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Removed Core from qp_create_ezfio.ml
This commit is contained in:
parent
83d3cafbb2
commit
da3ba4ef4b
@ -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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exception ElementError of string
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@ -14,7 +14,7 @@ type t =
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[@@deriving sexp]
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let of_string x =
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match (String.capitalize (String.lowercase x)) with
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match (String.capitalize_ascii (String.lowercase_ascii x)) with
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| "X" | "Dummy" -> X
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| "H" | "Hydrogen" -> H
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| "He" | "Helium" -> He
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@ -1,5 +1,6 @@
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(** CONTRL *)
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type scftyp_t = RHF | ROHF | MCSCF | NONE
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let string_of_scftyp = function
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| RHF -> "RHF"
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| ROHF -> "ROHF"
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@ -116,7 +117,7 @@ type guess_t =
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| Natural of (int*string)
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let guess_of_string s =
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match String.lowercase s with
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match String.lowercase_ascii s with
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| "huckel" -> Huckel
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| "hcore" -> Hcore
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| _ -> raise (Invalid_argument "Bad MO guess")
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@ -33,7 +33,7 @@ let to_string x =
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let of_string s =
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match (String.lowercase s) with
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match (String.lowercase_ascii s) with
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| "core" -> Core []
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| "inactive" -> Inactive []
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| "active" -> Active []
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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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type t =
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| Guess
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@ -8,7 +8,7 @@ type t =
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| Orthonormalized
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| None
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[@@deriving sexp]
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;;
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let to_string = function
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| Guess -> "Guess"
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@ -20,7 +20,7 @@ let to_string = function
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;;
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let of_string s =
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match String.lowercase (String.strip s) with
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match String.lowercase_ascii (String.trim s) with
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| "guess" -> Guess
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| "canonical" -> Canonical
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| "natural" -> Natural
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@ -1,5 +1,5 @@
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open Core;;
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open Qptypes;;
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open Qptypes
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open Sexplib.Std
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type t = {
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x : float ;
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@ -21,10 +21,10 @@ let of_string ~units s =
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| Units.Angstrom -> Units.angstrom_to_bohr
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in
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let l = s
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|> String.split ~on:' '
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|> List.filter ~f:(fun x -> x <> "")
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|> List.map ~f:Float.of_string
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|> Array.of_list
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|> String_ext.split ~on:' '
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|> List.filter (fun x -> x <> "")
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|> List.map float_of_string
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|> Array.of_list
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in
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{ x = l.(0) *. f ;
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y = l.(1) *. f ;
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@ -1,6 +1,6 @@
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open Qputils
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open Qptypes
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open Core
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open Sexplib.Std
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type element =
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| Element of Element.t
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@ -38,7 +38,7 @@ let dummy_centers ~threshold ~molecule ~nuclei =
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| _ -> assert false
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in
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aux [] (n-1,n-1)
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|> List.map ~f:(fun (i,x,j,y,r) ->
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|> List.map (fun (i,x,j,y,r) ->
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let f =
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x /. (x +. y)
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in
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@ -58,22 +58,22 @@ let dummy_centers ~threshold ~molecule ~nuclei =
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(** Returns the list of available basis sets *)
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let list_basis () =
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let basis_list =
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let ic = Pervasives.open_in (Qpackage.root ^ "/data/basis/00_README.rst") in
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let n = Pervasives.in_channel_length ic in
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let ic = open_in (Qpackage.root ^ "/data/basis/00_README.rst") in
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let n = in_channel_length ic in
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let s = Bytes.create n in
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Pervasives.really_input ic s 0 n;
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Pervasives.close_in ic;
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really_input ic s 0 n;
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close_in ic;
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Bytes.to_string s
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|> String.split ~on:'\n'
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|> List.filter ~f:(fun line -> String.length line > 1 && line.[0] <> '#')
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|> List.map ~f:(fun line ->
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match String.split ~on:'\'' line with
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|> String_ext.split ~on:'\n'
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|> List.filter (fun line -> String.length line > 1 && line.[0] <> '#')
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|> List.map (fun line ->
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match String_ext.split ~on:'\'' line with
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| file :: name :: descr :: _ ->
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Printf.sprintf "%s\n %s\n %s\n\n" file name (String.strip descr)
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Printf.sprintf "%s\n %s\n %s\n\n" file name (String.trim descr)
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| _ -> assert false
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)
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in
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List.sort basis_list ~compare:String.ascending
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List.sort compare basis_list
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(** Run the program *)
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@ -101,7 +101,7 @@ let run ?o b au c d m p cart xyz_file =
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**********)
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let basis_table =
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Hashtbl.Poly.create ()
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Hashtbl.create 63
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in
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(* Open basis set channels *)
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@ -111,10 +111,7 @@ let run ?o b au c d m p cart xyz_file =
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| Element e -> Element.to_string e
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| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
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in
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match Hashtbl.find basis_table key with
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| Some in_channel ->
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in_channel
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| None -> raise Caml.Not_found
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Hashtbl.find basis_table key
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in
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let temp_filename =
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@ -129,11 +126,11 @@ let run ?o b au c d m p cart xyz_file =
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Qpackage.root ^ "/data/basis/" ^ basis
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in
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match
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Sys.is_file basis,
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Sys.is_file long_basis
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Sys.file_exists basis,
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Sys.file_exists long_basis
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with
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| `Yes, _ -> In_channel.create basis
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| `No , `Yes -> In_channel.create long_basis
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| true , _ -> open_in basis
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| false, true -> open_in long_basis
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| _ -> failwith ("Basis "^basis^" not found")
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in
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@ -141,7 +138,7 @@ let run ?o b au c d m p cart xyz_file =
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| [] -> ()
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| elem_and_basis_name :: rest ->
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begin
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match (String.lsplit2 ~on:':' elem_and_basis_name) with
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match (String_ext.lsplit2 ~on:':' elem_and_basis_name) with
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| None -> (* Principal basis *)
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begin
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let basis =
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@ -150,14 +147,12 @@ let run ?o b au c d m p cart xyz_file =
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let new_channel =
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fetch_channel basis
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in
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List.iter nuclei ~f:(fun elem->
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List.iter (fun elem->
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let key =
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Element.to_string elem.Atom.element
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in
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match Hashtbl.add basis_table ~key:key ~data:new_channel with
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| `Ok -> ()
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| `Duplicate -> ()
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)
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Hashtbl.add basis_table key new_channel
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) nuclei
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end
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| Some (key, basis) -> (*Aux basis *)
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begin
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@ -166,12 +161,12 @@ let run ?o b au c d m p cart xyz_file =
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Element (Element.of_string key)
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with Element.ElementError _ ->
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let result =
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match (String.split ~on:',' key) with
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match (String_ext.split ~on:',' key) with
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| i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
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| _ -> failwith "Expected format is int,Element:basis"
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in Int_elem result
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and basis =
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String.lowercase basis
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String.lowercase_ascii basis
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in
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let key =
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match elem with
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@ -181,23 +176,13 @@ let run ?o b au c d m p cart xyz_file =
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let new_channel =
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fetch_channel basis
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in
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begin
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match Hashtbl.add basis_table ~key:key ~data:new_channel with
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| `Ok -> ()
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| `Duplicate ->
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let e =
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match elem with
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| Element e -> e
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| Int_elem (_,e) -> e
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in
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failwith ("Duplicate definition of basis for "^(Element.to_long_string e))
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end
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Hashtbl.add basis_table key new_channel
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end
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end;
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build_basis rest
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in
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String.split ~on:'|' b
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|> List.rev_map ~f:String.strip
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String_ext.split ~on:'|' b
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|> List.rev_map String.trim
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|> build_basis;
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@ -207,7 +192,7 @@ let run ?o b au c d m p cart xyz_file =
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***************)
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let pseudo_table =
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Hashtbl.Poly.create ()
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Hashtbl.create 63
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in
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(* Open pseudo channels *)
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@ -215,7 +200,7 @@ let run ?o b au c d m p cart xyz_file =
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let key =
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Element.to_string element
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in
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Hashtbl.find pseudo_table key
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Hashtbl.find_opt pseudo_table key
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in
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let temp_filename =
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Filename.temp_file "qp_create_" ".pseudo"
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@ -229,11 +214,11 @@ let run ?o b au c d m p cart xyz_file =
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Qpackage.root ^ "/data/pseudo/" ^ pseudo
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in
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match
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Sys.is_file pseudo,
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Sys.is_file long_pseudo
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Sys.file_exists pseudo,
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Sys.file_exists long_pseudo
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with
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| `Yes, _ -> In_channel.create pseudo
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| `No , `Yes -> In_channel.create long_pseudo
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| true , _ -> open_in pseudo
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| false, true-> open_in long_pseudo
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| _ -> failwith ("Pseudo file "^pseudo^" not found.")
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in
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@ -241,7 +226,7 @@ let run ?o b au c d m p cart xyz_file =
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| [] -> ()
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| elem_and_pseudo_name :: rest ->
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begin
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match (String.lsplit2 ~on:':' elem_and_pseudo_name) with
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match (String_ext.lsplit2 ~on:':' elem_and_pseudo_name) with
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| None -> (* Principal pseudo *)
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begin
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let pseudo =
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@ -250,21 +235,19 @@ let run ?o b au c d m p cart xyz_file =
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let new_channel =
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fetch_channel pseudo
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in
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List.iter nuclei ~f:(fun elem->
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List.iter (fun elem->
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let key =
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Element.to_string elem.Atom.element
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in
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match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
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| `Ok -> ()
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| `Duplicate -> ()
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)
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Hashtbl.add pseudo_table key new_channel
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) nuclei
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end
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| Some (key, pseudo) -> (*Aux pseudo *)
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begin
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let elem =
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Element.of_string key
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and pseudo =
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String.lowercase pseudo
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String.lowercase_ascii pseudo
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in
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let key =
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Element.to_string elem
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@ -272,11 +255,7 @@ let run ?o b au c d m p cart xyz_file =
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let new_channel =
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fetch_channel pseudo
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in
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begin
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match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
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| `Ok -> ()
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| `Duplicate -> failwith ("Duplicate definition of pseudo for "^(Element.to_long_string elem))
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end
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Hashtbl.add pseudo_table key new_channel
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end
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end;
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build_pseudo rest
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@ -285,8 +264,8 @@ let run ?o b au c d m p cart xyz_file =
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match p with
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| None -> ()
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| Some p ->
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String.split ~on:'|' p
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|> List.rev_map ~f:String.strip
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String_ext.split ~on:'|' p
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|> List.rev_map String.trim
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|> build_pseudo
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in
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@ -296,13 +275,13 @@ let run ?o b au c d m p cart xyz_file =
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| Some x -> x
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| None ->
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begin
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match String.rsplit2 ~on:'.' xyz_file with
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match String_ext.rsplit2 ~on:'.' xyz_file with
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| Some (x,"xyz")
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| Some (x,"zmt") -> x^".ezfio"
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| _ -> xyz_file^".ezfio"
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end
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in
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if Sys.file_exists_exn ezfio_file then
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if Sys.file_exists ezfio_file then
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failwith (ezfio_file^" already exists");
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let write_file () =
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@ -311,17 +290,17 @@ let run ?o b au c d m p cart xyz_file =
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(* Write Pseudo *)
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let pseudo =
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List.map nuclei ~f:(fun x ->
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List.map (fun x ->
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match pseudo_channel x.Atom.element with
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| Some channel -> Pseudo.read_element channel x.Atom.element
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| None -> Pseudo.empty x.Atom.element
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)
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) nuclei
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in
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let molecule =
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let n_elec_to_remove =
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List.fold pseudo ~init:0 ~f:(fun accu x ->
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accu + (Positive_int.to_int x.Pseudo.n_elec))
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List.fold_left (fun accu x ->
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accu + (Positive_int.to_int x.Pseudo.n_elec)) 0 pseudo
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in
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{ Molecule.elec_alpha =
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(Elec_alpha_number.to_int molecule.Molecule.elec_alpha)
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@ -333,14 +312,14 @@ let run ?o b au c d m p cart xyz_file =
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|> Elec_beta_number.of_int;
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Molecule.nuclei =
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let charges =
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List.map pseudo ~f:(fun x -> Positive_int.to_int x.Pseudo.n_elec
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|> Float.of_int)
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List.map (fun x -> Positive_int.to_int x.Pseudo.n_elec
|
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|> Float.of_int) pseudo
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|> Array.of_list
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in
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List.mapi molecule.Molecule.nuclei ~f:(fun i x ->
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List.mapi (fun i x ->
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{ x with Atom.charge = (Charge.to_float x.Atom.charge) -. charges.(i)
|
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|> Charge.of_float }
|
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)
|
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) molecule.Molecule.nuclei
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}
|
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in
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let nuclei =
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@ -356,13 +335,13 @@ let run ?o b au c d m p cart xyz_file =
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|
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(* Write Nuclei *)
|
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let labels =
|
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List.map ~f:(fun x->Element.to_string x.Atom.element) nuclei
|
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List.map (fun x->Element.to_string x.Atom.element) nuclei
|
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and charges =
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List.map ~f:(fun x-> Atom.(Charge.to_float x.charge)) nuclei
|
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List.map (fun x-> Atom.(Charge.to_float x.charge)) nuclei
|
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and coords =
|
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(List.map ~f:(fun x-> x.Atom.coord.Point3d.x) nuclei) @
|
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(List.map ~f:(fun x-> x.Atom.coord.Point3d.y) nuclei) @
|
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(List.map ~f:(fun x-> x.Atom.coord.Point3d.z) nuclei) in
|
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(List.map (fun x-> x.Atom.coord.Point3d.x) nuclei) @
|
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(List.map (fun x-> x.Atom.coord.Point3d.y) nuclei) @
|
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(List.map (fun x-> x.Atom.coord.Point3d.z) nuclei) in
|
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let nucl_num = (List.length labels) in
|
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Ezfio.set_nuclei_nucl_num nucl_num ;
|
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Ezfio.set_nuclei_nucl_label (Ezfio.ezfio_array_of_list
|
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@ -381,40 +360,41 @@ let run ?o b au c d m p cart xyz_file =
|
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in
|
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|
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let klocmax =
|
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List.fold pseudo ~init:0 ~f:(fun accu x ->
|
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List.fold_left (fun accu x ->
|
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let x =
|
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List.length x.Pseudo.local
|
||||
in
|
||||
if (x > accu) then x
|
||||
else accu
|
||||
)
|
||||
) 0 pseudo
|
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and lmax =
|
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List.fold pseudo ~init:0 ~f:(fun accu x ->
|
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List.fold_left (fun accu x ->
|
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let x =
|
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List.fold x.Pseudo.non_local ~init:0 ~f:(fun accu (x,_) ->
|
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List.fold_left (fun accu (x,_) ->
|
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let x =
|
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Positive_int.to_int x.Pseudo.GaussianPrimitive_non_local.proj
|
||||
in
|
||||
if (x > accu) then x
|
||||
else accu
|
||||
)
|
||||
) 0 x.Pseudo.non_local
|
||||
in
|
||||
if (x > accu) then x
|
||||
else accu
|
||||
)
|
||||
) 0 pseudo
|
||||
in
|
||||
|
||||
let kmax =
|
||||
Array.init (lmax+1) ~f:(fun i->
|
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List.map pseudo ~f:(fun x ->
|
||||
List.filter x.Pseudo.non_local ~f:(fun (y,_) ->
|
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(Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i)
|
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|> List.length )
|
||||
|> List.fold ~init:0 ~f:(fun accu x ->
|
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if accu > x then accu else x)
|
||||
)
|
||||
|> Array.fold ~init:0 ~f:(fun accu i ->
|
||||
if i > accu then i else accu)
|
||||
Array.init (lmax+1) (fun i->
|
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List.map (fun x ->
|
||||
List.filter (fun (y,_) ->
|
||||
(Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i)
|
||||
x.Pseudo.non_local
|
||||
|> List.length ) pseudo
|
||||
|> List.fold_left (fun accu x ->
|
||||
if accu > x then accu else x) 0
|
||||
)
|
||||
|> Array.fold_left (fun accu i ->
|
||||
if i > accu then i else accu) 0
|
||||
in
|
||||
|
||||
|
||||
@ -423,12 +403,12 @@ let run ?o b au c d m p cart xyz_file =
|
||||
Ezfio.set_pseudo_pseudo_kmax kmax;
|
||||
Ezfio.set_pseudo_pseudo_lmax lmax;
|
||||
let tmp_array_v_k, tmp_array_dz_k, tmp_array_n_k =
|
||||
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0. ,
|
||||
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0. ,
|
||||
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0
|
||||
Array.make_matrix klocmax nucl_num 0. ,
|
||||
Array.make_matrix klocmax nucl_num 0. ,
|
||||
Array.make_matrix klocmax nucl_num 0
|
||||
in
|
||||
List.iteri pseudo ~f:(fun j x ->
|
||||
List.iteri x.Pseudo.local ~f:(fun i (y,c) ->
|
||||
List.iteri (fun j x ->
|
||||
List.iteri (fun i (y,c) ->
|
||||
tmp_array_v_k.(i).(j) <- AO_coef.to_float c;
|
||||
let y, z =
|
||||
AO_expo.to_float y.Pseudo.GaussianPrimitive_local.expo,
|
||||
@ -436,11 +416,11 @@ let run ?o b au c d m p cart xyz_file =
|
||||
in
|
||||
tmp_array_dz_k.(i).(j) <- y;
|
||||
tmp_array_n_k.(i).(j) <- z;
|
||||
)
|
||||
);
|
||||
) x.Pseudo.local
|
||||
) pseudo ;
|
||||
let concat_2d tmp_array =
|
||||
let data =
|
||||
Array.map tmp_array ~f:Array.to_list
|
||||
Array.map Array.to_list tmp_array
|
||||
|> Array.to_list
|
||||
|> List.concat
|
||||
in
|
||||
@ -454,18 +434,18 @@ let run ?o b au c d m p cart xyz_file =
|
||||
|> Ezfio.set_pseudo_pseudo_n_k;
|
||||
|
||||
let tmp_array_v_kl, tmp_array_dz_kl, tmp_array_n_kl =
|
||||
Array.init (lmax+1) ~f:(fun _ ->
|
||||
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
|
||||
Array.init (lmax+1) ~f:(fun _ ->
|
||||
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
|
||||
Array.init (lmax+1) ~f:(fun _ ->
|
||||
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0 ))
|
||||
Array.init (lmax+1) (fun _ ->
|
||||
(Array.make_matrix kmax nucl_num 0. )),
|
||||
Array.init (lmax+1) (fun _ ->
|
||||
(Array.make_matrix kmax nucl_num 0. )),
|
||||
Array.init (lmax+1) (fun _ ->
|
||||
(Array.make_matrix kmax nucl_num 0 ))
|
||||
in
|
||||
List.iteri pseudo ~f:(fun j x ->
|
||||
List.iteri (fun j x ->
|
||||
let last_idx =
|
||||
Array.create ~len:(lmax+1) 0
|
||||
Array.make (lmax+1) 0
|
||||
in
|
||||
List.iter x.Pseudo.non_local ~f:(fun (y,c) ->
|
||||
List.iter (fun (y,c) ->
|
||||
let k, y, z =
|
||||
Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj,
|
||||
AO_expo.to_float y.Pseudo.GaussianPrimitive_non_local.expo,
|
||||
@ -478,14 +458,14 @@ let run ?o b au c d m p cart xyz_file =
|
||||
tmp_array_dz_kl.(k).(i).(j) <- y;
|
||||
tmp_array_n_kl.(k).(i).(j) <- z;
|
||||
last_idx.(k) <- i+1;
|
||||
)
|
||||
);
|
||||
) x.Pseudo.non_local
|
||||
) pseudo ;
|
||||
let concat_3d tmp_array =
|
||||
let data =
|
||||
Array.map tmp_array ~f:(fun x ->
|
||||
Array.map x ~f:Array.to_list
|
||||
Array.map (fun x ->
|
||||
Array.map Array.to_list x
|
||||
|> Array.to_list
|
||||
|> List.concat)
|
||||
|> List.concat) tmp_array
|
||||
|> Array.to_list
|
||||
|> List.concat
|
||||
in
|
||||
@ -518,7 +498,7 @@ let run ?o b au c d m p cart xyz_file =
|
||||
in
|
||||
let result = do_work [] 1 nuclei
|
||||
|> List.rev
|
||||
|> List.map ~f:(fun (x,i) ->
|
||||
|> List.map (fun (x,i) ->
|
||||
try
|
||||
let e =
|
||||
match x.Atom.element with
|
||||
@ -552,37 +532,38 @@ let run ?o b au c d m p cart xyz_file =
|
||||
let ao_num = List.length long_basis in
|
||||
Ezfio.set_ao_basis_ao_num ao_num;
|
||||
Ezfio.set_ao_basis_ao_basis b;
|
||||
let ao_prim_num = List.map long_basis ~f:(fun (_,g,_) -> List.length g.Gto.lc)
|
||||
and ao_nucl = List.map long_basis ~f:(fun (_,_,n) -> Nucl_number.to_int n)
|
||||
let ao_prim_num = List.map (fun (_,g,_) -> List.length g.Gto.lc) long_basis
|
||||
and ao_nucl = List.map (fun (_,_,n) -> Nucl_number.to_int n) long_basis
|
||||
and ao_power=
|
||||
let l = List.map long_basis ~f:(fun (x,_,_) -> x) in
|
||||
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) )@
|
||||
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) )@
|
||||
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) )
|
||||
let l = List.map (fun (x,_,_) -> x) long_basis in
|
||||
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) l)@
|
||||
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) l)@
|
||||
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) l)
|
||||
in
|
||||
let ao_prim_num_max = List.fold ~init:0 ~f:(fun s x ->
|
||||
let ao_prim_num_max = List.fold_left (fun s x ->
|
||||
if x > s then x
|
||||
else s) ao_prim_num
|
||||
else s) 0 ao_prim_num
|
||||
in
|
||||
let gtos =
|
||||
List.map long_basis ~f:(fun (_,x,_) -> x)
|
||||
List.map (fun (_,x,_) -> x) long_basis
|
||||
in
|
||||
|
||||
let create_expo_coef ec =
|
||||
let coefs =
|
||||
begin match ec with
|
||||
| `Coefs -> List.map gtos ~f:(fun x->
|
||||
List.map x.Gto.lc ~f:(fun (_,coef) -> AO_coef.to_float coef) )
|
||||
| `Expos -> List.map gtos ~f:(fun x->
|
||||
List.map x.Gto.lc ~f:(fun (prim,_) -> AO_expo.to_float
|
||||
prim.GaussianPrimitive.expo) )
|
||||
| `Coefs -> List.map (fun x->
|
||||
List.map (fun (_,coef) ->
|
||||
AO_coef.to_float coef) x.Gto.lc) gtos
|
||||
| `Expos -> List.map (fun x->
|
||||
List.map (fun (prim,_) -> AO_expo.to_float
|
||||
prim.GaussianPrimitive.expo) x.Gto.lc) gtos
|
||||
end
|
||||
in
|
||||
let rec get_n n accu = function
|
||||
| [] -> List.rev accu
|
||||
| h::tail ->
|
||||
let y =
|
||||
begin match List.nth h n with
|
||||
begin match List.nth_opt h n with
|
||||
| Some x -> x
|
||||
| None -> 0.
|
||||
end
|
||||
@ -621,9 +602,10 @@ let run ?o b au c d m p cart xyz_file =
|
||||
| ex ->
|
||||
begin
|
||||
begin
|
||||
match Sys.is_directory ezfio_file with
|
||||
| `Yes -> rmdir ezfio_file
|
||||
| _ -> ()
|
||||
try
|
||||
if Sys.is_directory ezfio_file then
|
||||
rmdir ezfio_file
|
||||
with _ -> ()
|
||||
end;
|
||||
raise ex;
|
||||
end
|
||||
@ -730,7 +712,7 @@ If a file with the same name as the basis set exists, this file will be read. O
|
||||
if basis = "show" then
|
||||
begin
|
||||
list_basis ()
|
||||
|> List.iter ~f:print_endline;
|
||||
|> List.iter print_endline;
|
||||
exit 0
|
||||
end;
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user