mirror of https://github.com/abinit/abipy.git
Preparing refactoring in robots
This commit is contained in:
Matteo Giantomassi
parent
2a2e5ef427
commit
5bbfc64d66
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@ -33,16 +33,16 @@ from abipy.abio.robots import GsrRobot, SigresRobot, MdfRobot, DdbRobot, abirobo
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from abipy.abio.inputs import AbinitInput, MultiDataset, AnaddbInput, OpticInput
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from abipy.abio.abivars import AbinitInputFile
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from abipy.abio.factories import *
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#from abipy.electrons import ElectronBands, ElectronDosPlotter, ElectronBandsPlotter
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from abipy.electrons.ebands import ElectronBands, ElectronDosPlotter, ElectronBandsPlotter, ebands_gridplot
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from abipy.electrons.ebands import (ElectronBands, ElectronDosPlotter, ElectronBandsPlotter,
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ebands_gridplot, ebands_animate)
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from abipy.electrons.gsr import GsrFile
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from abipy.electrons.psps import PspsFile
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from abipy.electrons.gw import SigresFile, SigresPlotter
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from abipy.electrons.bse import MdfFile
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from abipy.electrons.scissors import ScissorsBuilder
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from abipy.electrons.scr import ScrFile
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#from abipy.dfpt import PhbstFile, PhononBands, PhdosFile, PhdosReader
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from abipy.dfpt.phonons import PhbstFile, PhononBands, PhdosFile, PhdosReader, phbands_gridplot
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from abipy.dfpt.phonons import (PhbstFile, PhononBands, PhdosFile, PhdosReader,
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phbands_gridplot)
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from abipy.dfpt.ddb import DdbFile
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from abipy.dfpt.anaddbnc import AnaddbNcFile
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from abipy.dynamics.hist import HistFile
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@ -141,6 +141,16 @@ def abiopen(filepath):
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return cls.from_file(filepath)
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def print_frame(x):
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"""
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Print entire pandas DataFrame.
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"""
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import pandas as pd
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with pd.option_context('display.max_rows', len(x),
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'display.max_columns', len(list(x.keys()))):
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print(x)
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def software_stack():
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"""
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Import all the hard dependencies. Returns ordered dict: package --> string with version info.
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@ -75,8 +75,11 @@ class Robot(object):
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for label, ncfile in args:
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self.add_file(label, ncfile)
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#@abstractmethod
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#def get_dataframe(self, **kwargs):
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@classmethod
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def for_ext(cls, ext):
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def class_for_ext(cls, ext):
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"""Return the Robot subclass associated to the given extension."""
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for subcls in cls.__subclasses__():
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if subcls.EXT in (ext, ext.upper()):
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@ -86,6 +89,9 @@ class Robot(object):
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"The list of supported extensions is:\n%s" %
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[cls.EXT for cls in Robot.__subclasses__()])
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# Deprecated. Use class_for_ext
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for_ext = class_for_ext
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@classmethod
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def from_dir(cls, top, walk=True):
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"""
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@ -116,6 +122,19 @@ class Robot(object):
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return cls(*items)
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@classmethod
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def from_files(cls, filenames):
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"""
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Build a Robot from a list of files.
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"""
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from abipy.abilab import abiopen
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filenames = [f for f in filenames if f.endswith(cls.EXT + ".nc") or f.endswith(cls.EXT)]
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items = []
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for f in filenames:
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ncfile = abiopen(os.path.join(dirpath, f))
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if ncfile is not None: items.append((ncfile.filepath, ncfile))
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return cls(*items)
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@classmethod
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def from_flow(cls, flow, outdirs="all", nids=None):
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"""
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@ -166,7 +185,9 @@ class Robot(object):
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return robot
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def add_extfile_of_node(self, node, nids=None):
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"""Add the file produced by this node to the robot."""
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"""
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Add the file produced by this node to the robot.
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"""
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if nids and node.node_id not in nids: return
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filepath = node.outdir.has_abiext(self.EXT)
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if filepath:
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@ -231,7 +252,7 @@ class Robot(object):
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lines = ["%s with %d files in memory" % (self.__class__.__name__, len(self.ncfiles))]
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for i, f in enumerate(self.ncfiles):
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path = f.relpath if len(f.relpath) < len(f.filepath) else f.filepath
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lines.append(" [%d] %s" % (i, path))
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lines.append(" [%d] %s" % (i, path))
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return "\n".join(lines)
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__str__ = __repr__
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@ -281,18 +302,6 @@ class Robot(object):
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if nids is not None: raise ValueError("nids cannot be used when obj is a directory.")
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return cls.from_dir(obj)
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@staticmethod
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def _get_geodict(structure):
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"""
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Return a dictionary with info on the structure (used to build pandas dataframes).
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"""
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abc, angles = structure.lattice.abc, structure.lattice.angles
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return dict(
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a=abc[0], b=abc[1], c=abc[2], volume=structure.volume,
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angle0=angles[0], angle1=angles[1], angle2=angles[2],
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formula=structure.formula,
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)
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def _exec_funcs(self, funcs, arg):
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"""
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Execute list of callables funcs. Each func receives arg as argument.
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@ -342,30 +351,28 @@ class GsrRobot(Robot, NotebookWriter):
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the pandas :class:`DataFrame`
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funcs:
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Function or list of functions to execute to add more data to the DataFrame.
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Each function receives a GsrFile object and returns a tuple (key, value)
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Each function receives a :class:`GsrFile` object and returns a tuple (key, value)
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where key is a string with the name of column and value is the value to be inserted.
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"""
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# TODO add more columns
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# Add attributes specified by the users
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attrs = [
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"nsppol", "ecut", "pawecutdg", #"nspinor", "nspden", #"magnetization",
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"tsmear", "nkpts", "energy", "pressure", "max_force",
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"energy", "pressure", "max_force",
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"ecut", "pawecutdg",
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"tsmear", "nkpts",
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"nsppol", "nspinor", "nspden",
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] + kwargs.pop("attrs", [])
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rows, row_names = [], []
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for label, gsr in self:
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row_names.append(label)
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#d = {aname: getattr(gsr, aname) for aname in attrs}
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d = {}
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d = OrderedDict()
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for aname in attrs:
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try:
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d[aname] = getattr(gsr, aname)
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except NetcdfReaderError:
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pass
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d[aname] = getattr(gsr, aname, None)
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# Add info on structure.
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if kwargs.get("with_geo", True):
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d.update(self._get_geodict(gsr.structure))
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d.update(gsr.structure.get_geodict())
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# Execute funcs.
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d.update(self._exec_funcs(kwargs.get("funcs", []), gsr))
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@ -432,7 +439,9 @@ class GsrRobot(Robot, NotebookWriter):
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class SigresRobot(Robot):
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"""This robot analyzes the results contained in multiple SIGRES files."""
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"""
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This robot analyzes the results contained in multiple SIGRES files.
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"""
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EXT = "SIGRES"
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def merge_dataframes_sk(self, spin, kpoint, **kwargs):
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@ -458,7 +467,9 @@ class SigresRobot(Robot):
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rows, row_names = [], []
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for label, sigr in self:
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row_names.append(label)
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d = {aname: getattr(sigr, aname) for aname in attrs}
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d = OrderedDict()
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for aname in attrs:
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d[aname] = getattr(sig, aname, None)
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d.update({"qpgap": sigr.get_qpgap(spin, kpoint)})
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# Add convergence parameters
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@ -466,7 +477,7 @@ class SigresRobot(Robot):
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# Add info on structure.
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if kwargs.get("with_geo", False):
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d.update(self._get_geodict(sigr.structure))
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d.update(sigr.structure.get_geodict())
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# Execute funcs.
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d.update(self._exec_funcs(kwargs.get("funcs", []), sigr))
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@ -490,7 +501,9 @@ class SigresRobot(Robot):
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class MdfRobot(Robot):
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"""This robot analyzes the results contained in multiple MDF files."""
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"""
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This robot analyzes the results contained in multiple MDF files.
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"""
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EXT = "MDF.nc"
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def get_mdf_plotter(self):
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@ -504,11 +517,11 @@ class MdfRobot(Robot):
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rows, row_names = [], []
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for i, (label, mdf) in enumerate(self):
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row_names.append(label)
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d = dict(
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exc_mdf=mdf.exc_mdf,
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rpa_mdf=mdf.rpanlf_mdf,
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gwrpa_mdf=mdf.gwnlf_mdf,
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)
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d = OrderedDict([
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("exc_mdf", mdf.exc_mdf),
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("rpa_mdf", mdf.rpanlf_mdf),
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("gwrpa_mdf", mdf.gwnlf_mdf),
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])
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#d = {aname: getattr(mdf, aname) for aname in attrs}
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#d.update({"qpgap": mdf.get_qpgap(spin, kpoint)})
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@ -517,7 +530,7 @@ class MdfRobot(Robot):
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# Add info on structure.
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if kwargs.get("with_geo", False):
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d.update(self._get_geodict(mdf.structure))
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d.update(mdf.structure.get_geodict())
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# Execute funcs.
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d.update(self._exec_funcs(kwargs.get("funcs", []), mdf))
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@ -550,7 +563,9 @@ class DdbRobot(Robot):
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@property
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def qpoints_union(self):
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"""Return numpy array with the q-points in reduced coordinates found in the DDB files."""
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"""
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Return numpy array with the q-points in reduced coordinates found in the DDB files.
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"""
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qpoints = []
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for (label, ddb) in enumerate(self):
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qpoints.extend(q for q in ddb.qpoints if q not in qpoints)
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@ -585,7 +600,7 @@ class DdbRobot(Robot):
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rows, row_names = [], []
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for i, (label, ddb) in enumerate(self):
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row_names.append(label)
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d = dict(
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d = OrderedDict(
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# exc_mdf=mdf.exc_mdf,
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)
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#d = {aname: getattr(ddb, aname) for aname in attrs}
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@ -602,7 +617,7 @@ class DdbRobot(Robot):
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# Add info on structure.
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if kwargs.get("with_geo", True):
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d.update(self._get_geodict(phbands.structure))
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d.update(phbands.structure.get_geodict())
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# Execute funcs.
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d.update(self._exec_funcs(kwargs.get("funcs", []), ddb))
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@ -549,6 +549,35 @@ class Structure(pymatgen.Structure):
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return np.sqrt(self.dot(coords, coords, space=space,
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frac_coords=frac_coords))
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def get_geodict(self, with_spglib=True):
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"""
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Return a :class:`OrderedDict` with the most important structural parameters:
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- Chemical formula and number of atoms.
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- Lattice lengths, angles and volume.
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- The spacegroup number computed by Abinit (set to None if not available).
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- The spacegroup number and symbol computed by spglib (set to None not `with_spglib`).
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Useful to construct pandas DataFrames
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Args:
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with_spglib: If True, spglib is invoked to get the spacegroup symbol and number
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"""
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abc, angles = self.lattice.abc, self.lattice.angles
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# Get spacegroup info from spglib.
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spglib_symbol, spglib_number = None, None
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if with_spglib: spglib_symbol, spglib_number = self.get_spacegroup_info()
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# Get spacegroup number computed by Abinit if available.
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abispg_number = None if self.spacegroup is None else self.spacegroup.spgid
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return OrderedDict([
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("formula", self.formula), ("num_sites", self.num_sites),
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("angle0", angles[0]), ("angle1", angles[1]), ("angle2", angles[2]),
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("a", abc[0]), ("b", abc[1]), ("c", abc[2]), ("volume", self.volume),
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("abispg_num", abispg_number),
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("spglib_symb", spglib_symbol), ("spglib_num", spglib_number),
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])
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def show_bz(self, **kwargs):
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"""
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Gives the plot (as a matplotlib object) of the symmetry line path in the Brillouin Zone.
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@ -630,29 +659,6 @@ class Structure(pymatgen.Structure):
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else:
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raise visu.Error("Don't know how to export data for %s" % visu_name)
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def molecular_viewer(self, **kwargs):
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#from chemview import enable_notebook, MolecularViewer
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from chemview import MolecularViewer
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#from pymatgen.core.bonds import CovalentBond, get_bond_length
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#bonds = []
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#for j, site1 in enumerate(self):
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# for i, site2 in enumerate(self):
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# if j <= i: continue
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# if CovalentBond.is_bonded(site1, site2, tol=0.2):
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# bonds.append((i, j))
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#bonds = self.get_covalent_bonds(tol=0.2)
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#bonds=[(0, 1), (1, 0)]
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bonds = [(0, 0), (1, 1)]
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topology = dict(
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atom_types=[site.specie.symbol for site in self],
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bonds=bonds,
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)
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v = MolecularViewer(self.cart_coords, topology, **kwargs)
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return v
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def write_structure(self, filename):
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"""Write structure fo file."""
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if filename.endswith(".nc"):
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@ -1418,32 +1424,15 @@ def frame_from_structures(struct_objects, index=None, with_spglib=True):
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Support filenames, structure objects, Abinit input files, dicts and many more types.
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See `Structure.as_structure` for the complete list.
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index: Index of the dataframe.
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with_spglib: If True, spglib is invoked to get the spacegroup symbol and number
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with_spglib: If True, spglib is invoked to get the spacegroup symbol and number.
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Return:
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pandas :class:`DataFrame`
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"""
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structures = [Structure.as_structure(obj) for obj in struct_objects]
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dict_list = []
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for structure in structures:
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abc, angles = structure.lattice.abc, structure.lattice.angles
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# Get spacegroup info from spglib.
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spglib_symbol, spglib_number = None, None
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if with_spglib:
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spglib_symbol, spglib_number = structure.get_spacegroup_info()
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# Get spacegroup number computed by Abinit if available.
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abispg_number = None if structure.spacegroup is None else structure.spacegroup.spgid
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# Use OrderedDict to have columns ordered nicely.
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dict_list.append(OrderedDict([
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("formula", structure.formula), ("num_sites", structure.num_sites),
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("angle0", angles[0]), ("angle1", angles[1]), ("angle2", angles[2]),
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("a", abc[0]), ("b", abc[1]), ("c", abc[2]), ("volume", structure.volume),
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("abispg_num", abispg_number),
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("spglib_symb", spglib_symbol), ("spglib_num", spglib_number),
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]))
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# Use OrderedDict to have columns ordered nicely.
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odict_list = [(structure.get_geodict(with_spglib=with_spglib)) for structure in structures]
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import pandas as pd
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return pd.DataFrame(dict_list, index=index,
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columns=list(dict_list[0].keys()) if dict_list else None)
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return pd.DataFrame(odict_list, index=index,
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columns=list(odict_list[0].keys()) if odict_list else None)
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@ -28,6 +28,9 @@ class TestStructure(AbipyTest):
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# Call pymatgen machinery to get the high-symmetry stars.
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print(structure.hsym_stars)
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geodict = structure.get_geodict()
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assert geodict["abispg_num"] is not None
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if self.which("xcrysden") is not None:
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# Export data in Xcrysden format.
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structure.export(".xsf")
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@ -7,15 +7,143 @@ import argparse
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from abipy import abilab
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def abicomp_struct(options):
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"""
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Compare crystalline structures.
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"""
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paths = options.paths
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index = [os.path.relpath(p) for p in paths]
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frame = abilab.frame_from_structures(paths, index=None)
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print("File list:")
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for i, p in enumerate(paths):
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print("%d %s" % (i, p))
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print()
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abilab.print_frame(frame)
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return 0
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def abicomp_ebands(options):
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"""
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Plot electron bands on a grid.
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"""
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paths = options.paths
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eb_objects = paths
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titles = paths
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abilab.ebands_gridplot(eb_objects, titles=titles, edos_objects=None, edos_kwargs=None)
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#animate = True
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#if animate:
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# abilab.ebands_animate(eb_objects, edos_objects=None, edos_kwargs=None,
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# interval=250, savefile=None, show=True)
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return 0
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def abicomp_phbands(options):
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"""
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Plot phonon bands on a grid.
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"""
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paths = options.paths
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phb_objects = paths
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titles = paths
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abilab.phbands_gridplot(phb_objects, titles=titles, phdos_objects=None, phdos_kwargs=None)
|
||||
return 0
|
||||
|
||||
|
||||
#def abicomp_pseudos(options):
|
||||
# paths = options.paths
|
||||
# index = [os.path.relpath(p) for p in paths]
|
||||
# frame = abilab.frame_from_pseudos(paths, index=None)
|
||||
# print("File list:")
|
||||
# for i, p in enumerate(paths):
|
||||
# print("%d %s" % (i, p))
|
||||
# print()
|
||||
# abilab.print_frame(frame)
|
||||
# return 0
|
||||
|
||||
|
||||
def abicomp_robot(options):
|
||||
"""
|
||||
Analyze multiple files with a robot. The command has two different variants.
|
||||
|
||||
[1] The files can be listed explicitly as in:
|
||||
|
||||
abicomp.py robot out1_GSR.nc out1_GSR.nc
|
||||
|
||||
or, alternatively, with the shell syntax:
|
||||
|
||||
abicomp.py robot *_GSR.nc
|
||||
|
||||
[2] It's possible to use a directory as the first (and only) argument
|
||||
of the robot command followed by the Abinit file extension as in:
|
||||
|
||||
abicomp.py robot . GSR.nc
|
||||
|
||||
By default, the script with call `robot.get_dataframe()` to create an print a table
|
||||
with the most important results. For finer control, use --ipython to start an ipython
|
||||
console to interact with the robot directly.
|
||||
"""
|
||||
# To define an Help action
|
||||
#http://stackoverflow.com/questions/20094215/argparse-subparser-monolithic-help-output?rq=1
|
||||
paths = options.paths
|
||||
|
||||
# Temp code
|
||||
robot = abilab.abirobot(".", "GSR")
|
||||
print(robot)
|
||||
abilab.print_frame(robot.get_dataframe())
|
||||
return 0
|
||||
|
||||
if os.path.isdir(paths[0]):
|
||||
# Directory + extension
|
||||
top, ext = paths[:2]
|
||||
cls = Robot.class_for_ext(ext)
|
||||
robot = cls.from_dir(top, walk=True)
|
||||
else:
|
||||
# File list.
|
||||
#cls = Robot.class_for_ext(ext)
|
||||
robot = Robot.from_files(paths)
|
||||
|
||||
if options.ipython:
|
||||
import IPython
|
||||
IPython.embed(header=str(robot) + "\nType `robot` in the terminal and use <TAB> to list its methods", robot=robot)
|
||||
elif options.notebook:
|
||||
robot.make_and_open_notebook(nbpath=None, daemonize=True)
|
||||
else:
|
||||
print(robot)
|
||||
abilab.print_frame(robot.get_dataframe())
|
||||
|
||||
return 0
|
||||
|
||||
def abicomp_gs_scf(options):
|
||||
"""
|
||||
Compare ground-state SCF cycles.
|
||||
"""
|
||||
paths = options.paths
|
||||
f0 = abilab.AbinitOutputFile(paths[0])
|
||||
f0.compare_gs_scf_cycles(paths[1:])
|
||||
return 0
|
||||
|
||||
|
||||
def abicomp_dfpt2_scf(options):
|
||||
"""
|
||||
Compare DFPT SCF cycles.
|
||||
"""
|
||||
paths = options.paths
|
||||
f0 = abilab.AbinitOutputFile(paths[0])
|
||||
f0.compare_d2de_scf_cycles(paths[1:])
|
||||
return 0
|
||||
|
||||
|
||||
def main():
|
||||
def str_examples():
|
||||
return """\
|
||||
Usage example:\n
|
||||
|
||||
abidiff.py struct */*/outdata/out_GSR.nc => Compare structures in multiple files.
|
||||
abidiff.py ebands out1_GSR.nc out2_GSR.nc => Plot electron bands on a grid.
|
||||
abidiff.py gs_scf run1.abo run2.abo => Compare the SCF cycles in two output files.
|
||||
abidiff.py dfpt2_scf => Compare the DFPT SCF cycles in two output files.
|
||||
Usage example:
|
||||
abidiff.py struct */*/outdata/out_GSR.nc => Compare structures in multiple files.
|
||||
abidiff.py ebands out1_GSR.nc out2_GSR.nc => Plot electron bands on a grid.
|
||||
abidiff.py phbands out1_PHBST.nc out2_PHBST.nc => Plot electron bands on a grid.
|
||||
abidiff.py gs_scf run1.abo run2.abo => Compare the SCF cycles in two output files.
|
||||
abidiff.py dfpt2_scf => Compare the DFPT SCF cycles in two output files.
|
||||
"""
|
||||
|
||||
def show_examples_and_exit(err_msg=None, error_code=1):
|
||||
|
|
@ -41,20 +169,26 @@ Usage example:\n
|
|||
# Create the parsers for the sub-commands
|
||||
subparsers = parser.add_subparsers(dest='command', help='sub-command help', description="Valid subcommands")
|
||||
|
||||
# Subparser for gs_scf command.
|
||||
p_gs_scf = subparsers.add_parser('gs_scf', parents=[copts_parser], help="Compare ground-state SCF cycles.")
|
||||
|
||||
# Subparser for dfpt2_scf command.
|
||||
p_dftp2_scf = subparsers.add_parser('dfpt2_scf', parents=[copts_parser], help="Compare DFPT SCF cycles.")
|
||||
|
||||
# Subparser for struct command.
|
||||
p_struct = subparsers.add_parser('struct', parents=[copts_parser], help="Compare crystalline structures.")
|
||||
p_struct = subparsers.add_parser('struct', parents=[copts_parser], help=abicomp_struct.__doc__)
|
||||
|
||||
# Subparser for ebands command.
|
||||
p_ebands = subparsers.add_parser('ebands', parents=[copts_parser], help="Compare electron bands.")
|
||||
p_ebands = subparsers.add_parser('ebands', parents=[copts_parser], help=abicomp_ebands.__doc__)
|
||||
|
||||
# Subparser for gsr command.
|
||||
#p_gsr = subparsers.add_parser('gsr', parents=[copts_parser], help="Compare electron bands.")
|
||||
# Subparser for phbands command.
|
||||
p_phbands = subparsers.add_parser('phbands', parents=[copts_parser], help=abicomp_phbands.__doc__)
|
||||
|
||||
# Subparser for pseudos command.
|
||||
#p_pseudos = subparsers.add_parser('pseudos', parents=[copts_parser], help=abicomp_pseudos.__doc__)
|
||||
|
||||
# Subparser for robot command.
|
||||
p_robot = subparsers.add_parser('robot', parents=[copts_parser], help=abicomp_robot.__doc__)
|
||||
|
||||
# Subparser for gs_scf command.
|
||||
p_gs_scf = subparsers.add_parser('gs_scf', parents=[copts_parser], help=abicomp_gs_scf.__doc__)
|
||||
|
||||
# Subparser for dfpt2_scf command.
|
||||
p_dftp2_scf = subparsers.add_parser('dfpt2_scf', parents=[copts_parser], help=abicomp_dfpt2_scf.__doc__)
|
||||
|
||||
# Parse the command line.
|
||||
try:
|
||||
|
|
@ -76,37 +210,8 @@ Usage example:\n
|
|||
#sns.set(style='ticks', palette='Set2')
|
||||
#sns.despine()
|
||||
|
||||
paths = options.paths
|
||||
|
||||
if options.command == "gs_scf":
|
||||
f0 = abilab.AbinitOutputFile(paths[0])
|
||||
f0.compare_gs_scf_cycles(paths[1:])
|
||||
|
||||
elif options.command == "dfpt2_scf":
|
||||
f0 = abilab.AbinitOutputFile(paths[0])
|
||||
f0.compare_d2de_scf_cycles(paths[1:])
|
||||
|
||||
elif options.command == "struct":
|
||||
index = [os.path.relpath(p) for p in paths]
|
||||
frame = abilab.frame_from_structures(paths, index=None)
|
||||
print("File list:")
|
||||
for i, p in enumerate(paths):
|
||||
print("%d %s" % (i, p))
|
||||
print()
|
||||
print(frame)
|
||||
|
||||
elif options.command == "ebands":
|
||||
eb_objects = paths
|
||||
titles = paths
|
||||
abilab.ebands_gridplot(eb_objects, titles=titles, edos_objects=None, edos_kwargs=None)
|
||||
|
||||
else:
|
||||
raise RuntimeError("Don't know what to do with command: %s!" % options.command)
|
||||
|
||||
# Dispatch
|
||||
#return globals()["dojo_" + options.command](options)
|
||||
|
||||
return 0
|
||||
return globals()["abicomp_" + options.command](options)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
|
|
|||
Loading…
Reference in New Issue