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use kind_name as element tag in the xyz file #216

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use kind_name as element tag in the xyz file #216

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bcec6ee
use kind_name as atom symbol
superstar54 May 13, 2024
684235c
update docstring, and write the file directly
superstar54 May 13, 2024
d4901e6
fix pre-commit
superstar54 May 13, 2024
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14 changes: 10 additions & 4 deletions aiida_cp2k/calculations/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -407,9 +407,15 @@ def prepare_for_submission(self, folder):

@staticmethod
def _write_structure(structure, folder, name):
"""Function that writes a structure and takes care of element tags."""

xyz = _atoms_to_xyz(structure.get_ase())
"""Function that writes a structure to a xyz file.
The element tags being the names of the kind.
"""
elem_coords = [
f"{site.position[0]:25.16f} {site.position[1]:25.16f} {site.position[2]:25.16f}"
for site in structure.sites
]
xyz = f"{len(elem_coords)}\n\n"
xyz += "\n".join(map(add, structure.get_site_kindnames(), elem_coords))
with open(folder.get_abs_path(name), mode="w", encoding="utf-8") as fobj:
fobj.write(xyz)

Expand Down Expand Up @@ -475,7 +481,7 @@ def _trajectory_to_xyz_and_cell(trajectory):
if "cells" in trajectory.get_arraynames():
cell = "# Step Time [fs] Ax [Angstrom] Ay [Angstrom] Az [Angstrom] Bx [Angstrom] By [Angstrom] Bz [Angstrom] Cx [Angstrom] Cy [Angstrom] Cz [Angstrom] Volume [Angstrom^3]\n"
cell_vecs = [
f"{stepid+1} {(stepid+1)*0.5:6.3f} {cellvec[0][0]:25.16f} {cellvec[0][1]:25.16f} {cellvec[0][2]:25.16f} {cellvec[1][0]:25.16f} {cellvec[1][1]:25.16f} {cellvec[1][2]:25.16f} {cellvec[2][0]:25.16f} {cellvec[2][1]:25.16f} {cellvec[2][2]:25.16f} {np.dot(cellvec[0],np.cross(cellvec[1],cellvec[2]))}"
f"{stepid+1} {(stepid+1)*0.5:6.3f} {cellvec[0][0]:25.16f} {cellvec[0][1]:25.16f} {cellvec[0][2]:25.16f} {cellvec[1][0]:25.16f} {cellvec[1][1]:25.16f} {cellvec[1][2]:25.16f} {cellvec[2][0]:25.16f} {cellvec[2][1]:25.16f} {cellvec[2][2]:25.16f} {np.dot(cellvec[0], np.cross(cellvec[1], cellvec[2]))}"
for (stepid, cellvec) in zip(stepids, trajectory.get_array("cells"))
]
cell += "\n".join(cell_vecs)
Expand Down
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