##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################
from adaptivemd.generator import PythonRPCTaskGenerator
from adaptivemd.task import PythonTask
import shutil
import os
[docs]class Archiver(PythonRPCTaskGenerator):
[docs] def __init__(self, target):
"""
Generator to copy all files in a project to a specified location
Parameters
----------
target : `Directory`
the directory to dump all simulations to
"""
super(Archiver, self).__init__()
self.target = target
[docs] def to_dict(self):
return {
'target': self.target
}
[docs] def task_archive(self, files):
"""
Create a task that computes an msm using a given set of trajectories
Parameters
----------
files : list of `Trajectory`
the list of trajectory references to be used in the computation
Returns
-------
`Task`
a task object describing a simple python RPC call using pyemma
"""
t = PythonTask()
t.link(self.target, 'target_folder')
t.call(copy_files, files=files)
return t
[docs]def copy_files(files):
names = {}
for f in files:
n = os.path.basename(f)
if n not in names:
shutil.copy(f, os.path.join('target_folder', n))
names[n] = 1
else:
parts = n.split('.')
n2 = '.'.join(parts[:-1]) + '-{count:08d}.'.format(count=names[n]) + parts[-1]
shutil.copy(f, os.path.join('target_folder', n2))
names[n] += 1