ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4658 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2010-09-01 22:32:30 +00:00
parent 87e39e7610
commit 745d19c08a
4 changed files with 309 additions and 36 deletions
Download Patch File Download Diff File Expand all files Collapse all files

40
doc/fix_temp_rescale.html
View File

@ -9,14 +9,14 @@
<HR> <HR>
<H3>fix temp/rescale/eff command <H3>fix temp/rescale command
</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction <PRE>fix ID group-ID temp/rescale N Tstart Tstop window fraction
</PRE> </PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command <UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/rescale/eff = style name of this fix command <LI>temp/rescale = style name of this fix command
<LI>N = perform rescaling every N steps <LI>N = perform rescaling every N steps
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units) <LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>window = only rescale if temperature is outside this window (temperature units) <LI>window = only rescale if temperature is outside this window (temperature units)
@ -24,15 +24,21 @@
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0 <PRE>fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
</PRE> </PRE>
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>Reset the temperature of a group of atoms by explicitly rescaling <P>Reset the temperature of a group of atoms by explicitly rescaling
their velocities. their velocities.
</P> </P>
<P>The rescaling is applied to the translational degrees of freedom <P>The rescaling is applied to only 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. for the particles, which is an important consideration if extended
spherical or aspherical particles which have rotational degrees of
freedom are being thermostatted with this fix. The translational
degrees of freedom can also have a bias velocity removed from them
before thermostatting takes place; see the description below.
</P> </P>
<P>Rescaling is performed every N timesteps. The target temperature is a <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 ramped value between the <I>Tstart</I> and <I>Tstop</I> temperatures at the
@ -45,14 +51,15 @@ difference between the actual and desired temperature. E.g. if
<I>fraction</I> = 1.0, the temperature is reset to exactly the desired <I>fraction</I> = 1.0, the temperature is reset to exactly the desired
value. value.
</P> </P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt/eff</A> command which <P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
performs Nose/Hoover thermostatting AND time integration, this fix performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to does NOT perform time integration. It only modifies velocities to
effect thermostatting. Thus you must use a separate time integration 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 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
normally be used on atoms that also have their temperature controlled 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 by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
langevin/eff</A> commands. langevin</A> commands.
</P> </P>
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a <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 discussion of different ways to compute temperature and perform
@ -62,9 +69,10 @@ thermostatting.
creates its own compute of style "temp", as if one of this command had creates its own compute of style "temp", as if one of this command had
been issued: been issued:
</P> </P>
<PRE>compute fix-ID_temp group-ID temp/eff <PRE>compute fix-ID_temp group-ID temp
</PRE> </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 <P>See the <A HREF = "compute_temp.html">compute temp</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. group for the new compute is the same as the fix group.
</P> </P>
<P>Note that this is NOT the compute used by thermodynamic output (see <P>Note that this is NOT the compute used by thermodynamic output (see
@ -119,15 +127,11 @@ calculated by this fix is "extensive".
</P> </P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>. <P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B> none
</P>
<P>This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>
<P><A HREF = "fix_langevin.html">fix langevin/eff</A>, <A HREF = "fix_nh.html">fix nvt/eff</A>, <P><A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_nh.html">fix nvt</A>,
<A HREF = "fix_modify.html">fix_modify</A> <A HREF = "fix_modify.html">fix_modify</A>
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B> none

40
doc/fix_temp_rescale.txt
View File

@ -6,14 +6,14 @@
:line :line
fix temp/rescale/eff command :h3 fix temp/rescale command :h3
[Syntax:] [Syntax:]
fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction :pre fix ID group-ID temp/rescale N Tstart Tstop window fraction :pre
ID, group-ID are documented in "fix"_fix.html command ID, group-ID are documented in "fix"_fix.html command
temp/rescale/eff = style name of this fix command temp/rescale = style name of this fix command
N = perform rescaling every N steps N = perform rescaling every N steps
Tstart,Tstop = desired temperature at start/end of run (temperature units) Tstart,Tstop = desired temperature at start/end of run (temperature units)
window = only rescale if temperature is outside this window (temperature units) window = only rescale if temperature is outside this window (temperature units)
@ -21,15 +21,21 @@ fraction = rescale to target temperature by this fraction :ul
[Examples:] [Examples:]
fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0 :pre fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 :pre
[Description:] [Description:]
Reset the temperature of a group of atoms by explicitly rescaling Reset the temperature of a group of atoms by explicitly rescaling
their velocities. their velocities.
The rescaling is applied to the translational degrees of freedom The rescaling is applied to only 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. for the particles, which is an important consideration if extended
spherical or aspherical particles which have rotational degrees of
freedom are being thermostatted with this fix. 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 Rescaling is performed every N timesteps. The target temperature is a
ramped value between the {Tstart} and {Tstop} temperatures at the ramped value between the {Tstart} and {Tstop} temperatures at the
@ -42,14 +48,15 @@ difference between the actual and desired temperature. E.g. if
{fraction} = 1.0, the temperature is reset to exactly the desired {fraction} = 1.0, the temperature is reset to exactly the desired
value. value.
IMPORTANT NOTE: Unlike the "fix nvt/eff"_fix_nh.html command which IMPORTANT NOTE: Unlike the "fix nvt"_fix_nh.html command which
performs Nose/Hoover thermostatting AND time integration, this fix performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to does NOT perform time integration. It only modifies velocities to
effect thermostatting. Thus you must use a separate time integration 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 fix, like "fix nve"_fix_nve.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 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 by another fix - e.g. by "fix nvt"_fix_nh.html or "fix
langevin/eff"_fix_langevin_eff.html commands. langevin"_fix_langevin.html commands.
See "this howto section"_Section_howto.html#4_16 of the manual for a See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform discussion of different ways to compute temperature and perform
@ -59,9 +66,10 @@ 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 creates its own compute of style "temp", as if one of this command had
been issued: been issued:
compute fix-ID_temp group-ID temp/eff :pre compute fix-ID_temp group-ID temp :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 See the "compute temp"_compute_temp.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. group for the new compute is the same as the fix group.
Note that this is NOT the compute used by thermodynamic output (see Note that this is NOT the compute used by thermodynamic output (see
@ -116,15 +124,11 @@ This fix can ramp its target temperature over multiple runs, using the
This fix is not invoked during "energy minimization"_minimize.html. This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] [Restrictions:] none
This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:] [Related commands:]
"fix langevin/eff"_fix_langevin.html, "fix nvt/eff"_fix_nh.html, "fix langevin"_fix_langevin.html, "fix nvt"_fix_nh.html,
"fix_modify"_fix_modify.html "fix_modify"_fix_modify.html
[Default:] none [Default:] none

135
doc/fix_temp_rescale_eff.html Normal file
View File

@ -0,0 +1,135 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix temp/rescale/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/rescale/eff = style name of this fix command
<LI>N = perform rescaling every N steps
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>window = only rescale if temperature is outside this window (temperature units)
<LI>fraction = rescale to target temperature by this fraction
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Reset the temperature of a group of atoms 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>
<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
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
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes a global scalar which can be accessed by various
<A HREF = "Section_howto.html#4_15">output commands</A>. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
</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.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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>
<P><B>Default:</B> none
</P>
</HTML>

130
doc/fix_temp_rescale_eff.txt Normal file
View File

@ -0,0 +1,130 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix temp/rescale/eff command :h3
[Syntax:]
fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction :pre
ID, group-ID are documented in "fix"_fix.html command
temp/rescale/eff = style name of this fix command
N = perform rescaling every N steps
Tstart,Tstop = desired temperature at start/end of run (temperature units)
window = only rescale if temperature is outside this window (temperature units)
fraction = rescale to target temperature by this fraction :ul
[Examples:]
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
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.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is 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
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#4_15. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
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.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
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
[Default:] none