TREX Configuration file

As we expect our files to be archived in open-data repositories, we need to give the possibility to the users to store some metadata inside the files. We propose to store the list of names of the codes which have participated to the creation of the file, a list of authors of the file, and a textual description.

Variable	Type	Dimensions (for arrays)	Description
code_num	int		Number of codes used to produce the file
code	str	(metadata.code_num)	Names of the codes used
author_num	int		Number of authors of the file
author	str	(metadata.author_num)	Names of the authors of the file
package_version	str		TREXIO version used to produce the file
description	str		Text describing the content of file

We consider wave functions expressed in the spin-free formalism, where the number of ↑ and ↓ electrons is fixed.

Variable	Type	Dimensions	Description
up_num	int		Number of ↑-spin electrons
dn_num	int		Number of ↓-spin electrons

The nuclei are considered as fixed point charges. Coordinates are given in Cartesian \((x,y,z)\) format.

Variable	Type	Dimensions	Description
num	int		Number of nuclei
charge	float	(nucleus.num)	Charges of the nuclei
coord	float	(3,nucleus.num)	Coordinates of the atoms
label	str	(nucleus.num)	Atom labels
point_group	str		Symmetry point group

An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the core electrons of atom \(A\) is expressed as \[ V_A^{\text{ECP}} = V_{A \ell_{\max}} + \sum_{\ell=0}^{\ell_{\max} -1} \sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \left[ V_{A \ell} - V_{A \ell_{\max}} \right] \langle Y_{\ell m} | \]

The functions \(V_{A\ell}\) are parameterized as: \[ V_{A \ell}(\mathbf{r}) = \sum_{q=1}^{N_{q \ell}} \beta_{A q \ell}\, |\mathbf{r}-\mathbf{R}_{A}|^{n_{A q \ell}}\, e^{-\alpha_{A q \ell} |\mathbf{r}-\mathbf{R}_{A}|^2 } \]

See http://dx.doi.org/10.1063/1.4984046 for more info.

Variable	Type	Dimensions	Description
lmax_plus_1	int	(nucleus.num)	\(\ell_{\max} + 1\), one higher than the maximum angular momentum in the removed core orbitals
z_core	float	(nucleus.num)	Charges to remove
local_n	int	(nucleus.num)	Number of local functions \(N_{q \ell}\)
local_num_n_max	int		Maximum value of local_n, used for dimensioning arrays
local_exponent	float	(ecp.local_num_n_max, nucleus.num)	\(\alpha_{A q \ell_{\max}}\)
local_coef	float	(ecp.local_num_n_max, nucleus.num)	\(\beta_{A q \ell_{\max}}\)
local_power	int	(ecp.local_num_n_max, nucleus.num)	\(n_{A q \ell_{\max}}\)
non_local_n	int	(nucleus.num)	\(N_{q \ell_{\max}}\)
non_local_num_n_max	int		Maximum value of non_local_n, used for dimensioning arrays
non_local_exponent	float	(ecp.non_local_num_n_max, nucleus.num)	\(\alpha_{A q \ell}\)
non_local_coef	float	(ecp.non_local_num_n_max, nucleus.num)	\(\beta_{A q \ell}\)
non_local_power	int	(ecp.non_local_num_n_max, nucleus.num)	\(n_{A q \ell}\)

We consider here basis functions centered on nuclei. Hence, we enable the possibility to define dummy atoms to place basis functions in random positions.

The atomic basis set is defined as a list of shells. Each shell \(s\) is centered on a center \(A\), possesses a given angular momentum \(l\) and a radial function \(R_s\). The radial function is a linear combination of \(N_{\text{prim}}\) primitive functions that can be of type Slater (\(p=1\)) or Gaussian (\(p=2\)), parameterized by exponents \(\gamma_{ks}\) and coefficients \(a_{ks}\): \[ R_s(\mathbf{r}) = \mathcal{N}_s \vert\mathbf{r}-\mathbf{R}_A\vert^{n_s} \sum_{k=1}^{N_{\text{prim}}} a_{ks}\, f_{ks}(\gamma_{ks},p)\, \exp \left( - \gamma_{ks} \vert \mathbf{r}-\mathbf{R}_A \vert ^p \right). \]

In the case of Gaussian functions, \(n_s\) is always zero.

Different codes normalize functions at different levels. Computing normalization factors requires the ability to compute overlap integrals, so the normalization factors should be written in the file to ensure that the file is self-contained and does not need the client program to have the ability to compute such integrals.

Some codes assume that the contraction coefficients are for a linear combination of normalized primitives. This implies that a normalization constant for the primitive \(ks\) needs to be computed and stored. If this normalization factor is not required, \(f_{ks}=1\).

Some codes assume that the basis function are normalized. This implies the computation of an extra normalization factor, \(\mathcal{N}_s\). If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).

All the basis set parameters are stored in one-dimensional arrays:

Variable	Type	Dimensions	Description
type	str		Type of basis set: "Gaussian" or "Slater"
num	int		Total Number of shells
prim_num	int		Total number of primitives
nucleus_index	index	(nucleus.num)	Index of the first shell of each nucleus (\(A\))
nucleus_shell_num	int	(nucleus.num)	Number of shells for each nucleus
shell_ang_mom	int	(basis.num)	Angular momentum 0:S, 1:P, 2:D, ...
shell_prim_num	int	(basis.num)	Number of primitives in the shell (\(N_{\text{prim}}\))
shell_factor	float	(basis.num)	Normalization factor of the shell (\(\mathcal{N}_s\))
shell_prim_index	index	(basis.num)	Index of the first primitive in the complete list
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 (\(f_{ks}\))

For example, consider H₂ with the following basis set (in GAMESS format), where both the AOs and primitives are considered normalized:

HYDROGEN
S   5
1         3.387000E+01           6.068000E-03
2         5.095000E+00           4.530800E-02
3         1.159000E+00           2.028220E-01
4         3.258000E-01           5.039030E-01
5         1.027000E-01           3.834210E-01
S   1
1         3.258000E-01           1.000000E+00
S   1
1         1.027000E-01           1.000000E+00
P   1
1         1.407000E+00           1.000000E+00
P   1
1         3.880000E-01           1.000000E+00
D   1
1         1.057000E+00           1.0000000

we have:

type     = "Gaussian"
num      = 12
prim_num = 20

nucleus_index    = [0 , 6]
shell_ang_mom    = [0 , 0 , 0 , 1 , 1 , 2 , 0 , 0 , 0 , 1 , 1 , 2 ]
shell_prim_num   = [5 , 1 , 1 , 1 , 1 , 1 , 5 , 1 , 1 , 1 , 1 , 1 ]
shell_prim_index = [0 , 5 , 6 , 7 , 8 , 9 , 10, 15, 16, 17, 18, 19]
shell_factor     = [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.]

exponent =
[ 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407,
  0.388, 1.057, 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407,
  0.388, 1.057]

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,
  1.2929684417481876e-01, 2.1842769845268308e+00, 4.3649547399719840e-01,
  1.8135965626177861e+00, 1.0006253235944540e+01, 2.4169531573445120e+00,
  7.9610924849766440e-01, 3.0734305383061117e-01, 1.2929684417481876e-01,
  3.0734305383061117e-01, 1.2929684417481876e-01, 2.1842769845268308e+00,
  4.3649547399719840e-01, 1.8135965626177861e+00 ]

Going from the atomic basis set to AOs implies a systematic construction of all the angular functions of each shell. We consider two cases for the angular functions: the real-valued spherical harmonics, and the polynomials in Cartesian coordinates. In the case of spherical harmonics, the AOs are ordered in increasing magnetic quantum number (\(-l \le m \le l\)), and in the case of polynomials we impose the canonical ordering of the Libint2 library, i.e

\begin{eqnarray} p & : & p_x, p_y, p_z \nonumber \\ d & : & d_{xx}, d_{xy}, d_{xz}, d_{yy}, d_{yz}, d_{zz} \nonumber \\ f & : & f_{xxx}, f_{xxy}, f_{xxz}, f_{xyy}, f_{xyz}, f_{xzz}, f_{yyy}, f_{yyz}, f_{yzz}, …f_{zzz} \nonumber \\ {\rm etc.} \nonumber \end{eqnarray}

AOs are defined as

\[ \chi_i (\mathbf{r}) = \mathcal{N}_i\, P_{\eta(i)}(\mathbf{r})\, R_{\theta(i)} (\mathbf{r}) \]

where \(i\) is the atomic orbital index, \(P\) encodes for either the polynomials or the spherical harmonics, \(\theta(i)\) returns the shell on which the AO is expanded, and \(\eta(i)\) denotes which angular function is chosen. \(\mathcal{N}_i\) is a normalization factor that enables the possibility to have different normalization coefficients within a shell, as in the GAMESS convention where \(\mathcal{N}_{x^2} \ne \mathcal{N}_{xy}\) because \[ \left[ \iiint \left(x-X_A \right)^2 R_{\theta(i)} (\mathbf{r}) dx\, dy\, dz \right]^{-1/2} \ne \left[ \iiint \left( x-X_A \right) \left( y-Y_A \right) R_{\theta(i)} (\mathbf{r}) dx\, dy\, dz \right]^{-1/2}. \]

In such a case, one should set the normalization of the shell (in the Basis set section) to \(\mathcal{N}_{z^2}\), which is the normalization factor of the atomic orbitals in spherical coordinates. The normalization factor of the \(xy\) function which should be introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).

Variable	Type	Dimensions	Description
cartesian	int		1: true, 0: false
num	int		Total number of atomic orbitals
shell	index	(ao.num)	basis set shell for each AO
normalization	float	(ao.num)	Normalization factors

Variable	Type	Dimensions	Description
type	str		Free text to identify the set of MOs (HF, Natural, Local, CASSCF, etc)
num	int		Number of MOs
coefficient	float	(ao.num, mo.num)	MO coefficients
class	str	(mo.num)	Choose among: Core, Inactive, Active, Virtual, Deleted
symmetry	str	(mo.num)	Symmetry in the point group
occupation	float	(mo.num)	Occupation number

Variable	Type	Dimensions	Description
one_e	float	(mo.num, mo.num)
one_e_up	float	(mo.num, mo.num)
one_e_dn	float	(mo.num, mo.num)
two_e	float sparse	(mo.num, mo.num, mo.num, mo.num)

print("""#+begin_src python :tangle trex.json""")
print("""    "%s": {"""%(title))
indent = "        "
f1 = 0 ; f2 = 0 ; f3 = 0
for line in data:
    line = [ x.replace("~","") for x in line ]
    name = '"'+line[0]+'"'
    typ  = '"'+line[1]+'"'
    dims = line[2]
    if '(' in dims:
        dims = dims.strip()[1:-1]
        dims = [ '"'+x.strip()+'"' for x in dims.split(',') ]
        dims = "[ " + ", ".join(dims) + " ]"
    else:
        dims = "[ ]"
    f1 = max(f1, len(name))
    f2 = max(f2, len(typ))
    f3 = max(f3, len(dims))

fmt = "%%s%%%ds : [ %%%ds, %%%ds ]" % (f1, f2, f3)
for line in data:
    line = [ x.replace("~","") for x in line ]
    name = '"'+line[0]+'"'
    typ  = '"'+line[1]+'"'
    dims = line[2]
    if '(' in dims:
        dims = dims.strip()[1:-1]
        dims = [ '"'+x.strip()+'"' for x in dims.split(',') ]
        dims.reverse()
        dims = "[ " + ", ".join(dims) + " ]"
    else:
        if dims.strip() != "":
            dims = "ERROR"
        else:
            dims = "[]"
    buffer = fmt % (indent, name, typ.ljust(f2), dims.ljust(f3))
    indent = "      , "
    print(buffer)

if last == 0:
    print("    } ,")
else:
    print("    }")
print("""#+end_src""")