From e346151271c65c56a34d32f52ff5281d538e57ae Mon Sep 17 00:00:00 2001 From: Karl Hammond Date: Fri, 14 Oct 2022 17:40:22 -0500 Subject: [PATCH] Updated docs for fixes bond/break, bond/create, and bond/react for math/etc. --- doc/src/fix_bond_break.rst | 64 ++++----- doc/src/fix_bond_create.rst | 126 ++++++++-------- doc/src/fix_bond_react.rst | 280 +++++++++++++++++++----------------- 3 files changed, 241 insertions(+), 229 deletions(-) diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst index ba12e154c5..7aa620a8f6 100644 --- a/doc/src/fix_bond_break.rst +++ b/doc/src/fix_bond_break.rst @@ -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 ` 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 ` bond-order +This is different than a :doc:`pair-wise ` 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 ` 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 ` 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 ` 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 `. None of the :doc:`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 `. 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 +`. 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 ` command. This fix is not invoked during :doc:`energy minimization `. diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index c286482f81..bc5e1b83f8 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -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 ` 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 ` bond-order -potential such as Tersoff or AIREBO which infers bonds and many-body +This process is different than a :doc:`pair-wise ` 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 ` 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 ` 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 ` or :doc:`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 ` command, e.g. for a - percolation simulation. + atoms via the :doc:`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 ` or :doc:`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 ` 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 ` 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 ` command. @@ -203,20 +205,20 @@ define a :doc:`bond_style ` and use the :doc:`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 ` 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 ` 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 `. 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 ` command. This fix is not invoked during :doc:`energy minimization `. diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index a48675dcf2..85683f0ddd 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -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 ` 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 ` 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 ` 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 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 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 `) or +pairwise bond-order potential (e.g., :doc:`Tersoff ` or +:doc:`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 ` 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 ` 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 ` 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 `, :doc:`fix npt `, or +:doc:`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 ` 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 ` 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 `, 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 `. 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 `. 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 ` 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 ` 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 ` 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 ` 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 ` 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 `. 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 ` 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) ` +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 `. 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 ` command. ---------- @@ -649,20 +659,20 @@ allow for smooth restarts. None of the :doc:`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 `. 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 ` command. This fix is not invoked during :doc:`energy minimization `. -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 `", 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* ----------