From 745d19c08a8f54cce3c51bee73ab6427b2b6e9f7 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 1 Sep 2010 22:32:30 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4658 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_temp_rescale.html | 40 +++++----- doc/fix_temp_rescale.txt | 40 +++++----- doc/fix_temp_rescale_eff.html | 135 ++++++++++++++++++++++++++++++++++ doc/fix_temp_rescale_eff.txt | 130 ++++++++++++++++++++++++++++++++ 4 files changed, 309 insertions(+), 36 deletions(-) create mode 100644 doc/fix_temp_rescale_eff.html create mode 100644 doc/fix_temp_rescale_eff.txt diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html index 466d31f102..05896d6c36 100644 --- a/doc/fix_temp_rescale.html +++ b/doc/fix_temp_rescale.html @@ -9,14 +9,14 @@
-

fix temp/rescale/eff command +

fix temp/rescale command

Syntax:

-
fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction 
+
fix ID group-ID temp/rescale N Tstart Tstop window fraction 
 

 
 
Examples:
 

-
fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0 
+
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 
 

 
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.
+
The rescaling is applied to only the translational degrees of freedom
+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
 ramped value between the Tstart and Tstop temperatures at the
@@ -45,14 +51,15 @@ 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 command which
+
IMPORTANT NOTE: Unlike the fix nvt 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 to actually update the positions of atoms using the modified velocities.  Likewise, this fix should not
+fix, like fix nve 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 or fix
-langevin/eff commands.
+by another fix - e.g. by fix nvt or fix
+langevin commands.
 

 
See this howto section of the manual for a
 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
 been issued:
 

-
compute fix-ID_temp group-ID temp/eff 
+
compute fix-ID_temp group-ID temp 
 

-
See the compute temp/eff for details.  Note that the ID of the new compute is the fix-ID + underscore + "temp", and the
+
See the compute temp 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
@@ -119,15 +127,11 @@ calculated by this fix is "extensive".
 

 
This fix is not invoked during energy minimization.
 

-
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 for more info.
+
Restrictions: none
 

 
Related commands:
 

-
fix langevin/eff, fix nvt/eff,
+
fix langevin, fix nvt,
 fix_modify
 

 
Default: none
diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt
index 71bd847ba7..f972ce7413 100644
--- a/doc/fix_temp_rescale.txt
+++ b/doc/fix_temp_rescale.txt
@@ -6,14 +6,14 @@
 
 :line
 
-fix temp/rescale/eff command :h3
+fix temp/rescale command :h3
 
 [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
-temp/rescale/eff = style name of this fix command
+temp/rescale = 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)
@@ -21,15 +21,21 @@ 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
+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:]
 
 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.
+The rescaling is applied to only the translational degrees of freedom
+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
 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
 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
 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
+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
-by another fix - e.g. by "fix nvt/eff"_fix_nh.html or "fix
-langevin/eff"_fix_langevin_eff.html commands.
+by another fix - e.g. by "fix nvt"_fix_nh.html or "fix
+langevin"_fix_langevin.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
@@ -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
 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.
 
 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.
 
-[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.
+[Restrictions:] none
 
 [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
 
 [Default:] none
diff --git a/doc/fix_temp_rescale_eff.html b/doc/fix_temp_rescale_eff.html
new file mode 100644
index 0000000000..466d31f102
--- /dev/null
+++ b/doc/fix_temp_rescale_eff.html
@@ -0,0 +1,135 @@
+
+
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands 
+

+
+
+
+
+
+
+

+
+
fix temp/rescale/eff command 
+

+
Syntax:
+

+
fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction 
+

+
  • ID, group-ID are documented in fix 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 
+

+
Examples:
+

+
fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0 
+

+
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 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 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 or fix
+langevin/eff commands.
+

+
See this howto section 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 
+

+
See the compute temp/eff 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 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 command or print this temperature
+during thermodynamic output via the thermo_style
+custom 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 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 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 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.
+

+
The fix_modify temp option is supported by this
+fix.  You can use it to assign a temperature compute
+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 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.
+

+
This fix computes a global scalar which can be accessed by various
+output commands.  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 command.  See the
+run command for details of how to do this.
+

+
This fix is not invoked during energy minimization.
+

+
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 for more info.
+

+
Related commands:
+

+
fix langevin/eff, fix nvt/eff,
+fix_modify
+

+
Default: none
+

+
diff --git a/doc/fix_temp_rescale_eff.txt b/doc/fix_temp_rescale_eff.txt
new file mode 100644
index 0000000000..71bd847ba7
--- /dev/null
+++ b/doc/fix_temp_rescale_eff.txt
@@ -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