Function and class reference

atomicrex.Job

Class for handling an atomicrex fitjob.

atomicrex.AtomicStructure

Class for handling atomic structures.

This is the Python interface module for atomicrex. It primarily provides convenient access to the atomicrex job object and the atomic structures associated with it.

class atomicrex.AtomicStructure

Class for handling atomic structures.

property cell

simulation cell metric

Type

matrix

property cell_origin

origin point of the simulation cell in world coordinates

Type

vector

compute_energy(compute_forces=False, is_fitting=False, suppress_relaxation=False)

Computes the total energy and optionally the forces for this structure.

The function returns a scalar representing the energy of the structure. If the forces are computed they are stored in the structure object.

Parameters
  • compute_forces (bool) – Turns on the computation of forces.

  • is_fitting (bool) – Determines whether this DOF should be relaxed (usually the desired behavior depends on the program phase).

  • suppress_relaxation (bool) – If True structure relaxation will be suppressed.

compute_properties(is_fitting=False)

Computes all enabled properties of the structure.

Parameters

is_fitting (bool) – Determines whether this DOF should be relaxed (usually the desired behavior depends on the program phase).

deactivate_property(id, fit_enabled=False, output_enabled=False)

Deactivates a property in the structure, i.e. removes its contribution to the residual (objective function).

Parameters
  • id (string) – property identifier

  • fit_enabled (bool) – set to True in order to still include the property in the calculation of the objective function

  • output_enabled (bool) – set to True in order to still include the property when printing the results

deform_simulation_cell(deformation)

Applies an affine transformation to the cell and the atoms.

Parameters

deformation (3x3 matrix) – deformation matrix that is applied to the simulation cell.

property forces

list of atomic forces

Type

N x 3 doubles

get_atoms(job)

Returns the structure as an ASE atoms object.

Parameters

job – atomicrex job object; this is used to translate the atomicrex atom types to element names as understood by ASE

Returns

atomic structure

Return type

ASE atoms object

get_cell()
Returns

cell metric

Return type

matrix

get_forces()

Return the forces on the atoms in the form of an array.

Returns

atomic forces

Return type

list of vectors

get_number_of_atoms()
Returns

number of atoms in structure

Return type

int

get_pbc()

Periodic boundary conditions.

Returns

the periodic boundary conditions

Return type

list containing three booleans

get_positions()

Return the positions of the atoms

Returns

atomic positions

Return type

Nx3 array

get_potential_energy()
Returns

potential energy of structure

Return type

float

get_pressure_tensor(voigtIndex)
Parameters

filename (int) – voigtIndex Index of the pressure tensor component in Voigt notation.

Returns

pressure tensor entry

Return type

double

get_target_forces()

Get the target forces for a structure.

Returns

the target forces

Return type

Nx3 array of floats

get_types()

Return the atom types in the form of a list.

Notes

The atom type indices start at 0 (zero).

Returns

atom types

Return type

N ints

modify_property(id, target_value=None, relative_weight=1.0, fit_enabled=None, output_enabled=True)

Add and/or modify a property.

Parameters
  • id (string) – property identifier

  • target_value (double) – the target value [default: no target value]

  • relative_weight (double) – relative weight of the property if it is included in the calculation of the objective function

  • fit_enabled (bool) – calculation of the objective function

  • output_enabled (bool) – set to True in order to include the property when printing the results

property pbc

Periodic boundary conditions.

Type

list of three booleans

property positions

atomic positions

Type

N x 3 doubles

property potential_energy

potential energy of the structure

Type

float

print_properties(show_all=False)

Print properties that are enabled for output and/or fitting.

Parameters

show_all (bool) – set to True in order to show all properties regardless of their internal preference (as determined from output_enabled and fit_enabled)

Notes

Note that compute_properties() must be called first in order to update the stored values of the structure’s properties.

property properties

Properties associated with structure.

Type

dict

set_positions(positions)

Set atomic positions to some new values.

Parameters

pos (Nx3 array) – new atomic positions

set_target_forces(target_forces)

Set the target forces for a structure.

Parameters

target_forces (Nx3 array of floats) – list of atom vectors representing the target forces

set_types(types)

Set atom types.

Parameters

types (N array of ints) – new atom types

Notes

The atom type indices start at 0 (zero).

property tags

atom tags

Type

list of integers

property target_forces

Get the target forces for a structure.

Returns

the target forces

Return type

Nx3 array of floats

property types

atom types

Type

list of integers

write_lammps_dump(filename, ghosts=False)

Exports the structure to a LAMMPS dump file.

Parameters
  • filename (string) – Name of the output file.

  • ghosts (bool) – If True, ghost atoms used during computation of the energy will be included in the output.

write_poscar(filename, ghosts=False)

Exports the structure to a POSCAR file.

Parameters
  • filename (string) – Name of the output file.

  • ghosts (bool) – If True, ghost atoms used during computation of the energy will be included in the output.

class atomicrex.Job

Class for handling an atomicrex fitjob.

add_ase_structure(structure_id, atoms, structure_group=None)

Add a structure based on an ASE atoms object.

Parameters
  • structure_id (string) – structure name; to be used later for accessing structure in dictionary

  • atoms (ASE atoms object) – atomic configuration

  • structure_group (reference to a structure group) – reference to structure group, to which this structure is to be assigned; the default (None) implies the root group

add_library_structure(id, structure, params, structure_group=None)

Add a structure from the library of predefined structures.

Parameters
  • id (string) – structure name that will be used later to access the structure in the dictionary

  • structure (string) –

    type of structure

    single element: FCC, BCC, DIA, SC, HCP, DHCP, beta tin, omega etc.

    multiple elements: rocksalt, cesium chloride, zinc blende, D8a, L12, fluorite, C15, Bh, D2d, Ni17Th2, Th2Zn17, L10, wurtzite etc.

  • params (dictionary) – structural parameters including e.g, alat, clat, ca_ratio, type, type_A, type_B etc.

  • structure_group (reference to a structure group) – reference to structure group, to which this structure is to be assigned; the default (None) implies the root group

calculate_gradient(parameters=None, eps=0.0001)

Computes the gradient of the objective function with respect to the potential parameters using a central finite difference scheme.

Parameters
  • parameters (list of floats) – the parameter set, at which the derivative is to be computed

  • eps – step length for numerical differentiation

calculate_hessian(parameters=None, eps=0.0001)

Computes the matrix of second derivative of the objective function with respect to the potential parameters using a central finite difference scheme.

Parameters
  • parameters (list of floats) – the parameter set, at which the derivative is to be computed

  • eps – step length for numerical differentiation

calculate_residual(params=None, style='squared')

Calculates the the objective function to be minimized during fitting. This is the weighted sum of the deviations of all properties from their target values.

Parameters
  • params (list) – parameter vector, if specified it will overwrite the current parameter vector associated with this job

  • style (string) – method employed for calculating the residual contribution of this property to the objective function; possible values are: squared, squared_relative, user_defined, absolute_diff

property derived_properties

derived-properties associated with job.

Type

dict

get_potential_parameters()
Returns

potential parameters (DOFs) associated with job

Return type

list of floats

property name

name of fitjob

Type

str

output_results()

Write resulting potential parameters to file.

parse_input_file(filename)

Parse the general and potential parameters from an XML file.

Parameters

filename (str) – name of XML input file

perform_fitting()

Perform the actual fitting by minimizing the residual.

property potentials

potentials associated with job.

Type

dict

prepare_fitting()

Set up a list of all degrees of freedom and properties that are to be fitted. This function needs to be called prior to any computation. It is called automatically before a model is fitted via the perform_fitting() call.

print_potential_parameters(only_active=False)

Print potential parameters associated with job. By default all parameters (including inactive ones) are written to stdout.

Parameters

only_active (bool) – If True exclude inactive parameters

print_properties()

Print properties associated with job.

set_potential_parameters(values)
Parameters
  • the potential parameters (DOFs) associated with the job. (Sets) –

  • values (array) – list of double values representing the parameters

set_verbosity(verbosity)

Set the verbosity.

Parameters

verbosity (int) – verbosity level (0=none, 1=minimum, 2=medium, 3=maximum, 4=debug)

property structures

structures associated with job.

Type

dict