Merge pull request #536 from MDAnalysis/scipy-ncdf-precision

AMBER NetCDF file writing -- enforcing float32 precision
MDAnalysis · Nov 12, 2015 · 3754059 · 3754059
2 parents d168f86 + 4f0827f
commit 3754059
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Showing 3 changed files with 13 additions and 2 deletions.
diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -39,6 +39,7 @@ Changes
   * built html doc files are no longer version controlled (Issue #491)
 
 Fixes
+  * AMBER netcdf writer now correctly uses float32 precision (Issue #518)
   * Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
     (Issue #533)
   * Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)

diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py
@@ -691,14 +691,14 @@ def _init_netcdf(self, periodic=True):
         ncfile.createDimension('label', 5)  # needed for cell_angular
 
         # Create variables.
-        coords = ncfile.createVariable('coordinates', 'f8', ('frame', 'atom', 'spatial'),
+        coords = ncfile.createVariable('coordinates', 'f4', ('frame', 'atom', 'spatial'),
                                        zlib=self.zlib, complevel=self.cmplevel)
         setattr(coords, 'units', 'angstrom')
 
         spatial = ncfile.createVariable('spatial', 'c', ('spatial',))
         spatial[:] = np.asarray(list('xyz'))
 
-        time = ncfile.createVariable('time', 'f8', ('frame',),
+        time = ncfile.createVariable('time', 'f4', ('frame',),
                                      zlib=self.zlib, complevel=self.cmplevel)
         setattr(time, 'units', 'picosecond')
 

diff --git a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py
@@ -129,6 +129,16 @@ def test_write_trajectory(self):
         with self.Writer(self.outfile, t.n_atoms, dt=t.dt) as W:
             self._copy_traj(W)
         self._check_new_traj()
+        import netCDF4
+        #for issue #518 -- preserve float32 data in ncdf output
+        dataset = netCDF4.Dataset(self.outfile, 'r', format='NETCDF3')
+        variable_dict = dataset.variables
+        coords = variable_dict['coordinates']
+        time = variable_dict['time']
+        self.assertTrue('float32' in coords.__repr__(),
+                'ncdf coord output not float32')
+        self.assertTrue('float32' in time.__repr__(),
+                'ncdf time output not float32')
 
     def test_OtherWriter(self):
         t = self.universe.trajectory