additional tweaks to clarify fix sphere doc pages
This commit is contained in:
Steve Plimpton
@ -22,7 +22,7 @@ Syntax
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*disc* value = none = treat particles as 2d discs, not spheres
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* additional thermostat and barostat related keyword/value pairs from the :doc:`fix npt <fix_nh>` command can be appended
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* NOTE: additional thermostat and barostat and dipole related keyword/value pairs from the :doc:`fix npt <fix_nh>` command can be appended
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Examples
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""""""""
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@ -33,6 +33,7 @@ Examples
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fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
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fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 disc
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fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
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fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 update dipole
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fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
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Description
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@ -61,8 +62,9 @@ The only difference between discs and spheres in this context is their
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moment of inertia, as used in the time integration.
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Additional parameters affecting the thermostat and barostat are
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specified by keywords and values documented with the :doc:`fix npt <fix_nh>` command. See, for example, discussion of the *temp*,
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*iso*, *aniso*, and *dilate* keywords.
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specified by keywords and values documented with the :doc:`fix npt
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<fix_nh>` command. See, for example, discussion of the *temp*, *iso*,
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*aniso*, and *dilate* keywords.
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The particles in the fix group are the only ones whose velocities and
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positions are updated by the velocity/position update portion of the
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@ -87,8 +89,10 @@ this, the fix creates its own computes of style "temp/sphere" and
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compute fix-ID_temp all temp/sphere
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compute fix-ID_press all pressure fix-ID_temp
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See the :doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute pressure <compute_pressure>` commands for details. Note that the
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IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
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See the :doc:`compute temp/sphere <compute_temp_sphere>` and
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:doc:`compute pressure <compute_pressure>` commands for details. Note
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that the IDs of the new computes are the fix-ID + underscore + "temp"
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or fix_ID
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+ underscore + "press", and the group for the new computes is "all"
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since pressure is computed for the entire system.
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@ -170,7 +174,9 @@ defined by the :doc:`dimension <dimension>` keyword.
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Related commands
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""""""""""""""""
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:doc:`fix npt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`, :doc:`fix nvt_sphere <fix_nvt_sphere>`, :doc:`fix npt_asphere <fix_npt_asphere>`, :doc:`fix_modify <fix_modify>`
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:doc:`fix npt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`,
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:doc:`fix nvt_sphere <fix_nvt_sphere>`, :doc:`fix npt_asphere
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<fix_npt_asphere>`, :doc:`fix_modify <fix_modify>`
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Default
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"""""""
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@ -51,7 +51,8 @@ If the *update* keyword is used with the *dipole* value, then the
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orientation of the dipole moment of each particle is also updated
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during the time integration. This option should be used for models
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where a dipole moment is assigned to finite-size particles,
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e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole <atom_style>` command.
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e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole
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<atom_style>` command.
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The default dipole orientation integrator can be changed to the
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Dullweber-Leimkuhler-McLachlan integration scheme
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@ -75,11 +76,13 @@ moment of inertia, as used in the time integration.
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various :doc:`output commands <Howto_output>`.
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No information about this fix is written to :doc:`binary restart files
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<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
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relevant to this fix. No global or per-atom quantities are stored by
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this fix for access by various :doc:`output commands <Howto_output>`.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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the :doc:`run <run>` command. This fix is not invoked during
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:doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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@ -22,7 +22,7 @@ Syntax
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*disc* value = none = treat particles as 2d discs, not spheres
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* additional thermostat related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
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* NOTE: additional thermostat and dipole related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
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Examples
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""""""""
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@ -32,6 +32,7 @@ Examples
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fix 1 all nvt/sphere temp 300.0 300.0 100.0
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fix 1 all nvt/sphere temp 300.0 300.0 100.0 disc
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fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2
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fix 1 all nvt/sphere temp 300.0 300.0 100.0 update dipole
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Description
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"""""""""""
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@ -77,13 +78,13 @@ underscore + "temp", and the group for the new compute is the same as
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the fix group.
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Note that this is NOT the compute used by thermodynamic output (see
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the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*.
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This means you can change the attributes of this fix's temperature
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(e.g. its degrees-of-freedom) via the
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:doc:`compute_modify <compute_modify>` command or print this temperature
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during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
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It also means that changing attributes of *thermo_temp* will have no
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effect on this fix.
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the :doc:`thermo_style <thermo_style>` command) with ID =
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*thermo_temp*. This means you can change the attributes of this fix's
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temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify
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<compute_modify>` command or print this temperature during
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thermodynamic output via the :doc:`thermo_style custom <thermo_style>`
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command using the appropriate compute-ID. It also means that changing
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attributes of *thermo_temp* will have no effect on this fix.
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Like other fixes that perform thermostatting, this fix can be used
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with :doc:`compute commands <compute>` that remove a "bias" from the
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@ -148,7 +149,9 @@ defined by the :doc:`dimension <dimension>` keyword.
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Related commands
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""""""""""""""""
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:doc:`fix nvt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`, :doc:`fix nvt_asphere <fix_nvt_asphere>`, :doc:`fix npt_sphere <fix_npt_sphere>`, :doc:`fix_modify <fix_modify>`
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:doc:`fix nvt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`,
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:doc:`fix nvt_asphere <fix_nvt_asphere>`, :doc:`fix npt_sphere
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<fix_npt_sphere>`, :doc:`fix_modify <fix_modify>`
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Default
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"""""""
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