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Add ingredients for periodic calculations (#92)

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* Add ingredients for periodic calculations

* Add pbc group and k-point attribute

* Fix dimensions for k_point

* Remove dimensions for k_point

* Update the JSON output block for the MO
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Evgeny Posenitskiy 2022-05-25 10:07:59 +02:00 committed by GitHub
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1 changed files with 106 additions and 42 deletions
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@ -496,28 +496,38 @@ prim_factor =
over atomic orbitals. over atomic orbitals.
#+NAME: ao_1e_int #+NAME: ao_1e_int
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|--------------------+---------+--------------------+--------------------------------------------------------| |-----------------------+---------+--------------------+-----------------------------------------------------------------------------------|
| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ | | ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (real part, general case) |
| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ | | ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (real part, general case) |
| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ | | ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (real part, general case) |
| ~ecp~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ | | ~ecp~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ (real part, general case) |
| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ | | ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (real part, general case) |
| ~overlap_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (imaginary part) (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") #+CALL: json(data=ao_1e_int, title="ao_1e_int")
#+RESULTS: #+RESULTS:
:results: :RESULTS:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"ao_1e_int": { "ao_1e_int": {
"overlap" : [ "float", [ "ao.num", "ao.num" ] ] "overlap" : [ "float", [ "ao.num", "ao.num" ] ]
, "kinetic" : [ "float", [ "ao.num", "ao.num" ] ] , "kinetic" : [ "float", [ "ao.num", "ao.num" ] ]
, "potential_n_e" : [ "float", [ "ao.num", "ao.num" ] ] , "potential_n_e" : [ "float", [ "ao.num", "ao.num" ] ]
, "ecp" : [ "float", [ "ao.num", "ao.num" ] ] , "ecp" : [ "float", [ "ao.num", "ao.num" ] ]
, "core_hamiltonian" : [ "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_src
:end: :END:
** Two-electron integrals (~ao_2e_int~ group) ** Two-electron integrals (~ao_2e_int~ group)
:PROPERTIES: :PROPERTIES:
@ -560,14 +570,15 @@ prim_factor =
* Molecular orbitals (mo group) * Molecular orbitals (mo group)
#+NAME: mo #+NAME: mo
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|---------------+---------+--------------------+--------------------------------------------------------------------------| |------------------+---------+--------------------+--------------------------------------------------------------------------|
| ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) | | ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) |
| ~num~ | ~dim~ | | Number of MOs | | ~num~ | ~dim~ | | Number of MOs |
| ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients | | ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (real part, general case) |
| ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted | | ~coefficient_im~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (imaginary part, for periodic calculations) |
| ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group | | ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted |
| ~occupation~ | ~float~ | ~(mo.num)~ | Occupation number | | ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group |
| ~occupation~ | ~float~ | ~(mo.num)~ | Occupation number |
#+CALL: json(data=mo, title="mo") #+CALL: json(data=mo, title="mo")
@ -575,12 +586,13 @@ prim_factor =
:RESULTS: :RESULTS:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"mo": { "mo": {
"type" : [ "str" , [] ] "type" : [ "str" , [] ]
, "num" : [ "dim" , [] ] , "num" : [ "dim" , [] ]
, "coefficient" : [ "float", [ "mo.num", "ao.num" ] ] , "coefficient" : [ "float", [ "mo.num", "ao.num" ] ]
, "class" : [ "str" , [ "mo.num" ] ] , "coefficient_im" : [ "float", [ "mo.num", "ao.num" ] ]
, "symmetry" : [ "str" , [ "mo.num" ] ] , "class" : [ "str" , [ "mo.num" ] ]
, "occupation" : [ "float", [ "mo.num" ] ] , "symmetry" : [ "str" , [ "mo.num" ] ]
, "occupation" : [ "float", [ "mo.num" ] ]
} , } ,
#+end_src #+end_src
:END: :END:
@ -592,28 +604,38 @@ prim_factor =
the basis of molecular orbitals. the basis of molecular orbitals.
#+NAME: mo_1e_int #+NAME: mo_1e_int
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|--------------------+---------+--------------------+--------------------------------------------------------| |-----------------------+---------+--------------------+-----------------------------------------------------------------------------------|
| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ | | ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (real part, general case) |
| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ | | ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ (real part, general case) |
| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ | | ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (real part, general case) |
| ~ecp~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ | | ~ecp~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (real part, general case) |
| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ | | ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ (real part, general case) |
| ~overlap_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (imaginary part) (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") #+CALL: json(data=mo_1e_int, title="mo_1e_int")
#+RESULTS: #+RESULTS:
:results: :RESULTS:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"mo_1e_int": { "mo_1e_int": {
"overlap" : [ "float", [ "mo.num", "mo.num" ] ] "overlap" : [ "float", [ "mo.num", "mo.num" ] ]
, "kinetic" : [ "float", [ "mo.num", "mo.num" ] ] , "kinetic" : [ "float", [ "mo.num", "mo.num" ] ]
, "potential_n_e" : [ "float", [ "mo.num", "mo.num" ] ] , "potential_n_e" : [ "float", [ "mo.num", "mo.num" ] ]
, "ecp" : [ "float", [ "mo.num", "mo.num" ] ] , "ecp" : [ "float", [ "mo.num", "mo.num" ] ]
, "core_hamiltonian" : [ "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_src
:end: :END:
** Two-electron integrals (~mo_2e_int~ group) ** Two-electron integrals (~mo_2e_int~ group)
@ -778,6 +800,48 @@ prim_factor =
#+end_src #+end_src
:end: :end:
* Cell (cell group)
#+NAME: cell
| Variable | Type | Dimensions | Description |
|----------+---------+------------+-------------------------|
| ~a~ | ~float~ | ~(3)~ | First unit cell vector |
| ~b~ | ~float~ | ~(3)~ | Second unit cell vector |
| ~c~ | ~float~ | ~(3)~ | Third unit cell vector |
#+CALL: json(data=cell, title="cell")
#+RESULTS:
:RESULTS:
#+begin_src python :tangle trex.json
"cell": {
"a" : [ "float", [ "3" ] ]
, "b" : [ "float", [ "3" ] ]
, "c" : [ "float", [ "3" ] ]
} ,
#+end_src
:END:
* Periodic boundary calculations (pbc group)
#+NAME: pbc
| Variable | Type | Dimensions | Description |
|------------+---------+------------+-------------------------|
| ~periodic~ | ~int~ | | ~1~: true or ~0~: false |
| ~k_point~ | ~float~ | ~(3)~ | k-point sampling |
#+CALL: json(data=pbc, title="pbc")
#+RESULTS:
:RESULTS:
#+begin_src python :tangle trex.json
"pbc": {
"periodic" : [ "int" , [] ]
, "k_point" : [ "float", [ "3" ] ]
} ,
#+end_src
:END:
* Quantum Monte Carlo data (qmc group) * Quantum Monte Carlo data (qmc group)
In quantum Monte Carlo calculations, the wave function is evaluated In quantum Monte Carlo calculations, the wave function is evaluated