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@ -0,0 +1,356 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix bond/react command :h3
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[Syntax:]
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fix ID group-ID bond/react common_keyword values ...
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react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
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react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
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react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
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... :pre
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ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
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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"_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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Nevery = attempt reaction every this many steps :l
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Rmin = bonding pair atoms separated by less than Rmin can initiate reaction (distance units) :l
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template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l
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template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
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map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l
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zero or more individual keyword/value pairs may be appended to each react argument :l
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individual_keyword = {prob} or {stabilize_steps} :l
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{prob} values = fraction seed
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fraction = initiate reaction with this probability if otherwise eligible
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seed = random number seed (positive integer)
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{stabilize_steps} value = timesteps
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timesteps = number of timesteps to apply internally created nve/limit.html :pre
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:ule
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[Examples:]
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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 3.25 mol1 mol2 map_file.txt
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molecule mol1 pre_reacted_rxn1.txt
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molecule mol2 post_reacted_rxn1.txt
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molecule mol3 pre_reacted_rxn2.txt
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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 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
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react myrxn2 all 1 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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[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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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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atom-types, or atomic charges.
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Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
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pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
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determine bonding changes a priori. Rather, it uses a distance-based
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probabilistic criteria to effect predetermined topology changes in
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simulations using standard force fields.
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This fix was created to facilitate the dynamic creation of polymeric,
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amorphous or highly-crosslinked systems. A suggested workflow for
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using this fix is: 1) identify a reaction to be simulated 2) build a
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molecule template of the reaction site before the reaction has
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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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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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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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The {stabilization} keyword enables reaction site stabilization.
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Reaction site stabilization is performed by including reacting atoms
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in an internally created fix "nve/limit"_fix_nve_limit.html time
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integrator for a set number of timesteps given by the
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{stabilize_steps} keyword. While reacting atoms are being time
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integrated by the internal nve/limit, they are prevented from being
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involved in any new reactions. The {xmax} value keyword should
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typically be set to the maximum distance that non-reacting atoms move
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during the simulation.
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The group-ID set using the {stabilization} keyword should be a
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previously unused group-ID. The fix bond/react command creates a
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"dynamic group"_group.html of this name that excludes reacting atoms.
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This dynamic group-ID should then be used by a subsequent system-wide
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time integrator, as shown in the second example above. It is necessary
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to place the time integration command after the fix bond/react command
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due to the internal dynamic grouping performed by fix bond/react.
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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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timesteps.
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Two conditions must be met for a reaction to occur. First a bonding
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atom pair must be identified. Second, the topology surrounding the
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bonding atom pair must match the topology of the pre-reaction
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template. If both these conditions are met, the reaction site is
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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 be within a distance Rmin of each other. The atom
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types typei and typej are specified in the pre- and post-reaction
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templates. The distance calculation uses the pair neighbor list,
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therefore bonded neighbor exclusions may prevent a reaction between
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1st, 2nd or 3rd bonded neighbor atoms. If multiple bonding atom pairs
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are identified for an atom, the closest bonding atom partner is set as
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its "nearest" bonding partner. Then, if both an atomi and atomj have
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each other as their nearest bonding partners, these two atoms are
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identified as the bonding atom pair of the reaction site. Once this
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unique bonding atom pair is identified for each reaction, there could
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two or more reactions that involve a given atom on the same timestep.
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If this is the case, only one such reaction is permitted to occur.
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This reaction is chosen randomly from all potential reactions. This
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capability allows e.g. for different reaction pathways to proceed from
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identical 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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surrounding topology. As described below, the bonding atom pairs of
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the pre-reacted template are specified by atom ID in the map file. The
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pre-reacted molecule template should contain as few atoms as possible
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while still completely describing the topology of all atoms affected
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by the reaction. For example, if the force field contains dihedrals,
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the pre-reacted template should contain any atom within three bonds of
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reacting atoms.
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Some atoms in the pre-reacted template that are not reacting may have
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missing topology with respect to the simulation. For example, the
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pre-reacted template may contain an atom that would connect to the
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rest of a long polymer chain. These are referred to as edge atoms, and
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are also specified in the map file.
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Note that some care must be taken when a building a molecule template
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for a given simulation. All atom types in the pre-reacted template
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must be the same as those of a potential reaction site in the
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simulation. A detailed discussion of matching molecule template atom
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types with the simulation is provided on the "molecule"_molecule.html
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command page.
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The post-reacted molecule template contains a sample of the reaction
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site and its surrounding topology after the reaction has occurred. It
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must contain the same number of atoms as the pre-reacted template. A
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one-to-one correspondence between the atom IDs in the pre- and
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post-reacted templates is specified in the map file as described
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below. Note that during a reaction, an atom, bond, etc. type may
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change to one that was previously not present in the simulation. These
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new types must also be defined during the setup of a given simulation.
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A discussion of correctly handling this is also provided on the
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"molecule"_molecule.html command page.
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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 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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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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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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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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EdgeIDs :pre
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1 7 :pre
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Equivalences :pre
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1 1
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2 2
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3 3
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4 4
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5 5
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6 6
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7 7 :pre
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:line
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Once a reaction site has been successfully identified, data structures
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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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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 between the
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bonding atom pairs specified in the pre-reacted molecule template,
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this is not required.
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The optional keywords deal with the probability of a given reaction
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occurring as well as the stable equilibration of each reaction site as
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it occurs.
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The {prob} keyword can affect whether an eligible reaction actually
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occurs. The fraction setting must be a value between 0.0 and 1.0. A
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uniform random number between 0.0 and 1.0 is generated and the
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eligible reaction only occurs if the random number is less than the
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fraction.
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The {stabilize_steps} keyword allows for the specification of how many
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timesteps a reaction site is stabilized before being returned to the
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overall system thermostat.
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In order to produce the most physical behavior, this 'reaction site
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equilibration time' should be tuned to be as small as possible while
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retaining stability for a given system or reaction step. After a
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limited number of case studies, this number has been set to a default
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of 60 timesteps. Ideally, it should be individually tuned for each fix
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reaction step. Note that in some situations, decreasing rather than
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increasing this parameter will result in an increase in stability.
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A few other considerations:
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It may be beneficial to ensure reacting atoms are at a certain
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temperature before being released to the overall thermostat. For this,
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you can use the internally-created dynamic group named
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"bond_react_MASTER_group." For example, adding the following command
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would thermostat the group of all atoms currently involved in a
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reaction:
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fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1
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NOTE: This command must be added after the fix bond/react command, and
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will apply to all reaction steps.
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Computationally, each timestep this fix operates, it loops over
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neighbor lists and computes distances between pairs of atoms in the
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list. It also communicates between neighboring processors to
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coordinate which bonds are created. All of these operations increase
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the cost of a timestep. Thus you should be cautious about invoking
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this fix too frequently.
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You can dump out snapshots of the current bond topology via the dump
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local command.
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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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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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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this fix are "intensive".
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These is 1 quantity for each react argument:
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(1) cumulative # of reactions occurred :ul
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No parameter of this fix can be used with the {start/stop} keywords of
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the "run"_run.html command. This fix is not invoked during "energy
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minimization"_minimize.html.
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[Restrictions:]
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This fix is part of the USER-MISC package. It is only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"fix bond/create"_fix_bond_create.html, "fix
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bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
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"dump local"_dump.html, "special_bonds"_special_bonds.html
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[Default:]
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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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Steve Plimpton