├── .gitignore ├── LICENSE ├── README.md ├── docs ├── Makefile ├── make.bat └── source │ ├── conf.py │ └── index.rst ├── notebooks ├── data │ ├── CONTCAR_Li3PS4 │ ├── CONTCAR_Li7P3S11 │ ├── Li3PS4-γ_ICSD#180318_2011_Solid_State_Ionics.cif │ └── Li7P3S11 │ │ ├── XAS_input_10_1 │ │ ├── CONTCAR │ │ ├── CORE_DIELECTRIC_IMAG.dat │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ └── vasp.out │ │ ├── XAS_input_11_1 │ │ ├── CONTCAR │ │ ├── CORE_DIELECTRIC_IMAG.dat │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ └── vasp.out │ │ ├── XAS_input_1_1 │ │ ├── CONTCAR │ │ ├── CORE_DIELECTRIC_IMAG.dat │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ └── vasp.out │ │ ├── XAS_input_2_1 │ │ ├── CONTCAR │ │ ├── CORE_DIELECTRIC_IMAG.dat │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ └── vasp.out │ │ ├── XAS_input_3_1 │ │ ├── CONTCAR │ │ ├── CORE_DIELECTRIC_IMAG.dat │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ └── vasp.out │ │ ├── XAS_input_4_1 │ │ ├── CONTCAR │ │ ├── CORE_DIELECTRIC_IMAG.dat │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ └── vasp.out │ │ ├── XAS_input_5_1 │ │ ├── CONTCAR │ │ ├── CORE_DIELECTRIC_IMAG.dat │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ └── vasp.out │ │ ├── XAS_input_6_1 │ │ ├── CONTCAR │ │ ├── CORE_DIELECTRIC_IMAG.dat │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ └── vasp.out │ │ ├── XAS_input_7_1 │ │ ├── CONTCAR │ │ ├── CORE_DIELECTRIC_IMAG.dat │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ └── vasp.out │ │ ├── XAS_input_8_1 │ │ ├── CONTCAR │ │ ├── CORE_DIELECTRIC_IMAG.dat │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ └── vasp.out │ │ ├── XAS_input_9_1 │ │ ├── CONTCAR │ │ ├── CORE_DIELECTRIC_IMAG.dat │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ └── vasp.out │ │ └── XAS_input_SCF │ │ ├── CONTCAR │ │ ├── DOSCAR.bz2 │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR.bz2 │ │ ├── POSCAR │ │ ├── XDATCAR.bz2 │ │ └── vasp.out └── lps-example.ipynb ├── scripts ├── README.md ├── collect_xas_output.py └── make_xas_input.py ├── setup.py └── xas_tools ├── LDA-XAS.yaml ├── VERSION ├── __init__.py ├── spectra.py ├── tests ├── __init__.py ├── fixtures │ ├── CONTCAR_Li3PS4 │ └── CONTCAR_Li7P3S11 └── test_vasp.py ├── util.py └── vasp.py /.gitignore: -------------------------------------------------------------------------------- 1 | # make sure not to accidentally commit POTCAR files 2 | notebooks/Li3PS4_chp_input/ 3 | notebooks/Li7P3S11_chp_input/ 4 | 5 | # Emacs specific 6 | *~ 7 | .#* 8 | 9 | # Byte-compiled / optimized / DLL files 10 | __pycache__/ 11 | *.py[cod] 12 | *$py.class 13 | 14 | # C extensions 15 | *.so 16 | 17 | # Distribution / packaging 18 | .Python 19 | build/ 20 | develop-eggs/ 21 | dist/ 22 | downloads/ 23 | eggs/ 24 | .eggs/ 25 | lib/ 26 | lib64/ 27 | parts/ 28 | sdist/ 29 | var/ 30 | wheels/ 31 | pip-wheel-metadata/ 32 | share/python-wheels/ 33 | *.egg-info/ 34 | .installed.cfg 35 | *.egg 36 | MANIFEST 37 | 38 | # PyInstaller 39 | # Usually these files are written by a python script from a template 40 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 41 | *.manifest 42 | *.spec 43 | 44 | # Installer logs 45 | pip-log.txt 46 | pip-delete-this-directory.txt 47 | 48 | # Unit test / coverage reports 49 | htmlcov/ 50 | .tox/ 51 | .nox/ 52 | .coverage 53 | .coverage.* 54 | .cache 55 | nosetests.xml 56 | coverage.xml 57 | *.cover 58 | *.py,cover 59 | .hypothesis/ 60 | .pytest_cache/ 61 | 62 | # Translations 63 | *.mo 64 | *.pot 65 | 66 | # Django stuff: 67 | *.log 68 | local_settings.py 69 | db.sqlite3 70 | db.sqlite3-journal 71 | 72 | # Flask stuff: 73 | instance/ 74 | .webassets-cache 75 | 76 | # Scrapy stuff: 77 | .scrapy 78 | 79 | # Sphinx documentation 80 | docs/_build/ 81 | 82 | # PyBuilder 83 | target/ 84 | 85 | # Jupyter Notebook 86 | .ipynb_checkpoints 87 | 88 | # IPython 89 | profile_default/ 90 | ipython_config.py 91 | 92 | # pyenv 93 | .python-version 94 | 95 | # pipenv 96 | # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. 97 | # However, in case of collaboration, if having platform-specific dependencies or dependencies 98 | # having no cross-platform support, pipenv may install dependencies that don't work, or not 99 | # install all needed dependencies. 100 | #Pipfile.lock 101 | 102 | # PEP 582; used by e.g. github.com/David-OConnor/pyflow 103 | __pypackages__/ 104 | 105 | # Celery stuff 106 | celerybeat-schedule 107 | celerybeat.pid 108 | 109 | # SageMath parsed files 110 | *.sage.py 111 | 112 | # Environments 113 | .env 114 | .venv 115 | env/ 116 | venv/ 117 | ENV/ 118 | env.bak/ 119 | venv.bak/ 120 | 121 | # Spyder project settings 122 | .spyderproject 123 | .spyproject 124 | 125 | # Rope project settings 126 | .ropeproject 127 | 128 | # mkdocs documentation 129 | /site 130 | 131 | # mypy 132 | .mypy_cache/ 133 | .dmypy.json 134 | dmypy.json 135 | 136 | # Pyre type checker 137 | .pyre/ 138 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # xas-tools 2 | 3 | **Tools related to X-ray absorption spectroscopy (XAS) calculations**. 4 | 5 | Haoyue Guo (), Nong Artrith 6 | (), Alex Urban () 7 | 8 | See also:
9 | Haoyue Guo, Matthew R. Carbone, Chuntian Cao, Jianzhou Qu, Yonghua Du, Seong-Min Bak, Conan Weiland, Feng Wang, Shinjae Yoo, Nongnuch Artrith*, Alexander Urban*, Deyu Lu*, ["Simulated sulfur K-edge X-ray absorption spectroscopy database of lithium thiophosphate solid electrolytes", **2023**, https://doi.org/10.48550/arXiv.2302.00126](https://doi.org/10.48550/arXiv.2302.00126); Nature Scientific Data **10** , 349, 2023: (https://doi.org/10.1038/s41597-023-02262-4). 10 | 11 | ## Installation 12 | 13 | Install using `pip` 14 | 15 | pip install --user . 16 | 17 | Or install in editable (developer) mode with 18 | 19 | pip install --user -e . 20 | 21 | ## XAS calculations with VASP 22 | 23 | The package generates input files for XAS simulations with the supercell 24 | core-hole approach [1]. 25 | 26 | The following list describes the generak “workflow”: 27 | 28 | 1. Given an input atomic structure 29 | 2. All distinct absorbers are determined based on the symmetry of the 30 | structure 31 | 3. Multiplicities are determined based on the number of symmetrically 32 | equivalent absorbers 33 | 4. If requested, a supercell is created 34 | 5. VASP input files are generated for 35 | * A ground-state calculation without core hole 36 | * Core-hole potential calculations for all symmetrically distinct 37 | absorbers 38 | 6. VASP calculations are performed as usual 39 | 7. The VASP output is post-processed by 40 | * Alignment of the XAS lines for individual absorbers 41 | * Combining and broadening the XAS lines of all individual absorbers 42 | 43 | ## Reference 44 | 45 | [1] F. Karsai, M. Humer, E. Flage-Larsen, P. Blaha and G. Kresse, *Phys. Rev. B* **98** (2018) 235205 . 46 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SOURCEDIR = source 9 | BUILDDIR = build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=source 11 | set BUILDDIR=build 12 | 13 | if "%1" == "" goto help 14 | 15 | %SPHINXBUILD% >NUL 2>NUL 16 | if errorlevel 9009 ( 17 | echo. 18 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 19 | echo.installed, then set the SPHINXBUILD environment variable to point 20 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 21 | echo.may add the Sphinx directory to PATH. 22 | echo. 23 | echo.If you don't have Sphinx installed, grab it from 24 | echo.http://sphinx-doc.org/ 25 | exit /b 1 26 | ) 27 | 28 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 29 | goto end 30 | 31 | :help 32 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 33 | 34 | :end 35 | popd 36 | -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- 1 | # Configuration file for the Sphinx documentation builder. 2 | # 3 | # This file only contains a selection of the most common options. For a full 4 | # list see the documentation: 5 | # https://www.sphinx-doc.org/en/master/usage/configuration.html 6 | 7 | # -- Path setup -------------------------------------------------------------- 8 | 9 | # If extensions (or modules to document with autodoc) are in another directory, 10 | # add these directories to sys.path here. If the directory is relative to the 11 | # documentation root, use os.path.abspath to make it absolute, like shown here. 12 | # 13 | import os 14 | import sys 15 | sys.path.insert(0, os.path.abspath('../..')) 16 | 17 | 18 | # -- Project information ----------------------------------------------------- 19 | 20 | project = 'XAS Tools' 21 | copyright = '2022, The XAS Tools developers' 22 | author = 'The XAS Tools developers' 23 | 24 | # The full version, including alpha/beta/rc tags 25 | release = '0.1.0' 26 | 27 | 28 | # -- General configuration --------------------------------------------------- 29 | 30 | # Add any Sphinx extension module names here, as strings. They can be 31 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 32 | # ones. 33 | extensions = ['sphinx.ext.autodoc', 34 | 'sphinx.ext.viewcode', 35 | 'sphinx.ext.napoleon', 36 | 'sphinx.ext.mathjax'] 37 | 38 | # Add any paths that contain templates here, relative to this directory. 39 | templates_path = ['_templates'] 40 | 41 | # List of patterns, relative to source directory, that match files and 42 | # directories to ignore when looking for source files. 43 | # This pattern also affects html_static_path and html_extra_path. 44 | exclude_patterns = [] 45 | 46 | 47 | # -- Options for HTML output ------------------------------------------------- 48 | 49 | # The theme to use for HTML and HTML Help pages. See the documentation for 50 | # a list of builtin themes. 51 | # 52 | html_theme = 'alabaster' 53 | 54 | # Add any paths that contain custom static files (such as style sheets) here, 55 | # relative to this directory. They are copied after the builtin static files, 56 | # so a file named "default.css" will overwrite the builtin "default.css". 57 | html_static_path = ['_static'] 58 | -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- 1 | .. XAS Tools documentation master file, created by 2 | sphinx-quickstart on Mon Feb 14 13:19:05 2022. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to the XAS Tools documentation! 7 | ======================================= 8 | 9 | This package allows basic automation of X-ray absorption spectroscopy 10 | simulations with the supercell core-hole approach [1]. The package also 11 | provides functionality for the postprocessing of calculation results. 12 | 13 | [1] F. Karsai, M. Humer, E. Flage-Larsen, P. Blaha and G. Kresse, 14 | *Phys. Rev. B* **98**, 235205 (2018). 15 | 16 | 17 | 18 | .. toctree:: 19 | :maxdepth: 2 20 | :caption: Contents: 21 | 22 | 23 | 24 | Indices and tables 25 | ================== 26 | 27 | * :ref:`genindex` 28 | * :ref:`modindex` 29 | * :ref:`search` 30 | -------------------------------------------------------------------------------- /notebooks/data/CONTCAR_Li3PS4: -------------------------------------------------------------------------------- 1 | γ-Li3PS4 Li6 P2 S8 2 | 1.00000000000000 3 | 7.7728887530431452 -0.0000033681917313 0.0000011020054775 4 | -0.0000027248887747 6.6186469761244338 -0.0000003841750128 5 | 0.0000010357285640 -0.0000004507128427 6.2250567792974012 6 | Li P S 7 | 6 2 8 8 | Direct 9 | 0.2435623021061343 0.3168557575935761 -0.0000276211987660 10 | 0.2564381019141520 0.6831441890591163 0.4999719084053222 11 | 0.7435611655912444 0.6831434992933233 0.4999717768080432 12 | 0.7564385084591919 0.3168565213342524 -0.0000283052197278 13 | -0.0000002022956064 0.1433423811607082 0.4920524992366043 14 | 0.5000001100011322 0.8566575011659002 0.9920524276552353 15 | 0.0000004459212349 0.8183895641568136 0.0008237238071628 16 | 0.4999994910534741 0.1816104392205975 0.5008236991422910 17 | 0.2180289937774249 0.6737859652343253 0.8914540468516050 18 | 0.2819691231790888 0.3262152529442662 0.3914533684653503 19 | 0.7180305678642873 0.3262150763464409 0.3914527184322897 20 | 0.7819713061958816 0.6737862525889325 0.8914538150616318 21 | 0.0000003055071354 0.1120806960591720 0.8913364701868740 22 | 0.4999997684867032 0.8879169675626877 0.3913353072636300 23 | -0.0000001662142958 0.8086679840744586 0.3320856195908329 24 | 0.5000001784528179 0.1913318552054320 0.8320884975116104 25 | 26 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 27 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 28 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 29 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 30 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 31 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 32 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 33 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 34 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 35 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 36 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 37 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 38 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 39 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 40 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 41 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 42 | -------------------------------------------------------------------------------- /notebooks/data/CONTCAR_Li7P3S11: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892072299137546 -0.0045582927629227 0.0457425203370421 4 | 1.3472173211783336 6.1786729084373642 0.0192368121238670 5 | 5.0855915969651093 2.4906284758103654 11.4039621787899215 6 | Li P S 7 | 14 6 22 8 | Direct 9 | 0.6687429681853894 0.3523260262110126 0.9039712412362317 10 | 0.3312572099294600 0.6476712634939786 0.0960283951009658 11 | 0.6114585734705177 0.7343419829887414 0.1147873480188454 12 | 0.3885427908029592 0.2656559196982933 0.8852129292632063 13 | 0.1778128505142525 0.0049354053794799 0.2979970907895192 14 | 0.8221878062633918 0.9950642851196151 0.7020026166974888 15 | 0.9686144020561377 0.4556369208843891 0.7495712001414975 16 | 0.0313853150717303 0.5443640990176954 0.2504285290213179 17 | 0.2949205286317004 0.1981466305193354 0.7023827015199765 18 | 0.7050799199805200 0.8018536220907443 0.2976173714899878 19 | 0.6723444712504114 0.2017777806088064 0.4994633708840401 20 | 0.3276557097807620 0.7982227182604432 0.5005362951219575 21 | 0.1361429941051054 0.7067131908191373 0.8824014423855367 22 | 0.8638583120488356 0.2932863464507764 0.1175977826833790 23 | 0.7769408888468149 0.6321080916171602 0.5498679552055915 24 | 0.2230586287391673 0.3678920510938440 0.4501324242229064 25 | 0.4720538555832095 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0.1080083038135444 0.7046116534145491 42 | 0.4916935755691932 0.8919922714469746 0.2953888699840955 43 | 0.8208362858841207 0.7031896073070416 0.1006187763953790 44 | 0.1791636144595808 0.2968099712101095 0.8993811219681468 45 | 0.8585390477262619 0.2284035322807562 0.9433858695418907 46 | 0.1414608066159894 0.7715964700864949 0.0566142867473140 47 | 0.6807149810952434 0.9407450163164075 0.9116758906749631 48 | 0.3192848944202427 0.0592551200731378 0.0883243824922190 49 | 0.9730954522642765 0.8143715835613863 0.8015560597340347 50 | 0.0269045260670813 0.1856276311999048 0.1984439894228581 51 | 52 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 53 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 54 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 55 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 56 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 57 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 58 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 59 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 60 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 61 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 62 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 63 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 64 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 65 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 66 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 67 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 68 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 69 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 70 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 71 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 72 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 73 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 74 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 75 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 76 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 77 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 78 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 79 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 80 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 81 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 82 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 83 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 84 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 85 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 86 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 87 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 88 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 89 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 90 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 91 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 92 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 93 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 94 | -------------------------------------------------------------------------------- /notebooks/data/Li3PS4-γ_ICSD#180318_2011_Solid_State_Ionics.cif: -------------------------------------------------------------------------------- 1 | 2 | #(C) 2020 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure. All rights reserved. 3 | data_180318-ICSD 4 | _database_code_ICSD 180318 5 | _audit_creation_date 2011-08-01 6 | _chemical_name_common 'Trilithium tetrathiophosphate - gamma' 7 | _chemical_formula_structural 'Li3 (P S4)' 8 | _chemical_formula_sum 'Li3 P1 S4' 9 | _chemical_name_structure_type Enargite#Cu3AsS4 10 | _exptl_crystal_density_diffrn 1.93 11 | _diffrn_ambient_temperature 297. 12 | _citation_title 13 | 14 | ; 15 | Crystal structure and phase transitions of the lithium ionic conductor Li3 P 16 | S4 17 | ; 18 | loop_ 19 | _citation_id 20 | _citation_journal_full 21 | _citation_year 22 | _citation_journal_volume 23 | _citation_page_first 24 | _citation_page_last 25 | _citation_journal_id_ASTM 26 | primary 'Solid State Ionics' 2011 182 53 58 SSIOD3 27 | loop_ 28 | _citation_author_citation_id 29 | _citation_author_name 30 | primary 'Homma, K.' 31 | primary 'Yonemura, M.' 32 | primary 'Kobayashi, T.' 33 | primary 'Nagao, M.' 34 | primary 'Hirayama, M.' 35 | primary 'Kanno, R.' 36 | _cell_length_a 7.70829(11) 37 | _cell_length_b 6.53521(10) 38 | _cell_length_c 6.1365(7) 39 | _cell_angle_alpha 90. 40 | _cell_angle_beta 90. 41 | _cell_angle_gamma 90. 42 | _cell_volume 309.13 43 | _cell_formula_units_Z 2 44 | _space_group_name_H-M_alt 'P m n 21' 45 | _space_group_IT_number 31 46 | loop_ 47 | _space_group_symop_id 48 | _space_group_symop_operation_xyz 49 | 1 'x+1/2, -y, z+1/2' 50 | 2 '-x+1/2, -y, z+1/2' 51 | 3 '-x, y, z' 52 | 4 'x, y, z' 53 | loop_ 54 | _atom_type_symbol 55 | _atom_type_oxidation_number 56 | Li1+ 1 57 | P5+ 5 58 | S2- -2 59 | loop_ 60 | _atom_site_label 61 | _atom_site_type_symbol 62 | _atom_site_symmetry_multiplicity 63 | _atom_site_Wyckoff_symbol 64 | _atom_site_fract_x 65 | _atom_site_fract_y 66 | _atom_site_fract_z 67 | _atom_site_B_iso_or_equiv 68 | _atom_site_occupancy 69 | Li1 Li1+ 4 b 0.2502(4) 0.3309(5) 0.0179(3) 0.12(13) 1. 70 | Li2 Li1+ 2 a 0 0.145(2) 0.486(2) 0.12(13) 1. 71 | P1 P5+ 2 a 0 0.8218(3) 0.9942(3) 0.14(2) 1. 72 | S1 S2- 4 b 0.2185(17) 0.6717(2) 0.8857(2) 0.68(2) 0.97(3) 73 | S2 S2- 2 a 0 0.1083(4) 0.888(4) 0.59(6) 0.98(2) 74 | S3 S2- 2 a 0 0.8049(3) 0.3230(2) 0.77(3) 0.99(3) 75 | #End of TTdata_180318-ICSD -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_10_1/DOSCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_10_1/DOSCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_10_1/INCAR: -------------------------------------------------------------------------------- 1 | PREC = Accurate 2 | LREAL = Auto 3 | ALGO = Fast 4 | ENCUT = 400 5 | EDIFF = 1E-5 6 | ISMEAR = 0 7 | SIGMA = 0.05 8 | NBANDS = 704 9 | ISPIN = 2 10 | LORBIT = 11 11 | ICORELEVEL = 2 12 | CLNT = 1 13 | CLN = 1 14 | CLL = 0 15 | CLZ = 1.0 16 | CH_LSPEC = .TRUE. 17 | CH_SIGMA = 0.05 18 | LCHARG = .FALSE. 19 | LWAVE = .FALSE. -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_10_1/KPOINTS: -------------------------------------------------------------------------------- 1 | K-Points 2 | 0 3 | Gamma 4 | 3 3 3 5 | 0 0 0 6 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_10_1/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 0.118286308590E+04 0.11829E+04 -0.10156E+05 39424 0.342E+02 3 | DAV: 2 -0.262905815354E+03 -0.14458E+04 -0.13389E+04 51168 0.102E+02 4 | DAV: 3 -0.390590729306E+03 -0.12768E+03 -0.12578E+03 54208 0.286E+01 5 | DAV: 4 -0.399370437628E+03 -0.87797E+01 -0.87581E+01 62784 0.704E+00 6 | DAV: 5 -0.399470123334E+03 -0.99686E-01 -0.99677E-01 59200 0.739E-01 0.355E+01 7 | RMM: 6 -0.379646090907E+03 0.19824E+02 -0.14160E+01 45175 0.202E+00 0.168E+01 8 | RMM: 7 -0.390521174314E+03 -0.10875E+02 -0.44659E+00 51889 0.125E+00 0.884E+00 9 | RMM: 8 -0.395004537464E+03 -0.44834E+01 -0.94927E-01 50607 0.708E-01 0.430E+00 10 | RMM: 9 -0.396018906469E+03 -0.10144E+01 -0.27643E-01 54644 0.421E-01 0.145E+00 11 | RMM: 10 -0.396114202826E+03 -0.95296E-01 -0.10285E-01 60523 0.254E-01 0.617E-01 12 | RMM: 11 -0.396119169992E+03 -0.49672E-02 -0.22618E-02 62270 0.118E-01 0.341E-01 13 | RMM: 12 -0.396120764107E+03 -0.15941E-02 -0.35432E-03 61300 0.438E-02 0.128E-01 14 | RMM: 13 -0.396120775408E+03 -0.11301E-04 -0.82207E-04 62141 0.220E-02 0.466E-02 15 | RMM: 14 -0.396120740086E+03 0.35322E-04 -0.21747E-04 66527 0.985E-03 0.193E-02 16 | RMM: 15 -0.396120732720E+03 0.73668E-05 -0.36965E-05 60815 0.404E-03 17 | 1 F= -.39612073E+03 E0= -.39611678E+03 d E =-.791214E-02 mag= 0.8537 18 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_10_1/OUTCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_10_1/OUTCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_10_1/POSCAR: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892927170000000 0.0000000000000000 0.0000000000000000 4 | 2.6900120737000002 12.3583693090000004 0.0000000000000000 5 | 5.1267442849000000 2.5187865596000001 11.3793247881999999 6 | S Li P S 7 | 1 28 12 43 8 | Direct 9 | 0.6807149050000021 0.4703724680000008 0.9116758110000021 10 | 0.6687428950000012 0.1761630029999992 0.9039711949999969 11 | 0.6687428950000012 0.6761630179999969 0.9039711949999969 12 | 0.3312571940000026 0.3238356109999998 0.0960283880000006 13 | 0.3312571940000026 0.8238356109999998 0.0960283880000006 14 | 0.6114585400000010 0.3671709600000028 0.1147873399999995 15 | 0.6114585400000010 0.8671709300000003 0.1147873399999995 16 | 0.3885427709999973 0.1328279379999984 0.8852128979999989 17 | 0.3885427709999973 0.6328279379999984 0.8852128979999989 18 | 0.1778128300000006 0.0024677019999970 0.2979970570000035 19 | 0.1778128300000006 0.5024676920000033 0.2979970570000035 20 | 0.8221877220000025 0.4975320989999972 0.7020025850000025 21 | 0.8221877220000025 0.9975321289999997 0.7020025850000025 22 | 0.9686143400000020 0.2278184440000004 0.7495711449999973 23 | 0.9686143400000020 0.7278184290000027 0.7495711449999973 24 | 0.0313853099999974 0.2721820180000023 0.2504284979999980 25 | 0.0313853099999974 0.7721819879999998 0.2504284979999980 26 | 0.2949205039999967 0.0990733060000011 0.7023826240000020 27 | 0.2949205039999967 0.5990732910000034 0.7023826240000020 28 | 0.7050798539999974 0.4009267690000016 0.2976173460000027 29 | 0.7050798539999974 0.9009267690000016 0.2976173460000027 30 | 0.6723443870000025 0.1008888859999999 0.4994633499999992 31 | 0.6723443870000025 0.6008889080000017 0.4994633499999992 32 | 0.3276556730000024 0.3991113310000003 0.5005362630000008 33 | 0.3276556730000024 0.8991113310000003 0.5005362630000008 34 | 0.1361429840000028 0.3533565700000025 0.8824014070000032 35 | 0.1361429840000028 0.8533565999999979 0.8824014070000032 36 | 0.8638582230000011 0.1466431619999966 0.1175977739999965 37 | 0.8638582230000011 0.6466431619999966 0.1175977739999965 38 | 0.7769408229999968 0.3160540160000025 0.5498678679999998 39 | 0.7769408229999968 0.8160539869999965 0.5498678679999998 40 | 0.2230586109999990 0.1839460130000035 0.4501324000000011 41 | 0.2230586109999990 0.6839460130000035 0.4501324000000011 42 | 0.4720538259999998 0.3971497120000009 0.7272555229999966 43 | 0.4720538259999998 0.8971496819999984 0.7272555229999966 44 | 0.5279458170000026 0.1028505559999999 0.2727444169999984 45 | 0.5279458170000026 0.6028505559999999 0.2727444169999984 46 | 0.8348844650000018 0.4582849139999965 0.9417669179999990 47 | 0.8348844650000018 0.9582849140000036 0.9417669179999990 48 | 0.1651147449999968 0.0417154060000016 0.0582332390000033 49 | 0.1651147449999968 0.5417153839999997 0.0582332390000033 50 | 0.8209434150000021 0.2551785710000019 0.4022387269999967 51 | 0.8209434150000021 0.7551785710000019 0.4022387269999967 52 | 0.1790562119999990 0.2448210720000006 0.5977616309999974 53 | 0.1790562119999990 0.7448210720000006 0.5977616309999974 54 | 0.8125801679999967 0.2038727850000015 0.6833589669999967 55 | 0.8125801679999967 0.7038727999999992 0.6833589669999967 56 | 0.1874188330000024 0.2961274090000003 0.3166412409999992 57 | 0.1874188330000024 0.7961274390000028 0.3166412409999992 58 | 0.8374133109999988 0.4616349040000003 0.5170275569999987 59 | 0.8374133109999988 0.9616348739999978 0.5170275569999987 60 | 0.1625860779999968 0.0383653230000007 0.4829725330000016 61 | 0.1625860779999968 0.5383653040000027 0.4829725330000016 62 | 0.5900002719999975 0.3329958919999996 0.5765242579999992 63 | 0.5900002719999975 0.8329958919999996 0.5765242579999992 64 | 0.4099998180000028 0.1670047940000003 0.4234751159999988 65 | 0.4099998180000028 0.6670048240000028 0.4234751159999988 66 | 0.3173536059999975 0.4026352169999967 0.7017551060000002 67 | 0.3173536059999975 0.9026352169999967 0.7017551060000002 68 | 0.6826459170000021 0.0973652899999990 0.2982449229999986 69 | 0.6826459170000021 0.5973652599999966 0.2982449229999986 70 | 0.4775420429999997 0.2918528909999978 0.8781114820000013 71 | 0.4775420429999997 0.7918528909999978 0.8781114820000013 72 | 0.5224580759999995 0.2081471230000034 0.1218881309999986 73 | 0.5224580759999995 0.7081471090000022 0.1218881309999986 74 | 0.5083060259999996 0.0540041479999971 0.7046115990000033 75 | 0.5083060259999996 0.5540041329999994 0.7046115990000033 76 | 0.4916935560000013 0.4459961060000026 0.2953888480000018 77 | 0.4916935560000013 0.9459961060000026 0.2953888480000018 78 | 0.8208362459999989 0.3515947759999989 0.1006187719999971 79 | 0.8208362459999989 0.8515948060000014 0.1006187719999971 80 | 0.1791636049999994 0.1484049709999979 0.8993810420000017 81 | 0.1791636049999994 0.6484049560000003 0.8993810420000017 82 | 0.8585389850000027 0.1142017620000004 0.9433858390000012 83 | 0.8585389850000027 0.6142017840000022 0.9433858390000012 84 | 0.1414607910000001 0.3857982159999978 0.0566142830000018 85 | 0.1414607910000001 0.8857982159999978 0.0566142830000018 86 | 0.6807149050000021 0.9703724379999983 0.9116758110000021 87 | 0.3192848560000030 0.0296275580000014 0.0883243749999991 88 | 0.3192848560000030 0.5296275620000017 0.0883243749999991 89 | 0.9730954170000032 0.4071857630000011 0.8015559910000007 90 | 0.9730954170000032 0.9071857929999965 0.8015559910000007 91 | 0.0269045229999989 0.0928138049999987 0.1984439789999968 92 | 0.0269045229999989 0.5928137900000010 0.1984439789999968 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_10_1/vasp.out: -------------------------------------------------------------------------------- 1 | running on 32 total cores 2 | distrk: each k-point on 32 cores, 1 groups 3 | distr: one band on 1 cores, 32 groups 4 | using from now: INCAR 5 | vasp.6.1.1 19Jun20 (build Feb 22 2021 16:38:43) complex 6 | 7 | POSCAR found type information on POSCAR S LiP S 8 | POSCAR found : 4 types and 84 ions 9 | ----------------------------------------------------------------------------- 10 | | | 11 | | W W AA RRRRR N N II N N GGGG !!! | 12 | | W W A A R R NN N II NN N G G !!! | 13 | | W W A A R R N N N II N N N G !!! | 14 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 15 | | WW WW A A R R N NN II N NN G G | 16 | | W W A A R R N N II N N GGGG !!! | 17 | | | 18 | | You use a magnetic or noncollinear calculation, but did not specify | 19 | | the initial magnetic moment with the MAGMOM tag. Note that a | 20 | | default of 1 will be used for all atoms. This ferromagnetic setup | 21 | | may break the symmetry of the crystal, in particular it may rule | 22 | | out finding an antiferromagnetic solution. Thence, we recommend | 23 | | setting the initial magnetic moment manually or verifying carefully | 24 | | that this magnetic setup is desired. | 25 | | | 26 | ----------------------------------------------------------------------------- 27 | 28 | scaLAPACK will be used 29 | ----------------------------------------------------------------------------- 30 | | | 31 | | W W AA RRRRR N N II N N GGGG !!! | 32 | | W W A A R R NN N II NN N G G !!! | 33 | | W W A A R R N N N II N N N G !!! | 34 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 35 | | WW WW A A R R N NN II N NN G G | 36 | | W W A A R R N N II N N GGGG !!! | 37 | | | 38 | | For optimal performance we recommend to set | 39 | | NCORE = 4 - approx SQRT(number of cores). | 40 | | NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). | 41 | | This setting can greatly improve the performance of VASP for DFT. | 42 | | The default, NCORE=1 might be grossly inefficient on modern | 43 | | multi-core architectures or massively parallel machines. Do your | 44 | | own testing!!!! | 45 | | Unfortunately you need to use the default for GW and RPA | 46 | | calculations (for HF NCORE is supported but not extensively tested | 47 | | yet). | 48 | | | 49 | ----------------------------------------------------------------------------- 50 | 51 | LDA part: xc-table for Ceperly-Alder, standard interpolation 52 | POSCAR, INCAR and KPOINTS ok, starting setup 53 | FFT: planning ... 54 | WAVECAR not read 55 | entering main loop 56 | N E dE d eps ncg rms rms(c) 57 | DAV: 1 0.118286308590E+04 0.11829E+04 -0.10156E+05 39424 0.342E+02 58 | DAV: 2 -0.262905815354E+03 -0.14458E+04 -0.13389E+04 51168 0.102E+02 59 | DAV: 3 -0.390590729306E+03 -0.12768E+03 -0.12578E+03 54208 0.286E+01 60 | DAV: 4 -0.399370437628E+03 -0.87797E+01 -0.87581E+01 62784 0.704E+00 61 | DAV: 5 -0.399470123334E+03 -0.99686E-01 -0.99677E-01 59200 0.739E-01 0.355E+01 62 | RMM: 6 -0.379646090907E+03 0.19824E+02 -0.14160E+01 45175 0.202E+00 0.168E+01 63 | RMM: 7 -0.390521174314E+03 -0.10875E+02 -0.44659E+00 51889 0.125E+00 0.884E+00 64 | RMM: 8 -0.395004537464E+03 -0.44834E+01 -0.94927E-01 50607 0.708E-01 0.430E+00 65 | RMM: 9 -0.396018906469E+03 -0.10144E+01 -0.27643E-01 54644 0.421E-01 0.145E+00 66 | RMM: 10 -0.396114202826E+03 -0.95296E-01 -0.10285E-01 60523 0.254E-01 0.617E-01 67 | RMM: 11 -0.396119169992E+03 -0.49672E-02 -0.22618E-02 62270 0.118E-01 0.341E-01 68 | RMM: 12 -0.396120764107E+03 -0.15941E-02 -0.35432E-03 61300 0.438E-02 0.128E-01 69 | RMM: 13 -0.396120775408E+03 -0.11301E-04 -0.82207E-04 62141 0.220E-02 0.466E-02 70 | RMM: 14 -0.396120740086E+03 0.35322E-04 -0.21747E-04 66527 0.985E-03 0.193E-02 71 | RMM: 15 -0.396120732720E+03 0.73668E-05 -0.36965E-05 60815 0.404E-03 72 | 1 F= -.39612073E+03 E0= -.39611678E+03 d E =-.791214E-02 mag= 0.8537 73 | Starting Core_Hole_Spec 74 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 75 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 76 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 77 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 78 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 79 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 80 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 81 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 82 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 83 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 84 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 85 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 86 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 87 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 88 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 89 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 90 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 91 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 92 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 93 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 94 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 95 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 96 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 97 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 98 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 99 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 100 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 101 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 102 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 103 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 104 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 105 | Ending Core_Hole_Spec 106 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_11_1/DOSCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_11_1/DOSCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_11_1/INCAR: -------------------------------------------------------------------------------- 1 | PREC = Accurate 2 | LREAL = Auto 3 | ALGO = Fast 4 | ENCUT = 400 5 | EDIFF = 1E-5 6 | ISMEAR = 0 7 | SIGMA = 0.05 8 | NBANDS = 704 9 | ISPIN = 2 10 | LORBIT = 11 11 | ICORELEVEL = 2 12 | CLNT = 1 13 | CLN = 1 14 | CLL = 0 15 | CLZ = 1.0 16 | CH_LSPEC = .TRUE. 17 | CH_SIGMA = 0.05 18 | LCHARG = .FALSE. 19 | LWAVE = .FALSE. -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_11_1/KPOINTS: -------------------------------------------------------------------------------- 1 | K-Points 2 | 0 3 | Gamma 4 | 3 3 3 5 | 0 0 0 6 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_11_1/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 0.118284431738E+04 0.11828E+04 -0.10156E+05 39424 0.342E+02 3 | DAV: 2 -0.262906669884E+03 -0.14458E+04 -0.13390E+04 51232 0.102E+02 4 | DAV: 3 -0.390664145376E+03 -0.12776E+03 -0.12585E+03 54048 0.286E+01 5 | DAV: 4 -0.399438127184E+03 -0.87740E+01 -0.87524E+01 62656 0.704E+00 6 | DAV: 5 -0.399537885996E+03 -0.99759E-01 -0.99750E-01 59136 0.737E-01 0.355E+01 7 | RMM: 6 -0.379674095150E+03 0.19864E+02 -0.14251E+01 45130 0.204E+00 0.168E+01 8 | RMM: 7 -0.390529909554E+03 -0.10856E+02 -0.45258E+00 51733 0.125E+00 0.882E+00 9 | RMM: 8 -0.395027107199E+03 -0.44972E+01 -0.92952E-01 50687 0.703E-01 0.427E+00 10 | RMM: 9 -0.396036672258E+03 -0.10096E+01 -0.27457E-01 54490 0.422E-01 0.143E+00 11 | RMM: 10 -0.396123983194E+03 -0.87311E-01 -0.10205E-01 60683 0.254E-01 0.582E-01 12 | RMM: 11 -0.396128442356E+03 -0.44592E-02 -0.21669E-02 63068 0.116E-01 0.314E-01 13 | RMM: 12 -0.396129689820E+03 -0.12475E-02 -0.33766E-03 60783 0.427E-02 0.112E-01 14 | RMM: 13 -0.396129655333E+03 0.34487E-04 -0.80354E-04 63137 0.215E-02 0.363E-02 15 | RMM: 14 -0.396129637596E+03 0.17737E-04 -0.20407E-04 67568 0.926E-03 0.180E-02 16 | RMM: 15 -0.396129630918E+03 0.66789E-05 -0.30313E-05 58747 0.369E-03 17 | 1 F= -.39612963E+03 E0= -.39612744E+03 d E =-.438266E-02 mag= 0.9320 18 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_11_1/OUTCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_11_1/OUTCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_11_1/POSCAR: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892927170000000 0.0000000000000000 0.0000000000000000 4 | 2.6900120737000002 12.3583693090000004 0.0000000000000000 5 | 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0.9703724379999983 0.9116758110000021 88 | 0.3192848560000030 0.0296275580000014 0.0883243749999991 89 | 0.3192848560000030 0.5296275620000017 0.0883243749999991 90 | 0.9730954170000032 0.9071857929999965 0.8015559910000007 91 | 0.0269045229999989 0.0928138049999987 0.1984439789999968 92 | 0.0269045229999989 0.5928137900000010 0.1984439789999968 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_11_1/vasp.out: -------------------------------------------------------------------------------- 1 | running on 32 total cores 2 | distrk: each k-point on 32 cores, 1 groups 3 | distr: one band on 1 cores, 32 groups 4 | using from now: INCAR 5 | vasp.6.1.1 19Jun20 (build Feb 22 2021 16:38:43) complex 6 | 7 | POSCAR found type information on POSCAR S LiP S 8 | POSCAR found : 4 types and 84 ions 9 | ----------------------------------------------------------------------------- 10 | | | 11 | | W W AA RRRRR N N II N N GGGG !!! | 12 | | W W A A R R NN N II NN N G G !!! | 13 | | W W A A R R N N N II N N N G !!! | 14 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 15 | | WW WW A A R R N NN II N NN G G | 16 | | W W A A R R N N II N N GGGG !!! | 17 | | | 18 | | You use a magnetic or noncollinear calculation, but did not specify | 19 | | the initial magnetic moment with the MAGMOM tag. Note that a | 20 | | default of 1 will be used for all atoms. This ferromagnetic setup | 21 | | may break the symmetry of the crystal, in particular it may rule | 22 | | out finding an antiferromagnetic solution. Thence, we recommend | 23 | | setting the initial magnetic moment manually or verifying carefully | 24 | | that this magnetic setup is desired. | 25 | | | 26 | ----------------------------------------------------------------------------- 27 | 28 | scaLAPACK will be used 29 | ----------------------------------------------------------------------------- 30 | | | 31 | | W W AA RRRRR N N II N N GGGG !!! | 32 | | W W A A R R NN N II NN N G G !!! | 33 | | W W A A R R N N N II N N N G !!! | 34 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 35 | | WW WW A A R R N NN II N NN G G | 36 | | W W A A R R N N II N N GGGG !!! | 37 | | | 38 | | For optimal performance we recommend to set | 39 | | NCORE = 4 - approx SQRT(number of cores). | 40 | | NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). | 41 | | This setting can greatly improve the performance of VASP for DFT. | 42 | | The default, NCORE=1 might be grossly inefficient on modern | 43 | | multi-core architectures or massively parallel machines. Do your | 44 | | own testing!!!! | 45 | | Unfortunately you need to use the default for GW and RPA | 46 | | calculations (for HF NCORE is supported but not extensively tested | 47 | | yet). | 48 | | | 49 | ----------------------------------------------------------------------------- 50 | 51 | LDA part: xc-table for Ceperly-Alder, standard interpolation 52 | POSCAR, INCAR and KPOINTS ok, starting setup 53 | FFT: planning ... 54 | WAVECAR not read 55 | entering main loop 56 | N E dE d eps ncg rms rms(c) 57 | DAV: 1 0.118284431738E+04 0.11828E+04 -0.10156E+05 39424 0.342E+02 58 | DAV: 2 -0.262906669884E+03 -0.14458E+04 -0.13390E+04 51232 0.102E+02 59 | DAV: 3 -0.390664145376E+03 -0.12776E+03 -0.12585E+03 54048 0.286E+01 60 | DAV: 4 -0.399438127184E+03 -0.87740E+01 -0.87524E+01 62656 0.704E+00 61 | DAV: 5 -0.399537885996E+03 -0.99759E-01 -0.99750E-01 59136 0.737E-01 0.355E+01 62 | RMM: 6 -0.379674095150E+03 0.19864E+02 -0.14251E+01 45130 0.204E+00 0.168E+01 63 | RMM: 7 -0.390529909554E+03 -0.10856E+02 -0.45258E+00 51733 0.125E+00 0.882E+00 64 | RMM: 8 -0.395027107199E+03 -0.44972E+01 -0.92952E-01 50687 0.703E-01 0.427E+00 65 | RMM: 9 -0.396036672258E+03 -0.10096E+01 -0.27457E-01 54490 0.422E-01 0.143E+00 66 | RMM: 10 -0.396123983194E+03 -0.87311E-01 -0.10205E-01 60683 0.254E-01 0.582E-01 67 | RMM: 11 -0.396128442356E+03 -0.44592E-02 -0.21669E-02 63068 0.116E-01 0.314E-01 68 | RMM: 12 -0.396129689820E+03 -0.12475E-02 -0.33766E-03 60783 0.427E-02 0.112E-01 69 | RMM: 13 -0.396129655333E+03 0.34487E-04 -0.80354E-04 63137 0.215E-02 0.363E-02 70 | RMM: 14 -0.396129637596E+03 0.17737E-04 -0.20407E-04 67568 0.926E-03 0.180E-02 71 | RMM: 15 -0.396129630918E+03 0.66789E-05 -0.30313E-05 58747 0.369E-03 72 | 1 F= -.39612963E+03 E0= -.39612744E+03 d E =-.438266E-02 mag= 0.9320 73 | Starting Core_Hole_Spec 74 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 75 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 76 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 77 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 78 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 79 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 80 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 81 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 82 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 83 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 84 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 85 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 86 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 87 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 88 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 89 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 90 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 91 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 92 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 93 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 94 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 95 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 96 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 97 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 98 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 99 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 100 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 101 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 102 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 103 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 104 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 105 | Ending Core_Hole_Spec 106 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_1_1/DOSCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_1_1/DOSCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_1_1/INCAR: -------------------------------------------------------------------------------- 1 | PREC = Accurate 2 | LREAL = Auto 3 | ALGO = Fast 4 | ENCUT = 400 5 | EDIFF = 1E-5 6 | ISMEAR = 0 7 | SIGMA = 0.05 8 | NBANDS = 704 9 | ISPIN = 2 10 | LORBIT = 11 11 | ICORELEVEL = 2 12 | CLNT = 1 13 | CLN = 1 14 | CLL = 0 15 | CLZ = 1.0 16 | CH_LSPEC = .TRUE. 17 | CH_SIGMA = 0.05 18 | LCHARG = .FALSE. 19 | LWAVE = .FALSE. -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_1_1/KPOINTS: -------------------------------------------------------------------------------- 1 | K-Points 2 | 0 3 | Gamma 4 | 3 3 3 5 | 0 0 0 6 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_1_1/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 0.118257754379E+04 0.11826E+04 -0.10156E+05 39424 0.342E+02 3 | DAV: 2 -0.262992468845E+03 -0.14456E+04 -0.13388E+04 51136 0.102E+02 4 | DAV: 3 -0.390704996756E+03 -0.12771E+03 -0.12581E+03 53856 0.286E+01 5 | DAV: 4 -0.399469115211E+03 -0.87641E+01 -0.87423E+01 62816 0.704E+00 6 | DAV: 5 -0.399568640739E+03 -0.99526E-01 -0.99517E-01 58976 0.735E-01 0.355E+01 7 | RMM: 6 -0.379591517172E+03 0.19977E+02 -0.14348E+01 45224 0.207E+00 0.168E+01 8 | RMM: 7 -0.390455737567E+03 -0.10864E+02 -0.45303E+00 51765 0.126E+00 0.884E+00 9 | RMM: 8 -0.394994058618E+03 -0.45383E+01 -0.99176E-01 50841 0.715E-01 0.423E+00 10 | RMM: 9 -0.395973248959E+03 -0.97919E+00 -0.28010E-01 54571 0.429E-01 0.144E+00 11 | RMM: 10 -0.396060132773E+03 -0.86884E-01 -0.10647E-01 60600 0.257E-01 0.582E-01 12 | RMM: 11 -0.396064183225E+03 -0.40505E-02 -0.21871E-02 63254 0.116E-01 0.309E-01 13 | RMM: 12 -0.396065071430E+03 -0.88820E-03 -0.34432E-03 60222 0.429E-02 0.102E-01 14 | RMM: 13 -0.396064973989E+03 0.97441E-04 -0.81072E-04 64220 0.213E-02 0.327E-02 15 | RMM: 14 -0.396064956304E+03 0.17685E-04 -0.18796E-04 68328 0.872E-03 0.177E-02 16 | RMM: 15 -0.396064946256E+03 0.10047E-04 -0.25893E-05 57705 0.351E-03 0.830E-03 17 | RMM: 16 -0.396064943026E+03 0.32304E-05 -0.53284E-06 44376 0.232E-03 18 | 1 F= -.39606494E+03 E0= -.39606409E+03 d E =-.171133E-02 mag= 0.9769 19 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_1_1/OUTCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_1_1/OUTCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_1_1/POSCAR: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892927170000000 0.0000000000000000 0.0000000000000000 4 | 2.6900120737000002 12.3583693090000004 0.0000000000000000 5 | 5.1267442849000000 2.5187865596000001 11.3793247881999999 6 | S Li P S 7 | 1 28 12 43 8 | Direct 9 | 0.8209434150000021 0.2551785710000019 0.4022387269999967 10 | 0.6687428950000012 0.1761630029999992 0.9039711949999969 11 | 0.6687428950000012 0.6761630179999969 0.9039711949999969 12 | 0.3312571940000026 0.3238356109999998 0.0960283880000006 13 | 0.3312571940000026 0.8238356109999998 0.0960283880000006 14 | 0.6114585400000010 0.3671709600000028 0.1147873399999995 15 | 0.6114585400000010 0.8671709300000003 0.1147873399999995 16 | 0.3885427709999973 0.1328279379999984 0.8852128979999989 17 | 0.3885427709999973 0.6328279379999984 0.8852128979999989 18 | 0.1778128300000006 0.0024677019999970 0.2979970570000035 19 | 0.1778128300000006 0.5024676920000033 0.2979970570000035 20 | 0.8221877220000025 0.4975320989999972 0.7020025850000025 21 | 0.8221877220000025 0.9975321289999997 0.7020025850000025 22 | 0.9686143400000020 0.2278184440000004 0.7495711449999973 23 | 0.9686143400000020 0.7278184290000027 0.7495711449999973 24 | 0.0313853099999974 0.2721820180000023 0.2504284979999980 25 | 0.0313853099999974 0.7721819879999998 0.2504284979999980 26 | 0.2949205039999967 0.0990733060000011 0.7023826240000020 27 | 0.2949205039999967 0.5990732910000034 0.7023826240000020 28 | 0.7050798539999974 0.4009267690000016 0.2976173460000027 29 | 0.7050798539999974 0.9009267690000016 0.2976173460000027 30 | 0.6723443870000025 0.1008888859999999 0.4994633499999992 31 | 0.6723443870000025 0.6008889080000017 0.4994633499999992 32 | 0.3276556730000024 0.3991113310000003 0.5005362630000008 33 | 0.3276556730000024 0.8991113310000003 0.5005362630000008 34 | 0.1361429840000028 0.3533565700000025 0.8824014070000032 35 | 0.1361429840000028 0.8533565999999979 0.8824014070000032 36 | 0.8638582230000011 0.1466431619999966 0.1175977739999965 37 | 0.8638582230000011 0.6466431619999966 0.1175977739999965 38 | 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0.8125801679999967 0.7038727999999992 0.6833589669999967 55 | 0.1874188330000024 0.2961274090000003 0.3166412409999992 56 | 0.1874188330000024 0.7961274390000028 0.3166412409999992 57 | 0.8374133109999988 0.4616349040000003 0.5170275569999987 58 | 0.8374133109999988 0.9616348739999978 0.5170275569999987 59 | 0.1625860779999968 0.0383653230000007 0.4829725330000016 60 | 0.1625860779999968 0.5383653040000027 0.4829725330000016 61 | 0.5900002719999975 0.3329958919999996 0.5765242579999992 62 | 0.5900002719999975 0.8329958919999996 0.5765242579999992 63 | 0.4099998180000028 0.1670047940000003 0.4234751159999988 64 | 0.4099998180000028 0.6670048240000028 0.4234751159999988 65 | 0.3173536059999975 0.4026352169999967 0.7017551060000002 66 | 0.3173536059999975 0.9026352169999967 0.7017551060000002 67 | 0.6826459170000021 0.0973652899999990 0.2982449229999986 68 | 0.6826459170000021 0.5973652599999966 0.2982449229999986 69 | 0.4775420429999997 0.2918528909999978 0.8781114820000013 70 | 0.4775420429999997 0.7918528909999978 0.8781114820000013 71 | 0.5224580759999995 0.2081471230000034 0.1218881309999986 72 | 0.5224580759999995 0.7081471090000022 0.1218881309999986 73 | 0.5083060259999996 0.0540041479999971 0.7046115990000033 74 | 0.5083060259999996 0.5540041329999994 0.7046115990000033 75 | 0.4916935560000013 0.4459961060000026 0.2953888480000018 76 | 0.4916935560000013 0.9459961060000026 0.2953888480000018 77 | 0.8208362459999989 0.3515947759999989 0.1006187719999971 78 | 0.8208362459999989 0.8515948060000014 0.1006187719999971 79 | 0.1791636049999994 0.1484049709999979 0.8993810420000017 80 | 0.1791636049999994 0.6484049560000003 0.8993810420000017 81 | 0.8585389850000027 0.1142017620000004 0.9433858390000012 82 | 0.8585389850000027 0.6142017840000022 0.9433858390000012 83 | 0.1414607910000001 0.3857982159999978 0.0566142830000018 84 | 0.1414607910000001 0.8857982159999978 0.0566142830000018 85 | 0.6807149050000021 0.4703724680000008 0.9116758110000021 86 | 0.6807149050000021 0.9703724379999983 0.9116758110000021 87 | 0.3192848560000030 0.0296275580000014 0.0883243749999991 88 | 0.3192848560000030 0.5296275620000017 0.0883243749999991 89 | 0.9730954170000032 0.4071857630000011 0.8015559910000007 90 | 0.9730954170000032 0.9071857929999965 0.8015559910000007 91 | 0.0269045229999989 0.0928138049999987 0.1984439789999968 92 | 0.0269045229999989 0.5928137900000010 0.1984439789999968 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_1_1/vasp.out: -------------------------------------------------------------------------------- 1 | running on 32 total cores 2 | distrk: each k-point on 32 cores, 1 groups 3 | distr: one band on 1 cores, 32 groups 4 | using from now: INCAR 5 | vasp.6.1.1 19Jun20 (build Feb 22 2021 16:38:43) complex 6 | 7 | POSCAR found type information on POSCAR S LiP S 8 | POSCAR found : 4 types and 84 ions 9 | ----------------------------------------------------------------------------- 10 | | | 11 | | W W AA RRRRR N N II N N GGGG !!! | 12 | | W W A A R R NN N II NN N G G !!! | 13 | | W W A A R R N N N II N N N G !!! | 14 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 15 | | WW WW A A R R N NN II N NN G G | 16 | | W W A A R R N N II N N GGGG !!! | 17 | | | 18 | | You use a magnetic or noncollinear calculation, but did not specify | 19 | | the initial magnetic moment with the MAGMOM tag. Note that a | 20 | | default of 1 will be used for all atoms. This ferromagnetic setup | 21 | | may break the symmetry of the crystal, in particular it may rule | 22 | | out finding an antiferromagnetic solution. Thence, we recommend | 23 | | setting the initial magnetic moment manually or verifying carefully | 24 | | that this magnetic setup is desired. | 25 | | | 26 | ----------------------------------------------------------------------------- 27 | 28 | scaLAPACK will be used 29 | ----------------------------------------------------------------------------- 30 | | | 31 | | W W AA RRRRR N N II N N GGGG !!! | 32 | | W W A A R R NN N II NN N G G !!! | 33 | | W W A A R R N N N II N N N G !!! | 34 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 35 | | WW WW A A R R N NN II N NN G G | 36 | | W W A A R R N N II N N GGGG !!! | 37 | | | 38 | | For optimal performance we recommend to set | 39 | | NCORE = 4 - approx SQRT(number of cores). | 40 | | NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). | 41 | | This setting can greatly improve the performance of VASP for DFT. | 42 | | The default, NCORE=1 might be grossly inefficient on modern | 43 | | multi-core architectures or massively parallel machines. Do your | 44 | | own testing!!!! | 45 | | Unfortunately you need to use the default for GW and RPA | 46 | | calculations (for HF NCORE is supported but not extensively tested | 47 | | yet). | 48 | | | 49 | ----------------------------------------------------------------------------- 50 | 51 | LDA part: xc-table for Ceperly-Alder, standard interpolation 52 | POSCAR, INCAR and KPOINTS ok, starting setup 53 | FFT: planning ... 54 | WAVECAR not read 55 | entering main loop 56 | N E dE d eps ncg rms rms(c) 57 | DAV: 1 0.118257754379E+04 0.11826E+04 -0.10156E+05 39424 0.342E+02 58 | DAV: 2 -0.262992468845E+03 -0.14456E+04 -0.13388E+04 51136 0.102E+02 59 | DAV: 3 -0.390704996756E+03 -0.12771E+03 -0.12581E+03 53856 0.286E+01 60 | DAV: 4 -0.399469115211E+03 -0.87641E+01 -0.87423E+01 62816 0.704E+00 61 | DAV: 5 -0.399568640739E+03 -0.99526E-01 -0.99517E-01 58976 0.735E-01 0.355E+01 62 | RMM: 6 -0.379591517172E+03 0.19977E+02 -0.14348E+01 45224 0.207E+00 0.168E+01 63 | RMM: 7 -0.390455737567E+03 -0.10864E+02 -0.45303E+00 51765 0.126E+00 0.884E+00 64 | RMM: 8 -0.394994058618E+03 -0.45383E+01 -0.99176E-01 50841 0.715E-01 0.423E+00 65 | RMM: 9 -0.395973248959E+03 -0.97919E+00 -0.28010E-01 54571 0.429E-01 0.144E+00 66 | RMM: 10 -0.396060132773E+03 -0.86884E-01 -0.10647E-01 60600 0.257E-01 0.582E-01 67 | RMM: 11 -0.396064183225E+03 -0.40505E-02 -0.21871E-02 63254 0.116E-01 0.309E-01 68 | RMM: 12 -0.396065071430E+03 -0.88820E-03 -0.34432E-03 60222 0.429E-02 0.102E-01 69 | RMM: 13 -0.396064973989E+03 0.97441E-04 -0.81072E-04 64220 0.213E-02 0.327E-02 70 | RMM: 14 -0.396064956304E+03 0.17685E-04 -0.18796E-04 68328 0.872E-03 0.177E-02 71 | RMM: 15 -0.396064946256E+03 0.10047E-04 -0.25893E-05 57705 0.351E-03 0.830E-03 72 | RMM: 16 -0.396064943026E+03 0.32304E-05 -0.53284E-06 44376 0.232E-03 73 | 1 F= -.39606494E+03 E0= -.39606409E+03 d E =-.171133E-02 mag= 0.9769 74 | Starting Core_Hole_Spec 75 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 76 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 77 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 78 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 79 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 80 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 81 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 82 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 83 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 84 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 85 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 86 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 87 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 88 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 89 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 90 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 91 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 92 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 93 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 94 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 95 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 96 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 97 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 98 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 99 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 100 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 101 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 102 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 103 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 104 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 105 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 106 | Ending Core_Hole_Spec 107 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_2_1/DOSCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_2_1/DOSCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_2_1/INCAR: -------------------------------------------------------------------------------- 1 | PREC = Accurate 2 | LREAL = Auto 3 | ALGO = Fast 4 | ENCUT = 400 5 | EDIFF = 1E-5 6 | ISMEAR = 0 7 | SIGMA = 0.05 8 | NBANDS = 704 9 | ISPIN = 2 10 | LORBIT = 11 11 | ICORELEVEL = 2 12 | CLNT = 1 13 | CLN = 1 14 | CLL = 0 15 | CLZ = 1.0 16 | CH_LSPEC = .TRUE. 17 | CH_SIGMA = 0.05 18 | LCHARG = .FALSE. 19 | LWAVE = .FALSE. -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_2_1/KPOINTS: -------------------------------------------------------------------------------- 1 | K-Points 2 | 0 3 | Gamma 4 | 3 3 3 5 | 0 0 0 6 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_2_1/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 0.118263564927E+04 0.11826E+04 -0.10156E+05 39424 0.342E+02 3 | DAV: 2 -0.262917178386E+03 -0.14456E+04 -0.13388E+04 51264 0.102E+02 4 | DAV: 3 -0.390638122431E+03 -0.12772E+03 -0.12582E+03 54112 0.286E+01 5 | DAV: 4 -0.399423781153E+03 -0.87857E+01 -0.87639E+01 62912 0.706E+00 6 | DAV: 5 -0.399522997543E+03 -0.99216E-01 -0.99207E-01 59008 0.735E-01 0.355E+01 7 | RMM: 6 -0.379678486282E+03 0.19845E+02 -0.14235E+01 45099 0.205E+00 0.168E+01 8 | RMM: 7 -0.390556935183E+03 -0.10878E+02 -0.45327E+00 51882 0.127E+00 0.882E+00 9 | RMM: 8 -0.395084228613E+03 -0.45273E+01 -0.99301E-01 50847 0.718E-01 0.424E+00 10 | RMM: 9 -0.396067667037E+03 -0.98344E+00 -0.28021E-01 54549 0.429E-01 0.143E+00 11 | RMM: 10 -0.396152577828E+03 -0.84911E-01 -0.10626E-01 60672 0.257E-01 0.569E-01 12 | RMM: 11 -0.396156431816E+03 -0.38540E-02 -0.21773E-02 63657 0.116E-01 0.303E-01 13 | RMM: 12 -0.396157258837E+03 -0.82702E-03 -0.34065E-03 60286 0.429E-02 0.983E-02 14 | RMM: 13 -0.396157179755E+03 0.79083E-04 -0.82705E-04 64691 0.215E-02 0.319E-02 15 | RMM: 14 -0.396157164374E+03 0.15380E-04 -0.18748E-04 68084 0.865E-03 0.174E-02 16 | RMM: 15 -0.396157155016E+03 0.93582E-05 -0.28734E-05 57058 0.361E-03 17 | 1 F= -.39615716E+03 E0= -.39615687E+03 d E =-.577028E-03 mag= 0.9911 18 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_2_1/OUTCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_2_1/OUTCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_2_1/POSCAR: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892927170000000 0.0000000000000000 0.0000000000000000 4 | 2.6900120737000002 12.3583693090000004 0.0000000000000000 5 | 5.1267442849000000 2.5187865596000001 11.3793247881999999 6 | S Li P S 7 | 1 28 12 43 8 | Direct 9 | 0.8125801679999967 0.2038727850000015 0.6833589669999967 10 | 0.6687428950000012 0.1761630029999992 0.9039711949999969 11 | 0.6687428950000012 0.6761630179999969 0.9039711949999969 12 | 0.3312571940000026 0.3238356109999998 0.0960283880000006 13 | 0.3312571940000026 0.8238356109999998 0.0960283880000006 14 | 0.6114585400000010 0.3671709600000028 0.1147873399999995 15 | 0.6114585400000010 0.8671709300000003 0.1147873399999995 16 | 0.3885427709999973 0.1328279379999984 0.8852128979999989 17 | 0.3885427709999973 0.6328279379999984 0.8852128979999989 18 | 0.1778128300000006 0.0024677019999970 0.2979970570000035 19 | 0.1778128300000006 0.5024676920000033 0.2979970570000035 20 | 0.8221877220000025 0.4975320989999972 0.7020025850000025 21 | 0.8221877220000025 0.9975321289999997 0.7020025850000025 22 | 0.9686143400000020 0.2278184440000004 0.7495711449999973 23 | 0.9686143400000020 0.7278184290000027 0.7495711449999973 24 | 0.0313853099999974 0.2721820180000023 0.2504284979999980 25 | 0.0313853099999974 0.7721819879999998 0.2504284979999980 26 | 0.2949205039999967 0.0990733060000011 0.7023826240000020 27 | 0.2949205039999967 0.5990732910000034 0.7023826240000020 28 | 0.7050798539999974 0.4009267690000016 0.2976173460000027 29 | 0.7050798539999974 0.9009267690000016 0.2976173460000027 30 | 0.6723443870000025 0.1008888859999999 0.4994633499999992 31 | 0.6723443870000025 0.6008889080000017 0.4994633499999992 32 | 0.3276556730000024 0.3991113310000003 0.5005362630000008 33 | 0.3276556730000024 0.8991113310000003 0.5005362630000008 34 | 0.1361429840000028 0.3533565700000025 0.8824014070000032 35 | 0.1361429840000028 0.8533565999999979 0.8824014070000032 36 | 0.8638582230000011 0.1466431619999966 0.1175977739999965 37 | 0.8638582230000011 0.6466431619999966 0.1175977739999965 38 | 0.7769408229999968 0.3160540160000025 0.5498678679999998 39 | 0.7769408229999968 0.8160539869999965 0.5498678679999998 40 | 0.2230586109999990 0.1839460130000035 0.4501324000000011 41 | 0.2230586109999990 0.6839460130000035 0.4501324000000011 42 | 0.4720538259999998 0.3971497120000009 0.7272555229999966 43 | 0.4720538259999998 0.8971496819999984 0.7272555229999966 44 | 0.5279458170000026 0.1028505559999999 0.2727444169999984 45 | 0.5279458170000026 0.6028505559999999 0.2727444169999984 46 | 0.8348844650000018 0.4582849139999965 0.9417669179999990 47 | 0.8348844650000018 0.9582849140000036 0.9417669179999990 48 | 0.1651147449999968 0.0417154060000016 0.0582332390000033 49 | 0.1651147449999968 0.5417153839999997 0.0582332390000033 50 | 0.8209434150000021 0.2551785710000019 0.4022387269999967 51 | 0.8209434150000021 0.7551785710000019 0.4022387269999967 52 | 0.1790562119999990 0.2448210720000006 0.5977616309999974 53 | 0.1790562119999990 0.7448210720000006 0.5977616309999974 54 | 0.8125801679999967 0.7038727999999992 0.6833589669999967 55 | 0.1874188330000024 0.2961274090000003 0.3166412409999992 56 | 0.1874188330000024 0.7961274390000028 0.3166412409999992 57 | 0.8374133109999988 0.4616349040000003 0.5170275569999987 58 | 0.8374133109999988 0.9616348739999978 0.5170275569999987 59 | 0.1625860779999968 0.0383653230000007 0.4829725330000016 60 | 0.1625860779999968 0.5383653040000027 0.4829725330000016 61 | 0.5900002719999975 0.3329958919999996 0.5765242579999992 62 | 0.5900002719999975 0.8329958919999996 0.5765242579999992 63 | 0.4099998180000028 0.1670047940000003 0.4234751159999988 64 | 0.4099998180000028 0.6670048240000028 0.4234751159999988 65 | 0.3173536059999975 0.4026352169999967 0.7017551060000002 66 | 0.3173536059999975 0.9026352169999967 0.7017551060000002 67 | 0.6826459170000021 0.0973652899999990 0.2982449229999986 68 | 0.6826459170000021 0.5973652599999966 0.2982449229999986 69 | 0.4775420429999997 0.2918528909999978 0.8781114820000013 70 | 0.4775420429999997 0.7918528909999978 0.8781114820000013 71 | 0.5224580759999995 0.2081471230000034 0.1218881309999986 72 | 0.5224580759999995 0.7081471090000022 0.1218881309999986 73 | 0.5083060259999996 0.0540041479999971 0.7046115990000033 74 | 0.5083060259999996 0.5540041329999994 0.7046115990000033 75 | 0.4916935560000013 0.4459961060000026 0.2953888480000018 76 | 0.4916935560000013 0.9459961060000026 0.2953888480000018 77 | 0.8208362459999989 0.3515947759999989 0.1006187719999971 78 | 0.8208362459999989 0.8515948060000014 0.1006187719999971 79 | 0.1791636049999994 0.1484049709999979 0.8993810420000017 80 | 0.1791636049999994 0.6484049560000003 0.8993810420000017 81 | 0.8585389850000027 0.1142017620000004 0.9433858390000012 82 | 0.8585389850000027 0.6142017840000022 0.9433858390000012 83 | 0.1414607910000001 0.3857982159999978 0.0566142830000018 84 | 0.1414607910000001 0.8857982159999978 0.0566142830000018 85 | 0.6807149050000021 0.4703724680000008 0.9116758110000021 86 | 0.6807149050000021 0.9703724379999983 0.9116758110000021 87 | 0.3192848560000030 0.0296275580000014 0.0883243749999991 88 | 0.3192848560000030 0.5296275620000017 0.0883243749999991 89 | 0.9730954170000032 0.4071857630000011 0.8015559910000007 90 | 0.9730954170000032 0.9071857929999965 0.8015559910000007 91 | 0.0269045229999989 0.0928138049999987 0.1984439789999968 92 | 0.0269045229999989 0.5928137900000010 0.1984439789999968 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_2_1/vasp.out: -------------------------------------------------------------------------------- 1 | running on 32 total cores 2 | distrk: each k-point on 32 cores, 1 groups 3 | distr: one band on 1 cores, 32 groups 4 | using from now: INCAR 5 | vasp.6.1.1 19Jun20 (build Feb 22 2021 16:38:43) complex 6 | 7 | POSCAR found type information on POSCAR S LiP S 8 | POSCAR found : 4 types and 84 ions 9 | ----------------------------------------------------------------------------- 10 | | | 11 | | W W AA RRRRR N N II N N GGGG !!! | 12 | | W W A A R R NN N II NN N G G !!! | 13 | | W W A A R R N N N II N N N G !!! | 14 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 15 | | WW WW A A R R N NN II N NN G G | 16 | | W W A A R R N N II N N GGGG !!! | 17 | | | 18 | | You use a magnetic or noncollinear calculation, but did not specify | 19 | | the initial magnetic moment with the MAGMOM tag. Note that a | 20 | | default of 1 will be used for all atoms. This ferromagnetic setup | 21 | | may break the symmetry of the crystal, in particular it may rule | 22 | | out finding an antiferromagnetic solution. Thence, we recommend | 23 | | setting the initial magnetic moment manually or verifying carefully | 24 | | that this magnetic setup is desired. | 25 | | | 26 | ----------------------------------------------------------------------------- 27 | 28 | scaLAPACK will be used 29 | ----------------------------------------------------------------------------- 30 | | | 31 | | W W AA RRRRR N N II N N GGGG !!! | 32 | | W W A A R R NN N II NN N G G !!! | 33 | | W W A A R R N N N II N N N G !!! | 34 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 35 | | WW WW A A R R N NN II N NN G G | 36 | | W W A A R R N N II N N GGGG !!! | 37 | | | 38 | | For optimal performance we recommend to set | 39 | | NCORE = 4 - approx SQRT(number of cores). | 40 | | NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). | 41 | | This setting can greatly improve the performance of VASP for DFT. | 42 | | The default, NCORE=1 might be grossly inefficient on modern | 43 | | multi-core architectures or massively parallel machines. Do your | 44 | | own testing!!!! | 45 | | Unfortunately you need to use the default for GW and RPA | 46 | | calculations (for HF NCORE is supported but not extensively tested | 47 | | yet). | 48 | | | 49 | ----------------------------------------------------------------------------- 50 | 51 | LDA part: xc-table for Ceperly-Alder, standard interpolation 52 | POSCAR, INCAR and KPOINTS ok, starting setup 53 | FFT: planning ... 54 | WAVECAR not read 55 | entering main loop 56 | N E dE d eps ncg rms rms(c) 57 | DAV: 1 0.118263564927E+04 0.11826E+04 -0.10156E+05 39424 0.342E+02 58 | DAV: 2 -0.262917178386E+03 -0.14456E+04 -0.13388E+04 51264 0.102E+02 59 | DAV: 3 -0.390638122431E+03 -0.12772E+03 -0.12582E+03 54112 0.286E+01 60 | DAV: 4 -0.399423781153E+03 -0.87857E+01 -0.87639E+01 62912 0.706E+00 61 | DAV: 5 -0.399522997543E+03 -0.99216E-01 -0.99207E-01 59008 0.735E-01 0.355E+01 62 | RMM: 6 -0.379678486282E+03 0.19845E+02 -0.14235E+01 45099 0.205E+00 0.168E+01 63 | RMM: 7 -0.390556935183E+03 -0.10878E+02 -0.45327E+00 51882 0.127E+00 0.882E+00 64 | RMM: 8 -0.395084228613E+03 -0.45273E+01 -0.99301E-01 50847 0.718E-01 0.424E+00 65 | RMM: 9 -0.396067667037E+03 -0.98344E+00 -0.28021E-01 54549 0.429E-01 0.143E+00 66 | RMM: 10 -0.396152577828E+03 -0.84911E-01 -0.10626E-01 60672 0.257E-01 0.569E-01 67 | RMM: 11 -0.396156431816E+03 -0.38540E-02 -0.21773E-02 63657 0.116E-01 0.303E-01 68 | RMM: 12 -0.396157258837E+03 -0.82702E-03 -0.34065E-03 60286 0.429E-02 0.983E-02 69 | RMM: 13 -0.396157179755E+03 0.79083E-04 -0.82705E-04 64691 0.215E-02 0.319E-02 70 | RMM: 14 -0.396157164374E+03 0.15380E-04 -0.18748E-04 68084 0.865E-03 0.174E-02 71 | RMM: 15 -0.396157155016E+03 0.93582E-05 -0.28734E-05 57058 0.361E-03 72 | 1 F= -.39615716E+03 E0= -.39615687E+03 d E =-.577028E-03 mag= 0.9911 73 | Starting Core_Hole_Spec 74 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 75 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 76 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 77 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 78 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 79 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 80 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 81 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 82 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 83 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 84 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 85 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 86 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 87 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 88 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 89 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 90 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 91 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 92 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 93 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 94 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 95 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 96 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 97 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 98 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 99 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 100 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 101 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 102 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 103 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 104 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 105 | Ending Core_Hole_Spec 106 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_3_1/DOSCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_3_1/DOSCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_3_1/INCAR: -------------------------------------------------------------------------------- 1 | PREC = Accurate 2 | LREAL = Auto 3 | ALGO = Fast 4 | ENCUT = 400 5 | EDIFF = 1E-5 6 | ISMEAR = 0 7 | SIGMA = 0.05 8 | NBANDS = 704 9 | ISPIN = 2 10 | LORBIT = 11 11 | ICORELEVEL = 2 12 | CLNT = 1 13 | CLN = 1 14 | CLL = 0 15 | CLZ = 1.0 16 | CH_LSPEC = .TRUE. 17 | CH_SIGMA = 0.05 18 | LCHARG = .FALSE. 19 | LWAVE = .FALSE. -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_3_1/KPOINTS: -------------------------------------------------------------------------------- 1 | K-Points 2 | 0 3 | Gamma 4 | 3 3 3 5 | 0 0 0 6 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_3_1/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 0.118232915151E+04 0.11823E+04 -0.10156E+05 39424 0.342E+02 3 | DAV: 2 -0.263013072825E+03 -0.14453E+04 -0.13386E+04 51232 0.102E+02 4 | DAV: 3 -0.390685447965E+03 -0.12767E+03 -0.12577E+03 53984 0.286E+01 5 | DAV: 4 -0.399465698588E+03 -0.87803E+01 -0.87585E+01 63008 0.705E+00 6 | DAV: 5 -0.399564484136E+03 -0.98786E-01 -0.98777E-01 59200 0.732E-01 0.355E+01 7 | RMM: 6 -0.379696355343E+03 0.19868E+02 -0.14206E+01 45175 0.208E+00 0.168E+01 8 | RMM: 7 -0.390569827842E+03 -0.10873E+02 -0.45414E+00 51805 0.127E+00 0.884E+00 9 | RMM: 8 -0.395100889149E+03 -0.45311E+01 -0.10086E+00 50845 0.720E-01 0.424E+00 10 | RMM: 9 -0.396089051764E+03 -0.98816E+00 -0.28333E-01 54559 0.430E-01 0.143E+00 11 | RMM: 10 -0.396174245022E+03 -0.85193E-01 -0.10668E-01 60723 0.256E-01 0.583E-01 12 | RMM: 11 -0.396178243044E+03 -0.39980E-02 -0.21259E-02 63368 0.114E-01 0.306E-01 13 | RMM: 12 -0.396179057500E+03 -0.81446E-03 -0.33876E-03 60065 0.428E-02 0.100E-01 14 | RMM: 13 -0.396178970566E+03 0.86934E-04 -0.82170E-04 64534 0.214E-02 0.328E-02 15 | RMM: 14 -0.396178952793E+03 0.17772E-04 -0.18414E-04 67809 0.857E-03 0.177E-02 16 | RMM: 15 -0.396178942881E+03 0.99118E-05 -0.26063E-05 56939 0.350E-03 17 | 1 F= -.39617894E+03 E0= -.39617865E+03 d E =-.578582E-03 mag= 0.9909 18 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_3_1/OUTCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_3_1/OUTCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_3_1/POSCAR: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892927170000000 0.0000000000000000 0.0000000000000000 4 | 2.6900120737000002 12.3583693090000004 0.0000000000000000 5 | 5.1267442849000000 2.5187865596000001 11.3793247881999999 6 | S Li P S 7 | 1 28 12 43 8 | Direct 9 | 0.8374133109999988 0.4616349040000003 0.5170275569999987 10 | 0.6687428950000012 0.1761630029999992 0.9039711949999969 11 | 0.6687428950000012 0.6761630179999969 0.9039711949999969 12 | 0.3312571940000026 0.3238356109999998 0.0960283880000006 13 | 0.3312571940000026 0.8238356109999998 0.0960283880000006 14 | 0.6114585400000010 0.3671709600000028 0.1147873399999995 15 | 0.6114585400000010 0.8671709300000003 0.1147873399999995 16 | 0.3885427709999973 0.1328279379999984 0.8852128979999989 17 | 0.3885427709999973 0.6328279379999984 0.8852128979999989 18 | 0.1778128300000006 0.0024677019999970 0.2979970570000035 19 | 0.1778128300000006 0.5024676920000033 0.2979970570000035 20 | 0.8221877220000025 0.4975320989999972 0.7020025850000025 21 | 0.8221877220000025 0.9975321289999997 0.7020025850000025 22 | 0.9686143400000020 0.2278184440000004 0.7495711449999973 23 | 0.9686143400000020 0.7278184290000027 0.7495711449999973 24 | 0.0313853099999974 0.2721820180000023 0.2504284979999980 25 | 0.0313853099999974 0.7721819879999998 0.2504284979999980 26 | 0.2949205039999967 0.0990733060000011 0.7023826240000020 27 | 0.2949205039999967 0.5990732910000034 0.7023826240000020 28 | 0.7050798539999974 0.4009267690000016 0.2976173460000027 29 | 0.7050798539999974 0.9009267690000016 0.2976173460000027 30 | 0.6723443870000025 0.1008888859999999 0.4994633499999992 31 | 0.6723443870000025 0.6008889080000017 0.4994633499999992 32 | 0.3276556730000024 0.3991113310000003 0.5005362630000008 33 | 0.3276556730000024 0.8991113310000003 0.5005362630000008 34 | 0.1361429840000028 0.3533565700000025 0.8824014070000032 35 | 0.1361429840000028 0.8533565999999979 0.8824014070000032 36 | 0.8638582230000011 0.1466431619999966 0.1175977739999965 37 | 0.8638582230000011 0.6466431619999966 0.1175977739999965 38 | 0.7769408229999968 0.3160540160000025 0.5498678679999998 39 | 0.7769408229999968 0.8160539869999965 0.5498678679999998 40 | 0.2230586109999990 0.1839460130000035 0.4501324000000011 41 | 0.2230586109999990 0.6839460130000035 0.4501324000000011 42 | 0.4720538259999998 0.3971497120000009 0.7272555229999966 43 | 0.4720538259999998 0.8971496819999984 0.7272555229999966 44 | 0.5279458170000026 0.1028505559999999 0.2727444169999984 45 | 0.5279458170000026 0.6028505559999999 0.2727444169999984 46 | 0.8348844650000018 0.4582849139999965 0.9417669179999990 47 | 0.8348844650000018 0.9582849140000036 0.9417669179999990 48 | 0.1651147449999968 0.0417154060000016 0.0582332390000033 49 | 0.1651147449999968 0.5417153839999997 0.0582332390000033 50 | 0.8209434150000021 0.2551785710000019 0.4022387269999967 51 | 0.8209434150000021 0.7551785710000019 0.4022387269999967 52 | 0.1790562119999990 0.2448210720000006 0.5977616309999974 53 | 0.1790562119999990 0.7448210720000006 0.5977616309999974 54 | 0.8125801679999967 0.2038727850000015 0.6833589669999967 55 | 0.8125801679999967 0.7038727999999992 0.6833589669999967 56 | 0.1874188330000024 0.2961274090000003 0.3166412409999992 57 | 0.1874188330000024 0.7961274390000028 0.3166412409999992 58 | 0.8374133109999988 0.9616348739999978 0.5170275569999987 59 | 0.1625860779999968 0.0383653230000007 0.4829725330000016 60 | 0.1625860779999968 0.5383653040000027 0.4829725330000016 61 | 0.5900002719999975 0.3329958919999996 0.5765242579999992 62 | 0.5900002719999975 0.8329958919999996 0.5765242579999992 63 | 0.4099998180000028 0.1670047940000003 0.4234751159999988 64 | 0.4099998180000028 0.6670048240000028 0.4234751159999988 65 | 0.3173536059999975 0.4026352169999967 0.7017551060000002 66 | 0.3173536059999975 0.9026352169999967 0.7017551060000002 67 | 0.6826459170000021 0.0973652899999990 0.2982449229999986 68 | 0.6826459170000021 0.5973652599999966 0.2982449229999986 69 | 0.4775420429999997 0.2918528909999978 0.8781114820000013 70 | 0.4775420429999997 0.7918528909999978 0.8781114820000013 71 | 0.5224580759999995 0.2081471230000034 0.1218881309999986 72 | 0.5224580759999995 0.7081471090000022 0.1218881309999986 73 | 0.5083060259999996 0.0540041479999971 0.7046115990000033 74 | 0.5083060259999996 0.5540041329999994 0.7046115990000033 75 | 0.4916935560000013 0.4459961060000026 0.2953888480000018 76 | 0.4916935560000013 0.9459961060000026 0.2953888480000018 77 | 0.8208362459999989 0.3515947759999989 0.1006187719999971 78 | 0.8208362459999989 0.8515948060000014 0.1006187719999971 79 | 0.1791636049999994 0.1484049709999979 0.8993810420000017 80 | 0.1791636049999994 0.6484049560000003 0.8993810420000017 81 | 0.8585389850000027 0.1142017620000004 0.9433858390000012 82 | 0.8585389850000027 0.6142017840000022 0.9433858390000012 83 | 0.1414607910000001 0.3857982159999978 0.0566142830000018 84 | 0.1414607910000001 0.8857982159999978 0.0566142830000018 85 | 0.6807149050000021 0.4703724680000008 0.9116758110000021 86 | 0.6807149050000021 0.9703724379999983 0.9116758110000021 87 | 0.3192848560000030 0.0296275580000014 0.0883243749999991 88 | 0.3192848560000030 0.5296275620000017 0.0883243749999991 89 | 0.9730954170000032 0.4071857630000011 0.8015559910000007 90 | 0.9730954170000032 0.9071857929999965 0.8015559910000007 91 | 0.0269045229999989 0.0928138049999987 0.1984439789999968 92 | 0.0269045229999989 0.5928137900000010 0.1984439789999968 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_3_1/vasp.out: -------------------------------------------------------------------------------- 1 | running on 32 total cores 2 | distrk: each k-point on 32 cores, 1 groups 3 | distr: one band on 1 cores, 32 groups 4 | using from now: INCAR 5 | vasp.6.1.1 19Jun20 (build Feb 22 2021 16:38:43) complex 6 | 7 | POSCAR found type information on POSCAR S LiP S 8 | POSCAR found : 4 types and 84 ions 9 | ----------------------------------------------------------------------------- 10 | | | 11 | | W W AA RRRRR N N II N N GGGG !!! | 12 | | W W A A R R NN N II NN N G G !!! | 13 | | W W A A R R N N N II N N N G !!! | 14 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 15 | | WW WW A A R R N NN II N NN G G | 16 | | W W A A R R N N II N N GGGG !!! | 17 | | | 18 | | You use a magnetic or noncollinear calculation, but did not specify | 19 | | the initial magnetic moment with the MAGMOM tag. Note that a | 20 | | default of 1 will be used for all atoms. This ferromagnetic setup | 21 | | may break the symmetry of the crystal, in particular it may rule | 22 | | out finding an antiferromagnetic solution. Thence, we recommend | 23 | | setting the initial magnetic moment manually or verifying carefully | 24 | | that this magnetic setup is desired. | 25 | | | 26 | ----------------------------------------------------------------------------- 27 | 28 | scaLAPACK will be used 29 | ----------------------------------------------------------------------------- 30 | | | 31 | | W W AA RRRRR N N II N N GGGG !!! | 32 | | W W A A R R NN N II NN N G G !!! | 33 | | W W A A R R N N N II N N N G !!! | 34 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 35 | | WW WW A A R R N NN II N NN G G | 36 | | W W A A R R N N II N N GGGG !!! | 37 | | | 38 | | For optimal performance we recommend to set | 39 | | NCORE = 4 - approx SQRT(number of cores). | 40 | | NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). | 41 | | This setting can greatly improve the performance of VASP for DFT. | 42 | | The default, NCORE=1 might be grossly inefficient on modern | 43 | | multi-core architectures or massively parallel machines. Do your | 44 | | own testing!!!! | 45 | | Unfortunately you need to use the default for GW and RPA | 46 | | calculations (for HF NCORE is supported but not extensively tested | 47 | | yet). | 48 | | | 49 | ----------------------------------------------------------------------------- 50 | 51 | LDA part: xc-table for Ceperly-Alder, standard interpolation 52 | POSCAR, INCAR and KPOINTS ok, starting setup 53 | FFT: planning ... 54 | WAVECAR not read 55 | entering main loop 56 | N E dE d eps ncg rms rms(c) 57 | DAV: 1 0.118232915151E+04 0.11823E+04 -0.10156E+05 39424 0.342E+02 58 | DAV: 2 -0.263013072825E+03 -0.14453E+04 -0.13386E+04 51232 0.102E+02 59 | DAV: 3 -0.390685447965E+03 -0.12767E+03 -0.12577E+03 53984 0.286E+01 60 | DAV: 4 -0.399465698588E+03 -0.87803E+01 -0.87585E+01 63008 0.705E+00 61 | DAV: 5 -0.399564484136E+03 -0.98786E-01 -0.98777E-01 59200 0.732E-01 0.355E+01 62 | RMM: 6 -0.379696355343E+03 0.19868E+02 -0.14206E+01 45175 0.208E+00 0.168E+01 63 | RMM: 7 -0.390569827842E+03 -0.10873E+02 -0.45414E+00 51805 0.127E+00 0.884E+00 64 | RMM: 8 -0.395100889149E+03 -0.45311E+01 -0.10086E+00 50845 0.720E-01 0.424E+00 65 | RMM: 9 -0.396089051764E+03 -0.98816E+00 -0.28333E-01 54559 0.430E-01 0.143E+00 66 | RMM: 10 -0.396174245022E+03 -0.85193E-01 -0.10668E-01 60723 0.256E-01 0.583E-01 67 | RMM: 11 -0.396178243044E+03 -0.39980E-02 -0.21259E-02 63368 0.114E-01 0.306E-01 68 | RMM: 12 -0.396179057500E+03 -0.81446E-03 -0.33876E-03 60065 0.428E-02 0.100E-01 69 | RMM: 13 -0.396178970566E+03 0.86934E-04 -0.82170E-04 64534 0.214E-02 0.328E-02 70 | RMM: 14 -0.396178952793E+03 0.17772E-04 -0.18414E-04 67809 0.857E-03 0.177E-02 71 | RMM: 15 -0.396178942881E+03 0.99118E-05 -0.26063E-05 56939 0.350E-03 72 | 1 F= -.39617894E+03 E0= -.39617865E+03 d E =-.578582E-03 mag= 0.9909 73 | Starting Core_Hole_Spec 74 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 75 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 76 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 77 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 78 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 79 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 80 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 81 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 82 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 83 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 84 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 85 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 86 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 87 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 88 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 89 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 90 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 91 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 92 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 93 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 94 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 95 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 96 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 97 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 98 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 99 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 100 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 101 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 102 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 103 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 104 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 105 | Ending Core_Hole_Spec 106 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_4_1/DOSCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_4_1/DOSCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_4_1/INCAR: -------------------------------------------------------------------------------- 1 | PREC = Accurate 2 | LREAL = Auto 3 | ALGO = Fast 4 | ENCUT = 400 5 | EDIFF = 1E-5 6 | ISMEAR = 0 7 | SIGMA = 0.05 8 | NBANDS = 704 9 | ISPIN = 2 10 | LORBIT = 11 11 | ICORELEVEL = 2 12 | CLNT = 1 13 | CLN = 1 14 | CLL = 0 15 | CLZ = 1.0 16 | CH_LSPEC = .TRUE. 17 | CH_SIGMA = 0.05 18 | LCHARG = .FALSE. 19 | LWAVE = .FALSE. -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_4_1/KPOINTS: -------------------------------------------------------------------------------- 1 | K-Points 2 | 0 3 | Gamma 4 | 3 3 3 5 | 0 0 0 6 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_4_1/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 0.118336350632E+04 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0.19473E-04 -0.18306E-04 67916 0.861E-03 0.178E-02 16 | RMM: 15 -0.396079235637E+03 0.10908E-04 -0.26153E-05 56992 0.353E-03 0.844E-03 17 | RMM: 16 -0.396079231839E+03 0.37985E-05 -0.59462E-06 44449 0.239E-03 18 | 1 F= -.39607923E+03 E0= -.39607886E+03 d E =-.752712E-03 mag= 0.9905 19 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_5_1/OUTCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_5_1/OUTCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_5_1/POSCAR: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892927170000000 0.0000000000000000 0.0000000000000000 4 | 2.6900120737000002 12.3583693090000004 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0.3192848560000030 0.0296275580000014 0.0883243749999991 88 | 0.3192848560000030 0.5296275620000017 0.0883243749999991 89 | 0.9730954170000032 0.4071857630000011 0.8015559910000007 90 | 0.9730954170000032 0.9071857929999965 0.8015559910000007 91 | 0.0269045229999989 0.0928138049999987 0.1984439789999968 92 | 0.0269045229999989 0.5928137900000010 0.1984439789999968 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_5_1/vasp.out: -------------------------------------------------------------------------------- 1 | running on 32 total cores 2 | distrk: each k-point on 32 cores, 1 groups 3 | distr: one band on 1 cores, 32 groups 4 | using from now: INCAR 5 | vasp.6.1.1 19Jun20 (build Feb 22 2021 16:38:43) complex 6 | 7 | POSCAR found type information on POSCAR S LiP S 8 | POSCAR found : 4 types and 84 ions 9 | ----------------------------------------------------------------------------- 10 | | | 11 | | W W AA RRRRR N N II N N GGGG !!! | 12 | | W W A A R R NN N II NN N G G !!! | 13 | | W W A A R R N N N II N N N G !!! | 14 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 15 | | WW WW A A R R N NN II N NN G G | 16 | | W W A A R R N N II N N GGGG !!! | 17 | | | 18 | | You use a magnetic or noncollinear calculation, but did not specify | 19 | | the initial magnetic moment with the MAGMOM tag. Note that a | 20 | | default of 1 will be used for all atoms. This ferromagnetic setup | 21 | | may break the symmetry of the crystal, in particular it may rule | 22 | | out finding an antiferromagnetic solution. Thence, we recommend | 23 | | setting the initial magnetic moment manually or verifying carefully | 24 | | that this magnetic setup is desired. | 25 | | | 26 | ----------------------------------------------------------------------------- 27 | 28 | scaLAPACK will be used 29 | ----------------------------------------------------------------------------- 30 | | | 31 | | W W AA RRRRR N N II N N GGGG !!! | 32 | | W W A A R R NN N II NN N G G !!! | 33 | | W W A A R R N N N II N N N G !!! | 34 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 35 | | WW WW A A R R N NN II N NN G G | 36 | | W W A A R R N N II N N GGGG !!! | 37 | | | 38 | | For optimal performance we recommend to set | 39 | | NCORE = 4 - approx SQRT(number of cores). | 40 | | NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). | 41 | | This setting can greatly improve the performance of VASP for DFT. | 42 | | The default, NCORE=1 might be grossly inefficient on modern | 43 | | multi-core architectures or massively parallel machines. Do your | 44 | | own testing!!!! | 45 | | Unfortunately you need to use the default for GW and RPA | 46 | | calculations (for HF NCORE is supported but not extensively tested | 47 | | yet). | 48 | | | 49 | ----------------------------------------------------------------------------- 50 | 51 | LDA part: xc-table for Ceperly-Alder, standard interpolation 52 | POSCAR, INCAR and KPOINTS ok, starting setup 53 | FFT: planning ... 54 | WAVECAR not read 55 | entering main loop 56 | N E dE d eps ncg rms rms(c) 57 | DAV: 1 0.118278937902E+04 0.11828E+04 -0.10156E+05 39424 0.342E+02 58 | DAV: 2 -0.262869983359E+03 -0.14457E+04 -0.13389E+04 51168 0.102E+02 59 | DAV: 3 -0.390599536855E+03 -0.12773E+03 -0.12582E+03 54240 0.286E+01 60 | DAV: 4 -0.399370413378E+03 -0.87709E+01 -0.87493E+01 62560 0.704E+00 61 | DAV: 5 -0.399470273116E+03 -0.99860E-01 -0.99851E-01 59104 0.738E-01 0.355E+01 62 | RMM: 6 -0.379621599452E+03 0.19849E+02 -0.14169E+01 45191 0.205E+00 0.168E+01 63 | RMM: 7 -0.390467133167E+03 -0.10846E+02 -0.45305E+00 51829 0.127E+00 0.882E+00 64 | RMM: 8 -0.395011119377E+03 -0.45440E+01 -0.98351E-01 50807 0.715E-01 0.423E+00 65 | RMM: 9 -0.395989004791E+03 -0.97789E+00 -0.27805E-01 54510 0.428E-01 0.143E+00 66 | RMM: 10 -0.396074563267E+03 -0.85558E-01 -0.10534E-01 60631 0.257E-01 0.571E-01 67 | RMM: 11 -0.396078508726E+03 -0.39455E-02 -0.21750E-02 63353 0.116E-01 0.305E-01 68 | RMM: 12 -0.396079358752E+03 -0.85003E-03 -0.34250E-03 60398 0.428E-02 0.996E-02 69 | RMM: 13 -0.396079266018E+03 0.92735E-04 -0.79486E-04 64279 0.212E-02 0.325E-02 70 | RMM: 14 -0.396079246545E+03 0.19473E-04 -0.18306E-04 67916 0.861E-03 0.178E-02 71 | RMM: 15 -0.396079235637E+03 0.10908E-04 -0.26153E-05 56992 0.353E-03 0.844E-03 72 | RMM: 16 -0.396079231839E+03 0.37985E-05 -0.59462E-06 44449 0.239E-03 73 | 1 F= -.39607923E+03 E0= -.39607886E+03 d E =-.752712E-03 mag= 0.9905 74 | Starting Core_Hole_Spec 75 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 76 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 77 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 78 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 79 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 80 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 81 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 82 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 83 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 84 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 85 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 86 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 87 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 88 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 89 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 90 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 91 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 92 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 93 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 94 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 95 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 96 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 97 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 98 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 99 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 100 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 101 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 102 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 103 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 104 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 105 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 106 | Ending Core_Hole_Spec 107 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_6_1/DOSCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_6_1/DOSCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_6_1/INCAR: -------------------------------------------------------------------------------- 1 | PREC = Accurate 2 | LREAL = Auto 3 | ALGO = Fast 4 | ENCUT = 400 5 | EDIFF = 1E-5 6 | ISMEAR = 0 7 | SIGMA = 0.05 8 | NBANDS = 704 9 | ISPIN = 2 10 | LORBIT = 11 11 | ICORELEVEL = 2 12 | CLNT = 1 13 | CLN = 1 14 | CLL = 0 15 | CLZ = 1.0 16 | CH_LSPEC = .TRUE. 17 | CH_SIGMA = 0.05 18 | LCHARG = .FALSE. 19 | LWAVE = .FALSE. -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_6_1/KPOINTS: -------------------------------------------------------------------------------- 1 | K-Points 2 | 0 3 | Gamma 4 | 3 3 3 5 | 0 0 0 6 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_6_1/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 0.118269173395E+04 0.11827E+04 -0.10156E+05 39424 0.342E+02 3 | DAV: 2 -0.262830951402E+03 -0.14455E+04 -0.13388E+04 51232 0.102E+02 4 | DAV: 3 -0.390588583794E+03 -0.12776E+03 -0.12585E+03 54176 0.286E+01 5 | DAV: 4 -0.399371493316E+03 -0.87829E+01 -0.87614E+01 62656 0.705E+00 6 | DAV: 5 -0.399470860460E+03 -0.99367E-01 -0.99358E-01 58880 0.737E-01 0.355E+01 7 | RMM: 6 -0.379656397471E+03 0.19814E+02 -0.14316E+01 45214 0.206E+00 0.168E+01 8 | RMM: 7 -0.390511705868E+03 -0.10855E+02 -0.45785E+00 51779 0.127E+00 0.882E+00 9 | RMM: 8 -0.395058512414E+03 -0.45468E+01 -0.98973E-01 50691 0.718E-01 0.423E+00 10 | RMM: 9 -0.396043285692E+03 -0.98477E+00 -0.27898E-01 54452 0.430E-01 0.142E+00 11 | RMM: 10 -0.396128198866E+03 -0.84913E-01 -0.10632E-01 60733 0.257E-01 0.568E-01 12 | RMM: 11 -0.396132173761E+03 -0.39749E-02 -0.21558E-02 63482 0.115E-01 0.302E-01 13 | RMM: 12 -0.396133079816E+03 -0.90606E-03 -0.33600E-03 60266 0.425E-02 0.970E-02 14 | RMM: 13 -0.396133011931E+03 0.67885E-04 -0.80486E-04 64762 0.211E-02 0.310E-02 15 | RMM: 14 -0.396132999277E+03 0.12654E-04 -0.17832E-04 68290 0.840E-03 0.172E-02 16 | RMM: 15 -0.396132991127E+03 0.81497E-05 -0.25110E-05 56258 0.346E-03 17 | 1 F= -.39613299E+03 E0= -.39613268E+03 d E =-.630978E-03 mag= 0.9906 18 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_6_1/OUTCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_6_1/OUTCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_6_1/POSCAR: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892927170000000 0.0000000000000000 0.0000000000000000 4 | 2.6900120737000002 12.3583693090000004 0.0000000000000000 5 | 5.1267442849000000 2.5187865596000001 11.3793247881999999 6 | S Li P S 7 | 1 28 12 43 8 | Direct 9 | 0.4775420429999997 0.2918528909999978 0.8781114820000013 10 | 0.6687428950000012 0.1761630029999992 0.9039711949999969 11 | 0.6687428950000012 0.6761630179999969 0.9039711949999969 12 | 0.3312571940000026 0.3238356109999998 0.0960283880000006 13 | 0.3312571940000026 0.8238356109999998 0.0960283880000006 14 | 0.6114585400000010 0.3671709600000028 0.1147873399999995 15 | 0.6114585400000010 0.8671709300000003 0.1147873399999995 16 | 0.3885427709999973 0.1328279379999984 0.8852128979999989 17 | 0.3885427709999973 0.6328279379999984 0.8852128979999989 18 | 0.1778128300000006 0.0024677019999970 0.2979970570000035 19 | 0.1778128300000006 0.5024676920000033 0.2979970570000035 20 | 0.8221877220000025 0.4975320989999972 0.7020025850000025 21 | 0.8221877220000025 0.9975321289999997 0.7020025850000025 22 | 0.9686143400000020 0.2278184440000004 0.7495711449999973 23 | 0.9686143400000020 0.7278184290000027 0.7495711449999973 24 | 0.0313853099999974 0.2721820180000023 0.2504284979999980 25 | 0.0313853099999974 0.7721819879999998 0.2504284979999980 26 | 0.2949205039999967 0.0990733060000011 0.7023826240000020 27 | 0.2949205039999967 0.5990732910000034 0.7023826240000020 28 | 0.7050798539999974 0.4009267690000016 0.2976173460000027 29 | 0.7050798539999974 0.9009267690000016 0.2976173460000027 30 | 0.6723443870000025 0.1008888859999999 0.4994633499999992 31 | 0.6723443870000025 0.6008889080000017 0.4994633499999992 32 | 0.3276556730000024 0.3991113310000003 0.5005362630000008 33 | 0.3276556730000024 0.8991113310000003 0.5005362630000008 34 | 0.1361429840000028 0.3533565700000025 0.8824014070000032 35 | 0.1361429840000028 0.8533565999999979 0.8824014070000032 36 | 0.8638582230000011 0.1466431619999966 0.1175977739999965 37 | 0.8638582230000011 0.6466431619999966 0.1175977739999965 38 | 0.7769408229999968 0.3160540160000025 0.5498678679999998 39 | 0.7769408229999968 0.8160539869999965 0.5498678679999998 40 | 0.2230586109999990 0.1839460130000035 0.4501324000000011 41 | 0.2230586109999990 0.6839460130000035 0.4501324000000011 42 | 0.4720538259999998 0.3971497120000009 0.7272555229999966 43 | 0.4720538259999998 0.8971496819999984 0.7272555229999966 44 | 0.5279458170000026 0.1028505559999999 0.2727444169999984 45 | 0.5279458170000026 0.6028505559999999 0.2727444169999984 46 | 0.8348844650000018 0.4582849139999965 0.9417669179999990 47 | 0.8348844650000018 0.9582849140000036 0.9417669179999990 48 | 0.1651147449999968 0.0417154060000016 0.0582332390000033 49 | 0.1651147449999968 0.5417153839999997 0.0582332390000033 50 | 0.8209434150000021 0.2551785710000019 0.4022387269999967 51 | 0.8209434150000021 0.7551785710000019 0.4022387269999967 52 | 0.1790562119999990 0.2448210720000006 0.5977616309999974 53 | 0.1790562119999990 0.7448210720000006 0.5977616309999974 54 | 0.8125801679999967 0.2038727850000015 0.6833589669999967 55 | 0.8125801679999967 0.7038727999999992 0.6833589669999967 56 | 0.1874188330000024 0.2961274090000003 0.3166412409999992 57 | 0.1874188330000024 0.7961274390000028 0.3166412409999992 58 | 0.8374133109999988 0.4616349040000003 0.5170275569999987 59 | 0.8374133109999988 0.9616348739999978 0.5170275569999987 60 | 0.1625860779999968 0.0383653230000007 0.4829725330000016 61 | 0.1625860779999968 0.5383653040000027 0.4829725330000016 62 | 0.5900002719999975 0.3329958919999996 0.5765242579999992 63 | 0.5900002719999975 0.8329958919999996 0.5765242579999992 64 | 0.4099998180000028 0.1670047940000003 0.4234751159999988 65 | 0.4099998180000028 0.6670048240000028 0.4234751159999988 66 | 0.3173536059999975 0.4026352169999967 0.7017551060000002 67 | 0.3173536059999975 0.9026352169999967 0.7017551060000002 68 | 0.6826459170000021 0.0973652899999990 0.2982449229999986 69 | 0.6826459170000021 0.5973652599999966 0.2982449229999986 70 | 0.4775420429999997 0.7918528909999978 0.8781114820000013 71 | 0.5224580759999995 0.2081471230000034 0.1218881309999986 72 | 0.5224580759999995 0.7081471090000022 0.1218881309999986 73 | 0.5083060259999996 0.0540041479999971 0.7046115990000033 74 | 0.5083060259999996 0.5540041329999994 0.7046115990000033 75 | 0.4916935560000013 0.4459961060000026 0.2953888480000018 76 | 0.4916935560000013 0.9459961060000026 0.2953888480000018 77 | 0.8208362459999989 0.3515947759999989 0.1006187719999971 78 | 0.8208362459999989 0.8515948060000014 0.1006187719999971 79 | 0.1791636049999994 0.1484049709999979 0.8993810420000017 80 | 0.1791636049999994 0.6484049560000003 0.8993810420000017 81 | 0.8585389850000027 0.1142017620000004 0.9433858390000012 82 | 0.8585389850000027 0.6142017840000022 0.9433858390000012 83 | 0.1414607910000001 0.3857982159999978 0.0566142830000018 84 | 0.1414607910000001 0.8857982159999978 0.0566142830000018 85 | 0.6807149050000021 0.4703724680000008 0.9116758110000021 86 | 0.6807149050000021 0.9703724379999983 0.9116758110000021 87 | 0.3192848560000030 0.0296275580000014 0.0883243749999991 88 | 0.3192848560000030 0.5296275620000017 0.0883243749999991 89 | 0.9730954170000032 0.4071857630000011 0.8015559910000007 90 | 0.9730954170000032 0.9071857929999965 0.8015559910000007 91 | 0.0269045229999989 0.0928138049999987 0.1984439789999968 92 | 0.0269045229999989 0.5928137900000010 0.1984439789999968 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_6_1/vasp.out: -------------------------------------------------------------------------------- 1 | running on 32 total cores 2 | distrk: each k-point on 32 cores, 1 groups 3 | distr: one band on 1 cores, 32 groups 4 | using from now: INCAR 5 | vasp.6.1.1 19Jun20 (build Feb 22 2021 16:38:43) complex 6 | 7 | POSCAR found type information on POSCAR S LiP S 8 | POSCAR found : 4 types and 84 ions 9 | ----------------------------------------------------------------------------- 10 | | | 11 | | W W AA RRRRR N N II N N GGGG !!! | 12 | | W W A A R R NN N II NN N G G !!! | 13 | | W W A A R R N N N II N N N G !!! | 14 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 15 | | WW WW A A R R N NN II N NN G G | 16 | | W W A A R R N N II N N GGGG !!! | 17 | | | 18 | | You use a magnetic or noncollinear calculation, but did not specify | 19 | | the initial magnetic moment with the MAGMOM tag. Note that a | 20 | | default of 1 will be used for all atoms. This ferromagnetic setup | 21 | | may break the symmetry of the crystal, in particular it may rule | 22 | | out finding an antiferromagnetic solution. Thence, we recommend | 23 | | setting the initial magnetic moment manually or verifying carefully | 24 | | that this magnetic setup is desired. | 25 | | | 26 | ----------------------------------------------------------------------------- 27 | 28 | scaLAPACK will be used 29 | ----------------------------------------------------------------------------- 30 | | | 31 | | W W AA RRRRR N N II N N GGGG !!! | 32 | | W W A A R R NN N II NN N G G !!! | 33 | | W W A A R R N N N II N N N G !!! | 34 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 35 | | WW WW A A R R N NN II N NN G G | 36 | | W W A A R R N N II N N GGGG !!! | 37 | | | 38 | | For optimal performance we recommend to set | 39 | | NCORE = 4 - approx SQRT(number of cores). | 40 | | NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). | 41 | | This setting can greatly improve the performance of VASP for DFT. | 42 | | The default, NCORE=1 might be grossly inefficient on modern | 43 | | multi-core architectures or massively parallel machines. Do your | 44 | | own testing!!!! | 45 | | Unfortunately you need to use the default for GW and RPA | 46 | | calculations (for HF NCORE is supported but not extensively tested | 47 | | yet). | 48 | | | 49 | ----------------------------------------------------------------------------- 50 | 51 | LDA part: xc-table for Ceperly-Alder, standard interpolation 52 | POSCAR, INCAR and KPOINTS ok, starting setup 53 | FFT: planning ... 54 | WAVECAR not read 55 | entering main loop 56 | N E dE d eps ncg rms rms(c) 57 | DAV: 1 0.118269173395E+04 0.11827E+04 -0.10156E+05 39424 0.342E+02 58 | DAV: 2 -0.262830951402E+03 -0.14455E+04 -0.13388E+04 51232 0.102E+02 59 | DAV: 3 -0.390588583794E+03 -0.12776E+03 -0.12585E+03 54176 0.286E+01 60 | DAV: 4 -0.399371493316E+03 -0.87829E+01 -0.87614E+01 62656 0.705E+00 61 | DAV: 5 -0.399470860460E+03 -0.99367E-01 -0.99358E-01 58880 0.737E-01 0.355E+01 62 | RMM: 6 -0.379656397471E+03 0.19814E+02 -0.14316E+01 45214 0.206E+00 0.168E+01 63 | RMM: 7 -0.390511705868E+03 -0.10855E+02 -0.45785E+00 51779 0.127E+00 0.882E+00 64 | RMM: 8 -0.395058512414E+03 -0.45468E+01 -0.98973E-01 50691 0.718E-01 0.423E+00 65 | RMM: 9 -0.396043285692E+03 -0.98477E+00 -0.27898E-01 54452 0.430E-01 0.142E+00 66 | RMM: 10 -0.396128198866E+03 -0.84913E-01 -0.10632E-01 60733 0.257E-01 0.568E-01 67 | RMM: 11 -0.396132173761E+03 -0.39749E-02 -0.21558E-02 63482 0.115E-01 0.302E-01 68 | RMM: 12 -0.396133079816E+03 -0.90606E-03 -0.33600E-03 60266 0.425E-02 0.970E-02 69 | RMM: 13 -0.396133011931E+03 0.67885E-04 -0.80486E-04 64762 0.211E-02 0.310E-02 70 | RMM: 14 -0.396132999277E+03 0.12654E-04 -0.17832E-04 68290 0.840E-03 0.172E-02 71 | RMM: 15 -0.396132991127E+03 0.81497E-05 -0.25110E-05 56258 0.346E-03 72 | 1 F= -.39613299E+03 E0= -.39613268E+03 d E =-.630978E-03 mag= 0.9906 73 | Starting Core_Hole_Spec 74 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 75 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 76 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 77 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 78 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 79 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 80 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 81 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 82 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 83 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 84 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 85 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 86 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 87 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 88 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 89 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 90 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 91 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 92 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 93 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 94 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 95 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 96 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 97 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 98 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 99 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 100 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 101 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 102 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 103 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 104 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 105 | Ending Core_Hole_Spec 106 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_7_1/DOSCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_7_1/DOSCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_7_1/INCAR: -------------------------------------------------------------------------------- 1 | PREC = Accurate 2 | LREAL = Auto 3 | ALGO = Fast 4 | ENCUT = 400 5 | EDIFF = 1E-5 6 | ISMEAR = 0 7 | SIGMA = 0.05 8 | NBANDS = 704 9 | ISPIN = 2 10 | LORBIT = 11 11 | ICORELEVEL = 2 12 | CLNT = 1 13 | CLN = 1 14 | CLL = 0 15 | CLZ = 1.0 16 | CH_LSPEC = .TRUE. 17 | CH_SIGMA = 0.05 18 | LCHARG = .FALSE. 19 | LWAVE = .FALSE. -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_7_1/KPOINTS: -------------------------------------------------------------------------------- 1 | K-Points 2 | 0 3 | Gamma 4 | 3 3 3 5 | 0 0 0 6 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_7_1/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 0.118267912901E+04 0.11827E+04 -0.10156E+05 39424 0.342E+02 3 | DAV: 2 -0.262870902573E+03 -0.14456E+04 -0.13387E+04 51232 0.102E+02 4 | DAV: 3 -0.390596884213E+03 -0.12773E+03 -0.12583E+03 53856 0.286E+01 5 | DAV: 4 -0.399368952933E+03 -0.87721E+01 -0.87503E+01 62784 0.705E+00 6 | DAV: 5 -0.399468842852E+03 -0.99890E-01 -0.99881E-01 58912 0.737E-01 0.355E+01 7 | RMM: 6 -0.379583682373E+03 0.19885E+02 -0.14303E+01 45212 0.206E+00 0.168E+01 8 | RMM: 7 -0.390430739026E+03 -0.10847E+02 -0.45249E+00 51783 0.127E+00 0.882E+00 9 | RMM: 8 -0.394972371341E+03 -0.45416E+01 -0.10068E+00 50728 0.720E-01 0.423E+00 10 | RMM: 9 -0.395956990318E+03 -0.98462E+00 -0.27955E-01 54509 0.429E-01 0.143E+00 11 | RMM: 10 -0.396040419524E+03 -0.83429E-01 -0.10465E-01 60721 0.256E-01 0.575E-01 12 | RMM: 11 -0.396044416214E+03 -0.39967E-02 -0.21445E-02 63346 0.115E-01 0.302E-01 13 | RMM: 12 -0.396045215621E+03 -0.79941E-03 -0.34006E-03 60289 0.430E-02 0.982E-02 14 | RMM: 13 -0.396045123705E+03 0.91915E-04 -0.82811E-04 64345 0.216E-02 0.318E-02 15 | RMM: 14 -0.396045106788E+03 0.16917E-04 -0.18614E-04 67666 0.861E-03 0.176E-02 16 | RMM: 15 -0.396045096349E+03 0.10439E-04 -0.26719E-05 56636 0.352E-03 0.788E-03 17 | RMM: 16 -0.396045093344E+03 0.30056E-05 -0.61509E-06 44330 0.239E-03 18 | 1 F= -.39604509E+03 E0= -.39604492E+03 d E =-.337279E-03 mag= 0.9954 19 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_7_1/OUTCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_7_1/OUTCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_7_1/POSCAR: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892927170000000 0.0000000000000000 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PREC = Accurate 2 | LREAL = Auto 3 | ALGO = Fast 4 | ENCUT = 400 5 | EDIFF = 1E-5 6 | ISMEAR = 0 7 | SIGMA = 0.05 8 | NBANDS = 704 9 | ISPIN = 2 10 | LORBIT = 11 11 | ICORELEVEL = 2 12 | CLNT = 1 13 | CLN = 1 14 | CLL = 0 15 | CLZ = 1.0 16 | CH_LSPEC = .TRUE. 17 | CH_SIGMA = 0.05 18 | LCHARG = .FALSE. 19 | LWAVE = .FALSE. -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_8_1/KPOINTS: -------------------------------------------------------------------------------- 1 | K-Points 2 | 0 3 | Gamma 4 | 3 3 3 5 | 0 0 0 6 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_8_1/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 0.118280357976E+04 0.11828E+04 -0.10156E+05 39424 0.342E+02 3 | DAV: 2 -0.262932061673E+03 -0.14457E+04 -0.13389E+04 51168 0.102E+02 4 | DAV: 3 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0.4071857630000011 0.8015559910000007 90 | 0.9730954170000032 0.9071857929999965 0.8015559910000007 91 | 0.0269045229999989 0.0928138049999987 0.1984439789999968 92 | 0.0269045229999989 0.5928137900000010 0.1984439789999968 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_8_1/vasp.out: -------------------------------------------------------------------------------- 1 | running on 32 total cores 2 | distrk: each k-point on 32 cores, 1 groups 3 | distr: one band on 1 cores, 32 groups 4 | using from now: INCAR 5 | vasp.6.1.1 19Jun20 (build Feb 22 2021 16:38:43) complex 6 | 7 | POSCAR found type information on POSCAR S LiP S 8 | POSCAR found : 4 types and 84 ions 9 | ----------------------------------------------------------------------------- 10 | | | 11 | | W W AA RRRRR N N II N N GGGG !!! | 12 | | W W A A R R NN N II NN N G G !!! | 13 | | W W A A R R N N N II N N N G !!! | 14 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 15 | | WW WW A A R R N NN II N NN G G | 16 | | W W A A R R N N II N N GGGG !!! | 17 | | | 18 | | You use a magnetic or noncollinear calculation, but did not specify | 19 | | the initial magnetic moment with the MAGMOM tag. Note that a | 20 | | default of 1 will be used for all atoms. This ferromagnetic setup | 21 | | may break the symmetry of the crystal, in particular it may rule | 22 | | out finding an antiferromagnetic solution. Thence, we recommend | 23 | | setting the initial magnetic moment manually or verifying carefully | 24 | | that this magnetic setup is desired. | 25 | | | 26 | ----------------------------------------------------------------------------- 27 | 28 | scaLAPACK will be used 29 | ----------------------------------------------------------------------------- 30 | | | 31 | | W W AA RRRRR N N II N N GGGG !!! | 32 | | W W A A R R NN N II NN N G G !!! | 33 | | W W A A R R N N N II N N N G !!! | 34 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 35 | | WW WW A A R R N NN II N NN G G | 36 | | W W A A R R N N II N N GGGG !!! | 37 | | | 38 | | For optimal performance we recommend to set | 39 | | NCORE = 4 - approx SQRT(number of cores). | 40 | | NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). | 41 | | This setting can greatly improve the performance of VASP for DFT. | 42 | | The default, NCORE=1 might be grossly inefficient on modern | 43 | | multi-core architectures or massively parallel machines. Do your | 44 | | own testing!!!! | 45 | | Unfortunately you need to use the default for GW and RPA | 46 | | calculations (for HF NCORE is supported but not extensively tested | 47 | | yet). | 48 | | | 49 | ----------------------------------------------------------------------------- 50 | 51 | LDA part: xc-table for Ceperly-Alder, standard interpolation 52 | POSCAR, INCAR and KPOINTS ok, starting setup 53 | FFT: planning ... 54 | WAVECAR not read 55 | entering main loop 56 | N E dE d eps ncg rms rms(c) 57 | DAV: 1 0.118280357976E+04 0.11828E+04 -0.10156E+05 39424 0.342E+02 58 | DAV: 2 -0.262932061673E+03 -0.14457E+04 -0.13389E+04 51168 0.102E+02 59 | DAV: 3 -0.390616461894E+03 -0.12768E+03 -0.12578E+03 53888 0.286E+01 60 | DAV: 4 -0.399395121961E+03 -0.87787E+01 -0.87568E+01 62656 0.705E+00 61 | DAV: 5 -0.399494575063E+03 -0.99453E-01 -0.99444E-01 58624 0.738E-01 0.355E+01 62 | RMM: 6 -0.379712397278E+03 0.19782E+02 -0.14122E+01 45173 0.199E+00 0.168E+01 63 | RMM: 7 -0.390560714619E+03 -0.10848E+02 -0.44725E+00 51942 0.125E+00 0.880E+00 64 | RMM: 8 -0.395060423792E+03 -0.44997E+01 -0.95310E-01 50701 0.706E-01 0.426E+00 65 | RMM: 9 -0.396062408642E+03 -0.10020E+01 -0.27811E-01 54580 0.425E-01 0.143E+00 66 | RMM: 10 -0.396151240833E+03 -0.88832E-01 -0.10364E-01 60723 0.255E-01 0.583E-01 67 | RMM: 11 -0.396155435099E+03 -0.41943E-02 -0.21814E-02 63208 0.116E-01 0.319E-01 68 | RMM: 12 -0.396156706370E+03 -0.12713E-02 -0.34155E-03 61090 0.429E-02 0.113E-01 69 | RMM: 13 -0.396156681102E+03 0.25269E-04 -0.80427E-04 63058 0.215E-02 0.369E-02 70 | RMM: 14 -0.396156664942E+03 0.16160E-04 -0.20869E-04 67534 0.936E-03 0.181E-02 71 | RMM: 15 -0.396156659352E+03 0.55897E-05 -0.33408E-05 58787 0.380E-03 72 | 1 F= -.39615666E+03 E0= -.39615476E+03 d E =-.379699E-02 mag= 0.9451 73 | Starting Core_Hole_Spec 74 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 75 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 76 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 77 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 78 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 79 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 80 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 81 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 82 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 83 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 84 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 85 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 86 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 87 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 88 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 89 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 90 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 91 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 92 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 93 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 94 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 95 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 96 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 97 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 98 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 99 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 100 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 101 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 102 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 103 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 104 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 105 | Ending Core_Hole_Spec 106 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_9_1/DOSCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_9_1/DOSCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_9_1/INCAR: -------------------------------------------------------------------------------- 1 | PREC = Accurate 2 | LREAL = Auto 3 | ALGO = Fast 4 | ENCUT = 400 5 | EDIFF = 1E-5 6 | ISMEAR = 0 7 | SIGMA = 0.05 8 | NBANDS = 704 9 | ISPIN = 2 10 | LORBIT = 11 11 | ICORELEVEL = 2 12 | CLNT = 1 13 | CLN = 1 14 | CLL = 0 15 | CLZ = 1.0 16 | CH_LSPEC = .TRUE. 17 | CH_SIGMA = 0.05 18 | LCHARG = .FALSE. 19 | LWAVE = .FALSE. -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_9_1/KPOINTS: -------------------------------------------------------------------------------- 1 | K-Points 2 | 0 3 | Gamma 4 | 3 3 3 5 | 0 0 0 6 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_9_1/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 0.118258517607E+04 0.11826E+04 -0.10156E+05 39424 0.342E+02 3 | DAV: 2 -0.263018356919E+03 -0.14456E+04 -0.13389E+04 51264 0.102E+02 4 | DAV: 3 -0.390759408743E+03 -0.12774E+03 -0.12585E+03 53760 0.286E+01 5 | DAV: 4 -0.399534804211E+03 -0.87754E+01 -0.87535E+01 62880 0.704E+00 6 | DAV: 5 -0.399633190482E+03 -0.98386E-01 -0.98377E-01 58656 0.734E-01 0.355E+01 7 | RMM: 6 -0.379758287621E+03 0.19875E+02 -0.14162E+01 45132 0.202E+00 0.168E+01 8 | RMM: 7 -0.390608472281E+03 -0.10850E+02 -0.44959E+00 51925 0.126E+00 0.882E+00 9 | RMM: 8 -0.395084232027E+03 -0.44758E+01 -0.96240E-01 50722 0.709E-01 0.431E+00 10 | RMM: 9 -0.396098320778E+03 -0.10141E+01 -0.27666E-01 54622 0.423E-01 0.146E+00 11 | RMM: 10 -0.396198495677E+03 -0.10017E+00 -0.10508E-01 60391 0.256E-01 0.615E-01 12 | RMM: 11 -0.396203162187E+03 -0.46665E-02 -0.22897E-02 61986 0.119E-01 0.342E-01 13 | RMM: 12 -0.396204828145E+03 -0.16660E-02 -0.36273E-03 61637 0.442E-02 0.131E-01 14 | RMM: 13 -0.396204877086E+03 -0.48941E-04 -0.82680E-04 62375 0.219E-02 0.470E-02 15 | RMM: 14 -0.396204843615E+03 0.33471E-04 -0.21895E-04 66367 0.989E-03 0.191E-02 16 | RMM: 15 -0.396204837903E+03 0.57119E-05 -0.40416E-05 61010 0.419E-03 17 | 1 F= -.39620484E+03 E0= -.39620180E+03 d E =-.607719E-02 mag= 0.9042 18 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_9_1/OUTCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_9_1/OUTCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_9_1/POSCAR: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892927170000000 0.0000000000000000 0.0000000000000000 4 | 2.6900120737000002 12.3583693090000004 0.0000000000000000 5 | 5.1267442849000000 2.5187865596000001 11.3793247881999999 6 | S Li P S 7 | 1 28 12 43 8 | Direct 9 | 0.8585389850000027 0.1142017620000004 0.9433858390000012 10 | 0.6687428950000012 0.1761630029999992 0.9039711949999969 11 | 0.6687428950000012 0.6761630179999969 0.9039711949999969 12 | 0.3312571940000026 0.3238356109999998 0.0960283880000006 13 | 0.3312571940000026 0.8238356109999998 0.0960283880000006 14 | 0.6114585400000010 0.3671709600000028 0.1147873399999995 15 | 0.6114585400000010 0.8671709300000003 0.1147873399999995 16 | 0.3885427709999973 0.1328279379999984 0.8852128979999989 17 | 0.3885427709999973 0.6328279379999984 0.8852128979999989 18 | 0.1778128300000006 0.0024677019999970 0.2979970570000035 19 | 0.1778128300000006 0.5024676920000033 0.2979970570000035 20 | 0.8221877220000025 0.4975320989999972 0.7020025850000025 21 | 0.8221877220000025 0.9975321289999997 0.7020025850000025 22 | 0.9686143400000020 0.2278184440000004 0.7495711449999973 23 | 0.9686143400000020 0.7278184290000027 0.7495711449999973 24 | 0.0313853099999974 0.2721820180000023 0.2504284979999980 25 | 0.0313853099999974 0.7721819879999998 0.2504284979999980 26 | 0.2949205039999967 0.0990733060000011 0.7023826240000020 27 | 0.2949205039999967 0.5990732910000034 0.7023826240000020 28 | 0.7050798539999974 0.4009267690000016 0.2976173460000027 29 | 0.7050798539999974 0.9009267690000016 0.2976173460000027 30 | 0.6723443870000025 0.1008888859999999 0.4994633499999992 31 | 0.6723443870000025 0.6008889080000017 0.4994633499999992 32 | 0.3276556730000024 0.3991113310000003 0.5005362630000008 33 | 0.3276556730000024 0.8991113310000003 0.5005362630000008 34 | 0.1361429840000028 0.3533565700000025 0.8824014070000032 35 | 0.1361429840000028 0.8533565999999979 0.8824014070000032 36 | 0.8638582230000011 0.1466431619999966 0.1175977739999965 37 | 0.8638582230000011 0.6466431619999966 0.1175977739999965 38 | 0.7769408229999968 0.3160540160000025 0.5498678679999998 39 | 0.7769408229999968 0.8160539869999965 0.5498678679999998 40 | 0.2230586109999990 0.1839460130000035 0.4501324000000011 41 | 0.2230586109999990 0.6839460130000035 0.4501324000000011 42 | 0.4720538259999998 0.3971497120000009 0.7272555229999966 43 | 0.4720538259999998 0.8971496819999984 0.7272555229999966 44 | 0.5279458170000026 0.1028505559999999 0.2727444169999984 45 | 0.5279458170000026 0.6028505559999999 0.2727444169999984 46 | 0.8348844650000018 0.4582849139999965 0.9417669179999990 47 | 0.8348844650000018 0.9582849140000036 0.9417669179999990 48 | 0.1651147449999968 0.0417154060000016 0.0582332390000033 49 | 0.1651147449999968 0.5417153839999997 0.0582332390000033 50 | 0.8209434150000021 0.2551785710000019 0.4022387269999967 51 | 0.8209434150000021 0.7551785710000019 0.4022387269999967 52 | 0.1790562119999990 0.2448210720000006 0.5977616309999974 53 | 0.1790562119999990 0.7448210720000006 0.5977616309999974 54 | 0.8125801679999967 0.2038727850000015 0.6833589669999967 55 | 0.8125801679999967 0.7038727999999992 0.6833589669999967 56 | 0.1874188330000024 0.2961274090000003 0.3166412409999992 57 | 0.1874188330000024 0.7961274390000028 0.3166412409999992 58 | 0.8374133109999988 0.4616349040000003 0.5170275569999987 59 | 0.8374133109999988 0.9616348739999978 0.5170275569999987 60 | 0.1625860779999968 0.0383653230000007 0.4829725330000016 61 | 0.1625860779999968 0.5383653040000027 0.4829725330000016 62 | 0.5900002719999975 0.3329958919999996 0.5765242579999992 63 | 0.5900002719999975 0.8329958919999996 0.5765242579999992 64 | 0.4099998180000028 0.1670047940000003 0.4234751159999988 65 | 0.4099998180000028 0.6670048240000028 0.4234751159999988 66 | 0.3173536059999975 0.4026352169999967 0.7017551060000002 67 | 0.3173536059999975 0.9026352169999967 0.7017551060000002 68 | 0.6826459170000021 0.0973652899999990 0.2982449229999986 69 | 0.6826459170000021 0.5973652599999966 0.2982449229999986 70 | 0.4775420429999997 0.2918528909999978 0.8781114820000013 71 | 0.4775420429999997 0.7918528909999978 0.8781114820000013 72 | 0.5224580759999995 0.2081471230000034 0.1218881309999986 73 | 0.5224580759999995 0.7081471090000022 0.1218881309999986 74 | 0.5083060259999996 0.0540041479999971 0.7046115990000033 75 | 0.5083060259999996 0.5540041329999994 0.7046115990000033 76 | 0.4916935560000013 0.4459961060000026 0.2953888480000018 77 | 0.4916935560000013 0.9459961060000026 0.2953888480000018 78 | 0.8208362459999989 0.3515947759999989 0.1006187719999971 79 | 0.8208362459999989 0.8515948060000014 0.1006187719999971 80 | 0.1791636049999994 0.1484049709999979 0.8993810420000017 81 | 0.1791636049999994 0.6484049560000003 0.8993810420000017 82 | 0.8585389850000027 0.6142017840000022 0.9433858390000012 83 | 0.1414607910000001 0.3857982159999978 0.0566142830000018 84 | 0.1414607910000001 0.8857982159999978 0.0566142830000018 85 | 0.6807149050000021 0.4703724680000008 0.9116758110000021 86 | 0.6807149050000021 0.9703724379999983 0.9116758110000021 87 | 0.3192848560000030 0.0296275580000014 0.0883243749999991 88 | 0.3192848560000030 0.5296275620000017 0.0883243749999991 89 | 0.9730954170000032 0.4071857630000011 0.8015559910000007 90 | 0.9730954170000032 0.9071857929999965 0.8015559910000007 91 | 0.0269045229999989 0.0928138049999987 0.1984439789999968 92 | 0.0269045229999989 0.5928137900000010 0.1984439789999968 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_9_1/vasp.out: -------------------------------------------------------------------------------- 1 | running on 32 total cores 2 | distrk: each k-point on 32 cores, 1 groups 3 | distr: one band on 1 cores, 32 groups 4 | using from now: INCAR 5 | vasp.6.1.1 19Jun20 (build Feb 22 2021 16:38:43) complex 6 | 7 | POSCAR found type information on POSCAR S LiP S 8 | POSCAR found : 4 types and 84 ions 9 | ----------------------------------------------------------------------------- 10 | | | 11 | | W W AA RRRRR N N II N N GGGG !!! | 12 | | W W A A R R NN N II NN N G G !!! | 13 | | W W A A R R N N N II N N N G !!! | 14 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 15 | | WW WW A A R R N NN II N NN G G | 16 | | W W A A R R N N II N N GGGG !!! | 17 | | | 18 | | You use a magnetic or noncollinear calculation, but did not specify | 19 | | the initial magnetic moment with the MAGMOM tag. Note that a | 20 | | default of 1 will be used for all atoms. This ferromagnetic setup | 21 | | may break the symmetry of the crystal, in particular it may rule | 22 | | out finding an antiferromagnetic solution. Thence, we recommend | 23 | | setting the initial magnetic moment manually or verifying carefully | 24 | | that this magnetic setup is desired. | 25 | | | 26 | ----------------------------------------------------------------------------- 27 | 28 | scaLAPACK will be used 29 | ----------------------------------------------------------------------------- 30 | | | 31 | | W W AA RRRRR N N II N N GGGG !!! | 32 | | W W A A R R NN N II NN N G G !!! | 33 | | W W A A R R N N N II N N N G !!! | 34 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 35 | | WW WW A A R R N NN II N NN G G | 36 | | W W A A R R N N II N N GGGG !!! | 37 | | | 38 | | For optimal performance we recommend to set | 39 | | NCORE = 4 - approx SQRT(number of cores). | 40 | | NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). | 41 | | This setting can greatly improve the performance of VASP for DFT. | 42 | | The default, NCORE=1 might be grossly inefficient on modern | 43 | | multi-core architectures or massively parallel machines. Do your | 44 | | own testing!!!! | 45 | | Unfortunately you need to use the default for GW and RPA | 46 | | calculations (for HF NCORE is supported but not extensively tested | 47 | | yet). | 48 | | | 49 | ----------------------------------------------------------------------------- 50 | 51 | LDA part: xc-table for Ceperly-Alder, standard interpolation 52 | POSCAR, INCAR and KPOINTS ok, starting setup 53 | FFT: planning ... 54 | WAVECAR not read 55 | entering main loop 56 | N E dE d eps ncg rms rms(c) 57 | DAV: 1 0.118258517607E+04 0.11826E+04 -0.10156E+05 39424 0.342E+02 58 | DAV: 2 -0.263018356919E+03 -0.14456E+04 -0.13389E+04 51264 0.102E+02 59 | DAV: 3 -0.390759408743E+03 -0.12774E+03 -0.12585E+03 53760 0.286E+01 60 | DAV: 4 -0.399534804211E+03 -0.87754E+01 -0.87535E+01 62880 0.704E+00 61 | DAV: 5 -0.399633190482E+03 -0.98386E-01 -0.98377E-01 58656 0.734E-01 0.355E+01 62 | RMM: 6 -0.379758287621E+03 0.19875E+02 -0.14162E+01 45132 0.202E+00 0.168E+01 63 | RMM: 7 -0.390608472281E+03 -0.10850E+02 -0.44959E+00 51925 0.126E+00 0.882E+00 64 | RMM: 8 -0.395084232027E+03 -0.44758E+01 -0.96240E-01 50722 0.709E-01 0.431E+00 65 | RMM: 9 -0.396098320778E+03 -0.10141E+01 -0.27666E-01 54622 0.423E-01 0.146E+00 66 | RMM: 10 -0.396198495677E+03 -0.10017E+00 -0.10508E-01 60391 0.256E-01 0.615E-01 67 | RMM: 11 -0.396203162187E+03 -0.46665E-02 -0.22897E-02 61986 0.119E-01 0.342E-01 68 | RMM: 12 -0.396204828145E+03 -0.16660E-02 -0.36273E-03 61637 0.442E-02 0.131E-01 69 | RMM: 13 -0.396204877086E+03 -0.48941E-04 -0.82680E-04 62375 0.219E-02 0.470E-02 70 | RMM: 14 -0.396204843615E+03 0.33471E-04 -0.21895E-04 66367 0.989E-03 0.191E-02 71 | RMM: 15 -0.396204837903E+03 0.57119E-05 -0.40416E-05 61010 0.419E-03 72 | 1 F= -.39620484E+03 E0= -.39620180E+03 d E =-.607719E-02 mag= 0.9042 73 | Starting Core_Hole_Spec 74 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 75 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 76 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 77 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 78 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 79 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 80 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 81 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 82 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 83 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 84 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 85 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 86 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 87 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 88 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 89 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 90 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 91 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 92 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 93 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 94 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 95 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 96 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 97 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 98 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 99 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 100 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 101 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 102 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 103 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 104 | ZCORE= 10.0000000000000 ECORE= -2393.17085973796 105 | Ending Core_Hole_Spec 106 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_SCF/CONTCAR: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892072299137546 -0.0045582927629227 0.0457425203370421 4 | 1.3472173211783336 6.1786729084373642 0.0192368121238670 5 | 5.0855915969651093 2.4906284758103654 11.4039621787899215 6 | Li P S 7 | 14 6 22 8 | Direct 9 | 0.6687429681853914 0.3523260262110099 0.9039712412362348 10 | 0.3312572099294613 0.6476712634939759 0.0960283951009657 11 | 0.6114585734705145 0.7343419829887381 0.1147873480188437 12 | 0.3885427908029584 0.2656559196982897 0.8852129292632043 13 | 0.1778128505142504 0.0049354053794772 0.2979970907895222 14 | 0.8221878062633934 0.9950642851196179 0.7020026166974915 15 | 0.9686144020561400 0.4556369208843876 0.7495712001414958 16 | 0.0313853150717307 0.5443640990176988 0.2504285290213204 17 | 0.2949205286316996 0.1981466305193322 0.7023827015199799 18 | 0.7050799199805198 0.8018536220907464 0.2976173714899844 19 | 0.6723444712504119 0.2017777806088077 0.4994633708840368 20 | 0.3276557097807640 0.7982227182604404 0.5005362951219610 21 | 0.1361429941051071 0.7067131908191371 0.8824014423855360 22 | 0.8638583120488335 0.2932863464507776 0.1175977826833758 23 | 0.7769408888468163 0.6321080916171624 0.5498679552055918 24 | 0.2230586287391674 0.3678920510938468 0.4501324242229074 25 | 0.4720538555832121 0.7942995050150898 0.7272555808500982 26 | 0.5279458913772075 0.2057011350358238 0.2727444414263829 27 | 0.8348845149113302 0.9165698749929447 0.9417670004218905 28 | 0.1651147592327646 0.0834308187346409 0.0582332432232917 29 | 0.8209434782455105 0.5103571975189283 0.4022387616785821 30 | 0.1790562316988940 0.4896421674948783 0.5977617002079967 31 | 0.8125802272163227 0.4077455926264122 0.6833590422081670 32 | 0.1874188465469402 0.5922548555001370 0.3166412751091556 33 | 0.8374133762435036 0.9232698469554563 0.5170276185841658 34 | 0.1625860990918824 0.0767306561960197 0.4829725562982219 35 | 0.5900003420401418 0.6659918348026892 0.5765242958641963 36 | 0.4099998518898005 0.3340096124861489 0.4234751510165253 37 | 0.3173536323576371 0.8052704780631288 0.7017551399964077 38 | 0.6826459601173340 0.1947305883404198 0.2982449506878240 39 | 0.4775420705549607 0.5837058324516349 0.8781115613149524 40 | 0.5224581183105670 0.4162942842364501 0.1218881369542189 41 | 0.5083061068028556 0.1080083038135413 0.7046116534145526 42 | 0.4916935755691938 0.8919922714469735 0.2953888699840945 43 | 0.8208362858841198 0.7031896073070385 0.1006187763953790 44 | 0.1791636144595827 0.2968099712101093 0.8993811219681476 45 | 0.8585390477262607 0.2284035322807583 0.9433858695418920 46 | 0.1414608066159886 0.7715964700864930 0.0566142867473118 47 | 0.6807149810952424 0.9407450163164057 0.9116758906749638 48 | 0.3192848944202424 0.0592551200731393 0.0883243824922175 49 | 0.9730954522642747 0.8143715835613889 0.8015560597340325 50 | 0.0269045260670779 0.1856276311999068 0.1984439894228558 51 | 52 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 53 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 54 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 55 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 56 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 57 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 58 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 59 | 0.00000000E+00 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https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_SCF/DOSCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_SCF/INCAR: -------------------------------------------------------------------------------- 1 | ALGO = Fast 2 | EDIFF = 1e-05 3 | EDIFFG = -0.01 4 | ENCUT = 520 5 | IBRION = 2 6 | ICHARG = 1 7 | ISIF = 2 8 | ISMEAR = 0 9 | ISPIN = 2 10 | ISYM = 0 11 | LCHARG = False 12 | LORBIT = 11 13 | LREAL = Auto 14 | LWAVE = False 15 | NELM = 200 16 | NELMIN = 6 17 | NPAR = 4 18 | NSW = 0 19 | PREC = Accurate 20 | SIGMA = 0.05 21 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_SCF/KPOINTS: -------------------------------------------------------------------------------- 1 | Fully automatic kpoint scheme 2 | 0 3 | Automatic 4 | 25 5 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_SCF/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 0.881879785528E+03 0.88188E+03 -0.70309E+04 6336 0.112E+03 3 | DAV: 2 -0.984952533320E+02 -0.98038E+03 -0.93235E+03 7952 0.196E+02 4 | DAV: 3 -0.197688688929E+03 -0.99193E+02 -0.98210E+02 8104 0.660E+01 5 | DAV: 4 -0.199970715964E+03 -0.22820E+01 -0.22723E+01 7944 0.115E+01 6 | DAV: 5 -0.200037689133E+03 -0.66973E-01 -0.66900E-01 7824 0.195E+00 0.422E+01 7 | RMM: 6 -0.195577727055E+03 0.44600E+01 -0.13429E+01 6506 0.586E+00 0.258E+01 8 | RMM: 7 -0.202640651915E+03 -0.70629E+01 -0.10088E+01 7198 0.542E+00 0.105E+01 9 | RMM: 8 -0.203689350169E+03 -0.10487E+01 -0.22523E+00 7603 0.293E+00 0.411E+00 10 | RMM: 9 -0.203579265120E+03 0.11009E+00 -0.29557E-01 7892 0.131E+00 0.169E+00 11 | RMM: 10 -0.203561996163E+03 0.17269E-01 -0.15444E-01 7933 0.767E-01 0.718E-01 12 | RMM: 11 -0.203566704044E+03 -0.47079E-02 -0.23670E-02 8180 0.337E-01 0.506E-01 13 | RMM: 12 -0.203568138256E+03 -0.14342E-02 -0.67192E-03 8574 0.159E-01 0.284E-01 14 | RMM: 13 -0.203569168739E+03 -0.10305E-02 -0.17884E-03 7991 0.809E-02 0.902E-02 15 | RMM: 14 -0.203569337060E+03 -0.16832E-03 -0.63792E-04 8113 0.474E-02 0.449E-02 16 | RMM: 15 -0.203569340132E+03 -0.30720E-05 -0.16688E-04 8229 0.263E-02 0.299E-02 17 | RMM: 16 -0.203569343756E+03 -0.36236E-05 -0.58748E-05 7176 0.146E-02 18 | 1 F= -.20356934E+03 E0= -.20356934E+03 d E =-.443280E-15 mag= -0.0008 19 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_SCF/OUTCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_SCF/OUTCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_SCF/POSCAR: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892072299137546 -0.0045582927629227 0.0457425203370421 4 | 1.3472173211783336 6.1786729084373642 0.0192368121238670 5 | 5.0855915969651093 2.4906284758103654 11.4039621787899215 6 | Li P S 7 | 14 6 22 8 | Direct 9 | 0.6687429681853894 0.3523260262110126 0.9039712412362317 10 | 0.3312572099294600 0.6476712634939786 0.0960283951009658 11 | 0.6114585734705177 0.7343419829887414 0.1147873480188454 12 | 0.3885427908029592 0.2656559196982933 0.8852129292632063 13 | 0.1778128505142525 0.0049354053794799 0.2979970907895192 14 | 0.8221878062633918 0.9950642851196151 0.7020026166974888 15 | 0.9686144020561377 0.4556369208843891 0.7495712001414975 16 | 0.0313853150717303 0.5443640990176954 0.2504285290213179 17 | 0.2949205286317004 0.1981466305193354 0.7023827015199765 18 | 0.7050799199805200 0.8018536220907443 0.2976173714899878 19 | 0.6723444712504114 0.2017777806088064 0.4994633708840401 20 | 0.3276557097807620 0.7982227182604432 0.5005362951219575 21 | 0.1361429941051054 0.7067131908191373 0.8824014423855367 22 | 0.8638583120488356 0.2932863464507764 0.1175977826833790 23 | 0.7769408888468149 0.6321080916171602 0.5498679552055915 24 | 0.2230586287391673 0.3678920510938440 0.4501324242229064 25 | 0.4720538555832095 0.7942995050150896 0.7272555808501016 26 | 0.5279458913772060 0.2057011350358253 0.2727444414263824 27 | 0.8348845149113299 0.9165698749929417 0.9417670004218892 28 | 0.1651147592327670 0.0834308187346428 0.0582332432232888 29 | 0.8209434782455136 0.5103571975189255 0.4022387616785807 30 | 0.1790562316988965 0.4896421674948781 0.5977617002079981 31 | 0.8125802272163228 0.4077455926264148 0.6833590422081703 32 | 0.1874188465469407 0.5922548555001388 0.3166412751091553 33 | 0.8374133762435056 0.9232698469554576 0.5170276185841691 34 | 0.1625860990918834 0.0767306561960230 0.4829725562982253 35 | 0.5900003420401391 0.6659918348026909 0.5765242958641942 36 | 0.4099998518898000 0.3340096124861488 0.4234751510165256 37 | 0.3173536323576395 0.8052704780631271 0.7017551399964105 38 | 0.6826459601173318 0.1947305883404212 0.2982449506878265 39 | 0.4775420705549628 0.5837058324516330 0.8781115613149524 40 | 0.5224581183105674 0.4162942842364497 0.1218881369542215 41 | 0.5083061068028543 0.1080083038135444 0.7046116534145491 42 | 0.4916935755691932 0.8919922714469746 0.2953888699840955 43 | 0.8208362858841207 0.7031896073070416 0.1006187763953790 44 | 0.1791636144595808 0.2968099712101095 0.8993811219681468 45 | 0.8585390477262619 0.2284035322807562 0.9433858695418907 46 | 0.1414608066159894 0.7715964700864949 0.0566142867473140 47 | 0.6807149810952434 0.9407450163164075 0.9116758906749631 48 | 0.3192848944202427 0.0592551200731378 0.0883243824922190 49 | 0.9730954522642765 0.8143715835613863 0.8015560597340347 50 | 0.0269045260670813 0.1856276311999048 0.1984439894228581 51 | 52 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 53 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 54 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 55 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 56 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 57 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 58 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 59 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 60 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 61 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 62 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 63 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 64 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 65 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 66 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 67 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 68 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 69 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 70 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 71 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 72 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 73 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 74 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 75 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 76 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 77 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 78 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 79 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 80 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 81 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 82 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 83 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 84 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 85 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 86 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 87 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 88 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 89 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 90 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 91 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 92 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 93 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 94 | -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_SCF/XDATCAR.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/notebooks/data/Li7P3S11/XAS_input_SCF/XDATCAR.bz2 -------------------------------------------------------------------------------- /notebooks/data/Li7P3S11/XAS_input_SCF/vasp.out: -------------------------------------------------------------------------------- 1 | Wed Apr 14 13:11:41 EDT 2021 2 | running on 32 total cores 3 | distrk: each k-point on 32 cores, 1 groups 4 | distr: one band on 8 cores, 4 groups 5 | using from now: INCAR 6 | vasp.6.1.1 19Jun20 (build Mar 12 2021 19:31:03) complex 7 | 8 | POSCAR found type information on POSCAR LiP S 9 | POSCAR found : 3 types and 42 ions 10 | ----------------------------------------------------------------------------- 11 | | | 12 | | W W AA RRRRR N N II N N GGGG !!! | 13 | | W W A A R R NN N II NN N G G !!! | 14 | | W W A A R R N N N II N N N G !!! | 15 | | W WW W AAAAAA RRRRR N N N II N N N G GGG ! | 16 | | WW WW A A R R N NN II N NN G G | 17 | | W W A A R R N N II N N GGGG !!! | 18 | | | 19 | | You use a magnetic or noncollinear calculation, but did not specify | 20 | | the initial magnetic moment with the MAGMOM tag. Note that a | 21 | | default of 1 will be used for all atoms. This ferromagnetic setup | 22 | | may break the symmetry of the crystal, in particular it may rule | 23 | | out finding an antiferromagnetic solution. Thence, we recommend | 24 | | setting the initial magnetic moment manually or verifying carefully | 25 | | that this magnetic setup is desired. | 26 | | | 27 | ----------------------------------------------------------------------------- 28 | 29 | scaLAPACK will be used 30 | LDA part: xc-table for Ceperly-Alder, standard interpolation 31 | generate k-points for: 2 4 2 32 | POSCAR, INCAR and KPOINTS ok, starting setup 33 | FFT: planning ... 34 | WAVECAR not read 35 | WARNING: chargedensity file is incomplete 36 | entering main loop 37 | N E dE d eps ncg rms rms(c) 38 | DAV: 1 0.881879785528E+03 0.88188E+03 -0.70309E+04 6336 0.112E+03 39 | DAV: 2 -0.984952533320E+02 -0.98038E+03 -0.93235E+03 7952 0.196E+02 40 | DAV: 3 -0.197688688929E+03 -0.99193E+02 -0.98210E+02 8104 0.660E+01 41 | DAV: 4 -0.199970715964E+03 -0.22820E+01 -0.22723E+01 7944 0.115E+01 42 | DAV: 5 -0.200037689133E+03 -0.66973E-01 -0.66900E-01 7824 0.195E+00 0.422E+01 43 | RMM: 6 -0.195577727055E+03 0.44600E+01 -0.13429E+01 6506 0.586E+00 0.258E+01 44 | RMM: 7 -0.202640651915E+03 -0.70629E+01 -0.10088E+01 7198 0.542E+00 0.105E+01 45 | RMM: 8 -0.203689350169E+03 -0.10487E+01 -0.22523E+00 7603 0.293E+00 0.411E+00 46 | RMM: 9 -0.203579265120E+03 0.11009E+00 -0.29557E-01 7892 0.131E+00 0.169E+00 47 | RMM: 10 -0.203561996163E+03 0.17269E-01 -0.15444E-01 7933 0.767E-01 0.718E-01 48 | RMM: 11 -0.203566704044E+03 -0.47079E-02 -0.23670E-02 8180 0.337E-01 0.506E-01 49 | RMM: 12 -0.203568138256E+03 -0.14342E-02 -0.67192E-03 8574 0.159E-01 0.284E-01 50 | RMM: 13 -0.203569168739E+03 -0.10305E-02 -0.17884E-03 7991 0.809E-02 0.902E-02 51 | RMM: 14 -0.203569337060E+03 -0.16832E-03 -0.63792E-04 8113 0.474E-02 0.449E-02 52 | RMM: 15 -0.203569340132E+03 -0.30720E-05 -0.16688E-04 8229 0.263E-02 0.299E-02 53 | RMM: 16 -0.203569343756E+03 -0.36236E-05 -0.58748E-05 7176 0.146E-02 54 | 1 F= -.20356934E+03 E0= -.20356934E+03 d E =-.443280E-15 mag= -0.0008 55 | Wed Apr 14 13:14:21 EDT 2021 56 | -------------------------------------------------------------------------------- /scripts/README.md: -------------------------------------------------------------------------------- 1 | **How to use the scripts for X-ray absorption spectroscopy (XAS) calculations.** 2 | -------------------------------------------------------------------------------- /scripts/collect_xas_output.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | """ 4 | Extract XAS spectra from VASP core-hole potential calculations. 5 | 6 | """ 7 | 8 | import argparse 9 | 10 | from xas_tools.vasp import parse_vasp_chp_output 11 | 12 | __author__ = "Alexander Urban" 13 | __email__ = "aurban@atomistic.net" 14 | __date__ = "2021-06-09" 15 | __version__ = "0.11" 16 | 17 | 18 | def analyze_output(paths): 19 | for p in paths: 20 | parse_vasp_chp_output(p) 21 | 22 | 23 | def main(): 24 | 25 | parser = argparse.ArgumentParser( 26 | description=__doc__+"\n{} {}".format(__date__, __author__), 27 | formatter_class=argparse.RawDescriptionHelpFormatter) 28 | 29 | parser.add_argument( 30 | "paths", 31 | help="Paths to the base directories of VASP CHP calculations.", 32 | nargs="+") 33 | 34 | args = parser.parse_args() 35 | 36 | analyze_output(args.paths) 37 | 38 | 39 | if (__name__ == "__main__"): 40 | main() 41 | -------------------------------------------------------------------------------- /scripts/make_xas_input.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | """ 4 | Generate VASP input files for XAS core-hole potential calculations 5 | for a given input file in POSCAR format. 6 | 7 | """ 8 | 9 | import argparse 10 | import os 11 | 12 | import pymatgen as mg 13 | from xas_tools.vasp import CHPCalculation 14 | 15 | __author__ = "Alexander Urban" 16 | __email__ = "aurban@atomistic.net" 17 | __date__ = "2021-03-27" 18 | __version__ = "0.11" 19 | 20 | 21 | def make_input(poscar_files, supercell, band_multiple, element, level, 22 | core_hole, grid_points, ncore, vasp_set): 23 | 24 | for i, f in enumerate(poscar_files): 25 | struc = mg.core.Structure.from_file(f) 26 | chp = CHPCalculation(struc, element=element, n=level[0], 27 | ell=level[1], z=core_hole) 28 | path = os.path.basename("XAS_" + f + "_{}".format(i)) 29 | if vasp_set is not None: 30 | chp.write_vasp_input(supercell=supercell, 31 | path=path, 32 | band_multiple=band_multiple, 33 | grid_points=grid_points, 34 | ncore=ncore, 35 | vasp_set=vasp_set) 36 | else: 37 | chp.write_vasp_input(supercell=supercell, 38 | path=path, 39 | band_multiple=band_multiple, 40 | grid_points=grid_points, 41 | ncore=ncore) 42 | 43 | 44 | def main(): 45 | 46 | parser = argparse.ArgumentParser( 47 | description=__doc__+"\n{} {}".format(__date__, __author__), 48 | formatter_class=argparse.RawDescriptionHelpFormatter) 49 | 50 | parser.add_argument( 51 | "poscar_files", 52 | help="Path to one or more atomic structure file(s) in POSCAR format.", 53 | nargs="+") 54 | 55 | parser.add_argument( 56 | "--supercell", "-s", 57 | help="Supercell multiples (default: None).", 58 | type=int, 59 | default=None, 60 | nargs=3) 61 | 62 | parser.add_argument( 63 | "--band-multiple", "-n", 64 | help="Number of bands per valence electron (default: 1).", 65 | type=int, 66 | default=1) 67 | 68 | parser.add_argument( 69 | "--element", "-e", 70 | help="Chemical symbol of the element that is probed (default: S)", 71 | default="S") 72 | 73 | parser.add_argument( 74 | "--level", "-l", 75 | help="Principal and angular momentum quantum numbers of the level " 76 | "that is probed. For example, the K edge (excitation from " 77 | "the 1s orbitals) would be (1, 0). Default: (1, 0)", 78 | type=int, 79 | default=[1, 0], 80 | nargs=2) 81 | 82 | parser.add_argument( 83 | "--core-hole", "-c", 84 | help="Fraction of the core hole in electrons (default: 1.0).", 85 | type=float, 86 | default=1.0) 87 | 88 | parser.add_argument( 89 | "--grid-points", "-g", 90 | help="Number of grid points for the representation of " 91 | "spectral lines (default: 40000).", 92 | type=int, 93 | default=40000) 94 | 95 | parser.add_argument( 96 | "--ncore", 97 | help="VASP's NCORE parameter, which is usually square root of " 98 | "the number of cores (default: 1).", 99 | type=int, 100 | default=1) 101 | 102 | parser.add_argument( 103 | "--vasp-set", 104 | help="Path to a YAML file with VASP input file parameters.", 105 | default=None) 106 | 107 | args = parser.parse_args() 108 | 109 | make_input(args.poscar_files, args.supercell, args.band_multiple, 110 | args.element, args.level, args.core_hole, args.grid_points, 111 | args.ncore, args.vasp_set) 112 | 113 | 114 | if (__name__ == "__main__"): 115 | main() 116 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup, find_packages 2 | from codecs import open 3 | import os 4 | import glob 5 | 6 | __author__ = "The Atomistic.net Team" 7 | __email__ = "nartrith@atomistic.net" 8 | __maintainer__ = "Haoyue Guo, Alexander Urban, Nongnuch Artrith" 9 | __maintainer_email__ = "hg2568@columbia.edu, a.urban@columbia.edu, nartrith@atomistic.net" 10 | 11 | here = os.path.abspath(os.path.dirname(__file__)) 12 | package_name = 'xas_tools' 13 | package_description = 'Tools for X-ray absorption spectroscopy (XAS)' 14 | 15 | # Get the long description from the README file 16 | with open(os.path.join(here, 'README.md'), encoding='utf-8') as fp: 17 | long_description = fp.read() 18 | 19 | # Get version number from the VERSION file 20 | with open(os.path.join(here, package_name, 'VERSION')) as fp: 21 | version = fp.read().strip() 22 | 23 | setup( 24 | name=package_name, 25 | version=version, 26 | description=package_description, 27 | long_description=long_description, 28 | author=__author__, 29 | author_email=__email__, 30 | maintainer=__maintainer__, 31 | maintainer_email=__maintainer_email__, 32 | license='MPL', 33 | classifiers=[ 34 | 'Development Status :: 3 - Alpha', 35 | 'Intended Audience :: Science/Research', 36 | 'Topic :: Scientific/Engineering :: Physics', 37 | 'Topic :: Scientific/Engineering :: Chemistry', 38 | 'Topic :: Scientific/Engineering :: Artificial Intelligence', 39 | 'License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)', 40 | 'Programming Language :: Python :: 3' 41 | ], 42 | keywords=['materials science', 'spectroscopy'], 43 | packages=find_packages(exclude=['tests']), 44 | scripts=glob.glob(os.path.join("scripts", "*.py")), 45 | install_requires=['numpy', 'pymatgen', 'pyyaml'] 46 | ) 47 | -------------------------------------------------------------------------------- /xas_tools/LDA-XAS.yaml: -------------------------------------------------------------------------------- 1 | INCAR: 2 | ALGO: NORMAL 3 | EDIFF: 1.0e-05 4 | EDIFFG: -0.01 5 | ENCUT: 400 6 | ISMEAR: 0 7 | ISPIN: 2 8 | LORBIT: '11' 9 | LREAL: AUTO 10 | LWAVE: false 11 | PREC: Accurate 12 | SIGMA: 0.05 13 | LCHARG: .FALSE. 14 | LWAVE: .FALSE. 15 | KPOINTS: 16 | # length: 25 17 | grid_density: 6000 18 | POTCAR_FUNCTIONAL: "LDA_52" 19 | POTCAR: 20 | Li: 21 | symbol: Li_GW 22 | P: 23 | symbol: P_GW 24 | S: 25 | symbol: S_GW 26 | Ni: 27 | symbol: Ni_GW 28 | Mn: 29 | symbol: Mn_GW 30 | Co: 31 | symbol: Co_GW 32 | -------------------------------------------------------------------------------- /xas_tools/VERSION: -------------------------------------------------------------------------------- 1 | 0.1.0 2 | -------------------------------------------------------------------------------- /xas_tools/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/xas_tools/__init__.py -------------------------------------------------------------------------------- /xas_tools/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/atomisticnet/xas-tools/26dab3f425a6b23be794c01c80d7298a9356d188/xas_tools/tests/__init__.py -------------------------------------------------------------------------------- /xas_tools/tests/fixtures/CONTCAR_Li3PS4: -------------------------------------------------------------------------------- 1 | γ-Li3PS4 Li6 P2 S8 2 | 1.00000000000000 3 | 7.7728887530431452 -0.0000033681917313 0.0000011020054775 4 | -0.0000027248887747 6.6186469761244338 -0.0000003841750128 5 | 0.0000010357285640 -0.0000004507128427 6.2250567792974012 6 | Li P S 7 | 6 2 8 8 | Direct 9 | 0.2435623021061343 0.3168557575935761 -0.0000276211987660 10 | 0.2564381019141520 0.6831441890591163 0.4999719084053222 11 | 0.7435611655912444 0.6831434992933233 0.4999717768080432 12 | 0.7564385084591919 0.3168565213342524 -0.0000283052197278 13 | -0.0000002022956064 0.1433423811607082 0.4920524992366043 14 | 0.5000001100011322 0.8566575011659002 0.9920524276552353 15 | 0.0000004459212349 0.8183895641568136 0.0008237238071628 16 | 0.4999994910534741 0.1816104392205975 0.5008236991422910 17 | 0.2180289937774249 0.6737859652343253 0.8914540468516050 18 | 0.2819691231790888 0.3262152529442662 0.3914533684653503 19 | 0.7180305678642873 0.3262150763464409 0.3914527184322897 20 | 0.7819713061958816 0.6737862525889325 0.8914538150616318 21 | 0.0000003055071354 0.1120806960591720 0.8913364701868740 22 | 0.4999997684867032 0.8879169675626877 0.3913353072636300 23 | -0.0000001662142958 0.8086679840744586 0.3320856195908329 24 | 0.5000001784528179 0.1913318552054320 0.8320884975116104 25 | 26 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 27 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 28 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 29 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 30 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 31 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 32 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 33 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 34 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 35 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 36 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 37 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 38 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 39 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 40 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 41 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 42 | -------------------------------------------------------------------------------- /xas_tools/tests/fixtures/CONTCAR_Li7P3S11: -------------------------------------------------------------------------------- 1 | Li14 P6 S22 2 | 1.00000000000000 3 | 12.3892072299137546 -0.0045582927629227 0.0457425203370421 4 | 1.3472173211783336 6.1786729084373642 0.0192368121238670 5 | 5.0855915969651093 2.4906284758103654 11.4039621787899215 6 | Li P S 7 | 14 6 22 8 | Direct 9 | 0.6687429681853894 0.3523260262110126 0.9039712412362317 10 | 0.3312572099294600 0.6476712634939786 0.0960283951009658 11 | 0.6114585734705177 0.7343419829887414 0.1147873480188454 12 | 0.3885427908029592 0.2656559196982933 0.8852129292632063 13 | 0.1778128505142525 0.0049354053794799 0.2979970907895192 14 | 0.8221878062633918 0.9950642851196151 0.7020026166974888 15 | 0.9686144020561377 0.4556369208843891 0.7495712001414975 16 | 0.0313853150717303 0.5443640990176954 0.2504285290213179 17 | 0.2949205286317004 0.1981466305193354 0.7023827015199765 18 | 0.7050799199805200 0.8018536220907443 0.2976173714899878 19 | 0.6723444712504114 0.2017777806088064 0.4994633708840401 20 | 0.3276557097807620 0.7982227182604432 0.5005362951219575 21 | 0.1361429941051054 0.7067131908191373 0.8824014423855367 22 | 0.8638583120488356 0.2932863464507764 0.1175977826833790 23 | 0.7769408888468149 0.6321080916171602 0.5498679552055915 24 | 0.2230586287391673 0.3678920510938440 0.4501324242229064 25 | 0.4720538555832095 0.7942995050150896 0.7272555808501016 26 | 0.5279458913772060 0.2057011350358253 0.2727444414263824 27 | 0.8348845149113299 0.9165698749929417 0.9417670004218892 28 | 0.1651147592327670 0.0834308187346428 0.0582332432232888 29 | 0.8209434782455136 0.5103571975189255 0.4022387616785807 30 | 0.1790562316988965 0.4896421674948781 0.5977617002079981 31 | 0.8125802272163228 0.4077455926264148 0.6833590422081703 32 | 0.1874188465469407 0.5922548555001388 0.3166412751091553 33 | 0.8374133762435056 0.9232698469554576 0.5170276185841691 34 | 0.1625860990918834 0.0767306561960230 0.4829725562982253 35 | 0.5900003420401391 0.6659918348026909 0.5765242958641942 36 | 0.4099998518898000 0.3340096124861488 0.4234751510165256 37 | 0.3173536323576395 0.8052704780631271 0.7017551399964105 38 | 0.6826459601173318 0.1947305883404212 0.2982449506878265 39 | 0.4775420705549628 0.5837058324516330 0.8781115613149524 40 | 0.5224581183105674 0.4162942842364497 0.1218881369542215 41 | 0.5083061068028543 0.1080083038135444 0.7046116534145491 42 | 0.4916935755691932 0.8919922714469746 0.2953888699840955 43 | 0.8208362858841207 0.7031896073070416 0.1006187763953790 44 | 0.1791636144595808 0.2968099712101095 0.8993811219681468 45 | 0.8585390477262619 0.2284035322807562 0.9433858695418907 46 | 0.1414608066159894 0.7715964700864949 0.0566142867473140 47 | 0.6807149810952434 0.9407450163164075 0.9116758906749631 48 | 0.3192848944202427 0.0592551200731378 0.0883243824922190 49 | 0.9730954522642765 0.8143715835613863 0.8015560597340347 50 | 0.0269045260670813 0.1856276311999048 0.1984439894228581 51 | 52 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 53 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 54 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 55 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 56 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 57 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 58 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 59 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 60 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 61 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 62 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 63 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 64 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 65 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 66 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 67 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 68 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 69 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 70 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 71 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 72 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 73 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 74 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 75 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 76 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 77 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 78 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 79 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 80 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 81 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 82 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 83 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 84 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 85 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 86 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 87 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 88 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 89 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 90 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 91 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 92 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 93 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 94 | -------------------------------------------------------------------------------- /xas_tools/tests/test_vasp.py: -------------------------------------------------------------------------------- 1 | import unittest 2 | import tempfile 3 | import json 4 | import os 5 | 6 | import pymatgen as mg 7 | 8 | from xas_tools.vasp import CHPCalculation 9 | 10 | fixtures = os.path.join(os.path.dirname(__file__), 'fixtures') 11 | Li3PS4 = os.path.join(fixtures, 'CONTCAR_Li3PS4') 12 | 13 | 14 | class VaspTest(unittest.TestCase): 15 | 16 | def test_write_vasp_Li3PS4(self): 17 | struc = mg.Structure.from_file(Li3PS4) 18 | chp = CHPCalculation(struc, element="S", n=1, ell=0, z=1.0) 19 | with tempfile.TemporaryDirectory() as d: 20 | path = os.path.join(d, 'Li3PS4_chp_input') 21 | chp.write_vasp_input(supercell=(1, 2, 1), 22 | band_multiple=2, 23 | path=path) 24 | with open(os.path.join(path, 'metadata.json')) as fp: 25 | metadata = json.load(fp) 26 | self.assertEqual(metadata['multiplicity'][0], 2) 27 | 28 | def test_vasp_warning(self): 29 | raise NotImplementedError( 30 | 'The VASP test is only a stub and needs to be completed.') 31 | 32 | 33 | if __name__ == "__main__": 34 | unittest.main() 35 | -------------------------------------------------------------------------------- /xas_tools/util.py: -------------------------------------------------------------------------------- 1 | """ 2 | Utility functions. 3 | 4 | """ 5 | 6 | import numpy as np 7 | 8 | # Check if Numba is available 9 | try: 10 | from numba import jit 11 | numba_available = True 12 | except ImportError: 13 | numba_available = False 14 | 15 | # Define a no-op decorator 16 | def jit(*args, **kwargs): 17 | def decorator(func): 18 | return func 19 | return decorator 20 | 21 | __author__ = "Nong Artrith, Alexander Urban" 22 | __email__ = "nartrith@atomistic.net" 23 | __maintainer__ = "Nong Artrith, Alexander Urban" 24 | __maintainer_email__ = ("nartrith@atomistic.net" 25 | + ", aurban@atomistic.net") 26 | __date__ = "2021-06-08" 27 | __version__ = "0.1" 28 | 29 | @jit(nopython=True) 30 | def gauss_function(x, x0, s): 31 | """ 32 | Normalized Gaussian 33 | 34 | Args: 35 | x (float): argument 36 | x0 (float): mean 37 | s (float): standard deviation 38 | 39 | """ 40 | return np.exp(-0.5*((x-x0)/s)**2)/(s*np.sqrt(2.0*np.pi)) 41 | 42 | 43 | @jit(nopython=True) 44 | def lorentz_function(x, x0, w): 45 | """ 46 | Normalized Lorentz (Cauchy) function 47 | 48 | Args: 49 | x (float): argument 50 | x0 (float): center 51 | w (float): full width at half maximum (FWHM) 52 | 53 | """ 54 | return 2.0/(w*np.pi)/(1.0 + 4.0*(x - x0)**2/w**2) 55 | 56 | 57 | def variable_convolution(x, y, kernel_func, sigma_start, sigma_end=None, 58 | num_points=None, x_range=None): 59 | """ 60 | Apply convolution with a kernel of linearly varying or static 61 | width across the x range. 62 | 63 | Args: 64 | x (ndarray): X values. 65 | y (ndarray): Y values. 66 | kernel_func (function): Kernel function f(x, x_center, sigma). 67 | sigma_start (float): Initial standard deviation. 68 | sigma_end (float, optional): Final standard deviation. If None, 69 | sigma_start is used. 70 | num_points (int, optional): Number of points to evaluate the 71 | kernel function. If None, the number of points in the 72 | input x is used. 73 | x_range (2-tuple, optional): Min and max x values for output. 74 | If None, use min and max of `x`. 75 | 76 | Returns: 77 | x_out, y_out (ndarray): Convolved X and Y values. 78 | 79 | """ 80 | 81 | if sigma_end is None: 82 | sigma_end = sigma_start 83 | 84 | if num_points is None: 85 | num_points = len(x) 86 | 87 | if x_range is not None: 88 | x_min, x_max = x_range 89 | else: 90 | x_min, x_max = np.min(x), np.max(x) 91 | 92 | return _variable_convolution_numba(x, y, sigma_start, sigma_end, 93 | num_points, x_min, x_max) 94 | 95 | 96 | @jit(nopython=True) 97 | def _variable_convolution_numba(x, y, sigma_start, sigma_end, num_points, 98 | x_min, x_max): 99 | """ 100 | A helper function for Numba. See `variable_convolution` for the 101 | documentation of the arguments. 102 | 103 | """ 104 | sigmas = np.linspace(sigma_start, sigma_end, len(x)) 105 | x_out = np.linspace(x_min, x_max, num_points) 106 | y_out = np.zeros(num_points) 107 | 108 | for i in range(len(x)): 109 | sigma = sigmas[i] 110 | kernel = gauss_function(x_out, x[i], sigma) 111 | kernel_sum = np.sum(kernel) 112 | if kernel_sum != 0: 113 | kernel /= kernel_sum 114 | y_out += y[i] * kernel 115 | 116 | return x_out, y_out 117 | 118 | 119 | def broaden(x_in, y_in, fwhm, fwhm2=None, xlim=None, n=100, sigma=False, 120 | lorentz=False): 121 | """ 122 | Deprecated. Use the function `variable_convolution` instead. 123 | 124 | Broaden a line shape via convolution with a distribution function. 125 | A Gaussian function is used unless `lorentz` is set to True, in 126 | which case a Lorentzian function is used. 127 | 128 | Args: 129 | x_in, y_in (ndarray): X and Y values of the line shape 130 | fwhm (float): full width at half maximum (FWHM) of the distribution 131 | function 132 | fwhm2 (float): if specified, the FWHM is linearly varied from 133 | `fwhm` to `fwhm2` from the lowest to the highest X value 134 | xlim (tuple): Tuple (x0, x1) with the minimal and maximal X values 135 | n (int): number of discretization points 136 | sigma (bool): if True, assume that `fwhm` is the standard deviation 137 | lorentz (bool): if True, perform convolution with a Lorentzian function 138 | instead of a Gaussian function 139 | 140 | Returns: 141 | x, y (ndarray) 142 | 143 | """ 144 | 145 | if fwhm2 is None: 146 | scale = np.ones(n) 147 | else: 148 | scale = np.linspace(1.0, fwhm2/fwhm, n) 149 | 150 | if lorentz: 151 | func = lorentz_function 152 | sigma = True 153 | else: 154 | func = gauss_function 155 | 156 | if sigma or lorentz: 157 | s = fwhm 158 | else: 159 | s = fwhm/(2.0*np.sqrt(2.0*np.log(2.0))) 160 | 161 | x0 = np.min(x_in) 162 | x1 = np.max(x_in) 163 | if xlim is not None: 164 | if xlim[0] is not None: 165 | x0 = max(xlim[0], x0) 166 | if xlim[1] is not None: 167 | x1 = min(xlim[1], x1) 168 | 169 | # determine non-zero y values so that we can ignore exact zero 170 | # values at beginning and end of x range 171 | idx = [i for i in range(len(x_in)) if y_in[i] != 0.0] 172 | 173 | y = np.zeros(n) 174 | x = np.linspace(x0, x1, n) 175 | y[0] = y_in[0] 176 | y[-1] = y_in[-1] 177 | for i in range(max(idx[0], 1), min(idx[-1], len(x_in)-1)): 178 | dx = 0.5*(x_in[i+1]-x_in[i-1]) 179 | for j in range(1, n-1): 180 | y[j] += y_in[i]*func(x[j], x_in[i], scale[j]*s)*dx 181 | 182 | return x, y 183 | --------------------------------------------------------------------------------