pyiron.atomistics.master.murnaghan module

class pyiron.atomistics.master.murnaghan.DebyeModel(murnaghan, num_steps=50)[source]

Bases: object

Calculate Thermodynamic Properties based on the Murnaghan output

property debye_temperature
energy_vib(T, debye_T=None, low_T_limit=True)[source]
property num_steps
polynomial(poly_fit=None, volumes=None)[source]
property volume
class pyiron.atomistics.master.murnaghan.EnergyVolumeFit(volume_lst=None, energy_lst=None)[source]

Bases: object

Fit energy volume curves

Parameters
  • volume_lst (list/numpy.dnarray) – vector of volumes

  • energy_lst (list/numpy.dnarray) – vector of energies

.. attribute:: volume_lst

vector of volumes

.. attribute:: energy_lst

vector of energies

.. attribute:: fit_dict

dictionary of fit parameters

static birch(V, E0, B0, BP, V0)[source]

From Intermetallic compounds: Principles and Practice, Vol. I: Principles Chapter 9 pages 195-210 by M. Mehl. B. Klein, D. Papaconstantopoulos paper downloaded from Web

case where n=0

static birchmurnaghan_energy(V, E0, B0, BP, V0)[source]

BirchMurnaghan equation from PRB 70, 224107

property energy_lst
property fit_dict
fit_energy(volume_lst)[source]

Gives the energy value for the corresponding energy volume fit defined in the fit dictionary.

Parameters

volume_lst – list of volumes

Returns

list of energies

fit_eos_general(volume_lst=None, energy_lst=None, fittype='birchmurnaghan')[source]

Fit on of the equations of state

Parameters
  • volume_lst (list/numpy.dnarray/None) – vector of volumes

  • energy_lst (list/numpy.dnarray/None) – vector of energies

  • fittype (str) – on of the following [‘birch’, ‘birchmurnaghan’, ‘murnaghan’, ‘pouriertarantola’, ‘vinet’]

Returns

dictionary with fit results

Return type

dict

fit_eos_general_intern(fittype='birchmurnaghan')[source]
fit_polynomial(volume_lst=None, energy_lst=None, fit_order=3)[source]

Fit a polynomial

Parameters
  • volume_lst (list/numpy.dnarray/None) – vector of volumes

  • energy_lst (list/numpy.dnarray/None) – vector of energies

  • fit_order (int) – Degree of the polynomial

Returns

dictionary with fit results

Return type

dict

static get_error(x_lst, y_lst, p_fit)[source]
Parameters
  • x_lst

  • y_lst

  • p_fit

Returns

numpy.dnarray

static murnaghan(V, E0, B0, BP, V0)[source]

From PRB 28,5480 (1983

static pouriertarantola(V, E0, B0, BP, V0)[source]
static vinet_energy(V, E0, B0, BP, V0)[source]

Vinet equation from PRB 70, 224107

property volume_lst
class pyiron.atomistics.master.murnaghan.Murnaghan(project, job_name='murnaghan')[source]

Bases: pyiron.atomistics.master.parallel.AtomisticParallelMaster

collect_output()[source]

Collect the output files of the external executable and store the information in the HDF5 file. This method has to be implemented in the individual meta jobs derived from the ParallelMaster.

property equilibrium_energy
property equilibrium_volume
property fit
fit_birch_murnaghan(vol_erg_dic=None)[source]
fit_murnaghan(vol_erg_dic=None)[source]
fit_polynomial(fit_order=3, vol_erg_dic=None)[source]
fit_vinet(vol_erg_dic=None)[source]
get_structure(iteration_step=-1)[source]

Returns: Structure with equilibrium volume

list_structures()[source]
plot(num_steps=100, plt_show=True)[source]
poly_fit(fit_order=3, vol_erg_dic=None)[source]
class pyiron.atomistics.master.murnaghan.MurnaghanJobGenerator(job, no_job_checks=False)[source]

Bases: pyiron.base.master.parallel.JobGenerator

static job_name(parameter)[source]
modify_job(job, parameter)[source]
property parameter_list

Returns: (list)

pyiron.atomistics.master.murnaghan.birch(V, E0, B0, BP, V0)[source]

From Intermetallic compounds: Principles and Practice, Vol. I: Principles Chapter 9 pages 195-210 by M. Mehl. B. Klein, D. Papaconstantopoulos paper downloaded from Web

case where n=0

pyiron.atomistics.master.murnaghan.birchmurnaghan_energy(V, E0, B0, BP, V0)[source]

BirchMurnaghan equation from PRB 70, 224107

pyiron.atomistics.master.murnaghan.debye_function(x)[source]
pyiron.atomistics.master.murnaghan.debye_integral(x)[source]
pyiron.atomistics.master.murnaghan.fit_leastsq(p0, datax, datay, fittype='vinet')[source]

Least square fit

Parameters
  • p0 (list) – [E0, B0, BP, V0] list of fit parameters

  • datax (float/numpy.dnarray) – volumes to fit

  • datay (float/numpy.dnarray) – energies corresponding to the volumes

  • fittype (str) – on of the following [‘birch’, ‘birchmurnaghan’, ‘murnaghan’, ‘pouriertarantola’, ‘vinet’]

Returns

[E0, B0, BP, V0], [E0_err, B0_err, BP_err, V0_err]

Return type

list

pyiron.atomistics.master.murnaghan.fitfunction(parameters, vol, fittype='vinet')[source]

Fit the energy volume curve

Parameters
  • parameters (list) – [E0, B0, BP, V0] list of fit parameters

  • vol (float/numpy.dnarray) – single volume or a vector of volumes as numpy array

  • fittype (str) – on of the following [‘birch’, ‘birchmurnaghan’, ‘murnaghan’, ‘pouriertarantola’, ‘vinet’]

Returns

single energy as float or a vector of energies as numpy array

Return type

(float/numpy.dnarray)

pyiron.atomistics.master.murnaghan.murnaghan(V, E0, B0, BP, V0)[source]

From PRB 28,5480 (1983

pyiron.atomistics.master.murnaghan.pouriertarantola(V, E0, B0, BP, V0)[source]

Pourier-Tarantola equation from PRB 70, 224107

pyiron.atomistics.master.murnaghan.vinet_energy(V, E0, B0, BP, V0)[source]

Vinet equation from PRB 70, 224107