forked from lijiext/lammps
correctly render doc page
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jrgissing
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@ -20,14 +20,15 @@ ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb
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bond/react = style name of this fix command :l
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zero or more common keyword/value pairs may be appended directly after 'bond/react' :l
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these apply to all reaction specifications (below) :l
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common_keyword = {stabilization}
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{stabilization} values = group-ID xmax
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group-ID = user-assigned ID of an internally-created dynamic group that excludes reacting atoms, and can be used by a subsequent time integration fix such as nvt, npt, or nve (cannot be 'all')
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{xmax} value = distance
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distance = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator
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react = mandatory argument indicating new reaction specification
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react-ID = user-assigned name for the reaction
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react-group-ID = only atoms in this group are available for the reaction
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common_keyword = {stabilization} :l
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{stabilization} values = {no} or {yes} {group-ID} {xmax}
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{no} = no reaction site stabilization
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{yes} = perform reaction site stabilization
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{group-ID} = user-assigned ID of an internally-created dynamic group that excludes reacting atoms, and can be used by a subsequent time integration fix such as nvt, npt, or nve (cannot be 'all')
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{xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre
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react = mandatory argument indicating new reaction specification :l
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react-ID = user-assigned name for the reaction :l
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react-group-ID = only atoms in this group are available for the reaction :l
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Nevery = attempt reaction every this many steps :l
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Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l
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Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
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@ -47,7 +48,7 @@ react = mandatory argument indicating new reaction specification
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molecule mol1 pre_reacted_topology.txt
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molecule mol2 post_reacted_topology.txt
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fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt
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fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
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molecule mol1 pre_reacted_rxn1.txt
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molecule mol2 post_reacted_rxn1.txt
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@ -56,12 +57,12 @@ molecule mol4 post_reacted_rxn2.txt
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fix 5 all bond/react stabilization yes nvt_grp .03 &
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react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
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react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
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fix 6 nvt_grp nvt temp 300 300 100 # system-wide thermostat must be defined after bond/react :pre
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fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre
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[Description:]
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Initiate complex covalent bonding (topology) changes. These topology
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changes will be referred to as "reactions" throughout this
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changes will be referred to as 'reactions' throughout this
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documentation. Topology changes are defined in pre- and post-reaction
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molecule templates and can include creation and deletion of bonds,
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angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
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@ -81,10 +82,10 @@ occurred 3) build a molecule template of the reaction site after the
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reaction has occurred 4) create a map that relates the
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template-atom-IDs of each atom between pre- and post-reaction molecule
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templates 5) fill a simulation box with molecules and run a simulation
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with fix/bond react.
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with fix bond/react.
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Only one 'fix bond/react' command can be used at a time. Multiple
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reactions can be simultaneously applied by specifying multiple 'react'
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reactions can be simultaneously applied by specifying multiple {react}
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arguments to a single 'fix bond/react' command. This syntax is
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necessary because the 'common keywords' are applied to all reactions.
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@ -111,9 +112,9 @@ NOTE: The internally created group currently applies to all atoms in
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the system, i.e. you should generally not have a separate thermostat
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which acts on the 'all' group.
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The following comments pertain to each 'react' argument:
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The following comments pertain to each {react} argument:
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A check for possible new reaction sites is performed every Nevery
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A check for possible new reaction sites is performed every {Nevery}
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timesteps.
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Two conditions must be met for a reaction to occur. First a bonding
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@ -124,20 +125,20 @@ modified to match the post-reaction template.
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A bonding atom pair will be identified if several conditions are met.
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First, a pair of atoms within the specified react-group-ID of type
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typei and typej must separated by a distance between Rmin and Rmax. It
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is possible that multiple bonding atom pairs are identified: if the
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bonding atoms in the pre-reacted template are not 1-2, 1-3, or 1-4
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neighbors, the closest bonding atom partner is set as its bonding
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partner; otherwise, the farthest potential partner is chosen. Then, if
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both an atomi and atomj have each other as their nearest bonding
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partners, these two atoms are identified as the bonding atom pair of
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the reaction site. Once this unique bonding atom pair is identified
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for each reaction, there could two or more reactions that involve a
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given atom on the same timestep. If this is the case, only one such
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reaction is permitted to occur. This reaction is chosen randomly from
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all potential reactions. This capability allows e.g. for different
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reaction pathways to proceed from identical reaction sites with
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user-specified probabilities.
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typei and typej must separated by a distance between {Rmin} and
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{Rmax}. It is possible that multiple bonding atom pairs are
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identified: if the bonding atoms in the pre-reacted template are not
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1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
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its bonding partner; otherwise, the farthest potential partner is
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chosen. Then, if both an atomi and atomj have each other as their
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nearest bonding partners, these two atoms are identified as the
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bonding atom pair of the reaction site. Once this unique bonding atom
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pair is identified for each reaction, there could two or more
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reactions that involve a given atom on the same timestep. If this is
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the case, only one such reaction is permitted to occur. This reaction
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is chosen randomly from all potential reactions. This capability
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allows e.g. for different reaction pathways to proceed from identical
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reaction sites with user-specified probabilities.
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The pre-reacted molecule template is specified by a molecule command.
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This molecule template file contains a sample reaction site and its
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@ -175,77 +176,43 @@ A discussion of correctly handling this is also provided on the
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The map file is a text document with the following format:
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Format of the map file
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A map file has a header and a body. The header of map file the
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contains one mandatory keyword and one optional keyword. The mandatory
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keyword is 'equivalences' and the optional keyword is 'edgeIDs':
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A map file has a header and a body. The header appears first. The
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first line of the header is always skipped; it typically contains a
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description of the file. Lines can have a trailing comment starting
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with '#' that is ignored. If the line is blank (only whitespace after
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comment is deleted), it is skipped. If the line contains a header
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keyword, the corresponding value(s) is read from the line. If it
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doesn't contain a header keyword, the line begins the body of the
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file.
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N {equivalences} = # of atoms N in the reaction molecule templates
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N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template :pre
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The header contains one mandatory keyword and one optional keyword.
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The mandatory keyword is 'equivalences' and the optional keyword is
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'edgeIDs.' These specify the number of atoms in the pre- and
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post-reacted templates and the number of edge atoms in pre-reacted
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template, respectively.
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The body contains two mandatory sections and one optional section. The
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first section begins with the keyword 'BondingIDs' and lists the atom
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IDs of the bonding atom pair in the pre-reacted molecule template. The
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second mandatory section begins with the keyword 'Equivalences' and
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lists a one-to-one correspondence between atom IDs of the pre- and
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post-reacted templates. The optional section begins with the keyword
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'EdgeIDs' and list the atom IDs of edge atoms in the pre-reacted
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The body of the map file contains two mandatory sections and one
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optional section. The first mandatory section begins with the keyword
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'BondingIDs' and lists the atom IDs of the bonding atom pair in the
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pre-reacted molecule template. The second mandatory section begins
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with the keyword 'Equivalences' and lists a one-to-one correspondence
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between atom IDs of the pre- and post-reacted templates. The first
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column is an atom ID of the pre-reacted molecule template, and the
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second column is the corresponding atom ID of the post-reacted
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molecule template. The optional section begins with the keyword
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'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
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molecule template.
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Format of the header of the map file
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These are the recognized header keywords. Header lines can come in any
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order. The value(s) are read from the beginning of the line. Thus the
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keyword 'equivalences' should be in a line like "25 equivalences."
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equivalences = # of atoms in the pre- and post-reacted molecule
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templates edgeIDs = # of edge atoms in the pre-reacted molecule template :pre
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The edgeIDs keyword is optional.
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Format of the body of the map file
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These are the section keywords for the body of the file.
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BondingIDs, EdgeIDs = list of atom IDs of bonding and edge atoms in
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the pre-reacted molecule template
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Equivalences = a two column list where the first column is an atom ID
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of the pre-reacted molecule template, and the second column is the
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corresponding atom ID of the post-reacted molecule template
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The bondingIDs section will always contain two atom IDs, corresponding
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to the bonding atom pairs of the pre-reacted map file. The
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Equivalences section will contain as many rows as there are atoms in
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the pre- and post-reacted molecule templates. The edgeIDs section is
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optional, but would contain an atom ID for each edge atom in the
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pre-reacted molecule template.
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A sample map file is given below:
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:line
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# This is a map file :pre
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# this is a map file :pre
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2 edgeIDs
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7 equivalences :pre
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BondingIDs :pre
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3 5 :pre
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3
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5 :pre
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EdgeIDs :pre
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1 7 :pre
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1
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7 :pre
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Equivalences :pre
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@ -264,13 +231,13 @@ within LAMMPS that store bond topology are updated to reflect the
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post-reacted molecule template. All force fields with fixed bonds,
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angles, dihedrals or impropers are supported.
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A few capabilities to note: 1) You may specify as many 'react'
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A few capabilities to note: 1) You may specify as many {react}
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arguments as desired. For example, you could break down a complicated
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reaction mechanism into several reaction steps, each defined by its
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own 'react' argument. 2) While typically a bond is formed or removed
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own {react} argument. 2) While typically a bond is formed or removed
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between the bonding atom pairs specified in the pre-reacted molecule
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template, this is not required. 3) By reversing the order of the pre-
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and post- reacted molecule templates in another 'react' argument, you
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and post- reacted molecule templates in another {react} argument, you
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can allow for the possibility of one or more reverse reactions.
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The optional keywords deal with the probability of a given reaction
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@ -327,7 +294,7 @@ No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix.
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This fix computes one statistic for each 'react' argument that it
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This fix computes one statistic for each {react} argument that it
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stores in a global vector, of length 'number of react arguments', that
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can be accessed by various "output
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commands"_Section_howto.html#howto_15. The vector values calculated by
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@ -359,5 +326,5 @@ The option defaults are stabilization = no, stabilize_steps = 60
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:line
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:link(Gissinger) [(Gissinger)] Gissinger, Jensen and Wise, Polymer,
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128, 211 (2017).
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:link(Gissinger)
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[(Gissinger)] Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
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