Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

EpwCalculation: Allow restart from previous epw.x run #918

Draft
wants to merge 1 commit into
base: main
Choose a base branch
from
Draft

EpwCalculation: Allow restart from previous epw.x run #918

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
207 changes: 88 additions & 119 deletions src/aiida_quantumespresso/calculations/epw.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@
# -*- coding: utf-8 -*-
"""Plugin to create a Quantum Espresso epw.x input file."""
import os
from pathlib import Path

from aiida import orm
from aiida.common import datastructures, exceptions
import numpy as np

from aiida_quantumespresso.calculations import _lowercase_dict, _uppercase_dict
from aiida_quantumespresso.calculations.ph import PhCalculation
from aiida_quantumespresso.calculations.pw import PwCalculation
from aiida_quantumespresso.utils.convert import convert_input_to_namelist_entry

from .base import CalcJob
Expand All @@ -30,9 +31,7 @@ class EpwCalculation(CalcJob):
_DEFAULT_OUTPUT_FILE = 'aiida.out'
_OUTPUT_XML_TENSOR_FILE_NAME = 'tensors.xml'
_OUTPUT_SUBFOLDER = './out/'
_SAVE_PREFIX = '/save/'
_FOLDER_SAVE = 'save'
_VERBOSITY = 'high'
_FOLDER_DYNAMICAL_MATRIX = 'DYN_MAT'

# Not using symlink in pw to allow multiple nscf to run on top of the same scf
Expand All @@ -52,9 +51,12 @@ def define(cls, spec):
spec.input('qfpoints', valid_type=orm.KpointsData, help='fine qpoint mesh')
spec.input('parameters', valid_type=orm.Dict, help='')
spec.input('settings', valid_type=orm.Dict, required=False, help='')
spec.input('parent_folder_nscf', valid_type=orm.RemoteData,
help='the folder of a completed nscf `PwCalculation`')
spec.input('parent_folder_ph', valid_type=orm.RemoteData, help='the folder of a completed `PhCalculation`')
spec.input('parent_folder_nscf', required=False, valid_type=orm.RemoteData,
help='the folder of a completed nscf `PwCalculation`')
spec.input('parent_folder_ph', required=False, valid_type=orm.RemoteData,
help='the folder of a completed `PhCalculation`')
spec.input('parent_folder_epw', required=False, valid_type=(orm.RemoteData, orm.RemoteStashFolderData),
help='folder that contains all files required to restart an `EpwCalculation`')
# yapf: enable

def prepare_for_submission(self, folder):
Expand All @@ -68,7 +70,7 @@ def prepare_for_submission(self, folder):
:return: :class:`~aiida.common.datastructures.CalcInfo` instance.
"""

# pylint: disable=too-many-statements,too-many-branches
# pylint: disable=too-many-statements,too-many-branches, protected-access

def test_offset(offset):
"""Check if the grid has an offset."""
Expand All @@ -82,48 +84,99 @@ def test_offset(offset):
remote_copy_list = []
remote_symlink_list = []

parameters = _uppercase_dict(self.inputs.parameters.get_dict(), dict_name='parameters')
parameters = {k: _lowercase_dict(v, dict_name=k) for k, v in parameters.items()}

if 'INPUTEPW' not in parameters:
raise exceptions.InputValidationError('required namelist INPUTEPW not specified')

if 'settings' in self.inputs:
settings = _uppercase_dict(self.inputs.settings.get_dict(), dict_name='settings')
else:
settings = {}

# Copy nscf folder
parent_folder_nscf = self.inputs.parent_folder_nscf
parent_calc_nscf = parent_folder_nscf.creator
remote_list = remote_symlink_list if settings.pop(
'PARENT_FOLDER_SYMLINK', self._default_symlink_usage
) else remote_copy_list

if parent_calc_nscf is None:
raise exceptions.NotExistent(f'parent_folder<{parent_folder_nscf.pk}> has no parent calculation')
if 'parent_folder_nscf' in self.inputs:
parent_folder_nscf = self.inputs.parent_folder_nscf

# Also, the parent calculation must be on the same computer
if not self.node.computer.uuid == parent_calc_nscf.computer.uuid:
computer_label = parent_calc_nscf.computer.get_name()
raise exceptions.InputValidationError(
f'Calculation has to be launched on the same computer as that of the parent: {computer_label}'
)
remote_list.append((
parent_folder_nscf.computer.uuid,
Path(parent_folder_nscf.get_remote_path(), PwCalculation._OUTPUT_SUBFOLDER).as_posix(),
self._OUTPUT_SUBFOLDER,
))

# put by default, default_parent_output_folder = ./out
parent_calc_out_subfolder_nscf = parent_calc_nscf.process_class._OUTPUT_SUBFOLDER # pylint: disable=protected-access
if 'parent_folder_ph' in self.inputs:
parent_folder_ph = self.inputs.parent_folder_ph

# Now phonon folder
parent_folder_ph = self.inputs.parent_folder_ph
parent_calc_ph = parent_folder_ph.creator
# Create the save folder with dvscf and dyn files
folder.get_subfolder(self._FOLDER_SAVE, create=True)

# Also, the parent calculation must be on the same computer
if not self.node.computer.uuid == parent_calc_ph.computer.uuid:
computer_label = parent_calc_nscf.computer.get_name()
raise exceptions.InputValidationError(
f'Calculation has to be launched on the same computer as that of the parent: {computer_label}'
# List of IBZ q-point to be added below EPW. To be removed when removed from EPW.
qibz_ar = []
for key, value in sorted(parent_folder_ph.creator.outputs.output_parameters.get_dict().items()):
if key.startswith('dynamical_matrix_'):
qibz_ar.append(value['q_point'])

nqpt = len(qibz_ar)

# Append the required contents of the `save` folder to the remove copy list, copied from the `ph.x`
# calculation

prefix = self._PREFIX
outdir = self._OUTPUT_SUBFOLDER
fildvscf = PhCalculation._DVSCF_PREFIX
fildyn = PhCalculation._OUTPUT_DYNAMICAL_MATRIX_PREFIX

ph_path = Path(parent_folder_ph.get_remote_path())

remote_list.append(
(parent_folder_ph.computer.uuid, Path(ph_path, outdir, '_ph0', f'{prefix}.phsave').as_posix(), 'save')
)

# I put the first-level keys as uppercase (i.e., namelist and card names) and the second-level keys as lowercase
parameters = _uppercase_dict(self.inputs.parameters.get_dict(), dict_name='parameters')
parameters = {k: _lowercase_dict(v, dict_name=k) for k, v in parameters.items()}
for iqpt in range(1, nqpt + 1):
remote_list.append((
parent_folder_ph.computer.uuid,
Path(ph_path, outdir, '_ph0', '' if iqpt == 1 else f'{prefix}.q_{iqpt}',
f'{prefix}.{fildvscf}1').as_posix(), Path('save', f'{prefix}.dvscf_q{iqpt}').as_posix()
))
# remote_copy_list.append((
# parent_folder_ph.computer.uuid,
# Path(
# ph_path, outdir, '_ph0', '' if iqpt == 1 else f'{prefix}.q_{iqpt}', f'{prefix}.{fildvscf}_paw1'
# ).as_posix(),
# Path('save', f"{prefix}.dvscf_paw_q{iqpt}").as_posix()
# ))
remote_list.append((
parent_folder_ph.computer.uuid, Path(ph_path, f'{fildyn}{iqpt}').as_posix(),
Path('save', f'{prefix}.dyn_q{iqpt}').as_posix()
))

if 'INPUTEPW' not in parameters:
raise exceptions.InputValidationError('required namelist INPUTEPW not specified')
if 'parent_folder_epw' in self.inputs:

parent_folder_epw = self.inputs.parent_folder_epw
if isinstance(parent_folder_epw, orm.RemoteStashFolderData):
epw_path = Path(parent_folder_epw.target_basepath)
else:
epw_path = Path(parent_folder_epw.get_remote_path())

vme_fmt_dict = {
'dipole': 'dmedata.fmt',
'wannier': 'vmedata.fmt',
}

for filename in (
'crystal.fmt', 'epwdata.fmt', vme_fmt_dict[parameters['INPUTEPW']['vme']], f'{self._PREFIX}.kgmap',
f'{self._PREFIX}.kmap', f'{self._PREFIX}.ukk', self._OUTPUT_SUBFOLDER, self._FOLDER_SAVE
):
remote_list.append(
(parent_folder_epw.computer.uuid, Path(epw_path, filename).as_posix(), Path(filename).as_posix())
)

parameters['INPUTEPW']['outdir'] = self._OUTPUT_SUBFOLDER
parameters['INPUTEPW']['verbosity'] = self._VERBOSITY
parameters['INPUTEPW']['dvscf_dir'] = self._FOLDER_SAVE
parameters['INPUTEPW']['prefix'] = self._PREFIX

try:
Expand All @@ -132,7 +185,6 @@ def test_offset(offset):
parameters['INPUTEPW']['nq1'] = mesh[0]
parameters['INPUTEPW']['nq2'] = mesh[1]
parameters['INPUTEPW']['nq3'] = mesh[2]
postpend_text = None
except NotImplementedError as exception:
raise exceptions.InputValidationError('Cannot get the coarse q-point grid') from exception

Expand All @@ -142,7 +194,6 @@ def test_offset(offset):
parameters['INPUTEPW']['nk1'] = mesh[0]
parameters['INPUTEPW']['nk2'] = mesh[1]
parameters['INPUTEPW']['nk3'] = mesh[2]
postpend_text = None
except NotImplementedError as exception:
raise exceptions.InputValidationError('Cannot get the coarse k-point grid') from exception

Expand All @@ -152,7 +203,6 @@ def test_offset(offset):
parameters['INPUTEPW']['nqf1'] = mesh[0]
parameters['INPUTEPW']['nqf2'] = mesh[1]
parameters['INPUTEPW']['nqf3'] = mesh[2]
postpend_text = None
except NotImplementedError as exception:
raise exceptions.InputValidationError('Cannot get the fine q-point grid') from exception

Expand All @@ -162,7 +212,6 @@ def test_offset(offset):
parameters['INPUTEPW']['nkf1'] = mesh[0]
parameters['INPUTEPW']['nkf2'] = mesh[1]
parameters['INPUTEPW']['nkf3'] = mesh[2]
postpend_text = None
except NotImplementedError as exception:
raise exceptions.InputValidationError('Cannot get the fine k-point grid') from exception

Expand All @@ -177,28 +226,6 @@ def test_offset(offset):
except KeyError: # list of namelists not specified in the settings; do automatic detection
namelists_toprint = self._compulsory_namelists

# create the save folder with dvscf and dyn files.
folder.get_subfolder(self._FOLDER_SAVE, create=True)

# List of IBZ q-point to be added below EPW. To be removed when removed from EPW.
qibz_ar = []
for key, value in sorted(parent_folder_ph.creator.outputs.output_parameters.get_dict().items()):
if key.startswith('dynamical_matrix_'):
qibz_ar.append(value['q_point'])

qibz_node = orm.ArrayData()
qibz_node.set_array('qibz', np.array(qibz_ar))

list_of_points = qibz_node.get_array('qibz')
# Number of q-point in the irreducible Brillouin Zone.
nqpt = len(list_of_points[0, :])

# add here the list of point coordinates
if len(list_of_points) > 1:
postpend_text = f'{len(list_of_points)} cartesian\n'
for points in list_of_points:
postpend_text += '{0:18.10f} {1:18.10f} {2:18.10f} \n'.format(*points) # pylint: disable=consider-using-f-string

with folder.open(self.metadata.options.input_filename, 'w') as infile:
for namelist_name in namelists_toprint:
infile.write(f'&{namelist_name}\n')
Expand All @@ -208,70 +235,12 @@ def test_offset(offset):
infile.write(convert_input_to_namelist_entry(key, value))
infile.write('/\n')

# add list of qpoints if required
if postpend_text is not None:
infile.write(postpend_text)

if parameters:
raise exceptions.InputValidationError(
'The following namelists are specified in parameters, but are not valid namelists for the current type '
f'of calculation: {",".join(list(parameters.keys()))}'
)

# copy the parent scratch
symlink = settings.pop('PARENT_FOLDER_SYMLINK', self._default_symlink_usage) # a boolean
if symlink:
# I create a symlink to each file/folder in the parent ./out
folder.get_subfolder(self._OUTPUT_SUBFOLDER, create=True)

remote_symlink_list.append((
parent_folder_nscf.computer.uuid,
os.path.join(parent_folder_nscf.get_remote_path(), parent_calc_out_subfolder_nscf,
'*'), self._OUTPUT_SUBFOLDER
))

else:
# here I copy the whole folder ./out
remote_copy_list.append((
parent_folder_nscf.computer.uuid,
os.path.join(parent_folder_nscf.get_remote_path(),
parent_calc_out_subfolder_nscf), self._OUTPUT_SUBFOLDER
))

prefix = self._PREFIX

for iqpt in range(1, nqpt + 1):
label = str(iqpt)
tmp_path = os.path.join(self._FOLDER_DYNAMICAL_MATRIX, 'dynamical-matrix-0')
remote_copy_list.append((
parent_folder_ph.computer.uuid, os.path.join(parent_folder_ph.get_remote_path(),
tmp_path), 'save/' + prefix + '.dyn_q0'
))
tmp_path = os.path.join(self._FOLDER_DYNAMICAL_MATRIX, 'dynamical-matrix-' + label)
remote_copy_list.append((
parent_folder_ph.computer.uuid, os.path.join(parent_folder_ph.get_remote_path(),
tmp_path), 'save/' + prefix + '.dyn_q' + label
))

if iqpt == 1:
tmp_path = os.path.join(self._OUTPUT_SUBFOLDER, '_ph0/' + prefix + '.dvscf*')
remote_copy_list.append((
parent_folder_ph.computer.uuid, os.path.join(parent_folder_ph.get_remote_path(),
tmp_path), 'save/' + prefix + '.dvscf_q' + label
))
tmp_path = os.path.join(self._OUTPUT_SUBFOLDER, '_ph0/' + prefix + '.phsave')
remote_copy_list.append((
parent_folder_ph.computer.uuid, os.path.join(parent_folder_ph.get_remote_path(), tmp_path), 'save/'
))
else:
tmp_path = os.path.join(
self._OUTPUT_SUBFOLDER, '_ph0/' + prefix + '.q_' + label + '/' + prefix + '.dvscf*'
)
remote_copy_list.append((
parent_folder_ph.computer.uuid, os.path.join(parent_folder_ph.get_remote_path(),
tmp_path), 'save/' + prefix + '.dvscf_q' + label
))

codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = (list(settings.pop('CMDLINE', [])) + ['-in', self.metadata.options.input_filename])
codeinfo.stdout_name = self.metadata.options.output_filename
Expand Down
7 changes: 1 addition & 6 deletions tests/calculations/test_epw/test_epw_default.in
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
&INPUTEPW
dis_froz_max = 8.5000000000d+00
dis_win_max = 18
dvscf_dir = './save/'
dvscf_dir = 'save'
elecselfen = .true.
elph = .true.
epbwrite = .true.
Expand All @@ -22,10 +22,5 @@
outdir = './out/'
prefix = 'aiida'
proj(1) = 'Si : sp3'
verbosity = 'high'
wannierize = .true.
/
3 cartesian
0.0000000000 0.0000000000 0.0000000000
0.0000000000 0.5000000000 0.5000000000
0.5000000000 0.5000000000 0.5000000000