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Last change on this file since cadbc1 was 4eb4fe, checked in by Frederik Heber <heber@…>, 15 years ago

"-e <db path>" not necessary anymore.

Removed necessity of specifying path to databases (this was one check of molecuilder/test/testsuite.at which cannot be fulfilled anymore with boost::program_options)
For this to work a great number of small changes have been necessary:

class periodentafel:

all .db files merged into const char * arrays in elements_db.cpp
periodentafel rewritten:
- each database has its own function and uses a istream: LoadElementsDatabase(), LoadValenceDatabase(), LoadOrbitalsDatabase(), LoadHBondAngleDatabase(), LoadHBondLengthsDatabase()
- constructor periodentafel::LoadPeriodentafel() calls each function on the above const char * arrays
- it is still possible to call LoadPeriodentafel with an external path.
FindElement(), AskElement() and EnterElement return element * const instead of const element * (i.e. the contents of the pointer is const (the element) not the pointer itself which is very vexatious (i.e. FindElement() yields const element * which can subsequently not be used for RemoveElement(), ...)
parsedElems is not needed anymore. Instead we operate on map elements directly
new unittest periodentafelTest which is made friend of periodentafel to be able to access private loading functions directly

A number of unit tests had to be changed (all that create elements during setUp() which is now unnecessary)

element creation removed: AnalysisCorrelationToPointUnitTest, AnalysisCorrelationToSurfaceUnitTest, AnalysisPairCorrelationUnitTest, CountBondsTest, LinkedCellTest, ParserUnitTest, AnalysisBondsTest, BondGraphTest, ListOfBondsTest
adapted parsed bond table (carbon is no Z=6 not 2): AnalysisBondsTest, BondGraphTest

Some of the analysis_bonds function's signatures were changed in the process:

have const element * instead of element *: MinMeanMaxBondDistanceBetweenElements(), CountHydrogenBridgeBonds()

Finally, the respective tests are removed from molecuilder/tests/testsuite.at.

Property mode set to 100644

File size: 4.1 KB

Line
1	# Covalent radius of each element in Angstroem from CSD (binding is: [Rcov(A)+Rcov(B)-t,Rcov(A)+Rcov(B)+t] with t = 0.4A
2	#Element Name Symbol Period Group Block Atomic Number AtomicWeight Covalent Radius vdW Radius
3	Hydrogen H 1 1 s 1 1.008 0.23 1.09
4	Helium He 1 18 p 2 4.003 1.5 1.4
5	Lithium Li 2 1 s 3 6.941 0.68 1.82
6	Beryllium Be 2 2 s 4 9.012 0.35 2
7	Boron B 2 13 p 5 10.811 0.83 2
8	Carbon C 2 14 p 6 12.011 0.68 1.7
9	Nitrogen N 2 15 p 7 14.007 0.68 1.55
10	Oxygen O 2 16 p 8 15.999 0.68 1.52
11	Fluorine F 2 17 p 9 18.998 0.64 1.47
12	Neon Ne 2 18 p 10 20.18 1.5 1.54
13	Sodium Na 3 1 s 11 22.991 0.97 2.27
14	Magnesium Mg 3 2 s 12 24.305 1.1 1.73
15	Aluminium Al 3 13 p 13 26.982 1.35 2
16	Silicon Si 3 14 p 14 28.086 1.2 2.1
17	Phosphorus P 3 15 p 15 30.974 1.05 1.8
18	Sulphur S 3 16 p 16 32.066 1.02 1.8
19	Chlorine Cl 3 17 p 17 35.453 0.99 1.75
20	Argon Ar 3 18 p 18 39.948 1.51 1.88
21	Potassium K 4 1 s 19 39.098 1.33 2.75
22	Calcium Ca 4 2 s 20 40.078 0.99 2
23	Scandium Sc 4 3 d 21 44.956 1.44 2
24	Titanium Ti 4 4 d 22 47.867 1.47 2
25	Vanadium V 4 5 d 23 50.942 1.33 2
26	Chromium Cr 4 6 d 24 51.996 1.35 2
27	Manganese Mn 4 7 d 25 54.938 1.35 2
28	Iron Fe 4 8 d 26 55.845 1.34 2
29	Cobalt Co 4 9 d 27 58.933 1.33 2
30	Nickel Ni 4 10 d 28 58.693 1.5 1.63
31	Copper Cu 4 11 d 29 63.546 1.52 1.4
32	Zinc Zn 4 12 d 30 65.39 1.45 1.39
33	Gallium Ga 4 13 p 31 69.723 1.22 1.87
34	Germanium Ge 4 14 p 32 72.61 1.17 2
35	Arsenic As 4 15 p 33 74.922 1.21 1.85
36	Selenium Se 4 16 p 34 78.96 1.22 1.9
37	Bromine Br 4 17 p 35 79.904 1.21 1.85
38	Krypton Kr 4 18 p 36 83.8 1.5 2.02
39	Rubidium Rb 5 1 s 37 85.468 1.47 2
40	Strontium Sr 5 2 s 38 87.62 1.12 2
41	Yttrium Y 5 3 d 39 88.906 1.78 2
42	Zirconium Zr 5 4 d 40 91.224 1.56 2
43	Niobium Nb 5 5 d 41 92.906 1.48 2
44	Molybdenum Mo 5 6 d 42 95.94 1.47 2
45	Technetium Tc 5 7 d 43 98 1.35 2
46	Ruthenium Ru 5 8 d 44 101.07 1.4 2
47	Rhodium Rh 5 9 d 45 102.906 1.45 2
48	Palladium Pd 5 10 d 46 106.42 1.5 1.63
49	Silver Ag 5 11 d 47 107.868 1.59 1.72
50	Cadmium Cd 5 12 d 48 112.411 1.69 1.58
51	Indium In 5 13 p 49 114.818 1.63 1.93
52	Tin Sn 5 14 p 50 118.71 1.46 2.17
53	Antimony Sb 5 15 p 51 121.76 1.46 2
54	Tellurium Te 5 16 p 52 127.6 1.47 2.06
55	Iodine I 5 17 p 53 126.904 1.4 1.98
56	Xenon Xe 5 18 p 54 131.29 1.5 2.16
57	Caesium Cs 6 1 s 55 132.905 1.67 2
58	Barium Ba 6 2 s 56 137.327 1.34 2
59	Lanthanum La 6Lan 19 f 57 138.906 1.87 2
60	Cerium Ce 6Lan 19 f 58 140.116 1.83 2
61	Praseodymium Pr 6Lan 19 f 59 140.908 1.82 2
62	Neodymium Nd 6Lan 19 f 60 144.24 1.81 2
63	Promethium Pm 6Lan 19 f 61 145 1.8 2
64	Samarium Sm 6Lan 19 f 62 150.36 1.8 2
65	Europium Eu 6Lan 19 f 63 151.964 1.99 2
66	Gadolinium Gd 6Lan 19 f 64 157.25 1.79 2
67	Terbium Tb 6Lan 19 f 65 158.925 1.76 2
68	Dysprosium Dy 6Lan 19 f 66 162.5 1.75 2
69	Holmium Ho 6Lan 19 f 67 164.93 1.74 2
70	Erbium Er 6Lan 19 f 68 167.26 1.73 2
71	Thulium Tm 6Lan 19 f 69 168.934 1.72 2
72	Ytterbium Yb 6Lan 19 f 70 173.04 1.94 2
73	Lutetium Lu 6 3 d 71 174.967 1.72 2
74	Hafnium Hf 6 4 d 72 178.49 1.57 2
75	Tantalum Ta 6 5 d 73 180.948 1.43 2
76	Tungsten W 6 6 d 74 183.84 1.37 2
77	Rhenium Re 6 7 d 75 186.207 1.35 2
78	Osmium Os 6 8 d 76 190.23 1.37 2
79	Iridium Ir 6 9 d 77 192.217 1.32 2
80	Platinum Pt 6 10 d 78 195.078 1.5 1.72
81	Gold Au 6 11 d 79 196.967 1.5 1.66
82	Mercury Hg 6 12 d 80 200.59 1.7 1.55
83	Thallium Tl 6 13 p 81 204.383 1.55 1.96
84	Lead Pb 6 14 p 82 207.2 1.54 2.02
85	Bismuth Bi 6 15 p 83 208.98 1.54 2
86	Polonium Po 6 16 p 84 210 1.68 2
87	Astatine At 6 17 p 85 210 1.21 2
88	Radon Rn 6 18 p 86 222 1.5 2
89	Francium Fr 7 1 s 87 223 1.5 2
90	Radium Ra 7 2 s 88 226 1.9 2
91	Actinium Ac 7Act 20 f 89 227 1.88 2
92	Thorium Th 7Act 20 f 90 232.038 1.79 2
93	Protactinium Pa 7Act 20 f 91 231.036 1.61 2
94	Uranium U 7Act 20 f 92 238.029 1.58 1.86
95	Neptunium Np 7Act 20 f 93 237 1.55 2
96	Plutonium Pu 7Act 20 f 94 244 1.53 2
97	Americium Am 7Act 20 f 95 243 1.51 2
98	Curium Cm 7Act 20 f 96 247 0.99 2
99	Berkelium Bk 7Act 20 f 97 247 1.54 2
100	Californium Cf 7Act 20 f 98 251 1.83 2
101	Einsteinium Es 7Act 20 f 99 252 1.5 2
102	Fermium Fm 7Act 20 f 100 257 1.5 2
103	Mendelevium Md 7Act 20 f 101 258 1.5 2
104	Nobelium No 7Act 20 f 102 259 1.5 2
105	Lawrencium Lr 7 3 d 103 262 1.5 2
106	Rutherfordium Rf 7 4 d 104 261 1.5 2
107	Dubnium Db 7 5 d 105 262 1.5 2
108	Seaborgium Sg 7 6 d 106 266 1.5 2
109	Bohrium Bh 7 7 d 107 264 1.5 2
110	Hassium Hs 7 8 d 108 269 1.5 2
111	Meitnerium Mt 7 9 d 109 268 1.5 2
112	Darmstadtium Ds 7 10 d 110 271 1.5 2

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