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Changed dummy into ghost

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This commit is contained in:
Anthony Scemama 2024-02-28 18:15:25 +01:00
parent 3319d78816
commit 9927328138
4 changed files with 42 additions and 43 deletions
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3
ocaml/Angmom.ml
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@ -26,8 +26,7 @@ let of_string = function
| "J" | "j" -> J | "J" | "j" -> J
| "K" | "k" -> K | "K" | "k" -> K
| "L" | "l" -> L | "L" | "l" -> L
| x -> raise (Failure ("Angmom should be S|P|D|F|G|H|I|J|K|L, | x -> raise (Failure ("Angmom should be S|P|D|F|G|H|I|J|K|L, not "^x^"."))
not "^x^"."))
let of_char = function let of_char = function
| 'S' | 's' -> S | 'S' | 's' -> S

2
ocaml/Basis.ml
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@ -17,7 +17,7 @@ let read in_channel at_number =
(** Find an element in the basis set file *) (** Find an element in the basis set file *)
let find in_channel element = let find in_channel element =
seek_in in_channel 0; seek_in in_channel 0;
let element_read = ref Element.X in let element_read = ref Element.Og in
while !element_read <> element while !element_read <> element
do do
let buffer = input_line in_channel in let buffer = input_line in_channel in

38
ocaml/Element.ml
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@ -4,7 +4,7 @@ open Qptypes
exception ElementError of string exception ElementError of string
type t = X type t = X
|H |He |H |He
|Li|Be |B |C |N |O |F |Ne |Li|Be |B |C |N |O |F |Ne
|Na|Mg |Al|Si|P |S |Cl|Ar |Na|Mg |Al|Si|P |S |Cl|Ar
@ -20,7 +20,7 @@ type t = X
let of_string x = let of_string x =
match (String.capitalize_ascii (String.lowercase_ascii x)) with match (String.capitalize_ascii (String.lowercase_ascii x)) with
| "X" | "Dummy" -> X | "X" | "Ghost" -> X
| "H" | "Hydrogen" -> H | "H" | "Hydrogen" -> H
| "He" | "Helium" -> He | "He" | "Helium" -> He
| "Li" | "Lithium" -> Li | "Li" | "Lithium" -> Li
@ -265,7 +265,7 @@ let to_string = function
let to_long_string = function let to_long_string = function
| X -> "Dummy" | X -> "Ghost"
| H -> "Hydrogen" | H -> "Hydrogen"
| He -> "Helium" | He -> "Helium"
| Li -> "Lithium" | Li -> "Lithium"
@ -492,20 +492,20 @@ let to_charge c =
| No -> 102 | No -> 102
| Lr -> 103 | Lr -> 103
| Rf -> 104 | Rf -> 104
| Db -> 105 | Db -> 105
| Sg -> 106 | Sg -> 106
| Bh -> 107 | Bh -> 107
| Hs -> 108 | Hs -> 108
| Mt -> 109 | Mt -> 109
| Ds -> 110 | Ds -> 110
| Rg -> 111 | Rg -> 111
| Cn -> 112 | Cn -> 112
| Nh -> 113 | Nh -> 113
| Fl -> 114 | Fl -> 114
| Mc -> 115 | Mc -> 115
| Lv -> 116 | Lv -> 116
| Ts -> 117 | Ts -> 117
| Og -> 118 | Og -> 118
in Charge.of_int result in Charge.of_int result
@ -565,7 +565,7 @@ let of_charge c = match (Charge.to_int c) with
| 52 -> Te | 52 -> Te
| 53 -> I | 53 -> I
| 54 -> Xe | 54 -> Xe
| 55 -> Cs | 55 -> Cs
| 56 -> Ba | 56 -> Ba
| 57 -> La | 57 -> La
| 58 -> Ce | 58 -> Ce
@ -880,7 +880,7 @@ let vdw_radius x =
| Ts -> None | Ts -> None
| Og -> None | Og -> None
in in
match result x with match result x with
| Some y -> Some (Positive_float.of_float @@ Units.angstrom_to_bohr *. y ) | Some y -> Some (Positive_float.of_float @@ Units.angstrom_to_bohr *. y )
| None -> None | None -> None

42
ocaml/qp_create_ezfio.ml
View File

@ -6,8 +6,8 @@ type element =
| Element of Element.t | Element of Element.t
| Int_elem of (Nucl_number.t * Element.t) | Int_elem of (Nucl_number.t * Element.t)
(** Handle dummy atoms placed on bonds *) (** Handle ghost atoms placed on bonds *)
let dummy_centers ~threshold ~molecule ~nuclei = let ghost_centers ~threshold ~molecule ~nuclei =
let d = let d =
Molecule.distance_matrix molecule Molecule.distance_matrix molecule
in in
@ -68,11 +68,11 @@ let run ?o b au c d m p cart xyz_file =
(Molecule.of_file xyz_file ~charge:(Charge.of_int c) (Molecule.of_file xyz_file ~charge:(Charge.of_int c)
~multiplicity:(Multiplicity.of_int m) ) ~multiplicity:(Multiplicity.of_int m) )
in in
let dummy = let ghost =
dummy_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei ghost_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei
in in
let nuclei = let nuclei =
molecule.Molecule.nuclei @ dummy molecule.Molecule.nuclei @ ghost
in in
@ -145,8 +145,6 @@ let run ?o b au c d m p cart xyz_file =
| i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k) | i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
| _ -> failwith "Expected format is int,Element:basis" | _ -> failwith "Expected format is int,Element:basis"
in Int_elem result in Int_elem result
and basis =
String.lowercase_ascii basis
in in
let key = let key =
match elem with match elem with
@ -313,7 +311,7 @@ let run ?o b au c d m p cart xyz_file =
} }
in in
let nuclei = let nuclei =
molecule.Molecule.nuclei @ dummy molecule.Molecule.nuclei @ ghost
in in
@ -491,11 +489,7 @@ let run ?o b au c d m p cart xyz_file =
|> List.rev |> List.rev
|> list_map (fun (x,i) -> |> list_map (fun (x,i) ->
try try
let e = let e = x.Atom.element in
match x.Atom.element with
| Element.X -> Element.H
| e -> e
in
let key = let key =
Int_elem (i,x.Atom.element) Int_elem (i,x.Atom.element)
in in
@ -507,9 +501,15 @@ let run ?o b au c d m p cart xyz_file =
in in
try try
Basis.read_element (basis_channel key) i e Basis.read_element (basis_channel key) i e
with Not_found -> with _ ->
failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i) try
(Element.to_string x.Atom.element) ) if e = Element.X then
Basis.read_element (basis_channel key) i (Element.H)
else
raise Not_found
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 with
| End_of_file -> failwith | End_of_file -> failwith
("Element "^(Element.to_string x.Atom.element)^" not found in basis set.") ("Element "^(Element.to_string x.Atom.element)^" not found in basis set.")
@ -710,9 +710,9 @@ If a file with the same name as the basis set exists, this file will be read. O
arg=With_arg "<int>"; arg=With_arg "<int>";
doc="Total charge of the molecule. Default is 0. For negative values, use m instead of -, for ex m1"} ; 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"; { opt=Optional ; short='g'; long="ghost";
arg=With_arg "<float>"; arg=With_arg "<float>";
doc="Add dummy atoms. x * (covalent radii of the atoms)."} ; doc="Add ghost atoms. x * (covalent radii of the atoms)."} ;
{ opt=Optional ; short='m'; long="multiplicity"; { opt=Optional ; short='m'; long="multiplicity";
arg=With_arg "<int>"; arg=With_arg "<int>";
@ -756,8 +756,8 @@ If a file with the same name as the basis set exists, this file will be read. O
int_of_string x ) int_of_string x )
in in
let dummy = let ghost =
match Command_line.get "dummy" with match Command_line.get "ghost" with
| None -> 0. | None -> 0.
| Some x -> float_of_string x | Some x -> float_of_string x
in in
@ -782,7 +782,7 @@ If a file with the same name as the basis set exists, this file will be read. O
| x::_ -> x | x::_ -> x
in in
run ?o:output basis au charge dummy multiplicity pseudo cart xyz_filename run ?o:output basis au charge ghost multiplicity pseudo cart xyz_filename
) )
with with
(* | Failure txt -> Printf.eprintf "Fatal error: %s\n%!" txt *) (* | Failure txt -> Printf.eprintf "Fatal error: %s\n%!" txt *)