Pysic module

Pysic is an object based calculator for atomistic many-body interactions. It is controlled via several classes such as Pysic, which defines a calculator for the ASE simulation environment [1], and Potential, which defines potentials to be used by for calculating atomic interactions.

[1]	ASE: Comput. Sci. Eng., Vol. 4, 56-66, 2002; https://wiki.fysik.dtu.dk/ase/

Classes of the pysic module

• Pysic class
  • Calculators in ASE
  • Wrapping calculators
  • List of methods
  • Full documentation of the Pysic class
• Potential class
  • Cutoffs
  • Targets of a Potential
  • List of currently available potentials
  • List of methods
  • Full documentation of the Potential class
• ProductPotential class
  • Adding and multiplying potentials
  • Parameterization
  • List of methods
  • Full documentation of the ProductPotential class
• CoulombSummation class
  • Charge scaling
  • Automatic parameters
  • List of currently available summation algorithms
  • List of methods
  • Full documentation of the CoulombSummation class
• Coordinator class
  • Bond order potentials
  • Parameter wrapping
  • Bond order mixing
  • List of methods
  • Full documentation of the Coordinator class
• BondOrderParameters class
  • Bond order cutoffs
  • Atomic and pairwise factors
  • Defining parameters
  • List of currently available bond order factors
  • List of methods
  • Full documentation of the BondOrderParameters class
• CompoundPotential class
  • Using CompoundPotential
  • Defining new wrappers
  • List of corrently available compound potentials
  • List of methods
  • Full documentation of the CompoundPotential class
• ChargeRelaxation class
  • Connecting the structure, calculator and relaxation algorithm
  • Piping ChargeRelaxation algorithms
  • Observers
  • List of currently available relaxation methods
  • List of methods
  • Full documentation of the ChargeRelaxation class
• HybridCalculator class
  • Mechanical Embedding
  • Hydrogen links in Pysic
  • List of methods
  • Full documentation of the HybridCalculator class
• Subsystem class
  • Full documentation of the Subsystem class
  • Full documentation of the SubSystemInternal class
• Interaction class
  • Full documentation of the Interaction class
  • Full documentation of the InteractionInternal class
• FastNeighborList class
  • The benefit of neighbor lists
  • Faster neighbor search
  • Limitations in the implementation
  • Accessing neighbor lists
  • Methods inherited from ASE NeighborList
  • List of methods
  • Full documentation of the FastNeighborList class
• CoreMirror class
  • List of Methods
  • Full documentation of the CoreMirror class

List of methods

Below is a list of methods in pysic.

Potential and bond order factor inquiry

• list_potentials()
• list_valid_potentials()
• is_potential()
• is_valid_potential()
• list_bond_order_factors()
• list_valid_bond_order_factors()
• is_bond_order_factor()
• is_valid_bond_order_factor()
• number_of_targets()
• number_of_parameters()
• names_of_parameters()
• index_of_parameter()
• descriptions_of_parameters()
• description_of_potential()

Charge relaxation inquiry

• is_valid_charge_relaxation()
• is_charge_relaxation()

Message Parsing Interface

• finish_mpi()
• get_number_of_cpus()
• get_cpu_id()

Functions of the pysic module

The module defines a group of functions to directly access the Fortran core for information on available potentials.

pysic.list_potentials()

Same as list_valid_potentials()

pysic.list_valid_potentials()

A list of names of potentials currently known by the core.

The method retrieves from the core a list of the names of different potentials currently implemented. Since the fortran core is directly accessed, any updates made in the core source code should get noticed automatically.

pysic.is_potential(potential_name)

Same as is_valid_potential()

Parameters:

potential_name: string

the name of the potential

pysic.is_charge_relaxation(relaxation_name)

Same as is_valid_charge_relaxation()

Parameters:

relaxation_name: string

the name of the relaxation mode

pysic.is_valid_charge_relaxation(relaxation_name)

Tells if the given string is the name of a charge relaxation mode.

Parameters:

relaxation_name: string

the name of the relaxation mode

pysic.is_valid_potential(potential_name)

Tells if the given string is the name of a potential.

Parameters:

potential_name: string

the name of the potential

pysic.list_bond_order_factors()

Same as list_valid_bond_order_factors()

pysic.list_valid_bond_order_factors()

A list of names of bond order factors currently known by the core.

The method retrieves from the core a list of the names of different bond factors currently implemented. Since the fortran core is directly accessed, any updates made in the core source code should get noticed automatically.

pysic.is_bond_order_factor(bond_order_name)

Same as is_valid_bond_order_factor()

Parameters:

bond_order_name: string

the name of the bond order factor

pysic.is_valid_bond_order_factor(bond_order_name)

Tells if the given string is the name of a bond order factor.

Parameters:

bond_order_name: string

the name of the bond order factor

pysic.number_of_targets(potential_name)

Tells how many targets a potential or bond order factor acts on, i.e., is it pair or many-body.

Parameters:

potential_name: string

the name of the potential or bond order factor

pysic.number_of_parameters(potential_name, as_list=False)

Tells how many parameters a potential, bond order factor, charge relaxation mode or coulomb summation mode incorporates.

A potential has a simple list of parameters and thus the function returns by default a single number. A bond order factor can incorporate parameters for different number of targets (some for single elements, others for pairs, etc.), and so a list of numbers is returned, representing the number of single, pair etc. parameters. If the parameter ‘as_list’ is given and is True, the result is a list containing one number also for a potential.

Parameters:

potential_name: string

the name of the potential or bond order factor

as_list: logical

should the result always be a list

pysic.names_of_parameters(potential_name)

Lists the names of the parameters of a potential, bond order factor, charge relaxation mode or coulomb summation mode.

For a potential, a simple list of names is returned. For a bond order factor, the parameters are categorised according to the number of targets they apply to (single element, pair, etc.). So, for a bond order factor, a list of lists is returned, where the first list contains the single element parameters, the second list the pair parameters etc.

Parameters:

potential_name: string

the name of the potential or bond order factor

pysic.index_of_parameter(potential_name, parameter_name)

Tells the index of a parameter of a potential or bond order factor in the list of parameters the potential uses.

For a potential, the index of the specified parameter is given. For a bond order factor, a list of two integers is given. These give the number of targets (single element, pair etc.) the parameter is associated with and the list index.

Note especially that an index is returned, and these start counting from 0. So for a bond order factor, a parameter for pairs (2 targets) will return 1 as the index for number of targets.

Parameters:

potential_name: string

the name of the potential or bond order factor

parameter_name: string

the name of the parameter

pysic.descriptions_of_parameters(potential_name)

Returns a list of strings containing physical names of the parameters of a potential, bond order factor, or charge relaxation mode, e.g., ‘spring constant’ or ‘decay length’.

For a potential, a simple list of descriptions is returned. For a bond order factor, the parameters are categorised according to the number of targets they apply to (single element, pair, etc.). So, for a bond order factor, a list of lists is returned, where the first list contains the single element parameters, the second list the pair parameters etc.

Parameters:

potential_name: string

the name of the potential or bond order factor

pysic.description_of_potential(potential_name, parameter_values=None, cutoff=None, elements=None, tags=None, indices=None)

Prints a brief description of a potential.

If optional arguments are provided, they are incorporated in the description. That is, by default the method describes the general features of a potential, but it can also be used for describing a particular potential with set parameters.

Parameters:

potential_name: string

the name of the potential

pysic.finish_mpi()

Terminates the MPI framework.

If the Fortran core is compiled in MPI mode, pysic will automatically initialize MPI upon being imported. This method terminates the MPI.

pysic.get_number_of_cpus()

Gets the number of cpus from the Fortran MPI.

pysic.get_cpu_id()

Gets the cpu ID from the Fortran MPI.