calc_relax_dynamic.py
Calculation script functions
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integrator_info(integrator=None, p_xx=0.0, p_yy=0.0, p_zz=0.0, p_xy=0.0, p_xz=0.0, p_yz=0.0, temperature=0.0, randomseed=None, units='metal') Generates LAMMPS commands for velocity creation and fix integrators.
- Parameters
integrator (str or None, optional) – The integration method to use. Options are ‘npt’, ‘nvt’, ‘nph’, ‘nve’, ‘nve+l’, ‘nph+l’. The +l options use Langevin thermostat. (Default is None, which will use ‘nph+l’ for temperature == 0, and ‘npt’ otherwise.)
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).
p_xy (float, optional) – The value to relax the xy shear pressure component to (default is 0.0).
p_xz (float, optional) – The value to relax the xz shear pressure component to (default is 0.0).
p_yz (float, optional) – The value to relax the yz shear pressure component to (default is 0.0).
temperature (float, optional) – The temperature to relax at (default is 0.0).
randomseed (int or None, optional) – Random number seed used by LAMMPS in creating velocities and with the Langevin thermostat. (Default is None which will select a random int between 1 and 900000000.)
units (str, optional) – The LAMMPS units style to use (default is ‘metal’).
- Returns
The generated LAMMPS input lines for velocity create and fix integration commands.
- Return type
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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.)
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relax_dynamic(lammps_command, system, potential, mpi_command=None, p_xx=0.0, p_yy=0.0, p_zz=0.0, p_xy=0.0, p_xz=0.0, p_yz=0.0, temperature=0.0, integrator=None, runsteps=220000, thermosteps=100, dumpsteps=None, equilsteps=20000, randomseed=None) Performs a full dynamic relax on a given system at the given temperature to the specified pressure state.
- 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.
symbols (list of str) – The list of element-model symbols for the Potential that correspond to system’s atypes.
mpi_command (str, optional) – The MPI command for running LAMMPS in parallel. If not given, LAMMPS will run serially.
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).
temperature (float, optional) – The temperature to relax at (default is 0.0).
runsteps (int, optional) – The number of integration steps to perform (default is 220000).
integrator (str or None, optional) – The integration method to use. Options are ‘npt’, ‘nvt’, ‘nph’, ‘nve’, ‘nve+l’, ‘nph+l’. The +l options use Langevin thermostat. (Default is None, which will use ‘nph+l’ for temperature == 0, and ‘npt’ otherwise.)
thermosteps (int, optional) – Thermo values will be reported every this many steps (default is 100).
dumpsteps (int or None, optional) – Dump files will be saved every this many steps (default is None, which sets dumpsteps equal to runsteps).
equilsteps (int, optional) – The number of timesteps at the beginning of the simulation to exclude when computing average values (default is 20000).
randomseed (int or None, optional) – Random number seed used by LAMMPS in creating velocities and with the Langevin thermostat. (Default is None which will select a random int between 1 and 900000000.)
- Returns
Dictionary of results consisting of keys:
’relaxed_system’ (float) - The relaxed system.
’E_coh’ (float) - The mean measured cohesive energy.
’measured_pxx’ (float) - The measured x tensile pressure of the relaxed system.
’measured_pyy’ (float) - The measured y tensile pressure of the relaxed system.
’measured_pzz’ (float) - The measured z tensile pressure of the relaxed system.
’measured_pxy’ (float) - The measured xy shear pressure of the relaxed system.
’measured_pxz’ (float) - The measured xz shear pressure of the relaxed system.
’measured_pyz’ (float) - The measured yz shear pressure of the relaxed system.
’temp’ (float) - The mean measured temperature.
’E_coh_std’ (float) - The standard deviation in the measured cohesive energy values.
’measured_pxx_std’ (float) - The standard deviation in the measured x tensile pressure of the relaxed system.
’measured_pyy_std’ (float) - The standard deviation in the measured y tensile pressure of the relaxed system.
’measured_pzz_std’ (float) - The standard deviation in the measured z tensile pressure of the relaxed system.
’measured_pxy_std’ (float) - The standard deviation in the measured xy shear pressure of the relaxed system.
’measured_pxz_std’ (float) - The standard deviation in the measured xz shear pressure of the relaxed system.
’measured_pyz_std’ (float) - The standard deviation in the measured yz shear pressure of the relaxed system.
’temp_std’ (float) - The standard deviation in the measured temperature values.
- Return type