def __init__(self,
kernel,
context,
unit_config,
output_file="",
integrator="EulerBDIntegrator",
reaction_handler="Gillespie",
evaluate_topology_reactions=True,
evaluate_forces=True,
evaluate_observables=True,
skin=0):
"""
Creates a new simulation object
:param kernel: the kernel to use
:param context: the parent low level context object
:param unit_config: the unit configuration
:param output_file: the output file
:param integrator: the integrator
:param reaction_handler: the reaction handler
:param evaluate_topology_reactions: whether to evaluate topology reactions
:param evaluate_forces: whether to evaluate forces
:param evaluate_observables: whether to evaluate observables
:param skin: the skin size for neighbor lists
"""
available_kernels = _KernelProvider.get().available_kernels()
if kernel not in available_kernels:
raise ValueError(
"The selected kernel was \"{}\" but only {} "
"are available.".format(
kernel,
", ".join(['"{}"'.format(x) for x in available_kernels])))
self._unit_conf = unit_config
self._kernel = kernel
self._simulation = _Simulation()
self._simulation.set_kernel(kernel)
self._simulation.context = context
self.output_file = output_file
self._observables = _Observables(self)
self.integrator = integrator
self.reaction_handler = reaction_handler
self.evaluate_topology_reactions = evaluate_topology_reactions
self.evaluate_forces = evaluate_forces
self.evaluate_observables = evaluate_observables
self.skin = skin
self.simulation_scheme = "ReaDDyScheme"
self.show_progress = True
self._progress = None
if kernel == "CPU":
self._kernel_configuration = _CPUKernelConfiguration()
else:
self._kernel_configuration = _NOOPKernelConfiguration()
def __init__(self, kernel, context, unit_config, output_file="", integrator="EulerBDIntegrator",
reaction_handler="Gillespie", evaluate_topology_reactions=True, evaluate_forces=True,
evaluate_observables=True, skin=0):
"""
Creates a new simulation object
:param kernel: the kernel to use
:param context: the parent low level context object
:param unit_config: the unit configuration
:param output_file: the output file
:param integrator: the integrator
:param reaction_handler: the reaction handler
:param evaluate_topology_reactions: whether to evaluate topology reactions
:param evaluate_forces: whether to evaluate forces
:param evaluate_observables: whether to evaluate observables
:param skin: the skin size for neighbor lists
"""
available_kernels = _KernelProvider.get().available_kernels()
if kernel not in available_kernels:
raise ValueError("The selected kernel was \"{}\" but only {} "
"are available.".format(kernel, ", ".join(['"{}"'.format(x) for x in available_kernels])))
self._unit_conf = unit_config
self._kernel = kernel
self._simulation = _Simulation()
self._simulation.set_kernel(kernel)
self._simulation.context = context
self._evaluate_topology_reactions = True
self._evaluate_forces = True
self._evaluate_observables = True
self._skin = 0
self._integrator = "EulerBDIntegrator"
self._reaction_handler = "Gillespie"
self._simulation_scheme = "ReaDDyScheme"
self._output_file = ""
self.output_file = output_file
self._observables = _Observables(self)
self.integrator = integrator
self.reaction_handler = reaction_handler
self.evaluate_topology_reactions = evaluate_topology_reactions
self.evaluate_forces = evaluate_forces
self.evaluate_observables = evaluate_observables
self.skin = skin
self._show_progress = True
self._progress_output_stride = 10
self._progress = None
if kernel == "CPU":
self._kernel_configuration = _CPUKernelConfiguration()
else:
self._kernel_configuration = _NOOPKernelConfiguration()