From 8d79fee3b454f0638ad266898244f34bc8a54f80 Mon Sep 17 00:00:00 2001 From: Tulga-Erdene Sodjargal <128572046+tulga-rdn@users.noreply.github.com> Date: Fri, 20 Dec 2024 23:30:13 +0100 Subject: [PATCH 1/2] add tidynamics to requirements.txt --- package/requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/package/requirements.txt b/package/requirements.txt index accac1b49fd..341c720ee38 100644 --- a/package/requirements.txt +++ b/package/requirements.txt @@ -22,3 +22,4 @@ mdanalysis_sphinx_theme >=1.0.1 sphinx_sitemap threadpoolctl tqdm +tidynamics From 51d83ed699e5da7578623e3ccd9fd25c9cde8f80 Mon Sep 17 00:00:00 2001 From: Tulga-Erdene Sodjargal <128572046+tulga-rdn@users.noreply.github.com> Date: Fri, 20 Dec 2024 23:32:33 +0100 Subject: [PATCH 2/2] remove tidynamics not detected error --- package/MDAnalysis/analysis/msd.py | 14 +------------- 1 file changed, 1 insertion(+), 13 deletions(-) diff --git a/package/MDAnalysis/analysis/msd.py b/package/MDAnalysis/analysis/msd.py index 4515ed40983..75c7832c168 100644 --- a/package/MDAnalysis/analysis/msd.py +++ b/package/MDAnalysis/analysis/msd.py @@ -392,19 +392,7 @@ def _conclude_fft(self): # with FFT, np.float64 bit prescision required. r""" Calculates the MSD via the FCA fast correlation algorithm. """ - try: - import tidynamics - except ImportError: - raise ImportError("""ERROR --- tidynamics was not found! - - tidynamics is required to compute an FFT based MSD (default) - - try installing it using pip eg: - - pip install tidynamics - - or set fft=False""") - + import tidynamics positions = self._position_array.astype(np.float64) for n in tqdm(range(self.n_particles)): self.results.msds_by_particle[:, n] = tidynamics.msd(