Fixed kT vs k_B T in a couple of places and associated description

doc/src/compute_fep.rst

@@ -92,9 +92,9 @@ stepwise alchemical transformations during a simulation run:
 
 .. math::
 
-   \Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A = - kT
+   \Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A = - k_B T
    \sum_{i=0}^{n-1} \ln \left< \exp \left( - \frac{U(\lambda_{i+1}) -
-   U(\lambda_i)}{kT} \right) \right>_{\lambda_i}
+   U(\lambda_i)}{k_B T} \right) \right>_{\lambda_i}
 
 This compute is suitable for the finite-difference thermodynamic
 integration (FDTI) method :ref:`(Mezei) <Mezei>`, which is based on an
@@ -131,9 +131,9 @@ both the forward and reverse routes:
 
 .. math::
 
-   \left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /kT
+   \left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /k_B T
    \right]} \right>_0 = \left< \frac{1}{1 + \exp\left[\left(U_0 - U_1 +
-   \Delta_0^1A \right) /kT \right]} \right>_1
+   \Delta_0^1A \right) /k_B T \right]} \right>_1
 
 The value of the free energy difference is determined by numerical
 root finding to establish the equality.
@@ -276,8 +276,8 @@ trajectories during which the volume fluctuates or changes :ref:`(Allen and Tild
 
 .. math::
 
-   \Delta_0^1 A = - kT \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( -
-   \frac{U(\lambda_{i+1}) - U(\lambda_i)}{kT} \right)
+   \Delta_0^1 A = - k_B T \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( -
+   \frac{U(\lambda_{i+1}) - U(\lambda_i)}{k_B T} \right)
    \right>_{\lambda_i}}{\left< V \right>_{\lambda_i}}
 
 ----------
@@ -287,8 +287,8 @@ Output info
 
 This compute calculates a global vector of length 3 which contains the
 energy difference ( :math:`U_1-U_0` ) as c_ID[1], the
-Boltzmann factor :math:`\exp(-(U_1-U_0)/kT)`, or
-:math:`V \exp(-(U_1-U_0)/kT)`, as c_ID[2] and the
+Boltzmann factor :math:`\exp(-(U_1-U_0)/k_B T)`, or
+:math:`V \exp(-(U_1-U_0)/k_B T)`, as c_ID[2] and the
 volume of the simulation box :math:`V` as c_ID[3]. :math:`U_1` is the
 pair potential energy obtained with the perturbed parameters and
 :math:`U_0` is the pair potential energy obtained with the

doc/src/compute_fep_ta.rst

@@ -42,7 +42,7 @@ in a single simulation:
 .. math::
 
    \gamma = \lim_{\Delta \mathcal{A} \to 0} \left( \frac{\Delta A_{0 \to 1 }}{\Delta \mathcal{A}}\right)_{N,V,T}
-   = - \frac{kT}{\Delta \mathcal{A}} \ln \left\langle \exp\left(\frac{-(U_1 - U_0)}{kT}\right) \right\rangle_0
+   = - \frac{k_B T}{\Delta \mathcal{A}} \ln \left\langle \exp\left(\frac{-(U_1 - U_0)}{k_B T}\right) \right\rangle_0
 
 During the perturbation, both axes of *plane* are scaled by multiplying
 :math:`\sqrt{\mathrm{scale\_factor}}`, while the other axis divided by
@@ -62,7 +62,7 @@ Output info
 
 This compute calculates a global vector of length 3 which contains the
 energy difference :math:`(U_1-U_0)` as c_ID[1], the Boltzmann factor
-:math:`\exp\bigl(-(U_1-U_0)/kT\bigr)`, as c_ID[2] and the change in the *plane*
+:math:`\exp\bigl(-(U_1-U_0)/k_B T\bigr)`, as c_ID[2] and the change in the *plane*
 area :math:`\Delta \mathcal{A}` as c_ID[3]. :math:`U_1` is the potential
 energy of the perturbed state and :math:`U_0` is the potential energy of
 the reference state.  The energies include kspace terms if these are

doc/src/compute_temp_chunk.rst

@@ -69,11 +69,11 @@ The temperature is calculated by the formula
 
 .. math::
 
-  \text{KE} = \frac{\text{DOF}}{2} k T,
+  \text{KE} = \frac{\text{DOF}}{2} k_B T,
 
 where KE is the total kinetic energy of all atoms assigned to chunks
 (sum of :math:`\frac12 m v^2`), DOF is the the total number of degrees of
-freedom for those atoms, :math:`k` is Boltzmann constant, and :math:`T` is the
+freedom for those atoms, :math:`k_B` is Boltzmann constant, and :math:`T` is the
 absolute temperature.
 
 The DOF is calculated as :math:`N\times`\ *adof*
@@ -107,11 +107,11 @@ formula
 
 .. math::
 
-  \text{KE} = \frac{\text{DOF}}{2} k T,
+  \text{KE} = \frac{\text{DOF}}{2} k_B T,
 
 where KE is the total kinetic energy of the chunk of atoms (sum of
 :math:`\frac12 m v^2`), DOF is the total number of degrees of freedom for all
-atoms in the chunk, :math:`k` is the Boltzmann constant, and :math:`T` is the
+atoms in the chunk, :math:`k_B` is the Boltzmann constant, and :math:`T` is the
 absolute temperature.
 
 The number of degrees of freedom (DOF) in this case is calculated as

doc/src/compute_temp_profile.rst

@@ -81,15 +81,15 @@ each atom, the temperature is calculated by the formula
 .. math::
 
   \text{KE} = \left( \frac{\text{dim}}{N} - N_s N_x N_y N_z
-                        - \text{extra} \right) \frac{k T}{2},
+                        - \text{extra} \right) \frac{k_B T}{2},
 
 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_s =` 0, 1, 2, or 3 for streaming velocity subtracted in 0, 1, 2, or 3
 dimensions, respectively; *extra* is the number of  extra degrees of freedom;
-*N* is the number of atoms in the group; *k* is the Boltzmann constant, and
-*T* is the absolute temperature.  The :math:`N_s N_x N_y N_z` term is the
-number of degrees of freedom subtracted to adjust for the removal of the
+*N* is the number of atoms in the group; :math:`k_B` is the Boltzmann constant,
+and :math:`T` is the absolute temperature.  The :math:`N_s N_x N_y N_z` term is
+the number of 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
 :math:`\text{dim} - N_s` and accounts for overall conservation of