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Changed Symmetry into Angmom in OCaml

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This commit is contained in:
Anthony Scemama 2021-05-21 16:42:48 +02:00
parent 3ceea5e8b2
commit 68b33e4b35
14 changed files with 121 additions and 32 deletions
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6
ocaml/Symmetry.ml → ocaml/Angmom.ml
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@ -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

0
ocaml/Symmetry.mli → ocaml/Angmom.mli
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4
ocaml/GaussianPrimitive.ml
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@ -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)

8
ocaml/Gto.ml
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@ -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

2
ocaml/Gto.mli
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@ -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]

18
ocaml/Input_ao_basis.ml
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@ -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.Symmetry.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.x) l) ;
(list_map (fun a -> Positive_int.to_int a.Angmom.Xyz.y) 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

8
ocaml/Long_basis.ml
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@ -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"

8
ocaml/Long_basis.mli
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@ -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

4
ocaml/Primitive.mli
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@ -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

7
ocaml/qp_create_ezfio.ml
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@ -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 Symmetry.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.x)) l)@
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.y)) 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

47
src/basis/EZFIO.cfg Normal file
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@ -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

1
src/basis/NEED Normal file
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@ -0,0 +1 @@
nuclei

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

32
src/basis/basis.irp.f Normal file
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@ -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