from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import warnings
from gmx import context
from gmx import fileio
from gmx import exceptions
from gmx import util
__all__ = ['System']
[docs]class System(object):
"""Gromacs simulation system objects. (Deprecated)
.. deprecated:: 0.0.7
Instead, use :py:mod:`gmx.workflow` tools to set up a system for simulation.
Version 0.0.6 and earlier:
A System object connects all of the objects necessary to describe a molecular
system to be simulated.
Once a system is created, objects can be attached or edited, accessed through
the following properties.
Attributes:
workflow: element of work to be executed.
Example:
>>> my_sim = gmx.System._from_file(tpr_filename)
>>> status = my_sim.run()
Example:
>>> my_sim = gmx.System._from_file(tpr_filename)
>>> # Launch exectution of the runner and work on available resources.
>>> with gmx.context.DefaultContext(system) as session:
... # Run the work specified in the TPR file
... session.run()
... # Extend the simulation and run an additional 1000 steps.
... # (version 0.1.0)
... #status = session.run(1000)
... print(status)
...
gmx.Status(True)
Success
"""
def __init__(self):
warnings.warn("gmx.System handles are not meaningful in GROMACS versions >= 2019. See gmx.workflow",
DeprecationWarning)
self.__workflow = None
@property
def workflow(self):
return self.__workflow
@workflow.setter
def workflow(self, work):
self.__workflow = work
@staticmethod
def _from_file(inputrecord):
"""Process a file to create a System object. (Deprecated)
Calls an appropriate helper function to parse a file in the current
context and create a System object. If no Context is currently bound, a
local default context is created and bound.
We are still refining the meanings of paths and file locations, and the
semantics of turning file objects into API objects. For reference, see
https://github.com/kassonlab/gmxapi/issues/96
Until resolved, this helper method should not be part of the public
interface.
Args:
inputrecord (str): input file name
Returns:
gmx.System
Example:
simulation = gmx.System._from_file('membrane.tpr')
status = simulation.run()
"""
import gmx.workflow
if util._filetype(inputrecord) is fileio.TprFile:
# we use the API to process TPR files. We create a MD module and
# retrieve a system from its contents.
newsystem = gmx.workflow.from_tpr(inputrecord)
if newsystem is None:
raise gmx.Error("Got empty system when reading TPR file.")
else:
raise gmx.UsageError("Need a TPR file.")
system = System()
system.workflow = newsystem
return system
[docs] def run(self, parameters=None):
"""Launch execution.
If the System is attached to a Context, the Context is initialized, if
necessary, and its instance run()
method is called. If there is not yet a Context, one is created and then
used.
Note: currently always initializes new context informed by the runner.
Args:
parameters: optional parameters to pass to runner. Parameter type varies by runner type.
Returns:
Gromacs status object.
"""
with context.get_context(self.workflow) as session:
if parameters is None:
return session.run()
else:
return session.run(parameters)