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