Source code for abipy.panels.structure
""""GUIs for structure."""
from __future__ import annotations
import os
import io
import param
import panel as pn
import numpy as np
import panel.widgets as pnw
import bokeh.models.widgets as bkw
from abipy.core.structure import Structure
from abipy.panels.core import (AbipyParameterized, PanelWithStructure, dfc, mpl, ply,
depends_on_btn_click, Loading, add_mp_rest_docstring)
from abipy.tools.decorators import Appender
add_inp_docstring = Appender("""
kprra (number of **k**-points per reciprocal atom) defines the **k**-mesh for electrons.
AbiPy automatically computes the variables [[ngkpt]], [[nshiftk]] and [[shiftk]] from kprra.
The pseudopotentials are taken from the [PseudoDojo project](http://www.pseudo-dojo.org/)
according to value of `XC type` and `Pseudos type` and recommended values for [[ecut]]
and [[pawecutdg]] and [[nband]] are automatically added to the input.
At the end of the page, there is a button to download a targz file with all the required input files.
""", indents=0)
def _make_targz_bytes(inp_or_multi, remove_dir=True):
"""
Return bytesIO with the targz file containing input and pseudos.
"""
targz_path = inp_or_multi.make_targz()
output = io.BytesIO()
with open(targz_path, "rb") as fh:
output.write(fh.read())
output.seek(0)
return output
[docs]
class StructurePanel(PanelWithStructure):
"""
Panel with widgets to interact with an AbiPy Structure.
"""
def __init__(self, structure: Structure, with_inputs: bool = True, **params):
"""
Args:
structure: |Structure| object.
with_inputs: True if tabs for generating input files should be shown.
"""
PanelWithStructure.__init__(self, structure=structure, **params)
# Convert widgets.
self.output_format = pnw.Select(name="format", value="abinit",
options="abinit,cif,xsf,poscar,qe,siesta,wannier90,cssr,json".split(","))
# Spglib widgets
self.spglib_symprec = pnw.Spinner(name="symprec", value=0.01, start=0.0, end=None, step=0.01)
self.spglib_angtol = pnw.Spinner(name="angtol", value=5, start=0.0, end=None, step=1)
# Abisanitize widgets
self.abisanitize_btn = pnw.Button(name="Run abisanitize", button_type='primary')
self.select_primitive = pnw.Select(name='Select primitive',
options=['primitive', 'primitive_standard', "no_primitive"])
# K-path widgets
self.kpath_format = pnw.Select(name="format", value="abinit", options=["abinit", "siesta", "wannier90"])
self.line_density = pnw.Spinner(name="line density", value=10, step=5, start=0, end=None)
self.plot_kpath = pnw.Checkbox(name='Plot k-path', value=False)
# MP-match
self.mp_match_btn = pnw.Button(name="Connect to Materials Project", button_type='primary')
# MP-search
#mp_search_btn = pnw.Button(name="Connect to Materials Project", button_type='primary')
#mp_api_key
# Widgets to control the generation of input files.
self.kppra = pnw.Spinner(name="kppra", value=1000, step=500, start=0, end=None)
self.smearing_type = pnw.Select(name="Smearing type", value=None,
options=[None, "gaussian", "fermi_dirac"])
self.tsmear = pnw.Spinner(name="tsmear (Ha)", value=0.01, step=0.002, start=0.0, end=None)
# TODO: nspinor 2 should trigger a check on the table.
from abipy.flowtk.psrepos import get_installed_repos_and_root
installed_repos, repos_root = get_installed_repos_and_root()
options = [repo.name for repo in installed_repos]
default_repo = "ONCVPSP-PBE-SR-PDv0.4"
default_repo = None if default_repo not in options else default_repo
self.repos_name = pnw.Select(name="PP repos", value=default_repo, options=options)
self.table_name = pnw.Select(name="Table name", value="standard", options=["standard", "stringent"])
# widgets for GS input generator
self.gs_type = pnw.Select(name="GS type", value="scf", options=["scf", "relax"])
self.gs_input_btn = pnw.Button(name="Generate input", button_type='primary')
# widgets for e-bands input generator.
self.ebands_input_btn = pnw.Button(name="Generate input", button_type='primary')
self.edos_kppra = pnw.Spinner(name="edos_kppra", value=0, step=500, start=0, end=None)
# widgets for DFPT phonons input generator.
self.ph_input_btn = pnw.Button(name="Generate input", button_type='primary')
self.with_becs = pnw.Checkbox(name='BECS and epsilon_inf (semiconductors)', value=False)
#self.dfpt_ngqpt = pnw.LiteralInput(name='ngqpt (python list)', value=[None, None, None], type=list)
#self.dfpt_ngqpt = pnw.LiteralInput(name='ngqpt (python list)', value=[None, None, None], type=list)
self.label2mode = {
"unpolarized": 'unpolarized',
"polarized": 'polarized',
"non-collinear SOC with magnetism": "spinor",
"non-collinear SOC, no magnetism": "spinor_nomag",
"collinear anti-ferromagnetic": "afm",
}
self.spin_mode = pnw.Select(name="SpinMode", value="unpolarized", options=list(self.label2mode.keys()))
[docs]
@pn.depends("output_format.value")
def convert(self):
"""Convert the input structure to one of the format selected by the user."""
s = self.structure.convert(fmt=self.output_format.value)
return self.html_with_clipboard_btn(f"<pre> {s} </pre>")
[docs]
@pn.depends("spglib_symprec.value", "spglib_angtol.value")
def spglib_summary(self) -> pn.Row:
"""Call spglib to find space group symmetries and Wyckoff positions."""
s = self.structure.spget_summary(symprec=self.spglib_symprec.value,
angle_tolerance=self.spglib_angtol.value)
return pn.Row(bkw.PreText(text=s, sizing_mode='stretch_width'))
[docs]
@depends_on_btn_click('abisanitize_btn')
def on_abisanitize_btn(self) -> None:
"""
Returns a new structure in which:
- Structure is refined.
- Reduced to primitive settings.
- Lattice vectors are exchanged if the triple product is negative
**symprec**:
Symmetry precision used to refine the structure.
**angle_tolerance**:
Tolerance on angles.
**primitive**:
Returns most primitive structure found.
**primitive_standard**:
Whether to convert to a primitive cell using the standards defined in Setyawan, W., & Curtarolo, S. (2010).
High-throughput electronic band structure calculations: Challenges and tools.
Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010
"""
primitive, primitive_standard = False, False
if self.select_primitive.value in ('primitive', 'primitive_standard'):
primitive = True
primitive_standard = self.select_primitive.value == 'primitive_standard'
else:
assert self.select_primitive.value == "no_primitive"
#print("primitive", primitive, "primitive_standard", primitive_standard)
s = self.structure.abi_sanitize(symprec=self.spglib_symprec.value,
angle_tolerance=self.spglib_angtol.value,
primitive=primitive, primitive_standard=primitive_standard)
return pn.Row(
pn.Column("## Input Structure:", bkw.PreText(text=str(self.structure), sizing_mode='stretch_width')),
pn.Column("## Sanitized:", bkw.PreText(text=str(s), sizing_mode='stretch_width')),
sizing_mode='stretch_width')
[docs]
@pn.depends("kpath_format.value", "line_density.value")
def get_kpath(self) -> pn.Column:
"""
Generate high-symmetry k-path from input structure in the ABINIT format.
"""
col = pn.Column(sizing_mode='stretch_width'); ca = col.append
s = self.structure.get_kpath_input_string(fmt=self.kpath_format.value,
line_density=self.line_density.value)
ca(self.html_with_clipboard_btn(f"<pre> {s} </pre>"))
if self.plot_kpath.value:
# FIXME: I don't know why but these calls open in a new tab.
ca("## Brillouin zone and **k**-path:")
kpath_pane = ply(self.structure.plotly_bz(pmg_path=True, show=False), with_divider=False)
df_kpts = dfc(self.structure.hsym_kpoints.get_highsym_datataframe(), with_divider=False)
ca(pn.Row(kpath_pane, df_kpts))
ca(pn.layout.Divider())
return col
def _get_pseudos_ecut_pawecutdg(self) -> tuple:
#from abipy.data.hgh_pseudos import HGH_TABLE
#return HGH_TABLE
from abipy.flowtk.psrepos import get_repo_from_name
repo = get_repo_from_name(self.repos_name.value)
pseudos = repo.get_pseudos(self.table_name.value)
ecut = 0
pawecutdg = 0
for p in pseudos:
hint = p.hint_for_accuracy(accuracy="normal")
ecut = max(ecut, hint.ecut)
pawecutdg = max(pawecutdg, hint.pawecutdg)
return pseudos, ecut, pawecutdg
def _get_smearing(self):
smearing = None
if self.smearing_type.value is not None:
smearing = "%s:%s Ha" % (self.smearing_type.value, self.tsmear.value)
return smearing
def _finalize(self, inp_or_multi, header=None, validate=False):
# TODO chksymbreak should be set to 0 else Abinit may stop.
if validate:
if inp_or_multi.is_input:
this = inp_or_multi.deepcopy()
this.pop_vars("pseudos")
v = this.abivalidate()
v_list = [v]
else:
this = inp_or_multi.deepcopy()
this.pop_vars("pseudos")
v_list = this.abivalidate()
count = 0
for v in v_list:
if v.retcode != 0:
count += 1
print(v.stderr_file.read())
print(v.log_file.read())
if count != 0: raise RuntimeError("")
# Here we replace the absolute paths with their basenames
# so that we can create a targz file with the pseudos
# We do it at this level because absolute paths are needed for executing abinit.
inp_or_multi.set_vars(pseudos='"%s"' % ", ".join(p.basename for p in inp_or_multi.pseudos))
html = self.html_with_clipboard_btn(inp_or_multi._repr_html_())
pseudos = inp_or_multi.pseudos
nspinor = inp_or_multi.get("nspinor", 1)
if nspinor == 2 and any(not p.supports_soc for p in pseudos):
raise RuntimeError("The pseudopotential table selected does not support calculations with SOC!")
def download_input():
return _make_targz_bytes(inp_or_multi)
file_download = pnw.FileDownload(filename="input.tar.gz", callback=download_input)
alert = pn.pane.Alert( """
This input file has been automatically generated by AbiPy.
Several input parameters have **default values** that might not be suitable for your particular calculation.
Please check the input variables and modify them according to your needs.
Also note that running big calculations with lot of datasets is not the most efficient approach.
Examples of AbiPy scripts to automate calculations without datasets are available
[at this page](https://abinit.github.io/abipy/flow_gallery/index.html).
""", alert_type="danger")
items = [html, file_download, pn.layout.Divider(), alert]
if header: items.insert(0, header)
return pn.Column(*items, sizing_mode="stretch_width")
[docs]
def get_gs_input(self) -> AbinitInput:
"""
Return an AbinitInput for GS calculation from the parameters selected via the widgets.
"""
from abipy.abio.factories import gs_input
pseudos, ecut, pawecutdg = self._get_pseudos_ecut_pawecutdg()
gs_inp = gs_input(structure=self.structure,
pseudos=pseudos,
kppa=self.kppra.value,
ecut=ecut,
pawecutdg=pawecutdg,
spin_mode=self.label2mode[self.spin_mode.value],
smearing=self._get_smearing(),
charge=0.0,
)
gs_inp.set_mnemonics(False)
gs_inp.pop_vars(("charge", "chksymbreak"))
# TODO: ecut, ....
#gs_inp.set_vars(#ecut="?? # depends on pseudos",
# #nband="?? # depends on pseudos",
# pseudos='"%s"' % ", ".join(p.basename for p in gs_inp.pseudos),
# )
return gs_inp
[docs]
@depends_on_btn_click('gs_input_btn')
@add_inp_docstring
def on_gs_input_btn(self):
"""
This Tab provides widgets to generate a minimalistic ABINIT input file
for ground-state calculations or structural relaxations.
In the case of relaxation runs, the following variables are automatically added:
[[optcell]] = 2, [[ionmov]] = 2, [[ecutsm]] = 0.5 and [[dilatmx]] = 1.05.
"""
gs_inp = self.get_gs_input()
if self.gs_type.value == "relax":
gs_inp.set_vars(optcell=2, ionmov=2, ecutsm=0.5, dilatmx=1.05)
return self._finalize(gs_inp)
[docs]
@depends_on_btn_click('ebands_input_btn')
@add_inp_docstring
def on_ebands_input_btn(self):
"""
This Tab provides widgets to generate a minimalistic ABINIT input file
for band structure calculations.
The first dataset performs a GS run to obtain the density file.
The second dataset reads the DEN file and performs a NSCF calculation on
a high-symmetry **k**-path generated automatically according to the input structure.
[[ndivsm]] and [[kptbounds]]
Optionally, one can add a third dataset to compute the e-DOS via a NSCF run on a
much denser **k**-mesh.
"""
from abipy.abio.factories import ebands_input
dos_kppa = self.edos_kppra.value
if dos_kppa == 0.0: dos_kppa = None
pseudos, ecut, pawecutdg = self._get_pseudos_ecut_pawecutdg()
multi = ebands_input(structure=self.structure,
pseudos=pseudos,
kppa=self.kppra.value,
nscf_nband=None,
ndivsm=10,
ecut=ecut,
pawecutdg=pawecutdg,
scf_nband=None,
spin_mode=self.label2mode[self.spin_mode.value],
smearing=self._get_smearing(),
charge=0.0,
dos_kppa=dos_kppa,
)
# Add getwfk variables.
for inp in multi[1:]:
inp["getwfk"] = 1
multi.pop_vars(("charge", "chksymbreak"))
#multi.set_vars(#ecut="?? # depends on pseudos",
# #nband="?? # depends on pseudos",
# )
return self._finalize(multi)
[docs]
@depends_on_btn_click('ph_input_btn')
@add_inp_docstring
def on_ph_input_btn(self):
"""
This Tab provides widgets to generate a minimalistic ABINIT input file
for the DFPT computation of phonons, Born effective charges (BECS)
and macroscopic dieletric tensors.
"""
from abipy.abio.factories import phonons_from_gsinput
gs_inp = self.get_gs_input()
ngkpt = np.array(gs_inp["ngkpt"])
# TODO Find an easy way to specify the q-mesh.
# Use ngqpt a la Samuel?
ph_ngqpt = [2, 2, 2]
#ph_nqpt = qscale * ngkpt
#any(ngkp % ph_ngqpt != 0):
qpoints = gs_inp.abiget_ibz(ngkpt=ph_ngqpt, shiftk=[0, 0, 0], kptopt=1).points
ndtset = 1 + len(qpoints)
qstart = 1
with_becs = self.with_becs.value
if with_becs:
# Account for the DDK (2nd dataset)
ndtset += 1
qstart = 2
multi = gs_inp.replicate(ndtset)
if with_becs:
ddk_input = multi[qstart - 1]
ddk_input.set_vars(
rfelfd=2, # only the derivative of ground-state wavefunctions with respect to k
rfdir=[1, 1, 1],
nqpt=1,
qpt=(0, 0, 0),
kptopt=2, # 2 to take into account time-reversal symmetry.
iscf=-3, # The d/dk perturbation must be treated in a non-self-consistent way
getwfk=1,
comment="Response Function calculation: d/dk",
)
ddk_input.pop_tolerances()
ddk_input.set_vars(tolwfr=1.0e-22)
for qpt, ph_input in zip(qpoints, multi[qstart:]):
is_gamma = np.sum(qpt ** 2) < 1e-12
#if with_becs and is_gamma: continue
ph_input.set_vars(
kptopt=2 if is_gamma else 3, # use time-reversal if Gamma
rfphon=1, # Will consider phonon-type perturbation
nqpt=1, # One wavevector is to be considered
qpt=qpt, # q-wavevector.
rfatpol=[1, len(gs_inp.structure)],
rfdir=[1, 1, 1],
getwfk=1,
rfelfd=3 if (with_becs and is_gamma) else None,
getddk=2 if (with_becs and is_gamma) else None,
prtwf=-1,
comment="Input file for PH calculation with DFPT.",
)
ph_input.pop_tolerances()
ph_input.set_vars(tolvrs=1.0e-10)
header = f"""
## BZ sampling
- k-mesh for electrons: {ngkpt}
- qmesh for phonons: {ph_ngqpt}
"""
#multi = phonons_from_gsinput(gs_inp, ph_ngqpt=None, qpoints=None, with_ddk=True,
# with_dde=True, with_bec=False,
# ph_tol=None, ddk_tol=None, dde_tol=None, wfq_tol=None,
# qpoints_to_skip=None, manager=None)
# Add getwfk variables.
#for inp in multi[1:]:
# inp["getwfk"] = 1
#multi.pop_vars(("charge", "chksymbreak"))
#multi.set_vars(#ecut="?? # depends on pseudos",
# #nband="?? # depends on pseudos",
# pseudos='"%s"' % ", ".join(p.basename for p in multi.pseudos),
# )
return self._finalize(multi, header=header)
[docs]
@depends_on_btn_click('mp_match_btn', show_shared_wdg_warning=False)
@add_mp_rest_docstring
def on_mp_match_btn(self):
"""
Match your structure with the ones available in the MP database.
Produce table with lattice parameters and space group info.
"""
mp = self.structure.mp_match()
if not mp.structures:
return pn.Column("## No structure found in the MP database")
return pn.Column(dfc(mp.lattice_dataframe, transpose=True),
sizing_mode='stretch_width')
#@depends_on_btn_click('mp_search_btn')
#def on_mp_search_btn(self):
# from abipy.core.structure import mp_search
# chemsys_formula_id = self.stucture.formula
# mp = mp_search(chemsys_formula_id, api_key=None, endpoint=None, final=True)
# if not mp.structures:
# raise RuntimeError("No structure found in MP database")
# return pn.Column(dfc(mp.lattice_dataframe), sizing_mode='stretch_width')
[docs]
def get_panel(self, with_inputs=True, as_dict=False, **kwargs):
"""
Build panel with widgets to interact with the structure either in a notebook or in a bokeh app.
Args:
with_inputs: True if tabs for generating input files should be shown.
"""
d = dict()
d["Summary"] = self.get_summary_view_for_abiobj(self.structure)
d["Viewer"] = self.get_structure_view()
d["Spglib"] = pn.Row(
self.pws_col(['## Spglib options',
"spglib_symprec", "spglib_angtol",
]),
self.spglib_summary
)
d["AbiSanitize"] = pn.Row(
self.pws_col(['## Spglib options',
"spglib_symprec", "spglib_angtol", "select_primitive", "abisanitize_btn",
pn.layout.Divider(),
]),
self.on_abisanitize_btn
)
d["Kpath"] = pn.Row(
self.pws_col(['## K-path options',
"kpath_format", "line_density", "plot_kpath",
]),
self.get_kpath
)
d["Convert"] = pn.Row(
self.pws_col(["## Convert structure", "output_format",
]),
self.convert
)
if with_inputs:
# Add tabs to generate inputs from structure.
d["GS-input"] = pn.Row(
self.pws_col(['## Generate GS input',
"gs_type", "spin_mode", "kppra", "smearing_type", "tsmear",
"repos_name", "table_name",
"gs_input_btn",
]),
self.on_gs_input_btn
)
d["Ebands-input"] = pn.Row(
self.pws_col(['## Generate Ebands input',
"spin_mode", "kppra", "edos_kppra", "smearing_type", "tsmear",
"repos_name", "table_name",
"ebands_input_btn",
]),
self.on_ebands_input_btn
)
d["PH-input"] = pn.Row(
self.pws_col(['## Generate phonon input',
"spin_mode", "kppra", "smearing_type", "tsmear",
"with_becs",
"repos_name", "table_name",
"ph_input_btn",
]),
self.on_ph_input_btn
)
d["MP-match"] = pn.Column(self.on_mp_match_btn,
pn.layout.Divider(),
pn.Row(self.mp_match_btn, align="center"),
sizing_mode="stretch_width")
if as_dict: return d
return self.get_template_from_tabs(d, template=kwargs.get("template", None))
[docs]
class InputFileGenerator(AbipyParameterized):
abi_sanitize = param.Boolean(True, doc="Sanitize structure")
info_str = """
Generate ABINIT input files for performing basic:
- GS calculations
- NSCF band structure calculations
- DFPT calculations for phonons including Born effective charges and dielectric constant
starting from a crystalline structure provided by the user either via an external file
or through the Materials Project identifier (*mp-id*).
"""
def __init__(self, **params):
super().__init__(**params)
# Spglib widgets
#self.spglib_symprec = pnw.Spinner(name="symprec", value=0.01, start=0.0, end=None, step=0.01)
#self.spglib_angtol = pnw.Spinner(name="angtol", value=5, start=0.0, end=None, step=1)
help_md = pn.pane.Markdown(f"""
## Description
{self.info_str}
""")
self.main_area = pn.Column(help_md,
self.get_alert_data_transfer(),
sizing_mode="stretch_width")
self.file_input = pnw.FileInput(height=60, css_classes=["pnx-file-upload-area"])
self.file_input.param.watch(self.on_file_input, "value")
self.mpid_input = pnw.TextInput(name='mp-id', placeholder='Enter e.g. mp-149 for Silicon and press ⏎')
self.mpid_input.param.watch(self.on_mpid_input, "value")
self.mpid_err_wdg = pn.pane.Markdown("")
def _set_structure(self, structure):
if self.abi_sanitize:
structure = structure.abi_sanitize(symprec=1e-3, angle_tolerance=5,
primitive=True, primitive_standard=False)
self.input_structure = structure
[docs]
def on_file_input(self, event):
self.mpid_err_wdg.object = ""
#print("filename", self.file_input.filename)
if self.file_input.value is None: return None
#print("value", self.file_input.value)
import tempfile
workdir = tempfile.mkdtemp()
fd, tmp_path = tempfile.mkstemp(suffix=self.file_input.filename)
with open(tmp_path, "wb") as fh:
fh.write(self.file_input.value)
self._set_structure(Structure.from_file(tmp_path))
os.remove(tmp_path)
self.update_main_area()
[docs]
def on_mpid_input(self, event):
with Loading(self.mpid_input, err_wdg=self.mpid_err_wdg):
self._set_structure(Structure.from_mpid(self.mpid_input.value))
self.update_main_area()
[docs]
def update_main_area(self):
with Loading(self.main_area):
d = self.input_structure.get_panel(as_dict=True)
d = {k: d[k] for k in ("GS-input", "Ebands-input", "PH-input", "Summary")}
tabs = pn.Tabs(*d.items())
self.main_area.objects = [tabs]
[docs]
def get_panel(self):
col = pn.Column(
"## Upload (or drag & drop) **any file** with a structure (*.nc*, *.abi*, *.cif*, *.xsf*, *POSCAR*):",
self.get_fileinput_section(self.file_input),
"## or get the structure from the [Materials Project](https://materialsproject.org/) database:",
pn.Row(self.mpid_input, pn.Column(self.mpid_err_wdg)),
"## Invoke abi_sanitize to refine structure",
self.param.abi_sanitize,
sizing_mode="stretch_width")
main = pn.Column(col, self.main_area, sizing_mode="stretch_width")
cls, kwds = self.get_abinit_template_cls_kwds()
return cls(main=main, title="Input File Generator", **kwds)