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Fix documentation

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Anthony Scemama 2023-01-02 17:03:42 +01:00
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@ -46,17 +46,21 @@ I/O as for ~sparse~ data but without the need to write indices of the sparse val
For determinant lists (integer bit fields), the ~special~ attribute is present in the type. For determinant lists (integer bit fields), the ~special~ attribute is present in the type.
This means that the source code is not produced by the generator, but hand-written. This means that the source code is not produced by the generator, but hand-written.
Some data may be complex. In that case, the real part should be stored
in the variable, and the imaginary part will be stored in the variable
with the same name suffixed by ~_im~.
#+begin_src python :tangle trex.json :exports none #+begin_src python :tangle trex.json :exports none
{ {
#+end_src #+end_src
* Metadata (metadata group) * Metadata (metadata group)
As we expect our files to be archived in open-data repositories, we As we expect TREXIO files to be archived in open-data repositories,
need to give the possibility to the users to store some metadata we give the possibility to the users to store some metadata inside
inside the files. We propose to store the list of names of the codes the files. We propose to store the list of names of the codes which
which have participated to the creation of the file, a list of have participated to the creation of the file, a list of authors of
authors of the file, and a textual description. the file, and a textual description.
#+NAME: metadata #+NAME: metadata
| Variable | Type | Dimensions (for arrays) | Description | | Variable | Type | Dimensions (for arrays) | Description |
@ -69,7 +73,7 @@ This means that the source code is not produced by the generator, but hand-writt
| ~description~ | ~str~ | | Text describing the content of file | | ~description~ | ~str~ | | Text describing the content of file |
| ~unsafe~ | ~int~ | | ~1~: true, ~0~: false | | ~unsafe~ | ~int~ | | ~1~: true, ~0~: false |
**Note:** ~unsafe~ attribute of the ~metadata~ group indicates **Note:** The ~unsafe~ attribute of the ~metadata~ group indicates
whether the file has been previously opened with ~'u'~ mode. It is whether the file has been previously opened with ~'u'~ mode. It is
automatically written in the file upon the first unsafe opening. If automatically written in the file upon the first unsafe opening. If
the user has checked that the TREXIO file is valid (e.g. using the user has checked that the TREXIO file is valid (e.g. using
@ -181,7 +185,7 @@ This means that the source code is not produced by the generator, but hand-writt
The structure of this group is adapted for the [[https://github.com/dftlibs/numgrid][numgrid]] library. The structure of this group is adapted for the [[https://github.com/dftlibs/numgrid][numgrid]] library.
Feel free to submit a PR if you find missing options/functionalities. Feel free to submit a PR if you find missing options/functionalities.
#+name: grid #+NAME: grid
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|-----------------+---------+------------------+-------------------------------------------------------------------------| |-----------------+---------+------------------+-------------------------------------------------------------------------|
| ~description~ | ~str~ | | Details about the used quadratures can go here | | ~description~ | ~str~ | | Details about the used quadratures can go here |
@ -485,23 +489,25 @@ prim_factor =
| ~power~ | ~int~ | ~(ecp.num)~ | $n_{A q \ell}$ all ECP powers | | ~power~ | ~int~ | ~(ecp.num)~ | $n_{A q \ell}$ all ECP powers |
There might be some confusion in the meaning of the $\ell_{\max}$. There might be some confusion in the meaning of the $\ell_{\max}$.
It can be attributed to the maximum angular momentum occupied It can be attributed to the maximum angular momentum occupied in
in the core orbitals, which are removed by the ECP. the core orbitals, which are removed by the ECP. On the other
On the other hand, it can be attributed to the maximum angular momentum of the hand, it can be attributed to the maximum angular momentum of the
ECP that replaces the core electrons. ECP that replaces the core electrons.
*Note*, that the latter $\ell_{\max}$ is always higher by 1 than the former. *Note*, that the latter $\ell_{\max}$ is always higher by 1 than the former.
*Note for developers*: avoid having variables with similar prefix
*Note for developers*: avoid having variables with similar prefix in their name. in their name. The HDF5 back end might cause issues due to the way
HDF5 back end might cause issues due to the way ~find_dataset~ function works. ~find_dataset~ function works. For example, in the ECP group we
For example, in the ECP group we use ~max_ang_mom~ and not ~ang_mom_max~. use ~max_ang_mom~ and not ~ang_mom_max~. The latter causes issues
The latter causes issues when written before the ~ang_mom~ array in the TREXIO file. when written before the ~ang_mom~ array in the TREXIO file.
*Update*: in fact, the aforementioned issue has only been observed when using HDF5 version 1.10.4 *Update*: in fact, the aforementioned issue has only been observed
installed via ~apt-get~. Installing the same version from the ~conda-forge~ channel and running it in when using HDF5 version 1.10.4 installed via ~apt-get~. Installing
an isolated ~conda~ environment works just fine. Thus, it seems to be a bug in the ~apt~-provided package. the same version from the ~conda-forge~ channel and running it in
If you encounter the aforementioned issue, please report it to our [[https://github.com/TREX-CoE/trexio/issues][issue tracker on GitHub]]. an isolated ~conda~ environment works just fine. Thus, it seems to
be a bug in the ~apt~-provided package.
If you encounter the aforementioned issue, please report it to our
[[https://github.com/TREX-CoE/trexio/issues][issue tracker on GitHub]].
#+CALL: json(data=ecp, title="ecp") #+CALL: json(data=ecp, title="ecp")
@ -663,18 +669,18 @@ power = [
over atomic orbitals. over atomic orbitals.
#+NAME: ao_1e_int #+NAME: ao_1e_int
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|-----------------------+---------+--------------------+-----------------------------------------------------------------------------------| |-----------------------+---------+--------------------+--------------------------------------------------------------------------|
| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (real part, general case) | | ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (real part, general case) | | ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (real part, general case) | | ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
| ~ecp~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ (real part, general case) | | ~ecp~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ |
| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (real part, general case) | | ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
| ~overlap_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (imaginary part) (imaginary part) | | ~overlap_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (imaginary part) |
| ~kinetic_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (imaginary part) | | ~kinetic_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (imaginary part) |
| ~potential_n_e_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (imaginary part) | | ~potential_n_e_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (imaginary part) |
| ~ecp_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ECP}} \vert q \rangle$ (imaginary part) | | ~ecp_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ECP}} \vert q \rangle$ (imaginary part) |
| ~core_hamiltonian_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (imaginary part) | | ~core_hamiltonian_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (imaginary part) |
#+CALL: json(data=ao_1e_int, title="ao_1e_int") #+CALL: json(data=ao_1e_int, title="ao_1e_int")
@ -716,11 +722,21 @@ power = [
\sum_{j=1}^{i-1} \frac{\text{erf}(\vert \mathbf{r}_i - \sum_{j=1}^{i-1} \frac{\text{erf}(\vert \mathbf{r}_i -
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential \mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential
The Cholesky decomposition of the integrals can also be stored:
\[
A_{ijkl} = \sum_{\alpha} G_{il\alpha} G_{jl\alpha}
\]
#+NAME: ao_2e_int #+NAME: ao_2e_int
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|----------+----------------+------------------------------------+-----------------------------------------| |-----------------------+----------------+---------------------------------------------------+-----------------------------------------------|
| ~eri~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Electron repulsion integrals | | ~eri~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Electron repulsion integrals |
| ~eri_lr~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Long-range Electron repulsion integrals | | ~eri_lr~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Long-range Electron repulsion integrals |
| ~eri_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for ERI |
| ~eri_cholesky~ | ~float sparse~ | ~(ao.num, ao.num, ao_2e_int.eri_cholesky_num)~ | Cholesky decomposition of the ERI |
| ~eri_lr_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for long range ERI |
| ~eri_lr_cholesky~ | ~float sparse~ | ~(ao.num, ao.num, ao_2e_int.eri_lr_cholesky_num)~ | Cholesky decomposition of the long range ERI |
#+CALL: json(data=ao_2e_int, title="ao_2e_int") #+CALL: json(data=ao_2e_int, title="ao_2e_int")
@ -728,8 +744,12 @@ power = [
:results: :results:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"ao_2e_int": { "ao_2e_int": {
"eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ] "eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
, "eri_lr" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ] , "eri_lr" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
, "eri_cholesky_num" : [ "dim" , [] ]
, "eri_cholesky" : [ "float sparse", [ "ao_2e_int.eri_cholesky_num", "ao.num", "ao.num" ] ]
, "eri_lr_cholesky_num" : [ "dim" , [] ]
, "eri_lr_cholesky" : [ "float sparse", [ "ao_2e_int.eri_lr_cholesky_num", "ao.num", "ao.num" ] ]
} , } ,
#+end_src #+end_src
:end: :end:
@ -741,8 +761,8 @@ power = [
|------------------+---------+--------------------+--------------------------------------------------------------------------| |------------------+---------+--------------------+--------------------------------------------------------------------------|
| ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) | | ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) |
| ~num~ | ~dim~ | | Number of MOs | | ~num~ | ~dim~ | | Number of MOs |
| ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (real part, general case) | | ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients |
| ~coefficient_im~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (imaginary part, for periodic calculations) | | ~coefficient_im~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (imaginary part) |
| ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted | | ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted |
| ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group | | ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group |
| ~occupation~ | ~float~ | ~(mo.num)~ | Occupation number | | ~occupation~ | ~float~ | ~(mo.num)~ | Occupation number |
@ -775,18 +795,18 @@ power = [
the basis of molecular orbitals. the basis of molecular orbitals.
#+NAME: mo_1e_int #+NAME: mo_1e_int
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|-----------------------+---------+--------------------+-----------------------------------------------------------------------------------| |-----------------------+---------+--------------------+--------------------------------------------------------------------------|
| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (real part, general case) | | ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ |
| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ (real part, general case) | | ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ |
| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (real part, general case) | | ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ |
| ~ecp~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (real part, general case) | | ~ecp~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ |
| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ (real part, general case) | | ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
| ~overlap_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (imaginary part) (imaginary part) | | ~overlap_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (imaginary part) |
| ~kinetic_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ (imaginary part) | | ~kinetic_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ (imaginary part) |
| ~potential_n_e_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (imaginary part) | | ~potential_n_e_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (imaginary part) |
| ~ecp_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (imaginary part) | | ~ecp_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (imaginary part) |
| ~core_hamiltonian_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ (imaginary part) | | ~core_hamiltonian_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ (imaginary part) |
#+CALL: json(data=mo_1e_int, title="mo_1e_int") #+CALL: json(data=mo_1e_int, title="mo_1e_int")
@ -814,12 +834,6 @@ power = [
[[#ao_two_e][AO two-electron integrals section]]. Here, the integrals are given in [[#ao_two_e][AO two-electron integrals section]]. Here, the integrals are given in
the basis of molecular orbitals. the basis of molecular orbitals.
The Cholesky decomposition of the integrals can also be stored:
\[
A_{ijkl} = \sum_{\alpha} G_{il\alpha} G_{jl\alpha}
\]
#+NAME: mo_2e_int #+NAME: mo_2e_int
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|-----------------------+----------------+---------------------------------------------------+-----------------------------------------------| |-----------------------+----------------+---------------------------------------------------+-----------------------------------------------|
@ -845,18 +859,6 @@ power = [
} , } ,
#+end_src #+end_src
:end: :end:
:results:
#+begin_src python :tangle trex.json
"mo_2e_int": {
"eri" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "eri_lr" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "eri_cholesky_num" : [ "dim" , [] ]
, "eri_cholesky" : [ "float sparse", [ "mo_2e_int.eri_cholesky_num", "mo.num", "mo.num" ] ]
, "eri_lr_cholesky_num" : [ "dim" , [] ]
, "eri_lr_cholesky" : [ "float sparse", [ "mo_2e_int.eri_lr_cholesky_num", "mo.num", "mo.num" ] ]
} ,
#+end_src
:
* N-electron basis * N-electron basis
** Slater determinants (determinant group) ** Slater determinants (determinant group)
@ -1228,7 +1230,7 @@ power = [
| ~en_nucleus~ | ~index~ | ~(jastrow.en_num)~ | Nucleus relative to the eN parameter | | ~en_nucleus~ | ~index~ | ~(jastrow.en_num)~ | Nucleus relative to the eN parameter |
| ~een_nucleus~ | ~index~ | ~(jastrow.een_num)~ | Nucleus relative to the eeN parameter | | ~een_nucleus~ | ~index~ | ~(jastrow.een_num)~ | Nucleus relative to the eeN parameter |
| ~ee_scaling~ | ~float~ | | $\kappa$ value in CHAMP Jastrow for electron-electron distances | | ~ee_scaling~ | ~float~ | | $\kappa$ value in CHAMP Jastrow for electron-electron distances |
| ~eN_scaling~ | ~float~ | ~(nucleus.num)~ | $\kappa$ value in CHAMP Jastrow for electron-nucleus distances | | ~en_scaling~ | ~float~ | ~(nucleus.num)~ | $\kappa$ value in CHAMP Jastrow for electron-nucleus distances |
* Quantum Monte Carlo data (qmc group) * Quantum Monte Carlo data (qmc group)