# dump h5md command

## Syntax

``` LAMMPS
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](dump) doc page)

-   N = dump every this many timesteps

-   file.h5 = name of file to write to

-   args = *position* options or *image* or *velocity* options or
    *force* options or *species* options or *file_from* ID or *box*
    value or *create_group* value or *author* value = list of data
    elements to dump, with their dump \"sub-intervals\"

        *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

Note that at least one element must be specified and that *image* may
only be present if *position* is specified first.

For the elements *position*, *velocity*, *force* and *species*, a
sub-interval may be specified to write the data only every N_element
iterations of the dump (i.e. every N\*N_element time steps). This is
specified by this option directly following the element declaration:

    options = *every* N_element

## Examples

``` LAMMPS
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](https://www.hdfgroup.org/solutions/hdf5/)\_ based
[H5MD](https://nongnu.org/h5md/)\_ file format [(de Buyl)](h5md_cpc).
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
sub-interval 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.

:::: note
::: title
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.
::::

**Use from write_dump:**

It is possible to use this dump style with the [write_dump](write_dump)
command. In this case, the sub-intervals 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.

``` LAMMPS
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 H5MD package. It is only enabled if
LAMMPS was built with that package. See the [Build
package](Build_package) page for more info. It also requires (i)
building the ch5md library provided with LAMMPS (See the [Build
package](Build_package) page for more info.) and (ii) having the
[HDF5](https://www.hdfgroup.org/solutions/hdf5/)\_ library installed (C
bindings are sufficient) on your system. The library ch5md is compiled
with the h5cc wrapper provided by the HDF5 library.

------------------------------------------------------------------------

## Related commands

[dump](dump), [dump_modify](dump_modify), [undump](undump)

------------------------------------------------------------------------

::: {#h5md_cpc}
**(de Buyl)** de Buyl, Colberg and Hofling, H5MD: A structured,
efficient, and portable file format for molecular data, Comp. Phys.
Comm. 185(6), 1546-1553 (2014)
-[\[arXiv:1308.6382\]](https://arxiv.org/abs/1308.6382/)\_.
:::