dislocation_SDVPN Input Terms

Calculation Metadata

Specifies metadata descriptors common to all calculation styles.

  • branch: A metadata group name that the calculation can be parsed by. Primarily meant for differentiating runs with different settings parameters.

Initial System Configuration

Specifies the file and options to load for the initial atomic configuration.

  • load_file: The path to the initial configuration file to load.

  • load_style: The atomman.load() style indicating the format of the load_file.

  • load_options: A space-delimited list of key-value pairs for optional style-specific arguments used by atomman.load().

  • family: A metadata descriptor for relating the load_file back to the original crystal structure or prototype that the load_file was based on. If not given, will use the family field in load_file if load_style is ‘system_model’, or the file’s name otherwise.

  • symbols: A space-delimited list of the potential’s atom-model symbols to associate with the loaded system’s atom types. Required if load_file does not contain symbol/species information.

  • box_parameters: Specifies new box parameters to scale the loaded configuration by. Can be given either as a list of three or six numbers: ‘a b c’ for orthogonal boxes, or ‘a b c alpha beta gamma’ for triclinic boxes. The a, b, c parameters are in units of length and the alpha, beta, gamma angles are in degrees.

Elastic Constants

Specifies the computed elastic constants for the interatomic potential and crystal structure, relative to the loaded system’s orientation. If the values are specified with the Voigt Cij terms and the system is in a standard setting for a crystal type, then only the unique Cij values for that crystal type are necessary. If isotropic values are used, only two idependent parameters are necessary.

  • elasticconstants_file: The path to a record containing the elastic constants to use. If neither this or the individual Cij components (below) are given and load_style is ‘system_model’, this will be set to load_file.

  • C11: The C11 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C12: The C12 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C13: The C13 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C14: The C14 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C15: The C15 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C16: The C16 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C22: The C22 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C23: The C23 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C24: The C24 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C25: The C25 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C26: The C26 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C33: The C33 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C34: The C34 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C35: The C35 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C36: The C36 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C44: The C44 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C45: The C45 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C46: The C46 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C55: The C55 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C56: The C56 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C66: The C66 component of the 6x6 Cij Voigt Cij elastic stiffness tensor (units of pressure).

  • C_M: The isotropic P-wave modulus (units of pressure).

  • C_lambda: The isotropic Lame’s first parameter (units of pressure).

  • C_mu: The isotropic shear modulus (units of pressure).

  • C_E: The isotropic Young’s modulus (units of pressure).

  • C_nu: The isotropic Poisson’s ratio (unitless).

  • C_K: The isotropic bulk modulus (units of pressure).

Gamma Surface

Specifies the gamma surface results to load.

  • gammasurface_file: The path to a file that contains a data model associated with an atomman.defect.GammaSurface object. Can be a record for a finished stacking_fault_map_2D calculation.

Dislocation

Specifies the parameter set that defines a dislocation type and how to orient it relative to the atomic system.

  • dislocation_file: The path to a dislocation record file that collects the parameters for a specific dislocation type.

  • dislocation_slip_hkl: The Miller (hkl) slip plane for the dislocation given as three space-delimited integers.

  • dislocation_ξ_uvw: The Miller [uvw] line vector direction for the dislocation given as three space-delimited integers. The angle between burgers and ξ_uvw determines the dislocation’s character.

  • dislocation_burgers: The Miller Burgers vector for the dislocation given as three space-delimited floats.

  • dislocation_m: The Cartesian vector of the final system that the dislocation solution’s m vector (in-plane, perpendicular to ξ) should align with. Given as three space-delimited numbers. Limited to beingparallel to one of the three Cartesian axes.

  • dislocation_n: The Cartesian vector of the final system that the dislocation solution’s n vector (slip plane normal) should align with. Given as three space-delimited numbers. Limited to beingparallel to one of the three Cartesian axes.

  • dislocation_shift: A rigid body shift to apply to the atoms in the system after it has been rotated to the correct orientation. This controls where the dislocation is placed relative to the atomic positions as the dislocation line is always inserted at coordinates (0,0) for the two Cartesian axes aligned with m and n. Specified as three floating point numbers.

  • dislocation_shiftscale: boolean indicating if the dislocation_shift value is a Cartesian vector (False, default) or if it is scaled relative to the rotated cell’s box parameters prior to applying sizemults.

  • dislocation_shiftindex: An integer that if given will result in a shift being automatically determined and used such that the dislocation’s slip plane will be positioned halfway between two atomic planes. Changing the integer value changes which set of planes the slip plane is positioned between. Note that shiftindex values only shift atoms in the slip plane normal direction and therefore may not be the ideal positions for some dislocation cores.

  • sizemults: Multiplication parameters to construct a supercell from the rotated system. Limited to three values for dislocation generation. Values must be even for the two box vectors not aligned with the dislocation line. The system will be replicated equally in the positive and negative directions for those two box vectors.

  • amin: Specifies a minimum width in length units that the resulting system’s a box vector must have. The associated sizemult value will be increased if necessary to ensure this. Default value is 0.0.

  • bmin: Specifies a minimum width in length units that the resulting system’s b box vector must have. The associated sizemult value will be increased if necessary to ensure this. Default value is 0.0.

  • cmin: Specifies a minimum width in length units that the resulting system’s c box vector must have. The associated sizemult value will be increased if necessary to ensure this. Default value is 0.0.

Input/Output Units

Specifies the default units to use for the other input keys and to use for saving to the results file.

  • length_unit: The unit of length to use. Default value is ‘angstrom’.

  • pressure_unit: The unit of pressure to use. Default value is ‘GPa’.

  • energy_unit: The unit of energy to use. Default value is ‘eV’.

  • force_unit: The unit of force to use. Default value is ‘eV/angstrom’.

Run Parameters

  • xmax: The maximum value of the x-coordinates to use for the points where the disregistry is evaluated. The solution is centered around x=0, therefore this also corresponds to the minimum value of x used. The set of x-coordinates used is fully defined by giving at least two of xmax, xstep and xnum.

  • xstep: The step size (delta x) value between the x-coordinates used to evaluate the disregistry. The set of x-coordinates used is fully defined by giving at least two of xmax, xstep and xnum.

  • xnum: The total number of x-coordinates at which to evaluate the disregistry. The set of x-coordinates used is fully defined by giving at least two of xmax, xstep and xnum.

  • xscale: Boolean indicating if xmax and xstep are taken in angstroms (False) or relative to the unit cell’s a box vector (True). Default value is False.

  • minimize_style: The scipy.optimize.minimize method style to use when solving for the disregistry. Default value is ‘Powell’, which seems to do decently well for this problem.

  • minimize_options: Allows for the specification of the options dictionary used by scipy.optimize.minimize. This is given as ‘key value key value…’.

  • minimize_cycles: Specifies the number of times to run the minimization in succession. The minimization algorithms used by the underlying scipy code often benefit from restarting and rerunning the minimized configuration to achive a better fit. Default value is 10.

  • cutofflongrange: The radial cutoff (in distance units) to use for the long-range elastic energy. The long-range elastic energy is configuration-independent, so this value changes the dislocation’s energy but not the computed disregistry profile. Default value is 1000 angstroms.

  • tau_xy: Shear stress (in units of pressure) to apply to the system. Default value is 0 GPa.

  • tau_yy: Normal stress (in units of pressure) to apply to the system. Default value is 0 GPa.

  • tau_yz: Shear stress (in units of pressure) to apply to the system. Default value is 0 GPa.

  • alpha: Coefficient(s) (in pressure/length units) of the non-local energy correction term to use. Default value is 0.0, meaning this correction is not applied.

  • beta_xx: The xx component of the surface energy coefficient tensor (in units pressure-length) to use. Default value is 0.0 GPa-Angstrom.

  • beta_yy: The yy component of the surface energy coefficient tensor (in units pressure-length) to use. Default value is 0.0 GPa-Angstrom.

  • beta_zz: The zz component of the surface energy coefficient tensor (in units pressure-length) to use. Default value is 0.0 GPa-Angstrom.

  • beta_xy: The xy component of the surface energy coefficient tensor (in units pressure-length) to use. Default value is 0.0 GPa-Angstrom.

  • beta_xz: The xz component of the surface energy coefficient tensor (in units pressure-length) to use. Default value is 0.0 GPa-Angstrom.

  • beta_yz: The yz component of the surface energy coefficient tensor (in units pressure-length) to use. Default value is 0.0 GPa-Angstrom.

  • cdiffelastic: Boolean indicating if the dislocation density is computed using central difference for the elastic term. Default value is False

  • cdiffsurface: Boolean indicating if the dislocation density is computed using central difference for the surface term. Default value is True

  • cdiffstress: Boolean indicating if the dislocation density is computed using central difference for the stress term. Default value is False

  • halfwidth: The arctan disregistry halfwidth (in length units) to use for creating the initial disregistry guess.

  • normalizedisreg: Boolean indicating how the disregistry profile is handled. If True (default), the disregistry is scaled such that the minimum x value has a disregistry of 0 and the maximum x value has a disregistry equal to the dislocation’s Burgers vector. Note that the disregistry for these endpoints is fixed, so if you use False the initial disregistry should be close to the final solution.

  • fullstress: Boolean indicating which of two stress formulas to use. True uses the original full formulation, while False uses a newer, simpler representation. Default value is True.