Context Navigation

source: src/elements.db@ 51be2a

Visit:

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable

Last change on this file since 51be2a 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

Rev	Line
[14de469]	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
[4eb4fe]	4	Helium He 1 18 p 2 4.003 1.5 1.4
[14de469]	5	Lithium Li 2 1 s 3 6.941 0.68 1.82
[4eb4fe]	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
[14de469]	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
[4eb4fe]	12	Neon Ne 2 18 p 10 20.18 1.5 1.54
[14de469]	13	Sodium Na 3 1 s 11 22.991 0.97 2.27
[4eb4fe]	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
[14de469]	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
[4eb4fe]	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
[14de469]	33	Gallium Ga 4 13 p 31 69.723 1.22 1.87
[4eb4fe]	34	Germanium Ge 4 14 p 32 72.61 1.17 2
[14de469]	35	Arsenic As 4 15 p 33 74.922 1.21 1.85
[4eb4fe]	36	Selenium Se 4 16 p 34 78.96 1.22 1.9
[14de469]	37	Bromine Br 4 17 p 35 79.904 1.21 1.85
[4eb4fe]	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
[14de469]	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
[4eb4fe]	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
[14de469]	83	Thallium Tl 6 13 p 81 204.383 1.55 1.96
[4eb4fe]	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
[14de469]	94	Uranium U 7Act 20 f 92 238.029 1.58 1.86
[4eb4fe]	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

Note: See TracBrowser for help on using the repository browser.

Download in other formats:

Original Format