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Defect File Format*

  • This is a REQUIRED file.
  • Input file provides coordinates and parameters of defects in the initial configuration
  • The defect configuration provided by this file can be the final defect configuration from a previous simulation (if it is a restart a simulation)
  • This file provides the starting simulation time, simulation cell size, maximum number of defect types and maximum number of parameters that can be assigned to a defect.

Format@

Snap Shot@

 Configuration file  100
 # hash symbol marks the end of comment lines
    10000
    600    608    612
    40210
    4    5
    472    461    583    5    1  4    2  13858    3  9858    4  4000    5  2
    141    587    89    5    1  0    2  3    3  3    4  0    5  0
    388    381    511    5    1  0    2  45    3  45    4  0    5  0
    127    14    83    5    1  0    2  6    3  6    4  0    5  0
    9    519    573    5    1  3    2  1007    3  7    4  1000    5  0
    412    167    509    5    1  2    2  1000    3  0    4  1000    5  0
    498    519    525    5    1  2    2  1000    3  0    4  1000    5  0
    505    34    364    5    1  0    2  6    3  6    4  0    5  0

Description@

# :  Marks the end of comment line
10000 :  First line of the file corresponds after the comments to the starting simulation time (in seconds)
600 608 612 :  Simulation cell x, y, z dimensions in lattice units (LUs) (For a cubic-lattice one LU is equal to half-a-lattice-constant)
40210 :  Number of defects in the initial configuration
4 5 :  MAX_DTYPES-1 and MAX_NP-1
MAX_DTYPES is the maximum number of defect-complex types allowed in a simulation
MAX_NP is the maximum number of defect parameters IDs (pid) allowed
Note: In the above example, MAX_DTYPES = 5 and MAX_NP = 6
Important: MAX_NP ≥ MAX_DTYPES

Example

\(\underbrace{\color{blue}{472\quad 461\quad 583}}_{x,y,z~\text{coordinates}}~~~\underbrace{~~\color{red}{5}~~}_{\text{num. of}\\ \text{parameters}\\ \text{initialized}}~~ \underbrace{1\quad 4}_{pid1~~~pv1}~~ \underbrace{2 \quad 13858}_{pid2~~pv2}~~ \underbrace{3\quad 9858}_{pid3~~pv3}~~ \underbrace{4\quad 4000}_{pid4~~~pv4}~~ \underbrace{5\quad 2}_{pid5~~~~pv5}\) (pid = parameter id and pv = parameter id value )

  • The above line defines the HeV type defect. pid1=1 defines the * type* of a defect complex.
  • pid2=2 defines the total defect size. pid3=3 defines the size of I orV size in the defect complex.
  • pid4 = 4 defines the number of He atoms (or other defect type). pid5=5 defines non-size parameter. In the present snap shot
  • pid5 is used to define the 1D-direction of an SIA cluster.
  • For other defect complexes, pid5 has no meaning.

Hardwired Aspects@

  • pid1 = 1 always represents the type of defect complex.
  • pid2 = 2 always represents the total size of the defect complex.
  • pid3 = 3 always represents the size (or number) of V (Vacancy) or I (Interstitial) in a defect complex
  • Negative coordinates are NOT ALLOWED and should of integer type
  • Since the simulation cell dimensions, number of defect-complex types and the maximum number of parameters allowed are set via this input file. Hence, it is a REQUIRED file.
    • Initial configuration can have zero defects.
  • Parameter ID (pid) should be an integer.
  • Parameter values (pv) is a floating-point number and Default = 0.0
  • Number of defect types and the maximum number of parameters are of integer-type
  • Simulation cell dimensions should of integer-type
  • If there are n primary defect types, then from pid3 to pid(n+1) would define the sizes of primary defect types in a defect complex.
    • Note Any parameter after pid(n+1), e.g pid(n+2), pid(n+3), will be non-size parameter types.
Example: Hardwired Behavior of pids Representing Primary Defect Sizes

In a simulation with the three primary defects types, Vacancy(V), SIA(I) and helium (He), then total number of possible defect types are V, I, He, HeV, HeI. Hence, maximum number of defect types would be 5 or higher. (Note: It is assumed that HeVI defect complex would spontaneously becomes He). In this simulation:

  • pid2 = 2 defines the total size in the defect complex.
  • pid2 = 3 defines the size (or number of) of V (Vacancy) or I (Interstitial) in a defect complex.
  • pid2 = 4 defines the size (or number of) of He (Vacancy) in a defect complex.

V2:\(\quad\color{blue}{472\quad 461\quad 583}~~~~~\color{red}{5}~~~~ \underbrace{1\quad 0}_{pid1~~~pv1}~~ \underbrace{2 \quad 2}_{pid2~~pv2}~~ \underbrace{3\quad 2}_{pid3~~pv3}~~ \underbrace{4\quad 0}_{pid4~~~pv4}~~ \underbrace{5\quad 0}_{pid5~~~~pv5}\)

I2: \(\quad\color{blue}{472\quad 461\quad 583}~~~~~\color{red}{5}~~~~ \underbrace{1\quad 1}_{pid1~~~pv1}~~ \underbrace{2 \quad 2}_{pid2~~pv2}~~ \underbrace{3\quad 2}_{pid3~~pv3}~~ \underbrace{4\quad 0}_{pid4~~~pv4}~~ \underbrace{5\quad 1}_{pid5~~~~pv5}\)

He10:\(\quad\color{blue}{472\quad 461\quad 583}~~~~~\color{red}{5}~~~~ \underbrace{1\quad 2}_{pid1~~~pv1}~~ \underbrace{2 \quad 10}_{pid2~~pv2}~~ \underbrace{3\quad 0}_{pid3~~pv3}~~ \underbrace{4\quad 10}_{pid4~~~pv4}~~ \underbrace{5\quad 0}_{pid5~~~~pv5}\)

He10V2: \(\quad\color{blue}{472\quad 461\quad 583}~~~~~\color{red}{5}~~~~ \underbrace{1\quad 3}_{pid1~~~pv1}~~ \underbrace{2 \quad 12}_{pid2~~pv2}~~ \underbrace{3\quad 2}_{pid3~~pv3}~~ \underbrace{4\quad 10}_{pid4~~~pv4}~~ \underbrace{5\quad 0}_{pid5~~~~pv5}\)(helium-vacancy type defect-complex)(Note: pv2 = pv3+ pv4)

He10I2:\(\quad\color{blue}{472\quad 461\quad 583}~~~~~\color{red}{5}~~~~ \underbrace{1\quad 4}_{pid1~~~pv1}~~ \underbrace{2 \quad 12}_{pid2~~pv2}~~ \underbrace{3\quad 2}_{pid3~~pv3}~~ \underbrace{4\quad 10}_{pid4~~~pv4}~~ \underbrace{5\quad 1}_{pid5~~~~pv5}\)(helium-SIA type defect-complex)

Avoid

  • It is possible, but KSOME has never been tested with negative parameter IDs (pid)
  • Avoid using negative parameter values (pv) for parameter IDs (pid) representing the total size and size(or number) of primary defect types in a defect complex.

Possible Changes in Future@

  • This can be made an OPTIONAL input file by defining simulation cell dimensions, number of defect-complex types and the maximum number parameters in the input script file
    • Especially, when the there are NO defects in the starting simulation cell.
  • Possibility of using negative parameter values to represent the size of a annihilating defect type. E.g: If the number of interstitials in a defect complex is positive then, those of a vacancy would be a negative number.

Topics to Discuss@

  • Use of fake defects to create depth profiles. The fake defects will create real defects according the depth profile.












This page was last updated on Sep 16, 2020, 4:17 PM (PST)
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