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

debye_temperature
energy_vib(T, debye_T=None, low_T_limit=True)[source]
num_steps
polynomial(poly_fit=None, volumes=None)[source]
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

energy_lst
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

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.

equilibrium_energy
equilibrium_volume
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]
parameter_list

(list)

Type:Returns
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