Syntax: +
+dump ID group-ID h5md N file.h5 +
+Examples: +
+dump h5md1 all h5md 100 dump_h5md.h5 +
+Description: +
+Dump a snapshot of atom coordinates every N timesteps in the HDF5 +based H5MD file format. +
+ + +This dump style will write only one file, on the root node. +
+IMPORTANT NOTE: Because periodic boundary conditions are enforced only +on timesteps when neighbor lists are rebuilt, the coordinates of an +atom written to a dump file may be slightly outside the simulation +box. +
+Restrictions: +
+The h5md dump style is part of the USER-H5MD package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info. It also requires +(i) building the ch5md library provided with LAMMPS (See the Making +LAMMPS section for more info.) and +(ii) having the HDF5 library installed (C bindings are sufficient). +The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library. +
+ + +Related commands: +
+dump, dump_modify, undump +
+ diff --git a/doc/dump_h5md.txt b/doc/dump_h5md.txt new file mode 100644 index 0000000000..9b83b1e7cf --- /dev/null +++ b/doc/dump_h5md.txt @@ -0,0 +1,59 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +dump h5md command :h3 + +[Syntax:] + +dump ID group-ID h5md N file.h5 + +ID = user-assigned name for the dump :ulb,l +group-ID = ID of the group of atoms to be imaged :l +h5md = 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.h5 = name of file to write to :l +:ule + +[Examples:] + +dump h5md1 all h5md 100 dump_h5md.h5 + +[Description:] + +Dump a snapshot of atom coordinates every N timesteps in the "HDF5"_HDF5_ws +based "H5MD"_h5md file format. + +:link(h5md,http://nongnu.org/h5md/) + +This dump style will write only one file, on the root node. + +IMPORTANT NOTE: Because periodic boundary conditions are enforced only +on timesteps when neighbor lists are rebuilt, the coordinates of an +atom written to a dump file may be slightly outside the simulation +box. + +:line + +[Restrictions:] + +The {h5md} dump style is part of the USER-H5MD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. It also requires +(i) building the ch5md library provided with LAMMPS (See the "Making +LAMMPS"_Section_start.html#start_3 section for more info.) and +(ii) having the "HDF5"_HDF5_ws library installed (C bindings are sufficient). +The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library. + +:link(HDF5_ws,http://www.hdfgroup.org/HDF5/) + +:line + +[Related commands:] + +"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html +