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https://github.com/LCPQ/quantum_package
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Option to add automatically dummy basis functions
This commit is contained in:
parent
635ff3dc02
commit
d56c9dcb0f
@ -8,8 +8,8 @@ type t =
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coord : Point3d.t ;
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} with sexp
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(** Read xyz coordinates of the atom with unit u *)
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let of_string u s =
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(** Read xyz coordinates of the atom *)
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let of_string ~units s =
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let buffer = s
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|> String.split ~on:' '
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|> List.filter ~f:(fun x -> x <> "")
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@ -18,21 +18,21 @@ let of_string u 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 u (String.concat [x; y; z] ~sep:" ")
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coord = Point3d.of_string ~units (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 = Element.to_charge e;
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coord = Point3d.of_string u (String.concat [x; y; z] ~sep:" ")
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coord = Point3d.of_string ~units (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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let to_string u a =
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let to_string ~units a =
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[ Element.to_string a.element ;
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Charge.to_string a.charge ;
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Point3d.to_string u a.coord ]
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Point3d.to_string ~units a.coord ]
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|> String.concat ~sep:" "
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;;
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@ -5,5 +5,5 @@ type t = { element : Element.t; charge : Charge.t; coord : Point3d.t; }
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val t_of_sexp : Sexplib.Sexp.t -> t
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val sexp_of_t : t -> Sexplib.Sexp.t
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val of_string : Units.units -> string -> t
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val to_string : Units.units -> t -> string
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val of_string : units:Units.units -> string -> t
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val to_string : units:Units.units -> t -> string
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218
ocaml/Element.ml
218
ocaml/Element.ml
@ -1,4 +1,5 @@
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open Core.Std;;
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open Core.Std
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open Qptypes
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exception ElementError of string
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@ -8,49 +9,49 @@ type t =
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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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|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
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with sexp;;
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with sexp
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let of_string x =
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match (String.capitalize (String.lowercase x)) with
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| "X" | "Dummy" -> X
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| "H" | "Hydrogen" -> H
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| "He" | "Helium" -> He
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| "Li" | "Lithium" -> Li
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| "Be" | "Beryllium" -> Be
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| "B" | "Boron" -> B
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| "C" | "Carbon" -> C
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| "N" | "Nitrogen" -> N
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| "O" | "Oxygen" -> O
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| "F" | "Fluorine" -> F
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| "Ne" | "Neon" -> Ne
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| "Na" | "Sodium" -> Na
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| "Mg" | "Magnesium" -> Mg
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| "Al" | "Aluminum" -> Al
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| "Si" | "Silicon" -> Si
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| "P" | "Phosphorus" -> P
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| "S" | "Sulfur" -> S
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| "Cl" | "Chlorine" -> Cl
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| "Ar" | "Argon" -> Ar
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| "K" | "Potassium" -> K
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| "Ca" | "Calcium" -> Ca
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| "Sc" | "Scandium" -> Sc
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| "Ti" | "Titanium" -> Ti
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| "V" | "Vanadium" -> V
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| "Cr" | "Chromium" -> Cr
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| "Mn" | "Manganese" -> Mn
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| "Fe" | "Iron" -> Fe
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| "Co" | "Cobalt" -> Co
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| "Ni" | "Nickel" -> Ni
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| "Cu" | "Copper" -> Cu
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| "Zn" | "Zinc" -> Zn
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| "Ga" | "Gallium" -> Ga
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| "Ge" | "Germanium" -> Ge
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| "As" | "Arsenic" -> As
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| "Se" | "Selenium" -> Se
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| "Br" | "Bromine" -> Br
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| "Kr" | "Krypton" -> Kr
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| "X" | "Dummy" -> X
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| "H" | "Hydrogen" -> H
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| "He" | "Helium" -> He
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| "Li" | "Lithium" -> Li
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| "Be" | "Beryllium" -> Be
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| "B" | "Boron" -> B
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| "C" | "Carbon" -> C
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| "N" | "Nitrogen" -> N
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| "O" | "Oxygen" -> O
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| "F" | "Fluorine" -> F
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| "Ne" | "Neon" -> Ne
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| "Na" | "Sodium" -> Na
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| "Mg" | "Magnesium" -> Mg
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| "Al" | "Aluminum" -> Al
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| "Si" | "Silicon" -> Si
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| "P" | "Phosphorus" -> P
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| "S" | "Sulfur" -> S
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| "Cl" | "Chlorine" -> Cl
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| "Ar" | "Argon" -> Ar
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| "K" | "Potassium" -> K
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| "Ca" | "Calcium" -> Ca
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| "Sc" | "Scandium" -> Sc
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| "Ti" | "Titanium" -> Ti
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| "V" | "Vanadium" -> V
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| "Cr" | "Chromium" -> Cr
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| "Mn" | "Manganese" -> Mn
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| "Fe" | "Iron" -> Fe
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| "Co" | "Cobalt" -> Co
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| "Ni" | "Nickel" -> Ni
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| "Cu" | "Copper" -> Cu
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| "Zn" | "Zinc" -> Zn
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| "Ga" | "Gallium" -> Ga
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| "Ge" | "Germanium" -> Ge
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| "As" | "Arsenic" -> As
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| "Se" | "Selenium" -> Se
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| "Br" | "Bromine" -> Br
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| "Kr" | "Krypton" -> Kr
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| x -> raise (ElementError ("Element "^x^" unknown"))
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;;
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let to_string = function
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| X -> "X"
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@ -90,7 +91,7 @@ let to_string = function
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| Se -> "Se"
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| Br -> "Br"
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| Kr -> "Kr"
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;;
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let to_long_string = function
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| X -> "Dummy"
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@ -130,7 +131,7 @@ let to_long_string = function
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| Se -> "Selenium"
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| Br -> "Bromine"
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| Kr -> "Krypton"
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;;
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let to_charge c =
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let result = match c with
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@ -172,7 +173,7 @@ let to_charge c =
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| Br -> 35
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| Kr -> 36
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in Charge.of_int result
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;;
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let of_charge c = match (Charge.to_int c) with
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| 0 -> X
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@ -213,5 +214,134 @@ let of_charge c = match (Charge.to_int c) with
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| 35 -> Br
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| 36 -> Kr
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| x -> raise (ElementError ("Element of charge "^(string_of_int x)^" unknown"))
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;;
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let covalent_radius x =
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let result = function
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| X -> 0.
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| H -> 0.37
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| He -> 0.70
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| Li -> 1.23
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| Be -> 0.89
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| B -> 0.90
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| C -> 0.85
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| N -> 0.74
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| O -> 0.74
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| F -> 0.72
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| Ne -> 0.70
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| Na -> 1.00
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| Mg -> 1.36
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| Al -> 1.25
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| Si -> 1.17
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| P -> 1.10
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| S -> 1.10
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| Cl -> 0.99
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| Ar -> 0.70
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| K -> 2.03
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| Ca -> 1.74
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| Sc -> 1.44
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| Ti -> 1.32
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| V -> 1.22
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| Cr -> 0.00
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| Mn -> 1.16
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| Fe -> 0.00
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| Co -> 1.15
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| Ni -> 1.17
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| Cu -> 1.25
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| Zn -> 1.25
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| Ga -> 1.20
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| Ge -> 1.21
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| As -> 1.16
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| Se -> 0.70
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| Br -> 1.24
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| Kr -> 1.91
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in
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Units.angstrom_to_bohr *. (result x)
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|> Positive_float.of_float
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let vdw_radius x =
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let result = function
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| X -> 0.
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| H -> 1.20
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| He -> 1.70
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| Li -> 1.70
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| Be -> 1.70
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| B -> 1.70
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| C -> 1.70
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| N -> 1.55
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| O -> 1.52
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| F -> 1.47
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| Ne -> 1.70
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| Na -> 1.70
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| Mg -> 1.70
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| Al -> 1.94
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| Si -> 2.10
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| P -> 1.80
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| S -> 1.80
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| Cl -> 1.75
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| Ar -> 1.70
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| K -> 1.70
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| Ca -> 1.70
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| Sc -> 1.70
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| Ti -> 1.70
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| V -> 1.98
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| Cr -> 1.94
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| Mn -> 1.93
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| Fe -> 1.93
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| Co -> 1.92
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| Ni -> 1.70
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| Cu -> 1.70
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| Zn -> 1.70
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| Ga -> 2.02
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| Ge -> 1.70
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| As -> 1.96
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| Se -> 1.70
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| Br -> 2.10
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| Kr -> 1.70
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in
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Units.angstrom_to_bohr *. (result x)
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|> Positive_float.of_float
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let mass x =
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let result = function
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| X -> 0.
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| H -> 1.0079
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| He -> 4.00260
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| Li -> 6.941
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| Be -> 9.01218
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| B -> 10.81
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| C -> 12.011
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| N -> 14.0067
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| O -> 15.9994
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| F -> 18.998403
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| Ne -> 20.179
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| Na -> 22.98977
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| Mg -> 24.305
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| Al -> 26.98154
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| Si -> 28.0855
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| P -> 30.97376
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| S -> 32.06
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| Cl -> 35.453
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| Ar -> 39.948
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| K -> 39.0983
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| Ca -> 40.08
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| Sc -> 44.9559
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| Ti -> 47.90
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| V -> 50.9415
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| Cr -> 51.996
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| Mn -> 54.9380
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| Fe -> 55.9332
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| Co -> 58.9332
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| Ni -> 58.70
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| Cu -> 63.546
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| Zn -> 65.38
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| Ga -> 69.72
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| Ge -> 72.59
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| As -> 74.9216
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| Se -> 78.96
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| Br -> 79.904
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| Kr -> 83.80
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in
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result x
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|> Positive_float.of_float
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@ -13,6 +13,8 @@ val of_string : string -> t
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val to_string : t -> string
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val to_long_string : t -> string
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(** get the positive charge *)
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(** Properties *)
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val to_charge : t -> Charge.t
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val of_charge : Charge.t -> t
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val covalent_radius : t -> Qptypes.Positive_float.t
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val vdw_radius : t -> Qptypes.Positive_float.t
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@ -147,7 +147,7 @@ nucl_coord = %s
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(b.nucl_charge |> Array.to_list |> List.map
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~f:(Charge.to_string) |> String.concat ~sep:", " )
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(b.nucl_coord |> Array.to_list |> List.map
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~f:(Point3d.to_string Units.Bohr) |> String.concat ~sep:"\n" )
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~f:(Point3d.to_string ~units:Units.Bohr) |> String.concat ~sep:"\n" )
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;;
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@ -161,7 +161,7 @@ nucl_coord = %s
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Printf.sprintf " %-3s %d %s"
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(b.nucl_label.(i) |> Element.to_string)
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(b.nucl_charge.(i) |> Charge.to_int )
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(b.nucl_coord.(i) |> Point3d.to_string Units.Angstrom) )
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(b.nucl_coord.(i) |> Point3d.to_string ~units:Units.Angstrom) )
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) |> String.concat ~sep:"\n"
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in
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Printf.sprintf "
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@ -10,27 +10,36 @@ type t = {
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} with sexp
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let get_charge { nuclei ; elec_alpha ; elec_beta } =
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let result = (Elec_alpha_number.to_int elec_alpha) +
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(Elec_beta_number.to_int elec_beta) in
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let result =
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(Elec_alpha_number.to_int elec_alpha) +
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(Elec_beta_number.to_int elec_beta)
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in
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let rec nucl_charge = function
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| a::rest -> (Charge.to_float a.Atom.charge) +. nucl_charge rest
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| [] -> 0.
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in
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Charge.of_float (nucl_charge nuclei -. (Float.of_int result))
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;;
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let get_multiplicity m =
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let elec_alpha = m.elec_alpha in
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let elec_alpha =
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m.elec_alpha
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in
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Multiplicity.of_alpha_beta elec_alpha m.elec_beta
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;;
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let get_nucl_num m =
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let nmax = (List.length m.nuclei) in
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let nmax =
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List.length m.nuclei
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in
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Nucl_number.of_int nmax ~max:nmax
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;;
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let name m =
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let cm = Charge.to_int (get_charge m) in
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let cm =
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get_charge m
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|> Charge.to_int
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in
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let c =
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match cm with
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| 0 -> ""
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@ -39,8 +48,12 @@ 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 (get_multiplicity m) in
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let { nuclei ; elec_alpha ; elec_beta } = m in
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let mult =
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get_multiplicity m
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|> Multiplicity.to_string
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in
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let { nuclei ; elec_alpha ; elec_beta } = m
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in
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let rec build_list accu = function
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| a::rest ->
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begin
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@ -53,7 +66,9 @@ let name m =
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in
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let rec build_name accu = function
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| (a, n)::rest ->
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let a = Element.to_string a in
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let a =
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Element.to_string a
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in
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begin
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match n with
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| 1 -> build_name (a::accu) rest
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@ -64,19 +79,25 @@ let name m =
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end
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| [] -> accu
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in
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let result = build_list [] nuclei |> build_name [c ; ", " ; mult]
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let result =
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build_list [] nuclei |> build_name [c ; ", " ; mult]
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in
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String.concat (result)
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;;
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let to_string m =
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let { nuclei ; elec_alpha ; elec_beta } = m in
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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:(fun x -> Atom.to_string
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Units.Angstrom x) nuclei)
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let { nuclei ; elec_alpha ; elec_beta } = m
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in
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let n =
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List.length nuclei
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in
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let title =
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name m
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in
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[ Int.to_string n ; title ] @
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(List.map ~f:(fun x -> Atom.to_string Units.Angstrom x) nuclei)
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|> String.concat ~sep:"\n"
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;;
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let of_xyz_string
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?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
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@ -94,7 +115,9 @@ let of_xyz_string
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) + 1 - (Charge.to_int charge)
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|> Elec_number.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) =
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Multiplicity.to_alpha_beta ne multiplicity
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in
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let result =
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{ nuclei = l ;
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elec_alpha = na ;
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@ -109,7 +132,7 @@ let of_xyz_string
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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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@ -121,8 +144,33 @@ let of_xyz_file
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let (_,buffer) = String.lsplit2_exn buffer ~on:'\n' in
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of_xyz_string ~charge:charge ~multiplicity:multiplicity
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~units:units buffer
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;;
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include To_md5;;
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let distance_matrix molecule =
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let coord =
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molecule.nuclei
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|> List.map ~f:(fun x -> x.Atom.coord)
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|> Array.of_list
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in
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let n =
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Array.length coord
|
||||
in
|
||||
let result =
|
||||
Array.make_matrix ~dimx:n ~dimy:n 0.
|
||||
in
|
||||
for i = 0 to (n-1)
|
||||
do
|
||||
for j = 0 to (n-1)
|
||||
do
|
||||
result.(i).(j) <- Point3d.distance coord.(i) coord.(j)
|
||||
done;
|
||||
done;
|
||||
result
|
||||
|
||||
|
||||
|
||||
|
||||
include To_md5
|
||||
let to_md5 = to_md5 sexp_of_t
|
||||
;;
|
||||
|
||||
|
||||
@ -34,5 +34,9 @@ val of_xyz_string :
|
||||
?multiplicity:Multiplicity.t ->
|
||||
?units:Units.units -> string -> t
|
||||
|
||||
(** Creates the distance matrix between all the atoms *)
|
||||
val distance_matrix :
|
||||
t -> (float array) array
|
||||
|
||||
(** Computes the MD5 hash *)
|
||||
val to_md5 : t -> Qptypes.MD5.t
|
||||
|
||||
@ -7,9 +7,16 @@ type t = {
|
||||
z : float ;
|
||||
} with sexp
|
||||
|
||||
let of_tuple ~units (x,y,z) =
|
||||
let f = match units with
|
||||
| Units.Bohr -> 1.
|
||||
| Units.Angstrom -> Units.angstrom_to_bohr
|
||||
in
|
||||
{ x = x *. f ; y = y *. f ; z = z *. f }
|
||||
|
||||
(** Read x y z coordinates in string s with units u *)
|
||||
let of_string u s =
|
||||
let f = match u with
|
||||
let of_string ~units s =
|
||||
let f = match units with
|
||||
| Units.Bohr -> 1.
|
||||
| Units.Angstrom -> Units.angstrom_to_bohr
|
||||
in
|
||||
@ -22,7 +29,6 @@ let of_string u s =
|
||||
{ x = l.(0) *. f ;
|
||||
y = l.(1) *. f ;
|
||||
z = l.(2) *. f }
|
||||
;;
|
||||
|
||||
|
||||
let distance2 p1 p2 =
|
||||
@ -30,17 +36,18 @@ let distance2 p1 p2 =
|
||||
and { x=x2 ; y=y2 ; z=z2 } = p2 in
|
||||
(x2-.x1)*.(x2-.x1) +. (y2-.y1)*.(y2-.y1) +. (z2-.z1)*.(z2-.z1)
|
||||
|> Positive_float.of_float
|
||||
;;
|
||||
|
||||
let distance p1 p2 = sqrt (Positive_float.to_float (distance2 p1 p2))
|
||||
;;
|
||||
|
||||
let to_string u p =
|
||||
let f = match u with
|
||||
let distance p1 p2 =
|
||||
sqrt (Positive_float.to_float (distance2 p1 p2))
|
||||
|
||||
|
||||
let to_string ~units p =
|
||||
let f = match units with
|
||||
| Units.Bohr -> 1.
|
||||
| Units.Angstrom -> Units.bohr_to_angstrom
|
||||
in
|
||||
let { x=x ; y=y ; z=z } = p in
|
||||
Printf.sprintf "%16.8f %16.8f %16.8f" (x*.f) (y*.f) (z*.f)
|
||||
;;
|
||||
|
||||
|
||||
|
||||
@ -4,11 +4,14 @@ type t =
|
||||
z : float;
|
||||
} with sexp
|
||||
|
||||
(** Create from a tuple of floats *)
|
||||
val of_tuple : units:Units.units -> float*float*float -> t
|
||||
|
||||
(** Create from an xyz string *)
|
||||
val of_string : Units.units -> string -> t
|
||||
val of_string : units:Units.units -> string -> t
|
||||
|
||||
(** Convert to a string for printing *)
|
||||
val to_string : Units.units -> t -> string
|
||||
val to_string : units:Units.units -> t -> string
|
||||
|
||||
(** Computes the squared distance between 2 points *)
|
||||
val distance2 : t -> t -> Qptypes.Positive_float.t
|
||||
|
||||
@ -11,26 +11,92 @@ let spec =
|
||||
~doc:"string Name of basis set."
|
||||
+> flag "c" (optional_with_default 0 int)
|
||||
~doc:"int Total charge of the molecule. Default is 0."
|
||||
+> flag "d" (optional_with_default 0. float)
|
||||
~doc:"float Add dummy atoms. x * (covalent radii of the atoms)"
|
||||
+> flag "m" (optional_with_default 1 int)
|
||||
~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
|
||||
+> flag "p" no_arg
|
||||
~doc:" Using pseudopotentials"
|
||||
+> anon ("xyz_file" %: string)
|
||||
;;
|
||||
|
||||
let run ?o b c m p xyz_file =
|
||||
|
||||
let dummy_centers ~threshold ~molecule ~nuclei =
|
||||
let d =
|
||||
Molecule.distance_matrix molecule
|
||||
in
|
||||
let n =
|
||||
Array.length d
|
||||
in
|
||||
let nuclei =
|
||||
Array.of_list nuclei
|
||||
in
|
||||
let rec aux accu = function
|
||||
| (-1,_) -> accu
|
||||
| (i,-1) -> aux accu (i-1,i-1)
|
||||
| (i,j) when (i>j) ->
|
||||
let new_accu =
|
||||
let x,y =
|
||||
Element.covalent_radius (nuclei.(i)).Atom.element |> Positive_float.to_float,
|
||||
Element.covalent_radius (nuclei.(j)).Atom.element |> Positive_float.to_float
|
||||
in
|
||||
let r =
|
||||
( x +. y ) *. threshold
|
||||
in
|
||||
if d.(i).(j) < r then
|
||||
(i,x,j,y,d.(i).(j)) :: accu
|
||||
else
|
||||
accu
|
||||
in aux new_accu (i,j-1)
|
||||
| (i,j) when (i=j) -> aux accu (i,j-1)
|
||||
| _ -> assert false
|
||||
in
|
||||
aux [] (n-1,n-1)
|
||||
|> List.map ~f:(fun (i,x,j,y,r) ->
|
||||
let f =
|
||||
x /. (x +. y)
|
||||
in
|
||||
let u =
|
||||
Point3d.of_tuple ~units:Units.Bohr
|
||||
( nuclei.(i).Atom.coord.Point3d.x +.
|
||||
(nuclei.(j).Atom.coord.Point3d.x -. nuclei.(i).Atom.coord.Point3d.x) *. f,
|
||||
nuclei.(i).Atom.coord.Point3d.y +.
|
||||
(nuclei.(j).Atom.coord.Point3d.y -. nuclei.(i).Atom.coord.Point3d.y) *. f,
|
||||
nuclei.(i).Atom.coord.Point3d.z +.
|
||||
(nuclei.(j).Atom.coord.Point3d.z -. nuclei.(i).Atom.coord.Point3d.z) *. f)
|
||||
in
|
||||
Atom.{ element = Element.X ; charge = Charge.of_int 0 ; coord = u }
|
||||
)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
let run ?o b c d m p xyz_file =
|
||||
|
||||
(* Read molecule *)
|
||||
let molecule =
|
||||
(Molecule.of_xyz_file xyz_file ~charge:(Charge.of_int c)
|
||||
~multiplicity:(Multiplicity.of_int m) )
|
||||
in
|
||||
let nuclei = molecule.Molecule.nuclei in
|
||||
let dummy =
|
||||
dummy_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei
|
||||
in
|
||||
(*
|
||||
List.iter dummy ~f:(fun x ->
|
||||
Printf.printf "%s\n" (Atom.to_string ~units:Units.Angstrom x)
|
||||
);
|
||||
*)
|
||||
let nuclei =
|
||||
molecule.Molecule.nuclei @ dummy
|
||||
in
|
||||
|
||||
|
||||
let basis_table = Hashtbl.Poly.create () in
|
||||
(* Open basis set channels *)
|
||||
let basis_channel element =
|
||||
let key = Element.to_string element in
|
||||
let key =
|
||||
Element.to_string element
|
||||
in
|
||||
match Hashtbl.find basis_table key with
|
||||
| Some in_channel ->
|
||||
in_channel
|
||||
@ -80,7 +146,8 @@ let run ?o b c m p xyz_file =
|
||||
in
|
||||
Unix.unlink filename;
|
||||
List.iter nuclei ~f:(fun elem->
|
||||
let key = Element.to_string elem.Atom.element
|
||||
let key =
|
||||
Element.to_string elem.Atom.element
|
||||
in
|
||||
match Hashtbl.add basis_table ~key:key ~data:new_channel with
|
||||
| `Ok -> ()
|
||||
@ -92,7 +159,8 @@ let run ?o b c m p xyz_file =
|
||||
let elem = Element.of_string key
|
||||
and basis = String.lowercase basis
|
||||
in
|
||||
let key = Element.to_string elem
|
||||
let key =
|
||||
Element.to_string elem
|
||||
in
|
||||
let command =
|
||||
Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename ^
|
||||
@ -175,7 +243,12 @@ let run ?o b c m p xyz_file =
|
||||
|> List.rev
|
||||
|> List.map ~f:(fun (x,i) ->
|
||||
try
|
||||
Basis.read_element (basis_channel x.Atom.element) i x.Atom.element
|
||||
let e =
|
||||
match x.Atom.element with
|
||||
| Element.X -> Element.H
|
||||
| e -> e
|
||||
in
|
||||
Basis.read_element (basis_channel x.Atom.element) i e
|
||||
with
|
||||
| End_of_file ->
|
||||
begin
|
||||
@ -264,7 +337,7 @@ let run ?o b c m p xyz_file =
|
||||
| None -> failwith "Error in basis"
|
||||
| Some x -> Input.Ao_basis.write x
|
||||
|
||||
;;
|
||||
|
||||
|
||||
let command =
|
||||
Command.basic
|
||||
@ -279,13 +352,13 @@ elements can be defined as follows:
|
||||
|
||||
")
|
||||
spec
|
||||
(fun o b c m p xyz_file () ->
|
||||
run ?o b c m p xyz_file )
|
||||
;;
|
||||
(fun o b c d m p xyz_file () ->
|
||||
run ?o b c d m p xyz_file )
|
||||
|
||||
|
||||
let () =
|
||||
Command.run command
|
||||
;;
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -39,6 +39,15 @@ H 0.54386314 0.00000000 -0.92559535
|
||||
let m = Molecule.of_xyz_file "c2h6.xyz" in
|
||||
print_string (Molecule.to_string m);
|
||||
|
||||
print_string "\nDistance matrix\n";
|
||||
print_string "---------------\n";
|
||||
let d =
|
||||
Molecule.distance_matrix m
|
||||
in
|
||||
Array.iter d ~f:(fun x ->
|
||||
Array.iter x ~f:(fun y -> Printf.printf "%12.8f " y);
|
||||
print_newline ();
|
||||
)
|
||||
;;
|
||||
|
||||
test_molecule ();;
|
||||
|
||||
@ -9,7 +9,6 @@
|
||||
#
|
||||
|
||||
|
||||
|
||||
if [[ -z ${QP_ROOT} ]]
|
||||
then
|
||||
print "The QP_ROOT environment variable is not set."
|
||||
|
||||
@ -1,4 +1,5 @@
|
||||
name_to_elec = {"H": 1,
|
||||
name_to_elec = {"X": 0,
|
||||
"H": 1,
|
||||
"He": 2,
|
||||
"Li": 3,
|
||||
"Be": 4,
|
||||
|
||||
@ -58,17 +58,35 @@ def get_pseudo_str(l_atom):
|
||||
str_ = ""
|
||||
|
||||
for a in l_atom:
|
||||
l_cmd_atom = ["--atom", a]
|
||||
|
||||
l_cmd_head = [EMSL_path, "get_basis_data",
|
||||
"--db_path", db_path,
|
||||
"--basis", "BFD-Pseudo"]
|
||||
if a is not 'X':
|
||||
l_cmd_atom = ["--atom", a]
|
||||
|
||||
process = Popen(l_cmd_head + l_cmd_atom, stdout=PIPE, stderr=PIPE)
|
||||
l_cmd_head = [EMSL_path, "get_basis_data",
|
||||
"--db_path", db_path,
|
||||
"--basis", "BFD-Pseudo"]
|
||||
|
||||
stdout, _ = process.communicate()
|
||||
str_ += stdout.strip() + "\n"
|
||||
process = Popen(l_cmd_head + l_cmd_atom, stdout=PIPE, stderr=PIPE)
|
||||
|
||||
stdout, _ = process.communicate()
|
||||
str_ += stdout.strip() + "\n"
|
||||
|
||||
else: # Dummy atoms
|
||||
str_ += """Element Symbol: X
|
||||
Number of replaced protons: 0
|
||||
Number of projectors: 0
|
||||
|
||||
Pseudopotential data:
|
||||
|
||||
Local component:
|
||||
Coeff. r^n Exp.
|
||||
0.0 -1 0.
|
||||
0.0 1 0.
|
||||
0.0 0 0.
|
||||
|
||||
Non-local component:
|
||||
Coeff. r^n Exp. Proj.
|
||||
"""
|
||||
return str_
|
||||
|
||||
|
||||
|
||||
@ -525,7 +525,8 @@ integer function load_$ao_integrals(filename)
|
||||
integer*8 :: i
|
||||
integer(cache_key_kind), pointer :: key(:)
|
||||
real(integral_kind), pointer :: val(:)
|
||||
integer :: iknd, kknd, n, j
|
||||
integer :: iknd, kknd
|
||||
integer*8 :: n, j
|
||||
load_$ao_integrals = 1
|
||||
open(unit=66,file=filename,FORM='unformatted',STATUS='UNKNOWN')
|
||||
read(66,err=98,end=98) iknd, kknd
|
||||
@ -555,12 +556,8 @@ integer function load_$ao_integrals(filename)
|
||||
return
|
||||
99 continue
|
||||
call map_deinit($ao_integrals_map)
|
||||
FREE $ao_integrals_map
|
||||
if (.True.) then
|
||||
PROVIDE $ao_integrals_map
|
||||
endif
|
||||
stop 'Problem reading $ao_integrals_map file in work/'
|
||||
98 continue
|
||||
stop 'Problem reading $ao_integrals_map file in work/'
|
||||
|
||||
end
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user