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116
doc/fix_atom_swap.html
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@ -9,15 +9,15 @@
<HR> <HR>
<H3>fix atom_swap command <H3>fix atom/swap command
</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </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> </PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command <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 <LI>N = invoke this fix every N steps
@ -47,66 +47,72 @@
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2 <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 fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 delta_mu 4.3 -5.0
</PRE> </PRE>
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>This fix performs Monte Carlo swaps of atoms of one given atom type with atoms <P>This fix performs Monte Carlo swaps of atoms of one given atom type
of the other given atom types. The specified T is used in the Metropolis criterion with atoms of the other given atom types. The specified T is used in
dictating swap probabilities. the Metropolis criterion dictating swap probabilities.
</P> </P>
<P>Perform X swaps of atoms of one type with atoms of another type according to a <P>Perform X swaps of atoms of one type with atoms of another type
Monte Carlo probability. Swap candidates must be in the fix group, must be in according to a Monte Carlo probability. Swap candidates must be in the
the region (if specified), and must be of one of the listed types. Swaps are fix group, must be in the region (if specified), and must be of one of
attempted between candidates that are chosen randomly with equal probability the listed types. Swaps are attempted between candidates that are
among the candidate atoms. Swaps are not attempted between atoms of the same chosen randomly with equal probability among the candidate
type since nothing would happen. atoms. Swaps are not attempted between atoms of the same type since
nothing would happen.
</P> </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 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 in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
may be needed when running such a hybrid simulation, especially if be needed when running such a hybrid simulation, especially if the
the swapped atoms are not well equilibrated. swapped atoms are not well equilibrated.
</P> </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>
<P>The <I>ke</I> keyword can be set to <I>no</I> to turn off kinetic energy conservation <P>The <I>ke</I> keyword can be set to <I>no</I> to turn off kinetic energy
for swaps. The default is <I>yes</I>, which means that swapped atoms have their conservation for swaps. The default is <I>yes</I>, which means that swapped
velocities scaled by the ratio of the masses of the swapped atom types. This atoms have their velocities scaled by the ratio of the masses of the
ensures that the kinetic energy of each atom is the same after the swap as it swapped atom types. This ensures that the kinetic energy of each atom
was before the swap, even though the atom masses have changed. is the same after the swap as it was before the swap, even though the
atom masses have changed.
</P> </P>
<P>The <I>semi-grand</I> keyword can be set to <I>yes</I> to switch to the semi-grand <P>The <I>semi-grand</I> keyword can be set to <I>yes</I> to switch to the
canonical ensemble as discussed in <A HREF = "#Sadigh">(Sadigh)</A>. This means that the semi-grand canonical ensemble as discussed in <A HREF = "#Sadigh">(Sadigh)</A>. This
total number of each particle type does not need to be conserved. The default means that the total number of each particle type does not need to be
is <I>no</I>, which means that the only kind of swap allowed exchanges an atom of conserved. The default is <I>no</I>, which means that the only kind of swap
one type with an atom of a different given type. In other words, the relative allowed exchanges an atom of one type with an atom of a different
mole fractions of the swapped atoms remains constant. Whereas in the given type. In other words, the relative mole fractions of the swapped
semi-grand canonical ensemble, the composition of the system can change. Note atoms remains constant. Whereas in the semi-grand canonical ensemble,
that when using <I>semi-grand</I>, all atoms in the fix group are eligible for the composition of the system can change. Note that when using
attempted conversion to one of the given types, even if its current type is <I>semi-grand</I>, all atoms in the fix group are eligible for attempted
not one of the given types. An attempt is made to switch the selected atom to conversion to one of the given types, even if its current type is not
one of the listed <I>types</I> with equal probability. Acceptance of each attempt one of the given types. An attempt is made to switch the selected atom
depends upon the Metropolis criterion. to one of the listed <I>types</I> with equal probability. Acceptance of
each attempt depends upon the Metropolis criterion.
</P> </P>
<P>The <I>delta_mu</I> keyword allows users to specify non-zero chemical potentials <P>The <I>delta_mu</I> keyword allows users to specify non-zero chemical
for each of the atom types. All chemical potentials are relative to the first potentials for each of the atom types. All chemical potentials are
atom type, so no value is given for the first atom type. These parameters are relative to the first atom type, so no value is given for the first
useful for semi-grand canonical ensemble simulations where it may be atom type. These parameters are useful for semi-grand canonical
desirable to actively control the composition of the system. When given, ensemble simulations where it may be desirable to actively control the
there must be ntypes-1 values given, where ntypes is the number of atom composition of the system. When given, there must be ntypes-1 values
types in the simulated system. Note that a value for delta_mu is required for given, where ntypes is the number of atom types in the simulated
all atom types when using <I>semi-grand</I>, even for atom types not listed system. Note that a value for delta_mu is required for all atom types
following the <I>types</I> keyword. This is because when using <I>semi-grand</I>, it is when using <I>semi-grand</I>, even for atom types not listed following the
possible that any of the atom types in the system could be part of the fix <I>types</I> keyword. This is because when using <I>semi-grand</I>, it is
group and therefore are eligible for swapping to one of the listed atom types. 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>
<P>This command may optionally use the <I>region</I> keyword to define <P>This command may optionally use the <I>region</I> keyword to define swap
swap volume. The specified region must have been volume. The specified region must have been previously defined with a
previously defined with a <A HREF = "region.html">region</A> command. It must be <A HREF = "region.html">region</A> command. It must be defined with side = <I>in</I>.
defined with side = <I>in</I>. Swap attempts occur only between atoms that Swap attempts occur only between atoms that are both within the
are both within the specified region. Swaps are not otherwise attempted. specified region. Swaps are not otherwise attempted.
</P> </P>
<P>You should ensure you do not swap atoms belonging to a molecule, or <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. 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. swapping.
</P> </P>
<P>This fix checks to ensure all atoms of the given types have the same <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 atomic charge. LAMMPS doesn't enforce this in general, but it is
needed for this fix to simplify the swapping procedure. Successful swaps needed for this fix to simplify the swapping procedure. Successful
will swap the atom type and charge of the swapped atoms. swaps will swap the atom type and charge of the swapped atoms.
</P> </P>
<P>Since this fix computes total potential energies before and after <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: OK, including the following:
</P> </P>
<UL><LI> long-range electrostatics (kspace) <UL><LI> long-range electrostatics (kspace)

116
doc/fix_atom_swap.txt
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@ -6,14 +6,14 @@
:line :line
fix atom_swap command :h3 fix atom/swap command :h3
[Syntax:] [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 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 N = invoke this fix every N steps :l
X = number of swaps to attempt every N steps :l X = number of swaps to attempt every N steps :l
seed = random # seed (positive integer) :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:] [Examples:]
fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2 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 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:] [Description:]
This fix performs Monte Carlo swaps of atoms of one given atom type with atoms This fix performs Monte Carlo swaps of atoms of one given atom type
of the other given atom types. The specified T is used in the Metropolis criterion with atoms of the other given atom types. The specified T is used in
dictating swap probabilities. the Metropolis criterion dictating swap probabilities.
Perform X swaps of atoms of one type with atoms of another type according to a Perform X swaps of atoms of one type with atoms of another type
Monte Carlo probability. Swap candidates must be in the fix group, must be in according to a Monte Carlo probability. Swap candidates must be in the
the region (if specified), and must be of one of the listed types. Swaps are fix group, must be in the region (if specified), and must be of one of
attempted between candidates that are chosen randomly with equal probability the listed types. Swaps are attempted between candidates that are
among the candidate atoms. Swaps are not attempted between atoms of the same chosen randomly with equal probability among the candidate
type since nothing would happen. 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 integration displacements, e.g. via "fix_nvt"_fix_nvt.html, resulting
in a hybrid MC+MD simulation. A smaller-than-usual timestep size in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
may be needed when running such a hybrid simulation, especially if be needed when running such a hybrid simulation, especially if the
the swapped atoms are not well equilibrated. 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 The {ke} keyword can be set to {no} to turn off kinetic energy
for swaps. The default is {yes}, which means that swapped atoms have their conservation for swaps. The default is {yes}, which means that swapped
velocities scaled by the ratio of the masses of the swapped atom types. This atoms have their velocities scaled by the ratio of the masses of the
ensures that the kinetic energy of each atom is the same after the swap as it swapped atom types. This ensures that the kinetic energy of each atom
was before the swap, even though the atom masses have changed. 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 The {semi-grand} keyword can be set to {yes} to switch to the
canonical ensemble as discussed in "(Sadigh)"_#Sadigh. This means that the semi-grand canonical ensemble as discussed in "(Sadigh)"_#Sadigh. This
total number of each particle type does not need to be conserved. The default means that the total number of each particle type does not need to be
is {no}, which means that the only kind of swap allowed exchanges an atom of conserved. The default is {no}, which means that the only kind of swap
one type with an atom of a different given type. In other words, the relative allowed exchanges an atom of one type with an atom of a different
mole fractions of the swapped atoms remains constant. Whereas in the given type. In other words, the relative mole fractions of the swapped
semi-grand canonical ensemble, the composition of the system can change. Note atoms remains constant. Whereas in the semi-grand canonical ensemble,
that when using {semi-grand}, all atoms in the fix group are eligible for the composition of the system can change. Note that when using
attempted conversion to one of the given types, even if its current type is {semi-grand}, all atoms in the fix group are eligible for attempted
not one of the given types. An attempt is made to switch the selected atom to conversion to one of the given types, even if its current type is not
one of the listed {types} with equal probability. Acceptance of each attempt one of the given types. An attempt is made to switch the selected atom
depends upon the Metropolis criterion. 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 The {delta_mu} keyword allows users to specify non-zero chemical
for each of the atom types. All chemical potentials are relative to the first potentials for each of the atom types. All chemical potentials are
atom type, so no value is given for the first atom type. These parameters are relative to the first atom type, so no value is given for the first
useful for semi-grand canonical ensemble simulations where it may be atom type. These parameters are useful for semi-grand canonical
desirable to actively control the composition of the system. When given, ensemble simulations where it may be desirable to actively control the
there must be ntypes-1 values given, where ntypes is the number of atom composition of the system. When given, there must be ntypes-1 values
types in the simulated system. Note that a value for delta_mu is required for given, where ntypes is the number of atom types in the simulated
all atom types when using {semi-grand}, even for atom types not listed system. Note that a value for delta_mu is required for all atom types
following the {types} keyword. This is because when using {semi-grand}, it is when using {semi-grand}, even for atom types not listed following the
possible that any of the atom types in the system could be part of the fix {types} keyword. This is because when using {semi-grand}, it is
group and therefore are eligible for swapping to one of the listed atom types. 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 This command may optionally use the {region} keyword to define swap
swap volume. The specified region must have been volume. The specified region must have been previously defined with a
previously defined with a "region"_region.html command. It must be "region"_region.html command. It must be defined with side = {in}.
defined with side = {in}. Swap attempts occur only between atoms that Swap attempts occur only between atoms that are both within the
are both within the specified region. Swaps are not otherwise attempted. specified region. Swaps are not otherwise attempted.
You should ensure you do not swap atoms belonging to a molecule, or 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. 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. swapping.
This fix checks to ensure all atoms of the given types have the same 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 atomic charge. LAMMPS doesn't enforce this in general, but it is
needed for this fix to simplify the swapping procedure. Successful swaps needed for this fix to simplify the swapping procedure. Successful
will swap the atom type and charge of the swapped atoms. swaps will swap the atom type and charge of the swapped atoms.
Since this fix computes total potential energies before and after 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: OK, including the following:
long-range electrostatics (kspace) long-range electrostatics (kspace)