From a328741a0c644c6e844dc8c2248721e2acbe9031 Mon Sep 17 00:00:00 2001 From: q-posev Date: Fri, 25 Jun 2021 11:52:53 +0200 Subject: [PATCH] add headers to tables and group names --- trex.org | 111 +++++++++++++++++++++++++++++++++++-------------------- 1 file changed, 71 insertions(+), 40 deletions(-) diff --git a/trex.org b/trex.org index 6de2586..c3c0e02 100644 --- a/trex.org +++ b/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