Protocol Documentation

pd3/proto/config.proto

package pd3.proto

Config

General settings for setting up a given system.

Field	Type	Description
name	string	Name of this given study setup.

Physical Parameters

Field	Type	Description
lattice	double	Lattice length in FCC crystals in meters. This doubles as the units for our cartesian system.
mu	double	Shear modulus of the primary matrix.
nu	double	Possion's ratio of the primary matrix.
crystal_type	CrystalType	Crystal type for the system. Only FCC is supported in pd3, but drt can handle different cubic crystals.

Stacking Fault Energies

Field	Type	Description
sf_energy	double	Stacking fault energy should arise between partials in a perfect lattice. For non-partial simulations this can be ignored.
sisf_energy	double	Super intrinsic stacking fault energy arises between partials in a precipitate.
apb_energy	double	APB energy details the force induced by a sheared precipitate.
cf_energy	double	Complex stacking fault energy.

Geometric Parameters

Field	Type	Description
min_area	double	Note that all distances prescribed in this section should be provided in burgers vectors. Minimum triangular area allowed by the simulation. Coarsening will occur if a topology breaks this limit.
max_area	double	Maximum triangular area allowed by the simulation. Refinement will occur if a topology breaks this limit.
collision_horizon	double	The distance at which dislocations will be seen to be colliding. Note that this is also used as the core radius for a dislocation.
min_length	int32	Minimum length of a segment.
max_length	int32	Maximum length of a segment.
max_connections	int32	Unused. The number of connections that a physical dislocation can have. This is unlimited currently, but listed here for compatibility with DDLab.
topology_attempts	int32	Number of attempts at refinement before moving on
collision_cutoff	double	The length percentage to a node at which we consider node segment collision over segment segment collision
min_plane_distance	double	Provided that two dislocations are on the same slip-plane, this sets a threshold $\epsilon$ whether 2 dislocations are on exactly the same plane. i.e: $\text{normal}\cdot\text{line}_1 = \text{normal}\cdot\text{line}_2\pm\epsilon$

Time Parameters

Field	Type	Description
dt0	double	The initial $\Delta\text{t}$ to start integrating with. Note DDD typically dynamically changes integration steps.
max_steps	int32	The maximum number of steps the simulation will run to by default.
integration_convergence	int32	Maximum attempts for integration convegerence. An additional step will perform a refinement of backwards euler.
integration_limit	int32	Maximum attempt at integration. Each integration attempt wil shrink the $\Delta\text{t}$ value.
integration_tolerance	double	Maximum allowable convergence error in refinable integration techniques.
time_growth_max	double	The maximum step that our time factor can take when we are adaptivly increasing our $\Delta\text{t}$ value.
time_growth_pow	double	Influences the rate of time step growth. Larger numbers reduce the rate of growth, Default is ~20.
max_movement	double	The largest jump that a dislocation node can move in a given step.
fixed_timestep	bool	Run the simulations with a fixed timestep. integration_limit must be set to 0.

Lock Energy Parameters

Field	Type	Description
perfect_energy	double
shockley_energy	double
stair_rod_energy	double
hirth_energy	double
frank_energy	double
frank_energy_barrier	double	The term $\lambda$ to stop thrashing between dislocation states (example, partials and perfects)

Dislocation Type Parameters

Field	Type	Description
edge_coefficient	double
screw_coefficient	double
climb_coefficient	double
sense_coefficient	double

Debugging Parameters

Field	Type	Description
print_freq	int32	The number of steps between logging events.
debug_level	int32	Debug Level goes all the way to 4 Level 0 - No output at all Level 1 - Output for major events Level 2 - Debugging output is enabled. Level 3 - Remeshing is broken into atomic steps for easier Level 4 - PB dumps are created eery step. debugging.
logger_type	LoggerType	The logger to use. This will be used for primary and debugging events.
log_location	string	The location to which the logger should default output. (Unused)

Compute Parameters

Field	Type	Description
threads	int32

Boolean Flags

Field	Type	Description
do_seperation	bool
do_partials	bool
do_inclusion	bool
do_SFT	bool	Unused.
do_shielding	bool	Unused.
do_cross_slip	bool	Unused.
do_remesh	bool
do_collision	bool
do_precipitates	bool
do_validation	bool
do_interaction	bool
do_pk	bool
do_self	bool

Boundary Conditions

Field	Type	Description
periodicity	PeriodicCondition

PeriodicCondition

Periodic Conditions are prescribed by a rotation of the frame reference (by XZX Euler Angles) and a displacement. In addition, we have cell size given by the extents.

Field	Type	Description
alpha	double	Rotation about the X axis in $\pi$ radians (E.g. 1/4 = 45deg)
beta	double	Rotation about the Z axis in $\pi$ radians.
gamma	double	Rotation about the X' axis in $\pi$ radians.
extent_x	double	1/2 cell size in the rotated frame for x.
extent_y	double	1/2 cell size in the rotated frame for y.
extent_z	double	1/2 cell size in the rotated frame for z.
center_x	double	Displacement of periodicity frame for x.
center_y	double	Displacement of periodicity frame for y.
center_z	double	Displacement of periodicity frame for z.

CrystalType

Name	Number	Description
FCC	0	Face Centered Cubic (default)
BCC	1	Body Centered Cubic
SIMPLE	2	Simple cubic

LoggerType

Name	Number	Description
TXT	0	By default we'll use the text logger similar to DDLab.
PROTO	1	This provides a system description Series as detailed in
PARAVIEW	2	config.proto.

This logger creates a ParaView friendly output for quick viewing. | | PARADIS | 3 | This logger creates a Paradis restart file. |

Scalar Value Types

.proto Type	Notes	C++	Python
double		double	float
float		float	float
int32	Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint32 instead.	int32	int
int64	Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint64 instead.	int64	int/long
uint32	Uses variable-length encoding.	uint32	int/long
uint64	Uses variable-length encoding.	uint64	int/long
sint32	Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int32s.	int32	int
sint64	Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int64s.	int64	int/long
fixed32	Always four bytes. More efficient than uint32 if values are often greater than 2^28.	uint32	int
fixed64	Always eight bytes. More efficient than uint64 if values are often greater than 2^56.	uint64	int/long
sfixed32	Always four bytes.	int32	int
sfixed64	Always eight bytes.	int64	int/long
bool		bool	boolean
string	A string must always contain UTF-8 encoded or 7-bit ASCII text.	string	str/unicode
bytes	May contain any arbitrary sequence of bytes.	string	str