doc page changes

"x".

"x".

How the variable is converted to a text string depends on what style

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

It can be a variable that stores multiple text strings, and return one

of them.  The returned text string can be multiple "words" (space

of them.  The returned text string can be multiple "words" (space

separated) which will then be interpreted as multiple arguments in the

separated) which will then be interpreted as multiple arguments in the

rebuilt and atoms being migrated to new processors.  This also means

rebuilt and atoms being migrated to new processors.  This also means

you may be missing pairwise interactions that need to be computed.

you may be missing pairwise interactions that need to be computed.

The solution is to change the re-neighboring criteria via the

The solution is to change the re-neighboring criteria via the

"neigh_modify"_neigh_modify command.  The safest settings are "delay 0

"neigh_modify"_neigh_modify.html command.  The safest settings are

every 1 check yes".  Second, it may mean that an atom has moved far

"delay 0 every 1 check yes".  Second, it may mean that an atom has

outside a processor's sub-domain or even the entire simulation box.

moved far outside a processor's sub-domain or even the entire

This indicates bad physics, e.g. due to highly overlapping atoms, too

simulation box. This indicates bad physics, e.g. due to highly

large a timestep, etc. :dd

overlapping atoms, too large a timestep, etc. :dd

{Out of range atoms - cannot compute PPPM} :dt

{Out of range atoms - cannot compute PPPM} :dt

rebuilt and atoms being migrated to new processors.  This also means

rebuilt and atoms being migrated to new processors.  This also means

you may be missing pairwise interactions that need to be computed.

you may be missing pairwise interactions that need to be computed.

The solution is to change the re-neighboring criteria via the

The solution is to change the re-neighboring criteria via the

"neigh_modify"_neigh_modify command.  The safest settings are "delay 0

"neigh_modify"_neigh_modify.html command.  The safest settings are

every 1 check yes".  Second, it may mean that an atom has moved far

"delay 0 every 1 check yes".  Second, it may mean that an atom has

outside a processor's sub-domain or even the entire simulation box.

moved far outside a processor's sub-domain or even the entire

This indicates bad physics, e.g. due to highly overlapping atoms, too

simulation box. This indicates bad physics, e.g. due to highly

large a timestep, etc. :dd

overlapping atoms, too large a timestep, etc. :dd

{Out of range atoms - cannot compute PPPMDisp} :dt

{Out of range atoms - cannot compute PPPMDisp} :dt

rebuilt and atoms being migrated to new processors.  This also means

rebuilt and atoms being migrated to new processors.  This also means

you may be missing pairwise interactions that need to be computed.

you may be missing pairwise interactions that need to be computed.

The solution is to change the re-neighboring criteria via the

The solution is to change the re-neighboring criteria via the

"neigh_modify"_neigh_modify command.  The safest settings are "delay 0

"neigh_modify"_neigh_modify.html command.  The safest settings are

every 1 check yes".  Second, it may mean that an atom has moved far

"delay 0 every 1 check yes".  Second, it may mean that an atom has

outside a processor's sub-domain or even the entire simulation box.

moved far outside a processor's sub-domain or even the entire

This indicates bad physics, e.g. due to highly overlapping atoms, too

simulation box. This indicates bad physics, e.g. due to highly

large a timestep, etc. :dd

overlapping atoms, too large a timestep, etc. :dd

{Overflow of allocated fix vector storage} :dt

{Overflow of allocated fix vector storage} :dt

"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -

"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -

"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -

"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -

"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE

"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE

"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf

"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -

"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -

"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -

"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -

"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm

"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm

:line

:line

USER-NC-DUMP package :link(USER-NC-DUMP),h5

Contents: Dump styles for writing NetCDF format files.  NetCDF is a binary,

portable, self-describing file format on top of HDF5. The file format

contents follow the AMBER NetCDF trajectory conventions

(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions to this

convention. This package implements a "dump nc"_dump_nc.html command

and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots

in this format.  See src/USER-NC-DUMP/README for more details.

NetCDF files can be directly visualized with the following tools:

Ovito (http://www.ovito.org/). Ovito supports the AMBER convention

  and all of the above extensions. :ulb,l

VMD (http://www.ks.uiuc.edu/Research/vmd/) :l

AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains

  a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule

The person who created these files is Lars Pastewka at

Karlsruhe Institute of Technology (lars.pastewka at kit.edu).

Contact him directly if you have questions.

:line

USER-OMP package :link(USER-OMP),h5

USER-OMP package :link(USER-OMP),h5

Supporting info:

Supporting info:

order physical processors, or by config files that specify what

order physical processors, or by config files that specify what

physical processors to assign to each MPI rank.  The -reorder switch

physical processors to assign to each MPI rank.  The -reorder switch

simply gives you a portable way to do this without relying on MPI

simply gives you a portable way to do this without relying on MPI

itself.  See the "processors out"_processors command for how to output

itself.  See the "processors out"_processors.html command for how

info on the final assignment of physical processors to the LAMMPS

to output info on the final assignment of physical processors to

simulation domain.

the LAMMPS simulation domain.

-screen file :pre

-screen file :pre

efficiently. Although benefits can be seen by launching a MPI task

efficiently. Although benefits can be seen by launching a MPI task

for every hardware thread, for multinode simulations, we recommend

for every hardware thread, for multinode simulations, we recommend

that OpenMP threads are used for SMT instead, either with the

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

"KOKKOS package"_accelerate_kokkos.html. In the example above, up

to 36X speedups can be observed by using all 36 physical cores with

to 36X speedups can be observed by using all 36 physical cores with

LAMMPS. By using all 72 hardware threads, an additional 10-30%

LAMMPS. By using all 72 hardware threads, an additional 10-30%

Not all styles are supported in the USER-INTEL package. You can mix

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

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

this requires that these packages were installed at build time. This

can performed automatically by using "-sf hybrid intel opt" or

can performed automatically by using "-sf hybrid intel opt" or

"-sf hybrid intel omp" command-line options. Alternatively, the "opt"

"-sf hybrid intel omp" command-line options. Alternatively, the "opt"