Added new function for calculating the occupation matrix

src/mdevaluate/free_energy_landscape.py

@@ -9,10 +9,61 @@ import cmath
 import pandas as pd
 import multiprocessing as mp
 
-
 VALID_GEOMETRY = {"cylindrical", "slab"}
 
 
+def occupation_matrix(trajectory, edge_length=0.05, segments=1000, skip=0.1, nodes=8):
+    frame_indices = np.unique(
+        np.int_(np.linspace(len(trajectory) * skip, len(trajectory) - 1, num=segments))
+    )
+
+    box = trajectory[0].box
+    x_bins = np.arange(0, box[0][0] + edge_length, edge_length)
+    y_bins = np.arange(0, box[1][1] + edge_length, edge_length)
+    z_bins = np.arange(0, box[2][2] + edge_length, edge_length)
+    bins = [x_bins, y_bins, z_bins]
+    # Trajectory is split for parallel computing
+    size = math.ceil(len(frame_indices) / nodes)
+    indices = [
+        np.arange(len(frame_indices))[i : i + size]
+        for i in range(0, len(frame_indices), size)
+    ]
+    pool = mp.Pool(nodes)
+    results = pool.map(
+        partial(_calc_histogram, trajectory=trajectory, bins=bins), indices
+    )
+    pool.close()
+    matbin = np.sum(results, axis=0)
+    x = (x_bins[:-1] + x_bins[1:]) / 2
+    y = (y_bins[:-1] + y_bins[1:]) / 2
+    z = (z_bins[:-1] + z_bins[1:]) / 2
+
+    coords = np.array(np.meshgrid(x, y, z, indexing="ij"))
+    coords = np.array([x.flatten() for x in coords])
+    matbin_new = matbin.flatten()
+    occupation_df = pd.DataFrame(
+        {"x": coords[0], "y": coords[1], "z": coords[2], "occupation": matbin_new}
+    )
+    occupation_df = occupation_df.query("occupation != 0")
+    return occupation_df
+
+
+def _calc_histogram(numberlist, trajectory, bins):
+    matbin = None
+    for index in range(0, len(numberlist), 1000):
+        try:
+            indices = numberlist[index : index + 1000]
+        except IndexError:
+            indices = numberlist[index:]
+        frames = np.concatenate(np.array([trajectory.pbc[i] for i in indices]))
+        hist, _ = np.histogramdd(frames, bins=bins)
+        if matbin is None:
+            matbin = hist
+        else:
+            matbin += hist
+    return matbin
+
+
 def get_fel(
     traj,
     path,

test/test_free_energy_landscape.py

@@ -9,39 +9,39 @@ from mdevaluate import free_energy_landscape as fel
 
 @pytest.fixture
 def trajectory(request):
-    return mdevaluate.open(os.path.join(os.path.dirname(__file__), 'data/pore'))
+    return mdevaluate.open(os.path.join(os.path.dirname(__file__), "data/pore"))
 
 
 def test_get_fel(trajectory):
     test_array = np.array(
         [
             0.0,
-            13.162354034697204,
-            5.327100985208421,
-            9.558746399158396,
-            4.116475238453127,
-            6.305715728953043,
-            3.231102391108276,
-            5.896478799115712,
-            8.381981206446293,
-            5.1191684352849816,
-            5.361112857237105,
-            8.053932845998895,
-            6.895396051256847,
-            7.588888886900885,
-            11.223429636542576,
-            3.779149304024221,
-            40.64319010769286,
-            93.1120609754045,
-            136.99287780099627,
-            171.4403749377496,
+            12.87438176,
+            4.95868203,
+            11.02055197,
+            5.44195534,
+            6.73933442,
+            3.30971789,
+            6.10424055,
+            8.56153733,
+            5.45777331,
+            5.64545817,
+            8.42100423,
+            6.28132121,
+            7.4777172,
+            11.64839354,
+            4.52566354,
+            40.84730838,
+            93.86241602,
+            140.3039937,
+            173.55970021,
         ]
     )
 
     oxygens_water = trajectory.subset(atom_name="OW", residue_name="SOL")
     r, energy_differences = fel.get_fel(
         oxygens_water,
-        os.path.join(os.path.dirname(__file__), 'data/pore'),
+        os.path.join(os.path.dirname(__file__), "data/pore"),
         "cylindrical",
         225,
         edge=0.05,
@@ -51,4 +51,4 @@ def test_get_fel(trajectory):
         overwrite=True,
     )
 
-    assert (energy_differences == test_array).all()
+    assert (np.round(energy_differences) == np.round(test_array)).all()