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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11808 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2014-04-17 16:45:33 +00:00
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92
doc/fix_bond_create.html
View File

@ -29,7 +29,7 @@
<LI>zero or more keyword/value pairs may be appended to args
<LI>keyword = <I>iparam</I> or <I>jparam</I> or <I>prob</I>
<LI>keyword = <I>iparam</I> or <I>jparam</I> or <I>prob</I> or <I>atype</I> or <I>dtype</I> or <I>itype</I>
<PRE> <I>iparam</I> values = maxbond, newtype
maxbond = max # of bonds of bondtype the itype atom can have
@ -39,14 +39,21 @@
newtype = change the jtype atom to this type when maxbonds exist
<I>prob</I> values = fraction seed
fraction = create a bond with this probability if otherwise eligible
seed = random number seed (positive integer)
seed = random number seed (positive integer)
<I>atype</I> value = angletype
angletype = type of created angles
<I>dtype</I> value = dihedraltype
dihedraltype = type of created dihedrals
<I>itype</I> value = impropertype
impropertype = type of created impropers
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>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
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2
</PRE>
<P><B>Description:</B>
</P>
@ -55,11 +62,16 @@ 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 <A HREF = "bond_style.html">bond_style</A> command. Once the bond is created
it will be permanently in place. 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.
it will be permanently in place. Optionally, the creation of a bond
can also create angle, dihedral, and improper interactions that bond
is part of. See the discussion of the <I>atype</I>, <I>dtype</I>, and <I>itype</I>
keywords below.
</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 new bonds is performed every <I>Nevery</I> timesteps.
If two atoms I,J are within a distance <I>Rmin</I> of each other, if I is
@ -106,22 +118,37 @@ actually created. The <I>fraction</I> 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.
</P>
<P>Any bond that is created is assigned a bond type of <I>bondtype</I>. 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.
<P>Any bond that is created is assigned a bond type of <I>bondtype</I>
</P>
<P>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
new 3-body (angle) or 4-body (dihedral, improper) interactions, you
can choose to create new angles, dihedrals, impropers as well, using
the <I>atype</I>, <I>dtype</I>, and <I>itype</I> keywords. All of these changes
typically affect pairwise interactions between atoms that are now part
of new bonds, angles, etc.
</P>
<P>If the <I>atype</I> keyword is used and if an angle potential is defined
via the <A HREF = "angle.html">angle_style</A> command, then any new 3-body
interactions inferred by the creation of a bond will create new angles
of type <I>angletype</I>, with parameters assigned by the corresponding
<A HREF = "angle_coeff.html">angle_coeff</A> command. Likewise, the <I>dtype</I> and
<I>itype</I> keywords will create new dihedrals and impropers of type
<I>dihedraltype</I> and <I>impropertype</I>.
</P>
<P>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 bond per atom" parameter must be set to allow for it. See the
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command for
more details. Note that a data file with no atoms can be used if you
wish to add unbonded atoms via the <A HREF = "create_atoms.html">create atoms</A>
command, e.g. for a percolation simulation.
"extra bond per atom" parameter must be set to allow for it. Ditto
for "extra angle per atom", "extra dihedral per atom", and "extra
improper per atom" if angles, dihedrals, or impropers are being added
when bonds are created. See the <A HREF = "read_data.html">read_data</A> or
<A HREF = "create_box.html">create_box</A> command for more details. Note that a
data file with no atoms can be used if you wish to add unbonded atoms
via the <A HREF = "create_atoms.html">create atoms</A> command, e.g. for a
percolation simulation.
</P>
<P>IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a
list of 1st, 2nd, and 3rd neighbors of each atom (within the bond
@ -143,9 +170,14 @@ specified for the new types.
<P>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.
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
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
<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.
@ -157,7 +189,7 @@ 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.
resulting from created bonds (and angles, dihedrals, impropers).
</P>
<HR>
@ -187,22 +219,6 @@ 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 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 <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 creation of a new bond.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_bond_break.html">fix bond/break</A>, <A HREF = "fix_bond_swap.html">fix

92
doc/fix_bond_create.txt
View File

@ -19,7 +19,7 @@ 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
keyword = {iparam} or {jparam} or {prob} or {atype} or {dtype} or {itype} :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
@ -28,13 +28,20 @@ keyword = {iparam} or {jparam} or {prob} :l
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
seed = random number seed (positive integer)
{atype} value = angletype
angletype = type of created angles
{dtype} value = dihedraltype
dihedraltype = type of created dihedrals
{itype} value = impropertype
impropertype = type of created impropers :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
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2 :pre
[Description:]
@ -43,11 +50,16 @@ 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.
it will be permanently in place. Optionally, the creation of a bond
can also create angle, dihedral, and improper interactions that bond
is part of. See the discussion of the {atype}, {dtype}, and {itype}
keywords below.
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 new bonds is performed every {Nevery} timesteps.
If two atoms I,J are within a distance {Rmin} of each other, if I is
@ -94,22 +106,37 @@ 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.
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
new 3-body (angle) or 4-body (dihedral, improper) interactions, you
can choose to create new angles, dihedrals, impropers as well, using
the {atype}, {dtype}, and {itype} keywords. All of these changes
typically affect pairwise interactions between atoms that are now part
of new bonds, angles, etc.
If the {atype} keyword is used and if an angle potential is defined
via the "angle_style"_angle.html command, then any new 3-body
interactions inferred by the creation of a bond will create new angles
of type {angletype}, with parameters assigned by the corresponding
"angle_coeff"_angle_coeff.html command. Likewise, the {dtype} and
{itype} keywords will create new dihedrals and impropers of type
{dihedraltype} and {impropertype}.
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 bond per atom" parameter must be set to allow for it. See the
"read_data"_read_data.html or "create_box"_create_box.html command for
more details. Note that 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.
"extra bond per atom" parameter must be set to allow for it. Ditto
for "extra angle per atom", "extra dihedral per atom", and "extra
improper per atom" if angles, dihedrals, or impropers are being added
when bonds are created. See the "read_data"_read_data.html or
"create_box"_create_box.html command for more details. Note that 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 (within the bond
@ -131,9 +158,14 @@ 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.
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
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
"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.
@ -145,7 +177,7 @@ 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.
resulting from created bonds (and angles, dihedrals, impropers).
:line
@ -175,22 +207,6 @@ 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 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 *,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 creation of a new bond.
[Related commands:]
"fix bond/break"_fix_bond_break.html, "fix