forked from lijiext/lammps
Modify Howto and Tools
- add missing TOCs in Howto section - limit section numbering to maximum of 3 levels - add "Tool descriptions" header
This commit is contained in:
Richard Berger
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5436169c20
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703a795af8
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@ -21,68 +21,45 @@ also show how to setup and run various kinds of simulations.
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Tutorials howto :h3
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"Using GitHub with LAMMPS"_Howto_github.html
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"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
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"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
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<!-- RST
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General howto :h3
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.. toctree::
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:name: tutorials
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:maxdepth: 1
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"Restart a simulation"_Howto_restart.html
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"Visualize LAMMPS snapshots"_Howto_viz.html
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"Run multiple simulations from one input script"_Howto_multiple.html
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"Multi-replica simulations"_Howto_replica.html
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"Library interface to LAMMPS"_Howto_library.html
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"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
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Howto_github
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Howto_pylammps
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Howto_bash
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Settings howto :h3
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"2d simulations"_Howto_2d.html
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"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
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"Thermostats"_Howto_thermostat.html
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"Barostats"_Howto_barostat.html
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"Walls"_Howto_walls.html
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"NEMD simulations"_Howto_nemd.html
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"Long-range dispersion settings"_Howto_dispersion.html :all(b)
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Analysis howto :h3
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"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
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"Use chunks to calculate system properties"_Howto_chunk.html
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"Calculate temperature"_Howto_temperature.html
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"Calculate elastic constants"_Howto_elastic.html
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"Calculate thermal conductivity"_Howto_kappa.html
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"Calculate viscosity"_Howto_viscosity.html
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"Calculate diffusion coefficients"_Howto_diffusion.html :all(b)
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Force fields howto :h3
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"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
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"TIP3P water model"_Howto_tip3p.html
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"TIP4P water model"_Howto_tip4p.html
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"SPC water model"_Howto_spc.html :all(b)
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Packages howto :h3
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"Finite-size spherical and aspherical particles"_Howto_spherical.html
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"Granular models"_Howto_granular.html
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"Body style particles"_Howto_body.html
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"Polarizable models"_Howto_polarizable.html
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"Adiabatic core/shell model"_Howto_coreshell.html
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"Drude induced dipoles"_Howto_drude.html
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"Drude induced dipoles (extended)"_Howto_drude2.html
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"Manifolds (surfaces)"_Howto_manifold.html
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"Magnetic spins"_Howto_spins.html :all(b)
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END_RST -->
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<!-- HTML_ONLY -->
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External howto :h3
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"Using GitHub with LAMMPS"_Howto_github.html
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"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
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"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
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<!-- END_HTML_ONLY -->
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General howto :h3
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<!-- RST
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.. toctree::
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:name: general
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:maxdepth: 1
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Howto_restart
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Howto_viz
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Howto_multiple
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Howto_replica
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Howto_library
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Howto_couple
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END_RST -->
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<!-- HTML_ONLY -->
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"Restart a simulation"_Howto_restart.html
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"Visualize LAMMPS snapshots"_Howto_viz.html
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"Run multiple simulations from one input script"_Howto_multiple.html
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@ -90,8 +67,28 @@ General howto :h3
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"Library interface to LAMMPS"_Howto_library.html
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"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
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<!-- END_HTML_ONLY -->
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Settings howto :h3
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<!-- RST
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.. toctree::
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:name: settings
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:maxdepth: 1
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Howto_2d
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Howto_triclinic
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Howto_thermostat
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Howto_barostat
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Howto_walls
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Howto_nemd
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Howto_dispersion
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END_RST -->
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<!-- HTML_ONLY -->
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"2d simulations"_Howto_2d.html
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"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
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"Thermostats"_Howto_thermostat.html
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@ -100,8 +97,29 @@ Settings howto :h3
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"NEMD simulations"_Howto_nemd.html
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"Long-range dispersion settings"_Howto_dispersion.html :all(b)
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<!-- END_HTML_ONLY -->
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Analysis howto :h3
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<!-- RST
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.. toctree::
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:name: analysis
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:maxdepth: 1
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Howto_output
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Howto_chunk
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Howto_temperature
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Howto_elastic
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Howto_kappa
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Howto_viscosity
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Howto_diffusion
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END_RST -->
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<!-- HTML_ONLY -->
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"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
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"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
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"Calculate temperature"_Howto_temperature.html
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@ -110,15 +128,55 @@ Analysis howto :h3
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"Calculate viscosity"_Howto_viscosity.html
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"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
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<!-- END_HTML_ONLY -->
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Force fields howto :h3
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<!-- RST
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.. toctree::
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:name: force
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:maxdepth: 1
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Howto_bioFF
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Howto_tip3p
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Howto_tip4p
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Howto_spc
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END_RST -->
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<!-- HTML_ONLY -->
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"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
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"TIP3P water model"_Howto_tip3p.html
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"TIP4P water model"_Howto_tip4p.html
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"SPC water model"_Howto_spc.html :all(b)
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<!-- END_HTML_ONLY -->
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Packages howto :h3
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<!-- RST
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.. toctree::
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:name: packages
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:maxdepth: 1
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Howto_spherical
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Howto_granular
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Howto_body
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Howto_polarizable
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Howto_coreshell
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Howto_drude
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Howto_drude2
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Howto_manifold
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Howto_spins
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END_RST -->
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<!-- HTML_ONLY -->
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"Finite-size spherical and aspherical particles"_Howto_spherical.html
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"Granular models"_Howto_granular.html
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"Body style particles"_Howto_body.html
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@ -66,7 +66,7 @@ every LAMMPS command.
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.. toctree::
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:maxdepth: 2
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:numbered:
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:numbered: 3
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:caption: User Documentation
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:name: userdoc
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:includehidden:
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@ -89,6 +89,8 @@ Miscellaneous tools :h3
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:line
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Tool descriptions :h3
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amber2lmp tool :h4,link(amber)
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The amber2lmp sub-directory contains two Python scripts for converting
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