mirror of https://gitlab.com/scemama/QCaml.git
Added Angstrom
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0687671098
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@ -49,10 +49,10 @@ atoms_xyz:
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atoms_list:
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| { [] }
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| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { (Element.of_string $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }
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| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { (Element.of_string $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }
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| atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { (Element.of_int $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }
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| atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { (Element.of_int $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }
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| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { (Element.of_string $2, Coordinate.of_3_floats $4 $6 $8 `Angstrom ) :: $1 }
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| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { (Element.of_string $2, Coordinate.of_3_floats $4 $6 $8 `Angstrom ) :: $1 }
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| atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { (Element.of_int $2, Coordinate.of_3_floats $4 $6 $8 `Angstrom ) :: $1 }
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| atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { (Element.of_int $2, Coordinate.of_3_floats $4 $6 $8 `Angstrom ) :: $1 }
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@ -1,55 +1,97 @@
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type t = float array
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type t =
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| Bohr of float array
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| Angstrom of float array
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let zero =
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[| 0. ; 0. ; 0. |]
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(** Bohr radius, taken from https://physics.nist.gov/cgi-bin/cuu/Value?bohrrada0 *)
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let a0 =
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0.529_177_210_67
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let of_float_triplet (x,y,z) =
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[|x;y;z|]
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let zero = Bohr [| 0. ; 0. ; 0. |]
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let of_float_triplet (x,y,z) = function
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| `Bohr -> Bohr [|x;y;z|]
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| `Angstrom -> Angstrom [|x;y;z|]
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let of_3_floats x y z =
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[|x;y;z|]
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of_float_triplet (x,y,z)
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let to_string x =
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(string_of_float x.(0))^" "^(string_of_float x.(1))^" "^(string_of_float x.(2))
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let to_string y =
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let result x =
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(string_of_float x.(0))^" "^(string_of_float x.(1))^" "^(string_of_float x.(2))
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in
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match y with
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| Bohr x -> (result x) ^ " Bohr"
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| Angstrom x -> (result x) ^ " Angstrom"
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let to_float_array = function
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| Bohr a
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| Angstrom a -> a
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let x a = (to_float_array a).(0)
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let y a = (to_float_array a).(1)
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let z a = (to_float_array a).(2)
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let x a = a.(0)
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let y a = a.(1)
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let z a = a.(2)
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let coord a = function
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| 0 -> a.(0)
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| 1 -> a.(1)
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| 2 -> a.(2)
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| _ -> raise (Invalid_argument "Coordinate")
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| 0 -> (to_float_array a).(0)
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| 1 -> (to_float_array a).(1)
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| 2 -> (to_float_array a).(2)
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| _ -> raise (Invalid_argument "Coordinate")
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let to_float_array a = a
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(** Linear algebra *)
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let (|-) a b =
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match a,b with
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| [|x;y;z|], [|x';y';z'|] -> [| x-.x'; y-.y'; z-.z' |]
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| _ -> assert false
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let (|+) a b =
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match a,b with
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| [|x;y;z|], [|x';y';z'|] -> [| x+.x'; y+.y'; z+.z' |]
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| _ -> assert false
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let (|.) s a =
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match a with
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| [|x;y;z|] -> [| s*.x; s*.y; s*.z |]
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| Bohr [|x;y;z|] -> Bohr [| s*.x; s*.y; s*.z |]
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| Angstrom [|x;y;z|] -> Angstrom [| s*.x; s*.y; s*.z |]
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| _ -> assert false
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let to_Angstrom = function
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| Angstrom a -> Angstrom a
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| Bohr a -> Angstrom (a0 |. Bohr a |> to_float_array)
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let dot a b =
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match a,b with
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| [|x;y;z|], [|x';y';z'|] -> x*.x' +. y*.y' +. z*.z'
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| _ -> assert false
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let to_Bohr = function
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| Angstrom a -> Bohr (1./.a0 |. Angstrom a |> to_float_array)
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| Bohr a -> Bohr a
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let (|-), (|+) =
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let rec op f p q =
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match (p, q) with
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| (Angstrom a, Angstrom b) -> Angstrom (f a b)
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| (Bohr a, Bohr b) -> Bohr (f a b)
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| (Angstrom a, Bohr b) -> op f (to_Bohr p) q
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| (Bohr a, Angstrom b) -> op f p (to_Bohr q)
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in
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(op (fun a b ->
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match a,b with
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| [|x;y;z|], [|x';y';z'|] -> [| x-.x'; y-.y'; z-.z' |]
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| _ -> assert false
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) ,
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op (fun a b ->
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match a,b with
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| [|x;y;z|], [|x';y';z'|] -> [| x+.x'; y+.y'; z+.z' |]
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| _ -> assert false
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)
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)
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let dot =
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let rec op f p q =
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match (p, q) with
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| (Angstrom a, Angstrom b)
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| (Bohr a, Bohr b) -> f a b
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| (Angstrom a, Bohr b) -> op f (to_Bohr p) q
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| (Bohr a, Angstrom b) -> op f p (to_Bohr q)
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in
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op (fun a b ->
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match a,b with
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| [|x;y;z|], [|x';y';z'|] -> x*.x' +. y*.y' +. z*.z'
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| _ -> assert false
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)
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let norm u =
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sqrt @@ dot u u
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@ -1,7 +1,7 @@
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type t
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val zero : t
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val of_float_triplet : float * float * float -> t
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val of_3_floats : float -> float -> float -> t
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val of_float_triplet : float * float * float -> [< `Angstrom | `Bohr ] -> t
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val of_3_floats : float -> float -> float -> [< `Angstrom | `Bohr ] -> t
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val to_string : t -> string
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val x : t -> float
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val y : t -> float
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@ -32,6 +32,11 @@ let run ~coord ~basis =
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let () =
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let usage_msg = "Quantum Chemistry Package. Options available:" in
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let usage_msg = "Available options:" in
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Arg.parse speclist (fun _ -> ()) usage_msg;
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run ~coord:!coord_file ~basis:!basis_file
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try
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run ~coord:!coord_file ~basis:!basis_file
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with
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| Invalid_argument e ->
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(print_string "Error: " ; print_endline e; print_newline () ; Arg.usage speclist usage_msg)
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;
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