Sapphire10 k patch 1

.github/workflows/python-package-conda.yml

@@ -5,30 +5,37 @@ on: [push]
 jobs:
   build-linux:
     runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 5
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+
+    - name: Set up Miniconda
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: '3.10'
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install dependencies
-      run: |
-        conda env update --file environment.yml --name base
+        auto-update-conda: true
+        environment-file: environment.yml
+        activate-environment: base
+        auto-activate-base: true
+
     - name: Lint with flake8
       run: |
-        conda install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        conda run -n base python -m pip install flake8
+        conda run -n base flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        conda run -n base flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
     - name: Test with pytest
       run: |
-        conda install pytest
-        pytest -q -m "not slow"
+        conda run -n base python -m pip install pytest
+        conda run -n base pytest -q -m "not slow"
+
+    - name: Run simulation
+      run: |
+        mkdir -p outputs
+        conda run -n base python iro2_test_1.py
+        ls -R .
+
+    - name: Upload simulation outputs
+      uses: actions/upload-artifact@v4
+      with:
+        name: irO2-simulation-outputs
+        path: outputs/

.gitignore

@@ -17,8 +17,8 @@ build/
 .ipynb_checkpoints/
 
 # Common simulation outputs (adjust as needed)
-*.traj
+#*.traj
 *.xyz
 *.cif
-*.log
+#*.log
 *.out

iro2_test_1.py

@@ -1,119 +1,119 @@
-# pip install ase
-# conda config --add channels conda-forge
-# conda install xtb-python
-# conda search xtb-python --channel conda-forge
-# conda install qcelemental ase
-from pathlib import Path
-from ase.io import read
-import numpy as np
-from ase.constraints import FixAtoms
-from ase import Atom
-from ase.visualize import view
-from ase.io import write
-from ase.visualize import view
-from ase.data import covalent_radii
-from ase.constraints import FixAtoms
-from ase.neighborlist import neighbor_list
-from xtb.ase.calculator import XTB
-from ase.optimize import BFGS
-
-Path("outputs").mkdir(exist_ok=True)
-
-
-def run_relaxation(
-    qe_input: str = "slab_clean_2x2.in",
-    traj: str = "relax_H.traj",
-    log: str = "relax_H.log",
-    fmax: float = 0.05,
-    cut: float = 1.3,
-):
-
-    covalent_radii[1] = 0.6
-
-    slab = read("slab_clean_2x2.in", format="espresso-in")
-    # xTB does not support PBC multipoles in this mode → treat slab as cluster
-    slab.set_pbc((False, False, False))
-    print(slab)
-    print("Atoms:", len(slab))
-    print("Cell (Å):\n", slab.cell)
-    print("PBC:", slab.pbc)
-
-    # Get atomic symbols and positions
-    symbols = slab.get_chemical_symbols()
-    positions = slab.get_positions()
-
-    # Find top of slab
-    z_positions = positions[:, 2]
-    z_top = z_positions.max()
-
-    print(f"Top of slab z = {z_top:.3f} Å")
-
-    # Find surface O atoms within 1.5 Å of top
-    surface_O_indices = [
-        i for i, s in enumerate(symbols)
-        if s == "O" and (z_top - positions[i, 2]) < 1.5
-    ]
-
-    print("Candidate surface O atoms:")
-    for i in surface_O_indices:
-        x, y, z = positions[i]
-        print(f"Index {i}: position = ({x:.3f}, {y:.3f}, {z:.3f})")
-
-    #Adding H* on top of Oxygen 20
-
-    o_idx = 20
-    O_pos = slab.positions[o_idx]
-
-    # Typical O–H bond length
-    OH_distance = 1.0  # Å
-
-    # Place H above O along +z
-    H_pos = O_pos + np.array([0.0, 0.0, OH_distance])
-
-    # Add H atom
-    slab.append(Atom("H", position=H_pos))
-
-    #for atom in slab:
-        #if atom.symbol == "H":
-            #atom.tag = 1
+# # pip install ase
+# # conda config --add channels conda-forge
+# # conda install xtb-python
+# # conda search xtb-python --channel conda-forge
+# # conda install qcelemental ase
+# #from pathlib import Path
+# from ase.io import read
+# import numpy as np
+# from ase.constraints import FixAtoms
+# from ase import Atom
+# from ase.visualize import view
+# from ase.io import write
+# from ase.visualize import view
+# from ase.data import covalent_radii
+# from ase.constraints import FixAtoms
+# from ase.neighborlist import neighbor_list
+# from xtb.ase.calculator import XTB
+# from ase.optimize import BFGS
+
+# Path("outputs").mkdir(exist_ok=True)
+
+
+# def run_relaxation(
+#     qe_input: str = "slab_clean_2x2.in",
+#     traj: str = "relax_H.traj",
+#     log: str = "relax_H.log",
+#     fmax: float = 0.05,
+#     cut: float = 1.3,
+# ):
+
+#     covalent_radii[1] = 0.6
+
+#     slab = read("slab_clean_2x2.in", format="espresso-in")
+#     # xTB does not support PBC multipoles in this mode → treat slab as cluster
+#     slab.set_pbc((False, False, False))
+#     print(slab)
+#     print("Atoms:", len(slab))
+#     print("Cell (Å):\n", slab.cell)
+#     print("PBC:", slab.pbc)
+
+#     # Get atomic symbols and positions
+#     symbols = slab.get_chemical_symbols()
+#     positions = slab.get_positions()
+
+#     # Find top of slab
+#     z_positions = positions[:, 2]
+#     z_top = z_positions.max()
+
+#     print(f"Top of slab z = {z_top:.3f} Å")
+
+#     # Find surface O atoms within 1.5 Å of top
+#     surface_O_indices = [
+#         i for i, s in enumerate(symbols)
+#         if s == "O" and (z_top - positions[i, 2]) < 1.5
+#     ]
+
+#     print("Candidate surface O atoms:")
+#     for i in surface_O_indices:
+#         x, y, z = positions[i]
+#         print(f"Index {i}: position = ({x:.3f}, {y:.3f}, {z:.3f})")
+
+#     #Adding H* on top of Oxygen 20
+
+#     o_idx = 20
+#     O_pos = slab.positions[o_idx]
+
+#     # Typical O–H bond length
+#     OH_distance = 1.0  # Å
+
+#     # Place H above O along +z
+#     H_pos = O_pos + np.array([0.0, 0.0, OH_distance])
+
+#     # Add H atom
+#     slab.append(Atom("H", position=H_pos))
+
+#     #for atom in slab:
+#         #if atom.symbol == "H":
+#             #atom.tag = 1
 
-    #set_highlight_atoms([i for i,a in enumerate(slab) if a.symbol=="H"])
+#     #set_highlight_atoms([i for i,a in enumerate(slab) if a.symbol=="H"])
 
-    print("Total atoms:", len(slab))
-    print("Last atom symbol:", slab[-1].symbol)
-    print("Last atom position:", slab[-1].position)
+#     print("Total atoms:", len(slab))
+#     print("Last atom symbol:", slab[-1].symbol)
+#     print("Last atom position:", slab[-1].position)
 
-    print(f"Added H at position {H_pos}")
-    print("Total atoms now:", len(slab))
+#     print(f"Added H at position {H_pos}")
+#     print("Total atoms now:", len(slab))
 
-    write("slab_with_H.xyz", slab)
+#     write("slab_with_H.xyz", slab)
 
-    view(slab)
+#     view(slab)
 
-    z = slab.positions[:, 2]
-    z_freeze = 20.0   # Å (tune if needed)
+#     z = slab.positions[:, 2]
+#     z_freeze = 20.0   # Å (tune if needed)
 
-    freeze_mask = z < z_freeze
-    slab.set_constraint(FixAtoms(mask=freeze_mask))
+#     freeze_mask = z < z_freeze
+#     slab.set_constraint(FixAtoms(mask=freeze_mask))
 
-    print("Frozen atoms:", int(freeze_mask.sum()), "/", len(slab))
+#     print("Frozen atoms:", int(freeze_mask.sum()), "/", len(slab))
 
-    iH = len(slab) - 1  # last atom is H
-    cut = 1.3           # Å check radius around H
+#     iH = len(slab) - 1  # last atom is H
+#     cut = 1.3           # Å check radius around H
 
-    i, j, d = neighbor_list("ijd", slab, cutoff=[cut]*len(slab))
-    close = [(jj, dd) for ii, jj, dd in zip(i, j, d) if ii == iH]
+#     i, j, d = neighbor_list("ijd", slab, cutoff=[cut]*len(slab))
+#     close = [(jj, dd) for ii, jj, dd in zip(i, j, d) if ii == iH]
 
 
 
-    print("Neighbors within 1.3 Å of H:", close)
+#     print("Neighbors within 1.3 Å of H:", close)
 
-    # Optimize structure with xTB
-    slab.calc = XTB(method="GFN2-xTB")
-    opt = BFGS(slab, trajectory=traj, logfile=log)
-    opt.run(fmax=fmax)
+#     # Optimize structure with xTB
+#     slab.calc = XTB(method="GFN2-xTB")
+#     opt = BFGS(slab, trajectory=traj, logfile=log)
+#     opt.run(fmax=fmax)
 
-    return slab, close
+#     return slab, close
 
-if __name__ == "__main__":
-    run_relaxation()
+# if __name__ == "__main__":
+#     run_relaxation()