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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12160 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2014-06-27 23:45:33 +00:00
parent c8bbcb34de
commit 0c68c7f328
2 changed files with 86 additions and 50 deletions
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68
doc/fix_gcmc.html
View File

@ -25,7 +25,7 @@
<LI>M = number of MC displacements to attempt every N steps
<LI>type = atom type or molecule ID of exchanged gas
<LI>type = atom type to assign to inserted atoms (offset for molecule insertion)
<LI>seed = random # seed (positive integer)
@ -37,9 +37,12 @@
<LI>zero or more keyword/value pairs may be appended to args
<LI>keyword = <I>molecule</I>, <I>region</I>, <I>maxangle</I>, <I>pressure</I>, or <I>fugacity_coeff</I>
<LI>keyword = <I>mol</I>, <I>region</I>, <I>maxangle</I>, <I>pressure</I>, or <I>fugacity_coeff</I>
<PRE> <I>molecule</I> value = <I>no</I> or <I>yes</I>
<PRE> <I>mol</I> value = template-ID
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
<I>shake</I> value = fix-ID
fix-ID = ID of <A HREF = "fix_shake.html">fix shake</A> command
<I>region</I> value = region-ID
region-ID = ID of region to use as an exchange/move volume
<I>maxangle</I> value = maximum molecular rotation angle (degrees)
@ -51,7 +54,7 @@
<P><B>Examples:</B>
</P>
<PRE>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
fix 3 Kr gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes maxangle 180
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
</PRE>
<P><B>Description:</B>
@ -80,6 +83,13 @@ translations are attempted 100% of the time. For MC exchanges of either
molecular or atomic gasses, deletions and insertions are each attempted
with 50% probability.
</P>
<P>If inserted particles are individual atoms, they are assigned the
specified atom type. If they are molecules, the type of each atom in
the inserted molecule is specified in the file read by the
<A HREF = "molecule.html">molecule</A> command, and those values are added to the
specified atom type. E.g. if <I>type</I> = 2, and the file specifies atom
types 1,2,3, then the inserted molecule will have atom types 3,4,5.
</P>
<P>This fix cannot be used to perform MC insertions of gas atoms or
molecules other than the exchanged type, but MC deletions, translations,
and rotations can be performed on any atom/molecule in the fix group.
@ -120,21 +130,26 @@ coordinates for atoms in a molecule are taken from the template
molecule provided by the user. A random initial rotation is used in the
case of molecule insertions.
</P>
<P>If the setting for the <I>molecule</I> keyword is <I>no</I>, then only single
atoms are exchanged. In this case, you should ensure you do not
<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used. It
specifies a <I>template-ID</I> previously defined using the
<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
molecule. The coordinates, atom types, charges, etc, as well as any
bond/angle/etc and special neighbor information for the molecule can
be specified in the molecule file. See the <A HREF = "molecule.html">molecule</A>
command for details. The only settings required to be in this file
are the coordinates and types of atoms in the molecule.
</P>
<P>When not using the <I>mol</I> keyword, you should ensure you do not
delete only a portion of a molecule (only some of its atoms), or
LAMMPS will soon generate an error when it tries to find those atoms.
LAMMPS will warn you if any of the atoms eligible for deletion have a
non-zero molecule ID, but does not check for this at the time of
deletion.
</P>
<P>If the setting for the <I>molecule</I> keyword is <I>yes</I>, entire molecules
are exchanged. The user must supply a model molecule in the data
file to use as a template for exchanges, and that molecule's number
must be given in the fix GCMC command as the "type" of the exchanged
gas. Note that the model molecule must be present whenever the fix
is initialized. This is a limitation that will likely be remedied
in the not-to-distant future.
<P>If you wish to insert molecules via the <I>mol</I> keyword, that will have
their bonds or angles constrained via SHAKE, use the <I>shake</I> keyword,
specifying as its value the ID of a separate <A HREF = "fix_shake.html">fix
shake</A> command which also appears in your input script.
</P>
<P>Optionally, users may specify the maximum rotation angle for
molecular rotations using the <I>maxangle</I> keyword and specifying
@ -158,18 +173,20 @@ keyword, in which case the user-specified chemical potential is
ignored. For non-ideal gas reservoirs, the user may also specify the
fugacity coefficient using the <I>fugacity_coeff</I> keyword.
</P>
<P>Use of this fix typically will cause the number of atoms to fluctuate,
therefore, you will want to use the
<A HREF = "compute_modify.html">compute_modify</A> command to insure that the
current number of atoms is used as a normalizing factor each time
temperature is computed. Here is the necessary command:
</P>
<PRE>compute_modify thermo_temp dynamic yes
</PRE>
<P>If LJ units are used, note that a value of 0.18292026 is used by this
fix as the reduced value for Planck's constant. This value was
derived from LJ paramters for argon, where h* = h/sqrt(sigma^2 *
epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
mass = 39.948 amu.
</P>
<P>IMPORTANT NOTE: If you are monitoring the temperature of a system
where the particle count is changing due to adding/deleting particles,
you typically should use the <A HREF = "compute_modify.html">compute_modify dynamic
yes</A> command for the temperature compute you are
using.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the deposition to <A HREF = "restart.html">binary restart
@ -230,11 +247,12 @@ trigger an error, so it is better to run multiple shorter-duration
simulations. Likewise, very large molecules have not been tested
and may turn out to be problematic.
</P>
<P>Use of multiple fix gcmc commands in the same input using a template
molecule are not supported. There are multiple issues where the
current implmentation makes assumptions that are no longer valid
in this case. Resolving all of them require significant changes to
the implementation.
<P>Use of multiple fix gcmc commands in the same input script can be
problematic if using a template molecule. The issue is that the
user-referenced template molecule in the second fix gcmc command
may no longer exist since it might have been deleted by the first
fix gcmc command. An existing template molecule will need to be
referenced by the user for each subsequent fix gcmc command.
</P>
<P><B>Related commands:</B>
</P>
@ -244,7 +262,7 @@ the implementation.
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are molecule = no, maxangle = 10.
<P>The option defaults are mol = no, maxangle = 10.
</P>
<HR>

68
doc/fix_gcmc.txt
View File

@ -17,14 +17,17 @@ gcmc = style name of this fix command :l
N = invoke this fix every N steps :l
X = number of exchanges to attempt every N steps :l
M = number of MC displacements to attempt every N steps :l
type = atom type or molecule ID of exchanged gas :l
type = atom type to assign to inserted atoms (offset for molecule insertion) :l
seed = random # seed (positive integer) :l
T = temperature of the ideal gas reservoir (temperature units) :l
mu = chemical potential of the ideal gas reservoir (energy units) :l
displace = maximum Monte Carlo displacement distance (length units) :l
zero or more keyword/value pairs may be appended to args :l
keyword = {molecule}, {region}, {maxangle}, {pressure}, or {fugacity_coeff} :l
{molecule} value = {no} or {yes}
keyword = {mol}, {region}, {maxangle}, {pressure}, or {fugacity_coeff} :l
{mol} value = template-ID
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
{shake} value = fix-ID
fix-ID = ID of "fix shake"_fix_shake.html command
{region} value = region-ID
region-ID = ID of region to use as an exchange/move volume
{maxangle} value = maximum molecular rotation angle (degrees)
@ -35,7 +38,7 @@ keyword = {molecule}, {region}, {maxangle}, {pressure}, or {fugacity_coeff} :l
[Examples:]
fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
fix 3 Kr gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes maxangle 180
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk :pre
[Description:]
@ -64,6 +67,13 @@ translations are attempted 100% of the time. For MC exchanges of either
molecular or atomic gasses, deletions and insertions are each attempted
with 50% probability.
If inserted particles are individual atoms, they are assigned the
specified atom type. If they are molecules, the type of each atom in
the inserted molecule is specified in the file read by the
"molecule"_molecule.html command, and those values are added to the
specified atom type. E.g. if {type} = 2, and the file specifies atom
types 1,2,3, then the inserted molecule will have atom types 3,4,5.
This fix cannot be used to perform MC insertions of gas atoms or
molecules other than the exchanged type, but MC deletions, translations,
and rotations can be performed on any atom/molecule in the fix group.
@ -104,21 +114,26 @@ coordinates for atoms in a molecule are taken from the template
molecule provided by the user. A random initial rotation is used in the
case of molecule insertions.
If the setting for the {molecule} keyword is {no}, then only single
atoms are exchanged. In this case, you should ensure you do not
Individual atoms are inserted, unless the {mol} keyword is used. It
specifies a {template-ID} previously defined using the
"molecule"_molecule.html command, which reads a file that defines the
molecule. The coordinates, atom types, charges, etc, as well as any
bond/angle/etc and special neighbor information for the molecule can
be specified in the molecule file. See the "molecule"_molecule.html
command for details. The only settings required to be in this file
are the coordinates and types of atoms in the molecule.
When not using the {mol} keyword, you should ensure you do not
delete only a portion of a molecule (only some of its atoms), or
LAMMPS will soon generate an error when it tries to find those atoms.
LAMMPS will warn you if any of the atoms eligible for deletion have a
non-zero molecule ID, but does not check for this at the time of
deletion.
If the setting for the {molecule} keyword is {yes}, entire molecules
are exchanged. The user must supply a model molecule in the data
file to use as a template for exchanges, and that molecule's number
must be given in the fix GCMC command as the "type" of the exchanged
gas. Note that the model molecule must be present whenever the fix
is initialized. This is a limitation that will likely be remedied
in the not-to-distant future.
If you wish to insert molecules via the {mol} keyword, that will have
their bonds or angles constrained via SHAKE, use the {shake} keyword,
specifying as its value the ID of a separate "fix
shake"_fix_shake.html command which also appears in your input script.
Optionally, users may specify the maximum rotation angle for
molecular rotations using the {maxangle} keyword and specifying
@ -142,18 +157,20 @@ keyword, in which case the user-specified chemical potential is
ignored. For non-ideal gas reservoirs, the user may also specify the
fugacity coefficient using the {fugacity_coeff} keyword.
Use of this fix typically will cause the number of atoms to fluctuate,
therefore, you will want to use the
"compute_modify"_compute_modify.html command to insure that the
current number of atoms is used as a normalizing factor each time
temperature is computed. Here is the necessary command:
compute_modify thermo_temp dynamic yes :pre
If LJ units are used, note that a value of 0.18292026 is used by this
fix as the reduced value for Planck's constant. This value was
derived from LJ paramters for argon, where h* = h/sqrt(sigma^2 *
epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
mass = 39.948 amu.
IMPORTANT NOTE: If you are monitoring the temperature of a system
where the particle count is changing due to adding/deleting particles,
you typically should use the "compute_modify dynamic
yes"_compute_modify.html command for the temperature compute you are
using.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the deposition to "binary restart
@ -214,11 +231,12 @@ trigger an error, so it is better to run multiple shorter-duration
simulations. Likewise, very large molecules have not been tested
and may turn out to be problematic.
Use of multiple fix gcmc commands in the same input using a template
molecule are not supported. There are multiple issues where the
current implmentation makes assumptions that are no longer valid
in this case. Resolving all of them require significant changes to
the implementation.
Use of multiple fix gcmc commands in the same input script can be
problematic if using a template molecule. The issue is that the
user-referenced template molecule in the second fix gcmc command
may no longer exist since it might have been deleted by the first
fix gcmc command. An existing template molecule will need to be
referenced by the user for each subsequent fix gcmc command.
[Related commands:]
@ -228,7 +246,7 @@ the implementation.
[Default:]
The option defaults are molecule = no, maxangle = 10.
The option defaults are mol = no, maxangle = 10.
:line