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examples/illustrations/bulk-water-tip4p-anisotropic/analysis.py

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+#!/usr/bin/env python
+# coding: utf-8
+
+import numpy as np
+import MDAnalysis as mda
+import nmrformd
+
+import sys, os, git
+current_path = os.getcwd()
+git_repo = git.Repo(current_path, search_parent_directories=True)
+git_path = git_repo.git.rev_parse("--show-toplevel")
+
+sys.path.append(git_path + '/examples/shared/')
+from utilities import save_result, measure_N, measure_R1
+
+path = "/data/nmrformd-data/bulk-water-tip4p-vs-temperature/raw_data/"
+run = True
+R1_intra = 1e-5
+R1_inter = 1e-5
+T = 300
+while run:
+    # Read current status
+    name_intra = "N4000_intra_T" + str(T) + "K"
+    name_inter = "N4000_inter_T" + str(T) + "K"
+    n_intra = measure_N(name_intra)
+    n_inter = measure_N(name_inter)
+    # Import MDA universe
+    datapath = path + "N4000_" + str(T) + "K/"
+    u = mda.Universe(datapath+"prod.tpr", datapath+"prod.xtc")
+    hydrogen = u.select_atoms("name HW1 HW2")
+    n_hydrogen = hydrogen.n_atoms
+    if n_intra < n_hydrogen:
+        # Calculated NMR properties
+        intra = nmrformd.NMR(u, atom_group = hydrogen,
+                            neighbor_group = hydrogen,
+                            type_analysis = "intra_molecular", isotropic=False,
+                            number_i = 1)
+        save_result(intra, name = name_intra, aniso=True)
+        if np.random.random() < 0.2:
+            inter = nmrformd.NMR(u, atom_group = hydrogen,
+                                neighbor_group = hydrogen,
+                                type_analysis = "inter_molecular",  isotropic=False,
+                                number_i = 1)
+            save_result(inter, name = name_inter, aniso=True)
+    else:
+        run = False
+    # Print information
+    R1_intra = measure_R1(name_intra)
+    R1_inter = measure_R1(name_inter)
+    print("T =", T, "K --", n_intra, n_hydrogen, 
+        "R1:", np.round(R1_intra,2), np.round(R1_inter,2), 
+        "T1:", np.round(1/(R1_intra+R1_inter),2))