The library.h5 file format

Info

A library file is in the HDF5 format, which divide the data in groups (i.e., "folders") and datasets (i.e., "files"), the latter being array of data. Groups and datasets can have attributes.

The basis set library root contains at least two main (storage) groups: basis_sets and pseudopotentials. They are detailed below.

The basis_sets group

This group contains one subgroup per basis set (a basis set group), for which the name is the basis set name. In each basis set group, there is one subgroup for each atom (a atomic bs group). Finally, in that atomic bs subgroup, there is one atomic bs variant group for each variant. Thus, the following structure is valid:

*
|
+- basis_sets/         # `basis_sets` group
   |
   +- SZV-MOLOPT-GTH/  # a `basis set` group
   |  |
   |  +- C/            # an `atomic bs` group
   |  |  |
   |  |  +- q4/        # an `atomic bs variant` group (see below)
   |  |
   |  +- H/
   |  |  |
   |  |  +- q1/
   |  |
   |  +- ...
   |
   +- DZVP-MOLOPT-GTH/
      |
      +- C/
      |  |
      |  +- q4/
      |
      +- H/
      |  |
      |  +- q1/
      |
      +- ...

Each atomic bs variant group is composed of the following datasets, which are all mandatory:

Name	Shape	Attributes	Info
info	(2,)	---	contains (len(names), len(contractions))
names	(n,)	---	contains n=len(names) names
contraction_{i}_info	(4+n,)	nshell [mandatory]	contains (principle_n, l_min, l_max, nfunc, nshell[0], ..., nshell[n-1]) with n=attrs[nshell]
contraction_{i}_exp_coefs	(nfunc,1+sum(nshell))	---	contains exponents in [:, 0] and coefficients in [:, 1:]

The two last datasets are repeated with i=[0:len(contractions)].

Thus, the following structure, e.g., is valid:

*
|
+ basis_sets/TZVP-GTH/C/q4/   # contains two contractions
  |
  +- info                     # contains (2, 2)
  +- names                    # contains (TZVP-GTH-q4, TZVP-GTH)
  +- contraction_0_info       # contains (2, 0, 1, 5, 3, 3)
  |                           # and has attribute nshell=2
  +- contraction_0_exp_coefs  # of shape (5, 7)
  +- contraction_1_info       # contains (3, 2, 2, 1, 1)
  |                           # and has attribute nshell=1
  +- contraction_1_exp_coefs  # of shape (1, 2)

The pseudopotentials group

Again, this group contains one subgroup per pseudopotential familly (a pp family group), which name is the family name. In each pp family group, there is one subgroup for each basis set (a atomic pp group). Finally, in that atomic pp subgroup, there is one atomic pp variant group for each variant.

Thus, the following structure is valid:

*
|
+- pseudopotentials/   # the `pseudopotentials` group
   |
   +- GTH-BLYP/        # a `pp family group`
   |  |
   |  +- C/            # an `atomic pp` group
   |  |  |
   |  |  +- q4/        # an `atomic pp variant` group (see below)
   |  |
   |  +- H/
   |  |  |
   |  |  +- q1/
   |  |
   |  +- ...
   |
   +- GTH-PBE/
      |
      +- C/
      |  |
      |  +- q4/
      |
      +- ...

Each atomic pp variant group is composed of the following datasets, which are all mandatory:

Name	Shape	Attributes	Info
info	(3+n,)	nelec [mandatory]	contains (len(names), len(lcoefs), len(nlprojectors), nelec[0], ... nelec[n-1]) with n=attrs[nelec]
names	(n,)	---	contains n=len(names) names
local_radius_coefs	(1+n,)	---	contains (lradius, lcoef[0],..., lcoefs[n-1]) with n=len(lcoefs)
nlprojector_{i}_radius_coefs	(1+n,)	nfunc [mandatory]	contains (nlradius, nlcoefs[triu(n)[0]], ..., nlcoefs[triu(n)[n-1]]) with n=attrs[nfunc] and triu(N) gives the list of the upper triangular indices of a square matrix of size N.

The last dataset is repeated with i=[0:len(nlprojectors)].

The following structure, e.g., is valid:

*
|
+- pseudopotentials/GTH-BLYP/Ne/q8/
   |
   +- info                        # contains (2, 2, 2, 2, 6)
   |                              # and has attribute nelec=2
   +- names                       # contains (GTH-BLYP-q8, GTH-BLYP)
   +- local_radius_coefs          # of shape (3,)
   +- nlprojector_0_radius_coefs  # of shape (4,)
   |                              # and has attribute nfunc=2
   +- nlprojector_1_radius_coefs  # of shape (2,)
                                  # and has attribute nfunc=1

Metadata

The file may have the date_build attribute, indicating when it was created.

Each basis set and pp familly group might also have the following attributes:

Name	Type	Description
description	str	Description of the data
references	array	One-dimensional array of URLs to reference papers (DOI) or sources.
tags	array	One-dimensional array of tags

Each atomic bs variant and atomic pp variant may present a source attribute which indicate the URL to the source of this variant.

Those attributes are optional.