mirror of https://github.com/abinit/abipy.git
Replace old tensor objects with pmg tensors
This commit is contained in:
Matteo Giantomassi
parent
3d8ac10c87
commit
a4f35e1302
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@ -1,173 +0,0 @@
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# coding: utf-8
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"""
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This module contains classes representing tensors and helper functions to change lattice.
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"""
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from __future__ import print_function, division, unicode_literals, absolute_import
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import itertools
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import numpy as np
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from monty.dev import deprecated
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from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
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from abipy.core import Structure
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__all__ = [
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"Tensor",
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"SymmetricTensor",
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]
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def from_cart_to_red(cartesian_tensor,lattice):
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mat = lattice.inv_matrix
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red_tensor = np.dot(np.dot(np.transpose(mat), cartesian_tensor), mat)
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return red_tensor
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class Tensor(object):
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"""Representation of a 3x3 tensor"""
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# TODO Remove
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#@deprecated(message="abipy.core.Tensor is deprecated and will be replaced by pymatgen tensor in v0.4")
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def __init__(self, red_tensor, lattice, space="r"):
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"""
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Args:
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red_tensor: array-like object with the 9 cartesian components of the tensor
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lattice: Lattice object defining the reference system
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space:
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"r" if the lattice is a real space lattice
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"g" if the lattice is a reciprocal space lattice
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"""
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self._reduced_tensor = red_tensor
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self._lattice = lattice
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self.space = space
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if space == "g":
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self._is_real_space = False
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elif space == "r":
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self._is_real_space = True
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else:
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raise ValueError("space should be either 'g' or 'r'")
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def __eq__(self, other):
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if other is None: return False
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return (np.allclose(self.reduced_tensor, other.reduced_tensor) and
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self.lattice == other.lattice and
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self.space == other.space)
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def __ne__(self, other):
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return not (self == other)
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def __repr__(self):
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return self.to_string()
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def __str__(self):
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return repr(self)
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def to_string(self, verbose=0, with_reduced=False):
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lines = []
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app = lines.append
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app("Tensor in %s space." % self.space)
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app("")
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app("Cartesian coordinates:")
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app(str(self.cartesian_tensor))
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if with_reduced:
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app("")
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app(str(self.lattice))
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app("Reduced coordinates:")
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app(str(self.reduced_tensor))
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return "\n".join(lines)
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@property
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def lattice(self):
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return self._lattice
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@property
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def reduced_tensor(self):
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return self._reduced_tensor
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@property
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def is_real_space(self):
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return self._is_real_space
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@property
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def cartesian_tensor(self):
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mat = self._lattice.matrix
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return np.dot(np.dot(np.transpose(mat), self._reduced_tensor), mat)
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@classmethod
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def from_cartesian_tensor(cls, cartesian_tensor, lattice, space="r"):
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red_tensor = from_cart_to_red(cartesian_tensor, lattice)
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return cls(red_tensor, lattice,space)
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def symmetrize(self, structure):
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tensor = self._reduced_tensor
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if self._is_real_space:
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real_lattice = self._lattice
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else:
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real_lattice = self._lattice.reciprocal_lattice
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# I guess this is the reason why tensor.symmetrize (omega) is so slow!
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real_finder = SpacegroupAnalyzer(structure)
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real_symmops = real_finder.get_point_group_operations(cartesian=True)
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cartesian_tensor = self.cartesian_tensor
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sym_tensor = np.zeros((3,3))
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my_tensor = cartesian_tensor
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for real_sym in real_symmops:
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mat = real_sym.rotation_matrix
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prod_sym = np.dot(np.transpose(mat),np.dot(cartesian_tensor,mat))
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sym_tensor = sym_tensor + prod_sym
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sym_tensor = sym_tensor/len(real_symmops)
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self._reduced_tensor = from_cart_to_red(sym_tensor,self._lattice)
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class SymmetricTensor(Tensor):
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"""Representation of a 3x3 symmetric tensor"""
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@classmethod
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def from_directions(cls, qpoints, values, lattice, space):
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"""
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Build a `SymmetricTensor` from the values computed along 6 directions.
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Args:
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qpoints: fractional coordinates of 6 independent q-directions
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values: values of (q^T E q)/(q^T q) along the 6 qpoints
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lattice: `Lattice` object defining the reference system
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space: "r" if the lattice is a real space lattice
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"g" if the lattice is a reciprocal space lattice
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"""
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assert len(qpoints) == 6 and len(values) == len(qpoints)
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mat = lattice.matrix
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metric = np.dot(np.transpose(mat),mat)
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coeffs_red = np.zeros((6,6))
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for (iqpt,qpt) in enumerate(qpoints):
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metqpt = np.dot(metric,qpt)
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coeffs_red[iqpt,:] = [metqpt[0]**2,metqpt[1]**2,metqpt[2]**2,
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2*metqpt[0]*metqpt[1],2*metqpt[0]*metqpt[2],2*metqpt[1]*metqpt[2]]
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normqpt_red = np.dot(np.transpose(qpt),np.dot(metric,qpt))
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coeffs_red[iqpt,:] = coeffs_red[iqpt,:] / normqpt_red
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red_symm = np.linalg.solve(coeffs_red,values)
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red_tensor = [[red_symm[0],red_symm[3],red_symm[4]],
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[red_symm[3],red_symm[1],red_symm[5]],
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[red_symm[4],red_symm[5],red_symm[2]]]
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return cls(red_tensor, lattice, space)
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@ -1,52 +0,0 @@
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"""Tests for tensor"""
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from __future__ import print_function, division
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import numpy as np
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from pymatgen.core.structure import Structure
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from pymatgen.core.lattice import Lattice
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from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
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from abipy.core.tensor import *
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from abipy.core.testing import AbipyTest
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class TestTensor(AbipyTest):
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"""Unit tests for Tensor."""
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def test_tensor(self):
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"""Initialize Tensor"""
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lattice = Lattice.hexagonal(4,6)
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#rprimd = np.array([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]])
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#rprimd = rprimd*10
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#lattice = Lattice(rprimd)
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structure = Structure(lattice, ["Ga", "As"],
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[[0, 0, 0], [0.5, 0.5, 0.5]])
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#finder = SymmetryFinder(structure)
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finder = SpacegroupAnalyzer(structure)
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spacegroup = finder.get_space_group_operations()
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pointgroup = finder.get_point_group_symbol()
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cartesian_tensor = [[2,3,1.2],[3,4,1.0],[1.2,1.0,6]]
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tensor = Tensor.from_cartesian_tensor(cartesian_tensor,lattice.reciprocal_lattice,space="g")
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red_tensor = tensor.reduced_tensor
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tensor2 = Tensor(red_tensor,lattice.reciprocal_lattice,space="g")
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assert(((np.abs(tensor2.cartesian_tensor)-np.abs(cartesian_tensor)) < 1E-8).all())
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self.assertTrue(tensor==tensor2)
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print(tensor)
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#print("non-symmetrized cartesian_tensor = ",tensor2.cartesian_tensor)
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tensor2.symmetrize(structure)
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#print("symmetrized_cartesian_tensor = ",tensor2.cartesian_tensor)
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self.serialize_with_pickle(tensor)
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if __name__ == "__main__":
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import unittest
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unittest.main()
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@ -11,14 +11,13 @@ from collections import OrderedDict
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from monty.functools import lazy_property
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from monty.string import marquee
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from monty.termcolor import cprint
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from abipy.core.tensor import Tensor
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from abipy.core.mixins import AbinitNcFile, Has_Structure, NotebookWriter
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from abipy.abio.robots import Robot
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from abipy.iotools import ETSF_Reader
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from abipy.tools.plotting import add_fig_kwargs, get_axarray_fig_plt, rotate_ticklabels, set_visible
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from abipy.dfpt.phonons import InteratomicForceConstants
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from abipy.dfpt.ddb import Becs
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from abipy.dfpt.tensors import NLOpticalSusceptibilityTensor
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from abipy.dfpt.tensors import Tensor, DielectricTensor, NLOpticalSusceptibilityTensor
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from abipy.dfpt.elastic import ElasticData
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@ -91,6 +90,11 @@ class AnaddbNcFile(AbinitNcFile, Has_Structure, NotebookWriter):
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app("")
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app(self.structure.to_string(verbose=verbose, title="Structure"))
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import json
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app(marquee("Parameters", mark="="))
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app(json.dumps(self.params, indent=2, sort_keys=True))
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app("")
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if self.has_elastic_data:
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app("")
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df = self.elastic_data.get_average_elastic_dataframe(tensor="elastic_relaxed")
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@ -104,38 +108,58 @@ class AnaddbNcFile(AbinitNcFile, Has_Structure, NotebookWriter):
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app(df.T.to_string(index=True))
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if verbose:
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df = self.elastic_data.get_voigt_dataframe(["elastic_relaxed", "elastic_clamped"])
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df = self.elastic_data.get_voigt_dataframe()
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app(df.T.to_string())
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if self.emacro is not None:
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app("Macroscopic dielectric tensor (Cartesian coords)")
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app(str(self.emacro))
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app("")
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if self.emacro_rlx is not None:
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app("Relaxed ion Macroscopic dielectric tensor (Cartesian coords)")
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app(str(self.emacro_rlx))
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app("")
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#if self.becs is not None:
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if self.dchide is not None:
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app("Non-linear optical susceptibility tensor.")
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app(str(self.dchide))
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app("")
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if self.dchidt is not None:
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app("First-order change in the linear dielectric susceptibility.")
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app(str(self.dchidt))
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app("")
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#if self.has_piezoelectric_data:
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# df = self.elastic_data.get_piezoelectric_dataframe()
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#app(str(self.params))
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return "\n".join(lines)
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@lazy_property
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def emacro(self):
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"""
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Macroscopic dielectric tensor. None if the file does not contain this information.
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Macroscopic dielectric tensor.
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None if the file does not contain this information.
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"""
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try:
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return Tensor.from_cartesian_tensor(self.reader.read_value("emacro_cart"),
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self.structure.lattice, space="r")
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return DielectricTensor(self.reader.read_value("emacro_cart"))
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except Exception as exc:
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print(exc, "Returning None", sep="\n")
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#print(exc, "Returning None", sep="\n")
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return None
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@lazy_property
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def emacro_rlx(self):
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"""
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Relaxed ion Macroscopic dielectric tensor. None if the file does not contain this information.
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Relaxed ion Macroscopic dielectric tensor.
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None if the file does not contain this information.
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"""
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try:
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return Tensor.from_cartesian_tensor(self.reader.read_value("emacro_cart_rlx"),
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self.structure.lattice, space="r")
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return DielectricTensor(self.reader.read_value("emacro_cart_rlx"))
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except Exception as exc:
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print(exc, "Requires dieflag > 0", "Returning None", sep="\n")
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#print(exc, "Requires dieflag > 0", "Returning None", sep="\n")
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return None
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@lazy_property
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@ -147,7 +171,7 @@ class AnaddbNcFile(AbinitNcFile, Has_Structure, NotebookWriter):
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try:
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return Becs(self.reader.read_value("becs_cart"), self.structure, chneut=chneut, order="f")
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except Exception as exc:
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print(exc, "Returning None", sep="\n")
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#print(exc, "Returning None", sep="\n")
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return None
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@lazy_property
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@ -160,8 +184,8 @@ class AnaddbNcFile(AbinitNcFile, Has_Structure, NotebookWriter):
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try:
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return InteratomicForceConstants.from_file(self.filepath)
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except Exception as exc:
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print(exc)
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cprint("Interatomic force constants have not been calculated. Returning None", "red")
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#print(exc)
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#cprint("Interatomic force constants have not been calculated. Returning None", "red")
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return None
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@lazy_property
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@ -173,7 +197,7 @@ class AnaddbNcFile(AbinitNcFile, Has_Structure, NotebookWriter):
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try:
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return NLOpticalSusceptibilityTensor(self.reader.read_value("dchide"))
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except Exception as exc:
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print(exc, "Requires nlflag > 0", "Returning None", sep="\n")
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#print(exc, "Requires nlflag > 0", "Returning None", sep="\n")
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return None
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@lazy_property
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@ -186,19 +210,20 @@ class AnaddbNcFile(AbinitNcFile, Has_Structure, NotebookWriter):
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None if the file does not contain this information.
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"""
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try:
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a = self.reader.read_value("dchidt").T
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dchidt = []
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for i in a:
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d = []
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for j in i:
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d.append(Tensor.from_cartesian_tensor(j, self.structure.lattice, space="r"))
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dchidt.append(d)
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return dchidt
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a = self.reader.read_value("dchidt").T.copy()
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except Exception as exc:
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print(exc, "Requires 0 < nlflag < 3", "Returning None", sep="\n")
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#print(exc, "Requires 0 < nlflag < 3", "Returning None", sep="\n")
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return None
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dchidt = []
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for i in a:
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d = []
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for j in i:
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d.append(Tensor(j))
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dchidt.append(d)
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return dchidt
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@lazy_property
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def oscillator_strength(self):
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"""
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@ -209,7 +234,7 @@ class AnaddbNcFile(AbinitNcFile, Has_Structure, NotebookWriter):
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try:
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return self.reader.read_value("oscillator_strength", cmode="c")
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except Exception as exc:
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print(exc, "Oscillator strengths require dieflag == 1, 3 or 4", "Returning None", sep="\n")
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#print(exc, "Oscillator strengths require dieflag == 1, 3 or 4", "Returning None", sep="\n")
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return None
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@lazy_property
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@ -313,7 +338,6 @@ class AnaddbNcRobot(Robot):
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rows.append(d)
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#index = index if not abspath else self._to_relpaths(index)
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return pd.DataFrame(rows, index=index, columns=list(rows[0].keys() if rows else None))
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@add_fig_kwargs
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@ -16,7 +16,6 @@ from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, get_axarray_fig
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from abipy.core.func1d import Function1D
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from abipy.core.kpoints import Kpoint, KpointList
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from abipy.core.mixins import AbinitNcFile, Has_Structure, NotebookWriter
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from abipy.core.tensor import SymmetricTensor
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from abipy.iotools import ETSF_Reader
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from abipy.tools.plotting import set_axlims
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from abipy.tools import duck
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@ -54,7 +53,7 @@ class DielectricTensor(object):
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# One tensor for each frequency
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all_tensors = []
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for ifrq, freq in enumerate(mdf.wmesh):
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tensor = SymmetricTensor.from_directions(mdf.qfrac_coords, all_emacros[:,ifrq],
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tensor = _SymmetricTensor.from_directions(mdf.qfrac_coords, all_emacros[:,ifrq],
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structure.lattice.reciprocal_lattice, space="g")
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all_tensors.append(tensor)
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@ -1023,3 +1022,159 @@ class MdfRobot(Robot, RobotWithEbands):
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nb.cells.extend(self.get_ebands_code_cells())
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return self._write_nb_nbpath(nb, nbpath)
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def _from_cart_to_red(cartesian_tensor,lattice):
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mat = lattice.inv_matrix
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red_tensor = np.dot(np.dot(np.transpose(mat), cartesian_tensor), mat)
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return red_tensor
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# TODO Remove
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#@deprecated(message="abipy.core.Tensor is deprecated and will be replaced by pymatgen tensor in v0.4")
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class _Tensor(object):
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"""Representation of a 3x3 tensor"""
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def __init__(self, red_tensor, lattice, space="r"):
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"""
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Args:
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red_tensor: array-like object with the 9 cartesian components of the tensor
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lattice: Lattice object defining the reference system
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space:
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"r" if the lattice is a real space lattice
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"g" if the lattice is a reciprocal space lattice
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"""
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self._reduced_tensor = red_tensor
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self._lattice = lattice
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self.space = space
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if space == "g":
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self._is_real_space = False
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elif space == "r":
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self._is_real_space = True
|
||||
else:
|
||||
raise ValueError("space should be either 'g' or 'r'")
|
||||
|
||||
def __eq__(self, other):
|
||||
if other is None: return False
|
||||
return (np.allclose(self.reduced_tensor, other.reduced_tensor) and
|
||||
self.lattice == other.lattice and
|
||||
self.space == other.space)
|
||||
|
||||
def __ne__(self, other):
|
||||
return not (self == other)
|
||||
|
||||
def __repr__(self):
|
||||
return self.to_string()
|
||||
|
||||
def __str__(self):
|
||||
return repr(self)
|
||||
|
||||
def to_string(self, verbose=0, with_reduced=False):
|
||||
lines = []
|
||||
app = lines.append
|
||||
|
||||
app("Tensor in %s space." % self.space)
|
||||
app("")
|
||||
app("Cartesian coordinates:")
|
||||
app(str(self.cartesian_tensor))
|
||||
|
||||
if with_reduced:
|
||||
app("")
|
||||
app(str(self.lattice))
|
||||
app("Reduced coordinates:")
|
||||
app(str(self.reduced_tensor))
|
||||
|
||||
return "\n".join(lines)
|
||||
|
||||
@property
|
||||
def lattice(self):
|
||||
return self._lattice
|
||||
|
||||
@property
|
||||
def reduced_tensor(self):
|
||||
return self._reduced_tensor
|
||||
|
||||
@property
|
||||
def is_real_space(self):
|
||||
return self._is_real_space
|
||||
|
||||
@property
|
||||
def cartesian_tensor(self):
|
||||
mat = self._lattice.matrix
|
||||
return np.dot(np.dot(np.transpose(mat), self._reduced_tensor), mat)
|
||||
|
||||
@classmethod
|
||||
def from_cartesian_tensor(cls, cartesian_tensor, lattice, space="r"):
|
||||
red_tensor = _from_cart_to_red(cartesian_tensor, lattice)
|
||||
return cls(red_tensor, lattice,space)
|
||||
|
||||
def symmetrize(self, structure):
|
||||
tensor = self._reduced_tensor
|
||||
|
||||
if self._is_real_space:
|
||||
real_lattice = self._lattice
|
||||
else:
|
||||
real_lattice = self._lattice.reciprocal_lattice
|
||||
|
||||
# I guess this is the reason why tensor.symmetrize (omega) is so slow!
|
||||
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
|
||||
real_finder = SpacegroupAnalyzer(structure)
|
||||
|
||||
real_symmops = real_finder.get_point_group_operations(cartesian=True)
|
||||
|
||||
cartesian_tensor = self.cartesian_tensor
|
||||
|
||||
sym_tensor = np.zeros((3,3))
|
||||
|
||||
my_tensor = cartesian_tensor
|
||||
|
||||
for real_sym in real_symmops:
|
||||
mat = real_sym.rotation_matrix
|
||||
prod_sym = np.dot(np.transpose(mat),np.dot(cartesian_tensor,mat))
|
||||
sym_tensor = sym_tensor + prod_sym
|
||||
|
||||
sym_tensor = sym_tensor/len(real_symmops)
|
||||
|
||||
self._reduced_tensor = _from_cart_to_red(sym_tensor,self._lattice)
|
||||
|
||||
|
||||
class _SymmetricTensor(_Tensor):
|
||||
"""Representation of a 3x3 symmetric tensor"""
|
||||
|
||||
@classmethod
|
||||
def from_directions(cls, qpoints, values, lattice, space):
|
||||
"""
|
||||
Build a `_SymmetricTensor` from the values computed along 6 directions.
|
||||
|
||||
Args:
|
||||
qpoints: fractional coordinates of 6 independent q-directions
|
||||
values: values of (q^T E q)/(q^T q) along the 6 qpoints
|
||||
lattice: `Lattice` object defining the reference system
|
||||
space: "r" if the lattice is a real space lattice
|
||||
"g" if the lattice is a reciprocal space lattice
|
||||
"""
|
||||
assert len(qpoints) == 6 and len(values) == len(qpoints)
|
||||
|
||||
mat = lattice.matrix
|
||||
metric = np.dot(np.transpose(mat),mat)
|
||||
|
||||
coeffs_red = np.zeros((6,6))
|
||||
|
||||
for (iqpt,qpt) in enumerate(qpoints):
|
||||
metqpt = np.dot(metric,qpt)
|
||||
|
||||
coeffs_red[iqpt,:] = [metqpt[0]**2,metqpt[1]**2,metqpt[2]**2,
|
||||
2*metqpt[0]*metqpt[1],2*metqpt[0]*metqpt[2],2*metqpt[1]*metqpt[2]]
|
||||
|
||||
normqpt_red = np.dot(np.transpose(qpt),np.dot(metric,qpt))
|
||||
|
||||
coeffs_red[iqpt,:] = coeffs_red[iqpt,:] / normqpt_red
|
||||
|
||||
red_symm = np.linalg.solve(coeffs_red,values)
|
||||
|
||||
red_tensor = [[red_symm[0],red_symm[3],red_symm[4]],
|
||||
[red_symm[3],red_symm[1],red_symm[5]],
|
||||
[red_symm[4],red_symm[5],red_symm[2]]]
|
||||
|
||||
return cls(red_tensor, lattice, space)
|
||||
|
|
|
|||
|
|
@ -74,7 +74,7 @@ TODO list:
|
|||
|
||||
* Scheduler should report info on exceptions (especially if at the end when on_all_ok is invoked)
|
||||
|
||||
* Replace core.tensor with pymatgen tensor (postponed to v0.4)
|
||||
* ALMOST DONE: Replace core.tensor with pymatgen tensor
|
||||
Check DielectricTensor in Anaddb from DDB.
|
||||
Use pmg tensor for stress as well.
|
||||
|
||||
|
|
|
|||
|
|
@ -116,14 +116,6 @@ core Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tensor` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: abipy.core.tensor
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`testing` Module
|
||||
---------------------
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue