Source code for pymatgen.core.xcfunc

# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides
"""

from collections import namedtuple, OrderedDict
from monty.string import is_string
from monty.json import MSONable  # , MontyEncoder
from monty.functools import lazy_property
from pymatgen.core.libxcfunc import LibxcFunc

__author__ = "Matteo Giantomassi"
__copyright__ = "Copyright 2016, The Materials Project"
__version__ = "3.0.0"  # The libxc version used to generate this file!
__maintainer__ = "Matteo Giantomassi"
__email__ = "gmatteo@gmail.com"
__status__ = "Production"
__date__ = "May 16, 2016"


[docs]class XcFunc(MSONable): """ This object stores information about the XC correlation functional. Client code usually creates the object by calling the class methods: - from_name - from_type_name or code-specific methods such as: - from_abinit_ixc Ax XcFunc instance is hashable and can therefore be used as key in dictionaries. The implementation is based on the libxc conventions and is inspired to the XML specification for atomic PAW datasets documented at: https://wiki.fysik.dtu.dk/gpaw/setups/pawxml.html For convenience, part of the pawxml documentation is reported here. The xc_functional element defines the exchange-correlation functional used for generating the dataset. It has the two attributes type and name. The type attribute can be LDA, GGA, MGGA or HYB. The name attribute designates the exchange-correlation functional and can be specified in the following ways: [1] Taking the names from the LibXC library. The correlation and exchange names are stripped from their XC_ part and combined with a + sign. Here is an example for an LDA functional: <xc_functional type="LDA", name="LDA_X+LDA_C_PW"/> and this is what PBE will look like: <xc_functional type="GGA", name="GGA_X_PBE+GGA_C_PBE"/> [2] Using one of the following pre-defined aliases: type name LibXC equivalent Reference LDA PW LDA_X+LDA_C_PW LDA exchange; Perdew, Wang, PRB 45, 13244 (1992) GGA PW91 GGA_X_PW91+GGA_C_PW91 Perdew et al PRB 46, 6671 (1992) GGA PBE GGA_X_PBE+GGA_C_PBE Perdew, Burke, Ernzerhof, PRL 77, 3865 (1996) GGA RPBE GGA_X_RPBE+GGA_C_PBE Hammer, Hansen, Nørskov, PRB 59, 7413 (1999) GGA revPBE GGA_X_PBE_R+GGA_C_PBE Zhang, Yang, PRL 80, 890 (1998) GGA PBEsol GGA_X_PBE_SOL+GGA_C_PBE_SOL Perdew et al, PRL 100, 136406 (2008) GGA AM05 GGA_X_AM05+GGA_C_AM05 Armiento, Mattsson, PRB 72, 085108 (2005) GGA BLYP GGA_X_B88+GGA_C_LYP Becke, PRA 38, 3098 (1988); Lee, Yang, Parr, PRB 37, 785 """ type_name = namedtuple("type_name", "type, name") xcf = LibxcFunc defined_aliases = OrderedDict([ # (x, c) --> type_name # LDAs ((xcf.LDA_X, xcf.LDA_C_PW), type_name("LDA", "PW")), # ixc 7 ((xcf.LDA_X, xcf.LDA_C_PW_MOD), type_name("LDA", "PW_MOD")), ((xcf.LDA_X, xcf.LDA_C_PZ), type_name("LDA", "PZ")), # ixc 2 ((xcf.LDA_X, xcf.LDA_C_WIGNER), type_name("LDA", "W")), # ixc 4 ((xcf.LDA_X, xcf.LDA_C_HL), type_name("LDA", "HL")), # ixc 5 ((xcf.LDA_X, xcf.LDA_C_GL), type_name("LDA", "GL")), ((xcf.LDA_X, xcf.LDA_C_VWN), type_name("LDA", "VWN")), # GGAs ((xcf.GGA_X_PW91, xcf.GGA_C_PW91), type_name("GGA", "PW91")), ((xcf.GGA_X_PBE, xcf.GGA_C_PBE), type_name("GGA", "PBE")), ((xcf.GGA_X_RPBE, xcf.GGA_C_PBE), type_name("GGA", "RPBE")), # ixc 15 ((xcf.GGA_X_PBE_R, xcf.GGA_C_PBE), type_name("GGA", "revPBE")), # ixc 14 ((xcf.GGA_X_PBE_SOL, xcf.GGA_C_PBE_SOL), type_name("GGA", "PBEsol")), ((xcf.GGA_X_AM05, xcf.GGA_C_AM05), type_name("GGA", "AM05")), ((xcf.GGA_X_B88, xcf.GGA_C_LYP), type_name("GGA", "BLYP")), ]) del type_name # Correspondence between Abinit ixc notation and libxc notation. # see: http://www.abinit.org/doc/helpfiles/for-v7.8/input_variables/varbas.html#ixc # and 42_libpaw/m_pawpsp.F90 for the implementation. # Fortunately, all the other cases are handled with libxc. abinitixc_to_libxc = { 1: dict(xc=xcf.LDA_XC_TETER93), 2: dict(x=xcf.LDA_X, c=xcf.LDA_C_PZ), # PZ 001009 4: dict(x=xcf.LDA_X, c=xcf.LDA_C_WIGNER), # W 5: dict(x=xcf.LDA_X, c=xcf.LDA_C_HL), # HL 7: dict(x=xcf.LDA_X, c=xcf.LDA_C_PW), # PW 001012 11: dict(x=xcf.GGA_X_PBE, c=xcf.GGA_C_PBE), # PBE 14: dict(x=xcf.GGA_X_PBE_R, c=xcf.GGA_C_PBE), # revPBE 15: dict(x=xcf.GGA_X_RPBE, c=xcf.GGA_C_PBE), # RPBE } del xcf
[docs] @classmethod def aliases(cls): """List of registered names.""" return [nt.name for nt in cls.defined_aliases.values()]
[docs] @classmethod def asxc(cls, obj): """Convert object into Xcfunc.""" if isinstance(obj, cls): return obj if is_string(obj): return cls.from_name(obj) raise TypeError("Don't know how to convert <%s:%s> to Xcfunc" % (type(obj), str(obj)))
[docs] @classmethod def from_abinit_ixc(cls, ixc): """Build the object from Abinit ixc (integer)""" ixc = int(ixc) if ixc == 0: return None if ixc > 0: return cls(**cls.abinitixc_to_libxc[ixc]) # libxc notation employed in Abinit: a six-digit number in the form XXXCCC or CCCXXX # ixc = str(ixc) # assert len(ixc[1:]) == 6 # first, last = ixc[1:4], ixc[4:] ixc = abs(ixc) first = ixc // 1000 last = ixc - first * 1000 x, c = LibxcFunc(int(first)), LibxcFunc(int(last)) if not x.is_x_kind: x, c = c, x # Swap assert x.is_x_kind and c.is_c_kind return cls(x=x, c=c)
[docs] @classmethod def from_name(cls, name): """Build the object from one of the registered names""" return cls.from_type_name(None, name)
[docs] @classmethod def from_type_name(cls, typ, name): """Build the object from (type, name).""" # Try aliases first. for k, nt in cls.defined_aliases.items(): if typ is not None and typ != nt.type: continue # print(name, nt.name) if name == nt.name: if len(k) == 1: return cls(xc=k) if len(k) == 2: return cls(x=k[0], c=k[1]) raise ValueError("Wrong key: %s" % k) # At this point, we should have something in the form # name="GGA_X_PBE+GGA_C_PBE" or name=""LDA_XC_TETER93" if "+" in name: # if typ is not None: raise ValueError("typ: `%s` but name: `%s`" % (typ, name)) x, c = (s.strip() for s in name.split("+")) x, c = LibxcFunc[x], LibxcFunc[c] return cls(x=x, c=c) # if typ is not None: raise ValueError("typ: `%s` but name: `%s`" % (typ, name)) xc = LibxcFunc[name] return cls(xc=xc)
[docs] @classmethod def from_dict(cls, d): """ Makes XcFunc obey the general json interface used in pymatgen for easier serialization. """ return cls(xc=d.get("xc"), x=d.get("x"), c=d.get("c"))
[docs] def as_dict(self): """ Makes XcFunc obey the general json interface used in pymatgen for easier serialization. """ d = {"@module": self.__class__.__module__, "@class": self.__class__.__name__} # print("in as_dict", type(self.x), type(self.c), type(self.xc)) if self.x is not None: d["x"] = self.x.as_dict() if self.c is not None: d["c"] = self.c.as_dict() if self.xc is not None: d["xc"] = self.xc.as_dict() return d
# def to_json(self): # """ # Returns a json string representation of the MSONable object. # """ # return json.dumps(self.as_dict()) #, cls=MontyEncoder) def __init__(self, xc=None, x=None, c=None): """ Args: xc: LibxcFunc for XC functional. x, c: LibxcFunc for exchange and correlation part. Mutually exclusive with xc. """ # Consistency check if xc is None: if x is None or c is None: raise ValueError("x or c must be specified when xc is None") else: if x is not None or c is not None: raise ValueError("x and c should be None when xc is specified") self.xc, self.x, self.c = xc, x, c
[docs] @lazy_property def type(self): """The type of the functional.""" if self.xc in self.defined_aliases: return self.defined_aliases[self.xc].type xc = (self.x, self.c) if xc in self.defined_aliases: return self.defined_aliases[xc].type # If self is not in defined_aliases, use LibxcFunc family if self.xc is not None: return self.xc.family return "+".join([self.x.family, self.c.family])
[docs] @lazy_property def name(self): """ The name of the functional. If the functional is not found in the aliases, the string has the form X_NAME+C_NAME """ if self.xc in self.defined_aliases: return self.defined_aliases[self.xc].name xc = (self.x, self.c) if xc in self.defined_aliases: return self.defined_aliases[xc].name if self.xc is not None: return self.xc.name return "+".join([self.x.name, self.c.name])
def __repr__(self): return "%s" % self.name def __hash__(self): return hash(self.name) def __eq__(self, other): if other is None: return False if isinstance(other, XcFunc): return self.name == other.name # assume other is a string return self.name == other def __ne__(self, other): return not self == other
# @property # def refs(self): # def info_dict() # if self.xc is not None: # return {"xc", self.xc.info_dict} # else: # return {"x", self.x.info_dict, "c", self.c.info_dict}