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Updated docs for fixes bond/break, bond/create, and bond/react for math/etc.

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Karl Hammond
2022-10-14 17:40:22 -05:00
parent 3d0a7d774a
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64
doc/src/fix_bond_break.rst
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@ -6,7 +6,7 @@ fix bond/break command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID bond/break Nevery bondtype Rmax keyword values ...
@ -15,7 +15,7 @@ Syntax
* Nevery = attempt bond breaking every this many steps
* bondtype = type of bonds to break
* Rmax = bond longer than Rmax can break (distance units)
* zero or more keyword/value pairs may be appended to args
* zero or more keyword/value pairs may be appended
* keyword = *prob*
.. parsed-literal::
@ -43,42 +43,42 @@ pair of atoms computed by the :doc:`bond_style <bond_style>` command.
Once the bond is broken it will be permanently deleted, as will all
angle, dihedral, and improper interactions that bond is part of.
This is different than a :doc:`pairwise <pair_style>` bond-order
This is different than a :doc:`pair-wise <pair_style>` bond-order
potential such as Tersoff or AIREBO which infers bonds and many-body
interactions based on the current geometry of a small cluster of atoms
and effectively creates and destroys bonds and higher-order many-body
interactions from timestep to timestep as atoms move.
A check for possible bond breakage is performed every *Nevery*
timesteps. If two bonded atoms I,J are further than a distance *Rmax*
of each other, if the bond is of type *bondtype*, and if both I and J
are in the specified fix group, then I,J is labeled as a "possible"
bond to break.
timesteps. If two bonded atoms :math:`i` and :math:`j` are farther than the
distance *Rmax* from each other, the bond is of type *bondtype*, and both
:math:`i` and :math:`j` are in the specified fix group, then the bond between
:math:`i` and :math:`j` is labeled as a "possible" bond to break.
If several bonds involving an atom are stretched, it may have multiple
possible bonds to break. Every atom checks its list of possible bonds
to break and labels the longest such bond as its "sole" bond to break.
After this is done, if atom I is bonded to atom J in its sole bond,
and atom J is bonded to atom I in its sole bond, then the I,J bond is
"eligible" to be broken.
After this is done, if atom :math:`i` is bonded to atom :math:`j` in its sole
bond, and atom :math:`j` is bonded to atom :math:`j` in its sole bond, then the
bond between :math:`i` and :math:`j` is "eligible" to be broken.
Note that these rules mean an atom will only be part of at most one
broken bond on a given timestep. It also means that if atom I chooses
atom J as its sole partner, but atom J chooses atom K is its sole
partner (due to Rjk > Rij), then this means atom I will not be part of
a broken bond on this timestep, even if it has other possible bond
partners.
broken bond on a given time step. It also means that if atom :math:`i` chooses
atom :math:`j` as its sole partner, but atom :math:`j` chooses atom :math:`k`
as its sole partner (because :math:`R_{jk} > R_{ij}`), then this means atom
:math:`I` will not be part of a broken bond on this time step, even if it has
other possible bond partners.
The *prob* keyword can effect whether an eligible bond is actually
broken. The *fraction* setting must be a value between 0.0 and 1.0.
A uniform random number between 0.0 and 1.0 is generated and the
eligible bond is only broken if the random number < fraction.
eligible bond is only broken if the random number is less than *fraction*.
When a bond is broken, data structures within LAMMPS that store bond
topology are updated to reflect the breakage. Likewise, if the bond
topologies are updated to reflect the breakage. Likewise, if the bond
is part of a 3-body (angle) or 4-body (dihedral, improper)
interaction, that interaction is removed as well. These changes
typically affect pairwise interactions between atoms that used to be
typically affect pair-wise interactions between atoms that used to be
part of bonds, angles, etc.
.. note::
@ -88,17 +88,17 @@ part of bonds, angles, etc.
becomes two molecules due to the broken bond, all atoms in both new
molecules retain their original molecule IDs.
Computationally, each timestep this fix operates, it loops over all
Computationally, each time step this fix is invoked, it loops over all
the bonds in the system and computes distances between pairs of bonded
atoms. It also communicates between neighboring processors to
coordinate which bonds are broken. Moreover, if any bonds are broken,
neighbor lists must be immediately updated on the same timestep. This
is to insure that any pairwise interactions that should be turned "on"
neighbor lists must be immediately updated on the same time step. This
is to ensure that any pair-wise interactions that should be turned "on"
due to a bond breaking, because they are no longer excluded by the
presence of the bond and the settings of the
:doc:`special_bonds <special_bonds>` command, will be immediately
recognized. All of these operations increase the cost of a timestep.
Thus you should be cautious about invoking this fix too frequently.
recognized. All of these operations increase the cost of a time step.
Thus, you should be cautious about invoking this fix too frequently.
You can dump out snapshots of the current bond topology via the :doc:`dump local <dump>` command.
@ -107,11 +107,11 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local
Breaking a bond typically alters the energy of a system. You
should be careful not to choose bond breaking criteria that induce a
dramatic change in energy. For example, if you define a very stiff
harmonic bond and break it when 2 atoms are separated by a distance
far from the equilibrium bond length, then the 2 atoms will be
harmonic bond and break it when two atoms are separated by a distance
far from the equilibrium bond length, then the two atoms will be
dramatically released when the bond is broken. More generally, you
may need to thermostat your system to compensate for energy changes
resulting from broken bonds (and angles, dihedrals, impropers).
resulting from broken bonds (as well as angles, dihedrals, and impropers).
See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for more
information on related features in LAMMPS.
@ -124,14 +124,14 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
This fix computes two statistics which it stores in a global vector of
length 2, which can be accessed by various :doc:`output commands <Howto_output>`. The vector values calculated by this fix
are "intensive".
This fix computes two statistics, which it stores in a global vector of
length 2. This vector can be accessed by various :doc:`output commands
<Howto_output>`. The vector values calculated by this fix are "intensive".
These are the 2 quantities:
The two quantities in the global vector are
* (1) # of bonds broken on the most recent breakage timestep
* (2) cumulative # of bonds broken
(1) number of bonds broken on the most recent breakage time step
(2) cumulative number of bonds broken
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.

126
doc/src/fix_bond_create.rst
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@ -10,7 +10,7 @@ fix bond/create/angle command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ...
@ -58,83 +58,84 @@ Description
"""""""""""
Create bonds between pairs of atoms as a simulation runs according to
specified criteria. This can be used to model cross-linking of
specified criteria. This can be used to model the cross-linking of
polymers, the formation of a percolation network, etc. In this
context, a bond means an interaction between a pair of atoms computed
by the :doc:`bond_style <bond_style>` command. Once the bond is created
it will be permanently in place. Optionally, the creation of a bond
can also create angle, dihedral, and improper interactions that bond
can also create angle, dihedral, and improper interactions that the bond
is part of. See the discussion of the *atype*, *dtype*, and *itype*
keywords below.
This is different than a :doc:`pairwise <pair_style>` bond-order
potential such as Tersoff or AIREBO which infers bonds and many-body
This process is different than a :doc:`pair-wise <pair_style>` bond-order
potential such as Tersoff or AIREBO, which infer bonds and many-body
interactions based on the current geometry of a small cluster of atoms
and effectively creates and destroys bonds and higher-order many-body
interactions from timestep to timestep as atoms move.
and effectively create and destroy bonds and higher-order many-body
interactions from time step to time step as the atoms move.
A check for possible new bonds is performed every *Nevery* timesteps.
If two atoms I,J are within a distance *Rmin* of each other, if I is
of atom type *itype*, if J is of atom type *jtype*, if both I and J
are in the specified fix group, if a bond does not already exist
between I and J, and if both I and J meet their respective *maxbond*
requirement (explained below), then I,J is labeled as a "possible"
bond pair.
A check for possible new bonds is performed every *Nevery* time steps.
If two atoms :math:`i` and :math:`j` are within a distance *Rmin* of each
other, atom :math:`i` is of type *itype*, atom :math:`j` is of type *jtype*,
and both :math:`i` and :math:`j` are in the specified fix group, then if a bond
does not already exist between atoms :math:`i` and :math:`j`, and if both
:math:`i` and :math:`j` meet their respective *maxbond* requirements (explained
below), then :math:`i` and :math:`j` are labeled as a "possible" bond pair.
If several atoms are close to an atom, it may have multiple possible
bond partners. Every atom checks its list of possible bond partners
and labels the closest such partner as its "sole" bond partner. After
this is done, if atom I has atom J as its sole partner, and atom J has
atom I as its sole partner, then the I,J bond is "eligible" to be
formed.
this is done, if atom :math:`i` has atom :math:`j` as its sole partner and
atom :math:`j` has atom :math:`i` as its sole partner, then the
:math:`i,j` bond is "eligible" to be formed.
Note that these rules mean an atom will only be part of at most one
created bond on a given timestep. It also means that if atom I
chooses atom J as its sole partner, but atom J chooses atom K is its
sole partner (due to Rjk < Rij), then this means atom I will not form
a bond on this timestep, even if it has other possible bond partners.
Note that these rules mean that an atom will only be part of at most one
created bond on a given time step. It also means that if atom :math:`i`
chooses atom :math:`j` as its sole partner, but atom :math:`j` chooses atom
:math:`k` as its sole partner (because :math:`R_{jk} < R_{ij}`), then atom
:math:`i` will not form a bond on this time step, even if it has other possible
bond partners.
It is permissible to have *itype* = *jtype*\ . *Rmin* must be <= the
pairwise cutoff distance between *itype* and *jtype* atoms, as defined
It is permissible to have *itype* = *jtype*\ . *Rmin* must be :math:`\leq` the
pair-wise cutoff distance between *itype* and *jtype* atoms, as defined
by the :doc:`pair_style <pair_style>` command.
The *iparam* and *jparam* keywords can be used to limit the bonding
functionality of the participating atoms. Each atom keeps track of
how many bonds of *bondtype* it already has. If atom I of
itype already has *maxbond* bonds (as set by the *iparam*
keyword), then it will not form any more. Likewise for atom J. If
*maxbond* is set to 0, then there is no limit on the number of bonds
how many bonds of *bondtype* it already has. If atom :math:`i` of type
*itype* already has *maxbond* bonds (as set by the *iparam*
keyword), then it will not form any more, and likewise for atom :math:`j`.
If *maxbond* is set to 0, then there is no limit on the number of bonds
that can be formed with that atom.
The *newtype* value for *iparam* and *jparam* can be used to change
the atom type of atom I or J when it reaches *maxbond* number of bonds
of type *bondtype*\ . This means it can now interact in a pairwise
the atom type of atom :math:`i` or :math:`j` when it reaches *maxbond* number
of bonds of type *bondtype*\ . This means it can now interact in a pair-wise
fashion with other atoms in a different way by specifying different
:doc:`pair_coeff <pair_coeff>` coefficients. If you do not wish the
atom type to change, simply specify *newtype* as *itype* or *jtype*\ .
The *prob* keyword can also effect whether an eligible bond is
The *prob* keyword can also affect whether an eligible bond is
actually created. The *fraction* setting must be a value between 0.0
and 1.0. A uniform random number between 0.0 and 1.0 is generated and
the eligible bond is only created if the random number < fraction.
the eligible bond is only created if the random number is less than *fraction*.
The *aconstrain* keyword is only available with the fix
bond/create/angle command. It allows to specify a minimal and maximal
angle *amin* and *amax* between the two prospective bonding partners and
a third particle that is already bonded to one of the two partners.
Such a criterion can be important when new angles are defined together
with the formation of a new bond. Without a restriction on the
bond/create/angle command. It allows one to specify minimum and maximum
angles *amin* and *amax*, respectively, between the two prospective bonding
partners and a third particle that is already bonded to one of the two
partners. Such a criterion can be important when new angles are defined
together with the formation of a new bond. Without a restriction on the
permissible angle, and for stiffer angle potentials, very large energies
can arise and lead to uncontrolled behavior.
can arise and lead to unphysical behavior.
Any bond that is created is assigned a bond type of *bondtype*.
When a bond is created, data structures within LAMMPS that store bond
topology are updated to reflect the creation. If the bond is part of
topologies are updated to reflect the creation. If the bond is part of
new 3-body (angle) or 4-body (dihedral, improper) interactions, you
can choose to create new angles, dihedrals, impropers as well, using
can choose to create new angles, dihedrals, and impropers as well using
the *atype*, *dtype*, and *itype* keywords. All of these changes
typically affect pairwise interactions between atoms that are now part
typically affect pair-wise interactions between atoms that are now part
of new bonds, angles, etc.
.. note::
@ -165,19 +166,19 @@ of type *angletype*, with parameters assigned by the corresponding
when bonds are created. See the :doc:`read_data <read_data>` or
:doc:`create_box <create_box>` command for more details. Note that a
data file with no atoms can be used if you wish to add non-bonded
atoms via the :doc:`create atoms <create_atoms>` command, e.g. for a
percolation simulation.
atoms via the :doc:`create atoms <create_atoms>` command (e.g., for a
percolation simulation).
.. note::
LAMMPS stores and maintains a data structure with a list of the
first, second, and third neighbors of each atom (within the bond topology of
the system) for use in weighting pairwise interactions for bonded
the system) for use in weighting pair-wise interactions for bonded
atoms. Note that adding a single bond always adds a new first neighbor
but may also induce \*many\* new second and third neighbors, depending on the
but may also induce **many** new second and third neighbors, depending on the
molecular topology of your system. The "extra special per atom"
parameter must typically be set to allow for the new maximum total
size (first + second + third neighbors) of this per-atom list. There are 2
size (first + second + third neighbors) of this per-atom list. There are two
ways to do this. See the :doc:`read_data <read_data>` or
:doc:`create_box <create_box>` commands for details.
@ -186,15 +187,16 @@ of type *angletype*, with parameters assigned by the corresponding
Even if you do not use the *atype*, *dtype*, or *itype*
keywords, the list of topological neighbors is updated for atoms
affected by the new bond. This in turn affects which neighbors are
considered for pairwise interactions, using the weighting rules set by
considered for pair-wise interactions, using the weighting rules set by
the :doc:`special_bonds <special_bonds>` command. Consider a new bond
created between atoms I,J. If J has a bonded neighbor K, then K
becomes a second neighbor of I. Even if the *atype* keyword is not used
to create angle I-J-K, the pairwise interaction between I and K will
be potentially turned off or weighted by the 1-3 weighting specified
created between atoms :math:`i` and :math:`j`. If :math:`j` has a bonded
neighbor :math:`k`, then :math:`k` becomes a second neighbor of :math:`i`.
Even if the *atype* keyword is not used to create angle :math:`\angle ijk`,
the pair-wise interaction between :math:`i` and :math:`k` could potentially
be turned off or weighted by the 1--3 weighting specified
by the :doc:`special_bonds <special_bonds>` command. This is the case
even if the "angle yes" option was used with that command. The same
is true for third neighbors (1-4 interactions), the *dtype* keyword, and
is true for third neighbors (1--4 interactions), the *dtype* keyword, and
the "dihedral yes" option used with the
:doc:`special_bonds <special_bonds>` command.
@ -203,20 +205,20 @@ define a :doc:`bond_style <bond_style>` and use the
:doc:`bond_coeff <bond_coeff>` command to specify coefficients for the
*bondtype*\ . Similarly, if new atom types are specified by the
*iparam* or *jparam* keywords, they must be within the range of atom
types allowed by the simulation and pairwise coefficients must be
types allowed by the simulation and pair-wise coefficients must be
specified for the new types.
Computationally, each timestep this fix operates, it loops over
Computationally, each time step this fix is invoked, it loops over
neighbor lists and computes distances between pairs of atoms in the
list. It also communicates between neighboring processors to
coordinate which bonds are created. Moreover, if any bonds are
created, neighbor lists must be immediately updated on the same
timestep. This is to insure that any pairwise interactions that
time step. This is to ensure that any pair-wise interactions that
should be turned "off" due to a bond creation, because they are now
excluded by the presence of the bond and the settings of the
:doc:`special_bonds <special_bonds>` command, will be immediately
recognized. All of these operations increase the cost of a timestep.
Thus you should be cautious about invoking this fix too frequently.
recognized. All of these operations increase the cost of a time step.
Thus, you should be cautious about invoking this fix too frequently.
You can dump out snapshots of the current bond topology via the :doc:`dump local <dump>` command.
@ -225,8 +227,8 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local
Creating a bond typically alters the energy of a system. You
should be careful not to choose bond creation criteria that induce a
dramatic change in energy. For example, if you define a very stiff
harmonic bond and create it when 2 atoms are separated by a distance
far from the equilibrium bond length, then the 2 atoms will oscillate
harmonic bond and create it when two atoms are separated by a distance
far from the equilibrium bond length, then the two atoms will oscillate
dramatically when the bond is formed. More generally, you may need to
thermostat your system to compensate for energy changes resulting from
created bonds (and angles, dihedrals, impropers).
@ -245,10 +247,10 @@ length 2, which can be accessed by various :doc:`output commands
<Howto_output>`. The vector values calculated by this fix are
"intensive".
These are the 2 quantities:
The two quantities in the global vector are
* (1) # of bonds created on the most recent creation timestep
* (2) cumulative # of bonds created
(1) number of bonds created on the most recent creation time step
(2) cumulative number of bonds created
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.

280
doc/src/fix_bond_react.rst
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@ -6,12 +6,12 @@ fix bond/react command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID bond/react common_keyword values ...
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
fix ID group-ID bond/react common_keyword values &
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values &
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values &
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values &
...
* ID, group-ID are documented in :doc:`fix <fix>` command.
@ -22,11 +22,12 @@ Syntax
.. parsed-literal::
*stabilization* values = *no* or *yes* *group-ID* *xmax*
*no* = no reaction site stabilization (default)
*yes* = perform reaction site stabilization
*group-ID* = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
*xmax* = xmax value that is used by an internally-created :doc:`nve/limit <fix_nve_limit>` integrator
*stabilization* values = stabilize group_prefix xmax
stabilize = *yes* or *no*
*yes* = perform reaction site stabilization
*no* = no reaction site stabilization (default)
group_prefix = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
xmax = value that is used by an internally-created :doc:`nve/limit <fix_nve_limit>` integrator
*reset_mol_ids* values = *yes* or *no*
*yes* = update molecule IDs based on new global topology (default)
*no* = do not update molecule IDs
@ -51,18 +52,18 @@ Syntax
*max_rxn* value = N
N = maximum number of reactions allowed to occur
*stabilize_steps* value = timesteps
timesteps = number of timesteps to apply the internally-created :doc:`nve/limit <fix_nve_limit>` fix to reacting atoms
*custom_charges* value = *no* or *fragmentID*
no = update all atomic charges (default)
fragmentID = ID of molecule fragment whose charges are updated
timesteps = number of time steps to apply the internally-created :doc:`nve/limit <fix_nve_limit>` fix to reacting atoms
*custom_charges* value = *no* or fragment-ID
*no* = update all atomic charges (default)
fragment-ID = ID of molecule fragment whose charges are updated
*molecule* value = *off* or *inter* or *intra*
off = allow both inter- and intramolecular reactions (default)
inter = search for reactions between molecules with different IDs
intra = search for reactions within the same molecule
*modify_create* keyword values
*fit* value = *all* or *fragmentID*
all = use all eligible atoms for create-atoms fit (default)
fragmentID = ID of molecule fragment used for create-atoms fit
*off* = allow both inter- and intramolecular reactions (default)
*inter* = search for reactions between molecules with different IDs
*intra* = search for reactions within the same molecule
*modify_create* values = keyword arg
*fit* arg = *all* or fragment-ID
*all* = use all eligible atoms for create-atoms fit (default)
fragment-ID = ID of molecule fragment used for create-atoms fit
*overlap* value = R
R = only insert atom/molecule if further than R from existing particles (distance units)
@ -99,31 +100,32 @@ other molecules can be identified and deleted. Finally, atoms can be
created and inserted at specific positions relative to the reaction
site.
Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
Fix bond/react does not use quantum mechanical (e.g., :doc:`fix qmmm <fix_qmmm>`) or
pairwise bond-order potential (e.g., :doc:`Tersoff <pair_tersoff>` or
:doc:`AIREBO <pair_airebo>`) methods to
determine bonding changes a priori. Rather, it uses a distance-based
probabilistic criteria to effect predetermined topology changes in
simulations using standard force fields.
This fix was created to facilitate the dynamic creation of polymeric,
amorphous or highly cross-linked systems. A suggested workflow for
using this fix is: 1) identify a reaction to be simulated 2) build a
molecule template of the reaction site before the reaction has
occurred 3) build a molecule template of the reaction site after the
reaction has occurred 4) create a map that relates the
template-atom-IDs of each atom between pre- and post-reaction molecule
templates 5) fill a simulation box with molecules and run a simulation
with fix bond/react.
using this fix is
(1) identify a reaction to be simulated
(2) build a molecule template of the reaction site before the reaction has occurred
(3) build a molecule template of the reaction site after the reaction has occurred
(4) create a map that relates the template-atom-IDs of each atom between pre- and post-reaction molecule templates
(5) fill a simulation box with molecules and run a simulation with fix bond/react.
Only one 'fix bond/react' command can be used at a time. Multiple
reactions can be simultaneously applied by specifying multiple *react*
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.
The *stabilization* keyword enables reaction site stabilization.
Reaction site stabilization is performed by including reacting atoms
in an internally-created fix :doc:`nve/limit <fix_nve_limit>` time
integrator for a set number of timesteps given by the
integrator for a set number of time steps given by the
*stabilize_steps* keyword. While reacting atoms are being time
integrated by the internal nve/limit, they are prevented from being
involved in any new reactions. The *xmax* value keyword should
@ -133,53 +135,54 @@ during the simulation.
Fix bond/react creates and maintains two important dynamic groups of
atoms when using the *stabilization* keyword. The first group contains
all atoms currently involved in a reaction; this group is
automatically thermostatted by an internally-created
automatically time-integrated by an internally-created
:doc:`nve/limit <fix_nve_limit>` integrator. The second group contains
all atoms currently not involved in a reaction. This group should be
used by a thermostat in order to time integrate the system. The name
controlled by a thermostat in order to time integrate the system. The name
of this group of non-reacting atoms is created by appending '_REACT'
to the group-ID argument of the *stabilization* keyword, as shown in
the second example above.
.. note::
When using reaction stabilization, you should generally not have
a separate thermostat which acts on the 'all' group.
When using reaction stabilization, you should generally **not** have
a separate thermostat that 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
as "all". If the group-ID is previously unused, the fix bond/react
command creates a :doc:`dynamic group <group>` 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
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 atoms not involved in a reaction at a given timestep,
contains only atoms not involved in a reaction at a given time step,
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 (full examples can be found at examples/PACKAGES/reaction). The time
integrator such as :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, or
:doc:`fix nve <fix_nve>`, as shown in the second example
above (full examples can be found in examples/PACKAGES/reaction). 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.
should also be specified as this static group or a subset.
The *reset_mol_ids* keyword invokes the :doc:`reset_mol_ids <reset_mol_ids>`
command after a reaction occurs, to ensure that molecule IDs are
consistent with the new bond topology. The group-ID used for
:doc:`reset_mol_ids <reset_mol_ids>` is the group-ID for this fix.
Resetting molecule IDs is necessarily a global operation, and so can
Resetting molecule IDs is necessarily a global operation, so it can
be slow for very large systems.
The following comments pertain to each *react* argument (in other
words, can be customized for each reaction, or reaction step):
words, they can be customized for each reaction, or reaction step):
A check for possible new reaction sites is performed every *Nevery*
timesteps. *Nevery* can be specified with an equal-style
time steps. *Nevery* can be specified with an equal-style
:doc:`variable <variable>`, whose value is rounded up to the nearest
integer.
@ -194,11 +197,11 @@ reaction site is eligible to be modified to match the post-reaction
template.
An initiator atom pair will be identified if several conditions are
met. First, a pair of atoms I,J within the specified react-group-ID of
type itype and jtype must be separated by a distance between *Rmin*
and *Rmax*\ . *Rmin* and *Rmax* can be specified with equal-style
:doc:`variables <variable>`. For example, these reaction cutoffs can
be a function of the reaction conversion using the following commands:
met. First, a pair of atoms :math:`i` and :math:`j` within the specified
react-group-ID of type *itype* and *jtype* must be separated by a distance
between *Rmin* and *Rmax*\ . *Rmin* and *Rmax* can be specified with
equal-style :doc:`variables <variable>`. For example, these reaction cutoffs
can be functions of the reaction conversion using the following commands:
.. code-block:: LAMMPS
@ -207,23 +210,28 @@ be a function of the reaction conversion using the following commands:
variable rmax equal 3+f_myrxn[1]/100 # arbitrary function of reaction count
The following criteria are used if multiple candidate initiator atom
pairs are identified within the cutoff distance: 1) If the initiator
atoms in the pre-reaction template are not 1-2 neighbors (i.e. not
directly bonded) the closest potential partner is chosen. 2)
Otherwise, if the initiator atoms in the pre-reaction template are 1-2
neighbors (i.e. directly bonded) the farthest potential partner is
chosen. 3) Then, if both an atom I and atom J have each other as their
initiator partners, these two atoms are identified as the initiator
atom pair of the reaction site. Note that it can be helpful to select
pairs are identified within the cutoff distance:
(1) If the initiator atoms in the pre-reaction template are not 1--2
neighbors (i.e., not directly bonded) the closest potential partner is
chosen.
(2) Otherwise, if the initiator atoms in the pre-reaction template are 1--2
neighbors (i.e. directly bonded) the farthest potential partner is
chosen.
(3) Then, if both an atom :math:`i` and atom :math:`j` have each other as
initiator partners, these two atoms are identified as the initiator atom
pair of the reaction site.
Note that it can be helpful to select
unique atom types for the initiator atoms: if an initiator atom pair
is identified, as described in the previous steps, but does not
is identified, as described in the previous steps, but it does not
correspond to the same pair specified in the pre-reaction template, an
otherwise eligible reaction could be prevented from occurring. Once
this unique initiator atom pair is identified for each reaction, there
could be two or more reactions that involve the same atom on the same
timestep. If this is the case, only one such reaction is permitted to
time step. If this is the case, only one such reaction is permitted to
occur. This reaction is chosen randomly from all potential reactions
involving the overlapping atom. This capability allows e.g. for
involving the overlapping atom. This capability allows, for example,
different reaction pathways to proceed from identical reaction sites
with user-specified probabilities.
@ -247,19 +255,19 @@ pre-reaction template atoms should be linked to an initiator atom, via
at least one path that does not involve edge atoms. When the
pre-reaction template contains edge atoms, not all atoms, bonds,
charges, etc. specified in the reaction templates will be updated.
Specifically, topology that involves only atoms that are 'too near' to
template edges will not be updated. The definition of 'too near the
edge' depends on which interactions are defined in the simulation. If
Specifically, topology that involves only atoms that are "too near" to
template edges will not be updated. The definition of "too near the
edge" depends on which interactions are defined in the simulation. If
the simulation has defined dihedrals, atoms within two bonds of edge
atoms are considered 'too near the edge.' If the simulation defines
atoms are considered "too near the edge." If the simulation defines
angles, but not dihedrals, atoms within one bond of edge atoms are
considered 'too near the edge.' If just bonds are defined, only edge
atoms are considered 'too near the edge.'
considered "too near the edge." If just bonds are defined, only edge
atoms are considered "too near the edge."
.. note::
Small molecules, i.e. ones that have all their atoms contained
within the reaction templates, never have edge atoms.
Small molecules (i.e., ones that have all their atoms contained
within the reaction templates) never have edge atoms.
Note that some care must be taken when a building a molecule template
for a given simulation. All atom types in the pre-reacted template
@ -282,7 +290,7 @@ provided on the :doc:`molecule <molecule>` command page.
.. note::
When a reaction occurs, it is possible that the resulting
topology/atom (e.g. special bonds, dihedrals, etc.) exceeds that of
topology/atom (e.g., special bonds, dihedrals) exceeds that of
the existing system and reaction templates. As when inserting
molecules, enough space for this increased topology/atom must be
reserved by using the relevant "extra" keywords to the
@ -292,14 +300,14 @@ The map file is a text document with the following format:
A map file has a header and a body. The header of map file the
contains one mandatory keyword and five optional keywords. The
mandatory keyword is 'equivalences':
mandatory keyword is *equivalences*\ :
.. parsed-literal::
N *equivalences* = # of atoms N in the reaction molecule templates
The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and
'constraints':
The optional keywords are *edgeIDs*\ , *deleteIDs*\ , *chiralIDs*\ , and
*constraints*\ :
.. parsed-literal::
@ -311,25 +319,25 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and
The body of the map file contains two mandatory sections and five
optional sections. The first mandatory section begins with the keyword
'InitiatorIDs' and lists the two atom IDs of the initiator atom pair
"InitiatorIDs" and lists the two atom IDs of the initiator atom pair
in the pre-reacted molecule template. The second mandatory section
begins with the keyword 'Equivalences' and lists a one-to-one
begins with the keyword "Equivalences" and lists a one-to-one
correspondence between atom IDs of the pre- and post-reacted
templates. 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 first optional section begins with
the keyword 'EdgeIDs' and lists the atom IDs of edge atoms in the
the keyword "EdgeIDs" and lists the atom IDs of edge atoms in the
pre-reacted molecule template. The second optional section begins with
the keyword 'DeleteIDs' and lists the atom IDs of pre-reaction
the keyword "DeleteIDs" and lists the atom IDs of pre-reaction
template atoms to delete. The third optional section begins with the
keyword 'CreateIDs' and lists the atom IDs of the post-reaction
keyword "CreateIDs" and lists the atom IDs of the post-reaction
template atoms to create. The fourth optional section begins with the
keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose
keyword "ChiralIDs" lists the atom IDs of chiral atoms whose
handedness should be enforced. The fifth optional section begins with
the keyword 'Constraints' and lists additional criteria that must be
the keyword "Constraints" and lists additional criteria that must be
satisfied in order for the reaction to occur. Currently, there are
six types of constraints available, as discussed below: 'distance',
'angle', 'dihedral', 'arrhenius', 'rmsd', and 'custom'.
six types of constraints available, as discussed below: "distance",
"angle", "dihedral", "arrhenius", "rmsd", and "custom".
A sample map file is given below:
@ -384,13 +392,13 @@ two sub-keywords, *fit* and *overlap*. One or more of the sub-keywords
may be used after the *modify_create* keyword. The *fit* sub-keyword
can be used to specify which post-reaction atoms are used for the
optimal translation and rotation of the post-reaction template. The
*fragmentID* value of the *fit* sub-keyword must be the name of a
fragment-ID value of the *fit* sub-keyword must be the name of a
molecule fragment defined in the post-reaction :doc:`molecule
<molecule>` template, and only atoms in this fragment are used for the
fit. Atoms are created only if no current atom in the simulation is
within a distance R of any created atom, including the effect of
periodic boundary conditions if applicable. R is defined by the
*overlap* sub-keyword. Note that the default value for R is 0.0, which
within a distance :math:`R` of any created atom, including the effect of
periodic boundary conditions if applicable. :math:`R` is defined by the
*overlap* sub-keyword. Note that the default value for :math:`R` is 0.0, which
will allow atoms to strongly overlap if you are inserting where other
atoms are present. The velocity of each created atom is initialized in
a random direction with a magnitude calculated from the instantaneous
@ -406,40 +414,40 @@ and the relative position of the fourth bonded atom determines the
chiral center's handedness.
Any number of additional constraints may be specified in the
Constraints section of the map file. The constraint of type 'distance'
Constraints section of the map file. The constraint of type "distance"
has syntax as follows:
.. parsed-literal::
distance *ID1* *ID2* *rmin* *rmax*
where 'distance' is the required keyword, *ID1* and *ID2* are
where "distance" is the required keyword, *ID1* and *ID2* are
pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
two atoms must be separated by a distance between *rmin* and *rmax*
for the reaction to occur.
The constraint of type 'angle' has the following syntax:
The constraint of type "angle" has the following syntax:
.. parsed-literal::
angle *ID1* *ID2* *ID3* *amin* *amax*
where 'angle' is the required keyword, *ID1*, *ID2* and *ID3* are
where "angle" is the required keyword, *ID1*, *ID2* and *ID3* are
pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
three atoms must form an angle between *amin* and *amax* for the
reaction to occur (where *ID2* is the central atom). Angles must be
specified in degrees. This constraint can be used to enforce a certain
orientation between reacting molecules.
The constraint of type 'dihedral' has the following syntax:
The constraint of type "dihedral" has the following syntax:
.. parsed-literal::
dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2*
where 'dihedral' is the required keyword, and *ID1*, *ID2*, *ID3*
where "dihedral" is the required keyword, and *ID1*, *ID2*, *ID3*
and *ID4* are pre-reaction atom IDs (or molecule-fragment IDs, see
below). Dihedral angles are calculated in the interval (-180,180].
below). Dihedral angles are calculated in the interval :math:`(-180^\circ,180^\circ]`.
Refer to the :doc:`dihedral style <dihedral_style>` documentation for
further details on convention. If *amin* is less than *amax*, these
four atoms must form a dihedral angle greater than *amin* **and** less
@ -447,7 +455,7 @@ than *amax* for the reaction to occur. If *amin* is greater than
*amax*, these four atoms must form a dihedral angle greater than
*amin* **or** less than *amax* for the reaction to occur. Angles must
be specified in degrees. Optionally, a second range of permissible
angles *amin2*-*amax2* can be specified.
angles *amin2* to *amax2* can be specified.
For the 'distance', 'angle', and 'dihedral' constraints (explained
above), atom IDs can be replaced by pre-reaction molecule-fragment
@ -457,11 +465,11 @@ fragment. The molecule fragment must have been defined in the
:doc:`molecule <molecule>` command for the pre-reaction template.
The constraint of type 'arrhenius' imposes an additional reaction
probability according to the temperature-dependent Arrhenius equation:
probability according to the modified Arrhenius equation,
.. math::
k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}}
k = AT^{n}e^{-E_{a}/k_{B}T}.
The Arrhenius constraint has the following syntax:
@ -469,11 +477,11 @@ The Arrhenius constraint has the following syntax:
arrhenius *A* *n* *E_a* *seed*
where 'arrhenius' is the required keyword, *A* is the pre-exponential
where "arrhenius" is the required keyword, *A* is the pre-exponential
factor, *n* is the exponent of the temperature dependence, :math:`E_a`
is the activation energy (:doc:`units <units>` of energy), and *seed* is a
random number seed. The temperature is defined as the instantaneous
temperature averaged over all atoms in the reaction site, and is
temperature averaged over all atoms in the reaction site and is
calculated in the same manner as for example
:doc:`compute temp/chunk <compute_temp_chunk>`. Currently, there are no
options for additional temperature averaging or velocity-biased
@ -487,7 +495,7 @@ The constraint of type 'rmsd' has the following syntax:
rmsd *RMSDmax* *molfragment*
where 'rmsd' is the required keyword, and *RMSDmax* is the maximum
where "rmsd" is the required keyword, and *RMSDmax* is the maximum
root-mean-square deviation between atom positions of the pre-reaction
template and the local reaction site (distance units), after optimal
translation and rotation of the pre-reaction template. Optionally, the
@ -500,26 +508,26 @@ example, the molecule fragment could consist of only the backbone
atoms of a polymer chain. This constraint can be used to enforce a
specific relative position and orientation between reacting molecules.
The constraint of type 'custom' has the following syntax:
The constraint of type "custom" has the following syntax:
.. parsed-literal::
custom *varstring*
where 'custom' is the required keyword, and *varstring* is a
where "custom" is the required keyword, and *varstring* is a
variable expression. The expression must be a valid equal-style
variable formula that can be read by the :doc:`variable <variable>` command,
after any special reaction functions are evaluated. If the resulting
expression is zero, the reaction is prevented from occurring;
otherwise, it is permitted to occur. There are two special reaction
functions available, 'rxnsum' and 'rxnave'. These functions operate
functions available, "rxnsum" and "rxnave". These functions operate
over the atoms in a given reaction site, and have one mandatory
argument and one optional argument. The mandatory argument is the
identifier for an atom-style variable. The second, optional argument
is the name of a molecule fragment in the pre-reaction template, and
can be used to operate over a subset of atoms in the reaction site.
The 'rxnsum' function sums the atom-style variable over the reaction
site, while the 'rxnave' returns the average value. For example, a
The "rxnsum" function sums the atom-style variable over the reaction
site, while the "rxnave" returns the average value. For example, a
constraint on the total potential energy of atoms involved in the
reaction can be imposed as follows:
@ -535,8 +543,8 @@ reaction can be imposed as follows:
The above example prevents the reaction from occurring unless the
total potential energy of the reaction site is above 100. The variable
expression can be interpreted as the probability of the reaction
occurring by using an inequality and the 'random(x,y,z)' function
available as an equal-style variable input, similar to the 'arrhenius'
occurring by using an inequality and the :doc:`random(x,y,z) <variable>`
function available for equal-style variables, similar to the 'arrhenius'
constraint above.
By default, all constraints must be satisfied for the reaction to
@ -561,40 +569,42 @@ within LAMMPS that store bond topology are updated to reflect the
post-reacted molecule template. All force fields with fixed bonds,
angles, dihedrals or impropers are supported.
A few capabilities to note: 1) You may specify as many *react*
arguments as desired. For example, you could break down a complicated
reaction mechanism into several reaction steps, each defined by its
own *react* argument. 2) While typically a bond is formed or removed
between the initiator atoms specified in the pre-reacted molecule
template, this is not required. 3) By reversing the order of the pre-
and post- reacted molecule templates in another *react* argument, you
can allow for the possibility of one or more reverse reactions.
A few capabilities to note:
(1) You may specify as many *react* arguments as desired. For example, you
could break down a complicated reaction mechanism into several reaction
steps, each defined by its own *react* argument.
(2) While typically a bond is formed or removed between the initiator atoms
specified in the pre-reacted molecule template, this is not required.
(3) By reversing the order of the pre- and post-reacted molecule templates in
another *react* argument, you can allow for the possibility of one or
more reverse reactions.
The optional keywords deal with the probability of a given reaction
occurring as well as the stable equilibration of each reaction site as
it occurs:
it occurs.
The *prob* keyword can affect whether or not an eligible reaction
actually occurs. The fraction setting must be a value between 0.0 and
1.0, and can be specified with an equal-style :doc:`variable <variable>`.
A uniform random number between 0.0 and 1.0 is generated and the
eligible reaction only occurs if the random number is less than the
fraction. Up to N reactions are permitted to occur, as optionally
fraction. Up to :math:`N` reactions are permitted to occur, as optionally
specified by the *max_rxn* keyword.
The *stabilize_steps* keyword allows for the specification of how many
timesteps a reaction site is stabilized before being returned to the
time steps a reaction site is stabilized before being returned to the
overall system thermostat. In order to produce the most physical
behavior, this 'reaction site equilibration time' should be tuned to
behavior, this "reaction site equilibration time" should be tuned to
be as small as possible while retaining stability for a given system
or reaction step. After a limited number of case studies, this number
has been set to a default of 60 timesteps. Ideally, it should be
has been set to a default of 60 time steps. Ideally, it should be
individually tuned for each fix reaction step. Note that in some
situations, decreasing rather than increasing this parameter will
result in an increase in stability.
The *custom_charges* keyword can be used to specify which atoms'
atomic charges are updated. When the value is set to 'no', all atomic
atomic charges are updated. When the value is set to *no*\ , all atomic
charges are updated to those specified by the post-reaction template
(default). Otherwise, the value should be the name of a molecule
fragment defined in the pre-reaction molecule template. In this case,
@ -602,10 +612,10 @@ only the atomic charges of atoms in the molecule fragment are updated.
The *molecule* keyword can be used to force the reaction to be
intermolecular, intramolecular or either. When the value is set to
'off', molecule IDs are not considered when searching for reactions
(default). When the value is set to 'inter', the initiator atoms must
*off*\ , molecule IDs are not considered when searching for reactions
(default). When the value is set to *inter*\ , the initiator atoms must
have different molecule IDs in order to be considered for the
reaction. When the value is set to 'intra', only initiator atoms with
reaction. When the value is set to *intra*\ , only initiator atoms with
the same molecule ID are considered for the reaction.
A few other considerations:
@ -627,15 +637,15 @@ all currently-reacting atoms:
This command must be added after the fix bond/react command, and
will apply to all reactions.
Computationally, each timestep this fix operates, it loops over
Computationally, each time step this fix is invoked, it loops over
neighbor lists (for bond-forming reactions) and computes distances
between pairs of atoms in the list. It also communicates between
neighboring processors to coordinate which bonds are created and/or
removed. All of these operations increase the cost of a timestep. Thus
removed. All of these operations increase the cost of a time step. Thus,
you should be cautious about invoking this fix too frequently.
You can dump out snapshots of the current bond topology via the dump
local command.
You can dump out snapshots of the current bond topology via the
:doc:`dump local <dump>` command.
----------
@ -649,20 +659,20 @@ allow for smooth restarts. None of the :doc:`fix_modify <fix_modify>`
options are relevant to this fix.
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 :doc:`output commands <Howto_output>`. The
vector values calculated by this fix are "intensive".
These is 1 quantity for each react argument:
There is one quantity in the global vector for each *react* argument:
* (1) cumulative # of reactions occurred
(1) cumulative number of reactions that occurred
No parameter of this fix can be used with the *start/stop* keywords
of the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
When fix bond/react is 'unfixed', all internally-created groups are
deleted. Therefore, fix bond/react can only be unfixed after unfixing
all other fixes that use any group created by fix bond/react.
When fix bond/react is ":doc:`unfixed <unfix>`", all internally-created
groups are deleted. Therefore, fix bond/react can only be unfixed after
unfixing all other fixes that use any group created by fix bond/react.
Restrictions
""""""""""""
@ -683,7 +693,7 @@ Default
"""""""
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = no
reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = *fit all*
----------