Observers¶
SiteOccupancyObserver¶

class
mchammer.observers.
SiteOccupancyObserver
(cluster_space, sites, super_cell, interval=None)[source]¶ This class represents a site occupation factor (SOF) observer.
A SOF observer allows to compute the site occupation factors along the trajectory sampled by a Monte Carlo (MC) simulation.
Parameters:  cluster_space (icet.ClusterSpace) – cluster space from which the allowed species are extracted
 sites (dict(str, list(int))) – dictionary containing lists of sites that are to be considered, which keys will be taken as the names of the sites
 super_cell (ase.Atoms) – an atoms object that represents a typical super cell, which is used to determine the allowed species
 interval (int) – observation interval during the Monte Carlo simulation

tag
¶ name of observer
Type: str

interval
¶ observation interval
Type: int
Example
The following snippet illustrate how to use the site occupancy factor (SOF) observer in a Monte Carlo simulation of a surface slab. Here, the SOF observer is used to monitor the concentrations of different species at the surface, the first subsurface layer, and the remaining “bulk”. A minimal cluster expansion is used with slightly modified surface interactions in order to obtain an example that can be run without much ado. In practice, one should of course use a proper cluster expansion:
from ase.build import fcc111 from icet import ClusterExpansion, ClusterSpace from mchammer.calculators import ClusterExpansionCalculator from mchammer.ensembles import CanonicalEnsemble from mchammer.observers import SiteOccupancyObserver # prepare reference structure prim = fcc111('Au', size=(1, 1, 10), vacuum=10.0) prim.translate((0.1, 0.1, 0.0)) prim.wrap() prim.pbc = True # icet requires pbc in all directions # prepare cluster expansion cs = ClusterSpace(prim, cutoffs=[3.7], chemical_symbols=['Ag', 'Au']) params = [0] + 5 * [0] + 10 * [0.1] params[1] = 0.01 params[6] = 0.12 ce = ClusterExpansion(cs, params) print(ce) # prepare initial configuration based on a 2x2 supercell atoms = prim.repeat((2, 2, 1)) for k in range(20): atoms[k].symbol = 'Ag' # set up MC simulation calc = ClusterExpansionCalculator(atoms, ce) mc = CanonicalEnsemble(atoms=atoms, calculator=calc, temperature=600, data_container='myrun_sof.dc') # set up observer and attach it to the MC simulation sites = {'surface': [0, 9], 'subsurface': [1, 8], 'bulk': list(range(2, 8))} sof = SiteOccupancyObserver(cs, sites, atoms, interval=len(atoms)) mc.attach_observer(sof) # run 1000 trial steps mc.run(1000)
After having run this snippet one can access the SOFs via the data container:
print(mc.data_container.data)

get_observable
(atoms)[source]¶ Returns the site occupation factors for a given atomic configuration.
Parameters: atoms ( Atoms
) – input atomic structure.Return type: Dict
[str
,List
[float
]]

return_type
¶ Data type of the observed data.
Return type: type
BinaryShortRangeOrderObserver¶

class
mchammer.observers.
BinaryShortRangeOrderObserver
(cluster_space, structure, interval, radius)[source]¶ This class represents a short range order (SRO) observer for a binary system.
Parameters:  cluster_space (icet.ClusterSpace) – cluster space used for initialization
 structure (ase.Atoms) – defines the lattice which the observer will work on
 interval (int) – observation interval during the Monte Carlo simulation
 radius (float) – the maximum radius for the neigbhor shells considered

tag
¶ human readable observer name (BinaryShortRangeOrderObserver)
Type: str

interval
¶ observation interval
Type: int
Example
The following snippet illustrate how to use the shortrange order (SRO) observer in a Monte Carlo simulation of a bulk supercell. Here, the parameters of the cluster expansion are set to emulate a simple Ising model in order to obtain an example that can be run without modification. In practice, one should of course use a proper cluster expansion:
from ase.build import bulk from icet import ClusterExpansion, ClusterSpace from mchammer.calculators import ClusterExpansionCalculator from mchammer.ensembles import CanonicalEnsemble from mchammer.observers import BinaryShortRangeOrderObserver # prepare cluster expansion # the setup emulates a second nearestneighbor (NN) Ising model # (zerolet and singlet ECIs are zero; only first and second neighbor # pairs are included) prim = bulk('Au') cs = ClusterSpace(prim, cutoffs=[4.3], chemical_symbols=['Ag', 'Au']) ce = ClusterExpansion(cs, [0, 0, 0.1, 0.02]) # prepare initial configuration nAg = 10 atoms = prim.repeat(3) atoms.set_chemical_symbols(nAg * ['Ag'] + (len(atoms)  nAg) * ['Au']) # set up MC simulation calc = ClusterExpansionCalculator(atoms, ce) mc = CanonicalEnsemble(atoms=atoms, calculator=calc, temperature=600, data_container='myrun_sro.dc') # set up observer and attach it to the MC simulation sro = BinaryShortRangeOrderObserver(cs, atoms, interval=len(atoms), radius=4.3) mc.attach_observer(sro) # run 1000 trial steps mc.run(1000)
After having run this snippet one can access the SRO parameters via the data container:
print(mc.data_container.data)

get_observable
(atoms)[source]¶ Returns the value of the property from a cluster expansion model for a given atomic configurations.
Parameters: atoms ( Atoms
) – input atomic structureReturn type: Dict
[str
,float
]

return_type
¶ Data type of the observed data.
Return type: type
ClusterCountObserver¶

class
mchammer.observers.
ClusterCountObserver
(cluster_space, atoms, interval)[source]¶ This class represents a cluster count observer.
A cluster count observer enables one to keep track of the decoration of clusters along the trajectory sampled by a Monte Carlo (MC) simulation. For example, using this observer, several canonical MC simulations could be carried out at different temperatures and the temperature dependence of the number of nearest neigbhors of a particular species could be accessed with this observer.
Parameters:  cluster_space (icet.ClusterSpace) – cluster space to define the clusters to be counted
 atoms (ase.Atoms) – defines the lattice that the observer will work on
 interval (int) – observation interval during the Monte Carlo simulation

tag
¶ human readable observer name
Type: str

interval
¶ observation interval
Type: int

get_observable
(atoms)[source]¶ Returns the value of the property from a cluster expansion model for a given atomic configuration.
Parameters: atoms ( Atoms
) – input atomic structureReturn type: dict

return_type
¶ Data type of the observed data.
Return type: type
ClusterExpansionObserver¶

class
mchammer.observers.
ClusterExpansionObserver
(cluster_expansion, interval=None, tag='ClusterExpansionObserver')[source]¶ This class represents a cluster expansion (CE) observer.
A CE observer allows to compute a property described by a CE along the trajectory sampled by a Monte Carlo (MC) simulation. In general this CE differs from the CE that is used to generate the trajectory. For example in a canonical MC simulation the latter would usually represent an energy (total or mixing energy) whereas the former CE(s) could map lattice constant or band gap.
Parameters:  cluster_expansion (
icet.ClusterExpansion
cluster expansion model) – to be used for observation  tag (str) – human readable observer name (default: ClusterExpansionObserver)
 interval (int) – observation interval during the Monte Carlo simulation

tag
¶ name of observer
Type: str

interval
¶ observation interval
Type: int

get_observable
(atoms)[source]¶ Returns the value of the property from a cluster expansion model for a given atomic configuration.
Parameters: atoms ( Atoms
) – input atomic structure.Return type: float

return_type
¶ Data type of the observed data.
Return type: type
 cluster_expansion (