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FIX: data format in the basis group consistent with ECP

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q-posev 2021-10-18 17:40:53 +02:00
parent 5b6d78e015
commit 9b12332211
1 changed files with 41 additions and 30 deletions
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@ -215,20 +215,17 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
All the basis set parameters are stored in one-dimensional arrays: All the basis set parameters are stored in one-dimensional arrays:
#+NAME: basis #+NAME: basis
| Variable | Type | Dimensions | Description | | Variable | Type | Dimensions | Description |
|---------------------+---------+--------------------+----------------------------------------------------------| |-----------------+---------+---------------+------------------------------------------------------------------|
| ~type~ | ~str~ | | Type of basis set: "Gaussian" or "Slater" | | ~type~ | ~str~ | | Type of basis set: "Gaussian" or "Slater" |
| ~num~ | ~dim~ | | Total Number of shells | | ~num~ | ~dim~ | | Total number of primitives |
| ~prim_num~ | ~dim~ | | Total number of primitives | | ~nucleus_index~ | ~index~ | ~(basis.num)~ | One-to-one correspondence between primitives and atomic indices |
| ~nucleus_index~ | ~index~ | ~(nucleus.num)~ | Index of the first shell of each nucleus ($A$) | | ~ang_mom~ | ~int~ | ~(basis.num)~ | One-to-one correspondence between primitives and angular momenta |
| ~nucleus_shell_num~ | ~int~ | ~(nucleus.num)~ | Number of shells for each nucleus | | ~shell_index~ | ~index~ | ~(basis.num)~ | One-to-one correspondence between primitives and atomic shells |
| ~shell_ang_mom~ | ~int~ | ~(basis.num)~ | Angular momentum ~0:S, 1:P, 2:D, ...~ | | ~shell_factor~ | ~float~ | ~(basis.num)~ | Normalization factor of the shell ($\mathcal{N}_s$) |
| ~shell_prim_num~ | ~int~ | ~(basis.num)~ | Number of primitives in the shell ($N_{\text{prim}}$) | | ~exponent~ | ~float~ | ~(basis.num)~ | Exponents of the primitives ($\gamma_{ks}$) |
| ~shell_factor~ | ~float~ | ~(basis.num)~ | Normalization factor of the shell ($\mathcal{N}_s$) | | ~coefficient~ | ~float~ | ~(basis.num)~ | Coefficients of the primitives ($a_{ks}$) |
| ~shell_prim_index~ | ~index~ | ~(basis.num)~ | Index of the first primitive in the complete list | | ~prim_factor~ | ~float~ | ~(basis.num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
| ~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 ($f_{ks}$) |
#+CALL: json(data=basis, title="basis") #+CALL: json(data=basis, title="basis")
@ -252,6 +249,8 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
#+end_src #+end_src
:END: :END:
** Example
For example, consider H_2 with the following basis set (in GAMESS For example, consider H_2 with the following basis set (in GAMESS
format), where both the AOs and primitives are considered normalized: format), where both the AOs and primitives are considered normalized:
@ -272,31 +271,43 @@ P 1
P 1 P 1
1 3.880000E-01 1.000000E+00 1 3.880000E-01 1.000000E+00
D 1 D 1
1 1.057000E+00 1.0000000 1 1.057000E+00 1.000000E+00
#+END_EXAMPLE #+END_EXAMPLE
we have: In TREXIO representaion we have:
#+BEGIN_EXAMPLE #+BEGIN_EXAMPLE
type = "Gaussian" type = "Gaussian"
num = 12 num = 20
prim_num = 20
nucleus_index = [0 , 6] # 10 primitives per H atom
shell_ang_mom = [0 , 0 , 0 , 1 , 1 , 2 , 0 , 0 , 0 , 1 , 1 , 2 ] nucleus_index =
shell_prim_num = [5 , 1 , 1 , 1 , 1 , 1 , 5 , 1 , 1 , 1 , 1 , 1 ] [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
shell_prim_index = [0 , 5 , 6 , 7 , 8 , 9 , 10, 15, 16, 17, 18, 19] 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ]
shell_factor = [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.]
# 7 primitives for S (l=0), 2 primitives for P (l=1), 1 primitive for D (l=2) shells
ang_mom =
[ 0, 0, 0, 0, 0, 0, 0, 1, 1, 2,
0, 0, 0, 0, 0, 0, 0, 1, 1, 2 ]
# 5 primitives for first S shell and then 1 primitive per remaining shells
shell_index =
[ 0, 0, 0, 0, 0, 1, 2, 3, 4, 5,
0, 0, 0, 0, 0, 1, 2, 3, 4, 5 ]
# no need to normalize shells
shell_factor =
[ 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,
1., 1., 1., 1., 1., 1., 1., 1., 1., 1. ]
# parameters of the primitives
exponent = exponent =
[ 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407, [ 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407, 0.388, 1.057,
0.388, 1.057, 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407, 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407, 0.388, 1.057 ]
0.388, 1.057]
coefficient = coefficient =
[ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, [ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0,
1.0, 1.0, 1.0, 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0 ]
1.0, 1.0, 1.0]
prim_factor = prim_factor =
[ 1.0006253235944540e+01, 2.4169531573445120e+00, 7.9610924849766440e-01 [ 1.0006253235944540e+01, 2.4169531573445120e+00, 7.9610924849766440e-01