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
Line | |
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1 | /*
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2 | * Box.cpp
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3 | *
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4 | * Created on: Jun 30, 2010
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5 | * Author: crueger
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6 | */
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7 |
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8 | #include "Helpers/MemDebug.hpp"
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9 |
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10 | #include "Box.hpp"
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11 |
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12 | #include <cmath>
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13 |
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14 | #include "Matrix.hpp"
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15 | #include "vector.hpp"
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16 |
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17 | #include "Helpers/Assert.hpp"
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18 |
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19 | Box::Box()
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20 | {
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21 | M= new Matrix();
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22 | M->one();
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23 | Minv = new Matrix();
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24 | Minv->one();
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25 | }
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26 |
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27 | Box::Box(const Box& src){
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28 | M=new Matrix(*src.M);
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29 | Minv = new Matrix(*src.Minv);
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30 | }
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31 |
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32 | Box::~Box()
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33 | {
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34 | delete M;
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35 | delete Minv;
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36 | }
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37 |
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38 | const Matrix &Box::getM() const{
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39 | return *M;
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40 | }
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41 | const Matrix &Box::getMinv() const{
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42 | return *Minv;
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43 | }
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44 |
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45 | void Box::setM(Matrix _M){
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46 | ASSERT(_M.at(1,0)==_M.at(0,1),"Matrix used as cell_size was not symmetric");
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47 | ASSERT(_M.at(2,0)==_M.at(0,2),"Matrix used as cell_size was not symmetric");
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48 | ASSERT(_M.at(1,2)==_M.at(2,1),"Matrix used as cell_size was not symmetric");
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49 | *M =_M;
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50 | *Minv = M->invert();
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51 | }
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52 |
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53 | Vector Box::translateIn(const Vector &point){
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54 | return (*M) * point;
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55 | }
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56 |
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57 | Vector Box::translateOut(const Vector &point){
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58 | return (*Minv) * point;
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59 | }
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60 |
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61 | Vector Box::WrapPeriodically(const Vector &point){
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62 | Vector helper = translateOut(point);
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63 | for(int i=NDIM;i--;){
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64 | double intpart,fracpart;
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65 | fracpart = modf(helper.at(i),&intpart);
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66 | if(fracpart<0.)
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67 | fracpart+=1.;
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68 | helper.at(i)=fracpart;
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69 | }
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70 | return translateIn(helper);
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71 | }
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72 |
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73 | Box &Box::operator=(const Box &src){
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74 | if(&src!=this){
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75 | delete M;
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76 | delete Minv;
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77 | M = new Matrix(*src.M);
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78 | Minv = new Matrix(*src.Minv);
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79 | }
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80 | return *this;
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81 | }
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82 |
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83 | Box &Box::operator=(const Matrix &mat){
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84 | setM(mat);
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85 | return *this;
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86 | }
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