Skip to content
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

Add more operations #122

Merged
merged 13 commits into from
Jun 3, 2024
Merged

Add more operations #122

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
222da2c
rename operations
srmnitc May 29, 2024
53b54e9
rename prefix to operation
srmnitc May 29, 2024
122a02c
restructure vacancy operation
srmnitc May 29, 2024
6bcc054
add operation mapping for vacancy
srmnitc May 29, 2024
8a0c650
fix delete method to return copied vacancy structure if needed
srmnitc Jun 3, 2024
df6e4a7
add possibility to preserve structure when substituting
srmnitc Jun 3, 2024
40e3d42
fix bugs when adding substitute elements in succession
srmnitc Jun 3, 2024
62716f4
update substitution example
srmnitc Jun 3, 2024
17c8265
convert interstitial to operation
srmnitc Jun 3, 2024
a70c0e2
convert interstitial to operation
srmnitc Jun 3, 2024
d37576d
force conversions
srmnitc Jun 3, 2024
2f0ddab
update examples
srmnitc Jun 3, 2024
e495576
Bump version: 0.8.9 → 0.8.10
srmnitc Jun 3, 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
2 changes: 1 addition & 1 deletion .bumpversion.cfg
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
[bumpversion]
current_version = 0.8.9
current_version = 0.8.10
commit = True
tag = False

Expand Down
2 changes: 1 addition & 1 deletion CITATION.cff
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,4 +20,4 @@ url: 'https://atomrdf.pyscal.org'
license: "MIT"
repository-code: https://github.com/pyscal/atomRDF
type: software
version: 0.8.9
version: 0.8.10
10 changes: 9 additions & 1 deletion atomrdf/network/ontology.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,16 @@
- Add math operations, see sample.py for the complete list of items - at the moment, 4 cardinal operations,
but maybe more will be needed.

- StructureOperation: StructureRotation and associated vectors, see structure.py
- StructureOperation:
- RotationOperation and associated vectors, see structure.py
- TranslationOperation - no triples yet, see structure.py

- PROV activities
- DeleteAtom - to create vacancy - Now Just added as label to PROV activities
- AddAtom - to create impurity
- SubstituteAtom - to create impurity
"""

import os
from atomrdf.network.network import OntologyNetwork

Expand Down
287 changes: 182 additions & 105 deletions atomrdf/structure.py
View file
Open in desktop

Large diffs are not rendered by default.

2,742 changes: 1,438 additions & 1,304 deletions examples/03_point_defects.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

110 changes: 106 additions & 4 deletions examples/04_substitution.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

104 changes: 89 additions & 15 deletions examples/05_interstitials.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

setup(
name='atomrdf',
version='0.8.9',
version='0.8.10',
author='Abril Azocar Guzman, Sarath Menon',
author_email='sarath.menon@pyscal.org',
description='Ontology based structural manipulation and quering',
Expand Down
Loading