pyiron_atomistics.thermodynamics.interfacemethod

pyiron_atomistics.thermodynamics.interfacemethod#

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

Functions

analyse_minimized_structure(ham)

param ham:

analyse_structure(structure[, mode, diamond])

Use either common neighbor analysis or the diamond structure detector

calc_temp_iteration(basis, temperature_next, ...)

param basis:

check_diamond(structure)

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

check_for_holes(temperature_next, ...[, ...])

param temperature_next:

create_job_template(job_name, structure, ...)

Create a job template using the project_parameter dictionary.

fix_iso(job)

Add couple xyz to the fix_ensemble inside LAMMPS

fix_z_dir(job)

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

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.

generate_random_seed(project_parameter)

Generate random seed for project parameters

generate_structure(project_parameter)

param project_parameter:

get_center_point([strain_result_lst, ...])

param strain_result_lst:

get_initial_melting_temperature_guess(...[, ...])

param project_parameter:

get_nve_job_name(temperature_next, strain, ...)

param temperature_next:

get_press(ham[, step])

param ham:

get_strain_lst([fit_range, points, ...])

param fit_range:

get_voronoi_volume(temperature_next, ...)

param temperature_next:

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.

initialise_iterators(project_parameter)

param project_parameter:

minimize_pos(structure, project_parameter[, ...])

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

minimize_vol(structure, project_parameter[, ...])

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

next_calc(structure, temperature, ...[, ...])

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

next_step_funct(number_of_atoms, key_max, ...)

param number_of_atoms:

npt_liquid(temperature_solid, ...[, timestep])

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.

npt_solid(temperature, basis, project_parameter)

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

plot_equilibration(temperature_next, ...[, ...])

param temperature_next:

plot_melting_point_prediction(...[, ...])

param strain_value_lst:

plot_solid_liquid_ratio(temperature_next, ...)

param temperature_next:

ratio_selection(strain_lst, ratio_lst, ...)

param strain_lst:

remove_selective_dynamics(basis)

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

round_temperature_next(temperature_next)

Round temperature to the last two dicits

set_server(job, project_parameter)

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

setup_liquid_job(job_name, basis, ...[, ...])

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

strain_circle(basis_relative, ...[, ...])

param basis_relative:

validate_convergence(pr, temperature_left, ...)

param pr: