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Commit e076d08e authored by jrgissing's avatar jrgissing
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correctly render doc page

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