From 759fa6f097339d4db703e80fb21fd362dd381018 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 2 Jan 2018 22:02:01 +0100 Subject: [PATCH] Added mli files for Nuclei --- Nuclei/Charge.ml | 14 ++++ Nuclei/Charge.mli | 13 ++++ Nuclei/Element.ml | 183 +++++++++++++++++++++++++++++++++++++++++++++ Nuclei/Element.mli | 15 ++++ Nuclei/Mass.mli | 1 + Nuclei/Radius.mli | 1 + Positive_float.ml | 12 +++ Positive_float.mli | 5 ++ 8 files changed, 244 insertions(+) create mode 100644 Nuclei/Charge.ml create mode 100644 Nuclei/Charge.mli create mode 100644 Nuclei/Element.ml create mode 100644 Nuclei/Element.mli create mode 100644 Nuclei/Mass.mli create mode 100644 Nuclei/Radius.mli create mode 100644 Positive_float.ml create mode 100644 Positive_float.mli diff --git a/Nuclei/Charge.ml b/Nuclei/Charge.ml new file mode 100644 index 0000000..8896bef --- /dev/null +++ b/Nuclei/Charge.ml @@ -0,0 +1,14 @@ +type t = float + +let of_float x = x +let of_int i = Float.of_int i +let of_string s = Float.of_string s + +let to_float x = x +let to_int x = Float.to_int x +let to_string x = + if x >= 0. then + Printf.sprintf "+%f" x + else + Printf.sprintf "%f" x + diff --git a/Nuclei/Charge.mli b/Nuclei/Charge.mli new file mode 100644 index 0000000..83b09ad --- /dev/null +++ b/Nuclei/Charge.mli @@ -0,0 +1,13 @@ +type t = float + +(** Float conversion functions *) +val to_float : t -> float +val of_float : float -> t + +(** Int conversion functions *) +val to_int : t -> int +val of_int : int -> t + +(** String conversion functions *) +val to_string: t -> string +val of_string: string -> t diff --git a/Nuclei/Element.ml b/Nuclei/Element.ml new file mode 100644 index 0000000..248731c --- /dev/null +++ b/Nuclei/Element.ml @@ -0,0 +1,183 @@ +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 + +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_charge c = + begin + match c with + | 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 + end + |> Charge.of_int + + +let of_charge c = + match Charge.to_int c with + | 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 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 + Units.angstrom_to_bohr *. (result x) + |> Radius.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 + Units.angstrom_to_bohr *. (result x) + |> Radius.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 + diff --git a/Nuclei/Element.mli b/Nuclei/Element.mli new file mode 100644 index 0000000..81e7acf --- /dev/null +++ b/Nuclei/Element.mli @@ -0,0 +1,15 @@ +exception ElementError of string + +type t + +(** String conversion functions *) +val of_string : string -> t +val to_string : t -> string +val to_long_string : t -> string + +(** Properties *) +val to_charge : t -> Charge.t +val of_charge : Charge.t -> t +val covalent_radius : t -> Radius.t +val vdw_radius : t -> Radius.t +val mass : t -> Mass.t diff --git a/Nuclei/Mass.mli b/Nuclei/Mass.mli new file mode 100644 index 0000000..0c9e0cc --- /dev/null +++ b/Nuclei/Mass.mli @@ -0,0 +1 @@ +include Positive_float diff --git a/Nuclei/Radius.mli b/Nuclei/Radius.mli new file mode 100644 index 0000000..0c9e0cc --- /dev/null +++ b/Nuclei/Radius.mli @@ -0,0 +1 @@ +include Positive_float diff --git a/Positive_float.ml b/Positive_float.ml new file mode 100644 index 0000000..134c224 --- /dev/null +++ b/Positive_float.ml @@ -0,0 +1,12 @@ +type t + +let of_float x = + assert ( x >= 0. ); + x + +let to_float x = x + +let to_string x = string_of_float @@ to_float x + +let of_string x = of_float @@ float_of_string x + diff --git a/Positive_float.mli b/Positive_float.mli new file mode 100644 index 0000000..b0b6e73 --- /dev/null +++ b/Positive_float.mli @@ -0,0 +1,5 @@ +type t +val of_float : float -> t +val to_float : t -> float +val to_string : t -> string +val of_string : string -> t