Source code for ase2sprkkr.input_parameters.input_parameters
""" Containers for configuration parameters of SPR-KKR task.
These configuration parameters are supplied to SPR-KKR executables as input files.
The containers are also the objects, that take care about executing the SPR-KKR
executables.
"""
from __future__ import annotations
import os
import io
import pkgutil
import importlib
from . import definitions
from ..outputs import readers
from ..outputs.readers.default import DefaultProcess
from ..sprkkr.configuration import ConfigurationFile, ConfigurationSection
from ..common.decorators import cached_class_property
import shutil
from typing import Union
[docs]
class InputSection(ConfigurationSection):
""" Input parameters sections has nothing special, yet. """
[docs]
class InputParameters(ConfigurationFile):
""" It holds the configuration values for a SPR-KKR task and run the task
This class is a ConfigurationContainer, thus, it holds the configuration values
for the task. Moreover, according to its definition, it can run the task -
execute the executable with proper parameters - and instantiate the result class,
which then parse the output of the task.
"""
default_sprkkr_executable_suffix = os.getenv('SPRKKR_EXECUTABLE_SUFFIX', '')
""" This suffix is (if not stated otherwise) appended to the executable name. """
[docs]
def resolve_executable_suffix(self, postfix:Union[str,bool]):
"""" Return the postfix, that is appended after the name of SPR-KKR executable.
Parameters
----------
postfix
- If str is given, it is left as is.
- If True, return the default value:
default_sprkkr_executable_suffix
(content of SPRKKR_EXECUTABLE_SUFFIX or a user_defined_value)
- If False, return ''
"""
if postfix is False:
return ''
if postfix is True:
return self.default_sprkkr_executable_suffix
return postfix
[docs]
def __init__(self, definition, inputfile=None, outputfile=False):
super().__init__(definition)
self._inputfile = inputfile
self._outputfile = inputfile if outputfile is False else outputfile
@property
def task_name(self):
""" Return the task name, as defined in the definition of the parameters
(see InputParametersDefinition class) """
return self._definition.name
_default_mpi_runner = None
[docs]
@classmethod
def default_mpi_runner(cls, auto:bool=False):
""" Return the executable and its params to run a mpi task.
The runner is determined by autodetection.
Parameters
----------
auto:bool
If true,
- do not warn if no mpi is found
- check the number of available cpus, do not return a runner, if there is only one
Return
------
mpi_runner: list or False
List of strings with executable and its parameters to run a mpi task.
E.g. [ 'mpirun' ]
If no suitable runner is found, return False.
"""
if cls._default_mpi_runner is None:
for r in [ 'mpirun', 'mpirun.opmpirun', 'mpirun.mpich' ]:
if shutil.which(r):
cls._default_mpi_runner = [ r ]
return cls._default_mpi_runner
if not auto:
print("No MPI runner found. Disabling MPI!!!")
cls._default_mpi_runner=False
if auto and hasattr(os, 'sched_getaffinity') and len(os.sched_getaffinity(0))==1:
return None
return cls._default_mpi_runner
[docs]
def mpi_runner(self, mpi):
""" Return a shell command to execute a mpi task.
Parameters
----------
mpi_runner: Union[bool,str,list,int]
- If True is given, return the default mpi-runner
- If False is given, no mpi-runner is returned.
- If 'auto' is given, it is the same as True, however
* no warning is given if no mpi is found
* MPI is not used, if only one CPU is available
- If a string is given, it is interpreted as a list of one item
- If a list (of strings) is given, the user specified its own runner, use it as is
as the parameters for subprocess.run.
- If an integer is given, it is interpreted as the number of
processes: the default mpi-runner is used, and the parameters
to specify the number of processes.
Return
------
mpi_runner: list
List of strings with the executable and its parameters, e.g.
::
['mpirun', '-np', '4']
"""
if mpi is False or not self._definition.mpi:
return None
if isinstance(mpi, list):
return mpi
if isinstance(mpi, str):
if mpi == 'auto':
return self.default_mpi_runner(auto=True) or None
return [ mpi ]
runner = self.default_mpi_runner()
if not runner:
return None
if mpi is True:
return runner
if isinstance(mpi, int):
return runner + ['-np', str(mpi)]
raise Exception("Unknown mpi argument: " + str(mpi))
[docs]
def is_mpi(self, mpi=True):
""" Will be this task (the task described by this input parameters)
runned using mpi?
Parameters
----------
mpi: list or str or bool
Optional parameter. If False is given, return False regardless the type of the
task, otherwise it is ignored. See InputParameters.mpi_runner for the explanation of the
parameter.
Return
------
is_mpi: bool
Will be this task runned using mpi?
"""
return mpi and self._definition.mpi
[docs]
def run_process(self, calculator, input_file, output_file, directory='.', print_output=None, executable_suffix=None, mpi=None):
"""
Run the process that calculate the task specified by this input paameters
calculator: ase2sprkkr.sprkkr.calculator.SPRKKR
Calculator, used for running the task. Various configurations are readed from them.
directory: str
Where to run the calculation
input_file: file
File, where the input parameters for the task are stored.
output_file: file
File, where the output will be writed. It should be opened for writing (in binary mode)
print_output: bool or str
Print the output to the stdout, too? String value 'info' prints only selected infromations
(depending on the task runned)
executable_suffix: str or None
Postfix, appended to the name of the called executable (sometimes, SPRKKR executables are
compiled so that the resulting executables has postfixies)
mpi: list or str or bool
Run the task using mpi? See InputParameters.mpi_runner for the possible values of the parameter.
Return
------
out: mixed
The result of ase2sprkkr.common.process_output_reader.ProcessOutputReader.run() method: the
parsed output of the runned task.
"""
print_output = calculator.value_or_default('print_output', print_output)
executable_suffix = calculator.value_or_default('executable_suffix', executable_suffix)
mpi = calculator.value_or_default('mpi', mpi)
d = self._definition
executable = d.executable
executable += self.resolve_executable_suffix(executable_suffix)
process = self.result_reader(calculator)
try:
mpi = self.mpi_runner(mpi)
if mpi:
executable = mpi + [ executable + 'MPI', input_file.name ]
return process.run(executable, output_file, stdin = None, print_output=print_output, directory=directory)
else:
executable = [ executable ]
return process.run(executable, output_file, stdin = input_file, print_output=print_output, directory=directory)
except FileNotFoundError as e:
e.strerror = 'Cannot find SPRKKR executable. Maybe, the SPRKKR_EXECUTABLE_SUFFIX environment variable or InputParameters.default_sprkkr_executable_suffix attribute should be set?\n' + \
e.strerror
raise
finally:
input_file.close()
[docs]
def result_reader(self, calculator=None, directory=None):
""" Return the result readed: the class that parse the output
of the runned task
calculator
Calculator, which will be attached to the resulting class
for ruther processing the results
directory
Directory, to which will be related the relative paths
in the result.
If none, get the directory from the calculator, or the current
directory
"""
cls = self._definition.result_reader
if not directory and calculator.directory:
directory = calculator.directory
if cls is None:
task = self.TASK.TASK().lower()
try:
mod = importlib.import_module(f'.{task}', readers.__name__)
clsname = task.title() + 'Process'
cls = getattr(mod, clsname)
if not cls:
raise Exception(f"Can not determine the class to read the results of task {task}"
"No {clsname} class in the module {oo.__name__}.{task}")
except ModuleNotFoundError:
cls = DefaultProcess
return cls(self, calculator, directory)
[docs]
def read_output_from_file(self, filename, directory=None):
""" Read output of a previously runned task from a file and parse it in a same
way, as the process would be runned again.
filename
Filename, from which the result will be read
directory
A directory, to which are related the paths in the output
Default None means the directory, where the file is
"""
directory = directory or os.path.dirname(filename)
return self.result_reader(directory=directory).read_from_file(filename)
[docs]
def executable_params(self, directory=None, ):
"""
Return
------
([executable], stdin, stdout) params for process.Popen
"""
def __str__(self):
return f"<Configuration container {self._get_path()}>"
[docs]
def set_option(self, name, value):
for i in self._members:
if name in i:
self._members[i][name] = value
else:
raise KeyError("No option with name {} in any of the members".format(name))
@cached_class_property
def definitions():
# user = os.path.join(platformdirs.user_config_dir('ase2sprkkr', 'ase2sprkkr'), 'input_parameters')
names = (i for i in pkgutil.iter_modules(definitions.__path__))
im = importlib.import_module
modules = ( im('.definitions.' + i.name, __package__) for i in names )
return { m.__name__.rsplit('.',1)[1].upper(): m.input_parameters for m in modules if hasattr(m, 'input_parameters') }
[docs]
@classmethod
def is_it_a_input_parameters_name(cls, name):
name = name.upper()
return name if name in cls.definitions else False
[docs]
@classmethod
def create_input_parameters(cls, arg):
"""
Create input_parameters object
Parameters
----------
arg: str or InputParameters
If an InputParameters object is given, it is returned as is.
If a string is given, it is interpreted either as a filename
(from which the parameters are read) or the task name, for
which the default parameters are used
Return
------
input_parameters: InputParameters
"""
if isinstance(arg, str):
name = cls.is_it_a_input_parameters_name(arg)
if name:
return cls.create(arg)
return cls.from_file(arg)
if isinstance(arg, io.IOBase):
return cls.from_file(arg)
return arg
[docs]
@classmethod
def create(cls, name):
""" Create input parameters for the given task name
Parameters
----------
name: str
Name of the task (e.g. 'SCF', 'PHAGEN')
Return
------
input_parameters: InputParameters
Input parameters with the default values for the given task.
"""
return InputParameters(cls.task_definition(name))
[docs]
@classmethod
def default_parameters(cls):
""" Create default input parameters """
return cls.create('SCF')
[docs]
@classmethod
def from_file(cls, filename, allow_dangerous:bool=False):
""" Read an input file and create a new InputParameters object from the readed stuff
Parameters
----------
filename: str or file
Input file (either its filename, or an open file)
allow_dangerous
Allow to read dangerous values of options: i.e. the values that do not fullfil the
required type of the given option or its other requirements.
"""
definitions = cls.definitions
for d in definitions.values():
try:
out = d.read_from_file(filename, allow_dangerous=allow_dangerous)
return out
except Exception as e:
last = e
raise last
[docs]
def calculate(self, *args, **kwargs):
""" Create a calculator and run the input_parameters. See SPRKKR.calculate for the arguments """
calc = calculator.SPRKKR()
calc.calculate(input_parameters=self, *args, **kwargs)
def __repr__(self):
d = self._definition
out = d.configuration_type_name
out = out + ' for task ' + d.name.upper()
return out
[docs]
def change_task(self, task):
""" Change the task to the given task. Retain the value of the options,
that are present in the new task.
"""
vals = self.to_dict()
self._definition = self.task_definition(task)
self._init_members_from_the_definition()
self.set(vals, unknown = 'ignore', error='ignore')
[docs]
def save_to_file(self, file, atoms=None, *, validate='save'):
if self._definition.save_hook:
self._definition.save_hook(
getattr(file, "name", None),
atoms
)
super().save_to_file(file, atoms, validate=validate)
# at least, to avoid a circular import
from ..sprkkr import calculator # NOQA: E402