Commit 703a795a authored by Richard Berger's avatar Richard Berger
Browse files

Modify Howto and Tools 

- add missing TOCs in Howto section
- limit section numbering to maximum of 3 levels
- add "Tool descriptions" header
parent 5436169c

doc/src/Howto.txt

+107 −49
Original line number Diff line number Diff line
@@ -21,67 +21,44 @@ also show how to setup and run various kinds of simulations. 


Tutorials howto :h3



"Using GitHub with LAMMPS"_Howto_github.html

"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html

"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)

<!-- RST



General howto :h3

.. toctree::

   :name: tutorials

   :maxdepth: 1



"Restart a simulation"_Howto_restart.html

"Visualize LAMMPS snapshots"_Howto_viz.html

"Run multiple simulations from one input script"_Howto_multiple.html

"Multi-replica simulations"_Howto_replica.html

"Library interface to LAMMPS"_Howto_library.html

"Couple LAMMPS to other codes"_Howto_couple.html :all(b)

   Howto_github

   Howto_pylammps

   Howto_bash



Settings howto :h3

END_RST -->



"2d simulations"_Howto_2d.html

"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html

"Thermostats"_Howto_thermostat.html

"Barostats"_Howto_barostat.html

"Walls"_Howto_walls.html

"NEMD simulations"_Howto_nemd.html

"Long-range dispersion settings"_Howto_dispersion.html :all(b)

<!-- HTML_ONLY -->



Analysis howto :h3

"Using GitHub with LAMMPS"_Howto_github.html

"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html

"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)



"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html

"Use chunks to calculate system properties"_Howto_chunk.html

"Calculate temperature"_Howto_temperature.html

"Calculate elastic constants"_Howto_elastic.html

"Calculate thermal conductivity"_Howto_kappa.html

"Calculate viscosity"_Howto_viscosity.html

"Calculate diffusion coefficients"_Howto_diffusion.html :all(b)

<!-- END_HTML_ONLY -->



Force fields howto :h3

General howto :h3



"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html

"TIP3P water model"_Howto_tip3p.html

"TIP4P water model"_Howto_tip4p.html

"SPC water model"_Howto_spc.html :all(b)

<!-- RST



Packages howto :h3

.. toctree::

   :name: general

   :maxdepth: 1



"Finite-size spherical and aspherical particles"_Howto_spherical.html

"Granular models"_Howto_granular.html

"Body style particles"_Howto_body.html

"Polarizable models"_Howto_polarizable.html

"Adiabatic core/shell model"_Howto_coreshell.html

"Drude induced dipoles"_Howto_drude.html

"Drude induced dipoles (extended)"_Howto_drude2.html

"Manifolds (surfaces)"_Howto_manifold.html

"Magnetic spins"_Howto_spins.html :all(b)



<!-- HTML_ONLY -->

   Howto_restart

   Howto_viz

   Howto_multiple

   Howto_replica

   Howto_library

   Howto_couple



External howto :h3

END_RST -->



"Using GitHub with LAMMPS"_Howto_github.html

"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html

"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)



General howto :h3

<!-- HTML_ONLY -->



"Restart a simulation"_Howto_restart.html

"Visualize LAMMPS snapshots"_Howto_viz.html
@@ -90,8 +67,28 @@ General howto :h3 
"Library interface to LAMMPS"_Howto_library.html

"Couple LAMMPS to other codes"_Howto_couple.html :all(b)



<!-- END_HTML_ONLY -->



Settings howto :h3



<!-- RST



.. toctree::

   :name: settings

   :maxdepth: 1



   Howto_2d

   Howto_triclinic

   Howto_thermostat

   Howto_barostat

   Howto_walls

   Howto_nemd

   Howto_dispersion



END_RST -->



<!-- HTML_ONLY -->



"2d simulations"_Howto_2d.html

"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html

"Thermostats"_Howto_thermostat.html
@@ -100,8 +97,29 @@ Settings howto :h3 
"NEMD simulations"_Howto_nemd.html

"Long-range dispersion settings"_Howto_dispersion.html :all(b)



<!-- END_HTML_ONLY -->





Analysis howto :h3



<!-- RST



.. toctree::

   :name: analysis

   :maxdepth: 1



   Howto_output

   Howto_chunk

   Howto_temperature

   Howto_elastic

   Howto_kappa

   Howto_viscosity

   Howto_diffusion



END_RST -->



<!-- HTML_ONLY -->



"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html

"Use chunks to calculate system properties"_Howto_chunk.html :all(b)

"Calculate temperature"_Howto_temperature.html
@@ -110,15 +128,55 @@ Analysis howto :h3 
"Calculate viscosity"_Howto_viscosity.html

"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)



<!-- END_HTML_ONLY -->



Force fields howto :h3



<!-- RST



.. toctree::

   :name: force

   :maxdepth: 1



   Howto_bioFF

   Howto_tip3p

   Howto_tip4p

   Howto_spc



END_RST -->



<!-- HTML_ONLY -->



"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html

"TIP3P water model"_Howto_tip3p.html

"TIP4P water model"_Howto_tip4p.html

"SPC water model"_Howto_spc.html :all(b)



<!-- END_HTML_ONLY -->



Packages howto :h3



<!-- RST



.. toctree::

   :name: packages

   :maxdepth: 1



   Howto_spherical

   Howto_granular

   Howto_body

   Howto_polarizable

   Howto_coreshell

   Howto_drude

   Howto_drude2

   Howto_manifold

   Howto_spins



END_RST -->





<!-- HTML_ONLY -->



"Finite-size spherical and aspherical particles"_Howto_spherical.html

"Granular models"_Howto_granular.html

"Body style particles"_Howto_body.html

doc/src/Manual.txt

+1 −1
Original line number Diff line number Diff line
@@ -66,7 +66,7 @@ every LAMMPS command. 


.. toctree::

   :maxdepth: 2

   :numbered:

   :numbered: 3

   :caption: User Documentation

   :name: userdoc

   :includehidden:

doc/src/Tools.txt

+2 −0
Original line number Diff line number Diff line
@@ -89,6 +89,8 @@ Miscellaneous tools :h3 


:line



Tool descriptions :h3



amber2lmp tool :h4,link(amber)



The amber2lmp sub-directory contains two Python scripts for converting

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