added optimize_geometry, minor bug fixes

Author: mkphuthi

asimtools/scripts/optimize_geometry.py

@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+'''
+Relaxes structure using ASE while retaining symmetry. Requires ASE>=3.23
+
+Author: [email protected]
+'''
+from typing import Dict, Optional
+import ase.optimize
+from ase.constraints import ExpCellFilter
+from ase.spacegroup.symmetrize import FixSymmetry
+from ase.io.trajectory import Trajectory
+from asimtools.calculators import load_calc
+from asimtools.utils import get_atoms
+
+def optimize_geometry(
+    calc_id: str,
+    image: Dict,
+    optimizer: str = 'BFGS',
+    fmax: float = 0.003, #Roughly 0.48GPa
+    optimizer_args: Optional[Dict] = None,
+    expcellfilter_args: Optional[Dict] = None,
+) -> Dict:
+    """Relaxes cell (and atoms) using ase.constraints.ExpCellFilter while retaining symmetry
+
+    :param calc_id: calc_id in calc_input.yaml
+    :type calc_id: str
+    :param image: image specification
+    :type image: Dict
+    :param optimizer: Any optimizer from ase.optimize, defaults to 'BFGS'
+    :type optimizer: str, optional
+    :param fmax: fmax in optimizer, defaults to 0.003 which is ~0.48GPa
+    :type fmax: float, optional
+    :param expcellfilter_args: arguments for ase.constraints.ExpCellFilter, defaults to None
+    :type expcellfilter_args: Optional[Dict], optional
+    :return: Results including relaxed structure energy
+    :rtype: Dict
+    """
+    if expcellfilter_args is None:
+        expcellfilter_args = {}
+    if optimizer_args is None:
+        optimizer_args = {}
+
+    calc = load_calc(calc_id)
+    atoms = get_atoms(**image)
+    atoms.set_calculator(calc)
+
+    ecf = ExpCellFilter(atoms, **expcellfilter_args)
+
+    dyn = getattr(ase.optimize, optimizer)(ecf)
+    traj_file = 'cell_relax.traj'
+    traj = Trajectory(
+        traj_file,
+        'w',
+        atoms,
+        properties=['energy', 'forces', 'stress'],
+    )
+    dyn.attach(traj)
+    try:
+        dyn.run(fmax=fmax)
+    except Exception:
+        print('Failed to optimize atoms')
+        raise
+
+    image_file = 'image_output.xyz'
+    atoms.write(image_file, format='extxyz')
+
+    energy = float(atoms.get_potential_energy())
+    final_fmax = float(atoms.get_stress().max())
+
+    results = {
+        'energy': energy,
+        'final_fmax': final_fmax,
+        'files':{
+            'image': image_file,
+            'traj': traj_file,
+        }
+    }
+    return results

asimtools/scripts/sim_array.py

@@ -48,10 +48,9 @@ def sim_array(
     assert array_values is None or file_pattern is None, \
         'Provide only one of array_values or file_pattern'
 
-    print('fpattern', file_pattern)
     if file_pattern is not None:
         array_values = glob(file_pattern)
-
+    print(array_values)
     assert len(array_values) > 0, 'No array values or files found'
 
     if ids == 'str_btn':