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Merge pull request #331 from Exabyte-io/update/SOF-7691-1
update/SOF 7691 1
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‎lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md‎

Lines changed: 24 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -54,21 +54,33 @@ Find and open `create_grain_boundary_film.ipynb`. Edit the grain boundary parame
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`EDGE_INCLUSION_TOLERANCE = 0.0` -- Edge inclusion parameter, in Angstroms. Controls the overlap of the second phase onto the first phase.
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```python
57+
# Material selection
58+
MATERIAL_INDEX = 0 # Index in the list of materials
59+
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# Grain boundary parameters
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TARGET_TWIST_ANGLE = 9.0 # in degrees
59-
BOUNDARY_GAP = 0.0 # Gap between orientations in X direction
60-
XY_SUPERCELL_MATRIX = [[1, 0], [0, 2]]
62+
BOUNDARY_GAP = 0.0 # Gap between two orientations in X direction, in Angstroms
63+
XY_SUPERCELL_MATRIX = [[1, 0], [0, 2]] # Supercell matrix to be applied to each of the orientations before matching
64+
MILLER_INDICES = (0, 0, 1) # Miller indices for the supercell matching
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VACUUM = 10.0 # Vacuum thickness in Angstroms, added to the top and bottom of the grain boundary
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# Search algorithm parameters
63-
MAX_REPETITION = None
68+
MAX_REPETITION = None # Maximum supercell matrix element value
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ANGLE_TOLERANCE = 0.5 # in degrees
65-
RETURN_FIRST_MATCH = True
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RETURN_FIRST_MATCH = True # If True, returns first solution within tolerance
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67-
# Distance tolerance for atom merging
72+
# Distance tolerance for two atoms to be considered too close.
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# Used when merging two orientations to remove the atoms of the first one.
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# Should be less than the expected bond length
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DISTANCE_TOLERANCE = 1.43 # in Angstroms
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70-
# Edge inclusion parameter
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# How much to expand inclusion of the edge atoms for both orientations and fill in the gap region.
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# A fine-tuning parameter
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EDGE_INCLUSION_TOLERANCE = 0.0 # in Angstroms
80+
81+
# Visualization parameters
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SHOW_INTERMEDIATE_STEPS = True
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CELL_REPETITIONS_FOR_VISUALIZATION = [3, 3, 1]
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```
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![Notebook Setup](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/2-jl-setup-nb-gb.webp "Notebook Setup")
@@ -95,21 +107,16 @@ Open JupyterLite Session and find `create_point_defect.ipynb` notebook.
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Select the h-BN grain boundary structure as input material and configure the adatom defect parameters in the "1.1. Set Notebook Parameters" section:
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```python
98-
DEFECT_TYPE = "interstitial" # (e.g. "vacancy", "substitution", "interstitial")
99-
SITE_ID = None # Site index of the defect
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COORDINATE = [0.5, 0.45, 0.5] # Position of the defect in crystal coordinates
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APPROXIMATE_COORDINATE = None # Approximate coordinates of the defect in crystal coordinates
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CHEMICAL_ELEMENT = "N" # Element to be placed at the site (ignored for vacancy)
103-
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# Selected material will be used as a unit cell to create a supercell first.
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SUPERCELL_MATRIX = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
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106-
# List of dictionaries with defect parameters
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DEFECT_CONFIGS = [
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{
109-
"defect_type": DEFECT_TYPE,
110-
"coordinate": COORDINATE,
111-
"chemical_element": CHEMICAL_ELEMENT,
112-
}
115+
"type": "interstitial",
116+
"coordinate": [0.5, 0.45, 0.5], # Crystal coordinates
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"element": "N",
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"placement_method": "closest_site",
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},
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]
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```
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‎lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md‎

Lines changed: 32 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -53,47 +53,48 @@ Find and open the `create_adatom_defect.ipynb` notebook. Select MoS2 as input ma
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Set up the slab and defect parameters in the notebook:
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```python
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# Slab parameters
57-
MILLER_INDICES = (0, 0, 1) # MoS2 basal plane
58-
SLAB_THICKNESS = 1 # Single layer
59-
VACUUM = 10.0 # in Angstrom
60-
SUPERCELL_MATRIX = [[3, 0, 0], [0, 3, 0], [0, 0, 1]] # 3x3 supercell
56+
# Index in the list of materials, to access as materials[MATERIAL_INDEX]
57+
MATERIAL_INDEX = 0
58+
ELEMENT = "Pt" # Chemical element of the adatom
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62-
# Defect configurations for all Pt atoms
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# Dictionaries are validated and converted to AdatomDefectDict objects below
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DEFECT_CONFIGS = [
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{
65-
"defect_type": "adatom",
66-
"placement_method": "coordinate",
67-
"chemical_element": "Pt",
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"position_on_surface": [5/9, 4/9], # First Pt: atop central Mo
69-
"distance_z": 1.2, # Distance from surface S atoms
70-
"use_cartesian_coordinates": False
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"type": "adatom",
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"coordinate_2d": [5/9, 4/9], # Crystal coordinates on the surface (x, y)
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"distance_z": 1.2, # Method to place the adatom
66+
"element": ELEMENT,
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},
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{
73-
"defect_type": "adatom",
74-
"placement_method": "coordinate",
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"chemical_element": "Pt",
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"position_on_surface": [2/9, 4/9], # Second Pt: next clockwise atop Mo
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"distance_z": 1.2, # Distance from surface S atoms
78-
"use_cartesian_coordinates": False
69+
"type": "adatom",
70+
"coordinate_2d": [2/9, 4/9], # Crystal coordinates on the surface (x, y)
71+
"distance_z": 1.2, # Method to place the adatom
72+
"element": ELEMENT,
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},
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{
81-
"defect_type": "adatom",
82-
"placement_method": "coordinate",
83-
"chemical_element": "Pt",
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"position_on_surface": [5/9, 7/9], # Third Pt: next clockwise atop Mo
85-
"distance_z": 1.2, # Distance from surface S atoms
86-
"use_cartesian_coordinates": False
75+
"type": "adatom",
76+
"coordinate_2d": [5/9, 7/9], # Crystal coordinates on the surface (x, y)
77+
"distance_z": 1.2, # Method to place the adatom
78+
"element": ELEMENT,
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},
8880
{
89-
"defect_type": "adatom",
90-
"placement_method": "coordinate",
91-
"chemical_element": "Pt",
92-
"position_on_surface": [4/9, 5/9], # Fourth Pt: centered atop S
93-
"distance_z": 1.6, # Distance between Pt atom layers, in Angstrom
94-
"use_cartesian_coordinates": False
95-
}
81+
"type": "adatom",
82+
"coordinate_2d": [4/9, 5/9], # Crystal coordinates on the surface (x, y)
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"distance_z": 1.6, # Method to place the adatom
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"element": ELEMENT,
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},
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]
87+
88+
89+
PLACEMENT_METHOD = "new_crystal_site" # Method to place the adatom, e.g., "new_crystal_site", "exact_coordinate", "equidistant"
90+
91+
92+
# Slab parameters
93+
MILLER_INDICES = (0, 0, 1) # Miller indices of the surface
94+
SLAB_THICKNESS = 1 # Thickness of the slab in unit cells
95+
VACUUM = 10.0 # Vacuum thickness in Angstrom
96+
XY_SUPERCELL_MATRIX = [[3, 0], [0, 3]] # Supercell matrix for the slab
97+
TERMINATION_FORMULA = None # Stoichiometric formula of the slab termination to be used.
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```
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Key parameters explained:

‎lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md‎

Lines changed: 9 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -54,23 +54,21 @@ We'll modify its parameters to create the Sn-vacancy O-interstitial defects acco
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Replace the default parameters in section 1.1 with:
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```python
57-
# Supercell parameters.
57+
# Selected material will be used as a unit cell to create a supercell first.
5858
SUPERCELL_MATRIX = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
5959

60-
# Defect parameters.
6160
DEFECT_CONFIGS = [
6261
{
63-
"defect_type": "vacancy",
64-
# Coordiante will be resolved to nearest atom.
65-
"approximate_coordinate": [0.0, 0.25, 0.525],
62+
"type": "vacancy",
63+
"coordinate": [0.0, 0.25, 0.525], # Crystal coordinates
64+
"placement_method": "closest_site",
6665
},
6766
{
68-
"defect_type": "interstitial",
69-
# Coordiante will be resolved to nearest Voronoi site.
70-
"coordinate": [0.0, 0.25, 0.35],
71-
"chemical_element": "O",
72-
"placement_method": "voronoi_site"
73-
}
67+
"type": "interstitial",
68+
"coordinate": [0.0, 0.25, 0.35], # Crystal coordinates
69+
"element": "O",
70+
"placement_method": "voronoi_site",
71+
},
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]
7573
```
7674
![Defect Parameters](../../../images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/3-jl-setup-nb.webp "Defect parameters for O-interstitial in SnO")

‎lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md‎

Lines changed: 19 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -82,21 +82,28 @@ Next, edit `create_point_defect_pair.ipynb` notebook to modify the parameters by
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Copy the below content and edit the "1.1. Set up defect parameters" cell in the notebook as follows:
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```python
85+
from types import SimpleNamespace
86+
87+
# Selected material will be used as a unit cell to create a supercell first.
8588
SUPERCELL_MATRIX = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
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8790
# List of dictionaries with defect parameters
88-
PRIMARY_DEFECT_CONFIG = {
89-
"defect_type": "substitution",
90-
"approximate_coordinate": [1.608, 4.642, 5.240],
91-
"chemical_element": "Mg",
92-
"use_cartesian_coordinates": True,
93-
}
94-
95-
SECONDARY_DEFECT_CONFIG = {
96-
"defect_type": "vacancy",
97-
"approximate_coordinate": [1.608, 4.642, 7.210],
98-
"use_cartesian_coordinates": True,
99-
}
91+
PRIMARY_DEFECT_CONFIG = SimpleNamespace(
92+
defect_type="substitution",
93+
coordinate=[1.608, 4.642, 5.240], # Approx. coord that will be resolved to the closest site
94+
use_cartesian_coordinates=True, # Use cartesian or crystal coordinates
95+
chemical_element="Mg",
96+
# "site_id": 0, # Index of the atom in the host material
97+
# "coordinate": None, # Exact position (override the approximate coordinate)
98+
)
99+
100+
SECONDARY_DEFECT_CONFIG = SimpleNamespace(
101+
defect_type="vacancy",
102+
approximate_coordinate=[1.608, 4.642, 7.210], # Approx. coord that will be resolved to the closest site
103+
use_cartesian_coordinates=True,
104+
# "site_id": 0, # Index of the atom in the host material
105+
# "coordinate": None, # Exact position (override the approximate coordinate)
106+
)
100107
```
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Here's the visual of the updated content:

‎lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md‎

Lines changed: 21 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -73,39 +73,38 @@ Next, edit `create_point_defect.ipynb` notebook to modify the parameters by addi
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Copy the below content and edit the "1.1. Set up defect parameters" cell in the notebook as follows:
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```python
76-
DEFECT_TYPE = "substitution"
77-
SITE_ID = None # `from_site_id` method will be ignored
78-
COORDINATE = None # default method will be ignored
79-
APPROXIMATE_COORDINATE = None
80-
CHEMICAL_ELEMENT = "N"
76+
# Selected material will be used as a unit cell to create a supercell first.
8177
SUPERCELL_MATRIX = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
82-
USE_CARTESIAN_COORDINATES = True
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8479
DEFECT_CONFIGS = [
8580
{
86-
"defect_type": "substitution",
87-
"approximate_coordinate": [4.9, 2.85, 10],
88-
"chemical_element": CHEMICAL_ELEMENT,
89-
"use_cartesian_coordinates": USE_CARTESIAN_COORDINATES
81+
"type": "substitution",
82+
"coordinate": [4.9, 2.85, 10],
83+
"element": "N",
84+
"placement_method": "closest_site",
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"use_cartesian_coordinates": True
9086
},
9187
{
92-
"defect_type": "substitution",
93-
"approximate_coordinate": [3.7, 4.9, 10],
94-
"chemical_element": CHEMICAL_ELEMENT,
95-
"use_cartesian_coordinates": USE_CARTESIAN_COORDINATES
88+
"type": "substitution",
89+
"coordinate": [3.7, 4.9, 10],
90+
"element": "N",
91+
"placement_method": "closest_site",
92+
"use_cartesian_coordinates": True
9693
},
9794
{
98-
"defect_type": "substitution",
99-
"approximate_coordinate": [2.45, 2.85, 10],
100-
"chemical_element": CHEMICAL_ELEMENT,
101-
"use_cartesian_coordinates": USE_CARTESIAN_COORDINATES
95+
"type": "substitution",
96+
"coordinate": [2.45, 2.85, 10],
97+
"element": "N",
98+
"placement_method": "closest_site",
99+
"use_cartesian_coordinates": True
102100
},
103101
{
104-
"defect_type": "vacancy",
105-
"approximate_coordinate": [3.7, 3.55, 10],
106-
"use_cartesian_coordinates": USE_CARTESIAN_COORDINATES
102+
"type": "vacancy",
103+
"coordinate": [3.7, 3.55, 10],
104+
"placement_method": "closest_site",
105+
"use_cartesian_coordinates": True
107106
},
108-
]
107+
]
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```
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Here's the visual of the updated content:

‎lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md‎

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@@ -59,11 +59,15 @@ Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/
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Find and open `create_nanoribbon.ipynb` in the list of notebooks. Edit the nanoribbon parameters in section 1.1 of the notebook:
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6161
```python
62-
WIDTH = 3 # in number of unit cells
63-
LENGTH = 6 # in number of unit cells
64-
VACUUM_WIDTH = 0 # in number of unit cells
65-
VACUUM_LENGTH = 0 # in number of unit cells
66-
EDGE_TYPE = "zigzag" # "zigzag" or "armchair"
62+
# Index in the list of materials, to access as materials[MATERIAL_INDEX]
63+
MATERIAL_INDEX = 0
64+
65+
# Widths and lengths are in number of unit cells
66+
WIDTH = 3 # in unit cells
67+
LENGTH = 6 # in unit cells
68+
VACUUM_WIDTH = 0 # in Angstroms
69+
VACUUM_LENGTH = 0 # in Angstroms
70+
EDGE_TYPE = "zigzag" # "zigzag" or "armchair"
6771
```
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6973
![Nanoribbon Parameters](../../../images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/2-jl-nb-setup-nanoribbon.webp "Nanoribbon Parameters")
@@ -92,11 +96,14 @@ After creating the nanoribbon, we'll introduce the vacancy defect using the poin
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Open `create_point_defect.ipynb` and modify the defect configuration parameters:
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9498
```python
99+
# Selected material will be used as a unit cell to create a supercell first.
95100
SUPERCELL_MATRIX = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
101+
96102
DEFECT_CONFIGS = [
97103
{
98-
"defect_type": "vacancy",
99-
"approximate_coordinate": [0.5, 0.5, 0.5],
104+
"type": "vacancy",
105+
"coordinate": [0.5, 0.5, 0.5],
106+
"placement_method": "closest_site",
100107
"use_cartesian_coordinates": False
101108
}
102109
]

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