ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

bond/react: convert group-ID to group-ID-prefix

Browse Source 
enables consistent syntax when using custom groups
This commit is contained in:
jrgissing
2018-11-03 11:57:46 -06:00
parent 0c7c344e19
commit f7aa01d74a
3 changed files with 40 additions and 38 deletions
Download Patch File Download Diff File Expand all files Collapse all files

34
doc/src/fix_bond_react.txt
View File

@ -24,11 +24,11 @@ common_keyword = {stabilization} :l
{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
@ -51,7 +51,7 @@ react = mandatory argument indicating new reaction specification :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
@ -60,7 +60,7 @@ molecule mol4 post_reacted_rxn2.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:]
@ -104,20 +104,22 @@ during the simulation.
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, fix bond/react command
creates a "dynamic group"_group.html of this name that is initialized
to include all atoms. If the group-ID is that of an existing static
group, the group is converted into a dynamic group, whose atoms are
limited to those belonging to the original static group. In either
case, 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. The time integration command should be placed
after the fix bond/react command due to the internal dynamic grouping
performed by fix bond/react. By specifying an existing group, you may
thermostat non-reacting parts of your system separately.
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 group, or a subset.
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