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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12944 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-01-16 16:09:27 +00:00
parent dd36721943
commit bed966d556
8 changed files with 90 additions and 10 deletions
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12
doc/fix_adapt.html
View File

@ -234,6 +234,12 @@ over the course of a 1000-step simulation:
<PRE>variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter v_size
</PRE>
<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, this fix changes
parameters only on the outer loop (largest) timesteps, which means
that the frequency parameter <I>N</I> has to be commensurate with the step
numbers for those outer steps. Otherwise invocation will be less
frequent than expected.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
@ -246,7 +252,11 @@ commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
<P><B>Restrictions:</B>
</P>
<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, this fix is only
invoked on outer loop time steps that are also commensurate with
the frequency parameter <I>N</I>.
</P>
<P><B>Related commands:</B>
</P>

12
doc/fix_adapt.txt
View File

@ -220,6 +220,12 @@ over the course of a 1000-step simulation:
variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter v_size :pre
When the "run style"_run_style.html is {respa}, this fix changes
parameters only on the outer loop (largest) timesteps, which means
that the frequency parameter {N} has to be commensurate with the step
numbers for those outer steps. Otherwise invocation will be less
frequent than expected.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
@ -232,7 +238,11 @@ commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Restrictions:]
When the "run style"_run_style.html is {respa}, this fix is only
invoked on outer loop time steps that are also commensurate with
the frequency parameter {N}.
[Related commands:]

12
doc/fix_adapt_fep.html
View File

@ -246,6 +246,12 @@ over the course of a 1000-step simulation:
<PRE>variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter * v_size
</PRE>
<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, this fix changes
parameters only on the outer loop (largest) timesteps, which means
that the frequency parameter <I>N</I> has to be commensurate with the step
numbers for those outer steps. Otherwise invocation will be less
frequent than expected.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
@ -258,7 +264,11 @@ commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
<P><B>Restrictions:</B>
</P>
<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, this fix is only
invoked on outer loop time steps that are also commensurate with
the frequency parameter <I>N</I>.
</P>
<P><B>Related commands:</B>
</P>

12
doc/fix_adapt_fep.txt
View File

@ -232,6 +232,12 @@ over the course of a 1000-step simulation:
variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter * v_size :pre
When the "run style"_run_style.html is {respa}, this fix changes
parameters only on the outer loop (largest) timesteps, which means
that the frequency parameter {N} has to be commensurate with the step
numbers for those outer steps. Otherwise invocation will be less
frequent than expected.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
@ -244,7 +250,11 @@ commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Restrictions:]
When the "run style"_run_style.html is {respa}, this fix is only
invoked on outer loop time steps that are also commensurate with
the frequency parameter {N}.
[Related commands:]

4
doc/fix_ave_spatial.html
View File

@ -93,8 +93,8 @@ commands</A> such as <A HREF = "thermo_style.html">thermo_style
custom</A>, and can also be written to a file.
</P>
<P>The group specified with the command means only atoms within the group
contribute to bin averages. If the <I>region</I> keyword is used, the
atom must be in both the group and the specified geometric
contribute to bin averages. If the <I>region</I> keyword is used, the atom
must be in both the specified group and the specified geometric
<A HREF = "region.html">region</A> in order to contribute to bin averages.
</P>
<P>Each listed value can be an atom attribute (position, velocity, force

4
doc/fix_ave_spatial.txt
View File

@ -78,8 +78,8 @@ commands"_Section_howto.html#howto_15 such as "thermo_style
custom"_thermo_style.html, and can also be written to a file.
The group specified with the command means only atoms within the group
contribute to bin averages. If the {region} keyword is used, the
atom must be in both the group and the specified geometric
contribute to bin averages. If the {region} keyword is used, the atom
must be in both the specified group and the specified geometric
"region"_region.html in order to contribute to bin averages.
Each listed value can be an atom attribute (position, velocity, force

22
doc/minimize.html
View File

@ -50,6 +50,11 @@ slowly drains all kinetic energy from the system. The <A HREF = "pair_soft.html
soft</A> potential can be used to un-overlap atoms while
running dynamics.
</P>
<P>Note that you can minimize some atoms in the system while holding the
coordiates of other atoms fixed by applying <A HREF = "fix_setforce.html">fix
setforce</A> to the other atoms. See a fuller
discussion of using fixes while minimizing below.
</P>
<P>The <A HREF = "min_style.html">minimization styles</A> <I>cg</I>, <I>sd</I>, and <I>hftn</I>
involves an outer iteration loop which sets the search direction along
which atom coordinates are changed. An inner iteration is then
@ -211,8 +216,23 @@ during the minimization.
</P>
<P>Only a few other fixes (typically those that apply force constraints)
are invoked during minimization. See the doc pages for individual
<A HREF = "fix.html">fix</A> commands to see which ones are relevant.
<A HREF = "fix.html">fix</A> commands to see which ones are relevant. Current
examples of fixes that can be used include:
</P>
<UL><LI><A HREF = "fix_addforce.html">fix addforce</A>
<LI><A HREF = "fix_addtorque.html">fix addtorque</A>
<LI><A HREF = "fix_efield.html">fix efield</A>
<LI><A HREF = "fix_enforce2d.html">fix enforce2d</A>
<LI><A HREF = "fix_indent.html">fix indent</A>
<LI><A HREF = "fix_lineforce.html">fix lineforce</A>
<LI><A HREF = "fix_planeforce.html">fix planeforce</A>
<LI><A HREF = "fix_setforce.html">fix setforce</A>
<LI><A HREF = "fix_spring.html">fix spring</A>
<LI><A HREF = "fix_spring_self.html">fix spring/self</A>
<LI><A HREF = "fix_viscous.html">fix viscous</A>
<LI><A HREF = "fix_wall.html">fix wall</A>
<LI><A HREF = "fix_wall_region.html">fix wall/region</A>
</UL>
<P>IMPORTANT NOTE: Some fixes which are invoked during minimization have
an associated potential energy. For that energy to be included in the
total potential energy of the system (the quantity being minimized),

22
doc/minimize.txt
View File

@ -47,6 +47,11 @@ slowly drains all kinetic energy from the system. The "pair_style
soft"_pair_soft.html potential can be used to un-overlap atoms while
running dynamics.
Note that you can minimize some atoms in the system while holding the
coordiates of other atoms fixed by applying "fix
setforce"_fix_setforce.html to the other atoms. See a fuller
discussion of using fixes while minimizing below.
The "minimization styles"_min_style.html {cg}, {sd}, and {hftn}
involves an outer iteration loop which sets the search direction along
which atom coordinates are changed. An inner iteration is then
@ -208,7 +213,22 @@ during the minimization.
Only a few other fixes (typically those that apply force constraints)
are invoked during minimization. See the doc pages for individual
"fix"_fix.html commands to see which ones are relevant.
"fix"_fix.html commands to see which ones are relevant. Current
examples of fixes that can be used include:
"fix addforce"_fix_addforce.html
"fix addtorque"_fix_addtorque.html
"fix efield"_fix_efield.html
"fix enforce2d"_fix_enforce2d.html
"fix indent"_fix_indent.html
"fix lineforce"_fix_lineforce.html
"fix planeforce"_fix_planeforce.html
"fix setforce"_fix_setforce.html
"fix spring"_fix_spring.html
"fix spring/self"_fix_spring_self.html
"fix viscous"_fix_viscous.html
"fix wall"_fix_wall.html
"fix wall/region"_fix_wall_region.html :ul
IMPORTANT NOTE: Some fixes which are invoked during minimization have
an associated potential energy. For that energy to be included in the