From 2fba54092fb3a1c054ebd05f139f3165e66203f7 Mon Sep 17 00:00:00 2001 From: Orest Dubay Date: Mon, 3 Aug 2020 08:53:11 +0200 Subject: [PATCH] Add nglview support (#8) * Refactored structure viewer into its own object * Add unit tests for structure viewer - structure and arrows --- poetry.lock | 1156 ++++++++++++++++++++++++-------- pyproject.toml | 7 +- src/py4vasp/data/__init__.py | 1 + src/py4vasp/data/projectors.py | 4 +- src/py4vasp/data/structure.py | 86 +++ src/py4vasp/raw/file.py | 14 + src/py4vasp/raw/rawdata.py | 6 + tests/data/test_structure.py | 75 +++ tests/raw/test_file.py | 29 + 9 files changed, 1106 insertions(+), 272 deletions(-) create mode 100644 src/py4vasp/data/structure.py create mode 100644 tests/data/test_structure.py diff --git a/poetry.lock b/poetry.lock index b82283d..0720d57 100644 --- a/poetry.lock +++ b/poetry.lock @@ -12,7 +12,7 @@ description = "A small Python module for determining appropriate platform-specif name = "appdirs" optional = false python-versions = "*" -version = "1.4.3" +version = "1.4.4" [[package]] category = "main" @@ -23,13 +23,63 @@ optional = false python-versions = "*" version = "0.1.0" +[[package]] +category = "main" +description = "The secure Argon2 password hashing algorithm." +name = "argon2-cffi" +optional = false +python-versions = "*" +version = "20.1.0" + +[package.dependencies] +cffi = ">=1.0.0" +six = "*" + +[package.extras] +dev = ["coverage (>=5.0.2)", "hypothesis", "pytest", "sphinx", "wheel", "pre-commit"] +docs = ["sphinx"] +tests = ["coverage (>=5.0.2)", "hypothesis", "pytest"] + +[[package]] +category = "main" +description = "Atomic Simulation Environment" +name = "ase" +optional = false +python-versions = "*" +version = "3.19.2" + +[package.dependencies] +matplotlib = "*" +numpy = "*" +scipy = "*" + +[package.extras] +docs = ["pillow", "sphinx", "sphinx-rtd-theme"] + +[[package]] +category = "dev" +description = "An abstract syntax tree for Python with inference support." +name = "astroid" +optional = false +python-versions = ">=3.5" +version = "2.4.2" + +[package.dependencies] +lazy-object-proxy = ">=1.4.0,<1.5.0" +six = ">=1.12,<2.0" +wrapt = ">=1.11,<2.0" + +[package.dependencies.typed-ast] +python = "<3.8" +version = ">=1.4.0,<1.5" + [[package]] category = "dev" description = "Atomic file writes." name = "atomicwrites" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "1.3.0" +version = "1.4.0" [[package]] category = "main" @@ -62,7 +112,7 @@ description = "Specifications for callback functions passed in to an API" name = "backcall" optional = false python-versions = "*" -version = "0.1.0" +version = "0.2.0" [[package]] category = "dev" @@ -86,10 +136,11 @@ category = "main" description = "An easy safelist-based HTML-sanitizing tool." name = "bleach" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "3.1.0" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +version = "3.1.5" [package.dependencies] +packaging = "*" six = ">=1.9.0" webencodings = "*" @@ -99,37 +150,34 @@ description = "Python package for providing Mozilla's CA Bundle." name = "certifi" optional = false python-versions = "*" -version = "2019.11.28" +version = "2020.6.20" [[package]] category = "main" -description = "Universal encoding detector for Python 2 and 3" -name = "chardet" +description = "Foreign Function Interface for Python calling C code." +name = "cffi" optional = false python-versions = "*" -version = "3.0.4" +version = "1.14.1" + +[package.dependencies] +pycparser = "*" [[package]] category = "main" -description = "Utilities for interfacing with plotly's Chart Studio" -name = "chart-studio" +description = "Universal encoding detector for Python 2 and 3" +name = "chardet" optional = false python-versions = "*" -version = "1.0.0" - -[package.dependencies] -plotly = "*" -requests = "*" -retrying = ">=1.3.3" -six = "*" +version = "3.0.4" [[package]] category = "dev" description = "Composable command line interface toolkit" name = "click" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "7.0" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +version = "7.1.2" [[package]] category = "main" @@ -154,7 +202,7 @@ description = "Code coverage measurement for Python" name = "coverage" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" -version = "5.0" +version = "5.2.1" [package.extras] toml = ["toml"] @@ -165,10 +213,9 @@ description = "Productivity Tools for Plotly + Pandas" name = "cufflinks" optional = false python-versions = "*" -version = "0.17.0" +version = "0.17.3" [package.dependencies] -chart-studio = ">=1.0.0" colorlover = ">=0.2.1" ipython = ">=5.3.0" ipywidgets = ">=7.0.0" @@ -178,13 +225,24 @@ plotly = ">=4.1.1" setuptools = ">=34.4.1" six = ">=1.9.0" +[[package]] +category = "main" +description = "Composable style cycles" +name = "cycler" +optional = false +python-versions = "*" +version = "0.10.0" + +[package.dependencies] +six = "*" + [[package]] category = "main" description = "Decorators for Humans" name = "decorator" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*" -version = "4.4.1" +version = "4.4.2" [[package]] category = "main" @@ -228,7 +286,7 @@ description = "Internationalized Domain Names in Applications (IDNA)" name = "idna" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "2.8" +version = "2.10" [[package]] category = "dev" @@ -245,22 +303,22 @@ marker = "python_version < \"3.8\"" name = "importlib-metadata" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" -version = "1.3.0" +version = "1.7.0" [package.dependencies] zipp = ">=0.5" [package.extras] docs = ["sphinx", "rst.linker"] -testing = ["packaging", "importlib-resources"] +testing = ["packaging", "pep517", "importlib-resources (>=1.3)"] [[package]] category = "main" description = "IPython Kernel for Jupyter" name = "ipykernel" optional = false -python-versions = ">=3.4" -version = "5.1.3" +python-versions = ">=3.5" +version = "5.3.4" [package.dependencies] appnope = "*" @@ -270,15 +328,15 @@ tornado = ">=4.2" traitlets = ">=4.1.0" [package.extras] -test = ["pytest", "pytest-cov", "flaky", "nose"] +test = ["pytest (!=5.3.4)", "pytest-cov", "flaky", "nose"] [[package]] category = "main" description = "IPython: Productive Interactive Computing" name = "ipython" optional = false -python-versions = ">=3.6" -version = "7.10.2" +python-versions = ">=3.7" +version = "7.17.0" [package.dependencies] appnope = "*" @@ -294,7 +352,7 @@ setuptools = ">=18.5" traitlets = ">=4.2" [package.extras] -all = ["nose (>=0.10.1)", "qtconsole", "pygments", "nbconvert", "Sphinx (>=1.3)", "nbformat", "requests", "testpath", "ipykernel", "notebook", "ipyparallel", "ipywidgets", "numpy (>=1.14)"] +all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.14)", "pygments", "qtconsole", "requests", "testpath"] doc = ["Sphinx (>=1.3)"] kernel = ["ipykernel"] nbconvert = ["nbconvert"] @@ -333,27 +391,42 @@ version = ">=4.0.0" [package.extras] test = ["pytest (>=3.6.0)", "pytest-cov", "mock"] +[[package]] +category = "dev" +description = "A Python utility / library to sort Python imports." +name = "isort" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +version = "4.3.21" + +[package.extras] +pipfile = ["pipreqs", "requirementslib"] +pyproject = ["toml"] +requirements = ["pipreqs", "pip-api"] +xdg_home = ["appdirs (>=1.4.0)"] + [[package]] category = "main" description = "An autocompletion tool for Python that can be used for text editors." name = "jedi" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "0.15.1" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +version = "0.17.2" [package.dependencies] -parso = ">=0.5.0" +parso = ">=0.7.0,<0.8.0" [package.extras] -testing = ["colorama", "docopt", "pytest (>=3.1.0,<5.0.0)"] +qa = ["flake8 (3.7.9)"] +testing = ["Django (<3.1)", "colorama", "docopt", "pytest (>=3.9.0,<5.0.0)"] [[package]] category = "main" description = "A very fast and expressive template engine." name = "jinja2" optional = false -python-versions = "*" -version = "2.10.3" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +version = "2.11.2" [package.dependencies] MarkupSafe = ">=0.23" @@ -388,32 +461,47 @@ category = "main" description = "Jupyter protocol implementation and client libraries" name = "jupyter-client" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -version = "5.3.4" +python-versions = ">=3.5" +version = "6.1.6" [package.dependencies] jupyter-core = ">=4.6.0" python-dateutil = ">=2.1" -pywin32 = ">=1.0" pyzmq = ">=13" tornado = ">=4.1" traitlets = "*" [package.extras] -test = ["ipykernel", "ipython", "mock", "pytest"] +test = ["async-generator", "ipykernel", "ipython", "mock", "pytest", "pytest-asyncio", "pytest-timeout"] [[package]] category = "main" description = "Jupyter core package. A base package on which Jupyter projects rely." name = "jupyter-core" optional = false -python-versions = ">=2.7, !=3.0, !=3.1, !=3.2" -version = "4.6.1" +python-versions = "!=3.0,!=3.1,!=3.2,!=3.3,!=3.4,>=2.7" +version = "4.6.3" [package.dependencies] pywin32 = ">=1.0" traitlets = "*" +[[package]] +category = "main" +description = "A fast implementation of the Cassowary constraint solver" +name = "kiwisolver" +optional = false +python-versions = ">=3.6" +version = "1.2.0" + +[[package]] +category = "dev" +description = "A fast and thorough lazy object proxy." +name = "lazy-object-proxy" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +version = "1.4.3" + [[package]] category = "main" description = "Safely add untrusted strings to HTML/XML markup." @@ -422,6 +510,30 @@ optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" version = "1.1.1" +[[package]] +category = "main" +description = "Python plotting package" +name = "matplotlib" +optional = false +python-versions = ">=3.6" +version = "3.3.0" + +[package.dependencies] +cycler = ">=0.10" +kiwisolver = ">=1.0.1" +numpy = ">=1.15" +pillow = ">=6.2.0" +pyparsing = ">=2.0.3,<2.0.4 || >2.0.4,<2.1.2 || >2.1.2,<2.1.6 || >2.1.6" +python-dateutil = ">=2.1" + +[[package]] +category = "dev" +description = "McCabe checker, plugin for flake8" +name = "mccabe" +optional = false +python-versions = "*" +version = "0.6.1" + [[package]] category = "main" description = "The fastest markdown parser in pure Python" @@ -432,11 +544,30 @@ version = "0.8.4" [[package]] category = "main" +description = "Monty is the missing complement to Python." +name = "monty" +optional = false +python-versions = "*" +version = "3.0.4" + +[package.extras] +yaml = ["ruamel.yaml"] + +[[package]] +category = "dev" description = "More routines for operating on iterables, beyond itertools" name = "more-itertools" optional = false python-versions = ">=3.5" -version = "8.0.2" +version = "8.4.0" + +[[package]] +category = "main" +description = "Python library for arbitrary-precision floating-point arithmetic" +name = "mpmath" +optional = false +python-versions = "*" +version = "1.1.0" [[package]] category = "main" @@ -471,8 +602,8 @@ category = "main" description = "The Jupyter Notebook format" name = "nbformat" optional = false -python-versions = "*" -version = "4.4.0" +python-versions = ">=3.5" +version = "5.0.7" [package.dependencies] ipython-genutils = "*" @@ -483,42 +614,91 @@ traitlets = ">=4.1" [package.extras] test = ["pytest", "pytest-cov", "testpath"] +[[package]] +category = "main" +description = "Python package for creating and manipulating graphs and networks" +name = "networkx" +optional = false +python-versions = ">=3.5" +version = "2.4" + +[package.dependencies] +decorator = ">=4.3.0" + +[package.extras] +all = ["numpy", "scipy", "pandas", "matplotlib", "pygraphviz", "pydot", "pyyaml", "gdal", "lxml", "pytest"] +gdal = ["gdal"] +lxml = ["lxml"] +matplotlib = ["matplotlib"] +numpy = ["numpy"] +pandas = ["pandas"] +pydot = ["pydot"] +pygraphviz = ["pygraphviz"] +pytest = ["pytest"] +pyyaml = ["pyyaml"] +scipy = ["scipy"] + +[[package]] +category = "main" +description = "IPython widget to interactively view molecular structures and trajectories." +name = "nglview" +optional = false +python-versions = ">=3.6" +version = "2.7.7" + +[package.dependencies] +ipywidgets = ">=7" +numpy = "*" + +[package.extras] +MDAnalysis = ["mdanalysis"] +ParmEd = ["parmed"] +ase = ["ase"] +htmd = ["htmd"] +mdtraj = ["mdtraj"] +pytraj = ["pytraj"] +qcelemental = ["qcelemental"] +rdkit = ["rdkit"] +simpletraj = ["simpletraj"] + [[package]] category = "main" description = "A web-based notebook environment for interactive computing" name = "notebook" optional = false python-versions = ">=3.5" -version = "6.0.2" +version = "6.1.0" [package.dependencies] Send2Trash = "*" +argon2-cffi = "*" ipykernel = "*" ipython-genutils = "*" jinja2 = "*" jupyter-client = ">=5.3.4" -jupyter-core = ">=4.6.0" +jupyter-core = ">=4.6.1" nbconvert = "*" nbformat = "*" prometheus-client = "*" pyzmq = ">=17" -terminado = ">=0.8.1" +terminado = ">=0.8.3" tornado = ">=5.0" traitlets = ">=4.2.1" [package.extras] -test = ["nose", "coverage", "requests", "nose-warnings-filters", "nbval", "nose-exclude", "selenium", "pytest", "pytest-cov", "nose-exclude"] +docs = ["sphinx", "nbsphinx", "sphinxcontrib-github-alt"] +test = ["nose", "coverage", "requests", "nose-warnings-filters", "nbval", "nose-exclude", "selenium", "pytest", "pytest-cov", "requests-unixsocket", "nose-exclude"] [[package]] category = "main" description = "NumPy is the fundamental package for array computing with Python." name = "numpy" optional = false -python-versions = ">=3.5" -version = "1.17.4" +python-versions = ">=3.6" +version = "1.19.1" [[package]] -category = "dev" +category = "main" description = "Core utilities for Python packages" name = "packaging" optional = false @@ -529,6 +709,14 @@ version = "20.4" pyparsing = ">=2.0.2" six = "*" +[[package]] +category = "main" +description = "Color palettes for Python" +name = "palettable" +optional = false +python-versions = "*" +version = "3.3.0" + [[package]] category = "main" description = "Powerful data structures for data analysis, time series, and statistics" @@ -558,8 +746,8 @@ category = "main" description = "A Python Parser" name = "parso" optional = false -python-versions = "*" -version = "0.5.2" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +version = "0.7.1" [package.extras] testing = ["docopt", "pytest (>=3.0.7)"] @@ -571,7 +759,7 @@ marker = "python_version >= \"3.3\" and sys_platform != \"win32\" or sys_platfor name = "pexpect" optional = false python-versions = "*" -version = "4.7.0" +version = "4.8.0" [package.dependencies] ptyprocess = ">=0.5" @@ -586,11 +774,19 @@ version = "0.7.5" [[package]] category = "main" -description = "An open-source, interactive graphing library for Python" +description = "Python Imaging Library (Fork)" +name = "pillow" +optional = false +python-versions = ">=3.5" +version = "7.2.0" + +[[package]] +category = "main" +description = "An open-source, interactive data visualization library for Python" name = "plotly" optional = false python-versions = "*" -version = "4.4.1" +version = "4.9.0" [package.dependencies] retrying = ">=1.3.3" @@ -618,7 +814,7 @@ description = "Python client for the Prometheus monitoring system." name = "prometheus-client" optional = false python-versions = "*" -version = "0.7.1" +version = "0.8.0" [package.extras] twisted = ["twisted"] @@ -628,8 +824,8 @@ category = "main" description = "Library for building powerful interactive command lines in Python" name = "prompt-toolkit" optional = false -python-versions = ">=3.6" -version = "3.0.2" +python-versions = ">=3.6.1" +version = "3.0.5" [package.dependencies] wcwidth = "*" @@ -637,7 +833,7 @@ wcwidth = "*" [[package]] category = "main" description = "Run a subprocess in a pseudo terminal" -marker = "python_version >= \"3.3\" and sys_platform != \"win32\" or sys_platform != \"win32\" or os_name != \"nt\" or python_version >= \"3.3\" and sys_platform != \"win32\" and (python_version >= \"3.3\" and sys_platform != \"win32\" or sys_platform != \"win32\")" +marker = "sys_platform != \"win32\" or os_name != \"nt\" or python_version >= \"3.3\" and sys_platform != \"win32\"" name = "ptyprocess" optional = false python-versions = "*" @@ -649,18 +845,70 @@ description = "library with cross-python path, ini-parsing, io, code, log facili name = "py" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "1.8.0" +version = "1.9.0" + +[[package]] +category = "main" +description = "C parser in Python" +name = "pycparser" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +version = "2.20" [[package]] category = "main" description = "Pygments is a syntax highlighting package written in Python." name = "pygments" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -version = "2.5.2" +python-versions = ">=3.5" +version = "2.6.1" [[package]] category = "dev" +description = "python code static checker" +name = "pylint" +optional = false +python-versions = ">=3.5.*" +version = "2.5.3" + +[package.dependencies] +astroid = ">=2.4.0,<=2.5" +colorama = "*" +isort = ">=4.2.5,<5" +mccabe = ">=0.6,<0.7" +toml = ">=0.7.1" + +[[package]] +category = "main" +description = "Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. It is currently the core analysis code powering the Materials Project (https://www.materialsproject.org)." +name = "pymatgen" +optional = false +python-versions = ">=3.6" +version = "2020.7.18" + +[package.dependencies] +matplotlib = ">=1.5" +monty = ">=3.0.2" +networkx = ">=2.2" +numpy = ">=1.14.3" +palettable = ">=3.1.1" +pandas = "*" +plotly = ">=4.5.0" +requests = "*" +"ruamel.yaml" = ">=0.15.6" +scipy = ">=1.5.0" +spglib = ">=1.9.9.44" +sympy = "*" +tabulate = "*" + +[package.extras] +abinit = ["netcdf4"] +ase = ["ase (>=3.3)"] +provenance = ["pybtex"] +vis = ["vtk (>=6.0.0)"] + +[[package]] +category = "main" description = "Python parsing module" name = "pyparsing" optional = false @@ -673,7 +921,7 @@ description = "Persistent/Functional/Immutable data structures" name = "pyrsistent" optional = false python-versions = "*" -version = "0.15.6" +version = "0.16.0" [package.dependencies] six = "*" @@ -701,15 +949,15 @@ category = "dev" description = "Pytest plugin for measuring coverage." name = "pytest-cov" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "2.8.1" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +version = "2.9.0" [package.dependencies] coverage = ">=4.4" pytest = ">=3.6" [package.extras] -testing = ["fields", "hunter", "process-tests (2.0.2)", "six", "virtualenv"] +testing = ["fields", "hunter", "process-tests (2.0.2)", "six", "pytest-xdist", "virtualenv"] [[package]] category = "main" @@ -728,7 +976,7 @@ description = "World timezone definitions, modern and historical" name = "pytz" optional = false python-versions = "*" -version = "2019.3" +version = "2020.1" [[package]] category = "main" @@ -737,7 +985,7 @@ marker = "sys_platform == \"win32\"" name = "pywin32" optional = false python-versions = "*" -version = "227" +version = "228" [[package]] category = "main" @@ -754,7 +1002,7 @@ description = "Python bindings for 0MQ" name = "pyzmq" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*" -version = "18.1.1" +version = "19.0.2" [[package]] category = "main" @@ -762,16 +1010,16 @@ description = "Python HTTP for Humans." name = "requests" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -version = "2.22.0" +version = "2.24.0" [package.dependencies] certifi = ">=2017.4.17" -chardet = ">=3.0.2,<3.1.0" -idna = ">=2.5,<2.9" +chardet = ">=3.0.2,<4" +idna = ">=2.5,<3" urllib3 = ">=1.21.1,<1.25.0 || >1.25.0,<1.25.1 || >1.25.1,<1.26" [package.extras] -security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)"] +security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"] socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7)", "win-inet-pton"] [[package]] @@ -785,6 +1033,43 @@ version = "1.3.3" [package.dependencies] six = ">=1.7.0" +[[package]] +category = "main" +description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order" +name = "ruamel.yaml" +optional = false +python-versions = "*" +version = "0.16.10" + +[package.dependencies] +[package.dependencies."ruamel.yaml.clib"] +python = "<3.9" +version = ">=0.1.2" + +[package.extras] +docs = ["ryd"] +jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"] + +[[package]] +category = "main" +description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml" +marker = "platform_python_implementation == \"CPython\" and python_version < \"3.9\"" +name = "ruamel.yaml.clib" +optional = false +python-versions = "*" +version = "0.2.0" + +[[package]] +category = "main" +description = "SciPy: Scientific Library for Python" +name = "scipy" +optional = false +python-versions = ">=3.6" +version = "1.5.2" + +[package.dependencies] +numpy = ">=1.14.5" + [[package]] category = "main" description = "Send file to trash natively under Mac OS X, Windows and Linux." @@ -798,8 +1083,8 @@ category = "main" description = "Python 2 and 3 compatibility utilities" name = 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"anaconda"} cufflinks = {channel = "conda-forge", name = "cufflinks-py"} mdtraj = {channel = "conda-forge"} +ase = {channel = "conda-forge"} sphinx = {channel = "anaconda"} [build-system] diff --git a/src/py4vasp/data/__init__.py b/src/py4vasp/data/__init__.py index 6ff7f33..48de6b8 100644 --- a/src/py4vasp/data/__init__.py +++ b/src/py4vasp/data/__init__.py @@ -22,6 +22,7 @@ from .energy import Energy from .kpoints import Kpoints from .projectors import Projectors +from .structure import Structure import plotly.io as pio import cufflinks as cf diff --git a/src/py4vasp/data/projectors.py b/src/py4vasp/data/projectors.py index 503fd94..245a3a1 100644 --- a/src/py4vasp/data/projectors.py +++ b/src/py4vasp/data/projectors.py @@ -8,7 +8,7 @@ from py4vasp.data import _util from py4vasp.exceptions import UsageException -_selection_doc = """ +_selection_doc = r""" selection : str A string specifying the projection of the orbitals. There are three distinct possibilities: @@ -33,7 +33,7 @@ _end_spec = ")" _seperators = (" ", ",") _range_separator = "-" -_range = re.compile(r"^(\d+)" + re.escape(_range_separator) + "(\d+)$") +_range = re.compile(r"^(\d+)" + re.escape(_range_separator) + r"(\d+)$") _whitespace_begin_spec = re.compile(r"\s*" + re.escape(_begin_spec) + r"\s*") _whitespace_end_spec = re.compile(r"\s*" + re.escape(_end_spec) + r"\s*") _whitespace_range = re.compile(r"\s*" + re.escape(_range_separator) + r"\s*") diff --git a/src/py4vasp/data/structure.py b/src/py4vasp/data/structure.py new file mode 100644 index 0000000..5481460 --- /dev/null +++ b/src/py4vasp/data/structure.py @@ -0,0 +1,86 @@ +from py4vasp.data import _util +from py4vasp.exceptions import RefinementException +import functools +import numpy as np + + +class StructureViewer: + """Collection of data and elements to be displayed in a structure viewer""" + + def __init__(self, structure, show_cell=True, supercell=None, show_axes=False, axes_length=3, arrows=None): + self.structure = structure + self.show_cell = show_cell + self.supercell = supercell + self.show_axes = show_axes + self.axes_length = axes_length + self.arrows = arrows + + def with_arrows(self, arrows): + self.arrows = arrows + return self + + def show(self): + import nglview + from nglview.shape import Shape + + structure = self.structure.to_pymatgen() + if self.supercell is not None: + structure.make_supercell(self.supercell) + + view = nglview.show_pymatgen(structure) + if self.show_cell: + view.add_representation(repr_type="unitcell") + if self.show_axes or self.arrows is not None: + shape = Shape(view=view) + if self.show_axes: + shape.add_arrow( + [0, 0, 0], [self.axes_length, 0, 0], [1, 0, 0], 0.2) + shape.add_arrow( + [0, 0, 0], [0, self.axes_length, 0], [0, 1, 0], 0.2) + shape.add_arrow( + [0, 0, 0], [0, 0, self.axes_length], [0, 0, 1], 0.2) + if self.arrows is not None: + for (x, y, z), (vx, vy, vz) in zip(structure.cart_coords, self.arrows): + shape.add_arrow( + [x, y, z], [x+vx, y+vy, z+vz], [0.1, 0.1, 0.8], 0.2) + + return view + + +class Structure: + def __init__(self, raw_structure): + self._raw = raw_structure + self.structure_viewer = None + + def read(self): + return self.to_dict() + + def to_dict(self): + return { + "cell": self._raw.cell.lattice_vectors[:], + "cartesian_positions": self._raw.cartesian_positions[:], + "species": list(self._raw.species), + } + + def __len__(self): + return len(self._raw.cartesian_positions) + + def to_pymatgen(self): + import pymatgen as mg + return mg.Structure( + lattice=mg.Lattice(self._raw.cell.lattice_vectors), + species=[specie.decode("ascii") for specie in self._raw.species], + coords=self._raw.cartesian_positions, + coords_are_cartesian=True + ) + + def plot(self, show_cell=True, supercell=None, show_axes=False, axes_length=3): + self.structure_viewer = StructureViewer( + self, show_cell=show_cell, supercell=supercell, show_axes=show_axes, axes_length=axes_length) + return self.structure_viewer.show() + + def plot_arrows(self, arrows): + if self.structure_viewer is None: + self.plot() + self.structure_viewer = self.structure_viewer.with_arrows(arrows) + return self.structure_viewer.show() \ No newline at end of file diff --git a/src/py4vasp/raw/file.py b/src/py4vasp/raw/file.py index ca31247..ed5e329 100644 --- a/src/py4vasp/raw/file.py +++ b/src/py4vasp/raw/file.py @@ -129,6 +129,20 @@ def cell(self): lattice_vectors=self._h5f["results/positions/lattice_vectors"], ) + def structure(self): + """ Read the structure information. + + Returns + ------- + raw.Structure + """ + self._assert_not_closed() + return raw.Structure( + cell = self.cell(), + cartesian_positions = self._h5f["results/positions/cartesian_positions"], + species = self._h5f["results/positions/species"], + ) + def energy(self): """ Read the energies during the ionic convergence. diff --git a/src/py4vasp/raw/rawdata.py b/src/py4vasp/raw/rawdata.py index 962718f..3c2ff77 100644 --- a/src/py4vasp/raw/rawdata.py +++ b/src/py4vasp/raw/rawdata.py @@ -42,6 +42,12 @@ class Cell: "Lattice vectors defining the unit cell." __eq__ = _dataclass_equal +@dataclass +class Structure: + cell: Cell + cartesian_positions: np.ndarray + species: np.ndarray = None + __eq__ = _dataclass_equal @dataclass class Kpoints: diff --git a/tests/data/test_structure.py b/tests/data/test_structure.py new file mode 100644 index 0000000..3e99836 --- /dev/null +++ b/tests/data/test_structure.py @@ -0,0 +1,75 @@ +from py4vasp.data import Structure +from py4vasp.exceptions import RefinementException +import py4vasp.raw as raw +import pytest +import numpy as np + + +@pytest.fixture +def raw_structure(): + number_atoms = 20 + shape = (number_atoms, 3) + return raw.Structure( + cell=raw.Cell(scale=1.0, lattice_vectors=np.eye(3)), + cartesian_positions=np.arange(np.prod(shape)).reshape(shape), + species=np.array(["C"]*number_atoms, dtype="S2"), + ) + + +def test_read(raw_structure, Assert): + actual = Structure(raw_structure).read() + assert (actual["cell"] == raw_structure.cell.lattice_vectors).all() + Assert.allclose(actual["cartesian_positions"], + raw_structure.cartesian_positions) + assert (actual["species"] == raw_structure.species).all() + + +def test_to_pymatgen(raw_structure, Assert): + structure = Structure(raw_structure) + mg_structure = structure.to_pymatgen() + a, b, c = mg_structure.lattice.as_dict()["matrix"] + assert a == [1, 0, 0] + assert b == [0, 1, 0] + assert c == [0, 0, 1] + + +def test_plot(raw_structure, Assert): + structure = Structure(raw_structure) + assert structure.structure_viewer is None + view = structure.plot() + assert structure.structure_viewer is not None + + view = structure.plot(show_cell=False) + assert [(msg["methodName"], msg["args"]) + for msg in view.get_state()["_ngl_msg_archive"]][1:] == [] + + view = structure.plot(show_cell=True) + assert [(msg["methodName"], msg["args"]) for msg in view.get_state()[ + "_ngl_msg_archive"]][1:] == [('addRepresentation', ['unitcell'])] + + view = structure.plot(show_cell=False, show_axes=False) + assert [(msg["methodName"], msg["args"]) + for msg in view.get_state()["_ngl_msg_archive"]][1:] == [] + + view = structure.plot(show_cell=False, show_axes=True, axes_length=5) + assert [(msg["methodName"], msg["args"]) for msg in view.get_state()["_ngl_msg_archive"]][1:] == [ + ('addShape', [ + 'shape', [('arrow', [0, 0, 0], [5, 0, 0], [1, 0, 0], 0.2)]]), + ('addShape', [ + 'shape', [('arrow', [0, 0, 0], [0, 5, 0], [0, 1, 0], 0.2)]]), + ('addShape', [ + 'shape', [('arrow', [0, 0, 0], [0, 0, 5], [0, 0, 1], 0.2)]]), + ] + + +def test_plot_arrows(raw_structure, Assert): + structure = Structure(raw_structure) + assert structure.structure_viewer is None + view = structure.plot_arrows([(0, 0, 1) for i in range(len(structure))]) + assert structure.structure_viewer is not None + assert [(msg["methodName"], msg["args"]) for msg in view.get_state()[ + "_ngl_msg_archive"]][1] == ('addRepresentation', ['unitcell']) + assert [(msg["methodName"], msg["args"]) for msg in view.get_state()[ + "_ngl_msg_archive"]][2] == ('addShape', ['shape', [('arrow', [0.0, 1.0, 2.0], [0.0, 1.0, 3.0], [0.1, 0.1, 0.8], 0.2)]]) + assert sum(msg["methodName"] == 'addShape' for msg in view.get_state()[ + "_ngl_msg_archive"]) == len(structure) diff --git a/tests/raw/test_file.py b/tests/raw/test_file.py index 759ea0f..3d92313 100644 --- a/tests/raw/test_file.py +++ b/tests/raw/test_file.py @@ -283,3 +283,32 @@ def check_kpoints(file, reference): assert actual == reference assert isinstance(actual.number, Integral) assert isinstance(actual.mode, str) + + +def test_structure(tmpdir): + setup = SetupTest( + directory=tmpdir, + options=itertools.product((True, False)), + create_reference=reference_structure, + write_reference=write_structure, + check_actual=check_structure, + ) + generic_test(setup) + + +def reference_structure(): + structure = raw.Structure( + cell=reference_cell(), + cartesian_positions=np.linspace(np.zeros(3), np.ones(3), num_atoms), + species = np.array(["C"]*num_atoms, dtype="S2") + ) + return structure + +def write_structure(h5f, structure): + write_cell(h5f, structure.cell) + h5f["results/positions/cartesian_positions"] = structure.cartesian_positions + h5f["results/positions/species"] = structure.species + +def check_structure(file, reference): + actual = file.structure() + assert actual == reference