improved convergence N figure

simongravelle · Jan 24, 2024 · 5b04b75 · 5b04b75
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Showing 146 changed files with 74 additions and 63 deletions.
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/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/examples/illustrations/bulk-water-tip4p-vs-size/analysis.py b/examples/illustrations/bulk-water-tip4p-vs-size/analysis.py
@@ -18,8 +18,8 @@
 R1_intra = 1e-5
 R1_inter = 1e-5
 while run:
-    for N in [25, 39, 62, 99, 158, 251, 398, 631, 1002, 1589, 2521]:
-        for n in range(10):
+    for N in [25, 39, 62, 99, 158, 251, 398, 631, 1002, 1589, 2521, 6500, 10000]: 
+        for n in range(20):
             # Import MDA universe
             datapath = path + "N"+str(N)+"/"
             if os.path.exists(datapath+"prod-"+str(n)+".xtc"):
@@ -28,10 +28,14 @@
                 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")
-                hydrogen = u.select_atoms("type 2")
+                try:
+                    u = mda.Universe(datapath+"topology.data", datapath+"prod-"+str(n)+".xtc")
+                    hydrogen = u.select_atoms("type 2")
+                except:
+                    u = mda.Universe(datapath+"prod.tpr", datapath+"prod-"+str(n)+".xtc")
+                    hydrogen = u.select_atoms("type HW")
                 n_hydrogen = hydrogen.n_atoms
-                if n_intra < n_hydrogen:
+                if n_intra < n_hydrogen*2:
                     # Calculated NMR properties
                     intra = nmrformd.NMR(u, atom_group = hydrogen,
                                         neighbor_group = hydrogen,
@@ -44,13 +48,12 @@
                                             type_analysis = "inter_molecular",
                                             number_i = 1)
                         save_result(inter, name = name_inter)
-                else:
-                    print("N", N, "no calculation")
-                    #run = False
-                # Print information
-                R1_intra = measure_R1(name_intra)
-                R1_inter = measure_R1(name_inter)
-                print("N =", N, "n", n, "----", n_intra, n_hydrogen, 
-                    "R1:", np.round(R1_intra,2), np.round(R1_inter,2), 
-                    "T1:", np.round(1/(R1_intra+R1_inter),2))
+                    # Print information
+                    R1_intra = measure_R1(name_intra)
+                    R1_inter = measure_R1(name_inter)
+                    print("N =", N, "n", n, "----", n_intra, n_hydrogen, 
+                        "R1:", np.round(R1_intra,2), np.round(R1_inter,2), 
+                        "T1:", np.round(1/(R1_intra+R1_inter),2))
+                #else:
+                #    print("N", N, "no calculation")
     print(" ")
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_inter_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N1002_inter_n1.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/N1002_intra_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N1002_intra_n1.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_inter_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_inter_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_inter_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_inter_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_inter_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_inter_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_inter_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_inter_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_inter_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_inter_n5.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/N158_intra_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_intra_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_intra_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_intra_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_intra_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_intra_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_intra_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_intra_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_intra_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N158_intra_n5.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_inter_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_inter_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_inter_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_inter_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_inter_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_inter_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_inter_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_inter_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_inter_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_inter_n5.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/N251_intra_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_intra_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_intra_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_intra_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_intra_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_intra_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_intra_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_intra_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_intra_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N251_intra_n5.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_n10.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n10.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_inter_n6.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n6.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n7.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n7.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n8.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n8.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n9.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_inter_n9.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_n10.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n10.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/N25_intra_n6.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n6.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n7.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n7.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n8.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n8.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n9.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N25_intra_n9.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_inter_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_inter_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_inter_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_inter_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_inter_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_inter_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_inter_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_inter_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_inter_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_inter_n5.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/N398_intra_n1.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_intra_n1.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_intra_n2.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_intra_n2.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_intra_n3.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_intra_n3.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_intra_n4.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_intra_n4.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_intra_n5.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N398_intra_n5.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_n10.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n10.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_inter_n6.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n6.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n7.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n7.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n8.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n8.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n9.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_inter_n9.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_n10.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n10.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/N39_intra_n6.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n6.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n7.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n7.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n8.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n8.npy
diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n9.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N39_intra_n9.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_n10.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N62_inter_n10.npy
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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
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diff --git a/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N6500_inter_n0.npy b/examples/illustrations/bulk-water-tip4p-vs-size/raw_data/N6500_inter_n0.npy
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diff --git a/examples/illustrations/bulk-water.ipynb b/examples/illustrations/bulk-water.ipynb