Commit 2de01cef authored by Norbert Podhorszki's avatar Norbert Podhorszki
Browse files

Dump atom/adios and dump custom/adios command notifications

parent 1179beb5

doc/src/Commands_all.txt

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@@ -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,

doc/src/commands_list.txt

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@@ -32,6 +32,7 @@ Commands :h1 
   dimension

   displace_atoms

   dump

   dump_adios

   dump_cfg_uef

   dump_h5md

   dump_image

doc/src/dump.txt

+4 −1
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@@ -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

doc/src/dump_adios.txt

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"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

examples/USER/adios/in.adios_balance

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@@ -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

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