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update references to USER-MISC package

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This commit is contained in:
Axel Kohlmeyer
2021-07-25 10:42:35 -04:00
parent 41db4235d6
commit afc54639c4
32 changed files with 50 additions and 47 deletions
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2
doc/src/compute_ackland_atom.rst
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@ -69,7 +69,7 @@ LAMMPS output options.
Restrictions
""""""""""""
This compute is part of the USER-MISC package. It is only enabled if
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
The per-atom vector values will be unitless since they are the

4
doc/src/compute_basal_atom.rst
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@ -42,7 +42,7 @@ too frequently or to have multiple compute/dump commands, each of
which computes this quantity.
An example input script that uses this compute is provided
in examples/USER-MISC/basal.
in examples/PACKAGES/basal.
Output info
"""""""""""
@ -58,7 +58,7 @@ components of a unit vector.
Restrictions
""""""""""""
This compute is part of the USER-MISC package. It is only enabled if
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
The output of this compute will be meaningless unless the atoms are on

4
doc/src/compute_cnp_atom.rst
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@ -40,7 +40,7 @@ This parameter is computed using the following formula from
.. math::
Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}} \vec{R}_{ik} + \vec{R}_{jk} |^2
Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} \left | \sum_{k = 1}^{n_{ij}} \vec{R}_{ik} + \vec{R}_{jk} \right | ^{2}
where the index *j* goes over the :math:`n_i` nearest neighbors of atom
*i*\ , and the index *k* goes over the :math:`n_{ij}` common nearest neighbors
@ -110,7 +110,7 @@ values:
Restrictions
""""""""""""
This compute is part of the USER-MISC package. It is only enabled if
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_entropy_atom.rst
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@ -124,7 +124,7 @@ ordered environments.
Restrictions
""""""""""""
This compute is part of the USER-MISC package. It is only enabled if
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_gyration_shape.rst
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@ -80,7 +80,7 @@ distance\^2 :doc:`units <units>` while the sixth one is dimensionless.
Restrictions
""""""""""""
This compute is part of the USER-MISC package. It is only enabled if
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_gyration_shape_chunk.rst
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@ -81,7 +81,7 @@ distance\^2 :doc:`units <units>` while the sixth one is dimensionless.
Restrictions
""""""""""""
This compute is part of the USER-MISC package. It is only enabled if
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_hma.rst
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@ -169,7 +169,7 @@ scalar value will be in energy :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the USER-MISC package. It is enabled only
This compute is part of the EXTRA-COMPUTE package. It is enabled only
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Usage restricted to canonical (NVT) ensemble simulation only.

2
doc/src/compute_momentum.rst
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@ -43,7 +43,7 @@ value will be in mass\*velocity :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the USER-MISC package. It is only enabled if
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_pressure_cylinder.rst
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@ -67,7 +67,7 @@ calculations are also excluded. Note that this pressure compute outputs
the configurational terms only; the kinetic contribution is not included
and may be calculated from the number density output by P_kin=density\*k\*T.
This compute is part of the USER-MISC package. It is only enabled
This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_stress_mop.rst
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@ -92,7 +92,7 @@ The values produced by this compute can be accessed by various :doc:`output comm
Restrictions
""""""""""""
These styles are part of the USER-MISC package. They are only enabled if
These styles are part of the EXTRA-COMPUTE package. They are only enabled if
LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
doc page on for more info.

2
doc/src/compute_temp_rotate.rst
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@ -84,7 +84,7 @@ vector values will be in energy :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the USER-MISC package. It is only enabled if
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/compute_viscosity_cos.rst
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@ -137,7 +137,7 @@ The 7-th element of vector value will be in velocity :doc:`units <units>`.
Restrictions
""""""""""""
This command is only available when LAMMPS was built with the USER-MISC package.
This command is only available when LAMMPS was built with the MISC package.
Since this compute depends on :doc:`fix accelerate/cos <fix_accelerate_cos>` which can
only work for 3d systems, it cannot be used for 2d systems.

2
doc/src/fix_accelerate_cos.rst
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@ -86,7 +86,7 @@ This fix is not invoked during energy minimization.
Restrictions
""""""""""""
This command is only available when LAMMPS was built with the USER-MISC package.
This command is only available when LAMMPS was built with the MISC package.
Since this fix depends on the z-coordinate of atoms, it cannot be used in 2d simulations.
Related commands

2
doc/src/fix_ave_correlate_long.rst
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@ -127,7 +127,7 @@ the run command. This fix is not invoked during energy minimization.
Restrictions
""""""""""""
This compute is part of the USER-MISC package. It is only enabled if
This compute is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

4
doc/src/fix_electron_stopping.rst
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@ -153,7 +153,7 @@ atoms moving above some minimum cutoff velocity (i.e., kinetic energy).
These coefficients can be determined by fitting a quadratic polynomial to
electronic stopping data predicted by, for example, SRIM or TD-DFT. Multiple
'Ecut c1 c2' values can be provided for multi-species simulations in the order
of the atom types. There is an examples/USER-MISC/electron_stopping/ directory,
of the atom types. There is an examples/PACKAGES/electron_stopping/ directory,
which illustrates uses of this command. Details of this implementation are
further described in :ref:`Stewart2018 <Stewart2018>` and :ref:`Lee2020 <Lee2020>`.
@ -175,7 +175,7 @@ on this fix.
Restrictions
""""""""""""
This pair style is part of the USER-MISC package. It is only enabled if
This pair style is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.

2
doc/src/fix_ffl.rst
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@ -110,7 +110,7 @@ In order to perform constant-pressure simulations please use
:doc:`fix npt <fix_nh>`, to avoid duplicate integration of the
equations of motion.
This fix is part of the USER-MISC package. It is only enabled if
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

2
doc/src/fix_filter_corotate.rst
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@ -72,7 +72,7 @@ fixes are not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Currently, it does not support :doc:`molecule templates <molecule>`.

2
doc/src/fix_flow_gauss.rst
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@ -158,7 +158,7 @@ This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.

2
doc/src/fix_gle.rst
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@ -142,7 +142,7 @@ In order to perform constant-pressure simulations please use
:doc:`fix npt <fix_nh>`, to avoid duplicate integration of the
equations of motion.
This fix is part of the USER-MISC package. It is only enabled if
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

9
doc/src/fix_ipi.rst
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@ -84,10 +84,11 @@ coordinates are transferred. However, one could use this strategy to
define an external potential acting on the atoms that are moved by
i-PI.
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. Because of the
use of UNIX domain sockets, this fix will only work in a UNIX
environment.
This fix is part of the MISC package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` doc page for more info.
Because of the use of UNIX domain sockets, this fix will only
work in a UNIX environment.
Related commands
""""""""""""""""

2
doc/src/fix_momentum.rst
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@ -97,7 +97,7 @@ the :doc:`run <run>` command. This fix is not invoked during
Restrictions
""""""""""""
Fix momentum/chunk is part of the USER-MISC package. It is only enabled
Fix momentum/chunk is part of the EXTRA-FIX package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.

2
doc/src/fix_npt_cauchy.rst
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@ -554,7 +554,7 @@ This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not

5
doc/src/fix_nvk.rst
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@ -56,8 +56,9 @@ the simulation box. Therefore, the group must be set to all.
This fix has not yet been implemented to work with the RESPA integrator.
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""

4
doc/src/fix_orient.rst
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@ -177,11 +177,11 @@ This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the MISC package. It is only enabled if LAMMPS
These fixes are part of the ORIENT package. They are only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
This fix should only be used with fcc or bcc lattices.
These fixes should only be used with fcc or bcc lattices.
Related commands
""""""""""""""""

2
doc/src/fix_orient_eco.rst
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@ -122,7 +122,7 @@ the run command. This fix is not invoked during energy minimization.
Restrictions
""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
This fix is part of the ORIENT package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.

4
doc/src/fix_pafi.rst
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@ -45,7 +45,7 @@ projection is also calculated, whose time integral can be shown to be equal to
the true free energy gradient along the minimum free energy path local to the reference pathway.
A detailed discussion of the projection technique can be found in :ref:`(Swinburne) <Swinburne>`.
This fix can be used with LAMMPS as demonstrated in examples/USER-MISC/pafi,
This fix can be used with LAMMPS as demonstrated in examples/PACKAGES/pafi,
though it is primarily intended to be coupled with the PAFI C++ code, developed
at `https://github.com/tomswinburne/pafi <https://github.com/tomswinburne/pafi>`_,
which distributes multiple LAMMPS workers in parallel to compute and collate
@ -84,7 +84,7 @@ This fix produces a global vector each timestep which can be accessed by various
Restrictions
""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.

5
doc/src/fix_pimd.rst
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@ -152,8 +152,9 @@ related tasks for each of the partitions, e.g.
Restrictions
""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This fix is part of the REPLICA package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` doc page for more info.
A PIMD simulation can be initialized with a single data file read via
the :doc:`read_data <read_data>` command. However, this means all

4
doc/src/fix_rhok.rst
View File

@ -43,7 +43,7 @@ used to study crystal-liquid interfaces and determine melting
temperatures :ref:`(Pedersen) <Pedersen>`.
An example of using the interface pinning method is located in the
*examples/USER-MISC/rhok* directory.
*examples/PACKAGES/rhok* directory.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -70,7 +70,7 @@ This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.

5
doc/src/fix_ti_spring.rst
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@ -170,8 +170,9 @@ Related commands
Restrictions
""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` doc page for more info.
Default
"""""""

5
doc/src/fix_ttm.rst
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@ -322,9 +322,8 @@ of the :doc:`run <run>` command. The fixes are not invoked during
Restrictions
""""""""""""
Fix *ttm* is part of the MISC package. It is only enabled if LAMMPS
was built with that package. Fix *ttm/mod* is part of the USER-MISC
package. It is only enabled if LAMMPS was built with that package.
Fix *ttm* and *ttm/mod* are part of the EXTRA-FIX package. They are
only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` doc page for more info.
These fixes can only be used for 3d simulations and orthogonal

4
doc/src/fix_wall_ees.rst
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@ -117,7 +117,7 @@ ellipsoidal particles according to the EES potential introduced above.
Other details of this command are the same as for the :doc:`fix
wall/region <fix_wall_region>` command. One may also find an example
of using this fix in the examples/USER-MISC/ees/ directory.
of using this fix in the examples/PACKAGES/ees/ directory.
----------
@ -160,7 +160,7 @@ minimization, invoked by the :doc:`minimize <minimize>` command.
Restrictions
""""""""""""
These fixes are part of the USER-MISC package. They are only enabled
These fixes are part of the EXTRA-FIX package. They are only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.

2
doc/src/fix_wall_reflect_stochastic.rst
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@ -106,7 +106,7 @@ bodies such as those defined by the :doc:`fix rigid <fix_rigid>`
command. The wall velocity must lie on the same plane as the wall
itself.
This fix is part of the USER-MISC package. It is only enabled if
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands