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quantum_package/ocaml/qp_create_ezfio_from_xyz.ml
2014-10-30 16:26:31 +01:00

167 lines
5.1 KiB
OCaml

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 nmax = Nucl_number.get_max () in
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 ~max:nmax 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
;;