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73
doc/fix_temp_csvr.html
View File

@ -11,13 +11,17 @@
<H3>fix temp/csvr command
</H3>
<H3>fix temp/csld command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID temp/csvr Tstart Tstop Tdamp seed
</PRE>
<PRE>fix ID group-ID temp/csld Tstart Tstop Tdamp seed
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/csvr = style name of this fix command
<LI>temp/csvr or temp/csld = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run
@ -31,17 +35,26 @@
</P>
<PRE>fix 1 all temp/csvr 300.0 300.0 100.0 54324
</PRE>
<PRE>fix 1 all temp/csld 100.0 300.0 10.0 123321
</PRE>
<P><B>Description:</B>
</P>
<P>Adjust the temperature with a CSVR thermostat <A HREF = "#Bussi">(Bussi)</A>, which
updates the velocities to a linear combination of the current
velocities with a gaussian distribution at the desired temperature in
every timestep.
<P>Adjust the temperature with a canonical sampling thermostat that uses
global velocity rescaling with Hamiltonian dynamics (<I>temp/csvr</I>)
<A HREF = "#Bussi1">(Bussi1)</A>, or Langevin dynamics (<I>temp/csld</I>) <A HREF = "#Bussi2">(Bussi2)</A>.
In the case of <I>temp/csvr</I> the thermostat is similar to the empirical
Berendsen thermostat in <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>, but
chooses the actual scaling factor from a suitably chosen (gaussian)
distribution rather than having it determined from the time constant
directly. In the second case the velocities are updated to a linear
combination of the current velocities with a gaussian distribution
of velocities at the desired temperature. Both termostats are applied
in every timestep.
</P>
<P>The thermostat is applied to only the translational degrees of freedom
for the particles, which is an important consideration for finite-size
particles which have rotational degrees of freedom are being
thermostatted with this fix. The translational degrees of freedom can
thermostatted with these fixes. The translational degrees of freedom can
also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</P>
@ -64,11 +77,11 @@ keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent temperature.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to
performs Nose/Hoover thermostatting AND time integration, these fixes
do NOT perform time integration. They only modify velocities to
effect thermostatting. Thus you must use a separate time integration
fix, like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of
atoms using the modified velocities. Likewise, this fix should not
atoms using the modified velocities. Likewise, these fixes 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</A> or <A HREF = "fix_langevin.html">fix
langevin</A> commands.
@ -77,7 +90,7 @@ langevin</A> commands.
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
<P>These fixes compute a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:
</P>
@ -97,7 +110,7 @@ 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
<P>Like other fixes that perform thermostatting, these fixes 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
@ -116,24 +129,37 @@ thermal degrees of freedom, and the bias is added back in.
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
<P>No information about these fixes are written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
you have defined to this fix which will be used in its thermostatting
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by these
fixes. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
you have defined to these fixes which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
these fixes and by the compute should be the same.
</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
<P>These fixes 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.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
<P>These fixes are not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P>These fixes compute a global scalar which can be accessed by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
cummulative energy change due to the fix. The scalar value
calculated by this fix is "extensive".
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is not compatible with <A HREF = "fix_shake.html">fix shake</A>.
<P>These fixes are not compatible with <A HREF = "fix_shake.html">fix shake</A>.
</P>
<P>The fix can be used with dynamic groups as defined by the
<A HREF = "group.html">group</A> command. Likewise it can be used with groups to
which atoms are added or deleted over time, e.g. a deposition
simulation. However, the conservation properties of the thermostat
and barostat are defined for systems with a static set of atoms. You
may observe odd behavior if the atoms in a group vary dramatically
over time or the atom count becomes very small.
</P>
<P><B>Related commands:</B>
</P>
@ -146,8 +172,11 @@ temp/rescale</A>, <A HREF = "fix_langevin.html">fix langevin</A>,
</P>
<HR>
<A NAME = "Bussi"></A>
<A NAME = "Bussi1"></A>
<P><B>(Bussi)</B> Bussi and Parrinello, Phys. Rev. E (2007)
<A NAME = "Bussi2"></A><B>(Bussi1)</B> Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)
<P><B>(Bussi2)</B> Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)
</P>
</HTML>

70
doc/fix_temp_csvr.txt
View File

@ -7,13 +7,15 @@
:line
fix temp/csvr command :h3
fix temp/csld command :h3
[Syntax:]
fix ID group-ID temp/csvr Tstart Tstop Tdamp seed :pre
fix ID group-ID temp/csld Tstart Tstop Tdamp seed :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
temp/csvr = style name of this fix command :l
temp/csvr or temp/csld = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l
Tstart can be a variable (see below) :pre
Tdamp = temperature damping parameter (time units) :l
@ -22,18 +24,26 @@ seed = random number seed to use for white noise (positive integer) :l,ule
[Examples:]
fix 1 all temp/csvr 300.0 300.0 100.0 54324 :pre
fix 1 all temp/csld 100.0 300.0 10.0 123321 :pre
[Description:]
Adjust the temperature with a CSVR thermostat "(Bussi)"_#Bussi, which
updates the velocities to a linear combination of the current
velocities with a gaussian distribution at the desired temperature in
every timestep.
Adjust the temperature with a canonical sampling thermostat that uses
global velocity rescaling with Hamiltonian dynamics ({temp/csvr})
"(Bussi1)"_#Bussi1, or Langevin dynamics ({temp/csld}) "(Bussi2)"_#Bussi2.
In the case of {temp/csvr} the thermostat is similar to the empirical
Berendsen thermostat in "temp/berendsen"_fix_temp_berendsen.html, but
chooses the actual scaling factor from a suitably chosen (gaussian)
distribution rather than having it determined from the time constant
directly. In the second case the velocities are updated to a linear
combination of the current velocities with a gaussian distribution
of velocities at the desired temperature. Both termostats are applied
in every timestep.
The thermostat is applied to only the translational degrees of freedom
for the particles, which is an important consideration for finite-size
particles which have rotational degrees of freedom are being
thermostatted with this fix. The translational degrees of freedom can
thermostatted with these fixes. The translational degrees of freedom can
also have a bias velocity removed from them before thermostatting
takes place; see the description below.
@ -56,11 +66,11 @@ keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent temperature.
IMPORTANT NOTE: Unlike the "fix nvt"_fix_nh.html command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to
performs Nose/Hoover thermostatting AND time integration, these fixes
do NOT perform time integration. They only modify velocities to
effect thermostatting. Thus you must use a separate time integration
fix, like "fix nve"_fix_nve.html to actually update the positions of
atoms using the modified velocities. Likewise, this fix should not
atoms using the modified velocities. Likewise, these fixes should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html commands.
@ -69,7 +79,7 @@ See "this howto section"_Section_howto.html#howto_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
These fixes compute a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:
@ -89,7 +99,7 @@ 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
Like other fixes that perform thermostatting, these fixes 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
@ -108,24 +118,37 @@ thermal degrees of freedom, and the bias is added back in.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
No information about these fixes are written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a temperature "compute"_compute.html
you have defined to this fix which will be used in its thermostatting
The "fix_modify"_fix_modify.html {temp} option is supported by these
fixes. You can use it to assign a temperature "compute"_compute.html
you have defined to these fixes which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
these fixes and by the compute should be the same.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
These fixes 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.
This fix is not invoked during "energy minimization"_minimize.html.
These fixes are not invoked during "energy minimization"_minimize.html.
These fixes compute a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
cummulative energy change due to the fix. The scalar value
calculated by this fix is "extensive".
[Restrictions:]
This fix is not compatible with "fix shake"_fix_shake.html.
These fixes are not compatible with "fix shake"_fix_shake.html.
The fix can be used with dynamic groups as defined by the
"group"_group.html command. Likewise it can be used with groups to
which atoms are added or deleted over time, e.g. a deposition
simulation. However, the conservation properties of the thermostat
and barostat are defined for systems with a static set of atoms. You
may observe odd behavior if the atoms in a group vary dramatically
over time or the atom count becomes very small.
[Related commands:]
@ -138,6 +161,7 @@ temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html,
:line
:link(Bussi)
[(Bussi)] Bussi and Parrinello, Phys. Rev. E (2007)
:link(Bussi1)
[(Bussi1)] Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)
:link(Bussi2)
[(Bussi2)] Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)