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update docs to make wall fix restrictions more explicit

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This commit is contained in:
Axel Kohlmeyer
2024-08-16 16:29:45 -04:00
parent 5111170d8f
commit a2fa7d68d7
3 changed files with 93 additions and 68 deletions
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42
doc/src/pair_brownian.rst
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@ -48,11 +48,13 @@ torques on finite-size spherical particles. The former requires
monodisperse spherical particles; the latter allows for polydisperse monodisperse spherical particles; the latter allows for polydisperse
spherical particles. spherical particles.
These pair styles are designed to be used with either the :doc:`pair_style lubricate <pair_lubricate>` or :doc:`pair_style lubricateU <pair_lubricateU>` commands to provide thermostatting These pair styles are designed to be used with either the
when dissipative lubrication forces are acting. Thus the parameters :doc:`pair_style lubricate <pair_lubricate>` or :doc:`pair_style
*mu*, *flaglog*, *flagfld*, *cutinner*, and *cutoff* should be lubricateU <pair_lubricateU>` commands to provide thermostatting when
specified consistent with the settings in the lubrication pair styles. dissipative lubrication forces are acting. Thus the parameters *mu*,
For details, refer to either of the lubrication pair styles. *flaglog*, *flagfld*, *cutinner*, and *cutoff* should be specified
consistent with the settings in the lubrication pair styles. For
details, refer to either of the lubrication pair styles.
The *t_target* setting is used to specify the target temperature of The *t_target* setting is used to specify the target temperature of
the system. The random number *seed* is used to generate random the system. The random number *seed* is used to generate random
@ -85,25 +87,26 @@ must be specified.
Mixing, shift, table, tail correction, restart, rRESPA info Mixing, shift, table, tail correction, restart, rRESPA info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the two cutoff distances for this For atom type pairs I,J and I != J, the two cutoff distances for these
pair style can be mixed. The default mix value is *geometric*\ . See pair styles can be mixed. The default mix value is *geometric*\ . See
the "pair_modify" command for details. the "pair_modify" command for details.
This pair style does not support the :doc:`pair_modify <pair_modify>` These pair styles do not support the :doc:`pair_modify <pair_modify>`
shift option for the energy of the pair interaction. shift option for the energy of the pair interaction.
The :doc:`pair_modify <pair_modify>` table option is not relevant The :doc:`pair_modify <pair_modify>` table option is not relevant
for this pair style. for these pair styles.
This pair style does not support the :doc:`pair_modify <pair_modify>` These pair styles do not support the :doc:`pair_modify <pair_modify>`
tail option for adding long-range tail corrections to energy and tail option for adding long-range tail corrections to energy and
pressure. pressure.
This pair style writes its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need These pair styles write their information to :doc:`binary restart files
to be specified in an input script that reads a restart file. <restart>`, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the These pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the :doc:`run_style respa <run_style>` command. They do not support the
*inner*, *middle*, *outer* keywords. *inner*, *middle*, *outer* keywords.
---------- ----------
@ -111,14 +114,21 @@ This pair style can only be used via the *pair* keyword of the
Restrictions Restrictions
"""""""""""" """"""""""""
These styles are part of the COLLOID package. They are only enabled These styles are part of the COLLOID package. They are only enabled if
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info. LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Only spherical monodisperse particles are allowed for pair_style Only spherical monodisperse particles are allowed for pair_style
brownian. brownian.
Only spherical particles are allowed for pair_style brownian/poly. Only spherical particles are allowed for pair_style brownian/poly.
These pair styles are only compatible with the following wall fixes:
doc:`fix wall/lj93, fix wall/lj126, fix wall/lj1043, fix wall/colloid,
fix wall/harmonic, fix wall/lepton, fix wall/morse, fix wall/table
<fix_wall>`.
Related commands Related commands
"""""""""""""""" """"""""""""""""

25
doc/src/pair_lubricate.rst
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@ -104,10 +104,12 @@ as long as *flagVF* is set to 1 (default).
.. note:: .. note::
When using the FLD terms, these pair styles are designed to be When using the FLD terms, these pair styles are designed to be used
used with explicit time integration and a correspondingly small with explicit time integration and a correspondingly small timestep.
timestep. Thus either :doc:`fix nve/sphere <fix_nve_sphere>` or :doc:`fix nve/asphere <fix_nve_asphere>` should be used for time integration. Thus either :doc:`fix nve/sphere <fix_nve_sphere>` or :doc:`fix
To perform implicit FLD, see the :doc:`pair_style lubricateU <pair_lubricateU>` command. nve/asphere <fix_nve_asphere>` should be used for time integration.
To perform implicit FLD, see the :doc:`pair_style lubricateU
<pair_lubricateU>` command.
Style *lubricate* requires monodisperse spherical particles; style Style *lubricate* requires monodisperse spherical particles; style
*lubricate/poly* allows for polydisperse spherical particles. *lubricate/poly* allows for polydisperse spherical particles.
@ -123,17 +125,18 @@ hydrodynamic interactions accordingly. Volume changes due to fix
deform are accounted for when computing the volume fraction deform are accounted for when computing the volume fraction
corrections to R_FU. corrections to R_FU.
When computing the volume fraction corrections to R_FU, the presence When computing the volume fraction corrections to R_FU, the presence of
of walls (whether moving or stationary) will affect the volume walls (whether moving or stationary) will affect the volume fraction
fraction available to colloidal particles. This is currently accounted available to colloidal particles. This is currently accounted for with
for with the following types of walls: :doc:`wall/lj93 <fix_wall>`, the following types of walls: :doc:`wall/lj93 <fix_wall>`,
:doc:`wall/lj126 <fix_wall>`, :doc:`wall/colloid <fix_wall>`, and :doc:`wall/lj126 <fix_wall>`, :doc:`wall/colloid <fix_wall>`, and
:doc:`wall/harmonic <fix_wall>`. For these wall styles, the correct :doc:`wall/harmonic <fix_wall>`. For these wall styles, the correct
volume fraction will be used when walls do not coincide with the box volume fraction will be used when walls do not coincide with the box
boundary, as well as when walls move and thereby cause a change in the boundary, as well as when walls move and thereby cause a change in the
volume fraction. Other wall styles will still work, but they will volume fraction. Other wall styles may still work, but they will result
result in the volume fraction being computed based on the box in the volume fraction being computed based on the box boundaries.
boundaries. Several wall styles are not compatible with these pair styles and using
them will result in an error.
Since lubrication forces are dissipative, it is usually desirable to Since lubrication forces are dissipative, it is usually desirable to
thermostat the system at a constant temperature. If Brownian motion thermostat the system at a constant temperature. If Brownian motion

94
doc/src/pair_lubricateU.rst
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@ -97,27 +97,28 @@ corrections to R_FU are included if *flagVF* is set to 1 (default).
F\ *rest* represents the forces and torques due to all other types of F\ *rest* represents the forces and torques due to all other types of
interactions, e.g. Brownian, electrostatic etc. Note that this interactions, e.g. Brownian, electrostatic etc. Note that this
algorithm neglects the inertial terms, thereby removing the algorithm neglects the inertial terms, thereby removing the restriction
restriction of resolving the small interial time scale, which may not of resolving the small interial time scale, which may not be of interest
be of interest for colloidal particles. This pair style solves for for colloidal particles. These pair styles solve for the velocity such
the velocity such that the hydrodynamic force balances all other types that the hydrodynamic force balances all other types of forces, thereby
of forces, thereby resulting in a net zero force (zero inertia limit). resulting in a net zero force (zero inertia limit). When defining these
When defining this pair style, it must be defined last so that when pair styles, they must be defined last so that when these styles are
this style is invoked all other types of forces have already been invoked all other types of forces have already been computed. For the
computed. For the same reason, it won't work if additional non-pair same reason, they won't work if additional non-pair styles are defined
styles are defined (such as bond or Kspace forces) as they are (such as bond or Kspace forces) as they are calculated in LAMMPS after
calculated in LAMMPS after the pairwise interactions have been the pairwise interactions have been computed.
computed.
.. note:: .. note::
When using these styles, the these pair styles are designed to When using these styles, the pair styles are designed to be used with
be used with implicit time integration and a correspondingly larger implicit time integration and a correspondingly larger timestep.
timestep. Thus either :doc:`fix nve/noforce <fix_nve_noforce>` should Thus either :doc:`fix nve/noforce <fix_nve_noforce>` should be used
be used for spherical particles defined via :doc:`atom_style sphere <atom_style>` or :doc:`fix nve/asphere/noforce <fix_nve_asphere_noforce>` should be used for for spherical particles defined via :doc:`atom_style sphere
spherical particles defined via :doc:`atom_style ellipsoid <atom_style>`. This is because the velocity and angular <atom_style>` or :doc:`fix nve/asphere/noforce
momentum of each particle is set by the pair style, and should not be <fix_nve_asphere_noforce>` should be used for spherical particles
reset by the time integration fix. defined via :doc:`atom_style ellipsoid <atom_style>`. This is
because the velocity and angular momentum of each particle is set by
the pair style, and should not be reset by the time integration fix.
Style *lubricateU* requires monodisperse spherical particles; style Style *lubricateU* requires monodisperse spherical particles; style
*lubricateU/poly* allows for polydisperse spherical particles. *lubricateU/poly* allows for polydisperse spherical particles.
@ -128,17 +129,20 @@ hydrodynamic interactions accordingly. Volume changes due to fix
deform are accounted for when computing the volume fraction deform are accounted for when computing the volume fraction
corrections to R_FU. corrections to R_FU.
When computing the volume fraction corrections to R_FU, the presence When computing the volume fraction corrections to R_FU, the presence of
of walls (whether moving or stationary) will affect the volume walls (whether moving or stationary) will affect the volume fraction
fraction available to colloidal particles. This is currently accounted available to colloidal particles. This is currently accounted for with
for with the following types of walls: :doc:`wall/lj93 <fix_wall>`, the following types of walls: :doc:`wall/lj93 <fix_wall>`,
:doc:`wall/lj126 <fix_wall>`, :doc:`wall/colloid <fix_wall>`, and :doc:`wall/lj126 <fix_wall>`, :doc:`wall/colloid <fix_wall>`, and
:doc:`wall/harmonic <fix_wall>`. For these wall styles, the correct :doc:`wall/harmonic <fix_wall>`. For these wall styles, the correct
volume fraction will be used when walls do not coincide with the box volume fraction will be used when walls do not coincide with the box
boundary, as well as when walls move and thereby cause a change in the boundary, as well as when walls move and thereby cause a change in the
volume fraction. To use these wall styles with pair_style *lubricateU* volume fraction. To use these wall styles with pair_style *lubricateU*
or *lubricateU/poly*, the *fld yes* option must be specified in the or *lubricateU/poly*, the *fld yes* option must be specified in the fix
fix wall command. wall command. Other wall styles may still work, but they will result
in the volume fraction being computed based on the box boundaries.
Several wall styles are not compatible with these pair styles and using
them will result in an error.
Since lubrication forces are dissipative, it is usually desirable to Since lubrication forces are dissipative, it is usually desirable to
thermostat the system at a constant temperature. If Brownian motion thermostat the system at a constant temperature. If Brownian motion
@ -171,21 +175,22 @@ For atom type pairs I,J and I != J, the two cutoff distances for this
pair style can be mixed. The default mix value is *geometric*\ . See pair style can be mixed. The default mix value is *geometric*\ . See
the "pair_modify" command for details. the "pair_modify" command for details.
This pair style does not support the :doc:`pair_modify <pair_modify>` These pair styles do not support the :doc:`pair_modify <pair_modify>`
shift option for the energy of the pair interaction. shift option for the energy of the pair interaction.
The :doc:`pair_modify <pair_modify>` table option is not relevant The :doc:`pair_modify <pair_modify>` table option is not relevant
for this pair style. for these pair styles.
This pair style does not support the :doc:`pair_modify <pair_modify>` These pair styles do not support the :doc:`pair_modify <pair_modify>`
tail option for adding long-range tail corrections to energy and tail option for adding long-range tail corrections to energy and
pressure. pressure.
This pair style writes its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need These pair styles write their information to :doc:`binary restart files
to be specified in an input script that reads a restart file. <restart>`, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the These pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the :doc:`run_style respa <run_style>` command. They does not support the
*inner*, *middle*, *outer* keywords. *inner*, *middle*, *outer* keywords.
---------- ----------
@ -193,24 +198,31 @@ This pair style can only be used via the *pair* keyword of the
Restrictions Restrictions
"""""""""""" """"""""""""
These styles are part of the COLLOID package. They are only enabled These styles are part of the COLLOID package. They are only enabled if
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info. LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Currently, these pair styles assume that all other types of Currently, these pair styles assume that all other types of
forces/torques on the particles have been already been computed when forces/torques on the particles have been already been computed when it
it is invoked. This requires this style to be defined as the last of is invoked. This requires this style to be defined as the last of the
the pair styles, and that no fixes apply additional constraint forces. pair styles, and that no fixes apply additional constraint forces. One
One exception is the :doc:`fix wall/colloid <fix_wall>` commands, which exception is the :doc:`fix wall/colloid <fix_wall>` commands, which has
has an "fld" option to apply their wall forces correctly. an "fld" option to apply their wall forces correctly.
Only spherical monodisperse particles are allowed for pair_style Only spherical monodisperse particles are allowed for pair_style
lubricateU. lubricateU.
Only spherical particles are allowed for pair_style lubricateU/poly. Only spherical particles are allowed for pair_style lubricateU/poly.
For sheared suspensions, it is assumed that the shearing is done in For sheared suspensions, it is assumed that the shearing is done in the
the xy plane, with x being the velocity direction and y being the xy plane, with x being the velocity direction and y being the
velocity-gradient direction. In this case, one must use :doc:`fix deform <fix_deform>` with the same rate of shear (erate). velocity-gradient direction. In this case, one must use :doc:`fix deform
<fix_deform>` with the same rate of shear (erate).
These pair styles are only compatible with the following wall fixes:
doc:`fix wall/lj93, fix wall/lj126, fix wall/lj1043, fix wall/colloid,
fix wall/harmonic, fix wall/lepton, fix wall/morse, fix wall/table
<fix_wall>`.
Related commands Related commands
"""""""""""""""" """"""""""""""""