remove more \_ escapes from doc anchors and a bunch of other issues found in the process

doc/src/Intro_features.rst

@@ -87,7 +87,7 @@ commands)
 * water potentials: TIP3P, TIP4P, SPC
 * implicit solvent potentials: hydrodynamic lubrication, Debye
 * force-field compatibility with common CHARMM, AMBER, DREIDING,     OPLS, GROMACS, COMPASS options
-* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim\_init, kim\_interactions, and kim\_query <kim_commands>` commands
+* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim_init, kim_interactions, and kim_query <kim_commands>` commands
 * hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation
 * overlaid potentials: superposition of multiple pair potentials
 

doc/src/Packages_details.rst

@@ -927,7 +927,7 @@ Also several computes which calculate properties of rigid bodies.
 
 * src/RIGID: filenames -> commands
 * :doc:`compute erotate/rigid <compute_erotate_rigid>`
-* fix shake"_fix\_shake.html
+* :doc:`fix shake <fix_shake>`
 * :doc:`fix rattle <fix_shake>`
 * :doc:`fix rigid/\* <fix_rigid>`
 * examples/ASPHERE

doc/src/compute_hma.rst

@@ -54,19 +54,22 @@ effects, smaller timestep inaccuracy, faster equilibration and shorter
 decorrelation time.
 
 HMA should not be used if atoms are expected to diffuse.  It is also
-restricted to simulations in the NVT ensemble.  While this compute may be
+restricted to simulations in the NVT ensemble.  While this compute may
-used with any potential in LAMMPS, it will provide inaccurate results
+be used with any potential in LAMMPS, it will provide inaccurate results
 for potentials that do not go to 0 at the truncation distance;
-:doc:`pair\_lj\_smooth\_linear <pair_lj_smooth_linear>` and Ewald summation should
+:doc:`pair_style lj/smooth/linear <pair_lj_smooth_linear>` and Ewald
-work fine, while :doc:`pair_lj <pair_lj>` will perform poorly unless
+summation should work fine, while :doc:`pair_style lj/cut <pair_lj>`
-the potential is shifted (via :doc:`pair_modify <pair_modify>` shift) or the cutoff is large.  Furthermore, computation of the heat capacity with
+will perform poorly unless the potential is shifted (via
-this compute is restricted to those that implement the single\_hessian method
+:doc:`pair_modify <pair_modify>` shift) or the cutoff is large.
-in Pair.  Implementing single\_hessian in additional pair styles is simple.
+Furthermore, computation of the heat capacity with this compute is
-Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at
+restricted to those that implement the *single\_hessian* method in Pair.
-buffalo.edu) if your desired pair style does not have this method.  This is
+Implementing *single\_hessian* in additional pair styles is simple.
-the list of pair styles that currently implement pair\_hessian:
+Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke
+(kofke at buffalo.edu) if your desired pair style does not have this
+method.  This is the list of pair styles that currently implement
+*single\_hessian*:
 
-* :doc:`lj\_smooth\_linear <pair_lj_smooth_linear>`
+* :doc:`pair_style lj/smooth/linear <pair_lj_smooth_linear>`
 
 
 In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble

doc/src/dihedral_cosine_shift_exp.rst

@@ -92,7 +92,7 @@ Related commands
 """"""""""""""""
 
 :doc:`dihedral_coeff <dihedral_coeff>`,
-:doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`
+:doc:`angle_style cosine/shift/exp <angle_cosine_shift_exp>`
 
 **Default:** none
 

doc/src/fix_adapt_fep.rst

@@ -319,7 +319,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
+:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair_style \*/soft <pair_fep_soft>`
 
 Default
 """""""

doc/src/fix_bond_react.rst

@@ -390,7 +390,7 @@ the activation energy (:doc:`units <units>` of energy), and *seed* is a
 random number seed. The temperature is defined as the instantaneous
 temperature averaged over all atoms in the reaction site, and is
 calculated in the same manner as for example
-:doc:`compute\_temp\_chunk <compute_temp_chunk>`. Currently, there are no
+:doc:`compute temp/chunk <compute_temp_chunk>`. Currently, there are no
 options for additional temperature averaging or velocity-biased
 temperature calculations. A uniform random number between 0 and 1 is
 generated using *seed*\ ; if this number is less than the result of the

doc/src/fix_nh_uef.rst

@@ -89,14 +89,14 @@ in the LAMMPS frame. Only when the positions and velocities are
 updated is the system rotated to the flow frame, and it is rotated
 back to the LAMMPS frame immediately afterwards. For this reason, all
 vector-valued quantities (except for the tensors from
-:doc:`compute\_pressure/uef <compute_pressure_uef>` and
+:doc:`compute pressure/uef <compute_pressure_uef>` and
-:doc:`compute\_temp/uef <compute_temp_uef>`) will be computed in the
+:doc:`compute temp/uef <compute_temp_uef>`) will be computed in the
 LAMMPS frame. Rotationally invariant scalar quantities like the
 temperature and hydrostatic pressure are frame-invariant and will be
 computed correctly. Additionally, the system is in the LAMMPS frame
 during all of the output steps, and therefore trajectory files made
 using the dump command will be in the LAMMPS frame unless the
-:doc:`dump\_cfg/uef <dump_cfg_uef>` command is used.
+:doc:`dump cfg/uef <dump_cfg_uef>` command is used.
 
 
 ----------

doc/src/fix_precession_spin.rst

@@ -85,7 +85,7 @@ function for the same parameters.
 
 The temperature effects are accounted for by connecting the spin
 :math:`i` to a thermal bath using a Langevin thermostat (see
-:doc:`fix\_langevin\_spin <fix_langevin_spin>` for the definition of 
+:doc:`fix langevin/spin <fix_langevin_spin>` for the definition of 
 this thermostat).
 
 Style *anisotropy* is used to simulate an easy axis or an easy plane

doc/src/fix_wall_gran.rst

@@ -89,7 +89,7 @@ The nature of the wall/particle interactions are determined by the
 *pair\_coeff* command for the latter.  The equation for the force
 between the wall and particles touching it is the same as the
 corresponding equation on the :doc:`pair_style gran/\* <pair_gran>` and
-:doc:`pair\_style\_granular <pair_granular>` doc pages, in the limit of
+:doc:`pair_style granular <pair_granular>` doc pages, in the limit of
 one of the two particles going to infinite radius and mass (flat
 wall).  Specifically, delta = radius - r = overlap of particle with
 wall, m\_eff = mass of particle, and the effective radius of contact =

doc/src/fix_wall_gran_region.rst

@@ -160,7 +160,7 @@ The nature of the wall/particle interactions are determined by the
 *pair\_coeff* command for the latter.  The equation for the force
 between the wall and particles touching it is the same as the
 corresponding equation on the :doc:`pair_style gran/\* <pair_gran>` and
-:doc:`pair\_style\_granular <pair_granular>` doc pages, but the effective
+:doc:`pair_style granular <pair_granular>` doc pages, but the effective
 radius is calculated using the radius of the particle and the radius
 of curvature of the wall at the contact point.
 

doc/src/min_modify.rst

@@ -106,34 +106,31 @@ all atoms in the system:
 For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force
 norm is replaced by the spin-torque norm.
 
-Keywords *alpha\_damp* and *discrete\_factor* only make sense when
+Keywords *alpha\_damp* and *discrete\_factor* only make sense when a
-a :doc:`min_spin <min_spin>` command is declared.
+:doc:`min_spin <min_spin>` command is declared.  Keyword *alpha\_damp*
-Keyword *alpha\_damp* defines an analog of a magnetic Gilbert
+defines an analog of a magnetic Gilbert damping. It defines a relaxation
-damping. It defines a relaxation rate toward an equilibrium for
+rate toward an equilibrium for a given magnetic system.  Keyword
-a given magnetic system.
+*discrete\_factor* defines a discretization factor for the adaptive
-Keyword *discrete\_factor* defines a discretization factor for the
+timestep used in the *spin* minimization.  See :doc:`min_spin
-adaptive timestep used in the *spin* minimization.
+<min_spin>` for more information about those quantities.
-See :doc:`min_spin <min_spin>` for more information about those
-quantities.
 
-The choice of a line search algorithm for the *spin/cg* and
+The choice of a line search algorithm for the *spin/cg* and *spin/lbfgs*
-*spin/lbfgs* styles can be specified via the *line* keyword.
+styles can be specified via the *line* keyword.  The *spin\_cubic* and
-The *spin\_cubic* and  *spin\_none* only make sense when one of those 
+*spin\_none* options only make sense when one of those two minimization
-two minimization styles is declared.
+styles is declared.  The *spin\_cubic* option performs the line search
-The *spin\_cubic* performs the line search based on a cubic interpolation
+based on a cubic interpolation of the energy along the search
-of the energy along the search direction. The *spin\_none* keyword
+direction. The *spin\_none* option deactivates the line search
-deactivates the line search procedure.
+procedure.  The *spin\_none* option is a default value for *line*
-The *spin\_none* is a default value for *line* keyword for both *spin/lbfgs*
+keyword for both *spin/lbfgs* and *spin/cg*\ . Convergence of
-and *spin/cg*\ . Convergence of *spin/lbfgs* can be more robust if
+*spin/lbfgs* can be more robust if *spin\_cubic* line search is used.
-*spin\_cubic* line search is used.
 
 Restrictions
 """"""""""""
 
 
-For magnetic GNEB calculations, only *spin\_none* value for *line* keyword can be used
+For magnetic GNEB calculations, only the *spin\_none* value for *line* keyword can be used
-when styles *spin/cg* and *spin/lbfgs* are employed.
+when minimization styles *spin/cg* and *spin/lbfgs* are employed.
-See :doc:`neb/spin <neb_spin>` for more explanation.
+See :doc:`neb/spin <neb_spin>` for more explanations.
 
 Related commands
 """"""""""""""""

doc/src/min_spin.rst

@@ -70,14 +70,13 @@ discretization factor *discrete\_factor*.
 By default, style *spin/cg* does not employ the line search procedure 
 and uses the adaptive time-step technique in the same way as style *spin*\ .
 
-Style *spin/lbfgs* defines an orthogonal spin optimization
+Style *spin/lbfgs* defines an orthogonal spin optimization (OSO)
-(OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno 
+combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS)
-(L-BFGS) algorithm.
+algorithm.  By default, style *spin/lbfgs* does not employ line search
-By default, style *spin/lbfgs* does not employ line search procedure.
+procedure.  If the line search procedure is not used then the discrete
-If the line search procedure is not used then the discrete factor defines
+factor defines the maximum root mean squared rotation angle of spins by
-the maximum root mean squared rotation angle of spins by equation *pi/(5\*Kappa)*.
+equation *pi/(5\*Kappa)*.  The default value for Kappa is 10.  The
-The default value for Kappa is 10.
+*spin\_cubic* line search option can improve the convergence of the
-The *spin\_cubic* line search can improve the convergence of the 
 *spin/lbfgs* algorithm.
 
 The :doc:`min_modify <min_modify>` command can be used to

doc/src/neb_spin.rst

@@ -389,8 +389,9 @@ This command can only be used if LAMMPS was built with the SPIN
 package.  See the :doc:`Build package <Build_package>` doc
 page for more info.
 
-For magnetic GNEB calculations, only *spin\_none* value for *line* keyword can be used
+For magnetic GNEB calculations, only the *spin\_none* value for the
-when styles *spin/cg* and *spin/lbfgs* are employed.
+*line* keyword can be used when minimization styles *spin/cg* and
+*spin/lbfgs* are employed.
 
 
 ----------

doc/src/pair_class2.rst

@@ -133,7 +133,7 @@ cutoff distance.
 
 A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
 free energy calculations, is part of the USER-FEP package and is documented with
-the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
+the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is
 only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
 
 
@@ -203,7 +203,7 @@ LAMMPS was built with that package.  See the :doc:`Build package <Build_package>
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style */soft <pair_fep_soft>`
 
 **Default:** none
 

doc/src/pair_coul.rst

@@ -392,7 +392,7 @@ info.
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`pair\_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace_style <kspace_style>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace_style <kspace_style>`
 
 **Default:** none
 

doc/src/pair_fep_soft.rst

@@ -193,7 +193,7 @@ and Coulomb potentials modified by a soft core, with the functional form
 The *lj/class2/soft* style is a 9-6 potential with the exponent of the
 denominator of the first term in brackets taking the value 1.5 instead of 2
 (other details differ, see the form of the potential in
-:doc:`pair\_class2 <pair_class2>`).
+:doc:`pair_style lj/class2 <pair_class2>`).
 
 Coulomb interactions can also be damped with a soft core at short distance,
 
@@ -255,14 +255,14 @@ optional cutoffs.
 
 Style *lj/charmm/coul/long/soft* implements a soft-core version of the modified
 12-6 LJ potential used in CHARMM and documented in the
-:doc:`pair\_lj\_charmm <pair_charmm>` style. In the soft version the parameters n,
+:doc:`pair_style lj/charmm/coul/long <pair_charmm>` style. In the soft version the parameters n,
 alpha\_LJ and alpha\_C are set in the :doc:`pair_style <pair_style>` command, before
 the global cutoffs. The activation parameter lambda is introduced as an argument
 of the :doc:`pair_coeff <pair_coeff>` command, after epsilon and sigma and
 before the optional eps14 and sigma14.
 
 Style *lj/class2/soft* implements a soft-core version of the 9-6 potential in
-:doc:`pair\_class2 <pair_class2>`. In the soft version the parameters n, alpha\_LJ
+:doc:`pair_style lj/class2 <pair_class2>`. In the soft version the parameters n, alpha\_LJ
 and alpha\_C are set in the :doc:`pair_style <pair_style>` command, before the
 global cutoffs. The activation parameter lambda is introduced as an argument of
 the the :doc:`pair_coeff <pair_coeff>` command, after epsilon and sigma and before

doc/src/pair_lj.rst

@@ -348,7 +348,7 @@ pair\_style command.
 
 A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
 free energy calculations, is part of the USER-FEP package and is documented with
-the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
+the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is
 only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
 
 

doc/src/pair_lj_long.rst

@@ -180,7 +180,7 @@ specified in the pair\_style command.
 
 A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
 free energy calculations, is part of the USER-FEP package and is documented with
-the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
+the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is
 only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
 
 

doc/src/pair_morse.rst

@@ -95,7 +95,7 @@ the *morse* and *morse/smooth/linear* styles.
 
 A version of the *morse* style with a soft core, *morse/soft*\ , suitable for use in
 free energy calculations, is part of the USER-FEP package and is documented with
-the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is only
+the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is only
 available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
 
 
@@ -160,7 +160,7 @@ built with the USER-MISC package.  See the :doc:`Build package <Build_package>`
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style */soft <pair_fep_soft>`
 
 **Default:** none
 

doc/src/pair_spin_exchange.rst

@@ -55,7 +55,7 @@ in :ref:`(Tranchida) <Tranchida3>`.
 
 From this exchange interaction, each spin :math:`i` will be submitted
 to a magnetic torque :math:`\vec{\omega}`, and its associated atom can be submitted to a
-force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
+force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix nve/spin <fix_nve_spin>`),
 such as:
 
 .. math::

doc/src/pair_spin_magelec.rst

@@ -41,7 +41,7 @@ direction of a screened dielectric atomic polarization (in eV).
 
 From this magneto-electric interaction, each spin i will be submitted
 to a magnetic torque omega, and its associated atom can be submitted to a
-force F for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
+force F for spin-lattice calculations (see :doc:`fix nve/spin <fix_nve_spin>`),
 such as:
 
 .. image:: Eqs/pair_spin_me_forces.jpg
@@ -68,7 +68,7 @@ Related commands
 """"""""""""""""
 
 :doc:`atom_style spin <atom_style>`, :doc:`pair_coeff <pair_coeff>`,
-:doc:`pair\_spin\_exchange <pair_spin_exchange>`, :doc:`pair_eam <pair_eam>`,
+:doc:`pair_style spin/exchange <pair_spin_exchange>`, :doc:`pair_eam <pair_eam>`,
 
 **Default:** none
 

doc/src/temper_grem.rst

@@ -14,7 +14,7 @@ Syntax
 * N = total # of timesteps to run
 * M = attempt a tempering swap every this many steps
 * lambda = initial lambda for this ensemble
-* fix-ID = ID of fix\_grem
+* fix-ID = ID of *fix grem*
 * thermostat-ID = ID of the thermostat that controls kinetic temperature
 * seed1 = random # seed used to decide on adjacent temperature to partner with
 * seed2 = random # seed for Boltzmann factor in Metropolis swap