Changed Symmetry into Angmom in OCaml

ocaml/Angmom.ml

@@ -26,7 +26,7 @@ let of_string = function
   | "J" | "j" -> J
   | "K" | "k" -> K
   | "L" | "l" -> L
-  | x -> raise (Failure ("Symmetry should be S|P|D|F|G|H|I|J|K|L,
+  | x -> raise (Failure ("Angmom should be S|P|D|F|G|H|I|J|K|L,
 not "^x^"."))
 
 let of_char = function
@@ -40,7 +40,7 @@ let of_char = function
   | 'J' | 'j' -> J
   | 'K' | 'k' -> K
   | 'L' | 'l' -> L
-  | x -> raise (Failure ("Symmetry should be S|P|D|F|G|H|I|J|K|L"))
+  | x -> raise (Failure ("Angmom should be S|P|D|F|G|H|I|J|K|L"))
 
 let to_l = function
   | S -> Positive_int.of_int 0
@@ -68,7 +68,7 @@ let of_l i =
   | 7 -> J
   | 8 -> K
   | 9 -> L
-  | x -> raise (Failure ("Symmetry should be S|P|D|F|G|H|I|J|K|L"))
+  | x -> raise (Failure ("Angmom should be S|P|D|F|G|H|I|J|K|L"))
 
 
 type st = t

ocaml/GaussianPrimitive.ml

@@ -2,14 +2,14 @@ open Qptypes
 open Sexplib.Std
 
 type t =
-  { sym  : Symmetry.t ;
+  { sym  : Angmom.t ;
     expo : AO_expo.t ;
   } [@@deriving sexp]
 
 let to_string p =
   let { sym = s ; expo = e } = p in
   Printf.sprintf "(%s, %22e)"
-    (Symmetry.to_string s)
+    (Angmom.to_string s)
     (AO_expo.to_float e)
 
 

ocaml/Gto.ml

@@ -9,7 +9,7 @@ type fmt =
 | Gaussian
 
 type t =
-{ sym  : Symmetry.t ;
+{ sym  : Angmom.t ;
   lc   : ((GaussianPrimitive.t * AO_coef.t) list)
 } [@@deriving sexp]
 
@@ -47,7 +47,7 @@ let read_one in_channel =
   in
   let sym_str = String.sub buffer 0 2 in
   let   n_str = String.sub buffer 2 ((String.length buffer)-2) in
-  let sym = Symmetry.of_string (String_ext.strip sym_str) in
+  let sym = Angmom.of_string (String_ext.strip sym_str) in
   let n = int_of_string (String_ext.strip n_str) in
   (* Read all the primitives *)
   let rec read_lines result = function
@@ -82,7 +82,7 @@ let read_one in_channel =
 (** Write the GTO in Gamess format *)
 let to_string_gamess { sym = sym ; lc = lc } =
   let result =
-    Printf.sprintf "%s %3d" (Symmetry.to_string sym) (List.length lc)
+    Printf.sprintf "%s %3d" (Angmom.to_string sym) (List.length lc)
   in
   let rec do_work accu i = function
   | [] -> List.rev accu
@@ -102,7 +102,7 @@ let to_string_gamess { sym = sym ; lc = lc } =
 (** Write the GTO in Gaussian format *)
 let to_string_gaussian { sym = sym ; lc = lc } =
   let result =
-    Printf.sprintf "%s %3d   1.00" (Symmetry.to_string sym) (List.length lc)
+    Printf.sprintf "%s %3d   1.00" (Angmom.to_string sym) (List.length lc)
   in
   let rec do_work accu i = function
   | [] -> List.rev accu

ocaml/Gto.mli

@@ -5,7 +5,7 @@ type fmt =
 | Gaussian
 
 type t =
-  { sym : Symmetry.t ;
+  { sym : Angmom.t ;
     lc  : (GaussianPrimitive.t * Qptypes.AO_coef.t) list;
   } [@@deriving sexp]
 

ocaml/Input_ao_basis.ml

@@ -9,7 +9,7 @@ module Ao_basis : sig
       ao_prim_num     : AO_prim_number.t array;
       ao_prim_num_max : AO_prim_number.t;
       ao_nucl         : Nucl_number.t array;
-      ao_power        : Symmetry.Xyz.t array;
+      ao_power        : Angmom.Xyz.t array;
       ao_coef         : AO_coef.t array;
       ao_expo         : AO_expo.t array;
       ao_cartesian    : bool;
@@ -32,7 +32,7 @@ end = struct
       ao_prim_num     : AO_prim_number.t array;
       ao_prim_num_max : AO_prim_number.t;
       ao_nucl         : Nucl_number.t array;
-      ao_power        : Symmetry.Xyz.t array;
+      ao_power        : Angmom.Xyz.t array;
       ao_coef         : AO_coef.t array;
       ao_expo         : AO_expo.t array;
       ao_cartesian    : bool;
@@ -87,7 +87,7 @@ end = struct
       if (data.(2*dim+i-1) > 0) then
         result.(i-1) <- result.(i-1)^"z"^(string_of_int data.(2*dim+i-1));
     done;
-    Array.map Symmetry.Xyz.of_string result
+    Array.map Angmom.Xyz.of_string result
   ;;
 
   let read_ao_coef () =
@@ -133,7 +133,7 @@ end = struct
     let ao_num = AO_number.to_int b.ao_num in
     let gto_array = Array.init (AO_number.to_int b.ao_num)
       (fun i ->
-        let s = Symmetry.Xyz.to_symmetry b.ao_power.(i) in
+        let s = Angmom.Xyz.to_symmetry b.ao_power.(i) in
         let ao_prim_num = AO_prim_number.to_int b.ao_prim_num.(i) in
         let prims = List.init ao_prim_num (fun j ->
           let prim = { GaussianPrimitive.sym  = s ;
@@ -217,9 +217,9 @@ end = struct
      let ao_power =
        let l = Array.to_list ao_power in 
        List.concat [
-         (list_map (fun a -> Positive_int.to_int a.Symmetry.Xyz.x) l) ;
+         (list_map (fun a -> Positive_int.to_int a.Angmom.Xyz.x) l) ;
-         (list_map (fun a -> Positive_int.to_int a.Symmetry.Xyz.y) l) ;
+         (list_map (fun a -> Positive_int.to_int a.Angmom.Xyz.y) l) ;
-         (list_map (fun a -> Positive_int.to_int a.Symmetry.Xyz.z) l) ]
+         (list_map (fun a -> Positive_int.to_int a.Angmom.Xyz.z) l) ]
      in
      Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list
      ~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ;
@@ -409,7 +409,7 @@ end = struct
       | [] -> []
       | (i,n,x)::tail  ->
           (Printf.sprintf " %5d  %6d     %-8s\n" i (Nucl_number.to_int n)
-            (Symmetry.Xyz.to_string x)
+            (Angmom.Xyz.to_string x)
           )::(do_work tail)
       in do_work l
       |> String.concat ""
@@ -496,7 +496,7 @@ md5                     = %s
     (b.ao_nucl |> Array.to_list |> list_map Nucl_number.to_string |>
       String.concat ", ")
     (b.ao_power |> Array.to_list |> list_map (fun x->
-      "("^(Symmetry.Xyz.to_string x)^")" )|> String.concat ", ")
+      "("^(Angmom.Xyz.to_string x)^")" )|> String.concat ", ")
     (b.ao_coef  |> Array.to_list |> list_map AO_coef.to_string
       |> String.concat ", ")
     (b.ao_expo  |> Array.to_list |> list_map AO_expo.to_string

ocaml/Long_basis.ml

@@ -2,7 +2,7 @@ open Qptypes
 open Qputils
 open Sexplib.Std
 
-type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t ) list [@@deriving sexp]
+type t = (Angmom.Xyz.t * Gto.t * Nucl_number.t ) list [@@deriving sexp]
 
 let of_basis b =
   let rec do_work accu = function
@@ -10,7 +10,7 @@ let of_basis b =
     | (g,n)::tail ->
         begin
           let new_accu =
-            Symmetry.Xyz.of_symmetry g.Gto.sym
+            Angmom.Xyz.of_symmetry g.Gto.sym
             |> List.rev_map (fun x-> (x,g,n))
           in
           do_work (new_accu@accu) tail
@@ -25,7 +25,7 @@ let to_basis b =
   | [] -> List.rev accu
   | (s,g,n)::tail ->
     let first_sym =
-      Symmetry.Xyz.of_symmetry g.Gto.sym
+      Angmom.Xyz.of_symmetry g.Gto.sym
       |> List.hd
     in
     let new_accu =
@@ -42,7 +42,7 @@ let to_basis b =
 let to_string b =
   let middle = list_map (fun (x,y,z) ->
      "( "^((string_of_int (Nucl_number.to_int z)))^", "^
-     (Symmetry.Xyz.to_string x)^", "^(Gto.to_string y)
+     (Angmom.Xyz.to_string x)^", "^(Gto.to_string y)
      ^" )"
   ) b
   |> String.concat ",\n"

ocaml/Long_basis.mli

@@ -5,16 +5,16 @@ open Qptypes;;
   * all the D orbitals are converted to xx, xy, xz, yy, yx
   * etc
 *)
-type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list [@@deriving sexp]
+type t = (Angmom.Xyz.t * Gto.t * Nucl_number.t) list [@@deriving sexp]
 
 (** Transform a basis to a long basis *)
 val of_basis :
-  (Gto.t * Nucl_number.t) list -> (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list
+  (Gto.t * Nucl_number.t) list -> (Angmom.Xyz.t * Gto.t * Nucl_number.t) list
 
 (** Transform a long basis to a basis *)
 val to_basis :
-  (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list -> (Gto.t * Nucl_number.t) list
+  (Angmom.Xyz.t * Gto.t * Nucl_number.t) list -> (Gto.t * Nucl_number.t) list
 
 (** Convert the basis into its string representation *)
 val to_string :
-  (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list -> string
+  (Angmom.Xyz.t * Gto.t * Nucl_number.t) list -> string

ocaml/Primitive.mli

@@ -1,5 +1,5 @@
 type t =
-{ sym : Symmetry.t;
+{ sym : Angmom.t;
   expo : Qptypes.AO_expo.t;
 } [@@deriving sexp]
 
@@ -7,5 +7,5 @@ type t =
 val to_string : t -> string
 
 (** Creation *)
-val of_sym_expo : Symmetry.t -> Qptypes.AO_expo.t -> t
+val of_sym_expo : Angmom.t -> Qptypes.AO_expo.t -> t
 

ocaml/qp_create_ezfio.ml

@@ -512,13 +512,14 @@ let run ?o b au c d m p cart xyz_file =
       let ao_num = List.length long_basis in
       Ezfio.set_ao_basis_ao_num ao_num;
       Ezfio.set_ao_basis_ao_basis b;
+      Ezfio.set_basis_basis b;
       let ao_prim_num = list_map (fun (_,g,_) -> List.length g.Gto.lc) long_basis 
       and ao_nucl = list_map (fun (_,_,n) -> Nucl_number.to_int n) long_basis 
       and ao_power=
         let l = list_map (fun (x,_,_) -> x) long_basis in
-        (list_map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) l)@
+        (list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.x)) l)@
-        (list_map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) l)@
+        (list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.y)) l)@
-        (list_map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) l)
+        (list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.z)) l)
       in
       let ao_prim_num_max = List.fold_left (fun s x ->
         if x > s then x

src/basis/EZFIO.cfg

@@ -0,0 +1,47 @@
+[basis]
+type: character*(256)
+doc: Name of the |AO| basis set
+interface: ezfio
+
+[shell_num]
+type: integer
+doc: Number of shells
+interface: ezfio, provider
+
+[shell_normalization_factor]
+type: double precision
+doc: Number of primitives per |AO|
+size: (basis.shell_num)
+interface: ezfio, provider
+
+[shell_prim_num]
+type: integer
+doc: Max number of primitives in a shell
+size: (basis.shell_num)
+interface: ezfio, provider
+
+[shell_prim_index]
+type: integer
+doc: Max number of primitives in a shell
+size: (basis.shell_num)
+interface: ezfio, provider
+
+[shell_nucl]
+type: integer
+doc: Index of the nucleus on which the shell is centered
+size: (basis.shell_num)
+interface: ezfio, provider
+
+[shell_coef]
+type: double precision
+doc: Primitive coefficients
+size: (basis.shell_prim_num)
+interface: ezfio, provider
+
+[shell_expo]
+type: double precision
+doc: Exponents in the shell
+size: (basis.shell_prim_num)
+interface: ezfio, provider
+
+

src/basis/NEED

@@ -0,0 +1 @@
+nuclei

src/basis/README.rst

@@ -0,0 +1,8 @@
+======
+basis
+======
+
+This module contains the basis set information, which will then be used to build the atomic orbitals.
+
+
+

src/basis/basis.irp.f

@@ -0,0 +1,32 @@
+BEGIN_PROVIDER [ double precision, basis_normalization_factor, (shell_num) ]
+  implicit none
+  BEGIN_DOC
+  ! Normalization factors of the shells
+  END_DOC
+  double precision               :: norm,overlap_x,overlap_y,overlap_z,C_A(3), c
+  integer                        :: l, powA(3), nz
+  integer                        :: i,j,k
+  nz=100
+  C_A(1) = 0.d0
+  C_A(2) = 0.d0
+  C_A(3) = 0.d0
+
+  do i=1,shell_num
+    powA(1) = shell_ang_mom(i)
+    powA(2) = 0
+    powA(3) = 0
+
+    ! Normalization of the contracted basis functions
+    norm = 0.d0
+    do j=shell_prim_index(i), shell_prim_index(i)+shell_prim_num(i)-1
+     do k=shell_prim_index(i), shell_prim_index(i)+shell_prim_num(i)-1
+      call overlap_gaussian_xyz(C_A,C_A,shell_prim_expo(j),shell_prim_expo(k), &
+          powA,powA,overlap_x,overlap_y,overlap_z,c,nz)
+      norm = norm+c*shell_prim_coef(j)*shell_prim_coef(k)
+     enddo
+    enddo
+    basis_normalization_factor(i) = basis_normalization_factor(i) * sqrt(norm)
+
+  enddo
+
+END_PROVIDER