git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2781 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -345,7 +345,8 @@ description:
 <TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A> 
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A> 
 </TD></TR></TABLE></DIV>
 
 <P>These are compute styles contributed by users, which can be used if

doc/Section_commands.txt

@@ -474,6 +474,7 @@ description:
 "temp/com"_compute_temp_com.html,
 "temp/deform"_compute_temp_deform.html,
 "temp/partial"_compute_temp_partial.html,
+"temp/profile"_compute_temp_profile.html,
 "temp/ramp"_compute_temp_ramp.html,
 "temp/region"_compute_temp_region.html,
 "temp/sphere"_compute_temp_sphere.html :tb(c=6,ea=c)

doc/Section_howto.html

@@ -1178,6 +1178,7 @@ pressure</A> command calculates pressure.
 <LI><A HREF = "compute_temp_com.html">compute temp/com</A>
 <LI><A HREF = "compute_temp_deform.html">compute temp/deform</A>
 <LI><A HREF = "compute_temp_partial.html">compute temp/partial</A>
+<LI><A HREF = "compute_temp_profile.html">compute temp/profile</A>
 <LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
 <LI><A HREF = "compute_temp_region.html">compute temp/region</A> 
 </UL>
@@ -1186,9 +1187,10 @@ velocities) that are removed when computing the thermal temperature.
 <A HREF = "fix_temp_sphere.html">Fix temp/sphere</A> and <A HREF = "fix_temp_asphere.html">fix
 temp/asphere</A> compute kinetic energy for
 extended particles that includes rotational degrees of freedom.  They
-both allow, as an extra argument, another temperature compute that
+both allow, as an extra argument, which is another temperature compute
-subtracts a velocity bias, so the translational velocity of extended
+that subtracts a velocity bias.  This allows the translational
-spherical or aspherical particles can be adjusted in prescribed ways.
+velocity of extended spherical or aspherical particles to be adjusted
+in prescribed ways.
 </P>
 <P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>.  Four
 thermostatting fixes are currently available: Nose-Hoover (nvt),
@@ -1203,7 +1205,7 @@ Berendsen, Langevin, and direct rescaling (temp/rescale):
 <LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A> 
 </UL>
 <P><A HREF = "fix_nvt.html">Fix nvt</A> only thermostats the translational velocity of
-particles.  <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> does as well, except
+particles.  <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> also does this, except
 that it subtracts out a velocity bias due to a deforming box and
 integrates the SLLOD equations of motion.  See the <A HREF = "#4_13">NEMD
 simulations</A> section of this page for further details.  <A HREF = "fix_nvt_sphere.html">Fix
@@ -1225,8 +1227,9 @@ the x and z components of velocity by using it in conjunction with
 <P>IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
 they update the velocities and positions of particles due to forces
 and velocities respectively.  The other thermostat fixes only adjust
-velocities; they do NOT perform time integration.  Thus they should be
+velocities; they do NOT perform time integration updates.  Thus they
-used in conjunction with a constant NVE integration fix such as these:
+should be used in conjunction with a constant NVE integration fix such
+as these:
 </P>
 <UL><LI><A HREF = "fix_nve.html">fix nve</A>
 <LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
@@ -1258,12 +1261,15 @@ and aspherical particles.
 </P>
 <P>All of the barostatting fixes use the <A HREF = "compute_pressure.html">compute
 pressure</A> compute to calculate a current
-pressure.  The barostatting fixes can also use temperature computes
+pressure.  By default, this compute is created with a simple <A HREF = "compute_temp.html">compute
-that remove bias for the purpose of computing the current temperature
+temp</A> (see the last argument of the <A HREF = "compute_pressure.html">compute
-which contributes to the current pressure.  See the doc pages for the
+pressure</A> command), which is used to calculated
-individual fixes and for the <A HREF = "fix_modify.html">fix_modify</A> command for
+the kinetic componenet of the pressure.  The barostatting fixes can
-instructions on how to assign a temperature or pressure compute to a
+also use temperature computes that remove bias for the purpose of
-barostatting fix.
+computing the kinetic componenet which contributes to the current
+pressure.  See the doc pages for the individual fixes and for the
+<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
+a temperature or pressure compute to a barostatting fix.
 </P>
 <P>IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods (<A HREF = "fix_npt.html">fix
 npt</A> and <A HREF = "fix_nph.html">fix nph</A>) perform time

doc/Section_howto.txt

@@ -1169,6 +1169,7 @@ pressure"_compute_pressure.html command calculates pressure.
 "compute temp/com"_compute_temp_com.html
 "compute temp/deform"_compute_temp_deform.html
 "compute temp/partial"_compute_temp_partial.html
+"compute temp/profile"_compute_temp_profile.html
 "compute temp/ramp"_compute_temp_ramp.html
 "compute temp/region"_compute_temp_region.html :ul
 
@@ -1177,9 +1178,10 @@ velocities) that are removed when computing the thermal temperature.
 "Fix temp/sphere"_fix_temp_sphere.html and "fix
 temp/asphere"_fix_temp_asphere.html compute kinetic energy for
 extended particles that includes rotational degrees of freedom.  They
-both allow, as an extra argument, another temperature compute that
+both allow, as an extra argument, which is another temperature compute
-subtracts a velocity bias, so the translational velocity of extended
+that subtracts a velocity bias.  This allows the translational
-spherical or aspherical particles can be adjusted in prescribed ways.
+velocity of extended spherical or aspherical particles to be adjusted
+in prescribed ways.
 
 Thermostatting in LAMMPS is performed by "fixes"_fix.html.  Four
 thermostatting fixes are currently available: Nose-Hoover (nvt),
@@ -1194,7 +1196,7 @@ Berendsen, Langevin, and direct rescaling (temp/rescale):
 "fix temp/rescale"_fix_temp_rescale.html :ul
 
 "Fix nvt"_fix_nvt.html only thermostats the translational velocity of
-particles.  "Fix nvt/sllod"_fix_nvt_sllod.html does as well, except
+particles.  "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except
 that it subtracts out a velocity bias due to a deforming box and
 integrates the SLLOD equations of motion.  See the "NEMD
 simulations"_#4_13 section of this page for further details.  "Fix
@@ -1216,8 +1218,9 @@ the x and z components of velocity by using it in conjunction with
 IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
 they update the velocities and positions of particles due to forces
 and velocities respectively.  The other thermostat fixes only adjust
-velocities; they do NOT perform time integration.  Thus they should be
+velocities; they do NOT perform time integration updates.  Thus they
-used in conjunction with a constant NVE integration fix such as these:
+should be used in conjunction with a constant NVE integration fix such
+as these:
 
 "fix nve"_fix_nve.html
 "fix nve/sphere"_fix_nve_sphere.html
@@ -1249,12 +1252,15 @@ and aspherical particles.
 
 All of the barostatting fixes use the "compute
 pressure"_compute_pressure.html compute to calculate a current
-pressure.  The barostatting fixes can also use temperature computes
+pressure.  By default, this compute is created with a simple "compute
-that remove bias for the purpose of computing the current temperature
+temp"_compute_temp.html (see the last argument of the "compute
-which contributes to the current pressure.  See the doc pages for the
+pressure"_compute_pressure.html command), which is used to calculated
-individual fixes and for the "fix_modify"_fix_modify.html command for
+the kinetic componenet of the pressure.  The barostatting fixes can
-instructions on how to assign a temperature or pressure compute to a
+also use temperature computes that remove bias for the purpose of
-barostatting fix.
+computing the kinetic componenet which contributes to the current
+pressure.  See the doc pages for the individual fixes and for the
+"fix_modify"_fix_modify.html command for instructions on how to assign
+a temperature or pressure compute to a barostatting fix.
 
 IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods ("fix
 npt"_fix_npt.html and "fix nph"_fix_nph.html) perform time

doc/compute.html

@@ -130,6 +130,7 @@ available in LAMMPS:
 <LI><A HREF = "compute_temp_com.html">temp/com</A> - temperature after subtracting center-of-mass velocity
 <LI><A HREF = "compute_temp_deform.html">temp/deform</A> - temperature excluding box deformation velocity
 <LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
+<LI><A HREF = "compute_temp_profile.html">temp/profile</A> - temperature excluding a binned velocity profile
 <LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
 <LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
 <LI><A HREF = "compute_temp_sphere.html">temp/sphere</A> - temperature of spherical particles 

doc/compute.txt

@@ -127,6 +127,7 @@ available in LAMMPS:
 "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
 "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
 "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
+"temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
 "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
 "temp/region"_compute_temp_region.html - temperature of a region of atoms
 "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles :ul

doc/compute_temp_asphere.html

@@ -50,9 +50,11 @@ rotational motion to the extra degrees of freedom.  E.g. the <A HREF = "pair_gay
 pair potential</A> does not impart torque to spherical
 particles, so they do not rotate.
 </P>
-<P>The rotational kinetic energy is computed as 1/2 I w^2, where I is the
+<P>The translational kinetic energy is computed the same as is described
-inertia tensor for the aspherical particle and w is its angular
+by the <A HREF = "compute_temp.html">compute temp</A> command.  The rotational
-velocity, which is computed from its angular momentum.
+kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
+for the aspherical particle and w is its angular velocity, which is
+computed from its angular momentum.
 </P>
 <P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
 as ellipsoids, not ellipses, meaning their moments of inertia will be

doc/compute_temp_asphere.txt

@@ -47,9 +47,11 @@ rotational motion to the extra degrees of freedom.  E.g. the "GayBerne
 pair potential"_pair_gayberne.html does not impart torque to spherical
 particles, so they do not rotate.
 
-The rotational kinetic energy is computed as 1/2 I w^2, where I is the
+The translational kinetic energy is computed the same as is described
-inertia tensor for the aspherical particle and w is its angular
+by the "compute temp"_compute_temp.html command.  The rotational
-velocity, which is computed from its angular momentum.
+kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
+for the aspherical particle and w is its angular velocity, which is
+computed from its angular momentum.
 
 IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated
 as ellipsoids, not ellipses, meaning their moments of inertia will be

doc/compute_temp_com.html

@@ -33,7 +33,8 @@ command that computes a temperature,
 e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
 temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
 </P>
-<P>The temperature is calculated by the formula KE = dim/2 N k T, where
+<P>After the center-of-mass velocity has been subtracted from each atom,
+the temperature is calculated by the formula KE = dim/2 N k T, where
 KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
 dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
 in the group, k = Boltzmann constant, and T = temperature.

doc/compute_temp_com.txt

@@ -30,7 +30,8 @@ command that computes a temperature,
 e.g. "thermo_modify"_thermo_modify.html, "fix
 temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
 
-The temperature is calculated by the formula KE = dim/2 N k T, where
+After the center-of-mass velocity has been subtracted from each atom,
+the temperature is calculated by the formula KE = dim/2 N k T, where
 KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
 dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
 in the group, k = Boltzmann constant, and T = temperature.

doc/compute_temp_deform.html

@@ -36,10 +36,10 @@ that computes a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</
 <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
 </P>
 <P>The deformation fix changes the box size and/or shape over time, so
-each point in the simulation box can be thought of as having a
+each atom in the simulation box can be thought of as having a
 "streaming" velocity.  For example, if the box is being sheared in x,
-relative to y, then points at the bottom of the box (low y) have a
+relative to y, then atoms at the bottom of the box (low y) have a
-small x velocity, while points at the top of the box (hi y) have a
+small x velocity, while atoms at the top of the box (hi y) have a
 large x velocity.  This position-dependent streaming velocity is
 subtracted from each atom's actual velocity to yield a thermal
 velocity which is used to compute the temperature.
@@ -56,11 +56,12 @@ not changed, and thus they do NOT have the streaming velocity assumed
 by this compute.  LAMMPS will warn you if fix deform is defined and
 its remap setting is not consistent with this compute.
 </P>
-<P>The temperature is calculated by the formula KE = dim/2 N k T, where
+<P>After the streaming velocity has been subtracted from each atom, the
-KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
+temperature is calculated by the formula KE = dim/2 N k T, where KE =
-dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2
-in the group, k = Boltzmann constant, and T = temperature.  Note that
+or 3 = dimensionality of the simulation, N = number of atoms in the
-v in the kinetic energy formula is the atom's thermal velocity.
+group, k = Boltzmann constant, and T = temperature.  Note that v in
+the kinetic energy formula is the atom's thermal velocity.
 </P>
 <P>A 6-component kinetic energy tensor is also calculated by this compute
 for use in the computation of a pressure tensor.  The formula for the
@@ -104,8 +105,9 @@ the simulation.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>, <A HREF = "fix_deform.html">fix
+<P><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>, <A HREF = "compute_temp_profile.html">compute
-deform</A>, <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
+temp/profile</A>, <A HREF = "fix_deform.html">fix deform</A>,
+<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
 </P>
 <P><B>Default:</B> none
 </P>

doc/compute_temp_deform.txt

@@ -33,10 +33,10 @@ that computes a temperature, e.g. "thermo_modify"_thermo_modify.html,
 "fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
 
 The deformation fix changes the box size and/or shape over time, so
-each point in the simulation box can be thought of as having a
+each atom in the simulation box can be thought of as having a
 "streaming" velocity.  For example, if the box is being sheared in x,
-relative to y, then points at the bottom of the box (low y) have a
+relative to y, then atoms at the bottom of the box (low y) have a
-small x velocity, while points at the top of the box (hi y) have a
+small x velocity, while atoms at the top of the box (hi y) have a
 large x velocity.  This position-dependent streaming velocity is
 subtracted from each atom's actual velocity to yield a thermal
 velocity which is used to compute the temperature.
@@ -53,11 +53,12 @@ not changed, and thus they do NOT have the streaming velocity assumed
 by this compute.  LAMMPS will warn you if fix deform is defined and
 its remap setting is not consistent with this compute.
 
-The temperature is calculated by the formula KE = dim/2 N k T, where
+After the streaming velocity has been subtracted from each atom, the
-KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
+temperature is calculated by the formula KE = dim/2 N k T, where KE =
-dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
+total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2
-in the group, k = Boltzmann constant, and T = temperature.  Note that
+or 3 = dimensionality of the simulation, N = number of atoms in the
-v in the kinetic energy formula is the atom's thermal velocity.
+group, k = Boltzmann constant, and T = temperature.  Note that v in
+the kinetic energy formula is the atom's thermal velocity.
 
 A 6-component kinetic energy tensor is also calculated by this compute
 for use in the computation of a pressure tensor.  The formula for the
@@ -101,7 +102,8 @@ the simulation.
 
 [Related commands:]
 
-"compute temp/ramp"_compute_temp_ramp.html, "fix
+"compute temp/ramp"_compute_temp_ramp.html, "compute
-deform"_fix_deform.html, "fix nvt/sllod"_fix_nvt_sllod.html
+temp/profile"_compute_temp_profile.html, "fix deform"_fix_deform.html,
+"fix nvt/sllod"_fix_nvt_sllod.html
 
 [Default:] none

doc/compute_temp_ramp.html

@@ -28,20 +28,27 @@
 </PRE>
 <P><B>Examples:</B>
 </P>
-<PRE>temperature 2nd middle ramp vx 0 8 y 2 12 units lattice 
+<PRE>compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice 
 </PRE>
 <P><B>Description:</B>
 </P>
 <P>Define a computation that calculates the temperature of a group of
-atoms, after subtracting out an imposed velocity on the system before
+atoms, after subtracting out an ramped velocity profile before
 computing the kinetic energy.  A compute of this style can be used by
 any command that computes a temperature,
 e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
 temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
 </P>
-<P>The meaning of the arguments for this command is the same as for the
+<P>The meaning of the arguments for this command which define the
-<A HREF = "velocity.html">velocity ramp</A> command which was presumably used to
+velocity ramp are the same as for the <A HREF = "velocity.html">velocity ramp</A>
-impose the velocity.
+command which was presumably used to impose the velocity.
+</P>
+<P>After the ramp velocity has been subtracted from the specified
+dimension for each atom, the temperature is calculated by the formula
+KE = dim/2 N k T, where KE = total kinetic energy of the group of
+atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
+simulation, N = number of atoms in the group, k = Boltzmann constant,
+and T = temperature.
 </P>
 <P>The <I>units</I> keyword determines the meaning of the distance units used
 for coordinates (c1,c2) and velocities (vlo,vhi).  A <I>box</I> value
@@ -93,8 +100,8 @@ the simulation.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_region.html">compute
+<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_profile.html">compute
-temp/region</A>, <A HREF = "compute_temp_deform.html">compute
+temp/profie</A>, <A HREF = "compute_temp_deform.html">compute
 temp/deform</A>, <A HREF = "compute_pressure.html">compute
 pressure</A>
 </P>

doc/compute_temp_ramp.txt

@@ -24,20 +24,27 @@ keyword = {units} :ul
 
 [Examples:]
 
-temperature 2nd middle ramp vx 0 8 y 2 12 units lattice :pre
+compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice :pre
 
 [Description:]
 
 Define a computation that calculates the temperature of a group of
-atoms, after subtracting out an imposed velocity on the system before
+atoms, after subtracting out an ramped velocity profile before
 computing the kinetic energy.  A compute of this style can be used by
 any command that computes a temperature,
 e.g. "thermo_modify"_thermo_modify.html, "fix
 temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
 
-The meaning of the arguments for this command is the same as for the
+The meaning of the arguments for this command which define the
-"velocity ramp"_velocity.html command which was presumably used to
+velocity ramp are the same as for the "velocity ramp"_velocity.html
-impose the velocity.
+command which was presumably used to impose the velocity.
+
+After the ramp velocity has been subtracted from the specified
+dimension for each atom, the temperature is calculated by the formula
+KE = dim/2 N k T, where KE = total kinetic energy of the group of
+atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
+simulation, N = number of atoms in the group, k = Boltzmann constant,
+and T = temperature.
 
 The {units} keyword determines the meaning of the distance units used
 for coordinates (c1,c2) and velocities (vlo,vhi).  A {box} value
@@ -90,11 +97,10 @@ the simulation.
 [Related commands:]
 
 "compute temp"_compute_temp.html, "compute
-temp/region"_compute_temp_region.html, "compute
+temp/profie"_compute_temp_profile.html, "compute
 temp/deform"_compute_temp_deform.html, "compute
 pressure"_compute_pressure.html
 
 [Default:]
 
 The option default is units = lattice.
-

doc/compute_temp_sphere.html

@@ -36,9 +36,10 @@ particles with only translational kinetic energy.
 translational, 3 rotational).  For 2d spherical particles, each has 3
 degrees of freedom (2 translational, 1 rotational).
 </P>
-<P>The rotational kinetic energy is computed as 1/2 I w^2, where I is the
+<P>The translational kinetic energy is computed the same as is described
-moment of inertia for a sphere and w is the particle's angular
+by the <A HREF = "compute_temp.html">compute temp</A> command.  The rotational
-velocity.
+kinetic energy is computed as 1/2 I w^2, where I is the moment of
+inertia for a sphere and w is the particle's angular velocity.
 </P>
 <P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
 as spheres, not disks, meaning their moment of inertia will be the

doc/compute_temp_sphere.txt

@@ -33,9 +33,10 @@ For 3d spherical particles, each has 6 degrees of freedom (3
 translational, 3 rotational).  For 2d spherical particles, each has 3
 degrees of freedom (2 translational, 1 rotational).
 
-The rotational kinetic energy is computed as 1/2 I w^2, where I is the
+The translational kinetic energy is computed the same as is described
-moment of inertia for a sphere and w is the particle's angular
+by the "compute temp"_compute_temp.html command.  The rotational
-velocity.
+kinetic energy is computed as 1/2 I w^2, where I is the moment of
+inertia for a sphere and w is the particle's angular velocity.
 
 IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated
 as spheres, not disks, meaning their moment of inertia will be the

doc/fix_langevin.html

@@ -97,19 +97,17 @@ thermostatting.
 run from <I>Tstart</I> to <I>Tstop</I>.
 </P>
 <P>Like other fixes that perform thermostatting, this fix can be used
-with <A HREF = "compute.html">compute commands</A> that calculate a temperature
+with <A HREF = "compute.html">compute commands</A> that remove a "bias" from the
-after removing a "bias" from the atom velocities.  E.g. removing the
+atom velocities.  E.g. removing the center-of-mass velocity from a
-center-of-mass velocity from a group of atoms or only calculating
+group of atoms or removing the x-component of velocity from the
-temperature on the x-component of velocity or only calculating
+calculation.  This is not done by default, but only if the
-temperature for atoms in a geometric region.  This is not done by
+<A HREF = "fix_modify.html">fix_modify</A> command is used to assign a temperature
-default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
+compute to this fix that includes such a bias term.  See the doc pages
-to assign a temperature compute to this fix that includes such a bias
+for individual <A HREF = "compute.html">compute commands</A> to determine which ones
-term.  See the doc pages for individual <A HREF = "compute.html">compute
+include a bias.  In this case, the thermostat works in the following
-commands</A> to determine which ones include a bias.  In
+manner: bias is removed from each atom, thermostatting is performed on
-this case, the thermostat works in the following manner: the current
+the remaining thermal degrees of freedom, and the bias is added back
-temperature is calculated taking the bias into account, bias is
+in.
-removed from each atom, thermostatting is performed on the remaining
-thermal degrees of freedom, and the bias is added back in.
 </P>
 <P>The <I>damp</I> parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 100.0

doc/fix_langevin.txt

@@ -88,19 +88,17 @@ The desired temperature at each timestep is a ramped value during the
 run from {Tstart} to {Tstop}.
 
 Like other fixes that perform thermostatting, this fix can be used
-with "compute commands"_compute.html that calculate a temperature
+with "compute commands"_compute.html that remove a "bias" from the
-after removing a "bias" from the atom velocities.  E.g. removing the
+atom velocities.  E.g. removing the center-of-mass velocity from a
-center-of-mass velocity from a group of atoms or only calculating
+group of atoms or removing the x-component of velocity from the
-temperature on the x-component of velocity or only calculating
+calculation.  This is not done by default, but only if the
-temperature for atoms in a geometric region.  This is not done by
+"fix_modify"_fix_modify.html command is used to assign a temperature
-default, but only if the "fix_modify"_fix_modify.html command is used
+compute to this fix that includes such a bias term.  See the doc pages
-to assign a temperature compute to this fix that includes such a bias
+for individual "compute commands"_compute.html to determine which ones
-term.  See the doc pages for individual "compute
+include a bias.  In this case, the thermostat works in the following
-commands"_compute.html to determine which ones include a bias.  In
+manner: bias is removed from each atom, thermostatting is performed on
-this case, the thermostat works in the following manner: the current
+the remaining thermal degrees of freedom, and the bias is added back
-temperature is calculated taking the bias into account, bias is
+in.
-removed from each atom, thermostatting is performed on the remaining
-thermal degrees of freedom, and the bias is added back in.
 
 The {damp} parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 100.0