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<div class="section" id="compute-dipole-chunk-command">
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<span id="index-0"></span><h1>compute dipole/chunk command<a class="headerlink" href="#compute-dipole-chunk-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID dipole/chunk chunkID charge-correction
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
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<li>dipole/chunk = style name of this compute command</li>
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<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command</li>
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<li>charge-correction = <em>mass</em> or <em>geometry</em>, use COM or geometric center for charged chunk correction (optional)</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>compute 1 fluid dipole/chunk molchunk
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compute dw water dipole/chunk 1 geometry
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Define a computation that calculates the dipole vector and total dipole
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for multiple chunks of atoms.</p>
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<p>In LAMMPS, chunks are collections of atoms defined by a <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
|
||||
as chunkID. For example, a single chunk could be the atoms in a
|
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molecule or atoms in a spatial bin. See the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> doc page and “<a class="reference internal" href="Section_howto.html#howto-23"><span>Section_howto 23</span></a> for details of how chunks can be
|
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defined and examples of how they can be used to measure properties of
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a system.</p>
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<p>This compute calculates the x,y,z coordinates of the dipole vector
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and the total dipole moment for each chunk, which includes all effects
|
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due to atoms passing thru periodic boundaries. For chunks with a net
|
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charge the resulting dipole is made position independent by subtracting
|
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the position vector of the center of mass or geometric center times the
|
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net charge from the computed dipole vector.</p>
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<p>Note that only atoms in the specified group contribute to the
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calculation. The <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command
|
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defines its own group; atoms will have a chunk ID = 0 if they are not
|
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in that group, signifying they are not assigned to a chunk, and will
|
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thus also not contribute to this calculation. You can specify the
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“all” group for this command if you simply want to include atoms with
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non-zero chunk IDs.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">The coordinates of an atom contribute to the chunk’s
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dipole in “unwrapped” form, by using the image flags
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associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command
|
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for a discussion of “unwrapped” coordinates. See the Atoms section of
|
||||
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags
|
||||
and how they are set for each atom. You can reset the image flags
|
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(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
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</div>
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<p>The simplest way to output the results of the compute com/chunk
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calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>
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command, for example:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom molecule
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compute myChunk all dipole/chunk cc1
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fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
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</pre></div>
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</div>
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<p><strong>Output info:</strong></p>
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<p>This compute calculates a global array where the number of rows = the
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number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command. The number of columns =
|
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4 for the x,y,z dipole vector components and the total dipole of each
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chunk. These values can be accessed by any command that uses global
|
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array values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
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options.</p>
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<p>The array values are “intensive”. The array values will be in
|
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dipole units, i.e. charge units times distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
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</div>
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<div class="section" id="restrictions">
|
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
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<div>none</div></blockquote>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="compute_com_chunk.html"><em>compute com/chunk</em></a></p>
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<p><strong>Default:</strong> none</p>
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@ -0,0 +1,100 @@
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.. index:: compute dipole/chunk
|
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compute dipole/chunk 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 dipole/chunk chunkID charge-correction
|
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|
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* ID, group-ID are documented in :doc:`compute <compute>` command
|
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* dipole/chunk = style name of this compute command
|
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* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
|
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* charge-correction = *mass* or *geometry*, use COM or geometric center for charged chunk correction (optional)
|
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|
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Examples
|
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""""""""
|
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|
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.. parsed-literal::
|
||||
|
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compute 1 fluid dipole/chunk molchunk
|
||||
compute dw water dipole/chunk 1 geometry
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that calculates the dipole vector and total dipole
|
||||
for multiple chunks of atoms.
|
||||
|
||||
In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
|
||||
to a single chunk (or no chunk). The ID for this command is specified
|
||||
as chunkID. For example, a single chunk could be the atoms in a
|
||||
molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom <compute_chunk_atom>` doc page and ":ref:`Section_howto 23 <howto_23>` for details of how chunks can be
|
||||
defined and examples of how they can be used to measure properties of
|
||||
a system.
|
||||
|
||||
This compute calculates the x,y,z coordinates of the dipole vector
|
||||
and the total dipole moment for each chunk, which includes all effects
|
||||
due to atoms passing thru periodic boundaries. For chunks with a net
|
||||
charge the resulting dipole is made position independent by subtracting
|
||||
the position vector of the center of mass or geometric center times the
|
||||
net charge from the computed dipole vector.
|
||||
|
||||
Note that only atoms in the specified group contribute to the
|
||||
calculation. The :doc:`compute chunk/atom <compute_chunk_atom>` command
|
||||
defines its own group; atoms will have a chunk ID = 0 if they are not
|
||||
in that group, signifying they are not assigned to a chunk, and will
|
||||
thus also not contribute to this calculation. You can specify the
|
||||
"all" group for this command if you simply want to include atoms with
|
||||
non-zero chunk IDs.
|
||||
|
||||
.. note::
|
||||
|
||||
The coordinates of an atom contribute to the chunk's
|
||||
dipole in "unwrapped" form, by using the image flags
|
||||
associated with each atom. See the :doc:`dump custom <dump>` command
|
||||
for a discussion of "unwrapped" coordinates. See the Atoms section of
|
||||
the :doc:`read_data <read_data>` command for a discussion of image flags
|
||||
and how they are set for each atom. You can reset the image flags
|
||||
(e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
|
||||
|
||||
The simplest way to output the results of the compute com/chunk
|
||||
calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
|
||||
command, for example:
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
compute cc1 all chunk/atom molecule
|
||||
compute myChunk all dipole/chunk cc1
|
||||
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
|
||||
|
||||
**Output info:**
|
||||
|
||||
This compute calculates a global array where the number of rows = the
|
||||
number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns =
|
||||
4 for the x,y,z dipole vector components and the total dipole of each
|
||||
chunk. These values can be accessed by any command that uses global
|
||||
array values from a compute as input. See :ref:`Section_howto 15 <howto_15>` for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The array values are "intensive". The array values will be in
|
||||
dipole units, i.e. charge units times distance :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`compute com/chunk <compute_com_chunk>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
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.. _ld: Manual.html
|
||||
.. _lc: Section_commands.html#comm
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|
|
@ -0,0 +1,92 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
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|
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:line
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|
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compute dipole/chunk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID dipole/chunk chunkID charge-correction :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
dipole/chunk = style name of this compute command
|
||||
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command
|
||||
charge-correction = {mass} or {geometry}, use COM or geometric center for charged chunk correction (optional) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 fluid dipole/chunk molchunk
|
||||
compute dw water dipole/chunk 1 geometry :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the dipole vector and total dipole
|
||||
for multiple chunks of atoms.
|
||||
|
||||
In LAMMPS, chunks are collections of atoms defined by a "compute
|
||||
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
|
||||
to a single chunk (or no chunk). The ID for this command is specified
|
||||
as chunkID. For example, a single chunk could be the atoms in a
|
||||
molecule or atoms in a spatial bin. See the "compute
|
||||
chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
|
||||
23"_Section_howto.html#howto_23 for details of how chunks can be
|
||||
defined and examples of how they can be used to measure properties of
|
||||
a system.
|
||||
|
||||
This compute calculates the x,y,z coordinates of the dipole vector
|
||||
and the total dipole moment for each chunk, which includes all effects
|
||||
due to atoms passing thru periodic boundaries. For chunks with a net
|
||||
charge the resulting dipole is made position independent by subtracting
|
||||
the position vector of the center of mass or geometric center times the
|
||||
net charge from the computed dipole vector.
|
||||
|
||||
Note that only atoms in the specified group contribute to the
|
||||
calculation. The "compute chunk/atom"_compute_chunk_atom.html command
|
||||
defines its own group; atoms will have a chunk ID = 0 if they are not
|
||||
in that group, signifying they are not assigned to a chunk, and will
|
||||
thus also not contribute to this calculation. You can specify the
|
||||
"all" group for this command if you simply want to include atoms with
|
||||
non-zero chunk IDs.
|
||||
|
||||
NOTE: The coordinates of an atom contribute to the chunk's
|
||||
dipole in "unwrapped" form, by using the image flags
|
||||
associated with each atom. See the "dump custom"_dump.html command
|
||||
for a discussion of "unwrapped" coordinates. See the Atoms section of
|
||||
the "read_data"_read_data.html command for a discussion of image flags
|
||||
and how they are set for each atom. You can reset the image flags
|
||||
(e.g. to 0) before invoking this compute by using the "set
|
||||
image"_set.html command.
|
||||
|
||||
The simplest way to output the results of the compute com/chunk
|
||||
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
|
||||
command, for example:
|
||||
|
||||
compute cc1 all chunk/atom molecule
|
||||
compute myChunk all dipole/chunk cc1
|
||||
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a global array where the number of rows = the
|
||||
number of chunks {Nchunk} as calculated by the specified "compute
|
||||
chunk/atom"_compute_chunk_atom.html command. The number of columns =
|
||||
4 for the x,y,z dipole vector components and the total dipole of each
|
||||
chunk. These values can be accessed by any command that uses global
|
||||
array values from a compute as input. See "Section_howto
|
||||
15"_Section_howto.html#howto_15 for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The array values are "intensive". The array values will be in
|
||||
dipole units, i.e. charge units times distance "units"_units.html.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute com/chunk"_compute_com_chunk.html
|
||||
|
||||
[Default:] none
|
||||
Loading…
Reference in New Issue