diff --git a/src/msspec/utils.py b/src/msspec/utils.py
index b5f4843..1c37f92 100644
--- a/src/msspec/utils.py
+++ b/src/msspec/utils.py
@@ -19,8 +19,8 @@
# along with this msspec. If not, see .
#
# Source file : src/msspec/utils.py
-# Last modified: Thu, 06 Oct 2022 18:27:24 +0200
-# Committed by : Sylvain Tricot 1665073644 +0200
+# Last modified: Wed, 26 Feb 2025 11:15:03 +0100
+# Committed by : Sylvain Tricot
"""
@@ -468,8 +468,12 @@ def hemispherical_cluster(cluster, emitter_tag=0, emitter_plane=0, diameter=0,
# the symbol of your emitter
symbol = cluster[np.where(cluster.get_tags() == emitter_tag)[0][0]].symbol
- assert (diameter != 0 or planes != 0), \
- "At least one of diameter or planes parameter must be use."
+ if shape.lower() in ('spherical'):
+ assert (diameter != 0 or planes != 0), \
+ "At least one of diameter or planes parameter must be use."
+ elif shape.lower() in ('cylindrical'):
+ assert (diameter != 0 and planes != 0), \
+ "Diameter and planes parameters must be defined for cylindrical shape."
if diameter == 0:
# calculate the minimal diameter according to the number of planes
@@ -479,6 +483,7 @@ def hemispherical_cluster(cluster, emitter_tag=0, emitter_plane=0, diameter=0,
# number of repetition in each direction
rep = int(3*min_diameter/min(a, c))
+ #print("rep = ", rep)
# repeat the cluster
cluster = cluster.repeat((rep, rep, rep))
@@ -542,7 +547,7 @@ def hemispherical_cluster(cluster, emitter_tag=0, emitter_plane=0, diameter=0,
xplan, yplan = get_xypos(cluster, zplan)
radius = np.sqrt(xplan**2 + yplan**2 + zplan**2)
- if diameter != 0:
+ if diameter != 0 and shape in ('spherical'):
assert (radius <= diameter/2), ("The number of planes is too high "
"compared to the diameter.")
radius = max(radius, diameter/2)
@@ -575,3 +580,90 @@ def hemispherical_cluster(cluster, emitter_tag=0, emitter_plane=0, diameter=0,
Atoms.translate(cluster, [0, 0, -ze]) # put the emitter in (0,0,0)
return cluster
+
+def shape_cluster(primitive, emitter_tag=0, emitter_plane=0, diameter=0,
+ planes=0, shape='spherical'):
+
+ """Creates and returns a cluster based on an Atoms object and some
+ parameters.
+
+ :param cluster: the Atoms object used to create the cluster
+ :type cluster: Atoms object
+ :param emitter_tag: the tag of your emitter
+ :type emitter_tag: integer
+ :param diameter: the diameter of your cluster in Angströms
+ :type diameter: float
+ :param planes: the number of planes of your cluster
+ :type planes: integer
+ :param emitter_plane: the plane where your emitter will be starting by 0
+ for the first plane
+ :type emitter_plane: integer
+
+ See :ref:`hemispherical_cluster_faq` for more informations.
+ """
+ # We need the radius of the cluster and the number of planes
+ if shape.lower() in ('ispherical', 'cylindrical'):
+ assert (nplanes != 0 and diameter != 0), "nplanes and diameter cannot be zero for '{}' shape".format(shape)
+ elif shape.lower() in ('spherical'):
+ if diameter <= 0:
+ # find the diameter based on the number of planes
+ assert planes != 0, "planes should be > 0"
+
+
+ n = 3
+ natoms = 0
+ while True:
+ n += 2
+ cluster = primitive.copy()
+ # Repeat the primitive cell
+ cluster = cluster.repeat((n, n, n))
+ center_cluster(cluster)
+
+ # Find the emitter closest to the origin
+ all_tags = cluster.get_tags()
+ are_emitters = all_tags == emitter_tag
+ _ie = np.linalg.norm(cluster[are_emitters].positions, axis=1).argmin()
+ ie = np.nonzero(are_emitters)[0][_ie]
+ # Translate the cluster to this emitter position
+ cluster.translate(-cluster[ie].position)
+ # cut plane at surface and at bottom
+ all_z = np.unique(cluster.positions[:,2])
+ try:
+ zsurf = all_z[all_z >= 0][emitter_plane]
+ except IndexError:
+ # There are not enough planes above the emitter
+ zsurf = all_z.max()
+ try:
+ zbottom = all_z[all_z <= 0][::-1][planes - (emitter_plane+1)]
+ except IndexError:
+ # There are not enough planes below the emitter
+ zbottom = all_z.min()
+ cluster = cut_plane(cluster, z=[zbottom,zsurf])
+ # spherical shape
+ if shape.lower() in ('spherical'):
+ cluster = cut_sphere(cluster, radius=diameter/2, center=(0,0,zsurf))
+ if shape.lower() in ('ispherical'):
+ cluster = cut_sphere(cluster, radius=diameter/2, center=(0,0,0))
+ elif shape.lower() in ('cylindrical'):
+ cluster = cut_cylinder(cluster, radius=diameter/2)
+ else:
+ raise NameError("Unknown shape")
+ cluster.set_cell(primitive.cell)
+ if len(cluster) <= natoms:
+ break
+ else:
+ natoms = len(cluster)
+
+
+ return cluster
+
+
+
+
+
+
+
+
+
+
+