mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-10-12 10:51:31 +02:00
503 lines
9.0 KiB
OCaml
503 lines
9.0 KiB
OCaml
open Core
|
|
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 (String.lowercase 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
|
|
|
|
|