pyiron.atomistics.master package

Submodules

pyiron.atomistics.master.convergence_volume module

class pyiron.atomistics.master.convergence_volume.ConvergenceVolume(project, job_name)[source]

Bases: pyiron.atomistics.master.serial.SerialMaster

Parameters:
  • project
  • job_name
create_next(job_name=None)[source]
Parameters:job_name

Returns:

pyiron.atomistics.master.convergence_volume.convergence_goal(self, **qwargs)[source]

pyiron.atomistics.master.murnaghan module

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

Bases: object

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.Murnaghan(project, job_name='murnaghan')[source]

Bases: pyiron.atomistics.master.parallel.AtomisticParallelMaster

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

BirchMurnaghan equation from PRB 70, 224107

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_birch_murnaghan(vol_erg_dic=None)[source]
fit_leastsq(p0, datax, datay, function, fittype)[source]
fit_murnaghan(fit_order=3, vol_erg_dic=None)[source]
fit_vinet(vol_erg_dic=None)[source]
fitfunction(parameters, vol, fittype='birchmurnaghan')[source]
static get_error(x_lst, y_lst, p_fit)[source]
get_final_structure()[source]

Returns: Structure with equilibrium volume

plot(num_steps=100, plt_show=True)[source]
poly_fit(fit_order=3, vol_erg_dic=None)[source]
ref_job_initialize()[source]
run_if_interactive()[source]

For jobs which executables are available as Python library, those can also be executed with a library call instead of calling an external executable. This is usually faster than a single core python job.

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

Vinet equation from PRB 70, 224107

class pyiron.atomistics.master.murnaghan.MurnaghanInt(project, job_name)[source]

Bases: pyiron.atomistics.master.murnaghan.Murnaghan

class pyiron.atomistics.master.murnaghan.MurnaghanJobGenerator(job)[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.debye_function(x)[source]
pyiron.atomistics.master.murnaghan.debye_integral(x)[source]

pyiron.atomistics.master.parallel module

class pyiron.atomistics.master.parallel.AtomisticParallelMaster(project, job_name)[source]

Bases: pyiron.base.master.parallel.ParallelMaster, pyiron.atomistics.job.atomistic.AtomisticGenericJob

get_final_structure()[source]

Returns:

structure

type: Returns

class pyiron.atomistics.master.parallel.GenericOutput[source]

Bases: collections.OrderedDict

pyiron.atomistics.master.phonopy module

class pyiron.atomistics.master.phonopy.PhonopyJob(project, job_name)[source]

Bases: pyiron.atomistics.master.parallel.AtomisticParallelMaster

Parameters:
  • project
  • job_name
collect_output()[source]

Returns:

dos_energies

type: Returns

dos_total

type: Returns

dynamical_matrix

type: Returns

dynamical_matrix_at_q(q)[source]
Parameters:q

Returns:

from_hdf(hdf=None, group_name=None)[source]

Restore the ParallelMaster from an HDF5 file

Parameters:
  • hdf (ProjectHDFio) – HDF5 group object - optional
  • group_name (str) – HDF5 subgroup name - optional
get_hesse_matrix()[source]
get_thermal_properties(t_min=1, t_max=1500, t_step=50, temperatures=None)[source]
Parameters:
  • t_min
  • t_max
  • t_step
  • temperatures

Returns:

plot_dos(ax=None, *args, **qwargs)[source]
Parameters:
  • *args
  • ax
  • **qwargs

Returns:

run_static()[source]

The run static function is called by run to execute the simulation.

to_hdf(hdf=None, group_name=None)[source]

Store the ParallelMaster in an HDF5 file

Parameters:
  • hdf (ProjectHDFio) – HDF5 group object - optional
  • group_name (str) – HDF5 subgroup name - optional
write_phonopy_force_constants(file_name='FORCE_CONSTANTS', cwd=None)[source]
class pyiron.atomistics.master.phonopy.PhonopyJobGenerator(job)[source]

Bases: pyiron.base.master.parallel.JobGenerator

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

(list)

Type:Returns
class pyiron.atomistics.master.phonopy.PhonopyMaster(project, job_name)[source]

Bases: pyiron.atomistics.master.phonopy.PhonopyJob

Parameters:
  • project
  • job_name
class pyiron.atomistics.master.phonopy.PhonopyMaster2(project, job_name)[source]

Bases: pyiron.atomistics.master.phonopy.PhonopyJob

Parameters:
  • project
  • job_name
pyiron.atomistics.master.phonopy.atoms_to_phonopy(atom)[source]

Convert ASE-like Atoms to Phonopy Atoms :param atom: ASE-like Atoms

Returns:Phonopy Atoms
pyiron.atomistics.master.phonopy.phonopy_to_atoms(ph_atoms)[source]

Convert Phonopy Atoms to ASE-like Atoms :param ph_atoms: Phonopy Atoms object

Returns: ASE-like Atoms object

class pyiron.atomistics.master.phonopy.thermal(temps, fe, entropy, cv)[source]

Bases: object

Parameters:
  • temps
  • fe
  • entropy
  • cv

pyiron.atomistics.master.serial module

class pyiron.atomistics.master.serial.GenericOutput[source]

Bases: collections.OrderedDict

class pyiron.atomistics.master.serial.SerialMaster(project, job_name)[source]

Bases: pyiron.base.master.serial.SerialMasterBase, pyiron.atomistics.job.atomistic.AtomisticGenericJob

get_final_structure()[source]

Returns:

structure

type: Returns

Module contents