Skip to content

Fix the project to run https://github.com/DerekDardzinski/OgreInterface/blob/main/OgreInterface/example.py successfully. #5

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
hongyi-zhao wants to merge 3 commits into
base: main
Choose a base branch
from
Open

Fix the project to run https://github.com/DerekDardzinski/OgreInterface/blob/main/OgreInterface/example.py successfully. #5

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
9a74896
Fix the project to run <https://github.com/DerekDardzinski/OgreInterf…
hongyi-zhao Feb 13, 2024
df9a502
Fix the OgreInterface/example.py to use `center=True` to avoid atoms …
hongyi-zhao Feb 14, 2024
f36564e
Change `get_string` to `get_str` to fix the following problem:
hongyi-zhao Feb 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 8 additions & 10 deletions OgreInterface/example.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,9 @@
film="./poscars/POSCAR_Al_conv",
max_film_index=2,
max_substrate_index=2,
max_linear_strain=0.01,
max_angle_strain=0.01,
max_strain=0.01,
max_area_mismatch=0.01,
max_area=200,
convert_to_conventional=True,
max_area=200
)
ms.run_scan()
ms.plot_misfits(fontsize=14, labelrotation=-20, figure_scale=1)
Expand All @@ -35,8 +33,8 @@
)

# Select which Surface you want from the list of Surface's
sub = subs.slabs[0]
film = films.slabs[0]
sub = subs._slabs[0]
film = films._slabs[0]

# Optional way to remove layers from the substrate or film (Usefull for complete control of termination)
# sub.remove_layers(num_layers=3, top=False)
Expand All @@ -46,12 +44,12 @@
interface_generator = InterfaceGenerator(
substrate=sub,
film=film,
max_linear_strain=0.01,
max_angle_strain=0.01,
max_strain=0.01,
max_area_mismatch=0.01,
max_area=200,
interfacial_distance=2.0,
vacuum=40,
interfacial_distance=4.0,
vacuum=20,
center=True,
)

# Generate the interfaces
Expand Down
4 changes: 2 additions & 2 deletions OgreInterface/interfaces/interface.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -493,7 +493,7 @@ def write_file(
if relax:
poscar.selective_dynamics = to_relax

poscar_str = poscar.get_string()
poscar_str = poscar.get_str()

else:
syms = [site.specie.symbol for site in slab]
Expand Down Expand Up @@ -538,7 +538,7 @@ def write_file(
if relax:
poscar.selective_dynamics = to_relax

poscar_str = poscar.get_string().split("\n")
poscar_str = poscar.get_str().split("\n")
poscar_str[5] = " ".join(new_atom_types)
poscar_str[6] = " ".join(list(map(str, n_atoms)))
poscar_str = "\n".join(poscar_str)
Expand Down
4 changes: 2 additions & 2 deletions OgreInterface/interfaces/old_interface.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -944,7 +944,7 @@ def write_file(
if relax:
poscar.selective_dynamics = to_relax

poscar_str = poscar.get_string()
poscar_str = poscar.get_str()

else:
syms = [site.specie.symbol for site in slab]
Expand Down Expand Up @@ -987,7 +987,7 @@ def write_file(
if relax:
poscar.selective_dynamics = to_relax

poscar_str = poscar.get_string().split("\n")
poscar_str = poscar.get_str().split("\n")
poscar_str[5] = " ".join(new_atom_types)
poscar_str[6] = " ".join(list(map(str, n_atoms)))
poscar_str = "\n".join(poscar_str)
Expand Down
4 changes: 2 additions & 2 deletions OgreInterface/surfaces/surface.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -177,7 +177,7 @@ def write_file(
comment = self._get_base_poscar_comment_str(orthogonal=orthogonal)

if not self._passivated:
poscar_str = Poscar(slab, comment=comment).get_string()
poscar_str = Poscar(slab, comment=comment).get_str()
else:
if relax:
atomic_numbers = np.array(slab.atomic_numbers)
Expand Down Expand Up @@ -231,7 +231,7 @@ def write_file(
if relax:
poscar.selective_dynamics = selective_dynamics

poscar_str = poscar.get_string().split("\n")
poscar_str = poscar.get_str().split("\n")
poscar_str[5] = " ".join(new_atom_types)
poscar_str[6] = " ".join(list(map(str, n_atoms)))
poscar_str = "\n".join(poscar_str)
Expand Down