added analysis

Former-commit-id: 3620687
simongravelle · Jan 4, 2024 · 2c60fab · 2c60fab
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diff --git a/examples/illustrations/bulk-water-tip3p/analysis.ipynb b/examples/illustrations/bulk-water-tip3p/analysis.ipynb
@@ -100,16 +100,17 @@
    "outputs": [],
    "source": [
     "while 1<2:   \n",
-    "    # high res\n",
     "    for T in [280, 290, 300, 310, 320]:\n",
     "        datapath = git_path + \"/data/bulk-water-tip3p/bulk-water/raw-data/N4000_\" + str(T) + \"K/\"\n",
     "        xtc = [datapath+\"prod1.xtc\", datapath+\"prod2.xtc\"]\n",
     "        u = mda.Universe(datapath+\"prod1.tpr\", xtc)\n",
     "        dt = np.round(u.trajectory.dt,2)\n",
     "        hydrogen = u.select_atoms(\"name HW1 HW2\")\n",
     "        n_hydrogen = hydrogen.n_atoms\n",
-    "        intra = nmrformd.NMR(u, atom_group = hydrogen, neighbor_group = hydrogen, type_analysis = \"intra_molecular\", number_i=5)\n",
-    "        inter = nmrformd.NMR(u, atom_group = hydrogen, neighbor_group = hydrogen, type_analysis = \"inter_molecular\", number_i=1)\n",
+    "        intra = nmrformd.NMR(u, atom_group = hydrogen, neighbor_group = hydrogen,\n",
+    "                             type_analysis = \"intra_molecular\", number_i=5)\n",
+    "        inter = nmrformd.NMR(u, atom_group = hydrogen, neighbor_group = hydrogen,\n",
+    "                             type_analysis = \"inter_molecular\", number_i=1)\n",
     "        n_intra = save_result(intra, name = \"N4000_intra_T\" + str(T) + \"K\")\n",
     "        n_inter = save_result(inter, name = \"N4000_inter_T\" + str(T) + \"K\")\n",
     "        print(n_hydrogen, T, n_intra)"

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