def plot_magnon():
print_license()
parser = argparse.ArgumentParser(
description=
"TB2J_magnon: Plot magnon band structure from the TB2J magnetic interaction parameters"
)
parser.add_argument("--fname",
default='exchange.xml',
type=str,
help='exchange xml file name. default: exchange.xml')
parser.add_argument(
"--qpath",
default=None,
type=str,
help=
'The names of special q-points. If not given, the path will be automatically choosen. See https://wiki.fysik.dtu.dk/ase/ase/dft/kpoints.html for the table of special kpoints and the default path.'
)
parser.add_argument(
"--figfname",
default=None,
type=str,
help=
'The file name of the figure. It should be e.g. png, pdf or other types of files which could be generated by matplotlib.'
)
parser.add_argument(
"--Jq",
action="store_true",
help="To plot the eigenvalues of -J(q) instead of the magnon band",
default=False)
parser.add_argument("--show",
action="store_true",
help="whether to show magnon band structure.",
default=False)
args = parser.parse_args()
if args.Jq:
print(
"Plotting the eigenvalues of -J(q). The figure is written to %s" %
(args.figfname))
if args.figfname is None:
args.figfname = 'Eigen_Jq.pdf'
else:
print(
"Plotting the magnon band structure. The figure is written to %s" %
(args.figfname))
if args.figfname is None:
args.figfname = 'magnon_band.pdf'
plot_magnon_band(fname=args.fname,
knames=args.qpath,
npoints=300,
Jq=args.Jq,
show=args.show)
def run_wann2J():
print_license()
parser = argparse.ArgumentParser(
description=
"wann2J: Using magnetic force theorem to calculate exchange parameter J from wannier functions"
)
parser.add_argument('--path',
help="path to the wannier files",
default='./',
type=str)
parser.add_argument('--posfile',
help="name of the position file",
default='POSCAR',
type=str)
parser.add_argument('--prefix_spinor',
help="prefix to the spinor wannier files",
default='wannier90',
type=str)
parser.add_argument('--prefix_up',
help="prefix to the spin up wannier files",
default='wannier90.up',
type=str)
parser.add_argument('--prefix_down',
help="prefix to the spin down wannier files",
default='wannier90.dn',
type=str)
parser.add_argument('--elements',
help="elements to be considered in Heisenberg model",
default=None,
type=str,
nargs='*')
parser.add_argument(
'--groupby',
help=
"In the spinor case, the order of the orbitals have two conventions: 1: group by spin (orb1_up, orb2_up,... orb1_down, ...), 2,group by orbital (orb1_up, orb1_down, orb2_up, ...,). Use 'spin' in the former case and 'orbital' in the latter case. The default is spin.",
default='spin',
type=str,
)
parser.add_argument(
'--rcut',
help=
'cutoff of spin pair distance. The default is to calculate all commensurate R point to the k mesh.',
default=None,
type=float)
parser.add_argument('--efermi',
help='Fermi energy in eV',
default=None,
type=float)
parser.add_argument('--kmesh',
help='kmesh in the format of kx ky kz',
type=int,
nargs='*',
default=[5, 5, 5])
parser.add_argument('--emin',
help='energy minimum below efermi, default -14 eV',
type=float,
default=-14.0)
parser.add_argument('--emax',
help='energy maximum above efermi, default 0.0 eV',
type=float,
default=0.0)
parser.add_argument(
'--nz',
help='number of steps for semicircle contour, default: 100',
default=100,
type=int)
# parser.add_argument(
# '--height',
# help=
# 'energy contour, a small number (often between 0.1 to 0.5, default 0.1)',
# type=float,
# default=0.1)
# parser.add_argument('--nz1',
# help='number of steps 1, default: 50',
# default=50,
# type=int)
# parser.add_argument('--nz2',
# help='number of steps 2, default: 200',
# default=200,
# type=int)
# parser.add_argument('--nz3',
# help='number of steps 3, default: 50',
# default=50,
# type=int)
parser.add_argument(
'--cutoff',
help="The minimum of J amplitude to write, (in eV), default is 1e-5 eV",
default=1e-5,
type=float)
parser.add_argument(
'--exclude_orbs',
help=
"the indices of wannier functions to be excluded from magnetic site. counting start from 0",
default=[],
type=int,
nargs='+')
parser.add_argument(
'--np',
help='number of cpu cores to use in parallel, default: 1',
default=1,
type=int)
parser.add_argument(
'--use_cache',
help=
"whether to use disk file for temporary storing wavefunctions and hamiltonian to reduce memory usage. Default: False",
action='store_true',
default=False)
parser.add_argument(
"--description",
help=
"add description of the calculatiion to the xml file. Essential information, like the xc functional, U values, magnetic state should be given.",
type=str,
default="Calculated with TB2J.")
parser.add_argument("--spinor",
action="store_true",
help="Whether to use spinor wannier function.",
default=False)
parser.add_argument(
"--orb_decomposition",
default=False,
action='store_true',
help="whether to do orbital decomposition in the non-collinear mode.")
parser.add_argument(
"--output_path",
help="The path of the output directory, default is TB2J_results",
type=str,
default="TB2J_results")
parser.add_argument(
"--wannier_type",
help="The type of Wannier function, either Wannier90 or banddownfolder",
type=str,
default="Wannier90")
# parser.add_argument("--qspace",
# action="store_true",
# help="Whether to calculate J in qspace first and transform to real space.",
# default=False)
args = parser.parse_args()
if args.efermi is None:
print("Please input fermi energy using --efermi ")
sys.exit()
if args.elements is None:
print("Please input the magnetic elements, e.g. --elements Fe Ni")
sys.exit()
gen_exchange(
path=args.path,
colinear=(not args.spinor),
groupby=args.groupby,
posfile=args.posfile,
efermi=args.efermi,
kmesh=args.kmesh,
magnetic_elements=args.elements,
Rcut=args.rcut,
prefix_SOC=args.prefix_spinor,
prefix_up=args.prefix_up,
prefix_dn=args.prefix_down,
emin=args.emin,
emax=args.emax,
nz=args.nz,
# height=args.height,
# nz1=args.nz1,
# nz2=args.nz2,
# nz3=args.nz3,
use_cache=args.use_cache,
np=args.np,
description=args.description,
output_path=args.output_path,
exclude_orbs=args.exclude_orbs,
wannier_type=args.wannier_type,
# qspace=args.qspace,
orb_decomposition=args.orb_decomposition)
def run_wann2J():
print_license()
parser = argparse.ArgumentParser(
description=
"wann2J: Using magnetic force theorem to calculate exchange parameter J from wannier functions"
)
parser.add_argument('--path',
help="path to the wannier files",
default='./',
type=str)
parser.add_argument('--posfile',
help="name of the position file",
default='POSCAR',
type=str)
parser.add_argument('--prefix_spinor',
help="prefix to the spinor wannier files",
default='wannier90',
type=str)
parser.add_argument('--prefix_up',
help="prefix to the spin up wannier files",
default='wannier90.up',
type=str)
parser.add_argument('--prefix_down',
help="prefix to the spin down wannier files",
default='wannier90.dn',
type=str)
parser.add_argument('--elements',
help="elements to be considered in Heisenberg model",
default=None,
type=str,
nargs='*')
parser.add_argument(
'--orb_order',
help=
"In the spinor case, the order of the orbitals have two conventions: (orb1_up, orb2_up,... orb1_down, ...), (orb1_up, orb1_down, orb2_up, ...,). Use 1 in the former case and 2 in the latter case. The default is 1.",
default=1,
type=int,
)
parser.add_argument(
'--rcut',
help=
'cutoff of spin pair distance. The default is to calculate all commensurate R point to the k mesh.',
default=None,
type=float)
parser.add_argument('--efermi',
help='Fermi energy in eV',
default=None,
type=float)
parser.add_argument('--kmesh',
help='kmesh in the format of kx ky kz',
type=int,
nargs='*',
default=[5, 5, 5])
parser.add_argument('--emin',
help='energy minimum below efermi, default -14 eV',
type=float,
default=-14.0)
parser.add_argument('--emax',
help='energy maximum above efermi, default 0.0 eV',
type=float,
default=0.0)
parser.add_argument(
'--nz',
help='number of steps for semicircle contour, default: 100',
default=100,
type=int)
parser.add_argument(
'--height',
help=
'energy contour, a small number (often between 0.1 to 0.5, default 0.1)',
type=float,
default=0.1)
parser.add_argument('--nz1',
help='number of steps 1, default: 50',
default=50,
type=int)
parser.add_argument('--nz2',
help='number of steps 2, default: 200',
default=200,
type=int)
parser.add_argument('--nz3',
help='number of steps 3, default: 50',
default=50,
type=int)
parser.add_argument(
'--cutoff',
help="The minimum of J amplitude to write, (in eV), default is 1e-5 eV",
default=1e-5,
type=float)
parser.add_argument(
'--exclude_orbs',
help=
"the indices of wannier functions to be excluded from magnetic site. counting start from 0",
default=[],
type=int,
nargs='+')
parser.add_argument(
"--description",
help=
"add description of the calculatiion to the xml file. Essential information, like the xc functional, U values, magnetic state should be given.",
type=str,
default="Calculated with TB2J.")
parser.add_argument("--spinor",
action="store_true",
help="Whether to use spinor wannier function.",
default=False)
args = parser.parse_args()
if args.efermi is None:
print("Please input fermi energy using --efermi ")
sys.exit()
if args.elements is None:
print("Please input the magnetic elements, e.g. --elements Fe Ni")
sys.exit()
if args.orb_order not in (1, 2):
print("orb_order should be either 1 or 2.")
sys.exit()
gen_exchange(path=args.path,
colinear=(not args.spinor),
orb_order=args.orb_order,
posfile=args.posfile,
efermi=args.efermi,
kmesh=args.kmesh,
magnetic_elements=args.elements,
Rcut=args.rcut,
prefix_SOC=args.prefix_spinor,
prefix_up=args.prefix_up,
prefix_dn=args.prefix_down,
emin=args.emin,
emax=args.emax,
nz=args.nz,
height=args.height,
nz1=args.nz1,
nz2=args.nz2,
nz3=args.nz3,
description=args.description,
exclude_orbs=args.exclude_orbs)
def run_siesta2J():
print_license()
parser = argparse.ArgumentParser(
description=
"siesta2J: Using magnetic force theorem to calculate exchange parameter J from siesta Hamiltonian"
)
parser.add_argument('--fdf_fname',
help="path of the input fdf file",
default='./',
type=str)
parser.add_argument('--elements',
help="elements to be considered in Heisenberg model",
default=None,
type=str,
nargs='*')
parser.add_argument(
'--rcut',
help='range of R. The default is all the commesurate R to the kmesh',
default=None,
type=float)
parser.add_argument('--efermi',
help='Fermi energy in eV',
default=None,
type=float)
parser.add_argument(
'--kmesh',
help=
'kmesh in the format of kx ky kz. Monkhorst pack. If all the numbers are odd, it is Gamma cenetered. (strongly recommended)',
type=int,
nargs='*',
default=[5, 5, 5])
parser.add_argument('--emin',
help='energy minimum below efermi, default -14 eV',
type=float,
default=-14.0)
parser.add_argument('--emax',
help='energy maximum above efermi, default 0.0 eV',
type=float,
default=0.05)
#parser.add_argument(
# '--height',
# help=
# 'energy contour, a small number (often between 0.1 to 0.5, default 0.2)',
# type=float,
# default=0.1)
parser.add_argument('--nz',
help='number of integration steps, default: 50',
default=50,
type=int)
#parser.add_argument(
# '--nz2', help='number of steps 2, default: 200', default=200, type=int)
#parser.add_argument(
# '--nz3', help='number of steps 3, default: 50', default=50, type=int)
parser.add_argument(
'--cutoff',
help="The minimum of J amplitude to write, (in eV), default is 1e-5 eV",
default=1e-5,
type=float)
parser.add_argument(
'--exclude_orbs',
help=
"the indices of wannier functions to be excluded from magnetic site. counting start from 0",
default=[],
type=int,
nargs='+')
parser.add_argument(
"--description",
help=
"add description of the calculatiion to the xml file. Essential information, like the xc functional, U values, magnetic state should be given.",
type=str,
default="Calculated with TB2J.")
parser.add_argument("--fname",
default='exchange.xml',
type=str,
help='exchange xml file name. default: exchange.xml')
args = parser.parse_args()
if args.elements is None:
print("Please input the magnetic elements, e.g. --elements Fe Ni")
exit()
gen_exchange_siesta(
fdf_fname=args.fdf_fname,
kmesh=args.kmesh,
magnetic_elements=args.elements,
Rcut=args.rcut,
emin=args.emin,
emax=args.emax,
nz=args.nz,
#height=args.height,
#nz1=args.nz1,
#nz2=args.nz2,
#nz3=args.nz3,
description=args.description,
exclude_orbs=args.exclude_orbs)
def run_siesta2J():
print_license()
parser = argparse.ArgumentParser(
description=
"siesta2J: Using magnetic force theorem to calculate exchange parameter J from siesta Hamiltonian"
)
parser.add_argument('--fdf_fname',
help="path of the input fdf file",
default='./',
type=str)
parser.add_argument(
'--elements',
help=
"list of elements to be considered in Heisenberg model. For each element, a postfixes can be used to specify the orbitals(Only with Siesta backend), eg. Fe_3d, or Fe_3d_4s ",
default=None,
type=str,
nargs='*')
parser.add_argument(
'--rcut',
help='range of R. The default is all the commesurate R to the kmesh',
default=None,
type=float)
parser.add_argument('--efermi',
help='Fermi energy in eV. For test only. ',
default=None,
type=float)
parser.add_argument(
'--kmesh',
help=
'kmesh in the format of kx ky kz. Monkhorst pack. If all the numbers are odd, it is Gamma cenetered. (strongly recommended), Default: 5 5 5',
type=int,
nargs='*',
default=[5, 5, 5])
parser.add_argument('--emin',
help='energy minimum below efermi, default -14 eV',
type=float,
default=-14.0)
parser.add_argument('--emax',
help='energy maximum above efermi. Default 0.0 eV',
type=float,
default=0.05)
parser.add_argument(
'--use_cache',
help=
"whether to use disk file for temporary storing wavefunctions and hamiltonian to reduce memory usage. Default: False",
action='store_true',
default=False)
# parser.add_argument(
# '--height',
# help=
# 'energy contour, a small number (often between 0.1 to 0.5, default 0.2)',
# type=float,
# default=0.1)
parser.add_argument('--nz',
help='number of integration steps. Default: 50',
default=50,
type=int)
# parser.add_argument(
# '--nz2', help='number of steps 2, default: 200', default=200, type=int)
# parser.add_argument(
# '--nz3', help='number of steps 3, default: 50', default=50, type=int)
parser.add_argument(
'--cutoff',
help="The minimum of J amplitude to write, (in eV). Default: 1e-5 eV",
default=1e-5,
type=float)
parser.add_argument(
'--exclude_orbs',
help=
"the indices of wannier functions to be excluded from magnetic site. counting start from 0. Default is none.",
default=[],
type=int,
nargs='+')
parser.add_argument(
'--np',
help='number of cpu cores to use in parallel, default: 1',
default=1,
type=int)
parser.add_argument(
"--description",
help=
"add description of the calculatiion to the xml file. Essential information, like the xc functional, U values, magnetic state should be given.",
type=str,
default="Calculated with TB2J.")
parser.add_argument(
"--orb_decomposition",
default=False,
action='store_true',
help=
"whether to do orbital decomposition in the non-collinear mode. Default: False."
)
parser.add_argument("--fname",
default='exchange.xml',
type=str,
help='exchange xml file name. default: exchange.xml')
parser.add_argument(
"--output_path",
help="The path of the output directory, default is TB2J_results",
type=str,
default="TB2J_results")
args = parser.parse_args()
if args.elements is None:
print("Please input the magnetic elements, e.g. --elements Fe Ni")
sys.exit()
include_orbs = {}
for element in args.elements:
if "_" in element:
elem = element.split("_")[0]
orb = element.split("_")[1:]
include_orbs[elem] = orb
else:
include_orbs[element] = None
gen_exchange_siesta(fdf_fname=args.fdf_fname,
kmesh=args.kmesh,
magnetic_elements=list(include_orbs.keys()),
include_orbs=include_orbs,
Rcut=args.rcut,
emin=args.emin,
emax=args.emax,
nz=args.nz,
description=args.description,
output_path=args.output_path,
use_cache=args.use_cache,
np=args.np,
exclude_orbs=args.exclude_orbs,
orb_decomposition=args.orb_decomposition)