376 lines
17 KiB
Plaintext
376 lines
17 KiB
Plaintext
"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,Commands_all.html)
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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 Rmax 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 Rmax 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 Rmax 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} :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 prefix for the dynamic group of non-reacting atoms
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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 considered 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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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 atom-IDs 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} or {update_edges} :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 the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms
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{update_edges} value = {none} or {charges} or {custom}
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none = do not update topology near the edges of reaction templates
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charges = update atomic charges of all atoms in reaction templates
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custom = force the update of user-specified atomic charges :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 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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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 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_REACT 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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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 cross-linked 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 can be an existing
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static group or a previously-unused group-ID. It cannot be specified
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as 'all'. If the group-ID is previously unused, the fix bond/react
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command creates a "dynamic group"_group.html that is initialized to
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include all atoms. If the group-ID is that of an existing static
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group, the group is used as the parent group of new,
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internally-created dynamic group. In both cases, this new dynamic
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group is named by appending '_REACT' to the group-ID, e.g.
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nvt_grp_REACT. By specifying an existing group, you may thermostat
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constant-topology parts of your system separately. The dynamic group
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contains only non-reacting atoms at a given timestep, and therefore
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should be used by a subsequent system-wide time integrator such as
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nvt, npt, or nve, as shown in the second example above. The time
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integration command should be placed 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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NOTE: If the group-ID is an existing static group, react-group-IDs
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should also be specified as this static group, or a subset.
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NOTE: If the group-ID is previously unused, the internally-created
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group applies to all atoms in the system, i.e. you should generally
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not have a separate thermostat which acts on the 'all' group, or any
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other group.
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The following comments pertain to each {react} argument (in other
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words, can be customized for each reaction, or reaction step):
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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 I,J within the specified react-group-ID of type
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itype and jtype 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 atom I and atom J 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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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. When the pre-reaction template
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contains edge atoms, not all atoms, bonds, charges, etc. specified in
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the reaction templates will be updated. Specifically, topology that
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involves only atoms that are 'too near' to template edges will not be
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updated. The definition of 'too near the edge' depends on which
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interactions are defined in the simulation. If the simulation has
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defined dihedrals, atoms within two bonds of edge atoms are considered
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'too near the edge.' If the simulation defines angles, but not
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dihedrals, atoms within one bond of edge atoms are considered 'too
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near the edge.' If just bonds are defined, only edge atoms are
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considered 'too near the edge.'
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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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A map file has a header and a body. The header of map file the
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contains one mandatory keyword and two optional keywords. The
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mandatory keyword is 'equivalences' and the optional keywords are
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'edgeIDs' and 'customIDs':
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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
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N {customIDs} = # of atoms N that are specified for a custom update :pre
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The body of the map file contains two mandatory sections and two
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optional sections. 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 first 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. The second optional section begins with the keyword
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'Custom Edges' and allows for forcing the update of a specific atom's
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atomic charge. The first column is the ID of an atom near the edge of
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the pre-reacted molecule template, and the value of the second column
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is either 'none' or 'charges.' Further details are provided in the
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discussion of the 'update_edges' keyword.
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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
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5 :pre
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EdgeIDs :pre
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1
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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 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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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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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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The {update_edges} keyword can increase the number of atoms whose
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atomic charges are updated, when the pre-reaction template contains
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edge atoms. When the value is set to 'charges,' all atoms' atomic
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charges are updated to those specified by the post-reaction template,
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including atoms near the edge of reaction templates. When the value is
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set to 'custom,' an additional section must be included in the map
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file that specifies whether to update charges, on a per-atom basis.
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The format of this section is detailed above. Listing a pre-reaction
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atom ID with a value of 'charges' will force the update of the atom's
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charge, even if it is near a template edge. Atoms not near a template
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edge are unaffected by this setting.
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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 :pre
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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 reactions.
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Computationally, each timestep this fix operates, it loops over
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neighbor lists (for bond-forming reactions) and computes distances
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between pairs of atoms in the list. It also communicates between
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neighboring processors to coordinate which bonds are created and/or
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removed. All of these operations increase the cost of a timestep. Thus
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you should be cautious about invoking 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, aside from internally-created per-atom
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properties. None of the "fix_modify"_fix_modify.html options are
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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 commands"_Howto_output.html. The
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vector values calculated by 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 "Build
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package"_Build_package.html doc page 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, prob = 1.0, stabilize_steps = 60, update_edges = none
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:line
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:link(Gissinger)
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[(Gissinger)] Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
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