def _generate_NEBinputdata(self,neb_parameters,settings_dict):
"""
This methods generate the input data for the NEB part of the calculation
"""
# I put the first-level keys as uppercase (i.e., namelist and card names)
# and the second-level keys as lowercase
# (deeper levels are unchanged)
input_params = _uppercase_dict(neb_parameters.get_dict(),
dict_name='parameters')
input_params = {k: _lowercase_dict(v, dict_name=k)
for k, v in input_params.iteritems()}
# For the neb input there is no blocked keyword
# Create an empty dictionary for the compulsory namelist 'PATH'
# if not present
if 'PATH' not in input_params:
input_params['PATH'] = {}
# In case of climbing image, we need the corresponding card
climbing_image = False
if input_params['PATH'].get('ci_scheme','no-ci').lower() in ['manual']:
climbing_image = True
try:
climbing_image_list = settings_dict.pop("CLIMBING_IMAGES")
except KeyError:
raise InputValidationError("No climbing image specified for this calculation")
if not isinstance(climbing_image_list, list):
raise InputValidationError("Climbing images should be provided as a list")
if [ i for i in climbing_image_list if i<2 or i >= input_params['PATH'].get('num_of_images',2)]:
raise InputValidationError("The climbing images should be in the range between the first "
"and the last image")
climbing_image_card = "CLIMBING_IMAGES\n"
climbing_image_card += ", ".join([str(_) for _ in climbing_image_list]) + "\n"
inputfile = ""
inputfile += "&PATH\n"
# namelist content; set to {} if not present, so that we leave an
# empty namelist
namelist = input_params.pop('PATH', {})
for k, v in sorted(namelist.iteritems()):
inputfile += convert_input_to_namelist_entry(k, v)
inputfile += "/\n"
# Write cards now
if climbing_image:
inputfile += climbing_image_card
if input_params:
raise InputValidationError(
"The following namelists are specified in input_params, but are "
"not valid namelists for the current type of calculation: "
"{}".format(",".join(input_params.keys())))
return inputfile
def validate_input_parameters(self, input_nodes):
"""
Validate the parameters input node and create from it the input parameter dictionary that contains
all the necessary namelists and their flags that should be written to the input file of the calculation
:param input_nodes: dictionary of sanitized and validated input nodes
:returns: input_parameters a dictionary with input namelists and their flags
"""
qpoints = input_nodes[self.get_linkname('qpoints')]
parameters = input_nodes[self.get_linkname('parameters')].get_dict()
# Transform first-level keys (i.e. namelist and card names) to uppercase and second-level to lowercase
input_parameters = _uppercase_dict(parameters, dict_name='parameters')
input_parameters = {
k: _lowercase_dict(v, dict_name=k)
for k, v in input_parameters.iteritems()
}
# Check that required namelists are present
for namelist in self._compulsory_namelists:
if not namelist in input_parameters:
raise InputValidationError(
"the required namelist '{}' was not defined".format(
namelist))
# Check for presence of blocked keywords
for namelist, flag in self._blocked_keywords:
if namelist in input_parameters and flag in input_parameters[
namelist]:
raise InputValidationError(
"explicit definition of the '{}' "
"flag in the '{}' namelist or card is not allowed".format(
flag, namelist))
# Validate qpoint input node
try:
mesh, offset = qpoints.get_kpoints_mesh()
except AttributeError:
raise NotImplementedError(
'support for explicit qpoints is not implemented, only uniform meshes'
)
if any([i != 0. for i in offset]):
raise NotImplementedError(
'support for qpoint meshes with non-zero offsets is not implemented'
)
input_parameters['INPUTHP']['iverbosity'] = 2
input_parameters['INPUTHP']['outdir'] = self._OUTPUT_SUBFOLDER
input_parameters['INPUTHP']['prefix'] = self._PREFIX
input_parameters['INPUTHP']['nq1'] = mesh[0]
input_parameters['INPUTHP']['nq2'] = mesh[1]
input_parameters['INPUTHP']['nq3'] = mesh[2]
return input_parameters
def should_do_alltogheter(self):
"""Check if the z2pack calculations can be run concurrently."""
from aiida.schedulers.plugins.direct import DirectScheduler
computer = self.inputs.pw_code.computer
scheduler = computer.get_scheduler()
settings = _lowercase_dict(self.ctx.inputs.get('z2pack_settings', {}),
'z2pack_settings')
symlink = settings.get('parent_folder_symlink', False)
return False
return not isinstance(scheduler, DirectScheduler) and not symlink
def _generate_input_files(cls, neb_parameters, settings_dict):
"""Generate the input data for the NEB part of the calculation."""
# I put the first-level keys as uppercase (i.e., namelist and card names)
# and the second-level keys as lowercase
# (deeper levels are unchanged)
input_params = _uppercase_dict(neb_parameters.get_dict(), dict_name='parameters')
input_params = {k: _lowercase_dict(v, dict_name=k) for k, v in input_params.items()}
# Force default values for blocked keywords. NOTE: this is different from PW/CP
for blocked in cls._blocked_keywords:
namelist = blocked[0].upper()
key = blocked[1].lower()
value = blocked[2]
if namelist in input_params:
if key in input_params[namelist]:
raise InputValidationError(
f"You cannot specify explicitly the '{key}' key in the '{namelist}' namelist."
)
else:
input_params[namelist] = {}
input_params[namelist][key] = value
# Create an empty dictionary for the compulsory namelist 'PATH' if not present
if 'PATH' not in input_params:
input_params['PATH'] = {}
# In case of climbing image, we need the corresponding card
ci_scheme = input_params['PATH'].get('ci_scheme', 'no-ci').lower()
climbing_image_list = settings_dict.pop('CLIMBING_IMAGES', None)
if ci_scheme == 'manual':
manual_climbing_image = True
if climbing_image_list is None:
raise InputValidationError(
"'ci_scheme' is {}, but no climbing images were specified for this "
'calculation.'.format(ci_scheme)
)
if not isinstance(climbing_image_list, list):
raise InputValidationError('Climbing images should be provided as a list.')
num_of_images = input_params['PATH'].get('num_of_images', 2)
if any([(i < 2 or i >= num_of_images) for i in climbing_image_list]):
raise InputValidationError(
'The climbing images should be in the range between the first '
'and the last image (excluded).'
)
climbing_image_card = 'CLIMBING_IMAGES\n'
climbing_image_card += ', '.join([str(_) for _ in climbing_image_list]) + '\n'
else:
manual_climbing_image = False
if climbing_image_list is not None:
raise InputValidationError(f"Climbing images are not accepted when 'ci_scheme' is {ci_scheme}.")
input_data = '&PATH\n'
# namelist content; set to {} if not present, so that we leave an empty namelist
namelist = input_params.pop('PATH', {})
for key, value in sorted(namelist.items()):
input_data += convert_input_to_namelist_entry(key, value)
input_data += '/\n'
# Write CI cards now
if manual_climbing_image:
input_data += climbing_image_card
if input_params:
raise InputValidationError(
'The following namelists are specified in input_params, but are '
'not valid namelists for the current type of calculation: '
'{}'.format(','.join(list(input_params.keys())))
)
return input_data
def prepare_for_submission(self, folder):
"""Create the input files from the input nodes passed to this instance of the `CalcJob`.
:param folder: an `aiida.common.folders.Folder` to temporarily write files on disk
:return: `aiida.common.datastructures.CalcInfo` instance
"""
local_copy_list = []
remote_copy_list = []
remote_symlink_list = []
if 'settings' in self.inputs:
settings = _uppercase_dict(self.inputs.settings.get_dict(),
dict_name='settings')
else:
settings = {}
parent_folder = self.inputs.parent_folder
parent_calcs = parent_folder.get_incoming(
node_class=orm.CalcJobNode).all()
if not parent_calcs:
raise exceptions.NotExistent(
'parent_folder<{}> has no parent calculation'.format(
parent_folder.pk))
elif len(parent_calcs) > 1:
raise exceptions.UniquenessError(
'parent_folder<{}> has multiple parent calculations'.format(
parent_folder.pk))
parent_calc = parent_calcs[0].node
# If the parent calculation is a `PhCalculation` we are restarting
restart_flag = parent_calc.process_type == 'aiida.calculations:quantumespresso.ph'
# Also, the parent calculation must be on the same computer
if not self.node.computer.uuid == parent_calc.computer.uuid:
raise exceptions.InputValidationError(
'Calculation has to be launched on the same computer as that of the parent: {}'
.format(parent_calc.computer.get_name()))
# put by default, default_parent_output_folder = ./out
try:
default_parent_output_folder = parent_calc.process_class._OUTPUT_SUBFOLDER
except AttributeError:
try:
default_parent_output_folder = parent_calc._get_output_folder()
except AttributeError:
raise exceptions.InputValidationError(
'parent calculation does not have a default output subfolder'
)
parent_calc_out_subfolder = settings.pop('PARENT_CALC_OUT_SUBFOLDER',
default_parent_output_folder)
# 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 six.iteritems(parameters)
}
prepare_for_d3 = settings.pop('PREPARE_FOR_D3', False)
if prepare_for_d3:
self._blocked_keywords += [('INPUTPH', 'fildrho'),
('INPUTPH', 'drho_star%open'),
('INPUTPH', 'drho_star%ext'),
('INPUTPH', 'drho_star%dir')]
for namelist, flag in self._blocked_keywords:
if namelist in parameters:
if flag in parameters[namelist]:
raise exceptions.InputValidationError(
"Cannot specify explicitly the '{}' flag in the '{}' namelist or card."
.format(flag, namelist))
if 'INPUTPH' not in parameters:
raise exceptions.InputValidationError(
'required namelist INPUTPH not specified')
parameters['INPUTPH']['outdir'] = self._OUTPUT_SUBFOLDER
parameters['INPUTPH']['iverbosity'] = 1
parameters['INPUTPH']['prefix'] = self._PREFIX
parameters['INPUTPH']['fildyn'] = self._OUTPUT_DYNAMICAL_MATRIX_PREFIX
if prepare_for_d3:
parameters['INPUTPH']['fildrho'] = self._DRHO_PREFIX
parameters['INPUTPH']['drho_star%open'] = True
parameters['INPUTPH']['drho_star%ext'] = self._DRHO_STAR_EXT
parameters['INPUTPH']['drho_star%dir'] = self._FOLDER_DRHO
try:
mesh, offset = self.inputs.qpoints.get_kpoints_mesh()
if any([i != 0. for i in offset]):
raise NotImplementedError(
'Computation of phonons on a mesh with non zero offset is not implemented, at the level of ph.x'
)
parameters['INPUTPH']['ldisp'] = True
parameters['INPUTPH']['nq1'] = mesh[0]
parameters['INPUTPH']['nq2'] = mesh[1]
parameters['INPUTPH']['nq3'] = mesh[2]
postpend_text = None
except AttributeError:
# this is the case where no mesh was set. Maybe it's a list
try:
list_of_points = self.inputs.qpoints.get_kpoints(
cartesian=True)
except AttributeError:
# In this case, there are no info on the qpoints at all
raise exceptions.InputValidationError(
'Input `qpoints` contains neither a mesh nor a list of points'
)
# change to 2pi/a coordinates
lattice_parameter = numpy.linalg.norm(self.inputs.qpoints.cell[0])
list_of_points *= lattice_parameter / (2. * numpy.pi)
# add here the list of point coordinates
if len(list_of_points) > 1:
parameters['INPUTPH']['qplot'] = True
parameters['INPUTPH']['ldisp'] = True
postpend_text = u'{}\n'.format(len(list_of_points))
for points in list_of_points:
postpend_text += u'{0:18.10f} {1:18.10f} {2:18.10f} 1\n'.format(
*points)
# Note: the weight is fixed to 1, because ph.x calls these
# things weights but they are not such. If they are going to
# exist with the meaning of weights, they will be supported
else:
parameters['INPUTPH']['ldisp'] = False
postpend_text = u''
for points in list_of_points:
postpend_text += u'{0:18.10f} {1:18.10f} {2:18.10f}\n'.format(
*points)
# customized namelists, otherwise not present in the distributed ph code
try:
namelists_toprint = settings.pop('NAMELISTS')
if not isinstance(namelists_toprint, list):
raise exceptions.InputValidationError(
"The 'NAMELISTS' value, if specified in the settings input "
'node, must be a list of strings')
except KeyError: # list of namelists not specified in the settings; do automatic detection
namelists_toprint = self._compulsory_namelists
# create a folder for the dynamical matrices
if not restart_flag: # if it is a restart, it will be copied over
folder.get_subfolder(self._FOLDER_DYNAMICAL_MATRIX, create=True)
with folder.open(self.metadata.options.input_filename, 'w') as infile:
for namelist_name in namelists_toprint:
infile.write(u'&{0}\n'.format(namelist_name))
# namelist content; set to {} if not present, so that we leave an empty namelist
namelist = parameters.pop(namelist_name, {})
for key, value in sorted(six.iteritems(namelist)):
infile.write(convert_input_to_namelist_entry(key, value))
infile.write(u'/\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 of calculation: '
'{}'.format(','.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.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
parent_calc_out_subfolder,
'*'), self._OUTPUT_SUBFOLDER))
# I also create a symlink for the ./pseudo folder
# TODO: suppress this when the recover option of QE will be fixed
# (bug when trying to find pseudo file)
remote_symlink_list.append(
(parent_folder.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
self._get_pseudo_folder()),
self._get_pseudo_folder()))
else:
# here I copy the whole folder ./out
remote_copy_list.append(
(parent_folder.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
parent_calc_out_subfolder),
self._OUTPUT_SUBFOLDER))
# I also copy the ./pseudo folder
# TODO: suppress this when the recover option of QE will be fixed
# (bug when trying to find pseudo file)
remote_copy_list.append(
(parent_folder.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
self._get_pseudo_folder()),
self._get_pseudo_folder()))
if restart_flag: # in this case, copy in addition also the dynamical matrices
if symlink:
remote_symlink_list.append(
(parent_folder.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
self._FOLDER_DYNAMICAL_MATRIX),
self._FOLDER_DYNAMICAL_MATRIX))
else:
# copy the dynamical matrices
# no need to copy the _ph0, since I copied already the whole ./out folder
remote_copy_list.append(
(parent_folder.computer.uuid,
os.path.join(parent_folder.get_remote_path(),
self._FOLDER_DYNAMICAL_MATRIX), '.'))
# Create an `.EXIT` file if `only_initialization` flag in `settings` is set to `True`
if settings.pop('ONLY_INITIALIZATION', False):
with folder.open('{}.EXIT'.format(self._PREFIX), 'w') as handle:
handle.write('\n')
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = (
list(settings.pop('CMDLINE', [])) +
['-in', self.metadata.options.input_filename])
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.remote_symlink_list = remote_symlink_list
# Retrieve by default the output file and the xml file
filepath_xml_tensor = os.path.join(self._OUTPUT_SUBFOLDER, '_ph0',
'{}.phsave'.format(self._PREFIX))
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(self.metadata.options.output_filename)
calcinfo.retrieve_list.append(self._FOLDER_DYNAMICAL_MATRIX)
calcinfo.retrieve_list.append(
os.path.join(filepath_xml_tensor,
self._OUTPUT_XML_TENSOR_FILE_NAME))
calcinfo.retrieve_list += settings.pop('ADDITIONAL_RETRIEVE_LIST', [])
if settings:
unknown_keys = ', '.join(list(settings.keys()))
raise exceptions.InputValidationError(
'`settings` contained unexpected keys: {}'.format(
unknown_keys))
return calcinfo
def prepare_for_submission(self, folder): # pylint: disable=too-many-statements,too-many-branches
"""Prepare the calculation job for submission by transforming input nodes into input files.
In addition to the input files being written to the sandbox folder, a `CalcInfo` instance will be returned that
contains lists of files that need to be copied to the remote machine before job submission, as well as file
lists that are to be retrieved after job completion.
:param folder: a sandbox folder to temporarily write files on disk.
:return: :py:`~aiida.common.datastructures.CalcInfo` instance.
"""
def test_offset(offset):
"""Check if the grid has an offset."""
if any([i != 0. for i in offset]):
raise NotImplementedError(
'Computation of electron-phonon on a mesh with non zero offset is not implemented, '
'at the level of epw.x')
# pylint: disable=too-many-statements,too-many-branches
local_copy_list = []
remote_copy_list = []
remote_symlink_list = []
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
if parent_calc_nscf is None:
raise exceptions.NotExistent('parent_folder<{}> has no parent calculation'.format(parent_folder_nscf.pk))
# Also, the parent calculation must be on the same computer
if not self.node.computer.uuid == parent_calc_nscf.computer.uuid:
raise exceptions.InputValidationError(
'Calculation has to be launched on the same computer as that of the parent: {}'.format(
parent_calc_nscf.computer.get_name()))
# put by default, default_parent_output_folder = ./out
parent_calc_out_subfolder_nscf = parent_calc_nscf.process_class._OUTPUT_SUBFOLDER # pylint: disable=protected-access
# Now phonon folder
parent_folder_ph = self.inputs.parent_folder_ph
parent_calc_ph = parent_folder_ph.creator
# Also, the parent calculation must be on the same computer
if not self.node.computer.uuid == parent_calc_ph.computer.uuid:
raise exceptions.InputValidationError(
'Calculation has to be launched on the same computer as that of the parent: {}'.format(
parent_calc_ph.computer.get_name()))
# 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()}
if 'INPUTEPW' not in parameters:
raise exceptions.InputValidationError('required namelist INPUTEPW not specified')
parameters['INPUTEPW']['outdir'] = self._OUTPUT_SUBFOLDER
parameters['INPUTEPW']['iverbosity'] = 1
parameters['INPUTEPW']['prefix'] = self._PREFIX
try:
mesh, offset = self.inputs.qpoints.get_kpoints_mesh()
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
try:
mesh, offset = self.inputs.kpoints.get_kpoints_mesh()
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
try:
mesh, offset = self.inputs.qfpoints.get_kpoints_mesh()
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
try:
mesh, offset = self.inputs.kfpoints.get_kpoints_mesh()
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
# customized namelists, otherwise not present in the distributed epw code
try:
namelists_toprint = settings.pop('NAMELISTS')
if not isinstance(namelists_toprint, list):
raise exceptions.InputValidationError(
"The 'NAMELISTS' value, if specified in the settings input "
'node, must be a list of strings')
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 = '{} cartesian\n'.format(len(list_of_points))
for points in list_of_points:
postpend_text += '{0:18.10f} {1:18.10f} {2:18.10f} \n'.format(*points)
with folder.open(self.metadata.options.input_filename, 'w') as infile:
for namelist_name in namelists_toprint:
infile.write('&{0}\n'.format(namelist_name))
# namelist content; set to {} if not present, so that we leave an empty namelist
namelist = parameters.pop(namelist_name, {})
for key, value in sorted(namelist.items()):
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 of calculation: '
'{}'.format(','.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
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.remote_symlink_list = remote_symlink_list
# Retrieve by default the output file
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(self.metadata.options.output_filename)
calcinfo.retrieve_list += settings.pop('ADDITIONAL_RETRIEVE_LIST', [])
if settings:
unknown_keys = ', '.join(list(settings.keys()))
raise exceptions.InputValidationError('`settings` contained unexpected keys: {}'.format(unknown_keys))
return calcinfo
def _prepare_for_submission(self,tempfolder,inputdict):
"""
This is the routine to be called when you want to create
the input files and related stuff with a plugin.
:param tempfolder: a aiida.common.folders.Folder subclass where
the plugin should put all its files.
:param inputdict: a dictionary with the input nodes, as they would
be returned by get_inputdata_dict (without the Code!)
"""
try:
code = inputdict.pop(self.get_linkname('code'))
except KeyError:
raise InputValidationError("No code specified for this calculation")
local_copy_list = []
remote_copy_list = []
remote_symlink_list = []
try:
parameters = inputdict.pop(self.get_linkname('parameters'))
except KeyError:
raise InputValidationError("No parameters specified for this calculation")
if not isinstance(parameters, ParameterData):
raise InputValidationError("parameters is not of type ParameterData")
try:
qpoints = inputdict.pop(self.get_linkname('qpoints'))
except KeyError:
raise InputValidationError("No qpoints specified for this calculation")
if not isinstance(qpoints, KpointsData):
raise InputValidationError("qpoints is not of type KpointsData")
# Settings can be undefined, and defaults to an empty dictionary.
# They will be used for any input that doen't fit elsewhere.
settings = inputdict.pop(self.get_linkname('settings'),None)
if settings is None:
settings_dict = {}
else:
if not isinstance(settings, ParameterData):
raise InputValidationError("settings, if specified, must be of "
"type ParameterData")
# Settings converted to uppercase
settings_dict = _uppercase_dict(settings.get_dict(),
dict_name='settings')
parent_calc_folder = inputdict.pop(self.get_linkname('parent_folder'),None)
if parent_calc_folder is None:
raise InputValidationError("No parent calculation found, needed to "
"compute phonons")
# TODO: to be a PwCalculation is not sufficient: it could also be a nscf
# calculation that is invalid for phonons
if not isinstance(parent_calc_folder, RemoteData):
raise InputValidationError("parent_calc_folder, if specified,"
"must be of type RemoteData")
restart_flag = False
# extract parent calculation
parent_calcs = parent_calc_folder.get_inputs(node_type=JobCalculation)
n_parents = len(parent_calcs)
if n_parents != 1:
raise UniquenessError("Input RemoteData is child of {} "
"calculation{}, while it should have "
"a single parent".format(n_parents,
"" if n_parents==0 else "s"))
parent_calc = parent_calcs[0]
# check that it is a valid parent
self._check_valid_parent(parent_calc)
if not isinstance(parent_calc, PwCalculation):
restart_flag = True
# Also, the parent calculation must be on the same computer
new_comp = self.get_computer()
old_comp = parent_calc.get_computer()
if ( not new_comp.uuid == old_comp.uuid ):
raise InputValidationError("PhCalculation must be launched on the same computer"
" of the parent: {}".format(old_comp.get_name()))
# put by default, default_parent_output_folder = ./out
try:
default_parent_output_folder = parent_calc._OUTPUT_SUBFOLDER
except AttributeError:
try:
default_parent_output_folder = parent_calc._get_output_folder()
except AttributeError:
raise InputValidationError("Parent of PhCalculation does not "
"have a default output subfolder")
#os.path.join(
# parent_calc.OUTPUT_SUBFOLDER,
# '{}.save'.format(parent_calc.PREFIX))
parent_calc_out_subfolder = settings_dict.pop('PARENT_CALC_OUT_SUBFOLDER',
default_parent_output_folder)
# Here, there should be no other inputs
if inputdict:
raise InputValidationError("The following input data nodes are "
"unrecognized: {}".format(inputdict.keys()))
##############################
# END OF INITIAL INPUT CHECK #
##############################
# I put the first-level keys as uppercase (i.e., namelist and card names)
# and the second-level keys as lowercase
# (deeper levels are unchanged)
input_params = _uppercase_dict(parameters.get_dict(),
dict_name='parameters')
input_params = {k: _lowercase_dict(v, dict_name=k)
for k, v in input_params.iteritems()}
prepare_for_d3 = settings_dict.pop('PREPARE_FOR_D3',False)
if prepare_for_d3:
self._blocked_keywords += [('INPUTPH', 'fildrho'),
('INPUTPH', 'drho_star%open'),
('INPUTPH', 'drho_star%ext'),
('INPUTPH', 'drho_star%dir')]
# I remove unwanted elements (for the moment, instead, I stop; to change when
# we setup a reasonable logging)
for nl, flag in self._blocked_keywords:
if nl in input_params:
if flag in input_params[nl]:
raise InputValidationError(
"You cannot specify explicitly the '{}' flag in the '{}' "
"namelist or card.".format(flag, nl))
# Set some variables (look out at the case! NAMELISTS should be uppercase,
# internal flag names must be lowercase)
if 'INPUTPH' not in input_params:
raise InputValidationError("No namelist INPUTPH found in input") # I cannot decide what to do in the calculation
input_params['INPUTPH']['outdir'] = self._OUTPUT_SUBFOLDER
input_params['INPUTPH']['iverbosity'] = 1 # in human language 1=high
input_params['INPUTPH']['prefix'] = self._PREFIX
input_params['INPUTPH']['fildyn'] = self._OUTPUT_DYNAMICAL_MATRIX_PREFIX
if prepare_for_d3:
input_params['INPUTPH']['fildrho'] = self._DRHO_PREFIX
input_params['INPUTPH']['drho_star%open'] = True
input_params['INPUTPH']['drho_star%ext'] = self._DRHO_STAR_EXT
input_params['INPUTPH']['drho_star%dir'] = self._FOLDER_DRHO
# qpoints part
try:
mesh,offset = qpoints.get_kpoints_mesh()
if any([i!=0. for i in offset]):
raise NotImplementedError("Computation of phonons on a mesh with"
" non zero offset is not implemented, at the level of ph.x")
input_params["INPUTPH"]["ldisp"] = True
input_params["INPUTPH"]["nq1"] = mesh[0]
input_params["INPUTPH"]["nq2"] = mesh[1]
input_params["INPUTPH"]["nq3"] = mesh[2]
postpend_text = None
except AttributeError:
# this is the case where no mesh was set. Maybe it's a list
try:
list_of_points = qpoints.get_kpoints(cartesian=True)
except AttributeError as e:
# In this case, there are no info on the qpoints at all
raise InputValidationError("Neither a qpoints mesh or a valid "
"list of qpoints was found in input",
e.message)
# change to 2pi/a coordinates
lattice_parameter = numpy.linalg.norm(qpoints.cell[0])
list_of_points *= lattice_parameter / (2.*numpy.pi)
# add here the list of point coordinates
if len(list_of_points)>1:
input_params["INPUTPH"]["qplot"] = True
input_params["INPUTPH"]["ldisp"] = True
postpend_text = "{}\n".format(len(list_of_points))
for points in list_of_points:
postpend_text += "{} {} {} 1\n".format(*points)
# Note: the weight is fixed to 1, because ph.x calls these
# things weights but they are not such. If they are going to
# exist with the meaning of weights, they will be supported
else:
input_params["INPUTPH"]["ldisp"] = False
postpend_text = ""
for points in list_of_points:
postpend_text += "{} {} {}\n".format(*points)
# =================== NAMELISTS ========================
# customized namelists, otherwise not present in the distributed ph code
try:
namelists_toprint = settings_dict.pop('NAMELISTS')
if not isinstance(namelists_toprint, list):
raise InputValidationError(
"The 'NAMELISTS' value, if specified in the settings input "
"node, must be a list of strings")
except KeyError: # list of namelists not specified in the settings; do automatic detection
namelists_toprint = self._compulsory_namelists
input_filename = tempfolder.get_abs_path(self._INPUT_FILE_NAME)
# create a folder for the dynamical matrices
if not restart_flag: # if it is a restart, it will be copied over
tempfolder.get_subfolder(self._FOLDER_DYNAMICAL_MATRIX,
create=True)
with open(input_filename,'w') as infile:
infile.write('AiiDA calculation\n')
for namelist_name in namelists_toprint:
infile.write("&{0}\n".format(namelist_name))
# namelist content; set to {} if not present, so that we leave an
# empty namelist
namelist = input_params.pop(namelist_name,{})
for k, v in sorted(namelist.iteritems()):
infile.write(get_input_data_text(k,v))
infile.write("/\n")
# add list of qpoints if required
if postpend_text is not None:
infile.write(postpend_text)
#TODO: write nat_todo
if input_params:
raise InputValidationError(
"The following namelists are specified in input_params, but are "
"not valid namelists for the current type of calculation: "
"{}".format(",".join(input_params.keys())))
# copy the parent scratch
symlink = settings_dict.pop('PARENT_FOLDER_SYMLINK',
_default_symlink_usage) # a boolean
if symlink:
# I create a symlink to each file/folder in the parent ./out
tempfolder.get_subfolder(self._OUTPUT_SUBFOLDER, create=True)
remote_symlink_list.append( (parent_calc_folder.get_computer().uuid,
os.path.join(parent_calc_folder.get_remote_path(),
parent_calc_out_subfolder,
"*"),
self._OUTPUT_SUBFOLDER
) )
# I also create a symlink for the ./pseudo folder
# TODO: suppress this when the recover option of QE will be fixed
# (bug when trying to find pseudo file)
remote_symlink_list.append((parent_calc_folder.get_computer().uuid,
os.path.join(parent_calc_folder.get_remote_path(),
self._get_pseudo_folder()),
self._get_pseudo_folder()
))
#pass
else:
# here I copy the whole folder ./out
remote_copy_list.append(
(parent_calc_folder.get_computer().uuid,
os.path.join(parent_calc_folder.get_remote_path(),
parent_calc_out_subfolder),
self._OUTPUT_SUBFOLDER))
# I also copy the ./pseudo folder
# TODO: suppress this when the recover option of QE will be fixed
# (bug when trying to find pseudo file)
remote_copy_list.append(
(parent_calc_folder.get_computer().uuid,
os.path.join(parent_calc_folder.get_remote_path(),
self._get_pseudo_folder()),
self._get_pseudo_folder()))
if restart_flag: # in this case, copy in addition also the dynamical matrices
if symlink:
remote_symlink_list.append(
(parent_calc_folder.get_computer().uuid,
os.path.join(parent_calc_folder.get_remote_path(),
self._FOLDER_DYNAMICAL_MATRIX),
self._FOLDER_DYNAMICAL_MATRIX))
else:
# copy the dynamical matrices
remote_copy_list.append(
(parent_calc_folder.get_computer().uuid,
os.path.join(parent_calc_folder.get_remote_path(),
self._FOLDER_DYNAMICAL_MATRIX),
'.'))
# no need to copy the _ph0, since I copied already the whole ./out folder
# here we may create an aiida.EXIT file
create_exit_file = settings_dict.pop('ONLY_INITIALIZATION',False)
if create_exit_file:
exit_filename = tempfolder.get_abs_path(
'{}.EXIT'.format(self._PREFIX))
with open(exit_filename,'w') as f:
f.write('\n')
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
# Empty command line by default
cmdline_params = settings_dict.pop('CMDLINE', [])
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.remote_symlink_list = remote_symlink_list
codeinfo = CodeInfo()
codeinfo.cmdline_params = (list(cmdline_params)
+ ["-in", self._INPUT_FILE_NAME])
codeinfo.stdout_name = self._OUTPUT_FILE_NAME
codeinfo.code_uuid = code.uuid
calcinfo.codes_info = [codeinfo]
# Retrieve by default the output file and the xml file
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(self._OUTPUT_FILE_NAME)
calcinfo.retrieve_list.append(self._FOLDER_DYNAMICAL_MATRIX)
calcinfo.retrieve_list.append(
os.path.join(self._OUTPUT_SUBFOLDER,
'_ph0',
'{}.phsave'.format(self._PREFIX),
self._OUTPUT_XML_TENSOR_FILE_NAME))
extra_retrieved = settings_dict.pop('ADDITIONAL_RETRIEVE_LIST', [])
for extra in extra_retrieved:
calcinfo.retrieve_list.append( extra )
if settings_dict:
raise InputValidationError("The following keys have been found in "
"the settings input node, but were not understood: {}".format(
",".join(settings_dict.keys())))
return calcinfo
def _prepare_for_submission(self, tempfolder, inputdict):
"""
This is the routine to be called when you want to create
the input files and related stuff with a plugin.
:param tempfolder: a aiida.common.folders.Folder subclass where
the plugin should put all its files.
:param inputdict: a dictionary with the input nodes, as they would
be returned by get_inputdata_dict (without the Code!)
"""
local_copy_list = []
remote_copy_list = []
try:
code = inputdict.pop(self.get_linkname('code'))
except KeyError:
raise InputValidationError(
"No code specified for this calculation")
try:
parameters = inputdict.pop(self.get_linkname('parameters'))
except KeyError:
raise InputValidationError(
"No parameters specified for this calculation")
if not isinstance(parameters, ParameterData):
raise InputValidationError(
"parameters is not of type ParameterData")
# Settings can be undefined, and defaults to an empty dictionary
settings = inputdict.pop(self.get_linkname('settings'), None)
if settings is None:
settings_dict = {}
else:
if not isinstance(settings, ParameterData):
raise InputValidationError(
"settings, if specified, must be of "
"type ParameterData")
# Settings converted to uppercase
settings_dict = _uppercase_dict(settings.get_dict(),
dict_name='settings')
parent_calc_folder = inputdict.pop(self.get_linkname('parent_folder'),
None)
if parent_calc_folder is not None:
if not isinstance(parent_calc_folder, self._parent_folder_type):
if not isinstance(self._parent_folder_type, tuple):
possible_types = [self._parent_folder_type.__name__]
else:
possible_types = [
t.__name__ for t in self._parent_folder_type
]
raise InputValidationError("parent_calc_folder, if specified,"
"must be of type {}".format(
" or ".join(possible_types)))
following_text = self._get_following_text(inputdict, settings)
# Here, there should be no more parameters...
if inputdict:
raise InputValidationError("The following input data nodes are "
"unrecognized: {}".format(
inputdict.keys()))
##############################
# END OF INITIAL INPUT CHECK #
##############################
# I put the first-level keys as uppercase (i.e., namelist and card names)
# and the second-level keys as lowercase
# (deeper levels are unchanged)
input_params = _uppercase_dict(parameters.get_dict(),
dict_name='parameters')
input_params = {
k: _lowercase_dict(v, dict_name=k)
for k, v in input_params.iteritems()
}
# set default values. NOTE: this is different from PW/CP
for blocked in self._blocked_keywords:
namelist = blocked[0].upper()
key = blocked[1].lower()
value = blocked[2]
if namelist in input_params:
if key in input_params[namelist]:
raise InputValidationError(
"You cannot specify explicitly the '{}' key in the '{}' "
"namelist.".format(key, namelist))
# set to a default
if not input_params[namelist]:
input_params[namelist] = {}
input_params[namelist][key] = value
# =================== NAMELISTS AND CARDS ========================
try:
namelists_toprint = settings_dict.pop('NAMELISTS')
if not isinstance(namelists_toprint, list):
raise InputValidationError(
"The 'NAMELISTS' value, if specified in the settings input "
"node, must be a list of strings")
except KeyError: # list of namelists not specified; do automatic detection
namelists_toprint = self._default_namelists
input_filename = tempfolder.get_abs_path(self._INPUT_FILE_NAME)
with open(input_filename, 'w') as infile:
for namelist_name in namelists_toprint:
infile.write("&{0}\n".format(namelist_name))
# namelist content; set to {} if not present, so that we leave an
# empty namelist
namelist = input_params.pop(namelist_name, {})
for k, v in sorted(namelist.iteritems()):
infile.write(convert_input_to_namelist_entry(k, v))
infile.write("/\n")
# Write remaning text now, if any
infile.write(following_text)
# Check for specified namelists that are not expected
if input_params:
raise InputValidationError(
"The following namelists are specified in input_params, but are "
"not valid namelists for the current type of calculation: "
"{}".format(",".join(input_params.keys())))
# copy remote output dir, if specified
if parent_calc_folder is not None:
if isinstance(parent_calc_folder, RemoteData):
parent_calc_out_subfolder = settings_dict.pop(
'PARENT_CALC_OUT_SUBFOLDER', self._INPUT_SUBFOLDER)
remote_copy_list.append(
(parent_calc_folder.get_computer().uuid,
os.path.join(parent_calc_folder.get_remote_path(),
parent_calc_out_subfolder),
self._OUTPUT_SUBFOLDER))
elif isinstance(parent_calc_folder, FolderData):
local_copy_list.append(
(parent_calc_folder.get_abs_path(self._INPUT_SUBFOLDER),
self._OUTPUT_SUBFOLDER))
elif isinstance(parent_calc_folder, SinglefileData):
filename = parent_calc_folder.get_file_abs_path()
local_copy_list.append((filename, os.path.basename(filename)))
calcinfo = CalcInfo()
calcinfo.uuid = self.uuid
# Empty command line by default
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
codeinfo = CodeInfo()
codeinfo.cmdline_params = settings_dict.pop('CMDLINE', [])
codeinfo.stdin_name = self._INPUT_FILE_NAME
codeinfo.stdout_name = self._OUTPUT_FILE_NAME
codeinfo.code_uuid = code.uuid
calcinfo.codes_info = [codeinfo]
# Retrieve by default the output file and the xml file
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(self._OUTPUT_FILE_NAME)
settings_retrieve_list = settings_dict.pop('ADDITIONAL_RETRIEVE_LIST',
[])
calcinfo.retrieve_list += settings_retrieve_list
calcinfo.retrieve_list += self._internal_retrieve_list
calcinfo.retrieve_singlefile_list = self._retrieve_singlefile_list
if settings_dict:
try:
Parserclass = self.get_parserclass()
parser = Parserclass(self)
parser_opts = parser.get_parser_settings_key()
settings_dict.pop(parser_opts)
except (
KeyError, AttributeError
): # the key parser_opts isn't inside the dictionary, or it is set to None
raise InputValidationError(
"The following keys have been found in "
"the settings input node, but were not understood: {}".
format(",".join(settings_dict.keys())))
return calcinfo
def prepare_for_submission(self, folder): # pylint: disable=too-many-branches,too-many-statements
"""Prepare the calculation job for submission by transforming input nodes into input files.
In addition to the input files being written to the sandbox folder, a `CalcInfo` instance will be returned that
contains lists of files that need to be copied to the remote machine before job submission, as well as file
lists that are to be retrieved after job completion.
:param folder: a sandbox folder to temporarily write files on disk.
:return: :py:`~aiida.common.datastructures.CalcInfo` instance.
"""
# 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()}
# Same for settings.
if 'settings' in self.inputs:
settings = _uppercase_dict(self.inputs.settings.get_dict(), dict_name='settings')
else:
settings = {}
# Set default values. NOTE: this is different from PW/CP
for blocked in self._blocked_keywords:
namelist = blocked[0].upper()
key = blocked[1].lower()
value = blocked[2]
if namelist in parameters:
if key in parameters[namelist]:
raise exceptions.InputValidationError(
"You cannot specify explicitly the '{}' key in the '{}' "
'namelist.'.format(key, namelist))
else:
parameters[namelist] = {}
parameters[namelist][key] = value
# Restrict the plot output to the file types that we want to be able to parse
dimension_to_output_format = {
0: 0, # Spherical integration -> Gnuplot, 1D
1: 0, # 1D -> Gnuplot, 1D
2: 7, # 2D -> Gnuplot, 2D
3: 6, # 3D -> Gaussian cube
4: 0, # Polar on a sphere -> # Gnuplot, 1D
}
parameters['PLOT']['output_format'] = dimension_to_output_format[parameters['PLOT']['iflag']]
namelists_toprint = self._default_namelists
input_filename = self.inputs.metadata.options.input_filename
with folder.open(input_filename, 'w') as infile:
for namelist_name in namelists_toprint:
infile.write('&{0}\n'.format(namelist_name))
# namelist content; set to {} if not present, so that we leave an empty namelist
namelist = parameters.pop(namelist_name, {})
for key, value in sorted(namelist.items()):
infile.write(convert_input_to_namelist_entry(key, value))
infile.write('/\n')
# Check for specified namelists that are not expected
if parameters:
raise exceptions.InputValidationError(
'The following namelists are specified in parameters, but are '
'not valid namelists for the current type of calculation: '
'{}'.format(','.join(list(parameters.keys()))))
remote_copy_list = []
local_copy_list = []
# Copy remote output dir
parent_calc_folder = self.inputs.get('parent_folder', None)
if isinstance(parent_calc_folder, orm.RemoteData):
remote_copy_list.append((
parent_calc_folder.computer.uuid,
os.path.join(parent_calc_folder.get_remote_path(), self._INPUT_SUBFOLDER),
self._OUTPUT_SUBFOLDER
))
remote_copy_list.append((
parent_calc_folder.computer.uuid,
os.path.join(parent_calc_folder.get_remote_path(), self._PSEUDO_SUBFOLDER),
self._PSEUDO_SUBFOLDER
))
elif isinstance(parent_calc_folder, orm.FolderData):
for filename in parent_calc_folder.list_object_names():
local_copy_list.append((
parent_calc_folder.uuid,
filename,
os.path.join(self._OUTPUT_SUBFOLDER, filename)
))
local_copy_list.append((
parent_calc_folder.uuid,
filename,
os.path.join(self._PSEUDO_SUBFOLDER, filename)
))
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = settings.pop('CMDLINE', [])
codeinfo.stdin_name = self.inputs.metadata.options.input_filename
codeinfo.stdout_name = self.inputs.metadata.options.output_filename
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo = datastructures.CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
# Retrieve by default the output file
calcinfo.retrieve_list = [self.inputs.metadata.options.output_filename]
calcinfo.retrieve_temporary_list = []
# Depending on the `plot_num` and the corresponding parameters, more than one pair of `filplot` + `fileout`
# files may be written. In that case, the data files will have `filplot` as a prefix with some suffix to
# distinguish them from one another. The `fileout` filename will be the full data filename with the `fileout`
# value as a suffix.
retrieve_tuples = [
self._FILEOUT,
('{}_*{}'.format(self._FILPLOT, self._FILEOUT), '.', 0)
]
if self.inputs.metadata.options.keep_plot_file:
calcinfo.retrieve_list.extend(retrieve_tuples)
else:
calcinfo.retrieve_temporary_list.extend(retrieve_tuples)
return calcinfo
def prepare_for_submission(self, folder):
"""Create the input files from the input nodes passed to this instance of the `CalcJob`.
:param folder: an `aiida.common.folders.Folder` to temporarily write files on disk
:return: `aiida.common.datastructures.CalcInfo` instance
"""
if 'settings' in self.inputs:
settings = _uppercase_dict(self.inputs.settings.get_dict(),
dict_name='settings')
else:
settings = {}
following_text = self._get_following_text()
# Put the first-level keys as uppercase (i.e., namelist and card names) and the second-level keys as lowercase
if 'parameters' in self.inputs:
parameters = _uppercase_dict(self.inputs.parameters.get_dict(),
dict_name='parameters')
parameters = {
k: _lowercase_dict(v, dict_name=k)
for k, v in six.iteritems(parameters)
}
else:
parameters = {}
# Force default values for blocked keywords. NOTE: this is different from PW/CP
for blocked in self._blocked_keywords:
namelist = blocked[0].upper()
key = blocked[1].lower()
value = blocked[2]
if namelist in parameters:
if key in parameters[namelist]:
raise exceptions.InputValidationError(
"You cannot specify explicitly the '{}' key in the '{}' "
'namelist.'.format(key, namelist))
else:
parameters[namelist] = {}
parameters[namelist][key] = value
# =================== NAMELISTS AND CARDS ========================
try:
namelists_toprint = settings.pop('NAMELISTS')
if not isinstance(namelists_toprint, list):
raise exceptions.InputValidationError(
"The 'NAMELISTS' value, if specified in the settings input node, must be a list of strings"
)
except KeyError: # list of namelists not specified; do automatic detection
namelists_toprint = self._default_namelists
input_filename = self.inputs.metadata.options.input_filename
with folder.open(input_filename, 'w') as infile:
for namelist_name in namelists_toprint:
infile.write(u'&{0}\n'.format(namelist_name))
# namelist content; set to {} if not present, so that we leave an empty namelist
namelist = parameters.pop(namelist_name, {})
for key, value in sorted(six.iteritems(namelist)):
infile.write(convert_input_to_namelist_entry(key, value))
infile.write(u'/\n')
# Write remaning text now, if any
infile.write(following_text)
# Check for specified namelists that are not expected
if parameters:
raise exceptions.InputValidationError(
'The following namelists are specified in parameters, but are '
'not valid namelists for the current type of calculation: '
'{}'.format(','.join(list(parameters.keys()))))
remote_copy_list = []
local_copy_list = []
# copy remote output dir, if specified
parent_calc_folder = self.inputs.get('parent_folder', None)
if parent_calc_folder is not None:
if isinstance(parent_calc_folder, RemoteData):
parent_calc_out_subfolder = settings.pop(
'PARENT_CALC_OUT_SUBFOLDER', self._INPUT_SUBFOLDER)
remote_copy_list.append(
(parent_calc_folder.computer.uuid,
os.path.join(parent_calc_folder.get_remote_path(),
parent_calc_out_subfolder),
self._OUTPUT_SUBFOLDER))
elif isinstance(parent_calc_folder, FolderData):
# TODO: test me, especially with deep relative paths.
for filename in parent_calc_folder.list_object_names():
local_copy_list.append(
(parent_calc_folder.uuid, filename,
os.path.join(self._OUTPUT_SUBFOLDER, filename)))
elif isinstance(parent_calc_folder, SinglefileData):
# TODO: test me
single_file = parent_calc_folder
local_copy_list.append((single_file.uuid, single_file.filename,
single_file.filename))
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = settings.pop('CMDLINE', [])
codeinfo.stdin_name = self.inputs.metadata.options.input_filename
codeinfo.stdout_name = self.inputs.metadata.options.output_filename
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
# Retrieve by default the output file and the xml file
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(
self.inputs.metadata.options.output_filename)
settings_retrieve_list = settings.pop('ADDITIONAL_RETRIEVE_LIST', [])
calcinfo.retrieve_list += settings_retrieve_list
calcinfo.retrieve_list += self._internal_retrieve_list
calcinfo.retrieve_singlefile_list = self._retrieve_singlefile_list
# We might still have parser options in the settings dictionary: pop them.
_pop_parser_options(self, settings)
if settings:
unknown_keys = ', '.join(list(settings.keys()))
raise exceptions.InputValidationError(
'`settings` contained unexpected keys: {}'.format(
unknown_keys))
return calcinfo
def prepare_for_submission(self, folder):
"""Prepare the calculation job for submission by transforming input nodes into input files.
In addition to the input files being written to the sandbox folder, a `CalcInfo` instance will be returned that
contains lists of files that need to be copied to the remote machine before job submission, as well as file
lists that are to be retrieved after job completion.
:param folder: a sandbox folder to temporarily write files on disk.
:return: :py:`~aiida.common.datastructures.CalcInfo` instance.
"""
# pylint: disable=too-many-branches,too-many-statements
if 'settings' in self.inputs:
settings = _uppercase_dict(self.inputs.settings.get_dict(),
dict_name='settings')
else:
settings = {}
following_text = self._get_following_text()
# Put the first-level keys as uppercase (i.e., namelist and card names) and the second-level keys as lowercase
if 'parameters' in self.inputs:
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()
}
else:
parameters = {}
# =================== NAMELISTS AND CARDS ========================
try:
namelists_toprint = settings.pop('NAMELISTS')
if not isinstance(namelists_toprint, list):
raise exceptions.InputValidationError(
"The 'NAMELISTS' value, if specified in the settings input node, must be a list of strings"
)
except KeyError: # list of namelists not specified; do automatic detection
namelists_toprint = self._default_namelists
parameters = self.set_blocked_keywords(parameters)
parameters = self.filter_namelists(parameters, namelists_toprint)
file_content = self.generate_input_file(parameters)
file_content += '\n' + following_text
input_filename = self.inputs.metadata.options.input_filename
with folder.open(input_filename, 'w') as infile:
infile.write(file_content)
symlink = settings.pop('PARENT_FOLDER_SYMLINK', False)
remote_copy_list = []
local_copy_list = []
remote_symlink_list = []
ptr = remote_symlink_list if symlink else remote_copy_list
# copy remote output dir, if specified
parent_calc_folder = self.inputs.get('parent_folder', None)
if parent_calc_folder is not None:
if isinstance(parent_calc_folder, RemoteData):
parent_calc_out_subfolder = settings.pop(
'PARENT_CALC_OUT_SUBFOLDER', self._INPUT_SUBFOLDER)
ptr.append((parent_calc_folder.computer.uuid,
os.path.join(parent_calc_folder.get_remote_path(),
parent_calc_out_subfolder),
self._OUTPUT_SUBFOLDER))
elif isinstance(parent_calc_folder, FolderData):
for filename in parent_calc_folder.list_object_names():
local_copy_list.append(
(parent_calc_folder.uuid, filename,
os.path.join(self._OUTPUT_SUBFOLDER, filename)))
elif isinstance(parent_calc_folder, SinglefileData):
single_file = parent_calc_folder
local_copy_list.append((single_file.uuid, single_file.filename,
single_file.filename))
codeinfo = datastructures.CodeInfo()
codeinfo.cmdline_params = settings.pop('CMDLINE', [])
codeinfo.stdin_name = self.inputs.metadata.options.input_filename
codeinfo.stdout_name = self.inputs.metadata.options.output_filename
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo = datastructures.CalcInfo()
calcinfo.uuid = str(self.uuid)
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = local_copy_list
calcinfo.remote_copy_list = remote_copy_list
calcinfo.remote_symlink_list = remote_symlink_list
# Retrieve by default the output file and the xml file
calcinfo.retrieve_list = []
calcinfo.retrieve_list.append(
self.inputs.metadata.options.output_filename)
settings_retrieve_list = settings.pop('ADDITIONAL_RETRIEVE_LIST', [])
calcinfo.retrieve_list += settings_retrieve_list
calcinfo.retrieve_list += self._internal_retrieve_list
calcinfo.retrieve_singlefile_list = self._retrieve_singlefile_list
# We might still have parser options in the settings dictionary: pop them.
_pop_parser_options(self, settings)
if settings:
unknown_keys = ', '.join(list(settings.keys()))
raise exceptions.InputValidationError(
f'`settings` contained unexpected keys: {unknown_keys}')
return calcinfo
def prepare_z2pack(cls, folder):
input_filename = folder.get_abs_path(cls._INPUT_Z2PACK_FILE)
try:
pw_code = cls.inputs.pw_code
except AttributeError:
raise exceptions.InputValidationError(
'No nscf code specified for this calculation')
try:
overlap_code = cls.inputs.overlap_code
except AttributeError:
raise exceptions.InputValidationError(
'No overlap code specified for this calculation')
try:
wannier90_code = cls.inputs.wannier90_code
except AttributeError:
raise exceptions.InputValidationError(
'No Wannier90 code specified for this calculation')
try:
settings_dict = _lowercase_dict(cls.inputs.z2pack_settings.get_dict(),
dict_name='z2pack_settings')
except:
raise exceptions.InputValidationError(
'No settings specified for this calculation')
if 'npools' not in settings_dict:
pools_cmd = ''
else:
npools = settings_dict['npools']
if isinstance(npools, int):
pools_cmd = ' -nk ' + str(npools) + ' '
else:
raise exceptions.InputValidationError('npools must be an integer.')
try:
dim_mode = settings_dict['dimension_mode']
except KeyError:
raise exceptions.InputValidationError(
'No dimension_mode specified for this calculation')
try:
invariant = settings_dict['invariant'].lower()
except KeyError:
raise exceptions.InputValidationError(
'No invariant specified for this calculation')
if 'mpi_command' in settings_dict:
mpi_command = settings_dict['mpi_command']
else:
computer = cls.inputs.pw_code.computer
proc_per_machine = computer.get_default_mpiprocs_per_machine()
n_machines = cls.inputs.metadata.options.resources['num_machines']
mpi_procs = proc_per_machine * n_machines
mpi_command = computer.get_mpirun_command()
mpi_command = ' '.join(mpi_command).format(tot_num_mpiprocs=mpi_procs)
pos_tol = settings_dict.get('pos_tol', cls._DEFAULT_POS_TOLERANCE)
gap_tol = settings_dict.get('gap_tol', cls._DEFAULT_GAP_TOLERANCE)
move_tol = settings_dict.get('move_tol', cls._DEFAULT_MOVE_TOLERANCE)
num_lines = settings_dict.get('num_lines', cls._DEFAULT_NUM_LINES)
min_neighbour_dist = settings_dict.get('min_neighbour_dist',
cls._DEFAULT_MIN_NEIGHBOUR_DISTANCE)
iterator = settings_dict.get('iterator', cls._DEFAULT_ITERATOR)
# restart_mode = settings_dict.get('restart_mode', False)
prepend_code = settings_dict.get('prepend_code', '')
if dim_mode == '3D':
try:
surface = settings_dict['surface']
# surface = settings_dict.get_dict()['surface']
except KeyError:
raise exceptions.InputValidationError(
'A surface must be specified for dim_mode==3D ')
input_file_lines = []
input_file_lines.append('#!/usr/bin/env python')
input_file_lines.append('import z2pack')
input_file_lines.append('import json')
nscf_cmd = ' {} {}'.format(mpi_command, pw_code.get_execname())
overlap_cmd = ' {} {}'.format(mpi_command, overlap_code.get_execname())
wannier90_cmd = ' {}'.format(wannier90_code.get_execname())
pw_in_cmd = settings_dict.get('pw_in_command', '<')
z2cmd = (
"(\n '" + "ln -s ../out .; ln -s ../pseudo .;'\n '" +
wannier90_cmd + ' ' + cls._SEEDNAME + ' -pp;' + "' +\n '" +
nscf_cmd + pools_cmd + ' {} '.format(pw_in_cmd) +
cls._INPUT_PW_NSCF_FILE + ' >& ' + cls._OUTPUT_PW_NSCF_FILE +
";' +\n '" + overlap_cmd + ' {} '.format(pw_in_cmd) +
cls._INPUT_OVERLAP_FILE + ' >& ' + cls._OUTPUT_OVERLAP_FILE + ";'\n" +
')'
# yapf: disable
)
# yapf: disable
input_file_lines.append('')
input_file_lines.append('z2cmd =' + z2cmd)
input_file_lines.append('')
input_files = [cls._INPUT_PW_NSCF_FILE, cls._INPUT_OVERLAP_FILE,cls._INPUT_W90_FILE]
input_file_lines.append('input_files = ' + str(input_files))
input_file_lines.append('system = z2pack.fp.System(')
input_file_lines.append(' input_files = input_files,')
input_file_lines.append(' kpt_fct = [z2pack.fp.kpoint.qe_explicit, z2pack.fp.kpoint.wannier90_full],')
# input_file_lines.append(' build_folder= \'.\',')
# input_file_lines.append('\t kpt_fct=[z2pack.fp.kpoint.qe, z2pack.fp.kpoint.wannier90],')
input_file_lines.append(' kpt_path = ' + str([cls._INPUT_PW_NSCF_FILE, cls._INPUT_W90_FILE]) + ',')
input_file_lines.append(' command = z2cmd,')
input_file_lines.append(" executable = '/bin/bash',")
input_file_lines.append(" mmn_path = '{}.mmn'".format(cls._SEEDNAME))
input_file_lines.append(')')
input_file_lines.append('')
input_file_lines.append('gap_check={}')
input_file_lines.append('move_check={}')
input_file_lines.append('pos_check={}')
input_file_lines.append(
"res_dict={'convergence_report':{'GapCheck':{}, 'MoveCheck':{}, 'PosCheck':{}}, 'invariant':{}}"
)
# yapf: enable
input_file_lines.append('')
if prepend_code != '':
input_file_lines.append('\t' + prepend_code)
if dim_mode == '2D' or dim_mode == '3D':
input_file_lines.append('result = z2pack.surface.run(')
input_file_lines.append(' system = system,')
if dim_mode == '2D':
if invariant == 'z2':
input_file_lines.append(
' surface = lambda t1,t2: [t2, t1/2, 0],')
elif invariant == 'chern':
input_file_lines.append(
' surface = lambda t1,t2: [t1, t2, 0],')
elif dim_mode == '3D':
input_file_lines.append(' surface = ' + surface +
',')
input_file_lines.append(' pos_tol = ' + str(pos_tol) +
',')
input_file_lines.append(' gap_tol = ' + str(gap_tol) +
',')
input_file_lines.append(' move_tol = ' + str(move_tol) +
',')
input_file_lines.append(' num_lines = ' + str(num_lines) +
',')
input_file_lines.append(' min_neighbour_dist = ' +
str(min_neighbour_dist) + ',')
input_file_lines.append(' iterator = ' + str(iterator) +
',')
input_file_lines.append(' save_file = ' + "'" +
cls._OUTPUT_SAVE_FILE + "'" + ',')
if cls.restart_mode:
input_file_lines.append(' load = True')
input_file_lines.append(' )')
if invariant.lower() == 'z2':
input_file_lines.append('Z2 = z2pack.invariant.z2(result)')
input_file_lines.append("res_dict['invariant'].update({'Z2':Z2})")
elif invariant.lower() == 'chern':
input_file_lines.append('Chern = z2pack.invariant.chern(result)')
input_file_lines.append(
"res_dict['invariant'].update({'Chern':Chern})")
else:
raise exceptions.InputValidationError(
'Only dimension_mode 2D and 3D are currently implemented.')
input_file_lines.append('')
input_file_lines.append(
"gap_check['PASSED'] = "
"result.convergence_report['surface']['GapCheck']['PASSED']")
input_file_lines.append(
"gap_check['FAILED'] = "
"result.convergence_report['surface']['GapCheck']['FAILED']")
input_file_lines.append(
"move_check['PASSED'] = "
"result.convergence_report['surface']['MoveCheck']['PASSED']")
input_file_lines.append(
"move_check['FAILED'] = "
"result.convergence_report['surface']['MoveCheck']['FAILED']")
input_file_lines.append(
"pos_check['PASSED'] = "
"result.convergence_report['line']['PosCheck']['PASSED']")
input_file_lines.append(
"pos_check['FAILED'] = "
"result.convergence_report['line']['PosCheck']['FAILED']")
input_file_lines.append(
"pos_check['MISSING'] = "
"result.convergence_report['line']['PosCheck']['MISSING']")
input_file_lines.append('')
input_file_lines.append(
"res_dict['convergence_report']['GapCheck'].update(gap_check)")
input_file_lines.append(
"res_dict['convergence_report']['MoveCheck'].update(move_check)")
input_file_lines.append(
"res_dict['convergence_report']['PosCheck'].update(pos_check)")
input_file_lines.append('')
input_file_lines.append("with open('" + cls._OUTPUT_RESULT_FILE +
"', 'w') as fp:")
input_file_lines.append(' json.dump(res_dict, fp)')
input_file_lines.append('')
input_file_lines.append('')
input_file_lines.append('')
with open(input_filename, 'w') as file_input:
file_input.write('\n'.join(input_file_lines))
file_input.write('\n')
def prepare_for_submission(self, folder):
self.inputs.metadata.options.parser_name = 'z2pack.z2pack'
self.inputs.metadata.options.output_filename = self._OUTPUT_Z2PACK_FILE
self.inputs.metadata.options.input_filename = self._INPUT_Z2PACK_FILE
calcinfo = datastructures.CalcInfo()
codeinfo = datastructures.CodeInfo()
codeinfo.stdout_name = self._OUTPUT_Z2PACK_FILE
codeinfo.stdin_name = self._INPUT_Z2PACK_FILE
codeinfo.code_uuid = self.inputs.code.uuid
calcinfo.codes_info = [codeinfo]
calcinfo.codes_run_mode = datastructures.CodeRunMode.SERIAL
calcinfo.cmdline_params = []
calcinfo.retrieve_list = []
calcinfo.retrieve_temporary_list = []
calcinfo.local_copy_list = []
calcinfo.remote_copy_list = []
calcinfo.remote_symlink_list = []
inputs = [
self._INPUT_PW_NSCF_FILE,
self._INPUT_OVERLAP_FILE,
self._INPUT_W90_FILE,
]
outputs = [
self._OUTPUT_Z2PACK_FILE,
self._OUTPUT_SAVE_FILE,
self._OUTPUT_RESULT_FILE,
]
errors = [
os.path.join('build', a)
for a in [self._ERROR_W90_FILE, self._ERROR_PW_FILE]
]
calcinfo.retrieve_list.extend(outputs)
calcinfo.retrieve_list.extend(errors)
parent = self.inputs.parent_folder
rpath = parent.get_remote_path()
uuid = parent.computer.uuid
parent_type = parent.creator.process_class
if parent_type == Z2packCalculation:
self._set_inputs_from_parent_z2pack()
elif parent_type == PwCalculation:
self._set_inputs_from_parent_scf()
pw_dct = _lowercase_dict(self.inputs.pw_parameters.get_dict(),
'pw_dct')
sys = pw_dct['system']
if sys.get('noncolin', False) and sys.get('lspinorb', False):
self._blocked_keywords_wannier90.append(('spinors', True))
try:
settings = _lowercase_dict(self.inputs.z2pack_settings.get_dict(),
'z2pack_settings')
except AttributeError:
raise exceptions.InputValidationError(
'Must provide `z2pack_settings` input for `scf` calculation.')
symlink = settings.get('parent_folder_symlink', False)
self.restart_mode = settings.get('restart_mode', True)
ptr = calcinfo.remote_symlink_list if symlink else calcinfo.remote_copy_list
if parent_type == PwCalculation:
prepare_nscf(self, folder)
prepare_overlap(self, folder)
prepare_wannier90(self, folder)
elif parent_type == Z2packCalculation:
if self.restart_mode:
calcinfo.remote_copy_list.append((
uuid,
os.path.join(rpath, self._OUTPUT_SAVE_FILE),
self._OUTPUT_SAVE_FILE,
))
calcinfo.remote_copy_list.extend([(uuid, os.path.join(rpath,
inp), inp)
for inp in inputs])
else:
raise exceptions.ValidationError(
'parent node must be either from a PWscf or a Z2pack calculation.'
)
parent_files = [self._PSEUDO_SUBFOLDER, self._OUTPUT_SUBFOLDER]
ptr.extend([(uuid, os.path.join(rpath, fname), fname)
for fname in parent_files])
prepare_z2pack(self, folder)
return calcinfo
