86 KiB
Data stored in TREXIO
- Metadata (metadata group)
- System
- Basis functions
- Orbitals
- Multi-determinant information
- Correlation factors
- Quantum Monte Carlo data (qmc group)
For simplicity, the singular form is always used for the names of
groups and attributes, and all data are stored in atomic units.
The dimensions of the arrays in the tables below are given in
column-major order (as in Fortran), and the ordering of the dimensions
is reversed in the produced trex.json configuration file as the
library is written in C.
Dimensions are given both in row-major [] and column-major ()
formats. Pick the one adapted to the programming language in which
you use TREXIO (Numpy is by default row-major, and Fortran is column-major).
In the column-major representation, A(i,j) and A(i+1,j) are
contiguous in memory. In the row-major representation, A[i,j] and
A[i,j+1] are contiguous.
Metadata (metadata group)
As we expect TREXIO files to be archived in open-data repositories, we 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 | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
code_num |
dim |
Number of codes used to produce the file | ||
code |
str |
[metadata.code_num] |
(metadata.code_num) |
Names of the codes used |
author_num |
dim |
Number of authors of the file | ||
author |
str |
[metadata.author_num] |
(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 | ||
unsafe |
int |
1: true, 0: false |
Note: The unsafe attribute of the metadata group indicates
whether the file has been previously opened with 'u' mode. It is
automatically written in the file upon the first unsafe opening. If
the user has checked that the TREXIO file is valid (e.g. using
trexio-tools) after unsafe operations, then the unsafe attribute
value can be manually overwritten (in unsafe mode) from 1 to 0.
"metadata": {
"code_num" : [ "dim", [] ]
, "code" : [ "str", [ "metadata.code_num" ] ]
, "author_num" : [ "dim", [] ]
, "author" : [ "str", [ "metadata.author_num" ] ]
, "package_version" : [ "str", [] ]
, "description" : [ "str", [] ]
, "unsafe" : [ "int", [] ]
} ,System
Nucleus (nucleus group)
The nuclei are considered as fixed point charges. Coordinates are given in Cartesian $(x,y,z)$ format.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description | |
|---|---|---|---|---|---|
num |
dim |
Number of nuclei | |||
charge |
float |
[nucleus.num] |
(nucleus.num) |
Charges of the nuclei | |
coord |
float |
[nucleus.num, 3] |
(3, nucleus.num) |
Coordinates of the atoms | |
label |
str |
[nucleus.num] |
(nucleus.num) |
Atom labels | |
point_group |
str |
Symmetry point group | |||
repulsion |
float |
Nuclear repulsion energy |
"nucleus": {
"num" : [ "dim" , [] ]
, "charge" : [ "float", [ "nucleus.num" ] ]
, "coord" : [ "float", [ "nucleus.num", "3" ] ]
, "label" : [ "str" , [ "nucleus.num" ] ]
, "point_group" : [ "str" , [] ]
, "repulsion" : [ "float", [] ]
} ,Cell (cell group)
3 Lattice vectors to define a box containing the system, for example used in periodic calculations.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
a |
float |
[3] |
(3) |
First real space lattice vector |
b |
float |
[3] |
(3) |
Second real space lattice vector |
c |
float |
[3] |
(3) |
Third real space lattice vector |
g_a |
float |
[3] |
(3) |
First reciprocal space lattice vector |
g_b |
float |
[3] |
(3) |
Second reciprocal space lattice vector |
g_c |
float |
[3] |
(3) |
Third reciprocal space lattice vector |
two_pi |
int |
0 or 1. If two_pi=1, $2\pi$ is included in the reciprocal vectors. |
"cell": {
"a" : [ "float", [ "3" ] ]
, "b" : [ "float", [ "3" ] ]
, "c" : [ "float", [ "3" ] ]
, "g_a" : [ "float", [ "3" ] ]
, "g_b" : [ "float", [ "3" ] ]
, "g_c" : [ "float", [ "3" ] ]
, "two_pi" : [ "int" , [] ]
} ,Periodic boundary calculations (pbc group)
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
periodic |
int |
1: true or 0: false |
||
k_point_num |
dim |
Number of $k$-points | ||
k_point |
float |
[3] |
(3) |
$k$-point sampling |
k_point_weight |
float |
[pbc.k_point_num] |
(pbc.k_point_num) |
$k$-point weight |
"pbc": {
"periodic" : [ "int" , [] ]
, "k_point_num" : [ "dim" , [] ]
, "k_point" : [ "float", [ "3" ] ]
, "k_point_weight" : [ "float", [ "pbc.k_point_num" ] ]
} ,Electron (electron group)
The chemical system consists of nuclei and electrons, where the nuclei are considered as fixed point charges with Cartesian coordinates. The wave function is stored in the spin-free formalism, and therefore, it is necessary for the user to explicitly store the number of electrons with spin up ($N_\uparrow$) and spin down ($N_\downarrow$). These numbers correspond to the normalization of the spin-up and spin-down single-particle reduced density matrices.
We consider wave functions expressed in the spin-free formalism, where the number of ↑ and ↓ electrons is fixed.
#+NAME:electron
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
num |
dim |
Number of electrons | ||
up_num |
int |
Number of ↑-spin electrons | ||
dn_num |
int |
Number of ↓-spin electrons |
"electron": {
"num" : [ "dim", [] ]
, "up_num" : [ "int", [] ]
, "dn_num" : [ "int", [] ]
} ,Ground or excited states (state group)
This group contains information about excited states. Since only a single state can be stored in a TREXIO file, it is possible to store in the main TREXIO file the names of auxiliary files containing the information of the other states.
The file_name and label arrays have to be written only for the
main file, e.g. the one containing the ground state wave function
together with the basis set parameters, molecular orbitals,
integrals, etc.
The id and current_label attributes need to be specified for each file.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
num |
dim |
Number of states (including the ground state) | ||
id |
index |
Index of the current state (0 is ground state) | ||
energy |
float |
Energy of the current state | ||
current_label |
str |
Label of the current state | ||
label |
str |
[state.num] |
(state.num) |
Labels of all states |
file_name |
str |
[state.num] |
(state.num) |
Names of the TREXIO files linked to the current one (i.e. containing data for other states) |
"state": {
"num" : [ "dim" , [] ]
, "id" : [ "index", [] ]
, "energy" : [ "float", [] ]
, "current_label" : [ "str" , [] ]
, "label" : [ "str" , [ "state.num" ] ]
, "file_name" : [ "str" , [ "state.num" ] ]
} ,Basis functions
Basis set (basis group)
Gaussian and Slater-type orbitals
We consider here basis functions centered on nuclei. Hence, it is possibile to define dummy atoms to place basis functions in arbitrary 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 functions 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.
Numerical orbitals
Trexio supports numerical atom centered orbitals. The implementation is
based on the approach of FHI-aims [Blum, V. et al; Ab initio molecular
simulations with numeric atom-centered orbitals; Computer Physics
Communications 2009]. These orbitals are
defined by the atom they are centered on, their angular momentum and a
radial function $R_s$, which is of the form
\[
R_s(\mathbf{r}) = \mathcal{N}_s \frac{u_i(\mathbf{r})}{r^{-n_s}}.
\]
Where $u_i(\mathbf{r})$ is numerically tabulated on a dense logarithmic
grid. It is constructed to vanish for any $\mathbf{r}$
outside of the grid. The reference points are stored in nao_grid_r
and nao_grid_phi. Additionaly, a separate spline for the first and second
derivative of $u(\mathbf{r})$ can be stored in nao_grid_grad and nao_grid_lap.
Storing them in this form allows to calculate the actual first and
second derivatives easily as follows:
\[ \frac{\partial \phi}{\partial x} = \frac{x}{r^2}\left( u^\prime\left(r\right) - \frac{u\left(r\right)}{r}\right) \] \[ \frac{\partial^2 \phi}{\partial x^2} = \frac{1}{r^3}\left(x^2 u^{\prime\prime}(r) + \left( 3x^2-r^2\right) \left( \frac{u(r)}{r^2} - \frac{u'(r)}{r}\right) \right) \]
The index of the first data point for each shell is stored in
nao_grid_start, the number of data points per spline is stored
in nao_grid_size for convenience.
What kind of spline is used can be provided in the interpolator_kind field.
For example, FHI-aims uses a cubic spline, so the interpolator_kind is
\"Polynomial\" and the interp_coeff_cnt is $4$. In this case, the first
interpolation coefficient per data point is the absolute term, the second is for
the linear term etc.
The interpolation coefficients for the wave function are given in the
interpolator_phi array. The interpolator_grad and interpolator_lap
arrays provide a spline for the gradient and Laplacian, respectively.
The argument passed to the interpolants is on the logarithmic scale of
the reference points: If the argument is an integer $i$, the interpolant
will return the value of $u(\mathbf{r})$ at the $i$th reference point.
A radius is converted to this scale by (note the zero-indexing)
\[
i_{\log} = \frac{1}{c} \cdot \log \left( \frac{r}{r_0} \right)
\]
where
\[
c = \log\left(\frac{r_1}{r_0}\right)
\]
For convenience, this conversion and functions to evaluate the splines
are provided with trexio. Since these implementations are not adapted to
a specific software architecture, a programm using these orbitals should
reimplement them with consideration for its specific needs.
Plane waves
A plane wave is defined as
\[ \chi_j(\mathbf{r}) = \exp \left( -i \mathbf{G}_j \cdot \mathbf{r} \right) \]
The basis set is defined as the array of $k$-points in the
reciprocal space $\mathbf{G}_j$, defined in the pbc group. The
kinetic energy cutoff e_cut is the only input data relevant to
plane waves.
Oscillating orbitals
Basis functions can be made oscillating as \[ R_s(\mathbf{r}) = \mathcal{N}_s \vert\mathbf{r}-\mathbf{R}_A\vert^{n_s} \sum_{k=1}^{N_{\text{prim}}} a_{ks}\, f_{ks}(\gamma_{ks},p)\, \exp \left( - \gamma_{ks} \vert \mathbf{r}-\mathbf{R}_A \vert ^p \right)\, \cos \left( \beta_{ks} \vert \mathbf{r}-\mathbf{R}_A \vert ^q \right) \]
Oscillation kind can be:
Cos1for $q=1$Cos2for $q=2$
Data definitions
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
type |
str |
Type of basis set: "Gaussian", "Slater", "Numerical" or "PW" for plane waves | ||
prim_num |
dim |
Total number of primitives | ||
shell_num |
dim |
Total number of shells | ||
nao_grid_num |
dim |
Total number of grid points for numerical orbitals | ||
interp_coeff_cnt |
dim |
Number of coefficients for the numerical orbital interpolator | ||
nucleus_index |
index |
[basis.shell_num] |
(basis.shell_num) |
One-to-one correspondence between shells and atomic indices |
shell_ang_mom |
int |
[basis.shell_num] |
(basis.shell_num) |
One-to-one correspondence between shells and angular momenta |
shell_factor |
float |
[basis.shell_num] |
(basis.shell_num) |
Normalization factor of each shell ($\mathcal{N}_s$) |
r_power |
int |
[basis.shell_num] |
(basis.shell_num) |
Power to which $r$ is raised ($n_s$) |
nao_grid_start |
index |
[basis.shell_num] |
(basis.shell_num) |
Index of the first data point for a given numerical orbital |
nao_grid_size |
dim |
[basis.shell_num] |
(basis.shell_num) |
Number of data points per numerical orbital |
shell_index |
index |
[basis.prim_num] |
(basis.prim_num) |
One-to-one correspondence between primitives and shell index |
exponent |
float |
[basis.prim_num] |
(basis.prim_num) |
Exponents of the primitives ($\gamma_{ks}$) |
exponent_im |
float |
[basis.prim_num] |
(basis.prim_num) |
Imaginary part of the exponents of the primitives ($\gamma_{ks}$) |
coefficient |
float |
[basis.prim_num] |
(basis.prim_num) |
Coefficients of the primitives ($a_{ks}$) |
coefficient_im |
float |
[basis.prim_num] |
(basis.prim_num) |
Imaginary part of the coefficients of the primitives ($a_{ks}$) |
oscillation_arg |
float |
[basis.prim_num] |
(basis.prim_num) |
Additional argument to have oscillating orbitals ($\beta_{ks}$) |
oscillation_kind |
str |
Kind of Oscillating function:"Cos1" or "Cos2" | ||
prim_factor |
float |
[basis.prim_num] |
(basis.prim_num) |
Normalization coefficients for the primitives ($f_{ks}$) |
e_cut |
float |
Energy cut-off for plane-wave calculations | ||
nao_grid_radius |
float |
[basis.nao_grid_num] |
(basis.nao_grid_num) |
Radii of grid points for numerical orbitals |
nao_grid_phi |
float |
[basis.nao_grid_num] |
(basis.nao_grid_num) |
Wave function values for numerical orbitals |
nao_grid_grad |
float |
[basis.nao_grid_num] |
(basis.nao_grid_num) |
Radial gradient of numerical orbitals |
nao_grid_lap |
float |
[basis.nao_grid_num] |
(basis.nao_grid_num) |
Laplacian of numerical orbitals |
interpolator_kind |
str |
Kind of spline, e.g. "Polynomial" | ||
interpolator_phi |
float |
[basis.nao_grid_num, basis.interp_coeff_cnt] |
(basis.interp_coeff_cnt, basis.nao_grid_num) |
Coefficients for numerical orbital interpolation function |
interpolator_grad |
float |
[basis.nao_grid_num, basis.interp_coeff_cnt] |
(basis.interp_coeff_cnt, basis.nao_grid_num) |
Coefficients for numerical orbital gradient interpolation function |
interpolator_lap |
float |
[basis.nao_grid_num, basis.interp_coeff_cnt] |
(basis.interp_coeff_cnt, basis.nao_grid_num) |
Coefficients for numerical orbital laplacian interpolation function |
"basis": {
"type" : [ "str" , [] ]
, "prim_num" : [ "dim" , [] ]
, "shell_num" : [ "dim" , [] ]
, "nao_grid_num" : [ "dim" , [] ]
, "interp_coeff_cnt" : [ "dim" , [] ]
, "nucleus_index" : [ "index", [ "basis.shell_num" ] ]
, "shell_ang_mom" : [ "int" , [ "basis.shell_num" ] ]
, "shell_factor" : [ "float", [ "basis.shell_num" ] ]
, "r_power" : [ "int" , [ "basis.shell_num" ] ]
, "nao_grid_start" : [ "index", [ "basis.shell_num" ] ]
, "nao_grid_size" : [ "dim" , [ "basis.shell_num" ] ]
, "shell_index" : [ "index", [ "basis.prim_num" ] ]
, "exponent" : [ "float", [ "basis.prim_num" ] ]
, "exponent_im" : [ "float", [ "basis.prim_num" ] ]
, "coefficient" : [ "float", [ "basis.prim_num" ] ]
, "coefficient_im" : [ "float", [ "basis.prim_num" ] ]
, "oscillation_arg" : [ "float", [ "basis.prim_num" ] ]
, "oscillation_kind" : [ "str" , [] ]
, "prim_factor" : [ "float", [ "basis.prim_num" ] ]
, "e_cut" : [ "float", [] ]
, "nao_grid_radius" : [ "float", [ "basis.nao_grid_num" ] ]
, "nao_grid_phi" : [ "float", [ "basis.nao_grid_num" ] ]
, "nao_grid_grad" : [ "float", [ "basis.nao_grid_num" ] ]
, "nao_grid_lap" : [ "float", [ "basis.nao_grid_num" ] ]
, "interpolator_kind" : [ "str" , [] ]
, "interpolator_phi" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ]
, "interpolator_grad" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ]
, "interpolator_lap" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ]
} ,Example
For example, consider H_2 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 1.000000E+00
In TREXIO representaion we have:
type = "Gaussian" prim_num = 20 shell_num = 12 # 6 shells per H atom nucleus_index = [ 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1 ] # 3 shells in S (l=0), 2 in P (l=1), 1 in D (l=2) shell_ang_mom = [ 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. ] # 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 = [ 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 ]
Effective core potentials (ecp group)
An effective core potential (ECP) $V_A^{\text{ECP}}$ replacing the core electrons of atom $A$ can be expressed as \[ V_A^{\text{ECP}} = V_{A \ell_{\max}+1} + \sum_{\ell=0}^{\ell_{\max}} \delta V_{A \ell}\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \langle Y_{\ell m} | \]
The first term in this equation is attributed to the local channel, while the remaining terms correspond to non-local channel projections. $\ell_{\max}$ refers to the maximum angular momentum in the non-local component of the ECP. The functions \(\delta V_{A \ell}\) and \(V_{A \ell_{\max}+1}\) are parameterized as:
\begin{eqnarray} \delta 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 } \nonumber\\ V_{A \ell_{\max}+1}(\mathbf{r}) &=& -\frac{Z_\text{eff}}{|\mathbf{r}-\mathbf{R}_{A}|}+\delta V_{A \ell_{\max}+1}(\mathbf{r}) \end{eqnarray}where $Z_\text{eff}$ is the effective nuclear charge of the center.
See http://dx.doi.org/10.1063/1.4984046 or https://doi.org/10.1063/1.5121006 for more info.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
max_ang_mom_plus_1 |
int |
[nucleus.num] |
(nucleus.num) |
$\ell_{\max}+1$, one higher than the max angular momentum in the removed core orbitals |
z_core |
int |
[nucleus.num] |
(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] |
(ecp.num) |
One-to-one correspondence between ECP items and the angular momentum $\ell$ |
nucleus_index |
index |
[ecp.num] |
(ecp.num) |
One-to-one correspondence between ECP items and the atom index |
exponent |
float |
[ecp.num] |
(ecp.num) |
$\alpha_{A q \ell}$ all ECP exponents |
coefficient |
float |
[ecp.num] |
(ecp.num) |
$\beta_{A q \ell}$ all ECP coefficients |
power |
int |
[ecp.num] |
(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. The 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 the ang_mom array in the TREXIO file.
Update: in fact, the aforementioned issue has only been observed
when using HDF5 version 1.10.4 installed via apt-get. Installing
the same version from the conda-forge channel and running it in
an isolated conda environment works just fine. Thus, it seems to
be a bug in the apt-provided package.
If you encounter the aforementioned issue, please report it to our
issue tracker on GitHub.
"ecp": {
"max_ang_mom_plus_1" : [ "int" , [ "nucleus.num" ] ]
, "z_core" : [ "int" , [ "nucleus.num" ] ]
, "num" : [ "dim" , [] ]
, "ang_mom" : [ "int" , [ "ecp.num" ] ]
, "nucleus_index" : [ "index", [ "ecp.num" ] ]
, "exponent" : [ "float", [ "ecp.num" ] ]
, "coefficient" : [ "float", [ "ecp.num" ] ]
, "power" : [ "int" , [ "ecp.num" ] ]
} ,Example
For example, consider H_2 molecule with the following effective core potential (in GAMESS input format for the H atom):
H-ccECP GEN 0 1 3 1.00000000000000 1 21.24359508259891 21.24359508259891 3 21.24359508259891 -10.85192405303825 2 21.77696655044365 1 0.00000000000000 2 1.000000000000000
In TREXIO representation this would be:
num = 8 # lmax+1 per atom 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 ; 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 potential of 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 ] # 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 ] exponent = [ 21.24359508259891, 21.24359508259891, 21.77696655044365, 1.000000000000000, 21.24359508259891, 21.24359508259891, 21.77696655044365, 1.000000000000000 ] power = [ -1, 1, 0, 0, -1, 1, 0, 0 ]
Numerical integration grid (grid group)
In some applications, such as DFT calculations, integrals have to be computed numerically on a grid. A common choice for the angular grid is the one proposed by Lebedev and Laikov [Russian Academy of Sciences Doklady Mathematics, Volume 59, Number 3, 1999, pages 477-481]. For the radial grids, many approaches have been developed over the years.
The structure of this group is adapted for the numgrid library. Feel free to submit a PR if you find missing options/functionalities.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
description |
str |
Details about the used quadratures can go here | ||
rad_precision |
float |
Radial precision parameter (not used in some schemes like Krack-Köster) | ||
num |
dim |
Number of grid points | ||
max_ang_num |
int |
Maximum number of angular grid points (for pruning) | ||
min_ang_num |
int |
Minimum number of angular grid points (for pruning) | ||
coord |
float |
[grid.num] |
(grid.num) |
Discretized coordinate space |
weight |
float |
[grid.num] |
(grid.num) |
Grid weights according to a given partitioning (e.g. Becke) |
ang_num |
dim |
Number of angular integration points (if used) | ||
ang_coord |
float |
[grid.ang_num] |
(grid.ang_num) |
Discretized angular space (if used) |
ang_weight |
float |
[grid.ang_num] |
(grid.ang_num) |
Angular grid weights (if used) |
rad_num |
dim |
Number of radial integration points (if used) | ||
rad_coord |
float |
[grid.rad_num] |
(grid.rad_num) |
Discretized radial space (if used) |
rad_weight |
float |
[grid.rad_num] |
(grid.rad_num) |
Radial grid weights (if used) |
"grid": {
"description" : [ "str" , [] ]
, "rad_precision" : [ "float", [] ]
, "num" : [ "dim" , [] ]
, "max_ang_num" : [ "int" , [] ]
, "min_ang_num" : [ "int" , [] ]
, "coord" : [ "float", [ "grid.num" ] ]
, "weight" : [ "float", [ "grid.num" ] ]
, "ang_num" : [ "dim" , [] ]
, "ang_coord" : [ "float", [ "grid.ang_num" ] ]
, "ang_weight" : [ "float", [ "grid.ang_num" ] ]
, "rad_num" : [ "dim" , [] ]
, "rad_coord" : [ "float", [ "grid.rad_num" ] ]
, "rad_weight" : [ "float", [ "grid.rad_num" ] ]
} ,Orbitals
Atomic orbitals (ao group)
AOs are defined as
\[ \chi_i (\mathbf{r}) = \mathcal{N}_i'\, P_{\eta(i)}(\mathbf{r})\, R_{s(i)} (\mathbf{r}) \]
where $i$ is the atomic orbital index, $P$ refers to either polynomials in $x,y,z$ or real solid harmonics \[ S^m_{\ell}(\mathbf{r}) \equiv \sqrt{\frac{4\pi}{2\ell+1}}\; r^\ell Y^m_{\ell}(\theta,\varphi) \] (see Wikipedia), and $s(i)$ specifies the shell on which the AO is expanded.
$\eta(i)$ denotes the chosen angular function. The AOs can be expressed using real solid harmonics or polynomials in Cartesian coordinates. In the case of real solid harmonics, the AOs are ordered as $0, +1, -1, +2, -2, \dots, + m, -m$). In the case of polynomials, the canonical (or alphabetical) ordering is used,
| $p$ | $p_x, p_y, p_z$ |
| $d$ | $d_{xx}, d_{xy}, d_{xz}, d_{yy}, d_{yz}, d_{zz}$ |
| $f$ | $f_{xxx}, f_{xxy}, f_{xxz}, f_{xyy}, f_{xyz}$, |
| $f_{xzz}, f_{yyy}, f_{yyz}, f_{yzz}, f_{zzz}$ | |
| $\vdots$ |
Note that for \(p\) orbitals in spherical coordinates, the ordering is $0,+1,-1$ which corresponds to $p_z, p_x, p_y$.
$\mathcal{N}_i'$ is a normalization factor that allows for different
normalization coefficients within a single shell, as in the GAMESS
convention where each individual function is unit-normalized.
Using GAMESS convention, the normalization factor of the shell
$\mathcal{N}_d$ in the basis group is appropriate for instance
for the $d_z^2$ function (i.e.
$\mathcal{N}_{d}\equiv\mathcal{N}_{z^2}$) but not for the $d_{xy}$
AO, so the correction factor $\mathcal{N}_i'$ for $d_{xy}$ in the
ao groups is the ratio $\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}$.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
cartesian |
int |
1: true, 0: false |
||
num |
dim |
Total number of atomic orbitals | ||
shell |
index |
[ao.num] |
(ao.num) |
Basis set shell for each AO |
normalization |
float |
[ao.num] |
(ao.num) |
Normalization factor $\mathcal{N}_i$ |
"ao": {
"cartesian" : [ "int" , [] ]
, "num" : [ "dim" , [] ]
, "shell" : [ "index", [ "ao.num" ] ]
, "normalization" : [ "float", [ "ao.num" ] ]
} ,
One-electron integrals (ao_1e_int group)
- \[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}} \sum_{i=1}^{N_\text{elec}} \frac{-Z_A }{\vert \mathbf{R}_A - \mathbf{r}_i \vert} \] : electron-nucleus attractive potential,
- \[ \hat{T}_{\text{e}} = \sum_{i=1}^{N_\text{elec}} -\frac{1}{2}\hat{\Delta}_i \] : electronic kinetic energy
- $\hat{h} = \hat{T}_\text{e} + \hat{V}_\text{ne} + \hat{V}_\text{ECP}$ : core electronic Hamiltonian
The one-electron integrals for a one-electron operator $\hat{O}$ are \[ \langle p \vert \hat{O} \vert q \rangle \], returned as a matrix over atomic orbitals.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
overlap |
float |
[ao.num, ao.num] |
(ao.num, ao.num) |
$\langle p \vert q \rangle$ |
kinetic |
float |
[ao.num, ao.num] |
(ao.num, ao.num) |
$\langle p \vert \hat{T}_e \vert q \rangle$ |
potential_n_e |
float |
[ao.num, ao.num] |
(ao.num, ao.num) |
$\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
ecp |
float |
[ao.num, ao.num] |
(ao.num, ao.num) |
$\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ |
core_hamiltonian |
float |
[ao.num, ao.num] |
(ao.num, ao.num) |
$\langle p \vert \hat{h} \vert q \rangle$ |
overlap_im |
float |
[ao.num, ao.num] |
(ao.num, ao.num) |
$\langle p \vert q \rangle$ (imaginary part) |
kinetic_im |
float |
[ao.num, ao.num] |
(ao.num, ao.num) |
$\langle p \vert \hat{T}_e \vert q \rangle$ (imaginary part) |
potential_n_e_im |
float |
[ao.num, ao.num] |
(ao.num, ao.num) |
$\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (imaginary part) |
ecp_im |
float |
[ao.num, ao.num] |
(ao.num, ao.num) |
$\langle p \vert \hat{V}_{\text{ECP}} \vert q \rangle$ (imaginary part) |
core_hamiltonian_im |
float |
[ao.num, ao.num] |
(ao.num, ao.num) |
$\langle p \vert \hat{h} \vert q \rangle$ (imaginary part) |
"ao_1e_int": {
"overlap" : [ "float", [ "ao.num", "ao.num" ] ]
, "kinetic" : [ "float", [ "ao.num", "ao.num" ] ]
, "potential_n_e" : [ "float", [ "ao.num", "ao.num" ] ]
, "ecp" : [ "float", [ "ao.num", "ao.num" ] ]
, "core_hamiltonian" : [ "float", [ "ao.num", "ao.num" ] ]
, "overlap_im" : [ "float", [ "ao.num", "ao.num" ] ]
, "kinetic_im" : [ "float", [ "ao.num", "ao.num" ] ]
, "potential_n_e_im" : [ "float", [ "ao.num", "ao.num" ] ]
, "ecp_im" : [ "float", [ "ao.num", "ao.num" ] ]
, "core_hamiltonian_im" : [ "float", [ "ao.num", "ao.num" ] ]
} ,
Two-electron integrals (ao_2e_int group)
The two-electron integrals for a two-electron operator $\hat{O}$ are \[ \langle p q \vert \hat{O} \vert r s \rangle \] in physicists notation, where $p,q,r,s$ are indices over atomic orbitals.
- \[ \hat{W}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}} \sum_{j=1}^{i-1} \frac{1}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron repulsive potential operator.
- \[ \hat{W}^{lr}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}} \sum_{j=1}^{i-1} \frac{\text{erf}(\mu\, \vert \mathbf{r}_i - \mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential
The Cholesky decomposition of the integrals can also be stored:
\[ \langle ij | kl \rangle = \sum_{\alpha} G_{ik\alpha} G_{jl\alpha} \]
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
eri |
float sparse |
[ao.num, ao.num, ao.num, ao.num] |
(ao.num, ao.num, ao.num, ao.num) |
Electron repulsion integrals |
eri_lr |
float sparse |
[ao.num, ao.num, ao.num, ao.num] |
(ao.num, ao.num, ao.num, ao.num) |
Long-range electron repulsion integrals |
eri_cholesky_num |
dim |
Number of Cholesky vectors for ERI | ||
eri_cholesky |
float sparse |
[ao_2e_int.eri_cholesky_num, ao.num, ao.num] |
(ao.num, ao.num, ao_2e_int.eri_cholesky_num) |
Cholesky decomposition of the ERI |
eri_lr_cholesky_num |
dim |
Number of Cholesky vectors for long range ERI | ||
eri_lr_cholesky |
float sparse |
[ao_2e_int.eri_lr_cholesky_num, ao.num, ao.num] |
(ao.num, ao.num, ao_2e_int.eri_lr_cholesky_num) |
Cholesky decomposition of the long range ERI |
"ao_2e_int": {
"eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
, "eri_lr" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
, "eri_cholesky_num" : [ "dim" , [] ]
, "eri_cholesky" : [ "float sparse", [ "ao_2e_int.eri_cholesky_num", "ao.num", "ao.num" ] ]
, "eri_lr_cholesky_num" : [ "dim" , [] ]
, "eri_lr_cholesky" : [ "float sparse", [ "ao_2e_int.eri_lr_cholesky_num", "ao.num", "ao.num" ] ]
} ,Molecular orbitals (mo group)
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
type |
str |
Free text to identify the set of MOs (HF, Natural, Local, CASSCF, etc) | ||
num |
dim |
Number of MOs | ||
coefficient |
float |
[mo.num, ao.num] |
(ao.num, mo.num) |
MO coefficients |
coefficient_im |
float |
[mo.num, ao.num] |
(ao.num, mo.num) |
MO coefficients (imaginary part) |
class |
str |
[mo.num] |
(mo.num) |
Choose among: Core, Inactive, Active, Virtual, Deleted |
symmetry |
str |
[mo.num] |
(mo.num) |
Symmetry in the point group |
occupation |
float |
[mo.num] |
(mo.num) |
Occupation number |
energy |
float |
[mo.num] |
(mo.num) |
For canonical MOs, corresponding eigenvalue |
spin |
int |
[mo.num] |
(mo.num) |
For UHF wave functions, 0 is $\alpha$ and 1 is $\beta$ |
k_point |
index |
[mo.num] |
(mo.num) |
For periodic calculations, the $k$ point to which each MO belongs |
Warning: mo.num is the total number of MOs stored in the file.
For periodic calculations, this group contains all the MOs
belonging to all $k$ points so mo.num will be the sum of the
numbers of MOs in each $k$ point. For UHF wave functions, mo.num
is the number of spin-orbitals, twice the number of spatial orbitals.
"mo": {
"type" : [ "str" , [] ]
, "num" : [ "dim" , [] ]
, "coefficient" : [ "float", [ "mo.num", "ao.num" ] ]
, "coefficient_im" : [ "float", [ "mo.num", "ao.num" ] ]
, "class" : [ "str" , [ "mo.num" ] ]
, "symmetry" : [ "str" , [ "mo.num" ] ]
, "occupation" : [ "float", [ "mo.num" ] ]
, "energy" : [ "float", [ "mo.num" ] ]
, "spin" : [ "int" , [ "mo.num" ] ]
, "k_point" : [ "index", [ "mo.num" ] ]
} ,
One-electron integrals (mo_1e_int group)
The operators as the same as those defined in the AO one-electron integrals section. Here, the integrals are given in the basis of molecular orbitals.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
overlap |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
$\langle i \vert j \rangle$ |
kinetic |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
$\langle i \vert \hat{T}_e \vert j \rangle$ |
potential_n_e |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
$\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ |
ecp |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
$\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ |
core_hamiltonian |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
$\langle i \vert \hat{h} \vert j \rangle$ |
overlap_im |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
$\langle i \vert j \rangle$ (imaginary part) |
kinetic_im |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
$\langle i \vert \hat{T}_e \vert j \rangle$ (imaginary part) |
potential_n_e_im |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
$\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (imaginary part) |
ecp_im |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
$\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (imaginary part) |
core_hamiltonian_im |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
$\langle i \vert \hat{h} \vert j \rangle$ (imaginary part) |
"mo_1e_int": {
"overlap" : [ "float", [ "mo.num", "mo.num" ] ]
, "kinetic" : [ "float", [ "mo.num", "mo.num" ] ]
, "potential_n_e" : [ "float", [ "mo.num", "mo.num" ] ]
, "ecp" : [ "float", [ "mo.num", "mo.num" ] ]
, "core_hamiltonian" : [ "float", [ "mo.num", "mo.num" ] ]
, "overlap_im" : [ "float", [ "mo.num", "mo.num" ] ]
, "kinetic_im" : [ "float", [ "mo.num", "mo.num" ] ]
, "potential_n_e_im" : [ "float", [ "mo.num", "mo.num" ] ]
, "ecp_im" : [ "float", [ "mo.num", "mo.num" ] ]
, "core_hamiltonian_im" : [ "float", [ "mo.num", "mo.num" ] ]
} ,
Two-electron integrals (mo_2e_int group)
The operators are the same as those defined in the AO two-electron integrals section. Here, the integrals are given in the basis of molecular orbitals.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
eri |
float sparse |
[mo.num, mo.num, mo.num, mo.num] |
(mo.num, mo.num, mo.num, mo.num) |
Electron repulsion integrals |
eri_lr |
float sparse |
[mo.num, mo.num, mo.num, mo.num] |
(mo.num, mo.num, mo.num, mo.num) |
Long-range electron repulsion integrals |
eri_cholesky_num |
dim |
Number of Cholesky vectors for ERI | ||
eri_cholesky |
float sparse |
[mo_2e_int.eri_cholesky_num, mo.num, mo.num] |
(mo.num, mo.num, mo_2e_int.eri_cholesky_num) |
Cholesky decomposition of the ERI |
eri_lr_cholesky_num |
dim |
Number of Cholesky vectors for long range ERI | ||
eri_lr_cholesky |
float sparse |
[mo_2e_int.eri_lr_cholesky_num, mo.num, mo.num] |
(mo.num, mo.num, mo_2e_int.eri_lr_cholesky_num) |
Cholesky decomposition of the long range ERI |
"mo_2e_int": {
"eri" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "eri_lr" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "eri_cholesky_num" : [ "dim" , [] ]
, "eri_cholesky" : [ "float sparse", [ "mo_2e_int.eri_cholesky_num", "mo.num", "mo.num" ] ]
, "eri_lr_cholesky_num" : [ "dim" , [] ]
, "eri_lr_cholesky" : [ "float sparse", [ "mo_2e_int.eri_lr_cholesky_num", "mo.num", "mo.num" ] ]
} ,Multi-determinant information
Slater determinants (determinant group)
The configuration interaction (CI) wave function $\Psi$ can be expanded in the basis of Slater determinants $D_I$ as follows
\[ \Psi = \sum_I C_I D_I \]
For relatively small expansions, a given determinant can be represented as a list of occupied orbitals. However, this becomes unfeasible for larger expansions and requires more advanced data structures. The bit field representation is used here, namely a given determinant is represented as $N_{\text{int}}$ 64-bit integers where j-th bit is set to 1 if there is an electron in the j-th orbital and 0 otherwise. This gives access to larger determinant expansions by optimising the storage of the determinant lists in the memory.
\[ D_I = \alpha_1 \alpha_2 \ldots \alpha_{n_\uparrow} \beta_1 \beta_2 \ldots \beta_{n_\downarrow} \]
where $\alpha$ and $\beta$ denote ↑-spin and ↓-spin electrons, respectively,
$n_\uparrow$ and $n_\downarrow$ correspond to electron.up_num and electron.dn_num, respectively.
Note: the special attribute is present in the types, meaning that the source node is not
produced by the code generator.
An illustration on how to read determinants is presented in the examples.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
num |
dim readonly |
Number of determinants | ||
list |
int special |
[determinant.num] |
(determinant.num) |
List of determinants as integer bit fields |
coefficient |
float buffered |
[determinant.num] |
(determinant.num) |
Coefficients of the determinants from the CI expansion |
"determinant": {
"num" : [ "dim readonly" , [] ]
, "list" : [ "int special" , [ "determinant.num" ] ]
, "coefficient" : [ "float buffered", [ "determinant.num" ] ]
} ,Configuration state functions (csf group)
The configuration interaction (CI) wave function $\Psi$ can be expanded in the basis of configuration state functions (CSFs) $\Psi_I$ as follows
\[ \Psi = \sum_I C_I \psi_I. \]
Each CSF $\psi_I$ is a linear combination of Slater determinants. Slater
determinants are stored in the determinant section. In this group
we store the CI coefficients in the basis of CSFs, and the
matrix $\langle D_I | \psi_J \rangle$ needed to project the CSFs in
the basis of Slater determinants.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
num |
dim readonly |
Number of CSFs | ||
coefficient |
float buffered |
[csf.num] |
(csf.num) |
Coefficients $C_I$ of the CSF expansion |
det_coefficient |
float sparse |
[csf.num, determinant.num] |
(determinant.num, csf.num) |
Projection on the determinant basis |
"csf": {
"num" : [ "dim readonly" , [] ]
, "coefficient" : [ "float buffered", [ "csf.num" ] ]
, "det_coefficient" : [ "float sparse" , [ "csf.num", "determinant.num" ] ]
} ,Amplitudes (amplitude group)
The wave function may be expressed in terms of action of the cluster operator $\hat{T}$:
\[ \hat{T} = \hat{T}_1 + \hat{T}_2 + \hat{T}_3 + \dots \]
on a reference wave function $\Psi$, where $\hat{T}_1$ is the single excitation operator,
\[ \hat{T}_1 = \sum_{ia} t_{i}^{a}\, \hat{a}^\dagger_a \hat{a}_i, \]
$\hat{T}_2$ is the double excitation operator,
\[ \hat{T}_2 = \frac{1}{4} \sum_{ijab} t_{ij}^{ab}\, \hat{a}^\dagger_a \hat{a}^\dagger_b \hat{a}_j \hat{a}_i, \]
etc. Indices $i$, $j$, $a$ and $b$ denote molecular orbital indices.
Wave functions obtained with perturbation theory or configuration interaction are of the form
\[ |\Phi\rangle = \hat{T}|\Psi\rangle \]
and coupled-cluster wave functions are of the form
\[ |\Phi\rangle = e^{\hat{T}}| \Psi \rangle \]
The reference wave function is stored using the determinant and/or
csf groups, and the amplitudes are stored using the current group.
The attributes with the exp suffix correspond to exponentialized operators.
The order of the indices is chosen such that
t(i,a)= $t_{i}^{a}$.t(i,j,a,b)= $t_{ij}^{ab}$,t(i,j,k,a,b,c)= $t_{ijk}^{abc}$,t(i,j,k,l,a,b,c,d)= $t_{ijkl}^{abcd}$,- $\dots$
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
single |
float sparse |
[mo.num,mo.num] |
(mo.num,mo.num) |
Single excitation amplitudes |
single_exp |
float sparse |
[mo.num,mo.num] |
(mo.num,mo.num) |
Exponentialized single excitation amplitudes |
double |
float sparse |
[mo.num,mo.num,mo.num,mo.num] |
(mo.num,mo.num,mo.num,mo.num) |
Double excitation amplitudes |
double_exp |
float sparse |
[mo.num,mo.num,mo.num,mo.num] |
(mo.num,mo.num,mo.num,mo.num) |
Exponentialized double excitation amplitudes |
triple |
float sparse |
[mo.num,mo.num,mo.num,mo.num,mo.num,mo.num] |
(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num) |
Triple excitation amplitudes |
triple_exp |
float sparse |
[mo.num,mo.num,mo.num,mo.num,mo.num,mo.num] |
(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num) |
Exponentialized triple excitation amplitudes |
quadruple |
float sparse |
[mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num] |
(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num) |
Quadruple excitation amplitudes |
quadruple_exp |
float sparse |
[mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num] |
(mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num,mo.num) |
Exponentialized quadruple excitation amplitudes |
"amplitude": {
"single" : [ "float sparse", [ "mo.num", "mo.num" ] ]
, "single_exp" : [ "float sparse", [ "mo.num", "mo.num" ] ]
, "double" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "double_exp" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "triple" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "triple_exp" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "quadruple" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "quadruple_exp" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num", "mo.num" ] ]
} ,Reduced density matrices (rdm group)
The reduced density matrices are defined in the basis of molecular orbitals.
The ↑-spin and ↓-spin components of the one-body density matrix are given by
\begin{eqnarray*} \gamma_{ij}^{\uparrow} &=& \langle \Psi | \hat{a}^{\dagger}_{j\alpha}\, \hat{a}_{i\alpha} | \Psi \rangle \\ \gamma_{ij}^{\downarrow} &=& \langle \Psi | \hat{a}^{\dagger}_{j\beta} \, \hat{a}_{i\beta} | \Psi \rangle \end{eqnarray*}and the spin-summed one-body density matrix is \[ \gamma_{ij} = \gamma^{\uparrow}_{ij} + \gamma^{\downarrow}_{ij} \]
The $\uparrow \uparrow$, $\downarrow \downarrow$, $\uparrow \downarrow$ components of the two-body density matrix are given by
\begin{eqnarray*} \Gamma_{ijkl}^{\uparrow \uparrow} &=& \langle \Psi | \hat{a}^{\dagger}_{k\alpha}\, \hat{a}^{\dagger}_{l\alpha} \hat{a}_{j\alpha}\, \hat{a}_{i\alpha} | \Psi \rangle \\ \Gamma_{ijkl}^{\downarrow \downarrow} &=& \langle \Psi | \hat{a}^{\dagger}_{k\beta}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\beta} | \Psi \rangle \\ \Gamma_{ijkl}^{\uparrow \downarrow} &=& \langle \Psi | \hat{a}^{\dagger}_{k\alpha}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\alpha} | \Psi \rangle + \langle \Psi | \hat{a}^{\dagger}_{l\alpha}\, \hat{a}^{\dagger}_{k\beta} \hat{a}_{i\beta}\, \hat{a}_{j\alpha} | \Psi \rangle \\ \end{eqnarray*}and the spin-summed one-body density matrix is \[ \Gamma_{ijkl} = \Gamma_{ijkl}^{\uparrow \uparrow} + \Gamma_{ijkl}^{\downarrow \downarrow} + \Gamma_{ijkl}^{\uparrow \downarrow}. \]
The total energy can be computed as: \[ E = E_{\text{NN}} + \sum_{ij} \gamma_{ij} \langle j|h|i \rangle + \frac{1}{2} \sum_{ijlk} \Gamma_{ijkl} \langle k l | i j \rangle \]
To compress the storage, the Cholesky decomposition of the RDMs can be stored:
\[ \Gamma_{ijkl} = \sum_{\alpha} G_{ij\alpha} G_{kl\alpha} \]
Warning: as opposed to electron repulsion integrals, the decomposition is made such that the Cholesky vectors are expanded in a two-electron basis $f_{ij}(\mathbf{r}_1,\mathbf{r}_2) = \phi_i(\mathbf{r}_1) \phi_j(\mathbf{r}_2)$, whereas in electron repulsion integrals each Cholesky vector is expressed in a basis of a one-electron function $g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)$.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
1e |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
One body density matrix |
1e_up |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
↑-spin component of the one body density matrix |
1e_dn |
float |
[mo.num, mo.num] |
(mo.num, mo.num) |
↓-spin component of the one body density matrix |
1e_transition |
float |
[state.num, state.num, mo.num, mo.num] |
(mo.num, mo.num, state.num, state.num) |
One-particle transition density matrices |
2e |
float sparse |
[mo.num, mo.num, mo.num, mo.num] |
(mo.num, mo.num, mo.num, mo.num) |
Two-body reduced density matrix (spin trace) |
2e_upup |
float sparse |
[mo.num, mo.num, mo.num, mo.num] |
(mo.num, mo.num, mo.num, mo.num) |
↑↑ component of the two-body reduced density matrix |
2e_dndn |
float sparse |
[mo.num, mo.num, mo.num, mo.num] |
(mo.num, mo.num, mo.num, mo.num) |
↓↓ component of the two-body reduced density matrix |
2e_updn |
float sparse |
[mo.num, mo.num, mo.num, mo.num] |
(mo.num, mo.num, mo.num, mo.num) |
↑↓ component of the two-body reduced density matrix |
2e_transition |
float sparse |
[state.num, state.num, mo.num, mo.num, mo.num, mo.num] |
(mo.num, mo.num, mo.num, mo.num, state.num, state.num) |
Two-particle transition density matrices |
2e_cholesky_num |
dim |
Number of Cholesky vectors | ||
2e_cholesky |
float sparse |
[rdm.2e_cholesky_num, mo.num, mo.num] |
(mo.num, mo.num, rdm.2e_cholesky_num) |
Cholesky decomposition of the two-body RDM (spin trace) |
2e_upup_cholesky_num |
dim |
Number of Cholesky vectors | ||
2e_upup_cholesky |
float sparse |
[rdm.2e_upup_cholesky_num, mo.num, mo.num] |
(mo.num, mo.num, rdm.2e_upup_cholesky_num) |
Cholesky decomposition of the two-body RDM (↑↑) |
2e_dndn_cholesky_num |
dim |
Number of Cholesky vectors | ||
2e_dndn_cholesky |
float sparse |
[rdm.2e_dndn_cholesky_num, mo.num, mo.num] |
(mo.num, mo.num, rdm.2e_dndn_cholesky_num) |
Cholesky decomposition of the two-body RDM (↓↓) |
2e_updn_cholesky_num |
dim |
Number of Cholesky vectors | ||
2e_updn_cholesky |
float sparse |
[rdm.2e_updn_cholesky_num, mo.num, mo.num] |
(mo.num, mo.num, rdm.2e_updn_cholesky_num) |
Cholesky decomposition of the two-body RDM (↑↓) |
"rdm": {
"1e" : [ "float" , [ "mo.num", "mo.num" ] ]
, "1e_up" : [ "float" , [ "mo.num", "mo.num" ] ]
, "1e_dn" : [ "float" , [ "mo.num", "mo.num" ] ]
, "1e_transition" : [ "float" , [ "state.num", "state.num", "mo.num", "mo.num" ] ]
, "2e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_upup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_dndn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_updn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_transition" : [ "float sparse", [ "state.num", "state.num", "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_cholesky_num" : [ "dim" , [] ]
, "2e_cholesky" : [ "float sparse", [ "rdm.2e_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_upup_cholesky_num" : [ "dim" , [] ]
, "2e_upup_cholesky" : [ "float sparse", [ "rdm.2e_upup_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_dndn_cholesky_num" : [ "dim" , [] ]
, "2e_dndn_cholesky" : [ "float sparse", [ "rdm.2e_dndn_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_updn_cholesky_num" : [ "dim" , [] ]
, "2e_updn_cholesky" : [ "float sparse", [ "rdm.2e_updn_cholesky_num", "mo.num", "mo.num" ] ]
} ,Correlation factors
Jastrow factor (jastrow group)
The Jastrow factor is an $N$-electron function which multiplies the CI expansion: $\Psi = \Phi \times \exp(J)$,
In the following, we use the notations $r_{ij} = |\mathbf{r}_i - \mathbf{r}_j|$ and $R_{i\alpha} = |\mathbf{r}_i - \mathbf{R}_\alpha|$, where indices $i$ and $j$ refer to electrons and $\alpha$ to nuclei.
Parameters for multiple forms of Jastrow factors can be saved in
TREXIO files, and are described in the following sections. These
are identified by the type attribute. The type can be one of the
following:
CHAMPMu
CHAMP
The first form of Jastrow factor is the one used in the CHAMP program:
\[ J(\mathbf{r},\mathbf{R}) = J_{\text{eN}}(\mathbf{r},\mathbf{R}) + J_{\text{ee}}(\mathbf{r}) + J_{\text{eeN}}(\mathbf{r},\mathbf{R}) \]
$J_{\text{eN}}$ contains electron-nucleus terms:
\[ J_{\text{eN}}(\mathbf{r},\mathbf{R}) = \sum_{i=1}^{N_\text{elec}} \sum_{\alpha=1}^{N_\text{nucl}}\left[ \frac{a_{1,\alpha}\, f_\alpha(R_{i\alpha})}{1+a_{2,\alpha}\, f_\alpha(R_{i\alpha})} + \sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, [f_\alpha(R_{i\alpha})]^p - J_{\text{eN}}^\infty \right] \]
$J_{\text{ee}}$ contains electron-electron terms:
\[ J_{\text{ee}}(\mathbf{r}) = \sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \left[ \frac{\frac{1}{2}\big(1 + \delta^{\uparrow\downarrow}_{ij}\big)\,b_1\, f_{\text{ee}}(r_{ij})}{1+b_2\, f_{\text{ee}}(r_{ij})} + \sum_{p=2}^{N_\text{ord}^b} b_{p+1}\, [f_{\text{ee}}(r_{ij})]^p - J_{\text{ee},ij}^\infty \right] \]
$\delta^{\uparrow\downarrow}_{ij}$ is zero when the electrons $i$ and $j$ have the same spin, and one otherwise.
$J_{\text{eeN}}$ contains electron-electron-Nucleus terms:
\[ J_{\text{eeN}}(\mathbf{r},\mathbf{R}) = \sum_{\alpha=1}^{N_{\text{nucl}}} \sum_{i=1}^{N_{\text{elec}}} \sum_{j=1}^{i-1} \sum_{p=2}^{N_{\text{ord}}} \sum_{k=0}^{p-1} \sum_{l=0}^{p-k-2\delta_{k,0}} c_{lkp\alpha} \left[ g_{\text{ee}}({r}_{ij}) \right]^k \nonumber \\ \left[ \left[ g_\alpha({R}_{i\alpha}) \right]^l + \left[ g_\alpha({R}_{j\alpha}) \right]^l \right] \left[ g_\alpha({R}_{i\,\alpha}) \, g_\alpha({R}_{j\alpha}) \right]^{(p-k-l)/2} \] $c_{lkp\alpha}$ are non-zero only when $p-k-l$ is even.
The terms $J_{\text{ee},ij}^\infty$ and $J_{\text{eN}}^\infty$ are shifts to ensure that $J_{\text{eN}}$ and $J_{\text{ee}}$ have an asymptotic value of zero:
\[ J_{\text{eN}}^{\infty} = \frac{a_{1,\alpha}\, \kappa_\alpha^{-1}}{1+a_{2,\alpha}\, \kappa_\alpha^{-1}} + \sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, \kappa_\alpha^{-p} \] \[ J_{\text{ee},ij}^{\infty} = \frac{\frac{1}{2}\big(1 + \delta^{\uparrow\downarrow}_{ij}\big)\,b_1\, \kappa_{\text{ee}}^{-1}}{1+b_2\, \kappa_{\text{ee}}^{-1}} + \sum_{p=2}^{N_\text{ord}^b} b_{p+1}\, \kappa_{\text{ee}}^{-p} \]
$f$ and $g$ are scaling function defined as
\[ f_\alpha(r) = \frac{1-e^{-\kappa_\alpha\, r}}{\kappa_\alpha} \text{ and } g_\alpha(r) = e^{-\kappa_\alpha\, r}, \]
Mu
Mu-Jastrow is based on a one-parameter correlation factor that has been introduced in the context of transcorrelated methods. This correlation factor imposes the electron-electron cusp, and it is built such that the leading order in $1/r_{12}$ of the effective two-electron potential reproduces the long-range interaction of the range-separated density functional theory. Its analytical expression reads
\[ J(\mathbf{r}, \mathbf{R}) = J_{\text{eeN}}(\mathbf{r}, \mathbf{R}) + J_{\text{eN}}(\mathbf{r}, \mathbf{R}) \].
The electron-electron cusp is incorporated in the three-body term
\[ J_\text{eeN} (\mathbf{r}, \mathbf{R}) = \sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right) \, \Pi_{\alpha=1}^{N_{\text{nucl}}} \, E_\alpha({R}_{i\alpha}) \, E_\alpha({R}_{j\alpha}), \]
where ww$u$ is an electron-electron function
\[ u\left(\mu, r\right) = \frac{r}{2} \, \left[ 1 - \text{erf}(\mu\, r) \right] - \frac{1}{2 \, \mu \, \sqrt{\pi}} \exp \left[ -(\mu \, r)^2 \right]. \]
This electron-electron term is tuned by the parameter $\mu$ which controls the depth and the range of the Coulomb hole between electrons.
An envelope function has been introduced to cancel out the Jastrow effects between two-electrons when at least one is close to a nucleus (to perform a frozen-core calculation). The envelope function is given by
\[ E_\alpha(R) = 1 - \exp\left( - \gamma_{\alpha} \, R^2 \right). \]
In particular, if the parameters $\gamma_\alpha$ tend to zero, the Mu-Jastrow factor becomes a two-body Jastrow factor:
\[ J_{\text{ee}}(\mathbf{r}) = \sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right) \]
and for large $\gamma_\alpha$ it becomes zero.
To increase the flexibility of the Jastrow and improve the electron density the following electron-nucleus term is added
\[ J_{\text{eN}}(\mathbf{r},\mathbf{R}) = \sum_{i=1}^{N_\text{elec}} \sum_{\alpha=1}^{N_\text{nucl}} \, \left[ \exp\left( a_{\alpha} R_{i \alpha}^2 \right) - 1\right]. \]
The parameter $\mu$ is stored in the ee array, the parameters
$\gamma_\alpha$ are stored in the een array, and the parameters
$a_\alpha$ are stored in the en array.
Table of values
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
type |
str |
Type of Jastrow factor: CHAMP or Mu |
||
en_num |
dim |
Number of Electron-nucleus parameters | ||
ee_num |
dim |
Number of Electron-electron parameters | ||
een_num |
dim |
Number of Electron-electron-nucleus parameters | ||
en |
float |
[jastrow.en_num] |
(jastrow.en_num) |
Electron-nucleus parameters |
ee |
float |
[jastrow.ee_num] |
(jastrow.ee_num) |
Electron-electron parameters |
een |
float |
[jastrow.een_num] |
(jastrow.een_num) |
Electron-electron-nucleus parameters |
en_nucleus |
index |
[jastrow.en_num] |
(jastrow.en_num) |
Nucleus relative to the eN parameter |
een_nucleus |
index |
[jastrow.een_num] |
(jastrow.een_num) |
Nucleus relative to the eeN parameter |
ee_scaling |
float |
$\kappa$ value in CHAMP Jastrow for electron-electron distances | ||
en_scaling |
float |
[nucleus.num] |
(nucleus.num) |
$\kappa$ value in CHAMP Jastrow for electron-nucleus distances |
"jastrow": {
"type" : [ "str" , [] ]
, "en_num" : [ "dim" , [] ]
, "ee_num" : [ "dim" , [] ]
, "een_num" : [ "dim" , [] ]
, "en" : [ "float", [ "jastrow.en_num" ] ]
, "ee" : [ "float", [ "jastrow.ee_num" ] ]
, "een" : [ "float", [ "jastrow.een_num" ] ]
, "en_nucleus" : [ "index", [ "jastrow.en_num" ] ]
, "een_nucleus" : [ "index", [ "jastrow.een_num" ] ]
, "ee_scaling" : [ "float", [] ]
, "en_scaling" : [ "float", [ "nucleus.num" ] ]
} ,Quantum Monte Carlo data (qmc group)
In quantum Monte Carlo calculations, the wave function is evaluated at points of the 3N-dimensional space. Some algorithms require multiple independent walkers, so it is possible to store multiple coordinates, as well as some quantities evaluated at those points.
By convention, the electron coordinates contain first all the electrons of $\uparrow$-spin and then all the $\downarrow$-spin.
| Variable | Type | Row-major Dimensions | Column-major Dimensions | Description |
|---|---|---|---|---|
num |
dim |
Number of 3N-dimensional points | ||
point |
float |
[qmc.num, electron.num, 3] |
(3, electron.num, qmc.num) |
3N-dimensional points |
psi |
float |
[qmc.num] |
(qmc.num) |
Wave function evaluated at the points |
e_loc |
float |
[qmc.num] |
(qmc.num) |
Local energy evaluated at the points |
"qmc": {
"num" : [ "dim" , [] ]
, "point" : [ "float", [ "qmc.num", "electron.num", "3" ] ]
, "psi" : [ "float", [ "qmc.num" ] ]
, "e_loc" : [ "float", [ "qmc.num" ] ]
}