From a89d2cee5e789ad7c85f593f1a8b9d73ba1e50e6 Mon Sep 17 00:00:00 2001
From: James Graham <j.graham@soton.ac.uk>
Date: Thu, 18 Mar 2021 19:21:28 +0000
Subject: [PATCH] fix: cast unitcell to float32 to avoid numpy warn
---
pycgtool/frame.py | 6 +++++-
test/test_bondset.py | 2 +-
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/pycgtool/frame.py b/pycgtool/frame.py
index e7ede1c..8aa7275 100644
--- a/pycgtool/frame.py
+++ b/pycgtool/frame.py
@@ -119,6 +119,10 @@ class Frame:
self.time = traj.time
+ # Cast unitcell vectors to float32 to avoid warning - they're currently float64
+ if traj.unitcell_vectors is not None:
+ traj.unitcell_vectors = traj.unitcell_vectors.astype(np.float32)
+
@property
def residues(self):
"""Residues in the frame topology."""
@@ -204,7 +208,7 @@ class Frame:
def build_trajectory(self) -> None:
"""Build an MDTraj trajectory from atom coordinates and the values stored as attributes on this frame."""
- xyz = np.array([atom.coords for atom in self._topology.atoms])
+ xyz = np.array([atom.coords for atom in self._topology.atoms], dtype=np.float32)
# We currently have axes: 0 - each atom, 1 - timestep, 2 - xyz coords
# Need to convert to axes: 0 - timestep, 1 - each atom, 2 - xyz coords
diff --git a/test/test_bondset.py b/test/test_bondset.py
index aa34785..d990b52 100644
--- a/test/test_bondset.py
+++ b/test/test_bondset.py
@@ -1,9 +1,9 @@
-import unittest
import math
import os
import pathlib
import tempfile
+import unittest
from pycgtool.bondset import BondSet
from pycgtool.frame import Frame
--
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