add tests and fix bugs they exposed

aiida_quantumespresso/calculations/__init__.py

@@ -505,16 +505,15 @@ def _generate_PWCPinputdata(cls, parameters, settings, pseudos, structure, kpoin
         # ------------ ATOMIC_POSITIONS -----------
         coordinates = [site.position for site in structure.sites]
         if use_fractional:
-            atomic_positions_card_list = ['ATOMIC_POSITIONS crystal']
+            atomic_positions_card_header = 'ATOMIC_POSITIONS crystal\n'
             coordinates = numpy.dot(coordinates, numpy.linalg.inv(numpy.array(structure.cell))).tolist()
         else:
-            atomic_positions_card_list = ['ATOMIC_POSITIONS angstrom']
+            atomic_positions_card_header = 'ATOMIC_POSITIONS angstrom\n'
 
-        for site, site_coords in zip(structure.sites, coordinates):
-            atomic_positions_card_list.append(
-                '{0} {1:18.10f} {2:18.10f} {3:18.10f}'.  # pylint: disable=consider-using-f-string
-                format(site.kind_name.ljust(6), *site_coords)
-            )
+        atomic_positions_card_list = [
+            '{0} {1:18.10f} {2:18.10f} {3:18.10f}'.format(site.kind_name.ljust(6), *site_coords)  # pylint: disable=consider-using-f-string
+            for site, site_coords in zip(structure.sites, coordinates)
+        ]
 
         fixed_coords = settings.pop('FIXED_COORDS', None)
 
@@ -525,12 +524,15 @@ def _generate_PWCPinputdata(cls, parameters, settings, pseudos, structure, kpoin
                 raise exceptions.InputValidationError(
                     f'Input structure has {len(structure.sites)} sites, but fixed_coords has length {len(fixed_coords)}'
                 )
-            fixed_coords_strings = [' {:d} {:d} {:d}'.format(*row) for row in numpy.int32(fixed_coords).tolist()]  # pylint: disable=consider-using-f-string
-
-            for atomic_pos_str, fixed_coords_str in zip(atomic_positions_card_list[1:], fixed_coords_strings):
-                atomic_pos_str += fixed_coords_str
-
-        atomic_positions_card = '\n'.join(atomic_positions_card_list) + '\n'
+            fixed_coords_strings = [
+                ' {:d} {:d} {:d}'.format(*row) for row in numpy.int32(numpy.invert(fixed_coords)).tolist()  # pylint: disable=consider-using-f-string
+            ]
+            atomic_positions_card_list = [
+                atomic_pos_str + fixed_coords_str
+                for atomic_pos_str, fixed_coords_str in zip(atomic_positions_card_list, fixed_coords_strings)
+            ]
+
+        atomic_positions_card = atomic_positions_card_header + '\n'.join(atomic_positions_card_list) + '\n'
 
         # Optional ATOMIC_FORCES card
         atomic_forces = settings.pop('ATOMIC_FORCES', None)

aiida_quantumespresso/parsers/pw.py

@@ -250,13 +250,14 @@ def is_ionically_converged(self, trajectory, except_final_scf=False):
             return verify_convergence_trajectory(
                 trajectory=trajectory,
                 index=-1,
-                threshold_forces=threshold_forces
+                threshold_forces=threshold_forces,
+                fixed_coords=fixed_coords
             )
 
         if relax_type == 'vc-relax':
-            values = [threshold_forces, threshold_stress, external_pressure]
-            converged_relax = verify_convergence_trajectory(trajectory, -2, *values, fixed_coords)
-            converged_final = verify_convergence_trajectory(trajectory, -1, *values, fixed_coords)
+            values = [threshold_forces, threshold_stress, external_pressure, fixed_coords]
+            converged_relax = verify_convergence_trajectory(trajectory, -2, *values)
+            converged_final = verify_convergence_trajectory(trajectory, -1, *values)
 
             return converged_relax and (converged_final or except_final_scf)
 

tests/calculations/test_pw.py

@@ -320,3 +320,35 @@ def test_pw_validate_inputs_restart_nscf(
     inputs['parameters'] = orm.Dict(dict=parameters)
     with pytest.warns(Warning, match='`restart_mode` should be set to `from_scratch` for a `.*`.'):
         generate_calc_job(fixture_sandbox, entry_point_name, inputs)
+
+
+def test_fixed_coords(fixture_sandbox, generate_calc_job, generate_inputs_pw, file_regression):
+    """Test a ``PwCalculation`` where the ``fixed_coords`` setting was provided."""
+    entry_point_name = 'quantumespresso.pw'
+
+    inputs = generate_inputs_pw()
+    inputs['settings'] = orm.Dict(dict={'FIXED_COORDS': [[True, True, False], [False, True, False]]})
+    generate_calc_job(fixture_sandbox, entry_point_name, inputs)
+
+    with fixture_sandbox.open('aiida.in') as handle:
+        input_written = handle.read()
+
+    file_regression.check(input_written, encoding='utf-8', extension='.in')
+
+
+@pytest.mark.parametrize(['fixed_coords', 'error_message'], [
+    ([[True, True], [False, True]], 'The `fixed_coords` setting must be a list of lists with length 3.'),
+    ([[True, True, 1], [False, True, False]
+      ], 'All elements in the `fixed_coords` setting lists must be either `True` or `False`.'),
+    ([
+        [True, True, False],
+    ], 'Input structure has 2 sites, but fixed_coords has length 1'),
+])
+def test_fixed_coords_validation(fixture_sandbox, generate_calc_job, generate_inputs_pw, fixed_coords, error_message):
+    """Test the validation of the ``fixed_coords`` setting for the ``PwCalculation``."""
+    entry_point_name = 'quantumespresso.pw'
+
+    inputs = generate_inputs_pw()
+    inputs['settings'] = orm.Dict(dict={'FIXED_COORDS': fixed_coords})
+    with pytest.raises(ValueError, match=error_message):
+        generate_calc_job(fixture_sandbox, entry_point_name, inputs)

tests/calculations/test_pw/test_fixed_coords.in

@@ -0,0 +1,28 @@
+&CONTROL
+  calculation = 'scf'
+  outdir = './out/'
+  prefix = 'aiida'
+  pseudo_dir = './pseudo/'
+  verbosity = 'high'
+/
+&SYSTEM
+  ecutrho =   2.4000000000d+02
+  ecutwfc =   3.0000000000d+01
+  ibrav = 0
+  nat = 2
+  ntyp = 1
+/
+&ELECTRONS
+  electron_maxstep = 60
+/
+ATOMIC_SPECIES
+Si     28.0855 Si.upf
+ATOMIC_POSITIONS angstrom
+Si           0.0000000000       0.0000000000       0.0000000000 0 0 1
+Si           1.3575000000       1.3575000000       1.3575000000 1 0 1
+K_POINTS automatic
+2 2 2 0 0 0
+CELL_PARAMETERS angstrom
+      2.7150000000       2.7150000000       0.0000000000
+      2.7150000000       0.0000000000       2.7150000000
+      0.0000000000       2.7150000000       2.7150000000