diff --git a/trex.org b/trex.org index 9ef7438..e96cc38 100644 --- a/trex.org +++ b/trex.org @@ -133,11 +133,15 @@ with the same name suffixed by ~_im~. used in periodic calculations. #+NAME: cell - | Variable | Type | Dimensions | Description | - |----------+---------+------------+-----------------------| - | ~a~ | ~float~ | ~(3)~ | First lattice vector | - | ~b~ | ~float~ | ~(3)~ | Second lattice vector | - | ~c~ | ~float~ | ~(3)~ | Third lattice vector | + | Variable | Type | Dimensions | Description | + |----------+---------+------------+--------------------------------------------------------------------------| + | ~a~ | ~float~ | ~(3)~ | First real space lattice vector | + | ~b~ | ~float~ | ~(3)~ | Second real space lattice vector | + | ~c~ | ~float~ | ~(3)~ | Third real space lattice vector | + | ~G_a~ | ~float~ | ~(3)~ | First reciprocal space lattice vector | + | ~G_b~ | ~float~ | ~(3)~ | Second reciprocal space lattice vector | + | ~G_c~ | ~float~ | ~(3)~ | Third reciprocal space lattice vector | + | ~two_pi~ | ~int~ | | ~0~ or ~1~. If ~two_pi=1~, $2\pi$ is included in the reciprocal vectors. | #+CALL: json(data=cell, title="cell") @@ -145,9 +149,13 @@ with the same name suffixed by ~_im~. :results: #+begin_src python :tangle trex.json "cell": { - "a" : [ "float", [ "3" ] ] - , "b" : [ "float", [ "3" ] ] - , "c" : [ "float", [ "3" ] ] + "a" : [ "float", [ "3" ] ] + , "b" : [ "float", [ "3" ] ] + , "c" : [ "float", [ "3" ] ] + , "G_a" : [ "float", [ "3" ] ] + , "G_b" : [ "float", [ "3" ] ] + , "G_c" : [ "float", [ "3" ] ] + , "two_pi" : [ "int" , [] ] } , #+end_src :end: @@ -282,12 +290,13 @@ with the same name suffixed by ~_im~. A plane wave is defined as \[ - \chi_j(r) = \exp \left( -i \mathbf{k}_j \mathbf{r} \right) + \chi_j(\mathbf{r}) = \exp \left( -i \mathbf{G}_j \cdot \mathbf{r} \right) \] The basis set is defined as the array of $k$-points in the - reciprocal space, defined in the ~pbc~ group. The kinetic energy - cutoff ~e_cut~ is the only input data relevant to plane waves. + reciprocal space $\mathbf{G}_j$, defined in the ~pbc~ group. The + kinetic energy cutoff ~e_cut~ is the only input data relevant to + plane waves. *** Data definitions @@ -390,7 +399,7 @@ exponent = coefficient = [ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0, 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0 ] -` + prim_factor = [ 1.0006253235944540e+01, 2.4169531573445120e+00, 7.9610924849766440e-01 3.0734305383061117e-01, 1.2929684417481876e-01, 3.0734305383061117e-01, @@ -408,21 +417,20 @@ prim_factor = \[ V_A^{\text{ECP}} = V_{A \ell_{\max}+1} + - \sum_{\ell=0}^{\ell_{\max}} - \sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \left[ - V_{A \ell} - V_{A \ell_{\max}+1} \right] \langle Y_{\ell m} | + \sum_{\ell=0}^{\ell_{\max}} V_{A \ell} + \sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \langle Y_{\ell m} | \] The first term in the equation above is sometimes attributed to the local channel, while the remaining terms correspond to the non-local channel projections. - The functions $V_{A\ell}$ are parameterized as: + All the functions $V_{A\ell}$ are parameterized as: \[ - V_{A \ell}(\mathbf{r}) = + V_{A \ell}(\mathbf{r}) = \sum_{q=1}^{N_{q \ell}} \beta_{A q \ell}\, |\mathbf{r}-\mathbf{R}_{A}|^{n_{A q \ell}}\, e^{-\alpha_{A q \ell} |\mathbf{r}-\mathbf{R}_{A}|^2 } - \] + \]. See http://dx.doi.org/10.1063/1.4984046 or https://doi.org/10.1063/1.5121006 for more info. @@ -438,7 +446,6 @@ prim_factor = | ~coefficient~ | ~float~ | ~(ecp.num)~ | $\beta_{A q \ell}$ all ECP coefficients | | ~power~ | ~int~ | ~(ecp.num)~ | $n_{A q \ell}$ all ECP powers | - There might be some confusion in the meaning of the $\ell_{\max}$. It can be attributed to the maximum angular momentum occupied in the core orbitals, which are removed by the ECP. On the other