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Initial support for numerical atom-centered orbitals

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joguenzl 2023-03-31 13:01:51 +02:00
parent 1adaec0da0
commit fb97b44a5f
3 changed files with 461 additions and 29 deletions
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8
src/pytrexio.i
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@ -108,6 +108,14 @@ import_array();
/* For some reasons SWIG does not apply the proper bitfield_t typemap, so one has to manually specify int64_t* ARGOUT_ARRAY1 below */
%apply (int64_t* ARGOUT_ARRAY1, int32_t DIM1) {(bitfield_t* const bit_list, const int32_t N_int)};
/* NAO functions */
%apply double *OUTPUT { double* const log_r_out, double* const amplitude};
%apply (double *ARGOUT_ARRAY1, int DIM1) {(double* const amplitudes, int amplitude_cnt)};
%apply (double* IN_ARRAY1, int DIM1) {(double* grid_r, int n_grid_r),
(double* interpolator, int n_interp), (double* nucleus_coords, int n_nuc_co), (double* normalization, int n_norm)};
%apply (int64_t* IN_ARRAY1, int DIM1) {(int64_t* grid_start, int n_grid_st),
(int64_t* grid_size, int n_grid_si), (int64_t* nucleus_index, int n_nuc_id)};
/* This tells SWIG to treat char ** dset_in pattern as a special case
Enables access to trexio_[...]_write_dset_str set of functions directly, i.e.
by converting input list of strings from Python into char ** of C

369
src/templates_front/templator_front.org
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@ -42,6 +42,8 @@ typedef int32_t trexio_exit_code;
#include "config.h"
#endif
#define _USE_MATH_DEFINES
#include <math.h>
#include <pthread.h>
#include <assert.h>
#include <stdlib.h>
@ -5585,6 +5587,12 @@ def has_determinant_list(trexio_file) -> bool:
bitfield representation of the determinant. If the creation of the bitfield requires a change of sign, the return code is
~TREXIO_PHASE_CHANGE~.
~trexio_convert_nao_radius~ functions convert a radius from the center of an NAO to its logarithmic interpolation grid.
~trexio_evaluate_nao_radial~ function evaluates the radial function of an NAO for a given distance from the center.
~trexio_evaluate_nao_radial_all~ evaluates all radial functions at a given position in space.
** C
#+begin_src c :tangle prefix_front.h
@ -5603,6 +5611,35 @@ trexio_exit_code trexio_to_orbital_list_up_dn (const int32_t N_int, const bitfie
trexio_exit_code trexio_safe_to_orbital_list (const int32_t N_int, const bitfield_t* dset_in, const int64_t dim_in, int32_t* const dset_out, const int64_t dim_out, int32_t* const num);
trexio_exit_code trexio_safe_to_orbital_list_up_dn (const int32_t N_int, const bitfield_t* dset_in, const int64_t dim_in, int32_t* const dset_up_out, const int64_t dim_up_out, int32_t* const dset_dn_out, const int64_t dim_dn_out, int32_t* const num_up, int32_t* const num_dn);
trexio_exit_code trexio_to_bitfield_list (const int32_t* orb_list, const int32_t occupied_num, bitfield_t* const bit_list, const int32_t N_int);
trexio_exit_code trexio_convert_nao_radius_32 (const float r,
const float* const grid_r, float* const log_r_out);
trexio_exit_code trexio_convert_nao_radius_64 (const double r,
const double* const grid_r, double* const log_r_out);
trexio_exit_code trexio_convert_nao_radius_py (const double r,
double* grid_r, int32_t n_grid_r, double* const log_r_out);
trexio_exit_code trexio_evaluate_nao_radial (const int32_t shell_index,
const double r, const int32_t* const grid_start, const int32_t* const grid_size,
const double* const grid_r, const double* const interpolator,
const double* const normalization, double* const amplitude);
trexio_exit_code trexio_evaluate_nao_radial_all (const int32_t shell_num,
const int32_t* const nucleus_index, const double* const nucleus_coords,
const int32_t* const grid_start, const int32_t* const grid_size,
const double* const grid_r, const double* const interpolator, const double* const normalization,
const double rx, const double ry, const double rz, double* const amplitude);
trexio_exit_code trexio_evaluate_nao_radial_py (const int shell_index,
const double r, int64_t* grid_start, int n_grid_st, int64_t* grid_size,
int n_grid_si, double* grid_r, int n_grid_r, double* interpolator,
int n_interp, double* normalization, int n_norm, double* const amplitude);
trexio_exit_code trexio_evaluate_nao_radial_all_py (const int32_t shell_num,
int64_t* nucleus_index, int n_nuc_id, double* nucleus_coords, int n_nuc_co,
int64_t* grid_start, int n_grid_st, int64_t* grid_size, int n_grid_si,
double* grid_r, int n_grid_r, double* interpolator, int n_interp, double* normalization, int n_norm,
const double rx, const double ry, const double rz, double* const amplitudes, int amplitude_cnt);
#+end_src
@ -5740,7 +5777,174 @@ trexio_safe_to_orbital_list_up_dn (const int32_t N_int,
}
#+end_src
#+begin_src c :tangle trexio_private.h
#+begin_src c :tangle prefix_front.c
trexio_exit_code
trexio_convert_nao_radius_32 (const float r, const float* const grid_r, float* const log_r_out)
{
if (r < 0) return TREXIO_INVALID_ARG_1;
if (grid_r == NULL) return TREXIO_INVALID_ARG_2;
*log_r_out = log(r / grid_r[0]) / log(grid_r[1] / grid_r[0]);
return TREXIO_SUCCESS;
}
trexio_exit_code
trexio_convert_nao_radius_64 (const double r, const double* const grid_r, double* const log_r_out)
{
if (r < 0) return TREXIO_INVALID_ARG_1;
if (grid_r == NULL) return TREXIO_INVALID_ARG_2;
*log_r_out = log(r / grid_r[0]) / log(grid_r[1] / grid_r[0]);
return TREXIO_SUCCESS;
}
trexio_exit_code
trexio_convert_nao_radius_py (const double r, double* grid_r, int32_t n_grid, double* const log_r_out)
{
if (r < 0) return TREXIO_INVALID_ARG_1;
if (grid_r == NULL) return TREXIO_INVALID_ARG_2;
*log_r_out = log(r / grid_r[0]) / log(grid_r[1] / grid_r[0]);
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle prefix_front.c
trexio_exit_code
trexio_evaluate_nao_radial (const int32_t shell_index, const double r, const int32_t* const grid_start,
const int32_t* const grid_size, const double* const grid_r, const double* const interpolator, const double* const normalization, double* const amplitude)
{
if (shell_index < 0) return TREXIO_INVALID_ARG_1;
if (r < 0) return TREXIO_INVALID_ARG_2;
if (grid_start == 0) return TREXIO_INVALID_ARG_3;
if (grid_size == 0) return TREXIO_INVALID_ARG_4;
if (grid_r == NULL) return TREXIO_INVALID_ARG_5;
if (interpolator == 0) return TREXIO_INVALID_ARG_6;
if (normalization == 0) return TREXIO_INVALID_ARG_7;
const int32_t i0 = 4*grid_start[shell_index];
// Convert radius to logarithmic units
double r_log = 0;
trexio_convert_nao_radius_64 (r, grid_r + grid_start[shell_index], &r_log);
int32_t i_log = (int32_t) r_log;
if (i_log < 0)
i_log = 0;
else if (i_log >= grid_size[shell_index])
return 0; // NAOs vanish at the boundary by definition
double t = r_log - (double) i_log;
double val_spline = interpolator[i0 + 4*i_log + 0];
val_spline += t * interpolator[i0 + 4*i_log + 1];
val_spline += t * t * interpolator[i0 + 4*i_log + 2];
val_spline += t * t * t * interpolator[i0 + 4*i_log + 3];
*amplitude = val_spline * normalization[shell_index] / r;
return TREXIO_SUCCESS;
}
trexio_exit_code
trexio_evaluate_nao_radial_all (const int32_t shell_num, const int32_t* const nucleus_index, const double* const nucleus_coords, const int32_t* const grid_start,
const int32_t* const grid_size, const double* const grid_r, const double* const interpolator,
const double* const normalization, const double rx, const double ry, const double rz, double* const amplitude)
{
if (shell_num < 0) return TREXIO_INVALID_ARG_1;
if (nucleus_index == 0) return TREXIO_INVALID_ARG_2;
if (nucleus_coords == 0) return TREXIO_INVALID_ARG_3;
if (grid_start == 0) return TREXIO_INVALID_ARG_4;
if (grid_size == 0) return TREXIO_INVALID_ARG_5;
if (grid_r == NULL) return TREXIO_INVALID_ARG_6;
if (interpolator == 0) return TREXIO_INVALID_ARG_7;
if (normalization == 0) return TREXIO_INVALID_ARG_8;
for (int shell_index = 0; shell_index < shell_num; shell_index++) {
const int32_t nuc_index = nucleus_index[shell_index];
const double dx = nucleus_coords[3*nuc_index + 0] - rx;
const double dy = nucleus_coords[3*nuc_index + 1] - ry;
const double dz = nucleus_coords[3*nuc_index + 2] - rz;
const double r = sqrt(dx*dx + dy*dy + dz*dz);
// All possibly reported errors have been caught above
trexio_evaluate_nao_radial(shell_index, r, grid_start,
grid_size, grid_r, interpolator, normalization, &amplitude[shell_index]);
}
return TREXIO_SUCCESS;
}
trexio_exit_code trexio_evaluate_nao_radial_py (const int shell_index,
const double r, int64_t* grid_start, int n_grid_st,
int64_t* grid_size, int n_grid_si, double* grid_r, int n_grid_r,
double* interpolator, int n_interp, double* normalization, int n_norm, double* const amplitude)
{
// Code needs to be copied because of the use of int64_t mandated by Python
// If a 64-bit version is implemented, this can be avoided
if (shell_index < 0) return TREXIO_INVALID_ARG_1;
if (r < 0) return TREXIO_INVALID_ARG_2;
if (grid_start == 0) return TREXIO_INVALID_ARG_3;
if (grid_size == 0) return TREXIO_INVALID_ARG_4;
if (grid_r == NULL) return TREXIO_INVALID_ARG_5;
if (interpolator == 0) return TREXIO_INVALID_ARG_6;
if (normalization == 0) return TREXIO_INVALID_ARG_7;
const int32_t i0 = 4*grid_start[shell_index];
// Convert radius to logarithmic units
double r_log = 0;
trexio_convert_nao_radius_64 (r, grid_r + grid_start[shell_index], &r_log);
int32_t i_log = (int32_t) r_log;
if (i_log < 0)
i_log = 0;
else if (i_log >= grid_size[shell_index])
return 0; // NAOs vanish at the boundary by definition
double t = r_log - (double) i_log;
double val_spline = interpolator[i0 + 4*i_log + 0];
val_spline += t * interpolator[i0 + 4*i_log + 1];
val_spline += t * t * interpolator[i0 + 4*i_log + 2];
val_spline += t * t * t * interpolator[i0 + 4*i_log + 3];
*amplitude = val_spline * normalization[shell_index] / r;
return TREXIO_SUCCESS;
}
trexio_exit_code trexio_evaluate_nao_radial_all_py (const int32_t shell_num,
int64_t* nucleus_index, int n_nuc_id, double* nucleus_coords, int n_nuc_co,
int64_t* grid_start, int n_grid_st, int64_t* grid_size, int n_grid_si,
double* grid_r, int n_grid_r, double* interpolator, int n_interp,
double* normalization, int n_norm,
const double rx, const double ry, const double rz, double* const amplitudes, int amplitude_cnt)
{
if (shell_num < 0) return TREXIO_INVALID_ARG_1;
if (nucleus_index == 0) return TREXIO_INVALID_ARG_2;
if (nucleus_coords == 0) return TREXIO_INVALID_ARG_3;
if (grid_start == 0) return TREXIO_INVALID_ARG_4;
if (grid_size == 0) return TREXIO_INVALID_ARG_5;
if (grid_r == NULL) return TREXIO_INVALID_ARG_6;
if (interpolator == 0) return TREXIO_INVALID_ARG_7;
if (normalization == 0) return TREXIO_INVALID_ARG_8;
for (int shell_index = 0; shell_index < shell_num; shell_index++) {
const int32_t nuc_index = nucleus_index[shell_index];
const double dx = nucleus_coords[3*nuc_index + 0] - rx;
const double dy = nucleus_coords[3*nuc_index + 1] - ry;
const double dz = nucleus_coords[3*nuc_index + 2] - rz;
const double r = sqrt(dx*dx + dy*dy + dz*dz);
// All possibly reported errors have been caught above
trexio_evaluate_nao_radial_py(shell_index, r, grid_start, n_grid_st,
grid_size, n_grid_si, grid_r, n_grid_r, interpolator, n_interp, normalization, n_norm, &amplitudes[shell_index]);
}
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle trexio_private.h
/* Popcount and trailz */
#if TREXIO_INT_SIZE == 64
@ -5867,6 +6071,76 @@ interface
end interface
#+end_src
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer(trexio_exit_code) function trexio_convert_nao_radius_32(r, grid_r, log_r_out) &
bind(C, name="trexio_convert_nao_radius_32")
use, intrinsic :: iso_c_binding
import
real(c_float), intent(in), value :: r
real(c_float), intent(in) :: grid_r(*)
real(c_float), intent(out) :: log_r_out
end function trexio_convert_nao_radius_32
end interface
#+end_src
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer(trexio_exit_code) function trexio_convert_nao_radius_64(r, grid_r, log_r_out) &
bind(C, name="trexio_convert_nao_radius_64")
use, intrinsic :: iso_c_binding
import
real(c_double), intent(in), value :: r
real(c_double), intent(in) :: grid_r(*)
real(c_double), intent(out) :: log_r_out
end function trexio_convert_nao_radius_64
end interface
#+end_src
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer(trexio_exit_code) function trexio_evaluate_nao_radial (shell_index, r, &
grid_start, grid_size, grid_r, interpolator, normalization, amplitude) &
bind(C, name="trexio_evaluate_nao_radial")
use, intrinsic :: iso_c_binding
import
integer(c_int32_t), intent(in), value :: shell_index
real(c_double), intent(in), value :: r
integer(c_int32_t), intent(in) :: grid_start(*)
integer(c_int32_t), intent(in) :: grid_size(*)
real(c_double), intent(in) :: grid_r(*)
real(c_double), intent(in) :: interpolator(*)
real(c_double), intent(in) :: normalization(*)
real(c_double), intent(out) :: amplitude
end function trexio_evaluate_nao_radial
end interface
#+end_src
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer(trexio_exit_code) function trexio_evaluate_nao_radial_all (shell_num, &
nucleus_index, nucleus_coords, &
grid_start, grid_size, grid_r, interpolator, &
normalization, rx, ry, rz, amplitudes) &
bind(C, name="trexio_evaluate_nao_radial_all")
use, intrinsic :: iso_c_binding
import
integer(c_int32_t), intent(in), value :: shell_num
integer(c_int32_t), intent(in) :: nucleus_index(*)
real(c_double), intent(in) :: nucleus_coords(*)
integer(c_int32_t), intent(in) :: grid_start(*)
integer(c_int32_t), intent(in) :: grid_size(*)
real(c_double), intent(in) :: grid_r(*)
real(c_double), intent(in) :: interpolator(*)
real(c_double), intent(in) :: normalization(*)
real(c_double), intent(in), value :: rx
real(c_double), intent(in), value :: ry
real(c_double), intent(in), value :: rz
real(c_double), intent(out) :: amplitudes(*)
end function trexio_evaluate_nao_radial_all
end interface
#+end_src
** Python
#+begin_src python :tangle basic_python.py
@ -5967,6 +6241,99 @@ def to_orbital_list_up_dn(n_int: int, determinant: list) -> tuple:
return (orbital_list_up[0:occ_num_up], orbital_list_dn[0:occ_num_dn])
#+end_src
#+begin_src python :tangle basic_python.py
def convert_nao_radius(r: float, grid_r) -> float:
"""Converts the radius r as a distance from a nucleus to the shell
s logarithmic grid.
Input:
~r~ - the radius to be converted
~grid_r~ - The radial grid of the shell. Note that this is only the
grid of the shell of interest, not the array of all shells.
Returns:
Float that gives the radius in the shell's logarithmic units
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc, r_log = pytr.trexio_convert_nao_radius_py(r, grid_r)
if rc != TREXIO_SUCCESS:
raise Exception(rc)
return r_log
def evaluate_nao_radial(shell_index, r, grid_start, grid_size, grid_r, interpolator, normalization) -> float:
"""Evaluates the radial function of a given NAO shell at a distance from its center.
Input:
~shell_index~ - index of the shell of interest
~r~ - distance from the shell center
~grid_start~ - array of starting points of the individual splines
~grid_size~ - array of number of data points per spline
~grid_r~ - The radial grid of the shell. Note that this is only the
grid of the shell of interest, not the array of all shells.
~interpolator~ - Interpolator of the spline. It is assumed to contain a cubic spline.
An interpolator for a kinetic energy spline can also be passed.
~normalization~ - array of radial function normalization constants.
Returns:
Value of the spline at the given radius
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc, amplitude = pytr.trexio_evaluate_nao_radial_py(shell_index, r, grid_start, grid_size, grid_r, interpolator.flatten(), normalization)
if rc != TREXIO_SUCCESS:
raise Error(rc)
return amplitude
def evaluate_nao_radial_all(nucleus_index, nucleus_coords, grid_start,
grid_size, grid_r, interpolator, normalization, r) -> float:
"""Evaluates the radial functions of all NAO shells at a given position in space.
Input:
~nucleus_index~ - array giving the centers of the NAO
~nucleus_coords~ - array giving the coordinates of the NAO centers
~grid_start~ - array of starting points of the individual splines
~grid_size~ - array of number of data points per spline
~grid_r~ - The radial grid of the shell. Note that this is only the
grid of the shell of interest, not the array of all shells.
~interpolator~ - Interpolator of the spline. It is assumed to contain a cubic spline.
An interpolator for a kinetic energy spline can also be passed.
~normalization~ - array of radial function normalization constants.
~r~ - the position in space at which the functions are evaluated
Returns:
Array of spline values at ~r~
Raises:
- Exception if ~r~ is not three dimensional
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
if len(r) != 3:
raise Error(TREXIO_INVALID_ARG7)
shell_cnt = len(nucleus_index)
rc, amplitudes = pytr.trexio_evaluate_nao_radial_all_py(shell_cnt, \
nucleus_index, nucleus_coords.flatten(), grid_start, grid_size, grid_r, \
interpolator.flatten(), normalization, r[0], r[1], r[2], shell_cnt)
if rc != TREXIO_SUCCESS:
raise Exception(rc)
return amplitudes
#+end_src
* Fortran helper/wrapper functions
The function below adapts the original C-based ~trexio_open~ for Fortran.

113
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@ -254,6 +254,44 @@
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 [Reference to paper]. 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 ~numgrid_r~
and ~numgrid_phi~. Additionaly, a separate spline for the kinetic energy
can be stored in ~numgrid_kin~. The index of the first data point for
each shell is stored in ~numgrid_start~.
FHI-aims uses cubic interpolation between the reference points.
The interpolation coefficients are given in the ~interpolator~ array.
The number of coefficients per interpolation point is stored as
~interp_coeff_cnt~ so that other interpolation functions can be
implemented if needed. The ~interpolator_kin~ array provides a spline for
the kinetic energy.
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)
\[
i_{log} = \frac{1}{c} \cdot \log{\frac{r}{r_0}}
\]
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
@ -270,20 +308,30 @@
*** Data definitions
#+NAME: basis
| Variable | Type | Dimensions | Description |
|-----------------+---------+---------------------+-----------------------------------------------------------------|
| ~type~ | ~str~ | | Type of basis set: "Gaussian", "Slater" or "PW" for plane waves |
| ~prim_num~ | ~dim~ | | Total number of primitives |
| ~shell_num~ | ~dim~ | | Total number of shells |
| ~nucleus_index~ | ~index~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and atomic indices |
| ~shell_ang_mom~ | ~int~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and angular momenta |
| ~shell_factor~ | ~float~ | ~(basis.shell_num)~ | Normalization factor of each shell ($\mathcal{N}_s$) |
| ~r_power~ | ~int~ | ~(basis.shell_num)~ | Power to which $r$ is raised ($n_s$) |
| ~shell_index~ | ~index~ | ~(basis.prim_num)~ | One-to-one correspondence between primitives and shell index |
| ~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 ($f_{ks}$) |
| ~e_cut~ | ~float~ | | Energy cut-off for plane-wave calculations |
| Variable | Type | 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 | |
| ~numgrid_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)~ | One-to-one correspondence between shells and atomic indices | |
| ~shell_ang_mom~ | ~int~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and angular momenta | |
| ~shell_factor~ | ~float~ | ~(basis.shell_num)~ | Normalization factor of each shell ($\mathcal{N}_s$) | |
| ~r_power~ | ~int~ | ~(basis.shell_num)~ | Power to which $r$ is raised ($n_s$) | |
| ~numgrid_start~ | ~index~ | ~(basis.shell_num)~ | Index of the first data point for a given numerical orbital | |
| ~numgrid_size~ | ~dim~ | ~(basis.shell_num)~ | Number of data points per numerical orbital | |
| ~shell_index~ | ~index~ | ~(basis.prim_num)~ | One-to-one correspondence between primitives and shell index | |
| ~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 ($f_{ks}$) | |
| ~e_cut~ | ~float~ | | Energy cut-off for plane-wave calculations | |
| ~numgrid_radius~ | ~float~ | ~(basis.numgrid_num)~ | Radii of grid points for numerical orbitals | |
| ~numgrid_phi~ | ~float~ | ~(basis.numgrid_num)~ | Wave function values for numerical orbitals | |
| ~numgrid_kin~ | ~float~ | ~(basis.numgrid_num)~ | Kinetic energy of numerical orbitals | |
| ~interpolator~ | ~float~ | ~(basis.interp_coeff_cnt,basis.numgrid_num)~ | Coefficients for numerical orbital interpolation function | |
| ~interpolator_kin~ | ~float~ | ~(basis.interp_coeff_cnt,basis.numgrid_num)~ | Coefficients for numerical orbital kinetic energy interpolation function | |
#+CALL: json(data=basis, title="basis")
@ -291,20 +339,29 @@
#+RESULTS:
:results:
#+begin_src python :tangle trex.json
"basis": {
"type" : [ "str" , [] ]
, "prim_num" : [ "dim" , [] ]
, "shell_num" : [ "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" ] ]
, "shell_index" : [ "index", [ "basis.prim_num" ] ]
, "exponent" : [ "float", [ "basis.prim_num" ] ]
, "coefficient" : [ "float", [ "basis.prim_num" ] ]
, "prim_factor" : [ "float", [ "basis.prim_num" ] ]
, "e_cut" : [ "float", [] ]
} ,
"basis": {
"type" : [ "str" , [] ]
, "prim_num" : [ "dim" , [] ]
, "shell_num" : [ "dim" , [] ]
, "numgrid_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" ] ]
, "numgrid_start" : [ "index", [ "basis.shell_num" ] ]
, "numgrid_size" : [ "dim" , [ "basis.shell_num" ] ]
, "shell_index" : [ "index", [ "basis.prim_num" ] ]
, "exponent" : [ "float", [ "basis.prim_num" ] ]
, "coefficient" : [ "float", [ "basis.prim_num" ] ]
, "prim_factor" : [ "float", [ "basis.prim_num" ] ]
, "e_cut" : [ "float", [] ]
, "numgrid_radius" : [ "float", [ "basis.numgrid_num" ] ]
, "numgrid_phi" : [ "float", [ "basis.numgrid_num" ] ]
, "numgrid_kin" : [ "float", [ "basis.numgrid_num" ] ]
, "interpolator" : [ "float", [ "basis.numgrid_num", "basis.interp_coeff_cnt" ] ]
, "interpolator_kin" : [ "float", [ "basis.numgrid_num", "basis.interp_coeff_cnt" ] ]
} ,
#+end_src
:end: