quantum_package/plugins/Psiref_Utils/README.rst

===================
Psiref_utils Module
===================


Utilities related to the use of a reference wave function. This module
needs to be loaded with any psi_ref module.


Documentation
=============

.. Do not edit this section. It was auto-generated from the
.. by the `update_README.py` script.

`get_index_in_psi_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L182>`_
  Returns the index of the determinant in the ``psi_ref_sorted_bit`` array


`h_matrix_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L116>`_
  Undocumented


`holes_operators <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_excitations_operators.irp.f#L3>`_
  holes_operators represents an array of integers where all the holes have
  been done going from psi_ref to psi_non_ref
  particles_operators represents an array of integers where all the particles have
  been done going from psi_ref to psi_non_ref


`idx_non_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L20>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  idx_non_ref_rev gives the reverse.


`idx_non_ref_rev <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L21>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  idx_non_ref_rev gives the reverse.


`is_in_psi_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L168>`_
  True if the determinant ``det`` is in the wave function


`n_det_non_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L22>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  idx_non_ref_rev gives the reverse.


`particles_operators <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_excitations_operators.irp.f#L4>`_
  holes_operators represents an array of integers where all the holes have
  been done going from psi_ref to psi_non_ref
  particles_operators represents an array of integers where all the particles have
  been done going from psi_ref to psi_non_ref


`psi_coef_ref_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L128>`_
  Undocumented


`psi_non_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L18>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  idx_non_ref_rev gives the reverse.


`psi_non_ref_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L19>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  idx_non_ref_rev gives the reverse.


`psi_non_ref_coef_restart <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L62>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  But this is with respect to the restart wave function.


`psi_non_ref_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L104>`_
  Reference determinants sorted to accelerate the search of a random determinant in the wave
  function.


`psi_non_ref_restart <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L61>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  But this is with respect to the restart wave function.


`psi_non_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L103>`_
  Reference determinants sorted to accelerate the search of a random determinant in the wave
  function.


`psi_ref_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L5>`_
  Reference determinants sorted to accelerate the search of a random determinant in the wave
  function.


`psi_ref_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L147>`_
  Undocumented


`psi_ref_energy_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L129>`_
  Undocumented


`psi_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Psiref_Utils/psi_ref_utils.irp.f#L4>`_
  Reference determinants sorted to accelerate the search of a random determinant in the wave
  function.

Needed Modules
==============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.


.. image:: tree_dependency.png

* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_

Documentation
=============
.. Do not edit this section It was auto-generated
.. by the `update_README.py` script.


`a_coef <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L252>`_
  Undocumented


`add_poly <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L306>`_
  Add two polynomials
  D(t) =! D(t) +( B(t)+C(t))


`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L334>`_
  Add a polynomial multiplied by a constant
  D(t) =! D(t) +( cst * B(t))


`align_double <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L48>`_
  Compute 1st dimension such that it is aligned for vectorization.


`apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L320>`_
  Apply the rotation found by find_rotation


`approx_dble <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L371>`_
  Undocumented


`b_coef <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L257>`_
  Undocumented


`binom <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L31>`_
  Binomial coefficients


`binom_func <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L1>`_
  .. math                       ::
  .br
  \frac{i!}{j!(i-j)!}
  .br


`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L32>`_
  Binomial coefficients


`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L136>`_
  Undocumented


`dble_fact_even <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L153>`_
  n!!


`dble_fact_odd <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L197>`_
  n!!


`dble_logfact <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L231>`_
  n!!


`ddfact2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L243>`_
  Undocumented


`dset_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_216#L27>`_
  array A has already been sorted, and iorder has contains the new order of
  elements of A. This subroutine changes the order of x to match the new order of A.


`dset_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L94>`_
  array A has already been sorted, and iorder has contains the new order of
  elements of A. This subroutine changes the order of x to match the new order of A.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`dsort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L339>`_
  Sort array x(isize).
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`dtranspose <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/transpose.irp.f#L41>`_
  Transpose input matrix A into output matrix B


`erf0 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L105>`_
  Undocumented


`extract_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/extract_ref.irp.f#L1>`_
  Replaces the total wave function by the normalized projection on the reference


`f_integral <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L408>`_
  function that calculates the following integral
  \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx


`fact <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L63>`_
  n!


`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L123>`_
  1/n!


`find_rotation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L301>`_
  Find A.C = B


`gammln <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L271>`_
  Undocumented


`gammp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L133>`_
  Undocumented


`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L184>`_
  Gaussian product in 1D.
  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}


`gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L226>`_
  Gaussian product in 1D.
  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}


`gcf <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L211>`_
  Undocumented


`get_index_in_psi_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L225>`_
  Returns the index of the determinant in the ``psi_ref_sorted_bit`` array


`get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L247>`_
  Find C = A^-1


`give_explicit_poly_and_gaussian <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L46>`_
  Transforms the product of
  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
  into
  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )


`give_explicit_poly_and_gaussian_double <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L122>`_
  Transforms the product of
  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3)
  exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) exp(-(r-Nucl_center)^2 gama
  .br
  into
  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )


`give_explicit_poly_and_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L1>`_
  Transform the product of
  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
  into
  fact_k  (x-x_P)^iorder(1)  (y-y_P)^iorder(2)  (z-z_P)^iorder(3) exp(-p(r-P)^2)


`gser <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L167>`_
  Undocumented


`h_matrix_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L157>`_
  Undocumented


`heap_dsort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L210>`_
  Sort array x(isize) using the heap sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`heap_dsort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L273>`_
  Sort array x(isize) using the heap sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`heap_i2sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L744>`_
  Sort array x(isize) using the heap sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`heap_i2sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L807>`_
  Sort array x(isize) using the heap sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`heap_i8sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L566>`_
  Sort array x(isize) using the heap sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`heap_i8sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L629>`_
  Sort array x(isize) using the heap sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`heap_isort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L388>`_
  Sort array x(isize) using the heap sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`heap_isort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L451>`_
  Sort array x(isize) using the heap sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`heap_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L32>`_
  Sort array x(isize) using the heap sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`heap_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L95>`_
  Sort array x(isize) using the heap sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`hermite <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L540>`_
  Hermite polynomial


`holes_operators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_excitations_operators.irp.f#L3>`_
  holes_operators represents an array of integers where all the holes have
  been done going from psi_ref to psi_non_ref
  particles_operators represents an array of integers where all the particles have
  been done going from psi_ref to psi_non_ref


`i2radix_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_452#L327>`_
  Sort integer array x(isize) using the radix sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  iradix should be -1 in input.


`i2set_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_216#L102>`_
  array A has already been sorted, and iorder has contains the new order of
  elements of A. This subroutine changes the order of x to match the new order of A.


`i2set_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L271>`_
  array A has already been sorted, and iorder has contains the new order of
  elements of A. This subroutine changes the order of x to match the new order of A.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`i2sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L873>`_
  Sort array x(isize).
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`i8radix_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_452#L165>`_
  Sort integer array x(isize) using the radix sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  iradix should be -1 in input.


`i8radix_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_452#L651>`_
  Sort integer array x(isize) using the radix sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  iradix should be -1 in input.


`i8set_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_216#L77>`_
  array A has already been sorted, and iorder has contains the new order of
  elements of A. This subroutine changes the order of x to match the new order of A.


`i8set_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L212>`_
  array A has already been sorted, and iorder has contains the new order of
  elements of A. This subroutine changes the order of x to match the new order of A.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`i8sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L695>`_
  Sort array x(isize).
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`idx_non_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L61>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  idx_non_ref_rev gives the reverse.


`idx_non_ref_rev <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L62>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  idx_non_ref_rev gives the reverse.


`insertion_dsort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L180>`_
  Sort array x(isize) using the insertion sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`insertion_dsort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L61>`_
  Sort array x(isize) using the insertion sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`insertion_i2sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L714>`_
  Sort array x(isize) using the insertion sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`insertion_i2sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L238>`_
  Sort array x(isize) using the insertion sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`insertion_i8sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L536>`_
  Sort array x(isize) using the insertion sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`insertion_i8sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L179>`_
  Sort array x(isize) using the insertion sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`insertion_isort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L358>`_
  Sort array x(isize) using the insertion sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`insertion_isort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L120>`_
  Sort array x(isize) using the insertion sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`insertion_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L2>`_
  Sort array x(isize) using the insertion sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`insertion_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L2>`_
  Sort array x(isize) using the insertion sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`inv_int <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L278>`_
  1/i


`iradix_sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_452#L3>`_
  Sort integer array x(isize) using the radix sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  iradix should be -1 in input.


`iradix_sort_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_452#L489>`_
  Sort integer array x(isize) using the radix sort algorithm.
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.
  iradix should be -1 in input.


`is_in_psi_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L211>`_
  True if the determinant ``det`` is in the wave function


`iset_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_216#L52>`_
  array A has already been sorted, and iorder has contains the new order of
  elements of A. This subroutine changes the order of x to match the new order of A.


`iset_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L153>`_
  array A has already been sorted, and iorder has contains the new order of
  elements of A. This subroutine changes the order of x to match the new order of A.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`isort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L517>`_
  Sort array x(isize).
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L399>`_
  Diagonalize matrix H
  .br
  H is untouched between input and ouptut
  .br
  eigevalues(i) = ith lowest eigenvalue of the H matrix
  .br
  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
  .br


`lapack_diag_s2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L462>`_
  Diagonalize matrix H
  .br
  H is untouched between input and ouptut
  .br
  eigevalues(i) = ith lowest eigenvalue of the H matrix
  .br
  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
  .br


`lapack_diagd <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L332>`_
  Diagonalize matrix H
  .br
  H is untouched between input and ouptut
  .br
  eigevalues(i) = ith lowest eigenvalue of the H matrix
  .br
  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
  .br


`lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L528>`_
  Diagonalize matrix H
  .br
  H is untouched between input and ouptut
  .br
  eigevalues(i) = ith lowest eigenvalue of the H matrix
  .br
  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
  .br


`logfact <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L91>`_
  n!


`lowercase <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L395>`_
  Transform to lower case


`map_load_from_disk <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/map_functions.irp.f#L70>`_
  Undocumented


`map_save_to_disk <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/map_functions.irp.f#L1>`_
  Undocumented


`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L264>`_
  Multiply two polynomials
  D(t) =! D(t) +( B(t)*C(t))


`n_det_non_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L63>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  idx_non_ref_rev gives the reverse.


`normalize <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L348>`_
  Normalizes vector u
  u is expected to be aligned in memory.


`nproc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L304>`_
  Number of current OpenMP threads


`ortho_canonical <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L45>`_
  Compute C_new=C_old.U.s^-1/2 canonical orthogonalization.
  .br
  overlap : overlap matrix
  .br
  LDA : leftmost dimension of overlap array
  .br
  N : Overlap matrix is NxN (array is (LDA,N) )
  .br
  C : Coefficients of the vectors to orthogonalize. On exit,
  orthogonal vectors
  .br
  LDC : leftmost dimension of C
  .br
  m : Coefficients matrix is MxN, ( array is (LDC,N) )
  .br


`ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L162>`_
  Compute C_new=C_old.S^-1/2 orthogonalization.
  .br
  overlap : overlap matrix
  .br
  LDA : leftmost dimension of overlap array
  .br
  N : Overlap matrix is NxN (array is (LDA,N) )
  .br
  C : Coefficients of the vectors to orthogonalize. On exit,
  orthogonal vectors
  .br
  LDC : leftmost dimension of C
  .br
  m : Coefficients matrix is MxN, ( array is (LDC,N) )
  .br


`ortho_qr <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L128>`_
  Orthogonalization using Q.R factorization
  .br
  A : matrix to orthogonalize
  .br
  LDA : leftmost dimension of A
  .br
  n : Number of rows of A
  .br
  m : Number of columns of A
  .br


`overlap_a_b_c <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/one_e_integration.irp.f#L35>`_
  Undocumented


`overlap_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/one_e_integration.irp.f#L1>`_
  .. math::
  .br
  \sum_{-infty}^{+infty} (x-A_x)^ax (x-B_x)^bx exp(-alpha(x-A_x)^2) exp(-beta(x-B_X)^2) dx
  .br


`overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/one_e_integration.irp.f#L113>`_
  .. math::
  .br
  S_x = \int (x-A_x)^{a_x} exp(-\alpha(x-A_x)^2)  (x-B_x)^{b_x} exp(-beta(x-B_x)^2) dx \\
  S = S_x S_y S_z
  .br


`overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/one_e_integration.irp.f#L175>`_
  .. math                      ::
  .br
  \int_{-infty}^{+infty} (x-A_center)^(power_A) * (x-B_center)^power_B * exp(-alpha(x-A_center)^2) * exp(-beta(x-B_center)^2) dx
  .br


`particles_operators <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_excitations_operators.irp.f#L4>`_
  holes_operators represents an array of integers where all the holes have
  been done going from psi_ref to psi_non_ref
  particles_operators represents an array of integers where all the particles have
  been done going from psi_ref to psi_non_ref


`progress_active <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L29>`_
  Current status for displaying progress bars. Global variable.


`progress_bar <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L27>`_
  Current status for displaying progress bars. Global variable.


`progress_timeout <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L28>`_
  Current status for displaying progress bars. Global variable.


`progress_title <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L31>`_
  Current status for displaying progress bars. Global variable.


`progress_value <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L30>`_
  Current status for displaying progress bars. Global variable.


`psi_non_ref <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L59>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  idx_non_ref_rev gives the reverse.


`psi_non_ref_coef <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L60>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  idx_non_ref_rev gives the reverse.


`psi_non_ref_coef_restart <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L103>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  But this is with respect to the restart wave function.


`psi_non_ref_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L145>`_
  Reference determinants sorted to accelerate the search of a random determinant in the wave
  function.


`psi_non_ref_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L46>`_
  Transposed psi_non_ref_coef


`psi_non_ref_restart <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L102>`_
  Set of determinants which are not part of the reference, defined from the application
  of the reference bitmask on the determinants.
  idx_non_ref gives the indice of the determinant in psi_det.
  But this is with respect to the restart wave function.


`psi_non_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L144>`_
  Reference determinants sorted to accelerate the search of a random determinant in the wave
  function.


`psi_ref_coef_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L169>`_
  Undocumented


`psi_ref_coef_normalized <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L30>`_
  Normalized coefficients of the reference


`psi_ref_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L5>`_
  Reference determinants sorted to accelerate the search of a random determinant in the wave
  function.


`psi_ref_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L17>`_
  Transposed psi_ref_coef


`psi_ref_energy <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L190>`_
  Undocumented


`psi_ref_energy_diagonalized <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L170>`_
  Undocumented


`psi_ref_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L4>`_
  Reference determinants sorted to accelerate the search of a random determinant in the wave
  function.


`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L363>`_
  Recenter two polynomials


`ref_hamiltonian_matrix <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/psi_ref_utils.irp.f#L310>`_
  H matrix in the Reference space


`rint <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L436>`_
  .. math::
  .br
  \int_0^1 dx \exp(-p x^2) x^n
  .br


`rint1 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L596>`_
  Standard version of rint


`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L565>`_
  Version of rint for large values of n


`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/integration.irp.f#L484>`_
  Needed for the calculation of two-electron integrals.


`rinteg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L47>`_
  Undocumented


`rintgauss <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L31>`_
  Undocumented


`run_progress <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L45>`_
  Display a progress bar with documentation of what is happening


`sabpartial <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/need.irp.f#L2>`_
  Undocumented


`set_order <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_216#L2>`_
  array A has already been sorted, and iorder has contains the new order of
  elements of A. This subroutine changes the order of x to match the new order of A.


`set_order_big <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_283#L35>`_
  array A has already been sorted, and iorder has contains the new order of
  elements of A. This subroutine changes the order of x to match the new order of A.
  This is a version for very large arrays where the indices need
  to be in integer*8 format


`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L585>`_
  Undocumented


`sort <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/sort.irp.f_template_184#L161>`_
  Sort array x(isize).
  iorder in input should be (1,2,3,...,isize), and in output
  contains the new order of the elements.


`start_progress <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L1>`_
  Starts the progress bar


`stop_progress <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/progress.irp.f#L19>`_
  Stop the progress bar


`svd <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/LinearAlgebra.irp.f#L1>`_
  Compute A = U.D.Vt
  .br
  LDx : leftmost dimension of x
  .br
  Dimsneion of A is m x n
  .br


`transpose <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/transpose.irp.f#L2>`_
  Transpose input matrix A into output matrix B


`u_dot_u <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L334>`_
  Compute <u|u>


`u_dot_v <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L320>`_
  Compute <u|v>


`wall_time <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L289>`_
  The equivalent of cpu_time, but for the wall time.


`write_git_log <http://github.com/LCPQ/quantum_package/tree/master/plugins/Psiref_Utils/util.irp.f#L264>`_
  Write the last git commit in file iunit.