open Qputils;; open Qptypes;; open Core.Std;; let spec = let open Command.Spec in empty +> flag "o" (optional string) ~doc:"file Name of the created EZFIO file" +> flag "b" (required string) ~doc:"name Basis set." +> flag "c" (optional_with_default 0 int) ~doc:"int Total charge of the molecule. Default is 0." +> flag "m" (optional_with_default 1 int) ~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1" +> anon ("xyz_file" %: string) ;; let run ?o b c m xyz_file = (* Open basis set channel *) let basis_channel = In_channel.create (Qpackage.root ^ "/data/basis/" ^ (String.lowercase b)) in (* Read molecule *) let molecule = (Molecule.of_xyz_file xyz_file ~charge:(Charge.of_int c) ~multiplicity:(Multiplicity.of_int m) ) in (* Build EZFIO File name *) let ezfio_file = match o with | Some x -> x | None -> begin match String.rsplit2 ~on:'.' xyz_file with | Some (x,"xyz") -> x^".ezfio" | _ -> xyz_file^".ezfio" end in if Sys.file_exists_exn ezfio_file then failwith (ezfio_file^" already exists"); (* Create EZFIO *) Ezfio.set_file ezfio_file; (* Write Electrons *) Ezfio.set_electrons_elec_alpha_num ( Elec_alpha_number.to_int molecule.Molecule.elec_alpha ) ; Ezfio.set_electrons_elec_beta_num ( Elec_beta_number.to_int molecule.Molecule.elec_beta ) ; (* Write Nuclei *) let nuclei = molecule.Molecule.nuclei in let labels = List.map ~f:(fun x->Element.to_string x.Atom.element) nuclei and charges = List.map ~f:(fun x-> Atom.(Charge.to_float x.charge)) nuclei and coords = (List.map ~f:(fun x-> x.Atom.coord.Point3d.x) nuclei) @ (List.map ~f:(fun x-> x.Atom.coord.Point3d.y) nuclei) @ (List.map ~f:(fun x-> x.Atom.coord.Point3d.z) nuclei) in let nucl_num = (List.length labels) in Ezfio.set_nuclei_nucl_num nucl_num ; Ezfio.set_nuclei_nucl_label (Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| nucl_num |] ~data:labels); Ezfio.set_nuclei_nucl_charge (Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| nucl_num |] ~data:charges); Ezfio.set_nuclei_nucl_coord (Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| nucl_num ; 3 |] ~data:coords); (* Write Basis set *) let basis = let rec do_work (accu:(Atom.t*Nucl_number.t) list) (n:int) = function | [] -> accu | e::tail -> let new_accu = (e,(Nucl_number.of_int n))::accu in do_work new_accu (n+1) tail in do_work [] 1 nuclei |> List.rev |> List.map ~f:(fun (x,i) -> Basis.read_element basis_channel i x.Atom.element) |> List.concat in let long_basis = Long_basis.of_basis basis in 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) 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)) ) in let ao_prim_num_max = List.fold ~init:0 ~f:(fun s x -> if x > s then x else s) ao_prim_num in let gtos = List.map long_basis ~f:(fun (_,x,_) -> x) 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.Primitive.expo) ) end in let rec get_n n accu = function | [] -> List.rev accu | h::tail -> let y = begin match List.nth h n with | Some x -> x | None -> 0. end in get_n n (y::accu) tail in let rec build accu = function | n when n=ao_prim_num_max -> accu | n -> build ( accu @ (get_n n [] coefs) ) (n+1) in build [] 0 in let ao_coef = create_expo_coef `Coefs and ao_expo = create_expo_coef `Expos in Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ; Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ; Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ; Ezfio.set_ao_basis_ao_coef(Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_coef) ; Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ; ;; let command = Command.basic ~summary: "Quantum Package command" ~readme:(fun () -> "Creates an EZFIO directory from a standard xyz file ") spec (fun o b c m xyz_file () -> run ?o b c m xyz_file ) ;; let () = Command.run command ;;