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pylint (unused import)

This commit is contained in:
gmatteo 2019-10-16 01:13:50 +02:00
parent 5425a402d9
commit b22680d09b
68 changed files with 108 additions and 462 deletions
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3
abipy/abilab.py
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@ -3,7 +3,6 @@ This module gathers the most important classes and helper functions used for scr
"""
from __future__ import print_function, division, unicode_literals
import sys
import os
import collections
@ -24,7 +23,7 @@ ArrayWithUnit = units.ArrayWithUnit
####################
### Abipy import ###
####################
from abipy.flowtk import Pseudo, PseudoTable, Mrgscr, Mrgddb, Mrggkk, Flow, Work, TaskManager, AbinitBuild, flow_main
from abipy.flowtk import Pseudo, PseudoTable, Mrgscr, Mrgddb, Flow, Work, TaskManager, AbinitBuild, flow_main
from abipy.core.release import __version__, min_abinit_version
from abipy.core.globals import enable_notebook, in_notebook, disable_notebook
from abipy.core import restapi

3
abipy/abio/abivars.py
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@ -1,5 +1,4 @@
"""This module contains lookup table with the name of the ABINIT variables."""
import json
import os
import warnings
import numpy as np
@ -547,7 +546,7 @@ class AbinitInputParser(object):
if m:
tok = tok.replace("sqrt", "math.sqrt")
tok = str(eval(tok))
if "/" in tok: # Note true_division from __future__
if "/" in tok:
tok = str(eval(tok))
values.append(tok)
return values

4
abipy/abio/abivars_db.py
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@ -1,12 +1,8 @@
"""Database with the names of the input variables used in Abinit and in other main programs."""
import sys
import os
from collections import OrderedDict
# Unit names.
# Operators.
from abipy.abio.abivar_database.variables import ABI_UNITS, ABI_OPS
##############
# Public API #

1
abipy/abio/factories.py
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@ -9,7 +9,6 @@ from monty.collections import AttrDict
from monty.string import is_string
from monty.json import jsanitize, MontyDecoder
from pymatgen.util.serialization import pmg_serialize
from abipy.flowtk import PseudoTable
from abipy.core.structure import Structure
from abipy.abio.inputs import AbinitInput, MultiDataset
from abipy.abio.input_tags import *

18
abipy/abio/inputs.py
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@ -4,7 +4,6 @@ The syntax is similar to the one used in ABINIT with small differences.
"""
import os
import collections
import warnings
import itertools
import copy
import time
@ -263,10 +262,10 @@ class AbiAbstractInput(AbstractInput):
the corresponding variables to the input.
"""
d = {}
for aobj in abi_objects:
if not hasattr(aobj, "to_abivars"):
raise TypeError("type %s: %s does not have `to_abivars` method" % (type(aobj), repr(aobj)))
d.update(self.set_vars(aobj.to_abivars()))
for obj in abi_objects:
if not hasattr(obj, "to_abivars"):
raise TypeError("type %s: %s does not have `to_abivars` method" % (type(obj), repr(obj)))
d.update(self.set_vars(obj.to_abivars()))
return d
@abc.abstractmethod
@ -369,12 +368,9 @@ class AbinitInput(AbiAbstractInput, MSONable, Has_Structure):
import hashlib
sha1 = hashlib.sha1()
try:
tos = unicode
except NameError:
# Py3K
def tos(s):
return str(s).encode(encoding="utf-8")
# Py3K
def tos(s):
return str(s).encode(encoding="utf-8")
# Add key, values to sha1
# (not sure this is code is portable: roundoff errors and conversion to string)

2
abipy/abio/outputs.py
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@ -370,7 +370,7 @@ class AbinitOutputFile(AbinitTextFile, NotebookWriter):
if self.run_completed:
return self._get_structures("footer")
else:
print("Cannot extract final structures from file.\n %s" % str(exc))
cprint("Cannot extract final structures from file.\n %s" % self.filepath, "red")
return []
@lazy_property

2
abipy/abio/robots.py
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@ -692,7 +692,7 @@ Expecting callable or attribute name or key in abifile.params""" % (type(hue), s
if self._do_close.pop(abifile.filepath, False):
try:
abifile.close()
except Exception:
except Exception as exc:
print("Exception while closing: ", abifile.filepath)
print(exc)

1
abipy/abio/variable.py
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@ -1,5 +1,4 @@
import string
import warnings
import collections
import numpy as np

4
abipy/core/fields.py
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@ -8,7 +8,7 @@ import os
from collections import OrderedDict
from monty.collections import AttrDict
from monty.functools import lazy_property
from monty.string import is_string
from monty.string import is_string, marquee
from monty.termcolor import cprint
from monty.inspect import all_subclasses
from pymatgen.io.vasp.inputs import Poscar
@ -502,7 +502,7 @@ class _Field(Has_Structure):
elif self.nspinor == 2:
raise NotImplementedError()
ntot, mx, my, mz = scalvec_from_spinmat(res_nspden)
#ntot, mx, my, mz = scalvec_from_spinmat(res_nspden)
nup, ndown = 0.5 * (ntot + mz), 0.5 * (ntot - mz)
# Fill DataFrame row.

1
abipy/core/func1d.py
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@ -3,7 +3,6 @@
Function1D describes a function of a single variable and provides an easy-to-use API
for performing common tasks such as algebraic operations, integrations, differentiations, plots ...
"""
import itertools
import numpy as np
from io import StringIO

5
abipy/core/kpoints.py
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@ -8,10 +8,9 @@ import numpy as np
from itertools import product
from tabulate import tabulate
from monty.json import MSONable, MontyEncoder
from monty.json import MontyEncoder
from monty.collections import AttrDict, dict2namedtuple
from monty.functools import lazy_property
from monty.termcolor import cprint
from monty.string import marquee
from pymatgen.core.lattice import Lattice
from pymatgen.util.serialization import pmg_serialize
@ -348,7 +347,7 @@ def map_kpoints(other_kpoints, other_lattice, ref_lattice, ref_kpoints, ref_symr
found = False
for ik_ref, kref in enumerate(ref_kpoints):
if found: break
for tsign in tsign:
for tsign in tsigns:
for isym, symrec in enumerate(ref_symrecs):
krot = tsign * np.matmul(symrec, kref)
if issamek(okpt_red, krot):

5
abipy/core/mesh3d.py
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@ -3,10 +3,9 @@
import numpy as np
from itertools import product as iproduct
from collections import deque
#from itertools import product as iproduct
from monty.functools import lazy_property
from numpy.random import random
#from numpy.random import random
from numpy.fft import fftn, ifftn, fftshift, ifftshift, fftfreq
from abipy.tools import duck

5
abipy/core/mixins.py
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@ -5,15 +5,14 @@ import os
import collections
import tempfile
import pickle
import numpy as np
from time import ctime
import numpy as np
from monty.os.path import which
from monty.termcolor import cprint
from monty.string import is_string, list_strings
from monty.string import list_strings
from monty.collections import dict2namedtuple
from monty.functools import lazy_property
from abipy.flowtk.netcdf import NetcdfReader, NO_DEFAULT
__all__ = [

1
abipy/core/restapi.py
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@ -7,7 +7,6 @@ import sys
from collections import OrderedDict
from pprint import pprint
from monty.functools import lazy_property
from monty.collections import dict2namedtuple
from monty.string import marquee
from pymatgen import SETTINGS
from pymatgen.ext.matproj import MPRester, MPRestError

5
abipy/core/structure.py
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@ -11,7 +11,7 @@ import pickle
import pymatgen
import pymatgen.core.units as pmg_units
from pprint import pprint, pformat
from pprint import pformat
from warnings import warn
from collections import OrderedDict
from monty.collections import AttrDict, dict2namedtuple
@ -25,7 +25,7 @@ from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt
from abipy.flowtk import PseudoTable
from abipy.core.mixins import NotebookWriter
from abipy.core.symmetries import AbinitSpaceGroup
from abipy.iotools import as_etsfreader, Visualizer, xsf
from abipy.iotools import as_etsfreader, Visualizer
from abipy.flowtk.abiobjects import structure_from_abivars, structure_to_abivars
@ -1264,7 +1264,6 @@ class Structure(pymatgen.Structure, NotebookWriter):
"""
from pymatgen.electronic_structure.plotter import plot_brillouin_zone, plot_brillouin_zone_from_kpath
labels = None if not with_labels else self.hsym_kpath.kpath["kpoints"]
#pprint(labels)
if pmg_path:
return plot_brillouin_zone_from_kpath(self.hsym_kpath, ax=ax, show=False, **kwargs)
else:

21
abipy/core/symmetries.py
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@ -10,6 +10,7 @@ import spglib
from monty.string import is_string
from monty.itertools import iuptri
from monty.functools import lazy_property
from monty.termcolor import cprint
from monty.collections import dict2namedtuple
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.serialization import SlotPickleMixin
@ -699,17 +700,17 @@ class AbinitSpaceGroup(OpSequence):
has_timerev=has_timrev_from_kptopt(kptopt),
inord=inord)
@classmethod
def from_file(cls, ncfile, inord="F"):
"""
Initialize the object from a Netcdf file.
"""
r, closeit = as_etsfreader(ncfile)
new = cls.from_ncreader(r)
if closeit:
file.close()
#@classmethod
#def from_file(cls, ncfile, inord="F"):
# """
# Initialize the object from a Netcdf file.
# """
# r, closeit = as_etsfreader(ncfile)
# new = cls.from_ncreader(r)
# if closeit:
# file.close()
return new
# return new
@classmethod
def from_structure(cls, structure, has_timerev=True, symprec=1e-5, angle_tolerance=5):

3
abipy/dfpt/anaddbnc.py
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@ -199,8 +199,7 @@ class AnaddbNcFile(AbinitNcFile, Has_Structure, NotebookWriter):
try:
return InteratomicForceConstants.from_file(self.filepath)
except Exception as exc:
#print(exc)
#cprint("Interatomic force constants have not been calculated. Returning None", "red")
cprint("Interatomic force constants have not been calculated. Returning None", "red")
return None
@lazy_property

22
abipy/dfpt/ddb.py
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@ -11,12 +11,12 @@ import abipy.core.abinit_units as abu
from collections import OrderedDict
from functools import lru_cache
from monty.string import marquee, list_strings
from monty.collections import AttrDict, dict2namedtuple, tree
from monty.collections import AttrDict, dict2namedtuple
from monty.functools import lazy_property
from monty.termcolor import cprint
from monty.dev import deprecated
from pymatgen.core.units import eV_to_Ha, bohr_to_angstrom, ang_to_bohr, Energy
from abipy.flowtk import NetcdfReader, AnaddbTask
from pymatgen.core.units import eV_to_Ha, bohr_to_angstrom, Energy
from abipy.flowtk import AnaddbTask
from abipy.core.mixins import TextFile, Has_Structure, NotebookWriter
from abipy.core.symmetries import AbinitSpaceGroup
from abipy.core.structure import Structure
@ -28,7 +28,7 @@ from abipy.dfpt.phonons import PhononDosPlotter, PhononBandsPlotter
from abipy.dfpt.ifc import InteratomicForceConstants
from abipy.dfpt.elastic import ElasticData
from abipy.core.abinit_units import phfactor_ev2units, phunit_tag
from abipy.tools.plotting import Marker, add_fig_kwargs, get_ax_fig_plt, set_axlims, get_axarray_fig_plt
from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt
from abipy.tools import duck
from abipy.tools.tensors import DielectricTensor, ZstarTensor, Stress
from abipy.abio.robots import Robot
@ -1138,7 +1138,7 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
plotter: |PhononDosPlotter| object.
Client code can use ``plotter.gridplot()`` to visualize the results.
"""
num_cpus = get_ncpus() // 2 if num_cpus is None else num_cpus
#num_cpus = get_ncpus() // 2 if num_cpus is None else num_cpus
if num_cpus <= 0: num_cpus = 1
num_cpus = min(num_cpus, len(nqsmalls))
@ -1840,7 +1840,7 @@ class DielectricTensorGenerator(Has_Structure):
# the possible imaginary parts of degenerate modes will cancel.
if duck.is_listlike(gamma_ev):
gammas = np.asarray(gamma_ev)
assert len(gammas) == len(phfreqs)
assert len(gammas) == len(self.phfreqs)
else:
gammas = np.ones(len(self.phfreqs)) * float(gamma_ev)
@ -1850,17 +1850,9 @@ class DielectricTensorGenerator(Has_Structure):
t += self.oscillator_strength[i].real / (self.phfreqs[i]**2 - w**2 - 1j*g)
vol = self.structure.volume / bohr_to_angstrom ** 3
t = 4 * np.pi * t / vol / eV_to_Ha**2
t = 4 * np.pi * t / vol / eV_to_Ha ** 2
t += self.epsinf
#t = np.zeros((3, 3))
#w = w * eV_to_Ha
#for i in range(3, len(self.phfreqs)):
# phw = self.phfreqs[i] * eV_to_Ha
# t += self.oscillator_strength[i].real / (phw**2 - w**2)
#t *= 4 * np.pi / (self.structure.volume * ang_to_bohr ** 3)
#t += self.epsinf
return DielectricTensor(t)
@add_fig_kwargs

4
abipy/dfpt/phonons.py
View File

@ -1,5 +1,4 @@
# coding: utf-8
import sys
import functools
import numpy as np
import itertools
@ -11,7 +10,7 @@ import abipy.core.abinit_units as abu
from collections import OrderedDict
from monty.string import is_string, list_strings, marquee
from monty.collections import AttrDict, dict2namedtuple
from monty.collections import dict2namedtuple
from monty.functools import lazy_property
from monty.termcolor import cprint
from pymatgen.core.units import eV_to_Ha, Energy
@ -3671,7 +3670,6 @@ class PhononDosPlotter(NotebookWriter):
titles = list(self._phdoses_dict.keys())
phdos_list = list(self._phdoses_dict.values())
import matplotlib.pyplot as plt
nrows, ncols = 1, 1
numeb = len(phdos_list)
if numeb > 1:

1
abipy/display/utils.py
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@ -4,7 +4,6 @@
import ipywidgets as ipw
from collections import OrderedDict
from abipy.tools.plotting import get_ax_fig_plt
#def add_docstrings(*tuples):

8
abipy/electrons/bse.py
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@ -1,13 +1,11 @@
# coding: utf-8
"""Classes for the analysis of BSE calculations"""
import sys
import os
import itertools
import numpy as np
import pandas as pd
from collections import OrderedDict
from monty.collections import AttrDict
from monty.functools import lazy_property
from monty.string import marquee, is_string
from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt
@ -232,12 +230,6 @@ class DielectricFunction(object):
# """String with the type of calculation."""
# return self.info["calc_type"]
#def show_info(self, stream=sys.stdout):
# """Pretty print of the info."""
# import pprint
# printer = pprint.PrettyPrinter(self, width=80, depth=None, stream=stream)
# printer.pprint(self.info)
@add_fig_kwargs
def plot(self, ax=None, **kwargs):
"""

2
abipy/electrons/denpot.py
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@ -2,7 +2,7 @@
"""Density/potential files in netcdf/fortran format."""
import os
import tempfile
import numpy as np
#import numpy as np
from monty.string import marquee
from monty.termcolor import cprint

9
abipy/electrons/ebands.py
View File

@ -1,6 +1,5 @@
# coding: utf-8
"""Classes to analyse electronic structures."""
import sys
import os
import copy
import itertools
@ -16,7 +15,7 @@ from collections import OrderedDict, namedtuple
from collections.abc import Iterable
from monty.string import is_string, list_strings, marquee
from monty.termcolor import cprint
from monty.json import MSONable, MontyEncoder
from monty.json import MontyEncoder
from monty.collections import AttrDict, dict2namedtuple
from monty.functools import lazy_property
from monty.bisect import find_le, find_gt
@ -25,7 +24,7 @@ from pymatgen.electronic_structure.core import Spin as PmgSpin
from abipy.core.func1d import Function1D
from abipy.core.mixins import Has_Structure, NotebookWriter
from abipy.core.kpoints import (Kpoint, KpointList, Kpath, IrredZone, KSamplingInfo, KpointsReaderMixin,
Ktables, has_timrev_from_kptopt, map_grid2ibz, kmesh_from_mpdivs)
Ktables, has_timrev_from_kptopt, map_grid2ibz) #, kmesh_from_mpdivs)
from abipy.core.structure import Structure
from abipy.iotools import ETSF_Reader
from abipy.tools import gaussian, duck
@ -2951,7 +2950,6 @@ class ElectronBandsPlotter(NotebookWriter):
# Merge frames ignoring index (not meaningful)
data = pd.concat(frames, ignore_index=True)
import matplotlib.pyplot as plt
import seaborn as sns
if not spin_polarized:
ax, fig, plt = get_ax_fig_plt(ax=ax)
@ -2961,6 +2959,7 @@ class ElectronBandsPlotter(NotebookWriter):
sns.swarmplot(x="band", y="eig", data=data, hue="label", color=".25", ax=ax)
else:
# Generate two subplots for spin-up / spin-down channels.
import matplotlib.pyplot as plt
if ax is not None:
raise NotImplementedError("ax == None not implemented when nsppol==2")
fig, ax_list = plt.subplots(nrows=2, ncols=1, sharex=True, squeeze=False)
@ -3939,7 +3938,7 @@ class Bands3D(Has_Structure):
for ikuc, ik_ibz in enumerate(self.uc2ibz):
ucdata_sbk[:, :, ikuc] = scalars[:, :, ik_ibz]
else:
raise ValueError("Wrong inshape: %s" % str(insp))
raise ValueError("Wrong inshape: %s" % str(inshape))
return ucdata_sbk

9
abipy/electrons/fatbands.py
View File

@ -8,12 +8,12 @@ from collections import OrderedDict, defaultdict
from tabulate import tabulate
from monty.termcolor import cprint
from monty.functools import lazy_property
from monty.string import marquee, list_strings
from monty.string import marquee #, list_strings
from pymatgen.core.periodic_table import Element
from abipy.core.mixins import AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands, NotebookWriter
from abipy.electrons.ebands import ElectronsReader
from abipy.tools import gaussian
from abipy.tools.plotting import set_axlims, get_axarray_fig_plt, add_fig_kwargs, get_ax_fig_plt
from abipy.tools.plotting import set_axlims, get_axarray_fig_plt, add_fig_kwargs #, get_ax_fig_plt
def gaussians_dos(dos, mesh, width, values, energies, weights):
@ -256,7 +256,7 @@ class FatBandsFile(AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands, N
else:
print("natsph < natom. Will set to zero the PJDOS contributions for the atoms that are not included.")
assert self.natsph < self.natom
filedata = np.reshape(r.read_value(key),
filedata = np.reshape(self.reader.read_value(key),
(self.natsph, self.mbesslang**2, self.nsppol, self.mband, self.nkpt))
for i, iatom in enumerate(self.iatsph):
walm_sbk[iatom] = filedata[i]
@ -608,7 +608,7 @@ class FatBandsFile(AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands, N
# Build plot grid.
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec, GridSpecFromSubplotSpec
from matplotlib.gridspec import GridSpec #, GridSpecFromSubplotSpec
fig = plt.figure()
nrows, ncols = 2 * (mylmax+1), mylmax + 1
gspec = GridSpec(nrows=nrows, ncols=ncols, wspace=0.1, hspace=0.1)
@ -1407,6 +1407,7 @@ class FatBandsFile(AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands, N
# Build plot grid.
nrows, ncols = np.count_nonzero(self.has_atom), self.lsize
ax_mat = None
ax_mat, fig, plt = get_axarray_fig_plt(ax_mat, nrows=nrows, ncols=ncols,
sharex=True, sharey=True, squeeze=False)
ax_mat = np.reshape(ax_mat, (nrows, ncols))

3
abipy/electrons/fold2bloch.py
View File

@ -3,8 +3,7 @@
import os
import numpy as np
from collections import OrderedDict
from monty.string import marquee # is_string, list_strings,
from monty.string import marquee
from monty.functools import lazy_property
from monty.collections import dict2namedtuple
from monty.termcolor import cprint

6
abipy/electrons/gsr.py
View File

@ -7,13 +7,13 @@ import pandas as pd
import pymatgen.core.units as units
import abipy.core.abinit_units as abu
from collections import OrderedDict, defaultdict
from collections import OrderedDict
from tabulate import tabulate
from monty.string import is_string, list_strings, marquee
from monty.string import list_strings, marquee
from monty.termcolor import cprint
from monty.collections import AttrDict, dict2namedtuple
from monty.functools import lazy_property
from pymatgen.core.units import EnergyArray, ArrayWithUnit
from pymatgen.core.units import ArrayWithUnit
from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
from abipy.core.mixins import AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands, NotebookWriter
from abipy.tools.plotting import add_fig_kwargs, get_axarray_fig_plt

6
abipy/electrons/gw.py
View File

@ -6,11 +6,11 @@ import warnings
import numpy as np
import pandas as pd
from collections import namedtuple, OrderedDict, defaultdict
from collections import namedtuple, OrderedDict
from io import StringIO
from tabulate import tabulate
from monty.string import list_strings, is_string, marquee
from monty.collections import AttrDict, dict2namedtuple
from monty.collections import dict2namedtuple
from monty.functools import lazy_property
from monty.termcolor import cprint
from monty.bisect import find_le, find_ge
@ -19,7 +19,7 @@ from abipy.core.kpoints import Kpoint, KpointList, Kpath, IrredZone, has_timrev_
from abipy.core.mixins import AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter
from abipy.iotools import ETSF_Reader
from abipy.tools.plotting import (ArrayPlotter, add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt, Marker,
set_axlims, set_visible, rotate_ticklabels, ax_append_title)
set_axlims, set_visible, rotate_ticklabels)
from abipy.tools import duck
from abipy.abio.robots import Robot
from abipy.electrons.ebands import ElectronBands, RobotWithEbands

9
abipy/electrons/scr.py
View File

@ -1,22 +1,21 @@
# coding: utf-8
"""Objects to analyze the screening files produced by the GW code (optdriver 3)."""
import numpy as np
import abc
import pymatgen.core.units as pmgu
from monty.string import marquee # is_string, list_strings,
from monty.string import marquee
from monty.inspect import all_subclasses
from monty.termcolor import cprint
from monty.collections import AttrDict
from monty.functools import lazy_property
from monty.bisect import index as bs_index
from abipy.core.func1d import Function1D
from abipy.core.kpoints import Kpoint, KpointList
from abipy.core.kpoints import KpointList
from abipy.core.gsphere import GSphere
from abipy.core.mixins import AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands, NotebookWriter
from abipy.core.mixins import AbinitNcFile, Has_Header, Has_Structure, NotebookWriter
from abipy.electrons.ebands import ElectronBands
from abipy.iotools import ETSF_Reader
from abipy.tools.plotting import ArrayPlotter, plot_array, data_from_cplx_mode, add_fig_kwargs, get_ax_fig_plt, set_axlims
from abipy.tools.plotting import ArrayPlotter, data_from_cplx_mode, add_fig_kwargs, get_ax_fig_plt, set_axlims
from abipy.tools import duck
import logging

1
abipy/eph/a2f.py
View File

@ -1188,6 +1188,7 @@ class A2fRobot(Robot, RobotWithEbands, RobotWithPhbands):
if hue is None:
params_are_string = duck.is_string(params[0])
xvals = params if not params_are_string else range(len(params))
l = None
for iq, qsamp in enumerate(qsamps):
a2f_list = [ncfile.get_a2f_qsamp(qsamp) for ncfile in ncfiles]
yvals = [getattr(a2f, what) for a2f in a2f_list]

5
abipy/eph/eph_plotter.py
View File

@ -4,10 +4,7 @@ Objects to plot electronic, vibrational and e-ph properties.
"""
import numpy as np
from monty.string import marquee, list_strings
from monty.termcolor import cprint
from abipy.tools.plotting import (add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt, set_axlims, set_visible,
rotate_ticklabels, ax_append_title, set_ax_xylabels, ax_share)
from abipy.tools.plotting import (add_fig_kwargs, get_axarray_fig_plt, set_axlims, set_visible, ax_share)
from abipy.tools import duck
from abipy.electrons.ebands import ElectronBands
from abipy.dfpt.ddb import DdbFile

2
abipy/eph/gkq.py
View File

@ -8,7 +8,6 @@ import abipy.core.abinit_units as abu
from collections import OrderedDict
from monty.string import marquee
from monty.functools import lazy_property
from monty.termcolor import cprint
from abipy.core.kpoints import Kpoint
from abipy.core.mixins import AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands, NotebookWriter
from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt
@ -546,6 +545,7 @@ class GkqRobot(Robot, RobotWithEbands):
"""
nbformat, nbv, nb = self.get_nbformat_nbv_nb(title=None)
args = [(l, f.filepath) for l, f in self.items()]
nb.cells.extend([
#nbv.new_markdown_cell("# This is a markdown cell"),
nbv.new_code_cell("robot = abilab.GkqRobot(*%s)\nrobot.trim_paths()\nrobot" % str(args)),

2
abipy/eph/sigeph.py
View File

@ -27,7 +27,7 @@ from abipy.tools.plotting import (add_fig_kwargs, get_ax_fig_plt, get_axarray_fi
rotate_ticklabels, ax_append_title, set_ax_xylabels, linestyles)
from abipy.tools import gaussian, duck
from abipy.electrons.ebands import ElectronBands, ElectronDos, RobotWithEbands, ElectronBandsPlotter, ElectronDosPlotter
from abipy.dfpt.phonons import PhononDos # PhononBands, RobotWithPhbands, factor_ev2units, unit_tag, dos_label_from_units
#from abipy.dfpt.phonons import PhononDos # PhononBands, RobotWithPhbands, factor_ev2units, unit_tag, dos_label_from_units
from abipy.abio.robots import Robot
from abipy.eph.common import BaseEphReader

41
abipy/eph/transportfile.py
View File

@ -53,47 +53,6 @@ class TransportFile(AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands,
od = self.get_ebands_params()
return od
# These methods are related to the old Bolztrap2 interface
def get_transport_result(self,itemp=None,el_temp=300):
"""
Get one instance of TransportResult according to a temperature
Args:
itemp: the index of the temperature from which to create the TransportResult class
if None, read the transport value without tau
el_temp: temperature to use in the Fermi integrations
"""
reader = self.reader
wmesh, dos, idos = reader.read_dos()
if itemp is None:
wmesh, vvdos = reader.read_vvdos()
tau_temp = None
else:
wmesh, vvdos = reader.read_vvdos_tau(itemp)
tau_temp = reader.tmesh[itemp]
el_temp = tau_temp
# TODO spin
#self.nsppol
dos = dos[0]
vvdos = vvdos[:,:,0]
volume_b3 = self.structure.volume * abu.Ang_Bohr**3
fermi_ha = self.ebands.fermie * abu.eV_Ha
tr = TransportResult(wmesh,wmesh,dos,vvdos,fermi_ha,el_temp,volume_b3,self.nelect,
tau_temp=tau_temp,nsppol=reader.nsppol)
tr._L0,tr._L1,tr._L2 = reader.read_onsager(itemp)
tr._sigma,tr._seebeck,tr._kappa,_ = reader.read_transport(itemp)
return tr
def get_all_transport_results(self):
"""
Return multiple instances of TransportResults from the data in the TRANSPORT.nc file
"""
results = [self.get_transport_result(itemp=itemp) for itemp in list(range(self.ntemp))]
return TransportResultRobot(results)
@add_fig_kwargs
def plot_dos(self, ax=None, **kwargs):
"""

3
abipy/eph/v1qavg.py
View File

@ -7,7 +7,7 @@ import numpy as np
from collections import OrderedDict
from monty.string import list_strings, marquee
from monty.functools import lazy_property
from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt, linestyles
from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt
from abipy.core.mixins import AbinitNcFile, Has_Structure, NotebookWriter
from abipy.core.kpoints import Kpath
from abipy.abio.robots import Robot
@ -370,6 +370,7 @@ class V1qAvgRobot(Robot):
"""
nbformat, nbv, nb = self.get_nbformat_nbv_nb(title=None)
args = [(l, f.filepath) for l, f in self.items()]
nb.cells.extend([
#nbv.new_markdown_cell("# This is a markdown cell"),
nbv.new_code_cell("robot = abilab.V1qAvgRobot(*%s)\nrobot.trim_paths()\nrobot" % str(args)),

2
abipy/eph/v1qnu.py
View File

@ -7,7 +7,7 @@ import numpy as np
from collections import OrderedDict
from monty.string import marquee
from monty.functools import lazy_property
from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt
from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt
from abipy.core.mixins import AbinitNcFile, Has_Structure, NotebookWriter
from abipy.core.kpoints import KpointList, Kpoint
from abipy.tools import duck

7
abipy/eph/v1sym.py
View File

@ -37,10 +37,9 @@ class V1symFile(AbinitNcFile, Has_Structure, NotebookWriter):
"""
Determine the symmetrical perturbations. Meaning of pertsy:
0 for non-target perturbations.
1 for basis perturbations.
-1 for perturbations that can be found from basis perturbations.
0 for non-target perturbations.
1 for basis perturbations.
-1 for perturbations that can be found from basis perturbations.
"""
# Fortran array: nctkarr_t("pertsy_qpt", "int", "three, mpert, nqpt")))
return self.reader.read_value("pertsy_qpt")

1
abipy/examples/flows/run_ldaus.py
View File

@ -10,7 +10,6 @@ from __future__ import print_function, division, unicode_literals, absolute_impo
import sys
import os
import numpy as np
import abipy.data as abidata
import abipy.abilab as abilab
import abipy.flowtk as flowtk

2
abipy/examples/flows/run_si_ebands.py
View File

@ -16,7 +16,7 @@ import abipy.flowtk as flowtk
def make_scf_nscf_inputs(paral_kgb=0, usepaw=0):
"""Returns two input files: GS run and NSCF on a high symmetry k-mesh."""
pseudos = abidata.pseudos("14si.pspnc") if usepaw == 0 else data.pseudos("Si.GGA_PBE-JTH-paw.xml")
pseudos = abidata.pseudos("14si.pspnc") if usepaw == 0 else abidata.pseudos("Si.GGA_PBE-JTH-paw.xml")
# Get structure from cif file.
multi = abilab.MultiDataset(structure=abidata.cif_file("si.cif"), pseudos=pseudos, ndtset=2)

1
abipy/examples/flows/run_sic_relax.py
View File

@ -10,7 +10,6 @@ from __future__ import division, print_function, unicode_literals, absolute_impo
import sys
import os
import numpy as np
import abipy.abilab as abilab
import abipy.data as data

2
abipy/examples/plot/plot_fold2bloch.py
View File

@ -10,7 +10,7 @@ from __future__ import division, print_function
from abipy import abilab
import abipy.data as abidata
import numpy as np
with abilab.abiopen(abidata.ref_file("h6_FOLD2BLOCH.nc")) as ncfile:
print(ncfile)

2
abipy/flowtk/__init__.py
View File

@ -7,7 +7,7 @@ from pymatgen.io.abinit.pseudos import Pseudo, PseudoTable, PseudoParser
from pymatgen.io.abinit.netcdf import NetcdfReader
from .launcher import PyFlowScheduler, PyLauncher
from .qadapters import show_qparams, all_qtypes
from .wrappers import Mrgscr, Mrgddb, Mrggkk, Cut3D, Fold2Bloch
from .wrappers import Mrgscr, Mrgddb, Cut3D, Fold2Bloch
from .nodes import Status
from .tasks import *
from .tasks import EphTask, ElasticTask

2
abipy/flowtk/dfpt_works.py
View File

@ -1,8 +1,6 @@
# coding: utf-8
"""Work subclasses related to DFTP."""
import numpy as np
from .works import Work, MergeDdb

2
abipy/flowtk/events.py
View File

@ -12,7 +12,7 @@ import abc
import logging
import numpy as np
from monty.string import indent, is_string, list_strings
from monty.string import indent, is_string
from monty.fnmatch import WildCard
from monty.termcolor import colored
from monty.inspect import all_subclasses

193
abipy/flowtk/flows.py
View File

@ -10,10 +10,10 @@ import time
import collections
import warnings
import shutil
import copy
import tempfile
import numpy as np
from io import StringIO
from pprint import pprint
from tabulate import tabulate
from pydispatch import dispatcher
@ -30,14 +30,12 @@ from pymatgen.util.serialization import pmg_pickle_load, pmg_pickle_dump, pmg_se
from pymatgen.core.units import Memory
from pymatgen.util.io_utils import AtomicFile
from pymatgen.util.plotting import add_fig_kwargs, get_ax_fig_plt
from abipy.flowtk import wrappers
from .nodes import Status, Node, NodeError, NodeResults, Dependency, GarbageCollector, check_spectator
from .tasks import ScfTask, DdkTask, DdeTask, TaskManager, FixQueueCriticalError
from .tasks import ScfTask, TaskManager, FixQueueCriticalError
from .utils import File, Directory, Editor
from pymatgen.io.abinit.abiinspect import yaml_read_irred_perts
from .works import NodeContainer, Work, BandStructureWork, PhononWork, BecWork, G0W0Work, QptdmWork, DteWork
from .events import EventsParser # autodoc_event_handlers
from .events import EventsParser
import logging
@ -54,7 +52,6 @@ __all__ = [
"G0W0WithQptdmFlow",
"bandstructure_flow",
"g0w0_flow",
#"phonon_flow",
]
@ -1894,16 +1891,6 @@ class Flow(Node, NodeContainer, MSONable):
return self
#def new_from_input_decorators(self, new_workdir, decorators)
# """
# Return a new :class:`Flow` in which all the Abinit inputs have been
# decorated by decorators.
# """
# # The trick part here is how to assign a new id to the new nodes while maintaing the
# # correct dependencies! The safest approach would be to pass through __init__
# # instead of using copy.deepcopy()
# return flow
def show_dependencies(self, stream=sys.stdout):
"""Writes to the given stream the ASCII representation of the dependency tree."""
def child_iter(node):
@ -2883,177 +2870,3 @@ class NonLinearCoeffFlow(Flow):
print("retcode", retcode)
#if retcode != 0: return retcode
return retcode
#def phonon_flow(workdir, scf_input, ph_inputs, with_nscf=False, with_ddk=False, with_dde=False,
# manager=None, flow_class=PhononFlow, allocate=True):
# """
# Build a :class:`PhononFlow` for phonon calculations.
#
# Args:
# workdir: Working directory.
# scf_input: Input for the GS SCF run.
# ph_inputs: List of Inputs for the phonon runs.
# with_nscf: add an nscf task in front of al phonon tasks to make sure the q point is covered
# with_ddk: add the ddk step
# with_dde: add the dde step it the dde is set ddk is switched on automatically
# manager: :class:`TaskManager` used to submit the jobs
# Initialized from manager.yml if manager is None.
# flow_class: Flow class
#
# Returns:
# :class:`Flow` object
# """
# logger.critical("phonon_flow is deprecated and could give wrong results")
# if with_dde:
# with_ddk = True
#
# natom = len(scf_input.structure)
#
# # Create the container that will manage the different works.
# flow = flow_class(workdir, manager=manager)
#
# # Register the first work (GS calculation)
# # register_task creates a work for the task, registers it to the flow and returns the work
# # the 0the element of the work is the task
# scf_task = flow.register_task(scf_input, task_class=ScfTask)[0]
#
# # Build a temporary work with a shell manager just to run
# # ABINIT to get the list of irreducible pertubations for this q-point.
# shell_manager = flow.manager.to_shell_manager(mpi_procs=1)
#
# if with_ddk:
# logger.info('add ddk')
# # TODO
# # MG Warning: be careful here because one should use tolde or tolwfr (tolvrs shall not be used!)
# ddk_input = ph_inputs[0].deepcopy()
# ddk_input.set_vars(qpt=[0, 0, 0], rfddk=1, rfelfd=2, rfdir=[1, 1, 1])
# ddk_task = flow.register_task(ddk_input, deps={scf_task: 'WFK'}, task_class=DdkTask)[0]
#
# if with_dde:
# logger.info('add dde')
# dde_input = ph_inputs[0].deepcopy()
# dde_input.set_vars(qpt=[0, 0, 0], rfddk=1, rfelfd=2)
# dde_input_idir = dde_input.deepcopy()
# dde_input_idir.set_vars(rfdir=[1, 1, 1])
# dde_task = flow.register_task(dde_input, deps={scf_task: 'WFK', ddk_task: 'DDK'}, task_class=DdeTask)[0]
#
# if not isinstance(ph_inputs, (list, tuple)):
# ph_inputs = [ph_inputs]
#
# for i, ph_input in enumerate(ph_inputs):
# fake_input = ph_input.deepcopy()
#
# # Run abinit on the front-end to get the list of irreducible pertubations.
# tmp_dir = os.path.join(workdir, "__ph_run" + str(i) + "__")
# w = PhononWork(workdir=tmp_dir, manager=shell_manager)
# fake_task = w.register(fake_input)
#
# # Use the magic value paral_rf = -1 to get the list of irreducible perturbations for this q-point.
# abivars = dict(
# paral_rf=-1,
# rfatpol=[1, natom], # Set of atoms to displace.
# rfdir=[1, 1, 1], # Along this set of reduced coordinate axis.
# )
#
# fake_task.set_vars(abivars)
# w.allocate()
# w.start(wait=True)
#
# # Parse the file to get the perturbations.
# try:
# irred_perts = yaml_read_irred_perts(fake_task.log_file.path)
# except Exception:
# print("Error in %s" % fake_task.log_file.path)
# raise
#
# logger.info(irred_perts)
#
# w.rmtree()
#
# # Now we can build the final list of works:
# # One work per q-point, each work computes all
# # the irreducible perturbations for a singe q-point.
#
# work_qpt = PhononWork()
#
# if with_nscf:
# # MG: Warning this code assume 0 is Gamma!
# nscf_input = copy.deepcopy(scf_input)
# nscf_input.set_vars(kptopt=3, iscf=-3, qpt=irred_perts[0]['qpt'], nqpt=1)
# nscf_task = work_qpt.register_nscf_task(nscf_input, deps={scf_task: "DEN"})
# deps = {nscf_task: "WFQ", scf_task: "WFK"}
# else:
# deps = {scf_task: "WFK"}
#
# if with_ddk:
# deps[ddk_task] = 'DDK'
#
# logger.info(irred_perts[0]['qpt'])
#
# for irred_pert in irred_perts:
# #print(irred_pert)
# new_input = ph_input.deepcopy()
#
# #rfatpol 1 1 # Only the first atom is displaced
# #rfdir 1 0 0 # Along the first reduced coordinate axis
# qpt = irred_pert["qpt"]
# idir = irred_pert["idir"]
# ipert = irred_pert["ipert"]
#
# # TODO this will work for phonons, but not for the other types of perturbations.
# rfdir = 3 * [0]
# rfdir[idir - 1] = 1
# rfatpol = [ipert, ipert]
#
# new_input.set_vars(
# #rfpert=1,
# qpt=qpt,
# rfdir=rfdir,
# rfatpol=rfatpol,
# )
#
# if with_ddk:
# new_input.set_vars(rfelfd=3)
#
# work_qpt.register_phonon_task(new_input, deps=deps)
#
# flow.register_work(work_qpt)
#
# if allocate: flow.allocate()
#
# return flow
#
#
#def phonon_conv_flow(workdir, scf_input, qpoints, params, manager=None, allocate=True):
# """
# Create a :class:`Flow` to perform convergence studies for phonon calculations.
#
# Args:
# workdir: Working directory of the flow.
# scf_input: :class:`AbinitInput` object defining a GS-SCF calculation.
# qpoints: List of list of lists with the reduced coordinates of the q-point(s).
# params:
# To perform a converge study wrt ecut: params=["ecut", [2, 4, 6]]
# manager: :class:`TaskManager` object responsible for the submission of the jobs.
# If manager is None, the object is initialized from the yaml file
# located either in the working directory or in the user configuration dir.
# allocate: True if the flow should be allocated before returning.
#
# Return:
# :class:`Flow` object.
# """
# qpoints = np.reshape(qpoints, (-1, 3))
#
# flow = Flow(workdir=workdir, manager=manager)
#
# for qpt in qpoints:
# for gs_inp in scf_input.product(*params):
# # Register the SCF task
# work = flow.register_scf_task(gs_inp)
#
# # Add the PhononWork connected to this scf_task.
# flow.register_work(PhononWork.from_scf_task(work[0], qpoints=qpt))
#
# if allocate: flow.allocate()
# return flow

1
abipy/flowtk/gs_works.py
View File

@ -1,7 +1,6 @@
# coding: utf-8
"""Work subclasses related to GS calculations."""
import json
import numpy as np
from .works import Work
from abipy.core.structure import Structure

2
abipy/flowtk/nodes.py
View File

@ -424,8 +424,8 @@ def check_spectator(node_method):
node = args[0]
if node.in_spectator_mode:
#raise node.SpectatorError("You should not call this method when the node in spectator_mode")
#warnings.warn("You should not call %s when the node in spectator_mode" % node_method)
import warnings
#warnings.warn("You should not call %s when the node in spectator_mode" % node_method)
return node_method(*args, **kwargs)

5
abipy/flowtk/qha.py
View File

@ -4,12 +4,11 @@ Tools and workflows for calculations within the quasi-harmonic approximation.
WARNING: This code is still under development.
"""
import os
import numpy as np
from abipy.core.structure import Structure
from abipy.abio.inputs import AbinitInput
from abipy.flowtk.works import Work, RelaxWork, PhononWork, MergeDdb
#from abipy.abio.inputs import AbinitInput
from abipy.flowtk.works import Work, MergeDdb # RelaxWork, PhononWork,
from abipy.flowtk.flows import Flow
import logging

4
abipy/flowtk/tasks.py
View File

@ -25,7 +25,7 @@ from .utils import File, Directory, irdvars_for_ext, abi_splitext, FilepathFixer
from .qadapters import make_qadapter, QueueAdapter, QueueAdapterError
from . import qutils as qu
from .db import DBConnector
from .nodes import Status, Node, NodeError, NodeResults, NodeCorrections, FileNode, check_spectator
from .nodes import Status, Node, NodeError, NodeResults, FileNode #, check_spectator
from . import abiinspect
from . import events
from .abitimer import AbinitTimerParser
@ -539,7 +539,6 @@ class TaskManager(MSONable):
@classmethod
def autodoc(cls):
from abipy.flowtk.db import DBConnector
s = """
# TaskManager configuration file (YAML Format)
@ -564,7 +563,6 @@ batch_adapter:
"""
s += "policy: " + TaskPolicy.autodoc() + "\n"
s += "qadapter: " + QueueAdapter.autodoc() + "\n"
#s += "db_connector: " + DBConnector.autodoc()
return s
@classmethod

8
abipy/flowtk/utils.py
View File

@ -854,7 +854,7 @@ class SparseHistogram(object):
if num is None and step is None:
raise ValueError("Either num or step must be specified")
from collections import defaultdict, OrderedDict
from collections import defaultdict
values = [key(item) for item in items] if key is not None else items
start, stop = min(values), max(values)
@ -933,11 +933,11 @@ class Dirviz(object):
# Add input attributes.
if graph_attr is not None:
fg.graph_attr.update(**graph_attr)
g.graph_attr.update(**graph_attr)
if node_attr is not None:
fg.node_attr.update(**node_attr)
g.node_attr.update(**node_attr)
if edge_attr is not None:
fg.edge_attr.update(**edge_attr)
g.edge_attr.update(**edge_attr)
def node_kwargs(path):
return dict(

63
abipy/flowtk/wrappers.py
View File

@ -19,7 +19,6 @@ __date__ = "$Feb 21, 2013M$"
__all__ = [
"Mrgscr",
"Mrggkk",
"Mrgddb",
"Mrgdvdb",
]
@ -144,68 +143,6 @@ class Mrgscr(ExecWrapper):
self.execute(workdir)
class Mrggkk(ExecWrapper):
_name = "mrggkk"
def merge(self, workdir, gswfk_file, dfpt_files, gkk_files, out_gkk, binascii=0):
"""
Merge GGK files, return the absolute path of the new database.
Args:
gswfk_file: Ground-state WFK filename
dfpt_files: List of 1WFK files to merge.
gkk_files: List of GKK files to merge.
out_gkk: Name of the output GKK file
binascii: Integer flat. 0 --> binary output, 1 --> ascii formatted output
"""
raise NotImplementedError("This method should be tested")
#out_gkk = out_gkk if cwd is None else os.path.join(os.path.abspath(cwd), out_gkk)
# We work with absolute paths.
gswfk_file = os.path.absath(gswfk_file)
dfpt_files = [os.path.abspath(s) for s in list_strings(dfpt_files)]
gkk_files = [os.path.abspath(s) for s in list_strings(gkk_files)]
print("Will merge %d 1WF files, %d GKK file in output %s" %
(len(dfpt_files), len(gkk_files), out_gkk))
if self.verbose:
for i, f in enumerate(dfpt_files): print(" [%d] 1WF %s" % (i, f))
for i, f in enumerate(gkk_files): print(" [%d] GKK %s" % (i, f))
self.stdin_fname, self.stdout_fname, self.stderr_fname = \
map(os.path.join, 3 * [workdir], ["mrggkk.stdin", "mrggkk.stdout", "mrggkk.stderr"])
inp = StringIO()
inp.write(out_gkk + "\n") # Name of the output file
inp.write(str(binascii) + "\n") # Integer flag: 0 --> binary output, 1 --> ascii formatted output
inp.write(gswfk_file + "\n") # Name of the groud state wavefunction file WF
#dims = len(dfpt_files, gkk_files, ?)
dims = " ".join([str(d) for d in dims])
inp.write(dims + "\n") # Number of 1WF, of GKK files, and number of 1WF files in all the GKK files
# Names of the 1WF files...
for fname in dfpt_files:
inp.write(fname + "\n")
# Names of the GKK files...
for fname in gkk_files:
inp.write(fname + "\n")
self.stdin_data = [s for s in inp.getvalue()]
with open(self.stdin_fname, "w") as fh:
fh.writelines(self.stdin_data)
# Force OS to write data to disk.
fh.flush()
os.fsync(fh.fileno())
self.execute(workdir)
return out_gkk
class Mrgddb(ExecWrapper):
_name = "mrgddb"

4
abipy/integration_tests/itest_bse.py
View File

@ -1,10 +1,10 @@
"""Integration tests for BSE flows."""
import pytest
#import pytest
import abipy.data as abidata
import abipy.abilab as abilab
import abipy.flowtk as flowtk
from abipy.core.testing import has_abinit, has_matplotlib
#from abipy.core.testing import has_abinit, has_matplotlib
# TODO
#def itest_bse_with_mdf(fwp, tvars):

3
abipy/integration_tests/itest_gw.py
View File

@ -1,11 +1,10 @@
"""Integration tests for GW flows."""
import pytest
import abipy.data as abidata
import abipy.abilab as abilab
import abipy.flowtk as flowtk
from abipy.core.testing import has_abinit, has_matplotlib
#from abipy.core.testing import has_abinit, has_matplotlib
def make_g0w0_inputs(ngkpt, tvars):

2
abipy/integration_tests/itest_handlers.py
View File

@ -1,6 +1,4 @@
import sys
import os
import pytest
import abipy.data as abidata
import abipy.abilab as abilab

3
abipy/integration_tests/itest_relaxations.py
View File

@ -1,12 +1,11 @@
"""Integration tests for structural relaxations."""
import pytest
import numpy as np
import abipy.data as abidata
import abipy.abilab as abilab
import abipy.flowtk as flowtk
from abipy.core.testing import has_abinit, has_matplotlib
from abipy.core.testing import has_matplotlib
def ion_relaxation(tvars, ntime=50):

2
abipy/integration_tests/itest_scheduler.py
View File

@ -1,8 +1,6 @@
#!/usr/bin/env python
"""Integration tests for the scheduler."""
import sys
import os
import abipy.data as abidata
import abipy.abilab as abilab
import abipy.flowtk as flowtk

2
abipy/iotools/xsf.py
View File

@ -3,7 +3,7 @@
import numpy as np
from pymatgen.core.units import Energy, EnergyArray, ArrayWithUnit
from pymatgen.core.units import Energy, EnergyArray #, ArrayWithUnit
from abipy.tools import transpose_last3dims, add_periodic_replicas

2
abipy/scripts/abidoc.py
View File

@ -4,11 +4,9 @@ Interface to the database of ABINIT input variables
"""
import sys
import os
import argparse
import abipy.flowtk as flowtk
from pprint import pprint
from monty.functools import prof_main
from monty.termcolor import cprint
from abipy.core.release import __version__

2
abipy/scripts/abiopen.py
View File

@ -7,9 +7,7 @@ Alternatively, it is possible to generate automatically a jupyter notebook to ex
"""
import sys
import os
import io
import argparse
import tempfile
from monty.os.path import which
from monty.termcolor import cprint

1
abipy/scripts/abistruct.py
View File

@ -9,7 +9,6 @@ import numpy as np
from pprint import pprint
from tabulate import tabulate
from warnings import warn
from monty.string import marquee
from monty.functools import prof_main
from monty.termcolor import cprint

1
abipy/scripts/abiview.py
View File

@ -6,7 +6,6 @@ or convert data from Abinit files (usually netcdf) to other formats.
import sys
import os
import argparse
import numpy as np
from monty.functools import prof_main
from monty.termcolor import cprint

1
abipy/tools/bessel.py
View File

@ -2,7 +2,6 @@
"""This module provides functions to compute integrals of Bessel functions."""
import numpy as np
from collections import deque
from scipy.special import spherical_jn
from scipy.interpolate import UnivariateSpline
from scipy.integrate import simps # cumtrapz, quad

3
abipy/tools/fftprof.py
View File

@ -2,7 +2,6 @@
Python interface to fftprof. Provides objects to benchmark
the FFT libraries used by ABINIT and plot the results with matplotlib.
"""
import sys
import os
import tempfile
import numpy as np
@ -10,7 +9,7 @@ import numpy as np
from subprocess import Popen, PIPE
from monty.os.path import which
from monty.fnmatch import WildCard
from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt
from abipy.tools.plotting import add_fig_kwargs
__all__ = [
"FFTBenchmark",

1
abipy/tools/iotools.py
View File

@ -1,7 +1,6 @@
# coding: utf-8
"""IO related utilities."""
import os
import tempfile
from subprocess import call
from monty.termcolor import cprint

3
abipy/tools/numtools.py
View File

@ -1,7 +1,6 @@
# coding: utf-8
"""Numeric tools."""
import numpy as np
import bisect as bs
from monty.collections import dict2namedtuple
from abipy.tools import duck
@ -437,7 +436,7 @@ class BlochRegularGridInterpolator(object):
frac_coords = np.reshape(frac_coords, (-1, 3))
if cartesian:
red_from_cart = self.structure.lattice.inv_matrix.T
frac_coords = [np.dot(red_from, v) for v in frac_coords]
frac_coords = [np.dot(red_from_cart, v) for v in frac_coords]
uc_coords = np.reshape(frac_coords, (-1, 3)) % 1

2
abipy/tools/plotting.py
View File

@ -12,8 +12,6 @@ import itertools
import numpy as np
from collections import OrderedDict, namedtuple
from monty.string import list_strings
from monty.functools import lazy_property
from pymatgen.util.plotting import add_fig_kwargs, get_ax_fig_plt, get_ax3d_fig_plt, get_axarray_fig_plt
from .numtools import data_from_cplx_mode

8
abipy/waves/pwwave.py
View File

@ -1,13 +1,11 @@
# coding: utf-8
"""This module contains the class describing a planewave wavefunction."""
import tempfile
import copy
import itertools
#import copy
import numpy as np
from monty.termcolor import cprint
from abipy.core import Mesh3D
from abipy.core.kpoints import Kpoint
#from abipy.core.kpoints import Kpoint
from abipy.iotools import Visualizer
from abipy.iotools.xsf import xsf_write_structure, xsf_write_data
from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt
@ -23,7 +21,7 @@ def latex_label_ispinor(ispinor, nspinor):
return ""
elif nspinor == 2:
return {k: v.replace("myuparrow", "uparrow") for k, v in
{0: r"$\sigma=\myuparrow$", 1: r"$\sigma=\downarrow$"}.items()}[ispden]
{0: r"$\sigma=\myuparrow$", 1: r"$\sigma=\downarrow$"}.items()}[ispinor]
else:
raise ValueError("Wrong value for nspinor: %s" % nspinor)

6
abipy/waves/wfkfile.py
View File

@ -1,12 +1,12 @@
# coding: utf-8
"""Wavefunction file."""
import numpy as np
#import numpy as np
from monty.functools import lazy_property
from monty.string import marquee
from abipy.core import Mesh3D, GSphere, Structure
from abipy.core import Mesh3D, GSphere
from abipy.core.mixins import AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands, NotebookWriter
from abipy.iotools import ETSF_Reader, Visualizer
from abipy.iotools import Visualizer
from abipy.electrons.ebands import ElectronsReader
from abipy.waves.pwwave import PWWaveFunction
from abipy.tools import duck

10
setup.cfg
View File

@ -17,7 +17,13 @@ exclude-dir=abipy/gui
[pycodestyle]
count = True
ignore = E116,E121,E122,E123,E124,E126,E128,E129,E131,E133,E201,E203,E226,E231,E241,E242,E261,E262,E265,E266,E306,E401,E402,E704,W503,W504,W505,E701,E702,E731,E741,W605
max-line-length = 130
statistics = True
exclude=abipy/gui,abipy/abio/abivar_database,dev_scripts,docs,.ipynb_checkpoints,abipy/examples/flows/develop/,test_*.py,abipy/benchmarks,abipy/data/refs
ignore = E116,E121,E122,E123,E124,E126,E128,E129,E131,E133,E201,E203,E226,E231,E241,E242,E261,E262,E265,E266,E306,E401,E402,E704,W503,W504,W505,E701,E702,E731,E741,W605
exclude= .git,__pycache__,abipy/gui,abipy/abio/abivar_database,dev_scripts,docs,.ipynb_checkpoints,abipy/examples/flows/develop/,test_*.py,abipy/benchmarks,abipy/data/refs
[flake8]
# max-complexity = 10
max-line-length = 130
exclude= .git,__pycache__,abipy/gui,abipy/abio/abivar_database,dev_scripts,docs,.ipynb_checkpoints,abipy/examples/flows/develop/,test_*.py,abipy/benchmarks,abipy/data/refs
extend_ignore = E116,E121,E122,E123,E124,E126,E128,E129,E131,E133,E201,E203,E226,E231,E241,E242,E261,E262,E265,E266,E306,E401,E402,E704,W503,W504,W505,E701,E702,E731,E741,W605,F841