diff --git a/package/AUTHORS b/package/AUTHORS index 028e3a3ef25..245e6bd7345 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -213,6 +213,7 @@ Chronological list of authors - Ahmed Salah Ghoneim - Alexander Schlaich - Josh Vermaas + - Xiaoxu Ruan External code ------------- diff --git a/package/CHANGELOG b/package/CHANGELOG index 480bb224a6a..2d489056e09 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -16,7 +16,7 @@ The rules for this file: ??/??/?? IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae, ooprathamm, MeetB7, BFedder, v-parmar, MoSchaeffler, jbarnoud, jandom, - xhgchen, jaclark5, DrDomenicoMarson, AHMED-salah00, schlaicha + xhgchen, jaclark5, DrDomenicoMarson, AHMED-salah00, schlaicha, SophiaRuan * 2.5.0 Fixes @@ -49,6 +49,8 @@ Enhancements and SegmentGroup. (PR #3953) Changes + * Add progress bars to track the progress of _conclude() functions + (_conclude_simple() and _conclude_fft()) in msd.py (Issue #4070, PR #4072) * As per NEP29 the minimum supported NumPy version has been raised to 1.21 (note: in practice later versions of NumPy may be used depending on your architecture, operating system, or Python version) (PR #3983) diff --git a/package/MDAnalysis/analysis/msd.py b/package/MDAnalysis/analysis/msd.py index 6c3104a9ce6..c3d202e883a 100644 --- a/package/MDAnalysis/analysis/msd.py +++ b/package/MDAnalysis/analysis/msd.py @@ -250,6 +250,7 @@ from ..due import due, Doi from .base import AnalysisBase from ..core import groups +from tqdm import tqdm logger = logging.getLogger('MDAnalysis.analysis.msd') @@ -387,7 +388,7 @@ def _conclude_simple(self): """ lagtimes = np.arange(1, self.n_frames) positions = self._position_array.astype(np.float64) - for lag in lagtimes: + for lag in tqdm(lagtimes): disp = positions[:-lag, :, :] - positions[lag:, :, :] sqdist = np.square(disp).sum(axis=-1) self.results.msds_by_particle[lag, :] = np.mean(sqdist, axis=0) @@ -411,7 +412,7 @@ def _conclude_fft(self): # with FFT, np.float64 bit prescision required. or set fft=False""") positions = self._position_array.astype(np.float64) - for n in range(self.n_particles): + for n in tqdm(range(self.n_particles)): self.results.msds_by_particle[:, n] = tidynamics.msd( positions[:, n, :]) self.results.timeseries = self.results.msds_by_particle.mean(axis=1)