Merge branch 'develop'

# Conflicts:
#	.github/workflows/build_and_test.yml
#	.gitignore
#	defect_finder/BDM.py
#	setup.py

.github/workflows/build_and_test.yml

@@ -19,7 +19,7 @@ jobs:
       max-parallel: 5
 
       matrix:
-        python-version: ['3.8', '3.9']
+        python-version: ['3.8', '3.9']  # Excluding 3.10 for the moment, as hiphive requires Numpy <1.22 which is incompatible with Python 3.10, should be fixed soon...
 
     name: Python ${{ matrix.python-version }} Test Pop
 
@@ -40,6 +40,5 @@ jobs:
 
       - name: Test
         run:  |
-          pytest
+          pytest --ignore=tests/test_local.py  # Ignore local tests file, which tests INCAR and POTCAR file writing but not possible on GitHub Actions
           pytest tests/test_shakenbreak.py --mpl  # test output plots
-        

.gitignore

@@ -128,11 +128,12 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-# PyCharm
+# PyCharm files
 .idea/
 
-# MacOS
+# Mac OS Files
 .DS_Store
 
-# Affinity Logo ideas
+# Affinity Designer
 Affinity/
+.vscode/settings.json

Example_notebook/Defect_Finding_Example.ipynb

@@ -789,7 +789,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Then parse the energies by running the `BDM_parsing_script.sh` from the `defect-finder` folder, in the top-level folder containing your defect folders (e.g. `vac_2_Te_0` etc. (with subfolders: `vac_2_Te_0/BDM/vac_2_Te_0_10.0%_BDM_Distortion/vasp_gam` etc.). This will parse the energies and store them in a `{defect_name}.txt` file (in the `{defect_name}/BDM` folders) to allow easy plotting and analysis.\n",
+    "Then parse the energies by running the `BDM_parsing_script.sh` from the `ShakeNBreak` folder, in the top-level folder containing your defect folders (e.g. `vac_2_Te_0` etc. (with subfolders: `vac_2_Te_0/BDM/vac_2_Te_0_10.0%_BDM_Distortion/vasp_gam` etc.). This will parse the energies and store them in a `{defect_name}.txt` file (in the `{defect_name}/BDM` folders) to allow easy plotting and analysis.\n",
     "\n",
     "Also recommended to parse the final structures (CONTCARs) obtained with each BDM distortion to your local computer to ease the structural analysis. Can go to the local folder where BDM input is and use scp/rsync...\n",
     "```bash\n",
@@ -1528,7 +1528,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -1542,7 +1542,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,

README.md

@@ -1,2 +1,2 @@
-# `defect-finder`
+# `shakenbreak`
 Defect structure-searching method employing chemically-guided bond distortions to locate ground-state and metastable structures of point defects in solid materials.

data/CdTe_Bulk_Supercell_POSCAR

@@ -0,0 +1,72 @@
+Cd32 Te32
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data/CdTe_Int_Cd_2_-60%_Distortion_NN_10_POSCAR

@@ -0,0 +1,73 @@
+Cd33 Te32
+1.0
+13.086768 0.000000 0.000000
+0.000000 13.086768 0.000000
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+Cd Te Cd
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data/CdTe_Int_Cd_2_-60%_Distortion_Rattled_POSCAR

@@ -0,0 +1,73 @@
+Cd33 Te32
+1.0
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+0.000000 13.086768 0.000000
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+Cd Te Cd
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data/CdTe_Int_Cd_2_-60%_Distortion_Unrattled_POSCAR

@@ -0,0 +1,73 @@
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