Working on doc

data/.gitignore

@@ -1,2 +1,3 @@
 executables
 ezfio_defaults
+list_element.txt

data/module_gitignore

@@ -0,0 +1,44 @@
+IRPF90_temp/
+IRPF90_man/
+irpf90.make
+irpf90_entities
+tags
+AO_Basis
+AO_one_e_integrals
+Bitmask
+CIS
+CISD
+Davidson
+DavidsonDressed
+DavidsonUndressed
+Determinants
+Dressing
+dummy
+Electrons
+Ezfio_files
+FCI
+FourIdx
+Generators_CAS
+Generators_full
+gitignore
+Hartree_Fock
+Integrals_Bielec
+Iterations
+MO_Basis
+MOGuess
+MO_one_e_integrals
+MPI
+MRPT_Utils
+Nuclei
+Perturbation
+Pseudo
+Psiref_CAS
+Psiref_Utils
+Selectors_CASSD
+Selectors_full
+Selectors_Utils
+SingleRefMethod
+Slave
+Tools
+Utils
+ZMQ

docs/.gitignore

@@ -0,0 +1,2 @@
+
+build

docs/source/auto_generate.py

@@ -1,4 +1,4 @@
-#!/bin/env python2
+#!/usr/bin/env python2
 
 from __future__ import print_function
 import os
@@ -38,9 +38,9 @@ def generate_modules(abs_module, entities):
 
   providers = []
   subroutines = []
-  for k in entities:
+  for k in sorted(entities.keys()):
     e = entities[k]
-    if e["module"] == module:
+    if e["module"].lower() == module.lower():
         if "/" not in e["file"] and e["file"] != "ezfio_interface.irp.f":
             if e["type"] == 's':
                 subroutines.append(e)
@@ -51,13 +51,13 @@ def generate_modules(abs_module, entities):
     rst += [ "", "Providers", "---------", "" ]
     for p in providers:
         rst += [ """
-.. option:: %s
+.. c:var:: %s
 
     .. code:: text
 
         %s
 
-        File: %s
+    File: :file:`%s`
 
     %s
 
@@ -65,7 +65,31 @@ def generate_modules(abs_module, entities):
 """ % ( p["name"],
         "\n        ".join(p["decl"]),
         p["file"],
-        " ".join(p["doc"]).replace(".br","\n"),
+        " ".join(p["doc"]).replace("\n ","\n    "),
+      ) ]
+
+
+
+  if subroutines:
+    rst += [ "", "Subroutines / functions", "-----------------------", "" ]
+    for p in subroutines:
+        rst += [ """
+
+.. c:function:: %s
+
+    .. code:: text
+
+        %s
+
+    File: :file:`%s`
+
+    %s
+
+
+""" % ( p["name"],
+        "\n        ".join(p["decl"]),
+        p["file"],
+        " ".join(p["doc"]).replace("\n ","\n    "),
       ) ]
 
 
@@ -114,11 +138,14 @@ def generate_providers(abs_module):
                         state = 3
                         continue
                     if line.startswith(".SH Need"):
-                        break
+                        state = 0
+                        continue
                     if line.startswith(".SH Instability"):
-                        break
+                        state = 0
+                        continue
                     if line.startswith(".SH Call"):
-                        break
+                        state = 0
+                        continue
 
                     if state == 1:
                         entity["decl"] += [ line ]
@@ -129,17 +156,49 @@ def generate_providers(abs_module):
                         else:
                             entity["type"] = 'p'
                     elif state == 2:
+                        if line.startswith(".br"):
+                          line = "\n"
                         entity["doc"] += [ line ]
                     elif state == 3:
                         if line.startswith(".br"):
                             continue
-                        entity["file"] = line
+                        entity["file"] = line.split("/")[-1]
+                        try:
+                            entity["module"] = line.split("/")[-2]
+                        except: pass
+                        break
 
             entities [ entity["name"] ] = entity
 
   return entities
 
 
+def generate_index(entities):
+
+  rst_file = os.path.join('programmers_guide','index_providers.rst')
+
+  with open(rst_file,'w') as f: 
+    rst = [ "Index of Providers", 
+            "------------------", 
+            "" ]
+
+    for e in sorted(entities.keys()):
+        e = entities[e]
+        if e["type"] == 'p':
+            rst.append("* :c:data:`%s`" % (e["name"]))
+
+    rst += [ "",
+             "Index of Subroutines/Functions", 
+             "------------------------------", 
+             "" ]
+
+    for e in sorted(entities.keys()):
+        e = entities[e]
+        if e["type"] == 's':
+            rst.append("* :c:func:`%s`" % (e["name"]))
+
+    f.write("\n".join(rst))
+
 
 
 def main():
@@ -159,8 +218,14 @@ def main():
       if read_entities:
         for k in read_entities:
             entities[k] = read_entities[k]
+
+  for abs_module in os.listdir(SRC):
+    abs_module = os.path.join(SRC,abs_module)
+    if os.path.exists( os.path.join(abs_module, "README.rst") ):
         generate_modules(abs_module,entities)
 
+  generate_index(entities)
+
 if __name__ == '__main__':
   main()
 

docs/source/modules/ao_basis.rst

@@ -89,3 +89,460 @@ EZFIO parameters
     If |true|, use |AOs| in Cartesian coordinates (6d,10f,...)
 
     Default: false
+
+
+Providers
+---------
+
+
+.. c:var:: ao_coef_normalization_factor
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_coef_normalized	(ao_num,ao_prim_num_max)
+        double precision, allocatable	:: ao_coef_normalization_factor	(ao_num)
+
+    File: :file:`aos.irp.f`
+
+    Coefficients including the AO normalization
+
+
+
+
+.. c:var:: ao_coef_normalization_libint_factor
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_coef_normalization_libint_factor	(ao_num)
+
+    File: :file:`aos.irp.f`
+
+    Coefficients including the AO normalization
+
+
+
+
+.. c:var:: ao_coef_normalized
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_coef_normalized	(ao_num,ao_prim_num_max)
+        double precision, allocatable	:: ao_coef_normalization_factor	(ao_num)
+
+    File: :file:`aos.irp.f`
+
+    Coefficients including the AO normalization
+
+
+
+
+.. c:var:: ao_coef_normalized_ordered
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_coef_normalized_ordered	(ao_num,ao_prim_num_max)
+        double precision, allocatable	:: ao_expo_ordered	(ao_num,ao_prim_num_max)
+
+    File: :file:`aos.irp.f`
+
+    Sorted primitives to accelerate 4 index MO transformation
+
+
+
+
+.. c:var:: ao_coef_normalized_ordered_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_coef_normalized_ordered_transp	(ao_prim_num_max,ao_num)
+
+    File: :file:`aos.irp.f`
+
+    Transposed ao_coef_normalized_ordered
+
+
+
+
+.. c:var:: ao_expo_ordered
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_coef_normalized_ordered	(ao_num,ao_prim_num_max)
+        double precision, allocatable	:: ao_expo_ordered	(ao_num,ao_prim_num_max)
+
+    File: :file:`aos.irp.f`
+
+    Sorted primitives to accelerate 4 index MO transformation
+
+
+
+
+.. c:var:: ao_expo_ordered_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_expo_ordered_transp	(ao_prim_num_max,ao_num)
+
+    File: :file:`aos.irp.f`
+
+    Transposed ao_expo_ordered
+
+
+
+
+.. c:var:: ao_l
+
+    .. code:: text
+
+        integer, allocatable	:: ao_l	(ao_num)
+        integer	:: ao_l_max
+        character*(128), allocatable	:: ao_l_char	(ao_num)
+
+    File: :file:`aos.irp.f`
+
+    ao_l = l value of the AO: a+b+c in x^a y^b z^c
+
+
+
+
+.. c:var:: ao_l_char
+
+    .. code:: text
+
+        integer, allocatable	:: ao_l	(ao_num)
+        integer	:: ao_l_max
+        character*(128), allocatable	:: ao_l_char	(ao_num)
+
+    File: :file:`aos.irp.f`
+
+    ao_l = l value of the AO: a+b+c in x^a y^b z^c
+
+
+
+
+.. c:var:: ao_l_char_space
+
+    .. code:: text
+
+        character*(4), allocatable	:: ao_l_char_space	(ao_num)
+
+    File: :file:`aos.irp.f`
+
+    
+
+
+
+
+.. c:var:: ao_l_max
+
+    .. code:: text
+
+        integer, allocatable	:: ao_l	(ao_num)
+        integer	:: ao_l_max
+        character*(128), allocatable	:: ao_l_char	(ao_num)
+
+    File: :file:`aos.irp.f`
+
+    ao_l = l value of the AO: a+b+c in x^a y^b z^c
+
+
+
+
+.. c:var:: ao_prim_num_max
+
+    .. code:: text
+
+        integer	:: ao_prim_num_max
+
+    File: :file:`aos.irp.f`
+
+    max number of primitives
+
+
+
+
+.. c:var:: cart_to_sphe_0
+
+    .. code:: text
+
+        double precision, allocatable	:: cart_to_sphe_0	(1,1)
+
+    File: :file:`spherical_to_cartesian.irp.f`
+
+    Spherical -> Cartesian Transformation matrix for l=0
+
+
+
+
+.. c:var:: cart_to_sphe_1
+
+    .. code:: text
+
+        double precision, allocatable	:: cart_to_sphe_1	(3,3)
+
+    File: :file:`spherical_to_cartesian.irp.f`
+
+    Spherical -> Cartesian Transformation matrix for l=1
+
+
+
+
+.. c:var:: cart_to_sphe_2
+
+    .. code:: text
+
+        double precision, allocatable	:: cart_to_sphe_2	(6,5)
+
+    File: :file:`spherical_to_cartesian.irp.f`
+
+    Spherical -> Cartesian Transformation matrix for l=2
+
+
+
+
+.. c:var:: cart_to_sphe_3
+
+    .. code:: text
+
+        double precision, allocatable	:: cart_to_sphe_3	(10,7)
+
+    File: :file:`spherical_to_cartesian.irp.f`
+
+    Spherical -> Cartesian Transformation matrix for l=3
+
+
+
+
+.. c:var:: cart_to_sphe_4
+
+    .. code:: text
+
+        double precision, allocatable	:: cart_to_sphe_4	(15,9)
+
+    File: :file:`spherical_to_cartesian.irp.f`
+
+    Spherical -> Cartesian Transformation matrix for l=4
+
+
+
+
+.. c:var:: cart_to_sphe_5
+
+    .. code:: text
+
+        double precision, allocatable	:: cart_to_sphe_5	(21,11)
+
+    File: :file:`spherical_to_cartesian.irp.f`
+
+    Spherical -> Cartesian Transformation matrix for l=5
+
+
+
+
+.. c:var:: cart_to_sphe_6
+
+    .. code:: text
+
+        double precision, allocatable	:: cart_to_sphe_6	(28,13)
+
+    File: :file:`spherical_to_cartesian.irp.f`
+
+    Spherical -> Cartesian Transformation matrix for l=6
+
+
+
+
+.. c:var:: cart_to_sphe_7
+
+    .. code:: text
+
+        double precision, allocatable	:: cart_to_sphe_7	(36,15)
+
+    File: :file:`spherical_to_cartesian.irp.f`
+
+    Spherical -> Cartesian Transformation matrix for l=7
+
+
+
+
+.. c:var:: cart_to_sphe_8
+
+    .. code:: text
+
+        double precision, allocatable	:: cart_to_sphe_8	(45,17)
+
+    File: :file:`spherical_to_cartesian.irp.f`
+
+    Spherical -> Cartesian Transformation matrix for l=8
+
+
+
+
+.. c:var:: cart_to_sphe_9
+
+    .. code:: text
+
+        double precision, allocatable	:: cart_to_sphe_9	(55,19)
+
+    File: :file:`spherical_to_cartesian.irp.f`
+
+    Spherical -> Cartesian Transformation matrix for l=9
+
+
+
+
+.. c:var:: l_to_charater
+
+    .. code:: text
+
+        character*(128), allocatable	:: l_to_charater	(0:7)
+
+    File: :file:`aos.irp.f`
+
+    character corresponding to the "L" value of an AO orbital
+
+
+
+
+.. c:var:: n_aos_max
+
+    .. code:: text
+
+        integer, allocatable	:: nucl_n_aos	(nucl_num)
+        integer	:: n_aos_max
+
+    File: :file:`aos.irp.f`
+
+    Number of AOs per atom
+
+
+
+
+.. c:var:: n_pt_max_i_x
+
+    .. code:: text
+
+        integer	:: n_pt_max_integrals
+        integer	:: n_pt_max_i_x
+
+    File: :file:`dimensions_integrals.irp.f`
+
+    
+
+
+
+
+.. c:var:: n_pt_max_integrals
+
+    .. code:: text
+
+        integer	:: n_pt_max_integrals
+        integer	:: n_pt_max_i_x
+
+    File: :file:`dimensions_integrals.irp.f`
+
+    
+
+
+
+
+.. c:var:: nucl_aos
+
+    .. code:: text
+
+        integer, allocatable	:: nucl_aos	(nucl_num,N_AOs_max)
+
+    File: :file:`aos.irp.f`
+
+    List of AOs attached on each atom
+
+
+
+
+.. c:var:: nucl_list_shell_aos
+
+    .. code:: text
+
+        integer, allocatable	:: nucl_list_shell_aos	(nucl_num,N_AOs_max)
+        integer, allocatable	:: nucl_num_shell_aos	(nucl_num)
+
+    File: :file:`aos.irp.f`
+
+    Index of the shell type Aos and of the corresponding Aos Per convention, for P,D,F and G AOs, we take the index of the AO with the the corresponding power in the "X" axis
+
+
+
+
+.. c:var:: nucl_n_aos
+
+    .. code:: text
+
+        integer, allocatable	:: nucl_n_aos	(nucl_num)
+        integer	:: n_aos_max
+
+    File: :file:`aos.irp.f`
+
+    Number of AOs per atom
+
+
+
+
+.. c:var:: nucl_num_shell_aos
+
+    .. code:: text
+
+        integer, allocatable	:: nucl_list_shell_aos	(nucl_num,N_AOs_max)
+        integer, allocatable	:: nucl_num_shell_aos	(nucl_num)
+
+    File: :file:`aos.irp.f`
+
+    Index of the shell type Aos and of the corresponding Aos Per convention, for P,D,F and G AOs, we take the index of the AO with the the corresponding power in the "X" axis
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: ao_power_index
+
+    .. code:: text
+
+        integer function ao_power_index(nx,ny,nz)
+
+    File: :file:`aos.irp.f`
+
+    Unique index given to a triplet of powers: 
+    1/2 (l-n_x)*(l-n_x+1) + n_z + 1
+
+
+
+
+
+.. c:function:: ao_value
+
+    .. code:: text
+
+        double precision function ao_value(i,r)
+
+    File: :file:`aos_value.irp.f`
+
+    return the value of the ith ao at point r
+
+
+
+
+
+.. c:function:: give_all_aos_at_r
+
+    .. code:: text
+
+        subroutine give_all_aos_at_r(r,aos_array)
+
+    File: :file:`aos_value.irp.f`
+
+    gives the values of aos at a given point r
+
+

docs/source/modules/ao_one_e_integrals.rst

@@ -41,3 +41,880 @@ EZFIO parameters
     Read/Write |AO| one-electron integrals from/to disk [ Write | Read | None ]
 
     Default: None
+
+
+Providers
+---------
+
+
+.. c:var:: ao_cart_to_sphe_coef
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_cart_to_sphe_coef	(ao_num,ao_num)
+        integer	:: ao_cart_to_sphe_num
+
+    File: :file:`ao_ortho_canonical.irp.f`
+
+    ao_cart_to_sphe coefficients of the current basis set
+
+
+
+
+.. c:var:: ao_cart_to_sphe_inv
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_cart_to_sphe_inv	(ao_cart_to_sphe_num,ao_num)
+
+    File: :file:`ao_ortho_canonical.irp.f`
+
+    AO_cart_to_sphe_coef^(-1)
+
+
+
+
+.. c:var:: ao_cart_to_sphe_num
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_cart_to_sphe_coef	(ao_num,ao_num)
+        integer	:: ao_cart_to_sphe_num
+
+    File: :file:`ao_ortho_canonical.irp.f`
+
+    ao_cart_to_sphe coefficients of the current basis set
+
+
+
+
+.. c:var:: ao_cart_to_sphe_overlap
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_cart_to_sphe_overlap	(ao_cart_to_sphe_num,ao_cart_to_sphe_num)
+
+    File: :file:`ao_ortho_canonical.irp.f`
+
+    AO overlap matrix in the spherical basis set
+
+
+
+
+.. c:var:: ao_deriv2_x
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_deriv2_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv2_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv2_z	(ao_num,ao_num)
+
+    File: :file:`kin_ao_ints.irp.f`
+
+    Second derivatives matrix elements in the |AO| basis. 
+    math:`{\tt ao_deriv2_x} = \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle` 
+
+
+
+
+
+.. c:var:: ao_deriv2_y
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_deriv2_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv2_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv2_z	(ao_num,ao_num)
+
+    File: :file:`kin_ao_ints.irp.f`
+
+    Second derivatives matrix elements in the |AO| basis. 
+    math:`{\tt ao_deriv2_x} = \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle` 
+
+
+
+
+
+.. c:var:: ao_deriv2_z
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_deriv2_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv2_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv2_z	(ao_num,ao_num)
+
+    File: :file:`kin_ao_ints.irp.f`
+
+    Second derivatives matrix elements in the |AO| basis. 
+    math:`{\tt ao_deriv2_x} = \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle` 
+
+
+
+
+
+.. c:var:: ao_deriv_1_x
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_deriv_1_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv_1_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv_1_z	(ao_num,ao_num)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    array of the integrals of AO_i * d/dx  AO_j array of the integrals of AO_i * d/dy  AO_j array of the integrals of AO_i * d/dz  AO_j
+
+
+
+
+.. c:var:: ao_deriv_1_y
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_deriv_1_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv_1_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv_1_z	(ao_num,ao_num)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    array of the integrals of AO_i * d/dx  AO_j array of the integrals of AO_i * d/dy  AO_j array of the integrals of AO_i * d/dz  AO_j
+
+
+
+
+.. c:var:: ao_deriv_1_z
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_deriv_1_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv_1_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_deriv_1_z	(ao_num,ao_num)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    array of the integrals of AO_i * d/dx  AO_j array of the integrals of AO_i * d/dy  AO_j array of the integrals of AO_i * d/dz  AO_j
+
+
+
+
+.. c:var:: ao_dipole_x
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_dipole_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_dipole_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_dipole_z	(ao_num,ao_num)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    array of the integrals of AO_i * x AO_j array of the integrals of AO_i * y AO_j array of the integrals of AO_i * z AO_j
+
+
+
+
+.. c:var:: ao_dipole_y
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_dipole_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_dipole_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_dipole_z	(ao_num,ao_num)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    array of the integrals of AO_i * x AO_j array of the integrals of AO_i * y AO_j array of the integrals of AO_i * z AO_j
+
+
+
+
+.. c:var:: ao_dipole_z
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_dipole_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_dipole_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_dipole_z	(ao_num,ao_num)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    array of the integrals of AO_i * x AO_j array of the integrals of AO_i * y AO_j array of the integrals of AO_i * z AO_j
+
+
+
+
+.. c:var:: ao_kinetic_integral
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_kinetic_integral	(ao_num,ao_num)
+
+    File: :file:`kin_ao_ints.irp.f`
+
+    Array of the priminitve basis kinetic integrals. 
+    :math:`\langle \chi_i |\hat{T}| \chi_j \rangle`
+
+
+
+
+.. c:var:: ao_mono_elec_integral
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_mono_elec_integral	(ao_num,ao_num)
+        double precision, allocatable	:: ao_mono_elec_integral_diag	(ao_num)
+
+    File: :file:`ao_mono_ints.irp.f`
+
+    array of the mono electronic hamiltonian on the AOs basis : sum of the kinetic and nuclear electronic potential
+
+
+
+
+.. c:var:: ao_mono_elec_integral_diag
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_mono_elec_integral	(ao_num,ao_num)
+        double precision, allocatable	:: ao_mono_elec_integral_diag	(ao_num)
+
+    File: :file:`ao_mono_ints.irp.f`
+
+    array of the mono electronic hamiltonian on the AOs basis : sum of the kinetic and nuclear electronic potential
+
+
+
+
+.. c:var:: ao_nucl_elec_integral
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_nucl_elec_integral	(ao_num,ao_num)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Nucleus-electron interaction, in the |AO| basis set. 
+    :math:`\langle \chi_i | -\sum_A \frac{1}{|r-R_A|} | \chi_j \rangle`
+
+
+
+
+.. c:var:: ao_nucl_elec_integral_per_atom
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_nucl_elec_integral_per_atom	(ao_num,ao_num,nucl_num)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Nucleus-electron interaction in the |AO| basis set, per atom A. 
+    :math:`\langle \chi_i | -\frac{1}{|r-R_A|} | \chi_j \rangle`
+
+
+
+
+.. c:var:: ao_ortho_canonical_coef
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_ortho_canonical_coef	(ao_num,ao_num)
+        integer	:: ao_ortho_canonical_num
+
+    File: :file:`ao_ortho_canonical.irp.f`
+
+    matrix of the coefficients of the mos generated by the orthonormalization by the S^{-1/2} canonical transformation of the aos ao_ortho_canonical_coef(i,j) = coefficient of the ith ao on the jth ao_ortho_canonical orbital
+
+
+
+
+.. c:var:: ao_ortho_canonical_coef_inv
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_ortho_canonical_coef_inv	(ao_num,ao_num)
+
+    File: :file:`ao_ortho_canonical.irp.f`
+
+    ao_ortho_canonical_coef^(-1)
+
+
+
+
+.. c:var:: ao_ortho_canonical_num
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_ortho_canonical_coef	(ao_num,ao_num)
+        integer	:: ao_ortho_canonical_num
+
+    File: :file:`ao_ortho_canonical.irp.f`
+
+    matrix of the coefficients of the mos generated by the orthonormalization by the S^{-1/2} canonical transformation of the aos ao_ortho_canonical_coef(i,j) = coefficient of the ith ao on the jth ao_ortho_canonical orbital
+
+
+
+
+.. c:var:: ao_ortho_canonical_overlap
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_ortho_canonical_overlap	(ao_ortho_canonical_num,ao_ortho_canonical_num)
+
+    File: :file:`ao_ortho_canonical.irp.f`
+
+    overlap matrix of the ao_ortho_canonical. Expected to be the Identity
+
+
+
+
+.. c:var:: ao_overlap
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_overlap	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_z	(ao_num,ao_num)
+
+    File: :file:`ao_overlap.irp.f`
+
+    Overlap between atomic basis functions: :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+
+
+
+.. c:var:: ao_overlap_abs
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_overlap_abs	(ao_num,ao_num)
+
+    File: :file:`ao_overlap.irp.f`
+
+    Overlap between absolute value of atomic basis functions: :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
+
+
+
+
+.. c:var:: ao_overlap_x
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_overlap	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_z	(ao_num,ao_num)
+
+    File: :file:`ao_overlap.irp.f`
+
+    Overlap between atomic basis functions: :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+
+
+
+.. c:var:: ao_overlap_y
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_overlap	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_z	(ao_num,ao_num)
+
+    File: :file:`ao_overlap.irp.f`
+
+    Overlap between atomic basis functions: :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+
+
+
+.. c:var:: ao_overlap_z
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_overlap	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_overlap_z	(ao_num,ao_num)
+
+    File: :file:`ao_overlap.irp.f`
+
+    Overlap between atomic basis functions: :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+
+
+
+.. c:var:: ao_pseudo_integral
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_pseudo_integral	(ao_num,ao_num)
+
+    File: :file:`pot_ao_pseudo_ints.irp.f`
+
+    Pseudo-potential integrals
+
+
+
+
+.. c:var:: ao_pseudo_integral_local
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_pseudo_integral_local	(ao_num,ao_num)
+
+    File: :file:`pot_ao_pseudo_ints.irp.f`
+
+    Local pseudo-potential
+
+
+
+
+.. c:var:: ao_pseudo_integral_non_local
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_pseudo_integral_non_local	(ao_num,ao_num)
+
+    File: :file:`pot_ao_pseudo_ints.irp.f`
+
+    Local pseudo-potential
+
+
+
+
+.. c:var:: ao_spread_x
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_spread_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_spread_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_spread_z	(ao_num,ao_num)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    array of the integrals of AO_i * x^2 AO_j array of the integrals of AO_i * y^2 AO_j array of the integrals of AO_i * z^2 AO_j
+
+
+
+
+.. c:var:: ao_spread_y
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_spread_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_spread_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_spread_z	(ao_num,ao_num)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    array of the integrals of AO_i * x^2 AO_j array of the integrals of AO_i * y^2 AO_j array of the integrals of AO_i * z^2 AO_j
+
+
+
+
+.. c:var:: ao_spread_z
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_spread_x	(ao_num,ao_num)
+        double precision, allocatable	:: ao_spread_y	(ao_num,ao_num)
+        double precision, allocatable	:: ao_spread_z	(ao_num,ao_num)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    array of the integrals of AO_i * x^2 AO_j array of the integrals of AO_i * y^2 AO_j array of the integrals of AO_i * z^2 AO_j
+
+
+
+
+.. c:var:: i_x1_pol_mult_mono_elec
+
+    .. code:: text
+
+        recursive subroutine I_x1_pol_mult_mono_elec(a,c,R1x,R1xp,R2x,d,nd,n_pt_in)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Recursive routine involved in the electron-nucleus potential
+
+
+
+
+.. c:var:: i_x2_pol_mult_mono_elec
+
+    .. code:: text
+
+        recursive subroutine I_x2_pol_mult_mono_elec(c,R1x,R1xp,R2x,d,nd,dim)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Recursive routine involved in the electron-nucleus potential
+
+
+
+
+.. c:var:: pseudo_dz_k_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: pseudo_v_k_transp	(pseudo_klocmax,nucl_num)
+        integer, allocatable	:: pseudo_n_k_transp	(pseudo_klocmax,nucl_num)
+        double precision, allocatable	:: pseudo_dz_k_transp	(pseudo_klocmax,nucl_num)
+
+    File: :file:`pot_ao_pseudo_ints.irp.f`
+
+    Transposed arrays for pseudopotentials
+
+
+
+
+.. c:var:: pseudo_dz_kl_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: pseudo_v_kl_transp	(pseudo_kmax,0:pseudo_lmax,nucl_num)
+        integer, allocatable	:: pseudo_n_kl_transp	(pseudo_kmax,0:pseudo_lmax,nucl_num)
+        double precision, allocatable	:: pseudo_dz_kl_transp	(pseudo_kmax,0:pseudo_lmax,nucl_num)
+
+    File: :file:`pot_ao_pseudo_ints.irp.f`
+
+    Transposed arrays for pseudopotentials
+
+
+
+
+.. c:var:: pseudo_n_k_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: pseudo_v_k_transp	(pseudo_klocmax,nucl_num)
+        integer, allocatable	:: pseudo_n_k_transp	(pseudo_klocmax,nucl_num)
+        double precision, allocatable	:: pseudo_dz_k_transp	(pseudo_klocmax,nucl_num)
+
+    File: :file:`pot_ao_pseudo_ints.irp.f`
+
+    Transposed arrays for pseudopotentials
+
+
+
+
+.. c:var:: pseudo_n_kl_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: pseudo_v_kl_transp	(pseudo_kmax,0:pseudo_lmax,nucl_num)
+        integer, allocatable	:: pseudo_n_kl_transp	(pseudo_kmax,0:pseudo_lmax,nucl_num)
+        double precision, allocatable	:: pseudo_dz_kl_transp	(pseudo_kmax,0:pseudo_lmax,nucl_num)
+
+    File: :file:`pot_ao_pseudo_ints.irp.f`
+
+    Transposed arrays for pseudopotentials
+
+
+
+
+.. c:var:: pseudo_v_k_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: pseudo_v_k_transp	(pseudo_klocmax,nucl_num)
+        integer, allocatable	:: pseudo_n_k_transp	(pseudo_klocmax,nucl_num)
+        double precision, allocatable	:: pseudo_dz_k_transp	(pseudo_klocmax,nucl_num)
+
+    File: :file:`pot_ao_pseudo_ints.irp.f`
+
+    Transposed arrays for pseudopotentials
+
+
+
+
+.. c:var:: pseudo_v_kl_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: pseudo_v_kl_transp	(pseudo_kmax,0:pseudo_lmax,nucl_num)
+        integer, allocatable	:: pseudo_n_kl_transp	(pseudo_kmax,0:pseudo_lmax,nucl_num)
+        double precision, allocatable	:: pseudo_dz_kl_transp	(pseudo_kmax,0:pseudo_lmax,nucl_num)
+
+    File: :file:`pot_ao_pseudo_ints.irp.f`
+
+    Transposed arrays for pseudopotentials
+
+
+
+
+.. c:var:: read_ao_one_integrals
+
+    .. code:: text
+
+        logical	:: read_ao_one_integrals
+        logical	:: write_ao_one_integrals
+
+    File: :file:`read_write.irp.f`
+
+    One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
+
+
+
+
+.. c:var:: s_half
+
+    .. code:: text
+
+        double precision, allocatable	:: s_half	(ao_num,ao_num)
+
+    File: :file:`ao_overlap.irp.f`
+
+    S^{1/2}
+
+
+
+
+.. c:var:: s_half_inv
+
+    .. code:: text
+
+        double precision, allocatable	:: s_half_inv	(AO_num,AO_num)
+
+    File: :file:`ao_overlap.irp.f`
+
+    Matrix X = S^{-1/2} obtained by SVD
+
+
+
+
+.. c:var:: s_inv
+
+    .. code:: text
+
+        double precision, allocatable	:: s_inv	(ao_num,ao_num)
+
+    File: :file:`ao_overlap.irp.f`
+
+    S^-1
+
+
+
+
+.. c:var:: write_ao_one_integrals
+
+    .. code:: text
+
+        logical	:: read_ao_one_integrals
+        logical	:: write_ao_one_integrals
+
+    File: :file:`read_write.irp.f`
+
+    One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: give_polynom_mult_center_mono_elec
+
+    .. code:: text
+
+        subroutine give_polynom_mult_center_mono_elec(A_center,B_center,alpha,beta,power_A,power_B,C_center,n_pt_in,d,n_pt_out)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Returns the explicit polynomial in terms of the "t" variable of the following 
+    :math:`I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)`
+
+
+
+
+
+.. c:function:: int_gaus_pol
+
+    .. code:: text
+
+        double precision function int_gaus_pol(alpha,n)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Computes the integral: 
+    :math:`\int_{-\infty}^{\infty} x^n \exp(-\alpha x^2) dx`
+
+
+
+
+
+.. c:function:: nai_pol_mult
+
+    .. code:: text
+
+        double precision function NAI_pol_mult(A_center,B_center,power_A,power_B,alpha,beta,C_center,n_pt_in)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Computes the electron-nucleus attraction with two primitves. 
+    :math:`\langle g_i | \frac{1}{|r-R_c|} | g_j \rangle`
+
+
+
+
+
+.. c:function:: overlap_bourrin_deriv_x
+
+    .. code:: text
+
+        subroutine overlap_bourrin_deriv_x(i_component,A_center,B_center,alpha,beta,power_A,power_B,dx,lower_exp_val,overlap_x,nx)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: overlap_bourrin_dipole
+
+    .. code:: text
+
+        subroutine overlap_bourrin_dipole(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,lower_exp_val,dx,nx)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: overlap_bourrin_spread
+
+    .. code:: text
+
+        subroutine overlap_bourrin_spread(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,lower_exp_val,dx,nx)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: overlap_bourrin_x
+
+    .. code:: text
+
+        subroutine overlap_bourrin_x(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,lower_exp_val,dx,nx)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: overlap_bourrin_x_abs
+
+    .. code:: text
+
+        subroutine overlap_bourrin_x_abs(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,lower_exp_val,dx,nx)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: power
+
+    .. code:: text
+
+        double precision function power(n,x)
+
+    File: :file:`spread_dipole_ao.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: v_e_n
+
+    .. code:: text
+
+        double precision function V_e_n(a_x,a_y,a_z,b_x,b_y,b_z,alpha,beta)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Primitve nuclear attraction between the two primitves centered on the same atom. 
+    primitive_1 = x**(a_x) y**(a_y) z**(a_z) exp(-alpha * r**2) 
+    primitive_2 = x**(b_x) y**(b_y) z**(b_z) exp(- beta * r**2)
+
+
+
+
+
+.. c:function:: v_phi
+
+    .. code:: text
+
+        double precision function V_phi(n,m)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Computes the angular "phi" part of the nuclear attraction integral: 
+    :math:`\int_{0}^{2 \pi} \cos(\phi)^n \sin(\phi)^m d\phi`
+
+
+
+
+
+.. c:function:: v_r
+
+    .. code:: text
+
+        double precision function V_r(n,alpha)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Computes the radial part of the nuclear attraction integral: 
+    :math:`\int_{0}^{\infty} r^n  \exp(-\alpha  r^2)  dr` 
+
+
+
+
+
+
+.. c:function:: v_theta
+
+    .. code:: text
+
+        double precision function V_theta(n,m)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Computes the angular "theta" part of the nuclear attraction integral: 
+    :math:`\int_{0}^{\pi} \cos(\theta)^n \sin(\theta)^m d\theta`
+
+
+
+
+
+.. c:function:: wallis
+
+    .. code:: text
+
+        double precision function Wallis(n)
+
+    File: :file:`pot_ao_ints.irp.f`
+
+    Wallis integral: 
+    :math:`\int_{0}^{\pi} \cos(\theta)^n d\theta`
+
+

docs/source/modules/cis.rst

@@ -27,3 +27,91 @@ EZFIO parameters
 
     Variational CIS energy
 
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: cis
+
+    .. code:: text
+
+        subroutine cis
+
+    File: :file:`CIS.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: h_apply_cis
+
+    .. code:: text
+
+        subroutine H_apply_cis()
+
+    File: :file:`H_apply.irp.f_shell_8`
+
+    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.
+
+
+
+
+
+.. c:function:: h_apply_cis_diexc
+
+    .. code:: text
+
+        subroutine H_apply_cis_diexc(key_in, key_prev, hole_1,particl_1, hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+    File: :file:`H_apply.irp.f_shell_8`
+
+    
+
+
+
+
+
+.. c:function:: h_apply_cis_diexcorg
+
+    .. code:: text
+
+        subroutine H_apply_cis_diexcOrg(key_in,key_mask,hole_1,particl_1,hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+    File: :file:`H_apply.irp.f_shell_8`
+
+    Generate all double excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided.
+
+
+
+
+
+.. c:function:: h_apply_cis_diexcp
+
+    .. code:: text
+
+        subroutine H_apply_cis_diexcP(key_in, fs1, fh1, particl_1, fs2, fh2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+    File: :file:`H_apply.irp.f_shell_8`
+
+    
+
+
+
+
+
+.. c:function:: h_apply_cis_monoexc
+
+    .. code:: text
+
+        subroutine H_apply_cis_monoexc(key_in, hole_1,particl_1,fock_diag_tmp,i_generator,iproc_in  )
+
+    File: :file:`H_apply.irp.f_shell_8`
+
+    Generate all single excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided.
+
+

docs/source/modules/cisd.rst

@@ -27,3 +27,77 @@ EZFIO parameters
 
     Variational CISD energy
 
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: h_apply_cisd
+
+    .. code:: text
+
+        subroutine H_apply_cisd()
+
+    File: :file:`H_apply.irp.f_shell_8`
+
+    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.
+
+
+
+
+
+.. c:function:: h_apply_cisd_diexc
+
+    .. code:: text
+
+        subroutine H_apply_cisd_diexc(key_in, key_prev, hole_1,particl_1, hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+    File: :file:`H_apply.irp.f_shell_8`
+
+    
+
+
+
+
+
+.. c:function:: h_apply_cisd_diexcorg
+
+    .. code:: text
+
+        subroutine H_apply_cisd_diexcOrg(key_in,key_mask,hole_1,particl_1,hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+    File: :file:`H_apply.irp.f_shell_8`
+
+    Generate all double excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided.
+
+
+
+
+
+.. c:function:: h_apply_cisd_diexcp
+
+    .. code:: text
+
+        subroutine H_apply_cisd_diexcP(key_in, fs1, fh1, particl_1, fs2, fh2, particl_2, fock_diag_tmp, i_generator, iproc_in  )
+
+    File: :file:`H_apply.irp.f_shell_8`
+
+    
+
+
+
+
+
+.. c:function:: h_apply_cisd_monoexc
+
+    .. code:: text
+
+        subroutine H_apply_cisd_monoexc(key_in, hole_1,particl_1,fock_diag_tmp,i_generator,iproc_in  )
+
+    File: :file:`H_apply.irp.f_shell_8`
+
+    Generate all single excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided.
+
+

docs/source/modules/davidson.rst

@@ -56,3 +56,497 @@ EZFIO parameters
     If |true|, use the distributed algorithm
 
     Default: True
+
+
+Providers
+---------
+
+
+.. c:var:: ci_eigenvectors
+
+    .. code:: text
+
+        double precision, allocatable	:: ci_electronic_energy	(N_states_diag)
+        double precision, allocatable	:: ci_eigenvectors	(N_det,N_states_diag)
+        double precision, allocatable	:: ci_eigenvectors_s2	(N_states_diag)
+
+    File: :file:`diagonalize_CI.irp.f`
+
+    Eigenvectors/values of the CI matrix
+
+
+
+
+.. c:var:: ci_eigenvectors_s2
+
+    .. code:: text
+
+        double precision, allocatable	:: ci_electronic_energy	(N_states_diag)
+        double precision, allocatable	:: ci_eigenvectors	(N_det,N_states_diag)
+        double precision, allocatable	:: ci_eigenvectors_s2	(N_states_diag)
+
+    File: :file:`diagonalize_CI.irp.f`
+
+    Eigenvectors/values of the CI matrix
+
+
+
+
+.. c:var:: ci_electronic_energy
+
+    .. code:: text
+
+        double precision, allocatable	:: ci_electronic_energy	(N_states_diag)
+        double precision, allocatable	:: ci_eigenvectors	(N_det,N_states_diag)
+        double precision, allocatable	:: ci_eigenvectors_s2	(N_states_diag)
+
+    File: :file:`diagonalize_CI.irp.f`
+
+    Eigenvectors/values of the CI matrix
+
+
+
+
+.. c:var:: ci_energy
+
+    .. code:: text
+
+        double precision, allocatable	:: ci_energy	(N_states_diag)
+
+    File: :file:`diagonalize_CI.irp.f`
+
+    N_states lowest eigenvalues of the CI matrix
+
+
+
+
+.. c:var:: davidson_criterion
+
+    .. code:: text
+
+        character(64)	:: davidson_criterion
+
+    File: :file:`parameters.irp.f`
+
+    Can be : [  energy  | residual | both | wall_time | cpu_time | iterations ]
+
+
+
+
+.. c:var:: dressed_column_idx
+
+    .. code:: text
+
+        integer, allocatable	:: dressed_column_idx	(N_states)
+
+    File: :file:`diagonalization_hs2_dressed.irp.f`
+
+    Index of the dressed columns
+
+
+
+
+.. c:var:: n_states_diag
+
+    .. code:: text
+
+        integer	:: n_states_diag
+
+    File: :file:`input.irp.f`
+
+    Number of states to consider during the Davdison diagonalization
+
+
+
+
+.. c:var:: nthreads_davidson
+
+    .. code:: text
+
+        integer	:: nthreads_davidson
+
+    File: :file:`davidson_parallel.irp.f`
+
+    Number of threads for Davdison
+
+
+
+
+.. c:var:: psi_energy
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_energy	(N_states)
+
+    File: :file:`u0Hu0.irp.f`
+
+    Energy of the current wave function
+
+
+
+
+.. c:var:: psi_energy_with_nucl_rep
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_energy_with_nucl_rep	(N_states)
+
+    File: :file:`u0Hu0.irp.f`
+
+    Energy of the wave function with the nuclear repulsion energy.
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: davidson_collector
+
+    .. code:: text
+
+        subroutine davidson_collector(zmq_to_qp_run_socket, zmq_socket_pull, v0, s0, sze, N_st)
+
+    File: :file:`davidson_parallel.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: davidson_converged
+
+    .. code:: text
+
+        subroutine davidson_converged(energy,residual,wall,iterations,cpu,N_st,converged)
+
+    File: :file:`parameters.irp.f`
+
+    True if the Davidson algorithm is converged
+
+
+
+
+
+.. c:function:: davidson_diag_hjj_sjj
+
+    .. code:: text
+
+        subroutine davidson_diag_hjj_sjj(dets_in,u_in,H_jj,s2_out,energies,dim_in,sze,N_st,N_st_diag,Nint,dressing_state,converged)
+
+    File: :file:`diagonalization_hs2_dressed.irp.f`
+
+    Davidson diagonalization with specific diagonal elements of the H matrix 
+    H_jj : specific diagonal H matrix elements to diagonalize de Davidson 
+    S2_out : Output : s^2 
+    dets_in : bitmasks corresponding to determinants 
+    u_in : guess coefficients on the various states. Overwritten on exit 
+    dim_in : leftmost dimension of u_in 
+    sze : Number of determinants 
+    N_st : Number of eigenstates 
+    N_st_diag : Number of states in which H is diagonalized. Assumed > sze 
+    Initial guess vectors are not necessarily orthonormal
+
+
+
+
+
+.. c:function:: davidson_diag_hs2
+
+    .. code:: text
+
+        subroutine davidson_diag_hs2(dets_in,u_in,s2_out,dim_in,energies,sze,N_st,N_st_diag,Nint,dressing_state)
+
+    File: :file:`diagonalization_hs2_dressed.irp.f`
+
+    Davidson diagonalization. 
+    dets_in : bitmasks corresponding to determinants 
+    u_in : guess coefficients on the various states. Overwritten on exit 
+    dim_in : leftmost dimension of u_in 
+    sze : Number of determinants 
+    N_st : Number of eigenstates 
+    Initial guess vectors are not necessarily orthonormal
+
+
+
+
+
+.. c:function:: davidson_pull_results
+
+    .. code:: text
+
+        subroutine davidson_pull_results(zmq_socket_pull, v_t, s_t, imin, imax, task_id)
+
+    File: :file:`davidson_parallel.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: davidson_push_results
+
+    .. code:: text
+
+        subroutine davidson_push_results(zmq_socket_push, v_t, s_t, imin, imax, task_id)
+
+    File: :file:`davidson_parallel.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: davidson_run_slave
+
+    .. code:: text
+
+        subroutine davidson_run_slave(thread,iproc)
+
+    File: :file:`davidson_parallel.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: davidson_slave_inproc
+
+    .. code:: text
+
+        subroutine davidson_slave_inproc(i)
+
+    File: :file:`davidson_parallel.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: davidson_slave_tcp
+
+    .. code:: text
+
+        subroutine davidson_slave_tcp(i)
+
+    File: :file:`davidson_parallel.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: davidson_slave_work
+
+    .. code:: text
+
+        subroutine davidson_slave_work(zmq_to_qp_run_socket, zmq_socket_push, N_st, sze, worker_id)
+
+    File: :file:`davidson_parallel.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: diagonalize_ci
+
+    .. code:: text
+
+        subroutine diagonalize_CI
+
+    File: :file:`diagonalize_CI.irp.f`
+
+    Replace the coefficients of the CI states by the coefficients of the eigenstates of the CI matrix
+
+
+
+
+
+.. c:function:: find_reference
+
+    .. code:: text
+
+        subroutine find_reference(thresh,n_ref,result)
+
+    File: :file:`find_reference.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: h_s2_u_0_nstates_openmp
+
+    .. code:: text
+
+        subroutine H_S2_u_0_nstates_openmp(v_0,s_0,u_0,N_st,sze)
+
+    File: :file:`u0Hu0.irp.f`
+
+    Computes v_0 = H|u_0> and s_0 = S^2 |u_0> 
+    Assumes that the determinants are in psi_det 
+    istart, iend, ishift, istep are used in ZMQ parallelization.
+
+
+
+
+
+.. c:function:: h_s2_u_0_nstates_openmp_work
+
+    .. code:: text
+
+        subroutine H_S2_u_0_nstates_openmp_work(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
+
+    File: :file:`u0Hu0.irp.f`
+
+    Computes v_t = H|u_t> and s_t = S^2 |u_t> 
+    Default should be 1,N_det,0,1
+
+
+
+
+
+.. c:function:: h_s2_u_0_nstates_openmp_work_1
+
+    .. code:: text
+
+        subroutine H_S2_u_0_nstates_openmp_work_1(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
+
+    File: :file:`u0Hu0.irp.f_template_468`
+
+    Computes v_t = H|u_t> and s_t = S^2 |u_t> 
+    Default should be 1,N_det,0,1
+
+
+
+
+
+.. c:function:: h_s2_u_0_nstates_openmp_work_2
+
+    .. code:: text
+
+        subroutine H_S2_u_0_nstates_openmp_work_2(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
+
+    File: :file:`u0Hu0.irp.f_template_468`
+
+    Computes v_t = H|u_t> and s_t = S^2 |u_t> 
+    Default should be 1,N_det,0,1
+
+
+
+
+
+.. c:function:: h_s2_u_0_nstates_openmp_work_3
+
+    .. code:: text
+
+        subroutine H_S2_u_0_nstates_openmp_work_3(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
+
+    File: :file:`u0Hu0.irp.f_template_468`
+
+    Computes v_t = H|u_t> and s_t = S^2 |u_t> 
+    Default should be 1,N_det,0,1
+
+
+
+
+
+.. c:function:: h_s2_u_0_nstates_openmp_work_4
+
+    .. code:: text
+
+        subroutine H_S2_u_0_nstates_openmp_work_4(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
+
+    File: :file:`u0Hu0.irp.f_template_468`
+
+    Computes v_t = H|u_t> and s_t = S^2 |u_t> 
+    Default should be 1,N_det,0,1
+
+
+
+
+
+.. c:function:: h_s2_u_0_nstates_openmp_work_n_int
+
+    .. code:: text
+
+        subroutine H_S2_u_0_nstates_openmp_work_N_int(v_t,s_t,u_t,N_st,sze,istart,iend,ishift,istep)
+
+    File: :file:`u0Hu0.irp.f_template_468`
+
+    Computes v_t = H|u_t> and s_t = S^2 |u_t> 
+    Default should be 1,N_det,0,1
+
+
+
+
+
+.. c:function:: h_s2_u_0_nstates_zmq
+
+    .. code:: text
+
+        subroutine H_S2_u_0_nstates_zmq(v_0,s_0,u_0,N_st,sze)
+
+    File: :file:`davidson_parallel.irp.f`
+
+    Computes v_0 = H|u_0> and s_0 = S^2 |u_0> 
+    n : number of determinants 
+    H_jj : array of <j|H|j> 
+    S2_jj : array of <j|S^2|j>
+
+
+
+
+
+.. c:function:: u_0_h_u_0
+
+    .. code:: text
+
+        subroutine u_0_H_u_0(e_0,u_0,n,keys_tmp,Nint,N_st,sze)
+
+    File: :file:`u0Hu0.irp.f`
+
+    Computes e_0 = <u_0|H|u_0>/<u_0|u_0> 
+    n : number of determinants 
+
+
+
+
+
+
+.. c:function:: zmq_get_n_states_diag
+
+    .. code:: text
+
+        integer function zmq_get_N_states_diag(zmq_to_qp_run_socket, worker_id)
+
+    File: :file:`davidson_parallel.irp.f`
+
+    Get N_states_diag from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_put_n_states_diag
+
+    .. code:: text
+
+        integer function zmq_put_N_states_diag(zmq_to_qp_run_socket,worker_id)
+
+    File: :file:`davidson_parallel.irp.f`
+
+    Put N_states_diag on the qp_run scheduler
+
+

docs/source/modules/davidsonundressed.rst

@@ -11,3 +11,35 @@ DavidsonUndressed
 Module for main files Davidson's algorithm with no dressing.
 
 
+
+
+Providers
+---------
+
+
+.. c:var:: dressing_column_h
+
+    .. code:: text
+
+        double precision, allocatable	:: dressing_column_h	(N_det,N_states)
+        double precision, allocatable	:: dressing_column_s	(N_det,N_states)
+
+    File: :file:`null_dressing_vector.irp.f`
+
+    Null dressing vectors
+
+
+
+
+.. c:var:: dressing_column_s
+
+    .. code:: text
+
+        double precision, allocatable	:: dressing_column_h	(N_det,N_states)
+        double precision, allocatable	:: dressing_column_s	(N_det,N_states)
+
+    File: :file:`null_dressing_vector.irp.f`
+
+    Null dressing vectors
+
+

docs/source/modules/electrons.rst

@@ -42,3 +42,35 @@ EZFIO parameters
     Numbers total of electrons (alpha + beta)
 
     Default: = electrons.elec_alpha_num + electrons.elec_beta_num
+
+
+Providers
+---------
+
+
+.. c:var:: elec_num
+
+    .. code:: text
+
+        integer	:: elec_num
+        integer, allocatable	:: elec_num_tab	(2)
+
+    File: :file:`electrons.irp.f`
+
+    Numbers of alpha ("up") , beta ("down") and total electrons
+
+
+
+
+.. c:var:: elec_num_tab
+
+    .. code:: text
+
+        integer	:: elec_num
+        integer, allocatable	:: elec_num_tab	(2)
+
+    File: :file:`electrons.irp.f`
+
+    Numbers of alpha ("up") , beta ("down") and total electrons
+
+

docs/source/modules/ezfio_files.rst

@@ -13,3 +13,137 @@ This modules essentially contains the name of the |EZFIO| directory in the
 command-line, or as the :envvar:`QP_INPUT` environment variable.
 
 
+
+
+Providers
+---------
+
+
+.. c:var:: ezfio_filename
+
+    .. code:: text
+
+        character*(128)	:: ezfio_filename
+
+    File: :file:`ezfio.irp.f`
+
+    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.
+
+
+
+
+.. c:var:: ezfio_work_dir
+
+    .. code:: text
+
+        character*(128)	:: ezfio_work_dir
+
+    File: :file:`ezfio.irp.f`
+
+    EZFIO/work/
+
+
+
+
+.. c:var:: output_cpu_time_0
+
+    .. code:: text
+
+        double precision	:: output_wall_time_0
+        double precision	:: output_cpu_time_0
+
+    File: :file:`output.irp.f`
+
+    Initial CPU and wall times when printing in the output files
+
+
+
+
+.. c:var:: output_wall_time_0
+
+    .. code:: text
+
+        double precision	:: output_wall_time_0
+        double precision	:: output_cpu_time_0
+
+    File: :file:`output.irp.f`
+
+    Initial CPU and wall times when printing in the output files
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: getunitandopen
+
+    .. code:: text
+
+        integer function getUnitAndOpen(f,mode)
+
+    File: :file:`get_unit_and_open.irp.f`
+
+    :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:: write_bool
+
+    .. code:: text
+
+        subroutine write_bool(iunit,value,label)
+
+    File: :file:`output.irp.f`
+
+    Write an logical value in output
+
+
+
+
+
+.. c:function:: write_double
+
+    .. code:: text
+
+        subroutine write_double(iunit,value,label)
+
+    File: :file:`output.irp.f`
+
+    Write a double precision value in output
+
+
+
+
+
+.. c:function:: write_int
+
+    .. code:: text
+
+        subroutine write_int(iunit,value,label)
+
+    File: :file:`output.irp.f`
+
+    Write an integer value in output
+
+
+
+
+
+.. c:function:: write_time
+
+    .. code:: text
+
+        subroutine write_time(iunit)
+
+    File: :file:`output.irp.f`
+
+    Write a time stamp in the output for chronological reconstruction
+
+

docs/source/modules/fci.rst

@@ -137,235 +137,785 @@ Providers
 ---------
 
 
-.. option:: pt2_e0_denominator
-
-    .. code:: text
-
-        double precision, allocatable	:: pt2_e0_denominator	(N_states)
-
-        File: energy.irp.f
-
-    E0 in the denominator of the PT2
-
-
-
-
-.. option:: pt2_u_0
-
-    .. code:: text
-
-        double precision, allocatable	:: pt2_w	(N_det_generators)
-        double precision, allocatable	:: pt2_cw	(0:N_det_generators)
-        double precision	:: pt2_w_t
-        double precision	:: pt2_u_0
-        integer, allocatable	:: pt2_n_0	(pt2_N_teeth+1)
-
-        File: pt2_stoch_routines.irp.f
-
-    
-
-
-
-
-.. option:: pt2_r
-
-    .. code:: text
-
-        integer, allocatable	:: pt2_j	(N_det_generators)
-        integer, allocatable	:: pt2_r	(N_det_generators)
-
-        File: pt2_stoch_routines.irp.f
-
-    
-
-
-
-
-.. option:: pt2_w
-
-    .. code:: text
-
-        double precision, allocatable	:: pt2_w	(N_det_generators)
-        double precision, allocatable	:: pt2_cw	(0:N_det_generators)
-        double precision	:: pt2_w_t
-        double precision	:: pt2_u_0
-        integer, allocatable	:: pt2_n_0	(pt2_N_teeth+1)
-
-        File: pt2_stoch_routines.irp.f
-
-    
-
-
-
-
-.. option:: pt2_u
-
-    .. code:: text
-
-        double precision, allocatable	:: pt2_u	(N_det_generators)
-
-        File: pt2_stoch_routines.irp.f
-
-    
-
-
-
-
-.. option:: pt2_j
-
-    .. code:: text
-
-        integer, allocatable	:: pt2_j	(N_det_generators)
-        integer, allocatable	:: pt2_r	(N_det_generators)
-
-        File: pt2_stoch_routines.irp.f
-
-    
-
-
-
-
-.. option:: pt2_f
-
-    .. code:: text
-
-        integer, allocatable	:: pt2_f	(N_det_generators)
-        integer	:: pt2_n_tasks_max
-
-        File: pt2_stoch_routines.irp.f
-
-    
-
-
-
-
-.. option:: pt2_cw
-
-    .. code:: text
-
-        double precision, allocatable	:: pt2_w	(N_det_generators)
-        double precision, allocatable	:: pt2_cw	(0:N_det_generators)
-        double precision	:: pt2_w_t
-        double precision	:: pt2_u_0
-        integer, allocatable	:: pt2_n_0	(pt2_N_teeth+1)
-
-        File: pt2_stoch_routines.irp.f
-
-    
-
-
-
-
-.. option:: pt2_w_t
-
-    .. code:: text
-
-        double precision, allocatable	:: pt2_w	(N_det_generators)
-        double precision, allocatable	:: pt2_cw	(0:N_det_generators)
-        double precision	:: pt2_w_t
-        double precision	:: pt2_u_0
-        integer, allocatable	:: pt2_n_0	(pt2_N_teeth+1)
-
-        File: pt2_stoch_routines.irp.f
-
-    
-
-
-
-
-.. option:: pt2_n_tasks
-
-    .. code:: text
-
-        integer	:: pt2_n_tasks
-
-        File: pt2_stoch_routines.irp.f
-
-    Number of parallel tasks for the Monte Carlo
-
-
-
-
-.. option:: pt2_n_0
-
-    .. code:: text
-
-        double precision, allocatable	:: pt2_w	(N_det_generators)
-        double precision, allocatable	:: pt2_cw	(0:N_det_generators)
-        double precision	:: pt2_w_t
-        double precision	:: pt2_u_0
-        integer, allocatable	:: pt2_n_0	(pt2_N_teeth+1)
-
-        File: pt2_stoch_routines.irp.f
-
-    
-
-
-
-
-.. option:: pt2_n_tasks_max
-
-    .. code:: text
-
-        integer, allocatable	:: pt2_f	(N_det_generators)
-        integer	:: pt2_n_tasks_max
-
-        File: pt2_stoch_routines.irp.f
-
-    
-
-
-
-
-.. option:: pt2_n_teeth
-
-    .. code:: text
-
-        integer	:: pt2_n_teeth
-        integer	:: pt2_mindetinfirstteeth
-
-        File: pt2_stoch_routines.irp.f
-
-    
-
-
-
-
-.. option:: initialize_pt2_e0_denominator
+.. c:var:: initialize_pt2_e0_denominator
 
     .. code:: text
 
         logical	:: initialize_pt2_e0_denominator
 
-        File: energy.irp.f
+    File: :file:`energy.irp.f`
 
     If true, initialize pt2_E0_denominator
 
 
 
 
-.. option:: pt2_mindetinfirstteeth
+.. c:var:: pt2_cw
+
+    .. code:: text
+
+        double precision, allocatable	:: pt2_w	(N_det_generators)
+        double precision, allocatable	:: pt2_cw	(0:N_det_generators)
+        double precision	:: pt2_w_t
+        double precision	:: pt2_u_0
+        integer, allocatable	:: pt2_n_0	(pt2_N_teeth+1)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+.. c:var:: pt2_e0_denominator
+
+    .. code:: text
+
+        double precision, allocatable	:: pt2_e0_denominator	(N_states)
+
+    File: :file:`energy.irp.f`
+
+    E0 in the denominator of the PT2
+
+
+
+
+.. c:var:: pt2_f
+
+    .. code:: text
+
+        integer, allocatable	:: pt2_f	(N_det_generators)
+        integer	:: pt2_n_tasks_max
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+.. c:var:: pt2_j
+
+    .. code:: text
+
+        integer, allocatable	:: pt2_j	(N_det_generators)
+        integer, allocatable	:: pt2_r	(N_det_generators)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+.. c:var:: pt2_mindetinfirstteeth
 
     .. code:: text
 
         integer	:: pt2_n_teeth
         integer	:: pt2_mindetinfirstteeth
 
-        File: pt2_stoch_routines.irp.f
+    File: :file:`pt2_stoch_routines.irp.f`
 
     
 
 
 
 
-.. option:: pt2_stoch_istate
+.. c:var:: pt2_n_0
+
+    .. code:: text
+
+        double precision, allocatable	:: pt2_w	(N_det_generators)
+        double precision, allocatable	:: pt2_cw	(0:N_det_generators)
+        double precision	:: pt2_w_t
+        double precision	:: pt2_u_0
+        integer, allocatable	:: pt2_n_0	(pt2_N_teeth+1)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+.. c:var:: pt2_n_tasks
+
+    .. code:: text
+
+        integer	:: pt2_n_tasks
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    Number of parallel tasks for the Monte Carlo
+
+
+
+
+.. c:var:: pt2_n_tasks_max
+
+    .. code:: text
+
+        integer, allocatable	:: pt2_f	(N_det_generators)
+        integer	:: pt2_n_tasks_max
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+.. c:var:: pt2_n_teeth
+
+    .. code:: text
+
+        integer	:: pt2_n_teeth
+        integer	:: pt2_mindetinfirstteeth
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+.. c:var:: pt2_r
+
+    .. code:: text
+
+        integer, allocatable	:: pt2_j	(N_det_generators)
+        integer, allocatable	:: pt2_r	(N_det_generators)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+.. c:var:: pt2_stoch_istate
 
     .. code:: text
 
         integer	:: pt2_stoch_istate
 
-        File: pt2_stoch_routines.irp.f
+    File: :file:`pt2_stoch_routines.irp.f`
 
     State for stochatsic PT2
 
 
+
+
+.. c:var:: pt2_u
+
+    .. code:: text
+
+        double precision, allocatable	:: pt2_u	(N_det_generators)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+.. c:var:: pt2_u_0
+
+    .. code:: text
+
+        double precision, allocatable	:: pt2_w	(N_det_generators)
+        double precision, allocatable	:: pt2_cw	(0:N_det_generators)
+        double precision	:: pt2_w_t
+        double precision	:: pt2_u_0
+        integer, allocatable	:: pt2_n_0	(pt2_N_teeth+1)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+.. c:var:: pt2_w
+
+    .. code:: text
+
+        double precision, allocatable	:: pt2_w	(N_det_generators)
+        double precision, allocatable	:: pt2_cw	(0:N_det_generators)
+        double precision	:: pt2_w_t
+        double precision	:: pt2_u_0
+        integer, allocatable	:: pt2_n_0	(pt2_N_teeth+1)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+.. c:var:: pt2_w_t
+
+    .. code:: text
+
+        double precision, allocatable	:: pt2_w	(N_det_generators)
+        double precision, allocatable	:: pt2_cw	(0:N_det_generators)
+        double precision	:: pt2_w_t
+        double precision	:: pt2_u_0
+        integer, allocatable	:: pt2_n_0	(pt2_N_teeth+1)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: add_to_selection_buffer
+
+    .. code:: text
+
+        subroutine add_to_selection_buffer(b, det, val)
+
+    File: :file:`selection_buffer.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: bitstring_to_list_in_selection
+
+    .. code:: text
+
+        subroutine bitstring_to_list_in_selection( string, list, n_elements, Nint)
+
+    File: :file:`selection.irp.f`
+
+    Gives the inidices(+1) of the bits set to 1 in the bit string
+
+
+
+
+
+.. c:function:: create_selection_buffer
+
+    .. code:: text
+
+        subroutine create_selection_buffer(N, siz_, res)
+
+    File: :file:`selection_buffer.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: delete_selection_buffer
+
+    .. code:: text
+
+        subroutine delete_selection_buffer(b)
+
+    File: :file:`selection_buffer.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: fci_zmq
+
+    .. code:: text
+
+        subroutine fci_zmq
+
+    File: :file:`FCI.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: fill_buffer_double
+
+    .. code:: text
+
+        subroutine fill_buffer_double(i_generator, sp, h1, h2, bannedOrb, banned, fock_diag_tmp, E0, pt2, variance, norm, mat, buf)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: get_d0
+
+    .. code:: text
+
+        subroutine get_d0(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: get_d1
+
+    .. code:: text
+
+        subroutine get_d1(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: get_d2
+
+    .. code:: text
+
+        subroutine get_d2(gen, phasemask, bannedOrb, banned, mat, mask, h, p, sp, coefs)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: get_m0
+
+    .. code:: text
+
+        subroutine get_m0(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: get_m1
+
+    .. code:: text
+
+        subroutine get_m1(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: get_m2
+
+    .. code:: text
+
+        subroutine get_m2(gen, phasemask, bannedOrb, vect, mask, h, p, sp, coefs)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: get_mask_phase
+
+    .. code:: text
+
+        subroutine get_mask_phase(det1, pm, Nint)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: get_phase_bi
+
+    .. code:: text
+
+        double precision function get_phase_bi(phasemask, s1, s2, h1, p1, h2, p2, Nint)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: make_selection_buffer_s2
+
+    .. code:: text
+
+        subroutine make_selection_buffer_s2(b)
+
+    File: :file:`selection_buffer.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: merge_selection_buffers
+
+    .. code:: text
+
+        subroutine merge_selection_buffers(b1, b2)
+
+    File: :file:`selection_buffer.irp.f`
+
+    Merges the selection buffers b1 and b2 into b2
+
+
+
+
+
+.. c:function:: past_d1
+
+    .. code:: text
+
+        subroutine past_d1(bannedOrb, p)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: past_d2
+
+    .. code:: text
+
+        subroutine past_d2(banned, p, sp)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: pt2_collector
+
+    .. code:: text
+
+        subroutine pt2_collector(zmq_socket_pull, E, relative_error, pt2, error, variance, norm)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: pt2_find_sample
+
+    .. code:: text
+
+        integer function pt2_find_sample(v, w)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: pt2_find_sample_lr
+
+    .. code:: text
+
+        integer function pt2_find_sample_lr(v, w, l_in, r_in)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: pt2_slave_inproc
+
+    .. code:: text
+
+        subroutine pt2_slave_inproc(i)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: pt2_stoch
+
+    .. code:: text
+
+        subroutine pt2_stoch
+
+    File: :file:`PT2.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: pull_pt2_results
+
+    .. code:: text
+
+        subroutine pull_pt2_results(zmq_socket_pull, index, pt2, variance, norm, task_id, n_tasks)
+
+    File: :file:`run_pt2_slave.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: pull_selection_results
+
+    .. code:: text
+
+        subroutine pull_selection_results(zmq_socket_pull, pt2, variance, norm, val, det, N, task_id, ntask)
+
+    File: :file:`run_selection_slave.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: push_pt2_results
+
+    .. code:: text
+
+        subroutine push_pt2_results(zmq_socket_push, index, pt2, variance, norm, task_id, n_tasks)
+
+    File: :file:`run_pt2_slave.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: push_selection_results
+
+    .. code:: text
+
+        subroutine push_selection_results(zmq_socket_push, pt2, variance, norm, b, task_id, ntask)
+
+    File: :file:`run_selection_slave.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: run_pt2_slave
+
+    .. code:: text
+
+        subroutine run_pt2_slave(thread,iproc,energy)
+
+    File: :file:`run_pt2_slave.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: run_selection_slave
+
+    .. code:: text
+
+        subroutine run_selection_slave(thread,iproc,energy)
+
+    File: :file:`run_selection_slave.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: select_connected
+
+    .. code:: text
+
+        subroutine select_connected(i_generator,E0,pt2,variance,norm,b,subset,csubset)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: select_singles_and_doubles
+
+    .. code:: text
+
+        subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_diag_tmp,E0,pt2,variance,norm,buf,subset,csubset)
+
+    File: :file:`selection.irp.f`
+
+    WARNING /!\ : It is assumed that the generators and selectors are psi_det_sorted
+
+
+
+
+
+.. c:function:: selection_collector
+
+    .. code:: text
+
+        subroutine selection_collector(zmq_socket_pull, b, N, pt2, variance, norm)
+
+    File: :file:`zmq_selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: selection_slave_inproc
+
+    .. code:: text
+
+        subroutine selection_slave_inproc(i)
+
+    File: :file:`zmq_selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: sort_selection_buffer
+
+    .. code:: text
+
+        subroutine sort_selection_buffer(b)
+
+    File: :file:`selection_buffer.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: splash_pq
+
+    .. code:: text
+
+        subroutine splash_pq(mask, sp, det, i_gen, N_sel, bannedOrb, banned, mat, interesting)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: spot_isinwf
+
+    .. code:: text
+
+        subroutine spot_isinwf(mask, det, i_gen, N, banned, fullMatch, interesting)
+
+    File: :file:`selection.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: testteethbuilding
+
+    .. code:: text
+
+        logical function testTeethBuilding(minF, N)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: zmq_pt2
+
+    .. code:: text
+
+        subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm)
+
+    File: :file:`pt2_stoch_routines.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: zmq_selection
+
+    .. code:: text
+
+        subroutine ZMQ_selection(N_in, pt2, variance, norm)
+
+    File: :file:`zmq_selection.irp.f`
+
+    
+
+

docs/source/modules/fouridx.rst

@@ -11,3 +11,21 @@ FourIdx
 Four-index transformation.
 
 
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: four_idx
+
+    .. code:: text
+
+        subroutine four_idx
+
+    File: :file:`Four_idx_transform.irp.f`
+
+    4-index transformation from AO to MO integrals
+
+

docs/source/modules/generators_full.rst

@@ -14,3 +14,132 @@ 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
+
+    .. code:: text
+
+        integer	:: degree_max_generators
+
+    File: :file:`generators.irp.f`
+
+    Max degree of excitation (respect to HF) of the generators
+
+
+
+
+.. c:var:: n_det_generators
+
+    .. code:: text
+
+        integer	:: n_det_generators
+
+    File: :file:`generators.irp.f`
+
+    For Single reference wave functions, the number of generators is 1 : the Hartree-Fock determinant
+
+
+
+
+.. c:var:: psi_coef_generators
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_det_generators	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_coef_generators	(psi_det_size,N_states)
+
+    File: :file:`generators.irp.f`
+
+    For Single reference wave functions, the generator is the Hartree-Fock determinant
+
+
+
+
+.. c:var:: psi_coef_sorted_gen
+
+    .. code:: text
+
+        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)
+
+    File: :file:`generators.irp.f`
+
+    For Single reference wave functions, the generator is the Hartree-Fock determinant
+
+
+
+
+.. c:var:: psi_det_generators
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_det_generators	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_coef_generators	(psi_det_size,N_states)
+
+    File: :file:`generators.irp.f`
+
+    For Single reference wave functions, the generator is the Hartree-Fock determinant
+
+
+
+
+.. c:var:: psi_det_sorted_gen
+
+    .. code:: text
+
+        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)
+
+    File: :file:`generators.irp.f`
+
+    For Single reference wave functions, the generator is the Hartree-Fock determinant
+
+
+
+
+.. c:var:: psi_det_sorted_gen_order
+
+    .. code:: text
+
+        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)
+
+    File: :file:`generators.irp.f`
+
+    For Single reference wave functions, the generator is the Hartree-Fock determinant
+
+
+
+
+.. c:var:: select_max
+
+    .. code:: text
+
+        double precision, allocatable	:: select_max	(size_select_max)
+
+    File: :file:`generators.irp.f`
+
+    Memo to skip useless selectors
+
+
+
+
+.. c:var:: size_select_max
+
+    .. code:: text
+
+        integer	:: size_select_max
+
+    File: :file:`generators.irp.f`
+
+    Size of the select_max array
+
+

docs/source/modules/hartree_fock.rst

@@ -101,20 +101,104 @@ Providers
 ---------
 
 
-.. option:: fock_matrix_mo_alpha
+.. c:var:: ao_bi_elec_integral_alpha
 
     .. code:: text
 
-        double precision, allocatable	:: fock_matrix_mo_alpha	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: ao_bi_elec_integral_alpha	(ao_num,ao_num)
+        double precision, allocatable	:: ao_bi_elec_integral_beta	(ao_num,ao_num)
 
-        File: Fock_matrix.irp.f
+    File: :file:`Fock_matrix.irp.f`
 
-    Fock matrix on the MO basis
+    Alpha Fock matrix in AO basis set
 
 
 
 
-.. option:: extrapolate_fock_matrix
+.. c:var:: ao_bi_elec_integral_beta
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_bi_elec_integral_alpha	(ao_num,ao_num)
+        double precision, allocatable	:: ao_bi_elec_integral_beta	(ao_num,ao_num)
+
+    File: :file:`Fock_matrix.irp.f`
+
+    Alpha Fock matrix in AO basis set
+
+
+
+
+.. c:var:: diagonal_fock_matrix_mo
+
+    .. code:: text
+
+        double precision, allocatable	:: diagonal_fock_matrix_mo	(mo_tot_num)
+        double precision, allocatable	:: eigenvectors_fock_matrix_mo	(ao_num,mo_tot_num)
+
+    File: :file:`diagonalize_fock.irp.f`
+
+    Diagonal Fock matrix in the MO basis
+
+
+
+
+.. c:var:: diagonal_fock_matrix_mo_sum
+
+    .. code:: text
+
+        double precision, allocatable	:: diagonal_fock_matrix_mo_sum	(mo_tot_num)
+
+    File: :file:`diagonalize_fock.irp.f`
+
+    diagonal element of the fock matrix calculated as the sum over all the interactions with all the electrons in the RHF determinant diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
+
+
+
+
+.. c:var:: eigenvalues_fock_matrix_ao
+
+    .. code:: text
+
+        double precision, allocatable	:: eigenvalues_fock_matrix_ao	(AO_num)
+        double precision, allocatable	:: eigenvectors_fock_matrix_ao	(AO_num,AO_num)
+
+    File: :file:`DIIS.irp.f`
+
+    Eigenvalues and eigenvectors of the Fock matrix over the AO basis
+
+
+
+
+.. c:var:: eigenvectors_fock_matrix_ao
+
+    .. code:: text
+
+        double precision, allocatable	:: eigenvalues_fock_matrix_ao	(AO_num)
+        double precision, allocatable	:: eigenvectors_fock_matrix_ao	(AO_num,AO_num)
+
+    File: :file:`DIIS.irp.f`
+
+    Eigenvalues and eigenvectors of the Fock matrix over the AO basis
+
+
+
+
+.. c:var:: eigenvectors_fock_matrix_mo
+
+    .. code:: text
+
+        double precision, allocatable	:: diagonal_fock_matrix_mo	(mo_tot_num)
+        double precision, allocatable	:: eigenvectors_fock_matrix_mo	(ao_num,mo_tot_num)
+
+    File: :file:`diagonalize_fock.irp.f`
+
+    Diagonal Fock matrix in the MO basis
+
+
+
+
+.. c:var:: extrapolate_fock_matrix
 
     .. code:: text
 
@@ -124,286 +208,290 @@ Providers
         iteration_SCF,dim_DIIS                 &
         )
 
-        File: Roothaan_Hall_SCF.irp.f
+    File: :file:`Roothaan_Hall_SCF.irp.f`
 
     Compute the extrapolated Fock matrix using the DIIS procedure
 
 
 
 
-.. option:: fock_matrix_ao_alpha
-
-    .. code:: text
-
-        double precision, allocatable	:: fock_matrix_ao_alpha	(ao_num,ao_num)
-        double precision, allocatable	:: fock_matrix_ao_beta	(ao_num,ao_num)
-
-        File: Fock_matrix.irp.f
-
-    Alpha Fock matrix in AO basis set
-
-
-
-
-.. option:: hf_energy
-
-    .. code:: text
-
-        double precision	:: hf_energy
-
-        File: Fock_matrix.irp.f
-
-    Hartree-Fock energy
-
-
-
-
-.. option:: fock_matrix_diag_mo
-
-    .. code:: text
-
-        double precision, allocatable	:: fock_matrix_mo	(mo_tot_num,mo_tot_num)
-        double precision, allocatable	:: fock_matrix_diag_mo	(mo_tot_num)
-
-        File: Fock_matrix.irp.f
-
-    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 
-
-
-
-
-
-.. option:: fock_matrix_ao_beta
-
-    .. code:: text
-
-        double precision, allocatable	:: fock_matrix_ao_alpha	(ao_num,ao_num)
-        double precision, allocatable	:: fock_matrix_ao_beta	(ao_num,ao_num)
-
-        File: Fock_matrix.irp.f
-
-    Alpha Fock matrix in AO basis set
-
-
-
-
-.. option:: hf_density_matrix_ao
-
-    .. code:: text
-
-        double precision, allocatable	:: hf_density_matrix_ao	(ao_num,ao_num)
-
-        File: HF_density_matrix_ao.irp.f
-
-    S^{-1}.P.S^{-1}  where P = C.C^t
-
-
-
-
-.. option:: fps_spf_matrix_ao
-
-    .. code:: text
-
-        double precision, allocatable	:: fps_spf_matrix_ao	(AO_num,AO_num)
-
-        File: DIIS.irp.f
-
-    Commutator FPS - SPF
-
-
-
-
-.. option:: threshold_diis_nonzero
-
-    .. code:: text
-
-        double precision	:: threshold_diis_nonzero
-
-        File: DIIS.irp.f
-
-    If threshold_DIIS is zero, choose sqrt(thresh_scf)
-
-
-
-
-.. option:: ao_bi_elec_integral_alpha
-
-    .. code:: text
-
-        double precision, allocatable	:: ao_bi_elec_integral_alpha	(ao_num,ao_num)
-        double precision, allocatable	:: ao_bi_elec_integral_beta	(ao_num,ao_num)
-
-        File: Fock_matrix.irp.f
-
-    Alpha Fock matrix in AO basis set
-
-
-
-
-.. option:: eigenvectors_fock_matrix_ao
-
-    .. code:: text
-
-        double precision, allocatable	:: eigenvalues_fock_matrix_ao	(AO_num)
-        double precision, allocatable	:: eigenvectors_fock_matrix_ao	(AO_num,AO_num)
-
-        File: DIIS.irp.f
-
-    Eigenvalues and eigenvectors of the Fock matrix over the AO basis
-
-
-
-
-.. option:: fock_matrix_mo_beta
-
-    .. code:: text
-
-        double precision, allocatable	:: fock_matrix_mo_beta	(mo_tot_num,mo_tot_num)
-
-        File: Fock_matrix.irp.f
-
-    Fock matrix on the MO basis
-
-
-
-
-.. option:: eigenvectors_fock_matrix_mo
-
-    .. code:: text
-
-        double precision, allocatable	:: diagonal_fock_matrix_mo	(mo_tot_num)
-        double precision, allocatable	:: eigenvectors_fock_matrix_mo	(ao_num,mo_tot_num)
-
-        File: diagonalize_fock.irp.f
-
-    Diagonal Fock matrix in the MO basis
-
-
-
-
-.. option:: fock_matrix_mo
-
-    .. code:: text
-
-        double precision, allocatable	:: fock_matrix_mo	(mo_tot_num,mo_tot_num)
-        double precision, allocatable	:: fock_matrix_diag_mo	(mo_tot_num)
-
-        File: Fock_matrix.irp.f
-
-    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 
-
-
-
-
-
-.. option:: fps_spf_matrix_mo
-
-    .. code:: text
-
-        double precision, allocatable	:: fps_spf_matrix_mo	(mo_tot_num,mo_tot_num)
-
-        File: DIIS.irp.f
-
-    Commutator FPS - SPF in MO basis
-
-
-
-
-.. option:: diagonal_fock_matrix_mo_sum
-
-    .. code:: text
-
-        double precision, allocatable	:: diagonal_fock_matrix_mo_sum	(mo_tot_num)
-
-        File: diagonalize_fock.irp.f
-
-    diagonal element of the fock matrix calculated as the sum over all the interactions with all the electrons in the RHF determinant diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
-
-
-
-
-.. option:: hf_density_matrix_ao_alpha
-
-    .. code:: text
-
-        double precision, allocatable	:: hf_density_matrix_ao_alpha	(ao_num,ao_num)
-
-        File: HF_density_matrix_ao.irp.f
-
-    S^{-1}.P_alpha.S^{-1}
-
-
-
-
-.. option:: hf_density_matrix_ao_beta
-
-    .. code:: text
-
-        double precision, allocatable	:: hf_density_matrix_ao_beta	(ao_num,ao_num)
-
-        File: HF_density_matrix_ao.irp.f
-
-    S^{-1}.P_beta.S^{-1}
-
-
-
-
-.. option:: eigenvalues_fock_matrix_ao
-
-    .. code:: text
-
-        double precision, allocatable	:: eigenvalues_fock_matrix_ao	(AO_num)
-        double precision, allocatable	:: eigenvectors_fock_matrix_ao	(AO_num,AO_num)
-
-        File: DIIS.irp.f
-
-    Eigenvalues and eigenvectors of the Fock matrix over the AO basis
-
-
-
-
-.. option:: ao_bi_elec_integral_beta
-
-    .. code:: text
-
-        double precision, allocatable	:: ao_bi_elec_integral_alpha	(ao_num,ao_num)
-        double precision, allocatable	:: ao_bi_elec_integral_beta	(ao_num,ao_num)
-
-        File: Fock_matrix.irp.f
-
-    Alpha Fock matrix in AO basis set
-
-
-
-
-.. option:: fock_matrix_ao
+.. c:var:: fock_matrix_ao
 
     .. code:: text
 
         double precision, allocatable	:: fock_matrix_ao	(ao_num,ao_num)
 
-        File: Fock_matrix.irp.f
+    File: :file:`Fock_matrix.irp.f`
 
     Fock matrix in AO basis set
 
 
 
 
-.. option:: diagonal_fock_matrix_mo
+.. c:var:: fock_matrix_ao_alpha
 
     .. code:: text
 
-        double precision, allocatable	:: diagonal_fock_matrix_mo	(mo_tot_num)
-        double precision, allocatable	:: eigenvectors_fock_matrix_mo	(ao_num,mo_tot_num)
+        double precision, allocatable	:: fock_matrix_ao_alpha	(ao_num,ao_num)
+        double precision, allocatable	:: fock_matrix_ao_beta	(ao_num,ao_num)
 
-        File: diagonalize_fock.irp.f
+    File: :file:`Fock_matrix.irp.f`
 
-    Diagonal Fock matrix in the MO basis
+    Alpha Fock matrix in AO basis set
+
+
+
+
+.. c:var:: fock_matrix_ao_beta
+
+    .. code:: text
+
+        double precision, allocatable	:: fock_matrix_ao_alpha	(ao_num,ao_num)
+        double precision, allocatable	:: fock_matrix_ao_beta	(ao_num,ao_num)
+
+    File: :file:`Fock_matrix.irp.f`
+
+    Alpha Fock matrix in AO basis set
+
+
+
+
+.. c:var:: fock_matrix_diag_mo
+
+    .. code:: text
+
+        double precision, allocatable	:: fock_matrix_mo	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: fock_matrix_diag_mo	(mo_tot_num)
+
+    File: :file:`Fock_matrix.irp.f`
+
+    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 
+
+
+
+
+
+.. c:var:: fock_matrix_mo
+
+    .. code:: text
+
+        double precision, allocatable	:: fock_matrix_mo	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: fock_matrix_diag_mo	(mo_tot_num)
+
+    File: :file:`Fock_matrix.irp.f`
+
+    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 
+
+
+
+
+
+.. c:var:: fock_matrix_mo_alpha
+
+    .. code:: text
+
+        double precision, allocatable	:: fock_matrix_mo_alpha	(mo_tot_num,mo_tot_num)
+
+    File: :file:`Fock_matrix.irp.f`
+
+    Fock matrix on the MO basis
+
+
+
+
+.. c:var:: fock_matrix_mo_beta
+
+    .. code:: text
+
+        double precision, allocatable	:: fock_matrix_mo_beta	(mo_tot_num,mo_tot_num)
+
+    File: :file:`Fock_matrix.irp.f`
+
+    Fock matrix on the MO basis
+
+
+
+
+.. c:var:: fps_spf_matrix_ao
+
+    .. code:: text
+
+        double precision, allocatable	:: fps_spf_matrix_ao	(AO_num,AO_num)
+
+    File: :file:`DIIS.irp.f`
+
+    Commutator FPS - SPF
+
+
+
+
+.. c:var:: fps_spf_matrix_mo
+
+    .. code:: text
+
+        double precision, allocatable	:: fps_spf_matrix_mo	(mo_tot_num,mo_tot_num)
+
+    File: :file:`DIIS.irp.f`
+
+    Commutator FPS - SPF in MO basis
+
+
+
+
+.. c:var:: hf_density_matrix_ao
+
+    .. code:: text
+
+        double precision, allocatable	:: hf_density_matrix_ao	(ao_num,ao_num)
+
+    File: :file:`HF_density_matrix_ao.irp.f`
+
+    S^{-1}.P.S^{-1}  where P = C.C^t
+
+
+
+
+.. c:var:: hf_density_matrix_ao_alpha
+
+    .. code:: text
+
+        double precision, allocatable	:: hf_density_matrix_ao_alpha	(ao_num,ao_num)
+
+    File: :file:`HF_density_matrix_ao.irp.f`
+
+    S^{-1}.P_alpha.S^{-1}
+
+
+
+
+.. c:var:: hf_density_matrix_ao_beta
+
+    .. code:: text
+
+        double precision, allocatable	:: hf_density_matrix_ao_beta	(ao_num,ao_num)
+
+    File: :file:`HF_density_matrix_ao.irp.f`
+
+    S^{-1}.P_beta.S^{-1}
+
+
+
+
+.. c:var:: hf_energy
+
+    .. code:: text
+
+        double precision	:: hf_energy
+
+    File: :file:`Fock_matrix.irp.f`
+
+    Hartree-Fock energy
+
+
+
+
+.. c:var:: threshold_diis_nonzero
+
+    .. code:: text
+
+        double precision	:: threshold_diis_nonzero
+
+    File: :file:`DIIS.irp.f`
+
+    If threshold_DIIS is zero, choose sqrt(thresh_scf)
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: create_guess
+
+    .. code:: text
+
+        subroutine create_guess
+
+    File: :file:`SCF.irp.f`
+
+    Create a MO guess if no MOs are present in the EZFIO directory
+
+
+
+
+
+.. c:function:: damping_scf
+
+    .. code:: text
+
+        subroutine damping_SCF
+
+    File: :file:`damping_SCF.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: huckel_guess
+
+    .. code:: text
+
+        subroutine huckel_guess
+
+    File: :file:`huckel.irp.f`
+
+    Build the MOs using the extended Huckel model
+
+
+
+
+
+.. c:function:: roothaan_hall_scf
+
+    .. code:: text
+
+        subroutine Roothaan_Hall_SCF
+
+    File: :file:`Roothaan_Hall_SCF.irp.f`
+
+    Roothaan-Hall algorithm for SCF Hartree-Fock calculation
+
+
+
+
+
+.. c:function:: run
+
+    .. code:: text
+
+        subroutine run
+
+    File: :file:`SCF.irp.f`
+
+    Run SCF calculation
+
+
+
+
+
+.. c:function:: scf
+
+    .. code:: text
+
+        subroutine scf
+
+    File: :file:`SCF.irp.f`
+
+    Produce `Hartree_Fock` MO orbital output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ output: hartree_fock.energy optional: mo_basis.mo_coef
 
 

docs/source/modules/iterations.rst

@@ -35,3 +35,79 @@ EZFIO parameters
 
     The |PT2| correction at each iteration
 
+
+
+Providers
+---------
+
+
+.. c:var:: extrapolated_energy
+
+    .. code:: text
+
+        double precision, allocatable	:: extrapolated_energy	(N_iter,N_states)
+
+    File: :file:`iterations.irp.f`
+
+    Extrapolated energy, using E_var = f(PT2) where PT2=0
+
+
+
+
+.. c:var:: n_iter
+
+    .. code:: text
+
+        integer	:: n_iter
+
+    File: :file:`io.irp.f`
+
+    number of iterations
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: print_extrapolated_energy
+
+    .. code:: text
+
+        subroutine print_extrapolated_energy(e_,pt2_)
+
+    File: :file:`print_extrapolation.irp.f`
+
+    Print the extrapolated energy in the output
+
+
+
+
+
+.. c:function:: print_summary
+
+    .. code:: text
+
+        subroutine print_summary(e_,pt2_,error_,variance_,norm_)
+
+    File: :file:`print_summary.irp.f`
+
+    Print the extrapolated energy in the output
+
+
+
+
+
+.. c:function:: save_iterations
+
+    .. code:: text
+
+        subroutine save_iterations(e_, pt2_,n_)
+
+    File: :file:`iterations.irp.f`
+
+    Update the energy in the EZFIO file.
+
+

docs/source/modules/mo_basis.rst

@@ -63,3 +63,287 @@ EZFIO parameters
 
     MD5 checksum characterizing the |AO| basis set.
 
+
+
+Providers
+---------
+
+
+.. c:var:: mo_coef
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_coef	(ao_num,mo_tot_num)
+
+    File: :file:`mos.irp.f`
+
+    Molecular orbital coefficients on AO basis set mo_coef(i,j) = coefficient of the ith ao on the jth mo mo_label : Label characterizing the MOS (local, canonical, natural, etc)
+
+
+
+
+.. c:var:: mo_coef_in_ao_ortho_basis
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_coef_in_ao_ortho_basis	(ao_num,mo_tot_num)
+
+    File: :file:`mos.irp.f`
+
+    MO coefficients in orthogonalized AO basis 
+    C^(-1).C_mo
+
+
+
+
+.. c:var:: mo_coef_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_coef_transp	(mo_tot_num,ao_num)
+
+    File: :file:`mos.irp.f`
+
+    Molecular orbital coefficients on AO basis set
+
+
+
+
+.. c:var:: mo_label
+
+    .. code:: text
+
+        character*(64)	:: mo_label
+
+    File: :file:`mos.irp.f`
+
+    Molecular orbital coefficients on AO basis set mo_coef(i,j) = coefficient of the ith ao on the jth mo mo_label : Label characterizing the MOS (local, canonical, natural, etc)
+
+
+
+
+.. c:var:: mo_num
+
+    .. code:: text
+
+        integer	:: mo_num
+
+    File: :file:`mos.irp.f`
+
+    mo_tot_num without the highest deleted MOs
+
+
+
+
+.. c:var:: mo_occ
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_occ	(mo_tot_num)
+
+    File: :file:`mos.irp.f`
+
+    MO occupation numbers
+
+
+
+
+.. c:var:: mo_tot_num
+
+    .. code:: text
+
+        integer	:: mo_tot_num
+
+    File: :file:`mos.irp.f`
+
+    Number of MOs
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: ao_ortho_cano_to_ao
+
+    .. code:: text
+
+        subroutine ao_ortho_cano_to_ao(A_ao,LDA_ao,A,LDA)
+
+    File: :file:`mos.irp.f`
+
+    Transform A from the AO basis to the orthogonal AO basis 
+    C^(-1).A_ao.Ct^(-1)
+
+
+
+
+
+.. c:function:: ao_to_mo
+
+    .. code:: text
+
+        subroutine ao_to_mo(A_ao,LDA_ao,A_mo,LDA_mo)
+
+    File: :file:`mos.irp.f`
+
+    Transform A from the AO basis to the MO basis 
+    Ct.A_ao.C
+
+
+
+
+
+.. c:function:: give_all_mos_at_r
+
+    .. code:: text
+
+        subroutine give_all_mos_at_r(r,mos_array)
+
+    File: :file:`utils.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: give_specific_mos_at_r
+
+    .. code:: text
+
+        subroutine give_specific_mos_at_r(r,mos_array, mo_coef_specific)
+
+    File: :file:`utils.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: mix_mo_jk
+
+    .. code:: text
+
+        subroutine mix_mo_jk(j,k)
+
+    File: :file:`mos.irp.f`
+
+    subroutine that rotates the jth MO with the kth MO to give two new MO's that are '+' = 1/sqrt(2) (|j> + |k>) '-' = 1/sqrt(2) (|j> - |k>) by convention, the '+' MO is in the lower index (min(j,k)) by convention, the '-' MO is in the greater index (max(j,k))
+
+
+
+
+
+.. c:function:: mo_as_eigvectors_of_mo_matrix
+
+    .. code:: text
+
+        subroutine mo_as_eigvectors_of_mo_matrix(matrix,n,m,label,sign,output)
+
+    File: :file:`utils.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: mo_as_eigvectors_of_mo_matrix_sort_by_observable
+
+    .. code:: text
+
+        subroutine mo_as_eigvectors_of_mo_matrix_sort_by_observable(matrix,observable,n,m,label)
+
+    File: :file:`utils.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: mo_as_svd_vectors_of_mo_matrix
+
+    .. code:: text
+
+        subroutine mo_as_svd_vectors_of_mo_matrix(matrix,lda,m,n,label)
+
+    File: :file:`utils.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: mo_as_svd_vectors_of_mo_matrix_eig
+
+    .. code:: text
+
+        subroutine mo_as_svd_vectors_of_mo_matrix_eig(matrix,lda,m,n,eig,label)
+
+    File: :file:`utils.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: mo_sort_by_observable
+
+    .. code:: text
+
+        subroutine mo_sort_by_observable(observable,label)
+
+    File: :file:`utils.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: mo_to_ao_no_overlap
+
+    .. code:: text
+
+        subroutine mo_to_ao_no_overlap(A_mo,LDA_mo,A_ao,LDA_ao)
+
+    File: :file:`mos.irp.f`
+
+    Transform A from the MO basis to the S^-1 AO basis Useful for density matrix
+
+
+
+
+
+.. c:function:: save_mos
+
+    .. code:: text
+
+        subroutine save_mos
+
+    File: :file:`utils.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: save_mos_truncated
+
+    .. code:: text
+
+        subroutine save_mos_truncated(n)
+
+    File: :file:`utils.irp.f`
+
+    
+
+

docs/source/modules/mo_one_e_integrals.rst

@@ -36,3 +36,249 @@ EZFIO parameters
     Read/Write |MO| one-electron integrals from/to disk [ Write | Read | None ]
 
     Default: None
+
+
+Providers
+---------
+
+
+.. c:var:: mo_dipole_x
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_dipole_x	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_dipole_y	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_dipole_z	(mo_tot_num,mo_tot_num)
+
+    File: :file:`spread_dipole_mo.irp.f`
+
+    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
+
+
+
+
+.. c:var:: mo_dipole_y
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_dipole_x	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_dipole_y	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_dipole_z	(mo_tot_num,mo_tot_num)
+
+    File: :file:`spread_dipole_mo.irp.f`
+
+    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
+
+
+
+
+.. c:var:: mo_dipole_z
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_dipole_x	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_dipole_y	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_dipole_z	(mo_tot_num,mo_tot_num)
+
+    File: :file:`spread_dipole_mo.irp.f`
+
+    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
+
+
+
+
+.. c:var:: mo_kinetic_integral
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_kinetic_integral	(mo_tot_num,mo_tot_num)
+
+    File: :file:`kin_mo_ints.irp.f`
+
+    Kinetic energy integrals in the MO basis
+
+
+
+
+.. c:var:: mo_mono_elec_integral
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_mono_elec_integral	(mo_tot_num,mo_tot_num)
+
+    File: :file:`mo_mono_ints.irp.f`
+
+    array of the mono electronic hamiltonian on the MOs basis : sum of the kinetic and nuclear electronic potential (and pseudo potential if needed)
+
+
+
+
+.. c:var:: mo_nucl_elec_integral
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_nucl_elec_integral	(mo_tot_num,mo_tot_num)
+
+    File: :file:`pot_mo_ints.irp.f`
+
+    interaction nuclear electron on the MO basis
+
+
+
+
+.. c:var:: mo_nucl_elec_integral_per_atom
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_nucl_elec_integral_per_atom	(mo_tot_num,mo_tot_num,nucl_num)
+
+    File: :file:`pot_mo_ints.irp.f`
+
+    mo_nucl_elec_integral_per_atom(i,j,k) = -<MO(i)|1/|r-Rk|MO(j)> where Rk is the geometry of the kth atom
+
+
+
+
+.. c:var:: mo_overlap
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_overlap	(mo_tot_num,mo_tot_num)
+
+    File: :file:`mo_overlap.irp.f`
+
+    
+
+
+
+
+.. c:var:: mo_pseudo_integral
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_pseudo_integral	(mo_tot_num,mo_tot_num)
+
+    File: :file:`pot_mo_pseudo_ints.irp.f`
+
+    interaction nuclear electron on the MO basis
+
+
+
+
+.. c:var:: mo_spread_x
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_spread_x	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_spread_y	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_spread_z	(mo_tot_num,mo_tot_num)
+
+    File: :file:`spread_dipole_mo.irp.f`
+
+    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
+
+
+
+
+.. c:var:: mo_spread_y
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_spread_x	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_spread_y	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_spread_z	(mo_tot_num,mo_tot_num)
+
+    File: :file:`spread_dipole_mo.irp.f`
+
+    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
+
+
+
+
+.. c:var:: mo_spread_z
+
+    .. code:: text
+
+        double precision, allocatable	:: mo_spread_x	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_spread_y	(mo_tot_num,mo_tot_num)
+        double precision, allocatable	:: mo_spread_z	(mo_tot_num,mo_tot_num)
+
+    File: :file:`spread_dipole_mo.irp.f`
+
+    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
+
+
+
+
+.. c:var:: read_mo_one_integrals
+
+    .. code:: text
+
+        logical	:: read_mo_one_integrals
+        logical	:: write_mo_one_integrals
+
+    File: :file:`read_write.irp.f`
+
+    One level of abstraction for disk_access_mo_integrals
+
+
+
+
+.. c:var:: s_mo_coef
+
+    .. code:: text
+
+        double precision, allocatable	:: s_mo_coef	(ao_num,mo_tot_num)
+
+    File: :file:`ao_to_mo.irp.f`
+
+    Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix.
+
+
+
+
+.. c:var:: write_mo_one_integrals
+
+    .. code:: text
+
+        logical	:: read_mo_one_integrals
+        logical	:: write_mo_one_integrals
+
+    File: :file:`read_write.irp.f`
+
+    One level of abstraction for disk_access_mo_integrals
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: mo_to_ao
+
+    .. code:: text
+
+        subroutine mo_to_ao(A_mo,LDA_mo,A_ao,LDA_ao)
+
+    File: :file:`ao_to_mo.irp.f`
+
+    Transform A from the MO basis to the AO basis 
+    (S.C).A_mo.(S.C)t
+
+
+
+
+
+.. c:function:: orthonormalize_mos
+
+    .. code:: text
+
+        subroutine orthonormalize_mos
+
+    File: :file:`orthonormalize.irp.f`
+
+    
+
+

docs/source/modules/moguess.rst

@@ -11,3 +11,77 @@ MOGuess
 Guess for |MOs|.
 
 
+
+
+Providers
+---------
+
+
+.. c:var:: ao_ortho_canonical_nucl_elec_integral
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_ortho_canonical_nucl_elec_integral	(mo_tot_num,mo_tot_num)
+
+    File: :file:`pot_mo_ortho_canonical_ints.irp.f`
+
+    
+
+
+
+
+.. c:var:: ao_ortho_lowdin_coef
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_ortho_lowdin_coef	(ao_num,ao_num)
+
+    File: :file:`mo_ortho_lowdin.irp.f`
+
+    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
+
+
+
+
+.. c:var:: ao_ortho_lowdin_nucl_elec_integral
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_ortho_lowdin_nucl_elec_integral	(mo_tot_num,mo_tot_num)
+
+    File: :file:`pot_mo_ortho_lowdin_ints.irp.f`
+
+    
+
+
+
+
+.. c:var:: ao_ortho_lowdin_overlap
+
+    .. code:: text
+
+        double precision, allocatable	:: ao_ortho_lowdin_overlap	(ao_num,ao_num)
+
+    File: :file:`mo_ortho_lowdin.irp.f`
+
+    overlap matrix of the ao_ortho_lowdin supposed to be the Identity
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: hcore_guess
+
+    .. code:: text
+
+        subroutine hcore_guess
+
+    File: :file:`h_core_guess_routine.irp.f`
+
+    Produce `H_core` MO orbital
+
+

docs/source/modules/mpi.rst

@@ -10,3 +10,107 @@ MPI
 
 Contains all the functions and providers for parallelization with |MPI|.
 
+
+
+Providers
+---------
+
+
+.. c:var:: mpi_initialized
+
+    .. code:: text
+
+        logical	:: mpi_initialized
+
+    File: :file:`mpi.irp.f`
+
+    Always true. Initialized MPI
+
+
+
+
+.. c:var:: mpi_master
+
+    .. code:: text
+
+        logical	:: mpi_master
+
+    File: :file:`mpi.irp.f`
+
+    If true, rank is zero
+
+
+
+
+.. c:var:: mpi_rank
+
+    .. code:: text
+
+        integer	:: mpi_rank
+        integer	:: mpi_size
+
+    File: :file:`mpi.irp.f`
+
+    Rank of MPI process and number of MPI processes
+
+
+
+
+.. c:var:: mpi_size
+
+    .. code:: text
+
+        integer	:: mpi_rank
+        integer	:: mpi_size
+
+    File: :file:`mpi.irp.f`
+
+    Rank of MPI process and number of MPI processes
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: broadcast_chunks_double
+
+    .. code:: text
+
+        subroutine broadcast_chunks_double(A, LDA)
+
+    File: :file:`mpi.irp.f_template_97`
+
+    Broadcast with chunks of ~2GB
+
+
+
+
+
+.. c:function:: broadcast_chunks_integer
+
+    .. code:: text
+
+        subroutine broadcast_chunks_integer(A, LDA)
+
+    File: :file:`mpi.irp.f_template_97`
+
+    Broadcast with chunks of ~2GB
+
+
+
+
+
+.. c:function:: broadcast_chunks_integer8
+
+    .. code:: text
+
+        subroutine broadcast_chunks_integer8(A, LDA)
+
+    File: :file:`mpi.irp.f_template_97`
+
+    Broadcast with chunks of ~2GB
+
+

docs/source/modules/nuclei.rst

@@ -48,3 +48,304 @@ EZFIO parameters
 
     Nuclear repulsion (Computed automaticaly or Read in the |EZFIO|)
 
+
+
+Providers
+---------
+
+
+.. c:var:: center_of_mass
+
+    .. code:: text
+
+        double precision, allocatable	:: center_of_mass	(3)
+
+    File: :file:`nuclei.irp.f`
+
+    Center of mass of the molecule
+
+
+
+
+.. c:var:: element_mass
+
+    .. code:: text
+
+        character*(4), allocatable	:: element_name	(0:127)
+        double precision, allocatable	:: element_mass	(0:127)
+
+    File: :file:`nuclei.irp.f`
+
+    Array of the name of element, sorted by nuclear charge (integer)
+
+
+
+
+.. c:var:: element_name
+
+    .. code:: text
+
+        character*(4), allocatable	:: element_name	(0:127)
+        double precision, allocatable	:: element_mass	(0:127)
+
+    File: :file:`nuclei.irp.f`
+
+    Array of the name of element, sorted by nuclear charge (integer)
+
+
+
+
+.. c:var:: inertia_tensor
+
+    .. code:: text
+
+        double precision, allocatable	:: inertia_tensor	(3,3)
+
+    File: :file:`inertia.irp.f`
+
+    Inertia tensor
+
+
+
+
+.. c:var:: inertia_tensor_eigenvalues
+
+    .. code:: text
+
+        double precision, allocatable	:: inertia_tensor_eigenvectors	(3,3)
+        double precision, allocatable	:: inertia_tensor_eigenvalues	(3)
+
+    File: :file:`inertia.irp.f`
+
+    Eigenvectors/eigenvalues of the inertia_tensor. Used to find normal orientation.
+
+
+
+
+.. c:var:: inertia_tensor_eigenvectors
+
+    .. code:: text
+
+        double precision, allocatable	:: inertia_tensor_eigenvectors	(3,3)
+        double precision, allocatable	:: inertia_tensor_eigenvalues	(3)
+
+    File: :file:`inertia.irp.f`
+
+    Eigenvectors/eigenvalues of the inertia_tensor. Used to find normal orientation.
+
+
+
+
+.. c:var:: nucl_coord
+
+    .. code:: text
+
+        double precision, allocatable	:: nucl_coord	(nucl_num,3)
+
+    File: :file:`nuclei.irp.f`
+
+    Nuclear coordinates in the format (:, {x,y,z})
+
+
+
+
+.. c:var:: nucl_coord_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: nucl_coord_transp	(3,nucl_num)
+
+    File: :file:`nuclei.irp.f`
+
+    Transposed array of nucl_coord
+
+
+
+
+.. c:var:: nucl_dist
+
+    .. code:: text
+
+        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)
+
+    File: :file:`nuclei.irp.f`
+
+    nucl_dist     : Nucleus-nucleus distances nucl_dist_2   : Nucleus-nucleus distances squared nucl_dist_vec : Nucleus-nucleus distances vectors
+
+
+
+
+.. c:var:: nucl_dist_2
+
+    .. code:: text
+
+        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)
+
+    File: :file:`nuclei.irp.f`
+
+    nucl_dist     : Nucleus-nucleus distances nucl_dist_2   : Nucleus-nucleus distances squared nucl_dist_vec : Nucleus-nucleus distances vectors
+
+
+
+
+.. c:var:: nucl_dist_vec_x
+
+    .. code:: text
+
+        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)
+
+    File: :file:`nuclei.irp.f`
+
+    nucl_dist     : Nucleus-nucleus distances nucl_dist_2   : Nucleus-nucleus distances squared nucl_dist_vec : Nucleus-nucleus distances vectors
+
+
+
+
+.. c:var:: nucl_dist_vec_y
+
+    .. code:: text
+
+        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)
+
+    File: :file:`nuclei.irp.f`
+
+    nucl_dist     : Nucleus-nucleus distances nucl_dist_2   : Nucleus-nucleus distances squared nucl_dist_vec : Nucleus-nucleus distances vectors
+
+
+
+
+.. c:var:: nucl_dist_vec_z
+
+    .. code:: text
+
+        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)
+
+    File: :file:`nuclei.irp.f`
+
+    nucl_dist     : Nucleus-nucleus distances nucl_dist_2   : Nucleus-nucleus distances squared nucl_dist_vec : Nucleus-nucleus distances vectors
+
+
+
+
+.. c:var:: nuclear_repulsion
+
+    .. code:: text
+
+        double precision	:: nuclear_repulsion
+
+    File: :file:`nuclei.irp.f`
+
+    Nuclear repulsion energy
+
+
+
+
+.. c:var:: positive_charge_barycentre
+
+    .. code:: text
+
+        double precision, allocatable	:: positive_charge_barycentre	(3)
+
+    File: :file:`nuclei.irp.f`
+
+    Centroid of the positive charges
+
+
+
+
+.. c:var:: slater_bragg_radii
+
+    .. code:: text
+
+        double precision, allocatable	:: slater_bragg_radii	(100)
+
+    File: :file:`atomic_radii.irp.f`
+
+    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)
+
+
+
+
+.. c:var:: slater_bragg_radii_per_atom
+
+    .. code:: text
+
+        double precision, allocatable	:: slater_bragg_radii_per_atom	(nucl_num)
+
+    File: :file:`atomic_radii.irp.f`
+
+    
+
+
+
+
+.. c:var:: slater_bragg_radii_per_atom_ua
+
+    .. code:: text
+
+        double precision, allocatable	:: slater_bragg_radii_per_atom_ua	(nucl_num)
+
+    File: :file:`atomic_radii.irp.f`
+
+    
+
+
+
+
+.. c:var:: slater_bragg_radii_ua
+
+    .. code:: text
+
+        double precision, allocatable	:: slater_bragg_radii_ua	(100)
+
+    File: :file:`atomic_radii.irp.f`
+
+    
+
+
+
+
+.. c:var:: slater_bragg_type_inter_distance
+
+    .. code:: text
+
+        double precision, allocatable	:: slater_bragg_type_inter_distance	(nucl_num,nucl_num)
+
+    File: :file:`atomic_radii.irp.f`
+
+    
+
+
+
+
+.. c:var:: slater_bragg_type_inter_distance_ua
+
+    .. code:: text
+
+        double precision, allocatable	:: slater_bragg_type_inter_distance_ua	(nucl_num,nucl_num)
+
+    File: :file:`atomic_radii.irp.f`
+
+    
+
+

docs/source/modules/perturbation.rst

@@ -107,3 +107,694 @@ EZFIO parameters
     Type of zeroth-order Hamiltonian [ EN | Barycentric | Variance | SOP ]
 
     Default: EN
+
+
+Providers
+---------
+
+
+.. c:var:: fill_h_apply_buffer_selection
+
+    .. code:: text
+
+        subroutine fill_H_apply_buffer_selection(n_selected,det_buffer,e_2_pert_buffer,coef_pert_buffer, &
+        N_st,Nint,iproc,select_max_out)
+
+    File: :file:`selection.irp.f`
+
+    Fill the H_apply buffer with determiants for the selection
+
+
+
+
+.. c:var:: max_exc_pert
+
+    .. code:: text
+
+        integer	:: max_exc_pert
+
+    File: :file:`exc_max.irp.f`
+
+    
+
+
+
+
+.. c:var:: selection_criterion
+
+    .. code:: text
+
+        double precision	:: selection_criterion
+        double precision	:: selection_criterion_min
+        double precision	:: selection_criterion_factor
+
+    File: :file:`selection.irp.f`
+
+    Threshold to select determinants. Set by selection routines.
+
+
+
+
+.. c:var:: selection_criterion_factor
+
+    .. code:: text
+
+        double precision	:: selection_criterion
+        double precision	:: selection_criterion_min
+        double precision	:: selection_criterion_factor
+
+    File: :file:`selection.irp.f`
+
+    Threshold to select determinants. Set by selection routines.
+
+
+
+
+.. c:var:: selection_criterion_min
+
+    .. code:: text
+
+        double precision	:: selection_criterion
+        double precision	:: selection_criterion_min
+        double precision	:: selection_criterion_factor
+
+    File: :file:`selection.irp.f`
+
+    Threshold to select determinants. Set by selection routines.
+
+
+
+
+.. c:var:: var_pt2_ratio
+
+    .. code:: text
+
+        double precision	:: var_pt2_ratio
+
+    File: :file:`var_pt2_ratio_provider.irp.f`
+
+    The selection process stops when the energy ratio variational/(variational+PT2) is equal to var_pt2_ratio
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: i_h_psi_pert_new_minilist
+
+    .. code:: text
+
+        subroutine i_H_psi_pert_new_minilist(key,keys,idx_key,N_minilist,coef,Nint,Ndet,Ndet_max,Nstate,i_H_psi_array,coef_pert)
+
+    File: :file:`pt2_new.irp.f`
+
+    Computes <i|H|Psi> = \sum_J c_J <i|H|J>. 
+    Uses filter_connected_i_H_psi0 to get all the |J> to which |i> is connected. The |J> are searched in short pre-computed lists.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_decontracted
+
+    .. code:: text
+
+        subroutine perturb_buffer_by_mono_decontracted(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``decontracted`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_dummy
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``dummy`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_epstein_nesbet
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_epstein_nesbet_2x2
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_epstein_nesbet_2x2_no_ci_diag
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_epstein_nesbet_sc2
+
+    .. code:: text
+
+        subroutine perturb_buffer_by_mono_epstein_nesbet_sc2(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected
+
+    .. code:: text
+
+        subroutine perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_epstein_nesbet_sc2_projected
+
+    .. code:: text
+
+        subroutine perturb_buffer_by_mono_epstein_nesbet_sc2_projected(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_h_core
+
+    .. code:: text
+
+        subroutine perturb_buffer_by_mono_h_core(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_moller_plesset
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_moller_plesset_general
+
+    .. code:: text
+
+        subroutine perturb_buffer_by_mono_moller_plesset_general(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``moller_plesset_general`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_by_mono_qdpt
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``qdpt`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_decontracted
+
+    .. code:: text
+
+        subroutine perturb_buffer_decontracted(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``decontracted`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_dummy
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``dummy`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_epstein_nesbet
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_epstein_nesbet_2x2
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_epstein_nesbet_2x2_no_ci_diag
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_epstein_nesbet_sc2
+
+    .. code:: text
+
+        subroutine perturb_buffer_epstein_nesbet_sc2(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_epstein_nesbet_sc2_no_projected
+
+    .. code:: text
+
+        subroutine perturb_buffer_epstein_nesbet_sc2_no_projected(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_epstein_nesbet_sc2_projected
+
+    .. code:: text
+
+        subroutine perturb_buffer_epstein_nesbet_sc2_projected(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_h_core
+
+    .. code:: text
+
+        subroutine perturb_buffer_h_core(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_moller_plesset
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_moller_plesset_general
+
+    .. code:: text
+
+        subroutine perturb_buffer_moller_plesset_general(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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``moller_plesset_general`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: perturb_buffer_qdpt
+
+    .. code:: text
+
+        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)
+
+    File: :file:`perturbation.irp.f_shell_13`
+
+    Applly pertubration ``qdpt`` to the buffer of determinants generated in the H_apply routine.
+
+
+
+
+
+.. c:function:: pt2_decontracted
+
+    .. code:: text
+
+        subroutine pt2_decontracted (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)
+
+    File: :file:`pt2_equations.irp.f_template_606`
+
+    
+
+
+
+
+
+.. c:function:: pt2_dummy
+
+    .. code:: text
+
+        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)
+
+    File: :file:`pt2_equations.irp.f_template_606`
+
+    Dummy perturbation to add all connected determinants.
+
+
+
+
+
+.. c:function:: pt2_epstein_nesbet
+
+    .. code:: text
+
+        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)
+
+    File: :file:`pt2_equations.irp.f_template_606`
+
+    compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution 
+    for the various N_st states. 
+    c_pert(i) = <psi(i)|H|det_pert>/( E(i) - <det_pert|H|det_pert> ) 
+    e_2_pert(i) = <psi(i)|H|det_pert>^2/( E(i) - <det_pert|H|det_pert> ) 
+
+
+
+
+
+
+.. c:function:: pt2_epstein_nesbet_2x2
+
+    .. code:: text
+
+        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)
+
+    File: :file:`pt2_equations.irp.f_template_606`
+
+    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> 
+
+
+
+
+
+
+.. c:function:: pt2_epstein_nesbet_2x2_no_ci_diag
+
+    .. code:: text
+
+        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)
+
+    File: :file:`pt2_equations.irp.f_template_606`
+
+    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> 
+
+
+
+
+
+
+.. c:function:: pt2_epstein_nesbet_sc2
+
+    .. code:: text
+
+        subroutine pt2_epstein_nesbet_sc2 (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)
+
+    File: :file:`pt2_equations.irp.f_template_606`
+
+    compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution 
+    for the various N_st states, but with the CISD_SC2 energies and coefficients 
+    c_pert(i) = <psi(i)|H|det_pert>/( E(i) - <det_pert|H|det_pert> ) 
+    e_2_pert(i) = <psi(i)|H|det_pert>^2/( E(i) - <det_pert|H|det_pert> ) 
+
+
+
+
+
+
+.. c:function:: pt2_epstein_nesbet_sc2_no_projected
+
+    .. code:: text
+
+        subroutine pt2_epstein_nesbet_SC2_no_projected (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)
+
+    File: :file:`pt2_equations.irp.f_template_606`
+
+    compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution 
+    for the various N_st states, 
+    but  with the correction in the denominator 
+    comming from the interaction of that determinant with all the others determinants 
+    that can be repeated by repeating all the double excitations 
+    : you repeat all the correlation energy already taken into account in electronic_energy(1) 
+    that could be repeated to this determinant. 
+    In addition, for the perturbative energetic contribution you have the standard second order 
+    e_2_pert = <psi_i|H|det_pert>^2/(Delta_E) 
+    and also the purely projected contribution 
+    H_pert_diag = <HF|H|det_pert> c_pert
+
+
+
+
+
+.. c:function:: pt2_epstein_nesbet_sc2_projected
+
+    .. code:: text
+
+        subroutine pt2_epstein_nesbet_SC2_projected (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)
+
+    File: :file:`pt2_equations.irp.f_template_606`
+
+    compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution 
+    for the various N_st states, 
+    but  with the correction in the denominator 
+    comming from the interaction of that determinant with all the others determinants 
+    that can be repeated by repeating all the double excitations 
+    : you repeat all the correlation energy already taken into account in electronic_energy(1) 
+    that could be repeated to this determinant. 
+    In addition, for the perturbative energetic contribution you have the standard second order 
+    e_2_pert = <psi_i|H|det_pert>^2/(Delta_E) 
+    and also the purely projected contribution 
+    H_pert_diag = <HF|H|det_pert> c_pert
+
+
+
+
+
+.. c:function:: pt2_h_core
+
+    .. code:: text
+
+        subroutine pt2_h_core(det_pert,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
+
+    File: :file:`pert_single.irp.f`
+
+    compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution 
+    for the various N_st states. 
+    c_pert(i) = <psi(i)|H|det_pert>/( E(i) - <det_pert|H|det_pert> ) 
+    e_2_pert(i) = <psi(i)|H|det_pert>^2/( E(i) - <det_pert|H|det_pert> ) 
+
+
+
+
+
+
+.. c:function:: pt2_moller_plesset
+
+    .. code:: text
+
+        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)
+
+    File: :file:`pt2_equations.irp.f_template_606`
+
+    compute the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution 
+    for the various n_st states. 
+    c_pert(i) = <psi(i)|H|det_pert>/(difference of orbital energies) 
+    e_2_pert(i) = <psi(i)|H|det_pert>^2/(difference of orbital energies) 
+
+
+
+
+
+
+.. c:function:: pt2_moller_plesset_general
+
+    .. code:: text
+
+        subroutine pt2_moller_plesset_general (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)
+
+    File: :file:`pt2_equations.irp.f_template_606`
+
+    compute the general Moller-Plesset perturbative first order coefficient and second order energetic contribution 
+    for the various n_st states. 
+    c_pert(i) = <psi(i)|H|det_pert>/(difference of orbital energies) 
+    e_2_pert(i) = <psi(i)|H|det_pert>^2/(difference of orbital energies) 
+
+
+
+
+
+
+.. c:function:: pt2_qdpt
+
+    .. code:: text
+
+        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)
+
+    File: :file:`pt2_equations.irp.f_template_606`
+
+    compute the QDPT first order coefficient and second order energetic contribution 
+    for the various N_st states. 
+    c_pert(i) = <psi(i)|H|det_pert>/( <psi(i)|H|psi(i)> - <det_pert|H|det_pert> ) 
+
+
+
+
+
+
+.. c:function:: remove_small_contributions
+
+    .. code:: text
+
+        subroutine remove_small_contributions
+
+    File: :file:`selection.irp.f`
+
+    Remove determinants with small contributions. N_states is assumed to be provided.
+
+
+
+
+
+.. c:function:: repeat_all_e_corr
+
+    .. code:: text
+
+        double precision function repeat_all_e_corr(key_in)
+
+    File: :file:`pert_sc2.irp.f`
+
+    
+
+

docs/source/modules/psiref_cas.rst

@@ -12,3 +12,166 @@ Reference wave function is defined as a |CAS| wave function.
 This module is required for |CAS-SD|, |MRPT| or |MRCC|.
 
 
+
+
+Providers
+---------
+
+
+.. c:var:: idx_ref
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_ref	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_ref_coef	(psi_det_size,n_states)
+        integer, allocatable	:: idx_ref	(psi_det_size)
+        integer	:: n_det_ref
+
+    File: :file:`psi_ref.irp.f`
+
+    CAS wave function, defined from the application of the CAS bitmask on the determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+
+
+
+.. c:var:: inv_norm_psi_ref
+
+    .. code:: text
+
+        double precision, allocatable	:: norm_psi_ref	(N_states)
+        double precision, allocatable	:: inv_norm_psi_ref	(N_states)
+
+    File: :file:`psi_ref.irp.f`
+
+    
+
+
+
+
+.. c:var:: n_det_ref
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_ref	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_ref_coef	(psi_det_size,n_states)
+        integer, allocatable	:: idx_ref	(psi_det_size)
+        integer	:: n_det_ref
+
+    File: :file:`psi_ref.irp.f`
+
+    CAS wave function, defined from the application of the CAS bitmask on the determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+
+
+
+.. c:var:: norm_psi_ref
+
+    .. code:: text
+
+        double precision, allocatable	:: norm_psi_ref	(N_states)
+        double precision, allocatable	:: inv_norm_psi_ref	(N_states)
+
+    File: :file:`psi_ref.irp.f`
+
+    
+
+
+
+
+.. c:var:: psi_non_ref_coef_interm_norm
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_non_ref_coef_interm_norm	(N_det_non_ref,N_states)
+
+    File: :file:`psi_ref.irp.f`
+
+    
+
+
+
+
+.. c:var:: psi_ref
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_ref	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_ref_coef	(psi_det_size,n_states)
+        integer, allocatable	:: idx_ref	(psi_det_size)
+        integer	:: n_det_ref
+
+    File: :file:`psi_ref.irp.f`
+
+    CAS wave function, defined from the application of the CAS bitmask on the determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+
+
+
+.. c:var:: psi_ref_coef
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_ref	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_ref_coef	(psi_det_size,n_states)
+        integer, allocatable	:: idx_ref	(psi_det_size)
+        integer	:: n_det_ref
+
+    File: :file:`psi_ref.irp.f`
+
+    CAS wave function, defined from the application of the CAS bitmask on the determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+
+
+
+.. c:var:: psi_ref_coef_interm_norm
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_ref_coef_interm_norm	(N_det_ref,N_states)
+
+    File: :file:`psi_ref.irp.f`
+
+    
+
+
+
+
+.. c:var:: psi_ref_coef_inv
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_ref_coef_inv	(psi_det_size,n_states)
+
+    File: :file:`psi_ref.irp.f`
+
+    1/psi_ref_coef
+
+
+
+
+.. c:var:: psi_ref_coef_restart
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_ref_restart	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_ref_coef_restart	(psi_det_size,n_states)
+
+    File: :file:`psi_ref.irp.f`
+
+    Projection of the CAS wave function on the restart wave function.
+
+
+
+
+.. c:var:: psi_ref_restart
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_ref_restart	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_ref_coef_restart	(psi_det_size,n_states)
+
+    File: :file:`psi_ref.irp.f`
+
+    Projection of the CAS wave function on the restart wave function.
+
+

docs/source/modules/psiref_utils.rst

@@ -14,3 +14,369 @@ needs to be loaded with any `psi_ref_*` module.
 
 
 
+
+
+Providers
+---------
+
+
+.. c:var:: h_matrix_ref
+
+    .. code:: text
+
+        double precision, allocatable	:: h_matrix_ref	(N_det_ref,N_det_ref)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    
+
+
+
+
+.. c:var:: holes_operators
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: holes_operators	(N_int,2)
+        integer(bit_kind), allocatable	:: particles_operators	(N_int,2)
+
+    File: :file:`psi_ref_excitations_operators.irp.f`
+
+    holes_operators represents an array of integers where all the holes have been done going from psi_ref to psi_non_ref particles_operators represents an array of integers where all the particles have been done going from psi_ref to psi_non_ref
+
+
+
+
+.. c:var:: idx_non_ref
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_non_ref	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_non_ref_coef	(psi_det_size,n_states)
+        integer, allocatable	:: idx_non_ref	(psi_det_size)
+        integer, allocatable	:: idx_non_ref_rev	(psi_det_size)
+        integer	:: n_det_non_ref
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Set of determinants which are not part of the reference, defined from the application of the reference bitmask on the determinants. idx_non_ref gives the indice of the determinant in psi_det. idx_non_ref_rev gives the reverse.
+
+
+
+
+.. c:var:: idx_non_ref_from_sorted
+
+    .. code:: text
+
+        integer, allocatable	:: idx_non_ref_from_sorted	(N_det)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    
+
+
+
+
+.. c:var:: idx_non_ref_rev
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_non_ref	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_non_ref_coef	(psi_det_size,n_states)
+        integer, allocatable	:: idx_non_ref	(psi_det_size)
+        integer, allocatable	:: idx_non_ref_rev	(psi_det_size)
+        integer	:: n_det_non_ref
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Set of determinants which are not part of the reference, defined from the application of the reference bitmask on the determinants. idx_non_ref gives the indice of the determinant in psi_det. idx_non_ref_rev gives the reverse.
+
+
+
+
+.. c:var:: n_det_non_ref
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_non_ref	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_non_ref_coef	(psi_det_size,n_states)
+        integer, allocatable	:: idx_non_ref	(psi_det_size)
+        integer, allocatable	:: idx_non_ref_rev	(psi_det_size)
+        integer	:: n_det_non_ref
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Set of determinants which are not part of the reference, defined from the application of the reference bitmask on the determinants. idx_non_ref gives the indice of the determinant in psi_det. idx_non_ref_rev gives the reverse.
+
+
+
+
+.. c:var:: particles_operators
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: holes_operators	(N_int,2)
+        integer(bit_kind), allocatable	:: particles_operators	(N_int,2)
+
+    File: :file:`psi_ref_excitations_operators.irp.f`
+
+    holes_operators represents an array of integers where all the holes have been done going from psi_ref to psi_non_ref particles_operators represents an array of integers where all the particles have been done going from psi_ref to psi_non_ref
+
+
+
+
+.. c:var:: psi_non_ref
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_non_ref	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_non_ref_coef	(psi_det_size,n_states)
+        integer, allocatable	:: idx_non_ref	(psi_det_size)
+        integer, allocatable	:: idx_non_ref_rev	(psi_det_size)
+        integer	:: n_det_non_ref
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Set of determinants which are not part of the reference, defined from the application of the reference bitmask on the determinants. idx_non_ref gives the indice of the determinant in psi_det. idx_non_ref_rev gives the reverse.
+
+
+
+
+.. c:var:: psi_non_ref_coef
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_non_ref	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_non_ref_coef	(psi_det_size,n_states)
+        integer, allocatable	:: idx_non_ref	(psi_det_size)
+        integer, allocatable	:: idx_non_ref_rev	(psi_det_size)
+        integer	:: n_det_non_ref
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Set of determinants which are not part of the reference, defined from the application of the reference bitmask on the determinants. idx_non_ref gives the indice of the determinant in psi_det. idx_non_ref_rev gives the reverse.
+
+
+
+
+.. c:var:: psi_non_ref_coef_restart
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_non_ref_restart	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_non_ref_coef_restart	(psi_det_size,n_states)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Set of determinants which are not part of the reference, defined from the application of the reference bitmask on the determinants. idx_non_ref gives the indice of the determinant in psi_det. But this is with respect to the restart wave function.
+
+
+
+
+.. c:var:: psi_non_ref_coef_sorted_bit
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_non_ref_sorted_bit	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_non_ref_coef_sorted_bit	(psi_det_size,N_states)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Reference determinants sorted to accelerate the search of a random determinant in the wave function.
+
+
+
+
+.. c:var:: psi_non_ref_coef_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_non_ref_coef_transp	(n_states,psi_det_size)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Transposed psi_non_ref_coef
+
+
+
+
+.. c:var:: psi_non_ref_restart
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_non_ref_restart	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_non_ref_coef_restart	(psi_det_size,n_states)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Set of determinants which are not part of the reference, defined from the application of the reference bitmask on the determinants. idx_non_ref gives the indice of the determinant in psi_det. But this is with respect to the restart wave function.
+
+
+
+
+.. c:var:: psi_non_ref_sorted_bit
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_non_ref_sorted_bit	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_non_ref_coef_sorted_bit	(psi_det_size,N_states)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Reference determinants sorted to accelerate the search of a random determinant in the wave function.
+
+
+
+
+.. c:var:: psi_ref_coef_diagonalized
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_ref_coef_diagonalized	(N_det_ref,N_states)
+        double precision, allocatable	:: psi_ref_energy_diagonalized	(N_states)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    
+
+
+
+
+.. c:var:: psi_ref_coef_normalized
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_ref_coef_normalized	(psi_det_size,n_states)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Normalized coefficients of the reference
+
+
+
+
+.. c:var:: psi_ref_coef_sorted_bit
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_ref_sorted_bit	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_ref_coef_sorted_bit	(psi_det_size,N_states)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Reference determinants sorted to accelerate the search of a random determinant in the wave function.
+
+
+
+
+.. c:var:: psi_ref_coef_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_ref_coef_transp	(n_states,psi_det_size)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Transposed psi_ref_coef
+
+
+
+
+.. c:var:: psi_ref_energy
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_ref_energy	(N_states)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    
+
+
+
+
+.. c:var:: psi_ref_energy_diagonalized
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_ref_coef_diagonalized	(N_det_ref,N_states)
+        double precision, allocatable	:: psi_ref_energy_diagonalized	(N_states)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    
+
+
+
+
+.. c:var:: psi_ref_sorted_bit
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_ref_sorted_bit	(N_int,2,psi_det_size)
+        double precision, allocatable	:: psi_ref_coef_sorted_bit	(psi_det_size,N_states)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Reference determinants sorted to accelerate the search of a random determinant in the wave function.
+
+
+
+
+.. c:var:: ref_hamiltonian_matrix
+
+    .. code:: text
+
+        double precision, allocatable	:: ref_hamiltonian_matrix	(n_det_ref,n_det_ref)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    H matrix in the Reference space
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: extract_ref
+
+    .. code:: text
+
+        subroutine extract_ref
+
+    File: :file:`extract_ref.irp.f`
+
+    Replaces the total wave function by the normalized projection on the reference
+
+
+
+
+
+.. c:function:: get_index_in_psi_ref_sorted_bit
+
+    .. code:: text
+
+        integer function get_index_in_psi_ref_sorted_bit(key,Nint)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    Returns the index of the determinant in the ``psi_ref_sorted_bit`` array
+
+
+
+
+
+.. c:function:: is_in_psi_ref
+
+    .. code:: text
+
+        logical function is_in_psi_ref(key,Nint)
+
+    File: :file:`psi_ref_utils.irp.f`
+
+    True if the determinant ``det`` is in the wave function
+
+

docs/source/modules/selectors_full.rst

@@ -12,3 +12,48 @@ All the determinants are possible selectors. Only the largest contributions are
 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
+
+    .. code:: text
+
+        integer	:: n_det_selectors
+
+    File: :file:`selectors.irp.f`
+
+    For Single reference wave functions, the number of selectors is 1 : the Hartree-Fock determinant
+
+
+
+
+.. c:var:: psi_selectors
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_selectors	(N_int,2,psi_selectors_size)
+        double precision, allocatable	:: psi_selectors_coef	(psi_selectors_size,N_states)
+
+    File: :file:`selectors.irp.f`
+
+    Determinants on which we apply <i|H|psi> for perturbation.
+
+
+
+
+.. c:var:: psi_selectors_coef
+
+    .. code:: text
+
+        integer(bit_kind), allocatable	:: psi_selectors	(N_int,2,psi_selectors_size)
+        double precision, allocatable	:: psi_selectors_coef	(psi_selectors_size,N_states)
+
+    File: :file:`selectors.irp.f`
+
+    Determinants on which we apply <i|H|psi> for perturbation.
+
+

docs/source/modules/selectors_utils.rst

@@ -11,3 +11,352 @@ Selectors_Utils
 Helper functions for selectors.
 
 
+
+
+Providers
+---------
+
+
+.. c:var:: coef_hf_selector
+
+    .. code:: text
+
+        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
+
+    File: :file:`e_corr_selectors.irp.f`
+
+    energy of correlation per determinant respect to the Hartree Fock determinant 
+    for the all the double excitations in the selectors determinants 
+    E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> 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
+
+
+
+
+.. c:var:: delta_e_per_selector
+
+    .. code:: text
+
+        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
+
+    File: :file:`e_corr_selectors.irp.f`
+
+    energy of correlation per determinant respect to the Hartree Fock determinant 
+    for the all the double excitations in the selectors determinants 
+    E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> 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
+
+
+
+
+.. c:var:: double_index_selectors
+
+    .. code:: text
+
+        integer, allocatable	:: exc_degree_per_selectors	(N_det_selectors)
+        integer, allocatable	:: double_index_selectors	(N_det_selectors)
+        integer	:: n_double_selectors
+
+    File: :file:`e_corr_selectors.irp.f`
+
+    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
+
+
+
+
+.. c:var:: e_corr_double_only
+
+    .. code:: text
+
+        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
+
+    File: :file:`e_corr_selectors.irp.f`
+
+    energy of correlation per determinant respect to the Hartree Fock determinant 
+    for the all the double excitations in the selectors determinants 
+    E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> 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
+
+
+
+
+.. c:var:: e_corr_per_selectors
+
+    .. code:: text
+
+        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
+
+    File: :file:`e_corr_selectors.irp.f`
+
+    energy of correlation per determinant respect to the Hartree Fock determinant 
+    for the all the double excitations in the selectors determinants 
+    E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> 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
+
+
+
+
+.. c:var:: e_corr_second_order
+
+    .. code:: text
+
+        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
+
+    File: :file:`e_corr_selectors.irp.f`
+
+    energy of correlation per determinant respect to the Hartree Fock determinant 
+    for the all the double excitations in the selectors determinants 
+    E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> 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
+
+
+
+
+.. c:var:: exc_degree_per_selectors
+
+    .. code:: text
+
+        integer, allocatable	:: exc_degree_per_selectors	(N_det_selectors)
+        integer, allocatable	:: double_index_selectors	(N_det_selectors)
+        integer	:: n_double_selectors
+
+    File: :file:`e_corr_selectors.irp.f`
+
+    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
+
+
+
+
+.. c:var:: i_h_hf_per_selectors
+
+    .. code:: text
+
+        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
+
+    File: :file:`e_corr_selectors.irp.f`
+
+    energy of correlation per determinant respect to the Hartree Fock determinant 
+    for the all the double excitations in the selectors determinants 
+    E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> 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
+
+
+
+
+.. c:var:: inv_selectors_coef_hf
+
+    .. code:: text
+
+        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
+
+    File: :file:`e_corr_selectors.irp.f`
+
+    energy of correlation per determinant respect to the Hartree Fock determinant 
+    for the all the double excitations in the selectors determinants 
+    E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> 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
+
+
+
+
+.. c:var:: inv_selectors_coef_hf_squared
+
+    .. code:: text
+
+        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
+
+    File: :file:`e_corr_selectors.irp.f`
+
+    energy of correlation per determinant respect to the Hartree Fock determinant 
+    for the all the double excitations in the selectors determinants 
+    E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> 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
+
+
+
+
+.. c:var:: n_double_selectors
+
+    .. code:: text
+
+        integer, allocatable	:: exc_degree_per_selectors	(N_det_selectors)
+        integer, allocatable	:: double_index_selectors	(N_det_selectors)
+        integer	:: n_double_selectors
+
+    File: :file:`e_corr_selectors.irp.f`
+
+    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
+
+
+
+
+.. c:var:: psi_selectors_coef_transp
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_selectors_coef_transp	(N_states,psi_selectors_size)
+
+    File: :file:`selectors.irp.f`
+
+    Transposed psi_selectors
+
+
+
+
+.. c:var:: psi_selectors_diag_h_mat
+
+    .. code:: text
+
+        double precision, allocatable	:: psi_selectors_diag_h_mat	(psi_selectors_size)
+
+    File: :file:`selectors.irp.f`
+
+    Diagonal elements of the H matrix for each selectors
+
+
+
+
+.. c:var:: psi_selectors_size
+
+    .. code:: text
+
+        integer	:: psi_selectors_size
+
+    File: :file:`selectors.irp.f`
+
+    
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: zmq_get_n_det_generators
+
+    .. code:: text
+
+        integer function zmq_get_N_det_generators(zmq_to_qp_run_socket, worker_id)
+
+    File: :file:`zmq.irp.f_template_102`
+
+    Get N_det_generators from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_get_n_det_selectors
+
+    .. code:: text
+
+        integer function zmq_get_N_det_selectors(zmq_to_qp_run_socket, worker_id)
+
+    File: :file:`zmq.irp.f_template_102`
+
+    Get N_det_selectors from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_put_n_det_generators
+
+    .. code:: text
+
+        integer function zmq_put_N_det_generators(zmq_to_qp_run_socket,worker_id)
+
+    File: :file:`zmq.irp.f_template_102`
+
+    Put N_det_generators on the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_put_n_det_selectors
+
+    .. code:: text
+
+        integer function zmq_put_N_det_selectors(zmq_to_qp_run_socket,worker_id)
+
+    File: :file:`zmq.irp.f_template_102`
+
+    Put N_det_selectors on the qp_run scheduler
+
+

docs/source/modules/slave.rst

@@ -11,3 +11,63 @@ Slave
 Slave processes for distributed parallelism.
 
 
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: provide_everything
+
+    .. code:: text
+
+        subroutine provide_everything
+
+    File: :file:`slave_cipsi.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: qp_ao_ints
+
+    .. code:: text
+
+        subroutine qp_ao_ints
+
+    File: :file:`slave_eri.irp.f`
+
+    Slave for electron repulsion integrals
+
+
+
+
+
+.. c:function:: run_wf
+
+    .. code:: text
+
+        subroutine run_wf
+
+    File: :file:`slave_cipsi.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: slave
+
+    .. code:: text
+
+        subroutine slave
+
+    File: :file:`slave_cipsi.irp.f`
+
+    Helper program for distributed parallelism
+
+

docs/source/modules/tools.rst

@@ -10,3 +10,119 @@ Tools
 
 Useful tools are grouped in this module.
 
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: fcidump
+
+    .. code:: text
+
+        subroutine fcidump
+
+    File: :file:`fcidump.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: print_mos
+
+    .. code:: text
+
+        subroutine print_mos
+
+    File: :file:`molden.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: save_natorb
+
+    .. code:: text
+
+        subroutine save_natorb
+
+    File: :file:`save_natorb.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: save_ortho_mos
+
+    .. code:: text
+
+        subroutine save_ortho_mos
+
+    File: :file:`save_ortho_mos.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: write_ao_basis
+
+    .. code:: text
+
+        subroutine write_Ao_basis(i_unit_output)
+
+    File: :file:`molden.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: write_geometry
+
+    .. code:: text
+
+        subroutine write_geometry(i_unit_output)
+
+    File: :file:`molden.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: write_intro_gamess
+
+    .. code:: text
+
+        subroutine write_intro_gamess(i_unit_output)
+
+    File: :file:`molden.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: write_mo_basis
+
+    .. code:: text
+
+        subroutine write_Mo_basis(i_unit_output)
+
+    File: :file:`molden.irp.f`
+
+    
+
+

docs/source/modules/zmq.rst

@@ -12,3 +12,874 @@ Definition of |ZeroMQ| sockets and messages.
 
 
 
+
+
+Providers
+---------
+
+
+.. c:var:: qp_run_address
+
+    .. code:: text
+
+        character*(128)	:: qp_run_address
+        integer	:: zmq_port_start
+
+    File: :file:`utils.irp.f`
+
+    Address of the qp_run socket Example : tcp://130.120.229.139:12345
+
+
+
+
+.. c:var:: zmq_context
+
+    .. code:: text
+
+        integer(ZMQ_PTR)	:: zmq_context
+        integer(omp_lock_kind)	:: zmq_lock
+
+    File: :file:`utils.irp.f`
+
+    Context for the ZeroMQ library
+
+
+
+
+.. c:var:: zmq_lock
+
+    .. code:: text
+
+        integer(ZMQ_PTR)	:: zmq_context
+        integer(omp_lock_kind)	:: zmq_lock
+
+    File: :file:`utils.irp.f`
+
+    Context for the ZeroMQ library
+
+
+
+
+.. c:var:: zmq_port_start
+
+    .. code:: text
+
+        character*(128)	:: qp_run_address
+        integer	:: zmq_port_start
+
+    File: :file:`utils.irp.f`
+
+    Address of the qp_run socket Example : tcp://130.120.229.139:12345
+
+
+
+
+.. c:var:: zmq_socket_pair_inproc_address
+
+    .. code:: text
+
+        character*(128)	:: zmq_socket_pull_tcp_address
+        character*(128)	:: zmq_socket_pair_inproc_address
+        character*(128)	:: zmq_socket_push_tcp_address
+        character*(128)	:: zmq_socket_pull_inproc_address
+        character*(128)	:: zmq_socket_push_inproc_address
+        character*(128)	:: zmq_socket_sub_tcp_address
+
+    File: :file:`utils.irp.f`
+
+    Socket which pulls the results (2)
+
+
+
+
+.. c:var:: zmq_socket_pull_inproc_address
+
+    .. code:: text
+
+        character*(128)	:: zmq_socket_pull_tcp_address
+        character*(128)	:: zmq_socket_pair_inproc_address
+        character*(128)	:: zmq_socket_push_tcp_address
+        character*(128)	:: zmq_socket_pull_inproc_address
+        character*(128)	:: zmq_socket_push_inproc_address
+        character*(128)	:: zmq_socket_sub_tcp_address
+
+    File: :file:`utils.irp.f`
+
+    Socket which pulls the results (2)
+
+
+
+
+.. c:var:: zmq_socket_pull_tcp_address
+
+    .. code:: text
+
+        character*(128)	:: zmq_socket_pull_tcp_address
+        character*(128)	:: zmq_socket_pair_inproc_address
+        character*(128)	:: zmq_socket_push_tcp_address
+        character*(128)	:: zmq_socket_pull_inproc_address
+        character*(128)	:: zmq_socket_push_inproc_address
+        character*(128)	:: zmq_socket_sub_tcp_address
+
+    File: :file:`utils.irp.f`
+
+    Socket which pulls the results (2)
+
+
+
+
+.. c:var:: zmq_socket_push_inproc_address
+
+    .. code:: text
+
+        character*(128)	:: zmq_socket_pull_tcp_address
+        character*(128)	:: zmq_socket_pair_inproc_address
+        character*(128)	:: zmq_socket_push_tcp_address
+        character*(128)	:: zmq_socket_pull_inproc_address
+        character*(128)	:: zmq_socket_push_inproc_address
+        character*(128)	:: zmq_socket_sub_tcp_address
+
+    File: :file:`utils.irp.f`
+
+    Socket which pulls the results (2)
+
+
+
+
+.. c:var:: zmq_socket_push_tcp_address
+
+    .. code:: text
+
+        character*(128)	:: zmq_socket_pull_tcp_address
+        character*(128)	:: zmq_socket_pair_inproc_address
+        character*(128)	:: zmq_socket_push_tcp_address
+        character*(128)	:: zmq_socket_pull_inproc_address
+        character*(128)	:: zmq_socket_push_inproc_address
+        character*(128)	:: zmq_socket_sub_tcp_address
+
+    File: :file:`utils.irp.f`
+
+    Socket which pulls the results (2)
+
+
+
+
+.. c:var:: zmq_socket_sub_tcp_address
+
+    .. code:: text
+
+        character*(128)	:: zmq_socket_pull_tcp_address
+        character*(128)	:: zmq_socket_pair_inproc_address
+        character*(128)	:: zmq_socket_push_tcp_address
+        character*(128)	:: zmq_socket_pull_inproc_address
+        character*(128)	:: zmq_socket_push_inproc_address
+        character*(128)	:: zmq_socket_sub_tcp_address
+
+    File: :file:`utils.irp.f`
+
+    Socket which pulls the results (2)
+
+
+
+
+.. c:var:: zmq_state
+
+    .. code:: text
+
+        character*(128)	:: zmq_state
+
+    File: :file:`utils.irp.f`
+
+    Threads executing work through the ZeroMQ interface
+
+
+
+
+Subroutines / functions
+-----------------------
+
+
+
+.. c:function:: add_task_to_taskserver
+
+    .. code:: text
+
+        integer function add_task_to_taskserver(zmq_to_qp_run_socket,task)
+
+    File: :file:`utils.irp.f`
+
+    Get a task from the task server
+
+
+
+
+
+.. c:function:: connect_to_taskserver
+
+    .. code:: text
+
+        integer function connect_to_taskserver(zmq_to_qp_run_socket,worker_id,thread)
+
+    File: :file:`utils.irp.f`
+
+    Connect to the task server and obtain the worker ID
+
+
+
+
+
+.. c:function:: disconnect_from_taskserver
+
+    .. code:: text
+
+        integer function disconnect_from_taskserver(zmq_to_qp_run_socket, worker_id)
+
+    File: :file:`utils.irp.f`
+
+    Disconnect from the task server
+
+
+
+
+
+.. c:function:: disconnect_from_taskserver_state
+
+    .. code:: text
+
+        integer function disconnect_from_taskserver_state(zmq_to_qp_run_socket, worker_id, state)
+
+    File: :file:`utils.irp.f`
+
+    Disconnect from the task server
+
+
+
+
+
+.. c:function:: end_parallel_job
+
+    .. code:: text
+
+        subroutine end_parallel_job(zmq_to_qp_run_socket,zmq_socket_pull,name_in)
+
+    File: :file:`utils.irp.f`
+
+    End a new parallel job with name 'name'. The slave tasks execute subroutine 'slave'
+
+
+
+
+
+.. c:function:: end_zmq_pair_socket
+
+    .. code:: text
+
+        subroutine end_zmq_pair_socket(zmq_socket_pair)
+
+    File: :file:`utils.irp.f`
+
+    Terminate socket on which the results are sent.
+
+
+
+
+
+.. c:function:: end_zmq_pull_socket
+
+    .. code:: text
+
+        subroutine end_zmq_pull_socket(zmq_socket_pull)
+
+    File: :file:`utils.irp.f`
+
+    Terminate socket on which the results are sent.
+
+
+
+
+
+.. c:function:: end_zmq_push_socket
+
+    .. code:: text
+
+        subroutine end_zmq_push_socket(zmq_socket_push,thread)
+
+    File: :file:`utils.irp.f`
+
+    Terminate socket on which the results are sent.
+
+
+
+
+
+.. c:function:: end_zmq_sub_socket
+
+    .. code:: text
+
+        subroutine end_zmq_sub_socket(zmq_socket_sub)
+
+    File: :file:`utils.irp.f`
+
+    Terminate socket on which the results are sent.
+
+
+
+
+
+.. c:function:: end_zmq_to_qp_run_socket
+
+    .. code:: text
+
+        subroutine end_zmq_to_qp_run_socket(zmq_to_qp_run_socket)
+
+    File: :file:`utils.irp.f`
+
+    Terminate the socket from the application to qp_run
+
+
+
+
+
+.. c:function:: get_task_from_taskserver
+
+    .. code:: text
+
+        integer function get_task_from_taskserver(zmq_to_qp_run_socket,worker_id,task_id,task)
+
+    File: :file:`utils.irp.f`
+
+    Get a task from the task server
+
+
+
+
+
+.. c:function:: get_tasks_from_taskserver
+
+    .. code:: text
+
+        integer function get_tasks_from_taskserver(zmq_to_qp_run_socket,worker_id,task_id,task,n_tasks)
+
+    File: :file:`utils.irp.f`
+
+    Get multiple tasks from the task server
+
+
+
+
+
+.. c:function:: new_parallel_job
+
+    .. code:: text
+
+        subroutine new_parallel_job(zmq_to_qp_run_socket,zmq_socket_pull,name_in)
+
+    File: :file:`utils.irp.f`
+
+    Start a new parallel job with name 'name'. The slave tasks execute subroutine 'slave'
+
+
+
+
+
+.. c:function:: new_zmq_pair_socket
+
+    .. code:: text
+
+        function new_zmq_pair_socket(bind)
+
+    File: :file:`utils.irp.f`
+
+    Socket on which the collector and the main communicate
+
+
+
+
+
+.. c:function:: new_zmq_pull_socket
+
+    .. code:: text
+
+        function new_zmq_pull_socket()
+
+    File: :file:`utils.irp.f`
+
+    Socket on which the results are sent. If thread is 1, use inproc
+
+
+
+
+
+.. c:function:: new_zmq_push_socket
+
+    .. code:: text
+
+        function new_zmq_push_socket(thread)
+
+    File: :file:`utils.irp.f`
+
+    Socket on which the results are sent. If thread is 1, use inproc
+
+
+
+
+
+.. c:function:: new_zmq_sub_socket
+
+    .. code:: text
+
+        function new_zmq_sub_socket()
+
+    File: :file:`utils.irp.f`
+
+    Socket to read the state published by the Task server
+
+
+
+
+
+.. c:function:: new_zmq_to_qp_run_socket
+
+    .. code:: text
+
+        function new_zmq_to_qp_run_socket()
+
+    File: :file:`utils.irp.f`
+
+    Socket on which the qp_run process replies
+
+
+
+
+
+.. c:function:: reset_zmq_addresses
+
+    .. code:: text
+
+        subroutine reset_zmq_addresses
+
+    File: :file:`utils.irp.f`
+
+    Socket which pulls the results (2)
+
+
+
+
+
+.. c:function:: switch_qp_run_to_master
+
+    .. code:: text
+
+        subroutine switch_qp_run_to_master
+
+    File: :file:`utils.irp.f`
+
+    Address of the master qp_run socket Example : tcp://130.120.229.139:12345
+
+
+
+
+
+.. c:function:: task_done_to_taskserver
+
+    .. code:: text
+
+        integer function task_done_to_taskserver(zmq_to_qp_run_socket, worker_id, task_id)
+
+    File: :file:`utils.irp.f`
+
+    Get a task from the task server
+
+
+
+
+
+.. c:function:: tasks_done_to_taskserver
+
+    .. code:: text
+
+        integer function tasks_done_to_taskserver(zmq_to_qp_run_socket, worker_id, task_id, n_tasks)
+
+    File: :file:`utils.irp.f`
+
+    Get a task from the task server
+
+
+
+
+
+.. c:function:: wait_for_next_state
+
+    .. code:: text
+
+        subroutine wait_for_next_state(state)
+
+    File: :file:`utils.irp.f`
+
+    
+
+
+
+
+
+.. c:function:: wait_for_state
+
+    .. code:: text
+
+        subroutine wait_for_state(state_wait,state)
+
+    File: :file:`utils.irp.f`
+
+    Wait for the ZMQ state to be ready
+
+
+
+
+
+.. c:function:: wait_for_states
+
+    .. code:: text
+
+        subroutine wait_for_states(state_wait,state,n)
+
+    File: :file:`utils.irp.f`
+
+    Wait for the ZMQ state to be ready
+
+
+
+
+
+.. c:function:: zmq_abort
+
+    .. code:: text
+
+        integer function zmq_abort(zmq_to_qp_run_socket)
+
+    File: :file:`utils.irp.f`
+
+    Aborts a running parallel computation
+
+
+
+
+
+.. c:function:: zmq_delete_task
+
+    .. code:: text
+
+        integer function zmq_delete_task(zmq_to_qp_run_socket,zmq_socket_pull,task_id,more)
+
+    File: :file:`utils.irp.f`
+
+    When a task is done, it has to be removed from the list of tasks on the qp_run queue. This guarantees that the results have been received in the pull.
+
+
+
+
+
+.. c:function:: zmq_delete_tasks
+
+    .. code:: text
+
+        integer function zmq_delete_tasks(zmq_to_qp_run_socket,zmq_socket_pull,task_id,n_tasks,more)
+
+    File: :file:`utils.irp.f`
+
+    When a task is done, it has to be removed from the list of tasks on the qp_run queue. This guarantees that the results have been received in the pull.
+
+
+
+
+
+.. c:function:: zmq_delete_tasks_async_recv
+
+    .. code:: text
+
+        integer function zmq_delete_tasks_async_recv(zmq_to_qp_run_socket,zmq_socket_pull,task_id,n_tasks,more)
+
+    File: :file:`utils.irp.f`
+
+    When a task is done, it has to be removed from the list of tasks on the qp_run queue. This guarantees that the results have been received in the pull.
+
+
+
+
+
+.. c:function:: zmq_delete_tasks_async_send
+
+    .. code:: text
+
+        integer function zmq_delete_tasks_async_send(zmq_to_qp_run_socket,zmq_socket_pull,task_id,n_tasks,more)
+
+    File: :file:`utils.irp.f`
+
+    When a task is done, it has to be removed from the list of tasks on the qp_run queue. This guarantees that the results have been received in the pull.
+
+
+
+
+
+.. c:function:: zmq_get8_dvector
+
+    .. code:: text
+
+        integer function zmq_get8_dvector(zmq_to_qp_run_socket, worker_id, name, x, size_x)
+
+    File: :file:`put_get.irp.f`
+
+    Get a float vector from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_get8_ivector
+
+    .. code:: text
+
+        integer function zmq_get8_ivector(zmq_to_qp_run_socket, worker_id, name, x, size_x)
+
+    File: :file:`put_get.irp.f`
+
+    Get a vector of integers from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_get_dmatrix
+
+    .. code:: text
+
+        integer function zmq_get_dmatrix(zmq_to_qp_run_socket, worker_id, name, x, size_x1, size_x2, sze)
+
+    File: :file:`put_get.irp.f`
+
+    Get a float vector from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_get_dvector
+
+    .. code:: text
+
+        integer function zmq_get_dvector(zmq_to_qp_run_socket, worker_id, name, x, size_x)
+
+    File: :file:`put_get.irp.f`
+
+    Get a float vector from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_get_i8matrix
+
+    .. code:: text
+
+        integer function zmq_get_i8matrix(zmq_to_qp_run_socket, worker_id, name, x, size_x1, size_x2, sze)
+
+    File: :file:`put_get.irp.f`
+
+    Get a float vector from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_get_imatrix
+
+    .. code:: text
+
+        integer function zmq_get_imatrix(zmq_to_qp_run_socket, worker_id, name, x, size_x1, size_x2, sze)
+
+    File: :file:`put_get.irp.f`
+
+    Get a float vector from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_get_int
+
+    .. code:: text
+
+        integer function zmq_get_int(zmq_to_qp_run_socket, worker_id, name, x)
+
+    File: :file:`put_get.irp.f`
+
+    Get a vector of integers from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_get_int_nompi
+
+    .. code:: text
+
+        integer function zmq_get_int_nompi(zmq_to_qp_run_socket, worker_id, name, x)
+
+    File: :file:`put_get.irp.f`
+
+    Get a vector of integers from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_get_ivector
+
+    .. code:: text
+
+        integer function zmq_get_ivector(zmq_to_qp_run_socket, worker_id, name, x, size_x)
+
+    File: :file:`put_get.irp.f`
+
+    Get a vector of integers from the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_port
+
+    .. code:: text
+
+        function zmq_port(ishift)
+
+    File: :file:`utils.irp.f`
+
+    Return the value of the ZMQ port from the corresponding integer
+
+
+
+
+
+.. c:function:: zmq_put8_dvector
+
+    .. code:: text
+
+        integer function zmq_put8_dvector(zmq_to_qp_run_socket, worker_id, name, x, size_x)
+
+    File: :file:`put_get.irp.f`
+
+    Put a float vector on the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_put8_ivector
+
+    .. code:: text
+
+        integer function zmq_put8_ivector(zmq_to_qp_run_socket, worker_id, name, x, size_x)
+
+    File: :file:`put_get.irp.f`
+
+    Put a vector of integers on the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_put_dmatrix
+
+    .. code:: text
+
+        integer function zmq_put_dmatrix(zmq_to_qp_run_socket, worker_id, name, x, size_x1, size_x2, sze)
+
+    File: :file:`put_get.irp.f`
+
+    Put a float vector on the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_put_dvector
+
+    .. code:: text
+
+        integer function zmq_put_dvector(zmq_to_qp_run_socket, worker_id, name, x, size_x)
+
+    File: :file:`put_get.irp.f`
+
+    Put a float vector on the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_put_i8matrix
+
+    .. code:: text
+
+        integer function zmq_put_i8matrix(zmq_to_qp_run_socket, worker_id, name, x, size_x1, size_x2, sze)
+
+    File: :file:`put_get.irp.f`
+
+    Put a float vector on the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_put_imatrix
+
+    .. code:: text
+
+        integer function zmq_put_imatrix(zmq_to_qp_run_socket, worker_id, name, x, size_x1, size_x2, sze)
+
+    File: :file:`put_get.irp.f`
+
+    Put a float vector on the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_put_int
+
+    .. code:: text
+
+        integer function zmq_put_int(zmq_to_qp_run_socket, worker_id, name, x)
+
+    File: :file:`put_get.irp.f`
+
+    Put a vector of integers on the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_put_ivector
+
+    .. code:: text
+
+        integer function zmq_put_ivector(zmq_to_qp_run_socket, worker_id, name, x, size_x)
+
+    File: :file:`put_get.irp.f`
+
+    Put a vector of integers on the qp_run scheduler
+
+
+
+
+
+.. c:function:: zmq_set_running
+
+    .. code:: text
+
+        integer function zmq_set_running(zmq_to_qp_run_socket)
+
+    File: :file:`utils.irp.f`
+
+    Set the job to Running in QP-run
+
+

docs/source/programmers_guide/index.rst

@@ -12,23 +12,9 @@ Index of Modules
    /modules/*
 
 
-Index of Providers
-------------------
+.. Auto-generated file
 
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   /providers/*
+.. include:: index_providers.rst
 
 
-Index of Subroutines/Functions
-------------------------------
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   /subroutines/*
-
 

include/.gitignore

@@ -1,2 +1,3 @@
 zmq.h
 zmq_utils.h
+f77_zmq_free.h

src/AO_Basis/aos.irp.f

@@ -1,7 +1,7 @@
 BEGIN_PROVIDER [ integer, ao_prim_num_max ]
  implicit none
  BEGIN_DOC
- ! max number of primitives
+ ! Max number of primitives.
  END_DOC
  ao_prim_num_max = maxval(ao_prim_num)
 END_PROVIDER
@@ -10,7 +10,7 @@ END_PROVIDER
 &BEGIN_PROVIDER [ double precision, ao_coef_normalization_factor, (ao_num) ]
   implicit none
   BEGIN_DOC
-  ! Coefficients including the AO normalization
+  ! Coefficients including the |AO| normalization
   END_DOC
   double precision               :: norm,overlap_x,overlap_y,overlap_z,C_A(3), c
   integer                        :: l, powA(3), nz
@@ -46,7 +46,7 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, ao_coef_normalization_libint_factor, (ao_num) ]
   implicit none
   BEGIN_DOC
-  ! Coefficients including the AO normalization
+  ! |AO| normalization for interfacing with libint
   END_DOC
   double precision               :: norm,overlap_x,overlap_y,overlap_z,C_A(3), c
   integer                        :: l, powA(3), nz
@@ -80,7 +80,7 @@ END_PROVIDER
 &BEGIN_PROVIDER [ double precision, ao_expo_ordered, (ao_num,ao_prim_num_max) ]
   implicit none
   BEGIN_DOC
-   ! Sorted primitives to accelerate 4 index MO transformation
+  ! Sorted primitives to accelerate 4 index |MO| transformation
   END_DOC
   
   integer                        :: iorder(ao_prim_num_max)
@@ -105,7 +105,7 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, ao_coef_normalized_ordered_transp, (ao_prim_num_max,ao_num) ]
   implicit none
   BEGIN_DOC
-  ! Transposed ao_coef_normalized_ordered
+  ! Transposed :c:var:`ao_coef_normalized_ordered`
   END_DOC
   integer                        :: i,j
   do j=1, ao_num
@@ -119,7 +119,7 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, ao_expo_ordered_transp, (ao_prim_num_max,ao_num) ]
   implicit none
   BEGIN_DOC
-  ! Transposed ao_expo_ordered
+  ! Transposed :c:var:`ao_expo_ordered`
   END_DOC
   integer                        :: i,j
   do j=1, ao_num
@@ -135,7 +135,7 @@ END_PROVIDER
 &BEGIN_PROVIDER [ character*(128), ao_l_char, (ao_num) ]
  implicit none
  BEGIN_DOC
-! ao_l = l value of the AO: a+b+c in x^a y^b z^c
+! :math:`l` value of the |AO|: :math`a+b+c` in :math:`x^a y^b z^c`
  END_DOC
  integer :: i
  do i=1,ao_num
@@ -151,7 +151,7 @@ integer function ao_power_index(nx,ny,nz)
   BEGIN_DOC
   ! Unique index given to a triplet of powers:
   !
-  ! 1/2 (l-n_x)*(l-n_x+1) + n_z + 1
+  ! :math:`\frac{1}{2} (l-n_x) (l-n_x+1) + n_z + 1`
   END_DOC
   integer                        :: l
   l = nx + ny + nz
@@ -161,7 +161,7 @@ end
 
 BEGIN_PROVIDER [ character*(128), l_to_charater, (0:7)]
  BEGIN_DOC
- ! character corresponding to the "L" value of an AO orbital
+ ! Character corresponding to the "l" value of an |AO|
  END_DOC
  implicit none
  l_to_charater(0)='S'
@@ -178,10 +178,10 @@ END_PROVIDER
  BEGIN_PROVIDER [ integer, Nucl_N_Aos, (nucl_num)]
 &BEGIN_PROVIDER [ integer, N_AOs_max ]
  implicit none
- integer :: i
  BEGIN_DOC
- ! Number of AOs per atom
+ ! Number of |AOs| per atom
  END_DOC
+ integer :: i
  Nucl_N_Aos = 0
  do i = 1, ao_num
   Nucl_N_Aos(ao_nucl(i)) +=1
@@ -192,7 +192,7 @@ END_PROVIDER
  BEGIN_PROVIDER [ integer, Nucl_Aos, (nucl_num,N_AOs_max)]
  implicit none
  BEGIN_DOC
- ! List of AOs attached on each atom
+ ! List of |AOs| centered on each atom
  END_DOC
  integer :: i
  integer, allocatable :: nucl_tmp(:)
@@ -212,9 +212,9 @@ END_PROVIDER
  implicit none
  integer :: i,j,k
  BEGIN_DOC
- ! Index of the shell type Aos and of the corresponding Aos 
- ! Per convention, for P,D,F and G AOs, we take the index 
- ! of the AO with the the corresponding power in the "X" axis
+ ! Index of the shell type |AOs| and of the corresponding |AOs|
+ ! By convention, for p,d,f and g |AOs|, we take the index 
+ ! of the |AO| with the the corresponding power in the x axis
  END_DOC
  do i = 1, nucl_num
   Nucl_num_shell_Aos(i) = 0
@@ -258,6 +258,9 @@ END_PROVIDER
 
 BEGIN_PROVIDER [ character*(4), ao_l_char_space, (ao_num) ]
  implicit none
+ BEGIN_DOC
+! Converts an l value to a string
+ END_DOC
  integer :: i
  character*(4) :: give_ao_character_space
  do i=1,ao_num

src/AO_Basis/aos_value.irp.f

@@ -1,7 +1,7 @@
 double precision function ao_value(i,r)
  implicit none
  BEGIN_DOC
-! return the value of the ith ao at point r
+! Returns the value of the i-th |AO| at point r
  END_DOC
  double precision, intent(in) :: r(3)
  integer, intent(in) :: i
@@ -34,7 +34,7 @@ end
 subroutine give_all_aos_at_r(r,aos_array)
  implicit none
  BEGIN_dOC
-! gives the values of aos at a given point r
+! Gives the values of |AOs| at a given point r
  END_DOC
  double precision, intent(in) :: r(3)
  double precision, intent(out) :: aos_array(ao_num)
@@ -44,5 +44,4 @@ subroutine give_all_aos_at_r(r,aos_array)
   aos_array(i) = ao_value(i,r)
  enddo
 
-
 end

src/AO_Basis/dimensions_integrals.irp.f

@@ -1,6 +1,9 @@
  BEGIN_PROVIDER [ integer, n_pt_max_integrals ]
 &BEGIN_PROVIDER [ integer, n_pt_max_i_x]
  implicit none
+ BEGIN_DOC
+! Number of points used in the numerical integrations.
+ END_DOC
  integer :: n_pt_sup
  integer :: prim_power_l_max
  include 'Utils/constants.include.F'

src/AO_one_e_integrals/NEED

@@ -1 +1,2 @@
-AO_Basis Pseudo
+AO_Basis
+Pseudo

src/AO_one_e_integrals/ao_mono_ints.irp.f

@@ -3,8 +3,7 @@
   implicit none
   integer :: i,j,n,l
   BEGIN_DOC
- ! array of the mono electronic hamiltonian on the AOs basis
- ! : sum of the kinetic and nuclear electronic potential 
+ ! Array of the one-electron Hamiltonian on the |AO| basis.
   END_DOC
   do j = 1, ao_num
    do i = 1, ao_num

src/AO_one_e_integrals/ao_ortho_canonical.irp.f

@@ -2,7 +2,8 @@
 &BEGIN_PROVIDER [ integer, ao_cart_to_sphe_num ]
   implicit none
   BEGIN_DOC
-! ao_cart_to_sphe coefficients of the current basis set
+! Coefficients to go from cartesian to spherical coordinates in the current
+! basis set
   END_DOC
   integer :: i
   integer, external              :: ao_power_index
@@ -49,7 +50,7 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, ao_cart_to_sphe_overlap, (ao_cart_to_sphe_num,ao_cart_to_sphe_num) ]
  implicit none
  BEGIN_DOC
- ! AO overlap matrix in the spherical basis set
+ ! |AO| overlap matrix in the spherical basis set
  END_DOC
  double precision, allocatable :: S(:,:)
  allocate (S(ao_cart_to_sphe_num,ao_num))
@@ -71,7 +72,7 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, ao_cart_to_sphe_inv, (ao_cart_to_sphe_num,ao_num) ]
  implicit none
  BEGIN_DOC
- ! AO_cart_to_sphe_coef^(-1)
+ ! Inverse of :c:var:`ao_cart_to_sphe_coef`
  END_DOC
 
  call get_pseudo_inverse(ao_cart_to_sphe_coef,size(ao_cart_to_sphe_coef,1),&

src/AO_one_e_integrals/ao_overlap.irp.f

@@ -5,7 +5,8 @@
   implicit none
   BEGIN_DOC  
 ! Overlap between atomic basis functions:
-! :math:`\int \chi_i(r) \chi_j(r) dr)`
+!
+! :math:`\int \chi_i(r) \chi_j(r) dr`
   END_DOC
   integer :: i,j,n,l
   double precision :: f
@@ -73,8 +74,9 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, ao_overlap_abs,(ao_num,ao_num) ]
   implicit none
   BEGIN_DOC  
-! Overlap between absolute value of atomic basis functions:
-! :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
+! Overlap between absolute values of atomic basis functions:
+!
+! :math:`\int |\chi_i(r)| |\chi_j(r)| dr`
   END_DOC
   integer :: i,j,n,l
   double precision :: f
@@ -127,7 +129,7 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, S_inv,(ao_num,ao_num) ]
  implicit none
  BEGIN_DOC
-! S^-1
+! Inverse of the overlap matrix
  END_DOC
  call get_pseudo_inverse(ao_overlap,size(ao_overlap,1),ao_num,ao_num,S_inv,size(S_inv,1))
 END_PROVIDER
@@ -135,7 +137,7 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, S_half_inv, (AO_num,AO_num) ]
 
   BEGIN_DOC
-!   Matrix X = S^{-1/2} obtained by SVD
+!   :math:`X = S^{-1/2}` obtained by SVD
   END_DOC
 
   implicit none
@@ -194,7 +196,7 @@ END_PROVIDER
 BEGIN_PROVIDER [ double precision, S_half, (ao_num,ao_num)  ]
  implicit none
  BEGIN_DOC
- ! S^{1/2}
+ ! :math:`S^{1/2}`
  END_DOC
 
   integer :: i,j,k

src/AO_one_e_integrals/kin_ao_ints.irp.f

@@ -2,6 +2,13 @@
 &BEGIN_PROVIDER [ double precision, ao_deriv2_y,(ao_num,ao_num) ]
 &BEGIN_PROVIDER [ double precision, ao_deriv2_z,(ao_num,ao_num) ]
   implicit none
+  BEGIN_DOC
+  ! Second derivative matrix elements in the |AO| basis.
+  !
+  ! :math:`{\tt ao_deriv2_x} =
+  !  \langle \chi_i(x,y,z) | \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle`
+  !
+  END_DOC
   integer :: i,j,n,l
   double precision :: f
   integer :: dim1
@@ -12,12 +19,6 @@
   integer :: power_A(3), power_B(3)
   double precision :: d_a_2,d_2
   dim1=100
-  BEGIN_DOC
-  ! second derivatives matrix elements in the ao basis 
-  ! .. math::
-  !
-  !   {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
-  END_DOC
 
   ! -- Dummy call to provide everything
    A_center(:) = 0.d0
@@ -61,9 +62,6 @@
       beta = ao_expo_ordered_transp(l,i)
       call overlap_gaussian_xyz(A_center,B_center,alpha,beta,power_A,power_B,overlap_x0,overlap_y0,overlap_z0,overlap,dim1)
       c = ao_coef_normalized_ordered_transp(n,j) * ao_coef_normalized_ordered_transp(l,i)
-!     if (abs(c) < 1.d-8) then
-!       cycle
-!     endif
 
       power_A(1) = power_A(1)-2
       if (power_A(1)>-1) then
@@ -122,8 +120,9 @@ END_PROVIDER
 BEGIN_PROVIDER [double precision, ao_kinetic_integral, (ao_num,ao_num)]
   implicit none
   BEGIN_DOC
-  ! array of the priminitve basis kinetic integrals
-  !  \langle \chi_i |\hat{T}| \chi_j \rangle
+  ! Kinetic energy integrals in the |AO| basis.
+  !
+  ! :math:`\langle \chi_i |\hat{T}| \chi_j \rangle`
   END_DOC
   integer                        :: i,j,k,l
   

src/AO_one_e_integrals/pot_ao_ints.irp.f

@@ -1,6 +1,8 @@
 BEGIN_PROVIDER [ double precision, ao_nucl_elec_integral, (ao_num,ao_num)]
   BEGIN_DOC
-   ! interaction nuclear electron
+  !  Nucleus-electron interaction, in the |AO| basis set.
+  !
+  !  :math:`\langle \chi_i | -\sum_A \frac{1}{|r-R_A|} | \chi_j \rangle`
   END_DOC
   implicit none
   double precision               :: alpha, beta, gama, delta
@@ -59,11 +61,13 @@ BEGIN_PROVIDER [ double precision, ao_nucl_elec_integral, (ao_num,ao_num)]
               
               C_center(1:3) = nucl_coord(k,1:3)
               
-               c = c - Z*NAI_pol_mult(A_center,B_center,power_A,power_B,alpha,beta,C_center,n_pt_in)
+              c = c - Z * NAI_pol_mult(A_center,B_center,            &
+                  power_A,power_B,alpha,beta,C_center,n_pt_in)
               
             enddo
-             ao_nucl_elec_integral(i,j) = ao_nucl_elec_integral(i,j) +&
-                 ao_coef_normalized_ordered_transp(l,j)*ao_coef_normalized_ordered_transp(m,i)*c
+            ao_nucl_elec_integral(i,j) = ao_nucl_elec_integral(i,j)  &
+                + ao_coef_normalized_ordered_transp(l,j)             &
+                * ao_coef_normalized_ordered_transp(m,i) * c
           enddo
         enddo
       enddo
@@ -77,13 +81,13 @@ BEGIN_PROVIDER [ double precision, ao_nucl_elec_integral, (ao_num,ao_num)]
     print *,  'AO N-e integrals written to disk'
   endif
   
-   
 END_PROVIDER
 
- BEGIN_PROVIDER [ double precision, ao_nucl_elec_integral_per_atom, (ao_num,ao_num,nucl_num)]
+BEGIN_PROVIDER [ double precision, ao_nucl_elec_integral_per_atom, (ao_num,ao_num,nucl_num)]
   BEGIN_DOC
-! ao_nucl_elec_integral_per_atom(i,j,k) = -<AO(i)|1/|r-Rk|AO(j)> 
-! where Rk is the geometry of the kth atom
+! Nucleus-electron interaction in the |AO| basis set, per atom A.
+!
+! :math:`\langle \chi_i | -\frac{1}{|r-R_A|} | \chi_j \rangle`
   END_DOC
   implicit none
   double precision               :: alpha, beta, gama, delta
@@ -91,15 +95,15 @@ END_PROVIDER
   double precision               :: A_center(3),B_center(3),C_center(3)
   integer                        :: power_A(3),power_B(3)
   integer                        :: i,j,k,l,n_pt_in,m
- double precision ::overlap_x,overlap_y,overlap_z,overlap,dx,NAI_pol_mult
+  double precision               :: overlap_x,overlap_y,overlap_z,overlap,dx,NAI_pol_mult
   
   ao_nucl_elec_integral_per_atom = 0.d0
   
   !$OMP PARALLEL                                                    &
       !$OMP DEFAULT (NONE)                                          &
- !$OMP PRIVATE (i,j,k,l,m,alpha,beta,A_center,B_center,power_A,power_B, &
+      !$OMP PRIVATE (i,j,k,l,m,alpha,beta,A_center,B_center,power_A,power_B,&
       !$OMP  num_A,num_B,c,n_pt_in,C_center)                        &
- !$OMP SHARED (ao_num,ao_prim_num,ao_expo_ordered_transp,ao_power,ao_nucl,nucl_coord,ao_coef_normalized_ordered_transp, &
+      !$OMP SHARED (ao_num,ao_prim_num,ao_expo_ordered_transp,ao_power,ao_nucl,nucl_coord,ao_coef_normalized_ordered_transp,&
       !$OMP  n_pt_max_integrals,ao_nucl_elec_integral_per_atom,nucl_num)
   n_pt_in = n_pt_max_integrals
   !$OMP DO SCHEDULE (dynamic)
@@ -130,8 +134,10 @@ END_PROVIDER
           alpha = ao_expo_ordered_transp(l,j)
           do m=1,ao_prim_num(i)
             beta = ao_expo_ordered_transp(m,i)
-       c = c + NAI_pol_mult(A_center,B_center,power_A,power_B,alpha,beta,C_center,n_pt_in) &
-           * ao_coef_normalized_ordered_transp(l,j)*ao_coef_normalized_ordered_transp(m,i)
+            c = c + NAI_pol_mult(A_center,B_center,power_A,power_B,  &
+                alpha,beta,C_center,n_pt_in)                         &
+                * ao_coef_normalized_ordered_transp(l,j)             &
+                * ao_coef_normalized_ordered_transp(m,i)
           enddo
         enddo
         ao_nucl_elec_integral_per_atom(i,j,k) = -c
@@ -146,21 +152,24 @@ END_PROVIDER
 
 
 double precision function NAI_pol_mult(A_center,B_center,power_A,power_B,alpha,beta,C_center,n_pt_in)
-! function that calculate the folowing integral :
-!       int{dr} of (x-A_x)^ax (x-B_X)^bx exp(-alpha (x-A_x)^2 - beta (x-B_x)^2 ) 1/(r-R_c)
+  BEGIN_DOC
+! Computes the electron-nucleus attraction with two primitves.
+!
+! :math:`\langle g_i | \frac{1}{|r-R_c|} | g_j \rangle`
+  END_DOC
   
-implicit none
-integer, intent(in) :: n_pt_in
-double precision,intent(in) :: C_center(3),A_center(3),B_center(3),alpha,beta
-integer :: power_A(3),power_B(3)
-integer :: i,j,k,l,n_pt
-double precision :: P_center(3)
-double precision :: d(0:n_pt_in),pouet,coeff,rho,dist,const,pouet_2,p,p_inv,factor
-double precision :: I_n_special_exact,integrate_bourrin,I_n_bibi
-double precision ::  V_e_n,const_factor,dist_integral,tmp
-double precision :: accu,epsilo,rint
-integer :: n_pt_out,lmax
-include 'Utils/constants.include.F'
+  implicit none
+  integer, intent(in)            :: n_pt_in
+  double precision,intent(in)    :: C_center(3),A_center(3),B_center(3),alpha,beta
+  integer                        :: power_A(3),power_B(3)
+  integer                        :: i,j,k,l,n_pt
+  double precision               :: P_center(3)
+  double precision               :: d(0:n_pt_in),pouet,coeff,rho,dist,const,pouet_2,p,p_inv,factor
+  double precision               :: I_n_special_exact,integrate_bourrin,I_n_bibi
+  double precision               :: V_e_n,const_factor,dist_integral,tmp
+  double precision               :: accu,epsilo,rint
+  integer                        :: n_pt_out,lmax
+  include 'Utils/constants.include.F'
   if ( (A_center(1)/=B_center(1)).or.                                &
         (A_center(2)/=B_center(2)).or.                               &
         (A_center(3)/=B_center(3)).or.                               &
@@ -169,11 +178,11 @@ include 'Utils/constants.include.F'
         (A_center(3)/=C_center(3))) then
     continue
   else
-        NAI_pol_mult = V_e_n(power_A(1),power_A(2),power_A(3),power_B(1),power_B(2),power_B(3),alpha,beta)
+    NAI_pol_mult = V_e_n(power_A(1),power_A(2),power_A(3),           &
+        power_B(1),power_B(2),power_B(3),alpha,beta)
     return
   endif
   p = alpha + beta
-!  print*, "a"
   p_inv = 1.d0/p
   rho = alpha * beta * p_inv
   dist = 0.d0
@@ -214,9 +223,9 @@ include 'Utils/constants.include.F'
   endif
   accu = 0.d0
   
-! 1/r1 standard attraction integral
+  ! 1/r1 standard attraction integral
   epsilo = 1.d0
-! sum of integrals of type : int {t,[0,1]}  exp-(rho.(P-Q)^2 * t^2) * t^i
+  ! sum of integrals of type : int {t,[0,1]}  exp-(rho.(P-Q)^2 * t^2) * t^i
   do i =0 ,n_pt_out,2
     accu +=  d(i) * rint(i/2,const)
   enddo
@@ -226,25 +235,27 @@ end
 
 
 subroutine give_polynom_mult_center_mono_elec(A_center,B_center,alpha,beta,power_A,power_B,C_center,n_pt_in,d,n_pt_out)
-!!!! subroutine that returns the explicit polynom in term of the "t" variable of the following polynomw ::
-!!!!         I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)
-!!!! it is for the nuclear electron atraction
-implicit none
-integer, intent(in) :: n_pt_in
-integer,intent(out) :: n_pt_out
-double precision, intent(in) :: A_center(3), B_center(3),C_center(3)
-double precision, intent(in) :: alpha,beta
-integer, intent(in) :: power_A(3), power_B(3)
-integer :: a_x,b_x,a_y,b_y,a_z,b_z
-double precision :: d(0:n_pt_in)
-double precision :: d1(0:n_pt_in)
-double precision :: d2(0:n_pt_in)
-double precision :: d3(0:n_pt_in)
-double precision :: accu,  pq_inv, p10_1, p10_2, p01_1, p01_2
-double precision :: p,P_center(3),rho,p_inv,p_inv_2
-!print*,'n_pt_in = ',n_pt_in
+  implicit none
+  BEGIN_DOC
+! Returns the explicit polynomial in terms of the "t" variable of the following
+!
+! :math:`I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)`
+  END_DOC
+  integer, intent(in)            :: n_pt_in
+  integer,intent(out)            :: n_pt_out
+  double precision, intent(in)   :: A_center(3), B_center(3),C_center(3)
+  double precision, intent(in)   :: alpha,beta
+  integer, intent(in)            :: power_A(3), power_B(3)
+  integer                        :: a_x,b_x,a_y,b_y,a_z,b_z
+  double precision               :: d(0:n_pt_in)
+  double precision               :: d1(0:n_pt_in)
+  double precision               :: d2(0:n_pt_in)
+  double precision               :: d3(0:n_pt_in)
+  double precision               :: accu,  pq_inv, p10_1, p10_2, p01_1, p01_2
+  double precision               :: p,P_center(3),rho,p_inv,p_inv_2
+
   accu = 0.d0
-!COMPTEUR irp_rdtsc1 = irp_rdtsc()
+
   ASSERT (n_pt_in > 1)
   p = alpha+beta
   p_inv = 1.d0/p
@@ -252,21 +263,20 @@ double precision :: p,P_center(3),rho,p_inv,p_inv_2
   do i =1, 3
     P_center(i) = (alpha * A_center(i) + beta * B_center(i)) * p_inv
   enddo
-! print*,'passed the P_center'
   
   double precision               :: R1x(0:2), B01(0:2), R1xp(0:2),R2x(0:2)
   R1x(0)  = (P_center(1) - A_center(1))
   R1x(1)  = 0.d0
   R1x(2)  = -(P_center(1) - C_center(1))
- ! R1x = (P_x - A_x) - (P_x - C_x) t^2
+
   R1xp(0)  = (P_center(1) - B_center(1))
   R1xp(1)  = 0.d0
   R1xp(2)  =-(P_center(1) - C_center(1))
- !R1xp = (P_x - B_x) - (P_x - C_x) t^2
+
   R2x(0)  =  p_inv_2
   R2x(1)  = 0.d0
   R2x(2)  = -p_inv_2
- !R2x  = 0.5 / p - 0.5/p t^2
+
   do i = 0,n_pt_in
     d(i) = 0.d0
   enddo
@@ -286,7 +296,7 @@ double precision :: p,P_center(3),rho,p_inv,p_inv_2
   a_x = power_A(1)
   b_x = power_B(1)
   call I_x1_pol_mult_mono_elec(a_x,b_x,R1x,R1xp,R2x,d1,n_pt1,n_pt_in)
-! print*,'passed the first I_x1'
+
   if(n_pt1<0)then
     n_pt_out = -1
     do i = 0,n_pt_in
@@ -298,15 +308,15 @@ double precision :: p,P_center(3),rho,p_inv,p_inv_2
   R1x(0)  = (P_center(2) - A_center(2))
   R1x(1)  = 0.d0
   R1x(2)  = -(P_center(2) - C_center(2))
- ! R1x = (P_x - A_x) - (P_x - C_x) t^2
+
   R1xp(0)  = (P_center(2) - B_center(2))
   R1xp(1)  = 0.d0
   R1xp(2)  =-(P_center(2) - C_center(2))
- !R1xp = (P_x - B_x) - (P_x - C_x) t^2
+
   a_y = power_A(2)
   b_y = power_B(2)
   call I_x1_pol_mult_mono_elec(a_y,b_y,R1x,R1xp,R2x,d2,n_pt2,n_pt_in)
-! print*,'passed the second I_x1'
+
   if(n_pt2<0)then
     n_pt_out = -1
     do i = 0,n_pt_in
@@ -319,18 +329,16 @@ double precision :: p,P_center(3),rho,p_inv,p_inv_2
   R1x(0)  = (P_center(3) - A_center(3))
   R1x(1)  = 0.d0
   R1x(2)  = -(P_center(3) - C_center(3))
- ! R1x = (P_x - A_x) - (P_x - C_x) t^2
+
   R1xp(0)  = (P_center(3) - B_center(3))
   R1xp(1)  = 0.d0
   R1xp(2)  =-(P_center(3) - C_center(3))
- !R2x  = 0.5 / p - 0.5/p t^2
+
   a_z = power_A(3)
   b_z = power_B(3)
   
-! print*,'a_z = ',a_z
-! print*,'b_z = ',b_z
   call I_x1_pol_mult_mono_elec(a_z,b_z,R1x,R1xp,R2x,d3,n_pt3,n_pt_in)
-! print*,'passed the third I_x1'
+
   if(n_pt3<0)then
     n_pt_out = -1
     do i = 0,n_pt_in
@@ -354,12 +362,14 @@ end
 
 
 recursive subroutine I_x1_pol_mult_mono_elec(a,c,R1x,R1xp,R2x,d,nd,n_pt_in)
-!!!!  recursive function involved in the electron nucleus potential
   implicit none
+  BEGIN_DOC
+!  Recursive routine involved in the electron-nucleus potential
+  END_DOC
   integer , intent(in)           :: n_pt_in
   double precision,intent(inout) :: d(0:n_pt_in)
   integer,intent(inout)          :: nd
- integer, intent(in):: a,c
+  integer, intent(in)            :: a,c
   double precision, intent(in)   :: R1x(0:2),R1xp(0:2),R2x(0:2)
   include 'Utils/constants.include.F'
   double precision               :: X(0:max_dim)
@@ -367,8 +377,8 @@ recursive subroutine I_x1_pol_mult_mono_elec(a,c,R1x,R1xp,R2x,d,nd,n_pt_in)
   !DIR$ ATTRIBUTES ALIGN : $IRP_ALIGN :: X, Y
   integer                        :: nx, ix,dim,iy,ny
   dim = n_pt_in
-! print*,'a,c = ',a,c
-! print*,'nd_in = ',nd
+  ! print*,'a,c = ',a,c
+  ! print*,'nd_in = ',nd
   
   if( (a==0) .and. (c==0))then
     nd = 0
@@ -379,7 +389,6 @@ recursive subroutine I_x1_pol_mult_mono_elec(a,c,R1x,R1xp,R2x,d,nd,n_pt_in)
     return
   else if ((a==0).and.(c.ne.0)) then
     call I_x2_pol_mult_mono_elec(c,R1x,R1xp,R2x,d,nd,n_pt_in)
-!    print*,'nd 0,c',nd
   else if (a==1) then
     nx = nd
     do ix=0,n_pt_in
@@ -401,19 +410,16 @@ recursive subroutine I_x1_pol_mult_mono_elec(a,c,R1x,R1xp,R2x,d,nd,n_pt_in)
     enddo
     nx = 0
     call I_x1_pol_mult_mono_elec(a-2,c,R1x,R1xp,R2x,X,nx,n_pt_in)
-!    print*,'nx a-2,c= ',nx
     do ix=0,nx
       X(ix) *= dble(a-1)
     enddo
     call multiply_poly(X,nx,R2x,2,d,nd)
-!    print*,'nd out = ',nd
     
     nx = nd
     do ix=0,n_pt_in
       X(ix) = 0.d0
     enddo
     call I_x1_pol_mult_mono_elec(a-1,c-1,R1x,R1xp,R2x,X,nx,n_pt_in)
-!      print*,'nx a-1,c-1 = ',nx
     do ix=0,nx
       X(ix) *= dble(c)
     enddo
@@ -426,20 +432,20 @@ end
 
 recursive subroutine I_x2_pol_mult_mono_elec(c,R1x,R1xp,R2x,d,nd,dim)
   implicit none
+  BEGIN_DOC
+!  Recursive routine involved in the electron-nucleus potential
+  END_DOC
   integer , intent(in)           :: dim
   include 'Utils/constants.include.F'
   double precision               :: d(0:max_dim)
   integer,intent(inout)          :: nd
- integer, intent(in):: c
+  integer, intent(in)            :: c
   double precision, intent(in)   :: R1x(0:2),R1xp(0:2),R2x(0:2)
   integer                        :: i
-!print*,'X2,c = ',c
-!print*,'nd_in = ',nd
   
   if(c==0) then
     nd = 0
     d(0) = 1.d0
-!  print*,'nd  IX2 = ',nd
     return
   elseif ((nd<0).or.(c<0))then
     nd = -1
@@ -454,22 +460,16 @@ recursive subroutine I_x2_pol_mult_mono_elec(c,R1x,R1xp,R2x,d,nd,dim)
     enddo
     nx = 0
     call I_x1_pol_mult_mono_elec(0,c-2,R1x,R1xp,R2x,X,nx,dim)
-!      print*,'nx 0,c-2 = ',nx
     do ix=0,nx
       X(ix) *= dble(c-1)
     enddo
     call multiply_poly(X,nx,R2x,2,d,nd)
-!      print*,'nd = ',nd
     ny = 0
     do ix=0,dim
       Y(ix) = 0.d0
     enddo
     
     call I_x1_pol_mult_mono_elec(0,c-1,R1x,R1xp,R2x,Y,ny,dim)
-!      print*,'ny = ',ny
-!      do ix=0,ny
-!        print*,'Y(ix) = ',Y(ix)
-!      enddo
     if(ny.ge.0)then
       call multiply_poly(Y,ny,R1xp,2,d,nd)
     endif
@@ -477,38 +477,39 @@ recursive subroutine I_x2_pol_mult_mono_elec(c,R1x,R1xp,R2x,d,nd,dim)
 end
 
 double precision function V_e_n(a_x,a_y,a_z,b_x,b_y,b_z,alpha,beta)
-implicit none
-!!! primitve nuclear attraction between the two primitves centered on the same atom ::
-!!!!         primitive_1 = x**(a_x) y**(a_y) z**(a_z) exp(-alpha * r**2)
-!!!!         primitive_2 = x**(b_x) y**(b_y) z**(b_z) exp(- beta * r**2)
-integer :: a_x,a_y,a_z,b_x,b_y,b_z
-double precision :: alpha,beta
-double precision :: V_r, V_phi, V_theta
-if(iand((a_x+b_x),1)==1.or.iand(a_y+b_y,1)==1.or.iand((a_z+b_z),1)==1)then
+  implicit none
+  BEGIN_DOC
+! Primitve nuclear attraction between the two primitves centered on the same atom.
+!
+!         primitive_1 = x**(a_x) y**(a_y) z**(a_z) exp(-alpha * r**2)
+!
+!         primitive_2 = x**(b_x) y**(b_y) z**(b_z) exp(- beta * r**2)
+  END_DOC
+  integer                        :: a_x,a_y,a_z,b_x,b_y,b_z
+  double precision               :: alpha,beta
+  double precision               :: V_r, V_phi, V_theta
+  if(iand((a_x+b_x),1)==1.or.iand(a_y+b_y,1)==1.or.iand((a_z+b_z),1)==1)then
     V_e_n = 0.d0
-else
+  else
     V_e_n =   V_r(a_x+b_x+a_y+b_y+a_z+b_z+1,alpha+beta)              &
-&         * V_phi(a_x+b_x,a_y+b_y)                         &
-&         * V_theta(a_z+b_z,a_x+b_x+a_y+b_y+1)
-endif
+        * V_phi(a_x+b_x,a_y+b_y)                                     &
+        * V_theta(a_z+b_z,a_x+b_x+a_y+b_y+1)
+  endif
   
 end
 
 
 double precision function int_gaus_pol(alpha,n)
-!!!! calculate the integral of 
-!!     integral on "x" with boundaries (- infinity; + infinity) of [ x**n  exp(-alpha * x**2) ]
-implicit none
-double precision :: alpha
-integer :: n
-double precision :: dble_fact
-include 'Utils/constants.include.F'
-
-!if(iand(n,1).eq.1)then
-!  int_gaus_pol= 0.d0
-!else
-!  int_gaus_pol = dsqrt(pi/alpha) * dble_fact(n -1)/(alpha+alpha)**(n/2)
-!endif
+  implicit none
+  BEGIN_DOC
+! Computes the integral:
+!
+! :math:`\int_{-\infty}^{\infty} x^n \exp(-\alpha x^2) dx`
+  END_DOC
+  double precision               :: alpha
+  integer                        :: n
+  double precision               :: dble_fact
+  include 'Utils/constants.include.F'
   
   int_gaus_pol = 0.d0
   if(iand(n,1).eq.0)then
@@ -525,27 +526,33 @@ include 'Utils/constants.include.F'
 end
 
 double precision function V_r(n,alpha)
-!!!! calculate the radial part of the nuclear attraction integral which is the following integral :
-!!     integral on "r" with boundaries ( 0 ; + infinity) of [ r**n  exp(-alpha * r**2) ]
-!!! CAUTION  :: this function requires the constant sqpi = dsqrt(pi)
-implicit none
-double precision ::  alpha, fact
-integer :: n
-include 'Utils/constants.include.F'
-if(iand(n,1).eq.1)then
+  implicit none
+  BEGIN_DOC
+  ! Computes the radial part of the nuclear attraction integral:
+  !
+  ! :math:`\int_{0}^{\infty} r^n  \exp(-\alpha  r^2)  dr`
+  !
+  END_DOC
+  double precision               :: alpha, fact
+  integer                        :: n
+  include 'Utils/constants.include.F'
+  if(iand(n,1).eq.1)then
     V_r = 0.5d0 * fact(shiftr(n,1)) / (alpha ** (shiftr(n,1) + 1))
-else
+  else
     V_r = sqpi * fact(n) / fact(shiftr(n,1)) * (0.5d0/sqrt(alpha)) ** (n+1)
-endif
+  endif
 end
 
 
 double precision function V_phi(n,m)
-implicit none
-!!!! calculate the angular "phi" part of the nuclear attraction integral wich is the following integral :
-!!     integral on "phi" with boundaries ( 0 ; 2 pi) of [ cos(phi) **n  sin(phi) **m ]
-integer :: n,m, i
-double precision ::  prod, Wallis
+  implicit none
+  BEGIN_DOC
+  ! Computes the angular "phi" part of the nuclear attraction integral:
+  !
+  ! :math:`\int_{0}^{2 \pi} \cos(\phi)^n \sin(\phi)^m d\phi`
+  END_DOC
+  integer                        :: n,m, i
+  double precision               :: prod, Wallis
   prod = 1.d0
   do i = 0,shiftr(n,1)-1
     prod = prod/ (1.d0 + dfloat(m+1)/dfloat(n-i-i-1))
@@ -553,13 +560,17 @@ double precision ::  prod, Wallis
   V_phi = 4.d0 * prod * Wallis(m)
 end
 
+
 double precision function V_theta(n,m)
-implicit none
-!!!! calculate the angular "theta" part of the nuclear attraction integral wich is the following integral :
-!!     integral on "theta" with boundaries ( 0 ; pi) of [ cos(theta) **n  sin(theta) **m ]
-integer :: n,m,i
-double precision ::  Wallis, prod
-include 'Utils/constants.include.F'
+  implicit none
+  BEGIN_DOC
+  ! Computes the angular "theta" part of the nuclear attraction integral:
+  !
+  ! :math:`\int_{0}^{\pi} \cos(\theta)^n \sin(\theta)^m d\theta`
+  END_DOC
+  integer                        :: n,m,i
+  double precision               :: Wallis, prod
+  include 'Utils/constants.include.F'
   V_theta = 0.d0
   prod = 1.d0
   do i = 0,shiftr(n,1)-1
@@ -570,20 +581,23 @@ end
 
 
 double precision function Wallis(n)
-!!!! calculate the Wallis integral :
-!!     integral on "theta" with boundaries ( 0 ; pi/2) of [ cos(theta) **n ]
-implicit none
-double precision :: fact
-integer :: n,p
-include 'Utils/constants.include.F'
-if(iand(n,1).eq.0)then
+  implicit none
+  BEGIN_DOC
+  ! Wallis integral:
+  !
+  ! :math:`\int_{0}^{\pi} \cos(\theta)^n d\theta`
+  END_DOC
+  double precision               :: fact
+  integer                        :: n,p
+  include 'Utils/constants.include.F'
+  if(iand(n,1).eq.0)then
     Wallis = fact(shiftr(n,1))
     Wallis = pi * fact(n) / (dble(ibset(0_8,n)) * (Wallis+Wallis)*Wallis)
-else
+  else
     p = shiftr(n,1)
     Wallis = fact(p)
     Wallis = dble(ibset(0_8,p+p)) * Wallis*Wallis / fact(p+p+1)
-endif
+  endif
   
 end
 

src/AO_one_e_integrals/pot_ao_pseudo_ints.irp.f

@@ -1,7 +1,7 @@
 BEGIN_PROVIDER [ double precision, ao_pseudo_integral, (ao_num,ao_num)]
   implicit none
   BEGIN_DOC
-  ! Pseudo-potential integrals
+  ! Pseudo-potential integrals in the |AO| basis set.
   END_DOC
   
   if (read_ao_one_integrals) then
@@ -137,7 +137,7 @@ BEGIN_PROVIDER [ double precision, ao_pseudo_integral_local, (ao_num,ao_num)]
  BEGIN_PROVIDER [ double precision, ao_pseudo_integral_non_local, (ao_num,ao_num)]
   implicit none
   BEGIN_DOC
-  ! Local pseudo-potential
+  ! Non-local pseudo-potential
   END_DOC
   include 'Utils/constants.include.F'
   double precision               :: alpha, beta, gama, delta

src/AO_one_e_integrals/read_write.irp.f

@@ -2,7 +2,7 @@
 &BEGIN_PROVIDER [ logical, write_ao_one_integrals ]
    
    BEGIN_DOC
-   ! One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
+   ! If |true|, read/write one-electrons from/to disk.
    END_DOC
    implicit none
    

src/AO_one_e_integrals/spread_dipole_ao.irp.f

@@ -2,9 +2,11 @@
  &BEGIN_PROVIDER [ double precision, ao_spread_y, (ao_num,ao_num)]
  &BEGIN_PROVIDER [ double precision, ao_spread_z, (ao_num,ao_num)]
  BEGIN_DOC
- ! array of the integrals of AO_i * x^2 AO_j
- ! array of the integrals of AO_i * y^2 AO_j
- ! array of the integrals of AO_i * z^2 AO_j
+ ! * array of the integrals of AO_i * x^2 AO_j
+ !
+ ! * array of the integrals of AO_i * y^2 AO_j
+ !
+ ! * array of the integrals of AO_i * z^2 AO_j
  END_DOC
  implicit none
   integer :: i,j,n,l
@@ -73,9 +75,11 @@
  &BEGIN_PROVIDER [ double precision, ao_dipole_y, (ao_num,ao_num)]
  &BEGIN_PROVIDER [ double precision, ao_dipole_z, (ao_num,ao_num)]
  BEGIN_DOC
- ! array of the integrals of AO_i * x AO_j
- ! array of the integrals of AO_i * y AO_j
- ! array of the integrals of AO_i * z AO_j
+ ! * array of the integrals of AO_i * x AO_j
+ !
+ ! * array of the integrals of AO_i * y AO_j
+ !
+ ! * array of the integrals of AO_i * z AO_j
  END_DOC
  implicit none
   integer :: i,j,n,l
@@ -143,9 +147,11 @@
  &BEGIN_PROVIDER [ double precision, ao_deriv_1_y, (ao_num,ao_num)]
  &BEGIN_PROVIDER [ double precision, ao_deriv_1_z, (ao_num,ao_num)]
  BEGIN_DOC
- ! array of the integrals of AO_i * d/dx  AO_j
- ! array of the integrals of AO_i * d/dy  AO_j
- ! array of the integrals of AO_i * d/dz  AO_j
+ ! * array of the integrals of AO_i * d/dx  AO_j
+ !
+ ! * array of the integrals of AO_i * d/dy  AO_j
+ !
+ ! * array of the integrals of AO_i * d/dz  AO_j
  END_DOC
  implicit none
   integer :: i,j,n,l
@@ -214,47 +220,9 @@
 
 
 
- subroutine overlap_bourrin_x_abs(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,lower_exp_val,dx,nx)
- implicit none
-! compute the following integral :
-!  int [-infty ; +infty] of [(x-A_center)^(power_A) * (x-B_center)^power_B * exp(-alpha(x-A_center)^2) * exp(-beta(x-B_center)^2) ]
- integer :: i,j,k,l
- integer,intent(in) :: power_A,power_B
- double precision, intent(in) :: lower_exp_val
- double precision,intent(in) :: A_center, B_center,alpha,beta
- double precision, intent(out) :: overlap_x,dx
- integer, intent(in) :: nx
- double precision :: x_min,x_max,domain,x,power,factor,dist,p,p_inv,rho
- double precision :: P_center,pouet_timy
- if(power_A.lt.0.or.power_B.lt.0)then
-  overlap_x = 0.d0
-  dx = 0.d0
-  return
- endif
- p = alpha + beta
- p_inv= 1.d0/p
- rho = alpha * beta * p_inv
- dist = (A_center - B_center)*(A_center - B_center)
- P_center = (alpha * A_center + beta * B_center) * p_inv
- factor = dexp(-rho * dist)
- pouet_timy = dsqrt(lower_exp_val/p)
-  x_min = P_center - pouet_timy
-  x_max = P_center + pouet_timy
-!print*,'xmin = ',x_min
-!print*,'xmax = ',x_max
- domain = x_max-x_min
- dx = domain/dble(nx)
- overlap_x = 0.d0
- x = x_min
- do i = 1, nx
-  x += dx
-  overlap_x += (power(power_A,x-A_center) * power(power_B,x-B_center)) * dexp(-p * (x-P_center)*(x-P_center))
- enddo
- overlap_x *= factor * dx
-end
 
  subroutine overlap_bourrin_spread(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,lower_exp_val,dx,nx)
-! compute the following integral :
+! Computes the following integral :
 !  int [-infty ; +infty] of [(x-A_center)^(power_A) * (x-B_center)^power_B * exp(-alpha(x-A_center)^2) * exp(-beta(x-B_center)^2) * x ]
 !  needed for the dipole and those things
  implicit none
@@ -264,7 +232,7 @@ end
  double precision,intent(in) :: A_center, B_center,alpha,beta
  double precision, intent(out) :: overlap_x,dx
  integer, intent(in) :: nx
- double precision :: x_min,x_max,domain,x,power,factor,dist,p,p_inv,rho
+ double precision :: x_min,x_max,domain,x,factor,dist,p,p_inv,rho
  double precision :: P_center,pouet_timy
  if(power_A.lt.0.or.power_B.lt.0)then
   overlap_x = 0.d0
@@ -292,19 +260,12 @@ end
  x = x_min
  do i = 1, nx
   x += dx
-  overlap_x += power(power_A,x-A_center) * power(power_B,x-B_center) * dexp(-p * (x-P_center)*(x-P_center)) * x * x
+  overlap_x += (x-A_center)**(power_A) * (x-B_center)**(power_B) * dexp(-p * (x-P_center)*(x-P_center)) * x * x
  enddo
  overlap_x *= factor * dx
 
  end
 
- double precision function power(n,x)
- implicit none
- integer :: i,n
- double precision :: x,accu
- power = x**n
- return
- end
 
  subroutine overlap_bourrin_dipole(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,lower_exp_val,dx,nx)
 ! compute the following integral :
@@ -317,7 +278,7 @@ end
  double precision,intent(in) :: A_center, B_center,alpha,beta
  double precision, intent(out) :: overlap_x,dx
  integer, intent(in) :: nx
- double precision :: x_min,x_max,domain,x,power,factor,dist,p,p_inv,rho
+ double precision :: x_min,x_max,domain,x,factor,dist,p,p_inv,rho
  double precision :: P_center
  if(power_A.lt.0.or.power_B.lt.0)then
   overlap_x = 0.d0
@@ -347,7 +308,7 @@ end
  x = x_min
  do i = 1, nx
   x += dx
-  overlap_x += power(power_A,x-A_center) * power(power_B,x-B_center) * dexp(-p * (x-P_center)*(x-P_center)) * x
+  overlap_x += (x-A_center)**(power_A) * (x-B_center)**(power_B) * dexp(-p * (x-P_center)*(x-P_center)) * x
  enddo
  overlap_x *= factor * dx
 
@@ -378,7 +339,7 @@ end
  double precision,intent(in) :: A_center, B_center,alpha,beta
  double precision, intent(out) :: overlap_x,dx
  integer, intent(in) :: nx
- double precision :: x_min,x_max,domain,x,power,factor,dist,p,p_inv,rho
+ double precision :: x_min,x_max,domain,x,factor,dist,p,p_inv,rho
  double precision :: P_center,pouet_timy
  if(power_A.lt.0.or.power_B.lt.0)then
   overlap_x = 0.d0
@@ -406,7 +367,7 @@ end
  x = x_min
  do i = 1, nx
   x += dx
-  overlap_x += power(power_A,x-A_center) * power(power_B,x-B_center) * dexp(-p * (x-P_center)*(x-P_center))
+  overlap_x += (x-A_center)**(power_A) * (x-B_center)**(power_B) * dexp(-p * (x-P_center)*(x-P_center))
  enddo
  overlap_x *= factor * dx
  end

src/CIS/NEED

@@ -1 +1,3 @@
-Selectors_full SingleRefMethod DavidsonUndressed
+Selectors_full
+SingleRefMethod
+DavidsonUndressed

src/CISD/NEED

@@ -1 +1,3 @@
-Selectors_full SingleRefMethod DavidsonUndressed
+Selectors_full
+SingleRefMethod
+DavidsonUndressed

src/Determinants/NEED

@@ -1 +1,3 @@
-MO_Basis MO_one_e_integrals Integrals_Bielec 
+MO_Basis
+MO_one_e_integrals
+Integrals_Bielec 

src/FCI/NEED

@@ -1 +1,7 @@
-Perturbation Selectors_full Generators_full ZMQ MPI DavidsonUndressed Iterations
+Perturbation
+Selectors_full
+Generators_full
+ZMQ
+MPI
+DavidsonUndressed
+Iterations

src/Generators_full/NEED

@@ -1 +1,2 @@
-Determinants Hartree_Fock
+Determinants
+Hartree_Fock

src/Hartree_Fock/NEED

@@ -1 +1,4 @@
-Integrals_Bielec AO_one_e_integrals MOGuess Bitmask
+Integrals_Bielec
+AO_one_e_integrals
+MOGuess
+Bitmask

src/Integrals_Bielec/NEED

@@ -1 +1,7 @@
-AO_one_e_integrals MO_one_e_integrals Pseudo Bitmask ZMQ AO_Basis MO_Basis
+AO_one_e_integrals
+MO_one_e_integrals
+Pseudo
+Bitmask
+ZMQ
+AO_Basis
+MO_Basis

src/MOGuess/NEED

@@ -1 +1,2 @@
-MO_Basis MO_one_e_integrals
+MO_Basis
+MO_one_e_integrals

src/MO_Basis/NEED

@@ -1 +1,3 @@
-AO_Basis AO_one_e_integrals Electrons 
+AO_Basis
+AO_one_e_integrals
+Electrons

src/MO_one_e_integrals/NEED

@@ -1 +1,3 @@
-AO_one_e_integrals MO_Basis Pseudo
+AO_one_e_integrals
+MO_Basis
+Pseudo

src/MRPT_Utils/NEED

@@ -1 +1,3 @@
-Determinants Davidson Psiref_CAS
+Determinants
+Davidson
+Psiref_CAS

src/Nuclei/NEED

@@ -1 +1,2 @@
-Ezfio_files Utils
+Ezfio_files
+Utils

src/Perturbation/NEED

@@ -1 +1,4 @@
-Determinants Hartree_Fock Davidson  MRPT_Utils
+Determinants
+Hartree_Fock
+Davidson
+MRPT_Utils

src/Psiref_Utils/NEED

@@ -1 +1,2 @@
-Bitmask Determinants
+Bitmask
+Determinants

src/Selectors_full/NEED

@@ -1 +1,3 @@
-Determinants Hartree_Fock Selectors_Utils
+Determinants
+Hartree_Fock
+Selectors_Utils

src/Slave/NEED

@@ -1 +1,2 @@
-FCI MPI
+FCI
+MPI

src/dummy/NEED

@@ -1 +1,34 @@
-AO_Basis AO_one_e_integrals Bitmask CIS CISD Davidson DavidsonDressed DavidsonUndressed Determinants Dressing Electrons Ezfio_files FCI FourIdx Generators_CAS Generators_full Hartree_Fock Integrals_Bielec MO_Basis MOGuess MO_one_e_integrals MPI Nuclei Perturbation Pseudo Psiref_CAS Psiref_Utils Selectors_CASSD Selectors_full Selectors_Utils SingleRefMethod Utils ZMQ MRPT_Utils
+AO_Basis
+AO_one_e_integrals
+Bitmask
+CIS
+CISD
+Davidson
+DavidsonDressed
+DavidsonUndressed
+Determinants
+Dressing
+Electrons
+Ezfio_files
+FCI
+FourIdx
+Generators_CAS
+Generators_full
+Hartree_Fock
+Integrals_Bielec
+MO_Basis
+MOGuess
+MO_one_e_integrals
+MPI
+Nuclei
+Perturbation
+Pseudo
+Psiref_CAS
+Psiref_Utils
+Selectors_CASSD
+Selectors_full
+Selectors_Utils
+SingleRefMethod
+Utils
+ZMQ
+MRPT_Utils