use k_B for Boltzmann constant

doc/src/compute_temp.rst

@@ -36,11 +36,11 @@ The temperature is calculated by the formula
 
 .. math::
 
-    \mathrm{KE} = \frac{\text{dim}}{2} N k T,
+   \text{KE} = \frac{\text{dim}}{2} N k_B T,
 
 where KE = total kinetic energy of the group of atoms (sum of
 :math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
-:math:`N` is the number of atoms in the group, :math:`k` is the Boltzmann
+:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
 constant, and :math:`T` is the absolute temperature.
 
 A kinetic energy tensor, stored as a six-element vector, is also

doc/src/compute_temp_com.rst

@@ -37,12 +37,12 @@ the temperature is calculated by the formula
 
 .. math::
 
-  \text{KE} = \frac{\text{dim}}{2} N k T,
+   \text{KE} = \frac{\text{dim}}{2} N k_B T,
 
 where KE is the total kinetic energy of the group of atoms (sum of
-:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
-:math:`N` is number of atoms in the group, :math:`k` is the Boltzmann constant,
-and :math:`T` is the absolute temperature.
+:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the
+simulation, :math:`N` is number of atoms in the group, :math:`k_B` is
+the Boltzmann constant, and :math:`T` is the absolute temperature.
 
 A kinetic energy tensor, stored as a six-element vector, is also
 calculated by this compute for use in the computation of a pressure

doc/src/compute_temp_cs.rst

@@ -57,11 +57,11 @@ The temperature is calculated by the formula
 
 .. math::
 
-   \text{KE} = \frac{\text{dim}}{2} N k T,
+   \text{KE} = \frac{\text{dim}}{2} N k_B T,
 
 where KE is the total kinetic energy of the group of atoms (sum of
 :math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
-:math:`N` is the number of atoms in the group, :math:`k` is the Boltzmann
+:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
 constant, and :math:`T` is the absolute temperature.  Note that
 the velocity of each core or shell atom used in the KE calculation is
 the velocity of the center-of-mass (COM) of the core/shell pair the

doc/src/compute_temp_deform.rst

@@ -65,12 +65,13 @@ temperature is calculated by the formula
 
 .. math::
 
-  \text{KE} = \frac{\text{dim}}{2} N k T,
+   \text{KE} = \frac{\text{dim}}{2} N k_B T,
 
 where KE is the total kinetic energy of the group of atoms (sum of
-:math:`\frac12 m v^2`, dim = 2 or 3 is the dimensionality of the simulation,
-:math:`N` is the number of atoms in the group, :math:`k` is the Boltzmann
-constant, and :math:`T` is the temperature.  Note that :math:`v` in the kinetic energy formula is the atom's velocity.
+:math:`\frac12 m v^2`, dim = 2 or 3 is the dimensionality of the
+simulation, :math:`N` is the number of atoms in the group, :math:`k_B`
+is the Boltzmann constant, and :math:`T` is the temperature.  Note that
+:math:`v` in the kinetic energy formula is the atom's velocity.
 
 A kinetic energy tensor, stored as a six-element vector, is also
 calculated by this compute for use in the computation of a pressure

doc/src/compute_temp_eff.rst

@@ -34,7 +34,7 @@ The temperature is calculated by the formula
 
 .. math::
 
-   \text{KE} = \frac{\text{dim}}{2} N k T,
+   \text{KE} = \frac{\text{dim}}{2} N k_B T,
 
 where KE is the total kinetic energy of the group of atoms (sum of
 :math:`\frac12 m v^2` for nuclei and sum of
@@ -42,7 +42,7 @@ where KE is the total kinetic energy of the group of atoms (sum of
 includes the radial electron velocity contributions), dim = 2 or 3 is the
 dimensionality of the simulation, :math:`N` is the number of atoms (only total
 number of nuclei in the eFF (see the :doc:`pair_eff <pair_style>`
-command) in the group, :math:`k` is the Boltzmann constant, and :math:`T` is
+command) in the group, :math:`k_B` is the Boltzmann constant, and :math:`T` is
 the absolute temperature.  This expression is summed over all nuclear and
 electronic degrees of freedom, essentially by setting the kinetic contribution
 to the heat capacity to :math:`\frac32 k` (where only nuclei contribute). This

doc/src/compute_temp_partial.rst

@@ -34,11 +34,11 @@ The temperature is calculated by the formula
 
 .. math::
 
-  \text{KE} = \frac{\text{dim}}{2} N k T,
+   \text{KE} = \frac{\text{dim}}{2} N k_B T,
 
 where KE is the total kinetic energy of the group of atoms (sum of
 :math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
-:math:`N` is the number of atoms in the group, :math:`k` is the Boltzmann
+:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
 constant, and :math:`T` = temperature.  The calculation of KE excludes the
 :math:`x`, :math:`y`, or :math:`z` dimensions if *xflag*, *yflag*, or *zflag*
 is 0.  The dim parameter is adjusted to give the correct number of

doc/src/compute_temp_ramp.rst

@@ -48,17 +48,17 @@ dimension for each atom, the temperature is calculated by the formula
 
 .. math::
 
-  \text{KE} = \frac{\text{dim}}{2} N k T,
+   \text{KE} = \frac{\text{dim}}{2} N k_B T,
 
 where KE is the total kinetic energy of the group of atoms (sum of
 :math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
-:math:`N` is the number of atoms in the group, :math:`k` is the Boltzmann
+:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
 constant, and :math:`T` is the absolute temperature.
 
 The *units* keyword determines the meaning of the distance units used
 for coordinates (*clo*, *chi*) and velocities (*vlo*, *vhi*).  A *box* value
 selects standard distance units as defined by the :doc:`units <units>`
-command (e.g., :math:`\mathrm{\mathring A}` for units = real or metal).  A
+command (e.g., :math:`\mathrm{\mathring{A}}` for units = real or metal).  A
 *lattice* value means the distance units are in lattice spacings (i.e.,
 velocity in lattice spacings per unit time).  The :doc:`lattice <lattice>`
 command must have been previously used to define the lattice spacing.

doc/src/compute_temp_region.rst

@@ -42,11 +42,11 @@ The temperature is calculated by the formula
 
 .. math::
 
-  \text{KE} = \frac{\text{dim}}{2} N k T,
+   \text{KE} = \frac{\text{dim}}{2} N k_B T,
 
 where KE = is the total kinetic energy of the group of atoms (sum of
 :math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
-:math:`N` is the  number of atoms in both the group and region, :math:`k` is
+:math:`N` is the  number of atoms in both the group and region, :math:`k_B` is
 the Boltzmann constant, and :math:`T` temperature.
 
 A kinetic energy tensor, stored as a six-element vector, is also

doc/src/compute_temp_rotate.rst

@@ -36,11 +36,11 @@ each atom, the temperature is calculated by the formula
 
 .. math::
 
-  \text{KE} = \frac{\text{dim}}{2} N k T,
+   \text{KE} = \frac{\text{dim}}{2} N k_B T,
 
 where KE is the total kinetic energy of the group of atoms (sum of
 :math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
-:math:`N` is the number of atoms in the group, :math:`k` is the Boltzmann
+:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
 constant, and :math:`T` is the absolute temperature.
 
 A kinetic energy tensor, stored as a six-element vector, is also calculated by

doc/src/compute_viscosity_cos.rst

@@ -79,11 +79,11 @@ subtracted for each atom, the temperature is calculated by the formula
 
 .. math::
 
-  \text{KE} = \frac{\text{dim}}{2} N k T,
+   \text{KE} = \frac{\text{dim}}{2} N k_B T,
 
 where KE is the total kinetic energy of the group of atoms (sum of
 :math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
-:math:`N` is the number of atoms in the group, :math:`k` is the Boltzmann
+:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
 constant, and :math:`T` is the absolute temperature.
 
 A kinetic energy tensor, stored as a six-element vector, is also

doc/src/fix_gcmc.rst

@@ -259,9 +259,9 @@ pressure of the fictitious gas reservoir by:
 .. math::
 
    \mu^{id}  = & k T \ln{\rho \Lambda^3} \\
-             = & k T \ln{\frac{\phi P \Lambda^3}{k T}}
+             = & k T \ln{\frac{\phi P \Lambda^3}{k_B T}}
 
-where *k* is Boltzman's constant, *T* is the user-specified
+where :math:`k_B` is the Boltzmann constant, *T* is the user-specified
 temperature, :math:`\rho` is the number density, *P* is the pressure,
 and :math:`\phi` is the fugacity coefficient.  The constant
 :math:`\Lambda` is required for dimensional consistency.  For all unit
@@ -269,7 +269,7 @@ styles except *lj* it is defined as the thermal de Broglie wavelength
 
 .. math::
 
-   \Lambda = \sqrt{ \frac{h^2}{2 \pi m k T}}
+   \Lambda = \sqrt{ \frac{h^2}{2 \pi m k_B T}}
 
 where *h* is Planck's constant, and *m* is the mass of the exchanged atom
 or molecule.  For unit style *lj*, :math:`\Lambda` is simply set to

doc/src/fix_nh.rst

@@ -208,9 +208,9 @@ The relaxation rate of the barostat is set by its inertia :math:`W`:
 
 .. math::
 
-   W = (N + 1) k T_{\rm target} P_{\rm damp}^2
+   W = (N + 1) k_B T_{\rm target} P_{\rm damp}^2
 
-where :math:`N` is the number of atoms, :math:`k` is the Boltzmann constant,
+where :math:`N` is the number of atoms, :math:`k_B` is the Boltzmann constant,
 and :math:`T_{\rm target}` is the target temperature of the barostat :ref:`(Martyna) <nh-Martyna>`.
 If a thermostat is defined, :math:`T_{\rm target}` is the target temperature
 of the thermostat. If a thermostat is not defined, :math:`T_{\rm target}`

doc/src/fix_widom.rst

@@ -100,9 +100,9 @@ The excess chemical potential mu_ex is defined as:
 
 .. math::
 
-   \mu_{ex} = -kT \ln(<\exp(-(U_{N+1}-U_{N})/{kT})>)
+   \mu_{ex} = -kT \ln(<\exp(-(U_{N+1}-U_{N})/{k_B T})>)
 
-where *k* is Boltzman's constant, *T* is the user-specified temperature,
+where :math:`k_B` is the Boltzmann constant, *T* is the user-specified temperature,
 U_N and U_{N+1} is the potential energy of the system with N and N+1
 particles.
 

doc/src/pair_dpd_ext.rst

@@ -80,8 +80,8 @@ the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c
 )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight
 functions with coefficients :math:`s_\alpha` that vary between 0 and 1,
 :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the
-unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`,
-where :math:`k` is the Boltzmann constant and :math:`T` is the
+unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k_B T \gamma_{\alpha}}`,
+where :math:`k_B` is the Boltzmann constant and :math:`T` is the
 temperature in the pair\_style command.
 
 For the style *dpd/ext/tstat*, the force on atom I due to atom J is
@@ -121,7 +121,7 @@ as in the examples above:
 
 The last coefficient is optional. If not specified, the global DPD
 cutoff is used. Note that :math:`\sigma`'s are set equal to
-:math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by
+:math:`\sqrt{2 k_B T \gamma}`, where :math:`T` is the temperature set by
 the :doc:`pair_style <pair_style>` command so it does not need to be
 specified.