Updating Docs for commit 58018f4 made on 2023-10-06T07:32:22+00:00 fr…

…om refs/heads/main by hmcezar
Cascella-Group-UiO · Oct 6, 2023 · 6bf76db · 6bf76db
commit 6bf76db
Show file tree

Hide file tree

Showing 1,860 changed files with 587,829 additions and 0 deletions.
diff --git a/.nojekyll b/.nojekyll
diff --git a/README.md b/README.md
@@ -0,0 +1,14 @@
+<a href="https://cascella-group-uio.github.io/HyMD/">
+  <img src="https://github.com/Cascella-Group-UiO/HyMD/blob/main/docs/img/hymd_logo_text_black.png?raw=true" width="500" title="HylleraasMD">
+</a>
+
+### GitHub Pages Cache
+
+Nothing to see here. The contents of this branch are essentially a cache that's not intended to be viewed on github.com.
+
+
+If you're looking to update our documentation, check [the HylleraasMD documentation](https://cascella-group-uio.github.io/HyMD/index.html).
+
+For more information on how this documentation is built using Sphinx, Read the Docs, and GitHub Actions/Pages, see:
+
+ * https://tech.michaelaltfield.net/2020/07/18/sphinx-rtd-github-pages-1
diff --git a/index.html b/index.html
@@ -0,0 +1,9 @@
+<!DOCTYPE html>
+<html>
+  <head>
+    <title>Redirecting to main branch</title>
+    <meta charset="utf-8">
+    <meta http-equiv="refresh" content="0; url=./main/index.html">
+    <link rel="canonical" href="https://cascella-group-uio.github.io/HyMD/main/index.html">
+  </head>
+</html>
diff --git a/main/.buildinfo b/main/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: d1c53ca0a458bab63f3363f597dbef0e
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/main/.doctrees/doc_pages/api.doctree b/main/.doctrees/doc_pages/api.doctree
diff --git a/main/.doctrees/doc_pages/benchmarks.doctree b/main/.doctrees/doc_pages/benchmarks.doctree
diff --git a/main/.doctrees/doc_pages/command_line.doctree b/main/.doctrees/doc_pages/command_line.doctree
diff --git a/main/.doctrees/doc_pages/config_file.doctree b/main/.doctrees/doc_pages/config_file.doctree
diff --git a/main/.doctrees/doc_pages/constants_and_units.doctree b/main/.doctrees/doc_pages/constants_and_units.doctree
diff --git a/main/.doctrees/doc_pages/electrostatics.doctree b/main/.doctrees/doc_pages/electrostatics.doctree
diff --git a/main/.doctrees/doc_pages/examples.doctree b/main/.doctrees/doc_pages/examples.doctree
diff --git a/main/.doctrees/doc_pages/filtering.doctree b/main/.doctrees/doc_pages/filtering.doctree
diff --git a/main/.doctrees/doc_pages/installation.doctree b/main/.doctrees/doc_pages/installation.doctree
diff --git a/main/.doctrees/doc_pages/interaction_energy_functionals.doctree b/main/.doctrees/doc_pages/interaction_energy_functionals.doctree
diff --git a/main/.doctrees/doc_pages/interfaces.doctree b/main/.doctrees/doc_pages/interfaces.doctree
diff --git a/main/.doctrees/doc_pages/intramolecular_bonds.doctree b/main/.doctrees/doc_pages/intramolecular_bonds.doctree
diff --git a/main/.doctrees/doc_pages/overview.doctree b/main/.doctrees/doc_pages/overview.doctree
diff --git a/main/.doctrees/doc_pages/pressure.doctree b/main/.doctrees/doc_pages/pressure.doctree
diff --git a/main/.doctrees/doc_pages/theory.doctree b/main/.doctrees/doc_pages/theory.doctree
diff --git a/main/.doctrees/doc_pages/topology_input.doctree b/main/.doctrees/doc_pages/topology_input.doctree
diff --git a/main/.doctrees/environment.pickle b/main/.doctrees/environment.pickle
diff --git a/main/.doctrees/index.doctree b/main/.doctrees/index.doctree
diff --git a/main/_downloads/06277b09d9dbd669eb066a87bde69764/benchmarks-2.png b/main/_downloads/06277b09d9dbd669eb066a87bde69764/benchmarks-2.png
diff --git a/main/_downloads/65e54d27de07d1f3391023244e2c96b6/benchmarks-2.py b/main/_downloads/65e54d27de07d1f3391023244e2c96b6/benchmarks-2.py
@@ -0,0 +1,33 @@
+import numpy as np
+import matplotlib.pyplot as plt
+
+mesh_2048_cpus = [2048,     1024,     512,       256,       128,       64,        32,        16,        8,          4         , ]
+mesh_2048_time = [3.375108, 5.977880, 10.414429, 16.859782, 31.692761, 50.496983, 51.508302, 76.465812, 114.956267, 200.790592, ]
+
+mesh_1024_cpus = [2048,     1024,     512,      256,      128,      64,       32,       16,       8,         4,         2,         1        , ]
+mesh_1024_time = [0.439009, 0.662988, 1.172991, 2.024713, 3.625324, 7.148897, 7.330420, 9.117424, 13.209331, 22.204145, 41.150021, 71.836402, ]
+
+mesh_512_cpus = [1024,    512,      256,       128,      64,       32,       16,       8,        4,        2,       1        , ]
+mesh_512_time = [0.137271, 0.148182, 0.161536, 0.271535, 0.798458, 0.817093, 1.114978, 1.712410, 2.870377, 5.151649, 8.589524, ]
+
+mesh_256_cpus = [256, 128, 64, 32, 16, 8, 4, 2, 1]
+mesh_256_time = [0.033834, 0.037837, 0.053191, 0.070217, 0.115923, 0.200090, 0.336702, 0.665111, 1.127391]
+
+mesh_128_cpus = [64,       32,       16,       8,        4,        2,        1,        ]
+mesh_128_time = [0.012815, 0.018430, 0.022436, 0.037648, 0.055399, 0.093687, 0.169120, ]
+
+mesh_64_cpus = [64,       32,       16,       8,        4,        2,        1,        ]
+mesh_64_time = [0.012815, 0.018162, 0.018430, 0.037648, 0.037949, 0.055399, 0.093687, ]
+
+plt.loglog(mesh_2048_cpus, mesh_2048_time, "r-x", label="2048³")
+plt.loglog(mesh_1024_cpus, mesh_1024_time, "b-o", label="1024³")
+plt.loglog(mesh_512_cpus, mesh_512_time, "k-^", label="512³")
+plt.loglog(mesh_256_cpus, mesh_256_time, "c-v", label="256³")
+plt.loglog(mesh_128_cpus, mesh_128_time, "y-8", label="128³")
+plt.loglog(mesh_64_cpus, mesh_64_time, "g->", label="64³")
+plt.xlabel("CPUs", fontsize=15)
+plt.xscale('log', base=2)
+plt.yscale('log', base=2)
+plt.ylabel("Time per step, s", fontsize=15)
+plt.legend(loc="upper left", fontsize=15)
+plt.show()
diff --git a/main/_downloads/682597475ba7aeb79c5d27601a114807/benchmarks-1.png b/main/_downloads/682597475ba7aeb79c5d27601a114807/benchmarks-1.png
diff --git a/main/_downloads/9732f060c48ad320d8ef77b0255fa65c/benchmarks-2.hires.png b/main/_downloads/9732f060c48ad320d8ef77b0255fa65c/benchmarks-2.hires.png
diff --git a/main/_downloads/c2b4427af0abc490fea62e3654884461/benchmarks-1.py b/main/_downloads/c2b4427af0abc490fea62e3654884461/benchmarks-1.py
@@ -0,0 +1,38 @@
+import numpy as np
+import matplotlib.pyplot as plt
+nodes_small = np.array([1, 2, 5, 8, 12, 15, 17, 18], dtype=np.float64)
+time_small = np.array([
+   4.187099, 2.403876, 1.604452, 1.104753, 1.102880, 1.102931, 1.091972,
+   1.090594
+], dtype=np.float64)
+nodes_medium = np.array([
+   1, 3, 4, 7, 13, 14, 16, 25, 30, 31, 35, 40, 42, 46, 47, 50
+], dtype=np.float64,)
+time_medium = np.array([
+   11.201839, 5.281660, 3.693661, 2.317845, 1.566609, 1.425823, 1.437634,
+   0.962915, 0.955779, 0.958936, 0.966228, 0.973874, 0.974221, 0.976087,
+   0.982746, 0.950908,
+], dtype=np.float64)
+nodes_large = np.array([
+   1, 2, 3, 4, 5, 7, 12, 13, 16, 25, 26, 30, 37, 49, 55, 71, 80
+], dtype=np.float64)
+time_large = np.array([
+   20.77469, 12.257692, 9.430474, 6.560756, 5.340657, 3.760844, 3.655468,
+   2.623202, 2.315075, 1.668369, 1.497107, 1.533885, 1.414385, 1.417828,
+   1.404457, 1.411190, 1.435383,
+], dtype=np.float64)
+plt.plot(
+   nodes_small * 128, 1e6 * time_small / 10000.0, "r-o", label="224 k"
+)
+plt.plot(
+   nodes_medium * 128, 1e6 * time_medium / 10000.0, "b-x", label="533 k"
+)
+plt.plot(
+   nodes_large * 128, 1e6 * time_large / 10000.0, "k-^", label="1.04 M"
+)
+plt.xlabel("CPUs", fontsize=15)
+plt.ylabel("Time per step, us", fontsize=15)
+plt.legend(fontsize=15)
+plt.xscale('log', base=2)
+plt.yscale('log', base=2)
+plt.show()
diff --git a/main/_downloads/d3fab0727cec9bfe48cd44e3926f8b8b/benchmarks-1.pdf b/main/_downloads/d3fab0727cec9bfe48cd44e3926f8b8b/benchmarks-1.pdf
diff --git a/main/_downloads/d80367d2b3a595c564d561412e710698/benchmarks-1.hires.png b/main/_downloads/d80367d2b3a595c564d561412e710698/benchmarks-1.hires.png
diff --git a/main/_downloads/f62fcc5108e569ea2fe61890ff1f4f10/benchmarks-2.pdf b/main/_downloads/f62fcc5108e569ea2fe61890ff1f4f10/benchmarks-2.pdf
diff --git a/main/_images/benchmarks-1.png b/main/_images/benchmarks-1.png
diff --git a/main/_images/benchmarks-2.png b/main/_images/benchmarks-2.png
diff --git a/main/_images/hylleraas_centre_logo_black.png b/main/_images/hylleraas_centre_logo_black.png
diff --git a/main/_images/uio_full_logo_eng_pos.png b/main/_images/uio_full_logo_eng_pos.png