pyiron.thermodynamics.interfacemethod module

pyiron based implementation of the coexistence method. Currently this functionality is primarly used as part of the melting point simulation protocol which is available at: https://github.com/pyiron/pyiron_meltingpoint

pyiron.thermodynamics.interfacemethod.analyse_minimized_structure(ham)

Parameters

ham (GenericJob) –

Returns:

pyiron.thermodynamics.interfacemethod.analyse_structure(structure, mode='total', diamond=False)

Use either common neighbor analysis or the diamond structure detector

Parameters

• structure (pyiron.structure.atoms.Atoms) – The structure to analyze.

• mode ("total"/"numeric"/"str") –

  Controls the style and level of detail of the output. - total : return number of atoms belonging to each structure - numeric : return a per atom list of numbers- 0 for unknown,

  1 fcc, 2 hcp, 3 bcc and 4 icosa

  • str : return a per atom string of sructures

• diamond (bool) – Flag to either use the diamond structure detector or the common neighbor analysis.

Returns

(depends on mode)

pyiron.thermodynamics.interfacemethod.calc_temp_iteration(basis, temperature_next, project_parameter, timestep, nve_run_time_steps, fit_range, center, debug_plot=True)

Parameters

• basis –

• temperature_next –

• project_parameter –

• timestep –

• nve_run_time_steps –

• fit_range –

• center –

• debug_plot –

Returns:

pyiron.thermodynamics.interfacemethod.check_diamond(structure)

Utility function to check if the structure is fcc, bcc, hcp or diamond

Parameters

structure (pyiron.structure.atoms.Atoms) – Atomistic Structure object to check

Returns

true if diamond else false

Return type

bool

pyiron.thermodynamics.interfacemethod.check_for_holes(temperature_next, strain_value_lst, nve_run_time_steps, project_parameter, debug_plot=True)

Parameters

• temperature_next –

• strain_value_lst –

• nve_run_time_steps –

• project_parameter –

• debug_plot –

Returns:

pyiron.thermodynamics.interfacemethod.create_job_template(job_name, structure, project_parameter)

Create a job template using the project_parameter dictionary. The dictionary has to contain the following keys: - job_type: Type of Simulation code to be used - project: Project object used to create the job - potential: Interatomic Potential - queue (optional): HPC Job queue to be used

Parameters

• job_name (str) – Name of the job object

• structure (pyiron.structure.atoms.Atoms) – Atomistic Structure object to be set to the job as input sturcture

• project_parameter (dict) – Dictionary with the project parameters

Returns

New job object

Return type

GenericJob

pyiron.thermodynamics.interfacemethod.fix_iso(job)

Add couple xyz to the fix_ensemble inside LAMMPS

Parameters

job (LAMMPS) – Lammps job object

Returns

Return updated job object

Return type

LAMMPS

pyiron.thermodynamics.interfacemethod.fix_z_dir(job)

Rather than fixing all directions only fix the z-direction during an NPT simulation

Parameters

job (LAMMPS) – Lammps job object

Returns

Return updated job object

Return type

LAMMPS

pyiron.thermodynamics.interfacemethod.freeze_one_half(basis)

Split the structure into two parts along the z-axis and then freeze the position of the atoms of the upper part (z>0.5) by setting selective dynamics to False.

Parameters

basis (pyiron.structure.atoms.Atoms) – Atomistic structure object

Returns

Atomistic structure object with half of the atoms fixed

Return type

pyiron.structure.atoms.Atoms

pyiron.thermodynamics.interfacemethod.generate_random_seed(project_parameter)

Generate random seed for project parameters

Parameters

project_parameter (dict) –

Returns

The project parameters dictionary including the key ‘seed’

Return type

dict

pyiron.thermodynamics.interfacemethod.generate_structure(project_parameter)

Parameters

project_parameter –

Returns:

pyiron.thermodynamics.interfacemethod.get_center_point(strain_result_lst=None, pressure_result_lst=None, center=None)

Parameters

• strain_result_lst –

• pressure_result_lst –

• center –

Returns:

pyiron.thermodynamics.interfacemethod.get_initial_melting_temperature_guess(project_parameter, ham_minimize_vol, temperature_next=None)

Parameters

• project_parameter –

• ham_minimize_vol –

• temperature_next –

Returns:

pyiron.thermodynamics.interfacemethod.get_nve_job_name(temperature_next, strain, steps_lst, nve_run_time_steps)

Parameters

• temperature_next –

• strain –

• steps_lst –

• nve_run_time_steps –

Returns:

pyiron.thermodynamics.interfacemethod.get_press(ham, step=20)

Parameters

• ham –

• step –

Returns:

pyiron.thermodynamics.interfacemethod.get_strain_lst(fit_range=0.02, points=21, strain_result_lst=None, pressure_result_lst=None, center=None)

Parameters

• fit_range –

• points –

• strain_result_lst –

• pressure_result_lst –

• center –

Returns:

pyiron.thermodynamics.interfacemethod.get_voronoi_volume(temperature_next, strain_lst, nve_run_time_steps, project_parameter)

Parameters

• temperature_next –

• strain_lst –

• nve_run_time_steps –

• project_parameter –

Returns:

pyiron.thermodynamics.interfacemethod.half_velocity(job, temperature)

Rather than setting twice the kinetic energy at the beginning of a molecular dynamics simulation reduce the velocity to half the initial velocity. This is required to continue MD claculation.

Parameters

• job (LAMMPS) – Lammps job object

• temperature (float) – Temperature of the molecular dynamics calculation in K

Returns

Return updated job object

Return type

LAMMPS

pyiron.thermodynamics.interfacemethod.initialise_iterators(project_parameter)

Parameters

project_parameter –

Returns:

pyiron.thermodynamics.interfacemethod.minimize_pos(structure, project_parameter, max_iter=1000)

Minimize the positions in a given structure using the job type defined in the project_parameters, which contains the following keys: - job_type: Type of Simulation code to be used - project: Project object used to create the job - potential: Interatomic Potential - queue (optional): HPC Job queue to be used

Parameters

• structure (pyiron.structure.atoms.Atoms) – Atomistic Structure object to be set to the job as input sturcture

• project_parameter (dict) – Dictionary wtih the project parameters

• max_iter (int) – Maximum number of steps during minimization

Returns

job object used to execute the calculation

pyiron.thermodynamics.interfacemethod.minimize_vol(structure, project_parameter, max_iter=1000)

Minimize the volume for a given structure using the job type defined in the project_parameters, which contains the following keys: - job_type: Type of Simulation code to be used - project: Project object used to create the job - potential: Interatomic Potential - queue (optional): HPC Job queue to be used

Parameters

• structure (pyiron.structure.atoms.Atoms) – Atomistic Structure object to be set to the job as input sturcture

• project_parameter (dict) – Dictionary with the project parameters

• max_iter (int) – Maximum number of steps during minimization

Returns

job object used to execute the calculation

pyiron.thermodynamics.interfacemethod.next_calc(structure, temperature, project_parameter, run_time_steps=10000)

Calculate NPT ensemble at a given temperature using the job defined in the project parameters: - job_type: Type of Simulation code to be used - project: Project object used to create the job - potential: Interatomic Potential - queue (optional): HPC Job queue to be used

Parameters

• structure (pyiron.structure.atoms.Atoms) – Atomistic Structure object to be set to the job as input sturcture

• temperature (float) – Temperature of the Molecular dynamics calculation

• project_parameter (dict) – Dictionary with the project parameters

• run_time_steps (int) – Number of Molecular dynamics steps

Returns

Final Atomistic Structure object

pyiron.thermodynamics.interfacemethod.next_step_funct(number_of_atoms, key_max, structure_left, structure_right, temperature_left, temperature_right, distribution_initial_half, structure_after_minimization, run_time_steps, project_parameter)

Parameters

• number_of_atoms –

• key_max –

• structure_left –

• structure_right –

• temperature_left –

• temperature_right –

• distribution_initial_half –

• structure_after_minimization –

• run_time_steps –

• project_parameter –

Returns:

pyiron.thermodynamics.interfacemethod.npt_liquid(temperature_solid, temperature_liquid, basis, project_parameter, timestep=1.0)

Calculate NPT ensemble at a given temperature while initally freezing the position of the atoms of the upper part (z>0.5) and afterwards calculating the full sample at a lower temperature. These steps are used to construct the solid liquid interface as part of the coexistence approach. For the calculations the job object is defined in the project parameters: - job_type: Type of Simulation code to be used - project: Project object used to create the job - potential: Interatomic Potential - queue (optional): HPC Job queue to be used

Parameters

• temperature_solid (flaot) – Temperature to simulate the whole structure

• temperature_liquid (float) – Temperature to simulate the upper half of the structure

• basis (pyiron.structure.atoms.Atoms) – Atomistic Structure object to be set to the job as input sturcture

• project_parameter (dict) – Dictionary with the project parameters

• timestep (float) – Molecular dynamics time step

Returns

job object used to execute the calculation

pyiron.thermodynamics.interfacemethod.npt_solid(temperature, basis, project_parameter, timestep=1.0)

Calculate NPT ensemble at a given temperature using the job defined in the project parameters: - job_type: Type of Simulation code to be used - project: Project object used to create the job - potential: Interatomic Potential - queue (optional): HPC Job queue to be used

Parameters

• temperature (float) – Temperature of the Molecular dynamics calculation

• basis (pyiron.structure.atoms.Atoms) – Atomistic Structure object to be set to the job as input sturcture

• project_parameter (dict) – Dictionary with the project parameters

• timestep (float) – Molecular dynamics time step

Returns

job object used to execute the calculation

pyiron.thermodynamics.interfacemethod.plot_equilibration(temperature_next, strain_lst, nve_run_time_steps, project_parameter, debug_plot=True)

Parameters

• temperature_next –

• strain_lst –

• nve_run_time_steps –

• project_parameter –

• debug_plot –

Returns:

pyiron.thermodynamics.interfacemethod.plot_melting_point_prediction(strain_value_lst, pressure_value_lst, temperature_value_lst, boundary_value=0.25, debug_plot=True)

Parameters

• strain_value_lst –

• pressure_value_lst –

• temperature_value_lst –

• boundary_value –

• debug_plot –

Returns:

pyiron.thermodynamics.interfacemethod.plot_solid_liquid_ratio(temperature_next, strain_lst, nve_run_time_steps, project_parameter, debug_plot=True)

Parameters

• temperature_next –

• strain_lst –

• nve_run_time_steps –

• project_parameter –

• debug_plot –

Returns:

pyiron.thermodynamics.interfacemethod.ratio_selection(strain_lst, ratio_lst, pressure_lst, temperature_lst, ratio_boundary, debug_plot=True)

Parameters

• strain_lst –

• ratio_lst –

• pressure_lst –

• temperature_lst –

• ratio_boundary –

• debug_plot –

Returns:

pyiron.thermodynamics.interfacemethod.remove_selective_dynamics(basis)

If the selective dyanmics tag is set, allow all atoms to move by setting selective dynamics to True

Parameters

basis (pyiron.structure.atoms.Atoms) – Atomistic structure object

Returns

Atomistic structure object with selective dynamics set to True

Return type

Atoms

pyiron.thermodynamics.interfacemethod.round_temperature_next(temperature_next)

Round temperature to the last two dicits

Parameters

temperature_next (float) – Temperature

Returns

rounded temperature

Return type

float

pyiron.thermodynamics.interfacemethod.set_server(job, project_parameter)

Set the potential, queue and cpu_cores defined in the project_parameter dictionary to the job object.

Parameters

• job (GenericJob) – Job object

• project_parameter (dict) – Dictionary with the keys potential and cpu_cores and optionally queue

Returns

Updated job object

Return type

GenericJob

pyiron.thermodynamics.interfacemethod.setup_liquid_job(job_name, basis, temperature, project_parameter, timestep=1.0)

Calculate NPT ensemble at a given temperature while freezing the position of the atoms of the upper part (z>0.5) amd the using the job defined in the project parameters: - job_type: Type of Simulation code to be used - project: Project object used to create the job - potential: Interatomic Potential - queue (optional): HPC Job queue to be used

Parameters

• job_name (str) – Job name for the liquid calculation

• basis (pyiron.structure.atoms.Atoms) – Atomistic Structure object to be set to the job as input sturcture

• temperature (float) – Temperature of the Molecular dynamics calculation

• project_parameter (dict) – Dictionary with the project parameters

• timestep (float) – Molecular dynamics time step

Returns

job object used to execute the calculation

pyiron.thermodynamics.interfacemethod.strain_circle(basis_relative, temperature_next, nve_run_time_steps, project_parameter, timestep=1.0, strain_result_lst=None, pressure_result_lst=None, center=None, fit_range=0.02)

Parameters

• basis_relative –

• temperature_next –

• nve_run_time_steps –

• project_parameter –

• timestep –

• strain_result_lst –

• pressure_result_lst –

• center –

• fit_range –

Returns:

pyiron.thermodynamics.interfacemethod.validate_convergence(pr, temperature_left, temperature_next, temperature_right, enable_iteration, timestep_iter, timestep_lst, timestep, fit_range_iter, fit_range_lst, fit_range, nve_run_time_steps_iter, nve_run_time_steps_lst, nve_run_time_steps, strain_result_lst, pressure_result_lst, step_count, step_dict, boundary_value, ratio_boundary, convergence_goal, output_file='melting.json')

Parameters

• pr –

• temperature_left –

• temperature_next –

• temperature_right –

• enable_iteration –

• timestep_iter –

• timestep_lst –

• timestep –

• fit_range_iter –

• fit_range_lst –

• fit_range –

• nve_run_time_steps_iter –

• nve_run_time_steps_lst –

• nve_run_time_steps –

• strain_result_lst –

• pressure_result_lst –

• step_count –

• step_dict –

• boundary_value –

• ratio_boundary –

• convergence_goal –

• output_file –

Returns: