def define_vertices(self):
# Graph components
g = self.graph
g.delete_vacancy = DeleteAtom()
g.build_lambdas = BuildMixingPairs()
g.random_velocity = SerialList(RandomVelocity)
g.initial_forces = Zeros()
g.slice_structure = Slice()
g.check_steps = IsGEq()
g.verlet_positions = SerialList(VerletPositionUpdate)
g.reflect = SerialList(VoronoiReflection)
g.calc_full = SerialList(ExternalHamiltonian)
g.slice_positions = SerialList(Slice)
g.calc_vac = SerialList(ExternalHamiltonian)
g.slice_harmonic = SerialList(Slice)
g.harmonic = SerialList(HarmonicHamiltonian)
g.write_vac_forces = SerialList(Overwrite)
g.write_harmonic_forces = SerialList(Overwrite)
g.transpose_lambda = Transpose()
g.mix = SerialList(WeightedSum)
g.verlet_velocities = SerialList(VerletVelocityUpdate)
g.check_thermalized = IsGEq()
g.check_sampling_period = ModIsZero()
g.transpose_energies = Transpose()
g.addition = SerialList(WeightedSum)
g.average = SerialList(WelfordOnline)
g.clock = Counter()
def define_vertices(self):
# Graph components
g = self.graph
g.calc_static = ExternalHamiltonian()
g.clock = Counter()
g.check_steps = IsGEq()
g.force_norm = Norm()
g.max_force = Max()
g.check_force = IsGEq()
g.gradient_descent = GradientDescent()
def define_vertices(self):
# Graph components
g = self.graph
g.interpolate_images = InterpolatePositions()
g.check_steps = IsGEq()
g.calc_static = AutoList(ExternalHamiltonian)
g.neb_forces = NEBForces()
g.gradient_descent = SerialList(GradientDescent)
g.clock = Counter()
def define_vertices(self):
# Graph components
g = self.graph
g.initial_velocity = RandomVelocity()
g.initial_forces = Zeros()
g.check_steps = IsGEq()
g.clock = Counter()
g.calc_static = ExternalHamiltonian()
g.verlet_positions = VerletPositionUpdate()
g.verlet_velocities = VerletVelocityUpdate()
def define_vertices(self):
# Graph components
g = self.graph
ip = Pointer(self.input)
g.create_centroids = CreateJob()
g.initial_positions = InitialPositions()
g.initial_forces = Zeros()
g.initial_velocities = SerialList(RandomVelocity)
g.cutoff = CutoffDistance()
g.check_steps = IsGEq()
g.remove_images = RemoveJob()
g.create_images = CreateJob()
g.constrained_evo = ParallelList(_ConstrainedMD, sleep_time=ip.sleep_time)
g.check_thermalized = IsGEq()
g.mix = CentroidsRunningAverageMix()
g.smooth = CentroidsSmoothing()
g.reparameterize = CentroidsReparameterization()
g.calc_static_centroids = SerialList(ExternalHamiltonian)
g.recenter = SerialList(StringRecenter)
g.clock = Counter()
def define_vertices(self):
# Graph components
g = self.graph
g.check_steps = IsGEq()
g.verlet_positions = VerletPositionUpdate()
g.reflect_string = StringReflect()
g.reflect_atoms = SphereReflection()
g.calc_static = ExternalHamiltonian()
g.verlet_velocities = VerletVelocityUpdate()
g.running_average_pos = PositionsRunningAverage()
g.clock = Counter()
def define_vertices(self):
# Graph components
g = self.graph
g.initial_velocity = RandomVelocity()
g.initial_forces = Zeros()
g.check_steps = IsGEq()
g.verlet_positions = VerletPositionUpdate()
g.reflect = VoronoiReflection()
g.calc_static = ExternalHamiltonian()
g.harmonic = HarmonicHamiltonian()
g.mix = WeightedSum()
g.verlet_velocities = VerletVelocityUpdate()
g.clock = Counter()
def define_vertices(self):
# Graph components
g = self.graph
g.initial_velocities = RandomVelocity()
g.initial_forces = Zeros()
g.initial_pressures = Zeros()
g.cutoff = CutoffDistance()
g.check_steps = IsGEq()
g.clock = Counter()
g.barostat = BerendsenBarostat()
g.verlet_positions = VerletPositionUpdate()
g.reflect_atoms = SphereReflection()
g.calc_static = ExternalHamiltonian()
g.verlet_velocities = VerletVelocityUpdate()
def define_vertices(self):
# Graph components
g = self.graph
g.build_lambdas = BuildMixingPairs()
g.initial_forces = Zeros()
g.initial_velocity = SerialList(RandomVelocity)
g.check_steps = IsGEq()
g.verlet_positions = SerialList(VerletPositionUpdate)
g.reflect = SerialList(VoronoiReflection)
g.calc_static = AutoList(ExternalHamiltonian)
g.harmonic = SerialList(HarmonicHamiltonian)
g.transpose_forces = Transpose()
g.mix = SerialList(WeightedSum)
g.verlet_velocities = SerialList(VerletVelocityUpdate)
g.clock = Counter()
def define_vertices(self):
# Components
g = self.graph
g.partition = PartitionStructure()
g.calc_static_mm = ExternalHamiltonian()
g.calc_static_qm = ExternalHamiltonian()
g.clock = Counter()
g.force_norm_mm = Norm()
g.force_norm_qm = Norm()
g.max_force_mm = Max()
g.max_force_qm = Max()
g.check_force_mm = IsLEq()
g.check_force_qm = IsLEq()
g.check_steps = IsGEq()
g.update_buffer_qm = AddDisplacements()
g.update_core_mm = AddDisplacements()
g.gradient_descent_mm = GradientDescent()
g.gradient_descent_qm = GradientDescent()
g.calc_static_small = ExternalHamiltonian()
def define_vertices(self):
# Graph components
g = self.graph
g.initialize_images = CreateJob()
g.initialize_centroids = CreateJob()
g.initial_positions = InitialPositions()
g.initial_velocities = SerialList(RandomVelocity)
g.initial_forces = Zeros()
g.cutoff = CutoffDistance()
g.check_steps = IsGEq()
g.verlet_positions = SerialList(VerletPositionUpdate)
g.reflect_string = SerialList(StringReflect)
g.reflect_atoms = SerialList(SphereReflection)
g.calc_static_images = SerialList(ExternalHamiltonian)
g.verlet_velocities = SerialList(VerletVelocityUpdate)
g.running_average_pos = SerialList(PositionsRunningAverage)
g.check_sampling_period = ModIsZero()
g.mix = CentroidsRunningAverageMix()
g.smooth = CentroidsSmoothing()
g.reparameterize = CentroidsReparameterization()
g.calc_static_centroids = SerialList(ExternalHamiltonian)
g.recenter = SerialList(StringRecenter)
g.clock = Counter()