TREX/trexio
1
0
Fork 0
mirror of https://github.com/TREX-CoE/trexio.git synced 2024-11-03 20:54:07 +01:00
Code Issues Projects Releases Wiki Activity

Merge pull request #139 from TREX-CoE/transrdm

Browse Source 
Added 1e and 2e transition density matrices for GammCor
This commit is contained in:
Anthony Scemama 2024-02-21 13:01:48 +01:00 committed by GitHub
commit c368ac4c9d
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
1 changed files with 72 additions and 68 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

140
trex.org
View File

@ -326,29 +326,29 @@
*** Data definitions *** Data definitions
#+NAME: basis #+NAME: basis
| Variable | Type | Dimensions | Description | | | Variable | Type | Dimensions | Description | |
|---------------------+---------+----------------------------------------------+------------------------------------------------------------------------------+---| |---------------------+---------+-----------------------------------------------+------------------------------------------------------------------------------+---|
| ~type~ | ~str~ | | Type of basis set: "Gaussian", "Slater", "Numerical" or "PW" for plane waves | | | ~type~ | ~str~ | | Type of basis set: "Gaussian", "Slater", "Numerical" or "PW" for plane waves | |
| ~prim_num~ | ~dim~ | | Total number of primitives | | | ~prim_num~ | ~dim~ | | Total number of primitives | |
| ~shell_num~ | ~dim~ | | Total number of shells | | | ~shell_num~ | ~dim~ | | Total number of shells | |
| ~nao_grid_num~ | ~dim~ | | Total number of grid points for numerical orbitals | | | ~nao_grid_num~ | ~dim~ | | Total number of grid points for numerical orbitals | |
| ~interp_coeff_cnt~ | ~dim~ | | Number of coefficients for the numerical orbital interpolator | | | ~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 | | | ~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_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 ($\mathcal{N}_s$) | | | ~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 ($n_s$) | | | ~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_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 | | | ~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 | | | ~shell_index~ | ~index~ | ~(basis.prim_num)~ | One-to-one correspondence between primitives and shell index | |
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) | | | ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) | |
| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) | | | ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) | |
| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) | | | ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) | |
| ~e_cut~ | ~float~ | | Energy cut-off for plane-wave calculations | | | ~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_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_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_grad~ | ~float~ | ~(basis.nao_grid_num)~ | Radial gradient of numerical orbitals | |
| ~nao_grid_lap~ | ~float~ | ~(basis.nao_grid_num)~ | Laplacian 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_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_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_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 | | | ~interpolator_lap~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital laplacian interpolation function | |
@ -1124,23 +1124,25 @@ power = [
$g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)$. $g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)$.
#+NAME: rdm #+NAME: rdm
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|------------------------+----------------+----------------------------------------------+-----------------------------------------------------------------------| |------------------------+----------------+---------------------------------------------------------+-----------------------------------------------------------------------|
| ~1e~ | ~float~ | ~(mo.num, mo.num)~ | One body density matrix | | ~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_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 | | ~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) | | ~1e_transition~ | ~float~ | ~(mo.num, mo.num, state.num, state.num) | One-particle transition density matrices |
| ~2e_upup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\uparrow component of the two-body reduced density matrix | | ~2e~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Two-body reduced density matrix (spin trace) |
| ~2e_dndn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\downarrow component of the two-body reduced density matrix | | ~2e_upup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\uparrow 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_dndn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\downarrow component of the two-body reduced density matrix |
| ~2e_cholesky_num~ | ~dim~ | | Number of Cholesky vectors | | ~2e_updn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\downarrow component of the two-body reduced density matrix |
| ~2e_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the two-body RDM (spin trace) | | ~2e_transition~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num, state.num, state.num) | Two-particle transition density matrices |
| ~2e_upup_cholesky_num~ | ~dim~ | | Number of Cholesky vectors | | ~2e_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_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the two-body RDM (spin trace) |
| ~2e_dndn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors | | ~2e_upup_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_upup_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_upup_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\uparrow\uparrow) |
| ~2e_updn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors | | ~2e_dndn_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) | | ~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") #+CALL: json(data=rdm, title="rdm")
@ -1148,21 +1150,23 @@ power = [
:results: :results:
#+begin_src python :tangle trex.json #+begin_src python :tangle trex.json
"rdm": { "rdm": {
"1e" : [ "float" , [ "mo.num", "mo.num" ] ] "1e" : [ "float" , [ "mo.num", "mo.num" ] ]
, "1e_up" : [ "float" , [ "mo.num", "mo.num" ] ] , "1e_up" : [ "float" , [ "mo.num", "mo.num" ] ]
, "1e_dn" : [ "float" , [ "mo.num", "mo.num" ] ] , "1e_dn" : [ "float" , [ "mo.num", "mo.num" ] ]
, "2e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ] , "1e_transition" : [ "float" , [ "state.num", "state.num", "mo.num", "mo.num" ] ]
, "2e_upup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ] , "2e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_dndn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ] , "2e_upup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_updn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ] , "2e_dndn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_cholesky_num" : [ "dim" , [] ] , "2e_updn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_cholesky" : [ "float sparse", [ "rdm.2e_cholesky_num", "mo.num", "mo.num" ] ] , "2e_transition" : [ "float sparse", [ "state.num", "state.num", "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_upup_cholesky_num" : [ "dim" , [] ] , "2e_cholesky_num" : [ "dim" , [] ]
, "2e_upup_cholesky" : [ "float sparse", [ "rdm.2e_upup_cholesky_num", "mo.num", "mo.num" ] ] , "2e_cholesky" : [ "float sparse", [ "rdm.2e_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_dndn_cholesky_num" : [ "dim" , [] ] , "2e_upup_cholesky_num" : [ "dim" , [] ]
, "2e_dndn_cholesky" : [ "float sparse", [ "rdm.2e_dndn_cholesky_num", "mo.num", "mo.num" ] ] , "2e_upup_cholesky" : [ "float sparse", [ "rdm.2e_upup_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_updn_cholesky_num" : [ "dim" , [] ] , "2e_dndn_cholesky_num" : [ "dim" , [] ]
, "2e_updn_cholesky" : [ "float sparse", [ "rdm.2e_updn_cholesky_num", "mo.num", "mo.num" ] ] , "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_src
:end: :end:
@ -1325,19 +1329,19 @@ power = [
*** Table of values *** Table of values
#+name: jastrow #+name: jastrow
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|---------------+----------+---------------------+-----------------------------------------------------------------| |---------------+---------+---------------------+-----------------------------------------------------------------|
| ~type~ | ~str~ | | Type of Jastrow factor: ~CHAMP~ or ~Mu~ | | ~type~ | ~str~ | | Type of Jastrow factor: ~CHAMP~ or ~Mu~ |
| ~en_num~ | ~dim~ | | Number of Electron-nucleus parameters | | ~en_num~ | ~dim~ | | Number of Electron-nucleus parameters |
| ~ee_num~ | ~dim~ | | Number of Electron-electron parameters | | ~ee_num~ | ~dim~ | | Number of Electron-electron parameters |
| ~een_num~ | ~dim~ | | Number of Electron-electron-nucleus parameters | | ~een_num~ | ~dim~ | | Number of Electron-electron-nucleus parameters |
| ~en~ | ~float~ | ~(jastrow.en_num)~ | Electron-nucleus parameters | | ~en~ | ~float~ | ~(jastrow.en_num)~ | Electron-nucleus parameters |
| ~ee~ | ~float~ | ~(jastrow.ee_num)~ | Electron-electron parameters | | ~ee~ | ~float~ | ~(jastrow.ee_num)~ | Electron-electron parameters |
| ~een~ | ~float~ | ~(jastrow.een_num)~ | Electron-electron-nucleus parameters | | ~een~ | ~float~ | ~(jastrow.een_num)~ | Electron-electron-nucleus parameters |
| ~en_nucleus~ | ~index~ | ~(jastrow.en_num)~ | Nucleus relative to the eN parameter | | ~en_nucleus~ | ~index~ | ~(jastrow.en_num)~ | Nucleus relative to the eN parameter |
| ~een_nucleus~ | ~index~ | ~(jastrow.een_num)~ | Nucleus relative to the eeN 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 | | ~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 | | ~en_scaling~ | ~float~ | ~(nucleus.num)~ | $\kappa$ value in CHAMP Jastrow for electron-nucleus distances |
#+CALL: json(data=jastrow, title="jastrow") #+CALL: json(data=jastrow, title="jastrow")