git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1648 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_langevin.html

@@ -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>

doc/fix_langevin.txt

@@ -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:]
 

doc/fix_npt.html

@@ -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

doc/fix_npt.txt

@@ -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

doc/fix_npt_asphere.html

@@ -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, 
+<P>Perform constant NPT integration to update position, velocity,
-and angular velocity each timestep for aspherical or ellipsoidal 
+orientation, and angular velocity each timestep for aspherical or
-particles in the group using a Nose/Hoover temperature
+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>,
+<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
-<A HREF = "fix_modify.html">fix_modify</A>
+npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
 </P>
 <P><B>Default:</B>
 </P>

doc/fix_npt_asphere.txt

@@ -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, 
+Perform constant NPT integration to update position, velocity,
-and angular velocity each timestep for aspherical or ellipsoidal 
+orientation, and angular velocity each timestep for aspherical or
-particles in the group using a Nose/Hoover temperature
+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 npt"_fix_npt.html, "fix nve_asphere"_fix_nve_asphere.html, "fix
-"fix_modify"_fix_modify.html
+npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
 
 [Default:]
 

doc/fix_npt_sphere.html

@@ -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
+<PRE>fix 1 all npt/sphere 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/sphere 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 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/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial 
+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, 
+<P>Perform constant NPT integration to update position, velocity, and
-and angular velocity each timestep for aspherical or ellipsoidal 
+angular velocity each timestep for extended spherical particles in the
-particles in the group using a Nose/Hoover temperature
+group using a Nose/Hoover temperature thermostat and Nose/Hoover
-thermostat and Nose/Hoover pressure barostat.  P is pressure; T is
+pressure barostat.  P is pressure; T is temperature.  This creates a
-temperature.  This creates a system trajectory consistent with the
+system trajectory consistent with the isothermal-isobaric ensemble.
-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
+<P>This fix requires that particles be represented as extended spheres
-LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
+and not point particles.  This means they will have an angular
-LAMMPS</A> section for more info.
+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>,
+<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
-<A HREF = "fix_modify.html">fix_modify</A>
+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>

doc/fix_npt_sphere.txt

@@ -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 1 all npt/sphere 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/sphere 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 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/asphere 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial :pre
+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, 
+Perform constant NPT integration to update position, velocity, and
-and angular velocity each timestep for aspherical or ellipsoidal 
+angular velocity each timestep for extended spherical particles in the
-particles in the group using a Nose/Hoover temperature
+group using a Nose/Hoover temperature thermostat and Nose/Hoover
-thermostat and Nose/Hoover pressure barostat.  P is pressure; T is
+pressure barostat.  P is pressure; T is temperature.  This creates a
-temperature.  This creates a system trajectory consistent with the
+system trajectory consistent with the isothermal-isobaric ensemble.
-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
+This fix requires that particles be represented as extended spheres
-LAMMPS was built with that package.  See the "Making
+and not point particles.  This means they will have an angular
-LAMMPS"_Section_start.html#2_3 section for more info.
+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 npt"_fix_npt.html, "fix nve_sphere"_fix_nve_sphere.html, "fix
-"fix_modify"_fix_modify.html
+nvt_sphere"_fix_nvt_sphere.html, "fix
+npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
 
 [Default:]
 

doc/fix_nve.html

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

doc/fix_nve.txt

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

doc/fix_nve_asphere.html

@@ -24,10 +24,10 @@
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>Perform constant NVE updates of position, velocity, orientation, and
+<P>Perform constant NVE integration to update position, velocity,
-angular velocity for aspherical particles in the group each timestep.
+orientation, and angular velocity for aspherical particles in the
-V is volume; E is energy.  This creates a system trajectory consistent
+group each timestep.  V is volume; E is energy.  This creates a system
-with the microcanonical ensemble.
+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.

doc/fix_nve_asphere.txt

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

doc/fix_nve_sphere.html

@@ -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
+<P>Perform constant NVE integration to update position, velocity, and
-velocity for spherical particles in the group each timestep.  V is
+angular velocity for extended spherical particles in the group each
-volume; E is energy.  This creates a system trajectory consistent with
+timestep.  V is volume; E is energy.  This creates a system trajectory
-the microcanonical ensemble.
+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.

doc/fix_nve_sphere.txt

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

doc/fix_nvt.html

@@ -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

doc/fix_nvt.txt

@@ -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

doc/fix_nvt_asphere.html

@@ -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,
+<P>Perform constant NVT integration to update position, velocity,
-and angular velocities each timestep for aspherical or ellipsoidal 
+orientation, and angular velocity each timestep for aspherical or
-particles in the group using a Nose/Hoover temperature thermostat.  
+ellipsoidal particles in the group using a Nose/Hoover temperature
-V is volume; T is temperature.  This creates a system trajectory 
+thermostat.  V is volume; T is temperature.  This creates a system
-consistent with the canonical ensemble.
+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.

doc/fix_nvt_asphere.txt

@@ -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,
+Perform constant NVT integration to update position, velocity,
-and angular velocities each timestep for aspherical or ellipsoidal 
+orientation, and angular velocity each timestep for aspherical or
-particles in the group using a Nose/Hoover temperature thermostat.  
+ellipsoidal particles in the group using a Nose/Hoover temperature
-V is volume; T is temperature.  This creates a system trajectory 
+thermostat.  V is volume; T is temperature.  This creates a system
-consistent with the canonical ensemble.
+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.

doc/fix_nvt_sllod.html

@@ -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

doc/fix_nvt_sllod.txt

@@ -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

doc/fix_nvt_sphere.html

@@ -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
+<PRE>fix 1 all nvt/sphere 300.0 300.0 100.0
-fix 1 all nvt/asphere 300.0 300.0 100.0 drag 0.2 
+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,
+<P>Perform constant NVT integration to update position, velocity, and
-and angular velocities each timestep for aspherical or ellipsoidal 
+angular velocity each timestep for extended spherical particles in the
-particles in the group using a Nose/Hoover temperature thermostat.  
+group using a Nose/Hoover temperature thermostat.  V is volume; T is
-V is volume; T is temperature.  This creates a system trajectory 
+temperature.  This creates a system trajectory consistent with the
-consistent with the canonical ensemble.
+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
+<P>This fix requires that particles be represented as extended spheres
-LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
+and not point particles.  This means they will have an angular
-LAMMPS</A> section for more info.
+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
+<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
-npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
+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>

doc/fix_nvt_sphere.txt

@@ -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/sphere 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 drag 0.2 :pre
 
 [Description:]
 
-Perform constant NVT integration to update positions, velocities,
+Perform constant NVT integration to update position, velocity, and
-and angular velocities each timestep for aspherical or ellipsoidal 
+angular velocity each timestep for extended spherical particles in the
-particles in the group using a Nose/Hoover temperature thermostat.  
+group using a Nose/Hoover temperature thermostat.  V is volume; T is
-V is volume; T is temperature.  This creates a system trajectory 
+temperature.  This creates a system trajectory consistent with the
-consistent with the canonical ensemble.
+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
+This fix requires that particles be represented as extended spheres
-LAMMPS was built with that package.  See the "Making
+and not point particles.  This means they will have an angular
-LAMMPS"_Section_start.html#2_3 section for more info.
+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
+"fix nvt"_fix_nvt.html, "fix nve_sphere"_fix_nve_sphere.html, "fix
-npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
+nvt_asphere"_fix_nvt_asphere.html, "fix
+npt_sphere"_fix_npt_sphere.html, "fix_modify"_fix_modify.html
 
 [Default:]
 

doc/fix_temp_berendsen.html

@@ -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

doc/fix_temp_berendsen.txt

@@ -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

doc/fix_temp_rescale.html

@@ -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.

doc/fix_temp_rescale.txt

@@ -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.