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Add .pes file parser
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8 files changed

+434
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lines changed

8 files changed

+434
-1
lines changed

‎castep_outputs/parsers/__init__.py‎

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@@ -19,6 +19,7 @@
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parse_elf_fmt_file,
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parse_pot_fmt_file,
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)
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from .pes_file_parser import parse_pes_file
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from .phonon_dos_file_parser import parse_phonon_dos_file
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from .phonon_file_parser import parse_phonon_file
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from .tddft_file_parser import parse_tddft_file
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"parse_magres_file",
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"parse_md_geom_file",
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"parse_md_geom_file",
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"parse_pes_file",
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"parse_phonon_dos_file",
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"parse_phonon_file",
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"parse_pot_fmt_file",
@@ -73,6 +75,7 @@
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"err": parse_err_file,
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"phonon": parse_phonon_file,
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"epme": parse_epme_file,
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"pes": parse_pes_file,
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}
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#: Names of parsers/parsable file extensions (without ``"."``).

‎castep_outputs/parsers/pes_file_parser.py‎

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"""Parse castep .pes files."""
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from __future__ import annotations
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from typing import TextIO, TypedDict
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from ..utilities.datatypes import ThreeByThreeMatrix, ThreeVector
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from ..utilities.filewrapper import Block
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from ..utilities.utility import file_or_path, to_type
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class PESData(TypedDict):
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"""PES sample points."""
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pos: ThreeVector
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e: float
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f_opt: float | None
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class PESFileInfo(TypedDict, total=False):
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"""Full pes file information."""
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probe_species: str
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probe_method: str
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cell: ThreeByThreeMatrix
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date_started: str
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data: list[PESData]
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units: dict[str, str]
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samples: dict[str, int]
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def _parse_header(header: Block) -> PESFileInfo:
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accum: PESFileInfo = {"units": {}, "samples": {}, "data": []}
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header = map(str.strip, header)
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for line in header:
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if line.startswith("Job:"):
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_, accum["probe_method"] = line.split(": ")
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elif line.startswith("Probe species:"):
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_, accum["probe_species"] = line.split(": ")
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elif "unit:" in line:
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typ_, _, unit = line.split()
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accum["units"][typ_.lower()] = unit
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elif line.startswith("Number of samples"):
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*_, direc, count = line.split()
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accum["samples"][direc.strip(":")] = int(count)
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elif line.startswith("Cell Vectors"):
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*_, unit = line.split()
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accum["units"]["cell"] = unit.strip("()")
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accum["cell"] = tuple(to_type(cell.split(), float)
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for cell, _ in zip(header, range(3)))
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elif line.startswith("Date"):
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_, accum["date_started"] = line.split(": ", maxsplit=1)
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return accum
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@file_or_path(mode="r")
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def parse_pes_file(pes_file: TextIO) -> PESFileInfo:
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"""Parse castep .pes file.
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Parameters
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----------
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pes_file
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A handle to a CASTEP .pes file.
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Returns
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-------
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PESFileInfo
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Parsed data.
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"""
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line = next(pes_file)
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block = Block.from_re(line, pes_file, "BEGIN header", "END header")
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accum = _parse_header(block)
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line = next(pes_file)
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block = Block.from_re(line, pes_file, " BLOCK DATA", "ENDBLOCK DATA")
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block.remove_bounds(1, 1)
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data = accum["data"]
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for line in block:
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a, b, c, e, *extra = to_type(line.split(), float)
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curr = {}
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curr["pos"] = a, b, c
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curr["e"] = e
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curr["f_opt"] = extra[0] if extra else None
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data.append(curr)
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return accum

‎test/data_files/gen_data.py‎

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@@ -31,6 +31,7 @@
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"efield",
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"tddft",
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"err",
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"pes",
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"epme",
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("pp-md", "castep"),
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("si8-md", "castep"),
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argp.add_argument("datasets", nargs=REMAINDER, help="Sets to generate.", default=ALL_SETS)
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argp.add_argument(
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"--formats", nargs="+", help="Formats to generate.", default=("json", "pyyaml", "ruamel"),
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"--formats",
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nargs="+",
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help="Formats to generate.",
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default=("json", "pyyaml", "ruamel"),
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)
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args = argp.parse_args()
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‎test/data_files/pes.json‎

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{
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"units": {
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"energy": "eV",
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"force": "eV/A",
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"cell": "Bohr"
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},
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"samples": {
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"a": 10,
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"b": 10
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},
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"data": [
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{
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"pos": [
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0.5,
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0.5,
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0.50017
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],
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"e": -231.164733,
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"f_opt": 0.148
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},
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{
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"pos": [
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0.61111,
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0.5,
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0.50029
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],
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"e": -231.345479,
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"f_opt": 0.42
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},
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{
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"pos": [
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0.72222,
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0.5,
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0.50042
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],
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"e": -231.557748,
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"f_opt": 0.194
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},
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{
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"pos": [
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0.83333,
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0.5,
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0.50074
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],
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"e": -231.445747,
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"f_opt": -0.582
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},
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{
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"pos": [
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0.94444,
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0.5,
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0.50149
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],
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"e": -231.041607,
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"f_opt": -0.531
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},
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{
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"pos": [
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1.05556,
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0.5,
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0.50233
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],
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"e": -231.015796,
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"f_opt": 0.408
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},
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{
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"pos": [
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1.16667,
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0.5,
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0.50266
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],
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"e": -231.314431,
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"f_opt": 0.401
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},
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{
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"pos": [
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1.27778,
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0.5,
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0.50263
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],
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"e": -231.347231,
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"f_opt": -0.201
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},
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{
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"pos": [
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1.38889,
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0.5,
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0.50254
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],
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"e": -231.199074,
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"f_opt": -0.212
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},
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{
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"pos": [
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1.5,
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0.50258
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],
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"e": -231.166451,
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"f_opt": 0.16
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},
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{
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"pos": [
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1.5,
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0.61111,
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0.5027
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],
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"e": -231.336101,
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"f_opt": 0.413
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},
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{
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"pos": [
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1.38889,
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0.61111,
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0.5027
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],
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"e": -231.21672,
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"f_opt": 0.0254
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}
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],
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"date_started": "Fri Jun 27 13:43:56 +0100 2025",
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"probe_method": "min_c",
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"probe_species": "H",
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"cell": [
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[
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0.0,
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5.077705,
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5.077705
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],
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[
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5.077705,
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0.0,
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5.077705
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],
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[
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5.077705,
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5.077705,
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0.0
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]
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]
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}

‎test/data_files/pes.pyyaml‎

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cell: !!python/tuple
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- !!python/tuple
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- 0.0
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- 5.077705
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- 5.077705
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- !!python/tuple
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- 5.077705
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- 0.0
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- 5.077705
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- !!python/tuple
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- 5.077705
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- 5.077705
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- 0.0
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data:
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- e: -231.164733
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f_opt: 0.148
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pos: !!python/tuple
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- 0.5
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- 0.5
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- 0.50017
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- e: -231.345479
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f_opt: 0.42
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pos: !!python/tuple
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- 0.61111
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- 0.5
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- 0.50029
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- e: -231.557748
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f_opt: 0.194
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pos: !!python/tuple
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- 0.72222
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- 0.5
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- 0.50042
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- e: -231.445747
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f_opt: -0.582
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pos: !!python/tuple
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- 0.83333
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- 0.5
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- 0.50074
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- e: -231.041607
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f_opt: -0.531
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pos: !!python/tuple
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- 0.94444
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- 0.5
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- 0.50149
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- e: -231.015796
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f_opt: 0.408
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pos: !!python/tuple
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- 1.05556
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- 0.5
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- 0.50233
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- e: -231.314431
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f_opt: 0.401
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pos: !!python/tuple
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- 1.16667
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- 0.5
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- 0.50266
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- e: -231.347231
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f_opt: -0.201
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pos: !!python/tuple
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- 1.27778
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- 0.5
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- 0.50263
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- e: -231.199074
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f_opt: -0.212
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pos: !!python/tuple
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- 1.38889
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- 0.5
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- 0.50254
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- e: -231.166451
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f_opt: 0.16
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pos: !!python/tuple
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- 1.5
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- 0.5
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- 0.50258
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- e: -231.336101
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f_opt: 0.413
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pos: !!python/tuple
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- 1.5
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- 0.61111
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- 0.5027
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- e: -231.21672
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f_opt: 0.0254
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pos: !!python/tuple
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- 1.38889
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- 0.61111
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- 0.5027
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date_started: Fri Jun 27 13:43:56 +0100 2025
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probe_method: min_c
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probe_species: H
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samples:
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a: 10
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b: 10
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units:
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cell: Bohr
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energy: eV
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force: eV/A

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