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Axel Kohlmeyer
2022-12-26 06:34:53 -05:00
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doc/src/fix_atom_swap.rst
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@ -44,56 +44,55 @@ Examples
Description
"""""""""""
This fix performs Monte Carlo swaps of atoms of one given atom type
with atoms of the other given atom types. The specified :math:`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 scaling temperature
*T* is used in the Metropolis criterion dictating swap probabilities.
Perform :math:`X` swaps of atoms of one type with atoms of another type
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.
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
integration displacements (e.g., via :doc:`fix nvt <fix_nh>`), 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. If not using *semi-grand*, exactly two atom types
are required.
specified. If not using *semi-grand*, exactly two atom types are
required.
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.
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 :ref:`(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*, atoms in the fix group whose type is not
listed in the *types* keyword are ineligible for attempted
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 *semi-grand* keyword can be set to *yes* to switch to the semi-grand
canonical ensemble as discussed in :ref:`(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*,
atoms in the fix group whose type is not listed in the *types* keyword
are ineligible for attempted 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 *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.
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
@ -108,16 +107,16 @@ have a non-zero molecule ID, but does not check for this at the time of
swapping.
If not using *semi-grand* this fix checks to ensure all atoms of the
given types have the same atomic charge. LAMMPS does not enforce this
in general, but it is needed for this fix to simplify the swapping
given types have the same atomic charge. LAMMPS does not 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. Conversely, when using *semi-grand*, it is assumed that
all the atom types involved in switches have the same
charge. Otherwise, charge would not be conserved. As a consequence, no
checks on atomic charges are performed, and successful switches update
the atom type but not the atom charge. While it is possible to use
*semi-grand* with groups of atoms that have different charges, these
charges will not be changed when the atom types change.
all the atom types involved in switches have the same charge. Otherwise,
charge would not be conserved. As a consequence, no checks on atomic
charges are performed, and successful switches update the atom type but
not the atom charge. While it is possible to use *semi-grand* with
groups of atoms that have different charges, these charges will not be
changed when the atom types change.
Since this fix computes total potential energies before and after
proposed swaps, so even complicated potential energy calculations are
@ -145,18 +144,19 @@ Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the state of the fix to :doc:`binary restart files
<restart>`. This includes information about the random number
generator seed, the next timestep for MC exchanges, the number of
exchange attempts and successes, etc. See the :doc:`read_restart
<read_restart>` command for info on how to re-specify a fix in an
input script that reads a restart file, so that the operation of the
fix continues in an uninterrupted fashion.
<restart>`. This includes information about the random number generator
seed, the next timestep for MC exchanges, the number of exchange
attempts and successes, etc. See the :doc:`read_restart <read_restart>`
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
.. note::
For this to work correctly, the timestep must **not** be changed
after reading the restart with :doc:`reset_timestep <reset_timestep>`.
The fix will try to detect it and stop with an error.
after reading the restart with :doc:`reset_timestep
<reset_timestep>`. The fix will try to detect it and stop with an
error.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix.
@ -187,12 +187,12 @@ Related commands
:doc:`fix nvt <fix_nh>`, :doc:`neighbor <neighbor>`,
:doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
:doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`,
:doc:`fix mol/swap <fix_mol_swap>`
:doc:`fix mol/swap <fix_mol_swap>`, :doc:`fix sgcmc <fix_sgcmc>`
Default
"""""""
The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
The option defaults are *ke* = yes, *semi-grand* = no, *mu* = 0.0 for
all atom types.
----------