calc_relax_box.py

Calculation script functions

calc_cij(lammps_command, system, potential, mpi_command=None, p_xx=0.0, p_yy=0.0, p_zz=0.0, strainrange=1e-06, cycle=0)

Runs cij.in LAMMPS script to evaluate Cij, and E_coh of the current system, and define a new system with updated box dimensions to test.

Parameters

  • lammps_command (str) – Command for running LAMMPS.

  • system (atomman.System) – The system to perform the calculation on.

  • potential (atomman.lammps.Potential) – The LAMMPS implemented potential to use.

  • mpi_command (str, optional) – The MPI command for running LAMMPS in parallel. If not given, LAMMPS will run serially.

  • strainrange (float, optional) – The small strain value to apply when calculating the elastic constants (default is 1e-6).

  • p_xx (float, optional) – The value to relax the x tensile pressure component to (default is 0.0).

  • p_yy (float, optional) – The value to relax the y tensile pressure component to (default is 0.0).

  • p_zz (float, optional) – The value to relax the z tensile pressure component to (default is 0.0).

  • cycle (int, optional) – Indicates the iteration cycle of quick_a_Cij(). This is used to uniquely save the LAMMPS input and output files.

Returns

Dictionary of results consisting of keys:

  • ’E_coh’ (float) - The cohesive energy of the supplied system.

  • ’stress’ (numpy.array) - The measured stress state of the supplied system.

  • ’C_elastic’ (atomman.ElasticConstants) - The supplied system’s elastic constants.

  • ’system_new’ (atomman.System) - System with updated box dimensions.

Return type

dict

Raises

RuntimeError – If any of the new box dimensions are less than zero.

main(*args)

Main function called when script is executed directly.

process_input(input_dict, UUID=None, build=True)

Processes str input parameters, assigns default values if needed, and generates new, more complex terms as used by the calculation.

Parameters

  • input_dict (dict) – Dictionary containing the calculation input parameters with string values. The allowed keys depends on the calculation style.

  • UUID (str, optional) – Unique identifier to use for the calculation instance. If not given and a ‘UUID’ key is not in input_dict, then a random UUID4 hash tag will be assigned.

  • build (bool, optional) – Indicates if all complex terms are to be built. A value of False allows for default values to be assigned even if some inputs required by the calculation are incomplete. (Default is True.)

relax_box(lammps_command, system, potential, mpi_command=None, strainrange=1e-06, p_xx=0.0, p_yy=0.0, p_zz=0.0, p_xy=0.0, p_xz=0.0, p_yz=0.0, tol=1e-10, diverge_scale=3.0)

Quickly refines static orthorhombic system by evaluating the elastic constants and the virial pressure.

Parameters

  • lammps_command (str) – Command for running LAMMPS.

  • system (atomman.System) – The system to perform the calculation on.

  • potential (atomman.lammps.Potential) – The LAMMPS implemented potential to use.

  • mpi_command (str, optional) – The MPI command for running LAMMPS in parallel. If not given, LAMMPS will run serially.

  • strainrange (float, optional) – The small strain value to apply when calculating the elastic constants (default is 1e-6).

  • p_xx (float, optional) – The value to relax the x tensile pressure component to (default is 0.0).

  • p_yy (float, optional) – The value to relax the y tensile pressure component to (default is 0.0).

  • p_zz (float, optional) – The value to relax the z tensile pressure component to (default is 0.0).

  • tol (float, optional) – The relative tolerance used to determine if the lattice constants have converged (default is 1e-10).

  • diverge_scale (float, optional) – Factor to identify if the system’s dimensions have diverged. Divergence is identified if either any current box dimension is greater than the original dimension multiplied by diverge_scale, or if any current box dimension is less than the original dimension divided by diverge_scale. (Default is 3.0).

Returns

Dictionary of results consisting of keys:

  • ’a_lat’ (float) - The relaxed a lattice constant.

  • ’b_lat’ (float) - The relaxed b lattice constant.

  • ’c_lat’ (float) - The relaxed c lattice constant.

  • ’alpha_lat’ (float) - The alpha lattice angle.

  • ’beta_lat’ (float) - The beta lattice angle.

  • ’gamma_lat’ (float) - The gamma lattice angle.

  • ’E_coh’ (float) - The cohesive energy of the relaxed system.

  • ’stress’ (numpy.array) - The measured stress state of the relaxed system.

  • ’C_elastic’ (atomman.ElasticConstants) - The relaxed system’s elastic constants.

  • ’system_relaxed’ (atomman.System) - The relaxed system.

Return type

dict

Raises

RuntimeError – If system diverges or no convergence reached after 100 cycles.