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1368 lines
67 KiB
Org Mode
1368 lines
67 KiB
Org Mode
#+TITLE: Data stored in TREXIO
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#+STARTUP: latexpreview
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#+SETUPFILE: docs/theme.setup
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For simplicity, the singular form is always used for the names of
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groups and attributes, and all data are stored in atomic units.
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The dimensions of the arrays in the tables below are given in
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column-major order (as in Fortran), and the ordering of the dimensions
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is reversed in the produced ~trex.json~ configuration file as the
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library is written in C.
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#+begin_src python :tangle trex.json :exports none
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{
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#+end_src
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* Metadata (metadata group)
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As we expect TREXIO files to be archived in open-data repositories,
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we give the possibility to the users to store some metadata inside
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the files. We propose to store the list of names of the codes which
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have participated to the creation of the file, a list of authors of
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the file, and a textual description.
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#+NAME: metadata
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| Variable | Type | Dimensions (for arrays) | Description |
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|-------------------+-------+-------------------------+------------------------------------------|
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| ~code_num~ | ~dim~ | | Number of codes used to produce the file |
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| ~code~ | ~str~ | ~(metadata.code_num)~ | Names of the codes used |
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| ~author_num~ | ~dim~ | | Number of authors of the file |
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| ~author~ | ~str~ | ~(metadata.author_num)~ | Names of the authors of the file |
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| ~package_version~ | ~str~ | | TREXIO version used to produce the file |
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| ~description~ | ~str~ | | Text describing the content of file |
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| ~unsafe~ | ~int~ | | ~1~: true, ~0~: false |
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**Note:** The ~unsafe~ attribute of the ~metadata~ group indicates
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whether the file has been previously opened with ~'u'~ mode. It is
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automatically written in the file upon the first unsafe opening. If
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the user has checked that the TREXIO file is valid (e.g. using ~trexio-tools~) after unsafe operations, then the ~unsafe~ attribute
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value can be manually overwritten (in unsafe mode) from ~1~ to ~0~.
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#+CALL: json(data=metadata, title="metadata")
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#+RESULTS:
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:results:
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#+begin_src python :tangle trex.json
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"metadata": {
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"code_num" : [ "dim", [] ]
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, "code" : [ "str", [ "metadata.code_num" ] ]
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, "author_num" : [ "dim", [] ]
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, "author" : [ "str", [ "metadata.author_num" ] ]
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, "package_version" : [ "str", [] ]
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, "description" : [ "str", [] ]
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, "unsafe" : [ "int", [] ]
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} ,
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#+end_src
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:end:
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* System
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** Nucleus (nucleus group)
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The nuclei are considered as fixed point charges. Coordinates are
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given in Cartesian $(x,y,z)$ format.
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#+NAME: nucleus
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| Variable | Type | Dimensions | Description |
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|---------------+---------+-------------------+--------------------------|
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| ~num~ | ~dim~ | | Number of nuclei |
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| ~charge~ | ~float~ | ~(nucleus.num)~ | Charges of the nuclei |
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| ~coord~ | ~float~ | ~(3,nucleus.num)~ | Coordinates of the atoms |
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| ~label~ | ~str~ | ~(nucleus.num)~ | Atom labels |
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| ~point_group~ | ~str~ | | Symmetry point group |
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| ~repulsion~ | ~float~ | | Nuclear repulsion energy |
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#+CALL: json(data=nucleus, title="nucleus")
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#+RESULTS:
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:results:
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#+begin_src python :tangle trex.json
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"nucleus": {
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"num" : [ "dim" , [] ]
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, "charge" : [ "float", [ "nucleus.num" ] ]
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, "coord" : [ "float", [ "nucleus.num", "3" ] ]
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, "label" : [ "str" , [ "nucleus.num" ] ]
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, "point_group" : [ "str" , [] ]
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, "repulsion" : [ "float", [] ]
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} ,
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#+end_src
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:end:
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** Cell (cell group)
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3 Lattice vectors to define a box containing the system, for example
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used in periodic calculations.
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#+NAME: cell
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| Variable | Type | Dimensions | Description |
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|----------+---------+------------+--------------------------------------------------------------------------|
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| ~a~ | ~float~ | ~(3)~ | First real space lattice vector |
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| ~b~ | ~float~ | ~(3)~ | Second real space lattice vector |
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| ~c~ | ~float~ | ~(3)~ | Third real space lattice vector |
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| ~G_a~ | ~float~ | ~(3)~ | First reciprocal space lattice vector |
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| ~G_b~ | ~float~ | ~(3)~ | Second reciprocal space lattice vector |
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| ~G_c~ | ~float~ | ~(3)~ | Third reciprocal space lattice vector |
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| ~two_pi~ | ~int~ | | ~0~ or ~1~. If ~two_pi=1~, $2\pi$ is included in the reciprocal vectors. |
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#+CALL: json(data=cell, title="cell")
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#+RESULTS:
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:results:
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#+begin_src python :tangle trex.json
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"cell": {
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"a" : [ "float", [ "3" ] ]
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, "b" : [ "float", [ "3" ] ]
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, "c" : [ "float", [ "3" ] ]
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, "G_a" : [ "float", [ "3" ] ]
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, "G_b" : [ "float", [ "3" ] ]
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, "G_c" : [ "float", [ "3" ] ]
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, "two_pi" : [ "int" , [] ]
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} ,
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#+end_src
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:end:
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** Periodic boundary calculations (pbc group)
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A single $k$-point per TREXIO file can be stored. The $k$-point is
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defined in this group.
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#+NAME: pbc
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| Variable | Type | Dimensions | Description |
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|------------+---------+------------+-------------------------|
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| ~periodic~ | ~int~ | | ~1~: true or ~0~: false |
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| ~k_point~ | ~float~ | ~(3)~ | $k$-point sampling |
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#+CALL: json(data=pbc, title="pbc")
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#+RESULTS:
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:results:
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#+begin_src python :tangle trex.json
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"pbc": {
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"periodic" : [ "int" , [] ]
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, "k_point" : [ "float", [ "3" ] ]
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} ,
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#+end_src
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:end:
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** Electron (electron group)
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The chemical system consists of nuclei and electrons, where the
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nuclei are considered as fixed point charges with Cartesian
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coordinates. The wave function is stored in the spin-free
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formalism, and therefore, it is necessary for the user to
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explicitly store the number of electrons with spin up
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($N_\uparrow$) and spin down ($N_\downarrow$). These numbers
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correspond to the normalization of the spin-up and spin-down
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single-particle reduced density matrices.
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We consider wave functions expressed in the spin-free formalism, where
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the number of \uparrow and \downarrow electrons is fixed.
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#+NAME:electron
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| Variable | Type | Dimensions | Description |
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|----------+-------+------------+-------------------------------------|
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| ~num~ | ~dim~ | | Number of electrons |
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| ~up_num~ | ~int~ | | Number of \uparrow-spin electrons |
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| ~dn_num~ | ~int~ | | Number of \downarrow-spin electrons |
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#+CALL: json(data=electron, title="electron")
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#+RESULTS:
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:results:
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#+begin_src python :tangle trex.json
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"electron": {
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"num" : [ "dim", [] ]
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, "up_num" : [ "int", [] ]
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, "dn_num" : [ "int", [] ]
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} ,
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#+end_src
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:end:
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** Ground or excited states (state group)
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This group contains information about excited states. Since only a
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single state can be stored in a TREXIO file, it is possible to store
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in the main TREXIO file the names of auxiliary files containing the
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information of the other states.
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The ~file_name~ and ~label~ arrays have to be written only for the
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main file, e.g. the one containing the ground state wave function
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together with the basis set parameters, molecular orbitals,
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integrals, etc.
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The ~id~ and ~current_label~ attributes need to be specified for each file.
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#+NAME: state
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| Variable | Type | Dimensions | Description |
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|-----------------+-------+---------------+---------------------------------------------------------------------------------------------|
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| ~num~ | ~dim~ | | Number of states (including the ground state) |
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| ~id~ | ~int~ | | Index of the current state (0 is ground state) |
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| ~current_label~ | ~str~ | | Label of the current state |
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| ~label~ | ~str~ | ~(state.num)~ | Labels of all states |
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| ~file_name~ | ~str~ | ~(state.num)~ | Names of the TREXIO files linked to the current one (i.e. containing data for other states) |
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#+CALL: json(data=state, title="state")
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#+RESULTS:
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:results:
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#+begin_src python :tangle trex.json
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"state": {
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"num" : [ "dim", [] ]
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, "id" : [ "int", [] ]
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, "current_label" : [ "str", [] ]
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, "label" : [ "str", [ "state.num" ] ]
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, "file_name" : [ "str", [ "state.num" ] ]
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} ,
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#+end_src
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:end:
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* Basis functions
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** Basis set (basis group)
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*** Gaussian and Slater-type orbitals
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We consider here basis functions centered on nuclei. Hence, it is
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possibile to define /dummy atoms/ to place basis functions in
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arbitrary positions.
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The atomic basis set is defined as a list of shells. Each shell $s$ is
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centered on a center $A$, possesses a given angular momentum $l$ and a
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radial function $R_s$. The radial function is a linear combination of
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$N_{\text{prim}}$ /primitive/ functions that can be of type
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Slater ($p=1$) or Gaussian ($p=2$),
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parameterized by exponents $\gamma_{ks}$ and coefficients $a_{ks}$:
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\[
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R_s(\mathbf{r}) = \mathcal{N}_s \vert\mathbf{r}-\mathbf{R}_A\vert^{n_s}
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\sum_{k=1}^{N_{\text{prim}}} a_{ks}\, f_{ks}(\gamma_{ks},p)\,
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\exp \left( - \gamma_{ks}
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\vert \mathbf{r}-\mathbf{R}_A \vert ^p \right).
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\]
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In the case of Gaussian functions, $n_s$ is always zero.
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Different codes normalize functions at different levels. Computing
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normalization factors requires the ability to compute overlap
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integrals, so the normalization factors should be written in the
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file to ensure that the file is self-contained and does not need the
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client program to have the ability to compute such integrals.
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Some codes assume that the contraction coefficients are for a linear
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combination of /normalized/ primitives. This implies that a normalization
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constant for the primitive $ks$ needs to be computed and stored. If
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this normalization factor is not required, $f_{ks}=1$.
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Some codes assume that the basis function are normalized. This
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implies the computation of an extra normalization factor, $\mathcal{N}_s$.
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If the the basis function is not considered normalized, $\mathcal{N}_s=1$.
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All the basis set parameters are stored in one-dimensional arrays.
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*** Plane waves
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A plane wave is defined as
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\[
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\chi_j(\mathbf{r}) = \exp \left( -i \mathbf{G}_j \cdot \mathbf{r} \right)
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\]
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The basis set is defined as the array of $k$-points in the
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reciprocal space $\mathbf{G}_j$, defined in the ~pbc~ group. The
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kinetic energy cutoff ~e_cut~ is the only input data relevant to
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plane waves.
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*** Data definitions
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#+NAME: basis
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| Variable | Type | Dimensions | Description |
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|-----------------+---------+---------------------+-----------------------------------------------------------------|
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| ~type~ | ~str~ | | Type of basis set: "Gaussian", "Slater" or "PW" for plane waves |
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| ~prim_num~ | ~dim~ | | Total number of primitives |
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| ~shell_num~ | ~dim~ | | Total number of shells |
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| ~nucleus_index~ | ~index~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and atomic indices |
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| ~shell_ang_mom~ | ~int~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and angular momenta |
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| ~shell_factor~ | ~float~ | ~(basis.shell_num)~ | Normalization factor of each shell ($\mathcal{N}_s$) |
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| ~r_power~ | ~int~ | ~(basis.shell_num)~ | Power to which $r$ is raised ($n_s$) |
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| ~shell_index~ | ~index~ | ~(basis.prim_num)~ | One-to-one correspondence between primitives and shell index |
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| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) |
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| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) |
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| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
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| ~e_cut~ | ~float~ | | Energy cut-off for plane-wave calculations |
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#+CALL: json(data=basis, title="basis")
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#+RESULTS:
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:results:
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#+begin_src python :tangle trex.json
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"basis": {
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"type" : [ "str" , [] ]
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, "prim_num" : [ "dim" , [] ]
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, "shell_num" : [ "dim" , [] ]
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, "nucleus_index" : [ "index", [ "basis.shell_num" ] ]
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, "shell_ang_mom" : [ "int" , [ "basis.shell_num" ] ]
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, "shell_factor" : [ "float", [ "basis.shell_num" ] ]
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, "r_power" : [ "int" , [ "basis.shell_num" ] ]
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, "shell_index" : [ "index", [ "basis.prim_num" ] ]
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, "exponent" : [ "float", [ "basis.prim_num" ] ]
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, "coefficient" : [ "float", [ "basis.prim_num" ] ]
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, "prim_factor" : [ "float", [ "basis.prim_num" ] ]
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, "e_cut" : [ "float", [] ]
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} ,
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#+end_src
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:end:
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*** Example
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For example, consider H_2 with the following basis set (in GAMESS
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format), where both the AOs and primitives are considered normalized:
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#+BEGIN_EXAMPLE
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HYDROGEN
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S 5
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1 3.387000E+01 6.068000E-03
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2 5.095000E+00 4.530800E-02
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3 1.159000E+00 2.028220E-01
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4 3.258000E-01 5.039030E-01
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5 1.027000E-01 3.834210E-01
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S 1
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1 3.258000E-01 1.000000E+00
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S 1
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1 1.027000E-01 1.000000E+00
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P 1
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1 1.407000E+00 1.000000E+00
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P 1
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1 3.880000E-01 1.000000E+00
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D 1
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1 1.057000E+00 1.000000E+00
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#+END_EXAMPLE
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In TREXIO representaion we have:
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#+BEGIN_EXAMPLE
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type = "Gaussian"
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prim_num = 20
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shell_num = 12
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# 6 shells per H atom
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nucleus_index =
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[ 0, 0, 0, 0, 0, 0,
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1, 1, 1, 1, 1, 1 ]
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# 3 shells in S (l=0), 2 in P (l=1), 1 in D (l=2)
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shell_ang_mom =
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[ 0, 0, 0, 1, 1, 2,
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0, 0, 0, 1, 1, 2 ]
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# no need to renormalize shells
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shell_factor =
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[ 1., 1., 1., 1., 1., 1.,
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1., 1., 1., 1., 1., 1. ]
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# 5 primitives for the first S shell and then 1 primitive per remaining shells in each H atom
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shell_index =
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[ 0, 0, 0, 0, 0, 1, 2, 3, 4, 5,
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6, 6, 6, 6, 6, 7, 8, 9, 10, 11 ]
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# parameters of the primitives (10 per H atom)
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exponent =
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[ 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407, 0.388, 1.057,
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33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407, 0.388, 1.057 ]
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coefficient =
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[ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0,
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0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0 ]
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prim_factor =
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[ 1.0006253235944540e+01, 2.4169531573445120e+00, 7.9610924849766440e-01
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3.0734305383061117e-01, 1.2929684417481876e-01, 3.0734305383061117e-01,
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1.2929684417481876e-01, 2.1842769845268308e+00, 4.3649547399719840e-01,
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1.8135965626177861e+00, 1.0006253235944540e+01, 2.4169531573445120e+00,
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7.9610924849766440e-01, 3.0734305383061117e-01, 1.2929684417481876e-01,
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3.0734305383061117e-01, 1.2929684417481876e-01, 2.1842769845268308e+00,
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4.3649547399719840e-01, 1.8135965626177861e+00 ]
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#+END_EXAMPLE
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** Effective core potentials (ecp group)
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An effective core potential (ECP) $V_A^{\text{ECP}}$ replacing the
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core electrons of atom $A$ can be expressed as
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\[
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V_A^{\text{ECP}} =
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V_{A \ell_{\max}+1} +
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\sum_{\ell=0}^{\ell_{\max}} V_{A \ell}
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\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \langle Y_{\ell m} |
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\]
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The first term in the equation above is sometimes attributed to the local channel,
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while the remaining terms correspond to the non-local channel projections.
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All the functions $V_{A\ell}$ are parameterized as:
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\[
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V_{A \ell}(\mathbf{r}) =
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\sum_{q=1}^{N_{q \ell}}
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\beta_{A q \ell}\, |\mathbf{r}-\mathbf{R}_{A}|^{n_{A q \ell}}\,
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e^{-\alpha_{A q \ell} |\mathbf{r}-\mathbf{R}_{A}|^2 }
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\].
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See http://dx.doi.org/10.1063/1.4984046 or https://doi.org/10.1063/1.5121006 for more info.
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#+NAME: ecp
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| Variable | Type | Dimensions | Description |
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|----------------------+---------+-----------------+----------------------------------------------------------------------------------------|
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| ~max_ang_mom_plus_1~ | ~int~ | ~(nucleus.num)~ | $\ell_{\max}+1$, one higher than the max angular momentum in the removed core orbitals |
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| ~z_core~ | ~int~ | ~(nucleus.num)~ | Number of core electrons to remove per atom |
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| ~num~ | ~dim~ | | Total number of ECP functions for all atoms and all values of $\ell$ |
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| ~ang_mom~ | ~int~ | ~(ecp.num)~ | One-to-one correspondence between ECP items and the angular momentum $\ell$ |
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| ~nucleus_index~ | ~index~ | ~(ecp.num)~ | One-to-one correspondence between ECP items and the atom index |
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| ~exponent~ | ~float~ | ~(ecp.num)~ | $\alpha_{A q \ell}$ all ECP exponents |
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| ~coefficient~ | ~float~ | ~(ecp.num)~ | $\beta_{A q \ell}$ all ECP coefficients |
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| ~power~ | ~int~ | ~(ecp.num)~ | $n_{A q \ell}$ all ECP powers |
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There might be some confusion in the meaning of the $\ell_{\max}$.
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It can be attributed to the maximum angular momentum occupied in
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the core orbitals, which are removed by the ECP. On the other
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hand, it can be attributed to the maximum angular momentum of the
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ECP that replaces the core electrons.
|
|
*Note*, that the latter $\ell_{\max}$ is always higher by 1 than the former.
|
|
|
|
*Note for developers*: avoid having variables with similar prefix
|
|
in their name. The HDF5 back end might cause issues due to the way
|
|
~find_dataset~ function works. For example, in the ECP group we
|
|
use ~max_ang_mom~ and not ~ang_mom_max~. The latter causes issues
|
|
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 installed via ~apt-get~. Installing
|
|
the same version from the ~conda-forge~ channel and running it in
|
|
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")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"ecp": {
|
|
"max_ang_mom_plus_1" : [ "int" , [ "nucleus.num" ] ]
|
|
, "z_core" : [ "int" , [ "nucleus.num" ] ]
|
|
, "num" : [ "dim" , [] ]
|
|
, "ang_mom" : [ "int" , [ "ecp.num" ] ]
|
|
, "nucleus_index" : [ "index", [ "ecp.num" ] ]
|
|
, "exponent" : [ "float", [ "ecp.num" ] ]
|
|
, "coefficient" : [ "float", [ "ecp.num" ] ]
|
|
, "power" : [ "int" , [ "ecp.num" ] ]
|
|
} ,
|
|
#+end_src
|
|
:end:
|
|
|
|
*** Example
|
|
|
|
For example, consider H_2 molecule with the following
|
|
[[https://pseudopotentiallibrary.org/recipes/H/ccECP/H.ccECP.gamess][effective core potential]]
|
|
(in GAMESS input format for the H atom):
|
|
|
|
#+BEGIN_EXAMPLE
|
|
H-ccECP GEN 0 1
|
|
3
|
|
1.00000000000000 1 21.24359508259891
|
|
21.24359508259891 3 21.24359508259891
|
|
-10.85192405303825 2 21.77696655044365
|
|
1
|
|
0.00000000000000 2 1.000000000000000
|
|
#+END_EXAMPLE
|
|
|
|
In TREXIO representation this would be:
|
|
|
|
#+BEGIN_EXAMPLE
|
|
num = 8
|
|
|
|
# lmax+1 per atom
|
|
max_ang_mom_plus_1 = [ 1, 1 ]
|
|
|
|
# number of core electrons to remove per atom
|
|
zcore = [ 0, 0 ]
|
|
|
|
# first 4 ECP elements correspond to the first H atom ; the remaining 4 elements are for the second H atom
|
|
nucleus_index = [
|
|
0, 0, 0, 0,
|
|
1, 1, 1, 1
|
|
]
|
|
|
|
# 3 first ECP elements correspond to potential of the P orbital (l=1), then 1 element for the S orbital (l=0) ; similar for the second H atom
|
|
ang_mom = [
|
|
1, 1, 1, 0,
|
|
1, 1, 1, 0
|
|
]
|
|
|
|
# ECP quantities that can be attributed to atoms and/or angular momenta based on the aforementioned ecp_nucleus and ecp_ang_mom arrays
|
|
coefficient = [
|
|
1.00000000000000, 21.24359508259891, -10.85192405303825, 0.00000000000000,
|
|
1.00000000000000, 21.24359508259891, -10.85192405303825, 0.00000000000000
|
|
]
|
|
|
|
exponent = [
|
|
21.24359508259891, 21.24359508259891, 21.77696655044365, 1.000000000000000,
|
|
21.24359508259891, 21.24359508259891, 21.77696655044365, 1.000000000000000
|
|
]
|
|
|
|
power = [
|
|
-1, 1, 0, 0,
|
|
-1, 1, 0, 0
|
|
]
|
|
#+END_EXAMPLE
|
|
|
|
** Numerical integration grid (grid group)
|
|
|
|
In some applications, such as DFT calculations, integrals have to
|
|
be computed numerically on a grid. A common choice for the angular
|
|
grid is the one proposed by Lebedev and Laikov
|
|
[Russian Academy of Sciences Doklady Mathematics, Volume 59, Number 3, 1999, pages 477-481].
|
|
For the radial grids, many approaches have been developed over the years.
|
|
|
|
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.
|
|
|
|
#+NAME: grid
|
|
| Variable | Type | Dimensions | Description |
|
|
|-----------------+---------+------------------+-------------------------------------------------------------------------|
|
|
| ~description~ | ~str~ | | Details about the used quadratures can go here |
|
|
| ~rad_precision~ | ~float~ | | Radial precision parameter (not used in some schemes like Krack-Köster) |
|
|
| ~num~ | ~dim~ | | Number of grid points |
|
|
| ~max_ang_num~ | ~int~ | | Maximum number of angular grid points (for pruning) |
|
|
| ~min_ang_num~ | ~int~ | | Minimum number of angular grid points (for pruning) |
|
|
| ~coord~ | ~float~ | ~(grid.num)~ | Discretized coordinate space |
|
|
| ~weight~ | ~float~ | ~(grid.num)~ | Grid weights according to a given partitioning (e.g. Becke) |
|
|
| ~ang_num~ | ~dim~ | | Number of angular integration points (if used) |
|
|
| ~ang_coord~ | ~float~ | ~(grid.ang_num)~ | Discretized angular space (if used) |
|
|
| ~ang_weight~ | ~float~ | ~(grid.ang_num)~ | Angular grid weights (if used) |
|
|
| ~rad_num~ | ~dim~ | | Number of radial integration points (if used) |
|
|
| ~rad_coord~ | ~float~ | ~(grid.rad_num)~ | Discretized radial space (if used) |
|
|
| ~rad_weight~ | ~float~ | ~(grid.rad_num)~ | Radial grid weights (if used) |
|
|
|
|
#+CALL: json(data=grid, title="grid")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"grid": {
|
|
"description" : [ "str" , [] ]
|
|
, "rad_precision" : [ "float", [] ]
|
|
, "num" : [ "dim" , [] ]
|
|
, "max_ang_num" : [ "int" , [] ]
|
|
, "min_ang_num" : [ "int" , [] ]
|
|
, "coord" : [ "float", [ "grid.num" ] ]
|
|
, "weight" : [ "float", [ "grid.num" ] ]
|
|
, "ang_num" : [ "dim" , [] ]
|
|
, "ang_coord" : [ "float", [ "grid.ang_num" ] ]
|
|
, "ang_weight" : [ "float", [ "grid.ang_num" ] ]
|
|
, "rad_num" : [ "dim" , [] ]
|
|
, "rad_coord" : [ "float", [ "grid.rad_num" ] ]
|
|
, "rad_weight" : [ "float", [ "grid.rad_num" ] ]
|
|
} ,
|
|
#+end_src
|
|
:end:
|
|
|
|
* Orbitals
|
|
** Atomic orbitals (ao group)
|
|
|
|
AOs are defined as
|
|
|
|
\[
|
|
\chi_i (\mathbf{r}) = \mathcal{N}_i'\, P_{\eta(i)}(\mathbf{r})\, R_{s(i)} (\mathbf{r})
|
|
\]
|
|
|
|
where $i$ is the atomic orbital index, $P$ refers to either
|
|
polynomials or spherical harmonics, and $s(i)$ specifies the shell
|
|
on which the AO is expanded.
|
|
|
|
$\eta(i)$ denotes the chosen angular function. The AOs can be
|
|
expressed using real spherical harmonics or polynomials in Cartesian
|
|
coordinates. In the case of real spherical harmonics, the AOs are
|
|
ordered as $0, +1, -1, +2, -2, \dots, + m, -m$ (see [[https://en.wikipedia.org/wiki/Table_of_spherical_harmonics#Real_spherical_harmonics][Wikipedia]]). In
|
|
the case of polynomials, the canonical (or alphabetical) ordering is
|
|
used,
|
|
|
|
| $p$ | $p_x, p_y, p_z$ |
|
|
| $d$ | $d_{xx}, d_{xy}, d_{xz}, d_{yy}, d_{yz}, d_{zz}$ |
|
|
| $f$ | $f_{xxx}, f_{xxy}, f_{xxz}, f_{xyy}, f_{xyz}$, |
|
|
| | $f_{xzz}, f_{yyy}, f_{yyz}, f_{yzz}, f_{zzz}$ |
|
|
| $\vdots$ | |
|
|
|
|
Note that for \(p\) orbitals in spherical coordinates, the ordering
|
|
is $0,+1,-1$ which corresponds to $p_z, p_x, p_y$.
|
|
|
|
$\mathcal{N}_i'$ is a normalization factor that allows for different
|
|
normalization coefficients within a single shell, as in the GAMESS
|
|
convention where each individual function is unit-normalized.
|
|
Using GAMESS convention, the normalization factor of the shell
|
|
$\mathcal{N}_d$ in the ~basis~ group is appropriate for instance
|
|
for the $d_z^2$ function (i.e.
|
|
$\mathcal{N}_{d}\equiv\mathcal{N}_{z^2}$) but not for the $d_{xy}$
|
|
AO, so the correction factor $\mathcal{N}_i'$ for $d_{xy}$ in the
|
|
~ao~ groups is the ratio $\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}$.
|
|
|
|
|
|
#+NAME: ao
|
|
| Variable | Type | Dimensions | Description |
|
|
|-----------------+---------+------------+--------------------------------------|
|
|
| ~cartesian~ | ~int~ | | ~1~: true, ~0~: false |
|
|
| ~num~ | ~dim~ | | Total number of atomic orbitals |
|
|
| ~shell~ | ~index~ | ~(ao.num)~ | Basis set shell for each AO |
|
|
| ~normalization~ | ~float~ | ~(ao.num)~ | Normalization factor $\mathcal{N}_i$ |
|
|
|
|
#+CALL: json(data=ao, title="ao")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"ao": {
|
|
"cartesian" : [ "int" , [] ]
|
|
, "num" : [ "dim" , [] ]
|
|
, "shell" : [ "index", [ "ao.num" ] ]
|
|
, "normalization" : [ "float", [ "ao.num" ] ]
|
|
} ,
|
|
#+end_src
|
|
:end:
|
|
|
|
*** One-electron integrals (~ao_1e_int~ group)
|
|
:PROPERTIES:
|
|
:CUSTOM_ID: ao_one_e
|
|
:END:
|
|
|
|
- \[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
|
|
\sum_{i=1}^{N_\text{elec}} \frac{-Z_A }{\vert \mathbf{R}_A -
|
|
\mathbf{r}_i \vert} \] : electron-nucleus attractive potential,
|
|
- \[ \hat{T}_{\text{e}} =
|
|
\sum_{i=1}^{N_\text{elec}} -\frac{1}{2}\hat{\Delta}_i \] : electronic kinetic energy
|
|
- $\hat{h} = \hat{T}_\text{e} + \hat{V}_\text{ne} + \hat{V}_\text{ECP}$ : core electronic Hamiltonian
|
|
|
|
The one-electron integrals for a one-electron operator $\hat{O}$ are
|
|
\[ \langle p \vert \hat{O} \vert q \rangle \], returned as a matrix
|
|
over atomic orbitals.
|
|
|
|
#+NAME: ao_1e_int
|
|
| 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~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ |
|
|
| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
|
|
| ~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) |
|
|
| ~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) |
|
|
| ~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")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"ao_1e_int": {
|
|
"overlap" : [ "float", [ "ao.num", "ao.num" ] ]
|
|
, "kinetic" : [ "float", [ "ao.num", "ao.num" ] ]
|
|
, "potential_n_e" : [ "float", [ "ao.num", "ao.num" ] ]
|
|
, "ecp" : [ "float", [ "ao.num", "ao.num" ] ]
|
|
, "core_hamiltonian" : [ "float", [ "ao.num", "ao.num" ] ]
|
|
, "overlap_im" : [ "float", [ "ao.num", "ao.num" ] ]
|
|
, "kinetic_im" : [ "float", [ "ao.num", "ao.num" ] ]
|
|
, "potential_n_e_im" : [ "float", [ "ao.num", "ao.num" ] ]
|
|
, "ecp_im" : [ "float", [ "ao.num", "ao.num" ] ]
|
|
, "core_hamiltonian_im" : [ "float", [ "ao.num", "ao.num" ] ]
|
|
} ,
|
|
#+end_src
|
|
:end:
|
|
|
|
*** Two-electron integrals (~ao_2e_int~ group)
|
|
:PROPERTIES:
|
|
:CUSTOM_ID: ao_two_e
|
|
:END:
|
|
|
|
The two-electron integrals for a two-electron operator $\hat{O}$ are
|
|
\[ \langle p q \vert \hat{O} \vert r s \rangle \] in physicists
|
|
notation, where $p,q,r,s$ are indices over atomic orbitals.
|
|
|
|
# TODO: Physicist / Chemist functions
|
|
# Functions are provided to get the indices in physicists or chemists
|
|
# notation.
|
|
|
|
- \[ \hat{W}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}} \sum_{j=1}^{i-1} \frac{1}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron repulsive potential operator.
|
|
- \[ \hat{W}^{lr}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}}
|
|
\sum_{j=1}^{i-1} \frac{\text{erf}(\mu\, \vert \mathbf{r}_i -
|
|
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential
|
|
|
|
The Cholesky decomposition of the integrals can also be stored:
|
|
|
|
\[
|
|
\langle ij | kl \rangle = \sum_{\alpha} G_{ik\alpha} G_{jl\alpha}
|
|
\]
|
|
|
|
#+NAME: ao_2e_int
|
|
| 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 |
|
|
| ~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")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"ao_2e_int": {
|
|
"eri" : [ "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:
|
|
|
|
** Molecular orbitals (mo group)
|
|
|
|
#+NAME: mo
|
|
| Variable | Type | Dimensions | Description |
|
|
|------------------+---------+--------------------+--------------------------------------------------------------------------|
|
|
| ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) |
|
|
| ~num~ | ~dim~ | | Number of MOs |
|
|
| ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients |
|
|
| ~coefficient_im~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (imaginary part) |
|
|
| ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted |
|
|
| ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group |
|
|
| ~occupation~ | ~float~ | ~(mo.num)~ | Occupation number |
|
|
| ~energy~ | ~float~ | ~(mo.num)~ | For canonical MOs, corresponding eigenvalue |
|
|
| ~spin~ | ~int~ | ~(mo.num)~ | For UHF wave functions, 0 is $\alpha$ and 1 is $\beta$ |
|
|
|
|
#+CALL: json(data=mo, title="mo")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"mo": {
|
|
"type" : [ "str" , [] ]
|
|
, "num" : [ "dim" , [] ]
|
|
, "coefficient" : [ "float", [ "mo.num", "ao.num" ] ]
|
|
, "coefficient_im" : [ "float", [ "mo.num", "ao.num" ] ]
|
|
, "class" : [ "str" , [ "mo.num" ] ]
|
|
, "symmetry" : [ "str" , [ "mo.num" ] ]
|
|
, "occupation" : [ "float", [ "mo.num" ] ]
|
|
, "energy" : [ "float", [ "mo.num" ] ]
|
|
, "spin" : [ "int" , [ "mo.num" ] ]
|
|
} ,
|
|
#+end_src
|
|
:end:
|
|
|
|
*** 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
|
|
| 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~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ |
|
|
| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
|
|
| ~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) |
|
|
| ~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) |
|
|
| ~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")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"mo_1e_int": {
|
|
"overlap" : [ "float", [ "mo.num", "mo.num" ] ]
|
|
, "kinetic" : [ "float", [ "mo.num", "mo.num" ] ]
|
|
, "potential_n_e" : [ "float", [ "mo.num", "mo.num" ] ]
|
|
, "ecp" : [ "float", [ "mo.num", "mo.num" ] ]
|
|
, "core_hamiltonian" : [ "float", [ "mo.num", "mo.num" ] ]
|
|
, "overlap_im" : [ "float", [ "mo.num", "mo.num" ] ]
|
|
, "kinetic_im" : [ "float", [ "mo.num", "mo.num" ] ]
|
|
, "potential_n_e_im" : [ "float", [ "mo.num", "mo.num" ] ]
|
|
, "ecp_im" : [ "float", [ "mo.num", "mo.num" ] ]
|
|
, "core_hamiltonian_im" : [ "float", [ "mo.num", "mo.num" ] ]
|
|
} ,
|
|
#+end_src
|
|
:end:
|
|
|
|
*** Two-electron integrals (~mo_2e_int~ group)
|
|
|
|
The operators are the same as those defined in the
|
|
[[#ao_two_e][AO two-electron integrals section]]. Here, the integrals are given in
|
|
the basis of molecular orbitals.
|
|
|
|
#+NAME: mo_2e_int
|
|
| 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 |
|
|
| ~eri_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for ERI |
|
|
| ~eri_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, mo_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~ | ~(mo.num, mo.num, mo_2e_int.eri_lr_cholesky_num)~ | Cholesky decomposition of the long range ERI |
|
|
|
|
#+CALL: json(data=mo_2e_int, title="mo_2e_int")
|
|
|
|
#+RESULTS:
|
|
: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
|
|
:end:
|
|
|
|
* Multi-determinant information
|
|
** Slater determinants (determinant group)
|
|
|
|
The configuration interaction (CI) wave function $\Psi$
|
|
can be expanded in the basis of Slater determinants $D_I$ as follows
|
|
|
|
\[
|
|
\Psi = \sum_I C_I D_I
|
|
\]
|
|
|
|
For relatively small expansions, a given determinant can be represented as a list of occupied orbitals.
|
|
However, this becomes unfeasible for larger expansions and requires more advanced data structures.
|
|
The bit field representation is used here, namely a given determinant is represented as $N_{\text{int}}$
|
|
64-bit integers where j-th bit is set to 1 if there is an electron in the j-th orbital and 0 otherwise.
|
|
This gives access to larger determinant expansions by optimising the storage of the determinant lists
|
|
in the memory.
|
|
|
|
\[
|
|
D_I = \alpha_1 \alpha_2 \ldots \alpha_{n_\uparrow} \beta_1 \beta_2 \ldots \beta_{n_\downarrow}
|
|
\]
|
|
|
|
where $\alpha$ and $\beta$ denote \uparrow-spin and \downarrow-spin electrons, respectively,
|
|
$n_\uparrow$ and $n_\downarrow$ correspond to ~electron.up_num~ and ~electron.dn_num~, respectively.
|
|
|
|
Note: the ~special~ attribute is present in the types, meaning that the source node is not
|
|
produced by the code generator.
|
|
|
|
An illustration on how to read determinants is presented in the [[./examples.html][examples]].
|
|
|
|
#+NAME: determinant
|
|
| Variable | Type | Dimensions | Description |
|
|
|---------------+------------------+---------------------+--------------------------------------------------------|
|
|
| ~num~ | ~dim readonly~ | | Number of determinants |
|
|
| ~list~ | ~int special~ | ~(determinant.num)~ | List of determinants as integer bit fields |
|
|
| ~coefficient~ | ~float buffered~ | ~(determinant.num)~ | Coefficients of the determinants from the CI expansion |
|
|
|
|
#+CALL: json(data=determinant, title="determinant")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"determinant": {
|
|
"num" : [ "dim readonly" , [] ]
|
|
, "list" : [ "int special" , [ "determinant.num" ] ]
|
|
, "coefficient" : [ "float buffered", [ "determinant.num" ] ]
|
|
} ,
|
|
#+end_src
|
|
:end:
|
|
|
|
** Configuration state functions (csf group)
|
|
|
|
The configuration interaction (CI) wave function $\Psi$ can be
|
|
expanded in the basis of [[https://en.wikipedia.org/wiki/Configuration_state_function][configuration state functions]] (CSFs)
|
|
$\Psi_I$ as follows
|
|
|
|
\[
|
|
\Psi = \sum_I C_I \psi_I.
|
|
\]
|
|
|
|
Each CSF $\psi_I$ is a linear combination of Slater determinants. Slater
|
|
determinants are stored in the =determinant= section. In this group
|
|
we store the CI coefficients in the basis of CSFs, and the
|
|
matrix $\langle D_I | \psi_J \rangle$ needed to project the CSFs in
|
|
the basis of Slater determinants.
|
|
|
|
#+NAME: csf
|
|
| Variable | Type | Dimensions | Description |
|
|
|-------------------+------------------+-----------------------------+-----------------------------------------|
|
|
| ~num~ | ~dim readonly~ | | Number of CSFs |
|
|
| ~coefficient~ | ~float buffered~ | ~(csf.num)~ | Coefficients $C_I$ of the CSF expansion |
|
|
| ~det_coefficient~ | ~float sparse~ | ~(determinant.num,csf.num)~ | Projection on the determinant basis |
|
|
|
|
#+CALL: json(data=csf, title="csf")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"csf": {
|
|
"num" : [ "dim readonly" , [] ]
|
|
, "coefficient" : [ "float buffered", [ "csf.num" ] ]
|
|
, "det_coefficient" : [ "float sparse" , [ "csf.num", "determinant.num" ] ]
|
|
} ,
|
|
#+end_src
|
|
:end:
|
|
|
|
** Amplitudes (amplitude group)
|
|
|
|
The wave function may be expressed in terms of action of the cluster
|
|
operator $\hat{T}$:
|
|
|
|
\[
|
|
\hat{T} = \hat{T}_1 + \hat{T}_2 + \hat{T}_3 + \dots
|
|
\]
|
|
|
|
on a reference wave function $\Psi$, where $\hat{T}_1$ is the single excitation operator,
|
|
|
|
\[
|
|
\hat{T}_1 = \sum_{ia} t_{i}^{a}\, \hat{a}^\dagger_a \hat{a}_i,
|
|
\]
|
|
|
|
$\hat{T}_2$ is the double excitation operator,
|
|
|
|
\[
|
|
\hat{T}_2 = \frac{1}{4} \sum_{ijab} t_{ij}^{ab}\, \hat{a}^\dagger_a \hat{a}^\dagger_b \hat{a}_j \hat{a}_i,
|
|
\]
|
|
|
|
/etc/. Indices $i$, $j$, $a$ and $b$ denote molecular orbital indices.
|
|
|
|
Wave functions obtained with perturbation theory or configuration
|
|
interaction are of the form
|
|
|
|
\[ |\Phi\rangle = \hat{T}|\Psi\rangle \]
|
|
|
|
and coupled-cluster wave functions are of the form
|
|
|
|
\[ |\Phi\rangle = e^{\hat{T}}| \Psi \rangle \]
|
|
|
|
The reference wave function is stored using the ~determinant~ and/or
|
|
~csf~ groups, and the amplitudes are stored using the current group.
|
|
The attributes with the ~exp~ suffix correspond to exponentialized operators.
|
|
|
|
The order of the indices is chosen such that
|
|
- ~t(i,a)~ = $t_{i}^{a}$.
|
|
- ~t(i,j,a,b)~ = $t_{ij}^{ab}$,
|
|
- ~t(i,j,k,a,b,c)~ = $t_{ijk}^{abc}$,
|
|
- ~t(i,j,k,l,a,b,c,d)~ = $t_{ijkl}^{abcd}$,
|
|
- $\dots$
|
|
|
|
#+NAME: amplitude
|
|
| Variable | Type | Dimensions | Description |
|
|
|-----------------+----------------+-------------------------------------------------------------+-------------------------------------------------|
|
|
| ~single~ | ~float sparse~ | ~(mo.num,mo.num)~ | Single excitation amplitudes |
|
|
| ~single_exp~ | ~float sparse~ | ~(mo.num,mo.num)~ | Exponentialized single excitation amplitudes |
|
|
| ~double~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num)~ | Double excitation amplitudes |
|
|
| ~double_exp~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num)~ | Exponentialized double excitation amplitudes |
|
|
| ~triple~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Triple excitation amplitudes |
|
|
| ~triple_exp~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Exponentialized triple excitation amplitudes |
|
|
| ~quadruple~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Quadruple excitation amplitudes |
|
|
| ~quadruple_exp~ | ~float sparse~ | ~(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num)~ | Exponentialized quadruple excitation amplitudes |
|
|
|
|
#+CALL: json(data=amplitude, title="amplitude")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"amplitude": {
|
|
"single" : [ "float sparse", [ "mo.num", "mo.num" ] ]
|
|
, "single_exp" : [ "float sparse", [ "mo.num", "mo.num" ] ]
|
|
, "double" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
|
, "double_exp" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
|
, "triple" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
|
, "triple_exp" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
|
, "quadruple" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
|
, "quadruple_exp" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
|
} ,
|
|
#+end_src
|
|
:end:
|
|
|
|
** Reduced density matrices (rdm group)
|
|
|
|
The reduced density matrices are defined in the basis of molecular
|
|
orbitals.
|
|
|
|
The \uparrow-spin and \downarrow-spin components of the one-body
|
|
density matrix are given by
|
|
\begin{eqnarray*}
|
|
\gamma_{ij}^{\uparrow} &=& \langle \Psi | \hat{a}^{\dagger}_{j\alpha}\, \hat{a}_{i\alpha} | \Psi \rangle \\
|
|
\gamma_{ij}^{\downarrow} &=& \langle \Psi | \hat{a}^{\dagger}_{j\beta} \, \hat{a}_{i\beta} | \Psi \rangle
|
|
\end{eqnarray*}
|
|
and the spin-summed one-body density matrix is
|
|
\[
|
|
\gamma_{ij} = \gamma^{\uparrow}_{ij} + \gamma^{\downarrow}_{ij}
|
|
\]
|
|
|
|
The $\uparrow \uparrow$, $\downarrow \downarrow$, $\uparrow \downarrow$ components of the two-body density matrix are given by
|
|
\begin{eqnarray*}
|
|
\Gamma_{ijkl}^{\uparrow \uparrow} &=&
|
|
\langle \Psi | \hat{a}^{\dagger}_{k\alpha}\, \hat{a}^{\dagger}_{l\alpha} \hat{a}_{j\alpha}\, \hat{a}_{i\alpha} | \Psi \rangle \\
|
|
\Gamma_{ijkl}^{\downarrow \downarrow} &=&
|
|
\langle \Psi | \hat{a}^{\dagger}_{k\beta}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\beta} | \Psi \rangle \\
|
|
\Gamma_{ijkl}^{\uparrow \downarrow} &=&
|
|
\langle \Psi | \hat{a}^{\dagger}_{k\alpha}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\alpha} | \Psi \rangle
|
|
+ \langle \Psi | \hat{a}^{\dagger}_{l\alpha}\, \hat{a}^{\dagger}_{k\beta} \hat{a}_{i\beta}\, \hat{a}_{j\alpha} | \Psi \rangle \\
|
|
\end{eqnarray*}
|
|
and the spin-summed one-body density matrix is
|
|
\[
|
|
\Gamma_{ijkl} = \Gamma_{ijkl}^{\uparrow \uparrow} +
|
|
\Gamma_{ijkl}^{\downarrow \downarrow} + \Gamma_{ijkl}^{\uparrow \downarrow}.
|
|
\]
|
|
|
|
The total energy can be computed as:
|
|
\[
|
|
E = E_{\text{NN}} + \sum_{ij} \gamma_{ij} \langle j|h|i \rangle +
|
|
\frac{1}{2} \sum_{ijlk} \Gamma_{ijkl} \langle k l | i j \rangle
|
|
\]
|
|
|
|
|
|
To compress the storage, the Cholesky decomposition of the RDMs can
|
|
be stored:
|
|
|
|
\[
|
|
\Gamma_{ijkl} = \sum_{\alpha} G_{ij\alpha} G_{kl\alpha}
|
|
\]
|
|
|
|
Warning: as opposed to electron repulsion integrals, the
|
|
decomposition is made such that the Cholesky vectors are expanded
|
|
in a two-electron basis
|
|
$f_{ij}(\mathbf{r}_1,\mathbf{r}_2) = \phi_i(\mathbf{r}_1) \phi_j(\mathbf{r}_2)$,
|
|
whereas in electron repulsion integrals each Cholesky vector is
|
|
expressed in a basis of a one-electron function
|
|
$g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)$.
|
|
|
|
#+NAME: rdm
|
|
| Variable | Type | Dimensions | Description |
|
|
|------------------------+----------------+----------------------------------------------+-----------------------------------------------------------------------|
|
|
| ~1e~ | ~float~ | ~(mo.num, mo.num)~ | One body density matrix |
|
|
| ~1e_up~ | ~float~ | ~(mo.num, mo.num)~ | \uparrow-spin component of the one body density matrix |
|
|
| ~1e_dn~ | ~float~ | ~(mo.num, mo.num)~ | \downarrow-spin component of the one body density matrix |
|
|
| ~2e~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Two-body reduced density matrix (spin trace) |
|
|
| ~2e_upup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\uparrow component of the two-body reduced density matrix |
|
|
| ~2e_dndn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\downarrow component of the two-body reduced density matrix |
|
|
| ~2e_updn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\downarrow component of the two-body reduced density matrix |
|
|
| ~2e_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
|
|
| ~2e_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the two-body RDM (spin trace) |
|
|
| ~2e_upup_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
|
|
| ~2e_upup_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_upup_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\uparrow\uparrow) |
|
|
| ~2e_dndn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
|
|
| ~2e_dndn_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_dndn_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\downarrow\downarrow) |
|
|
| ~2e_updn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
|
|
| ~2e_updn_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_updn_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\uparrow\downarrow) |
|
|
|
|
#+CALL: json(data=rdm, title="rdm")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"rdm": {
|
|
"1e" : [ "float" , [ "mo.num", "mo.num" ] ]
|
|
, "1e_up" : [ "float" , [ "mo.num", "mo.num" ] ]
|
|
, "1e_dn" : [ "float" , [ "mo.num", "mo.num" ] ]
|
|
, "2e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
|
, "2e_upup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
|
, "2e_dndn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
|
, "2e_updn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
|
, "2e_cholesky_num" : [ "dim" , [] ]
|
|
, "2e_cholesky" : [ "float sparse", [ "rdm.2e_cholesky_num", "mo.num", "mo.num" ] ]
|
|
, "2e_upup_cholesky_num" : [ "dim" , [] ]
|
|
, "2e_upup_cholesky" : [ "float sparse", [ "rdm.2e_upup_cholesky_num", "mo.num", "mo.num" ] ]
|
|
, "2e_dndn_cholesky_num" : [ "dim" , [] ]
|
|
, "2e_dndn_cholesky" : [ "float sparse", [ "rdm.2e_dndn_cholesky_num", "mo.num", "mo.num" ] ]
|
|
, "2e_updn_cholesky_num" : [ "dim" , [] ]
|
|
, "2e_updn_cholesky" : [ "float sparse", [ "rdm.2e_updn_cholesky_num", "mo.num", "mo.num" ] ]
|
|
} ,
|
|
#+end_src
|
|
:end:
|
|
|
|
* Correlation factors
|
|
** Jastrow factor (jastrow group)
|
|
|
|
The Jastrow factor is an $N$-electron function which multiplies the CI
|
|
expansion: $\Psi = \Phi \times \exp(J)$,
|
|
|
|
In the following, we use the notations $r_{ij} = |\mathbf{r}_i - \mathbf{r}_j|$ and
|
|
$R_{i\alpha} = |\mathbf{r}_i - \mathbf{R}_\alpha|$, where indices
|
|
$i$ and $j$ refer to electrons and $\alpha$ to nuclei.
|
|
|
|
Parameters for multiple forms of Jastrow factors can be saved in
|
|
TREXIO files, and are described in the following sections. These
|
|
are identified by the ~type~ attribute. The type can be one of the
|
|
following:
|
|
- ~CHAMP~
|
|
- ~Mu~
|
|
|
|
*** CHAMP
|
|
|
|
The first form of Jastrow factor is the one used in
|
|
the [[https://trex-coe.eu/trex-quantum-chemistry-codes/champ][CHAMP]] program:
|
|
|
|
\[
|
|
J(\mathbf{r},\mathbf{R}) = J_{\text{eN}}(\mathbf{r},\mathbf{R}) + J_{\text{ee}}(\mathbf{r}) + J_{\text{eeN}}(\mathbf{r},\mathbf{R})
|
|
\]
|
|
|
|
|
|
$J_{\text{eN}}$ contains electron-nucleus terms:
|
|
|
|
\[
|
|
J_{\text{eN}}(\mathbf{r},\mathbf{R}) = \sum_{i=1}^{N_\text{elec}} \sum_{\alpha=1}^{N_\text{nucl}}\left[
|
|
\frac{a_{1,\alpha}\, f_\alpha(R_{i\alpha})}{1+a_{2,\alpha}\,
|
|
f_\alpha(R_{i\alpha})} + \sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, [f_\alpha(R_{i\alpha})]^p - J_{\text{eN}}^\infty
|
|
\right]
|
|
\]
|
|
|
|
$J_{\text{ee}}$ contains electron-electron terms:
|
|
|
|
\[
|
|
J_{\text{ee}}(\mathbf{r}) =
|
|
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1}
|
|
\left[
|
|
\frac{\frac{1}{2}\big(1 + \delta^{\uparrow\downarrow}_{ij}\big)\,b_1\, f_{\text{ee}}(r_{ij})}{1+b_2\, f_{\text{ee}}(r_{ij})} +
|
|
\sum_{p=2}^{N_\text{ord}^b} b_{p+1}\, [f_{\text{ee}}(r_{ij})]^p - J_{\text{ee},ij}^\infty
|
|
\right]
|
|
\]
|
|
|
|
$\delta^{\uparrow\downarrow}_{ij}$ is zero when the electrons $i$ and
|
|
$j$ have the same spin, and one otherwise.
|
|
|
|
$J_{\text{eeN}}$ contains electron-electron-Nucleus terms:
|
|
|
|
\[
|
|
J_{\text{eeN}}(\mathbf{r},\mathbf{R}) =
|
|
\sum_{\alpha=1}^{N_{\text{nucl}}}
|
|
\sum_{i=1}^{N_{\text{elec}}}
|
|
\sum_{j=1}^{i-1}
|
|
\sum_{p=2}^{N_{\text{ord}}}
|
|
\sum_{k=0}^{p-1}
|
|
\sum_{l=0}^{p-k-2\delta_{k,0}}
|
|
c_{lkp\alpha} \left[ g_{\text{ee}}({r}_{ij}) \right]^k \nonumber \\
|
|
\left[ \left[ g_\alpha({R}_{i\alpha}) \right]^l + \left[ g_\alpha({R}_{j\alpha}) \right]^l \right]
|
|
\left[ g_\alpha({R}_{i\,\alpha}) \,
|
|
g_\alpha({R}_{j\alpha}) \right]^{(p-k-l)/2}
|
|
\]
|
|
$c_{lkp\alpha}$ are non-zero only when $p-k-l$ is even.
|
|
|
|
The terms $J_{\text{ee},ij}^\infty$ and $J_{\text{eN}}^\infty$ are shifts to ensure that
|
|
$J_{\text{eN}}$ and $J_{\text{ee}}$ have an asymptotic value of zero:
|
|
|
|
\[
|
|
J_{\text{eN}}^{\infty} =
|
|
\frac{a_{1,\alpha}\, \kappa_\alpha^{-1}}{1+a_{2,\alpha}\,
|
|
\kappa_\alpha^{-1}} + \sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, \kappa_\alpha^{-p}
|
|
\]
|
|
\[
|
|
J_{\text{ee},ij}^{\infty} =
|
|
\frac{\frac{1}{2}\big(1 + \delta^{\uparrow\downarrow}_{ij}\big)\,b_1\,
|
|
\kappa_{\text{ee}}^{-1}}{1+b_2\, \kappa_{\text{ee}}^{-1}} +
|
|
\sum_{p=2}^{N_\text{ord}^b} b_{p+1}\, \kappa_{\text{ee}}^{-p}
|
|
\]
|
|
|
|
$f$ and $g$ are scaling function defined as
|
|
|
|
\[
|
|
f_\alpha(r) = \frac{1-e^{-\kappa_\alpha\, r}}{\kappa_\alpha} \text{ and }
|
|
g_\alpha(r) = e^{-\kappa_\alpha\, r},
|
|
\]
|
|
|
|
|
|
*** Mu
|
|
|
|
[[https://aip.scitation.org/doi/10.1063/5.0044683][Mu-Jastrow]] is based on a one-parameter correlation factor that has
|
|
been introduced in the context of transcorrelated methods. This
|
|
correlation factor imposes the electron-electron cusp, and it is
|
|
built such that the leading order in $1/r_{12}$ of the effective
|
|
two-electron potential reproduces the long-range interaction of the
|
|
range-separated density functional theory. Its analytical
|
|
expression reads
|
|
|
|
\[
|
|
J(\mathbf{r}, \mathbf{R}) = J_{\text{eeN}}(\mathbf{r}, \mathbf{R}) +
|
|
J_{\text{eN}}(\mathbf{r}, \mathbf{R})
|
|
\].
|
|
|
|
The electron-electron cusp is incorporated in the three-body term
|
|
|
|
\[
|
|
J_\text{eeN} (\mathbf{r}, \mathbf{R}) =
|
|
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right) \,
|
|
\Pi_{\alpha=1}^{N_{\text{nucl}}} \, E_\alpha({R}_{i\alpha}) \, E_\alpha({R}_{j\alpha}),
|
|
\]
|
|
|
|
where ww$u$ is an electron-electron function
|
|
|
|
\[
|
|
u\left(\mu, r\right) = \frac{r}{2} \, \left[ 1 - \text{erf}(\mu\, r) \right] - \frac{1}{2 \, \mu \, \sqrt{\pi}} \exp \left[ -(\mu \, r)^2 \right].
|
|
\]
|
|
|
|
This electron-electron term is tuned by the parameter $\mu$ which
|
|
controls the depth and the range of the Coulomb hole between
|
|
electrons.
|
|
|
|
An envelope function has been introduced to cancel out the Jastrow
|
|
effects between two-electrons when at least one is close to a nucleus
|
|
(to perform a frozen-core calculation). The envelope function is
|
|
given by
|
|
|
|
\[
|
|
E_\alpha(R) = 1 - \exp\left( - \gamma_{\alpha} \, R^2 \right).
|
|
\]
|
|
|
|
In particular, if the parameters $\gamma_\alpha$ tend to zero, the
|
|
Mu-Jastrow factor becomes a two-body Jastrow factor:
|
|
|
|
\[
|
|
J_{\text{ee}}(\mathbf{r}) =
|
|
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right)
|
|
\]
|
|
|
|
and for large $\gamma_\alpha$ it becomes zero.
|
|
|
|
To increase the flexibility of the Jastrow and improve the
|
|
electron density the following electron-nucleus term is added
|
|
|
|
\[
|
|
J_{\text{eN}}(\mathbf{r},\mathbf{R}) = \sum_{i=1}^{N_\text{elec}} \sum_{\alpha=1}^{N_\text{nucl}} \,
|
|
\left[ \exp\left( a_{\alpha} R_{i \alpha}^2 \right) - 1\right].
|
|
\]
|
|
|
|
|
|
The parameter $\mu$ is stored in the ~ee~ array, the parameters
|
|
$\gamma_\alpha$ are stored in the ~een~ array, and the parameters
|
|
$a_\alpha$ are stored in the ~en~ array.
|
|
|
|
*** Table of values
|
|
|
|
#+name: jastrow
|
|
| Variable | Type | Dimensions | Description |
|
|
|---------------+----------+---------------------+-----------------------------------------------------------------|
|
|
| ~type~ | ~string~ | | Type of Jastrow factor: ~CHAMP~ or ~Mu~ |
|
|
| ~en_num~ | ~dim~ | | Number of Electron-nucleus parameters |
|
|
| ~ee_num~ | ~dim~ | | Number of Electron-electron parameters |
|
|
| ~een_num~ | ~dim~ | | Number of Electron-electron-nucleus parameters |
|
|
| ~en~ | ~float~ | ~(jastrow.en_num)~ | Electron-nucleus parameters |
|
|
| ~ee~ | ~float~ | ~(jastrow.ee_num)~ | Electron-electron parameters |
|
|
| ~een~ | ~float~ | ~(jastrow.een_num)~ | Electron-electron-nucleus parameters |
|
|
| ~en_nucleus~ | ~index~ | ~(jastrow.en_num)~ | Nucleus relative to the eN 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 |
|
|
| ~en_scaling~ | ~float~ | ~(nucleus.num)~ | $\kappa$ value in CHAMP Jastrow for electron-nucleus distances |
|
|
|
|
#+CALL: json(data=jastrow, title="jastrow")
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"jastrow": {
|
|
"type" : [ "string", [] ]
|
|
, "en_num" : [ "dim" , [] ]
|
|
, "ee_num" : [ "dim" , [] ]
|
|
, "een_num" : [ "dim" , [] ]
|
|
, "en" : [ "float" , [ "jastrow.en_num" ] ]
|
|
, "ee" : [ "float" , [ "jastrow.ee_num" ] ]
|
|
, "een" : [ "float" , [ "jastrow.een_num" ] ]
|
|
, "en_nucleus" : [ "index" , [ "jastrow.en_num" ] ]
|
|
, "een_nucleus" : [ "index" , [ "jastrow.een_num" ] ]
|
|
, "ee_scaling" : [ "float" , [] ]
|
|
, "en_scaling" : [ "float" , [ "nucleus.num" ] ]
|
|
} ,
|
|
#+end_src
|
|
:end:
|
|
|
|
* Quantum Monte Carlo data (qmc group)
|
|
|
|
In quantum Monte Carlo calculations, the wave function is evaluated
|
|
at points of the 3N-dimensional space. Some algorithms require multiple
|
|
independent /walkers/, so it is possible to store multiple coordinates,
|
|
as well as some quantities evaluated at those points.
|
|
|
|
By convention, the electron coordinates contain first all the electrons
|
|
of $\uparrow$-spin and then all the $\downarrow$-spin.
|
|
|
|
#+name: qmc
|
|
| Variable | Type | Dimensions | Description |
|
|
|----------+---------+------------------------------+---------------------------------------|
|
|
| ~num~ | ~dim~ | | Number of 3N-dimensional points |
|
|
| ~point~ | ~float~ | ~(3, electron.num, qmc.num)~ | 3N-dimensional points |
|
|
| ~psi~ | ~float~ | ~(qmc.num)~ | Wave function evaluated at the points |
|
|
| ~e_loc~ | ~float~ | ~(qmc.num)~ | Local energy evaluated at the points |
|
|
|
|
#+CALL: json(data=qmc, title="qmc", last=1)
|
|
|
|
#+RESULTS:
|
|
:results:
|
|
#+begin_src python :tangle trex.json
|
|
"qmc": {
|
|
"num" : [ "dim" , [] ]
|
|
, "point" : [ "float", [ "qmc.num", "electron.num", "3" ] ]
|
|
, "psi" : [ "float", [ "qmc.num" ] ]
|
|
, "e_loc" : [ "float", [ "qmc.num" ] ]
|
|
}
|
|
#+end_src
|
|
:end:
|
|
|
|
* Appendix :noexport:
|
|
** Python script from table to json
|
|
|
|
#+NAME: json
|
|
#+begin_src python :var data=nucleus title="nucleus" last=0 :results output drawer
|
|
print("""#+begin_src python :tangle trex.json""")
|
|
print(""" "%s": {"""%(title))
|
|
indent = " "
|
|
f1 = 0 ; f2 = 0 ; f3 = 0
|
|
for line in data:
|
|
line = [ x.replace("~","") for x in line ]
|
|
name = '"'+line[0]+'"'
|
|
typ = '"'+line[1]+'"'
|
|
dims = line[2]
|
|
if '(' in dims:
|
|
dims = dims.strip()[1:-1]
|
|
dims = [ '"'+x.strip()+'"' for x in dims.split(',') ]
|
|
dims = "[ " + ", ".join(dims) + " ]"
|
|
else:
|
|
dims = "[ ]"
|
|
f1 = max(f1, len(name))
|
|
f2 = max(f2, len(typ))
|
|
f3 = max(f3, len(dims))
|
|
|
|
fmt = "%%s%%%ds : [ %%%ds, %%%ds ]" % (f1, f2, f3)
|
|
for line in data:
|
|
line = [ x.replace("~","") for x in line ]
|
|
name = '"'+line[0]+'"'
|
|
typ = '"'+line[1]+'"'
|
|
dims = line[2]
|
|
if '(' in dims:
|
|
dims = dims.strip()[1:-1]
|
|
dims = [ '"'+x.strip()+'"' for x in dims.split(',') ]
|
|
dims.reverse()
|
|
dims = "[ " + ", ".join(dims) + " ]"
|
|
else:
|
|
if dims.strip() != "":
|
|
dims = "ERROR"
|
|
else:
|
|
dims = "[]"
|
|
buffer = fmt % (indent, name, typ.ljust(f2), dims.ljust(f3))
|
|
indent = " , "
|
|
print(buffer)
|
|
|
|
if last == 0:
|
|
print(" } ,")
|
|
else:
|
|
print(" }")
|
|
print("""#+end_src""")
|
|
|
|
#+end_src
|
|
|
|
|
|
#+begin_src python :tangle trex.json :results output drawer :exports none
|
|
}
|
|
#+end_src
|