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Merge pull request #2013 from wverestek/master

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small modification to fix bond/react to allow equal style variables as probability input
This commit is contained in:
Axel Kohlmeyer
2020-04-28 10:51:07 -04:00
committed by GitHub
parent b38e95f88c d946c61789
commit 8f9323a3d7
7 changed files with 678 additions and 94 deletions
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52
doc/src/fix_bond_react.rst Normal file → Executable file
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@ -158,7 +158,9 @@ The following comments pertain to each *react* argument (in other
words, can be customized for each reaction, or reaction step):
A check for possible new reaction sites is performed every *Nevery*
timesteps.
timesteps. *Nevery* can be specified with an equal-style
:doc:`variable <variable>`, whose value is rounded up to the nearest
integer.
Three physical conditions must be met for a reaction to occur. First,
a bonding atom pair must be identified within the reaction distance
@ -171,19 +173,29 @@ modified to match the post-reaction template.
A bonding atom pair will be identified if several conditions are met.
First, a pair of atoms I,J within the specified react-group-ID of type
itype and jtype must be separated by a distance between *Rmin* and
*Rmax*\ . 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.
*Rmax*\ . *Rmin* and *Rmax* can be specified with equal-style
:doc:`variables <variable>`. For example, these reaction cutoffs can
be a function of the reaction conversion using the following commands:
.. code-block:: LAMMPS
variable rmax equal 0 # initialize variable before bond/react
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 pre-reacted molecule template is specified by a molecule command.
This molecule template file contains a sample reaction site and its
@ -419,7 +431,8 @@ it occurs:
The *prob* keyword can affect whether or not an eligible reaction
actually occurs. The fraction setting must be a value between 0.0 and
1.0. A uniform random number between 0.0 and 1.0 is generated and the
1.0, and can be specified with an equal-style :doc:`variable <variable>`.
A uniform random number between 0.0 and 1.0 is generated and the
eligible reaction only occurs if the random number is less than the
fraction. Up to N reactions are permitted to occur, as optionally
specified by the *max_rxn* keyword.
@ -489,10 +502,11 @@ local command.
**Restart, fix_modify, output, run start/stop, minimize info:**
Cumulative reaction counts for each reaction are written to :doc:`binary restart files <restart>`. These values are associated with the
reaction name (react-ID). Additionally, internally-created per-atom
properties are stored to allow for smooth restarts. None of the
:doc:`fix_modify <fix_modify>` options are relevant to this fix.
Cumulative reaction counts for each reaction are written to :doc:`binary restart files <restart>`.
These values are associated with the reaction name (react-ID).
Additionally, internally-created per-atom properties are stored to
allow for smooth restarts. None of the :doc:`fix_modify <fix_modify>`
options are relevant to this fix.
This fix computes one statistic for each *react* argument that it
stores in a global vector, of length 'number of react arguments', that