Local changes for hero run; disentangle later

src/aiida_quantumespresso/calculations/__init__.py

@@ -734,6 +734,9 @@ def _generate_PWCPinputdata(cls, parameters, settings, pseudos, structure, kpoin
                     'namelists using the NAMELISTS inside the `settings` input node'
                 ) from exception
 
+        if 'DIRECT_MINIMIZATION' in input_params:
+            namelists_toprint.append('DIRECT_MINIMIZATION')
+
         inputfile = ''
         for namelist_name in namelists_toprint:
             inputfile += f'&{namelist_name}\n'

src/aiida_quantumespresso/calculations/pw.py

@@ -13,7 +13,7 @@
 class PwCalculation(BasePwCpInputGenerator):
     """`CalcJob` implementation for the pw.x code of Quantum ESPRESSO."""
 
-    _default_namelists = ('CONTROL', 'SYSTEM', 'ELECTRONS', 'DIRECT_MINIMIZATION')
+    _default_namelists = ('CONTROL', 'SYSTEM', 'ELECTRONS')
 
     _automatic_namelists = {
         'scf': _default_namelists,
@@ -161,6 +161,8 @@ def define(cls, spec):
         spec.exit_code(542, 'ERROR_RADIAL_FFT_SIGNIFICANT_VOLUME_CONTRACTION',
             message=('The cell relaxation caused a significant volume contraction '
                      'and there is not enough space allocated for radial FFT.'))
+        spec.exit_code(543, 'ERROR_SYMMETRY_OPERATIONS_NOT_SATISFIED',
+            message='The variable cell optimization caused the symmetry operations to not be satisfied.')
 
         # Strong warnings about calculation results, but something tells us that you're ok with that
         spec.exit_code(710, 'WARNING_ELECTRONIC_CONVERGENCE_NOT_REACHED',

src/aiida_quantumespresso/parsers/parse_raw/pw.py

@@ -243,7 +243,7 @@ def detect_important_message(logs, line):
         'error': {
             'Maximum CPU time exceeded': 'ERROR_OUT_OF_WALLTIME',
             'convergence NOT achieved after': 'ERROR_ELECTRONIC_CONVERGENCE_NOT_REACHED',
-            'history already reset at previous step: stopping': 'ERROR_IONIC_CYCLE_BFGS_HISTORY_FAILURE',
+            'history already reset at previous step: ': 'ERROR_IONIC_CYCLE_BFGS_HISTORY_FAILURE',
             'problems computing cholesky': 'ERROR_DIAGONALIZATION_CHOLESKY_DECOMPOSITION',
             'charge is wrong': 'ERROR_CHARGE_IS_WRONG',
             'not orthogonal operation': 'ERROR_SYMMETRY_NON_ORTHOGONAL_OPERATION',
@@ -258,6 +258,7 @@ def detect_important_message(logs, line):
             'Error in routine broyden': 'ERROR_BROYDEN_FACTORIZATION',
             'Not enough space allocated for radial FFT: try restarting with a larger cell_factor': 'ERROR_RADIAL_FFT_SIGNIFICANT_VOLUME_CONTRACTION',
             REG_ERROR_NPOOLS_TOO_HIGH: 'ERROR_NPOOLS_TOO_HIGH',
+            'some of the original symmetry operations not satisfied': 'ERROR_SYMMETRY_OPERATIONS_NOT_SATISFIED'
         },
         'warning': {
             'Warning:': None,

src/aiida_quantumespresso/parsers/parse_xml/parse.py

@@ -11,7 +11,7 @@
 
 from .exceptions import XMLParseError
 from .versions import get_default_schema_filepath, get_schema_filepath
-
+from ..pw import fix_sirius_xml_prints
 
 def raise_parsing_error(message):
     raise XMLParseError(message)
@@ -511,8 +511,8 @@ def parse_xml_post_6_2(xml):
 
     for atom in outputs['atomic_structure']['atomic_positions']['atom']:
         atomic_species_name.append(atom['@name'])
-        atoms.append([atom['@name'], [coord * CONSTANTS.bohr_to_ang for coord in atom['$']]])
-
+        atoms.append([atom['@name'], [fix_sirius_xml_prints(coord) * CONSTANTS.bohr_to_ang for coord in atom['$']]])
+        
     species = outputs['atomic_species']['species']
     structure_data = {
         'atomic_positions_units': 'Angstrom',
@@ -568,7 +568,7 @@ def parse_xml_post_6_2(xml):
 
 def parse_step_to_trajectory(trajectory, data, skip_structure=False):
     """."""
-    from ..pw import fix_sirius_xml_prints
+    from ..pw import fix_sirius_xml_prints # Do we really need that here? If we use it in other parts of the parser maybe we put it in the beginning? 
 
     if 'scf_conv' in data and 'n_scf_steps' in data['scf_conv']:
         scf_iterations = data['scf_conv']['n_scf_steps']  # Can be zero in case of initialization-only calculation
@@ -602,9 +602,9 @@ def parse_step_to_trajectory(trajectory, data, skip_structure=False):
     if 'forces' in data and '$' in data['forces']:
         forces = np.array(data['forces']['$'])
         dimensions = data['forces']['@dims']  # Like [3, 2], should be reversed to reshape the forces array
-        trajectory['forces'].append(forces.reshape(dimensions[::-1]))
+        trajectory['forces'].append(fix_sirius_xml_prints(forces.reshape(dimensions[::-1])))
 
     if 'stress' in data and '$' in data['stress']:
         stress = np.array(data['stress']['$'])
         dimensions = data['stress']['@dims']  # Like [3, 3], should be reversed to reshape the stress array
-        trajectory['stress'].append(stress.reshape(dimensions[::-1]))
+        trajectory['stress'].append(fix_sirius_xml_prints(stress.reshape(dimensions[::-1])))

src/aiida_quantumespresso/workflows/pw/base.py

@@ -640,3 +640,21 @@ def handle_electronic_convergence_warning(self, calculation):
         self.report_error_handled(calculation, action)
         self.results()  # Call the results method to attach the output nodes
         return ProcessHandlerReport(True, self.exit_codes.WARNING_ELECTRONIC_CONVERGENCE_NOT_REACHED)
+
+
+    @process_handler(priority=541, exit_codes=[
+        PwCalculation.exit_codes.ERROR_SYMMETRY_NON_ORTHOGONAL_OPERATION,
+        PwCalculation.exit_codes.ERROR_SYMMETRY_OPERATIONS_NOT_SATISFIED,
+    ])
+    def handle_symmetry_non_orthogonal_warning(self, calculation):
+        """Handle `ERROR_SYMMETRY_NON_ORTHOGONAL_OPERATION` and `ERROR_SYMMETRY_OPERATIONS_NOT_SATISFIED`
+
+        Use the structure from the last relaxation step as the starting point and restart from scratch.
+        """
+
+        self.ctx.inputs.structure = calculation.outputs.output_structure
+        action = 'initialised the structure again and restarting from scratch.'
+
+        self.set_restart_type(RestartType.FROM_SCRATCH)
+        self.report_error_handled(calculation, action)
+        return ProcessHandlerReport(True)

src/aiida_quantumespresso/workflows/pw/relax.py

@@ -267,7 +267,7 @@ def should_run_relax(self):
             self.report('Pulay stresses still present, running another geometry optimizatio.')
             return True
 
-        # If the kpoints are defined as a density, make sure the kpoints mesh is the same for the new structur
+        # If the kpoints are defined as a density, make sure the kpoints mesh is the same for the new structure
         if 'kpoints_distance' in self.ctx.relax_inputs:
             input_kpts_mesh, _ = base_relax_workchain.base.links.get_outgoing(
                 link_label_filter='iteration_01'