pyiron.lammps.control module

class pyiron.lammps.control.LammpsControl(input_file_name=None, **qwargs)[source]

Bases: pyiron.base.generic.parameters.GenericParameters

calc_md(temperature=None, pressure=None, n_ionic_steps=1000, time_step=1.0, n_print=100, temperature_damping_timescale=100.0, pressure_damping_timescale=1000.0, seed=None, tloop=None, initial_temperature=None, langevin=False, delta_temp=None, delta_press=None, job_name='', rotation_matrix=None)[source]

Set an MD calculation within LAMMPS. Nosé Hoover is used by default.

Parameters
  • temperature (None/float/list) – Target temperature value(-s). If set to None, an NVE calculation is performed. It is required when the pressure is set or langevin is set It can be a list of temperature values, containing the initial target temperature and the final target temperature (in between the target value is varied linearly).

  • pressure (None/float/numpy.ndarray/list) – Target pressure. If set to None, an NVE or an NVT calculation is performed. A list of up to length 6 can be given to specify xx, yy, zz, xy, xz, and yz components of the pressure tensor, respectively. These values can mix floats and None to allow only certain degrees of cell freedom to change. (Default is None, run isochorically.)

  • n_ionic_steps (int) – Number of ionic steps

  • time_step (float) – Step size in fs between two steps.

  • n_print (int) – Print frequency

  • temperature_damping_timescale (float) – The time associated with the thermostat adjusting the temperature. (In fs. After rescaling to appropriate time units, is equivalent to Lammps’ Tdamp.)

  • pressure_damping_timescale (float) – The time associated with the barostat adjusting the temperature. (In fs. After rescaling to appropriate time units, is equivalent to Lammps’ Pdamp.)

  • seed (int) – Seed for the random number generation (required for the velocity creation)

  • tloop

  • initial_temperature (None/float) – Initial temperature according to which the initial velocity field is created. If None, the initial temperature will be twice the target temperature (which would go immediately down to the target temperature as described in equipartition theorem). If 0, the velocity field is not initialized (in which case the initial velocity given in structure will be used). If any other number is given, this value is going to be used for the initial temperature.

  • langevin (bool) – (True or False) Activate Langevin dynamics

  • delta_temp (float) – Thermostat timescale, but in your Lammps time units, whatever those are. (DEPRECATED.)

  • delta_press (float) – Barostat timescale, but in your Lammps time units, whatever those are. (DEPRECATED.)

  • job_name (str) – Job name of the job to generate a unique random seed.

  • rotation_matrix (numpy.ndarray) – The rotation matrix from the pyiron to Lammps coordinate frame.

calc_minimize(ionic_energy_tolerance=0.0, ionic_force_tolerance=0.0001, max_iter=100000, pressure=None, n_print=100, style='cg', rotation_matrix=None)[source]

Sets parameters required for minimization.

Parameters
  • ionic_energy_tolerance (float) – If the magnitude of difference between energies of two consecutive steps is lower than or equal to ionic_energy_tolerance, the minimisation terminates. (Default is 0.0 eV.)

  • ionic_force_tolerance (float) – If the magnitude of the global force vector at a step is lower than or equal to ionic_force_tolerance, the minimisation terminates. (Default is 1e-4 eV/angstrom.)

  • e_tol (float) – Sam as ionic_energy_tolerance (deprecated)

  • f_tol (float) – Sam as ionic_force_tolerance (deprecated)

  • max_iter (int) – Maximum number of minimisation steps to carry out. If the minimisation converges before max_iter steps, terminate at the converged step. If the minimisation does not converge up to max_iter steps, terminate at the max_iter step. (Default is 100000.)

  • pressure (None/float/numpy.ndarray/list) – Target pressure. If set to None, an NVE or an NVT calculation is performed. A list of up to length 6 can be given to specify xx, yy, zz, xy, xz, and yz components of the pressure tensor, respectively. These values can mix floats and None to allow only certain degrees of cell freedom to change. (Default is None, run isochorically.)

  • n_print (int) – Write (dump or print) to the output file every n steps (Default: 100)

  • style ('cg'/'sd'/other values from Lammps docs) – The style of the numeric minimization, either conjugate gradient, steepest descent, or other keys permissible from the Lammps docs on ‘min_style’. (Default is ‘cg’ – conjugate gradient.)

  • rotation_matrix (numpy.ndarray) – The rotation matrix from the pyiron to Lammps coordinate frame.

calc_static()[source]
calc_vcsgc(mu, ordered_element_list, target_concentration=None, kappa=1000.0, mc_step_interval=100, swap_fraction=0.1, temperature_mc=None, window_size=None, window_moves=None, temperature=None, pressure=None, n_ionic_steps=1000, time_step=1.0, n_print=100, temperature_damping_timescale=100.0, pressure_damping_timescale=1000.0, seed=None, initial_temperature=None, langevin=False, job_name='')[source]

Run variance-constrained semi-grand-canonical MD/MC for a binary system. In addition to VC-SGC arguments, all arguments for a regular MD calculation are also accepted.

https://vcsgc-lammps.materialsmodeling.org

Note

For easy visualization later (with get_structure), it is highly recommended that the initial structure contain at least one atom of each species.

Warning

Assumes the units are metal, otherwise units for the constraints may be off.

Parameters
  • mu (dict) – A dictionary of chemical potentials, one for each element the potential treats, where the dictionary keys are just the chemical symbol. Note that only the relative chemical potentials are used here, such that the swap acceptance probability is influenced by the chemical potential difference between the two species (a more negative value increases the odds of swapping to that element.)

  • ordered_element_list (list) – A list of the chemical species symbols in the order they appear in the definition of the potential in the Lammps’ input file.

  • target_concentration – A dictionary of target simulation domain concentrations for each species in the potential. Dictionary keys should be the chemical symbol of the corresponding species, and the sum of all concentrations must be 1. (Default is None, which runs regular semi-grand-canonical MD/MC without any variance constraint.)

  • kappa – Variance constraint for the MC. Larger value means a tighter adherence to the target concentrations. (Default is 1000.)

  • mc_step_interval (int) – How many steps of MD between each set of MC moves. (Default is 100.) Must divide the number of ionic steps evenly.

  • swap_fraction (float) – The fraction of atoms whose species is swapped at each MC phase. (Default is 0.1.)

  • temperature_mc (float) – The temperature for accepting MC steps. (Default is None, which uses the MD temperature.)

  • window_size (float) – The size of the sampling window for parallel calculations as a fraction of something unspecified in the VC-SGC docs, but it must lie between 0.5 and 1. (Default is None, window is determined automatically.)

  • window_moves (int) – The number of times the sampling window is moved during one MC cycle. (Default is None, number of moves is determined automatically.)

property dataset
energy_pot_per_atom()[source]
static generate_seed_from_job(job_name='', seed=0)[source]

Generate a unique seed from the job name.

Parameters
  • job_name (str) – job_name of the current job to generate the seed

  • seed (int) – integer to access part of the seed

Returns

random seed generated based on the hash

Return type

int

load_default(file_content=None)[source]

Load defaults resets the dataset in the background to be empty

measure_mean_value(key, every=1, repeat=None, name=None, atom=False)[source]
Parameters
  • key (str) – property to take an average value of (e.g. ‘energy_pot’ v.i.)

  • every (int) – number of steps there should be between two measurements

  • repeat (int) – number of measurements for each output (default: n_print/every)

  • name (str) – name to give in the output string (ignored if a pyiron predefined tag is used)

Comments:
Currently available keys: ‘energy_pot’, ‘energy_tot’, ‘temperature’, ‘volume’,

‘pressures’, ‘positions’, ‘forces, ‘velocities’

Future keys: ‘cells’

pressure_to_lammps(pressure, rotation_matrix)[source]

Convert a singular value, list of values, or combination of values to the appropriate six elements for Lammps pxx, pyy, pzz, pxy, pxz, and pyz pressure tensor representation.

Lammps handles complex cells in a particular way, namely by using an upper triangular cell. This means we may need to convert our pressure tensor to a new coordinate frame. We also handle that transformation here.

Finally, we also ensure that the units are converted from pyiron’s GPa to whatever Lammps needs.

Parameters
  • pressure (float/list/tuple/numpy.ndarray) – The pressure(s) to convert.

  • rotation_matrix (numpy.ndarray) – The 3x3 matrix rotating from the pyiron to Lammps coordinate frame.

Returns

pxx, pyy, pzz, pxy, pxz, and pyz to be passed to Lammps.

Return type

(numpy.ndarray)

set_initial_velocity(temperature, seed=None, gaussian=False, append_value=False, zero_lin_momentum=True, zero_rot_momentum=True, job_name='')[source]

Create initial velocities via velocity all create. More information can be found on LAMMPS website: https://lammps.sandia.gov/doc/velocity.html

Parameters
  • temperature – (int or float)

  • seed – (int) Seed for the initial random number generator

  • gaussian – (True/False) Create velocity according to the Gaussian distribution (otherwise uniform)

  • append_value – (True/False) Add the velocity values to the current velocities (probably not functional now)

  • zero_lin_momentum – (True/False) Cancel the total linear momentum

  • zero_rot_momentum – (True/False) Cancel the total angular momentum

  • job_name – (str) job name to generate seed