Source code for chemcoord.internal_coordinates.zmat_functions

# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function,
                        unicode_literals, with_statement)

import numpy as np
import sympy

from chemcoord import export
from chemcoord.internal_coordinates.zmat_class_main import Zmat

[docs]class DummyManipulation(object): """Contextmanager that controls the behaviour of :meth:`~chemcoord.Zmat.safe_loc` and :meth:`~chemcoord.Zmat.safe_iloc`. In the following examples it is assumed, that using the assignment with :meth:`~chemcoord.Zmat.safe_loc` would lead to an invalid reference. Then there are two possible usecases:: with DummyManipulation(zmat, True): zmat.safe_loc[...] = ... # This inserts required dummy atoms and removes them, # if they are not needed anymore. # Removes only dummy atoms, that were automatically inserted. with DummyManipulation(zmat, False): zmat.safe_loc[...] = ... # This raises an exception # :class:`~chemcoord.exceptions.InvalidReference`. # which can be handled appropiately. # The zmat instance is unmodified, if an exception was raised. """ def __init__(self, dummy_manipulation_allowed, cls=None): if cls is None: cls = Zmat self.cls = cls self.dummy_manipulation_allowed = dummy_manipulation_allowed self.old_value = self.cls.dummy_manipulation_allowed def __enter__(self): self.cls.dummy_manipulation_allowed = self.dummy_manipulation_allowed def __exit__(self, exc_type, exc_value, traceback): self.cls.dummy_manipulation_allowed = self.old_value
[docs]class TestOperators(object): """Switch the validity testing of zmatrices resulting from operators. The following examples is done with ``+`` it is assumed, that adding ``zmat_1`` and ``zmat_2`` leads to a zmatrix with an invalid reference:: with TestOperators(True): zmat_1 + zmat_2 # Raises InvalidReference Exception """ def __init__(self, test_operators, cls=None): if cls is None: cls = Zmat self.cls = cls self.test_operators = test_operators self.old_value = self.cls.test_operators def __enter__(self): self.cls.test_operators = self.test_operators def __exit__(self, exc_type, exc_value, traceback): self.cls.test_operators = self.old_value
[docs]def apply_grad_cartesian_tensor(grad_X, zmat_dist): """Apply the gradient for transformation to cartesian space onto zmat_dist. Args: grad_X (:class:`numpy.ndarray`): A ``(3, n, n, 3)`` array. The mathematical details of the index layout is explained in :meth:`~chemcoord.Cartesian.get_grad_zmat()`. zmat_dist (:class:`~chemcoord.Zmat`): Distortions in Zmatrix space. Returns: :class:`~chemcoord.Cartesian`: Distortions in cartesian space. """ columns = ['bond', 'angle', 'dihedral'] C_dist = zmat_dist.loc[:, columns].values.T try: C_dist = C_dist.astype('f8') C_dist[[1, 2], :] = np.radians(C_dist[[1, 2], :]) except (TypeError, AttributeError): C_dist[[1, 2], :] = sympy.rad(C_dist[[1, 2], :]) cart_dist = np.tensordot(grad_X, C_dist, axes=([3, 2], [0, 1])).T from chemcoord.cartesian_coordinates.cartesian_class_main import Cartesian return Cartesian(atoms=zmat_dist['atom'], coords=cart_dist, index=zmat_dist.index)