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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13119 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2015-02-16 17:52:45 +00:00
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doc/compute_temp_chunk.html
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@ -21,14 +21,15 @@
<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
<LI>zero or more values can be listed
<LI>zero or more values can be listed as value1,value2,etc
<LI>value = <I>temp</I> or <I>kecom</I> or <I>internal</I>
<LI> temp = temperature of each chunk
<PRE> temp = temperature of each chunk
kecom = kinetic energy of each chunk based on velocity of center of mass
internal = internal kinetic energy of each chunk
zero or more keyword/value pairs may be appended
internal = internal kinetic energy of each chunk
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>com</I> or <I>bias</I> or <I>adof</I> or <I>cdof</I>
@ -69,9 +70,9 @@ defined and examples of how they can be used to measure properties of
a system.
</P>
<P>The temperature is calculated by the formula KE = DOF k T, where KE =
total kinetic energy of all atoms both in the group and assigned to
chunks (sum of 1/2 m v^2), DOF = the total number of degrees of
freedom for those atoms, k = Boltzmann constant, and T = temperature.
total kinetic energy of all atoms assigned to chunks (sum of 1/2 m
v^2), DOF = the total number of degrees of freedom for those atoms, k
= Boltzmann constant, and T = temperature.
</P>
<P>The DOF is calculated as N*adof + Nchunk*cdof, where N = number of
atoms contributing to the KE, adof = degrees of freedom per atom, and
@ -133,25 +134,26 @@ concept is somewhat ill-defined. In some cases, you can use the
<I>adof</I> and <I>cdof</I> keywords to adjust the calculated degress of freedom
appropriately, as explained below.
</P>
<P>Note that this compute and the <A HREF = "fix_ave_chunk.html">fix ave/chunk temp</A>
command can calculate different things. This compute calculates the
temperature for each chunk for a single snapshot. Fix ave/chunk can
do that but can time average those values over many snapshots, or it
can compute a temperature as if the atoms in the chunk on different
timesteps were collected together as one set of atoms to calculate
their temperature. This compute allows the center-of-mass velocity of
each chunk to be subtracted before calculating the temperature; fix
ave/chunk does not.
<P>Note that the per-chunk temperature calulated by this compute and the
<A HREF = "fix_ave_chunk.html">fix ave/chunk temp</A> command can be different.
This compute calculates the temperature for each chunk for a single
snapshot. Fix ave/chunk can do that but can also time average those
values over many snapshots, or it can compute a temperature as if the
atoms in the chunk on different timesteps were collected together as
one set of atoms to calculate their temperature. This compute allows
the center-of-mass velocity of each chunk to be subtracted before
calculating the temperature; fix ave/chunk does not.
</P>
<P>Note that only atoms in the specified group contribute to the
calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> 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.
<P>IMPORTANT NOTE: Only atoms in the specified group contribute to the
calculations performed by this compute. The <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> 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.
</P>
<P>The simplest way to output the pre-chunk results of the compute
<P>The simplest way to output the per-chunk results of the compute
temp/chunk calculation to a file is to use the <A HREF = "fix_ave_time.html">fix
ave/time</A> command, for example:
</P>