Source code for pyretis.inout.setup.common

# -*- coding: utf-8 -*-
# Copyright (c) 2021, PyRETIS Development Team.
# Distributed under the LGPLv2.1+ License. See LICENSE for more info.
"""This module defines common methods for the settings handling.

Important methods defined here
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

create_external (:py:func:`.create_external`)
    Method to create objects from settings.

check_settings (:py:func:`.check_settings`)
    Check that required simulation settings are actually given.

create_engine (:py:func:`.create_engine`)
    Method to create an engine from settings.

create_orderparameter (:py:func:`.create_orderparameter`)
    Method to create order parameters from settings.

create_potential (:py:func:`.create_potential`)
    Method to create a potential from settings.

import_from (:py:func:`.import_from`)
    A method to dynamically import method/classes etc. from user
    specified modules.
"""
import sys
import importlib
import logging
import os
from pyretis.core.common import initiate_instance
from pyretis.engines import engine_factory
from pyretis.orderparameter import order_factory
from pyretis.orderparameter.orderparameter import CompositeOrderParameter
from pyretis.forcefield.factory import potential_factory
logger = logging.getLogger(__name__)  # pylint: disable=invalid-name
logger.addHandler(logging.NullHandler())


__all__ = ['create_external', 'check_settings', 'import_from',
           'create_orderparameter', 'create_engine', 'create_potential']


[docs]def import_from(module_path, function_name): """Import a method/class from a module. This method will dynamically import a specified method/object from a module and return it. If the module can not be imported or if we can't find the method/class in the module we will raise exceptions. Parameters ---------- module_path : string The path/filename to load from. function_name : string The name of the method/class to load. Returns ------- out : object The thing we managed to import. Note ---- Here we need to handle different versions of python. This is due to the ``imp`` module being deprecated and the same time ``importlib`` is changing between versions 3.4 and 3.5 [#]_. References ---------- .. [#] http://bugs.python.org/issue21436 """ try: module_name = os.path.basename(module_path) module_name = os.path.splitext(module_name)[0] spec = importlib.util.spec_from_file_location( module_name, module_path ) module = importlib.util.module_from_spec(spec) spec.loader.exec_module(module) sys.modules[module_name] = module logger.debug('Imported module: %s', module) return getattr(module, function_name) except (ImportError, IOError) as err: msg = f'Could not import module: {module_path}' logger.critical(msg) raise ValueError(msg) from err except AttributeError as err: msg = f'Could not import "{function_name}" from "{module_path}"' logger.critical(msg) raise ValueError(msg) from err
[docs]def check_settings(settings, required): """Check that required simulation settings are actually given. This method will look for required settings in the given `settings`. If one or more keys from the given `required` list of strings are not found, this method will return False. Otherwise, it will return True. Typically, an exception should be raised if False is returned, this is handled outside the method in case someone wants to add some magic handling of missing settings. Parameters ---------- settings : dict This dict contains the given settings required : list of strings This list contains the settings that are required and which we will check the presence of. Returns ------- result : boolean True if all required settings are present, False otherwise. not_found : list of strings There are the required settings we did not find. """ result = True not_found = [] for setting in required: if setting not in settings: result = False not_found.append(setting) return result, not_found
[docs]def create_external(settings, key, factory, required_methods, key_settings=None): """Create external objects from settings. This method will handle the creation of objects from settings. The requested objects can be PyRETIS internals or defined in external modules. Parameters ---------- settings : dict This dictionary contains the settings for the simulation. key : string The setting we are creating for. factory : callable A method to call that can handle the creation of internal objects for us. required_methods : list of strings The methods we need to have if creating an object from external files. key_settings : dict, optional This dictionary contains the settings for the specific key we are processing. If this is not given, we will try to obtain these settings by `settings[key]`. The reason why we make it possible to pass these as settings is in case we are processing a key which does not give a simple setting, but a list of settings. It that case `settings[key]` will give a list to process. That list is iterated somewhere else and `key_settings` can then be used to process these elements. Returns ------- out : object This object represents the class we are requesting here. """ if key_settings is None: try: key_settings = settings[key] except KeyError: logger.debug('No "%s" setting found. Skipping set-up', key) return None module = key_settings.get('module', None) klass = None try: klass = key_settings['class'] except KeyError: logger.debug('No "class" setting for "%s" specified. Skipping set-up', key) return None if module is None: return factory(key_settings) # Here we assume we are to load from a file. Before we import # we need to check that the path is ok or if we should include # the 'exe-path' from settings. # 1) Check if we can find the module: if os.path.isfile(module): obj = import_from(module, klass) else: if 'exe-path' in settings['simulation']: module = os.path.join(settings['simulation']['exe-path'], module) obj = import_from(module, klass) else: msg = f'Could not find module "{module}" for {key}!' raise ValueError(msg) # run some checks: for function in required_methods: objfunc = getattr(obj, function, None) if not objfunc: msg = f'Could not find method {klass}.{function}' logger.critical(msg) raise ValueError(msg) if not callable(objfunc): msg = f'Method {klass}.{function} is not callable!' logger.critical(msg) raise ValueError(msg) return initiate_instance(obj, key_settings)
[docs]def create_orderparameter(settings): """Create order parameters from settings. Parameters ---------- settings : dict This dictionary contains the settings for the simulation. Returns ------- out : object like :py:class:`.OrderParameter` This object represents the order parameter. """ main_order = create_external( settings, 'orderparameter', order_factory, ['calculate'], ) if main_order is None: logger.info('No order parameter created') return None logger.info('Created main order parameter:\n%s', main_order) extra_cv = [] order_settings = settings.get('collective-variable', []) for order_setting in order_settings: order = create_external( settings, 'collective-variable', order_factory, ['calculate'], key_settings=order_setting ) logger.info('Created additional collective variable:\n%s', order) extra_cv.append(order) if not extra_cv: return main_order all_order = [main_order] + extra_cv order = CompositeOrderParameter(order_parameters=all_order) logger.info('Composite order parameter:\n%s', order) return order
[docs]def create_engine(settings): """Create an engine from settings. Parameters ---------- settings : dict This dictionary contains the settings for the simulation. Returns ------- out : object like :py:class:`.EngineBase` This object represents the engine. """ engine = create_external(settings, 'engine', engine_factory, ['integration_step']) if not engine: raise ValueError('Could not create engine from settings!') return engine
[docs]def create_potential(settings, key_settings): """Create a potential from settings. Parameters ---------- settings : dict This dictionary contains the settings for the simulation. key_settings : dict Settings for the potential we are creating. Returns ------- out : object like :py:class:`.PotentialFunction` The object representing the potential function. """ return create_external(settings, 'potential', potential_factory, ['force', 'potential', 'potential_and_force'], key_settings=key_settings)