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simplify, formatting

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This commit is contained in:
Jacob Gissinger
2022-07-29 23:34:37 -04:00
parent f0a421eb25
commit ed6fe96909
1 changed files with 11 additions and 11 deletions
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doc/src/fix_bond_react.rst
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@ -536,16 +536,16 @@ only one value, e.g. bond force. This value is returned by the
fragment in the pre-reaction template. The fragment must contain
exactly two atoms, corresponding to the atoms involved in the bond
whose value should be calculated. An example of a constraint that uses
the force experienced by a bond in the reaction site is provided
below. The 'rxnsum' and 'rxnave' functions operate over the atoms in a
given reaction site, and have one mandatory argument and one optional
argument. The mandatory argument is the identifier for an atom-style
variable. The second, optional argument is the name of a molecule
fragment in the pre-reaction template, and can be used to operate over
a subset of atoms in the reaction site. The 'rxnsum' function sums the
atom-style variable over the reaction site, while the 'rxnave' returns
the average value. For example, a constraint on the total potential
energy of atoms involved in the reaction can be imposed as follows:
the force experienced by a bond is provided below. The 'rxnsum' and
'rxnave' functions operate over the atoms in a given reaction site,
and have one mandatory argument and one optional argument. The
mandatory argument is the identifier for an atom-style variable. The
second, optional argument is the name of a molecule fragment in the
pre-reaction template, and can be used to operate over a subset of
atoms in the reaction site. The 'rxnsum' function sums the atom-style
variable over the reaction site, while the 'rxnave' returns the
average value. For example, a constraint on the total potential energy
of atoms involved in the reaction can be imposed as follows:
.. code-block:: LAMMPS
@ -578,7 +578,7 @@ Arrhenius constraint that depends on the bond force of a specific bond:
# in Constraints section of map file
custom "exp(-(v_E_a-rxnbond(c_bondforce,bond1frag))/(2/3*rxnsum(v_ke)*v_natoms)) < random(0,1,12345)"
custom "exp(-(v_E_a-rxnbond(c_bondforce,bond1frag))/(2/3\*rxnsum(v_ke)\*v_natoms)) < random(0,1,12345)"
By using an inequality and the 'random(x,y,z)' function, the left-hand
side can be interpreted as the probability of the reaction occurring,