ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Update documentation of h5md dump style.

Browse Source
This commit is contained in:
Pierre de Buyl
2014-08-22 11:12:10 +02:00
committed by Pierre de Buyl
parent 8ee4b05d2b
commit e5c8e4acdc
1 changed files with 32 additions and 4 deletions
Download Patch File Download Diff File Expand all files Collapse all files

36
doc/dump_h5md.txt
View File

@ -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/.