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pseudos.py
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pseudos.py
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"""
This module provides objects describing the basic parameters of the
pseudopotentials used in Abinit, and a parser to instantiate pseudopotential objects..
"""
from __future__ import annotations
import abc
import collections
import logging
import os
import sys
from collections import defaultdict, namedtuple
import numpy as np
from monty.collections import AttrDict, Namespace
# from monty.dev import deprecated
from monty.functools import lazy_property
from monty.itertools import iterator_from_slice
from monty.json import MontyDecoder, MSONable
from monty.os.path import find_exts
from monty.string import is_string, list_strings
from tabulate import tabulate
from pymatgen.core.periodic_table import Element
from pymatgen.core.xcfunc import XcFunc
from pymatgen.util.plotting import add_fig_kwargs, get_ax_fig_plt
logger = logging.getLogger(__name__)
__all__ = [
"Pseudo",
"PseudoTable",
]
__author__ = "Matteo Giantomassi"
__version__ = "0.1"
__maintainer__ = "Matteo Giantomassi"
# Tools and helper functions.
def straceback():
"""Returns a string with the traceback."""
import traceback
return "\n".join((traceback.format_exc(), str(sys.exc_info()[0])))
def _read_nlines(filename, nlines):
"""
Read at most nlines lines from file filename.
If nlines is < 0, the entire file is read.
"""
if nlines < 0:
with open(filename) as fh:
return fh.readlines()
lines = []
with open(filename) as fh:
for lineno, line in enumerate(fh):
if lineno == nlines:
break
lines.append(line)
return lines
_l2str = {0: "s", 1: "p", 2: "d", 3: "f", 4: "g", 5: "h", 6: "i"}
_str2l = {v: k for k, v in _l2str.items()}
def l2str(l_ang_mom):
"""Convert the angular momentum l (int) to string."""
try:
return _l2str[l_ang_mom]
except KeyError:
return f"Unknown angular momentum, received {l_ang_mom = }"
def str2l(s):
"""Convert a string to the angular momentum l (int)"""
return _str2l[s]
class Pseudo(MSONable, metaclass=abc.ABCMeta):
"""
Abstract base class defining the methods that must be
implemented by the concrete pseudo-potential sub-classes.
"""
@classmethod
def as_pseudo(cls, obj):
"""
Convert obj into a pseudo. Accepts:
* Pseudo object.
* string defining a valid path.
"""
return obj if isinstance(obj, cls) else cls.from_file(obj)
@staticmethod
def from_file(filename):
"""
Build an instance of a concrete Pseudo subclass from filename.
Note: the parser knows the concrete class that should be instantiated
Client code should rely on the abstract interface provided by Pseudo.
"""
return PseudoParser().parse(filename)
def __eq__(self, other: object) -> bool:
needed_attrs = ("md5", "Z", "Z_val", "l_max")
if not all(hasattr(other, attr) for attr in needed_attrs):
return NotImplemented
return (
all(getattr(self, attr) == getattr(other, attr) for attr in needed_attrs)
and self.__class__ == other.__class__
)
def __repr__(self):
try:
return f"<{type(self).__name__} at {os.path.relpath(self.filepath)}>"
except Exception:
# relpath can fail if the code is executed in demon mode.
return f"<{type(self).__name__} at {self.filepath}>"
def __str__(self):
return self.to_string()
def to_string(self, verbose=0):
"""String representation."""
# pylint: disable=E1101
lines = []
app = lines.append
app(f"<{type(self).__name__}: {self.basename}>")
app(" summary: " + self.summary.strip())
app(f" number of valence electrons: {self.Z_val}")
app(f" maximum angular momentum: {l2str(self.l_max)}")
app(f" angular momentum for local part: {l2str(self.l_local)}")
app(f" XC correlation: {self.xc}")
app(f" supports spin-orbit: {self.supports_soc}")
if self.isnc:
app(f" radius for non-linear core correction: {self.nlcc_radius}")
if self.has_hints:
for accuracy in ("low", "normal", "high"):
hint = self.hint_for_accuracy(accuracy=accuracy)
app(f" hint for {accuracy} accuracy: {hint}")
return "\n".join(lines)
@property
@abc.abstractmethod
def summary(self):
"""String summarizing the most important properties."""
@property
def filepath(self):
"""Absolute path to pseudopotential file."""
# pylint: disable=E1101
return os.path.abspath(self.path)
@property
def basename(self):
"""File basename."""
# pylint: disable=E1101
return os.path.basename(self.filepath)
@property
@abc.abstractmethod
def Z(self):
"""The atomic number of the atom."""
@property
@abc.abstractmethod
def Z_val(self):
"""Valence charge."""
@property
def type(self):
"""Type of pseudo."""
return type(self).__name__
@property
def element(self):
"""Pymatgen :class:`Element`."""
try:
return Element.from_Z(self.Z)
except (KeyError, IndexError):
return Element.from_Z(int(self.Z))
@property
def symbol(self):
"""Element symbol."""
return self.element.symbol
@property
@abc.abstractmethod
def l_max(self):
"""Maximum angular momentum."""
@property
@abc.abstractmethod
def l_local(self):
"""Angular momentum used for the local part."""
@property
def isnc(self):
"""True if norm-conserving pseudopotential."""
return isinstance(self, NcPseudo)
@property
def ispaw(self):
"""True if PAW pseudopotential."""
return isinstance(self, PawPseudo)
@lazy_property
def md5(self):
"""MD5 hash value."""
# if self.has_dojo_report and "md5" in self.dojo_report: return self.dojo_report["md5"]
return self.compute_md5()
def compute_md5(self):
"""Compute and erturn MD5 hash value."""
# pylint: disable=E1101
import hashlib
with open(self.path) as fh:
text = fh.read()
m = hashlib.md5(text.encode("utf-8"))
return m.hexdigest()
@property
@abc.abstractmethod
def supports_soc(self):
"""
True if the pseudo can be used in a calculation with spin-orbit coupling.
Base classes should provide a concrete implementation that computes this value.
"""
def as_dict(self, **kwargs):
"""Return dictionary for MSONable protocol."""
# pylint: disable=E1101
return {
"@module": type(self).__module__,
"@class": type(self).__name__,
"basename": self.basename,
"type": self.type,
"symbol": self.symbol,
"Z": self.Z,
"Z_val": self.Z_val,
"l_max": self.l_max,
"md5": self.md5,
"filepath": self.filepath,
# "xc": self.xc.as_dict(),
}
@classmethod
def from_dict(cls, d):
"""Build instance from dictionary (MSONable protocol)."""
new = cls.from_file(d["filepath"])
# Consistency test based on md5
if "md5" in d and d["md5"] != new.md5:
raise ValueError(
f"The md5 found in file does not agree with the one in dict\nReceived {d['md5']}\nComputed {new.md5}"
)
return new
def as_tmpfile(self, tmpdir=None):
"""
Copy the pseudopotential to a temporary a file and returns a new pseudopotential object.
Useful for unit tests in which we have to change the content of the file.
Args:
tmpdir: If None, a new temporary directory is created and files are copied here
else tmpdir is used.
"""
# pylint: disable=E1101
import shutil
import tempfile
tmpdir = tempfile.mkdtemp() if tmpdir is None else tmpdir
new_path = os.path.join(tmpdir, self.basename)
shutil.copy(self.filepath, new_path)
# Copy dojoreport file if present.
root, ext = os.path.splitext(self.filepath)
djrepo = root + ".djrepo"
if os.path.exists(djrepo):
shutil.copy(djrepo, os.path.join(tmpdir, os.path.basename(djrepo)))
# Build new object and copy dojo_report if present.
new = type(self).from_file(new_path)
if self.has_dojo_report:
new.dojo_report = self.dojo_report.deepcopy()
return new
@property
def has_dojo_report(self):
"""True if the pseudo has an associated `DOJO_REPORT` section."""
# pylint: disable=E1101
return hasattr(self, "dojo_report") and bool(self.dojo_report)
@property
def djrepo_path(self):
"""The path of the djrepo file. None if file does not exist."""
# pylint: disable=E1101
root, ext = os.path.splitext(self.filepath)
path = root + ".djrepo"
return path
# if os.path.exists(path): return path
# return None
def hint_for_accuracy(self, accuracy="normal"):
"""
Returns a :class:`Hint` object with the suggested value of ecut [Ha] and
pawecutdg [Ha] for the given accuracy.
ecut and pawecutdg are set to zero if no hint is available.
Args:
accuracy: ["low", "normal", "high"]
"""
# pylint: disable=E1101
if not self.has_dojo_report:
return Hint(ecut=0.0, pawecutdg=0.0)
# Get hints from dojoreport. Try first in hints then in ppgen_hints.
if "hints" in self.dojo_report:
return Hint.from_dict(self.dojo_report["hints"][accuracy])
if "ppgen_hints" in self.dojo_report:
return Hint.from_dict(self.dojo_report["ppgen_hints"][accuracy])
return Hint(ecut=0.0, pawecutdg=0.0)
@property
def has_hints(self):
"""
True if self provides hints on the cutoff energy.
"""
for acc in ["low", "normal", "high"]:
try:
if self.hint_for_accuracy(acc) is None:
return False
except KeyError:
return False
return True
def open_pspsfile(self, ecut=20, pawecutdg=None):
"""
Calls Abinit to compute the internal tables for the application of the
pseudopotential part. Returns :class:`PspsFile` object providing methods
to plot and analyze the data or None if file is not found or it's not readable.
Args:
ecut: Cutoff energy in Hartree.
pawecutdg: Cutoff energy for the PAW double grid.
"""
from abipy.abio.factories import gs_input
from abipy.core.structure import Structure
from abipy.electrons.psps import PspsFile
from abipy.flowtk import AbinitTask
# Build fake structure.
lattice = 10 * np.eye(3)
structure = Structure(lattice, [self.element], coords=[[0, 0, 0]])
if self.ispaw and pawecutdg is None:
pawecutdg = ecut * 4
inp = gs_input(
structure,
pseudos=[self],
ecut=ecut,
pawecutdg=pawecutdg,
spin_mode="unpolarized",
kppa=1,
)
# Add prtpsps = -1 to make Abinit print the PSPS.nc file and stop.
inp["prtpsps"] = -1
# Build temporary task and run it (ignore retcode because we don't exit cleanly)
task = AbinitTask.temp_shell_task(inp)
task.start_and_wait()
filepath = task.outdir.has_abiext("_PSPS.nc")
if not filepath:
logger.critical(f"Cannot find PSPS.nc file in {task.outdir}")
return None
# Open the PSPS.nc file.
try:
return PspsFile(filepath)
except Exception as exc:
logger.critical(f"Exception while reading PSPS file at {filepath}:\n{exc}")
return None
class NcPseudo(metaclass=abc.ABCMeta):
"""
Abstract class defining the methods that must be implemented
by the concrete classes representing norm-conserving pseudopotentials.
"""
@property
@abc.abstractmethod
def nlcc_radius(self):
"""
Radius at which the core charge vanish (i.e. cut-off in a.u.).
Returns 0.0 if nlcc is not used.
"""
@property
def has_nlcc(self):
"""True if the pseudo is generated with non-linear core correction."""
return self.nlcc_radius > 0.0
@property
def rcore(self):
"""Radius of the pseudization sphere in a.u."""
try:
return self._core
except AttributeError:
return None
class PawPseudo(metaclass=abc.ABCMeta):
"""
Abstract class that defines the methods that must be implemented
by the concrete classes representing PAW pseudopotentials.
"""
# def nlcc_radius(self):
# """
# Radius at which the core charge vanish (i.e. cut-off in a.u.).
# Returns 0.0 if nlcc is not used.
# """
# return 0.0
#
# @property
# def has_nlcc(self):
# """True if the pseudo is generated with non-linear core correction."""
# return True
@property
@abc.abstractmethod
def paw_radius(self):
"""Radius of the PAW sphere in a.u."""
@property
def rcore(self):
"""Alias of paw_radius."""
return self.paw_radius
class AbinitPseudo(Pseudo):
"""
An AbinitPseudo is a pseudopotential whose file contains an abinit header.
"""
def __init__(self, path, header):
"""
Args:
path: Filename.
header: :class:`AbinitHeader` instance.
"""
self.path = path
self.header = header
self._summary = header.summary
# Build xc from header.
self.xc = XcFunc.from_abinit_ixc(header["pspxc"])
for attr_name in header:
value = header.get(attr_name)
# Hide these attributes since one should always use the public interface.
setattr(self, "_" + attr_name, value)
@property
def summary(self):
"""Summary line reported in the ABINIT header."""
return self._summary.strip()
@property
def Z(self):
# pylint: disable=E1101
return self._zatom
@property
def Z_val(self):
# pylint: disable=E1101
return self._zion
@property
def l_max(self):
# pylint: disable=E1101
return self._lmax
@property
def l_local(self):
# pylint: disable=E1101
return self._lloc
@property
def supports_soc(self):
# Treat ONCVPSP pseudos
# pylint: disable=E1101
if self._pspcod == 8:
switch = self.header["extension_switch"]
if switch in (0, 1):
return False
if switch in (2, 3):
return True
raise ValueError(f"Don't know how to handle extension_switch: {switch}")
# TODO Treat HGH HGHK pseudos
# As far as I know, other Abinit pseudos do not support SOC.
return False
class NcAbinitPseudo(NcPseudo, AbinitPseudo):
"""Norm-conserving pseudopotential in the Abinit format."""
@property
def summary(self):
return self._summary.strip()
@property
def Z(self):
# pylint: disable=E1101
return self._zatom
@property
def Z_val(self):
"""Number of valence electrons."""
# pylint: disable=E1101
return self._zion
@property
def l_max(self):
# pylint: disable=E1101
return self._lmax
@property
def l_local(self):
# pylint: disable=E1101
return self._lloc
@property
def nlcc_radius(self):
# pylint: disable=E1101
return self._rchrg
class PawAbinitPseudo(PawPseudo, AbinitPseudo):
"""Paw pseudopotential in the Abinit format."""
@property
def paw_radius(self):
# pylint: disable=E1101
return self._r_cut
# def orbitals(self):
@property
def supports_soc(self):
return True
class Hint:
"""
Suggested value for the cutoff energy [Hartree units]
and the cutoff energy for the dense grid (only for PAW pseudos).
"""
def __init__(self, ecut, pawecutdg=None):
self.ecut = ecut
self.pawecutdg = ecut if pawecutdg is None else pawecutdg
def __str__(self):
if self.pawecutdg is not None:
return f"ecut: {self.ecut}, pawecutdg: {self.pawecutdg}"
return f"ecut: {self.ecut}"
def as_dict(self):
"""Return dictionary for MSONable protocol."""
return {
"@module": type(self).__module__,
"@class": type(self).__name__,
"ecut": self.ecut,
"pawecutdg": self.pawecutdg,
}
@classmethod
def from_dict(cls, d):
"""Build instance from dictionary (MSONable protocol)."""
return cls(**{k: v for k, v in d.items() if not k.startswith("@")})
def _dict_from_lines(lines, key_nums, sep=None):
"""
Helper function to parse formatted text structured like:
value1 value2 ... sep key1, key2 ...
key_nums is a list giving the number of keys for each line. 0 if line should be skipped.
sep is a string denoting the character that separates the keys from the value (None if
no separator is present).
Returns:
dict{key1 : value1, key2 : value2, ...}
Raises:
ValueError if parsing fails.
"""
if is_string(lines):
lines = [lines]
if not isinstance(key_nums, collections.abc.Iterable):
key_nums = list(key_nums)
if len(lines) != len(key_nums):
raise ValueError(f"{lines = }\n{key_nums = }")
kwargs = Namespace()
for i, nk in enumerate(key_nums):
if nk == 0:
continue
line = lines[i]
tokens = [t.strip() for t in line.split()]
values, keys = tokens[:nk], "".join(tokens[nk:])
# Sanitize keys: In some case we might get strings in the form: foo[,bar]
keys.replace("[", "").replace("]", "")
keys = keys.split(",")
if sep is not None:
check = keys[0][0]
if check != sep:
raise ValueError(f"Expecting separator {sep}, got {check}")
keys[0] = keys[0][1:]
if len(values) != len(keys):
msg = f"line: {line}\n len(keys) != len(value)\nkeys: {keys}\n values: {values}"
raise ValueError(msg)
kwargs.update(zip(keys, values))
return kwargs
class AbinitHeader(dict):
"""Dictionary whose keys can be also accessed as attributes."""
def __getattr__(self, name):
try:
# Default behavior
return super().__getattribute__(name)
except AttributeError:
try:
# Try in the dictionary.
return self[name]
except KeyError as exc:
raise AttributeError(str(exc))
def _int_from_str(string):
"""
Convert string into integer
Raise:
TypeError if string is not a valid integer
"""
float_num = float(string)
int_num = int(float_num)
if float_num == int_num:
return int_num
# Needed to handle pseudos with fractional charge
int_num = np.rint(float_num)
logger.warning(f"Converting float {float_num} to int {int_num}")
return int_num
class NcAbinitHeader(AbinitHeader):
"""The abinit header found in the NC pseudopotential files."""
_attr_desc = namedtuple("_attr_desc", "default astype")
_VARS = {
# Mandatory
"zatom": _attr_desc(None, _int_from_str),
"zion": _attr_desc(None, float),
"pspdat": _attr_desc(None, float),
"pspcod": _attr_desc(None, int),
"pspxc": _attr_desc(None, int),
"lmax": _attr_desc(None, int),
"lloc": _attr_desc(None, int),
"r2well": _attr_desc(None, float),
"mmax": _attr_desc(None, float),
# Optional variables for non linear-core correction. HGH does not have it.
"rchrg": _attr_desc(0.0, float), # radius at which the core charge vanish (i.e. cut-off in a.u.)
"fchrg": _attr_desc(0.0, float),
"qchrg": _attr_desc(0.0, float),
}
del _attr_desc
def __init__(self, summary, **kwargs):
super().__init__()
# pseudos generated by APE use llocal instead of lloc.
if "llocal" in kwargs:
kwargs["lloc"] = kwargs.pop("llocal")
self.summary = summary.strip()
for key, desc in NcAbinitHeader._VARS.items():
default, astype = desc.default, desc.astype
value = kwargs.pop(key, None)
if value is None:
value = default
if default is None:
raise RuntimeError(f"Attribute {key} must be specified")
else:
try:
value = astype(value)
except Exception:
raise RuntimeError(f"Conversion Error for key {key}, value {value}")
self[key] = value
# Add remaining arguments, e.g. extension_switch
if kwargs:
self.update(kwargs)
@staticmethod
def fhi_header(filename, ppdesc):
"""
Parse the FHI abinit header. Example:
Troullier-Martins psp for element Sc Thu Oct 27 17:33:22 EDT 1994
21.00000 3.00000 940714 zatom, zion, pspdat
1 1 2 0 2001 .00000 pspcod,pspxc,lmax,lloc,mmax,r2well
1.80626423934776 .22824404341771 1.17378968127746 rchrg,fchrg,qchrg
"""
lines = _read_nlines(filename, 4)
try:
header = _dict_from_lines(lines[:4], [0, 3, 6, 3])
except ValueError:
# The last record with rchrg ... seems to be optional.
header = _dict_from_lines(lines[:3], [0, 3, 6])
summary = lines[0]
return NcAbinitHeader(summary, **header)
@staticmethod
def hgh_header(filename, ppdesc):
"""
Parse the HGH abinit header. Example:
Hartwigsen-Goedecker-Hutter psp for Ne, from PRB58, 3641 (1998)
10 8 010605 zatom,zion,pspdat
3 1 1 0 2001 0 pspcod,pspxc,lmax,lloc,mmax,r2well
"""
lines = _read_nlines(filename, 3)
header = _dict_from_lines(lines[:3], [0, 3, 6])
summary = lines[0]
return NcAbinitHeader(summary, **header)
@staticmethod
def gth_header(filename, ppdesc):
"""
Parse the GTH abinit header. Example:
Goedecker-Teter-Hutter Wed May 8 14:27:44 EDT 1996
1 1 960508 zatom,zion,pspdat
2 1 0 0 2001 0. pspcod,pspxc,lmax,lloc,mmax,r2well
0.2000000 -4.0663326 0.6778322 0 0 rloc, c1, c2, c3, c4
0 0 0 rs, h1s, h2s
0 0 rp, h1p
1.36 .2 0.6 rcutoff, rloc
"""
lines = _read_nlines(filename, 7)
header = _dict_from_lines(lines[:3], [0, 3, 6])
summary = lines[0]
return NcAbinitHeader(summary, **header)
@staticmethod
def oncvpsp_header(filename, ppdesc):
"""
Parse the ONCVPSP abinit header. Example:
Li ONCVPSP r_core= 2.01 3.02
3.0000 3.0000 140504 zatom,zion,pspd
8 2 1 4 600 0 pspcod,pspxc,lmax,lloc,mmax,r2well
5.99000000 0.00000000 0.00000000 rchrg fchrg qchrg
2 2 0 0 0 nproj
0 extension_switch
0 -2.5000025868368D+00 -1.2006906995331D+00
1 0.0000000000000D+00 0.0000000000000D+00 0.0000000000000D+00
2 1.0000000000000D-02 4.4140499497377D-02 1.9909081701712D-02
"""
lines = _read_nlines(filename, 6)
header = _dict_from_lines(lines[:3], [0, 3, 6])
summary = lines[0]
# Replace pspd with pspdata
header.update({"pspdat": header["pspd"]})
header.pop("pspd")
# Read extension switch
header["extension_switch"] = int(lines[5].split()[0])
return NcAbinitHeader(summary, **header)
@staticmethod
def tm_header(filename, ppdesc):
"""
Parse the TM abinit header. Example:
Troullier-Martins psp for element Fm Thu Oct 27 17:28:39 EDT 1994
100.00000 14.00000 940714 zatom, zion, pspdat
1 1 3 0 2001 .00000 pspcod,pspxc,lmax,lloc,mmax,r2well
0 4.085 6.246 0 2.8786493 l,e99.0,e99.9,nproj,rcpsp
.00000000 .0000000000 .0000000000 .00000000 rms,ekb1,ekb2,epsatm
1 3.116 4.632 1 3.4291849 l,e99.0,e99.9,nproj,rcpsp
.00000000 .0000000000 .0000000000 .00000000 rms,ekb1,ekb2,epsatm
2 4.557 6.308 1 2.1865358 l,e99.0,e99.9,nproj,rcpsp
.00000000 .0000000000 .0000000000 .00000000 rms,ekb1,ekb2,epsatm
3 23.251 29.387 1 2.4776730 l,e99.0,e99.9,nproj,rcpsp
.00000000 .0000000000 .0000000000 .00000000 rms,ekb1,ekb2,epsatm
3.62474762267880 .07409391739104 3.07937699839200 rchrg,fchrg,qchrg
"""
lines = _read_nlines(filename, -1)
header = []
for lineno, line in enumerate(lines):
header.append(line)
if lineno == 2:
# Read lmax.
tokens = line.split()
pspcod, pspxc, lmax, lloc = map(int, tokens[:4])
mmax, r2well = map(float, tokens[4:6])
# if tokens[-1].strip() != "pspcod,pspxc,lmax,lloc,mmax,r2well":
# raise RuntimeError("%s: Invalid line\n %s" % (filename, line))
lines = lines[3:]
break
# TODO
# Parse the section with the projectors.
# 0 4.085 6.246 0 2.8786493 l,e99.0,e99.9,nproj,rcpsp
# .00000000 .0000000000 .0000000000 .00000000 rms,ekb1,ekb2,epsatm
projectors = {}
for idx in range(2 * (lmax + 1)):
line = lines[idx]
if idx % 2 == 0:
proj_info = [
line,
]
if idx % 2 == 1:
proj_info.append(line)
d = _dict_from_lines(proj_info, [5, 4])
projectors[int(d["l"])] = d
# Add the last line with info on nlcc.
header.append(lines[idx + 1])
summary = header[0]
header = _dict_from_lines(header, [0, 3, 6, 3])
return NcAbinitHeader(summary, **header)
class PawAbinitHeader(AbinitHeader):
"""The abinit header found in the PAW pseudopotential files."""
_attr_desc = namedtuple("_attr_desc", "default astype")
_VARS = {
"zatom": _attr_desc(None, _int_from_str),
"zion": _attr_desc(None, float),
"pspdat": _attr_desc(None, float),
"pspcod": _attr_desc(None, int),
"pspxc": _attr_desc(None, int),
"lmax": _attr_desc(None, int),
"lloc": _attr_desc(None, int),
"mmax": _attr_desc(None, int),
"r2well": _attr_desc(None, float),
"pspfmt": _attr_desc(None, str),
"creatorID": _attr_desc(None, int),
"basis_size": _attr_desc(None, int),
"lmn_size": _attr_desc(None, int),
"orbitals": _attr_desc(None, list),
"number_of_meshes": _attr_desc(None, int),
"r_cut": _attr_desc(None, float), # r_cut(PAW) in the header
"shape_type": _attr_desc(None, int),
"rshape": _attr_desc(None, float),
}
del _attr_desc
def __init__(self, summary, **kwargs):
super().__init__()
self.summary = summary.strip()
for key, desc in self._VARS.items():
default, astype = desc.default, desc.astype
value = kwargs.pop(key, None)
if value is None:
value = default
if default is None:
raise RuntimeError(f"Attribute {key} must be specified")
else:
try:
value = astype(value)
except Exception:
raise RuntimeError(f"Conversion Error for key {key}, with value {value}")
self[key] = value
if kwargs:
raise RuntimeError(f"kwargs should be empty but got {str(kwargs)}")
@staticmethod
def paw_header(filename, ppdesc):
"""
Parse the PAW abinit header. Examples:
Paw atomic data for element Ni - Generated by AtomPAW (N. Holzwarth) + AtomPAW2Abinit v3.0.5
28.000 18.000 20061204 : zatom,zion,pspdat
7 7 2 0 350 0. : pspcod,pspxc,lmax,lloc,mmax,r2well
paw3 1305 : pspfmt,creatorID
5 13 : basis_size,lmn_size
0 0 1 1 2 : orbitals
3 : number_of_meshes
1 3 350 1.1803778368E-05 3.5000000000E-02 : mesh 1, type,size,rad_step[,log_step]
2 1 921 2.500000000000E-03 : mesh 2, type,size,rad_step[,log_step]
3 3 391 1.1803778368E-05 3.5000000000E-02 : mesh 3, type,size,rad_step[,log_step]
2.3000000000 : r_cut(SPH)
2 0.
Another format:
C (US d-loc) - PAW data extracted from US-psp (D.Vanderbilt) - generated by USpp2Abinit v2.3.0
6.000 4.000 20090106 : zatom,zion,pspdat
7 11 1 0 560 0. : pspcod,pspxc,lmax,lloc,mmax,r2well
paw4 2230 : pspfmt,creatorID
4 8 : basis_size,lmn_size
0 0 1 1 : orbitals
5 : number_of_meshes
1 2 560 1.5198032759E-04 1.6666666667E-02 : mesh 1, type,size,rad_step[,log_step]
2 2 556 1.5198032759E-04 1.6666666667E-02 : mesh 2, type,size,rad_step[,log_step]
3 2 576 1.5198032759E-04 1.6666666667E-02 : mesh 3, type,size,rad_step[,log_step]
4 2 666 1.5198032759E-04 1.6666666667E-02 : mesh 4, type,size,rad_step[,log_step]
5 2 673 1.5198032759E-04 1.6666666667E-02 : mesh 5, type,size,rad_step[,log_step]
1.5550009124 : r_cut(PAW)
3 0. : shape_type,rshape
Yet nnother one:
Paw atomic data for element Si - Generated by atompaw v3.0.1.3 & AtomPAW2Abinit v3.3.1
14.000 4.000 20120814 : zatom,zion,pspdat
7 11 1 0 663 0. : pspcod,pspxc,lmax,lloc,mmax,r2well
paw5 1331 : pspfmt,creatorID
4 8 : basis_size,lmn_size
0 0 1 1 : orbitals
5 : number_of_meshes
1 2 663 8.2129718540404674E-04 1.1498160595656655E-02 : mesh 1, type,size,rad_step[,log_step]
2 2 658 8.2129718540404674E-04 1.1498160595656655E-02 : mesh 2, type,size,rad_step[,log_step]
3 2 740 8.2129718540404674E-04 1.1498160595656655E-02 : mesh 3, type,size,rad_step[,log_step]
4 2 819 8.2129718540404674E-04 1.1498160595656655E-02 : mesh 4, type,size,rad_step[,log_step]
5 2 870 8.2129718540404674E-04 1.1498160595656655E-02 : mesh 5, type,size,rad_step[,log_step]
1.5669671236 : r_cut(PAW)
2 0. : shape_type,rshape
"""
supported_formats = ["paw3", "paw4", "paw5"]
if ppdesc.format not in supported_formats:
raise NotImplementedError(f"format {ppdesc.format} not in {supported_formats}")
lines = _read_nlines(filename, -1)
summary = lines[0]
header = _dict_from_lines(lines[:5], [0, 3, 6, 2, 2], sep=":")