tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11779 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2014-04-11 20:23:37 +00:00
parent 0916861315
commit d4518d2fd1
2 changed files with 44 additions and 64 deletions
Download Patch File Download Diff File Expand all files Collapse all files

54
doc/fix_bond_break.html
View File

@ -47,12 +47,14 @@ 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 <A HREF = "bond_style.html">bond_style</A> command.
Once the bond is broken it will be permanently deleted. This is
different than a <A HREF = "pair_style.html">pairwise</A> 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.
Once the bond is broken it will be permanently deleted, as will all
angle, dihedral, and improper interactions that bond is part of.
</P>
<P>This is different than a <A HREF = "pair_style.html">pairwise</A> 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.
</P>
<P>A check for possible bond breakage is performed every <I>Nevery</I>
timesteps. If two bonded atoms I,J are further than a distance <I>Rmax</I>
@ -80,17 +82,21 @@ A uniform random number between 0.0 and 1.0 is generated and the
eligible bond is only broken if the random number < fraction.
</P>
<P>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.
topology 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.
</P>
<P>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.
<P>Computationally, each timestep this fix operates, 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"
due to a bond breaking, because they are no longer excluded by the
presence of the bond and the settings of the
<A HREF = "special_bonds.html">special_bonds</A> 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.
</P>
<P>You can dump out snapshots of the current bond topology via the <A HREF = "dump.html">dump
local</A> command.
@ -132,22 +138,6 @@ minimization</A>.
built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>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.
</P>
<P>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
<A HREF = "angle_style.html">angle_style</A> or
<A HREF = "dihedral_style.html">dihedral_style</A>.
</P>
<P>This fix requires that the pairwise weightings defined by the
<A HREF = "special_bonds.html">special_bonds</A> command be *,1,1 for 1-3 and 1-4
neighbors within the bond topology (the 1-2 setting is not
restricted). This means that the pairwise interaction of I with J's
other bond partners is unaffected by the breaking of the bond.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_bond_create.html">fix bond/create</A>, <A HREF = "fix_bond_swap.html">fix

54
doc/fix_bond_break.txt
View File

@ -36,12 +36,14 @@ 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.
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 "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 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}
@ -69,17 +71,21 @@ 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.
topology 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.
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.
Computationally, each timestep this fix operates, 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"
due to a bond breaking, because they are no longer excluded by the
presence of the bond and the settings of the
"special_bonds"_special_bonds.html 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.
You can dump out snapshots of the current bond topology via the "dump
local"_dump.html command.
@ -121,22 +127,6 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
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 *,1,1 for 1-3 and 1-4
neighbors within the bond topology (the 1-2 setting is not
restricted). This means that the pairwise interaction of I with J's
other bond partners is unaffected by the breaking of the bond.
[Related commands:]
"fix bond/create"_fix_bond_create.html, "fix