matscipy.calculators.fitting

Helper routines for potential fitting

Classes

CombinedFit(calc, par, targets)

Fit(calc, par)

Parameter optimization class.

FitB2(calc, par, els, Ec, a0[, B, C11, C12, ...])

FitBCC(calc, par, els, Ec, a0[, B, C11, ...])

FitCubicCrystal(calc, par, els, Ec, a0[, B, ...])

FitDiamond(calc, par, els, Ec, a0[, B, C11, ...])

FitDiamond100(calc, par, els, crystal, Esurf)

FitDiamond110(calc, par, els, crystal, Esurf)

FitDiamond111(calc, par, els, crystal, Esurf)

FitDimer(calc, par, els, D0, r0[, w_D0, ...])

FitFCC(calc, par, els, Ec, a0[, B, C11, ...])

FitGraphene(calc, par, els, Ec, a0, c0[, ...])

FitGraphite(calc, par, els, Ec, a0, c0[, ...])

FitHexagonalCrystal(calc, par, els, Ec, a0, c0)

FitL1_0(calc, par, els, Ec, a0, c0[, c_a, ...])

FitL1_2(calc, par, els, Ec, a0[, B, C11, ...])

FitSC(calc, par, els, Ec, a0[, B, C11, C12, ...])

FitSinglePoint(calc, par, atoms[, w_energy, ...])

FitSurface(calc, par, els, crystal, Esurf[, ...])

FitTetragonalCrystal(calc, par, els, Ec, a0, c0)

Parameters(default, constant, derived[, ...])

Stores a parameter set for fitting purposes.

Penalty(calc, par, func)

RotatingFit(par, targets)

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)