Updated documentation

INSTALL.rst

@@ -46,7 +46,7 @@ Requirements
 - `GMP <https://gmplib.org/>`_ : Gnu Multiple Precision Arithmetic Library
 - |OCaml| compiler with |OPAM| package manager 
 - `Bubblewrap <https://github.com/projectatomic/bubblewrap>`_ : Sandboxing tool required by Opam
-- `libcap https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git`_ : POSIX capabilities required by Bubblewrap
+- `libcap <https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git>`_ : POSIX capabilities required by Bubblewrap
 - |Ninja| : a parallel build system
 
 

docs/source/modules/ao_two_e_erf_ints.rst

@@ -176,6 +176,7 @@ Providers
        * :c:data:`ao_num`
        * :c:data:`ao_power`
        * :c:data:`ao_prim_num`
+       * :c:data:`mu_erf`
        * :c:data:`n_pt_max_integrals`
        * :c:data:`nucl_coord`
 
@@ -214,6 +215,7 @@ Providers
        * :c:data:`ao_prim_num`
        * :c:data:`ezfio_filename`
        * :c:data:`io_ao_two_e_integrals_erf`
+       * :c:data:`mu_erf`
        * :c:data:`n_pt_max_integrals`
        * :c:data:`nproc`
        * :c:data:`nucl_coord`
@@ -290,6 +292,7 @@ Subroutines / functions
        * :c:data:`ao_power`
        * :c:data:`ao_expo_ordered_transp`
        * :c:data:`ao_prim_num`
+       * :c:data:`mu_erf`
        * :c:data:`ao_nucl`
        * :c:data:`nucl_coord`
 

docs/source/modules/ao_two_e_ints.rst

@@ -1016,6 +1016,70 @@ Subroutines / functions
        * :c:func:`two_e_integrals_index`
 
  
+.. c:function:: get_ao_two_e_integrals_non_zero_jl:
+
+
+    File : :file:`ao_two_e_ints/map_integrals.irp.f`
+
+    .. code:: fortran
+
+        subroutine get_ao_two_e_integrals_non_zero_jl(j,l,thresh,sze_max,sze,out_val,out_val_index,non_zero_int)
+
+
+    Gets multiple AO bi-electronic integral from the AO map .
+    All non-zero i are retrieved for j,k,l fixed.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_map`
+       * :c:data:`ao_overlap_abs`
+       * :c:data:`ao_two_e_integral_schwartz`
+       * :c:data:`ao_two_e_integrals_in_map`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`map_get`
+       * :c:func:`two_e_integrals_index`
+
+ 
+.. c:function:: get_ao_two_e_integrals_non_zero_jl_from_list:
+
+
+    File : :file:`ao_two_e_ints/map_integrals.irp.f`
+
+    .. code:: fortran
+
+        subroutine get_ao_two_e_integrals_non_zero_jl_from_list(j,l,thresh,list,n_list,sze_max,out_val,out_val_index,non_zero_int)
+
+
+    Gets multiple AO two-electron integrals from the AO map .
+    All non-zero i are retrieved for j,k,l fixed.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_map`
+       * :c:data:`ao_overlap_abs`
+       * :c:data:`ao_two_e_integral_schwartz`
+       * :c:data:`ao_two_e_integrals_in_map`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`map_get`
+       * :c:func:`two_e_integrals_index`
+
+ 
 .. c:function:: give_polynom_mult_center_x:
 
 
@@ -1243,6 +1307,8 @@ Subroutines / functions
        * :c:func:`get_ao_two_e_integral_erf`
        * :c:func:`get_ao_two_e_integrals_erf_non_zero`
        * :c:func:`get_ao_two_e_integrals_non_zero`
+       * :c:func:`get_ao_two_e_integrals_non_zero_jl`
+       * :c:func:`get_ao_two_e_integrals_non_zero_jl_from_list`
        * :c:func:`get_mo_two_e_integral_erf`
        * :c:func:`get_mo_two_e_integrals_coulomb_ii`
        * :c:func:`get_mo_two_e_integrals_erf`

docs/source/modules/becke_numerical_grid.rst

@@ -93,6 +93,12 @@ EZFIO parameters
     Total number of grid points
  
  
+.. option:: thresh_grid
+ 
+    threshold on the weight of a given grid point
+ 
+    Default: 1.e-20
+ 
  
 Providers 
 --------- 
@@ -210,6 +216,7 @@ Providers
        * :c:data:`n_points_final_grid`
        * :c:data:`n_points_radial_grid`
        * :c:data:`nucl_num`
+       * :c:data:`thresh_grid`
 
     Needed by:
 
@@ -244,6 +251,40 @@ Providers
        * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r`
 
  
+.. c:var:: final_grid_points_per_atom
+
+
+    File : :file:`becke_numerical_grid/grid_becke_per_atom.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: final_grid_points_per_atom	(3,n_pts_max_per_atom,nucl_num)
+        double precision, allocatable	:: final_weight_at_r_vector_per_atom	(n_pts_max_per_atom,nucl_num)
+        integer, allocatable	:: index_final_points_per_atom	(3,n_pts_max_per_atom,nucl_num)
+        integer, allocatable	:: index_final_points_per_atom_reverse	(n_points_integration_angular,n_points_radial_grid,nucl_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`n_pts_per_atom`
+       * :c:data:`nucl_num`
+       * :c:data:`thresh_grid`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_in_r_array_per_atom`
+
+ 
 .. c:var:: final_weight_at_r
 
 
@@ -263,10 +304,10 @@ Providers
 
        * :c:data:`alpha_knowles`
        * :c:data:`angular_quadrature_points`
+       * :c:data:`grid_atomic_number`
        * :c:data:`grid_points_radial`
        * :c:data:`m_knowles`
        * :c:data:`n_points_radial_grid`
-       * :c:data:`nucl_charge`
        * :c:data:`nucl_num`
        * :c:data:`weight_at_r`
 
@@ -276,6 +317,9 @@ Providers
        :columns: 3
 
        * :c:data:`final_grid_points`
+       * :c:data:`final_grid_points_per_atom`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`n_pts_per_atom`
 
  
 .. c:var:: final_weight_at_r_vector
@@ -309,6 +353,7 @@ Providers
        * :c:data:`n_points_final_grid`
        * :c:data:`n_points_radial_grid`
        * :c:data:`nucl_num`
+       * :c:data:`thresh_grid`
 
     Needed by:
 
@@ -343,6 +388,69 @@ Providers
        * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r`
 
  
+.. c:var:: final_weight_at_r_vector_per_atom
+
+
+    File : :file:`becke_numerical_grid/grid_becke_per_atom.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: final_grid_points_per_atom	(3,n_pts_max_per_atom,nucl_num)
+        double precision, allocatable	:: final_weight_at_r_vector_per_atom	(n_pts_max_per_atom,nucl_num)
+        integer, allocatable	:: index_final_points_per_atom	(3,n_pts_max_per_atom,nucl_num)
+        integer, allocatable	:: index_final_points_per_atom_reverse	(n_points_integration_angular,n_points_radial_grid,nucl_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`n_pts_per_atom`
+       * :c:data:`nucl_num`
+       * :c:data:`thresh_grid`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_in_r_array_per_atom`
+
+ 
+.. c:var:: grid_atomic_number
+
+
+    File : :file:`becke_numerical_grid/atomic_number.irp.f`
+
+    .. code:: fortran
+
+        integer, allocatable	:: grid_atomic_number	(nucl_num)
+
+
+    Atomic number used to adjust the grid
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+
+ 
 .. c:var:: grid_points_per_atom
 
 
@@ -362,10 +470,10 @@ Providers
 
        * :c:data:`alpha_knowles`
        * :c:data:`angular_quadrature_points`
+       * :c:data:`grid_atomic_number`
        * :c:data:`grid_points_radial`
        * :c:data:`m_knowles`
        * :c:data:`n_points_radial_grid`
-       * :c:data:`nucl_charge`
        * :c:data:`nucl_coord`
        * :c:data:`nucl_num`
 
@@ -375,6 +483,7 @@ Providers
        :columns: 3
 
        * :c:data:`final_grid_points`
+       * :c:data:`final_grid_points_per_atom`
        * :c:data:`one_e_dm_alpha_in_r`
        * :c:data:`weight_at_r`
 
@@ -439,6 +548,7 @@ Providers
        * :c:data:`n_points_final_grid`
        * :c:data:`n_points_radial_grid`
        * :c:data:`nucl_num`
+       * :c:data:`thresh_grid`
 
     Needed by:
 
@@ -473,6 +583,74 @@ Providers
        * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r`
 
  
+.. c:var:: index_final_points_per_atom
+
+
+    File : :file:`becke_numerical_grid/grid_becke_per_atom.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: final_grid_points_per_atom	(3,n_pts_max_per_atom,nucl_num)
+        double precision, allocatable	:: final_weight_at_r_vector_per_atom	(n_pts_max_per_atom,nucl_num)
+        integer, allocatable	:: index_final_points_per_atom	(3,n_pts_max_per_atom,nucl_num)
+        integer, allocatable	:: index_final_points_per_atom_reverse	(n_points_integration_angular,n_points_radial_grid,nucl_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`n_pts_per_atom`
+       * :c:data:`nucl_num`
+       * :c:data:`thresh_grid`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_in_r_array_per_atom`
+
+ 
+.. c:var:: index_final_points_per_atom_reverse
+
+
+    File : :file:`becke_numerical_grid/grid_becke_per_atom.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: final_grid_points_per_atom	(3,n_pts_max_per_atom,nucl_num)
+        double precision, allocatable	:: final_weight_at_r_vector_per_atom	(n_pts_max_per_atom,nucl_num)
+        integer, allocatable	:: index_final_points_per_atom	(3,n_pts_max_per_atom,nucl_num)
+        integer, allocatable	:: index_final_points_per_atom_reverse	(n_points_integration_angular,n_points_radial_grid,nucl_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`n_pts_per_atom`
+       * :c:data:`nucl_num`
+       * :c:data:`thresh_grid`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_in_r_array_per_atom`
+
+ 
 .. c:var:: index_final_points_reverse
 
 
@@ -504,6 +682,7 @@ Providers
        * :c:data:`n_points_final_grid`
        * :c:data:`n_points_radial_grid`
        * :c:data:`nucl_num`
+       * :c:data:`thresh_grid`
 
     Needed by:
 
@@ -576,8 +755,10 @@ Providers
     .. hlist::
        :columns: 3
 
+       * :c:data:`final_weight_at_r`
        * :c:data:`n_points_radial_grid`
        * :c:data:`nucl_num`
+       * :c:data:`thresh_grid`
 
     Needed by:
 
@@ -681,11 +862,13 @@ Providers
 
        * :c:data:`angular_quadrature_points`
        * :c:data:`final_grid_points`
+       * :c:data:`final_grid_points_per_atom`
        * :c:data:`final_weight_at_r`
        * :c:data:`grid_points_per_atom`
        * :c:data:`grid_points_radial`
        * :c:data:`n_points_final_grid`
        * :c:data:`n_points_grid_per_atom`
+       * :c:data:`n_pts_per_atom`
        * :c:data:`one_e_dm_alpha_in_r`
        * :c:data:`weight_at_r`
 
@@ -721,15 +904,81 @@ Providers
 
        * :c:data:`angular_quadrature_points`
        * :c:data:`final_grid_points`
+       * :c:data:`final_grid_points_per_atom`
        * :c:data:`final_weight_at_r`
        * :c:data:`grid_points_per_atom`
        * :c:data:`grid_points_radial`
        * :c:data:`n_points_final_grid`
        * :c:data:`n_points_grid_per_atom`
+       * :c:data:`n_pts_per_atom`
        * :c:data:`one_e_dm_alpha_in_r`
        * :c:data:`weight_at_r`
 
  
+.. c:var:: n_pts_max_per_atom
+
+
+    File : :file:`becke_numerical_grid/grid_becke_per_atom.irp.f`
+
+    .. code:: fortran
+
+        integer, allocatable	:: n_pts_per_atom	(nucl_num)
+        integer	:: n_pts_max_per_atom	
+
+
+    Number of points which are non zero
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`nucl_num`
+       * :c:data:`thresh_grid`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_in_r_array_per_atom`
+       * :c:data:`final_grid_points_per_atom`
+
+ 
+.. c:var:: n_pts_per_atom
+
+
+    File : :file:`becke_numerical_grid/grid_becke_per_atom.irp.f`
+
+    .. code:: fortran
+
+        integer, allocatable	:: n_pts_per_atom	(nucl_num)
+        integer	:: n_pts_max_per_atom	
+
+
+    Number of points which are non zero
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`nucl_num`
+       * :c:data:`thresh_grid`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_in_r_array_per_atom`
+       * :c:data:`final_grid_points_per_atom`
+
+ 
 .. c:var:: weight_at_r
 
 
@@ -754,7 +1003,6 @@ Providers
 
        * :c:data:`grid_points_per_atom`
        * :c:data:`n_points_radial_grid`
-       * :c:data:`nucl_charge`
        * :c:data:`nucl_coord_transp`
        * :c:data:`nucl_dist_inv`
        * :c:data:`nucl_num`
@@ -824,7 +1072,6 @@ Subroutines / functions
        * :c:data:`nucl_dist_inv`
        * :c:data:`slater_bragg_type_inter_distance_ua`
        * :c:data:`nucl_coord_transp`
-       * :c:data:`nucl_charge`
        * :c:data:`nucl_num`
 
  

docs/source/modules/cipsi.rst

@@ -727,9 +727,40 @@ Providers
        * :c:data:`c0_weight`
        * :c:data:`n_states`
        * :c:data:`pt2_match_weight`
+       * :c:data:`state_average_weight`
+       * :c:data:`variance_match_weight`
+       * :c:data:`weight_selection`
 
 
  
+.. c:var:: variance_match_weight
+
+
+    File : :file:`cipsi/selection.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: variance_match_weight	(N_states)
+
+
+    Weights adjusted along the selection to make the variances
+    of each state coincide.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_states`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`selection_weight`
+
+ 
  
 Subroutines / functions 
 ----------------------- 
@@ -879,6 +910,7 @@ Subroutines / functions
        * :c:data:`selection_weight`
        * :c:data:`mo_num`
        * :c:data:`n_states`
+       * :c:data:`weight_selection`
        * :c:data:`n_int`
        * :c:data:`psi_det_hii`
        * :c:data:`do_only_1h1p`
@@ -1181,6 +1213,7 @@ Subroutines / functions
        :columns: 3
 
        * :c:data:`generators_bitmask`
+       * :c:data:`selection_weight`
        * :c:data:`pt2_stoch_istate`
        * :c:data:`psi_selectors`
        * :c:data:`psi_det`
@@ -1203,6 +1236,7 @@ Subroutines / functions
        * :c:data:`n_det_generators`
        * :c:data:`psi_det_generators`
        * :c:data:`n_int`
+       * :c:data:`pseudo_sym`
        * :c:data:`psi_det_generators`
 
     Called by:
@@ -1551,12 +1585,14 @@ Subroutines / functions
        * :c:data:`correlation_energy_ratio_max`
        * :c:data:`n_iter`
        * :c:data:`psi_energy_with_nucl_rep`
+       * :c:data:`selection_factor`
        * :c:data:`psi_occ_pattern`
        * :c:data:`n_det_max`
        * :c:data:`n_states`
        * :c:data:`h_apply_buffer_allocated`
        * :c:data:`n_det`
        * :c:data:`s2_eig`
+       * :c:data:`variance_max`
        * :c:data:`do_pt2`
        * :c:data:`psi_energy`
        * :c:data:`pt2_relative_error`
@@ -1619,6 +1655,7 @@ Subroutines / functions
        * :c:data:`pt2_stoch_istate`
        * :c:data:`state_average_weight`
        * :c:data:`threshold_generators`
+       * :c:data:`variance_match_weight`
 
  
 .. c:function:: run_pt2_slave:
@@ -1776,16 +1813,18 @@ Subroutines / functions
        * :c:data:`psi_bilinear_matrix_values`
        * :c:data:`psi_bilinear_matrix_transp_values`
        * :c:data:`mo_num`
+       * :c:data:`psi_det_sorted`
        * :c:data:`psi_bilinear_matrix_transp_rows_loc`
        * :c:data:`n_states`
        * :c:data:`pt2_f`
-       * :c:data:`psi_bilinear_matrix_values`
        * :c:data:`elec_alpha_num`
+       * :c:data:`psi_bilinear_matrix_values`
+       * :c:data:`weight_selection`
        * :c:data:`psi_bilinear_matrix_transp_values`
        * :c:data:`n_int`
        * :c:data:`psi_det_alpha_unique`
        * :c:data:`psi_det_sorted`
-       * :c:data:`psi_det_sorted`
+       * :c:data:`pseudo_sym`
        * :c:data:`psi_bilinear_matrix_columns_loc`
        * :c:data:`psi_selectors_coef_transp`
 
@@ -1859,6 +1898,7 @@ Subroutines / functions
        * :c:data:`pt2_e0_denominator`
        * :c:data:`pt2_stoch_istate`
        * :c:data:`read_wf`
+       * :c:data:`selection_weight`
        * :c:data:`state_average_weight`
        * :c:data:`threshold_generators`
 
@@ -1879,6 +1919,7 @@ Subroutines / functions
     .. hlist::
        :columns: 3
 
+       * :c:data:`selection_weight`
        * :c:data:`pt2_stoch_istate`
        * :c:data:`psi_det`
        * :c:data:`zmq_state`
@@ -1935,6 +1976,7 @@ Subroutines / functions
 
        * :c:data:`pt2_e0_denominator`
        * :c:data:`pt2_stoch_istate`
+       * :c:data:`selection_weight`
        * :c:data:`state_average_weight`
        * :c:data:`threshold_generators`
 
@@ -1959,6 +2001,7 @@ Subroutines / functions
        * :c:data:`correlation_energy_ratio_max`
        * :c:data:`n_iter`
        * :c:data:`psi_energy_with_nucl_rep`
+       * :c:data:`selection_factor`
        * :c:data:`psi_occ_pattern`
        * :c:data:`pt2_max`
        * :c:data:`n_det_max`
@@ -2028,6 +2071,7 @@ Subroutines / functions
        * :c:data:`pt2_stoch_istate`
        * :c:data:`state_average_weight`
        * :c:data:`threshold_generators`
+       * :c:data:`variance_match_weight`
 
  
 .. c:function:: select_connected:
@@ -2351,6 +2395,43 @@ Subroutines / functions
        * :c:func:`check_mem`
 
  
+.. c:function:: update_pt2_and_variance_weights:
+
+
+    File : :file:`cipsi/selection.irp.f`
+
+    .. code:: fortran
+
+        subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_st)
+
+
+    Updates the rPT2- and Variance- matching weights.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`pt2_match_weight`
+       * :c:data:`variance_match_weight`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`zmq_pt2`
+       * :c:func:`zmq_selection`
+
+    Touches:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`pt2_match_weight`
+       * :c:data:`variance_match_weight`
+
+ 
 .. c:function:: zmq_pt2:
 
 
@@ -2368,6 +2449,7 @@ Subroutines / functions
        :columns: 3
 
        * :c:data:`psi_det_sorted`
+       * :c:data:`selection_weight`
        * :c:data:`pt2_stoch_istate`
        * :c:data:`psi_selectors`
        * :c:data:`psi_bilinear_matrix_values`
@@ -2378,7 +2460,7 @@ Subroutines / functions
        * :c:data:`state_average_weight`
        * :c:data:`n_det`
        * :c:data:`s2_eig`
-       * :c:data:`pt2_match_weight`
+       * :c:data:`psi_det_sorted`
        * :c:data:`pt2_j`
        * :c:data:`mo_two_e_integrals_in_map`
        * :c:data:`psi_bilinear_matrix_transp_values`
@@ -2396,7 +2478,7 @@ Subroutines / functions
        * :c:data:`threshold_generators`
        * :c:data:`psi_det_beta_unique`
        * :c:data:`det_to_occ_pattern`
-       * :c:data:`psi_det_sorted`
+       * :c:data:`global_selection_buffer`
        * :c:data:`psi_bilinear_matrix_transp_rows_loc`
        * :c:data:`n_states`
        * :c:data:`pt2_f`
@@ -2405,7 +2487,7 @@ Subroutines / functions
        * :c:data:`n_int`
        * :c:data:`psi_det_hii`
        * :c:data:`pt2_j`
-       * :c:data:`global_selection_buffer`
+       * :c:data:`pseudo_sym`
        * :c:data:`pt2_w`
        * :c:data:`pt2_u`
 
@@ -2434,6 +2516,7 @@ Subroutines / functions
        * :c:func:`pt2_slave_inproc`
        * :c:func:`remove_duplicates_in_selection_buffer`
        * :c:func:`resident_memory`
+       * :c:func:`update_pt2_and_variance_weights`
        * :c:func:`write_double`
        * :c:func:`write_int`
        * :c:func:`zmq_selection`
@@ -2453,6 +2536,7 @@ Subroutines / functions
        * :c:data:`pt2_match_weight`
        * :c:data:`pt2_stoch_istate`
        * :c:data:`state_average_weight`
+       * :c:data:`variance_match_weight`
 
  
 .. c:function:: zmq_selection:
@@ -2472,12 +2556,12 @@ Subroutines / functions
        :columns: 3
 
        * :c:data:`psi_det_sorted`
+       * :c:data:`selection_weight`
        * :c:data:`psi_selectors`
        * :c:data:`psi_bilinear_matrix_values`
        * :c:data:`n_det`
        * :c:data:`psi_bilinear_matrix_columns_loc`
        * :c:data:`n_det_selectors`
-       * :c:data:`psi_bilinear_matrix_transp_values`
        * :c:data:`psi_det_alpha_unique`
        * :c:data:`psi_bilinear_matrix_transp_values`
        * :c:data:`state_average_weight`
@@ -2493,8 +2577,9 @@ Subroutines / functions
        * :c:data:`n_states`
        * :c:data:`pt2_f`
        * :c:data:`n_det_generators`
-       * :c:data:`pt2_match_weight`
+       * :c:data:`psi_bilinear_matrix_transp_values`
        * :c:data:`n_int`
+       * :c:data:`pseudo_sym`
 
     Called by:
 
@@ -2519,6 +2604,7 @@ Subroutines / functions
        * :c:func:`save_wavefunction`
        * :c:func:`selection_collector`
        * :c:func:`selection_slave_inproc`
+       * :c:func:`update_pt2_and_variance_weights`
        * :c:func:`write_double`
 
     Touches:
@@ -2534,4 +2620,5 @@ Subroutines / functions
        * :c:data:`psi_det_size`
        * :c:data:`psi_det_sorted_bit`
        * :c:data:`pt2_match_weight`
+       * :c:data:`variance_match_weight`
 

docs/source/modules/davidson.rst

@@ -1756,6 +1756,40 @@ Subroutines / functions
        * :c:func:`i_wee_j_single`
 
  
+.. c:function:: print_energy_components:
+
+
+    File : :file:`davidson/print_e_components.irp.f`
+
+    .. code:: fortran
+
+        subroutine print_energy_components()
+
+
+    Prints the different components of the energy.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_integrals_n_e`
+       * :c:data:`n_states`
+       * :c:data:`mo_pseudo_integrals`
+       * :c:data:`mo_kinetic_integrals`
+       * :c:data:`mo_num`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`psi_energy`
+       * :c:data:`one_e_dm_mo_alpha`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`print_summary`
+
+ 
 .. c:function:: u_0_h_u_0:
 
 

docs/source/modules/determinants.rst

@@ -61,12 +61,18 @@ EZFIO parameters
  
     Default: True
  
-.. option:: used_weight
+.. option:: weight_one_e_dm
  
     Weight used in the calculation of the one-electron density matrix. 0: 1./(c_0^2), 1: 1/N_states, 2: input state-average weight, 3: 1/(Norm_L3(Psi))
  
     Default: 1
  
+.. option:: weight_selection
+ 
+    Weight used in the selection. 0: input state-average weight, 1: 1./(c_0^2), 2: rPT2 matching, 3: variance matching, 4: variance and rPT2 matching, 5: variance minimization and matching
+ 
+    Default: 2
+ 
 .. option:: threshold_generators
  
     Thresholds on generators (fraction of the square of the norm)
@@ -119,6 +125,12 @@ EZFIO parameters
     Weight of the states in state-average calculations.
  
  
+.. option:: selection_factor
+ 
+    f such that the number of determinants to add is f * N_det * sqrt(N_states)
+ 
+    Default: 1.
+ 
 .. option:: thresh_sym
  
     Thresholds to check if a determinant is connected with HF
@@ -3638,7 +3650,7 @@ Providers
 
        * :c:data:`c0_weight`
        * :c:data:`n_states`
-       * :c:data:`used_weight`
+       * :c:data:`weight_one_e_dm`
 
     Needed by:
 
@@ -3648,6 +3660,7 @@ Providers
        * :c:data:`det_alpha_norm`
        * :c:data:`one_e_dm_mo_alpha_average`
        * :c:data:`psi_average_norm_contrib`
+       * :c:data:`selection_weight`
 
  
 .. c:var:: weight_occ_pattern

docs/source/modules/dft_utils_in_r.rst

@@ -199,6 +199,70 @@ Providers
        * :c:data:`potential_xc_alpha_ao_sr_lda`
 
  
+.. c:var:: aos_in_r_array_per_atom
+
+
+    File : :file:`dft_utils_in_r/ao_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: aos_in_r_array_per_atom	(ao_num,n_pts_max_per_atom,nucl_num)
+        double precision, allocatable	:: aos_in_r_array_per_atom_transp	(n_pts_max_per_atom,ao_num,nucl_num)
+
+
+    aos_in_r_array_per_atom(i,j,k)        = value of the ith ao on the jth grid point attached on the kth atom
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_coef_normalized_ordered_transp_per_nucl`
+       * :c:data:`ao_expo_ordered_transp_per_nucl`
+       * :c:data:`ao_num`
+       * :c:data:`ao_power_ordered_transp_per_nucl`
+       * :c:data:`ao_prim_num`
+       * :c:data:`final_grid_points_per_atom`
+       * :c:data:`n_pts_per_atom`
+       * :c:data:`nucl_aos_transposed`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_n_aos`
+       * :c:data:`nucl_num`
+
+
+ 
+.. c:var:: aos_in_r_array_per_atom_transp
+
+
+    File : :file:`dft_utils_in_r/ao_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: aos_in_r_array_per_atom	(ao_num,n_pts_max_per_atom,nucl_num)
+        double precision, allocatable	:: aos_in_r_array_per_atom_transp	(n_pts_max_per_atom,ao_num,nucl_num)
+
+
+    aos_in_r_array_per_atom(i,j,k)        = value of the ith ao on the jth grid point attached on the kth atom
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_coef_normalized_ordered_transp_per_nucl`
+       * :c:data:`ao_expo_ordered_transp_per_nucl`
+       * :c:data:`ao_num`
+       * :c:data:`ao_power_ordered_transp_per_nucl`
+       * :c:data:`ao_prim_num`
+       * :c:data:`final_grid_points_per_atom`
+       * :c:data:`n_pts_per_atom`
+       * :c:data:`nucl_aos_transposed`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_n_aos`
+       * :c:data:`nucl_num`
+
+
+ 
 .. c:var:: aos_in_r_array_transp
 
 

docs/source/modules/ezfio_files.rst

@@ -146,6 +146,7 @@ Providers
        * :c:data:`read_wf`
        * :c:data:`s2_eig`
        * :c:data:`scf_algorithm`
+       * :c:data:`selection_factor`
        * :c:data:`state_following`
        * :c:data:`target_energy`
        * :c:data:`thresh_scf`
@@ -153,8 +154,9 @@ Providers
        * :c:data:`threshold_davidson`
        * :c:data:`threshold_diis`
        * :c:data:`threshold_generators`
-       * :c:data:`used_weight`
        * :c:data:`variance_max`
+       * :c:data:`weight_one_e_dm`
+       * :c:data:`weight_selection`
 
  
 .. c:var:: ezfio_work_dir
@@ -296,6 +298,7 @@ Providers
        * :c:data:`read_wf`
        * :c:data:`s2_eig`
        * :c:data:`scf_algorithm`
+       * :c:data:`selection_factor`
        * :c:data:`state_following`
        * :c:data:`target_energy`
        * :c:data:`thresh_scf`
@@ -303,8 +306,9 @@ Providers
        * :c:data:`threshold_davidson`
        * :c:data:`threshold_diis`
        * :c:data:`threshold_generators`
-       * :c:data:`used_weight`
        * :c:data:`variance_max`
+       * :c:data:`weight_one_e_dm`
+       * :c:data:`weight_selection`
 
  
 .. c:var:: output_wall_time_0
@@ -411,6 +415,7 @@ Providers
        * :c:data:`read_wf`
        * :c:data:`s2_eig`
        * :c:data:`scf_algorithm`
+       * :c:data:`selection_factor`
        * :c:data:`state_following`
        * :c:data:`target_energy`
        * :c:data:`thresh_scf`
@@ -418,8 +423,9 @@ Providers
        * :c:data:`threshold_davidson`
        * :c:data:`threshold_diis`
        * :c:data:`threshold_generators`
-       * :c:data:`used_weight`
        * :c:data:`variance_max`
+       * :c:data:`weight_one_e_dm`
+       * :c:data:`weight_selection`
 
  
 .. c:var:: qp_kill_filename
@@ -764,6 +770,7 @@ Subroutines / functions
        * :c:func:`roothaan_hall_scf`
        * :c:data:`s2_eig`
        * :c:data:`scf_algorithm`
+       * :c:data:`selection_factor`
        * :c:data:`state_following`
        * :c:data:`target_energy`
        * :c:data:`thresh_scf`
@@ -771,8 +778,9 @@ Subroutines / functions
        * :c:data:`threshold_davidson`
        * :c:data:`threshold_diis`
        * :c:data:`threshold_generators`
-       * :c:data:`used_weight`
        * :c:data:`variance_max`
+       * :c:data:`weight_one_e_dm`
+       * :c:data:`weight_selection`
 
     Calls:
 

docs/source/modules/iterations.rst

@@ -160,6 +160,13 @@ Subroutines / functions
        * :c:func:`run_cipsi`
        * :c:func:`run_stochastic_cipsi`
 
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`print_energy_components`
+
  
 .. c:function:: save_iterations:
 

docs/source/modules/mpi.rst

@@ -174,6 +174,7 @@ Providers
        * :c:data:`read_wf`
        * :c:data:`s2_eig`
        * :c:data:`scf_algorithm`
+       * :c:data:`selection_factor`
        * :c:data:`state_following`
        * :c:data:`target_energy`
        * :c:data:`thresh_scf`
@@ -181,8 +182,9 @@ Providers
        * :c:data:`threshold_davidson`
        * :c:data:`threshold_diis`
        * :c:data:`threshold_generators`
-       * :c:data:`used_weight`
        * :c:data:`variance_max`
+       * :c:data:`weight_one_e_dm`
+       * :c:data:`weight_selection`
 
  
 .. c:var:: mpi_rank

docs/source/programmers_guide/index_providers.rst

@@ -103,6 +103,8 @@ Index of Providers
     * :c:data:`aos_grad_in_r_array_transp` 
     * :c:data:`aos_grad_in_r_array_transp_xyz` 
     * :c:data:`aos_in_r_array` 
+    * :c:data:`aos_in_r_array_per_atom` 
+    * :c:data:`aos_in_r_array_per_atom_transp` 
     * :c:data:`aos_in_r_array_transp` 
     * :c:data:`aos_lapl_in_r_array` 
     * :c:data:`aos_lapl_in_r_array_transp` 
@@ -251,8 +253,10 @@ Index of Providers
     * :c:data:`fact_inv` 
     * :c:data:`file_lock` 
     * :c:data:`final_grid_points` 
+    * :c:data:`final_grid_points_per_atom` 
     * :c:data:`final_weight_at_r` 
     * :c:data:`final_weight_at_r_vector` 
+    * :c:data:`final_weight_at_r_vector_per_atom` 
     * :c:data:`fock_matrix_alpha_no_xc_ao` 
     * :c:data:`fock_matrix_ao` 
     * :c:data:`fock_matrix_ao_alpha` 
@@ -282,6 +286,7 @@ Index of Providers
     * :c:data:`give_polynomial_mult_center_one_e_erf_opt` 
     * :c:data:`global_selection_buffer` 
     * :c:data:`global_selection_buffer_lock` 
+    * :c:data:`grid_atomic_number` 
     * :c:data:`grid_points_per_atom` 
     * :c:data:`grid_points_radial` 
     * :c:data:`grid_type_sgn` 
@@ -313,6 +318,8 @@ Index of Providers
     * :c:data:`inact_bitmask` 
     * :c:data:`inact_virt_bitmask` 
     * :c:data:`index_final_points` 
+    * :c:data:`index_final_points_per_atom` 
+    * :c:data:`index_final_points_per_atom_reverse` 
     * :c:data:`index_final_points_reverse` 
     * :c:data:`index_holes_bitmask` 
     * :c:data:`index_particl_bitmask` 
@@ -460,6 +467,8 @@ Index of Providers
     * :c:data:`n_points_radial_grid` 
     * :c:data:`n_pt_max_i_x` 
     * :c:data:`n_pt_max_integrals` 
+    * :c:data:`n_pts_max_per_atom` 
+    * :c:data:`n_pts_per_atom` 
     * :c:data:`n_single_exc_bitmasks` 
     * :c:data:`n_states` 
     * :c:data:`n_states_diag` 
@@ -754,6 +763,7 @@ Index of Providers
     * :c:data:`selection_criterion` 
     * :c:data:`selection_criterion_factor` 
     * :c:data:`selection_criterion_min` 
+    * :c:data:`selection_factor` 
     * :c:data:`selection_weight` 
     * :c:data:`short_range_hartree` 
     * :c:data:`short_range_hartree_operator` 
@@ -775,6 +785,7 @@ Index of Providers
     * :c:data:`state_following` 
     * :c:data:`target_energy` 
     * :c:data:`theta_angular_integration_lebedev` 
+    * :c:data:`thresh_grid` 
     * :c:data:`thresh_scf` 
     * :c:data:`thresh_sym` 
     * :c:data:`threshold_davidson` 
@@ -792,11 +803,14 @@ Index of Providers
     * :c:data:`unpaired_alpha_electrons` 
     * :c:data:`used_weight` 
     * :c:data:`var_pt2_ratio` 
+    * :c:data:`variance_match_weight` 
     * :c:data:`variance_max` 
     * :c:data:`virt_bitmask` 
     * :c:data:`virt_bitmask_4` 
     * :c:data:`weight_at_r` 
     * :c:data:`weight_occ_pattern` 
+    * :c:data:`weight_one_e_dm` 
+    * :c:data:`weight_selection` 
     * :c:data:`weights_angular_integration_lebedev` 
     * :c:data:`weights_angular_points` 
     * :c:data:`write_ao_integrals_e_n` 
@@ -1033,6 +1047,8 @@ Index of Subroutines/Functions
     * :c:func:`get_ao_two_e_integrals_erf` 
     * :c:func:`get_ao_two_e_integrals_erf_non_zero` 
     * :c:func:`get_ao_two_e_integrals_non_zero` 
+    * :c:func:`get_ao_two_e_integrals_non_zero_jl` 
+    * :c:func:`get_ao_two_e_integrals_non_zero_jl_from_list` 
     * :c:func:`get_d0` 
     * :c:func:`get_d1` 
     * :c:func:`get_d2` 
@@ -1280,6 +1296,7 @@ Index of Subroutines/Functions
     * :c:func:`print_ci_vectors` 
     * :c:func:`print_det` 
     * :c:func:`print_e_conv` 
+    * :c:func:`print_energy_components` 
     * :c:func:`print_extrapolated_energy` 
     * :c:func:`print_generators_bitmasks_holes` 
     * :c:func:`print_generators_bitmasks_holes_for_one_generator` 
@@ -1418,6 +1435,7 @@ Index of Subroutines/Functions
     * :c:func:`u_0_s2_u_0` 
     * :c:func:`u_dot_u` 
     * :c:func:`u_dot_v` 
+    * :c:func:`update_pt2_and_variance_weights` 
     * :c:func:`v_e_n` 
     * :c:func:`v_grad_rho_oc_to_v_grad_rho_ab` 
     * :c:func:`v_phi` 

docs/source/programs/fci.rst

@@ -89,5 +89,7 @@ fci
     * :c:data:`pt2_match_weight` 
     * :c:data:`pt2_stoch_istate` 
     * :c:data:`read_wf` 
+    * :c:data:`selection_weight` 
     * :c:data:`state_average_weight` 
     * :c:data:`threshold_generators` 
+    * :c:data:`variance_match_weight` 

docs/source/programs/pt2.rst

@@ -55,5 +55,6 @@ pt2
     * :c:data:`pt2_e0_denominator` 
     * :c:data:`pt2_stoch_istate` 
     * :c:data:`read_wf` 
+    * :c:data:`selection_weight` 
     * :c:data:`state_average_weight` 
     * :c:data:`threshold_generators` 

docs/source/programs/rotate_mos.rst

@@ -0,0 +1,37 @@
+.. _rotate_mos: 
+ 
+.. program:: rotate_mos 
+ 
+========== 
+rotate_mos 
+========== 
+ 
+ 
+ 
+ 
+ Rotates molecular orbitals i and j by combining them as 
+ $1/\sqrt{2} ( \phi_i + \phi_j )$ and 
+ $1/\sqrt{2} ( \phi_i - \phi_j )$. 
+ 
+ Needs: 
+ 
+ .. hlist:: 
+    :columns: 3 
+ 
+    * :c:data:`ao_num` 
+    * :c:data:`mo_num` 
+    * :c:data:`mo_coef` 
+ 
+ Calls: 
+ 
+ .. hlist:: 
+    :columns: 3 
+ 
+    * :c:func:`save_mos` 
+ 
+ Touches: 
+ 
+ .. hlist:: 
+    :columns: 3 
+ 
+    * :c:data:`mo_coef` 

docs/source/programs/sort_by_fock_energies.rst

@@ -0,0 +1,39 @@
+.. _sort_by_fock_energies: 
+ 
+.. program:: sort_by_fock_energies 
+ 
+===================== 
+sort_by_fock_energies 
+===================== 
+ 
+ 
+ 
+ 
+ Program that saves the current |MOs| ordered by diagonal element of the Fock operator. 
+  
+ Warning : the Fock operator, and therefore its matrix elements, depends on the occupancy. 
+ 
+ Needs: 
+ 
+ .. hlist:: 
+    :columns: 3 
+ 
+    * :c:data:`fock_matrix_mo` 
+    * :c:data:`ao_num` 
+    * :c:data:`mo_num` 
+    * :c:data:`mo_coef` 
+ 
+ Calls: 
+ 
+ .. hlist:: 
+    :columns: 3 
+ 
+    * :c:func:`dsort` 
+    * :c:func:`save_mos` 
+ 
+ Touches: 
+ 
+ .. hlist:: 
+    :columns: 3 
+ 
+    * :c:data:`mo_coef` 

docs/source/programs/swap_mos.rst

@@ -0,0 +1,27 @@
+.. _swap_mos: 
+ 
+.. program:: swap_mos 
+ 
+======== 
+swap_mos 
+======== 
+ 
+ 
+ 
+ 
+ Swaps the indices of two molecular orbitals 
+ 
+ Needs: 
+ 
+ .. hlist:: 
+    :columns: 3 
+ 
+    * :c:data:`ao_num` 
+    * :c:data:`mo_coef` 
+ 
+ Calls: 
+ 
+ .. hlist:: 
+    :columns: 3 
+ 
+    * :c:func:`save_mos` 

docs/source/programs/test.rst

@@ -0,0 +1,19 @@
+.. _test: 
+ 
+.. program:: test 
+ 
+==== 
+test 
+==== 
+ 
+ 
+ 
+ 
+ 
+ Calls: 
+ 
+ .. hlist:: 
+    :columns: 3 
+ 
+    * :c:func:`two_e_integrals_index` 
+    * :c:func:`two_e_integrals_index_reverse` 

man/cis.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "CIS" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "CIS" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 cis \-  | Quantum Package >
 .

man/cisd.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "CISD" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "CISD" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 cisd \-  | Quantum Package >
 .

man/configure.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "CONFIGURE" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "CONFIGURE" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 configure \-  | Quantum Package >
 .

man/diagonalize_h.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "DIAGONALIZE_H" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "DIAGONALIZE_H" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 diagonalize_h \-  | Quantum Package >
 .

man/excited_states.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "EXCITED_STATES" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "EXCITED_STATES" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 excited_states \-  | Quantum Package >
 .

man/fci.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "FCI" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "FCI" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 fci \-  | Quantum Package >
 .
@@ -125,10 +125,10 @@ Touches:
 \fBpsi_occ_pattern\fP
 .IP \(bu 2
 \fBc0_weight\fP
-.UNINDENT
-.INDENT 2.0
 .IP \(bu 2
 \fBdistributed_davidson\fP
+.UNINDENT
+.INDENT 2.0
 .IP \(bu 2
 \fBpsi_coef\fP
 .IP \(bu 2
@@ -143,10 +143,10 @@ Touches:
 \fBpsi_energy\fP
 .IP \(bu 2
 \fBpsi_occ_pattern\fP
-.UNINDENT
-.INDENT 2.0
 .IP \(bu 2
 \fBpsi_energy\fP
+.UNINDENT
+.INDENT 2.0
 .IP \(bu 2
 \fBpt2_e0_denominator\fP
 .IP \(bu 2
@@ -156,9 +156,13 @@ Touches:
 .IP \(bu 2
 \fBread_wf\fP
 .IP \(bu 2
+\fBselection_weight\fP
+.IP \(bu 2
 \fBstate_average_weight\fP
 .IP \(bu 2
 \fBthreshold_generators\fP
+.IP \(bu 2
+\fBvariance_match_weight\fP
 .UNINDENT
 .UNINDENT
 .UNINDENT

man/fcidump.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "FCIDUMP" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "FCIDUMP" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 fcidump \-  | Quantum Package >
 .

man/four_idx_transform.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "FOUR_IDX_TRANSFORM" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "FOUR_IDX_TRANSFORM" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 four_idx_transform \-  | Quantum Package >
 .

man/interfaces.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "INTERFACES" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "INTERFACES" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 interfaces \-  | Quantum Package >
 .

man/ks_scf.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "KS_SCF" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "KS_SCF" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 ks_scf \-  | Quantum Package >
 .

man/molden.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "MOLDEN" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "MOLDEN" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 molden \-  | Quantum Package >
 .

man/natural_orbitals.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "NATURAL_ORBITALS" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "NATURAL_ORBITALS" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 natural_orbitals \-  | Quantum Package >
 .

man/plugins.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "PLUGINS" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "PLUGINS" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 plugins \-  | Quantum Package >
 .

man/print_ci_vectors.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "PRINT_CI_VECTORS" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "PRINT_CI_VECTORS" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 print_ci_vectors \-  | Quantum Package >
 .

man/print_e_conv.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "PRINT_E_CONV" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "PRINT_E_CONV" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 print_e_conv \-  | Quantum Package >
 .

man/print_wf.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "PRINT_WF" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "PRINT_WF" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 print_wf \-  | Quantum Package >
 .

man/printing.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "PRINTING" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "PRINTING" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 printing \-  | Quantum Package >
 .

man/pt2.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "PT2" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "PT2" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 pt2 \-  | Quantum Package >
 .
@@ -104,6 +104,8 @@ Touches:
 .IP \(bu 2
 \fBread_wf\fP
 .IP \(bu 2
+\fBselection_weight\fP
+.IP \(bu 2
 \fBstate_average_weight\fP
 .IP \(bu 2
 \fBthreshold_generators\fP

man/qp_convert_output_to_ezfio.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_CONVERT_OUTPUT_TO_EZFIO" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QP_CONVERT_OUTPUT_TO_EZFIO" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_convert_output_to_ezfio \-  | Quantum Package >
 .

man/qp_create_ezfio.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_CREATE_EZFIO" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QP_CREATE_EZFIO" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_create_ezfio \-  | Quantum Package >
 .

man/qp_edit.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_EDIT" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QP_EDIT" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_edit \-  | Quantum Package >
 .

man/qp_export_as_tgz.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_EXPORT_AS_TGZ" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QP_EXPORT_AS_TGZ" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_export_as_tgz \-  | Quantum Package >
 .

man/qp_plugins.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_PLUGINS" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QP_PLUGINS" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_plugins \-  | Quantum Package >
 .

man/qp_reset.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_RESET" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QP_RESET" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_reset \-  | Quantum Package >
 .

man/qp_run.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_RUN" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QP_RUN" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_run \-  | Quantum Package >
 .

man/qp_set_frozen_core.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_SET_FROZEN_CORE" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QP_SET_FROZEN_CORE" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_set_frozen_core \-  | Quantum Package >
 .

man/qp_set_mo_class.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_SET_MO_CLASS" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QP_SET_MO_CLASS" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_set_mo_class \-  | Quantum Package >
 .

man/qp_stop.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_STOP" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QP_STOP" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_stop \-  | Quantum Package >
 .

man/qp_update.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QP_UPDATE" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QP_UPDATE" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qp_update \-  | Quantum Package >
 .

man/qpsh.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "QPSH" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "QPSH" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 qpsh \-  | Quantum Package >
 .

man/rotate_mos.1

@@ -0,0 +1,85 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "ROTATE_MOS" "1" "Jun 15, 2019" "2.0" "Quantum Package"
+.SH NAME
+rotate_mos \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.INDENT 0.0
+.INDENT 3.5
+Rotates molecular orbitals i and j by combining them as
+$1/sqrt{2} ( phi_i + phi_j )$ and
+$1/sqrt{2} ( phi_i \- phi_j )$.
+.sp
+Needs:
+.INDENT 0.0
+.INDENT 2.0
+.IP \(bu 2
+\fBao_num\fP
+.UNINDENT
+.INDENT 2.0
+.IP \(bu 2
+\fBmo_num\fP
+.UNINDENT
+.INDENT 2.0
+.IP \(bu 2
+\fBmo_coef\fP
+.UNINDENT
+.UNINDENT
+.sp
+Calls:
+.INDENT 0.0
+.INDENT 2.0
+.IP \(bu 2
+\fBsave_mos()\fP
+.UNINDENT
+.INDENT 2.0
+.UNINDENT
+.INDENT 2.0
+.UNINDENT
+.UNINDENT
+.sp
+Touches:
+.INDENT 0.0
+.INDENT 2.0
+.IP \(bu 2
+\fBmo_coef\fP
+.UNINDENT
+.INDENT 2.0
+.UNINDENT
+.INDENT 2.0
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2019, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.

man/rs_ks_scf.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "RS_KS_SCF" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "RS_KS_SCF" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 rs_ks_scf \-  | Quantum Package >
 .

man/save_natorb.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "SAVE_NATORB" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "SAVE_NATORB" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 save_natorb \-  | Quantum Package >
 .

man/save_one_e_dm.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "SAVE_ONE_E_DM" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "SAVE_ONE_E_DM" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 save_one_e_dm \-  | Quantum Package >
 .

man/save_ortho_mos.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "SAVE_ORTHO_MOS" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "SAVE_ORTHO_MOS" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 save_ortho_mos \-  | Quantum Package >
 .

man/scf.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "SCF" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "SCF" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 scf \-  | Quantum Package >
 .

man/sort_by_fock_energies.1

@@ -0,0 +1,89 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "SORT_BY_FOCK_ENERGIES" "1" "Jun 15, 2019" "2.0" "Quantum Package"
+.SH NAME
+sort_by_fock_energies \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.INDENT 0.0
+.INDENT 3.5
+Program that saves the current MOs ordered by diagonal element of the Fock operator.
+.sp
+Warning : the Fock operator, and therefore its matrix elements, depends on the occupancy.
+.sp
+Needs:
+.INDENT 0.0
+.INDENT 2.0
+.IP \(bu 2
+\fBfock_matrix_mo\fP
+.IP \(bu 2
+\fBao_num\fP
+.UNINDENT
+.INDENT 2.0
+.IP \(bu 2
+\fBmo_num\fP
+.UNINDENT
+.INDENT 2.0
+.IP \(bu 2
+\fBmo_coef\fP
+.UNINDENT
+.UNINDENT
+.sp
+Calls:
+.INDENT 0.0
+.INDENT 2.0
+.IP \(bu 2
+\fBdsort()\fP
+.UNINDENT
+.INDENT 2.0
+.IP \(bu 2
+\fBsave_mos()\fP
+.UNINDENT
+.INDENT 2.0
+.UNINDENT
+.UNINDENT
+.sp
+Touches:
+.INDENT 0.0
+.INDENT 2.0
+.IP \(bu 2
+\fBmo_coef\fP
+.UNINDENT
+.INDENT 2.0
+.UNINDENT
+.INDENT 2.0
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2019, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.

man/swap_mos.1

@@ -0,0 +1,69 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "SWAP_MOS" "1" "Jun 15, 2019" "2.0" "Quantum Package"
+.SH NAME
+swap_mos \-  | Quantum Package >
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.INDENT 0.0
+.INDENT 3.5
+Swaps the indices of two molecular orbitals
+.sp
+Needs:
+.INDENT 0.0
+.INDENT 2.0
+.IP \(bu 2
+\fBao_num\fP
+.UNINDENT
+.INDENT 2.0
+.IP \(bu 2
+\fBmo_coef\fP
+.UNINDENT
+.INDENT 2.0
+.UNINDENT
+.UNINDENT
+.sp
+Calls:
+.INDENT 0.0
+.INDENT 2.0
+.IP \(bu 2
+\fBsave_mos()\fP
+.UNINDENT
+.INDENT 2.0
+.UNINDENT
+.INDENT 2.0
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.UNINDENT
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2019, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.

man/write_integrals_erf.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "WRITE_INTEGRALS_ERF" "1" "May 28, 2019" "2.0" "Quantum Package"
+.TH "WRITE_INTEGRALS_ERF" "1" "Jun 15, 2019" "2.0" "Quantum Package"
 .SH NAME
 write_integrals_erf \-  | Quantum Package >
 .

src/tools/rotate_mos.irp.f

@@ -1,17 +1,26 @@
 program rotate_mos
   implicit none
+  BEGIN_DOC
+  ! Rotates molecular orbitals i and j by combining them as
+  ! $1/\sqrt{2} ( \phi_i + \phi_j )$ and
+  ! $1/\sqrt{2} ( \phi_i - \phi_j )$.
+  END_DOC
   integer                        :: iorb,jorb
- read(5,*)iorb,jorb
- double precision, allocatable :: mo_coef_tmp(:,:)
- allocate(mo_coef_tmp(ao_num,mo_num))
- mo_coef_tmp = mo_coef
   integer                        :: i,j
   double precision               :: dsqrt2_inv
+  double precision, allocatable  :: mo_coef_tmp(:,:)
+
+  read(5,*)iorb,jorb
+
+  allocate(mo_coef_tmp(ao_num,mo_num))
+  mo_coef_tmp = mo_coef
+
   dsqrt2_inv = 1.d0/dsqrt(2.d0)
   do i = 1, ao_num
     mo_coef(i,iorb) = dsqrt2_inv * ( mo_coef_tmp(i,iorb) + mo_coef_tmp(i,jorb) )
     mo_coef(i,jorb) = dsqrt2_inv * ( mo_coef_tmp(i,iorb) - mo_coef_tmp(i,jorb) )
   enddo
+
   touch mo_coef
   call save_mos
   

src/tools/sort_by_fock_energies.irp.f

@@ -1,23 +1,28 @@
 program sort_by_fock_energies
   BEGIN_DOC
-! programs that save the current mos ordered by Diagonal element of the Fock operator. 
+  ! Program that saves the current |MOs| ordered by diagonal element of the Fock operator.
-!
+  !
-! Warning : the Fock operator, and therefore its matrix elements, depends on the occupancy. 
+  ! Warning : the Fock operator, and therefore its matrix elements, depends on the occupancy.
   END_DOC
   implicit none
   integer                        :: i,j,k
   integer, allocatable           :: iorder(:)
   double precision, allocatable  :: fock_energies_tmp(:), new_mo_coef(:,:)
+
   allocate(iorder(mo_num), fock_energies_tmp(mo_num),new_mo_coef(ao_num,mo_num))
+
   do i = 1, mo_num
     fock_energies_tmp(i) = Fock_matrix_diag_mo(i)
     print*,'fock_energies_tmp(i) = ',fock_energies_tmp(i)
     iorder(i) = i
   enddo
+
   print*,''
   print*,'Sorting by Fock energies'
   print*,''
+
   call dsort(fock_energies_tmp,iorder,mo_num)
+
   do i = 1, mo_num
     k = iorder(i)
     print*,'fock_energies_new(i) = ',fock_energies_tmp(i)
@@ -25,6 +30,7 @@ program sort_by_fock_energies
       new_mo_coef(j,i) = mo_coef(j,k)
     enddo
   enddo
+
   mo_coef = new_mo_coef
   touch mo_coef
   call save_mos

src/tools/swap_mos.irp.f

@@ -1,5 +1,8 @@
 program swap_mos
   implicit none
+  BEGIN_DOC
+  ! Swaps the indices of two molecular orbitals
+  END_DOC
   integer                        :: i,j, i1, i2
   double precision               :: x
   print *,  'MOs to swap?'