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Added kpoint to MO group #138

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merged 7 commits into from
May 13, 2024
Merged

Added kpoint to MO group #138

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6fbd52e
Added kpoint to MO group
scemama Feb 15, 2024
982c8bf
Merge branch 'master' into kpoint
scemama Mar 1, 2024
ffef984
Added k-vector info
scemama Mar 1, 2024
8fb0335
Created json blocks
scemama Mar 1, 2024
f8aad19
Merge branch 'master' into kpoint
scemama Mar 13, 2024
5ebbecb
Added k-point weights
scemama Mar 13, 2024
8c93ed1
Merge branch 'master' into kpoint
scemama May 13, 2024
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101 changes: 55 additions & 46 deletions trex.org
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Original file line number Diff line number Diff line change
Expand Up @@ -121,23 +121,23 @@

** Periodic boundary calculations (pbc group)

A single $k$-point per TREXIO file can be stored. The $k$-point is
defined in this group.

#+NAME: pbc
| Variable | Type | Dimensions | Description |
|------------+---------+------------+-------------------------|
| ~periodic~ | ~int~ | | ~1~: true or ~0~: false |
| ~k_point~ | ~float~ | ~(3)~ | $k$-point sampling |
| Variable | Type | Dimensions | Description |
|---------------+---------+------------------------+-------------------------|
| ~periodic~ | ~int~ | | ~1~: true or ~0~: false |
| ~k_point_num~ | ~dim~ | | Number of $k$-points |
| ~k_point~ | ~float~ | ~(3, pbc.k_point_num)~ | $k$-point sampling |

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

#+RESULTS:
:results:
#+begin_src python :tangle trex.json
"pbc": {
"periodic" : [ "int" , [] ]
, "k_point" : [ "float", [ "3" ] ]
"periodic" : [ "int" , [] ]
, "k_point_num" : [ "dim" , [] ]
, "k_point" : [ "float", [ "pbc.k_point_num", "3" ] ]
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} ,
#+end_src
:end:
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Expand Down Expand Up @@ -326,32 +326,32 @@
*** 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 |



Expand Down Expand Up @@ -811,15 +811,22 @@ power = [
| 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 $\beta$ |
| ~k_point~ | ~index~ | ~(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:
Expand All @@ -835,10 +842,12 @@ power = [
, "occupation" : [ "float", [ "mo.num" ] ]
, "energy" : [ "float", [ "mo.num" ] ]
, "spin" : [ "int" , [ "mo.num" ] ]
, "k_point" : [ "index", [ "mo.num" ] ]
} ,
#+end_src
:end:


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

The operators as the same as those defined in the
Expand Down Expand Up @@ -1349,17 +1358,17 @@ power = [
:results:
#+begin_src python :tangle trex.json
"jastrow": {
"type" : [ "str" , [] ]
, "en_num" : [ "dim" , [] ]
, "ee_num" : [ "dim" , [] ]
, "een_num" : [ "dim" , [] ]
, "en" : [ "float" , [ "jastrow.en_num" ] ]
, "ee" : [ "float" , [ "jastrow.ee_num" ] ]
, "een" : [ "float" , [ "jastrow.een_num" ] ]
, "en_nucleus" : [ "index" , [ "jastrow.en_num" ] ]
, "een_nucleus" : [ "index" , [ "jastrow.een_num" ] ]
, "ee_scaling" : [ "float" , [] ]
, "en_scaling" : [ "float" , [ "nucleus.num" ] ]
"type" : [ "str" , [] ]
, "en_num" : [ "dim" , [] ]
, "ee_num" : [ "dim" , [] ]
, "een_num" : [ "dim" , [] ]
, "en" : [ "float", [ "jastrow.en_num" ] ]
, "ee" : [ "float", [ "jastrow.ee_num" ] ]
, "een" : [ "float", [ "jastrow.een_num" ] ]
, "en_nucleus" : [ "index", [ "jastrow.en_num" ] ]
, "een_nucleus" : [ "index", [ "jastrow.een_num" ] ]
, "ee_scaling" : [ "float", [] ]
, "en_scaling" : [ "float", [ "nucleus.num" ] ]
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} ,
#+end_src
:end:
Expand Down
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