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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><B>Description:</B>
</P> </P>
<P>Change or adapt one or more specific simulation attributes or settings <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>
<P>This is a version of the <A HREF = "fix_adapt.html">fix_adapt</A> with two <P>This is an enhanced version of the <A HREF = "fix_adapt.html">fix_adapt</A> command
differences, with two differences,
</P> </P>
<UL><LI>It is possible to modify the charges of chosen atom types only, instead of scaling all the charges in the system. <UL><LI>It is possible to modify the charges of chosen atom types only,
<LI>There is a new option <I>after</I> for better compatibility with "fixave/time". 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> </UL>
<P>This version is suited for free energy calculations using <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>. <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. initial values after the run.
</P> </P>
<P>If the <I>after</I> keyword is set to <I>yes</I>, then the parameters are <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 changed one timestep after the multiple of N. In this manner, if a fix
fix such as "fix ave/time" is used to calculate averages at every N such as "fix ave/time" is used to calculate averages at every N
timesteps, all the contributions to the average will be obtained with timesteps, all the contributions to the average will be obtained with
the same values of the parameters. the same values of the parameters.
</P> </P>
<HR> <HR>
@ -259,9 +262,8 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>
<P><A HREF = "compute_fep.html">compute fep</A> <P><A HREF = "compute_fep.html">compute fep</A>, <A HREF = "fix_adapt.html">fix_adapt</A>, <A HREF = "compute_ti.html">compute
<A HREF = "fix_adapt.html">fix_adapt</A> ti</A>
<A HREF = "compute_ti.html">compute ti</A>
</P> </P>
<P><B>Default:</B> <P><B>Default:</B>
</P> </P>

26
doc/fix_adapt_fep.txt
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@ -52,15 +52,16 @@ fix 1 all adapt/fep 10 atom diameter 1 v_size :pre
[Description:] [Description:]
Change or adapt one or more specific simulation attributes or settings 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 This is an enhanced version of the "fix_adapt"_fix_adapt.html command
differences, with two differences,
It is possible to modify the charges of chosen atom types only, \ It is possible to modify the charges of chosen atom types only,
instead of scaling all the charges in the system. instead of scaling all the charges in the system. :ulb,l
There is a new option {after} for better compatibility with "fix\
ave/time". :ul There is a new option {after} for better compatibility with "fix
ave/time". :l,ule
This version is suited for free energy calculations using This version is suited for free energy calculations using
"compute_ti"_compute_ti.html or "compute_fep"_compute_fep.html. "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. initial values after the run.
If the {after} keyword is set to {yes}, then the parameters are 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 changed one timestep after the multiple of N. In this manner, if a fix
fix such as "fix ave/time" is used to calculate averages at every N such as "fix ave/time" is used to calculate averages at every N
timesteps, all the contributions to the average will be obtained with timesteps, all the contributions to the average will be obtained with
the same values of the parameters. the same values of the parameters.
:line :line
@ -247,9 +248,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Related commands:] [Related commands:]
"compute fep"_compute_fep.html "compute fep"_compute_fep.html, "fix_adapt"_fix_adapt.html, "compute
"fix_adapt"_fix_adapt.html ti"_compute_ti.html
"compute ti"_compute_ti.html
[Default:] [Default:]