diff --git a/Snakefile b/Snakefile index 24b5c09..834ceda 100644 --- a/Snakefile +++ b/Snakefile @@ -396,7 +396,7 @@ for start_diff in [0, 2, 4, 6, 8, 10, 15, 20]: f"llzo_many_{n}_{start_diff}" input: 'src/code/llzo/many_runs.py', - f'src/data/llzo/traj{n}.xyz' + # f'src/data/llzo/traj{n}.xyz' output: f'src/data/llzo/diffusion_{n}_{start_diff}.npz' diff --git a/showyourwork.yml b/showyourwork.yml index 194a876..b4843b1 100644 --- a/showyourwork.yml +++ b/showyourwork.yml @@ -12,27 +12,17 @@ margin_icons: horizontal_offset: -4 # datasets: -# 10.5281/zenodo.7602139: +# 10.5281/zenodo.10532134: # contents: -# traj0.xyz: src/data/llzo/traj0.xyz -# traj1.xyz: src/data/llzo/traj1.xyz -# traj2.xyz: src/data/llzo/traj2.xyz -# traj3.xyz: src/data/llzo/traj3.xyz -# traj4.xyz: src/data/llzo/traj4.xyz -# traj5.xyz: src/data/llzo/traj5.xyz -# traj6.xyz: src/data/llzo/traj6.xyz -# traj7.xyz: src/data/llzo/traj7.xyz -# traj8.xyz: src/data/llzo/traj8.xyz -# traj9.xyz: src/data/llzo/traj9.xyz -# traj10.xyz: src/data/llzo/traj10.xyz -# traj11.xyz: src/data/llzo/traj11.xyz -# traj12.xyz: src/data/llzo/traj12.xyz -# traj13.xyz: src/data/llzo/traj13.xyz -# traj14.xyz: src/data/llzo/traj14.xyz -# traj15.xyz: src/data/llzo/traj15.xyz +# traj0.out: src/data/llzo/traj0.out +# traj1.out: src/data/llzo/traj1.out +# traj2.out: src/data/llzo/traj2.out +# traj3.out: src/data/llzo/traj3.out +# traj4.out: src/data/llzo/traj4.out +# traj5.out: src/data/llzo/traj5.out dependencies: - src/ms.tex: + src/tex/ms.tex: - src/tex/bib.bib src/scripts/glswlsols.py: - src/data/random_walks/numerical/glswlsols_1_128_128.npz diff --git a/src/tex/bib.bib b/src/tex/bib.bib index 52c9295..d64992f 100644 --- a/src/tex/bib.bib +++ b/src/tex/bib.bib @@ -264,15 +264,6 @@ @article{coles_correlation_2020 title = {Correlation Length in Concentrated Electrolytes: Insights from All-Atom Molecular Dynamics Simulations}, journal = {J. Phys. Chem. B} } - -@misc{coles_llzo_zenodo_2022, - title = {{LLZO} simulation trajectories}, - doi = {10.5281/zenodo.7602139}, - publisher={Zenodo}, - author={Coles, S. W.}, - year={2022}, - month={Jul} -} @book{cramer_mathematical_1946, author = {H. Cram\'{e}r}, @@ -683,10 +674,10 @@ @article{mccluskey_bayesian_2019 @misc{mccluskey_github_2022, author = {McCluskey, A. R. and Coles, S. W. and Morgan, B. J.}, license = {CC BY 4.0/MIT}, - month = {5}, + month = {1}, title = {{msd-errors-0.0.1}}, howpublished = {https://github.com/arm61/msd-errors}, - year = {2023} + year = {2024} } @software{mccluskey_kinisi_2022, @@ -716,8 +707,8 @@ @software{mccluskey_uravu_2022 month = {9}, title = {{uravu-1.2.9}}, url = {https://github.com/arm61/uravu}, - version = {1.2.8}, - year = {2022} + version = {1.2.9}, + year = {2023} } @misc{mccluskey_zenodo_2022, @@ -732,13 +723,13 @@ @misc{mccluskey_zenodo_2022 @misc{coles_llzo_zenodo_2022, - title = {{LLZO} simulation trajectories}, - doi = {10.5281/zenodo.7602139}, - url = {https://doi.org/10.5281/zenodo.7602139}, + title = {Molecular dynamics simulations of cubic {LLZO} at 700 K}, + howpublished = {DOI: 10.5072/zenodo.10532134}, + doi = {10.5281/zenodo.10532134}, publisher={Zenodo}, author={Coles, S. W.}, - year={2022}, - month={Jul} + year={2024}, + month={1} } @article{michaudagrawal_mdanalysis_2011,