mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-07-22 10:47:43 +02:00
add headers to tables and group names
This commit is contained in:
parent
81755ed821
commit
a328741a0c
111
trex.org
111
trex.org
@ -2,22 +2,29 @@
|
||||
#+STARTUP: latexpreview
|
||||
#+SETUPFILE: docs/theme.setup
|
||||
|
||||
This page contains information about the general structure of the
|
||||
TREXIO library. The source code of the library can be automatically
|
||||
generated based on the contents of the ~trex.json~ file, which is
|
||||
compiled from different sections (groups) presented below.
|
||||
|
||||
All the quantities are saved in atomic units.
|
||||
For more information about the automatic generation on the source code
|
||||
or regarding possible modifications, please contact the TREXIO developers.
|
||||
|
||||
All quantities are saved in TREXIO file in atomic units.
|
||||
The dimensions of the arrays in the tables below are given in
|
||||
column-major order (as in Fortran), and the ordering of the dimensions
|
||||
is reversed in the produces JSON configuration file as the library is
|
||||
is reversed in the produced JSON configuration file as the library is
|
||||
written in C.
|
||||
|
||||
In Fortran, the arrays are 1-based and in most other languages the
|
||||
arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
arrays are 0-based. Hence, we introduce the ~index~ type which is an
|
||||
1-based ~int~ in the Fortran interface and 0-based otherwise.
|
||||
|
||||
#+begin_src python :tangle trex.json
|
||||
#+begin_src python :tangle trex.json :exports none
|
||||
{
|
||||
#+end_src
|
||||
|
||||
* Metadata
|
||||
* Metadata (metadata group)
|
||||
|
||||
As we expect our files to be archived in open-data repositories, we
|
||||
need to give the possibility to the users to store some metadata
|
||||
@ -26,6 +33,8 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
authors of the file, and a textual description.
|
||||
|
||||
#+NAME: metadata
|
||||
| Variable | Type | Dimensions (for arrays) | Description |
|
||||
|---------------+-------+-------------------------+------------------------------------------|
|
||||
| ~code_num~ | ~int~ | | Number of codes used to produce the file |
|
||||
| ~code~ | ~str~ | ~(metadata.code_num)~ | Names of the codes used |
|
||||
| ~author_num~ | ~int~ | | Number of authors of the file |
|
||||
@ -46,14 +55,16 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
* Electron
|
||||
* Electron (electron group)
|
||||
|
||||
We consider wave functions expressed in the spin-free formalism, where
|
||||
the number of \uparrow and \downarrow electrons is fixed.
|
||||
|
||||
#+NAME:electron
|
||||
| ~up_num~ | ~int~ | | Number of \uparrow-spin electrons |
|
||||
| ~dn_num~ | ~int~ | | Number of \downarrow-spin electrons |
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|----------+-------+------------+-------------------------------------|
|
||||
| ~up_num~ | ~int~ | | Number of \uparrow-spin electrons |
|
||||
| ~dn_num~ | ~int~ | | Number of \downarrow-spin electrons |
|
||||
|
||||
#+CALL: json(data=electron, title="electron")
|
||||
#+RESULTS:
|
||||
@ -66,12 +77,14 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
* Nucleus
|
||||
* Nucleus (nucleus group)i
|
||||
|
||||
The nuclei are considered as fixed point charges. Coordinates are
|
||||
given in Cartesian $(x,y,z)$ format.
|
||||
|
||||
#+NAME: nucleus
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|---------------+---------+-------------------+--------------------------|
|
||||
| ~num~ | ~int~ | | Number of nuclei |
|
||||
| ~charge~ | ~float~ | ~(nucleus.num)~ | Charges of the nuclei |
|
||||
| ~coord~ | ~float~ | ~(3,nucleus.num)~ | Coordinates of the atoms |
|
||||
@ -92,7 +105,7 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
* TODO Effective core potentials
|
||||
* TODO Effective core potentials (ecp group)
|
||||
|
||||
An effective core potential (ECP) $V_A^{\text{pp}}$ replacing the
|
||||
core electrons of atom $A$ is the sum of a local component
|
||||
@ -126,6 +139,8 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
- $\hat{V}_\text{ecp,nl} = \sum_A \hat{V}_A^{\text{nl}}$ : non-local component
|
||||
|
||||
#+NAME: ecp
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|-----------------------+---------+------------------------------------------+----------------------------|
|
||||
| ~lmax_plus_1~ | ~int~ | ~(nucleus.num)~ | $l_{\max} + 1$ |
|
||||
| ~z_core~ | ~float~ | ~(nucleus.num)~ | Charges to remove |
|
||||
| ~local_n~ | ~int~ | ~(nucleus.num)~ | Number of local function |
|
||||
@ -161,7 +176,7 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
* Basis set
|
||||
* Basis set (basis group)
|
||||
|
||||
We consider here basis functions centered on nuclei. Hence, we enable
|
||||
the possibility to define /dummy atoms/ to place basis functions in
|
||||
@ -201,6 +216,8 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
All the basis set parameters are stored in one-dimensional arrays:
|
||||
|
||||
#+NAME: basis
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|---------------------+---------+--------------------+----------------------------------------------------------|
|
||||
| ~type~ | ~str~ | | Type of basis set: "Gaussian" or "Slater" |
|
||||
| ~num~ | ~int~ | | Total Number of shells |
|
||||
| ~prim_num~ | ~int~ | | Total number of primitives |
|
||||
@ -210,7 +227,7 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
| ~shell_prim_num~ | ~int~ | ~(basis.num)~ | Number of primitives in the shell ($N_{\text{prim}}$) |
|
||||
| ~shell_factor~ | ~float~ | ~(basis.num)~ | Normalization factor of the shell ($\mathcal{N}_s$) |
|
||||
| ~shell_prim_index~ | ~index~ | ~(basis.num)~ | Index of the first primitive in the complete list |
|
||||
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) |
|
||||
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) |
|
||||
| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) |
|
||||
| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
|
||||
|
||||
@ -292,7 +309,7 @@ prim_factor =
|
||||
4.3649547399719840e-01, 1.8135965626177861e+00 ]
|
||||
#+END_EXAMPLE
|
||||
|
||||
* Atomic orbitals
|
||||
* Atomic orbitals (ao group)
|
||||
|
||||
Going from the atomic basis set to AOs implies a systematic
|
||||
construction of all the angular functions of each shell. We
|
||||
@ -337,6 +354,8 @@ prim_factor =
|
||||
introduced here should be $\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}$.
|
||||
|
||||
#+NAME: ao
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|-----------------+---------+------------+---------------------------------|
|
||||
| ~cartesian~ | ~int~ | | ~1~: true, ~0~: false |
|
||||
| ~num~ | ~int~ | | Total number of atomic orbitals |
|
||||
| ~shell~ | ~index~ | ~(ao.num)~ | basis set shell for each AO |
|
||||
@ -356,7 +375,7 @@ prim_factor =
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
** One-electron integrals
|
||||
** One-electron integrals (ao_1e_int group)
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: ao_one_e
|
||||
:END:
|
||||
@ -374,12 +393,14 @@ prim_factor =
|
||||
over atomic orbitals.
|
||||
|
||||
#+NAME: ao_1e_int
|
||||
| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
|
||||
| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
|
||||
| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
|
||||
| ~ecp_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,l}} \vert q \rangle$ |
|
||||
| ~ecp_non_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,nl}} \vert q \rangle$ |
|
||||
| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|--------------------+---------+--------------------+-----------------------------------------------------------|
|
||||
| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
|
||||
| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
|
||||
| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
|
||||
| ~ecp_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,l}} \vert q \rangle$ |
|
||||
| ~ecp_non_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,nl}} \vert q \rangle$ |
|
||||
| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
|
||||
|
||||
#+CALL: json(data=ao_1e_int, title="ao_1e_int")
|
||||
|
||||
@ -397,7 +418,7 @@ prim_factor =
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
** Two-electron integrals
|
||||
** Two-electron integrals (ao_2e_int group)
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: ao_two_e
|
||||
:END:
|
||||
@ -418,8 +439,10 @@ prim_factor =
|
||||
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential
|
||||
|
||||
#+NAME: ao_2e_int
|
||||
| ~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 |
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|----------+----------------+------------------------------------+-----------------------------------------|
|
||||
| ~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 |
|
||||
|
||||
#+CALL: json(data=ao_2e_int, title="ao_2e_int")
|
||||
|
||||
@ -433,9 +456,11 @@ prim_factor =
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
* Molecular orbitals
|
||||
* Molecular orbitals (mo group)
|
||||
|
||||
#+NAME: mo
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|---------------+---------+--------------------+------------------------------------------|
|
||||
| ~type~ | ~str~ | | String identify the set of MOs |
|
||||
| ~num~ | ~int~ | | Number of MOs |
|
||||
| ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients |
|
||||
@ -459,19 +484,21 @@ prim_factor =
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
** One-electron integrals
|
||||
** One-electron integrals (mo_1e_int group)
|
||||
|
||||
The operators as the same as those defined in the
|
||||
[[#ao_one_e][AO one-electron integrals section]]. Here, the integrals are given in
|
||||
the basis of molecular orbitals.
|
||||
|
||||
#+NAME: mo_1e_int
|
||||
| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ |
|
||||
| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ |
|
||||
| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ |
|
||||
| ~ecp_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,l}} \vert j \rangle$ |
|
||||
| ~ecp_non_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,nl}} \vert j \rangle$ |
|
||||
| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|--------------------+---------+--------------------+-----------------------------------------------------------|
|
||||
| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ |
|
||||
| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ |
|
||||
| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ |
|
||||
| ~ecp_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,l}} \vert j \rangle$ |
|
||||
| ~ecp_non_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,nl}} \vert j \rangle$ |
|
||||
| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
|
||||
|
||||
#+CALL: json(data=mo_1e_int, title="mo_1e_int")
|
||||
|
||||
@ -489,15 +516,17 @@ prim_factor =
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
** Two-electron integrals
|
||||
** Two-electron integrals (mo_2e_int group)
|
||||
|
||||
The operators as the same as those defined in the
|
||||
[[#ao_one_e][AO one-electron integrals section]]. Here, the integrals are given in
|
||||
the basis of molecular orbitals.
|
||||
|
||||
#+NAME: mo_2e_int
|
||||
| ~eri~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Electron repulsion integrals |
|
||||
| ~eri_lr~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Long-range Electron repulsion integrals |
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|----------+----------------+------------------------------------+-----------------------------------------|
|
||||
| ~eri~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Electron repulsion integrals |
|
||||
| ~eri_lr~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Long-range Electron repulsion integrals |
|
||||
|
||||
#+CALL: json(data=mo_2e_int, title="mo_2e_int")
|
||||
|
||||
@ -512,13 +541,15 @@ prim_factor =
|
||||
:end:
|
||||
|
||||
* TODO Slater determinants
|
||||
* TODO Reduced density matrices
|
||||
* TODO Reduced density matrices (rdm group)
|
||||
|
||||
#+NAME: rdm
|
||||
| ~one_e~ | ~float~ | ~(mo.num, mo.num)~ |
|
||||
| ~one_e_up~ | ~float~ | ~(mo.num, mo.num)~ |
|
||||
| ~one_e_dn~ | ~float~ | ~(mo.num, mo.num)~ |
|
||||
| ~two_e~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ |
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|------------+----------------+------------------------------------+-------------|
|
||||
| ~one_e~ | ~float~ | ~(mo.num, mo.num)~ | |
|
||||
| ~one_e_up~ | ~float~ | ~(mo.num, mo.num)~ | |
|
||||
| ~one_e_dn~ | ~float~ | ~(mo.num, mo.num)~ | |
|
||||
| ~two_e~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | |
|
||||
|
||||
#+CALL: json(data=rdm, title="rdm", last=1)
|
||||
|
||||
@ -587,6 +618,6 @@ print("""#+end_src""")
|
||||
#+end_src
|
||||
|
||||
|
||||
#+begin_src python :tangle trex.json :results output drawer
|
||||
#+begin_src python :tangle trex.json :results output drawer :exports none
|
||||
}
|
||||
#+end_src
|
||||
|
||||
Loading…
Reference in New Issue
Block a user