Merge branch 'main' into rework_raman

setup.cfg

@@ -37,10 +37,12 @@ include =
 
 [options.entry_points]
 console_scripts =
+	ase_compare_structures = tdeptools.scripts.ase_compare_structures:app
 	ase_geometry_info = tdeptools.scripts.ase_geometry_info:app
 	ase_geometry_refine = tdeptools.scripts.ase_geometry_refine:app
 	ase_get_distance_table = tdeptools.scripts.ase_get_distance_table:app
 	ase_join_pw_ph = tdeptools.scripts.ase_join_pw_ph:app
+	ase_match_lattices = tdeptools.scripts.ase_match_lattices:app
 	ase_strain_sample = tdeptools.scripts.ase_strain_sample:app
 	ase_suggest_kpoints = tdeptools.scripts.ase_suggest_kpoints:app
 	tdep_compute_raman_intensities = tdeptools.scripts.tdep_compute_raman_intensities:app

tdeptools/scripts/ase_compare_structures.py

@@ -0,0 +1,55 @@
+#! /usr/bin/env python3
+
+from pathlib import Path
+
+import typer
+from ase.io import read
+from rich import print as echo
+import numpy as np
+
+
+def guess_format(file: Path):
+    if "geometry.in" in file.name:
+        return "aims"
+    elif "poscar" in file.name.lower():
+        return "vasp"
+    else:
+        return None
+
+
+app = typer.Typer(pretty_exceptions_show_locals=False)
+
+
+@app.command()
+def main(
+    file1: Path,
+    file2: Path,
+    format: str = None,
+):
+    """Compare two structures, find supercell matrices etc."""
+    echo(f"Match structures in {file1} and {file2}")
+    echo(f"... read '{file1}'")
+    atoms1 = read(file1, format=guess_format(file1))
+    echo(atoms1)
+    echo(f"... read '{file2}'")
+    atoms2 = read(file2, format=guess_format(file2))
+    echo(atoms2)
+
+    echo("MATCH LATTICES")
+    echo()
+
+    cell1 = np.array(atoms1.cell)
+    cell2 = np.array(atoms2.cell)
+    smatrix = np.linalg.inv(cell1).T @ cell2
+    echo("... supercell matrix:")
+    echo(smatrix)
+
+    echo("... round to integers:")
+    echo(smatrix.round().astype(int))
+
+    echo("... for TDEP `generate_structure`")
+    echo(" ".join([f"{m:d}" for m in smatrix.round().astype(int).T.flatten()]))
+
+
+if __name__ == "__main__":
+    app()

tdeptools/scripts/ase_geometry_info.py

@@ -88,7 +88,7 @@ def inform(atoms, symprec=default_symprec, max_atoms=20, verbose=False):
             for key, val in atoms.cell.bandpath().special_points.items():
                 echo(f"    {key}: {val}")
 
-    if symprec is not None:
+    if symprec is not None and all(atoms.pbc):
         echo()
         echo("Report symmetry information from spglib:")
         sds = get_symmetry_dataset(atoms, symprec=symprec)
@@ -106,7 +106,7 @@ def inform(atoms, symprec=default_symprec, max_atoms=20, verbose=False):
                 echo(f"    {vec}")
 
     # Info
-    for (key, val) in atoms.info.items():
+    for key, val in atoms.info.items():
         echo(f"  {key:10s}: {val}")
 
 

tdeptools/scripts/ase_match_lattices.py

@@ -0,0 +1,68 @@
+#! /usr/bin/env python3
+
+from pathlib import Path
+
+import typer
+from ase.io import read
+from rich import print as echo
+import numpy as np
+
+
+def guess_format(file: Path):
+    if "geometry.in" in file.name:
+        return "aims"
+    elif "poscar" in file.name.lower():
+        return "vasp"
+    else:
+        return None
+
+
+app = typer.Typer(pretty_exceptions_show_locals=False)
+
+
+@app.command()
+def main(
+    file1: Path,
+    file2: Path,
+    scale_atoms: bool = True,
+    tolerance_volume: float = 0.1,
+    format: str = None,
+    outfile: str = None,
+):
+    """Match lattice vectors of structure in FILE2 to that in FILE1."""
+    echo(f"Match lattices of structures in {file1} and {file2}")
+    echo(f"... read '{file1}'")
+    atoms1 = read(file1, format=guess_format(file1))
+    echo(atoms1)
+    echo(f"... read '{file2}'")
+    atoms2 = read(file2, format=guess_format(file2))
+    echo(atoms2)
+
+    echo("MATCH LATTICES")
+    echo()
+
+    cell1 = np.array(atoms1.cell)
+    cell2 = np.array(atoms2.cell)
+    smatrix = np.linalg.inv(cell1).T @ cell2
+    echo("... supercell matrix:")
+    echo(smatrix)
+    echo()
+
+    volume_change = np.linalg.det(smatrix - np.eye(3))
+
+    echo(f"... volume change: {volume_change}")
+
+    if abs(volume_change) > tolerance_volume:
+        raise ValueError("DETERMINANT OF cell changes by more than tolerance!")
+
+    atoms2.set_cell(atoms1.cell, scale_atoms=scale_atoms)
+
+    if outfile is None:
+        outfile = file2.name + ".matched"
+
+    echo(f'... write to "{outfile}"')
+    atoms2.write(outfile, format=format)
+
+
+if __name__ == "__main__":
+    app()

tdeptools/scripts/tdep_create_next_iteration.py

@@ -69,6 +69,7 @@ def main(
     create_sample_folder: bool = True,
     file_geometry: str = "geometry.in",
     files_control: List[Path] = None,
+    files_aux: List[Path] = None,
     predictions: bool = False,
     file_predictions: Path = "predictions.nc",
     format: str = "aims",
@@ -115,6 +116,11 @@ def main(
         for file in files_control:
             shutil.copy(file, folder_new)
 
+    if files_aux is not None:
+        echo(f".. copy aux files: {files_aux}")
+        for file in files_aux:
+            shutil.copy(file, folder_new)
+
     if create_sample_folder:
         files = sorted(folder_new.glob("contcar_conf*"))
         create_sample_folders(

tdeptools/scripts/tdep_displace_atoms.py

@@ -16,6 +16,7 @@
 def main(
     file: Path,
     file_unitcell: Path = None,
+    nmax: int = None,
     plusminus: bool = True,
     displacement: float = typer.Option(default_displacement, help="displacement in Å"),
     format: str = "vasp",
@@ -60,8 +61,16 @@ def main(
     else:
         signs = (1,)
 
+    natoms = len(atoms)
+
+    if nmax is None:
+        nmax = natoms
+
+    echo(f"... number of atoms:         {natoms}")
+    echo(f"... number of displacements: {nmax}")
+
     counter = 0
-    for nn in list_match:
+    for nn in list_match[:nmax]:
         for ii in range(3):
             for ss in signs:
                 counter += 1

tdeptools/scripts/tdep_relax_cell.py

@@ -28,7 +28,7 @@ def _array_to_str(array, decimals=6):
     return f"[ {rep} ]"
 
 
-app = typer.Typer()
+app = typer.Typer(pretty_exceptions_show_locals=False)
 
 
 @app.command()