Merge branch 'LCPQ-master'

.gitignore

@@ -6,3 +6,4 @@ build.ninja
 bin/
 lib/
 config/qp_create_ninja.pickle
+src/*/.gitignore

config/gfortran.cfg

@@ -10,7 +10,7 @@
 #
 #
 [COMMON]
-FC           : gfortran -ffree-line-length-none -I . -mavx
+FC           : gfortran -g -ffree-line-length-none -I .
 LAPACK_LIB   : -llapack -lblas
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32
@@ -35,7 +35,7 @@ OPENMP  : 1          ; Append OpenMP flags
 #                           -ffast-math and the Fortran-specific
 #                           -fno-protect-parens and -fstack-arrays.
 [OPT]
-FCFLAGS : -Ofast -g
+FCFLAGS : -Ofast 
 
 # Profiling flags
 #################

configure

@@ -7,15 +7,16 @@ Usage: configure <config_file> (--production | --development)
 
 Options:
 
-    config_file   A config file with all the information for the compilation
+    config_file   A config file with all the information for compiling.
                   Example config_files are given in config/
 
-   --production   You can only compile all the modules with this flag,
-                  but the compilation will be lighting fast
+   --production   You can only compile **all** the modules with this flag,
+                  but it will compile lighting fast.
+
+   --development  this will create a build.ninja for each directory which 
+                  contains a binary. In a second step you may compile them
+                  individually if you like.
 
-   --development  It will create a build.ninja for each directory
-                  who contains a binary, than you can compile then
-                  individualy if you want
 
 Examples:
 
@@ -163,7 +164,7 @@ def find_path(bin_, l_installed, var_for_qp_root=False):
 # | |_| | | (_  |_ | (_) | |
 #
 def check_output(*popenargs, **kwargs):
-    """Run command with arguments and return its output as a byte string.
+    """Run command with arguments and return its output as a string.
 
     Backported from Python 2.7 as it's implemented as pure python on stdlib.
 
@@ -189,7 +190,7 @@ def check_output(*popenargs, **kwargs):
 def checking(d_dependency):
     """
     For each key in d_dependency check if it
-    it avalabie or not
+    is avalabie or not
     """
 
     def check_python():
@@ -205,8 +206,8 @@ def checking(d_dependency):
 
     def check_availability(binary):
         """
-        If avalable return the path who can find the
-        binary else return 0
+        If avalable return the path where the binary 
+        can be found, else return 0
         """
 
         if binary == "python":
@@ -254,7 +255,7 @@ def checking(d_dependency):
 
     """
 
-    print "Checking what you need to install and what is it avalaible"
+    print "Checking what you need to install and what is avalaible"
     print ""
     l_installed = dict()
     l_needed = []
@@ -327,7 +328,7 @@ _|_ | | _>  |_ (_| | | (_|  |_ | (_) | |
     d_print = {
         "install_ninja": "Install ninja...",
         "build": "Creating build.ninja...",
-        "install": "Installing the dependency through ninja..."
+        "install": "Installing the dependencies with Ninja..."
     }
 
     length = max(map(len, d_print.values()))
@@ -486,7 +487,7 @@ def create_ninja_and_rc(l_installed):
             subprocess.check_call(" ".join(l), shell=True,stderr=dnull)
     except:
         print "[ FAIL ]"
-        print "Check the valididy of the config file provided ({0})".format(sys.argv[1])
+        print "Check the validity of the config file provided ({0})".format(sys.argv[1])
         print "Exit..."
         sys.exit(1)
 
@@ -498,6 +499,11 @@ def recommendation():
     path = join(QP_ROOT, "quantum_package.rc")
     print "Now :"
     print "   source {0}".format(path)
+    print ""
+    print "Then, install the modules you want to install using :"
+    print "    qp_install_module.py "
+    print ""
+    print "Finally :"
     print "   ninja"
     print "   make -C ocaml"
     print ""

ocaml/.gitignore

@@ -1,50 +1,47 @@
-.gitignore
-ezfio.ml
-Qptypes.ml
-qptypes_generator.byte
 _build
-qp_create_ezfio_from_xyz.native
-qp_set_ddci.native
-qp_print.native
-qp_edit.native
-qp_set_mo_class.native
-qp_basis_clean.native
-qp_run.native
-qp_edit.native
-test_mo_label.byte
-test_point3d.byte
-test_gto.byte
-test_excitation.byte
-test_determinants.byte
-test_basis.byte
-test_molecule.byte
-test_elements.byte
-test_bitlist.byte
-test_atom.byte
-test_mo_label
-test_point3d
-test_gto
-test_excitation
-test_determinants
-test_basis
-test_molecule
-test_elements
-test_bitlist
-test_atom
-qp_create_ezfio_from_xyz
-qp_set_ddci
-qp_print
-qp_edit
-qp_set_mo_class
-qp_basis_clean
-qp_run
-Input_determinants.ml
-Input_integrals_bielec.ml
-Input_pseudo.ml
-Input_perturbation.ml
-Input_hartree_fock.ml
-Input_properties.ml
-qp_edit.ml
-qp_edit
-qp_edit.native
+ezfio.ml
+.gitignore
 Input_auto_generated.ml
+Input_determinants.ml
+Input_hartree_fock.ml
+Input_integrals_bielec.ml
+Input_perturbation.ml
+Input_properties.ml
+Input_pseudo.ml
+qp_basis_clean
+qp_basis_clean.native
+qp_create_ezfio_from_xyz
+qp_create_ezfio_from_xyz.native
+qp_edit
+qp_edit.ml
+qp_edit.native
+qp_print
+qp_print.native
+qp_run
+qp_run.native
+qp_set_ddci
+qp_set_ddci.native
+qp_set_mo_class
+qp_set_mo_class.native
+qptypes_generator.byte
+Qptypes.ml
+test_atom
+test_atom.byte
+test_basis
+test_basis.byte
+test_bitlist
+test_bitlist.byte
+test_determinants
+test_determinants.byte
+test_elements
+test_elements.byte
+test_excitation
+test_excitation.byte
+test_gto
+test_gto.byte
+test_mo_label
+test_mo_label.byte
+test_molecule
+test_molecule.byte
+test_point3d
+test_point3d.byte

ocaml/Makefile

@@ -30,7 +30,7 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore
 	qp_edit.ml qp_edit qp_edit.native Input_auto_generated.ml;\
 	do \
 	   echo $$i ; \
-	done > .gitignore
+	done |sort | uniq > .gitignore
 
 executables: $(QP_ROOT)/data/executables
 

plugins/CAS_SD/README.rst

@@ -118,101 +118,69 @@ Documentation
   Undocumented
 
 
-`h_apply_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L536>`_
+`h_apply_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L414>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L3>`_
-  Undocumented
-
-
-`h_apply_cas_sd_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L118>`_
+`h_apply_cas_sd_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L96>`_
-  Undocumented
-
-
-`h_apply_cas_sd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L386>`_
+`h_apply_cas_sd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L269>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_pt2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L3171>`_
+`h_apply_cas_sd_pt2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2610>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2537>`_
-  Undocumented
-
-
-`h_apply_cas_sd_pt2_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2674>`_
+`h_apply_cas_sd_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2118>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_pt2_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2641>`_
-  Undocumented
-
-
-`h_apply_cas_sd_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2983>`_
+`h_apply_cas_sd_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2427>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2288>`_
+`h_apply_cas_sd_selected <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1872>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_selected_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1618>`_
-  Undocumented
-
-
-`h_apply_cas_sd_selected_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1757>`_
+`h_apply_cas_sd_selected_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1346>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1723>`_
-  Undocumented
-
-
-`h_apply_cas_sd_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L2086>`_
+`h_apply_cas_sd_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1675>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected_no_skip <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1397>`_
+`h_apply_cas_sd_selected_no_skip <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1128>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_cas_sd_selected_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L727>`_
-  Undocumented
-
-
-`h_apply_cas_sd_selected_no_skip_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L866>`_
+`h_apply_cas_sd_selected_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L602>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_cas_sd_selected_no_skip_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L832>`_
-  Undocumented
-
-
-`h_apply_cas_sd_selected_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L1195>`_
+`h_apply_cas_sd_selected_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CAS_SD/H_apply.irp.f_shell_22#L931>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/CIS/README.rst

@@ -48,3 +48,44 @@ Needed Modules
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
+* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`cis <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/super_ci.irp.f#L1>`_
+  Undocumented
+
+
+`h_apply_cis <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/H_apply.irp.f_shell_8#L414>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cis_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/H_apply.irp.f_shell_8#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cis_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/H_apply.irp.f_shell_8#L269>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`super_ci <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/super_ci.irp.f#L9>`_
+  Undocumented
+

plugins/CISD/.gitignore

@@ -20,7 +20,6 @@ Pseudo
 Selectors_full
 SingleRefMethod
 Utils
-cisd
 cisd_lapack
 ezfio_interface.irp.f
 irpf90.make

plugins/CISD/README.rst

@@ -42,3 +42,40 @@ Documentation
   particles.
   Assume N_int is already provided.
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
+* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`cisd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/cisd_lapack.irp.f#L1>`_
+  Undocumented
+
+
+`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L414>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD/H_apply.irp.f_shell_8#L269>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+

plugins/CISD/cisd.irp.f

@@ -14,6 +14,7 @@ program cisd
   enddo
 
   call save_wavefunction
+  call ezfio_set_cisd_energy(CI_energy(1))
 ! call CISD_SC2(psi_det,psi_coef,eigvalues,size(psi_coef,1),N_det,N_states,N_int)
 ! do i = 1, N_states
 !  print*,'eigvalues(i) = ',eigvalues(i)

plugins/CISD_selected/EZFIO.cfg

@@ -0,0 +1,10 @@
+[energy]
+type: double precision
+doc: Variational Selected CISD energy
+interface: ezfio
+
+[energy_pt2]
+type: double precision
+doc: Estimated CISD energy (including PT2)
+interface: ezfio
+

plugins/CISD_selected/README.rst

@@ -179,3 +179,197 @@ Needed Modules
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation>`_
+* `CISD <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`cisd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/cisd_selection.irp.f#L1>`_
+  Undocumented
+
+
+`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L414>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_8#L269>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f#L13>`_
+  Undocumented
+
+
+`h_apply_cisd_selection_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5931>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_delta_rho_one_point_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5405>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_delta_rho_one_point_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5734>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L5159>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_dipole_moment_z_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4633>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_dipole_moment_z_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4962>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3615>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4387>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_2x2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3861>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_2x2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L4190>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3089>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L3418>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2843>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2317>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2646>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L2071>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1545>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_no_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1874>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1299>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L773>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_epstein_nesbet_sc2_projected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1102>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L527>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_h_core_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_h_core_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L330>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L6703>`_
+  Calls H_apply on the HF determinant and selects all connected single and double
+  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
+
+
+`h_apply_cisd_selection_moller_plesset_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L6177>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cisd_selection_moller_plesset_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CISD_selected/H_apply.irp.f_shell_10#L6506>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+

plugins/CISD_selected/cisd_selection.irp.f

@@ -43,4 +43,6 @@ program cisd
   call diagonalize_CI
   deallocate(pt2,norm_pert,H_pert_diag)
     call save_wavefunction
+  call ezfio_set_cisd_selected_energy(CI_energy)
+  call ezfio_set_cisd_selected_energy_pt2(CI_energy+pt2)
 end

plugins/FCIdump/.gitignore

@@ -1,23 +1,23 @@
-# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-IRPF90_temp
-IRPF90_man
-irpf90_entities
-tags
-irpf90.make
-Makefile
-Makefile.depend
-.ninja_log
+# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
 .ninja_deps
-ezfio_interface.irp.f
-Ezfio_files
+.ninja_log
+AO_Basis
+Bitmask
 Determinants
+Electrons
+Ezfio_files
+IRPF90_man
+IRPF90_temp
+Integrals_Bielec
 Integrals_Monoelec
 MO_Basis
-Utils
-Pseudo
-Bitmask
-AO_Basis
-Electrons
+Makefile
+Makefile.depend
 Nuclei
-Integrals_Bielec
+Pseudo
+Utils
+ezfio_interface.irp.f
 fcidump
+irpf90.make
+irpf90_entities
+tags

plugins/FCIdump/README.rst

@@ -23,3 +23,22 @@ Needed Modules
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`fcidump <http://github.com/LCPQ/quantum_package/tree/master/plugins/FCIdump/fcidump.irp.f#L1>`_
+  Undocumented
+

plugins/Full_CI/.gitignore

@@ -1,32 +0,0 @@
-# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-.ninja_deps
-.ninja_log
-AO_Basis
-Bitmask
-Determinants
-Electrons
-Ezfio_files
-Generators_full
-Hartree_Fock
-IRPF90_man
-IRPF90_temp
-Integrals_Bielec
-Integrals_Monoelec
-MOGuess
-MO_Basis
-Makefile
-Makefile.depend
-Nuclei
-Perturbation
-Properties
-Pseudo
-Selectors_full
-Utils
-ezfio_interface.irp.f
-full_ci
-full_ci_no_skip
-irpf90.make
-irpf90_entities
-tags
-target_pt2
-var_pt2_ratio

plugins/Full_CI/README.rst

@@ -27,201 +27,137 @@ Documentation
   Undocumented
 
 
-`h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L673>`_
+`h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L527>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_fci_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3>`_
-  Undocumented
-
-
-`h_apply_fci_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L142>`_
+`h_apply_fci_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L108>`_
-  Undocumented
-
-
-`h_apply_fci_mono <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3329>`_
+`h_apply_fci_mono <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2744>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_fci_mono_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2657>`_
-  Undocumented
-
-
-`h_apply_fci_mono_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2796>`_
+`h_apply_fci_mono_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2216>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_mono_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2762>`_
-  Undocumented
-
-
-`h_apply_fci_mono_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3125>`_
+`h_apply_fci_mono_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2545>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L471>`_
+`h_apply_fci_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L330>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_no_skip <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2436>`_
+`h_apply_fci_no_skip <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1998>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_fci_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1766>`_
-  Undocumented
-
-
-`h_apply_fci_no_skip_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1905>`_
+`h_apply_fci_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1472>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_no_skip_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1871>`_
-  Undocumented
-
-
-`h_apply_fci_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2234>`_
+`h_apply_fci_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1801>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1556>`_
+`h_apply_fci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1265>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_fci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L922>`_
-  Undocumented
-
-
-`h_apply_fci_pt2_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1059>`_
+`h_apply_fci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L773>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_fci_pt2_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1026>`_
-  Undocumented
-
-
-`h_apply_fci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1368>`_
+`h_apply_fci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L1082>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5135>`_
+`h_apply_pt2_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4258>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_pt2_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4499>`_
-  Undocumented
-
-
-`h_apply_pt2_mono_delta_rho_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4636>`_
+`h_apply_pt2_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3764>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_mono_delta_rho_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4603>`_
-  Undocumented
-
-
-`h_apply_pt2_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4945>`_
+`h_apply_pt2_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4073>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L6898>`_
+`h_apply_pt2_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5729>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_pt2_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L6264>`_
-  Undocumented
-
-
-`h_apply_pt2_mono_di_delta_rho_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L6401>`_
+`h_apply_pt2_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5237>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_pt2_mono_di_delta_rho_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L6368>`_
-  Undocumented
-
-
-`h_apply_pt2_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L6710>`_
+`h_apply_pt2_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5546>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_select_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4250>`_
+`h_apply_select_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3518>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_select_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3578>`_
-  Undocumented
-
-
-`h_apply_select_mono_delta_rho_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3717>`_
+`h_apply_select_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L2990>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_select_mono_delta_rho_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3683>`_
-  Undocumented
-
-
-`h_apply_select_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4046>`_
+`h_apply_select_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L3319>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_select_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L6015>`_
+`h_apply_select_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4991>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_select_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5345>`_
-  Undocumented
-
-
-`h_apply_select_mono_di_delta_rho_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5484>`_
+`h_apply_select_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4465>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_select_mono_di_delta_rho_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5450>`_
-  Undocumented
-
-
-`h_apply_select_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L5813>`_
+`h_apply_select_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/Full_CI/H_apply.irp.f_shell_43#L4794>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.

plugins/Full_CI/target_pt2.irp.f

@@ -26,6 +26,9 @@ program var_pt2_ratio_run
     soft_touch N_det psi_det psi_coef
     call diagonalize_CI
     ratio = (CI_energy(1) - HF_energy) / (CI_energy(1)+pt2(1) - HF_energy)
+    if (N_det > 20000) then
+      exit
+    endif
   enddo
 
   threshold_selectors = 1.d0

plugins/Hartree_Fock/Fock_matrix.irp.f

@@ -111,18 +111,27 @@ END_PROVIDER
  integer*8                      :: p,q
  double precision               :: integral
  double precision               :: ao_bielec_integral
- if (do_direct_integrals) then
+ double precision, allocatable  :: ao_bi_elec_integral_alpha_tmp(:,:)
+ double precision, allocatable  :: ao_bi_elec_integral_beta_tmp(:,:)
+ !DIR$ ATTRIBUTES ALIGN : $IRP_ALIGN :: ao_bi_elec_integral_beta_tmp
+ !DIR$ ATTRIBUTES ALIGN : $IRP_ALIGN :: ao_bi_elec_integral_alpha_tmp
 
  ao_bi_elec_integral_alpha = 0.d0
  ao_bi_elec_integral_beta  = 0.d0
+ if (do_direct_integrals) then
+
    !$OMP PARALLEL DEFAULT(NONE)                                      &
-       !$OMP PRIVATE(i,j,l,k1,k,integral,ii,jj,kk,ll,i8,keys,values,p,q,r,s)&
-       !$OMP SHARED(ao_num,HF_density_matrix_ao_alpha,HF_density_matrix_ao_beta,&
+       !$OMP PRIVATE(i,j,l,k1,k,integral,ii,jj,kk,ll,i8,keys,values,p,q,r,s, &
+       !$OMP ao_bi_elec_integral_alpha_tmp,ao_bi_elec_integral_beta_tmp)&
+       !$OMP SHARED(ao_num,ao_num_align,HF_density_matrix_ao_alpha,HF_density_matrix_ao_beta,&
        !$OMP ao_integrals_map,ao_integrals_threshold, ao_bielec_integral_schwartz, &
-       !$OMP ao_overlap_abs) &
-       !$OMP REDUCTION(+:ao_bi_elec_integral_alpha,ao_bi_elec_integral_beta)
+       !$OMP ao_overlap_abs, ao_bi_elec_integral_alpha, ao_bi_elec_integral_beta)  
 
    allocate(keys(1), values(1))
+   allocate(ao_bi_elec_integral_alpha_tmp(ao_num_align,ao_num), &
+            ao_bi_elec_integral_beta_tmp(ao_num_align,ao_num))
+   ao_bi_elec_integral_alpha_tmp = 0.d0
+   ao_bi_elec_integral_beta_tmp  = 0.d0
 
    q = ao_num*ao_num*ao_num*ao_num
    !$OMP DO SCHEDULE(dynamic)
@@ -160,15 +169,21 @@ END_PROVIDER
              k = kk(k2)
              l = ll(k2)
              integral = (HF_density_matrix_ao_alpha(k,l)+HF_density_matrix_ao_beta(k,l)) * values(1)
-             ao_bi_elec_integral_alpha(i,j) += integral
-             ao_bi_elec_integral_beta (i,j) += integral
+             ao_bi_elec_integral_alpha_tmp(i,j) += integral
+             ao_bi_elec_integral_beta_tmp (i,j) += integral
              integral = values(1)
-             ao_bi_elec_integral_alpha(l,j) -= HF_density_matrix_ao_alpha(k,i) * integral
-             ao_bi_elec_integral_beta (l,j) -= HF_density_matrix_ao_beta (k,i) * integral
+             ao_bi_elec_integral_alpha_tmp(l,j) -= HF_density_matrix_ao_alpha(k,i) * integral
+             ao_bi_elec_integral_beta_tmp (l,j) -= HF_density_matrix_ao_beta (k,i) * integral
            enddo
    enddo
-   !$OMP END DO
-   deallocate(keys,values)
+   !$OMP END DO NOWAIT
+   !$OMP CRITICAL
+   ao_bi_elec_integral_alpha += ao_bi_elec_integral_alpha_tmp
+   !$OMP END CRITICAL
+   !$OMP CRITICAL
+   ao_bi_elec_integral_beta  += ao_bi_elec_integral_beta_tmp
+   !$OMP END CRITICAL
+   deallocate(keys,values,ao_bi_elec_integral_alpha_tmp,ao_bi_elec_integral_beta_tmp)
    !$OMP END PARALLEL
  else
    PROVIDE ao_bielec_integrals_in_map 
@@ -180,16 +195,18 @@ END_PROVIDER
    integer(key_kind), allocatable :: keys(:)
    double precision, allocatable  :: values(:)
 
-   ao_bi_elec_integral_alpha = 0.d0
-   ao_bi_elec_integral_beta  = 0.d0
    !$OMP PARALLEL DEFAULT(NONE)                                      &
-       !$OMP PRIVATE(i,j,l,k1,k,integral,ii,jj,kk,ll,i8,keys,values,n_elements_max,n_elements)&
-       !$OMP SHARED(ao_num,HF_density_matrix_ao_alpha,HF_density_matrix_ao_beta,&
-       !$OMP ao_integrals_map) &
-       !$OMP REDUCTION(+:ao_bi_elec_integral_alpha,ao_bi_elec_integral_beta)
+       !$OMP PRIVATE(i,j,l,k1,k,integral,ii,jj,kk,ll,i8,keys,values,n_elements_max, &
+       !$OMP  n_elements,ao_bi_elec_integral_alpha_tmp,ao_bi_elec_integral_beta_tmp)&
+       !$OMP SHARED(ao_num,ao_num_align,HF_density_matrix_ao_alpha,HF_density_matrix_ao_beta,&
+       !$OMP  ao_integrals_map, ao_bi_elec_integral_alpha, ao_bi_elec_integral_beta) 
 
    call get_cache_map_n_elements_max(ao_integrals_map,n_elements_max)
    allocate(keys(n_elements_max), values(n_elements_max))
+   allocate(ao_bi_elec_integral_alpha_tmp(ao_num_align,ao_num), &
+            ao_bi_elec_integral_beta_tmp(ao_num_align,ao_num))
+   ao_bi_elec_integral_alpha_tmp = 0.d0
+   ao_bi_elec_integral_beta_tmp  = 0.d0
 
    !$OMP DO SCHEDULE(dynamic)
    do i8=0_8,ao_integrals_map%map_size
@@ -207,16 +224,22 @@ END_PROVIDER
          k = kk(k2)
          l = ll(k2)
          integral = (HF_density_matrix_ao_alpha(k,l)+HF_density_matrix_ao_beta(k,l)) * values(k1)
-         ao_bi_elec_integral_alpha(i,j) += integral
-         ao_bi_elec_integral_beta (i,j) += integral
+         ao_bi_elec_integral_alpha_tmp(i,j) += integral
+         ao_bi_elec_integral_beta_tmp (i,j) += integral
          integral = values(k1)
-         ao_bi_elec_integral_alpha(l,j) -= HF_density_matrix_ao_alpha(k,i) * integral
-         ao_bi_elec_integral_beta (l,j) -= HF_density_matrix_ao_beta (k,i) * integral
+         ao_bi_elec_integral_alpha_tmp(l,j) -= HF_density_matrix_ao_alpha(k,i) * integral
+         ao_bi_elec_integral_beta_tmp (l,j) -= HF_density_matrix_ao_beta (k,i) * integral
        enddo
      enddo
    enddo
-   !$OMP END DO
-   deallocate(keys,values)
+   !$OMP END DO NOWAIT
+   !$OMP CRITICAL
+   ao_bi_elec_integral_alpha += ao_bi_elec_integral_alpha_tmp
+   !$OMP END CRITICAL
+   !$OMP CRITICAL
+   ao_bi_elec_integral_beta  += ao_bi_elec_integral_beta_tmp
+   !$OMP END CRITICAL
+   deallocate(keys,values,ao_bi_elec_integral_alpha_tmp,ao_bi_elec_integral_beta_tmp)
    !$OMP END PARALLEL
 
  endif

plugins/Hartree_Fock/README.rst

@@ -66,11 +66,11 @@ Documentation
   Alpha Fock matrix in AO basis set
 
 
-`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L231>`_
+`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L254>`_
   Fock matrix on the MO basis
 
 
-`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L289>`_
+`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L312>`_
   Fock matrix in AO basis set
 
 
@@ -78,7 +78,7 @@ Documentation
   Alpha Fock matrix in AO basis set
 
 
-`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L251>`_
+`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L274>`_
   Fock matrix on the MO basis
 
 
@@ -114,7 +114,7 @@ Documentation
   .br
 
 
-`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L332>`_
+`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L355>`_
   Undocumented
 
 
@@ -134,7 +134,7 @@ Documentation
   S^-1 Beta density matrix in the AO basis x S^-1
 
 
-`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L270>`_
+`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L293>`_
   Hartree-Fock energy
 
 

plugins/Hartree_Fock/damping_SCF.irp.f

@@ -30,9 +30,12 @@ subroutine damping_SCF
   
   call write_time(output_hartree_fock)
 
-  write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), '====','================','================','================', '===='
-  write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), '  N ', 'Energy  ', 'Energy diff  ', 'Density diff  ', 'Save'
-  write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), '====','================','================','================', '===='
+  write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), &
+    '====','================','================','================', '===='
+  write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), &
+    '  N ', 'Energy  ', 'Energy diff  ', 'Density diff  ', 'Save'
+  write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), &
+    '====','================','================','================', '===='
 
   E = HF_energy + 1.d0
   E_min = HF_energy

plugins/MRCC_Utils/README.rst

@@ -258,11 +258,7 @@ Documentation
   N_states lowest eigenvalues of the dressed CI matrix
 
 
-`create_minilist <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L17>`_
-  Undocumented
-
-
-`davidson_diag_hjj_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/davidson.irp.f#L59>`_
+`davidson_diag_hjj_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/davidson.irp.f#L56>`_
   Davidson diagonalization with specific diagonal elements of the H matrix
   .br
   H_jj : specific diagonal H matrix elements to diagonalize de Davidson
@@ -283,7 +279,7 @@ Documentation
   Initial guess vectors are not necessarily orthonormal
 
 
-`davidson_diag_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/davidson.irp.f#L4>`_
+`davidson_diag_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/davidson.irp.f#L1>`_
   Davidson diagonalization.
   .br
   dets_in : bitmasks corresponding to determinants
@@ -374,7 +370,7 @@ Documentation
   Find A.C = B
 
 
-`find_triples_and_quadruples <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L271>`_
+`find_triples_and_quadruples <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L206>`_
   Undocumented
 
 
@@ -435,26 +431,18 @@ Documentation
   Undocumented
 
 
-`h_apply_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L552>`_
+`h_apply_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L422>`_
   Calls H_apply on the HF determinant and selects all connected single and double
   excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
 
 
-`h_apply_mrcc_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L3>`_
-  Undocumented
-
-
-`h_apply_mrcc_diexcorg <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L126>`_
+`h_apply_mrcc_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L1>`_
   Generate all double excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
 
 
-`h_apply_mrcc_diexcp <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L100>`_
-  Undocumented
-
-
-`h_apply_mrcc_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L398>`_
+`h_apply_mrcc_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/H_apply.irp.f_shell_27#L273>`_
   Generate all single excitations of key_in using the bit masks of holes and
   particles.
   Assume N_int is already provided.
@@ -464,15 +452,7 @@ Documentation
   Dressed H with Delta_ij
 
 
-`h_u_0_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/davidson.irp.f#L385>`_
-  Computes v_0 = H|u_0>
-  .br
-  n : number of determinants
-  .br
-  H_jj : array of <j|H|j>
-
-
-`h_u_0_mrcc_org <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/davidson.irp.f#L489>`_
+`h_u_0_mrcc <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/davidson.irp.f#L360>`_
   Computes v_0 = H|u_0>
   .br
   n : number of determinants
@@ -777,11 +757,11 @@ Documentation
   n!
 
 
-`mrcc_dress <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L65>`_
+`mrcc_dress <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L15>`_
   Undocumented
 
 
-`mrcc_dress_simple <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L225>`_
+`mrcc_dress_simple <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L160>`_
   Undocumented
 
 
@@ -875,7 +855,7 @@ Documentation
   Current status for displaying progress bars. Global variable.
 
 
-`psi_ref_lock <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L4>`_
+`psi_ref_lock <http://github.com/LCPQ/quantum_package/tree/master/plugins/MRCC_Utils/mrcc_dress.irp.f#L3>`_
   Locks on ref determinants to fill delta_ij
 
 

plugins/Perturbation/README.rst

@@ -112,42 +112,42 @@ Documentation
   routine.
 
 
-`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L266>`_
+`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L56>`_
   Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L371>`_
+`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L266>`_
   Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L476>`_
+`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L371>`_
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L791>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L896>`_
   Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L686>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L791>`_
   Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L581>`_
+`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L686>`_
   Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L896>`_
+`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L476>`_
   Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L56>`_
+`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L581>`_
   Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
   routine.
 
@@ -157,42 +157,42 @@ Documentation
   routine.
 
 
-`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L215>`_
+`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L5>`_
   Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L320>`_
+`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L215>`_
   Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L425>`_
+`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L320>`_
   Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L740>`_
+`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L845>`_
   Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L635>`_
+`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L740>`_
   Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L530>`_
+`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L635>`_
   Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L845>`_
+`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L425>`_
   Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
   routine.
 
 
-`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L5>`_
+`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/plugins/Perturbation/perturbation.irp.f_shell_13#L530>`_
   Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
   routine.
 

plugins/QmcChem/README.rst

@@ -43,3 +43,44 @@ Needed Modules
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`ao_pseudo_grid <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/pot_ao_pseudo_ints.irp.f#L2>`_
+  Grid points for f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C
+  .br
+  <img src="http://latex.codecogs.com/gif.latex?f(|r-r_A|)&space;=&space;\int&space;Y_{lm}^{C}&space;(|r-r_C|,&space;\Omega_C)&space;\chi_i^{A}&space;(r-r_A)&space;d\Omega_C"
+  title="f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C" />
+
+
+`mo_pseudo_grid <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/pot_ao_pseudo_ints.irp.f#L56>`_
+  Grid points for f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \phi_i^{A} (r-r_A) d\Omega_C
+  .br
+  <img src="http://latex.codecogs.com/gif.latex?f(|r-r_A|)&space;=&space;\int&space;Y_{lm}^{C}&space;(|r-r_C|,&space;\Omega_C)&space;\chi_i^{A}&space;(r-r_A)&space;d\Omega_C"
+  title="f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C" />
+
+
+`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/save_for_qmcchem.irp.f#L1>`_
+  Undocumented
+
+
+`test_pseudo_grid_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/pot_ao_pseudo_ints.irp.f#L111>`_
+  Undocumented
+
+
+`write_pseudopotential <http://github.com/LCPQ/quantum_package/tree/master/plugins/QmcChem/pseudo.irp.f#L1>`_
+  Write the pseudo_potential into the EZFIO file
+

plugins/SingleRefMethod/README.rst

@@ -43,3 +43,41 @@ Needed Modules
 
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+.. image:: tree_dependency.png
+
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+
+`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod/generators.irp.f#L3>`_
+  For Single reference wave functions, the number of generators is 1 : the
+  Hartree-Fock determinant
+
+
+`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod/generators.irp.f#L13>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+
+`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod/generators.irp.f#L12>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+
+`select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod/generators.irp.f#L41>`_
+  Memo to skip useless selectors
+
+
+`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod/generators.irp.f#L49>`_
+  Size of select_max
+

scripts/get_basis.sh

@@ -8,6 +8,8 @@
 # Prints in stdout the name of a temporary file containing the basis set.
 #
 
+
+
 if [[ -z ${QP_ROOT} ]]
 then
   print "The QP_ROOT environment variable is not set."
@@ -15,6 +17,7 @@ then
   exit -1
 fi
 
+
 export EMSL_API_ROOT="${QP_ROOT}"/install/emsl
 
 tmpfile="$1"

scripts/module/qp_install_module.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 """
 Usage:
-       qp_install_module.py create -n <name> [<children_module>...]
+       qp_install_module.py create -n <name> [<children_modules>...]
        qp_install_module.py download -n <name> [<path_folder>...]
        qp_install_module.py install <name>...
        qp_install_module.py list (--installed | --available-local)
@@ -10,7 +10,7 @@ Usage:
 
 
 Options:
-    list: List all the module available
+    list: List all the modules available
     create: Create a new module
 """
 
@@ -25,8 +25,8 @@ try:
     from qp_update_readme import D_KEY
     from qp_path import QP_SRC, QP_PLUGINS, QP_ROOT
 except ImportError:
-    print "Please check if you have sourced the .quantum_package.rc"
-    print "(`source .quantum_package.rc`)"
+    print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc"
+    print "(`source ${QP_ROOT}/quantum_package.rc`)"
     print sys.exit(1)
 
 
@@ -39,7 +39,7 @@ def save_new_module(path, l_child):
     try:
         os.makedirs(path)
     except OSError:
-        print "The module ({0}) already exist...".format(path)
+        print "The module ({0}) already exists...".format(path)
         sys.exit(1)
 
     with open(os.path.join(path, "NEEDED_CHILDREN_MODULES"), "w") as f:
@@ -78,39 +78,41 @@ if __name__ == '__main__':
     elif arguments["create"]:
         m_instance = ModuleHandler([QP_SRC])
 
-        l_children = arguments["<children_module>"]
+        l_children = arguments["<children_modules>"]
 
         name = arguments["<name>"][0]
 
         path = os.path.join(QP_PLUGINS, name)
 
-        print "You will create the module:"
-        print path
+        print "Created module:"
+        print path, '\n'
 
         for children in l_children:
             if children not in m_instance.dict_descendant:
-                print "This module ({0}) is not a valide module.".format(children)
-                print "Run `list` flag for the list of module available"
-                print "Maybe you need to install some module first"
+                print "This module ({0}) is not a valid module.".format(children)
+                print "Run `list` for the list of available modules."
+                print "Maybe you need to install some other module first."
                 print "Aborting..."
                 sys.exit(1)
 
-        print "You ask for this submodule:"
-        print l_children
+        print "Needed module:"
+        print l_children, '\n'
 
-        print "You can use all the routine in this module"
-        print l_children + m_instance.l_descendant_unique(l_children)
+        print "This corresponds to using the following modules:"
+        print l_children + m_instance.l_descendant_unique(l_children), '\n'
 
-        print "This can be reduce to:"
+        print "Which is reduced to:"
         l_child_reduce = m_instance.l_reduce_tree(l_children)
-        print l_child_reduce
+        print l_child_reduce, '\n'
+
         print "Installation",
         save_new_module(path, l_child_reduce)
 
         print "    [ OK ]"
-        print "You can now install it normaly. Type:"
-        print "` {0} install {1} `".format(os.path.basename(__file__), name)
-        print "And don't forgot to add this to the git if you want"
+        print "Your module is created in the `plugins` directory."
+        print "You need to create some `.irp.f` to be able to install it."
+#        print "` {0} install {1} `".format(os.path.basename(__file__), name)
+        print ""
 
     elif arguments["download"]:
         pass
@@ -203,4 +205,5 @@ if __name__ == '__main__':
             try:
                 os.unlink(os.path.join(QP_SRC, module))
             except OSError:
-                print "%s is a core module which can not be renmoved" % module
+                print "%s is a core module which can't be removed" % module
+

scripts/save_current_mos.sh

@@ -4,6 +4,7 @@
 # directory, where xxx is the corresponding mo_label.
 # Wed Apr  2 14:35:15 CEST 2014
 
+
 if [[ -z ${QP_ROOT} ]]
 then
   print "The QP_ROOT environment variable is not set."
@@ -11,40 +12,40 @@ then
   exit -1
 fi
 
-EZFIO=$1
+EZFIO="$1"
 
-if [[ -z ${EZFIO} ]]
+if [[ -z "${EZFIO}" ]]
 then
   echo "Error in $0"
   exit 1
 fi
 
-if [[ ! -f ${EZFIO}/mo_basis/mo_label ]]
+if [[ ! -f "${EZFIO}/mo_basis/mo_label" ]]
 then
   LABEL='no_label'
 else
-  LABEL=$(head -1 ${EZFIO}/mo_basis/mo_label)
+  LABEL=$(head -1 "${EZFIO}/mo_basis/mo_label")
 fi
 
 DESTINATION="save/mo_basis/${LABEL}"
 
-cd ${EZFIO}
+cd "${EZFIO}"
 
 if [[ ! -d save/mo_basis ]]
 then
         mkdir -p save/mo_basis
 fi
 
-BACKUP=${DESTINATION}.old 
-if [[ -d ${BACKUP} ]]
+BACKUP="${DESTINATION}.old"
+if [[ -d "${BACKUP}" ]]
 then
-        rm -rf ${BACKUP}
+        rm -rf "${BACKUP}"
 fi
 
-if [[ -d ${DESTINATION} ]]
+if [[ -d "${DESTINATION}" ]]
 then
-        mv ${DESTINATION} ${BACKUP}
+        mv "${DESTINATION}" "${BACKUP}"
 fi
 
-cp -r mo_basis ${DESTINATION}
+cp -r mo_basis "${DESTINATION}"
 

src/Determinants/.gitignore

@@ -1,27 +0,0 @@
-# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-.ninja_deps
-.ninja_log
-AO_Basis
-Bitmask
-Electrons
-Ezfio_files
-IRPF90_man
-IRPF90_temp
-Integrals_Bielec
-Integrals_Monoelec
-MO_Basis
-Makefile
-Makefile.depend
-Nuclei
-Pseudo
-Utils
-ezfio_interface.irp.f
-guess_doublet
-guess_singlet
-guess_triplet
-irpf90.make
-irpf90_entities
-program_initial_determinants
-save_natorb
-tags
-truncate_wf

src/Determinants/H_apply.template.f

@@ -102,15 +102,38 @@ subroutine $subroutine_diexcP(key_in, fs1, fh1, particl_1, fs2, fh2, particl_2,
   integer                               :: n_minilist, n_alpha, n_beta, deg(2), i, ni
   $declarations
   
-  p1_mask(:,:) = 0
-  p2_mask(:,:) = 0
+  p1_mask(:,:) = 0_bit_kind
+  p2_mask(:,:) = 0_bit_kind
   p1_mask(ishft(fh1,-bit_kind_shift) + 1, fs1) = ishft(1,iand(fh1-1,bit_kind_size-1))
   p2_mask(ishft(fh2,-bit_kind_shift) + 1, fs2) = ishft(1,iand(fh2-1,bit_kind_size-1))
   
   key_mask(:,:) = key_in(:,:)
+
   key_mask(ishft(fh1,-bit_kind_shift) + 1, fs1) -= ishft(1,iand(fh1-1,bit_kind_size-1))
   key_mask(ishft(fh2,-bit_kind_shift) + 1, fs2) -= ishft(1,iand(fh2-1,bit_kind_size-1))
 
+!   do i=1,N_int
+!     n_alpha = n_alpha + popcnt(key_mask(i, 1))
+!     n_beta = n_beta + popcnt(key_mask(i, 2))
+!   end do
+!   
+!   do i=1, N_det
+!     deg(1) = n_alpha
+!     deg(2) = n_beta
+!     
+!     do ni = 1, N_int
+! !       deg(1) = deg(1) - popcnt(iand(key_mask(ni, 1), psi_non_ref(ni, 1, i)))
+! !       deg(2) = deg(2) - popcnt(iand(key_mask(ni, 2), psi_non_ref(ni, 2, i)))
+!     end do
+!     
+!     
+!     if(deg(1) + deg(2) <= 2) then
+! !       ndet_out = ndet_out + 1
+! !       idx(ndet_out) = i
+!     end if
+!   end do
+>>>>>>> 9107aee5ac0e251a0c91d82ef9c686fcef599fb5
+
   call $subroutine_diexcOrg(key_in, key_mask, p1_mask, particl_1, p2_mask, particl_2, i_generator, iproc_in $parameters )
 end subroutine
 
@@ -412,7 +435,7 @@ subroutine $subroutine_monoexc(key_in, hole_1,particl_1,i_generator,iproc_in $pa
   
   logical :: check_double_excitation 
   
-  key_mask(:,:) = 0_8
+  key_mask(:,:) = 0_bit_kind
   
   iproc = iproc_in
 

src/Determinants/README.rst

@@ -54,7 +54,11 @@ Documentation
 .. by the `update_README.py` script.
 
 
+`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1108>`_
   Needed for diag_H_mat_elem
+
+
+`abs_psi_coef_max <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L451>`_
   Max and min values of the coefficients
 
 

src/Determinants/slater_rules.irp.f

@@ -962,7 +962,7 @@ subroutine get_excitation_degree_vector(key1,key2,degree,Nint,sze,idx)
   integer, intent(out)           :: degree(sze)
   integer, intent(out)           :: idx(0:sze)
   
-  integer                        :: i,l,d
+  integer                        :: i,l,d,m
   
   ASSERT (Nint > 0)
   ASSERT (sze > 0)
@@ -1025,9 +1025,9 @@ subroutine get_excitation_degree_vector(key1,key2,degree,Nint,sze,idx)
     do i=1,sze
       d = 0
       !DEC$ LOOP COUNT MIN(4)
-      do l=1,Nint
-        d = d + popcnt(xor( key1(l,1,i), key2(l,1)))                 &
-              + popcnt(xor( key1(l,2,i), key2(l,2)))
+      do m=1,Nint
+        d = d + popcnt(xor( key1(m,1,i), key2(m,1)))                 &
+              + popcnt(xor( key1(m,2,i), key2(m,2)))
       enddo
       if (d > 4) then
         cycle

src/Ezfio_files/README.rst

@@ -203,8 +203,8 @@ Documentation
   Output file for Bitmask
 
 
-`output_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
-  Output file for CAS_SD
+`output_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
+  Output file for CISD
 
 
 `output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L2>`_
@@ -227,42 +227,42 @@ Documentation
   Output file for Full_CI
 
 
-`output_generators_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
-  Output file for Generators_CAS
-
-
-`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
+`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
   Output file for Generators_full
 
 
-`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
+`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
   Output file for Hartree_Fock
 
 
-`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
+`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
   Output file for Integrals_Bielec
 
 
-`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
+`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
   Output file for Integrals_Monoelec
 
 
-`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
+`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
   Output file for MO_Basis
 
 
-`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
+`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
   Output file for MOGuess
 
 
-`output_mrcc_cassd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
+`output_mrcc_cassd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
   Output file for MRCC_CASSD
 
 
-`output_mrcc_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
+`output_mrcc_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
   Output file for MRCC_Utils
 
 
+`output_myhartreefock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
+  Output file for MyHartreeFock
+
+
 `output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
   Output file for Nuclei
 
@@ -291,7 +291,11 @@ Documentation
   Output file for Selectors_full
 
 
-`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L461>`_
+`output_singlerefmethod <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L461>`_
+  Output file for SingleRefMethod
+
+
+`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L481>`_
   Output file for Utils
 
 

src/Integrals_Bielec/read_write.irp.f

@@ -20,7 +20,13 @@ implicit none
         read_ao_integrals = .False.
         write_ao_integrals = .False.
 
-    else if (disk_access_mo_integrals.EQ.'Read') then
+    else
+        print *, 'bielec_integrals/disk_access_ao_integrals has a wrong type'
+        stop 1
+
+    endif
+
+    if (disk_access_mo_integrals.EQ.'Read') then
         read_mo_integrals =  .True.
         write_mo_integrals = .False.
 
@@ -33,8 +39,8 @@ implicit none
         write_mo_integrals = .False.
 
     else
-        print *, 'bielec_integrals/disk_acces not of a the good type'
-        stop "1"
+        print *, 'bielec_integrals/disk_access_mo_integrals has a wrong type'
+        stop 1
 
     endif