git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10364 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-07-25 22:21:01 +00:00
parent be3847ff31
commit a26ee56443
2 changed files with 41 additions and 21 deletions

View File

@ -21,8 +21,9 @@
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>N_k = number of terms in the Prony series representation of the memory kernel
seed = random number seed to use for white noise (positive integer)
<LI>N_k = number of terms in the Prony series representation of the memory kernel
<LI>seed = random number seed to use for white noise (positive integer)
<LI>series = <I>pprony</I> is presently the only available option
@ -35,9 +36,8 @@ seed = random number seed to use for white noise (positive integer)
<PRE>keyword = <I>frozen</I> or <I>zero</I>
<I>frozen</I> value = <I>no</I> or <I>yes</I>
<I>no</I> = initialize extended variables using values drawn from equilibrium distribution at Tstart
<I>yes</I> = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature)
</PRE>
<PRE> <I>zero</I> value = <I>no</I> or <I>yes</I>
<I>yes</I> = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature)
<I>zero</I> value = <I>no</I> or <I>yes</I>
<I>no</I> = do not set total random force to zero
<I>yes</I> = set total random force to zero
</PRE>
@ -58,6 +58,13 @@ Fluctuation-Dissipation Theorem. The functional form of the memory
kernel associated with the temporally non-local force is constrained
to be a Prony series.
</P>
<P>IMPORTANT NOTE: While this fix bears many similarities to <A HREF = "fix_langevin.html">fix
langevin</A>, it has one significant
difference. Namely, <A HREF = "fix_gld.html">fix gld</A> performs time integration,
whereas <A HREF = "fix_langevin.html">fix langevin</A> does NOT. To this end, the
specification of another fix to perform time integration, such as <A HREF = "fix_nve.html">fix
nve</A>, is NOT necessary.
</P>
<P>With this fix active, the force on the <I>j</I>th atom is given as
</P>
<CENTER><IMG SRC = "Eqs/fix_gld1.jpg">
@ -89,13 +96,6 @@ the Newtonian and Langevin limits. Details of these limits, and the
associated numerical concerns are discussed in
<A HREF = "#Baczewski">(Baczewski)</A>.
</P>
<P>While this fix bears many similarities to <A HREF = "fix_langevin.html">fix
langevin</A>, it has one significant
difference. Namely, <A HREF = "fix_gld.html">fix gld</A> performs time integration,
whereas <A HREF = "fix_langevin.html">fix langevin</A> does NOT. To this end, the
specification of another fix to perform time integration, such as <A HREF = "fix_nve.html">fix
nve</A>, is NOT necessary.
</P>
<P>The desired temperature at each timestep is ramped from <I>Tstart</I> to
<I>Tstop</I> over the course of the next run.
</P>
@ -126,6 +126,8 @@ to zero by subtracting off an equal part of it from each atom in the
group. As a result, the center-of-mass of a system with zero initial
momentum will not drift over time.
</P>
<HR>
<P><B>Restart, run start/stop, minimize info:</B>
</P>
<P>The instantaneous values of the extended variables are written to
@ -135,6 +137,10 @@ do "exact" restarts with this fix, where the simulation continues on
the same as if no restart had taken place. However, in a statistical
sense, a restarted simulation should produce the same behavior.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various <A HREF = "Section_howto.html#howto_15">output commands</A>.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
@ -143,6 +149,10 @@ sense, a restarted simulation should produce the same behavior.
</P>
<P><B>Restrictions:</B> none
</P>
<P>This fix is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_viscous.html">fix viscous</A>,

View File

@ -15,7 +15,7 @@ fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k key
ID, group-ID are documented in "fix"_fix.html command :ulb,l
gld = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
N_k = number of terms in the Prony series representation of the memory kernel
N_k = number of terms in the Prony series representation of the memory kernel :l
seed = random number seed to use for white noise (positive integer) :l
series = {pprony} is presently the only available option :l
c_k = the weight of the kth term in the Prony series (mass per time units) :l
@ -24,7 +24,7 @@ zero or more keyword/value pairs may be appended :l
keyword = {frozen} or {zero}
{frozen} value = {no} or {yes}
{no} = initialize extended variables using values drawn from equilibrium distribution at Tstart
{yes} = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature) :pre
{yes} = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature)
{zero} value = {no} or {yes}
{no} = do not set total random force to zero
{yes} = set total random force to zero :pre
@ -45,6 +45,13 @@ Fluctuation-Dissipation Theorem. The functional form of the memory
kernel associated with the temporally non-local force is constrained
to be a Prony series.
IMPORTANT NOTE: While this fix bears many similarities to "fix
langevin"_fix_langevin.html, it has one significant
difference. Namely, "fix gld"_fix_gld.html performs time integration,
whereas "fix langevin"_fix_langevin.html does NOT. To this end, the
specification of another fix to perform time integration, such as "fix
nve"_fix_nve.html, is NOT necessary.
With this fix active, the force on the {j}th atom is given as
:c,image(Eqs/fix_gld1.jpg)
@ -76,13 +83,6 @@ the Newtonian and Langevin limits. Details of these limits, and the
associated numerical concerns are discussed in
"(Baczewski)"_#Baczewski.
While this fix bears many similarities to "fix
langevin"_fix_langevin.html, it has one significant
difference. Namely, "fix gld"_fix_gld.html performs time integration,
whereas "fix langevin"_fix_langevin.html does NOT. To this end, the
specification of another fix to perform time integration, such as "fix
nve"_fix_nve.html, is NOT necessary.
The desired temperature at each timestep is ramped from {Tstart} to
{Tstop} over the course of the next run.
@ -113,6 +113,8 @@ to zero by subtracting off an equal part of it from each atom in the
group. As a result, the center-of-mass of a system with zero initial
momentum will not drift over time.
:line
[Restart, run start/stop, minimize info:]
The instantaneous values of the extended variables are written to
@ -122,6 +124,10 @@ do "exact" restarts with this fix, where the simulation continues on
the same as if no restart had taken place. However, in a statistical
sense, a restarted simulation should produce the same behavior.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various "output commands"_Section_howto.html#howto_15.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
@ -130,6 +136,10 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
This fix is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"fix langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html,