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simongravelle · Jan 22, 2024 · 2e67f47 · 2e67f47
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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/examples/illustrations/bulk-water-tip4p-vs-size/analysis.py b/examples/illustrations/bulk-water-tip4p-vs-size/analysis.py
@@ -22,13 +22,13 @@
         for n in range(10):
             # Import MDA universe
             datapath = path + "N"+str(N)+"/"
-            if os.path.exists(datapath+"prod"+str(n)+".xtc"):
+            if os.path.exists(datapath+"prod-"+str(n)+".xtc"):
                 # Read current status
                 name_intra = "N"+str(N)+"_intra_n"+str(n)
                 name_inter = "N"+str(N)+"_inter_n"+str(n) 
                 n_intra = measure_N(name_intra)
                 n_inter = measure_N(name_inter)
-                u = mda.Universe(datapath+"topology.data", datapath+"prod"+str(n)+".xtc")
+                u = mda.Universe(datapath+"topology.data", datapath+"prod-"+str(n)+".xtc")
                 hydrogen = u.select_atoms("type 2")
                 n_hydrogen = hydrogen.n_atoms
                 if n_intra < n_hydrogen:

diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N1002_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N1002_inter_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N1002_intra_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N1002_intra_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N1589_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N1589_inter_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N1589_intra_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N1589_intra_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_inter_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_intra_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_intra_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_inter_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_intra_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_intra_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N2521_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N2521_inter_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N2521_intra_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N2521_intra_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n5.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n5.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_inter_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_intra_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_intra_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n5.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n5.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n5.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_intra_n5.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N631_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N631_inter_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N631_intra_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N631_intra_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_inter_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_inter_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_inter_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_inter_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_inter_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_inter_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_inter_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_inter_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_inter_n5.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_intra_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_intra_n0.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_intra_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_intra_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_intra_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_intra_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_intra_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_intra_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_intra_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N99_intra_n5.npy
diff --git a/examples/illustrations/bulk-water.ipynb b/examples/illustrations/bulk-water.ipynb
diff --git a/nmrformd-data/polymer-in-water b/nmrformd-data/polymer-in-water
diff --git a/nmrformd-data/water-in-silica b/nmrformd-data/water-in-silica