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116
doc/fix_atom_swap.html
View File

@ -9,15 +9,15 @@
<HR>
<H3>fix atom_swap command
<H3>fix atom/swap command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID atom_swap N X seed T keyword values ...
<PRE>fix ID group-ID atom/swap N X seed T keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>atom_swap = style name of this fix command
<LI>atom/swap = style name of this fix command
<LI>N = invoke this fix every N steps
@ -47,66 +47,72 @@
<P><B>Examples:</B>
</P>
<PRE>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix atom_swap_fix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
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>
<P><B>Description:</B>
</P>
<P>This fix performs Monte Carlo swaps of atoms of one given atom type with atoms
of the other given atom types. The specified T is used in the Metropolis criterion
dictating swap probabilities.
<P>This fix performs Monte Carlo swaps of atoms of one given atom type
with atoms of the other given atom types. The specified T is used in
the Metropolis criterion dictating swap probabilities.
</P>
<P>Perform X swaps of atoms of one type with atoms of another type according to a
Monte Carlo probability. Swap candidates must be in the fix group, must be in
the region (if specified), and must be of one of the listed types. Swaps are
attempted between candidates that are chosen randomly with equal probability
among the candidate atoms. Swaps are not attempted between atoms of the same
type since nothing would happen.
<P>Perform X swaps of atoms of one type with atoms of another type
according to a Monte Carlo probability. Swap candidates must be in the
fix group, must be in the region (if specified), and must be of one of
the listed types. Swaps are attempted between candidates that are
chosen randomly with equal probability among the candidate
atoms. Swaps are not attempted between atoms of the same type since
nothing would happen.
</P>
<P>All atoms in the simulation domain can be moved using regular time
<P>All atoms in the simulation domain can be moved using regular time
integration displacements, e.g. via <A HREF = "fix_nvt.html">fix_nvt</A>, resulting
in a hybrid MC+MD simulation. A smaller-than-usual timestep size
may be needed when running such a hybrid simulation, especially if
the swapped atoms are not well equilibrated.
in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
be needed when running such a hybrid simulation, especially if the
swapped atoms are not well equilibrated.
</P>
<P>The <I>types</I> keyword is required. At least two atom types must be specified.
<P>The <I>types</I> keyword is required. At least two atom types must be
specified.
</P>
<P>The <I>ke</I> keyword can be set to <I>no</I> to turn off kinetic energy conservation
for swaps. The default is <I>yes</I>, which means that swapped atoms have their
velocities scaled by the ratio of the masses of the swapped atom types. This
ensures that the kinetic energy of each atom is the same after the swap as it
was before the swap, even though the atom masses have changed.
<P>The <I>ke</I> keyword can be set to <I>no</I> to turn off kinetic energy
conservation for swaps. The default is <I>yes</I>, which means that swapped
atoms have their velocities scaled by the ratio of the masses of the
swapped atom types. This ensures that the kinetic energy of each atom
is the same after the swap as it was before the swap, even though the
atom masses have changed.
</P>
<P>The <I>semi-grand</I> keyword can be set to <I>yes</I> to switch to the semi-grand
canonical ensemble as discussed in <A HREF = "#Sadigh">(Sadigh)</A>. This means that the
total number of each particle type does not need to be conserved. The default
is <I>no</I>, which means that the only kind of swap allowed exchanges an atom of
one type with an atom of a different given type. In other words, the relative
mole fractions of the swapped atoms remains constant. Whereas in the
semi-grand canonical ensemble, the composition of the system can change. Note
that when using <I>semi-grand</I>, all atoms in the fix group are eligible for
attempted conversion to one of the given types, even if its current type is
not one of the given types. An attempt is made to switch the selected atom to
one of the listed <I>types</I> with equal probability. Acceptance of each attempt
depends upon the Metropolis criterion.
<P>The <I>semi-grand</I> keyword can be set to <I>yes</I> to switch to the
semi-grand canonical ensemble as discussed in <A HREF = "#Sadigh">(Sadigh)</A>. This
means that the total number of each particle type does not need to be
conserved. The default is <I>no</I>, which means that the only kind of swap
allowed exchanges an atom of one type with an atom of a different
given type. In other words, the relative mole fractions of the swapped
atoms remains constant. Whereas in the semi-grand canonical ensemble,
the composition of the system can change. Note that when using
<I>semi-grand</I>, all atoms in the fix group are eligible for attempted
conversion to one of the given types, even if its current type is not
one of the given types. An attempt is made to switch the selected atom
to one of the listed <I>types</I> 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 relative to the first
atom type, so no value is given for the first atom type. These parameters are
useful for semi-grand canonical ensemble simulations where it may be
desirable to actively control the composition of the system. When given,
there must be ntypes-1 values given, where ntypes is the number of atom
types in the simulated system. Note that a value for delta_mu is required for
all atom types when using <I>semi-grand</I>, even for atom types not listed
following the <I>types</I> keyword. This is because when using <I>semi-grand</I>, it is
possible that any of the atom types in the system could be part of the fix
group and therefore are eligible for swapping to one of the listed atom types.
<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
relative to the first atom type, so no value is given for the first
atom type. These parameters are useful for semi-grand canonical
ensemble simulations where it may be desirable to actively control the
composition of the system. When given, there must be ntypes-1 values
given, where ntypes is the number of atom types in the simulated
system. Note that a value for delta_mu is required for all atom types
when using <I>semi-grand</I>, even for atom types not listed following the
<I>types</I> keyword. This is because when using <I>semi-grand</I>, it is
possible that any of the atom types in the system could be part of the
fix group and therefore are eligible for swapping to one of the listed
atom types.
</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 <A HREF = "region.html">region</A> command. It must be
defined with side = <I>in</I>. Swap attempts occur only between atoms that
are both within the specified region. Swaps are not otherwise attempted.
<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
<A HREF = "region.html">region</A> command. It must be defined with side = <I>in</I>.
Swap attempts occur only between atoms that are both within the
specified region. Swaps are not otherwise attempted.
</P>
<P>You should ensure you do not swap atoms belonging to a molecule, or
LAMMPS will soon generate an error when it tries to find those atoms.
@ -115,12 +121,12 @@ non-zero molecule ID, but does not check for this at the time of
swapping.
</P>
<P>This fix checks to ensure all atoms of the given types have the same
atomic charge. LAMMPS doesn't enforce this in general, but it is
needed for this fix to simplify the swapping procedure. Successful swaps
will swap the atom type and charge of the swapped atoms.
atomic charge. LAMMPS doesn't enforce this in general, but it is
needed for this fix to simplify the swapping procedure. Successful
swaps will swap the atom type and charge of the swapped atoms.
</P>
<P>Since this fix computes total potential energies before and after
proposed swaps, so even complicated potential energy calculations are
proposed swaps, so even complicated potential energy calculations are
OK, including the following:
</P>
<UL><LI> long-range electrostatics (kspace)

116
doc/fix_atom_swap.txt
View File

@ -6,14 +6,14 @@
:line
fix atom_swap command :h3
fix atom/swap command :h3
[Syntax:]
fix ID group-ID atom_swap N X seed T keyword values ... :pre
fix ID group-ID atom/swap N X seed T keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
atom_swap = style name of this fix command :l
atom/swap = style name of this fix command :l
N = invoke this fix every N steps :l
X = number of swaps to attempt every N steps :l
seed = random # seed (positive integer) :l
@ -35,66 +35,72 @@ keyword = {types} or {delta_mu} or {ke} or {semi-grand} or {region} :l
[Examples:]
fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix atom_swap_fix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
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
[Description:]
This fix performs Monte Carlo swaps of atoms of one given atom type with atoms
of the other given atom types. The specified T is used in the Metropolis criterion
dictating swap probabilities.
This fix performs Monte Carlo swaps of atoms of one given atom type
with atoms of the other given atom types. The specified T is used in
the Metropolis criterion dictating swap probabilities.
Perform X swaps of atoms of one type with atoms of another type according to a
Monte Carlo probability. Swap candidates must be in the fix group, must be in
the region (if specified), and must be of one of the listed types. Swaps are
attempted between candidates that are chosen randomly with equal probability
among the candidate atoms. Swaps are not attempted between atoms of the same
type since nothing would happen.
Perform X swaps of atoms of one type with atoms of another type
according to a Monte Carlo probability. Swap candidates must be in the
fix group, must be in the region (if specified), and must be of one of
the listed types. Swaps are attempted between candidates that are
chosen randomly with equal probability among the candidate
atoms. Swaps are not attempted between atoms of the same type since
nothing would happen.
All atoms in the simulation domain can be moved using regular time
All atoms in the simulation domain can be moved using regular time
integration displacements, e.g. via "fix_nvt"_fix_nvt.html, resulting
in a hybrid MC+MD simulation. A smaller-than-usual timestep size
may be needed when running such a hybrid simulation, especially if
the swapped atoms are not well equilibrated.
in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
be needed when running such a hybrid simulation, especially if the
swapped atoms are not well equilibrated.
The {types} keyword is required. At least two atom types must be specified.
The {types} keyword is required. At least two atom types must be
specified.
The {ke} keyword can be set to {no} to turn off kinetic energy conservation
for swaps. The default is {yes}, which means that swapped atoms have their
velocities scaled by the ratio of the masses of the swapped atom types. This
ensures that the kinetic energy of each atom is the same after the swap as it
was before the swap, even though the atom masses have changed.
The {ke} keyword can be set to {no} to turn off kinetic energy
conservation for swaps. The default is {yes}, which means that swapped
atoms have their velocities scaled by the ratio of the masses of the
swapped atom types. This ensures that the kinetic energy of each atom
is the same after the swap as it was before the swap, even though the
atom masses have changed.
The {semi-grand} keyword can be set to {yes} to switch to the semi-grand
canonical ensemble as discussed in "(Sadigh)"_#Sadigh. This means that the
total number of each particle type does not need to be conserved. The default
is {no}, which means that the only kind of swap allowed exchanges an atom of
one type with an atom of a different given type. In other words, the relative
mole fractions of the swapped atoms remains constant. Whereas in the
semi-grand canonical ensemble, the composition of the system can change. Note
that when using {semi-grand}, all atoms in the fix group are eligible for
attempted conversion to one of the given types, even if its current type is
not one of the given types. An attempt is made to switch the selected atom to
one of the listed {types} with equal probability. Acceptance of each attempt
depends upon the Metropolis criterion.
The {semi-grand} keyword can be set to {yes} to switch to the
semi-grand canonical ensemble as discussed in "(Sadigh)"_#Sadigh. This
means that the total number of each particle type does not need to be
conserved. The default is {no}, which means that the only kind of swap
allowed exchanges an atom of one type with an atom of a different
given type. In other words, the relative mole fractions of the swapped
atoms remains constant. Whereas in the semi-grand canonical ensemble,
the composition of the system can change. Note that when using
{semi-grand}, all atoms in the fix group are eligible for attempted
conversion to one of the given types, even if its current type is not
one of the given types. An attempt is made to switch the selected atom
to one of the 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 relative to the first
atom type, so no value is given for the first atom type. These parameters are
useful for semi-grand canonical ensemble simulations where it may be
desirable to actively control the composition of the system. When given,
there must be ntypes-1 values given, where ntypes is the number of atom
types in the simulated system. Note that a value for delta_mu is required for
all atom types when using {semi-grand}, even for atom types not listed
following the {types} keyword. This is because when using {semi-grand}, it is
possible that any of the atom types in the system could be part of the fix
group and therefore are eligible for swapping to one of the listed atom types.
The {delta_mu} keyword allows users to specify non-zero chemical
potentials for each of the atom types. All chemical potentials are
relative to the first atom type, so no value is given for the first
atom type. These parameters are useful for semi-grand canonical
ensemble simulations where it may be desirable to actively control the
composition of the system. When given, there must be ntypes-1 values
given, where ntypes is the number of atom types in the simulated
system. Note that a value for delta_mu is required for all atom types
when using {semi-grand}, even for atom types not listed following the
{types} keyword. This is because when using {semi-grand}, it is
possible that any of the atom types in the system could be part of the
fix group and therefore are eligible for swapping to one of the listed
atom types.
This command may optionally use the {region} keyword to define
swap volume. The specified region must have been
previously defined with a "region"_region.html command. It must be
defined with side = {in}. Swap attempts occur only between atoms that
are both within the specified region. Swaps are not otherwise attempted.
This command may optionally use the {region} keyword to define swap
volume. The specified region must have been previously defined with a
"region"_region.html command. It must be defined with side = {in}.
Swap attempts occur only between atoms that are both within the
specified region. Swaps are not otherwise attempted.
You should ensure you do not swap atoms belonging to a molecule, or
LAMMPS will soon generate an error when it tries to find those atoms.
@ -103,12 +109,12 @@ non-zero molecule ID, but does not check for this at the time of
swapping.
This fix checks to ensure all atoms of the given types have the same
atomic charge. LAMMPS doesn't enforce this in general, but it is
needed for this fix to simplify the swapping procedure. Successful swaps
will swap the atom type and charge of the swapped atoms.
atomic charge. LAMMPS doesn't enforce this in general, but it is
needed for this fix to simplify the swapping procedure. Successful
swaps will swap the atom type and charge of the swapped atoms.
Since this fix computes total potential energies before and after
proposed swaps, so even complicated potential energy calculations are
proposed swaps, so even complicated potential energy calculations are
OK, including the following:
long-range electrostatics (kspace)