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split the basis format to depend on shell_num and prim_num

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q-posev 2021-10-21 15:51:21 +02:00
parent 64b3e25da5
commit 9321213a21
1 changed files with 37 additions and 34 deletions
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@ -215,17 +215,18 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
All the basis set parameters are stored in one-dimensional arrays:
#+NAME: basis
| Variable | Type | Dimensions | Description |
|-----------------+---------+---------------+------------------------------------------------------------------|
| ~type~ | ~str~ | | Type of basis set: "Gaussian" or "Slater" |
| ~num~ | ~dim~ | | Total number of primitives |
| ~nucleus_index~ | ~index~ | ~(basis.num)~ | One-to-one correspondence between primitives and atomic indices |
| ~ang_mom~ | ~int~ | ~(basis.num)~ | One-to-one correspondence between primitives and angular momenta |
| ~shell_index~ | ~index~ | ~(basis.num)~ | One-to-one correspondence between primitives and atomic shells |
| ~shell_factor~ | ~float~ | ~(basis.num)~ | Normalization factor of the shell ($\mathcal{N}_s$) |
| ~exponent~ | ~float~ | ~(basis.num)~ | Exponents of the primitives ($\gamma_{ks}$) |
| ~coefficient~ | ~float~ | ~(basis.num)~ | Coefficients of the primitives ($a_{ks}$) |
| ~prim_factor~ | ~float~ | ~(basis.num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
| Variable | Type | Dimensions | Description |
|-----------------+---------+---------------------+--------------------------------------------------------------|
| ~type~ | ~str~ | | Type of basis set: "Gaussian" or "Slater" |
| ~prim_num~ | ~dim~ | | Total number of primitives |
| ~shell_num~ | ~dim~ | | Total number of shells |
| ~nucleus_index~ | ~index~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and atomic indices |
| ~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_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 ($f_{ks}$) |
#+CALL: json(data=basis, title="basis")
@ -233,15 +234,16 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
:RESULTS:
#+begin_src python :tangle trex.json
"basis": {
"type" : [ "str" , [] ]
, "num" : [ "dim" , [] ]
, "nucleus_index" : [ "index", [ "basis.num" ] ]
, "ang_mom" : [ "int" , [ "basis.num" ] ]
, "shell_index" : [ "index", [ "basis.num" ] ]
, "shell_factor" : [ "float", [ "basis.num" ] ]
, "exponent" : [ "float", [ "basis.num" ] ]
, "coefficient" : [ "float", [ "basis.num" ] ]
, "prim_factor" : [ "float", [ "basis.num" ] ]
"type" : [ "str" , [] ]
, "prim_num" : [ "dim" , [] ]
, "shell_num" : [ "dim" , [] ]
, "nucleus_index" : [ "index", [ "basis.shell_num" ] ]
, "ang_mom" : [ "int" , [ "basis.shell_num" ] ]
, "shell_factor" : [ "float", [ "basis.shell_num" ] ]
, "shell_index" : [ "index", [ "basis.prim_num" ] ]
, "exponent" : [ "float", [ "basis.prim_num" ] ]
, "coefficient" : [ "float", [ "basis.prim_num" ] ]
, "prim_factor" : [ "float", [ "basis.prim_num" ] ]
} ,
#+end_src
:END:
@ -275,27 +277,28 @@ D 1
#+BEGIN_EXAMPLE
type = "Gaussian"
num = 20
prim_num = 20
shell_num = 12
# 10 primitives per H atom
# 6 shells per H atom
nucleus_index =
[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ]
[ 0, 0, 0, 0, 0, 0,
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
# 3 shells in S (l=0), 2 in P (l=1), 1 in D (l=2)
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 ]
[ 0, 0, 0, 1, 1, 2,
0, 0, 0, 1, 1, 2 ]
# no need to renormalize shells
shell_factor =
[ 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,
1., 1., 1., 1., 1., 1., 1., 1., 1., 1. ]
[ 1., 1., 1., 1., 1., 1.,
1., 1., 1., 1., 1., 1. ]
# 5 primitives for the first S shell and then 1 primitive per remaining shells in each H atom
shell_index =
[ 0, 0, 0, 0, 0, 1, 2, 3, 4, 5,
6, 6, 6, 6, 6, 7, 8, 9, 10, 11 ]
# parameters of the primitives (10 per H atom)
exponent =