Iteration

Makefile

@@ -22,29 +22,29 @@ format:
 
 test:
 	${python} -m pytest -rs \
-	tests/test_acsf_linear_angles.py \
-	tests/test_acsf.py \
-	tests/test_arad.py \
-	tests/test_armp.py \
-	tests/test_compound.py \
-	tests/test_distance.py \
-	tests/test_energy_krr_atomic_cmat.py \
-	tests/test_energy_krr_bob.py \
-	tests/test_energy_krr_cmat.py \
-	tests/test_fchl_acsf_energy.py \
-	tests/test_fchl_acsf_forces.py \
-	tests/test_fchl_acsf.py \
-	tests/test_fchl_electric_field.py \
-	tests/test_fchl_force.py \
-	tests/test_fchl_scalar.py \
-	tests/test_kernel_derivatives.py \
-	tests/test_kernels.py \
-	tests/test_mrmp.py \
-	tests/test_neural_network.py \
-	tests/test_representations.py \
-	tests/test_slatm.py \
-	tests/test_solvers.py \
-	tests/test_symm_funct.py
+		tests/test_distance.py \
+		tests/test_kernels.py \
+		tests/test_representations.py \
+		tests/test_slatm.py \
+		tests/test_solvers.py
+		# tests/test_fchl_acsf.py
+		# tests/test_fchl_acsf_energy.py
+		# tests/test_fchl_acsf_forces.py \
+		# tests/test_fchl_electric_field.py \
+		# tests/test_fchl_force.py \
+		# tests/test_fchl_scalar.py
+	# REMOVE tests/test_acsf_linear_angles.py \
+	# REMOVE tests/test_acsf.py \
+	# tests/test_arad.py \
+	# REMOVE tests/test_armp.py \
+	# REMOVE tests/test_compound.py \
+	# integration tests/test_energy_krr_atomic_cmat.py \
+	# integration tests/test_energy_krr_bob.py \
+	# integration tests/test_energy_krr_cmat.py \
+	# tests/test_kernel_derivatives.py \
+	# REMOVE tests/test_mrmp.py \
+	# REMOVE tests/test_neural_network.py \
+	# REMOVE tests/test_symm_funct.py
 
 types:
 	${python} -m monkeytype run $(which pytest) ./tests/

src/qmllib/representations/slatm.py

@@ -1,4 +1,4 @@
-import itertools as itl
+import itertools
 
 import numpy as np
 import scipy.spatial.distance as spatial_distance
@@ -50,15 +50,15 @@ def update_m(obj, ia, rcut=9.0, pbc=None):
 
     n1s, n2s, n3s = nns
 
-    n123s_ = np.array(list(itl.product(n1s, n2s, n3s)))
+    n123s_ = np.array(list(itertools.product(n1s, n2s, n3s)))
     n123s = []
     for n123 in n123s_:
         n123u = list(n123)
         if n123u != [0, 0, 0]:
             n123s.append(n123u)
 
     nau = len(n123s)
-    n123s = np.array(n123s, np.float)
+    n123s = np.array(n123s, np.float64)
 
     na = len(zs)
     cia = coords[ia]
@@ -134,13 +134,14 @@ def get_sbop(
         assert ia is not None, "#ERROR: plz specify `za and `ia "
 
     if pbc != "000":
-        if rcut < 9.0:
-            raise ValueError()
-        assert iloc, "#ERROR: for periodic system, plz use atomic rpst"
-        zs, coords = update_m(obj, ia, rcut=rcut, pbc=pbc)
+        raise NotImplementedError("Periodic boundary conditions not implemented")
+        # if rcut < 9.0:
+        #     raise ValueError()
+        # assert iloc, "#ERROR: for periodic system, plz use atomic rpst"
+        # zs, coords = update_m(obj, ia, rcut=rcut, pbc=pbc)
 
         # after update of `m, the query atom `ia will become the first atom
-        ia = 0
+        # ia = 0
 
     # bop potential distribution
     r0 = 0.1
@@ -174,11 +175,12 @@ def get_sbot(
         assert ia is not None, "#ERROR: plz specify `za and `ia "
 
     if pbc != "000":
-        assert iloc, "#ERROR: for periodic system, plz use atomic rpst"
-        zs, coords = update_m(obj, ia, rcut=rcut, pbc=pbc)
+        raise NotImplementedError("Periodic boundary conditions not implemented")
+        # assert iloc, "#ERROR: for periodic system, plz use atomic rpst"
+        # zs, coords = update_m(obj, ia, rcut=rcut, pbc=pbc)
 
-        # after update of `m, the query atom `ia will become the first atom
-        ia = 0
+        # # after update of `m, the query atom `ia will become the first atom
+        # ia = 0
 
     # for a normalized gaussian distribution, u should multiply this coeff
     coeff = 1 / np.sqrt(2 * sigma**2 * np.pi) if normalize else 1.0

tests/conftest.py

@@ -1,3 +1,54 @@
 from pathlib import Path
 
+import numpy as np
+
 ASSETS = Path("./tests/assets")
+
+
+def get_asize(list_of_atoms, pad):
+    """TODO Anders what is asize"""
+
+    asize: dict[int, int] = dict()
+
+    # WHAT
+
+    for atoms in list_of_atoms:
+
+        unique_atoms, unique_counts = np.unique(atoms, return_counts=True)
+
+        for atom, count in zip(unique_atoms, unique_counts):
+
+            prev = asize.get(atom, None)
+
+            if prev is None:
+                asize[atom] = count + pad
+                continue
+
+            asize[atom] = max(asize[atom], count + pad)
+
+        # for key, value in mol.natypes.items():
+        #     try:
+        #         asize[key] = max(asize[key], value + pad)
+        #     except KeyError:
+        #         asize[key] = value + pad
+
+    return asize
+
+
+def get_energies(filename: Path):
+    """Returns a dictionary with heats of formation for each xyz-file."""
+
+    with open(filename, "r") as f:
+        lines = f.readlines()
+
+    energies = dict()
+
+    for line in lines:
+        tokens = line.split()
+
+        xyz_name = tokens[0]
+        hof = float(tokens[1])
+
+        energies[xyz_name] = hof
+
+    return energies