pyiron.atomistics.master.murnaghan module¶
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class
pyiron.atomistics.master.murnaghan.
DebyeModel
(murnaghan, num_steps=50)[source]¶ Bases:
object
Calculate Thermodynamic Properties based on the Murnaghan output
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property
debye_temperature
¶
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property
num_steps
¶
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property
volume
¶
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property
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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
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.. attribute:: volume_lst
vector of volumes
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.. attribute:: energy_lst
vector of energies
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.. attribute:: fit_dict
dictionary of fit parameters
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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
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static
birchmurnaghan_energy
(V, E0, B0, BP, V0)[source]¶ BirchMurnaghan equation from PRB 70, 224107
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property
energy_lst
¶
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property
fit_dict
¶
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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
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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
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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
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static
get_error
(x_lst, y_lst, p_fit)[source]¶ - Parameters
x_lst –
y_lst –
p_fit –
- Returns
numpy.dnarray
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property
volume_lst
¶
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class
pyiron.atomistics.master.murnaghan.
Murnaghan
(project, job_name='murnaghan')[source]¶ Bases:
pyiron.atomistics.master.parallel.AtomisticParallelMaster
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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.
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property
equilibrium_energy
¶
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property
equilibrium_volume
¶
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property
fit
¶
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class
pyiron.atomistics.master.murnaghan.
MurnaghanJobGenerator
(master)[source]¶ Bases:
pyiron_base.master.parallel.JobGenerator
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static
job_name
(parameter)[source]¶ Return new job name from parameter object. The next child job created will have this name. Subclasses may override this to give custom job names.
- Parameters
parameter (type) – current parameter object drawn from :attribute:`.parameter_list`.
- Returns
job name for the next child job
- Return type
str
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modify_job
(job, parameter)[source]¶ Modify next job with the parameter object. job is already the newly created job object cloned from the template job, so this function has to return the same instance, but may (and should) modify it.
- Parameters
job (
GenericJob
) – new job instanceparameter (type) – current parameter object drawn from :attribute:`.parameter_list`.
- Returns
must be the given job
- Return type
GenericJob
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property
parameter_list
¶ Returns: (list)
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static
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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
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pyiron.atomistics.master.murnaghan.
birchmurnaghan_energy
(V, E0, B0, BP, V0)[source]¶ BirchMurnaghan equation from PRB 70, 224107
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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
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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)