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Changed dummy into ghost
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3319d78816
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@ -26,8 +26,7 @@ let of_string = function
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| "J" | "j" -> J
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| "J" | "j" -> J
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| "K" | "k" -> K
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| "K" | "k" -> K
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| "L" | "l" -> L
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| "L" | "l" -> L
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| x -> raise (Failure ("Angmom should be S|P|D|F|G|H|I|J|K|L,
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| x -> raise (Failure ("Angmom should be S|P|D|F|G|H|I|J|K|L, not "^x^"."))
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not "^x^"."))
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let of_char = function
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let of_char = function
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| 'S' | 's' -> S
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| 'S' | 's' -> S
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@ -17,7 +17,7 @@ let read in_channel at_number =
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(** Find an element in the basis set file *)
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(** Find an element in the basis set file *)
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let find in_channel element =
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let find in_channel element =
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seek_in in_channel 0;
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seek_in in_channel 0;
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let element_read = ref Element.X in
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let element_read = ref Element.Og in
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while !element_read <> element
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while !element_read <> element
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do
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do
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let buffer = input_line in_channel in
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let buffer = input_line in_channel in
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@ -4,7 +4,7 @@ open Qptypes
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exception ElementError of string
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exception ElementError of string
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type t = X
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type t = X
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|H |He
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|H |He
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|Li|Be |B |C |N |O |F |Ne
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|Li|Be |B |C |N |O |F |Ne
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|Na|Mg |Al|Si|P |S |Cl|Ar
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|Na|Mg |Al|Si|P |S |Cl|Ar
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@ -20,7 +20,7 @@ type t = X
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let of_string x =
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let of_string x =
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match (String.capitalize_ascii (String.lowercase_ascii x)) with
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match (String.capitalize_ascii (String.lowercase_ascii x)) with
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| "X" | "Dummy" -> X
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| "X" | "Ghost" -> X
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| "H" | "Hydrogen" -> H
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| "H" | "Hydrogen" -> H
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| "He" | "Helium" -> He
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| "He" | "Helium" -> He
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| "Li" | "Lithium" -> Li
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| "Li" | "Lithium" -> Li
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@ -265,7 +265,7 @@ let to_string = function
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let to_long_string = function
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let to_long_string = function
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| X -> "Dummy"
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| X -> "Ghost"
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| H -> "Hydrogen"
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| H -> "Hydrogen"
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| He -> "Helium"
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| He -> "Helium"
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| Li -> "Lithium"
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| Li -> "Lithium"
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@ -492,20 +492,20 @@ let to_charge c =
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| No -> 102
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| No -> 102
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| Lr -> 103
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| Lr -> 103
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| Rf -> 104
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| Rf -> 104
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| Db -> 105
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| Db -> 105
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| Sg -> 106
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| Sg -> 106
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| Bh -> 107
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| Bh -> 107
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| Hs -> 108
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| Hs -> 108
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| Mt -> 109
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| Mt -> 109
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| Ds -> 110
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| Ds -> 110
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| Rg -> 111
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| Rg -> 111
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| Cn -> 112
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| Cn -> 112
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| Nh -> 113
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| Nh -> 113
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| Fl -> 114
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| Fl -> 114
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| Mc -> 115
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| Mc -> 115
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| Lv -> 116
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| Lv -> 116
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| Ts -> 117
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| Ts -> 117
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| Og -> 118
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| Og -> 118
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in Charge.of_int result
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in Charge.of_int result
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@ -565,7 +565,7 @@ let of_charge c = match (Charge.to_int c) with
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| 52 -> Te
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| 52 -> Te
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| 53 -> I
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| 53 -> I
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| 54 -> Xe
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| 54 -> Xe
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| 55 -> Cs
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| 55 -> Cs
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| 56 -> Ba
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| 56 -> Ba
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| 57 -> La
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| 57 -> La
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| 58 -> Ce
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| 58 -> Ce
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@ -880,7 +880,7 @@ let vdw_radius x =
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| Ts -> None
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| Ts -> None
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| Og -> None
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| Og -> None
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in
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in
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match result x with
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match result x with
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| Some y -> Some (Positive_float.of_float @@ Units.angstrom_to_bohr *. y )
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| Some y -> Some (Positive_float.of_float @@ Units.angstrom_to_bohr *. y )
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| None -> None
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| None -> None
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@ -6,8 +6,8 @@ type element =
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| Element of Element.t
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| Element of Element.t
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| Int_elem of (Nucl_number.t * Element.t)
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| Int_elem of (Nucl_number.t * Element.t)
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(** Handle dummy atoms placed on bonds *)
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(** Handle ghost atoms placed on bonds *)
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let dummy_centers ~threshold ~molecule ~nuclei =
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let ghost_centers ~threshold ~molecule ~nuclei =
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let d =
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let d =
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Molecule.distance_matrix molecule
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Molecule.distance_matrix molecule
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in
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in
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@ -68,11 +68,11 @@ let run ?o b au c d m p cart xyz_file =
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(Molecule.of_file xyz_file ~charge:(Charge.of_int c)
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(Molecule.of_file xyz_file ~charge:(Charge.of_int c)
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~multiplicity:(Multiplicity.of_int m) )
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~multiplicity:(Multiplicity.of_int m) )
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in
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in
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let dummy =
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let ghost =
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dummy_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei
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ghost_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei
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in
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in
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let nuclei =
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let nuclei =
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molecule.Molecule.nuclei @ dummy
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molecule.Molecule.nuclei @ ghost
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in
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in
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@ -145,8 +145,6 @@ let run ?o b au c d m p cart xyz_file =
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| i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
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| i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
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| _ -> failwith "Expected format is int,Element:basis"
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| _ -> failwith "Expected format is int,Element:basis"
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in Int_elem result
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in Int_elem result
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and basis =
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String.lowercase_ascii basis
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in
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in
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let key =
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let key =
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match elem with
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match elem with
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@ -313,7 +311,7 @@ let run ?o b au c d m p cart xyz_file =
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}
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}
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in
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in
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let nuclei =
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let nuclei =
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molecule.Molecule.nuclei @ dummy
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molecule.Molecule.nuclei @ ghost
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in
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in
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@ -491,11 +489,7 @@ let run ?o b au c d m p cart xyz_file =
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|> List.rev
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|> List.rev
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|> list_map (fun (x,i) ->
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|> list_map (fun (x,i) ->
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try
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try
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let e =
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let e = x.Atom.element in
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match x.Atom.element with
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| Element.X -> Element.H
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| e -> e
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in
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let key =
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let key =
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Int_elem (i,x.Atom.element)
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Int_elem (i,x.Atom.element)
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in
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in
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@ -507,9 +501,15 @@ let run ?o b au c d m p cart xyz_file =
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in
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in
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try
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try
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Basis.read_element (basis_channel key) i e
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Basis.read_element (basis_channel key) i e
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with Not_found ->
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with _ ->
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failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i)
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try
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(Element.to_string x.Atom.element) )
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if e = Element.X then
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Basis.read_element (basis_channel key) i (Element.H)
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else
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raise Not_found
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with Not_found ->
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failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i)
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(Element.to_string x.Atom.element) )
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with
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with
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| End_of_file -> failwith
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| End_of_file -> failwith
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("Element "^(Element.to_string x.Atom.element)^" not found in basis set.")
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("Element "^(Element.to_string x.Atom.element)^" not found in basis set.")
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@ -710,9 +710,9 @@ If a file with the same name as the basis set exists, this file will be read. O
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arg=With_arg "<int>";
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arg=With_arg "<int>";
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doc="Total charge of the molecule. Default is 0. For negative values, use m instead of -, for ex m1"} ;
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doc="Total charge of the molecule. Default is 0. For negative values, use m instead of -, for ex m1"} ;
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{ opt=Optional ; short='d'; long="dummy";
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{ opt=Optional ; short='g'; long="ghost";
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arg=With_arg "<float>";
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arg=With_arg "<float>";
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doc="Add dummy atoms. x * (covalent radii of the atoms)."} ;
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doc="Add ghost atoms. x * (covalent radii of the atoms)."} ;
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{ opt=Optional ; short='m'; long="multiplicity";
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{ opt=Optional ; short='m'; long="multiplicity";
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arg=With_arg "<int>";
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arg=With_arg "<int>";
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@ -756,8 +756,8 @@ If a file with the same name as the basis set exists, this file will be read. O
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int_of_string x )
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int_of_string x )
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in
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in
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let dummy =
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let ghost =
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match Command_line.get "dummy" with
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match Command_line.get "ghost" with
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| None -> 0.
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| None -> 0.
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| Some x -> float_of_string x
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| Some x -> float_of_string x
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in
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in
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@ -782,7 +782,7 @@ If a file with the same name as the basis set exists, this file will be read. O
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| x::_ -> x
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| x::_ -> x
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in
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in
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run ?o:output basis au charge dummy multiplicity pseudo cart xyz_filename
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run ?o:output basis au charge ghost multiplicity pseudo cart xyz_filename
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)
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)
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with
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with
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(* | Failure txt -> Printf.eprintf "Fatal error: %s\n%!" txt *)
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(* | Failure txt -> Printf.eprintf "Fatal error: %s\n%!" txt *)
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