def __init__(self):
# must set this here since we need it to generate the state,
# will get called again in the superclass method
self.getState_kwargs = dict(GET_STATE_KWARG_DEFAULTS)
if self.GET_STATE_KWARGS is not None:
self.getState_kwargs.update(self.GET_STATE_KWARGS)
test_sys = LennardJonesPair()
init_state = self.make_state(test_sys.system, test_sys.positions)
super().__init__(
distance=PairDistance(),
init_state=init_state,
system=test_sys.system,
topology=test_sys.topology,
)
hdf5_filename = 'results.wepy.h5'
setup_state_filename = 'setup.pkl'
restart_state_filename = 'restart.pkl'
# normalize the input paths
json_top_path = osp.join(inputs_dir, json_top_filename)
# normalize the output paths
hdf5_path = osp.join(outputs_dir, hdf5_filename)
setup_state_path = osp.join(outputs_dir, setup_state_filename)
restart_state_path = osp.join(outputs_dir, restart_state_filename)
## System and OpenMMRunner
# make the test system from openmmtools
test_sys = LennardJonesPair()
# make the integrator
integrator = omm.LangevinIntegrator(TEMPERATURE, FRICTION_COEFFICIENT,
STEP_SIZE)
# make a context and set the positions
context = omm.Context(test_sys.system, copy(integrator))
context.setPositions(test_sys.positions)
# get the data from this context so we have a state to start the
# simulation with
get_state_kwargs = dict(GET_STATE_KWARG_DEFAULTS)
init_sim_state = context.getState(**get_state_kwargs)
init_state = OpenMMState(init_sim_state)
from simtk.openmm import *
from openmmtools.testsystems import LennardJonesPair
from openmmtools import alchemy
import numpy as np
from simtk.openmm.vec3 import Vec3
from openforcefield.topology import Molecule, Topology
from openmmforcefields.generators import SystemGenerator
platform = openmm.Platform.getPlatformByName('CPU')
# platform.setPropertyDefaultValue('Precision', 'double')
'''
---SYSTEM PREPARATION---
'''
test_system = LennardJonesPair()
[system, topology, positions] = [test_system.system, test_system.topology , test_system.positions]
reference_force = system.getForces()[0]
sterics_mixing_rules = ()
expression = ('U_sterics;'
'U_sterics = (1.0-lambda)*4*epsilon*x*(x-1.0);'
'x = (sigma/reff_sterics)^6;'
'reff_sterics = (softcore_alpha*lambda*(sigma^softcore_n) + r^softcore_n)^(1.0/softcore_n);'
'epsilon = sqrt(epsilon1*epsilon2);'
'sigma = 0.5*(sigma1 + sigma2);')
force = openmm.CustomNonbondedForce(expression)