Adding ENVIRON namelists

aiida_quantumespresso/parsers/parse_raw/pw.py

@@ -267,7 +267,7 @@ def detect_important_message(logs, line):
             logs.warning.append(message)
 
 
-def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None):
+def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None, settings={}):
     """Parses the stdout content of a Quantum ESPRESSO `pw.x` calculation.
 
     :param stdout: the stdout content as a string
@@ -306,6 +306,9 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
     # Determine whether the input switched on an electric field
     lelfield = input_parameters.get('CONTROL', {}).get('lelfield', False)
 
+    # Determine if an ENVIRON calculation run
+    is_environ = 'ENVIRON' in setttings
+
     # Find some useful quantities.
     if not parsed_xml.get('number_of_bands', None):
         try:
@@ -743,7 +746,7 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
                     parsed_data['fermi_energy' + units_suffix] = default_energy_units
                 except Exception:
                     logs.warning.append('Error while parsing Fermi energy from the output file.')
-            elif 'Gaussian-smeared nuclei' in line:
+            elif is_environ and 'Gaussian-smeared nuclei' in line:
                 try:
                     value_potential_shift = float(line.split()[-2])
                     unit_potential_shift = line.split()[-1]

aiida_quantumespresso/parsers/pw.py

@@ -44,7 +44,7 @@ def parse(self, **kwargs):
 
         parameters = self.node.inputs.parameters.get_dict()
         parsed_xml, logs_xml = self.parse_xml(dir_with_bands, parser_options)
-        parsed_stdout, logs_stdout = self.parse_stdout(parameters, parser_options, parsed_xml)
+        parsed_stdout, logs_stdout = self.parse_stdout(parameters, parser_options, parsed_xml, settings)
 
         parsed_bands = parsed_stdout.pop('bands', {})
         parsed_structure = parsed_stdout.pop('structure', {})
@@ -295,7 +295,7 @@ def parse_xml(self, dir_with_bands=None, parser_options=None):
 
         return parsed_data, logs
 
-    def parse_stdout(self, parameters, parser_options=None, parsed_xml=None):
+    def parse_stdout(self, parameters, parser_options=None, parsed_xml=None, settings={}):
         """Parse the stdout output file.
 
         :param parameters: the input parameters dictionary
@@ -321,7 +321,7 @@ def parse_stdout(self, parameters, parser_options=None, parsed_xml=None):
             return parsed_data, logs
 
         try:
-            parsed_data, logs = parse_stdout(stdout, parameters, parser_options, parsed_xml)
+            parsed_data, logs = parse_stdout(stdout, parameters, parser_options, parsed_xml, settings)
         except Exception:
             logs.critical.append(traceback.format_exc())
             self.exit_code_stdout = self.exit_codes.ERROR_UNEXPECTED_PARSER_EXCEPTION

tests/calculations/test_pw.py

@@ -73,7 +73,7 @@ def test_pw_ibrav(
     calc_info = generate_calc_job(fixture_sandbox, entry_point_name, inputs)
 
     cmdline_params = ['-in', 'aiida.in']
-    local_copy_list = [(upf.uuid, upf.filename, u'./pseudo/Si.upf')]
+    local_copy_list = [(upf.uuid, upf.filename, './pseudo/Si.upf')]
     retrieve_list = ['aiida.out', './out/aiida.save/data-file-schema.xml', './out/aiida.save/data-file.xml']
     retrieve_temporary_list = [['./out/aiida.save/K*[0-9]/eigenval*.xml', '.', 2]]
 
@@ -252,7 +252,7 @@ def test_pw_parallelization_duplicate_cmdline_flag(fixture_sandbox, generate_cal
     assert 'Conflicting' in str(exc.value)
 
 
-def test_environ_pw_namelists(fixture_sandbox, generate_calc_job, generate_inputs_pw, file_regression):
+def test_environ_namelists(fixture_sandbox, generate_calc_job, generate_inputs_pw, file_regression):
     """Test that Environ does not change the contents of the pw file created."""
     entry_point_name = 'quantumespresso.pw'
 
@@ -276,38 +276,11 @@ def test_environ_pw_namelists(fixture_sandbox, generate_calc_job, generate_input
 
     with fixture_sandbox.open('aiida.in') as handle:
         input_written = handle.read()
-
-    # Checks on the files written to the sandbox folder as raw input
-    assert sorted(fixture_sandbox.get_content_list()) == sorted(['aiida.in', 'pseudo', 'out', 'environ.in'])
-    # Check the aiida.in files are written correctly
-    file_regression.check(input_written, encoding='utf-8', extension='.in')
-
-def test_environ_namelists(fixture_sandbox, generate_calc_job, generate_inputs_pw, file_regression):
-    """Test that Environ namelists are created."""
-    entry_point_name = 'quantumespresso.pw'
-
-    inputs = generate_inputs_pw()
-    inputs['settings'] = orm.Dict(
-        dict={
-            'ENVIRON': {
-                'electrolyte_linearized': True,
-                'environ_type': 'input',
-            },
-            'BOUNDARY': {
-                'solvent_mode': 'electronic',
-                'electrolyte_mode': 'electronic',
-            },
-            'ELECTROSTATIC': {
-                'pbc_correction': 'parabolic',
-            }
-        },
-    )
-    generate_calc_job(fixture_sandbox, entry_point_name, inputs)
-
     with fixture_sandbox.open('environ.in') as handle:
         environ_written = handle.read()
 
     # Checks on the files written to the sandbox folder as raw input
     assert sorted(fixture_sandbox.get_content_list()) == sorted(['aiida.in', 'pseudo', 'out', 'environ.in'])
-    # Checks on the files written to the sandbox folder as raw input
-    file_regression.check(environ_written, encoding='utf-8', extension='.in')
+    # Check the aiida.in files are written correctly
+    file_regression.check(input_written, encoding='utf-8', extension='.aiida.in')
+    file_regression.check(environ_written, encoding='utf-8', extension='.environ.in')