From 7618445eb9068cc02fa2193fd9951c326565dbcb Mon Sep 17 00:00:00 2001 From: hp115 <77673542+hp115@users.noreply.github.com> Date: Tue, 6 Apr 2021 16:05:56 +0100 Subject: [PATCH] Add Transformation to set box dimensions (#3175) Fixes #2691 Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> Co-authored-by: Irfan Alibay --- package/AUTHORS | 1 + package/CHANGELOG | 4 +- .../MDAnalysis/transformations/__init__.py | 1 + .../transformations/boxdimensions.py | 87 +++++++++++++++++++ .../trajectory_transformations.rst | 1 + .../transformations/boxdimensions.rst | 1 + .../transformations/test_boxdimensions.py | 83 ++++++++++++++++++ 7 files changed, 177 insertions(+), 1 deletion(-) create mode 100644 package/MDAnalysis/transformations/boxdimensions.py create mode 100644 package/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst create mode 100644 testsuite/MDAnalysisTests/transformations/test_boxdimensions.py diff --git a/package/AUTHORS b/package/AUTHORS index 30d4700df19..a1c15d1d50d 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -159,6 +159,7 @@ Chronological list of authors - Jan Stevens - Orion Cohen - Dimitrios Papageorgiou + - Hannah Pollak External code ------------- diff --git a/package/CHANGELOG b/package/CHANGELOG index 40176d12565..6d1fed563ec 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -17,7 +17,7 @@ The rules for this file: lilyminium, daveminh, jbarnoud, yuxuanzhuang, VOD555, ianmkenney, calcraven，xiki-tempula, mieczyslaw, manuel.nuno.melo, PicoCentauri, hanatok, rmeli, aditya-kamath, tirkarthi, LeonardoBarneschi, hejamu, - biogen98, orioncohen, z3y50n + biogen98, orioncohen, z3y50n, hp115 * 2.0.0 @@ -89,6 +89,8 @@ Fixes * Fix syntax warning over comparison of literals using is (Issue #3066) Enhancements + * Add `set_dimensions` transformation class for setting constant + box dimensions for all timesteps in trajectory (Issue #2691) * Added a ValueError raised when not given a gridcenter while providing grid dimensions to DensityAnalysis, also added check for NaN in the input (Issue #3148, PR #3154) diff --git a/package/MDAnalysis/transformations/__init__.py b/package/MDAnalysis/transformations/__init__.py index 91083fff18b..7fd56d2eab6 100644 --- a/package/MDAnalysis/transformations/__init__.py +++ b/package/MDAnalysis/transformations/__init__.py @@ -130,3 +130,4 @@ def wrapped(ts): from .positionaveraging import PositionAverager from .fit import fit_translation, fit_rot_trans from .wrap import wrap, unwrap +from .boxdimensions import set_dimensions diff --git a/package/MDAnalysis/transformations/boxdimensions.py b/package/MDAnalysis/transformations/boxdimensions.py new file mode 100644 index 00000000000..5a6569caa90 --- /dev/null +++ b/package/MDAnalysis/transformations/boxdimensions.py @@ -0,0 +1,87 @@ +# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- +# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 +# +# MDAnalysis --- https://www.mdanalysis.org +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) +# +# Released under the GNU Public Licence, v2 or any higher version +# +# Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# doi: 10.25080/majora-629e541a-00e +# +# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. +# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. +# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 +# + +"""\ +Set box dimensions --- :mod:`MDAnalysis.transformations.boxdimensions` +======================================================================= + +Set dimensions of the simulation box to a constant vector across all timesteps. + + +.. autoclass:: set_dimensions +""" +import numpy as np + + +class set_dimensions: + """ + Set simulation box dimensions. + + Timestep dimensions are modified in place. + + Example + ------- + + e.g. set simulation box dimensions to a vector containing unit cell + dimensions [*a*, *b*, *c*, *alpha*, *beta*, *gamma*], lengths *a*, + *b*, *c* are in the MDAnalysis length unit (Å), and angles are in degrees. + + .. code-block:: python + + dim = [2, 2, 2, 90, 90, 90] + transform = mda.transformations.boxdimensions.set_dimensions(dim) + u.trajectory.add_transformations(transform) + + Parameters + ---------- + dimensions: iterable of floats + vector that contains unit cell lengths and angles. + Expected shapes are (6, 0) or (1, 6) + + Returns + ------- + :class:`~MDAnalysis.coordinates.base.Timestep` object + """ + + def __init__(self, dimensions): + self.dimensions = dimensions + + try: + self.dimensions = np.asarray(self.dimensions, np.float32) + except ValueError: + errmsg = (f'{self.dimensions} cannot be converted into ' + 'np.float32 numpy.ndarray') + raise ValueError(errmsg) + try: + self.dimensions = self.dimensions.reshape(6, ) + except ValueError: + errmsg = (f'{self.dimensions} array does not have valid box ' + 'dimension shape.\nSimulation box dimensions are ' + 'given by an float array of shape (6, ), ' + ' containing 3 lengths and 3 angles: ' + '[a, b, c, alpha, beta, gamma]') + raise ValueError(errmsg) + + def __call__(self, ts): + ts.dimensions = self.dimensions + return ts diff --git a/package/doc/sphinx/source/documentation_pages/trajectory_transformations.rst b/package/doc/sphinx/source/documentation_pages/trajectory_transformations.rst index 9662f687442..4d885cb0c45 100644 --- a/package/doc/sphinx/source/documentation_pages/trajectory_transformations.rst +++ b/package/doc/sphinx/source/documentation_pages/trajectory_transformations.rst @@ -233,4 +233,5 @@ Currently implemented transformations ./transformations/positionaveraging ./transformations/fit ./transformations/wrap + ./transformations/boxdimensions diff --git a/package/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst b/package/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst new file mode 100644 index 00000000000..e40789ae657 --- /dev/null +++ b/package/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst @@ -0,0 +1 @@ +.. automodule:: MDAnalysis.transformations.boxdimensions diff --git a/testsuite/MDAnalysisTests/transformations/test_boxdimensions.py b/testsuite/MDAnalysisTests/transformations/test_boxdimensions.py new file mode 100644 index 00000000000..f85ee564a58 --- /dev/null +++ b/testsuite/MDAnalysisTests/transformations/test_boxdimensions.py @@ -0,0 +1,83 @@ +# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- +# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 +# +# MDAnalysis --- https://www.mdanalysis.org +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) +# +# Released under the GNU Public Licence, v2 or any higher version +# +# Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# doi: 10.25080/majora-629e541a-00e +# +# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. +# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. +# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 +# + +import numpy as np +import pytest +from numpy.testing import assert_array_almost_equal + +import MDAnalysis as mdanalysis +from MDAnalysis.transformations import set_dimensions +from MDAnalysisTests import make_Universe + + +@pytest.fixture() +def boxdimensions_universe(): + # create Universe objects for tests + new_u = make_Universe(trajectory=True) + return new_u + + +def test_boxdimensions_dims(boxdimensions_universe): + new_dims = np.float32([2, 2, 2, 90, 90, 90]) + set_dimensions(new_dims)(boxdimensions_universe.trajectory.ts) + assert_array_almost_equal(boxdimensions_universe.dimensions, + new_dims, decimal=6) + + +@pytest.mark.parametrize('dim_vector_shapes', ( + [1, 1, 1, 90, 90], + [1, 1, 1, 1, 90, 90, 90], + np.array([[1], [1], [90], [90], [90]]), + np.array([1, 1, 1, 90, 90]), + np.array([1, 1, 1, 1, 90, 90, 90]), + [1, 1, 1, 90, 90], + 111909090) + ) +def test_dimensions_vector(boxdimensions_universe, dim_vector_shapes): + # wrong box dimension vector shape + ts = boxdimensions_universe.trajectory.ts + with pytest.raises(ValueError, match='valid box dimension shape'): + set_dimensions(dim_vector_shapes)(ts) + + +@pytest.mark.parametrize('dim_vector_forms_dtypes', ( + ['a', 'b', 'c', 'd', 'e', 'f'], + np.array(['a', 'b', 'c', 'd', 'e', 'f']), + 'abcd') + ) +def test_dimensions_vector_asarray(boxdimensions_universe, + dim_vector_forms_dtypes): + # box dimension input type not convertible into array + ts = boxdimensions_universe.trajectory.ts + with pytest.raises(ValueError, match='cannot be converted'): + set_dimensions(dim_vector_forms_dtypes)(ts) + + +def test_dimensions_transformations_api(boxdimensions_universe): + # test if transformation works with on-the-fly transformations API + new_dims = np.float32([2, 2, 2, 90, 90, 90]) + transform = set_dimensions(new_dims) + boxdimensions_universe.trajectory.add_transformations(transform) + for ts in boxdimensions_universe.trajectory: + assert_array_almost_equal(boxdimensions_universe.dimensions, + new_dims, decimal=6)