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@1648 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2008-03-19 22:51:12 +00:00
parent cf8e38d63f
commit ad6bfadf6c
26 changed files with 431 additions and 128 deletions
Download Patch File Download Diff File Expand all files Collapse all files

14
doc/fix_langevin.html
View File

@ -67,6 +67,14 @@ 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>Note that the thermostat effect of this fix 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.
</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
@ -111,10 +119,6 @@ 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
@ -158,7 +162,7 @@ fix for access by various <A HREF = "Section_howto.html#4_15">output commands</A
<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>
viscous</A>, <A HREF = "fix_nvt.html">fix nvt</A>
</P>
<P><B>Default:</B>
</P>

15
doc/fix_langevin.txt
View File

@ -17,6 +17,7 @@ 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
@ -57,6 +58,14 @@ 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.
Note that the thermostat effect of this fix 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.
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
@ -101,10 +110,6 @@ 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
@ -148,7 +153,7 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Related commands:]
"fix nvt"_fix_nvt.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
viscous"_fix_viscous.html
viscous"_fix_viscous.html, "fix nvt"_fix_nvt.html
[Default:]

5
doc/fix_npt.html
View File

@ -58,6 +58,11 @@ thermostat <A HREF = "#Hoover1">(Hoover1)</A> and Nose/Hoover pressure barostat
creates a system trajectory consistent with the isothermal-isobaric
ensemble.
</P>
<P>The thermostat is applied to only the translational degrees of freedom
for the particles. The translational degrees of freedom can also have
a bias velocity removed from them before thermostatting takes place;
see the description below.
</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

5
doc/fix_npt.txt
View File

@ -47,6 +47,11 @@ thermostat "(Hoover1)"_#Hoover1 and Nose/Hoover pressure barostat
creates a system trajectory consistent with the isothermal-isobaric
ensemble.
The thermostat is applied to only the translational degrees of freedom
for the particles. The translational degrees of freedom can also have
a bias velocity removed from them before thermostatting takes place;
see the description below.
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

37
doc/fix_npt_asphere.html
View File

@ -50,13 +50,20 @@ fix 2 water npt/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NPT integration to update positions, velocities,
and angular velocity each timestep for aspherical or ellipsoidal
particles in the group using a Nose/Hoover temperature
<P>Perform constant NPT integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover temperature
thermostat and Nose/Hoover pressure barostat. P is pressure; T is
temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
</P>
<P>The thermostat is applied to both the translational and rotational
degrees of freedom for the aspherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</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
@ -150,6 +157,21 @@ custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</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>This fix writes the state of the Nose/Hoover thermostat and barostat
@ -189,6 +211,11 @@ this.
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix requires that particles be represented as extended ellipsoids
and not point particles. This means they will have an angular
momentum and a shape which is determined by the <A HREF = "shape.html">shape</A>
command.
</P>
<P>Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
@ -199,8 +226,8 @@ the Nose/Hoover formulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_npt.html">fix npt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>,
<A HREF = "fix_modify.html">fix_modify</A>
<P><A HREF = "fix_npt.html">fix npt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_npt_asphere.html">fix
npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B>
</P>

37
doc/fix_npt_asphere.txt
View File

@ -39,13 +39,20 @@ fix 2 water npt/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0
[Description:]
Perform constant NPT integration to update positions, velocities,
and angular velocity each timestep for aspherical or ellipsoidal
particles in the group using a Nose/Hoover temperature
Perform constant NPT integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover temperature
thermostat and Nose/Hoover pressure barostat. P is pressure; T is
temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
The thermostat is applied to both the translational and rotational
degrees of freedom for the aspherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
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
@ -139,6 +146,21 @@ custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} 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:]
This fix writes the state of the Nose/Hoover thermostat and barostat
@ -178,6 +200,11 @@ This fix is part of the "asphere" 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.
This fix requires that particles be represented as extended ellipsoids
and not point particles. This means they will have an angular
momentum and a shape which is determined by the "shape"_shape.html
command.
Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
non-periodic or periodic.
@ -188,8 +215,8 @@ the Nose/Hoover formulation.
[Related commands:]
"fix npt"_fix_npt.html, "fix nve_asphere"_fix_nve_asphere.html,
"fix_modify"_fix_modify.html
"fix npt"_fix_npt.html, "fix nve_asphere"_fix_nve_asphere.html, "fix
npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
[Default:]

66
doc/fix_npt_sphere.html
View File

@ -9,15 +9,15 @@
<HR>
<H3>fix npt/asphere command
<H3>fix npt/sphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID npt/asphere Tstart Tstop Tdamp p-style args keyword value ...
<PRE>fix ID group-ID npt/sphere Tstart Tstop Tdamp p-style args keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>npt/asphere = style name of this fix command
<LI>npt/sphere = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run
@ -43,19 +43,28 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all npt/asphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
fix 2 water npt/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial
<PRE>fix 1 all npt/sphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
fix 2 water npt/sphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NPT integration to update positions, velocities,
and angular velocity each timestep for aspherical or ellipsoidal
particles in the group using a Nose/Hoover temperature
thermostat and Nose/Hoover pressure barostat. P is pressure; T is
temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
<P>Perform constant NPT integration to update position, velocity, and
angular velocity each timestep for extended spherical particles in the
group using a Nose/Hoover temperature thermostat and Nose/Hoover
pressure barostat. P is pressure; T is temperature. This creates a
system trajectory consistent with the isothermal-isobaric ensemble.
</P>
<P>This fix differs from the <A HREF = "fix_npt.html">fix npt</A> command, which
assumes point particles and only updates their position and velocity.
</P>
<P>The thermostat is applied to both the translational and rotational
degrees of freedom for the spherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</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
@ -131,10 +140,10 @@ timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp/asphere
<PRE>compute fix-ID_temp group-ID temp/sphere
compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<P>See the <A HREF = "compute_temp_asphere.html">compute temp/asphere</A> and <A HREF = "compute_pressure.html">compute
<P>See the <A HREF = "compute_temp_sphere.html">compute temp/sphere</A> and <A HREF = "compute_pressure.html">compute
pressure</A> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press", and the group for the new computes is the same
@ -150,6 +159,21 @@ custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</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>This fix writes the state of the Nose/Hoover thermostat and barostat
@ -185,9 +209,10 @@ this.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "asphere" 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>This fix requires that particles be represented as extended spheres
and not point particles. This means they will have an angular
velocity and a diameter which is determined by the <A HREF = "shape.html">shape</A>
command.
</P>
<P>Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
@ -199,8 +224,9 @@ the Nose/Hoover formulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_npt.html">fix npt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>,
<A HREF = "fix_modify.html">fix_modify</A>
<P><A HREF = "fix_npt.html">fix npt</A>, <A HREF = "fix_nve_sphere.html">fix nve_sphere</A>, <A HREF = "fix_nvt_sphere.html">fix
nvt_sphere</A>, <A HREF = "fix_npt_asphere.html">fix
npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B>
</P>

66
doc/fix_npt_sphere.txt
View File

@ -6,14 +6,14 @@
:line
fix npt/asphere command :h3
fix npt/sphere command :h3
[Syntax:]
fix ID group-ID npt/asphere Tstart Tstop Tdamp p-style args keyword value ... :pre
fix ID group-ID npt/sphere Tstart Tstop Tdamp p-style args keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
npt/asphere = style name of this fix command :l
npt/sphere = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l
Tdamp = temperature damping parameter (time units) :l
p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
@ -32,19 +32,28 @@ keyword = {drag} or {dilate} :l
[Examples:]
fix 1 all npt/asphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
fix 2 water npt/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial :pre
fix 1 all npt/sphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
fix 2 all npt/sphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
fix 2 water npt/sphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial :pre
[Description:]
Perform constant NPT integration to update positions, velocities,
and angular velocity each timestep for aspherical or ellipsoidal
particles in the group using a Nose/Hoover temperature
thermostat and Nose/Hoover pressure barostat. P is pressure; T is
temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
Perform constant NPT integration to update position, velocity, and
angular velocity each timestep for extended spherical particles in the
group using a Nose/Hoover temperature thermostat and Nose/Hoover
pressure barostat. P is pressure; T is temperature. This creates a
system trajectory consistent with the isothermal-isobaric ensemble.
This fix differs from the "fix npt"_fix_npt.html command, which
assumes point particles and only updates their position and velocity.
The thermostat is applied to both the translational and rotational
degrees of freedom for the spherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
@ -120,10 +129,10 @@ This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
compute fix-ID_temp group-ID temp/asphere
compute fix-ID_temp group-ID temp/sphere
compute fix-ID_press group-ID pressure fix-ID_temp :pre
See the "compute temp/asphere"_compute_temp_asphere.html and "compute
See the "compute temp/sphere"_compute_temp_sphere.html and "compute
pressure"_compute_pressure.html commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press", and the group for the new computes is the same
@ -139,6 +148,21 @@ custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} 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:]
This fix writes the state of the Nose/Hoover thermostat and barostat
@ -174,9 +198,10 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the "asphere" 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.
This fix requires that particles be represented as extended spheres
and not point particles. This means they will have an angular
velocity and a diameter which is determined by the "shape"_shape.html
command.
Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be
@ -188,8 +213,9 @@ the Nose/Hoover formulation.
[Related commands:]
"fix npt"_fix_npt.html, "fix nve_asphere"_fix_nve_asphere.html,
"fix_modify"_fix_modify.html
"fix npt"_fix_npt.html, "fix nve_sphere"_fix_nve_sphere.html, "fix
nvt_sphere"_fix_nvt_sphere.html, "fix
npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
[Default:]

7
doc/fix_nve.html
View File

@ -24,9 +24,10 @@
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVE updates of position and velocity for atoms in the
group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
<P>Perform constant NVE integration to update position and velocity for
atoms in the group each timestep. V is volume; E is energy. This
creates a system trajectory consistent with the microcanonical
ensemble.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>

7
doc/fix_nve.txt
View File

@ -21,9 +21,10 @@ fix 1 all nve :pre
[Description:]
Perform constant NVE updates of position and velocity for atoms in the
group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
Perform constant NVE integration to update position and velocity for
atoms in the group each timestep. V is volume; E is energy. This
creates a system trajectory consistent with the microcanonical
ensemble.
[Restart, fix_modify, output, run start/stop, minimize info:]

8
doc/fix_nve_asphere.html
View File

@ -24,10 +24,10 @@
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVE updates of position, velocity, orientation, and
angular velocity for aspherical particles in the group each timestep.
V is volume; E is energy. This creates a system trajectory consistent
with the microcanonical ensemble.
<P>Perform constant NVE integration to update position, velocity,
orientation, and angular velocity for aspherical particles in the
group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
</P>
<P>This fix differs from the <A HREF = "fix_nve.html">fix nve</A> command, which
assumes point particles and only updates their position and velocity.

8
doc/fix_nve_asphere.txt
View File

@ -21,10 +21,10 @@ fix 1 all nve/asphere :pre
[Description:]
Perform constant NVE updates of position, velocity, orientation, and
angular velocity for aspherical particles in the group each timestep.
V is volume; E is energy. This creates a system trajectory consistent
with the microcanonical ensemble.
Perform constant NVE integration to update position, velocity,
orientation, and angular velocity for aspherical particles in the
group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
This fix differs from the "fix nve"_fix_nve.html command, which
assumes point particles and only updates their position and velocity.

8
doc/fix_nve_sphere.html
View File

@ -35,10 +35,10 @@ fix 1 all nve/sphere update dipole
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVE updates of position, velocity, and angular
velocity for spherical particles in the group each timestep. V is
volume; E is energy. This creates a system trajectory consistent with
the microcanonical ensemble.
<P>Perform constant NVE integration to update position, velocity, and
angular velocity for extended spherical particles in the group each
timestep. V is volume; E is energy. This creates a system trajectory
consistent with the microcanonical ensemble.
</P>
<P>This fix differs from the <A HREF = "fix_nve.html">fix nve</A> command, which
assumes point particles and only updates their position and velocity.

8
doc/fix_nve_sphere.txt
View File

@ -27,10 +27,10 @@ fix 1 all nve/sphere update dipole :pre
[Description:]
Perform constant NVE updates of position, velocity, and angular
velocity for spherical particles in the group each timestep. V is
volume; E is energy. This creates a system trajectory consistent with
the microcanonical ensemble.
Perform constant NVE integration to update position, velocity, and
angular velocity for extended spherical particles in the group each
timestep. V is volume; E is energy. This creates a system trajectory
consistent with the microcanonical ensemble.
This fix differs from the "fix nve"_fix_nve.html command, which
assumes point particles and only updates their position and velocity.

5
doc/fix_nvt.html
View File

@ -43,6 +43,11 @@ each timestep for atoms in the group using a Nose/Hoover temperature
thermostat <A HREF = "#Hoover">(Hoover)</A>. V is volume; T is temperature. This
creates a system trajectory consistent with the canonical ensemble.
</P>
<P>The thermostat is applied to only the translational degrees of freedom
for the particles. The translational degrees of freedom can also have
a bias velocity removed from them before thermostatting takes place;
see the description below.
</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

5
doc/fix_nvt.txt
View File

@ -34,6 +34,11 @@ each timestep for atoms in the group using a Nose/Hoover temperature
thermostat "(Hoover)"_#Hoover. V is volume; T is temperature. This
creates a system trajectory consistent with the canonical ensemble.
The thermostat is applied to only the translational degrees of freedom
for the particles. The translational degrees of freedom can also have
a bias velocity removed from them before thermostatting takes place;
see the description below.
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

37
doc/fix_nvt_asphere.html
View File

@ -38,11 +38,18 @@ fix 1 all nvt/asphere 300.0 300.0 100.0 drag 0.2
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVT integration to update positions, velocities,
and angular velocities each timestep for aspherical or ellipsoidal
particles in the group using a Nose/Hoover temperature thermostat.
V is volume; T is temperature. This creates a system trajectory
consistent with the canonical ensemble.
<P>Perform constant NVT integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover temperature
thermostat. V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
</P>
<P>The thermostat is applied to both the translational and rotational
degrees of freedom for the aspherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</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
@ -82,6 +89,21 @@ 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>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
@ -116,6 +138,11 @@ commands</A>.
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix requires that particles be represented as extended ellipsoids
and not point particles. This means they will have an angular
momentum and a shape which is determined by the <A HREF = "shape.html">shape</A>
command.
</P>
<P>The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in
the Nose/Hoover formulation.

37
doc/fix_nvt_asphere.txt
View File

@ -29,11 +29,18 @@ fix 1 all nvt/asphere 300.0 300.0 100.0 drag 0.2 :pre
[Description:]
Perform constant NVT integration to update positions, velocities,
and angular velocities each timestep for aspherical or ellipsoidal
particles in the group using a Nose/Hoover temperature thermostat.
V is volume; T is temperature. This creates a system trajectory
consistent with the canonical ensemble.
Perform constant NVT integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover temperature
thermostat. V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
The thermostat is applied to both the translational and rotational
degrees of freedom for the aspherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
@ -73,6 +80,21 @@ 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:]
This fix writes the state of the Nose/Hoover thermostat to "binary
@ -107,6 +129,11 @@ This fix is part of the "asphere" 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.
This fix requires that particles be represented as extended ellipsoids
and not point particles. This means they will have an angular
momentum and a shape which is determined by the "shape"_shape.html
command.
The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in
the Nose/Hoover formulation.

15
doc/fix_nvt_sllod.html
View File

@ -108,6 +108,21 @@ 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>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary

15
doc/fix_nvt_sllod.txt
View File

@ -99,6 +99,21 @@ 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:]
This fix writes the state of the Nose/Hoover thermostat to "binary

63
doc/fix_nvt_sphere.html
View File

@ -9,15 +9,15 @@
<HR>
<H3>fix nvt/asphere command
<H3>fix nvt/sphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nvt/asphere Tstart Tstop Tdamp keyword value ...
<PRE>fix ID group-ID nvt/sphere Tstart Tstop Tdamp keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nvt/asphere = style name of this fix command
<LI>nvt/sphere = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run
@ -33,16 +33,26 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nvt/asphere 300.0 300.0 100.0
fix 1 all nvt/asphere 300.0 300.0 100.0 drag 0.2
<PRE>fix 1 all nvt/sphere 300.0 300.0 100.0
fix 1 all nvt/sphere 300.0 300.0 100.0 drag 0.2
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVT integration to update positions, velocities,
and angular velocities each timestep for aspherical or ellipsoidal
particles in the group using a Nose/Hoover temperature thermostat.
V is volume; T is temperature. This creates a system trajectory
consistent with the canonical ensemble.
<P>Perform constant NVT integration to update position, velocity, and
angular velocity each timestep for extended spherical particles in the
group using a Nose/Hoover temperature thermostat. V is volume; T is
temperature. This creates a system trajectory consistent with the
canonical ensemble.
</P>
<P>This fix differs from the <A HREF = "fix_nvt.html">fix nvt</A> command, which
assumes point particles and only updates their position and velocity.
</P>
<P>The thermostat is applied to both the translational and rotational
degrees of freedom for the spherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</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
@ -62,12 +72,12 @@ to determine if the drag term is working. Typically a value between
0.2 to 2.0 is sufficient to damp oscillations after a few periods.
</P>
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/asphere", as if this command
creates its own compute of style "temp/sphere", as if this command
had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp/asphere
<PRE>compute fix-ID_temp group-ID temp/sphere
</PRE>
<P>See the <A HREF = "compute_temp_asphere.html">compute temp/asphere</A> command for
<P>See the <A HREF = "compute_temp_sphere.html">compute temp/sphere</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.
@ -82,6 +92,21 @@ 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>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
@ -112,9 +137,10 @@ commands</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "asphere" 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>This fix requires that particles be represented as extended spheres
and not point particles. This means they will have an angular
velocity and a diameter which is determined by the <A HREF = "shape.html">shape</A>
command.
</P>
<P>The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in
@ -122,8 +148,9 @@ the Nose/Hoover formulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_npt_asphere.html">fix
npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
<P><A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_nve_sphere.html">fix nve_sphere</A>, <A HREF = "fix_nvt_asphere.html">fix
nvt_asphere</A>, <A HREF = "fix_npt_sphere.html">fix
npt_sphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B>
</P>

63
doc/fix_nvt_sphere.txt
View File

@ -6,14 +6,14 @@
:line
fix nvt/asphere command :h3
fix nvt/sphere command :h3
[Syntax:]
fix ID group-ID nvt/asphere Tstart Tstop Tdamp keyword value ... :pre
fix ID group-ID nvt/sphere Tstart Tstop Tdamp keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
nvt/asphere = style name of this fix command :l
nvt/sphere = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l
Tdamp = temperature damping parameter (time units) :l
@ -24,16 +24,26 @@ keyword = {drag} :l
[Examples:]
fix 1 all nvt/asphere 300.0 300.0 100.0
fix 1 all nvt/asphere 300.0 300.0 100.0 drag 0.2 :pre
fix 1 all nvt/sphere 300.0 300.0 100.0
fix 1 all nvt/sphere 300.0 300.0 100.0 drag 0.2 :pre
[Description:]
Perform constant NVT integration to update positions, velocities,
and angular velocities each timestep for aspherical or ellipsoidal
particles in the group using a Nose/Hoover temperature thermostat.
V is volume; T is temperature. This creates a system trajectory
consistent with the canonical ensemble.
Perform constant NVT integration to update position, velocity, and
angular velocity each timestep for extended spherical particles in the
group using a Nose/Hoover temperature thermostat. V is volume; T is
temperature. This creates a system trajectory consistent with the
canonical ensemble.
This fix differs from the "fix nvt"_fix_nvt.html command, which
assumes point particles and only updates their position and velocity.
The thermostat is applied to both the translational and rotational
degrees of freedom for the spherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
@ -53,12 +63,12 @@ to determine if the drag term is working. Typically a value between
0.2 to 2.0 is sufficient to damp oscillations after a few periods.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/asphere", as if this command
creates its own compute of style "temp/sphere", as if this command
had been issued:
compute fix-ID_temp group-ID temp/asphere :pre
compute fix-ID_temp group-ID temp/sphere :pre
See the "compute temp/asphere"_compute_temp_asphere.html command for
See the "compute temp/sphere"_compute_temp_sphere.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.
@ -73,6 +83,21 @@ 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:]
This fix writes the state of the Nose/Hoover thermostat to "binary
@ -103,9 +128,10 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the "asphere" 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.
This fix requires that particles be represented as extended spheres
and not point particles. This means they will have an angular
velocity and a diameter which is determined by the "shape"_shape.html
command.
The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in
@ -113,8 +139,9 @@ the Nose/Hoover formulation.
[Related commands:]
"fix nvt"_fix_nvt.html, "fix nve_asphere"_fix_nve_asphere.html, "fix
npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
"fix nvt"_fix_nvt.html, "fix nve_sphere"_fix_nve_sphere.html, "fix
nvt_asphere"_fix_nvt_asphere.html, "fix
npt_sphere"_fix_npt_sphere.html, "fix_modify"_fix_modify.html
[Default:]

7
doc/fix_temp_berendsen.html
View File

@ -30,6 +30,13 @@
thermostat <A HREF = "#Berendsen">(Berendsen)</A>, which rescales their velocities
every timestep.
</P>
<P>The thermostat 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.
</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

7
doc/fix_temp_berendsen.txt
View File

@ -27,6 +27,13 @@ Reset the temperature of a group of atoms by using a Berendsen
thermostat "(Berendsen)"_#Berendsen, which rescales their velocities
every timestep.
The thermostat 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.
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

7
doc/fix_temp_rescale.html
View File

@ -33,6 +33,13 @@ fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
<P>Reset the temperature of a group of atoms by explicitly rescaling
their velocities.
</P>
<P>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.
</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.

7
doc/fix_temp_rescale.txt
View File

@ -30,6 +30,13 @@ fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 :pre
Reset the temperature of a group of atoms by explicitly rescaling
their velocities.
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
beginning and end of the run.