diff --git a/tests/refs/ref_new/example_7.xyz b/tests/testresources/refs/ref_new/example_7.xyz similarity index 100% rename from tests/refs/ref_new/example_7.xyz rename to tests/testresources/refs/ref_new/example_7.xyz diff --git a/tests/refs/ref_new/example_8.report b/tests/testresources/refs/ref_new/example_8.report similarity index 100% rename from tests/refs/ref_new/example_8.report rename to tests/testresources/refs/ref_new/example_8.report diff --git a/tests/refs/ref_new/example_8.xyz b/tests/testresources/refs/ref_new/example_8.xyz similarity index 100% rename from tests/refs/ref_new/example_8.xyz rename to tests/testresources/refs/ref_new/example_8.xyz diff --git a/tests/refs/ref_new/molcas_caspt2.qcin b/tests/testresources/refs/ref_new/molcas_caspt2.qcin similarity index 100% rename from tests/refs/ref_new/molcas_caspt2.qcin rename to tests/testresources/refs/ref_new/molcas_caspt2.qcin diff --git a/tests/refs/ref_new/molcas_caspt2.report b/tests/testresources/refs/ref_new/molcas_caspt2.report similarity index 100% rename from tests/refs/ref_new/molcas_caspt2.report rename to tests/testresources/refs/ref_new/molcas_caspt2.report diff --git a/tests/refs/ref_new/molcas_caspt2.xyz b/tests/testresources/refs/ref_new/molcas_caspt2.xyz similarity index 100% rename from tests/refs/ref_new/molcas_caspt2.xyz rename to tests/testresources/refs/ref_new/molcas_caspt2.xyz diff --git a/tests/refs/ref_new/molcas_casscf.qcin b/tests/testresources/refs/ref_new/molcas_casscf.qcin similarity index 100% rename from tests/refs/ref_new/molcas_casscf.qcin rename to tests/testresources/refs/ref_new/molcas_casscf.qcin diff --git a/tests/refs/ref_new/molcas_casscf.report b/tests/testresources/refs/ref_new/molcas_casscf.report similarity index 100% rename from tests/refs/ref_new/molcas_casscf.report rename to tests/testresources/refs/ref_new/molcas_casscf.report diff --git a/tests/refs/ref_new/molcas_casscf.xyz b/tests/testresources/refs/ref_new/molcas_casscf.xyz similarity index 100% rename from tests/refs/ref_new/molcas_casscf.xyz rename to tests/testresources/refs/ref_new/molcas_casscf.xyz diff --git a/tests/refs/ref_new/orca_ccsdt.qcin b/tests/testresources/refs/ref_new/orca_ccsdt.qcin similarity index 100% rename from tests/refs/ref_new/orca_ccsdt.qcin rename to tests/testresources/refs/ref_new/orca_ccsdt.qcin diff --git a/tests/refs/ref_new/orca_ccsdt.report b/tests/testresources/refs/ref_new/orca_ccsdt.report similarity index 100% rename from tests/refs/ref_new/orca_ccsdt.report rename to tests/testresources/refs/ref_new/orca_ccsdt.report diff --git a/tests/refs/ref_new/orca_ccsdt.xyz b/tests/testresources/refs/ref_new/orca_ccsdt.xyz similarity index 100% rename from tests/refs/ref_new/orca_ccsdt.xyz rename to tests/testresources/refs/ref_new/orca_ccsdt.xyz diff --git a/tests/refs/ref_new/orca_dft.qcin b/tests/testresources/refs/ref_new/orca_dft.qcin similarity index 100% rename from tests/refs/ref_new/orca_dft.qcin rename to tests/testresources/refs/ref_new/orca_dft.qcin diff --git a/tests/refs/ref_new/orca_dft.report b/tests/testresources/refs/ref_new/orca_dft.report similarity index 100% rename from tests/refs/ref_new/orca_dft.report rename to tests/testresources/refs/ref_new/orca_dft.report diff --git a/tests/refs/ref_new/orca_dft.xyz b/tests/testresources/refs/ref_new/orca_dft.xyz similarity index 100% rename from tests/refs/ref_new/orca_dft.xyz rename to tests/testresources/refs/ref_new/orca_dft.xyz diff --git a/tests/refs/tetrahedral_1_noff.report b/tests/testresources/refs/tetrahedral_1_noff.report similarity index 100% rename from tests/refs/tetrahedral_1_noff.report rename to tests/testresources/refs/tetrahedral_1_noff.report diff --git a/tests/testresources/refs/tetrahedral_1_noff.xyz b/tests/testresources/refs/tetrahedral_1_noff.xyz new file mode 100644 index 00000000..ef1fdd0a --- /dev/null +++ b/tests/testresources/refs/tetrahedral_1_noff.xyz @@ -0,0 +1,15 @@ +13 +10/26/2021 11:00, XYZ structure generated by mol3D Class, molSimplify +Co 0.000000 0.000000 0.000000 +O 2.010020 -0.000000 0.000000 +H 2.616218 0.027327 -0.782547 +H 2.616204 -0.027327 0.782547 +O -0.670013 -1.291396 -1.386886 +H -0.172026 -1.667654 -2.155678 +H -1.572146 -1.694076 -1.454629 +O -0.670019 1.846773 -0.424942 +H -0.150583 2.615195 -0.771809 +H -1.593605 2.192279 -0.334391 +O -0.670021 -0.555396 1.811817 +H -1.010153 0.026841 2.537015 +H -0.734041 -1.472633 2.179461 diff --git a/tests/refs/tetrahedral_2_noff.report b/tests/testresources/refs/tetrahedral_2_noff.report similarity index 100% rename from tests/refs/tetrahedral_2_noff.report rename to tests/testresources/refs/tetrahedral_2_noff.report diff --git a/tests/refs/tetrahedral_2_noff.xyz b/tests/testresources/refs/tetrahedral_2_noff.xyz similarity index 100% rename from tests/refs/tetrahedral_2_noff.xyz rename to tests/testresources/refs/tetrahedral_2_noff.xyz diff --git a/tests/refs/tutorial_09_part_one.report b/tests/testresources/refs/tutorial_09_part_one.report similarity index 100% rename from tests/refs/tutorial_09_part_one.report rename to tests/testresources/refs/tutorial_09_part_one.report diff --git a/tests/refs/tutorial_09_part_one.xyz b/tests/testresources/refs/tutorial_09_part_one.xyz similarity index 100% rename from tests/refs/tutorial_09_part_one.xyz rename to tests/testresources/refs/tutorial_09_part_one.xyz diff --git a/tests/refs/tutorial_09_part_two.report b/tests/testresources/refs/tutorial_09_part_two.report similarity index 100% rename from tests/refs/tutorial_09_part_two.report rename to tests/testresources/refs/tutorial_09_part_two.report diff --git a/tests/testresources/refs/tutorial_09_part_two.xyz b/tests/testresources/refs/tutorial_09_part_two.xyz new file mode 100644 index 00000000..7cfcd5d5 --- /dev/null +++ b/tests/testresources/refs/tutorial_09_part_two.xyz @@ -0,0 +1,27 @@ +25 +08/10/2020 15:20, XYZ structure generated by mol3D Class, molSimplify +Zn -0.195653 0.009149 0.718395 +C 2.020403 0.671841 -0.078088 +C 2.061021 -0.757836 0.321456 +N 0.657954 -1.162802 0.265974 +N 0.826951 1.175104 0.597126 +H 1.881333 0.732044 -1.186333 +H 2.957806 1.221601 0.180064 +H 2.443850 -0.839985 1.358134 +H 2.735858 -1.355827 -0.333656 +H 0.520161 -2.055398 0.785394 +H 0.449242 -1.313973 -0.755174 +H 0.577438 2.063047 0.106757 +H 1.145840 1.545865 1.515468 +O 1.438187 0.154958 3.222649 +O -0.395159 0.067383 4.454483 +O -0.537446 -0.095021 2.100430 +C 0.223039 0.016226 3.248666 +H 0.105444 0.232962 5.270613 +N -1.459486 1.244963 -0.339476 +H -2.471390 0.991737 -0.258987 +H -1.488937 2.261222 -0.086587 +H -1.254328 1.216064 -1.366289 +O -1.745904 -1.266647 0.356920 +H -1.760757 -2.141303 0.828099 +H -2.500159 -1.355786 -0.280263 diff --git a/tests/refs/tutorial_10_part_one.report b/tests/testresources/refs/tutorial_10_part_one.report similarity index 100% rename from tests/refs/tutorial_10_part_one.report rename to tests/testresources/refs/tutorial_10_part_one.report diff --git a/tests/refs/tutorial_10_part_one.xyz b/tests/testresources/refs/tutorial_10_part_one.xyz similarity index 100% rename from tests/refs/tutorial_10_part_one.xyz rename to tests/testresources/refs/tutorial_10_part_one.xyz diff --git a/tests/refs/tutorial_10_part_two.report b/tests/testresources/refs/tutorial_10_part_two.report similarity index 100% rename from tests/refs/tutorial_10_part_two.report rename to tests/testresources/refs/tutorial_10_part_two.report diff --git a/tests/refs/tutorial_10_part_two.xyz b/tests/testresources/refs/tutorial_10_part_two.xyz similarity index 100% rename from tests/refs/tutorial_10_part_two.xyz rename to tests/testresources/refs/tutorial_10_part_two.xyz diff --git a/tests/refs/tutorial_2.xyz b/tests/testresources/refs/tutorial_2.xyz similarity index 100% rename from tests/refs/tutorial_2.xyz rename to tests/testresources/refs/tutorial_2.xyz diff --git a/tests/refs/tutorial_3.report b/tests/testresources/refs/tutorial_3.report similarity index 100% rename from tests/refs/tutorial_3.report rename to tests/testresources/refs/tutorial_3.report diff --git a/tests/refs/tutorial_3.xyz b/tests/testresources/refs/tutorial_3.xyz similarity index 100% rename from tests/refs/tutorial_3.xyz rename to tests/testresources/refs/tutorial_3.xyz diff --git a/tests/testresources/refs/tutorial_4/dissimres.smi b/tests/testresources/refs/tutorial_4/dissimres.smi new file mode 100644 index 00000000..ea846774 --- /dev/null +++ b/tests/testresources/refs/tutorial_4/dissimres.smi @@ -0,0 +1,10 @@ +N#CC 1 +c1c(nc(cc1)F)F 3 +N1(C=CNC1)C 4 +[nH]1cncc1 1 +N1=CNCC=C1 1 +FC1CCNC1 5 +Nc1cncc(Cl)n1 1 +ClCc1cnccc1 5 +N(C)CC 1 +c1ccc(cc1N)F 7 diff --git a/tests/testresources/refs/tutorial_4/simres.smi b/tests/testresources/refs/tutorial_4/simres.smi new file mode 100644 index 00000000..b069a89f --- /dev/null +++ b/tests/testresources/refs/tutorial_4/simres.smi @@ -0,0 +1,15 @@ +N#CC 1 +c1c(nc(cc1)F)F 3 +FC1CCNC1 5 +N1(C=CNC1)C 4 +c1ccc(cc1N)F 7 +Nc1cncc(Cl)n1 1 +N(C)CC 1 +ClCc1cnccc1 5 +N1=CNCC=C1 1 +[nH]1cncc1 1 +C(#N)c1ncncc1 2 +N(CC#N)CC#N 1 +c1(nc(ccn1)N)N 2 +[nH]1ncnc1 1 +c1(ccccc1)C#N 8 diff --git a/tests/testresources/refs/tutorial_4/simres_human.smi b/tests/testresources/refs/tutorial_4/simres_human.smi new file mode 100644 index 00000000..3f7f5c59 --- /dev/null +++ b/tests/testresources/refs/tutorial_4/simres_human.smi @@ -0,0 +1,5 @@ +c1cc2c(c(c1)C(F)(F)F)nc(cc2[C](O)CN1CCN(CC1)CCNC[C](c1c2cccc(c2nc(c1)C(F)(F)F)C(F)(F)F)O)C(F)(F)F 21,26 +Cc1cc(cc2nnc(Nc3ccc(cc3)S(=O)(=O)NCCN3CCCC3)nc12)c1cc(O)ccc1Br 20,23 +N1(CCN(CC1)C(CN1CCC(CC1)N1CCCCC1)c1ccccc1)C(=O)C1OCCC1 4,9 +O=P(O)(CCN(CCN(CCn1c2c(nc1)c(=O)[nH]cn2)CCP(=O)(O)O)CCO)O 6,9 +N1(CCN(CC1)CCNCc1onc(c1)C(C)C)C(=O)c1cc(cc(c1)C(F)(F)F)C(F)(F)F 4,9 diff --git a/tests/refs/tutorial_6.xyz b/tests/testresources/refs/tutorial_6.xyz similarity index 100% rename from tests/refs/tutorial_6.xyz rename to tests/testresources/refs/tutorial_6.xyz diff --git a/tests/refs/tutorial_8_part_one.report b/tests/testresources/refs/tutorial_8_part_one.report similarity index 100% rename from tests/refs/tutorial_8_part_one.report rename to tests/testresources/refs/tutorial_8_part_one.report diff --git a/tests/refs/tutorial_8_part_one.xyz b/tests/testresources/refs/tutorial_8_part_one.xyz similarity index 100% rename from tests/refs/tutorial_8_part_one.xyz rename to tests/testresources/refs/tutorial_8_part_one.xyz diff --git a/tests/refs/tutorial_8_part_two.report b/tests/testresources/refs/tutorial_8_part_two.report similarity index 100% rename from tests/refs/tutorial_8_part_two.report rename to tests/testresources/refs/tutorial_8_part_two.report diff --git a/tests/refs/tutorial_8_part_two.xyz b/tests/testresources/refs/tutorial_8_part_two.xyz similarity index 100% rename from tests/refs/tutorial_8_part_two.xyz rename to tests/testresources/refs/tutorial_8_part_two.xyz diff --git a/tests/refs/tutorial_qm9_part_one.xyz b/tests/testresources/refs/tutorial_qm9_part_one.xyz similarity index 100% rename from tests/refs/tutorial_qm9_part_one.xyz rename to tests/testresources/refs/tutorial_qm9_part_one.xyz diff --git a/tests/refs/xtb_ANC_fail.report b/tests/testresources/refs/xtb_ANC_fail.report similarity index 100% rename from tests/refs/xtb_ANC_fail.report rename to tests/testresources/refs/xtb_ANC_fail.report diff --git a/tests/refs/xtb_ANC_fail.xyz b/tests/testresources/refs/xtb_ANC_fail.xyz similarity index 100% rename from tests/refs/xtb_ANC_fail.xyz rename to tests/testresources/refs/xtb_ANC_fail.xyz diff --git a/tests/refs/xtb_H2O_before.report b/tests/testresources/refs/xtb_H2O_before.report similarity index 100% rename from tests/refs/xtb_H2O_before.report rename to tests/testresources/refs/xtb_H2O_before.report diff --git a/tests/refs/xtb_H2O_before.xyz b/tests/testresources/refs/xtb_H2O_before.xyz similarity index 100% rename from tests/refs/xtb_H2O_before.xyz rename to tests/testresources/refs/xtb_H2O_before.xyz diff --git a/tests/refs/xtb_bipy_spin5.report b/tests/testresources/refs/xtb_bipy_spin5.report similarity index 100% rename from tests/refs/xtb_bipy_spin5.report rename to tests/testresources/refs/xtb_bipy_spin5.report diff --git a/tests/refs/xtb_bipy_spin5.xyz b/tests/testresources/refs/xtb_bipy_spin5.xyz similarity index 100% rename from tests/refs/xtb_bipy_spin5.xyz rename to tests/testresources/refs/xtb_bipy_spin5.xyz diff --git a/tests/refs/xtb_final_opt.report b/tests/testresources/refs/xtb_final_opt.report similarity index 100% rename from tests/refs/xtb_final_opt.report rename to tests/testresources/refs/xtb_final_opt.report diff --git a/tests/refs/xtb_final_opt.xyz b/tests/testresources/refs/xtb_final_opt.xyz similarity index 100% rename from tests/refs/xtb_final_opt.xyz rename to tests/testresources/refs/xtb_final_opt.xyz diff --git a/tests/refs/xtb_imidazole_BA.report b/tests/testresources/refs/xtb_imidazole_BA.report similarity index 100% rename from tests/refs/xtb_imidazole_BA.report rename to tests/testresources/refs/xtb_imidazole_BA.report diff --git a/tests/refs/xtb_imidazole_BA.xyz b/tests/testresources/refs/xtb_imidazole_BA.xyz similarity index 100% rename from tests/refs/xtb_imidazole_BA.xyz rename to tests/testresources/refs/xtb_imidazole_BA.xyz