Updated documentation to reflect changes in compute_temp_profile

doc/src/compute_temp_profile.rst

@@ -76,13 +76,20 @@ velocity for each atom.  Note that if there is only one atom in the
 bin, its thermal velocity will thus be 0.0.
 
 After the spatially-averaged velocity field has been subtracted from
-each atom, the temperature is calculated by the formula KE = (dim\*N
-- dim\*Nx\*Ny\*Nz) k T/2, 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 dim\*Nx\*Ny\*Nz term are degrees of freedom
-subtracted to adjust for the removal of the center-of-mass velocity in
-each of Nx\*Ny\*Nz bins, as discussed in the :ref:`(Evans) <Evans1>` paper.
+each atom, the temperature is calculated by the formula
+KE = (dim\*N - stream\*Nx\*Ny\*Nz - extra ) k T/2, 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, stream = 0, 1, 2 or 3 for
+streaming velocity subtracted in 0, 1, 2 or 3 dimensions, extra = extra
+degrees-of-freedom, N = number of atoms in the group, k = Boltzmann
+constant, and T = temperature.  The stream\*Nx\*Ny\*Nz term is degrees
+of freedom subtracted to adjust for the removal of the center-of-mass
+velocity in each direction of the Nx\*Ny\*Nz bins, as discussed in the
+:ref:`(Evans) <Evans1>` paper.  The extra term defaults to (dim - stream)
+and accounts for overall conservation of center-of-mass velocity across
+the group in directions where streaming velocity is not subtracted. This
+can be altered using the *extra* option of the
+:doc:`compute_modify <compute_modify>` command.
 
 If the *out* keyword is used with a *tensor* value, which is the
 default, a kinetic energy tensor, stored as a 6-element vector, is
@@ -123,10 +130,13 @@ needed, the subtracted degrees-of-freedom can be altered using the
 .. note::
 
    When using the *out* keyword with a value of *bin*\ , the
-   calculated temperature for each bin does not include the
-   degrees-of-freedom adjustment described in the preceding paragraph,
-   for fixes that constrain molecular motion.  It does include the
-   adjustment due to the *extra* option, which is applied to each bin.
+   calculated temperature for each bin includes the degrees-of-freedom
+   adjustment described in the preceding paragraph for fixes that
+   constrain molecular motion, as well as the adjustment due to
+   the *extra* option (which defaults to dim - stream as described above),
+   by fractionally applying them based on the fraction of atoms in each
+   bin, so that the degrees-of-freedom summed over all bins is consistent
+   with the degrees-of-freedom in the scalar temperature calculation.
 
 See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
 discussion of different ways to compute temperature and perform