From 2b589450bb1c3c2c7ead2122d19fdde0d304f0da Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 23 Jan 2009 18:49:48 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2523 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_bond_break.html | 160 ++++++++++++++++++++++++++++ doc/fix_bond_break.txt | 147 ++++++++++++++++++++++++++ doc/fix_bond_create.html | 218 +++++++++++++++++++++++++++++++++++++++ doc/fix_bond_create.txt | 204 ++++++++++++++++++++++++++++++++++++ 4 files changed, 729 insertions(+) create mode 100644 doc/fix_bond_break.html create mode 100755 doc/fix_bond_break.txt create mode 100644 doc/fix_bond_create.html create mode 100755 doc/fix_bond_create.txt diff --git a/doc/fix_bond_break.html b/doc/fix_bond_break.html new file mode 100644 index 0000000000..61b37fc6e1 --- /dev/null +++ b/doc/fix_bond_break.html @@ -0,0 +1,160 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

fix bond/break command +

+

Syntax: +

+
fix ID group-ID bond/break Nevery bondtype Rmax keyword values ... 
+
+ +

Examples: +

+
fix 5 all bond/break 10 2 1.2
+fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829 
+
+

Description: +

+

Break bonds between pairs of atoms as a simulation runs according to +specified criteria. This can be used to model the dissolution of a +polymer network due to stretching of the simulation box or other +deformations. In this context, a bond means an interaction between a +pair of atoms computed by the bond_style command. +Once the bond is broken it will be permanently deleted. This is +different than a pairwise 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 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. +

+

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. +

+

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. +

+

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. +

+

When a bond is broken, data structures within LAMMPS that store bond +topology are updated to reflect the breakage. This can also affect +subsequent computation of pairwise interactions involving the atoms in +the bond. See the Restriction section below for additional +information. +

+

Computationally, each timestep this fix operates, it loops over bond +lists and computes distances between pairs of bonded atoms in the +list. It also communicates between neighboring processors to +coordinate which bonds are broken. Thus it will increase the cost of +a timestep. Thus you should be cautious about invoking this fix too +frequently. +

+

You can dump out snapshots of the current bond topology via the dump +bond command. +

+

IMPORTANT NOTE: 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 equilibribum bond length, then the 2 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. +

+
+ +

Restart, fix_modify, output, run start/stop, minimize info: +

+

No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. +

+

This fix computes two statistics which it stores in a vector of length +2, which can be accessed by various output +commands. The vector values +calculated by this fix are "extensive", meaning they scale with the +number of atoms in the simulation. +

+

These are the 2 quantities: +

+ +

No parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +

+

Restrictions: +

+

Currently, there are 2 restrictions for using this fix. We may relax +these in the future if there are new models that would be enabled by +it. +

+

When a bond is broken, you might wish to turn off angle and dihedral +interactions that include that bond. However, LAMMPS does not check +for these angles and dihedrals, even if your simulation defines an +angle_style or +dihedral_style. +

+

This fix requires that the pairwise weightings defined by the +special_bonds command be 0,1,1 for 1-2, 1-3, and +1-4 neighbors within the bond topology. This effectively means that +the pairwise interaction between atoms I and J is turned off when a +bond between them exists and will be turned on when the bond is +broken. It also means that the pairwise interaction of I with J's +other bond partners is unaffected by the existence of the bond. +

+

Related commands: +

+

fix bond/create, fix +bond/swap, dump bond, +special_bonds +

+

Default: +

+

The option defaults are prob = 1.0. +

+ diff --git a/doc/fix_bond_break.txt b/doc/fix_bond_break.txt new file mode 100755 index 0000000000..423e6b9bb4 --- /dev/null +++ b/doc/fix_bond_break.txt @@ -0,0 +1,147 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix bond/break command :h3 + +[Syntax:] + +fix ID group-ID bond/break Nevery bondtype Rmax keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +bond/break = style name of this fix command :l +Nevery = attempt bond breaking every this many steps :l +bondtype = type of bonds to break :l +Rmax = bond longer than Rmax can break (distance units) :l +zero or more keyword/value pairs may be appended to args :l +keyword = {prob} :l + {prob} values = fraction seed + fraction = break a bond with this probability if otherwise eligible + seed = random number seed (positive integer) :pre +:ule + +[Examples:] + +fix 5 all bond/break 10 2 1.2 +fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829 :pre + +[Description:] + +Break bonds between pairs of atoms as a simulation runs according to +specified criteria. This can be used to model the dissolution of a +polymer network due to stretching of the simulation box or other +deformations. In this context, a bond means an interaction between a +pair of atoms computed by the "bond_style"_bond_style.html command. +Once the bond is broken it will be permanently deleted. This is +different than a "pairwise"_pair_style.html 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 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. + +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. + +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. + +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. + +When a bond is broken, data structures within LAMMPS that store bond +topology are updated to reflect the breakage. This can also affect +subsequent computation of pairwise interactions involving the atoms in +the bond. See the Restriction section below for additional +information. + +Computationally, each timestep this fix operates, it loops over bond +lists and computes distances between pairs of bonded atoms in the +list. It also communicates between neighboring processors to +coordinate which bonds are broken. Thus it will increase the cost of +a timestep. Thus you should be cautious about invoking this fix too +frequently. + +You can dump out snapshots of the current bond topology via the "dump +bond"_dump.html command. + +IMPORTANT NOTE: 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 equilibribum bond length, then the 2 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. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. + +This fix computes two statistics which it stores in a vector of length +2, which can be accessed by various "output +commands"_Section_howto.html#4_15. The vector values +calculated by this fix are "extensive", meaning they scale with the +number of atoms in the simulation. + +These are the 2 quantities: + +(1) # of bonds broken on the most recent breakage timestep +(2) cummulative # of bonds broken :ul + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +Currently, there are 2 restrictions for using this fix. We may relax +these in the future if there are new models that would be enabled by +it. + +When a bond is broken, you might wish to turn off angle and dihedral +interactions that include that bond. However, LAMMPS does not check +for these angles and dihedrals, even if your simulation defines an +"angle_style"_angle_style.html or +"dihedral_style"_dihedral_style.html. + +This fix requires that the pairwise weightings defined by the +"special_bonds"_special_bonds.html command be 0,1,1 for 1-2, 1-3, and +1-4 neighbors within the bond topology. This effectively means that +the pairwise interaction between atoms I and J is turned off when a +bond between them exists and will be turned on when the bond is +broken. It also means that the pairwise interaction of I with J's +other bond partners is unaffected by the existence of the bond. + +[Related commands:] + +"fix bond/create"_fix_bond_create.html, "fix +bond/swap"_fix_bond_swap.html, "dump bond"_dump.html, +"special_bonds"_special_bonds.html + +[Default:] + +The option defaults are prob = 1.0. diff --git a/doc/fix_bond_create.html b/doc/fix_bond_create.html new file mode 100644 index 0000000000..922a9394af --- /dev/null +++ b/doc/fix_bond_create.html @@ -0,0 +1,218 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

fix bond/create command +

+

Syntax: +

+
fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ... 
+
+ +

Examples: +

+
fix 5 all bond/create 10 1 2 0.8 1
+fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 
+
+

Description: +

+

Create bonds between pairs of atoms as a simulation runs according to +specified criteria. This can be used to model 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 bond_style command. Once the bond is created +it will be permanently in place. This is different than a +pairwise 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 from timestep to timestep as 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. +

+

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. +

+

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. +

+

It is permissible to have itype = jtype. Rmin must be <= the +pairwise cutoff distance between itype and jtype atoms, as defined +by the 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 +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 +fashion with other atoms in a different way by specifying different +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 +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. +

+

Any bond that is created is assigned a bond type of bondtype. Data +structures within LAMMPS that store bond topology are updated to +reflect the new bond. This can also affect subsequent computation of +pairwise interactions involving the atoms in the bond. See the +Restriction section below for additional information. +

+

IMPORTANT NOTE: To create a new bond, the internal LAMMPS data +structures that store this information must have space for it. When +LAMMPS is initialized from a data file, the list of bonds is scanned +and the maximum number of bonds per atom is tallied. If some atom +will acquire more bonds than this limit as this fix operates, then the +"extra bonds per atom" parameter in the data file header must be set +to allow for it. See the read_data command for more +details. Note that if this parameter needs to be set, it means a data +file must be used to initialize the system, even if it initially has +no bonds. A data file with no atoms can be used if you wish to add +unbonded atoms via the create atoms command, +e.g. for a percolation simulation. +

+

IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a +list of 1st, 2nd, and 3rd neighbors of each atom (in the bond topology +of the system) for use in weighting pairwise interactions for bonded +atoms. Adding a bond adds a single entry to this list. The "extra" +keyword of the special_bonds command should be +used to leave space for new bonds if the maximum number of entries for +any atom will be exceeded as this fix operates. See the +special_bonds command for details. +

+

Note that even if your simulation starts with no bonds, you must +define a bond_style and use the +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 +specified for the new types. +

+

Computationally, each timestep this fix operates, 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. Thus it roughly doubles the cost +of a timestep. Thus you should be cautious about invoking this fix +too frequently. +

+

You can dump out snapshots of the current bond topology via the dump +bond command. +

+

IMPORTANT NOTE: 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 equilibribum bond length, then the 2 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. +

+
+ +

Restart, fix_modify, output, run start/stop, minimize info: +

+

No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. +

+

This fix computes two statistics which it stores in a vector of length +2, which can be accessed by various output +commands. The vector values +calculated by this fix are "extensive", meaning they scale with the +number of atoms in the simulation. +

+

These are the 2 quantities: +

+ +

No parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +

+

Restrictions: +

+

Currently, there are 2 restrictions for using this fix. We may relax +these in the future if there are new models that would be enabled by +it. +

+

When a bond is created, you might wish to induce new angle and +dihedral interactions that include that bond. However, LAMMPS does +not create these angles and dihedrals, even if your simulation defines +an angle_style or +dihedral_style. +

+

This fix requires that the pairwise weightings defined by the +special_bonds command be 0,1,1 for 1-2, 1-3, and +1-4 neighbors within the bond topology. This effectively means that +the pairwise interaction between atoms I and J will be turned off when +a bond between them is created. It also means that the pairwise +interaction of I with J's other bond partners will be unaffected by +the new bond. +

+

Related commands: +

+

fix bond/break, fix +bond/swap, dump bond, +special_bonds +

+

Default: +

+

The option defaults are iparam = (0,itype), jparam = (0,jtype), and +prob = 1.0. +

+ diff --git a/doc/fix_bond_create.txt b/doc/fix_bond_create.txt new file mode 100755 index 0000000000..7ad5272f0a --- /dev/null +++ b/doc/fix_bond_create.txt @@ -0,0 +1,204 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix bond/create command :h3 + +[Syntax:] + +fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +bond/create = style name of this fix command :l +Nevery = attempt bond creation every this many steps :l +itype,jtype = atoms of itype can bond to atoms of jtype :l +Rmin = 2 atoms separated by less than Rmin can bond (distance units) :l +bondtype = type of created bonds :l +zero or more keyword/value pairs may be appended to args :l +keyword = {iparam} or {jparam} or {prob} :l + {iparam} values = maxbond, newtype + maxbond = max # of bonds of bondtype the itype atom can have + newtype = change the itype atom to this type when maxbonds exist + {jparam} values = maxbond, newtype + maxbond = max # of bonds of bondtype the jtype atom can have + newtype = change the jtype atom to this type when maxbonds exist + {prob} values = fraction seed + fraction = create a bond with this probability if otherwise eligible + seed = random number seed (positive integer) :pre +:ule + +[Examples:] + +fix 5 all bond/create 10 1 2 0.8 1 +fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 :pre + +[Description:] + +Create bonds between pairs of atoms as a simulation runs according to +specified criteria. This can be used to model 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 "bond_style"_bond_style.html command. Once the bond is created +it will be permanently in place. This is different than a +"pairwise"_pair_style.html 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 from timestep to timestep as 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. + +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. + +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. + +It is permissible to have {itype} = {jtype}. {Rmin} must be <= the +pairwise cutoff distance between {itype} and {jtype} atoms, as defined +by the "pair_style"_pair_style.html 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 +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 +fashion with other atoms in a different way by specifying different +"pair_coeff"_pair_coeff.html 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 +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. + +Any bond that is created is assigned a bond type of {bondtype}. Data +structures within LAMMPS that store bond topology are updated to +reflect the new bond. This can also affect subsequent computation of +pairwise interactions involving the atoms in the bond. See the +Restriction section below for additional information. + +IMPORTANT NOTE: To create a new bond, the internal LAMMPS data +structures that store this information must have space for it. When +LAMMPS is initialized from a data file, the list of bonds is scanned +and the maximum number of bonds per atom is tallied. If some atom +will acquire more bonds than this limit as this fix operates, then the +"extra bonds per atom" parameter in the data file header must be set +to allow for it. See the "read_data"_read_data.html command for more +details. Note that if this parameter needs to be set, it means a data +file must be used to initialize the system, even if it initially has +no bonds. A data file with no atoms can be used if you wish to add +unbonded atoms via the "create atoms"_create_atoms.html command, +e.g. for a percolation simulation. + +IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a +list of 1st, 2nd, and 3rd neighbors of each atom (in the bond topology +of the system) for use in weighting pairwise interactions for bonded +atoms. Adding a bond adds a single entry to this list. The "extra" +keyword of the "special_bonds"_special_bonds.html command should be +used to leave space for new bonds if the maximum number of entries for +any atom will be exceeded as this fix operates. See the +"special_bonds"_special_bonds.html command for details. + +Note that even if your simulation starts with no bonds, you must +define a "bond_style"_bond_style.html and use the +"bond_coeff"_bond_coeff.html 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 +specified for the new types. + +Computationally, each timestep this fix operates, 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. Thus it roughly doubles the cost +of a timestep. Thus you should be cautious about invoking this fix +too frequently. + +You can dump out snapshots of the current bond topology via the "dump +bond"_dump.html command. + +IMPORTANT NOTE: 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 equilibribum bond length, then the 2 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. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. + +This fix computes two statistics which it stores in a vector of length +2, which can be accessed by various "output +commands"_Section_howto.html#4_15. The vector values +calculated by this fix are "extensive", meaning they scale with the +number of atoms in the simulation. + +These are the 2 quantities: + +(1) # of bonds created on the most recent creation timestep +(2) cummulative # of bonds created :ul + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +Currently, there are 2 restrictions for using this fix. We may relax +these in the future if there are new models that would be enabled by +it. + +When a bond is created, you might wish to induce new angle and +dihedral interactions that include that bond. However, LAMMPS does +not create these angles and dihedrals, even if your simulation defines +an "angle_style"_angle_style.html or +"dihedral_style"_dihedral_style.html. + +This fix requires that the pairwise weightings defined by the +"special_bonds"_special_bonds.html command be 0,1,1 for 1-2, 1-3, and +1-4 neighbors within the bond topology. This effectively means that +the pairwise interaction between atoms I and J will be turned off when +a bond between them is created. It also means that the pairwise +interaction of I with J's other bond partners will be unaffected by +the new bond. + +[Related commands:] + +"fix bond/break"_fix_bond_break.html, "fix +bond/swap"_fix_bond_swap.html, "dump bond"_dump.html, +"special_bonds"_special_bonds.html + +[Default:] + +The option defaults are iparam = (0,itype), jparam = (0,jtype), and +prob = 1.0.