mirror of
https://github.com/QuantumPackage/qp2.git
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Removing Core
This commit is contained in:
parent
da3ba4ef4b
commit
f203fbad2d
@ -1,4 +1,4 @@
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open Core
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open Sexplib.Std
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exception AtomError of string
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exception AtomError of string
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@ -11,20 +11,20 @@ type t =
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(** Read xyz coordinates of the atom *)
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(** Read xyz coordinates of the atom *)
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let of_string ~units s =
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let of_string ~units s =
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let buffer = s
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let buffer = s
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|> String.split ~on:' '
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|> String_ext.split ~on:' '
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|> List.filter ~f:(fun x -> x <> "")
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|> List.filter (fun x -> x <> "")
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in
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in
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match buffer with
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match buffer with
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| [ name; charge; x; y; z ] ->
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| [ name; charge; x; y; z ] ->
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{ element = Element.of_string name ;
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{ element = Element.of_string name ;
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charge = Charge.of_string charge ;
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charge = Charge.of_string charge ;
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coord = Point3d.of_string ~units (String.concat [x; y; z] ~sep:" ")
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coord = Point3d.of_string ~units (String.concat " " [x; y; z] )
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}
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}
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| [ name; x; y; z ] ->
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| [ name; x; y; z ] ->
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let e = Element.of_string name in
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let e = Element.of_string name in
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{ element = e ;
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{ element = e ;
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charge = Element.to_charge e;
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charge = Element.to_charge e;
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coord = Point3d.of_string ~units (String.concat [x; y; z] ~sep:" ")
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coord = Point3d.of_string ~units (String.concat " " [x; y; z])
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}
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}
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| _ -> raise (AtomError s)
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| _ -> raise (AtomError s)
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@ -33,7 +33,7 @@ let to_string ~units a =
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[ Element.to_string a.element ;
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[ Element.to_string a.element ;
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Charge.to_string a.charge ;
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Charge.to_string a.charge ;
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Point3d.to_string ~units a.coord ]
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Point3d.to_string ~units a.coord ]
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|> String.concat ~sep:" "
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|> String.concat " "
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let to_xyz a =
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let to_xyz a =
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12
ocaml/Bit.ml
12
ocaml/Bit.ml
@ -1,4 +1,4 @@
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open Core;;
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open Sexplib.Std
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(*
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(*
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Type for bits
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Type for bits
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@ -16,31 +16,31 @@ type t =
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let to_string = function
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let to_string = function
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| Zero -> "0"
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| Zero -> "0"
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| One -> "1"
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| One -> "1"
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;;
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let and_operator a b =
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let and_operator a b =
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match a, b with
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match a, b with
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| Zero, _ -> Zero
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| Zero, _ -> Zero
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| _, Zero -> Zero
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| _, Zero -> Zero
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| _, _ -> One
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| _, _ -> One
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;;
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let or_operator a b =
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let or_operator a b =
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match a, b with
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match a, b with
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| One, _ -> One
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| One, _ -> One
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| _, One -> One
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| _, One -> One
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| _, _ -> Zero
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| _, _ -> Zero
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;;
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let xor_operator a b =
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let xor_operator a b =
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match a, b with
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match a, b with
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| One, Zero -> One
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| One, Zero -> One
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| Zero, One -> One
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| Zero, One -> One
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| _, _ -> Zero
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| _, _ -> Zero
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;;
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let not_operator = function
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let not_operator = function
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| One -> Zero
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| One -> Zero
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| Zero -> One
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| Zero -> One
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;;
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@ -1,5 +1,4 @@
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open Qptypes
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open Qptypes
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open Core
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(*
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(*
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Type for bits strings
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Type for bits strings
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@ -22,15 +21,15 @@ let to_string b =
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let of_string ?(zero='0') ?(one='1') s =
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let of_string ?(zero='0') ?(one='1') s =
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String.to_list s
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List.init (String.length s) (String.get s)
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|> List.rev_map ~f:( fun c ->
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|> List.rev_map ( fun c ->
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if (c = zero) then Bit.Zero
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if (c = zero) then Bit.Zero
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else if (c = one) then Bit.One
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else if (c = one) then Bit.One
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else (failwith ("Error in bitstring ") ) )
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else (failwith ("Error in bitstring ") ) )
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let of_string_mp s =
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let of_string_mp s =
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String.to_list s
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List.init (String.length s) (String.get s)
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|> List.rev_map ~f:(function
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|> List.rev_map (function
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| '-' -> Bit.Zero
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| '-' -> Bit.Zero
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| '+' -> Bit.One
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| '+' -> Bit.One
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| _ -> failwith ("Error in bitstring ") )
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| _ -> failwith ("Error in bitstring ") )
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@ -44,7 +43,7 @@ let of_int64 i =
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| 1L -> Bit.One :: accu |> List.rev
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| 1L -> Bit.One :: accu |> List.rev
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| i ->
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| i ->
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let b =
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let b =
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match (Int64.bit_and i 1L ) with
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match (Int64.logand i 1L ) with
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| 0L -> Bit.Zero
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| 0L -> Bit.Zero
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| 1L -> Bit.One
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| 1L -> Bit.One
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| _ -> raise (Failure "i land 1 not in (0,1)")
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| _ -> raise (Failure "i land 1 not in (0,1)")
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@ -70,18 +69,18 @@ let to_int64 l =
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let rec do_work accu = function
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let rec do_work accu = function
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| [] -> accu
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| [] -> accu
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| Bit.Zero::tail -> do_work Int64.(shift_left accu 1) tail
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| Bit.Zero::tail -> do_work Int64.(shift_left accu 1) tail
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| Bit.One::tail -> do_work Int64.(bit_or one (shift_left accu 1)) tail
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| Bit.One::tail -> do_work Int64.(logor one (shift_left accu 1)) tail
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in do_work Int64.zero (List.rev l)
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in do_work Int64.zero (List.rev l)
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(* Create a bit list from a list of int64 *)
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(* Create a bit list from a list of int64 *)
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let of_int64_list l =
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let of_int64_list l =
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List.map ~f:of_int64 l
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List.map of_int64 l
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|> List.concat
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|> List.concat
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(* Create a bit list from an array of int64 *)
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(* Create a bit list from an array of int64 *)
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let of_int64_array l =
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let of_int64_array l =
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Array.map ~f:of_int64 l
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Array.map of_int64 l
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|> Array.to_list
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|> Array.to_list
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|> List.concat
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|> List.concat
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@ -116,7 +115,7 @@ let to_int64_list l =
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in
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in
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let l = do_work [] [] 1 l
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let l = do_work [] [] 1 l
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in
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in
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List.rev_map ~f:to_int64 l
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List.rev_map to_int64 l
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(* Create an array of int64 from a bit list *)
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(* Create an array of int64 from a bit list *)
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let to_int64_array l =
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let to_int64_array l =
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@ -127,8 +126,8 @@ let to_int64_array l =
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let of_mo_number_list n_int l =
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let of_mo_number_list n_int l =
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let n_int = N_int_number.to_int n_int in
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let n_int = N_int_number.to_int n_int in
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let length = n_int*64 in
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let length = n_int*64 in
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let a = Array.create length (Bit.Zero) in
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let a = Array.make length (Bit.Zero) in
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List.iter ~f:(fun i-> a.((MO_number.to_int i)-1) <- Bit.One) l;
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List.iter (fun i-> a.((MO_number.to_int i)-1) <- Bit.One) l;
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Array.to_list a
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Array.to_list a
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@ -183,10 +182,10 @@ let not_operator b = logical_operator1 Bit.not_operator b
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let popcnt b =
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let popcnt b =
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List.fold_left b ~init:0 ~f:(fun accu -> function
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List.fold_left (fun accu -> function
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| Bit.One -> accu+1
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| Bit.One -> accu+1
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| Bit.Zero -> accu
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| Bit.Zero -> accu
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)
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) 0 b
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@ -1,14 +1,14 @@
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open Core
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open Sexplib.Std
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type t = float [@@deriving sexp]
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type t = float [@@deriving sexp]
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let of_float x = x
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let of_float x = x
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let of_int i = Float.of_int i
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let of_int i = float_of_int i
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let of_string s = Float.of_string s
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let of_string s = float_of_string s
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let to_float x = x
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let to_float x = x
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let to_int x = Float.to_int x
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let to_int x = int_of_float x
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let to_string x =
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let to_string x =
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if x >= 0. then
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if x >= 0. then
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Printf.sprintf "+%f" x
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Printf.sprintf "+%f" x
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@ -1,4 +1,3 @@
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open Core
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open Qptypes
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open Qptypes
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module Hole = struct
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module Hole = struct
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@ -56,7 +55,7 @@ let to_string = function
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"," ;
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"," ;
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(MO_class.to_string (Particle.to_mo_class p));
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(MO_class.to_string (Particle.to_mo_class p));
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"]"]
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"]"]
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|> String.concat ~sep:" "
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|> String.concat " "
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| Double (h1,p1,h2,p2) ->
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| Double (h1,p1,h2,p2) ->
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[ "Double Exc. : [" ;
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[ "Double Exc. : [" ;
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(MO_class.to_string (Hole.to_mo_class h1));
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(MO_class.to_string (Hole.to_mo_class h1));
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@ -67,6 +66,6 @@ let to_string = function
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"," ;
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"," ;
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(MO_class.to_string (Particle.to_mo_class p2));
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(MO_class.to_string (Particle.to_mo_class p2));
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"]"]
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"]"]
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|> String.concat ~sep:" "
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|> String.concat " "
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@ -1,10 +1,10 @@
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open Qptypes
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open Qptypes
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open Core
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open Sexplib.Std
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type t =
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type t =
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{ sym : Symmetry.t ;
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{ sym : Symmetry.t ;
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expo : AO_expo.t ;
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expo : AO_expo.t ;
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} [@@deriving sexp]
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} [@@deriving sexp]
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let to_string p =
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let to_string p =
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let { sym = s ; expo = e } = p in
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let { sym = s ; expo = e } = p in
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@ -1,5 +1,6 @@
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open Core;;
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open Sexplib
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open Qptypes;;
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open Sexplib.Std
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open Qptypes
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let fail_msg str (ex,range) =
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let fail_msg str (ex,range) =
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@ -15,25 +16,25 @@ let fail_msg str (ex,range) =
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let start_pos = range.start_pos.offset
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let start_pos = range.start_pos.offset
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and end_pos = range.end_pos.offset
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and end_pos = range.end_pos.offset
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in
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in
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let pre = String.sub ~pos:0 ~len:start_pos str
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let pre = String.sub str 0 start_pos
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and mid = String.sub ~pos:start_pos ~len:(end_pos-start_pos) str
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and mid = String.sub str start_pos (end_pos-start_pos)
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and post = String.sub ~pos:(end_pos)
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and post = String.sub str (end_pos)
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~len:((String.length str)-(end_pos)) str
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((String.length str)-(end_pos))
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in
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in
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let str = Printf.sprintf "%s ## %s ## %s" pre mid post
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let str = Printf.sprintf "%s ## %s ## %s" pre mid post
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in
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in
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let str = String.tr str ~target:'(' ~replacement:' '
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let str = String_ext.tr str ~target:'(' ~replacement:' '
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|> String.split ~on:')'
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|> String_ext.split ~on:')'
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|> List.map ~f:String.strip
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|> List.map String_ext.strip
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|> List.filter ~f:(fun x ->
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|> List.filter (fun x ->
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match String.substr_index x ~pos:0 ~pattern:"##" with
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match String_ext.substr_index ~pos:0 ~pattern:"##" x with
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| None -> false
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| None -> false
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| Some _ -> true
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| Some _ -> true
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)
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)
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|> String.concat ~sep:"\n"
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|> String.concat "\n"
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in
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in
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Printf.eprintf "Error: (%s)\n\n %s\n\n" msg str;
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Printf.eprintf "Error: (%s)\n\n %s\n\n" msg str
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;;
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let evaluate_sexp t_of_sexp s =
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let evaluate_sexp t_of_sexp s =
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@ -41,20 +42,19 @@ let evaluate_sexp t_of_sexp s =
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match ( Sexp.of_string_conv sexp t_of_sexp ) with
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match ( Sexp.of_string_conv sexp t_of_sexp ) with
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| `Result r -> Some r
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| `Result r -> Some r
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| `Error ex -> ( fail_msg sexp ex; None)
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| `Error ex -> ( fail_msg sexp ex; None)
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;;
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|
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let of_rst t_of_sexp s =
|
let of_rst t_of_sexp s =
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Rst_string.to_string s
|
Rst_string.to_string s
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|> String.split ~on:'\n'
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|> String_ext.split ~on:'\n'
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|> List.filter ~f:(fun line ->
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|> List.filter (fun line -> String.contains line '=')
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String.contains line '=')
|
|> List.map (fun line ->
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|> List.map ~f:(fun line ->
|
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"("^(
|
"("^(
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String.tr line ~target:'=' ~replacement:' '
|
String_ext.tr ~target:'=' ~replacement:' ' line
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)^")" )
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)^")" )
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|> String.concat
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|> String.concat ""
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|> evaluate_sexp t_of_sexp
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|> evaluate_sexp t_of_sexp
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;;
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|
@ -1,4 +1,4 @@
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open Core
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open Sexplib.Std
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open Qptypes
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open Qptypes
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|
|
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(** New job : Request to create a new multi-tasked job *)
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(** New job : Request to create a new multi-tasked job *)
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@ -161,7 +161,7 @@ end = struct
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}
|
}
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let create ~state ~tasks = { state = State.of_string state ; tasks }
|
let create ~state ~tasks = { state = State.of_string state ; tasks }
|
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let to_string x =
|
let to_string x =
|
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Printf.sprintf "add_task %s %s" (State.to_string x.state) (String.concat ~sep:"|" x.tasks)
|
Printf.sprintf "add_task %s %s" (State.to_string x.state) (String.concat "|" x.tasks)
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end
|
end
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|
|
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|
|
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@ -193,12 +193,12 @@ end = struct
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}
|
}
|
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let create ~state ~task_ids =
|
let create ~state ~task_ids =
|
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{ state = State.of_string state ;
|
{ state = State.of_string state ;
|
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task_ids = List.map ~f:Id.Task.of_int task_ids
|
task_ids = List.map Id.Task.of_int task_ids
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}
|
}
|
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let to_string x =
|
let to_string x =
|
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Printf.sprintf "del_task %s %s"
|
Printf.sprintf "del_task %s %s"
|
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(State.to_string x.state)
|
(State.to_string x.state)
|
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(String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
|
(String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
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end
|
end
|
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|
|
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|
|
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@ -219,7 +219,7 @@ end = struct
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else "done"
|
else "done"
|
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in
|
in
|
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Printf.sprintf "del_task_reply %s %s"
|
Printf.sprintf "del_task_reply %s %s"
|
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more (String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
|
more (String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
|
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end
|
end
|
||||||
|
|
||||||
|
|
||||||
@ -303,11 +303,11 @@ end = struct
|
|||||||
"get_tasks_reply ok"
|
"get_tasks_reply ok"
|
||||||
let to_string_list x =
|
let to_string_list x =
|
||||||
"get_tasks_reply ok" :: (
|
"get_tasks_reply ok" :: (
|
||||||
List.map x ~f:(fun (task_id, task) ->
|
List.map (fun (task_id, task) ->
|
||||||
match task_id with
|
match task_id with
|
||||||
| Some task_id -> Printf.sprintf "%d %s" (Id.Task.to_int task_id) task
|
| Some task_id -> Printf.sprintf "%d %s" (Id.Task.to_int task_id) task
|
||||||
| None -> Printf.sprintf "0 terminate"
|
| None -> Printf.sprintf "0 terminate"
|
||||||
) )
|
) x )
|
||||||
|
|
||||||
end
|
end
|
||||||
|
|
||||||
@ -408,14 +408,14 @@ end = struct
|
|||||||
let create ~state ~client_id ~task_ids =
|
let create ~state ~client_id ~task_ids =
|
||||||
{ client_id = Id.Client.of_int client_id ;
|
{ client_id = Id.Client.of_int client_id ;
|
||||||
state = State.of_string state ;
|
state = State.of_string state ;
|
||||||
task_ids = List.map ~f:Id.Task.of_int task_ids;
|
task_ids = List.map Id.Task.of_int task_ids;
|
||||||
}
|
}
|
||||||
|
|
||||||
let to_string x =
|
let to_string x =
|
||||||
Printf.sprintf "task_done %s %d %s"
|
Printf.sprintf "task_done %s %d %s"
|
||||||
(State.to_string x.state)
|
(State.to_string x.state)
|
||||||
(Id.Client.to_int x.client_id)
|
(Id.Client.to_int x.client_id)
|
||||||
(String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
|
(String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
|
||||||
end
|
end
|
||||||
|
|
||||||
(** Terminate *)
|
(** Terminate *)
|
||||||
@ -460,7 +460,7 @@ end = struct
|
|||||||
type t = string
|
type t = string
|
||||||
let create x = x
|
let create x = x
|
||||||
let to_string x =
|
let to_string x =
|
||||||
String.concat ~sep:" " [ "error" ; x ]
|
String.concat " " [ "error" ; x ]
|
||||||
end
|
end
|
||||||
|
|
||||||
|
|
||||||
|
@ -207,7 +207,7 @@ let distance_matrix molecule =
|
|||||||
|
|
||||||
|
|
||||||
|
|
||||||
open Core ;;
|
|
||||||
include To_md5
|
include To_md5
|
||||||
let to_md5 = to_md5 sexp_of_t
|
let to_md5 = to_md5 sexp_of_t
|
||||||
|
|
||||||
|
@ -1,10 +1,11 @@
|
|||||||
open Core;;
|
open Qptypes
|
||||||
open Qptypes ;;
|
open Sexplib.Std
|
||||||
|
|
||||||
type t = Strictly_positive_int.t [@@deriving sexp]
|
type t = Strictly_positive_int.t [@@deriving sexp]
|
||||||
|
|
||||||
let of_int = Strictly_positive_int.of_int ;;
|
let of_int = Strictly_positive_int.of_int
|
||||||
let to_int = Strictly_positive_int.to_int ;;
|
|
||||||
|
let to_int = Strictly_positive_int.to_int
|
||||||
|
|
||||||
let to_string m =
|
let to_string m =
|
||||||
match (to_int m) with
|
match (to_int m) with
|
||||||
@ -18,7 +19,7 @@ let to_string m =
|
|||||||
| 8 -> "Octet"
|
| 8 -> "Octet"
|
||||||
| 9 -> "Nonet"
|
| 9 -> "Nonet"
|
||||||
| i -> Printf.sprintf "%d-et" i
|
| i -> Printf.sprintf "%d-et" i
|
||||||
;;
|
|
||||||
|
|
||||||
let of_alpha_beta a b =
|
let of_alpha_beta a b =
|
||||||
let a = Elec_alpha_number.to_int a
|
let a = Elec_alpha_number.to_int a
|
||||||
@ -26,11 +27,11 @@ let of_alpha_beta a b =
|
|||||||
in
|
in
|
||||||
assert (a >= b);
|
assert (a >= b);
|
||||||
of_int (1 + a - b)
|
of_int (1 + a - b)
|
||||||
;;
|
|
||||||
|
|
||||||
let to_alpha_beta ne m =
|
let to_alpha_beta ne m =
|
||||||
let ne = Elec_number.to_int ne in
|
let ne = Elec_number.to_int ne in
|
||||||
let nb = (ne-(to_int m)+1)/2 in
|
let nb = (ne-(to_int m)+1)/2 in
|
||||||
let na = ne - nb in
|
let na = ne - nb in
|
||||||
(Elec_alpha_number.of_int na, Elec_beta_number.of_int nb)
|
(Elec_alpha_number.of_int na, Elec_beta_number.of_int nb)
|
||||||
;;
|
|
||||||
|
@ -1,5 +1,3 @@
|
|||||||
open Core
|
|
||||||
|
|
||||||
type t =
|
type t =
|
||||||
{
|
{
|
||||||
title: string;
|
title: string;
|
||||||
@ -7,14 +5,14 @@ type t =
|
|||||||
cur_value : float;
|
cur_value : float;
|
||||||
end_value : float;
|
end_value : float;
|
||||||
bar_length : int;
|
bar_length : int;
|
||||||
init_time : Time.t;
|
init_time : float;
|
||||||
dirty : bool;
|
dirty : bool;
|
||||||
next : Time.t;
|
next : float;
|
||||||
}
|
}
|
||||||
|
|
||||||
let init ?(bar_length=20) ?(start_value=0.) ?(end_value=1.) ~title =
|
let init ?(bar_length=20) ?(start_value=0.) ?(end_value=1.) ~title =
|
||||||
{ title ; start_value ; end_value ; bar_length ; cur_value=start_value ;
|
{ title ; start_value ; end_value ; bar_length ; cur_value=start_value ;
|
||||||
init_time= Time.now () ; dirty = false ; next = Time.now () }
|
init_time= Unix.time () ; dirty = false ; next = Unix.time () }
|
||||||
|
|
||||||
let update ~cur_value bar =
|
let update ~cur_value bar =
|
||||||
{ bar with cur_value ; dirty=true }
|
{ bar with cur_value ; dirty=true }
|
||||||
@ -40,23 +38,23 @@ let display_tty bar =
|
|||||||
|> Float.to_int
|
|> Float.to_int
|
||||||
in
|
in
|
||||||
let hashes =
|
let hashes =
|
||||||
String.init bar.bar_length ~f:(fun i ->
|
String.init bar.bar_length (fun i ->
|
||||||
if (i < n_hashes) then '#'
|
if (i < n_hashes) then '#'
|
||||||
else ' '
|
else ' '
|
||||||
)
|
)
|
||||||
in
|
in
|
||||||
let now =
|
let now =
|
||||||
Time.now ()
|
Unix.time ()
|
||||||
in
|
in
|
||||||
let running_time =
|
let running_time =
|
||||||
Time.abs_diff now bar.init_time
|
now -. bar.init_time
|
||||||
in
|
in
|
||||||
Printf.eprintf "%s : [%s] %4.1f%% | %10s\r%!"
|
Printf.eprintf "%s : [%s] %4.1f%% | %8.0f s\r%!"
|
||||||
bar.title
|
bar.title
|
||||||
hashes
|
hashes
|
||||||
percent
|
percent
|
||||||
(Time.Span.to_string running_time);
|
running_time;
|
||||||
{ bar with dirty = false ; next = Time.add now (Time.Span.of_sec 0.1) }
|
{ bar with dirty = false ; next = now +. 0.1 }
|
||||||
|
|
||||||
|
|
||||||
let display_file bar =
|
let display_file bar =
|
||||||
@ -65,19 +63,19 @@ let display_file bar =
|
|||||||
(bar.end_value -. bar.start_value)
|
(bar.end_value -. bar.start_value)
|
||||||
in
|
in
|
||||||
let running_time =
|
let running_time =
|
||||||
Time.abs_diff (Time.now ()) bar.init_time
|
(Unix.time ()) -. bar.init_time
|
||||||
in
|
in
|
||||||
Printf.eprintf "%5.2f %% in %20s \n%!"
|
Printf.eprintf "%5.2f %% in %20.0f seconds \n%!"
|
||||||
percent
|
percent
|
||||||
(Time.Span.to_string running_time);
|
running_time;
|
||||||
{ bar with dirty = false ; next = Time.add (Time.now ()) (Time.Span.of_sec 10.) }
|
{ bar with dirty = false ; next = (Unix.time ()) +. 10. }
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
let display bar =
|
let display bar =
|
||||||
if (not bar.dirty) then
|
if (not bar.dirty) then
|
||||||
bar
|
bar
|
||||||
else if (Time.now () < bar.next) then
|
else if (Unix.time () < bar.next) then
|
||||||
bar
|
bar
|
||||||
else
|
else
|
||||||
begin
|
begin
|
||||||
|
@ -1,4 +1,4 @@
|
|||||||
open Core
|
open Sexplib.Std
|
||||||
open Qptypes
|
open Qptypes
|
||||||
|
|
||||||
|
|
||||||
@ -81,12 +81,12 @@ let to_string_local = function
|
|||||||
| t ->
|
| t ->
|
||||||
"Local component:" ::
|
"Local component:" ::
|
||||||
( Printf.sprintf "%20s %8s %20s" "Coeff." "r^n" "Exp." ) ::
|
( Printf.sprintf "%20s %8s %20s" "Coeff." "r^n" "Exp." ) ::
|
||||||
( List.map t ~f:(fun (l,c) -> Printf.sprintf "%20f %8d %20f"
|
( List.map (fun (l,c) -> Printf.sprintf "%20f %8d %20f"
|
||||||
(AO_coef.to_float c)
|
(AO_coef.to_float c)
|
||||||
(R_power.to_int l.GaussianPrimitive_local.r_power)
|
(R_power.to_int l.GaussianPrimitive_local.r_power)
|
||||||
(AO_expo.to_float l.GaussianPrimitive_local.expo)
|
(AO_expo.to_float l.GaussianPrimitive_local.expo)
|
||||||
) )
|
) t )
|
||||||
|> String.concat ~sep:"\n"
|
|> String.concat "\n"
|
||||||
|
|
||||||
|
|
||||||
(** Transform the non-local component of the pseudopotential to a string *)
|
(** Transform the non-local component of the pseudopotential to a string *)
|
||||||
@ -95,7 +95,7 @@ let to_string_non_local = function
|
|||||||
| t ->
|
| t ->
|
||||||
"Non-local component:" ::
|
"Non-local component:" ::
|
||||||
( Printf.sprintf "%20s %8s %20s %8s" "Coeff." "r^n" "Exp." "Proj") ::
|
( Printf.sprintf "%20s %8s %20s %8s" "Coeff." "r^n" "Exp." "Proj") ::
|
||||||
( List.map t ~f:(fun (l,c) ->
|
( List.map (fun (l,c) ->
|
||||||
let p =
|
let p =
|
||||||
Positive_int.to_int l.GaussianPrimitive_non_local.proj
|
Positive_int.to_int l.GaussianPrimitive_non_local.proj
|
||||||
in
|
in
|
||||||
@ -104,8 +104,8 @@ let to_string_non_local = function
|
|||||||
(R_power.to_int l.GaussianPrimitive_non_local.r_power)
|
(R_power.to_int l.GaussianPrimitive_non_local.r_power)
|
||||||
(AO_expo.to_float l.GaussianPrimitive_non_local.expo)
|
(AO_expo.to_float l.GaussianPrimitive_non_local.expo)
|
||||||
p p
|
p p
|
||||||
) )
|
) t )
|
||||||
|> String.concat ~sep:"\n"
|
|> String.concat "\n"
|
||||||
|
|
||||||
(** Transform the Pseudopotential to a string *)
|
(** Transform the Pseudopotential to a string *)
|
||||||
let to_string t =
|
let to_string t =
|
||||||
@ -116,29 +116,30 @@ let to_string t =
|
|||||||
:: to_string_local t.local
|
:: to_string_local t.local
|
||||||
:: to_string_non_local t.non_local
|
:: to_string_non_local t.non_local
|
||||||
:: []
|
:: []
|
||||||
|> List.filter ~f:(fun x -> x <> "")
|
|> List.filter (fun x -> x <> "")
|
||||||
|> String.concat ~sep:"\n"
|
|> String.concat "\n"
|
||||||
|
|
||||||
|
|
||||||
(** Find an element in the file *)
|
(** Find an element in the file *)
|
||||||
let find in_channel element =
|
let find in_channel element =
|
||||||
In_channel.seek in_channel 0L;
|
seek_in in_channel 0;
|
||||||
|
|
||||||
let loop, element_read, old_pos =
|
let loop, element_read, old_pos =
|
||||||
ref true,
|
ref true,
|
||||||
ref None,
|
ref None,
|
||||||
ref (In_channel.pos in_channel)
|
ref (pos_in in_channel)
|
||||||
in
|
in
|
||||||
|
|
||||||
while !loop
|
while !loop
|
||||||
do
|
do
|
||||||
try
|
try
|
||||||
let buffer =
|
let buffer =
|
||||||
old_pos := In_channel.pos in_channel;
|
old_pos := pos_in in_channel;
|
||||||
match In_channel.input_line in_channel with
|
try
|
||||||
| Some line -> String.split ~on:' ' line
|
input_line in_channel
|
||||||
|> List.hd_exn
|
|> String_ext.split ~on:' '
|
||||||
| None -> raise End_of_file
|
|> List.hd
|
||||||
|
with _ -> raise End_of_file
|
||||||
in
|
in
|
||||||
element_read := Some (Element.of_string buffer);
|
element_read := Some (Element.of_string buffer);
|
||||||
loop := !element_read <> (Some element)
|
loop := !element_read <> (Some element)
|
||||||
@ -146,7 +147,7 @@ let find in_channel element =
|
|||||||
| Element.ElementError _ -> ()
|
| Element.ElementError _ -> ()
|
||||||
| End_of_file -> loop := false
|
| End_of_file -> loop := false
|
||||||
done ;
|
done ;
|
||||||
In_channel.seek in_channel !old_pos;
|
seek_in in_channel !old_pos;
|
||||||
!element_read
|
!element_read
|
||||||
|
|
||||||
|
|
||||||
@ -156,13 +157,13 @@ let read_element in_channel element =
|
|||||||
| Some e when e = element ->
|
| Some e when e = element ->
|
||||||
begin
|
begin
|
||||||
let rec read result =
|
let rec read result =
|
||||||
match In_channel.input_line in_channel with
|
try
|
||||||
| None -> result
|
let line = input_line in_channel in
|
||||||
| Some line ->
|
if (String.trim line = "") then
|
||||||
if (String.strip line = "") then
|
|
||||||
result
|
result
|
||||||
else
|
else
|
||||||
read (line::result)
|
read (line::result)
|
||||||
|
with _ -> result
|
||||||
in
|
in
|
||||||
|
|
||||||
let data =
|
let data =
|
||||||
@ -171,20 +172,20 @@ let read_element in_channel element =
|
|||||||
in
|
in
|
||||||
|
|
||||||
let debug_data =
|
let debug_data =
|
||||||
String.concat ~sep:"\n" data
|
String.concat "\n" data
|
||||||
in
|
in
|
||||||
|
|
||||||
let decode_first_line = function
|
let decode_first_line = function
|
||||||
| first_line :: rest ->
|
| first_line :: rest ->
|
||||||
begin
|
begin
|
||||||
let first_line_split =
|
let first_line_split =
|
||||||
String.split first_line ~on:' '
|
String_ext.split first_line ~on:' '
|
||||||
|> List.filter ~f:(fun x -> (String.strip x) <> "")
|
|> List.filter (fun x -> (String.trim x) <> "")
|
||||||
in
|
in
|
||||||
match first_line_split with
|
match first_line_split with
|
||||||
| e :: "GEN" :: n :: p ->
|
| e :: "GEN" :: n :: p ->
|
||||||
{ element = Element.of_string e ;
|
{ element = Element.of_string e ;
|
||||||
n_elec = Int.of_string n |> Positive_int.of_int ;
|
n_elec = int_of_string n |> Positive_int.of_int ;
|
||||||
local = [] ;
|
local = [] ;
|
||||||
non_local = []
|
non_local = []
|
||||||
}, rest
|
}, rest
|
||||||
@ -200,18 +201,18 @@ let read_element in_channel element =
|
|||||||
| (n,line::rest) ->
|
| (n,line::rest) ->
|
||||||
begin
|
begin
|
||||||
match
|
match
|
||||||
String.split line ~on:' '
|
String_ext.split line ~on:' '
|
||||||
|> List.filter ~f:(fun x -> String.strip x <> "")
|
|> List.filter (fun x -> String.trim x <> "")
|
||||||
with
|
with
|
||||||
| c :: i :: e :: [] ->
|
| c :: i :: e :: [] ->
|
||||||
let i =
|
let i =
|
||||||
Int.of_string i
|
int_of_string i
|
||||||
in
|
in
|
||||||
let elem =
|
let elem =
|
||||||
( create_primitive
|
( create_primitive
|
||||||
(Float.of_string e |> AO_expo.of_float)
|
(float_of_string e |> AO_expo.of_float)
|
||||||
(i-2 |> R_power.of_int),
|
(i-2 |> R_power.of_int),
|
||||||
Float.of_string c |> AO_coef.of_float
|
float_of_string c |> AO_coef.of_float
|
||||||
)
|
)
|
||||||
in
|
in
|
||||||
loop create_primitive (elem::accu) (n-1, rest)
|
loop create_primitive (elem::accu) (n-1, rest)
|
||||||
@ -230,8 +231,8 @@ let read_element in_channel element =
|
|||||||
match data with
|
match data with
|
||||||
| n :: rest ->
|
| n :: rest ->
|
||||||
let n =
|
let n =
|
||||||
String.strip n
|
String.trim n
|
||||||
|> Int.of_string
|
|> int_of_string
|
||||||
|> Positive_int.of_int
|
|> Positive_int.of_int
|
||||||
in
|
in
|
||||||
decode_local_n n rest
|
decode_local_n n rest
|
||||||
@ -250,8 +251,8 @@ let read_element in_channel element =
|
|||||||
match data with
|
match data with
|
||||||
| n :: rest ->
|
| n :: rest ->
|
||||||
let n =
|
let n =
|
||||||
String.strip n
|
String.trim n
|
||||||
|> Int.of_string
|
|> int_of_string
|
||||||
|> Positive_int.of_int
|
|> Positive_int.of_int
|
||||||
in
|
in
|
||||||
let result =
|
let result =
|
||||||
|
@ -1,45 +1,45 @@
|
|||||||
open Core;;
|
open Qptypes
|
||||||
open Qptypes;;
|
open Qputils
|
||||||
open Qputils;;
|
|
||||||
|
|
||||||
(** Variables related to the quantum package installation *)
|
(** Variables related to the quantum package installation *)
|
||||||
|
|
||||||
let root =
|
let root =
|
||||||
match (Sys.getenv "QP_ROOT") with
|
match (Sys.getenv_opt "QP_ROOT") with
|
||||||
| None -> failwith "QP_ROOT environment variable is not set.
|
| None -> failwith "QP_ROOT environment variable is not set.
|
||||||
Please source the quantum_package.rc file."
|
Please source the quantum_package.rc file."
|
||||||
| Some x -> x
|
| Some x -> x
|
||||||
;;
|
|
||||||
|
|
||||||
let bit_kind_size = lazy (
|
let bit_kind_size = lazy (
|
||||||
let filename = root^"/src/bitmask/bitmasks_module.f90" in
|
let filename = root^"/src/bitmask/bitmasks_module.f90" in
|
||||||
if not (Sys.file_exists_exn filename) then
|
if not (Sys.file_exists filename) then
|
||||||
raise (Failure ("File "^filename^" not found"));
|
raise (Failure ("File "^filename^" not found"));
|
||||||
|
|
||||||
let in_channel = In_channel.create filename in
|
let in_channel = open_in filename in
|
||||||
let lines = In_channel.input_lines in_channel in
|
let lines = input_lines in_channel in
|
||||||
In_channel.close in_channel;
|
close_in in_channel;
|
||||||
|
|
||||||
let rec get_data = function
|
let rec get_data = function
|
||||||
| [] -> raise (Failure ("bit_kind_size not found in "^filename))
|
| [] -> raise (Failure ("bit_kind_size not found in "^filename))
|
||||||
| line::tail ->
|
| line::tail ->
|
||||||
let line =
|
let line =
|
||||||
begin match String.split ~on:'!' line |> List.hd with
|
try
|
||||||
| Some x -> x
|
String_ext.split ~on:'!' line
|
||||||
| None -> ""
|
|> List.hd
|
||||||
end in
|
with _ -> line
|
||||||
begin match (String.rsplit2 ~on:':' line) with
|
in
|
||||||
|
begin match (String_ext.rsplit2 ~on:':' line) with
|
||||||
| Some (_ ,buffer) ->
|
| Some (_ ,buffer) ->
|
||||||
begin match (String.split ~on:'=' buffer |> List.map ~f:String.strip) with
|
begin match (String_ext.split ~on:'=' buffer |> List.map String.trim) with
|
||||||
| ["bit_kind_size"; x] ->
|
| ["bit_kind_size"; x] ->
|
||||||
Int.of_string x |> Bit_kind_size.of_int
|
int_of_string x |> Bit_kind_size.of_int
|
||||||
| _ -> get_data tail
|
| _ -> get_data tail
|
||||||
end
|
end
|
||||||
| _ -> get_data tail
|
| _ -> get_data tail
|
||||||
end
|
end
|
||||||
in
|
in
|
||||||
get_data lines )
|
get_data lines )
|
||||||
;;
|
|
||||||
|
|
||||||
let bit_kind = lazy (
|
let bit_kind = lazy (
|
||||||
Lazy.force bit_kind_size
|
Lazy.force bit_kind_size
|
||||||
@ -47,23 +47,26 @@ let bit_kind = lazy (
|
|||||||
|> fun x -> x / 8
|
|> fun x -> x / 8
|
||||||
|> Bit_kind.of_int
|
|> Bit_kind.of_int
|
||||||
)
|
)
|
||||||
;;
|
|
||||||
|
|
||||||
let executables = lazy (
|
let executables = lazy (
|
||||||
let filename = root^"/data/executables"
|
let filename = root^"/data/executables" in
|
||||||
and func in_channel =
|
let lines =
|
||||||
In_channel.input_lines in_channel
|
let in_channel = open_in filename in
|
||||||
|> List.map ~f:(fun x ->
|
let result = input_lines in_channel in
|
||||||
let e = String.split ~on:' ' x
|
close_in in_channel;
|
||||||
|> List.filter ~f:(fun x -> x <> "")
|
result
|
||||||
|
in
|
||||||
|
lines
|
||||||
|
|> List.map (fun x ->
|
||||||
|
let e = String_ext.split ~on:' ' x
|
||||||
|
|> List.filter (fun x -> x <> "")
|
||||||
in
|
in
|
||||||
match e with
|
match e with
|
||||||
| [a;b] -> (a,String.substr_replace_all ~pattern:"$QP_ROOT" ~with_:root b)
|
| [a;b] -> (a,String_ext.substr_replace_all ~pattern:"$QP_ROOT" ~with_:root b)
|
||||||
| _ -> ("","")
|
| _ -> ("","")
|
||||||
)
|
)
|
||||||
in
|
|> List.sort (fun (x,_) (y,_) ->
|
||||||
In_channel.with_file filename ~f:func
|
|
||||||
|> List.sort ~compare:(fun (x,_) (y,_) ->
|
|
||||||
if x < y then -1
|
if x < y then -1
|
||||||
else if x > y then 1
|
else if x > y then 1
|
||||||
else 0)
|
else 0)
|
||||||
@ -72,33 +75,37 @@ let executables = lazy (
|
|||||||
|
|
||||||
|
|
||||||
let get_ezfio_default_in_file ~directory ~data ~filename =
|
let get_ezfio_default_in_file ~directory ~data ~filename =
|
||||||
let lines = In_channel.with_file filename ~f:(fun in_channel ->
|
let lines =
|
||||||
In_channel.input_lines in_channel) in
|
let in_channel = open_in filename in
|
||||||
|
let result = input_lines in_channel in
|
||||||
|
close_in in_channel;
|
||||||
|
result
|
||||||
|
in
|
||||||
let rec find_dir = function
|
let rec find_dir = function
|
||||||
| line :: rest ->
|
| line :: rest ->
|
||||||
if ((String.strip line) = directory) then
|
if ((String.trim line) = directory) then
|
||||||
rest
|
rest
|
||||||
else
|
else
|
||||||
find_dir rest
|
find_dir rest
|
||||||
| [] -> raise Caml.Not_found
|
| [] -> raise Not_found
|
||||||
in
|
in
|
||||||
let rec find_data = function
|
let rec find_data = function
|
||||||
| line :: rest ->
|
| line :: rest ->
|
||||||
if (line = "") then
|
if (line = "") then
|
||||||
raise Caml.Not_found
|
raise Not_found
|
||||||
else if (line.[0] <> ' ') then
|
else if (line.[0] <> ' ') then
|
||||||
raise Caml.Not_found
|
raise Not_found
|
||||||
else
|
else
|
||||||
begin
|
begin
|
||||||
match (String.lsplit2 ~on:' ' (String.strip line)) with
|
match (String_ext.lsplit2 ~on:' ' (String.trim line)) with
|
||||||
| Some (l,r) ->
|
| Some (l,r) ->
|
||||||
if (l = data) then
|
if (l = data) then
|
||||||
String.strip r
|
String.trim r
|
||||||
else
|
else
|
||||||
find_data rest
|
find_data rest
|
||||||
| None -> raise Caml.Not_found
|
| None -> raise Not_found
|
||||||
end
|
end
|
||||||
| [] -> raise Caml.Not_found
|
| [] -> raise Not_found
|
||||||
in
|
in
|
||||||
find_dir lines
|
find_dir lines
|
||||||
|> find_data ;
|
|> find_data ;
|
||||||
@ -111,7 +118,7 @@ let get_ezfio_default directory data =
|
|||||||
| [] ->
|
| [] ->
|
||||||
begin
|
begin
|
||||||
Printf.printf "%s/%s not found\n%!" directory data;
|
Printf.printf "%s/%s not found\n%!" directory data;
|
||||||
raise Caml.Not_found
|
raise Not_found
|
||||||
end
|
end
|
||||||
| filename :: tail ->
|
| filename :: tail ->
|
||||||
let filename =
|
let filename =
|
||||||
@ -120,7 +127,7 @@ let get_ezfio_default directory data =
|
|||||||
try
|
try
|
||||||
get_ezfio_default_in_file ~directory ~data ~filename
|
get_ezfio_default_in_file ~directory ~data ~filename
|
||||||
with
|
with
|
||||||
| Caml.Not_found -> aux tail
|
| Not_found -> aux tail
|
||||||
in
|
in
|
||||||
Sys.readdir dirname
|
Sys.readdir dirname
|
||||||
|> Array.to_list
|
|> Array.to_list
|
||||||
@ -131,10 +138,7 @@ let ezfio_work ezfio_file =
|
|||||||
let result =
|
let result =
|
||||||
Filename.concat ezfio_file "work"
|
Filename.concat ezfio_file "work"
|
||||||
in
|
in
|
||||||
begin
|
if not (Sys.file_exists result) then
|
||||||
match Sys.is_directory result with
|
( Ezfio.set_file ezfio_file ; Ezfio.set_work_empty false);
|
||||||
| `Yes -> ()
|
|
||||||
| _ -> ( Ezfio.set_file ezfio_file ; Ezfio.set_work_empty false)
|
|
||||||
end;
|
|
||||||
result
|
result
|
||||||
;;
|
;;
|
||||||
|
@ -42,3 +42,11 @@ let rmdir dirname =
|
|||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
let input_lines ic =
|
||||||
|
let n = in_channel_length ic in
|
||||||
|
let s = Bytes.create n in
|
||||||
|
really_input ic s 0 n;
|
||||||
|
close_in ic;
|
||||||
|
Bytes.to_string s
|
||||||
|
|> String_ext.split ~on:'\n'
|
||||||
|
|
||||||
|
@ -3,27 +3,6 @@ include String
|
|||||||
(** Split a string on a given character *)
|
(** Split a string on a given character *)
|
||||||
let split ?(on=' ') str =
|
let split ?(on=' ') str =
|
||||||
split_on_char on str
|
split_on_char on str
|
||||||
(*
|
|
||||||
let rec do_work ?(accu=[]) ?(left="") = function
|
|
||||||
| "" -> List.rev (left::accu)
|
|
||||||
| s ->
|
|
||||||
let new_s =
|
|
||||||
(length s) - 1
|
|
||||||
|> sub s 1
|
|
||||||
in
|
|
||||||
if (s.[0] = on) then
|
|
||||||
let new_accu =
|
|
||||||
left :: accu
|
|
||||||
in
|
|
||||||
do_work ~accu:new_accu new_s
|
|
||||||
else
|
|
||||||
let new_left =
|
|
||||||
concat "" [ left ; make 1 s.[0] ]
|
|
||||||
in
|
|
||||||
do_work ~accu ~left:new_left new_s
|
|
||||||
in
|
|
||||||
do_work str
|
|
||||||
*)
|
|
||||||
|
|
||||||
|
|
||||||
(** Strip blanks on the left of a string *)
|
(** Strip blanks on the left of a string *)
|
||||||
@ -101,7 +80,7 @@ let rsplit2_exn ?(on=' ') s =
|
|||||||
else
|
else
|
||||||
do_work (i-1)
|
do_work (i-1)
|
||||||
in
|
in
|
||||||
do_work length
|
do_work (length-1)
|
||||||
|
|
||||||
|
|
||||||
let lsplit2 ?(on=' ') s =
|
let lsplit2 ?(on=' ') s =
|
||||||
@ -140,3 +119,23 @@ let is_prefix ~prefix s =
|
|||||||
|
|
||||||
let of_char c =
|
let of_char c =
|
||||||
String.make 1 c
|
String.make 1 c
|
||||||
|
|
||||||
|
let tr ~target ~replacement s =
|
||||||
|
String.map (fun c -> if c = target then replacement else c) s
|
||||||
|
|
||||||
|
|
||||||
|
let substr_index ?(pos=0) ~pattern s =
|
||||||
|
try
|
||||||
|
let regexp =
|
||||||
|
Str.regexp pattern
|
||||||
|
in
|
||||||
|
Some (Str.search_forward regexp s pos)
|
||||||
|
with Not_found -> None
|
||||||
|
|
||||||
|
|
||||||
|
let substr_replace_all ~pattern ~with_ s =
|
||||||
|
let regexp =
|
||||||
|
Str.regexp pattern
|
||||||
|
in
|
||||||
|
Str.global_replace regexp with_ s
|
||||||
|
|
||||||
|
@ -33,7 +33,7 @@ type t =
|
|||||||
|
|
||||||
let debug_env =
|
let debug_env =
|
||||||
try
|
try
|
||||||
Sys.getenv "QP_TASK_DEBUG"; true
|
Sys.getenv "QP_TASK_DEBUG" = "1"
|
||||||
with Not_found -> false
|
with Not_found -> false
|
||||||
|
|
||||||
|
|
||||||
|
@ -4,9 +4,8 @@ SHA1=$(git log -1 | head -1 | cut -d ' ' -f 2)
|
|||||||
DATE=$(git log -1 | grep Date | cut -d ':' -f 2-)
|
DATE=$(git log -1 | grep Date | cut -d ':' -f 2-)
|
||||||
MESSAGE=$(git log -1 | tail -1 | sed 's/"/\\"/g')
|
MESSAGE=$(git log -1 | tail -1 | sed 's/"/\\"/g')
|
||||||
cat << EOF > Git.ml
|
cat << EOF > Git.ml
|
||||||
open Core
|
let sha1 = "$SHA1" |> String.trim
|
||||||
let sha1 = "$SHA1" |> String_ext.strip
|
let date = "$DATE" |> String.trim
|
||||||
let date = "$DATE" |> String_ext.strip
|
let message = "$MESSAGE" |> String.trim
|
||||||
let message = "$MESSAGE" |> String_ext.strip
|
|
||||||
EOF
|
EOF
|
||||||
|
|
||||||
|
@ -1,4 +1,3 @@
|
|||||||
open Core
|
|
||||||
open Qptypes
|
open Qptypes
|
||||||
open Element
|
open Element
|
||||||
|
|
||||||
@ -6,9 +5,10 @@ let () =
|
|||||||
let indices =
|
let indices =
|
||||||
Array.init 78 (fun i -> i)
|
Array.init 78 (fun i -> i)
|
||||||
in
|
in
|
||||||
Out_channel.with_file (Qpackage.root ^ "/data/list_element.txt")
|
let out_channel =
|
||||||
~f:(fun out_channel ->
|
open_out (Qpackage.root ^ "/data/list_element.txt")
|
||||||
Array.init 110 ~f:(fun i ->
|
in
|
||||||
|
Array.init 110 (fun i ->
|
||||||
let element =
|
let element =
|
||||||
try
|
try
|
||||||
Some (of_charge (Charge.of_int i))
|
Some (of_charge (Charge.of_int i))
|
||||||
@ -21,7 +21,6 @@ let () =
|
|||||||
i (to_string x) (to_long_string x) (Positive_float.to_float @@ mass x )
|
i (to_string x) (to_long_string x) (Positive_float.to_float @@ mass x )
|
||||||
)
|
)
|
||||||
|> Array.to_list
|
|> Array.to_list
|
||||||
|> String.concat ~sep:""
|
|> String.concat ""
|
||||||
|> Out_channel.output_string out_channel
|
|> Printf.fprintf out_channel "%s"
|
||||||
)
|
|
||||||
|
|
||||||
|
Loading…
Reference in New Issue
Block a user