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Documentation #109

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merged 14 commits into from
Aug 28, 2023
Merged

Documentation #109

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c956300
Work on documentation
bjorgve Jan 18, 2023
e3eee98
Add hydrogen atom example
bjorgve Jan 28, 2023
1fe40c9
Add helium atom
bjorgve Jan 28, 2023
2a9d10b
Avoid killed kernel with badly defined analytic functions
bjorgve Jan 28, 2023
aa5e6a3
update convolution operator and add comment to error catch
bjorgve Jan 30, 2023
90a5983
Add Beryllium atom notebook
bjorgve Jan 30, 2023
f0858fc
Update notebooks
bjorgve Feb 16, 2023
df79192
Update link to current mrcpp master
bjorgve Feb 17, 2023
ca264d0
Run clang-format
robertodr Aug 25, 2023
c67a6ae
Update MRCPP version to fetch
robertodr Aug 26, 2023
3228706
Add matplotlib, safeguard in plotter.py
robertodr Aug 26, 2023
5c4b91c
Run black+isort on Python files
robertodr Aug 26, 2023
fc76393
better solvent notebook (#107)
Gabrielgerez Aug 28, 2023
05a1788
Add authorship and instruction cells above executable cells (#110)
Gabrielgerez Aug 28, 2023
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4 changes: 3 additions & 1 deletion .gitignore
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Expand Up @@ -3,12 +3,14 @@ install*
debug*
.idea
.ipynb_checkpoints
*.ipynb
*.swp
cmake-build-debug
.direnv
.pytest_cache

# Editor junk
.vscode

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
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2 changes: 1 addition & 1 deletion cmake/custom/fetch_mrcpp.cmake
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Expand Up @@ -18,7 +18,7 @@ else()
GIT_REPOSITORY
https://github.com/MRChemSoft/mrcpp.git
GIT_TAG
v1.5.0
5320eb433dcea82b177f5181ce12ab89f0b04a92
)

set(CMAKE_CXX_COMPILER ${CMAKE_CXX_COMPILER})
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14 changes: 14 additions & 0 deletions docs/bibliography.bib
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Expand Up @@ -35,3 +35,17 @@ @ARTICLE{Anderson2019-bx
issn = "2590-0552",
doi = "10.1016/j.jcpx.2019.100033"
}

@article{Tomasi2005,
author = {Tomasi, Jacopo and Mennucci, Benedetta and Cammi, Roberto},
title = {Quantum Mechanical Continuum Solvation Models},
journal = {Chemical Reviews},
volume = {105},
number = {8},
pages = {2999-3094},
year = {2005},
doi = {10.1021/cr9904009},
note ={PMID: 16092826},
URL = { https://doi.org/10.1021/cr9904009},
eprint = { https://doi.org/10.1021/cr9904009 }
}
6 changes: 0 additions & 6 deletions docs/conf.py
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Expand Up @@ -109,9 +109,3 @@ def version_from_file(f):
},
}

html_sidebars = {
"**": [
"searchbox.html",
"sbt-sidebar-nav.html",
]
}
10 changes: 9 additions & 1 deletion docs/index.rst
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Expand Up @@ -19,7 +19,15 @@ Check out the :doc:`usage` section for further information, including how to :re
:caption: Contents

usage
notebooks/vampyr_intro
notebooks/introduction
notebooks/function_representations
notebooks/multiwavelets
notebooks/poisson_equation
notebooks/helmholtz_equation
notebooks/hydrogen_atom
notebooks/helium_atom
notebooks/beryllium_atom
notebooks/multiwavelets
notebooks/PCMSolvent

.. toctree::
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