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72
doc/fix_temp_rescale_eff.html
View File

@ -28,69 +28,14 @@
</PRE>
<P><B>Description:</B>
</P>
<P>Reset the temperature of a group of atoms by explicitly rescaling
<P>Reset the temperature of a group of nuclei and electrons in the
<A HREF = "pair_eff.html">electron force field</A> model by explicitly rescaling
their velocities.
</P>
<P>The rescaling is applied to the translational degrees of freedom
for all particles, and the electronic radial degrees of freedom. The translational degrees of freedom can also have a bias velocity removed from them before thermostatting takes place; see the description below.
</P>
<P>Rescaling is performed every N timesteps. The target temperature is a
ramped value between the <I>Tstart</I> and <I>Tstop</I> temperatures at the
beginning and end of the run.
</P>
<P>Rescaling is only performed if the difference between the current and
desired temperatures is greater than the <I>window</I> value. The amount
of rescaling that is applied is a <I>fraction</I> (from 0.0 to 1.0) of the
difference between the actual and desired temperature. E.g. if
<I>fraction</I> = 1.0, the temperature is reset to exactly the desired
value.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt/eff</A> command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to
effect thermostatting. Thus you must use a separate time integration
fix, like <A HREF = "fix_nve_eff.html">fix nve/eff</A> to actually update the positions of atoms using the modified velocities. Likewise, this fix should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt/eff</A> or <A HREF = "fix_langevin_eff.html">fix
langevin/eff</A> commands.
</P>
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
</P>
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if one of this command had
been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp/eff
</PRE>
<P>See the <A HREF = "compute_temp_eff.html">compute temp/eff</A> for details. Note that the ID of the new compute is the fix-ID + underscore + "temp", and the
group for the new compute is the same as the fix group.
</P>
<P>Note that this is NOT the compute used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, this fix can be used
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
<P>The operation of this fix is exactly like that described by the <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A> command, except that the rescaling
is also applied to the radial electron velocity for electron
particles.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
@ -127,8 +72,9 @@ LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_langevin.html">fix langevin/eff</A>, <A HREF = "fix_nh.html">fix nvt/eff</A>,
<A HREF = "fix_modify.html">fix_modify</A>
<P><A HREF = "fix_langevin_eff.html">fix langevin/eff</A>, <A HREF = "fix_nh_eff.html">fix
nvt/eff</A>, <A HREF = "fix_modify.html">fix_modify</A>,
<A HREF = "fix_temp_rescale.html">fix_temp_rescale</A>,
</P>
<P><B>Default:</B> none
</P>

72
doc/fix_temp_rescale_eff.txt
View File

@ -25,69 +25,14 @@ fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0 :pre
[Description:]
Reset the temperature of a group of atoms by explicitly rescaling
Reset the temperature of a group of nuclei and electrons in the
"electron force field"_pair_eff.html model by explicitly rescaling
their velocities.
The rescaling is applied to the translational degrees of freedom
for all particles, and the electronic radial degrees of freedom. The translational degrees of freedom can also have a bias velocity removed from them before thermostatting takes place; see the description below.
Rescaling is performed every N timesteps. The target temperature is a
ramped value between the {Tstart} and {Tstop} temperatures at the
beginning and end of the run.
Rescaling is only performed if the difference between the current and
desired temperatures is greater than the {window} value. The amount
of rescaling that is applied is a {fraction} (from 0.0 to 1.0) of the
difference between the actual and desired temperature. E.g. if
{fraction} = 1.0, the temperature is reset to exactly the desired
value.
IMPORTANT NOTE: Unlike the "fix nvt/eff"_fix_nh.html command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to
effect thermostatting. Thus you must use a separate time integration
fix, like "fix nve/eff"_fix_nve_eff.html to actually update the positions of atoms using the modified velocities. Likewise, this fix should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by "fix nvt/eff"_fix_nh.html or "fix
langevin/eff"_fix_langevin_eff.html commands.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if one of this command had
been issued:
compute fix-ID_temp group-ID temp/eff :pre
See the "compute temp/eff"_compute_temp_eff.html for details. Note that the ID of the new compute is the fix-ID + underscore + "temp", and the
group for the new compute is the same as the fix group.
Note that this is NOT the compute used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the "fix_modify"_fix_modify.html command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
The operation of this fix is exactly like that described by the "fix
temp/rescale"_fix_temp_rescale.html command, except that the rescaling
is also applied to the radial electron velocity for electron
particles.
[Restart, fix_modify, output, run start/stop, minimize info:]
@ -124,7 +69,8 @@ LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"fix langevin/eff"_fix_langevin.html, "fix nvt/eff"_fix_nh.html,
"fix_modify"_fix_modify.html
"fix langevin/eff"_fix_langevin_eff.html, "fix
nvt/eff"_fix_nh_eff.html, "fix_modify"_fix_modify.html,
"fix_temp_rescale"_fix_temp_rescale.html,
[Default:] none