Merge pull request #53 from vishnu2709/master

Added documentation for lsms using ReadTheDocs

.readthedocs.yaml

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+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.10"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/source/conf.py

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

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+sphinx==7.1.2
+sphinx-rtd-theme==1.3.0rc1

docs/source/acquisition.rst

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+************
+Getting LSMS
+************
+
+The code can be obtained from the github repo (https://github.com/mstsuite/lsms)
+
+.. parsed-literal::
+   git clone https://github.com/mstsuite/lsms.git
+
+LSMS has the following dependencies
+
+1. Fortran and C++
+2. Cmake
+3. HDF5
+4. BLAS and LAPACK
+5. MPI
+6. (Optional) CUDA/ROCm for GPU acceleration
+
+Lua and LibXC are included - if you would like to use a pre-existing lua or LibXC installation it can be linked during the build process

docs/source/conductivity.rst

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+************************
+Electrical Resistivity
+************************
+
+lsms can also calculate electrical resistivity from the Kubo-Greenwood equation. To do this, first perform a standard self-consistent calculation. Then copy the converged potential to the starting potential and copy the restart file
+
+.. parsed-literal::
+   cp w_<systemid> v_<systemid>
+   cp i_lsms.restart i_lsms.dos
+
+Change the mode to conductivity
+
+.. parsed-literal::
+   lsmsMode="kubo"
+
+Then run lsms
+
+.. parsed-literal::
+   mpirun -np <number of MPI ranks> $LSMS_PATH/lsms i_lsms.kubo
+
+The stdout will print the electrical resistivity in units of :math:`\mu\Omega`-cm
+
+.. parsed-literal::
+   TOTAL RESISTIVITY (in microOhm-cm)
+   412.992   -1.32721   -1.86057
+   0.540036   408.027   -0.912385
+   -2.64419   -0.598773   416.019
+
+For a spin-polarized system, the spin up and down resistivities are calculated separately and the resistors are added in parallel.
+
+.. parsed-literal::
+   RESISTIVITY SPIN 1 (in microOhm-cm)
+   289.029  -0.206822  0.193379
+   -0.222593  289.206  0.0590624
+   0.0231963  -0.48124  289.46
+
+   RESISTIVITY SPIN 2 (in microOhm-cm)
+   262.711  0.162251  -0.491042
+   -0.173043  261.377  0.476058
+   -0.993332  1.08469  262.733
+
+   TOTAL RESISTIVITY (in microOhm-cm)
+   137.621   -0.00159926   -0.0911053
+   -0.0977167   137.294   0.144432
+   -0.26754   0.190146   137.724
+
+Currently the resistivity implementation is non-relativistic. A relativistic implementation will be added in the future. 

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+
+# -- Project information
+
+project = 'LSMS'
+copyright = '2023, mstsuite'
+author = 'Markus Eisenbach et al'
+
+release = '0.4'
+version = '0.4.0'
+
+# -- General configuration
+
+extensions = [
+    'sphinx.ext.duration',
+    'sphinx.ext.doctest',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+]
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
+}
+intersphinx_disabled_domains = ['std']
+
+templates_path = ['_templates']
+
+# -- Options for HTML output
+
+html_theme = 'sphinx_rtd_theme'
+
+# -- Options for EPUB output
+epub_show_urls = 'footnote'

docs/source/dos.rst

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+******************
+Density of States
+******************
+
+To get DOS, first a standard self-consistent calculation (as described in the previous sections) must be performed. Once that is done, copy the restart file to a new input file and the converged potential as the new starting potential
+
+.. parsed-literal::
+   cp i_lsms.restart i_lsms.dos
+   cp w_<systemid> v_<systemid>
+
+Edit the i_lsms.dos for dos calculations. First set the mode for DOS
+
+.. parsed-literal::
+   lsmsMode="dos"
+
+Change the energy contour settings so that the points are parallel to the real energy axis
+
+.. parsed-literal::
+   energyContour.grid=3
+   energyContour.npts= <number of energy points>
+   energyContour.ebot= <starting energy value>
+   energyContour.etop= <final energy value>
+   energyContour.eibot= <imaginary part>
+
+It is important to specify ``energyContour.eibot`` as we cannot traverse the real energy line due to singularities. Hence adding a small imaginary part to the energy is necessary. Generallyvalues between 0.001 and 0.005 Ryd are good choices.
+
+lsms will generate an output file called ``dos.out`` with three columns
+
+1. Real part of the energy.
+2. Imaginary part of the energy.
+3. Total Density of States

docs/source/gfm.rst

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+******************************************
+Green's Function at Matsubara Frequencies
+******************************************
+
+lsms can write out the Green's function at the Matsubara frequencies. To do this, set the mode and the required temperature
+
+.. parsed-literal::
+   lsmsMode = "gf_out"
+   temperature = <Temperature in Kelvin>
+
+The relevant energy points are given by
+
+.. math::
+   E_n = E_F + \pi ik_B T(2n + 1)
+
+To generate these energy points, we need to set the appropriate contour in the input file
+
+.. parsed-literal::
+   energyContour.grid=4
+   energyContour.npts= <number of points>
+
+lsms will generate output files of the form ``greens_functions_<atom index>.out``, containing the local Green's function in blocks for each energy. There are five columns in each energy block
+
+1. Spin index
+2. L = (l,m) index
+3. L' = (l',m') index
+4. Real part of G(L,L')
+5. Imaginary part of G(L,L') 

docs/source/index.rst

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+Welcome to the LSMS documentation!
+===================================
+
+**LSMS** is a high-performance software package for scalable first-principles calculations of materials using locally self-consistent multiple scattering theory.
+
+Use the sidebar to navigate to the required section. 
+
+.. note::
+
+   This project is under active development.
+
+.. toctree::
+   :hidden:
+
+   acquisition
+   installation
+   running
+   inputfile
+   outputfile
+   dos
+   gfm
+   conductivity