modernize LaTeX for formatting text in math mode

doc/src/Howto_peri.rst

@@ -197,7 +197,7 @@ The LPS model has a force scalar state
 .. math::
 
    \underline{t} = \frac{3K\theta}{m}\underline{\omega}\,\underline{x} +
-   \alpha \underline{\omega}\,\underline{e}^{\rm d}, \qquad\qquad\textrm{(3)}
+   \alpha \underline{\omega}\,\underline{e}^\mathrm{d}, \qquad\qquad\textrm{(3)}
 
 with :math:`K` the bulk modulus and :math:`\alpha` related to the shear
 modulus :math:`G` as
@@ -242,14 +242,14 @@ scalar state are defined, respectively, as
 
 .. math::
 
-   \underline{e}^{\rm i}=\frac{\theta \underline{x}}{3}, \qquad
+   \underline{e}^\mathrm{i}=\frac{\theta \underline{x}}{3}, \qquad
-   \underline{e}^{\rm d} = \underline{e}- \underline{e}^{\rm i},
+   \underline{e}^\mathrm{d} = \underline{e}- \underline{e}^\mathrm{i},
 
 
 where the arguments of the state functions and the vectors on which they
 operate are omitted for simplicity. We note that the LPS model is linear
 in the dilatation :math:`\theta`, and in the deviatoric part of the
-extension :math:`\underline{e}^{\rm d}`.
+extension :math:`\underline{e}^\mathrm{d}`.
 
 .. note::
 

doc/src/Howto_triclinic.rst

@@ -249,23 +249,23 @@ as follows:
 
 .. math::
 
-  a   = & {\rm lx} \\
+  a   = & \mathrm{lx} \\
-  b^2 = &  {\rm ly}^2 +  {\rm xy}^2 \\
+  b^2 = &  \mathrm{ly}^2 + \mathrm{xy}^2 \\
-  c^2 = &  {\rm lz}^2 +  {\rm xz}^2 +  {\rm yz}^2 \\
+  c^2 = &  \mathrm{lz}^2 + \mathrm{xz}^2 + \mathrm{yz}^2 \\
-  \cos{\alpha} = & \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\
+  \cos{\alpha} = & \frac{\mathrm{xy}*\mathrm{xz} + \mathrm{ly}*\mathrm{yz}}{b*c} \\
-  \cos{\beta}  = & \frac{\rm xz}{c} \\
+  \cos{\beta}  = & \frac{\mathrm{xz}}{c} \\
-  \cos{\gamma} = & \frac{\rm xy}{b} \\
+  \cos{\gamma} = & \frac{\mathrm{xy}}{b} \\
 
 The inverse relationship can be written as follows:
 
 .. math::
 
-  {\rm lx}   = & a \\
+  \mathrm{lx}   = & a \\
-  {\rm xy}   = & b \cos{\gamma}  \\
+  \mathrm{xy}   = & b \cos{\gamma}  \\
-  {\rm xz}   = & c \cos{\beta}\\
+  \mathrm{xz}   = & c \cos{\beta}\\
-  {\rm ly}^2 = & b^2 - {\rm xy}^2 \\
+  \mathrm{ly}^2 = & b^2 - \mathrm{xy}^2 \\
-  {\rm yz}   = & \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
+  \mathrm{yz}   = & \frac{b*c \cos{\alpha} - \mathrm{xy}*\mathrm{xz}}{\mathrm{ly}} \\
-  {\rm lz}^2 = & c^2 - {\rm xz}^2 - {\rm yz}^2 \\
+  \mathrm{lz}^2 = & c^2 - \mathrm{xz}^2 - \mathrm{yz}^2 \\
 
 The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and
 :math:`\gamma` can be printed out or accessed by computes using the

doc/src/compute_cna_atom.rst

@@ -67,7 +67,7 @@ following relation should also be satisfied:
 
 .. math::
 
-  r_c + r_s > 2*{\rm cutoff}
+  r_c + r_s > 2*\mathrm{cutoff}
 
 where :math:`r_c` is the cutoff distance of the potential, :math:`r_s`
 is the skin

doc/src/compute_cnp_atom.rst

@@ -74,7 +74,7 @@ following relation should also be satisfied:
 
 .. math::
 
-  r_c + r_s > 2*{\rm cutoff}
+  r_c + r_s > 2*\mathrm{cutoff}
 
 where :math:`r_c` is the cutoff distance of the potential, :math:`r_s` is
 the skin

doc/src/compute_efield_wolf_atom.rst

@@ -50,9 +50,9 @@ the potential energy using the Wolf summation method, described in
 
 .. math::
    E_i = \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
+   \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} +
    \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
+   \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
 
 where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()*
 are error-function and complementary error-function terms.  This

doc/src/compute_hexorder_atom.rst

@@ -40,7 +40,7 @@ is a complex number (stored as two real numbers) defined as follows:
 
 .. math::
 
-   q_n = \frac{1}{nnn}\sum_{j = 1}^{nnn} e^{n i \theta({\bf r}_{ij})}
+   q_n = \frac{1}{nnn}\sum_{j = 1}^{nnn} e^{n i \theta({\textbf{r}}_{ij})}
 
 where the sum is over the *nnn* nearest neighbors
 of the central atom. The angle :math:`\theta`

doc/src/compute_stress_atom.rst

@@ -65,7 +65,7 @@ In case of compute *stress/atom*, the virial contribution is:
 
    W_{ab} & = \frac{1}{2} \sum_{n = 1}^{N_p} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) + \frac{1}{2} \sum_{n = 1}^{N_b} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b})  \\
   & + \frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b}) + \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) \\
-  & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
+  & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + \mathrm{Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
 
 The first term is a pairwise energy contribution where :math:`n` loops
 over the :math:`N_p` neighbors of atom :math:`I`, :math:`\mathbf{r}_1`
@@ -97,7 +97,7 @@ In case of compute *centroid/stress/atom*, the virial contribution is:
 .. math::
 
    W_{ab} & = \sum_{n = 1}^{N_p} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_b} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_a} r_{I0_a}  F_{I_b} + \sum_{n = 1}^{N_d} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_i} r_{I0_a} F_{I_b} \\
-  & + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
+  & + \mathrm{Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
 
 As with compute *stress/atom*, the first, second, third, fourth and
 fifth terms are pairwise, bond, angle, dihedral and improper

doc/src/fitpod_command.rst

@@ -263,10 +263,10 @@ then the globally defined weights from the ``fitting_weight_energy`` and
 POD Potential
 """""""""""""
 
-We consider a multi-element system of *N* atoms with :math:`N_{\rm e}`
+We consider a multi-element system of *N* atoms with :math:`N_\mathrm{e}`
 unique elements.  We denote by :math:`\boldsymbol r_n` and :math:`Z_n`
 position vector and type of an atom *n* in the system,
-respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e}
+respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_\mathrm{e}
 \}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots,
 \boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1,
 Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The total energy of the

doc/src/fix_nh.rst

@@ -208,19 +208,19 @@ The relaxation rate of the barostat is set by its inertia :math:`W`:
 
 .. math::
 
-   W = (N + 1) k_B T_{\rm target} P_{\rm damp}^2
+   W = (N + 1) k_B T_\mathrm{target} P_\mathrm{damp}^2
 
 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>`.
+and :math:`T_\mathrm{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
+If a thermostat is defined, :math:`T_\mathrm{target}` is the target temperature
-of the thermostat. If a thermostat is not defined, :math:`T_{\rm target}`
+of the thermostat. If a thermostat is not defined, :math:`T_\mathrm{target}`
 is set to the current temperature of the system when the barostat is initialized.
 If this temperature is too low the simulation will quit with an error.
-Note: in previous versions of LAMMPS, :math:`T_{\rm target}` would default to
+Note: in previous versions of LAMMPS, :math:`T_\mathrm{target}` would default to
 a value of 1.0 for *lj* units and 300.0 otherwise if the system had a temperature
 of exactly zero.
 
-If a thermostat is not specified by this fix, :math:`T_{\rm target}` can be
+If a thermostat is not specified by this fix, :math:`T_\mathrm{target}` can be
 manually specified using the *Ptemp* parameter. This may be useful if the
 barostat is initialized when the current temperature does not reflect the
 steady state temperature of the system. This keyword may also be useful in
@@ -512,8 +512,8 @@ according to the following factorization of the Liouville propagator
 .. math::
 
    \exp \left(\mathrm{i} L \Delta t \right) = & \hat{E}
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\
    &\times \left[
@@ -526,8 +526,8 @@ according to the following factorization of the Liouville propagator
    &\times
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
    &+ \mathcal{O} \left(\Delta t^3 \right)
 
 This factorization differs somewhat from that of Tuckerman et al, in

doc/src/fix_npt_cauchy.rst

@@ -426,8 +426,8 @@ according to the following factorization of the Liouville propagator
 .. math::
 
    \exp \left(\mathrm{i} L \Delta t \right) = & \hat{E}
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\
    &\times \left[
@@ -440,8 +440,8 @@ according to the following factorization of the Liouville propagator
    &\times
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
    &+ \mathcal{O} \left(\Delta t^3 \right)
 
 This factorization differs somewhat from that of Tuckerman et al, in

doc/src/fix_orient.rst

@@ -62,19 +62,19 @@ The potential energy added to atom I is given by these formulas
 
 .. math::
 
-   \xi_{i} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j} - \mathbf{r}_{j}^{\rm I} \right| \qquad\qquad\left(1\right) \\
+   \xi_{i} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j} - \mathbf{r}_{j}^\mathrm{I} \right| \qquad\qquad\left(1\right) \\
    \\
-  \xi_{\rm IJ} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j}^{\rm J} - \mathbf{r}_{j}^{\rm I} \right| \qquad\qquad\left(2\right)\\
+  \xi_\mathrm{IJ} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j}^\mathrm{J} - \mathbf{r}_{j}^\mathrm{I} \right| \qquad\qquad\left(2\right)\\
   \\
-  \xi_{\rm low}  = & {\rm cutlo} \, \xi_{\rm IJ}  \qquad\qquad\qquad\left(3\right)\\
+  \xi_\mathrm{low}  = & \mathrm{cutlo} \, \xi_\mathrm{IJ}  \qquad\qquad\qquad\left(3\right)\\
-  \xi_{\rm high}  = & {\rm cuthi} \, \xi_{\rm IJ} \qquad\qquad\qquad\left(4\right) \\
+  \xi_\mathrm{high}  = & \mathrm{cuthi} \, \xi_\mathrm{IJ} \qquad\qquad\qquad\left(4\right) \\
   \\
-  \omega_{i} = & \frac{\pi}{2} \frac{\xi_{i} - \xi_{\rm low}}{\xi_{\rm high} - \xi_{\rm low}} \qquad\qquad\left(5\right)\\
+  \omega_{i} = & \frac{\pi}{2} \frac{\xi_{i} - \xi_\mathrm{low}}{\xi_\mathrm{high} - \xi_\mathrm{low}} \qquad\qquad\left(5\right)\\
   \\
-  u_{i}  = & 0 \quad\quad\qquad\qquad\qquad \textrm{ for } \qquad \xi_{i} < \xi_{\rm low}\\
+  u_{i}  = & 0 \quad\quad\qquad\qquad\qquad \textrm{ for } \qquad \xi_{i} < \xi_\mathrm{low}\\
-         = & {\rm dE}\,\frac{1 - \cos(2 \omega_{i})}{2}
+         = & \mathrm{dE}\,\frac{1 - \cos(2 \omega_{i})}{2}
-   \qquad \mathrm{ for }\qquad \xi_{\rm low} < \xi_{i} < \xi_{\rm high}  \quad \left(6\right) \\
+   \qquad \mathrm{for }\qquad \xi_\mathrm{low} < \xi_{i} < \xi_\mathrm{high}  \quad \left(6\right) \\
-         = & {\rm dE} \quad\qquad\qquad\qquad\textrm{ for } \qquad \xi_{\rm high} < \xi_{i}
+         = & \mathrm{dE} \quad\qquad\qquad\qquad\textrm{ for } \qquad \xi_\mathrm{high} < \xi_{i}
 
 which are fully explained in :ref:`(Janssens) <Janssens>`.  For fcc crystals
 this order parameter Xi for atom I in equation (1) is a sum over the

doc/src/min_modify.rst

@@ -98,14 +98,14 @@ all atoms
 
 .. math::
 
-   || \vec{F} ||_{max} = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
+   || \vec{F} ||_{max} = \mathrm{max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
 
 The *inf* norm takes the maximum component across the forces of
 all atoms in the system:
 
 .. math::
 
-   || \vec{F} ||_{inf} = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right)
+   || \vec{F} ||_{inf} = \mathrm{max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right)
 
 For the min styles *spin*, *spin/cg* and *spin/lbfgs*, the force
 norm is replaced by the spin-torque norm.

doc/src/min_spin.rst

@@ -50,9 +50,9 @@ system:
 
 .. math::
 
-   {\Delta t}_{\rm max} = \frac{2\pi}{\kappa \left|\vec{\omega}_{\rm max} \right|}
+   {\Delta t}_\mathrm{max} = \frac{2\pi}{\kappa \left|\vec{\omega}_\mathrm{max} \right|}
 
-with :math:`\left|\vec{\omega}_{\rm max}\right|` the norm of the largest precession
+with :math:`\left|\vec{\omega}_\mathrm{max}\right|` the norm of the largest precession
 frequency in the system (across all processes, and across all replicas if a
 spin/neb calculation is performed).
 

doc/src/neb_spin.rst

@@ -148,7 +148,7 @@ spin i, :math:`\omega_i^{\nu}` is a rotation angle defined as:
 
 .. math::
 
-   \omega_i^{\nu} = (\nu - 1) \Delta \omega_i {\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
+   \omega_i^{\nu} = (\nu - 1) \Delta \omega_i \mathrm{~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
 
 with :math:`\nu` the image number, Q the total number of images, and
 :math:`\omega_i` the total rotation between the initial and final spins.

doc/src/pair_aip_water_2dm.rst

@@ -53,14 +53,14 @@ materials as described in :ref:`(Feng1) <Feng1>` and :ref:`(Feng2) <Feng2>`.
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
    \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
    \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

doc/src/pair_coul.rst

@@ -241,9 +241,9 @@ summation method, described in :ref:`Wolf <Wolf1>`, given by:
 .. math::
 
    E_i = \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
+   \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} +
    \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
+   \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
 
 where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()*
 are error-function and complementary error-function terms.  This

doc/src/pair_coul_shield.rst

@@ -40,8 +40,8 @@ the pair style :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
 .. math::
 
    E      = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij} = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\
+   V_{ij} = & \mathrm{Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\
-   {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                           70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                           84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                           35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

doc/src/pair_dpd_ext.rst

@@ -62,8 +62,8 @@ a sum of 3 terms
 
    \mathbf{f}  = & f^C + f^D + f^R \qquad \qquad r < r_c \\
    f^C      = & A_{ij} w(r) \hat{\mathbf{r}}_{ij} \\
-   f^D      = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij}  - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \mathbf{v}_{ij} \\
+   f^D      = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij}  - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^\mathrm{T} ) \mathbf{v}_{ij} \\
-   f^R      = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij}  + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\
+   f^R      = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij}  + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^\mathrm{T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\
    w(r)     = & 1 - r/r_c \\
 
 where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D`

doc/src/pair_hbond_dreiding.rst

@@ -68,21 +68,21 @@ force field, given by:
 
 .. math::
 
-   E  = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_{\rm in} \\
+   E  = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_\mathrm{in} \\
-      = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
+      = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_\mathrm{in} < r < r_\mathrm{out} \\
-      = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_{\rm out} \\
+      = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_\mathrm{out} \\
    LJ(r)  = & AR^{-12}-BR^{-10}cos^n\theta=
          \epsilon\left\lbrace 5\left[ \frac{\sigma}{r}\right]^{12}-
          6\left[ \frac{\sigma}{r}\right]^{10}  \right\rbrace cos^n\theta\\
    Morse(r)  = & D_0\left\lbrace \chi^2 - 2\chi\right\rbrace cos^n\theta=
          D_{0}\left\lbrace e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)}
          \right\rbrace cos^n\theta \\
-   S(r)  = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
+   S(r)  = & \frac{ \left[r_\mathrm{out}^2 - r^2\right]^2
-   \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
+   \left[r_\mathrm{out}^2 + 2r^2 - 3{r_\mathrm{in}^2}\right]}
-   { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
+   { \left[r_\mathrm{out}^2 - {r_\mathrm{in}}^2\right]^3 }
 
-where :math:`r_{\rm in}` is the inner spline distance cutoff,
+where :math:`r_\mathrm{in}` is the inner spline distance cutoff,
-:math:`r_{\rm out}` is the outer distance cutoff, :math:`\theta_c` is
+:math:`r_\mathrm{out}` is the outer distance cutoff, :math:`\theta_c` is
 the angle cutoff, and :math:`n` is the power of the cosine of the angle
 :math:`\theta`.
 
@@ -189,8 +189,8 @@ follows:
 * :math:`\epsilon` (energy units)
 * :math:`\sigma` (distance units)
 * *n* = exponent in formula above
-* distance cutoff :math:`r_{\rm in}` (distance units)
+* distance cutoff :math:`r_\mathrm{in}` (distance units)
-* distance cutoff :math:`r_{\rm out}` (distance units)
+* distance cutoff :math:`r_\mathrm{out}` (distance units)
 * angle cutoff (degrees)
 
 For the *hbond/dreiding/morse* style the list of coefficients is as
@@ -202,7 +202,7 @@ follows:
 * :math:`\alpha` (1/distance units)
 * :math:`r_0` (distance units)
 * *n* = exponent in formula above
-* distance cutoff :math:`r_{\rm in}` (distance units)
+* distance cutoff :math:`r_\mathrm{in}` (distance units)
 * distance cutoff :math:`r_{out}` (distance units)
 * angle cutoff (degrees)
 

doc/src/pair_ilp_graphene_hbn.rst

@@ -44,14 +44,14 @@ in :ref:`(Kolmogorov) <Kolmogorov2>`.
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
    \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
    \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

doc/src/pair_ilp_tmd.rst

@@ -41,14 +41,14 @@ as described in :ref:`(Ouyang7) <Ouyang7>` and :ref:`(Jiang) <Jiang>`.
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
    \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
    \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

doc/src/pair_lj_cut_coul.rst

@@ -194,9 +194,9 @@ summation method, described in :ref:`Wolf <Wolf3>`, given by:
 .. math::
 
    E_i = \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
+   \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} +
    \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
+   \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
 
 where :math:`\alpha` is the damping parameter, and erfc() is the
 complementary error-function terms.  This potential is essentially a

doc/src/pair_mesodpd.rst

@@ -200,7 +200,7 @@ force :math:`F_{ij}^C` are expressed as
   \mathbf{F}_{ij}^{D} & = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij}  \\
   \mathbf{F}_{ij}^{R} & = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij} \\
   \omega_{C}(r) & = 1 - r/r_c \\
-  \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^{\rm power_f} \\
+  \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^\mathrm{power_f} \\
   \sigma^2 = 2\gamma k_B T
 
 The concentration flux between two tDPD particles includes the Fickian
@@ -211,7 +211,7 @@ by
 
    Q_{ij}^D & = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right) \\
    Q_{ij}^R & = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij} \\
-   w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power_{cc}} \\
+   w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^\mathrm{power_{cc}} \\
    \epsilon_{ij}^2 & = m_s^2\kappa_{ij}\rho
 
 where the parameters kappa and epsilon determine the strength of the

doc/src/pair_mgpt.rst

@@ -33,7 +33,7 @@ elemental bulk material in the form
 
 .. math::
 
-   E_{\rm tot}({\bf R}_1 \ldots {\bf R}_N) = NE_{\rm vol}(\Omega )
+   E_\mathrm{tot}({\bf R}_1 \ldots {\bf R}_N) = NE_\mathrm{vol}(\Omega )
    + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega )
    + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega )
    + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega )

doc/src/pair_saip_metal.rst

@@ -41,14 +41,14 @@ potential (ILP) potential for hetero-junctions formed with hexagonal
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
    \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
    \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

doc/src/pair_spin_dipole.rst

@@ -43,7 +43,7 @@ vector omega and mechanical force between particles I and J.
 
 .. math::
 
-   \mathcal{H}_{\rm long} & =
+   \mathcal{H}_\mathrm{long} & =
    -\frac{\mu_{0} \left( \mu_B\right)^2}{4\pi}
    \sum_{i,j,i\neq j}^{N}
     \frac{g_i g_j}{r_{ij}^3}

doc/src/pair_spin_dmi.rst

@@ -52,7 +52,7 @@ particle i:
 .. math::
 
     \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right)
-    ~~{\rm and}~~
+    ~~\mathrm{and}~~
     \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right)
 
 More details about the derivation of these torques/forces are reported in

doc/src/pair_spin_exchange.rst

@@ -94,7 +94,7 @@ submitted to a force :math:`\vec{F}_{i}` for spin-lattice calculations (see
 
    \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J}
    \left(r_{ij} \right)\,\vec{s}_{j}
-   ~~{\rm and}~~
+   ~~\mathrm{and}~~
    \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
    \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
 

doc/utils/sphinx-config/conf.py.in

@@ -290,7 +290,7 @@ rst_prolog = r"""
 
 .. only:: html
 
-   :math:`\renewcommand{\AA}{\text{Å}}`
+   :math:`\renewcommand{\AA}{\textup{\r{A}}`
 
 .. role:: lammps(code)
     :language: LAMMPS

tools/lammps-gui/org.lammps.lammps-gui.yml

@@ -110,5 +110,5 @@ modules:
       - -D BUILD_WHAM=yes
     sources:
       - type: git
-        url: https://github.com/lammps/lammps.git
+        url: https://github.com/akohlmey/lammps.git
-        branch: release
+        branch: collected-small-fixes