Loading doc/src/Section_commands.txt +1 −1 Original line number Diff line number Diff line Loading @@ -106,7 +106,7 @@ the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and "x". How the variable is converted to a text string depends on what style of variable it is; see the "variable"_variable doc page for details. of variable it is; see the "variable"_variable.html doc page for details. It can be a variable that stores multiple text strings, and return one of them. The returned text string can be multiple "words" (space separated) which will then be interpreted as multiple arguments in the Loading doc/src/Section_errors.txt +15 −15 Original line number Diff line number Diff line Loading @@ -8116,11 +8116,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the "neigh_modify"_neigh_modify command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd "neigh_modify"_neigh_modify.html command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd {Out of range atoms - cannot compute PPPM} :dt Loading @@ -8132,11 +8132,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the "neigh_modify"_neigh_modify command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd "neigh_modify"_neigh_modify.html command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd {Out of range atoms - cannot compute PPPMDisp} :dt Loading @@ -8148,11 +8148,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the "neigh_modify"_neigh_modify command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd "neigh_modify"_neigh_modify.html command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd {Overflow of allocated fix vector storage} :dt Loading doc/src/Section_start.txt +3 −3 Original line number Diff line number Diff line Loading @@ -1601,9 +1601,9 @@ implementations, either by environment variables that specify how to order physical processors, or by config files that specify what physical processors to assign to each MPI rank. The -reorder switch simply gives you a portable way to do this without relying on MPI itself. See the "processors out"_processors command for how to output info on the final assignment of physical processors to the LAMMPS simulation domain. itself. See the "processors out"_processors.html command for how to output info on the final assignment of physical processors to the LAMMPS simulation domain. -screen file :pre Loading doc/src/accelerate_intel.txt +2 −2 Original line number Diff line number Diff line Loading @@ -151,7 +151,7 @@ can start running so that the CPU pipeline is still being used efficiently. Although benefits can be seen by launching a MPI task for every hardware thread, for multinode simulations, we recommend that OpenMP threads are used for SMT instead, either with the USER-INTEL package, "USER-OMP package"_accelerate_omp.html", or USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or "KOKKOS package"_accelerate_kokkos.html. In the example above, up to 36X speedups can be observed by using all 36 physical cores with LAMMPS. By using all 72 hardware threads, an additional 10-30% Loading Loading @@ -343,7 +343,7 @@ when using offload. Not all styles are supported in the USER-INTEL package. You can mix the USER-INTEL package with styles from the "OPT"_accelerate_opt.html package or the "USER-OMP package"_accelerate_omp.html". Of course, package or the "USER-OMP package"_accelerate_omp.html. Of course, this requires that these packages were installed at build time. This can performed automatically by using "-sf hybrid intel opt" or "-sf hybrid intel omp" command-line options. Alternatively, the "opt" Loading doc/src/atom_style.txt +1 −1 Original line number Diff line number Diff line Loading @@ -166,7 +166,7 @@ stores a per-particle mass and size and orientation (i.e. the corner points of the triangle). The {template} style allows molecular topolgy (bonds,angles,etc) to be defined via a molecule template using the "molecule"_molecule.txt defined via a molecule template using the "molecule"_molecule.html command. The template stores one or more molecules with a single copy of the topology info (bonds,angles,etc) of each. Individual atoms only store a template index and template atom to identify which Loading Loading
doc/src/Section_commands.txt +1 −1 Original line number Diff line number Diff line Loading @@ -106,7 +106,7 @@ the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and "x". How the variable is converted to a text string depends on what style of variable it is; see the "variable"_variable doc page for details. of variable it is; see the "variable"_variable.html doc page for details. It can be a variable that stores multiple text strings, and return one of them. The returned text string can be multiple "words" (space separated) which will then be interpreted as multiple arguments in the Loading
doc/src/Section_errors.txt +15 −15 Original line number Diff line number Diff line Loading @@ -8116,11 +8116,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the "neigh_modify"_neigh_modify command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd "neigh_modify"_neigh_modify.html command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd {Out of range atoms - cannot compute PPPM} :dt Loading @@ -8132,11 +8132,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the "neigh_modify"_neigh_modify command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd "neigh_modify"_neigh_modify.html command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd {Out of range atoms - cannot compute PPPMDisp} :dt Loading @@ -8148,11 +8148,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the "neigh_modify"_neigh_modify command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd "neigh_modify"_neigh_modify.html command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly overlapping atoms, too large a timestep, etc. :dd {Overflow of allocated fix vector storage} :dt Loading
doc/src/Section_start.txt +3 −3 Original line number Diff line number Diff line Loading @@ -1601,9 +1601,9 @@ implementations, either by environment variables that specify how to order physical processors, or by config files that specify what physical processors to assign to each MPI rank. The -reorder switch simply gives you a portable way to do this without relying on MPI itself. See the "processors out"_processors command for how to output info on the final assignment of physical processors to the LAMMPS simulation domain. itself. See the "processors out"_processors.html command for how to output info on the final assignment of physical processors to the LAMMPS simulation domain. -screen file :pre Loading
doc/src/accelerate_intel.txt +2 −2 Original line number Diff line number Diff line Loading @@ -151,7 +151,7 @@ can start running so that the CPU pipeline is still being used efficiently. Although benefits can be seen by launching a MPI task for every hardware thread, for multinode simulations, we recommend that OpenMP threads are used for SMT instead, either with the USER-INTEL package, "USER-OMP package"_accelerate_omp.html", or USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or "KOKKOS package"_accelerate_kokkos.html. In the example above, up to 36X speedups can be observed by using all 36 physical cores with LAMMPS. By using all 72 hardware threads, an additional 10-30% Loading Loading @@ -343,7 +343,7 @@ when using offload. Not all styles are supported in the USER-INTEL package. You can mix the USER-INTEL package with styles from the "OPT"_accelerate_opt.html package or the "USER-OMP package"_accelerate_omp.html". Of course, package or the "USER-OMP package"_accelerate_omp.html. Of course, this requires that these packages were installed at build time. This can performed automatically by using "-sf hybrid intel opt" or "-sf hybrid intel omp" command-line options. Alternatively, the "opt" Loading
doc/src/atom_style.txt +1 −1 Original line number Diff line number Diff line Loading @@ -166,7 +166,7 @@ stores a per-particle mass and size and orientation (i.e. the corner points of the triangle). The {template} style allows molecular topolgy (bonds,angles,etc) to be defined via a molecule template using the "molecule"_molecule.txt defined via a molecule template using the "molecule"_molecule.html command. The template stores one or more molecules with a single copy of the topology info (bonds,angles,etc) of each. Individual atoms only store a template index and template atom to identify which Loading
