Coverage for /builds/ase/ase/ase/calculators/exciting/exciting.py: 84.29%
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1# fmt: off
3"""ASE Calculator for the ground state exciting DFT code.
5Exciting calculator class in this file allow for writing exciting input
6files using ASE Atoms object that allow for the compiled exciting binary
7to run DFT on the geometry/material defined in the Atoms object. Also gives
8access to developer to a lightweight parser (lighter weight than NOMAD or
9the exciting parser in the exciting repository) to capture ground state
10properties.
12Note: excitingtools must be installed using `pip install excitingtools` to
13use this calculator.
14"""
16from os import PathLike
17from pathlib import Path
18from typing import Any, Mapping
20import ase.io.exciting
21from ase.calculators.calculator import PropertyNotImplementedError
22from ase.calculators.exciting.runner import (
23 SimpleBinaryRunner,
24 SubprocessRunResults,
25)
26from ase.calculators.genericfileio import (
27 BaseProfile,
28 CalculatorTemplate,
29 GenericFileIOCalculator,
30)
33class ExcitingProfile(BaseProfile):
34 """Defines all quantities that are configurable for a given machine.
36 Follows the generic pattern BUT currently not used by our calculator as:
37 * species_path is part of the input file in exciting.
38 * OnlyTypo fix part of the profile used in the base class is the run
39 method, which is part of the BinaryRunner class.
40 """
41 configvars = {'species_path'}
43 def __init__(self, command, species_path=None, **kwargs):
44 super().__init__(command, **kwargs)
46 self.species_path = species_path
48 def version(self):
49 """Return exciting version."""
50 # TARP No way to get the version for the binary in use
51 return
53 # Machine specific config files in the config
54 # species_file goes in the config
55 # binary file in the config.
56 # options for that, parallel info dictionary.
57 # Number of threads and stuff like that.
59 def get_calculator_command(self, input_file):
60 """Returns command to run binary as a list of strings."""
61 # input_file unused for exciting, it looks for input.xml in run
62 # directory.
63 if input_file is None:
64 return []
65 else:
66 return [str(input_file)]
69class ExcitingGroundStateTemplate(CalculatorTemplate):
70 """Template for Ground State Exciting Calculator
72 Abstract methods inherited from the base class:
73 * write_input
74 * execute
75 * read_results
76 """
78 parser = {'info.xml': ase.io.exciting.parse_output}
79 output_names = list(parser)
80 # Use frozenset since the CalculatorTemplate enforces it.
81 implemented_properties = frozenset(['energy', 'forces'])
82 _label = 'exciting'
84 def __init__(self):
85 """Initialise with constant class attributes.
87 :param program_name: The DFT program, should always be exciting.
88 :param implemented_properties: What properties should exciting
89 calculate/read from output.
90 """
91 super().__init__('exciting', self.implemented_properties)
92 self.errorname = f'{self._label}.err'
94 @staticmethod
95 def _require_forces(input_parameters):
96 """Expect ASE always wants forces, enforce setting in input_parameters.
98 :param input_parameters: exciting ground state input parameters, either
99 as a dictionary or ExcitingGroundStateInput.
100 :return: Ground state input parameters, with "compute
101 forces" set to true.
102 """
103 from excitingtools import ExcitingGroundStateInput
105 input_parameters = ExcitingGroundStateInput(input_parameters)
106 input_parameters.tforce = True
107 return input_parameters
109 def write_input(
110 self,
111 profile: ExcitingProfile, # ase test linter enforces method signatures
112 # be consistent with the
113 # abstract method that it implements
114 directory: PathLike,
115 atoms: ase.Atoms,
116 parameters: dict,
117 properties=None,
118 ):
119 """Write an exciting input.xml file based on the input args.
121 :param profile: an Exciting code profile
122 :param directory: Directory in which to run calculator.
123 :param atoms: ASE atoms object.
124 :param parameters: exciting ground state input parameters, in a
125 dictionary. Expect species_path, title and ground_state data,
126 either in an object or as dict.
127 :param properties: Base method's API expects the physical properties
128 expected from a ground state calculation, for example energies
129 and forces. For us this is not used.
130 """
131 # Create a copy of the parameters dictionary so we don't
132 # modify the callers dictionary.
133 parameters_dict = parameters
134 assert set(parameters_dict.keys()) == {
135 'title', 'species_path', 'ground_state_input',
136 'properties_input'}, \
137 'Keys should be defined by ExcitingGroundState calculator'
138 file_name = Path(directory) / 'input.xml'
139 species_path = parameters_dict.pop('species_path')
140 title = parameters_dict.pop('title')
141 # We can also pass additional parameters which are actually called
142 # properties in the exciting input xml. We don't use this term
143 # since ASE use properties to refer to results of a calculation
144 # (e.g. force, energy).
145 if 'properties_input' not in parameters_dict:
146 parameters_dict['properties_input'] = None
148 ase.io.exciting.write_input_xml_file(
149 file_name=file_name, atoms=atoms,
150 ground_state_input=parameters_dict['ground_state_input'],
151 species_path=species_path, title=title,
152 properties_input=parameters_dict['properties_input'])
154 def execute(
155 self, directory: PathLike,
156 profile) -> SubprocessRunResults:
157 """Given an exciting calculation profile, execute the calculation.
159 :param directory: Directory in which to execute the calculator
160 exciting_calculation: Base method `execute` expects a profile,
161 however it is simply used to execute the program, therefore we
162 just pass a SimpleBinaryRunner.
163 :param profile: This name comes from the superclass CalculatorTemplate.
164 It contains machine specific information to run the
165 calculation.
167 :return: Results of the subprocess.run command.
168 """
169 return profile.run(directory, f"{directory}/input.xml", None,
170 erorrfile=self.errorname)
172 def read_results(self, directory: PathLike) -> Mapping[str, Any]:
173 """Parse results from each ground state output file.
175 Note we allow for the ability for there to be multiple output files.
177 :param directory: Directory path to output file from exciting
178 simulation.
179 :return: Dictionary containing important output properties.
180 """
181 results = {}
182 for file_name in self.output_names:
183 full_file_path = Path(directory) / file_name
184 result: dict = self.parser[file_name](full_file_path)
185 results.update(result)
186 return results
188 def load_profile(self, cfg, **kwargs):
189 """ExcitingProfile can be created via a config file.
191 Alternative to this method the profile can be created with it's
192 init method. This method allows for more settings to be passed.
193 """
194 return ExcitingProfile.from_config(cfg, self.name, **kwargs)
197class ExcitingGroundStateResults:
198 """Exciting Ground State Results."""
200 def __init__(self, results: dict) -> None:
201 self.results = results
202 self.final_scl_iteration = list(results['scl'].keys())[-1]
204 def total_energy(self) -> float:
205 """Return total energy of system."""
206 # TODO(Alex) We should a common list of keys somewhere
207 # such that parser -> results -> getters are consistent
208 return float(
209 self.results['scl'][self.final_scl_iteration]['Total energy']
210 )
212 def band_gap(self) -> float:
213 """Return the estimated fundamental gap from the exciting sim."""
214 return float(
215 self.results['scl'][self.final_scl_iteration][
216 'Estimated fundamental gap'
217 ]
218 )
220 def forces(self):
221 """Return forces present on the system.
223 Currently, not all exciting simulations return forces. We leave this
224 definition for future revisions.
225 """
226 raise PropertyNotImplementedError
228 def stress(self):
229 """Get the stress on the system.
231 Right now exciting does not yet calculate the stress on the system so
232 this won't work for the time being.
233 """
234 raise PropertyNotImplementedError
237class ExcitingGroundStateCalculator(GenericFileIOCalculator):
238 """Class for the ground state calculation.
240 :param runner: Binary runner that will execute an exciting calculation and
241 return a result.
242 :param ground_state_input: dictionary of ground state settings for example
243 {'rgkmax': 8.0, 'autormt': True} or an object of type
244 ExcitingGroundStateInput.
245 :param directory: Directory in which to run the job.
246 :param species_path: Path to the location of exciting's species files.
247 :param title: job name written to input.xml
249 :return: Results returned from running the calculate method.
252 Typical usage:
254 gs_calculator = ExcitingGroundState(runner, ground_state_input)
256 results: ExcitingGroundStateResults = gs_calculator.calculate(
257 atoms: Atoms)
258 """
260 def __init__(
261 self,
262 *,
263 runner: SimpleBinaryRunner,
264 ground_state_input,
265 directory='./',
266 species_path='./',
267 title='ASE-generated input',
268 ):
269 self.runner = runner
270 # Package data to be passed to
271 # ExcitingGroundStateTemplate.write_input(..., input_parameters, ...)
272 # Structure not included, as it's passed when one calls .calculate
273 # method directly
274 self.exciting_inputs = {
275 'title': title,
276 'species_path': species_path,
277 'ground_state_input': ground_state_input,
278 }
279 self.directory = Path(directory)
281 # GenericFileIOCalculator expects a `profile`
282 # containing machine-specific settings, however, in exciting's case,
283 # the species file are defined in the input XML (hence passed in the
284 # parameters argument) and the only other machine-specific setting is
285 # the BinaryRunner. Furthermore, in GenericFileIOCalculator.calculate,
286 # profile is only used to provide a run method. We therefore pass the
287 # BinaryRunner in the place of a profile.
288 super().__init__(
289 profile=runner,
290 template=ExcitingGroundStateTemplate(),
291 directory=directory,
292 parameters=self.exciting_inputs,
293 )