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Elements org

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Anthony Scemama 2020-12-28 23:27:33 +01:00
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6 changed files with 551 additions and 188 deletions
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#+begin_src elisp tangle: no :results none :exports none
(setq pwd (file-name-directory buffer-file-name))
(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
(setq lib (concat pwd "lib/"))
(setq testdir (concat pwd "test/"))
(setq mli (concat lib name ".mli"))
(setq ml (concat lib name ".ml"))
(setq test-ml (concat testdir name ".ml"))
(org-babel-tangle)
#+end_src
* Element
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
Chemical elements.
** Type
#+NAME: types
#+begin_src ocaml :tangle (eval mli)
type t =
|X
|H |He
|Li|Be |B |C |N |O |F |Ne
|Na|Mg |Al|Si|P |S |Cl|Ar
|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
|Pt
exception ElementError of string
open Common
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
<<types>>
#+end_src
** Conversion
#+begin_src ocaml :tangle (eval mli)
val of_string : string -> t
val to_string : t -> string
val to_long_string : t -> string
val to_int : t -> int
val of_int : int -> t
val to_charge : t -> Charge.t
val of_charge : Charge.t -> t
#+end_src
| ~of_string~ | Creates an ~Element.t~ from a chemical symbol or from the full name of the element (case insensitive) |
| ~to_string~ | Gets the chemical symbol of the ~Element.t~ in a string |
| ~to_long_string~ | Gets the full name of the ~Element.t~ in a string |
| ~to_int~ | Convert to the atomic charge, with ~int~ type |
| ~of_int~ | Create from the atomic charge, with ~int~ type |
| ~to_charge~ | Convert to the atomic charge, with ~Charge.t~ type |
| ~of_charge~ | Create from the atomic charge, with ~Charge.t~ type |
#+begin_example
Element.of_string "Fe" ;;
- : Element.t = Particles.Element.Fe
Element.of_string "hydrogen" ;;
- : Element.t = Particles.Element.H
Element.of_string "Kryptonite" ;;
Exception: Particles.Element.ElementError "Element Kryptonite unknown".
Element.(to_long_string Fe) ;;
- : string = "Iron"
Element.(to_string Fe);;
- : string = "Fe"
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let of_string x =
match (String.capitalize_ascii (String.lowercase_ascii x)) with
| "X" | "Dummy" -> X | "H" | "Hydrogen" -> H
| "He" | "Helium" -> He | "Li" | "Lithium" -> Li
| "Be" | "Beryllium" -> Be | "B" | "Boron" -> B
| "C" | "Carbon" -> C | "N" | "Nitrogen" -> N
| "O" | "Oxygen" -> O | "F" | "Fluorine" -> F
| "Ne" | "Neon" -> Ne | "Na" | "Sodium" -> Na
| "Mg" | "Magnesium" -> Mg | "Al" | "Aluminum" -> Al
| "Si" | "Silicon" -> Si | "P" | "Phosphorus" -> P
| "S" | "Sulfur" -> S | "Cl" | "Chlorine" -> Cl
| "Ar" | "Argon" -> Ar | "K" | "Potassium" -> K
| "Ca" | "Calcium" -> Ca | "Sc" | "Scandium" -> Sc
| "Ti" | "Titanium" -> Ti | "V" | "Vanadium" -> V
| "Cr" | "Chromium" -> Cr | "Mn" | "Manganese" -> Mn
| "Fe" | "Iron" -> Fe | "Co" | "Cobalt" -> Co
| "Ni" | "Nickel" -> Ni | "Cu" | "Copper" -> Cu
| "Zn" | "Zinc" -> Zn | "Ga" | "Gallium" -> Ga
| "Ge" | "Germanium" -> Ge | "As" | "Arsenic" -> As
| "Se" | "Selenium" -> Se | "Br" | "Bromine" -> Br
| "Kr" | "Krypton" -> Kr | "Rb" | "Rubidium" -> Rb
| "Sr" | "Strontium" -> Sr | "Y" | "Yttrium" -> Y
| "Zr" | "Zirconium" -> Zr | "Nb" | "Niobium" -> Nb
| "Mo" | "Molybdenum" -> Mo | "Tc" | "Technetium" -> Tc
| "Ru" | "Ruthenium" -> Ru | "Rh" | "Rhodium" -> Rh
| "Pd" | "Palladium" -> Pd | "Ag" | "Silver" -> Ag
| "Cd" | "Cadmium" -> Cd | "In" | "Indium" -> In
| "Sn" | "Tin" -> Sn | "Sb" | "Antimony" -> Sb
| "Te" | "Tellurium" -> Te | "I" | "Iodine" -> I
| "Xe" | "Xenon" -> Xe | "Pt" | "Platinum" -> Pt
| x -> raise (ElementError ("Element "^x^" unknown"))
let to_string = function
| X -> "X" | H -> "H" | He -> "He" | Li -> "Li"
| Be -> "Be" | B -> "B" | C -> "C" | N -> "N"
| O -> "O" | F -> "F" | Ne -> "Ne" | Na -> "Na"
| Mg -> "Mg" | Al -> "Al" | Si -> "Si" | P -> "P"
| S -> "S" | Cl -> "Cl" | Ar -> "Ar" | K -> "K"
| Ca -> "Ca" | Sc -> "Sc" | Ti -> "Ti" | V -> "V"
| Cr -> "Cr" | Mn -> "Mn" | Fe -> "Fe" | Co -> "Co"
| Ni -> "Ni" | Cu -> "Cu" | Zn -> "Zn" | Ga -> "Ga"
| Ge -> "Ge" | As -> "As" | Se -> "Se" | Br -> "Br"
| Kr -> "Kr" | Rb -> "Rb" | Sr -> "Sr" | Y -> "Y"
| Zr -> "Zr" | Nb -> "Nb" | Mo -> "Mo" | Tc -> "Tc"
| Ru -> "Ru" | Rh -> "Rh" | Pd -> "Pd" | Ag -> "Ag"
| Cd -> "Cd" | In -> "In" | Sn -> "Sn" | Sb -> "Sb"
| Te -> "Te" | I -> "I" | Xe -> "Xe" | Pt -> "Pt"
let to_long_string = function
| X -> "Dummy" | H -> "Hydrogen" | He -> "Helium"
| Li -> "Lithium" | Be -> "Beryllium" | B -> "Boron"
| C -> "Carbon" | N -> "Nitrogen" | O -> "Oxygen"
| F -> "Fluorine" | Ne -> "Neon" | Na -> "Sodium"
| Mg -> "Magnesium" | Al -> "Aluminum" | Si -> "Silicon"
| P -> "Phosphorus" | S -> "Sulfur" | Cl -> "Chlorine"
| Ar -> "Argon" | K -> "Potassium" | Ca -> "Calcium"
| Sc -> "Scandium" | Ti -> "Titanium" | V -> "Vanadium"
| Cr -> "Chromium" | Mn -> "Manganese" | Fe -> "Iron"
| Co -> "Cobalt" | Ni -> "Nickel" | Cu -> "Copper"
| Zn -> "Zinc" | Ga -> "Gallium" | Ge -> "Germanium"
| As -> "Arsenic" | Se -> "Selenium" | Br -> "Bromine"
| Kr -> "Krypton" | Rb -> "Rubidium" | Sr -> "Strontium"
| Y -> "Yttrium" | Zr -> "Zirconium" | Nb -> "Niobium"
| Mo -> "Molybdenum" | Tc -> "Technetium" | Ru -> "Ruthenium"
| Rh -> "Rhodium" | Pd -> "Palladium" | Ag -> "Silver"
| Cd -> "Cadmium" | In -> "Indium" | Sn -> "Tin"
| Sb -> "Antimony" | Te -> "Tellurium" | I -> "Iodine"
| Xe -> "Xenon" | Pt -> "Platinum"
let to_int = function
| X -> 0 | H -> 1 | He -> 2 | Li -> 3
| Be -> 4 | B -> 5 | C -> 6 | N -> 7
| O -> 8 | F -> 9 | Ne -> 10 | Na -> 11
| Mg -> 12 | Al -> 13 | Si -> 14 | P -> 15
| S -> 16 | Cl -> 17 | Ar -> 18 | K -> 19
| Ca -> 20 | Sc -> 21 | Ti -> 22 | V -> 23
| Cr -> 24 | Mn -> 25 | Fe -> 26 | Co -> 27
| Ni -> 28 | Cu -> 29 | Zn -> 30 | Ga -> 31
| Ge -> 32 | As -> 33 | Se -> 34 | Br -> 35
| Kr -> 36 | Rb -> 37 | Sr -> 38 | Y -> 39
| Zr -> 40 | Nb -> 41 | Mo -> 42 | Tc -> 43
| Ru -> 44 | Rh -> 45 | Pd -> 46 | Ag -> 47
| Cd -> 48 | In -> 49 | Sn -> 50 | Sb -> 51
| Te -> 52 | I -> 53 | Xe -> 54 | Pt -> 78
let to_charge c =
to_int c |> Charge.of_int
let of_int = function
| 0 -> X | 1 -> H | 2 -> He | 3 -> Li
| 4 -> Be | 5 -> B | 6 -> C | 7 -> N
| 8 -> O | 9 -> F | 10 -> Ne | 11 -> Na
| 12 -> Mg | 13 -> Al | 14 -> Si | 15 -> P
| 16 -> S | 17 -> Cl | 18 -> Ar | 19 -> K
| 20 -> Ca | 21 -> Sc | 22 -> Ti | 23 -> V
| 24 -> Cr | 25 -> Mn | 26 -> Fe | 27 -> Co
| 28 -> Ni | 29 -> Cu | 30 -> Zn | 31 -> Ga
| 32 -> Ge | 33 -> As | 34 -> Se | 35 -> Br
| 36 -> Kr | 37 -> Rb | 38 -> Sr | 39 -> Y
| 40 -> Zr | 41 -> Nb | 42 -> Mo | 43 -> Tc
| 44 -> Ru | 45 -> Rh | 46 -> Pd | 47 -> Ag
| 48 -> Cd | 49 -> In | 50 -> Sn | 51 -> Sb
| 52 -> Te | 53 -> I | 54 -> Xe | 78 -> Pt
| x -> raise (ElementError ("Element of charge "^(string_of_int x)^" unknown"))
let of_charge c =
Charge.to_int c |> of_int
#+end_src
** Database information
#+begin_src ocaml :tangle (eval mli)
val covalent_radius : t -> Non_negative_float.t
val vdw_radius : t -> Non_negative_float.t
val mass : t -> Mass.t
val small_core : t -> int
val large_core : t -> int
#+end_src
| ~covalent_radius~ | Covalent radii of the elements, in atomic units |
| ~vdw_radius~ | Van der Waals radii of the elements, in atomic units |
| ~mass~ | Atomic mass of the elements, in atomic units) |
| ~small_core~ | Number of electrons in the small core model (all except the outermost two shells) |
| ~large_core~ | Number of electrons in the large core model (all except the outermost shell) |
#+begin_src ocaml :tangle (eval ml) :exports none
let covalent_radius x =
let result = function
| X -> 0. | H -> 0.37 | He -> 0.70 | Li -> 1.23
| Be -> 0.89 | B -> 0.90 | C -> 0.85 | N -> 0.74
| O -> 0.74 | F -> 0.72 | Ne -> 0.70 | Na -> 1.00
| Mg -> 1.36 | Al -> 1.25 | Si -> 1.17 | P -> 1.10
| S -> 1.10 | Cl -> 0.99 | Ar -> 0.70 | K -> 2.03
| Ca -> 1.74 | Sc -> 1.44 | Ti -> 1.32 | V -> 1.22
| Cr -> 0.00 | Mn -> 1.16 | Fe -> 0.00 | Co -> 1.15
| Ni -> 1.17 | Cu -> 1.25 | Zn -> 1.25 | Ga -> 1.20
| Ge -> 1.21 | As -> 1.16 | Se -> 0.70 | Br -> 1.24
| Kr -> 1.91 | Rb -> 2.20 | Sr -> 1.95 | Y -> 1.90
| Zr -> 1.75 | Nb -> 1.64 | Mo -> 1.54 | Tc -> 1.47
| Ru -> 1.46 | Rh -> 1.42 | Pd -> 1.39 | Ag -> 1.45
| Cd -> 1.44 | In -> 1.42 | Sn -> 1.39 | Sb -> 1.39
| Te -> 1.38 | I -> 1.39 | Xe -> 1.40 | Pt -> 1.30
in
Constants.a0 *. (result x)
|> Non_negative_float.of_float
let vdw_radius x =
let result = function
| X -> 0. | H -> 1.20 | He -> 1.70 | Li -> 1.70
| Be -> 1.70 | B -> 1.70 | C -> 1.70 | N -> 1.55
| O -> 1.52 | F -> 1.47 | Ne -> 1.70 | Na -> 1.70
| Mg -> 1.70 | Al -> 1.94 | Si -> 2.10 | P -> 1.80
| S -> 1.80 | Cl -> 1.75 | Ar -> 1.70 | K -> 1.70
| Ca -> 1.70 | Sc -> 1.70 | Ti -> 1.70 | V -> 1.98
| Cr -> 1.94 | Mn -> 1.93 | Fe -> 1.93 | Co -> 1.92
| Ni -> 1.70 | Cu -> 1.70 | Zn -> 1.70 | Ga -> 2.02
| Ge -> 1.70 | As -> 1.96 | Se -> 1.70 | Br -> 2.10
| Kr -> 1.70 | Rb -> 3.03 | Sr -> 2.49 | Y -> 0.
| Zr -> 0. | Nb -> 0. | Mo -> 0. | Tc -> 0.
| Ru -> 0. | Rh -> 0. | Pd -> 1.63 | Ag -> 1.72
| Cd -> 1.58 | In -> 1.93 | Sn -> 2.17 | Sb -> 2.06
| Te -> 2.06 | I -> 1.98 | Xe -> 2.16 | Pt -> 1.75
in
Constants.a0 *. (result x)
|> Non_negative_float.of_float
let mass c =
begin
match c with
| X -> 0. | H -> 1.0079 | He -> 4.00260 | Li -> 6.941
| Be -> 9.01218 | B -> 10.81 | C -> 12.011 | N -> 14.0067
| O -> 15.9994 | F -> 18.998403 | Ne -> 20.179 | Na -> 22.98977
| Mg -> 24.305 | Al -> 26.98154 | Si -> 28.0855 | P -> 30.97376
| S -> 32.06 | Cl -> 35.453 | Ar -> 39.948 | K -> 39.0983
| Ca -> 40.08 | Sc -> 44.9559 | Ti -> 47.90 | V -> 50.9415
| Cr -> 51.996 | Mn -> 54.9380 | Fe -> 55.9332 | Co -> 58.9332
| Ni -> 58.70 | Cu -> 63.546 | Zn -> 65.38 | Ga -> 69.72
| Ge -> 72.59 | As -> 74.9216 | Se -> 78.96 | Br -> 79.904
| Kr -> 83.80 | Rb -> 85.4678 | Sr -> 87.62 | Y -> 88.90584
| Zr -> 91.224 | Nb -> 92.90637 | Mo -> 95.95 | Tc -> 98.
| Ru -> 101.07 | Rh -> 102.90550 | Pd -> 106.42 | Ag -> 107.8682
| Cd -> 112.414 | In -> 114.818 | Sn -> 118.710 | Sb -> 121.760
| Te -> 127.60 | I -> 126.90447 | Xe -> 131.293 | Pt -> 195.084
end
|> Mass.of_float
let noble_gas =
[ He ; Ne ; Ar ; Kr ; Xe ]
let large_core t =
let num = to_int t in
let rec loop = function
| gas :: rest ->
if gas < num then
gas
else
loop rest
| [] -> 0
in
List.rev_map to_int noble_gas
|> loop
let small_core t =
let num = to_int t in
let rec loop = function
| large :: small :: rest ->
if large < num then
small
else
loop (small :: rest)
| small :: [] ->
if small < num then
small
else
0
| [] -> 0
in
List.rev_map to_int noble_gas
|> loop
#+end_src
** Printers
#+begin_src ocaml :tangle (eval mli)
val pp : Format.formatter -> t -> unit
val pp_long : Format.formatter -> t -> unit
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
let pp ppf t =
Format.fprintf ppf "@[%s@]" (to_string t)
let pp_long ppf t =
Format.fprintf ppf "@[%s@]" (to_long_string t)
#+end_src

8
particles/lib/electrons.ml
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@ -1,4 +1,4 @@
(* [[file:../electrons.org::*Type][Type:2]] *)
(* [[file:~/QCaml/particles/electrons.org::*Type][Type:2]] *)
type t = {
n_alfa : int ;
n_beta : int ;
@ -11,7 +11,7 @@ type t = {
* | ~of_atoms~ | Creates the data relative to electrons for a molecular system described by ~Nuclei.t~ for a given total charge and spin multiplicity. | *)
(* [[file:../electrons.org::*Creation][Creation:2]] *)
(* [[file:~/QCaml/particles/electrons.org::*Creation][Creation:2]] *)
open Common
let make n_alfa n_beta =
@ -42,7 +42,7 @@ let of_atoms ?multiplicity:(multiplicity=1) ?charge:(charge=0) nuclei =
* | ~multiplicity~ | Spin multiplicity: $2S+1$ | *)
(* [[file:../electrons.org::*Access][Access:2]] *)
(* [[file:~/QCaml/particles/electrons.org::*Access][Access:2]] *)
let charge e =
- (e.n_alfa + e.n_beta)
|> Charge.of_int
@ -56,7 +56,7 @@ let n_elec t = t.n_alfa + t.n_beta
let multiplicity t = t.n_alfa - t.n_beta + 1
(* Access:2 ends here *)
(* [[file:../electrons.org::*Printers][Printers:2]] *)
(* [[file:~/QCaml/particles/electrons.org::*Printers][Printers:2]] *)
let pp ppf t =
Format.fprintf ppf "@[n_alfa=%d, n_beta=%d@]" t.n_alfa t.n_beta
(* Printers:2 ends here *)

8
particles/lib/electrons.mli
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@ -2,14 +2,14 @@
*
* #+NAME: types *)
(* [[file:../electrons.org::types][types]] *)
(* [[file:~/QCaml/particles/electrons.org::types][types]] *)
type t
(* types ends here *)
(* Creation *)
(* [[file:../electrons.org::*Creation][Creation:1]] *)
(* [[file:~/QCaml/particles/electrons.org::*Creation][Creation:1]] *)
open Common
val make : int -> int -> t
@ -25,7 +25,7 @@ val of_atoms : ?multiplicity:int -> ?charge:int -> Nuclei.t -> t
(* Access *)
(* [[file:../electrons.org::*Access][Access:1]] *)
(* [[file:~/QCaml/particles/electrons.org::*Access][Access:1]] *)
val charge : t -> Charge.t
val n_elec : t -> int
val n_alfa : t -> int
@ -36,6 +36,6 @@ val multiplicity : t -> int
(* Printers *)
(* [[file:../electrons.org::*Printers][Printers:1]] *)
(* [[file:~/QCaml/particles/electrons.org::*Printers][Printers:1]] *)
val pp : Format.formatter -> t -> unit
(* Printers:1 ends here *)

235
particles/lib/element.ml
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@ -1,16 +1,47 @@
open Common
(* [[file:../element.org::*Type][Type:2]] *)
type t =
|X
|H |He
|Li|Be |B |C |N |O |F |Ne
|Na|Mg |Al|Si|P |S |Cl|Ar
|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
|Pt
exception ElementError of string
type t =
|X
|H |He
|Li|Be |B |C |N |O |F |Ne
|Na|Mg |Al|Si|P |S |Cl|Ar
|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
|Pt
open Common
(* Type:2 ends here *)
(* | ~of_string~ | Creates an ~Element.t~ from a chemical symbol or from the full name of the element (case insensitive) |
* | ~to_string~ | Gets the chemical symbol of the ~Element.t~ in a string |
* | ~to_long_string~ | Gets the full name of the ~Element.t~ in a string |
* | ~to_int~ | Convert to the atomic charge, with ~int~ type |
* | ~of_int~ | Create from the atomic charge, with ~int~ type |
* | ~to_charge~ | Convert to the atomic charge, with ~Charge.t~ type |
* | ~of_charge~ | Create from the atomic charge, with ~Charge.t~ type |
*
* #+begin_example
* Element.of_string "Fe" ;;
* - : Element.t = Particles.Element.Fe
*
* Element.of_string "hydrogen" ;;
* - : Element.t = Particles.Element.H
*
* Element.of_string "Kryptonite" ;;
* Exception: Particles.Element.ElementError "Element Kryptonite unknown".
*
* Element.(to_long_string Fe) ;;
* - : string = "Iron"
*
* Element.(to_string Fe);;
* - : string = "Fe"
* #+end_example *)
(* [[file:../element.org::*Conversion][Conversion:2]] *)
let of_string x =
match (String.capitalize_ascii (String.lowercase_ascii x)) with
| "X" | "Dummy" -> X | "H" | "Hydrogen" -> H
@ -45,58 +76,58 @@ let of_string x =
let to_string = function
| X -> "X" | H -> "H" | He -> "He" | Li -> "Li"
| Be -> "Be" | B -> "B" | C -> "C" | N -> "N"
| O -> "O" | F -> "F" | Ne -> "Ne" | Na -> "Na"
| Mg -> "Mg" | Al -> "Al" | Si -> "Si" | P -> "P"
| S -> "S" | Cl -> "Cl" | Ar -> "Ar" | K -> "K"
| Ca -> "Ca" | Sc -> "Sc" | Ti -> "Ti" | V -> "V"
| Cr -> "Cr" | Mn -> "Mn" | Fe -> "Fe" | Co -> "Co"
| Ni -> "Ni" | Cu -> "Cu" | Zn -> "Zn" | Ga -> "Ga"
| Ge -> "Ge" | As -> "As" | Se -> "Se" | Br -> "Br"
| Kr -> "Kr" | Rb -> "Rb" | Sr -> "Sr" | Y -> "Y"
| Zr -> "Zr" | Nb -> "Nb" | Mo -> "Mo" | Tc -> "Tc"
| Ru -> "Ru" | Rh -> "Rh" | Pd -> "Pd" | Ag -> "Ag"
| Cd -> "Cd" | In -> "In" | Sn -> "Sn" | Sb -> "Sb"
| Te -> "Te" | I -> "I" | Xe -> "Xe" | Pt -> "Pt"
| X -> "X" | H -> "H" | He -> "He" | Li -> "Li"
| Be -> "Be" | B -> "B" | C -> "C" | N -> "N"
| O -> "O" | F -> "F" | Ne -> "Ne" | Na -> "Na"
| Mg -> "Mg" | Al -> "Al" | Si -> "Si" | P -> "P"
| S -> "S" | Cl -> "Cl" | Ar -> "Ar" | K -> "K"
| Ca -> "Ca" | Sc -> "Sc" | Ti -> "Ti" | V -> "V"
| Cr -> "Cr" | Mn -> "Mn" | Fe -> "Fe" | Co -> "Co"
| Ni -> "Ni" | Cu -> "Cu" | Zn -> "Zn" | Ga -> "Ga"
| Ge -> "Ge" | As -> "As" | Se -> "Se" | Br -> "Br"
| Kr -> "Kr" | Rb -> "Rb" | Sr -> "Sr" | Y -> "Y"
| Zr -> "Zr" | Nb -> "Nb" | Mo -> "Mo" | Tc -> "Tc"
| Ru -> "Ru" | Rh -> "Rh" | Pd -> "Pd" | Ag -> "Ag"
| Cd -> "Cd" | In -> "In" | Sn -> "Sn" | Sb -> "Sb"
| Te -> "Te" | I -> "I" | Xe -> "Xe" | Pt -> "Pt"
let to_long_string = function
| X -> "Dummy" | H -> "Hydrogen" | He -> "Helium"
| Li -> "Lithium" | Be -> "Beryllium" | B -> "Boron"
| C -> "Carbon" | N -> "Nitrogen" | O -> "Oxygen"
| F -> "Fluorine" | Ne -> "Neon" | Na -> "Sodium"
| Mg -> "Magnesium" | Al -> "Aluminum" | Si -> "Silicon"
| P -> "Phosphorus" | S -> "Sulfur" | Cl -> "Chlorine"
| Ar -> "Argon" | K -> "Potassium" | Ca -> "Calcium"
| Sc -> "Scandium" | Ti -> "Titanium" | V -> "Vanadium"
| Cr -> "Chromium" | Mn -> "Manganese" | Fe -> "Iron"
| Co -> "Cobalt" | Ni -> "Nickel" | Cu -> "Copper"
| Zn -> "Zinc" | Ga -> "Gallium" | Ge -> "Germanium"
| As -> "Arsenic" | Se -> "Selenium" | Br -> "Bromine"
| Kr -> "Krypton" | Rb -> "Rubidium" | Sr -> "Strontium"
| Y -> "Yttrium" | Zr -> "Zirconium" | Nb -> "Niobium"
| Mo -> "Molybdenum" | Tc -> "Technetium" | Ru -> "Ruthenium"
| Rh -> "Rhodium" | Pd -> "Palladium" | Ag -> "Silver"
| Cd -> "Cadmium" | In -> "Indium" | Sn -> "Tin"
| Sb -> "Antimony" | Te -> "Tellurium" | I -> "Iodine"
| Xe -> "Xenon" | Pt -> "Platinum"
| X -> "Dummy" | H -> "Hydrogen" | He -> "Helium"
| Li -> "Lithium" | Be -> "Beryllium" | B -> "Boron"
| C -> "Carbon" | N -> "Nitrogen" | O -> "Oxygen"
| F -> "Fluorine" | Ne -> "Neon" | Na -> "Sodium"
| Mg -> "Magnesium" | Al -> "Aluminum" | Si -> "Silicon"
| P -> "Phosphorus" | S -> "Sulfur" | Cl -> "Chlorine"
| Ar -> "Argon" | K -> "Potassium" | Ca -> "Calcium"
| Sc -> "Scandium" | Ti -> "Titanium" | V -> "Vanadium"
| Cr -> "Chromium" | Mn -> "Manganese" | Fe -> "Iron"
| Co -> "Cobalt" | Ni -> "Nickel" | Cu -> "Copper"
| Zn -> "Zinc" | Ga -> "Gallium" | Ge -> "Germanium"
| As -> "Arsenic" | Se -> "Selenium" | Br -> "Bromine"
| Kr -> "Krypton" | Rb -> "Rubidium" | Sr -> "Strontium"
| Y -> "Yttrium" | Zr -> "Zirconium" | Nb -> "Niobium"
| Mo -> "Molybdenum" | Tc -> "Technetium" | Ru -> "Ruthenium"
| Rh -> "Rhodium" | Pd -> "Palladium" | Ag -> "Silver"
| Cd -> "Cadmium" | In -> "Indium" | Sn -> "Tin"
| Sb -> "Antimony" | Te -> "Tellurium" | I -> "Iodine"
| Xe -> "Xenon" | Pt -> "Platinum"
let to_int = function
| X -> 0 | H -> 1 | He -> 2 | Li -> 3
| Be -> 4 | B -> 5 | C -> 6 | N -> 7
| O -> 8 | F -> 9 | Ne -> 10 | Na -> 11
| Mg -> 12 | Al -> 13 | Si -> 14 | P -> 15
| S -> 16 | Cl -> 17 | Ar -> 18 | K -> 19
| Ca -> 20 | Sc -> 21 | Ti -> 22 | V -> 23
| Cr -> 24 | Mn -> 25 | Fe -> 26 | Co -> 27
| Ni -> 28 | Cu -> 29 | Zn -> 30 | Ga -> 31
| Ge -> 32 | As -> 33 | Se -> 34 | Br -> 35
| Kr -> 36 | Rb -> 37 | Sr -> 38 | Y -> 39
| Zr -> 40 | Nb -> 41 | Mo -> 42 | Tc -> 43
| Ru -> 44 | Rh -> 45 | Pd -> 46 | Ag -> 47
| Cd -> 48 | In -> 49 | Sn -> 50 | Sb -> 51
| Te -> 52 | I -> 53 | Xe -> 54 | Pt -> 78
| X -> 0 | H -> 1 | He -> 2 | Li -> 3
| Be -> 4 | B -> 5 | C -> 6 | N -> 7
| O -> 8 | F -> 9 | Ne -> 10 | Na -> 11
| Mg -> 12 | Al -> 13 | Si -> 14 | P -> 15
| S -> 16 | Cl -> 17 | Ar -> 18 | K -> 19
| Ca -> 20 | Sc -> 21 | Ti -> 22 | V -> 23
| Cr -> 24 | Mn -> 25 | Fe -> 26 | Co -> 27
| Ni -> 28 | Cu -> 29 | Zn -> 30 | Ga -> 31
| Ge -> 32 | As -> 33 | Se -> 34 | Br -> 35
| Kr -> 36 | Rb -> 37 | Sr -> 38 | Y -> 39
| Zr -> 40 | Nb -> 41 | Mo -> 42 | Tc -> 43
| Ru -> 44 | Rh -> 45 | Pd -> 46 | Ag -> 47
| Cd -> 48 | In -> 49 | Sn -> 50 | Sb -> 51
| Te -> 52 | I -> 53 | Xe -> 54 | Pt -> 78
let to_charge c =
@ -104,27 +135,37 @@ let to_charge c =
let of_int = function
| 0 -> X | 1 -> H | 2 -> He | 3 -> Li
| 4 -> Be | 5 -> B | 6 -> C | 7 -> N
| 8 -> O | 9 -> F | 10 -> Ne | 11 -> Na
| 12 -> Mg | 13 -> Al | 14 -> Si | 15 -> P
| 16 -> S | 17 -> Cl | 18 -> Ar | 19 -> K
| 20 -> Ca | 21 -> Sc | 22 -> Ti | 23 -> V
| 24 -> Cr | 25 -> Mn | 26 -> Fe | 27 -> Co
| 28 -> Ni | 29 -> Cu | 30 -> Zn | 31 -> Ga
| 32 -> Ge | 33 -> As | 34 -> Se | 35 -> Br
| 36 -> Kr | 37 -> Rb | 38 -> Sr | 39 -> Y
| 40 -> Zr | 41 -> Nb | 42 -> Mo | 43 -> Tc
| 44 -> Ru | 45 -> Rh | 46 -> Pd | 47 -> Ag
| 48 -> Cd | 49 -> In | 50 -> Sn | 51 -> Sb
| 52 -> Te | 53 -> I | 54 -> Xe | 78 -> Pt
| x -> raise (ElementError ("Element of charge "^(string_of_int x)^" unknown"))
| 0 -> X | 1 -> H | 2 -> He | 3 -> Li
| 4 -> Be | 5 -> B | 6 -> C | 7 -> N
| 8 -> O | 9 -> F | 10 -> Ne | 11 -> Na
| 12 -> Mg | 13 -> Al | 14 -> Si | 15 -> P
| 16 -> S | 17 -> Cl | 18 -> Ar | 19 -> K
| 20 -> Ca | 21 -> Sc | 22 -> Ti | 23 -> V
| 24 -> Cr | 25 -> Mn | 26 -> Fe | 27 -> Co
| 28 -> Ni | 29 -> Cu | 30 -> Zn | 31 -> Ga
| 32 -> Ge | 33 -> As | 34 -> Se | 35 -> Br
| 36 -> Kr | 37 -> Rb | 38 -> Sr | 39 -> Y
| 40 -> Zr | 41 -> Nb | 42 -> Mo | 43 -> Tc
| 44 -> Ru | 45 -> Rh | 46 -> Pd | 47 -> Ag
| 48 -> Cd | 49 -> In | 50 -> Sn | 51 -> Sb
| 52 -> Te | 53 -> I | 54 -> Xe | 78 -> Pt
| x -> raise (ElementError ("Element of charge "^(string_of_int x)^" unknown"))
let of_charge c =
Charge.to_int c |> of_int
(* Conversion:2 ends here *)
(* | ~covalent_radius~ | Covalent radii of the elements, in atomic units |
* | ~vdw_radius~ | Van der Waals radii of the elements, in atomic units |
* | ~mass~ | Atomic mass of the elements, in atomic units) |
* | ~small_core~ | Number of electrons in the small core model (all except the outermost two shells) |
* | ~large_core~ | Number of electrons in the large core model (all except the outermost shell) | *)
(* [[file:../element.org::*Database information][Database information:2]] *)
let covalent_radius x =
let result = function
| X -> 0. | H -> 0.37 | He -> 0.70 | Li -> 1.23
@ -188,25 +229,47 @@ let mass c =
|> Mass.of_float
let small_core = function
| X -> 0 | H -> 0 | He -> 0 | Li -> 2
| Be -> 2 | B -> 2 | C -> 2 | N -> 2
| O -> 2 | F -> 2 | Ne -> 2 | Na -> 10
| Mg -> 10 | Al -> 10 | Si -> 10 | P -> 10
| S -> 10 | Cl -> 10 | Ar -> 10 | K -> 10
| Ca -> 10 | Sc -> 10 | Ti -> 10 | V -> 10
| Cr -> 10 | Mn -> 10 | Fe -> 10 | Co -> 10
| Ni -> 10 | Cu -> 10 | Zn -> 10 | Ga -> 10
| Ge -> 10 | As -> 10 | Se -> 10 | Br -> 10
| Kr -> 10 | Rb -> 28 | Sr -> 28 | Y -> 28
| Zr -> 28 | Nb -> 28 | Mo -> 28 | Tc -> 28
| Ru -> 28 | Rh -> 28 | Pd -> 28 | Ag -> 28
| Cd -> 28 | In -> 28 | Sn -> 28 | Sb -> 28
| Te -> 28 | I -> 28 | Xe -> 28 | Pt -> 60
let noble_gas =
[ He ; Ne ; Ar ; Kr ; Xe ]
let large_core t =
let num = to_int t in
let rec loop = function
| gas :: rest ->
if gas < num then
gas
else
loop rest
| [] -> 0
in
List.rev_map to_int noble_gas
|> loop
let small_core t =
let num = to_int t in
let rec loop = function
| large :: small :: rest ->
if large < num then
small
else
loop (small :: rest)
| small :: [] ->
if small < num then
small
else
0
| [] -> 0
in
List.rev_map to_int noble_gas
|> loop
(* Database information:2 ends here *)
(* [[file:../element.org::*Printers][Printers:2]] *)
let pp ppf t =
Format.fprintf ppf "@[%s@]" (to_string t)
let pp_long ppf t =
Format.fprintf ppf "@[%s@]" (to_long_string t)
(* Printers:2 ends here *)

82
particles/lib/element.mli
View File

@ -1,80 +1,52 @@
(** Chemical elements. *)
(* Type
*
* #+NAME: types *)
open Common
(* [[file:../element.org::types][types]] *)
type t =
|X
|H |He
|Li|Be |B |C |N |O |F |Ne
|Na|Mg |Al|Si|P |S |Cl|Ar
|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
|Pt
exception ElementError of string
type t =
|X
|H |He
|Li|Be |B |C |N |O |F |Ne
|Na|Mg |Al|Si|P |S |Cl|Ar
|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
|Pt
open Common
(* types ends here *)
(* Conversion *)
(* [[file:../element.org::*Conversion][Conversion:1]] *)
val of_string : string -> t
(** Creates an {!Element.t} from a chemical symbol or from the full name of the
element (case insensitive).
@raise ElementError upon failure
Examples:
{[
Element.of_string "Fe" -> Element.Fe
Element.of_string "hydrogen" -> Element.H
Element.of_string "pouet" -> ElementError "Element pouet unknown"
]}
*)
val to_string : t -> string
(** Gets the chemical symbol of the {!Element.t} in a string.
Example:
[Element.(to_string Fe) -> "Fe"]
*)
val to_long_string : t -> string
(** Gets the full name of the {!Element.t} in a string.
Example:
[Element.(to_long_string Fe) -> "Iron"]
*)
val to_int : t -> int
(** Convert to the atomic charge, with [int] type. *)
val of_int : int -> t
(** Create from the atomic charge, with [int] type. *)
val to_charge : t -> Charge.t
(** Convert to the atomic charge, with {!Charge.t} type. *)
val of_charge : Charge.t -> t
(** Create from the atomic charge, with {!Charge.t} type. *)
(* Conversion:1 ends here *)
(* Database information *)
(* [[file:../element.org::*Database information][Database information:1]] *)
val covalent_radius : t -> Non_negative_float.t
(** Covalent radii of the elements, in atomic units. *)
val vdw_radius : t -> Non_negative_float.t
(** Van der Waals radii of the elements, in atomic units. *)
val mass : t -> Mass.t
(** Atomic mass of the elements, in atomic units. *)
val small_core : t -> int
(** Number of electrons in the small core model (all except the outermost two shells). *)
(*
val large_core : t -> int
(** Number of electrons in the large core model (all except the outermost shell). *)
*)
(* Database information:1 ends here *)
(* Printers *)
(** Pretty printers *)
(* [[file:../element.org::*Printers][Printers:1]] *)
val pp : Format.formatter -> t -> unit
val pp_long : Format.formatter -> t -> unit
(* Printers:1 ends here *)

8
particles/test/electrons.ml
View File

@ -1,4 +1,4 @@
(* [[file:../electrons.org::*Type][Type:3]] *)
(* [[file:~/QCaml/particles/electrons.org::*Type][Type:3]] *)
open Common
open Particles
open Alcotest
@ -16,12 +16,12 @@ H 0.756950272703377558 0. -0.585882234512562827
let e = Electrons.of_atoms nuclei in
(* Type:3 ends here *)
(* [[file:../electrons.org::*Creation][Creation:3]] *)
(* [[file:~/QCaml/particles/electrons.org::*Creation][Creation:3]] *)
check int "of_atoms alfa" 5 (Electrons.n_alfa e);
check int "of_atoms beta" 5 (Electrons.n_beta e);
(* Creation:3 ends here *)
(* [[file:../electrons.org::*Access][Access:3]] *)
(* [[file:~/QCaml/particles/electrons.org::*Access][Access:3]] *)
check int "charge " (-10) (Charge.to_int @@ Electrons.charge e);
check int "n_elec" 10 (Electrons.n_elec e);
check int "multiplicity" 1 (Electrons.multiplicity e);
@ -38,7 +38,7 @@ check bool "make" true (Electrons.make 6 4 = Electrons.(of_atoms ~multiplicity:3
(* Tests *)
(* [[file:../electrons.org::*Tests][Tests:1]] *)
(* [[file:~/QCaml/particles/electrons.org::*Tests][Tests:1]] *)
()
let tests = [