Fix the ph tests

Author: mbercx

src/aiida_quantumespresso/parsers/parse_raw/ph.py

@@ -146,10 +146,48 @@ def parse_ph_text_output(lines, logs):
     :return: dictionary with parsed values
     """
 
+    def parse_qpoints(lines):
+        """Parse the q-points from the corresponding lines in the stdout."""
+
+        return {int(line.split()[0]): [float(coord) for coord in line.split()[1:4]] for line in lines}
+
+    def parse_mode_symmetries(lines, num_atoms):
+        """Parse the mode symmetries from the block after diagonalization of the dynamical matrix."""
+
+        q_data = {}
+        symlabel_q_point = [float(i) for i in lines[2].split('q = (')[-1].split(')')[0].split()]
+
+        q_data['mode_symmetry'] = []
+
+        for line in lines:
+
+            if 'Mode symmetry' in line:
+                q_data['point_group'] = line.split('Mode symmetry,')[1].split('point group:')[0].strip()
+
+            if '-->' in line:
+                freq_start = int(line.split('(')[1].split(')')[0].split('-')[0])
+                freq_end = int(line.split('(')[1].split(')')[0].split('-')[1])
+
+                if line.split()[-1] == 'I':
+                    symm_label = line.split()[-2]
+                else:
+                    symm_label = line.split()[-1]
+
+                q_data['mode_symmetry'].extend([symm_label] * (freq_end - freq_start + 1))
+
+        # If the mode symmetries are not printed, set those for the non-symmetry case
+        if 'point_group' not in q_data:
+            q_data['point_group'] = 'C_1'
+            q_data['mode_symmetry'] = ['A'] * (3 * num_atoms)
+
+        return symlabel_q_point, q_data
+
     parsed_data = {}
 
+    parsed_data['num_q_found'] = 0
+
     # Parse number of q-points and number of atoms
-    for line in lines:
+    for count, line in enumerate(lines):
 
         if 'q-points for this run' in line:
             try:

src/aiida_quantumespresso/parsers/ph.py

@@ -67,8 +67,14 @@ def parse_stdout(cls, stdout: str, tensor_file: str, dynmat_files: list) -> tupl
         from aiida_quantumespresso.parsers.parse_raw.ph import parse_raw_ph_output as parse_stdout
 
         parsed_base, logs_base = super().parse_stdout(stdout)
+
+        # if logs_base['error']:
+        #     return parsed_base, logs_base
+
         parsed_data, logs = parse_stdout(stdout, tensor_file, dynmat_files)
 
+
+
         parsed_data.update(parsed_base)
         for log_level, log_items in logs_base.items():
             logs[log_level].extend(log_items)

tests/parsers/test_ph.py

@@ -22,7 +22,7 @@ def test_ph_default(test_name, fixture_localhost, generate_calc_job_node, genera
 
     assert calcfunction.is_finished, calcfunction.exception
     assert calcfunction.is_finished_ok, calcfunction.exit_message
-    assert not orm.Log.collection.get_logs_for(node)
+    assert not [log for log in orm.Log.objects.get_logs_for(node) if log.levelname == 'ERROR']
     assert 'output_parameters' in results
     data_regression.check(results['output_parameters'].get_dict())
 

tests/parsers/test_ph/test_ph_default_default_.yml

@@ -56,4 +56,5 @@ number_of_atoms: 2
 number_of_irr_representations_for_each_q:
 - 2
 number_of_qpoints: 1
+wall_time: 15.25s
 wall_time_seconds: 15.25

tests/parsers/test_ph/test_ph_default_no_modes_printed_.yml

@@ -1,3 +1,4 @@
+code_version: v.6.8
 dynamical_matrix_1:
   frequencies:
   - 147.433165
@@ -24,4 +25,5 @@ number_of_atoms: 2
 number_of_irr_representations_for_each_q:
 - 6
 number_of_qpoints: 1
+wall_time: 26.71s
 wall_time_seconds: 26.71

tests/parsers/test_ph/test_ph_default_single_qpoint_.yml

@@ -1,3 +1,4 @@
+code_version: v.7.0
 dynamical_matrix_1:
   frequencies:
   - -3.206051
@@ -18,4 +19,5 @@ number_of_atoms: 1
 number_of_irr_representations_for_each_q:
 - 2
 number_of_qpoints: 1
+wall_time: 23.37s
 wall_time_seconds: 23.37

tests/parsers/test_ph/test_ph_not_converged.yml

@@ -3,4 +3,5 @@ number_of_atoms: 2
 number_of_irr_representations_for_each_q:
 - 2
 number_of_qpoints: 8
+wall_time: 3m21.58s
 wall_time_seconds: 201.57999999999998

tests/parsers/test_ph/test_ph_out_of_walltime.yml

@@ -3,4 +3,5 @@ number_of_atoms: 2
 number_of_irr_representations_for_each_q:
 - 2
 number_of_qpoints: 3
+wall_time: 7.13s
 wall_time_seconds: 7.13

tests/workflows/ph/test_base/test_merge_outputs_merge_outputs_.yml

@@ -1,3 +1,4 @@
+code_version: v.7.0
 dynamical_matrix_1:
   frequencies:
   - -3.205876
@@ -53,4 +54,5 @@ number_of_irr_representations_for_each_q:
 - 3
 - 3
 number_of_qpoints: 4
+wall_time: 55.47s
 wall_time_seconds: 113.61

tests/workflows/ph/test_base/test_merge_outputs_merge_outputs_singleq_.yml

@@ -1,3 +1,4 @@
+code_version: v.7.0
 dynamical_matrix_1:
   frequencies:
   - -3.151844
@@ -18,4 +19,5 @@ number_of_atoms: 1
 number_of_irr_representations_for_each_q:
 - 2
 number_of_qpoints: 1
+wall_time: 7.40s
 wall_time_seconds: 27.53