diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt index f137ccffd9..e6f364f2c9 100644 --- a/doc/src/Commands_all.txt +++ b/doc/src/Commands_all.txt @@ -48,6 +48,7 @@ An alphabetic list of all general LAMMPS commands. "dimension"_dimension.html, "displace_atoms"_displace_atoms.html, "dump"_dump.html, +"dump adios"_dump_adios.html, "dump image"_dump_image.html, "dump_modify"_dump_modify.html, "dump movie"_dump_image.html, diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt index 78fa9fbf87..9b3185bda8 100644 --- a/doc/src/commands_list.txt +++ b/doc/src/commands_list.txt @@ -32,6 +32,7 @@ Commands :h1 dimension displace_atoms dump + dump_adios dump_cfg_uef dump_h5md dump_image diff --git a/doc/src/dump.txt b/doc/src/dump.txt index 9999f5bbff..a776ff70fc 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -13,6 +13,7 @@ dump command :h3 "dump netcdf"_dump_netcdf.html command :h3 "dump image"_dump_image.html command :h3 "dump movie"_dump_image.html command :h3 +"dump adios"_dump_adios.html command :h3 [Syntax:] @@ -27,10 +28,12 @@ args = list of arguments for a particular style :l {atom} args = none {atom/gz} args = none {atom/mpiio} args = none + {atom/adios} args = none, discussed on "dump adios"_dump_adios.html doc page {cfg} args = same as {custom} args, see below {cfg/gz} args = same as {custom} args, see below {cfg/mpiio} args = same as {custom} args, see below {custom}, {custom/gz}, {custom/mpiio} args = see below + {custom/adios} args = same as {custom} args, discussed on "dump adios"_dump_adios.html doc page {dcd} args = none {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page {image} args = discussed on "dump image"_dump_image.html doc page @@ -653,7 +656,7 @@ package"_Build_package.html doc page for more info. [Related commands:] -"dump h5md"_dump_h5md.html, "dump image"_dump_image.html, +"dump adios"_dump_adios.html "dump h5md"_dump_h5md.html, "dump image"_dump_image.html, "dump molfile"_dump_molfile.html, "dump_modify"_dump_modify.html, "undump"_undump.html diff --git a/doc/src/dump_adios.txt b/doc/src/dump_adios.txt new file mode 100644 index 0000000000..d6424d664a --- /dev/null +++ b/doc/src/dump_adios.txt @@ -0,0 +1,73 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +dump atoms/adios command :h3 +dump custom/adios command :h3 + +[Syntax:] + +dump ID group-ID atoms/adios N file.bp :pre +dump ID group-ID custom/adios N file.bp args :pre + +ID = user-assigned name for the dump :ulb,l +group-ID = ID of the group of atoms to be imaged :l +adios = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l +N = dump every this many timesteps :l +file.bp = name of file/stream to write to :l +args = same options as in "{dump custom}"_dump.html command :l +:ule + + +[Examples:] + +dump adios1 all atom/adios 100 atoms.bp +dump 4a all custom/adios 100 dump_adios.bp id v_p x y z +dump 2 subgroup custom/adios 100 dump_adios.bp mass type xs ys zs vx vy vz :pre + +[Description:] + +Dump a snapshot of atom coordinates every N timesteps in the +"ADIOS"_adios based "BP" file format, or using different I/O solutions in ADIOS, +to a stream that can be read on-line by another program. +ADIOS-BP files are binary, portable and self-describing. + +:link(adios,https://github.com/ornladios/ADIOS2) + + +[Use from write_dump:] + +It is possible to use these dump styles with the +"write_dump"_write_dump.html command. In this case, the sub-intervals +must not be set at all. The write_dump command can be used to +create a new file at each individual dump. + +dump 4 all atom/adios 100 dump.bp +write_dump all atom/adios singledump.bp :pre + +:line + +[Restrictions:] + +The number of atoms per snapshot CAN change with the adios style. +When using the ADIOS tool 'bpls' to list the content of a .bp file, +bpls will print "__" for the size of the output table indicating that +its size is changing every step. + +The {atom/adios} and {custom/adios} dump styles are part of the USER-adios package. +They are only enabled if LAMMPS was built with that package. See the +"Build package"_Build_package.html doc page for more info. + + +:line + +[Related commands:] + +"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html + +:line + diff --git a/examples/USER/adios/in.adios_balance b/examples/USER/adios/in.adios_balance index b44870afbb..d89ae52b41 100644 --- a/examples/USER/adios/in.adios_balance +++ b/examples/USER/adios/in.adios_balance @@ -54,3 +54,4 @@ thermo_style custom step temp epair press f_10[3] f_10 thermo 100 run 200 +write_dump all atom/adios balance_atom_final.bp