from uibcdf_systems._private_tools.exceptions import *
from uibcdf_systems import puw
from uibcdf_systems.systems._molecular_system import MolecularSystem
import openmm as mm
import openmm.app as app
import openmm.unit as unit
import numpy as np
[docs]class FreeParticle(MolecularSystem):
"""Free particles
Free particles test system
Attributes
----------
parameters :
Dictionary with parameters to initializate the molecular system
topology : openmm.topology
Openmm topology
coordinates :
Position of particles
system : openmm.system
Openmm system
"""
[docs] def __init__(self, n_particles=1, mass='16 amu', density=None, coordinates=None, box=None, pbc=False):
"""Creating a new instance of FreeParticle
A new test system is returned with the openmm system of particles behaving freely -no
potential external potential-.
Parameters
----------
n_particles: int
Number of particles in the system
mass: unit.Quantity
Mass of the particles (in unites of mass) # mass of CH4
Examples
--------
>>> from uibcdf_test_systems import FreeParticle
>>> from openmm import unit
>>> free_particle = FreeParticle(n_particles=1, mass=16*unit.amu)
Notes
-----
See `the free particle documentation in the user guide section
<../../systems/free_particle.html>`_.
"""
super().__init__()
# Parameters
mass = puw.convert(mass)
self.parameters['n_particles']=n_particles
self.parameters['mass']=mass
if (box is not None) or (density is not None):
pbc = True
self.parameters['pbc']=pbc
if pbc:
if (box is None) or (density is None):
raise ValueError('Either the "box" input argument or the "density" needs to beed provided.')
if density is not None:
# box initialization upon density
raise NotImplementedMethodError()
# OpenMM topology
self.topology = app.Topology()
try:
dummy_element = app.element.get_by_symbol('DUM')
except:
dummy_element = app.Element(0, 'DUM', 'DUM', 0.0 * unit.amu)
chain = self.topology.addChain('A')
for ii in range(n_particles):
residue = self.topology.addResidue('DUM', chain)
atom = self.topology.addAtom(name='DUM', element= dummy_element, residue=residue)
# OpenMM system
self.system = mm.System()
for ii in range(n_particles):
self.system.addParticle(mass)
# Coordinates
if coordinates is None:
coordinates = np.zeros([self.parameters['n_particles'], 3], np.float32) * unit.nanometers
self.set_coordinates(coordinates)
# Box
if pbc:
self.set_box(box)
