Forgot files

docs/source/modules/ao_two_e_erf_ints.rst

@@ -0,0 +1,905 @@
+.. _module_ao_two_e_erf_ints: 
+ 
+.. program:: ao_two_e_erf_ints 
+ 
+.. default-role:: option 
+ 
+======================
+ao_two_e_erf_ints
+======================
+
+Here, all two-electron integrals (:math:`erf(\mu r_{12})/r_{12}`) are computed.
+As they have 4 indices and many are zero, they are stored in a map, as defined
+in :file:`utils/map_module.f90`.
+
+The main parameter of this module is :option:`ao_two_e_erf_ints mu_erf` which is the range-separation parameter.
+
+To fetch an |AO| integral, use the
+`get_ao_two_e_integral_erf(i,j,k,l,ao_integrals_erf_map)` function.
+
+
+The conventions are:
+* For |AO| integrals : (ij|kl) = (11|22) = <ik|jl> = <12|12>
+
+
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: io_ao_two_e_integrals_erf
+ 
+    Read/Write |AO| integrals with the long range interaction from/to disk [ Write | Read | None ]
+ 
+    Default: None
+ 
+.. option:: mu_erf
+ 
+    cutting of the interaction in the range separated model
+ 
+    Default: 0.5
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: ao_integrals_erf_cache
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: ao_integrals_erf_cache	(0:64*64*64*64)
+
+
+    Cache of |AO| integrals for fast access
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_cache_min`
+       * :c:data:`ao_integrals_erf_map`
+       * :c:data:`ao_two_e_integrals_erf_in_map`
+
+
+ 
+.. c:var:: ao_integrals_erf_cache_max
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        integer	:: ao_integrals_erf_cache_min	
+        integer	:: ao_integrals_erf_cache_max	
+
+
+    Min and max values of the AOs for which the integrals are in the cache
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_cache`
+
+ 
+.. c:var:: ao_integrals_erf_cache_min
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        integer	:: ao_integrals_erf_cache_min	
+        integer	:: ao_integrals_erf_cache_max	
+
+
+    Min and max values of the AOs for which the integrals are in the cache
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_cache`
+
+ 
+.. c:var:: ao_integrals_erf_map
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        type(map_type)	:: ao_integrals_erf_map	
+
+
+    |AO| integrals
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_cache`
+       * :c:data:`ao_two_e_integrals_erf_in_map`
+       * :c:data:`mo_two_e_int_erf_jj_from_ao`
+
+ 
+.. c:var:: ao_two_e_integral_erf_schwartz
+
+
+    File : :file:`ao_two_e_erf_ints/providers_ao_erf.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: ao_two_e_integral_erf_schwartz	(ao_num,ao_num)
+
+
+    Needed to compute Schwartz inequalities
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_coef_normalized_ordered_transp`
+       * :c:data:`ao_expo_ordered_transp`
+       * :c:data:`ao_nucl`
+       * :c:data:`ao_num`
+       * :c:data:`ao_power`
+       * :c:data:`ao_prim_num`
+       * :c:data:`n_pt_max_integrals`
+       * :c:data:`nucl_coord`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_two_e_int_erf_jj_from_ao`
+
+ 
+.. c:var:: ao_two_e_integrals_erf_in_map
+
+
+    File : :file:`ao_two_e_erf_ints/providers_ao_erf.irp.f`
+
+    .. code:: fortran
+
+        logical	:: ao_two_e_integrals_erf_in_map	
+
+
+    Map of Atomic integrals
+       i(r1) j(r2) 1/r12 k(r1) l(r2)
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_coef_normalized_ordered_transp`
+       * :c:data:`ao_expo_ordered_transp`
+       * :c:data:`ao_integrals_erf_map`
+       * :c:data:`ao_nucl`
+       * :c:data:`ao_num`
+       * :c:data:`ao_power`
+       * :c:data:`ao_prim_num`
+       * :c:data:`ezfio_filename`
+       * :c:data:`io_ao_two_e_integrals_erf`
+       * :c:data:`n_pt_max_integrals`
+       * :c:data:`nproc`
+       * :c:data:`nucl_coord`
+       * :c:data:`read_ao_two_e_integrals_erf`
+       * :c:data:`zmq_context`
+       * :c:data:`zmq_socket_pull_tcp_address`
+       * :c:data:`zmq_state`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_cache`
+       * :c:data:`mo_two_e_int_erf_jj_from_ao`
+       * :c:data:`mo_two_e_integrals_erf_in_map`
+
+ 
+.. c:function:: general_primitive_integral_erf:
+
+
+    File : :file:`ao_two_e_erf_ints/two_e_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        double precision function general_primitive_integral_erf(dim,            &
+      P_new,P_center,fact_p,p,p_inv,iorder_p,                        &
+      Q_new,Q_center,fact_q,q,q_inv,iorder_q)
+
+
+    Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mu_erf`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`add_poly_multiply`
+       * :c:func:`give_polynom_mult_center_x`
+       * :c:func:`multiply_poly`
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: ao_two_e_integral_erf:
+
+
+    File : :file:`ao_two_e_erf_ints/two_e_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        double precision function ao_two_e_integral_erf(i,j,k,l)
+
+
+    integral of the AO basis <ik|jl> or (ij|kl)
+       i(r1) j(r1) 1/r12 k(r2) l(r2)
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_pt_max_integrals`
+       * :c:data:`ao_coef_normalized_ordered_transp`
+       * :c:data:`ao_power`
+       * :c:data:`ao_expo_ordered_transp`
+       * :c:data:`ao_prim_num`
+       * :c:data:`ao_nucl`
+       * :c:data:`nucl_coord`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`give_explicit_poly_and_gaussian`
+
+ 
+.. c:function:: ao_two_e_integral_schwartz_accel_erf:
+
+
+    File : :file:`ao_two_e_erf_ints/two_e_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        double precision function ao_two_e_integral_schwartz_accel_erf(i,j,k,l)
+
+
+    integral of the AO basis <ik|jl> or (ij|kl)
+       i(r1) j(r1) 1/r12 k(r2) l(r2)
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_pt_max_integrals`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_coef_normalized_ordered_transp`
+       * :c:data:`ao_power`
+       * :c:data:`ao_expo_ordered_transp`
+       * :c:data:`ao_prim_num`
+       * :c:data:`ao_nucl`
+       * :c:data:`nucl_coord`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`give_explicit_poly_and_gaussian`
+
+ 
+.. c:function:: ao_two_e_integrals_erf_in_map_collector:
+
+
+    File : :file:`ao_two_e_erf_ints/integrals_erf_in_map_slave.irp.f`
+
+    .. code:: fortran
+
+        subroutine ao_two_e_integrals_erf_in_map_collector(zmq_socket_pull)
+
+
+    Collects results from the AO integral calculation
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_map`
+       * :c:data:`ao_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_two_e_integrals_erf_in_map`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`end_zmq_to_qp_run_socket`
+       * :c:func:`insert_into_ao_integrals_erf_map`
+
+ 
+.. c:function:: ao_two_e_integrals_erf_in_map_slave:
+
+
+    File : :file:`ao_two_e_erf_ints/integrals_erf_in_map_slave.irp.f`
+
+    .. code:: fortran
+
+        subroutine ao_two_e_integrals_erf_in_map_slave(thread,iproc)
+
+
+    Computes a buffer of integrals
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ao_two_e_integrals_erf_in_map_slave_inproc`
+       * :c:func:`ao_two_e_integrals_erf_in_map_slave_tcp`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`compute_ao_integrals_erf_jl`
+       * :c:func:`end_zmq_push_socket`
+       * :c:func:`end_zmq_to_qp_run_socket`
+       * :c:func:`push_integrals`
+
+ 
+.. c:function:: ao_two_e_integrals_erf_in_map_slave_inproc:
+
+
+    File : :file:`ao_two_e_erf_ints/integrals_erf_in_map_slave.irp.f`
+
+    .. code:: fortran
+
+        subroutine ao_two_e_integrals_erf_in_map_slave_inproc(i)
+
+
+    Computes a buffer of integrals. i is the ID of the current thread.
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_two_e_integrals_erf_in_map`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ao_two_e_integrals_erf_in_map_slave`
+
+ 
+.. c:function:: ao_two_e_integrals_erf_in_map_slave_tcp:
+
+
+    File : :file:`ao_two_e_erf_ints/integrals_erf_in_map_slave.irp.f`
+
+    .. code:: fortran
+
+        subroutine ao_two_e_integrals_erf_in_map_slave_tcp(i)
+
+
+    Computes a buffer of integrals. i is the ID of the current thread.
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ao_two_e_integrals_erf_in_map_slave`
+
+ 
+.. c:function:: clear_ao_erf_map:
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        subroutine clear_ao_erf_map
+
+
+    Frees the memory of the |AO| map
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_map`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`map_deinit`
+
+ 
+.. c:function:: compute_ao_integrals_erf_jl:
+
+
+    File : :file:`ao_two_e_erf_ints/two_e_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        subroutine compute_ao_integrals_erf_jl(j,l,n_integrals,buffer_i,buffer_value)
+
+
+    Parallel client for AO integrals
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_overlap_abs`
+       * :c:data:`ao_num`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_two_e_integral_erf_schwartz`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ao_two_e_integrals_erf_in_map_slave`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`two_e_integrals_index`
+
+ 
+.. c:function:: compute_ao_two_e_integrals_erf:
+
+
+    File : :file:`ao_two_e_erf_ints/two_e_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        subroutine compute_ao_two_e_integrals_erf(j,k,l,sze,buffer_value)
+
+
+    Compute AO 1/r12 integrals for all i and fixed j,k,l
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_overlap_abs`
+       * :c:data:`ao_num`
+       * :c:data:`ao_two_e_integral_erf_schwartz`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_two_e_int_erf_jj_from_ao`
+
+ 
+.. c:function:: dump_ao_integrals_erf:
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        subroutine dump_ao_integrals_erf(filename)
+
+
+    Save to disk the |AO| erf integrals
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_map`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_set_work_empty`
+
+ 
+.. c:function:: eri_erf:
+
+
+    File : :file:`ao_two_e_erf_ints/two_e_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        double precision function ERI_erf(alpha,beta,delta,gama,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z)
+
+
+    Atomic primtive two-electron integral between the 4 primitives :
+    
+    * primitive 1 : $x_1^{a_x} y_1^{a_y} z_1^{a_z} \exp(-\alpha * r1^2)$
+    * primitive 2 : $x_1^{b_x} y_1^{b_y} z_1^{b_z} \exp(- \beta * r1^2)$
+    * primitive 3 : $x_2^{c_x} y_2^{c_y} z_2^{c_z} \exp(-\delta * r2^2)$
+    * primitive 4 : $x_2^{d_x} y_2^{d_y} z_2^{d_z} \exp(-\gamma * r2^2)$
+    
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mu_erf`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`integrale_new_erf`
+
+ 
+.. c:function:: get_ao_erf_map_size:
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        function get_ao_erf_map_size()
+
+
+    Returns the number of elements in the |AO| map
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_map`
+
+ 
+.. c:function:: get_ao_two_e_integral_erf:
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        double precision function get_ao_two_e_integral_erf(i,j,k,l,map) result(result)
+
+
+    Gets one |AO| two-electron integral from the |AO| map
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_cache_min`
+       * :c:data:`ao_overlap_abs`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_integrals_erf_cache`
+       * :c:data:`ao_two_e_integral_erf_schwartz`
+       * :c:data:`ao_two_e_integrals_erf_in_map`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`map_get`
+       * :c:func:`two_e_integrals_index`
+
+ 
+.. c:function:: get_ao_two_e_integrals_erf:
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        subroutine get_ao_two_e_integrals_erf(j,k,l,sze,out_val)
+
+
+    Gets multiple |AO| two-electron integral from the |AO| map .
+    All i are retrieved for j,k,l fixed.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_map`
+       * :c:data:`ao_overlap_abs`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_two_e_integrals_erf_in_map`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`add_integrals_to_map_erf`
+
+ 
+.. c:function:: get_ao_two_e_integrals_erf_non_zero:
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        subroutine get_ao_two_e_integrals_erf_non_zero(j,k,l,sze,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_erf_map`
+       * :c:data:`ao_overlap_abs`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_two_e_integral_erf_schwartz`
+       * :c:data:`ao_two_e_integrals_erf_in_map`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_two_e_int_erf_jj_from_ao`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`map_get`
+       * :c:func:`two_e_integrals_index`
+
+ 
+.. c:function:: insert_into_ao_integrals_erf_map:
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        subroutine insert_into_ao_integrals_erf_map(n_integrals,buffer_i, buffer_values)
+
+
+    Create new entry into |AO| map
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_map`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ao_two_e_integrals_erf_in_map_collector`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`map_append`
+
+ 
+.. c:function:: integrale_new_erf:
+
+
+    File : :file:`ao_two_e_erf_ints/two_e_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        subroutine integrale_new_erf(I_f,a_x,b_x,c_x,d_x,a_y,b_y,c_y,d_y,a_z,b_z,c_z,d_z,p,q,n_pt)
+
+
+    Calculate the integral of the polynomial :
+    
+    $I_x1(a_x+b_x, c_x+d_x,p,q) \, I_x1(a_y+b_y, c_y+d_y,p,q) \, I_x1(a_z+b_z, c_z+d_z,p,q)$
+    
+    between $( 0 ; 1)$
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mu_erf`
+       * :c:data:`n_pt_max_integrals`
+       * :c:data:`gauleg_t2`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`eri_erf`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`i_x1_new`
+
+ 
+.. c:function:: load_ao_integrals_erf:
+
+
+    File : :file:`ao_two_e_erf_ints/map_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        integer function load_ao_integrals_erf(filename)
+
+
+    Read from disk the |AO| erf integrals
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_map`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`cache_map_reallocate`
+       * :c:func:`map_deinit`
+       * :c:func:`map_sort`
+
+ 
+.. c:function:: save_erf_two_e_integrals_ao:
+
+
+    File : :file:`ao_two_e_erf_ints/routines_save_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        subroutine save_erf_two_e_integrals_ao
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_map`
+       * :c:data:`ezfio_filename`
+       * :c:data:`ao_two_e_integrals_erf_in_map`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`routine`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_set_ao_two_e_erf_ints_io_ao_two_e_integrals_erf`
+       * :c:func:`ezfio_set_work_empty`
+       * :c:func:`map_save_to_disk`
+
+ 
+.. c:function:: save_erf_two_e_ints_ao_into_ints_ao:
+
+
+    File : :file:`ao_two_e_erf_ints/routines_save_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        subroutine save_erf_two_e_ints_ao_into_ints_ao
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_erf_map`
+       * :c:data:`ezfio_filename`
+       * :c:data:`ao_two_e_integrals_erf_in_map`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_set_ao_two_e_ints_io_ao_two_e_integrals`
+       * :c:func:`ezfio_set_work_empty`
+       * :c:func:`map_save_to_disk`
+

docs/source/modules/aux_quantities.rst

@@ -0,0 +1,52 @@
+.. _module_aux_quantities: 
+ 
+.. program:: aux_quantities 
+ 
+.. default-role:: option 
+ 
+==============
+aux_quantities
+==============
+
+
+This module contains some global variables (such as densities and energies)
+which are stored in the EZFIO folder in a different place than determinants.
+This is used in practice to store density matrices which can be obtained from
+any methods, as long as they are stored in the same MO basis which is used for
+the calculations. In |RSDFT| calculations, this can be done to perform damping
+on the density in order to speed up convergence.
+
+The main providers of that module are:
+
+* `data_one_e_dm_alpha_mo` and `data_one_e_dm_beta_mo` which are the
+  one-body alpha and beta densities which are necessary read from the EZFIO
+  folder.
+
+
+Thanks to these providers you can use any density matrix that does not
+necessary corresponds to that of the current wave function.
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: data_energy_var
+ 
+    Variational energy computed with the wave function
+ 
+ 
+.. option:: data_energy_proj
+ 
+    Projected energy computed with the wave function
+ 
+ 
+.. option:: data_one_e_dm_alpha_mo
+ 
+    Alpha one body density matrix on the |MO| basis computed with the wave function
+ 
+ 
+.. option:: data_one_e_dm_beta_mo
+ 
+    Beta one body density matrix on the |MO| basis computed with the wave function
+ 

docs/source/modules/becke_numerical_grid.rst

@@ -0,0 +1,833 @@
+.. _module_becke_numerical_grid: 
+ 
+.. program:: becke_numerical_grid 
+ 
+.. default-role:: option 
+ 
+====================
+becke_numerical_grid
+====================
+
+This module contains all quantities needed to build Becke's grid used in general for DFT integration. Note that it can be used for whatever integration in R^3 as long as the functions to be integrated are mostly concentrated near the atomic regions.
+
+This grid is built as the reunion of a spherical grid around each atom. Each spherical grid contains
+a certain number of radial and angular points. No pruning is done on the angular part of the grid.
+
+The main keyword for that module is:
+
+* :option:`becke_numerical_grid grid_type_sgn` which controls the precision of the grid according the standard **SG-n** grids. This keyword controls the two providers `n_points_integration_angular` `n_points_radial_grid`.
+
+The main providers of that module are:
+
+* `n_points_integration_angular` which is the number of angular integration points. WARNING: it obeys to specific rules so it cannot be any integer number. Some of the possible values are [ 50 | 74 | 170 | 194 | 266 | 302 | 590 | 1202 | 2030 | 5810 ] for instance. See :file:`angular.f` for more details.
+* `n_points_radial_grid` which is the number of radial angular points. This can be any strictly positive integer. Nevertheless, a minimum of 50 is in general necessary.
+* `final_grid_points` which are the (x,y,z) coordinates of the grid points.
+* `final_weight_at_r_vector` which are the weights at each grid point
+
+
+For a simple example of how to use the grid, see :file:`example.irp.f`.
+
+The spherical integration uses Lebedev-Laikov grids, which was used from the code distributed through CCL (http://www.ccl.net/).
+See next section for explanations and citation policies.
+
+.. code-block:: text
+
+       This subroutine is part of a set of subroutines that generate
+       Lebedev grids [1-6] for integration on a sphere. The original
+       C-code [1] was kindly provided by Dr. Dmitri N. Laikov and
+       translated into fortran by Dr. Christoph van Wuellen.
+       This subroutine was translated using a C to fortran77 conversion
+       tool written by Dr. Christoph van Wuellen.
+
+       Users of this code are asked to include reference [1] in their
+       publications, and in the user- and programmers-manuals
+       describing their codes.
+
+       This code was distributed through CCL (http://www.ccl.net/).
+
+       [1] V.I. Lebedev, and D.N. Laikov
+           "A quadrature formula for the sphere of the 131st
+            algebraic order of accuracy"
+           Doklady Mathematics, Vol. 59, No. 3, 1999, pp. 477-481.
+
+       [2] V.I. Lebedev
+           "A quadrature formula for the sphere of 59th algebraic
+            order of accuracy"
+           Russian Acad. Sci. Dokl. Math., Vol. 50, 1995, pp. 283-286.
+
+       [3] V.I. Lebedev, and A.L. Skorokhodov
+           "Quadrature formulas of orders 41, 47, and 53 for the sphere"
+           Russian Acad. Sci. Dokl. Math., Vol. 45, 1992, pp. 587-592.
+
+       [4] V.I. Lebedev
+           "Spherical quadrature formulas exact to orders 25-29"
+           Siberian Mathematical Journal, Vol. 18, 1977, pp. 99-107.
+
+       [5] V.I. Lebedev
+           "Quadratures on a sphere"
+           Computational Mathematics and Mathematical Physics, Vol. 16,
+           1976, pp. 10-24.
+
+       [6] V.I. Lebedev
+           "Values of the nodes and weights of ninth to seventeenth
+            order Gauss-Markov quadrature formulae invariant under the
+            octahedron group with inversion"
+           Computational Mathematics and Mathematical Physics, Vol. 15,
+           1975, pp. 44-51.
+
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: grid_type_sgn
+ 
+    Type of grid used for the Becke's numerical grid. Can be, by increasing accuracy: [ 0 | 1 | 2 | 3 ]
+ 
+    Default: 2
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: alpha_knowles
+
+
+    File : :file:`becke_numerical_grid/integration_radial.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: alpha_knowles	(100)
+
+
+    Recommended values for the alpha parameters according to the paper of Knowles (JCP, 104, 1996)
+    as a function of the nuclear charge
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+
+ 
+.. c:var:: angular_quadrature_points
+
+
+    File : :file:`becke_numerical_grid/grid_becke.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: angular_quadrature_points	(n_points_integration_angular,3)
+        double precision, allocatable	:: weights_angular_points	(n_points_integration_angular)
+
+
+    weights and grid points for the integration on the angular variables on
+    the unit sphere centered on (0,0,0)
+    According to the LEBEDEV scheme
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_points_radial_grid`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+
+ 
+.. c:var:: dr_radial_integral
+
+
+    File : :file:`becke_numerical_grid/grid_becke.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: grid_points_radial	(n_points_radial_grid)
+        double precision	:: dr_radial_integral	
+
+
+    points in [0,1] to map the radial integral [0,\infty]
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_points_radial_grid`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+
+ 
+.. c:var:: final_grid_points
+
+
+    File : :file:`becke_numerical_grid/grid_becke_vector.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: final_grid_points	(3,n_points_final_grid)
+        double precision, allocatable	:: final_weight_at_r_vector	(n_points_final_grid)
+        integer, allocatable	:: index_final_points	(3,n_points_final_grid)
+        integer, allocatable	:: index_final_points_reverse	(n_points_integration_angular,n_points_radial_grid,nucl_num)
+
+
+     final_grid_points(1:3,j) = (/ x, y, z /) of the jth grid point
+    
+    final_weight_at_r_vector(i) = Total weight function of the ith grid point which contains the Lebedev, Voronoi and radial weights contributions
+    
+    index_final_points(1:3,i) = gives the angular, radial and atomic indices associated to the ith grid point
+    
+    index_final_points_reverse(i,j,k) = index of the grid point having i as angular, j as radial and l as atomic indices
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_grad_in_r_array`
+       * :c:data:`aos_in_r_array`
+       * :c:data:`aos_lapl_in_r_array`
+       * :c:data:`aos_sr_vc_alpha_lda_w`
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_lda_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`energy_sr_x_lda`
+       * :c:data:`energy_sr_x_pbe`
+       * :c:data:`energy_x_lda`
+       * :c:data:`energy_x_pbe`
+       * :c:data:`mos_in_r_array`
+       * :c:data:`one_e_dm_alpha_at_r`
+       * :c:data:`one_e_dm_and_grad_alpha_in_r`
+
+ 
+.. c:var:: final_weight_at_r
+
+
+    File : :file:`becke_numerical_grid/grid_becke.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: final_weight_at_r	(n_points_integration_angular,n_points_radial_grid,nucl_num)
+
+
+    Total weight on each grid point which takes into account all Lebedev, Voronoi and radial weights.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`alpha_knowles`
+       * :c:data:`angular_quadrature_points`
+       * :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`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_grid_points`
+       * :c:data:`n_points_final_grid`
+
+ 
+.. c:var:: final_weight_at_r_vector
+
+
+    File : :file:`becke_numerical_grid/grid_becke_vector.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: final_grid_points	(3,n_points_final_grid)
+        double precision, allocatable	:: final_weight_at_r_vector	(n_points_final_grid)
+        integer, allocatable	:: index_final_points	(3,n_points_final_grid)
+        integer, allocatable	:: index_final_points_reverse	(n_points_integration_angular,n_points_radial_grid,nucl_num)
+
+
+     final_grid_points(1:3,j) = (/ x, y, z /) of the jth grid point
+    
+    final_weight_at_r_vector(i) = Total weight function of the ith grid point which contains the Lebedev, Voronoi and radial weights contributions
+    
+    index_final_points(1:3,i) = gives the angular, radial and atomic indices associated to the ith grid point
+    
+    index_final_points_reverse(i,j,k) = index of the grid point having i as angular, j as radial and l as atomic indices
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_grad_in_r_array`
+       * :c:data:`aos_in_r_array`
+       * :c:data:`aos_lapl_in_r_array`
+       * :c:data:`aos_sr_vc_alpha_lda_w`
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_lda_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`energy_sr_x_lda`
+       * :c:data:`energy_sr_x_pbe`
+       * :c:data:`energy_x_lda`
+       * :c:data:`energy_x_pbe`
+       * :c:data:`mos_in_r_array`
+       * :c:data:`one_e_dm_alpha_at_r`
+       * :c:data:`one_e_dm_and_grad_alpha_in_r`
+
+ 
+.. c:var:: grid_points_per_atom
+
+
+    File : :file:`becke_numerical_grid/grid_becke.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: grid_points_per_atom	(3,n_points_integration_angular,n_points_radial_grid,nucl_num)
+
+
+    x,y,z coordinates of grid points used for integration in 3d space
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`alpha_knowles`
+       * :c:data:`angular_quadrature_points`
+       * :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`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_grid_points`
+       * :c:data:`one_e_dm_alpha_in_r`
+       * :c:data:`weight_at_r`
+
+ 
+.. c:var:: grid_points_radial
+
+
+    File : :file:`becke_numerical_grid/grid_becke.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: grid_points_radial	(n_points_radial_grid)
+        double precision	:: dr_radial_integral	
+
+
+    points in [0,1] to map the radial integral [0,\infty]
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_points_radial_grid`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+
+ 
+.. c:var:: index_final_points
+
+
+    File : :file:`becke_numerical_grid/grid_becke_vector.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: final_grid_points	(3,n_points_final_grid)
+        double precision, allocatable	:: final_weight_at_r_vector	(n_points_final_grid)
+        integer, allocatable	:: index_final_points	(3,n_points_final_grid)
+        integer, allocatable	:: index_final_points_reverse	(n_points_integration_angular,n_points_radial_grid,nucl_num)
+
+
+     final_grid_points(1:3,j) = (/ x, y, z /) of the jth grid point
+    
+    final_weight_at_r_vector(i) = Total weight function of the ith grid point which contains the Lebedev, Voronoi and radial weights contributions
+    
+    index_final_points(1:3,i) = gives the angular, radial and atomic indices associated to the ith grid point
+    
+    index_final_points_reverse(i,j,k) = index of the grid point having i as angular, j as radial and l as atomic indices
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_grad_in_r_array`
+       * :c:data:`aos_in_r_array`
+       * :c:data:`aos_lapl_in_r_array`
+       * :c:data:`aos_sr_vc_alpha_lda_w`
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_lda_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`energy_sr_x_lda`
+       * :c:data:`energy_sr_x_pbe`
+       * :c:data:`energy_x_lda`
+       * :c:data:`energy_x_pbe`
+       * :c:data:`mos_in_r_array`
+       * :c:data:`one_e_dm_alpha_at_r`
+       * :c:data:`one_e_dm_and_grad_alpha_in_r`
+
+ 
+.. c:var:: index_final_points_reverse
+
+
+    File : :file:`becke_numerical_grid/grid_becke_vector.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: final_grid_points	(3,n_points_final_grid)
+        double precision, allocatable	:: final_weight_at_r_vector	(n_points_final_grid)
+        integer, allocatable	:: index_final_points	(3,n_points_final_grid)
+        integer, allocatable	:: index_final_points_reverse	(n_points_integration_angular,n_points_radial_grid,nucl_num)
+
+
+     final_grid_points(1:3,j) = (/ x, y, z /) of the jth grid point
+    
+    final_weight_at_r_vector(i) = Total weight function of the ith grid point which contains the Lebedev, Voronoi and radial weights contributions
+    
+    index_final_points(1:3,i) = gives the angular, radial and atomic indices associated to the ith grid point
+    
+    index_final_points_reverse(i,j,k) = index of the grid point having i as angular, j as radial and l as atomic indices
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_grad_in_r_array`
+       * :c:data:`aos_in_r_array`
+       * :c:data:`aos_lapl_in_r_array`
+       * :c:data:`aos_sr_vc_alpha_lda_w`
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_lda_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`energy_sr_x_lda`
+       * :c:data:`energy_sr_x_pbe`
+       * :c:data:`energy_x_lda`
+       * :c:data:`energy_x_pbe`
+       * :c:data:`mos_in_r_array`
+       * :c:data:`one_e_dm_alpha_at_r`
+       * :c:data:`one_e_dm_and_grad_alpha_in_r`
+
+ 
+.. c:var:: m_knowles
+
+
+    File : :file:`becke_numerical_grid/grid_becke.irp.f`
+
+    .. code:: fortran
+
+        integer	:: m_knowles	
+
+
+    value of the "m" parameter in the equation (7) of the paper of Knowles (JCP, 104, 1996)
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+
+ 
+.. c:var:: n_points_final_grid
+
+
+    File : :file:`becke_numerical_grid/grid_becke_vector.irp.f`
+
+    .. code:: fortran
+
+        integer	:: n_points_final_grid	
+
+
+    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`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_grad_in_r_array`
+       * :c:data:`aos_in_r_array`
+       * :c:data:`aos_lapl_in_r_array`
+       * :c:data:`aos_sr_vc_alpha_lda_w`
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_lda_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`energy_sr_x_lda`
+       * :c:data:`energy_sr_x_pbe`
+       * :c:data:`energy_x_lda`
+       * :c:data:`energy_x_pbe`
+       * :c:data:`final_grid_points`
+       * :c:data:`mos_grad_in_r_array`
+       * :c:data:`mos_in_r_array`
+       * :c:data:`mos_lapl_in_r_array`
+       * :c:data:`one_e_dm_alpha_at_r`
+       * :c:data:`one_e_dm_and_grad_alpha_in_r`
+       * :c:data:`potential_sr_c_alpha_ao_lda`
+       * :c:data:`potential_sr_x_alpha_ao_lda`
+       * :c:data:`potential_sr_x_alpha_ao_pbe`
+       * :c:data:`potential_x_alpha_ao_lda`
+       * :c:data:`potential_x_alpha_ao_pbe`
+
+ 
+.. c:var:: n_points_grid_per_atom
+
+
+    File : :file:`becke_numerical_grid/grid_becke.irp.f`
+
+    .. code:: fortran
+
+        integer	:: n_points_grid_per_atom	
+
+
+    Number of grid points per atom
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_points_radial_grid`
+
+
+ 
+.. c:var:: n_points_integration_angular
+
+
+    File : :file:`becke_numerical_grid/grid_becke.irp.f`
+
+    .. code:: fortran
+
+        integer	:: n_points_radial_grid	
+        integer	:: n_points_integration_angular	
+
+
+    n_points_radial_grid = number of radial grid points per atom
+    
+    n_points_integration_angular = number of angular grid points per atom
+    
+    These numbers are automatically set by setting the grid_type_sgn parameter
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`grid_type_sgn`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`angular_quadrature_points`
+       * :c:data:`final_grid_points`
+       * :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:`one_e_dm_alpha_in_r`
+       * :c:data:`weight_at_r`
+
+ 
+.. c:var:: n_points_radial_grid
+
+
+    File : :file:`becke_numerical_grid/grid_becke.irp.f`
+
+    .. code:: fortran
+
+        integer	:: n_points_radial_grid	
+        integer	:: n_points_integration_angular	
+
+
+    n_points_radial_grid = number of radial grid points per atom
+    
+    n_points_integration_angular = number of angular grid points per atom
+    
+    These numbers are automatically set by setting the grid_type_sgn parameter
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`grid_type_sgn`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`angular_quadrature_points`
+       * :c:data:`final_grid_points`
+       * :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:`one_e_dm_alpha_in_r`
+       * :c:data:`weight_at_r`
+
+ 
+.. c:var:: weight_at_r
+
+
+    File : :file:`becke_numerical_grid/grid_becke.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: weight_at_r	(n_points_integration_angular,n_points_radial_grid,nucl_num)
+
+
+    Weight function at grid points : w_n(r) according to the equation (22)
+    of Becke original paper (JCP, 88, 1988)
+    
+    The "n" discrete variable represents the nucleis which in this array is
+    represented by the last dimension and the points are labelled by the
+    other dimensions.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`nucl_coord_transp`
+       * :c:data:`nucl_dist_inv`
+       * :c:data:`nucl_num`
+       * :c:data:`slater_bragg_type_inter_distance_ua`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+
+ 
+.. c:var:: weights_angular_points
+
+
+    File : :file:`becke_numerical_grid/grid_becke.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: angular_quadrature_points	(n_points_integration_angular,3)
+        double precision, allocatable	:: weights_angular_points	(n_points_integration_angular)
+
+
+    weights and grid points for the integration on the angular variables on
+    the unit sphere centered on (0,0,0)
+    According to the LEBEDEV scheme
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_points_radial_grid`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`final_weight_at_r`
+       * :c:data:`grid_points_per_atom`
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: cell_function_becke:
+
+
+    File : :file:`becke_numerical_grid/step_function_becke.irp.f`
+
+    .. code:: fortran
+
+        double precision function cell_function_becke(r,atom_number)
+
+
+    atom_number :: atom on which the cell function of Becke (1988, JCP,88(4))
+    r(1:3)                       :: x,y,z coordinantes of the current point
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_dist_inv`
+       * :c:data:`slater_bragg_type_inter_distance_ua`
+       * :c:data:`nucl_coord_transp`
+       * :c:data:`nucl_num`
+
+ 
+.. c:function:: derivative_knowles_function:
+
+
+    File : :file:`becke_numerical_grid/integration_radial.irp.f`
+
+    .. code:: fortran
+
+        double precision function derivative_knowles_function(alpha,m,x)
+
+
+    Derivative of the function proposed by Knowles (JCP, 104, 1996) for distributing the radial points
+
+ 
+.. c:function:: example_becke_numerical_grid:
+
+
+    File : :file:`becke_numerical_grid/example.irp.f`
+
+    .. code:: fortran
+
+        subroutine example_becke_numerical_grid
+
+
+    subroutine that illustrates the main features available in becke_numerical_grid
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_points_final_grid`
+       * :c:data:`final_weight_at_r`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`final_grid_points`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_num`
+
+ 
+.. c:function:: f_function_becke:
+
+
+    File : :file:`becke_numerical_grid/step_function_becke.irp.f`
+
+    .. code:: fortran
+
+        double precision function f_function_becke(x)
+
+
+
+ 
+.. c:function:: knowles_function:
+
+
+    File : :file:`becke_numerical_grid/integration_radial.irp.f`
+
+    .. code:: fortran
+
+        double precision function knowles_function(alpha,m,x)
+
+
+    Function proposed by Knowles (JCP, 104, 1996) for distributing the radial points :
+    the Log "m" function ( equation (7) in the paper )
+
+ 
+.. c:function:: step_function_becke:
+
+
+    File : :file:`becke_numerical_grid/step_function_becke.irp.f`
+
+    .. code:: fortran
+
+        double precision function step_function_becke(x)
+
+
+    Step function of the Becke paper (1988, JCP,88(4))
+

docs/source/modules/cis.rst

@@ -0,0 +1,280 @@
+.. _module_cis: 
+ 
+.. program:: cis 
+ 
+.. default-role:: option 
+ 
+===
+cis
+===
+
+This module contains a |CIS| program.
+
+The user point of view
+----------------------
+
+The :ref:`cis` program performs the CI to obtain the ROHF reference + all
+single excitations on top of it. This program can be very useful to:
+
+* **Ground state calculations**: generate a guess for the ground state wave
+  function if one is not sure that the :ref:`scf` program gave the lowest |SCF|
+  solution. In combination with :ref:`save_natorb` it can produce new |MOs| in
+  order to reperform an :ref:`scf` optimization.
+
+* **Excited states calculations**: generate guesses for all the
+  :option:`determinants n_states` wave functions, that will be used by the
+  :ref:`fci` program.
+
+
+The main keywords/options to be used are:
+
+* :option:`determinants n_states`: number of states to consider for the |CIS| calculation
+
+* :option:`determinants s2_eig`: force all states to have the desired value of |S^2|
+
+* :option:`determinants expected_s2`: desired value of |S^2|
+
+
+
+
+The programmer's point of view
+------------------------------
+
+This module was built by setting the following rules:
+
+* The only generator determinant is the Hartree-Fock (single-reference method)
+* All generated singly excited determinants are included in the wave function (no perturbative
+  selection)
+
+These rules are set in the ``H_apply.irp.f`` file.
+
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: energy
+ 
+    Variational |CIS| energy
+ 
+ 
+ 
+Programs 
+-------- 
+ 
+ * :ref:`cis` 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: h_apply_cis:
+
+
+    File : :file:`h_apply.irp.f_shell_8`
+
+    .. code:: fortran
+
+        subroutine H_apply_cis()
+
+
+    Calls H_apply on the |HF| determinant and selects all connected single and double
+    excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`psi_coef`
+       * :c:data:`n_states`
+       * :c:data:`generators_bitmask`
+       * :c:data:`mo_num`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`h_apply_buffer_allocated`
+       * :c:data:`n_det`
+       * :c:data:`s2_eig`
+       * :c:data:`n_det_generators`
+       * :c:data:`i_bitmask_gen`
+       * :c:data:`n_int`
+       * :c:data:`psi_det`
+       * :c:data:`psi_det_generators`
+       * :c:data:`psi_det_generators`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`build_fock_tmp`
+       * :c:func:`copy_h_apply_buffer_to_wf`
+       * :c:func:`dsort`
+       * :c:func:`h_apply_cis_diexc`
+       * :c:func:`h_apply_cis_monoexc`
+       * :c:func:`make_s2_eigenfunction`
+       * :c:func:`wall_time`
+
+    Touches:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det`
+       * :c:data:`psi_occ_pattern`
+       * :c:data:`c0_weight`
+       * :c:data:`psi_coef`
+       * :c:data:`psi_det_sorted_bit`
+       * :c:data:`psi_det`
+       * :c:data:`psi_det_size`
+       * :c:data:`psi_det_sorted_bit`
+       * :c:data:`psi_occ_pattern`
+
+ 
+.. c:function:: h_apply_cis_diexc:
+
+
+    File : :file:`h_apply.irp.f_shell_8`
+
+    .. code:: fortran
+
+        subroutine H_apply_cis_diexc(key_in, key_prev, hole_1,particl_1, hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_int`
+       * :c:data:`n_det`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cis`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cis_diexcp`
+
+ 
+.. c:function:: h_apply_cis_diexcorg:
+
+
+    File : :file:`h_apply.irp.f_shell_8`
+
+    .. code:: fortran
+
+        subroutine H_apply_cis_diexcOrg(key_in,key_mask,hole_1,particl_1,hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+
+    Generate all double excitations of key_in using the bit masks of holes and
+    particles.
+    Assume N_int is already provided.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_int`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cis_diexcp`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`bitstring_to_list_ab`
+       * :c:func:`fill_h_apply_buffer_no_selection`
+
+ 
+.. c:function:: h_apply_cis_diexcp:
+
+
+    File : :file:`h_apply.irp.f_shell_8`
+
+    .. code:: fortran
+
+        subroutine H_apply_cis_diexcP(key_in, fs1, fh1, particl_1, fs2, fh2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_int`
+       * :c:data:`n_det`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cis_diexc`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cis_diexcorg`
+
+ 
+.. c:function:: h_apply_cis_monoexc:
+
+
+    File : :file:`h_apply.irp.f_shell_8`
+
+    .. code:: fortran
+
+        subroutine H_apply_cis_monoexc(key_in, hole_1,particl_1,fock_diag_tmp,i_generator,iproc_in  )
+
+
+    Generate all single excitations of key_in using the bit masks of holes and
+    particles.
+    Assume N_int is already provided.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_int`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cis`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`bitstring_to_list_ab`
+       * :c:func:`fill_h_apply_buffer_no_selection`
+

docs/source/modules/cisd.rst

@@ -0,0 +1,273 @@
+.. _module_cisd: 
+ 
+.. program:: cisd 
+ 
+.. default-role:: option 
+ 
+====
+cisd
+====
+
+This module contains a CI of single and double excitations.
+
+The user point of view
+----------------------
+
+The :command:`cisd` program performs the CI of the ROHF-like + all single and double excitations on top of it.
+This program can be very useful to :
+
+* **Ground state calculations**: generate a guess for the ground state wave function if one is not sure that the :c:func:`scf` program gave the lowest SCF solution. In combination with :c:func:`save_natorb` it can produce new |MOs| in order to reperform an :c:func:`scf` optimization.
+
+* **Excited states calculations**: generate guess for all the :option:`determinants n_states` wave functions, that will be used by the :c:func:`fci` program.
+
+
+The main keywords/options to be used are:
+
+* :option:`determinants n_states` : number of states to consider for the |cisd| calculation
+
+* :option:`determinants s2_eig` : force all states to have the desired value of :math:`S^2`
+
+* :option:`determinants expected_s2` : desired value of :math:`S^2`
+
+The programmer point of view
+----------------------------
+
+This module have been built by setting the following rules:
+
+
+* The only generator determinant is the Hartree-Fock (single-reference method)
+* All generated determinants are included in the wave function (no perturbative
+  selection)
+
+These rules are set in the ``H_apply.irp.f`` file.
+
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: energy
+ 
+    Variational |CISD| energy
+ 
+ 
+ 
+Programs 
+-------- 
+ 
+ * :ref:`cisd` 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: h_apply_cisd:
+
+
+    File : :file:`h_apply.irp.f_shell_8`
+
+    .. code:: fortran
+
+        subroutine H_apply_cisd()
+
+
+    Calls H_apply on the |HF| determinant and selects all connected single and double
+    excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`psi_coef`
+       * :c:data:`n_states`
+       * :c:data:`generators_bitmask`
+       * :c:data:`mo_num`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`h_apply_buffer_allocated`
+       * :c:data:`n_det`
+       * :c:data:`s2_eig`
+       * :c:data:`n_det_generators`
+       * :c:data:`i_bitmask_gen`
+       * :c:data:`n_int`
+       * :c:data:`psi_det`
+       * :c:data:`psi_det_generators`
+       * :c:data:`psi_det_generators`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`build_fock_tmp`
+       * :c:func:`copy_h_apply_buffer_to_wf`
+       * :c:func:`dsort`
+       * :c:func:`h_apply_cisd_diexc`
+       * :c:func:`h_apply_cisd_monoexc`
+       * :c:func:`make_s2_eigenfunction`
+       * :c:func:`wall_time`
+
+    Touches:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det`
+       * :c:data:`psi_occ_pattern`
+       * :c:data:`c0_weight`
+       * :c:data:`psi_coef`
+       * :c:data:`psi_det_sorted_bit`
+       * :c:data:`psi_det`
+       * :c:data:`psi_det_size`
+       * :c:data:`psi_det_sorted_bit`
+       * :c:data:`psi_occ_pattern`
+
+ 
+.. c:function:: h_apply_cisd_diexc:
+
+
+    File : :file:`h_apply.irp.f_shell_8`
+
+    .. code:: fortran
+
+        subroutine H_apply_cisd_diexc(key_in, key_prev, hole_1,particl_1, hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_int`
+       * :c:data:`n_det`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cisd`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cisd_diexcp`
+
+ 
+.. c:function:: h_apply_cisd_diexcorg:
+
+
+    File : :file:`h_apply.irp.f_shell_8`
+
+    .. code:: fortran
+
+        subroutine H_apply_cisd_diexcOrg(key_in,key_mask,hole_1,particl_1,hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+
+    Generate all double excitations of key_in using the bit masks of holes and
+    particles.
+    Assume N_int is already provided.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_int`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cisd_diexcp`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`bitstring_to_list_ab`
+       * :c:func:`fill_h_apply_buffer_no_selection`
+
+ 
+.. c:function:: h_apply_cisd_diexcp:
+
+
+    File : :file:`h_apply.irp.f_shell_8`
+
+    .. code:: fortran
+
+        subroutine H_apply_cisd_diexcP(key_in, fs1, fh1, particl_1, fs2, fh2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_int`
+       * :c:data:`n_det`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cisd_diexc`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cisd_diexcorg`
+
+ 
+.. c:function:: h_apply_cisd_monoexc:
+
+
+    File : :file:`h_apply.irp.f_shell_8`
+
+    .. code:: fortran
+
+        subroutine H_apply_cisd_monoexc(key_in, hole_1,particl_1,fock_diag_tmp,i_generator,iproc_in  )
+
+
+    Generate all single excitations of key_in using the bit masks of holes and
+    particles.
+    Assume N_int is already provided.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_int`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`h_apply_cisd`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`bitstring_to_list_ab`
+       * :c:func:`fill_h_apply_buffer_no_selection`
+

docs/source/modules/davidson_dressed.rst

@@ -0,0 +1,13 @@
+.. _module_davidson_dressed: 
+ 
+.. program:: davidson_dressed 
+ 
+.. default-role:: option 
+ 
+================
+davidson_dressed
+================
+
+Davidson with single-column dressing.
+
+ 

docs/source/modules/davidson_undressed.rst

@@ -0,0 +1,75 @@
+.. _module_davidson_undressed: 
+ 
+.. program:: davidson_undressed 
+ 
+.. default-role:: option 
+ 
+==================
+davidson_undressed
+==================
+
+Module for main files Davidson's algorithm with no dressing.
+
+ 
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: dressing_column_h
+
+
+    File : :file:`davidson_undressed/null_dressing_vector.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: dressing_column_h	(N_det,N_states)
+        double precision, allocatable	:: dressing_column_s	(N_det,N_states)
+
+
+    Null dressing vectors
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det`
+       * :c:data:`n_states`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ci_electronic_energy`
+
+ 
+.. c:var:: dressing_column_s
+
+
+    File : :file:`davidson_undressed/null_dressing_vector.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: dressing_column_h	(N_det,N_states)
+        double precision, allocatable	:: dressing_column_s	(N_det,N_states)
+
+
+    Null dressing vectors
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det`
+       * :c:data:`n_states`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ci_electronic_energy`
+

docs/source/modules/density_for_dft.rst

@@ -0,0 +1,306 @@
+.. _module_density_for_dft: 
+ 
+.. program:: density_for_dft 
+ 
+.. default-role:: option 
+ 
+===============
+density_for_dft
+===============
+
+
+This module defines the *provider* of the density used for the DFT related calculations.
+This definition is done through the keyword :option:`density_for_dft density_for_dft`.
+The density can be:
+
+* WFT : the density is computed with a potentially multi determinant wave function (see variables `psi_det` and `psi_det`)# input_density : the density is set to a density previously stored in the |EZFIO| folder (see ``aux_quantities``)
+* damping_rs_dft : the density is damped between the input_density and the WFT density, with a damping factor of :option:`density_for_dft damping_for_rs_dft`
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: density_for_dft
+ 
+    Type of density used for DFT calculation. If set to WFT , it uses the density of the wave function stored in (psi_det,psi_coef). If set to input_density it uses the one-body dm stored in aux_quantities/ . If set to damping_rs_dft it uses the damped density between WFT and input_density. In the ks_scf and rs_ks_scf programs, it is set to WFT.
+ 
+    Default: WFT
+ 
+.. option:: damping_for_rs_dft
+ 
+    damping factor for the density used in RSFT.
+ 
+    Default: 0.5
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: one_body_dm_mo_alpha_one_det
+
+
+    File : :file:`density_for_dft/density_for_dft.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_body_dm_mo_alpha_one_det	(mo_num,mo_num,N_states)
+        double precision, allocatable	:: one_body_dm_mo_beta_one_det	(mo_num,mo_num,N_states)
+
+
+    One body density matrix on the |MO| basis for a single determinant
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`mo_num`
+       * :c:data:`n_states`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`one_e_dm_mo_alpha_for_dft`
+       * :c:data:`one_e_dm_mo_beta_for_dft`
+
+ 
+.. c:var:: one_body_dm_mo_beta_one_det
+
+
+    File : :file:`density_for_dft/density_for_dft.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_body_dm_mo_alpha_one_det	(mo_num,mo_num,N_states)
+        double precision, allocatable	:: one_body_dm_mo_beta_one_det	(mo_num,mo_num,N_states)
+
+
+    One body density matrix on the |MO| basis for a single determinant
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`mo_num`
+       * :c:data:`n_states`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`one_e_dm_mo_alpha_for_dft`
+       * :c:data:`one_e_dm_mo_beta_for_dft`
+
+ 
+.. c:var:: one_e_dm_alpha_ao_for_dft
+
+
+    File : :file:`density_for_dft/density_for_dft.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_alpha_ao_for_dft	(ao_num,ao_num,N_states)
+        double precision, allocatable	:: one_e_dm_beta_ao_for_dft	(ao_num,ao_num,N_states)
+
+
+    one body density matrix on the AO basis based on one_e_dm_mo_alpha_for_dft
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+       * :c:data:`n_states`
+       * :c:data:`one_e_dm_mo_alpha_for_dft`
+       * :c:data:`one_e_dm_mo_beta_for_dft`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`one_e_dm_alpha_at_r`
+       * :c:data:`one_e_dm_alpha_in_r`
+       * :c:data:`one_e_dm_and_grad_alpha_in_r`
+
+ 
+.. c:var:: one_e_dm_average_mo_for_dft
+
+
+    File : :file:`density_for_dft/density_for_dft.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_average_mo_for_dft	(mo_num,mo_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_num`
+       * :c:data:`n_states`
+       * :c:data:`one_e_dm_mo_for_dft`
+       * :c:data:`state_average_weight`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`short_range_hartree_operator`
+
+ 
+.. c:var:: one_e_dm_beta_ao_for_dft
+
+
+    File : :file:`density_for_dft/density_for_dft.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_alpha_ao_for_dft	(ao_num,ao_num,N_states)
+        double precision, allocatable	:: one_e_dm_beta_ao_for_dft	(ao_num,ao_num,N_states)
+
+
+    one body density matrix on the AO basis based on one_e_dm_mo_alpha_for_dft
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+       * :c:data:`n_states`
+       * :c:data:`one_e_dm_mo_alpha_for_dft`
+       * :c:data:`one_e_dm_mo_beta_for_dft`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`one_e_dm_alpha_at_r`
+       * :c:data:`one_e_dm_alpha_in_r`
+       * :c:data:`one_e_dm_and_grad_alpha_in_r`
+
+ 
+.. c:var:: one_e_dm_mo_alpha_for_dft
+
+
+    File : :file:`density_for_dft/density_for_dft.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_mo_alpha_for_dft	(mo_num,mo_num,N_states)
+
+
+    density matrix for alpha electrons in the MO basis used for all DFT calculations based on the density
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`damping_for_rs_dft`
+       * :c:data:`data_one_e_dm_alpha_mo`
+       * :c:data:`density_for_dft`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+       * :c:data:`n_states`
+       * :c:data:`one_body_dm_mo_alpha_one_det`
+       * :c:data:`one_e_dm_mo_alpha`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+       * :c:data:`one_e_dm_mo_for_dft`
+       * :c:data:`psi_dft_energy_kinetic`
+       * :c:data:`trace_v_xc`
+
+ 
+.. c:var:: one_e_dm_mo_beta_for_dft
+
+
+    File : :file:`density_for_dft/density_for_dft.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_mo_beta_for_dft	(mo_num,mo_num,N_states)
+
+
+    density matrix for beta  electrons in the MO basis used for all DFT calculations based on the density
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`damping_for_rs_dft`
+       * :c:data:`data_one_e_dm_beta_mo`
+       * :c:data:`density_for_dft`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+       * :c:data:`n_states`
+       * :c:data:`one_body_dm_mo_alpha_one_det`
+       * :c:data:`one_e_dm_mo_alpha`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+       * :c:data:`one_e_dm_mo_for_dft`
+       * :c:data:`psi_dft_energy_kinetic`
+       * :c:data:`trace_v_xc`
+
+ 
+.. c:var:: one_e_dm_mo_for_dft
+
+
+    File : :file:`density_for_dft/density_for_dft.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_mo_for_dft	(mo_num,mo_num,N_states)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_num`
+       * :c:data:`n_states`
+       * :c:data:`one_e_dm_mo_alpha_for_dft`
+       * :c:data:`one_e_dm_mo_beta_for_dft`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`one_e_dm_average_mo_for_dft`
+       * :c:data:`short_range_hartree_operator`
+

docs/source/modules/dft_keywords.rst

@@ -0,0 +1,68 @@
+.. _module_dft_keywords: 
+ 
+.. program:: dft_keywords 
+ 
+.. default-role:: option 
+ 
+============
+dft_keywords
+============
+
+This module contains the main keywords related to a DFT calculation or RS-DFT calculation, such as:
+
+* :option:`dft_keywords exchange_functional`
+* :option:`dft_keywords correlation_functional`
+* :option:`dft_keywords HF_exchange`  : only relevent for the :c:func:`rs_ks_scf` program
+
+The keyword for the **range separation parameter**  :math:`\mu` is the :option:`ao_two_e_erf_ints mu_erf` keyword.
+
+The keyword for the type of density used in RS-DFT calculation with a multi-configurational wave function is the :option:`density_for_dft density_for_dft` keyword.
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: exchange_functional
+ 
+    name of the exchange functional
+ 
+    Default: short_range_LDA
+ 
+.. option:: correlation_functional
+ 
+    name of the correlation functional
+ 
+    Default: short_range_LDA
+ 
+.. option:: HF_exchange
+ 
+    Percentage of HF exchange in the DFT model
+ 
+    Default: 0.
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: dft_type
+
+
+    File : :file:`dft_keywords/keywords.irp.f`
+
+    .. code:: fortran
+
+        character*(32)	:: dft_type	
+
+
+    defines the type of DFT applied: LDA, GGA etc ...
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`correlation_functional`
+       * :c:data:`exchange_functional`
+
+

docs/source/modules/dft_utils_in_r.rst

@@ -0,0 +1,882 @@
+.. _module_dft_utils_in_r: 
+ 
+.. program:: dft_utils_in_r 
+ 
+.. default-role:: option 
+ 
+==============
+dft_utils_in_r
+==============
+
+This module contains most of the fundamental quantities (AOs, MOs or density derivatives) evaluated in real-space representation that are needed for the various DFT modules.
+
+As these quantities might be used and re-used, the values at each point of the grid are stored (see ``becke_numerical_grid`` for more information on the grid).
+
+The main providers for this module are:
+
+* `aos_in_r_array`: values of the |AO| basis on the grid point.
+* `mos_in_r_array`: values of the |MO| basis on the grid point.
+* `one_e_dm_and_grad_alpha_in_r`: values of the density and its gradienst on the grid points.
+
+ 
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: aos_grad_in_r_array
+
+
+    File : :file:`dft_utils_in_r/ao_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: aos_grad_in_r_array	(ao_num,n_points_final_grid,3)
+        double precision, allocatable	:: aos_grad_in_r_array_transp	(n_points_final_grid,ao_num,3)
+        double precision, allocatable	:: aos_grad_in_r_array_transp_xyz	(3,n_points_final_grid,ao_num)
+
+
+    aos_grad_in_r_array(i,j,k)          = value of the kth component of the gradient of ith ao on the jth grid point
+    
+    aos_grad_in_r_array_transp(i,j,k)   = value of the kth component of the gradient of jth ao on the ith grid point
+    
+    k = 1 : x, k= 2, y, k  3, z
+
+    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`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`nucl_aos_transposed`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_n_aos`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`mos_grad_in_r_array`
+       * :c:data:`potential_sr_x_alpha_ao_pbe`
+       * :c:data:`potential_x_alpha_ao_pbe`
+
+ 
+.. c:var:: aos_grad_in_r_array_transp
+
+
+    File : :file:`dft_utils_in_r/ao_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: aos_grad_in_r_array	(ao_num,n_points_final_grid,3)
+        double precision, allocatable	:: aos_grad_in_r_array_transp	(n_points_final_grid,ao_num,3)
+        double precision, allocatable	:: aos_grad_in_r_array_transp_xyz	(3,n_points_final_grid,ao_num)
+
+
+    aos_grad_in_r_array(i,j,k)          = value of the kth component of the gradient of ith ao on the jth grid point
+    
+    aos_grad_in_r_array_transp(i,j,k)   = value of the kth component of the gradient of jth ao on the ith grid point
+    
+    k = 1 : x, k= 2, y, k  3, z
+
+    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`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`nucl_aos_transposed`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_n_aos`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`mos_grad_in_r_array`
+       * :c:data:`potential_sr_x_alpha_ao_pbe`
+       * :c:data:`potential_x_alpha_ao_pbe`
+
+ 
+.. c:var:: aos_grad_in_r_array_transp_xyz
+
+
+    File : :file:`dft_utils_in_r/ao_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: aos_grad_in_r_array	(ao_num,n_points_final_grid,3)
+        double precision, allocatable	:: aos_grad_in_r_array_transp	(n_points_final_grid,ao_num,3)
+        double precision, allocatable	:: aos_grad_in_r_array_transp_xyz	(3,n_points_final_grid,ao_num)
+
+
+    aos_grad_in_r_array(i,j,k)          = value of the kth component of the gradient of ith ao on the jth grid point
+    
+    aos_grad_in_r_array_transp(i,j,k)   = value of the kth component of the gradient of jth ao on the ith grid point
+    
+    k = 1 : x, k= 2, y, k  3, z
+
+    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`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`nucl_aos_transposed`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_n_aos`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`mos_grad_in_r_array`
+       * :c:data:`potential_sr_x_alpha_ao_pbe`
+       * :c:data:`potential_x_alpha_ao_pbe`
+
+ 
+.. c:var:: aos_in_r_array
+
+
+    File : :file:`dft_utils_in_r/ao_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: aos_in_r_array	(ao_num,n_points_final_grid)
+        double precision, allocatable	:: aos_in_r_array_transp	(n_points_final_grid,ao_num)
+
+
+    aos_in_r_array(i,j)        = value of the ith ao on the jth grid point
+    
+    aos_in_r_array_transp(i,j) = value of the jth ao on the ith grid point
+
+    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`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`nucl_aos_transposed`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_n_aos`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_sr_vc_alpha_lda_w`
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_lda_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`potential_sr_c_alpha_ao_lda`
+       * :c:data:`potential_sr_x_alpha_ao_lda`
+       * :c:data:`potential_sr_x_alpha_ao_pbe`
+       * :c:data:`potential_x_alpha_ao_lda`
+       * :c:data:`potential_x_alpha_ao_pbe`
+
+ 
+.. c:var:: aos_in_r_array_transp
+
+
+    File : :file:`dft_utils_in_r/ao_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: aos_in_r_array	(ao_num,n_points_final_grid)
+        double precision, allocatable	:: aos_in_r_array_transp	(n_points_final_grid,ao_num)
+
+
+    aos_in_r_array(i,j)        = value of the ith ao on the jth grid point
+    
+    aos_in_r_array_transp(i,j) = value of the jth ao on the ith grid point
+
+    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`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`nucl_aos_transposed`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_n_aos`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_sr_vc_alpha_lda_w`
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_lda_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`potential_sr_c_alpha_ao_lda`
+       * :c:data:`potential_sr_x_alpha_ao_lda`
+       * :c:data:`potential_sr_x_alpha_ao_pbe`
+       * :c:data:`potential_x_alpha_ao_lda`
+       * :c:data:`potential_x_alpha_ao_pbe`
+
+ 
+.. c:var:: aos_lapl_in_r_array
+
+
+    File : :file:`dft_utils_in_r/ao_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: aos_lapl_in_r_array	(ao_num,n_points_final_grid,3)
+        double precision, allocatable	:: aos_lapl_in_r_array_transp	(n_points_final_grid,ao_num,3)
+
+
+    aos_lapl_in_r_array(i,j,k)          = value of the kth component of the laplacian of ith ao on the jth grid point
+    
+    aos_lapl_in_r_array_transp(i,j,k)   = value of the kth component of the laplacian of jth ao on the ith grid point
+    
+    k = 1 : x, k= 2, y, k  3, z
+
+    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`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`nucl_aos_transposed`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_n_aos`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mos_lapl_in_r_array`
+
+ 
+.. c:var:: aos_lapl_in_r_array_transp
+
+
+    File : :file:`dft_utils_in_r/ao_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: aos_lapl_in_r_array	(ao_num,n_points_final_grid,3)
+        double precision, allocatable	:: aos_lapl_in_r_array_transp	(n_points_final_grid,ao_num,3)
+
+
+    aos_lapl_in_r_array(i,j,k)          = value of the kth component of the laplacian of ith ao on the jth grid point
+    
+    aos_lapl_in_r_array_transp(i,j,k)   = value of the kth component of the laplacian of jth ao on the ith grid point
+    
+    k = 1 : x, k= 2, y, k  3, z
+
+    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`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`nucl_aos_transposed`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_n_aos`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mos_lapl_in_r_array`
+
+ 
+.. c:var:: mos_grad_in_r_array
+
+
+    File : :file:`dft_utils_in_r/mo_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mos_grad_in_r_array	(mo_num,n_points_final_grid,3)
+
+
+    mos_grad_in_r_array(i,j,k)          = value of the kth component of the gradient of ith mo on the jth grid point
+    
+    mos_grad_in_r_array_transp(i,j,k)   = value of the kth component of the gradient of jth mo on the ith grid point
+    
+    k = 1 : x, k= 2, y, k  3, z
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`aos_grad_in_r_array`
+       * :c:data:`mo_coef_transp`
+       * :c:data:`mo_num`
+       * :c:data:`n_points_final_grid`
+
+
+ 
+.. c:var:: mos_in_r_array
+
+
+    File : :file:`dft_utils_in_r/mo_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mos_in_r_array	(mo_num,n_points_final_grid)
+        double precision, allocatable	:: mos_in_r_array_transp	(n_points_final_grid,mo_num)
+
+
+    mos_in_r_array(i,j)        = value of the ith mo on the jth grid point
+    
+    mos_in_r_array_transp(i,j) = value of the jth mo on the ith grid point
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`final_grid_points`
+       * :c:data:`mo_coef_transp`
+       * :c:data:`mo_num`
+       * :c:data:`n_points_final_grid`
+
+
+ 
+.. c:var:: mos_in_r_array_transp
+
+
+    File : :file:`dft_utils_in_r/mo_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mos_in_r_array	(mo_num,n_points_final_grid)
+        double precision, allocatable	:: mos_in_r_array_transp	(n_points_final_grid,mo_num)
+
+
+    mos_in_r_array(i,j)        = value of the ith mo on the jth grid point
+    
+    mos_in_r_array_transp(i,j) = value of the jth mo on the ith grid point
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`final_grid_points`
+       * :c:data:`mo_coef_transp`
+       * :c:data:`mo_num`
+       * :c:data:`n_points_final_grid`
+
+
+ 
+.. c:var:: mos_lapl_in_r_array
+
+
+    File : :file:`dft_utils_in_r/mo_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mos_lapl_in_r_array	(mo_num,n_points_final_grid,3)
+
+
+    mos_lapl_in_r_array(i,j,k)          = value of the kth component of the laplacian of ith mo on the jth grid point
+    
+    mos_lapl_in_r_array_transp(i,j,k)   = value of the kth component of the laplacian of jth mo on the ith grid point
+    
+    k = 1 : x, k= 2, y, k  3, z
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`aos_lapl_in_r_array`
+       * :c:data:`mo_coef_transp`
+       * :c:data:`mo_num`
+       * :c:data:`n_points_final_grid`
+
+
+ 
+.. c:var:: one_e_dm_alpha_at_r
+
+
+    File : :file:`dft_utils_in_r/dm_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_alpha_at_r	(n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_dm_beta_at_r	(n_points_final_grid,N_states)
+
+
+    one_e_dm_alpha_at_r(i,istate) = n_alpha(r_i,istate)
+    one_e_dm_beta_at_r(i,istate) =  n_beta(r_i,istate)
+    where r_i is the ith point of the grid and istate is the state number
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`final_grid_points`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`n_states`
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_sr_vc_alpha_lda_w`
+       * :c:data:`aos_vc_alpha_lda_w`
+       * :c:data:`energy_sr_x_lda`
+       * :c:data:`energy_x_lda`
+
+ 
+.. c:var:: one_e_dm_alpha_in_r
+
+
+    File : :file:`dft_utils_in_r/dm_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_alpha_in_r	(n_points_integration_angular,n_points_radial_grid,nucl_num,N_states)
+        double precision, allocatable	:: one_e_dm_beta_in_r	(n_points_integration_angular,n_points_radial_grid,nucl_num,N_states)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`mo_num`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`n_states`
+       * :c:data:`nucl_num`
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+
+
+ 
+.. c:var:: one_e_dm_and_grad_alpha_in_r
+
+
+    File : :file:`dft_utils_in_r/dm_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_and_grad_alpha_in_r	(4,n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_dm_and_grad_beta_in_r	(4,n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_grad_2_dm_alpha_at_r	(n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_grad_2_dm_beta_at_r	(n_points_final_grid,N_states)
+
+
+    one_e_dm_and_grad_alpha_in_r(1,i,i_state) = d\dx n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(2,i,i_state) = d\dy n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(3,i,i_state) = d\dz n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(4,i,i_state) = n_alpha(r_i,istate)
+    one_e_grad_2_dm_alpha_at_r(i,istate)      = d\dx n_alpha(r_i,istate)^2 + d\dy n_alpha(r_i,istate)^2 + d\dz n_alpha(r_i,istate)^2
+    where r_i is the ith point of the grid and istate is the state number
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`final_grid_points`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`n_states`
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`energy_sr_x_pbe`
+       * :c:data:`energy_x_pbe`
+
+ 
+.. c:var:: one_e_dm_and_grad_beta_in_r
+
+
+    File : :file:`dft_utils_in_r/dm_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_and_grad_alpha_in_r	(4,n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_dm_and_grad_beta_in_r	(4,n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_grad_2_dm_alpha_at_r	(n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_grad_2_dm_beta_at_r	(n_points_final_grid,N_states)
+
+
+    one_e_dm_and_grad_alpha_in_r(1,i,i_state) = d\dx n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(2,i,i_state) = d\dy n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(3,i,i_state) = d\dz n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(4,i,i_state) = n_alpha(r_i,istate)
+    one_e_grad_2_dm_alpha_at_r(i,istate)      = d\dx n_alpha(r_i,istate)^2 + d\dy n_alpha(r_i,istate)^2 + d\dz n_alpha(r_i,istate)^2
+    where r_i is the ith point of the grid and istate is the state number
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`final_grid_points`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`n_states`
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`energy_sr_x_pbe`
+       * :c:data:`energy_x_pbe`
+
+ 
+.. c:var:: one_e_dm_beta_at_r
+
+
+    File : :file:`dft_utils_in_r/dm_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_alpha_at_r	(n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_dm_beta_at_r	(n_points_final_grid,N_states)
+
+
+    one_e_dm_alpha_at_r(i,istate) = n_alpha(r_i,istate)
+    one_e_dm_beta_at_r(i,istate) =  n_beta(r_i,istate)
+    where r_i is the ith point of the grid and istate is the state number
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`final_grid_points`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`n_states`
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_sr_vc_alpha_lda_w`
+       * :c:data:`aos_vc_alpha_lda_w`
+       * :c:data:`energy_sr_x_lda`
+       * :c:data:`energy_x_lda`
+
+ 
+.. c:var:: one_e_dm_beta_in_r
+
+
+    File : :file:`dft_utils_in_r/dm_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_alpha_in_r	(n_points_integration_angular,n_points_radial_grid,nucl_num,N_states)
+        double precision, allocatable	:: one_e_dm_beta_in_r	(n_points_integration_angular,n_points_radial_grid,nucl_num,N_states)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`grid_points_per_atom`
+       * :c:data:`mo_num`
+       * :c:data:`n_points_radial_grid`
+       * :c:data:`n_states`
+       * :c:data:`nucl_num`
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+
+
+ 
+.. c:var:: one_e_grad_2_dm_alpha_at_r
+
+
+    File : :file:`dft_utils_in_r/dm_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_and_grad_alpha_in_r	(4,n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_dm_and_grad_beta_in_r	(4,n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_grad_2_dm_alpha_at_r	(n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_grad_2_dm_beta_at_r	(n_points_final_grid,N_states)
+
+
+    one_e_dm_and_grad_alpha_in_r(1,i,i_state) = d\dx n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(2,i,i_state) = d\dy n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(3,i,i_state) = d\dz n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(4,i,i_state) = n_alpha(r_i,istate)
+    one_e_grad_2_dm_alpha_at_r(i,istate)      = d\dx n_alpha(r_i,istate)^2 + d\dy n_alpha(r_i,istate)^2 + d\dz n_alpha(r_i,istate)^2
+    where r_i is the ith point of the grid and istate is the state number
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`final_grid_points`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`n_states`
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`energy_sr_x_pbe`
+       * :c:data:`energy_x_pbe`
+
+ 
+.. c:var:: one_e_grad_2_dm_beta_at_r
+
+
+    File : :file:`dft_utils_in_r/dm_in_r.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: one_e_dm_and_grad_alpha_in_r	(4,n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_dm_and_grad_beta_in_r	(4,n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_grad_2_dm_alpha_at_r	(n_points_final_grid,N_states)
+        double precision, allocatable	:: one_e_grad_2_dm_beta_at_r	(n_points_final_grid,N_states)
+
+
+    one_e_dm_and_grad_alpha_in_r(1,i,i_state) = d\dx n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(2,i,i_state) = d\dy n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(3,i,i_state) = d\dz n_alpha(r_i,istate)
+    one_e_dm_and_grad_alpha_in_r(4,i,i_state) = n_alpha(r_i,istate)
+    one_e_grad_2_dm_alpha_at_r(i,istate)      = d\dx n_alpha(r_i,istate)^2 + d\dy n_alpha(r_i,istate)^2 + d\dz n_alpha(r_i,istate)^2
+    where r_i is the ith point of the grid and istate is the state number
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`final_grid_points`
+       * :c:data:`n_points_final_grid`
+       * :c:data:`n_states`
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`aos_sr_vc_alpha_pbe_w`
+       * :c:data:`aos_vc_alpha_pbe_w`
+       * :c:data:`energy_sr_x_pbe`
+       * :c:data:`energy_x_pbe`
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: density_and_grad_alpha_beta_and_all_aos_and_grad_aos_at_r:
+
+
+    File : :file:`dft_utils_in_r/dm_in_r.irp.f`
+
+    .. code:: fortran
+
+        subroutine density_and_grad_alpha_beta_and_all_aos_and_grad_aos_at_r(r,dm_a,dm_b, grad_dm_a, grad_dm_b, aos_array, grad_aos_array)
+
+
+    input:
+    
+    * r(1) ==> r(1) = x, r(2) = y, r(3) = z
+    
+    output:
+    
+    * dm_a = alpha density evaluated at r
+    * dm_b = beta  density evaluated at r
+    * aos_array(i) = ao(i) evaluated at r
+    * grad_dm_a(1) = X gradient of the alpha density evaluated in r
+    * grad_dm_a(1) = X gradient of the beta  density evaluated in r
+    * grad_aos_array(1) = X gradient of the aos(i) evaluated at r
+    
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+       * :c:data:`n_states`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`one_e_dm_and_grad_alpha_in_r`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dsymv`
+       * :c:func:`give_all_aos_and_grad_at_r`
+
+ 
+.. c:function:: dm_dft_alpha_beta_and_all_aos_at_r:
+
+
+    File : :file:`dft_utils_in_r/dm_in_r.irp.f`
+
+    .. code:: fortran
+
+        subroutine dm_dft_alpha_beta_and_all_aos_at_r(r,dm_a,dm_b,aos_array)
+
+
+    input: r(1) ==> r(1) = x, r(2) = y, r(3) = z
+    output : dm_a = alpha density evaluated at r
+    output : dm_b = beta  density evaluated at r
+    output : aos_array(i) = ao(i) evaluated at r
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+       * :c:data:`n_states`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dsymv`
+       * :c:func:`give_all_aos_at_r`
+
+ 
+.. c:function:: dm_dft_alpha_beta_at_r:
+
+
+    File : :file:`dft_utils_in_r/dm_in_r.irp.f`
+
+    .. code:: fortran
+
+        subroutine dm_dft_alpha_beta_at_r(r,dm_a,dm_b)
+
+
+    input: r(1) ==> r(1) = x, r(2) = y, r(3) = z
+    output : dm_a = alpha density evaluated at r(3)
+    output : dm_b = beta  density evaluated at r(3)
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`one_e_dm_alpha_ao_for_dft`
+       * :c:data:`n_states`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`one_e_dm_alpha_at_r`
+       * :c:data:`one_e_dm_alpha_in_r`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dgemv`
+       * :c:func:`give_all_aos_at_r`
+

docs/source/modules/dressing.rst

@@ -0,0 +1,36 @@
+.. _module_dressing: 
+ 
+.. program:: dressing 
+ 
+.. default-role:: option 
+ 
+=========
+dress_zmq
+=========
+
+Module to facilitate the construction of modules using dressed
+Hamiltonians, parallelized with |ZeroMQ|.
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: thresh_dressed_ci
+ 
+    Threshold on the convergence of the dressed |CI| energy
+ 
+    Default: 1.e-5
+ 
+.. option:: n_it_max_dressed_ci
+ 
+    Maximum number of dressed |CI| iterations
+ 
+    Default: 10
+ 
+.. option:: dress_relative_error
+ 
+    Stop stochastic dressing when the relative error is smaller than :option:`perturbation PT2_relative_error`
+ 
+    Default: 0.001

docs/source/modules/electrons.rst

@@ -0,0 +1,114 @@
+.. _module_electrons: 
+ 
+.. program:: electrons 
+ 
+.. default-role:: option 
+ 
+=========
+electrons
+=========
+
+Describes the electrons. For the moment, only the number of alpha
+and beta electrons are provided by this module.
+
+
+Assumptions
+===========
+
+* `elec_num` >= 0
+* `elec_alpha_num` >= 0
+* `elec_beta_num` >= 0
+* `elec_alpha_num` >= `elec_beta_num`
+
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: elec_alpha_num
+ 
+    Numbers of electrons alpha ("up")
+ 
+ 
+.. option:: elec_beta_num
+ 
+    Numbers of electrons beta ("down")
+ 
+ 
+.. option:: elec_num
+ 
+    Numbers total of electrons (alpha + beta)
+ 
+    Default: = electrons.elec_alpha_num + electrons.elec_beta_num
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: elec_num
+
+
+    File : :file:`electrons/electrons.irp.f`
+
+    .. code:: fortran
+
+        integer	:: elec_num	
+        integer, allocatable	:: elec_num_tab	(2)
+
+
+    Numbers of alpha ("up") , beta ("down") and total electrons
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`ezfio_filename`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`diagonal_h_matrix_on_psi_det`
+       * :c:data:`psi_det_hii`
+       * :c:data:`psi_selectors_diag_h_mat`
+       * :c:data:`pt2_f`
+
+ 
+.. c:var:: elec_num_tab
+
+
+    File : :file:`electrons/electrons.irp.f`
+
+    .. code:: fortran
+
+        integer	:: elec_num	
+        integer, allocatable	:: elec_num_tab	(2)
+
+
+    Numbers of alpha ("up") , beta ("down") and total electrons
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`ezfio_filename`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`diagonal_h_matrix_on_psi_det`
+       * :c:data:`psi_det_hii`
+       * :c:data:`psi_selectors_diag_h_mat`
+       * :c:data:`pt2_f`
+

docs/source/modules/ezfio_files.rst

@@ -0,0 +1,760 @@
+.. _module_ezfio_files: 
+ 
+.. program:: ezfio_files 
+ 
+.. default-role:: option 
+ 
+===========
+ezfio_files
+===========
+
+This modules essentially contains the name of the |EZFIO| directory in the
+:c:data:`ezfio_filename` variable. This is read as the first argument of the
+command-line, or as the :envvar:`QP_INPUT` environment variable.
+
+ 
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: ezfio_filename
+
+
+    File : :file:`ezfio_files/ezfio.irp.f`
+
+    .. code:: fortran
+
+        character*(128)	:: ezfio_filename	
+
+
+    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.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_initialized`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_cartesian`
+       * :c:data:`ao_coef`
+       * :c:data:`ao_expo`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_md5`
+       * :c:data:`ao_nucl`
+       * :c:data:`ao_num`
+       * :c:data:`ao_power`
+       * :c:data:`ao_prim_num`
+       * :c:data:`ao_two_e_integrals_erf_in_map`
+       * :c:data:`ao_two_e_integrals_in_map`
+       * :c:data:`cas_bitmask`
+       * :c:data:`correlation_energy_ratio_max`
+       * :c:data:`data_energy_proj`
+       * :c:data:`data_energy_var`
+       * :c:data:`data_one_e_dm_alpha_mo`
+       * :c:data:`data_one_e_dm_beta_mo`
+       * :c:data:`davidson_sze_max`
+       * :c:data:`disk_access_nuclear_repulsion`
+       * :c:data:`disk_based_davidson`
+       * :c:data:`distributed_davidson`
+       * :c:data:`do_direct_integrals`
+       * :c:data:`do_pseudo`
+       * :c:data:`do_pt2`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`elec_num`
+       * :c:data:`energy_iterations`
+       * :c:data:`ezfio_work_dir`
+       * :c:data:`frozen_orb_scf`
+       * :c:data:`generators_bitmask`
+       * :c:data:`generators_bitmask_restart`
+       * :c:data:`io_ao_integrals_e_n`
+       * :c:data:`io_ao_integrals_kinetic`
+       * :c:data:`io_ao_integrals_overlap`
+       * :c:data:`io_ao_integrals_pseudo`
+       * :c:data:`io_ao_one_e_integrals`
+       * :c:data:`io_ao_two_e_integrals`
+       * :c:data:`io_ao_two_e_integrals_erf`
+       * :c:data:`io_mo_integrals_e_n`
+       * :c:data:`io_mo_integrals_kinetic`
+       * :c:data:`io_mo_integrals_pseudo`
+       * :c:data:`io_mo_one_e_integrals`
+       * :c:data:`io_mo_two_e_integrals`
+       * :c:data:`io_mo_two_e_integrals_erf`
+       * :c:data:`level_shift`
+       * :c:data:`max_dim_diis`
+       * :c:data:`mo_class`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_guess_type`
+       * :c:data:`mo_integrals_threshold`
+       * :c:data:`mo_label`
+       * :c:data:`mo_num`
+       * :c:data:`mo_occ`
+       * :c:data:`mo_two_e_integrals_erf_in_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`mu_erf`
+       * :c:data:`n_cas_bitmask`
+       * :c:data:`n_det`
+       * :c:data:`n_det_iterations`
+       * :c:data:`n_det_max`
+       * :c:data:`n_det_max_full`
+       * :c:data:`n_det_print_wf`
+       * :c:data:`n_generators_bitmask`
+       * :c:data:`n_generators_bitmask_restart`
+       * :c:data:`n_it_scf_max`
+       * :c:data:`n_iter`
+       * :c:data:`n_states`
+       * :c:data:`n_states_diag`
+       * :c:data:`no_ivvv_integrals`
+       * :c:data:`no_vvv_integrals`
+       * :c:data:`no_vvvv_integrals`
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_charge_remove`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_label`
+       * :c:data:`nucl_num`
+       * :c:data:`only_expected_s2`
+       * :c:data:`pseudo_dz_k`
+       * :c:data:`pseudo_dz_kl`
+       * :c:data:`pseudo_grid_rmax`
+       * :c:data:`pseudo_grid_size`
+       * :c:data:`pseudo_klocmax`
+       * :c:data:`pseudo_kmax`
+       * :c:data:`pseudo_lmax`
+       * :c:data:`pseudo_n_k`
+       * :c:data:`pseudo_n_kl`
+       * :c:data:`pseudo_v_k`
+       * :c:data:`pseudo_v_kl`
+       * :c:data:`psi_coef`
+       * :c:data:`psi_det`
+       * :c:data:`psi_det_size`
+       * :c:data:`pt2_iterations`
+       * :c:data:`pt2_max`
+       * :c:data:`pt2_relative_error`
+       * :c:data:`qp_stop_filename`
+       * :c:data:`read_wf`
+       * :c:data:`s2_eig`
+       * :c:data:`scf_algorithm`
+       * :c:data:`state_following`
+       * :c:data:`target_energy`
+       * :c:data:`thresh_scf`
+       * :c:data:`threshold_davidson`
+       * :c:data:`threshold_diis`
+       * :c:data:`threshold_generators`
+       * :c:data:`used_weight`
+
+ 
+.. c:var:: ezfio_work_dir
+
+
+    File : :file:`ezfio_files/ezfio.irp.f`
+
+    .. code:: fortran
+
+        character*(128)	:: ezfio_work_dir	
+
+
+    EZFIO/work/
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ezfio_filename`
+
+
+ 
+.. c:var:: file_lock
+
+
+    File : :file:`ezfio_files/lock.irp.f`
+
+    .. code:: fortran
+
+        integer(omp_lock_kind)	:: file_lock	
+
+
+    OpenMP Lock for I/O
+
+
+ 
+.. c:var:: output_cpu_time_0
+
+
+    File : :file:`ezfio_files/output.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: output_wall_time_0	
+        double precision	:: output_cpu_time_0	
+
+
+    Initial CPU and wall times when printing in the output files
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_cartesian`
+       * :c:data:`ao_coef`
+       * :c:data:`ao_expo`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_md5`
+       * :c:data:`ao_nucl`
+       * :c:data:`ao_num`
+       * :c:data:`ao_power`
+       * :c:data:`ao_prim_num`
+       * :c:data:`ci_energy`
+       * :c:data:`correlation_energy_ratio_max`
+       * :c:data:`data_energy_proj`
+       * :c:data:`data_energy_var`
+       * :c:data:`data_one_e_dm_alpha_mo`
+       * :c:data:`data_one_e_dm_beta_mo`
+       * :c:data:`davidson_sze_max`
+       * :c:data:`disk_access_nuclear_repulsion`
+       * :c:data:`disk_based_davidson`
+       * :c:data:`distributed_davidson`
+       * :c:data:`do_direct_integrals`
+       * :c:data:`do_pseudo`
+       * :c:data:`do_pt2`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`energy_iterations`
+       * :c:data:`frozen_orb_scf`
+       * :c:data:`io_ao_integrals_e_n`
+       * :c:data:`io_ao_integrals_kinetic`
+       * :c:data:`io_ao_integrals_overlap`
+       * :c:data:`io_ao_integrals_pseudo`
+       * :c:data:`io_ao_one_e_integrals`
+       * :c:data:`io_ao_two_e_integrals`
+       * :c:data:`io_ao_two_e_integrals_erf`
+       * :c:data:`io_mo_integrals_e_n`
+       * :c:data:`io_mo_integrals_kinetic`
+       * :c:data:`io_mo_integrals_pseudo`
+       * :c:data:`io_mo_one_e_integrals`
+       * :c:data:`io_mo_two_e_integrals`
+       * :c:data:`io_mo_two_e_integrals_erf`
+       * :c:data:`level_shift`
+       * :c:data:`max_dim_diis`
+       * :c:data:`mo_class`
+       * :c:data:`mo_guess_type`
+       * :c:data:`mo_integrals_threshold`
+       * :c:data:`mu_erf`
+       * :c:data:`n_det_generators`
+       * :c:data:`n_det_iterations`
+       * :c:data:`n_det_max`
+       * :c:data:`n_det_max_full`
+       * :c:data:`n_det_print_wf`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_it_scf_max`
+       * :c:data:`n_iter`
+       * :c:data:`n_states`
+       * :c:data:`n_states_diag`
+       * :c:data:`no_ivvv_integrals`
+       * :c:data:`no_vvv_integrals`
+       * :c:data:`no_vvvv_integrals`
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_charge_remove`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_label`
+       * :c:data:`nucl_num`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`only_expected_s2`
+       * :c:data:`pseudo_dz_k`
+       * :c:data:`pseudo_dz_kl`
+       * :c:data:`pseudo_grid_rmax`
+       * :c:data:`pseudo_grid_size`
+       * :c:data:`pseudo_klocmax`
+       * :c:data:`pseudo_kmax`
+       * :c:data:`pseudo_lmax`
+       * :c:data:`pseudo_n_k`
+       * :c:data:`pseudo_n_kl`
+       * :c:data:`pseudo_v_k`
+       * :c:data:`pseudo_v_kl`
+       * :c:data:`pt2_iterations`
+       * :c:data:`pt2_max`
+       * :c:data:`pt2_relative_error`
+       * :c:data:`read_wf`
+       * :c:data:`s2_eig`
+       * :c:data:`scf_algorithm`
+       * :c:data:`state_following`
+       * :c:data:`target_energy`
+       * :c:data:`thresh_scf`
+       * :c:data:`threshold_davidson`
+       * :c:data:`threshold_diis`
+       * :c:data:`threshold_generators`
+       * :c:data:`used_weight`
+
+ 
+.. c:var:: output_wall_time_0
+
+
+    File : :file:`ezfio_files/output.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: output_wall_time_0	
+        double precision	:: output_cpu_time_0	
+
+
+    Initial CPU and wall times when printing in the output files
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_cartesian`
+       * :c:data:`ao_coef`
+       * :c:data:`ao_expo`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_md5`
+       * :c:data:`ao_nucl`
+       * :c:data:`ao_num`
+       * :c:data:`ao_power`
+       * :c:data:`ao_prim_num`
+       * :c:data:`ci_energy`
+       * :c:data:`correlation_energy_ratio_max`
+       * :c:data:`data_energy_proj`
+       * :c:data:`data_energy_var`
+       * :c:data:`data_one_e_dm_alpha_mo`
+       * :c:data:`data_one_e_dm_beta_mo`
+       * :c:data:`davidson_sze_max`
+       * :c:data:`disk_access_nuclear_repulsion`
+       * :c:data:`disk_based_davidson`
+       * :c:data:`distributed_davidson`
+       * :c:data:`do_direct_integrals`
+       * :c:data:`do_pseudo`
+       * :c:data:`do_pt2`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`energy_iterations`
+       * :c:data:`frozen_orb_scf`
+       * :c:data:`io_ao_integrals_e_n`
+       * :c:data:`io_ao_integrals_kinetic`
+       * :c:data:`io_ao_integrals_overlap`
+       * :c:data:`io_ao_integrals_pseudo`
+       * :c:data:`io_ao_one_e_integrals`
+       * :c:data:`io_ao_two_e_integrals`
+       * :c:data:`io_ao_two_e_integrals_erf`
+       * :c:data:`io_mo_integrals_e_n`
+       * :c:data:`io_mo_integrals_kinetic`
+       * :c:data:`io_mo_integrals_pseudo`
+       * :c:data:`io_mo_one_e_integrals`
+       * :c:data:`io_mo_two_e_integrals`
+       * :c:data:`io_mo_two_e_integrals_erf`
+       * :c:data:`level_shift`
+       * :c:data:`max_dim_diis`
+       * :c:data:`mo_class`
+       * :c:data:`mo_guess_type`
+       * :c:data:`mo_integrals_threshold`
+       * :c:data:`mu_erf`
+       * :c:data:`n_det_generators`
+       * :c:data:`n_det_iterations`
+       * :c:data:`n_det_max`
+       * :c:data:`n_det_max_full`
+       * :c:data:`n_det_print_wf`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_it_scf_max`
+       * :c:data:`n_iter`
+       * :c:data:`n_states`
+       * :c:data:`n_states_diag`
+       * :c:data:`no_ivvv_integrals`
+       * :c:data:`no_vvv_integrals`
+       * :c:data:`no_vvvv_integrals`
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_charge_remove`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_label`
+       * :c:data:`nucl_num`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`only_expected_s2`
+       * :c:data:`pseudo_dz_k`
+       * :c:data:`pseudo_dz_kl`
+       * :c:data:`pseudo_grid_rmax`
+       * :c:data:`pseudo_grid_size`
+       * :c:data:`pseudo_klocmax`
+       * :c:data:`pseudo_kmax`
+       * :c:data:`pseudo_lmax`
+       * :c:data:`pseudo_n_k`
+       * :c:data:`pseudo_n_kl`
+       * :c:data:`pseudo_v_k`
+       * :c:data:`pseudo_v_kl`
+       * :c:data:`pt2_iterations`
+       * :c:data:`pt2_max`
+       * :c:data:`pt2_relative_error`
+       * :c:data:`read_wf`
+       * :c:data:`s2_eig`
+       * :c:data:`scf_algorithm`
+       * :c:data:`state_following`
+       * :c:data:`target_energy`
+       * :c:data:`thresh_scf`
+       * :c:data:`threshold_davidson`
+       * :c:data:`threshold_diis`
+       * :c:data:`threshold_generators`
+       * :c:data:`used_weight`
+
+ 
+.. c:var:: qp_kill_filename
+
+
+    File : :file:`ezfio_files/qp_stop.irp.f`
+
+    .. code:: fortran
+
+        character*(128)	:: qp_stop_filename	
+        character*(128)	:: qp_kill_filename	
+        integer	:: qp_stop_variable	
+
+
+    Name of the file to check for qp stop
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ezfio_filename`
+
+
+ 
+.. c:var:: qp_stop_filename
+
+
+    File : :file:`ezfio_files/qp_stop.irp.f`
+
+    .. code:: fortran
+
+        character*(128)	:: qp_stop_filename	
+        character*(128)	:: qp_kill_filename	
+        integer	:: qp_stop_variable	
+
+
+    Name of the file to check for qp stop
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ezfio_filename`
+
+
+ 
+.. c:var:: qp_stop_variable
+
+
+    File : :file:`ezfio_files/qp_stop.irp.f`
+
+    .. code:: fortran
+
+        character*(128)	:: qp_stop_filename	
+        character*(128)	:: qp_kill_filename	
+        integer	:: qp_stop_variable	
+
+
+    Name of the file to check for qp stop
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ezfio_filename`
+
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: getunitandopen:
+
+
+    File : :file:`ezfio_files/get_unit_and_open.irp.f`
+
+    .. code:: fortran
+
+        integer function getUnitAndOpen(f,mode)
+
+
+    :f:
+       file name
+    
+    :mode:
+       'R' : READ, UNFORMATTED
+       'W' : WRITE, UNFORMATTED
+       'r' : READ, FORMATTED
+       'w' : WRITE, FORMATTED
+       'a' : APPEND, FORMATTED
+       'x' : READ/WRITE, FORMATTED
+    
+
+ 
+.. c:function:: qp_stop:
+
+
+    File : :file:`ezfio_files/qp_stop.irp.f`
+
+    .. code:: fortran
+
+        logical function qp_stop()
+
+
+    Checks if the qp_stop command was invoked for the clean termination of the program
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`qp_stop_filename`
+
+ 
+.. c:function:: write_bool:
+
+
+    File : :file:`ezfio_files/output.irp.f`
+
+    .. code:: fortran
+
+        subroutine write_bool(iunit,value,label)
+
+
+    Write an logical value in output
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_master`
+
+ 
+.. c:function:: write_double:
+
+
+    File : :file:`ezfio_files/output.irp.f`
+
+    .. code:: fortran
+
+        subroutine write_double(iunit,value,label)
+
+
+    Write a double precision value in output
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_master`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ci_energy`
+       * :c:func:`damping_scf`
+       * :c:func:`davidson_diag_hjj_sjj`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`psi_coef_max`
+       * :c:data:`pt2_e0_denominator`
+       * :c:func:`roothaan_hall_scf`
+       * :c:func:`run_cipsi`
+       * :c:func:`run_slave_main`
+       * :c:func:`run_stochastic_cipsi`
+       * :c:func:`zmq_pt2`
+       * :c:func:`zmq_selection`
+
+ 
+.. c:function:: write_int:
+
+
+    File : :file:`ezfio_files/output.irp.f`
+
+    .. code:: fortran
+
+        subroutine write_int(iunit,value,label)
+
+
+    Write an integer value in output
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_master`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`davidson_diag_hjj_sjj`
+       * :c:func:`make_s2_eigenfunction`
+       * :c:data:`mo_num`
+       * :c:data:`n_cas_bitmask`
+       * :c:data:`n_core_orb`
+       * :c:data:`n_det`
+       * :c:data:`n_det_generators`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_generators_bitmask`
+       * :c:data:`n_generators_bitmask_restart`
+       * :c:data:`n_int`
+       * :c:data:`nthreads_davidson`
+       * :c:data:`nthreads_pt2`
+       * :c:data:`psi_cas`
+       * :c:data:`psi_det_alpha_unique`
+       * :c:data:`psi_det_beta_unique`
+       * :c:data:`psi_det_size`
+       * :c:data:`pt2_n_teeth`
+       * :c:data:`qp_max_mem`
+       * :c:func:`remove_small_contributions`
+       * :c:func:`save_wavefunction_general`
+       * :c:func:`save_wavefunction_specified`
+       * :c:func:`zmq_pt2`
+
+ 
+.. c:function:: write_time:
+
+
+    File : :file:`ezfio_files/output.irp.f`
+
+    .. code:: fortran
+
+        subroutine write_time(iunit)
+
+
+    Write a time stamp in the output for chronological reconstruction
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`output_wall_time_0`
+       * :c:data:`mpi_master`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_cartesian`
+       * :c:data:`ao_coef`
+       * :c:data:`ao_expo`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_md5`
+       * :c:data:`ao_nucl`
+       * :c:data:`ao_num`
+       * :c:data:`ao_power`
+       * :c:data:`ao_prim_num`
+       * :c:data:`ci_energy`
+       * :c:data:`correlation_energy_ratio_max`
+       * :c:func:`damping_scf`
+       * :c:data:`data_energy_proj`
+       * :c:data:`data_energy_var`
+       * :c:data:`data_one_e_dm_alpha_mo`
+       * :c:data:`data_one_e_dm_beta_mo`
+       * :c:func:`davidson_diag_hjj_sjj`
+       * :c:data:`davidson_sze_max`
+       * :c:data:`disk_access_nuclear_repulsion`
+       * :c:data:`disk_based_davidson`
+       * :c:data:`distributed_davidson`
+       * :c:data:`do_direct_integrals`
+       * :c:data:`do_pseudo`
+       * :c:data:`do_pt2`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`energy_iterations`
+       * :c:data:`frozen_orb_scf`
+       * :c:data:`io_ao_integrals_e_n`
+       * :c:data:`io_ao_integrals_kinetic`
+       * :c:data:`io_ao_integrals_overlap`
+       * :c:data:`io_ao_integrals_pseudo`
+       * :c:data:`io_ao_one_e_integrals`
+       * :c:data:`io_ao_two_e_integrals`
+       * :c:data:`io_ao_two_e_integrals_erf`
+       * :c:data:`io_mo_integrals_e_n`
+       * :c:data:`io_mo_integrals_kinetic`
+       * :c:data:`io_mo_integrals_pseudo`
+       * :c:data:`io_mo_one_e_integrals`
+       * :c:data:`io_mo_two_e_integrals`
+       * :c:data:`io_mo_two_e_integrals_erf`
+       * :c:data:`level_shift`
+       * :c:func:`make_s2_eigenfunction`
+       * :c:data:`max_dim_diis`
+       * :c:func:`mo_as_eigvectors_of_mo_matrix`
+       * :c:func:`mo_as_svd_vectors_of_mo_matrix`
+       * :c:func:`mo_as_svd_vectors_of_mo_matrix_eig`
+       * :c:data:`mo_class`
+       * :c:data:`mo_guess_type`
+       * :c:data:`mo_integrals_threshold`
+       * :c:data:`mu_erf`
+       * :c:data:`n_det_generators`
+       * :c:data:`n_det_iterations`
+       * :c:data:`n_det_max`
+       * :c:data:`n_det_max_full`
+       * :c:data:`n_det_print_wf`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_it_scf_max`
+       * :c:data:`n_iter`
+       * :c:data:`n_states`
+       * :c:data:`n_states_diag`
+       * :c:data:`no_ivvv_integrals`
+       * :c:data:`no_vvv_integrals`
+       * :c:data:`no_vvvv_integrals`
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_charge_remove`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_label`
+       * :c:data:`nucl_num`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`only_expected_s2`
+       * :c:data:`pseudo_dz_k`
+       * :c:data:`pseudo_dz_kl`
+       * :c:data:`pseudo_grid_rmax`
+       * :c:data:`pseudo_grid_size`
+       * :c:data:`pseudo_klocmax`
+       * :c:data:`pseudo_kmax`
+       * :c:data:`pseudo_lmax`
+       * :c:data:`pseudo_n_k`
+       * :c:data:`pseudo_n_kl`
+       * :c:data:`pseudo_v_k`
+       * :c:data:`pseudo_v_kl`
+       * :c:data:`pt2_iterations`
+       * :c:data:`pt2_max`
+       * :c:data:`pt2_relative_error`
+       * :c:data:`read_wf`
+       * :c:func:`roothaan_hall_scf`
+       * :c:data:`s2_eig`
+       * :c:data:`scf_algorithm`
+       * :c:data:`state_following`
+       * :c:data:`target_energy`
+       * :c:data:`thresh_scf`
+       * :c:data:`threshold_davidson`
+       * :c:data:`threshold_diis`
+       * :c:data:`threshold_generators`
+       * :c:data:`used_weight`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`cpu_time`
+       * :c:func:`print_memory_usage`
+       * :c:func:`wall_time`
+

docs/source/modules/fci.rst

@@ -0,0 +1,160 @@
+.. _module_fci: 
+ 
+.. program:: fci 
+ 
+.. default-role:: option 
+ 
+===
+fci
+===
+
+
+|CIPSI| algorithm in the full configuration interaction space.
+
+
+The user point of view
+----------------------
+
+* :ref:`fci` performs |CIPSI| calculations using a stochastic scheme for both
+  the selection and the |PT2| contribution,
+
+* :ref:`pt2` computes the |PT2| contribution using the wave function stored in
+  the |EZFIO| database.
+
+
+The main keywords/options for this module are:
+
+* :option:`determinants n_det_max` : maximum number of Slater determinants in
+  the |CIPSI| wave function. The :ref:`fci` program will stop when the size of
+  the |CIPSI| wave function will exceed :option:`determinants n_det_max`.
+
+* :option:`perturbation pt2_max` : absolute value of the |PT2| to stop the
+  |CIPSI| calculation. Once the abs(|PT2|) :math:`<` :option:`perturbation pt2_max`,
+  the |CIPSI| calculation stops.
+
+* :option:`determinants n_states` : number of states to consider in the |CIPSI|
+  calculation.
+
+* :option:`determinants read_wf` : if |false|, starts with a |ROHF|-like
+  determinant, if |true|, starts with the current wave function(s) stored in
+  the |EZFIO| directory.
+
+.. note::
+   For a multi-state calculation, it is recommended to start with :ref:`cis`
+   or :ref:`cisd` wave functions as a guess.
+
+* :option:`determinants expected_s2` : expected value of |S^2| for the
+  desired spin multiplicity.
+
+* :option:`determinants s2_eig` : if |true|, systematically add all the
+  determinants needed to have a pure value of |S^2|. Also, if |true|, it
+  tracks only the states having the good :option:`determinants expected_s2`.
+
+
+
+
+The programmer's point of view
+------------------------------
+
+This module was created with the :ref:`module_cipsi` module.
+
+.. seealso::
+
+    The documentation of the :ref:`module_cipsi` module.
+
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: energy
+ 
+    Calculated Selected |FCI| energy
+ 
+ 
+.. option:: energy_pt2
+ 
+    Calculated |FCI| energy + |PT2|
+ 
+ 
+ 
+Programs 
+-------- 
+ 
+ * :ref:`fci` 
+ * :ref:`pt2` 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: do_ddci
+
+
+    File : :file:`fci/class.irp.f`
+
+    .. code:: fortran
+
+        logical	:: do_only_1h1p	
+        logical	:: do_ddci	
+
+
+    In the FCI case, all those are always false
+
+
+ 
+.. c:var:: do_only_1h1p
+
+
+    File : :file:`fci/class.irp.f`
+
+    .. code:: fortran
+
+        logical	:: do_only_1h1p	
+        logical	:: do_ddci	
+
+
+    In the FCI case, all those are always false
+
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: save_energy:
+
+
+    File : :file:`fci/save_energy.irp.f`
+
+    .. code:: fortran
+
+        subroutine save_energy(E,pt2)
+
+
+    Saves the energy in |EZFIO|.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_states`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`run_cipsi`
+       * :c:func:`run_stochastic_cipsi`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_set_fci_energy`
+       * :c:func:`ezfio_set_fci_energy_pt2`
+

docs/source/modules/generators_cas.rst

@@ -0,0 +1,19 @@
+.. _module_generators_cas: 
+ 
+.. program:: generators_cas 
+ 
+.. default-role:: option 
+ 
+==============
+generators_cas
+==============
+
+Module defining the generator determinants as those belonging to a |CAS|.
+The |MOs| belonging to the |CAS| are those which were set as active with
+the :ref:`qp_set_mo_class` command.
+
+This module is intended to be included in the :file:`NEED` file to define
+the generators as the |CAS| determinants, which can be useful to define post-CAS approaches (see cassd module for instance).
+
+
+ 

docs/source/modules/generators_full.rst

@@ -0,0 +1,295 @@
+.. _module_generators_full: 
+ 
+.. program:: generators_full 
+ 
+.. default-role:: option 
+ 
+===============
+generators_full
+===============
+
+Module defining the generator determinants as all the determinants of the
+variational space.
+
+This module is intended to be included in the :file:`NEED` file to define
+a full set of generators.
+ 
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: degree_max_generators
+
+
+    File : :file:`generators_full/generators.irp.f`
+
+    .. code:: fortran
+
+        integer	:: degree_max_generators	
+
+
+    Max degree of excitation (respect to HF) of the generators
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`hf_bitmask`
+       * :c:data:`n_det_generators`
+       * :c:data:`n_int`
+       * :c:data:`psi_det_generators`
+
+
+ 
+.. c:var:: n_det_generators
+
+
+    File : :file:`generators_full/generators.irp.f`
+
+    .. code:: fortran
+
+        integer	:: n_det_generators	
+
+
+    For Single reference wave functions, the number of generators is 1 : the
+    Hartree-Fock determinant
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_master`
+       * :c:data:`n_det`
+       * :c:data:`output_wall_time_0`
+       * :c:data:`psi_det_sorted`
+       * :c:data:`threshold_generators`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`degree_max_generators`
+       * :c:data:`n_det_selectors`
+       * :c:data:`pt2_f`
+       * :c:data:`pt2_j`
+       * :c:data:`pt2_n_tasks`
+       * :c:data:`pt2_n_teeth`
+       * :c:data:`pt2_u`
+       * :c:data:`pt2_w`
+
+ 
+.. c:var:: psi_coef_generators
+
+
+    File : :file:`generators_full/generators.irp.f`
+
+    .. code:: fortran
+
+        integer(bit_kind), allocatable	:: psi_det_generators	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_coef_generators	(psi_det_size,N_states)
+
+
+    For Single reference wave functions, the generator is the
+    Hartree-Fock determinant
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det`
+       * :c:data:`n_int`
+       * :c:data:`n_states`
+       * :c:data:`psi_det_size`
+       * :c:data:`psi_det_sorted`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`degree_max_generators`
+
+ 
+.. c:var:: psi_coef_sorted_gen
+
+
+    File : :file:`generators_full/generators.irp.f`
+
+    .. code:: fortran
+
+        integer(bit_kind), allocatable	:: psi_det_sorted_gen	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_coef_sorted_gen	(psi_det_size,N_states)
+        integer, allocatable	:: psi_det_sorted_gen_order	(psi_det_size)
+
+
+    For Single reference wave functions, the generator is the
+    Hartree-Fock determinant
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_int`
+       * :c:data:`n_states`
+       * :c:data:`psi_det_size`
+       * :c:data:`psi_det_sorted`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`pt2_f`
+       * :c:data:`pt2_n_teeth`
+       * :c:data:`pt2_w`
+
+ 
+.. c:var:: psi_det_generators
+
+
+    File : :file:`generators_full/generators.irp.f`
+
+    .. code:: fortran
+
+        integer(bit_kind), allocatable	:: psi_det_generators	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_coef_generators	(psi_det_size,N_states)
+
+
+    For Single reference wave functions, the generator is the
+    Hartree-Fock determinant
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det`
+       * :c:data:`n_int`
+       * :c:data:`n_states`
+       * :c:data:`psi_det_size`
+       * :c:data:`psi_det_sorted`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`degree_max_generators`
+
+ 
+.. c:var:: psi_det_sorted_gen
+
+
+    File : :file:`generators_full/generators.irp.f`
+
+    .. code:: fortran
+
+        integer(bit_kind), allocatable	:: psi_det_sorted_gen	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_coef_sorted_gen	(psi_det_size,N_states)
+        integer, allocatable	:: psi_det_sorted_gen_order	(psi_det_size)
+
+
+    For Single reference wave functions, the generator is the
+    Hartree-Fock determinant
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_int`
+       * :c:data:`n_states`
+       * :c:data:`psi_det_size`
+       * :c:data:`psi_det_sorted`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`pt2_f`
+       * :c:data:`pt2_n_teeth`
+       * :c:data:`pt2_w`
+
+ 
+.. c:var:: psi_det_sorted_gen_order
+
+
+    File : :file:`generators_full/generators.irp.f`
+
+    .. code:: fortran
+
+        integer(bit_kind), allocatable	:: psi_det_sorted_gen	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_coef_sorted_gen	(psi_det_size,N_states)
+        integer, allocatable	:: psi_det_sorted_gen_order	(psi_det_size)
+
+
+    For Single reference wave functions, the generator is the
+    Hartree-Fock determinant
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_int`
+       * :c:data:`n_states`
+       * :c:data:`psi_det_size`
+       * :c:data:`psi_det_sorted`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`pt2_f`
+       * :c:data:`pt2_n_teeth`
+       * :c:data:`pt2_w`
+
+ 
+.. c:var:: select_max
+
+
+    File : :file:`generators_full/generators.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: select_max	(size_select_max)
+
+
+    Memo to skip useless selectors
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`size_select_max`
+
+
+ 
+.. c:var:: size_select_max
+
+
+    File : :file:`generators_full/generators.irp.f`
+
+    .. code:: fortran
+
+        integer	:: size_select_max	
+
+
+    Size of the select_max array
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`select_max`
+

docs/source/modules/hartree_fock.rst

@@ -0,0 +1,406 @@
+.. _module_hartree_fock: 
+ 
+.. program:: hartree_fock 
+ 
+.. default-role:: option 
+ 
+============
+hartree_fock
+============
+
+
+The :ref:`scf` program performs *Restricted* Hartree-Fock
+calculations (the spatial part of the |MOs| is common for alpha and beta
+spinorbitals).
+
+The Hartree-Fock algorithm is a |SCF| and therefore is based on the
+:ref:`module_scf_utils` module. 
+
+The Fock matrix is defined in :file:`fock_matrix_hf.irp.f`.
+
+
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: energy
+ 
+    Energy HF
+ 
+ 
+ 
+Programs 
+-------- 
+ 
+ * :ref:`scf` 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: ao_two_e_integral_alpha
+
+
+    File : :file:`hartree_fock/fock_matrix_hf.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: ao_two_e_integral_alpha	(ao_num,ao_num)
+        double precision, allocatable	:: ao_two_e_integral_beta	(ao_num,ao_num)
+
+
+    Alpha Fock matrix in AO basis set
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_coef_normalized_ordered_transp`
+       * :c:data:`ao_expo_ordered_transp`
+       * :c:data:`ao_integrals_map`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_nucl`
+       * :c:data:`ao_num`
+       * :c:data:`ao_overlap_abs`
+       * :c:data:`ao_power`
+       * :c:data:`ao_prim_num`
+       * :c:data:`ao_two_e_integral_schwartz`
+       * :c:data:`ao_two_e_integrals_in_map`
+       * :c:data:`do_direct_integrals`
+       * :c:data:`n_pt_max_integrals`
+       * :c:data:`nucl_coord`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`hf_energy`
+
+ 
+.. c:var:: ao_two_e_integral_beta
+
+
+    File : :file:`hartree_fock/fock_matrix_hf.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: ao_two_e_integral_alpha	(ao_num,ao_num)
+        double precision, allocatable	:: ao_two_e_integral_beta	(ao_num,ao_num)
+
+
+    Alpha Fock matrix in AO basis set
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_coef_normalized_ordered_transp`
+       * :c:data:`ao_expo_ordered_transp`
+       * :c:data:`ao_integrals_map`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_nucl`
+       * :c:data:`ao_num`
+       * :c:data:`ao_overlap_abs`
+       * :c:data:`ao_power`
+       * :c:data:`ao_prim_num`
+       * :c:data:`ao_two_e_integral_schwartz`
+       * :c:data:`ao_two_e_integrals_in_map`
+       * :c:data:`do_direct_integrals`
+       * :c:data:`n_pt_max_integrals`
+       * :c:data:`nucl_coord`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`hf_energy`
+
+ 
+.. c:var:: extra_e_contrib_density
+
+
+    File : :file:`hartree_fock/hf_energy.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: extra_e_contrib_density	
+
+
+    Extra contribution to the SCF energy coming from the density.
+    
+    For a Hartree-Fock calculation: extra_e_contrib_density = 0
+    
+    For a Kohn-Sham or Range-separated Kohn-Sham: the exchange/correlation - trace of the V_xc potential
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`scf_energy`
+
+ 
+.. c:var:: fock_matrix_ao_alpha
+
+
+    File : :file:`hartree_fock/fock_matrix_hf.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: fock_matrix_ao_alpha	(ao_num,ao_num)
+        double precision, allocatable	:: fock_matrix_ao_beta	(ao_num,ao_num)
+
+
+    Alpha Fock matrix in AO basis set
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_two_e_integral_alpha`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao`
+       * :c:data:`fock_matrix_mo_alpha`
+       * :c:data:`fock_matrix_mo_beta`
+       * :c:data:`scf_energy`
+
+ 
+.. c:var:: fock_matrix_ao_beta
+
+
+    File : :file:`hartree_fock/fock_matrix_hf.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: fock_matrix_ao_alpha	(ao_num,ao_num)
+        double precision, allocatable	:: fock_matrix_ao_beta	(ao_num,ao_num)
+
+
+    Alpha Fock matrix in AO basis set
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_two_e_integral_alpha`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao`
+       * :c:data:`fock_matrix_mo_alpha`
+       * :c:data:`fock_matrix_mo_beta`
+       * :c:data:`scf_energy`
+
+ 
+.. c:var:: hf_energy
+
+
+    File : :file:`hartree_fock/hf_energy.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: hf_energy	
+        double precision	:: hf_two_electron_energy	
+        double precision	:: hf_one_electron_energy	
+
+
+    Hartree-Fock energy containing the nuclear repulsion, and its one- and two-body components.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+
+ 
+.. c:var:: hf_one_electron_energy
+
+
+    File : :file:`hartree_fock/hf_energy.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: hf_energy	
+        double precision	:: hf_two_electron_energy	
+        double precision	:: hf_one_electron_energy	
+
+
+    Hartree-Fock energy containing the nuclear repulsion, and its one- and two-body components.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+
+ 
+.. c:var:: hf_two_electron_energy
+
+
+    File : :file:`hartree_fock/hf_energy.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: hf_energy	
+        double precision	:: hf_two_electron_energy	
+        double precision	:: hf_one_electron_energy	
+
+
+    Hartree-Fock energy containing the nuclear repulsion, and its one- and two-body components.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: create_guess:
+
+
+    File : :file:`hartree_fock/scf.irp.f`
+
+    .. code:: fortran
+
+        subroutine create_guess
+
+
+    Create a MO guess if no MOs are present in the EZFIO directory
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ezfio_filename`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_guess_type`
+       * :c:data:`mo_one_e_integrals`
+       * :c:data:`ao_ortho_lowdin_coef`
+       * :c:data:`mo_label`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`scf`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_has_mo_basis_mo_coef`
+       * :c:func:`huckel_guess`
+       * :c:func:`mo_as_eigvectors_of_mo_matrix`
+
+    Touches:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_label`
+
+ 
+.. c:function:: run:
+
+
+    File : :file:`hartree_fock/scf.irp.f`
+
+    .. code:: fortran
+
+        subroutine run
+
+
+    Run SCF calculation
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`scf_energy`
+       * :c:data:`mo_label`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`pt2`
+       * :c:func:`scf`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_set_hartree_fock_energy`
+       * :c:func:`roothaan_hall_scf`
+
+    Touches:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`mo_coef`
+       * :c:data:`level_shift`
+       * :c:data:`mo_coef`
+

docs/source/modules/iterations.rst

@@ -0,0 +1,204 @@
+.. _module_iterations: 
+ 
+.. program:: iterations 
+ 
+.. default-role:: option 
+ 
+==========
+iterations
+==========
+
+Module which saves the computed energies for an extrapolation to
+the |FCI| limit.
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: n_iter
+ 
+    Number of saved iterations
+ 
+    Default: 1
+ 
+.. option:: n_det_iterations
+ 
+    Number of determinants at each iteration
+ 
+ 
+.. option:: energy_iterations
+ 
+    The variational energy at each iteration
+ 
+ 
+.. option:: pt2_iterations
+ 
+    The |PT2| correction at each iteration
+ 
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: extrapolated_energy
+
+
+    File : :file:`iterations/iterations.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: extrapolated_energy	(N_iter,N_states)
+
+
+    Extrapolated energy, using E_var = f(PT2) where PT2=0
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`energy_iterations`
+       * :c:data:`n_det`
+       * :c:data:`n_iter`
+       * :c:data:`n_states`
+       * :c:data:`pt2_iterations`
+
+
+ 
+.. c:var:: n_iter
+
+
+    File : :file:`iterations/io.irp.f`
+
+    .. code:: fortran
+
+        integer	:: n_iter	
+
+
+    number of iterations
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ezfio_filename`
+       * :c:data:`mpi_master`
+       * :c:data:`n_states`
+       * :c:data:`output_wall_time_0`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`extrapolated_energy`
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: print_extrapolated_energy:
+
+
+    File : :file:`iterations/print_extrapolation.irp.f`
+
+    .. code:: fortran
+
+        subroutine print_extrapolated_energy
+
+
+    Print the extrapolated energy in the output
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`extrapolated_energy`
+       * :c:data:`n_states`
+       * :c:data:`n_det`
+       * :c:data:`pt2_iterations`
+       * :c:data:`n_iter`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`run_cipsi`
+       * :c:func:`run_stochastic_cipsi`
+
+ 
+.. c:function:: print_summary:
+
+
+    File : :file:`iterations/print_summary.irp.f`
+
+    .. code:: fortran
+
+        subroutine print_summary(e_,pt2_,error_,variance_,norm_,n_det_,n_occ_pattern_,n_st,s2_)
+
+
+    Print the extrapolated energy in the output
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`do_pt2`
+       * :c:data:`s2_eig`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`run_cipsi`
+       * :c:func:`run_stochastic_cipsi`
+
+ 
+.. c:function:: save_iterations:
+
+
+    File : :file:`iterations/iterations.irp.f`
+
+    .. code:: fortran
+
+        subroutine save_iterations(e_, pt2_,n_)
+
+
+    Update the energy in the EZFIO file.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_iter`
+       * :c:data:`energy_iterations`
+       * :c:data:`n_states`
+       * :c:data:`pt2_iterations`
+       * :c:data:`n_det_iterations`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`run_cipsi`
+       * :c:func:`run_stochastic_cipsi`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_set_iterations_energy_iterations`
+       * :c:func:`ezfio_set_iterations_n_det_iterations`
+       * :c:func:`ezfio_set_iterations_n_iter`
+       * :c:func:`ezfio_set_iterations_pt2_iterations`
+

docs/source/modules/kohn_sham.rst

@@ -0,0 +1,101 @@
+.. _module_kohn_sham: 
+ 
+.. program:: kohn_sham 
+ 
+.. default-role:: option 
+ 
+=========
+kohn_sham
+=========
+
+
+The Kohn-Sham module performs *Restricted* Kohn-Sham calculations (the
+spatial part of the |MOs| is common for alpha and beta spinorbitals).
+
+The Kohn-Sham in an SCF and therefore is based on the ``scf_utils`` structure.
+It performs the following actions:
+
+#. Compute/Read all the one- and two-electron integrals, and store them in memory
+#. Check in the |EZFIO| database if there is a set of |MOs|. If there is, it
+   will read them as initial guess. Otherwise, it will create a guess.
+#. Perform the |SCF| iterations
+
+The definition of the Fock matrix is in :file:`kohn_sham fock_matrix_ks.irp.f`
+For the keywords related to the |SCF| procedure, see the ``scf_utils`` directory where you will find all options.
+The main are:
+
+#. :option:`scf_utils thresh_scf`
+#. :option:`scf_utils level_shift`
+
+At each iteration, the |MOs| are saved in the |EZFIO| database. Hence, if the calculation
+crashes for any unexpected reason, the calculation can be restarted by running again
+the |SCF| with the same |EZFIO| database.
+
+The `DIIS`_ algorithm is implemented, as well as the `level-shifting`_ method.
+If the |SCF| does not converge, try again with a higher value of :option:`level_shift`.
+
+To start a calculation from scratch, the simplest way is to remove the
+``mo_basis`` directory from the |EZFIO| database, and run the |SCF| again.
+
+
+
+
+.. _DIIS: https://en.wikipedia.org/w/index.php?title=DIIS
+.. _level-shifting: https://doi.org/10.1002/qua.560070407
+
+
+
+ 
+ 
+ 
+Programs 
+-------- 
+ 
+ * :ref:`ks_scf` 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: ks_energy
+
+
+    File : :file:`ks_enery.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: ks_energy	
+        double precision	:: two_e_energy	
+        double precision	:: one_e_energy	
+        double precision	:: fock_matrix_energy	
+        double precision	:: trace_potential_xc	
+
+
+    Kohn-Sham energy containing the nuclear repulsion energy, and the various components of this quantity.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_potential_alpha_xc`
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`e_correlation_dft`
+       * :c:data:`e_exchange_dft`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`extra_e_contrib_density`
+
+ 
+ 
+Subroutines / functions 
+----------------------- 

docs/source/modules/kohn_sham_rs.rst

@@ -0,0 +1,468 @@
+.. _module_kohn_sham_rs: 
+ 
+.. program:: kohn_sham_rs 
+ 
+.. default-role:: option 
+ 
+============
+kohn_sham_rs
+============
+
+
+The Range-separated Kohn-Sham module performs *Restricted* Kohn-Sham calculations (the
+spatial part of the |MOs| is common for alpha and beta spinorbitals) where the coulomb interaction is partially treated using exact exchange.
+The splitting of the interaction between long- and short-range is determined by the range-separation parameter :option:`ao_two_e_erf_ints mu_erf`. The long-range part of the interaction is explicitly treated with exact exchange, and the short-range part of the interaction is treated with appropriate DFT functionals.
+
+The Range-separated Kohn-Sham in an SCF and therefore is based on the ``scf_utils`` structure.
+It performs the following actions:
+
+#. Compute/Read all the one- and two-electron integrals, and store them in memory
+#. Check in the |EZFIO| database if there is a set of |MOs|. If there is, it
+   will read them as initial guess. Otherwise, it will create a guess.
+#. Perform the |SCF| iterations
+
+The definition of the Fock matrix is in :file:`kohn_sham_rs fock_matrix_rs_ks.irp.f`
+For the keywords related to the |SCF| procedure, see the ``scf_utils`` directory where you will find all options.
+The main are:
+# :option:`scf_utils thresh_scf`
+# :option:`scf_utils level_shift`
+
+
+At each iteration, the |MOs| are saved in the |EZFIO| database. Hence, if the calculation
+crashes for any unexpected reason, the calculation can be restarted by running again
+the |SCF| with the same |EZFIO| database.
+
+The `DIIS`_ algorithm is implemented, as well as the `level-shifting`_ method.
+If the |SCF| does not converge, try again with a higher value of :option:`level_shift`.
+
+To start a calculation from scratch, the simplest way is to remove the
+``mo_basis`` directory from the |EZFIO| database, and run the |SCF| again.
+
+
+.. _DIIS: https://en.wikipedia.org/w/index.php?title=DIIS
+.. _level-shifting: https://doi.org/10.1002/qua.560070407
+
+
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: energy
+ 
+    Energy range separated hybrid
+ 
+ 
+ 
+Programs 
+-------- 
+ 
+ * :ref:`rs_ks_scf` 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: ao_potential_alpha_xc
+
+
+    File : :file:`pot_functionals.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: ao_potential_alpha_xc	(ao_num,ao_num)
+        double precision, allocatable	:: ao_potential_beta_xc	(ao_num,ao_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`potential_x_alpha_ao`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`rs_ks_energy`
+
+ 
+.. c:var:: ao_potential_beta_xc
+
+
+    File : :file:`pot_functionals.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: ao_potential_alpha_xc	(ao_num,ao_num)
+        double precision, allocatable	:: ao_potential_beta_xc	(ao_num,ao_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`potential_x_alpha_ao`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`rs_ks_energy`
+
+ 
+.. c:var:: e_correlation_dft
+
+
+    File : :file:`pot_functionals.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: e_correlation_dft	
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`energy_x`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`extra_e_contrib_density`
+       * :c:data:`rs_ks_energy`
+
+ 
+.. c:var:: e_exchange_dft
+
+
+    File : :file:`pot_functionals.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: e_exchange_dft	
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`energy_x`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`extra_e_contrib_density`
+       * :c:data:`rs_ks_energy`
+
+ 
+.. c:var:: fock_matrix_alpha_no_xc_ao
+
+
+    File : :file:`fock_matrix_rs_ks.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: fock_matrix_alpha_no_xc_ao	(ao_num,ao_num)
+        double precision, allocatable	:: fock_matrix_beta_no_xc_ao	(ao_num,ao_num)
+
+
+    Mono electronic an Coulomb matrix in AO basis set
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_two_e_integral_alpha`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao_alpha`
+
+ 
+.. c:var:: fock_matrix_beta_no_xc_ao
+
+
+    File : :file:`fock_matrix_rs_ks.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: fock_matrix_alpha_no_xc_ao	(ao_num,ao_num)
+        double precision, allocatable	:: fock_matrix_beta_no_xc_ao	(ao_num,ao_num)
+
+
+    Mono electronic an Coulomb matrix in AO basis set
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_two_e_integral_alpha`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao_alpha`
+
+ 
+.. c:var:: fock_matrix_energy
+
+
+    File : :file:`rs_ks_energy.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: rs_ks_energy	
+        double precision	:: two_e_energy	
+        double precision	:: one_e_energy	
+        double precision	:: fock_matrix_energy	
+        double precision	:: trace_potential_xc	
+
+
+    Range-separated Kohn-Sham energy containing the nuclear repulsion energy, and the various components of this quantity.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_potential_alpha_xc`
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`e_correlation_dft`
+       * :c:data:`e_exchange_dft`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`extra_e_contrib_density`
+
+ 
+.. c:var:: one_e_energy
+
+
+    File : :file:`rs_ks_energy.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: rs_ks_energy	
+        double precision	:: two_e_energy	
+        double precision	:: one_e_energy	
+        double precision	:: fock_matrix_energy	
+        double precision	:: trace_potential_xc	
+
+
+    Range-separated Kohn-Sham energy containing the nuclear repulsion energy, and the various components of this quantity.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_potential_alpha_xc`
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`e_correlation_dft`
+       * :c:data:`e_exchange_dft`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`extra_e_contrib_density`
+
+ 
+.. c:var:: rs_ks_energy
+
+
+    File : :file:`rs_ks_energy.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: rs_ks_energy	
+        double precision	:: two_e_energy	
+        double precision	:: one_e_energy	
+        double precision	:: fock_matrix_energy	
+        double precision	:: trace_potential_xc	
+
+
+    Range-separated Kohn-Sham energy containing the nuclear repulsion energy, and the various components of this quantity.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_potential_alpha_xc`
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`e_correlation_dft`
+       * :c:data:`e_exchange_dft`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`extra_e_contrib_density`
+
+ 
+.. c:var:: trace_potential_xc
+
+
+    File : :file:`rs_ks_energy.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: rs_ks_energy	
+        double precision	:: two_e_energy	
+        double precision	:: one_e_energy	
+        double precision	:: fock_matrix_energy	
+        double precision	:: trace_potential_xc	
+
+
+    Range-separated Kohn-Sham energy containing the nuclear repulsion energy, and the various components of this quantity.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_potential_alpha_xc`
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`e_correlation_dft`
+       * :c:data:`e_exchange_dft`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`extra_e_contrib_density`
+
+ 
+.. c:var:: two_e_energy
+
+
+    File : :file:`rs_ks_energy.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: rs_ks_energy	
+        double precision	:: two_e_energy	
+        double precision	:: one_e_energy	
+        double precision	:: fock_matrix_energy	
+        double precision	:: trace_potential_xc	
+
+
+    Range-separated Kohn-Sham energy containing the nuclear repulsion energy, and the various components of this quantity.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`ao_potential_alpha_xc`
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`e_correlation_dft`
+       * :c:data:`e_exchange_dft`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`extra_e_contrib_density`
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: check_coherence_functional:
+
+
+    File : :file:`rs_ks_scf.irp.f`
+
+    .. code:: fortran
+
+        subroutine check_coherence_functional
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`exchange_functional`
+       * :c:data:`correlation_functional`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`rs_ks_scf`
+

docs/source/modules/mo_basis.rst

@@ -0,0 +1,815 @@
+.. _module_mo_basis: 
+ 
+.. program:: mo_basis 
+ 
+.. default-role:: option 
+ 
+========
+mo_basis
+========
+
+Molecular orbitals are expressed as
+
+.. math::
+
+  \phi_k({\bf r}) = \sum_i C_{ik} \chi_k({\bf r})
+
+
+where :math:`\chi_k` are *normalized* atomic basis functions.
+
+The current set of |MOs| has a label `mo_label`.
+When the orbitals are modified, the label should also be updated to keep
+everything consistent.
+
+When saving the |MOs|, the :file:`mo_basis` directory of the |EZFIO| database
+is copied in the :file:`save` directory, named by the current `mo_label`. All
+this is done with the script named :file:`save_current_mos.sh` in the
+:file:`$QP_ROOT/scripts` directory.
+
+
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: mo_num
+ 
+    Total number of |MOs|
+ 
+ 
+.. option:: mo_coef
+ 
+    Coefficient of the i-th |AO| on the j-th |MO|
+ 
+ 
+.. option:: mo_label
+ 
+    Label characterizing the MOS (Local, Canonical, Natural, *etc*)
+ 
+ 
+.. option:: mo_occ
+ 
+    |MO| occupation numbers
+ 
+ 
+.. option:: mo_class
+ 
+    [ Core | Inactive | Active | Virtual | Deleted ], as defined by :ref:`qp_set_mo_class`
+ 
+ 
+.. option:: ao_md5
+ 
+    MD5 checksum characterizing the |AO| basis set.
+ 
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: mo_coef
+
+
+    File : :file:`mo_basis/mos.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_coef	(ao_num,mo_num)
+
+
+    Molecular orbital coefficients on |AO| basis set
+    
+    mo_coef(i,j) = coefficient of the i-th |AO| on the jth mo
+    
+    mo_label : Label characterizing the MOS (local, canonical, natural, etc)
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_ortho_canonical_coef`
+       * :c:data:`ezfio_filename`
+       * :c:data:`mo_num`
+       * :c:data:`mpi_master`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`eigenvectors_fock_matrix_mo`
+       * :c:data:`fock_matrix_mo_alpha`
+       * :c:data:`fock_matrix_mo_beta`
+       * :c:data:`fps_spf_matrix_mo`
+       * :c:data:`mo_coef_in_ao_ortho_basis`
+       * :c:data:`mo_coef_transp`
+       * :c:data:`mo_dipole_x`
+       * :c:data:`mo_integrals_n_e`
+       * :c:data:`mo_integrals_n_e_per_atom`
+       * :c:data:`mo_kinetic_integrals`
+       * :c:data:`mo_overlap`
+       * :c:data:`mo_pseudo_integrals`
+       * :c:data:`mo_spread_x`
+       * :c:data:`mo_two_e_int_erf_jj_from_ao`
+       * :c:data:`mo_two_e_integral_jj_from_ao`
+       * :c:data:`mo_two_e_integrals_erf_in_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`mo_two_e_integrals_vv_from_ao`
+       * :c:data:`one_e_dm_ao_alpha`
+       * :c:data:`one_e_spin_density_ao`
+       * :c:data:`psi_det`
+       * :c:data:`s_mo_coef`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+ 
+.. c:var:: mo_coef_begin_iteration
+
+
+    File : :file:`mo_basis/track_orb.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_coef_begin_iteration	(ao_num,mo_num)
+
+
+    Void provider to store the coefficients of the |MO| basis at the beginning of the SCF iteration
+    
+    Usefull to track some orbitals
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: mo_coef_in_ao_ortho_basis
+
+
+    File : :file:`mo_basis/mos.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_coef_in_ao_ortho_basis	(ao_num,mo_num)
+
+
+    |MO| coefficients in orthogonalized |AO| basis
+    
+    :math:`C^{-1}.C_{mo}` 
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_ortho_canonical_coef_inv`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: mo_coef_transp
+
+
+    File : :file:`mo_basis/mos.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_coef_transp	(mo_num,ao_num)
+
+
+    |MO| coefficients on |AO| basis set
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_two_e_int_erf_jj_from_ao`
+       * :c:data:`mo_two_e_integral_jj_from_ao`
+       * :c:data:`mo_two_e_integrals_erf_in_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`mo_two_e_integrals_vv_from_ao`
+
+ 
+.. c:var:: mo_label
+
+
+    File : :file:`mo_basis/mos.irp.f`
+
+    .. code:: fortran
+
+        character*(64)	:: mo_label	
+
+
+    |MO| coefficients on |AO| basis set
+    
+    mo_coef(i,j) = coefficient of the i-th |AO| on the j-th |MO|
+    
+    mo_label : Label characterizing the |MOs| (local, canonical, natural, etc)
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ezfio_filename`
+       * :c:data:`mpi_master`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det`
+       * :c:data:`psi_coef`
+       * :c:data:`psi_det`
+
+ 
+.. c:var:: mo_num
+
+
+    File : :file:`mo_basis/mos.irp.f`
+
+    .. code:: fortran
+
+        integer	:: mo_num	
+
+
+    Number of MOs
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_ortho_canonical_coef`
+       * :c:data:`ezfio_filename`
+       * :c:data:`mpi_master`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_ortho_canonical_nucl_elec_integrals`
+       * :c:data:`ao_ortho_lowdin_nucl_elec_integrals`
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`core_fock_operator`
+       * :c:data:`core_fock_operator_erf`
+       * :c:data:`data_one_e_dm_alpha_mo`
+       * :c:data:`data_one_e_dm_beta_mo`
+       * :c:data:`eigenvectors_fock_matrix_mo`
+       * :c:data:`fock_matrix_ao`
+       * :c:data:`fock_matrix_mo`
+       * :c:data:`fock_matrix_mo_alpha`
+       * :c:data:`fock_matrix_mo_beta`
+       * :c:data:`fock_operator_closed_shell_ref_bitmask`
+       * :c:data:`fock_wee_closed_shell`
+       * :c:data:`fps_spf_matrix_mo`
+       * :c:data:`full_ijkl_bitmask`
+       * :c:data:`int_erf_3_index`
+       * :c:data:`list_core_inact_act`
+       * :c:data:`list_inact`
+       * :c:data:`mo_class`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_coef_begin_iteration`
+       * :c:data:`mo_coef_in_ao_ortho_basis`
+       * :c:data:`mo_coef_transp`
+       * :c:data:`mo_dipole_x`
+       * :c:data:`mo_integrals_cache_min`
+       * :c:data:`mo_integrals_erf_cache_min`
+       * :c:data:`mo_integrals_erf_map`
+       * :c:data:`mo_integrals_map`
+       * :c:data:`mo_integrals_n_e`
+       * :c:data:`mo_integrals_n_e_per_atom`
+       * :c:data:`mo_kinetic_integrals`
+       * :c:data:`mo_occ`
+       * :c:data:`mo_one_e_integrals`
+       * :c:data:`mo_overlap`
+       * :c:data:`mo_pseudo_integrals`
+       * :c:data:`mo_spread_x`
+       * :c:data:`mo_two_e_int_erf_jj`
+       * :c:data:`mo_two_e_int_erf_jj_from_ao`
+       * :c:data:`mo_two_e_integral_jj_from_ao`
+       * :c:data:`mo_two_e_integrals_erf_in_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`mo_two_e_integrals_jj`
+       * :c:data:`mo_two_e_integrals_vv_from_ao`
+       * :c:data:`n_core_orb`
+       * :c:data:`n_int`
+       * :c:data:`one_e_dm_ao_alpha`
+       * :c:data:`one_e_dm_dagger_mo_spin_index`
+       * :c:data:`one_e_dm_mo`
+       * :c:data:`one_e_dm_mo_alpha`
+       * :c:data:`one_e_dm_mo_alpha_average`
+       * :c:data:`one_e_dm_mo_diff`
+       * :c:data:`one_e_dm_mo_spin_index`
+       * :c:data:`one_e_spin_density_ao`
+       * :c:data:`one_e_spin_density_mo`
+       * :c:data:`psi_energy_h_core`
+       * :c:data:`s_mo_coef`
+       * :c:data:`singles_alpha_csc_idx`
+       * :c:data:`singles_beta_csc_idx`
+
+ 
+.. c:var:: mo_occ
+
+
+    File : :file:`mo_basis/mos.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_occ	(mo_num)
+
+
+    |MO| occupation numbers
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`ezfio_filename`
+       * :c:data:`mo_num`
+       * :c:data:`mpi_master`
+
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: ao_ortho_cano_to_ao:
+
+
+    File : :file:`mo_basis/mos.irp.f`
+
+    .. code:: fortran
+
+        subroutine ao_ortho_cano_to_ao(A_ao,LDA_ao,A,LDA)
+
+
+    Transform A from the |AO| basis to the orthogonal |AO| basis
+    
+    $C^{-1}.A_{ao}.C^{\dagger-1}$
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_ortho_canonical_coef_inv`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dgemm`
+
+ 
+.. c:function:: ao_to_mo:
+
+
+    File : :file:`mo_basis/mos.irp.f`
+
+    .. code:: fortran
+
+        subroutine ao_to_mo(A_ao,LDA_ao,A_mo,LDA_mo)
+
+
+    Transform A from the |AO| basis to the |MO| basis
+    
+    $C^\dagger.A_{ao}.C$
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_mo_alpha`
+       * :c:data:`fock_matrix_mo_beta`
+       * :c:data:`fps_spf_matrix_mo`
+       * :c:data:`mo_dipole_x`
+       * :c:data:`mo_integrals_n_e`
+       * :c:data:`mo_integrals_n_e_per_atom`
+       * :c:data:`mo_kinetic_integrals`
+       * :c:data:`mo_pseudo_integrals`
+       * :c:data:`mo_spread_x`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dgemm`
+
+ 
+.. c:function:: give_all_mos_and_grad_and_lapl_at_r:
+
+
+    File : :file:`mo_basis/mos_in_r.irp.f`
+
+    .. code:: fortran
+
+        subroutine give_all_mos_and_grad_and_lapl_at_r(r,mos_array,mos_grad_array,mos_lapl_array)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`give_all_aos_and_grad_and_lapl_at_r`
+
+ 
+.. c:function:: give_all_mos_and_grad_at_r:
+
+
+    File : :file:`mo_basis/mos_in_r.irp.f`
+
+    .. code:: fortran
+
+        subroutine give_all_mos_and_grad_at_r(r,mos_array,mos_grad_array)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`give_all_aos_and_grad_at_r`
+
+ 
+.. c:function:: give_all_mos_at_r:
+
+
+    File : :file:`mo_basis/mos_in_r.irp.f`
+
+    .. code:: fortran
+
+        subroutine give_all_mos_at_r(r,mos_array)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef_transp`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dgemv`
+       * :c:func:`give_all_aos_at_r`
+
+ 
+.. c:function:: initialize_mo_coef_begin_iteration:
+
+
+    File : :file:`mo_basis/track_orb.irp.f`
+
+    .. code:: fortran
+
+        subroutine initialize_mo_coef_begin_iteration
+
+
+    
+    Initialize :c:data:`mo_coef_begin_iteration` to the current :c:data:`mo_coef`
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_coef_begin_iteration`
+       * :c:data:`mo_coef`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`damping_scf`
+       * :c:func:`roothaan_hall_scf`
+
+ 
+.. c:function:: mix_mo_jk:
+
+
+    File : :file:`mo_basis/mos.irp.f`
+
+    .. code:: fortran
+
+        subroutine mix_mo_jk(j,k)
+
+
+    Rotates the j-th |MO| with the k-th |MO| to give two new |MOs| that are
+    
+    * $+ = \frac{1}{\sqrt{2}} ( | j\rangle +  | k\rangle)$
+    
+    * $- = \frac{1}{\sqrt{2}} ( | j\rangle -  | k\rangle)$
+    
+    by convention, the '+' |MO| is in the lowest  index (min(j,k))
+    by convention, the '-' |MO| is in the highest index (max(j,k))
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`mo_coef`
+
+ 
+.. c:function:: mo_as_eigvectors_of_mo_matrix:
+
+
+    File : :file:`mo_basis/utils.irp.f`
+
+    .. code:: fortran
+
+        subroutine mo_as_eigvectors_of_mo_matrix(matrix,n,m,label,sign,output)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_label`
+       * :c:data:`ao_num`
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_guess`
+       * :c:func:`damping_scf`
+       * :c:func:`hcore_guess`
+       * :c:func:`roothaan_hall_scf`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dgemm`
+       * :c:func:`lapack_diag`
+       * :c:func:`write_time`
+
+ 
+.. c:function:: mo_as_svd_vectors_of_mo_matrix:
+
+
+    File : :file:`mo_basis/utils.irp.f`
+
+    .. code:: fortran
+
+        subroutine mo_as_svd_vectors_of_mo_matrix(matrix,lda,m,n,label)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_label`
+       * :c:data:`ao_num`
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dgemm`
+       * :c:func:`svd`
+       * :c:func:`write_time`
+
+ 
+.. c:function:: mo_as_svd_vectors_of_mo_matrix_eig:
+
+
+    File : :file:`mo_basis/utils.irp.f`
+
+    .. code:: fortran
+
+        subroutine mo_as_svd_vectors_of_mo_matrix_eig(matrix,lda,m,n,eig,label)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_label`
+       * :c:data:`ao_num`
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`set_natural_mos`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dgemm`
+       * :c:func:`svd`
+       * :c:func:`write_time`
+
+ 
+.. c:function:: reorder_core_orb:
+
+
+    File : :file:`mo_basis/track_orb.irp.f`
+
+    .. code:: fortran
+
+        subroutine reorder_core_orb
+
+
+    routines that takes the current :c:data:`mo_coef` and reorder the core orbitals (see :c:data:`list_core` and :c:data:`n_core_orb`) according to the overlap with :c:data:`mo_coef_begin_iteration`
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef_begin_iteration`
+       * :c:data:`mo_coef`
+       * :c:data:`ao_overlap`
+       * :c:data:`n_core_orb`
+       * :c:data:`ao_num`
+       * :c:data:`list_inact`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`damping_scf`
+       * :c:func:`roothaan_hall_scf`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dsort`
+
+ 
+.. c:function:: save_mos:
+
+
+    File : :file:`mo_basis/utils.irp.f`
+
+    .. code:: fortran
+
+        subroutine save_mos
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_occ`
+       * :c:data:`ao_md5`
+       * :c:data:`ezfio_filename`
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef`
+       * :c:data:`ao_num`
+       * :c:data:`mo_label`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`damping_scf`
+       * :c:func:`hcore_guess`
+       * :c:func:`huckel_guess`
+       * :c:func:`roothaan_hall_scf`
+       * :c:func:`save_natural_mos`
+       * :c:func:`save_ortho_mos`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_set_mo_basis_ao_md5`
+       * :c:func:`ezfio_set_mo_basis_mo_coef`
+       * :c:func:`ezfio_set_mo_basis_mo_label`
+       * :c:func:`ezfio_set_mo_basis_mo_num`
+       * :c:func:`ezfio_set_mo_basis_mo_occ`
+       * :c:func:`system`
+
+ 
+.. c:function:: save_mos_truncated:
+
+
+    File : :file:`mo_basis/utils.irp.f`
+
+    .. code:: fortran
+
+        subroutine save_mos_truncated(n)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_occ`
+       * :c:data:`ao_md5`
+       * :c:data:`ezfio_filename`
+       * :c:data:`mo_coef`
+       * :c:data:`ao_num`
+       * :c:data:`mo_label`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_set_mo_basis_ao_md5`
+       * :c:func:`ezfio_set_mo_basis_mo_coef`
+       * :c:func:`ezfio_set_mo_basis_mo_label`
+       * :c:func:`ezfio_set_mo_basis_mo_num`
+       * :c:func:`ezfio_set_mo_basis_mo_occ`
+       * :c:func:`system`
+

docs/source/modules/mo_guess.rst

@@ -0,0 +1,160 @@
+.. _module_mo_guess: 
+ 
+.. program:: mo_guess 
+ 
+.. default-role:: option 
+ 
+========
+mo_guess
+========
+
+Guess for |MOs|.
+
+ 
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: ao_ortho_canonical_nucl_elec_integrals
+
+
+    File : :file:`mo_guess/pot_mo_ortho_canonical_ints.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: ao_ortho_canonical_nucl_elec_integrals	(mo_num,mo_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_n_e`
+       * :c:data:`ao_num`
+       * :c:data:`ao_ortho_canonical_coef`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: ao_ortho_lowdin_coef
+
+
+    File : :file:`mo_guess/mo_ortho_lowdin.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: ao_ortho_lowdin_coef	(ao_num,ao_num)
+
+
+    matrix of the coefficients of the mos generated by the
+    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
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_overlap`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_ortho_lowdin_nucl_elec_integrals`
+       * :c:data:`ao_ortho_lowdin_overlap`
+
+ 
+.. c:var:: ao_ortho_lowdin_nucl_elec_integrals
+
+
+    File : :file:`mo_guess/pot_mo_ortho_lowdin_ints.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: ao_ortho_lowdin_nucl_elec_integrals	(mo_num,mo_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_n_e`
+       * :c:data:`ao_num`
+       * :c:data:`ao_ortho_lowdin_coef`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: ao_ortho_lowdin_overlap
+
+
+    File : :file:`mo_guess/mo_ortho_lowdin.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: ao_ortho_lowdin_overlap	(ao_num,ao_num)
+
+
+    overlap matrix of the ao_ortho_lowdin
+    supposed to be the Identity
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_ortho_lowdin_coef`
+       * :c:data:`ao_overlap`
+
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: hcore_guess:
+
+
+    File : :file:`mo_guess/h_core_guess_routine.irp.f`
+
+    .. code:: fortran
+
+        subroutine hcore_guess
+
+
+    Produce `H_core` MO orbital
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_label`
+       * :c:data:`mo_one_e_integrals`
+       * :c:data:`mo_coef`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`mo_as_eigvectors_of_mo_matrix`
+       * :c:func:`save_mos`
+
+    Touches:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_coef`
+       * :c:data:`mo_label`
+

docs/source/modules/mo_one_e_ints.rst

@@ -0,0 +1,571 @@
+.. _module_mo_one_e_ints: 
+ 
+.. program:: mo_one_e_ints 
+ 
+.. default-role:: option 
+ 
+==================
+mo_one_e_integrals
+==================
+
+All the one-electron integrals in |MO| basis are defined here.
+
+The most important providers for usual quantum-chemistry calculation are:
+
+* `mo_kinetic_integrals` which are the kinetic operator integrals on the |AO| basis (see :file:`kin_mo_ints.irp.f`)
+* `mo_integrals_n_e` which are the nuclear-elctron operator integrals on the |AO| basis (see :file:`pot_mo_ints.irp.f`)
+* `mo_one_e_integrals` which are the the h_core operator integrals on the |AO| basis (see :file:`mo_mono_ints.irp.f`)
+
+Note that you can find other interesting integrals related to the position operator in :file:`spread_dipole_mo.irp.f`.
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: mo_integrals_e_n
+ 
+    Nucleus-electron integrals in |MO| basis set
+ 
+ 
+.. option:: io_mo_integrals_e_n
+ 
+    Read/Write |MO| electron-nucleus attraction integrals from/to disk [ Write | Read | None ]
+ 
+    Default: None
+ 
+.. option:: mo_integrals_kinetic
+ 
+    Kinetic energy integrals in |MO| basis set
+ 
+ 
+.. option:: io_mo_integrals_kinetic
+ 
+    Read/Write |MO| one-electron kinetic integrals from/to disk [ Write | Read | None ]
+ 
+    Default: None
+ 
+.. option:: mo_integrals_pseudo
+ 
+    Pseudopotential integrals in |MO| basis set
+ 
+ 
+.. option:: io_mo_integrals_pseudo
+ 
+    Read/Write |MO| pseudopotential integrals from/to disk [ Write | Read | None ]
+ 
+    Default: None
+ 
+.. option:: mo_one_e_integrals
+ 
+    One-electron integrals in |MO| basis set
+ 
+ 
+.. option:: io_mo_one_e_integrals
+ 
+    Read/Write |MO| one-electron integrals from/to disk [ Write | Read | None ]
+ 
+    Default: None
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: mo_dipole_x
+
+
+    File : :file:`mo_one_e_ints/spread_dipole_mo.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_dipole_x	(mo_num,mo_num)
+        double precision, allocatable	:: mo_dipole_y	(mo_num,mo_num)
+        double precision, allocatable	:: mo_dipole_z	(mo_num,mo_num)
+
+
+    array of the integrals of MO_i * x MO_j
+    array of the integrals of MO_i * y MO_j
+    array of the integrals of MO_i * z MO_j
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_dipole_x`
+       * :c:data:`ao_num`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: mo_dipole_y
+
+
+    File : :file:`mo_one_e_ints/spread_dipole_mo.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_dipole_x	(mo_num,mo_num)
+        double precision, allocatable	:: mo_dipole_y	(mo_num,mo_num)
+        double precision, allocatable	:: mo_dipole_z	(mo_num,mo_num)
+
+
+    array of the integrals of MO_i * x MO_j
+    array of the integrals of MO_i * y MO_j
+    array of the integrals of MO_i * z MO_j
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_dipole_x`
+       * :c:data:`ao_num`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: mo_dipole_z
+
+
+    File : :file:`mo_one_e_ints/spread_dipole_mo.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_dipole_x	(mo_num,mo_num)
+        double precision, allocatable	:: mo_dipole_y	(mo_num,mo_num)
+        double precision, allocatable	:: mo_dipole_z	(mo_num,mo_num)
+
+
+    array of the integrals of MO_i * x MO_j
+    array of the integrals of MO_i * y MO_j
+    array of the integrals of MO_i * z MO_j
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_dipole_x`
+       * :c:data:`ao_num`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: mo_integrals_n_e
+
+
+    File : :file:`mo_one_e_ints/pot_mo_ints.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_integrals_n_e	(mo_num,mo_num)
+
+
+    Nucleus-electron interaction on the |MO| basis
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_n_e`
+       * :c:data:`ao_num`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+       * :c:data:`read_mo_integrals_e_n`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_one_e_integrals`
+       * :c:data:`ref_bitmask_energy`
+
+ 
+.. c:var:: mo_integrals_n_e_per_atom
+
+
+    File : :file:`mo_one_e_ints/pot_mo_ints.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_integrals_n_e_per_atom	(mo_num,mo_num,nucl_num)
+
+
+    mo_integrals_n_e_per_atom(i,j,k) =
+    :math:`\langle \phi_i| -\frac{1}{|r-R_k|} | \phi_j \rangle` .
+    where R_k is the coordinate of the k-th nucleus.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_integrals_n_e_per_atom`
+       * :c:data:`ao_num`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+       * :c:data:`nucl_num`
+
+
+ 
+.. c:var:: mo_kinetic_integrals
+
+
+    File : :file:`mo_one_e_ints/kin_mo_ints.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_kinetic_integrals	(mo_num,mo_num)
+
+
+    Kinetic energy integrals in the MO basis
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_kinetic_integrals`
+       * :c:data:`ao_num`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+       * :c:data:`read_mo_integrals_kinetic`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_one_e_integrals`
+       * :c:data:`ref_bitmask_energy`
+
+ 
+.. c:var:: mo_one_e_integrals
+
+
+    File : :file:`mo_one_e_ints/mo_one_e_ints.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_one_e_integrals	(mo_num,mo_num)
+
+
+    array of the mono electronic hamiltonian on the MOs basis :
+    sum of the kinetic and nuclear electronic potential (and pseudo potential if needed)
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`do_pseudo`
+       * :c:data:`mo_integrals_n_e`
+       * :c:data:`mo_kinetic_integrals`
+       * :c:data:`mo_num`
+       * :c:data:`mo_pseudo_integrals`
+       * :c:data:`read_mo_one_e_integrals`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`core_energy`
+       * :c:data:`core_energy_erf`
+       * :c:data:`fock_operator_closed_shell_ref_bitmask`
+       * :c:data:`psi_energy_h_core`
+       * :c:data:`ref_bitmask_energy`
+
+ 
+.. c:var:: mo_overlap
+
+
+    File : :file:`mo_one_e_ints/mo_overlap.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_overlap	(mo_num,mo_num)
+
+
+    Provider to check that the MOs are indeed orthonormal.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_overlap`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: mo_pseudo_integrals
+
+
+    File : :file:`mo_one_e_ints/pot_mo_pseudo_ints.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_pseudo_integrals	(mo_num,mo_num)
+
+
+    Pseudopotential integrals in |MO| basis
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_pseudo_integrals`
+       * :c:data:`do_pseudo`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+       * :c:data:`read_mo_integrals_pseudo`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_one_e_integrals`
+
+ 
+.. c:var:: mo_spread_x
+
+
+    File : :file:`mo_one_e_ints/spread_dipole_mo.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_spread_x	(mo_num,mo_num)
+        double precision, allocatable	:: mo_spread_y	(mo_num,mo_num)
+        double precision, allocatable	:: mo_spread_z	(mo_num,mo_num)
+
+
+    array of the integrals of MO_i * x^2 MO_j
+    array of the integrals of MO_i * y^2 MO_j
+    array of the integrals of MO_i * z^2 MO_j
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_spread_x`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: mo_spread_y
+
+
+    File : :file:`mo_one_e_ints/spread_dipole_mo.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_spread_x	(mo_num,mo_num)
+        double precision, allocatable	:: mo_spread_y	(mo_num,mo_num)
+        double precision, allocatable	:: mo_spread_z	(mo_num,mo_num)
+
+
+    array of the integrals of MO_i * x^2 MO_j
+    array of the integrals of MO_i * y^2 MO_j
+    array of the integrals of MO_i * z^2 MO_j
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_spread_x`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: mo_spread_z
+
+
+    File : :file:`mo_one_e_ints/spread_dipole_mo.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: mo_spread_x	(mo_num,mo_num)
+        double precision, allocatable	:: mo_spread_y	(mo_num,mo_num)
+        double precision, allocatable	:: mo_spread_z	(mo_num,mo_num)
+
+
+    array of the integrals of MO_i * x^2 MO_j
+    array of the integrals of MO_i * y^2 MO_j
+    array of the integrals of MO_i * z^2 MO_j
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_spread_x`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: s_mo_coef
+
+
+    File : :file:`mo_one_e_ints/ao_to_mo.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: s_mo_coef	(ao_num,mo_num)
+
+
+    Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_overlap`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao`
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: mo_to_ao:
+
+
+    File : :file:`mo_one_e_ints/ao_to_mo.irp.f`
+
+    .. code:: fortran
+
+        subroutine mo_to_ao(A_mo,LDA_mo,A_ao,LDA_ao)
+
+
+    Transform A from the MO basis to the AO basis
+    
+    $(S.C).A_{mo}.(S.C)^\dagger$
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`s_mo_coef`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dgemm`
+
+ 
+.. c:function:: mo_to_ao_no_overlap:
+
+
+    File : :file:`mo_one_e_ints/ao_to_mo.irp.f`
+
+    .. code:: fortran
+
+        subroutine mo_to_ao_no_overlap(A_mo,LDA_mo,A_ao,LDA_ao)
+
+
+    $C.A_{mo}.C^\dagger$
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dgemm`
+
+ 
+.. c:function:: orthonormalize_mos:
+
+
+    File : :file:`mo_one_e_ints/orthonormalize.irp.f`
+
+    .. code:: fortran
+
+        subroutine orthonormalize_mos
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_label`
+       * :c:data:`ao_num`
+       * :c:data:`mo_overlap`
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`save_ortho_mos`
+       * :c:func:`scf`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ortho_lowdin`
+
+    Touches:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_coef`
+       * :c:data:`mo_label`
+

docs/source/modules/mpi.rst

@@ -0,0 +1,291 @@
+.. _module_mpi: 
+ 
+.. program:: mpi 
+ 
+.. default-role:: option 
+ 
+===
+mpi
+===
+
+Contains all the functions and providers for parallelization with |MPI|.
+ 
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: mpi_initialized
+
+
+    File : :file:`mpi/mpi.irp.f`
+
+    .. code:: fortran
+
+        logical	:: mpi_initialized	
+
+
+    Always true. Initialized MPI
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ezfio_filename`
+
+ 
+.. c:var:: mpi_master
+
+
+    File : :file:`mpi/mpi.irp.f`
+
+    .. code:: fortran
+
+        logical	:: mpi_master	
+
+
+    If true, rank is zero
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_rank`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_cartesian`
+       * :c:data:`ao_coef`
+       * :c:data:`ao_expo`
+       * :c:data:`ao_integrals_threshold`
+       * :c:data:`ao_md5`
+       * :c:data:`ao_nucl`
+       * :c:data:`ao_num`
+       * :c:data:`ao_power`
+       * :c:data:`ao_prim_num`
+       * :c:data:`ao_two_e_integrals_in_map`
+       * :c:data:`cas_bitmask`
+       * :c:data:`ci_energy`
+       * :c:data:`correlation_energy_ratio_max`
+       * :c:data:`data_energy_proj`
+       * :c:data:`data_energy_var`
+       * :c:data:`data_one_e_dm_alpha_mo`
+       * :c:data:`data_one_e_dm_beta_mo`
+       * :c:data:`davidson_sze_max`
+       * :c:data:`disk_access_nuclear_repulsion`
+       * :c:data:`disk_based_davidson`
+       * :c:data:`distributed_davidson`
+       * :c:data:`do_direct_integrals`
+       * :c:data:`do_pseudo`
+       * :c:data:`do_pt2`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`element_name`
+       * :c:data:`energy_iterations`
+       * :c:data:`frozen_orb_scf`
+       * :c:data:`generators_bitmask`
+       * :c:data:`generators_bitmask_restart`
+       * :c:data:`io_ao_integrals_e_n`
+       * :c:data:`io_ao_integrals_kinetic`
+       * :c:data:`io_ao_integrals_overlap`
+       * :c:data:`io_ao_integrals_pseudo`
+       * :c:data:`io_ao_one_e_integrals`
+       * :c:data:`io_ao_two_e_integrals`
+       * :c:data:`io_ao_two_e_integrals_erf`
+       * :c:data:`io_mo_integrals_e_n`
+       * :c:data:`io_mo_integrals_kinetic`
+       * :c:data:`io_mo_integrals_pseudo`
+       * :c:data:`io_mo_one_e_integrals`
+       * :c:data:`io_mo_two_e_integrals`
+       * :c:data:`io_mo_two_e_integrals_erf`
+       * :c:data:`level_shift`
+       * :c:data:`max_dim_diis`
+       * :c:data:`mo_class`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_guess_type`
+       * :c:data:`mo_integrals_threshold`
+       * :c:data:`mo_label`
+       * :c:data:`mo_num`
+       * :c:data:`mo_occ`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`mu_erf`
+       * :c:data:`n_cas_bitmask`
+       * :c:data:`n_core_orb`
+       * :c:data:`n_det`
+       * :c:data:`n_det_generators`
+       * :c:data:`n_det_iterations`
+       * :c:data:`n_det_max`
+       * :c:data:`n_det_max_full`
+       * :c:data:`n_det_print_wf`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_generators_bitmask`
+       * :c:data:`n_generators_bitmask_restart`
+       * :c:data:`n_int`
+       * :c:data:`n_it_scf_max`
+       * :c:data:`n_iter`
+       * :c:data:`n_states`
+       * :c:data:`n_states_diag`
+       * :c:data:`no_ivvv_integrals`
+       * :c:data:`no_vvv_integrals`
+       * :c:data:`no_vvvv_integrals`
+       * :c:data:`nthreads_davidson`
+       * :c:data:`nthreads_pt2`
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_charge_remove`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_label`
+       * :c:data:`nucl_num`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`only_expected_s2`
+       * :c:data:`pseudo_dz_k`
+       * :c:data:`pseudo_dz_kl`
+       * :c:data:`pseudo_grid_rmax`
+       * :c:data:`pseudo_grid_size`
+       * :c:data:`pseudo_klocmax`
+       * :c:data:`pseudo_kmax`
+       * :c:data:`pseudo_lmax`
+       * :c:data:`pseudo_n_k`
+       * :c:data:`pseudo_n_kl`
+       * :c:data:`pseudo_v_k`
+       * :c:data:`pseudo_v_kl`
+       * :c:data:`psi_cas`
+       * :c:data:`psi_coef`
+       * :c:data:`psi_coef_max`
+       * :c:data:`psi_det`
+       * :c:data:`psi_det_alpha_unique`
+       * :c:data:`psi_det_beta_unique`
+       * :c:data:`psi_det_size`
+       * :c:data:`pt2_e0_denominator`
+       * :c:data:`pt2_iterations`
+       * :c:data:`pt2_max`
+       * :c:data:`pt2_n_teeth`
+       * :c:data:`pt2_relative_error`
+       * :c:data:`qp_max_mem`
+       * :c:data:`read_wf`
+       * :c:data:`s2_eig`
+       * :c:data:`scf_algorithm`
+       * :c:data:`state_following`
+       * :c:data:`target_energy`
+       * :c:data:`thresh_scf`
+       * :c:data:`threshold_davidson`
+       * :c:data:`threshold_diis`
+       * :c:data:`threshold_generators`
+       * :c:data:`used_weight`
+
+ 
+.. c:var:: mpi_rank
+
+
+    File : :file:`mpi/mpi.irp.f`
+
+    .. code:: fortran
+
+        integer	:: mpi_rank	
+        integer	:: mpi_size	
+
+
+    Rank of MPI process and number of MPI processes
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_master`
+
+ 
+.. c:var:: mpi_size
+
+
+    File : :file:`mpi/mpi.irp.f`
+
+    .. code:: fortran
+
+        integer	:: mpi_rank	
+        integer	:: mpi_size	
+
+
+    Rank of MPI process and number of MPI processes
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_master`
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: broadcast_chunks_double:
+
+
+    File : :file:`mpi/mpi.irp.f_template_97`
+
+    .. code:: fortran
+
+        subroutine broadcast_chunks_double(A, LDA)
+
+
+    Broadcast with chunks of ~2GB
+
+ 
+.. c:function:: broadcast_chunks_integer:
+
+
+    File : :file:`mpi/mpi.irp.f_template_97`
+
+    .. code:: fortran
+
+        subroutine broadcast_chunks_integer(A, LDA)
+
+
+    Broadcast with chunks of ~2GB
+
+ 
+.. c:function:: broadcast_chunks_integer8:
+
+
+    File : :file:`mpi/mpi.irp.f_template_97`
+
+    .. code:: fortran
+
+        subroutine broadcast_chunks_integer8(A, LDA)
+
+
+    Broadcast with chunks of ~2GB
+
+ 
+.. c:function:: mpi_print:
+
+
+    File : :file:`mpi/mpi.irp.f`
+
+    .. code:: fortran
+
+        subroutine mpi_print(string)
+
+
+    Print string to stdout if the MPI rank is zero.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_master`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`run_slave_main`
+

docs/source/modules/nuclei.rst

@@ -0,0 +1,666 @@
+.. _module_nuclei: 
+ 
+.. program:: nuclei 
+ 
+.. default-role:: option 
+ 
+======
+nuclei
+======
+
+This module contains data relative to the nuclei (coordinates, charge,
+nuclear repulsion energy, etc).
+The coordinates are expressed in atomic units.
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: nucl_num
+ 
+    Number of nuclei
+ 
+ 
+.. option:: nucl_label
+ 
+    Nuclear labels
+ 
+ 
+.. option:: nucl_charge
+ 
+    Nuclear charges
+ 
+ 
+.. option:: nucl_coord
+ 
+    Nuclear coordinates in the format (:, {x,y,z})
+ 
+ 
+.. option:: disk_access_nuclear_repulsion
+ 
+    Read/Write Nuclear Repulsion from/to disk [ Write | Read | None ]
+ 
+    Default: None
+ 
+.. option:: nuclear_repulsion
+ 
+    Nuclear repulsion (Computed automaticaly or Read in the |EZFIO|)
+ 
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: center_of_mass
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: center_of_mass	(3)
+
+
+    Center of mass of the molecule
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`element_name`
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`inertia_tensor`
+
+ 
+.. c:var:: element_mass
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        character*(4), allocatable	:: element_name	(0:127)
+        double precision, allocatable	:: element_mass	(0:127)
+
+
+    Array of the name of element, sorted by nuclear charge (integer)
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_master`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`center_of_mass`
+       * :c:data:`inertia_tensor`
+
+ 
+.. c:var:: element_name
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        character*(4), allocatable	:: element_name	(0:127)
+        double precision, allocatable	:: element_mass	(0:127)
+
+
+    Array of the name of element, sorted by nuclear charge (integer)
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_master`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`center_of_mass`
+       * :c:data:`inertia_tensor`
+
+ 
+.. c:var:: inertia_tensor
+
+
+    File : :file:`nuclei/inertia.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: inertia_tensor	(3,3)
+
+
+    Inertia tensor
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`center_of_mass`
+       * :c:data:`element_name`
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`inertia_tensor_eigenvectors`
+
+ 
+.. c:var:: inertia_tensor_eigenvalues
+
+
+    File : :file:`nuclei/inertia.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: inertia_tensor_eigenvectors	(3,3)
+        double precision, allocatable	:: inertia_tensor_eigenvalues	(3)
+
+
+    Eigenvectors/eigenvalues of the inertia_tensor. Used to find normal orientation.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`inertia_tensor`
+
+
+ 
+.. c:var:: inertia_tensor_eigenvectors
+
+
+    File : :file:`nuclei/inertia.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: inertia_tensor_eigenvectors	(3,3)
+        double precision, allocatable	:: inertia_tensor_eigenvalues	(3)
+
+
+    Eigenvectors/eigenvalues of the inertia_tensor. Used to find normal orientation.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`inertia_tensor`
+
+
+ 
+.. c:var:: nucl_coord
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: nucl_coord	(nucl_num,3)
+
+
+    Nuclear coordinates in the format (:, {x,y,z})
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ezfio_filename`
+       * :c:data:`mpi_master`
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_label`
+       * :c:data:`nucl_num`
+       * :c:data:`output_wall_time_0`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_deriv2_x`
+       * :c:data:`ao_deriv_1_x`
+       * :c:data:`ao_dipole_x`
+       * :c:data:`ao_integrals_n_e`
+       * :c:data:`ao_integrals_n_e_per_atom`
+       * :c:data:`ao_overlap`
+       * :c:data:`ao_overlap_abs`
+       * :c:data:`ao_pseudo_integrals_local`
+       * :c:data:`ao_pseudo_integrals_non_local`
+       * :c:data:`ao_spread_x`
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`ao_two_e_integral_erf_schwartz`
+       * :c:data:`ao_two_e_integral_schwartz`
+       * :c:data:`ao_two_e_integrals_erf_in_map`
+       * :c:data:`ao_two_e_integrals_in_map`
+       * :c:data:`center_of_mass`
+       * :c:data:`inertia_tensor`
+       * :c:data:`nucl_coord_transp`
+       * :c:data:`nucl_dist_2`
+       * :c:data:`nuclear_repulsion`
+
+ 
+.. c:var:: nucl_coord_transp
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: nucl_coord_transp	(3,nucl_num)
+
+
+    Transposed array of nucl_coord
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_num`
+
+
+ 
+.. c:var:: nucl_dist
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: nucl_dist_2	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_x	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_y	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_z	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist	(nucl_num,nucl_num)
+
+
+    nucl_dist     : Nucleus-nucleus distances
+    nucl_dist_2   : Nucleus-nucleus distances squared
+    nucl_dist_vec : Nucleus-nucleus distances vectors
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_dist_inv`
+
+ 
+.. c:var:: nucl_dist_2
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: nucl_dist_2	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_x	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_y	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_z	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist	(nucl_num,nucl_num)
+
+
+    nucl_dist     : Nucleus-nucleus distances
+    nucl_dist_2   : Nucleus-nucleus distances squared
+    nucl_dist_vec : Nucleus-nucleus distances vectors
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_dist_inv`
+
+ 
+.. c:var:: nucl_dist_inv
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: nucl_dist_inv	(nucl_num,nucl_num)
+
+
+    Inverse of the distance between nucleus I and nucleus J
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_dist_2`
+       * :c:data:`nucl_num`
+
+
+ 
+.. c:var:: nucl_dist_vec_x
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: nucl_dist_2	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_x	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_y	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_z	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist	(nucl_num,nucl_num)
+
+
+    nucl_dist     : Nucleus-nucleus distances
+    nucl_dist_2   : Nucleus-nucleus distances squared
+    nucl_dist_vec : Nucleus-nucleus distances vectors
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_dist_inv`
+
+ 
+.. c:var:: nucl_dist_vec_y
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: nucl_dist_2	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_x	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_y	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_z	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist	(nucl_num,nucl_num)
+
+
+    nucl_dist     : Nucleus-nucleus distances
+    nucl_dist_2   : Nucleus-nucleus distances squared
+    nucl_dist_vec : Nucleus-nucleus distances vectors
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_dist_inv`
+
+ 
+.. c:var:: nucl_dist_vec_z
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: nucl_dist_2	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_x	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_y	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist_vec_z	(nucl_num,nucl_num)
+        double precision, allocatable	:: nucl_dist	(nucl_num,nucl_num)
+
+
+    nucl_dist     : Nucleus-nucleus distances
+    nucl_dist_2   : Nucleus-nucleus distances squared
+    nucl_dist_vec : Nucleus-nucleus distances vectors
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_dist_inv`
+
+ 
+.. c:var:: nuclear_repulsion
+
+
+    File : :file:`nuclei/nuclei.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: nuclear_repulsion	
+
+
+    Nuclear repulsion energy
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`disk_access_nuclear_repulsion`
+       * :c:data:`mpi_master`
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_num`
+       * :c:data:`output_wall_time_0`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ci_energy`
+       * :c:data:`core_energy`
+       * :c:data:`core_energy_erf`
+       * :c:data:`hf_energy`
+       * :c:data:`psi_energy_with_nucl_rep`
+       * :c:data:`pt2_e0_denominator`
+       * :c:data:`scf_energy`
+
+ 
+.. c:var:: slater_bragg_radii
+
+
+    File : :file:`nuclei/atomic_radii.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: slater_bragg_radii	(100)
+
+
+    atomic radii in Angstrom defined in table I of JCP 41, 3199 (1964) Slater
+    execpt for the Hydrogen atom where we took the value of Becke (1988, JCP)
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`slater_bragg_radii_per_atom`
+       * :c:data:`slater_bragg_radii_ua`
+
+ 
+.. c:var:: slater_bragg_radii_per_atom
+
+
+    File : :file:`nuclei/atomic_radii.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: slater_bragg_radii_per_atom	(nucl_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_num`
+       * :c:data:`slater_bragg_radii`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`slater_bragg_type_inter_distance`
+
+ 
+.. c:var:: slater_bragg_radii_per_atom_ua
+
+
+    File : :file:`nuclei/atomic_radii.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: slater_bragg_radii_per_atom_ua	(nucl_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_charge`
+       * :c:data:`nucl_num`
+       * :c:data:`slater_bragg_radii_ua`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`slater_bragg_type_inter_distance_ua`
+
+ 
+.. c:var:: slater_bragg_radii_ua
+
+
+    File : :file:`nuclei/atomic_radii.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: slater_bragg_radii_ua	(100)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`slater_bragg_radii`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`slater_bragg_radii_per_atom_ua`
+
+ 
+.. c:var:: slater_bragg_type_inter_distance
+
+
+    File : :file:`nuclei/atomic_radii.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: slater_bragg_type_inter_distance	(nucl_num,nucl_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_num`
+       * :c:data:`slater_bragg_radii_per_atom`
+
+
+ 
+.. c:var:: slater_bragg_type_inter_distance_ua
+
+
+    File : :file:`nuclei/atomic_radii.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: slater_bragg_type_inter_distance_ua	(nucl_num,nucl_num)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_num`
+       * :c:data:`slater_bragg_radii_per_atom_ua`
+
+

docs/source/modules/perturbation.rst

@@ -0,0 +1,998 @@
+.. _module_perturbation: 
+ 
+.. program:: perturbation 
+ 
+.. default-role:: option 
+ 
+============
+perturbation
+============
+
+
+All subroutines in ``*.irp.f`` starting with `pt2_` in the current directory are
+perturbation computed using the routine `i_H_psi`. Other cases are not allowed.
+The arguments of the `pt2_` are always:
+
+.. code-block:: fortran
+
+  subroutine pt2_...(                                          &
+      psi_ref,                                                 &
+      psi_ref_coefs,                                           &
+      E_refs,                                                  &
+      det_pert,                                                &
+      c_pert,                                                  &
+      e_2_pert,                                                &
+      H_pert_diag,                                             &
+      Nint,                                                    &
+      Ndet,                                                    &
+      N_st )
+
+
+  integer          , intent(in)  :: Nint,Ndet,N_st
+  integer(bit_kind), intent(in)  :: psi_ref(Nint,2,Ndet)
+  double precision , intent(in)  :: psi_ref_coefs(Ndet,N_st)
+  double precision , intent(in)  :: E_refs(N_st)
+  integer(bit_kind), intent(in)  :: det_pert(Nint,2)
+  double precision , intent(out) :: c_pert(N_st),e_2_pert(N_st),H_pert_diag
+
+
+`psi_ref`
+  bitstring of the determinants present in the various `N_st` states
+
+`psi_ref_coefs`
+  coefficients of the determinants on the various `N_st` states
+
+`E_refs`
+  Energy of the various `N_st` states
+
+`det_pert`
+  Perturber determinant
+
+`c_pert`
+  Perturbative coefficients for the various states
+
+`e_2_pert`
+  Perturbative energetic contribution for the various states
+
+`H_pert_diag`
+  Diagonal |H| matrix element of the perturber
+
+`Nint`
+  Should be equal to `N_int`
+
+`Ndet`
+  Number of determinants `i` in |Psi| on which we apply <det_pert | |H| | `i`>
+
+`N_st`
+  Number of states
+
+
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: do_pt2
+ 
+    If `True`, compute the |PT2| contribution
+ 
+    Default: True
+ 
+.. option:: pt2_max
+ 
+    The selection process stops when the largest |PT2| (for all the state) is lower
+
+    than `pt2_max` in absolute value
+ 
+    Default: 0.0001
+ 
+.. option:: pt2_relative_error
+ 
+    Stop stochastic |PT2| when the relative error is smaller than `PT2_relative_error`
+ 
+    Default: 0.002
+ 
+.. option:: correlation_energy_ratio_max
+ 
+    The selection process stops at a fixed correlation ratio (useful for getting same accuracy between molecules).
+
+    Defined as :math:`{E_{CI}-E_{HF}}/{E_{CI}+E_{PT2} - E_{HF}}`.
+ 
+    Default: 1.00
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: h0_type
+
+
+    File : :file:`perturbation/h0_type.irp.f`
+
+    .. code:: fortran
+
+        character*32	:: h0_type	
+
+
+    Type of zeroth-order Hamiltonian
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`s2_eig`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`pt2_e0_denominator`
+
+ 
+.. c:var:: max_exc_pert
+
+
+    File : :file:`perturbation/exc_max.irp.f`
+
+    .. code:: fortran
+
+        integer	:: max_exc_pert	
+
+
+
+
+ 
+.. c:var:: selection_criterion
+
+
+    File : :file:`perturbation/selection.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: selection_criterion	
+        double precision	:: selection_criterion_min	
+        double precision	:: selection_criterion_factor	
+
+
+    Threshold to select determinants. Set by selection routines.
+
+
+ 
+.. c:var:: selection_criterion_factor
+
+
+    File : :file:`perturbation/selection.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: selection_criterion	
+        double precision	:: selection_criterion_min	
+        double precision	:: selection_criterion_factor	
+
+
+    Threshold to select determinants. Set by selection routines.
+
+
+ 
+.. c:var:: selection_criterion_min
+
+
+    File : :file:`perturbation/selection.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: selection_criterion	
+        double precision	:: selection_criterion_min	
+        double precision	:: selection_criterion_factor	
+
+
+    Threshold to select determinants. Set by selection routines.
+
+
+ 
+.. c:var:: var_pt2_ratio
+
+
+    File : :file:`perturbation/var_pt2_ratio_provider.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: var_pt2_ratio	
+
+
+    The selection process stops when the energy ratio variational/(variational+PT2)
+    is equal to var_pt2_ratio
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`correlation_energy_ratio_max`
+
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: fill_h_apply_buffer_selection:
+
+
+    File : :file:`perturbation/selection.irp.f`
+
+    .. code:: fortran
+
+        subroutine fill_H_apply_buffer_selection(n_selected,det_buffer,e_2_pert_buffer,coef_pert_buffer, N_st,Nint,iproc,select_max_out)
+
+
+    Fill the H_apply buffer with determiants for the selection
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`selection_criterion`
+       * :c:data:`h_apply_buffer_allocated`
+       * :c:data:`n_det`
+       * :c:data:`n_int`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`omp_set_lock`
+       * :c:func:`omp_unset_lock`
+       * :c:func:`resize_h_apply_buffer`
+
+ 
+.. c:function:: perturb_buffer_by_mono_dummy:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_by_mono_dummy(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``dummy`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_num`
+       * :c:data:`psi_selectors`
+       * :c:data:`n_det`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_det_generators`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`pt2_dummy`
+
+ 
+.. c:function:: perturb_buffer_by_mono_epstein_nesbet:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_by_mono_epstein_nesbet(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_num`
+       * :c:data:`psi_selectors`
+       * :c:data:`n_det`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_det_generators`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`pt2_epstein_nesbet`
+
+ 
+.. c:function:: perturb_buffer_by_mono_epstein_nesbet_2x2:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_by_mono_epstein_nesbet_2x2(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_num`
+       * :c:data:`psi_selectors`
+       * :c:data:`n_det`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_det_generators`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`pt2_epstein_nesbet_2x2`
+
+ 
+.. c:function:: perturb_buffer_by_mono_epstein_nesbet_2x2_no_ci_diag:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_by_mono_epstein_nesbet_2x2_no_ci_diag(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_num`
+       * :c:data:`psi_selectors`
+       * :c:data:`n_det`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_det_generators`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`pt2_epstein_nesbet_2x2_no_ci_diag`
+
+ 
+.. c:function:: perturb_buffer_by_mono_moller_plesset:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_by_mono_moller_plesset(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_num`
+       * :c:data:`psi_selectors`
+       * :c:data:`n_det`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_det_generators`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`pt2_moller_plesset`
+
+ 
+.. c:function:: perturb_buffer_by_mono_qdpt:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_by_mono_qdpt(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``qdpt`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_num`
+       * :c:data:`psi_selectors`
+       * :c:data:`n_det`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_det_generators`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`pt2_qdpt`
+
+ 
+.. c:function:: perturb_buffer_dummy:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_dummy(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``dummy`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_det_generators`
+       * :c:data:`mo_num`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_microlist`
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`getmobiles`
+       * :c:func:`pt2_dummy`
+
+ 
+.. c:function:: perturb_buffer_epstein_nesbet:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_epstein_nesbet(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_det_generators`
+       * :c:data:`mo_num`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_microlist`
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`getmobiles`
+       * :c:func:`pt2_epstein_nesbet`
+
+ 
+.. c:function:: perturb_buffer_epstein_nesbet_2x2:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_epstein_nesbet_2x2(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_det_generators`
+       * :c:data:`mo_num`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_microlist`
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`getmobiles`
+       * :c:func:`pt2_epstein_nesbet_2x2`
+
+ 
+.. c:function:: perturb_buffer_epstein_nesbet_2x2_no_ci_diag:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_epstein_nesbet_2x2_no_ci_diag(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_det_generators`
+       * :c:data:`mo_num`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_microlist`
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`getmobiles`
+       * :c:func:`pt2_epstein_nesbet_2x2_no_ci_diag`
+
+ 
+.. c:function:: perturb_buffer_moller_plesset:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_moller_plesset(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_det_generators`
+       * :c:data:`mo_num`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_microlist`
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`getmobiles`
+       * :c:func:`pt2_moller_plesset`
+
+ 
+.. c:function:: perturb_buffer_qdpt:
+
+
+    File : :file:`perturbation/perturbation.irp.f_shell_13`
+
+    .. code:: fortran
+
+        subroutine perturb_buffer_qdpt(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
+
+
+    Apply pertubration ``qdpt`` to the buffer of determinants generated in the H_apply
+    routine.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_det_generators`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_det_generators`
+       * :c:data:`mo_num`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_microlist`
+       * :c:func:`create_minilist`
+       * :c:func:`create_minilist_find_previous`
+       * :c:func:`getmobiles`
+       * :c:func:`pt2_qdpt`
+
+ 
+.. c:function:: pt2_dummy:
+
+
+    File : :file:`perturbation/pt2_equations.irp.f_template_305`
+
+    .. code:: fortran
+
+        subroutine pt2_dummy (electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
+
+
+    Dummy perturbation to add all connected determinants.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`selection_criterion`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_selectors_size`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`perturb_buffer_by_mono_dummy`
+       * :c:func:`perturb_buffer_dummy`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`i_h_psi_minilist`
+
+ 
+.. c:function:: pt2_epstein_nesbet:
+
+
+    File : :file:`perturbation/pt2_equations.irp.f_template_305`
+
+    .. code:: fortran
+
+        subroutine pt2_epstein_nesbet (electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
+
+
+    Compute the standard Epstein-Nesbet perturbative first order coefficient and
+    second order energetic contribution for the various N_st states.
+    
+    `c_pert(i)` = $\frac{\langle i|H|\alpha \rangle}{ E_n - \langle \alpha|H|\alpha \rangle }$.
+    
+    `e_2_pert(i)` = $\frac{\langle i|H|\alpha \rangle^2}{ E_n - \langle \alpha|H|\alpha \rangle }$.
+    
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`selection_criterion`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_selectors_size`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`perturb_buffer_by_mono_epstein_nesbet`
+       * :c:func:`perturb_buffer_epstein_nesbet`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`i_h_psi_minilist`
+
+ 
+.. c:function:: pt2_epstein_nesbet_2x2:
+
+
+    File : :file:`perturbation/pt2_equations.irp.f_template_305`
+
+    .. code:: fortran
+
+        subroutine pt2_epstein_nesbet_2x2 (electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
+
+
+    Computes the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution
+    for the various N_st states.
+    
+    `e_2_pert(i)` = $\frac{1}{2} ( \langle \alpha|H|\alpha \rangle -  E_n) - \sqrt{ (\langle \alpha|H|\alpha \rangle -  E_n)^2 + 4 \langle i|H|\alpha \rangle^2 }$.
+    
+    `c_pert(i)` = `e_2_pert(i)` $\times \frac{1}{ \langle i|H|\alpha \rangle}$.
+    
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_selectors_size`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`perturb_buffer_by_mono_epstein_nesbet_2x2`
+       * :c:func:`perturb_buffer_epstein_nesbet_2x2`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`i_h_psi`
+
+ 
+.. c:function:: pt2_epstein_nesbet_2x2_no_ci_diag:
+
+
+    File : :file:`perturbation/pt2_equations.irp.f_template_305`
+
+    .. code:: fortran
+
+        subroutine pt2_epstein_nesbet_2x2_no_ci_diag(electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
+
+
+    compute the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution
+    
+    for the various N_st states.
+    
+    e_2_pert(i) = 0.5 * (( <det_pert|H|det_pert> -  E(i) )  - sqrt( ( <det_pert|H|det_pert> -  E(i)) ^2 + 4 <psi(i)|H|det_pert>^2  )
+    
+    c_pert(i) = e_2_pert(i)/ <psi(i)|H|det_pert>
+    
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_selectors_size`
+       * :c:data:`psi_energy`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`perturb_buffer_by_mono_epstein_nesbet_2x2_no_ci_diag`
+       * :c:func:`perturb_buffer_epstein_nesbet_2x2_no_ci_diag`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`i_h_psi`
+
+ 
+.. c:function:: pt2_moller_plesset:
+
+
+    File : :file:`perturbation/pt2_equations.irp.f_template_305`
+
+    .. code:: fortran
+
+        subroutine pt2_moller_plesset (electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
+
+
+    Computes the standard Moller-Plesset perturbative first order coefficient and second
+    order energetic contribution for the various N_st states.
+    
+    `c_pert(i)` = $\frac{\langle i|H|\alpha \rangle}{\text{difference of orbital energies}}$.
+    
+    `e_2_pert(i)` = $\frac{\langle i|H|\alpha \rangle^2}{\text{difference of orbital energies}}$.
+    
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ref_bitmask`
+       * :c:data:`psi_selectors_size`
+       * :c:data:`psi_selectors`
+       * :c:data:`mo_num`
+       * :c:data:`n_det_selectors`
+       * :c:data:`fock_matrix_mo`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`perturb_buffer_by_mono_moller_plesset`
+       * :c:func:`perturb_buffer_moller_plesset`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`decode_exc`
+       * :c:func:`get_excitation`
+       * :c:func:`i_h_psi_minilist`
+
+ 
+.. c:function:: pt2_qdpt:
+
+
+    File : :file:`perturbation/pt2_equations.irp.f_template_305`
+
+    .. code:: fortran
+
+        subroutine pt2_qdpt (electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
+
+
+    Computes the QDPT first order coefficient and second order energetic contribution
+    for the various N_st states.
+    
+    `c_pert(i)` = $\frac{\langle i|H|\alpha \rangle}{\langle i|H|i \rangle - \langle \alpha|H|\alpha \rangle}$.
+    
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`selection_criterion`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_selectors_size`
+       * :c:data:`mo_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`perturb_buffer_by_mono_qdpt`
+       * :c:func:`perturb_buffer_qdpt`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`get_excitation_degree`
+       * :c:func:`i_h_j`
+       * :c:func:`i_h_psi_minilist`
+
+ 
+.. c:function:: remove_small_contributions:
+
+
+    File : :file:`perturbation/selection.irp.f`
+
+    .. code:: fortran
+
+        subroutine remove_small_contributions
+
+
+    Remove determinants with small contributions. N_states is assumed to be
+    provided.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`psi_coef`
+       * :c:data:`selection_criterion`
+       * :c:data:`n_states`
+       * :c:data:`n_det`
+       * :c:data:`psi_det_size`
+       * :c:data:`n_det_generators`
+       * :c:data:`n_int`
+       * :c:data:`psi_det_sorted`
+       * :c:data:`psi_det`
+       * :c:data:`psi_det_sorted`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`diagonalize_ci`
+       * :c:func:`i_h_psi`
+       * :c:func:`write_int`
+
+    Touches:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ci_electronic_energy`
+       * :c:data:`ci_electronic_energy`
+       * :c:data:`ci_energy`
+       * :c:data:`ci_electronic_energy`
+       * :c:data:`n_det`
+       * :c:data:`psi_coef`
+       * :c:data:`psi_det`
+

docs/source/modules/pseudo.rst

@@ -0,0 +1,94 @@
+.. _module_pseudo: 
+ 
+.. program:: pseudo 
+ 
+.. default-role:: option 
+ 
+======
+pseudo
+======
+
+This module defines the |EZFIO| parameters of the effective core potentials.
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: nucl_charge_remove
+ 
+    Nuclear charges removed per atom
+ 
+ 
+.. option:: pseudo_klocmax
+ 
+    Maximum value of k for the local component
+ 
+ 
+.. option:: pseudo_n_k
+ 
+    Number of gaussians in the local component
+ 
+ 
+.. option:: pseudo_v_k
+ 
+    Coefficients in the local component
+ 
+ 
+.. option:: pseudo_dz_k
+ 
+    Exponents in the local component
+ 
+ 
+.. option:: pseudo_lmax
+ 
+    Maximum angular momentum
+ 
+ 
+.. option:: pseudo_kmax
+ 
+    Maximum number of functions in the non-local component
+ 
+ 
+.. option:: pseudo_n_kl
+ 
+    Number of functions in the non-local component
+ 
+ 
+.. option:: pseudo_v_kl
+ 
+    Coefficients in the non-local component
+ 
+ 
+.. option:: pseudo_dz_kl
+ 
+    Exponents in the non-local component
+ 
+ 
+.. option:: do_pseudo
+ 
+    If `True`, pseudo-potentials are used.
+ 
+    Default: False
+ 
+.. option:: pseudo_grid_size
+ 
+    Nb of points of the grid for the QMC interfaces
+ 
+    Default: 1000
+ 
+.. option:: pseudo_grid_rmax
+ 
+    R_max of the QMC grid
+ 
+    Default: 10.0
+ 
+.. option:: ao_pseudo_grid
+ 
+    Grid for the QMC interface
+ 
+ 
+.. option:: mo_pseudo_grid
+ 
+    Grid for the QMC interface
+ 

docs/source/modules/psiref_cas.rst

@@ -0,0 +1,14 @@
+.. _module_psiref_cas: 
+ 
+.. program:: psiref_cas 
+ 
+.. default-role:: option 
+ 
+==========
+psiref_cas
+==========
+
+Reference wave function is defined as a |CAS| wave function.
+This module is required for |CAS-SD|, |MRPT| or |MRCC|.
+
+ 

docs/source/modules/psiref_utils.rst

@@ -0,0 +1,16 @@
+.. _module_psiref_utils: 
+ 
+.. program:: psiref_utils 
+ 
+.. default-role:: option 
+ 
+============
+psiref_utils
+============
+
+
+Utilities related to the use of a reference wave function. This module
+needs to be loaded with any `psi_ref_*` module.
+
+
+ 

docs/source/modules/scf_utils.rst

@@ -0,0 +1,795 @@
+.. _module_scf_utils: 
+ 
+.. program:: scf_utils 
+ 
+.. default-role:: option 
+ 
+=========
+scf_utils
+=========
+
+
+
+The scf_utils module is an abstract module which contains the basics to perform *Restricted* SCF calculations (the
+spatial part of the |MOs| is common for alpha and beta spinorbitals) based on a single-determinant wave function.
+
+This module does not produce any executable *and must not do*, but instead it contains everything one needs to perform an orbital optimization based on an Fock matrix.
+The ``scf_utils`` module is meant to be included in the :file:`NEED` of the various single determinant SCF procedures, such as ``hartree_fock`` or ``kohn_sham``, where a specific definition of the Fock matrix is given (see :file:`hartree_fock fock_matrix_hf.irp.f` for an example).
+
+All SCF programs perform the following actions:
+
+
+#. Compute/Read all the one- and two-electron integrals, and store them in memory
+
+#. Check in the |EZFIO| database if there is a set of |MOs|. If there is, it
+   will read them as initial guess. Otherwise, it will create a guess.
+#. Perform the |SCF| iterations based on the definition of the Fock matrix
+
+
+The main keywords/options are:
+
+* :option:`scf_utils thresh_scf`
+* :option:`scf_utils level_shift`
+
+At each iteration, the |MOs| are saved in the |EZFIO| database. Hence, if the calculation
+crashes for any unexpected reason, the calculation can be restarted by running again
+the |SCF| with the same |EZFIO| database.
+
+The `DIIS`_ algorithm is implemented, as well as the `level-shifting`_ method.
+If the |SCF| does not converge, try again with a higher value of :option:`level_shift`.
+
+To start a calculation from scratch, the simplest way is to remove the
+``mo_basis`` directory from the |EZFIO| database, and run the |SCF| again.
+
+.. _DIIS: https://en.wikipedia.org/w/index.php?title=DIIS
+.. _level-shifting: https://doi.org/10.1002/qua.560070407
+
+ 
+ 
+ 
+EZFIO parameters 
+---------------- 
+ 
+.. option:: max_dim_diis
+ 
+    Maximum size of the DIIS extrapolation procedure
+ 
+    Default: 15
+ 
+.. option:: threshold_diis
+ 
+    Threshold on the convergence of the DIIS error vector during a Hartree-Fock calculation. If 0. is chosen, the square root of thresh_scf will be used.
+ 
+    Default: 0.
+ 
+.. option:: thresh_scf
+ 
+    Threshold on the convergence of the Hartree Fock energy.
+ 
+    Default: 1.e-10
+ 
+.. option:: n_it_scf_max
+ 
+    Maximum number of SCF iterations
+ 
+    Default: 500
+ 
+.. option:: level_shift
+ 
+    Energy shift on the virtual MOs to improve SCF convergence
+ 
+    Default: 0.
+ 
+.. option:: scf_algorithm
+ 
+    Type of SCF algorithm used. Possible choices are [ Simple | DIIS]
+ 
+    Default: DIIS
+ 
+.. option:: mo_guess_type
+ 
+    Initial MO guess. Can be [ Huckel | HCore ]
+ 
+    Default: Huckel
+ 
+.. option:: energy
+ 
+    Calculated HF energy
+ 
+ 
+.. option:: frozen_orb_scf
+ 
+    If true, leave untouched all the orbitals defined as core and optimize all the orbitals defined as active with qp_set_mo_class
+ 
+    Default: False
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: eigenvalues_fock_matrix_ao
+
+
+    File : :file:`scf_utils/diis.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: eigenvalues_fock_matrix_ao	(AO_num)
+        double precision, allocatable	:: eigenvectors_fock_matrix_ao	(AO_num,AO_num)
+
+
+    Eigenvalues and eigenvectors of the Fock matrix over the AO basis
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`fock_matrix_ao`
+       * :c:data:`s_half_inv`
+
+
+ 
+.. c:var:: eigenvectors_fock_matrix_ao
+
+
+    File : :file:`scf_utils/diis.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: eigenvalues_fock_matrix_ao	(AO_num)
+        double precision, allocatable	:: eigenvectors_fock_matrix_ao	(AO_num,AO_num)
+
+
+    Eigenvalues and eigenvectors of the Fock matrix over the AO basis
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`fock_matrix_ao`
+       * :c:data:`s_half_inv`
+
+
+ 
+.. c:var:: eigenvectors_fock_matrix_mo
+
+
+    File : :file:`scf_utils/diagonalize_fock.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: eigenvectors_fock_matrix_mo	(ao_num,mo_num)
+
+
+    Eigenvector of the Fock matrix in the MO basis obtained with level shift.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`fock_matrix_mo`
+       * :c:data:`frozen_orb_scf`
+       * :c:data:`level_shift`
+       * :c:data:`list_inact`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+       * :c:data:`n_core_orb`
+
+
+ 
+.. c:function:: extrapolate_fock_matrix:
+
+
+    File : :file:`scf_utils/roothaan_hall_scf.irp.f`
+
+    .. code:: fortran
+
+        subroutine extrapolate_Fock_matrix(               &
+           error_matrix_DIIS,Fock_matrix_DIIS,    &
+           Fock_matrix_AO_,size_Fock_matrix_AO,   &
+           iteration_SCF,dim_DIIS                 &
+           )
+
+
+    Compute the extrapolated Fock matrix using the DIIS procedure
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`max_dim_diis`
+       * :c:data:`ao_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`roothaan_hall_scf`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`dgemm`
+       * :c:func:`dsysvx`
+
+ 
+.. c:var:: fock_matrix_ao
+
+
+    File : :file:`scf_utils/fock_matrix.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: fock_matrix_ao	(ao_num,ao_num)
+
+
+    Fock matrix in AO basis set
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`fock_matrix_mo`
+       * :c:data:`frozen_orb_scf`
+       * :c:data:`level_shift`
+       * :c:data:`mo_num`
+       * :c:data:`s_mo_coef`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`eigenvalues_fock_matrix_ao`
+       * :c:data:`fps_spf_matrix_ao`
+
+ 
+.. c:var:: fock_matrix_diag_mo
+
+
+    File : :file:`scf_utils/fock_matrix.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: fock_matrix_mo	(mo_num,mo_num)
+        double precision, allocatable	:: fock_matrix_diag_mo	(mo_num)
+
+
+    Fock matrix on the MO basis.
+    For open shells, the ROHF Fock Matrix is ::
+    
+          |   F-K    |  F + K/2  |    F     |
+          |---------------------------------|
+          | F + K/2  |     F     |  F - K/2 |
+          |---------------------------------|
+          |    F     |  F - K/2  |  F + K   |
+    
+    
+    F = 1/2 (Fa + Fb)
+    
+    K = Fb - Fa
+    
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`fock_matrix_mo_alpha`
+       * :c:data:`fock_matrix_mo_beta`
+       * :c:data:`frozen_orb_scf`
+       * :c:data:`list_inact`
+       * :c:data:`mo_num`
+       * :c:data:`n_core_orb`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`eigenvectors_fock_matrix_mo`
+       * :c:data:`fock_matrix_ao`
+
+ 
+.. c:var:: fock_matrix_mo
+
+
+    File : :file:`scf_utils/fock_matrix.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: fock_matrix_mo	(mo_num,mo_num)
+        double precision, allocatable	:: fock_matrix_diag_mo	(mo_num)
+
+
+    Fock matrix on the MO basis.
+    For open shells, the ROHF Fock Matrix is ::
+    
+          |   F-K    |  F + K/2  |    F     |
+          |---------------------------------|
+          | F + K/2  |     F     |  F - K/2 |
+          |---------------------------------|
+          |    F     |  F - K/2  |  F + K   |
+    
+    
+    F = 1/2 (Fa + Fb)
+    
+    K = Fb - Fa
+    
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`fock_matrix_mo_alpha`
+       * :c:data:`fock_matrix_mo_beta`
+       * :c:data:`frozen_orb_scf`
+       * :c:data:`list_inact`
+       * :c:data:`mo_num`
+       * :c:data:`n_core_orb`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`eigenvectors_fock_matrix_mo`
+       * :c:data:`fock_matrix_ao`
+
+ 
+.. c:var:: fock_matrix_mo_alpha
+
+
+    File : :file:`scf_utils/fock_matrix.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: fock_matrix_mo_alpha	(mo_num,mo_num)
+
+
+    Fock matrix on the MO basis
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_mo`
+
+ 
+.. c:var:: fock_matrix_mo_beta
+
+
+    File : :file:`scf_utils/fock_matrix.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: fock_matrix_mo_beta	(mo_num,mo_num)
+
+
+    Fock matrix on the MO basis
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_mo`
+
+ 
+.. c:var:: fps_spf_matrix_ao
+
+
+    File : :file:`scf_utils/diis.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: fps_spf_matrix_ao	(AO_num,AO_num)
+
+
+    Commutator FPS - SPF
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_overlap`
+       * :c:data:`fock_matrix_ao`
+       * :c:data:`scf_density_matrix_ao`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fps_spf_matrix_mo`
+
+ 
+.. c:var:: fps_spf_matrix_mo
+
+
+    File : :file:`scf_utils/diis.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: fps_spf_matrix_mo	(mo_num,mo_num)
+
+
+    Commutator FPS - SPF in MO basis
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`fps_spf_matrix_ao`
+       * :c:data:`mo_coef`
+       * :c:data:`mo_num`
+
+
+ 
+.. c:var:: scf_density_matrix_ao
+
+
+    File : :file:`scf_utils/scf_density_matrix_ao.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: scf_density_matrix_ao	(ao_num,ao_num)
+
+
+    S^{-1}.P.S^{-1}  where P = C.C^t
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fps_spf_matrix_ao`
+
+ 
+.. c:var:: scf_density_matrix_ao_alpha
+
+
+    File : :file:`scf_utils/scf_density_matrix_ao.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: scf_density_matrix_ao_alpha	(ao_num,ao_num)
+
+
+    S^{-1}.P_alpha.S^{-1}
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`elec_alpha_num`
+       * :c:data:`mo_coef`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`hf_energy`
+       * :c:data:`scf_density_matrix_ao`
+       * :c:data:`scf_energy`
+
+ 
+.. c:var:: scf_density_matrix_ao_beta
+
+
+    File : :file:`scf_utils/scf_density_matrix_ao.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: scf_density_matrix_ao_beta	(ao_num,ao_num)
+
+
+    S^{-1}.P_beta.S^{-1}
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`elec_beta_num`
+       * :c:data:`mo_coef`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`hf_energy`
+       * :c:data:`scf_density_matrix_ao`
+       * :c:data:`scf_energy`
+
+ 
+.. c:var:: scf_energy
+
+
+    File : :file:`scf_utils/fock_matrix.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: scf_energy	
+
+
+    Hartree-Fock energy
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_num`
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`extra_e_contrib_density`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`nuclear_repulsion`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+
+
+ 
+.. c:var:: threshold_diis_nonzero
+
+
+    File : :file:`scf_utils/diis.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: threshold_diis_nonzero	
+
+
+    If threshold_DIIS is zero, choose sqrt(thresh_scf)
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`thresh_scf`
+       * :c:data:`threshold_diis`
+
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: damping_scf:
+
+
+    File : :file:`scf_utils/damping_scf.irp.f`
+
+    .. code:: fortran
+
+        subroutine damping_SCF
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_coef`
+       * :c:data:`eigenvectors_fock_matrix_mo`
+       * :c:data:`scf_energy`
+       * :c:data:`scf_density_matrix_ao_beta`
+       * :c:data:`fock_matrix_mo`
+       * :c:data:`ao_num`
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`fock_matrix_ao`
+       * :c:data:`mo_label`
+       * :c:data:`n_it_scf_max`
+       * :c:data:`thresh_scf`
+       * :c:data:`frozen_orb_scf`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_set_hartree_fock_energy`
+       * :c:func:`initialize_mo_coef_begin_iteration`
+       * :c:func:`mo_as_eigvectors_of_mo_matrix`
+       * :c:func:`reorder_core_orb`
+       * :c:func:`save_mos`
+       * :c:func:`write_double`
+       * :c:func:`write_time`
+
+    Touches:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`scf_density_matrix_ao_alpha`
+       * :c:data:`scf_density_matrix_ao_beta`
+       * :c:data:`mo_coef`
+
+ 
+.. c:function:: huckel_guess:
+
+
+    File : :file:`scf_utils/huckel.irp.f`
+
+    .. code:: fortran
+
+        subroutine huckel_guess
+
+
+    Build the MOs using the extended Huckel model
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`ao_one_e_integrals`
+       * :c:data:`mo_coef`
+       * :c:data:`eigenvectors_fock_matrix_mo`
+       * :c:data:`ao_overlap`
+       * :c:data:`ao_num`
+       * :c:data:`ao_two_e_integral_alpha`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`fock_matrix_ao_alpha`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`create_guess`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`save_mos`
+
+    Touches:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`mo_coef`
+
+ 
+.. c:function:: roothaan_hall_scf:
+
+
+    File : :file:`scf_utils/roothaan_hall_scf.irp.f`
+
+    .. code:: fortran
+
+        subroutine Roothaan_Hall_SCF
+
+
+    Roothaan-Hall algorithm for SCF Hartree-Fock calculation
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`max_dim_diis`
+       * :c:data:`mo_occ`
+       * :c:data:`ao_md5`
+       * :c:data:`mo_coef`
+       * :c:data:`level_shift`
+       * :c:data:`fps_spf_matrix_mo`
+       * :c:data:`eigenvectors_fock_matrix_mo`
+       * :c:data:`scf_energy`
+       * :c:data:`mo_num`
+       * :c:data:`thresh_scf`
+       * :c:data:`scf_algorithm`
+       * :c:data:`fock_matrix_mo`
+       * :c:data:`ao_num`
+       * :c:data:`fock_matrix_ao`
+       * :c:data:`mo_label`
+       * :c:data:`n_it_scf_max`
+       * :c:data:`threshold_diis_nonzero`
+       * :c:data:`frozen_orb_scf`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`fps_spf_matrix_ao`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`run`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`extrapolate_fock_matrix`
+       * :c:func:`initialize_mo_coef_begin_iteration`
+       * :c:func:`mo_as_eigvectors_of_mo_matrix`
+       * :c:func:`reorder_core_orb`
+       * :c:func:`save_mos`
+       * :c:func:`write_double`
+       * :c:func:`write_time`
+
+    Touches:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`fock_matrix_ao_alpha`
+       * :c:data:`mo_coef`
+       * :c:data:`level_shift`
+       * :c:data:`mo_coef`
+

docs/source/modules/selectors_cassd.rst

@@ -0,0 +1,13 @@
+.. _module_selectors_cassd: 
+ 
+.. program:: selectors_cassd 
+ 
+.. default-role:: option 
+ 
+===============
+selectors_cassd
+===============
+
+Selectors for |CAS-SD| calculations. The selectors are defined as first the
+generators from :ref:`module_generators_cas`, and then the rest of the wave function.
+ 

docs/source/modules/selectors_full.rst

@@ -0,0 +1,153 @@
+.. _module_selectors_full: 
+ 
+.. program:: selectors_full 
+ 
+.. default-role:: option 
+ 
+==============
+selectors_full
+==============
+
+All the determinants are possible selectors. Only the largest contributions are kept, where
+a threshold is applied to the squared norm of the wave function, with the :option:`determinants
+threshold_selectors` flag.
+ 
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: n_det_selectors
+
+
+    File : :file:`selectors_full/selectors.irp.f`
+
+    .. code:: fortran
+
+        integer	:: n_det_selectors	
+
+
+    For Single reference wave functions, the number of selectors is 1 : the
+    Hartree-Fock determinant
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mpi_master`
+       * :c:data:`n_det`
+       * :c:data:`n_det_generators`
+       * :c:data:`output_wall_time_0`
+       * :c:data:`psi_det_sorted`
+       * :c:data:`threshold_selectors`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`coef_hf_selector`
+       * :c:data:`exc_degree_per_selectors`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_selectors_coef_transp`
+       * :c:data:`psi_selectors_diag_h_mat`
+       * :c:data:`pt2_f`
+
+ 
+.. c:var:: psi_selectors
+
+
+    File : :file:`selectors_full/selectors.irp.f`
+
+    .. code:: fortran
+
+        integer(bit_kind), allocatable	:: psi_selectors	(N_int,2,psi_selectors_size)
+        double precision, allocatable	:: psi_selectors_coef	(psi_selectors_size,N_states)
+
+
+    Determinants on which we apply <i|H|psi> for perturbation.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`n_states`
+       * :c:data:`psi_det_sorted`
+       * :c:data:`psi_selectors_size`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`coef_hf_selector`
+       * :c:data:`exc_degree_per_selectors`
+       * :c:data:`psi_selectors_coef_transp`
+       * :c:data:`psi_selectors_diag_h_mat`
+
+ 
+.. c:var:: psi_selectors_coef
+
+
+    File : :file:`selectors_full/selectors.irp.f`
+
+    .. code:: fortran
+
+        integer(bit_kind), allocatable	:: psi_selectors	(N_int,2,psi_selectors_size)
+        double precision, allocatable	:: psi_selectors_coef	(psi_selectors_size,N_states)
+
+
+    Determinants on which we apply <i|H|psi> for perturbation.
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`n_states`
+       * :c:data:`psi_det_sorted`
+       * :c:data:`psi_selectors_size`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`coef_hf_selector`
+       * :c:data:`exc_degree_per_selectors`
+       * :c:data:`psi_selectors_coef_transp`
+       * :c:data:`psi_selectors_diag_h_mat`
+
+ 
+.. c:var:: threshold_selectors
+
+
+    File : :file:`selectors_full/selectors.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: threshold_selectors	
+
+
+    Thresholds on selectors (fraction of the square of the norm)
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`threshold_generators`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+

docs/source/modules/selectors_utils.rst

@@ -0,0 +1,649 @@
+.. _module_selectors_utils: 
+ 
+.. program:: selectors_utils 
+ 
+.. default-role:: option 
+ 
+===============
+selectors_utils
+===============
+
+Helper functions for selectors.
+
+ 
+ 
+ 
+Providers 
+--------- 
+ 
+.. c:var:: coef_hf_selector
+
+
+    File : :file:`selectors_utils/e_corr_selectors.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: coef_hf_selector	
+        double precision	:: inv_selectors_coef_hf	
+        double precision	:: inv_selectors_coef_hf_squared	
+        double precision, allocatable	:: e_corr_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: i_h_hf_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: delta_e_per_selector	(N_det_selectors)
+        double precision	:: e_corr_double_only	
+        double precision	:: e_corr_second_order	
+
+
+    Correlation energy per determinant with respect to the Hartree-Fock determinant
+    for the all the double excitations in the selectors determinants.
+    
+    E_corr_per_selectors(i) = :math:`\langle D_i | H | \text{HF}\rangle  c(D_i)/c(HF)` if :math:`| D_i \rangle` is a double excitation.
+    
+    E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+    
+    coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`exc_degree_per_selectors`
+       * :c:data:`mo_integrals_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`ref_bitmask`
+       * :c:data:`ref_bitmask_energy`
+
+
+ 
+.. c:var:: delta_e_per_selector
+
+
+    File : :file:`selectors_utils/e_corr_selectors.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: coef_hf_selector	
+        double precision	:: inv_selectors_coef_hf	
+        double precision	:: inv_selectors_coef_hf_squared	
+        double precision, allocatable	:: e_corr_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: i_h_hf_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: delta_e_per_selector	(N_det_selectors)
+        double precision	:: e_corr_double_only	
+        double precision	:: e_corr_second_order	
+
+
+    Correlation energy per determinant with respect to the Hartree-Fock determinant
+    for the all the double excitations in the selectors determinants.
+    
+    E_corr_per_selectors(i) = :math:`\langle D_i | H | \text{HF}\rangle  c(D_i)/c(HF)` if :math:`| D_i \rangle` is a double excitation.
+    
+    E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+    
+    coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`exc_degree_per_selectors`
+       * :c:data:`mo_integrals_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`ref_bitmask`
+       * :c:data:`ref_bitmask_energy`
+
+
+ 
+.. c:var:: double_index_selectors
+
+
+    File : :file:`selectors_utils/e_corr_selectors.irp.f`
+
+    .. code:: fortran
+
+        integer, allocatable	:: exc_degree_per_selectors	(N_det_selectors)
+        integer, allocatable	:: double_index_selectors	(N_det_selectors)
+        integer	:: n_double_selectors	
+
+
+    Degree of excitation respect to Hartree Fock for the wave function
+    for the all the selectors determinants.
+    
+    double_index_selectors = list of the index of the double excitations
+    
+    n_double_selectors = number of double excitations in the selectors determinants
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`ref_bitmask`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`coef_hf_selector`
+
+ 
+.. c:var:: e_corr_double_only
+
+
+    File : :file:`selectors_utils/e_corr_selectors.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: coef_hf_selector	
+        double precision	:: inv_selectors_coef_hf	
+        double precision	:: inv_selectors_coef_hf_squared	
+        double precision, allocatable	:: e_corr_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: i_h_hf_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: delta_e_per_selector	(N_det_selectors)
+        double precision	:: e_corr_double_only	
+        double precision	:: e_corr_second_order	
+
+
+    Correlation energy per determinant with respect to the Hartree-Fock determinant
+    for the all the double excitations in the selectors determinants.
+    
+    E_corr_per_selectors(i) = :math:`\langle D_i | H | \text{HF}\rangle  c(D_i)/c(HF)` if :math:`| D_i \rangle` is a double excitation.
+    
+    E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+    
+    coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`exc_degree_per_selectors`
+       * :c:data:`mo_integrals_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`ref_bitmask`
+       * :c:data:`ref_bitmask_energy`
+
+
+ 
+.. c:var:: e_corr_per_selectors
+
+
+    File : :file:`selectors_utils/e_corr_selectors.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: coef_hf_selector	
+        double precision	:: inv_selectors_coef_hf	
+        double precision	:: inv_selectors_coef_hf_squared	
+        double precision, allocatable	:: e_corr_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: i_h_hf_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: delta_e_per_selector	(N_det_selectors)
+        double precision	:: e_corr_double_only	
+        double precision	:: e_corr_second_order	
+
+
+    Correlation energy per determinant with respect to the Hartree-Fock determinant
+    for the all the double excitations in the selectors determinants.
+    
+    E_corr_per_selectors(i) = :math:`\langle D_i | H | \text{HF}\rangle  c(D_i)/c(HF)` if :math:`| D_i \rangle` is a double excitation.
+    
+    E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+    
+    coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`exc_degree_per_selectors`
+       * :c:data:`mo_integrals_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`ref_bitmask`
+       * :c:data:`ref_bitmask_energy`
+
+
+ 
+.. c:var:: e_corr_second_order
+
+
+    File : :file:`selectors_utils/e_corr_selectors.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: coef_hf_selector	
+        double precision	:: inv_selectors_coef_hf	
+        double precision	:: inv_selectors_coef_hf_squared	
+        double precision, allocatable	:: e_corr_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: i_h_hf_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: delta_e_per_selector	(N_det_selectors)
+        double precision	:: e_corr_double_only	
+        double precision	:: e_corr_second_order	
+
+
+    Correlation energy per determinant with respect to the Hartree-Fock determinant
+    for the all the double excitations in the selectors determinants.
+    
+    E_corr_per_selectors(i) = :math:`\langle D_i | H | \text{HF}\rangle  c(D_i)/c(HF)` if :math:`| D_i \rangle` is a double excitation.
+    
+    E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+    
+    coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`exc_degree_per_selectors`
+       * :c:data:`mo_integrals_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`ref_bitmask`
+       * :c:data:`ref_bitmask_energy`
+
+
+ 
+.. c:var:: exc_degree_per_selectors
+
+
+    File : :file:`selectors_utils/e_corr_selectors.irp.f`
+
+    .. code:: fortran
+
+        integer, allocatable	:: exc_degree_per_selectors	(N_det_selectors)
+        integer, allocatable	:: double_index_selectors	(N_det_selectors)
+        integer	:: n_double_selectors	
+
+
+    Degree of excitation respect to Hartree Fock for the wave function
+    for the all the selectors determinants.
+    
+    double_index_selectors = list of the index of the double excitations
+    
+    n_double_selectors = number of double excitations in the selectors determinants
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`ref_bitmask`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`coef_hf_selector`
+
+ 
+.. c:var:: i_h_hf_per_selectors
+
+
+    File : :file:`selectors_utils/e_corr_selectors.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: coef_hf_selector	
+        double precision	:: inv_selectors_coef_hf	
+        double precision	:: inv_selectors_coef_hf_squared	
+        double precision, allocatable	:: e_corr_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: i_h_hf_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: delta_e_per_selector	(N_det_selectors)
+        double precision	:: e_corr_double_only	
+        double precision	:: e_corr_second_order	
+
+
+    Correlation energy per determinant with respect to the Hartree-Fock determinant
+    for the all the double excitations in the selectors determinants.
+    
+    E_corr_per_selectors(i) = :math:`\langle D_i | H | \text{HF}\rangle  c(D_i)/c(HF)` if :math:`| D_i \rangle` is a double excitation.
+    
+    E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+    
+    coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`exc_degree_per_selectors`
+       * :c:data:`mo_integrals_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`ref_bitmask`
+       * :c:data:`ref_bitmask_energy`
+
+
+ 
+.. c:var:: inv_selectors_coef_hf
+
+
+    File : :file:`selectors_utils/e_corr_selectors.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: coef_hf_selector	
+        double precision	:: inv_selectors_coef_hf	
+        double precision	:: inv_selectors_coef_hf_squared	
+        double precision, allocatable	:: e_corr_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: i_h_hf_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: delta_e_per_selector	(N_det_selectors)
+        double precision	:: e_corr_double_only	
+        double precision	:: e_corr_second_order	
+
+
+    Correlation energy per determinant with respect to the Hartree-Fock determinant
+    for the all the double excitations in the selectors determinants.
+    
+    E_corr_per_selectors(i) = :math:`\langle D_i | H | \text{HF}\rangle  c(D_i)/c(HF)` if :math:`| D_i \rangle` is a double excitation.
+    
+    E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+    
+    coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`exc_degree_per_selectors`
+       * :c:data:`mo_integrals_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`ref_bitmask`
+       * :c:data:`ref_bitmask_energy`
+
+
+ 
+.. c:var:: inv_selectors_coef_hf_squared
+
+
+    File : :file:`selectors_utils/e_corr_selectors.irp.f`
+
+    .. code:: fortran
+
+        double precision	:: coef_hf_selector	
+        double precision	:: inv_selectors_coef_hf	
+        double precision	:: inv_selectors_coef_hf_squared	
+        double precision, allocatable	:: e_corr_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: i_h_hf_per_selectors	(N_det_selectors)
+        double precision, allocatable	:: delta_e_per_selector	(N_det_selectors)
+        double precision	:: e_corr_double_only	
+        double precision	:: e_corr_second_order	
+
+
+    Correlation energy per determinant with respect to the Hartree-Fock determinant
+    for the all the double excitations in the selectors determinants.
+    
+    E_corr_per_selectors(i) = :math:`\langle D_i | H | \text{HF}\rangle  c(D_i)/c(HF)` if :math:`| D_i \rangle` is a double excitation.
+    
+    E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+    
+    coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`big_array_coulomb_integrals`
+       * :c:data:`exc_degree_per_selectors`
+       * :c:data:`mo_integrals_map`
+       * :c:data:`mo_two_e_integrals_in_map`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`ref_bitmask`
+       * :c:data:`ref_bitmask_energy`
+
+
+ 
+.. c:var:: n_double_selectors
+
+
+    File : :file:`selectors_utils/e_corr_selectors.irp.f`
+
+    .. code:: fortran
+
+        integer, allocatable	:: exc_degree_per_selectors	(N_det_selectors)
+        integer, allocatable	:: double_index_selectors	(N_det_selectors)
+        integer	:: n_double_selectors	
+
+
+    Degree of excitation respect to Hartree Fock for the wave function
+    for the all the selectors determinants.
+    
+    double_index_selectors = list of the index of the double excitations
+    
+    n_double_selectors = number of double excitations in the selectors determinants
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`ref_bitmask`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`coef_hf_selector`
+
+ 
+.. c:var:: psi_selectors_coef_transp
+
+
+    File : :file:`selectors_utils/selectors.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: psi_selectors_coef_transp	(N_states,psi_selectors_size)
+
+
+    Transposed psi_selectors
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_states`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_selectors_size`
+
+
+ 
+.. c:var:: psi_selectors_diag_h_mat
+
+
+    File : :file:`selectors_utils/selectors.irp.f`
+
+    .. code:: fortran
+
+        double precision, allocatable	:: psi_selectors_diag_h_mat	(psi_selectors_size)
+
+
+    Diagonal elements of the H matrix for each selectors
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`elec_num`
+       * :c:data:`n_det_selectors`
+       * :c:data:`n_int`
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_selectors_size`
+       * :c:data:`ref_bitmask`
+       * :c:data:`ref_bitmask_energy`
+
+
+ 
+.. c:var:: psi_selectors_size
+
+
+    File : :file:`selectors_utils/selectors.irp.f`
+
+    .. code:: fortran
+
+        integer	:: psi_selectors_size	
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`psi_det_size`
+
+    Needed by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`psi_selectors`
+       * :c:data:`psi_selectors_coef_transp`
+       * :c:data:`psi_selectors_diag_h_mat`
+
+ 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: zmq_get_n_det_generators:
+
+
+    File : :file:`selectors_utils/zmq.irp.f_template_102`
+
+    .. code:: fortran
+
+        integer function zmq_get_N_det_generators(zmq_to_qp_run_socket, worker_id)
+
+
+    Get N_det_generators from the qp_run scheduler
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_generators`
+       * :c:data:`zmq_state`
+       * :c:data:`mpi_master`
+
+ 
+.. c:function:: zmq_get_n_det_selectors:
+
+
+    File : :file:`selectors_utils/zmq.irp.f_template_102`
+
+    .. code:: fortran
+
+        integer function zmq_get_N_det_selectors(zmq_to_qp_run_socket, worker_id)
+
+
+    Get N_det_selectors from the qp_run scheduler
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`zmq_state`
+       * :c:data:`mpi_master`
+
+ 
+.. c:function:: zmq_put_n_det_generators:
+
+
+    File : :file:`selectors_utils/zmq.irp.f_template_102`
+
+    .. code:: fortran
+
+        integer function zmq_put_N_det_generators(zmq_to_qp_run_socket,worker_id)
+
+
+    Put N_det_generators on the qp_run scheduler
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_generators`
+       * :c:data:`zmq_state`
+
+ 
+.. c:function:: zmq_put_n_det_selectors:
+
+
+    File : :file:`selectors_utils/zmq.irp.f_template_102`
+
+    .. code:: fortran
+
+        integer function zmq_put_N_det_selectors(zmq_to_qp_run_socket,worker_id)
+
+
+    Put N_det_selectors on the qp_run scheduler
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_det_selectors`
+       * :c:data:`zmq_state`
+

docs/source/modules/single_ref_method.rst

@@ -0,0 +1,14 @@
+.. _module_single_ref_method: 
+ 
+.. program:: single_ref_method 
+ 
+.. default-role:: option 
+ 
+=================
+single_ref_method
+=================
+
+Include this module for single reference methods.
+Using this module, the only generator determinant is the Hartree-Fock determinant.
+
+ 

docs/source/modules/tools.rst

@@ -0,0 +1,246 @@
+.. _module_tools: 
+ 
+.. program:: tools 
+ 
+.. default-role:: option 
+ 
+=====
+tools
+=====
+
+Useful tools are grouped in this module.
+ 
+ 
+ 
+Programs 
+-------- 
+ 
+ * :ref:`diagonalize_h` 
+ * :ref:`fcidump` 
+ * :ref:`four_idx_transform` 
+ * :ref:`molden` 
+ * :ref:`print_e_conv` 
+ * :ref:`print_wf` 
+ * :ref:`save_natorb` 
+ * :ref:`save_one_e_dm` 
+ * :ref:`save_ortho_mos` 
+ * :ref:`write_integrals_erf` 
+ 
+Subroutines / functions 
+----------------------- 
+ 
+.. c:function:: routine:
+
+
+    File : :file:`write_integrals_erf.irp.f`
+
+    .. code:: fortran
+
+        subroutine routine
+
+
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`diagonalize_h`
+       * :c:func:`print_wf`
+       * :c:func:`write_integrals_erf`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`save_erf_two_e_integrals_ao`
+       * :c:func:`save_erf_two_e_integrals_mo`
+
+ 
+.. c:function:: routine_e_conv:
+
+
+    File : :file:`print_e_conv.irp.f`
+
+    .. code:: fortran
+
+        subroutine routine_e_conv
+
+
+    routine called by :c:func:`print_e_conv`
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`n_states`
+       * :c:data:`ezfio_filename`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`print_e_conv`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_get_iterations_energy_iterations`
+       * :c:func:`ezfio_get_iterations_n_det_iterations`
+       * :c:func:`ezfio_get_iterations_n_iter`
+       * :c:func:`ezfio_get_iterations_pt2_iterations`
+
+ 
+.. c:function:: routine_save_one_e_dm:
+
+
+    File : :file:`save_one_e_dm.irp.f`
+
+    .. code:: fortran
+
+        subroutine routine_save_one_e_dm
+
+
+    routine called by :c:func:`save_one_e_dm`
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`one_e_dm_mo_alpha`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`save_one_e_dm`
+
+    Calls:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`ezfio_set_aux_quantities_data_one_e_dm_alpha_mo`
+       * :c:func:`ezfio_set_aux_quantities_data_one_e_dm_beta_mo`
+
+ 
+.. c:function:: write_ao_basis:
+
+
+    File : :file:`molden.irp.f`
+
+    .. code:: fortran
+
+        subroutine write_Ao_basis(i_unit_output)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_list_shell_aos`
+       * :c:data:`ao_coef`
+       * :c:data:`ao_num`
+       * :c:data:`ao_prim_num`
+       * :c:data:`nucl_charge`
+       * :c:data:`ao_l`
+       * :c:data:`ao_expo`
+       * :c:data:`element_name`
+       * :c:data:`nucl_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`molden`
+
+ 
+.. c:function:: write_geometry:
+
+
+    File : :file:`molden.irp.f`
+
+    .. code:: fortran
+
+        subroutine write_geometry(i_unit_output)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`nucl_coord`
+       * :c:data:`nucl_charge`
+       * :c:data:`element_name`
+       * :c:data:`nucl_num`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`molden`
+
+ 
+.. c:function:: write_intro_gamess:
+
+
+    File : :file:`molden.irp.f`
+
+    .. code:: fortran
+
+        subroutine write_intro_gamess(i_unit_output)
+
+
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`molden`
+
+ 
+.. c:function:: write_mo_basis:
+
+
+    File : :file:`molden.irp.f`
+
+    .. code:: fortran
+
+        subroutine write_Mo_basis(i_unit_output)
+
+
+
+    Needs:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:data:`mo_num`
+       * :c:data:`mo_coef`
+       * :c:data:`ao_num`
+       * :c:data:`ao_l_char_space`
+       * :c:data:`nucl_charge`
+       * :c:data:`ao_nucl`
+       * :c:data:`element_name`
+
+    Called by:
+
+    .. hlist::
+       :columns: 3
+
+       * :c:func:`molden`
+

man/qp_reset.1

@@ -0,0 +1,66 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "QP_RESET" "1" "Jan 29, 2019" "2.0" "Quantum Package"
+.SH NAME
+qp_reset \-  | 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
+..
+.sp
+This command resets parts of the \fI\%EZFIO\fP directory.
+.SH USAGE
+.INDENT 0.0
+.INDENT 3.5
+.sp
+.nf
+.ft C
+qp_reset [\-adhm] EZFIO_DIR
+.ft P
+.fi
+.UNINDENT
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-a, \-\-all
+Reset to the state in which the directory is after after running qp_create_ezfio\&.
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-d, \-\-dets
+Deletes the determinants and CI coefficients.
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-m, \-\-mos
+Deletes the MOs, and consequently the determinants and CI coefficients.
+.UNINDENT
+.SH AUTHOR
+A. Scemama, E. Giner
+.SH COPYRIGHT
+2019, A. Scemama, E. Giner
+.\" Generated by docutils manpage writer.
+.