Add structure parsing

aiida_quantumespresso/parsers/pp.py

@@ -217,7 +217,7 @@ def detect_important_message(logs, line):
  split_line = line.split('=')
  if 'negative/imaginary' in line: # QE6.1
  output_dict['negative_core_charge'] = float(split_line[-1].split()[0])
- output_dict['imaginary_core_charge'] = float(split_line.split()[-1])
+ output_dict['imaginary_core_charge'] = float(split_line[-1].split()[-1])
  else: # QE6.4
  output_dict['negative_core_charge'] = float(split_line[1])
  if 'Min, Max, imaginary charge:' in line:
@@ -335,10 +335,15 @@ def parse_gaussian(self, data_file_str):
  """
  lines = data_file_str.splitlines()
 
+ title = lines[0]
+ comment = lines[1]
+
  atoms_line = lines[2].split()
- atoms = int(atoms_line[0]) # The number of atoms listed in the file
- header = lines[:6 + atoms] # Header of the file: comments, the voxel, and the number of atoms and datapoints
- data_lines = lines[6 + atoms:] # The actual data: atoms and volumetric data
+ natoms = int(atoms_line[0]) # The number of atoms listed in the file
+ origin = np.array(atoms_line[1:], dtype=float)
+
+ header = lines[:6 + natoms] # Header of the file: comments, the voxel, and the number of atoms and datapoints
+ data_lines = lines[6 + natoms:] # The actual data: atoms and volumetric data
 
  # Parse the declared dimensions of the volumetric data
  x_line = header[3].split()
@@ -352,6 +357,12 @@ 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)
@@ -368,7 +379,9 @@ def parse_gaussian(self, data_file_str):
  arraydata = orm.ArrayData()
  arraydata.set_array('voxel', voxel_array)
  arraydata.set_array('data', data_array)
- arraydata.set_array('coordinates_units', np.array(coordinates_units))
  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