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more doc changes for USER-SPH

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This commit is contained in:
Steve Plimpton
2020-04-30 16:52:32 -06:00
parent 4eb4839f6d
commit ec9b7c787d
3 changed files with 31 additions and 30 deletions
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6
doc/src/Commands_compute.rst
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@ -79,9 +79,6 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
* :doc:`ke/eff <compute_ke_eff>`
* :doc:`ke/rigid <compute_ke_rigid>`
* :doc:`meso/e/atom <compute_meso_e_atom>`
* :doc:`meso/rho/atom <compute_meso_rho_atom>`
* :doc:`meso/t/atom <compute_meso_t_atom>`
* :doc:`momentum <compute_momentum>`
* :doc:`msd <compute_msd>`
* :doc:`msd/chunk <compute_msd_chunk>`
@ -133,6 +130,9 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`sna/atom <compute_sna_atom>`
* :doc:`snad/atom <compute_sna_atom>`
* :doc:`snav/atom <compute_sna_atom>`
* :doc:`sph/e/atom <compute_sph_e_atom>`
* :doc:`sph/rho/atom <compute_sph_rho_atom>`
* :doc:`sph/t/atom <compute_sph_t_atom>`
* :doc:`spin <compute_spin>`
* :doc:`stress/atom <compute_stress_atom>`
* :doc:`stress/mop <compute_stress_mop>`

4
doc/src/Commands_fix.rst
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@ -94,9 +94,7 @@ OPT.
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`meso <fix_meso>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`meso/stationary <fix_meso_stationary>`
* :doc:`momentum (k) <fix_momentum>`
* :doc:`move <fix_move>`
* :doc:`mscg <fix_mscg>`
@ -201,6 +199,8 @@ OPT.
* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
* :doc:`smd/setvel <fix_smd_setvel>`
* :doc:`smd/wall_surface <fix_smd_wall_surface>`
* :doc:`sph <fix_sph>`
* :doc:`sph/stationary <fix_sph_stationary>`
* :doc:`spring <fix_spring>`
* :doc:`spring/chunk <fix_spring_chunk>`
* :doc:`spring/rg <fix_spring_rg>`

51
doc/src/Modify_atom.rst
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@ -38,31 +38,32 @@ but the last 2 strings you do not need to specify any of
(id,type,x,v,f). Those are included automatically as needed in the
other strings.
+-------------------------+--------------------------------------------------------------------------------+
| fields_grow | full list of properties which is allocated and stored |
+-------------------------+--------------------------------------------------------------------------------+
| fields_copy | list of properties to copy atoms are rearranged on-processor |
+-------------------------+--------------------------------------------------------------------------------+
| fields_comm | list of properties communicated to ghost atoms every step |
+-------------------------+--------------------------------------------------------------------------------+
| fields_comm_vel | additional properties communicated if :doc:`comm_modify vel <atom_style>` is used |
+-------------------------+--------------------------------------------------------------------------------+
| fields_reverse | list of properties summed from ghost atoms every step |
+-------------------------+--------------------------------------------------------------------------------+
| fields_border | list of properties communicated with ghost atoms every reneighboring step |
+-------------------------+--------------------------------------------------------------------------------+
| fields_border_vel | additional properties communicated if :doc:`comm_modify vel <atom_style>` is used |
+-------------------------+--------------------------------------------------------------------------------+
| fields_exchange | list of properties communicated when an atom migrates to another processor |
+-------------------------+--------------------------------------------------------------------------------+
| fields_restart | list of properties written/read to/from a restart file |
+-------------------------+--------------------------------------------------------------------------------+
| fields_create | list of properties defined when an atom is created by :doc:`create_atoms <create_atoms>` |
+-------------------------+--------------------------------------------------------------------------------+
| fields_data_atom | list of properties (in order) in the Atoms section of a data file, as read by :doc:`read_data <read_data>` |
+-------------------------+--------------------------------------------------------------------------------+
| fields_data_vel | list of properties (in order) in the Velocities section of a data file, as read by :doc:`read_data <read_data>` |
+-------------------------+--------------------------------------------------------------------------------+
.. list-table::
* - fields_grow
- full list of properties which is allocated and stored
* - fields_copy
- list of properties to copy atoms are rearranged on-processor
* - fields_comm
- list of properties communicated to ghost atoms every step
* - fields_comm_vel
- additional properties communicated if :doc:`comm_modify vel <atom_style>` is used
* - fields_reverse
- list of properties summed from ghost atoms every step
* - fields_border
- list of properties communicated with ghost atoms every reneighboring step
* - fields_border_vel
- additional properties communicated if :doc:`comm_modify vel <atom_style>` is used
* - fields_exchange
- list of properties communicated when an atom migrates to another processor
* - fields_restart
- list of properties written/read to/from a restart file
* - fields_create
- list of properties defined when an atom is created by :doc:`create_atoms <create_atoms>`
* - fields_data_atom
- list of properties (in order) in the Atoms section of a data file, as read by :doc:`read_data <read_data>`
* - fields_data_vel
- list of properties (in order) in the Velocities section of a data file, as read by :doc:`read_data <read_data>`
In these strings you can list variable names which LAMMPS already
defines (in some other atom style), or you can create new variable