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Updated documentation

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Anthony Scemama 2014-05-14 00:01:31 +02:00
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commit 3e7c65d858
20 changed files with 505 additions and 376 deletions
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2
scripts/update_README.py
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@ -148,7 +148,7 @@ def update_documentation(data):
# Search for the documentation in the IRPF90_man directory # Search for the documentation in the IRPF90_man directory
for item in tmp : for item in tmp :
item, _, line = item.split('\t') item, _, line = item.strip().split('\t')
doc = extract_doc(item) doc = extract_doc(item)
items.append( (item, filename, doc, line) ) items.append( (item, filename, doc, line) )

3
src/AOs/NEEDED_MODULES
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@ -1 +1,2 @@
Ezfio_files Nuclei Utils Ezfio_files Nuclei Output Utils

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src/AOs/README.rst
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@ -41,6 +41,7 @@ Needed Modules
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_ * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_ * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_ * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
Documentation Documentation
@ -49,55 +50,43 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/&BEGIN_PROVIDER [ double precision, ao_coef, (ao_num_align,ao_prim_num_max) ]/;" `ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L21>`_
>`_ Coefficients, exponents and powers of x,y and z
coefficient of the primitives on the AO basis
ao_coef(i,j) = coefficient of the jth primitive on the ith ao ao_coef(i,j) = coefficient of the jth primitive on the ith ao
`ao_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/BEGIN_PROVIDER [ double precision, ao_coef_transp, (ao_prim_num_max_align,ao_num) ]/;" `ao_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L136>`_
>`_
Transposed ao_coef and ao_expo Transposed ao_coef and ao_expo
`ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/&BEGIN_PROVIDER [ double precision, ao_expo, (ao_num_align,ao_prim_num_max) ]/;" `ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L20>`_
>`_ Coefficients, exponents and powers of x,y and z
coefficient of the primitives on the AO basis
ao_coef(i,j) = coefficient of the jth primitive on the ith ao ao_coef(i,j) = coefficient of the jth primitive on the ith ao
`ao_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/&BEGIN_PROVIDER [ double precision, ao_expo_transp, (ao_prim_num_max_align,ao_num) ]/;" `ao_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L137>`_
>`_
Transposed ao_coef and ao_expo Transposed ao_coef and ao_expo
`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/BEGIN_PROVIDER [ integer, ao_nucl, (ao_num)]/;" `ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L186>`_
>`_
Index of the nuclei on which the ao is centered Index of the nuclei on which the ao is centered
`ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/BEGIN_PROVIDER [ integer, ao_num ]/;" `ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L1>`_
>`_
Number of atomic orbitals Number of atomic orbitals
`ao_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/&BEGIN_PROVIDER [ integer, ao_num_align ]/;" `ao_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L2>`_
>`_
Number of atomic orbitals Number of atomic orbitals
`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/BEGIN_PROVIDER [ double precision, ao_overlap, (ao_num_align,ao_num) ]/;" `ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L96>`_
>`_
matrix of the overlap for tha AOs matrix of the overlap for tha AOs
S(i,j) = overlap between the ith and the jth atomic basis function S(i,j) = overlap between the ith and the jth atomic basis function
`ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/BEGIN_PROVIDER [ integer, ao_power, (ao_num_align,3) ]/;" `ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L19>`_
>`_ Coefficients, exponents and powers of x,y and z
coefficient of the primitives on the AO basis
ao_coef(i,j) = coefficient of the jth primitive on the ith ao ao_coef(i,j) = coefficient of the jth primitive on the ith ao
`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/BEGIN_PROVIDER [ integer, ao_prim_num, (ao_num_align) ]/;" `ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L154>`_
>`_
Number of primitives per atomic orbital Number of primitives per atomic orbital
`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/BEGIN_PROVIDER [ integer, ao_prim_num_max ]/;" `ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L176>`_
>`_
None None
`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L/&BEGIN_PROVIDER [ integer, ao_prim_num_max_align ]/;" `ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L177>`_
>`_
None None

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src/BiInts/README.rst
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@ -32,204 +32,161 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L1 `ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L1>`_
>`_
integral of the AO basis <ik|jl> or (ij|kl) integral of the AO basis <ik|jl> or (ij|kl)
i(r1) j(r1) 1/r12 k(r2) l(r2) i(r1) j(r1) 1/r12 k(r2) l(r2)
`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L331 `ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L326>`_
>`_
Needed to compuet Schwartz inequalities Needed to compuet Schwartz inequalities
`ao_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L192 `ao_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L189>`_
>`_
Map of Atomic integrals Map of Atomic integrals
i(r1) j(r2) 1/r12 k(r1) l(r2) i(r1) j(r2) 1/r12 k(r1) l(r2)
`compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L148 `compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L148>`_
>`_
Compute AO 1/r12 integrals for all i and fixed j,k,l Compute AO 1/r12 integrals for all i and fixed j,k,l
`eri <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L492 `eri <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L487>`_
>`_
ATOMIC PRIMTIVE bielectronic integral between the 4 primitives :: ATOMIC PRIMTIVE bielectronic integral between the 4 primitives ::
primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2) primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2)
primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2) primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2)
primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2) primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2)
primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2) primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2)
`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L357 `general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L352>`_
>`_
Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives
`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L637 `give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L632>`_
>`_
subroutine that returns the explicit polynom in term of the "t" subroutine that returns the explicit polynom in term of the "t"
variable of the following polynomw : variable of the following polynomw :
I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q) I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)
`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L581 `i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L576>`_
>`_
recursive function involved in the bielectronic integral recursive function involved in the bielectronic integral
`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L700 `i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L695>`_
>`_
recursive function involved in the bielectronic integral recursive function involved in the bielectronic integral
`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L820 `i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L815>`_
>`_
recursive function involved in the bielectronic integral recursive function involved in the bielectronic integral
`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L874 `i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L869>`_
>`_
recursive function involved in the bielectronic integral recursive function involved in the bielectronic integral
`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L734 `i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L729>`_
>`_
recursive function involved in the bielectronic integral recursive function involved in the bielectronic integral
`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L604 `i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L599>`_
>`_
recursive function involved in the bielectronic integral recursive function involved in the bielectronic integral
`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L936 `i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L931>`_
>`_
recursive function involved in the bielectronic integral recursive function involved in the bielectronic integral
`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L536 `integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L531>`_
>`_
calculate the integral of the polynom :: calculate the integral of the polynom ::
I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q) I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q)
between ( 0 ; 1) between ( 0 ; 1)
`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L623 `n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L618>`_
>`_
Returns the upper boundary of the degree of the polynom involved in the Returns the upper boundary of the degree of the polynom involved in the
bielctronic integral : bielctronic integral :
Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z) Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z)
`gauleg <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L20 `gauleg <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L20>`_
>`_
Gauss-Legendre Gauss-Legendre
`gauleg_t2 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L1 `gauleg_t2 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L1>`_
>`_
t_w(i,1,k) = w(i) t_w(i,1,k) = w(i)
t_w(i,2,k) = t(i) t_w(i,2,k) = t(i)
`gauleg_w <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L2 `gauleg_w <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L2>`_
>`_
t_w(i,1,k) = w(i) t_w(i,1,k) = w(i)
t_w(i,2,k) = t(i) t_w(i,2,k) = t(i)
`ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L6 `ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L6>`_
>`_
AO integrals AO integrals
`bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L17 `bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L17>`_
>`_
None None
`clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L128 `clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L128>`_
>`_
Frees the memory of the AO map Frees the memory of the AO map
`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L243 `clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L243>`_
>`_
Frees the memory of the MO map Frees the memory of the MO map
`get_ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L33 `get_ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L33>`_
>`_
Gets one AO bi-electronic integral from the AO map Gets one AO bi-electronic integral from the AO map
`get_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L51 `get_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L51>`_
>`_
Gets multiple AO bi-electronic integral from the AO map . Gets multiple AO bi-electronic integral from the AO map .
All i are retrieved for j,k,l fixed. All i are retrieved for j,k,l fixed.
`get_ao_bielec_integrals_non_zero <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L84 `get_ao_bielec_integrals_non_zero <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L84>`_
>`_
Gets multiple AO bi-electronic integral from the AO map . Gets multiple AO bi-electronic integral from the AO map .
All non-zero i are retrieved for j,k,l fixed. All non-zero i are retrieved for j,k,l fixed.
`get_ao_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L120 `get_ao_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L120>`_
>`_
Returns the number of elements in the AO map Returns the number of elements in the AO map
`get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L184 `get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L184>`_
>`_
Returns one integral <ij|kl> in the MO basis Returns one integral <ij|kl> in the MO basis
`get_mo_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L213 `get_mo_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L213>`_
>`_
Returns multiple integrals <ij|kl> in the MO basis, all Returns multiple integrals <ij|kl> in the MO basis, all
i for j,k,l fixed. i for j,k,l fixed.
`get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L235 `get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L235>`_
>`_
Return the number of elements in the MO map Return the number of elements in the MO map
`insert_into_ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L153 `insert_into_ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L153>`_
>`_
Create new entry into AO map Create new entry into AO map
`insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L168 `insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L168>`_
>`_
Create new entry into MO map, or accumulate in an existing entry Create new entry into MO map, or accumulate in an existing entry
`mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L201 `mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L201>`_
>`_
Returns one integral <ij|kl> in the MO basis Returns one integral <ij|kl> in the MO basis
`mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L142 `mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L142>`_
>`_
MO integrals MO integrals
`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L40 `add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L40>`_
>`_
Adds integrals to tha MO map according to some bitmask Adds integrals to tha MO map according to some bitmask
`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L300 `mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L296>`_
>`_
Transform Bi-electronic integrals <ij|ij> and <ij|ji> Transform Bi-electronic integrals <ij|ij> and <ij|ji>
`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L302 `mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L298>`_
>`_
Transform Bi-electronic integrals <ij|ij> and <ij|ji> Transform Bi-electronic integrals <ij|ij> and <ij|ji>
`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L301 `mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L297>`_
>`_
Transform Bi-electronic integrals <ij|ij> and <ij|ji> Transform Bi-electronic integrals <ij|ij> and <ij|ji>
`mo_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L21 `mo_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L21>`_
>`_
If True, the map of MO bielectronic integrals is provided If True, the map of MO bielectronic integrals is provided
`mo_bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L1 `mo_bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L1>`_
>`_
Computes an unique index for i,j,k,l integrals Computes an unique index for i,j,k,l integrals
`ao_integrals_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L73 `ao_integrals_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L73>`_
>`_
If <pq|rs> < ao_integrals_threshold, <pq|rs> = 0 If <pq|rs> < ao_integrals_threshold, <pq|rs> = 0
`mo_integrals_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L92 `do_direct_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L111>`_
>`_ If True, compute integrals on the fly
`mo_integrals_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L92>`_
If <ij|kl> < mo_integrals_threshold, <ij|kl> = 0 If <ij|kl> < mo_integrals_threshold, <ij|kl> = 0
`read_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L55 `read_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L55>`_
>`_
If true, read AO integrals in EZFIO If true, read AO integrals in EZFIO
`read_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L37 `read_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L37>`_
>`_
If true, read MO integrals in EZFIO If true, read MO integrals in EZFIO
`write_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L19 `write_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L19>`_
>`_
If true, write AO integrals in EZFIO If true, write AO integrals in EZFIO
`write_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L1 `write_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/options.irp.f#L1>`_
>`_
If true, write MO integrals in EZFIO If true, write MO integrals in EZFIO

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.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`full_ijkl_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L/BEGIN_PROVIDER [ integer(bit_kind), full_ijkl_bitmask, (N_int,4) ]/;" `full_ijkl_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L12>`_
>`_
Bitmask to include all possible MOs Bitmask to include all possible MOs
`hf_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L/BEGIN_PROVIDER [ integer(bit_kind), HF_bitmask, (N_int,2)]/;" `hf_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L32>`_
>`_
Hartree Fock bit mask Hartree Fock bit mask
`n_int <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L/BEGIN_PROVIDER [ integer, N_int ]/;" `n_int <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L3>`_
>`_
Number of 64-bit integers needed to represent determinants as binary strings Number of 64-bit integers needed to represent determinants as binary strings
`ref_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L/BEGIN_PROVIDER [ integer(bit_kind), ref_bitmask, (N_int,2)]/;" `ref_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L50>`_
>`_
Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask
`bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L/subroutine bitstring_to_hexa( output, string, Nint )/;" `bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L95>`_
>`_
Transform a bit string to a string in hexadecimal format for printing Transform a bit string to a string in hexadecimal format for printing
`bitstring_to_list <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L/subroutine bitstring_to_list( string, list, n_elements, Nint)/;" `bitstring_to_list <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L1>`_
>`_
Gives the inidices(+1) of the bits set to 1 in the bit string Gives the inidices(+1) of the bits set to 1 in the bit string
`bitstring_to_str <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L/subroutine bitstring_to_str( output, string, Nint )/;" `bitstring_to_str <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L62>`_
>`_
Transform a bit string to a string for printing Transform a bit string to a string for printing
`list_to_bitstring <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L/subroutine list_to_bitstring( string, list, n_elements, Nint)/;" `debug_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L117>`_
>`_ None
`list_to_bitstring <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L29>`_
return the physical string "string(N_int,2)" from the array of occupations "list(N_int*bit_kind_size,2) return the physical string "string(N_int,2)" from the array of occupations "list(N_int*bit_kind_size,2)
list list
<== ipos ==> <== ipos ==>

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@ -23,5 +23,14 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`fill_h_apply_buffer_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f#L6>`_
Fill the H_apply buffer with determiants for CISD
`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f#L43>`_
Calls H_apply on the HF determinant and selects all connected single and double
excitations (of the same symmetry).
`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/cisd.irp.f#L1>`_
None

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====================
DensityMatrix Module
====================
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

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@ -50,5 +50,110 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L93>`_
None
`h_apply_buffer_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L82>`_
Buffer of determinants/coefficients for H_apply. Uninitialized. Filled by H_apply subroutines.
`h_apply_buffer_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L81>`_
Buffer of determinants/coefficients for H_apply. Uninitialized. Filled by H_apply subroutines.
`h_apply_buffer_n_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L83>`_
Buffer of determinants/coefficients for H_apply. Uninitialized. Filled by H_apply subroutines.
`h_apply_buffer_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L22>`_
Size of the H_apply buffer.
`h_apply_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L3>`_
Theshold on | <Di|H|Dj> |
`resize_h_apply_buffer_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L31>`_
None
`n_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L11>`_
Number of determinants in the wave function
`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L47>`_
Number of generator determinants in the wave function
`n_states <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L3>`_
Number of states to consider
`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L20>`_
The wave function. Initialized with Hartree-Fock
`psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L19>`_
The wave function. Initialized with Hartree-Fock
`psi_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L55>`_
Determinants on which H is applied
`double_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L40>`_
double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1
double_exc_bitmask(:,2,i) is the bitmask for particles of excitation 1
double_exc_bitmask(:,3,i) is the bitmask for holes of excitation 2
double_exc_bitmask(:,4,i) is the bitmask for particles of excitation 2
for a given couple of hole/particle excitations i.
`n_double_exc_bitmasks <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L31>`_
Number of double excitation bitmasks
`n_single_exc_bitmasks <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L8>`_
Number of single excitation bitmasks
`single_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L17>`_
single_exc_bitmask(:,1,i) is the bitmask for holes
single_exc_bitmask(:,2,i) is the bitmask for particles
for a given couple of hole/particle excitations i.
`get_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L1>`_
Returns <S^2>
`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L842>`_
Needed for diag_H_mat_elem
`ac_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L887>`_
Needed for diag_H_mat_elem
`decode_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L76>`_
Decodes the exc arrays returned by get_excitation.
h1,h2 : Holes
p1,p2 : Particles
s1,s2 : Spins (1:alpha, 2:beta)
degree : Degree of excitation
`diag_h_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L779>`_
Computes <i|H|i>
`filter_connected <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L602>`_
Filters out the determinants that are not connected by H
`filter_connected_i_h_psi0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L687>`_
None
`get_double_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L140>`_
Returns the two excitation operators between two doubly excited determinants and the phase
`get_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L30>`_
Returns the excitation operators between two determinants and the phase
`get_excitation_degree <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1>`_
Returns the excitation degree between two determinants
`get_excitation_degree_vector <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L518>`_
Applies get_excitation_degree to an array of determinants
`get_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L273>`_
Returns the excitation operator between two singly excited determinants and the phase
`get_occ_from_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L935>`_
Returns a list of occupation numbers from a bitstring
`i_h_j <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L354>`_
Returns <i|H|j> where i and j are determinants
`i_h_psim <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L490>`_
None
`h_matrix_all_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/utils.irp.f#L1>`_
H matrix on the basis of the slater deter;inants defined by psi_det

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determinants
N_int integer
bit_kind integer
n_dets integer
n_states integer
psi_coef double precision (determinants_n_dets,determinants_n_states)
psi_det integer (determinants_N_int*determinants_bit_kind/4,2,determinants_n_dets)
H_apply_threshold double precision

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@ -34,20 +34,16 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`elec_alpha_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L/BEGIN_PROVIDER [ integer, elec_alpha_num ]/;" `elec_alpha_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L1>`_
>`_
Numbers of alpha ("up") , beta ("down") and total electrons Numbers of alpha ("up") , beta ("down") and total electrons
`elec_beta_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L/&BEGIN_PROVIDER [ integer, elec_beta_num ]/;" `elec_beta_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L2>`_
>`_
Numbers of alpha ("up") , beta ("down") and total electrons Numbers of alpha ("up") , beta ("down") and total electrons
`elec_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L/&BEGIN_PROVIDER [ integer, elec_num ]/;" `elec_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L3>`_
>`_
Numbers of alpha ("up") , beta ("down") and total electrons Numbers of alpha ("up") , beta ("down") and total electrons
`elec_num_tab <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L/&BEGIN_PROVIDER [ integer, elec_num_tab, (2) ]/;" `elec_num_tab <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L4>`_
>`_
Numbers of alpha ("up") , beta ("down") and total electrons Numbers of alpha ("up") , beta ("down") and total electrons

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@ -11,13 +11,11 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`ezfio_filename <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/ezfio.irp.f#L/BEGIN_PROVIDER [ character*(128), ezfio_filename ]/;" `ezfio_filename <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/ezfio.irp.f#L1>`_
>`_
Name of EZFIO file. It is obtained from the QPACKAGE_INPUT environment Name of EZFIO file. It is obtained from the QPACKAGE_INPUT environment
variable if it is set, or as the 1st argument of the command line. variable if it is set, or as the 1st argument of the command line.
`getunitandopen <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/get_unit_and_open.irp.f#L/integer function getUnitAndOpen(f,mode)/;" `getunitandopen <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/get_unit_and_open.irp.f#L1>`_
>`_
:f: :f:
file name file name
.br .br

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.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L46 `fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L83>`_
>`_ Alpha Fock matrix in AO basis set
`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L172>`_
Fock matrix on the MO basis
`fock_matrix_beta_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L84>`_
Alpha Fock matrix in AO basis set
`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L192>`_
Fock matrix on the MO basis
`fock_matrix_diag_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L2>`_
Fock matrix on the MO basis.
For open shells, the ROHF Fock Matrix is
.br
| F-K | F + K/2 | F |
|---------------------------------|
| F + K/2 | F | F - K/2 |
|---------------------------------|
| F | F - K/2 | F + K |
.br
F = 1/2 (Fa + Fb)
.br
K = Fb - Fa
.br
`fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L1>`_
Fock matrix on the MO basis.
For open shells, the ROHF Fock Matrix is
.br
| F-K | F + K/2 | F |
|---------------------------------|
| F + K/2 | F | F - K/2 |
|---------------------------------|
| F | F - K/2 | F + K |
.br
F = 1/2 (Fa + Fb)
.br
K = Fb - Fa
.br
`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L211>`_
Hartree-Fock energy
`hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L46>`_
Density matrix in the AO basis Density matrix in the AO basis
`hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L1 `hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L1>`_
>`_
Alpha and Beta density matrix in the AO basis Alpha and Beta density matrix in the AO basis
`hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L2 `hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L2>`_
>`_
Alpha and Beta density matrix in the AO basis Alpha and Beta density matrix in the AO basis
`diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L1 `diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
>`_
Diagonal Fock matrix in the MO basis Diagonal Fock matrix in the MO basis
`eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L2 `eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
>`_
Diagonal Fock matrix in the MO basis Diagonal Fock matrix in the MO basis
`scf_iteration <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/mo_SCF_iterations.irp.f#L1 `scf_iteration <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/mo_SCF_iterations.irp.f#L1>`_
>`_
None None
`do_diis <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/options.irp.f#L41 `do_diis <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/options.irp.f#L41>`_
>`_
If True, compute integrals on the fly If True, compute integrals on the fly
`n_it_scf_max <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/options.irp.f#L22 `n_it_scf_max <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/options.irp.f#L22>`_
>`_
Maximum number of SCF iterations Maximum number of SCF iterations
`thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/options.irp.f#L1 `thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/options.irp.f#L1>`_
>`_
Threshold on the convergence of the Hartree Fock energy Threshold on the convergence of the Hartree Fock energy
`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L5 `bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L5>`_
>`_
Energy of the reference bitmask used in Slater rules Energy of the reference bitmask used in Slater rules
`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L3 `kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L3>`_
>`_
Energy of the reference bitmask used in Slater rules Energy of the reference bitmask used in Slater rules
`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L2 `mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L2>`_
>`_
Energy of the reference bitmask used in Slater rules Energy of the reference bitmask used in Slater rules
`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L4 `nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L4>`_
>`_
Energy of the reference bitmask used in Slater rules Energy of the reference bitmask used in Slater rules
`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L1 `ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L1>`_
>`_
Energy of the reference bitmask used in Slater rules Energy of the reference bitmask used in Slater rules

12
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@ -22,22 +22,18 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`h_core_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/H_CORE_guess.irp.f#L1 `h_core_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/H_CORE_guess.irp.f#L1>`_
>`_
None None
`ao_ortho_lowdin_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/mo_ortho_lowdin.irp.f#L2 `ao_ortho_lowdin_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/mo_ortho_lowdin.irp.f#L2>`_
>`_
matrix of the coefficients of the mos generated by the matrix of the coefficients of the mos generated by the
orthonormalization by the S^{-1/2} canonical transformation of the aos orthonormalization by the S^{-1/2} canonical transformation of the aos
ao_ortho_lowdin_coef(i,j) = coefficient of the ith ao on the jth ao_ortho_lowdin orbital ao_ortho_lowdin_coef(i,j) = coefficient of the ith ao on the jth ao_ortho_lowdin orbital
`ao_ortho_lowdin_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/mo_ortho_lowdin.irp.f#L26 `ao_ortho_lowdin_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/mo_ortho_lowdin.irp.f#L26>`_
>`_
overlap matrix of the ao_ortho_lowdin overlap matrix of the ao_ortho_lowdin
supposed to be the Identity supposed to be the Identity
`ao_ortho_lowdin_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/pot_mo_ortho_lowdin_ints.irp.f#L1 `ao_ortho_lowdin_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/pot_mo_ortho_lowdin_ints.irp.f#L1>`_
>`_
None None

2
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@ -1 +1 @@
AOs Ezfio_files Nuclei Utils AOs Ezfio_files Nuclei Output Utils

31
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@ -25,6 +25,7 @@ Needed Modules
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_ * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_ * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_ * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_ * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
Documentation Documentation
@ -33,36 +34,28 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L/BEGIN_PROVIDER [ double precision, mo_coef, (ao_num_align,mo_tot_num) ]/;" `mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L22>`_
>`_
Molecular orbital coefficients on AO basis set Molecular orbital coefficients on AO basis set
mo_coef(i,j) = coefficient of the ith ao on the jth mo mo_coef(i,j) = coefficient of the ith ao on the jth mo
mo_label : Label characterizing the MOS (local, canonical, natural, etc)
`mo_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L/BEGIN_PROVIDER [ double precision, mo_coef_transp, (mo_tot_num_align,ao_num) ]/;" `mo_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L61>`_
>`_
Molecular orbital coefficients on AO basis set Molecular orbital coefficients on AO basis set
`mo_energy <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L/BEGIN_PROVIDER [ double precision, mo_energy, (mo_tot_num) ]/;" `mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L23>`_
>`_ Molecular orbital coefficients on AO basis set
Fock diagonal elements mo_coef(i,j) = coefficient of the ith ao on the jth mo
mo_label : Label characterizing the MOS (local, canonical, natural, etc)
`mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L/BEGIN_PROVIDER [ character*(64), mo_label ]/;" `mo_tot_num <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L1>`_
>`_
Label characterizing the MOS (local, canonical, natural, etc)
`mo_tot_num <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L/BEGIN_PROVIDER [ integer, mo_tot_num ]/;"
>`_
Total number of molecular orbitals and the size of the keys corresponding Total number of molecular orbitals and the size of the keys corresponding
`mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L/BEGIN_PROVIDER [ integer, mo_tot_num_align ]/;" `mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L12>`_
>`_
Aligned variable for dimensioning of arrays Aligned variable for dimensioning of arrays
`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L/subroutine mo_as_eigvectors_of_mo_matrix(matrix,n,m,label)/;" `mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L21>`_
>`_
None None
`save_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L/subroutine save_mos/;" `save_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L1>`_
>`_
None None

93
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@ -17,127 +17,96 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`ao_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L122 `ao_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L122>`_
>`_
array of the mono electronic hamiltonian on the AOs basis array of the mono electronic hamiltonian on the AOs basis
: sum of the kinetic and nuclear electronic potential : sum of the kinetic and nuclear electronic potential
`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L1 `ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L1>`_
>`_
Overlap between atomic basis functions: Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)` :math:`\int \chi_i(r) \chi_j(r) dr)`
`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L65 `ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L65>`_
>`_
Overlap between absolute value of atomic basis functions: Overlap between absolute value of atomic basis functions:
:math:`\int |\chi_i(r)| |\chi_j(r)| dr)` :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
`ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L2 `ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L2>`_
>`_
Overlap between atomic basis functions: Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)` :math:`\int \chi_i(r) \chi_j(r) dr)`
`ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L3 `ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L3>`_
>`_
Overlap between atomic basis functions: Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)` :math:`\int \chi_i(r) \chi_j(r) dr)`
`ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L4 `ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L4>`_
>`_
Overlap between atomic basis functions: Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)` :math:`\int \chi_i(r) \chi_j(r) dr)`
`check_ortho <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/check_orthonormality.irp.f#L1 `check_ortho <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/check_orthonormality.irp.f#L1>`_
>`_
None None
`do_print <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/check_orthonormality.irp.f#L11 `do_print <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/check_orthonormality.irp.f#L11>`_
>`_
None None
`n_pt_max_i_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/dimensions.irp.f#L2 `n_pt_max_i_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/dimensions.irp.f#L2>`_
>`_
None None
`n_pt_max_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/dimensions.irp.f#L1 `n_pt_max_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/dimensions.irp.f#L1>`_
>`_
None None
`ao_deriv2_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L1 `ao_deriv2_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L1>`_
>`_
second derivatives matrix elements in the ao basis second derivatives matrix elements in the ao basis
.. math:: .. math::
.br .br
{\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
`ao_deriv2_y <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L2 `ao_deriv2_y <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L2>`_
>`_
second derivatives matrix elements in the ao basis second derivatives matrix elements in the ao basis
.. math:: .. math::
.br .br
{\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
`ao_deriv2_z <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L3 `ao_deriv2_z <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L3>`_
>`_
second derivatives matrix elements in the ao basis second derivatives matrix elements in the ao basis
.. math:: .. math::
.br .br
{\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
`ao_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L125 `ao_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L125>`_
>`_
array of the priminitve basis kinetic integrals array of the priminitve basis kinetic integrals
\langle \chi_i |\hat{T}| \chi_j \rangle \langle \chi_i |\hat{T}| \chi_j \rangle
`mo_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_mo_ints.irp.f#L1 `mo_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_mo_ints.irp.f#L1>`_
>`_
None None
`mo_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L35 `mo_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L35>`_
>`_
array of the mono electronic hamiltonian on the MOs basis array of the mono electronic hamiltonian on the MOs basis
: sum of the kinetic and nuclear electronic potential : sum of the kinetic and nuclear electronic potential
`mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L1 `mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L1>`_
>`_
None None
`orthonormalize_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/orthonormalize.irp.f#L1 `orthonormalize_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/orthonormalize.irp.f#L1>`_
>`_
None None
`ao_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L1 `ao_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L1>`_
>`_
interaction nuclear electron interaction nuclear electron
`give_polynom_mult_center_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L157 `give_polynom_mult_center_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L157>`_
>`_
None None
`i_x1_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L285 `i_x1_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L285>`_
>`_
None None
`i_x2_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L357 `i_x2_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L357>`_
>`_
None None
`int_gaus_pol <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L428 `int_gaus_pol <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L428>`_
>`_
None None
`nai_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L82 `nai_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L82>`_
>`_
None None
`v_e_n <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L409 `v_e_n <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L409>`_
>`_
None None
`v_phi <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L473 `v_phi <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L473>`_
>`_
None None
`v_r <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L457 `v_r <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L457>`_
>`_
None None
`v_theta <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L486 `v_theta <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L486>`_
>`_
None None
`wallis <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L502 `wallis <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L502>`_
>`_
None None
`mo_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_mo_ints.irp.f#L1 `mo_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_mo_ints.irp.f#L1>`_
>`_
None None
`save_ortho_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/save_ortho_mos.irp.f#L1 `save_ortho_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/save_ortho_mos.irp.f#L1>`_
>`_
None None

36
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@ -22,62 +22,50 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`nucl_charge <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/BEGIN_PROVIDER [ double precision, nucl_charge, (nucl_num) ]/;" `nucl_charge <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L23>`_
>`_
Nuclear charges Nuclear charges
`nucl_coord <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num_aligned,3) ]/;" `nucl_coord <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L55>`_
>`_
Nuclear coordinates in the format (:, {x,y,z}) Nuclear coordinates in the format (:, {x,y,z})
`nucl_coord_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/BEGIN_PROVIDER [ double precision, nucl_coord_transp, (3,nucl_num) ]/;" `nucl_coord_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L110>`_
>`_
Transposed array of nucl_coord Transposed array of nucl_coord
`nucl_dist <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/&BEGIN_PROVIDER [ double precision, nucl_dist, (nucl_num_aligned,nucl_num) ]/;" `nucl_dist <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L129>`_
>`_
nucl_dist : Nucleus-nucleus distances nucl_dist : Nucleus-nucleus distances
nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_2 : Nucleus-nucleus distances squared
nucl_dist_vec : Nucleus-nucleus distances vectors nucl_dist_vec : Nucleus-nucleus distances vectors
`nucl_dist_2 <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/BEGIN_PROVIDER [ double precision, nucl_dist_2, (nucl_num_aligned,nucl_num) ]/;" `nucl_dist_2 <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L125>`_
>`_
nucl_dist : Nucleus-nucleus distances nucl_dist : Nucleus-nucleus distances
nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_2 : Nucleus-nucleus distances squared
nucl_dist_vec : Nucleus-nucleus distances vectors nucl_dist_vec : Nucleus-nucleus distances vectors
`nucl_dist_vec_x <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/&BEGIN_PROVIDER [ double precision, nucl_dist_vec_x, (nucl_num_aligned,nucl_num) ]/;" `nucl_dist_vec_x <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L126>`_
>`_
nucl_dist : Nucleus-nucleus distances nucl_dist : Nucleus-nucleus distances
nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_2 : Nucleus-nucleus distances squared
nucl_dist_vec : Nucleus-nucleus distances vectors nucl_dist_vec : Nucleus-nucleus distances vectors
`nucl_dist_vec_y <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/&BEGIN_PROVIDER [ double precision, nucl_dist_vec_y, (nucl_num_aligned,nucl_num) ]/;" `nucl_dist_vec_y <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L127>`_
>`_
nucl_dist : Nucleus-nucleus distances nucl_dist : Nucleus-nucleus distances
nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_2 : Nucleus-nucleus distances squared
nucl_dist_vec : Nucleus-nucleus distances vectors nucl_dist_vec : Nucleus-nucleus distances vectors
`nucl_dist_vec_z <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/&BEGIN_PROVIDER [ double precision, nucl_dist_vec_z, (nucl_num_aligned,nucl_num) ]/;" `nucl_dist_vec_z <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L128>`_
>`_
nucl_dist : Nucleus-nucleus distances nucl_dist : Nucleus-nucleus distances
nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_2 : Nucleus-nucleus distances squared
nucl_dist_vec : Nucleus-nucleus distances vectors nucl_dist_vec : Nucleus-nucleus distances vectors
`nucl_label <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/BEGIN_PROVIDER [ character*(32), nucl_label, (nucl_num) ]/;" `nucl_label <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L41>`_
>`_
Nuclear labels Nuclear labels
`nucl_num <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/BEGIN_PROVIDER [ integer, nucl_num ]/;" `nucl_num <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L1>`_
>`_
Number of nuclei Number of nuclei
`nucl_num_aligned <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/&BEGIN_PROVIDER [ integer, nucl_num_aligned ]/;" `nucl_num_aligned <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L2>`_
>`_
Number of nuclei Number of nuclei
`nuclear_repulsion <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L/BEGIN_PROVIDER [ double precision, nuclear_repulsion ]/;" `nuclear_repulsion <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L171>`_
>`_
Nuclear repulsion energy Nuclear repulsion energy

15
src/Output/README.rst
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@ -39,24 +39,19 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L2 `output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L2>`_
>`_
Initial CPU and wall times when printing in the output files Initial CPU and wall times when printing in the output files
`output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L1 `output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L1>`_
>`_
Initial CPU and wall times when printing in the output files Initial CPU and wall times when printing in the output files
`write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L49 `write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L49>`_
>`_
Write a double precision value in output Write a double precision value in output
`write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L64 `write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L64>`_
>`_
Write an integer value in output Write an integer value in output
`write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L33 `write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L33>`_
>`_
Write a time stamp in the output for chronological reconstruction Write a time stamp in the output for chronological reconstruction

114
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@ -10,53 +10,42 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file. .. NEEDED_MODULES file.
`apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L/subroutine apply_rotation(A,LDA,R,LDR,B,LDB,m,n)/;" `apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L146>`_
>`_
Apply the rotation found by find_rotation Apply the rotation found by find_rotation
`find_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L/subroutine find_rotation(A,LDA,B,m,C,n)/;" `find_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L127>`_
>`_
Find A.C = B Find A.C = B
`get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L/subroutine get_pseudo_inverse(A,m,n,C,LDA)/;" `get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L73>`_
>`_
Find C = A^-1 Find C = A^-1
`lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L/subroutine lapack_diag(eigvalues,eigvectors,H,nmax,n)/;" `lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L158>`_
>`_
Diagonalize matrix H Diagonalize matrix H
`ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L/subroutine ortho_lowdin(overlap,lda,n,C,ldc,m)/;" `ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L1>`_
>`_
Compute U.S^-1/2 canonical orthogonalization Compute U.S^-1/2 canonical orthogonalization
`add_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/subroutine add_poly(b,nb,c,nc,d,nd)/;" `add_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L243>`_
>`_
Add two polynomials Add two polynomials
D(t) =! D(t) +( B(t)+C(t)) D(t) =! D(t) +( B(t)+C(t))
`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/subroutine add_poly_multiply(b,nb,cst,d,nd)/;" `add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L271>`_
>`_
Add a polynomial multiplied by a constant Add a polynomial multiplied by a constant
D(t) =! D(t) +( cst * B(t)) D(t) =! D(t) +( cst * B(t))
`f_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/double precision function F_integral(n,p)/;" `f_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L345>`_
>`_
function that calculates the following integral function that calculates the following integral
\int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx
`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/subroutine gaussian_product(a,xa,b,xb,k,p,xp)/;" `gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L121>`_
>`_
Gaussian product in 1D. 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} 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/src/Utils/integration.irp.f#L/subroutine gaussian_product_x(a,xa,b,xb,k,p,xp)/;" `gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L163>`_
>`_
Gaussian product in 1D. 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} e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
`give_explicit_poly_and_gaussian <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/subroutine give_explicit_poly_and_gaussian(P_new,P_center,p,fact_k,iorder,alpha,beta,a,b,A_center,B_center,dim)/;" `give_explicit_poly_and_gaussian <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L46>`_
>`_
Transforms the product of 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) (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 into
@ -64,112 +53,105 @@ Documentation
* [ 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_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 ) * [ 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/src/Utils/integration.irp.f#L/subroutine give_explicit_poly_and_gaussian_x(P_new,P_center,p,fact_k,iorder,alpha,beta,a,b,A_center,B_center,dim)/;" `give_explicit_poly_and_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L1>`_
>`_
Transform the product of 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) (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 into
fact_k (x-x_P)^iorder(1) (y-y_P)^iorder(2) (z-z_P)^iorder(3) exp(-p(r-P)^2) fact_k (x-x_P)^iorder(1) (y-y_P)^iorder(2) (z-z_P)^iorder(3) exp(-p(r-P)^2)
`hermite <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/double precision function hermite(n,x)/;" `hermite <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L468>`_
>`_
Hermite polynomial Hermite polynomial
`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/subroutine multiply_poly(b,nb,c,nc,d,nd)/;" `multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L201>`_
>`_
Multiply two polynomials Multiply two polynomials
D(t) =! D(t) +( B(t)*C(t)) D(t) =! D(t) +( B(t)*C(t))
`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/subroutine recentered_poly2(P_new,x_A,x_P,a,P_new2,x_B,x_Q,b)/;" `recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L300>`_
>`_
Recenter two polynomials Recenter two polynomials
`rint <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/double precision function rint(n,rho)/;" `rint <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L373>`_
>`_
.. math:: .. math::
.br .br
\int_0^1 dx \exp(-p x^2) x^n \int_0^1 dx \exp(-p x^2) x^n
.br .br
`rint1 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/double precision function rint1(n,rho)/;" `rint1 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L524>`_
>`_
Standard version of rint Standard version of rint
`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/double precision function rint_large_n(n,rho)/;" `rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L493>`_
>`_
Version of rint for large values of n Version of rint for large values of n
`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L/double precision function rint_sum(n_pt_out,rho,d1)/;" `rint_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L417>`_
>`_
Needed for the calculation of two-electron integrals. Needed for the calculation of two-electron integrals.
`overlap_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L/double precision function overlap_gaussian_x(A_center,B_center,alpha,beta,power_A,power_B,dim)/;" `overlap_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L1>`_
>`_
.. math:: .. math::
.br .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 \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 .br
`overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L/subroutine overlap_gaussian_xyz(A_center,B_center,alpha,beta,power_A,& `overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L37>`_
>`_
.. math:: .. math::
.br .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_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 S = S_x S_y S_z
.br .br
`overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L/subroutine overlap_x_abs(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,lower_exp_val,dx,nx)/;" `overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L99>`_
>`_
.. math :: .. math ::
.br .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 \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 .br
`align_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L/integer function align_double(n)/;" `align_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L65>`_
>`_
Compute 1st dimension such that it is aligned for vectorization. Compute 1st dimension such that it is aligned for vectorization.
`binom <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L/BEGIN_PROVIDER [ double precision, binom, (0:20,0:20) ]/;" `all_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L1>`_
>`_ Dummy provider to provide all utils
`binom <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L47>`_
Binomial coefficients Binomial coefficients
`binom_func <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L/double precision function binom_func(i,j)/;" `binom_func <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L16>`_
>`_
.. math :: .. math ::
.br .br
\frac{i!}{j!(i-j)!} \frac{i!}{j!(i-j)!}
.br .br
`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L/&BEGIN_PROVIDER [ double precision, binom_transp, (0:20,0:20) ]/;" `binom_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L48>`_
>`_
Binomial coefficients Binomial coefficients
`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L/double precision function dble_fact(n) result(fact2)/;" `dble_fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L124>`_
>`_
n!! n!!
`fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L/double precision function fact(n)/;" `fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L80>`_
>`_
n! n!
`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L/BEGIN_PROVIDER [ double precision, fact_inv, (128) ]/;" `fact_inv <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L112>`_
>`_
1/n! 1/n!
`inv_int <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L/BEGIN_PROVIDER [ double precision, inv_int, (128) ]/;" `inv_int <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L171>`_
>`_
1/i 1/i
`nproc <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L/BEGIN_PROVIDER [ integer, nproc ]/;" `normalize <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L272>`_
>`_ Normalizes vector u
u is expected to be aligned in memory.
`nproc <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L197>`_
Number of current OpenMP threads Number of current OpenMP threads
`wall_time <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L/subroutine wall_time(t)/;" `u_dot_u <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L244>`_
>`_ Compute <u|u>
u is expected to be aligned in memory.
`u_dot_v <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L213>`_
Compute <u|v>
u and v are expected to be aligned in memory.
`wall_time <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L182>`_
The equivalent of cpu_time, but for the wall time. The equivalent of cpu_time, but for the wall time.
`write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L/subroutine write_git_log(iunit)/;" `write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L157>`_
>`_
Write the last git commit in file iunit. Write the last git commit in file iunit.

102
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@ -1,15 +1,15 @@
BEGIN_PROVIDER [ logical, all_utils ] BEGIN_PROVIDER [ logical, all_utils ]
implicit none implicit none
BEGIN_DOC BEGIN_DOC
! Dummy provider to provide all utils ! Dummy provider to provide all utils
END_DOC END_DOC
! Do not move this : it greps itself ! Do not move this : it greps itself
BEGIN_SHELL [ /bin/bash ] BEGIN_SHELL [ /bin/bash ]
for i in $(grep "BEGIN_PROVIDER" $QPACKAGE_ROOT/src/Utils/*.irp.f | cut -d ',' -f 2 | cut -d ']' -f 1 | tail --lines=+3 ) for i in $(grep "BEGIN_PROVIDER" $QPACKAGE_ROOT/src/Utils/*.irp.f | cut -d ',' -f 2 | cut -d ']' -f 1 | tail --lines=+3 )
do do
echo PROVIDE $i echo PROVIDE $i
done done
END_SHELL END_SHELL
END_PROVIDER END_PROVIDER
@ -209,3 +209,89 @@ BEGIN_PROVIDER [ integer, nproc ]
!$OMP END PARALLEL !$OMP END PARALLEL
END_PROVIDER END_PROVIDER
double precision function u_dot_v(u,v,sze)
implicit none
BEGIN_DOC
! Compute <u|v>
! u and v are expected to be aligned in memory.
END_DOC
integer, intent(in) :: sze
double precision, intent(in) :: u(sze),v(sze)
integer :: i,t1, t2, t3, t4
ASSERT (sze > 0)
t1 = 0
t2 = sze/4
t3 = t2+t2
t4 = t3+t2
u_dot_v = 0.d0
!DIR$ VECTOR ALWAYS
!DIR$ VECTOR ALIGNED
do i=1,t2
u_dot_v = u_dot_v + u(t1+i)*v(t1+i) + u(t2+i)*v(t2+i) + &
u(t3+i)*v(t3+i) + u(t4+i)*v(t4+i)
enddo
!DIR$ VECTOR ALWAYS
!DIR$ VECTOR ALIGNED
do i=t4+t2+1,sze
u_dot_v = u_dot_v + u(i)*v(i)
enddo
end
double precision function u_dot_u(u,sze)
implicit none
BEGIN_DOC
! Compute <u|u>
! u is expected to be aligned in memory.
END_DOC
integer, intent(in) :: sze
double precision, intent(in) :: u(sze)
integer :: i
integer :: t1, t2, t3, t4
ASSERT (sze > 0)
t1 = 0
t2 = sze/4
t3 = t2+t2
t4 = t3+t2
u_dot_u = 0.d0
do i=1,t2
u_dot_u = u_dot_u + u(t1+i)*u(t1+i) + u(t2+i)*u(t2+i) + &
u(t3+i)*u(t3+i) + u(t4+i)*u(t4+i)
enddo
do i=t4+t2+1,sze
u_dot_u = u_dot_u+u(i)*u(i)
enddo
end
subroutine normalize(u,sze)
implicit none
BEGIN_DOC
! Normalizes vector u
! u is expected to be aligned in memory.
END_DOC
integer, intent(in) :: sze
double precision, intent(inout):: u(sze)
double precision :: d
double precision, external :: u_dot_u
integer :: i
!DIR$ FORCEINLINE
d = 1.d0/dsqrt( u_dot_u(u,sze) )
if (d /= 1.d0) then
do i=1,sze
u(i) = d*u(i)
enddo
endif
end