Update to qe-tools 2.0.0rc1.

aiida_quantumespresso/calculations/pwimmigrant.py

@@ -199,7 +199,7 @@ class or using the ``set_`` methods (e.g. ``set_remote_workdir``).
  # Parse the input file.
  local_path = os.path.join(folder.abspath, self._INPUT_FILE_NAME)
  with open(local_path) as fin:
- pwinputfile = pwinputparser.PwInputFile(fin)
+ pwinputfile = pwinputparser.PwInputFile(fin.read())
 
  # Determine PREFIX, if it hasn't already been set by the user.
  if self._PREFIX is None:

aiida_quantumespresso/cli/data/structure.py

@@ -21,7 +21,8 @@ def cmd_import(filename, dry_run):
  """Import a `StructureData` from a Quantum ESPRESSO input file."""
  from aiida_quantumespresso.tools.pwinputparser import PwInputFile
 
- parser = PwInputFile(filename)
+ with open(filename, 'r') as input_file:
+ parser = PwInputFile(input_file.read())
  structure = parser.get_structuredata()
  formula = structure.get_formula()
 

aiida_quantumespresso/data/force_constants.py

@@ -2,8 +2,8 @@
 """Sub class of `Data` to handle interatomic force constants produced by the Quantum ESPRESSO q2r.x code."""
 import numpy
 
-from qe_tools.constants import bohr_to_ang
 from aiida.orm import SinglefileData
+from qe_tools import CONSTANTS
 
 
 class ForceConstantsData(SinglefileData):
@@ -147,7 +147,9 @@ def parse_q2r_force_constants_file(lines, also_force_constants=False):
 
  # read cell data
  cell = tuple(
- tuple(float(c) * celldm[0] * bohr_to_ang for c in l.split()) for l in lines[current_line:current_line + 3]
+ tuple(float(c) * celldm[0] * CONSTANTS.bohr_to_ang
+ for c in l.split())
+ for l in lines[current_line:current_line + 3]
  )
  parsed_data['cell'] = cell
  current_line += 3
@@ -169,7 +171,7 @@ def parse_q2r_force_constants_file(lines, also_force_constants=False):
  line[0] = atom_type_list[ityp - 1][0] # string with element name
  line[1] = atom_type_list[ityp - 1][1] # element mass in amu_ry
  # Convert atomic positions (in cartesian) from alat to Angstrom:
- line[2:] = [pos * celldm[0] * bohr_to_ang for pos in line[2:]]
+ line[2:] = [pos * celldm[0] * CONSTANTS.bohr_to_ang for pos in line[2:]]
  atom_list.append(tuple(line))
  current_line += 1
 

aiida_quantumespresso/parsers/cp.py

@@ -5,7 +5,7 @@
 from aiida.common import NotExistent
 from aiida.orm import Dict, TrajectoryData
 
-from qe_tools.constants import bohr_to_ang, hartree_to_ev, timeau_to_sec
+from qe_tools import CONSTANTS
 from aiida_quantumespresso.parsers.parse_raw.cp import parse_cp_raw_output, parse_cp_traj_stanzas
 from .base import Parser
 
@@ -66,9 +66,12 @@ def parse(self, **kwargs):
  return self.exit(self.exit_codes.ERROR_READING_POS_FILE)
 
  trajectories = [
- ('positions', 'pos', bohr_to_ang, out_dict['number_of_atoms']),
- ('cells', 'cel', bohr_to_ang, 3),
- ('velocities', 'vel', bohr_to_ang / timeau_to_sec * 10**12, out_dict['number_of_atoms']),
+ ('positions', 'pos', CONSTANTS.bohr_to_ang, out_dict['number_of_atoms']),
+ ('cells', 'cel', CONSTANTS.bohr_to_ang, 3),
+ (
+ 'velocities', 'vel', CONSTANTS.bohr_to_ang / CONSTANTS.timeau_to_sec * 10**12,
+ out_dict['number_of_atoms']
+ ),
  ]
 
  for name, extension, scale, elements in trajectories:
@@ -109,26 +112,26 @@ def parse(self, **kwargs):
  #print "New version"
  raw_trajectory['steps'] = numpy.array(matrix[:, 0], dtype=int)
  raw_trajectory['evp_times'] = matrix[:, 1] # TPS, ps
- raw_trajectory['electronic_kinetic_energy'] = matrix[:, 2] * hartree_to_ev # EKINC, eV
+ raw_trajectory['electronic_kinetic_energy'] = matrix[:, 2] * CONSTANTS.hartree_to_ev # EKINC, eV
  raw_trajectory['cell_temperature'] = matrix[:, 3] # TEMPH, K
  raw_trajectory['ionic_temperature'] = matrix[:, 4] # TEMPP, K
- raw_trajectory['scf_total_energy'] = matrix[:, 5] * hartree_to_ev # ETOT, eV
- raw_trajectory['enthalpy'] = matrix[:, 6] * hartree_to_ev # ENTHAL, eV
- raw_trajectory['enthalpy_plus_kinetic'] = matrix[:, 7] * hartree_to_ev # ECONS, eV
- raw_trajectory['energy_constant_motion'] = matrix[:, 8] * hartree_to_ev # ECONT, eV
- raw_trajectory['volume'] = matrix[:, 9] * (bohr_to_ang**3) # volume, angstrom^3
+ raw_trajectory['scf_total_energy'] = matrix[:, 5] * CONSTANTS.hartree_to_ev # ETOT, eV
+ raw_trajectory['enthalpy'] = matrix[:, 6] * CONSTANTS.hartree_to_ev # ENTHAL, eV
+ raw_trajectory['enthalpy_plus_kinetic'] = matrix[:, 7] * CONSTANTS.hartree_to_ev # ECONS, eV
+ raw_trajectory['energy_constant_motion'] = matrix[:, 8] * CONSTANTS.hartree_to_ev # ECONT, eV
+ raw_trajectory['volume'] = matrix[:, 9] * (CONSTANTS.bohr_to_ang**3) # volume, angstrom^3
  raw_trajectory['pressure'] = matrix[:, 10] # out_press, GPa
  else:
  #print "Old version"
  raw_trajectory['steps'] = numpy.array(matrix[:, 0], dtype=int)
- raw_trajectory['electronic_kinetic_energy'] = matrix[:, 1] * hartree_to_ev # EKINC, eV
+ raw_trajectory['electronic_kinetic_energy'] = matrix[:, 1] * CONSTANTS.hartree_to_ev # EKINC, eV
  raw_trajectory['cell_temperature'] = matrix[:, 2] # TEMPH, K
  raw_trajectory['ionic_temperature'] = matrix[:, 3] # TEMPP, K
- raw_trajectory['scf_total_energy'] = matrix[:, 4] * hartree_to_ev # ETOT, eV
- raw_trajectory['enthalpy'] = matrix[:, 5] * hartree_to_ev # ENTHAL, eV
- raw_trajectory['enthalpy_plus_kinetic'] = matrix[:, 6] * hartree_to_ev # ECONS, eV
- raw_trajectory['energy_constant_motion'] = matrix[:, 7] * hartree_to_ev # ECONT, eV
- raw_trajectory['volume'] = matrix[:, 8] * (bohr_to_ang**3) # volume, angstrom^3
+ raw_trajectory['scf_total_energy'] = matrix[:, 4] * CONSTANTS.hartree_to_ev # ETOT, eV
+ raw_trajectory['enthalpy'] = matrix[:, 5] * CONSTANTS.hartree_to_ev # ENTHAL, eV
+ raw_trajectory['enthalpy_plus_kinetic'] = matrix[:, 6] * CONSTANTS.hartree_to_ev # ECONS, eV
+ raw_trajectory['energy_constant_motion'] = matrix[:, 7] * CONSTANTS.hartree_to_ev # ECONT, eV
+ raw_trajectory['volume'] = matrix[:, 8] * (CONSTANTS.bohr_to_ang**3) # volume, angstrom^3
  raw_trajectory['pressure'] = matrix[:, 9] # out_press, GPa
  raw_trajectory['evp_times'] = matrix[:, 10] # TPS, ps
 

aiida_quantumespresso/parsers/matdyn.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 from aiida import orm
 from aiida.common import exceptions
-from qe_tools.constants import invcm_to_THz
+from qe_tools import CONSTANTS
 
 from aiida_quantumespresso.calculations.matdyn import MatdynCalculation
 from .base import Parser
@@ -114,7 +114,7 @@ def parse_raw_matdyn_phonon_file(phonon_frequencies):
  for i in range(num_kpoints):
  for j in range(num_bands):
  try:
- freq_matrix[i, j] = corrected_data[counter] * invcm_to_THz # from cm-1 to THz
+ freq_matrix[i, j] = corrected_data[counter] * CONSTANTS.invcm_to_THz # from cm-1 to THz
  except ValueError:
  parsed_data['warnings'].append('Error while parsing the frequencies')
  except IndexError:

aiida_quantumespresso/parsers/parse_raw/neb.py

@@ -5,7 +5,7 @@
 specific functionalities. The parsing will try to convert whatever it can in some dictionary, which by operative
 decision doesn't have much structure encoded, [the values are simple ]
 """
-from qe_tools.constants import bohr_to_ang
+from qe_tools import CONSTANTS
 
 from aiida_quantumespresso.parsers import QEOutputParsingError, get_parser_info
 from aiida_quantumespresso.parsers.parse_raw import convert_qe_time_to_sec
@@ -148,10 +148,10 @@ def parse_neb_text_output(data, input_dict={}):
  for count, line in enumerate(lines):
  if 'initial path length' in line:
  initial_path_length = float(line.split('=')[1].split('bohr')[0])
- parsed_data['initial_path_length'] = initial_path_length * bohr_to_ang
+ parsed_data['initial_path_length'] = initial_path_length * CONSTANTS.bohr_to_ang
  elif 'initial inter-image distance' in line:
  initial_image_dist = float(line.split('=')[1].split('bohr')[0])
- parsed_data['initial_image_dist'] = initial_image_dist * bohr_to_ang
+ parsed_data['initial_image_dist'] = initial_image_dist * CONSTANTS.bohr_to_ang
  elif 'string_method' in line:
  parsed_data['string_method'] = line.split('=')[1].strip()
  elif 'restart_mode' in line:
@@ -235,9 +235,9 @@ def parse_neb_text_output(data, input_dict={}):
  iteration_data['climbing_image_auto'].append([int(_) for _ in line.split('=')[1].split(',')])
  elif 'path length' in line:
  path_length = float(line.split('=')[1].split('bohr')[0])
- iteration_data['path_length'].append(path_length * bohr_to_ang)
+ iteration_data['path_length'].append(path_length * CONSTANTS.bohr_to_ang)
  elif 'inter-image distance' in line:
  image_dist = float(line.split('=')[1].split('bohr')[0])
- iteration_data['image_dist'].append(image_dist * bohr_to_ang)
+ iteration_data['image_dist'].append(image_dist * CONSTANTS.bohr_to_ang)
 
  return parsed_data, dict(iteration_data), list(critical_warnings.values())

aiida_quantumespresso/parsers/parse_raw/ph.py

@@ -6,7 +6,7 @@
 """
 import numpy
 
-from qe_tools.constants import *
+from qe_tools import CONSTANTS
 
 from aiida_quantumespresso.parsers import QEOutputParsingError, get_parser_info
 from aiida_quantumespresso.parsers.parse_raw.base import convert_qe_time_to_sec
@@ -282,7 +282,7 @@ def parse_ph_dynmat(data, logs, lattice_parameter=None, also_eigenvectors=False,
  header_dict['ibrav'] = int(pieces[2])
  header_dict['celldm'] = [float(i) for i in pieces[3:]]
  # In angstrom
- alat = header_dict['celldm'][0] * bohr_to_ang
+ alat = header_dict['celldm'][0] * CONSTANTS.bohr_to_ang
  if abs(alat) < 1.e-5:
  raise QEOutputParsingError(
  'Lattice constant=0! Probably you are using an '
@@ -318,7 +318,7 @@ def parse_ph_dynmat(data, logs, lattice_parameter=None, also_eigenvectors=False,
  try:
  if int(pieces[0]) != idx:
  raise QEOutputParsingError('Error with the indices of the species')
- species.append([pieces[1].strip(), float(pieces[2]) / amu_Ry])
+ species.append([pieces[1].strip(), float(pieces[2]) / CONSTANTS.amu_Ry])
  except ValueError:
  raise QEOutputParsingError('Error parsing the species')
 

aiida_quantumespresso/parsers/parse_raw/pw.py

@@ -7,7 +7,7 @@
 """
 import re
 import numpy
-from qe_tools.constants import ry_to_ev, bohr_to_ang, ry_si, bohr_si
+from qe_tools import CONSTANTS
 
 from aiida_quantumespresso.parsers import QEOutputParsingError
 from aiida_quantumespresso.parsers.parse_raw import convert_qe_time_to_sec
@@ -334,8 +334,8 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
  elif 'Smooth grid' in line:
  smooth_FFT_grid = [int(g) for g in line.split('(')[1].split(')')[0].split(',')]
  break
- alat *= bohr_to_ang
- volume *= bohr_to_ang**3
+ alat *= CONSTANTS.bohr_to_ang
+ volume *= CONSTANTS.bohr_to_ang**3
  parsed_data['lattice_parameter_initial'] = alat
  parsed_data['number_of_bands'] = nbnd
  try:
@@ -514,19 +514,19 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
  )
 
  if 'alat' in lattice[0].lower():
- a1 = [alat * bohr_to_ang * float(s) for s in a1]
- a2 = [alat * bohr_to_ang * float(s) for s in a2]
- a3 = [alat * bohr_to_ang * float(s) for s in a3]
+ a1 = [alat * CONSTANTS.bohr_to_ang * float(s) for s in a1]
+ a2 = [alat * CONSTANTS.bohr_to_ang * float(s) for s in a2]
+ a3 = [alat * CONSTANTS.bohr_to_ang * float(s) for s in a3]
  lattice_parameter_b = float(lattice[1])
  if abs(lattice_parameter_b - alat) > lattice_tolerance:
  raise QEOutputParsingError(
  'Lattice parameters mismatch! ' + '{} vs {}'.format(lattice_parameter_b, alat)
  )
  elif 'bohr' in lattice[0].lower():
- lattice_parameter_b *= bohr_to_ang
- a1 = [bohr_to_ang * float(s) for s in a1]
- a2 = [bohr_to_ang * float(s) for s in a2]
- a3 = [bohr_to_ang * float(s) for s in a3]
+ lattice_parameter_b *= CONSTANTS.bohr_to_ang
+ a1 = [CONSTANTS.bohr_to_ang * float(s) for s in a1]
+ a2 = [CONSTANTS.bohr_to_ang * float(s) for s in a2]
+ a3 = [CONSTANTS.bohr_to_ang * float(s) for s in a3]
  trajectory_data.setdefault('lattice_vectors_relax', []).append([a1, a2, a3])
 
  except Exception:
@@ -550,7 +550,7 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
  if metric == 'alat':
  tau = [alat * float(s) for s in tau]
  elif metric == 'bohr':
- tau = [bohr_to_ang * float(s) for s in tau]
+ tau = [CONSTANTS.bohr_to_ang * float(s) for s in tau]
  positions.append(tau)
  trajectory_data.setdefault(this_key, []).append(positions)
  except Exception:
@@ -590,7 +590,7 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
  # If for some step this line is not printed, the later check with the scf_accuracy array length should catch it
  elif 'estimated scf accuracy' in line:
  try:
- value = float(line.split()[-2]) * ry_to_ev
+ value = float(line.split()[-2]) * CONSTANTS.ry_to_ev
  trajectory_data.setdefault('scf_accuracy', []).append(value)
  except Exception:
  logs.warning.append('Error while parsing scf accuracy.')
@@ -654,7 +654,7 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
  elif '!' in line:
  try:
 
- En = float(line.split('=')[1].split('Ry')[0]) * ry_to_ev
+ En = float(line.split('=')[1].split('Ry')[0]) * CONSTANTS.ry_to_ev
 
  # Up till v6.5, the line after total energy would be the Harris-Foulkes estimate, followed by the
  # estimated SCF accuracy. However, pw.x v6.6 removed the HF estimate line.
@@ -663,7 +663,7 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
  subline = data_step[count + i]
  if marker in subline:
  try:
- E_acc = float(subline.split('<')[1].split('Ry')[0]) * ry_to_ev
+ E_acc = float(subline.split('<')[1].split('Ry')[0]) * CONSTANTS.ry_to_ev
  except Exception:
  pass
  else:
@@ -754,7 +754,7 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
  if 'atom ' in line2:
  line2 = line2.split('=')[1].split()
  # CONVERT FORCES IN eV/Ang
- vec = [float(s) * ry_to_ev / bohr_to_ang for s in line2]
+ vec = [float(s) * CONSTANTS.ry_to_ev / CONSTANTS.bohr_to_ang for s in line2]
  forces.append(vec)
  if len(forces) == nat:
  break
@@ -767,7 +767,7 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
 
  elif 'Total force =' in line:
  try: # note that I can't check the units: not written in output!
- value = float(line.split('=')[1].split('Total')[0]) * ry_to_ev / bohr_to_ang
+ value = float(line.split('=')[1].split('Total')[0]) * CONSTANTS.ry_to_ev / CONSTANTS.bohr_to_ang
  trajectory_data.setdefault('total_force', []).append(value)
  parsed_data['total_force' + units_suffix] = default_force_units
  except Exception:
@@ -791,7 +791,7 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
  raise QEOutputParsingError('Error while parsing stress: unexpected units.')
  for k in range(3):
  line2 = data_step[count2 + k + 1].split()
- vec = [float(s) * 10**(-9) * ry_si / (bohr_si)**3 for s in line2[0:3]]
+ vec = [float(s) * 10**(-9) * CONSTANTS.ry_si / (CONSTANTS.bohr_si)**3 for s in line2[0:3]]
  stress.append(vec)
  trajectory_data.setdefault('stress', []).append(stress)
  parsed_data['stress' + units_suffix] = default_stress_units
@@ -910,6 +910,6 @@ def parse_stdout(stdout, input_parameters, parser_options=None, parsed_xml=None)
 
 def grep_energy_from_line(line):
  try:
- return float(line.split('=')[1].split('Ry')[0]) * ry_to_ev
+ return float(line.split('=')[1].split('Ry')[0]) * CONSTANTS.ry_to_ev
  except Exception:
  raise QEOutputParsingError('Error while parsing energy')