more flexibility and prefixes

Author: mkphuthi

asimtools/scripts/atom_relax.py

@@ -4,7 +4,7 @@
 optimizers
 '''
 
-from typing import Dict, Tuple
+from typing import Dict, Tuple, Optional
 import numpy as np
 import ase.optimize
 from ase.io.trajectory import Trajectory
@@ -17,6 +17,7 @@ def atom_relax(
     optimizer: str = 'GPMin', #GPMin is fastest according to ASE docs
     properties: Tuple[str] = ('energy', 'forces'),
     fmax: float = 0.02,
+    prefix: Optional[str] = None,
 ) -> Dict:
     """Relaxes the given tomic structure using ASE's built-in structure
     optimizers
@@ -39,7 +40,12 @@ def atom_relax(
     atoms.set_calculator(calc)
     logger = get_logger()
 
-    traj_file = 'atom_relax.traj'
+    if prefix is not None:
+        prefix = prefix + '_'
+    else:
+        prefix = ''
+
+    traj_file = prefix + 'atom_relax.traj'
     dyn = getattr(ase.optimize, optimizer)(atoms)
     traj = Trajectory(
         traj_file,
@@ -54,7 +60,7 @@ def atom_relax(
         logger.error('Failed to relax atoms')
         raise
 
-    image_file = 'image_output.xyz'
+    image_file = prefix + 'image_output.xyz'
     atoms.write(image_file, format='extxyz')
 
     energy = float(atoms.get_potential_energy())

asimtools/scripts/cell_relax.py

@@ -19,10 +19,10 @@
 def cell_relax(
     calc_id: str,
     image: Dict,
-    prefix: str = '',
     optimizer: str = 'BFGS',
-    smax: float = 0.002,
+    fmax: float = 0.002,
     mask: Optional[Sequence] = None,
+    prefix: Optional[str] = None,
 ) -> Dict:
     """Relax cell using ASE Optimizer
 
@@ -34,8 +34,8 @@ def cell_relax(
     :type prefix: str, optional
     :param optimizer: Optimizer class to use from ase.optimize, defaults to 'BFGS'
     :type optimizer: str, optional
-    :param smax: Maximum stress in eV/$\AA^3$, defaults to 0.002
-    :type smax: float, optional
+    :param fmax: Maximum stress in eV/$\AA^3$, defaults to 0.002
+    :type fmax: float, optional
     :param mask: Mask to constrain cell deformation while relaxing, defaults to None
     :type mask: Optional[Sequence], optional
     :return: Dictionary of results including, final energy, stress and output files
@@ -45,6 +45,11 @@ def cell_relax(
     atoms = get_atoms(**image)
     atoms.set_calculator(calc)
 
+    if prefix is not None:
+        prefix = prefix + '_'
+    else:
+        prefix = ''
+
     traj_file = join_names([prefix, 'cell_relax.traj'])
     sf = StrainFilter(atoms, mask=mask)
     dyn = getattr(ase.optimize, optimizer)(sf)
@@ -56,7 +61,7 @@ def cell_relax(
     )
     dyn.attach(traj)
     try:
-        dyn.run(fmax=smax)
+        dyn.run(fmax=fmax)
     except Exception:
         print('Failed to optimize atoms')
         raise
@@ -65,11 +70,11 @@ def cell_relax(
     atoms.write(image_file, format='extxyz')
 
     energy = float(atoms.get_potential_energy())
-    final_smax = float(atoms.get_stress().max())
+    final_fmax = float(atoms.get_stress().max())
 
     results = {
         'energy': energy,
-        'final_smax': final_smax,
+        'final_fmax': final_fmax,
         'files':{
             'image': image_file,
             'traj': traj_file,

asimtools/scripts/parity.py

@@ -199,7 +199,7 @@ def parity(
         )
 
         rmse_val = rmse(res[prop]['ref'], res[prop]['pred'])
-        results[f'{prop}_rmse'] = rmse_val
+        results[f'{prop}_rmse'] = float(rmse_val)
 
         _, ax = plt.subplots()
         lims = np.array(get_axis_lims(res[prop]['ref'], res[prop]['pred']))

asimtools/scripts/singlepoint.py

@@ -5,7 +5,7 @@
 Author: [email protected]
 '''
 
-from typing import Tuple, Dict
+from typing import Tuple, Dict, Optional
 import logging
 from asimtools.calculators import load_calc
 from asimtools.utils import (
@@ -16,6 +16,7 @@ def singlepoint(
     calc_id: str,
     image: Dict,
     properties: Tuple[str] = ('energy', 'forces'),
+    prefix: Optional[str] = None,
 ) -> Dict:
     """Evaluates the properties of a single image, currently implemented
     properties are energy, forces and stress
@@ -33,6 +34,11 @@ def singlepoint(
     atoms = get_atoms(**image)
     atoms.set_calculator(calc)
 
+    if prefix is not None:
+        prefix = prefix + '_'
+    else:
+        prefix = ''
+
     if 'energy' in properties:
         try:
             energy = atoms.get_potential_energy()
@@ -57,7 +63,7 @@ def singlepoint(
             logging.error('Failed to calculate stress')
             raise
 
-    image_file = 'image_output.xyz'
+    image_file = prefix + 'image_output.xyz'
     atoms.write(image_file, format='extxyz')
 
     results = {

asimtools/scripts/surface_energies/surface_energies.py

@@ -15,6 +15,7 @@
 from pymatgen.core.surface import generate_all_slabs
 from pymatgen.io.ase import AseAtomsAdaptor as AAA
 from asimtools.calculators import load_calc
+from asimtools.scripts.atom_relax import atom_relax
 from asimtools.utils import (
     get_atoms,
 )
@@ -40,6 +41,7 @@ def surface_energies(
     image: Dict,
     calc_id: str,
     millers: Union[str,Sequence] = 'all',
+    atom_relax_args: Optional[Dict] = None,
     generate_all_slabs_args: Optional[Dict] = None,
 ) -> Dict:
     '''
@@ -51,6 +53,9 @@ def surface_energies(
     bulk = get_atoms(**image)
     bulk.set_calculator(calc)
 
+    if atom_relax_args is None:
+        atom_relax_args = {}
+
     default_pymatgen_kwargs = {
         'max_index': 3,
         'min_slab_size': 14,
@@ -83,6 +88,18 @@ def surface_energies(
             atoms = AAA.get_atoms(big_slab)
             atoms.write(f'{miller}.xyz')
 
+            relax_results = atom_relax(
+                calc_id=calc_id,
+                image={'atoms': atoms},
+                optimizer=atom_relax_args.get('optimizer', 'BFGS'),
+                properties=('energy','forces'),
+                fmax=atom_relax_args.get('fmax', 0.02),
+                prefix=f'{miller}_relaxed'
+            )
+            atoms = get_atoms(
+                image_file = relax_results.get('files', {}).get('image')
+            )
+
             assert np.allclose(atoms.pbc, (True, True, True)), \
                 f'Check pbcs for {miller}: {atoms.pbc}'
             assert atoms.cell[2][2] > pymargs['min_vacuum_size'] + \

asimtools/utils.py

@@ -204,7 +204,7 @@ def get_images(
     patterns: List[str] = None,
     images: Iterable[Atoms] = None,
     index: Union[str, int] = ':',
-    skip_failed: bool = True,
+    skip_failed: bool = False,
     **kwargs
 ) -> List[Atoms]:
     """Return a list of atoms objects based on the input arguments. Options \
@@ -239,6 +239,7 @@ def get_images(
         "Please specify file, pattern or iterable"
 
     if image_file is not None:
+        image_file = Path(image_file).resolve()
         images = read(image_file, index=index, **kwargs)
         if not isinstance(images, list):
                 images = [images]
@@ -249,11 +250,21 @@ def get_images(
 
         images = []
         for image_file in image_files:
+            image_file = Path(image_file).resolve()
             try:
-                new_images = read(image_file, index=index, **kwargs)
+                new_images = read(
+                    image_file,
+                    index=index,
+                    **kwargs
+                )
             except Exception as exc:
                 if not skip_failed:
-                    raise IOError(f"Failed to read {image_file}") from exc
+                    raise IOError(
+                        f"Failed to read {image_file} from {os.getcwd()}"
+                    ) from exc
+                else:
+                    new_images = []
+
             # Output of read can either be list of atoms or Atoms, depending on index
             if not isinstance(new_images, list):
                 new_images = [new_images]