Merge pull request #79 from jotelha/202107_electrochemistry_tests_fix

202107 electrochemistry tests fix
libAtoms · Jul 29, 2021 · 23be0e4 · 23be0e4
2 parents 41e0ad0 + 919ed89
commit 23be0e4
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Showing 5 changed files with 14 additions and 13 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,5 @@
 .gitignore
+.idea
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

diff --git a/examples/electrochemistry/samples_pnp_by_fenics_fem.py b/examples/electrochemistry/samples_pnp_by_fenics_fem.py
@@ -7,7 +7,7 @@
 #       extension: .py
 #       format_name: percent
 #       format_version: '1.3'
-#       jupytext_version: 1.6.0
+#       jupytext_version: 1.9.1
 #   kernelspec:
 #     display_name: Python 3
 #     language: python
@@ -84,7 +84,7 @@ def make_patch_spines_invisible(ax):
 # # Convergence in both cases
 
 # %%
-# Test case parameters   oö
+# Test case parameters
 c=[1.0, 1.0]
 z=[ 1, -1]
 L=10e-8 # 200 nm

diff --git a/scripts/electrochemistry/c2d.py b/scripts/electrochemistry/c2d.py
@@ -284,7 +284,7 @@ def __call__(self, parser, namespace, values, option_string=None):
 
     if not args.outfile:
         outfile = sys.stdout
-        outfile_format = 'xyz'
+        outfile_format = '.xyz'
     else:
         outfile = args.outfile
         _, outfile_format = os.path.splitext(outfile)
@@ -302,7 +302,7 @@ def __call__(self, parser, namespace, values, option_string=None):
     # species names have been specified on command line.
 
     else:  # elif outfile_format == '.xyz'
-        ase.io.write(outfile, system, format='xyz')
+        ase.io.write(outfile, system, format='extxyz')
 
     logger.info('Done.')
 

diff --git a/scripts/electrochemistry/stericify.py b/scripts/electrochemistry/stericify.py
@@ -228,7 +228,7 @@ def __call__(self, parser, namespace, value, option_string=None):
         system = ase.io.read(
             infile, format='lammps-data', units="real", style='full')
     else:  # elif outfile_format == '.xyz'
-        system = ase.io.read(infile, format='xyz')
+        system = ase.io.read(infile, format='extxyz')
 
     n = len(system)  # total number of particles
     logger.info('Read "{}" system within bounding box'.format(system.symbols))
@@ -364,7 +364,7 @@ def __call__(self, parser, namespace, value, option_string=None):
 
     if not args.outfile:
         outfile = sys.stdout
-        outfile_format = 'xyz'
+        outfile_format = '.xyz'
     else:
         outfile = args.outfile
         _, outfile_format = os.path.splitext(outfile)
@@ -377,7 +377,7 @@ def __call__(self, parser, namespace, value, option_string=None):
             format='lammps-data', units="real", atom_style='full',
             specorder=specorder)
     else:  # elif outfile_format == '.xyz'
-        ase.io.write(outfile, system, format='xyz')
+        ase.io.write(outfile, system, format='extxyz')
 
     logger.info('Done.')
 

diff --git a/tests/test_c2d.py b/tests/test_c2d.py
@@ -73,7 +73,7 @@ def test_c2d_input_format_npz_output_format_xyz(self):
                 [ 'c2d', os.path.join(self.data_path,'NaCl.npz'), 'NaCl.xyz' ],
                 check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
                 cwd=tmpdir, env=self.myenv)
-            xyz = ase.io.read(os.path.join(tmpdir,'NaCl.xyz'))
+            xyz = ase.io.read(os.path.join(tmpdir,'NaCl.xyz'), format='extxyz')
             self.assertEqual(len(xyz),len(self.ref_xyz))
             self.assertTrue( ( xyz.symbols == self.ref_xyz.symbols ).all() )
             self.assertTrue( ( xyz.get_initial_charges() ==
@@ -88,12 +88,12 @@ def test_c2d_input_format_txt_output_format_xyz(self):
                 [ 'c2d', os.path.join(self.data_path,'NaCl.txt'), 'NaCl.xyz' ],
                 check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
                 cwd=tmpdir, env=self.myenv)
-            xyz = ase.io.read(os.path.join(tmpdir,'NaCl.xyz'))
+            xyz = ase.io.read(os.path.join(tmpdir,'NaCl.xyz'), format='extxyz')
             self.assertEqual(len(xyz), len(self.ref_xyz))
-            self.assertTrue( ( xyz.symbols ==  self.ref_xyz.symbols ).all() )
+            self.assertTrue( ( xyz.symbols == self.ref_xyz.symbols ).all() )
             self.assertTrue( ( xyz.get_initial_charges()
-                ==  self.ref_xyz.get_initial_charges() ).all() )
-            self.assertTrue( ( xyz.cell ==  self.ref_xyz.cell ).all() )
+                == self.ref_xyz.get_initial_charges() ).all() )
+            self.assertTrue( ( xyz.cell == self.ref_xyz.cell ).all() )
 
     @unittest.skipUnless(LooseVersion(ase.__version__) > LooseVersion('3.19.0'),
         """ LAMMPS data file won't work for ASE version up until 3.18.1,
@@ -169,7 +169,7 @@ def test_pnp_c2d_pipeline_mode(self):
 
             c2d_output = c2d.communicate()[0]
             with io.StringIO(c2d_output) as xyz_instream:
-                xyz = ase.io.read(xyz_instream, format='xyz')
+                xyz = ase.io.read(xyz_instream, format='extxyz')
             self.assertEqual(len(xyz),len(self.ref_xyz))
             self.assertTrue( ( xyz.symbols == self.ref_xyz.symbols ).all() )
             self.assertTrue( ( xyz.get_initial_charges()