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Add ingredients for periodic calculations (#92)
* 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
This commit is contained in:
Evgeny Posenitskiy
GitHub
parent
9186a9493f
commit
a308146ded
148
trex.org
148
trex.org
@ -496,28 +496,38 @@ prim_factor =
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over atomic orbitals.
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#+NAME: ao_1e_int
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| Variable | Type | Dimensions | Description |
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|--------------------+---------+--------------------+--------------------------------------------------------|
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| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
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| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
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| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
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| ~ecp~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ |
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| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
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| Variable | Type | Dimensions | Description |
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|-----------------------+---------+--------------------+-----------------------------------------------------------------------------------|
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| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (real part, general case) |
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| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (real part, general case) |
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| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (real part, general case) |
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| ~ecp~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ (real part, general case) |
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| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (real part, general case) |
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| ~overlap_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (imaginary part) (imaginary part) |
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| ~kinetic_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (imaginary part) |
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| ~potential_n_e_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (imaginary part) |
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| ~ecp_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ECP}} \vert q \rangle$ (imaginary part) |
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| ~core_hamiltonian_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (imaginary part) |
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#+CALL: json(data=ao_1e_int, title="ao_1e_int")
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#+RESULTS:
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:results:
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:RESULTS:
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#+begin_src python :tangle trex.json
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"ao_1e_int": {
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"overlap" : [ "float", [ "ao.num", "ao.num" ] ]
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, "kinetic" : [ "float", [ "ao.num", "ao.num" ] ]
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, "potential_n_e" : [ "float", [ "ao.num", "ao.num" ] ]
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, "ecp" : [ "float", [ "ao.num", "ao.num" ] ]
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, "core_hamiltonian" : [ "float", [ "ao.num", "ao.num" ] ]
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"overlap" : [ "float", [ "ao.num", "ao.num" ] ]
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, "kinetic" : [ "float", [ "ao.num", "ao.num" ] ]
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, "potential_n_e" : [ "float", [ "ao.num", "ao.num" ] ]
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, "ecp" : [ "float", [ "ao.num", "ao.num" ] ]
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, "core_hamiltonian" : [ "float", [ "ao.num", "ao.num" ] ]
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, "overlap_im" : [ "float", [ "ao.num", "ao.num" ] ]
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, "kinetic_im" : [ "float", [ "ao.num", "ao.num" ] ]
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, "potential_n_e_im" : [ "float", [ "ao.num", "ao.num" ] ]
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, "ecp_im" : [ "float", [ "ao.num", "ao.num" ] ]
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, "core_hamiltonian_im" : [ "float", [ "ao.num", "ao.num" ] ]
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} ,
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#+end_src
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:end:
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:END:
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** Two-electron integrals (~ao_2e_int~ group)
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:PROPERTIES:
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@ -560,14 +570,15 @@ prim_factor =
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* Molecular orbitals (mo group)
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#+NAME: mo
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| Variable | Type | Dimensions | Description |
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|---------------+---------+--------------------+--------------------------------------------------------------------------|
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| ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) |
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| ~num~ | ~dim~ | | Number of MOs |
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| ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients |
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| ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted |
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| ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group |
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| ~occupation~ | ~float~ | ~(mo.num)~ | Occupation number |
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| Variable | Type | Dimensions | Description |
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|------------------+---------+--------------------+--------------------------------------------------------------------------|
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| ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) |
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| ~num~ | ~dim~ | | Number of MOs |
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| ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (real part, general case) |
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| ~coefficient_im~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (imaginary part, for periodic calculations) |
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| ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted |
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| ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group |
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| ~occupation~ | ~float~ | ~(mo.num)~ | Occupation number |
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#+CALL: json(data=mo, title="mo")
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@ -575,12 +586,13 @@ prim_factor =
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:RESULTS:
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#+begin_src python :tangle trex.json
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"mo": {
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"type" : [ "str" , [] ]
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, "num" : [ "dim" , [] ]
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, "coefficient" : [ "float", [ "mo.num", "ao.num" ] ]
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, "class" : [ "str" , [ "mo.num" ] ]
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, "symmetry" : [ "str" , [ "mo.num" ] ]
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, "occupation" : [ "float", [ "mo.num" ] ]
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"type" : [ "str" , [] ]
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, "num" : [ "dim" , [] ]
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, "coefficient" : [ "float", [ "mo.num", "ao.num" ] ]
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, "coefficient_im" : [ "float", [ "mo.num", "ao.num" ] ]
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, "class" : [ "str" , [ "mo.num" ] ]
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, "symmetry" : [ "str" , [ "mo.num" ] ]
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, "occupation" : [ "float", [ "mo.num" ] ]
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} ,
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#+end_src
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:END:
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@ -592,28 +604,38 @@ prim_factor =
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the basis of molecular orbitals.
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#+NAME: mo_1e_int
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| Variable | Type | Dimensions | Description |
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|--------------------+---------+--------------------+--------------------------------------------------------|
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| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ |
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| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ |
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| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ |
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| ~ecp~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ |
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| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
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| Variable | Type | Dimensions | Description |
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|-----------------------+---------+--------------------+-----------------------------------------------------------------------------------|
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| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (real part, general case) |
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| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ (real part, general case) |
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| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (real part, general case) |
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| ~ecp~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (real part, general case) |
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| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ (real part, general case) |
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| ~overlap_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (imaginary part) (imaginary part) |
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| ~kinetic_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ (imaginary part) |
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| ~potential_n_e_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (imaginary part) |
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| ~ecp_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (imaginary part) |
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| ~core_hamiltonian_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ (imaginary part) |
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#+CALL: json(data=mo_1e_int, title="mo_1e_int")
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#+RESULTS:
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:results:
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:RESULTS:
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#+begin_src python :tangle trex.json
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"mo_1e_int": {
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"overlap" : [ "float", [ "mo.num", "mo.num" ] ]
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, "kinetic" : [ "float", [ "mo.num", "mo.num" ] ]
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, "potential_n_e" : [ "float", [ "mo.num", "mo.num" ] ]
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, "ecp" : [ "float", [ "mo.num", "mo.num" ] ]
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, "core_hamiltonian" : [ "float", [ "mo.num", "mo.num" ] ]
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"overlap" : [ "float", [ "mo.num", "mo.num" ] ]
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, "kinetic" : [ "float", [ "mo.num", "mo.num" ] ]
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, "potential_n_e" : [ "float", [ "mo.num", "mo.num" ] ]
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, "ecp" : [ "float", [ "mo.num", "mo.num" ] ]
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, "core_hamiltonian" : [ "float", [ "mo.num", "mo.num" ] ]
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, "overlap_im" : [ "float", [ "mo.num", "mo.num" ] ]
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, "kinetic_im" : [ "float", [ "mo.num", "mo.num" ] ]
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, "potential_n_e_im" : [ "float", [ "mo.num", "mo.num" ] ]
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, "ecp_im" : [ "float", [ "mo.num", "mo.num" ] ]
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, "core_hamiltonian_im" : [ "float", [ "mo.num", "mo.num" ] ]
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} ,
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#+end_src
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:end:
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:END:
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** Two-electron integrals (~mo_2e_int~ group)
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@ -778,6 +800,48 @@ prim_factor =
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#+end_src
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:end:
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* Cell (cell group)
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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 unit cell vector |
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| ~b~ | ~float~ | ~(3)~ | Second unit cell vector |
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| ~c~ | ~float~ | ~(3)~ | Third unit cell vector |
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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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} ,
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#+end_src
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:END:
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* Periodic boundary calculations (pbc 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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* Quantum Monte Carlo data (qmc group)
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In quantum Monte Carlo calculations, the wave function is evaluated
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