fix ttm doc formatting fixes

doc/src/fix_ttm.rst

@@ -136,23 +136,23 @@ transfer between the subsystems:
   \bigtriangledown (\kappa_e \bigtriangledown T_e) -
   g_p (T_e - T_a) + g_s T_a'
 
-where C_e is the specific heat, rho_e is the density, kappa_e is the
+where :math:`C_e` is the specific heat, :math:`\rho_e` is the density,
-thermal conductivity, T is temperature, the "e" and "a" subscripts
+:math:`\kappa_e` is the thermal conductivity, *T* is temperature, the
-represent electronic and atomic subsystems respectively, g_p is the
+"e" and "a" subscripts represent electronic and atomic subsystems
-coupling constant for the electron-ion interaction, and g_s is the
+respectively, :math:`g_p` is the coupling constant for the electron-ion
-electron stopping coupling parameter.  C_e, rho_e, and kappa_e are
+interaction, and :math:`g_s` is the electron stopping coupling
-specified as parameters to the fix.  The other quantities are derived.
+parameter.  :math:`C_e`, :math:`\rho_e`, and :math:`\kappa_e` are
-The form of the heat diffusion equation used here is almost the same
+specified as parameters to the fix *ttm* or *ttm/grid*.  The other
-as that in equation 6 of :ref:`(Duffy) <Duffy>`, with the exception that the
+quantities are derived.  The form of the heat diffusion equation used
-electronic density is explicitly represented, rather than being part
+here is almost the same as that in equation 6 of :ref:`(Duffy) <Duffy>`,
-of the specific heat parameter.
+with the exception that the electronic density is explicitly
+represented, rather than being part of the specific heat parameter.
 
 Currently, the TTM fixes assume that none of the user-supplied
-parameters will vary with temperature. Note that :ref:`(Duffy)
+parameters will vary with temperature. Note that :ref:`(Duffy) <Duffy>`
-<Duffy>` used a tanh() functional form for the temperature dependence
+used a tanh() functional form for the temperature dependence of the
-of the electronic specific heat, but ignored temperature dependencies
+electronic specific heat, but ignored temperature dependencies of any of
-of any of the other parameters.  See more discussion below for fix
+the other parameters.  See more discussion below for fix *ttm/mod*.
-ttm/mod.
 
 .. note::
 
@@ -265,27 +265,27 @@ heat sources (e.g. laser heating in ablation simulations):
   \bigtriangledown (\kappa_e \bigtriangledown T_e) -
   g_p (T_e - T_a) + g_s T_a' + \theta (x-x_{surface})I_0 \exp(-x/l_{skin})
 
-where theta is the Heaviside step function, I_0 is the (absorbed)
+where :math:`\theta` is the Heaviside step function, :math:`I_0` is the
-laser pulse intensity for ablation simulations, l_skin is the depth
+(absorbed) laser pulse intensity for ablation simulations,
-of skin-layer, and all other designations have the same meaning as in
+:math:`l_{skin}` is the depth of the skin-layer, and all other
-the former equation. The duration of the pulse is set by the parameter
+designations have the same meaning as in the former equation. The
-*tau* in the *init_file*.
+duration of the pulse is set by the parameter *tau* in the *init_file*.
 
-Fix ttm/mod also allows users to specify the dependencies of C_e and
+Fix *ttm/mod* also allows users to specify the dependencies of
-kappa_e on the electronic temperature. The specific heat is expressed
+:math:`C_e` and :math:`\kappa_e` on the electronic temperature. The
-as
+specific heat is expressed as
 
 .. math::
 
   C_e = C_0 + (a_0 + a_1 X + a_2 X^2 + a_3 X^3 + a_4 X^4) \exp (-(AX)^2)
 
-where *X* = T_e/1000, and the thermal conductivity is defined as
+where :math:`X = \frac{T_e}{1000}`, and the thermal conductivity is
-kappa_e = D_e\*rho_e\*C_e, where D_e is the thermal diffusion
+defined as :math:`\kappa_e = D_e \cdot rho_e \cdot C_e`, where
-coefficient.
+:math:`D_e` is the thermal diffusion coefficient.
 
-Electronic pressure effects are included in the TTM model to account
+Electronic pressure effects are included in the TTM model to account for
-for the blast force acting on ions because of electronic pressure
+the blast force acting on ions because of electronic pressure gradient
-gradient (see :ref:`(Chen) <Chen>`, :ref:`(Norman) <Norman>`).  The total force
+(see :ref:`(Chen) <Chen>`, :ref:`(Norman) <Norman>`).  The total force
 acting on an ion is:
 
 .. math::
@@ -293,13 +293,14 @@ acting on an ion is:
   {\vec F}_i = - \partial U / \partial {\vec r}_i + {\vec
   F}_{langevin} - \nabla P_e/n_{ion}
 
-where F_langevin is a force from Langevin thermostat simulating
+where :math:`F_{langevin}` is a force from Langevin thermostat
-electron-phonon coupling, and nabla P_e/n_ion is the electron blast
+simulating electron-phonon coupling, and :math:`\nabla P_e/n_{ion}` is
-force.
+the electron blast force.
 
-The electronic pressure is taken to be P_e = B\*rho_e\*C_e\*T_e
+The electronic pressure is taken to be :math:`P_e = B \cdot rho_e \cdot
+C_e \cdot T_e`
 
-The current fix ttm/mod implementation allows TTM simulations with a
+The current fix *ttm/mod* implementation allows TTM simulations with a
 vacuum. The vacuum region is defined as the grid cells with zero
 electronic temperature. The numerical scheme does not allow energy
 exchange with such cells. Since the material can expand to previously
@@ -319,10 +320,10 @@ electronic pressure gradient is calculated as
   \frac{x}{x+\lambda}\frac{(C_e{}T_e)_{x+\Delta
   x}-(C_e{}T_e)_{x}}{\Delta x} \right]
 
-where lambda is the electron mean free path (see :ref:`(Norman) <Norman>`,
+where :math:`\lambda` is the electron mean free path (see :ref:`(Norman)
-:ref:`(Pisarev) <Pisarev>`)
+<Norman>`, :ref:`(Pisarev) <Pisarev>`)
 
-The fix ttm/mod parameter file *init_file* has the following syntax.
+The fix *ttm/mod* parameter file *init_file* has the following syntax.
 Every line with an odd number is considered as a comment and
 ignored. The lines with the even numbers are treated as follows: