forked from lijiext/lammps
204 lines
8.1 KiB
Plaintext
204 lines
8.1 KiB
Plaintext
.. index:: fix atom/swap
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fix atom/swap command
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=====================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID atom/swap N X seed T keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* atom/swap = style name of this fix command
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* N = invoke this fix every N steps
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* X = number of swaps to attempt every N steps
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* seed = random # seed (positive integer)
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* T = scaling temperature of the MC swaps (temperature units)
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* one or more keyword/value pairs may be appended to args
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* keyword = *types* or *mu* or *ke* or *semi-grand* or *region*
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.. parsed-literal::
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*types* values = two or more atom types
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*mu* values = chemical potential of swap types (energy units)
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*ke* value = *no* or *yes*
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*no* = no conservation of kinetic energy after atom swaps
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*yes* = kinetic energy is conserved after atom swaps
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*semi-grand* value = *no* or *yes*
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*no* = particle type counts and fractions conserved
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*yes* = semi-grand canonical ensemble, particle fractions not conserved
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*region* value = region-ID
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region-ID = ID of region to use as an exchange/move volume
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Examples
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""""""""
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.. parsed-literal::
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fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
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fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
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fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
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Description
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"""""""""""
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This fix performs Monte Carlo swaps of atoms of one given atom type
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with atoms of the other given atom types. The specified T is used in
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the Metropolis criterion dictating swap probabilities.
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Perform X swaps of atoms of one type with atoms of another type
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according to a Monte Carlo probability. Swap candidates must be in the
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fix group, must be in the region (if specified), and must be of one of
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the listed types. Swaps are attempted between candidates that are
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chosen randomly with equal probability among the candidate
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atoms. Swaps are not attempted between atoms of the same type since
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nothing would happen.
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All atoms in the simulation domain can be moved using regular time
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integration displacements, e.g. via :doc:`fix nvt <fix_nh>`, resulting
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in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
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be needed when running such a hybrid simulation, especially if the
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swapped atoms are not well equilibrated.
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The *types* keyword is required. At least two atom types must be
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specified.
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The *ke* keyword can be set to *no* to turn off kinetic energy
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conservation for swaps. The default is *yes*\ , which means that swapped
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atoms have their velocities scaled by the ratio of the masses of the
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swapped atom types. This ensures that the kinetic energy of each atom
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is the same after the swap as it was before the swap, even though the
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atom masses have changed.
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The *semi-grand* keyword can be set to *yes* to switch to the
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semi-grand canonical ensemble as discussed in :ref:`(Sadigh) <Sadigh>`. This
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means that the total number of each particle type does not need to be
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conserved. The default is *no*\ , which means that the only kind of swap
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allowed exchanges an atom of one type with an atom of a different
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given type. In other words, the relative mole fractions of the swapped
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atoms remains constant. Whereas in the semi-grand canonical ensemble,
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the composition of the system can change. Note that when using
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*semi-grand*\ , atoms in the fix group whose type is not listed
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in the *types* keyword are ineligible for attempted
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conversion. An attempt is made to switch
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the selected atom (if eligible) to one of the other listed types
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with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
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The *mu* keyword allows users to specify chemical
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potentials. This is required and allowed only when using *semi-grand*\ .
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All chemical potentials are absolute, so there is one for
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each swap type listed following the *types* keyword.
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In semi-grand canonical ensemble simulations the chemical composition
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of the system is controlled by the difference in these values. So
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shifting all values by a constant amount will have no effect
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on the simulation.
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This command may optionally use the *region* keyword to define swap
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volume. The specified region must have been previously defined with a
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:doc:`region <region>` command. It must be defined with side = *in*\ .
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Swap attempts occur only between atoms that are both within the
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specified region. Swaps are not otherwise attempted.
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You should ensure you do not swap atoms belonging to a molecule, or
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LAMMPS will soon generate an error when it tries to find those atoms.
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LAMMPS will warn you if any of the atoms eligible for swapping have a
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non-zero molecule ID, but does not check for this at the time of
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swapping.
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If not using *semi-grand* this fix checks to ensure all atoms of the
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given types have the same atomic charge. LAMMPS doesn't enforce this
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in general, but it is needed for this fix to simplify the
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swapping procedure. Successful swaps will swap the atom type and charge
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of the swapped atoms. Conversely, when using *semi-grand*\ , it is assumed that all the atom
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types involved in switches have the same charge. Otherwise, charge
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would not be conserved. As a consequence, no checks on atomic charges are
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performed, and successful switches update the atom type but not the
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atom charge. While it is possible to use *semi-grand* with groups of
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atoms that have different charges, these charges will not be changed when the
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atom types change.
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Since this fix computes total potential energies before and after
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proposed swaps, so even complicated potential energy calculations are
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OK, including the following:
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* long-range electrostatics (kspace)
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* many body pair styles
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* hybrid pair styles
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* eam pair styles
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* triclinic systems
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* need to include potential energy contributions from other fixes
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Some fixes have an associated potential energy. Examples of such fixes
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include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
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:doc:`addforce <fix_addforce>`, :doc:`langevin <fix_langevin>`,
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:doc:`restrain <fix_restrain>`, :doc:`temp/berendsen <fix_temp_berendsen>`,
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:doc:`temp/rescale <fix_temp_rescale>`, and :doc:`wall fixes <fix_wall>`.
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For that energy to be included in the total potential energy of the
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system (the quantity used when performing GCMC moves),
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you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for
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that fix. The doc pages for individual :doc:`fix <fix>` commands
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specify if this should be done.
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Restart, fix_modify, output, run start/stop, minimize info
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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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This fix writes the state of the fix to :doc:`binary restart files <restart>`. This includes information about the random
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number generator seed, the next timestep for MC exchanges, etc. See
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the :doc:`read_restart <read_restart>` command for info on how to
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re-specify a fix in an input script that reads a restart file, so that
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the operation of the fix continues in an uninterrupted fashion.
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None of the :doc:`fix_modify <fix_modify>` options are relevant to this
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fix.
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This fix computes a global vector of length 2, which can be accessed
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by various :ref:`output commands <howto_15>`. The vector
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values are the following global cumulative quantities:
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* 1 = swap attempts
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* 2 = swap successes
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The vector values calculated by this fix are "extensive".
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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This fix is part of the MC package. It is only enabled if LAMMPS was
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built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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Related commands
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""""""""""""""""
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:doc:`fix nvt <fix_nh>`, :doc:`neighbor <neighbor>`,
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:doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
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:doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`
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Default
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"""""""
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The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
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all atom types.
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----------
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.. _Sadigh:
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**(Sadigh)** B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and
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L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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