Make c surface an option.

usnistgov · Apr 25, 2024 · 105160b · 105160b
1 parent 191c6ce
commit 105160b
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Showing 3 changed files with 24 additions and 20 deletions.
diff --git a/jarvis/__init__.py b/jarvis/__init__.py
@@ -1,6 +1,6 @@
 """Version number."""
 
-__version__ = "2024.4.10"
+__version__ = "2024.4.20"
 
 import os
 

diff --git a/jarvis/analysis/defects/surface.py b/jarvis/analysis/defects/surface.py
@@ -35,10 +35,11 @@ def __init__(
         atoms=None,
         indices=[0, 0, 1],
         layers=3,
-        thickness=25,
+        thickness=None,
         vacuum=18.0,
         tol=1e-10,
         from_conventional_structure=True,
+        use_thickness_c=True,
     ):
         """Initialize the class.
 
@@ -67,6 +68,7 @@ def __init__(
         self.vacuum = vacuum
         self.layers = layers
         self.thickness = thickness
+        self.use_thickness_c = use_thickness_c
         # Note thickness overwrites layers
 
     def to_dict(self):
@@ -147,24 +149,26 @@ def make_surface(self):
             cartesian=True,
         )
         if self.thickness is not None and (self.thickness) > 0:
-            new_lat = new_atoms.lattice_mat  # lat_lengths()
-            a1 = new_lat[0]
-            a2 = new_lat[1]
-            a3 = new_lat[2]
-            new_lat = np.array(
-                [
-                    a1,
-                    a2,
-                    np.cross(a1, a2)
-                    * np.dot(a3, np.cross(a1, a2))
-                    / norm(np.cross(a1, a2)) ** 2,
-                ]
-            )
-
-            a3 = new_lat[2]
-            self.layers = int(self.thickness / np.linalg.norm(a3)) + 1
+            if not self.use_thickness_c:
+                new_lat = new_atoms.lattice_mat  # lat_lengths()
+                a1 = new_lat[0]
+                a2 = new_lat[1]
+                a3 = new_lat[2]
+                new_lat = np.array(
+                    [
+                        a1,
+                        a2,
+                        np.cross(a1, a2)
+                        * np.dot(a3, np.cross(a1, a2))
+                        / norm(np.cross(a1, a2)) ** 2,
+                    ]
+                )
+
+                a3 = new_lat[2]
+                self.layers = int(self.thickness / np.linalg.norm(a3)) + 1
+            else:
+                self.layers = int(self.thickness / new_atoms.lattice.c) + 1
             # print("self.layers", self.layers)
-            # self.layers = int(self.thickness / new_atoms.lattice.c) + 1
             # dims=get_supercell_dims(new_atoms,enforce_c_size=self.thickness)
             # print ('dims=',dims,self.layers)
             # surf_atoms = new_atoms.make_supercell_matrix([1, 1, dims[2]])

diff --git a/setup.py b/setup.py
@@ -12,7 +12,7 @@
 
 setup(
     name="jarvis-tools",
-    version="2024.4.10",
+    version="2024.4.20",
     long_description=long_d,
     install_requires=[
         "numpy>=1.20.1",