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Merge branch 'develop' into lubricate_patch

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This commit is contained in:
Axel Kohlmeyer
2024-10-04 17:09:27 -04:00
parent 8827dec5a9 36dd4de3bc
commit aec43d0f00
78 changed files with 11888 additions and 11008 deletions
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4
doc/src/compute_composition_atom.rst
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@ -88,6 +88,10 @@ too frequently.
----------
.. include:: accel_styles.rst
----------
Output info
"""""""""""

4
doc/src/compute_pressure.rst
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@ -125,10 +125,6 @@ where thermo_temp is the ID of a similarly defined compute of style
----------
.. include:: accel_styles.rst
----------
Output info
"""""""""""

2
doc/src/compute_rheo_property_atom.rst
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@ -81,7 +81,7 @@ includes *xx*, *xy*, *yx*, and *yy*. In 3D, this includes *xx*, *xy*, *xz*,
Many properties require their respective fixes, listed below in related
commands, be defined. For instance, the *viscosity* attribute is the
viscosity of a particle calculated by
:doc:`fix rheo/viscous <fix_rheo_viscosity>`. The meaning of less obvious
:doc:`fix rheo/viscosity <fix_rheo_viscosity>`. The meaning of less obvious
properties is described below.
The *phase* property indicates whether the particle is in a fluid state,

6
doc/src/compute_temp_deform.rst
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@ -128,6 +128,12 @@ See the :doc:`Howto thermostat <Howto_thermostat>` page for a
discussion of different ways to compute temperature and perform
thermostatting.
----------
.. include:: accel_styles.rst
----------
Output info
"""""""""""

6
doc/src/compute_temp_partial.rst
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@ -82,12 +82,6 @@ See the :doc:`Howto thermostat <Howto_thermostat>` page for a
discussion of different ways to compute temperature and perform
thermostatting.
----------
.. include:: accel_styles.rst
----------
Output info
"""""""""""

4
doc/src/fix_addforce.rst
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@ -115,10 +115,6 @@ correctly, the minimization will not converge properly.
----------
.. include:: accel_styles.rst
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

4
doc/src/fix_aveforce.rst
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@ -71,10 +71,6 @@ to it.
----------
.. include:: accel_styles.rst
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

7
doc/src/fix_nonaffine_displacement.rst
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@ -102,7 +102,6 @@ zeroed. The *update* reference style implies the reference state will be updated
*nstep* timesteps. The *offset* reference will update the reference state *nstep*
timesteps before a multiple of *nevery* timesteps.
----------
Restart, fix_modify, output, run start/stop, minimize info
@ -129,6 +128,12 @@ 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>` page for more info.
As this fix depends on a run including specific reference timesteps, it
currently does not update peratom values if used in conjunction with the
:doc:`rerun command <rerun>` since it cannot ensure the necessary reference
timesteps are included.
Related commands
""""""""""""""""

2
doc/src/fix_nph_body.rst
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@ -79,8 +79,6 @@ It also means that changing attributes of *thermo_temp* or
----------
.. include:: accel_styles.rst
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

2
doc/src/fix_npt_body.rst
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@ -103,8 +103,6 @@ remaining thermal degrees of freedom, and the bias is added back in.
----------
.. include:: accel_styles.rst
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

2
doc/src/fix_nvt_body.rst
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@ -85,8 +85,6 @@ remaining thermal degrees of freedom, and the bias is added back in.
----------
.. include:: accel_styles.rst
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

16
doc/src/fix_pour.rst
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@ -155,6 +155,22 @@ many timesteps until the desired # of particles has been inserted.
the :doc:`compute_modify dynamic/dof yes <compute_modify>` command
for the temperature compute you are using.
.. admonition:: Implementation Notes
:class: Hint
The exact insertion procedure depends on many factors (e.g. the range of
diameters inserted or whether molecules are being inserted). However, in
the simplest scenario of monodisperse atoms, the procedure works as
follows. First, the number of timesteps between two insertion events is
calculated as the time for a particle to fall through the insertion region,
accounting for gravity and any region motion. Next, the target number of
particles inserted per event (assuming no failed insertions due to overlaps)
is calculated as the product of the volume fraction and the volume of the
insertion region divided by the volume of a particle (or area in 2D).
Events are repeated until all N particles have been inserted, where
the final event is likely interrupted upon reaching N. Estimates of this
process are printed to the log/screen at the start of a run.
----------
All other keywords are optional with defaults as shown below.

3
doc/src/fix_rheo.rst
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@ -16,8 +16,7 @@ Syntax
* kstyle = *quintic* or *RK0* or *RK1* or *RK2*
* zmin = minimal number of neighbors for reproducing kernels
* zero or more keyword/value pairs may be appended to args
* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or
*shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or *shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
.. parsed-literal::

6
doc/src/fix_wall_flow.rst
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@ -123,6 +123,12 @@ also be potentially mitigated by using more multiple walls.
conservative as possible (every timestep if needed). Those are the
default settings.
----------
.. include:: accel_styles.rst
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

2
doc/src/min_style.rst
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@ -3,6 +3,8 @@
min_style cg command
====================
Accelerator Variant: *cg/kk*
min_style hftn command
======================

25
doc/src/pair_coul.rst
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@ -182,16 +182,17 @@ coulomb styles in :doc:`hybrid pair styles <pair_hybrid>`.
.. versionadded:: TBD
Style *coul/ctip* computes the Coulomb interations as described in
Style *coul/ctip* computes the Coulomb interactions as described in
:ref:`Plummer <Plummer1>`. It uses the the damped shifted model as in
style *coul/dsf* but is further extended to the second derivative of
the potential and incorporates empirical charge shielding meant to
approximate the more expensive Coulomb integrals used in style *coul/streitz*.
More details can be found in the referenced paper. Like the style *coul/streitz*,
style *coul/ctip* is a variable charge potential and must be hybridized
with a short-range potential via the :doc:`pair_style hybrid/overlay <pair_hybrid>`
command. Charge equilibration must be performed with the :doc:`fix qeq/ctip
<fix_qeq>` command. For example:
style *coul/dsf* but is further extended to the second derivative of the
potential and incorporates empirical charge shielding meant to
approximate the more expensive Coulomb integrals used in style
*coul/streitz*. More details can be found in the referenced paper. Like
the style *coul/streitz*, style *coul/ctip* is a variable charge
potential and must be hybridized with a short-range potential via the
:doc:`pair_style hybrid/overlay <pair_hybrid>` command. Charge
equilibration must be performed with the :doc:`fix qeq/ctip <fix_qeq>`
command. For example:
.. code-block:: LAMMPS
@ -200,9 +201,9 @@ command. Charge equilibration must be performed with the :doc:`fix qeq/ctip
pair_coeff * * coul/ctip NiO.ctip Ni O
fix 1 all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
See the examples/ctip directory for an example input script using the CTIP
potential. An Ni-O CTIP and EAM/FS parametrization are included for use with
the example.
See the examples/ctip directory for an example input script using the
CTIP potential. An Ni-O CTIP and EAM/FS parameterization are included
for use with the example.
----------

4
doc/src/pair_coul_diel.rst
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@ -71,6 +71,10 @@ The global cutoff (:math:`r_c`) specified in the pair_style command is used.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

4
doc/src/pair_coul_slater.rst
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@ -77,6 +77,10 @@ The global decay length of the charge (:math:`\lambda`) specified in the pair_st
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

4
doc/src/pair_granular.rst
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@ -741,10 +741,6 @@ atom types.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

4
doc/src/pair_mesodpd.rst
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@ -287,6 +287,10 @@ concentration profiles of the two chemical species as
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

4
doc/src/pair_mie.rst
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@ -62,6 +62,10 @@ cutoff specified in the pair_style command is used.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

4
doc/src/pair_sph_heatconduction.rst
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@ -39,6 +39,10 @@ above.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

4
doc/src/pair_sph_lj.rst
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@ -43,6 +43,10 @@ above.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

4
doc/src/pair_sph_taitwater.rst
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@ -52,6 +52,10 @@ above.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""