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
      
      
      
| Rev | Line |   | 
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| [14de469] | 1 | /** \file element.cpp
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 | 2 |  * 
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 | 3 |  * Function implementations for the class element.
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 | 4 |  * 
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 | 5 |  */
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 | 6 | 
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| [112b09] | 7 | #include "Helpers/MemDebug.hpp"
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 | 8 | 
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| [cd4ccc] | 9 | #include <iomanip>
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 | 10 | #include <fstream>
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 | 11 | 
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 | 12 | #include "element.hpp"
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| [14de469] | 13 | 
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| [ead4e6] | 14 | using namespace std;
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 | 15 | 
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| [14de469] | 16 | /************************************* Functions for class element **********************************/
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 | 17 | 
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 | 18 | /** Constructor of class element.
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 | 19 |  */
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| [d5af3e] | 20 | element::element() :
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 | 21 |   mass(0),
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 | 22 |   CovalentRadius(0),
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 | 23 |   VanDerWaalsRadius(0),
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 | 24 |         Z(-1),
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 | 25 |         previous(NULL),
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 | 26 |         next(NULL),
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 | 27 |         sort(NULL),
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 | 28 |         No(-1),
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 | 29 |         Valence(0),
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 | 30 |         NoValenceOrbitals(0)
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 | 31 | {
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| [27c6be] | 32 | };
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| [14de469] | 33 | 
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 | 34 | /** Destructor of class element.
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 | 35 |  */
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 | 36 | element::~element() {};
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 | 37 | 
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 | 38 | /** Prints element data to \a *out.
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 | 39 |  * \param *out outstream
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 | 40 |  */
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| [ead4e6] | 41 | bool element::Output(ostream * const out) const
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| [14de469] | 42 | { 
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| [042f82] | 43 |   if (out != NULL) {
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 | 44 |     *out << name << "\t" << symbol << "\t" << period << "\t" << group << "\t" << block << "\t" << Z << "\t" << mass << "\t" << CovalentRadius << "\t" << VanDerWaalsRadius << endl;
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 | 45 |     //*out << Z << "\t"  << fixed << setprecision(11) << showpoint << mass << "g/mol\t" << name << "\t" << symbol << "\t" << endl;
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 | 46 |     return true;
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 | 47 |   } else
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 | 48 |     return false;
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| [14de469] | 49 | };
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 | 50 | 
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 | 51 | /** Prints element data to \a *out.
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 | 52 |  * \param *out outstream
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| [042f82] | 53 |  * \param No  cardinal number of element
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| [14de469] | 54 |  * \param NoOfAtoms total number of atom of this element type
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 | 55 |  */
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| [ead4e6] | 56 | bool element::Checkout(ostream * const out, const int Number, const int NoOfAtoms) const
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| [14de469] | 57 | { 
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| [042f82] | 58 |   if (out != NULL) {
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 | 59 |     *out << "Ion_Type" << Number << "\t" << NoOfAtoms << "\t" << Z << "\t1.0\t3\t3\t" << fixed << setprecision(11) << showpoint << mass << "\t" << name << "\t" << symbol <<endl;
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 | 60 |     return true;
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 | 61 |   } else
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 | 62 |     return false;
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| [14de469] | 63 | };
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| [ead4e6] | 64 | 
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 | 65 | atomicNumber_t element::getNumber() const{
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 | 66 |   return Z;
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 | 67 | }
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 | 68 | 
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 | 69 | string element::getSymbol() const{
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 | 70 |   return string(symbol);
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 | 71 | }
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