status: Accepted in H5MD 1.1
Define a consistent scheme to store lists of particles and particle tuples (pairs, triples, etc.) in an H5MD file. This is of importance to define arbitrary groups of particles or connectivity among particles.
The group I work with does a fair amount of analysis on bond lengths, angle distributions and dihedral angle distributions as validation for force field development. So our main use case for a 'topology' module would be to store the pairs, 3- and 4-tuples of atoms that define the bonds, angles and dihedrals. That said, I have use cases for wanting to store lists of non-bonded pairs of atoms such as opposing carbons on a ring or designated 'endpoint' atoms that can be used to represent the overall orientation of a larger molecule, and in this use case a specific 'bond' list would not really be appropriate. (...) I would definitely agree that a standard storage scheme, would be useful, even if the structure of a 'topology' section varies by module. That way, even if the location of the lists varies, at least the same routines can be used to read/write the data when it is located. As a possible example: <tuple-list> +-- type: String +-- dimension: Integer \-- values: Integer[n-tuples][D] Where a pair list would be dimension(D) = 2, and the values in list would be the particle IDs. Given what Konrad pointed out about flexibility vs. specificity ,the "type" string could have specific list of acceptable values, much like the boundary attribute in the 'box' item. For my particular use cases, I can see the following types of atom-tuple lists being useful as topology/connectivity information: bonds, angles, dihedrals, chains, and 'other'.
A specific problem of 2) is that for non-trivial forcefields (proteins etc.), a simple bond list is not of much use. What you want is *all* forcefield terms. I can't think of any practical use for just the bonds.
A list of particles is an H5MD element:
<list_name>: Integer[N] +-- particles_group: String
N is the length of the list and
particles_group is the
name of an existing group within
Note: Alternatives to store
particles_group point to the respective group in
/particles using a hard/soft link, which ensures that this group
Use an object reference to point to the appropriate particle group. The reference must be an “Object reference” and not a “Dataset region reference” (see https://www.hdfgroup.org/HDF5/doc/RM/RM_H5R.html#Reference-Create).
If the corresponding
particles_group does not possess the
element, the values in
list_name correspond to the indexing of the
particles_group. Else, the values in
be put in correspondence with the equal values in the
If a fill value (see § 6.6 in (“HDF5 User’s guide,” n.d.)) is defined, entries whose value is set to this value are ignored.
A list of tuples is an H5MD element:
<tuples_list_name>: Integer[N,T] +-- particles_group: String
N is the length of the list,
T is the size of the tuples
particles_group is the name an existing group within
T may indicate variable dimensions.
The interpretation of the values stored within the tuples is done as for a list of particles.
If a fill value (see § 6.6 in (“HDF5 User’s guide,” n.d.)) is defined, tuples with all entries set to this value are ignored. If only certain entries within a tuple are set to the fill value, these entries are ignored decreasing the size of this tuple.
**Note:** The scheme should also allow for the storage of neighbour lists, i.e., the size of the tuples is not fixed.
As the lists of particles and tuples above are H5MD elements, they can be stored either as time-dependent groups or time-independent datasets.
As an example, a time-dependent list of pairs is stored as:
<pair_list_name> +-- particles_group: String \-- value: Integer[variable,N,2] \-- step: Integer[variable] \-- time: Float[variable]
The dimension denoted by
N may be variable.
“HDF5 User’s guide.” n.d. http://www.hdfgroup.org/HDF5/doc/UG.