update documentation
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Megan J. McCarthy
@ -32,85 +32,91 @@ Examples
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compute 1 all local_composition/atom cutoff 9.0
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comm_modify cutoff 9.0
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..
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****** UNDER CONSTRUCTION ******
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Description
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"""""""""""
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.. versionadded:: 24May2023
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Description
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"""""""""""
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Define a computation that calculates the local composition for each atom based on its neighbors inside a spherical
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cutoff. If an atom has :math:`M` neighbors, then its local mass density is
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calculated as the sum of its mass and its :math:`M` neighbor masses, divided
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by the volume of the cutoff sphere (or circle in 2d). The local
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temperature of the atom is calculated as the temperature of the
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collection of :math:`M+1` atoms, after subtracting the center-of-mass velocity
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of the :math:`M+1` atoms from each of the :math:`M+1` atom's velocities. This
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is effectively the thermal velocity of the neighborhood of the central
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atom, similar to :doc:`compute temp/com <compute_temp_com>`.
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.. versionadded:: 24May2023
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The optional keyword *cutoff* defines the distance cutoff used when
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searching for neighbors. The default value is the cutoff specified by
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the pair style. If no pair style is defined, then a cutoff must be
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defined using this keyword. If the specified cutoff is larger than
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that of the pair_style plus neighbor skin (or no pair style is
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defined), the *comm_modify cutoff* option must also be set to match
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that of the *cutoff* keyword.
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Define a computation that calculates the local composition of atom types for a
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central atom based on its neighbors inside a spherical cutoff. For a simulation with
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:math:`N` atom types and an atom with :math:`M` neighbors within the cutoff, the
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fraction of each atom type is counted and divided by the total number of atoms in the
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sphere, including the central atom (:math:`M+1`). The sum of all fractions will
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always add to one.
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The neighbor list needed to compute this quantity is constructed each
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time the calculation is performed (i.e. each time a snapshot of atoms
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is dumped). Thus it can be inefficient to compute/dump this quantity
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too frequently.
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.. note::
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.. note::
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This compute uses the number of atom types, not chemical species, assigned in
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:doc:`pair_coeff <pair_style>` command. If an interatomic potential has two
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species (i.e., Cu and Ni) assigned to four different atom types in
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:doc:`pair_coeff <pair_coeff>` (i.e., 'Cu Cu Ni Ni'), the local composition will
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output four fractional values. In those cases, the user may desire an extra
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calculation step to consolidate per-type fractions into per-species fractions.
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This calculation can be conducted within LAMMPS using another compute such as
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:doc:`compute reduce <compute_reduce>`, an atom-style :doc:`variable`, or as a
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post-processing step.
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If you have a bonded system, then the settings of
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:doc:`special_bonds <special_bonds>` command can remove pairwise
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interactions between atoms in the same bond, angle, or dihedral.
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This is the default setting for the :doc:`special_bonds
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<special_bonds>` command, and means those pairwise interactions do
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not appear in the neighbor list. Because this compute uses the
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neighbor list, it also means those pairs will not be included in
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the order parameter. This difficulty can be circumvented by
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writing a dump file, and using the :doc:`rerun <rerun>` command to
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compute the order parameter for snapshots in the dump file. The
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rerun script can use a :doc:`special_bonds <special_bonds>` command
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that includes all pairs in the neighbor list.
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----------
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----------
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The optional keyword *cutoff* defines the distance cutoff used when
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searching for neighbors. The default value is the cutoff specified by
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the pair style. If no pair style is defined, then a cutoff must be
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defined using this keyword. If the specified cutoff is larger than
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that of the pair_style plus neighbor skin (or no pair style is
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defined), the *comm_modify cutoff* option must also be set to match
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that of the *cutoff* keyword.
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The neighbor list needed to compute this quantity is constructed each
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time the calculation is performed (i.e. each time a snapshot of atoms
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is dumped). Thus it can be inefficient to compute/dump this quantity
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too frequently.
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.. note::
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If you have a bonded system, then the settings of
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:doc:`special_bonds <special_bonds>` command can remove pairwise
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interactions between atoms in the same bond, angle, or dihedral.
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This is the default setting for the :doc:`special_bonds
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<special_bonds>` command, and means those pairwise interactions do
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not appear in the neighbor list. Because this compute uses the
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neighbor list, it also means those pairs will not be included in
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the order parameter. This difficulty can be circumvented by
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writing a dump file, and using the :doc:`rerun <rerun>` command to
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compute the order parameter for snapshots in the dump file. The
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rerun script can use a :doc:`special_bonds <special_bonds>` command
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that includes all pairs in the neighbor list.
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----------
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.. include:: accel_styles.rst
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.. include:: accel_styles.rst
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----------
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----------
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Output info
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"""""""""""
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Output info
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"""""""""""
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This compute calculates a per-atom array with two columns: mass
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density in density :doc:`units <units>` and temperature in temperature
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:doc:`units <units>`.
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This compute calculates a per-atom array with :math:`1 + N` columns, where :math:`N` is the number of atom types. The first column is a count of the number of atoms used to calcuate composition (including the central atom), and each subsequent column indicates the fraction of that atom type detected within the cutoff range.
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These values can be accessed by any command that uses per-atom values
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from a compute as input. See the :doc:`Howto output <Howto_output>`
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doc page for an overview of LAMMPS output options.
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These values can be accessed by any command that uses per-atom values
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from a compute as input. See the :doc:`Howto output <Howto_output>`
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doc page for an overview of LAMMPS output options.
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Restrictions
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""""""""""""
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Restrictions
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""""""""""""
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This compute is part of the EXTRA-COMPUTE package. It is only enabled
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if LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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This compute is part of the EXTRA-COMPUTE package. It is only enabled
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if LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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Related commands
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""""""""""""""""
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Related commands
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""""""""""""""""
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:doc:`comm_modify <comm_modify>`
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:doc:`comm_modify <comm_modify>`
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Default
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"""""""
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Default
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"""""""
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The option defaults are *cutoff* = pair style cutoff.
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..
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The option defaults are *cutoff* = pair style cutoff.
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