Reactions*
- This is a
REQUIREDfile. - All possible reaction processes (events) that can occur in a simulation are specified in this file.
- If a reaction process between two defects is
not foundin the DB, then simulationquits. The error message would specify the missing reaction event. - When the capture radius of a defect cluster is
zero, it never interacts with other defects even when possible reaction processes are specified in the reaction event DB. - Explicit reaction events are not hardwired, instead reaction event types (emission, transformation, coalescence or annihilation etc) are hardwired.
Warning
- It is user's
RESPONSIBILITYto make sure that the entries in the reaction event database are correct.NOerror flags are raised. - Most likely an error in a reaction event will result in the formation of an unknown defect type thereby causing the code to quit. However, this is not always guaranteed
List of Key-Alphabets@
Table 1: List of all key-alphabets that can be used in define a reaction event.
| Key-Alphabets | Purpose | Description |
|---|---|---|
# | marks end of comments section | Always placed at the beginning of the DB |
f or n | creation of new a defect cluster | Both key-alphabets are equivalent. |
c | Combine or compare | Coalescence and compare depending on the position of the alphabet |
s(S) | Subtract | Recombination between opposite defect types with different sizes |
a(A) | Add | Adds sizes of individual defect types in a defect complex |
e | Emit | Emission and trap mutation events |
t | Transform | Transformation. Used to for the rotation or transformation of a defect type to a different defect type. |
r | random number (Integer) | Integer Random number generator between [a,b], where a and b both are integers |
m(M) | multiply | multiply values of defect parameters of reacting defects |
d(D) | divide | divide values of defect parameters of reacting defects |
R | random number (real number) | Floating-point random number generator between [a,b] |
k | annihilate (kill) | Invoked when SIA and Vacancy clusters have equal sizes resulting annihilation of both defect types |
i | ignore | When specified, comparison of a parameter between reacting defects is ignored |
* | Detrapping | This allows for the detrapping or emission of a defect-type from a complex as a whole. |
Hardwired Aspects of Reaction Events@
- Only self-interstitials and vacancies are defects of opposite types, i.e., they annihilate each other.
- Reaction is allowed between only two defects.
- After a coalescence reaction event (
c),- Only one defect survives after a reaction is performed. Multiple reaction products are not allowed
- Modifies the defect with a larger size and deletes the smaller one.
- In case of an emission event (
e)- Emission of multiple defect sizes is allowed.
- Emission of simultaneous emission of multiple defect clusters with different sizes is allowed.
- The size of the parent defect is calculated automatically based on the size of emitted defects.
Except for the size, all other parameters can be specified by the user.
- Transformation event (
t)- This reaction event can change any parameter of a defect.
-
Creation event (
norf)- Only the creation of individual defect clusters is allowed
- All the parameters of the newly created have to be specified by the user.
-
A reaction event between two different defects is triggered when they are closer to each than the sum of their capture radii and is always considered a non-activated event, i.e. it is assumed to occur in zero time.
- Coalescence type events (
c) are considered to be non-activated event types
- Coalescence type events (
- All other reaction event types are considered as activated event types. Hence, the execution of these events requires the use of both the activated event and reaction event databases.
Note
c,t,e,fornare the hard-wired reaction event types.- The user specifies the execution of these event types in the reaction event database.
Reaction Database format@
Before going into additional details on key-alphabets it is important to understand the format of the reaction event database.
Table 2: Formation of reaction event database presented in a tabular format.
| № | Event Type | ID | № of parameters matched | Parameter comparison | № of Defects modified | Defect-1 | Defect-2 | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | p1 | v1 | v2 | p2 | v1 | v2 | np | p1 | v1 | p2 | v2 | np | p1 | v1 | p2 | v2 | p3 | v3 | ||||
| 2 | c | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 3 | a | ||||||||||
| 3 | c | 1 | 2 | 1 | 1 | 0 | 3 | c | e | 1 | 1 | 1 | k | |||||||||
| 4 | c | 1 | 2 | 1 | 1 | 0 | 3 | c | g | 1 | 2 | 1 | 1 | 3 | s | |||||||
| 5 | c | 1 | 2 | 1 | 1 | 0 | 3 | c | l | 1 | 2 | 1 | 1 | 3 | s | |||||||
| 6 | e | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 3 | 1 | 1 | 3 | 1 | 5 | 1R4 | |||||
| 7 | e | 2 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 3 | 1 | 1 | 3 | 2 | 5 | 1R4 | |||||
| 8 | t | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 5 | 1 | ||||||||||
| 9 | t | 2 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 5 | 2 | ||||||||||
| 10 | e | 1 | 1 | 1 | 2 | 2 | 2 | 1 | 1 | 3 | 2 | 1 | 1 | 3 | -1 | |||||||
| p = parameter ID v1 = parameter value for Defect-1 v2 = parameter value for Defect-2 np = number of parameters | ||||||||||||||||||||||
List of Reaction Events Given in Table. 2 in Chemical Equation Notation
Coalescence Events
Line 1: \(\small ~~~~~I_{n_1}+I_{n_1} \to I_{n_1+n_2}~~~~\), where n1 and n2 are the sizes of interstitial clusters
Recombination Events
Line 2: \(\small ~~~~~I_{n_1}+V_{n_2} \to \varnothing~~\text{when}~~n_1 = n_2~~~\) where n1 and n2 are the sizes of interstitial and vacancy clusters, respectively. This is an annihilation event.
Line 3: \(\small ~~~~~I_{n_1}+V_{n_2} \to I_{n_1-n_2}~~\text{when}~~n_1>n_2~~~\)
Line 4: \(\small ~~~~~I_{n_1}+V_{n_2} \to V_{n_2-n_1}~~\text{when}~~n_1<n_2~~~\)
Emission Events
Line 5: \(\small ~~~~~I_{n_1} \to I_{n_1-1}+I_1~~~~\)(Emission of an mono-SIA)
(The parameter represents the orientation of SIA's burgers vector direction)
(1R4 then an integer random number between [1,4] is assigned to the parameter)
(If it is 1r4, a floating point random number between [1,4] is assigned to the parameter)
Line 6: \(\small ~~~~~I_{n_1} \to I_{n_1-1}+I_1~~~~\)(Emission of a size 2 SIA cluster)
Transformation Events
Line 7: \(\small I_{n}^{\langle111\rangle} \to I_{n}^{\langle\overline{1}11\rangle}\)
Line 8: \(\small I_{n}^{\langle\overline{1}11\rangle} \to I_{n}^{\langle1\overline{1}1\rangle}\)
Line 7 & 8 are events that change the direction of SIA's burgers vector.
Trap Mutation Event or Loop Punching Event
Line 9: \(~~~~\small He_n \to He_{n-1}V_1+I_1\)
Location of Key-Alphabets@
The location of the key-alphabets determines whether they are used to identify a reaction event type or to perform an operation on any of the defect parameters or to identify a possible reaction event.
At the beginning of a Reaction Event Specification
key-alphabets located at the beginning of a reaction event specifies the type of the reaction event
c, e, t, f, n
Within a Reaction Event Specification
- key-alphabets located on the left-hand side of number of defects to be modified shown in table.2 determine the aspects of a defect (size, orientation etc) that are used to identify the possible reaction
- key-alphabets on the right-hand side determines the how the new value of a particular parameter of the new defect is calculated.
Left-hand-side:c, g, l, e, i
Right-hand-side:s(S), a(A), d (D), r, R, k, *, h
Exception
Only c in the above key-alphabets is used both at the beginning and middle of a reaction event specification.
In a future upgrade it will be modified to m
Use of # Symbol
- Any text above the
#(hash) symbol is considered as comments.(marks the end of the comment section) - It should
alwaysbe placed at thebeginningof the DB.
35← Number of reactions in the DB
c 1 1 1 1 1 1 2 1 1 3 a
Description of Key-Alphabets@
At the Beginning@
c (combine)@
This is option is used to specify whether a specified reaction event in the database is for a coalescence event. This key-alphabet is always specified at the beginning of the reaction event.
Coalescence event between defects of the same type
SIA Clusters: c 1 1 1 1 1 1 2 1 1 3 a (\(I_{n_1}+I_{n_2} \to I_{n_1+n_2}\)) (Same as Line: 1 in the table. 2)
Vacancy Clusters : c 1 1 1 0 0 1 2 1 0 3 a (\(V_{n_1}+V_{n_2} \to V_{n_1+n_2}\))
Annihilation of SIA and Vacancy
(see Reaction DB formatting on how to specify reaction events)
f or n (create)@
This option is used to specify the creation of individual defect clusters of various types and sizes. This option uses the idea of fake defects. Newly created defect clusters are placed randomly with in the simulation box. Additionally, the coordinates of the fake defect can be used to restrict or place additional conditions on where the newly created defects can be placed within the simulation box.
In KSOME, new defects can be created three different ways (1) by reading defects from a file (cascade insertion for irradiation simulation) (2) based on implantation rate (3) as an activated event (thermal creation of defects)
t (transformation)@
An example of a transformation event is the rotation of Burgers vector \((I^{\langle 111\rangle} \to I^{\langle 1\bar{1}1 \rangle})\) of a 1D diffusing SIA cluster in BCC metals. Below shows snap shots of the SIA specification in the input configuration and the corresponding lines in the activated event DB.
Input Configuration
46 38 46 5 1 1 2 1 3 1 4 0 5 1
The SIA is assumed to be in BCC metal and 5 1 (where pid = 5 and piv = 1)corresponds to its orientation (Burgers vector). There are four \(\langle 111 \rangle\) orientations. Therefore, depending on the SIA's orientation, piv can be 1, 2, 3, and 4. If the SIA can change its orientation (rotation) by overcoming an energy barrier, then they have to be specified in the activation event DB, as shown below.
Activated Event DB
4 1 1.0 2 1.0 3 1.0 5 1.0 5 d 2 3.00e12 0 0.05 6 0.05 t 3 3.00e12 2 0.38 3 0.38 4 0.38
4 1 1.0 2 1.0 3 1.0 5 2.0 5 d 2 3.00e12 1 0.05 7 0.05 t 3 3.00e12 1 0.38 3 0.38 4 0.38
4 1 1.0 2 1.0 3 1.0 5 3.0 5 d 2 3.00e12 2 0.05 4 0.05 t 3 3.00e12 1 0.38 2 0.38 4 0.38
4 1 1.0 2 1.0 3 1.0 5 4.0 5 d 2 3.00e12 3 0.05 5 0.05 t 3 3.00e12 1 0.38 2 0.38 3 0.38
4 1 1.0 2 1.0 3 1.0 5 1.0 5 d 2 3.00e12 0 0.05 6 0.05 t 3 3.00e12 2 0.38 3 0.38 4 0.38 defines the diffusion and rotation of an SIA with orientation 5 1.
If 5 1 corresponds to the SIA oriented along \(\langle 111\rangle\), then t 3 3.00e12 2 0.38 3 0.38 4 0.38 defines the rotation of the SIA to \(\langle \bar{1}11 \rangle\), \(\langle \bar{1}\bar{1}1 \rangle\) and \(\langle 1\bar{1}1 \rangle\) orientations.
Warning
It can be used to change even the size of a defect cluster, but it is not advised.
e (Emission/Trap Mutation)@
Note
Trap mutationis considered as an emission-type event in KSOME.Detrappingis also considered as an emission-type event, but in this case, a defect of given type is assumed to detach as whole from a trap.
On the Right-hand Side@
h (Detrapping Event)@
Detrapping event is a type of emission (e) event, where a defect cluster of a particular type is emitted as a whole from a parent defect complex.
Detrapping of an SIA cluster from a trap or an impurity
In the case of an SIA cluster that only diffuses in 1D, due to trapping and detrapping, there are two possibilities as shown in the figures below:
In the case, of 1DC the parameter related to the 1D direction has to be saved. That is, the parameter 5 of an SIA cluster is transferred to the trap+SIA defect complex when the SIA cluster is trapped.
Snap shot of lines from the DB
- The parameter 5 is equal to zero by default for all types of defect complexes, except for the SIA clusters and SIA-type defect complexes.
Below are the relevant lines from the reaction DB that specify the execution of trapping and detrapping events.
1. e 1 1 1 4 4 2 1 1 2 3 1 1 3 * 5 * ← Detrapping event corresponds to \(\color{blue}{T_rI_n^{\langle111\rangle} \to T_r + I_n^{\langle111\rangle}}\) where \(T_r\) is the trap, \(I_n\) is the SIA cluster of size n and \(T_rI_n\) is the trap-SIA complex. In this case the burger vector is retained even after detrapping.
2. c 1 3 1 4 1 2 c e 3 c l 1 4 1 4 3 a 4 a 5 h ← trapping event between SIA+trap and SIA, for the case where the size of the trapped SIA cluster smaller than the SIA cluster being trapped
3. c 1 3 1 4 1 2 c g 3 c l 1 4 1 4 3 a 4 a 5 h ← trapping event between SIA+trap and SIA
page updated: Jan 13, 2023 Time: 7:52 PM (PST)