diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index bd52ca9dc5..afaa2c9d67 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -22,7 +22,7 @@ Syntax *disc* value = none = treat particles as 2d discs, not spheres -* additional thermostat and barostat related keyword/value pairs from the :doc:`fix npt ` command can be appended +* NOTE: additional thermostat and barostat and dipole related keyword/value pairs from the :doc:`fix npt ` command can be appended Examples """""""" @@ -33,6 +33,7 @@ Examples fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 disc fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2 + fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 update dipole fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial Description @@ -61,8 +62,9 @@ The only difference between discs and spheres in this context is their moment of inertia, as used in the time integration. Additional parameters affecting the thermostat and barostat are -specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*, -*iso*, *aniso*, and *dilate* keywords. +specified by keywords and values documented with the :doc:`fix npt +` command. See, for example, discussion of the *temp*, *iso*, +*aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -87,8 +89,10 @@ this, the fix creates its own computes of style "temp/sphere" and compute fix-ID_temp all temp/sphere compute fix-ID_press all pressure fix-ID_temp -See the :doc:`compute temp/sphere ` and :doc:`compute pressure ` commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID +See the :doc:`compute temp/sphere ` and +:doc:`compute pressure ` commands for details. Note +that the IDs of the new computes are the fix-ID + underscore + "temp" +or fix_ID + underscore + "press", and the group for the new computes is "all" since pressure is computed for the entire system. @@ -170,7 +174,9 @@ defined by the :doc:`dimension ` keyword. Related commands """""""""""""""" -:doc:`fix npt `, :doc:`fix nve_sphere `, :doc:`fix nvt_sphere `, :doc:`fix npt_asphere `, :doc:`fix_modify ` +:doc:`fix npt `, :doc:`fix nve_sphere `, + :doc:`fix nvt_sphere `, :doc:`fix npt_asphere + `, :doc:`fix_modify ` Default """"""" diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst index 0230255b42..df177a2eca 100644 --- a/doc/src/fix_nve_sphere.rst +++ b/doc/src/fix_nve_sphere.rst @@ -51,7 +51,8 @@ If the *update* keyword is used with the *dipole* value, then the orientation of the dipole moment of each particle is also updated during the time integration. This option should be used for models where a dipole moment is assigned to finite-size particles, -e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole ` command. +e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole +` command. The default dipole orientation integrator can be changed to the Dullweber-Leimkuhler-McLachlan integration scheme @@ -75,11 +76,13 @@ moment of inertia, as used in the time integration. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various :doc:`output commands `. +No information about this fix is written to :doc:`binary restart files +`. None of the :doc:`fix_modify ` options are +relevant to this fix. No global or per-atom quantities are stored by +this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of -the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. +the :doc:`run ` command. This fix is not invoked during +:doc:`energy minimization `. Restrictions """""""""""" diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst index 91575d4c48..f107940af9 100644 --- a/doc/src/fix_nvt_sphere.rst +++ b/doc/src/fix_nvt_sphere.rst @@ -22,7 +22,7 @@ Syntax *disc* value = none = treat particles as 2d discs, not spheres -* additional thermostat related keyword/value pairs from the :doc:`fix nvt ` command can be appended +* NOTE: additional thermostat and dipole related keyword/value pairs from the :doc:`fix nvt ` command can be appended Examples """""""" @@ -32,6 +32,7 @@ Examples fix 1 all nvt/sphere temp 300.0 300.0 100.0 fix 1 all nvt/sphere temp 300.0 300.0 100.0 disc fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2 + fix 1 all nvt/sphere temp 300.0 300.0 100.0 update dipole Description """"""""""" @@ -77,13 +78,13 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo_style ` command) with ID = *thermo_temp*. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -:doc:`compute_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. -It also means that changing attributes of *thermo_temp* will have no -effect on this fix. +the :doc:`thermo_style ` command) with ID = +*thermo_temp*. This means you can change the attributes of this fix's +temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify +` command or print this temperature during +thermodynamic output via the :doc:`thermo_style custom ` +command using the appropriate compute-ID. It also means that changing +attributes of *thermo_temp* will have no effect on this fix. Like other fixes that perform thermostatting, this fix can be used with :doc:`compute commands ` that remove a "bias" from the @@ -148,7 +149,9 @@ defined by the :doc:`dimension ` keyword. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix nve_sphere `, :doc:`fix nvt_asphere `, :doc:`fix npt_sphere `, :doc:`fix_modify ` +:doc:`fix nvt `, :doc:`fix nve_sphere `, + :doc:`fix nvt_asphere `, :doc:`fix npt_sphere + `, :doc:`fix_modify ` Default """""""