+
+ +
+

dump h5md command

+
+

Syntax

+
dump ID group-ID h5md N file.h5 args
+
+
+
    +
  • ID = user-assigned name for the dump
    • +
  • group-ID = ID of the group of atoms to be imaged
    • +
  • 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 doc page)
    • +
  • N = dump every this many timesteps
    • +
  • file.h5 = name of file to write to
    • +
  • 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.
    • +
+
+position options
+image
+velocity options
+force options
+species options
+file_from ID: do not open a new file, re-use the already opened file from dump ID
+box value = yes or no
+create_group value = yes or no
+author value = quoted string
+
+

For the elements position, velocity, force and species, one +may specify a sub-interval to write the data only every N_element +iterations of the dump (i.e. every N*N_element time steps). This is +specified by the option

+
every N_element
+
+
+

that follows directly the element declaration.

+
+
+

Examples

+
dump h5md1 all h5md 100 dump_h5md.h5 position image
+dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
+dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe"
+
+
+
+
+

Description

+

Dump a snapshot of atom coordinates every N timesteps in the +HDF5 based H5MD file format (de Buyl). +HDF5 files are binary, portable and self-describing. This dump style +will write only one file, on the root node.

+

Several dumps may write to the same file, by using file_from and +referring to a previously defined dump. Several groups may also be +stored within the same file by defining several dumps. A dump that +refers (via file_from) to an already open dump ID and that concerns +another particle group must specify create_group yes.

+

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. image must be given after position in any case. 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.

+
+

Warning

+

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.

+
+

Use from write_dump:

+

It is possible to use this dump style with the +write_dump command. In this case, the subintervals +must not be set at all. The write_dump command can be used either to +create a new file or to add current data to an existing dump file by +using the file_from keyword.

+

Typically, the species data is fixed. The following two commands +store the position data every 100 timesteps, with the image data, and +store once the species data in the same file.

+
dump h5md1 all h5md 100 dump.h5 position image
+write_dump all h5md dump.h5 file_from h5md1 species
+
+
+
+
+
+

Restrictions

+

The number of atoms per snapshot cannot change with the h5md style. +The position data is stored wrapped (box boundaries not enforced, see +note above). Only orthogonal domains are currently supported. This is +a limitation of the present dump h5md command and not of H5MD itself.

+

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) on your system. The library ch5md is compiled with the +h5cc wrapper provided by the HDF5 library.

+
+
+ +
+ + +
+