def __call__(self, **options):
# Process the keyword arguments
self.setCallOptions(options)
# Check if the universe has features not supported by the integrator
Features.checkFeatures(self, self.universe)
# Get the universe variables needed by the integrator
configuration = self.universe.configuration()
masses = self.universe.masses()
velocities = self.universe.velocities()
if velocities is None:
raise ValueError("no velocities")
# Get the friction coefficients. First check if a keyword argument
# 'friction' was given to the integrator. Its value can be a
# ParticleScalar or a plain number (used for all atoms). If no
# such argument is given, collect the values of the attribute
# 'friction' from all atoms (default is zero).
try:
friction = self.getOption('friction')
except KeyError:
friction = self.universe.getParticleScalar('friction')
if not ParticleProperties.isParticleProperty(friction):
var = ParticleProperties.ParticleScalar(self.universe)
var.array[:] = friction
friction = var
# Construct a C evaluator object for the force field, using
# the specified number of threads or the default value
nt = self.getOption('threads')
evaluator = self.universe.energyEvaluator(threads=nt).CEvaluator()
# Run the C integrator
MMTK_langevin.integrateLD(self.universe,
configuration.array, velocities.array,
masses.array, friction.array, evaluator,
self.getOption('temperature'),
self.getOption('delta_t'),
self.getOption('steps'),
self.getActions())
def __call__(self, **options):
# Process the keyword arguments
self.setCallOptions(options)
# Check if the universe has features not supported by the integrator
Features.checkFeatures(self, self.universe)
#the following two lines are required due to MMTK mixing up atom indices. This sorts them.
#atoms = self.universe.atomList()
#atoms.sort(key=operator.attrgetter('index'))
# Get the universe variables needed by the integrator
configuration = self.universe.configuration()
velocities = self.universe.velocities()
if velocities is None:
raise ValueError("no velocities")
# Get the friction coefficients. First check if a keyword argument
# 'friction' was given to the integrator. Its value can be a
# ParticleScalar or a plain number (used for all atoms). If no
# such argument is given, collect the values of the attribute
# 'friction' from all atoms (default is zero).
friction = self.getOption('friction')
#call this method to create the OpenMM System. Without this, creating
#the forces will fail!!
self.initOmmSystem()
#call this method to ensure that the forcefield parameters get
#passed to OpenMM. Without this, there will be no forces to integrate!
self.createOmmForces()
#The restraint option must be included in the creation of the integrator for this part to be executed
try:
restraint = self.getOption('restraint')
except ValueError:
restraint = None
print 'No restraints (Value Error)'
except:
print sys.exc_info()[0]
if restraint != None:
self.addRestraint(restraint)
#ugly hack to get timestep skip information
skip = -1
if ('actions' in self.call_options):
actions = self.call_options['actions']
for action in actions:
if isinstance(action, Dynamics.TranslationRemover):
self.addOmmCMRemover(action.skip)
if isinstance(action, Trajectory.LogOutput):
break # to avoid Logoutput skip setting problem PNR NFF SJC
if isinstance(action, Trajectory.TrajectoryOutput):
skip = action.skip
action.skip = 1
if skip < 0 :
for action in actions:
if issubclass(action.__class__, Trajectory.TrajectoryOutput):
skip = action.skip
action.skip = 1
break
#we are not logging anything, so we don't have to report any intermediate values
if skip < 0:
skip = 100
steps = 1
# Run the C integrator
atoms = self.universe.atomList()
masses = [atom.mass() for atom in atoms]
natoms = len(atoms)
nmolecules = len(self.universe.objectList(Molecule))
molecule_lengths = N.zeros(nmolecules, dtype=N.int32, order='C')
for i in range(0,len(self.universe.objectList(Molecule))):
molecule_lengths[i] = len(self.universe.objectList(Molecule)[i].atomList())
MMTK_langevin.integrateLD(self.universe, configuration.array,
velocities.array, N.array(masses, dtype=N.float64),
friction,
self.getOption('temperature'),
self.getOption('delta_t'),
self.getOption('steps'), skip, natoms, self.nbeads,
nmolecules, molecule_lengths,
self.getActions())
#call this to clean up after ourselves
self.destroyOmmSystem()
def __call__(self, **options):
# Process the keyword arguments
self.setCallOptions(options)
# Check if the universe has features not supported by the integrator
Features.checkFeatures(self, self.universe)
#the following two lines are required due to MMTK mixing up atom indices. This sorts them.
#atoms = self.universe.atomList()
#atoms.sort(key=operator.attrgetter('index'))
# Get the universe variables needed by the integrator
configuration = self.universe.configuration()
velocities = self.universe.velocities()
if velocities is None:
raise ValueError("no velocities")
# Get the friction coefficients. First check if a keyword argument
# 'friction' was given to the integrator. Its value can be a
# ParticleScalar or a plain number (used for all atoms). If no
# such argument is given, collect the values of the attribute
# 'friction' from all atoms (default is zero).
friction = self.getOption('friction')
#call this method to create the OpenMM System. Without this, creating
#the forces will fail!!
self.initOmmSystem()
#call this method to ensure that the forcefield parameters get
#passed to OpenMM. Without this, there will be no forces to integrate!
self.createOmmForces()
#The restraint option must be included in the creation of the integrator for this part to be executed
try:
restraint = self.getOption('restraint')
except ValueError:
restraint = None
print 'No restraints (Value Error)'
except:
print sys.exc_info()[0]
if restraint != None:
self.addRestraint(restraint)
#ugly hack to get timestep skip information
skip = -1
if ('actions' in self.call_options):
actions = self.call_options['actions']
for action in actions:
if isinstance(action, Dynamics.TranslationRemover):
self.addOmmCMRemover(action.skip)
if isinstance(action, Trajectory.LogOutput):
break # to avoid Logoutput skip setting problem PNR NFF SJC
if isinstance(action, Trajectory.TrajectoryOutput):
skip = action.skip
action.skip = 1
if skip < 0:
for action in actions:
if issubclass(action.__class__,
Trajectory.TrajectoryOutput):
skip = action.skip
action.skip = 1
break
#we are not logging anything, so we don't have to report any intermediate values
if skip < 0:
skip = 100
steps = 1
# Run the C integrator
atoms = self.universe.atomList()
masses = [atom.mass() for atom in atoms]
natoms = len(atoms)
nmolecules = len(self.universe.objectList(Molecule))
molecule_lengths = N.zeros(nmolecules, dtype=N.int32, order='C')
for i in range(0, len(self.universe.objectList(Molecule))):
molecule_lengths[i] = len(
self.universe.objectList(Molecule)[i].atomList())
MMTK_langevin.integrateLD(self.universe, configuration.array,
velocities.array,
N.array(masses, dtype=N.float64), friction,
self.getOption('temperature'),
self.getOption('delta_t'),
self.getOption('steps'), skip, natoms,
self.nbeads, nmolecules, molecule_lengths,
self.getActions())
#call this to clean up after ourselves
self.destroyOmmSystem()
