diff --git a/doc/dump_h5md.txt b/doc/dump_h5md.txt index 9b83b1e7cf..b0743ba3be 100644 --- a/doc/dump_h5md.txt +++ b/doc/dump_h5md.txt @@ -10,27 +10,43 @@ dump h5md command :h3 [Syntax:] -dump ID group-ID h5md N file.h5 +dump ID group-ID h5md N file.h5 args :pre 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 +args = list of data elements to dump, with their dump "subintervals". +At least one element must be given and image may only be present if +position is specified first. :l + position N_position + image + velocity N_velocity + force N_force + species N_species :pre + :ule [Examples:] -dump h5md1 all h5md 100 dump_h5md.h5 +dump h5md1 all h5md 100 dump_h5md.h5 position 1 image +dump h5md1 all h5md 100 dump_h5md.h5 position 1 velocity 10 :pre [Description:] Dump a snapshot of atom coordinates every N timesteps in the "HDF5"_HDF5_ws -based "H5MD"_h5md file format. +based "H5MD"_h5md file format "(de Buyl et al.)"_#h5md_cpc. +HDF5 files are binary, portable and self-describing. +This dump style will write only one file, on the root node. :link(h5md,http://nongnu.org/h5md/) -This dump style will write only one file, on the root node. +Each data element is written every N*N_element steps. For {image}, no +subinterval is needed as it must be present at the same interval as {position}. +The box information (edges in each dimension) is stored at the same interval +than the {position} element, if present. Else it is stored every N steps. + IMPORTANT NOTE: Because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, the coordinates of an @@ -41,6 +57,12 @@ box. [Restrictions:] +:ulb +The number of atoms per snapshot cannot change with the h5md style. :l +The position data is stored wrapped (box boundaries not enforced, see note above). :l +It is not possible yet to store several groups in a single H5MD file. :l +:ule + 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 @@ -57,3 +79,9 @@ The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library "dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html +:line + +:link(h5md_cpc) +[(de Buyl et al.)] de Buyl, Colberg and Hofling, H5MD: A structured, efficient, +and portable file format for molecular data, Comp. Phys. Comm. 185(6), +1546-1553 (2014) - "\[arXiv:1308.6382\]"_http://arxiv.org/abs/1308.6382/.