Merge pull request #7 from LCPQ/master

Merge with V2

ocaml/Makefile

@@ -25,9 +25,12 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore
 
 .gitignore: $(MLFILES)
 	@for i in .gitignore ezfio.ml Qptypes.ml qptypes_generator.byte _build $(ALL_EXE) $(ALL_TESTS) \
-	$(patsubst %.ml,%,$(wildcard test_*.ml)) $(patsubst %.ml,%,$(wildcard qp_*.ml)) ; do \
+	$(patsubst %.ml,%,$(wildcard test_*.ml)) $(patsubst %.ml,%,$(wildcard qp_*.ml)) \
+	$(shell grep Input Input_auto_generated.ml | awk '{print $$2 ".ml"}') \
+	Input_auto_generated.ml;\
+	do \
 	   echo $$i ; \
-	done >> .gitignore
+	done > .gitignore
 
 executables: $(QPACKAGE_ROOT)/data/executables
 

scripts/build_modules.sh

@@ -30,6 +30,7 @@ Build failed for module $MODULE
 "
     fi
   fi
+  ${QPACKAGE_ROOT}/scripts/create_gitignore.sh
   cd ${OLDPWD}
 done
 ${QPACKAGE_ROOT}/scripts/create_executables_list.sh

scripts/create_gitignore.sh

@@ -35,4 +35,4 @@ then
 fi
 
 find . -type l | sed "s@./@@" >> .gitignore
-
+find . -type f -executable -print | sed "s@./@@" >> .gitignore

scripts/ezfio_interface/convert_ezfio.sh

@@ -1,27 +0,0 @@
-#!/bin/bash
-#  Convert a old ezfio file (with option.irp.f ezfio_default)
-# into a new EZFIO.cfg type
-
-# Hartree Fock
-# Changin the case, don't know if is needed or not 
-mv $1/Hartree_Fock $1/hartree_fock 2> /dev/null
-
-mv $1/hartree_Fock/thresh_SCF $1/hartree_fock/thresh_scf 2> /dev/null
-
-# BiInts
-mv $1/bi_integrals $1/bielect_integrals 2> /dev/null
-
-if [ -f  $1/bielect_integrals/read_ao_integrals ]; then
-    if [ `cat $1/bielect_integrals/read_ao_integrals` -eq "True" ]
-    then
-            echo "Read" > $1/bielect_integrals/disk_access_ao_integrals
-    
-    elif [ `cat bielect_integrals/write_ao_integrals` -eq "True" ]
-    then
-            echo "Write" > $1/bielect_integrals/disk_access_ao_integrals
-    
-    else
-            echo "None" > $1/bielect_integrals/disk_access_ao_integrals
-    
-    fi
-fi

scripts/ezfio_interface/ei_handler.py

@@ -70,9 +70,9 @@ def is_bool(str_):
     Take a string, if is a bool return the conversion into
         fortran and ocaml.
     """
-    if str_.lower() in ['true', '.true.']:
+    if "true" in str_.lower():
         return Type(None, "true", ".True.")
-    elif str_.lower() in ['false', '.false.']:
+    elif "false" in str_.lower():
         return Type(None, "false", ".False")
     else:
         raise TypeError

scripts/update_README.py

@@ -1,16 +1,16 @@
 #!/usr/bin/env python
 
 """Updates the README.rst file as the include directive is disabled on GitHub."""
-__date__     = "Thu Apr  3 23:06:18 CEST 2014"
+__date__ = "Thu Apr  3 23:06:18 CEST 2014"
 __author__ = "Anthony Scemama <scemama@irsamc.ups-tlse.fr>"
 
 
-README="README.rst"
+README = "README.rst"
-Assum_key="Assumptions\n===========\n"
+Assum_key = "Assumptions\n===========\n"
-Needed_key="Needed Modules\n==============\n"
+Needed_key = "Needed Modules\n==============\n"
-Doc_key="Documentation\n=============\n"
+Doc_key = "Documentation\n=============\n"
-Sentinel="@@$%&@@"
+Sentinel = "@@$%&@@"
-URL="http://github.com/LCPQ/quantum_package/tree/master/src/"
+URL = "http://github.com/LCPQ/quantum_package/tree/master/src/"
 
 import os
 import subprocess
@@ -22,11 +22,11 @@ header = """
 """
 
 try:
-# subprocess.check_output("git status".split())
+    # subprocess.check_output("git status".split())
-# has_git = True
+    has_git = True
-  pass
 except OSError:
-  has_git = False
+    has_git = False
+
 
 def fetch_splitted_data():
     """Read the README.rst file and split it in strings:
@@ -37,14 +37,14 @@ def fetch_splitted_data():
     The result is given as a list of strings
     """
 
-    file = open(README,'r')
+    file = open(README, 'r')
     data = file.read()
     file.close()
 
     # Place sentinels
-    data = data.replace(Assum_key,Sentinel+Assum_key)
+    data = data.replace(Assum_key, Sentinel + Assum_key)
-    data = data.replace(Doc_key,Sentinel+Doc_key)
+    data = data.replace(Doc_key, Sentinel + Doc_key)
-    data = data.replace(Needed_key,Sentinel+Needed_key)
+    data = data.replace(Needed_key, Sentinel + Needed_key)
 
     # Now Split data using the sentinels
     result = data.split(Sentinel)
@@ -56,9 +56,9 @@ def update_assumptions(data):
     """Read the ASSUMPTIONS.rst file, and replace the data with it."""
 
     try:
-        file = open('ASSUMPTIONS.rst','r')
+        file = open('ASSUMPTIONS.rst', 'r')
     except IOError:
-        file = open('ASSUMPTIONS.rst','w')
+        file = open('ASSUMPTIONS.rst', 'w')
         assumptions = ""
     else:
         assumptions = file.read()
@@ -74,7 +74,7 @@ def update_assumptions(data):
             data[i] = assumptions
 
     if not has_assumptions:
-        data.insert(1,assumptions)
+        data.insert(1, assumptions)
 
     return data
 
@@ -83,12 +83,12 @@ def update_needed(data):
     """Read the NEEDED_MODULES file, and replace the data with it.
     Create the links to the GitHub pages."""
 
-    file = open('NEEDED_MODULES','r')
+    file = open('NEEDED_MODULES', 'r')
     modules = file.read()
     file.close()
 
     if modules.strip() != "":
-        modules = [ '* `%s <%s%s>`_'%(x,URL,x) for x in  modules.split() ]
+        modules = ['* `%s <%s%s>`_' % (x, URL, x) for x in modules.split()]
         modules = "\n".join(modules)
         modules = Needed_key + header + modules + '\n\n'
 
@@ -105,112 +105,114 @@ def update_needed(data):
 
 
 def update_documentation(data):
-  """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
+    """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
 
-  # If the file does not exist, don't do anything
+    # If the file does not exist, don't do anything
-  try:
+    try:
-    file = open('tags','r')
+        file = open('tags', 'r')
-  except:
+    except:
-    return
+        return
-  tags = file.readlines()
+    tags = file.readlines()
-  file.close()
-
-  def extract_doc(item):
-    """Extracts the documentation contained in IRPF90_man file"""
-    file = open("IRPF90_man/%s.l"%(item),'r')
-    lines = file.readlines()
     file.close()
-    result = []
-    inside = False
-    for line in lines:
-      if not inside:
-        inside = line.startswith(".SH Description")
-      else:
-        if line.startswith(".SH"):
-          break
-        result.append("  "+line.strip())
 
-    if result == []:
+    def extract_doc(item):
-      result = ["  Undocumented"]
+        """Extracts the documentation contained in IRPF90_man file"""
-    return "\n".join(result)+'\n'
+        file = open("IRPF90_man/%s.l" % (item), 'r')
+        lines = file.readlines()
+        file.close()
+        result = []
+        inside = False
+        for line in lines:
+            if not inside:
+                inside = line.startswith(".SH Description")
+            else:
+                if line.startswith(".SH"):
+                    break
+                result.append("  " + line.strip())
 
+        if result == []:
+            result = ["  Undocumented"]
+        return "\n".join(result) + '\n'
 
+    items = []
+    dirname = os.path.basename(os.getcwd())
+    command = "git ls-tree --full-tree --name-only HEAD:src/%s"
+    command = command % (dirname)
+    try:
+        if dirname != 'src':
+            p = subprocess.Popen(command.split(), stdout=subprocess.PIPE)
+            tracked_files = p.stdout.read()
+        else:
+            tracked_files = ""
+        tracked_files = tracked_files.splitlines()
+    except:
+        tracked_files = []
+    for filename in tracked_files:
+        if filename.endswith('.irp.f'):
+                    # Search for providers, subroutines and functions in each file using
+                    # the tags file
+            search = "\t" + filename + "\t"
+            tmp = filter(lambda line: search in line, tags)
 
-  items = []
+            # Search for the documentation in the IRPF90_man directory
-  dirname = os.path.basename(os.getcwd())
+            for item in tmp:
-  command = "git ls-tree --full-tree --name-only HEAD:src/%s"
+                item, _, line = item.strip().split('\t')
-  command = command%(dirname)
+                doc = extract_doc(item)
-  try:
+                items.append((item, filename, doc, line))
-    if dirname != 'src':
-      p = subprocess.Popen(command.split(),stdout=subprocess.PIPE)
-      tracked_files = p.stdout.read()
-    else:
-      tracked_files = ""
-    tracked_files = tracked_files.splitlines()
-  except:
-    tracked_files = []
-  for filename in tracked_files:
-      if filename.endswith('.irp.f'):
-          # Search for providers, subroutines and functions in each file using
-          # the tags file
-          search = "\t"+filename+"\t"
-          tmp = filter(lambda line: search in line, tags)
 
-          # Search for the documentation in the IRPF90_man directory
+    dirname = os.path.basename(os.getcwd())
-          for item in tmp :
+    # Write the documentation in the README
-              item, _, line = item.strip().split('\t')
+    template = "`%(item)s <%(url)s%(dirname)s/%(filename)s#L%(line)s>`_\n%(doc)s\n"
-              doc = extract_doc(item)
-              items.append( (item, filename, doc, line) )
 
-  dirname = os.path.basename(os.getcwd())
+    documentation = Doc_key + header
-  # Write the documentation in the README
+    url = URL
-  template = "`%(item)s <%(url)s%(dirname)s/%(filename)s#L%(line)s>`_\n%(doc)s\n"
+    for item, filename, doc, line in items:
+        documentation += template % locals()
+    documentation += '\n\n'
 
-  documentation = Doc_key + header 
+    has_doc = False
-  url = URL
+    for i in range(len(data)):
-  for item, filename, doc, line in items:
+        if data[i].startswith(Doc_key):
-    documentation += template%locals()
+            has_doc = True
-  documentation += '\n\n'
+            data[i] = documentation
 
-  has_doc = False
+    if not has_doc:
-  for i in range(len(data)):
+        data.append(documentation)
-      if data[i].startswith(Doc_key):
-          has_doc = True
-          data[i] = documentation
 
-  if not has_doc:
+    return data
-      data.append(documentation)
-
-  return data
 
 
 def git_add():
     """Executes:
     git add README.rst
-    if git is present on the machine."""
+    throw an error if git is not precent"""
-    command = "git add "+README
+
-    os.system(command+" &> /dev/null")
+    import subprocess
+
+    try:
+        # pipe output to /dev/null for silence
+        null = open("/dev/null", "w")
+        subprocess.Popen("git add README.rst", stdout=null, stderr=null)
+        null.close()
+
+    except OSError:
+        raise
 
 
 def main():
-    if not has_git:
-        return
     data = fetch_splitted_data()
     data = update_assumptions(data)
     data = update_documentation(data)
     data = update_needed(data)
     output = ''.join(data)
 
-    file = open(README,'w')
+    with open(README, 'w') as f:
-    file.write(output)
+        f.write(output)
-    file.close()
-
-    git_add()
 
+    try:
+        git_add()
+    except OSError:
+        pass
 
 if __name__ == '__main__':
-    try:
+    main()
-      main()
-    except:
-      pass
-

src/AOs/README.rst

@@ -50,21 +50,65 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L1>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L65>`_
+  Overlap between absolute value of atomic basis functions:
+  :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
+
+`ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L2>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+`ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L3>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+`ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L4>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
 `ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L21>`_
   Coefficients, exponents and powers of x,y and z
-  ao_coef(i,j) = coefficient of the jth primitive on the ith ao
 
-`ao_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L96>`_
+`ao_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L157>`_
   Transposed ao_coef and ao_expo
 
+`ao_coef_unnormalized <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L116>`_
+  Coefficients, exponents and powers of x,y and z as in the EZFIO file
+  ao_coef(i,j) = coefficient of the jth primitive on the ith ao
+  ao_l = l value of the AO: a+b+c in x^a y^b z^c
+
 `ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L20>`_
   Coefficients, exponents and powers of x,y and z
-  ao_coef(i,j) = coefficient of the jth primitive on the ith ao
 
-`ao_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L97>`_
+`ao_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L158>`_
   Transposed ao_coef and ao_expo
 
-`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L146>`_
+`ao_expo_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L117>`_
+  Coefficients, exponents and powers of x,y and z as in the EZFIO file
+  ao_coef(i,j) = coefficient of the jth primitive on the ith ao
+  ao_l = l value of the AO: a+b+c in x^a y^b z^c
+
+`ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L118>`_
+  Coefficients, exponents and powers of x,y and z as in the EZFIO file
+  ao_coef(i,j) = coefficient of the jth primitive on the ith ao
+  ao_l = l value of the AO: a+b+c in x^a y^b z^c
+
+`ao_l_char <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L119>`_
+  Coefficients, exponents and powers of x,y and z as in the EZFIO file
+  ao_coef(i,j) = coefficient of the jth primitive on the ith ao
+  ao_l = l value of the AO: a+b+c in x^a y^b z^c
+
+`ao_l_char_space <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L309>`_
+  Undocumented
+
+`ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L400>`_
+  MD5 key characteristic of the AO basis
+
+`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L207>`_
   Index of the nuclei on which the ao is centered
 
 `ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L1>`_
@@ -75,16 +119,37 @@ Documentation
 
 `ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L19>`_
   Coefficients, exponents and powers of x,y and z
-  ao_coef(i,j) = coefficient of the jth primitive on the ith ao
 
-`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L114>`_
+`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L175>`_
   Number of primitives per atomic orbital
 
-`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L136>`_
+`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L197>`_
   Undocumented
 
-`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L137>`_
+`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L198>`_
   Undocumented
 
+`l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L216>`_
+  character corresponding to the "L" value of an AO orbital
+
+`n_aos_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L229>`_
+  Number of AOs per atom
+
+`nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L242>`_
+  List of AOs attached on each atom
+
+`nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L260>`_
+  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
+
+`nucl_n_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L228>`_
+  Number of AOs per atom
+
+`nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L261>`_
+  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
+
 
 

src/Bielec_integrals/README.rst

@@ -32,152 +32,193 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L1>`_
+`ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1>`_
   integral of the AO basis <ik|jl> or (ij|kl)
   i(r1) j(r1) 1/r12 k(r2) l(r2)
 
-`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L350>`_
+`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L490>`_
-  Needed to compuet Schwartz inequalities
+  Needed to compute Schwartz inequalities
 
-`ao_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L188>`_
+`ao_bielec_integral_schwartz_accel <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L107>`_
+  integral of the AO basis <ik|jl> or (ij|kl)
+  i(r1) j(r1) 1/r12 k(r2) l(r2)
+
+`ao_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L322>`_
   Map of Atomic integrals
   i(r1) j(r2) 1/r12 k(r1) l(r2)
 
-`compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L147>`_
+`ao_l4 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L279>`_
+  Computes the product of l values of i,j,k,and l
+
+`compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L290>`_
   Compute AO 1/r12 integrals for all i and fixed j,k,l
 
-`eri <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L511>`_
+`eri <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L653>`_
   ATOMIC PRIMTIVE bielectronic integral between the 4 primitives ::
   primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2)
   primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2)
   primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2)
   primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2)
 
-`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L376>`_
+`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L515>`_
   Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives
 
-`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L656>`_
+`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L851>`_
   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)
 
-`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L600>`_
+`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L772>`_
   recursive function involved in the bielectronic integral
 
-`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L719>`_
+`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L914>`_
   recursive function involved in the bielectronic integral
 
-`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L839>`_
+`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1034>`_
   recursive function involved in the bielectronic integral
 
-`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L893>`_
+`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1088>`_
   recursive function involved in the bielectronic integral
 
-`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L753>`_
+`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L948>`_
   recursive function involved in the bielectronic integral
 
-`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L623>`_
+`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L807>`_
   recursive function involved in the bielectronic integral
 
-`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L955>`_
+`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1150>`_
   recursive function involved in the bielectronic integral
 
-`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L555>`_
+`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L698>`_
   calculate the integral of the polynom ::
   I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q)
   between ( 0 ; 1)
 
-`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L642>`_
+`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L837>`_
-  Returns the upper boundary of the degree of the polynom involved in the
+  Returns the upper boundary of the degree of the polynomial involved in the
   bielctronic integral :
   Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z)
 
-`gauleg <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L20>`_
+`gauleg <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L29>`_
   Gauss-Legendre
 
-`gauleg_t2 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L1>`_
+`gauleg_t2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L10>`_
   t_w(i,1,k) = w(i)
   t_w(i,2,k) = t(i)
 
-`gauleg_w <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L2>`_
+`gauleg_w <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L11>`_
   t_w(i,1,k) = w(i)
   t_w(i,2,k) = t(i)
 
-`ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L6>`_
+`n_pt_max_integrals_16 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L1>`_
+  Aligned n_pt_max_integrals
+
+`ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L6>`_
   AO integrals
 
-`bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L17>`_
+`bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L19>`_
   Undocumented
 
-`clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L128>`_
+`bielec_integrals_index_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L36>`_
+  Undocumented
+
+`clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L223>`_
   Frees the memory of the AO map
 
-`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L285>`_
+`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L399>`_
   Frees the memory of the MO map
 
-`get_ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L33>`_
+`get_ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L113>`_
   Gets one AO bi-electronic integral from the AO map
 
-`get_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L51>`_
+`get_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L137>`_
   Gets multiple AO bi-electronic integral from the AO map .
   All i are retrieved for j,k,l fixed.
 
-`get_ao_bielec_integrals_non_zero <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L84>`_
+`get_ao_bielec_integrals_non_zero <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L172>`_
   Gets multiple AO bi-electronic integral from the AO map .
   All non-zero i are retrieved for j,k,l fixed.
 
-`get_ao_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L120>`_
+`get_ao_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L214>`_
   Returns the number of elements in the AO map
 
-`get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L184>`_
+`get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L281>`_
   Returns one integral <ij|kl> in the MO basis
 
-`get_mo_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L213>`_
+`get_mo_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L310>`_
   Returns multiple integrals <ij|kl> in the MO basis, all
   i for j,k,l fixed.
 
-`get_mo_bielec_integrals_existing_ik <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L235>`_
+`get_mo_bielec_integrals_existing_ik <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L341>`_
   Returns multiple integrals <ij|kl> in the MO basis, all
+  i(1)j(1) 1/r12 k(2)l(2)
   i for j,k,l fixed.
 
-`get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L277>`_
+`get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L391>`_
   Return the number of elements in the MO map
 
-`insert_into_ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L153>`_
+`insert_into_ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L250>`_
   Create new entry into AO map
 
-`insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L168>`_
+`insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L265>`_
   Create new entry into MO map, or accumulate in an existing entry
 
-`mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L201>`_
+`mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L298>`_
   Returns one integral <ij|kl> in the MO basis
 
-`mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L142>`_
+`mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L237>`_
   MO integrals
 
-`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L40>`_
+`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L42>`_
   Adds integrals to tha MO map according to some bitmask
 
-`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L314>`_
+`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L464>`_
   mo_bielec_integral_jj(i,j) = J_ij
-  mo_bielec_integral_jj_exchange(i,j) = J_ij
+  mo_bielec_integral_jj_exchange(i,j) = K_ij
   mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
 
-`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L316>`_
+`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L466>`_
   mo_bielec_integral_jj(i,j) = J_ij
-  mo_bielec_integral_jj_exchange(i,j) = J_ij
+  mo_bielec_integral_jj_exchange(i,j) = K_ij
   mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
 
-`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L315>`_
+`mo_bielec_integral_jj_anti_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L326>`_
+  mo_bielec_integral_jj_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
+
+`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L465>`_
   mo_bielec_integral_jj(i,j) = J_ij
-  mo_bielec_integral_jj_exchange(i,j) = J_ij
+  mo_bielec_integral_jj_exchange(i,j) = K_ij
   mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
 
-`mo_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L21>`_
+`mo_bielec_integral_jj_exchange_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L325>`_
+  mo_bielec_integral_jj_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
+
+`mo_bielec_integral_jj_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L324>`_
+  mo_bielec_integral_jj_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
+
+`mo_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L22>`_
   If True, the map of MO bielectronic integrals is provided
 
-`mo_bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L1>`_
+`mo_bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L1>`_
   Computes an unique index for i,j,k,l integrals
 
+`read_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L1>`_
+  One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
+
+`read_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L2>`_
+  One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
+
+`write_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L3>`_
+  One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
+
+`write_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L4>`_
+  One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
+
 
 

src/Bitmask/README.rst

@@ -54,6 +54,24 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+`is_a_two_holes_two_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L206>`_
+  Undocumented
+
+`number_of_holes <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L1>`_
+  Undocumented
+
+`number_of_holes_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L394>`_
+  Undocumented
+
+`number_of_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L103>`_
+  Undocumented
+
+`number_of_particles_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L422>`_
+  Undocumented
+
+`cas_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L173>`_
+  Bitmasks for CAS reference determinants. (N_int, alpha/beta, CAS reference)
+
 `cis_ijkl_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L32>`_
   Bitmask to include all possible single excitations from Hartree-Fock
 
@@ -61,23 +79,35 @@ Documentation
   Bitmask to include all possible MOs
 
 `generators_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L100>`_
-  Bitmasks for generator determinants. (N_int, alpha/beta, hole/particle, generator).
+  Bitmasks for generator determinants.
+  (N_int, alpha/beta, hole/particle, generator).
+  .br
   3rd index is :
+  .br
   * 1 : hole     for single exc
-  * 1 : particle for single exc
+  .br
+  * 2 : particle for single exc
+  .br
   * 3 : hole     for 1st exc of double
+  .br
   * 4 : particle for 1st exc of double
-  * 5 : hole     for 2dn exc of double
+  .br
-  * 6 : particle for 2dn exc of double
+  * 5 : hole     for 2nd exc of double
+  .br
+  * 6 : particle for 2nd exc of double
+  .br
 
 `hf_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L44>`_
   Hartree Fock bit mask
 
-`i_bitmask_gen <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L186>`_
+`i_bitmask_gen <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L211>`_
   Current bitmask for the generators
 
-`i_bitmask_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L194>`_
+`inact_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L193>`_
-  Current bitmask for the reference
+  Bitmasks for the inactive orbitals that are excited in post CAS method
+
+`n_cas_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L143>`_
+  Number of bitmasks for CAS
 
 `n_generators_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L70>`_
   Number of bitmasks for generators
@@ -85,36 +115,31 @@ Documentation
 `n_int <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L3>`_
   Number of 64-bit integers needed to represent determinants as binary strings
 
-`n_reference_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L134>`_
-  Number of bitmasks for reference
-
 `ref_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L62>`_
   Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask
 
-`reference_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L164>`_
+`virt_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L194>`_
-  Bitmasks for reference determinants. (N_int, alpha/beta, hole/particle, reference)
+  Bitmasks for the inactive orbitals that are excited in post CAS method
 
-`bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L95>`_
+`bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L98>`_
   Transform a bit string to a string in hexadecimal format for printing
 
 `bitstring_to_list <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L1>`_
   Gives the inidices(+1) of the bits set to 1 in the bit string
 
-`bitstring_to_str <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L62>`_
+`bitstring_to_str <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L65>`_
   Transform a bit string to a string for printing
 
-`debug_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L117>`_
+`debug_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L120>`_
-  Undocumented
+  Subroutine to print the content of a determinant in '+-' notation and
+  hexadecimal representation.
 
 `list_to_bitstring <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L29>`_
-  return the physical string "string(N_int,2)" from the array of occupations "list(N_int*bit_kind_size,2)
+  Returns the physical string "string(N_int,2)" from the array of
-  list
+  occupations "list(N_int*bit_kind_size,2)
-  <== ipos ==>
+
-  |
+`print_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L138>`_
-  v
+  Subroutine to print the content of a determinant using the '+-' notation
-  string :|------------------------|-------------------------|------------------------|
-  <==== bit_kind_size ====> <==== bit_kind_size ====> <==== bit_kind_size ====>
-  {        iint            } {         iint         } {         iint         }
 
 
 

src/CAS_SD/EZFIO.cfg

@@ -8,7 +8,7 @@ default: 10000
 type: logical
 doc: If true, compute the PT2 at the end of the selection
 interface: input
-default: true
+default: True
 
 [PT2_max]
 type: PT2_energy

src/CAS_SD/README.rst

@@ -7,3 +7,38 @@ Selected CAS + SD module.
 1) Set the different MO classes using the ``qp_set_mo_class`` command
 2) Run the selected CAS+SD program
 
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/cas_sd_selected.irp.f#L1>`_
+  Undocumented
+
+
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
+* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+

src/CID/README.rst

@@ -16,19 +16,20 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 
 Documentation
 =============

src/CID_SC2_selected/README.rst

@@ -20,20 +20,21 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
-* `SC2 <http://github.com/LCPQ/quantum_package/tree/master/src/SC2>`_
 * `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

src/CID_selected/README.rst

@@ -23,19 +23,21 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 

src/CIS/README.rst

@@ -32,17 +32,18 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 

src/CISD/README.rst

@@ -16,19 +16,20 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 
 Documentation
 =============

src/CISD_SC2_selected/EZFIO.cfg

@@ -8,7 +8,7 @@ default: 10000
 type: logical
 doc: If true, compute the PT2 at the end of the selection
 interface: input
-default: true
+default: True
 
 [PT2_max]
 type: PT2_energy

src/CISD_SC2_selected/README.rst

@@ -8,6 +8,9 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+`cisd_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/cisd_sc2_selection.irp.f#L1>`_
+  Undocumented
+
 
 
 Needed Modules
@@ -17,20 +20,21 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
-* `SC2 <http://github.com/LCPQ/quantum_package/tree/master/src/SC2>`_
 * `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

src/CISD_selected/README.rst

@@ -14,6 +14,12 @@ Documentation
 `cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/cisd_selection.irp.f#L1>`_
   Undocumented
 
+`n_det_max_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/options.irp.f#L1>`_
+  Get n_det_max_cisd from EZFIO file
+
+`pt2_max <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/options.irp.f#L18>`_
+  Get pt2_max from EZFIO file
+
 
 
 Needed Modules
@@ -23,19 +29,21 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 

src/DDCI_selected/README.rst

@@ -2,3 +2,38 @@
 DDCI_selected Module
 ====================
 
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/ddci.irp.f#L1>`_
+  Undocumented
+
+
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
+* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+

src/Dets/README.rst

@@ -33,11 +33,10 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
@@ -50,18 +49,23 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L95>`_
+`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L100>`_
   Copies the H_apply buffer to psi_coef. You need to touch psi_det, psi_coef and N_det
   after calling this function.
+  After calling this subroutine, N_det, psi_det and psi_coef need to be touched
 
-`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L181>`_
+`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L187>`_
   Fill the H_apply buffer with determiants for CISD
 
-`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L14>`_
+`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L15>`_
   Buffer of determinants/coefficients/perturbative energy for H_apply.
   Uninitialized. Filled by H_apply subroutines.
 
-`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L45>`_
+`h_apply_buffer_lock <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L16>`_
+  Buffer of determinants/coefficients/perturbative energy for H_apply.
+  Uninitialized. Filled by H_apply subroutines.
+
+`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L48>`_
   Undocumented
 
 `cisd_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/SC2.irp.f#L1>`_
@@ -80,26 +84,43 @@ Documentation
   .br
   Initial guess vectors are not necessarily orthonormal
 
-`repeat_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/SC2.irp.f#L220>`_
+`connected_to_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L155>`_
   Undocumented
 
-`connected_to_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L95>`_
+`connected_to_ref_by_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L253>`_
   Undocumented
 
-`det_is_not_or_may_be_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L191>`_
+`det_is_not_or_may_be_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L359>`_
   If true, det is not in ref
   If false, det may be in ref
 
-`is_in_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L1>`_
+`det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L1>`_
-  Undocumented
+  Return an integer*8 corresponding to a determinant index for searching
 
-`key_pattern_not_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L225>`_
+`get_index_in_psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L48>`_
+  Returns the index of the determinant in the ``psi_det_sorted_bit`` array
+
+`is_in_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L34>`_
+  True if the determinant ``det`` is in the wave function
+
+`key_pattern_not_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L393>`_
   Min and max values of the integers of the keys of the reference
 
-`davidson_converged <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L383>`_
+`occ_pattern_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L17>`_
+  Return an integer*8 corresponding to a determinant index for searching
+
+`do_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/create_excitations.irp.f#L1>`_
+  Apply the mono excitation operator : a^{dager}_(i_particle) a_(i_hole) of spin = ispin
+  on key_in
+  ispin = 1  == alpha
+  ispin = 2  == beta
+  i_ok = 1  == the excitation is possible
+  i_ok = -1 == the excitation is not possible
+
+`davidson_converged <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L382>`_
   True if the Davidson algorithm is converged
 
-`davidson_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L373>`_
+`davidson_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L372>`_
   Can be : [  energy  | residual | both | wall_time | cpu_time | iterations ]
 
 `davidson_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L18>`_
@@ -146,10 +167,10 @@ Documentation
 `davidson_sze_max <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L9>`_
   Max number of Davidson sizes
 
-`davidson_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L374>`_
+`davidson_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L373>`_
   Can be : [  energy  | residual | both | wall_time | cpu_time | iterations ]
 
-`one_body_dm_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L73>`_
+`one_body_dm_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L164>`_
   One-body density matrix
 
 `one_body_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L1>`_
@@ -158,63 +179,162 @@ Documentation
 `one_body_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L2>`_
   Alpha and beta one-body density matrix for each state
 
-`save_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L97>`_
+`one_body_single_double_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L80>`_
+  Alpha and beta one-body density matrix for each state
+
+`one_body_single_double_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L81>`_
+  Alpha and beta one-body density matrix for each state
+
+`one_body_spin_density_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L172>`_
+  rho(alpha) - rho(beta)
+
+`save_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L196>`_
   Save natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis
 
-`set_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L81>`_
+`set_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L180>`_
   Set natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis
 
-`state_average_weight <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L108>`_
+`state_average_weight <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L207>`_
   Weights in the state-average calculation of the density matrix
 
-`det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L295>`_
+`det_svd <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/det_svd.irp.f#L1>`_
-  Return an integer*8 corresponding to a determinant index for searching
+  Computes the SVD of the Alpha x Beta determinant coefficient matrix
+
+`create_wf_of_psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L741>`_
+  Matrix of wf coefficients. Outer product of alpha and beta determinants
+
+`filter_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L552>`_
+  Returns a determinant with only the 3 highest electrons
+
+`generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L796>`_
+  Create a wave function from all possible alpha x beta determinants
+
+`int_of_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L517>`_
+  Returns an integer*8 as :
+  .br
+  |_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->|
+  .br
+  |0<---   i1    ---><---   i2    ---><---   i3    --->|
+  .br
+  It encodes the value of the indices of the 3 highest MOs
+  in descending order
+  .br
+
+`max_degree_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L32>`_
+  Maximum degree of excitation in the wf
 
 `n_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L3>`_
   Number of determinants in the wave function
 
-`psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L208>`_
+`n_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L348>`_
+  Unique alpha determinants
+
+`n_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L385>`_
+  Unique beta determinants
+
+`psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L276>`_
   Contribution of determinants to the state-averaged density
 
-`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L229>`_
+`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L432>`_
   Wave function sorted by determinants contribution to the norm (state-averaged)
 
-`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L153>`_
+`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L230>`_
   The wave function coefficients. Initialized with Hartree-Fock if the EZFIO file
   is empty
 
-`psi_coef_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L228>`_
+`psi_coef_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L431>`_
   Wave function sorted by determinants contribution to the norm (state-averaged)
 
-`psi_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L259>`_
+`psi_coef_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L579>`_
-  Determinants on which we apply <i|H|psi> for perturbation.
+  Determinants on which we apply <i|H|j>.
-  o They are sorted by determinants interpreted as integers. Useful
+  They are sorted by the 3 highest electrons in the alpha part,
-  to accelerate the search of a determinant
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
 
-`psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L53>`_
+`psi_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L462>`_
+  Determinants on which we apply <i|H|psi> for perturbation.
+  They are sorted by determinants interpreted as integers. Useful
+  to accelerate the search of a random determinant in the wave
+  function.
+
+`psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L65>`_
   The wave function determinants. Initialized with Hartree-Fock if the EZFIO file
   is empty
 
-`psi_det_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L35>`_
+`psi_det_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L319>`_
+  List of alpha determinants of psi_det
+
+`psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L347>`_
+  Unique alpha determinants
+
+`psi_det_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L333>`_
+  List of beta determinants of psi_det
+
+`psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L384>`_
+  Unique beta determinants
+
+`psi_det_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L47>`_
   Size of the psi_det/psi_coef arrays
 
-`psi_det_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L227>`_
+`psi_det_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L430>`_
   Wave function sorted by determinants contribution to the norm (state-averaged)
 
-`psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L258>`_
+`psi_det_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L578>`_
-  Determinants on which we apply <i|H|psi> for perturbation.
+  Determinants on which we apply <i|H|j>.
-  o They are sorted by determinants interpreted as integers. Useful
+  They are sorted by the 3 highest electrons in the alpha part,
-  to accelerate the search of a determinant
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
 
-`read_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L104>`_
+`psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L461>`_
+  Determinants on which we apply <i|H|psi> for perturbation.
+  They are sorted by determinants interpreted as integers. Useful
+  to accelerate the search of a random determinant in the wave
+  function.
+
+`psi_det_sorted_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L580>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+`psi_svd_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L826>`_
+  SVD wave function
+
+`psi_svd_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L827>`_
+  SVD wave function
+
+`psi_svd_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L828>`_
+  SVD wave function
+
+`psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L709>`_
+  Matrix of wf coefficients. Outer product of alpha and beta determinants
+
+`read_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L880>`_
   Reads the determinants from the EZFIO file
 
-`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L310>`_
+`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L927>`_
   Save the wave function into the EZFIO file
 
-`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L319>`_
+`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L946>`_
   Save the wave function into the EZFIO file
 
+`save_wavefunction_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L937>`_
+  Save the wave function into the EZFIO file
+
+`sort_dets_by_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L600>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+`sort_dets_by_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L475>`_
+  Determinants are sorted are sorted according to their det_search_key.
+  Useful to accelerate the search of a random determinant in the wave
+  function.
+
+`spin_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L303>`_
+  Return an integer*8 corresponding to a determinant index for searching
+
 `double_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L40>`_
   double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1
   double_exc_bitmask(:,2,i) is the bitmask for particles of excitation 1
@@ -233,10 +353,13 @@ Documentation
   single_exc_bitmask(:,2,i) is the bitmask for particles
   for a given couple of hole/particle excitations i.
 
-`ci_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L36>`_
+`ci_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L37>`_
   Eigenvectors/values of the CI matrix
 
-`ci_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L35>`_
+`ci_eigenvectors_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L38>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L36>`_
   Eigenvectors/values of the CI matrix
 
 `ci_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L18>`_
@@ -245,7 +368,7 @@ Documentation
 `diag_algorithm <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L1>`_
   Diagonalization algorithm (Davidson or Lapack)
 
-`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L73>`_
+`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L96>`_
   Replace the coefficients of the CI states by the coefficients of the
   eigenstates of the CI matrix
 
@@ -256,15 +379,31 @@ Documentation
   Eigenvectors/values of the CI matrix
 
 `ci_sc2_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L1>`_
-  N_states lowest eigenvalues of the CI matrix
+  N_states_diag lowest eigenvalues of the CI matrix
 
 `diagonalize_ci_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L46>`_
-  Replace the coefficients of the CI states by the coefficients of the
+  Replace the coefficients of the CI states_diag by the coefficients of the
   eigenstates of the CI matrix
 
 `threshold_convergence_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L18>`_
   convergence of the correlation energy of SC2 iterations
 
+`ci_eigenvectors_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L2>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_eigenvectors_s2_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L3>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_electronic_energy_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L1>`_
+  Eigenvectors/values of the CI matrix
+
+`diagonalize_ci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L59>`_
+  Replace the coefficients of the CI states by the coefficients of the
+  eigenstates of the CI matrix
+
+`apply_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/excitations_utils.irp.f#L1>`_
+  Undocumented
+
 `filter_connected <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L2>`_
   Filters out the determinants that are not connected by H
   .br
@@ -276,9 +415,16 @@ Documentation
   .br
   idx(0) is the number of determinants that interact with key1
 
-`filter_connected_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L101>`_
+`filter_connected_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L163>`_
   Filters out the determinants that are not connected by H
+  returns the array idx which contains the index of the
+  determinants in the array key1 that interact
+  via the H operator with key2.
   .br
+  idx(0) is the number of determinants that interact with key1
+  key1 should come from psi_det_sorted_ab.
+
+`filter_connected_i_h_psi0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L293>`_
   returns the array idx which contains the index of the
   .br
   determinants in the array key1 that interact
@@ -287,16 +433,7 @@ Documentation
   .br
   idx(0) is the number of determinants that interact with key1
 
-`filter_connected_i_h_psi0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L233>`_
+`filter_connected_i_h_psi0_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L392>`_
-  returns the array idx which contains the index of the
-  .br
-  determinants in the array key1 that interact
-  .br
-  via the H operator with key2.
-  .br
-  idx(0) is the number of determinants that interact with key1
-
-`filter_connected_i_h_psi0_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L332>`_
   standard filter_connected_i_H_psi but returns in addition
   .br
   the array of the index of the non connected determinants to key1
@@ -307,31 +444,156 @@ Documentation
   .br
   to repeat the excitations
 
+`filter_connected_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L101>`_
+  Filters out the determinants that are not connected by H
+  returns the array idx which contains the index of the
+  determinants in the array key1 that interact
+  via the H operator with key2.
+  idx(0) is the number of determinants that interact with key1
+  .br
+  Determinants are taken from the psi_det_sorted_ab array
+
+`put_gess <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/guess_triplet.irp.f#L1>`_
+  Undocumented
+
+`det_to_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L2>`_
+  Transform a determinant to an occupation pattern
+
+`make_s2_eigenfunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L251>`_
+  Undocumented
+
+`n_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L143>`_
+  array of the occ_pattern present in the wf
+  psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
+  psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
+
+`occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L42>`_
+  Generate all possible determinants for a give occ_pattern
+
+`occ_pattern_to_dets_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L20>`_
+  Number of possible determinants for a given occ_pattern
+
+`psi_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L142>`_
+  array of the occ_pattern present in the wf
+  psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
+  psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
+
+`rec_occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L102>`_
+  Undocumented
+
+`n_states_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/options.irp.f#L40>`_
+  Number of states to consider for the diagonalization
+
+`pouet <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/program_beginer_determinants.irp.f#L1>`_
+  Undocumented
+
+`routine <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/program_beginer_determinants.irp.f#L7>`_
+  Undocumented
+
+`idx_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L5>`_
+  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.
+
+`idx_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L62>`_
+  Set of determinants which are not part of the CAS, defined from the application
+  of the CAS bitmask on the determinants.
+  idx_non_cas gives the indice of the determinant in psi_det.
+
+`n_det_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L6>`_
+  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.
+
+`n_det_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L63>`_
+  Set of determinants which are not part of the CAS, defined from the application
+  of the CAS bitmask on the determinants.
+  idx_non_cas gives the indice of the determinant in psi_det.
+
+`psi_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L3>`_
+  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.
+
+`psi_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L4>`_
+  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.
+
+`psi_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L47>`_
+  CAS determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+`psi_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L46>`_
+  CAS determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+`psi_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L60>`_
+  Set of determinants which are not part of the CAS, defined from the application
+  of the CAS bitmask on the determinants.
+  idx_non_cas gives the indice of the determinant in psi_det.
+
+`psi_non_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L61>`_
+  Set of determinants which are not part of the CAS, defined from the application
+  of the CAS bitmask on the determinants.
+  idx_non_cas gives the indice of the determinant in psi_det.
+
+`psi_non_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L100>`_
+  CAS determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+`psi_non_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L99>`_
+  CAS determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L5>`_
+  Energy of the reference bitmask used in Slater rules
+
+`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L3>`_
+  Energy of the reference bitmask used in Slater rules
+
+`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L2>`_
+  Energy of the reference bitmask used in Slater rules
+
+`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L4>`_
+  Energy of the reference bitmask used in Slater rules
+
+`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L1>`_
+  Energy of the reference bitmask used in Slater rules
+
+`expected_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L48>`_
+  Expected value of S2 : S*(S+1)
+
 `get_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L1>`_
   Returns <S^2>
 
-`get_s2_u0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L46>`_
+`get_s2_u0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L82>`_
   Undocumented
 
+`s2_values <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L67>`_
+  array of the averaged values of the S^2 operator on the various states
+
 `s_z <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L36>`_
-  Undocumented
+  z component of the Spin
 
 `s_z2_sz <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L37>`_
+  z component of the Spin
+
+`prog_save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_casino.irp.f#L266>`_
+  Undocumented
+
+`save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_casino.irp.f#L1>`_
   Undocumented
 
 `save_dets_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L1>`_
   Undocumented
 
-`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L37>`_
+`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L48>`_
   Undocumented
 
 `save_natorb <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_natorb.irp.f#L1>`_
   Undocumented
 
-`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L721>`_
+`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L962>`_
   Needed for diag_H_mat_elem
 
-`ac_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L766>`_
+`ac_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1007>`_
   Needed for diag_H_mat_elem
 
 `decode_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L76>`_
@@ -341,10 +603,10 @@ Documentation
   s1,s2 : Spins (1:alpha, 2:beta)
   degree : Degree of excitation
 
-`det_connections <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L898>`_
+`det_connections <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1139>`_
-  .br
+  Build connection proxy between determinants
 
-`diag_h_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L659>`_
+`diag_h_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L900>`_
   Computes <i|H|i>
 
 `get_double_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L141>`_
@@ -356,16 +618,16 @@ Documentation
 `get_excitation_degree <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1>`_
   Returns the excitation degree between two determinants
 
-`get_excitation_degree_vector <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L575>`_
+`get_excitation_degree_vector <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L816>`_
   Applies get_excitation_degree to an array of determinants
 
 `get_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L274>`_
   Returns the excitation operator between two singly excited determinants and the phase
 
-`get_occ_from_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L814>`_
+`get_occ_from_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1055>`_
   Returns a list of occupation numbers from a bitstring
 
-`h_u_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L830>`_
+`h_u_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1071>`_
   Computes v_0 = H|u_0>
   .br
   n : number of determinants
@@ -375,10 +637,13 @@ Documentation
 `i_h_j <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L355>`_
   Returns <i|H|j> where i and j are determinants
 
-`i_h_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L491>`_
+`i_h_j_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L492>`_
+  Returns <i|H|j> where i and j are determinants
+
+`i_h_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L631>`_
   <key|H|psi> for the various Nstates
 
-`i_h_psi_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L527>`_
+`i_h_psi_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L713>`_
   <key|H|psi> for the various Nstate
   .br
   returns in addition
@@ -391,11 +656,33 @@ Documentation
   .br
   to repeat the excitations
 
-`n_con_int <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L890>`_
+`i_h_psi_sc2_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L760>`_
+  <key|H|psi> for the various Nstate
+  .br
+  returns in addition
+  .br
+  the array of the index of the non connected determinants to key1
+  .br
+  in order to know what double excitation can be repeated on key1
+  .br
+  idx_repeat(0) is the number of determinants that can be used
+  .br
+  to repeat the excitations
+
+`i_h_psi_sec_ord <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L666>`_
+  <key|H|psi> for the various Nstates
+
+`n_con_int <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1131>`_
   Number of integers to represent the connections between determinants
 
+`write_spindeterminants <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L1>`_
+  Undocumented
+
+`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/truncate_wf.irp.f#L1>`_
+  Undocumented
+
 `h_matrix_all_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/utils.irp.f#L1>`_
-  H matrix on the basis of the slater deter;inants defined by psi_det
+  H matrix on the basis of the slater determinants defined by psi_det
 
 
 

src/FCIdump/README.rst

@@ -4,3 +4,32 @@ FCIdump Module
 
 Interface for the `NECI <https://github.com/ghb24/NECI_STABLE>`_ Full-CI QMC program.
 
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`fcidump <http://github.com/LCPQ/quantum_package/tree/master/src/FCIdump/fcidump.irp.f#L1>`_
+  Undocumented
+
+
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+

src/Full_CI/EZFIO.cfg

@@ -14,7 +14,7 @@ default: 10000
 type: logical
 doc: If true, compute the PT2 at the end of the selection
 interface: input
-default: true
+default: True
 
 [PT2_max]
 type: PT2_energy

src/Full_CI/README.rst

@@ -10,7 +10,10 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/full_ci.irp.f#L1>`_
+`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/full_ci_no_skip.irp.f#L1>`_
+  Undocumented
+
+`var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/var_pt2_ratio.irp.f#L1>`_
   Undocumented
 
 
@@ -22,18 +25,20 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 

src/Generators_CAS/README.rst

@@ -3,3 +3,55 @@ Generators_CAS Module
 =====================
 
 The generator determinants are those filtered by the ``cas_bitmask`` mask.
+Assumptions
+===========
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+The active space is defined by the ``reference_bitmask``.
+
+
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L3>`_
+  Number of generator detetrminants
+
+`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L35>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L34>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L78>`_
+  Memo to skip useless selectors
+
+`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L70>`_
+  Size of the select_max array
+
+
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+

src/Generators_full/README.rst

@@ -11,20 +11,26 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L22>`_
+`degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L55>`_
+  Max degree of excitation (respect to HF) of the generators
+
+`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L15>`_
   For Single reference wave functions, the number of generators is 1 : the
   Hartree-Fock determinant
 
-`psi_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L44>`_
+`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L38>`_
   For Single reference wave functions, the generator is the
   Hartree-Fock determinant
 
-`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L60>`_
+`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L37>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L78>`_
   Memo to skip useless selectors
 
-`threshold_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L3>`_
+`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L70>`_
-  Percentage of the norm of the state-averaged wave function to
+  Size of the select_max array
-  consider for the generators
 
 
 
@@ -35,12 +41,13 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_

src/Hartree_Fock/README.rst

@@ -11,11 +11,12 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
@@ -36,16 +37,16 @@ Documentation
 `fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L83>`_
   Alpha Fock matrix in AO basis set
 
-`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L194>`_
+`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L231>`_
   Fock matrix on the MO basis
 
-`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L242>`_
+`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L289>`_
   Fock matrix in AO basis set
 
 `fock_matrix_beta_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L84>`_
   Alpha Fock matrix in AO basis set
 
-`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L214>`_
+`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L251>`_
   Fock matrix on the MO basis
 
 `fock_matrix_diag_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L2>`_
@@ -78,24 +79,30 @@ Documentation
   K = Fb - Fa
   .br
 
-`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L285>`_
+`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L332>`_
   Undocumented
 
-`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L233>`_
+`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L270>`_
   Hartree-Fock energy
 
 `hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L27>`_
-  Density matrix in the AO basis
+  S^-1 Density matrix in the AO basis S^-1
 
 `hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L1>`_
-  Alpha density matrix in the AO basis
+  S^-1 x Alpha density matrix in the AO basis x S^-1
 
 `hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L14>`_
-  Beta density matrix in the AO basis
+  S^-1 Beta density matrix in the AO basis x S^-1
 
-`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L7>`_
+`guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Huckel_guess.irp.f#L1>`_
   Undocumented
 
+`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L8>`_
+  Create an MO guess if no MOs are present in the EZFIO directory
+
+`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L33>`_
+  Run SCF calculation
+
 `scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L2>`_
   Undocumented
 
@@ -105,7 +112,7 @@ Documentation
 `diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
   Diagonal Fock matrix in the MO basis
 
-`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L57>`_
+`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L67>`_
   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
@@ -113,20 +120,8 @@ Documentation
 `eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
   Diagonal Fock matrix in the MO basis
 
-`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L5>`_
+`huckel_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/huckel.irp.f#L1>`_
-  Energy of the reference bitmask used in Slater rules
+  Build the MOs using the extended Huckel model
-
-`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L3>`_
-  Energy of the reference bitmask used in Slater rules
-
-`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L2>`_
-  Energy of the reference bitmask used in Slater rules
-
-`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L4>`_
-  Energy of the reference bitmask used in Slater rules
-
-`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L1>`_
-  Energy of the reference bitmask used in Slater rules
 
 
 

src/MOs/README.rst

@@ -23,11 +23,11 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 
 Documentation
 =============
@@ -45,29 +45,58 @@ Documentation
 `mo_density_matrix_virtual <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L64>`_
   Density matrix in MO basis (virtual MOs)
 
-`mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L22>`_
+`mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mo_overlap.irp.f#L2>`_
+  Undocumented
+
+`ao_to_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L126>`_
+  Transform A from the AO basis to the MO basis
+
+`mix_mo_jk <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L210>`_
+  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))
+
+`mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L28>`_
   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)
 
-`mo_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L60>`_
+`mo_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L71>`_
   Molecular orbital coefficients on AO basis set
 
-`mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L23>`_
+`mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L29>`_
   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)
 
-`mo_occ <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L78>`_
+`mo_occ <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L102>`_
   MO occupation numbers
 
+`mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L152>`_
+  Transform A from the MO basis to the AO basis
+
+`mo_to_ao_no_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L184>`_
+  Transform A from the MO basis to the S^-1 AO basis
+
 `mo_tot_num <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L1>`_
   Total number of molecular orbitals and the size of the keys corresponding
 
-`mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L12>`_
+`mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L18>`_
   Aligned variable for dimensioning of arrays
 
-`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L22>`_
+`s_mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L89>`_
+  Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix.
+
+`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L24>`_
+  Undocumented
+
+`mo_as_eigvectors_of_mo_matrix_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L62>`_
+  Undocumented
+
+`mo_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L144>`_
   Undocumented
 
 `save_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L1>`_

src/MP2/README.rst

@@ -8,7 +8,7 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/mp2.irp.f#L1>`_
+`mp2 <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/mp2.irp.f#L1>`_
   Undocumented
 
 
@@ -20,18 +20,20 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/MRCC/README.rst

@@ -5,5 +5,87 @@ MRCC Module
 Needed Modules
 ==============
 
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
+* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+
 Documentation
 =============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L1>`_
+  Undocumented
+
+`run <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L10>`_
+  Undocumented
+
+`run_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L42>`_
+  Undocumented
+
+`run_mrcc_test <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L29>`_
+  Undocumented
+
+`find_triples_and_quadruples <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L202>`_
+  Undocumented
+
+`mrcc_dress <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L15>`_
+  Undocumented
+
+`mrcc_dress_simple <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L156>`_
+  Undocumented
+
+`psi_cas_lock <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L3>`_
+  Locks on CAS determinants to fill delta_ij
+
+`ci_eigenvectors_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L79>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_eigenvectors_s2_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L80>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_electronic_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L78>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L132>`_
+  N_states lowest eigenvalues of the dressed CI matrix
+
+`delta_ij <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L43>`_
+  Dressing matrix in N_det basis
+
+`delta_ij_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L34>`_
+  Dressing matrix in SD basis
+
+`diagonalize_ci_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L147>`_
+  Replace the coefficients of the CI states by the coefficients of the
+  eigenstates of the CI matrix
+
+`dressing_type <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L26>`_
+  [ Simple | MRCC ]
+
+`h_matrix_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L63>`_
+  Dressed H with Delta_ij
+
+`lambda_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L2>`_
+  cm/<Psi_0|H|D_m>
+
+
+

src/Makefile

@@ -16,6 +16,10 @@ default: ezfio
 
 veryclean:
 	$(QPACKAGE_ROOT)/scripts/clean_modules.sh $(ALL_MODULES)
+	# Define the dict [type in EZFIO.cfg] = ocaml type , f90 type
+	# If you change the qptypes_generator.ml, you need to rm this
+	# For simplicity add this to the veryclean rule
+	rm $(QPACKAGE_ROOT)/scripts/ezfio_interface/fancy_type.p
 
 $(ALL_MODULES): ezfio
 	$(QPACKAGE_ROOT)/scripts/build_modules.sh $@ 

src/Molden/README.rst

@@ -2,3 +2,40 @@
 Molden Module
 =============
 
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`print_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Molden/print_mo.irp.f#L1>`_
+  Undocumented
+
+`write_ao_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Molden/print_mo.irp.f#L63>`_
+  Undocumented
+
+`write_geometry <http://github.com/LCPQ/quantum_package/tree/master/src/Molden/print_mo.irp.f#L45>`_
+  Undocumented
+
+`write_intro_gamess <http://github.com/LCPQ/quantum_package/tree/master/src/Molden/print_mo.irp.f#L26>`_
+  Undocumented
+
+`write_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Molden/print_mo.irp.f#L112>`_
+  Undocumented
+
+
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+

src/MonoInts/README.rst

@@ -18,30 +18,10 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`ao_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L122>`_
+`ao_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L1>`_
   array of the mono electronic hamiltonian on the AOs basis
   : sum of the kinetic and nuclear electronic potential
 
-`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L1>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
-`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L65>`_
-  Overlap between absolute value of atomic basis functions:
-  :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
-
-`ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L2>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
-`ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L3>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
-`ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L4>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
 `check_ortho <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/check_orthonormality.irp.f#L1>`_
   Undocumented
 
@@ -72,58 +52,63 @@ Documentation
   .br
   {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
 
-`ao_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L126>`_
+`ao_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L125>`_
   array of the priminitve basis kinetic integrals
   \langle \chi_i |\hat{T}| \chi_j \rangle
 
 `mo_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_mo_ints.irp.f#L1>`_
   Undocumented
 
-`mo_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L35>`_
+`mo_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L1>`_
   array of the mono electronic hamiltonian on the MOs basis
   : sum of the kinetic and nuclear electronic potential
 
-`mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L1>`_
-  Undocumented
-
 `orthonormalize_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/orthonormalize.irp.f#L1>`_
   Undocumented
 
 `ao_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L1>`_
   interaction nuclear electron
 
-`give_polynom_mult_center_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L161>`_
+`ao_nucl_elec_integral_per_atom <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L67>`_
+  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
+
+`give_polynom_mult_center_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L214>`_
   Undocumented
 
-`i_x1_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L289>`_
+`i_x1_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L342>`_
   Undocumented
 
-`i_x2_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L361>`_
+`i_x2_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L413>`_
   Undocumented
 
-`int_gaus_pol <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L432>`_
+`int_gaus_pol <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L484>`_
   Undocumented
 
-`nai_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L82>`_
+`nai_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L135>`_
   Undocumented
 
-`v_e_n <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L413>`_
+`v_e_n <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L465>`_
   Undocumented
 
-`v_phi <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L477>`_
+`v_phi <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L529>`_
   Undocumented
 
-`v_r <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L461>`_
+`v_r <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L513>`_
   Undocumented
 
-`v_theta <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L490>`_
+`v_theta <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L542>`_
   Undocumented
 
-`wallis <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L506>`_
+`wallis <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L558>`_
   Undocumented
 
 `mo_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_mo_ints.irp.f#L1>`_
-  Undocumented
+  interaction nuclear electron on the MO basis
+
+`mo_nucl_elec_integral_per_atom <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_mo_ints.irp.f#L30>`_
+  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
 
 `save_ortho_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/save_ortho_mos.irp.f#L1>`_
   Undocumented
@@ -173,7 +158,7 @@ Documentation
   array of the integrals of AO_i * y^2 AO_j
   array of the integrals of AO_i * z^2 AO_j
 
-`overlap_bourrin_deriv_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L359>`_
+`overlap_bourrin_deriv_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L365>`_
   Undocumented
 
 `overlap_bourrin_dipole <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L318>`_
@@ -182,7 +167,7 @@ Documentation
 `overlap_bourrin_spread <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L265>`_
   Undocumented
 
-`overlap_bourrin_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L374>`_
+`overlap_bourrin_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L380>`_
   Undocumented
 
 `overlap_bourrin_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L226>`_

src/Nuclei/README.rst

@@ -22,6 +22,9 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+`element_name <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L215>`_
+  Array of the name of element, sorted by nuclear charge (integer)
+
 `nucl_charge <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L23>`_
   Nuclear charges
 
@@ -65,8 +68,11 @@ Documentation
 `nucl_num_aligned <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L2>`_
   Number of nuclei
 
-`nuclear_repulsion <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L171>`_
+`nuclear_repulsion <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L187>`_
   Nuclear repulsion energy
 
+`positive_charge_barycentre <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L171>`_
+  Centroid of the positive charges
+
 
 

src/Output/README.rst

@@ -39,5 +39,23 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+`output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L2>`_
+  Initial CPU and wall times when printing in the output files
+
+`output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L1>`_
+  Initial CPU and wall times when printing in the output files
+
+`write_bool <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L88>`_
+  Write an logical value in output
+
+`write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L58>`_
+  Write a double precision value in output
+
+`write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L73>`_
+  Write an integer value in output
+
+`write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L42>`_
+  Write a time stamp in the output for chronological reconstruction
+
 
 

src/Selectors_full/README.rst

@@ -8,7 +8,18 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-`coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L27>`_
+`coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L28>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+`delta_e_per_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L33>`_
   energy of correlation per determinant respect to the Hartree Fock determinant
   .br
   for the all the double excitations in the selectors determinants
@@ -28,7 +39,29 @@ Documentation
   .br
   n_double_selectors = number of double excitations in the selectors determinants
 
-`e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L28>`_
+`e_corr_double_only <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L34>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+`e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L31>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+`e_corr_second_order <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L35>`_
   energy of correlation per determinant respect to the Hartree Fock determinant
   .br
   for the all the double excitations in the selectors determinants
@@ -48,6 +81,39 @@ Documentation
   .br
   n_double_selectors = number of double excitations in the selectors determinants
 
+`i_h_hf_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L32>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+`inv_selectors_coef_hf <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L29>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+`inv_selectors_coef_hf_squared <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L30>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
 `n_double_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L5>`_
   degree of excitation respect to Hartree Fock for the wave function
   .br
@@ -57,23 +123,40 @@ Documentation
   .br
   n_double_selectors = number of double excitations in the selectors determinants
 
-`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L26>`_
+`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L20>`_
   For Single reference wave functions, the number of selectors is 1 : the
   Hartree-Fock determinant
 
-`psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L48>`_
+`psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L42>`_
   Determinants on which we apply <i|H|psi> for perturbation.
 
-`psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L49>`_
+`psi_selectors_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L76>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+`psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L43>`_
   Determinants on which we apply <i|H|psi> for perturbation.
 
-`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L21>`_
+`psi_selectors_coef_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L77>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+`psi_selectors_diag_h_mat <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L63>`_
+  Diagonal elements of the H matrix for each selectors
+
+`psi_selectors_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L78>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L15>`_
   Undocumented
 
-`threshold_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L3>`_
-  Percentage of the norm of the state-averaged wave function to
-  consider for the selectors
-
 
 
 Needed Modules
@@ -83,12 +166,13 @@ Needed Modules
 .. NEEDED_MODULES file.
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_

src/Utils/README.rst

@@ -10,35 +10,104 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+`apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L168>`_
+  Apply the rotation found by find_rotation
+
+`find_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L149>`_
+  Find A.C = B
+
+`get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L95>`_
+  Find C = A^-1
+
+`lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L247>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+`lapack_diag_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L310>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+`lapack_diagd <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L180>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+`lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L376>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+`ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L1>`_
+  Compute C_new=C_old.S^-1/2 canonical orthogonalization.
+  .br
+  overlap : overlap matrix
+  .br
+  LDA : leftmost dimension of overlap array
+  .br
+  N : Overlap matrix is NxN (array is (LDA,N) )
+  .br
+  C : Coefficients of the vectors to orthogonalize. On exit,
+  orthogonal vectors
+  .br
+  LDC : leftmost dimension of C
+  .br
+  m : Coefficients matrix is MxN, ( array is (LDC,N) )
+  .br
+
+`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L433>`_
+  Undocumented
+
 `abort_all <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L1>`_
   If True, all the calculation is aborted
 
-`abort_here <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L10>`_
+`abort_here <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L11>`_
   If True, all the calculation is aborted
 
-`catch_signal <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L33>`_
+`catch_signal <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L30>`_
   What to do on Ctrl-C. If two Ctrl-C are pressed within 1 sec, the calculation if aborted.
 
-`trap_signals <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L18>`_
+`trap_signals <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L19>`_
   What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine.
 
-`add_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L243>`_
+`add_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L306>`_
   Add two polynomials
   D(t) =! D(t) +( B(t)+C(t))
 
-`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L271>`_
+`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L334>`_
   Add a polynomial multiplied by a constant
   D(t) =! D(t) +( cst * B(t))
 
-`f_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L345>`_
+`f_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L408>`_
   function that calculates the following integral
   \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx
 
-`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L121>`_
+`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L184>`_
   Gaussian product in 1D.
   e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
 
-`gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L163>`_
+`gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L226>`_
   Gaussian product in 1D.
   e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
 
@@ -50,106 +119,146 @@ Documentation
   * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
   * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
 
+`give_explicit_poly_and_gaussian_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L122>`_
+  Transforms the product of
+  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3)
+  exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) exp(-(r-Nucl_center)^2 gama
+  .br
+  into
+  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
+  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
+  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
+
 `give_explicit_poly_and_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L1>`_
   Transform the product of
   (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
   into
   fact_k  (x-x_P)^iorder(1)  (y-y_P)^iorder(2)  (z-z_P)^iorder(3) exp(-p(r-P)^2)
 
-`hermite <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L477>`_
+`hermite <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L540>`_
   Hermite polynomial
 
-`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L201>`_
+`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L264>`_
   Multiply two polynomials
   D(t) =! D(t) +( B(t)*C(t))
 
-`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L300>`_
+`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L363>`_
   Recenter two polynomials
 
-`rint <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L373>`_
+`rint <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L436>`_
   .. math::
   .br
   \int_0^1 dx \exp(-p x^2) x^n
   .br
 
-`rint1 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L533>`_
+`rint1 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L596>`_
   Standard version of rint
 
-`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L502>`_
+`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L565>`_
   Version of rint for large values of n
 
-`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L421>`_
+`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L484>`_
   Needed for the calculation of two-electron integrals.
 
+`overlap_a_b_c <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L35>`_
+  Undocumented
+
 `overlap_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L1>`_
   .. math::
   .br
   \sum_{-infty}^{+infty} (x-A_x)^ax (x-B_x)^bx exp(-alpha(x-A_x)^2) exp(-beta(x-B_X)^2) dx
   .br
 
-`overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L37>`_
+`overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L113>`_
   .. math::
   .br
   S_x = \int (x-A_x)^{a_x} exp(-\alpha(x-A_x)^2)  (x-B_x)^{b_x} exp(-beta(x-B_x)^2) dx \\
   S = S_x S_y S_z
   .br
 
-`overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L99>`_
+`overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L175>`_
   .. math                      ::
   .br
   \int_{-infty}^{+infty} (x-A_center)^(power_A) * (x-B_center)^power_B * exp(-alpha(x-A_center)^2) * exp(-beta(x-B_center)^2) dx
   .br
 
-`align_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L70>`_
+`progress_active <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L29>`_
+  Current status for displaying progress bars. Global variable.
+
+`progress_bar <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L27>`_
+  Current status for displaying progress bars. Global variable.
+
+`progress_timeout <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L28>`_
+  Current status for displaying progress bars. Global variable.
+
+`progress_title <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L31>`_
+  Current status for displaying progress bars. Global variable.
+
+`progress_value <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L30>`_
+  Current status for displaying progress bars. Global variable.
+
+`run_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L45>`_
+  Display a progress bar with documentation of what is happening
+
+`start_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L1>`_
+  Starts the progress bar
+
+`stop_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L19>`_
+  Stop the progress bar
+
+`align_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L48>`_
   Compute 1st dimension such that it is aligned for vectorization.
 
-`all_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L1>`_
+`approx_dble <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L341>`_
-  Dummy provider to provide all utils
-
-`approx_dble <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L299>`_
   Undocumented
 
-`binom <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L52>`_
+`binom <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L31>`_
   Binomial coefficients
 
-`binom_func <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L21>`_
+`binom_func <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L1>`_
   .. math                       ::
   .br
   \frac{i!}{j!(i-j)!}
   .br
 
-`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L53>`_
+`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L32>`_
   Binomial coefficients
 
-`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L129>`_
+`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L137>`_
   n!!
 
-`fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L85>`_
+`dble_logfact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L171>`_
+  n!!
+
+`fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L63>`_
   n!
 
-`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L117>`_
+`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L125>`_
   1/n!
 
-`inv_int <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L176>`_
+`inv_int <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L218>`_
   1/i
 
-`normalize <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L275>`_
+`logfact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L93>`_
+  n!
+
+`normalize <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L317>`_
   Normalizes vector u
   u is expected to be aligned in memory.
 
-`nproc <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L202>`_
+`nproc <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L244>`_
   Number of current OpenMP threads
 
-`u_dot_u <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L244>`_
+`u_dot_u <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L286>`_
   Compute <u|u>
 
-`u_dot_v <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L218>`_
+`u_dot_v <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L260>`_
   Compute <u|v>
 
-`wall_time <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L187>`_
+`wall_time <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L229>`_
   The equivalent of cpu_time, but for the wall time.
 
-`write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L162>`_
+`write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L204>`_
   Write the last git commit in file iunit.