diff --git a/README.md b/README.md
index 81461cc365a045d660d52e92185e99cf4538d070..d8d862a1d619fdbd815b156c9f857f49fdf5d306 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,5 @@
-This repository contains the data presented in the publication "The Uncertainty Inherent to DEM Simulations: Insights from an Interlocking Parcel Model" by Maier, Mitterlindner, Benabchiasli, Fasching, and Radl (2024) in Scientific Reports
+This repository contains the simulation code and postprocessing presented in the publication "The Uncertainty Inherent to DEM Simulations: Insights from an Interlocking Parcel Model" by Maier, Mitterlindner, Benabchiasli, Fasching, and Radl (2024) in Scientific Reports
-- The folder "data" contains the data corresponding to the presented figures and tables, labeled using the same variables as in the paper.
- The folder "runfiles" contains the respective codebase to setup the DEM simulations using the settings and conditions described within the paper.
- The folder "postprocessing" uses the simulation data (i.e., "*.liggghts"-files) to extract the relevant data and analyse it statistically.
- The folder "demo" contains demo-"*.liggghts"-files for direct postprocessing without the need to run the simulation to test the postprocessing routines.
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/output_0.25_0.25.csv b/demo/Drawdown_L_10_D_14_scale_0.006/output_0.25_0.25.csv
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rename from demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/output_0.25_0.25.csv
rename to demo/Drawdown_L_10_D_14_scale_0.006/output_0.25_0.25.csv
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_39451.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39451.liggghts
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rename from demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_39451.liggghts
rename to demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39451.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_39511.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39511.liggghts
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rename to demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39511.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_39563.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39563.liggghts
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rename from demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_39563.liggghts
rename to demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39563.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_39799.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39799.liggghts
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rename from demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_39799.liggghts
rename to demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39799.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_39847.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39847.liggghts
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rename to demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39847.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_39857.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39857.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_39937.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_39937.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_40151.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_40151.liggghts
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rename to demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_40151.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_40193.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_40193.liggghts
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rename to demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_40193.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_40519.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_40519.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_40961.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_40961.liggghts
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rename to demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_40961.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_41231.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41231.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_41269.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41269.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_41467.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41467.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_41507.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41507.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_41539.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41539.liggghts
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rename to demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41539.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_41579.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41579.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_41621.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41621.liggghts
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rename to demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41621.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_41641.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41641.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_41669.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41669.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_41851.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41851.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_14_cohe_3.1e5_scale_0.006/results/particles_drawdown_0.25_seed_41893.liggghts b/demo/Drawdown_L_10_D_14_scale_0.006/results/particles_drawdown_0.25_seed_41893.liggghts
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diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41351.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41351.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41351.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41351.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41467.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41467.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41467.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41467.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41609.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41609.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41609.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41609.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41611.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41611.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41611.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41611.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41617.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41617.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41617.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41617.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41911.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41911.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_41911.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_41911.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42023.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42023.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42023.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42023.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42101.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42101.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42101.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42101.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42169.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42169.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42169.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42169.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42299.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42299.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42299.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42299.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42433.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42433.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42433.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42433.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42437.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42437.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42437.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42437.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42457.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42457.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42457.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42457.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42557.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42557.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42557.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42557.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42767.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42767.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0085/results/particles_drawdown_0.25_seed_42767.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0085/results/particles_drawdown_0.25_seed_42767.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/output_0.25_0.25.csv b/demo/Drawdown_L_10_D_8_scale_0.0095/output_0.25_0.25.csv
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/output_0.25_0.25.csv
rename to demo/Drawdown_L_10_D_8_scale_0.0095/output_0.25_0.25.csv
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39383.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39383.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39383.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39383.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39451.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39451.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39451.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39451.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39461.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39461.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39461.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39461.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39521.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39521.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39521.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39521.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39671.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39671.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39671.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39671.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39709.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39709.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39709.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39709.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39877.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39877.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39877.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39877.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39971.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39971.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_39971.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_39971.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40093.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40093.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40093.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40093.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40111.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40111.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40111.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40111.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40289.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40289.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40289.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40289.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40493.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40493.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40493.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40493.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40597.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40597.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40597.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40597.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40759.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40759.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40759.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40759.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40763.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40763.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40763.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40763.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40819.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40819.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40819.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40819.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40993.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40993.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_40993.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_40993.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_41077.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_41077.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_41077.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_41077.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_41177.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_41177.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_41177.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_41177.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_41269.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_41269.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_41269.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_41269.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42071.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42071.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42071.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42071.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42073.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42073.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42073.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42073.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42209.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42209.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42209.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42209.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42397.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42397.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42397.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42397.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42403.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42403.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42403.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42403.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42443.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42443.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42443.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42443.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42499.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42499.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42499.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42499.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42649.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42649.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42649.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42649.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42727.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42727.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42727.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42727.liggghts
diff --git a/demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42737.liggghts b/demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42737.liggghts
similarity index 100%
rename from demo/Drawdown_insertion_seeds_master_L_10_D_8_cohe_3.1e5_scale_0.0095/results/particles_drawdown_0.25_seed_42737.liggghts
rename to demo/Drawdown_L_10_D_8_scale_0.0095/results/particles_drawdown_0.25_seed_42737.liggghts
diff --git a/demo/datafile.csv b/demo/datafile.csv
deleted file mode 100644
index 0fd97b29c53646d8810b510c787543b61e064351..0000000000000000000000000000000000000000
--- a/demo/datafile.csv
+++ /dev/null
@@ -1,9 +0,0 @@
-D,L,scale,Nparcels,Arch,Heap_mean,Heap_std,Heap_ci_lower,Heap_ci_upper,Heap_var,Heap_index_of_dispersion,Heap_num_data_points,Height_mean,Height_std,Height_ci_lower,Height_ci_upper,Height_num_data_points,NumAtoms_mean,NumAtoms_std,NumAtoms_ci_lower,NumAtoms_ci_upper,NumAtoms_num_data_points,ParticleVolumeFraction_mean,ParticleVolumeFraction_ci_lower,ParticleVolumeFraction_ci_upper,Inverse_NumAtoms,Necessary_Sample_Size,Necessary_Sample_Size_noarch,Fraction_arched
-4.0,10.0,0.01,7.743708943705963,1,0.3472435827026237,0.0684615271444725,0.2753976161555079,0.4190895492497395,0.0046869806989533,0.0134976740605951,6,0.1214341333333333,0.0172220994430605,0.1033606483839527,0.1395076182827138,6,1812.8333333333333,19.67146834038239,1792.1893933678505,1833.477273298816,6,0.0197158590330054,0.0194913414213964,0.0199403766446145,0.1291370849898476,135.5248582070885,135.5248582070885,0.2857142857142857
-4.0,8.0,0.01,9.388819051395927,1,,,,,,,0,,,,,0,,,,,0,,,,0.106509667991878,6.8114977342059015,6.8114977342059015,0.0
-4.0,10.0,0.01,7.743708943705963,0,0.676665061755185,0.0534337949714501,0.6470744124042463,0.7062557111061237,0.0028551704450509,0.0042194737196051,15,0.1886446666666667,0.011092299817355,0.1825019557743146,0.1947873775590188,15,1809.4,14.617992826845766,1801.3048253977686,1817.495174602232,15,0.0196785190774956,0.0195904782640516,0.0197665598909397,0.1291370849898476,135.5248582070885,135.5248582070885,0.7142857142857143
-4.0,8.0,0.01,9.388819051395927,0,0.6970318462899359,0.0353844540302686,0.6598981391323108,0.734165553447561,0.0012520595870201,0.0017962731454588,6,0.1879185,0.0111928239644872,0.1761723516205852,0.1996646483794148,6,1803.3333333333333,21.86016163404714,1780.3925006206773,1826.2741660459887,6,0.0196125397386337,0.0193630417756683,0.0198620377015991,0.106509667991878,6.8114977342059015,6.8114977342059015,1.0
-8.0,16.0,0.01,4.694409525697964,1,,,,,,,0,,,,,0,,,,,0,,,,0.2130193359837561,6.8114977342059015,6.8114977342059015,0.0
-4.0,8.0,0.01,9.388819051395927,1,,,,,,,0,,,,,0,,,,,0,,,,0.106509667991878,6.8114977342059015,6.8114977342059015,0.0
-8.0,16.0,0.01,4.694409525697964,0,0.6970318462899359,0.0353844540302686,0.6598981391323108,0.734165553447561,0.0012520595870201,0.0017962731454588,6,0.1879185,0.0111928239644872,0.1761723516205852,0.1996646483794148,6,1803.3333333333333,21.86016163404714,1780.3925006206773,1826.2741660459887,6,0.1569003179090699,0.1549043342053465,0.1588963016127933,0.2130193359837561,6.8114977342059015,6.8114977342059015,1.0
-4.0,8.0,0.01,9.388819051395927,0,0.6970318462899359,0.0353844540302686,0.6598981391323108,0.734165553447561,0.0012520595870201,0.0017962731454588,6,0.1879185,0.0111928239644872,0.1761723516205852,0.1996646483794148,6,1803.3333333333333,21.86016163404714,1780.3925006206773,1826.2741660459887,6,0.0196125397386337,0.0193630417756683,0.0198620377015991,0.106509667991878,6.8114977342059015,6.8114977342059015,1.0
diff --git a/demo/datafile.pdf b/demo/datafile.pdf
deleted file mode 100644
index 3e1b0e7088d3c2a3b4c2e802b7dfbeb5e407ed45..0000000000000000000000000000000000000000
Binary files a/demo/datafile.pdf and /dev/null differ
diff --git a/demo/datafile.xlsx b/demo/datafile.xlsx
index 257ef7ecbc34d61ca34cc44ee14ed2683542f665..1e40fad89d67e1fd0d69220d3307d6496645d7e0 100644
Binary files a/demo/datafile.xlsx and b/demo/datafile.xlsx differ
diff --git a/postprocessing/helper.py b/postprocessing/helper.py
index 519987e163fb26415ab8ade34ce86c5f3f38fd20..5d6df050bc02785ce1c5440300778b057e92b3b5 100644
--- a/postprocessing/helper.py
+++ b/postprocessing/helper.py
@@ -20,10 +20,10 @@ def round_to_significant_digits(n, sig_digits):
float: The number rounded to the specified number of significant digits.
If the number `n` is 0, the function will return 0. For non-zero numbers,
- the function calculates the order of magnitude of the number and scales
- it accordingly to round it to the given number of significant digits.
+ the function calculates the order of magnitude of the number and scales
+ it accordingly to round it to the given number of significant digits.
After rounding, the number is scaled back to its original range.
-
+
Example:
round_to_significant_digits(12345.6789, 3) -> 12300
round_to_significant_digits(0.001234, 2) -> 0.0012
@@ -102,17 +102,17 @@ def create_dataframe(data_dict, arch_value):
Create a Pandas DataFrame from a dictionary of data with associated architecture value.
Args:
- data_dict (dict): A dictionary where the keys are tuples of the form
- (Nparcels, cohE) and the values are dictionaries containing
+ data_dict (dict): A dictionary where the keys are tuples of the form
+ (Nparcels, cohE) and the values are dictionaries containing
various metrics and statistics for each combination.
- arch_value (str or int): The architecture value that will be assigned to the "Arch" column
+ arch_value (str or int): The architecture value that will be assigned to the "Arch" column
of the DataFrame.
Returns:
- pd.DataFrame: A DataFrame containing all the data from `data_dict`, with each row
- representing one combination of `Nparcels` and `cohE`. The columns in the
+ pd.DataFrame: A DataFrame containing all the data from `data_dict`, with each row
+ representing one combination of `Nparcels` and `cohE`. The columns in the
DataFrame include various statistics and metrics such as:
-
+
- D
- xi
- Nparcels
@@ -124,7 +124,7 @@ def create_dataframe(data_dict, arch_value):
- Inverse_NumAtoms
- Necessary_Sample_Size, Necessary_Sample_Size_noarch
- The function iterates over each (Nparcels, cohE) pair in `data_dict`, extracts the corresponding
+ The function iterates over each (Nparcels, cohE) pair in `data_dict`, extracts the corresponding
values, and appends them as rows to the DataFrame. It then sorts the DataFrame by "Nparcels".
Example:
@@ -185,9 +185,9 @@ def create_dataframe(data_dict, arch_value):
def combine_csvs_to_excel(csv_files, output_file):
"""
- Combine multiple CSV files into a single Excel workbook, with each CSV file
- placed in a separate sheet. The sheet name is derived from the CSV file name
- (without path and extension). Each sheet is formatted with a table and column
+ Combine multiple CSV files into a single Excel workbook, with each CSV file
+ placed in a separate sheet. The sheet name is derived from the CSV file name
+ (without path and extension). Each sheet is formatted with a table and column
widths are auto-adjusted.
Args:
@@ -196,11 +196,11 @@ def combine_csvs_to_excel(csv_files, output_file):
Process:
1. Iterates over the list of CSV files.
- 2. Reads each CSV into a Pandas DataFrame and writes it to a new sheet in
+ 2. Reads each CSV into a Pandas DataFrame and writes it to a new sheet in
the Excel file.
3. The sheet name is the CSV file name (without its extension).
4. Adds a table for each sheet, with a default "TableStyleMedium22" style.
- 5. Automatically adjusts column widths based on the longest cell content
+ 5. Automatically adjusts column widths based on the longest cell content
in each column.
6. Writes the combined data into an Excel workbook using the "openpyxl" engine.
@@ -263,4 +263,3 @@ def combine_csvs_to_excel(csv_files, output_file):
worksheet.column_dimensions[column].width = adjusted_width
print(f"Combined CSV files into {output_file}")
-
diff --git a/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allins.sh b/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allins.sh
index f82794f9161f837b7a4a57e562301be2d59df4c4..aa9d6b7ed6596a99ee1d87b2c2db60a2a10fa546 100644
--- a/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allins.sh
+++ b/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allins.sh
@@ -2,41 +2,39 @@
# Shell Script for LIGGGHTS Simulations with Random Prime Seeds
-# This script is used to run multiple LIGGGHTS simulations by generating random prime numbers to use as seeds.
-# It executes LIGGGHTS insertion simulations repeatedly until a specified number of restart files are generated
+# This script is used to run multiple LIGGGHTS simulations by generating random prime numbers to use as seeds.
+# It executes LIGGGHTS insertion simulations repeatedly until a specified number of restart files are generated
# in the target directory.
# Key Components:
# - **LIGGGHTS_EXEC**: Specifies the LIGGGHTS executable to use for the simulations (e.g., 'liggghts-cg_heat').
# - **LIGGGHTS_SCRIPT_INS**: Specifies the LIGGGHTS script used for particle insertion ($(insertion.in)).
-# - **LIGGGHTS_SCRIPT_SETTLING**: Placeholder for another LIGGGHTS script for settling ($(ins.in)), though not executed
+# - **LIGGGHTS_SCRIPT_SETTLING**: Placeholder for another LIGGGHTS script for settling ($(ins.in)), though not executed
# in this script.
# Functions:
# - **is_prime()**: Checks if a given number is prime. Returns $(0) if the number is prime, otherwise returns $(1).
-# - **generate_random_prime()**: Generates a random prime number greater than 10,000 to be used as the seed for each
+# - **generate_random_prime()**: Generates a random prime number greater than 10,000 to be used as the seed for each
# LIGGGHTS simulation.
# Steps:
-# 1. **Directory Setup**: The script sets $(directory="restart") to monitor the number of files generated in the restart
+# 1. **Directory Setup**: The script sets $(directory="restart") to monitor the number of files generated in the restart
# directory.
# 2. **Folder and Scale Extraction**: The script determines its location and extracts the scaling factor from the folder name.
-# 3. **Prime Seed Generation**: The script enters a loop where it repeatedly generates a random prime number and uses it
+# 3. **Prime Seed Generation**: The script enters a loop where it repeatedly generates a random prime number and uses it
# as a seed for running the LIGGGHTS insertion simulation.
-# 4. **Simulation Execution**: It runs the LIGGGHTS simulation ($(${LIGGGHTS_EXEC})) with the prime number as a random seed
+# 4. **Simulation Execution**: It runs the LIGGGHTS simulation ($(${LIGGGHTS_EXEC})) with the prime number as a random seed
# and the extracted scaling factor, using the $(insertion.in) script.
-# 5. **Stopping Condition**: The script continues running simulations until the number of files in the $(restart) directory
+# 5. **Stopping Condition**: The script continues running simulations until the number of files in the $(restart) directory
# reaches 300.
# Notes:
# - Ensure that the LIGGGHTS executable and input scripts are correctly set and available in the environment where the script runs.
# - The script will stop once 300 restart files are found in the $(restart) directory.
-
LIGGGHTS_EXEC='liggghts-cg_heat'
LIGGGHTS_SCRIPT_INS="insertion.in"
-
is_prime() {
n=$1
if [ $n -le 1 ]; then
diff --git a/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allmake.sh b/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allmake.sh
index 0ff627e033859c8e6eb7b3ed3b9498bf9956cf52..5bbfd0a968e4c38ca1797189567258f97fadad4f 100644
--- a/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allmake.sh
+++ b/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allmake.sh
@@ -4,26 +4,26 @@
# This script performs the following tasks:
-# 1. **Extract L and D Values**:
+# 1. **Extract L and D Values**:
# - Retrieves the script's current directory and extracts the parent folder name.
-# - Parses the folder name to extract the `L` (tetrapod length) and `D` (sphere diameter) values using regular expressions.
+# - Parses the folder name to extract the `L` (tetrapod length) and `D` (sphere diameter) values using regular expressions.
# - The values are used for further file generation.
-# 2. **Validation**:
+# 2. **Validation**:
# - Ensures that valid `L` and `D` values have been extracted. If either is missing or invalid, the script exits with an error message.
-# 3. **Generate Multisphere Data File**:
+# 3. **Generate Multisphere Data File**:
# - Creates a new directory (`multisphere_data`) and generates a multisphere data file (`tetraeder.multisphere`) with the extracted `L` and `D` values.
# - The content of the file includes the coordinates for a tetrahedron structure, with each line representing the coordinates and radius (`D`) of a sphere.
-# 4. **Cleanup Files**:
+# 4. **Cleanup Files**:
# - Removes all files in the current directory except those with `.in` and `.sh` extensions.
# - Clears the contents of any directories starting with "post", but leaves the directories themselves intact.
# Steps:
-# - **L and D Extraction**:
+# - **L and D Extraction**:
# - `L` is extracted using `sed` to handle decimal values, while `D` is extracted using `grep` with a regular expression for proper matching.
-
+
# - **File Generation**:
# - The multisphere data file (`tetraeder.multisphere`) is populated with the extracted `L` and `D` values, using the format required for tetrahedron coordinates and sphere radii.
@@ -37,7 +37,6 @@
# Example folder name format for extraction: `simulation_L1.5_D3`.
-
# Get the directory where the script is located
script_dir=$(dirname "$(realpath "$0")")
@@ -55,8 +54,8 @@ echo "Extracted D: $D"
# Handle cases where L or D might be empty or invalid
if [ -z "$L" ] || [ -z "$D" ]; then
- echo "Error: Could not extract L and/or D values from folder name."
- exit 1
+ echo "Error: Could not extract L and/or D values from folder name."
+ exit 1
fi
# Calculate new values
@@ -71,7 +70,7 @@ output_file="multisphere_data/tetraeder.multisphere"
# Create the output file with the desired content
mkdir -p "$(dirname "$output_file")"
-cat <<EOL > "$output_file"
+cat <<EOL >"$output_file"
$L $L $L 0.$radius
$L -$L -$L 0.$radius
-$L $L -$L 0.$radius
diff --git a/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allrun.sh b/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allrun.sh
index 22a626a4b859ecac9fef9cf6db7011a4ba5baaa6..e0086c949ce4137258c94ecb940798652128165d 100644
--- a/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allrun.sh
+++ b/runfiles/Drawdown_L_10_D_14_scale_0.0075/Allrun.sh
@@ -30,7 +30,6 @@
# - LIGGGHTS must be installed and accessible in the environment where this script is executed.
# - Ensure that the SLURM job configuration aligns with the resources required for the simulations.
-
LIGGGHTS_EXEC='liggghts-cg_heat'
LIGGGHTS_SCRIPT_SETTLING="settling.in"
diff --git a/runfiles/Drawdown_L_10_D_14_scale_0.0075/README.md b/runfiles/Drawdown_L_10_D_14_scale_0.0075/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..859ad4835acb69287f80d065e43b47fa6bf91661
--- /dev/null
+++ b/runfiles/Drawdown_L_10_D_14_scale_0.0075/README.md
@@ -0,0 +1,11 @@
+This folder contains all simulation code used within the present contribution, exemplarily shown using a specific configuration.
+There are two main filetypes:
+- *in-files: LIGGGHTS runfiles which directly state the instructions used for the simulation
+- *sh-files: Bashscripts used for preprocessing and copying simulation data automatically to the right location
+
+To execute 10 simulations with different random seeds:
+- execute ./Allins.sh: generation of correct tetrapod-geometry based on foldername (L=coordinate of vertices of tetrahedron in mm, D=diameter of spheres), insertion of tetrapods into simulation domain using 10 different random seeds
+- execute ./Allrun.sh: settling in upper box and drawdown-test
+
+The exact parameter usage and functions within each file are described in the respective docstrings at the beginning of each file.
+The files within the "in" directory are parameters used within the simulation, as defined in the present contribution in Table 1.
\ No newline at end of file
diff --git a/runfiles/README.md b/runfiles/README.md
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..85d0f2bf5ad5550b0173c0b0377d5c935149393f 100644
--- a/runfiles/README.md
+++ b/runfiles/README.md
@@ -0,0 +1 @@
+Example usage of simulation code.
\ No newline at end of file