diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html
index 794356816..44e745318 100644
--- a/doc/fix_langevin.html
+++ b/doc/fix_langevin.html
@@ -1,174 +1,175 @@
<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 langevin command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID langevin Tstart Tstop damp seed keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>langevin = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>damp = damping parameter (time units)
<LI>seed = random # seed to use for white noise (positive integer)
<LI>zero or more keyword/value pairs may be appended
-keyword = <I>scale</I>
+<PRE>keyword = <I>scale</I>
<I>scale</I> values = type ratio
type = atom type (1-N)
- ratio = factor to scale the damping coefficient by
+ ratio = factor by which to scale the damping coefficient
+</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 boundary langevin 1.0 1.0 1000.0 699483
fix 1 all langevin 1.0 1.1 100.0 48279 axes 0 1 1
fix 3 boundary langevin 1.0 1.0 1000.0 699483 region boundary
</PRE>
<P><B>Description:</B>
</P>
<P>Apply a Langevin thermostat to a group of atoms which models an
interaction with a background implicit solvent. Used with <A HREF = "fix_nve.html">fix
nve</A>, this command performs Brownian dynamics (BD), since
the total force on each atom will have the form:
</P>
<PRE>F = Fc + Ff + Fr
</PRE>
<P>Fc is the conservative force computed via the usual inter-particle
interactions (<A HREF = "pair_style.html">pair_style</A>,
<A HREF = "bond_style.html">bond_style</A>, etc).
</P>
<P>The Ff and Fr terms are added by this fix. Ff = - gamma v and is a
frictional drag or viscous damping term proportional to the particle's
velocity. Gamma for each atom is computed as m/damp, where m is the
mass of the particle and damp is the damping factor specified by the
user.
</P>
<P>Fr is a force due to solvent atoms at a temperature T randomly bumping
into the particle. As derived from the fluctuation/dissipation
theorem, its magnitude is proportional to sqrt(T m / dt damp), where T
is the desired temperature, m is the mass of the particle, dt is the
timestep size, and damp is the damping factor. Random numbers are
used to randomize the direction and magnitude of this force as
described in <A HREF = "#Dunweg">(Dunweg)</A>, where a uniform random number is used
(instead of a Gaussian random number) for speed.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nvt.html">fix nvt</A> command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies forces 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 velocities and
positions of atoms using the the modified forces. 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_nvt.html">fix nvt</A> or <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A> commands.
</P>
<HR>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>.
</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>The <I>damp</I> parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 100.0
means to relax the temperature in a timespan of (roughly) 100 time
units (tau or fmsec or psec - see the <A HREF = "units.html">units</A> command).
The damp factor can be thought of as inversely related to the
viscosity of the solvent. I.e. a small relaxation time implies a
hi-viscosity solvent and vice versa. See the discussion about gamma
and viscosity in the documentation for the <A HREF = "fix_viscous.html">fix
viscous</A> command for more details.
</P>
<P>The random # <I>seed</I> must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.
</P>
<P>The keyword <I>axes</I> can be used to specify which dimensions to add Ff
and Fr to. A flag of 0 means skip that dimension; a flag of 1 means
include that dimension. The default is 1 for all 3 dimensions.
</P>
<P>The keyword <I>scale</I> allows the damp factor to be scaled up or down by
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
specifying a ratio of 2 increase the relaxation time which is
equivalent to the the solvent's viscosity acting on particles with 1/2
the diameter. This is the opposite effect of scale factors used by
the <A HREF = "fix_viscous.html">fix viscous</A> command, since the damp factor in
fix <I>langevin</I> is inversely related to the gamma factor in fix
<I>viscous</I>. Also note that the damping factor in fix <I>langevin</I>
includes the particle mass in Ff, unlike fix <I>viscous</I>. Thus the mass
and size of different atom types should be accounted for in the choice
of ratio values.
</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>. Because the state of the random number generator
is not saved in restart files, this means you cannot 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>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>No global scalar or vector or per-atom quantities are stored by this
fix for access by various <A HREF = "Section_howto.html#4_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.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_viscous.html">fix
viscous</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are axes = 1 1 1, scale = 1.0 for all types, no
region, and weight = 1.0.
</P>
<A NAME = "Dunweg"></A>
<P><B>(Dunweg)</B> Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
</P>
</HTML>
diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt
index 74a60aa63..4d43aa15e 100644
--- a/doc/fix_langevin.txt
+++ b/doc/fix_langevin.txt
@@ -1,162 +1,162 @@
"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 langevin command :h3
[Syntax:]
fix ID group-ID langevin Tstart Tstop damp seed keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
langevin = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
damp = damping parameter (time units) :l
seed = random # seed to use for white noise (positive integer) :l
zero or more keyword/value pairs may be appended :l
keyword = {scale}
{scale} values = type ratio
type = atom type (1-N)
- ratio = factor to scale the damping coefficient by
+ ratio = factor by which to scale the damping coefficient :pre
:ule
[Examples:]
fix 3 boundary langevin 1.0 1.0 1000.0 699483
fix 1 all langevin 1.0 1.1 100.0 48279 axes 0 1 1
fix 3 boundary langevin 1.0 1.0 1000.0 699483 region boundary :pre
[Description:]
Apply a Langevin thermostat to a group of atoms which models an
interaction with a background implicit solvent. Used with "fix
nve"_fix_nve.html, this command performs Brownian dynamics (BD), since
the total force on each atom will have the form:
F = Fc + Ff + Fr :pre
Fc is the conservative force computed via the usual inter-particle
interactions ("pair_style"_pair_style.html,
"bond_style"_bond_style.html, etc).
The Ff and Fr terms are added by this fix. Ff = - gamma v and is a
frictional drag or viscous damping term proportional to the particle's
velocity. Gamma for each atom is computed as m/damp, where m is the
mass of the particle and damp is the damping factor specified by the
user.
Fr is a force due to solvent atoms at a temperature T randomly bumping
into the particle. As derived from the fluctuation/dissipation
theorem, its magnitude is proportional to sqrt(T m / dt damp), where T
is the desired temperature, m is the mass of the particle, dt is the
timestep size, and damp is the damping factor. Random numbers are
used to randomize the direction and magnitude of this force as
described in "(Dunweg)"_#Dunweg, where a uniform random number is used
(instead of a Gaussian random number) for speed.
IMPORTANT NOTE: Unlike the "fix nvt"_fix_nvt.html command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies forces to effect
thermostatting. Thus you must use a separate time integration fix,
like "fix nve"_fix_nve.html to actually update the velocities and
positions of atoms using the the modified forces. Likewise, this fix
should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. by "fix nvt"_fix_nvt.html or "fix
temp/rescale"_fix_temp_rescale.html commands.
:line
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}.
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 {damp} parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 100.0
means to relax the temperature in a timespan of (roughly) 100 time
units (tau or fmsec or psec - see the "units"_units.html command).
The damp factor can be thought of as inversely related to the
viscosity of the solvent. I.e. a small relaxation time implies a
hi-viscosity solvent and vice versa. See the discussion about gamma
and viscosity in the documentation for the "fix
viscous"_fix_viscous.html command for more details.
The random # {seed} must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.
The keyword {axes} can be used to specify which dimensions to add Ff
and Fr to. A flag of 0 means skip that dimension; a flag of 1 means
include that dimension. The default is 1 for all 3 dimensions.
The keyword {scale} allows the damp factor to be scaled up or down by
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
specifying a ratio of 2 increase the relaxation time which is
equivalent to the the solvent's viscosity acting on particles with 1/2
the diameter. This is the opposite effect of scale factors used by
the "fix viscous"_fix_viscous.html command, since the damp factor in
fix {langevin} is inversely related to the gamma factor in fix
{viscous}. Also note that the damping factor in fix {langevin}
includes the particle mass in Ff, unlike fix {viscous}. Thus the mass
and size of different atom types should be accounted for in the choice
of ratio values.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. Because the state of the random number generator
is not saved in restart files, this means you cannot 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.
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.
No global scalar or vector or per-atom quantities are stored by this
fix for access by various "output commands"_Section_howto.html#4_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.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"fix nvt"_fix_nvt.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
viscous"_fix_viscous.html
[Default:]
The option defaults are axes = 1 1 1, scale = 1.0 for all types, no
region, and weight = 1.0.
:link(Dunweg)
[(Dunweg)] Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
diff --git a/doc/fix_temp_berendsen.html b/doc/fix_temp_berendsen.html
index 0d8a2bea2..14b4fab74 100644
--- a/doc/fix_temp_berendsen.html
+++ b/doc/fix_temp_berendsen.html
@@ -1,125 +1,122 @@
<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/berendsen command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID temp/berendsen Tstart Tstop Tdamp
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/berendsen = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run
<LI>Tdamp = temperature damping parameter (time units)
</UL>
<P><B>Examples:</B>
</P>
-<PRE>fix 1 all nvt 300.0 300.0 100.0
-fix 1 all nvt 300.0 300.0 100.0 drag 0.2
+<PRE>fix 1 all nvt 300.0 300.0 100.0
</PRE>
<P><B>Description:</B>
</P>
<P>Reset the temperature of a group of atoms by using a Berendsen
thermostat <A HREF = "#Berendsen">(Berendsen)</A>, which rescale their velocities
every timestep.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nvt.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
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
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
langevin</A> commands.
</P>
-<HR>
-
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> command 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>No global scalar or vector or per-atom quantities are stored by this
fix for access by various <A HREF = "Section_howto.html#4_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.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_langevin.html">fix langevin</A>,
<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp.html">compute temp</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Berendsen"></A>
<P><B>(Berendsen)</B> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
Phys, 81, 3684 (1984).
</P>
</HTML>
diff --git a/doc/fix_temp_berendsen.txt b/doc/fix_temp_berendsen.txt
index ed8611ede..03e9d4328 100644
--- a/doc/fix_temp_berendsen.txt
+++ b/doc/fix_temp_berendsen.txt
@@ -1,120 +1,117 @@
"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/berendsen command :h3
[Syntax:]
fix ID group-ID temp/berendsen Tstart Tstop Tdamp :pre
ID, group-ID are documented in "fix"_fix.html command
temp/berendsen = style name of this fix command
Tstart,Tstop = desired temperature at start/end of run
Tdamp = temperature damping parameter (time units) :ul
[Examples:]
-fix 1 all nvt 300.0 300.0 100.0
-fix 1 all nvt 300.0 300.0 100.0 drag 0.2 :pre
+fix 1 all nvt 300.0 300.0 100.0 :pre
[Description:]
Reset the temperature of a group of atoms by using a Berendsen
thermostat "(Berendsen)"_#Berendsen, which rescale their velocities
every timestep.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
"units"_units.html command).
IMPORTANT NOTE: Unlike the "fix nvt"_fix_nvt.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"_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"_fix_nvt.html or "fix
langevin"_fix_langevin.html commands.
-:line
-
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:
compute fix-ID_temp group-ID temp :pre
See the "compute temp"_compute_temp.html command 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.
No global scalar or vector or per-atom quantities are stored by this
fix for access by various "output commands"_Section_howto.html#4_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.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"fix nve"_fix_nve.html, "fix nvt"_fix_nvt.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html,
"fix_modify"_fix_modify.html, "compute temp"_compute_temp.html
[Default:] none
:line
:link(Berendsen)
[(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
Phys, 81, 3684 (1984).
diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html
index 960b26f37..d328d0d1f 100644
--- a/doc/fix_temp_rescale.html
+++ b/doc/fix_temp_rescale.html
@@ -1,137 +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 command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID temp/rescale N Tstart Tstop window fraction keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/rescale = 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 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>
<P><B>Description:</B>
</P>
<P>Reset the temperature of a group of atoms by explicitly rescaling
their velocities.
</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_nvt.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
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
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
langevin</A> commands.
</P>
-<HR>
-
<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
</PRE>
<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.
</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>. Note that because this fix is invoked
every N steps and thermodynamic info is printed every M steps, that
unless M is a multiple of N, the energy contribution will be zero.
</P>
<P>The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>. The scalar value calculated by
this fix is "extensive", meaning it scales with the number of atoms in
the simulation.
</P>
<P>The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
</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> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_nvt.html">fix nvt</A>,
<A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt
index d1cc20397..58a4a310e 100644
--- a/doc/fix_temp_rescale.txt
+++ b/doc/fix_temp_rescale.txt
@@ -1,132 +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 command :h3
[Syntax:]
fix ID group-ID temp/rescale N Tstart Tstop window fraction keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html 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)
fraction = rescale to target temperature by this fraction :ul
[Examples:]
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.
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"_fix_nvt.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"_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"_fix_nvt.html or "fix
langevin"_fix_langevin.html commands.
-:line
-
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 :pre
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
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. Note that because this fix is invoked
every N steps and thermodynamic info is printed every M steps, that
unless M is a multiple of N, the energy contribution will be zero.
The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various "output
commands"_Section_howto.html#4_15. The scalar value calculated by
this fix is "extensive", meaning it scales with the number of atoms in
the simulation.
The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
"thermo_style custom"_thermo_style.html command for details.
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:] none
[Related commands:]
"fix langevin"_fix_langevin.html, "fix nvt"_fix_nvt.html,
"fix_modify"_fix_modify.html
[Default:] none