-
Notifications
You must be signed in to change notification settings - Fork 14
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Added kpoint to MO group #138
Conversation
trex.org
Outdated
| 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 | |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Spaces
trex.org
Outdated
| 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: |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
The modification is here
trex.org
Outdated
, "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 |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
... and here
trex.org
Outdated
*** 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 | |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Spaces
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 |
@kousuke-nakano ping! |
@q-posev : I think we can merge this branch now... |
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.