git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12985 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
pscrozi
@ -37,7 +37,7 @@
|
||||
|
||||
<LI>zero or more keyword/value pairs may be appended to args
|
||||
|
||||
<LI>keyword = <I>mol</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>, <I>fugacity_coeff</I>, <I>full_energy</I>, or <I>charge</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
|
||||
@ -48,23 +48,25 @@
|
||||
<I>maxangle</I> value = maximum molecular rotation angle (degrees)
|
||||
<I>pressure</I> value = pressue of the gas reservoir (pressure units)
|
||||
<I>fugacity_coeff</I> value = fugacity coefficient of the gas reservoir (unitless)
|
||||
<I>full_energy</I> = compute the entire system energy when performing MC moves
|
||||
<I>charge</I> value = charge of inserted atoms (charge units)
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
|
||||
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180
|
||||
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
|
||||
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
|
||||
atoms or molecules of the given type with an imaginary ideal gas
|
||||
reservoir at the specified T and chemical potential (mu) as discussed
|
||||
in <A HREF = "#Frenkel">(Frenkel)</A>. If used with the <A HREF = "fix_nh.html">fix nvt</A>
|
||||
command, simulations in the grand canonical enemble (muVT, constant
|
||||
chemical potential, constant volume, and constant temperature) can be
|
||||
atoms or molecules of the given type with an imaginary ideal gas reservoir at
|
||||
the specified T and chemical potential (mu) as discussed in
|
||||
<A HREF = "#Frenkel">(Frenkel)</A>. If used with the <A HREF = "fix_nh.html">fix nvt</A> command,
|
||||
simulations in the grand canonical ensemble (muVT, constant chemical
|
||||
potential, constant volume, and constant temperature) can be
|
||||
performed. Specific uses include computing isotherms in microporous
|
||||
materials, or computing vapor-liquid coexistence curves.
|
||||
</P>
|
||||
@ -103,16 +105,16 @@ smaller-than-usual timestep size may be needed when running such a
|
||||
hybrid simulation, especially if the inserted molecules are not well
|
||||
equilibrated.
|
||||
</P>
|
||||
<P>This command may optionally use the <I>region</I> keyword to define an
|
||||
exchange and move volume. The specified region must have been
|
||||
previously defined with a <A HREF = "region.html">region</A> command. It must be
|
||||
defined with side = <I>in</I>. Insertion attempts occur only within the
|
||||
specified region. Move and deletion attempt candidates are selected
|
||||
from gas atoms or molecules within the region. If no candidate can be
|
||||
found within the specified region after randomly selecting candidates
|
||||
1000 times, the move or deletion attempt is considered a
|
||||
failure. Moves must start within the specified region, but may move
|
||||
the atom or molecule slightly outside of the region.
|
||||
<P>This command may optionally use the <I>region</I> keyword to define an
|
||||
exchange and move volume. The specified region must have been
|
||||
previously defined with a <A HREF = "region.html">region</A> command. It must be
|
||||
defined with side = <I>in</I>. Insertion attempts occur only within the
|
||||
specified region. Move and deletion attempt candidates are selected
|
||||
from gas atoms or molecules within the region. If no candidate can be
|
||||
found within the specified region after randomly selecting candidates
|
||||
1000 times, the move or deletion attempt is considered a failure. Moves
|
||||
must start and end with the atom or molecule center-of-mass within the
|
||||
specified region. Moves are not otherwise attempted.
|
||||
</P>
|
||||
<P>If used with <A HREF = "fix_nvt.html">fix_nvt</A>, the temperature of the imaginary
|
||||
reservoir, T, should be set to be equivalent to the target temperature
|
||||
@ -160,7 +162,10 @@ the angle in degrees. The specified angle will apply to all three
|
||||
Euler angles used internally to define the rotation matrix for
|
||||
molecular rotations. The max angle can be set to zero, but rotations
|
||||
will be pointless. Note that the default is ten degrees for each
|
||||
Euler angle.
|
||||
Euler angle. Also note that fix GCMC does not do configurational bias
|
||||
MC. In other words, while inserted molecules have different rotations,
|
||||
they all have the same molecular configuration, which was specified
|
||||
in the molecule command input.
|
||||
</P>
|
||||
<P>For atomic gasses, inserted atoms have the specified atom type, but
|
||||
deleted atoms are any atoms that have been inserted or that belong
|
||||
@ -176,6 +181,42 @@ 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>The <I>full_energy</I> option means that fix GCMC will compute the total
|
||||
potential energy of the entire simulated system. The total system
|
||||
energy before and after the proposed GCMC move is then used in the
|
||||
Metropolis criterion to determine whether or not to accept the
|
||||
proposed GCMC move. By default, this option is off, in which case
|
||||
only partial energies are computed to determine the difference in
|
||||
energy that would be caused by the proposed GCMC move.
|
||||
</P>
|
||||
<P>The <I>full_energy</I> option is needed for systems with complicated
|
||||
potential energy calculations, including the following:
|
||||
</P>
|
||||
<UL><LI> long-range electrostatics (kspace)
|
||||
<LI> many body pair styles
|
||||
<LI> hybrid pair styles
|
||||
<LI> eam pair styles
|
||||
<LI> triclinic systems
|
||||
<LI> need to include potential energy contributions from other fixes
|
||||
</UL>
|
||||
<P>Some fixes have an associated potential energy. Examples of such fixes
|
||||
include: <A HREF = "fix_efield.html">efield</A>, <A HREF = "fix_gravity.html">gravity</A>,
|
||||
<A HREF = "fix_addforce.html">addforce</A>, <A HREF = "fix_langevin.html">langevin</A>,
|
||||
<A HREF = "fix_restrain.html">restrain</A>, <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>,
|
||||
<A HREF = "fix_temp_rescale.html">temp/rescale</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
|
||||
For that energy to be included in the total potential energy of the
|
||||
system (the quantity used when performing GCMC moves),
|
||||
you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
|
||||
that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
|
||||
specify if this should be done.
|
||||
</P>
|
||||
<P>Use the <I>charge</I> option to insert atoms with a user-specified point
|
||||
charge. Note that doing so will cause the system to become non-neutral.
|
||||
LAMMPS issues a warning when using long-range electrostatics (kspace)
|
||||
with non-neutral systems. See the
|
||||
<A HREF = "compute_group_group.html">compute_group_group</A> documentation for more
|
||||
details about simulating non-neutral systems with kspace on.
|
||||
</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
|
||||
@ -192,7 +233,7 @@ mass = 39.948 amu.
|
||||
</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
|
||||
<P>This fix writes the state of the fix to <A HREF = "restart.html">binary restart
|
||||
files</A>. This includes information about the random
|
||||
number generator seed, the next timestep for MC exchanges, etc. See
|
||||
the <A HREF = "read_restart.html">read_restart</A> command for info on how to
|
||||
@ -202,9 +243,9 @@ the operation of the fix continues in an uninterrupted fashion.
|
||||
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
|
||||
fix.
|
||||
</P>
|
||||
<P>This fix computes a global vector of length 6, which can be accessed
|
||||
<P>This fix computes a global vector of length 8, which can be accessed
|
||||
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
|
||||
values are the following global cummulative quantities:
|
||||
values are the following global cumulative quantities:
|
||||
</P>
|
||||
<UL><LI>1 = displacement attempts
|
||||
<LI>2 = displacement successes
|
||||
@ -230,19 +271,8 @@ LAMMPS</A> section for more info.
|
||||
<P>Do not set "neigh_modify once yes" or else this fix will never be
|
||||
called. Reneighboring is required.
|
||||
</P>
|
||||
<P>Only pairwise interactions, as defined by the
|
||||
<A HREF = "pair_style.html">pair_style</A> command, are included in this
|
||||
calculation. Long-range interactions due to a
|
||||
<A HREF = "kspace_style.html">kspace_style</A> command are not included. Not all
|
||||
pair potentials can be evaluated in a pairwise mode as required by
|
||||
this fix. For example, 3-body potentials, such as
|
||||
<A HREF = "pair_tersoff.html">Tersoff</A> and <A HREF = "pair_sw.html">Stillinger-Weber</A> cannot
|
||||
be used. <A HREF = "pair_eam.html">EAM</A> potentials for metals only include the
|
||||
pair potential portion of the EAM interaction, not the embedding term.
|
||||
</P>
|
||||
<P>Can be run in parallel, but aspects of the GCMC part will not scale
|
||||
well in parallel. Only usable for 3D simulations with orthogonal
|
||||
simulation cells.
|
||||
well in parallel. Only usable for 3D simulations.
|
||||
</P>
|
||||
<P>Note that very lengthy simulations involving insertions/deletions of
|
||||
billions of gas molecules may run out of atom or molecule IDs and
|
||||
@ -259,13 +289,14 @@ referenced by the user for each subsequent fix gcmc command.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_nvt.html">fix_nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
|
||||
<P><A HREF = "fix_atom_swap.html">fix_atom_swap</A>,
|
||||
<A HREF = "fix_nvt.html">fix_nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
|
||||
<A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_evaporate.html">fix_evaporate</A>,
|
||||
<A HREF = "delete_atoms.html">delete_atoms</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The option defaults are mol = no, maxangle = 10.
|
||||
<P>The option defaults are mol = no, maxangle = 10, full_energy = no.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
||||
101
doc/fix_gcmc.txt
101
doc/fix_gcmc.txt
@ -23,7 +23,7 @@ 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 = {mol}, {region}, {maxangle}, {pressure}, or {fugacity_coeff} :l
|
||||
keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energy}, or {charge} :l
|
||||
{mol} value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
|
||||
{shake} value = fix-ID
|
||||
@ -32,23 +32,25 @@ keyword = {mol}, {region}, {maxangle}, {pressure}, or {fugacity_coeff} :l
|
||||
region-ID = ID of region to use as an exchange/move volume
|
||||
{maxangle} value = maximum molecular rotation angle (degrees)
|
||||
{pressure} value = pressue of the gas reservoir (pressure units)
|
||||
{fugacity_coeff} value = fugacity coefficient of the gas reservoir (unitless) :pre
|
||||
{fugacity_coeff} value = fugacity coefficient of the gas reservoir (unitless)
|
||||
{full_energy} = compute the entire system energy when performing MC moves
|
||||
{charge} value = charge of inserted atoms (charge units) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
|
||||
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180
|
||||
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
|
||||
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This fix performs grand canonical Monte Carlo (GCMC) exchanges of
|
||||
atoms or molecules of the given type with an imaginary ideal gas
|
||||
reservoir at the specified T and chemical potential (mu) as discussed
|
||||
in "(Frenkel)"_#Frenkel. If used with the "fix nvt"_fix_nh.html
|
||||
command, simulations in the grand canonical enemble (muVT, constant
|
||||
chemical potential, constant volume, and constant temperature) can be
|
||||
atoms or molecules of the given type with an imaginary ideal gas reservoir at
|
||||
the specified T and chemical potential (mu) as discussed in
|
||||
"(Frenkel)"_#Frenkel. If used with the "fix nvt"_fix_nh.html command,
|
||||
simulations in the grand canonical ensemble (muVT, constant chemical
|
||||
potential, constant volume, and constant temperature) can be
|
||||
performed. Specific uses include computing isotherms in microporous
|
||||
materials, or computing vapor-liquid coexistence curves.
|
||||
|
||||
@ -87,16 +89,16 @@ smaller-than-usual timestep size may be needed when running such a
|
||||
hybrid simulation, especially if the inserted molecules are not well
|
||||
equilibrated.
|
||||
|
||||
This command may optionally use the {region} keyword to define an
|
||||
exchange and move volume. The specified region must have been
|
||||
previously defined with a "region"_region.html command. It must be
|
||||
defined with side = {in}. Insertion attempts occur only within the
|
||||
specified region. Move and deletion attempt candidates are selected
|
||||
from gas atoms or molecules within the region. If no candidate can be
|
||||
found within the specified region after randomly selecting candidates
|
||||
1000 times, the move or deletion attempt is considered a
|
||||
failure. Moves must start within the specified region, but may move
|
||||
the atom or molecule slightly outside of the region.
|
||||
This command may optionally use the {region} keyword to define an
|
||||
exchange and move volume. The specified region must have been
|
||||
previously defined with a "region"_region.html command. It must be
|
||||
defined with side = {in}. Insertion attempts occur only within the
|
||||
specified region. Move and deletion attempt candidates are selected
|
||||
from gas atoms or molecules within the region. If no candidate can be
|
||||
found within the specified region after randomly selecting candidates
|
||||
1000 times, the move or deletion attempt is considered a failure. Moves
|
||||
must start and end with the atom or molecule center-of-mass within the
|
||||
specified region. Moves are not otherwise attempted.
|
||||
|
||||
If used with "fix_nvt"_fix_nvt.html, the temperature of the imaginary
|
||||
reservoir, T, should be set to be equivalent to the target temperature
|
||||
@ -144,7 +146,10 @@ the angle in degrees. The specified angle will apply to all three
|
||||
Euler angles used internally to define the rotation matrix for
|
||||
molecular rotations. The max angle can be set to zero, but rotations
|
||||
will be pointless. Note that the default is ten degrees for each
|
||||
Euler angle.
|
||||
Euler angle. Also note that fix GCMC does not do configurational bias
|
||||
MC. In other words, while inserted molecules have different rotations,
|
||||
they all have the same molecular configuration, which was specified
|
||||
in the molecule command input.
|
||||
|
||||
For atomic gasses, inserted atoms have the specified atom type, but
|
||||
deleted atoms are any atoms that have been inserted or that belong
|
||||
@ -160,6 +165,42 @@ 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.
|
||||
|
||||
The {full_energy} option means that fix GCMC will compute the total
|
||||
potential energy of the entire simulated system. The total system
|
||||
energy before and after the proposed GCMC move is then used in the
|
||||
Metropolis criterion to determine whether or not to accept the
|
||||
proposed GCMC move. By default, this option is off, in which case
|
||||
only partial energies are computed to determine the difference in
|
||||
energy that would be caused by the proposed GCMC move.
|
||||
|
||||
The {full_energy} option is needed for systems with complicated
|
||||
potential energy calculations, including the following:
|
||||
|
||||
long-range electrostatics (kspace)
|
||||
many body pair styles
|
||||
hybrid pair styles
|
||||
eam pair styles
|
||||
triclinic systems
|
||||
need to include potential energy contributions from other fixes :ul
|
||||
|
||||
Some fixes have an associated potential energy. Examples of such fixes
|
||||
include: "efield"_fix_efield.html, "gravity"_fix_gravity.html,
|
||||
"addforce"_fix_addforce.html, "langevin"_fix_langevin.html,
|
||||
"restrain"_fix_restrain.html, "temp/berendsen"_fix_temp_berendsen.html,
|
||||
"temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html.
|
||||
For that energy to be included in the total potential energy of the
|
||||
system (the quantity used when performing GCMC moves),
|
||||
you MUST enable the "fix_modify"_fix_modify.html {energy} option for
|
||||
that fix. The doc pages for individual "fix"_fix.html commands
|
||||
specify if this should be done.
|
||||
|
||||
Use the {charge} option to insert atoms with a user-specified point
|
||||
charge. Note that doing so will cause the system to become non-neutral.
|
||||
LAMMPS issues a warning when using long-range electrostatics (kspace)
|
||||
with non-neutral systems. See the
|
||||
"compute_group_group"_compute_group_group.html documentation for more
|
||||
details about simulating non-neutral systems with kspace on.
|
||||
|
||||
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
|
||||
@ -176,7 +217,7 @@ mass = 39.948 amu.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
This fix writes the state of the deposition to "binary restart
|
||||
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
|
||||
@ -186,9 +227,9 @@ 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 6, which can be accessed
|
||||
This fix computes a global vector of length 8, which can be accessed
|
||||
by various "output commands"_Section_howto.html#howto_15. The vector
|
||||
values are the following global cummulative quantities:
|
||||
values are the following global cumulative quantities:
|
||||
|
||||
1 = displacement attempts
|
||||
2 = displacement successes
|
||||
@ -214,19 +255,8 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
Do not set "neigh_modify once yes" or else this fix will never be
|
||||
called. Reneighboring is required.
|
||||
|
||||
Only pairwise interactions, as defined by the
|
||||
"pair_style"_pair_style.html command, are included in this
|
||||
calculation. Long-range interactions due to a
|
||||
"kspace_style"_kspace_style.html command are not included. Not all
|
||||
pair potentials can be evaluated in a pairwise mode as required by
|
||||
this fix. For example, 3-body potentials, such as
|
||||
"Tersoff"_pair_tersoff.html and "Stillinger-Weber"_pair_sw.html cannot
|
||||
be used. "EAM"_pair_eam.html potentials for metals only include the
|
||||
pair potential portion of the EAM interaction, not the embedding term.
|
||||
|
||||
Can be run in parallel, but aspects of the GCMC part will not scale
|
||||
well in parallel. Only usable for 3D simulations with orthogonal
|
||||
simulation cells.
|
||||
well in parallel. Only usable for 3D simulations.
|
||||
|
||||
Note that very lengthy simulations involving insertions/deletions of
|
||||
billions of gas molecules may run out of atom or molecule IDs and
|
||||
@ -243,13 +273,14 @@ referenced by the user for each subsequent fix gcmc command.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix_atom_swap"_fix_atom_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
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are mol = no, maxangle = 10.
|
||||
The option defaults are mol = no, maxangle = 10, full_energy = no.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
Reference in New Issue
Block a user