diff --git a/aiida_quantumespresso/parsers/pp.py b/aiida_quantumespresso/parsers/pp.py index b98d76284..a2dd0732c 100644 --- a/aiida_quantumespresso/parsers/pp.py +++ b/aiida_quantumespresso/parsers/pp.py @@ -213,9 +213,9 @@ def detect_important_message(logs, line): # Parse useful data from stdout for line in stdout_lines: - if 'Check:' in line: + if 'Check:' in line: # QE < 6.5 split_line = line.split('=') - if 'negative/imaginary' in line: # QE6.1 + if 'negative/imaginary' in line: # QE6.1-6.3 output_dict['negative_core_charge'] = float(split_line[-1].split()[0]) output_dict['imaginary_core_charge'] = float(split_line[-1].split()[-1]) else: # QE6.4 @@ -354,12 +354,6 @@ def parse_gaussian(self, data_file_str): voxel_array = np.array([[x_line[1], x_line[2], x_line[3]], [y_line[1], y_line[2], y_line[3]], [z_line[1], z_line[2], z_line[3]]], dtype=np.float64) - atomic_numbers = np.empty(natoms, int) - coordinates = np.empty((natoms, 3)) - for i in range(natoms): - line = header[6 + i].split() - atomic_numbers[i] = int(line[0]) - coordinates[i] = [float(s) for s in line[2:]] # Get the volumetric data data_array = np.empty(xdim * ydim * zdim, dtype=float) @@ -378,7 +372,5 @@ def parse_gaussian(self, data_file_str): arraydata.set_array('data', data_array) arraydata.set_array('data_units', np.array(data_units)) arraydata.set_array('coordinates_units', np.array(coordinates_units)) - arraydata.set_array('coordinates', coordinates) - arraydata.set_array('atomic_numbers', atomic_numbers) return arraydata diff --git a/tests/parsers/test_pp.py b/tests/parsers/test_pp.py index 8e92890dd..502b76e87 100644 --- a/tests/parsers/test_pp.py +++ b/tests/parsers/test_pp.py @@ -271,7 +271,7 @@ def test_pp_default_3d( assert calcfunction.is_finished_ok, calcfunction.exit_message assert 'output_parameters' in results assert 'output_data' in results - assert len(results['output_data'].get_arraynames()) == 6 + assert len(results['output_data'].get_arraynames()) == 4 data_array = results['output_data'].get_array('data').flatten() voxel_array = results['output_data'].get_array('voxel').flatten() data_units_array = results['output_data'].get_array('data_units') @@ -313,7 +313,7 @@ def test_pp_default_3d_keep_plot_file( assert calcfunction.is_finished_ok, calcfunction.exit_message assert 'output_parameters' in results assert 'output_data' in results - assert len(results['output_data'].get_arraynames()) == 6 + assert len(results['output_data'].get_arraynames()) == 4 def test_pp_default_3d_multiple(aiida_profile, generate_calc_job_node, generate_parser, generate_inputs_3d): @@ -334,7 +334,7 @@ def test_pp_default_3d_multiple(aiida_profile, generate_calc_job_node, generate_ for key in ['K001_B001', 'K001_B002']: assert key in results['output_data_multiple'] node = results['output_data_multiple'][key] - assert len(node.get_arraynames()) == 6 + assert len(node.get_arraynames()) == 4 def test_pp_default_3d_failed_missing(