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import shlex
from abc import ABC, abstractmethod
from contextlib import ExitStack
from os import PathLike
from pathlib import Path
from typing import Any, Iterable, List, Mapping, Optional, Set
from ase.calculators.abc import GetOutputsMixin
from ase.calculators.calculator import (
BadConfiguration,
BaseCalculator,
_validate_command,
)
from ase.config import cfg as _cfg
link_calculator_docs = (
"https://wiki.fysik.dtu.dk/ase/ase/calculators/"
"calculators.html#calculator-configuration"
)
class BaseProfile(ABC):
configvars: Set[str] = set()
def __init__(self, command):
self.command = _validate_command(command)
@property
def _split_command(self):
return shlex.split(self.command)
def get_command(self, inputfile, calc_command=None) -> List[str]:
"""
Get the command to run. This should be a list of strings.
Parameters
----------
inputfile : str
calc_command: list[str]: calculator command (used for sockets)
Returns
-------
list of str
The command to run.
"""
if calc_command is None:
calc_command = self.get_calculator_command(inputfile)
return [*self._split_command, *calc_command]
@abstractmethod
def get_calculator_command(self, inputfile):
"""
The calculator specific command as a list of strings.
Parameters
----------
inputfile : str
Returns
-------
list of str
The command to run.
"""
def run(
self, directory: Path, inputfile: Optional[str],
outputfile: str, errorfile: Optional[str] = None,
append: bool = False
) -> None:
"""
Run the command in the given directory.
Parameters
----------
directory : pathlib.Path
The directory to run the command in.
inputfile : Optional[str]
The name of the input file.
outputfile : str
The name of the output file.
errorfile: Optional[str]
the stderror file
append: bool
if True then use append mode
"""
import os
from subprocess import check_call
argv_command = self.get_command(inputfile)
mode = 'wb' if not append else 'ab'
with ExitStack() as stack:
output_path = directory / outputfile
fd_out = stack.enter_context(open(output_path, mode))
if errorfile is not None:
error_path = directory / errorfile
fd_err = stack.enter_context(open(error_path, mode))
else:
fd_err = None
check_call(
argv_command,
cwd=directory,
stdout=fd_out,
stderr=fd_err,
env=os.environ,
)
@abstractmethod
def version(self):
"""Get the version of the code.
Returns
-------
str
The version of the code.
"""
@classmethod
def from_config(cls, cfg, section_name):
"""Create a profile from a configuration file.
Parameters
----------
cfg : ase.config.Config
The configuration object.
section_name : str
The name of the section in the configuration file. E.g. the name
of the template that this profile is for.
Returns
-------
BaseProfile
The profile object.
"""
section = cfg.parser[section_name]
command = section['command']
kwargs = {
varname: section[varname]
for varname in cls.configvars if varname in section
}
try:
return cls(command=command, **kwargs)
except TypeError as err:
raise BadConfiguration(*err.args)
def read_stdout(args, createfile=None):
"""Run command in tempdir and return standard output.
Helper function for getting version numbers of DFT codes.
Most DFT codes don't implement a --version flag, so in order to
determine the code version, we just run the code until it prints
a version number."""
import tempfile
from subprocess import PIPE, Popen
with tempfile.TemporaryDirectory() as directory:
if createfile is not None:
path = Path(directory) / createfile
path.touch()
proc = Popen(
args,
stdout=PIPE,
stderr=PIPE,
stdin=PIPE,
cwd=directory,
encoding='utf-8', # Make this a parameter if any non-utf8/ascii
)
stdout, _ = proc.communicate()
# Exit code will be != 0 because there isn't an input file
return stdout
class CalculatorTemplate(ABC):
def __init__(self, name: str, implemented_properties: Iterable[str]):
self.name = name
self.implemented_properties = frozenset(implemented_properties)
@abstractmethod
def write_input(self, profile, directory, atoms, parameters, properties):
...
@abstractmethod
def execute(self, directory, profile):
...
@abstractmethod
def read_results(self, directory: PathLike) -> Mapping[str, Any]:
...
@abstractmethod
def load_profile(self, cfg):
...
def socketio_calculator(
self,
profile,
parameters,
directory,
# We may need quite a few socket kwargs here
# if we want to expose all the timeout etc. from
# SocketIOCalculator.
unixsocket=None,
port=None,
):
import os
from subprocess import Popen
from ase.calculators.socketio import SocketIOCalculator
if port and unixsocket:
raise TypeError(
'For the socketio_calculator only a UNIX '
'(unixsocket) or INET (port) socket can be used'
' not both.'
)
if not port and not unixsocket:
raise TypeError(
'For the socketio_calculator either a '
'UNIX (unixsocket) or INET (port) socket '
'must be used'
)
if not (
hasattr(self, 'socketio_argv')
and hasattr(self, 'socketio_parameters')
):
raise TypeError(
f'Template {self} does not implement mandatory '
'socketio_argv() and socketio_parameters()'
)
# XXX need socketio ABC or something
argv = profile.get_command(
inputfile=None,
calc_command=self.socketio_argv(profile, unixsocket, port)
)
parameters = {
**self.socketio_parameters(unixsocket, port),
**parameters,
}
# Not so elegant that socket args are passed to this function
# via socketiocalculator when we could make a closure right here.
def launch(atoms, properties, port, unixsocket):
directory.mkdir(exist_ok=True, parents=True)
self.write_input(
atoms=atoms,
profile=profile,
parameters=parameters,
properties=properties,
directory=directory,
)
with open(directory / self.outputname, 'w') as out_fd:
return Popen(argv, stdout=out_fd, cwd=directory, env=os.environ)
return SocketIOCalculator(
launch_client=launch, unixsocket=unixsocket, port=port
)
class GenericFileIOCalculator(BaseCalculator, GetOutputsMixin):
cfg = _cfg
def __init__(
self,
*,
template,
profile,
directory,
parameters=None,
):
self.template = template
if profile is None:
if template.name not in self.cfg.parser:
raise BadConfiguration(
f"No configuration of '{template.name}'. "
f"See '{link_calculator_docs}'"
)
try:
profile = template.load_profile(self.cfg)
except Exception as err:
configvars = self.cfg.as_dict()
raise BadConfiguration(
f'Failed to load section [{template.name}] '
f'from configuration: {configvars}'
) from err
self.profile = profile
# Maybe we should allow directory to be a factory, so
# calculators e.g. produce new directories on demand.
self.directory = Path(directory)
super().__init__(parameters)
def set(self, *args, **kwargs):
raise RuntimeError(
'No setting parameters for now, please. '
'Just create new calculators.'
)
def __repr__(self):
return f'{type(self).__name__}({self.template.name})'
@property
def implemented_properties(self):
return self.template.implemented_properties
@property
def name(self):
return self.template.name
def write_inputfiles(self, atoms, properties):
# SocketIOCalculators like to write inputfiles
# without calculating.
self.directory.mkdir(exist_ok=True, parents=True)
self.template.write_input(
profile=self.profile,
atoms=atoms,
parameters=self.parameters,
properties=properties,
directory=self.directory,
)
def calculate(self, atoms, properties, system_changes):
self.write_inputfiles(atoms, properties)
self.template.execute(self.directory, self.profile)
self.results = self.template.read_results(self.directory)
# XXX Return something useful?
def _outputmixin_get_results(self):
return self.results
def socketio(self, **socketkwargs):
return self.template.socketio_calculator(
directory=self.directory,
parameters=self.parameters,
profile=self.profile,
**socketkwargs,
)
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