diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt index 285220e6c6db278bf172848c5359aa7750d2deed..f1aa4bb6712dd65ca24ba9e97a6f05cd0486e1fa 100644 --- a/doc/src/Build_package.txt +++ b/doc/src/Build_package.txt @@ -42,7 +42,7 @@ packages: "KOKKOS"_Build_extras.html#kokkos, "LATTE"_Build_extras.html#latte, "MEAM"_Build_extras.html#meam, -"MESSAGE"_#Build_extras.html#message, +"MESSAGE"_Build_extras.html#message, "MSCG"_Build_extras.html#mscg, "OPT"_Build_extras.html#opt, "POEMS"_Build_extras.html#poems, @@ -59,7 +59,7 @@ packages: "USER-OMP"_Build_extras.html#user-omp, "USER-QMMM"_Build_extras.html#user-qmmm, "USER-QUIP"_Build_extras.html#user-quip, -"USER-SCAFACOS"_#Build_extras.html#user-scafacos, +"USER-SCAFACOS"_Build_extras.html#user-scafacos, "USER-SMD"_Build_extras.html#user-smd, "USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l) diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt index 714c23f0669eed55eaa15e31f100d117e5e2448c..061c4efb682566ecedbd4cefd93d2a79e95f1cc6 100644 --- a/doc/src/Howto_client_server.txt +++ b/doc/src/Howto_client_server.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -Using LAMMPS in client/server mode +Using LAMMPS in client/server mode :h3 Client/server coupling of two codes is where one code is the "client" and sends request messages to a "server" code. The server responds to diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 443d78922c5ec161c209feadff8b8329b9868977..b0b72f1f131f97c952e7bdd800c8080d58de7d7c 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -92,7 +92,7 @@ as contained in the file name. "USER-QTB"_#PKG-USER-QTB, "USER-QUIP"_#PKG-USER-QUIP, "USER-REAXC"_#PKG-USER-REAXC, -"USER-SCAFACOS"_#USER-SCAFACOS, +"USER-SCAFACOS"_#PKG-USER-SCAFACOS, "USER-SMD"_#PKG-USER-SMD, "USER-SMTBQ"_#PKG-USER-SMTBQ, "USER-SPH"_#PKG-USER-SPH, @@ -1860,7 +1860,7 @@ examples/reax :ul :line -USER-SCAFACOS package :link(USER-SCAFACOS),h4 +USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4 [Contents:] diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt index 27f436ed55e4825886789259778e22f0b51819ce..1fc00bc2e3c0f99a9650e633458d9688a0a665d2 100644 --- a/doc/src/Run_options.txt +++ b/doc/src/Run_options.txt @@ -176,7 +176,7 @@ Option -plog will override the name of the partition log files file.N. :line -[-mpicolor] color :link(mpi) +[-mpicolor] color :link(mpicolor) If used, this must be the first command-line argument after the LAMMPS executable name. It is only used when LAMMPS is launched by an mpirun diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt index 8fae57a718f55599c089712ab73d0ccb36b467ee..db3ef36ddf074cb133d04a95dd5961ae86955e5c 100644 --- a/doc/src/commands_list.txt +++ b/doc/src/commands_list.txt @@ -89,6 +89,8 @@ Commands :h1 run run_style server + server_mc + server_md set shell special_bonds diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt index 5b62d5617d547ff2f2da7b65f484ab0e9022b256..77f6b82c5e2ae076fb83baa2efee86753edce92d 100644 --- a/doc/src/fix_client_md.txt +++ b/doc/src/fix_client_md.txt @@ -50,7 +50,7 @@ md"_server_md.html doc page. Note that when using LAMMPS as an MD client, your LAMMPS input script should not normally contain force field commands, like a -"pair_style"_doc/pair_style.html, "bond_style"_doc/bond_style.html, or +"pair_style"_pair_style.html, "bond_style"_bond_style.html, or "kspace_style"_kspace_style.html commmand. However it is possible for a server code to only compute a portion of the full force-field, while LAMMPS computes the remaining part. Your LAMMPS script can also diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index 7a45ed8086a14cdc201eea9cce5f28f80b4df00e..f2f257b1346240f56256dbd4107198f437d30e27 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -26,6 +26,7 @@ Fixes :h1 fix_bond_swap fix_bond_react fix_box_relax + fix_client_md fix_cmap fix_colvars fix_controller diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 7e4032366400c97f4ca0b61be2e78339e13bb6f2..41973601d7d6f9a6db471304fdbde302c3c6611b 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -133,7 +133,7 @@ the code will stop with an error message. When this option is set to For a typical application, using the automatic parameter generation will provide simulations that are either inaccurate or slow. Using this option is thus not recommended. For guidelines on how to obtain good -parameters, see the "How-To"_Section_howto.html#howto_24 discussion. +parameters, see the "How-To"_Howto_dispersion.html discussion. :line diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index ddf4e15703a126f32d84fa6d626ed15dd36aa5ec..6d8a2894708477ec6b686c2c1c0a8565c6c030a9 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -383,8 +383,8 @@ dimensions. The only exception is if the slab option is set with must be periodic and the z dimension must be non-periodic. The scafacos KSpace style will only be enabled if LAMMPS is built with -the USER-SCAFACOS package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +the USER-SCAFACOS package. See the "Build package"_Build_package.html +doc page for more info. The use of ScaFaCos in LAMMPS does not yet support molecular charged systems where the short-range Coulombic interactions between atoms in diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 72a07945e7aee608931a25c41c6fb45d55f986a9..828863ae67d0afa794ce315b05d69b77587ada5e 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -67,6 +67,7 @@ Howto_multiple.html Howto_replica.html Howto_library.html Howto_couple.html +Howto_client_server.html Howto_output.html Howto_chunk.html Howto_2d.html