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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13405 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2015-04-11 23:48:54 +00:00
parent 12d466fc3b
commit 5b30a58492
4 changed files with 44 additions and 32 deletions
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21
doc/compute_temp_chunk.html
View File

@ -69,7 +69,7 @@ chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_how
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 =
<P>The temperature is calculated by the formula KE = DOF/2 k T, where KE =
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.
@ -187,20 +187,23 @@ not on a per-chunk basis.
<P>The <I>adof</I> and <I>cdof</I> keywords define the values used in the degree of
freedom (DOF) formulas used for the global or per-chunk temperature,
as described above. They can be used to calculate a more appropriate
temperature for some kinds of chunks. Here are 3 examples.
temperature for some kinds of chunks. Here are 3 examples:
</P>
<P>If spatially binned chunks contain some number of water molecules and
<A HREF = "fix_shake.html">fix shake</A> is used to make each molecule rigid, then
you could calculate a temperature with 6 degrees of freedom (DOF) (3
translational, 3 rotational) per molecule by setting <I>adof</I> to 2.0.
If <A HREF = "compute_temp_partial.html">compute temp/partial</A> is used with the
</P>
<P>If <A HREF = "compute_temp_partial.html">compute temp/partial</A> is used with the
<I>bias</I> keyword to only allow the x component of velocity to contribute
to the temperature, then <I>adof</I> = 1.0 would be appropriate. If each
chunk consists of a large molecule, with some number of its bonds
constrained by <A HREF = "fix_shake.html">fix shake</A> or the entire molecule by
<A HREF = "fix_rigid.html">fix rigid/small</A>, then <I>cdof</I> could be set to the
remaining degrees of freedom for the entire molecule (entire chunk in
this case).
to the temperature, then <I>adof</I> = 1.0 would be appropriate.
</P>
<P>If each chunk consists of a large molecule, with some number of its
bonds constrained by <A HREF = "fix_shake.html">fix shake</A> or the entire molecule
by <A HREF = "fix_rigid.html">fix rigid/small</A>, <I>adof</I> = 0.0 and <I>cdof</I> could be
set to the remaining degrees of freedom for the entire molecule
(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
molecule.
</P>
<HR>

19
doc/compute_temp_chunk.txt
View File

@ -57,7 +57,7 @@ chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
defined and examples of how they can be used to measure properties of
a system.
The temperature is calculated by the formula KE = DOF k T, where KE =
The temperature is calculated by the formula KE = DOF/2 k T, where KE =
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.
@ -175,20 +175,23 @@ not on a per-chunk basis.
The {adof} and {cdof} keywords define the values used in the degree of
freedom (DOF) formulas used for the global or per-chunk temperature,
as described above. They can be used to calculate a more appropriate
temperature for some kinds of chunks. Here are 3 examples.
temperature for some kinds of chunks. Here are 3 examples:
If spatially binned chunks contain some number of water molecules and
"fix shake"_fix_shake.html is used to make each molecule rigid, then
you could calculate a temperature with 6 degrees of freedom (DOF) (3
translational, 3 rotational) per molecule by setting {adof} to 2.0.
If "compute temp/partial"_compute_temp_partial.html is used with the
{bias} keyword to only allow the x component of velocity to contribute
to the temperature, then {adof} = 1.0 would be appropriate. If each
chunk consists of a large molecule, with some number of its bonds
constrained by "fix shake"_fix_shake.html or the entire molecule by
"fix rigid/small"_fix_rigid.html, then {cdof} could be set to the
remaining degrees of freedom for the entire molecule (entire chunk in
this case).
to the temperature, then {adof} = 1.0 would be appropriate.
If each chunk consists of a large molecule, with some number of its
bonds constrained by "fix shake"_fix_shake.html or the entire molecule
by "fix rigid/small"_fix_rigid.html, {adof} = 0.0 and {cdof} could be
set to the remaining degrees of freedom for the entire molecule
(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
molecule.
:line

19
doc/fix_ave_chunk.html
View File

@ -337,20 +337,23 @@ bias.
freedom (DOF) formula described above for for temperature calculation
for each chunk. They are only used when the <I>temp</I> value is
calculated. They can be used to calculate a more appropriate
temperature for some kinds of chunks. Here are 3 examples.
temperature for some kinds of chunks. Here are 3 examples:
</P>
<P>If spatially binned chunks contain some number of water molecules and
<A HREF = "fix_shake.html">fix shake</A> is used to make each molecule rigid, then
you could calculate a temperature with 6 degrees of freedom (DOF) (3
translational, 3 rotational) per molecule by setting <I>adof</I> to 2.0.
If <A HREF = "compute_temp_partial.html">compute temp/partial</A> is used with the
</P>
<P>If <A HREF = "compute_temp_partial.html">compute temp/partial</A> is used with the
<I>bias</I> keyword to only allow the x component of velocity to contribute
to the temperature, then <I>adof</I> = 1.0 would be appropriate. If each
chunk consists of a large molecule, with some number of its bonds
constrained by <A HREF = "fix_shake.html">fix shake</A> or the entire molecule by
<A HREF = "fix_rigid.html">fix rigid/small</A>, then <I>cdof</I> could be set to the
remaining degrees of freedom for the entire molecule (entire chunk in
this case).
to the temperature, then <I>adof</I> = 1.0 would be appropriate.
</P>
<P>If each chunk consists of a large molecule, with some number of its
bonds constrained by <A HREF = "fix_shake.html">fix shake</A> or the entire molecule
by <A HREF = "fix_rigid.html">fix rigid/small</A>, <I>adof</I> = 0.0 and <I>cdof</I> could be
set to the remaining degrees of freedom for the entire molecule
(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
molecule.
</P>
<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
timesteps, a section of chunk info will be written to a text file in

17
doc/fix_ave_chunk.txt
View File

@ -323,20 +323,23 @@ The {adof} and {cdof} keywords define the values used in the degree of
freedom (DOF) formula described above for for temperature calculation
for each chunk. They are only used when the {temp} value is
calculated. They can be used to calculate a more appropriate
temperature for some kinds of chunks. Here are 3 examples.
temperature for some kinds of chunks. Here are 3 examples:
If spatially binned chunks contain some number of water molecules and
"fix shake"_fix_shake.html is used to make each molecule rigid, then
you could calculate a temperature with 6 degrees of freedom (DOF) (3
translational, 3 rotational) per molecule by setting {adof} to 2.0.
If "compute temp/partial"_compute_temp_partial.html is used with the
{bias} keyword to only allow the x component of velocity to contribute
to the temperature, then {adof} = 1.0 would be appropriate. If each
chunk consists of a large molecule, with some number of its bonds
constrained by "fix shake"_fix_shake.html or the entire molecule by
"fix rigid/small"_fix_rigid.html, then {cdof} could be set to the
remaining degrees of freedom for the entire molecule (entire chunk in
this case).
to the temperature, then {adof} = 1.0 would be appropriate.
If each chunk consists of a large molecule, with some number of its
bonds constrained by "fix shake"_fix_shake.html or the entire molecule
by "fix rigid/small"_fix_rigid.html, {adof} = 0.0 and {cdof} could be
set to the remaining degrees of freedom for the entire molecule
(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
molecule.
The {file} keyword allows a filename to be specified. Every {Nfreq}
timesteps, a section of chunk info will be written to a text file in