156 lines
6.0 KiB
Plaintext
156 lines
6.0 KiB
Plaintext
.. index:: compute pair/local
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compute pair/local command
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==========================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID pair/local value1 value2 ... keyword args ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* pair/local = style name of this compute command
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* one or more values may be appended
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* value = *dist* or *eng* or *force* or *fx* or *fy* or *fz* or *pN*
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.. parsed-literal::
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*dist* = pairwise distance
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*eng* = pairwise energy
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*force* = pairwise force
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*fx*\ ,\ *fy*\ ,\ *fz* = components of pairwise force
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*pN* = pair style specific quantities for allowed N values
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* zero or more keyword/arg pairs may be appended
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* keyword = *cutoff*
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.. parsed-literal::
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*cutoff* arg = *type* or *radius*
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Examples
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""""""""
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.. parsed-literal::
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compute 1 all pair/local eng
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compute 1 all pair/local dist eng force
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compute 1 all pair/local dist eng fx fy fz
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compute 1 all pair/local dist fx fy fz p1 p2 p3
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Description
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"""""""""""
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Define a computation that calculates properties of individual pairwise
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interactions. The number of datums generated, aggregated across all
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processors, equals the number of pairwise interactions in the system.
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The local data stored by this command is generated by looping over the
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pairwise neighbor list. Info about an individual pairwise interaction
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will only be included if both atoms in the pair are in the specified
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compute group, and if the current pairwise distance is less than the
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force cutoff distance for that interaction, as defined by the
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:doc:`pair_style <pair_style>` and :doc:`pair_coeff <pair_coeff>`
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commands.
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The value *dist* is the distance bewteen the pair of atoms.
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The value *eng* is the interaction energy for the pair of atoms.
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The value *force* is the force acting between the pair of atoms, which
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is positive for a repulsive force and negative for an attractive
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force. The values *fx*\ , *fy*\ , and *fz* are the xyz components of
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*force* on atom I.
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A pair style may define additional pairwise quantities which can be
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accessed as *p1* to *pN*\ , where N is defined by the pair style. Most
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pair styles do not define any additional quantities, so N = 0. An
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example of ones that do are the :doc:`granular pair styles <pair_gran>`
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which calculate the tangential force between two particles and return
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its components and magnitude acting on atom I for N = 1,2,3,4. See
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individual pair styles for detils.
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The value *dist* will be in distance :doc:`units <units>`. The value
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*eng* will be in energy :doc:`units <units>`. The values *force*\ , *fx*\ ,
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*fy*\ , and *fz* will be in force :doc:`units <units>`. The values *pN*
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will be in whatever units the pair style defines.
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The optional *cutoff* keyword determines how the force cutoff distance
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for an interaction is determined. For the default setting of *type*\ ,
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the pairwise cutoff defined by the :doc:`pair_style <pair_style>`
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command for the types of the two atoms is used. For the *radius*
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setting, the sum of the radii of the two particles is used as a
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cutoff. For example, this is appropriate for granular particles which
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only interact when they are overlapping, as computed by `granular pair styles <pair_gran.txt>`_.
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Note that as atoms migrate from processor to processor, there will be
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no consistent ordering of the entries within the local vector or array
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from one timestep to the next. The only consistency that is
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guaranteed is that the ordering on a particular timestep will be the
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same for local vectors or arrays generated by other compute commands.
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For example, pair output from the :doc:`compute property/local <compute_property_local>` command can be combined
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with data from this command and output by the :doc:`dump local <dump>`
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command in a consistent way.
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Here is an example of how to do this:
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.. parsed-literal::
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compute 1 all property/local patom1 patom2
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compute 2 all pair/local dist eng force
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dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_2[1] c_2[2] c_2[3]
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.. note::
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For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4
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interactions within the molecular topology, their pairwise interaction
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may be turned off, and thus they may not appear in the neighbor list,
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and will not be part of the local data created by this command. More
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specifically, this will be true of I,J pairs with a weighting factor
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of 0.0; pairs with a non-zero weighting factor are included. The
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weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set
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by the :doc:`special_bonds <special_bonds>` command. An exception is if
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long-range Coulombics are being computed via the
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:doc:`kspace_style <kspace_style>` command, then atom pairs with
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weighting factors of zero are still included in the neighbor list, so
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that a portion of the long-range interaction contribution can be
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computed in the pair style. Hence in that case, those atom pairs will
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be part of the local data created by this command.
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**Output info:**
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This compute calculates a local vector or local array depending on the
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number of keywords. The length of the vector or number of rows in the
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array is the number of pairs. If a single keyword is specified, a
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local vector is produced. If two or more keywords are specified, a
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local array is produced where the number of columns = the number of
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keywords. The vector or array can be accessed by any command that
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uses local values from a compute as input. See :ref:`this section <howto_15>` for an overview of LAMMPS output
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options.
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The output for *dist* will be in distance :doc:`units <units>`. The
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output for *eng* will be in energy :doc:`units <units>`. The output for
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*force*\ , *fx*\ , *fy*\ , and *fz* will be in force :doc:`units <units>`.
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The outpur for *pN* will be in whatever units the pair style defines.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
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Default
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"""""""
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The keyword default is cutoff = type.
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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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