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Added kpoint to MO group #138

Merged
merged 7 commits into from
May 13, 2024
Merged

Added kpoint to MO group #138

merged 7 commits into from
May 13, 2024

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scemama
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@scemama scemama commented Feb 15, 2024

I have added an array kpoint to the MO group.
With this modification, the users can store all the MOs of all kpoints in a single file. This is necessary because for correlated calculations (CI or CC), it is necessary to have 2-electron integrals involving MOs of different kpoints.
With this modification, it is possible to extend the format to correlated periodic calculations without breaking backwards compatibility.

scemama
scemama commented Feb 15, 2024
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Comment on lines 1328 to 1349
| Variable | Type | Dimensions | Description |
|---------------+----------+---------------------+-----------------------------------------------------------------|
| ~type~ | ~str~ | | 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 |
| Variable | Type | Dimensions | Description |
|---------------+---------+---------------------+-----------------------------------------------------------------|
| ~type~ | ~str~ | | 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 |
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scemama
scemama commented Feb 15, 2024
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scemama
scemama commented Feb 15, 2024
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Comment on lines 811 to 832
| Variable | Type | Dimensions | Description |
|------------------+---------+--------------------+--------------------------------------------------------------------------|
| ~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 stored in the file |
| ~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 $\beta$ |
| ~kpoint~ | ~int~ | ~(mo.num)~ | For periodic calculations, the $k$ point to which each MO belongs |

**Warning**: ~mo.num~ is the total number of MOs stored in the file.
For periodic calculations, this group contains all the MOs
belonging to all $k$ points so ~mo.num~ will be the sum of the
numbers of MOs in each $k$ point. For UHF wave functions, ~mo.num~
is the number of spin-orbitals, twice the number of spatial orbitals.

#+CALL: json(data=mo, title="mo")

#+RESULTS:
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The modification is here

scemama
scemama commented Feb 15, 2024
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Comment on lines 842 to 853
, "occupation" : [ "float", [ "mo.num" ] ]
, "energy" : [ "float", [ "mo.num" ] ]
, "spin" : [ "int" , [ "mo.num" ] ]
, "kpoint" : [ "int" , [ "mo.num" ] ]
} ,
#+end_src
:end:


*** One-electron integrals (~mo_1e_int~ group)

The operators as the same as those defined in the
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... and here

scemama
scemama commented Feb 15, 2024
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Comment on lines 326 to 354
*** Data definitions

#+NAME: basis
| Variable | Type | Dimensions | Description | |
|---------------------+---------+----------------------------------------------+------------------------------------------------------------------------------+---|
| ~type~ | ~str~ | | Type of basis set: "Gaussian", "Slater", "Numerical" or "PW" for plane waves | |
| ~prim_num~ | ~dim~ | | Total number of primitives | |
| ~shell_num~ | ~dim~ | | Total number of shells | |
| ~nao_grid_num~ | ~dim~ | | Total number of grid points for numerical orbitals | |
| ~interp_coeff_cnt~ | ~dim~ | | Number of coefficients for the numerical orbital interpolator | |
| ~nucleus_index~ | ~index~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and atomic indices | |
| ~shell_ang_mom~ | ~int~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and angular momenta | |
| ~shell_factor~ | ~float~ | ~(basis.shell_num)~ | Normalization factor of each shell ($\mathcal{N}_s$) | |
| ~r_power~ | ~int~ | ~(basis.shell_num)~ | Power to which $r$ is raised ($n_s$) | |
| ~nao_grid_start~ | ~index~ | ~(basis.shell_num)~ | Index of the first data point for a given numerical orbital | |
| ~nao_grid_size~ | ~dim~ | ~(basis.shell_num)~ | Number of data points per numerical orbital | |
| ~shell_index~ | ~index~ | ~(basis.prim_num)~ | One-to-one correspondence between primitives and shell index | |
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) | |
| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) | |
| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) | |
| ~e_cut~ | ~float~ | | Energy cut-off for plane-wave calculations | |
| ~nao_grid_radius~ | ~float~ | ~(basis.nao_grid_num)~ | Radii of grid points for numerical orbitals | |
| ~nao_grid_phi~ | ~float~ | ~(basis.nao_grid_num)~ | Wave function values for numerical orbitals | |
| ~nao_grid_grad~ | ~float~ | ~(basis.nao_grid_num)~ | Radial gradient of numerical orbitals | |
| ~nao_grid_lap~ | ~float~ | ~(basis.nao_grid_num)~ | Laplacian of numerical orbitals | |
| ~interpolator_kind~ | ~str~ | | Kind of spline, e.g. "Polynomial" | |
| ~interpolator_phi~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital interpolation function | |
| ~interpolator_grad~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital gradient interpolation function | |
| ~interpolator_lap~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital laplacian interpolation function | |
| Variable | Type | Dimensions | Description |
|---------------------+---------+-----------------------------------------------+------------------------------------------------------------------------------|
| ~type~ | ~str~ | | Type of basis set: "Gaussian", "Slater", "Numerical" or "PW" for plane waves |
| ~prim_num~ | ~dim~ | | Total number of primitives |
| ~shell_num~ | ~dim~ | | Total number of shells |
| ~nao_grid_num~ | ~dim~ | | Total number of grid points for numerical orbitals |
| ~interp_coeff_cnt~ | ~dim~ | | Number of coefficients for the numerical orbital interpolator |
| ~nucleus_index~ | ~index~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and atomic indices |
| ~shell_ang_mom~ | ~int~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and angular momenta |
| ~shell_factor~ | ~float~ | ~(basis.shell_num)~ | Normalization factor of each shell ($\mathcal{N}_s$) |
| ~r_power~ | ~int~ | ~(basis.shell_num)~ | Power to which $r$ is raised ($n_s$) |
| ~nao_grid_start~ | ~index~ | ~(basis.shell_num)~ | Index of the first data point for a given numerical orbital |
| ~nao_grid_size~ | ~dim~ | ~(basis.shell_num)~ | Number of data points per numerical orbital |
| ~shell_index~ | ~index~ | ~(basis.prim_num)~ | One-to-one correspondence between primitives and shell index |
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) |
| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) |
| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
| ~e_cut~ | ~float~ | | Energy cut-off for plane-wave calculations |
| ~nao_grid_radius~ | ~float~ | ~(basis.nao_grid_num)~ | Radii of grid points for numerical orbitals |
| ~nao_grid_phi~ | ~float~ | ~(basis.nao_grid_num)~ | Wave function values for numerical orbitals |
| ~nao_grid_grad~ | ~float~ | ~(basis.nao_grid_num)~ | Radial gradient of numerical orbitals |
| ~nao_grid_lap~ | ~float~ | ~(basis.nao_grid_num)~ | Laplacian of numerical orbitals |
| ~interpolator_kind~ | ~str~ | | Kind of spline, e.g. "Polynomial" |
| ~interpolator_phi~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital interpolation function |
| ~interpolator_grad~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital gradient interpolation function |
| ~interpolator_lap~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital laplacian interpolation function |
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@scemama scemama changed the title sAdded kpoint to MO group Added kpoint to MO group Feb 16, 2024
@q-posev
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q-posev commented Feb 16, 2024

I let @kousuke-nakano decide. He will know if it posses issues for the files produced in the past where we had TREXIO file per k-point.

Also, it is not clear to me how you want to arrange the data with the new mo_num. For example, the mo_coefficient matrix: one has to be extremely careful not to screw up the data ordering if all k-points go in the same array.

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scemama commented Mar 1, 2024

@kousuke-nakano ping!

kousuke-nakano
kousuke-nakano requested changes Mar 1, 2024
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scemama commented Mar 1, 2024
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addman2 reviewed Mar 13, 2024
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scemama commented May 13, 2024

@q-posev : I think we can merge this branch now...

@q-posev q-posev merged commit 1117a5b into master May 13, 2024
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@q-posev q-posev deleted the kpoint branch May 13, 2024 15:06
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@q-posev q-posev q-posev approved these changes

@kousuke-nakano kousuke-nakano Awaiting requested review from kousuke-nakano

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@scemama @q-posev @addman2 @kousuke-nakano