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

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This commit is contained in:
Axel Kohlmeyer
2020-01-31 00:45:13 -05:00
parent 5962e880d4
commit e4cf0a07a0
22 changed files with 68 additions and 68 deletions
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2
doc/src/Intro_features.rst
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@ -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

2
doc/src/Packages_details.rst
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@ -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

25
doc/src/compute_hma.rst
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@ -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
used with any potential in LAMMPS, it will provide inaccurate results
restricted to simulations in the NVT ensemble. While this compute may
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
work fine, while :doc:`pair_lj <pair_lj>` will perform poorly unless
the potential is shifted (via :doc:`pair_modify <pair_modify>` shift) or the cutoff is large. Furthermore, computation of the heat capacity with
this compute is restricted to those that implement the single\_hessian method
in Pair. Implementing single\_hessian in additional pair styles is simple.
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 pair\_hessian:
:doc:`pair_style lj/smooth/linear <pair_lj_smooth_linear>` and Ewald
summation should work fine, while :doc:`pair_style lj/cut <pair_lj>`
will perform poorly unless the potential is shifted (via
:doc:`pair_modify <pair_modify>` shift) or the cutoff is large.
Furthermore, computation of the heat capacity with this compute is
restricted to those that implement the *single\_hessian* method in Pair.
Implementing *single\_hessian* in additional pair styles is simple.
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

2
doc/src/dihedral_cosine_shift_exp.rst
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@ -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

2
doc/src/fix_adapt_fep.rst
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@ -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
"""""""

2
doc/src/fix_bond_react.rst
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@ -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

6
doc/src/fix_nh_uef.rst
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@ -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\_temp/uef <compute_temp_uef>`) will be computed in the
:doc:`compute pressure/uef <compute_pressure_uef>` and
: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.
----------

2
doc/src/fix_precession_spin.rst
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@ -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

2
doc/src/fix_wall_gran.rst
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@ -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 =

2
doc/src/fix_wall_gran_region.rst
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@ -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.

41
doc/src/min_modify.rst
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@ -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
a :doc:`min_spin <min_spin>` command is declared.
Keyword *alpha\_damp* defines an analog of a magnetic Gilbert
damping. It defines a relaxation rate toward an equilibrium for
a given magnetic system.
Keyword *discrete\_factor* defines a discretization factor for the
adaptive timestep used in the *spin* minimization.
See :doc:`min_spin <min_spin>` for more information about those
quantities.
Keywords *alpha\_damp* and *discrete\_factor* only make sense when a
:doc:`min_spin <min_spin>` command is declared. Keyword *alpha\_damp*
defines an analog of a magnetic Gilbert damping. It defines a relaxation
rate toward an equilibrium for a given magnetic system. Keyword
*discrete\_factor* defines a discretization factor for the adaptive
timestep used in the *spin* minimization. See :doc:`min_spin
<min_spin>` for more information about those quantities.
The choice of a line search algorithm for the *spin/cg* and
*spin/lbfgs* styles can be specified via the *line* keyword.
The *spin\_cubic* and *spin\_none* only make sense when one of those
two minimization styles is declared.
The *spin\_cubic* performs the line search based on a cubic interpolation
of the energy along the search direction. The *spin\_none* keyword
deactivates the line search procedure.
The *spin\_none* is a default value for *line* keyword for both *spin/lbfgs*
and *spin/cg*\ . Convergence of *spin/lbfgs* can be more robust if
*spin\_cubic* line search is used.
The choice of a line search algorithm for the *spin/cg* and *spin/lbfgs*
styles can be specified via the *line* keyword. The *spin\_cubic* and
*spin\_none* options only make sense when one of those two minimization
styles is declared. The *spin\_cubic* option performs the line search
based on a cubic interpolation of the energy along the search
direction. The *spin\_none* option deactivates the line search
procedure. The *spin\_none* option is a default value for *line*
keyword for both *spin/lbfgs* and *spin/cg*\ . Convergence of
*spin/lbfgs* can be more robust if *spin\_cubic* line search is used.
Restrictions
""""""""""""
For magnetic GNEB calculations, only *spin\_none* value for *line* keyword can be used
when styles *spin/cg* and *spin/lbfgs* are employed.
See :doc:`neb/spin <neb_spin>` for more explanation.
For magnetic GNEB calculations, only the *spin\_none* value for *line* keyword can be used
when minimization styles *spin/cg* and *spin/lbfgs* are employed.
See :doc:`neb/spin <neb_spin>` for more explanations.
Related commands
""""""""""""""""

15
doc/src/min_spin.rst
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@ -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
(OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno
(L-BFGS) algorithm.
By default, style *spin/lbfgs* does not employ line search procedure.
If the line search procedure is not used then the discrete factor defines
the maximum root mean squared rotation angle of spins by equation *pi/(5\*Kappa)*.
The default value for Kappa is 10.
The *spin\_cubic* line search can improve the convergence of the
Style *spin/lbfgs* defines an orthogonal spin optimization (OSO)
combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS)
algorithm. By default, style *spin/lbfgs* does not employ line search
procedure. If the line search procedure is not used then the discrete
factor defines the maximum root mean squared rotation angle of spins by
equation *pi/(5\*Kappa)*. The default value for Kappa is 10. The
*spin\_cubic* line search option can improve the convergence of the
*spin/lbfgs* algorithm.
The :doc:`min_modify <min_modify>` command can be used to

5
doc/src/neb_spin.rst
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@ -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
when styles *spin/cg* and *spin/lbfgs* are employed.
For magnetic GNEB calculations, only the *spin\_none* value for the
*line* keyword can be used when minimization styles *spin/cg* and
*spin/lbfgs* are employed.
----------

4
doc/src/pair_class2.rst
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@ -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

2
doc/src/pair_coul.rst
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@ -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

6
doc/src/pair_fep_soft.rst
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@ -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

2
doc/src/pair_lj.rst
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@ -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.

2
doc/src/pair_lj_long.rst
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@ -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.

4
doc/src/pair_morse.rst
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@ -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

2
doc/src/pair_spin_exchange.rst
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@ -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::

4
doc/src/pair_spin_magelec.rst
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@ -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

2
doc/src/temper_grem.rst
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@ -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