ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

bond/react: clarify how reactions are searched for

Browse Source 
thanks to Ben Jensen (NASA Langley)
This commit is contained in:
jrgissing
2020-10-26 11:22:35 -04:00
parent b67950e130
commit 406d6e27ce
1 changed files with 20 additions and 13 deletions
Download Patch File Download Diff File Expand all files Collapse all files

33
doc/src/fix_bond_react.rst
View File

@ -194,19 +194,26 @@ be a function of the reaction conversion using the following commands:
fix myrxn all bond/react react myrxn1 all 1 0 v_rmax mol1 mol2 map_file.txt
variable rmax equal 3+f_myrxn[1]/100 # arbitrary function of reaction count
It is possible that multiple bonding atom pairs are identified: if the
bonding atoms in the pre-reacted template are 1-2 neighbors, i.e.
directly bonded, the farthest bonding atom partner is set as its
bonding partner; otherwise, the closest potential partner is chosen.
Then, if both an atom I and atom J have each other as their bonding
partners, these two atoms are identified as the bonding atom pair of
the reaction site. Once this unique bonding atom pair is identified
for each reaction, there could two or more reactions that involve a
given atom on the same timestep. If this is the case, only one such
reaction is permitted to occur. This reaction is chosen randomly from
all potential reactions. This capability allows e.g. for different
reaction pathways to proceed from identical reaction sites with
user-specified probabilities.
The following criteria are used if multiple candidate bonding atom
pairs are identified within the cutoff distance: 1) If the bonding
atoms in the pre-reaction template are not 1-2 neighbors (i.e. not
directly bonded) the closest potential partner is chosen. 2)
Otherwise, if the bonding atoms in the pre-reaction template are 1-2
neighbors (i.e. directly bonded) the farthest potential partner is
chosen. 3) Then, if both an atom I and atom J have each other as their
bonding partners, these two atoms are identified as the bonding atom
pair of the reaction site. Note that it can be helpful to select
unique atom types for the bonding atoms: if a bonding atom pair is
identified, as described in the previous steps, but does not
correspond to the same pair specified in the pre-reaction template, an
otherwise eligible reaction could be prevented from occurring. Once
this unique bonding atom pair is identified for each reaction, there
could be two or more reactions that involve the same atom on the same
timestep. If this is the case, only one such reaction is permitted to
occur. This reaction is chosen randomly from all potential reactions
involving the overlapping atom. This capability allows e.g. for
different reaction pathways to proceed from identical reaction sites
with user-specified probabilities.
The pre-reacted molecule template is specified by a molecule command.
This molecule template file contains a sample reaction site and its