Transform +/- -> 10

.travis.yml

@@ -24,7 +24,6 @@ python:
 
 script: 
   - ./configure  --production ./config/gfortran.cfg
-  - source ./quantum_package.rc ; cd tests ; bats bats/qp.bats
   - source ./quantum_package.rc ; qp_module.py install Full_CI Hartree_Fock CAS_SD MRCC_CASSD
   - source ./quantum_package.rc ; ninja
   - source ./quantum_package.rc ; cd ocaml ; make ; cd -

ocaml/qp_edit.ml

@@ -18,9 +18,9 @@ type keyword =
 | Mo_basis
 | Nuclei
 | Determinants
-| Integrals_bielec
-| Pseudo
 | Perturbation
+| Pseudo
+| Integrals_bielec
 | Properties
 | Hartree_fock
 ;;
@@ -33,9 +33,9 @@ let keyword_to_string = function
 | Mo_basis              -> "MO basis"
 | Nuclei                -> "Molecule"
 | Determinants -> "Determinants"
-| Integrals_bielec -> "Integrals_bielec"
-| Pseudo -> "Pseudo"
 | Perturbation -> "Perturbation"
+| Pseudo -> "Pseudo"
+| Integrals_bielec -> "Integrals_bielec"
 | Properties -> "Properties"
 | Hartree_fock -> "Hartree_fock"
 ;;
@@ -88,12 +88,12 @@ let get s =
            f Determinants_by_hand.(read, to_rst)
          | Determinants ->
            f Determinants.(read, to_rst)
-         | Integrals_bielec ->
-           f Integrals_bielec.(read, to_rst)
-         | Pseudo ->
-           f Pseudo.(read, to_rst)
          | Perturbation ->
            f Perturbation.(read, to_rst)
+         | Pseudo ->
+           f Pseudo.(read, to_rst)
+         | Integrals_bielec ->
+           f Integrals_bielec.(read, to_rst)
          | Properties ->
            f Properties.(read, to_rst)
          | Hartree_fock ->
@@ -136,9 +136,9 @@ let set str s =
       let open Input in
         match s with
         | Determinants -> write Determinants.(of_rst, write) s
-        | Integrals_bielec -> write Integrals_bielec.(of_rst, write) s
-        | Pseudo -> write Pseudo.(of_rst, write) s
         | Perturbation -> write Perturbation.(of_rst, write) s
+        | Pseudo -> write Pseudo.(of_rst, write) s
+        | Integrals_bielec -> write Integrals_bielec.(of_rst, write) s
         | Properties -> write Properties.(of_rst, write) s
         | Hartree_fock -> write Hartree_fock.(of_rst, write) s
         | Electrons        -> write Electrons.(of_rst, write) s
@@ -189,9 +189,9 @@ let run check_only ezfio_filename =
       Ao_basis;
       Electrons ;
       Determinants ; 
-      Integrals_bielec ; 
-      Pseudo ; 
       Perturbation ; 
+      Pseudo ; 
+      Integrals_bielec ; 
       Properties ; 
       Hartree_fock ; 
       Mo_basis;

ocaml/qp_print_basis.ml

@@ -35,7 +35,26 @@ let mo () =
   |> print_endline
 
 
+let psi_det () =
+  let ezfio_filename =
+    Sys.argv.(1)
+  in
+  if (not (Sys.file_exists_exn ezfio_filename)) then
+    failwith "Error reading EZFIO file";
+  Ezfio.set_file ezfio_filename;
+  let psi_det =
+    match Input.Determinants_by_hand.read () with
+    | Some psi_det -> psi_det
+    | _ -> failwith "Error reading the mo set"
+  in
+  Input.Determinants_by_hand.to_rst psi_det 
+  |> Rst_string.to_string
+  |> print_endline
+
+
+
 let () = 
   basis ();
-  mo ()
+  mo ();
+  psi_det ();
 

plugins/qmcpack/qp_convert_qmcpack_to_ezfio.py

@@ -17,7 +17,7 @@ ezfio.set_file(ezfio_path)
 do_pseudo = ezfio.get_pseudo_do_pseudo()
 if do_pseudo:
     print "do_pseudo True"
-    zcore = ezfio.get_pseudo_nucl_charge_remove()
+    print "The charge of nucl will be decreasced for taking into acount the pseudo potentiel"
 else:
     print "do_pseudo False"
 
@@ -68,11 +68,7 @@ print "nucl_num", len(l_label)
 print "Atomic coord in Bohr"
 
 for i, t in enumerate(zip(l_label, l_charge, l_coord_str)):
-    try:
+    print list_to_string(t)
-        l = (t[0], t[1] + zcore[i], t[2])
-    except NameError:
-        l = t
-    print list_to_string(l)
 
 #
 # Call externet process to get the sysmetry
@@ -83,7 +79,8 @@ process = subprocess.Popen(
     stdout=subprocess.PIPE)
 out, err = process.communicate()
 
-basis_raw, sym_raw, _= out.split("\n\n\n")
+print len(out.split("\n\n\n"))
+basis_raw, sym_raw, _ , det_raw, _ = out.split("\n\n\n")
 
 #  _                 __        
 # |_)  _.  _ o  _   (_   _ _|_ 
@@ -175,6 +172,9 @@ def get_nb_permutation(str_):
 
 
 def order_l_l_sym(l_l_sym):
+
+    l_order_mo = [i for i,_ in enumerate(l_l_sym)]
+
     n = 1
     for i in range(len(l_l_sym)):
         if n != 1:
@@ -184,11 +184,11 @@ def order_l_l_sym(l_l_sym):
         l = l_l_sym[i]
         n = get_nb_permutation(l[2])
 
-        l_l_sym[i:i + n] = sorted(l_l_sym[i:i + n],
+        l_l_sym[i:i + n], l_order_mo[i:i+n] = zip(*sorted(zip(l_l_sym[i:i + n],l_order_mo[i:i+n]),
-                                  key=lambda x: x[2],
+                                              key=lambda x: x[0][2],
-                                  cmp=compare_gamess_style)
+                                              cmp=compare_gamess_style))
 
-    return l_l_sym
+    return l_l_sym, l_order_mo
 
 
 #==========================
@@ -197,8 +197,13 @@ def order_l_l_sym(l_l_sym):
 
 l_sym_without_header = sym_raw.split("\n")[3:-2]
 l_l_sym_raw = [i.split() for i in l_sym_without_header]
+print len(l_l_sym_raw)
+
 l_l_sym_expend_sym = expend_sym_l(l_l_sym_raw)
-l_l_sym_ordered = order_l_l_sym(l_l_sym_expend_sym)
+print len(l_l_sym_expend_sym)
+
+l_l_sym_ordered, l_order_mo = order_l_l_sym(l_l_sym_expend_sym)
+
 
 #========
 #MO COEF
@@ -305,8 +310,8 @@ if do_pseudo:
             if l_dump:
                 l_str.append(l_dump)
 
-        str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE {2} AND LMAX {3} ARE"
+        str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE -1 AND LMAX {2} ARE"
-        print str_.format(a, i + 1, int(zcore[i]), int(len(l_str) - 1))
+        print str_.format(a, i + 1, int(len(l_str) - 1))
 
         for i, l in enumerate(l_str):
             str_ = "FOR L= {0} COEFF N ZETA"
@@ -314,8 +319,7 @@ if do_pseudo:
             for ii, ll in enumerate(l):
                 print " ", ii + 1, ll
 
-    str_ = "THE ECP RUN REMOVES {0} CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
+    str_ = "THE ECP RUN REMOVES -1 CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
-    print str_.format(sum(zcore))
     print "END_PSEUDO"
 
 #  _         
@@ -329,31 +333,29 @@ print "mo_num", mo_num
 print "det_num", n_det
 print ""
 
-psi_det = ezfio.get_determinants_psi_det()
-psi_coef = ezfio.get_determinants_psi_coef()[0]
 
-for c, (l_det_bit_alpha, l_det_bit_beta) in zip(psi_coef, psi_det):
-    print c
 
-    bin_det = ""
+token = "Determinants ::"
-    for i,int_det in enumerate(l_det_bit_alpha):
+pos = det_raw.rfind(token) + len(token)
-        bin_det_raw = "{0:b}".format(int_det)[::-1]
-        if mo_num - 64*(i+1) > 0:
-            bin_det += bin_det_raw + "0" * (64*(i+1) - len(bin_det_raw))
-        else:
-            bin_det += bin_det_raw + "0" * (mo_num-64*i - len(bin_det_raw))
 
-    print bin_det
+d_rep={"+":"1","-":"0"}
 
-    bin_det = ""
+det_without_header = det_raw[pos+2::]
-    for i,int_det in enumerate(l_det_bit_beta):
-        bin_det_raw = "{0:b}".format(int_det)[::-1]
-        if mo_num - 64*(i+1) > 0:
-            bin_det += bin_det_raw + "0" * (64*(i+1) - len(bin_det_raw))
-        else:
-            bin_det += bin_det_raw + "0" * (mo_num-64*i - len(bin_det_raw))
 
-    print bin_det
+for line_raw in det_without_header.split("\n"):
-    print ""
+    line = line_raw
+
+    if line_raw:
+        try:
+            float(line)
+        except ValueError:
+            print line_raw.strip(), len(line_raw.strip())
+            print l_order_mo, len(l_order_mo)
+
+            line_order = [line_raw[i] for i in l_order_mo]
+            line= "".join([d_rep[x] if x in d_rep else x for x in line_order])
+
+    print line
 
 print "END_DET"
+

scripts/compilation/qp_create_ninja.py

@@ -38,6 +38,7 @@ from qp_path import QP_ROOT, QP_SRC, QP_EZFIO
 LIB = "" # join(QP_ROOT, "lib", "rdtsc.o") 
 EZFIO_LIB = join(QP_ROOT, "lib", "libezfio_irp.a") 
 ZMQ_LIB   = join(QP_ROOT, "lib", "libf77zmq.a") + " "  + join(QP_ROOT, "lib", "libzmq.a") + " -lstdc++ -lrt"
+INT_LIB = "/home/razoa/libint/libint-2.1.0-beta2/lib/.libs/libint2.a"
 ROOT_BUILD_NINJA = join(QP_ROOT, "config", "build.ninja")
 
 header = r"""#
@@ -96,7 +97,8 @@ def ninja_create_env_variable(pwd_config_file):
         l_string.append(str_)
 
     lib_lapack = get_compilation_option(pwd_config_file, "LAPACK_LIB")
-    l_string.append("LIB = {0} {1} {2} {3}".format(LIB, lib_lapack, EZFIO_LIB, ZMQ_LIB))
+    str_lib = " ".join([LIB, lib_lapack, EZFIO_LIB, ZMQ_LIB, INT_LIB])
+    l_string.append("LIB = {0} ".format(str_lib))
 
     l_string.append("")
 
@@ -387,6 +389,8 @@ def get_l_file_for_module(path_module):
             l_src.append(f)
             obj = '{0}.o'.format(os.path.splitext(f)[0])
             l_obj.append(obj)
+        elif f.lower().endswith(".o"):
+             l_obj.append(join(path_module.abs, f))
         elif f == "EZFIO.cfg":
             l_depend.append(join(path_module.abs, "ezfio_interface.irp.f"))
 

src/AO_Basis/aos.irp.f

@@ -54,6 +54,13 @@ END_PROVIDER
       ao_coef_normalized(i,j) = ao_coef_normalized(i,j) * ao_coef_normalization_factor(i)
     enddo
   enddo
+
+!   do i=1,ao_num
+!   do j=1,ao_prim_num(i)
+!       ao_coef_normalized(i,j) = ao_coef(i,j)
+!    enddo
+!    enddo
+
 END_PROVIDER
 
  BEGIN_PROVIDER [ double precision, ao_coef_normalized_ordered, (ao_num_align,ao_prim_num_max) ]
@@ -72,8 +79,8 @@ END_PROVIDER
        d(j,1) = ao_expo(i,j)
        d(j,2) = ao_coef_normalized(i,j)
      enddo
-     call dsort(d(1,1),iorder,ao_prim_num(i))
+!     call dsort(d(1,1),iorder,ao_prim_num(i))
-     call dset_order(d(1,2),iorder,ao_prim_num(i))
+!     call dset_order(d(1,2),iorder,ao_prim_num(i))
      do j=1,ao_prim_num(i)
        ao_expo_ordered(i,j) = d(j,1)
        ao_coef_normalized_ordered(i,j) = d(j,2)

src/Integrals_Bielec/ao_bi_integrals.irp.f

@@ -4,6 +4,12 @@ double precision function ao_bielec_integral(i,j,k,l)
   !  integral of the AO basis <ik|jl> or (ij|kl)
   !     i(r1) j(r1) 1/r12 k(r2) l(r2)
   END_DOC
+ 
+ ! use libint_module
+ ! call init_libint(trim(ezfio_filename)//char(0))
+ ! ao_bielec_integral = ao_bielec_integral_libint(i,j,k,l)
+ ! return
+
   integer,intent(in)             :: i,j,k,l
   integer                        :: p,q,r,s
   double precision               :: I_center(3),J_center(3),K_center(3),L_center(3)
@@ -288,11 +294,18 @@ end
 subroutine compute_ao_bielec_integrals(j,k,l,sze,buffer_value)
   implicit none
   use map_module
-  
+  use  libint_module
+
   BEGIN_DOC
   ! Compute AO 1/r12 integrals for all i and fixed j,k,l
   END_DOC
-  
+
+!  include 'Utils/constants.include.F'
+!  integer, intent(in)            :: j,k,l,sze
+!  real(integral_kind), intent(out) :: buffer_value(sze)
+!
+!  call compute_ao_bielec_integrals_libint(j,k,l,sze,buffer_value)
+
   include 'Utils/constants.include.F'
   integer, intent(in)            :: j,k,l,sze
   real(integral_kind), intent(out) :: buffer_value(sze)