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elements_db.cpp@ 25a549

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Last change on this file since 25a549 was 06f141, 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 100755

File size: 8.0 KB

Line
1	/*
2	* elements_db.cpp
3	*
4	* Created on: 17.05.2010
5	* Author: heber
6	*/
7
8	const char *elementsDB =\
9	"# 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\n\
10	#Element Name Symbol Period Group Block Atomic Number AtomicWeight Covalent Radius vdW Radius\n\
11	Hydrogen H 1 1 s 1 1.008 0.23 1.09\n\
12	Helium He 1 18 p 2 4.003 1.50 1.40\n\
13	Lithium Li 2 1 s 3 6.941 0.68 1.82\n\
14	Beryllium Be 2 2 s 4 9.012 0.35 2.00\n\
15	Boron B 2 13 p 5 10.811 0.83 2.00\n\
16	Carbon C 2 14 p 6 12.011 0.68 1.70\n\
17	Nitrogen N 2 15 p 7 14.007 0.68 1.55\n\
18	Oxygen O 2 16 p 8 15.999 0.68 1.52\n\
19	Fluorine F 2 17 p 9 18.998 0.64 1.47\n\
20	Neon Ne 2 18 p 10 20.180 1.50 1.54\n\
21	Sodium Na 3 1 s 11 22.991 0.97 2.27\n\
22	Magnesium Mg 3 2 s 12 24.305 1.10 1.73\n\
23	Aluminium Al 3 13 p 13 26.982 1.35 2.00\n\
24	Silicon Si 3 14 p 14 28.086 1.20 2.10\n\
25	Phosphorus P 3 15 p 15 30.974 1.05 1.80\n\
26	Sulphur S 3 16 p 16 32.066 1.02 1.80\n\
27	Chlorine Cl 3 17 p 17 35.453 0.99 1.75\n\
28	Argon Ar 3 18 p 18 39.948 1.51 1.88\n\
29	Potassium K 4 1 s 19 39.098 1.33 2.75\n\
30	Calcium Ca 4 2 s 20 40.078 0.99 2.00\n\
31	Scandium Sc 4 3 d 21 44.956 1.44 2.00\n\
32	Titanium Ti 4 4 d 22 47.867 1.47 2.00\n\
33	Vanadium V 4 5 d 23 50.942 1.33 2.00\n\
34	Chromium Cr 4 6 d 24 51.996 1.35 2.00\n\
35	Manganese Mn 4 7 d 25 54.938 1.35 2.00\n\
36	Iron Fe 4 8 d 26 55.845 1.34 2.00\n\
37	Cobalt Co 4 9 d 27 58.933 1.33 2.00\n\
38	Nickel Ni 4 10 d 28 58.693 1.50 1.63\n\
39	Copper Cu 4 11 d 29 63.546 1.52 1.40\n\
40	Zinc Zn 4 12 d 30 65.390 1.45 1.39\n\
41	Gallium Ga 4 13 p 31 69.723 1.22 1.87\n\
42	Germanium Ge 4 14 p 32 72.610 1.17 2.00\n\
43	Arsenic As 4 15 p 33 74.922 1.21 1.85\n\
44	Selenium Se 4 16 p 34 78.960 1.22 1.90\n\
45	Bromine Br 4 17 p 35 79.904 1.21 1.85\n\
46	Krypton Kr 4 18 p 36 83.800 1.50 2.02\n\
47	Rubidium Rb 5 1 s 37 85.468 1.47 2.00\n\
48	Strontium Sr 5 2 s 38 87.620 1.12 2.00\n\
49	Yttrium Y 5 3 d 39 88.906 1.78 2.00\n\
50	Zirconium Zr 5 4 d 40 91.224 1.56 2.00\n\
51	Niobium Nb 5 5 d 41 92.906 1.48 2.00\n\
52	Molybdenum Mo 5 6 d 42 95.940 1.47 2.00\n\
53	Technetium Tc 5 7 d 43 98 1.35 2.00\n\
54	Ruthenium Ru 5 8 d 44 101.070 1.40 2.00\n\
55	Rhodium Rh 5 9 d 45 102.906 1.45 2.00\n\
56	Palladium Pd 5 10 d 46 106.420 1.50 1.63\n\
57	Silver Ag 5 11 d 47 107.868 1.59 1.72\n\
58	Cadmium Cd 5 12 d 48 112.411 1.69 1.58\n\
59	Indium In 5 13 p 49 114.818 1.63 1.93\n\
60	Tin Sn 5 14 p 50 118.71 1.46 2.17\n\
61	Antimony Sb 5 15 p 51 121.760 1.46 2.00\n\
62	Tellurium Te 5 16 p 52 127.600 1.47 2.06\n\
63	Iodine I 5 17 p 53 126.904 1.40 1.98\n\
64	Xenon Xe 5 18 p 54 131.290 1.50 2.16\n\
65	Caesium Cs 6 1 s 55 132.905 1.67 2.00\n\
66	Barium Ba 6 2 s 56 137.327 1.34 2.00\n\
67	Lutetium Lu 6 3 d 71 174.967 1.72 2.00\n\
68	Hafnium Hf 6 4 d 72 178.490 1.57 2.00\n\
69	Tantalum Ta 6 5 d 73 180.948 1.43 2.00\n\
70	Tungsten W 6 6 d 74 183.840 1.37 2.00\n\
71	Rhenium Re 6 7 d 75 186.207 1.35 2.00\n\
72	Osmium Os 6 8 d 76 190.230 1.37 2.00\n\
73	Iridium Ir 6 9 d 77 192.217 1.32 2.00\n\
74	Platinum Pt 6 10 d 78 195.078 1.50 1.72\n\
75	Gold Au 6 11 d 79 196.967 1.50 1.66\n\
76	Mercury Hg 6 12 d 80 200.590 1.70 1.55\n\
77	Thallium Tl 6 13 p 81 204.383 1.55 1.96\n\
78	Lead Pb 6 14 p 82 207.200 1.54 2.02\n\
79	Bismuth Bi 6 15 p 83 208.980 1.54 2.00\n\
80	Polonium Po 6 16 p 84 210 1.68 2.00\n\
81	Astatine At 6 17 p 85 210 1.21 2.00\n\
82	Radon Rn 6 18 p 86 222 1.50 2.00\n\
83	Cerium Ce 6Lan 19 f 58 140.116 1.83 2.00\n\
84	Dysprosium Dy 6Lan 19 f 66 162.500 1.75 2.00\n\
85	Erbium Er 6Lan 19 f 68 167.260 1.73 2.00\n\
86	Europium Eu 6Lan 19 f 63 151.964 1.99 2.00\n\
87	Gadolinium Gd 6Lan 19 f 64 157.250 1.79 2.00\n\
88	Holmium Ho 6Lan 19 f 67 164.930 1.74 2.00\n\
89	Lanthanum La 6Lan 19 f 57 138.906 1.87 2.00\n\
90	Neodymium Nd 6Lan 19 f 60 144.240 1.81 2.00\n\
91	Promethium Pm 6Lan 19 f 61 145 1.80 2.00\n\
92	Praseodymium Pr 6Lan 19 f 59 140.908 1.82 2.00\n\
93	Samarium Sm 6Lan 19 f 62 150.360 1.80 2.00\n\
94	Terbium Tb 6Lan 19 f 65 158.925 1.76 2.00\n\
95	Thulium Tm 6Lan 19 f 69 168.934 1.72 2.00\n\
96	Ytterbium Yb 6Lan 19 f 70 173.040 1.94 2.00\n\
97	Francium Fr 7 1 s 87 223 1.50 2.00\n\
98	Radium Ra 7 2 s 88 226 1.90 2.00\n\
99	Lawrencium Lr 7 3 d 103 262 1.50 2.00\n\
100	Rutherfordium Rf 7 4 d 104 261 1.50 2.00\n\
101	Dubnium Db 7 5 d 105 262 1.50 2.00\n\
102	Seaborgium Sg 7 6 d 106 266 1.50 2.00\n\
103	Bohrium Bh 7 7 d 107 264 1.50 2.00\n\
104	Hassium Hs 7 8 d 108 269 1.50 2.00\n\
105	Meitnerium Mt 7 9 d 109 268 1.50 2.00\n\
106	Darmstadtium Ds 7 10 d 110 271 1.50 2.00\n\
107	Actinium Ac 7Act 20 f 89 227 1.88 2.00\n\
108	Americium Am 7Act 20 f 95 243 1.51 2.00\n\
109	Berkelium Bk 7Act 20 f 97 247 1.54 2.00\n\
110	Californium Cf 7Act 20 f 98 251 1.83 2.00\n\
111	Curium Cm 7Act 20 f 96 247 0.99 2.00\n\
112	Einsteinium Es 7Act 20 f 99 252 1.50 2.00\n\
113	Fermium Fm 7Act 20 f 100 257 1.50 2.00\n\
114	Mendelevium Md 7Act 20 f 101 258 1.50 2.00\n\
115	Nobelium No 7Act 20 f 102 259 1.50 2.00\n\
116	Neptunium Np 7Act 20 f 93 237 1.55 2.00\n\
117	Protactinium Pa 7Act 20 f 91 231.036 1.61 2.00\n\
118	Plutonium Pu 7Act 20 f 94 244 1.53 2.00\n\
119	Thorium Th 7Act 20 f 90 232.038 1.79 2.00\n\
120	Uranium U 7Act 20 f 92 238.029 1.58 1.86\n\
121	";
122
123	const char *HbonddistanceDB =\
124	"#atomic number bond distances for single, double and triple bond (-1 no bond)\n\
125	1 0.74 -1 -1\n\
126	2 0.77429209 -1 -1\n\
127	5 1.23 1.19 1.18\n\
128	6 1.09 1.076 1.06\n\
129	7 1.04 1.02 1.01\n\
130	8 0.96 0.957 -1\n\
131	14 1.48 1.48 1.48\n\
132	15 1.42 -1 -1\n\
133	16 1.35 -1 -1\n\
134	17 1.29 -1 -1\n\
135	20 1.09 1.09 -1\n\
136	34 1.47 -1 -1\n\
137	35 1.44 -1 -1\n\
138	";
139
140	const char *HbondangleDB =\
141	"# atomicnumber angles for single, double and triple bond (-1 no angle)\n\
142	1 180 -1 -1\n\
143	5 180 131.0 109.2\n\
144	6 180 120 109.47\n\
145	7 180 110 106.67\n\
146	8 180 104.5 -1\n\
147	14 180 120 109.47\n\
148	15 180 -1 -1\n\
149	16 180 -1 -1\n\
150	17 180 -1 -1\n\
151	20 180 120 109.47\n\
152	34 180 -1 -1\n\
153	35 180 -1 -1\n\
154	";
155
156	const char *orbitalsDB =\
157	"# atomicnumber numberoforbitals\n\
158	1 1\n\
159	2 0\n\
160	3 1\n\
161	4 2\n\
162	5 3\n\
163	6 4\n\
164	7 3\n\
165	8 2\n\
166	9 1\n\
167	10 0\n\
168	11 1\n\
169	12 2\n\
170	13 3\n\
171	14 4\n\
172	15 3\n\
173	16 2\n\
174	17 1\n\
175	18 0\n\
176	19 1\n\
177	20 4\n\
178	21 3\n\
179	22 4\n\
180	23 5\n\
181	24 6\n\
182	25 4\n\
183	26 3\n\
184	27 3\n\
185	28 2\n\
186	29 2\n\
187	30 2\n\
188	31 3\n\
189	32 4\n\
190	33 3\n\
191	34 2\n\
192	35 1\n\
193	36 0\n\
194	37 1\n\
195	38 2\n\
196	39 3\n\
197	40 4\n\
198	41 5\n\
199	42 6\n\
200	43 6\n\
201	44 8\n\
202	45 4\n\
203	46 4\n\
204	47 1\n\
205	48 2\n\
206	49 3\n\
207	50 4\n\
208	51 3\n\
209	52 2\n\
210	53 1\n\
211	54 0\n\
212	55 1\n\
213	56 2\n\
214	57 3\n\
215	58 4\n\
216	59 3\n\
217	60 4\n\
218	61 3\n\
219	62 3\n\
220	63 3\n\
221	64 3\n\
222	65 4\n\
223	66 3\n\
224	67 3\n\
225	68 3\n\
226	69 3 \n\
227	70 3\n\
228	71 3\n\
229	72 4\n\
230	73 5\n\
231	74 6\n\
232	75 7\n\
233	76 8\n\
234	77 6\n\
235	78 6\n\
236	79 3\n\
237	80 2\n\
238	81 3\n\
239	82 4\n\
240	83 3\n\
241	84 4\n\
242	86 0\n\
243	88 2\n\
244	89 3\n\
245	90 4\n\
246	91 5\n\
247	92 6\n\
248	";
249
250	const char *valenceDB =\
251	"#atomicnumber numberofvalenceorbitals\n\
252	1 0.10000000000000E+01\n\
253	2 0.20000000000000E+01\n\
254	3 0.10000000000000E+01\n\
255	4 0.20000000000000E+01\n\
256	5 0.30000000000000E+01\n\
257	6 0.40000000000000E+01\n\
258	7 0.50000000000000E+01\n\
259	8 0.60000000000000E+01\n\
260	9 0.70000000000000E+01\n\
261	10 0.80000000000000E+01\n\
262	11 0.10000000000000E+01\n\
263	12 0.40000000000000E+01\n\
264	13 .3000000000000000E+01\n\
265	14 0.40000000000000E+01\n\
266	15 0.50000000000000E+01\n\
267	16 0.60000000000000E+01\n\
268	17 0.70000000000000E+01\n\
269	18 0.80000000000000E+01\n\
270	19 0.30000000000000E+01\n\
271	20 0.40000000000000E+01\n\
272	21 0.30000000000000E+01\n\
273	22 0.40000000000000E+01\n\
274	23 0.50000000000000E+01\n\
275	24 0.60000000000000E+01\n\
276	25 0.70000000000000E+01\n\
277	26 0.80000000000000E+01\n\
278	27 0.90000000000000E+01\n\
279	28 0.10000000000000E+02\n\
280	29 0.11000000000000E+02\n\
281	30 0.12000000000000E+02\n\
282	31 3.00000000000000000\n\
283	32 0.40000000000000E+01\n\
284	33 5.00000000000000000\n\
285	34 0.60000000000000E+01\n\
286	35 0.70000000000000E+01\n\
287	36 0.80000000000000E+01\n\
288	37 0.10000000000000E+01\n\
289	38 0.20000000000000E+01\n\
290	39 0.30000000000000E+01\n\
291	40 0.40000000000000E+01\n\
292	41 0.50000000000000E+01\n\
293	42 0.60000000000000E+01\n\
294	43 0.70000000000000E+01\n\
295	44 0.80000000000000E+01\n\
296	45 0.90000000000000E+01\n\
297	46 0.10000000000000E+02\n\
298	47 0.11000000000000E+02\n\
299	48 0.12000000000000E+02\n\
300	49 0.30000000000000E+01\n\
301	50 0.40000000000000E+01\n\
302	51 0.50000000000000E+01\n\
303	52 0.60000000000000E+01\n\
304	53 0.70000000000000E+01\n\
305	54 0.80000000000000E+01\n\
306	55 0.10000000000000E+01\n\
307	56 0.20000000000000E+01\n\
308	72 0.40000000000000E+01\n\
309	73 0.50000000000000E+01\n\
310	74 0.60000000000000E+01\n\
311	75 0.70000000000000E+01\n\
312	76 0.80000000000000E+01\n\
313	77 0.90000000000000E+01\n\
314	78 0.10000000000000E+02\n\
315	79 0.11000000000000E+02\n\
316	80 0.12000000000000E+02\n\
317	";

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