Test without data files

Author: arm61

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'
 

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

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,