Remove parsing of coordinates and atomic numbers

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

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(