Merge branch 'master' into user-cgdna

[Related commands:]

"fix bond/create"_fix_bond_create.html, "fix

bond/swap"_fix_bond_swap.html, "dump local"_dump.html,

"special_bonds"_special_bonds.html

bond/react"_fix_bond_react.html, "fix bond/swap"_fix_bond_swap.html,

"dump local"_dump.html, "special_bonds"_special_bonds.html

[Default:]

[Related commands:]

"fix bond/break"_fix_bond_break.html, "fix

bond/swap"_fix_bond_swap.html, "dump local"_dump.html,

"special_bonds"_special_bonds.html

bond/react"_fix_bond_react.html, "fix bond/swap"_fix_bond_swap.html,

"dump local"_dump.html, "special_bonds"_special_bonds.html

[Default:]

  {stabilization} values = {no} or {yes} {group-ID} {xmax}

    {no} = no reaction site stabilization

    {yes} = perform reaction site stabilization

      {group-ID} = user-assigned ID for all non-reacting atoms (group created internally)

      {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms

      {xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre

react = mandatory argument indicating new reaction specification :l

  react-ID = user-assigned name for the reaction :l

  react-group-ID = only atoms in this group are available for the reaction :l

  react-group-ID = only atoms in this group are considered for the reaction :l

  Nevery = attempt reaction every this many steps :l

  Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l

  Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l

molecule mol1 pre_reacted_topology.txt

molecule mol2 post_reacted_topology.txt

fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre

fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre

molecule mol1 pre_reacted_rxn1.txt

molecule mol2 post_reacted_rxn1.txt

fix 5 all bond/react stabilization yes nvt_grp .03 &

  react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &

  react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345

fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre

fix 6 nvt_grp_REACT nvt temp 300 300 100 # set thermostat after bond/react :pre

[Description:]

typically be set to the maximum distance that non-reacting atoms move

during the simulation.

The group-ID set using the {stabilization} keyword should be a

previously unused group-ID. It cannot be specified as 'all'. The fix

bond/react command creates a "dynamic group"_group.html of this name

that includes all non-reacting atoms. This dynamic group-ID should

then be used by a subsequent system-wide time integrator such as nvt,

npt, or nve, as shown in the second example above. It is currently

necessary to place the time integration command after the fix

bond/react command due to the internal dynamic grouping performed by

fix bond/react.

NOTE: The internally created group currently applies to all atoms in

the system, i.e. you should generally not have a separate thermostat

which acts on the 'all' group.

The group-ID set using the {stabilization} keyword can be an existing

static group or a previously-unused group-ID. It cannot be specified

as 'all'. If the group-ID is previously unused, the fix bond/react

command creates a "dynamic group"_group.html that is initialized to

include all atoms. If the group-ID is that of an existing static

group, the group is used as the parent group of new,

internally-created dynamic group. In both cases, this new dynamic

group is named by appending '_REACT' to the group-ID, e.g.

nvt_grp_REACT. By specifying an existing group, you may thermostat

constant-topology parts of your system separately. The dynamic group

contains only non-reacting atoms at a given timestep, and therefore

should be used by a subsequent system-wide time integrator such as

nvt, npt, or nve, as shown in the second example above. The time

integration command should be placed after the fix bond/react command

due to the internal dynamic grouping performed by fix bond/react.

NOTE: If the group-ID is an existing static group, react-group-IDs

should also be specified as this static group, or a subset.

NOTE: If the group-ID is previously unused, the internally created

group applies to all atoms in the system, i.e. you should generally

not have a separate thermostat which acts on the 'all' group, or any

other group.

The following comments pertain to each {react} argument:

per-atom values are 0.0, are removed from the dynamic group. If the {property}

keyword is used, the per-atom property name must be a previously defined

per-atom property.  The per-atom property is evaluated and atoms whose

values are 0.0 are removed from the dynamic group, otherwise they

are added to the group.

values are 0.0 are removed from the dynamic group.

The assignment of atoms to a dynamic group is done at the beginning of

each run and on every timestep that is a multiple of {N}, which is the

  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map

# stable at 800K

fix 1 statted_grp nvt temp 800 800 100

fix 1 statted_grp_REACT nvt temp 800 800 100

# in order to customize behavior of reacting atoms,

# you can use the internally created 'bond_react_MASTER_group', like so: