Allow explicitly specifying 'ibrav'.

aiida_quantumespresso/calculations/__init__.py

@@ -7,9 +7,12 @@
 from aiida.common import datastructures, exceptions
 from aiida.common.lang import classproperty
 
+from qe_tools.converters import get_parameters_from_cell
+
 from aiida_quantumespresso.utils.convert import convert_input_to_namelist_entry
 
 from .base import CalcJob
+from .helpers import QEInputValidationError
 
 
 class BasePwCpInputGenerator(CalcJob):
@@ -23,6 +26,7 @@ class BasePwCpInputGenerator(CalcJob):
  _DATAFILE_XML_PRE_6_2 = 'data-file.xml'
  _DATAFILE_XML_POST_6_2 = 'data-file-schema.xml'
  _ENVIRON_INPUT_FILE_NAME = 'environ.in'
+ _DEFAULT_IBRAV = 0
 
  # Additional files that should always be retrieved for the specific plugin
  _internal_retrieve_list = []
@@ -285,10 +289,15 @@ def _generate_PWCPinputdata(cls, parameters, settings, pseudos, structure, kpoin
 
  # ============ I prepare the input site data =============
  # ------------ CELL_PARAMETERS -----------
- cell_parameters_card = 'CELL_PARAMETERS angstrom\n'
- for vector in structure.cell:
- cell_parameters_card += ('{0:18.10f} {1:18.10f} {2:18.10f}'
- '\n'.format(*vector))
+
+ # Specify cell parameters only if 'ibrav' is zero.
+ if input_params.get('SYSTEM', {}).get('ibrav', cls._DEFAULT_IBRAV) == 0:
+ cell_parameters_card = 'CELL_PARAMETERS angstrom\n'
+ for vector in structure.cell:
+ cell_parameters_card += ('{0:18.10f} {1:18.10f} {2:18.10f}'
+ '\n'.format(*vector))
+ else:
+ cell_parameters_card = ''
 
  # ------------- ATOMIC_SPECIES ------------
  atomic_species_card_list = []
@@ -448,7 +457,18 @@ def _generate_PWCPinputdata(cls, parameters, settings, pseudos, structure, kpoin
  # Set some variables (look out at the case! NAMELISTS should be
  # uppercase, internal flag names must be lowercase)
  input_params.setdefault('SYSTEM', {})
- input_params['SYSTEM']['ibrav'] = 0
+ input_params['SYSTEM'].setdefault('ibrav', cls._DEFAULT_IBRAV)
+ ibrav = input_params['SYSTEM']['ibrav']
+ if ibrav != 0:
+ try:
+ structure_parameters = get_parameters_from_cell(
+ ibrav=ibrav,
+ cell=structure.get_attribute('cell'),
+ tolerance=settings.pop('IBRAV_CELL_TOLERANCE', 1e-6)
+ )
+ except ValueError as exc:
+ raise QEInputValidationError('Cannot get structure parameters from cell: {}'.format(exc)) from exc
+ input_params['SYSTEM'].update(structure_parameters)
  input_params['SYSTEM']['nat'] = len(structure.sites)
  input_params['SYSTEM']['ntyp'] = len(structure.kinds)
 

aiida_quantumespresso/calculations/cp.py

@@ -52,7 +52,6 @@ class CpCalculation(BasePwCpInputGenerator):
  ('CONTROL', 'pseudo_dir'), # set later
  ('CONTROL', 'outdir'), # set later
  ('CONTROL', 'prefix'), # set later
- ('SYSTEM', 'ibrav'), # set later
  ('SYSTEM', 'celldm'),
  ('SYSTEM', 'nat'), # set later
  ('SYSTEM', 'ntyp'), # set later

aiida_quantumespresso/calculations/helpers/__init__.py

@@ -158,7 +158,6 @@ def pw_input_helper(input_params, structure, stop_at_first_error=False, flat_mod
  i.lower() for i in [
  'pseudo_dir',
  'outdir',
- 'ibrav',
  'celldm',
  'nat',
  'ntyp',

aiida_quantumespresso/calculations/pw.py

@@ -27,7 +27,6 @@ class PwCalculation(BasePwCpInputGenerator):
  ('CONTROL', 'pseudo_dir'),
  ('CONTROL', 'outdir'),
  ('CONTROL', 'prefix'),
- ('SYSTEM', 'ibrav'),
  ('SYSTEM', 'celldm'),
  ('SYSTEM', 'nat'),
  ('SYSTEM', 'ntyp'),

aiida_quantumespresso/tools/pwinputparser.py

@@ -96,9 +96,6 @@ def create_builder_from_file(input_folder, input_file_name, code, metadata, pseu
  builder.structure = parsed_file.get_structuredata()
  builder.kpoints = parsed_file.get_kpointsdata()
 
- if parsed_file.namelists['SYSTEM']['ibrav'] != 0:
- raise NotImplementedError('Found ibrav != 0: `aiida-quantumespresso` currently only supports ibrav = 0.')
-
  # Then, strip the namelist items that the plugin doesn't allow or sets later.
  # NOTE: If any of the position or cell units are in alat or crystal
  # units, that will be taken care of by the input parsing tools, and

docs/source/user_guide/calculation_plugins/cp.rst

@@ -35,7 +35,6 @@ Inputs
  'CONTROL', 'pseudo_dir': pseudopotential directory
  'CONTROL', 'outdir': scratch directory
  'CONTROL', 'prefix': file prefix
- 'SYSTEM', 'ibrav': cell shape
  'SYSTEM', 'celldm': cell dm
  'SYSTEM', 'nat': number of atoms
  'SYSTEM', 'ntyp': number of species
@@ -48,6 +47,8 @@ Inputs
 
  Those keywords should not be specified, otherwise the submission will fail.
 
+ The `SYSTEM`, `ibrav` keyword is optional. If it is not specified, `ibrav=0` is used. When a non-zero `ibrav` is given, `aiida-quantumespresso` automatically extracts the cell parameters. As a consistency check, the cell is re-constructed from these parameters and compared to the input cell. The input structure needs to match the convention detailed in the `pw.x documentation <https://www.quantum-espresso.org/Doc/INPUT_PW.html#idm199>`_. The tolerance used in this check can be adjusted with the `IBRAV_CELL_TOLERANCE` key in the `settings` dictionary. It defines the absolute tolerance on each element of the cell matrix.
+
 * **structure**, class :py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`
  The initial ionic configuration of the CP molecular dynamics.
 * **settings**, class :py:class:`Dict <aiida.orm.nodes.data.dict.Dict>` (optional)

docs/source/user_guide/calculation_plugins/pw.rst

@@ -81,7 +81,6 @@ This can then be used directly in the process builder of for example a ``PwCalcu
  'CONTROL', 'pseudo_dir': pseudopotential directory
  'CONTROL', 'outdir': scratch directory
  'CONTROL', 'prefix': file prefix
- 'SYSTEM', 'ibrav': cell shape
  'SYSTEM', 'celldm': cell dm
  'SYSTEM', 'nat': number of atoms
  'SYSTEM', 'ntyp': number of species
@@ -94,6 +93,8 @@ This can then be used directly in the process builder of for example a ``PwCalcu
 
  Those keywords should not be specified, otherwise the submission will fail.
 
+ The `SYSTEM`, `ibrav` keyword is optional. If it is not specified, `ibrav=0` is used. When a non-zero `ibrav` is given, `aiida-quantumespresso` automatically extracts the cell parameters. As a consistency check, the cell is re-constructed from these parameters and compared to the input cell. The input structure needs to match the convention detailed in the `pw.x documentation <https://www.quantum-espresso.org/Doc/INPUT_PW.html#idm199>`_. The tolerance used in this check can be adjusted with the `IBRAV_CELL_TOLERANCE` key in the `settings` dictionary. It defines the absolute tolerance on each element of the cell matrix.
+
 * **structure**, class :py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`
 * **settings**, class :py:class:`Dict <aiida.orm.nodes.data.dict.Dict>` (optional)
  An optional dictionary that activates non-default operations. For a list of possible

setup.json

@@ -92,7 +92,8 @@
  "aiida_core[atomic_tools]~=1.3",
  "packaging",
  "qe-tools~=2.0rc1",
- "xmlschema~=1.2"
+ "xmlschema~=1.2",
+ "numpy"
  ],
  "license": "MIT License",
  "name": "aiida_quantumespresso",

tests/calculations/test_pw.py

@@ -1,6 +1,12 @@
 # -*- coding: utf-8 -*-
 """Tests for the `PwCalculation` class."""
+
+import pytest
+
+from aiida import orm
 from aiida.common import datastructures
+from aiida_quantumespresso.utils.resources import get_default_options
+from aiida_quantumespresso.calculations.helpers import QEInputValidationError
 
 
 def test_pw_default(fixture_sandbox, generate_calc_job, generate_inputs_pw, file_regression):
@@ -30,3 +36,122 @@ def test_pw_default(fixture_sandbox, generate_calc_job, generate_inputs_pw, file
  # Checks on the files written to the sandbox folder as raw input
  assert sorted(fixture_sandbox.get_content_list()) == sorted(['aiida.in', 'pseudo', 'out'])
  file_regression.check(input_written, encoding='utf-8', extension='.in')
+
+
+def test_pw_ibrav(
+ fixture_sandbox, generate_calc_job, fixture_code, generate_kpoints_mesh, generate_upf_data, file_regression
+):
+ """Test a `PwCalculation` where `ibrav` is explicitly specified."""
+ entry_point_name = 'quantumespresso.pw'
+
+ parameters = {'CONTROL': {'calculation': 'scf'}, 'SYSTEM': {'ecutrho': 240.0, 'ecutwfc': 30.0, 'ibrav': 2}}
+
+ # The structure needs to be rotated in the same way QE does it for ibrav=2.
+ param = 5.43
+ cell = [[-param / 2., 0, param / 2.], [0, param / 2., param / 2.], [-param / 2., param / 2., 0]]
+ structure = orm.StructureData(cell=cell)
+ structure.append_atom(position=(0., 0., 0.), symbols='Si', name='Si')
+ structure.append_atom(position=(param / 4., param / 4., param / 4.), symbols='Si', name='Si')
+
+ upf = generate_upf_data('Si')
+ inputs = {
+ 'code': fixture_code(entry_point_name),
+ 'structure': structure,
+ 'kpoints': generate_kpoints_mesh(2),
+ 'parameters': orm.Dict(dict=parameters),
+ 'pseudos': {
+ 'Si': upf
+ },
+ 'metadata': {
+ 'options': get_default_options()
+ }
+ }
+
+ calc_info = generate_calc_job(fixture_sandbox, entry_point_name, inputs)
+
+ cmdline_params = ['-in', 'aiida.in']
+ local_copy_list = [(upf.uuid, upf.filename, u'./pseudo/Si.upf')]
+ retrieve_list = ['aiida.out', './out/aiida.save/data-file-schema.xml', './out/aiida.save/data-file.xml']
+ retrieve_temporary_list = [['./out/aiida.save/K*[0-9]/eigenval*.xml', '.', 2]]
+
+ # Check the attributes of the returned `CalcInfo`
+ assert isinstance(calc_info, datastructures.CalcInfo)
+ assert sorted(calc_info.cmdline_params) == sorted(cmdline_params)
+ assert sorted(calc_info.local_copy_list) == sorted(local_copy_list)
+ assert sorted(calc_info.retrieve_list) == sorted(retrieve_list)
+ assert sorted(calc_info.retrieve_temporary_list) == sorted(retrieve_temporary_list)
+ assert sorted(calc_info.remote_symlink_list) == sorted([])
+
+ with fixture_sandbox.open('aiida.in') as handle:
+ input_written = handle.read()
+
+ # Checks on the files written to the sandbox folder as raw input
+ assert sorted(fixture_sandbox.get_content_list()) == sorted(['aiida.in', 'pseudo', 'out'])
+ file_regression.check(input_written, encoding='utf-8', extension='.in')
+
+
+def test_pw_wrong_ibrav(fixture_sandbox, generate_calc_job, fixture_code, generate_kpoints_mesh, generate_upf_data):
+ """Test that a `PwCalculation` with an incorrect `ibrav` raises."""
+ entry_point_name = 'quantumespresso.pw'
+
+ parameters = {'CONTROL': {'calculation': 'scf'}, 'SYSTEM': {'ecutrho': 240.0, 'ecutwfc': 30.0, 'ibrav': 2}}
+
+ # Here we use the wrong order of unit cell vectors on purpose.
+ param = 5.43
+ cell = [[0, param / 2., param / 2.], [-param / 2., 0, param / 2.], [-param / 2., param / 2., 0]]
+ structure = orm.StructureData(cell=cell)
+ structure.append_atom(position=(0., 0., 0.), symbols='Si', name='Si')
+ structure.append_atom(position=(param / 4., param / 4., param / 4.), symbols='Si', name='Si')
+
+ upf = generate_upf_data('Si')
+ inputs = {
+ 'code': fixture_code(entry_point_name),
+ 'structure': structure,
+ 'kpoints': generate_kpoints_mesh(2),
+ 'parameters': orm.Dict(dict=parameters),
+ 'pseudos': {
+ 'Si': upf
+ },
+ 'metadata': {
+ 'options': get_default_options()
+ }
+ }
+
+ with pytest.raises(QEInputValidationError):
+ generate_calc_job(fixture_sandbox, entry_point_name, inputs)
+
+
+def test_pw_ibrav_tol(fixture_sandbox, generate_calc_job, fixture_code, generate_kpoints_mesh, generate_upf_data):
+ """Test that `IBRAV_TOLERANCE` controls the tolerance when checking cell consistency."""
+ entry_point_name = 'quantumespresso.pw'
+
+ parameters = {'CONTROL': {'calculation': 'scf'}, 'SYSTEM': {'ecutrho': 240.0, 'ecutwfc': 30.0, 'ibrav': 2}}
+
+ # The structure needs to be rotated in the same way QE does it for ibrav=2.
+ param = 5.43
+ eps = 0.1
+ cell = [[-param / 2., eps, param / 2.], [-eps, param / 2. + eps, param / 2.], [-param / 2., param / 2., 0]]
+ structure = orm.StructureData(cell=cell)
+ structure.append_atom(position=(0., 0., 0.), symbols='Si', name='Si')
+ structure.append_atom(position=(param / 4., param / 4., param / 4.), symbols='Si', name='Si')
+
+ upf = generate_upf_data('Si')
+ inputs = {
+ 'code': fixture_code(entry_point_name),
+ 'structure': structure,
+ 'kpoints': generate_kpoints_mesh(2),
+ 'parameters': orm.Dict(dict=parameters),
+ 'pseudos': {
+ 'Si': upf
+ },
+ 'metadata': {
+ 'options': get_default_options()
+ },
+ }
+ # Without adjusting the tolerance, the check fails.
+ with pytest.raises(QEInputValidationError):
+ generate_calc_job(fixture_sandbox, entry_point_name, inputs)
+
+ # After adjusting the tolerance, the input validation no longer fails.
+ inputs['settings'] = orm.Dict(dict={'ibrav_cell_tolerance': eps})
+ generate_calc_job(fixture_sandbox, entry_point_name, inputs)

tests/calculations/test_pw/test_pw_ibrav.in

@@ -0,0 +1,24 @@
+&CONTROL
+ calculation = 'scf'
+ outdir = './out/'
+ prefix = 'aiida'
+ pseudo_dir = './pseudo/'
+ verbosity = 'high'
+/
+&SYSTEM
+ a = 5.4300000000d+00
+ ecutrho = 2.4000000000d+02
+ ecutwfc = 3.0000000000d+01
+ ibrav = 2
+ nat = 2
+ ntyp = 1
+/
+&ELECTRONS
+/
+ATOMIC_SPECIES
+Si 28.0855 Si.upf
+ATOMIC_POSITIONS angstrom
+Si 0.0000000000 0.0000000000 0.0000000000 
+Si 1.3575000000 1.3575000000 1.3575000000 
+K_POINTS automatic
+2 2 2 0 0 0

tests/tools/test_immigrate.py

@@ -2,6 +2,8 @@
 """Tests for immigrating `PwCalculation`s."""
 import os
 
+import numpy as np
+
 from aiida_quantumespresso.tools.pwinputparser import create_builder_from_file
 
 
@@ -47,10 +49,68 @@ def test_create_builder(fixture_sandbox, fixture_code, generate_upf_data, genera
  },
  'SYSTEM': {
  'ecutrho': 240.0,
- 'ecutwfc': 30.0
+ 'ecutwfc': 30.0,
+ 'ibrav': 0,
+ }
+ }
+ assert 'kpoints' in builder
+ assert 'structure' in builder
+
+ generate_calc_job(fixture_sandbox, entry_point_name, builder)
+
+
+def test_create_builder_nonzero_ibrav(fixture_sandbox, fixture_code, generate_upf_data, generate_calc_job):
+ """Test the `create_builder_from_file` method that parses an existing `pw.x` folder into a process builder.
+
+ The input file used is the one generated for `tests.calculations.test_pw.test_pw_ibrav`.
+ """
+ entry_point_name = 'quantumespresso.pw'
+ code = fixture_code(entry_point_name)
+
+ metadata = {
+ 'options': {
+ 'resources': {
+ 'num_machines': 1,
+ 'num_mpiprocs_per_machine': 32,
+ },
+ 'max_memory_kb': 1000,
+ 'max_wallclock_seconds': 60 * 60 * 12,
+ 'withmpi': True,
+ }
+ }
+
+ in_foldername = os.path.join('tests', 'calculations', 'test_pw')
+ in_folderpath = os.path.abspath(in_foldername)
+
+ upf_foldername = os.path.join('tests', 'fixtures', 'pseudos')
+ upf_folderpath = os.path.abspath(upf_foldername)
+ si_upf = generate_upf_data('Si')
+ si_upf.store()
+
+ builder = create_builder_from_file(
+ in_folderpath, 'test_pw_ibrav.in', code, metadata, upf_folderpath, use_first=True
+ )
+
+ assert builder['code'] == code
+ assert builder['metadata'] == metadata
+ pseudo_hash = si_upf.get_hash()
+ assert pseudo_hash is not None
+ assert builder['pseudos']['Si'].get_hash() == pseudo_hash
+ assert builder['parameters'].get_dict() == {
+ 'CONTROL': {
+ 'calculation': 'scf',
+ 'verbosity': 'high'
+ },
+ 'SYSTEM': {
+ 'ecutrho': 240.0,
+ 'ecutwfc': 30.0,
+ 'ibrav': 2,
  }
  }
  assert 'kpoints' in builder
  assert 'structure' in builder
+ param = 5.43
+ np.testing.assert_allclose([[-param / 2., 0, param / 2.], [0, param / 2., param / 2.], [-param / 2., param / 2., 0]
+ ], builder.structure.get_attribute('cell'))
 
  generate_calc_job(fixture_sandbox, entry_point_name, builder)