forked from lijiext/lammps
111 lines
3.7 KiB
Plaintext
111 lines
3.7 KiB
Plaintext
.. index:: fix evaporate
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fix evaporate 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 evaporate N M region-ID seed
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* evaporate = style name of this fix command
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* N = delete atoms every this many timesteps
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* M = number of atoms to delete each time
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* region-ID = ID of region within which to perform deletions
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* seed = random number seed to use for choosing atoms to delete
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* zero or more keyword/value pairs may be appended
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.. parsed-literal::
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keyword = *molecule*
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*molecule* value = *no* or *yes*
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Examples
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""""""""
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.. parsed-literal::
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fix 1 solvent evaporate 1000 10 surface 49892
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fix 1 solvent evaporate 1000 10 surface 38277 molecule yes
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Description
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"""""""""""
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Remove M atoms from the simulation every N steps. This can be used,
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for example, to model evaporation of solvent particles or moleclues
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(i.e. drying) of a system. Every N steps, the number of atoms in the
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fix group and within the specifed region are counted. M of these are
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chosen at random and deleted. If there are less than M eligible
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particles, then all of them are deleted.
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If the setting for the *molecule* keyword is *no*\ , then only single
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atoms are deleted. In this case, you should insure you do not delete
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only a portion of a molecule (only some of its atoms), or LAMMPS will
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soon generate an error when it tries to find those atoms. LAMMPS will
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warn you if any of the atoms eligible for deletion have a non-zero
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molecule ID, but does not check for this at the time of deletion.
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If the setting for the *molecule* keyword is *yes*\ , then when an atom
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is chosen for deletion, the entire molecule it is part of is deleted.
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The count of deleted atoms is incremented by the number of atoms in
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the molecule, which may make it exceed *M*\ . If the molecule ID of the
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chosen atom is 0, then it is assumed to not be part of a molecule, and
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just the single atom is deleted.
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As an example, if you wish to delete 10 water molecules every *N*
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steps, you should set *M* to 30. If only the water's oxygen atoms
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were in the fix group, then two hydrogen atoms would be deleted when
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an oxygen atom is selected for deletion, whether the hydrogens are
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inside the evaporation region or not.
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Note that neighbor lists are re-built on timesteps that atoms are
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removed. Thus you should not remove atoms too frequently or you will
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incur overhead due to the cost of building neighbor lists.
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.. note::
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If you are monitoring the temperature of a system where the atom
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count is changing due to evaporation, you typically should use the
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:doc:`compute_modify dynamic yes <compute_modify>` command for the
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temperature compute you are using.
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Restart, fix_modify, output, run start/stop, minimize info
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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
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are relevant to this fix.
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This fix computes a global scalar, which can be accessed by various
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:ref:`output commands <howto_15>`. The scalar is the
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cummulative number of deleted atoms. The scalar value calculated by
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this fix is "intensive".
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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 MISC package. It is only enabled if LAMMPS
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was 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 deposit <fix_deposit>`
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Default
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"""""""
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The option defaults are molecule = no.
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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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