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Fix typos in manager examples. use ulimit -s unlimited

This commit is contained in:
Matteo Giantomassi 2018-02-13 20:51:04 +01:00
parent 77043672a1
commit d38cfe8d7c
22 changed files with 315 additions and 170 deletions
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4
abipy/core/structure.py
View File

@ -1059,6 +1059,10 @@ class Structure(pymatgen.Structure, NotebookWriter):
@add_fig_kwargs
def plot(self, **kwargs):
"""
Plot structure with matplotlib. Return matplotlib Figure
See plot_structure for kwargs
"""
from abipy.tools.plotting import plot_structure
return plot_structure(self, **kwargs)

4
abipy/data/managers/dragon1_manager.yml
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@ -11,9 +11,7 @@ job: &job
PATH: "/home/users/g/m/gmatteo/git/abinit/_build_dragon1-intel-mpich-mkl.ac/src/98_main:$PATH"
modules:
- mpich/3.0.4/intel-13.0.0
# pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit unlimited
pre_run: "ulimit -s unlimited"
# queues
qadapters:

4
abipy/data/managers/hercules_manager.yml
View File

@ -12,9 +12,9 @@ job: &job
modules:
- impi/5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26
- imkl/11.3.3.210-iimpi-2016b
# pre_run is a string in verbatim mode (note |)
# here pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit unlimited
ulimit -s unlimited
# queues
qadapters:

4
abipy/data/managers/hmem_manager.yml
View File

@ -24,9 +24,7 @@ job: &job
PATH: "/home/users/g/m/gmatteo/git_repos/abinit/_build_hmem_intel_openmpi-mkl.ac/src/98_main/:$PATH"
modules:
- openmpi/1.5.3/intel-12.0.0.084
# pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit unlimited
pre_run: "ulimit -s unlimited"
# queues
qadapters:

4
abipy/data/managers/jureca_manager.yml
View File

@ -24,9 +24,7 @@ job: &job
PATH: $HOME/abinit/801-private/jureca_mpi/src/98_main:$PATH
modules:
- intel-para/2015.07
# pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit unlimited
pre_run: "ulimit -s unlimited"
# queues
qadapters:

4
abipy/data/managers/lemaitre2_manager.yml
View File

@ -11,9 +11,7 @@ job: &job
PATH: "/home/users/g/m/gmatteo/git_repos/abinit/_build_lemaitre2-intel-openmpi-mkl.ac/src/98_main/:$PATH"
modules: # Abinit compiled with abiconfig settings
- openmpi/1.6.5/intel-13.0.1.117
# pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit unlimited
pre_run: "ulimit -s unlimited"
# queues
qadapters:

12
abipy/data/managers/manneback_manager.yml
View File

@ -22,12 +22,12 @@ job: &job
mpi_runner: mpirun
shell_env:
PATH: /home/users/g/m/gmatteo/git_repos/abinit/_build_manneback-gcc-openmpi.ac/src/98_main/:$PATH
pre_run: |
ulimit -s unlimited # pre_run is a string in verbatim mode (note |)
export OMP_NUM_THREADS=1
unset SLURM_CPUS_PER_TASK
module purge
module load gompi/2016a FFTW/3.3.4-gompi-2016a
pre_run:
- "ulimit -s unlimited"
- "export OMP_NUM_THREADS=1"
- "unset SLURM_CPUS_PER_TASK"
- "module purge"
- "module load gompi/2016a FFTW/3.3.4-gompi-2016a"
#policy:
# frozen_timeout: 0-12:0:0

3
abipy/data/managers/nic4_manager.yml
View File

@ -10,8 +10,7 @@ job: &job
mpi_runner_options: "--bind-to none"
shell_env:
PATH: "/home/users/g/m/gmatteo/git_repos/abinit/_build_nic4-intel-openmpi-mkl-hdf5.ac/src/98_main:$PATH"
pre_run:
- "ulimit -s unlimited"
pre_run: "ulimit -s unlimited"
modules:
- shared
- openmpi/1.7.5/intel2013_sp1.1.106

4
abipy/data/managers/vega_manager.yml
View File

@ -11,9 +11,7 @@ job: &job
PATH: "/gpfsuser/home/users/g/m/gmatteo/git_repos/abinit/_build_vega-intel-impi-mkl.ac/src/98_main/:$PATH"
modules:
- intel/2015a
# pre_run is a string in verbatim mode (note |)
#pre_run: |
# "ulimit -s unlimited"
#pre_run: "ulimit -s unlimited"
# queues
qadapters:

6
abipy/data/managers/viper_manager.yml
View File

@ -7,9 +7,9 @@ hardware: &hardware
job: &job
mpi_runner: ~/bin/mpirun.openmpi
# pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit -s unlimited
source ~/.bashrc
pre_run:
- "ulimit -s unlimited"
- "source ~/.bashrc"
# queues
qadapters:

3
abipy/data/managers/zenobe_manager.yml
View File

@ -20,8 +20,7 @@ job: &job
- compiler/intel/composerxe/2013_sp1.1.106
- intelmpi
- python/2.7
pre_run: |
ulimit # pre_run is a string in verbatim mode (note |)
pre_run: "ulimit -s unlimited"
# List of qdapters.
qadapters:

2
abipy/dfpt/phonons.py
View File

@ -3975,7 +3975,7 @@ class RobotWithPhbands(object):
nbv.new_code_cell("#robot.plot_phdispl(qpoint=(0, 0, 0));"),
]
# TODO: PhdosRobot
class PhbstRobot(Robot, RobotWithPhbands):
"""
This robot analyzes the results contained in multiple PHBST.nc files.

2
abipy/display/mvtk.py
View File

@ -155,7 +155,7 @@ def plot_structure(structure, frac_coords=False, to_unit_cell=False, style="poin
Args:
structure: |Structure| object
frac_coords:
to_unit_cell: True if sites should be wrapped to the first unit cell.
to_unit_cell: True if sites should be wrapped into the first unit cell.
style: "points+labels" to show atoms sites with labels.
unit_cell_color:
color_scheme: color scheme for atom types. Allowed values in ("Jmol", "VESTA")

307
abipy/electrons/ebands.py
View File

@ -12,7 +12,7 @@ import numpy as np
import pymatgen.core.units as units
from collections import OrderedDict, namedtuple, Iterable
from monty.string import is_string, marquee
from monty.string import is_string, list_strings, marquee
from monty.termcolor import cprint
from monty.json import MSONable, MontyEncoder
from monty.collections import AttrDict, dict2namedtuple
@ -32,7 +32,7 @@ from abipy.core.structure import Structure
from abipy.iotools import ETSF_Reader
from abipy.tools import gaussian, duck
from abipy.tools.plotting import (set_axlims, add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt,
get_ax3d_fig_plt, rotate_ticklabels, plot_unit_cell)
get_ax3d_fig_plt, rotate_ticklabels, set_visible, plot_unit_cell)
import logging
logger = logging.getLogger(__name__)
@ -1335,6 +1335,25 @@ class ElectronBands(Has_Structure):
#print("ebands.fermie", self.fermie, "edos.fermie", edos.fermie)
return edos
def compare_gauss_edos(self, widths, step=0.1):
"""
Compute the electronic DOS with the Gaussian method for different values
of the broadening. Return plotter object.
Args:
widths: List with the tandard deviation (eV) of the gaussian.
step: Energy step (eV) of the linear mesh.
Return: |ElectronDosPlotter|
"""
edos_plotter = ElectronDosPlotter()
for width in widths:
edos = self.get_edos(method="gaussian", step=0.1, width=width)
label=r"$\sigma = %s$ [eV]" % width
edos_plotter.add_edos(label, edos)
return edos_plotter
@add_fig_kwargs
def plot_transitions(self, omega_ev, qpt=(0, 0, 0), atol_ev=0.1, atol_kdiff=1e-4,
ylims=None, ax=None, alpha=0.4, **kwargs):
@ -1794,11 +1813,11 @@ class ElectronBands(Has_Structure):
# Build axes and align bands and DOS.
fig = plt.figure()
gspec = GridSpec(1, 2, width_ratios=width_ratios, wspace=0.05)
ax1 = plt.subplot(gspec[0])
ax2 = plt.subplot(gspec[1], sharey=ax1)
ax0 = plt.subplot(gspec[0])
ax1 = plt.subplot(gspec[1], sharey=ax0)
else:
# Take them from ax_list.
ax1, ax2 = ax_list
ax0, ax1 = ax_list
fig = plt.gcf()
# Define the zero of energy.
@ -1813,27 +1832,27 @@ class ElectronBands(Has_Structure):
opts = {"color": "red", "linewidth": 2.0}
for band in range(self.mband):
self.plot_ax(ax1, e0, spin=spin, band=band, **opts)
self.plot_ax(ax0, e0, spin=spin, band=band, **opts)
self.decorate_ax(ax1, klabels=klabels)
set_axlims(ax1, ylims, "y")
self.decorate_ax(ax0, klabels=klabels)
set_axlims(ax0, ylims, "y")
# Plot the DOS
if self.nsppol == 1:
opts = {"color": "black", "linewidth": 2.0}
edos.plot_ax(ax2, e0, exchange_xy=True, **opts)
edos.plot_ax(ax1, e0, exchange_xy=True, **opts)
else:
for spin in self.spins:
if spin == 0:
opts = {"color": "black", "linewidth": 2.0}
else:
opts = {"color": "red", "linewidth": 2.0}
edos.plot_ax(ax2, e0, spin=spin, exchange_xy=True, **opts)
edos.plot_ax(ax1, e0, spin=spin, exchange_xy=True, **opts)
ax2.grid(True)
ax2.yaxis.set_ticks_position("right")
ax2.yaxis.set_label_position("right")
set_axlims(ax2, ylims, "y")
ax1.grid(True)
ax1.yaxis.set_ticks_position("right")
ax1.yaxis.set_label_position("right")
set_axlims(ax1, ylims, "y")
return fig
@ -2337,13 +2356,13 @@ class ElectronBandsPlotter(NotebookWriter):
# Build grid with two axes.
gspec = GridSpec(1, 2, width_ratios=width_ratios, wspace=0.05)
# bands and DOS will share the y-axis
ax1 = plt.subplot(gspec[0])
ax2 = plt.subplot(gspec[1], sharey=ax1)
ax_list = [ax1, ax2]
ax0 = plt.subplot(gspec[0])
ax1 = plt.subplot(gspec[1], sharey=ax0)
ax_list = [ax0, ax1]
else:
# One axis for bands only
ax1 = fig.add_subplot(111)
ax_list = [ax1]
ax0 = fig.add_subplot(111)
ax_list = [ax0]
for ax in ax_list:
ax.grid(True)
@ -2368,7 +2387,7 @@ class ElectronBandsPlotter(NotebookWriter):
else:
mye0 = ebands.get_e0(e0)
l = ebands.plot_ax(ax1, mye0, spin=None, band=None, **my_kwargs)
l = ebands.plot_ax(ax0, mye0, spin=None, band=None, **my_kwargs)
lines.append(l[0])
# Use relative paths if label is a file.
@ -2379,9 +2398,9 @@ class ElectronBandsPlotter(NotebookWriter):
# Set ticks and labels, legends.
if i == 0:
ebands.decorate_ax(ax1)
ebands.decorate_ax(ax0)
ax1.legend(lines, legends, loc='upper right', fontsize=fontsize, shadow=True)
ax0.legend(lines, legends, loc='upper right', fontsize=fontsize, shadow=True)
# Add DOSes
if self.edoses_dict:
@ -2464,18 +2483,18 @@ class ElectronBandsPlotter(NotebookWriter):
for i, (ebands, edos) in enumerate(zip(ebands_list, edos_list)):
subgrid = GridSpecFromSubplotSpec(1, 2, subplot_spec=gspec[i], width_ratios=[2, 1], wspace=0.05)
# Get axes and align bands and DOS.
ax1 = plt.subplot(subgrid[0])
ax2 = plt.subplot(subgrid[1], sharey=ax1)
ax0 = plt.subplot(subgrid[0])
ax1 = plt.subplot(subgrid[1], sharey=ax0)
set_axlims(ax0, ylims, "y")
set_axlims(ax1, ylims, "y")
set_axlims(ax2, ylims, "y")
# Define the zero of energy and plot
mye0 = ebands.get_e0(e0) if e0 != "edos_fermie" else edos.fermie
ebands.plot_with_edos(edos, e0=mye0, ax_list=(ax1, ax2), show=False)
ebands.plot_with_edos(edos, e0=mye0, ax_list=(ax0, ax1), show=False)
if titles is not None: ax1.set_title(titles[i], fontsize=fontsize)
if titles is not None: ax0.set_title(titles[i], fontsize=fontsize)
if i % ncols != 0:
for ax in (ax1, ax2):
for ax in (ax0, ax1):
ax.set_ylabel("")
return fig
@ -2625,18 +2644,18 @@ class ElectronBandsPlotter(NotebookWriter):
# Animation with band structures + DOS.
from matplotlib.gridspec import GridSpec
gspec = GridSpec(1, 2, width_ratios=width_ratios, wspace=0.05)
ax1 = plt.subplot(gspec[0])
ax2 = plt.subplot(gspec[1], sharey=ax1)
ebands_list[0].decorate_ax(ax1)
ax2.grid(True)
ax2.yaxis.set_ticks_position("right")
ax2.yaxis.set_label_position("right")
ax0 = plt.subplot(gspec[0])
ax1 = plt.subplot(gspec[1], sharey=ax0)
ebands_list[0].decorate_ax(ax0)
ax1.grid(True)
ax1.yaxis.set_ticks_position("right")
ax1.yaxis.set_label_position("right")
for i, (ebands, edos) in enumerate(zip(ebands_list, edos_list)):
# Define the zero of energy to align bands and dos
mye0 = ebands.get_e0(e0) if e0 != "edos_fermie" else edos.fermie
ebands_lines = ebands.plot_ax(ax1, mye0, **plotax_kwargs)
edos_lines = edos.plot_ax(ax2, mye0, exchange_xy=True, **plotax_kwargs)
ebands_lines = ebands.plot_ax(ax0, mye0, **plotax_kwargs)
edos_lines = edos.plot_ax(ax1, mye0, exchange_xy=True, **plotax_kwargs)
lines = ebands_lines + edos_lines
#if titles is not None: lines += [ax.set_title(titles[i])]
artists.append(lines)
@ -2964,17 +2983,22 @@ class ElectronDos(object):
Return: list of lines added to the axis.
"""
dosf, idosf = self.dos_idos(spin=spin)
opts = [c.lower() for c in what]
dosf, idosf = self.dos_idos(spin=spin)
e0 = self.get_e0(e0)
lines = []
for c in opts:
if c == "d": f = dosf
if c == "i": f = idosf
if c == "d":
f = dosf
elif c == "i":
f = idosf
else:
raise ValueError("Unknown value for what: `%s`" % str(c))
xx, yy = f.mesh - e0, f.values * fact
if exchange_xy: xx, yy = yy, xx
lines.extend(ax.plot(xx, yy, **kwargs))
return lines
@add_fig_kwargs
@ -2984,11 +3008,9 @@ class ElectronDos(object):
Args:
e0: Option used to define the zero of energy in the band structure plot. Possible values:
* ``fermie``: shift all eigenvalues to have zero energy at the Fermi energy (``self.fermie``).
* Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
* None: Don't shift energies, equivalent to ``e0 = 0``.
- ``fermie``: shift all eigenvalues to have zero energy at the Fermi energy (``self.fermie``).
- Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
- None: Don't shift energies, equivalent to ``e0 = 0``.
spin: Selects the spin component, None if total DOS is wanted.
ax: |matplotlib-Axes| or None if a new figure should be created.
xlims: Set the data limits for the x-axis. Accept tuple e.g. ``(left, right)``
@ -2998,24 +3020,27 @@ class ElectronDos(object):
Return: |matplotlib-Figure|
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
e0 = self.get_e0(e0)
if not kwargs:
kwargs = {"color": "black", "linewidth": 1.0}
for spin in range(self.nsppol):
if spin == 0:
opts = {"color": "black", "linewidth": 1.0}
else:
opts = {"color": "red", "linewidth": 1.0}
opts.update(kwargs)
spin_sign = +1 if spin == 0 else -1
x, y = self.spin_dos[spin].mesh - e0, spin_sign * self.spin_dos[spin].values
ax.plot(x, y, **kwargs)
ax.plot(x, y, **opts)
ax.grid(True)
ax.set_xlabel('Energy [eV]')
ax.set_ylabel('DOS [states/eV]')
set_axlims(ax, xlims, "x")
return fig
@add_fig_kwargs
def plot_dos_idos(self, e0="fermie", xlims=None, height_ratios=(1, 2), **kwargs):
def plot_dos_idos(self, e0="fermie", ax_list=None, xlims=None, height_ratios=(1, 2), **kwargs):
"""
Plot electronic DOS and Integrated DOS on two different subplots.
@ -3024,6 +3049,8 @@ class ElectronDos(object):
- ``fermie``: shift all eigenvalues to have zero energy at the Fermi energy (``self.fermie``).
- Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
- None: Don't shift energies, equivalent to ``e0 = 0``.
ax_list: The axes for the DOS and IDOS plot. If ax_list is None, a new figure
is created and the two axes are automatically generated.
xlims: Set the data limits for the x-axis. Accept tuple e.g. ``(left, right)``
or scalar e.g. ``left``. If left (right) is None, default values are used
height_ratios:
@ -3034,18 +3061,22 @@ class ElectronDos(object):
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
fig = plt.figure()
gspec = GridSpec(2, 1, height_ratios=height_ratios, wspace=0.05)
ax1 = plt.subplot(gspec[0])
ax2 = plt.subplot(gspec[1], sharex=ax1)
if ax_list is None:
fig = plt.figure()
gspec = GridSpec(2, 1, height_ratios=height_ratios, wspace=0.05)
ax0 = plt.subplot(gspec[0])
ax1 = plt.subplot(gspec[1], sharex=ax0)
ax_list = [ax0, ax1]
for ax in (ax1, ax2):
ax.grid(True)
set_axlims(ax, xlims, "x")
for ax in ax_list:
ax.grid(True)
set_axlims(ax, xlims, "x")
ax1.set_ylabel("TOT IDOS")
ax2.set_ylabel("TOT DOS")
ax2.set_xlabel('Energy [eV]')
ax0.set_ylabel("TOT IDOS")
ax1.set_ylabel("TOT DOS")
ax1.set_xlabel('Energy [eV]')
else:
fig = ax_list[0].get_figure()
for spin in range(self.nsppol):
if spin == 0:
@ -3054,9 +3085,8 @@ class ElectronDos(object):
opts = {"color": "red", "linewidth": 1.0}
# Plot Total dos if unpolarized.
if self.nsppol == 1: spin = None
self.plot_ax(ax1, e0, spin=spin, what="i", **opts)
self.plot_ax(ax2, e0, spin=spin, what="d", **opts)
self.plot_ax(ax_list[0], e0, spin=spin, what="i", **opts)
self.plot_ax(ax_list[1], e0, spin=spin, what="d", **opts)
return fig
@ -3093,7 +3123,7 @@ class ElectronDos(object):
ax.grid(True)
set_axlims(ax, xlims, "x")
#ax.set_xlabel('DOS (UP - DOWN)')
#ax.set_ylabel('DOS (UP - DOWN)')
ax.set_xlabel('Energy [eV]')
return fig
@ -3112,12 +3142,16 @@ class ElectronDosPlotter(NotebookWriter):
plotter.add_edos("bar dos", "bar.nc")
fig = plotter.gridplot()
"""
# TODO: down-up option animate?
def __init__(self, key_edos=None, edos_kwargs=None):
if key_edos is None: key_edos = []
key_edos = [(k, ElectronDos.as_edos(v, edos_kwargs)) for k, v in key_edos]
self.edoses_dict = OrderedDict(key_edos)
def __len__(self):
return len(self.edoses_dict)
@property
def edos_list(self):
"""List of DOSes"""
@ -3148,68 +3182,96 @@ class ElectronDosPlotter(NotebookWriter):
self.edoses_dict[label] = ElectronDos.as_edos(edos, edos_kwargs)
@add_fig_kwargs
def combiplot(self, ax=None, e0="fermie", xlims=None, fontsize=8, **kwargs):
def combiplot(self, what_list="dos", spin_mode="total", e0="fermie",
ax_list=None, xlims=None, fontsize=8, **kwargs):
"""
Plot the the DOSes on the same figure. Use ``gridplot`` to plot DOSes on different figures.
Args:
ax: |matplotlib-Axes| or None if a new figure should be created.
e0: Option used to define the zero of energy in the band structure plot. Possible values::
* ``fermie``: shift all eigenvalues to have zero energy at the Fermi energy (``self.fermie``).
* Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
* None: Don't shift energies, equivalent to ``e0 = 0``
what_list: Selects quantities to plot e.g. ["dos", "idos"] to plot DOS and integrated DOS.
"dos" for DOS only and "idos" for IDOS only
spin_mode: "total" for total (I)DOS, "resolved" for plotting individual contributions.
Meaningful only if nsppol == 2.
e0: Option used to define the zero of energy in the band structure plot. Possible values:
- ``fermie``: shift all eigenvalues to have zero energy at the Fermi energy (``self.fermie``).
- Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
- None: Don't shift energies, equivalent to ``e0 = 0``
ax_list: List of |matplotlib-Axes| or None if a new figure should be created.
xlims: Set the data limits for the x-axis. Accept tuple e.g. ``(left, right)``
or scalar e.g. ``left``. If left (right) is None, default values are used
fontsize: fontsize for titles and legend
fontsize (int): fontsize for titles and legend
Return: |matplotlib-Figure|
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
what_list = list_strings(what_list)
nrows, ncols = len(what_list), 1
ax_list, fig, plt = get_axarray_fig_plt(ax_list, nrows=nrows, ncols=ncols,
sharex=True, sharey=False, squeeze=False)
ax_list = ax_list.ravel()
can_use_basename = self._can_use_basenames_as_labels()
for label, dos in self.edoses_dict.items():
if can_use_basename:
label = os.path.basename(label)
else:
# Use relative paths if label is a file.
if os.path.isfile(label): label = os.path.relpath(label)
dos.plot_ax(ax, e0, label=label)
for i, (what, ax) in enumerate(zip(what_list, ax_list)):
wax = dict(dos="d", idos="i")[what]
for label, edos in self.edoses_dict.items():
if can_use_basename:
label = os.path.basename(label)
else:
# Use relative paths if label is a file.
if os.path.isfile(label): label = os.path.relpath(label)
ax.grid(True)
ax.set_xlabel("Energy [eV]")
ax.set_ylabel('DOS [states/eV]')
set_axlims(ax, xlims, "x")
ax.legend(loc="best", shadow=True, fontsize=fontsize)
# Here I handle spin and spin_mode.
if edos.nsppol == 1 or spin_mode == "total":
# Plot total values
edos.plot_ax(ax, e0, what=wax, spin=None, label=label)
elif spin_mode == "resolved":
# Plot spin resolved quantiies with sign.
# Note get_color to have same color for both spins.
for spin in range(edos.nsppol):
fact = 1 if spin == 0 else -1
lines = edos.plot_ax(ax, e0, what=wax, spin=spin, fact=fact,
color=None if spin == 0 else lines[0].get_color(),
label=label if spin == 0 else None)
else:
raise ValueError("Wrong value for spin_mode: `%s`:" % str(spin_mode))
ax.grid(True)
if i == len(what_list) - 1:
ax.set_xlabel("Energy [eV]")
ax.set_ylabel('DOS [states/eV]' if what == "dos" else "IDOS")
set_axlims(ax, xlims, "x")
ax.legend(loc="best", shadow=True, fontsize=fontsize)
return fig
def plot(self, *args, **kwargs):
"""An alias for combiplot."""
return self.combiplot(*args, **kwargs)
# An alias for combiplot.
plot = combiplot
@add_fig_kwargs
def gridplot(self, e0="fermie", xlims=None, **kwargs):
def gridplot(self, what="dos", spin_mode="total", e0="fermie",
sharex=True, sharey=True, xlims=None, fontsize=8, **kwargs):
"""
Plot multiple DOSes on a grid.
Args:
e0: Option used to define the zero of energy in the band structure plot. Possible values::
* ``fermie``: shift all eigenvalues and the DOS to have zero energy at the Fermi energy.
Note that, by default, the Fermi energy is taken from the band structure object
i.e. the Fermi energy computed at the end of the SCF file that produced the density.
This should be ok in semiconductors. In metals, however, a better value of the Fermi energy
can be obtained from the DOS provided that the k-sampling for the DOS is much denser than
the one used to compute the density. See ``edos_fermie``.
* ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
Available only if edos_objects is not None
* Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
* None: Don't shift energies, equivalent to ``e0 = 0``.
what: "dos" to plot DOS, "idos" for integrated DOS.
spin_mode: "total" for total (I)DOS, "resolved" for plotting individual contributions.
Meaningful only if nsppol == 2.
e0: Option used to define the zero of energy in the band structure plot. Possible values:
- ``fermie``: shift all eigenvalues and the DOS to have zero energy at the Fermi energy.
Note that, by default, the Fermi energy is taken from the band structure object
i.e. the Fermi energy computed at the end of the SCF file that produced the density.
This should be ok in semiconductors. In metals, however, a better value of the Fermi energy
can be obtained from the DOS provided that the k-sampling for the DOS is much denser than
the one used to compute the density. See ``edos_fermie``.
- ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
Available only if edos_objects is not None
- Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
- None: Don't shift energies, equivalent to ``e0 = 0``.
sharex, sharey: True if x (y) axis should be shared.
xlims: Set the data limits for the x-axis. Accept tuple e.g. ``(left, right)``
or scalar e.g. ``left``. If left (right) is None, default values are used
fontsize: Label and title fontsize.
Return: |matplotlib-Figure|
"""
@ -3224,19 +3286,42 @@ class ElectronDosPlotter(NotebookWriter):
# Build Grid
ax_list, fig, plt = get_axarray_fig_plt(None, nrows=nrows, ncols=ncols,
sharex=False, sharey=True, squeeze=False)
sharex=sharex, sharey=sharey, squeeze=False)
ax_list = ax_list.ravel()
# don't show the last ax if numeb is odd.
if numeb % ncols != 0: ax_list[-1].axis("off")
for i, (label, edos) in enumerate(self.edoses_dict.items()):
ax = ax_list[i]
edos.plot(ax=ax, e0=e0, show=False)
ax.set_title(label)
wax = dict(dos="d", idos="i")[what]
for i, ((label, edos), ax) in enumerate(zip(self.edoses_dict.items(), ax_list)):
irow, icol = divmod(i, ncols)
# Here I handle spin and spin_mode.
if edos.nsppol == 1 or spin_mode == "total":
opts = {"color": "black", "linewidth": 1.0}
edos.plot_ax(ax, e0=e0, what=wax, spin=None, **opts)
elif spin_mode == "resolved":
# Plot spin resolved quantiies with sign.
# Note get_color to have same color for both spins.
for spin in range(edos.nsppol):
fact = 1 if spin == 0 else -1
lines = edos.plot_ax(ax, e0, what=wax, spin=spin, fact=fact,
color=None if spin == 0 else lines[0].get_color(),
label=label if spin == 0 else None)
else:
raise ValueError("Wrong value for spin_mode: `%s`:" % str(spin_mode))
ax.grid(True)
ax.set_title(label, fontsize=fontsize)
set_axlims(ax, xlims, "x")
if i % ncols != 0:
ax.set_ylabel("")
if icol == 0:
ax.set_ylabel('DOS [states/eV]' if what == "dos" else "IDOS")
if irow == nrows - 1:
ax.set_xlabel("Energy [eV]")
#ax.legend(loc="best", shadow=True, fontsize=fontsize)
return fig
@ -3594,7 +3679,7 @@ class Bands3D(Has_Structure):
return figure
@add_fig_kwargs
def plot_contour(self, band, spin=0, plane="xy", elevation=0, ax=None, fontsize=10, **kwargs):
def plot_contour(self, band, spin=0, plane="xy", elevation=0, ax=None, fontsize=8, **kwargs):
"""
Contour plot with matplotlib_.

14
abipy/electrons/tests/test_ebands.py
View File

@ -97,6 +97,20 @@ class ElectronBandsTest(AbipyTest):
ni_edos = ni_ebands_kmesh.get_edos()
repr(ni_edos); str(ni_edos)
assert ni_edos.to_string(verbose=2)
# Get ElectronDosPlotter with nsppol == 2 and test matplotlib methods.
edos_plotter = ni_ebands_kmesh.compare_gauss_edos(widths=[0.2, 0.4], step=0.2)
assert len(edos_plotter) == 2
if self.has_matplotlib():
# Combiplot.
assert edos_plotter.combiplot(title="default values", show=False)
assert edos_plotter.combiplot(what_list=("dos", "idos"), spin_mode="resolved", show=False)
assert edos_plotter.combiplot(e0=0, what_list="dos", spin_mode="resolved", fontsize=12, show=False)
# Gridplot
assert edos_plotter.gridplot(title="default values", show=False)
assert edos_plotter.gridplot(what="idos", spin_mode="resolved", xlims=(-10, 10), show=False)
assert edos_plotter.gridplot(e0=0, what="dos", spin_mode="resolved", fontsize=12, show=False)
ni_ebands_kpath = ElectronBands.from_file(abidata.ref_file("ni_kpath_GSR.nc"))

43
abipy/eph/sigeph.py
View File

@ -101,6 +101,8 @@ class QpTempState(namedtuple("QpTempState", "tmesh e0 qpe ze0 spin kpoint band")
def get_dataframe(self, index=None, params=None):
"""
Build pandas dataframe with QP data
Args:
index: dataframe index.
params: Optional (Ordered) dictionary with extra parameters.
@ -689,13 +691,14 @@ class SigEPhFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter)
return pd.concat(df_list)
def get_dataframe_sk(self, spin, kpoint, index=None, with_params=True, ignore_imag=False):
def get_dataframe_sk(self, spin, kpoint, itemp=None, index=None, with_params=True, ignore_imag=False):
"""
Returns |pandas-DataFrame| with QP results for the given (spin, k-point).
Args:
spin: Spin index.
kpoint: K-point in self-energy. Accepts |Kpoint|, vector or index.
itemp: Temperature index, if None all temperatures are returned.
index: dataframe index.
with_params: False to exclude calculation parameters from the dataframe.
ignore_imag: Only real part is returned if ``ignore_imag``.
@ -708,7 +711,9 @@ class SigEPhFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter)
# Convert to dataframe and add other entries useful when comparing different calculations.
rows.append(qp.get_dataframe(params=self.params if with_params else None))
return pd.concat(rows)
df = pd.concat(rows)
if itemp is not None: df = df[df["tmesh"] == self.tmesh[itemp]]
return df
#def get_dirgaps_dataframe(self):
@ -1033,7 +1038,7 @@ class SigEPhRobot(Robot, RobotWithEbands):
@add_fig_kwargs
def plot_qpgaps_t(self, plot_qpmks=False, sortby=None, hue=None, fontsize=8, **kwargs):
"""
Compare the QP(T) direct gaps for all the k-points available on file.
Compare the QP(T) direct gaps for all the k-points available in the robot.
Args:
plot_qpmks: If True, plot QP_gap - KS_gap
@ -1054,7 +1059,7 @@ class SigEPhRobot(Robot, RobotWithEbands):
ax_list = None
for i, ((label, ncfile, param), lineopt) in enumerate(zip(self.sortby(sortby), self.iter_lineopt())):
fig = ncfile.plot_qpgaps_t(ax_list=ax_list, plot_qpmks=plot_qpmks,
label=label, show=False, fontsize=fontsize, **lineopt)
label=label if i == 0 else None, show=False, fontsize=fontsize, **lineopt)
ax_list = fig.axes
else:
# (nkcalc, ngroups) subplots
@ -1074,13 +1079,18 @@ class SigEPhRobot(Robot, RobotWithEbands):
for ax in ax_mat[:, ig]:
set_visible(ax, False, "ylabel")
# Hide legends except first one
if nrows > 1:
for ax in ax_mat[1:, :].ravel():
set_visible(ax, False, "legend")
return fig
@add_fig_kwargs
def plot_qpgaps_convergence(self, itemp=0, sortby=None, hue=None, fontsize=8, **kwargs):
def plot_qpgaps_convergence(self, itemp=0, sortby=None, hue=None, plot_qpmks=False, fontsize=8, **kwargs):
"""
Plot the convergence of the direct QP gaps at given temperature
for all the k-points available on file.
for all the k-points treated by the robot.
Args:
itemp: Temperature index.
@ -1093,6 +1103,7 @@ class SigEPhRobot(Robot, RobotWithEbands):
Accepts callable or string
If string, it's assumed that the abifile has an attribute with the same name and getattr is invoked.
If callable, the output of hue(abifile) is used.
plot_qpmks: If True, plot QP_gap - KS_gap
fontsize: legend and label fontsize.
Returns: |matplotlib-Figure|
@ -1105,7 +1116,7 @@ class SigEPhRobot(Robot, RobotWithEbands):
# Build grid with (nkpt, 1) plots.
ncols, nrows = 1, len(sigma_kpoints)
ax_list, fig, plt = get_axarray_fig_plt(None, nrows=nrows, ncols=ncols,
sharex=True, sharey=True, squeeze=False)
sharex=True, sharey=False, squeeze=False)
ax_list = ax_list.ravel()
if hue is None:
@ -1113,26 +1124,33 @@ class SigEPhRobot(Robot, RobotWithEbands):
else:
groups = self.group_and_sortby(hue, sortby)
name = "QP dirgap" if not plot_qpmks else "QP-KS dirgap"
for ik, (kpt, ax) in enumerate(zip(sigma_kpoints, ax_list)):
for spin in range(nsppol):
ax.set_title("QP dirgap k:%s, T = %.1f K" % (repr(kpt), nc0.tmesh[itemp]), fontsize=fontsize)
ax.set_title("%s k:%s, T = %.1f K" % (
name, repr(kpt), nc0.tmesh[itemp]), fontsize=fontsize)
# Extract QP dirgap for [spin, kpt, itemp]
if hue is None:
yvals = [ncfile.qp_dirgaps_t[spin, ik, itemp] for ncfile in ncfiles]
if plot_qpmks:
yvals = np.array(yvals) - np.array([ncfile.ks_dirgaps[spin, ik] for ncfile in ncfiles])
ax.plot(params, yvals, marker=nc0.marker_spin[spin])
else:
for g in groups:
yvals = [ncfile.qp_dirgaps_t[spin, ik, itemp] for ncfile in g.abifiles]
if plot_qpmks:
yvals = np.array(yvals) - np.array([ncfile.ks_dirgaps[spin, ik] for ncfile in g.abifiles])
label = "%s: %s" % (self._get_label(hue), g.hvalue)
ax.plot(g.xvalues, yvals, marker=nc0.marker_spin[spin], label=label)
ax.grid(True)
ax.set_ylabel("%s [eV]" % name)
if ik == len(sigma_kpoints) - 1:
ax.set_xlabel("%s" % self._get_label(sortby))
if sortby is None: rotate_ticklabels(ax, 15)
ax.set_ylabel("QP direct gap [eV]")
ax.legend(loc="best", fontsize=fontsize, shadow=True)
if hue is not None:
ax.legend(loc="best", fontsize=fontsize, shadow=True)
return fig
@ -1201,14 +1219,15 @@ class SigEPhRobot(Robot, RobotWithEbands):
# Extract QP data.
yvals = [getattr(qp, what)[itemp] for qp in qplist]
label = "%s: %s" % (self._get_label(hue), g.hvalue)
ax.plot(g.xvalues, yvals, marker=nc0.marker_spin[spin], label=label)
ax.plot(g.xvalues, yvals, marker=nc0.marker_spin[spin],
label=label if i == 0 else None)
ax.grid(True)
ax.set_ylabel(what)
if i == len(what_list) - 1:
ax.set_xlabel("%s" % self._get_label(sortby))
if sortby is None: rotate_ticklabels(ax, 15)
if i == 0:
if i == 0 and hue is not None:
ax.legend(loc="best", fontsize=fontsize, shadow=True)
if "title" not in kwargs:

4
abipy/eph/tests/test_sigeph.py
View File

@ -60,6 +60,10 @@ class SigEPhFileTest(AbipyTest):
assert np.all(data_sk["spin"] == 0)
self.assert_almost_equal(data_sk["kpoint"].values[0].frac_coords, [0.5, 0.0, 0.0])
itemp = 0
data_sk = ncfile.get_dataframe_sk(spin=0, kpoint=[0.5, 0.0, 0.0], itemp=itemp)
self.assert_equal(data_sk["tmesh"].values, ncfile.tmesh[itemp])
data = ncfile.get_dataframe()
assert "ze0" in data

33
abipy/examples/plot/plot_edos_vs_broad.py
View File

@ -7,25 +7,32 @@ This example shows how to compute and plot multiple
electron DOSes obtained with different values of the gaussian broadening.
"""
import abipy.data as abidata
from abipy.abilab import abiopen, ElectronDosPlotter
from abipy import abilab
# Open the wavefunction file computed with a homogeneous sampling of the BZ
# and extract the band structure on the k-mesh.
with abiopen(abidata.ref_file("si_scf_WFK.nc")) as gs_wfk:
with abilab.abiopen(abidata.ref_file("si_scf_WFK.nc")) as gs_wfk:
gs_bands = gs_wfk.ebands
# Compute the DOS with the Gaussian method.
# Plot bands and DOS.
# Compute the DOS with different values of the Gaussian smearing.
widths = [0.1, 0.2, 0.3]
step = 0.1
plotter = ElectronDosPlotter()
edos_plotter = gs_bands.compare_gauss_edos(widths, step=0.1)
for width in widths:
# Compute DOS and add it to the plotter.
edos = gs_bands.get_edos(method="gaussian", step=step, width=width)
label = r"$\sigma = %s$ [eV]" % width
plotter.add_edos(label, edos)
# Invoke ElectronDosPlotter methods to plot results.
edos_plotter.combiplot(title="e-DOS as function of the Gaussian broadening")
plotter.combiplot()
#plotter.animate()
edos_plotter.gridplot(title="gridplot version")
with abilab.abiopen(abidata.ref_file("ni_666k_GSR.nc")) as gsr:
ni_ebands_kmesh = gsr.ebands
edos_plotter = ni_ebands_kmesh.compare_gauss_edos(widths=[0.1, 0.2, 0.3], step=0.2)
title="e-DOS as function of the Gaussian broadening"
edos_plotter.combiplot(dos_mode="idos+dos")
edos_plotter.combiplot(dos_mode="dos", spin_mode="resolved")
edos_plotter.gridplot(title="gridplot version")
edos_plotter.gridplot(spin_mode="resolved")

20
abipy/examples/plot/plot_structure.py Executable file
View File

@ -0,0 +1,20 @@
#!/usr/bin/env python
r"""
Unit cell
=========
This example shows how to display the unit cell with matplotlib.
"""
from abipy.abilab import abiopen
import abipy.data as abidata
# Extract structure from netcdf file.
with abiopen(abidata.ref_file("sio2_kpath_GSR.nc")) as gsr:
structure = gsr.structure
# Visualize sites structure.
structure.plot(color_scheme="Jmol")
# Wrap sites into first unit cell.
# sphinx_gallery_thumbnail_number = 2
structure.plot(to_unit_cell=True)

4
abipy/integration_tests/TODO.md
View File

@ -25,7 +25,7 @@ TODO list:
* Almost DONE: Add support for https://mybinder.readthedocs.io/en/latest/sample_repos.html#conda-environment-with-environment-yml
* Rename EPH.nc
* Rename EPH.nc (A2F.nc, ELI.nc)
* DONE Add https://github.com/mcmtroffaes/sphinxcontrib-bibtex
@ -168,3 +168,5 @@ TODO list:
* lobster interface from Guido
* interface abistruct with marylin
* Remove Prettytable

2
abipy/tools/plotting.py
View File

@ -484,7 +484,7 @@ def plot_structure(structure, ax=None, to_unit_cell=False, alpha=0.7,
structure: Structure object
ax: matplotlib :class:`Axes3D` or None if a new figure should be created.
alpha: The alpha blending value, between 0 (transparent) and 1 (opaque)
to_unit_cell: True if sites should be wrapped to the first unit cell.
to_unit_cell: True if sites should be wrapped into the first unit cell.
style: "points+labels" to show atoms sites with labels.
color_scheme: color scheme for atom types. Allowed values in ("Jmol", "VESTA")

2
docs/links.rst
View File

@ -90,8 +90,10 @@
.. |AbinitInput| replace:: :class:`abipy.abio.inputs.AbinitInput`
.. |MultiDataset| replace:: :class:`abipy.abio.inputs.MultiDataset`
.. |ElectronBands| replace:: :class:`abipy.electrons.ebands.ElectronBands`
.. |ElectronBandsPlotter| replace:: :class:`abipy.electrons.ebands.ElectronBandsPlotter`
.. |SkwInterpolator| replace:: :class:`abipy.core.skw.SkwInterpolator`
.. |ElectronDos| replace:: :class:`abipy.electrons.ebands.ElectronDos`
.. |ElectronDosPlotter| replace:: :class:`abipy.electrons.ebands.ElectronDosPlotter`
.. |PhononBands| replace:: :class:`abipy.dfpt.phonons.PhononBands`
.. |Task| replace:: :class:`pymatgen.io.abinit.tasks.Task`
.. |ScfTask| replace:: :class:`pymatgen.io.abinit.tasks.ScfTask`