Update for TREXIOv2

bin/qp_convert_output_to_ezfio

@@ -195,48 +195,52 @@ def write_ezfio(res, filename):
     # P a r s i n g #
     # ~#~#~#~#~#~#~ #
 
+    inucl = {}
+    for i, a in enumerate(res.geometry):
+       inucl[a.coord] = i
+
     nbasis = 0
-    nucl_center = []
+    nucl_index = []
     curr_center = -1
     nucl_shell_num = []
     ang_mom = []
     nshell = 0
-    shell_prim_index = [1]
+    nshell_tot = 0
+    shell_index = []
     shell_prim_num = []
     for b in res.basis:
         s = b.sym
         if str.count(s, "y") + str.count(s, "x") == 0:
-          c = b.center
+          c = inucl[b.center]
           nshell += 1
+          nshell_tot += 1
           if c != curr_center:
              curr_center = c
-             nucl_center.append(nbasis+1)
              nucl_shell_num.append(nshell)
              nshell = 0
           nbasis += 1
+          nucl_index.append(c+1)
           coefficient += b.coef[:len(b.prim)]
           exponent += [p.expo for p in b.prim]
           ang_mom.append(str.count(s, "z"))
-          shell_prim_index.append(len(exponent)+1)
           shell_prim_num.append(len(b.prim))
-
+          shell_index += [nshell_tot+1] * len(b.prim)
-    nucl_shell_num.append(nshell+1)
-    nucl_shell_num = nucl_shell_num[1:]
 
     # ~#~#~#~#~ #
     # W r i t e #
     # ~#~#~#~#~ #
 
     ezfio.set_basis_basis("Read from ResultsFile")
-    ezfio.set_basis_basis_nucleus_index(nucl_center)
-    ezfio.set_basis_prim_num(len(coefficient))
     ezfio.set_basis_shell_num(len(ang_mom))
+    ezfio.set_basis_basis_nucleus_index(nucl_index)
+    ezfio.set_basis_prim_num(len(coefficient))
+
     ezfio.set_basis_nucleus_shell_num(nucl_shell_num)
     ezfio.set_basis_prim_coef(coefficient)
     ezfio.set_basis_prim_expo(exponent)
     ezfio.set_basis_shell_ang_mom(ang_mom)
     ezfio.set_basis_shell_prim_num(shell_prim_num)
-    ezfio.set_basis_shell_prim_index(shell_prim_index)
+    ezfio.set_basis_shell_index(shell_index)
 
     print("OK")
 

config/ifort_2021_avx.cfg

@@ -7,7 +7,7 @@
 #
 [COMMON]
 FC           : ifort -fpic
-LAPACK_LIB   : -mkl=parallel -lirc -lsvml -limf -lipps
+LAPACK_LIB   : -qmkl=parallel -lirc -lsvml -limf -lipps
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 -DINTEL 
 

config/ifort_2021_avx_mpi.cfg

@@ -7,7 +7,7 @@
 #
 [COMMON]
 FC           : mpiifort -fpic
-LAPACK_LIB   : -mkl=parallel -lirc -lsvml -limf -lipps
+LAPACK_LIB   : -qmkl=parallel -lirc -lsvml -limf -lipps
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL 
 

config/ifort_2021_sse4.cfg

@@ -7,7 +7,7 @@
 #
 [COMMON]
 FC           : ifort -fpic
-LAPACK_LIB   : -mkl=parallel -lirc -lsvml -limf -lipps
+LAPACK_LIB   : -qmkl=parallel -lirc -lsvml -limf -lipps
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 -DINTEL 
 

config/ifort_2021_sse4_mpi.cfg

@@ -7,7 +7,7 @@
 #
 [COMMON]
 FC           : mpiifort -fpic
-LAPACK_LIB   : -mkl=parallel -lirc -lsvml -limf -lipps
+LAPACK_LIB   : -qmkl=parallel -lirc -lsvml -limf -lipps
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL 
 

config/ifort_2021_xHost.cfg

@@ -7,7 +7,7 @@
 #
 [COMMON]
 FC           : ifort -fpic
-LAPACK_LIB   : -mkl=parallel -lirc -lsvml -limf -lipps
+LAPACK_LIB   : -qmkl=parallel -lirc -lsvml -limf -lipps
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=64 -DINTEL 
 

ocaml/qp_create_ezfio.ml

@@ -585,12 +585,18 @@ let run ?o b au c d m p cart xyz_file =
         let shell_prim_num =
           list_map List.length  lc
         in
-        let shell_prim_idx =
+        Printf.printf "Coucou\n%!";
+        let shell_idx =
+          Printf.printf "Coucou\n%!";
+          let rec make_list n accu = function
+          | 0 -> accu
+          | i -> make_list n (n :: accu) (i-1)
+          in
           let rec aux count accu = function
           | [] -> List.rev accu
           | l::rest ->
-            let newcount = count+(List.length l) in
+            let new_l = make_list count accu (List.length l) in
-            aux newcount (count::accu) rest
+            aux (count+1) new_l rest
           in
           aux 1 [] lc
         in
@@ -602,20 +608,12 @@ let run ?o b au c d m p cart xyz_file =
           ~rank:1 ~dim:[| shell_num |] ~data:shell_prim_num);
         Ezfio.set_basis_shell_ang_mom (Ezfio.ezfio_array_of_list
           ~rank:1 ~dim:[| shell_num |] ~data:ang_mom ) ;
-        Ezfio.set_basis_shell_prim_index (Ezfio.ezfio_array_of_list
+        Ezfio.set_basis_shell_index (Ezfio.ezfio_array_of_list
-          ~rank:1 ~dim:[| shell_num |] ~data:shell_prim_idx) ;
+          ~rank:1 ~dim:[| prim_num |] ~data:shell_idx) ;
         Ezfio.set_basis_basis_nucleus_index (Ezfio.ezfio_array_of_list
-          ~rank:1 ~dim:[| nucl_num |]
+          ~rank:1 ~dim:[| shell_num |]
-          ~data:(
+          ~data:( list_map (fun (_,n) -> Nucl_number.to_int n) basis) 
-          list_map (fun (_,n) -> Nucl_number.to_int n) basis
+          ) ;
-          |> List.fold_left (fun accu i -> 
-            match accu with 
-            | [] -> []
-            | (h,j) :: rest -> if j == i then ((h+1,j)::rest) else ((h+1,i)::(h+1,j)::rest)
-          ) [(0,0)]
-          |> List.rev
-          |> List.map fst
-          )) ;
         Ezfio.set_basis_nucleus_shell_num(Ezfio.ezfio_array_of_list
           ~rank:1 ~dim:[| nucl_num |]
           ~data:(

src/basis/EZFIO.cfg

@@ -37,16 +37,16 @@ doc: Number of primitives in a shell
 size: (basis.shell_num)
 interface: ezfio, provider
 
-[shell_prim_index]
+[shell_index]
 type: integer
-doc: Index of the first primitive of the shell
+doc: Index of the shell for each primitive
-size: (basis.shell_num)
+size: (basis.prim_num)
 interface: ezfio, provider
 
 [basis_nucleus_index]
 type: integer
-doc: Index of the nucleus on which the shell is centered
+doc: Nucleus on which the shell is centered
-size: (nuclei.nucl_num)
+size: (basis.shell_num)
 interface: ezfio, provider
 
 [prim_normalization_factor]

src/basis/basis.irp.f

@@ -30,8 +30,10 @@ BEGIN_PROVIDER [ double precision, shell_normalization_factor , (shell_num) ]
         powA(3) = 0
 
         norm = 0.d0
-        do k=shell_prim_index(i),shell_prim_index(i)+shell_prim_num(i)-1
+        do k=1, prim_num
-          do j=shell_prim_index(i),shell_prim_index(i)+shell_prim_num(i)-1
+          if (shell_index(k) /= i) cycle
+          do j=1, prim_num
+            if (shell_index(j) /= i) cycle
             call overlap_gaussian_xyz(C_A,C_A,prim_expo(j),prim_expo(k), &
               powA,powA,overlap_x,overlap_y,overlap_z,c,nz)
             norm = norm+c*prim_coef(j)*prim_coef(k) * prim_normalization_factor(j) * prim_normalization_factor(k)
@@ -91,7 +93,8 @@ BEGIN_PROVIDER [ double precision, prim_normalization_factor , (prim_num) ]
         powA(2) = 0
         powA(3) = 0
 
-        do k=shell_prim_index(i),shell_prim_index(i)+shell_prim_num(i)-1
+        do k=1, prim_num
+          if (shell_index(k) /= i) cycle
             call overlap_gaussian_xyz(C_A,C_A,prim_expo(k),prim_expo(k), &
               powA,powA,overlap_x,overlap_y,overlap_z,norm,nz)
             prim_normalization_factor(k) = 1.d0/dsqrt(norm)