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"jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] + +[metadata] +lock-version = "2.0" +python-versions = ">=3.8" +content-hash = "a634dae8b22403743fea76423cb174c5487e3c529b7f3582230bf94b19fb6ee5" diff --git a/pyproject.toml b/pyproject.toml index 8831fe97..82380dc2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,6 @@ h5py = ">=3.7.0" pandas = ">=1.4.3" nglview = ">=3.0.5" ase = ">=3.22.1" -mrcfile = ">=1.3.0" plotly = ">=5.9.0" kaleido = ">=0.2.1,<0.2.1.post1 || >0.2.1.post1" ipython = ">=8.12" diff --git a/src/py4vasp/_third_party/viewer/viewer3d.py b/src/py4vasp/_third_party/viewer/viewer3d.py deleted file mode 100644 index 96e5d30d..00000000 --- a/src/py4vasp/_third_party/viewer/viewer3d.py +++ /dev/null @@ -1,200 +0,0 @@ -# Copyright © VASP Software GmbH, -# Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) -import collections -import os -import tempfile -from typing import NamedTuple - -import numpy as np - -from py4vasp import exception -from py4vasp._util import import_ - -mrcfile = import_.optional("mrcfile") -nglview = import_.optional("nglview") - - -class _Arrow3d(NamedTuple): - tail: np.ndarray - tip: np.ndarray - color: np.ndarray - radius: float = 0.2 - - def to_serializable(self): - return list(self.tail), list(self.tip), list(self.color), float(self.radius) - - -def _rotate(arrow, transformation): - return _Arrow3d( - transformation @ arrow.tail, transformation @ arrow.tip, arrow.color - ) - - -_x_axis = _Arrow3d(tail=np.zeros(3), tip=np.array((3, 0, 0)), color=[1, 0, 0]) -_y_axis = _Arrow3d(tail=np.zeros(3), tip=np.array((0, 3, 0)), color=[0, 1, 0]) -_z_axis = _Arrow3d(tail=np.zeros(3), tip=np.array((0, 0, 3)), color=[0, 0, 1]) - - -class Viewer3d: - """Collection of data and elements to be displayed in a structure viewer. - - Parameters - ---------- - viewer : nglview.NGLWidget - The raw viewer used to display the structure. Currently we are only - supporting the nglview package. - """ - - _positions = None - _lengths = None - _angles = None - _number_cells = 1 - _axes = None - - def __init__(self, viewer): - self._ngl = viewer - self._arrows = [] - - @classmethod - def from_structure(cls, structure, supercell=None): - """Generate a new Viewer3d from a structure. - - Parameters - ---------- - structure : data.Structure - Defines the structure of the Vasp calculation. - supercell : int or np.ndarray - If present the cell is extended by the specified factor along each axis. - """ - ase = structure.to_ase(supercell) - res = cls(nglview.show_ase(ase)) - # ngl works with the standard form, so we need to store the positions in the same format - standard_cell, transformation = ase.cell.standard_form() - ase.set_cell(standard_cell, scale_atoms=True) - res._lengths = tuple(ase.cell.lengths()) - res._angles = tuple(ase.cell.angles()) - res._positions = ase.positions - res._number_cells = res._calculate_number_cells(supercell) - res._transformation = transformation - # res._transformation = np.eye(3) - return res - - def _calculate_number_cells(self, supercell): - if isinstance(supercell, collections.abc.Iterable): - return np.prod(supercell) - if isinstance(supercell, int): - return supercell**3 - if isinstance(supercell, float) and supercell.is_integer(): - return supercell**3 - return 1 - - @classmethod - def from_trajectory(cls, trajectory): - """Generate a new Viewer3d from a trajectory. - - Parameters - ---------- - trajectory : data.Structure - Defines the trajectory of the Vasp MD run. - supercell : int or np.ndarray - If present the cell is extended by the specified factor along each axis. - """ - ngl_trajectory = nglview.MDTrajTrajectory(trajectory.to_mdtraj()) - return cls(nglview.NGLWidget(ngl_trajectory)) - - def _ipython_display_(self): - self._ngl._ipython_display_() - - def show_cell(self): - """Show the unit cell of the crystal.""" - self._ngl.add_unitcell() - - def hide_cell(self): - """Hide the unit cell of the crystal.""" - self._ngl.remove_unitcell() - - def show_axes(self): - """Show the cartesian axis in the corner of the figure.""" - if self._axes is not None: - return - self._axes = ( - self._make_arrow(_rotate(_x_axis, self._transformation)), - self._make_arrow(_rotate(_y_axis, self._transformation)), - self._make_arrow(_rotate(_z_axis, self._transformation)), - ) - - def hide_axes(self): - """Hide the cartesian axis.""" - if self._axes is None: - return - for axis in self._axes: - self._ngl.remove_component(axis) - self._axes = None - - def show_arrows_at_atoms(self, arrows, color=[0.1, 0.1, 0.8]): - """Add arrows at all the atoms. - - Parameters - ---------- - arrows : np.ndarray - An array containing the direction of an arrow for every atom in the - unit cell. This arrow will be drawn in the figure. - color : np.ndarray - rgb values of the arrow, defaulting to blue. - - Notes - ----- - If you are working on a supercell, the code will automatically extend the - size of the array to show arrows in the supercell, too. - """ - if self._positions is None: - raise exception.RefinementError("Positions of atoms are not known.") - arrows = np.repeat(arrows @ self._transformation.T, self._number_cells, axis=0) - for tail, arrow in zip(self._positions, arrows): - tip = tail + arrow - arrow = _Arrow3d(tail, tip, color) - self._arrows.append(self._make_arrow(arrow)) - - def hide_arrows_at_atoms(self): - """Remove all arrows from the atoms. - - Notes - ----- - If two different kind of atoms have been added to the system, there is - currently no option to distinguish between them.""" - for arrow in self._arrows: - self._ngl.remove_component(arrow) - self._arrows = [] - - def _make_arrow(self, arrow): - return self._ngl.shape.add_arrow(*(arrow.to_serializable())) - - def show_isosurface(self, volume_data, **kwargs): - """Add an isosurface to the structure. - - Parameters - ---------- - volume_data : np.ndarray - The raw data represented on a 3d grid. Make sure the grid aligns with - the FFT grid used in the Vasp calculation. - kwargs - Additional parameters passed on to the visualizer. Most relevant is - the isolevel changing the position at which the isosurface is drawn. - """ - with tempfile.TemporaryDirectory() as tmp: - filename = os.path.join(tmp, "data.mrc") - self._make_mrc_file(filename, volume_data) - self._make_isosurface(filename, **kwargs) - - def _make_mrc_file(self, filename, volume_data): - with mrcfile.new(filename, overwrite=True) as data_file: - data_file.set_data(volume_data.astype(np.float32)) - data_file.header.cella = self._lengths - data_file.header.cellb = self._angles - - def _make_isosurface(self, filename, **kwargs): - if len(kwargs) == 0: - self._ngl.add_component(filename) - else: - component = self._ngl.add_component(filename, defaultRepresentation=False) - component.add_surface(**kwargs) diff --git a/tests/third_party/test_viewer3d.py b/tests/third_party/test_viewer3d.py deleted file mode 100644 index e8f52169..00000000 --- a/tests/third_party/test_viewer3d.py +++ /dev/null @@ -1,228 +0,0 @@ -# Copyright © VASP Software GmbH, -# Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) -import types -from unittest.mock import patch - -import numpy as np -import pytest - -from py4vasp import calculation, exception -from py4vasp._third_party.viewer.viewer3d import ( - Viewer3d, - _Arrow3d, - _x_axis, - _y_axis, - _z_axis, -) -from py4vasp._util import import_ - -json = import_.optional("ipykernel.jsonutil") -nglview = import_.optional("nglview") - - -@pytest.fixture -def assert_arrow_message(Assert): - def _assert_arrow_message(message, arrow): - assert message[0] == "addShape" - args = message[1] - assert args[0] == "shape" - params = args[1][0] - assert params[0] == "arrow" - Assert.allclose(params[1], arrow.tail) - Assert.allclose(params[2], arrow.tip) - assert params[3] == arrow.color - assert params[4] == arrow.radius - - return _assert_arrow_message - - -@pytest.fixture -def viewer3d(raw_data, not_core): - pytest.xfail("old version of viewer") - structure = calculation.structure.from_data(raw_data.structure("Sr2TiO4")) - return make_viewer(structure) - - -@pytest.fixture -def nonstandard_form(raw_data, not_core): - raw_structure = raw_data.structure("Sr2TiO4") - x = np.sqrt(0.5) - raw_structure.cell.lattice_vectors = np.array([[[x, x, 0], [-x, x, 0], [0, 0, 1]]]) - raw_structure.positions += 0.1 # shift to avoid small comparisons - viewer = make_viewer(calculation.structure.from_data(raw_structure)) - viewer.ref.transformation = np.array([[x, x, 0], [-x, x, 0], [0, 0, 1]]) - return viewer - - -def make_viewer(structure, supercell=None): - viewer = structure.plot(supercell) - viewer.ref = types.SimpleNamespace() - viewer.ref.positions = structure.cartesian_positions() - viewer.default_messages = count_messages(viewer, setup=True) - return viewer - - -def count_messages(viewer, setup=False): - n = viewer.default_messages if not setup else 0 - return len(viewer._ngl.get_state()["_ngl_msg_archive"]) - n - - -def last_messages(viewer, n=1, get_msg_kwargs=False): - num_messages = count_messages(viewer) - if num_messages >= n: - index = viewer.default_messages + num_messages - n - messages = viewer._ngl.get_state()["_ngl_msg_archive"][index:] - if get_msg_kwargs: - get_msg_tuple = lambda msg: (msg["methodName"], msg["args"], msg["kwargs"]) - else: - get_msg_tuple = lambda msg: (msg["methodName"], msg["args"]) - return [get_msg_tuple(msg) for msg in messages] - else: - return [] - - -def test_ipython(viewer3d): - cm_display = patch.object(nglview.NGLWidget, "_ipython_display_", autospec=True) - with cm_display as display: - assert viewer3d._ngl is not None - viewer3d._ipython_display_() - display.assert_called_once() - - -def test_cell(viewer3d): - viewer3d.show_cell() - assert_add_unitcell(*last_messages(viewer3d)) - viewer3d.hide_cell() - assert last_messages(viewer3d) == [("removeRepresentationsByName", ["unitcell", 0])] - - -def test_axes(viewer3d, assert_arrow_message): - viewer3d.show_axes() - messages = last_messages(viewer3d, n=3) - assert_arrow_message(messages[0], _x_axis) - assert_arrow_message(messages[1], _y_axis) - assert_arrow_message(messages[2], _z_axis) - viewer3d.show_axes() - viewer3d.hide_axes() - # ngl deletes the sent messages to indicate removal of the shapes - assert count_messages(viewer3d) == 0 - viewer3d.hide_axes() - - -def test_arrows(viewer3d, assert_arrow_message): - number_atoms = len(viewer3d.ref.positions) - color = [0.1, 0.1, 0.8] - arrows = create_arrows(viewer3d, number_atoms) - messages = last_messages(viewer3d, number_atoms) - assert len(messages) == number_atoms - for message, tail, arrow in zip(messages, viewer3d.ref.positions, arrows): - tip = tail + arrow - assert_arrow_message(message, _Arrow3d(tail, tip, color)) - viewer3d.show_arrows_at_atoms(arrows) - assert count_messages(viewer3d) == 2 * number_atoms - viewer3d.hide_arrows_at_atoms() - # ngl deletes the sent messages to indicate removal of the shapes - assert count_messages(viewer3d) == 0 - viewer3d.hide_arrows_at_atoms() - - -@pytest.mark.xfail -def test_supercell(raw_data, not_core): - structure = calculation.structure.from_data(raw_data.structure("Sr2TiO4")) - number_atoms = structure.number_atoms() - supercell = (1, 2, 3) - viewer = make_viewer(structure, supercell) - create_arrows(viewer, number_atoms) - assert count_messages(viewer) == np.prod(supercell) * number_atoms - supercell = 2 # meaning 2 along every direction - viewer = make_viewer(structure, supercell) - create_arrows(viewer, number_atoms) - assert count_messages(viewer) == supercell**3 * number_atoms - - -def test_bare_ngl_cannot_add_arrows_at_atoms(viewer3d): - viewer = Viewer3d(viewer3d._ngl) - with pytest.raises(exception.RefinementError): - create_arrows(viewer, 1) - - -def create_arrows(viewer, number_atoms): - arrows = np.repeat([(0.2, 0.4, 0.6)], number_atoms, axis=0) - viewer.show_arrows_at_atoms(arrows) - return arrows - - -def test_serializable(not_core): - arrow = _Arrow3d(np.zeros(3), np.ones(3), np.ones(1)) - for element in arrow.to_serializable(): - json.json_clean(element) - - -@pytest.mark.xfail(reason="Not compatible with density plotting") -def test_nonstandard_form(nonstandard_form, Assert, assert_arrow_message): - viewer = nonstandard_form - Assert.allclose(viewer._positions, viewer.ref.positions) - viewer.show_axes() - messages = last_messages(viewer, n=3) - assert_arrow_message(messages[0], rotate(_x_axis, viewer.ref.transformation)) - assert_arrow_message(messages[1], rotate(_y_axis, viewer.ref.transformation)) - assert_arrow_message(messages[2], rotate(_z_axis, viewer.ref.transformation)) - # - color = [0.1, 0.1, 0.8] - number_atoms = len(viewer.ref.positions) - arrows = create_arrows(viewer, number_atoms) - messages = last_messages(viewer, number_atoms) - for message, tail, arrow in zip(messages, viewer.ref.positions, arrows): - tip = tail + viewer.ref.transformation @ arrow - assert_arrow_message(message, _Arrow3d(tail, tip, color)) - - -def rotate(arrow, transformation): - return _Arrow3d( - transformation @ arrow.tail, transformation @ arrow.tip, arrow.color - ) - - -@pytest.mark.xfail -def test_isosurface(raw_data, not_core): - raw_density = raw_data.density("Fe3O4 collinear") - viewer = make_viewer(calculation.structure.from_data(raw_density.structure)) - viewer.show_isosurface(raw_density.charge) - messages = last_messages(viewer, n=1, get_msg_kwargs=True) - assert_load_file(messages[0], binary=True, default=True) - # - kwargs = {"isolevel": 0.1, "color": "red"} - viewer.show_isosurface(raw_density.charge, **kwargs) - messages = last_messages(viewer, n=2, get_msg_kwargs=True) - assert_load_file(messages[0], binary=True, default=False) - assert_add_surface(messages[1], kwargs) - - -@pytest.mark.xfail -def test_trajectory(raw_data, not_core): - structure = calculation.structure.from_data(raw_data.structure("Sr2TiO4")) - viewer = structure[:].plot() - viewer.default_messages = 0 - n = count_messages(viewer) - assert n == 2 - messages = last_messages(viewer, n, get_msg_kwargs=True) - assert_load_file(messages[0], binary=False, default=True) - assert_add_unitcell(messages[1]) - - -def assert_load_file(message, binary, default): - assert message[0] == "loadFile" - assert message[1][0]["binary"] == binary - assert message[2]["defaultRepresentation"] == default - - -def assert_add_unitcell(message): - assert message[0] == "addRepresentation" - assert message[1][0] == "unitcell" - - -def assert_add_surface(message, kwargs): - assert message[0] == "addRepresentation" - assert message[1][0] == "surface" - for key, val in kwargs.items(): - assert message[2][key] == val