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https://github.com/LCPQ/quantum_package
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Working on the basis set in xyz->ezfio
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@ -1,13 +1,14 @@
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open Core.Std;;
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open Qptypes;;
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type t = Gto.t list;;
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type t = (Gto.t * Atom_number.t) list;;
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(** Read all the basis functions of an element *)
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let read in_channel =
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let read in_channel at_number =
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let rec read result =
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try
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let gto = Gto.read_one in_channel in
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read (gto::result)
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read ( (gto,at_number)::result)
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with
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| Gto.End_Of_Basis -> List.rev result
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in read []
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@ -28,12 +29,15 @@ let find in_channel element =
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!element_read
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;;
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let read_element in_channel element =
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(** Read an element from the file *)
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let read_element in_channel at_number element =
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ignore (find in_channel element) ;
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read in_channel ;
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read in_channel at_number ;
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;;
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let to_string b =
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List.map ~f:Gto.to_string b
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List.map ~f:(fun (g,n) ->
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let n = Atom_number.to_int n in
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(Int.to_string n)^":"^(Gto.to_string g)) b
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|> String.concat ~sep:"\n"
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;;
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17
ocaml/Basis.mli
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17
ocaml/Basis.mli
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@ -0,0 +1,17 @@
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open Qptypes;;
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type t = (Gto.t * Atom_number.t) list
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(** Read all the basis functions of an element and set the number of the
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* atom *)
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val read : in_channel -> Atom_number.t -> (Gto.t * Atom_number.t) list
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(** Find an element in the basis set file *)
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val find : in_channel -> Element.t -> Element.t
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(** Read the basis of an element from the file *)
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val read_element :
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in_channel -> Atom_number.t -> Element.t -> (Gto.t * Atom_number.t) list
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(** Convert the basis to a string *)
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val to_string : (Gto.t * Atom_number.t) list -> string
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@ -1,15 +1,16 @@
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open Core.Std;;
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open Qptypes;;
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type t = (Symmetry.Xyz.t * Gto.t) list;;
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type t = (Symmetry.Xyz.t * Gto.t * Atom_number.t ) list;;
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let of_basis b =
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let rec do_work accu = function
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| [] -> accu
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| g::tail ->
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| (g,n)::tail ->
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begin
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let new_accu =
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Symmetry.Xyz.of_symmetry g.Gto.sym
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|> List.map ~f:(fun x-> (x,g))
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|> List.map ~f:(fun x-> (x,g,n))
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in
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do_work (new_accu@accu) tail
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end
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@ -20,7 +21,8 @@ let of_basis b =
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let to_string b =
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List.map ~f:(fun (x,y) ->
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List.map ~f:(fun (x,y,z) ->
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(Int.to_string (Atom_number.to_int z))^":"^
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(Symmetry.Xyz.to_string x)^" "^(Gto.to_string y)
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) b
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|> String.concat ~sep:"\n"
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16
ocaml/Long_basis.mli
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16
ocaml/Long_basis.mli
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@ -0,0 +1,16 @@
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open Qptypes;;
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(** A long basis is a basis set where
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* all the P orbitals are converted to x, y, z
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* all the D orbitals are converted to xx, xy, xz, yy, yx
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* etc
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*)
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type t = (Symmetry.Xyz.t * Gto.t * Atom_number.t) list
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(** Transform a basis to a long basis *)
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val of_basis :
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(Gto.t * Atom_number.t) list -> (Symmetry.Xyz.t * Gto.t * Atom_number.t) list
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(** Convert the basis into its string representation *)
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val to_string :
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(Symmetry.Xyz.t * Gto.t * Atom_number.t) list -> string
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@ -13,7 +13,7 @@ endif
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LIBS=
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PKGS=
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OCAMLCFLAGS=-g
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OCAMLBUILD=ocamlbuild -cflags $(OCAMLCFLAGS) -lflags -g
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OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags -g
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MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml
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MLIFILES=$(wildcard *.mli)
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ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml))
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@ -26,7 +26,8 @@ default: $(ALL_TESTS) $(ALL_EXE)
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executables: $(ALL_EXE)
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%.inferred.mli: $(MLFILES)
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$(OCAMLBUILD) $*.inferred.mli -cflags -i -use-ocamlfind $(PKGS)
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$(OCAMLBUILD) $*.inferred.mli -use-ocamlfind $(PKGS)
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mv _build/$*.inferred.mli .
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%.byte: $(MLFILES) $(MLIFILES)
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$(OCAMLBUILD) $*.byte -use-ocamlfind $(PKGS)
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@ -82,7 +82,36 @@ File : %s\n" c m b xyz_file;
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(* Write Basis set *)
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let basis =
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let long_basis = Long_basis
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let rec do_work (accu:(Atom.t*Atom_number.t) list) (n:int) = function
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| [] -> accu
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| e::tail -> let new_accu = (e,(Atom_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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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) -> Atom_number.to_int n)
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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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(*
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ao_basis
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ao_power integer (ao_basis_ao_num,3)
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ao_prim_num_max integer = maxval(ao_basis_ao_prim_num)
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ao_coef double precision (ao_basis_ao_num,ao_basis_ao_prim_num_max)
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ao_expo double precision (ao_basis_ao_num,ao_basis_ao_prim_num_max)
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*)
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;;
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@ -28,6 +28,13 @@ let input_data = "
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* Non_empty_string : string
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assert (x <> \"\") ;
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* Atom_number : int
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assert (x > 0) ;
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if (x > 1000) then
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warning \"More than 1000 atoms\";
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if (Ezfio.has_nuclei_nucl_num ()) then
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assert (x <= (Ezfio.get_nuclei_nucl_num ()));
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* MO_number : int
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assert (x > 0) ;
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if (x > 1000) then
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@ -1,5 +1,6 @@
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open Core.Std;;
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open Qputils;;
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open Qptypes;;
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let test_module () =
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@ -13,9 +14,11 @@ let test_module () =
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Molecule.of_xyz_file xyz_file
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in
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let nuclei = molecule.Molecule.nuclei in
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let basis =
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(Basis.read_element basis_channel Element.F) @
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(Basis.read_element basis_channel Element.F)
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(Basis.read_element basis_channel (Atom_number.of_int 1) Element.F) @
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(Basis.read_element basis_channel (Atom_number.of_int 2) Element.F)
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in
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Long_basis.of_basis basis
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@ -23,14 +23,14 @@ let test_gto_1 () =
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let test_gto_2 () =
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let in_channel = open_in "/home/scemama/quantum_package/data/basis/cc-pvdz" in
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ignore (input_line in_channel);
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let basis = Basis.read in_channel in
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List.iter basis ~f:(fun x-> Printf.printf "%s\n" (Gto.to_string x))
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let basis = Basis.read in_channel (Atom_number.of_int 1) in
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List.iter basis ~f:(fun (x,n)-> Printf.printf "%d:%s\n" (Atom_number.to_int n) (Gto.to_string x))
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;;
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let test_gto () =
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let in_channel = open_in "/home/scemama/quantum_package/data/basis/cc-pvdz" in
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let basis = Basis.read_element in_channel Element.C in
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List.iter basis ~f:(fun x-> Printf.printf "%s\n" (Gto.to_string x))
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let basis = Basis.read_element in_channel (Atom_number.of_int 1) Element.C in
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List.iter basis ~f:(fun (x,n)-> Printf.printf "%d:%s\n" (Atom_number.to_int n) (Gto.to_string x))
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;;
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let test_module () =
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