Merge lpqsv26:/home/caffarel/quantum_package

2024-12-22 20:35:19 +01:00 · 2015-12-04 20:08:25 +01:00 · 2015-12-04 20:08:25 +01:00 · 989b087f59
commit 989b087f59
parent cdf11866c4 df6ca0ee05
25 changed files with 221 additions and 166 deletions
--- a/2
+++ b/2
@ -134,7 +134,7 @@ ezfio = Info(
    default_path=join(QP_ROOT_INSTALL, "EZFIO"))

 zeromq = Info(
-    url='http://download.zeromq.org/zeromq-4.1.3.tar.gz',
+    url='http://download.zeromq.org/zeromq-4.0.7.tar.gz',
    description=' ZeroMQ',
    default_path=join(QP_ROOT_LIB, "libzmq.a"))

--- a/install/scripts/install_zeromq.sh
+++ b/install/scripts/install_zeromq.sh
@ -14,12 +14,15 @@ function _install()
  cd "${BUILD}"
  ./configure --without-libsodium || exit 1
  make -j 8 || exit 1
-  rm -f -- "${QP_ROOT}"/lib/libzmq.a "${QP_ROOT}"/lib/libzmq.so "${QP_ROOT}"/lib/libzmq.so.5
-  cp .libs/libzmq.a  "${QP_ROOT}"/lib 
-  cp .libs/libzmq.so "${QP_ROOT}"/lib/libzmq.so.5
+  rm -f -- "${QP_ROOT}"/lib/libzmq.a "${QP_ROOT}"/lib/libzmq.so "${QP_ROOT}"/lib/libzmq.so.?
+# cp .libs/libzmq.a  "${QP_ROOT}"/lib 
+# cp .libs/libzmq.so "${QP_ROOT}"/lib/libzmq.so.5
+  cp src/.libs/libzmq.a  "${QP_ROOT}"/lib 
+  cp src/.libs/libzmq.so "${QP_ROOT}"/lib/libzmq.so.4
  cp include/{zmq.h,zmq_utils.h} "${QP_ROOT}"/lib
  cd "${QP_ROOT}"/lib
-  ln -s libzmq.so.5 libzmq.so
+# ln -s libzmq.so.5 libzmq.so
+  ln -s libzmq.so.4 libzmq.so
  cd ${ORIG}
  return 0
 }
--- a/ocaml/qp_edit.ml
+++ b/ocaml/qp_edit.ml
@ -17,12 +17,12 @@ type keyword =
 | Electrons
 | Mo_basis
 | Nuclei
-| Determinants
-| Hartree_fock
-| Integrals_bielec
 | Perturbation
-| Properties
+| Hartree_fock
 | Pseudo
+| Integrals_bielec
+| Determinants
+| Properties
 ;;


@ -32,12 +32,12 @@ let keyword_to_string = function
 | Electrons             -> "Electrons"
 | Mo_basis              -> "MO basis"
 | Nuclei                -> "Molecule"
-| Determinants -> "Determinants"
-| Hartree_fock -> "Hartree_fock"
-| Integrals_bielec -> "Integrals_bielec"
 | Perturbation -> "Perturbation"
-| Properties -> "Properties"
+| Hartree_fock -> "Hartree_fock"
 | Pseudo -> "Pseudo"
+| Integrals_bielec -> "Integrals_bielec"
+| Determinants -> "Determinants"
+| Properties -> "Properties"
 ;;


@ -86,18 +86,18 @@ let get s =
           f Ao_basis.(read, to_rst)
         | Determinants_by_hand ->
           f Determinants_by_hand.(read, to_rst)
-         | Determinants ->
-           f Determinants.(read, to_rst)
-         | Hartree_fock ->
-           f Hartree_fock.(read, to_rst)
-         | Integrals_bielec ->
-           f Integrals_bielec.(read, to_rst)
         | Perturbation ->
           f Perturbation.(read, to_rst)
-         | Properties ->
-           f Properties.(read, to_rst)
+         | Hartree_fock ->
+           f Hartree_fock.(read, to_rst)
         | Pseudo ->
           f Pseudo.(read, to_rst)
+         | Integrals_bielec ->
+           f Integrals_bielec.(read, to_rst)
+         | Determinants ->
+           f Determinants.(read, to_rst)
+         | Properties ->
+           f Properties.(read, to_rst)
      end
    with
    | Sys_error msg -> (Printf.eprintf "Info: %s\n%!" msg ; "")
@ -135,12 +135,12 @@ let set str s =
      in
      let open Input in
        match s with
-        | Determinants -> write Determinants.(of_rst, write) s
-        | Hartree_fock -> write Hartree_fock.(of_rst, write) s
-        | Integrals_bielec -> write Integrals_bielec.(of_rst, write) s
        | Perturbation -> write Perturbation.(of_rst, write) s
-        | Properties -> write Properties.(of_rst, write) s
+        | Hartree_fock -> write Hartree_fock.(of_rst, write) s
        | Pseudo -> write Pseudo.(of_rst, write) s
+        | Integrals_bielec -> write Integrals_bielec.(of_rst, write) s
+        | Determinants -> write Determinants.(of_rst, write) s
+        | Properties -> write Properties.(of_rst, write) s
        | Electrons        -> write Electrons.(of_rst, write) s
        | Determinants_by_hand     -> write Determinants_by_hand.(of_rst, write) s
        | Nuclei           -> write Nuclei.(of_rst, write) s
@ -188,12 +188,12 @@ let run check_only ezfio_filename =
      Nuclei ;
      Ao_basis;
      Electrons ;
-      Determinants ; 
-      Hartree_fock ; 
-      Integrals_bielec ; 
      Perturbation ; 
-      Properties ; 
+      Hartree_fock ; 
      Pseudo ; 
+      Integrals_bielec ; 
+      Determinants ; 
+      Properties ; 
      Mo_basis;
      Determinants_by_hand ;
  ]
@ -212,7 +212,7 @@ let run check_only ezfio_filename =
  match check_only with
  | true  -> ()
  | false -> 
-    Printf.sprintf "%s %s ; tput sgr0 2> /dev/null" editor temp_filename 
+    Printf.sprintf "%s %s" editor temp_filename 
    |> Sys.command_exn 
  ;

--- a/plugins/CISD/.gitignore
+++ b/plugins/CISD/.gitignore
@ -20,6 +20,7 @@ Pseudo
 Selectors_full
 SingleRefMethod
 Utils
+ZMQ
 cisd
 cisd_lapack
 ezfio_interface.irp.f
--- a/plugins/CISD_selected/.gitignore
+++ b/plugins/CISD_selected/.gitignore
@ -23,6 +23,7 @@ Pseudo
 Selectors_full
 SingleRefMethod
 Utils
+ZMQ
 cisd_selection
 ezfio_interface.irp.f
 irpf90.make
--- a/plugins/CISD_selected/README.rst
+++ b/plugins/CISD_selected/README.rst
@ -196,6 +196,10 @@ Documentation
 .. 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
  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.
--- a/plugins/FCIdump/.gitignore
+++ b/plugins/FCIdump/.gitignore
@ -16,6 +16,7 @@ Makefile.depend
 Nuclei
 Pseudo
 Utils
+ZMQ
 ezfio_interface.irp.f
 fcidump
 irpf90.make
--- a/plugins/Full_CI/.gitignore
+++ b/plugins/Full_CI/.gitignore
@ -22,6 +22,7 @@ Properties
 Pseudo
 Selectors_full
 Utils
+ZMQ
 ezfio_interface.irp.f
 full_ci
 full_ci_no_skip
--- a/plugins/Hartree_Fock/.gitignore
+++ b/plugins/Hartree_Fock/.gitignore
@ -18,6 +18,7 @@ Nuclei
 Pseudo
 SCF
 Utils
+ZMQ
 ezfio_interface.irp.f
 irpf90.make
 irpf90_entities
--- a/plugins/Hartree_Fock/README.rst
+++ b/plugins/Hartree_Fock/README.rst
@ -52,7 +52,7 @@ Documentation
  Diagonal Fock matrix in the MO basis


-`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/diagonalize_fock.irp.f#L67>`_
+`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/diagonalize_fock.irp.f#L112>`_
  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
@ -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#L375>`_
+`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/plugins/Hartree_Fock/Fock_matrix.irp.f#L392>`_
  Undocumented


--- a/plugins/MP2/.gitignore
+++ b/plugins/MP2/.gitignore
@ -22,8 +22,10 @@ Pseudo
 Selectors_full
 SingleRefMethod
 Utils
+ZMQ
 ezfio_interface.irp.f
 irpf90.make
 irpf90_entities
 mp2
+mp2_wf
 tags
--- a/plugins/MP2/README.rst
+++ b/plugins/MP2/README.rst
@ -83,6 +83,35 @@ h_apply_mp2_monoexc
  Assume N_int is already provided.


+h_apply_mp2_selection
+  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_mp2_selection_diexc
+  Undocumented
+
+
+h_apply_mp2_selection_diexcorg
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+h_apply_mp2_selection_diexcp
+  Undocumented
+
+
+h_apply_mp2_selection_monoexc
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
 `mp2 <http://github.com/LCPQ/quantum_package/tree/master/plugins/MP2/mp2.irp.f#L1>`_
  Undocumented

+
+`mp2_wf <http://github.com/LCPQ/quantum_package/tree/master/plugins/MP2/mp2_wf.irp.f#L1>`_
+  Save the MP2 wave function
+
--- a/plugins/MRCC_Utils/mrcc_dress.irp.f
+++ b/plugins/MRCC_Utils/mrcc_dress.irp.f
@ -14,54 +14,6 @@ BEGIN_PROVIDER [ integer(omp_lock_kind), psi_ref_lock, (psi_det_size) ]
 END_PROVIDER


-! subroutine create_minilist(key_mask, fullList, miniList, idx_miniList, N_fullList, N_miniList, Nint)
-!   use bitmasks
-!   implicit none
-!   
-!   integer(bit_kind), intent(in)            :: fullList(Nint, 2, N_fullList)
-!   integer, intent(in)                      :: N_fullList
-!   integer(bit_kind),intent(out)            :: miniList(Nint, 2, N_fullList)
-!   integer,intent(out)                      :: idx_miniList(N_fullList), N_miniList
-!   integer, intent(in)                      :: Nint
-!   integer(bit_kind)                        :: key_mask(Nint, 2)
-!   integer                                  :: ni, i, n_a, n_b, e_a, e_b
-!   
-!   
-!   n_a = 0
-!   n_b = 0
-!   do ni=1,nint
-!     n_a = n_a + popcnt(key_mask(ni,1))
-!     n_b = n_b + popcnt(key_mask(ni,2))
-!   end do
-!   
-!   if(n_a == 0) then
-!     N_miniList = N_fullList
-!     miniList(:,:,:) = fullList(:,:,:)
-!     do i=1,N_fullList
-!       idx_miniList(i) = i
-!     end do
-!     return
-!   end if
-!   
-!   N_miniList = 0
-!   
-!   do i=1,N_fullList
-!     e_a = n_a
-!     e_b = n_b
-!     do ni=1,nint
-!       e_a -= popcnt(iand(fullList(ni, 1, i), key_mask(ni, 1)))
-!       e_b -= popcnt(iand(fullList(ni, 2, i), key_mask(ni, 2)))
-!     end do
-!     
-!     if(e_a + e_b <= 2) then
-!       N_miniList = N_miniList + 1
-!       miniList(:,:,N_miniList) = fullList(:,:,i)
-!       idx_miniList(N_miniList) = i
-!     end if
-!   end do
-! end subroutine
-
-
 subroutine mrcc_dress(delta_ij_, delta_ii_, Ndet_ref, Ndet_non_ref,i_generator,n_selected,det_buffer,Nint,iproc,key_mask)
 use bitmasks
 implicit none
@ -273,22 +225,9 @@ subroutine find_triples_and_quadruples(i_generator,n_selected,det_buffer,Nint,tq
  
  
  i_loop : do i=1,N_selected
-    if(is_connected_to(det_buffer(ni,1,i), miniList, Nint, N_miniList)) then
+    if(is_connected_to(det_buffer(1,1,i), miniList, Nint, N_miniList)) then
      cycle
    end if
-!     do j=1,N_miniList
-!       nt = 0
-!       do ni=1,Nint
-!         nt += popcnt(xor(miniList(ni,1,j), det_buffer(ni,1,i))) + popcnt(xor(miniList(ni,2,j), det_buffer(ni,2,i)))
-!       end do
-!       if(nt <= 4) then
-!         cycle i_loop
-!       end if
-!     end do
-!     if(connected_to_ref(det_buffer(1,1,i),psi_det_generators,Nint, &
-!        i_generator,N_det_generators) /= 0) then
-!         cycle i_loop
-!     end if

    ! Select determinants that are triple or quadruple excitations
    ! from the ref
--- a/plugins/QmcChem/.gitignore
+++ b/plugins/QmcChem/.gitignore
@ -16,6 +16,7 @@ Makefile.depend
 Nuclei
 Pseudo
 Utils
+ZMQ
 ezfio_interface.irp.f
 irpf90.make
 irpf90_entities
--- a/src/AO_Basis/README.rst
+++ b/src/AO_Basis/README.rst
@ -117,7 +117,7 @@ Documentation
  :math:`\int \chi_i(r) \chi_j(r) dr)`


-`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L65>`_
+`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L66>`_
  Overlap between absolute value of atomic basis functions:
  :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`

--- a/src/Bitmask/README.rst
+++ b/src/Bitmask/README.rst
@ -80,7 +80,7 @@ Documentation
  Bitmask to include all possible single excitations from Hartree-Fock


-`core_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L350>`_
+`core_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L344>`_
  Reunion of the inactive, active and virtual bitmasks


@ -142,7 +142,7 @@ Documentation
  Hartree Fock bit mask


-`i_bitmask_gen <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L364>`_
+`i_bitmask_gen <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L358>`_
  Current bitmask for the generators


@ -150,7 +150,7 @@ Documentation
  Bitmasks for the inactive orbitals that are excited in post CAS method


-`inact_virt_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L338>`_
+`inact_virt_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L332>`_
  Reunion of the inactive and virtual bitmasks


@ -158,7 +158,7 @@ Documentation
  Undocumented


-`list_inact <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L304>`_
+`list_inact <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L298>`_
  Undocumented


@ -167,7 +167,7 @@ Documentation
  occupations "list(N_int*bit_kind_size,2)


-`list_virt <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L305>`_
+`list_virt <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L299>`_
  Undocumented


@ -219,11 +219,11 @@ Documentation
  Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask


-`reunion_of_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L325>`_
+`reunion_of_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L319>`_
  Reunion of the inactive, active and virtual bitmasks


-`unpaired_alpha_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L373>`_
+`unpaired_alpha_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L367>`_
  Bitmask reprenting the unpaired alpha electrons in the HF_bitmask


--- a/src/Determinants/README.rst
+++ b/src/Determinants/README.rst
@ -316,7 +316,7 @@ Documentation
  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/Determinants/filter_connected.irp.f#L205>`_
+`filter_connected_i_h_psi0_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L197>`_
  standard filter_connected_i_H_psi but returns in addition
  .br
  the array of the index of the non connected determinants to key1
--- a/src/Ezfio_files/README.rst
+++ b/src/Ezfio_files/README.rst
@ -203,6 +203,14 @@ output_bitmask
  Output file for Bitmask


+output_cisd
+  Output file for CISD
+
+
+output_cisd_selected
+  Output file for CISD_selected
+
+
 `output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L2>`_
  Initial CPU and wall times when printing in the output files

@ -219,6 +227,10 @@ output_ezfio_files
  Output file for Ezfio_files


+output_fcidump
+  Output file for FCIdump
+
+
 output_full_ci
  Output file for Full_CI

@ -247,12 +259,8 @@ output_moguess
  Output file for MOGuess


-output_mrcc_cassd
-  Output file for MRCC_CASSD
-
-
-output_mrcc_utils
-  Output file for MRCC_Utils
+output_mp2
+  Output file for MP2


 output_nuclei
@ -271,18 +279,14 @@ output_pseudo
  Output file for Pseudo


-output_psiref_cas
-  Output file for Psiref_CAS
-
-
-output_psiref_utils
-  Output file for Psiref_Utils
-
-
 output_selectors_full
  Output file for Selectors_full


+output_singlerefmethod
+  Output file for SingleRefMethod
+
+
 output_utils
  Output file for Utils

@ -291,6 +295,10 @@ output_utils
  Initial CPU and wall times when printing in the output files


+output_zmq
+  Output file for ZMQ
+
+
 `write_bool <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L88>`_
  Write an logical value in output

--- a/src/Integrals_Bielec/.gitignore
+++ b/src/Integrals_Bielec/.gitignore
@ -13,6 +13,7 @@ Makefile.depend
 Nuclei
 Pseudo
 Utils
+ZMQ
 ezfio_interface.irp.f
 irpf90.make
 irpf90_entities
--- a/src/Integrals_Bielec/README.rst
+++ b/src/Integrals_Bielec/README.rst
@ -31,6 +31,7 @@ Needed Modules

 * `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `ZMQ <http://github.com/LCPQ/quantum_package/tree/master/src/ZMQ>`_

 Documentation
 =============
@ -47,7 +48,7 @@ Documentation
  i(r1) j(r1) 1/r12 k(r2) l(r2)


-`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L501>`_
+`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L442>`_
  Needed to compute Schwartz inequalities


@ -61,6 +62,14 @@ Documentation
  i(r1) j(r2) 1/r12 k(r1) l(r2)


+`ao_bielec_integrals_in_map_collector <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bielec_integrals_in_map_slave.irp.f#L57>`_
+  Collects results from the AO integral calculation
+
+
+`ao_bielec_integrals_in_map_slave <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bielec_integrals_in_map_slave.irp.f#L1>`_
+  Computes a buffer of integrals
+
+
 `ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L6>`_
  AO integrals

@ -89,7 +98,7 @@ Documentation
  Frees the memory of the AO map


-`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L422>`_
+`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L508>`_
  Frees the memory of the MO map


@ -97,6 +106,10 @@ Documentation
  Compute AO 1/r12 integrals for all i and fixed j,k,l


+`compute_ao_integrals_jl <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1202>`_
+  Parallel client for AO integrals
+
+
 `disk_access_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ezfio_interface.irp.f#L28>`_
  Read/Write AO integrals from/to disk [ Write | Read | None ]

@ -109,15 +122,15 @@ Documentation
  Compute integrals on the fly


-`dump_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_567#L3>`_
+`dump_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_562#L3>`_
  Save to disk the $ao integrals


-`dump_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_567#L137>`_
+`dump_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_562#L137>`_
  Save to disk the $ao integrals


-`eri <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L664>`_
+`eri <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L605>`_
  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)
@ -139,7 +152,7 @@ Documentation
  t_w(i,2,k) = t(i)


-`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L526>`_
+`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L467>`_
  Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives


@ -161,11 +174,11 @@ Documentation
  Returns the number of elements in the AO map


-`get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L281>`_
+`get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L280>`_
  Returns one integral <ij|kl> in the MO basis


-`get_mo_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L299>`_
+`get_mo_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L298>`_
  Returns one integral <ij|kl> in the MO basis


@ -174,47 +187,47 @@ Documentation
  i for j,k,l fixed.


-`get_mo_bielec_integrals_existing_ik <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L364>`_
+`get_mo_bielec_integrals_ij <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L364>`_
  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.
+  i(1)j(2) 1/r12 k(1)l(2)
+  i, j for k,l fixed.


-`get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L414>`_
+`get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L418>`_
  Return the number of elements in the MO map


-`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L874>`_
+`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L819>`_
  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/Integrals_Bielec/ao_bi_integrals.irp.f#L795>`_
+`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L738>`_
  recursive function involved in the bielectronic integral


-`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L937>`_
+`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L882>`_
  recursive function involved in the bielectronic integral


-`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1057>`_
+`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1002>`_
  recursive function involved in the bielectronic integral


-`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1111>`_
+`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1056>`_
  recursive function involved in the bielectronic integral


-`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L971>`_
+`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L916>`_
  recursive function involved in the bielectronic integral


-`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L830>`_
+`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L774>`_
  recursive function involved in the bielectronic integral


-`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1173>`_
+`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1118>`_
  recursive function involved in the bielectronic integral


@ -222,21 +235,21 @@ Documentation
  Create new entry into AO map


-`insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L265>`_
+`insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f#L264>`_
  Create new entry into MO map, or accumulate in an existing entry


-`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L721>`_
+`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L662>`_
  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)


-`load_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_567#L89>`_
+`load_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_562#L89>`_
  Read from disk the $ao integrals


-`load_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_567#L223>`_
+`load_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/map_integrals.irp.f_template_562#L223>`_
  Read from disk the $ao integrals


@ -244,43 +257,43 @@ Documentation
  Returns one integral <ij|kl> in the MO basis


-`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L465>`_
+`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L464>`_
  mo_bielec_integral_jj(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/Integrals_Bielec/mo_bi_integrals.irp.f#L467>`_
+`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L466>`_
  mo_bielec_integral_jj(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_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L327>`_
+`mo_bielec_integral_jj_anti_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/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/Integrals_Bielec/mo_bi_integrals.irp.f#L466>`_
+`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L465>`_
  mo_bielec_integral_jj(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_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L326>`_
+`mo_bielec_integral_jj_exchange_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/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/Integrals_Bielec/mo_bi_integrals.irp.f#L325>`_
+`mo_bielec_integral_jj_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/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_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L492>`_
+`mo_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L491>`_
  Needed to compute Schwartz inequalities


@ -304,7 +317,7 @@ Documentation
  Aligned n_pt_max_integrals


-`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L860>`_
+`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L805>`_
  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)
--- a/src/MOGuess/.gitignore
+++ b/src/MOGuess/.gitignore
@ -15,6 +15,8 @@ Nuclei
 Pseudo
 Utils
 ezfio_interface.irp.f
+guess_overlap
 irpf90.make
 irpf90_entities
-tags
+tags
+truncate_mos
--- a/src/MOGuess/README.rst
+++ b/src/MOGuess/README.rst
@ -43,6 +43,10 @@ Documentation
  supposed to be the Identity


+`guess_mimi <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/guess_overlap.irp.f#L1>`_
+  Produce `H_core` MO orbital
+
+
 `h_core_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/H_CORE_guess.irp.f#L1>`_
  Produce `H_core` MO orbital
  output:  mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
@ -51,3 +55,7 @@ Documentation
 `hcore_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/h_core_guess_routine.irp.f#L1>`_
  Produce `H_core` MO orbital

+
+`prog_truncate_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/truncate_mos.irp.f#L1>`_
+  Truncate MO set
+
--- a/src/MO_Basis/README.rst
+++ b/src/MO_Basis/README.rst
@ -76,11 +76,11 @@ Documentation
  by convention, the '-' MO is in the greater index (max(j,k))


-`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L24>`_
+`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L47>`_
  Undocumented


-`mo_as_eigvectors_of_mo_matrix_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L62>`_
+`mo_as_eigvectors_of_mo_matrix_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L103>`_
  Undocumented


@ -116,7 +116,7 @@ Documentation
  Undocumented


-`mo_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L144>`_
+`mo_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L185>`_
  Undocumented


@ -143,3 +143,7 @@ Documentation
 `save_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L1>`_
  Undocumented

+
+`save_mos_truncated <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L24>`_
+  Undocumented
+
--- a/src/Utils/README.rst
+++ b/src/Utils/README.rst
@ -36,7 +36,7 @@ Documentation
  Compute 1st dimension such that it is aligned for vectorization.


-`apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L168>`_
+`apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L196>`_
  Apply the rotation found by find_rotation


@ -122,7 +122,7 @@ Documentation
  1/n!


-`find_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L149>`_
+`find_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L177>`_
  Find A.C = B


@ -148,7 +148,7 @@ Documentation
  Undocumented


-`get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L95>`_
+`get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L123>`_
  Find C = A^-1


@ -420,7 +420,7 @@ Documentation
  contains the new order of the elements.


-`lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L247>`_
+`lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L275>`_
  Diagonalize matrix H
  .br
  H is untouched between input and ouptut
@ -431,7 +431,7 @@ Documentation
  .br


-`lapack_diag_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L310>`_
+`lapack_diag_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L338>`_
  Diagonalize matrix H
  .br
  H is untouched between input and ouptut
@ -442,7 +442,7 @@ Documentation
  .br


-`lapack_diagd <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L180>`_
+`lapack_diagd <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L208>`_
  Diagonalize matrix H
  .br
  H is untouched between input and ouptut
@ -453,7 +453,7 @@ Documentation
  .br


-`lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L376>`_
+`lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L404>`_
  Diagonalize matrix H
  .br
  H is untouched between input and ouptut
@ -482,7 +482,7 @@ Documentation
  Number of current OpenMP threads


-`ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L1>`_
+`ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L46>`_
  Compute C_new=C_old.S^-1/2 canonical orthogonalization.
  .br
  overlap : overlap matrix
@ -597,7 +597,7 @@ Documentation
  to be in integer*8 format


-`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L433>`_
+`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L461>`_
  Undocumented


@ -615,6 +615,15 @@ Documentation
  Stop the progress bar


+`svd <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L1>`_
+  Compute A = U.D.Vt
+  .br
+  LDx : leftmost dimension of x
+  .br
+  Dimsneion of A is m x n
+  .br
+
+
 `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.

--- a/src/ZMQ/README.rst
+++ b/src/ZMQ/README.rst
@ -5,11 +5,38 @@ ZMQ
 Socket address : defined as an environment variable : QP_RUN_ADDRESS


-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
 Documentation
 =============
 .. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
+
+
+`qp_run_address <http://github.com/LCPQ/quantum_package/tree/master/src/ZMQ/zmq.irp.f#L13>`_
+  Address of the qp_run socket
+  Example : tcp://130.120.229.139:12345
+
+
+`zmq_context <http://github.com/LCPQ/quantum_package/tree/master/src/ZMQ/zmq.irp.f#L4>`_
+  Context for the ZeroMQ library
+
+
+`zmq_port <http://github.com/LCPQ/quantum_package/tree/master/src/ZMQ/zmq.irp.f#L38>`_
+  Undocumented
+
+
+`zmq_port_start <http://github.com/LCPQ/quantum_package/tree/master/src/ZMQ/zmq.irp.f#L14>`_
+  Address of the qp_run socket
+  Example : tcp://130.120.229.139:12345
+
+
+`zmq_socket_pull <http://github.com/LCPQ/quantum_package/tree/master/src/ZMQ/zmq.irp.f#L87>`_
+  Socket which pulls the results (2)
+
+
+`zmq_socket_push <http://github.com/LCPQ/quantum_package/tree/master/src/ZMQ/zmq.irp.f#L70>`_
+  Socket on which to push the results (1)
+
+
+`zmq_to_qp_run_socket <http://github.com/LCPQ/quantum_package/tree/master/src/ZMQ/zmq.irp.f#L47>`_
+  Socket on which the qp_run process replies
+