matscipy.calculators.fitting

Helper routines for potential fitting

Classes

`CombinedFit`(calc, par, targets)	Attributes:
`Fit`(calc, par)	Parameter optimization class.
`FitB2`(calc, par, els, Ec, a0[, B, C11, C12, ...])	Attributes:
`FitBCC`(calc, par, els, Ec, a0[, B, C11, ...])	Attributes:
`FitCubicCrystal`(calc, par, els, Ec, a0[, B, ...])	Attributes:
`FitDiamond`(calc, par, els, Ec, a0[, B, C11, ...])	Attributes:
`FitDiamond100`(calc, par, els, crystal, Esurf)	Attributes:
`FitDiamond110`(calc, par, els, crystal, Esurf)	Attributes:
`FitDiamond111`(calc, par, els, crystal, Esurf)	Attributes:
`FitDimer`(calc, par, els, D0, r0[, w_D0, ...])	Attributes:
`FitFCC`(calc, par, els, Ec, a0[, B, C11, ...])	Attributes:
`FitGraphene`(calc, par, els, Ec, a0, c0[, ...])	Attributes:
`FitGraphite`(calc, par, els, Ec, a0, c0[, ...])	Attributes:
`FitHexagonalCrystal`(calc, par, els, Ec, a0, c0)	Attributes:
`FitL1_0`(calc, par, els, Ec, a0, c0[, c_a, ...])	Attributes:
`FitL1_2`(calc, par, els, Ec, a0[, B, C11, ...])	Attributes:
`FitSC`(calc, par, els, Ec, a0[, B, C11, C12, ...])	Attributes:
`FitSinglePoint`(calc, par, atoms[, w_energy, ...])	Attributes:
`FitSurface`(calc, par, els, crystal, Esurf[, ...])	Attributes:
`FitTetragonalCrystal`(calc, par, els, Ec, a0, c0)	Attributes:
`Parameters`(default, constant, derived[, ...])	Stores a parameter set for fitting purposes.
`Penalty`(calc, par, func)	Attributes:
`RotatingFit`(par, targets)	Attributes:

class matscipy.calculators.fitting.Parameters(default, constant, derived, ranges={}, hidden=[])

Bases: object

Stores a parameter set for fitting purposes.

In particular, it distinguishes between variable parameters (to be fitted), constant parameter and derived parameters, the latter ones having a functional dependence on the other parameters.

Attributes:

constant
default
derived
hidden
parameters
range_mapping
ranges
variable

Methods

get
get_array
get_constant
get_derived
get_dict
get_lower_bounds
get_upper_bounds
get_variable
in_range
set
set_array
set_constant
set_derived
set_dict
set_range_derived
set_variable

__init__(default, constant, derived, ranges={}, hidden=[])

Parameters:

default (dict) – Dictionary with the default parameter set
constant (list) – List of parameters that are constant
derived (dict) – Dictionary with derived parameters and a function to get those derived values.

default

constant

derived

ranges

hidden

parameters

range_mapping

set_range_derived()

set_variable(variable)

get_variable()

set_constant(constant)

get_constant()

set_derived(derived)

get_derived()

set(key, value)

get(key)

set_dict(d)

get_dict()

set_array(a, keys=None)

get_array(keys=None)

get_lower_bounds(keys=None)

get_upper_bounds(keys=None)

in_range(key=None)

variable

class matscipy.calculators.fitting.Fit(calc, par)

Bases: object

Parameter optimization class.

Attributes:

atoms
calc
cost_history
minimal_cost
par
par_at_minimal_cost
residuals_history

Methods

get_cohesive_energy
get_cost_function
get_cost_history
get_parameters_at_minimal_cost
get_potential_energy
get_residuals_history
get_square_residuals
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator_class
set_parameters
set_parameters_from_array

__init__(calc, par)

calc

par

minimal_cost

par_at_minimal_cost

cost_history

residuals_history

set_parameters_from_array(p)

set_calculator_class(calc)

set_parameters(par)

get_potential_energy()

get_cohesive_energy()

get_square_residuals(p=None, log=None)

get_cost_function(p=None, log=None, store_history=False)

get_residuals_history()

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_openopt(solver='interalg')

atoms

class matscipy.calculators.fitting.CombinedFit(calc, par, targets)

Bases: Fit

Attributes:

atoms
calc
cost_history
minimal_cost
par
par_at_minimal_cost
residuals_history
targets

Methods

get_cohesive_energy
get_cost_function
get_cost_history
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator_class
set_parameters
set_parameters_from_array

__init__(calc, par, targets)

targets

set_parameters_from_array(p)

set_parameters(p)

set_calculator_class(calc)

get_residuals(log=None)

get_potential_energy()

atoms

calc

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par

par_at_minimal_cost

residuals_history

class matscipy.calculators.fitting.RotatingFit(par, targets)

Bases: object

Attributes:

par
targets

Methods

optimize

__init__(par, targets)

par

targets

optimize(pmax=0.001, mix=None, **kwargs)

class matscipy.calculators.fitting.Penalty(calc, par, func)

Bases: Fit

Attributes:

atoms
calc
cost_history
func
minimal_cost
par
par_at_minimal_cost
residuals_history

Methods

set_calculator(calc)

Set the calculator

get_cohesive_energy
get_cost_function
get_cost_history
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator_class
set_parameters
set_parameters_from_array

__init__(calc, par, func)

func

set_calculator(calc): Set the calculator

get_residuals(log=None)

atoms

calc

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par

par_at_minimal_cost

residuals_history

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitSinglePoint(calc, par, atoms, w_energy=None, w_forces=None, w_stress=None)

Bases: Fit

Attributes:

atoms
calc
cost_history
energy
forces
minimal_cost
par
par_at_minimal_cost
residuals_history
stress
w_energy
w_forces
w_stress

Methods

set_calculator(calc)

Set the calculator

get_cohesive_energy
get_cost_function
get_cost_history
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator_class
set_parameters
set_parameters_from_array

__init__(calc, par, atoms, w_energy=None, w_forces=None, w_stress=None)

w_energy

w_forces

w_stress

energy

forces

stress

atoms

set_calculator(calc): Set the calculator

get_residuals(log=None)

calc

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par

par_at_minimal_cost

residuals_history

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitDimer(calc, par, els, D0, r0, w_D0=1.0, w_r0=1.0, vacuum=10.0, fmax=1e-06)

Bases: Fit

Attributes:

D0
atoms
calc
cost_history
fmax
minimal_cost
par
par_at_minimal_cost
r0
residuals_history
w_D0
w_r0

Methods

set_calculator(calc)

Set the calculator, and relax the structure to its ground-state.

get_cohesive_energy
get_cost_function
get_cost_history
get_distance
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_dimer
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator_class
set_parameters
set_parameters_from_array

__init__(calc, par, els, D0, r0, w_D0=1.0, w_r0=1.0, vacuum=10.0, fmax=1e-06)

D0

r0

w_D0

w_r0

calc

par

fmax

atoms

new_dimer()

set_calculator(calc): Set the calculator, and relax the structure to its ground-state.

get_distance()

get_residuals(log=None)

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitCubicCrystal(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

Bases: Fit

Attributes:

Ec
a0
atoms
calc
cost_history
crystal
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

get_C11
get_C44
get_Cp
get_SFE
get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

__init__(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

a0

Ec

w_a0

w_Ec

fmax

atoms

new_bulk()

set_calculator(calc)

get_lattice_constant()

get_SFE()

get_C11()

get_Cp()

get_C44()

get_residuals(log=None)

calc

crystal

par

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitTetragonalCrystal(calc, par, els, Ec, a0, c0, c_a=None, B=None, C11=None, C12=None, C13=None, C33=None, C44=None, C66=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_c0=1.0, w_c_a=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C13=1.0, w_C33=1.0, w_C44=1.0, w_C66=1.0, w_Cp=1.0, w_SFE=None, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

Bases: Fit

Attributes:

Ec
a0
atoms
c0
calc
cost_history
crystal
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0
w_c0

Methods

get_C33
get_C44
get_C66
get_D1
get_D2
get_D4
get_SFE
get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

__init__(calc, par, els, Ec, a0, c0, c_a=None, B=None, C11=None, C12=None, C13=None, C33=None, C44=None, C66=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_c0=1.0, w_c_a=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C13=1.0, w_C33=1.0, w_C44=1.0, w_C66=1.0, w_Cp=1.0, w_SFE=None, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

a0

c0

Ec

w_a0

w_c0

w_Ec

fmax

atoms

new_bulk()

set_calculator(calc)

get_SFE()

get_lattice_constant()

get_C33()

get_C44()

get_C66()

get_D1()

get_D2()

get_D4()

get_residuals(log=None)

calc

crystal

par

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitHexagonalCrystal(calc, par, els, Ec, a0, c0, w_Ec=1.0, w_a0=1.0, fmax=0.01)

Bases: Fit

Attributes:

Ec
a0
atoms
c0
calc
cost_history
crystal
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

__init__(calc, par, els, Ec, a0, c0, w_Ec=1.0, w_a0=1.0, fmax=0.01)

Ec

a0

c0

w_Ec

w_a0

fmax

atoms

new_bulk()

set_calculator(calc)

get_lattice_constant()

get_residuals(log=None)

calc

crystal

par

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitSurface(calc, par, els, crystal, Esurf, w_Esurf=1.0)

Bases: Fit

Attributes:

Ec
a0
atoms
calc
cost_history
crystal
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

get_cohesive_energy
get_cost_function
get_cost_history
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
get_surface_energy
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

__init__(calc, par, els, crystal, Esurf, w_Esurf=1.0)

calc

par

crystal

set_calculator(calc)

get_surface_energy()

get_residuals(log=None)

a0

Ec

fmax

w_a0

w_Ec

atoms

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitSC(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

Bases: FitCubicCrystal

Attributes:

Ec
a0
atoms
calc
cost_history
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

crystal
get_C11
get_C44
get_Cp
get_SFE
get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

crystal

crystalstr = 'sc'

a0

calc

Ec

fmax

par

w_a0

w_Ec

__init__(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

atoms

cost_history

get_C11()

get_C44()

get_Cp()

get_SFE()

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_lattice_constant()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

new_bulk()

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitBCC(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

Bases: FitCubicCrystal

Attributes:

Ec
a0
atoms
calc
cost_history
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

crystal
get_C11
get_C44
get_Cp
get_SFE
get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

crystal

crystalstr = 'bcc'

a0

calc

Ec

fmax

par

w_a0

w_Ec

__init__(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

atoms

cost_history

get_C11()

get_C44()

get_Cp()

get_SFE()

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_lattice_constant()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

new_bulk()

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitFCC(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

Bases: FitCubicCrystal

Attributes:

Ec
a0
atoms
calc
cost_history
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

crystal
get_C11
get_C44
get_Cp
get_SFE
get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

crystal

crystalstr = 'fcc'

a0

calc

Ec

fmax

par

w_a0

w_Ec

__init__(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

atoms

cost_history

get_C11()

get_C44()

get_Cp()

get_SFE()

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_lattice_constant()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

new_bulk()

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitB2(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

Bases: FitCubicCrystal

Attributes:

Ec
a0
atoms
calc
cost_history
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

crystal
get_C11
get_C44
get_Cp
get_SFE
get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

crystal

crystalstr = 'B2'

a0

calc

Ec

fmax

par

w_a0

w_Ec

__init__(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

atoms

cost_history

get_C11()

get_C44()

get_Cp()

get_SFE()

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_lattice_constant()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

new_bulk()

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitL1_0(calc, par, els, Ec, a0, c0, c_a=None, B=None, C11=None, C12=None, C13=None, C33=None, C44=None, C66=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_c0=1.0, w_c_a=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C13=1.0, w_C33=1.0, w_C44=1.0, w_C66=1.0, w_Cp=1.0, w_SFE=None, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

Bases: FitTetragonalCrystal

Attributes:

Ec
a0
atoms
c0
calc
cost_history
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0
w_c0

Methods

crystal
get_C33
get_C44
get_C66
get_D1
get_D2
get_D4
get_SFE
get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

crystal

crystalstr = 'L1_0'

a0

c0

calc

Ec

fmax

par

w_a0

w_c0

w_Ec

__init__(calc, par, els, Ec, a0, c0, c_a=None, B=None, C11=None, C12=None, C13=None, C33=None, C44=None, C66=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_c0=1.0, w_c_a=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C13=1.0, w_C33=1.0, w_C44=1.0, w_C66=1.0, w_Cp=1.0, w_SFE=None, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

atoms

cost_history

get_C33()

get_C44()

get_C66()

get_D1()

get_D2()

get_D4()

get_SFE()

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_lattice_constant()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

new_bulk()

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitL1_2(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

Bases: FitCubicCrystal

Attributes:

Ec
a0
atoms
calc
cost_history
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

crystal
get_C11
get_C44
get_Cp
get_SFE
get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

crystal

crystalstr = 'L1_2'

a0

calc

Ec

fmax

par

w_a0

w_Ec

__init__(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

atoms

cost_history

get_C11()

get_C44()

get_Cp()

get_SFE()

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_lattice_constant()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

new_bulk()

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitDiamond(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

Bases: FitCubicCrystal

Attributes:

Ec
a0
atoms
calc
cost_history
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

crystal
get_C11
get_C44
get_Cp
get_SFE
get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

crystal

crystalstr = 'dia'

a0

calc

Ec

fmax

par

w_a0

w_Ec

__init__(calc, par, els, Ec, a0, B=None, C11=None, C12=None, C44=None, Cp=None, SFE=None, w_Ec=1.0, w_a0=1.0, w_B=1.0, w_C11=1.0, w_C12=1.0, w_C44=1.0, w_Cp=1.0, w_SFE=1.0, fmax=1e-06, eps=0.001, ecoh_ref=None, size=[1, 1, 1])

atoms

cost_history

get_C11()

get_C44()

get_Cp()

get_SFE()

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_lattice_constant()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

new_bulk()

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitGraphite(calc, par, els, Ec, a0, c0, w_Ec=1.0, w_a0=1.0, fmax=0.01)

Bases: FitHexagonalCrystal

Attributes:

Ec
a0
atoms
c0
calc
cost_history
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

crystal
get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

crystal

crystalstr = 'gra'

a0

c0

calc

Ec

fmax

par

w_a0

w_Ec

__init__(calc, par, els, Ec, a0, c0, w_Ec=1.0, w_a0=1.0, fmax=0.01)

atoms

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_lattice_constant()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

new_bulk()

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitGraphene(calc, par, els, Ec, a0, c0, w_Ec=1.0, w_a0=1.0, fmax=0.01)

Bases: FitHexagonalCrystal

Attributes:

Ec
a0
atoms
c0
calc
cost_history
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

crystal
get_cohesive_energy
get_cost_function
get_cost_history
get_lattice_constant
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
new_bulk
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

crystal

crystalstr = 'grp'

a0

c0

calc

Ec

fmax

par

w_a0

w_Ec

__init__(calc, par, els, Ec, a0, c0, w_Ec=1.0, w_a0=1.0, fmax=0.01)

atoms

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_lattice_constant()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

minimal_cost

new_bulk()

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitDiamond100(calc, par, els, crystal, Esurf, w_Esurf=1.0)

Bases: FitSurface

Attributes:

Ec
a0
atoms
calc
cost_history
crystal
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

get_cohesive_energy
get_cost_function
get_cost_history
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
get_surface_energy
new_surface
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

surfstr = 'dia-100'

new_surface(a0)

a0

calc

crystal

Ec

fmax

par

w_a0

w_Ec

__init__(calc, par, els, crystal, Esurf, w_Esurf=1.0)

atoms

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

get_surface_energy()

minimal_cost

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitDiamond110(calc, par, els, crystal, Esurf, w_Esurf=1.0)

Bases: FitSurface

Attributes:

Ec
a0
atoms
calc
cost_history
crystal
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

get_cohesive_energy
get_cost_function
get_cost_history
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
get_surface_energy
new_surface
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

surfstr = 'dia-110'

new_surface(a0)

a0

calc

crystal

Ec

fmax

par

w_a0

w_Ec

__init__(calc, par, els, crystal, Esurf, w_Esurf=1.0)

atoms

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

get_surface_energy()

minimal_cost

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)

class matscipy.calculators.fitting.FitDiamond111(calc, par, els, crystal, Esurf, w_Esurf=1.0)

Bases: FitSurface

Attributes:

Ec
a0
atoms
calc
cost_history
crystal
fmax
minimal_cost
par
par_at_minimal_cost
residuals_history
w_Ec
w_a0

Methods

get_cohesive_energy
get_cost_function
get_cost_history
get_parameters_at_minimal_cost
get_potential_energy
get_residuals
get_residuals_history
get_square_residuals
get_surface_energy
new_surface
optimize
optimize_anneal
optimize_brute
optimize_leastsq
optimize_openopt
set_calculator
set_calculator_class
set_parameters
set_parameters_from_array

surfstr = 'dia-111'

a0

calc

crystal

Ec

fmax

par

w_a0

w_Ec

__init__(calc, par, els, crystal, Esurf, w_Esurf=1.0)

atoms

cost_history

get_cohesive_energy()

get_cost_function(p=None, log=None, store_history=False)

get_cost_history()

get_parameters_at_minimal_cost(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

get_potential_energy()

get_residuals(log=None)

get_residuals_history()

get_square_residuals(p=None, log=None)

get_surface_energy()

minimal_cost

new_surface(a0)

optimize(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, **kwargs)

optimize_anneal(**kwargs)

optimize_brute(**kwargs)

optimize_leastsq(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

optimize_openopt(solver='interalg')

par_at_minimal_cost

residuals_history

set_calculator(calc)

set_calculator_class(calc)

set_parameters(par)

set_parameters_from_array(p)