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https://github.com/LCPQ/quantum_package
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Fixed Pseudo and dummy atoms
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parent
5e1b077576
commit
2dcb4eba0d
244
ocaml/Pseudo.ml
244
ocaml/Pseudo.ml
@ -124,23 +124,27 @@ let to_string t =
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let find in_channel element =
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let find in_channel element =
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In_channel.seek in_channel 0L;
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In_channel.seek in_channel 0L;
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let element_read, old_pos =
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let loop, element_read, old_pos =
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ref Element.X,
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ref true,
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ref None,
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ref (In_channel.pos in_channel)
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ref (In_channel.pos in_channel)
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in
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in
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while !element_read <> element
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while !loop
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do
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do
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let buffer =
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old_pos := In_channel.pos in_channel;
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match In_channel.input_line in_channel with
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| Some line -> String.split ~on:' ' line
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|> List.hd_exn
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| None -> ""
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in
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try
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try
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element_read := Element.of_string buffer
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let buffer =
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old_pos := In_channel.pos in_channel;
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match In_channel.input_line in_channel with
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| Some line -> String.split ~on:' ' line
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|> List.hd_exn
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| None -> raise End_of_file
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in
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element_read := Some (Element.of_string buffer);
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loop := !element_read <> (Some element)
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with
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with
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| Element.ElementError _ -> ()
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| Element.ElementError _ -> ()
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| End_of_file -> loop := false
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done ;
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done ;
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In_channel.seek in_channel !old_pos;
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In_channel.seek in_channel !old_pos;
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!element_read
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!element_read
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@ -148,124 +152,126 @@ let find in_channel element =
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(** Read the Pseudopotential in GAMESS format *)
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(** Read the Pseudopotential in GAMESS format *)
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let read_element in_channel element =
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let read_element in_channel element =
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ignore (find in_channel element);
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match find in_channel element with
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| Some e when e = element ->
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let rec read result =
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match In_channel.input_line in_channel with
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| None -> result
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| Some line ->
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if (String.strip line = "") then
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result
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else
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read (line::result)
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in
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let data =
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read []
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|> List.rev
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in
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let debug_data =
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String.concat ~sep:"\n" data
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in
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let decode_first_line = function
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| first_line :: rest ->
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begin
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begin
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let first_line_split =
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let rec read result =
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String.split first_line ~on:' '
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match In_channel.input_line in_channel with
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|> List.filter ~f:(fun x -> (String.strip x) <> "")
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| None -> result
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| Some line ->
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if (String.strip line = "") then
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result
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else
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read (line::result)
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in
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in
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match first_line_split with
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| e :: "GEN" :: n :: p ->
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{ element = Element.of_string e ;
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n_elec = Int.of_string n |> Positive_int.of_int ;
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local = [] ;
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non_local = []
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}, rest
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| _ -> failwith (
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Printf.sprintf "Unable to read Pseudopotential : \n%s\n"
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debug_data )
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end
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| _ -> failwith ("Error reading pseudopotential\n"^debug_data)
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in
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let rec loop create_primitive accu = function
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let data =
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| (0,rest) -> List.rev accu, rest
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read []
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| (n,line::rest) ->
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|> List.rev
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begin
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in
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match
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String.split line ~on:' '
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let debug_data =
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|> List.filter ~f:(fun x -> String.strip x <> "")
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String.concat ~sep:"\n" data
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with
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in
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| c :: i :: e :: [] ->
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let i =
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let decode_first_line = function
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Int.of_string i
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| first_line :: rest ->
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in
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begin
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let elem =
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let first_line_split =
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( create_primitive
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String.split first_line ~on:' '
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(Float.of_string e |> AO_expo.of_float)
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|> List.filter ~f:(fun x -> (String.strip x) <> "")
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(i-2 |> R_power.of_int),
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in
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Float.of_string c |> AO_coef.of_float
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match first_line_split with
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)
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| e :: "GEN" :: n :: p ->
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in
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{ element = Element.of_string e ;
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loop create_primitive (elem::accu) (n-1, rest)
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n_elec = Int.of_string n |> Positive_int.of_int ;
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local = [] ;
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non_local = []
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}, rest
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| _ -> failwith (
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Printf.sprintf "Unable to read Pseudopotential : \n%s\n"
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debug_data )
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end
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| _ -> failwith ("Error reading pseudopotential\n"^debug_data)
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| _ -> failwith ("Error reading pseudopotential\n"^debug_data)
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end
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in
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| _ -> failwith ("Error reading pseudopotential\n"^debug_data)
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in
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let decode_local (pseudo,data) =
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let rec loop create_primitive accu = function
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let decode_local_n n rest =
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| (0,rest) -> List.rev accu, rest
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let result, rest =
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| (n,line::rest) ->
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loop Primitive_local.of_expo_r_power [] (Positive_int.to_int n,rest)
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begin
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match
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String.split line ~on:' '
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|> List.filter ~f:(fun x -> String.strip x <> "")
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with
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| c :: i :: e :: [] ->
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let i =
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Int.of_string i
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in
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let elem =
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( create_primitive
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(Float.of_string e |> AO_expo.of_float)
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(i-2 |> R_power.of_int),
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Float.of_string c |> AO_coef.of_float
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)
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in
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loop create_primitive (elem::accu) (n-1, rest)
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| _ -> failwith ("Error reading pseudopotential\n"^debug_data)
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end
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| _ -> failwith ("Error reading pseudopotential\n"^debug_data)
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in
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in
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{ pseudo with local = result }, rest
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in
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let decode_local (pseudo,data) =
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match data with
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let decode_local_n n rest =
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| n :: rest ->
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let result, rest =
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let n =
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loop Primitive_local.of_expo_r_power [] (Positive_int.to_int n,rest)
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String.strip n
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in
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|> Int.of_string
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{ pseudo with local = result }, rest
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|> Positive_int.of_int
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in
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in
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decode_local_n n rest
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match data with
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| _ -> failwith ("Unable to read (non-)local pseudopotential\n"^debug_data)
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| n :: rest ->
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in
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let n =
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String.strip n
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let decode_non_local (pseudo,data) =
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|> Int.of_string
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let decode_non_local_n proj n (pseudo,data) =
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|> Positive_int.of_int
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let result, rest =
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in
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loop (Primitive_non_local.of_proj_expo_r_power proj)
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decode_local_n n rest
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[] (Positive_int.to_int n, data)
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| _ -> failwith ("Unable to read (non-)local pseudopotential\n"^debug_data)
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in
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in
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{ pseudo with non_local = pseudo.non_local @ result }, rest
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in
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let rec new_proj (pseudo,data) proj =
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match data with
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| n :: rest ->
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let n =
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String.strip n
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|> Int.of_string
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|> Positive_int.of_int
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in
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let result =
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decode_non_local_n proj n (pseudo,rest)
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and proj_next =
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(Positive_int.to_int proj)+1
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|> Positive_int.of_int
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in
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new_proj result proj_next
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| _ -> pseudo
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in
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new_proj (pseudo,data) (Positive_int.of_int 0)
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in
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decode_first_line data
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let decode_non_local (pseudo,data) =
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|> decode_local
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let decode_non_local_n proj n (pseudo,data) =
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|> decode_non_local
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let result, rest =
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loop (Primitive_non_local.of_proj_expo_r_power proj)
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[] (Positive_int.to_int n, data)
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in
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{ pseudo with non_local = pseudo.non_local @ result }, rest
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in
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let rec new_proj (pseudo,data) proj =
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match data with
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| n :: rest ->
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let n =
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String.strip n
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|> Int.of_string
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|> Positive_int.of_int
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in
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let result =
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decode_non_local_n proj n (pseudo,rest)
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and proj_next =
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(Positive_int.to_int proj)+1
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|> Positive_int.of_int
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in
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new_proj result proj_next
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| _ -> pseudo
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in
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new_proj (pseudo,data) (Positive_int.of_int 0)
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in
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decode_first_line data
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|> decode_local
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|> decode_non_local
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end
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| _ -> empty element
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include To_md5
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include To_md5
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@ -1,7 +1,7 @@
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program e_curve
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program e_curve
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use bitmasks
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use bitmasks
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implicit none
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implicit none
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integer :: i,j,k, nab, m, l
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integer :: i,j,k, kk, nab, m, l
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double precision :: norm, E, hij, num, ci, cj
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double precision :: norm, E, hij, num, ci, cj
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integer, allocatable :: iorder(:)
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integer, allocatable :: iorder(:)
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double precision , allocatable :: norm_sort(:)
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double precision , allocatable :: norm_sort(:)
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@ -60,7 +60,7 @@ program e_curve
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num = 0.d0
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num = 0.d0
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norm = 0.d0
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norm = 0.d0
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m = 0
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m = 0
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!$OMP PARALLEL DEFAULT(SHARED) PRIVATE(k,l,det_i,det_j,ci,cj,hij) REDUCTION(+:norm,m,num)
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!$OMP PARALLEL DEFAULT(SHARED) PRIVATE(k,kk,l,det_i,det_j,ci,cj,hij) REDUCTION(+:norm,m,num)
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allocate( det_i(N_int,2), det_j(N_int,2))
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allocate( det_i(N_int,2), det_j(N_int,2))
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!$OMP DO SCHEDULE(guided)
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!$OMP DO SCHEDULE(guided)
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do k=1,n_det
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do k=1,n_det
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@ -68,15 +68,19 @@ program e_curve
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cycle
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cycle
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endif
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endif
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ci = psi_bilinear_matrix_values(k,1)
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ci = psi_bilinear_matrix_values(k,1)
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det_i(:,1) = psi_det_alpha_unique(:,psi_bilinear_matrix_rows(k))
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do kk=1,N_int
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det_i(:,2) = psi_det_beta_unique(:,psi_bilinear_matrix_columns(k))
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det_i(kk,1) = psi_det_alpha_unique(kk,psi_bilinear_matrix_rows(k))
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det_i(kk,2) = psi_det_beta_unique(kk,psi_bilinear_matrix_columns(k))
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enddo
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do l=1,n_det
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do l=1,n_det
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if (psi_bilinear_matrix_values(l,1) == 0.d0) then
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if (psi_bilinear_matrix_values(l,1) == 0.d0) then
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cycle
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cycle
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endif
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endif
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cj = psi_bilinear_matrix_values(l,1)
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cj = psi_bilinear_matrix_values(l,1)
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det_j(:,1) = psi_det_alpha_unique(:,psi_bilinear_matrix_rows(l))
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do kk=1,N_int
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det_j(:,2) = psi_det_beta_unique(:,psi_bilinear_matrix_columns(l))
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det_j(kk,1) = psi_det_alpha_unique(kk,psi_bilinear_matrix_rows(l))
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det_j(kk,2) = psi_det_beta_unique(kk,psi_bilinear_matrix_columns(l))
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enddo
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call i_h_j(det_i, det_j, N_int, hij)
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call i_h_j(det_i, det_j, N_int, hij)
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num = num + ci*cj*hij
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num = num + ci*cj*hij
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enddo
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enddo
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