From d0286b3de1126aaad678c3c9780e28c88c1884d2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 2 Jun 2019 20:19:17 -0400 Subject: [PATCH 1/4] remove mention of USER-CUDA package and fix typo --- doc/src/variable.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/variable.txt b/doc/src/variable.txt index e90e9bd04b..d75391d354 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -865,7 +865,7 @@ The {is_active()} function allows to query for active settings which are grouped by categories. Currently supported categories and arguments are: -{package} (argument = {cuda} or {gpu} or {intel} or {kokkos} or {omp}) +{package} (argument = {gpu} or {intel} or {kokkos} or {omp}) {newton} (argument = {pair} or {bond} or {any}) {pair} (argument = {single} or {respa} or {manybody} or {tail} or {shift}) {comm_style} (argument = {brick} or {tiled}) @@ -894,7 +894,7 @@ kspace_style pppm :pre Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step -timestep $(2.0*(1.0+*is_active(pair,respa)) +timestep $(2.0*(1.0+2.0*is_active(pair,respa)) if $(is_active(pair,respa)) then "run_style respa 4 3 2 2 improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2 improper 1 pair 2 kspace 3" :pre The {is_defined()} function allows to query categories like {compute}, From 674e3975a8e3227ce60ac1d5894a727e0483199d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 2 Jun 2019 21:41:28 -0400 Subject: [PATCH 2/4] add section to the Commands chapter listing and explaining removed packages and styles --- doc/src/Commands.txt | 7 +++++ doc/src/Commands_removed.txt | 55 ++++++++++++++++++++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 doc/src/Commands_removed.txt diff --git a/doc/src/Commands.txt b/doc/src/Commands.txt index bb3fab3683..bcbbe524a8 100644 --- a/doc/src/Commands.txt +++ b/doc/src/Commands.txt @@ -33,6 +33,11 @@ commands in it are used to define a LAMMPS simulation. Commands_bond Commands_kspace +.. toctree:: + :maxdepth: 1 + + Commands_removed + END_RST --> @@ -49,5 +54,7 @@ END_RST --> "Bond, angle, dihedral, improper commands"_Commands_bond.html "KSpace solvers"_Commands_kspace.html :all(b) +"Removed commands and packages"_Commands_removed.html :all(b) + diff --git a/doc/src/Commands_removed.txt b/doc/src/Commands_removed.txt new file mode 100644 index 0000000000..dc41c81981 --- /dev/null +++ b/doc/src/Commands_removed.txt @@ -0,0 +1,55 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html) + +:line + +Removed commands and packages :h3 + +This page lists LAMMPS commands and packages that have been removed from +the distribution and provides suggestions for alternatives or replacements. + +Fix ave/spatial and fix ave/spatial/sphere :h4 + +The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS +since they were superseded by the more general and extensible "chunk +infrastructure". Here the system is partitioned in one of many possible +ways through the "compute chunk/atom"_compute_chunk_atom.html command +and then averaging is done using "fix ave/chunk"_fix_ave_chunk.html. +Please refer to the "chunk HOWTO"_Howto_chunk.html section for an overview. + +MEAM package :h4 + +The MEAM package has been removed since it was superseded by the +"USER-MEAMC package"_Package_details.html#PKG-USER-MEAMC. The code in +the USER-MEAMC package is a translation of the Fortran code of MEAM into C++, +which removes several restrictions (e.g. there can be multiple instances +in hybrid pair styles) and allows for some optimizations leading +to better performance. The new pair style "meam/c"_pair_meamc.html has +the exact same syntax as the old "meam" pair style and thus pair style +"meam"_pair_meamc.html is an alias to the new style and backward +compatibility of old inputs is preserved. + +REAX package :h4 + +The REAX package has been removed since it was superseded by the +"USER-REAXC package"_Package_details.html#PKG-USER-REAXC. The USER-REAXC +package has been tested to yield equivalent results to the REAX package, +offers better performance, supports OpenMP multi-threading via USER-OMP, +and GPU and threading parallelization through KOKKOS. The new pair styles +are not syntax compatible with the removed reax pair style, so input +files will have to be adapted. + +USER-CUDA package :h4 + +The USER-CUDA package had been removed, since it had been unmaintained +for a long time and had known bugs and problems. Significant parts of +the design were transferred to the +"KOKKOS package"_Package_details.html#PKG-KOKKOS, which has similar +performance characteristics on Nvidia GPUs. Both, the KOKKOS +and the "GPU package"_Package_details.html#PKG-GPU are maintained +and allow running LAMMPS with GPU acceleration. + From 5f79a9ef805003abb21a645fbc97ad3b6396f21d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 2 Jun 2019 21:51:06 -0400 Subject: [PATCH 3/4] mention dummy commands with error messages that have been added instead of removed commands --- doc/src/Commands_removed.txt | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/src/Commands_removed.txt b/doc/src/Commands_removed.txt index dc41c81981..934f826e0c 100644 --- a/doc/src/Commands_removed.txt +++ b/doc/src/Commands_removed.txt @@ -11,6 +11,9 @@ Removed commands and packages :h3 This page lists LAMMPS commands and packages that have been removed from the distribution and provides suggestions for alternatives or replacements. +LAMMPS has special dummy styles implemented, that will stop LAMMPS and +print a suitable error message in most cases, when a style/command is used +that has been removed. Fix ave/spatial and fix ave/spatial/sphere :h4 From a98162694811396c2a02f652056b644a51c88547 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 3 Jun 2019 09:01:22 -0400 Subject: [PATCH 4/4] mention restart2data as removed feature as well --- doc/src/Commands_removed.txt | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/doc/src/Commands_removed.txt b/doc/src/Commands_removed.txt index 934f826e0c..1eee6e45e0 100644 --- a/doc/src/Commands_removed.txt +++ b/doc/src/Commands_removed.txt @@ -56,3 +56,11 @@ performance characteristics on Nvidia GPUs. Both, the KOKKOS and the "GPU package"_Package_details.html#PKG-GPU are maintained and allow running LAMMPS with GPU acceleration. +restart2data tool :h4 + +The functionality of the restart2data tool has been folded into the +LAMMPS executable directly instead of having a separate tool. A +combination of the commands "read_restart"_read_restart.html and +"write_data"_write_data.html can be used to the same effect. For added +convenience this conversion can also be triggered by "command line +flags"_Run_options.html