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qp2
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Removed Core from qp_create_ezfio.ml

This commit is contained in:
Anthony Scemama 2019-03-13 11:35:21 +01:00
parent 83d3cafbb2
commit da3ba4ef4b
6 changed files with 131 additions and 148 deletions
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4
ocaml/Element.ml
View File

@ -1,4 +1,4 @@
open Core
open Sexplib.Std
open Qptypes
exception ElementError of string
@ -14,7 +14,7 @@ type t =
[@@deriving sexp]
let of_string x =
match (String.capitalize (String.lowercase x)) with
match (String.capitalize_ascii (String.lowercase_ascii x)) with
| "X" | "Dummy" -> X
| "H" | "Hydrogen" -> H
| "He" | "Helium" -> He

3
ocaml/Gamess.ml
View File

@ -1,5 +1,6 @@
(** CONTRL *)
type scftyp_t = RHF | ROHF | MCSCF | NONE
let string_of_scftyp = function
| RHF -> "RHF"
| ROHF -> "ROHF"
@ -116,7 +117,7 @@ type guess_t =
| Natural of (int*string)
let guess_of_string s =
match String.lowercase s with
match String.lowercase_ascii s with
| "huckel" -> Huckel
| "hcore" -> Hcore
| _ -> raise (Invalid_argument "Bad MO guess")

2
ocaml/MO_class.ml
View File

@ -33,7 +33,7 @@ let to_string x =
let of_string s =
match (String.lowercase s) with
match (String.lowercase_ascii s) with
| "core" -> Core []
| "inactive" -> Inactive []
| "active" -> Active []

6
ocaml/MO_label.ml
View File

@ -1,4 +1,4 @@
open Core;;
open Sexplib.Std
type t =
| Guess
@ -8,7 +8,7 @@ type t =
| Orthonormalized
| None
[@@deriving sexp]
;;
let to_string = function
| Guess -> "Guess"
@ -20,7 +20,7 @@ let to_string = function
;;
let of_string s =
match String.lowercase (String.strip s) with
match String.lowercase_ascii (String.trim s) with
| "guess" -> Guess
| "canonical" -> Canonical
| "natural" -> Natural

12
ocaml/Point3d.ml
View File

@ -1,5 +1,5 @@
open Core;;
open Qptypes;;
open Qptypes
open Sexplib.Std
type t = {
x : float ;
@ -21,10 +21,10 @@ let of_string ~units s =
| Units.Angstrom -> Units.angstrom_to_bohr
in
let l = s
|> String.split ~on:' '
|> List.filter ~f:(fun x -> x <> "")
|> List.map ~f:Float.of_string
|> Array.of_list
|> String_ext.split ~on:' '
|> List.filter (fun x -> x <> "")
|> List.map float_of_string
|> Array.of_list
in
{ x = l.(0) *. f ;
y = l.(1) *. f ;

252
ocaml/qp_create_ezfio.ml
View File

@ -1,6 +1,6 @@
open Qputils
open Qptypes
open Core
open Sexplib.Std
type element =
| Element of Element.t
@ -38,7 +38,7 @@ let dummy_centers ~threshold ~molecule ~nuclei =
| _ -> assert false
in
aux [] (n-1,n-1)
|> List.map ~f:(fun (i,x,j,y,r) ->
|> List.map (fun (i,x,j,y,r) ->
let f =
x /. (x +. y)
in
@ -58,22 +58,22 @@ let dummy_centers ~threshold ~molecule ~nuclei =
(** Returns the list of available basis sets *)
let list_basis () =
let basis_list =
let ic = Pervasives.open_in (Qpackage.root ^ "/data/basis/00_README.rst") in
let n = Pervasives.in_channel_length ic in
let ic = open_in (Qpackage.root ^ "/data/basis/00_README.rst") in
let n = in_channel_length ic in
let s = Bytes.create n in
Pervasives.really_input ic s 0 n;
Pervasives.close_in ic;
really_input ic s 0 n;
close_in ic;
Bytes.to_string s
|> String.split ~on:'\n'
|> List.filter ~f:(fun line -> String.length line > 1 && line.[0] <> '#')
|> List.map ~f:(fun line ->
match String.split ~on:'\'' line with
|> String_ext.split ~on:'\n'
|> List.filter (fun line -> String.length line > 1 && line.[0] <> '#')
|> List.map (fun line ->
match String_ext.split ~on:'\'' line with
| file :: name :: descr :: _ ->
Printf.sprintf "%s\n %s\n %s\n\n" file name (String.strip descr)
Printf.sprintf "%s\n %s\n %s\n\n" file name (String.trim descr)
| _ -> assert false
)
in
List.sort basis_list ~compare:String.ascending
List.sort compare basis_list
(** Run the program *)
@ -101,7 +101,7 @@ let run ?o b au c d m p cart xyz_file =
**********)
let basis_table =
Hashtbl.Poly.create ()
Hashtbl.create 63
in
(* Open basis set channels *)
@ -111,10 +111,7 @@ let run ?o b au c d m p cart xyz_file =
| Element e -> Element.to_string e
| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
in
match Hashtbl.find basis_table key with
| Some in_channel ->
in_channel
| None -> raise Caml.Not_found
Hashtbl.find basis_table key
in
let temp_filename =
@ -129,11 +126,11 @@ let run ?o b au c d m p cart xyz_file =
Qpackage.root ^ "/data/basis/" ^ basis
in
match
Sys.is_file basis,
Sys.is_file long_basis
Sys.file_exists basis,
Sys.file_exists long_basis
with
| `Yes, _ -> In_channel.create basis
| `No , `Yes -> In_channel.create long_basis
| true , _ -> open_in basis
| false, true -> open_in long_basis
| _ -> failwith ("Basis "^basis^" not found")
in
@ -141,7 +138,7 @@ let run ?o b au c d m p cart xyz_file =
| [] -> ()
| elem_and_basis_name :: rest ->
begin
match (String.lsplit2 ~on:':' elem_and_basis_name) with
match (String_ext.lsplit2 ~on:':' elem_and_basis_name) with
| None -> (* Principal basis *)
begin
let basis =
@ -150,14 +147,12 @@ let run ?o b au c d m p cart xyz_file =
let new_channel =
fetch_channel basis
in
List.iter nuclei ~f:(fun elem->
List.iter (fun elem->
let key =
Element.to_string elem.Atom.element
in
match Hashtbl.add basis_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> ()
)
Hashtbl.add basis_table key new_channel
) nuclei
end
| Some (key, basis) -> (*Aux basis *)
begin
@ -166,12 +161,12 @@ let run ?o b au c d m p cart xyz_file =
Element (Element.of_string key)
with Element.ElementError _ ->
let result =
match (String.split ~on:',' key) with
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 basis
String.lowercase_ascii basis
in
let key =
match elem with
@ -181,23 +176,13 @@ let run ?o b au c d m p cart xyz_file =
let new_channel =
fetch_channel basis
in
begin
match Hashtbl.add basis_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate ->
let e =
match elem with
| Element e -> e
| Int_elem (_,e) -> e
in
failwith ("Duplicate definition of basis for "^(Element.to_long_string e))
end
Hashtbl.add basis_table key new_channel
end
end;
build_basis rest
in
String.split ~on:'|' b
|> List.rev_map ~f:String.strip
String_ext.split ~on:'|' b
|> List.rev_map String.trim
|> build_basis;
@ -207,7 +192,7 @@ let run ?o b au c d m p cart xyz_file =
***************)
let pseudo_table =
Hashtbl.Poly.create ()
Hashtbl.create 63
in
(* Open pseudo channels *)
@ -215,7 +200,7 @@ let run ?o b au c d m p cart xyz_file =
let key =
Element.to_string element
in
Hashtbl.find pseudo_table key
Hashtbl.find_opt pseudo_table key
in
let temp_filename =
Filename.temp_file "qp_create_" ".pseudo"
@ -229,11 +214,11 @@ let run ?o b au c d m p cart xyz_file =
Qpackage.root ^ "/data/pseudo/" ^ pseudo
in
match
Sys.is_file pseudo,
Sys.is_file long_pseudo
Sys.file_exists pseudo,
Sys.file_exists long_pseudo
with
| `Yes, _ -> In_channel.create pseudo
| `No , `Yes -> In_channel.create long_pseudo
| true , _ -> open_in pseudo
| false, true-> open_in long_pseudo
| _ -> failwith ("Pseudo file "^pseudo^" not found.")
in
@ -241,7 +226,7 @@ let run ?o b au c d m p cart xyz_file =
| [] -> ()
| elem_and_pseudo_name :: rest ->
begin
match (String.lsplit2 ~on:':' elem_and_pseudo_name) with
match (String_ext.lsplit2 ~on:':' elem_and_pseudo_name) with
| None -> (* Principal pseudo *)
begin
let pseudo =
@ -250,21 +235,19 @@ let run ?o b au c d m p cart xyz_file =
let new_channel =
fetch_channel pseudo
in
List.iter nuclei ~f:(fun elem->
List.iter (fun elem->
let key =
Element.to_string elem.Atom.element
in
match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> ()
)
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 pseudo
String.lowercase_ascii pseudo
in
let key =
Element.to_string elem
@ -272,11 +255,7 @@ let run ?o b au c d m p cart xyz_file =
let new_channel =
fetch_channel pseudo
in
begin
match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> failwith ("Duplicate definition of pseudo for "^(Element.to_long_string elem))
end
Hashtbl.add pseudo_table key new_channel
end
end;
build_pseudo rest
@ -285,8 +264,8 @@ let run ?o b au c d m p cart xyz_file =
match p with
| None -> ()
| Some p ->
String.split ~on:'|' p
|> List.rev_map ~f:String.strip
String_ext.split ~on:'|' p
|> List.rev_map String.trim
|> build_pseudo
in
@ -296,13 +275,13 @@ let run ?o b au c d m p cart xyz_file =
| Some x -> x
| None ->
begin
match String.rsplit2 ~on:'.' xyz_file with
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_exn ezfio_file then
if Sys.file_exists ezfio_file then
failwith (ezfio_file^" already exists");
let write_file () =
@ -311,17 +290,17 @@ let run ?o b au c d m p cart xyz_file =
(* Write Pseudo *)
let pseudo =
List.map nuclei ~f:(fun x ->
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 molecule =
let n_elec_to_remove =
List.fold pseudo ~init:0 ~f:(fun accu x ->
accu + (Positive_int.to_int x.Pseudo.n_elec))
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)
@ -333,14 +312,14 @@ let run ?o b au c d m p cart xyz_file =
|> Elec_beta_number.of_int;
Molecule.nuclei =
let charges =
List.map pseudo ~f:(fun x -> Positive_int.to_int x.Pseudo.n_elec
|> Float.of_int)
List.map (fun x -> Positive_int.to_int x.Pseudo.n_elec
|> Float.of_int) pseudo
|> Array.of_list
in
List.mapi molecule.Molecule.nuclei ~f:(fun i x ->
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 =
@ -356,13 +335,13 @@ let run ?o b au c d m p cart xyz_file =
(* Write Nuclei *)
let labels =
List.map ~f:(fun x->Element.to_string x.Atom.element) nuclei
List.map (fun x->Element.to_string x.Atom.element) nuclei
and charges =
List.map ~f:(fun x-> Atom.(Charge.to_float x.charge)) nuclei
List.map (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
(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
@ -381,40 +360,41 @@ let run ?o b au c d m p cart xyz_file =
in
let klocmax =
List.fold pseudo ~init:0 ~f:(fun accu x ->
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 pseudo ~init:0 ~f:(fun accu x ->
List.fold_left (fun accu x ->
let x =
List.fold x.Pseudo.non_local ~init:0 ~f:(fun accu (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) ~f:(fun i->
List.map pseudo ~f:(fun x ->
List.filter x.Pseudo.non_local ~f:(fun (y,_) ->
(Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i)
|> List.length )
|> List.fold ~init:0 ~f:(fun accu x ->
if accu > x then accu else x)
)
|> Array.fold ~init:0 ~f:(fun accu i ->
if i > accu then i else accu)
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
@ -423,12 +403,12 @@ let run ?o b au c d m p cart xyz_file =
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 ~dimx:klocmax ~dimy:nucl_num 0. ,
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0. ,
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0
Array.make_matrix klocmax nucl_num 0. ,
Array.make_matrix klocmax nucl_num 0. ,
Array.make_matrix klocmax nucl_num 0
in
List.iteri pseudo ~f:(fun j x ->
List.iteri x.Pseudo.local ~f:(fun i (y,c) ->
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,
@ -436,11 +416,11 @@ let run ?o b au c d m p cart xyz_file =
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 tmp_array ~f:Array.to_list
Array.map Array.to_list tmp_array
|> Array.to_list
|> List.concat
in
@ -454,18 +434,18 @@ let run ?o b au c d m p cart xyz_file =
|> Ezfio.set_pseudo_pseudo_n_k;
let tmp_array_v_kl, tmp_array_dz_kl, tmp_array_n_kl =
Array.init (lmax+1) ~f:(fun _ ->
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
Array.init (lmax+1) ~f:(fun _ ->
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
Array.init (lmax+1) ~f:(fun _ ->
(Array.make_matrix ~dimx:kmax ~dimy: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. )),
Array.init (lmax+1) (fun _ ->
(Array.make_matrix kmax nucl_num 0 ))
in
List.iteri pseudo ~f:(fun j x ->
List.iteri (fun j x ->
let last_idx =
Array.create ~len:(lmax+1) 0
Array.make (lmax+1) 0
in
List.iter x.Pseudo.non_local ~f:(fun (y,c) ->
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,
@ -478,14 +458,14 @@ let run ?o b au c d m p cart xyz_file =
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 tmp_array ~f:(fun x ->
Array.map x ~f:Array.to_list
Array.map (fun x ->
Array.map Array.to_list x
|> Array.to_list
|> List.concat)
|> List.concat) tmp_array
|> Array.to_list
|> List.concat
in
@ -518,7 +498,7 @@ let run ?o b au c d m p cart xyz_file =
in
let result = do_work [] 1 nuclei
|> List.rev
|> List.map ~f:(fun (x,i) ->
|> List.map (fun (x,i) ->
try
let e =
match x.Atom.element with
@ -552,37 +532,38 @@ let run ?o b au c d m p cart xyz_file =
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)
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 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)) )
let l = List.map (fun (x,_,_) -> x) long_basis in
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) l)@
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) l)@
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) l)
in
let ao_prim_num_max = List.fold ~init:0 ~f:(fun s x ->
let ao_prim_num_max = List.fold_left (fun s x ->
if x > s then x
else s) ao_prim_num
else s) 0 ao_prim_num
in
let gtos =
List.map long_basis ~f:(fun (_,x,_) -> x)
List.map (fun (_,x,_) -> x) long_basis
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.GaussianPrimitive.expo) )
| `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 h n with
begin match List.nth_opt h n with
| Some x -> x
| None -> 0.
end
@ -621,9 +602,10 @@ let run ?o b au c d m p cart xyz_file =
| ex ->
begin
begin
match Sys.is_directory ezfio_file with
| `Yes -> rmdir ezfio_file
| _ -> ()
try
if Sys.is_directory ezfio_file then
rmdir ezfio_file
with _ -> ()
end;
raise ex;
end
@ -730,7 +712,7 @@ If a file with the same name as the basis set exists, this file will be read. O
if basis = "show" then
begin
list_basis ()
|> List.iter ~f:print_endline;
|> List.iter print_endline;
exit 0
end;