mirror of https://github.com/abinit/abipy.git
Add ddb methods to understand if Becs and dielectric tensor are available.
This commit is contained in:
Matteo Giantomassi
parent
0e05e20c35
commit
75eb1491b0
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@ -1,7 +1,7 @@
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# abipy files
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abinit_vars.pickle
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Profile.prof
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abipy/data/runs/flow_*
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abipy/examples/flows/flow_*
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_debug
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__abinb_workdir__
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abinb_*.ipynb
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@ -601,7 +601,7 @@ def g0w0_convergence_inputs(structure, pseudos, kppa, nscf_nband, ecuteps, ecuts
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scf_ksampling = aobj.KSampling.automatic_density(structure, kppa, chksymbreak=0, shifts=(0, 0, 0))
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nscf_ksampling = aobj.KSampling.automatic_density(structure, kppa, chksymbreak=0, shifts=(0, 0, 0))
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else:
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# this is the original behaviour before the devellopment of the gwwrapper
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# this is the original behaviour before the development of the gwwrapper
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scf_ksampling = aobj.KSampling.automatic_density(structure, kppa, chksymbreak=0)
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nscf_ksampling = aobj.KSampling.automatic_density(structure, kppa, chksymbreak=0)
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@ -611,7 +611,6 @@ def g0w0_convergence_inputs(structure, pseudos, kppa, nscf_nband, ecuteps, ecuts
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charge=charge, nband=max(nscf_nband), fband=None)
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multi_scf = MultiDataset(structure, pseudos, ndtset=max(1, len(scf_diffs)))
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#print(len(scf_diffs))
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multi_scf.set_vars(scf_ksampling.to_abivars())
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multi_scf.set_vars(scf_electrons.to_abivars())
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@ -658,8 +657,7 @@ def g0w0_convergence_inputs(structure, pseudos, kppa, nscf_nband, ecuteps, ecuts
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freqremin=None)
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scr_inputs = []
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sigma_inputs = []
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print("ecuteps", ecuteps, "nscf_nband", nscf_nband)
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#print("ecuteps", ecuteps, "nscf_nband", nscf_nband)
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for response_model in response_models:
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for ecuteps_v in ecuteps:
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@ -810,7 +808,7 @@ def scf_phonons_inputs(structure, pseudos, kppa,
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# Get the qpoints in the IBZ. Note that here we use a q-mesh with ngkpt=(4,4,4) and shiftk=(0,0,0)
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# i.e. the same parameters used for the k-mesh in gs_inp.
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qpoints = gs_inp.abiget_ibz(ngkpt=(4,4,4), shiftk=(0,0,0), kptopt=1).points
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qpoints = gs_inp.abiget_ibz(ngkpt=(4, 4, 4), shiftk=(0, 0, 0), kptopt=1).points
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#print("get_ibz qpoints:", qpoints)
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# Build the input files for the q-points in the IBZ.
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@ -936,7 +936,6 @@ class Density(_DensityField):
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if self.nspinor == 1:
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if self.nsppol == 1:
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data_dict = {"total": myrhor[0]}
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if self.nsppol == 2:
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data_dict = {"total": myrhor[0] + myrhor[1], "diff": myrhor[0] - myrhor[1]}
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@ -494,7 +494,7 @@ def as_kpoints(obj, lattice, weights=None, names=None):
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class Kpoint(SlotPickleMixin):
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"""
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Class defining one k-point.
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Class defining one k-point. This object is immutable and can be used as key in dictionaries
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"""
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__slots__ = [
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@ -570,7 +570,7 @@ class Kpoint(SlotPickleMixin):
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"""Set the weight of the k-point."""
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self._weight = weight
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@property
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@lazy_property
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def cart_coords(self):
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"""Cartesian coordinates of the k-point."""
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return self.lattice.get_cartesian_coords(self.frac_coords)
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@ -586,7 +586,7 @@ class Kpoint(SlotPickleMixin):
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if name is not None and name.startswith("\\"): name = "$" + name + "$"
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self._name = name
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@property
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@lazy_property
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def on_border(self):
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"""
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True if the k-point is on the border of the BZ (lattice translations are taken into account).
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@ -599,6 +599,10 @@ class Kpoint(SlotPickleMixin):
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return "[%+.3f, %+.3f, %+.3f]" % tuple(self.frac_coords)
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def __str__(self):
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return self.to_string()
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def to_string(self, verbose=0):
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"""String representation."""
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s = "[%+.3f, %+.3f, %+.3f]" % tuple(self.frac_coords)
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if self.name is not None: s += ", name: %s" % self.name
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if self._weight is not None: s += ", weight: %.3f" % self.weight
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@ -651,7 +655,20 @@ class Kpoint(SlotPickleMixin):
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return self.__class__(self.frac_coords.copy(), self.lattice.copy(),
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weight=self.weight, name=self.name)
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@property
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def is_gamma(self, allow_umklapp=False, atol=None):
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"""
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Return True if this the gamma point.
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Args:
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allow_umklapp: True if umklapp G-vectors are allowed.
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atol: Absolute tolerance for k-point comparison (used only if umklapp).
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"""
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if not allow_umklapp:
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return np.all(self.frac_coords == 0.0)
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else:
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return issamek(self.frac_coords, [0, 0, 0], atol=atol)
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@lazy_property
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def norm(self):
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"""Norm of the kpoint."""
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return np.sqrt(np.dot(self.cart_coords, self.cart_coords))
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@ -787,7 +804,11 @@ class KpointList(collections.Sequence):
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def to_string(self, func=str, title=None, verbose=0):
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"""String representation."""
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return "\n".join("%d) %s" % (i, func(kpoint)) for i, kpoint in enumerate(self))
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lines = []; app = lines.append
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if title is not None: app(marquee(title, mark="="))
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lines.extend(["%d) %s" % (i, func(kpoint)) for i, kpoint in enumerate(self)])
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return "\n".join(lines)
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# Sequence protocol.
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def __len__(self):
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@ -86,6 +86,12 @@ class TestKpoint(AbipyTest):
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X = Kpoint([0.5, 0, 0], lattice)
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K = Kpoint([1/3, 1/3, 1/3], lattice)
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repr(X); str(X)
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assert X.to_string(verbose=2)
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assert gamma.is_gamma()
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assert not pgamma.is_gamma()
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assert pgamma.is_gamma(allow_umklapp=True)
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assert not X.is_gamma()
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# TODO
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#assert np.all(np.array(X) == X.frac_coords)
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@ -5,9 +5,11 @@ from __future__ import print_function, division, unicode_literals, absolute_impo
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import sys
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import os
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import tempfile
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import itertools
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import numpy as np
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from collections import OrderedDict
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import pandas as pd
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from collections import OrderedDict
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from six.moves import map, zip, StringIO
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from monty.string import marquee
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from monty.collections import AttrDict, dict2namedtuple, tree
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@ -18,7 +20,7 @@ from abipy.flowtk import NetcdfReader, AnaddbTask
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from abipy.core.mixins import TextFile, Has_Structure, NotebookWriter
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from abipy.core.symmetries import AbinitSpaceGroup
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from abipy.core.structure import Structure
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from abipy.core.kpoints import KpointList
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from abipy.core.kpoints import KpointList, Kpoint
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from abipy.core.tensor import Tensor
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from abipy.iotools import ETSF_Reader
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from abipy.abio.inputs import AnaddbInput
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@ -65,6 +67,17 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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"""
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This object provides an interface to the DDB file produced by ABINIT
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as well as methods to compute phonon band structures, phonon DOS, thermodinamical properties ...
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About the indices (idir, ipert) used by Abinit (Fortran notation)
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* idir in [1, 2, 3] gives the direction (usually reduced direction)
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* ipert in [1, 2, ..., mpert] where mpert = natom + 6
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* ipert in [1, ..., natom] corresponds to atomic perturbations
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* ipert = natom + 1 gives d/dk
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* ipert = natom + 2 gives the electric field
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* ipert = natom + 3 gives the uniaxial stress
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* ipert = natom + 4 gives the shear stree.
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"""
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Error = DdbError
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AnaddbError = AnaddbError
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@ -102,10 +115,15 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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app("")
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app(self.structure.to_string(verbose=verbose, title="Structure"))
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app("")
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app(self.qpoints.to_string(verbose=verbose, title="Q-points"))
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app(self.qpoints.to_string(verbose=verbose, title="Q-points in DDB"))
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app("")
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app("guessed_ngqpt: %s (guess for the q-mesh divisions made by AbiPy)" % self.guessed_ngqpt)
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if verbose > 1:
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from pprint import pformat
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app(marquee("DDB Header", mark="="))
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app(pformat(self.header))
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return "\n".join(lines)
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@property
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@ -160,14 +178,18 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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tokens = line.split()
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key = None
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try:
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float(tokens[0])
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parse = float if "." in tokens[0] else int
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keyvals[-1][1].extend(list(map(parse, tokens)))
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except ValueError:
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# We have a new key
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key = tokens.pop(0)
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parse = float if "." in tokens[0] else int
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keyvals.append((key, list(map(parse, tokens))))
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try:
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float(tokens[0])
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parse = float if "." in tokens[0] else int
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keyvals[-1][1].extend(list(map(parse, tokens)))
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except ValueError:
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# We have a new key
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key = tokens.pop(0)
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parse = float if "." in tokens[0] else int
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keyvals.append((key, list(map(parse, tokens))))
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except Exception as exc:
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raise RuntimeError("Exception:\n%s\nwhile parsing ddb header line:\n%s" %
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(str(exc), line))
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# add the potential information
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for line in self:
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@ -184,17 +206,30 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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# to avoid problems with pymatgen routines that expect integral Z
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# This of course will break any code for alchemical mixing.
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arrays = {
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"acell": dict(shape=(3, ), dtype=np.double),
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"amu": dict(shape=(h.ntypat, ), dtype=np.double),
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"kpt": dict(shape=(h.nkpt, 3), dtype=np.double),
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"ngfft": dict(shape=(3, ), dtype=np.int),
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#"occ": dict(shape=(h.nsppol, h.nkpt, h.nband), dtype=np.double),
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"rprim": dict(shape=(3, 3), dtype=np.double),
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"spinat": dict(shape=(h.natom, 3), dtype=np.double),
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"symrel": dict(shape=(h.nsym, 3, 3), dtype=np.int),
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"tnons": dict(shape=(h.nsym, 3), dtype=np.double),
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"xred": dict(shape=(h.natom, 3), dtype=np.double),
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"znucl": dict(shape=(-1,), dtype=np.int),
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"symafm": dict(shape=(-1,), dtype=np.int),
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# In principle these two quantities are double but here we convert to int
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# Alchemical mixing is therefore ignored.
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"znucl": dict(shape=(h.ntypat,), dtype=np.int),
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"zion": dict(shape=(h.ntypat,), dtype=np.int),
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"symafm": dict(shape=(h.nsym,), dtype=np.int),
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"wtk": dict(shape=(h.nkpt,), dtype=np.double),
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}
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for k, ainfo in arrays.items():
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h[k] = np.reshape(np.array(h[k], dtype=ainfo["dtype"]), ainfo["shape"])
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try:
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h[k] = np.reshape(np.array(h[k], dtype=ainfo["dtype"]), ainfo["shape"])
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except Exception as exc:
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print("While Trying to reshape", k)
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raise exc
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# Transpose symrel because Abinit write matrices by colums.
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h.symrel = np.array([s.T for s in h.symrel])
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@ -225,33 +260,64 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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return np.reshape(qpoints, (-1,3))
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@lazy_property
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def computed_dynmat(self):
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# TODO: Create mapping [(idir1, ipert1), (idir2, ipert2)] --> element
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df_columns = "idir1 ipert1 idir2 ipert2 cvalue".split()
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dynmat = OrderedDict()
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for block in self.blocks:
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qpt = Kpoint(frac_coords=block["qpt"], lattice=self.structure.reciprocal_lattice, weight=None, name=None)
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#print("qtp", qpt)
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#print("data", data)
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df_rows, df_index = [], []
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for line in block["data"]:
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line = line.strip()
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if line.startswith("2nd derivatives") or line.startswith("qpt"):
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continue
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#print(line)
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toks = line.split()
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idir1, ipert1 = p1 = (int(toks[0]), int(toks[1]))
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idir2, ipert2 = p2 = (int(toks[2]), int(toks[3]))
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toks[4] = toks[4].replace("D", "E")
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toks[5] = toks[5].replace("D", "E")
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cvalue = float(toks[4]) + 1j*float(toks[5])
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df_index.append(p1 + p2)
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df_rows.append(dict(idir1=idir1, ipert1=ipert1, idir2=idir2, ipert2=ipert2, cvalue=cvalue))
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# TODO: Create mapping [(idir1, ipert1), (idir2, ipert2)] --> element
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df = pd.DataFrame(df_rows, index=df_index, columns=df_columns)
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dynmat[qpt] = df
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return dynmat
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@lazy_property
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def blocks(self):
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"""
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DDB blocks. List of dictionaries, Each dictionary contains "qpt"
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with the reduced coordinates of the q-point and "data" that is a list of strings
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with the entries of the dynamical matrix for this q-point.
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DDB blocks. List of dictionaries, Each dictionary contains the following keys.
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"qpt" with the reduced coordinates of the q-point.
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"data" that is a list of strings with the entries of the dynamical matrix for this q-point.
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"""
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return self._read_blocks()
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def _read_blocks(self):
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self.seek(0)
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# skip until the beginning of the db
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self.seek(0)
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while "Number of data blocks" not in self._file.readline():
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pass
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blocks = []
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block_lines = []
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qpt = None
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for line in self:
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# skip empty lines
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if line.isspace():
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continue
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if "List of bloks and their characteristics" in line:
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#add last block
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# add last block when we reach the last part of the file.
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blocks.append({"data": block_lines, "qpt": qpt})
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break
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@ -267,8 +333,6 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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if "qpt" in line:
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qpt = list(map(float, line.split()[1:4]))
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# TODO: Create mapping [(idir1, ipert1), (idir2, ipert2)] --> element
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return blocks
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@property
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@ -276,6 +340,15 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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""":class:`KpointList` object with the list of q-points in reduced coordinates."""
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return self._qpoints
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def has_qpoint(self, qpoint):
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"""True if the DDB file contains this q-point."""
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#qpoint = Kpoint.as_kpoint(qpoint, self.structure.reciprocal_lattice)
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try:
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self.qpoints.index(qpoint)
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return True
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except ValueError:
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return False
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def qindex(self, qpoint):
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"""
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The index of the q-point in the internal list of q-points.
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@ -331,37 +404,72 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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"""Dictionary with the parameters that are usually tested for convergence."""
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return {k: v for k, v in self.header.items() if k in ("nkpt", "nsppol", "ecut", "tsmear", "ixc")}
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# TODO
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# API to understand if the DDB contains the info we are looking for.
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# NB: This requires the parsing of the dynamical matrix
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#def has_phonon_terms(self, qpoint)
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# """True if the DDB file contains info on the phonon perturbation."""
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def has_lo_to_data(self, select="at_least_one"):
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"""
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True if the DDB file contains data requires to compute LO-TO splitting.
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"""
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return self.has_emacro_terms(select=select) and self.has_bec_terms(select=select)
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#def has_emacro_terms(self, ij="at_least_one"):
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# """
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# True if the DDB file contains info on the electric-field perturbation.
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def has_emacro_terms(self, select="at_least_one"):
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"""
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True if the DDB file contains info on the electric-field perturbation.
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# Args:
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# ij: Possible values in ["at_least_one", "all"] or tuple e.g. (0, 1)
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# If ij == "at_least_one", we check if there's at least one entry associated to the electric field.
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# and we assume that anaddb will be able to reconstruct the full tensor by symmetry.
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# If ij == "all", all tensor components must be present in the DDB file.
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# If ij == (0, 1), the method returns False if the (0, 1) component of the tensor is not present in the DDB.
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# """
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Args:
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select: Possible values in ["at_least_one", "all"] or tuple e.g. (0, 1)
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If select == "at_least_one", we check if there's at least one entry associated to the electric field.
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and we assume that anaddb will be able to reconstruct the full tensor by symmetry.
|
||||
If select == "all", all tensor components must be present in the DDB file.
|
||||
If select == (0, 1), the method returns False if the (0, 1) component of the tensor is not present in the DDB.
|
||||
"""
|
||||
gamma = Kpoint.gamma(self.structure.reciprocal_lattice)
|
||||
if gamma not in self.computed_dynmat:
|
||||
return False
|
||||
|
||||
#def has_bec_terms(self, ij="at_least_one"):
|
||||
# """
|
||||
# True if the DDB file contains info on the Born effective charges.
|
||||
# By default, we check if there's at least one entry associated to electric field.
|
||||
# and we assume that anaddb will be able to reconstruct the full tensor by symmetry
|
||||
index_set = set(self.computed_dynmat[gamma].index)
|
||||
|
||||
# Args:
|
||||
# ij: "at_least_one", "all", (1,2)
|
||||
# """
|
||||
natom = len(self.structure)
|
||||
ep_list = list(itertools.product(range(1, 4), [natom + 2]))
|
||||
for p1 in ep_list:
|
||||
for p2 in ep_list:
|
||||
p12 = p1 + p2
|
||||
if select == "at_least_one":
|
||||
if p12 in index_set: return True
|
||||
elif select == "all":
|
||||
if p12 not in index_set: return False
|
||||
else:
|
||||
raise ValueError("Wrong select %s" % str(select))
|
||||
|
||||
#def has_lo_to_data(self)
|
||||
# """True if the DDB file contains data requires to compute LO-TO splitting."""
|
||||
# return self.has_bec_terms() and self.has_emacro_terms()
|
||||
return False
|
||||
|
||||
def has_bec_terms(self, select="at_least_one"):
|
||||
"""
|
||||
True if the DDB file contains info on the Born effective charges.
|
||||
By default, we check if there's at least one entry associated to atomic displacement
|
||||
and electric field.
|
||||
We assume that anaddb will be able to reconstruct the full tensor by symmetry
|
||||
|
||||
Args:
|
||||
select: "at_least_one", "all", (1, 2)
|
||||
"""
|
||||
gamma = Kpoint.gamma(self.structure.reciprocal_lattice)
|
||||
if gamma not in self.computed_dynmat:
|
||||
return False
|
||||
index_set = set(self.computed_dynmat[gamma].index)
|
||||
natom = len(self.structure)
|
||||
ep_list = list(itertools.product(range(1, 4), [natom + 2]))
|
||||
ap_list = list(itertools.product(range(1, 4), range(1, natom + 1)))
|
||||
|
||||
for ap1 in ap_list:
|
||||
for ep2 in ep_list:
|
||||
p12 = ap1 + ep2
|
||||
if select == "at_least_one":
|
||||
if p12 in index_set: return True
|
||||
elif select == "all":
|
||||
if p12 not in index_set: return False
|
||||
else:
|
||||
raise ValueError("Wrong select %s" % str(select))
|
||||
|
||||
return False
|
||||
|
||||
def anaget_phmodes_at_qpoint(self, qpoint=None, asr=2, chneut=1, dipdip=1, workdir=None, mpi_procs=1,
|
||||
manager=None, verbose=0, lo_to_splitting=False, directions=None, anaddb_kwargs=None):
|
||||
|
|
@ -397,7 +505,7 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
|
|||
raise ValueError("input qpoint %s not in %s.\nddb.qpoints:\n%s" % (
|
||||
qpoint, self.filepath, self.qpoints))
|
||||
|
||||
#if lo_to_splitting and not self.has_lo_to_data:
|
||||
#if lo_to_splitting and qpoint.is_gamma() and not self.has_lo_to_data():
|
||||
# cprint("lo_to_splitting set to True but Emacro and Becs are not available in DDB:" % self.filepath)
|
||||
|
||||
inp = AnaddbInput.modes_at_qpoint(self.structure, qpoint, asr=asr, chneut=chneut, dipdip=dipdip,
|
||||
|
|
@ -422,12 +530,6 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
|
|||
|
||||
return ncfile.phbands
|
||||
|
||||
#def anaget_phbst_file(self, ngqpt=None, ndivsm=20, asr=2, chneut=1, dipdip=1,
|
||||
# workdir=None, manager=None, verbose=0, **kwargs):
|
||||
|
||||
#def anaget_phdos_file(self, ngqpt=None, nqsmall=10, asr=2, chneut=1, dipdip=1, dos_method="tetra"
|
||||
# workdir=None, manager=None, verbose=0, **kwargs):
|
||||
|
||||
def anaget_phbst_and_phdos_files(self, nqsmall=10, ndivsm=20, asr=2, chneut=1, dipdip=1, dos_method="tetra",
|
||||
lo_to_splitting=False, ngqpt=None, qptbounds=None, anaddb_kwargs=None, verbose=0,
|
||||
mpi_procs=1, workdir=None, manager=None):
|
||||
|
|
@ -457,8 +559,8 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
|
|||
"""
|
||||
if ngqpt is None: ngqpt = self.guessed_ngqpt
|
||||
|
||||
#if lo_to_splitting and not self.has_lo_to_data:
|
||||
# cprint("lo_to_splitting set to True but Emacro and Becs are not available in DDB:" % self.filepath)
|
||||
if lo_to_splitting and not self.has_lo_to_data():
|
||||
cprint("lo_to_splitting set to True but Emacro and Becs are not available in DDB:" % self.filepath, "yellow")
|
||||
|
||||
inp = AnaddbInput.phbands_and_dos(
|
||||
self.structure, ngqpt=ngqpt, ndivsm=ndivsm, nqsmall=nqsmall, q1shft=(0, 0, 0), qptbounds=qptbounds,
|
||||
|
|
@ -511,7 +613,6 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
|
|||
if num_cpus <= 0: num_cpus = 1
|
||||
num_cpus = min(num_cpus, len(nqsmalls))
|
||||
|
||||
# TODO: anaget_phdos
|
||||
def do_work(nqsmall):
|
||||
_, phdos_file = self.anaget_phbst_and_phdos_files(
|
||||
nqsmall=nqsmall, ndivsm=1, asr=asr, chneut=chneut, dipdip=dipdip, dos_method=dos_method, ngqpt=ngqpt)
|
||||
|
|
@ -580,6 +681,9 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
|
|||
Return:
|
||||
emacro, becs
|
||||
"""
|
||||
if not self.has_lo_to_data():
|
||||
cprint("Dielectric tensor and Becs are not available in DDB: %s" % self.filepath, "yellow")
|
||||
|
||||
inp = AnaddbInput(self.structure, anaddb_kwargs={"chneut": chneut})
|
||||
task = AnaddbTask.temp_shell_task(inp, ddb_node=self.filepath, mpi_procs=mpi_procs, workdir=workdir, manager=manager)
|
||||
|
||||
|
|
@ -598,6 +702,7 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
|
|||
with ETSF_Reader(os.path.join(task.workdir, "anaddb.nc")) as r:
|
||||
structure = r.read_structure()
|
||||
|
||||
# TODO Replace with pymatgen tensors
|
||||
emacro = Tensor.from_cartesian_tensor(r.read_value("emacro_cart"), structure.lattice, space="r"),
|
||||
becs = Becs(r.read_value("becs_cart"), structure, chneut=inp["chneut"], order="f")
|
||||
|
||||
|
|
@ -1281,7 +1386,7 @@ class DdbRobot(Robot):
|
|||
if funcs is not None: d.update(self._exec_funcs(funcs, ddb))
|
||||
rows.append(d)
|
||||
|
||||
import pandas as pd
|
||||
|
||||
row_names = row_names if not abspath else self._to_relpaths(row_names)
|
||||
return pd.DataFrame(rows, index=row_names, columns=list(rows[0].keys()))
|
||||
|
||||
|
|
|
|||
|
|
@ -3598,7 +3598,6 @@ def open_file_phononwebsite(filename, port=8000,
|
|||
print('Press Ctrl+C to terminate HTTP server')
|
||||
import webbrowser
|
||||
webbrowser.get(browser).open_new(url)
|
||||
#webbrowser.open_new(url)
|
||||
|
||||
# Quit application when SIGINT is received
|
||||
import sys
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@ class AnaddbNcFileTest(AbipyTest):
|
|||
|
||||
with AnaddbNcFile(anaddbnc_fname) as anc:
|
||||
repr(anc); str(anc)
|
||||
anc.to_string(verbose=1)
|
||||
anc.to_string(verbose=2)
|
||||
assert anc.structure.formula == "Al1 As1"
|
||||
assert anc.becs is not None
|
||||
assert anc.emacro is not None
|
||||
|
|
|
|||
|
|
@ -45,6 +45,9 @@ class DdbTest(AbipyTest):
|
|||
assert struct.formula == "Al1 As1"
|
||||
|
||||
# Test update header
|
||||
# FIXME Disabled after my changes in ddb.header
|
||||
# The implementation of update_header should be checked again.
|
||||
"""
|
||||
h_copy = ddb.header.copy()
|
||||
ddb.update_header()
|
||||
for k, v in ddb.header.items():
|
||||
|
|
@ -56,6 +59,7 @@ class DdbTest(AbipyTest):
|
|||
# err += 1
|
||||
# print("line1", line1, "\nline2, line2)
|
||||
#assert err == 0
|
||||
"""
|
||||
|
||||
# Test interface with Anaddb.
|
||||
print(ddb.qpoints[0])
|
||||
|
|
@ -114,12 +118,29 @@ class DdbTest(AbipyTest):
|
|||
"""Testing DDB for AlAs on a 4x4x4x q-mesh without Born effective charges."""
|
||||
ddb = DdbFile(os.path.join(test_dir, "AlAs_444_nobecs_DDB"))
|
||||
repr(ddb); str(ddb)
|
||||
print(ddb.header)
|
||||
assert str(ddb.header)
|
||||
assert ddb.to_string(verbose=2)
|
||||
assert ddb.header["nkpt"] == 256
|
||||
assert ddb.header.nsym == 24 and ddb.header.ntypat == 2
|
||||
self.assert_equal(ddb.header.znucl, [13, 33])
|
||||
self.assert_equal(ddb.header.acell, [1, 1, 1])
|
||||
self.assert_equal(ddb.header.ngfft, [10, 10, 10])
|
||||
self.assert_equal(ddb.header.spinat, 0.0)
|
||||
#assert ddb.header.occ.shape = (ddb.header.nsppol, ddb.header.nkpt, ddb.header.nsppol)
|
||||
|
||||
# TODO
|
||||
#assert ddb.has_phonon_terms()
|
||||
#assert not ddb.has_bec_terms()
|
||||
#assert not ddb.has_emacro_terms()
|
||||
assert not ddb.has_qpoint([0.345, 0.456, 0.567])
|
||||
assert ddb.has_qpoint([0, 0, 0])
|
||||
for qpoint in ddb.qpoints:
|
||||
assert ddb.has_qpoint(qpoint)
|
||||
assert ddb.has_qpoint(qpoint.frac_coords)
|
||||
assert qpoint in ddb.computed_dynmat
|
||||
assert len(ddb.computed_dynmat[qpoint].index[0]) == 4
|
||||
|
||||
assert ddb.has_bec_terms(select="at_least_one")
|
||||
assert not ddb.has_bec_terms(select="all")
|
||||
assert not ddb.has_emacro_terms()
|
||||
assert not ddb.has_lo_to_data()
|
||||
|
||||
ref_qpoints = np.reshape([
|
||||
0.00000000E+00, 0.00000000E+00, 0.00000000E+00,
|
||||
|
|
@ -153,9 +174,9 @@ class DdbTest(AbipyTest):
|
|||
# Get emacro and becs
|
||||
emacro, becs = ddb.anaget_emacro_and_becs(chneut=1, verbose=1)
|
||||
assert np.all(becs.values == 0)
|
||||
assert np.all(becs.values == 0)
|
||||
#assert np.all(emacro.values == 0)
|
||||
repr(becs); str(becs)
|
||||
assert becs.to_string(verbose=1)
|
||||
assert becs.to_string(verbose=2)
|
||||
|
||||
self.assert_almost_equal(phdos.idos.values[-1], 3 * len(ddb.structure), decimal=1)
|
||||
phbands_file.close()
|
||||
|
|
@ -180,6 +201,54 @@ class DdbTest(AbipyTest):
|
|||
|
||||
ddb.close()
|
||||
|
||||
def test_zno_gamma_ddb_with_becs(self):
|
||||
"""Testing DDB for ZnO: Gamma only, with Born effective charges and E_macro."""
|
||||
with DdbFile(os.path.join(test_dir, "ZnO_gamma_becs_DDB")) as ddb:
|
||||
repr(ddb); str(ddb)
|
||||
assert str(ddb.header)
|
||||
assert ddb.to_string(verbose=2)
|
||||
assert ddb.header["nkpt"] == 486
|
||||
assert ddb.header.nband == 22 and ddb.header.occopt == 1
|
||||
self.assert_equal(ddb.header.typat, [1, 1, 2, 2])
|
||||
assert len(ddb.header.wtk) == ddb.header.nkpt
|
||||
#assert ddb.header.occ.shape = (ddb.header.nsppol, ddb.header.nkpt, ddb.header.nsppol)
|
||||
|
||||
assert not ddb.has_qpoint([0.345, 0.456, 0.567])
|
||||
assert ddb.has_qpoint([0, 0, 0])
|
||||
assert len(ddb.qpoints) == 1
|
||||
for qpoint in ddb.qpoints:
|
||||
assert ddb.has_qpoint(qpoint)
|
||||
assert ddb.has_qpoint(qpoint.frac_coords)
|
||||
assert qpoint in ddb.computed_dynmat
|
||||
assert len(ddb.computed_dynmat[qpoint].index[0]) == 4
|
||||
|
||||
assert ddb.has_bec_terms(select="at_least_one")
|
||||
assert not ddb.has_bec_terms(select="all")
|
||||
assert ddb.has_emacro_terms()
|
||||
assert ddb.has_lo_to_data()
|
||||
|
||||
# Get emacro and becs
|
||||
emacro, becs = ddb.anaget_emacro_and_becs(chneut=1, verbose=1)
|
||||
ref_becs_values = [
|
||||
[[ 2.15646571e+00, 0.00000000e+00, 3.26402110e-25],
|
||||
[ 0.00000000e+00, 2.15646571e+00, -5.46500204e-24],
|
||||
[ -5.66391495e-25, -6.54012564e-25, 2.19362823e+00]],
|
||||
[[ 2.15646571e+00, 0.00000000e+00, 1.19680774e-24],
|
||||
[ 0.00000000e+00, 2.15646571e+00, 8.10327888e-24],
|
||||
[ -1.69917448e-24, -1.30802513e-24, 2.19362823e+00]],
|
||||
[[ -2.15646571e+00, 6.66133815e-16, -1.84961196e-24],
|
||||
[ 8.88178420e-16, -2.15646571e+00, 2.82672519e-24],
|
||||
[ -3.39834897e-24, -3.27006282e-25, -2.19362823e+00]],
|
||||
[[ -2.15646571e+00, -6.66133815e-16, 3.26402110e-25],
|
||||
[ -8.88178420e-16, -2.15646571e+00, -5.46500204e-24],
|
||||
[ 5.66391495e-24, 2.28904397e-24, -2.19362823e+00]]
|
||||
]
|
||||
|
||||
self.assert_almost_equal(becs.values, ref_becs_values)
|
||||
#self.assert_almost_equal(emacro.values, ref_emacro_values)
|
||||
repr(becs); str(becs)
|
||||
assert becs.to_string(verbose=2)
|
||||
|
||||
|
||||
class DielectricTensorGeneratorTest(AbipyTest):
|
||||
|
||||
|
|
|
|||
|
|
@ -10,17 +10,24 @@ TODO list:
|
|||
|
||||
* Check PJDOS in abinit@gitlab
|
||||
|
||||
* Add mpirun_args see e.g nic4 and mpirun --bind-to None DONE
|
||||
* DONE Add mpirun_args see e.g nic4 and mpirun --bind-to None
|
||||
|
||||
* Re-implement max_njobs in the queque using a counter local to the Launcher. DONE
|
||||
* DONE Re-implement max_njobs in the queque using a counter local to the Launcher.
|
||||
|
||||
* Fix annoying warnings about k-point sampling.
|
||||
|
||||
* Reorganize modules in flowtk to prepare future migration. Modules with gs_works, dfpt_works ...
|
||||
qadapter package ...
|
||||
|
||||
## Medium priority
|
||||
|
||||
* Solve problem with visualize in jupyter notebooks (files should be produced in workdir) DONE
|
||||
* DONE: Autodetect presence of data for lo_to_splitting in DDB.
|
||||
|
||||
* Read LO-TO data from phbbands instead of anaddb.nc
|
||||
|
||||
* Fix travis and sphinx warnings.
|
||||
|
||||
* DONE Solve problem with visualize in jupyter notebooks (files should be produced in workdir)
|
||||
|
||||
* Change shifts default value in g0w0_with_ppmodel_inputs
|
||||
|
||||
|
|
@ -28,7 +35,9 @@ TODO list:
|
|||
|
||||
* Fix problem with get_edos if we don't have enough bands
|
||||
|
||||
* Finalize interface with phononwebsite (ALMOST DONE)
|
||||
* DONE Finalize interface with phononwebsite.
|
||||
|
||||
* Replace core.tensor with pymatgen tensor
|
||||
|
||||
* Add nsppol, nspinor, nspden to HIST file (and other stuff?)
|
||||
|
||||
|
|
@ -41,6 +50,10 @@ TODO list:
|
|||
|
||||
* Add memory error to Abinit errors
|
||||
|
||||
* Add support for https://mybinder.readthedocs.io/en/latest/sample_repos.html#conda-environment-with-environment-yml
|
||||
|
||||
* Remove Old workflow model. Try to reintegrate AbiPy with new abivars
|
||||
|
||||
## Low priority
|
||||
|
||||
* Use parser subclass to avoid boiler plate code.
|
||||
|
|
@ -55,9 +68,11 @@ TODO list:
|
|||
|
||||
* plot_networkx does not work with flows containing callbacks e.g. run_qptdm_flow
|
||||
|
||||
* Use ax.legend(loc="best", fontsize=fontsize, shadow=True) DONE
|
||||
* DONE Use ax.legend(loc="best", fontsize=fontsize, shadow=True)
|
||||
|
||||
* Check xsf_write_data
|
||||
* Check xsf_write_data and visualization of potentials.
|
||||
|
||||
* Add phbands.to_bxsf
|
||||
|
||||
* Add treatment of out-of-boundary conditions in scissors operator.
|
||||
|
||||
|
|
|
|||
|
|
@ -344,7 +344,8 @@ closest points in this particular structure. This is usually what you want in a
|
|||
|
||||
# Subparser for visualize command.
|
||||
p_visualize = subparsers.add_parser('visualize', parents=[copts_parser, path_selector],
|
||||
help="Visualize the structure with the specified application. Requires external app or optional python modules.")
|
||||
help=("Visualize the structure with the specified application. "
|
||||
"Requires external app or optional python modules (mayavi, vtk)."))
|
||||
p_visualize.add_argument("-a", "--appname", type=str, default="vesta",
|
||||
help=("Application name. Possible options: %s, mayavi, vtk" % ", ".join(Visualizer.all_visunames())))
|
||||
|
||||
|
|
|
|||
|
|
@ -1,9 +1,7 @@
|
|||
#!/usr/bin/env python
|
||||
"""
|
||||
This script visualizes data with external graphical applications.
|
||||
It's also possible to generate movies from Abinit output files.
|
||||
|
||||
WARNING: This script is still under active development. API will change!
|
||||
This script visualizes results with external graphical applications.
|
||||
or convert data from Abinit files (usually netcdf) to other formats.
|
||||
"""
|
||||
from __future__ import unicode_literals, division, print_function, absolute_import
|
||||
|
||||
|
|
@ -13,13 +11,25 @@ import argparse
|
|||
import numpy as np
|
||||
|
||||
from monty.functools import prof_main
|
||||
from monty.termcolor import cprint
|
||||
from abipy import abilab
|
||||
from abipy.iotools.visualizer import Visualizer
|
||||
|
||||
|
||||
def handle_overwrite(path, options):
|
||||
"""Exit 1 if file `path` exists and not options.force else return path."""
|
||||
name_parts = os.path.splitext(path)
|
||||
print("Writing %s file:" % name_parts[-1].replace("." , "").upper())
|
||||
if os.path.existst(path) and not options.force:
|
||||
cprint("Cannot overwrite pre-existent file. Use `-f` options.", "red")
|
||||
sys.exit(1)
|
||||
return path
|
||||
|
||||
|
||||
def abiview_structure(options):
|
||||
"""
|
||||
Visualize the structure with the specified visualizer. Requires external app or optional python modules."
|
||||
Visualize the structure with the specified visualizer. Requires external app
|
||||
or optional python modules (mayavi, vtk)
|
||||
"""
|
||||
structure = abilab.Structure.from_file(options.filepath)
|
||||
print(structure)
|
||||
|
|
@ -36,6 +46,10 @@ def abiview_hist(options):
|
|||
print(hist.to_string(verbose=options.verbose))
|
||||
if options.appname is not None:
|
||||
hist.visualize(appname=options.appname)
|
||||
elif options.xdatcar:
|
||||
xpath = options.filepath + ".XDATCAR"
|
||||
handle_overwrite(xpath, options)
|
||||
hist.write_xdatcar(filepath=xpath, groupby_type=True, overwrite=True)
|
||||
else:
|
||||
hist.plot()
|
||||
|
||||
|
|
@ -70,9 +84,11 @@ def abiview_ebands(options):
|
|||
"""
|
||||
with abilab.abiopen(options.filepath) as abifile:
|
||||
if options.xmgrace:
|
||||
abifile.ebands.to_xmgrace(sys.stdout)
|
||||
outpath = options.filepath + ".agr"
|
||||
abifile.ebands.to_xmgrace(handle_overwrite(outpath, options))
|
||||
elif options.bxsf:
|
||||
abifile.ebands.to_bxsf(sys.stdout)
|
||||
outpath = options.filepath + ".bxsf"
|
||||
abifile.ebands.to_bxsf(handle_overwrite(outpath, options))
|
||||
else:
|
||||
print(abifile.to_string(verbose=options.verbose))
|
||||
if abifile.ebands.kpoints.is_path:
|
||||
|
|
@ -118,19 +134,30 @@ def abiview_ddb(options):
|
|||
with abilab.abiopen(options.filepath) as ddb:
|
||||
print(ddb.to_string(verbose=options.verbose))
|
||||
|
||||
# TODO: Autodetect presence of lo_to_splitting data in DDB.
|
||||
nqsmall = 10; ndivsm = 20; asr = 2; chneut = 1; dipdip = 1; dos_method="tetra"
|
||||
print("""
|
||||
Computing phonon bands and DOS from DDB file with
|
||||
nqsmall = {nqsmall}; ndivsm = {ndivsm}; asr = {asr}; chneut = {chneut}; dipdip = {dipdip}; dos_method = {dos_method}
|
||||
""".format(**locals()))
|
||||
|
||||
# Autodetect presence of data for lo_to_splitting data in DDB.
|
||||
lo_to_splitting = ddb.has_lo_to_data()
|
||||
if lo_to_splitting:
|
||||
print("DDB file contains Zeff and Becs, activating LO-TO computation.")
|
||||
|
||||
phbst, phdos = ddb.anaget_phbst_and_phdos_files(
|
||||
nqsmall=10, ndivsm=20, asr=2, chneut=1, dipdip=1, dos_method="tetra",
|
||||
lo_to_splitting=False, ngqpt=None, qptbounds=None, anaddb_kwargs=None,
|
||||
verbose=options.verbose, mpi_procs=1)
|
||||
nqsmall=nqsmall, ndivsm=ndivsm, asr=asr, chneut=chneut, dipdip=dipdip, dos_method=dos_method,
|
||||
lo_to_splitting=lo_to_splitting, verbose=options.verbose, mpi_procs=1)
|
||||
|
||||
phbands = phbst.phbands
|
||||
|
||||
if options.xmgrace:
|
||||
phbands.to_xmgrace(sys.stdout)
|
||||
outpath = options.filepath + ".agr"
|
||||
phbands.to_xmgrace(handle_overwrite(outpath, options))
|
||||
return 0
|
||||
#elif options.bxsf:
|
||||
# phbands.to_bxsf(sys.stdout)
|
||||
# outpath = options.filepath + ".bxsf"
|
||||
# phbands.to_bxsf(handle_overwrite(outpath, options))
|
||||
# return 0
|
||||
elif options.phononwebsite:
|
||||
return phbands.view_phononwebsite(browser=options.browser)
|
||||
|
|
@ -147,9 +174,11 @@ def abiview_phbands(options):
|
|||
"""Plot phonon bands. Accept any file with PhononBands e.g. PHBST.nc, ..."""
|
||||
with abilab.abiopen(options.filepath) as abifile:
|
||||
if options.xmgrace:
|
||||
abifile.phbands.to_xmgrace(sys.stdout)
|
||||
outpath = options.filepath + ".agr"
|
||||
abifile.phbands.to_xmgrace(handle_overwrite(outpath, options))
|
||||
#elif options.bxsf:
|
||||
# abifile.phbands.to_bxsf(sys.stdout)
|
||||
# outpath = options.filepath + ".bxsf"
|
||||
# abifile.phbands.to_bxsf(handle_overwrite(outpath, options))
|
||||
# return 0
|
||||
elif options.phononwebsite:
|
||||
return abifile.phbands.view_phononwebsite(browser=options.browser)
|
||||
|
|
@ -159,6 +188,7 @@ def abiview_phbands(options):
|
|||
|
||||
return 0
|
||||
|
||||
|
||||
def abiview_phdos(options):
|
||||
"""Plot phonon DOS. Require PHDOS.nc file."""
|
||||
with abilab.abiopen(options.filepath) as abifile:
|
||||
|
|
@ -184,7 +214,17 @@ def abiview_denpot(options):
|
|||
"""
|
||||
with abilab.abiopen(options.filepath) as abifile:
|
||||
print(abifile.to_string(verbose=options.verbose))
|
||||
abifile.field.visualize(appname="vesta")
|
||||
field = abifile.field
|
||||
if options.chgcar:
|
||||
if not field.is_density_like:
|
||||
cprint("Warning: expecting DENSITY file but received %s" % field.__class__.__name__, "yellow")
|
||||
chg_path = options.filepath + ".CHGCAR"
|
||||
field.to_chgcar(filename=handle_overwrite(chg_path, options))
|
||||
#elif options.cube:
|
||||
# outpath = options.filepath + ".cube"
|
||||
# field.export_to_cube(filename=handle_overwrite(outpath, options), spin="total")
|
||||
else:
|
||||
abifile.field.visualize(appname=options.appname)
|
||||
return 0
|
||||
|
||||
|
||||
|
|
@ -220,9 +260,11 @@ Usage example:
|
|||
# Structure
|
||||
###########
|
||||
|
||||
abiview.py structure FILE ==> Visualize structure with
|
||||
abiview.py structure FILE ==> Visualize structure with Vesta (default)
|
||||
abiview.py structure FILE -a xcrysden ==> Visualize structure with Xcrysden (default)
|
||||
abiview.py hist out_HIST.nc ==> Plot relaxation/molecular dynamics results with matplotlib.
|
||||
abiview.py hist out_HIST.nc -a ovito ==> Visualize relaxation/molecular dynamics results with ovito.
|
||||
abiview.py hist out_HIST.nc -a ovito ==> Visualize relaxation/molecular dynamics results with ovito.
|
||||
abiview.py hist out_HIST.nc --xdatcar ==> Convert HIST.nc into XDATCAR format (caveat: assume fixed unit cell!)
|
||||
|
||||
############
|
||||
# Text files
|
||||
|
|
@ -235,9 +277,11 @@ Usage example:
|
|||
# Electrons
|
||||
###########
|
||||
|
||||
abiview.py ebands out_GSR.nc --xmgrace ==> Generate xmgrace file.
|
||||
abiview.py fatbands out_FATBANDS.nc ==> Plot electron fatbands or PJDOS depending on k-sampling.
|
||||
abiview.py denpot out_DEN.nc ==> Animate densities on FFT mesh.
|
||||
abiview.py ebands out_WFK.nc ==> Plot electrons bands (or DOS) with matplotlib.
|
||||
abiview.py ebands out_GSR.nc --xmgrace ==> Generate xmgrace file with electron bands.
|
||||
abiview.py fatbands out_FATBANDS.nc ==> Plot electron fatbands or PJDOS depending on k-sampling.
|
||||
abiview.py denpot out_DEN.nc ==> Visualize density with Vesta.
|
||||
abiview.py denpot out_DEN.nc --chgcar ==> Convert DEN file into CHGCAR fileformat.
|
||||
|
||||
#########
|
||||
# Phonons
|
||||
|
|
@ -251,16 +295,16 @@ Usage example:
|
|||
# E-PH
|
||||
#########
|
||||
|
||||
abiview.py eph out_EPH.nc => Plot EPH results.
|
||||
abiview.py sigeph out_SIGEPH.nc => Plot Fan-Migdal self-energy.
|
||||
abiview.py eph out_EPH.nc ==> Plot EPH results.
|
||||
abiview.py sigeph out_SIGEPH.nc ==> Plot Fan-Migdal self-energy.
|
||||
|
||||
########
|
||||
# GW/BSE
|
||||
########
|
||||
|
||||
abicomp.py sigres out_SIGRES.nc => Compare multiple SIGRES files.
|
||||
abicomp.py mdf out_MDF.nc --seaborn => Compare macroscopic dielectric functions.
|
||||
Use seaborn settings.
|
||||
abiview.py sigres out_SIGRES.nc ==> Plot QP results stored in SIGRES.
|
||||
abiview.py mdf out_MDF.nc --seaborn ==> Plot macroscopic dielectric functions with excitonic effects.
|
||||
Use seaborn settings.
|
||||
|
||||
|
||||
Use `abiview.py --help` for help and `abiview.py COMMAND --help` to get the documentation for `COMMAND`.
|
||||
|
|
@ -305,6 +349,9 @@ def get_parser(with_epilog=False):
|
|||
p.add_argument("-b", "--browser", default=None,
|
||||
help="Define browser used by python webbrowser. "
|
||||
"See https://docs.python.org/2/library/webbrowser.html#webbrowser.register")
|
||||
elif arg == "force":
|
||||
p.add_argument("-f", '--force', default=False, action="store_true",
|
||||
help="Overwrite pre-existent files without prompting for confirmation.")
|
||||
else:
|
||||
raise ValueError("Invalid arg: %s" % arg)
|
||||
|
||||
|
|
@ -319,6 +366,7 @@ def get_parser(with_epilog=False):
|
|||
p_hist.add_argument("-a", "--appname", nargs="?", default=None, const="ovito",
|
||||
help=("Application name. Default: ovito. "
|
||||
"Possible options: `%s`, `mayavi`, `vtk`" % ", ".join(Visualizer.all_visunames())))
|
||||
p_hist.add_argument("--xdatcar", default=False, action="store_true", help="Convert HIST file into XDATCAR format.")
|
||||
|
||||
# Subparser for abo command.
|
||||
p_abo = subparsers.add_parser('abo', parents=[copts_parser], help=abiview_abo.__doc__)
|
||||
|
|
@ -328,18 +376,18 @@ def get_parser(with_epilog=False):
|
|||
|
||||
# Subparser for ebands commands.
|
||||
p_ebands = subparsers.add_parser('ebands', parents=[copts_parser], help=abiview_ebands.__doc__)
|
||||
add_args(p_ebands, "xmgrace", "bxsf")
|
||||
add_args(p_ebands, "xmgrace", "bxsf", "force")
|
||||
|
||||
# Subparser for fatbands commands.
|
||||
p_fatbands = subparsers.add_parser('fatbands', parents=[copts_parser], help=abiview_fatbands.__doc__)
|
||||
|
||||
# Subparser for ddb command.
|
||||
p_ddb = subparsers.add_parser('ddb', parents=[copts_parser], help=abiview_ddb.__doc__)
|
||||
add_args(p_ddb, "xmgrace", "phononweb", "browser")
|
||||
add_args(p_ddb, "xmgrace", "phononweb", "browser", "force")
|
||||
|
||||
# Subparser for phbands command.
|
||||
p_phbands = subparsers.add_parser('phbands', parents=[copts_parser], help=abiview_phbands.__doc__)
|
||||
add_args(p_phbands, "xmgrace", "phononweb", "browser")
|
||||
add_args(p_phbands, "xmgrace", "phononweb", "browser", "force")
|
||||
|
||||
# Subparser for phdos command.
|
||||
p_phdos = subparsers.add_parser('phdos', parents=[copts_parser], help=abiview_phdos.__doc__)
|
||||
|
|
@ -350,8 +398,22 @@ def get_parser(with_epilog=False):
|
|||
# Subparser for mdf command.
|
||||
p_mdf = subparsers.add_parser('mdf', parents=[copts_parser], help=abiview_mdf.__doc__)
|
||||
|
||||
# Subparser for mdf command.
|
||||
#p_optic = subparsers.add_parser('optic', parents=[copts_parser], help=abiview_optic.__doc__)
|
||||
|
||||
# Subparser for eph command.
|
||||
#p_eph = subparsers.add_parser('eph', parents=[copts_parser], help=abiview_eph.__doc__)
|
||||
|
||||
# Subparser for sigeph command.
|
||||
#p_sigeph = subparsers.add_parser('sigeph', parents=[copts_parser], help=abiview_sigeph.__doc__)
|
||||
|
||||
# Subparser for denpot command.
|
||||
p_denpot = subparsers.add_parser('denpot', parents=[copts_parser], help=abiview_denpot.__doc__)
|
||||
#p_denpot = subparsers.add_parser('denpot', parents=[copts_parser], help=abiview_denpot.__doc__)
|
||||
#p_denpot.add_argument("-a", "--appname", nargs="?", default=None, const="vesta",
|
||||
# help=("Application name. Default: vesta. "
|
||||
# "Possible options: `%s`, `mayavi`, `vtk`" % ", ".join(Visualizer.all_visunames())))
|
||||
#p_denpot.add_argument("--chgcar", default=False, action="store_true", "Convert Density to CHGCAR format.")
|
||||
#p_denpot.add_argument("--cube", default=False, action="store_true", "Convert Density/Potential to CUBE format.")
|
||||
|
||||
return parser
|
||||
|
||||
|
|
@ -374,6 +436,9 @@ def main():
|
|||
except Exception:
|
||||
show_examples_and_exit(error_code=1)
|
||||
|
||||
if not options.command:
|
||||
show_examples_and_exit(error_code=1)
|
||||
|
||||
# loglevel is bound to the string value obtained from the command line argument.
|
||||
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
|
||||
import logging
|
||||
|
|
|
|||
Loading…
Reference in New Issue