Commit ee50fd70 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1810 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent e021fcc4

doc/JPG/bondswap.jpg

0 → 100644
+10.3 KiB
Loading image diff...

doc/Section_commands.txt

+1 −0
Original line number Diff line number Diff line
@@ -380,6 +380,7 @@ of each style or click on the style itself for a full description: 
"ave/atom"_fix_ave_atom.html,

"ave/spatial"_fix_ave_spatial.html,

"ave/time"_fix_ave_time.html,

"bond/swap"_fix_bond_swap.html,

"com"_fix_com.html,

"coord/original"_fix_coord_original.html,

"deform"_fix_deform.html,

doc/fix.txt

+1 −0
Original line number Diff line number Diff line
@@ -105,6 +105,7 @@ list of fix styles available in LAMMPS: 
"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities

"ave/spatial"_fix_ave_spatial.html - output per-atom quantities by layer

"ave/time"_fix_ave_time.html - output time-averaged compute quantities

"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping

"com"_fix_com.html - compute a center-of-mass

"coord/original"_fix_coord_original.html - store original coords of each atom

"deform"_fix_deform.html - change the simulation box size/shape

doc/fix_bond_swap.html

0 → 100644
+182 −0
Original line number Diff line number Diff line 
<HTML>

<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> 

</CENTER>













<HR>



<H3>fix bond/swap command 

</H3>

<P><B>Syntax:</B>

</P>

<PRE>fix ID group-ID bond/swap fraction cutoff seed 

</PRE>

<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command

<LI>bond/swap = style name of this fix command

<LI>fraction = fraction of group atoms to consider for swapping

<LI>cutoff = distance at which swapping will be considered (distance units)

<LI>seed = random # seed (positive integer) 

</UL>

<P><B>Examples:</B>

</P>

<PRE>fix 1 all bond/swap 0.5 1.5 598934 

</PRE>

<P><B>Description:</B>

</P>

<P>In a simulation of polymer chains, this command attempts to swap bonds

between two different chains, effectively grafting the end of one

chain onto another chain and vice versa.  This is done via Monte Carlo

rules using the Boltzmann acceptance criterion.  The purpose is to

lower the energy of the system more rapidly than dynamics alone would

do it, by enabling instantaneous large conformational changes in a

dense polymer melt.  It is designed for use with systems of

<A HREF = "bond_fene.html">FENE</A> bead-spring polymer chains where each polymer is

a linear chain of monomers, but LAMMPS does not enforce this

requirement.

</P>

<P>A schematic of the kinds of bond swaps that can occur is shown here:

</P>

<CENTER><IMG SRC = "JPG/bondswap.jpg">

</CENTER>

<P>On the left, the red and blue chains have two monomers A1 and B1 close

to each other, which are currently bonded to monomers A2 and B2

respectively within their own chains.  The bond swap operation will

attempt to delete the A1-A2 and B1-B2 bonds and replace them with

A1-B2 and B1-A2 bonds.  If the swap is energetically favorable, the

two chains on the right are the result and each polymer chain has

undergone a dramatic conformational change.  This reference provides

more details on how the algorithm works and its application:

<A HREF = "#Sides">(Sides)</A>.

</P>

<P>The bond swapping operation is invoked each time neighbor lists are

built during a simulation, since it potentially alters the list of

which neighbors are considered for pairwise interaction.  At each

reneighboring step, each processor considers a random specified

<I>fraction</I> of its atoms as potential swapping monomers for this

timestep.  Choosing a small <I>fraction</I> value can reduce the likelihood

of a reverse swap occurring soon after an initial swap.

</P>

<P>For each monomer A1, its neighbors are examined to find a possible B1

monomer.  Both A1 and B1 must be in the fix group, their separation

must be less than the specified <I>cutoff</I>, and the molecule IDs of A1

and B1 must be the same (see below).  If a suitable partner is found,

the energy change due to swapping the 2 bonds is computed.  This

includes changes in pairwise, bond, and angle energies due to the

altered connectivity of the 2 chains.  Dihedral and improper

interactions are not allowed to be defined when this fix is used.

</P>

<P>If the energy decreases due to the swap operation, the bond swap is

accepted.  If the energy increases it is accepted with probability

exp(-delta/kT) where delta is the increase in energy, k is the

Boltzmann constant, and T is the current temperature of the system.

Whether the swap is accepted or rejected, no other swaps are attempted

by this processor on this timestep.

</P>

<P>The criterion for matching molecule IDs is how bond swaps performed by

this fix conserve chain length.  To use this features you must setup

the molecule IDs for your polymer chains in a certain way, typically

in the data file, read by the <A HREF = "read_data.html">read_data</A> comand.

Consider a system of 6-mer chains.  You have 3 choices.  If the

molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then

swaps will conserve length.  For a particular momoner there will be

only one other monomer on another chain which is a potential swap

partner.  If the molecule IDs for monomers on each chain are set to

1,2,3,3,2,1 then swaps will conserve length but swaps will be able to

occur at either end of a chain.  Thus for a particular monomer there

will be 2 possible swap partners on another chain.  In this scenario,

swaps can also occur within a single chain, i.e. the two ends of a

chain swap with each other.  The third choice is to give all monomers

on all chains the same molecule ID, e.g. 0.  This will allow a wide

variety of swaps to occur, but will NOT conserve chain lengths.

</P>

<P>IMPORTANT NOTE: If your simulation uses molecule IDs in the usual way,

where all monomers on a single chain are assigned the same ID

(different for each chain), then swaps will only occur within the same

chain and will NOT conserve chain length.  This is probably not what

you want for this fix.

</P>

<HR>



<P>This fix computes a temperature each time it is invoked for use by the

Boltzmann criterion.  To do this, the fix creates its own compute of

style <I>temp</I>, as if this command had been issued:

</P>

<PRE>compute fix-ID_temp all temp 

</PRE>

<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details.  Note

that the ID of the new compute is the fix-ID with underscore + "temp"

appended and the group for the new compute is "all", so that the

temperature of the entire system is used.

</P>

<P>Note that this is NOT the compute used by thermodynamic output (see

the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.

This means you can change the attributes of this fix's temperature

(e.g. its degrees-of-freedom) via the

<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature

during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style

custom</A> command using the appropriate compute-ID.

It also means that changing attributes of <I>thermo_temp</I> will have no

effect on this fix.

</P>

<HR>



<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>

</P>

<P>No information about this fix is written to <A HREF = "restart.html">binary restart

files</A>.  Because the state of the random number generator

is not saved in restart files, this means you cannot do "exact"

restarts with this fix, where the simulation continues on the same as

if no restart had taken place.  However, in a statistical sense, a

restarted simulation should produce the same behavior.  Also note that

each processor generates possible swaps independently of other

processors.  Thus if you repeat the same simulation on a different number

of processors, the specific swaps performed will be different.

</P>

<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this

fix.  You can use it to assign a <A HREF = "compute.html">compute</A> you have

defined to this fix which will be used to compute the temperature for

the Boltzmann criterion.

</P>

<P>This fix computes two statistical quantities as a 2-vector of output,

which can be accessed by various <A HREF = "Section_howto.html#4_15">output

commands</A>.  The first component of the vector

is the cummulative number of swaps performed by all processors.  The

second component of the vector is the cummulative number of swaps

attempted (whether accepted or rejected).  Note that a swap "attempt"

only occurs when swap partners meeting the criteria described above

are found on a particular timestep.  The vector values calculated by

this fix are "extensive", meaning they scale with the number of atoms

in the simulation.

</P>

<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of

the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy

minimization</A>.

</P>

<P><B>Restrictions:</B>

</P>

<P>The setings of the "special_bond" command must be 0,1,1 in order to

use this fix, which is typical of FENE bead-spring chains.

I.e. pairwise interactions between bonded atoms are turned off, but

are turned on between atoms two or three hops away along the chain

backbone.

</P>

<P>Currently, energy changes in dihedral and improper interactions due to

a bond swap are not considered.  Thus a simulation that uses this fix

cannot use a dihedral or improper potential.

</P>

<P><B>Related commands:</B> none

</P>

<P><B>Default:</B> none

</P>

<HR>



<A NAME = "Sides"></A>



<P><B>(Sides)</B> Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42,

199-208 (2004).

</P>

</HTML>

doc/fix_bond_swap.txt

0 → 100755
+176 −0
Original line number Diff line number Diff line 
"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/swap command :h3



[Syntax:]



fix ID group-ID bond/swap fraction cutoff seed :pre



ID, group-ID are documented in "fix"_fix.html command

bond/swap = style name of this fix command

fraction = fraction of group atoms to consider for swapping

cutoff = distance at which swapping will be considered (distance units)

seed = random # seed (positive integer) :ul



[Examples:]



fix 1 all bond/swap 0.5 1.5 598934 :pre



[Description:]



In a simulation of polymer chains, this command attempts to swap bonds

between two different chains, effectively grafting the end of one

chain onto another chain and vice versa.  This is done via Monte Carlo

rules using the Boltzmann acceptance criterion.  The purpose is to

lower the energy of the system more rapidly than dynamics alone would

do it, by enabling instantaneous large conformational changes in a

dense polymer melt.  It is designed for use with systems of

"FENE"_bond_fene.html bead-spring polymer chains where each polymer is

a linear chain of monomers, but LAMMPS does not enforce this

requirement.



A schematic of the kinds of bond swaps that can occur is shown here:



:c,image(JPG/bondswap.jpg)



On the left, the red and blue chains have two monomers A1 and B1 close

to each other, which are currently bonded to monomers A2 and B2

respectively within their own chains.  The bond swap operation will

attempt to delete the A1-A2 and B1-B2 bonds and replace them with

A1-B2 and B1-A2 bonds.  If the swap is energetically favorable, the

two chains on the right are the result and each polymer chain has

undergone a dramatic conformational change.  This reference provides

more details on how the algorithm works and its application:

"(Sides)"_#Sides.



The bond swapping operation is invoked each time neighbor lists are

built during a simulation, since it potentially alters the list of

which neighbors are considered for pairwise interaction.  At each

reneighboring step, each processor considers a random specified

{fraction} of its atoms as potential swapping monomers for this

timestep.  Choosing a small {fraction} value can reduce the likelihood

of a reverse swap occurring soon after an initial swap.



For each monomer A1, its neighbors are examined to find a possible B1

monomer.  Both A1 and B1 must be in the fix group, their separation

must be less than the specified {cutoff}, and the molecule IDs of A1

and B1 must be the same (see below).  If a suitable partner is found,

the energy change due to swapping the 2 bonds is computed.  This

includes changes in pairwise, bond, and angle energies due to the

altered connectivity of the 2 chains.  Dihedral and improper

interactions are not allowed to be defined when this fix is used.



If the energy decreases due to the swap operation, the bond swap is

accepted.  If the energy increases it is accepted with probability

exp(-delta/kT) where delta is the increase in energy, k is the

Boltzmann constant, and T is the current temperature of the system.

Whether the swap is accepted or rejected, no other swaps are attempted

by this processor on this timestep.



The criterion for matching molecule IDs is how bond swaps performed by

this fix conserve chain length.  To use this features you must setup

the molecule IDs for your polymer chains in a certain way, typically

in the data file, read by the "read_data"_read_data.html comand.

Consider a system of 6-mer chains.  You have 3 choices.  If the

molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then

swaps will conserve length.  For a particular momoner there will be

only one other monomer on another chain which is a potential swap

partner.  If the molecule IDs for monomers on each chain are set to

1,2,3,3,2,1 then swaps will conserve length but swaps will be able to

occur at either end of a chain.  Thus for a particular monomer there

will be 2 possible swap partners on another chain.  In this scenario,

swaps can also occur within a single chain, i.e. the two ends of a

chain swap with each other.  The third choice is to give all monomers

on all chains the same molecule ID, e.g. 0.  This will allow a wide

variety of swaps to occur, but will NOT conserve chain lengths.



IMPORTANT NOTE: If your simulation uses molecule IDs in the usual way,

where all monomers on a single chain are assigned the same ID

(different for each chain), then swaps will only occur within the same

chain and will NOT conserve chain length.  This is probably not what

you want for this fix.



:line



This fix computes a temperature each time it is invoked for use by the

Boltzmann criterion.  To do this, the fix creates its own compute of

style {temp}, as if this command had been issued:



compute fix-ID_temp all temp :pre



See the "compute temp"_compute_temp.html command for details.  Note

that the ID of the new compute is the fix-ID with underscore + "temp"

appended and the group for the new compute is "all", so that the

temperature of the entire system is used.



Note that this is NOT the compute used by thermodynamic output (see

the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.

This means you can change the attributes of this fix's temperature

(e.g. its degrees-of-freedom) via the

"compute_modify"_compute_modify.html command or print this temperature

during thermodyanmic output via the "thermo_style

custom"_thermo_style.html command using the appropriate compute-ID.

It also means that changing attributes of {thermo_temp} will have no

effect on this fix.



:line



[Restart, fix_modify, thermo output, run start/stop, minimize info:]



No information about this fix is written to "binary restart

files"_restart.html.  Because the state of the random number generator

is not saved in restart files, this means you cannot do "exact"

restarts with this fix, where the simulation continues on the same as

if no restart had taken place.  However, in a statistical sense, a

restarted simulation should produce the same behavior.  Also note that

each processor generates possible swaps independently of other

processors.  Thus if you repeat the same simulation on a different number

of processors, the specific swaps performed will be different.



The "fix_modify"_fix_modify.html {temp} option is supported by this

fix.  You can use it to assign a "compute"_compute.html you have

defined to this fix which will be used to compute the temperature for

the Boltzmann criterion.



This fix computes two statistical quantities as a 2-vector of output,

which can be accessed by various "output

commands"_Section_howto.html#4_15.  The first component of the vector

is the cummulative number of swaps performed by all processors.  The

second component of the vector is the cummulative number of swaps

attempted (whether accepted or rejected).  Note that a swap "attempt"

only occurs when swap partners meeting the criteria described above

are found on a particular timestep.  The vector values calculated by

this fix are "extensive", meaning they scale with the number of atoms

in the simulation.



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:]



The setings of the "special_bond" command must be 0,1,1 in order to

use this fix, which is typical of FENE bead-spring chains.

I.e. pairwise interactions between bonded atoms are turned off, but

are turned on between atoms two or three hops away along the chain

backbone.



Currently, energy changes in dihedral and improper interactions due to

a bond swap are not considered.  Thus a simulation that uses this fix

cannot use a dihedral or improper potential.



[Related commands:] none



[Default:] none



:line



:link(Sides)

[(Sides)] Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42,

199-208 (2004).

CRA Git | Maintained and supported by SUSTech CRA and CCSE