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Allow the use of external potential files. 

A new keyword in TMatrixParameters allows to use an external
file for the potential energy of atoms. It should be used like
this:
    calc.tmatrix_parameters.potential = 'spkkr'
    calc.tmatrix_parameters.potential_file = 'Cu.pot' # the name does not matter
This commit is contained in:
Sylvain Tricot 2020-03-26 18:26:27 +01:00
parent 15b344cf5f
commit 927ac8a8a3
3 changed files with 130 additions and 108 deletions
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33
src/msspec/calculator.py
View File

@ -1,5 +1,5 @@
# coding: utf-8
# vim: set et sw=4 ts=4 sts=4 nu ai cc=+0 fdm=indent mouse=a:
# vim: set et sw=4 ts=4 sts=4 nu ai cc=+0 fdm=indent mouse=a tw=80:
"""
Module calculator
=================
@ -47,7 +47,8 @@ import numpy as np
from msspec import iodata
from msspec.data import electron_be
from msspec.config import Config
from msspec.misc import (UREG, LOGGER, get_call_info, get_level_from_electron_configuration,
from msspec.misc import (UREG, LOGGER, get_call_info,
get_level_from_electron_configuration,
XRaySource, set_log_output, log_process_output)
from msspec.utils import get_atom_index
@ -62,9 +63,9 @@ from msspec.calcio import PhagenIO, SpecIO
from msspec.phagen.fortran.libphagen import main as do_phagen
from msspec.spec.fortran import phd_se_noso_nosp_nosym, phd_mi_noso_nosp_nosym
from msspec.spec.fortran import eig_mi
from msspec.spec.fortran import eig_pw
from msspec.spec.fortran import _phd_se_noso_nosp_nosym, _phd_mi_noso_nosp_nosym
from msspec.spec.fortran import _eig_mi
from msspec.spec.fortran import _eig_pw
from terminaltables.ascii_table import AsciiTable
@ -289,14 +290,21 @@ class _MSCALCULATOR(Calculator):
# run phagen
#self._make('tmatrix')
os.chdir(os.path.join(self.tmp_folder, 'output'))
# copy external potential file to the workspace
if self.tmatrix_parameters.potential in ('lmto', 'spkkr', 'msf'):
fname = os.path.join(self.init_folder,
self.tmatrix_parameters.potential_file)
shutil.copy(fname, 'fort.2')
do_phagen()
# rename some output files to be more explicit
#os.rename('fort.10', 'cluster.clu')
#os.rename('fort.35', 'tmatrix.tl')
#os.rename('fort.55', 'tmatrix.rad')
shutil.copy('fort.10', 'cluster.clu')
#shutil.copy('fort.10', 'cluster.clu')
shutil.copy('clus/clus.out', 'cluster.clu')
shutil.copy('fort.35', 'tmatrix.tl')
shutil.copy('fort.55', 'tmatrix.rad')
os.chdir(self.init_folder)
@ -362,9 +370,9 @@ class _MSCALCULATOR(Calculator):
# Get the spec function to launch
if self.global_parameters.spectroscopy == 'PED':
if self.global_parameters.algorithm == 'expansion':
do_spec = phd_se_noso_nosp_nosym.run
do_spec = _phd_se_noso_nosp_nosym.run
elif self.global_parameters.algorithm == 'inversion':
do_spec = phd_mi_noso_nosp_nosym.run
do_spec = _phd_mi_noso_nosp_nosym.run
else:
LOGGER.error("\'{}\' spectroscopy with \'{}\' algorithm is not "
"an allowed combination.".format(self.global_parameters.spectroscopy,
@ -372,9 +380,9 @@ class _MSCALCULATOR(Calculator):
raise ValueError
elif self.global_parameters.spectroscopy == 'EIG':
if self.global_parameters.algorithm == 'inversion':
do_spec = eig_mi.run
do_spec = _eig_mi.run
elif self.global_parameters.algorithm == 'power':
do_spec = eig_pw.run
do_spec = _eig_pw.run
else:
LOGGER.error("\'{}\' spectroscopy with \'{}\' algorithm is not "
"an allowed combination.".format(self.global_parameters.spectroscopy,
@ -745,7 +753,10 @@ class _PED(_MSCALCULATOR):
filename = os.path.join(self.tmp_folder, 'output/cluster.clu')
self.phagenio.load_cluster_file(filename)
filename = os.path.join(self.tmp_folder, 'bin/plot/plot_vc.dat')
if self.phagen_parameters.potgen in ('in'):
filename = os.path.join(self.tmp_folder, 'output/plot/plot_vc.dat')
else:
filename = os.path.join(self.tmp_folder, 'output/plot/plot_v.dat')
pot_data = self.phagenio.load_potential_file(filename)
cluster = self.phagen_parameters.get_parameter('atoms').value

174
src/msspec/misc.py
View File

@ -1,86 +1,88 @@
# coding: utf-8
"""
Module misc
===========
"""
import logging
from pint import UnitRegistry
import numpy as np
import inspect
import re
class XRaySource(object):
MG_KALPHA = 1253.6
AL_KALPHA = 1486.6
def __init__(self):
pass
UREG = UnitRegistry()
UREG.define('rydberg = c * h * rydberg_constant = Ry')
UREG.define('bohr_radius = 4 * pi * epsilon_0 * hbar**2 / electron_mass / e**2 = a0')
logging.basicConfig(level=logging.INFO)
LOGGER = logging.getLogger('msspec')
np.set_printoptions(formatter={'float': lambda x:'%.2f' % x}, threshold=5)
def set_log_level(level):
lvl = getattr(logging, level.upper())
LOGGER.setLevel(lvl)
def set_log_output(stream):
LOGGER.parent.handlers[0].stream = stream
def get_call_info(frame):
args, varargs, varkw, loc = inspect.getargvalues(frame)
_, _, function, _, _ = inspect.getframeinfo(frame)
s = '%s called with:\n' % function
for kws in (args, varargs, varkw):
if kws != None:
if isinstance(kws, (tuple, list)):
for kw in kws:
s += '\t\t%s = %r\n' % (kw, loc[kw])
else:
s += '\t\t%s = %r\n' % (kws, loc[kws])
return s.strip()
def log_process_output(process, logger=None, severity=logging.INFO):
if logger == None:
logger = logging
else:
logger = logging.getLogger(logger)
logger.setLevel(LOGGER.getEffectiveLevel())
for line in iter(process.stdout.readline, b''):
logger.log(severity, line.rstrip('\n'))
process.stdout.close()
process.wait()
def get_level_from_electron_configuration(notation):
l_letters = 'spdfghiklmnoqrtuv'
n_letters = 'klmnopqrstuv'
pattern = re.compile(r'(?P<n>\d+)(?P<l>[%s%s])'
r'((?P<j>\d)/2)?' % (l_letters, l_letters.upper()))
m = pattern.match(notation)
assert m, 'Not a valid notation'
n, l, _, j = m.groups()
n = int(n)
l = l_letters.index(l.lower())
assert (l < n), 'Invalid l'
j1 = abs(l - 0.5)
j2 = abs(l + 0.5)
if j:
j = int(j) / 2.
else:
j = j1
assert j in (j1, j2), 'Invalid j'
letter = n_letters[n - 1]
subscript = str(int((2 * (l + j) + 1) / 2))
if letter == 'k':
subscript = ''
return '{}{}'.format(letter, subscript)
# coding: utf-8
# vim: set fdm=indent ts=4 sw=4 sts=4 et tw=80 ai cc=+0 mouse=a nu : #
"""
Module misc
===========
"""
import logging
from pint import UnitRegistry
import numpy as np
import inspect
import re
import os
class XRaySource(object):
MG_KALPHA = 1253.6
AL_KALPHA = 1486.6
def __init__(self):
pass
UREG = UnitRegistry()
UREG.define('rydberg = c * h * rydberg_constant = Ry')
UREG.define('bohr_radius = 4 * pi * epsilon_0 * hbar**2 / electron_mass / e**2 = a0')
logging.basicConfig(level=logging.INFO)
LOGGER = logging.getLogger('msspec')
np.set_printoptions(formatter={'float': lambda x:'%.2f' % x}, threshold=5)
def set_log_level(level):
lvl = getattr(logging, level.upper())
LOGGER.setLevel(lvl)
def set_log_output(stream):
LOGGER.parent.handlers[0].stream = stream
def get_call_info(frame):
args, varargs, varkw, loc = inspect.getargvalues(frame)
_, _, function, _, _ = inspect.getframeinfo(frame)
s = '%s called with:\n' % function
for kws in (args, varargs, varkw):
if kws != None:
if isinstance(kws, (tuple, list)):
for kw in kws:
s += '\t\t%s = %r\n' % (kw, loc[kw])
else:
s += '\t\t%s = %r\n' % (kws, loc[kws])
return s.strip()
def log_process_output(process, logger=None, severity=logging.INFO):
if logger == None:
logger = logging
else:
logger = logging.getLogger(logger)
logger.setLevel(LOGGER.getEffectiveLevel())
for line in iter(process.stdout.readline, b''):
logger.log(severity, line.rstrip('\n'))
process.stdout.close()
process.wait()
def get_level_from_electron_configuration(notation):
l_letters = 'spdfghiklmnoqrtuv'
n_letters = 'klmnopqrstuv'
pattern = re.compile(r'(?P<n>\d+)(?P<l>[%s%s])'
r'((?P<j>\d)/2)?' % (l_letters, l_letters.upper()))
m = pattern.match(notation)
assert m, 'Not a valid notation'
n, l, _, j = m.groups()
n = int(n)
l = l_letters.index(l.lower())
assert (l < n), 'Invalid l'
j1 = abs(l - 0.5)
j2 = abs(l + 0.5)
if j:
j = int(j) / 2.
else:
j = j1
assert j in (j1, j2), 'Invalid j'
letter = n_letters[n - 1]
subscript = str(int((2 * (l + j) + 1) / 2))
if letter == 'k':
subscript = ''
return '{}{}'.format(letter, subscript)

31
src/msspec/parameters.py
View File

@ -265,6 +265,7 @@ class BaseParameters(object):
class PhagenParameters(BaseParameters):
def __init__(self):
parameters = (
Parameter('version', types=(str,), fmt='>3s', default='1.1'),
Parameter('calctype', allowed_values=('xpd', 'xas', 'aed', 'led',
'rex', 'els', 'e2e'#, 'dos'
),
@ -273,7 +274,7 @@ class PhagenParameters(BaseParameters):
types=(str,), default='cis'),
Parameter('coor', allowed_values=('angs', 'au'), types=(str,),
default='angs'),
Parameter('enunit', allowed_values=('ryd', 'eV'), fmt='3>s',
Parameter('enunit', allowed_values=('ryd', 'eV'), fmt='>3s',
types=(str,), default='ryd'),
Parameter('einc', types=(int, float), limits=(0, None), fmt='.1f',
default=700.),
@ -281,7 +282,7 @@ class PhagenParameters(BaseParameters):
default=580.),
Parameter('scangl', types=(int, float), limits=(0, 360), fmt='.2f',
default=0.),
Parameter('lambda', types=(int, float), fmt='.2f', default=20.),
Parameter('lambda', types=(int, float), fmt='.1f', default=0.),
Parameter('emin', types=(int, float), limits=(0, None), fmt='.4f',
default=13.5236),
Parameter('emax', types=(int, float), limits=(0, None), fmt='.4f',
@ -294,9 +295,9 @@ class PhagenParameters(BaseParameters):
default='in'),
Parameter('potype', allowed_values=('hdrel', 'hedin', 'xalph',
'dhrel', 'dhcmp',
#'lmto', 'msf', 'spkkr'
'lmto', 'msf', 'spkkr'
),
types=(str,), fmt='5>s', default='hedin'),
types=(str,), fmt='>5s', default='hedin'),
Parameter('relc', allowed_values=('nr', 'sr', 'so'), types=(str,),
default='nr'),
Parameter('norman', allowed_values=('stdcrm', 'scaled', 'extrad'),
@ -308,9 +309,9 @@ class PhagenParameters(BaseParameters):
Parameter('charelx', allowed_values=('ex', 'gs'), types=(str,),
default='gs'),
Parameter('ionzst', allowed_values=('neutral', 'ionic'),
types=(str,), fmt='7>s', default='neutral'),
types=(str,), fmt='>7s', default='neutral'),
Parameter('eikappr', allowed_values=('yes', 'no'), types=(str,),
fmt='3>s', default='no'),
fmt='>3s', default='no'),
Parameter('db', types=(int, float), fmt='.2f', default=0.01),
Parameter('optrsh', allowed_values=('y', 'n'), types=(str,),
default='n'),
@ -885,11 +886,12 @@ class TMatrixParameters(BaseParameters):
def __init__(self, phagen_parameters):
parameters = (
Parameter('potential', types=str,
allowed_values=('muffin_tin', 'lmto'),
allowed_values=('muffin_tin', 'lmto', 'spkkr', 'msf'),
default='muffin_tin', doc=textwrap.dedent("""
This option allows to choose which kind of potential is used to compute the T-Matrix. For now,
only the internal *Muffin-Tin* potential is supported.
""")),
Parameter('potential_file', types=(str,type(None)), default=None),
Parameter('exchange_correlation', types=str,
allowed_values=('hedin_lundqvist_real',
'hedin_lundqvist_complex',
@ -955,8 +957,12 @@ class TMatrixParameters(BaseParameters):
self.freeze()
def bind_potential(self, p):
mapping = {'muffin_tin': 'in', 'lmto': 'ex'}
self.phagen_parameters.potgen = mapping[p.value]
mapping = {'muffin_tin': 'in', 'lmto': 'ex', 'spkkr': 'ex', 'msf': 'ex'}
if p.value.lower() in ('muffin_tin'):
self.phagen_parameters.potgen = 'in'
elif p.value.lower() in ('spkkr', 'lmto', 'msf'):
self.phagen_parameters.potgen = 'ex'
self.phagen_parameters.potype = p.value.lower()
def bind_exchange_correlation(self, p):
potential = self.get_parameter('potential').value
@ -969,8 +975,11 @@ class TMatrixParameters(BaseParameters):
'dirac_hara_complex': 'dhcmp'
}
self.phagen_parameters.potype = mapping[p.value]
elif potential == 'lmto':
self.phagen_parameters.potype = 'lmto'
else:
self.phagen_parameters.potype = potential
def bind_potential_file(self, p):
pass
def bind_imaginery_part(self, p):
self.phagen_parameters.gamma = p.value