diff --git a/trex.org b/trex.org index 1841692..9fc315d 100644 --- a/trex.org +++ b/trex.org @@ -118,7 +118,7 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an * Effective core potentials (ecp group) An effective core potential (ECP) $V_A^{\text{ECP}}$ replacing the - core electrons of atom $A$ is expressed as + core electrons of atom $A$ can be expressed as \[ V_A^{\text{ECP}} = V_{A \ell_{\max}+1} + @@ -127,6 +127,9 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an V_{A \ell} - V_{A \ell_{\max}+1} \right] \langle Y_{\ell m} | \] + 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: \[ V_{A \ell}(\mathbf{r}) = @@ -135,13 +138,13 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an e^{-\alpha_{A q \ell} |\mathbf{r}-\mathbf{R}_{A}|^2 } \] - See http://dx.doi.org/10.1063/1.4984046 for more info. + See http://dx.doi.org/10.1063/1.4984046 or https://doi.org/10.1063/1.5121006for more info. #+NAME: ecp | Variable | Type | Dimensions | Description | |----------------------+---------+-----------------+----------------------------------------------------------------------------------------| | ~max_ang_mom_plus_1~ | ~int~ | ~(nucleus.num)~ | $\ell_{\max}+1$, one higher than the max angular momentum in the removed core orbitals | - | ~z_core~ | ~float~ | ~(nucleus.num)~ | Charges to remove | + | ~z_core~ | ~float~ | ~(nucleus.num)~ | Number of core electrons to remove per atom | | ~num~ | ~dim~ | | Total number of ECP functions for all atoms and all values of $\ell$ | | ~ang_mom~ | ~int~ | ~(ecp.num)~ | One-to-one correspondence between ECP items and the angular momentum $\ell$ | | ~nucleus_index~ | ~index~ | ~(ecp.num)~ | One-to-one correspondence between ECP items and the atom index | @@ -150,10 +153,17 @@ arrays are 0-based. Hence, we introduce the ~index~ type which is an | ~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 hand, it can be attributed to the maximum angular momentum of the +ECP that replaces the core electrons. +*Note*, that the latter $\ell_{\max}$ is always higher by 1 than the former. + + *Note for developers*: avoid having variables with similar prefix in their name. -HDF5 back end might cause issues due to the way `find_dataset` function works -in the H5LT module. For example, in the ECP group we use ~max_ang_mom~ and -~ang_mom_max~ due to this. +HDF5 back end might cause issues due to the way `find_dataset` function works. +For example, in the ECP group we use ~max_ang_mom~ and not ~ang_mom_max~. The latter causes issues when written before ~ang_mom~ in the TREXIO file. @@ -202,19 +212,19 @@ max_ang_mom_plus_1 = [ 1, 1 ] # number of core electrons to remove per atom zcore = [ 0, 0 ] -# first 4 ECP elements correspond to the first H atom, same for the second H atom +# first 4 ECP elements correspond to the first H atom; the remaining 4 elements are for the second H atom nucleus_index = [ 0, 0, 0, 0, 1, 1, 1, 1 ] -# 3 first ECP elements correspond to l=1 of the first H atom, then 1 ECP for l=0; same for the second H atom +# 3 first ECP elements correspond to the P orbital (l=1), then 1 element for the S orbital (l=0) ; similar for the second H atom ang_mom = [ 1, 1, 1, 0, 1, 1, 1, 0 ] -# flat arrays with ECP quantities that can be parsed based on the aforementioned ecp_ang_mom and ecp_nucleus +# ECP quantities that can be attributed to atoms and/or angular momenta based on the aforementioned ecp_nucleus and ecp_ang_mom arrays coefficient = [ 1.00000000000000, 21.24359508259891, -10.85192405303825, 0.00000000000000, 1.00000000000000, 21.24359508259891, -10.85192405303825, 0.00000000000000