mirror of
https://github.com/LCPQ/quantum_package
synced 2024-11-04 05:03:54 +01:00
94 lines
2.4 KiB
OCaml
94 lines
2.4 KiB
OCaml
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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
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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 ( Positive_int.to_int
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molecule.Molecule.elec_alpha ) ;
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Ezfio.set_electrons_elec_beta_num ( Positive_int.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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;;
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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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