fix doc and tests

docs/use.rst

@@ -596,6 +596,7 @@ The output depends on the value of ``-V``, which can be:
       There is no way to change this behavior.
     + By default, the program also include the base tensors calculated in the process.
       The ``-S`` option prevents this (that may be useful in the case of electric field differentiation)
+    + If you want to add results to existing ``molecule_nd.h5`` file, you can use the ```--append`` option.
     + Projection over normal mode of all the geometrical derivatives is requested via the ``-p`` option, but you can also request that the cartesian hessian used to do so is different, with the ``-H`` option (which accepts FCHK and dalton archives with cartesian hessian in it as argument).
 
 

nachos/bake.py

@@ -148,10 +148,11 @@ def main():
     storage = files.ComputationalResults(recipe, directory=recipe_directory)
     storage.read(args.data)
 
-    original_cf = ChemistryDataFile()
+    original_cf = None
     if args.append:
         with open(args.output) as f:
             try:
+                original_cf = ChemistryDataFile()
                 original_cf.read(f)
             except BadChemistryDataFile as e:
                 return exit_failure('Cannot append data to `{}`: {}'.format(args.output, e))

tests/tests_nachos_bake.py

@@ -44,9 +44,9 @@ def test_bake_gaussian_F(self):
 
         storage = files.ComputationalResults(r, directory=directory)
         storage.read(storage_path)
-        baker = baking.Baker(r, storage, directory=directory)
 
         # with energy:
+        baker = baking.Baker(r, storage, directory=directory)
         cf_with_energy = baker.bake(only=[(derivatives.Derivative(), 3)])
 
         self.assertIn('F', cf_with_energy.derivatives)
@@ -64,6 +64,7 @@ def test_bake_gaussian_F(self):
             electrical_derivatives['FFF']['static'], cf_with_energy.derivatives['FFF']['static'])
 
         # with mu:
+        baker = baking.Baker(r, storage, directory=directory)
         cf_with_mu = baker.bake(only=[(derivatives.Derivative('F'), 2)])
 
         self.assertIn('FF', cf_with_mu.derivatives)
@@ -79,6 +80,7 @@ def test_bake_gaussian_F(self):
             delta=.01)
 
         # with alpha:
+        baker = baking.Baker(r, storage, directory=directory)
         cf_with_alpha = baker.bake(only=[(derivatives.Derivative('FF'), 1)])
 
         self.assertIn('FFF', cf_with_alpha.derivatives)
@@ -89,6 +91,7 @@ def test_bake_gaussian_F(self):
             cf_with_alpha.derivatives['FFF']['static'])
 
         # dynamic
+        baker = baking.Baker(r, storage, directory=directory)
         cf_with_alpha = baker.bake(only=[(derivatives.Derivative('dD'), 1)])
 
         self.assertIn('dDF', cf_with_alpha.derivatives)
@@ -159,9 +162,8 @@ def test_bake_gaussian_G(self):
 
         geometrical_derivatives = fchk.property('geometrical_derivatives')
 
-        baker = baking.Baker(r, storage, directory=directory)
-
         # with energy:
+        baker = baking.Baker(r, storage, directory=directory)
         cf_with_energy = baker.bake(only=[(derivatives.Derivative(), 2)])
 
         self.assertIn('G', cf_with_energy.derivatives)
@@ -175,6 +177,7 @@ def test_bake_gaussian_G(self):
             geometrical_derivatives['GG'], cf_with_energy.derivatives['GG'])
 
         # try with all
+        baker = baking.Baker(r, storage, directory=directory)
         cf = baker.bake()
 
         self.assertIn('G', cf.derivatives)
@@ -212,6 +215,7 @@ def test_bake_gaussian_G(self):
                 math.fabs(ph[i, i]), mwh.frequencies[i] ** 2, places=5)
 
         # now, bake and steal results from zero field
+        baker = baking.Baker(r, storage, directory=directory)
         cf_with_copy = baker.bake(only=[(derivatives.Derivative(), 0)], copy_zero_field_basis=True)
 
         # gradient and hessian ...