git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12881 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
177
doc/fix_atom_swap.html
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177
doc/fix_atom_swap.html
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<HTML>
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<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>
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</CENTER>
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<HR>
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<H3>fix atom/swap command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID atom/swap N X type_1 type_2 seed T keyword values ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>atom/swap = style name of this fix command
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<LI>N = invoke this fix every N steps
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<LI>X = number of swaps to attempt every N steps
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<LI>type_1 = first atom type to swap
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<LI>type_2 = second atom type to swap
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<LI>seed = random # seed (positive integer)
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<LI>T = scaling temperature of the MC swaps (temperature units)
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<LI>zero or more keyword/value pairs may be appended to args
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<LI>keyword = <I>region</I>
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<PRE> <I>region</I> value = region-ID
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region-ID = ID of region to use as a swap volume
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 2 all atom/swap 1 1 1 2 29494 300.0
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fix atom_swap_fix all atom/swap 100 1 5 6 12345 298.0 region my_swap_region
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This fix performs Monte Carlo swaps of atoms of one type with atoms of
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a second type. The specified temperature <I>T</I> is used to scale the
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energy in the criterion for accepting or rejecting each swap. The fix
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is invoked once every <I>N</I> steps. Each time the fix is invoked <I>X</I>
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swap attempts are made, one after the other, bewteen pairs of randomly
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selected atoms. Two attributes of the atoms in the pair are swapped:
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the atom type and the atom charge (if defined). Each attempted swap
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is accepted or rejected based on the Metropolis criterion using the
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Boltzmann factor exp(-Edelta / kT), where Edelta is the change in the
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system potential energy due to the swap, k is the Boltzmann constant,
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and <I>T</I> is the specified temperature.
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</P>
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<P>In addition to the MC swaps, atoms in the simulation domain will move
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via normal dynamic timestepping if a time integration fix is defined,
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e.g. <A HREF = "fix_nvt.html">fix_nvt</A>, which will result in a hybrid MC+MD
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simulation. If a swap produces a poorly equilibrated system, a
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smaller-than-usual timestep size may be needed when running such a
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simulation.
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</P>
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<P>If the <I>region</I> keyword is not used, all atoms of <I>type_1</I> and
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<I>type_2</I> which are in the specified group are candidates for swapping.
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If the <I>region</I> keyword is used, swappable atoms must also be in the
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specified region. Each time a swap is performed one random atom is
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chosen from the list of candidate <I>type_1</I> atoms, and one random atom
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from the list of candidate <I>type_2</I> atoms. A pair of swapped atoms
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can thus be far apart geometrically. If multiple swaps are attempted
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in the same timestep, an individual atom may be swapped multiple
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times.
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</P>
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<P>An additional requirement for charged systems is that all swappable
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atoms of <I>type_1</I> must have the same charge, and likewise for <I>type_2</I>.
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Atoms of <I>type_1</I> need not have the same charge as atoms of <I>type_2</I>.
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</P>
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<P>Note that this fix computes total potential energies before and after
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attempted swaps, so even systems with complicated potential energy
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calculations can be used, including the following:
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</P>
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<UL><LI>long-range electrostatics (KSpace)
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<LI>many-body pair styles
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<LI>hybrid pair styles
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<LI>EAM pair styles
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<LI>triclinic systems
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</UL>
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<P>Some fixes have an associated potential energy. Currently, the
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potential energy contribution due to these fixes is not included in
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the Metropolis criterion dictating atom swap probabilities. Examples
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of such fixes include: <A HREF = "fix_efield.html">efield</A>,
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<A HREF = "fix_gravity.html">gravity</A>, <A HREF = "fix_addforce.html">addforce</A>,
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<A HREF = "fix_restrain.html">restrain</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
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</P>
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<P>IMPORTANT NOTE: During the swaps performed within a single timestep,
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this fix performs minimal communication to update the state of the
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system. If the cutoff distance for all type pairs, as defined by the
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<A HREF = "pair_style.html">pair_style</A> is the same, the neighbor list does not
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need to be rebuilt when a swap takes place. The CPU cost per swap
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will then be equivalent to roughly a single MD timestep. If the
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cutoff distances are not the same for all type pairs, then the
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neighbor list will be rebuilt, and the CPU cost per swap will be
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higher.
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</P>
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<HR>
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<P>IMPORTANT NOTE: If you only wish to use this fix to relax a system
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without dynamics, e.g. to model surface segregation in an alloy, then
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you do not need to define a time integration fix. In this scenario an
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MC-only simulation can be run in a single timestep or multiple
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timesteps as follows:
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</P>
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<PRE>fix mc all atom/swap 1 100000 ...
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run 1
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</PRE>
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<P>or
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</P>
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<PRE>fix mc all atom/swap 1 1000 ...
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run 100
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</PRE>
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<P>In the first case, 100000 swaps are attempted in the first (only)
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timestep. A neighbor list will only be built once, which is
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sufficient since atoms are not moving.
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</P>
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<P>In the second case, the same 100000 swaps are spread across 100
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timesteps. This will require 100 neighbor list builds (once each time
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the fix is invoked, which should still be relatively cheap), but also
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|
allows you to monitor or analyze various quantities such as the
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evolution of the system energy as a function of timestep, as if the
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system were evolving over time.
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>This fix writes the state of the fix to <A HREF = "restart.html">binary restart
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files</A>. This includes information about the random
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number generator seed, the next timestep for MC exchanges, etc. See
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the <A HREF = "read_restart.html">read_restart</A> command for info on how to
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re-specify a fix in an input script that reads a restart file, so that
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the operation of the fix continues in an uninterrupted fashion.
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</P>
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<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
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fix.
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</P>
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<P>This fix computes a global vector of length 2, which can be accessed
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by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
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values are the following global cumulative quantities:
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</P>
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<UL><LI>1 = swap attempts
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<LI>2 = swap successes
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</UL>
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<P>The vector values calculated by this fix are "extensive".
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This fix is part of the MC package. It is only enabled if LAMMPS was
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built with that package. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_bond_swap.html">fix bond/swap</A>, <A HREF = "fix_nvt.html">fix_nvt</A>,
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<A HREF = "neighbor.html">neighbor</A>, <A HREF = "fix_deposit.html">fix_deposit</A>,
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<A HREF = "fix_evaporate.html">fix_evaporate</A>, <A HREF = "delete_atoms.html">delete_atoms</A>,
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<A HREF = "fix_gcmc.html">fix_gcmc</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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161
doc/fix_atom_swap.txt
Normal file
161
doc/fix_atom_swap.txt
Normal file
@ -0,0 +1,161 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix atom/swap command :h3
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[Syntax:]
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fix ID group-ID atom/swap N X type_1 type_2 seed T keyword values ... :pre
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|
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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|
atom/swap = style name of this fix command :l
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|
N = invoke this fix every N steps :l
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|
X = number of swaps to attempt every N steps :l
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type_1 = first atom type to swap :l
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type_2 = second atom type to swap :l
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seed = random # seed (positive integer) :l
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T = scaling temperature of the MC swaps (temperature units) :l
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zero or more keyword/value pairs may be appended to args :l
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keyword = {region} :l
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{region} value = region-ID
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|
region-ID = ID of region to use as a swap volume :pre
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|
:ule
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|
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|
[Examples:]
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|
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||||||
|
fix 2 all atom/swap 1 1 1 2 29494 300.0
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||||||
|
fix atom_swap_fix all atom/swap 100 1 5 6 12345 298.0 region my_swap_region :pre
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||||||
|
|
||||||
|
[Description:]
|
||||||
|
|
||||||
|
This fix performs Monte Carlo swaps of atoms of one type with atoms of
|
||||||
|
a second type. The specified temperature {T} is used to scale the
|
||||||
|
energy in the criterion for accepting or rejecting each swap. The fix
|
||||||
|
is invoked once every {N} steps. Each time the fix is invoked {X}
|
||||||
|
swap attempts are made, one after the other, bewteen pairs of randomly
|
||||||
|
selected atoms. Two attributes of the atoms in the pair are swapped:
|
||||||
|
the atom type and the atom charge (if defined). Each attempted swap
|
||||||
|
is accepted or rejected based on the Metropolis criterion using the
|
||||||
|
Boltzmann factor exp(-Edelta / kT), where Edelta is the change in the
|
||||||
|
system potential energy due to the swap, k is the Boltzmann constant,
|
||||||
|
and {T} is the specified temperature.
|
||||||
|
|
||||||
|
In addition to the MC swaps, atoms in the simulation domain will move
|
||||||
|
via normal dynamic timestepping if a time integration fix is defined,
|
||||||
|
e.g. "fix_nvt"_fix_nvt.html, which will result in a hybrid MC+MD
|
||||||
|
simulation. If a swap produces a poorly equilibrated system, a
|
||||||
|
smaller-than-usual timestep size may be needed when running such a
|
||||||
|
simulation.
|
||||||
|
|
||||||
|
If the {region} keyword is not used, all atoms of {type_1} and
|
||||||
|
{type_2} which are in the specified group are candidates for swapping.
|
||||||
|
If the {region} keyword is used, swappable atoms must also be in the
|
||||||
|
specified region. Each time a swap is performed one random atom is
|
||||||
|
chosen from the list of candidate {type_1} atoms, and one random atom
|
||||||
|
from the list of candidate {type_2} atoms. A pair of swapped atoms
|
||||||
|
can thus be far apart geometrically. If multiple swaps are attempted
|
||||||
|
in the same timestep, an individual atom may be swapped multiple
|
||||||
|
times.
|
||||||
|
|
||||||
|
An additional requirement for charged systems is that all swappable
|
||||||
|
atoms of {type_1} must have the same charge, and likewise for {type_2}.
|
||||||
|
Atoms of {type_1} need not have the same charge as atoms of {type_2}.
|
||||||
|
|
||||||
|
Note that this fix computes total potential energies before and after
|
||||||
|
attempted swaps, so even systems with complicated potential energy
|
||||||
|
calculations can be used, including the following:
|
||||||
|
|
||||||
|
long-range electrostatics (KSpace)
|
||||||
|
many-body pair styles
|
||||||
|
hybrid pair styles
|
||||||
|
EAM pair styles
|
||||||
|
triclinic systems :ul
|
||||||
|
|
||||||
|
Some fixes have an associated potential energy. Currently, the
|
||||||
|
potential energy contribution due to these fixes is not included in
|
||||||
|
the Metropolis criterion dictating atom swap probabilities. Examples
|
||||||
|
of such fixes include: "efield"_fix_efield.html,
|
||||||
|
"gravity"_fix_gravity.html, "addforce"_fix_addforce.html,
|
||||||
|
"restrain"_fix_restrain.html, and "wall fixes"_fix_wall.html.
|
||||||
|
|
||||||
|
IMPORTANT NOTE: During the swaps performed within a single timestep,
|
||||||
|
this fix performs minimal communication to update the state of the
|
||||||
|
system. If the cutoff distance for all type pairs, as defined by the
|
||||||
|
"pair_style"_pair_style.html is the same, the neighbor list does not
|
||||||
|
need to be rebuilt when a swap takes place. The CPU cost per swap
|
||||||
|
will then be equivalent to roughly a single MD timestep. If the
|
||||||
|
cutoff distances are not the same for all type pairs, then the
|
||||||
|
neighbor list will be rebuilt, and the CPU cost per swap will be
|
||||||
|
higher.
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
IMPORTANT NOTE: If you only wish to use this fix to relax a system
|
||||||
|
without dynamics, e.g. to model surface segregation in an alloy, then
|
||||||
|
you do not need to define a time integration fix. In this scenario an
|
||||||
|
MC-only simulation can be run in a single timestep or multiple
|
||||||
|
timesteps as follows:
|
||||||
|
|
||||||
|
fix mc all atom/swap 1 100000 ...
|
||||||
|
run 1 :pre
|
||||||
|
|
||||||
|
or
|
||||||
|
|
||||||
|
fix mc all atom/swap 1 1000 ...
|
||||||
|
run 100 :pre
|
||||||
|
|
||||||
|
In the first case, 100000 swaps are attempted in the first (only)
|
||||||
|
timestep. A neighbor list will only be built once, which is
|
||||||
|
sufficient since atoms are not moving.
|
||||||
|
|
||||||
|
In the second case, the same 100000 swaps are spread across 100
|
||||||
|
timesteps. This will require 100 neighbor list builds (once each time
|
||||||
|
the fix is invoked, which should still be relatively cheap), but also
|
||||||
|
allows you to monitor or analyze various quantities such as the
|
||||||
|
evolution of the system energy as a function of timestep, as if the
|
||||||
|
system were evolving over time.
|
||||||
|
|
||||||
|
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||||
|
|
||||||
|
This fix writes the state of the fix to "binary restart
|
||||||
|
files"_restart.html. This includes information about the random
|
||||||
|
number generator seed, the next timestep for MC exchanges, etc. See
|
||||||
|
the "read_restart"_read_restart.html command for info on how to
|
||||||
|
re-specify a fix in an input script that reads a restart file, so that
|
||||||
|
the operation of the fix continues in an uninterrupted fashion.
|
||||||
|
|
||||||
|
None of the "fix_modify"_fix_modify.html options are relevant to this
|
||||||
|
fix.
|
||||||
|
|
||||||
|
This fix computes a global vector of length 2, which can be accessed
|
||||||
|
by various "output commands"_Section_howto.html#howto_15. The vector
|
||||||
|
values are the following global cumulative quantities:
|
||||||
|
|
||||||
|
1 = swap attempts
|
||||||
|
2 = swap successes :ul
|
||||||
|
|
||||||
|
The vector values calculated by this fix are "extensive".
|
||||||
|
|
||||||
|
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:]
|
||||||
|
|
||||||
|
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.
|
||||||
|
|
||||||
|
[Related commands:]
|
||||||
|
|
||||||
|
"fix bond/swap"_fix_bond_swap.html, "fix_nvt"_fix_nvt.html,
|
||||||
|
"neighbor"_neighbor.html, "fix_deposit"_fix_deposit.html,
|
||||||
|
"fix_evaporate"_fix_evaporate.html, "delete_atoms"_delete_atoms.html,
|
||||||
|
"fix_gcmc"_fix_gcmc.html
|
||||||
|
|
||||||
|
[Default:] none
|
||||||
Reference in New Issue
Block a user