xyz to ezfio works

ocaml/Atom.ml

@@ -26,7 +26,8 @@ type t =
   coord   : Point3d.t ;
 }
 
-let of_string s =
+(** Read xyz coordinates of the atom with unit u *)
+let of_string u s =
   let buffer = s
   |> String.split ~on:' '
   |> List.filter ~f:(fun x -> x <> "")
@@ -35,13 +36,13 @@ let of_string s =
   | [ name; charge; x; y; z ] ->
     { element = Element.of_string name ;
       charge  = Charge.of_string  charge ;
-      coord   = Point3d.of_string (String.concat [x; y; z] ~sep:" ")
+      coord   = Point3d.of_string u (String.concat [x; y; z] ~sep:" ")
     }
   | [ name; x; y; z ] ->
     let e = Element.of_string name in
     { element = e ;
       charge  = Charge.of_int (Element.charge e);
-      coord   = Point3d.of_string (String.concat [x; y; z] ~sep:" ")
+      coord   = Point3d.of_string u (String.concat [x; y; z] ~sep:" ")
     }
   | _ -> raise (AtomError s)
 ;;

ocaml/Gto.ml

@@ -6,7 +6,7 @@ exception End_Of_Basis
 
 type t =
 { sym  : Symmetry.t ;
-  lc   : ((Primitive.t * float) list)
+  lc   : ((Primitive.t * AO_coef.t) list)
 }
 ;;
 
@@ -56,7 +56,7 @@ let read_one in_channel =
                     Primitive.expo = Positive_float.of_float
                         (Float.of_string expo)
                   }
-          and c = Float.of_string coef in
+          and c = AO_coef.of_float (Float.of_string coef) in
           read_lines ( (p,c)::result) (i-1)
         end
       | _ -> raise (GTO_Read_Failure line_buffer)
@@ -68,7 +68,7 @@ let read_one in_channel =
 
 (** Transform the gto to a string *)
 let to_string { sym = sym ; lc = lc } =
-  let f (p,c) = Printf.sprintf "( %s, %f )" (Primitive.to_string p) c
+  let f (p,c) = Printf.sprintf "( %s, %f )" (Primitive.to_string p) (AO_coef.to_float c)
   in
   Printf.sprintf "[ %s : %s ]" (Symmetry.to_string sym)
     (String.concat (List.map ~f:f lc) ~sep:", ")

ocaml/Makefile

@@ -12,7 +12,7 @@ endif
 
 LIBS=
 PKGS=
-OCAMLCFLAGS=-g
+OCAMLCFLAGS=-g 
 OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags -g 
 MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml
 MLIFILES=$(wildcard *.mli) 

ocaml/Molecule.ml

@@ -76,10 +76,11 @@ let to_string m =
 
 let of_xyz_string
     ?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
+    ?(units=Point3d.Angstrom)
     s =
   let l = String.split s ~on:'\n'
        |> List.filter ~f:(fun x -> x <> "")
-       |> List.map ~f:Atom.of_string 
+       |> List.map ~f:(fun x -> Atom.of_string units x)
   in
   let ne = ( get_charge { 
         nuclei=l ;

ocaml/Point3d.ml

@@ -1,21 +1,33 @@
 open Core.Std;;
 
+type units = 
+| Bohr
+| Angstrom
+;;
+
 type t = {
   x : float ;
   y : float ;
   z : float ;
 }
 
-let of_string s =
+(** Read x y z coordinates in string s with units u *)
+let of_string u s =
+  let f = 
+    begin match u with
+    | Bohr -> 1.
+    | Angstrom -> 1. /. 0.52917721092
+    end
+  in
   let l = s
   |> String.split ~on:' '
   |> List.filter ~f:(fun x -> x <> "")
   |> List.map ~f:Float.of_string
   |> Array.of_list
   in
-  { x = l.(0) ;
-    y = l.(1) ;
-    z = l.(2) }
+  { x = l.(0) *. f ;
+    y = l.(1) *. f ;
+    z = l.(2) *. f }
 ;;
            
 

ocaml/Qputils.ml

@@ -1,4 +1,14 @@
 let (/) (a:string) (b:string) = a^"/"^b;;
 
+let rec transpose = function
+| []          -> []
+| []::tail    -> transpose tail
+| (x::t1)::t2 ->
+    let new_head = (x::(List.map List.hd t2)) 
+    and new_tail =  (transpose (t1 :: (List.map List.tl t2) ))
+    in 
+    new_head @ new_tail
+;;
+
 
 

ocaml/Symmetry.ml

@@ -58,7 +58,9 @@ type st = t
 ;;
 
 module Xyz : sig
-  type t
+  type t = { x: Positive_int.t ;
+             y: Positive_int.t ;
+             z: Positive_int.t }
   val  of_string : string -> t
   val  to_string : t -> string 
   val  get_l     : t -> Positive_int.t
@@ -67,7 +69,6 @@ end = struct
   type t = { x: Positive_int.t ;
              y: Positive_int.t ;
              z: Positive_int.t }
-
   type state_type = Null | X | Y | Z
 
   (** Builds an XYZ triplet from a string.

ocaml/Symmetry.mli

@@ -0,0 +1,18 @@
+open Qptypes;;
+
+type t = S | P | D | F | G | H | I | J | K | L
+val to_string : t -> string
+val of_string : string -> t
+val of_char : char -> t
+val to_l : t -> Positive_int.t
+type st = t
+module Xyz :
+  sig
+    type t = { x: Positive_int.t ;
+               y: Positive_int.t ;
+               z: Positive_int.t }
+    val of_string : string -> t
+    val to_string : t -> string
+    val get_l : t -> Positive_int.t
+    val of_symmetry : st -> t list
+  end

ocaml/qp_create_ezfio_from_xyz.ml

@@ -98,21 +98,59 @@ File : %s\n" c m b xyz_file;
   Ezfio.set_ao_basis_ao_num ao_num;
   let ao_prim_num = List.map long_basis ~f:(fun (_,g,_) -> List.length g.Gto.lc) 
   and ao_nucl = List.map long_basis ~f:(fun (_,_,n) -> Atom_number.to_int n)
+  and ao_power= 
+    let l = List.map long_basis ~f:(fun (x,_,_) -> x) in
+    (List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) )@
+    (List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) )@
+    (List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) ) 
+  in
+  let ao_prim_num_max = List.fold ~init:0 ~f:(fun s x ->
+    if x > s then x
+    else s) ao_prim_num
+  in
+  let gtos = List.map long_basis ~f:(fun (_,x,_) -> x) in
+
+  let create_expo_coef ec = 
+      let coefs = 
+        begin match ec with
+        | `Coefs -> List.map gtos ~f:(fun x->
+          List.map x.Gto.lc ~f:(fun (_,coef) -> AO_coef.to_float coef) )
+        | `Expos -> List.map gtos ~f:(fun x->
+          List.map x.Gto.lc ~f:(fun (prim,_) -> Positive_float.to_float
+          prim.Primitive.expo) )
+        end
+      in
+      let rec get_n n accu = function
+        | [] -> List.rev accu  
+        | h::tail ->
+            let y =
+            begin match List.nth h n with
+            | Some x -> x
+            | None -> 0.
+            end
+            in 
+            get_n n (y::accu) tail
+      in
+      let rec build accu = function
+        | n when n=ao_prim_num_max -> accu
+        | n -> build ( accu @ (get_n n [] coefs) ) (n+1)
+      in
+      build [] 0
+  in
+
+  let ao_coef = create_expo_coef `Coefs
+  and ao_expo = create_expo_coef `Expos
   in
   Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
     ~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
   Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list
     ~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
-
-(*
-ao_basis
-  ao_power           integer       (ao_basis_ao_num,3)
-  ao_prim_num_max    integer       = maxval(ao_basis_ao_prim_num)
-  ao_coef            double precision (ao_basis_ao_num,ao_basis_ao_prim_num_max)
-  ao_expo            double precision (ao_basis_ao_num,ao_basis_ao_prim_num_max)
-
-*)
-
+  Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list
+  ~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ;
+  Ezfio.set_ao_basis_ao_coef(Ezfio.ezfio_array_of_list
+  ~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_coef) ;
+  Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list
+  ~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
 ;;
 
 let command = 

ocaml/qptypes_generator.ml

@@ -54,7 +54,7 @@ let input_data = "
   if (x > 100) then
     warning \"N_int > 100\";
   if (Ezfio.has_determinants_n_int ()) then
-    assert (x == (Ezfio.get_determinants_n_int ()));
+    assert (x = (Ezfio.get_determinants_n_int ()));
 
 * Det_number : int 
   assert (x > 0) ; 
@@ -75,6 +75,10 @@ let input_data = "
   | _ -> raise (Failure \"Bit_kind should be (1|2|4|8).\")
   end;
 
+* MO_coef : float
+
+* AO_coef : float
+
 "
 ;;
 
@@ -84,17 +88,19 @@ module %s : sig
   type t
   val to_%s : t -> %s
   val of_%s : %s -> t
+  val to_string : %s -> string
 end = struct
   type t = %s
   let to_%s x = x
   let of_%s x = ( %s x )
+  let to_string x = %s.to_string x
 end
 
 "
 ;;
 
 let parse_input input=
-  print_string "let warning = print_string;;\n" ;
+  print_string "open Core.Std;;\nlet warning = print_string;;\n" ;
   let rec parse result = function
     | [] -> result
     | ( "" , ""   )::tail -> parse result tail
@@ -102,10 +108,10 @@ let parse_input input=
         let  name , typ  = String.lsplit2_exn ~on:':' t
         in
         let typ  = String.strip typ
-        and name = String.strip name
-        in
-        let newstring = Printf.sprintf template name typ typ typ typ typ typ typ
-        ( String.strip text )
+        and name = String.strip name in
+        let typ_cap = String.capitalize typ in
+        let newstring = Printf.sprintf template name typ typ typ typ typ typ typ typ 
+          ( String.strip text ) typ_cap
         in
         List.rev (parse (newstring::result) tail )
   in

ocaml/test_atom.ml

@@ -1,5 +1,5 @@
 let test_atom = 
   let line = "C  6.0  1.  2. 3." in
-  let atom = Atom.of_string line in
+  let atom = Atom.of_string Point3d.Bohr line in
   print_string (Atom.to_string atom)
 ;;

ocaml/test_point3d.ml

@@ -1,13 +1,15 @@
 let test_point3d_1 () =
   let input = "7.4950000 -0.1499810    0.5085570" in
-  let p3d = Point3d.of_string input in
-  print_string (Point3d.to_string p3d)
+  let p3d = Point3d.of_string Point3d.Angstrom input in
+  print_endline(Point3d.to_string p3d);
+  let p3d = Point3d.of_string Point3d.Bohr input in
+  print_endline (Point3d.to_string p3d)
 ;;
 
 let test_point3d () =
-  let p1 = Point3d.of_string "1. 2. 3." 
-  and p2 = Point3d.of_string "-2. 1. 1.5" in
+  let p1 = Point3d.of_string Point3d.Bohr "1. 2. 3." 
+  and p2 = Point3d.of_string Point3d.Bohr "-2. 1. 1.5" in
   Printf.printf "%f\n" (Point3d.distance p1 p2)
 ;;
 
-test_point3d ();
+test_point3d_1 ();

robots.txt

@@ -1,2 +0,0 @@
-User-agent: *
-Allow: /

src/MOs/mos.irp.f

@@ -4,7 +4,13 @@ BEGIN_PROVIDER [ integer, mo_tot_num ]
   ! Total number of molecular orbitals and the size of the keys corresponding
   END_DOC
   PROVIDE ezfio_filename
-  call ezfio_get_mo_basis_mo_tot_num(mo_tot_num)
+  logical                        :: exists
+  call ezfio_has_mo_basis_mo_tot_num(exists)
+  if (exists) then
+    call ezfio_get_mo_basis_mo_tot_num(mo_tot_num)
+  else
+    mo_tot_num = ao_num
+  endif
   ASSERT (mo_tot_num > 0)
 END_PROVIDER
 
@@ -42,18 +48,23 @@ END_PROVIDER
   endif
   
   ! Coefs
-  allocate(buffer(ao_num,mo_tot_num))
-  buffer = 0.d0
-  call ezfio_get_mo_basis_mo_coef(buffer)
-  do i=1,mo_tot_num
-    do j=1,ao_num
-      mo_coef(j,i) = buffer(j,i)
+  call ezfio_has_mo_basis_mo_coef(exists)
+  if (exists) then
+    allocate(buffer(ao_num,mo_tot_num))
+    buffer = 0.d0
+    call ezfio_get_mo_basis_mo_coef(buffer)
+    do i=1,mo_tot_num
+      do j=1,ao_num
+        mo_coef(j,i) = buffer(j,i)
+      enddo
+      do j=ao_num+1,ao_num_align
+        mo_coef(j,i) = 0.d0
+      enddo
     enddo
-    do j=ao_num+1,ao_num_align
-      mo_coef(j,i) = 0.d0
-    enddo
-  enddo
-  deallocate(buffer)
+    deallocate(buffer)
+  else
+    mo_coef = 0.d0
+  endif
   
 END_PROVIDER
 

src/MOs/utils.irp.f

@@ -5,6 +5,7 @@ subroutine save_mos
   
   call system('$QPACKAGE_ROOT/scripts/save_current_mos.sh '//trim(ezfio_filename))
   
+  call ezfio_set_mo_basis_mo_tot_num(mo_tot_num)
   call ezfio_set_mo_basis_mo_label(mo_label)
   allocate ( buffer(ao_num,mo_tot_num) )
   buffer = 0.d0