Commit c44228b0 authored by Richard Berger's avatar Richard Berger
Browse files

Created more complete TOC and indices 

This adds index sections on the main navigation bar and finally silences the
missing TOC warnings.
parent 90f6395d

doc/src/Manual.txt

+17 −0
Original line number Diff line number Diff line
@@ -106,6 +106,9 @@ it gives quick access to documentation for all LAMMPS commands. 
.. toctree::

   :maxdepth: 2

   :numbered:

   :caption: User Documentation

   :name: userdoc

   :includehidden:

   

   Section_intro

   Section_start
@@ -121,6 +124,20 @@ it gives quick access to documentation for all LAMMPS commands. 
   Section_errors

   Section_history



.. toctree::

   :caption: Index

   :name: index

   :hidden:



   tutorials

   commands

   fixes

   computes

   pairs

   bonds

   angles

   dihedrals

   impropers



Indices and tables

==================

doc/src/Section_accelerate.txt

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@@ -157,11 +157,25 @@ packages"_Section_packages.html. 
These are the accelerator packages

currently in LAMMPS, either as standard or user packages:



"GPU Package"_accelerate_gpu.html with CUDA and OpenCL support for Nvidia GPUs and others :h5

"USER-INTEL Package"_accelerate_intel.html for Intel CPUs and Intel Xeon Phi :h5

"KOKKOS Package"_accelerate_kokkos.html for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading :h5

"USER-OMP Package "_accelerate_omp.html for OpenMP threading and generic CPU optimizations :h5

"OPT Package"_accelerate_opt.html generic CPU optimizations :h5

"GPU Package"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support

"USER-INTEL Package"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi

"KOKKOS Package"_accelerate_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading

"USER-OMP Package"_accelerate_omp.html : for OpenMP threading and generic CPU optimizations

"OPT Package"_accelerate_opt.html : generic CPU optimizations :tb(s=:)



<!-- RST



.. toctree::

   :maxdepth: 1

   :hidden:



   accelerate_gpu

   accelerate_intel

   accelerate_kokkos

   accelerate_omp

   accelerate_opt



END_RST -->



Inverting this list, LAMMPS currently has acceleration support for

three kinds of hardware, via the listed packages:

doc/src/angles.txt

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Angle Styles :h1



<!-- RST



.. toctree::

   :maxdepth: 1



   angle_charmm

   angle_class2

   angle_cosine

   angle_cosine_delta

   angle_cosine_periodic

   angle_cosine_shift

   angle_cosine_shift_exp

   angle_cosine_squared

   angle_dipole

   angle_fourier

   angle_fourier_simple

   angle_harmonic

   angle_hybrid

   angle_none

   angle_quartic

   angle_sdk

   angle_table

   angle_zero



END_RST -->

doc/src/bonds.txt

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Bonds :h1



<!-- RST



.. toctree::

   :maxdepth: 1



   bond_class2

   bond_fene

   bond_fene_expand

   bond_harmonic

   bond_harmonic_shift

   bond_harmonic_shift_cut

   bond_hybrid

   bond_morse

   bond_none

   bond_nonlinear

   bond_quartic

   bond_table

   bond_zero



END_RST -->

doc/src/commands.txt

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+109 −0
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Commands :h1



<!-- RST



.. toctree::

   :maxdepth: 1



   angle_coeff

   angle_style

   atom_modify

   atom_style

   balance

   bond_coeff

   bond_style

   bond_write

   boundary

   box

   change_box

   clear

   comm_modify

   comm_style

   compute

   compute_modify

   create_atoms

   create_bonds

   create_box

   delete_atoms

   delete_bonds

   dielectric

   dihedral_coeff

   dihedral_style

   dimension

   displace_atoms

   dump

   dump_custom_vtk

   dump_h5md

   dump_image

   dump_modify

   dump_molfile

   echo

   fix

   fix_modify

   group

   group2ndx

   if

   improper_coeff

   improper_style

   include

   info

   jump

   kspace_modify

   kspace_style

   label

   lattice

   log

   mass

   min_modify

   min_style

   minimize

   molecule

   neb

   neigh_modify

   neighbor

   newton

   next

   package

   pair_coeff

   pair_modify

   pair_style

   pair_write

   partition

   prd

   print

   processors

   python

   quit

   read_data

   read_dump

   read_restart

   region

   replicate

   rerun

   reset_timestep

   restart

   run

   run_style

   set

   shell

   special_bonds

   suffix

   tad

   temper

   thermo

   thermo_modify

   thermo_style

   timer

   timestep

   uncompute

   undump

   unfix

   units

   variable

   velocity

   write_coeff

   write_data

   write_dump

   write_restart



END_RST -->

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