bandu 1.3.5__py3-none-any.whl → 1.3.7__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- bandu/abinit_reader.py +1094 -1094
- bandu/bandu.py +320 -313
- bandu/brillouin_zone.py +185 -185
- bandu/colors.py +46 -46
- bandu/isosurface_class.py +235 -235
- bandu/plotter.py +599 -599
- bandu/translate.py +37 -37
- bandu/wfk_class.py +557 -556
- bandu/xsf_reader.py +91 -90
- {bandu-1.3.5.dist-info → bandu-1.3.7.dist-info}/METADATA +192 -192
- bandu-1.3.7.dist-info/RECORD +14 -0
- {bandu-1.3.5.dist-info → bandu-1.3.7.dist-info}/WHEEL +1 -1
- {bandu-1.3.5.dist-info → bandu-1.3.7.dist-info}/licenses/LICENSE +21 -21
- bandu-1.3.5.dist-info/RECORD +0 -14
- {bandu-1.3.5.dist-info → bandu-1.3.7.dist-info}/top_level.txt +0 -0
bandu/abinit_reader.py
CHANGED
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@@ -1,1095 +1,1095 @@
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-
import struct
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import numpy as np
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from typing import Generator, Union
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import sys
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from . import wfk_class as wc
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np.set_printoptions(threshold=sys.maxsize)
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7
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def bytes2float(bin_data)->float:
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return struct.unpack('<d', bin_data)[0]
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def bytes2int(bin_data)->int:
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return int.from_bytes(bin_data, 'little', signed=True)
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class Abinit7WFK():
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def __init__(
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self, filename:str
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):
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self.filename = filename
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self._ReadHeader()
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#---------------------------------------------------------------------------------------------------------------------#
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#------------------------------------------------------ METHODS ------------------------------------------------------#
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#---------------------------------------------------------------------------------------------------------------------#
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# method to read wavefunction header for abinit version 7
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def _ReadHeader(
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self
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)->None:
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wfk = open(self.filename, 'rb')
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print('Reading WFK header')
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#---------------#
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# unpack integers
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self.header = bytes2int(wfk.read(4))
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self.version = wfk.read(6).decode()
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self.headform = bytes2int(wfk.read(4))
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self.fform = bytes2int(wfk.read(4))
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wfk.read(8)
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self.bandtot = bytes2int(wfk.read(4))
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self.date = bytes2int(wfk.read(4))
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self.intxc = bytes2int(wfk.read(4))
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self.ixc = bytes2int(wfk.read(4))
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self.natom = bytes2int(wfk.read(4))
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self.ngfftx = bytes2int(wfk.read(4))
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self.ngffty = bytes2int(wfk.read(4))
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self.ngfftz = bytes2int(wfk.read(4))
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self.nkpt = bytes2int(wfk.read(4))
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self.nspden = bytes2int(wfk.read(4))
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self.nspinor = bytes2int(wfk.read(4))
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self.nsppol = bytes2int(wfk.read(4))
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self.nsym = bytes2int(wfk.read(4))
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self.npsp = bytes2int(wfk.read(4))
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self.ntypat = bytes2int(wfk.read(4))
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self.occopt = bytes2int(wfk.read(4))
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self.pertcase = bytes2int(wfk.read(4))
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self.usepaw = bytes2int(wfk.read(4))
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if self.usepaw == 1:
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raise NotImplementedError(
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f'''PAW potentials are not supported by this program for Abinit v{self.version}.
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This program supports PAW potentials in Abinit v10, consider upgrading to the latest version.
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'''
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)
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#--------------#
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# unpack doubles
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self.ecut = bytes2float(wfk.read(8))
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self.ecutdg = bytes2float(wfk.read(8))
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self.ecutsm = bytes2float(wfk.read(8))
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self.ecut_eff = bytes2float(wfk.read(8))
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self.qptnx = bytes2float(wfk.read(8))
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self.qptny = bytes2float(wfk.read(8))
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self.qptnz = bytes2float(wfk.read(8))
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rprimd_ax = bytes2float(wfk.read(8))
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rprimd_ay = bytes2float(wfk.read(8))
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rprimd_az = bytes2float(wfk.read(8))
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rprimd_bx = bytes2float(wfk.read(8))
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rprimd_by = bytes2float(wfk.read(8))
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rprimd_bz = bytes2float(wfk.read(8))
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rprimd_cx = bytes2float(wfk.read(8))
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rprimd_cy = bytes2float(wfk.read(8))
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rprimd_cz = bytes2float(wfk.read(8))
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#------------------------#
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# convert Bohr to Angstrom
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self.real_lattice = 0.529177*np.array([[rprimd_ax, rprimd_ay, rprimd_az],
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[rprimd_bx, rprimd_by, rprimd_bz],
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[rprimd_cx, rprimd_cy, rprimd_cz]]).reshape((3,3))
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self.stmbias = bytes2float(wfk.read(8))
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self.tphysel = bytes2float(wfk.read(8))
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self.tsmear = bytes2float(wfk.read(8))
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#---------------#
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# unpack integers
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self.usewvl = bytes2int(wfk.read(4))
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wfk.read(8)
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self.istwfk:list[int] = []
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for i in range(self.nkpt):
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val = bytes2int(wfk.read(4))
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self.istwfk.append(val)
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self.bands:list[int] = []
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for i in range(self.nkpt*self.nsppol):
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val = bytes2int(wfk.read(4))
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self.bands.append(val)
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self.npwarr:list[int] = []
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for i in range(self.nkpt):
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val = bytes2int(wfk.read(4))
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self.npwarr.append(val)
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self.so_psp:list[int] = []
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for i in range(self.npsp):
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val = bytes2int(wfk.read(4))
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self.so_psp.append(val)
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self.symafm:list[int] = []
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for i in range(self.nsym):
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val = bytes2int(wfk.read(4))
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self.symafm.append(val)
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self.symrel:list[np.ndarray] = []
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for i in range(self.nsym):
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arr = np.zeros((3,3))
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arr[0,0] = bytes2int(wfk.read(4))
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arr[1,0] = bytes2int(wfk.read(4))
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arr[2,0] = bytes2int(wfk.read(4))
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arr[0,1] = bytes2int(wfk.read(4))
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arr[1,1] = bytes2int(wfk.read(4))
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arr[2,1] = bytes2int(wfk.read(4))
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arr[0,2] = bytes2int(wfk.read(4))
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arr[1,2] = bytes2int(wfk.read(4))
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arr[2,2] = bytes2int(wfk.read(4))
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self.symrel.append(arr)
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self.typat:list[int] = []
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for i in range(self.natom):
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val = bytes2int(wfk.read(4))
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self.typat.append(val)
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#--------------#
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# unpack doubles
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self.kpts:list[np.ndarray] = []
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for i in range(self.nkpt):
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vec = np.zeros(3)
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vec[0] = bytes2float(wfk.read(8))
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vec[1] = bytes2float(wfk.read(8))
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vec[2] = bytes2float(wfk.read(8))
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self.kpts.append(vec)
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self.occ:list[float] = []
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for i in range(self.bandtot):
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val = bytes2float(wfk.read(8))
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self.occ.append(val)
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self.tnons:list[np.ndarray] = []
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for i in range(self.nsym):
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vec = np.zeros(3)
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vec[0] = bytes2float(wfk.read(8))
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vec[1] = bytes2float(wfk.read(8))
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vec[2] = bytes2float(wfk.read(8))
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self.tnons.append(vec)
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self.znucltypat:list[float] = []
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for i in range(self.ntypat):
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val = bytes2float(wfk.read(8))
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self.znucltypat.append(val)
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self.wtk:list[float] = []
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for i in range(self.nkpt):
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val = bytes2float(wfk.read(8))
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self.wtk.append(val)
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#-----------------------#
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# unpack pseudopotentials
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wfk.read(4)
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self.title:list[str] = []
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self.znuclpsp:list[float] = []
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self.zionpsp:list[float] = []
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self.pspso:list[int] = []
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self.pspdat:list[int] = []
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self.pspcod:list[int] = []
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self.pspxc:list[int] = []
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self.lmn_size:list[int] = []
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for i in range(self.npsp):
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wfk.read(4)
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self.title.append(wfk.read(132).decode())
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self.znuclpsp.append(bytes2float(wfk.read(8)))
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self.zionpsp.append(bytes2float(wfk.read(8)))
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self.pspso.append(bytes2int(wfk.read(4)))
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self.pspdat.append(bytes2int(wfk.read(4)))
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self.pspcod.append(bytes2int(wfk.read(4)))
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self.pspxc.append(bytes2int(wfk.read(4)))
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self.lmn_size.append(bytes2int(wfk.read(4)))
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wfk.read(4)
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#------------------#
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# unpack coordinates
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wfk.read(4)
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self.residm = bytes2float(wfk.read(8))
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self.xred:list[np.ndarray] = []
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for i in range(self.natom):
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vec = np.zeros(3)
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vec[0] = bytes2float(wfk.read(8))
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vec[1] = bytes2float(wfk.read(8))
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vec[2] = bytes2float(wfk.read(8))
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self.xred.append(vec)
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#------------------------------------#
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# unpack total energy and fermi energy
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190
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self.etotal = bytes2float(wfk.read(8))
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self.fermi = bytes2float(wfk.read(8))
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192
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wfk.read(4)
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print('WFK header read')
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wfk.close()
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#-----------------------------------------------------------------------------------------------------------------#
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# check for time reversal symmetry
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197
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def _CheckTimeRev(
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self
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):
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# if system is centrosymmetric, do not double reciprocal symmetry operations
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if True in [np.array_equal(-np.identity(3),mat) for mat in self.symrel]:
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self.time_reversal = False
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else:
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self.time_reversal = True
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print((
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'Noncentrosymmetric system identified, assuming time reversal symmetry\n'
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'To change this, set "check_time_rev" keyword to False when calling ReadWFK() or ReadEigenvalues()'
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))
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#-----------------------------------------------------------------------------------------------------------------#
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# method to read entire body of abinit version 7 wavefunction file
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211
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def ReadWFK(
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self, energy_level=np.nan, width=np.nan, check_time_rev:bool=True
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)->Generator[wc.WFK, None, None]:
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'''
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Method that constructs WFK objects from ABINIT v7 WFK file
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Parameters
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----------
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energy_level : float
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The energy level to pull plane wave coefficients from
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This is relative to the Fermi energy
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If not defined but width is defined, default is 0 Hartree
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width : float
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Defines range about energy_level to search for plane wave coefficients
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Total range is equal to width, so look width/2 above and below energy_level
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If not defined but energy_level is defined, default is 0.005 Hartree
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'''
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# check for time reversal symmetry
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if check_time_rev:
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self._CheckTimeRev()
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else:
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self.time_reversal = False
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# read wfk file
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wfk = open(self.filename, 'rb')
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skip = True
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if energy_level is np.nan:
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if width is np.nan:
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skip = False
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else:
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energy_level = 0
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else:
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if width is np.nan:
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width = 0.005
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#-----------#
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246
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# skip header
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247
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wfk.read(298)
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248
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wfk.read(4*(2*self.nkpt + self.nkpt*self.nsppol + self.npsp + 10*self.nsym + self.natom))
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wfk.read(8*(4*self.nkpt + self.bandtot + 3*self.nsym + self.ntypat + 3*self.natom))
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wfk.read(self.npsp*(176))
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251
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#-------------------------------#
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252
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# begin reading wavefunction body
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253
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for i in range(self.nsppol):
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254
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for j in range(self.nkpt):
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print(f'Reading kpoint {j+1} of {self.nkpt}', end='\r')
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256
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if j+1 == self.nkpt:
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print('\n', end='')
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pw_indices:list[tuple] = []
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eigenvalues:list[float] = []
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260
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wfk.read(4)
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npw = bytes2int(wfk.read(4))
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262
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self.nspinor = bytes2int(wfk.read(4))
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263
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nband_temp = bytes2int(wfk.read(4))
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264
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wfk.read(8)
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265
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for pw in range(npw):
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266
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kx = bytes2int(wfk.read(4))
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ky = bytes2int(wfk.read(4))
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kz = bytes2int(wfk.read(4))
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pw_indices.append((kx, ky, kz))
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270
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wfk.read(8)
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for nband in range(nband_temp):
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eigenval = bytes2float(wfk.read(8))
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eigenvalues.append(eigenval)
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# skip reading coefficients if they energy level of interest is not in band
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|
275
|
-
if skip:
|
|
276
|
-
min_val = self.fermi + energy_level - width/2
|
|
277
|
-
max_val = self.fermi + energy_level + width/2
|
|
278
|
-
eig_found = False
|
|
279
|
-
for eigval in eigenvalues:
|
|
280
|
-
if min_val <= eigval <= max_val:
|
|
281
|
-
eig_found = True
|
|
282
|
-
break
|
|
283
|
-
if eig_found:
|
|
284
|
-
yield self._ReadCoeffs(
|
|
285
|
-
wfk,
|
|
286
|
-
nband_temp,
|
|
287
|
-
npw,
|
|
288
|
-
eigenvalues,
|
|
289
|
-
pw_indices,
|
|
290
|
-
ind=j
|
|
291
|
-
)
|
|
292
|
-
else:
|
|
293
|
-
wfk.read(nband_temp*8)
|
|
294
|
-
wfk.read(4)
|
|
295
|
-
wfk.read(nband_temp*(8 + npw*16))
|
|
296
|
-
else:
|
|
297
|
-
yield self._ReadCoeffs(
|
|
298
|
-
wfk,
|
|
299
|
-
nband_temp,
|
|
300
|
-
npw,
|
|
301
|
-
eigenvalues,
|
|
302
|
-
pw_indices,
|
|
303
|
-
ind=j
|
|
304
|
-
)
|
|
305
|
-
print('WFK body read')
|
|
306
|
-
wfk.close()
|
|
307
|
-
#-----------------------------------------------------------------------------------------------------------------#
|
|
308
|
-
# method to read in plane wave coefficients
|
|
309
|
-
def _ReadCoeffs(
|
|
310
|
-
self, wfk_file, nbands, npws, eigs, pw_inds, ind
|
|
311
|
-
)->wc.WFK:
|
|
312
|
-
occupancies = np.zeros((1,nbands), dtype=float)
|
|
313
|
-
coeffs = np.zeros((nbands,npws), dtype=complex)
|
|
314
|
-
for nband in range(nbands):
|
|
315
|
-
occ = bytes2float(wfk_file.read(8))
|
|
316
|
-
occupancies[:,nband] = occ
|
|
317
|
-
wfk_file.read(4)
|
|
318
|
-
for nband in range(nbands):
|
|
319
|
-
wfk_file.read(4)
|
|
320
|
-
cg:np.ndarray = np.zeros((1,npws), dtype=complex)
|
|
321
|
-
for pw in range(npws):
|
|
322
|
-
cg1 = bytes2float(wfk_file.read(8))
|
|
323
|
-
cg2 = bytes2float(wfk_file.read(8))
|
|
324
|
-
cg[:,pw] = cg1 + 1j*cg2
|
|
325
|
-
coeffs[nband,:] = cg
|
|
326
|
-
wfk_file.read(4)
|
|
327
|
-
return wc.WFK(
|
|
328
|
-
eigenvalues=np.array(eigs),
|
|
329
|
-
wfk_coeffs=np.array(coeffs),
|
|
330
|
-
pw_indices=np.array(pw_inds),
|
|
331
|
-
kpoints=np.array(self.kpts[ind]),
|
|
332
|
-
nkpt=self.nkpt,
|
|
333
|
-
nbands=self.bands[0],
|
|
334
|
-
ngfftx=self.ngfftx,
|
|
335
|
-
ngffty=self.ngffty,
|
|
336
|
-
ngfftz=self.ngfftz,
|
|
337
|
-
symrel=np.array(self.symrel),
|
|
338
|
-
nsym=self.nsym,
|
|
339
|
-
lattice=self.real_lattice,
|
|
340
|
-
natom=self.natom,
|
|
341
|
-
xred=np.array(self.xred),
|
|
342
|
-
typat=self.typat,
|
|
343
|
-
znucltypat=self.znucltypat,
|
|
344
|
-
fermi_energy=self.fermi,
|
|
345
|
-
non_symm_vecs=np.array(self.tnons),
|
|
346
|
-
time_reversal=self.time_reversal
|
|
347
|
-
)
|
|
348
|
-
#-----------------------------------------------------------------------------------------------------------------#
|
|
349
|
-
# method to read only eigenvalues from body of abinit version 7 wavefunction file
|
|
350
|
-
def ReadEigenvalues(
|
|
351
|
-
self, check_time_rev:bool=True
|
|
352
|
-
)->Generator[wc.WFK, None, None]:
|
|
353
|
-
'''
|
|
354
|
-
Method that constructs WFK objects from ABINIT v7 WFK file.
|
|
355
|
-
'''
|
|
356
|
-
# check for time reversal symmetry
|
|
357
|
-
if check_time_rev:
|
|
358
|
-
self._CheckTimeRev()
|
|
359
|
-
else:
|
|
360
|
-
self.time_reversal = False
|
|
361
|
-
# read wfk
|
|
362
|
-
wfk = open(self.filename, 'rb')
|
|
363
|
-
#-----------#
|
|
364
|
-
# skip header
|
|
365
|
-
wfk.read(298)
|
|
366
|
-
wfk.read(4*(2*self.nkpt + self.nkpt*self.nsppol + self.npsp + 10*self.nsym + self.natom))
|
|
367
|
-
wfk.read(8*(4*self.nkpt + self.bandtot + 3*self.nsym + self.ntypat + 3*self.natom))
|
|
368
|
-
wfk.read(self.npsp*(176))
|
|
369
|
-
#-------------------------------#
|
|
370
|
-
# begin reading wavefunction body
|
|
371
|
-
for i in range(self.nsppol):
|
|
372
|
-
for j in range(self.nkpt):
|
|
373
|
-
print(f'Reading kpoint {j+1} of {self.nkpt}', end='\r')
|
|
374
|
-
if j+1 == self.nkpt:
|
|
375
|
-
print('\n', end='')
|
|
376
|
-
eigenvalues:list[float] = []
|
|
377
|
-
wfk.read(4)
|
|
378
|
-
npw = bytes2int(wfk.read(4))
|
|
379
|
-
self.nspinor = bytes2int(wfk.read(4))
|
|
380
|
-
nband_temp = bytes2int(wfk.read(4))
|
|
381
|
-
wfk.read(8)
|
|
382
|
-
wfk.read(12*npw)
|
|
383
|
-
wfk.read(8)
|
|
384
|
-
#------------------------------------------------------------------#
|
|
385
|
-
# only need eigenvalues for Fermi surface, skip over everything else
|
|
386
|
-
for nband in range(nband_temp):
|
|
387
|
-
eigenval = bytes2float(wfk.read(8))
|
|
388
|
-
eigenvalues.append(eigenval)
|
|
389
|
-
wfk.read(nband_temp*8)
|
|
390
|
-
wfk.read(4)
|
|
391
|
-
wfk.read(nband_temp*(8 + npw*16))
|
|
392
|
-
yield wc.WFK(
|
|
393
|
-
eigenvalues=np.array(eigenvalues),
|
|
394
|
-
kpoints=np.array(self.kpts[j]),
|
|
395
|
-
nkpt=self.nkpt,
|
|
396
|
-
nbands=self.bands[0],
|
|
397
|
-
ngfftx=self.ngfftx,
|
|
398
|
-
ngffty=self.ngffty,
|
|
399
|
-
ngfftz=self.ngfftz,
|
|
400
|
-
symrel=np.array(self.symrel),
|
|
401
|
-
nsym=self.nsym,
|
|
402
|
-
lattice=self.real_lattice,
|
|
403
|
-
natom=self.natom,
|
|
404
|
-
xred=np.array(self.xred),
|
|
405
|
-
typat=self.typat,
|
|
406
|
-
znucltypat=self.znucltypat,
|
|
407
|
-
fermi_energy=self.fermi,
|
|
408
|
-
non_symm_vecs=np.array(self.tnons),
|
|
409
|
-
time_reversal=self.time_reversal
|
|
410
|
-
)
|
|
411
|
-
print('WFK body read')
|
|
412
|
-
wfk.close()
|
|
413
|
-
|
|
414
|
-
#---------------------------------------------------------------------------------------------------------------------#
|
|
415
|
-
#----------------------------------------------------- END CLASS -----------------------------------------------------#
|
|
416
|
-
#---------------------------------------------------------------------------------------------------------------------#
|
|
417
|
-
|
|
418
|
-
class Abinit10WFK():
|
|
419
|
-
def __init__(
|
|
420
|
-
self, filename:str
|
|
421
|
-
):
|
|
422
|
-
self.filename = filename
|
|
423
|
-
self._ReadHeader()
|
|
424
|
-
#---------------------------------------------------------------------------------------------------------------------#
|
|
425
|
-
#------------------------------------------------------ METHODS ------------------------------------------------------#
|
|
426
|
-
#---------------------------------------------------------------------------------------------------------------------#
|
|
427
|
-
# method to read wavefunction header for abinit version 7
|
|
428
|
-
def _ReadHeader(
|
|
429
|
-
self
|
|
430
|
-
)->None:
|
|
431
|
-
wfk = open(self.filename, 'rb')
|
|
432
|
-
print('Reading WFK header')
|
|
433
|
-
#---------------#
|
|
434
|
-
# unpack integers
|
|
435
|
-
self.header = bytes2int(wfk.read(4))
|
|
436
|
-
self.version = wfk.read(6).decode()
|
|
437
|
-
wfk.read(2)
|
|
438
|
-
self.headform = bytes2int(wfk.read(4))
|
|
439
|
-
self.fform = bytes2int(wfk.read(4))
|
|
440
|
-
wfk.read(8)
|
|
441
|
-
self.bandtot = bytes2int(wfk.read(4))
|
|
442
|
-
self.date = bytes2int(wfk.read(4))
|
|
443
|
-
self.intxc = bytes2int(wfk.read(4))
|
|
444
|
-
self.ixc = bytes2int(wfk.read(4))
|
|
445
|
-
self.natom = bytes2int(wfk.read(4))
|
|
446
|
-
self.ngfftx = bytes2int(wfk.read(4))
|
|
447
|
-
self.ngffty = bytes2int(wfk.read(4))
|
|
448
|
-
self.ngfftz = bytes2int(wfk.read(4))
|
|
449
|
-
self.nkpt = bytes2int(wfk.read(4))
|
|
450
|
-
self.nspden = bytes2int(wfk.read(4))
|
|
451
|
-
self.nspinor = bytes2int(wfk.read(4))
|
|
452
|
-
self.nsppol = bytes2int(wfk.read(4))
|
|
453
|
-
self.nsym = bytes2int(wfk.read(4))
|
|
454
|
-
self.npsp = bytes2int(wfk.read(4))
|
|
455
|
-
self.ntypat = bytes2int(wfk.read(4))
|
|
456
|
-
self.occopt = bytes2int(wfk.read(4))
|
|
457
|
-
self.pertcase = bytes2int(wfk.read(4))
|
|
458
|
-
self.usepaw = bytes2int(wfk.read(4))
|
|
459
|
-
#--------------#
|
|
460
|
-
# unpack doubles
|
|
461
|
-
self.ecut = bytes2float(wfk.read(8))
|
|
462
|
-
self.ecutdg = bytes2float(wfk.read(8))
|
|
463
|
-
self.ecutsm = bytes2float(wfk.read(8))
|
|
464
|
-
self.ecut_eff = bytes2float(wfk.read(8))
|
|
465
|
-
self.qptnx = bytes2float(wfk.read(8))
|
|
466
|
-
self.qptny = bytes2float(wfk.read(8))
|
|
467
|
-
self.qptnz = bytes2float(wfk.read(8))
|
|
468
|
-
rprimd_ax = bytes2float(wfk.read(8))
|
|
469
|
-
rprimd_ay = bytes2float(wfk.read(8))
|
|
470
|
-
rprimd_az = bytes2float(wfk.read(8))
|
|
471
|
-
rprimd_bx = bytes2float(wfk.read(8))
|
|
472
|
-
rprimd_by = bytes2float(wfk.read(8))
|
|
473
|
-
rprimd_bz = bytes2float(wfk.read(8))
|
|
474
|
-
rprimd_cx = bytes2float(wfk.read(8))
|
|
475
|
-
rprimd_cy = bytes2float(wfk.read(8))
|
|
476
|
-
rprimd_cz = bytes2float(wfk.read(8))
|
|
477
|
-
#------------------------#
|
|
478
|
-
# convert Bohr to Angstrom
|
|
479
|
-
self.real_lattice = 0.529177*np.array([
|
|
480
|
-
[rprimd_ax, rprimd_ay, rprimd_az],
|
|
481
|
-
[rprimd_bx, rprimd_by, rprimd_bz],
|
|
482
|
-
[rprimd_cx, rprimd_cy, rprimd_cz]
|
|
483
|
-
]).reshape((3,3))
|
|
484
|
-
self.stmbias = bytes2float(wfk.read(8))
|
|
485
|
-
self.tphysel = bytes2float(wfk.read(8))
|
|
486
|
-
self.tsmear = bytes2float(wfk.read(8))
|
|
487
|
-
#---------------#
|
|
488
|
-
# unpack integers
|
|
489
|
-
self.usewvl = bytes2int(wfk.read(4))
|
|
490
|
-
self.nshiftk_orig = bytes2int(wfk.read(4))
|
|
491
|
-
self.nshiftk = bytes2int(wfk.read(4))
|
|
492
|
-
self.mband = bytes2int(wfk.read(4))
|
|
493
|
-
wfk.read(8)
|
|
494
|
-
self.istwfk:list[int] = []
|
|
495
|
-
for _ in range(self.nkpt):
|
|
496
|
-
val = bytes2int(wfk.read(4))
|
|
497
|
-
self.istwfk.append(val)
|
|
498
|
-
self.bands:list[int] = []
|
|
499
|
-
for _ in range(self.nkpt*self.nsppol):
|
|
500
|
-
val = bytes2int(wfk.read(4))
|
|
501
|
-
self.bands.append(val)
|
|
502
|
-
self.npwarr:list[int] = []
|
|
503
|
-
for _ in range(self.nkpt):
|
|
504
|
-
val = bytes2int(wfk.read(4))
|
|
505
|
-
self.npwarr.append(val)
|
|
506
|
-
self.so_psp:list[int] = []
|
|
507
|
-
for _ in range(self.npsp):
|
|
508
|
-
val = bytes2int(wfk.read(4))
|
|
509
|
-
self.so_psp.append(val)
|
|
510
|
-
self.symafm:list[int] = []
|
|
511
|
-
for _ in range(self.nsym):
|
|
512
|
-
val = bytes2int(wfk.read(4))
|
|
513
|
-
self.symafm.append(val)
|
|
514
|
-
self.symrel:list[np.ndarray] = []
|
|
515
|
-
for _ in range(self.nsym):
|
|
516
|
-
arr = np.zeros((3,3))
|
|
517
|
-
arr[0,0] = bytes2int(wfk.read(4))
|
|
518
|
-
arr[1,0] = bytes2int(wfk.read(4))
|
|
519
|
-
arr[2,0] = bytes2int(wfk.read(4))
|
|
520
|
-
arr[0,1] = bytes2int(wfk.read(4))
|
|
521
|
-
arr[1,1] = bytes2int(wfk.read(4))
|
|
522
|
-
arr[2,1] = bytes2int(wfk.read(4))
|
|
523
|
-
arr[0,2] = bytes2int(wfk.read(4))
|
|
524
|
-
arr[1,2] = bytes2int(wfk.read(4))
|
|
525
|
-
arr[2,2] = bytes2int(wfk.read(4))
|
|
526
|
-
self.symrel.append(arr)
|
|
527
|
-
self.typat:list[int] = []
|
|
528
|
-
for _ in range(self.natom):
|
|
529
|
-
val = bytes2int(wfk.read(4))
|
|
530
|
-
self.typat.append(val)
|
|
531
|
-
#--------------#
|
|
532
|
-
# unpack doubles
|
|
533
|
-
self.kpts:list[np.ndarray] = []
|
|
534
|
-
for _ in range(self.nkpt):
|
|
535
|
-
vec = np.zeros(3)
|
|
536
|
-
vec[0] = bytes2float(wfk.read(8))
|
|
537
|
-
vec[1] = bytes2float(wfk.read(8))
|
|
538
|
-
vec[2] = bytes2float(wfk.read(8))
|
|
539
|
-
self.kpts.append(vec)
|
|
540
|
-
self.occ:list[float] = []
|
|
541
|
-
for _ in range(self.bandtot):
|
|
542
|
-
val = bytes2float(wfk.read(8))
|
|
543
|
-
self.occ.append(val)
|
|
544
|
-
self.tnons:list[np.ndarray] = []
|
|
545
|
-
for _ in range(self.nsym):
|
|
546
|
-
vec = np.zeros(3)
|
|
547
|
-
vec[0] = bytes2float(wfk.read(8))
|
|
548
|
-
vec[1] = bytes2float(wfk.read(8))
|
|
549
|
-
vec[2] = bytes2float(wfk.read(8))
|
|
550
|
-
self.tnons.append(vec)
|
|
551
|
-
self.znucltypat:list[float] = []
|
|
552
|
-
for _ in range(self.ntypat):
|
|
553
|
-
val = bytes2float(wfk.read(8))
|
|
554
|
-
self.znucltypat.append(val)
|
|
555
|
-
self.wtk:list[float] = []
|
|
556
|
-
for _ in range(self.nkpt):
|
|
557
|
-
val = bytes2float(wfk.read(8))
|
|
558
|
-
self.wtk.append(val)
|
|
559
|
-
#------------------#
|
|
560
|
-
# unpack coordinates
|
|
561
|
-
wfk.read(8)
|
|
562
|
-
self.residm = bytes2float(wfk.read(8))
|
|
563
|
-
self.xred:list[np.ndarray] = []
|
|
564
|
-
for _ in range(self.natom):
|
|
565
|
-
vec = np.zeros(3)
|
|
566
|
-
vec[0] = bytes2float(wfk.read(8))
|
|
567
|
-
vec[1] = bytes2float(wfk.read(8))
|
|
568
|
-
vec[2] = bytes2float(wfk.read(8))
|
|
569
|
-
self.xred.append(vec)
|
|
570
|
-
#------------------------------------#
|
|
571
|
-
# unpack total energy and fermi energy
|
|
572
|
-
self.etotal = bytes2float(wfk.read(8))
|
|
573
|
-
self.fermi = bytes2float(wfk.read(8))
|
|
574
|
-
#-------------#
|
|
575
|
-
# unpack floats
|
|
576
|
-
self.amu:list[float] = []
|
|
577
|
-
for _ in range(self.ntypat):
|
|
578
|
-
val = bytes2float(wfk.read(8))
|
|
579
|
-
self.amu.append(val)
|
|
580
|
-
#----------------------------#
|
|
581
|
-
# unpack reciprocal space info
|
|
582
|
-
wfk.read(8)
|
|
583
|
-
self.kptopt = bytes2int(wfk.read(4))
|
|
584
|
-
self.pawcpxocc = bytes2int(wfk.read(4))
|
|
585
|
-
self.nelect = bytes2float(wfk.read(8))
|
|
586
|
-
self.cellcharge = bytes2float(wfk.read(8))
|
|
587
|
-
self.icoulomb = bytes2int(wfk.read(4))
|
|
588
|
-
rec_latt_ax = bytes2int(wfk.read(4))
|
|
589
|
-
rec_latt_ay = bytes2int(wfk.read(4))
|
|
590
|
-
rec_latt_az = bytes2int(wfk.read(4))
|
|
591
|
-
rec_latt_bx = bytes2int(wfk.read(4))
|
|
592
|
-
rec_latt_by = bytes2int(wfk.read(4))
|
|
593
|
-
rec_latt_bz = bytes2int(wfk.read(4))
|
|
594
|
-
rec_latt_cx = bytes2int(wfk.read(4))
|
|
595
|
-
rec_latt_cy = bytes2int(wfk.read(4))
|
|
596
|
-
rec_latt_cz = bytes2int(wfk.read(4))
|
|
597
|
-
self.kptr_latt = np.array([
|
|
598
|
-
[rec_latt_ax, rec_latt_ay, rec_latt_az],
|
|
599
|
-
[rec_latt_bx, rec_latt_by, rec_latt_bz],
|
|
600
|
-
[rec_latt_cx, rec_latt_cy, rec_latt_cz]
|
|
601
|
-
]).reshape((3,3))
|
|
602
|
-
rec_latt_ax = bytes2int(wfk.read(4))
|
|
603
|
-
rec_latt_ay = bytes2int(wfk.read(4))
|
|
604
|
-
rec_latt_az = bytes2int(wfk.read(4))
|
|
605
|
-
rec_latt_bx = bytes2int(wfk.read(4))
|
|
606
|
-
rec_latt_by = bytes2int(wfk.read(4))
|
|
607
|
-
rec_latt_bz = bytes2int(wfk.read(4))
|
|
608
|
-
rec_latt_cx = bytes2int(wfk.read(4))
|
|
609
|
-
rec_latt_cy = bytes2int(wfk.read(4))
|
|
610
|
-
rec_latt_cz = bytes2int(wfk.read(4))
|
|
611
|
-
self.kptr_latt_orig = np.array([
|
|
612
|
-
[rec_latt_ax, rec_latt_ay, rec_latt_az],
|
|
613
|
-
[rec_latt_bx, rec_latt_by, rec_latt_bz],
|
|
614
|
-
[rec_latt_cx, rec_latt_cy, rec_latt_cz]
|
|
615
|
-
]).reshape((3,3))
|
|
616
|
-
shift_orig_x = bytes2float(wfk.read(8))
|
|
617
|
-
shift_orig_y = bytes2float(wfk.read(8))
|
|
618
|
-
shift_orig_z = bytes2float(wfk.read(8))
|
|
619
|
-
self.origin_shift = [shift_orig_x, shift_orig_y, shift_orig_z]
|
|
620
|
-
shift_kx = bytes2float(wfk.read(8))
|
|
621
|
-
shift_ky = bytes2float(wfk.read(8))
|
|
622
|
-
shift_kz = bytes2float(wfk.read(8))
|
|
623
|
-
self.kpt_shift = [shift_kx, shift_ky, shift_kz]
|
|
624
|
-
#-----------------------#
|
|
625
|
-
# unpack pseudopotentials
|
|
626
|
-
wfk.read(4)
|
|
627
|
-
self.title:list[str] = []
|
|
628
|
-
self.znuclpsp:list[float] = []
|
|
629
|
-
self.zionpsp:list[float] = []
|
|
630
|
-
self.pspso:list[int] = []
|
|
631
|
-
self.pspdat:list[int] = []
|
|
632
|
-
self.pspcod:list[int] = []
|
|
633
|
-
self.pspxc:list[int] = []
|
|
634
|
-
self.lmn_size:list[int] = []
|
|
635
|
-
self.md5_pseudos:list[str] = []
|
|
636
|
-
for _ in range(self.npsp):
|
|
637
|
-
wfk.read(4)
|
|
638
|
-
self.title.append(wfk.read(132).decode())
|
|
639
|
-
self.znuclpsp.append(bytes2float(wfk.read(8)))
|
|
640
|
-
self.zionpsp.append(bytes2float(wfk.read(8)))
|
|
641
|
-
self.pspso.append(bytes2int(wfk.read(4)))
|
|
642
|
-
self.pspdat.append(bytes2int(wfk.read(4)))
|
|
643
|
-
self.pspcod.append(bytes2int(wfk.read(4)))
|
|
644
|
-
self.pspxc.append(bytes2int(wfk.read(4)))
|
|
645
|
-
self.lmn_size.append(bytes2int(wfk.read(4)))
|
|
646
|
-
self.md5_pseudos.append(wfk.read(32).decode())
|
|
647
|
-
wfk.read(4)
|
|
648
|
-
#---------------#
|
|
649
|
-
# unpack PAW data
|
|
650
|
-
if self.usepaw == 1:
|
|
651
|
-
wfk.read(4)
|
|
652
|
-
self.nrho:list[int] = []
|
|
653
|
-
for _ in range(self.natom):
|
|
654
|
-
for _ in range(self.nspden):
|
|
655
|
-
nrhoij = bytes2int(wfk.read(4))
|
|
656
|
-
self.nrho.append(nrhoij)
|
|
657
|
-
self.cplex = bytes2int(wfk.read(4))
|
|
658
|
-
self.nspden_paw = bytes2int(wfk.read(4))
|
|
659
|
-
wfk.read(8)
|
|
660
|
-
self.irho:list[int] = []
|
|
661
|
-
for i in range(self.natom):
|
|
662
|
-
for _ in range(self.nspden_paw):
|
|
663
|
-
nrhoij = self.nrho[i]
|
|
664
|
-
for _ in range(nrhoij):
|
|
665
|
-
rhoij = bytes2int(wfk.read(4))
|
|
666
|
-
self.irho.append(rhoij)
|
|
667
|
-
wfk.read(4)
|
|
668
|
-
self.rho:list[float] = []
|
|
669
|
-
for i in range(self.natom):
|
|
670
|
-
for _ in range(self.nspden_paw):
|
|
671
|
-
nrhoij = self.nrho[i]
|
|
672
|
-
for _ in range(nrhoij):
|
|
673
|
-
rhoij = bytes2float(wfk.read(8))
|
|
674
|
-
self.rho.append(rhoij)
|
|
675
|
-
wfk.read(4)
|
|
676
|
-
print('WFK header read')
|
|
677
|
-
wfk.close()
|
|
678
|
-
#-----------------------------------------------------------------------------------------------------------------#
|
|
679
|
-
# check for time reversal symmetry
|
|
680
|
-
def _CheckTimeRev(
|
|
681
|
-
self
|
|
682
|
-
):
|
|
683
|
-
# if system is centrosymmetric, do not double reciprocal symmetry operations
|
|
684
|
-
if True in [np.array_equal(-np.identity(3),mat) for mat in self.symrel]:
|
|
685
|
-
self.time_reversal = False
|
|
686
|
-
else:
|
|
687
|
-
self.time_reversal = True
|
|
688
|
-
print((
|
|
689
|
-
'Noncentrosymmetric system identified, assuming time reversal symmetry\n'
|
|
690
|
-
'To change this, set "check_time_rev" keyword to False when calling ReadWFK() or ReadEigenvalues()'
|
|
691
|
-
))
|
|
692
|
-
#-----------------------------------------------------------------------------------------------------------------#
|
|
693
|
-
# method to read entire body of abinit version 7 wavefunction file
|
|
694
|
-
def ReadWFK(
|
|
695
|
-
self, energy_level=np.nan, width=np.nan, check_time_rev:bool=True
|
|
696
|
-
)->Generator[wc.WFK, None, None]:
|
|
697
|
-
'''
|
|
698
|
-
Method that constructs WFK objects from ABINIT v10 WFK file.
|
|
699
|
-
|
|
700
|
-
Parameters
|
|
701
|
-
----------
|
|
702
|
-
energy_level : float
|
|
703
|
-
The energy level to pull plane wave coefficients from
|
|
704
|
-
This is relative to the Fermi energy
|
|
705
|
-
If not defined but width is defined, default is 0 Hartree
|
|
706
|
-
|
|
707
|
-
width : float
|
|
708
|
-
Defines range about energy_level to search for plane wave coefficients
|
|
709
|
-
Total range is equal to width, so look width/2 above and below energy_level
|
|
710
|
-
If not defined but energy_level is defined, default is 0.005 Hartree
|
|
711
|
-
'''
|
|
712
|
-
# check for time reversal symmetry
|
|
713
|
-
if check_time_rev:
|
|
714
|
-
self._CheckTimeRev()
|
|
715
|
-
else:
|
|
716
|
-
self.time_reversal = False
|
|
717
|
-
# read wfk
|
|
718
|
-
wfk = open(self.filename, 'rb')
|
|
719
|
-
skip = True
|
|
720
|
-
if energy_level is np.nan:
|
|
721
|
-
if width is np.nan:
|
|
722
|
-
skip = False
|
|
723
|
-
else:
|
|
724
|
-
energy_level = 0
|
|
725
|
-
else:
|
|
726
|
-
if width is np.nan:
|
|
727
|
-
width = 0.005
|
|
728
|
-
#-----------#
|
|
729
|
-
# skip header
|
|
730
|
-
wfk.read(468)
|
|
731
|
-
wfk.read(4*(2*self.nkpt + self.nkpt*self.nsppol + self.npsp + 10*self.nsym + self.natom))
|
|
732
|
-
wfk.read(8*(4*self.nkpt + self.bandtot + 3*self.nsym + 2*self.ntypat + 3*self.natom))
|
|
733
|
-
wfk.read(self.npsp*(208))
|
|
734
|
-
if self.usepaw == 1:
|
|
735
|
-
wfk.read(4)
|
|
736
|
-
for _ in range(self.natom):
|
|
737
|
-
for _ in range(self.nspden):
|
|
738
|
-
_ = wfk.read(4)
|
|
739
|
-
wfk.read(4)
|
|
740
|
-
wfk.read(4)
|
|
741
|
-
wfk.read(8)
|
|
742
|
-
for i in range(self.natom):
|
|
743
|
-
for _ in range(self.nspden_paw):
|
|
744
|
-
nrhoij = self.nrho[i]
|
|
745
|
-
for _ in range(nrhoij):
|
|
746
|
-
_ = wfk.read(4)
|
|
747
|
-
wfk.read(4)
|
|
748
|
-
for i in range(self.natom):
|
|
749
|
-
for _ in range(self.nspden_paw):
|
|
750
|
-
nrhoij = self.nrho[i]
|
|
751
|
-
for _ in range(nrhoij):
|
|
752
|
-
_ = wfk.read(8)
|
|
753
|
-
wfk.read(4)
|
|
754
|
-
#-------------------------------#
|
|
755
|
-
# begin reading wavefunction body
|
|
756
|
-
for i in range(self.nsppol):
|
|
757
|
-
for j in range(self.nkpt):
|
|
758
|
-
print(f'Reading kpoint {j+1} of {self.nkpt}', end='\r')
|
|
759
|
-
if j+1 == self.nkpt:
|
|
760
|
-
print('\n', end='')
|
|
761
|
-
wfk.read(4)
|
|
762
|
-
npw = bytes2int(wfk.read(4))
|
|
763
|
-
self.nspinor = bytes2int(wfk.read(4))
|
|
764
|
-
nband_temp = bytes2int(wfk.read(4))
|
|
765
|
-
pw_indices = np.zeros((npw,3), dtype=int)
|
|
766
|
-
eigenvalues = np.zeros(nband_temp, dtype=float)
|
|
767
|
-
wfk.read(8)
|
|
768
|
-
for pw in range(npw):
|
|
769
|
-
kx = bytes2int(wfk.read(4))
|
|
770
|
-
ky = bytes2int(wfk.read(4))
|
|
771
|
-
kz = bytes2int(wfk.read(4))
|
|
772
|
-
pw_indices[pw,:] = [kx, ky, kz]
|
|
773
|
-
wfk.read(8)
|
|
774
|
-
for nband in range(nband_temp):
|
|
775
|
-
eigenval = bytes2float(wfk.read(8))
|
|
776
|
-
eigenvalues[nband] = eigenval
|
|
777
|
-
# skip reading coefficients if they energy level of interest is not in band
|
|
778
|
-
if skip:
|
|
779
|
-
min_val = self.fermi + energy_level - width/2
|
|
780
|
-
max_val = self.fermi + energy_level + width/2
|
|
781
|
-
eig_found = False
|
|
782
|
-
for eigval in eigenvalues:
|
|
783
|
-
if min_val <= eigval <= max_val:
|
|
784
|
-
eig_found = True
|
|
785
|
-
break
|
|
786
|
-
if eig_found:
|
|
787
|
-
yield self._ReadCoeffs(
|
|
788
|
-
wfk,
|
|
789
|
-
nband_temp,
|
|
790
|
-
npw,
|
|
791
|
-
eigenvalues,
|
|
792
|
-
pw_indices,
|
|
793
|
-
ind=j
|
|
794
|
-
)
|
|
795
|
-
else:
|
|
796
|
-
wfk.read(nband_temp*8)
|
|
797
|
-
wfk.read(4)
|
|
798
|
-
wfk.read(nband_temp*(8 + npw*16))
|
|
799
|
-
# if not skip, read full wavefunction
|
|
800
|
-
else:
|
|
801
|
-
yield self._ReadCoeffs(
|
|
802
|
-
wfk,
|
|
803
|
-
nband_temp,
|
|
804
|
-
npw,
|
|
805
|
-
eigenvalues,
|
|
806
|
-
pw_indices,
|
|
807
|
-
ind=j
|
|
808
|
-
)
|
|
809
|
-
print('WFK body read')
|
|
810
|
-
wfk.close()
|
|
811
|
-
#-----------------------------------------------------------------------------------------------------------------#
|
|
812
|
-
# method to read in plane wave coefficients
|
|
813
|
-
def _ReadCoeffs(
|
|
814
|
-
self, wfk_file, nbands, npws, eigs, pw_inds, ind
|
|
815
|
-
)->wc.WFK:
|
|
816
|
-
occupancies = np.zeros((1,nbands), dtype=float)
|
|
817
|
-
coeffs = np.zeros((nbands,npws), dtype=complex)
|
|
818
|
-
for nband in range(nbands):
|
|
819
|
-
occ = bytes2float(wfk_file.read(8))
|
|
820
|
-
occupancies[:,nband] = occ
|
|
821
|
-
wfk_file.read(4)
|
|
822
|
-
for nband in range(nbands):
|
|
823
|
-
wfk_file.read(4)
|
|
824
|
-
cg:np.ndarray = np.zeros((1,npws), dtype=complex)
|
|
825
|
-
for pw in range(npws):
|
|
826
|
-
cg1 = bytes2float(wfk_file.read(8))
|
|
827
|
-
cg2 = bytes2float(wfk_file.read(8))
|
|
828
|
-
cg[:,pw] = cg1 + 1j*cg2
|
|
829
|
-
coeffs[nband,:] = cg
|
|
830
|
-
wfk_file.read(4)
|
|
831
|
-
return wc.WFK(
|
|
832
|
-
eigenvalues=np.array(eigs),
|
|
833
|
-
wfk_coeffs=np.array(coeffs),
|
|
834
|
-
pw_indices=np.array(pw_inds),
|
|
835
|
-
kpoints=np.array(self.kpts[ind]),
|
|
836
|
-
nkpt=self.nkpt,
|
|
837
|
-
nbands=self.bands[0],
|
|
838
|
-
ngfftx=self.ngfftx,
|
|
839
|
-
ngffty=self.ngffty,
|
|
840
|
-
ngfftz=self.ngfftz,
|
|
841
|
-
symrel=np.array(self.symrel),
|
|
842
|
-
nsym=self.nsym,
|
|
843
|
-
lattice=self.real_lattice,
|
|
844
|
-
natom=self.natom,
|
|
845
|
-
xred=np.array(self.xred),
|
|
846
|
-
typat=self.typat,
|
|
847
|
-
znucltypat=self.znucltypat,
|
|
848
|
-
fermi_energy=self.fermi,
|
|
849
|
-
non_symm_vecs=np.array(self.tnons),
|
|
850
|
-
time_reversal=self.time_reversal
|
|
851
|
-
)
|
|
852
|
-
#-----------------------------------------------------------------------------------------------------------------#
|
|
853
|
-
# method to read only eigenvalues from body of abinit version 10 wavefunction file
|
|
854
|
-
def ReadEigenvalues(
|
|
855
|
-
self, check_time_rev:bool=True
|
|
856
|
-
)->Generator[wc.WFK, None, None]:
|
|
857
|
-
'''
|
|
858
|
-
Method that constructs WFK objects from ABINIT v10 WFK file.
|
|
859
|
-
'''
|
|
860
|
-
# check for time reversal symmetry
|
|
861
|
-
if check_time_rev:
|
|
862
|
-
self._CheckTimeRev()
|
|
863
|
-
else:
|
|
864
|
-
self.time_reversal = False
|
|
865
|
-
# read wfk
|
|
866
|
-
wfk = open(self.filename, 'rb')
|
|
867
|
-
#-----------#
|
|
868
|
-
# skip header
|
|
869
|
-
wfk.read(468)
|
|
870
|
-
wfk.read(4*(2*self.nkpt + self.nkpt*self.nsppol + self.npsp + 10*self.nsym + self.natom))
|
|
871
|
-
wfk.read(8*(4*self.nkpt + self.bandtot + 3*self.nsym + 2*self.ntypat + 3*self.natom))
|
|
872
|
-
wfk.read(self.npsp*(208))
|
|
873
|
-
if self.usepaw == 1:
|
|
874
|
-
wfk.read(4)
|
|
875
|
-
for _ in range(self.natom):
|
|
876
|
-
for _ in range(self.nspden):
|
|
877
|
-
_ = wfk.read(4)
|
|
878
|
-
wfk.read(4)
|
|
879
|
-
wfk.read(4)
|
|
880
|
-
wfk.read(8)
|
|
881
|
-
for i in range(self.natom):
|
|
882
|
-
for _ in range(self.nspden_paw):
|
|
883
|
-
nrhoij = self.nrho[i]
|
|
884
|
-
for _ in range(nrhoij):
|
|
885
|
-
_ = wfk.read(4)
|
|
886
|
-
wfk.read(4)
|
|
887
|
-
for i in range(self.natom):
|
|
888
|
-
for _ in range(self.nspden_paw):
|
|
889
|
-
nrhoij = self.nrho[i]
|
|
890
|
-
for _ in range(nrhoij):
|
|
891
|
-
_ = wfk.read(8)
|
|
892
|
-
wfk.read(4)
|
|
893
|
-
#-------------------------------#
|
|
894
|
-
# begin reading wavefunction body
|
|
895
|
-
for i in range(self.nsppol):
|
|
896
|
-
for j in range(self.nkpt):
|
|
897
|
-
print(f'Reading kpoint {j+1} of {self.nkpt}', end='\r')
|
|
898
|
-
if j+1 == self.nkpt:
|
|
899
|
-
print('\n', end='')
|
|
900
|
-
wfk.read(4)
|
|
901
|
-
npw = bytes2int(wfk.read(4))
|
|
902
|
-
self.nspinor = bytes2int(wfk.read(4))
|
|
903
|
-
nband_temp = bytes2int(wfk.read(4))
|
|
904
|
-
eigenvalues = np.zeros((1,nband_temp), dtype=float)
|
|
905
|
-
wfk.read(8)
|
|
906
|
-
wfk.read(12*npw)
|
|
907
|
-
wfk.read(8)
|
|
908
|
-
#------------------------------------------------------------------#
|
|
909
|
-
# only need eigenvalues for Fermi surface, skip over everything else
|
|
910
|
-
for nband in range(nband_temp):
|
|
911
|
-
eigenval = bytes2float(wfk.read(8))
|
|
912
|
-
eigenvalues[:,nband] = eigenval
|
|
913
|
-
wfk.read(nband_temp*8)
|
|
914
|
-
wfk.read(4)
|
|
915
|
-
wfk.read(nband_temp*(8 + npw*16))
|
|
916
|
-
yield wc.WFK(
|
|
917
|
-
eigenvalues=np.array(eigenvalues),
|
|
918
|
-
kpoints=np.array(self.kpts[j]),
|
|
919
|
-
nkpt=self.nkpt,
|
|
920
|
-
nbands=self.bands[0],
|
|
921
|
-
ngfftx=self.ngfftx,
|
|
922
|
-
ngffty=self.ngffty,
|
|
923
|
-
ngfftz=self.ngfftz,
|
|
924
|
-
symrel=np.array(self.symrel),
|
|
925
|
-
nsym=self.nsym,
|
|
926
|
-
lattice=self.real_lattice,
|
|
927
|
-
natom=self.natom,
|
|
928
|
-
xred=np.array(self.xred),
|
|
929
|
-
typat=self.typat,
|
|
930
|
-
znucltypat=self.znucltypat,
|
|
931
|
-
fermi_energy=self.fermi,
|
|
932
|
-
non_symm_vecs=np.array(self.tnons),
|
|
933
|
-
time_reversal=self.time_reversal
|
|
934
|
-
)
|
|
935
|
-
print('WFK body read')
|
|
936
|
-
wfk.close()
|
|
937
|
-
|
|
938
|
-
#---------------------------------------------------------------------------------------------------------------------#
|
|
939
|
-
#----------------------------------------------------- END CLASS -----------------------------------------------------#
|
|
940
|
-
#---------------------------------------------------------------------------------------------------------------------#
|
|
941
|
-
|
|
942
|
-
class AbinitNetCDF():
|
|
943
|
-
def __init__(
|
|
944
|
-
self, filename:str
|
|
945
|
-
):
|
|
946
|
-
print('WFK found with netCDF4 format')
|
|
947
|
-
self.filename = filename
|
|
948
|
-
self.dataset = self._GetDataset()
|
|
949
|
-
self.kpts:np.ndarray = self.dataset.variables['reduced_coordinates_of_kpoints'][:]
|
|
950
|
-
self.nkpt:int = self.dataset.dimensions['number_of_kpoints'].size
|
|
951
|
-
self.xred:np.ndarray = self.dataset.variables['reduced_atom_positions'][:]
|
|
952
|
-
self.natom:int = self.dataset.dimensions['number_of_atoms'].size
|
|
953
|
-
self.tnons:np.ndarray = self.dataset.variables['reduced_symmetry_translations'][:]
|
|
954
|
-
self.symrel:np.ndarray = self.dataset.variables['reduced_symmetry_matrices'][:]
|
|
955
|
-
self.symrel = np.array([op.T for op in self.symrel])
|
|
956
|
-
self.nsym:int = self.dataset.dimensions['number_of_symmetry_operations'].size
|
|
957
|
-
self.fermi:float = self.dataset['fermi_energy'][:]
|
|
958
|
-
self.real_lattice:np.ndarray = self.dataset['primitive_vectors'][:]
|
|
959
|
-
self.real_lattice *= 0.529177
|
|
960
|
-
self.ngfftx:int = self.dataset.dimensions['number_of_grid_points_vector1'].size
|
|
961
|
-
self.ngffty:int = self.dataset.dimensions['number_of_grid_points_vector2'].size
|
|
962
|
-
self.ngfftz:int = self.dataset.dimensions['number_of_grid_points_vector3'].size
|
|
963
|
-
self.nband:int = int(self.dataset.dimensions['bantot'].size / self.nkpt)
|
|
964
|
-
self.typat:list = self.dataset.variables['atom_species'][:].tolist()
|
|
965
|
-
self.zion:np.ndarray = self.dataset.variables['atomic_numbers'][:]
|
|
966
|
-
self.znucltypat:list = [int(nuc) for nuc in self.zion]
|
|
967
|
-
self.bands = [self.nband]
|
|
968
|
-
#---------------------------------------------------------------------------------------------------------------------#
|
|
969
|
-
#------------------------------------------------------ METHODS ------------------------------------------------------#
|
|
970
|
-
#---------------------------------------------------------------------------------------------------------------------#
|
|
971
|
-
# create netCDF dataset
|
|
972
|
-
def _GetDataset(
|
|
973
|
-
self
|
|
974
|
-
):
|
|
975
|
-
from netCDF4 import Dataset
|
|
976
|
-
return Dataset(self.filename,format='NETCDF4')
|
|
977
|
-
#-----------------------------------------------------------------------------------------------------------------#
|
|
978
|
-
# check for time reversal symmetry
|
|
979
|
-
def _CheckTimeRev(
|
|
980
|
-
self
|
|
981
|
-
):
|
|
982
|
-
# if system is centrosymmetric, do not double reciprocal symmetry operations
|
|
983
|
-
if True in [np.array_equal(-np.identity(3),mat) for mat in self.symrel]:
|
|
984
|
-
self.time_reversal = False
|
|
985
|
-
else:
|
|
986
|
-
self.time_reversal = True
|
|
987
|
-
print((
|
|
988
|
-
'Noncentrosymmetric system identified, assuming time reversal symmetry\n'
|
|
989
|
-
'To change this, set "check_time_rev" keyword to False when calling ReadWFK() or ReadEigenvalues()'
|
|
990
|
-
))
|
|
991
|
-
#-----------------------------------------------------------------------------------------------------------------#
|
|
992
|
-
# fetch wavefunction coefficients from netcdf dataset
|
|
993
|
-
def ReadWFK(
|
|
994
|
-
self, energy_level:float=np.nan, width:float=np.nan, check_time_rev:bool=True
|
|
995
|
-
)->Generator[wc.WFK, None, None]:
|
|
996
|
-
# check for time reversal symmetry
|
|
997
|
-
if check_time_rev:
|
|
998
|
-
self._CheckTimeRev()
|
|
999
|
-
else:
|
|
1000
|
-
self.time_reversal = False
|
|
1001
|
-
eigs:np.ndarray = self.dataset.variables['eigenvalues'][:][0]
|
|
1002
|
-
pw_inds:np.ndarray = self.dataset.variables['reduced_coordinates_of_plane_waves'][:]
|
|
1003
|
-
# restructure wavefunction coefficients
|
|
1004
|
-
for kpt in range(self.nkpt):
|
|
1005
|
-
print(f'Reading kpoint {kpt+1} of {self.nkpt}', end='\r')
|
|
1006
|
-
kpt_coeffs = []
|
|
1007
|
-
# format plane wave indices
|
|
1008
|
-
kpt_pw_inds = pw_inds[kpt]
|
|
1009
|
-
kpt_pw_inds = kpt_pw_inds[~kpt_pw_inds.mask]
|
|
1010
|
-
kpt_pw_inds = kpt_pw_inds.reshape((-1,3))
|
|
1011
|
-
kpt_pw_inds = np.ma.getdata(kpt_pw_inds)
|
|
1012
|
-
coeffs = self.dataset.variables['coefficients_of_wavefunctions'][0,kpt]
|
|
1013
|
-
for band in coeffs:
|
|
1014
|
-
band = band[0]
|
|
1015
|
-
band = band[~band.mask]
|
|
1016
|
-
band = band.reshape((-1,2))
|
|
1017
|
-
band = np.ma.getdata(band)
|
|
1018
|
-
kpt_coeffs.append(band[:,0] + 1j*band[:,1])
|
|
1019
|
-
yield wc.WFK(
|
|
1020
|
-
eigenvalues=eigs[kpt,:],
|
|
1021
|
-
wfk_coeffs=np.array(kpt_coeffs),
|
|
1022
|
-
pw_indices=kpt_pw_inds,
|
|
1023
|
-
kpoints=self.kpts[kpt],
|
|
1024
|
-
nkpt=self.nkpt,
|
|
1025
|
-
nbands=self.nband,
|
|
1026
|
-
ngfftx=self.ngfftx,
|
|
1027
|
-
ngffty=self.ngffty,
|
|
1028
|
-
ngfftz=self.ngfftz,
|
|
1029
|
-
symrel=self.symrel,
|
|
1030
|
-
nsym=self.nsym,
|
|
1031
|
-
lattice=self.real_lattice,
|
|
1032
|
-
natom=self.natom,
|
|
1033
|
-
xred=self.xred,
|
|
1034
|
-
typat=self.typat,
|
|
1035
|
-
znucltypat=self.znucltypat,
|
|
1036
|
-
fermi_energy=self.fermi,
|
|
1037
|
-
non_symm_vecs=self.tnons,
|
|
1038
|
-
time_reversal=self.time_reversal
|
|
1039
|
-
)
|
|
1040
|
-
#-----------------------------------------------------------------------------------------------------------------#
|
|
1041
|
-
# fetch eigenvalues from netcdf dataset
|
|
1042
|
-
def ReadEigenvalues(
|
|
1043
|
-
self, energy_level:float=np.nan, width:float=np.nan, check_time_rev:bool=True
|
|
1044
|
-
)->Generator[wc.WFK, None, None]:
|
|
1045
|
-
# check for time reversal symmetry
|
|
1046
|
-
if check_time_rev:
|
|
1047
|
-
self._CheckTimeRev()
|
|
1048
|
-
else:
|
|
1049
|
-
self.time_reversal = False
|
|
1050
|
-
eigs:np.ndarray = self.dataset.variables['eigenvalues'][:][0]
|
|
1051
|
-
for i, kpt in enumerate(self.kpts):
|
|
1052
|
-
print(f'Reading kpoint {i+1} of {self.nkpt}', end='\r')
|
|
1053
|
-
yield wc.WFK(
|
|
1054
|
-
eigenvalues=eigs[i,:],
|
|
1055
|
-
kpoints=kpt,
|
|
1056
|
-
nkpt=self.nkpt,
|
|
1057
|
-
nbands=self.nband,
|
|
1058
|
-
ngfftx=self.ngfftx,
|
|
1059
|
-
ngffty=self.ngffty,
|
|
1060
|
-
ngfftz=self.ngfftz,
|
|
1061
|
-
symrel=self.symrel,
|
|
1062
|
-
nsym=self.nsym,
|
|
1063
|
-
lattice=self.real_lattice,
|
|
1064
|
-
natom=self.natom,
|
|
1065
|
-
xred=self.xred,
|
|
1066
|
-
typat=self.typat,
|
|
1067
|
-
znucltypat=self.znucltypat,
|
|
1068
|
-
fermi_energy=self.fermi,
|
|
1069
|
-
non_symm_vecs=self.tnons,
|
|
1070
|
-
time_reversal=self.time_reversal
|
|
1071
|
-
)
|
|
1072
|
-
|
|
1073
|
-
#---------------------------------------------------------------------------------------------------------------------#
|
|
1074
|
-
#----------------------------------------------------- END CLASS -----------------------------------------------------#
|
|
1075
|
-
#---------------------------------------------------------------------------------------------------------------------#
|
|
1076
|
-
|
|
1077
|
-
def AbinitWFK(
|
|
1078
|
-
filename:str
|
|
1079
|
-
)->Union[Abinit10WFK, Abinit7WFK, AbinitNetCDF]:
|
|
1080
|
-
'''
|
|
1081
|
-
A function for identifying ABINIT version and constructing respective AbinitWFK object.
|
|
1082
|
-
'''
|
|
1083
|
-
if filename.endswith('.nc'):
|
|
1084
|
-
return AbinitNetCDF(filename)
|
|
1085
|
-
wfk = open(filename, 'rb')
|
|
1086
|
-
wfk.read(4)
|
|
1087
|
-
version = wfk.read(6).decode()
|
|
1088
|
-
wfk.close()
|
|
1089
|
-
if version.strip().split('.')[0] == '7':
|
|
1090
|
-
return Abinit7WFK(filename)
|
|
1091
|
-
elif version.strip().split('.')[0] == '10':
|
|
1092
|
-
return Abinit10WFK(filename)
|
|
1093
|
-
else:
|
|
1094
|
-
print(f'Version {version} may not be supported, attempting to analyze with v10 procedure.')
|
|
1
|
+
import struct
|
|
2
|
+
import numpy as np
|
|
3
|
+
from typing import Generator, Union
|
|
4
|
+
import sys
|
|
5
|
+
from . import wfk_class as wc
|
|
6
|
+
np.set_printoptions(threshold=sys.maxsize)
|
|
7
|
+
|
|
8
|
+
def bytes2float(bin_data)->float:
|
|
9
|
+
return struct.unpack('<d', bin_data)[0]
|
|
10
|
+
|
|
11
|
+
def bytes2int(bin_data)->int:
|
|
12
|
+
return int.from_bytes(bin_data, 'little', signed=True)
|
|
13
|
+
|
|
14
|
+
class Abinit7WFK():
|
|
15
|
+
def __init__(
|
|
16
|
+
self, filename:str
|
|
17
|
+
):
|
|
18
|
+
self.filename = filename
|
|
19
|
+
self._ReadHeader()
|
|
20
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
21
|
+
#------------------------------------------------------ METHODS ------------------------------------------------------#
|
|
22
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
23
|
+
# method to read wavefunction header for abinit version 7
|
|
24
|
+
def _ReadHeader(
|
|
25
|
+
self
|
|
26
|
+
)->None:
|
|
27
|
+
wfk = open(self.filename, 'rb')
|
|
28
|
+
print('Reading WFK header')
|
|
29
|
+
#---------------#
|
|
30
|
+
# unpack integers
|
|
31
|
+
self.header = bytes2int(wfk.read(4))
|
|
32
|
+
self.version = wfk.read(6).decode()
|
|
33
|
+
self.headform = bytes2int(wfk.read(4))
|
|
34
|
+
self.fform = bytes2int(wfk.read(4))
|
|
35
|
+
wfk.read(8)
|
|
36
|
+
self.bandtot = bytes2int(wfk.read(4))
|
|
37
|
+
self.date = bytes2int(wfk.read(4))
|
|
38
|
+
self.intxc = bytes2int(wfk.read(4))
|
|
39
|
+
self.ixc = bytes2int(wfk.read(4))
|
|
40
|
+
self.natom = bytes2int(wfk.read(4))
|
|
41
|
+
self.ngfftx = bytes2int(wfk.read(4))
|
|
42
|
+
self.ngffty = bytes2int(wfk.read(4))
|
|
43
|
+
self.ngfftz = bytes2int(wfk.read(4))
|
|
44
|
+
self.nkpt = bytes2int(wfk.read(4))
|
|
45
|
+
self.nspden = bytes2int(wfk.read(4))
|
|
46
|
+
self.nspinor = bytes2int(wfk.read(4))
|
|
47
|
+
self.nsppol = bytes2int(wfk.read(4))
|
|
48
|
+
self.nsym = bytes2int(wfk.read(4))
|
|
49
|
+
self.npsp = bytes2int(wfk.read(4))
|
|
50
|
+
self.ntypat = bytes2int(wfk.read(4))
|
|
51
|
+
self.occopt = bytes2int(wfk.read(4))
|
|
52
|
+
self.pertcase = bytes2int(wfk.read(4))
|
|
53
|
+
self.usepaw = bytes2int(wfk.read(4))
|
|
54
|
+
if self.usepaw == 1:
|
|
55
|
+
raise NotImplementedError(
|
|
56
|
+
f'''PAW potentials are not supported by this program for Abinit v{self.version}.
|
|
57
|
+
This program supports PAW potentials in Abinit v10, consider upgrading to the latest version.
|
|
58
|
+
'''
|
|
59
|
+
)
|
|
60
|
+
#--------------#
|
|
61
|
+
# unpack doubles
|
|
62
|
+
self.ecut = bytes2float(wfk.read(8))
|
|
63
|
+
self.ecutdg = bytes2float(wfk.read(8))
|
|
64
|
+
self.ecutsm = bytes2float(wfk.read(8))
|
|
65
|
+
self.ecut_eff = bytes2float(wfk.read(8))
|
|
66
|
+
self.qptnx = bytes2float(wfk.read(8))
|
|
67
|
+
self.qptny = bytes2float(wfk.read(8))
|
|
68
|
+
self.qptnz = bytes2float(wfk.read(8))
|
|
69
|
+
rprimd_ax = bytes2float(wfk.read(8))
|
|
70
|
+
rprimd_ay = bytes2float(wfk.read(8))
|
|
71
|
+
rprimd_az = bytes2float(wfk.read(8))
|
|
72
|
+
rprimd_bx = bytes2float(wfk.read(8))
|
|
73
|
+
rprimd_by = bytes2float(wfk.read(8))
|
|
74
|
+
rprimd_bz = bytes2float(wfk.read(8))
|
|
75
|
+
rprimd_cx = bytes2float(wfk.read(8))
|
|
76
|
+
rprimd_cy = bytes2float(wfk.read(8))
|
|
77
|
+
rprimd_cz = bytes2float(wfk.read(8))
|
|
78
|
+
#------------------------#
|
|
79
|
+
# convert Bohr to Angstrom
|
|
80
|
+
self.real_lattice = 0.529177*np.array([[rprimd_ax, rprimd_ay, rprimd_az],
|
|
81
|
+
[rprimd_bx, rprimd_by, rprimd_bz],
|
|
82
|
+
[rprimd_cx, rprimd_cy, rprimd_cz]]).reshape((3,3))
|
|
83
|
+
self.stmbias = bytes2float(wfk.read(8))
|
|
84
|
+
self.tphysel = bytes2float(wfk.read(8))
|
|
85
|
+
self.tsmear = bytes2float(wfk.read(8))
|
|
86
|
+
#---------------#
|
|
87
|
+
# unpack integers
|
|
88
|
+
self.usewvl = bytes2int(wfk.read(4))
|
|
89
|
+
wfk.read(8)
|
|
90
|
+
self.istwfk:list[int] = []
|
|
91
|
+
for i in range(self.nkpt):
|
|
92
|
+
val = bytes2int(wfk.read(4))
|
|
93
|
+
self.istwfk.append(val)
|
|
94
|
+
self.bands:list[int] = []
|
|
95
|
+
for i in range(self.nkpt*self.nsppol):
|
|
96
|
+
val = bytes2int(wfk.read(4))
|
|
97
|
+
self.bands.append(val)
|
|
98
|
+
self.npwarr:list[int] = []
|
|
99
|
+
for i in range(self.nkpt):
|
|
100
|
+
val = bytes2int(wfk.read(4))
|
|
101
|
+
self.npwarr.append(val)
|
|
102
|
+
self.so_psp:list[int] = []
|
|
103
|
+
for i in range(self.npsp):
|
|
104
|
+
val = bytes2int(wfk.read(4))
|
|
105
|
+
self.so_psp.append(val)
|
|
106
|
+
self.symafm:list[int] = []
|
|
107
|
+
for i in range(self.nsym):
|
|
108
|
+
val = bytes2int(wfk.read(4))
|
|
109
|
+
self.symafm.append(val)
|
|
110
|
+
self.symrel:list[np.ndarray] = []
|
|
111
|
+
for i in range(self.nsym):
|
|
112
|
+
arr = np.zeros((3,3))
|
|
113
|
+
arr[0,0] = bytes2int(wfk.read(4))
|
|
114
|
+
arr[1,0] = bytes2int(wfk.read(4))
|
|
115
|
+
arr[2,0] = bytes2int(wfk.read(4))
|
|
116
|
+
arr[0,1] = bytes2int(wfk.read(4))
|
|
117
|
+
arr[1,1] = bytes2int(wfk.read(4))
|
|
118
|
+
arr[2,1] = bytes2int(wfk.read(4))
|
|
119
|
+
arr[0,2] = bytes2int(wfk.read(4))
|
|
120
|
+
arr[1,2] = bytes2int(wfk.read(4))
|
|
121
|
+
arr[2,2] = bytes2int(wfk.read(4))
|
|
122
|
+
self.symrel.append(arr)
|
|
123
|
+
self.typat:list[int] = []
|
|
124
|
+
for i in range(self.natom):
|
|
125
|
+
val = bytes2int(wfk.read(4))
|
|
126
|
+
self.typat.append(val)
|
|
127
|
+
#--------------#
|
|
128
|
+
# unpack doubles
|
|
129
|
+
self.kpts:list[np.ndarray] = []
|
|
130
|
+
for i in range(self.nkpt):
|
|
131
|
+
vec = np.zeros(3)
|
|
132
|
+
vec[0] = bytes2float(wfk.read(8))
|
|
133
|
+
vec[1] = bytes2float(wfk.read(8))
|
|
134
|
+
vec[2] = bytes2float(wfk.read(8))
|
|
135
|
+
self.kpts.append(vec)
|
|
136
|
+
self.occ:list[float] = []
|
|
137
|
+
for i in range(self.bandtot):
|
|
138
|
+
val = bytes2float(wfk.read(8))
|
|
139
|
+
self.occ.append(val)
|
|
140
|
+
self.tnons:list[np.ndarray] = []
|
|
141
|
+
for i in range(self.nsym):
|
|
142
|
+
vec = np.zeros(3)
|
|
143
|
+
vec[0] = bytes2float(wfk.read(8))
|
|
144
|
+
vec[1] = bytes2float(wfk.read(8))
|
|
145
|
+
vec[2] = bytes2float(wfk.read(8))
|
|
146
|
+
self.tnons.append(vec)
|
|
147
|
+
self.znucltypat:list[float] = []
|
|
148
|
+
for i in range(self.ntypat):
|
|
149
|
+
val = bytes2float(wfk.read(8))
|
|
150
|
+
self.znucltypat.append(val)
|
|
151
|
+
self.wtk:list[float] = []
|
|
152
|
+
for i in range(self.nkpt):
|
|
153
|
+
val = bytes2float(wfk.read(8))
|
|
154
|
+
self.wtk.append(val)
|
|
155
|
+
#-----------------------#
|
|
156
|
+
# unpack pseudopotentials
|
|
157
|
+
wfk.read(4)
|
|
158
|
+
self.title:list[str] = []
|
|
159
|
+
self.znuclpsp:list[float] = []
|
|
160
|
+
self.zionpsp:list[float] = []
|
|
161
|
+
self.pspso:list[int] = []
|
|
162
|
+
self.pspdat:list[int] = []
|
|
163
|
+
self.pspcod:list[int] = []
|
|
164
|
+
self.pspxc:list[int] = []
|
|
165
|
+
self.lmn_size:list[int] = []
|
|
166
|
+
for i in range(self.npsp):
|
|
167
|
+
wfk.read(4)
|
|
168
|
+
self.title.append(wfk.read(132).decode())
|
|
169
|
+
self.znuclpsp.append(bytes2float(wfk.read(8)))
|
|
170
|
+
self.zionpsp.append(bytes2float(wfk.read(8)))
|
|
171
|
+
self.pspso.append(bytes2int(wfk.read(4)))
|
|
172
|
+
self.pspdat.append(bytes2int(wfk.read(4)))
|
|
173
|
+
self.pspcod.append(bytes2int(wfk.read(4)))
|
|
174
|
+
self.pspxc.append(bytes2int(wfk.read(4)))
|
|
175
|
+
self.lmn_size.append(bytes2int(wfk.read(4)))
|
|
176
|
+
wfk.read(4)
|
|
177
|
+
#------------------#
|
|
178
|
+
# unpack coordinates
|
|
179
|
+
wfk.read(4)
|
|
180
|
+
self.residm = bytes2float(wfk.read(8))
|
|
181
|
+
self.xred:list[np.ndarray] = []
|
|
182
|
+
for i in range(self.natom):
|
|
183
|
+
vec = np.zeros(3)
|
|
184
|
+
vec[0] = bytes2float(wfk.read(8))
|
|
185
|
+
vec[1] = bytes2float(wfk.read(8))
|
|
186
|
+
vec[2] = bytes2float(wfk.read(8))
|
|
187
|
+
self.xred.append(vec)
|
|
188
|
+
#------------------------------------#
|
|
189
|
+
# unpack total energy and fermi energy
|
|
190
|
+
self.etotal = bytes2float(wfk.read(8))
|
|
191
|
+
self.fermi = bytes2float(wfk.read(8))
|
|
192
|
+
wfk.read(4)
|
|
193
|
+
print('WFK header read')
|
|
194
|
+
wfk.close()
|
|
195
|
+
#-----------------------------------------------------------------------------------------------------------------#
|
|
196
|
+
# check for time reversal symmetry
|
|
197
|
+
def _CheckTimeRev(
|
|
198
|
+
self
|
|
199
|
+
):
|
|
200
|
+
# if system is centrosymmetric, do not double reciprocal symmetry operations
|
|
201
|
+
if True in [np.array_equal(-np.identity(3),mat) for mat in self.symrel]:
|
|
202
|
+
self.time_reversal = False
|
|
203
|
+
else:
|
|
204
|
+
self.time_reversal = True
|
|
205
|
+
print((
|
|
206
|
+
'Noncentrosymmetric system identified, assuming time reversal symmetry\n'
|
|
207
|
+
'To change this, set "check_time_rev" keyword to False when calling ReadWFK() or ReadEigenvalues()'
|
|
208
|
+
))
|
|
209
|
+
#-----------------------------------------------------------------------------------------------------------------#
|
|
210
|
+
# method to read entire body of abinit version 7 wavefunction file
|
|
211
|
+
def ReadWFK(
|
|
212
|
+
self, energy_level=np.nan, width=np.nan, check_time_rev:bool=True
|
|
213
|
+
)->Generator[wc.WFK, None, None]:
|
|
214
|
+
'''
|
|
215
|
+
Method that constructs WFK objects from ABINIT v7 WFK file
|
|
216
|
+
|
|
217
|
+
Parameters
|
|
218
|
+
----------
|
|
219
|
+
energy_level : float
|
|
220
|
+
The energy level to pull plane wave coefficients from
|
|
221
|
+
This is relative to the Fermi energy
|
|
222
|
+
If not defined but width is defined, default is 0 Hartree
|
|
223
|
+
|
|
224
|
+
width : float
|
|
225
|
+
Defines range about energy_level to search for plane wave coefficients
|
|
226
|
+
Total range is equal to width, so look width/2 above and below energy_level
|
|
227
|
+
If not defined but energy_level is defined, default is 0.005 Hartree
|
|
228
|
+
'''
|
|
229
|
+
# check for time reversal symmetry
|
|
230
|
+
if check_time_rev:
|
|
231
|
+
self._CheckTimeRev()
|
|
232
|
+
else:
|
|
233
|
+
self.time_reversal = False
|
|
234
|
+
# read wfk file
|
|
235
|
+
wfk = open(self.filename, 'rb')
|
|
236
|
+
skip = True
|
|
237
|
+
if energy_level is np.nan:
|
|
238
|
+
if width is np.nan:
|
|
239
|
+
skip = False
|
|
240
|
+
else:
|
|
241
|
+
energy_level = 0
|
|
242
|
+
else:
|
|
243
|
+
if width is np.nan:
|
|
244
|
+
width = 0.005
|
|
245
|
+
#-----------#
|
|
246
|
+
# skip header
|
|
247
|
+
wfk.read(298)
|
|
248
|
+
wfk.read(4*(2*self.nkpt + self.nkpt*self.nsppol + self.npsp + 10*self.nsym + self.natom))
|
|
249
|
+
wfk.read(8*(4*self.nkpt + self.bandtot + 3*self.nsym + self.ntypat + 3*self.natom))
|
|
250
|
+
wfk.read(self.npsp*(176))
|
|
251
|
+
#-------------------------------#
|
|
252
|
+
# begin reading wavefunction body
|
|
253
|
+
for i in range(self.nsppol):
|
|
254
|
+
for j in range(self.nkpt):
|
|
255
|
+
print(f'Reading kpoint {j+1} of {self.nkpt}', end='\r')
|
|
256
|
+
if j+1 == self.nkpt:
|
|
257
|
+
print('\n', end='')
|
|
258
|
+
pw_indices:list[tuple] = []
|
|
259
|
+
eigenvalues:list[float] = []
|
|
260
|
+
wfk.read(4)
|
|
261
|
+
npw = bytes2int(wfk.read(4))
|
|
262
|
+
self.nspinor = bytes2int(wfk.read(4))
|
|
263
|
+
nband_temp = bytes2int(wfk.read(4))
|
|
264
|
+
wfk.read(8)
|
|
265
|
+
for pw in range(npw):
|
|
266
|
+
kx = bytes2int(wfk.read(4))
|
|
267
|
+
ky = bytes2int(wfk.read(4))
|
|
268
|
+
kz = bytes2int(wfk.read(4))
|
|
269
|
+
pw_indices.append((kx, ky, kz))
|
|
270
|
+
wfk.read(8)
|
|
271
|
+
for nband in range(nband_temp):
|
|
272
|
+
eigenval = bytes2float(wfk.read(8))
|
|
273
|
+
eigenvalues.append(eigenval)
|
|
274
|
+
# skip reading coefficients if they energy level of interest is not in band
|
|
275
|
+
if skip:
|
|
276
|
+
min_val = self.fermi + energy_level - width/2
|
|
277
|
+
max_val = self.fermi + energy_level + width/2
|
|
278
|
+
eig_found = False
|
|
279
|
+
for eigval in eigenvalues:
|
|
280
|
+
if min_val <= eigval <= max_val:
|
|
281
|
+
eig_found = True
|
|
282
|
+
break
|
|
283
|
+
if eig_found:
|
|
284
|
+
yield self._ReadCoeffs(
|
|
285
|
+
wfk,
|
|
286
|
+
nband_temp,
|
|
287
|
+
npw,
|
|
288
|
+
eigenvalues,
|
|
289
|
+
pw_indices,
|
|
290
|
+
ind=j
|
|
291
|
+
)
|
|
292
|
+
else:
|
|
293
|
+
wfk.read(nband_temp*8)
|
|
294
|
+
wfk.read(4)
|
|
295
|
+
wfk.read(nband_temp*(8 + npw*16))
|
|
296
|
+
else:
|
|
297
|
+
yield self._ReadCoeffs(
|
|
298
|
+
wfk,
|
|
299
|
+
nband_temp,
|
|
300
|
+
npw,
|
|
301
|
+
eigenvalues,
|
|
302
|
+
pw_indices,
|
|
303
|
+
ind=j
|
|
304
|
+
)
|
|
305
|
+
print('WFK body read')
|
|
306
|
+
wfk.close()
|
|
307
|
+
#-----------------------------------------------------------------------------------------------------------------#
|
|
308
|
+
# method to read in plane wave coefficients
|
|
309
|
+
def _ReadCoeffs(
|
|
310
|
+
self, wfk_file, nbands, npws, eigs, pw_inds, ind
|
|
311
|
+
)->wc.WFK:
|
|
312
|
+
occupancies = np.zeros((1,nbands), dtype=float)
|
|
313
|
+
coeffs = np.zeros((nbands,npws), dtype=complex)
|
|
314
|
+
for nband in range(nbands):
|
|
315
|
+
occ = bytes2float(wfk_file.read(8))
|
|
316
|
+
occupancies[:,nband] = occ
|
|
317
|
+
wfk_file.read(4)
|
|
318
|
+
for nband in range(nbands):
|
|
319
|
+
wfk_file.read(4)
|
|
320
|
+
cg:np.ndarray = np.zeros((1,npws), dtype=complex)
|
|
321
|
+
for pw in range(npws):
|
|
322
|
+
cg1 = bytes2float(wfk_file.read(8))
|
|
323
|
+
cg2 = bytes2float(wfk_file.read(8))
|
|
324
|
+
cg[:,pw] = cg1 + 1j*cg2
|
|
325
|
+
coeffs[nband,:] = cg
|
|
326
|
+
wfk_file.read(4)
|
|
327
|
+
return wc.WFK(
|
|
328
|
+
eigenvalues=np.array(eigs),
|
|
329
|
+
wfk_coeffs=np.array(coeffs),
|
|
330
|
+
pw_indices=np.array(pw_inds),
|
|
331
|
+
kpoints=np.array(self.kpts[ind]),
|
|
332
|
+
nkpt=self.nkpt,
|
|
333
|
+
nbands=self.bands[0],
|
|
334
|
+
ngfftx=self.ngfftx,
|
|
335
|
+
ngffty=self.ngffty,
|
|
336
|
+
ngfftz=self.ngfftz,
|
|
337
|
+
symrel=np.array(self.symrel),
|
|
338
|
+
nsym=self.nsym,
|
|
339
|
+
lattice=self.real_lattice,
|
|
340
|
+
natom=self.natom,
|
|
341
|
+
xred=np.array(self.xred),
|
|
342
|
+
typat=self.typat,
|
|
343
|
+
znucltypat=self.znucltypat,
|
|
344
|
+
fermi_energy=self.fermi,
|
|
345
|
+
non_symm_vecs=np.array(self.tnons),
|
|
346
|
+
time_reversal=self.time_reversal
|
|
347
|
+
)
|
|
348
|
+
#-----------------------------------------------------------------------------------------------------------------#
|
|
349
|
+
# method to read only eigenvalues from body of abinit version 7 wavefunction file
|
|
350
|
+
def ReadEigenvalues(
|
|
351
|
+
self, check_time_rev:bool=True
|
|
352
|
+
)->Generator[wc.WFK, None, None]:
|
|
353
|
+
'''
|
|
354
|
+
Method that constructs WFK objects from ABINIT v7 WFK file.
|
|
355
|
+
'''
|
|
356
|
+
# check for time reversal symmetry
|
|
357
|
+
if check_time_rev:
|
|
358
|
+
self._CheckTimeRev()
|
|
359
|
+
else:
|
|
360
|
+
self.time_reversal = False
|
|
361
|
+
# read wfk
|
|
362
|
+
wfk = open(self.filename, 'rb')
|
|
363
|
+
#-----------#
|
|
364
|
+
# skip header
|
|
365
|
+
wfk.read(298)
|
|
366
|
+
wfk.read(4*(2*self.nkpt + self.nkpt*self.nsppol + self.npsp + 10*self.nsym + self.natom))
|
|
367
|
+
wfk.read(8*(4*self.nkpt + self.bandtot + 3*self.nsym + self.ntypat + 3*self.natom))
|
|
368
|
+
wfk.read(self.npsp*(176))
|
|
369
|
+
#-------------------------------#
|
|
370
|
+
# begin reading wavefunction body
|
|
371
|
+
for i in range(self.nsppol):
|
|
372
|
+
for j in range(self.nkpt):
|
|
373
|
+
print(f'Reading kpoint {j+1} of {self.nkpt}', end='\r')
|
|
374
|
+
if j+1 == self.nkpt:
|
|
375
|
+
print('\n', end='')
|
|
376
|
+
eigenvalues:list[float] = []
|
|
377
|
+
wfk.read(4)
|
|
378
|
+
npw = bytes2int(wfk.read(4))
|
|
379
|
+
self.nspinor = bytes2int(wfk.read(4))
|
|
380
|
+
nband_temp = bytes2int(wfk.read(4))
|
|
381
|
+
wfk.read(8)
|
|
382
|
+
wfk.read(12*npw)
|
|
383
|
+
wfk.read(8)
|
|
384
|
+
#------------------------------------------------------------------#
|
|
385
|
+
# only need eigenvalues for Fermi surface, skip over everything else
|
|
386
|
+
for nband in range(nband_temp):
|
|
387
|
+
eigenval = bytes2float(wfk.read(8))
|
|
388
|
+
eigenvalues.append(eigenval)
|
|
389
|
+
wfk.read(nband_temp*8)
|
|
390
|
+
wfk.read(4)
|
|
391
|
+
wfk.read(nband_temp*(8 + npw*16))
|
|
392
|
+
yield wc.WFK(
|
|
393
|
+
eigenvalues=np.array(eigenvalues),
|
|
394
|
+
kpoints=np.array(self.kpts[j]),
|
|
395
|
+
nkpt=self.nkpt,
|
|
396
|
+
nbands=self.bands[0],
|
|
397
|
+
ngfftx=self.ngfftx,
|
|
398
|
+
ngffty=self.ngffty,
|
|
399
|
+
ngfftz=self.ngfftz,
|
|
400
|
+
symrel=np.array(self.symrel),
|
|
401
|
+
nsym=self.nsym,
|
|
402
|
+
lattice=self.real_lattice,
|
|
403
|
+
natom=self.natom,
|
|
404
|
+
xred=np.array(self.xred),
|
|
405
|
+
typat=self.typat,
|
|
406
|
+
znucltypat=self.znucltypat,
|
|
407
|
+
fermi_energy=self.fermi,
|
|
408
|
+
non_symm_vecs=np.array(self.tnons),
|
|
409
|
+
time_reversal=self.time_reversal
|
|
410
|
+
)
|
|
411
|
+
print('WFK body read')
|
|
412
|
+
wfk.close()
|
|
413
|
+
|
|
414
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
415
|
+
#----------------------------------------------------- END CLASS -----------------------------------------------------#
|
|
416
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
417
|
+
|
|
418
|
+
class Abinit10WFK():
|
|
419
|
+
def __init__(
|
|
420
|
+
self, filename:str
|
|
421
|
+
):
|
|
422
|
+
self.filename = filename
|
|
423
|
+
self._ReadHeader()
|
|
424
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
425
|
+
#------------------------------------------------------ METHODS ------------------------------------------------------#
|
|
426
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
427
|
+
# method to read wavefunction header for abinit version 7
|
|
428
|
+
def _ReadHeader(
|
|
429
|
+
self
|
|
430
|
+
)->None:
|
|
431
|
+
wfk = open(self.filename, 'rb')
|
|
432
|
+
print('Reading WFK header')
|
|
433
|
+
#---------------#
|
|
434
|
+
# unpack integers
|
|
435
|
+
self.header = bytes2int(wfk.read(4))
|
|
436
|
+
self.version = wfk.read(6).decode()
|
|
437
|
+
wfk.read(2)
|
|
438
|
+
self.headform = bytes2int(wfk.read(4))
|
|
439
|
+
self.fform = bytes2int(wfk.read(4))
|
|
440
|
+
wfk.read(8)
|
|
441
|
+
self.bandtot = bytes2int(wfk.read(4))
|
|
442
|
+
self.date = bytes2int(wfk.read(4))
|
|
443
|
+
self.intxc = bytes2int(wfk.read(4))
|
|
444
|
+
self.ixc = bytes2int(wfk.read(4))
|
|
445
|
+
self.natom = bytes2int(wfk.read(4))
|
|
446
|
+
self.ngfftx = bytes2int(wfk.read(4))
|
|
447
|
+
self.ngffty = bytes2int(wfk.read(4))
|
|
448
|
+
self.ngfftz = bytes2int(wfk.read(4))
|
|
449
|
+
self.nkpt = bytes2int(wfk.read(4))
|
|
450
|
+
self.nspden = bytes2int(wfk.read(4))
|
|
451
|
+
self.nspinor = bytes2int(wfk.read(4))
|
|
452
|
+
self.nsppol = bytes2int(wfk.read(4))
|
|
453
|
+
self.nsym = bytes2int(wfk.read(4))
|
|
454
|
+
self.npsp = bytes2int(wfk.read(4))
|
|
455
|
+
self.ntypat = bytes2int(wfk.read(4))
|
|
456
|
+
self.occopt = bytes2int(wfk.read(4))
|
|
457
|
+
self.pertcase = bytes2int(wfk.read(4))
|
|
458
|
+
self.usepaw = bytes2int(wfk.read(4))
|
|
459
|
+
#--------------#
|
|
460
|
+
# unpack doubles
|
|
461
|
+
self.ecut = bytes2float(wfk.read(8))
|
|
462
|
+
self.ecutdg = bytes2float(wfk.read(8))
|
|
463
|
+
self.ecutsm = bytes2float(wfk.read(8))
|
|
464
|
+
self.ecut_eff = bytes2float(wfk.read(8))
|
|
465
|
+
self.qptnx = bytes2float(wfk.read(8))
|
|
466
|
+
self.qptny = bytes2float(wfk.read(8))
|
|
467
|
+
self.qptnz = bytes2float(wfk.read(8))
|
|
468
|
+
rprimd_ax = bytes2float(wfk.read(8))
|
|
469
|
+
rprimd_ay = bytes2float(wfk.read(8))
|
|
470
|
+
rprimd_az = bytes2float(wfk.read(8))
|
|
471
|
+
rprimd_bx = bytes2float(wfk.read(8))
|
|
472
|
+
rprimd_by = bytes2float(wfk.read(8))
|
|
473
|
+
rprimd_bz = bytes2float(wfk.read(8))
|
|
474
|
+
rprimd_cx = bytes2float(wfk.read(8))
|
|
475
|
+
rprimd_cy = bytes2float(wfk.read(8))
|
|
476
|
+
rprimd_cz = bytes2float(wfk.read(8))
|
|
477
|
+
#------------------------#
|
|
478
|
+
# convert Bohr to Angstrom
|
|
479
|
+
self.real_lattice = 0.529177*np.array([
|
|
480
|
+
[rprimd_ax, rprimd_ay, rprimd_az],
|
|
481
|
+
[rprimd_bx, rprimd_by, rprimd_bz],
|
|
482
|
+
[rprimd_cx, rprimd_cy, rprimd_cz]
|
|
483
|
+
]).reshape((3,3))
|
|
484
|
+
self.stmbias = bytes2float(wfk.read(8))
|
|
485
|
+
self.tphysel = bytes2float(wfk.read(8))
|
|
486
|
+
self.tsmear = bytes2float(wfk.read(8))
|
|
487
|
+
#---------------#
|
|
488
|
+
# unpack integers
|
|
489
|
+
self.usewvl = bytes2int(wfk.read(4))
|
|
490
|
+
self.nshiftk_orig = bytes2int(wfk.read(4))
|
|
491
|
+
self.nshiftk = bytes2int(wfk.read(4))
|
|
492
|
+
self.mband = bytes2int(wfk.read(4))
|
|
493
|
+
wfk.read(8)
|
|
494
|
+
self.istwfk:list[int] = []
|
|
495
|
+
for _ in range(self.nkpt):
|
|
496
|
+
val = bytes2int(wfk.read(4))
|
|
497
|
+
self.istwfk.append(val)
|
|
498
|
+
self.bands:list[int] = []
|
|
499
|
+
for _ in range(self.nkpt*self.nsppol):
|
|
500
|
+
val = bytes2int(wfk.read(4))
|
|
501
|
+
self.bands.append(val)
|
|
502
|
+
self.npwarr:list[int] = []
|
|
503
|
+
for _ in range(self.nkpt):
|
|
504
|
+
val = bytes2int(wfk.read(4))
|
|
505
|
+
self.npwarr.append(val)
|
|
506
|
+
self.so_psp:list[int] = []
|
|
507
|
+
for _ in range(self.npsp):
|
|
508
|
+
val = bytes2int(wfk.read(4))
|
|
509
|
+
self.so_psp.append(val)
|
|
510
|
+
self.symafm:list[int] = []
|
|
511
|
+
for _ in range(self.nsym):
|
|
512
|
+
val = bytes2int(wfk.read(4))
|
|
513
|
+
self.symafm.append(val)
|
|
514
|
+
self.symrel:list[np.ndarray] = []
|
|
515
|
+
for _ in range(self.nsym):
|
|
516
|
+
arr = np.zeros((3,3))
|
|
517
|
+
arr[0,0] = bytes2int(wfk.read(4))
|
|
518
|
+
arr[1,0] = bytes2int(wfk.read(4))
|
|
519
|
+
arr[2,0] = bytes2int(wfk.read(4))
|
|
520
|
+
arr[0,1] = bytes2int(wfk.read(4))
|
|
521
|
+
arr[1,1] = bytes2int(wfk.read(4))
|
|
522
|
+
arr[2,1] = bytes2int(wfk.read(4))
|
|
523
|
+
arr[0,2] = bytes2int(wfk.read(4))
|
|
524
|
+
arr[1,2] = bytes2int(wfk.read(4))
|
|
525
|
+
arr[2,2] = bytes2int(wfk.read(4))
|
|
526
|
+
self.symrel.append(arr)
|
|
527
|
+
self.typat:list[int] = []
|
|
528
|
+
for _ in range(self.natom):
|
|
529
|
+
val = bytes2int(wfk.read(4))
|
|
530
|
+
self.typat.append(val)
|
|
531
|
+
#--------------#
|
|
532
|
+
# unpack doubles
|
|
533
|
+
self.kpts:list[np.ndarray] = []
|
|
534
|
+
for _ in range(self.nkpt):
|
|
535
|
+
vec = np.zeros(3)
|
|
536
|
+
vec[0] = bytes2float(wfk.read(8))
|
|
537
|
+
vec[1] = bytes2float(wfk.read(8))
|
|
538
|
+
vec[2] = bytes2float(wfk.read(8))
|
|
539
|
+
self.kpts.append(vec)
|
|
540
|
+
self.occ:list[float] = []
|
|
541
|
+
for _ in range(self.bandtot):
|
|
542
|
+
val = bytes2float(wfk.read(8))
|
|
543
|
+
self.occ.append(val)
|
|
544
|
+
self.tnons:list[np.ndarray] = []
|
|
545
|
+
for _ in range(self.nsym):
|
|
546
|
+
vec = np.zeros(3)
|
|
547
|
+
vec[0] = bytes2float(wfk.read(8))
|
|
548
|
+
vec[1] = bytes2float(wfk.read(8))
|
|
549
|
+
vec[2] = bytes2float(wfk.read(8))
|
|
550
|
+
self.tnons.append(vec)
|
|
551
|
+
self.znucltypat:list[float] = []
|
|
552
|
+
for _ in range(self.ntypat):
|
|
553
|
+
val = bytes2float(wfk.read(8))
|
|
554
|
+
self.znucltypat.append(val)
|
|
555
|
+
self.wtk:list[float] = []
|
|
556
|
+
for _ in range(self.nkpt):
|
|
557
|
+
val = bytes2float(wfk.read(8))
|
|
558
|
+
self.wtk.append(val)
|
|
559
|
+
#------------------#
|
|
560
|
+
# unpack coordinates
|
|
561
|
+
wfk.read(8)
|
|
562
|
+
self.residm = bytes2float(wfk.read(8))
|
|
563
|
+
self.xred:list[np.ndarray] = []
|
|
564
|
+
for _ in range(self.natom):
|
|
565
|
+
vec = np.zeros(3)
|
|
566
|
+
vec[0] = bytes2float(wfk.read(8))
|
|
567
|
+
vec[1] = bytes2float(wfk.read(8))
|
|
568
|
+
vec[2] = bytes2float(wfk.read(8))
|
|
569
|
+
self.xred.append(vec)
|
|
570
|
+
#------------------------------------#
|
|
571
|
+
# unpack total energy and fermi energy
|
|
572
|
+
self.etotal = bytes2float(wfk.read(8))
|
|
573
|
+
self.fermi = bytes2float(wfk.read(8))
|
|
574
|
+
#-------------#
|
|
575
|
+
# unpack floats
|
|
576
|
+
self.amu:list[float] = []
|
|
577
|
+
for _ in range(self.ntypat):
|
|
578
|
+
val = bytes2float(wfk.read(8))
|
|
579
|
+
self.amu.append(val)
|
|
580
|
+
#----------------------------#
|
|
581
|
+
# unpack reciprocal space info
|
|
582
|
+
wfk.read(8)
|
|
583
|
+
self.kptopt = bytes2int(wfk.read(4))
|
|
584
|
+
self.pawcpxocc = bytes2int(wfk.read(4))
|
|
585
|
+
self.nelect = bytes2float(wfk.read(8))
|
|
586
|
+
self.cellcharge = bytes2float(wfk.read(8))
|
|
587
|
+
self.icoulomb = bytes2int(wfk.read(4))
|
|
588
|
+
rec_latt_ax = bytes2int(wfk.read(4))
|
|
589
|
+
rec_latt_ay = bytes2int(wfk.read(4))
|
|
590
|
+
rec_latt_az = bytes2int(wfk.read(4))
|
|
591
|
+
rec_latt_bx = bytes2int(wfk.read(4))
|
|
592
|
+
rec_latt_by = bytes2int(wfk.read(4))
|
|
593
|
+
rec_latt_bz = bytes2int(wfk.read(4))
|
|
594
|
+
rec_latt_cx = bytes2int(wfk.read(4))
|
|
595
|
+
rec_latt_cy = bytes2int(wfk.read(4))
|
|
596
|
+
rec_latt_cz = bytes2int(wfk.read(4))
|
|
597
|
+
self.kptr_latt = np.array([
|
|
598
|
+
[rec_latt_ax, rec_latt_ay, rec_latt_az],
|
|
599
|
+
[rec_latt_bx, rec_latt_by, rec_latt_bz],
|
|
600
|
+
[rec_latt_cx, rec_latt_cy, rec_latt_cz]
|
|
601
|
+
]).reshape((3,3))
|
|
602
|
+
rec_latt_ax = bytes2int(wfk.read(4))
|
|
603
|
+
rec_latt_ay = bytes2int(wfk.read(4))
|
|
604
|
+
rec_latt_az = bytes2int(wfk.read(4))
|
|
605
|
+
rec_latt_bx = bytes2int(wfk.read(4))
|
|
606
|
+
rec_latt_by = bytes2int(wfk.read(4))
|
|
607
|
+
rec_latt_bz = bytes2int(wfk.read(4))
|
|
608
|
+
rec_latt_cx = bytes2int(wfk.read(4))
|
|
609
|
+
rec_latt_cy = bytes2int(wfk.read(4))
|
|
610
|
+
rec_latt_cz = bytes2int(wfk.read(4))
|
|
611
|
+
self.kptr_latt_orig = np.array([
|
|
612
|
+
[rec_latt_ax, rec_latt_ay, rec_latt_az],
|
|
613
|
+
[rec_latt_bx, rec_latt_by, rec_latt_bz],
|
|
614
|
+
[rec_latt_cx, rec_latt_cy, rec_latt_cz]
|
|
615
|
+
]).reshape((3,3))
|
|
616
|
+
shift_orig_x = bytes2float(wfk.read(8))
|
|
617
|
+
shift_orig_y = bytes2float(wfk.read(8))
|
|
618
|
+
shift_orig_z = bytes2float(wfk.read(8))
|
|
619
|
+
self.origin_shift = [shift_orig_x, shift_orig_y, shift_orig_z]
|
|
620
|
+
shift_kx = bytes2float(wfk.read(8))
|
|
621
|
+
shift_ky = bytes2float(wfk.read(8))
|
|
622
|
+
shift_kz = bytes2float(wfk.read(8))
|
|
623
|
+
self.kpt_shift = [shift_kx, shift_ky, shift_kz]
|
|
624
|
+
#-----------------------#
|
|
625
|
+
# unpack pseudopotentials
|
|
626
|
+
wfk.read(4)
|
|
627
|
+
self.title:list[str] = []
|
|
628
|
+
self.znuclpsp:list[float] = []
|
|
629
|
+
self.zionpsp:list[float] = []
|
|
630
|
+
self.pspso:list[int] = []
|
|
631
|
+
self.pspdat:list[int] = []
|
|
632
|
+
self.pspcod:list[int] = []
|
|
633
|
+
self.pspxc:list[int] = []
|
|
634
|
+
self.lmn_size:list[int] = []
|
|
635
|
+
self.md5_pseudos:list[str] = []
|
|
636
|
+
for _ in range(self.npsp):
|
|
637
|
+
wfk.read(4)
|
|
638
|
+
self.title.append(wfk.read(132).decode())
|
|
639
|
+
self.znuclpsp.append(bytes2float(wfk.read(8)))
|
|
640
|
+
self.zionpsp.append(bytes2float(wfk.read(8)))
|
|
641
|
+
self.pspso.append(bytes2int(wfk.read(4)))
|
|
642
|
+
self.pspdat.append(bytes2int(wfk.read(4)))
|
|
643
|
+
self.pspcod.append(bytes2int(wfk.read(4)))
|
|
644
|
+
self.pspxc.append(bytes2int(wfk.read(4)))
|
|
645
|
+
self.lmn_size.append(bytes2int(wfk.read(4)))
|
|
646
|
+
self.md5_pseudos.append(wfk.read(32).decode())
|
|
647
|
+
wfk.read(4)
|
|
648
|
+
#---------------#
|
|
649
|
+
# unpack PAW data
|
|
650
|
+
if self.usepaw == 1:
|
|
651
|
+
wfk.read(4)
|
|
652
|
+
self.nrho:list[int] = []
|
|
653
|
+
for _ in range(self.natom):
|
|
654
|
+
for _ in range(self.nspden):
|
|
655
|
+
nrhoij = bytes2int(wfk.read(4))
|
|
656
|
+
self.nrho.append(nrhoij)
|
|
657
|
+
self.cplex = bytes2int(wfk.read(4))
|
|
658
|
+
self.nspden_paw = bytes2int(wfk.read(4))
|
|
659
|
+
wfk.read(8)
|
|
660
|
+
self.irho:list[int] = []
|
|
661
|
+
for i in range(self.natom):
|
|
662
|
+
for _ in range(self.nspden_paw):
|
|
663
|
+
nrhoij = self.nrho[i]
|
|
664
|
+
for _ in range(nrhoij):
|
|
665
|
+
rhoij = bytes2int(wfk.read(4))
|
|
666
|
+
self.irho.append(rhoij)
|
|
667
|
+
wfk.read(4)
|
|
668
|
+
self.rho:list[float] = []
|
|
669
|
+
for i in range(self.natom):
|
|
670
|
+
for _ in range(self.nspden_paw):
|
|
671
|
+
nrhoij = self.nrho[i]
|
|
672
|
+
for _ in range(nrhoij):
|
|
673
|
+
rhoij = bytes2float(wfk.read(8))
|
|
674
|
+
self.rho.append(rhoij)
|
|
675
|
+
wfk.read(4)
|
|
676
|
+
print('WFK header read')
|
|
677
|
+
wfk.close()
|
|
678
|
+
#-----------------------------------------------------------------------------------------------------------------#
|
|
679
|
+
# check for time reversal symmetry
|
|
680
|
+
def _CheckTimeRev(
|
|
681
|
+
self
|
|
682
|
+
):
|
|
683
|
+
# if system is centrosymmetric, do not double reciprocal symmetry operations
|
|
684
|
+
if True in [np.array_equal(-np.identity(3),mat) for mat in self.symrel]:
|
|
685
|
+
self.time_reversal = False
|
|
686
|
+
else:
|
|
687
|
+
self.time_reversal = True
|
|
688
|
+
print((
|
|
689
|
+
'Noncentrosymmetric system identified, assuming time reversal symmetry\n'
|
|
690
|
+
'To change this, set "check_time_rev" keyword to False when calling ReadWFK() or ReadEigenvalues()'
|
|
691
|
+
))
|
|
692
|
+
#-----------------------------------------------------------------------------------------------------------------#
|
|
693
|
+
# method to read entire body of abinit version 7 wavefunction file
|
|
694
|
+
def ReadWFK(
|
|
695
|
+
self, energy_level=np.nan, width=np.nan, check_time_rev:bool=True
|
|
696
|
+
)->Generator[wc.WFK, None, None]:
|
|
697
|
+
'''
|
|
698
|
+
Method that constructs WFK objects from ABINIT v10 WFK file.
|
|
699
|
+
|
|
700
|
+
Parameters
|
|
701
|
+
----------
|
|
702
|
+
energy_level : float
|
|
703
|
+
The energy level to pull plane wave coefficients from
|
|
704
|
+
This is relative to the Fermi energy
|
|
705
|
+
If not defined but width is defined, default is 0 Hartree
|
|
706
|
+
|
|
707
|
+
width : float
|
|
708
|
+
Defines range about energy_level to search for plane wave coefficients
|
|
709
|
+
Total range is equal to width, so look width/2 above and below energy_level
|
|
710
|
+
If not defined but energy_level is defined, default is 0.005 Hartree
|
|
711
|
+
'''
|
|
712
|
+
# check for time reversal symmetry
|
|
713
|
+
if check_time_rev:
|
|
714
|
+
self._CheckTimeRev()
|
|
715
|
+
else:
|
|
716
|
+
self.time_reversal = False
|
|
717
|
+
# read wfk
|
|
718
|
+
wfk = open(self.filename, 'rb')
|
|
719
|
+
skip = True
|
|
720
|
+
if energy_level is np.nan:
|
|
721
|
+
if width is np.nan:
|
|
722
|
+
skip = False
|
|
723
|
+
else:
|
|
724
|
+
energy_level = 0
|
|
725
|
+
else:
|
|
726
|
+
if width is np.nan:
|
|
727
|
+
width = 0.005
|
|
728
|
+
#-----------#
|
|
729
|
+
# skip header
|
|
730
|
+
wfk.read(468)
|
|
731
|
+
wfk.read(4*(2*self.nkpt + self.nkpt*self.nsppol + self.npsp + 10*self.nsym + self.natom))
|
|
732
|
+
wfk.read(8*(4*self.nkpt + self.bandtot + 3*self.nsym + 2*self.ntypat + 3*self.natom))
|
|
733
|
+
wfk.read(self.npsp*(208))
|
|
734
|
+
if self.usepaw == 1:
|
|
735
|
+
wfk.read(4)
|
|
736
|
+
for _ in range(self.natom):
|
|
737
|
+
for _ in range(self.nspden):
|
|
738
|
+
_ = wfk.read(4)
|
|
739
|
+
wfk.read(4)
|
|
740
|
+
wfk.read(4)
|
|
741
|
+
wfk.read(8)
|
|
742
|
+
for i in range(self.natom):
|
|
743
|
+
for _ in range(self.nspden_paw):
|
|
744
|
+
nrhoij = self.nrho[i]
|
|
745
|
+
for _ in range(nrhoij):
|
|
746
|
+
_ = wfk.read(4)
|
|
747
|
+
wfk.read(4)
|
|
748
|
+
for i in range(self.natom):
|
|
749
|
+
for _ in range(self.nspden_paw):
|
|
750
|
+
nrhoij = self.nrho[i]
|
|
751
|
+
for _ in range(nrhoij):
|
|
752
|
+
_ = wfk.read(8)
|
|
753
|
+
wfk.read(4)
|
|
754
|
+
#-------------------------------#
|
|
755
|
+
# begin reading wavefunction body
|
|
756
|
+
for i in range(self.nsppol):
|
|
757
|
+
for j in range(self.nkpt):
|
|
758
|
+
print(f'Reading kpoint {j+1} of {self.nkpt}', end='\r')
|
|
759
|
+
if j+1 == self.nkpt:
|
|
760
|
+
print('\n', end='')
|
|
761
|
+
wfk.read(4)
|
|
762
|
+
npw = bytes2int(wfk.read(4))
|
|
763
|
+
self.nspinor = bytes2int(wfk.read(4))
|
|
764
|
+
nband_temp = bytes2int(wfk.read(4))
|
|
765
|
+
pw_indices = np.zeros((npw,3), dtype=int)
|
|
766
|
+
eigenvalues = np.zeros(nband_temp, dtype=float)
|
|
767
|
+
wfk.read(8)
|
|
768
|
+
for pw in range(npw):
|
|
769
|
+
kx = bytes2int(wfk.read(4))
|
|
770
|
+
ky = bytes2int(wfk.read(4))
|
|
771
|
+
kz = bytes2int(wfk.read(4))
|
|
772
|
+
pw_indices[pw,:] = [kx, ky, kz]
|
|
773
|
+
wfk.read(8)
|
|
774
|
+
for nband in range(nband_temp):
|
|
775
|
+
eigenval = bytes2float(wfk.read(8))
|
|
776
|
+
eigenvalues[nband] = eigenval
|
|
777
|
+
# skip reading coefficients if they energy level of interest is not in band
|
|
778
|
+
if skip:
|
|
779
|
+
min_val = self.fermi + energy_level - width/2
|
|
780
|
+
max_val = self.fermi + energy_level + width/2
|
|
781
|
+
eig_found = False
|
|
782
|
+
for eigval in eigenvalues:
|
|
783
|
+
if min_val <= eigval <= max_val:
|
|
784
|
+
eig_found = True
|
|
785
|
+
break
|
|
786
|
+
if eig_found:
|
|
787
|
+
yield self._ReadCoeffs(
|
|
788
|
+
wfk,
|
|
789
|
+
nband_temp,
|
|
790
|
+
npw,
|
|
791
|
+
eigenvalues,
|
|
792
|
+
pw_indices,
|
|
793
|
+
ind=j
|
|
794
|
+
)
|
|
795
|
+
else:
|
|
796
|
+
wfk.read(nband_temp*8)
|
|
797
|
+
wfk.read(4)
|
|
798
|
+
wfk.read(nband_temp*(8 + npw*16))
|
|
799
|
+
# if not skip, read full wavefunction
|
|
800
|
+
else:
|
|
801
|
+
yield self._ReadCoeffs(
|
|
802
|
+
wfk,
|
|
803
|
+
nband_temp,
|
|
804
|
+
npw,
|
|
805
|
+
eigenvalues,
|
|
806
|
+
pw_indices,
|
|
807
|
+
ind=j
|
|
808
|
+
)
|
|
809
|
+
print('WFK body read')
|
|
810
|
+
wfk.close()
|
|
811
|
+
#-----------------------------------------------------------------------------------------------------------------#
|
|
812
|
+
# method to read in plane wave coefficients
|
|
813
|
+
def _ReadCoeffs(
|
|
814
|
+
self, wfk_file, nbands, npws, eigs, pw_inds, ind
|
|
815
|
+
)->wc.WFK:
|
|
816
|
+
occupancies = np.zeros((1,nbands), dtype=float)
|
|
817
|
+
coeffs = np.zeros((nbands,npws), dtype=complex)
|
|
818
|
+
for nband in range(nbands):
|
|
819
|
+
occ = bytes2float(wfk_file.read(8))
|
|
820
|
+
occupancies[:,nband] = occ
|
|
821
|
+
wfk_file.read(4)
|
|
822
|
+
for nband in range(nbands):
|
|
823
|
+
wfk_file.read(4)
|
|
824
|
+
cg:np.ndarray = np.zeros((1,npws), dtype=complex)
|
|
825
|
+
for pw in range(npws):
|
|
826
|
+
cg1 = bytes2float(wfk_file.read(8))
|
|
827
|
+
cg2 = bytes2float(wfk_file.read(8))
|
|
828
|
+
cg[:,pw] = cg1 + 1j*cg2
|
|
829
|
+
coeffs[nband,:] = cg
|
|
830
|
+
wfk_file.read(4)
|
|
831
|
+
return wc.WFK(
|
|
832
|
+
eigenvalues=np.array(eigs),
|
|
833
|
+
wfk_coeffs=np.array(coeffs),
|
|
834
|
+
pw_indices=np.array(pw_inds),
|
|
835
|
+
kpoints=np.array(self.kpts[ind]),
|
|
836
|
+
nkpt=self.nkpt,
|
|
837
|
+
nbands=self.bands[0],
|
|
838
|
+
ngfftx=self.ngfftx,
|
|
839
|
+
ngffty=self.ngffty,
|
|
840
|
+
ngfftz=self.ngfftz,
|
|
841
|
+
symrel=np.array(self.symrel),
|
|
842
|
+
nsym=self.nsym,
|
|
843
|
+
lattice=self.real_lattice,
|
|
844
|
+
natom=self.natom,
|
|
845
|
+
xred=np.array(self.xred),
|
|
846
|
+
typat=self.typat,
|
|
847
|
+
znucltypat=self.znucltypat,
|
|
848
|
+
fermi_energy=self.fermi,
|
|
849
|
+
non_symm_vecs=np.array(self.tnons),
|
|
850
|
+
time_reversal=self.time_reversal
|
|
851
|
+
)
|
|
852
|
+
#-----------------------------------------------------------------------------------------------------------------#
|
|
853
|
+
# method to read only eigenvalues from body of abinit version 10 wavefunction file
|
|
854
|
+
def ReadEigenvalues(
|
|
855
|
+
self, check_time_rev:bool=True
|
|
856
|
+
)->Generator[wc.WFK, None, None]:
|
|
857
|
+
'''
|
|
858
|
+
Method that constructs WFK objects from ABINIT v10 WFK file.
|
|
859
|
+
'''
|
|
860
|
+
# check for time reversal symmetry
|
|
861
|
+
if check_time_rev:
|
|
862
|
+
self._CheckTimeRev()
|
|
863
|
+
else:
|
|
864
|
+
self.time_reversal = False
|
|
865
|
+
# read wfk
|
|
866
|
+
wfk = open(self.filename, 'rb')
|
|
867
|
+
#-----------#
|
|
868
|
+
# skip header
|
|
869
|
+
wfk.read(468)
|
|
870
|
+
wfk.read(4*(2*self.nkpt + self.nkpt*self.nsppol + self.npsp + 10*self.nsym + self.natom))
|
|
871
|
+
wfk.read(8*(4*self.nkpt + self.bandtot + 3*self.nsym + 2*self.ntypat + 3*self.natom))
|
|
872
|
+
wfk.read(self.npsp*(208))
|
|
873
|
+
if self.usepaw == 1:
|
|
874
|
+
wfk.read(4)
|
|
875
|
+
for _ in range(self.natom):
|
|
876
|
+
for _ in range(self.nspden):
|
|
877
|
+
_ = wfk.read(4)
|
|
878
|
+
wfk.read(4)
|
|
879
|
+
wfk.read(4)
|
|
880
|
+
wfk.read(8)
|
|
881
|
+
for i in range(self.natom):
|
|
882
|
+
for _ in range(self.nspden_paw):
|
|
883
|
+
nrhoij = self.nrho[i]
|
|
884
|
+
for _ in range(nrhoij):
|
|
885
|
+
_ = wfk.read(4)
|
|
886
|
+
wfk.read(4)
|
|
887
|
+
for i in range(self.natom):
|
|
888
|
+
for _ in range(self.nspden_paw):
|
|
889
|
+
nrhoij = self.nrho[i]
|
|
890
|
+
for _ in range(nrhoij):
|
|
891
|
+
_ = wfk.read(8)
|
|
892
|
+
wfk.read(4)
|
|
893
|
+
#-------------------------------#
|
|
894
|
+
# begin reading wavefunction body
|
|
895
|
+
for i in range(self.nsppol):
|
|
896
|
+
for j in range(self.nkpt):
|
|
897
|
+
print(f'Reading kpoint {j+1} of {self.nkpt}', end='\r')
|
|
898
|
+
if j+1 == self.nkpt:
|
|
899
|
+
print('\n', end='')
|
|
900
|
+
wfk.read(4)
|
|
901
|
+
npw = bytes2int(wfk.read(4))
|
|
902
|
+
self.nspinor = bytes2int(wfk.read(4))
|
|
903
|
+
nband_temp = bytes2int(wfk.read(4))
|
|
904
|
+
eigenvalues = np.zeros((1,nband_temp), dtype=float)
|
|
905
|
+
wfk.read(8)
|
|
906
|
+
wfk.read(12*npw)
|
|
907
|
+
wfk.read(8)
|
|
908
|
+
#------------------------------------------------------------------#
|
|
909
|
+
# only need eigenvalues for Fermi surface, skip over everything else
|
|
910
|
+
for nband in range(nband_temp):
|
|
911
|
+
eigenval = bytes2float(wfk.read(8))
|
|
912
|
+
eigenvalues[:,nband] = eigenval
|
|
913
|
+
wfk.read(nband_temp*8)
|
|
914
|
+
wfk.read(4)
|
|
915
|
+
wfk.read(nband_temp*(8 + npw*16))
|
|
916
|
+
yield wc.WFK(
|
|
917
|
+
eigenvalues=np.array(eigenvalues),
|
|
918
|
+
kpoints=np.array(self.kpts[j]),
|
|
919
|
+
nkpt=self.nkpt,
|
|
920
|
+
nbands=self.bands[0],
|
|
921
|
+
ngfftx=self.ngfftx,
|
|
922
|
+
ngffty=self.ngffty,
|
|
923
|
+
ngfftz=self.ngfftz,
|
|
924
|
+
symrel=np.array(self.symrel),
|
|
925
|
+
nsym=self.nsym,
|
|
926
|
+
lattice=self.real_lattice,
|
|
927
|
+
natom=self.natom,
|
|
928
|
+
xred=np.array(self.xred),
|
|
929
|
+
typat=self.typat,
|
|
930
|
+
znucltypat=self.znucltypat,
|
|
931
|
+
fermi_energy=self.fermi,
|
|
932
|
+
non_symm_vecs=np.array(self.tnons),
|
|
933
|
+
time_reversal=self.time_reversal
|
|
934
|
+
)
|
|
935
|
+
print('WFK body read')
|
|
936
|
+
wfk.close()
|
|
937
|
+
|
|
938
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
939
|
+
#----------------------------------------------------- END CLASS -----------------------------------------------------#
|
|
940
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
941
|
+
|
|
942
|
+
class AbinitNetCDF():
|
|
943
|
+
def __init__(
|
|
944
|
+
self, filename:str
|
|
945
|
+
):
|
|
946
|
+
print('WFK found with netCDF4 format')
|
|
947
|
+
self.filename = filename
|
|
948
|
+
self.dataset = self._GetDataset()
|
|
949
|
+
self.kpts:np.ndarray = self.dataset.variables['reduced_coordinates_of_kpoints'][:]
|
|
950
|
+
self.nkpt:int = self.dataset.dimensions['number_of_kpoints'].size
|
|
951
|
+
self.xred:np.ndarray = self.dataset.variables['reduced_atom_positions'][:]
|
|
952
|
+
self.natom:int = self.dataset.dimensions['number_of_atoms'].size
|
|
953
|
+
self.tnons:np.ndarray = self.dataset.variables['reduced_symmetry_translations'][:]
|
|
954
|
+
self.symrel:np.ndarray = self.dataset.variables['reduced_symmetry_matrices'][:]
|
|
955
|
+
self.symrel = np.array([op.T for op in self.symrel])
|
|
956
|
+
self.nsym:int = self.dataset.dimensions['number_of_symmetry_operations'].size
|
|
957
|
+
self.fermi:float = self.dataset['fermi_energy'][:]
|
|
958
|
+
self.real_lattice:np.ndarray = self.dataset['primitive_vectors'][:]
|
|
959
|
+
self.real_lattice *= 0.529177
|
|
960
|
+
self.ngfftx:int = self.dataset.dimensions['number_of_grid_points_vector1'].size
|
|
961
|
+
self.ngffty:int = self.dataset.dimensions['number_of_grid_points_vector2'].size
|
|
962
|
+
self.ngfftz:int = self.dataset.dimensions['number_of_grid_points_vector3'].size
|
|
963
|
+
self.nband:int = int(self.dataset.dimensions['bantot'].size / self.nkpt)
|
|
964
|
+
self.typat:list = self.dataset.variables['atom_species'][:].tolist()
|
|
965
|
+
self.zion:np.ndarray = self.dataset.variables['atomic_numbers'][:]
|
|
966
|
+
self.znucltypat:list = [int(nuc) for nuc in self.zion]
|
|
967
|
+
self.bands = [self.nband]
|
|
968
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
969
|
+
#------------------------------------------------------ METHODS ------------------------------------------------------#
|
|
970
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
971
|
+
# create netCDF dataset
|
|
972
|
+
def _GetDataset(
|
|
973
|
+
self
|
|
974
|
+
):
|
|
975
|
+
from netCDF4 import Dataset
|
|
976
|
+
return Dataset(self.filename,format='NETCDF4')
|
|
977
|
+
#-----------------------------------------------------------------------------------------------------------------#
|
|
978
|
+
# check for time reversal symmetry
|
|
979
|
+
def _CheckTimeRev(
|
|
980
|
+
self
|
|
981
|
+
):
|
|
982
|
+
# if system is centrosymmetric, do not double reciprocal symmetry operations
|
|
983
|
+
if True in [np.array_equal(-np.identity(3),mat) for mat in self.symrel]:
|
|
984
|
+
self.time_reversal = False
|
|
985
|
+
else:
|
|
986
|
+
self.time_reversal = True
|
|
987
|
+
print((
|
|
988
|
+
'Noncentrosymmetric system identified, assuming time reversal symmetry\n'
|
|
989
|
+
'To change this, set "check_time_rev" keyword to False when calling ReadWFK() or ReadEigenvalues()'
|
|
990
|
+
))
|
|
991
|
+
#-----------------------------------------------------------------------------------------------------------------#
|
|
992
|
+
# fetch wavefunction coefficients from netcdf dataset
|
|
993
|
+
def ReadWFK(
|
|
994
|
+
self, energy_level:float=np.nan, width:float=np.nan, check_time_rev:bool=True
|
|
995
|
+
)->Generator[wc.WFK, None, None]:
|
|
996
|
+
# check for time reversal symmetry
|
|
997
|
+
if check_time_rev:
|
|
998
|
+
self._CheckTimeRev()
|
|
999
|
+
else:
|
|
1000
|
+
self.time_reversal = False
|
|
1001
|
+
eigs:np.ndarray = self.dataset.variables['eigenvalues'][:][0]
|
|
1002
|
+
pw_inds:np.ndarray = self.dataset.variables['reduced_coordinates_of_plane_waves'][:]
|
|
1003
|
+
# restructure wavefunction coefficients
|
|
1004
|
+
for kpt in range(self.nkpt):
|
|
1005
|
+
print(f'Reading kpoint {kpt+1} of {self.nkpt}', end='\r')
|
|
1006
|
+
kpt_coeffs = []
|
|
1007
|
+
# format plane wave indices
|
|
1008
|
+
kpt_pw_inds = pw_inds[kpt]
|
|
1009
|
+
kpt_pw_inds = kpt_pw_inds[~kpt_pw_inds.mask]
|
|
1010
|
+
kpt_pw_inds = kpt_pw_inds.reshape((-1,3))
|
|
1011
|
+
kpt_pw_inds = np.ma.getdata(kpt_pw_inds)
|
|
1012
|
+
coeffs = self.dataset.variables['coefficients_of_wavefunctions'][0,kpt]
|
|
1013
|
+
for band in coeffs:
|
|
1014
|
+
band = band[0]
|
|
1015
|
+
band = band[~band.mask]
|
|
1016
|
+
band = band.reshape((-1,2))
|
|
1017
|
+
band = np.ma.getdata(band)
|
|
1018
|
+
kpt_coeffs.append(band[:,0] + 1j*band[:,1])
|
|
1019
|
+
yield wc.WFK(
|
|
1020
|
+
eigenvalues=eigs[kpt,:],
|
|
1021
|
+
wfk_coeffs=np.array(kpt_coeffs),
|
|
1022
|
+
pw_indices=kpt_pw_inds,
|
|
1023
|
+
kpoints=self.kpts[kpt],
|
|
1024
|
+
nkpt=self.nkpt,
|
|
1025
|
+
nbands=self.nband,
|
|
1026
|
+
ngfftx=self.ngfftx,
|
|
1027
|
+
ngffty=self.ngffty,
|
|
1028
|
+
ngfftz=self.ngfftz,
|
|
1029
|
+
symrel=self.symrel,
|
|
1030
|
+
nsym=self.nsym,
|
|
1031
|
+
lattice=self.real_lattice,
|
|
1032
|
+
natom=self.natom,
|
|
1033
|
+
xred=self.xred,
|
|
1034
|
+
typat=self.typat,
|
|
1035
|
+
znucltypat=self.znucltypat,
|
|
1036
|
+
fermi_energy=self.fermi,
|
|
1037
|
+
non_symm_vecs=self.tnons,
|
|
1038
|
+
time_reversal=self.time_reversal
|
|
1039
|
+
)
|
|
1040
|
+
#-----------------------------------------------------------------------------------------------------------------#
|
|
1041
|
+
# fetch eigenvalues from netcdf dataset
|
|
1042
|
+
def ReadEigenvalues(
|
|
1043
|
+
self, energy_level:float=np.nan, width:float=np.nan, check_time_rev:bool=True
|
|
1044
|
+
)->Generator[wc.WFK, None, None]:
|
|
1045
|
+
# check for time reversal symmetry
|
|
1046
|
+
if check_time_rev:
|
|
1047
|
+
self._CheckTimeRev()
|
|
1048
|
+
else:
|
|
1049
|
+
self.time_reversal = False
|
|
1050
|
+
eigs:np.ndarray = self.dataset.variables['eigenvalues'][:][0]
|
|
1051
|
+
for i, kpt in enumerate(self.kpts):
|
|
1052
|
+
print(f'Reading kpoint {i+1} of {self.nkpt}', end='\r')
|
|
1053
|
+
yield wc.WFK(
|
|
1054
|
+
eigenvalues=eigs[i,:],
|
|
1055
|
+
kpoints=kpt,
|
|
1056
|
+
nkpt=self.nkpt,
|
|
1057
|
+
nbands=self.nband,
|
|
1058
|
+
ngfftx=self.ngfftx,
|
|
1059
|
+
ngffty=self.ngffty,
|
|
1060
|
+
ngfftz=self.ngfftz,
|
|
1061
|
+
symrel=self.symrel,
|
|
1062
|
+
nsym=self.nsym,
|
|
1063
|
+
lattice=self.real_lattice,
|
|
1064
|
+
natom=self.natom,
|
|
1065
|
+
xred=self.xred,
|
|
1066
|
+
typat=self.typat,
|
|
1067
|
+
znucltypat=self.znucltypat,
|
|
1068
|
+
fermi_energy=self.fermi,
|
|
1069
|
+
non_symm_vecs=self.tnons,
|
|
1070
|
+
time_reversal=self.time_reversal
|
|
1071
|
+
)
|
|
1072
|
+
|
|
1073
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
1074
|
+
#----------------------------------------------------- END CLASS -----------------------------------------------------#
|
|
1075
|
+
#---------------------------------------------------------------------------------------------------------------------#
|
|
1076
|
+
|
|
1077
|
+
def AbinitWFK(
|
|
1078
|
+
filename:str
|
|
1079
|
+
)->Union[Abinit10WFK, Abinit7WFK, AbinitNetCDF]:
|
|
1080
|
+
'''
|
|
1081
|
+
A function for identifying ABINIT version and constructing respective AbinitWFK object.
|
|
1082
|
+
'''
|
|
1083
|
+
if filename.endswith('.nc'):
|
|
1084
|
+
return AbinitNetCDF(filename)
|
|
1085
|
+
wfk = open(filename, 'rb')
|
|
1086
|
+
wfk.read(4)
|
|
1087
|
+
version = wfk.read(6).decode()
|
|
1088
|
+
wfk.close()
|
|
1089
|
+
if version.strip().split('.')[0] == '7':
|
|
1090
|
+
return Abinit7WFK(filename)
|
|
1091
|
+
elif version.strip().split('.')[0] == '10':
|
|
1092
|
+
return Abinit10WFK(filename)
|
|
1093
|
+
else:
|
|
1094
|
+
print(f'Version {version} may not be supported, attempting to analyze with v10 procedure.')
|
|
1095
1095
|
return Abinit10WFK(filename)
|