Merge pull request #5 from raulf2012/dev

Merge work from last several months into master

.gitignore

@@ -1,6 +1,9 @@
 # My additions #
 ################
 *.pyc
+* conflicted copy *
+*__pycache__*
+
 
 # Compiled source #
 ###################

README.md

@@ -1,7 +1,7 @@
-# Python modules used in my research
-
-# Author(s):
-Raul Flores
-
-# Workflowy Development List
-https://workflowy.com/#/63d9234f4c4a
+# Python modules used in my research
+
+# Author(s):
+Raul Flores
+
+# Workflowy Development List
+https://workflowy.com/#/63d9234f4c4a

__init__.py

@@ -1 +1 @@
-#TEMP TEMP 171030
+#TEMP TEMP 171030

ase_modules/__init__.py

@@ -1 +1 @@
-## 171030
+## 171030

ase_modules/add_adsorbate.py

@@ -1,147 +1,147 @@
-#!/usr/bin/env python
-
-"""Methods to add atoms/adsorbates to surfaces."""
-
-#| - Import Modules
-import numpy as np
-import copy
-import math
-
-from operator import itemgetter
-from ase.build import add_adsorbate
-from misc_modules.numpy_methods import angle_between
-#__|
-
-def add_adsorbate_centered(active_element, slab, adsorbate, ads_height=2.5):
-    """Add adsorbate to surface.
-
-    Places an adsorbate above an active element/atom of a slab. If multiple
-    active elements are present within a unit cell, the adsorbate will be placed
-    above the atom closest to the center.
-
-    Args:
-        active_element: String
-        slab: ASE atoms object
-        adsorbate: ASE atoms object
-        ads_height: Float
-    """
-    #| - add_adsorbate_centered
-    center = (sum(slab.cell)) / 2
-    act_metals = []
-    for atom in slab:
-        if atom.symbol == active_element:
-            act_metals.append([
-                atom.index,
-                np.linalg.norm(atom.position - center),
-                ])
-
-    active_metal = slab[sorted(act_metals, key=itemgetter(1))[0][0]]
-    ads_pos = (active_metal.position[0], active_metal.position[1])
-    add_adsorbate(slab, adsorbate, ads_height, position=ads_pos)
-
-    return slab
-    #__|
-
-
-def add_graphene_layer(
-    slab,
-    graphene_units=1,
-    graph_surf_d=3.0,
-    graph_bond_d_real=1.4237,
-    ):
-    """
-    Add graphene layer above surface of hexagonal unit cell slab.
-
-    Args:
-        slab:
-        graphene_units:
-        graph_surf_d:
-        graph_bond_d_real:
-    """
-    #| - add_graphene_layer
-    slab = copy.deepcopy(slab)
-
-    # num_graph_units = graphene_units + 1
-    graphene_units = int(graphene_units)
-
-    num_graph_units = int(graphene_units)
-    ngu = num_graph_units
-
-    num_graph_bond_lengths = (2. + 1.) * ngu
-
-    v1 = slab.cell[0]
-    v2 = slab.cell[1]
-
-    angle = angle_between(v1, v2)
-    angle = math.degrees(angle)
-    # print("Angle between lattice vectors: " + str(angle))
-
-    mag1 = np.linalg.norm(v1)
-    mag2 = np.linalg.norm(v2)
-
-    assert round(mag1) == round(mag2)
-
-    graph_bond_d = mag1 / num_graph_bond_lengths
-
-    xy_cell = slab.cell[0:2, 0:2]  # x and y components of unit cell
-    x_unit_v = xy_cell[0]
-    y_unit_v = xy_cell[1]
-
-    x_unit_v = x_unit_v / np.linalg.norm(x_unit_v)
-    y_unit_v = y_unit_v / np.linalg.norm(y_unit_v)
-
-
-    #| - STRAIN
-    tmp = mag1 / num_graph_bond_lengths
-    strain = 100. * (graph_bond_d_real - tmp) / graph_bond_d_real
-    print("Strain: " + str(strain))
-    #__|
-
-    patt_cnt_x = 0
-    patt_cnt_y = 0
-    C_pos_lst = []
-    for y_ind in range(graphene_units * 3):
-        patt_cnt_x = patt_cnt_y
-        for x_ind in range(graphene_units * 3):
-
-            if patt_cnt_x == 0 or patt_cnt_x == 1:
-
-                pos_x = x_ind * graph_bond_d * x_unit_v
-                pos_y = y_ind * graph_bond_d * y_unit_v
-
-                pos_i = np.array(pos_x) + np.array(pos_y)
-                pos_i = np.append(pos_i, 0.)
-
-                C_pos_lst.append(pos_i)
-                # atom_cent = (origin[0] + x_ind * graph_bond_d
-                # - graph_bond_d * y_ind * y_unit_v[0], origin[1] + y_ind
-                # * graph_bond_d)
-
-                add_adsorbate(
-                    slab,
-                    "C",
-                    graph_surf_d,
-                    position=(pos_i[0], pos_i[1]),
-                    )
-
-                patt_cnt_x += 1
-
-            elif patt_cnt_x == 2:
-                patt_cnt_x = 0
-
-        if patt_cnt_y == 0:
-            patt_cnt_y = 2
-            continue
-
-        if patt_cnt_y == 2:
-            patt_cnt_y = 1
-            continue
-
-        elif patt_cnt_y == 1:
-            patt_cnt_y = 0
-            continue
-
-    C_pos_lst = np.array(C_pos_lst)
-
-    return(slab)
-    #__|
+#!/usr/bin/env python
+
+"""Methods to add atoms/adsorbates to surfaces."""
+
+#| - Import Modules
+import numpy as np
+import copy
+import math
+
+from operator import itemgetter
+from ase.build import add_adsorbate
+from misc_modules.numpy_methods import angle_between
+#__|
+
+def add_adsorbate_centered(active_element, slab, adsorbate, ads_height=2.5):
+    """Add adsorbate to surface.
+
+    Places an adsorbate above an active element/atom of a slab. If multiple
+    active elements are present within a unit cell, the adsorbate will be placed
+    above the atom closest to the center.
+
+    Args:
+        active_element: String
+        slab: ASE atoms object
+        adsorbate: ASE atoms object
+        ads_height: Float
+    """
+    #| - add_adsorbate_centered
+    center = (sum(slab.cell)) / 2
+    act_metals = []
+    for atom in slab:
+        if atom.symbol == active_element:
+            act_metals.append([
+                atom.index,
+                np.linalg.norm(atom.position - center),
+                ])
+
+    active_metal = slab[sorted(act_metals, key=itemgetter(1))[0][0]]
+    ads_pos = (active_metal.position[0], active_metal.position[1])
+    add_adsorbate(slab, adsorbate, ads_height, position=ads_pos)
+
+    return slab
+    #__|
+
+
+def add_graphene_layer(
+    slab,
+    graphene_units=1,
+    graph_surf_d=3.0,
+    graph_bond_d_real=1.4237,
+    ):
+    """
+    Add graphene layer above surface of hexagonal unit cell slab.
+
+    Args:
+        slab:
+        graphene_units:
+        graph_surf_d:
+        graph_bond_d_real:
+    """
+    #| - add_graphene_layer
+    slab = copy.deepcopy(slab)
+
+    # num_graph_units = graphene_units + 1
+    graphene_units = int(graphene_units)
+
+    num_graph_units = int(graphene_units)
+    ngu = num_graph_units
+
+    num_graph_bond_lengths = (2. + 1.) * ngu
+
+    v1 = slab.cell[0]
+    v2 = slab.cell[1]
+
+    angle = angle_between(v1, v2)
+    angle = math.degrees(angle)
+    # print("Angle between lattice vectors: " + str(angle))
+
+    mag1 = np.linalg.norm(v1)
+    mag2 = np.linalg.norm(v2)
+
+    assert round(mag1) == round(mag2)
+
+    graph_bond_d = mag1 / num_graph_bond_lengths
+
+    xy_cell = slab.cell[0:2, 0:2]  # x and y components of unit cell
+    x_unit_v = xy_cell[0]
+    y_unit_v = xy_cell[1]
+
+    x_unit_v = x_unit_v / np.linalg.norm(x_unit_v)
+    y_unit_v = y_unit_v / np.linalg.norm(y_unit_v)
+
+
+    #| - STRAIN
+    tmp = mag1 / num_graph_bond_lengths
+    strain = 100. * (graph_bond_d_real - tmp) / graph_bond_d_real
+    print("Strain: " + str(strain))
+    #__|
+
+    patt_cnt_x = 0
+    patt_cnt_y = 0
+    C_pos_lst = []
+    for y_ind in range(graphene_units * 3):
+        patt_cnt_x = patt_cnt_y
+        for x_ind in range(graphene_units * 3):
+
+            if patt_cnt_x == 0 or patt_cnt_x == 1:
+
+                pos_x = x_ind * graph_bond_d * x_unit_v
+                pos_y = y_ind * graph_bond_d * y_unit_v
+
+                pos_i = np.array(pos_x) + np.array(pos_y)
+                pos_i = np.append(pos_i, 0.)
+
+                C_pos_lst.append(pos_i)
+                # atom_cent = (origin[0] + x_ind * graph_bond_d
+                # - graph_bond_d * y_ind * y_unit_v[0], origin[1] + y_ind
+                # * graph_bond_d)
+
+                add_adsorbate(
+                    slab,
+                    "C",
+                    graph_surf_d,
+                    position=(pos_i[0], pos_i[1]),
+                    )
+
+                patt_cnt_x += 1
+
+            elif patt_cnt_x == 2:
+                patt_cnt_x = 0
+
+        if patt_cnt_y == 0:
+            patt_cnt_y = 2
+            continue
+
+        if patt_cnt_y == 2:
+            patt_cnt_y = 1
+            continue
+
+        elif patt_cnt_y == 1:
+            patt_cnt_y = 0
+            continue
+
+    C_pos_lst = np.array(C_pos_lst)
+
+    return(slab)
+    #__|