source: src/Element/element.hpp@ f47efd4

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 Candidate_v1.7.0 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 f47efd4 was 31bd9c, checked in by Frederik Heber <heber@…>, 11 years ago

Added ion class, derived from element.
  • Property mode set to 100644
File size: 3.4 KB
Line 
1/*
2 * element.hpp
3 *
4 * Created on: Aug 3, 2009
5 * Author: heber
6 */
7
8#ifndef ELEMENT_HPP_
9#define ELEMENT_HPP_
10
11/*********************************************** includes ***********************************/
12
13// include config.h
14#ifdef HAVE_CONFIG_H
15#include <config.h>
16#endif
17
18#include <iosfwd>
19#include <string>
20
21#include "types.hpp"
22
23#include "boost/serialization/array.hpp"
24#include "boost/serialization/string.hpp"
25
26class periodentafel;
27class IonTest;
28
29/********************************************** declarations *******************************/
30
31/** Chemical element.
32 * Class incorporates data for a certain chemical element to be referenced from atom class.
33 */
34class element {
35 friend class periodentafel;
36 friend class IonTest;
37 public:
38 element();
39 element(const element&);
40 virtual ~element();
41
42 element &operator=(const element&);
43
44 // accessor functions
45 double getMass() const;
46 const unsigned char *getColor() const;
47 double getCovalentRadius() const;
48 double getElectronegativity() const;
49 double getVanDerWaalsRadius() const;
50 atomicNumber_t getAtomicNumber() const;
51 virtual double getCharge() const
52 { return 0.; }
53 virtual double getValence() const;
54 virtual int getNoValenceOrbitals() const;
55 double getHBondDistance(const size_t i) const;
56 double getHBondAngle(const size_t i) const;
57
58 const std::string &getSymbol() const;
59 void setSymbol(const std::string &temp);
60
61 const std::string &getName() const;
62 void setName(const std::string &temp);
63
64 bool operator==(const element &other) const;
65
66 bool operator!=(const element &other) const {
67 return !(*this == other);
68 }
69
70 private:
71 friend class boost::serialization::access;
72 // serialization
73 template<class Archive>
74 void serialize(Archive & ar, const unsigned int version)
75 {
76 ar & mass;
77 ar & CovalentRadius;
78 ar & Electronegativity;
79 ar & VanDerWaalsRadius;
80 ar & Z;
81 ar & period;
82 ar & group;
83 ar & block;
84 ar & Valence;
85 ar & NoValenceOrbitals;
86 ar & boost::serialization::make_array<double>(HBondDistance, 3);
87 ar & boost::serialization::make_array<double>(HBondAngle, 3);
88 ar & boost::serialization::make_array<unsigned char>(color, 3);
89 ar & name;
90 ar & symbol;
91 }
92
93 protected:
94
95 double mass; //!< mass in g/mol
96 double CovalentRadius; //!< covalent radius
97 double Electronegativity; //!< electronegativity in Pauling units
98 double VanDerWaalsRadius; //!< van-der-Waals radius
99 atomicNumber_t Z; //!< atomic number
100 std::string period; //!< period: n quantum number
101 std::string group; //!< group: l quantum number
102 std::string block; //!< block: l quantum number
103 double Valence; //!< number of valence electrons for this element
104 int NoValenceOrbitals; //!< number of valence orbitals, used for determining bond degree in molecule::CreateConnectmatrix()
105 double HBondDistance[3]; //!< distance in Angstrom of this element to hydrogen (for single, double and triple bonds)
106 double HBondAngle[3]; //!< typical angle for one, two, three bonded hydrogen (in degrees)
107 unsigned char color[3]; //!< typical color for this element (from Jmol)
108
109 std::string name; //!< atom name, i.e. "Hydrogen"
110 std::string symbol; //!< short form of the atom, i.e. "H"
111};
112
113std::ostream &operator<<(std::ostream&,const element&);
114
115#endif /* ELEMENT_HPP_ */
Note: See TracBrowser for help on using the repository browser.