mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-11-04 21:23:56 +01:00
788 lines
23 KiB
OCaml
788 lines
23 KiB
OCaml
open Qputils
|
|
open Qptypes
|
|
open Sexplib.Std
|
|
|
|
type element =
|
|
| Element of Element.t
|
|
| Int_elem of (Nucl_number.t * Element.t)
|
|
|
|
(** Handle dummy atoms placed on bonds *)
|
|
let dummy_centers ~threshold ~molecule ~nuclei =
|
|
let d =
|
|
Molecule.distance_matrix molecule
|
|
in
|
|
let n =
|
|
Array.length d
|
|
in
|
|
let nuclei =
|
|
Array.of_list nuclei
|
|
in
|
|
let rec aux accu = function
|
|
| (-1,_) -> accu
|
|
| (i,-1) -> aux accu (i-1,i-1)
|
|
| (i,j) when (i>j) ->
|
|
let new_accu =
|
|
let x,y =
|
|
Element.covalent_radius (nuclei.(i)).Atom.element |> Positive_float.to_float,
|
|
Element.covalent_radius (nuclei.(j)).Atom.element |> Positive_float.to_float
|
|
in
|
|
let r =
|
|
( x +. y ) *. threshold
|
|
in
|
|
if d.(i).(j) < r then
|
|
(i,x,j,y,d.(i).(j)) :: accu
|
|
else
|
|
accu
|
|
in aux new_accu (i,j-1)
|
|
| (i,j) when (i=j) -> aux accu (i,j-1)
|
|
| _ -> assert false
|
|
in
|
|
aux [] (n-1,n-1)
|
|
|> list_map (fun (i,x,j,y,r) ->
|
|
let f =
|
|
x /. (x +. y)
|
|
in
|
|
let u =
|
|
Point3d.of_tuple ~units:Units.Bohr
|
|
( nuclei.(i).Atom.coord.Point3d.x +.
|
|
(nuclei.(j).Atom.coord.Point3d.x -. nuclei.(i).Atom.coord.Point3d.x) *. f,
|
|
nuclei.(i).Atom.coord.Point3d.y +.
|
|
(nuclei.(j).Atom.coord.Point3d.y -. nuclei.(i).Atom.coord.Point3d.y) *. f,
|
|
nuclei.(i).Atom.coord.Point3d.z +.
|
|
(nuclei.(j).Atom.coord.Point3d.z -. nuclei.(i).Atom.coord.Point3d.z) *. f)
|
|
in
|
|
Atom.{ element = Element.X ; charge = Charge.of_int 0 ; coord = u }
|
|
)
|
|
|
|
|
|
|
|
(** Run the program *)
|
|
let run ?o b au c d m p cart xyz_file =
|
|
|
|
(* Read molecule *)
|
|
let molecule =
|
|
if au then
|
|
(Molecule.of_file xyz_file ~charge:(Charge.of_int c)
|
|
~multiplicity:(Multiplicity.of_int m) ~units:Units.Bohr)
|
|
else
|
|
(Molecule.of_file xyz_file ~charge:(Charge.of_int c)
|
|
~multiplicity:(Multiplicity.of_int m) )
|
|
in
|
|
let dummy =
|
|
dummy_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei
|
|
in
|
|
let nuclei =
|
|
molecule.Molecule.nuclei @ dummy
|
|
in
|
|
|
|
|
|
(**********
|
|
Basis set
|
|
**********)
|
|
|
|
let basis_table =
|
|
Hashtbl.create 63
|
|
in
|
|
|
|
(* Open basis set channels *)
|
|
let basis_channel element =
|
|
let key =
|
|
match element with
|
|
| Element e -> Element.to_string e
|
|
| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
|
|
in
|
|
Hashtbl.find basis_table key
|
|
in
|
|
|
|
let temp_filename =
|
|
Filename.temp_file "qp_create_" ".basis"
|
|
in
|
|
let () =
|
|
Sys.remove temp_filename
|
|
in
|
|
|
|
let fetch_channel basis =
|
|
let long_basis =
|
|
Qpackage.root ^ "/data/basis/" ^ basis
|
|
in
|
|
match
|
|
Sys.file_exists basis,
|
|
Sys.file_exists long_basis
|
|
with
|
|
| true , _ -> open_in basis
|
|
| false, true -> open_in long_basis
|
|
| _ -> failwith ("Basis "^basis^" not found")
|
|
in
|
|
|
|
let rec build_basis = function
|
|
| [] -> ()
|
|
| elem_and_basis_name :: rest ->
|
|
begin
|
|
match (String_ext.lsplit2 ~on:':' elem_and_basis_name) with
|
|
| None -> (* Principal basis *)
|
|
begin
|
|
let basis =
|
|
elem_and_basis_name
|
|
in
|
|
let new_channel =
|
|
fetch_channel basis
|
|
in
|
|
List.iter (fun elem->
|
|
let key =
|
|
Element.to_string elem.Atom.element
|
|
in
|
|
Hashtbl.add basis_table key new_channel
|
|
) nuclei
|
|
end
|
|
| Some (key, basis) -> (*Aux basis *)
|
|
begin
|
|
let elem =
|
|
try
|
|
Element (Element.of_string key)
|
|
with Element.ElementError _ ->
|
|
let result =
|
|
match (String_ext.split ~on:',' key) with
|
|
| i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
|
|
| _ -> failwith "Expected format is int,Element:basis"
|
|
in Int_elem result
|
|
and basis =
|
|
String.lowercase_ascii basis
|
|
in
|
|
let key =
|
|
match elem with
|
|
| Element e -> Element.to_string e
|
|
| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
|
|
in
|
|
let new_channel =
|
|
fetch_channel basis
|
|
in
|
|
Hashtbl.add basis_table key new_channel
|
|
end
|
|
end;
|
|
build_basis rest
|
|
in
|
|
String_ext.split ~on:'|' b
|
|
|> List.rev_map String.trim
|
|
|> build_basis;
|
|
|
|
|
|
|
|
(***************
|
|
Pseudopotential
|
|
***************)
|
|
|
|
let pseudo_table =
|
|
Hashtbl.create 63
|
|
in
|
|
|
|
(* Open pseudo channels *)
|
|
let pseudo_channel element =
|
|
let key =
|
|
Element.to_string element
|
|
in
|
|
Hashtbl.find_opt pseudo_table key
|
|
in
|
|
let temp_filename =
|
|
Filename.temp_file "qp_create_" ".pseudo"
|
|
in
|
|
let () =
|
|
Sys.remove temp_filename
|
|
in
|
|
|
|
let fetch_channel pseudo =
|
|
let long_pseudo =
|
|
Qpackage.root ^ "/data/pseudo/" ^ pseudo
|
|
in
|
|
match
|
|
Sys.file_exists pseudo,
|
|
Sys.file_exists long_pseudo
|
|
with
|
|
| true , _ -> open_in pseudo
|
|
| false, true-> open_in long_pseudo
|
|
| _ -> failwith ("Pseudo file "^pseudo^" not found.")
|
|
in
|
|
|
|
let rec build_pseudo = function
|
|
| [] -> ()
|
|
| elem_and_pseudo_name :: rest ->
|
|
begin
|
|
match (String_ext.lsplit2 ~on:':' elem_and_pseudo_name) with
|
|
| None -> (* Principal pseudo *)
|
|
begin
|
|
let pseudo =
|
|
elem_and_pseudo_name
|
|
in
|
|
let new_channel =
|
|
fetch_channel pseudo
|
|
in
|
|
List.iter (fun elem->
|
|
let key =
|
|
Element.to_string elem.Atom.element
|
|
in
|
|
Hashtbl.add pseudo_table key new_channel
|
|
) nuclei
|
|
end
|
|
| Some (key, pseudo) -> (*Aux pseudo *)
|
|
begin
|
|
let elem =
|
|
Element.of_string key
|
|
and pseudo =
|
|
String.lowercase_ascii pseudo
|
|
in
|
|
let key =
|
|
Element.to_string elem
|
|
in
|
|
let new_channel =
|
|
fetch_channel pseudo
|
|
in
|
|
Hashtbl.add pseudo_table key new_channel
|
|
end
|
|
end;
|
|
build_pseudo rest
|
|
in
|
|
let () =
|
|
match p with
|
|
| None -> ()
|
|
| Some p ->
|
|
String_ext.split ~on:'|' p
|
|
|> List.rev_map String.trim
|
|
|> build_pseudo
|
|
in
|
|
|
|
(* Build EZFIO File name *)
|
|
let ezfio_file =
|
|
match o with
|
|
| Some x -> x
|
|
| None ->
|
|
begin
|
|
match String_ext.rsplit2 ~on:'.' xyz_file with
|
|
| Some (x,"xyz")
|
|
| Some (x,"zmt") -> x^".ezfio"
|
|
| _ -> xyz_file^".ezfio"
|
|
end
|
|
in
|
|
if Sys.file_exists ezfio_file then
|
|
failwith (ezfio_file^" already exists");
|
|
|
|
let write_file () =
|
|
(* Create EZFIO *)
|
|
Ezfio.set_file ezfio_file;
|
|
|
|
(* Write Pseudo *)
|
|
let pseudo =
|
|
list_map (fun x ->
|
|
match pseudo_channel x.Atom.element with
|
|
| Some channel -> Pseudo.read_element channel x.Atom.element
|
|
| None -> Pseudo.empty x.Atom.element
|
|
) nuclei
|
|
in
|
|
|
|
let z_core =
|
|
List.map (fun x ->
|
|
Positive_int.to_int x.Pseudo.n_elec
|
|
|> float_of_int
|
|
) pseudo
|
|
in
|
|
let nucl_num = (List.length z_core) in
|
|
Ezfio.set_pseudo_nucl_charge_remove (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| nucl_num |] ~data:z_core);
|
|
|
|
let molecule =
|
|
let n_elec_to_remove =
|
|
List.fold_left (fun accu x ->
|
|
accu + (Positive_int.to_int x.Pseudo.n_elec)) 0 pseudo
|
|
in
|
|
{ Molecule.elec_alpha =
|
|
(Elec_alpha_number.to_int molecule.Molecule.elec_alpha)
|
|
- n_elec_to_remove/2
|
|
|> Elec_alpha_number.of_int;
|
|
Molecule.elec_beta =
|
|
(Elec_beta_number.to_int molecule.Molecule.elec_beta)
|
|
- (n_elec_to_remove - n_elec_to_remove/2)
|
|
|> Elec_beta_number.of_int;
|
|
Molecule.nuclei =
|
|
let charges =
|
|
list_map (fun x -> Positive_int.to_int x.Pseudo.n_elec
|
|
|> Float.of_int) pseudo
|
|
|> Array.of_list
|
|
in
|
|
List.mapi (fun i x ->
|
|
{ x with Atom.charge = (Charge.to_float x.Atom.charge) -. charges.(i)
|
|
|> Charge.of_float }
|
|
) molecule.Molecule.nuclei
|
|
}
|
|
in
|
|
let nuclei =
|
|
molecule.Molecule.nuclei @ dummy
|
|
in
|
|
|
|
|
|
(* 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 labels =
|
|
list_map (fun x->Element.to_string x.Atom.element) nuclei
|
|
and charges =
|
|
list_map (fun x-> Atom.(Charge.to_float x.charge)) nuclei
|
|
and coords =
|
|
(list_map (fun x-> x.Atom.coord.Point3d.x) nuclei) @
|
|
(list_map (fun x-> x.Atom.coord.Point3d.y) nuclei) @
|
|
(list_map (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 pseudopotential *)
|
|
let () =
|
|
match p with
|
|
| None -> Ezfio.set_pseudo_do_pseudo false
|
|
| _ -> Ezfio.set_pseudo_do_pseudo true
|
|
in
|
|
|
|
let klocmax =
|
|
List.fold_left (fun accu x ->
|
|
let x =
|
|
List.length x.Pseudo.local
|
|
in
|
|
if (x > accu) then x
|
|
else accu
|
|
) 0 pseudo
|
|
and lmax =
|
|
List.fold_left (fun accu x ->
|
|
let x =
|
|
List.fold_left (fun accu (x,_) ->
|
|
let x =
|
|
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) (fun i->
|
|
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
|
|
|
|
|
|
let () =
|
|
Ezfio.set_pseudo_pseudo_klocmax klocmax;
|
|
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 klocmax nucl_num 0. ,
|
|
Array.make_matrix klocmax nucl_num 0. ,
|
|
Array.make_matrix klocmax nucl_num 0
|
|
in
|
|
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,
|
|
R_power.to_int y.Pseudo.GaussianPrimitive_local.r_power
|
|
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 Array.to_list tmp_array
|
|
|> Array.to_list
|
|
|> List.concat
|
|
in
|
|
Ezfio.ezfio_array_of_list ~rank:2 ~dim:[|nucl_num ; klocmax|] ~data
|
|
in
|
|
concat_2d tmp_array_v_k
|
|
|> Ezfio.set_pseudo_pseudo_v_k ;
|
|
concat_2d tmp_array_dz_k
|
|
|> Ezfio.set_pseudo_pseudo_dz_k;
|
|
concat_2d tmp_array_n_k
|
|
|> Ezfio.set_pseudo_pseudo_n_k;
|
|
|
|
let tmp_array_v_kl, tmp_array_dz_kl, tmp_array_n_kl =
|
|
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 (fun j x ->
|
|
let last_idx =
|
|
Array.make (lmax+1) 0
|
|
in
|
|
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,
|
|
R_power.to_int y.Pseudo.GaussianPrimitive_non_local.r_power
|
|
in
|
|
let i =
|
|
last_idx.(k)
|
|
in
|
|
tmp_array_v_kl.(k).(i).(j) <- AO_coef.to_float c;
|
|
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 (fun x ->
|
|
Array.map Array.to_list x
|
|
|> Array.to_list
|
|
|> List.concat) tmp_array
|
|
|> Array.to_list
|
|
|> List.concat
|
|
in
|
|
Ezfio.ezfio_array_of_list ~rank:3 ~dim:[|nucl_num ; kmax ; lmax+1|] ~data
|
|
in
|
|
concat_3d tmp_array_v_kl
|
|
|> Ezfio.set_pseudo_pseudo_v_kl ;
|
|
concat_3d tmp_array_dz_kl
|
|
|> Ezfio.set_pseudo_pseudo_dz_kl ;
|
|
concat_3d tmp_array_n_kl
|
|
|> Ezfio.set_pseudo_pseudo_n_kl ;
|
|
in
|
|
|
|
|
|
|
|
|
|
(* 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
|
|
let result = do_work [] 1 nuclei
|
|
|> List.rev
|
|
|> list_map (fun (x,i) ->
|
|
try
|
|
let e =
|
|
match x.Atom.element with
|
|
| Element.X -> Element.H
|
|
| e -> e
|
|
in
|
|
let key =
|
|
Int_elem (i,x.Atom.element)
|
|
in
|
|
try
|
|
Basis.read_element (basis_channel key) i e
|
|
with Not_found ->
|
|
let key =
|
|
Element x.Atom.element
|
|
in
|
|
try
|
|
Basis.read_element (basis_channel key) i e
|
|
with Not_found ->
|
|
failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i)
|
|
(Element.to_string x.Atom.element) )
|
|
with
|
|
| End_of_file -> failwith
|
|
("Element "^(Element.to_string x.Atom.element)^" not found in basis set.")
|
|
)
|
|
|> List.concat
|
|
in
|
|
(* close all in_channels *)
|
|
result
|
|
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;
|
|
Ezfio.set_basis_basis b;
|
|
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 (fun (x,_,_) -> x) long_basis in
|
|
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.x)) l)@
|
|
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.y)) l)@
|
|
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.z)) l)
|
|
in
|
|
let ao_prim_num_max = List.fold_left (fun s x ->
|
|
if x > s then x
|
|
else s) 0 ao_prim_num
|
|
in
|
|
let gtos =
|
|
list_map (fun (_,x,_) -> x) long_basis
|
|
in
|
|
|
|
let create_expo_coef ec =
|
|
let coefs =
|
|
begin match ec with
|
|
| `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_opt 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
|
|
let () =
|
|
let shell_num = List.length basis in
|
|
let lc : (GaussianPrimitive.t * Qptypes.AO_coef.t) list list =
|
|
list_map ( fun (g,_) -> g.Gto.lc ) basis
|
|
in
|
|
let ang_mom =
|
|
list_map (fun (l : (GaussianPrimitive.t * Qptypes.AO_coef.t) list) ->
|
|
let x, _ = List.hd l in
|
|
Angmom.to_l x.GaussianPrimitive.sym |> Qptypes.Positive_int.to_int
|
|
) lc
|
|
in
|
|
let expo =
|
|
list_map (fun l -> list_map (fun (x,_) -> Qptypes.AO_expo.to_float x.GaussianPrimitive.expo) l ) lc
|
|
|> List.concat
|
|
in
|
|
let coef =
|
|
list_map (fun l ->
|
|
list_map (fun (_,x) -> Qptypes.AO_coef.to_float x) l
|
|
) lc
|
|
|> List.concat
|
|
in
|
|
let shell_prim_num =
|
|
list_map List.length lc
|
|
in
|
|
let shell_idx =
|
|
let rec make_list n accu = function
|
|
| 0 -> accu
|
|
| i -> make_list n (n :: accu) (i-1)
|
|
in
|
|
let rec aux count accu = function
|
|
| [] -> List.rev accu
|
|
| l::rest ->
|
|
let new_l = make_list count accu (List.length l) in
|
|
aux (count+1) new_l rest
|
|
in
|
|
aux 1 [] lc
|
|
in
|
|
let prim_num = List.length coef in
|
|
Ezfio.set_basis_typ "Gaussian";
|
|
Ezfio.set_basis_shell_num shell_num;
|
|
Ezfio.set_basis_prim_num prim_num ;
|
|
Ezfio.set_basis_shell_prim_num (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| shell_num |] ~data:shell_prim_num);
|
|
Ezfio.set_basis_shell_ang_mom (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| shell_num |] ~data:ang_mom ) ;
|
|
Ezfio.set_basis_shell_index (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| prim_num |] ~data:shell_idx) ;
|
|
Ezfio.set_basis_basis_nucleus_index (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| shell_num |]
|
|
~data:( list_map (fun (_,n) -> Nucl_number.to_int n) basis)
|
|
) ;
|
|
Ezfio.set_basis_nucleus_shell_num(Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| nucl_num |]
|
|
~data:(
|
|
list_map (fun (_,n) -> Nucl_number.to_int n) basis
|
|
|> List.fold_left (fun accu i ->
|
|
match accu with
|
|
| [] -> [(1,i)]
|
|
| (h,j) :: rest -> if j == i then ((h+1,j)::rest) else ((1,i)::(h,j)::rest)
|
|
) []
|
|
|> List.rev
|
|
|> List.map fst
|
|
)) ;
|
|
Ezfio.set_basis_prim_coef (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| prim_num |] ~data:coef) ;
|
|
Ezfio.set_basis_prim_expo (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| prim_num |] ~data:expo) ;
|
|
|
|
|
|
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) ;
|
|
Ezfio.set_ao_basis_ao_cartesian(cart);
|
|
in
|
|
match Input.Ao_basis.read () with
|
|
| None -> failwith "Error in basis"
|
|
| Some x -> Input.Ao_basis.write x
|
|
in
|
|
let () =
|
|
try write_file () with
|
|
| ex ->
|
|
begin
|
|
begin
|
|
try
|
|
if Sys.is_directory ezfio_file then
|
|
rmdir ezfio_file
|
|
with _ -> ()
|
|
end;
|
|
raise ex;
|
|
end
|
|
in
|
|
ignore @@ Sys.command ("qp_edit -c "^ezfio_file);
|
|
print_endline ezfio_file
|
|
|
|
|
|
|
|
|
|
let () =
|
|
|
|
try (
|
|
|
|
let open Command_line in
|
|
begin
|
|
"Creates an EZFIO directory from a standard xyz file or from a z-matrix file in Gaussian format. The basis set is defined as a single string if all the atoms are taken from the same basis set, otherwise specific elements can be defined as follows:
|
|
|
|
-b \"cc-pcvdz | H:cc-pvdz | C:6-31g\"
|
|
-b \"cc-pvtz | 1,H:sto-3g | 3,H:6-31g\"
|
|
|
|
If a file with the same name as the basis set exists, this file will be read. Otherwise, the basis set is obtained from the database.
|
|
" |> set_description_doc ;
|
|
set_header_doc (Sys.argv.(0) ^ " - Quantum Package command");
|
|
|
|
[ { opt=Optional ; short='o'; long="output";
|
|
arg=With_arg "EZFIO_DIR";
|
|
doc="Name of the created EZFIO directory."} ;
|
|
|
|
{ opt=Mandatory; short='b'; long="basis";
|
|
arg=With_arg "<string>";
|
|
doc="Name of basis set file. Searched in ${QP_ROOT}/data/basis if not found."} ;
|
|
|
|
{ opt=Optional ; short='a'; long="au";
|
|
arg=Without_arg;
|
|
doc="Input geometry is in atomic units."} ;
|
|
|
|
{ opt=Optional ; short='c'; long="charge";
|
|
arg=With_arg "<int>";
|
|
doc="Total charge of the molecule. Default is 0. For negative values, use m instead of -, for ex m1"} ;
|
|
|
|
{ opt=Optional ; short='d'; long="dummy";
|
|
arg=With_arg "<float>";
|
|
doc="Add dummy atoms. x * (covalent radii of the atoms)."} ;
|
|
|
|
{ opt=Optional ; short='m'; long="multiplicity";
|
|
arg=With_arg "<int>";
|
|
doc="Spin multiplicity (2S+1) of the molecule. Default is 1."} ;
|
|
|
|
{ opt=Optional ; short='p'; long="pseudo";
|
|
arg=With_arg "<string>";
|
|
doc="Name of the pseudopotential."} ;
|
|
|
|
{ opt=Optional ; short='x'; long="cartesian";
|
|
arg=Without_arg;
|
|
doc="Compute AOs in the Cartesian basis set (6d, 10f, ...)."} ;
|
|
|
|
anonymous "FILE" Mandatory "Input file in xyz format or z-matrix.";
|
|
]
|
|
|> set_specs
|
|
end;
|
|
|
|
|
|
(* Handle options *)
|
|
let output =
|
|
Command_line.get "output"
|
|
in
|
|
|
|
let basis =
|
|
match Command_line.get "basis" with
|
|
| None -> ""
|
|
| Some x -> x
|
|
in
|
|
|
|
let au =
|
|
Command_line.get_bool "au"
|
|
in
|
|
|
|
let charge =
|
|
match Command_line.get "charge" with
|
|
| None -> 0
|
|
| Some x -> ( if x.[0] = 'm' then
|
|
~- (int_of_string (String.sub x 1 (String.length x - 1)))
|
|
else
|
|
int_of_string x )
|
|
in
|
|
|
|
let dummy =
|
|
match Command_line.get "dummy" with
|
|
| None -> 0.
|
|
| Some x -> float_of_string x
|
|
in
|
|
|
|
let multiplicity =
|
|
match Command_line.get "multiplicity" with
|
|
| None -> 1
|
|
| Some n -> int_of_string n
|
|
in
|
|
|
|
let pseudo =
|
|
Command_line.get "pseudo"
|
|
in
|
|
|
|
let cart =
|
|
Command_line.get_bool "cartesian"
|
|
in
|
|
|
|
let xyz_filename =
|
|
match Command_line.anon_args () with
|
|
| [] -> failwith "input file is missing"
|
|
| x::_ -> x
|
|
in
|
|
|
|
run ?o:output basis au charge dummy multiplicity pseudo cart xyz_filename
|
|
)
|
|
with
|
|
| Failure txt -> Printf.eprintf "Fatal error: %s\n%!" txt
|
|
| Command_line.Error txt -> Printf.eprintf "Command line error: %s\n%!" txt
|
|
|
|
|