removed submodule

simongravelle · Jan 5, 2024 · d43b0c4 · d43b0c4
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diff --git a/.gitmodules b/.gitmodules
diff --git a/data/HEWL-in-water b/data/HEWL-in-water
diff --git a/data/bulk-water-high-dumping-rate b/data/bulk-water-high-dumping-rate
diff --git a/data/bulk-water-tip3p b/data/bulk-water-tip3p
diff --git a/data/bulk-water-tip4p b/data/bulk-water-tip4p
diff --git a/data/lennard-jones-fluid b/data/lennard-jones-fluid
diff --git a/data/polymer-in-water b/data/polymer-in-water
diff --git a/data/water-in-silica b/data/water-in-silica
diff --git a/docs/source/figures/illustrations/bulk-water/effect_L_on_R1-dark.png b/docs/source/figures/illustrations/bulk-water/effect_L_on_R1-dark.png
diff --git a/docs/source/figures/illustrations/bulk-water/effect_L_on_R1-light.png b/docs/source/figures/illustrations/bulk-water/effect_L_on_R1-light.png
diff --git a/docs/source/figures/illustrations/bulk-water/effect_N_on_G-dark.png b/docs/source/figures/illustrations/bulk-water/effect_N_on_G-dark.png
diff --git a/docs/source/figures/illustrations/bulk-water/effect_N_on_G-light.png b/docs/source/figures/illustrations/bulk-water/effect_N_on_G-light.png
diff --git a/docs/source/figures/illustrations/bulk-water/effect_dt_on_G-dark.png b/docs/source/figures/illustrations/bulk-water/effect_dt_on_G-dark.png
diff --git a/docs/source/figures/illustrations/bulk-water/effect_dt_on_G-light.png b/docs/source/figures/illustrations/bulk-water/effect_dt_on_G-light.png
diff --git a/docs/source/figures/illustrations/bulk-water/effect_dt_on_R1-dark.png b/docs/source/figures/illustrations/bulk-water/effect_dt_on_R1-dark.png
diff --git a/docs/source/figures/illustrations/bulk-water/effect_dt_on_R1-light.png b/docs/source/figures/illustrations/bulk-water/effect_dt_on_R1-light.png
diff --git a/docs/source/figures/illustrations/bulk-water/effect_of_anisotropy-dark.png b/docs/source/figures/illustrations/bulk-water/effect_of_anisotropy-dark.png
diff --git a/docs/source/figures/illustrations/bulk-water/effect_of_anisotropy-light.png b/docs/source/figures/illustrations/bulk-water/effect_of_anisotropy-light.png
diff --git a/docs/source/figures/illustrations/bulk-water/experimental_comparison-dark.png b/docs/source/figures/illustrations/bulk-water/experimental_comparison-dark.png
diff --git a/docs/source/figures/illustrations/bulk-water/experimental_comparison-light.png b/docs/source/figures/illustrations/bulk-water/experimental_comparison-light.png
diff --git a/docs/source/figures/illustrations/bulk-water/water_spectrum-dark.png b/docs/source/figures/illustrations/bulk-water/water_spectrum-dark.png
diff --git a/docs/source/figures/illustrations/bulk-water/water_spectrum-light.png b/docs/source/figures/illustrations/bulk-water/water_spectrum-light.png
diff --git a/examples/illustrations/bulk-water-tip3p/analysis.ipynb b/examples/illustrations/bulk-water-tip3p/analysis.ipynb
@@ -2,9 +2,18 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/simon/.local/lib/python3.11/site-packages/MDAnalysis/topology/TPRParser.py:161: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13\n",
+      "  import xdrlib\n"
+     ]
+    }
+   ],
    "source": [
     "import numpy as np\n",
     "import MDAnalysis as mda\n",
@@ -13,7 +22,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -25,7 +34,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -95,9 +104,183 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "8000 280 209\n",
+      "8000 290 209\n",
+      "8000 300 208\n",
+      "8000 310 207\n",
+      "8000 320 207\n",
+      "8000 280 210\n",
+      "8000 290 210\n",
+      "8000 300 209\n",
+      "8000 310 208\n",
+      "8000 320 208\n",
+      "8000 280 211\n",
+      "8000 290 211\n",
+      "8000 300 210\n",
+      "8000 310 209\n",
+      "8000 320 209\n",
+      "8000 280 212\n",
+      "8000 290 212\n",
+      "8000 300 211\n",
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+      "8000 290 225\n",
+      "8000 300 224\n",
+      "8000 310 223\n",
+      "8000 320 223\n",
+      "8000 280 226\n",
+      "8000 290 226\n",
+      "8000 300 225\n",
+      "8000 310 224\n",
+      "8000 320 224\n",
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+      "8000 300 226\n",
+      "8000 310 225\n",
+      "8000 320 225\n",
+      "8000 280 228\n",
+      "8000 290 228\n",
+      "8000 300 227\n",
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+      "8000 320 226\n",
+      "8000 280 229\n",
+      "8000 290 229\n",
+      "8000 300 228\n",
+      "8000 310 227\n",
+      "8000 320 227\n",
+      "8000 280 230\n",
+      "8000 290 230\n",
+      "8000 300 229\n",
+      "8000 310 228\n",
+      "8000 320 228\n",
+      "8000 280 231\n",
+      "8000 290 231\n",
+      "8000 300 230\n",
+      "8000 310 229\n",
+      "8000 320 229\n",
+      "8000 280 232\n",
+      "8000 290 232\n",
+      "8000 300 231\n",
+      "8000 310 230\n",
+      "8000 320 230\n",
+      "8000 280 233\n",
+      "8000 290 233\n",
+      "8000 300 232\n",
+      "8000 310 231\n",
+      "8000 320 231\n",
+      "8000 280 234\n",
+      "8000 290 234\n",
+      "8000 300 233\n",
+      "8000 310 232\n",
+      "8000 320 232\n",
+      "8000 280 235\n",
+      "8000 290 235\n",
+      "8000 300 234\n",
+      "8000 310 233\n",
+      "8000 320 233\n",
+      "8000 280 236\n",
+      "8000 290 236\n",
+      "8000 300 235\n",
+      "8000 310 234\n",
+      "8000 320 234\n",
+      "8000 280 237\n",
+      "8000 290 237\n",
+      "8000 300 236\n",
+      "8000 310 235\n",
+      "8000 320 235\n",
+      "8000 280 238\n",
+      "8000 290 238\n",
+      "8000 300 237\n",
+      "8000 310 236\n",
+      "8000 320 236\n",
+      "8000 280 239\n",
+      "8000 290 239\n",
+      "8000 300 238\n",
+      "8000 310 237\n",
+      "8000 320 237\n",
+      "8000 280 240\n",
+      "8000 290 240\n",
+      "8000 300 239\n",
+      "8000 310 238\n",
+      "8000 320 238\n",
+      "8000 280 241\n",
+      "8000 290 241\n",
+      "8000 300 240\n",
+      "8000 310 239\n",
+      "8000 320 239\n",
+      "8000 280 242\n",
+      "8000 290 242\n"
+     ]
+    }
+   ],
    "source": [
     "while 1<2:   \n",
     "    for T in [280, 290, 300, 310, 320]:\n",

diff --git a/examples/illustrations/bulk-water-tip3p/raw_data/N4000_inter_T280K.npy b/examples/illustrations/bulk-water-tip3p/raw_data/N4000_inter_T280K.npy
diff --git a/examples/illustrations/bulk-water-tip3p/raw_data/N4000_inter_T290K.npy b/examples/illustrations/bulk-water-tip3p/raw_data/N4000_inter_T290K.npy
diff --git a/examples/illustrations/bulk-water-tip3p/raw_data/N4000_inter_T300K.npy b/examples/illustrations/bulk-water-tip3p/raw_data/N4000_inter_T300K.npy
diff --git a/examples/illustrations/bulk-water-tip3p/raw_data/N4000_inter_T310K.npy b/examples/illustrations/bulk-water-tip3p/raw_data/N4000_inter_T310K.npy
diff --git a/examples/illustrations/bulk-water-tip3p/raw_data/N4000_inter_T320K.npy b/examples/illustrations/bulk-water-tip3p/raw_data/N4000_inter_T320K.npy
diff --git a/examples/illustrations/bulk-water-tip3p/raw_data/N4000_intra_T280K.npy b/examples/illustrations/bulk-water-tip3p/raw_data/N4000_intra_T280K.npy
diff --git a/examples/illustrations/bulk-water-tip3p/raw_data/N4000_intra_T290K.npy b/examples/illustrations/bulk-water-tip3p/raw_data/N4000_intra_T290K.npy
diff --git a/examples/illustrations/bulk-water-tip3p/raw_data/N4000_intra_T300K.npy b/examples/illustrations/bulk-water-tip3p/raw_data/N4000_intra_T300K.npy
diff --git a/examples/illustrations/bulk-water-tip3p/raw_data/N4000_intra_T310K.npy b/examples/illustrations/bulk-water-tip3p/raw_data/N4000_intra_T310K.npy
diff --git a/examples/illustrations/bulk-water-tip3p/raw_data/N4000_intra_T320K.npy b/examples/illustrations/bulk-water-tip3p/raw_data/N4000_intra_T320K.npy