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qp2/ocaml/Element.ml

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OCaml
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open Sexplib.Std
open Qptypes
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
[@@deriving sexp]
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 =
let result = 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
in Charge.of_int result
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)
|> Positive_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
Units.angstrom_to_bohr *. (result x)
|> Positive_float.of_float
let mass x =
let result = function
| 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
in
result x
|> Positive_float.of_float
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