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Fixed triclinic bug in gcmc and qtype bug atom/swap

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14039 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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athomps
2015-09-11 23:08:52 +00:00
parent 886e170098
commit 0da2e1782b
2 changed files with 24 additions and 22 deletions
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23
doc/fix_atom_swap.html
View File

@ -29,10 +29,10 @@
<LI>one or more keyword/value pairs may be appended to args
<LI>keyword = <I>types</I> or <I>delta_mu</I> or <I>ke</I> or <I>semi-grand</I> or <I>region</I>
<LI>keyword = <I>types</I> or <I>mu</I> or <I>ke</I> or <I>semi-grand</I> or <I>region</I>
<PRE> <I>types</I> values = two or more atom types
<I>delta_mu</I> values = chemical potential of swap types (energy units)
<I>mu</I> values = chemical potential of swap types (energy units)
<I>ke</I> value = <I>no</I> or <I>yes</I>
<I>no</I> = no conservation of kinetic energy after atom swaps
<I>yes</I> = kinetic energy is conserved after atom swaps
@ -48,7 +48,7 @@
</P>
<PRE>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 delta_mu 4.3 -5.0
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 4.3 -5.0
</PRE>
<P><B>Description:</B>
</P>
@ -94,13 +94,14 @@ conversion. An attempt is made to switch
the selected atom (if eligible) to one of the other listed types
with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
</P>
<P>The <I>delta_mu</I> keyword allows users to specify non-zero chemical
potentials for each of the atom types. All chemical potentials are
absolute, so there should be one for each swap type listed following
the <I>types</I> keyword.
These parameters are required for semi-grand canonical
ensemble simulations where it may be desirable to actively control the
composition of the system.
<P>The <I>mu</I> keyword allows users to specify chemical
potentials. This is required and allowed only when using <I>semi-grand</I>.
All chemical potentials are absolute, so there is one for
each swap type listed following the <I>types</I> keyword.
In semi-grand canonical ensemble simulations the chemical composition
of the system is controlled by the difference in these values. So
shifting all values by a constant amount will have no effect
on the simulation.
</P>
<P>This command may optionally use the <I>region</I> keyword to define swap
volume. The specified region must have been previously defined with a
@ -187,7 +188,7 @@ LAMMPS</A> section for more info.
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are ke = yes, semi-grand = no, delta_mu = 0.0 for
<P>The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
all atom types.
</P>
<HR>

23
doc/fix_atom_swap.txt
View File

@ -19,9 +19,9 @@ X = number of swaps to attempt every N steps :l
seed = random # seed (positive integer) :l
T = scaling temperature of the MC swaps (temperature units) :l
one or more keyword/value pairs may be appended to args :l
keyword = {types} or {delta_mu} or {ke} or {semi-grand} or {region} :l
keyword = {types} or {mu} or {ke} or {semi-grand} or {region} :l
{types} values = two or more atom types
{delta_mu} values = chemical potential of swap types (energy units)
{mu} values = chemical potential of swap types (energy units)
{ke} value = {no} or {yes}
{no} = no conservation of kinetic energy after atom swaps
{yes} = kinetic energy is conserved after atom swaps
@ -36,7 +36,7 @@ keyword = {types} or {delta_mu} or {ke} or {semi-grand} or {region} :l
fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 delta_mu 4.3 -5.0 :pre
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 4.3 -5.0 :pre
[Description:]
@ -82,13 +82,14 @@ conversion. An attempt is made to switch
the selected atom (if eligible) to one of the other listed types
with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
The {delta_mu} keyword allows users to specify non-zero chemical
potentials for each of the atom types. All chemical potentials are
absolute, so there should be one for each swap type listed following
the {types} keyword.
These parameters are required for semi-grand canonical
ensemble simulations where it may be desirable to actively control the
composition of the system.
The {mu} keyword allows users to specify chemical
potentials. This is required and allowed only when using {semi-grand}.
All chemical potentials are absolute, so there is one for
each swap type listed following the {types} keyword.
In semi-grand canonical ensemble simulations the chemical composition
of the system is controlled by the difference in these values. So
shifting all values by a constant amount will have no effect
on the simulation.
This command may optionally use the {region} keyword to define swap
volume. The specified region must have been previously defined with a
@ -175,7 +176,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Default:]
The option defaults are ke = yes, semi-grand = no, delta_mu = 0.0 for
The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
all atom types.
:line