diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt index 48069d3120048e9d59ead6a3f2959be296d078de..0cf433d53a5bef331c65654a97d76eb2f7347796 100644 --- a/doc/src/Commands_bond.txt +++ b/doc/src/Commands_bond.txt @@ -95,7 +95,7 @@ OPT. "helix (o)"_dihedral_helix.html, "multi/harmonic (o)"_dihedral_multi_harmonic.html, "nharmonic (o)"_dihedral_nharmonic.html, -"opls (iko)"_dihedral_opls.htm;, +"opls (iko)"_dihedral_opls.html, "quadratic (o)"_dihedral_quadratic.html, "spherical (o)"_dihedral_spherical.html, "table (o)"_dihedral_table.html, diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt index 1e737df655462c2fc0e1059ac7bc56ecdb120287..4dfe4e2f6c88eab104e813e0051138c25434b4ef 100644 --- a/doc/src/Howto_spherical.txt +++ b/doc/src/Howto_spherical.txt @@ -159,7 +159,7 @@ ellipsoidal particles: The advantage of these fixes is that those which thermostat the particles include the rotational degrees of freedom in the temperature -calculation and thermostatting. The "fix langevin"_fix_langevin +calculation and thermostatting. The "fix langevin"_fix_langevin.html command can also be used with its {omgea} or {angmom} options to thermostat the rotational degrees of freedom for spherical or ellipsoidal particles. Other thermostatting fixes only operate on the diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 892774be383f379ade01ca6265e69ea6b6f4bcfc..e4ca846cc37cd2302e8f40bb8ee439f05f4f19c0 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -297,7 +297,7 @@ lib/gpu/README "Section 2.6 -sf gpu"_Run_options.html "Section 2.6 -pk gpu"_Run_options.html "package gpu"_package.html -"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g) +"Commands all"_lc pages (pair,kspace) for styles followed by (g) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line @@ -412,7 +412,7 @@ lib/kokkos/README "Section 2.6 -sf kk"_Run_options.html "Section 2.6 -pk kokkos"_Run_options.html "package kokkos"_package.html -"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k) +"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (k) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line @@ -1392,7 +1392,7 @@ src/USER-INTEL/README "Section 2.6 -sf intel"_Run_options.html "Section 2.6 -pk intel"_Run_options.html "package intel"_package.html -"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i) +"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (i) src/USER-INTEL/TEST "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul @@ -1698,7 +1698,7 @@ src/USER-OMP/README "Section 2.6 -sf omp"_Run_options.html "Section 2.6 -pk omp"_Run_options.html "package omp"_package.html -"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o) +"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (o) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt index 029c8f831cc537da73f898ac5ba3172036a54faf..3854552188857b0c90090520abc7324ffae8e475 100644 --- a/doc/src/Python_call.txt +++ b/doc/src/Python_call.txt @@ -59,7 +59,7 @@ and callbacks to LAMMPS. The "fix python/invoke"_fix_python_invoke.html command can execute Python code at selected timesteps during a simulation run. -The "pair_style python"_pair_python command allows you to define +The "pair_style python"_pair_python.html command allows you to define pairwise potentials as python code which encodes a single pairwise interaction. This is useful for rapid-developement and debugging of a new potential. diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt index ef876a7d42108a3ae8aad4f6c2f65670f65e0223..3b25ade4d29cb02ade5c092b2a20b0c5f8c37b19 100644 --- a/doc/src/Speed_intel.txt +++ b/doc/src/Speed_intel.txt @@ -400,7 +400,7 @@ within the input script to automatically append the "omp" suffix to styles when USER-INTEL styles are not available. NOTE: For simulations on higher node counts, add "processors * * * -grid numa"_processors.html" to the beginning of the input script for +grid numa"_processors.html to the beginning of the input script for better scalability. When running on many nodes, performance might be better when using diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt index 6c837885cd4dd5272e9b7925d84aa01ee8f9ab79..4c87091e7e20c675413c605738ec776813b52b9b 100644 --- a/doc/src/Speed_packages.txt +++ b/doc/src/Speed_packages.txt @@ -72,7 +72,7 @@ Lennard-Jones "pair_style lj/cut"_pair_lj.html: "pair_style lj/cut/opt"_pair_lj.html :ul To see what accelerate styles are currently available for a particular -style, find the style name in the "Commands_all"_Commands_all.html +style, find the style name in the "Commands_all"_lc style pages (fix,compute,pair,etc) and see what suffixes are listed (g,i,k,o,t) with it. The doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list