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FIX: data format in the basis group consistent with ECP
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trex.org
71
trex.org
@ -215,20 +215,17 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
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All the basis set parameters are stored in one-dimensional arrays:
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#+NAME: basis
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| Variable | Type | Dimensions | Description |
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|---------------------+---------+--------------------+----------------------------------------------------------|
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| ~type~ | ~str~ | | Type of basis set: "Gaussian" or "Slater" |
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| ~num~ | ~dim~ | | Total Number of shells |
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| ~prim_num~ | ~dim~ | | Total number of primitives |
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| ~nucleus_index~ | ~index~ | ~(nucleus.num)~ | Index of the first shell of each nucleus ($A$) |
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| ~nucleus_shell_num~ | ~int~ | ~(nucleus.num)~ | Number of shells for each nucleus |
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| ~shell_ang_mom~ | ~int~ | ~(basis.num)~ | Angular momentum ~0:S, 1:P, 2:D, ...~ |
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| ~shell_prim_num~ | ~int~ | ~(basis.num)~ | Number of primitives in the shell ($N_{\text{prim}}$) |
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| ~shell_factor~ | ~float~ | ~(basis.num)~ | Normalization factor of the shell ($\mathcal{N}_s$) |
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| ~shell_prim_index~ | ~index~ | ~(basis.num)~ | Index of the first primitive in the complete list |
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| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) |
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| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) |
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| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
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| Variable | Type | Dimensions | Description |
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|-----------------+---------+---------------+------------------------------------------------------------------|
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| ~type~ | ~str~ | | Type of basis set: "Gaussian" or "Slater" |
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| ~num~ | ~dim~ | | Total number of primitives |
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| ~nucleus_index~ | ~index~ | ~(basis.num)~ | One-to-one correspondence between primitives and atomic indices |
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| ~ang_mom~ | ~int~ | ~(basis.num)~ | One-to-one correspondence between primitives and angular momenta |
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| ~shell_index~ | ~index~ | ~(basis.num)~ | One-to-one correspondence between primitives and atomic shells |
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| ~shell_factor~ | ~float~ | ~(basis.num)~ | Normalization factor of the shell ($\mathcal{N}_s$) |
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| ~exponent~ | ~float~ | ~(basis.num)~ | Exponents of the primitives ($\gamma_{ks}$) |
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| ~coefficient~ | ~float~ | ~(basis.num)~ | Coefficients of the primitives ($a_{ks}$) |
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| ~prim_factor~ | ~float~ | ~(basis.num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
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#+CALL: json(data=basis, title="basis")
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@ -252,6 +249,8 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an
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#+end_src
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:END:
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** Example
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For example, consider H_2 with the following basis set (in GAMESS
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format), where both the AOs and primitives are considered normalized:
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@ -272,31 +271,43 @@ P 1
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P 1
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1 3.880000E-01 1.000000E+00
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D 1
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1 1.057000E+00 1.0000000
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1 1.057000E+00 1.000000E+00
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#+END_EXAMPLE
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we have:
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In TREXIO representaion we have:
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#+BEGIN_EXAMPLE
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type = "Gaussian"
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num = 12
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prim_num = 20
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type = "Gaussian"
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num = 20
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nucleus_index = [0 , 6]
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shell_ang_mom = [0 , 0 , 0 , 1 , 1 , 2 , 0 , 0 , 0 , 1 , 1 , 2 ]
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shell_prim_num = [5 , 1 , 1 , 1 , 1 , 1 , 5 , 1 , 1 , 1 , 1 , 1 ]
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shell_prim_index = [0 , 5 , 6 , 7 , 8 , 9 , 10, 15, 16, 17, 18, 19]
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shell_factor = [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.]
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# 10 primitives per H atom
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nucleus_index =
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[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ]
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# 7 primitives for S (l=0), 2 primitives for P (l=1), 1 primitive for D (l=2) shells
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ang_mom =
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[ 0, 0, 0, 0, 0, 0, 0, 1, 1, 2,
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0, 0, 0, 0, 0, 0, 0, 1, 1, 2 ]
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# 5 primitives for first S shell and then 1 primitive per remaining shells
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shell_index =
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[ 0, 0, 0, 0, 0, 1, 2, 3, 4, 5,
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0, 0, 0, 0, 0, 1, 2, 3, 4, 5 ]
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# no need to normalize shells
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shell_factor =
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[ 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,
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1., 1., 1., 1., 1., 1., 1., 1., 1., 1. ]
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# parameters of the primitives
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exponent =
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[ 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407,
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0.388, 1.057, 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407,
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0.388, 1.057]
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[ 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407, 0.388, 1.057,
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33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407, 0.388, 1.057 ]
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coefficient =
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[ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0,
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1.0, 1.0, 1.0, 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0,
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1.0, 1.0, 1.0]
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[ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0,
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0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0 ]
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prim_factor =
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[ 1.0006253235944540e+01, 2.4169531573445120e+00, 7.9610924849766440e-01
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