diff --git a/.cruft.json b/.cruft.json new file mode 100644 index 0000000..46ee67b --- /dev/null +++ b/.cruft.json @@ -0,0 +1,26 @@ +{ + "template": "https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin", + "commit": "c40010ce548126347c5fd7b36c2a5031bcd0b34b", + "checkout": null, + "context": { + "cookiecutter": { + "full_name": "Jose M. Pizarro", + "email": "jose.pizarro@physik.hu-berlin.de", + "github_username": "JosePizarro3", + "plugin_name": "nomad-parser-wannier90", + "module_name": "nomad_parser_wannier90", + "short_description": "NOMAD parser plugin for Wannier90 input/output files.", + "version": "0.0.1", + "license": "Apache Software License 2.0", + "include_schema_package": true, + "include_normalizer": false, + "include_parser": true, + "include_app": false, + "_copy_without_render": [ + "*.html" + ], + "_template": "https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin" + } + }, + "directory": null +} diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml new file mode 100644 index 0000000..f80ffed --- /dev/null +++ b/.github/workflows/actions.yml @@ -0,0 +1,74 @@ +name: install-and-test +on: [push] + +# https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs +# `contents` is for permission to the contents of the repository. +# `pull-requests` is for permission to pull request +permissions: + contents: write + checks: write + pull-requests: write + +jobs: + install-and-test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Set up Python 3.9 + uses: actions/setup-python@v5 + with: + python-version: 3.9 + - name: Install dependencies + run: | + pip install --upgrade pip + pip install uv + uv pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple --system + uv pip install coveralls --system + - name: mypy + run: | + python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional src/nomad_parser_wannier90/schema_packages src/nomad_parser_wannier90/parsers tests + - name: Build coverage file + run: | + pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=src tests | tee pytest-coverage.txt + - name: Pytest coverage comment + uses: MishaKav/pytest-coverage-comment@main + with: + pytest-coverage-path: pytest-coverage.txt + junitxml-path: pytest.xml + - name: Submit to coveralls + continue-on-error: true + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: | + coveralls --service=github + build-and-install: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Set up Python 3.9 + uses: actions/setup-python@v5 + with: + python-version: 3.9 + - name: Build the package + run: | + pip install uv + uv pip install --upgrade pip --system + uv pip install build --system + python -m build --sdist + - name: Install the package + run: | + uv pip install dist/*.tar.gz --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple --system + ruff-linting: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: chartboost/ruff-action@v1 + with: + args: "check ." + ruff-formatting: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: chartboost/ruff-action@v1 + with: + args: "format . --check --verbose" diff --git a/.github/workflows/mkdocs-deploy.yml b/.github/workflows/mkdocs-deploy.yml new file mode 100644 index 0000000..c46ff23 --- /dev/null +++ b/.github/workflows/mkdocs-deploy.yml @@ -0,0 +1,24 @@ +name: Deploy MkDocs Site + +on: + push: + branches: + - main # Triggers deployment on push to the main branch + +permissions: + contents: write + +jobs: + deploy: + runs-on: ubuntu-latest + + steps: + - name: Checkout Repository + uses: actions/checkout@v4 + + - name: Deploy docs + uses: mhausenblas/mkdocs-deploy-gh-pages@master + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + CONFIG_FILE: mkdocs.yml + REQUIREMENTS: requirements_docs.txt diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..d4e4675 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,43 @@ +# This workflow will upload a Python Package using Twine when a release is created +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries + +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Build and Publish Python Package + +on: + release: + types: [published] + +permissions: + contents: read + +jobs: + deploy: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python 3.9 + uses: actions/setup-python@v3 + with: + python-version: '3.9' + + - name: Install dependencies + run: | + pip install --upgrade pip + pip install build + + - name: Build package + run: python -m build + + - name: Publish package to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + password: ${{ secrets.PYPI_API_TOKEN }} \ No newline at end of file diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b1619d4 --- /dev/null +++ b/.gitignore @@ -0,0 +1,130 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ +.pyenv + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..04985fc --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,17 @@ +{ + "editor.rulers": [ + 90 + ], + "editor.renderWhitespace": "all", + "editor.tabSize": 4, + "files.trimTrailingWhitespace": true, + "[python]": { + "editor.formatOnSave": true, + "editor.defaultFormatter": "charliermarsh.ruff" + }, + "python.testing.pytestArgs": [ + "tests" + ], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true +} diff --git a/LICENSE b/LICENSE index 261eeb9..427417b 100644 --- a/LICENSE +++ b/LICENSE @@ -1,3 +1,4 @@ + Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ @@ -178,7 +179,7 @@ APPENDIX: How to apply the Apache License to your work. To apply the Apache License to your work, attach the following - boilerplate notice, with the fields enclosed by brackets "[]" + boilerplate notice, with the fields enclosed by brackets "{}" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a @@ -186,7 +187,7 @@ same "printed page" as the copyright notice for easier identification within third-party archives. - Copyright [yyyy] [name of copyright owner] + Copyright {yyyy} {name of copyright owner} Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..b5ccc2d --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1 @@ +recursive-include * nomad_plugin.yaml diff --git a/README.md b/README.md index fcf513e..33075f2 100644 --- a/README.md +++ b/README.md @@ -1,84 +1,93 @@ -# nomad-plugin-template -A template repository for creating a repository with a NOMAD plugin package. +# nomad-nomad-parser-wannier90 +NOMAD parser plugin for Wannier90 input/output files. -## Getting started +---- -1. Click on the `Use this template` button and create a new plugin repository. The form will ask you to fill out the name for the new plugin repository. +This `nomad`_ plugin was generated with `Cookiecutter`_ along with `@nomad`_'s `cookiecutter-nomad-plugin`_ template. -2. In the newly created repository, start a new Github Codespace and generate the plugin structure. -Run the following command to create a new NOMAD plugin project using cookiecutter-nomad-plugin: +### Install + +You should create a virtual environment. You will need the `nomad-lab` package (and `pytest`). +We recommend using Python 3.9. ```sh -cruft create https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin +python3 -m venv .pyenv +source .pyenv/bin/activate +pip install --upgrade pip +pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple ``` -Cookiecutter prompts you for information regarding your plugin: - -```no-highlight -full_name [John Doe]: Citizen Kane -email [john.doe@physik.hu-berlin.de]: citizen@kane.de -github_username [foo]: kane -plugin_name [foobar]: awesome-tools -module_name [awesome_tools]: awesome_tools -short_description [NOMAD example template]: An awesome plugin for NOMAD -version [0.1.0]: -Select license: -1 - MIT -2 - BSD-3 -3 - GNU GPL v3.0+ -Choose from 1, 2, 3 [1]: 2 -include_schema_package [y/n] (y): y -include_normalizer [y/n] (y): n -include_parser [y/n] (y): y -include_app [y/n] (y): n - -INFO:post_gen_project:Initializing python for package - src -.. -INFO:post_gen_project:Remove temporary folder: licenses -INFO:post_gen_project:Remove temporary folder: macros -INFO:post_gen_project:Remove temporary folder: py_sources +**Note!** +Until we have an official pypi NOMAD release with the plugins functionality. Make +sure to include NOMAD's internal package registry (e.g. via `--index-url`). + +### Testing + +You can run automated tests with `pytest`: + +```sh +pytest -svx tests ``` +### Run linting + +```sh +ruff check . +``` +### Run auto-formatting +This is entirely optional. To add this as a check in github actions pipeline, uncomment the `ruff-formatting` step in `./github/workflows/actions.yaml`. -There you go - you just created a minimal NOMAD plugin: - -> [!NOTE] -> In the above prompt, we pressed `y` for schema_package and parser, this creates a python package with two plugin entry points: one for parser and one for schema_package. - -```no-highlight -nomad-awesome-tools/ -├── LICENSE -├── README.rst -├── pyproject.toml -├── move_template_files.sh -├── src -│ └── nomad_awesome_tools -│ ├── __init__.py -| ├── schema_packages -│ | ├── __init__.py -│ | └── plugin.py -| └── parsers -│ ├── __init__.py -│ └── plugin.py -| -├── tests -│ ├── conftest.py -│ └── test_awesome.py -└── MANIFEST.in +```sh +ruff format . ``` +### Developing a NOMAD plugin + +Follow the [guide](https://nomad-lab.eu/prod/v1/staging/docs/howto/plugins/plugins.html) on how to develop NOMAD plugins. + +### Build the python package -> [!NOTE] -> The project `nomad-awesome-tools` is created in a new directory, we have included a helper script to move all the files to the parent level of the repository. +The `pyproject.toml` file contains everything that is necessary to turn the project +into a pip installable python package. Run the python build tool to create a package distribution: + +``` +pip install build +python -m build --sdist +``` +You can install the package with pip: + +``` +pip install dist/nomad-nomad-parser-wannier90-0.0.1 +``` + +Read more about python packages, `pyproject.toml`, and how to upload packages to PyPI +on the [PyPI documentation](https://packaging.python.org/en/latest/tutorials/packaging-projects/). + +### Documentation on Github pages + +To deploy documentation on Github pages, make sure to [enable GitHub pages via the repo settings](https://docs.github.com/en/pages/getting-started-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site#publishing-from-a-branch). + +To view the documentation locally, install the documentation related packages using: ```sh -sh CHANGE_TO_PLUGIN_NAME/move_template_files.sh +pip install -r requirements_docs.txt ``` -> [!IMPORTANT] -> The `CHANGE_TO_PLUGIN_NAME` should be substituted by the name of the plugin you've created. In the above case it'll be `sh nomad-awesome-tools/move_template_files.sh`. +Run the documentation server: +```sh +mkdocs serve +``` + +### Template update + +We use cruft to update the project based on template changes. A `cruft-update.yml` is included in Github workflows to automatically check for updates and create pull requests to apply updates. Follow the [instructions](https://github.blog/changelog/2022-05-03-github-actions-prevent-github-actions-from-creating-and-approving-pull-requests/) on how to enable Github Actions to create pull requests. + +To run the check for updates locally, follow the instructions on [`cruft` website](https://cruft.github.io/cruft/#updating-a-project). + +### License +Distributed under the terms of the `Apache Software License 2.0`_ license, "nomad-nomad-parser-wannier90" is free and open source software diff --git a/docs/assets/.gitignore b/docs/assets/.gitignore new file mode 100644 index 0000000..3881e38 --- /dev/null +++ b/docs/assets/.gitignore @@ -0,0 +1 @@ +nomad-oasis*.zip \ No newline at end of file diff --git a/docs/assets/favicon.png b/docs/assets/favicon.png new file mode 100644 index 0000000..f84c78f Binary files /dev/null and b/docs/assets/favicon.png differ diff --git a/docs/assets/nomad-plugin-logo.png b/docs/assets/nomad-plugin-logo.png new file mode 100644 index 0000000..149856c Binary files /dev/null and b/docs/assets/nomad-plugin-logo.png differ diff --git a/docs/explanation/explanation.md b/docs/explanation/explanation.md new file mode 100644 index 0000000..a2035f6 --- /dev/null +++ b/docs/explanation/explanation.md @@ -0,0 +1,4 @@ +# Explanation + +!!! note "Attention" + TODO diff --git a/docs/how_to/contribute_to_the_documentation.md b/docs/how_to/contribute_to_the_documentation.md new file mode 100644 index 0000000..173dce1 --- /dev/null +++ b/docs/how_to/contribute_to_the_documentation.md @@ -0,0 +1,4 @@ +# Contribute to the documentation + +!!! note "Attention" + TODO diff --git a/docs/how_to/contribute_to_this_plugin.md b/docs/how_to/contribute_to_this_plugin.md new file mode 100644 index 0000000..48d405a --- /dev/null +++ b/docs/how_to/contribute_to_this_plugin.md @@ -0,0 +1,5 @@ +# Contribute to This Plugin + +!!! note "Attention" + TODO + diff --git a/docs/how_to/install_this_plugin.md b/docs/how_to/install_this_plugin.md new file mode 100644 index 0000000..2b45e0f --- /dev/null +++ b/docs/how_to/install_this_plugin.md @@ -0,0 +1,4 @@ +# Install This Plugin + +!!! note "Attention" + TODO diff --git a/docs/how_to/use_this_plugin.md b/docs/how_to/use_this_plugin.md new file mode 100644 index 0000000..ad93966 --- /dev/null +++ b/docs/how_to/use_this_plugin.md @@ -0,0 +1,10 @@ +# How to Use This Plugin + +This plugin can be used in a NOMAD Oasis installation. + +## Add This Plugin to Your NOMAD installation + +Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/plugins/plugins.html#add-a-plugin-to-your-nomad) for all details on how to deploy the plugin on your NOMAD instance. + +!!! note "Attention" + TODO diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..2a2461b --- /dev/null +++ b/docs/index.md @@ -0,0 +1,48 @@ +# Welcome to the `nomad-parser-wannier90` documentation + +NOMAD parser plugin for Wannier90 input/output files. + +## Introduction + +!!! note "Attention" + TODO + +
+
+ +### Tutorial + +TODO + +- [Tutorial](tutorial/tutorial.md) + +
+
+ +### How-to guides + +How-to guides provide step-by-step instructions for a wide range of tasks, with the overarching topics: + +- [Install this plugin](how_to/install_this_plugin.md) +- [Use this plugin](how_to/use_this_plugin.md) +- [Contribute to this plugin](how_to/contribute_to_this_plugin.md) +- [Contribute to the documentation](how_to/contribute_to_the_documentation.md) + +
+ +
+ +### Explanation + +The explanation [section](explanation/explanation.md) provides background knowledge on this plugin. + +
+
+ +### Reference + +The reference [section](reference/references.md) includes all CLI commands and arguments, all configuration options, +the possible schema annotations and their arguments, and a glossary of used terms. + +
+
diff --git a/docs/reference/references.md b/docs/reference/references.md new file mode 100644 index 0000000..c199e70 --- /dev/null +++ b/docs/reference/references.md @@ -0,0 +1,4 @@ +# References + +!!! note "Attention" + TODO diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css new file mode 100644 index 0000000..321e087 --- /dev/null +++ b/docs/stylesheets/extra.css @@ -0,0 +1,69 @@ + +.md-header__button.md-logo :where(img,svg) { + width: 100%; + height: 30px; +} + +.md-header, .md-header__inner { + background-color: #fff; + color: #2A4CDF; +} + +.md-header[data-md-state=shadow] { + box-shadow: 0px 2px 4px -1px rgb(0 0 0 / 20%), 0px 4px 5px 0px rgb(0 0 0 / 14%), 0px 1px 10px 0px rgb(0 0 0 / 12%); + transition: box-shadow 200ms linear; +} + +.md-header__inner { + height: 80px; +} + +.md-header__topic { + font-size: 24px; +} + +.md-footer { + background-color: #2A4CDF; +} + +.md-search__form:hover { + background-color: rgba(0,0,0,.13); +} + +.md-typeset h1 { + color: black; + font-weight: 700; +} + +.youtube { + position: relative; + width: 100%; + height: 0; + padding-bottom: 56.25%; +} + +.youtube iframe { + position: absolute; + top: 0; + left: 0; + width: 100%; + height: 100%; +} + +.home-grid { + display: grid; + grid-template-columns: 1fr 1fr; + grid-column-gap: 24px; + row-gap: 24px; +} + +.home-grid div { + border-radius: 4px; + padding: 24px; + background-color: #f3e9d9; +} + +.home-grid h3 { + margin-top: 0; + font-weight: 700; +} \ No newline at end of file diff --git a/docs/theme/partials/header.html b/docs/theme/partials/header.html new file mode 100644 index 0000000..5b091f3 --- /dev/null +++ b/docs/theme/partials/header.html @@ -0,0 +1,86 @@ +{#- + This file was automatically generated - do not edit +-#} +{% set class = "md-header" %} +{% if "navigation.tabs.sticky" in features %} + {% set class = class ~ " md-header--lifted" %} +{% endif %} +
+ + {% if "navigation.tabs.sticky" in features %} + {% if "navigation.tabs" in features %} + {% include "partials/tabs.html" %} + {% endif %} + {% endif %} +
\ No newline at end of file diff --git a/docs/tutorial/tutorial.md b/docs/tutorial/tutorial.md new file mode 100644 index 0000000..a24d72a --- /dev/null +++ b/docs/tutorial/tutorial.md @@ -0,0 +1,4 @@ +# Tutorial + +!!! note "Attention" + TODO diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..7ce93b2 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,60 @@ +site_name: nomad-parser-wannier90 +site_description: NOMAD parser plugin for Wannier90 input/output files. +site_author: Jose M. Pizarro + +repo_url: https://github.com/FAIRmat-NFDI/nomad-parser-wannier90 +edit_uri: "" + +nav: + - Home: index.md + - Tutorial: tutorial/tutorial.md + - How-to guides: + - Install this Plugin: how_to/install_this_plugin.md + - Use this Plugin: how_to/use_this_plugin.md + - Contribute to this plugin: how_to/contribute_to_this_plugin.md + - Contribute to the documentation: how_to/contribute_to_the_documentation.md + - Explanation: explanation/explanation.md + - Reference: reference/references.md +plugins: + - search +theme: + name: material + palette: + primary: "#2A4CDF" + accent: "#008A67" + font: + text: "Titillium Web" + logo: assets/nomad-plugin-logo.png + favicon: assets/favicon.png + features: + - navigation.instant + custom_dir: docs/theme + icon: + repo: fontawesome/brands/github +markdown_extensions: + - attr_list + - md_in_html + - admonition + - pymdownx.details + - pymdownx.highlight: + anchor_linenums: true + - pymdownx.inlinehilite + - pymdownx.snippets + - pymdownx.superfences + - toc: + permalink: True + - pymdownx.arithmatex: + generic: true + - attr_list + - mkdocs-click + - pymdownx.extra +extra: + generator: false + homepage: https://nomad-lab.eu +use_directory_urls: false +extra_css: + - stylesheets/extra.css +extra_javascript: + - javascript.js + - https://polyfill.io/v3/polyfill.min.js?features=es6 + - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js diff --git a/move_template_files.sh b/move_template_files.sh new file mode 100644 index 0000000..f193801 --- /dev/null +++ b/move_template_files.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +rsync -avh nomad-nomad-parser-wannier90/ . +rm -rfv nomad-nomad-parser-wannier90 diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..305413e --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,137 @@ +[build-system] +requires = ["setuptools>=61.0.0", "setuptools-scm>=8.0"] +build-backend = "setuptools.build_meta" + +[project] +classifiers = [ + "Intended Audience :: Developers", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3.9", + "License :: OSI Approved :: Apache Software License", +] +name = "nomad-parser-wannier90" +description = "A NOMAD parser plugin for Wannier90 input/output files." +dynamic = ["version"] +readme = "README.md" +requires-python = ">=3.9" +authors = [ + { name = "Jose M. Pizarro", email = "jose.pizarro@physik.hu-berlin.de" }, +] +maintainers = [ + { name = "Jose M. Pizarro", email = "jose.pizarro@physik.hu-berlin.de" }, +] +license = { file = "LICENSE" } +dependencies = [ + "nomad-lab>=1.3.0", + "nomad-schema-plugin-simulation-workflow@git+https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git@develop", + "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@develop", + "nomad-simulations@git+https://github.com/nomad-coe/nomad-simulations.git@develop", +] + +[project.urls] +"Homepage" = "https://github.com/FAIRmat-NFDI/nomad-parser-wannier90" +"Bug Tracker" = "https://github.com/FAIRmat-NFDI/nomad-parser-wannier90/issues" +"Documentation" = "https://FAIRmat-NFDI.github.io/nomad-parser-wannier90/" + +[project.optional-dependencies] +[project.optional-dependencies] +dev = [ + "mypy==1.0.1", + "ruff", + "pytest", + "pytest-timeout", + "pytest-cov", + "structlog" +] + +[tool.ruff] +# Exclude a variety of commonly ignored directories. +exclude = [ + ".bzr", + ".direnv", + ".eggs", + ".git", + ".git-rewrite", + ".hg", + ".mypy_cache", + ".nox", + ".pants.d", + ".pytype", + ".ruff_cache", + ".svn", + ".tox", + ".venv", + "__pypackages__", + "_build", + "buck-out", + "build", + "dist", + "node_modules", + "venv", +] + +# Same as Black. +line-length = 88 +indent-width = 4 + + +[tool.ruff.lint] +select = [ + "E", # pycodestyle + "W", # pycodestyle + "PL", # pylint +] + +ignore = [ + "E501", # Line too long ({width} > {limit} characters) + "E701", # Multiple statements on one line (colon) + "E731", # Do not assign a lambda expression, use a def + "E402", # Module level import not at top of file + "PLR0911", # Too many return statements + "PLR0912", # Too many branches + "PLR0913", # Too many arguments in function definition + "PLR0915", # Too many statements + "PLR2004", # Magic value used instead of constant + "PLW0603", # Using the global statement + "PLW2901", # redefined-loop-name + "PLR1714", # consider-using-in + "PLR5501", # else-if-used +] + +fixable = ["ALL"] + +# Allow unused variables when underscore-prefixed. +dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$" + +# this is entirely optional, you can remove this if you wish to +[tool.ruff.format] +# use single quotes for strings. +quote-style = "single" + +# indent with spaces, rather than tabs. +indent-style = "space" + +# Like Black, respect magic trailing commas. +skip-magic-trailing-comma = false + +# Like Black, automatically detect the appropriate line ending. +line-ending = "auto" + +[tool.setuptools] +package-dir = { "" = "src" } + +[tool.setuptools.packages.find] +where = ["src"] + +[tool.setuptools_scm] +write_to = "src/nomad_parser_wannier90/_version.py" + +[project.entry-points.'nomad.plugin'] +nomad_parser_wannier90_plugin = "nomad_parser_wannier90.parsers:nomad_parser_wannier90_plugin" +nomad_parser_wannier90_schema = "nomad_parser_wannier90.schema_packages:nomad_parser_wannier90_schema" + + +[tool.cruft] +# Avoid updating workflow files, this leads to permissions issues +skip = [".github/*"] diff --git a/requirements_docs.txt b/requirements_docs.txt new file mode 100644 index 0000000..bacf1ed --- /dev/null +++ b/requirements_docs.txt @@ -0,0 +1,4 @@ +mkdocs +mkdocs-material==8.1.1 +pymdown-extensions +mkdocs-click diff --git a/src/nomad_parser_wannier90/__init__.py b/src/nomad_parser_wannier90/__init__.py new file mode 100644 index 0000000..ce2e284 --- /dev/null +++ b/src/nomad_parser_wannier90/__init__.py @@ -0,0 +1,4 @@ +try: + from ._version import version as __version__ +except ImportError: + __version__ = '' diff --git a/src/nomad_parser_wannier90/parsers/__init__.py b/src/nomad_parser_wannier90/parsers/__init__.py new file mode 100644 index 0000000..2487247 --- /dev/null +++ b/src/nomad_parser_wannier90/parsers/__init__.py @@ -0,0 +1,19 @@ +from nomad.config.models.plugins import ParserEntryPoint +from pydantic import Field + + +class Wannier90ParserEntryPoint(ParserEntryPoint): + parameter: int = Field(0, description='Custom configuration parameter') + + def load(self): + from nomad_parser_wannier90.parsers.parser import Wannier90Parser + + return Wannier90Parser(**self.dict()) + + +nomad_parser_wannier90_plugin = Wannier90ParserEntryPoint( + name='Wannier90ParserEntryPoint', + description='Entry point for the Wannier90 parser.', + level=1, + mainfile_contents_re=r'\|\s*WANNIER90\s*\|', +) diff --git a/src/nomad_parser_wannier90/parsers/band_parser.py b/src/nomad_parser_wannier90/parsers/band_parser.py new file mode 100644 index 0000000..0ca6128 --- /dev/null +++ b/src/nomad_parser_wannier90/parsers/band_parser.py @@ -0,0 +1,106 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. +# See https://nomad-lab.eu for further info. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +import numpy as np +from typing import Optional, List +from structlog.stdlib import BoundLogger + +from nomad.parsing.file_parser import DataTextParser + +from nomad_simulations.schema.model_method import Wannier +from nomad_simulations.schema.model_system import ModelSystem +from nomad_simulations.schema.numerical_settings import ( + KSpace, + KLinePath as KLinePathSettings, +) +from nomad_simulations.schema.properties import ElectronicBandStructure +from nomad_simulations.schema.variables import KLinePath + + +class Wannier90BandParser: + def __init__(self, band_file: str = ''): + if not band_file: + raise ValueError('Band structure `*band.dat` file not found.') + self.band_parser = DataTextParser(mainfile=band_file) + + def parse_k_line_path_settings( + self, + reciprocal_lattice_vectors: Optional[np.ndarray], + k_line_path: KLinePathSettings, + logger: BoundLogger, + ) -> None: + """ + Parse the `KLinePath` settings from the `*band.dat` file using the `KLinePath.resolve_points` method. The + information is then stored under `KLinePath.points`, and will be used to extract the `ElectronicBandStructure` variables + points. + + Args: + reciprocal_lattice_vectors (Optional[np.ndarray]): The reciprocal lattice vectors. + k_line_path (KLinePathSettings): The `KLinePath` settings section + logger (BoundLogger): The logger to log messages. + """ + try: + kpath_norms = self.band_parser.data.transpose()[0] + k_line_path.resolve_points( + points_norm=kpath_norms, + reciprocal_lattice_vectors=reciprocal_lattice_vectors, + logger=logger, + ) + except Exception: + logger.info('Error parsing `KLinePath` settings.') + + def parse_band_structure( + self, + wannier_method: Optional[Wannier], + k_space: Optional[KSpace], + model_systems: List[ModelSystem], + logger: BoundLogger, + ) -> Optional[ElectronicBandStructure]: + if wannier_method is None: + logger.warning('Could not parse the `Wannier` method.') + return None, None + n_orbitals = wannier_method.n_orbitals + if k_space is None: + logger.info('`KSpace` settings not found.') + return None + + # Resolving `reciprocal_lattice_vectors` from `KSpace` method + rlv = k_space.resolve_reciprocal_lattice_vectors(model_systems, logger) + # And parsing the points from the `*band.dat` file + k_line_path = k_space.k_line_path + self.parse_k_line_path_settings( + reciprocal_lattice_vectors=rlv, + k_line_path=k_line_path, + logger=logger, + ) + if k_line_path.points is None: + logger.warning('Could not resolve the `KLinePath` points.') + return None + + # Parse the band structure data + band_structure = ElectronicBandStructure(n_bands=n_orbitals) + if self.band_parser.data is None: + logger.warning('Could not parse the band structure data.') + return None + k_line_path_variables = KLinePath() + k_line_path_variables.points = k_line_path # ! Wait for @amirgolpv to check + band_structure.variables = [k_line_path_variables] + data = self.band_parser.data.transpose()[1:].transpose() + band_structure.value = data + return band_structure diff --git a/src/nomad_parser_wannier90/parsers/dos_parser.py b/src/nomad_parser_wannier90/parsers/dos_parser.py new file mode 100644 index 0000000..95bd795 --- /dev/null +++ b/src/nomad_parser_wannier90/parsers/dos_parser.py @@ -0,0 +1,49 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. +# See https://nomad-lab.eu for further info. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +import numpy as np +from typing import Optional + +from nomad.units import ureg +from nomad.parsing.file_parser import DataTextParser + +from nomad_simulations.schema_packages.properties import ElectronicDensityOfStates +from nomad_simulations.schema_packages.variables import Energy2 + + +class Wannier90DosParser: + def __init__(self, dos_file: str = ''): + if not dos_file: + raise ValueError('DOS `*dos.dat` file not found.') + self.dos_parser = DataTextParser(mainfile=dos_file) + + def parse_dos(self) -> Optional[ElectronicDensityOfStates]: + """ + Parse the `ElectronicDensityOfStates` section from the `*dos.dat` file. + + Returns: + (Optional[ElectronicDensityOfStates]): The parsed `ElectronicDensityOfStates` property. + """ + # TODO add spin polarized case + data = np.transpose(self.dos_parser.data) + sec_dos = ElectronicDensityOfStates() + energies = Energy2(points=data[0] * ureg.eV) + sec_dos.variables.append(energies) + sec_dos.value = data[1] / ureg.eV + return sec_dos diff --git a/src/nomad_parser_wannier90/parsers/hr_parser.py b/src/nomad_parser_wannier90/parsers/hr_parser.py new file mode 100644 index 0000000..a9a222c --- /dev/null +++ b/src/nomad_parser_wannier90/parsers/hr_parser.py @@ -0,0 +1,112 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. +# See https://nomad-lab.eu for further info. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +import numpy as np +from typing import Optional, Tuple +from structlog.stdlib import BoundLogger + +from nomad.units import ureg +from nomad.parsing.file_parser import TextParser, Quantity + +from nomad_simulations.schema_packages.model_method import Wannier +from nomad_simulations.schema_packages.properties import HoppingMatrix, CrystalFieldSplitting +from nomad_simulations.schema_packages.variables import WignerSeitz + + +class HrParser(TextParser): + def init_quantities(self): + self._quantities = [ + Quantity('degeneracy_factors', r'\s*written on[\s\w]*:\d*:\d*\s*([\d\s]+)'), + Quantity('hoppings', rf'\s*([-\d\s.]+)', repeats=False), + ] + + +class Wannier90HrParser: + def __init__(self, hr_file: str = ''): + if not hr_file: + raise ValueError('Hopping `*hr.dat` file not found.') + self.hr_parser = HrParser(mainfile=hr_file) + + def parse_hoppings( + self, wannier_method: Optional[Wannier], logger: BoundLogger + ) -> Tuple[Optional[HoppingMatrix], Optional[CrystalFieldSplitting]]: + """ + Parse the `HoppingMatrix` and `CrystalFieldSplitting` sections from the `*hr.dat` file. + + Args: + wannier_method (Wannier): The `Wannier` method section which contains the number of orbitals information. + logger (BoundLogger): The logger to log messages. + + Returns: + (Tuple[Optional[HoppingMatrix], Optional[CrystalFieldSplitting]]): The parsed `HoppingMatrix` and + `CrystalFieldSplitting` properties]. + """ + if wannier_method is None: + logger.warning('Could not parse the `Wannier` method.') + return None, None + n_orbitals = wannier_method.n_orbitals + + # Parsing the `HoppingMatrix` and `CrystalFieldSplitting` sections + crystal_field_splitting = CrystalFieldSplitting( + n_orbitals=n_orbitals, variables=[] + ) + hopping_matrix = HoppingMatrix(n_orbitals=n_orbitals) + + # Parse the `degeneracy_factors` and `value` of the `HoppingMatrix` + deg_factors = self.hr_parser.get('degeneracy_factors', []) + if deg_factors is None or len(deg_factors) == 0: + logger.warning('Could not parse the degeneracy factors.') + return None, None + + # Define the variables `WignerSeitz` + n_wigner_seitz_points = deg_factors[1] + wigner_seitz = WignerSeitz( + n_points=n_wigner_seitz_points + ) # delete crystal field Wigner-Seitz point from `HoppingMatrix` variable + hopping_matrix.variables.append(wigner_seitz) + + # deg_factors and full_hoppings contain both the `CrystalFieldSplitting` and `HoppingMatrix` values + degeneracy_factors = deg_factors[2:] + full_hoppings = self.hr_parser.get('hoppings', []) + try: + hops = np.reshape( + full_hoppings, + (n_wigner_seitz_points, n_orbitals, n_orbitals, 7), + ) + + # storing the crystal field splitting values + ws0 = int((n_wigner_seitz_points - 1) / 2) + crystal_fields = [ + hops[ws0, i, i, 5] for i in range(n_orbitals) + ] # only real elements + crystal_field_splitting.value = crystal_fields * ureg('eV') + + # delete repeated points for different orbitals + ws_points = hops[:, :, :, :3] + ws_points = np.unique(ws_points.reshape(-1, 3), axis=0) + wigner_seitz.points = ws_points + + # passing hoppings + hoppings = hops[:, :, :, -2] + 1j * hops[:, :, :, -1] + hopping_matrix.value = hoppings * ureg('eV') + hopping_matrix.degeneracy_factors = degeneracy_factors + except Exception: + logger.warning('Could not parse the hopping matrix values.') + return None, None + return hopping_matrix, crystal_field_splitting diff --git a/src/nomad_parser_wannier90/parsers/parser.py b/src/nomad_parser_wannier90/parsers/parser.py new file mode 100644 index 0000000..5a87325 --- /dev/null +++ b/src/nomad_parser_wannier90/parsers/parser.py @@ -0,0 +1,1060 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. +# See https://nomad-lab.eu for further info. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +import os +import logging +import numpy as np +from typing import List, Optional +from structlog.stdlib import BoundLogger + +from nomad.config import config +from nomad.units import ureg +from nomad.datamodel import EntryArchive +from nomad.parsing.file_parser import TextParser, Quantity, DataTextParser +from nomad.parsing.parser import MatchingParser +from simulationworkflowschema import SinglePoint +from runschema.run import Run, Program +from runschema.calculation import ( + Calculation, + Dos, + DosValues, + BandStructure, + BandEnergies, + Energy, + HoppingMatrix, +) +from runschema.method import Method, AtomParameters, KMesh, Wannier, TB +from runschema.system import System, Atoms, AtomsGroup + +# New schema +from nomad_simulations.schema_packages.general import Simulation, Program as BaseProgram +from nomad_simulations.schema_packages.model_system import ModelSystem, AtomicCell +from nomad_simulations.schema_packages.atoms_state import ( + AtomsState, + CoreHole, +) +from nomad_simulations.schema_packages.model_method import ( + ModelMethod, + Wannier as ModelWannier, +) +from nomad_simulations.schema_packages.numerical_settings import ( + KMesh as ModelKMesh, + KSpace, + KLinePath, +) + +from nomad_simulations.schema_packages.outputs import Outputs +from nomad_simulations.schema_packages.variables import Temperature +from nomad_simulations.schema_packages.properties import ElectronicBandGap + +from nomad_parser_wannier90.parsers.utils import get_files +from nomad_parser_wannier90.parsers.win_parser import WInParser, Wannier90WInParser +from nomad_parser_wannier90.parsers.hr_parser import HrParser, Wannier90HrParser +from nomad_parser_wannier90.parsers.dos_parser import Wannier90DosParser +from nomad_parser_wannier90.parsers.band_parser import Wannier90BandParser + +re_n = r'[\n\r]' + +configuration = config.get_plugin_entry_point( + 'nomad_parser_wannier90.parsers:nomad_parser_wannier90_plugin' +) + + +def test(template, atom_indices: list[int], **kwargs): + simulation = Simulation() + template.m_add_sub_section(EntryArchive.data, simulation) + simulation.program = Program(name='VASP', version='4.6.35') + model_system = ModelSystem() + simulation.model_system.append(model_system) + atomic_cell = AtomicCell( + lattice_vectors=[ + [5.76372622e-10, 0.0, 0.0], + [0.0, 5.76372622e-10, 0.0], + [0.0, 0.0, 4.0755698899999997e-10], + ], + positions=[ + [2.88186311e-10, 0.0, 2.0377849449999999e-10], + [0.0, 2.88186311e-10, 2.0377849449999999e-10], + [0.0, 0.0, 0.0], + [2.88186311e-10, 2.88186311e-10, 0.0], + ], + periodic_boundary_conditions=[True, True, True], + ) + model_system.cell.append(atomic_cell) + atoms_state = [ + AtomsState(chemical_symbol='Br'), + AtomsState(chemical_symbol='K'), + AtomsState(chemical_symbol='Si'), + AtomsState(chemical_symbol='Si'), + ] + atomic_cell.atoms_state = atoms_state + elements = [atom.chemical_symbol for atom in model_system.cell[0].atoms_state] + + # set atom_parameters and core_holes + list_terms = {'j_quantum_number', 'mj_quantum_number'} + for active_index, atom_index in enumerate(atom_indices): + atom_state = atomic_cell.atoms_state[atom_index] + core_hole = CoreHole() + for k, v in kwargs.items(): + try: + if k not in list_terms and isinstance( + v, list + ): # this supports lists of several quantities for multiple core-holes + if len(v): + setattr(core_hole, k, v[active_index]) + else: + setattr(core_hole, k, []) + else: + setattr(core_hole, k, v) + except AttributeError: + pass + atom_state.core_hole = core_hole + model_system2 = ModelSystem( + type='active_atom', + branch_label=elements[atom_index], + atom_indices=[atom_index], + ) + model_system.model_system.append(model_system2) + return template + + +class WOutParser(TextParser): + def __init__(self): + super().__init__(None) + + def init_quantities(self): + kmesh_quantities = [ + Quantity('n_points', r'Total points[\s=]*(\d+)', dtype=int, repeats=False), + Quantity( + 'grid', r'Grid size *\= *(\d+) *x *(\d+) *x *(\d+)', repeats=False + ), + Quantity('k_points', r'\|[\s\d]*(-*\d.[^\|]+)', repeats=True, dtype=float), + ] + + klinepath_quantities = [ + Quantity( + 'high_symm_name', + r'\| *From\: *([a-zA-Z]+) [\d\.\-\s]*To\: *([a-zA-Z]+)', + repeats=True, + ), + Quantity( + 'high_symm_value', + r'\| *From\: *[a-zA-Z]* *([\d\.\-\s]+)To\: *[a-zA-Z]* *([\d\.\-\s]+)\|', + repeats=True, + ), + ] + + disentangle_quantities = [ + Quantity( + 'outer', + r'\|\s*Outer:\s*([-\d.]+)\s*\w*\s*([-\d.]+)\s*\((?P<__unit>\w+)\)', + dtype=float, + repeats=False, + ), + Quantity( + 'inner', + r'\|\s*Inner:\s*([-\d.]+)\s*\w*\s*([-\d.]+)\s*\((?P<__unit>\w+)\)', + dtype=float, + repeats=False, + ), + ] + + structure_quantities = [ + Quantity('labels', r'\|\s*([A-Z][a-z]*)', repeats=True), + Quantity( + 'positions', + rf'\|\s*([\-\d\.]+)\s*([\-\d\.]+)\s*([\-\d\.]+)', + repeats=True, + dtype=float, + ), + ] + + self._quantities = [ + # Program quantities + Quantity( + Program.version, r'\s*\|\s*Release\:\s*([\d\.]+)\s*', repeats=False + ), + # System quantities + Quantity('lattice_vectors', r'\s*a_\d\s*([\d\-\s\.]+)', repeats=True), + Quantity( + 'reciprocal_lattice_vectors', r'\s*b_\d\s*([\d\-\s\.]+)', repeats=True + ), + Quantity( + 'structure', + rf'(\s*Fractional Coordinate[\s\S]+?)(?:{re_n}\s*(PROJECTIONS|K-POINT GRID))', + repeats=False, + sub_parser=TextParser(quantities=structure_quantities), + ), + # Method quantities + Quantity( + 'k_mesh', + rf'\s*(K-POINT GRID[\s\S]+?)(?:-\s*MAIN)', + repeats=False, + sub_parser=TextParser(quantities=kmesh_quantities), + ), + Quantity( + 'k_line_path', + rf'\s*(K-space path sections\:[\s\S]+?)(?:\*-------)', + repeats=False, + sub_parser=TextParser(quantities=klinepath_quantities), + ), + Quantity( + 'Nwannier', + r'\|\s*Number of Wannier Functions\s*\:\s*(\d+)', + repeats=False, + ), + Quantity( + 'Nband', + r'\|\s*Number of input Bloch states\s*\:\s*(\d+)', + repeats=False, + ), + Quantity( + 'Niter', r'\|\s*Total number of iterations\s*\:\s*(\d+)', repeats=False + ), + Quantity( + 'conv_tol', + r'\|\s*Convergence tolerence\s*\:\s*([\d.eE-]+)', + repeats=False, + ), + Quantity( + 'energy_windows', + rf'(\|\s*Energy\s*Windows\s*\|[\s\S]+?)(?:Number of target bands to extract:)', + repeats=False, + sub_parser=TextParser(quantities=disentangle_quantities), + ), + # Band related quantities + Quantity( + 'n_k_segments', + r'\|\s*Number of K-path sections\s*\:\s*(\d+)', + repeats=False, + ), + Quantity( + 'div_first_k_segment', + r'\|\s*Divisions along first K-path section\s*\:\s*(\d+)', + repeats=False, + ), + Quantity( + 'band_segments_points', + r'\|\s*From\:\s*\w+([\d\s\-\.]+)To\:\s*\w+([\d\s\-\.]+)', + repeats=True, + ), + ] + + +class Wannier90ParserData(MatchingParser): + level = 1 + + def __init__(self, *args, **kwargs): + self.wout_parser = WOutParser() + + self._dft_codes = [ + 'quantumespresso', + 'abinit', + 'vasp', + 'siesta', + 'wien2k', + 'fleur', + 'openmx', + 'gpaw', + ] + + self._input_projection_mapping = { + 'Nwannier': 'n_orbitals', + 'Nband': 'n_bloch_bands', + # "conv_tol": "convergence_tolerance_max_localization", + } + + def parse_atoms_state(self, labels: List[str]) -> List[AtomsState]: + """ + Parse the `AtomsState` from the labels by storing them as the `chemical_symbols`. + + Args: + labels (List[str]): List of chemical element labels. + + Returns: + (List[AtomsState]): List of `AtomsState` sections. + """ + atoms_state = [] + for label in labels: + atoms_state.append(AtomsState(chemical_symbol=label)) + return atoms_state + + def parse_atomic_cell(self) -> AtomicCell: + """ + Parse the `AtomicCell` from the `lattice_vectors` and `structure` regex quantities in `WOutParser`. + + Returns: + (AtomicCell): The parsed `AtomicCell` section. + """ + atomic_cell = AtomicCell() + + # Parsing `lattice_vectors` + if self.wout_parser.get('lattice_vectors', []): + lattice_vectors = np.vstack( + self.wout_parser.get('lattice_vectors', [])[-3:] + ) + atomic_cell.lattice_vectors = lattice_vectors * ureg.angstrom + # and `periodic_boundary_conditions` + pbc = ( + [True, True, True] if lattice_vectors is not None else [False, False, False] + ) + atomic_cell.periodic_boundary_conditions = pbc + + # Parsing `atoms_state` from `structure` + labels = self.wout_parser.get('structure', {}).get('labels') + if labels is not None: + atoms_state = self.parse_atoms_state(labels) + atomic_cell.atoms_state = atoms_state + # and parsing `positions` + if self.wout_parser.get('structure', {}).get('positions') is not None: + atomic_cell.positions = ( + self.wout_parser.get('structure', {}).get('positions') * ureg.angstrom + ) + return atomic_cell + + def parse_model_system(self, logger: BoundLogger) -> Optional[ModelSystem]: + """ + Parse the `ModelSystem` with the `AtomicCell` information. If the `structure` is not recognized in `WOutParser`, then return `None`. + + Returns: + (Optional[ModelSystem]): The parsed `ModelSystem` section. + """ + model_system = ModelSystem() + model_system.is_representative = True + + # If the `structure` is not parsed, return None + if self.wout_parser.get('structure') is None: + logger.error('Error parsing the structure from .wout') + return None + + atomic_cell = self.parse_atomic_cell() + model_system.cell.append(atomic_cell) + return model_system + + def parse_wannier(self) -> ModelWannier: + """ + Parse the `ModelWannier` section from the `WOutParser` quantities. + + Returns: + (ModelWannier): The parsed `ModelWannier` section. + """ + model_wannier = ModelWannier() + for key in self._input_projection_mapping.keys(): + setattr( + model_wannier, + self._input_projection_mapping[key], + self.wout_parser.get(key), + ) + if self.wout_parser.get('Niter'): + model_wannier.is_maximally_localized = self.wout_parser.get('Niter', 0) > 1 + model_wannier.energy_window_outer = self.wout_parser.get( + 'energy_windows', {} + ).get('outer') + model_wannier.energy_window_inner = self.wout_parser.get( + 'energy_windows', {} + ).get('inner') + return model_wannier + + def parse_k_mesh(self) -> Optional[ModelKMesh]: + """ + Parse the `ModelKMesh` section from the `WOutParser` quantities. + + Returns: + (Optional[ModelKMesh]): The parsed `ModelKMesh` section. + """ + sec_k_mesh = None + k_mesh = self.wout_parser.get('k_mesh') + if k_mesh is None: + return sec_k_mesh + sec_k_mesh = ModelKMesh() + sec_k_mesh.n_points = k_mesh.get('n_points') + sec_k_mesh.grid = k_mesh.get('grid', []) + if k_mesh.get('k_points') is not None: + sec_k_mesh.points = np.complex128(k_mesh.k_points[::2]) + return sec_k_mesh + + def parse_k_line_path(self) -> Optional[KLinePath]: + """ + Parse the `KLinePath` section from the `WOutParser` quantities. + + Returns: + (Optional[KLinePath]): The parsed `KLinePath` section. + """ + sec_k_line_path = None + k_line_path = self.wout_parser.get('k_line_path') + if k_line_path is None: + return sec_k_line_path + + # Store the list of high symmetry names and values for the section `KLinePath` + high_symm_names = k_line_path.get('high_symm_name') + high_symm_values = [ + np.reshape(val, (2, 3)) for val in k_line_path.get('high_symm_value') + ] + # Start with the first element of the first pair + names = [high_symm_names[0][0]] + values = [high_symm_values[0][0]] + for i, pair in enumerate(high_symm_names): + # Add the second element if it's not the last one in the list + if pair[1] != names[-1]: + names.append(pair[1]) + values.append(high_symm_values[i][1]) + sec_k_line_path = KLinePath( + high_symmetry_path_names=names, high_symmetry_path_values=values + ) # `points` are extracted in the `Wannier90BandParser` using the `KLinePath.resolve_points` method + return sec_k_line_path + + def parse_model_method(self, simulation: Simulation) -> ModelMethod: + """ + Parse the `ModelWannier(ModelMethod)` section from the `WOutParser` quantities. + + Returns: + (ModelMethod): The parsed `ModelWannier(ModelMethod)` section. + """ + # `ModelMethod` section + model_wannier = self.parse_wannier() + + # `NumericalSettings` sections + k_mesh = self.parse_k_mesh() + if k_mesh is not None: + k_space = KSpace(k_mesh=[k_mesh]) + model_wannier.numerical_settings.append(k_space) + + k_line_path = self.parse_k_line_path() + if k_line_path is not None: + if k_space is None: + k_space = KSpace() + model_wannier.numerical_settings.append(k_space) + k_space.k_line_path = k_line_path + + return model_wannier + + def parse_outputs(self, simulation: Simulation, logger: BoundLogger) -> Outputs: + outputs = Outputs() + if simulation.model_system is not None: + outputs.model_system_ref = simulation.model_system[-1] + + # TESTING ############################################## + # Scalar band gap + bg = ElectronicBandGap(type='direct') + bg.variables = [] + bg.value = 1.0 * ureg.eV + outputs.electronic_band_gaps.append(bg) + # T-dependent band gap + bg = ElectronicBandGap(type='direct') + bg.variables = [Temperature(points=[1, 2, 3] * ureg.kelvin)] + value = [1.0, 1.1, 1.2] * ureg.eV + bg.value = value + outputs.electronic_band_gaps.append(bg) + # TESTING ############################################## + + # Parse hoppings + hr_files = get_files('*hr.dat', self.filepath, self.mainfile) + if len(hr_files) > 1: + logger.info('Multiple `*hr.dat` files found.') + # contains information about `n_orbitals` + wannier_method = simulation.m_xpath('model_method[-1]', dict=False) + for hr_file in hr_files: + hopping_matrix, crystal_field_splitting = Wannier90HrParser( + hr_file + ).parse_hoppings(wannier_method=wannier_method, logger=logger) + if hopping_matrix is not None: + outputs.hopping_matrices.append(hopping_matrix) + if crystal_field_splitting is not None: + outputs.crystal_field_splittings.append(crystal_field_splitting) + + # Parse DOS + dos_files = get_files('*dos.dat', self.filepath, self.mainfile) + if len(dos_files) > 1: + logger.info('Multiple `*dos.dat` files found.') + for dos_file in dos_files: + electronic_dos = Wannier90DosParser(dos_file).parse_dos() + if electronic_dos is not None: + outputs.electronic_dos.append(electronic_dos) + + # Parse BandStructure + band_files = get_files('*band.dat', self.filepath, self.mainfile) + # contains information about `k_line_path` + k_space = simulation.m_xpath( + 'model_method[-1].numerical_settings[-1]', dict=False + ) + # getting the list of `ModelSystem` to extract the reciprocal_lattice_vectors + model_systems = simulation.m_xpath('model_system', dict=False) + if len(band_files) > 1: + logger.info('Multiple `*band.dat` files found.') + for band_file in band_files: + band_structure = Wannier90BandParser(band_file).parse_band_structure( + k_space=k_space, + wannier_method=wannier_method, + model_systems=model_systems, + logger=logger, + ) + if band_structure is not None: + outputs.electronic_band_structures.append(band_structure) + + return outputs + + def init_parser(self, logger: BoundLogger): + self.wout_parser.mainfile = self.filepath + self.wout_parser.logger = logger + + def parse(self, filepath: str, archive: EntryArchive, logger: BoundLogger): + self.filepath = filepath + self.archive = archive + self.maindir = os.path.dirname(self.filepath) + self.mainfile = os.path.basename(self.filepath) + + self.init_parser(logger) + + # Adding Simulation to data + simulation = Simulation() + simulation.program = BaseProgram( + name='Wannier90', + version=self.wout_parser.get('version', ''), + link='https://wannier.org/', + ) + archive.m_add_sub_section(EntryArchive.data, simulation) + + # `ModelSystem` parsing + model_system = self.parse_model_system(logger) + if model_system is not None: + simulation.model_system.append(model_system) + + # Child `ModelSystem` and `OrbitalsState` parsing + win_files = get_files('*.win', self.filepath, self.mainfile) + if len(win_files) > 1: + logger.warning( + 'Multiple `*.win` files found. We will parse the first one.' + ) + if win_files is not None: + child_model_systems = Wannier90WInParser( + win_files[0] + ).parse_child_model_systems(model_system, logger) + model_system.model_system = child_model_systems + + # `ModelWannier(ModelMethod)` parsing + model_method = self.parse_model_method(simulation) + simulation.model_method.append(model_method) + + # `Outputs` parsing + outputs = self.parse_outputs(simulation, logger) + simulation.outputs.append(outputs) + + +class Wannier90Parser: + level = 1 + + def __init__(self, *args, **kwargs): + self.wout_parser = WOutParser() + self.win_parser = WInParser() + self.band_dat_parser = DataTextParser() + self.dos_dat_parser = DataTextParser() + self.hr_parser = HrParser() + + self._input_projection_mapping = { + 'Nwannier': 'n_projected_orbitals', + 'Nband': 'n_bands', + 'conv_tol': 'convergence_tolerance_max_localization', + } + + self._input_projection_mapping2 = { + 'Nwannier': 'n_orbitals', + 'Nband': 'n_bloch_bands', + 'conv_tol': 'convergence_tolerance_max_localization', + } + + self._input_projection_units = {'Ang': 'angstrom', 'Bohr': 'bohr'} + + # Angular momentum [l, mr] following Wannier90 tables 3.1 and 3.2 + # TODO move to normalization or utils in nomad? + self._angular_momentum_orbital_map = { + (0, 1): 's', + (1, 1): 'px', + (1, 2): 'py', + (1, 3): 'pz', + (2, 1): 'dz2', + (2, 2): 'dxz', + (2, 3): 'dyz', + (2, 4): 'dx2-y2', + (2, 5): 'dxy', + (3, 1): 'fz3', + (3, 2): 'fxz2', + (3, 3): 'fyz2', + (3, 4): 'fz(x2-y2)', + (3, 5): 'fxyz', + (3, 6): 'fx(x2-3y2)', + (3, 7): 'fy(3x2-y2)', + (-1, 1): 'sp-1', + (-1, 2): 'sp-2', + (-2, 1): 'sp2-1', + (-2, 2): 'sp2-2', + (-2, 3): 'sp2-3', + (-3, 1): 'sp3-1', + (-3, 2): 'sp3-2', + (-3, 3): 'sp3-3', + (-3, 4): 'sp3-4', + (-4, 1): 'sp3d-1', + (-4, 2): 'sp3d-2', + (-4, 3): 'sp3d-3', + (-4, 4): 'sp3d-4', + (-4, 5): 'sp3d-5', + (-5, 1): 'sp3d2-1', + (-5, 2): 'sp3d2-2', + (-5, 3): 'sp3d2-3', + (-5, 4): 'sp3d2-4', + (-5, 5): 'sp3d2-5', + (-5, 6): 'sp3d2-6', + } + + self._dft_codes = [ + 'quantumespresso', + 'abinit', + 'vasp', + 'siesta', + 'wien2k', + 'fleur', + 'openmx', + 'gpaw', + ] + + def parse_system(self): + sec_run = self.archive.run[-1] + sec_system = System() + sec_run.system.append(sec_system) + + structure = self.wout_parser.get('structure') + if structure is None: + self.logger.error('Error parsing the structure from .wout') + return + + sec_atoms = Atoms() + sec_system.atoms = sec_atoms + if self.wout_parser.get('lattice_vectors', []): + lattice_vectors = np.vstack( + self.wout_parser.get('lattice_vectors', [])[-3:] + ) + sec_atoms.lattice_vectors = lattice_vectors * ureg.angstrom + if self.wout_parser.get('reciprocal_lattice_vectors') is not None: + sec_atoms.lattice_vectors_reciprocal = ( + np.vstack(self.wout_parser.get('reciprocal_lattice_vectors')[-3:]) + / ureg.angstrom + ) + + pbc = ( + [True, True, True] if lattice_vectors is not None else [False, False, False] + ) + sec_atoms.periodic = pbc + sec_atoms.labels = structure.get('labels') + if structure.get('positions') is not None: + sec_atoms.positions = structure.get('positions') * ureg.angstrom + + def parse_method(self): + sec_run = self.archive.run[-1] + sec_method = Method() + sec_run.method.append(sec_method) + sec_proj = TB() + sec_method.tb = sec_proj + sec_wann = Wannier() + sec_proj.wannier = sec_wann + + # k_mesh section + kmesh = self.wout_parser.get('k_mesh') + if kmesh: + sec_k_mesh = KMesh() + sec_method.k_mesh = sec_k_mesh + sec_k_mesh.n_points = kmesh.get('n_points') + sec_k_mesh.grid = kmesh.get('grid', []) + if kmesh.get('k_points') is not None: + sec_k_mesh.points = np.complex128(kmesh.k_points[::2]) + + # Wannier90 section + for key in self._input_projection_mapping.keys(): + setattr( + sec_wann, self._input_projection_mapping[key], self.wout_parser.get(key) + ) + if self.wout_parser.get('Niter'): + sec_wann.is_maximally_localized = self.wout_parser.get('Niter', 0) > 1 + if self.wout_parser.get('energy_windows'): + sec_wann.energy_window_outer = self.wout_parser.get('energy_windows').outer + sec_wann.energy_window_inner = self.wout_parser.get('energy_windows').inner + + def parse_winput(self): + sec_run = self.archive.run[-1] + try: + sec_system = sec_run.system[-1] + sec_atoms = sec_system.atoms + sec_method = sec_run.method[-1] + except Exception: + self.logger.warning( + 'Could not extract system.atoms and method sections for parsing win.' + ) + return + + # Parsing from input + win_files = get_files('*.win', self.filepath, self.mainfile) + if not win_files: + self.logger.warning('Input .win file not found.') + return + if len(win_files) > 1: + self.logger.warning( + 'Multiple win files found. We will parse the first one.' + ) + self.win_parser.mainfile = win_files[0] + + def fract_cart_sites(sec_atoms, units, val): + for pos in sec_atoms.positions.to(units): + if np.array_equal(val, pos.magnitude): + index = sec_atoms.positions.magnitude.tolist().index( + pos.magnitude.tolist() + ) + return sec_atoms.labels[index] + + # Set units in case these are defined in .win + projections = self.win_parser.get('projections', []) + if projections: + if not isinstance(projections, list): + projections = [projections] + if projections[0][0] in ['Bohr', 'Angstrom']: + sec_run.x_wannier90_units = self._input_projection_units[ + projections[0][0] + ] + projections.pop(0) + else: + sec_run.x_wannier90_units = 'angstrom' + if projections[0][0] == 'random': + return + + # Populating AtomsGroup for projected atoms + sec_run.x_wannier90_n_atoms_proj = len(projections) + for nat in range(sec_run.x_wannier90_n_atoms_proj): + sec_atoms_group = AtomsGroup() + sec_system.atoms_group.append(sec_atoms_group) + sec_atoms_group.type = 'active_orbitals' + sec_atoms_group.index = ( + 0 # Always first index (projection on a projection does not exist) + ) + sec_atoms_group.is_molecule = False + + # atom label always index=0 + try: + atom = projections[nat][0] + if atom.startswith('f='): # fractional coordinates + val = [float(x) for x in atom.replace('f=', '').split(',')] + val = np.dot(val, sec_atoms.lattice_vectors.magnitude) + sites = fract_cart_sites(sec_atoms, sec_run.x_wannier90_units, val) + elif atom.startswith('c='): # cartesian coordinates + val = [float(x) for x in atom.replace('c=', '').split(',')] + sites = fract_cart_sites(sec_atoms, sec_run.x_wannier90_units, val) + else: # atom label directly specified + sites = atom + sec_atoms_group.n_atoms = len( + sites + ) # always 1 (only one atom per proj) # TODO: either add a check or default to 1 + sec_atoms_group.label = 'projection' + sec_atoms_group.atom_indices = np.where( + [x == sites for x in sec_atoms.labels] + )[0] + except Exception: + self.logger.warning( + 'Error finding the atom labels for the projection from win.' + ) + + # orbital angular momentum always index=1 + # suggestion: shift to wout for projection? + try: + orbitals = projections[nat][1].split(';') + sec_atom_parameters = AtomParameters() + sec_method.atom_parameters.append(sec_atom_parameters) + sec_atom_parameters.n_orbitals = len(orbitals) + angular_momentum = [] + for orb in orbitals: + if orb.startswith('l='): # using angular momentum numbers + lmom = int(orb.split(',mr')[0].replace('l=', '').split(',')[0]) + mrmom = int(orb.split(',mr')[-1].replace('=', '').split(',')[0]) + if ( + orb_ang_mom := self._angular_momentum_orbital_map.get( + (lmom, mrmom) + ) + ): # shouldn't a missing numerical code rather generate a warning? + angular_momentum.append(orb_ang_mom) + else: # ang mom label directly specified + angular_momentum.append(orb) + sec_atom_parameters.orbitals = np.array(angular_momentum) + except Exception: + self.logger.warning('Projected orbital labels not found from win.') + + def parse_hoppings(self): + hr_files = get_files('*hr.dat', self.filepath, self.mainfile) + if not hr_files: + return + self.hr_parser.mainfile = hr_files[0] + + # Assuming method.tb is parsed before + sec_scc = self.archive.run[-1].calculation[-1] + sec_hopping_matrix = HoppingMatrix() + sec_scc.hopping_matrix.append(sec_hopping_matrix) + sec_hopping_matrix.n_orbitals = ( + self.archive.run[-1].method[-1].tb.wannier.n_projected_orbitals + ) + deg_factors = self.hr_parser.get('degeneracy_factors', []) + if deg_factors is not None: + sec_hopping_matrix.n_wigner_seitz_points = deg_factors[1] + sec_hopping_matrix.degeneracy_factors = deg_factors[2:] + full_hoppings = self.hr_parser.get('hoppings', []) + try: + sec_hopping_matrix.value = np.reshape( + full_hoppings, + ( + sec_hopping_matrix.n_wigner_seitz_points, + sec_hopping_matrix.n_orbitals * sec_hopping_matrix.n_orbitals, + 7, + ), + ) + except Exception: + self.logger.warning( + 'Could not parse the hopping matrix values. Please, revise your output files.' + ) + try: + sec_scc_energy = Energy() + sec_scc.energy = sec_scc_energy + # Setting Fermi level to the first orbital onsite energy + n_wigner_seitz_points_half = int( + 0.5 * sec_hopping_matrix.n_wigner_seitz_points + ) + energy_fermi = ( + sec_hopping_matrix.value[n_wigner_seitz_points_half][0][5] * ureg.eV + ) + sec_scc_energy.fermi = energy_fermi + sec_scc_energy.highest_occupied = energy_fermi + except Exception: + return + + def get_k_points(self): + if self.wout_parser.get('reciprocal_lattice_vectors') is None: + return + reciprocal_lattice_vectors = np.vstack( + self.wout_parser.get('reciprocal_lattice_vectors') + ) + + n_k_segments = self.wout_parser.get('n_k_segments', []) + k_symm_points = [] + k_symm_points_cart = [] + for ns in range(n_k_segments): + k_segments = np.split(self.wout_parser.get('band_segments_points')[ns], 2) + [ + k_symm_points_cart.append( + np.dot(k_segments[i], reciprocal_lattice_vectors) + ) + for i in range(2) + ] + [k_symm_points.append(k_segments[i]) for i in range(2)] + + n_k_segments_points_1 = self.wout_parser.get('div_first_k_segment') + delta_k = ( + np.linalg.norm(k_symm_points_cart[1] - k_symm_points_cart[0]) + / n_k_segments_points_1 + ) + band_segments_points = [] + for ns in range(n_k_segments): + n_k_segments_points = round( + np.linalg.norm( + k_symm_points_cart[2 * ns + 1] - k_symm_points_cart[2 * ns] + ) + / delta_k + ) + band_segments_points.append(n_k_segments_points) + + kpoints = [] + for n in range(len(band_segments_points)): + kpoints_segment = [ + k_symm_points[2 * n] + + i + * (k_symm_points[2 * n + 1] - k_symm_points[2 * n]) + / band_segments_points[n] + for i in range(band_segments_points[n]) + ] + kpoints.append(kpoints_segment) + + # TODO check having to add manually last point (?) + band_segments_points[-1] = band_segments_points[-1] + 1 + kpoints[-1].append(k_symm_points[-1]) + n_kpoints = sum(band_segments_points) + + return (n_kpoints, band_segments_points, kpoints) + + def parse_bandstructure(self): + sec_scc = self.archive.run[-1].calculation[-1] + + try: + energy_fermi = sec_scc.energy.fermi + except Exception: + self.logger.warning( + 'Error setting the Fermi level: not found from hoppings. Setting it to 0 eV' + ) + energy_fermi = 0.0 * ureg.eV + energy_fermi_eV = energy_fermi.to('electron_volt').magnitude + + band_files = get_files('*band.dat', self.filepath, self.mainfile) + if not band_files: + return + if len(band_files) > 1: + self.logger.warning('Multiple bandstructure data files found.') + # Parsing only first *_band.dat file + self.band_dat_parser.mainfile = band_files[0] + + sec_k_band = BandStructure() + sec_scc.band_structure_electronic.append(sec_k_band) + sec_k_band.energy_fermi = energy_fermi + try: + sec_k_band.reciprocal_cell = ( + self.archive.run[-1].system[0].atoms.lattice_vectors_reciprocal + ) + except Exception: + self.logger.warning( + 'Reciprocal cell in band_structure_electronic not set up.' + ) + + if self.band_dat_parser.data is None: + return + data = np.transpose(self.band_dat_parser.data) + + (n_kpoints, band_segments_points, kpoints) = self.get_k_points() + n_segments = len(band_segments_points) + n_bands = round((len(data[0])) / n_kpoints) + n_spin = 1 + + # reshaping bands into the NOMAD band_structure style + try: + bands = np.transpose(np.reshape(data[1], (n_bands, n_kpoints))) + except Exception: + self.logger.warning( + 'Could not reshape the bands into the NOMAD dimensions.' + ) + return + bkp_init = 0 + for n in range(n_segments): + sec_k_band_segment = BandEnergies() + sec_k_band.segment.append(sec_k_band_segment) + sec_k_band_segment.n_kpoints = band_segments_points[n] + sec_k_band_segment.kpoints = kpoints[n] + + bkp_last = bkp_init + band_segments_points[n] + energies = np.reshape( + bands[bkp_init:bkp_last, :], (n_spin, band_segments_points[n], n_bands) + ) + occs = np.reshape( + np.array( + [ + 2.0 if energies[i, j, k] < energy_fermi_eV else 0.0 + for i in range(n_spin) + for j in range(band_segments_points[n]) + for k in range(n_bands) + ] + ), + (n_spin, band_segments_points[n], n_bands), + ) + bkp_init = bkp_last + sec_k_band_segment.energies = energies * ureg.eV + sec_k_band_segment.occupations = occs + + def parse_dos(self): + sec_scc = self.archive.run[-1].calculation[-1] + + try: + energy_fermi = sec_scc.energy.fermi + except Exception: + self.logger.warning( + 'Error setting the Fermi level: not found from hoppings. Setting it to 0 eV' + ) + energy_fermi = 0.0 * ureg.eV + + dos_files = get_files('*dos.dat', self.filepath, self.mainfile) + if not dos_files: + return + if len(dos_files) > 1: + self.logger.warning('Multiple dos data files found.') + # Parsing only first *dos.dat file + self.dos_dat_parser.mainfile = dos_files[0] + + # TODO add spin polarized case + sec_dos = Dos() + sec_scc.dos_electronic.append(sec_dos) + sec_dos.energy_fermi = energy_fermi + data = np.transpose(self.dos_dat_parser.data) + sec_dos.n_energies = len(data[0]) + sec_dos.energies = data[0] * ureg.eV + sec_dos_values = DosValues() + sec_dos.total.append(sec_dos_values) + sec_dos_values.value = data[1] / ureg.eV + + def parse_scc(self): + sec_run = self.archive.run[-1] + sec_scc = Calculation() + sec_run.calculation.append(sec_scc) + + # Refs for calculation + sec_scc.method_ref = sec_run.method[-1] + sec_scc.system_ref = sec_run.system[-1] + + # Wannier90 hoppings section + self.parse_hoppings() + + # Wannier band structure + self.parse_bandstructure() + + # Wannier DOS + self.parse_dos() + + def init_parser(self): + self.wout_parser.mainfile = self.filepath + self.wout_parser.logger = self.logger + self.hr_parser.logger = self.logger + + def parse(self, filepath, archive, logger): + self.filepath = filepath + self.archive = archive + self.maindir = os.path.dirname(self.filepath) + self.mainfile = os.path.basename(self.filepath) + self.logger = logging.getLogger(__name__) if logger is None else logger + + self.init_parser() + + sec_run = Run() + self.archive.run.append(sec_run) + + # Program section + sec_run.program = Program( + name='Wannier90', version=self.wout_parser.get('version', '') + ) + # TODO TimeRun section + + self.parse_system() + + self.parse_method() + + # Parsing AtomsGroup and AtomParameters for System and Method from the input file .win + self.parse_winput() + + self.parse_scc() + + workflow = SinglePoint() + self.archive.workflow2 = workflow + + # Adding `data` section + p = Wannier90ParserData() + p.parse(filepath, archive, logger) diff --git a/src/nomad_parser_wannier90/parsers/utils/__init__.py b/src/nomad_parser_wannier90/parsers/utils/__init__.py new file mode 100644 index 0000000..d5ed6a4 --- /dev/null +++ b/src/nomad_parser_wannier90/parsers/utils/__init__.py @@ -0,0 +1,19 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. +# See https://nomad-lab.eu for further info. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from .utils import get_files diff --git a/src/nomad_parser_wannier90/parsers/utils/utils.py b/src/nomad_parser_wannier90/parsers/utils/utils.py new file mode 100644 index 0000000..b7edb29 --- /dev/null +++ b/src/nomad_parser_wannier90/parsers/utils/utils.py @@ -0,0 +1,51 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. +# See https://nomad-lab.eu for further info. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +import os +from glob import glob + + +def get_files(pattern: str, filepath: str, stripname: str = '', deep: bool = True): + """Get files following the `pattern` with respect to the file `stripname` (usually this + being the mainfile of the given parser) up to / down from the `filepath` (`deep=True` going + down, `deep=False` up) + + Args: + pattern (str): targeted pattern to be found + filepath (str): filepath to start the search + stripname (str, optional): name with respect to which do the search. Defaults to ''. + deep (bool, optional): boolean setting the path in the folders to scan (down or up). Defaults to down=True. + + Returns: + list: List of found files. + """ + for _ in range(10): + filenames = glob(f'{os.path.dirname(filepath)}/{pattern}') + pattern = os.path.join('**' if deep else '..', pattern) + if filenames: + break + + if len(filenames) > 1: + # filter files that match + suffix = os.path.basename(filepath).strip(stripname) + matches = [f for f in filenames if suffix in f] + filenames = matches if matches else filenames + + filenames = [f for f in filenames if os.access(f, os.F_OK)] + return filenames diff --git a/src/nomad_parser_wannier90/parsers/win_parser.py b/src/nomad_parser_wannier90/parsers/win_parser.py new file mode 100644 index 0000000..f74b578 --- /dev/null +++ b/src/nomad_parser_wannier90/parsers/win_parser.py @@ -0,0 +1,272 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. +# See https://nomad-lab.eu for further info. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +import numpy as np +from typing import List, Optional, Tuple, Union +from structlog.stdlib import BoundLogger + +from nomad.parsing.file_parser import TextParser, Quantity + +from nomad_simulations.schema_packages.model_system import ModelSystem, AtomicCell +from nomad_simulations.schema_packages.atoms_state import OrbitalsState + + +class WInParser(TextParser): + def init_quantities(self): + def str_proj_to_list(val_in): + # To avoid inconsistent regex that can contain or not spaces + val_n = [x for x in val_in.split('\n') if x] + return [v.strip('[]').replace(' ', '').split(':') for v in val_n] + + self._quantities = [ + Quantity( + 'energy_fermi', rf'\n\rfermi_energy\s*=\s*([\d\.\-]+)', repeats=False + ), + Quantity( + 'projections', + rf'[bB]egin [pP]rojections([\s\S]+?)(?:[eE]nd [pP]rojections)', + repeats=False, + str_operation=str_proj_to_list, + ), + ] + + +class Wannier90WInParser: + def __init__(self, win_file: str = ''): + if not win_file: + raise ValueError('Input `*.win` file not found.') + self.win_parser = WInParser(mainfile=win_file) + + self._input_projection_units = {'Ang': 'angstrom', 'Bohr': 'bohr'} + + # Angular momentum [l, mr] following Wannier90 tables 3.1 and 3.2 + self._wannier_orbital_symbols_map = { + 's': ('s', ''), + 'px': ('p', 'x'), + 'py': ('p', 'y'), + 'pz': ('p', 'z'), + 'dz2': ('d', 'z^2'), + 'dxz': ('d', 'xz'), + 'dyz': ('d', 'yz'), + 'dx2-y2': ('d', 'x^2-y^2'), + 'dxy': ('d', 'xy'), + 'fz3': ('f', 'z^3'), + 'fxz2': ('f', 'xz^2'), + 'fyz2': ('f', 'yz^2'), + 'fz(x2-y2)': ('f', 'z(x^2-y^2)'), + 'fxyz': ('f', 'xyz'), + 'fx(x2-3y2)': ('f', 'x(x^2-3y^2)'), + 'fy(3x2-y2)': ('f', 'y(3x^2-y^2)'), + } + self._wannier_orbital_numbers_map = { + (0, 1): ('s', ''), + (1, 1): ('p', 'x'), + (1, 2): ('p', 'y'), + (1, 3): ('p', 'z'), + (2, 1): ('d', 'z^2'), + (2, 2): ('d', 'xz'), + (2, 3): ('d', 'yz'), + (2, 4): ('d', 'x^2-y^2'), + (2, 5): ('d', 'xy'), + (3, 1): ('f', 'z^3'), + (3, 2): ('f', 'xz^2'), + (3, 3): ('f', 'yz^2'), + (3, 4): ('f', 'z(x^2-y^2)'), + (3, 5): ('f', 'xyz'), + (3, 6): ('f', 'x(x^2-3y^2)'), + (3, 7): ('f', 'y(3x^2-y^2)'), + } + + def _convert_positions_to_symbols( + self, atomic_cell: AtomicCell, units: str, positions: List[float] + ) -> Optional[str]: + """ + Convert the atom `positions` in fractional or cartesian coordinates to the atom `chemical_symbols`. + + Args: + atomic_cell (AtomicCell): The `AtomicCell` section to which `positions` are extracted + units (str): The units in which the positions are defined. + positions (List[float]): The positions in fractional or cartesian coordinates to be converted to `chemical_symbols`. + + Returns: + (Optional[str]): The `chemical_symbols` of the atom at the position `val`. + """ + for cell_position in atomic_cell.positions.to(units): + if np.array_equal(positions, cell_position.magnitude): + index = atomic_cell.positions.magnitude.tolist().index( + cell_position.magnitude.tolist() + ) + return atomic_cell.atoms_state[index].chemical_symbol + return None + + def parse_child_atom_indices( + self, + atom: Union[str, int], + atomic_cell: AtomicCell, + units: str, + ) -> Tuple[Optional[str], List[int]]: + """ + Parse the atom indices for the child model system. + + Args: + atom (Union[str, int]): The atom string containing the positions information. In some older version, + this can be an integer index pointing to the atom. + atomic_cell (AtomicCell): The `AtomicCell` section where `positions` are stored + units (str): The units in which the positions are defined. + + Returns: + (Tuple[str, List[int]]): The `branch_label` and `atom_indices` for the child model system. + """ + if isinstance(atom, int): + return '', [atom] + if atom.startswith('f='): # fractional coordinates + positions = [float(x) for x in atom.replace('f=', '').split(',')] + positions = np.dot(positions, atomic_cell.lattice_vectors.magnitude) + sites = self._convert_positions_to_symbols(atomic_cell, units, positions) + elif atom.startswith('c='): # cartesian coordinates + positions = [float(x) for x in atom.replace('c=', '').split(',')] + sites = self._convert_positions_to_symbols(atomic_cell, units, positions) + else: # atom label directly specified + sites = atom + + # Find the `atom_indices` which coincide with the `sites` + branch_label = sites + atom_indices = np.where( + [atom.chemical_symbol == branch_label for atom in atomic_cell.atoms_state] + )[0].tolist() + return branch_label, atom_indices + + def populate_orbitals_state( + self, + projection: List[str], + model_system_child: ModelSystem, + atomic_cell: AtomicCell, + logger: BoundLogger, + ) -> None: + """ + Populate the `OrbitalsState` sections for the AtomsState relevant for the Wannier projection. + + Args: + projection (List[Union[int, str]]): The projection information for the atom. + model_system_child (ModelSystem): The child model system to get the `atom_indices`. + atomic_cell (AtomicCell): The `AtomicCell` section where `positions` are stored. + logger (BoundLogger): The logger to log messages. + """ + atom = projection[0] + for atom_index in model_system_child.atom_indices: + if atomic_cell.atoms_state is None or len(atomic_cell.atoms_state) == 0: + logger.warning( + 'Could not extract the `AtomicCell.atoms_state` sections.' + ) + continue + atom_state = atomic_cell.atoms_state[atom_index] + + # To avoid issues when `atom` is an integer + if isinstance(atom, str) and atom != atom_state.chemical_symbol: + continue + + # Try to get the orbitals information + try: + orbitals = projection[1].split(';') + angular_momentum = None + for orb in orbitals: + orbital_state = OrbitalsState() + if orb.startswith('l='): # using angular momentum numbers + lmom = int(orb.split(',mr')[0].replace('l=', '').split(',')[0]) + mrmom = int(orb.split(',mr')[-1].replace('=', '').split(',')[0]) + angular_momentum = self._wannier_orbital_numbers_map.get( + (lmom, mrmom) + ) + else: # ang mom label directly specified + angular_momentum = self._wannier_orbital_symbols_map.get(orb) + ( + orbital_state.l_quantum_symbol, + orbital_state.ml_quantum_symbol, + ) = angular_momentum + atom_state.orbitals_state.append(orbital_state) + except Exception: + logger.warning('Projected orbital labels not found from win.') + return None + return None + + def parse_child_model_systems( + self, + model_system: ModelSystem, + logger: BoundLogger, + ) -> Optional[List[ModelSystem]]: + """ + Parse the child model systems from the `*.win` file to be added as sub-sections of the parent `ModelSystem` section. We + also store the `OrbitalsState` information of the projected atoms. + + Args: + model_system (ModelSystem): The parent `ModelSystem` to which the child model systems will be added. + logger (BoundLogger): The logger to log messages. + + Returns: + (Optional[List[ModelSystem]]): The list of child model systems with the projected atoms information. + """ + # Check if `atomic_cell` is present in `model_system`` + if model_system.cell is None or len(model_system.cell) == 0: + logger.warning( + 'Could not extract `model_system.cell` section from mainfile `*.wout`.' + ) + return None + atomic_cell = model_system.cell[0] + + # Set units in case these are defined in .win + projections = self.win_parser.get('projections', []) + if projections: + if not isinstance(projections, list): + projections = [projections] + if projections[0][0] in ['Bohr', 'Angstrom']: + wannier90_units = self._input_projection_units[projections[0][0]] + projections.pop(0) + else: + wannier90_units = 'angstrom' + if projections[0][0] == 'random': + return None + + # Populating AtomsGroup for projected atoms + model_system_childs = [] + for nat in range(len(projections)): + model_system_child = ModelSystem() + model_system_child.type = 'active_atom' + + # atom positions information always index=0 for `projections[nat]` + projection = projections[nat] + atom = projection[0] + try: + branch_label, atom_indices = self.parse_child_atom_indices( + atom, atomic_cell, wannier90_units + ) + model_system_child.branch_label = branch_label + model_system_child.atom_indices = atom_indices + except Exception: + logger.warning( + 'Error finding the atom labels for the projection from win.' + ) + return None + + # orbital angular momentum information always index=1 for `projections[nat]` + self.populate_orbitals_state( + projection, model_system_child, atomic_cell, logger + ) + model_system_childs.append(model_system_child) + + return model_system_childs diff --git a/src/nomad_parser_wannier90/schema_packages/__init__.py b/src/nomad_parser_wannier90/schema_packages/__init__.py new file mode 100644 index 0000000..88c04b5 --- /dev/null +++ b/src/nomad_parser_wannier90/schema_packages/__init__.py @@ -0,0 +1,17 @@ +from nomad.config.models.plugins import SchemaPackageEntryPoint +from pydantic import Field + + +class Wannier90SchemaPackageEntryPoint(SchemaPackageEntryPoint): + parameter: int = Field(0, description='Custom configuration parameter') + + def load(self): + from nomad_parser_wannier90.schema_packages.package import m_package + + return m_package + + +nomad_parser_wannier90_schema = Wannier90SchemaPackageEntryPoint( + name='Wannier90SchemaPackage', + description='Entry point for the Wannier90 code-specific schema.', +) diff --git a/src/nomad_parser_wannier90/schema_packages/package.py b/src/nomad_parser_wannier90/schema_packages/package.py new file mode 100644 index 0000000..2bb22d9 --- /dev/null +++ b/src/nomad_parser_wannier90/schema_packages/package.py @@ -0,0 +1,38 @@ +from typing import ( + TYPE_CHECKING, +) + +if TYPE_CHECKING: + from nomad.datamodel.datamodel import ( + EntryArchive, + ) + from structlog.stdlib import ( + BoundLogger, + ) + +from nomad.config import config +from nomad.datamodel.data import Schema +from nomad.datamodel.metainfo.annotations import ELNAnnotation, ELNComponentEnum +from nomad.metainfo import Quantity, SchemaPackage + +configuration = config.get_plugin_entry_point( + 'nomad_parser_wannier90.schema_packages:nomad_parser_wannier90_schema' +) + +m_package = SchemaPackage() + + +class MySchema(Schema): + name = Quantity( + type=str, a_eln=ELNAnnotation(component=ELNComponentEnum.StringEditQuantity) + ) + message = Quantity(type=str) + + def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None: + super().normalize(archive, logger) + + logger.info('MySchema.normalize', parameter=configuration.parameter) + self.message = f'Hello {self.name}!' + + +m_package.__init_metainfo__() diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..8176ffc --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1,22 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +from nomad import utils + + +logger = utils.get_logger(__name__) diff --git a/tests/data/lco_mlwf/lco-dos.dat b/tests/data/lco_mlwf/lco-dos.dat new file mode 100644 index 0000000..6612ae2 --- /dev/null +++ b/tests/data/lco_mlwf/lco-dos.dat @@ -0,0 +1,692 @@ + 0.97541072E+01 0.35878051E-14 + 0.97641109E+01 0.53229803E-14 + 0.97741147E+01 0.78828609E-14 + 0.97841184E+01 0.11652380E-13 + 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0.16616681E+02 0.64677260E-40 + 0.16626685E+02 0.32085127E-40 + 0.16636689E+02 0.15880527E-40 + 0.16646692E+02 0.78419365E-41 + 0.16656696E+02 0.38632619E-41 + 0.16666700E+02 0.18988369E-41 diff --git a/tests/data/lco_mlwf/lco.win b/tests/data/lco_mlwf/lco.win new file mode 100644 index 0000000..3c3a2a0 --- /dev/null +++ b/tests/data/lco_mlwf/lco.win @@ -0,0 +1,433 @@ +begin unit_cell_cart +ang +-1.909144696 1.909144696 6.603098061 + 1.909144696 -1.909144696 6.603098061 + 1.909144696 1.909144696 -6.603098061 +end unit_cell_cart + +begin atoms_cart +ang +La -0.0000000000 -0.0000000000 4.7702839137 +La 1.9091446961 1.9091446961 1.8328141469 +Cu -0.0000000000 -0.0000000000 -0.0000000000 +O -0.0000000000 1.9091446961 0.0000000000 +O 1.9091446961 -0.0000000000 0.0000000000 +O -0.0000000000 -0.0000000000 2.4522239552 +O 1.9091446961 1.9091446961 4.1508741055 +end atoms_cart + +! system +num_wann = 1 +num_bands = 5 +mp_grid 7 7 7 + +! job control +exclude_bands : 1-28,34-40 +iprint = 2 + +! plotting +wannier_plot = false +wannier_plot_supercell = 3 +bands_plot = true +bands_num_points = 100 +bands_plot_format = gnuplot +write_hr = true +write_u_matrices = true + +! disentanglement +dis_win_min = 10.0 +dis_win_max = 16.0 +dis_froz_min = 12.3 +dis_froz_max = 16.0 +dis_num_iter = 1000 +dis_conv_tol = 1.0E-12 +!dis_mix_ratio = 0.9 + +! wannierisation +num_iter = 1000 +conv_window = 5 +conv_tol = 1e-12 + +! pp tools +kpath = false +kpath_task = bands +kpath_bands_colour = spin +kpath_num_points=500 +begin kpoint_path + G 0.00 0.00 0.00 N 0.25 -0.25 0.25 + N 0.25 -0.25 0.25 X 0.00 0.00 0.50 + X 0.00 0.00 0.50 G 0.00 0.00 0.00 + G 0.00 0.00 0.00 M 0.25 0.25 -0.25 +end kpoint_path + +kslice = false +kslice_task = fermi_lines +fermi_energy = 11.375 +kslice_2dkmesh = 200 200 +kslice_corner = 0.00 0.00 0.00 +!kslice_b1 = -0.27259 0.27259 0.27259 +!kslice_b2 = 0.27259 -0.27259 0.27259 +kslice_b1 = -0.25 0.25 0.25 +kslice_b2 = 0.25 -0.25 0.25 +!kslice_b1 = 0.00 0.50 0.00 +!kslice_b2 = 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| + | Nicola Marzari (EPFL) | + | Ivo Souza (Universidad del Pais Vasco) | + | Arash A. Mostofi (Imperial College London) | + | Jonathan R. Yates (University of Oxford) | + | | + | For the full list of Wannier90 3.x authors, | + | please check the code documentation and the | + | README on the GitHub page of the code | + | | + | | + | Please cite | + | | + | [ref] "Wannier90 as a community code: | + | new features and applications", | + | G. Pizzi et al., J. Phys. Cond. Matt. 32, | + | 165902 (2020). | + | http://doi.org/10.1088/1361-648X/ab51ff | + | | + | in any publications arising from the use of | + | this code. For the method please cite | + | | + | [ref] "Maximally Localized Generalised Wannier | + | Functions for Composite Energy Bands" | + | N. Marzari and D. Vanderbilt | + | Phys. Rev. B 56 12847 (1997) | + | | + | [ref] "Maximally Localized Wannier Functions | + | for Entangled Energy Bands" | + | I. Souza, N. Marzari and D. Vanderbilt | + | Phys. Rev. B 65 035109 (2001) | + | | + | | + | Copyright (c) 1996-2020 | + | The Wannier90 Developer Group and | + | individual contributors | + | | + | Release: 3.1.0 5th March 2020 | + | | + | This program is free software; you can | + | redistribute it and/or modify it under the terms | + | of the GNU General Public License as published by | + | the Free Software Foundation; either version 2 of | + | the License, or (at your option) any later version| + | | + | This program is distributed in the hope that it | + | will be useful, but WITHOUT ANY WARRANTY; without | + | even the implied warranty of MERCHANTABILITY or | + | FITNESS FOR A PARTICULAR PURPOSE. See the GNU | + | General Public License for more details. | + | | + | You should have received a copy of the GNU General| + | Public License along with this program; if not, | + | write to the Free Software Foundation, Inc., | + | 675 Mass Ave, Cambridge, MA 02139, USA. | + | | + +---------------------------------------------------+ + | Execution started on 3May2022 at 14:04:17 | + +---------------------------------------------------+ + + ****************************************************************************** + * -> Using CODATA 2006 constant values * + * (http://physics.nist.gov/cuu/Constants/index.html) * + * -> Using Bohr value from CODATA * + ****************************************************************************** + + + Running in serial (with parallel executable) + + ------ + SYSTEM + ------ + + Lattice Vectors (Ang) + a_1 -1.909145 1.909145 6.603098 + a_2 1.909145 -1.909145 6.603098 + a_3 1.909145 1.909145 -6.603098 + + Unit Cell Volume: 96.26877 (Ang^3) + + Reciprocal-Space Vectors (Ang^-1) + b_1 -0.000000 1.645550 0.475776 + b_2 1.645550 -0.000000 0.475776 + b_3 1.645550 1.645550 -0.000000 + + *----------------------------------------------------------------------------* + | Site Fractional Coordinate Cartesian Coordinate (Ang) | + +----------------------------------------------------------------------------+ + | La 1 0.36122 0.36122 -0.00000 | -0.00000 -0.00000 4.77028 | + | La 2 0.63878 0.63878 1.00000 | 1.90914 1.90914 1.83281 | + | Cu 1 0.00000 0.00000 0.00000 | -0.00000 -0.00000 -0.00000 | + | O 1 0.50000 -0.00000 0.50000 | -0.00000 1.90914 0.00000 | + | O 2 -0.00000 0.50000 0.50000 | 1.90914 -0.00000 0.00000 | + | O 3 0.18569 0.18569 -0.00000 | -0.00000 -0.00000 2.45222 | + | O 4 0.81431 0.81431 1.00000 | 1.90914 1.90914 4.15087 | + *----------------------------------------------------------------------------* + ----------- + PROJECTIONS + ----------- + + +----------------------------------------------------------------------------+ + | Frac. Coord. l mr r z-axis x-axis Z/a | + +----------------------------------------------------------------------------+ + | 0.00 0.00 0.00 2 4 1 0.000 0.000 1.000 1.000 0.000 0.000 1.0 | + +----------------------------------------------------------------------------+ + + ------------ + K-POINT GRID + ------------ + + Grid size = 7 x 7 x 7 Total points = 343 + + *----------------------------------------------------------------------------* + | k-point Fractional Coordinate Cartesian Coordinate (Ang^-1) | + +----------------------------------------------------------------------------+ + | 1 0.00000 0.00000 0.00000 | 0.00000 0.00000 0.00000 | + | 2 0.00000 0.00000 0.14286 | 0.23508 0.23508 -0.00000 | + | 3 0.00000 0.00000 0.28571 | 0.47016 0.47016 -0.00000 | + | 4 0.00000 0.00000 0.42857 | 0.70524 0.70524 -0.00000 | + | 5 0.00000 0.00000 0.57143 | 0.94031 0.94031 -0.00000 | + | 6 0.00000 0.00000 0.71429 | 1.17539 1.17539 -0.00000 | + | 7 0.00000 0.00000 0.85714 | 1.41047 1.41047 -0.00000 | + | 8 0.00000 0.14286 0.00000 | 0.23508 -0.00000 0.06797 | + | 9 0.00000 0.14286 0.14286 | 0.47016 0.23508 0.06797 | + | 10 0.00000 0.14286 0.28571 | 0.70524 0.47016 0.06797 | + | 11 0.00000 0.14286 0.42857 | 0.94031 0.70524 0.06797 | + | 12 0.00000 0.14286 0.57143 | 1.17539 0.94031 0.06797 | + | 13 0.00000 0.14286 0.71429 | 1.41047 1.17539 0.06797 | + | 14 0.00000 0.14286 0.85714 | 1.64555 1.41047 0.06797 | + | 15 0.00000 0.28571 0.00000 | 0.47016 -0.00000 0.13594 | + | 16 0.00000 0.28571 0.14286 | 0.70524 0.23508 0.13594 | + | 17 0.00000 0.28571 0.28571 | 0.94031 0.47016 0.13594 | + | 18 0.00000 0.28571 0.42857 | 1.17539 0.70524 0.13594 | + | 19 0.00000 0.28571 0.57143 | 1.41047 0.94031 0.13594 | + | 20 0.00000 0.28571 0.71429 | 1.64555 1.17539 0.13594 | + | 21 0.00000 0.28571 0.85714 | 1.88063 1.41047 0.13594 | + | 22 0.00000 0.42857 0.00000 | 0.70524 -0.00000 0.20390 | + | 23 0.00000 0.42857 0.14286 | 0.94031 0.23508 0.20390 | + | 24 0.00000 0.42857 0.28571 | 1.17539 0.47016 0.20390 | 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0.33984 | + | 42 0.00000 0.71429 0.85714 | 2.58586 1.41047 0.33984 | + | 43 0.00000 0.85714 0.00000 | 1.41047 -0.00000 0.40781 | + | 44 0.00000 0.85714 0.14286 | 1.64555 0.23508 0.40781 | + | 45 0.00000 0.85714 0.28571 | 1.88063 0.47016 0.40781 | + | 46 0.00000 0.85714 0.42857 | 2.11571 0.70524 0.40781 | + | 47 0.00000 0.85714 0.57143 | 2.35079 0.94031 0.40781 | + | 48 0.00000 0.85714 0.71429 | 2.58586 1.17539 0.40781 | + | 49 0.00000 0.85714 0.85714 | 2.82094 1.41047 0.40781 | + | 50 0.14286 0.00000 0.00000 | -0.00000 0.23508 0.06797 | + | 51 0.14286 0.00000 0.14286 | 0.23508 0.47016 0.06797 | + | 52 0.14286 0.00000 0.28571 | 0.47016 0.70524 0.06797 | + | 53 0.14286 0.00000 0.42857 | 0.70524 0.94031 0.06797 | + | 54 0.14286 0.00000 0.57143 | 0.94031 1.17539 0.06797 | + | 55 0.14286 0.00000 0.71429 | 1.17539 1.41047 0.06797 | + | 56 0.14286 0.00000 0.85714 | 1.41047 1.64555 0.06797 | + | 57 0.14286 0.14286 0.00000 | 0.23508 0.23508 0.13594 | + | 58 0.14286 0.14286 0.14286 | 0.47016 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1.64555 1.17539 0.27187 | + | 76 0.14286 0.42857 0.71429 | 1.88063 1.41047 0.27187 | + | 77 0.14286 0.42857 0.85714 | 2.11571 1.64555 0.27187 | + | 78 0.14286 0.57143 0.00000 | 0.94031 0.23508 0.33984 | + | 79 0.14286 0.57143 0.14286 | 1.17539 0.47016 0.33984 | + | 80 0.14286 0.57143 0.28571 | 1.41047 0.70524 0.33984 | + | 81 0.14286 0.57143 0.42857 | 1.64555 0.94031 0.33984 | + | 82 0.14286 0.57143 0.57143 | 1.88063 1.17539 0.33984 | + | 83 0.14286 0.57143 0.71429 | 2.11571 1.41047 0.33984 | + | 84 0.14286 0.57143 0.85714 | 2.35079 1.64555 0.33984 | + | 85 0.14286 0.71429 0.00000 | 1.17539 0.23508 0.40781 | + | 86 0.14286 0.71429 0.14286 | 1.41047 0.47016 0.40781 | + | 87 0.14286 0.71429 0.28571 | 1.64555 0.70524 0.40781 | + | 88 0.14286 0.71429 0.42857 | 1.88063 0.94031 0.40781 | + | 89 0.14286 0.71429 0.57143 | 2.11571 1.17539 0.40781 | + | 90 0.14286 0.71429 0.71429 | 2.35079 1.41047 0.40781 | + | 91 0.14286 0.71429 0.85714 | 2.58586 1.64555 0.40781 | + | 92 0.14286 0.85714 0.00000 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0.14286 0.42857 | 0.94031 1.17539 0.20390 | + | 110 0.28571 0.14286 0.57143 | 1.17539 1.41047 0.20390 | + | 111 0.28571 0.14286 0.71429 | 1.41047 1.64555 0.20390 | + | 112 0.28571 0.14286 0.85714 | 1.64555 1.88063 0.20390 | + | 113 0.28571 0.28571 0.00000 | 0.47016 0.47016 0.27187 | + | 114 0.28571 0.28571 0.14286 | 0.70524 0.70524 0.27187 | + | 115 0.28571 0.28571 0.28571 | 0.94031 0.94031 0.27187 | + | 116 0.28571 0.28571 0.42857 | 1.17539 1.17539 0.27187 | + | 117 0.28571 0.28571 0.57143 | 1.41047 1.41047 0.27187 | + | 118 0.28571 0.28571 0.71429 | 1.64555 1.64555 0.27187 | + | 119 0.28571 0.28571 0.85714 | 1.88063 1.88063 0.27187 | + | 120 0.28571 0.42857 0.00000 | 0.70524 0.47016 0.33984 | + | 121 0.28571 0.42857 0.14286 | 0.94031 0.70524 0.33984 | + | 122 0.28571 0.42857 0.28571 | 1.17539 0.94031 0.33984 | + | 123 0.28571 0.42857 0.42857 | 1.41047 1.17539 0.33984 | + | 124 0.28571 0.42857 0.57143 | 1.64555 1.41047 0.33984 | + | 125 0.28571 0.42857 0.71429 | 1.88063 1.64555 0.33984 | + | 126 0.28571 0.42857 0.85714 | 2.11571 1.88063 0.33984 | + | 127 0.28571 0.57143 0.00000 | 0.94031 0.47016 0.40781 | + | 128 0.28571 0.57143 0.14286 | 1.17539 0.70524 0.40781 | + | 129 0.28571 0.57143 0.28571 | 1.41047 0.94031 0.40781 | + | 130 0.28571 0.57143 0.42857 | 1.64555 1.17539 0.40781 | + | 131 0.28571 0.57143 0.57143 | 1.88063 1.41047 0.40781 | + | 132 0.28571 0.57143 0.71429 | 2.11571 1.64555 0.40781 | + | 133 0.28571 0.57143 0.85714 | 2.35079 1.88063 0.40781 | + | 134 0.28571 0.71429 0.00000 | 1.17539 0.47016 0.47578 | + | 135 0.28571 0.71429 0.14286 | 1.41047 0.70524 0.47578 | + | 136 0.28571 0.71429 0.28571 | 1.64555 0.94031 0.47578 | + | 137 0.28571 0.71429 0.42857 | 1.88063 1.17539 0.47578 | + | 138 0.28571 0.71429 0.57143 | 2.11571 1.41047 0.47578 | + | 139 0.28571 0.71429 0.71429 | 2.35079 1.64555 0.47578 | + | 140 0.28571 0.71429 0.85714 | 2.58586 1.88063 0.47578 | + | 141 0.28571 0.85714 0.00000 | 1.41047 0.47016 0.54374 | + | 142 0.28571 0.85714 0.14286 | 1.64555 0.70524 0.54374 | + | 143 0.28571 0.85714 0.28571 | 1.88063 0.94031 0.54374 | + | 144 0.28571 0.85714 0.42857 | 2.11571 1.17539 0.54374 | + | 145 0.28571 0.85714 0.57143 | 2.35079 1.41047 0.54374 | + | 146 0.28571 0.85714 0.71429 | 2.58586 1.64555 0.54374 | + | 147 0.28571 0.85714 0.85714 | 2.82094 1.88063 0.54374 | + | 148 0.42857 0.00000 0.00000 | -0.00000 0.70524 0.20390 | + | 149 0.42857 0.00000 0.14286 | 0.23508 0.94031 0.20390 | + | 150 0.42857 0.00000 0.28571 | 0.47016 1.17539 0.20390 | + | 151 0.42857 0.00000 0.42857 | 0.70524 1.41047 0.20390 | + | 152 0.42857 0.00000 0.57143 | 0.94031 1.64555 0.20390 | + | 153 0.42857 0.00000 0.71429 | 1.17539 1.88063 0.20390 | + | 154 0.42857 0.00000 0.85714 | 1.41047 2.11571 0.20390 | + | 155 0.42857 0.14286 0.00000 | 0.23508 0.70524 0.27187 | + | 156 0.42857 0.14286 0.14286 | 0.47016 0.94031 0.27187 | + | 157 0.42857 0.14286 0.28571 | 0.70524 1.17539 0.27187 | + | 158 0.42857 0.14286 0.42857 | 0.94031 1.41047 0.27187 | + | 159 0.42857 0.14286 0.57143 | 1.17539 1.64555 0.27187 | + | 160 0.42857 0.14286 0.71429 | 1.41047 1.88063 0.27187 | + | 161 0.42857 0.14286 0.85714 | 1.64555 2.11571 0.27187 | + | 162 0.42857 0.28571 0.00000 | 0.47016 0.70524 0.33984 | + | 163 0.42857 0.28571 0.14286 | 0.70524 0.94031 0.33984 | + | 164 0.42857 0.28571 0.28571 | 0.94031 1.17539 0.33984 | + | 165 0.42857 0.28571 0.42857 | 1.17539 1.41047 0.33984 | + | 166 0.42857 0.28571 0.57143 | 1.41047 1.64555 0.33984 | + | 167 0.42857 0.28571 0.71429 | 1.64555 1.88063 0.33984 | + | 168 0.42857 0.28571 0.85714 | 1.88063 2.11571 0.33984 | + | 169 0.42857 0.42857 0.00000 | 0.70524 0.70524 0.40781 | + | 170 0.42857 0.42857 0.14286 | 0.94031 0.94031 0.40781 | + | 171 0.42857 0.42857 0.28571 | 1.17539 1.17539 0.40781 | + | 172 0.42857 0.42857 0.42857 | 1.41047 1.41047 0.40781 | + | 173 0.42857 0.42857 0.57143 | 1.64555 1.64555 0.40781 | + | 174 0.42857 0.42857 0.71429 | 1.88063 1.88063 0.40781 | + | 175 0.42857 0.42857 0.85714 | 2.11571 2.11571 0.40781 | + | 176 0.42857 0.57143 0.00000 | 0.94031 0.70524 0.47578 | + | 177 0.42857 0.57143 0.14286 | 1.17539 0.94031 0.47578 | + | 178 0.42857 0.57143 0.28571 | 1.41047 1.17539 0.47578 | + | 179 0.42857 0.57143 0.42857 | 1.64555 1.41047 0.47578 | + | 180 0.42857 0.57143 0.57143 | 1.88063 1.64555 0.47578 | + | 181 0.42857 0.57143 0.71429 | 2.11571 1.88063 0.47578 | + | 182 0.42857 0.57143 0.85714 | 2.35079 2.11571 0.47578 | + | 183 0.42857 0.71429 0.00000 | 1.17539 0.70524 0.54374 | + | 184 0.42857 0.71429 0.14286 | 1.41047 0.94031 0.54374 | + | 185 0.42857 0.71429 0.28571 | 1.64555 1.17539 0.54374 | + | 186 0.42857 0.71429 0.42857 | 1.88063 1.41047 0.54374 | + | 187 0.42857 0.71429 0.57143 | 2.11571 1.64555 0.54374 | + | 188 0.42857 0.71429 0.71429 | 2.35079 1.88063 0.54374 | + | 189 0.42857 0.71429 0.85714 | 2.58586 2.11571 0.54374 | + | 190 0.42857 0.85714 0.00000 | 1.41047 0.70524 0.61171 | + | 191 0.42857 0.85714 0.14286 | 1.64555 0.94031 0.61171 | + | 192 0.42857 0.85714 0.28571 | 1.88063 1.17539 0.61171 | + | 193 0.42857 0.85714 0.42857 | 2.11571 1.41047 0.61171 | + | 194 0.42857 0.85714 0.57143 | 2.35079 1.64555 0.61171 | + | 195 0.42857 0.85714 0.71429 | 2.58586 1.88063 0.61171 | + | 196 0.42857 0.85714 0.85714 | 2.82094 2.11571 0.61171 | + | 197 0.57143 0.00000 0.00000 | -0.00000 0.94031 0.27187 | + | 198 0.57143 0.00000 0.14286 | 0.23508 1.17539 0.27187 | + | 199 0.57143 0.00000 0.28571 | 0.47016 1.41047 0.27187 | + | 200 0.57143 0.00000 0.42857 | 0.70524 1.64555 0.27187 | + | 201 0.57143 0.00000 0.57143 | 0.94031 1.88063 0.27187 | + | 202 0.57143 0.00000 0.71429 | 1.17539 2.11571 0.27187 | + | 203 0.57143 0.00000 0.85714 | 1.41047 2.35079 0.27187 | + | 204 0.57143 0.14286 0.00000 | 0.23508 0.94031 0.33984 | + | 205 0.57143 0.14286 0.14286 | 0.47016 1.17539 0.33984 | + | 206 0.57143 0.14286 0.28571 | 0.70524 1.41047 0.33984 | + | 207 0.57143 0.14286 0.42857 | 0.94031 1.64555 0.33984 | + | 208 0.57143 0.14286 0.57143 | 1.17539 1.88063 0.33984 | + | 209 0.57143 0.14286 0.71429 | 1.41047 2.11571 0.33984 | + | 210 0.57143 0.14286 0.85714 | 1.64555 2.35079 0.33984 | + | 211 0.57143 0.28571 0.00000 | 0.47016 0.94031 0.40781 | + | 212 0.57143 0.28571 0.14286 | 0.70524 1.17539 0.40781 | + | 213 0.57143 0.28571 0.28571 | 0.94031 1.41047 0.40781 | + | 214 0.57143 0.28571 0.42857 | 1.17539 1.64555 0.40781 | + | 215 0.57143 0.28571 0.57143 | 1.41047 1.88063 0.40781 | + | 216 0.57143 0.28571 0.71429 | 1.64555 2.11571 0.40781 | + | 217 0.57143 0.28571 0.85714 | 1.88063 2.35079 0.40781 | + | 218 0.57143 0.42857 0.00000 | 0.70524 0.94031 0.47578 | + | 219 0.57143 0.42857 0.14286 | 0.94031 1.17539 0.47578 | + | 220 0.57143 0.42857 0.28571 | 1.17539 1.41047 0.47578 | + | 221 0.57143 0.42857 0.42857 | 1.41047 1.64555 0.47578 | + | 222 0.57143 0.42857 0.57143 | 1.64555 1.88063 0.47578 | + | 223 0.57143 0.42857 0.71429 | 1.88063 2.11571 0.47578 | + | 224 0.57143 0.42857 0.85714 | 2.11571 2.35079 0.47578 | + | 225 0.57143 0.57143 0.00000 | 0.94031 0.94031 0.54374 | + | 226 0.57143 0.57143 0.14286 | 1.17539 1.17539 0.54374 | + | 227 0.57143 0.57143 0.28571 | 1.41047 1.41047 0.54374 | + | 228 0.57143 0.57143 0.42857 | 1.64555 1.64555 0.54374 | + | 229 0.57143 0.57143 0.57143 | 1.88063 1.88063 0.54374 | + | 230 0.57143 0.57143 0.71429 | 2.11571 2.11571 0.54374 | + | 231 0.57143 0.57143 0.85714 | 2.35079 2.35079 0.54374 | + | 232 0.57143 0.71429 0.00000 | 1.17539 0.94031 0.61171 | + | 233 0.57143 0.71429 0.14286 | 1.41047 1.17539 0.61171 | + | 234 0.57143 0.71429 0.28571 | 1.64555 1.41047 0.61171 | + | 235 0.57143 0.71429 0.42857 | 1.88063 1.64555 0.61171 | + | 236 0.57143 0.71429 0.57143 | 2.11571 1.88063 0.61171 | + | 237 0.57143 0.71429 0.71429 | 2.35079 2.11571 0.61171 | + | 238 0.57143 0.71429 0.85714 | 2.58586 2.35079 0.61171 | + | 239 0.57143 0.85714 0.00000 | 1.41047 0.94031 0.67968 | + | 240 0.57143 0.85714 0.14286 | 1.64555 1.17539 0.67968 | + | 241 0.57143 0.85714 0.28571 | 1.88063 1.41047 0.67968 | + | 242 0.57143 0.85714 0.42857 | 2.11571 1.64555 0.67968 | + | 243 0.57143 0.85714 0.57143 | 2.35079 1.88063 0.67968 | + | 244 0.57143 0.85714 0.71429 | 2.58586 2.11571 0.67968 | + | 245 0.57143 0.85714 0.85714 | 2.82094 2.35079 0.67968 | + | 246 0.71429 0.00000 0.00000 | -0.00000 1.17539 0.33984 | + | 247 0.71429 0.00000 0.14286 | 0.23508 1.41047 0.33984 | + | 248 0.71429 0.00000 0.28571 | 0.47016 1.64555 0.33984 | + | 249 0.71429 0.00000 0.42857 | 0.70524 1.88063 0.33984 | + | 250 0.71429 0.00000 0.57143 | 0.94031 2.11571 0.33984 | + | 251 0.71429 0.00000 0.71429 | 1.17539 2.35079 0.33984 | + | 252 0.71429 0.00000 0.85714 | 1.41047 2.58586 0.33984 | + | 253 0.71429 0.14286 0.00000 | 0.23508 1.17539 0.40781 | + | 254 0.71429 0.14286 0.14286 | 0.47016 1.41047 0.40781 | + | 255 0.71429 0.14286 0.28571 | 0.70524 1.64555 0.40781 | + | 256 0.71429 0.14286 0.42857 | 0.94031 1.88063 0.40781 | + | 257 0.71429 0.14286 0.57143 | 1.17539 2.11571 0.40781 | + | 258 0.71429 0.14286 0.71429 | 1.41047 2.35079 0.40781 | + | 259 0.71429 0.14286 0.85714 | 1.64555 2.58586 0.40781 | + | 260 0.71429 0.28571 0.00000 | 0.47016 1.17539 0.47578 | + | 261 0.71429 0.28571 0.14286 | 0.70524 1.41047 0.47578 | + | 262 0.71429 0.28571 0.28571 | 0.94031 1.64555 0.47578 | + | 263 0.71429 0.28571 0.42857 | 1.17539 1.88063 0.47578 | + | 264 0.71429 0.28571 0.57143 | 1.41047 2.11571 0.47578 | + | 265 0.71429 0.28571 0.71429 | 1.64555 2.35079 0.47578 | + | 266 0.71429 0.28571 0.85714 | 1.88063 2.58586 0.47578 | + | 267 0.71429 0.42857 0.00000 | 0.70524 1.17539 0.54374 | + | 268 0.71429 0.42857 0.14286 | 0.94031 1.41047 0.54374 | + | 269 0.71429 0.42857 0.28571 | 1.17539 1.64555 0.54374 | + | 270 0.71429 0.42857 0.42857 | 1.41047 1.88063 0.54374 | + | 271 0.71429 0.42857 0.57143 | 1.64555 2.11571 0.54374 | + | 272 0.71429 0.42857 0.71429 | 1.88063 2.35079 0.54374 | + | 273 0.71429 0.42857 0.85714 | 2.11571 2.58586 0.54374 | + | 274 0.71429 0.57143 0.00000 | 0.94031 1.17539 0.61171 | + | 275 0.71429 0.57143 0.14286 | 1.17539 1.41047 0.61171 | + | 276 0.71429 0.57143 0.28571 | 1.41047 1.64555 0.61171 | + | 277 0.71429 0.57143 0.42857 | 1.64555 1.88063 0.61171 | + | 278 0.71429 0.57143 0.57143 | 1.88063 2.11571 0.61171 | + | 279 0.71429 0.57143 0.71429 | 2.11571 2.35079 0.61171 | + | 280 0.71429 0.57143 0.85714 | 2.35079 2.58586 0.61171 | + | 281 0.71429 0.71429 0.00000 | 1.17539 1.17539 0.67968 | + | 282 0.71429 0.71429 0.14286 | 1.41047 1.41047 0.67968 | + | 283 0.71429 0.71429 0.28571 | 1.64555 1.64555 0.67968 | + | 284 0.71429 0.71429 0.42857 | 1.88063 1.88063 0.67968 | + | 285 0.71429 0.71429 0.57143 | 2.11571 2.11571 0.67968 | + | 286 0.71429 0.71429 0.71429 | 2.35079 2.35079 0.67968 | + | 287 0.71429 0.71429 0.85714 | 2.58586 2.58586 0.67968 | + | 288 0.71429 0.85714 0.00000 | 1.41047 1.17539 0.74765 | + | 289 0.71429 0.85714 0.14286 | 1.64555 1.41047 0.74765 | + | 290 0.71429 0.85714 0.28571 | 1.88063 1.64555 0.74765 | + | 291 0.71429 0.85714 0.42857 | 2.11571 1.88063 0.74765 | + | 292 0.71429 0.85714 0.57143 | 2.35079 2.11571 0.74765 | + | 293 0.71429 0.85714 0.71429 | 2.58586 2.35079 0.74765 | + | 294 0.71429 0.85714 0.85714 | 2.82094 2.58586 0.74765 | + | 295 0.85714 0.00000 0.00000 | -0.00000 1.41047 0.40781 | + | 296 0.85714 0.00000 0.14286 | 0.23508 1.64555 0.40781 | + | 297 0.85714 0.00000 0.28571 | 0.47016 1.88063 0.40781 | + | 298 0.85714 0.00000 0.42857 | 0.70524 2.11571 0.40781 | + | 299 0.85714 0.00000 0.57143 | 0.94031 2.35079 0.40781 | + | 300 0.85714 0.00000 0.71429 | 1.17539 2.58586 0.40781 | + | 301 0.85714 0.00000 0.85714 | 1.41047 2.82094 0.40781 | + | 302 0.85714 0.14286 0.00000 | 0.23508 1.41047 0.47578 | + | 303 0.85714 0.14286 0.14286 | 0.47016 1.64555 0.47578 | + | 304 0.85714 0.14286 0.28571 | 0.70524 1.88063 0.47578 | + | 305 0.85714 0.14286 0.42857 | 0.94031 2.11571 0.47578 | + | 306 0.85714 0.14286 0.57143 | 1.17539 2.35079 0.47578 | + | 307 0.85714 0.14286 0.71429 | 1.41047 2.58586 0.47578 | + | 308 0.85714 0.14286 0.85714 | 1.64555 2.82094 0.47578 | + | 309 0.85714 0.28571 0.00000 | 0.47016 1.41047 0.54374 | + | 310 0.85714 0.28571 0.14286 | 0.70524 1.64555 0.54374 | + | 311 0.85714 0.28571 0.28571 | 0.94031 1.88063 0.54374 | + | 312 0.85714 0.28571 0.42857 | 1.17539 2.11571 0.54374 | + | 313 0.85714 0.28571 0.57143 | 1.41047 2.35079 0.54374 | + | 314 0.85714 0.28571 0.71429 | 1.64555 2.58586 0.54374 | + | 315 0.85714 0.28571 0.85714 | 1.88063 2.82094 0.54374 | + | 316 0.85714 0.42857 0.00000 | 0.70524 1.41047 0.61171 | + | 317 0.85714 0.42857 0.14286 | 0.94031 1.64555 0.61171 | + | 318 0.85714 0.42857 0.28571 | 1.17539 1.88063 0.61171 | + | 319 0.85714 0.42857 0.42857 | 1.41047 2.11571 0.61171 | + | 320 0.85714 0.42857 0.57143 | 1.64555 2.35079 0.61171 | + | 321 0.85714 0.42857 0.71429 | 1.88063 2.58586 0.61171 | + | 322 0.85714 0.42857 0.85714 | 2.11571 2.82094 0.61171 | + | 323 0.85714 0.57143 0.00000 | 0.94031 1.41047 0.67968 | + | 324 0.85714 0.57143 0.14286 | 1.17539 1.64555 0.67968 | + | 325 0.85714 0.57143 0.28571 | 1.41047 1.88063 0.67968 | + | 326 0.85714 0.57143 0.42857 | 1.64555 2.11571 0.67968 | + | 327 0.85714 0.57143 0.57143 | 1.88063 2.35079 0.67968 | + | 328 0.85714 0.57143 0.71429 | 2.11571 2.58586 0.67968 | + | 329 0.85714 0.57143 0.85714 | 2.35079 2.82094 0.67968 | + | 330 0.85714 0.71429 0.00000 | 1.17539 1.41047 0.74765 | + | 331 0.85714 0.71429 0.14286 | 1.41047 1.64555 0.74765 | + | 332 0.85714 0.71429 0.28571 | 1.64555 1.88063 0.74765 | + | 333 0.85714 0.71429 0.42857 | 1.88063 2.11571 0.74765 | + | 334 0.85714 0.71429 0.57143 | 2.11571 2.35079 0.74765 | + | 335 0.85714 0.71429 0.71429 | 2.35079 2.58586 0.74765 | + | 336 0.85714 0.71429 0.85714 | 2.58586 2.82094 0.74765 | + | 337 0.85714 0.85714 0.00000 | 1.41047 1.41047 0.81562 | + | 338 0.85714 0.85714 0.14286 | 1.64555 1.64555 0.81562 | + | 339 0.85714 0.85714 0.28571 | 1.88063 1.88063 0.81562 | + | 340 0.85714 0.85714 0.42857 | 2.11571 2.11571 0.81562 | + | 341 0.85714 0.85714 0.57143 | 2.35079 2.35079 0.81562 | + | 342 0.85714 0.85714 0.71429 | 2.58586 2.58586 0.81562 | + | 343 0.85714 0.85714 0.85714 | 2.82094 2.82094 0.81562 | + *----------------------------------------------------------------------------* + + + *---------------------------------- MAIN ------------------------------------* + | Number of Wannier Functions : 1 | + | Number of Objective Wannier Functions : 1 | + | Number of input Bloch states : 5 | + | Output verbosity (1=low, 5=high) : 2 | + | Timing Level (1=low, 5=high) : 1 | + | Optimisation (0=memory, 3=speed) : 3 | + | Length Unit : Ang | + | Post-processing setup (write *.nnkp) : F | + | Using Gamma-only branch of algorithms : F | + *----------------------------------------------------------------------------* + *------------------------------- WANNIERISE ---------------------------------* + | Total number of iterations : 1000 | + | Number of CG steps before reset : 5 | + | Trial step length for line search : 2.000 | + | Convergence tolerence : 0.100E-11 | + | Convergence window : 5 | + | Iterations between writing output : 1 | + | Iterations between backing up to disk : 100 | + | Write r^2_nm to file : F | + | Write xyz WF centres to file : F | + | Write on-site energies <0n|H|0n> to file : F | + | Use guiding centre to control phases : F | + | Use phases for initial projections : F | + *----------------------------------------------------------------------------* + *------------------------------- DISENTANGLE --------------------------------* + | Using band disentanglement : T | + | Total number of iterations : 1000 | + | Mixing ratio : 0.500 | + | Convergence tolerence : 1.000E-12 | + | Convergence window : 3 | + *----------------------------------------------------------------------------* + *-------------------------------- PLOTTING ----------------------------------* + | Plotting interpolated bandstructure : T | + | Number of K-path sections : 4 | + | Divisions along first K-path section : 100 | + | Output format : gnuplot | + | Output mode : s-k | + *----------------------------------------------------------------------------* + | K-space path sections: | + | From: G 0.000 0.000 0.000 To: N 0.250 -0.250 0.250 | + | From: N 0.250 -0.250 0.250 To: X 0.000 0.000 0.500 | + | From: X 0.000 0.000 0.500 To: G 0.000 0.000 0.000 | + | From: G 0.000 0.000 0.000 To: M 0.250 0.250 -0.250 | + *----------------------------------------------------------------------------* + | Plotting Hamiltonian in WF basis : T | + *----------------------------------------------------------------------------* + Time to read parameters 0.061 (sec) + + *---------------------------------- K-MESH ----------------------------------* + +----------------------------------------------------------------------------+ + | Distance to Nearest-Neighbour Shells | + | ------------------------------------ | + | Shell Distance (Ang^-1) Multiplicity | + | ----- ----------------- ------------ | + | 1 0.135936 2 | + | 2 0.244707 8 | + | 3 0.271872 2 | + | 4 0.311189 8 | + | 5 0.332451 4 | + | 6 0.359169 8 | + | 7 0.407808 2 | + | 8 0.413223 8 | + | 9 0.429463 8 | + | 10 0.470157 4 | + | 11 0.489414 8 | + | 12 0.526147 8 | + | 13 0.530028 16 | + | 14 0.530683 8 | + | 15 0.543104 8 | + | 16 0.543743 2 | + | 17 0.563814 16 | + | 18 0.622378 8 | + | 19 0.625940 16 | + | 20 0.637323 8 | + | 21 0.655326 8 | + | 22 0.664903 4 | + | 23 0.678656 8 | + | 24 0.679679 2 | + | 25 0.708503 8 | + | 26 0.708994 16 | + | 27 0.718338 8 | + | 28 0.718822 8 | + | 29 0.734121 8 | + | 30 0.743384 8 | + | 31 0.755710 16 | + | 32 0.756629 8 | + | 33 0.780002 8 | + | 34 0.782846 8 | + | 35 0.783734 8 | + | 36 0.791539 16 | + +----------------------------------------------------------------------------+ + | The b-vectors are chosen automatically | + | Shell: 1 w_b 27.0583842 (Ang^2) | + | Shell: 1 w_b 22.5344732 (Ang^2) | + | Shell: 2 w_b 4.5239110 (Ang^2) | + | The following shells are used: 1, 2 | + +----------------------------------------------------------------------------+ + | Shell # Nearest-Neighbours | + | ----- -------------------- | + | 1 2 | + | 2 8 | + +----------------------------------------------------------------------------+ + | Completeness relation is fully satisfied [Eq. (B1), PRB 56, 12847 (1997)] | + +----------------------------------------------------------------------------+ + | b_k Vectors (Ang^-1) and Weights (Ang^2) | + | ---------------------------------------- | + | No. b_k(x) b_k(y) b_k(z) w_b | + | --- -------------------------------- -------- | + | 1 0.000000 0.000000 0.135936 22.534473 | + | 2 -0.000000 0.000000 -0.135936 22.534473 | + | 3 0.235079 -0.000000 0.067968 4.523911 | + | 4 -0.000000 0.235079 0.067968 4.523911 | + | 5 -0.235079 0.000000 -0.067968 4.523911 | + | 6 0.000000 0.235079 -0.067968 4.523911 | + | 7 0.000000 -0.235079 -0.067968 4.523911 | + | 8 0.235079 0.000000 -0.067968 4.523911 | + | 9 0.000000 -0.235079 0.067968 4.523911 | + | 10 -0.235079 0.000000 0.067968 4.523911 | + +----------------------------------------------------------------------------+ + | b_k Directions (Ang^-1) | + | ----------------------- | + | No. x y z | + | --- -------------------------------- | + | 1 0.000000 0.000000 0.135936 | + | 2 0.235079 -0.000000 0.067968 | + | 3 -0.000000 0.235079 0.067968 | + | 4 0.000000 0.235079 -0.067968 | + | 5 0.235079 0.000000 -0.067968 | + +----------------------------------------------------------------------------+ + + Time to get kmesh 0.125 (sec) + *============================================================================* + | MEMORY ESTIMATE | + | Maximum RAM allocated during each phase of the calculation | + *============================================================================* + | Disentanglement 1.83 Mb | + | Wannierise: 0.45 Mb | + | | + | N.B. by setting optimisation=0 memory usage will be reduced to: | + | Disentanglement 1.83 Mb | + | Wannierise: 0.40 Mb | + | However, this will result in more i/o and slow down the calculation | + | plot_wannier: 0.45 Mb | + *----------------------------------------------------------------------------* + + Starting a new Wannier90 calculation ... + + + Reading overlaps from lco.mmn : Created on 1May2022 at 12:42:29 + + Reading projections from lco.amn : Created on 1May2022 at 12:42:24 + + Time to read overlaps 0.102 (sec) + + *------------------------------- DISENTANGLE --------------------------------* + +----------------------------------------------------------------------------+ + | Energy Windows | + | --------------- | + | Outer: 10.00000 to 16.00000 (eV) | + | Inner: 12.30000 to 16.00000 (eV) | + +----------------------------------------------------------------------------+ + | K-points with Frozen States | + | --------------------------- | + | 3 4 5 6 9 10 11 12 13 16 17 18 | + | 19 22 23 24 25 26 27 28 29 30 31 32 | + | 33 34 35 39 40 41 42 45 46 47 48 49 | + | 51 52 53 54 55 58 59 60 61 64 65 66 | + | 67 68 71 72 73 74 75 77 78 79 80 81 | + | 82 83 84 85 86 87 88 89 90 91 94 95 | + | 96 97 100 101 102 103 106 107 108 109 110 113 | + | 114 115 116 120 121 122 123 126 127 128 129 130 | + | 132 133 134 135 136 137 138 139 140 141 142 143 | + | 144 145 146 147 148 149 150 151 152 153 154 155 | + | 156 157 158 159 161 162 163 164 165 168 169 170 | + | 171 175 176 177 178 181 182 183 184 185 187 188 | + | 189 190 191 192 193 194 195 196 197 198 199 200 | + | 201 202 203 204 205 206 207 208 209 210 211 212 | + | 213 214 216 217 218 219 220 223 224 225 226 230 | + | 231 232 233 236 237 238 239 240 242 243 244 245 | + | 249 250 251 252 253 254 255 256 257 258 259 260 | + | 261 262 263 264 265 266 267 268 269 271 272 273 | + | 274 275 278 279 280 281 285 286 287 288 291 292 | + | 293 294 297 298 299 300 301 304 305 306 307 309 | + | 310 311 312 313 314 315 316 317 318 319 320 321 | + | 322 323 324 326 327 328 329 330 333 334 335 336 | + | 340 341 342 343 | + +----------------------------------------------------------------------------+ + Number of target bands to extract: 1 + +----------------------------------------------------------------------------+ + | Windows | + | ------- | + | K-point Ndimwin Ndimfroz Nfirstwin | + | ---------------------------------------------- | + | 1 5 0 1 | + | 2 5 0 1 | + | 3 5 1 1 | + | 4 5 1 1 | + | 5 5 1 1 | + | 6 5 1 1 | + | 7 5 0 1 | + | 8 5 0 1 | + | 9 5 1 1 | + | 10 5 1 1 | + | 11 5 1 1 | + | 12 5 1 1 | + | 13 5 1 1 | + | 14 5 0 1 | + | 15 5 0 1 | + | 16 5 1 1 | + | 17 5 1 1 | + | 18 5 1 1 | + | 19 5 1 1 | + | 20 5 0 1 | + | 21 5 0 1 | + | 22 5 1 1 | + | 23 5 1 1 | + | 24 5 1 1 | + | 25 5 1 1 | + | 26 5 1 1 | + | 27 5 1 1 | + | 28 5 1 1 | + | 29 5 1 1 | + | 30 5 1 1 | + | 31 5 1 1 | + | 32 5 1 1 | + | 33 5 1 1 | + | 34 5 1 1 | + | 35 5 1 1 | + | 36 5 0 1 | + | 37 5 0 1 | + | 38 5 0 1 | + | 39 5 1 1 | + | 40 5 1 1 | + | 41 5 1 1 | + | 42 5 1 1 | + | 43 5 0 1 | + | 44 5 0 1 | + | 45 5 1 1 | + | 46 5 1 1 | + | 47 5 1 1 | + | 48 5 1 1 | + | 49 5 1 1 | + | 50 5 0 1 | + | 51 5 1 1 | + | 52 5 1 1 | + | 53 5 1 1 | + | 54 5 1 1 | + | 55 5 1 1 | + | 56 5 0 1 | + | 57 5 0 1 | + | 58 5 1 1 | + | 59 5 1 1 | + | 60 5 1 1 | + | 61 5 1 1 | + | 62 5 0 1 | + | 63 5 0 1 | + | 64 5 1 1 | + | 65 5 1 1 | + | 66 5 1 1 | + | 67 5 1 1 | + | 68 5 1 1 | + | 69 5 0 1 | + | 70 5 0 1 | + | 71 5 1 1 | + | 72 5 1 1 | + | 73 5 1 1 | + | 74 5 1 1 | + | 75 5 1 1 | + | 76 5 0 1 | + | 77 5 1 1 | + | 78 5 1 1 | + | 79 5 1 1 | + | 80 5 1 1 | + | 81 5 1 1 | + | 82 5 1 1 | + | 83 5 1 1 | + | 84 5 1 1 | + | 85 5 1 1 | + | 86 5 1 1 | + | 87 5 1 1 | + | 88 5 1 1 | + | 89 5 1 1 | + | 90 5 1 1 | + | 91 5 1 1 | + | 92 5 0 1 | + | 93 5 0 1 | + | 94 5 1 1 | + | 95 5 1 1 | + | 96 5 1 1 | + | 97 5 1 1 | + | 98 5 0 1 | + | 99 5 0 1 | + | 100 5 1 1 | + | 101 5 1 1 | + | 102 5 1 1 | + | 103 5 1 1 | + | 104 5 0 1 | + | 105 5 0 1 | + | 106 5 1 1 | + | 107 5 1 1 | + | 108 5 1 1 | + | 109 5 1 1 | + | 110 5 1 1 | + | 111 5 0 1 | + | 112 5 0 1 | + | 113 5 1 1 | + | 114 5 1 1 | + | 115 5 1 1 | + | 116 5 1 1 | + | 117 5 0 1 | + | 118 5 0 1 | + | 119 5 0 1 | + | 120 5 1 1 | + | 121 5 1 1 | + | 122 5 1 1 | + | 123 5 1 1 | + | 124 5 0 1 | + | 125 5 0 1 | + | 126 5 1 1 | + | 127 5 1 1 | + | 128 5 1 1 | + | 129 5 1 1 | + | 130 5 1 1 | + | 131 5 0 1 | + | 132 5 1 1 | + | 133 5 1 1 | + | 134 5 1 1 | + | 135 5 1 1 | + | 136 5 1 1 | + | 137 5 1 1 | + | 138 5 1 1 | + | 139 5 1 1 | + | 140 5 1 1 | + | 141 5 1 1 | + | 142 5 1 1 | + | 143 5 1 1 | + | 144 5 1 1 | + | 145 5 1 1 | + | 146 5 1 1 | + | 147 5 1 1 | + | 148 5 1 1 | + | 149 5 1 1 | + | 150 5 1 1 | + | 151 5 1 1 | + | 152 5 1 1 | + | 153 5 1 1 | + | 154 5 1 1 | + | 155 5 1 1 | + | 156 5 1 1 | + | 157 5 1 1 | + | 158 5 1 1 | + | 159 5 1 1 | + | 160 5 0 1 | + | 161 5 1 1 | + | 162 5 1 1 | + | 163 5 1 1 | + | 164 5 1 1 | + | 165 5 1 1 | + | 166 5 0 1 | + | 167 5 0 1 | + | 168 5 1 1 | + | 169 5 1 1 | + | 170 5 1 1 | + | 171 5 1 1 | + | 172 5 0 1 | + | 173 5 0 1 | + | 174 5 0 1 | + | 175 5 1 1 | + | 176 5 1 1 | + | 177 5 1 1 | + | 178 5 1 1 | + | 179 5 0 1 | + | 180 5 0 1 | + | 181 5 1 1 | + | 182 5 1 1 | + | 183 5 1 1 | + | 184 5 1 1 | + | 185 5 1 1 | + | 186 5 0 1 | + | 187 5 1 1 | + | 188 5 1 1 | + | 189 5 1 1 | + | 190 5 1 1 | + | 191 5 1 1 | + | 192 5 1 1 | + | 193 5 1 1 | + | 194 5 1 1 | + | 195 5 1 1 | + | 196 5 1 1 | + | 197 5 1 1 | + | 198 5 1 1 | + | 199 5 1 1 | + | 200 5 1 1 | + | 201 5 1 1 | + | 202 5 1 1 | + | 203 5 1 1 | + | 204 5 1 1 | + | 205 5 1 1 | + | 206 5 1 1 | + | 207 5 1 1 | + | 208 5 1 1 | + | 209 5 1 1 | + | 210 5 1 1 | + | 211 5 1 1 | + | 212 5 1 1 | + | 213 5 1 1 | + | 214 5 1 1 | + | 215 5 0 1 | + | 216 5 1 1 | + | 217 5 1 1 | + | 218 5 1 1 | + | 219 5 1 1 | + | 220 5 1 1 | + | 221 5 0 1 | + | 222 5 0 1 | + | 223 5 1 1 | + | 224 5 1 1 | + | 225 5 1 1 | + | 226 5 1 1 | + | 227 5 0 1 | + | 228 5 0 1 | + | 229 5 0 1 | + | 230 5 1 1 | + | 231 5 1 1 | + | 232 5 1 1 | + | 233 5 1 1 | + | 234 5 0 1 | + | 235 5 0 1 | + | 236 5 1 1 | + | 237 5 1 1 | + | 238 5 1 1 | + | 239 5 1 1 | + | 240 5 1 1 | + | 241 5 0 1 | + | 242 5 1 1 | + | 243 5 1 1 | + | 244 5 1 1 | + | 245 5 1 1 | + | 246 5 0 1 | + | 247 5 0 1 | + | 248 5 0 1 | + | 249 5 1 1 | + | 250 5 1 1 | + | 251 5 1 1 | + | 252 5 1 1 | + | 253 5 1 1 | + | 254 5 1 1 | + | 255 5 1 1 | + | 256 5 1 1 | + | 257 5 1 1 | + | 258 5 1 1 | + | 259 5 1 1 | + | 260 5 1 1 | + | 261 5 1 1 | + | 262 5 1 1 | + | 263 5 1 1 | + | 264 5 1 1 | + | 265 5 1 1 | + | 266 5 1 1 | + | 267 5 1 1 | + | 268 5 1 1 | + | 269 5 1 1 | + | 270 5 0 1 | + | 271 5 1 1 | + | 272 5 1 1 | + | 273 5 1 1 | + | 274 5 1 1 | + | 275 5 1 1 | + | 276 5 0 1 | + | 277 5 0 1 | + | 278 5 1 1 | + | 279 5 1 1 | + | 280 5 1 1 | + | 281 5 1 1 | + | 282 5 0 1 | + | 283 5 0 1 | + | 284 5 0 1 | + | 285 5 1 1 | + | 286 5 1 1 | + | 287 5 1 1 | + | 288 5 1 1 | + | 289 5 0 1 | + | 290 5 0 1 | + | 291 5 1 1 | + | 292 5 1 1 | + | 293 5 1 1 | + | 294 5 1 1 | + | 295 5 0 1 | + | 296 5 0 1 | + | 297 5 1 1 | + | 298 5 1 1 | + | 299 5 1 1 | + | 300 5 1 1 | + | 301 5 1 1 | + | 302 5 0 1 | + | 303 5 0 1 | + | 304 5 1 1 | + | 305 5 1 1 | + | 306 5 1 1 | + | 307 5 1 1 | + | 308 5 0 1 | + | 309 5 1 1 | + | 310 5 1 1 | + | 311 5 1 1 | + | 312 5 1 1 | + | 313 5 1 1 | + | 314 5 1 1 | + | 315 5 1 1 | + | 316 5 1 1 | + | 317 5 1 1 | + | 318 5 1 1 | + | 319 5 1 1 | + | 320 5 1 1 | + | 321 5 1 1 | + | 322 5 1 1 | + | 323 5 1 1 | + | 324 5 1 1 | + | 325 5 0 1 | + | 326 5 1 1 | + | 327 5 1 1 | + | 328 5 1 1 | + | 329 5 1 1 | + | 330 5 1 1 | + | 331 5 0 1 | + | 332 5 0 1 | + | 333 5 1 1 | + | 334 5 1 1 | + | 335 5 1 1 | + | 336 5 1 1 | + | 337 5 0 1 | + | 338 5 0 1 | + | 339 5 0 1 | + | 340 5 1 1 | + | 341 5 1 1 | + | 342 5 1 1 | + | 343 5 1 1 | + +----------------------------------------------------------------------------+ + + Unitarised projection of Wannier functions + ------------------------------------------ + A_mn = --> S = A.A^+ --> U = S^-1/2.A + In dis_project... done + Using an inner window (linner = T) + In dis_proj_froz... done + + Extraction of optimally-connected subspace + ------------------------------------------ + +---------------------------------------------------------------------+<-- DIS + | Iter Omega_I(i-1) Omega_I(i) Delta (frac.) Time |<-- DIS + +---------------------------------------------------------------------+<-- DIS + 1 5.89559078 5.44227136 8.330E-02 0.00 <-- DIS + 2 5.45984098 5.33858007 2.271E-02 0.01 <-- DIS + 3 5.37242352 5.28492535 1.656E-02 0.01 <-- DIS + 4 5.31028874 5.25296985 1.091E-02 0.01 <-- DIS + 5 5.26905304 5.23313613 6.863E-03 0.02 <-- DIS + 6 5.24235247 5.22055535 4.175E-03 0.02 <-- DIS + 7 5.22522493 5.21245466 2.450E-03 0.02 <-- DIS + 8 5.21429150 5.20718138 1.365E-03 0.02 <-- DIS + 9 5.20734333 5.20372089 6.961E-04 0.03 <-- DIS + 10 5.20295484 5.20143641 2.919E-04 0.03 <-- DIS + 11 5.20020881 5.19992154 5.525E-05 0.03 <-- DIS + 12 5.19851492 5.19891364 -7.669E-05 0.03 <-- DIS + 13 5.19749270 5.19824136 -1.440E-04 0.03 <-- DIS + 14 5.19689673 5.19779208 -1.723E-04 0.03 <-- DIS + 15 5.19656869 5.19749138 -1.775E-04 0.04 <-- DIS + 16 5.19640664 5.19728989 -1.699E-04 0.04 <-- DIS + 17 5.19634516 5.19715477 -1.558E-04 0.04 <-- DIS + 18 5.19634254 5.19706408 -1.388E-04 0.04 <-- DIS + 19 5.19637247 5.19700319 -1.214E-04 0.04 <-- DIS + 20 5.19641859 5.19696228 -1.046E-04 0.04 <-- DIS + 21 5.19647092 5.19693479 -8.926E-05 0.04 <-- DIS + 22 5.19652364 5.19691631 -7.556E-05 0.05 <-- DIS + 23 5.19657349 5.19690388 -6.358E-05 0.05 <-- DIS + 24 5.19661885 5.19689553 -5.324E-05 0.05 <-- DIS + 25 5.19665907 5.19688991 -4.442E-05 0.05 <-- DIS + 26 5.19669412 5.19688613 -3.695E-05 0.05 <-- DIS + 27 5.19672425 5.19688358 -3.066E-05 0.06 <-- DIS + 28 5.19674992 5.19688187 -2.539E-05 0.06 <-- DIS + 29 5.19677161 5.19688072 -2.100E-05 0.06 <-- DIS + 30 5.19678984 5.19687995 -1.734E-05 0.06 <-- DIS + 31 5.19680509 5.19687942 -1.430E-05 0.06 <-- DIS + 32 5.19681781 5.19687907 -1.179E-05 0.06 <-- DIS + 33 5.19682838 5.19687884 -9.709E-06 0.07 <-- DIS + 34 5.19683715 5.19687868 -7.992E-06 0.07 <-- DIS + 35 5.19684440 5.19687857 -6.575E-06 0.07 <-- DIS + 36 5.19685040 5.19687850 -5.407E-06 0.07 <-- DIS + 37 5.19685535 5.19687845 -4.445E-06 0.07 <-- DIS + 38 5.19685943 5.19687842 -3.653E-06 0.07 <-- DIS + 39 5.19686280 5.19687840 -3.002E-06 0.07 <-- DIS + 40 5.19686557 5.19687838 -2.466E-06 0.08 <-- DIS + 41 5.19686785 5.19687837 -2.025E-06 0.08 <-- DIS + 42 5.19686972 5.19687837 -1.663E-06 0.08 <-- DIS + 43 5.19687126 5.19687836 -1.366E-06 0.08 <-- DIS + 44 5.19687253 5.19687836 -1.121E-06 0.08 <-- DIS + 45 5.19687357 5.19687836 -9.207E-07 0.08 <-- DIS + 46 5.19687443 5.19687835 -7.558E-07 0.09 <-- DIS + 47 5.19687513 5.19687835 -6.204E-07 0.09 <-- DIS + 48 5.19687571 5.19687835 -5.092E-07 0.09 <-- DIS + 49 5.19687618 5.19687835 -4.179E-07 0.09 <-- DIS + 50 5.19687657 5.19687835 -3.430E-07 0.09 <-- DIS + 51 5.19687689 5.19687835 -2.815E-07 0.09 <-- DIS + 52 5.19687715 5.19687835 -2.310E-07 0.10 <-- DIS + 53 5.19687737 5.19687835 -1.896E-07 0.10 <-- DIS + 54 5.19687754 5.19687835 -1.556E-07 0.10 <-- DIS + 55 5.19687769 5.19687835 -1.277E-07 0.10 <-- DIS + 56 5.19687781 5.19687835 -1.048E-07 0.10 <-- DIS + 57 5.19687791 5.19687835 -8.597E-08 0.10 <-- DIS + 58 5.19687799 5.19687835 -7.054E-08 0.10 <-- DIS + 59 5.19687805 5.19687835 -5.788E-08 0.11 <-- DIS + 60 5.19687810 5.19687835 -4.750E-08 0.11 <-- DIS + 61 5.19687815 5.19687835 -3.897E-08 0.11 <-- DIS + 62 5.19687819 5.19687835 -3.198E-08 0.11 <-- DIS + 63 5.19687822 5.19687835 -2.624E-08 0.11 <-- DIS + 64 5.19687824 5.19687835 -2.153E-08 0.11 <-- DIS + 65 5.19687826 5.19687835 -1.766E-08 0.12 <-- DIS + 66 5.19687828 5.19687835 -1.449E-08 0.12 <-- DIS + 67 5.19687829 5.19687835 -1.189E-08 0.12 <-- DIS + 68 5.19687830 5.19687835 -9.757E-09 0.12 <-- DIS + 69 5.19687831 5.19687835 -8.006E-09 0.12 <-- DIS + 70 5.19687832 5.19687835 -6.569E-09 0.12 <-- DIS + 71 5.19687832 5.19687835 -5.389E-09 0.13 <-- DIS + 72 5.19687833 5.19687835 -4.422E-09 0.13 <-- DIS + 73 5.19687833 5.19687835 -3.628E-09 0.13 <-- DIS + 74 5.19687834 5.19687835 -2.977E-09 0.13 <-- DIS + 75 5.19687834 5.19687835 -2.442E-09 0.13 <-- DIS + 76 5.19687834 5.19687835 -2.004E-09 0.13 <-- DIS + 77 5.19687834 5.19687835 -1.644E-09 0.14 <-- DIS + 78 5.19687834 5.19687835 -1.349E-09 0.14 <-- DIS + 79 5.19687835 5.19687835 -1.107E-09 0.14 <-- DIS + 80 5.19687835 5.19687835 -9.080E-10 0.14 <-- DIS + 81 5.19687835 5.19687835 -7.450E-10 0.14 <-- DIS + 82 5.19687835 5.19687835 -6.112E-10 0.14 <-- DIS + 83 5.19687835 5.19687835 -5.015E-10 0.14 <-- DIS + 84 5.19687835 5.19687835 -4.114E-10 0.15 <-- DIS + 85 5.19687835 5.19687835 -3.376E-10 0.15 <-- DIS + 86 5.19687835 5.19687835 -2.769E-10 0.15 <-- DIS + 87 5.19687835 5.19687835 -2.272E-10 0.15 <-- DIS + 88 5.19687835 5.19687835 -1.864E-10 0.15 <-- DIS + 89 5.19687835 5.19687835 -1.530E-10 0.15 <-- DIS + 90 5.19687835 5.19687835 -1.255E-10 0.16 <-- DIS + 91 5.19687835 5.19687835 -1.030E-10 0.16 <-- DIS + 92 5.19687835 5.19687835 -8.447E-11 0.16 <-- DIS + 93 5.19687835 5.19687835 -6.930E-11 0.16 <-- DIS + 94 5.19687835 5.19687835 -5.686E-11 0.16 <-- DIS + 95 5.19687835 5.19687835 -4.665E-11 0.16 <-- DIS + 96 5.19687835 5.19687835 -3.827E-11 0.17 <-- DIS + 97 5.19687835 5.19687835 -3.140E-11 0.17 <-- DIS + 98 5.19687835 5.19687835 -2.576E-11 0.17 <-- DIS + 99 5.19687835 5.19687835 -2.114E-11 0.17 <-- DIS + 100 5.19687835 5.19687835 -1.734E-11 0.17 <-- DIS + 101 5.19687835 5.19687835 -1.423E-11 0.17 <-- DIS + 102 5.19687835 5.19687835 -1.167E-11 0.18 <-- DIS + 103 5.19687835 5.19687835 -9.577E-12 0.18 <-- DIS + 104 5.19687835 5.19687835 -7.858E-12 0.18 <-- DIS + 105 5.19687835 5.19687835 -6.447E-12 0.18 <-- DIS + 106 5.19687835 5.19687835 -5.289E-12 0.18 <-- DIS + 107 5.19687835 5.19687835 -4.340E-12 0.18 <-- DIS + 108 5.19687835 5.19687835 -3.561E-12 0.19 <-- DIS + 109 5.19687835 5.19687835 -2.921E-12 0.19 <-- DIS + 110 5.19687835 5.19687835 -2.396E-12 0.19 <-- DIS + 111 5.19687835 5.19687835 -1.967E-12 0.19 <-- DIS + 112 5.19687835 5.19687835 -1.614E-12 0.19 <-- DIS + 113 5.19687835 5.19687835 -1.323E-12 0.19 <-- DIS + 114 5.19687835 5.19687835 -1.086E-12 0.20 <-- DIS + 115 5.19687835 5.19687835 -8.906E-13 0.20 <-- DIS + 116 5.19687835 5.19687835 -7.319E-13 0.20 <-- DIS + 117 5.19687835 5.19687835 -6.002E-13 0.20 <-- DIS + + <<< Delta < 1.000E-12 over 3 iterations >>> + <<< Disentanglement convergence criteria satisfied >>> + + Final Omega_I 5.19687835 (Ang^2) + + +----------------------------------------------------------------------------+ + + Time to disentangle bands 0.211 (sec) + + Writing checkpoint file lco.chk... done + + + *------------------------------- WANNIERISE ---------------------------------* + +--------------------------------------------------------------------+<-- CONV + | Iter Delta Spread RMS Gradient Spread (Ang^2) Time |<-- CONV + +--------------------------------------------------------------------+<-- CONV + + ------------------------------------------------------------------------------ + Initial State + WF centre and spread 1 ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + Sum of centres and spreads ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + + 0 0.520E+01 0.0000000000 5.1968783518 0.21 <-- CONV + O_D= 0.0000000 O_OD= 0.0000000 O_TOT= 5.1968784 <-- SPRD + ------------------------------------------------------------------------------ + Cycle: 1 + WF centre and spread 1 ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + Sum of centres and spreads ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + + 1 0.000E+00 0.0000000019 5.1968783518 0.21 <-- CONV + O_D= 0.0000000 O_OD= 0.0000000 O_TOT= 5.1968784 <-- SPRD + Delta: O_D= -0.2191079E-19 O_OD= 0.0000000E+00 O_TOT= 0.0000000E+00 <-- DLTA + ------------------------------------------------------------------------------ + Cycle: 2 + WF centre and spread 1 ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + Sum of centres and spreads ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + + 2 0.000E+00 0.0000000019 5.1968783518 0.21 <-- CONV + O_D= 0.0000000 O_OD= 0.0000000 O_TOT= 5.1968784 <-- SPRD + Delta: O_D= -0.2159428E-19 O_OD= 0.0000000E+00 O_TOT= 0.0000000E+00 <-- DLTA + ------------------------------------------------------------------------------ + Cycle: 3 + WF centre and spread 1 ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + Sum of centres and spreads ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + + 3 0.000E+00 0.0000000019 5.1968783518 0.21 <-- CONV + O_D= 0.0000000 O_OD= 0.0000000 O_TOT= 5.1968784 <-- SPRD + Delta: O_D= -0.2128269E-19 O_OD= 0.0000000E+00 O_TOT= 0.0000000E+00 <-- DLTA + ------------------------------------------------------------------------------ + Cycle: 4 + WF centre and spread 1 ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + Sum of centres and spreads ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + + 4 0.000E+00 0.0000000018 5.1968783518 0.22 <-- CONV + O_D= 0.0000000 O_OD= 0.0000000 O_TOT= 5.1968784 <-- SPRD + Delta: O_D= -0.2097595E-19 O_OD= 0.0000000E+00 O_TOT= 0.0000000E+00 <-- DLTA + ------------------------------------------------------------------------------ + Cycle: 5 + WF centre and spread 1 ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + Sum of centres and spreads ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + + 5 0.000E+00 0.0000000018 5.1968783518 0.22 <-- CONV + O_D= 0.0000000 O_OD= 0.0000000 O_TOT= 5.1968784 <-- SPRD + Delta: O_D= -0.2067398E-19 O_OD= 0.0000000E+00 O_TOT= 0.0000000E+00 <-- DLTA + ------------------------------------------------------------------------------ + + <<< Delta < 1.000E-12 over 5 iterations >>> + <<< Wannierisation convergence criteria satisfied >>> + + Final State + WF centre and spread 1 ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + Sum of centres and spreads ( -0.000000, -0.000000, 0.000000 ) 5.19687835 + + Spreads (Ang^2) Omega I = 5.196878352 + ================ Omega D = 0.000000000 + Omega OD = 0.000000000 + Final Spread (Ang^2) Omega Total = 5.196878352 + ------------------------------------------------------------------------------ + Time for wannierise 0.009 (sec) + + Writing checkpoint file lco.chk... done + + *---------------------------------------------------------------------------* + | PLOTTING | + *---------------------------------------------------------------------------* + + + Calculating interpolated band-structure + + Time to calculate interpolated band structure 0.018 (sec) + + Time for plotting 0.090 (sec) + Total Execution Time 0.599 (sec) + + *===========================================================================* + | TIMING INFORMATION | + *===========================================================================* + | Tag Ncalls Time (s)| + |---------------------------------------------------------------------------| + |kmesh: get : 1 0.125| + |overlap: allocate : 1 0.000| + |overlap: read : 1 0.102| + |dis: main : 1 0.211| + |wann: main : 1 0.009| + |plot: main : 1 0.090| + *---------------------------------------------------------------------------* + + All done: wannier90 exiting diff --git a/tests/data/lco_mlwf/lco_band.dat b/tests/data/lco_mlwf/lco_band.dat new 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1 1 0.000090 -0.000000 diff --git a/tests/data/lk99_liangsi_1/k000.win b/tests/data/lk99_liangsi_1/k000.win new file mode 100644 index 0000000..dfd5287 --- /dev/null +++ b/tests/data/lk99_liangsi_1/k000.win @@ -0,0 +1,507 @@ + num_bands = 2 + num_wann = 2 + +!!! Disentanglement parameters !!! + dis_froz_min = -0.1 + dis_froz_max = 0.1 + dis_mix_ratio = 0.5 + +!!! Iterations &c. !!! + iprint = 1 + num_iter = 10000 + num_print_cycles = 100 + conv_window = 3 +!conv_tol = 1e-10 + dis_num_iter = 10000 +!dis_conv_window = 3 +!dis_conv_tol = 1e-10 +!restart = default ! wannierise ! plot ! transport + +!!! Post-processing options !!! + write_proj = .true. + write_xyz = .true. + translate_home_cell = .true. + hr_plot = .true. + fermi_surface_plot = .true. +!dos = .false. +!dos_project = +!dos_kmesh = 50 50 1 +!dos_energy_min = -1.8 +!dos_energy_max = +1.5 + +!!! Band structure !!! +!!! needs `kpoint_path' block +!bands_plot = .true. + bands_num_points = 300 +!bands_plot_format = gnuplot xmgrace + bands_plot_project = 1 +!bands_plot_mode = s-k | cut [Slater-Koster | truncate Hamiltonian] + + +begin unit_cell_cart +Bohr + 15.809981 -9.127897 0.000000 + 0.000000 18.255794 0.000000 + 0.000000 0.000000 13.655482 +end unit_cell_cart + +begin atoms_cart +Bohr + 1 0.00000000 0.00000000 0.00000000 + 2 14.16532166 2.17390004 3.34034938 + 3 6.84466788 2.05268139 3.34034938 + 4 10.60997320 -4.22658143 3.34034938 + 5 0.00000000 0.00000000 6.70581120 + 6 5.26999374 9.12789709 6.63786152 + 7 14.46626465 -2.18121130 10.18626583 + 8 10.46583344 4.49086134 10.18626583 + 9 6.68786464 -2.30965003 10.18626583 + 10 5.26999374 9.12789709 13.45649432 + 11 1.20126341 6.00411167 3.06588785 + 12 10.00963643 7.16616580 3.06588785 + 13 4.59908153 14.21341353 3.06588785 + 14 0.75795153 12.80413935 10.29799499 + 15 4.34229565 3.38223261 10.29799499 + 16 10.70973419 11.19731904 10.29799499 + 17 15.20122325 -1.85833020 1.12119701 + 18 9.81873091 4.96591361 1.12119701 + 19 6.60000858 -3.10758341 1.12119701 + 20 3.98933782 6.28814444 2.21702212 + 21 8.36961963 9.43869267 2.21702212 + 22 3.45102392 11.65685389 2.21702212 + 23 12.81870649 7.99226804 3.35177902 + 24 2.47912097 16.23308845 3.35177902 + 25 0.51215391 3.15833451 3.35177902 + 26 0.78089182 7.37275767 5.64348298 + 27 9.03454002 6.11779032 5.64348298 + 28 5.99454953 13.89314301 5.64348298 + 29 15.02416727 3.89997624 7.81613844 + 30 4.92041924 1.93342541 7.81613844 + 31 11.67537623 -5.83340165 7.81613844 + 32 5.70503699 5.97934768 10.43734918 + 33 7.77919588 11.07893013 10.43734918 + 34 2.32574849 10.32541319 10.43734918 + 35 2.51956290 15.17969280 10.46136917 + 36 1.40420033 3.72005608 10.46136917 + 37 11.88621814 8.48394212 10.46136917 + 38 14.60705254 3.86126482 12.47101915 + 39 5.16250167 1.59154916 12.47101915 + 40 11.85040853 -5.45281398 12.47101915 + 41 10.53998747 0.00000018 4.08283891 +end atoms_cart + +!!! BZ-Path for band structure !!! +bands_plot = T +begin kpoint_path + G 0.00000 0.00000 0.00000 M 0.50000 -0.50000 0.00000 + M 0.50000 -0.50000 0.00000 K 0.66667 -0.33333 0.00000 + K 0.66667 -0.33333 0.00000 G 0.00000 0.00000 0.00000 + G 0.00000 0.00000 0.00000 A 0.00000 0.00000 0.50000 + A 0.00000 0.00000 0.50000 L 0.50000 -0.50000 0.50000 + L 0.50000 -0.50000 0.50000 H 0.66667 -0.33333 0.50000 + H 0.66667 -0.33333 0.50000 A 0.00000 0.00000 0.50000 +end kpoint_path + +!!!! Dummy `projections' block for guiding centres !!! +guiding_centres = T +begin projections + 10:s + 10:s +end projections + +!!! 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0.857142857142857 0.857142857142857 0.500000000000000 + 0.857142857142857 0.857142857142857 0.625000000000000 + 0.857142857142857 0.857142857142857 0.750000000000000 + 0.857142857142857 0.857142857142857 0.875000000000000 +end kpoints diff --git a/tests/data/lk99_liangsi_1/k000.wout b/tests/data/lk99_liangsi_1/k000.wout new file mode 100644 index 0000000..e189653 --- /dev/null +++ b/tests/data/lk99_liangsi_1/k000.wout @@ -0,0 +1,349 @@ + + +---------------------------------------------------+ + | | + | WANNIER90 | + | | + +---------------------------------------------------+ + | | + | Welcome to the Maximally-Localized | + | Generalized Wannier Functions code | + | http://www.wannier.org | + | | + | Wannier90 v2.0 Authors: | + | Arash A. Mostofi (Imperial College London) | + | Giovanni Pizzi (EPFL) | + | Ivo Souza (Universidad del Pais Vasco) | + | Jonathan R. Yates (University of Oxford) | + | | + | Wannier90 Contributors: | + | Young-Su Lee (KIST, S. Korea) | + | Matthew Shelley (Imperial College London) | + | Nicolas Poilvert (Penn State University) | + | Raffaello Bianco (Paris 6 and CNRS) | + | Gabriele Sclauzero (ETH Zurich) | + | | + | Wannier77 Authors: | + | Nicola Marzari (EPFL) | + | Ivo Souza (Universidad del Pais Vasco) | + | David Vanderbilt (Rutgers University) | + | | + | Please cite | + | | + | [ref] "Wannier90: A Tool for Obtaining Maximally | + | Localised Wannier Functions" | + | A. A. Mostofi, J. R. Yates, Y.-S. Lee, | + | I. Souza, D. Vanderbilt and N. Marzari | + | Comput. Phys. Commun. 178, 685 (2008) | + | | + | in any publications arising from the use of | + | this code. For the method please cite | + | | + | [ref] "Maximally Localized Generalised Wannier | + | Functions for Composite Energy Bands" | + | N. Marzari and D. Vanderbilt | + | Phys. Rev. B 56 12847 (1997) | + | | + | [ref] "Maximally Localized Wannier Functions | + | for Entangled Energy Bands" | + | I. Souza, N. Marzari and D. Vanderbilt | + | Phys. Rev. B 65 035109 (2001) | + | | + | | + | Copyright (c) 1996-2015 | + | Arash A. Mostofi, Jonathan R. Yates, | + | Young-Su Lee, Giovanni Pizzi, Ivo Souza, | + | David Vanderbilt and Nicola Marzari | + | | + | Release: 2.0.1 2nd April 2015 | + | | + | This program is free software; you can | + | redistribute it and/or modify it under the terms | + | of the GNU General Public License as published by | + | the Free Software Foundation; either version 2 of | + | the License, or (at your option) any later version| + | | + | This program is distributed in the hope that it | + | will be useful, but WITHOUT ANY WARRANTY; without | + | even the implied warranty of MERCHANTABILITY or | + | FITNESS FOR A PARTICULAR PURPOSE. See the GNU | + | General Public License for more details. | + | | + | You should have received a copy of the GNU General| + | Public License along with this program; if not, | + | write to the Free Software Foundation, Inc., | + | 675 Mass Ave, Cambridge, MA 02139, USA. | + | | + +---------------------------------------------------+ + | Execution started on 7Aug2023 at 06:31:05 | + +---------------------------------------------------+ + + ****************************************************************************** + * -> Using CODATA 2006 constant values * + * (http://physics.nist.gov/cuu/Constants/index.html) * + * -> Using Bohr value from CODATA * + ****************************************************************************** + + + ------ + SYSTEM + ------ + + Lattice Vectors (Ang) + a_1 8.366282 -4.830275 0.000000 + a_2 0.000000 9.660550 0.000000 + a_3 0.000000 0.000000 7.226170 + + Unit Cell Volume: 584.03988 (Ang^3) + + Reciprocal-Space Vectors (Ang^-1) + b_1 0.751013 0.000000 0.000000 + b_2 0.375506 0.650396 -0.000000 + b_3 -0.000000 0.000000 0.869504 + + *----------------------------------------------------------------------------* + | Site Fractional Coordinate Cartesian Coordinate (Ang) | + +----------------------------------------------------------------------------+ + | 1 1 0.00000 0.00000 0.00000 | 0.00000 0.00000 0.00000 | + | 2 1 0.89597 0.56707 0.24462 | 7.49597 1.15038 1.76764 | + | 3 1 0.43293 0.32891 0.24462 | 3.62204 1.08623 1.76764 | + | 4 1 0.67109 0.10403 0.24462 | 5.61456 -2.23661 1.76764 | + | 5 1 0.00000 0.00000 0.49107 | 0.00000 0.00000 3.54856 | + | 6 1 0.33333 0.66667 0.48609 | 2.78876 4.83028 3.51261 | + | 7 1 0.91501 0.33802 0.74595 | 7.65522 -1.15425 5.39034 | + | 8 1 0.66198 0.57698 0.74595 | 5.53828 2.37646 5.39034 | + | 9 1 0.42302 0.08499 0.74595 | 3.53907 -1.22221 5.39034 | + | 1 1 0.33333 0.66667 0.98543 | 2.78876 4.83028 7.12087 | + | 1 1 0.07598 0.36688 0.22452 | 0.63568 3.17724 1.62240 | + | 1 1 0.63312 0.70910 0.22452 | 5.29687 3.79217 1.62240 | + | 1 1 0.29090 0.92402 0.22452 | 2.43373 7.52141 1.62240 | + | 1 1 0.04794 0.72534 0.75413 | 0.40109 6.77566 5.44946 | + | 1 1 0.27466 0.32260 0.75413 | 2.29784 1.78980 5.44946 | + | 1 1 0.67740 0.95206 0.75413 | 5.66735 5.92537 5.44946 | + | 1 1 0.96150 0.37895 0.08211 | 8.04414 -0.98339 0.59331 | + | 1 1 0.62105 0.58254 0.08211 | 5.19585 2.62785 0.59331 | + | 1 1 0.41746 0.03850 0.08211 | 3.49257 -1.64446 0.59331 | + | 2 1 0.25233 0.47061 0.16235 | 2.11107 3.32754 1.17320 | + | 2 1 0.52939 0.78172 0.16235 | 4.42901 4.99474 1.17320 | + | 2 1 0.21828 0.74767 0.16235 | 1.82620 6.16854 1.17320 | + | 2 1 0.81080 0.84319 0.24545 | 6.78337 4.22933 1.77369 | + | 2 1 0.15681 0.96761 0.24545 | 1.31189 8.59018 1.77369 | + | 2 1 0.03239 0.18920 0.24545 | 0.27102 1.67132 1.77369 | + | 2 1 0.04939 0.42855 0.41328 | 0.41323 3.90150 2.98640 | + | 2 1 0.57145 0.62084 0.41328 | 4.78087 3.23740 2.98640 | + | 2 1 0.37916 0.95061 0.41328 | 3.17218 7.35193 2.98640 | + | 2 1 0.95030 0.68878 0.57238 | 7.95045 2.06378 4.13612 | + | 3 1 0.31122 0.26152 0.57238 | 2.60377 1.02312 4.13612 | + | 3 1 0.73848 0.04970 0.57238 | 6.17834 -3.08690 4.13612 | + | 3 1 0.36085 0.50796 0.76433 | 3.01898 3.16413 5.52321 | + | 3 1 0.49204 0.85289 0.76433 | 4.11657 5.86272 5.52321 | + | 3 1 0.14711 0.63915 0.76433 | 1.23073 5.46397 5.52321 | + | 3 1 0.15937 0.91118 0.76609 | 1.33330 8.03275 5.53592 | + | 3 1 0.08882 0.24818 0.76609 | 0.74307 1.96857 5.53592 | + | 3 1 0.75182 0.84063 0.76609 | 6.28992 4.48951 5.53592 | + | 3 1 0.92391 0.67347 0.91326 | 7.72972 2.04329 6.59938 | + | 3 1 0.32653 0.25045 0.91326 | 2.73188 0.84221 6.59938 | + | 4 1 0.74955 0.07609 0.91326 | 6.27097 -2.88550 6.59938 | + | 4 1 0.66667 0.33333 0.29899 | 5.57752 0.00000 2.16055 | + *----------------------------------------------------------------------------* + + ------------ + K-POINT GRID + ------------ + + Grid size = 7 x 7 x 8 Total points = 392 + + + *---------------------------------- MAIN ------------------------------------* + | Number of Wannier Functions : 2 | + | Number of input Bloch states : 2 | + | Output verbosity (1=low, 5=high) : 1 | + | Timing Level (1=low, 5=high) : 1 | + | Optimisation (0=memory, 3=speed) : 3 | + | Length Unit : Ang | + | Post-processing setup (write *.nnkp) : F | + | Using Gamma-only branch of algorithms : F | + *----------------------------------------------------------------------------* + *------------------------------- WANNIERISE ---------------------------------* + | Total number of iterations : 10000 | + | Number of CG steps before reset : 5 | + | Trial step length for line search : 2.000 | + | Convergence tolerence : 0.100E-09 | + | Convergence window : 3 | + | Iterations between writing output : 100 | + | Iterations between backing up to disk : 100 | + | Write r^2_nm to file : F | + | Write xyz WF centres to file : T | + | Write on-site energies <0n|H|0n> to file : F | + | Use guiding centre to control phases : T | + | Use phases for initial projections : F | + | Iterations before starting guiding centres: 0 | + | Iterations between using guiding centres : 1 | + *----------------------------------------------------------------------------* + *-------------------------------- PLOTTING ----------------------------------* + | Plotting Fermi surface : T | + | Number of plotting points (along b_1) : 50 | + | Plotting format : xcrysden | + *----------------------------------------------------------------------------* + | Plotting interpolated bandstructure : T | + | Number of K-path sections : 7 | + | Divisions along first K-path section : 300 | + | Output format : gnuplot | + | Output mode : s-k | + *----------------------------------------------------------------------------* + | K-space path sections: | + | From: G 0.000 0.000 0.000 To: M 0.500 -0.500 0.000 | + | From: M 0.500 -0.500 0.000 To: K 0.667 -0.333 0.000 | + | From: K 0.667 -0.333 0.000 To: G 0.000 0.000 0.000 | + | From: G 0.000 0.000 0.000 To: A 0.000 0.000 0.500 | + | From: A 0.000 0.000 0.500 To: L 0.500 -0.500 0.500 | + | From: L 0.500 -0.500 0.500 To: H 0.667 -0.333 0.500 | + | From: H 0.667 -0.333 0.500 To: A 0.000 0.000 0.500 | + *----------------------------------------------------------------------------* + | Plotting Hamiltonian in WF basis : T | + *----------------------------------------------------------------------------* + Time to read parameters 0.028 (sec) + + *---------------------------------- K-MESH ----------------------------------* + +----------------------------------------------------------------------------+ + | Distance to Nearest-Neighbour Shells | + | ------------------------------------ | + | Shell Distance (Ang^-1) Multiplicity | + | ----- ----------------- ------------ | + | 1 0.107288 6 | + | 2 0.108688 2 | + | 3 0.152721 12 | + | 4 0.185827 6 | + | 5 0.214575 6 | + | 6 0.215279 12 | + | 7 0.217376 2 | + | 8 0.240532 12 | + | 9 0.242411 12 | + | 10 0.283856 12 | + | 11 0.285979 12 | + | 12 0.303953 24 | + +----------------------------------------------------------------------------+ + | The b-vectors are chosen automatically | + | The following shells are used: 1, 2 | + +----------------------------------------------------------------------------+ + | Shell # Nearest-Neighbours | + | ----- -------------------- | + | 1 6 | + | 2 2 | + +----------------------------------------------------------------------------+ + | Completeness relation is fully satisfied [Eq. (B1), PRB 56, 12847 (1997)] | + +----------------------------------------------------------------------------+ + | b_k Vectors (Ang^-1) and Weights (Ang^2) | + | ---------------------------------------- | + | No. b_k(x) b_k(y) b_k(z) w_b | + | --- -------------------------------- -------- | + | 1 0.053644 0.092914 0.000000 28.958766 | + | 2 0.107288 0.000000 0.000000 28.958766 | + | 3 -0.053644 -0.092914 0.000000 28.958766 | + | 4 0.053644 -0.092914 0.000000 28.958766 | + | 5 -0.107288 0.000000 0.000000 28.958766 | + | 6 -0.053644 0.092914 0.000000 28.958766 | + | 7 0.000000 0.000000 0.108688 42.325936 | + | 8 0.000000 0.000000 -0.108688 42.325936 | + +----------------------------------------------------------------------------+ + | b_k Directions (Ang^-1) | + | ----------------------- | + | No. x y z | + | --- -------------------------------- | + | 1 0.053644 0.092914 0.000000 | + | 2 0.107288 0.000000 0.000000 | + | 3 0.053644 -0.092914 0.000000 | + | 4 0.000000 0.000000 0.108688 | + +----------------------------------------------------------------------------+ + + *============================================================================* + | MEMORY ESTIMATE | + | Maximum RAM allocated during each phase of the calculation | + *============================================================================* + | Wannierise: 0.87 Mb | + *----------------------------------------------------------------------------* + + Starting a new Wannier90 calculation ... + + Time to get kmesh 0.652 (sec) + + Reading overlaps from k000.mmn : blebleble + + Reading projections from k000.amn : blebleble + + Time to read overlaps 0.040 (sec) + + Writing checkpoint file k000.chk... done + + + *------------------------------- WANNIERISE ---------------------------------* + +--------------------------------------------------------------------+<-- CONV + | Iter Delta Spread RMS Gradient Spread (Ang^2) Time |<-- CONV + +--------------------------------------------------------------------+<-- CONV + + ------------------------------------------------------------------------------ + Initial State + WF centre and spread 1 ( 3.176859, 5.086575, 7.516859 ) 8.48502060 + WF centre and spread 2 ( 2.401703, 4.574920, 7.516859 ) 8.48428253 + Sum of centres and spreads ( 5.578562, 9.661495, 15.033719 ) 16.96930313 + + 0 0.170E+02 0.0000000000 16.9693024092 0.72 <-- CONV + O_D= 0.3390287 O_OD= 0.6971141 O_TOT= 16.9693024 <-- SPRD + ------------------------------------------------------------------------------ + Cycle: 1 + WF centre and spread 1 ( 3.176724, 5.086712, 7.516907 ) 8.47078532 + WF centre and spread 2 ( 2.401848, 4.574778, 7.516894 ) 8.47204985 + Sum of centres and spreads ( 5.578572, 9.661490, 15.033801 ) 16.94283517 + + 1 -0.265E-01 0.2151304013 16.9428344482 0.73 <-- CONV + O_D= 0.3180817 O_OD= 0.6915932 O_TOT= 16.9428344 <-- SPRD + Delta: O_D= -0.2094698E-01 O_OD= -0.5520977E-02 O_TOT= -0.2646796E-01 <-- DLTA + ------------------------------------------------------------------------------ + + <<< Delta < 1.000E-10 over 3 iterations >>> + <<< Wannierisation convergence criteria satisfied >>> + + Final State + WF centre and spread 1 ( 3.176560, 5.087064, 7.516938 ) 8.46045406 + WF centre and spread 2 ( 2.401945, 4.574512, 7.516899 ) 8.46368813 + Sum of centres and spreads ( 5.578506, 9.661576, 15.033837 ) 16.92414219 + + Spreads (Ang^2) Omega I = 15.933159609 + ================ Omega D = 0.302788812 + Omega OD = 0.688193044 + Final Spread (Ang^2) Omega Total = 16.924141465 + ------------------------------------------------------------------------------ + + Wannier centres written to file k000_centres.xyz + Time for wannierise 0.217 (sec) + + Writing checkpoint file k000.chk... done + + *---------------------------------------------------------------------------* + | PLOTTING | + *---------------------------------------------------------------------------* + + + Calculating interpolated band-structure + + Time to calculate interpolated band structure 0.180 (sec) + + + Calculating Fermi surface + + Time to calculate interpolated Fermi surface 11.320 (sec) + + Time for plotting 11.541 (sec) + Total Execution Time 12.480 (sec) + + *===========================================================================* + | TIMING INFORMATION | + *===========================================================================* + | Tag Ncalls Time (s)| + |---------------------------------------------------------------------------| + |kmesh: get : 1 0.652| + |overlap: read : 1 0.040| + |wann: main : 1 0.217| + |plot: main : 1 11.541| + *---------------------------------------------------------------------------* + + All done: wannier90 exiting diff --git a/tests/data/lk99_liangsi_1/k000_band.dat b/tests/data/lk99_liangsi_1/k000_band.dat new file mode 100644 index 0000000..b5201c1 --- /dev/null +++ b/tests/data/lk99_liangsi_1/k000_band.dat @@ -0,0 +1,3974 @@ + 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0.000011 -0.000000 + 4 3 4 2 2 -0.000034 -0.000000 diff --git a/tests/old_testing.py b/tests/old_testing.py new file mode 100644 index 0000000..4db63f7 --- /dev/null +++ b/tests/old_testing.py @@ -0,0 +1,96 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +import pytest +import numpy as np + +from nomad.datamodel import EntryArchive +from nomad_parser_wannier90.parsers.parser import Wannier90Parser + + +def approx(value, abs=0, rel=1e-6): + return pytest.approx(value, abs=abs, rel=rel) + + +@pytest.fixture(scope='module') +def parser(): + return Wannier90Parser() + + +def test_lco(parser): + archive = EntryArchive() + parser.parse('tests/data/wannier90/lco_mlwf/lco.wout', archive, None) + + sec_run = archive.run[-1] + sec_program = sec_run.program + assert sec_program.name == 'Wannier90' + assert sec_program.version == '3.1.0' + + assert len(sec_run.system) == 1 + sec_system = sec_run.system[-1] + assert sec_system.atoms.labels[-1] == 'O' + assert (sec_system.atoms.positions[2].magnitude == np.array([0.0, 0.0, 0.0])).all() + assert sec_system.atoms.lattice_vectors[0][0].magnitude == approx(-1.909145e-10) + assert sec_system.atoms.periodic == [True, True, True] + assert sec_system.m_xpath('atoms_group') + assert len(sec_system.atoms_group) == 1 + assert sec_system.atoms_group[-1].label == 'projection' + assert sec_system.atoms_group[-1].type == 'active_orbitals' + assert sec_system.atoms_group[-1].index == 0 + assert sec_system.atoms_group[-1].atom_indices[0] == 2 + + assert len(sec_run.method) == 1 + sec_method = sec_run.method[-1] + assert sec_method.k_mesh.n_points == 343 + assert ( + sec_method.k_mesh.points[303] == np.array([0.85714, 0.14286, 0.28571]) + ).all() + assert (sec_method.k_mesh.grid == np.array([7, 7, 7])).all() + sec_wannier = sec_method.tb.wannier + assert sec_wannier.n_projected_orbitals == 1 + assert sec_wannier.n_bands == 5 + assert sec_wannier.is_maximally_localized is True + assert sec_method.atom_parameters[-1].n_orbitals == 1 + assert sec_method.atom_parameters[-1].orbitals[0] == 'dx2-y2' + + # Band tests + assert len(sec_run.calculation) == 1 + sec_scc = sec_run.calculation[-1] + assert len(sec_scc.band_structure_electronic[0].segment) == 4 + assert sec_scc.band_structure_electronic[0].segment[0].n_kpoints == 100 + assert sec_scc.band_structure_electronic[0].segment[0].n_kpoints == len( + sec_scc.band_structure_electronic[0].segment[0].energies[0] + ) + assert sec_scc.energy.fermi == sec_scc.band_structure_electronic[0].energy_fermi + assert sec_scc.band_structure_electronic[0].energy_fermi.to( + 'eV' + ).magnitude == approx(12.895622) + # DOS tests + sec_dos = sec_scc.dos_electronic + assert len(sec_dos) == 1 + assert sec_dos[0].n_energies == 692 + assert sec_dos[0].n_energies == len(sec_dos[0].energies) + assert len(sec_dos[0].total[0].value) == sec_dos[0].n_energies + # x_wannier90 tests + sec_hoppings = sec_scc.hopping_matrix[0] + assert sec_hoppings.n_wigner_seitz_points == 397 + assert sec_hoppings.n_wigner_seitz_points == len(sec_hoppings.degeneracy_factors) + assert sec_hoppings.n_orbitals == sec_wannier.n_projected_orbitals + assert sec_hoppings.value.shape[0] == sec_hoppings.n_wigner_seitz_points + assert sec_hoppings.value.shape[1] == sec_hoppings.n_orbitals + assert sec_hoppings.value.shape[2] == 7 diff --git a/tests/test_parser.py b/tests/test_parser.py new file mode 100644 index 0000000..b89a86b --- /dev/null +++ b/tests/test_parser.py @@ -0,0 +1,60 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +import pytest +import numpy as np +import os + +from nomad.datamodel import EntryArchive +from nomad_parser_wannier90.parsers.parser import Wannier90Parser + +from . import logger + + +def approx(value, abs=0, rel=1e-6): + return pytest.approx(value, abs=abs, rel=rel) + + +@pytest.fixture(scope='module') +def parser(): + return Wannier90Parser() + + +def test_single_point_La2CuO4(parser): + archive = EntryArchive() + parser.parse( + os.path.join(os.path.dirname(__file__), 'data/lco_mlwf/lco.wout'), + archive, + logger, + ) + simulation = archive.data + assert simulation.program.name == 'Wannier90' + assert simulation.program.version == '3.1.0' + + +def test_single_point_LK99(parser): + archive = EntryArchive() + assert True + # parser.parse( + # os.path.join(os.path.dirname(__file__), 'data/lk99_liangsi_1/k000.wout'), + # archive, + # logger, + # ) + # simulation = archive.data + # assert simulation.program.name == 'Wannier90' + # assert simulation.program.version == '2.0.1'