mirror of https://github.com/abinit/abipy.git
Add plot_phdispl
This commit is contained in:
Matteo Giantomassi
parent
8fc326c25e
commit
0330ad222f
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@ -16,7 +16,7 @@ from monty.string import is_string, list_strings
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from monty.termcolor import cprint
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from abipy.core.mixins import NotebookWriter
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from abipy.tools.plotting import (plot_xy_with_hue, add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt,
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rotate_ticklabels)
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rotate_ticklabels, set_visible)
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class Robot(NotebookWriter):
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@ -949,10 +949,10 @@ Not all entries are sortable (Please select number-like quantities)""" % (self._
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for i, (ax, item) in enumerate(zip(ax_list.ravel(), items)):
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self.plot_convergence(item, sortby=sortby, hue=hue, ax=ax, fontsize=fontsize,
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marker=marker, show=False)
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if i != 0 and ax.legend():
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ax.legend().set_visible(False)
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if i != len(items) - 1 and ax.xaxis.label:
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ax.xaxis.label.set_visible(False)
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if i != 0:
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set_visible(ax, False, "legend")
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if i != len(items) - 1:
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set_visible(ax, False, "xlabel")
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return fig
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@ -590,7 +590,10 @@ class Kpoint(SlotPickleMixin):
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return np.any(diff < _ATOL_KDIFF)
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def __repr__(self):
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return "[%+.3f, %+.3f, %+.3f]" % tuple(self.frac_coords)
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s = "[%+.3f, %+.3f, %+.3f]" % tuple(self.frac_coords)
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if self.name is not None:
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s += " %s" % self.name
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return s
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def __str__(self):
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return self.to_string()
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@ -598,7 +601,8 @@ class Kpoint(SlotPickleMixin):
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def to_string(self, verbose=0):
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"""String representation."""
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s = "[%+.3f, %+.3f, %+.3f]" % tuple(self.frac_coords)
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if self.name is not None: s += ", name: %s" % self.name
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if self.name is not None:
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s += ", name: %s" % self.name
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if self._weight is not None: s += ", weight: %.3f" % self.weight
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return s
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@ -715,7 +715,7 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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return phbands_plotter
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def anacompare_phdos(self, nqsmalls, asr=2, chneut=1, dipdip=1, dos_method="tetra", ngqpt=None,
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num_cpus=1, stream=sys.stdout):
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verbose=0, num_cpus=1, stream=sys.stdout):
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"""
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Invoke Anaddb to compute Phonon DOS with different q-meshes. The ab-initio dynamical matrix
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reported in the DDB_ file will be Fourier-interpolated on the list of q-meshes specified
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@ -728,6 +728,7 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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dos_method: Technique for DOS computation in Possible choices: "tetra", "gaussian" or "gaussian:0.001 eV".
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In the later case, the value 0.001 eV is used as gaussian broadening
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ngqpt: Number of divisions for the ab-initio q-mesh in the DDB file. Auto-detected if None (default)
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verbose: Verbosity level.
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num_cpus: Number of CPUs (threads) used to parallellize the calculation of the DOSes. Autodetected if None.
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stream: File-like object used for printing.
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@ -756,7 +757,8 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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else:
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# Threads
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print("Computing %d phonon DOS with %d threads" % (len(nqsmalls), num_cpus) )
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if verbose:
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print("Computing %d phonon DOS with %d threads" % (len(nqsmalls), num_cpus) )
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phdoses = [None] * len(nqsmalls)
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def worker():
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@ -790,8 +792,9 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
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for i, phdos in enumerate(phdoses[:-1]):
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splined_dos = phdos.spline_on_mesh(last_mesh)
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abs_diff = (splined_dos - phdoses[-1]).abs()
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print(" Delta(Phdos[%d] - Phdos[%d]) / Phdos[%d]: %f" %
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(i, len(phdoses)-1, len(phdoses)-1, abs_diff.integral().values[-1]), file=stream)
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if verbose:
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print(" Delta(Phdos[%d] - Phdos[%d]) / Phdos[%d]: %f" %
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(i, len(phdoses)-1, len(phdoses)-1, abs_diff.integral().values[-1]), file=stream)
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# Fill the plotter.
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plotter = PhononDosPlotter()
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@ -23,7 +23,7 @@ from abipy.core.mixins import AbinitNcFile, Has_Structure, Has_PhononBands, Note
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from abipy.core.kpoints import Kpoint, Kpath
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from abipy.iotools import ETSF_Reader
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from abipy.tools import gaussian, duck
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from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, set_axlims, get_axarray_fig_plt
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from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, set_axlims, get_axarray_fig_plt, set_visible
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from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine
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from pymatgen.phonon.dos import CompletePhononDos as PmgCompletePhononDos, PhononDos as PmgPhononDos
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@ -485,8 +485,7 @@ class PhononBands(object):
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def qindex_qpoint(self, qpoint):
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"""Returns (qindex, qpoint) from an integer or a qpoint."""
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qindex = self.qindex(qpoint)
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qpoint = self.qpoints(qindex)
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return qindex, qpoint
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return qindex, self.qpoints[qindex]
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def get_unstable_modes(self, below_mev=-5.0):
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"""
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@ -1277,7 +1276,7 @@ class PhononBands(object):
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axlist: The axes for the bandstructure plot and the DOS plot. If axlist is None, a new figure
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is created and the two axes are automatically generated.
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width_ratios: Ratio between the width of the bands plots and the DOS plots.
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Used if `axlist` is None
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Used if ``axlist`` is None
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Returns: |matplotlib-Figure|
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"""
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@ -1321,6 +1320,111 @@ class PhononBands(object):
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return fig
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@add_fig_kwargs
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def plot_phdispl(self, qpoint, cart_dir=None, ax=None, units="eV",
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colormap="viridis", hatches="default", fontsize=12, **kwargs):
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"""
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Plot vertical bars with the contribution of the different atomic types to the phonon displacements
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at a given q-point. The contribution is given by the ratio :math:`\dfrac{|d_{type}|^2} {|d|^2}`
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where d is the (complex) phonon displacement in cartesian coordinates and d_{type} selects only the
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terms associated to the atomic type ``type``.
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Args:
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qpoint: integer, vector of reduced coordinates or |Kpoint| object.
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cart_dir: "x", "y", or "z" to select a particular Cartesian directions.
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None if no projection is wanted.
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ax: |matplotlib-Axes| or None if a new figure should be created.
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units: Units for phonon frequencies. Possible values in ("eV", "meV", "Ha", "cm-1", "Thz").
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Case-insensitive.
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colormap: Matplotlib colormap used for atom type.
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hatches: List of strings with matplotlib hatching patterns. None or empty list to disable hatching.
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fontsize: Legend and title fontsize.
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Returns: |matplotlib-Figure|
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"""
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factor = abu.phfactor_ev2units(units)
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icart = {"x": 0, "y": 1, "z": 2, None: None}[cart_dir]
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iq, qpoint = self.qindex_qpoint(qpoint)
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ax, fig, plt = get_ax_fig_plt(ax=ax)
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cmap = plt.get_cmap(colormap)
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ntypat = self.structure.ntypesp
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ax.set_title("qpoint = %s" % repr(qpoint), fontsize=fontsize)
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ax.set_xlabel('Frequency %s' % abu.phunit_tag(units))
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#ax.set_ylabel(r"Contribution of atomic types to phonon displacement $d_{q,\nu}**2$")
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if icart is None:
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ax.set_ylabel(r"${|\vec{d}|^2} / {|\vec{d}({type})|^2}$")
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else:
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ax.set_ylabel(r"${|\vec{d}_{%s}|^2} / {|\vec{d}({type})|^2}$" % cart_dir)
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# {Mg: [0], B: [1, 2]}
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symbol2indices = {symbol: np.array(self.structure.indices_from_symbol(symbol))
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for symbol in self.structure.symbol_set}
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#print(symbol2indices)
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width, pad = 4, 1
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pad = width + pad
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xticks, xticklabels = [], []
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if hatches == "default":
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hatches = ["/", "\\", "'", "|", "-", "+", "x", "o", "O", ".", "*"]
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else:
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hatches = list_strings(hatches) if hatches is not None else []
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x = 0
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for nu in self.branches:
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w_qnu = self.phfreqs[iq, nu] * factor
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dcart_qnu = np.reshape(self.phdispl_cart[iq, nu], (len(self.structure), 3))
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d2norm = sum(np.linalg.norm(d)**2 for d in dcart_qnu)
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# Make a bar plot with rectangles bounded by (x - width/2, x + width/2, bottom, bottom + height)
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# The align keyword controls if x is interpreted as the center or the left edge of the rectangle.
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bottom, height = 0.0, 0.0
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for itype, (symbol, inds) in enumerate(symbol2indices.items()):
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if icart is None:
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assert all(len(d) == 3 for d in dcart_qnu[inds])
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height = sum(np.linalg.norm(d)**2 for d in dcart_qnu[inds]) / d2norm
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else:
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height = sum(np.linalg.norm(d)**2 for d in dcart_qnu[inds, icart]) / d2norm
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ax.bar(x, height, width, bottom, align="center",
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color=cmap(float(itype) / max(1, ntypat - 1)),
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label=symbol if nu == 0 else None, edgecolor='black',
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hatch=hatches[itype % len(hatches)] if hatches else None,
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)
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bottom += height
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xticks.append(x)
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xticklabels.append("%.3f" % w_qnu)
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x += (width + pad) / 2
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ax.set_xticks(xticks)
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ax.set_xticklabels((xticklabels))
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ax.legend(loc="best", fontsize=fontsize, shadow=False)
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#ax.legend(bbox_to_anchor=(0, 1.02, 1, 0.2), loc="lower left", mode="expand", borderaxespad=0, ncol=ntypat)
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return fig
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@add_fig_kwargs
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def plot_phdispl_cartdirs(self, qpoint, units="eV", colormap="viridis", hatches="default", fontsize=12, **kwargs):
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"""
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Plot vertical bars with the contribution of the different atomic types to the phonon displacements
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at a gven q-point. See plot_phdispl for API documentation.
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"""
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ax_list, fig, plt = get_axarray_fig_plt(None, nrows=3, ncols=1,
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sharex=True, sharey=True, squeeze=False)
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cart_dirs = ["x", "y", "z"]
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for i, (cart_dir, ax) in enumerate(zip(cart_dirs, ax_list.ravel())):
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self.plot_phdispl(qpoint, cart_dir=cart_dir, ax=ax, units=units, colormap=colormap,
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fontsize=fontsize, hatches=hatches, show=False)
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# Disable artists.
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if i != 0:
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set_visible(ax, False, "legend", "title")
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if i != len(cart_dirs) - 1:
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set_visible(ax, False, "xlabel")
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return fig
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def get_dataframe(self):
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"""
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Return a |pandas-DataFrame| with the following columns:
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@ -1478,7 +1582,7 @@ class PhononBands(object):
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the maximum breaking with sign
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the absolute value of the maximum breaking
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"""
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gamma_ind = self.qpoints.index((0,0,0))
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gamma_ind = self.qpoints.index((0, 0, 0))
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ind = self.acoustic_indices(gamma_ind, threshold=threshold, raise_on_no_indices=raise_on_no_indices)
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asr_break = self.phfreqs[0, ind] * abu.phfactor_ev2units(units)
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@ -2071,6 +2175,7 @@ class PhdosFile(AbinitNcFile, Has_Structure, NotebookWriter):
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"""
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Human-readable string with useful information such as structure...
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Args:
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verbose: Verbosity level.
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"""
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lines = []; app = lines.append
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@ -2078,7 +2183,6 @@ class PhdosFile(AbinitNcFile, Has_Structure, NotebookWriter):
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app(marquee("File Info", mark="="))
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app(self.filestat(as_string=True))
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app("")
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app(self.structure.to_string(verbose=verbose, title="Structure"))
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app("")
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@ -2867,7 +2971,7 @@ class PhononBandsPlotter(NotebookWriter):
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mode_range: Only bands such as ``mode_range[0] <= nu_index < mode_range[1]`` are included in the plot.
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units: Units for phonon plots. Possible values in ("eV", "meV", "Ha", "cm-1", "Thz"). Case-insensitive.
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swarm: True to show the datapoints on top of the boxes
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ax: matplotlib :class:`Axes` or None if a new figure should be created.
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ax: |matplotlib-Axes| or None if a new figure should be created.
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kwargs: Keyword arguments passed to seaborn_ boxplot.
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"""
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frames = []
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@ -40,6 +40,7 @@ class PhononBandsTest(AbipyTest):
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assert any(q.name is not None for q in nc.qpoints)
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same_phbands_nc = PhononBands.as_phbands(nc)
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self.assert_equal(same_phbands_nc.phfreqs, phbands.phfreqs)
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assert phbands.phdispl_cart.shape == (phbands.nqpt, phbands.num_branches, phbands.num_branches)
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# a + b gives plotter
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assert hasattr(same_phbands_nc + phbands, "combiplot")
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@ -103,6 +104,8 @@ class PhononBandsTest(AbipyTest):
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assert phbands.plot_fatbands(units="ha", qlabels=qlabels, show=False)
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assert phbands.plot_fatbands(phdos_file=abidata.ref_file("trf2_5.out_PHDOS.nc"), units="thz", show=False)
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assert phbands.plot_colored_matched(units="cm^-1", show=False)
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assert phbands.plot_phdispl(qpoint=(0, 0, 0), units="cm^-1", hatches=None, show=False)
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assert phbands.plot_phdispl_cartdirs(qpoint=(0, 0, 0), units="cm^-1", show=False)
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assert phbands.boxplot(units="ev", mode_range=[2, 4], show=False)
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# Cannot compute PHDOS with q-path
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@ -153,8 +156,9 @@ class PhbstFileTest(AbipyTest):
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ii = ncfile.qindex(qpt)
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#print("iq", iq, "qpt", qpt, "ii", ii, "qpoints[ii]", ncfile.qpoints[ii])
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same_ii, same_qpt = ncfile.qindex_qpoint(ii)
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assert same_ii == ii
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assert qpt == same_qpt
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assert same_ii == ii and qpt == same_qpt
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same_ii, same_qpt = ncfile.phbands.qindex_qpoint(qpt)
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assert same_ii == ii and qpt == same_qpt
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qpoint = ncfile.qpoints[0]
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frame = ncfile.get_phframe(qpoint)
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@ -184,6 +184,10 @@ class GsrFile(AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands, Notebo
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"""
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return self.reader.read_abinit_xcfunc()
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@lazy_property
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def energy_terms(self):
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return self.reader.read_energy_terms(unit="eV")
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@lazy_property
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def params(self):
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""":class:`OrderedDict` with parameters that might be subject to convergence studies."""
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@ -273,7 +277,9 @@ if gsr.ebands.kpoints.is_ibz:
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class EnergyTerms(AttrDict):
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"""Contributions to the total GS energy. See energies_type in m_energies.F90"""
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"""
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Contributions to the total GS energy. See energies_type in m_energies.F90.
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"""
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_NAME2DOC = OrderedDict([
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# (Name, help)
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@ -317,6 +323,15 @@ class EnergyTerms(AttrDict):
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return self.to_string(with_doc=False)
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__repr__ = __str__
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def to_string(self, verbose=0, with_doc=True):
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"""String representation, with documentation if with_doc."""
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lines = [str(self.table)]
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if with_doc:
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for k, doc in self._NAME2DOC.items():
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lines.append("%s: %s" % (k, doc))
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return "\n".join(lines)
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@property
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def table(self):
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"""PrettyTable object with the results."""
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@ -326,14 +341,13 @@ class EnergyTerms(AttrDict):
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table.add_row([k, self[k]])
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return table
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def to_string(self, verbose=0, with_doc=True):
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"""String representation, with documentation if with_doc."""
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lines = [str(self.table)]
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if with_doc:
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for k, doc in self._NAME2DOC.items():
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lines.append("%s: %s" % (k, doc))
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return "\n".join(lines)
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#def get_dataframe(self):
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# """
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# Return a |pandas-DataFrame|
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# """
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# d = {k: float(self[k]) for k in self}
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# return pd.DataFrame(d, index=[None], columns=list(d.keys()))
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# #return pd.DataFrame(d, columns=list(d.keys()))
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class GsrReader(ElectronsReader):
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@ -486,6 +500,69 @@ class GsrRobot(Robot, RobotWithEbands):
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dataframe = pd.DataFrame(rows, index=index, columns=list(rows[0].keys()) if rows else None)
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return dict2namedtuple(fits=fits, dataframe=dataframe)
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def get_energyterms_dataframe(self, abspath=False):
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rows, row_names = [], []
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for label, gsr in self.items():
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row_names.append(label)
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rows.append(gsr.energy_terms)
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row_names = row_names if not abspath else self._to_relpaths(row_names)
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df = pd.DataFrame(rows, index=row_names, columns=list(rows[0].keys()))
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first_row = df.iloc[[0]].values[0]
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df = df.apply(lambda row: row - first_row, axis=1)
|
||||
return df
|
||||
|
||||
@add_fig_kwargs
|
||||
def plot_energyterms(self, fontsize=6, **kwargs):
|
||||
items = ["e_eigenvalues", "e_localpsp", "e_ewald"]
|
||||
|
||||
# Build grid of plots.
|
||||
nrows, ncols = len(items), 1
|
||||
ax_list, fig, plt = get_axarray_fig_plt(None, nrows=nrows, ncols=ncols,
|
||||
sharex=True, sharey=False, squeeze=False)
|
||||
|
||||
df = self.get_energyterms_dataframe()
|
||||
|
||||
#for i, (item, ax) in enumerate(zip(items, ax_list.ravel())):
|
||||
# print(item, "\n", df[item])
|
||||
# df.plot(x=None, y=item, kind='bar', ax=ax, legend=i==0, fontsize=fontsize)
|
||||
|
||||
for i, (item, ax) in enumerate(zip(items, ax_list.ravel())):
|
||||
#values = [float(afile.energy_terms[item]) for afile in self.abifiles]
|
||||
bottom = 0
|
||||
width, pad = 4, 1
|
||||
pad = width + pad
|
||||
xticks, xticklabels = [], []
|
||||
x = 0
|
||||
for j, (label, abifile) in enumerate(self):
|
||||
height = float(abifile.energy_terms[item])
|
||||
if j == 0: h0 = height
|
||||
height -= h0
|
||||
ax.bar(x, height, width, bottom, align="center",
|
||||
label=label,
|
||||
#color=cmap(float(itype) / max(1, ntypat - 1)),
|
||||
edgecolor='black',
|
||||
#hatch=hatches[itype % len(hatches)] if hatches else None,
|
||||
)
|
||||
xticks.append(x)
|
||||
xticklabels.append(label)
|
||||
x += (width + pad) / 2
|
||||
|
||||
ax.set_xticks(xticks)
|
||||
ax.set_xticklabels((xticklabels))
|
||||
ax.legend(loc="best", fontsize=fontsize, shadow=False)
|
||||
|
||||
#rows, row_names = [], []
|
||||
#for label, gsr in self.items():
|
||||
# row_names.append(label)
|
||||
# rows.append(gsr.energy_terms)
|
||||
#row_names = row_names if not abspath else self._to_relpaths(row_names)
|
||||
#data = pd.DataFrame(rows, index=row_names, columns=list(rows[0].keys()))
|
||||
#ax, fig, plt = get_ax_fig_plt(ax=None)
|
||||
#sns.barplot(x="day", y="total_bill", hue="sex", data=data)
|
||||
|
||||
return fig
|
||||
|
||||
@add_fig_kwargs
|
||||
def gridplot_eos(self, eos_names="all", fontsize=6, **kwargs):
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -107,18 +107,17 @@ if __name__ == "__main__":
|
|||
#
|
||||
# abicomp.py ddb flow_mgb2_phonons_nkpt_tsmear/w*/outdata/*_DDB -ipy
|
||||
#
|
||||
# to build a robot from all the output DDB files and start the ipython shell.
|
||||
# to build a robot from the output DDB files and start the ipython shell.
|
||||
#
|
||||
# then, inside the ipython shell, use:
|
||||
#
|
||||
# .. code-block:: ipython
|
||||
#
|
||||
# In [1]: %matplotlib
|
||||
# In [2]: p = robot.anaget_phonon_plotters()
|
||||
# In [3]: p.phbands_plotter.combiplot()
|
||||
# In [2]: r = robot.anaget_phonon_plotters(nqsmall=0)
|
||||
# In [3]: r.phbands_plotter.gridplot_with_hue("tsmear")
|
||||
#
|
||||
# to compute the phonon bands and the DOS for all DDB files with Anaddb
|
||||
# and plot the results on the same figure.
|
||||
# to compute the phonon bands with Anaddb and plot the results groupe by "tsmear".
|
||||
#
|
||||
# .. image:: https://github.com/abinit/abipy_assets/blob/master/run_mgb2_edoses.png?raw=true
|
||||
# .. image:: https://github.com/abinit/abipy_assets/blob/master/run_mgb2_phonons_nkpt_tsmear.png?raw=true
|
||||
# :alt: Convergence of electronic DOS in MgB2 wrt k-points.
|
||||
|
|
|
|||
|
|
@ -728,8 +728,12 @@ Usage example:
|
|||
|
||||
TIP:
|
||||
|
||||
Use Unix find to select all files with the a given extension and pass them to abicomp.py.
|
||||
For instance:
|
||||
The python code operates on a list of files/directories passed via the command line interface.
|
||||
The arguments are interpreted by the shell before invoking the script.
|
||||
This means that one can use the bash syntax and the unix tools to precompute the list of files/directories.
|
||||
|
||||
For example, one can use Unix find to select all files with the a given extension and pass them to abicomp.py.
|
||||
For command:
|
||||
|
||||
abicomp.py structure `find . -name "*_GSR.nc"`
|
||||
|
||||
|
|
@ -744,6 +748,14 @@ and this trick can be used to select files/directories as in:
|
|||
|
||||
abicomp.py structure w1/t{2..4}/outdata/*_GSR.nc
|
||||
|
||||
The [!name] syntax can be used to exclude patterns, so
|
||||
|
||||
abicomp.py structure w1/t[!2]*/outdata/*_GSR.nc
|
||||
|
||||
excludes all the GSR.nc files in the t2/outdata directory.
|
||||
|
||||
See also http://wiki.bash-hackers.org/syntax/pattern
|
||||
|
||||
NOTE: The `gsr`, `ddb`, `sigres`, `mdf` commands use robots to analyze files.
|
||||
In this case, one can provide a list of files and/or list of directories on the command-line interface e.g.:
|
||||
|
||||
|
|
|
|||
|
|
@ -60,6 +60,20 @@ def set_axlims(ax, lims, axname):
|
|||
return left, right
|
||||
|
||||
|
||||
def set_visible(ax, boolean, *args):
|
||||
"""
|
||||
Hide/Show the artists of axis ax listed in args.
|
||||
"""
|
||||
if "legend" in args and ax.legend():
|
||||
ax.legend().set_visible(boolean)
|
||||
if "title" in args and ax.title:
|
||||
ax.title.set_visible(boolean)
|
||||
if "xlabel" in args and ax.xaxis.label:
|
||||
ax.xaxis.label.set_visible(boolean)
|
||||
if "ylabel" in args and ax.yaxis.label:
|
||||
ax.yaxis.label.set_visible(boolean)
|
||||
|
||||
|
||||
def rotate_ticklabels(ax, rotation, axname="x"):
|
||||
"""Rotate the ticklables of axis ``ax``"""
|
||||
if "x" in axname:
|
||||
|
|
|
|||
Loading…
Reference in New Issue