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Fix errors (only two errors left)

This commit is contained in:
Matteo Giantomassi 2024-07-25 01:01:43 +02:00
parent 090fca1cbe
commit d56b647a87
27 changed files with 542 additions and 595 deletions
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37
.github/workflows/gh-pages.yml vendored
View File

@ -33,6 +33,11 @@ jobs:
python: '3.11'
runs-on: ubuntu-latest
env:
PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
# This is used in the flow scripts to generate the graph with graphviz.
READTHEDOCS: 1
steps:
- name: Check out Abipy repo
uses: actions/checkout@v4
@ -54,26 +59,28 @@ jobs:
mpirun -n 1 abinit --build
pip install --editable .
mkdir -p $HOME/.abinit/abipy/
cp abipy/data/managers/travis_manager.yml $HOME/.abinit/abipy/manager.yml
cp abipy/data/managers/simple_scheduler.yml $HOME/.abinit/abipy/scheduler.yml
cp abipy/data/managers/gh_manager.yml $HOME/.abinit/abipy/manager.yml
cp abipy/data/managers/gh_scheduler.yml $HOME/.abinit/abipy/scheduler.yml
- name: Build docs with Sphinx
run: |
conda activate abipy
cd docs
cd docs
source install.sh
make
#- name: Upload artifact
# uses: actions/upload-pages-artifact@v2
- name: Upload artifact
uses: actions/upload-pages-artifact@v2
with:
path: site/ # Important. Set to your output dir in MkDocs
#deploy:
# environment:
# name: github-pages
# url: ${{ steps.deployment.outputs.page_url }}
# runs-on: ubuntu-latest
# needs: build
# steps:
# - name: Deploy to GitHub Pages
# id: deployment
# uses: actions/deploy-pages@v2
deploy:
environment:
name: github-pages
url: ${{ steps.deployment.outputs.page_url }}
runs-on: ubuntu-latest
needs: build
steps:
- name: Deploy to GitHub Pages
id: deployment
uses: actions/deploy-pages@v3

8
.github/workflows/test.yml vendored
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@ -25,12 +25,10 @@ jobs:
config:
- os: ubuntu-latest
python: '3.11'
#python: '>3.9'
runs-on: ${{ matrix.config.os }}
#env:
# PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
env:
PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
steps:
- name: Check out Abipy repo
@ -57,7 +55,7 @@ jobs:
run: |
conda activate abipy
pip install -r requirements-tests.txt
pytest -v .
pytest -v .
- name: integration_tests
run: |

2
README.rst
View File

@ -447,7 +447,7 @@ AbiPy is released under the GNU GPL license. For more details see the LICENSE fi
.. |download-with-anaconda| image:: https://anaconda.org/abinit/abipy/badges/installer/conda.svg
:alt: Download with Anaconda
:target: https://conda.anaconda.org/abinit
:target: https://anaconda.org/conda-forge/abinit
.. |launch-binder| image:: https://mybinder.org/badge.svg
:alt: Launch binder

220
abipy/core/restapi.py
View File

@ -17,7 +17,6 @@ from abipy.tools.printing import print_dataframe
from abipy.core.mixins import NotebookWriter
MP_DEFAULT_ENDPOINT = "https://materialsproject.org/rest/v2"
MP_KEYS_FOR_DATAFRAME = (
"pretty_formula", "e_above_hull", "energy_per_atom",
@ -27,132 +26,113 @@ MP_KEYS_FOR_DATAFRAME = (
)
def get_mprester(api_key=None, endpoint=None) -> MyMPRester:
def get_mprester():
"""
Args:
api_key (str): A String API key for accessing the MaterialsProject
REST interface. Please apply on the Materials Project website for one.
If this is None, the code will check if there is a `PMG_MAPI_KEY` in
your .pmgrc.yaml. If so, it will use that environment
This makes easier for heavy users to simply add
this environment variable to their setups and MPRester can
then be called without any arguments.
endpoint (str): Url of endpoint to access the MaterialsProject REST interface.
Defaults to the standard Materials Project REST address, but
can be changed to other urls implementing a similar interface.
"""
if api_key is None:
try:
from pymatgen.core import SETTINGS
except ImportError:
from pymatgen import SETTINGS
api_key = SETTINGS.get("PMG_MAPI_KEY")
if api_key is None:
raise RuntimeError("Cannot find PMG_MAPI_KEY in pymatgen settings. Add it to $HOME/.pmgrc.yaml")
if endpoint is None: endpoint = MP_DEFAULT_ENDPOINT
return MyMPRester(api_key=api_key, endpoint=endpoint)
rester = MPRester()
#print(f"{type(rester)=}")
return rester
class MyMPRester(MPRester):
"""
Subclass Materials project Rester.
See :cite:`Jain2013,Ong2015`.
.. rubric:: Inheritance Diagram
.. inheritance-diagram:: MyMPRester
"""
Error = MPRestError
def get_phasediagram_results(self, elements) -> PhaseDiagramResults:
"""
Contact the materials project database, fetch entries and build :class:``PhaseDiagramResults`` instance.
Args:
elements: List of chemical elements.
"""
entries = self.get_entries_in_chemsys(elements, inc_structure="final")
return PhaseDiagramResults(entries)
#class MyMPRester(MPRester):
# """
# Subclass Materials project Rester.
# See :cite:`Jain2013,Ong2015`.
#
# .. rubric:: Inheritance Diagram
# .. inheritance-diagram:: MyMPRester
# """
# Error = MPRestError
#
# def get_phasediagram_results(self, elements) -> PhaseDiagramResults:
# """
# Contact the materials project database, fetch entries and build :class:``PhaseDiagramResults`` instance.
#
# Args:
# elements: List of chemical elements.
# """
# entries = self.get_entries_in_chemsys(elements, inc_structure="final")
# return PhaseDiagramResults(entries)
class PhaseDiagramResults:
"""
Simplified interface to phase-diagram pymatgen API.
Inspired to:
https://anaconda.org/matsci/plotting-and-analyzing-a-phase-diagram-using-the-materials-api/notebook
See also: :cite:`Ong2008,Ong2010`
"""
def __init__(self, entries):
self.entries = entries
# Convert pymatgen structure to Abipy.
from abipy.core.structure import Structure
for e in entries:
e.structure.__class__ = Structure
self.structures = [e.structure for e in entries]
self.mpids = [e.entry_id for e in entries]
# Create phase diagram.
from pymatgen.analysis.phase_diagram import PhaseDiagram
self.phasediagram = PhaseDiagram(self.entries)
def plot(self, show_unstable=True, show=True):
"""
Plot phase diagram.
Args:
show_unstable (float): Whether unstable phases will be plotted as
well as red crosses. If a number > 0 is entered, all phases with
ehull < show_unstable will be shown.
show: True to show plot.
Return: plotter object.
"""
from pymatgen.analysis.phase_diagram import PDPlotter
plotter = PDPlotter(self.phasediagram, show_unstable=show_unstable)
if show:
plotter.show()
return plotter
@lazy_property
def dataframe(self) -> pd.DataFrame:
"""Pandas dataframe with the most important results."""
rows = []
for e in self.entries:
d = e.structure.get_dict4pandas(with_spglib=True)
decomp, ehull = self.phasediagram.get_decomp_and_e_above_hull(e)
rows.append(OrderedDict([
("Materials ID", e.entry_id),
("spglib_symb", d["spglib_symb"]), ("spglib_num", d["spglib_num"]),
("Composition", e.composition.reduced_formula),
("Ehull", ehull), # ("Equilibrium_reaction_energy", pda.get_equilibrium_reaction_energy(e)),
("Decomposition", " + ".join(["%.2f %s" % (v, k.composition.formula) for k, v in decomp.items()])),
]))
import pandas as pd
return pd.DataFrame(rows, columns=list(rows[0].keys()) if rows else None)
def print_dataframes(self, with_spglib=False, file=sys.stdout, verbose=0) -> None:
"""
Print pandas dataframe to file `file`.
Args:
with_spglib: True to compute spacegroup with spglib.
file: Output stream.
verbose: Verbosity level.
"""
print_dataframe(self.dataframe, file=file)
if verbose:
from abipy.core.structure import dataframes_from_structures
dfs = dataframes_from_structures(self.structures, index=self.mpids, with_spglib=with_spglib)
print_dataframe(dfs.lattice, title="Lattice parameters:", file=file)
if verbose > 1:
print_dataframe(dfs.coords, title="Atomic positions (columns give the site index):", file=file)
#class PhaseDiagramResults:
# """
# Simplified interface to phase-diagram pymatgen API.
#
# Inspired to:
#
# https://anaconda.org/matsci/plotting-and-analyzing-a-phase-diagram-using-the-materials-api/notebook
#
# See also: :cite:`Ong2008,Ong2010`
# """
# def __init__(self, entries):
# self.entries = entries
# # Convert pymatgen structure to Abipy.
# from abipy.core.structure import Structure
# for e in entries:
# e.structure.__class__ = Structure
#
# self.structures = [e.structure for e in entries]
# self.mpids = [e.entry_id for e in entries]
#
# # Create phase diagram.
# from pymatgen.analysis.phase_diagram import PhaseDiagram
# self.phasediagram = PhaseDiagram(self.entries)
#
# def plot(self, show_unstable=True, show=True):
# """
# Plot phase diagram.
#
# Args:
# show_unstable (float): Whether unstable phases will be plotted as
# well as red crosses. If a number > 0 is entered, all phases with
# ehull < show_unstable will be shown.
# show: True to show plot.
#
# Return: plotter object.
# """
# from pymatgen.analysis.phase_diagram import PDPlotter
# plotter = PDPlotter(self.phasediagram, show_unstable=show_unstable)
# if show:
# plotter.show()
# return plotter
#
# @lazy_property
# def dataframe(self) -> pd.DataFrame:
# """Pandas dataframe with the most important results."""
# rows = []
# for e in self.entries:
# d = e.structure.get_dict4pandas(with_spglib=True)
# decomp, ehull = self.phasediagram.get_decomp_and_e_above_hull(e)
#
# rows.append(OrderedDict([
# ("Materials ID", e.entry_id),
# ("spglib_symb", d["spglib_symb"]), ("spglib_num", d["spglib_num"]),
# ("Composition", e.composition.reduced_formula),
# ("Ehull", ehull), # ("Equilibrium_reaction_energy", pda.get_equilibrium_reaction_energy(e)),
# ("Decomposition", " + ".join(["%.2f %s" % (v, k.composition.formula) for k, v in decomp.items()])),
# ]))
#
# import pandas as pd
# return pd.DataFrame(rows, columns=list(rows[0].keys()) if rows else None)
#
# def print_dataframes(self, with_spglib=False, file=sys.stdout, verbose=0) -> None:
# """
# Print pandas dataframe to file `file`.
#
# Args:
# with_spglib: True to compute spacegroup with spglib.
# file: Output stream.
# verbose: Verbosity level.
# """
# print_dataframe(self.dataframe, file=file)
# if verbose:
# from abipy.core.structure import dataframes_from_structures
# dfs = dataframes_from_structures(self.structures, index=self.mpids, with_spglib=with_spglib)
# print_dataframe(dfs.lattice, title="Lattice parameters:", file=file)
# if verbose > 1:
# print_dataframe(dfs.coords, title="Atomic positions (columns give the site index):", file=file)
class DatabaseStructures(NotebookWriter):

59
abipy/core/structure.py
View File

@ -41,14 +41,12 @@ __all__ = [
]
def mp_match_structure(obj, api_key=None, endpoint=None, final=True):
def mp_match_structure(obj):
"""
Finds matching structures on the Materials Project database.
Args:
obj: filename or |Structure| object.
api_key (str): A String API key for accessing the MaterialsProject REST interface.
endpoint (str): Url of endpoint to access the MaterialsProject REST interface.
final (bool): Whether to get the final structure, or the initial
(pre-relaxation) structure. Defaults to True.
@ -62,12 +60,14 @@ def mp_match_structure(obj, api_key=None, endpoint=None, final=True):
from abipy.core import restapi
structures, mpids = [], []
with restapi.get_mprester(api_key=api_key, endpoint=endpoint) as rest:
with restapi.get_mprester() as rest:
try:
if getattr(rest, "get_data") is None:
raise RuntimeError("mp_match_structure requires mp-api, please install it with `pip install mp-api`")
mpids = rest.find_structure(structure)
if mpids:
structures = [Structure.from_mpid(mid, final=final, api_key=api_key, endpoint=endpoint)
for mid in mpids]
structures = [Structure.from_mpid(mid) for mid in mpids]
except Exception as exc:
cprint(str(exc), "red")
@ -80,7 +80,7 @@ def mp_match_structure(obj, api_key=None, endpoint=None, final=True):
return restapi.MpStructures(structures=structures, ids=mpids)
def mp_search(chemsys_formula_id, api_key=None, endpoint=None):
def mp_search(chemsys_formula_id):
"""
Connect to the materials project database.
Get a list of structures corresponding to a chemical system, formula, or materials_id.
@ -88,32 +88,32 @@ def mp_search(chemsys_formula_id, api_key=None, endpoint=None):
Args:
chemsys_formula_id (str): A chemical system (e.g., Li-Fe-O),
or formula (e.g., Fe2O3) or materials_id (e.g., mp-1234).
api_key (str): A String API key for accessing the MaterialsProject REST interface.
If this is None, the code will check if there is a `PMG_MAPI_KEY` in your .pmgrc.yaml.
endpoint (str): Url of endpoint to access the MaterialsProject REST interface.
Returns:
:class:`MpStructures` object with
List of Structure objects, Materials project ids associated to structures.
and List of dictionaries with MP data (same order as structures).
Note that the attributes evalute to False if no match is found
Note that the attributes evalute to False if no match is found.
"""
chemsys_formula_id = chemsys_formula_id.replace(" ", "")
structures, mpids, data = [], [], None
from abipy.core import restapi
with restapi.get_mprester(api_key=api_key, endpoint=endpoint) as rest:
from pymatgen.ext.matproj import MPRestError
with restapi.get_mprester() as rest:
try:
if getattr(rest, "get_data") is None:
raise RuntimeError("mp_search requires mp-api, please install it with `pip install mp-api`")
data = rest.get_data(chemsys_formula_id, prop="")
if data:
structures = [Structure.from_str(d["cif"], fmt="cif", primitive=False, sort=False)
for d in data]
structures = [Structure.from_str(d["cif"], fmt="cif", primitive=False, sort=False) for d in data]
mpids = [d["material_id"] for d in data]
# Want AbiPy structure.
structures = list(map(Structure.as_structure, structures))
except rest.Error as exc:
except MPRestError:
cprint(str(exc), "magenta")
return restapi.MpStructures(structures, mpids, data=data)
@ -194,10 +194,13 @@ class Structure(pmg_Structure, NotebookWriter):
- Objects with a ``structure`` attribute.
- ASE atoms.
"""
if isinstance(obj, cls): return obj
if isinstance(obj, cls):
return obj
if isinstance(obj, pmg_Structure):
obj.__class__ = cls
return obj
if hasattr(obj, "ase_objtype"):
# ASE Atoms.
from pymatgen.io.ase import AseAtomsAdaptor
@ -331,7 +334,7 @@ class Structure(pmg_Structure, NotebookWriter):
return new
@classmethod
def from_mpid(cls, material_id: str, final=True, api_key=None, endpoint=None) -> Structure:
def from_mpid(cls, material_id: str) -> Structure:
"""
Get a Structure corresponding to a material_id.
@ -339,15 +342,6 @@ class Structure(pmg_Structure, NotebookWriter):
material_id (str): Materials Project material_id (a string, e.g., mp-1234).
final (bool): Whether to get the final structure, or the initial
(pre-relaxation) structure. Defaults to True.
api_key (str): A String API key for accessing the MaterialsProject
REST interface. Please apply on the Materials Project website for one.
If this is None, the code will check if there is a ``PMG_MAPI_KEY`` in your .pmgrc.yaml.
If so, it will use that environment
This makes easier for heavy users to simply add this environment variable
to their setups and MPRester can then be called without any arguments.
endpoint (str): Url of endpoint to access the MaterialsProject REST interface.
Defaults to the standard Materials Project REST address, but
can be changed to other urls implementing a similar interface.
Returns: |Structure| object.
"""
@ -357,9 +351,8 @@ class Structure(pmg_Structure, NotebookWriter):
# Get pytmatgen structure and convert it to abipy structure
from abipy.core import restapi
with restapi.get_mprester(api_key=api_key, endpoint=endpoint) as rest:
new = rest.get_structure_by_material_id(material_id, final=final)
#new = rest.get_structure_by_material_id(material_id)
with restapi.get_mprester() as rest:
new = rest.get_structure_by_material_id(material_id)
return cls.as_structure(new)
@classmethod
@ -841,8 +834,14 @@ class Structure(pmg_Structure, NotebookWriter):
s = self.get_sorted_structure()
ase_adaptor = AseAtomsAdaptor()
ase_atoms = ase_adaptor.get_atoms(structure=s)
standardized = spglib.standardize_cell(ase_atoms, to_primitive=1, no_idealize=no_idealize,
#standardized = spglib.standardize_cell(ase_atoms, to_primitive=1, no_idealize=no_idealize,
# symprec=symprec, angle_tolerance=angle_tolerance)
spglib_cell = (ase_atoms.cell, ase_atoms.get_scaled_positions(), ase_atoms.get_atomic_numbers())
standardized = spglib.standardize_cell(spglib_cell, to_primitive=1, no_idealize=no_idealize,
symprec=symprec, angle_tolerance=angle_tolerance)
standardized_ase_atoms = Atoms(scaled_positions=standardized[1], numbers=standardized[2], cell=standardized[0])
standardized_structure = ase_adaptor.get_structure(standardized_ase_atoms)

3
abipy/core/testing.py
View File

@ -340,7 +340,8 @@ class AbipyTest(PymatgenTest):
@staticmethod
def test_mprester():
"""Skip MP rester tests."""
raise unittest.SkipTest("MPRester tests have been disabled")
#raise unittest.SkipTest("MPRester tests have been disabled")
return True
@staticmethod
def has_matplotlib(version: Optional[str] = None, op: str = ">=") -> bool:

3
abipy/data/managers/travis_manager.yml → abipy/data/managers/gh_manager.yml
View File

@ -1,8 +1,9 @@
# Manager used for github actions.
qadapters:
-
priority: 1
queue:
qname: travis
qname: github
qtype: shell
job:
mpi_runner: mpirun

0
abipy/data/managers/travis_scheduler.yml → abipy/data/managers/gh_scheduler.yml
View File

25
abipy/dfpt/ddb.py
View File

@ -127,7 +127,7 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
return cls(tmp_filepath)
@classmethod
def from_mpid(cls, material_id, api_key=None, endpoint=None) -> DdbFile:
def from_mpid(cls, material_id) -> DdbFile:
"""
Fetch DDB file corresponding to a materials project ``material_id``,
save it to temporary file and return new DdbFile object.
@ -136,17 +136,17 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
Args:
material_id (str): Materials Project material_id (e.g., mp-1234).
api_key (str): A String API key for accessing the MaterialsProject REST interface.
If None, the code will check if there is a `PMG_MAPI_KEY` in your .pmgrc.yaml.
endpoint (str): Url of endpoint to access the MaterialsProject REST interface.
Defaults to the standard Materials Project REST address
"""
material_id = str(material_id)
if not material_id.startswith("mp-"):
raise ValueError("Materials project ID should start with mp-")
from abipy.core import restapi
with restapi.get_mprester(api_key=api_key, endpoint=endpoint) as rest:
with restapi.get_mprester() as rest:
if getattr(rest, "_make_request") is None:
raise RuntimeError("from_mpid requires mp-api, please install it with `pip install mp-api`")
ddb_string = rest._make_request("/materials/%s/abinit_ddb" % material_id)
_, tmpfile = tempfile.mkstemp(prefix=material_id, suffix='_DDB')
@ -2926,16 +2926,12 @@ class DdbRobot(Robot):
return filename.endswith("_" + cls.EXT)
@classmethod
def from_mpid_list(cls, mpid_list, api_key=None, endpoint=None):
def from_mpid_list(cls, mpid_list):
"""
Build a DdbRobot from list of materials-project ids.
Args:
mpid_list: List of Materials Project material_ids (e.g., ["mp-1234", "mp-1245"]).
api_key (str): A String API key for accessing the MaterialsProject REST interface.
If None, the code will check if there is a `PMG_MAPI_KEY` in your .pmgrc.yaml.
endpoint (str): Url of endpoint to access the MaterialsProject REST interface.
Defaults to the standard Materials Project REST address
"""
from abipy.core import restapi
ddb_files = []
@ -2943,10 +2939,15 @@ class DdbRobot(Robot):
if not mpid_list:
raise RuntimeError("No structure found in the MP database")
if any(not s.startswith("mp-") for s in mpid_list):
raise ValueError(f"Invalid mp-in in list:\n{mpid_list}")
with restapi.get_mprester(api_key=api_key, endpoint=endpoint) as rest:
with restapi.get_mprester() as rest:
if getattr(rest, "_make_request") is None:
raise RuntimeError("from_mpid_list requires mp-api, please install it with `pip install mp-api`")
for mpid in mpid_list:
try:
ddb_string = rest._make_request("/materials/%s/abinit_ddb" % mpid)

22
abipy/electrons/ebands.py
View File

@ -458,7 +458,7 @@ class ElectronBands(Has_Structure):
raise TypeError("Don't know how to extract ebands from object `%s`" % type(obj))
@classmethod
def from_mpid(cls, material_id, api_key=None, endpoint=None,
def from_mpid(cls, material_id,
nelect=None, has_timerev=True,
nspinor=1, nspden=None, line_mode=True) -> ElectronBands:
"""
@ -467,16 +467,6 @@ class ElectronBands(Has_Structure):
Args:
material_id (str): Materials Project material_id (a string, e.g., mp-1234).
api_key (str): A String API key for accessing the MaterialsProject
REST interface. Please apply on the Materials Project website for one.
If this is None, the code will check if there is a `PMG_MAPI_KEY` in
your .pmgrc.yaml. If so, it will use that environment
This makes easier for heavy users to simply add
this environment variable to their setups and MPRester can
then be called without any arguments.
endpoint (str): Url of endpoint to access the MaterialsProject REST interface.
Defaults to the standard Materials Project REST address, but
can be changed to other urls implementing a similar interface.
nelect: Number of electrons in the unit cell.
If None, this value is automatically computed using the Fermi level (if metal)
or the VBM indices reported in the JSON document sent by the MP database.
@ -491,7 +481,11 @@ class ElectronBands(Has_Structure):
# Get pytmatgen structure and convert it to an AbiPy structure
from abipy.core import restapi
with restapi.get_mprester(api_key=api_key, endpoint=endpoint) as rest:
with restapi.get_mprester() as rest:
if getattr(rest, "get_structure_by_material_id") is None:
raise RuntimeError("from_mpid requires mp-api, please install it with `pip install mp-api`")
pmgb = rest.get_bandstructure_by_material_id(material_id=material_id, line_mode=line_mode)
if pmgb is None: return None
@ -5487,9 +5481,9 @@ class Bands3D(Has_Structure):
except ImportError:
try:
from skimage.measure import marching_cubes
except ImportError:
except ImportError as exc:
raise ImportError("scikit-image not installed.\n"
"Please install with it with `conda install scikit-image` or `pip install scikit-image`")
"Please install with it with `conda install scikit-image` or `pip install scikit-image`") from exc
e0 = self.get_e0(e0)
isobands = self.get_isobands(e0)

3
abipy/ppcodes/oncv_parser.py
View File

@ -206,8 +206,7 @@ class OncvParser(BaseParser):
if self.rc5 is None:
raise self.Error(f"Cannot find magic line starting with `{header}` in: {self.filepath}")
# Parse ATOM and Reference configuration
# Example:
# Parse ATOM and Reference configuration. Example:
"""
#
# n l f energy (Ha)

25
abipy/ppcodes/ppgen.py
View File

@ -310,25 +310,34 @@ class OncvGenerator(_PseudoGenerator):
"""
@classmethod
def from_file(cls, path: str, calc_type: str, workdir: Optional[str] = None) -> OncvGenerator:
def from_file(cls, path: str, calc_type: str, use_mgga: bool, workdir: Optional[str] = None) -> OncvGenerator:
"""
Build the object from a file containing the input parameters.
"""
with open(path, "rt") as fh:
input_str = fh.read()
return cls(input_str, calc_type, workdir=workdir)
return cls(input_str, calc_type, use_mgga=use_mgga, workdir=workdir)
def __init__(self, input_str: str, calc_type: str, workdir: Optional[str] = None):
def __init__(self, input_str: str, calc_type: str, use_mgga: bool, workdir: Optional[str] = None):
super().__init__(workdir=workdir)
self._input_str = input_str
self.calc_type = calc_type
self.use_mgga = use_mgga
self._executable = {
"non-relativistic": which("oncvpspnr.x"),
"scalar-relativistic": which("oncvpsp.x"),
"fully-relativistic": which("oncvpspr.x"),
}[calc_type]
if self.use_mgga:
if calc_type != "scalar-relativistic":
raise ValueError("Only scalar-relativistic pseudos are supported in metagga mode!")
self._executable = {
"scalar-relativistic": which("oncvpspm.x"),
}[calc_type]
else:
self._executable = {
"non-relativistic": which("oncvpspnr.x"),
"scalar-relativistic": which("oncvpsp.x"),
"fully-relativistic": which("oncvpspr.x"),
}[calc_type]
if self._executable is None:
msg = "Cannot find oncvpsp executable in $PATH. Use `export PATH=dir_with_oncvps_executable:$PATH`"

62
abipy/scripts/abistruct.py
View File

@ -15,14 +15,13 @@ from tabulate import tabulate
from monty.string import marquee
from monty.functools import prof_main
from monty.termcolor import cprint
from pymatgen.io.vasp.outputs import Xdatcar
from abipy import abilab
from abipy.core.symmetries import AbinitSpaceGroup
from abipy.core.kpoints import Ktables, Kpoint, IrredZone
from abipy.core.structure import diff_structures
from abipy.iotools.visualizer import Visualizer
from abipy.iotools.xsf import xsf_write_structure
from abipy.abio import factories
from abipy import abilab
def save_structure(structure, options) -> None:
@ -131,7 +130,7 @@ Usage example:
`Ir-O-*` for wildcard pattern matching.
Print info and Abinit input files. Use e.g. `-f POSCAR`
to change output format. `-f None` to disable structure output.
abistruct.py mp_pd FILE-or-elements => Generate phase diagram with entries from the Materials Project.
abistruct.py mp_ebands FILE => Fetch electron band structure from MP database. Print gaps.
Accept FILE with structure if ebands from structure is wanted
or mp id e.g. "mp-149 or list of elements e.g `Li-Fe-O` or chemical formula.
@ -141,6 +140,8 @@ Use `abistruct.py --help` for help and `abistruct.py COMMAND --help` to get the
Use `-v` to increase verbosity level (can be supplied multiple times e.g -vv).
"""
#abistruct.py mp_pd FILE-or-elements => Generate phase diagram with entries from the Materials Project.
def get_parser(with_epilog=False):
@ -440,9 +441,6 @@ closest points in this particular structure. This is usually what you want in a
# Options for commands accessing the materials project database.
mp_rest_parser = argparse.ArgumentParser(add_help=False)
mp_rest_parser.add_argument("--mapi-key", default=None,
help="Pymatgen PMG_MAPI_KEY. Use value in .pmgrc.yaml if not specified.")
mp_rest_parser.add_argument("--endpoint", help="Pymatgen database.", default="https://www.materialsproject.org/rest/v2")
mp_rest_parser.add_argument("-b", "--browser", default=False, action='store_true',
help="Open materials-project webpages in browser")
@ -467,15 +465,15 @@ closest points in this particular structure. This is usually what you want in a
add_format_arg(p_mpsearch, default="abivars")
# Subparser for mp_pd command.
p_mp_pda = subparsers.add_parser('mp_pd', parents=[mp_rest_parser, copts_parser],
help=("Generate phase diagram with entries from the Materials Project. "
"Requires internet connection and PMG_MAPI_KEY"))
p_mp_pda.add_argument("file_or_elements", type=str, default=None,
help="FILE with structure or elements e.g., Li-Fe-O).")
p_mp_pda.add_argument("-u", "--show-unstable", type=int, default=0,
help="""Whether unstable phases will be plotted as
well as red crosses. If a number > 0 is entered, all phases with
ehull < show_unstable will be shown.""")
#p_mp_pda = subparsers.add_parser('mp_pd', parents=[mp_rest_parser, copts_parser],
# help=("Generate phase diagram with entries from the Materials Project. "
# "Requires internet connection and PMG_MAPI_KEY"))
#p_mp_pda.add_argument("file_or_elements", type=str, default=None,
# help="FILE with structure or elements e.g., Li-Fe-O).")
#p_mp_pda.add_argument("-u", "--show-unstable", type=int, default=0,
# help="""Whether unstable phases will be plotted as
#well as red crosses. If a number > 0 is entered, all phases with
#ehull < show_unstable will be shown.""")
# Subparser for mp_ebands command.
p_mp_ebands = subparsers.add_parser('mp_ebands', parents=[copts_parser, mp_rest_parser],
@ -916,7 +914,7 @@ def main():
print(structure.spget_summary(verbose=options.verbose))
print("\n")
print(marquee("Little Group", mark="="))
print(marquee("Little group", mark="="))
ltk = spgrp.find_little_group(kpoint=options.kpoint)
print(ltk.to_string(verbose=options.verbose))
@ -952,8 +950,7 @@ def main():
elif options.command == "mp_id":
# Get the Structure corresponding to material_id.
structure = abilab.Structure.from_mpid(options.mpid, final=True,
api_key=options.mapi_key, endpoint=options.endpoint)
structure = abilab.Structure.from_mpid(options.mpid)
# Convert to format and print it.
print(structure.convert(fmt=options.format))
@ -990,30 +987,30 @@ def main():
if options.browser:
mp.open_browser(limit=None if options.verbose == 2 else 10)
elif options.command == "mp_pd":
if os.path.exists(options.file_or_elements):
structure = abilab.Structure.from_file(options.file_or_elements)
elements = structure.symbol_set
else:
elements = options.file_or_elements.split("-")
#elif options.command == "mp_pd":
# if os.path.exists(options.file_or_elements):
# structure = abilab.Structure.from_file(options.file_or_elements)
# elements = structure.symbol_set
# else:
# elements = options.file_or_elements.split("-")
if options.verbose > 1: print("Building phase-diagram for elements:", elements)
with abilab.restapi.get_mprester(api_key=options.mapi_key, endpoint=options.endpoint) as rest:
pdr = rest.get_phasediagram_results(elements)
pdr.print_dataframes(verbose=options.verbose)
pdr.plot(show_unstable=options.show_unstable)
# if options.verbose > 1: print("Building phase-diagram for elements:", elements)
# with abilab.restapi.get_mprester() as rest:
# pdr = rest.get_phasediagram_results(elements)
# pdr.print_dataframes(verbose=options.verbose)
# pdr.plot(show_unstable=options.show_unstable)
elif options.command == "mp_ebands":
if os.path.exists(options.chemsys_formula_id):
mp = abilab.mp_match_structure(options.chemsys_formula_id)
for mpid in mp.ids:
ebands = abilab.ElectronBands.from_mpid(mpid, api_key=options.mapi_key, endpoint=options.endpoint)
ebands = abilab.ElectronBands.from_mpid(mpid)
print(ebands)
else:
if options.chemsys_formula_id.startswith("mp-"):
# Assume valid mp identifier.
mpid = options.chemsys_formula_id
ebands = abilab.ElectronBands.from_mpid(mpid, api_key=options.mapi_key, endpoint=options.endpoint)
ebands = abilab.ElectronBands.from_mpid(mpid)
print(ebands)
else:
mp = abilab.mp_search(options.chemsys_formula_id)
@ -1025,7 +1022,7 @@ def main():
if structure is None:
cprint("ignoring mpid %s because cannot find structure" % mpid, "red")
continue
ebands = abilab.ElectronBands.from_mpid(mpid, api_key=options.mapi_key, endpoint=options.endpoint)
ebands = abilab.ElectronBands.from_mpid(mpid)
if ebands is None:
cprint("Cannot get ebands for structure:\n%s" % str(structure), "red")
else:
@ -1058,6 +1055,7 @@ def main():
structures = hist.structures
elif "XDATCAR" in filepath:
from pymatgen.io.vasp.outputs import Xdatcar
structures = Xdatcar(filepath).structures
if not structures:
raise RuntimeError("Your Xdatcar contains only one structure. Due to a bug "

5
abipy/scripts/oncv.py
View File

@ -181,7 +181,7 @@ def oncv_run(options):
fr="fully-relativistic")[options.rel]
# Build Generator and start generation.
psgen = OncvGenerator.from_file(in_path, calc_type, workdir=None)
psgen = OncvGenerator.from_file(in_path, calc_type, options.use_mgga, workdir=None)
print(psgen.input_str)
print("Using executable:\n\t", psgen.executable)
@ -209,7 +209,7 @@ def oncv_run(options):
# Transfer final output file.
shutil.copy(psgen.stdout_path, out_path)
# Parse the output file
# Parse the output file.
onc_parser = OncvParser(out_path).scan()
if not onc_parser.run_completed:
cprint("oncvpsp output is not completed. Exiting", "red")
@ -332,6 +332,7 @@ def get_parser(with_epilog=False):
p_run = subparsers.add_parser('run', parents=[copts_parser, plot_parser], help=oncv_run.__doc__)
p_run.add_argument("--rel", default="from_file", help=("Relativistic treatment: `nor` for non-relativistic, "
"`sr` for scalar-relativistic, `fr` for fully-relativistic. Default: `from_file` i.e. detected from file"))
p_run.add_argument("--use-mgga", action='store_true', default=False, help="Produce mega-gga pseudo with oncvpspm.x")
# Subparser for print command.
p_print = subparsers.add_parser('print', parents=[copts_parser], help=oncv_print.__doc__)

2
abipy/tools/notebooks.py
View File

@ -85,7 +85,7 @@ def print_doc(function, **kwargs): # pragma: no cover
def ipw_listdir(top=".", recurse=True, widget_type="dropdown"): # pragma: no cover
"""
Return an ipython widget listing all the files located within the directory ``top``
that can be inspected with :ref:`abiopen.py`. The user can select the file in the widget
that can be inspected with abiopen.py. The user can select the file in the widget
and print info on the corresponding file inside the notebook.
Args:

30
dev_scripts/conda_get.sh
View File

@ -1,30 +0,0 @@
#!/bin/bash
set -e # exit on first error, -v print each command
# Install conda with travis: https://conda.io/docs/travis.html
if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
curl -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh;
else
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
fi
bash miniconda.sh -b -p ${HOME}/miniconda
export PATH="${HOME}/miniconda/bin:${PATH}"
hash -r
conda config --set always_yes yes --set changeps1 yes
conda update -q conda
# Useful for debugging any issues with conda
conda info -a
conda config --add channels conda-forge
echo "Installing abinit from abinit channel in abinit-environment..."
conda create -q -n abinit-environment python=${TRAVIS_PYTHON_VERSION}
source activate abinit-environment
#conda install -y -c abinit abinit=${ABINIT_VERSION}
conda install -y -c conda-forge abinit=${ABINIT_VERSION}
abinit --version
abinit --build
echo "Creating test-environment for python stack..."
conda create -q -n test-environment python=${TRAVIS_PYTHON_VERSION}
source activate test-environment

17
dev_scripts/conda_install.sh
View File

@ -1,17 +0,0 @@
#!/bin/bash
set -e # exit on first error
echo "Installing bader executable (http://theory.cm.utexas.edu/henkelman/code/bader/) from matsci ..."
conda install -y -c matsci bader
#conda install -c abinit apscheduler==2.1.0
#pip install apscheduler==2.1.0
echo "Installing requirements listed requirements.txt and requirements-optional.txt ..."
# https://github.com/ContinuumIO/anaconda-issues/issues/542
conda install -y -c anaconda setuptools
conda install nomkl
conda install -y --file ./requirements.txt
conda install -y --file ./requirements-optional.txt
conda install -y -c conda-forge graphviz python-graphviz
echo "Installation completed"

2
docs/api/embedding_api.rst
View File

@ -21,7 +21,7 @@ embedding Package
:show-inheritance:
:mod:`utils_ifc` Module
----------------------
-----------------------
.. automodule:: abipy.embedding.utils_ifc
:members:

2
docs/api/flowtk_api.rst
View File

@ -86,7 +86,7 @@ flowtk Package
:show-inheritance:
:mod:`gw_works` Module
----------------
----------------------
.. automodule:: abipy.flowtk.gw_works
:members:

2
docs/api/index.rst
View File

@ -20,6 +20,8 @@ API documentation
flowtk_api.rst
iotools_api.rst
lumi_api.rst
ml_api.rst
ppcodes_api.rst
panels_api.rst
tools_api.rst
waves_api.rst

2
docs/api/ml.rst → docs/api/ml_api.rst
View File

@ -37,7 +37,7 @@ ml Package
:mod:`ml_phonopy` Package
-------------------------------
-------------------------
.. automodule:: abipy.ml.ml_phonopy
:members:

24
docs/flows_howto.rst
View File

@ -4,7 +4,7 @@
Flows How-To
************
This is a list of FAQs about the AbiPy flows and the :ref:`abirun.py` script.
This is a list of FAQs about the AbiPy flows and the abirun.py_ script.
Feel free to suggest new entries!
.. important::
@ -16,7 +16,7 @@ Feel free to suggest new entries!
Suggestions:
* Start with the examples available in examples/flows before embarking on large scale calculations.
* Make sure the Abinit executable compiled on the machine can be executed both on the front end
* Make sure the Abinit executable compiled on the machine can be executed both on the front end
and the compute node (ask your sysadmin)
* If you are running on clusters in which the architecture of the compute node is completely different
from the one available on the front end, use ``shell_runner``
@ -25,8 +25,8 @@ Suggestions:
Do not:
* Change manually the input files and the submission scripts
* Submit jobs manually when the scheduler is running
* Use a too small delay for the scheduler
* Submit jobs manually when the scheduler is running
* Use a too small delay for the scheduler
.. contents::
@ -35,7 +35,7 @@ Do not:
How to get all the TaskManager options
--------------------------------------
The :ref:`abidoc.py` script provides three commands to get the documentation
The abidoc.py_ script provides three commands to get the documentation
for the options supported in ``manager.yml`` and ``scheduler.yml``.
Use::
@ -84,10 +84,10 @@ Add the following options to scheduler.yml
# Maximum number of cores that can be used by the scheduler.
max_ncores_used: 4
How to reduce the number of files produced by the Flow
How to reduce the number of files produced by the Flow
------------------------------------------------------
When running many calculations,
When running many calculations,
Use ``prtwf -1`` to tell Abinit to produce the wavefunction file only
if SCF cycle didn't converged so that AbiPy can reuse the file to restart the calculation.
@ -102,14 +102,14 @@ How to extend tasks/works with specialized code
-----------------------------------------------
Remember that pickle_ does not support classes defined inside scripts (`__main__`).
This means that `abirun.py` will likely raise an exception when trying to
This means that `abirun.py` will likely raise an exception when trying to
reconstruct the object from the pickle file:
.. code-block:: python
AttributeError: Cannot get attribute 'MyWork' on <module '__main__'
AttributeError: Cannot get attribute 'MyWork' on <module '__main__'
If you need to subclass one of the AbiPy Tasks/Works/Flows, define the subclass
If you need to subclass one of the AbiPy Tasks/Works/Flows, define the subclass
in a separated python module and import the module inside your script.
We suggest to create a python module in the AbiPy package e.g. `abipy/flowtk/my_works.py`
in order to have an absolute import that allows one to use
@ -133,12 +133,12 @@ to cancel all jobs of the flow that are in queue and kill the scheduler.
Compare multiple output files
-----------------------------
The :ref:`abicomp.py` script
The abicomp.py_ script
Try to understand why a task failed
-----------------------------------
There are several reasons why a task could fail.
Some of these reasons could be related to hardware failure, disk quota,
Some of these reasons could be related to hardware failure, disk quota,
OS errors or resource manager errors.
Others are related to Abinit-specific errors.

5
docs/links.rst
View File

@ -68,8 +68,11 @@
.. Links to abipy scripts.
.. _abiopen.py: https://abinit.github.io/abipy/scripts/abiopen.html
.. _abistruct.py: https://abinit.github.io/abipy/scripts/abistruct.html
.. _abidoc.py: https://abinit.github.io/abipy/scripts/abidoc.html
.. _abiview.py: https://abinit.github.io/abipy/scripts/abiview.html
.. _abicomp.py: https://abinit.github.io/abipy/scripts/abicomp.html
.. _abinp.py: https://abinit.github.io/abipy/scripts/abinp.html
.. _abicheck.py: https://abinit.github.io/abipy/scripts/abicheck.html
.. _abips.py: https://abinit.github.io/abipy/scripts/abips.html
.. _oncv.py: https://abinit.github.io/abipy/scripts/oncv.html
@ -167,7 +170,7 @@
.. |download-with-anaconda| image:: https://anaconda.org/abinit/abipy/badges/installer/conda.svg
:alt: Download with Anaconda
:target: https://conda.anaconda.org/abinit
:target: https://anaconda.org/conda-forge/abinit
.. |abipy-license| image:: https://img.shields.io/badge/license-GPL-blue.svg
:alt: AbiPy license

90
docs/postprocessing_howto.rst
View File

@ -4,26 +4,26 @@
Post-processing How-To
***********************
This is a list of FAQs about the usage of the AbiPy scripts.
This is a list of FAQs about the usage of the AbiPy scripts.
Feel free to suggest new entries!
.. contents::
:backlinks: top
Preliminary considerations
Preliminary considerations
---------------------------
The AbiPy scripts detect the file type by looking at the file extension
The AbiPy scripts detect the file type by looking at the file extension
so **don't change the file extension**.
Also, remember that it is possible to get the documentation by just adding
Also, remember that it is possible to get the documentation by just adding
the ``--help`` option to the command line.
For example:
.. code-block:: shell
abistruct.py --help
gives the documentation and usage examples for the abistruct.py_ script while:
.. code-block:: shell
@ -38,7 +38,7 @@ Get information about a generic ``FILE``
Use::
abiopen.py FILE --print
abiopen.py FILE --print
to print information about a file inside the terminal or
@ -46,7 +46,7 @@ to print information about a file inside the terminal or
to generate multiple matplotlib figures depending on FILE.
Use ``--verbose`` or ``-v`` to increase verbosity level.
Use ``--verbose`` or ``-v`` to increase verbosity level.
The option can be can be supplied multiple times e.g. ``-vv``.
Get all file extensions supported by ``abiopen.py``
@ -59,7 +59,7 @@ Use::
.. command-output:: abiopen.py --help
Convert the structure stored in ``FILE`` to a different format
Convert the structure stored in ``FILE`` to a different format
--------------------------------------------------------------
Use::
@ -69,7 +69,7 @@ Use::
to read the structure from ``FILE`` and generate a CIF_ file (default behaviour).
The majority of the netcdf_ files produced by Abinit contain structural information
so this command can be used with netcdf output files as well as Abinit input/output
so this command can be used with netcdf output files as well as Abinit input/output
files and all the other formats supported by pymatgen e.g. POSCAR files.
Other formats can be specified with the ``-f`` option.
For example::
@ -97,13 +97,13 @@ First of all, one can use::
to print the crystalline structure and find the space group with the spglib_ library.
If the structure looks good, use the :ref:`abinp.py` script with the ``validate`` command as in::
If the structure looks good, use the abinp.py_ script with the ``validate`` command as in::
abinp.py validate run.abi
abinp.py validate run.abi
to validate the input file with Abinit (requires ``manager.yml`` and, obviously, Abinit).
The script provides other options to invoke Abinit
The script provides other options to invoke Abinit
to get space group information, the list of k-points in the IBZ.
the list of atomic perturbations for phonons or the list of autoparal configurations.
See ``abinp.py --help`` for further info.
@ -143,8 +143,8 @@ A similar interface is also available via::
Get a quick look to a file
--------------------------
The :ref:`abiview.py` script is especially designed for this task.
The syntax is ``abiview.py COMMAND FILE`` where ``COMMAND`` is either
The abiview.py_ script is especially designed for this task.
The syntax is ``abiview.py COMMAND FILE`` where ``COMMAND`` is either
the Abinit file extension (without ``.nc``, if any) or the AbiPy object we want to visualize.
To get a quick look at the DDB file, use::
@ -157,9 +157,9 @@ If ``FILE`` contains electronic band energies, use e.g.::
abiview.py ebands out_GSR.nc
to plot the KS eigenvalues (the same command works for other files such as ``WFK.nc``, ``DEN.nc`` etc.
to plot the KS eigenvalues (the same command works for other files such as ``WFK.nc``, ``DEN.nc`` etc.
Note that :ref:`abiview.py` uses a predefined logic to visualize the data.
Note that abiview.py_ uses a predefined logic to visualize the data.
There are options to tune some parameters and/or export data in different formats
but exposing the AbiPy API from the command line is not easy.
@ -179,15 +179,15 @@ Visualize a structure
---------------------
The visualization of the structure is delegated to external graphical applications
that must be installed on your machine.
AbiPy will extract the structure from ``FILE``, convert it to one of the formats
that must be installed on your machine.
AbiPy will extract the structure from ``FILE``, convert it to one of the formats
supported by the graphical application and finally invoke the executable.
If you have vesta_ installed in one of the standard
If you have vesta_ installed in one of the standard
locations of your machine, you can simply execute::
abistruct.py visualize FILE
inside the terminal.
inside the terminal.
Other applications can be specified with the ``--application`` option.
At present, AbiPy supports vesta_, ovito_, xcrysden_, avogadro_, and v_sim_.
@ -251,7 +251,7 @@ with Abinit and a tolerance larger that the default value::
abistruct.py abispg problematic.cif --tolsym=1e-6
Hopefully, the code will detect the correct spacegroup, will re-symmetrize
Hopefully, the code will detect the correct spacegroup, will re-symmetrize
the initial lattice vectors and atomic positions and print the new symmetrized structure to terminal.
@ -287,7 +287,7 @@ Use::
abistruct.py mp_search LiF
to search on the `materials project`_ database for structures corresponding to a
to search on the `materials project`_ database for structures corresponding to a
chemical system or formula e.g. ``Fe2O3`` or ``Li-Fe-O`` or
``Ir-O-*`` for wildcard pattern matching.
@ -314,7 +314,7 @@ The script prints the results to terminal in tabular form:
The script will try to connect to the materials project server.
You need a ``~/.pmgrc.yaml`` configuration file inside your home directory
with the authentication token **PMG_MAPI_KEY**.
For further info please refer to the
For further info please refer to the
`pymatgen documentation <http://pymatgen.org/usage.html#pymatgen-matproj-rest-integration-with-the-materials-project-rest-api>`_
The script provides other commands to get (experimental) structures from the COD_ database,
@ -326,7 +326,7 @@ Compare my structure with the Materials Project database
Let's assume we have performed a structural relaxation and we want
to compare our results with the Materials Project data.
One can use the :ref:`abicomp.py` structure to extract the structure from the HIST.nc_
One can use the abicomp.py_ structure to extract the structure from the HIST.nc_
file and compare the data with the database::
abicomp.py mp_structure ../abipy/data/refs/sic_relax_HIST.nc
@ -370,23 +370,23 @@ to plot the SCF iterations or the steps of the structural relaxations or the DFP
(depending on the content of run.abo).
Note that one can also use::
abiview.py log run.log
to print the warnings/comments/errors reported in the Abinit log file ``run.log``.
Export bands to xmgrace format
Export bands to xmgrace format
------------------------------
Both |ElectronBands| and |PhononBands| provide a ``to_xmgrace`` method to produce xmgrace_ files.
To export the data to xmgrace, use :ref:`abiview.py` with the ``--xmgrace`` option.
To export the data to xmgrace, use abiview.py_ with the ``--xmgrace`` option.
For electrons, use::
abiview.py ebands out_GSR.nc --xmgrace
and::
abiview.py phbands out_PHBST.nc -xmgrace
abiview.py phbands out_PHBST.nc -xmgrace
for phonons.
@ -407,7 +407,7 @@ to visualize the Fermi surface with xcrysden_
.. code-block:: ipython
abifile.ebands.to_bxsf("mgb2.bxsf")
abifile.ebands.to_bxsf("mgb2.bxsf")
.. important::
@ -416,23 +416,23 @@ to visualize the Fermi surface with xcrysden_
Visualize phonon displacements
------------------------------
AbiPy is interfaced with the phononwebsite_ project
AbiPy is interfaced with the phononwebsite_ project
If you have already installed the python package from `github <https://github.com/henriquemiranda/phononwebsite>`_
it's possbile to export the ``PHBST.nc`` to JSON and then load the file via the web-interface.
Alternatively, it's possible to automate the entire procedure with the :ref:`abiview.py` script.
Alternatively, it's possible to automate the entire procedure with the abiview.py_ script.
Use::
abiview.py phbands out_PHBST.nc -web
to start a local web server and open the HTML page inside the default browser
to start a local web server and open the HTML page inside the default browser
(the browser can be changed with the ``--browser`` option).
It is also possible to visualize the phonon modes starting directly from a DDB_ file with::
abiview.py ddb -web
In this case, AbiPy will invoke anaddb to produce the ``PHBST.nc`` file on an automatically
In this case, AbiPy will invoke anaddb to produce the ``PHBST.nc`` file on an automatically
generated q-path and then start the web server.
Visualize the results of a structural relaxation
@ -442,10 +442,10 @@ The quickest way is to use::
abiview hist out_HIST.nc
to plot the results with matplotlib or::
to plot the results with matplotlib or::
abiopen.py out_HIST.nc -p
to print the most important results to terminal.
Note that it's possible to generate a ``XDATCAR`` file with::
@ -484,8 +484,8 @@ the AbiPy scripts are quite handy for a quick analysis of the results.
Compare multiple files
----------------------
The :ref:`abicomp.py` script is explicitly designed for this kind of task.
It operates on multiple files (usually files with the same extension) and
The abicomp.py_ script is explicitly designed for this kind of task.
It operates on multiple files (usually files with the same extension) and
either produces matplotlib_ plots or creates AbiPy robots providing methods
to analyze the results, perform convergence studies and build pandas DataFrames_.
@ -510,10 +510,10 @@ Remember that it is possible to use the shell syntax ``*_GSR.nc`` to select all
If you have nested directories, use unix ``find`` to scan the directory tree for files matching a given pattern
For example::
abicomp.py ebands `find . -name *_GSR.nc`
abicomp.py ebands `find . -name *_GSR.nc`
finds all ``GSR.nc`` files contained withing the current working directory.
The output of ``find`` is then passed to the :ref:`abicomp.py` script.
The output of ``find`` is then passed to the abicomp.py_ script.
.. note::
@ -523,8 +523,8 @@ The output of ``find`` is then passed to the :ref:`abicomp.py` script.
Profile the scripts
-------------------
All AbiPy script can be executed in profile mode by just prepending the ``prof`` keyword
to the command line arguments.
All AbiPy script can be executed in profile mode by just prepending the ``prof`` keyword
to the command line arguments.
This option could be useful if the script seems to be slow and you need to understand what's happening.
Use::
@ -537,10 +537,10 @@ or::
if the script requires a ``COMMAND`` argument.
Get the description of a variable
Get the description of a variable
---------------------------------
The :ref:`abidoc.py` script provides a simplified interface to the Abinit documentation.
The abidoc.py_ script provides a simplified interface to the Abinit documentation.
Use::
@ -558,7 +558,7 @@ Avoid transfering files from the cluster to localhost just to use matplotlib
----------------------------------------------------------------------------
Use `SSHFS <https://www.digitalocean.com/community/tutorials/how-to-use-sshfs-to-mount-remote-file-systems-over-ssh>`_
to mount the remote file system over SSH.
to mount the remote file system over SSH.
Now one can execute the AbiPy scripts in a terminal running on the local machine.
to open/visualize the files stored on the cluster.

428
docs/sg_execution_times.rst
View File

@ -6,7 +6,7 @@
Computation times
=================
**01:32.521** total execution time for 109 files **from all galleries**:
**01:25.939** total execution time for 109 files **from all galleries**:
.. container::
@ -33,329 +33,329 @@ Computation times
- Time
- Mem (MB)
* - :ref:`sphx_glr_gallery_plot_qha_vs_qmesh.py` (``../abipy/examples/plot/plot_qha_vs_qmesh.py``)
- 00:10.314
- 00:10.151
- 0.0
* - :ref:`sphx_glr_gallery_plot_ddb_asr.py` (``../abipy/examples/plot/plot_ddb_asr.py``)
- 00:04.750
- 00:04.590
- 0.0
* - :ref:`sphx_glr_gallery_plot_phonons_msqd.py` (``../abipy/examples/plot/plot_phonons_msqd.py``)
- 00:04.432
- 00:03.910
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_mgb2_phonons_nkpt_tsmear.py` (``../abipy/examples/flows/run_mgb2_phonons_nkpt_tsmear.py``)
- 00:03.683
- 00:03.448
- 0.0
* - :ref:`sphx_glr_gallery_plot_lumi_1D_nv_center.py` (``../abipy/examples/plot/plot_lumi_1D_nv_center.py``)
- 00:03.131
- 00:02.743
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_gkq.py` (``../abipy/examples/flows/run_gkq.py``)
- 00:02.525
- 00:02.557
- 0.0
* - :ref:`sphx_glr_gallery_plot_phbands_nkpt_tsmear.py` (``../abipy/examples/plot/plot_phbands_nkpt_tsmear.py``)
- 00:02.431
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_eph_pot.py` (``../abipy/examples/flows/run_eph_pot.py``)
- 00:01.970
- 00:02.362
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_eph_mob.py` (``../abipy/examples/flows/run_eph_mob.py``)
- 00:01.926
- 00:02.255
- 0.0
* - :ref:`sphx_glr_gallery_plot_mdf.py` (``../abipy/examples/plot/plot_mdf.py``)
- 00:01.924
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_eph_al.py` (``../abipy/examples/flows/run_eph_al.py``)
- 00:01.857
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_phonons_wkq.py` (``../abipy/examples/flows/run_phonons_wkq.py``)
- 00:01.827
* - :ref:`sphx_glr_flow_gallery_run_eph_pot.py` (``../abipy/examples/flows/run_eph_pot.py``)
- 00:02.025
- 0.0
* - :ref:`sphx_glr_gallery_plot_efatbands_spin.py` (``../abipy/examples/plot/plot_efatbands_spin.py``)
- 00:01.774
- 00:01.959
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_phonons.py` (``../abipy/examples/flows/run_phonons.py``)
- 00:01.492
- 00:01.858
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_phonons_wkq.py` (``../abipy/examples/flows/run_phonons_wkq.py``)
- 00:01.842
- 0.0
* - :ref:`sphx_glr_gallery_plot_mdf.py` (``../abipy/examples/plot/plot_mdf.py``)
- 00:01.758
- 0.0
* - :ref:`sphx_glr_gallery_plot_a2f.py` (``../abipy/examples/plot/plot_a2f.py``)
- 00:01.457
- 00:01.366
- 0.0
* - :ref:`sphx_glr_gallery_plot_efatbands.py` (``../abipy/examples/plot/plot_efatbands.py``)
- 00:01.363
- 00:01.330
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_eph_al.py` (``../abipy/examples/flows/run_eph_al.py``)
- 00:01.303
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_lumi_Eu_doped_SLA.py` (``../abipy/examples/flows/run_lumi_Eu_doped_SLA.py``)
- 00:01.323
- 0.0
* - :ref:`sphx_glr_gallery_plot_phbands_grid.py` (``../abipy/examples/plot/plot_phbands_grid.py``)
- 00:01.136
- 00:01.218
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_conducwork.py` (``../abipy/examples/flows/run_conducwork.py``)
- 00:01.104
- 00:01.067
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_phonons_with_quad.py` (``../abipy/examples/flows/run_phonons_with_quad.py``)
- 00:01.007
- 0.0
* - :ref:`sphx_glr_gallery_plot_ebands.py` (``../abipy/examples/plot/plot_ebands.py``)
- 00:00.990
* - :ref:`sphx_glr_gallery_plot_phbands_grid.py` (``../abipy/examples/plot/plot_phbands_grid.py``)
- 00:01.059
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_becs_and_epsilon_vs_kpts.py` (``../abipy/examples/flows/run_becs_and_epsilon_vs_kpts.py``)
- 00:00.986
- 00:00.979
- 0.0
* - :ref:`sphx_glr_gallery_plot_wannier90_abiwan.py` (``../abipy/examples/plot/plot_wannier90_abiwan.py``)
- 00:00.980
- 0.0
* - :ref:`sphx_glr_gallery_plot_ebands_boxplot.py` (``../abipy/examples/plot/plot_ebands_boxplot.py``)
- 00:00.969
- 0.0
* - :ref:`sphx_glr_gallery_plot_lumi_1D_Eu_doped.py` (``../abipy/examples/plot/plot_lumi_1D_Eu_doped.py``)
- 00:00.922
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_si_ebands.py` (``../abipy/examples/flows/run_si_ebands.py``)
- 00:00.920
* - :ref:`sphx_glr_flow_gallery_run_phonons_with_quad.py` (``../abipy/examples/flows/run_phonons_with_quad.py``)
- 00:00.966
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_flexoelectric.py` (``../abipy/examples/flows/run_flexoelectric.py``)
- 00:00.908
- 0.0
* - :ref:`sphx_glr_gallery_plot_speed_of_sound.py` (``../abipy/examples/plot/plot_speed_of_sound.py``)
- 00:00.831
- 00:00.869
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_raman_optic.py` (``../abipy/examples/flows/run_raman_optic.py``)
- 00:00.826
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_optic.py` (``../abipy/examples/flows/run_optic.py``)
- 00:00.819
- 00:00.827
- 0.0
* - :ref:`sphx_glr_gallery_plot_qpbands_with_interpolation.py` (``../abipy/examples/plot/plot_qpbands_with_interpolation.py``)
- 00:00.818
- 00:00.814
- 0.0
* - :ref:`sphx_glr_gallery_plot_ebands_spin.py` (``../abipy/examples/plot/plot_ebands_spin.py``)
- 00:00.792
- 0.0
* - :ref:`sphx_glr_gallery_plot_ebands_grid.py` (``../abipy/examples/plot/plot_ebands_grid.py``)
- 00:00.778
* - :ref:`sphx_glr_flow_gallery_run_optic.py` (``../abipy/examples/flows/run_optic.py``)
- 00:00.793
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_elastic.py` (``../abipy/examples/flows/run_elastic.py``)
- 00:00.770
- 00:00.773
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_gwconv_ecuteps.py` (``../abipy/examples/flows/run_gwconv_ecuteps.py``)
- 00:00.763
* - :ref:`sphx_glr_gallery_plot_ebands_spin.py` (``../abipy/examples/plot/plot_ebands_spin.py``)
- 00:00.738
- 0.0
* - :ref:`sphx_glr_gallery_plot_speed_of_sound.py` (``../abipy/examples/plot/plot_speed_of_sound.py``)
- 00:00.717
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_nonlinear.py` (``../abipy/examples/flows/run_nonlinear.py``)
- 00:00.726
- 00:00.713
- 0.0
* - :ref:`sphx_glr_gallery_plot_qha.py` (``../abipy/examples/plot/plot_qha.py``)
- 00:00.716
* - :ref:`sphx_glr_gallery_plot_ebands_grid.py` (``../abipy/examples/plot/plot_ebands_grid.py``)
- 00:00.703
- 0.0
* - :ref:`sphx_glr_gallery_plot_lumi_1D_Eu_doped.py` (``../abipy/examples/plot/plot_lumi_1D_Eu_doped.py``)
- 00:00.689
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_relax_vs_kpts_tsmear.py` (``../abipy/examples/flows/run_relax_vs_kpts_tsmear.py``)
- 00:00.692
- 00:00.676
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_lumi_NV_center.py` (``../abipy/examples/flows/run_lumi_NV_center.py``)
- 00:00.680
* - :ref:`sphx_glr_flow_gallery_run_gwconv_ecuteps.py` (``../abipy/examples/flows/run_gwconv_ecuteps.py``)
- 00:00.665
- 0.0
* - :ref:`sphx_glr_gallery_plot_phonons_infrared.py` (``../abipy/examples/plot/plot_phonons_infrared.py``)
- 00:00.675
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_frohlich_zpr.py` (``../abipy/examples/flows/run_frohlich_zpr.py``)
- 00:00.661
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_effmass_dfpt.py` (``../abipy/examples/flows/run_effmass_dfpt.py``)
- 00:00.656
* - :ref:`sphx_glr_gallery_plot_qha.py` (``../abipy/examples/plot/plot_qha.py``)
- 00:00.663
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_screening.py` (``../abipy/examples/flows/run_screening.py``)
- 00:00.648
- 00:00.649
- 0.0
* - :ref:`sphx_glr_gallery_plot_qpbands_with_scissor.py` (``../abipy/examples/plot/plot_qpbands_with_scissor.py``)
- 00:00.620
* - :ref:`sphx_glr_flow_gallery_run_lumi_NV_center.py` (``../abipy/examples/flows/run_lumi_NV_center.py``)
- 00:00.640
- 0.0
* - :ref:`sphx_glr_gallery_plot_gruneisen.py` (``../abipy/examples/plot/plot_gruneisen.py``)
- 00:00.618
* - :ref:`sphx_glr_gallery_plot_phonons_infrared.py` (``../abipy/examples/plot/plot_phonons_infrared.py``)
- 00:00.621
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_raman_bse.py` (``../abipy/examples/flows/run_raman_bse.py``)
- 00:00.615
- 00:00.616
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_phfrozen_ebands.py` (``../abipy/examples/flows/run_phfrozen_ebands.py``)
- 00:00.606
- 0.0
* - :ref:`sphx_glr_gallery_plot_efatbands_lm.py` (``../abipy/examples/plot/plot_efatbands_lm.py``)
- 00:00.569
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_eos.py` (``../abipy/examples/flows/run_eos.py``)
- 00:00.566
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_ldaus.py` (``../abipy/examples/flows/run_ldaus.py``)
- 00:00.553
* - :ref:`sphx_glr_flow_gallery_run_frohlich_zpr.py` (``../abipy/examples/flows/run_frohlich_zpr.py``)
- 00:00.594
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_si_g0w0.py` (``../abipy/examples/flows/run_si_g0w0.py``)
- 00:00.551
- 00:00.591
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_fe_ebands.py` (``../abipy/examples/flows/run_fe_ebands.py``)
- 00:00.515
- 0.0
* - :ref:`sphx_glr_gallery_plot_qps.py` (``../abipy/examples/plot/plot_qps.py``)
- 00:00.514
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_mgb2_edoses.py` (``../abipy/examples/flows/run_mgb2_edoses.py``)
- 00:00.509
- 0.0
* - :ref:`sphx_glr_gallery_plot_ebands_edos.py` (``../abipy/examples/plot/plot_ebands_edos.py``)
- 00:00.504
- 0.0
* - :ref:`sphx_glr_gallery_plot_phonon_fatbands.py` (``../abipy/examples/plot/plot_phonon_fatbands.py``)
- 00:00.498
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_frohlich_zpr_from_ddb.py` (``../abipy/examples/flows/run_frohlich_zpr_from_ddb.py``)
- 00:00.488
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_gs_vs_kpts.py` (``../abipy/examples/flows/run_gs_vs_kpts.py``)
- 00:00.486
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_effmass_finitediff.py` (``../abipy/examples/flows/run_effmass_finitediff.py``)
- 00:00.481
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_ht_si_g0w0ppm.py` (``../abipy/examples/flows/run_ht_si_g0w0ppm.py``)
- 00:00.481
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_gwr_g0w0.py` (``../abipy/examples/flows/run_gwr_g0w0.py``)
- 00:00.478
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_ht_si_ebands.py` (``../abipy/examples/flows/run_ht_si_ebands.py``)
- 00:00.472
- 0.0
* - :ref:`sphx_glr_gallery_plot_qpconvergence.py` (``../abipy/examples/plot/plot_qpconvergence.py``)
- 00:00.464
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_gaas_ebands_soc.py` (``../abipy/examples/flows/run_gaas_ebands_soc.py``)
- 00:00.462
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_relax_and_ebands.py` (``../abipy/examples/flows/run_relax_and_ebands.py``)
- 00:00.460
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_relax_vs_kpts.py` (``../abipy/examples/flows/run_relax_vs_kpts.py``)
- 00:00.453
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_ht_si_bsemdf.py` (``../abipy/examples/flows/run_ht_si_bsemdf.py``)
- 00:00.451
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_relax.py` (``../abipy/examples/flows/run_relax.py``)
- 00:00.432
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_phonopy_si.py` (``../abipy/examples/flows/run_phonopy_si.py``)
- 00:00.428
* - :ref:`sphx_glr_gallery_plot_qpbands_with_scissor.py` (``../abipy/examples/plot/plot_qpbands_with_scissor.py``)
- 00:00.589
- 0.0
* - :ref:`sphx_glr_gallery_plot_ifcs.py` (``../abipy/examples/plot/plot_ifcs.py``)
- 00:00.582
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_effmass_dfpt.py` (``../abipy/examples/flows/run_effmass_dfpt.py``)
- 00:00.576
- 0.0
* - :ref:`sphx_glr_gallery_plot_gruneisen.py` (``../abipy/examples/plot/plot_gruneisen.py``)
- 00:00.572
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_eos.py` (``../abipy/examples/flows/run_eos.py``)
- 00:00.545
- 0.0
* - :ref:`sphx_glr_gallery_plot_efatbands_lm.py` (``../abipy/examples/plot/plot_efatbands_lm.py``)
- 00:00.531
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_ldaus.py` (``../abipy/examples/flows/run_ldaus.py``)
- 00:00.520
- 0.0
* - :ref:`sphx_glr_gallery_plot_qps.py` (``../abipy/examples/plot/plot_qps.py``)
- 00:00.496
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_relax_vs_kpts.py` (``../abipy/examples/flows/run_relax_vs_kpts.py``)
- 00:00.487
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_fe_ebands.py` (``../abipy/examples/flows/run_fe_ebands.py``)
- 00:00.485
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_frohlich_zpr_from_ddb.py` (``../abipy/examples/flows/run_frohlich_zpr_from_ddb.py``)
- 00:00.482
- 0.0
* - :ref:`sphx_glr_gallery_plot_phonon_fatbands.py` (``../abipy/examples/plot/plot_phonon_fatbands.py``)
- 00:00.481
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_mgb2_edoses.py` (``../abipy/examples/flows/run_mgb2_edoses.py``)
- 00:00.481
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_gs_vs_kpts.py` (``../abipy/examples/flows/run_gs_vs_kpts.py``)
- 00:00.466
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_ht_si_g0w0ppm.py` (``../abipy/examples/flows/run_ht_si_g0w0ppm.py``)
- 00:00.466
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_effmass_finitediff.py` (``../abipy/examples/flows/run_effmass_finitediff.py``)
- 00:00.464
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_ht_si_ebands.py` (``../abipy/examples/flows/run_ht_si_ebands.py``)
- 00:00.454
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_relax_and_ebands.py` (``../abipy/examples/flows/run_relax_and_ebands.py``)
- 00:00.452
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_ht_si_bsemdf.py` (``../abipy/examples/flows/run_ht_si_bsemdf.py``)
- 00:00.432
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_si_ebands.py` (``../abipy/examples/flows/run_si_ebands.py``)
- 00:00.427
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_gwr_g0w0.py` (``../abipy/examples/flows/run_gwr_g0w0.py``)
- 00:00.421
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_relax.py` (``../abipy/examples/flows/run_relax.py``)
- 00:00.417
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_gaas_ebands_soc.py` (``../abipy/examples/flows/run_gaas_ebands_soc.py``)
- 00:00.415
- 0.0
* - :ref:`sphx_glr_gallery_plot_qpconvergence.py` (``../abipy/examples/plot/plot_qpconvergence.py``)
- 00:00.413
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_phonopy_si.py` (``../abipy/examples/flows/run_phonopy_si.py``)
- 00:00.412
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_from_files.py` (``../abipy/examples/flows/run_from_files.py``)
- 00:00.399
- 0.0
* - :ref:`sphx_glr_gallery_plot_kpath_from_ibz.py` (``../abipy/examples/plot/plot_kpath_from_ibz.py``)
- 00:00.395
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_sic_relax.py` (``../abipy/examples/flows/run_sic_relax.py``)
- 00:00.386
- 0.0
* - :ref:`sphx_glr_gallery_plot_phonons.py` (``../abipy/examples/plot/plot_phonons.py``)
- 00:00.381
- 0.0
* - :ref:`sphx_glr_gallery_plot_edos_vs_broad.py` (``../abipy/examples/plot/plot_edos_vs_broad.py``)
- 00:00.358
- 0.0
* - :ref:`sphx_glr_gallery_plot_phbands_and_dos.py` (``../abipy/examples/plot/plot_phbands_and_dos.py``)
- 00:00.352
- 0.0
* - :ref:`sphx_glr_gallery_plot_multiple_mdf.py` (``../abipy/examples/plot/plot_multiple_mdf.py``)
- 00:00.350
- 00:00.383
- 0.0
* - :ref:`sphx_glr_gallery_plot_optic.py` (``../abipy/examples/plot/plot_optic.py``)
- 00:00.349
- 00:00.382
- 0.0
* - :ref:`sphx_glr_gallery_plot_kpath_from_ibz.py` (``../abipy/examples/plot/plot_kpath_from_ibz.py``)
- 00:00.372
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_sic_relax.py` (``../abipy/examples/flows/run_sic_relax.py``)
- 00:00.371
- 0.0
* - :ref:`sphx_glr_gallery_plot_ebands.py` (``../abipy/examples/plot/plot_ebands.py``)
- 00:00.364
- 0.0
* - :ref:`sphx_glr_gallery_plot_edos_vs_broad.py` (``../abipy/examples/plot/plot_edos_vs_broad.py``)
- 00:00.336
- 0.0
* - :ref:`sphx_glr_gallery_plot_phbands_and_dos.py` (``../abipy/examples/plot/plot_phbands_and_dos.py``)
- 00:00.333
- 0.0
* - :ref:`sphx_glr_gallery_plot_scqpgw.py` (``../abipy/examples/plot/plot_scqpgw.py``)
- 00:00.348
- 00:00.330
- 0.0
* - :ref:`sphx_glr_gallery_plot_multiple_mdf.py` (``../abipy/examples/plot/plot_multiple_mdf.py``)
- 00:00.322
- 0.0
* - :ref:`sphx_glr_gallery_plot_wannier90_abiwan.py` (``../abipy/examples/plot/plot_wannier90_abiwan.py``)
- 00:00.312
- 0.0
* - :ref:`sphx_glr_gallery_plot_convergence.py` (``../abipy/examples/plot/plot_convergence.py``)
- 00:00.314
- 00:00.293
- 0.0
* - :ref:`sphx_glr_gallery_plot_ejdos.py` (``../abipy/examples/plot/plot_ejdos.py``)
- 00:00.309
- 0.0
* - :ref:`sphx_glr_gallery_plot_scr_matrix.py` (``../abipy/examples/plot/plot_scr_matrix.py``)
- 00:00.301
- 0.0
* - :ref:`sphx_glr_gallery_plot_den.py` (``../abipy/examples/plot/plot_den.py``)
- 00:00.300
- 00:00.283
- 0.0
* - :ref:`sphx_glr_gallery_plot_multiple_hist.py` (``../abipy/examples/plot/plot_multiple_hist.py``)
- 00:00.290
- 00:00.272
- 0.0
* - :ref:`sphx_glr_gallery_plot_den.py` (``../abipy/examples/plot/plot_den.py``)
- 00:00.267
- 0.0
* - :ref:`sphx_glr_gallery_plot_scr_matrix.py` (``../abipy/examples/plot/plot_scr_matrix.py``)
- 00:00.263
- 0.0
* - :ref:`sphx_glr_gallery_plot_dfpt_cycle.py` (``../abipy/examples/plot/plot_dfpt_cycle.py``)
- 00:00.270
- 00:00.258
- 0.0
* - :ref:`sphx_glr_gallery_plot_ebands_edos.py` (``../abipy/examples/plot/plot_ebands_edos.py``)
- 00:00.254
- 0.0
* - :ref:`sphx_glr_gallery_plot_phonons.py` (``../abipy/examples/plot/plot_phonons.py``)
- 00:00.249
- 0.0
* - :ref:`sphx_glr_gallery_plot_wfk.py` (``../abipy/examples/plot/plot_wfk.py``)
- 00:00.262
- 00:00.243
- 0.0
* - :ref:`sphx_glr_gallery_plot_lobster_files.py` (``../abipy/examples/plot/plot_lobster_files.py``)
- 00:00.259
- 0.0
* - :ref:`sphx_glr_gallery_plot_phonons_lo_to.py` (``../abipy/examples/plot/plot_phonons_lo_to.py``)
* - :ref:`sphx_glr_gallery_plot_ebands_boxplot.py` (``../abipy/examples/plot/plot_ebands_boxplot.py``)
- 00:00.240
- 0.0
* - :ref:`sphx_glr_gallery_plot_potentials.py` (``../abipy/examples/plot/plot_potentials.py``)
- 00:00.227
* - :ref:`sphx_glr_gallery_plot_lobster_files.py` (``../abipy/examples/plot/plot_lobster_files.py``)
- 00:00.220
- 0.0
* - :ref:`sphx_glr_gallery_plot_phonons_lo_to.py` (``../abipy/examples/plot/plot_phonons_lo_to.py``)
- 00:00.213
- 0.0
* - :ref:`sphx_glr_gallery_plot_lobster_cohp.py` (``../abipy/examples/plot/plot_lobster_cohp.py``)
- 00:00.225
- 0.0
* - :ref:`sphx_glr_gallery_plot_hist.py` (``../abipy/examples/plot/plot_hist.py``)
- 00:00.224
- 0.0
* - :ref:`sphx_glr_gallery_plot_ebands_scatter3d.py` (``../abipy/examples/plot/plot_ebands_scatter3d.py``)
- 00:00.210
- 0.0
* - :ref:`sphx_glr_gallery_plot_hist.py` (``../abipy/examples/plot/plot_hist.py``)
- 00:00.207
- 0.0
* - :ref:`sphx_glr_gallery_plot_ebands_scatter3d.py` (``../abipy/examples/plot/plot_ebands_scatter3d.py``)
- 00:00.201
- 0.0
* - :ref:`sphx_glr_gallery_plot_potentials.py` (``../abipy/examples/plot/plot_potentials.py``)
- 00:00.186
- 0.0
* - :ref:`sphx_glr_gallery_plot_phonon_pjdos.py` (``../abipy/examples/plot/plot_phonon_pjdos.py``)
- 00:00.191
- 0.0
* - :ref:`sphx_glr_gallery_plot_gw_spectral_functions.py` (``../abipy/examples/plot/plot_gw_spectral_functions.py``)
- 00:00.179
- 0.0
* - :ref:`sphx_glr_gallery_plot_bz.py` (``../abipy/examples/plot/plot_bz.py``)
- 00:00.179
- 00:00.183
- 0.0
* - :ref:`sphx_glr_gallery_plotly_phbands_and_dos.py` (``../abipy/examples/plot/plotly_phbands_and_dos.py``)
- 00:00.175
- 00:00.164
- 0.0
* - :ref:`sphx_glr_gallery_plot_scr.py` (``../abipy/examples/plot/plot_scr.py``)
* - :ref:`sphx_glr_gallery_plot_gw_spectral_functions.py` (``../abipy/examples/plot/plot_gw_spectral_functions.py``)
- 00:00.158
- 0.0
* - :ref:`sphx_glr_gallery_plot_scr.py` (``../abipy/examples/plot/plot_scr.py``)
- 00:00.138
- 0.0
* - :ref:`sphx_glr_gallery_plot_effmass.py` (``../abipy/examples/plot/plot_effmass.py``)
- 00:00.153
- 00:00.137
- 0.0
* - :ref:`sphx_glr_gallery_plot_wannier90_wout.py` (``../abipy/examples/plot/plot_wannier90_wout.py``)
- 00:00.149
- 00:00.136
- 0.0
* - :ref:`sphx_glr_gallery_plot_fold2bloch.py` (``../abipy/examples/plot/plot_fold2bloch.py``)
- 00:00.145
- 0.0
* - :ref:`sphx_glr_gallery_plot_edos_grid.py` (``../abipy/examples/plot/plot_edos_grid.py``)
- 00:00.130
- 0.0
* - :ref:`sphx_glr_gallery_plot_lruj.py` (``../abipy/examples/plot/plot_lruj.py``)
- 00:00.121
- 00:00.109
- 0.0
* - :ref:`sphx_glr_gallery_plot_edos.py` (``../abipy/examples/plot/plot_edos.py``)
- 00:00.115
* - :ref:`sphx_glr_gallery_plot_bz.py` (``../abipy/examples/plot/plot_bz.py``)
- 00:00.103
- 0.0
* - :ref:`sphx_glr_gallery_plot_gscycle.py` (``../abipy/examples/plot/plot_gscycle.py``)
- 00:00.111
- 00:00.095
- 0.0
* - :ref:`sphx_glr_gallery_plot_edos.py` (``../abipy/examples/plot/plot_edos.py``)
- 00:00.092
- 0.0
* - :ref:`sphx_glr_gallery_plot_phthermo.py` (``../abipy/examples/plot/plot_phthermo.py``)
- 00:00.097
- 00:00.090
- 0.0
* - :ref:`sphx_glr_gallery_plot_edos_grid.py` (``../abipy/examples/plot/plot_edos_grid.py``)
- 00:00.075
- 0.0
* - :ref:`sphx_glr_gallery_plot_phdos_grid.py` (``../abipy/examples/plot/plot_phdos_grid.py``)
- 00:00.078
- 00:00.074
- 0.0
* - :ref:`sphx_glr_gallery_plot_xrd.py` (``../abipy/examples/plot/plot_xrd.py``)
- 00:00.071
- 0.0
* - :ref:`sphx_glr_gallery_plot_funcs.py` (``../abipy/examples/plot/plot_funcs.py``)
- 00:00.046
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_gruneisen_abinit.py` (``../abipy/examples/flows/run_gruneisen_abinit.py``)
- 00:00.036
* - :ref:`sphx_glr_gallery_plot_funcs.py` (``../abipy/examples/plot/plot_funcs.py``)
- 00:00.042
- 0.0
* - :ref:`sphx_glr_flow_gallery_run_gruneisen_abinit.py` (``../abipy/examples/flows/run_gruneisen_abinit.py``)
- 00:00.035
- 0.0

55
docs/workflows/manager_examples.rst
View File

@ -45,6 +45,34 @@ Dragon1
job: *job
Gh
--
.. code-block:: yaml
# Manager used for github actions.
qadapters:
-
priority: 1
queue:
qname: github
qtype: shell
job:
mpi_runner: mpirun
pre_run:
- conda activate abipy
limits:
min_cores: 1
max_cores: 2
timelimit: 0:10:0
hardware:
num_nodes: 1
sockets_per_node: 1
cores_per_socket: 2
mem_per_node: 4 GB
Gmac
----
@ -582,33 +610,6 @@ Shell_nompi
mem_per_node: 4 GB
Travis
------
.. code-block:: yaml
qadapters:
-
priority: 1
queue:
qname: travis
qtype: shell
job:
mpi_runner: mpirun
pre_run:
- conda activate abipy
limits:
min_cores: 1
max_cores: 2
timelimit: 0:10:0
hardware:
num_nodes: 1
sockets_per_node: 1
cores_per_socket: 2
mem_per_node: 4 GB
Ubu
---

4
requirements.txt
View File

@ -7,11 +7,11 @@ tqdm
pyyaml>=3.11
ruamel.yaml>=0.16.12
pandas
#numpy
numpy<2.0.0
scipy
sympy
spglib
pymatgen==2023.7.17
pymatgen
netCDF4
matplotlib
seaborn