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https://github.com/LCPQ/quantum_package
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Added Molecule.of_xyz_file
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@ -1,3 +1,5 @@
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#TODO : Opam auto-installer in makefile
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# Check if QPACKAGE_ROOT is defined
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ifndef QPACKAGE_ROOT
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@ -33,13 +33,13 @@ let of_string s =
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| [ name; charge; x; y; z ] ->
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{ element = Element.of_string name ;
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charge = Charge.of_string charge ;
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coord = Point3d.of_string (String.concat [x; y; z] ?sep:(Some " "))
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coord = Point3d.of_string (String.concat [x; y; z] ~sep:" ")
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}
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| [ name; x; y; z ] ->
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let e = Element.of_string name in
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{ element = e ;
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charge = Charge.of_int (Element.charge e);
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coord = Point3d.of_string (String.concat [x; y; z] ?sep:(Some " "))
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coord = Point3d.of_string (String.concat [x; y; z] ~sep:" ")
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}
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| _ -> raise (AtomError s)
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;;
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@ -91,7 +91,7 @@ let find in_channel element =
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;;
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let read_basis_of_element in_channel element =
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find in_channel element ;
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ignore (find in_channel element) ;
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read_basis in_channel ;
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;;
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@ -100,5 +100,5 @@ let to_string { sym = sym ; lc = lc } =
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let f (p,c) = Printf.sprintf "( %s, %f )" (Primitive.to_string p) c
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in
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Printf.sprintf "[ %s : %s ]" (Symmetry.to_string sym)
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(String.concat (List.map ~f:f lc) ?sep:(Some ", "))
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(String.concat (List.map ~f:f lc) ~sep:", ")
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;;
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@ -9,7 +9,7 @@ type t = {
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elec_beta : Positive_int.t ;
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}
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let charge { nuclei ; elec_alpha ; elec_beta } =
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let get_charge { nuclei ; elec_alpha ; elec_beta } =
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let result = Positive_int.(to_int elec_alpha + to_int elec_beta) in
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let rec nucl_charge = function
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| a::rest -> Atom.(Charge.to_float a.charge) +. nucl_charge rest
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@ -18,12 +18,12 @@ let charge { nuclei ; elec_alpha ; elec_beta } =
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nucl_charge nuclei -. (Float.of_int result)
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;;
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let multiplicity m =
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let get_multiplicity m =
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Multiplicity.of_alpha_beta m.elec_alpha m.elec_beta
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;;
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let name m =
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let cm = Float.to_int (charge m) in
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let cm = Float.to_int (get_charge m) in
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let c =
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match cm with
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| 0 -> ""
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@ -32,7 +32,7 @@ let name m =
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| i when i>1 -> Printf.sprintf " (%d+)" i
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| i -> Printf.sprintf " (%d-)" (-i)
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in
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let mult = Multiplicity.to_string (multiplicity m) in
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let mult = Multiplicity.to_string (get_multiplicity m) in
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let { nuclei ; elec_alpha ; elec_beta } = m in
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let rec build_list accu = function
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| a::rest ->
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@ -67,35 +67,47 @@ let to_string m =
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let n = List.length nuclei in
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let title = name m in
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[ Int.to_string n ; title ] @ (List.map ~f:Atom.to_string nuclei)
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|> String.concat ?sep:(Some "\n")
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|> String.concat ~sep:"\n"
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;;
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let of_xyz_string s charge' multiplicity' =
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let of_xyz_string
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?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
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s =
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let l = String.split s ~on:'\n'
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|> List.filter ~f:(fun x -> x <> "")
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|> List.map ~f:Atom.of_string
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in
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let ne = ( charge {
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let ne = ( get_charge {
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nuclei=l ;
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elec_alpha=(Positive_int.of_int 0) ;
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elec_beta=(Positive_int.of_int 0) }
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|> Float.to_int
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)- charge'
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)- charge
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|> Positive_int.of_int
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in
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let (na,nb) = Multiplicity.to_alpha_beta ne multiplicity' in
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let (na,nb) = Multiplicity.to_alpha_beta ne multiplicity in
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let result =
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{ nuclei = l ;
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elec_alpha = (Positive_int.of_int na) ;
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elec_beta = (Positive_int.of_int nb) }
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in
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if ((multiplicity result) <> multiplicity') then
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if ((get_multiplicity result) <> multiplicity) then
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let msg = Printf.sprintf
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"With %d electrons multiplicity %d is impossible"
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(Positive_int.to_int ne)
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(Multiplicity.to_int multiplicity')
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(Multiplicity.to_int multiplicity)
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in
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raise (MultiplicityError msg);
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else () ;
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result
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;;
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let of_xyz_file
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?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
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filename =
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let (_,buffer) = In_channel.read_all filename
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|> String.lsplit2_exn ~on:'\n' in
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let (_,buffer) = String.lsplit2_exn buffer ~on:'\n' in
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of_xyz_string ~charge:charge ~multiplicity:multiplicity buffer
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;;
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@ -10,14 +10,18 @@ H 1.0 0.54386314 0.00000000 -0.92559535
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"
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in
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try ignore (Molecule.of_xyz_string xyz 1 (Strictly_positive_int.of_int 1))
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with
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| Molecule.MultiplicityError _ -> print_string "OK\n"
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;
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print_string "---\n";
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let m = Molecule.of_xyz_string xyz 0 (Strictly_positive_int.of_int 1)
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begin
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try (
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ignore (Molecule.of_xyz_string xyz ~multiplicity:(Multiplicity.of_int 2)) ;
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print_string "Failed in MultiplicityError\n" )
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with
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| Molecule.MultiplicityError _ -> print_string "MultiplicityError OK\n"
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end ;
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print_string "---\n";
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let m = Molecule.of_xyz_string xyz
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in print_endline (Molecule.name m) ;
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let m = Molecule.of_xyz_string xyz 1 (Strictly_positive_int.of_int 2)
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let m = Molecule.of_xyz_string xyz ~charge:1 ~multiplicity:(Multiplicity.of_int 2)
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in print_endline (Molecule.name m) ;
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let xyz =
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@ -27,9 +31,14 @@ O 1.65102147 0.00000000 -2.35602344
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H 0.54386314 0.00000000 -0.92559535
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"
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in
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let m = Molecule.of_xyz_string xyz (-2) (Strictly_positive_int.of_int 1)
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let m = Molecule.of_xyz_string xyz ~charge:(-2)
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in print_endline (Molecule.name m) ;
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print_endline (Molecule.to_string m);
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print_string "---------\n";
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let m = Molecule.of_xyz_file "c2h6.xyz" in
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print_string (Molecule.to_string m);
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;;
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test_molecule ();;
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