Merge pull request #6 from raulf2012/dev

Merging all changes up to PROJ_irox publication
raulf2012 · May 18, 2020 · 08568f4 · 08568f4
2 parents 7b22ba8 + 98a7aed
commit 08568f4
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Showing 69 changed files with 3,289 additions and 2,833 deletions.
diff --git a/__misc__/sc_temp_methods.py b/__misc__/sc_temp_methods.py
@@ -14,7 +14,7 @@ def color_scale_interp(
     ):
     """
     """
-    #| - color_scale_interp
+    # | - color_scale_interp
 #     cl.scales["8"]["seq"]["Purples"]
 
     black_white_cs = [
@@ -69,4 +69,4 @@ def clamp(x):
 
     return(color_out)
 
-    #__|
+    # __|
diff --git a/ase_modules/add_adsorbate.py b/ase_modules/add_adsorbate.py
@@ -2,15 +2,15 @@
 
 """Methods to add atoms/adsorbates to surfaces."""
 
-#| - Import Modules
+# | - 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.
@@ -25,7 +25,7 @@ def add_adsorbate_centered(active_element, slab, adsorbate, ads_height=2.5):
         adsorbate: ASE atoms object
         ads_height: Float
     """
-    #| - add_adsorbate_centered
+    # | - add_adsorbate_centered
     center = (sum(slab.cell)) / 2
     act_metals = []
     for atom in slab:
@@ -40,7 +40,7 @@ def add_adsorbate_centered(active_element, slab, adsorbate, ads_height=2.5):
     add_adsorbate(slab, adsorbate, ads_height, position=ads_pos)
 
     return slab
-    #__|
+    # __|
 
 
 def add_graphene_layer(
@@ -58,7 +58,7 @@ def add_graphene_layer(
         graph_surf_d:
         graph_bond_d_real:
     """
-    #| - add_graphene_layer
+    # | - add_graphene_layer
     slab = copy.deepcopy(slab)
 
     # num_graph_units = graphene_units + 1
@@ -91,11 +91,11 @@ def add_graphene_layer(
     y_unit_v = y_unit_v / np.linalg.norm(y_unit_v)
 
 
-    #| - STRAIN
+    # | - 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
@@ -144,4 +144,4 @@ def add_graphene_layer(
     C_pos_lst = np.array(C_pos_lst)
 
     return(slab)
-    #__|
+    # __|
diff --git a/ase_modules/adsorbates.py b/ase_modules/adsorbates.py
@@ -2,23 +2,23 @@
 
 """Adsorbate related methods."""
 
-#| - IMPORT MODULES
+# | - IMPORT MODULES
 from ase import Atoms
 from ase.build import molecule
 
 import numpy as np
-#__|
+# __|
 
 class Adsorbate:
     """Adsorbate atoms object class."""
 
-    #| - Adsorbate ************************************************************
+    # | - Adsorbate ************************************************************
 
     def __init__(self):
         """Initialize Adsorbate class instance."""
-        #| - __init__
+        # | - __init__
         self.tmp = 42
-        #__|
+        # __|
 
     def ooh(self,
         OO_bl=1.359,
@@ -36,7 +36,7 @@ def ooh(self,
             OO_angle:
             H_up_down:
         """
-        #| - ooh
+        # | - ooh
         O_1_x = OO_bl * np.sin(np.radians(OO_angle))
         O_1_y = OO_bl * np.cos(np.radians(OO_angle))
 
@@ -62,19 +62,19 @@ def ooh(self,
             )
 
         return(ooh_mol)
-        #__|
+        # __|
 
     def o(self):
         """*O adsorbate."""
-        #| - o
+        # | - o
         o_mol = Atoms(['O'],
             positions=[
                 (0, 0, 0),
                 ]
             )
 
         return(o_mol)
-        #__|
+        # __|
 
     def oh(self,
         OH_bl=0.978,
@@ -85,15 +85,15 @@ def oh(self,
             OH_bl:
                 O-H bond length
         """
-        #| - oh
+        # | - oh
         oh_mol = Atoms(["O", "H"],
             positions=[
                 (0, 0, 0),
                 (0, 0, OH_bl),
                 ]
             )
         return(oh_mol)
-        #__|
+        # __|
 
     def h2o(self,
         H_up_down="up",
@@ -104,7 +104,7 @@ def h2o(self,
             H_up_down:
                 Hydrogen atom pointing up or down
         """
-        #| - h2o
+        # | - h2o
         h2o_mol = molecule("H2O")
 
         if H_up_down == "up":
@@ -113,7 +113,7 @@ def h2o(self,
             pass
 
         return(h2o_mol)
-        #__|
+        # __|
 
     def get_adsorbate(self, adsorbate, **kwargs):
         """
@@ -123,10 +123,10 @@ def get_adsorbate(self, adsorbate, **kwargs):
             adsorbate:
             kwargs:
         """
-        #| - get_adsorbate
+        # | - get_adsorbate
         ads = getattr(self, adsorbate)(**kwargs)
 
         return(ads)
-        #__|
+        # __|
 
-    #__| **********************************************************************
+    # __| **********************************************************************