Updating or adapting the Fleur Parsers¶
Note
A more detailed walkthrough of the important design decisions concerning the implementation Fleur XML parsers and IO capabilities can be found in this document
Each input and output file for Fleur has a correspong XML-Schema, where the structure of these files are defined.
To be able to parse such files efficiently and without hardcoding their structure
we extract all necessary information about the schemas in the modules under
fleur_schema
. The resulting python dictionaries
can be accessed via the classes InputSchemaDict
and OutputSchemaDict
.
The easiest way to instantiate one of these objects is to use the
InputSchemaDict.fromVersion()
or OutputSchemaDict.fromVersion()
methods
by providing the desired version string.
Adding/modifying a Fleur Schema:¶
The command masci-tools fleur-schema add <path-to-schema-file>
can be used to add
the schema to the repository. If the schema for the specified version already exists
an error is raised. To ignore this error the option --overwrite
can be used.
Adapting the outxml_parser:¶
In contrast to the input file parser inpxml_parser()
, which parses all information available,
the outxml_parser()
has to be more flexible. The out file has much more information which might
not be always useful for users. Therefore the selection of what is parsed has to be much more specific.
This selection is expressed in the context of tasks. In general this corresponds to things like: - Total energy - Charge density distances - Magnetic moments - and so on …
These are expressed in a definition in form of a dictionary. Below a simple example
(Total energy) is shown, which parses the value
and units
attribute of the
totalEnergy
tag. The hardcoded known parsing tasks can be found in
default_parse_tasks
.
total_energy_definition = {
'energy_hartree': {
'parse_type': 'singleValue',
'path_spec': {
'name': 'totalEnergy'
}
},
}
The definition of a task can consist of multiple keys (in this case only energy_hartree
),
which by default correspond to the keys in the resulting output dictionary. Each key has
to contain the parse_type
and path_spec
key. The parse_type
defines the
method used to extract the information.
The following are possible:
- attrib:
Will parse the value of the given attribute
- text:
Will parse the text of the given tag
- numberNodes:
Will return the number of nodes for the given tag
- exists:
Will return, whether the given tag exists
- attrib_exists:
Will return, whether the given attribute exists
- allAttribs:
Will parse all known attributes at the given tag into a dictionary
- parentAttribs:
Will parse all known attributes at the given tag into a dictionary, but for the parent of the tag
- singleValue:
Special case of allAttribs to parse value and units attribute for the given tag
- xmlGetter:
Will execute a function in the module
xml_getters
given in thename
entry
The path_spec
key specifies how the key can be uniquely identified.
It can contain the following specifications:
- name:
Name of the wanted tag/attribute
- contains:
A phrase, which has to occur in the path
- not_contains:
A phrase, which has to not occur in the path
- exclude:
list of str. Only valid for attributes (these are sorted into different categories
unique
,unique_path
andother
). This attribute can exclude one or more of these categories
All except the name
key are optional and should be constructed so that there is only one
possible choice. Otherwise an exception is raised. There are other keywords, which can be entered
here. These control how the parsed data is entered into the output dictionary.
For a definition of these keywords, please refer to
default_parse_tasks
.
Each task can also contain a number of control keys, determining when to perform the tasks. Each of these keys begins with an underscore. All of these are optional. The following are valid:
- _general:
bool, if True (default False) the task is not performed for each iteration but once on the root of the file
- _minimal:
bool, if True the task is performed even when
minimal_mode = True
is given- _modes:
list of tuples specifying requirements on the
fleur_modes
for the task. For example[('jspins', 2), ('soc', True)]
will only perform the task for a magnetic SOC calculation- _conversions:
list of str, giving the names of functions to call after this task. Functions given here have to be decorated with the
conversion_function()
decorator- _special:
bool, if True (default False) this task is NEVER added automatically and has to be added by hand
Migrating the parsing tasks¶
These task definitions might have to be adapted for new fleur versions. Some changes
might be possible to make in default_parse_tasks
directly without breaking backwards compatibility. If this is not possible there is
a decorator register_migration()
to define a function that is recognized
by the outxml_parser()
to convert between versions. A usage example is shown below.
from masci_tools.io.parsers.fleur import register_migration
import copy
@register_migration(base_version='0.33', target_version='0.34')
def migrate_033_to034(definition_dict):
"""
Fictitious migration from 0.33 to 0.34
Moves the `number_of_atom_types` attribute from reading a simple
attribute to counting the number of atomGroups in the input section
And removes orbital_magnetic_moments task
"""
#IMPORTANT: First copy the original dict
new_dict = copy.deepcopy(definition_dict)
#If a task is incompatible remove it from the defintion_dict
new_dict.pop('orbital_magnetic_moments')
new_dict['general_out_info'].pop('number_of_atom_types')
new_dict['general_inp_info']['number_of_atom_types'] = {
'parse_type': 'numberNodes',
'path_spec': {
'name': 'atomGroup'
}
}
return new_dict