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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11961 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2014-05-09 16:23:11 +00:00
parent 358568b55d
commit f4f7e8b1b5
2 changed files with 26 additions and 24 deletions
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24
doc/fix_adapt_fep.html
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@ -64,13 +64,16 @@ fix 1 all adapt/fep 10 atom diameter 1 v_size
<P><B>Description:</B>
</P>
<P>Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs.
over time as a simulation runs.
</P>
<P>This is a version of the <A HREF = "fix_adapt.html">fix_adapt</A> with two
differences,
<P>This is an enhanced version of the <A HREF = "fix_adapt.html">fix_adapt</A> command
with two differences,
</P>
<UL><LI>It is possible to modify the charges of chosen atom types only, instead of scaling all the charges in the system.
<LI>There is a new option <I>after</I> for better compatibility with "fixave/time".
<UL><LI>It is possible to modify the charges of chosen atom types only,
instead of scaling all the charges in the system.
<LI>There is a new option <I>after</I> for better compatibility with "fix
ave/time".
</UL>
<P>This version is suited for free energy calculations using
<A HREF = "compute_ti.html">compute_ti</A> or <A HREF = "compute_fep.html">compute_fep</A>.
@ -98,10 +101,10 @@ the parameters themselves are actually altered; make sure you use the
initial values after the run.
</P>
<P>If the <I>after</I> keyword is set to <I>yes</I>, then the parameters are
changed one timestep after the multiple of N. In this manner, if a
fix such as "fix ave/time" is used to calculate averages at every N
changed one timestep after the multiple of N. In this manner, if a fix
such as "fix ave/time" is used to calculate averages at every N
timesteps, all the contributions to the average will be obtained with
the same values of the parameters.
the same values of the parameters.
</P>
<HR>
@ -259,9 +262,8 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_fep.html">compute fep</A>
<A HREF = "fix_adapt.html">fix_adapt</A>
<A HREF = "compute_ti.html">compute ti</A>
<P><A HREF = "compute_fep.html">compute fep</A>, <A HREF = "fix_adapt.html">fix_adapt</A>, <A HREF = "compute_ti.html">compute
ti</A>
</P>
<P><B>Default:</B>
</P>

26
doc/fix_adapt_fep.txt
View File

@ -52,15 +52,16 @@ fix 1 all adapt/fep 10 atom diameter 1 v_size :pre
[Description:]
Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs.
over time as a simulation runs.
This is a version of the "fix_adapt"_fix_adapt.html with two
differences,
This is an enhanced version of the "fix_adapt"_fix_adapt.html command
with two differences,
It is possible to modify the charges of chosen atom types only, \
instead of scaling all the charges in the system.
There is a new option {after} for better compatibility with "fix\
ave/time". :ul
It is possible to modify the charges of chosen atom types only,
instead of scaling all the charges in the system. :ulb,l
There is a new option {after} for better compatibility with "fix
ave/time". :l,ule
This version is suited for free energy calculations using
"compute_ti"_compute_ti.html or "compute_fep"_compute_fep.html.
@ -88,10 +89,10 @@ the parameters themselves are actually altered; make sure you use the
initial values after the run.
If the {after} keyword is set to {yes}, then the parameters are
changed one timestep after the multiple of N. In this manner, if a
fix such as "fix ave/time" is used to calculate averages at every N
changed one timestep after the multiple of N. In this manner, if a fix
such as "fix ave/time" is used to calculate averages at every N
timesteps, all the contributions to the average will be obtained with
the same values of the parameters.
the same values of the parameters.
:line
@ -247,9 +248,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Related commands:]
"compute fep"_compute_fep.html
"fix_adapt"_fix_adapt.html
"compute ti"_compute_ti.html
"compute fep"_compute_fep.html, "fix_adapt"_fix_adapt.html, "compute
ti"_compute_ti.html
[Default:]