Changeset a679d1 for src


Ignore:
Timestamp:
Jun 26, 2010, 12:35:18 PM (15 years ago)
Author:
Tillmann Crueger <crueger@…>
Branches:
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
Children:
4d206f
Parents:
436f04
Message:

Replaced Matrix access with direct access at several places

Location:
src
Files:
3 edited

Legend:

Unmodified
Added
Removed

  • src/boundary.cpp

    r436f04 ra679d1  
    836836            }
    837837
    838             Rotations.at(0,0) =   cos(phi[0])            *cos(phi[2]) + (sin(phi[0])*sin(phi[1])*sin(phi[2]));
    839             Rotations.at(0,1) =   sin(phi[0])            *cos(phi[2]) - (cos(phi[0])*sin(phi[1])*sin(phi[2]));
    840             Rotations.at(0,2) =               cos(phi[1])*sin(phi[2])                                     ;
    841             Rotations.at(1,0) = - sin(phi[0])*cos(phi[1])                                                ;
    842             Rotations.at(1,1) =   cos(phi[0])*cos(phi[1])                                                ;
    843             Rotations.at(1,2) =               sin(phi[1])                                                ;
    844             Rotations.at(2,0) = - cos(phi[0])            *sin(phi[2]) + (sin(phi[0])*sin(phi[1])*cos(phi[2]));
    845             Rotations.at(2,1) = - sin(phi[0])            *sin(phi[2]) - (cos(phi[0])*sin(phi[1])*cos(phi[2]));
    846             Rotations.at(2,2) =               cos(phi[1])*cos(phi[2])                                     ;
     838            Rotations.set(0,0,  cos(phi[0])            *cos(phi[2]) + (sin(phi[0])*sin(phi[1])*sin(phi[2])));
     839            Rotations.set(0,1,  sin(phi[0])            *cos(phi[2]) - (cos(phi[0])*sin(phi[1])*sin(phi[2])));
     840            Rotations.set(0,2,              cos(phi[1])*sin(phi[2])                                        );
     841            Rotations.set(1,0, -sin(phi[0])*cos(phi[1])                                                    );
     842            Rotations.set(1,1,  cos(phi[0])*cos(phi[1])                                                    );
     843            Rotations.set(1,2,              sin(phi[1])                                                    );
     844            Rotations.set(2,0, -cos(phi[0])            *sin(phi[2]) + (sin(phi[0])*sin(phi[1])*cos(phi[2])));
     845            Rotations.set(2,1, -sin(phi[0])            *sin(phi[2]) - (cos(phi[0])*sin(phi[1])*cos(phi[2])));
     846            Rotations.set(2,2,              cos(phi[1])*cos(phi[2])                                        );
    847847          }
    848848

  • src/ellipsoid.cpp

    r436f04 ra679d1  
    5252  theta = EllipsoidAngle[1];
    5353  phi = EllipsoidAngle[2];
    54   Matrix.at(0,0) = cos(psi)*cos(phi) - sin(psi)*cos(theta)*sin(phi);
    55   Matrix.at(1,0) = -cos(psi)*sin(phi) - sin(psi)*cos(theta)*cos(phi);
    56   Matrix.at(2,0) = sin(psi)*sin(theta);
    57   Matrix.at(0,1) = sin(psi)*cos(phi) + cos(psi)*cos(theta)*sin(phi);
    58   Matrix.at(1,1) = cos(psi)*cos(theta)*cos(phi) - sin(psi)*sin(phi);
    59   Matrix.at(2,1) = -cos(psi)*sin(theta);
    60   Matrix.at(0,2) = sin(theta)*sin(phi);
    61   Matrix.at(1,2) = sin(theta)*cos(phi);
    62   Matrix.at(2,2) = cos(theta);
     54  Matrix.set(0,0, cos(psi)*cos(phi) - sin(psi)*cos(theta)*sin(phi));
     55  Matrix.set(1,0, -cos(psi)*sin(phi) - sin(psi)*cos(theta)*cos(phi));
     56  Matrix.set(2,0, sin(psi)*sin(theta));
     57  Matrix.set(0,1, sin(psi)*cos(phi) + cos(psi)*cos(theta)*sin(phi));
     58  Matrix.set(1,1, cos(psi)*cos(theta)*cos(phi) - sin(psi)*sin(phi));
     59  Matrix.set(2,1, -cos(psi)*sin(theta));
     60  Matrix.set(0,2, sin(theta)*sin(phi));
     61  Matrix.set(1,2, sin(theta)*cos(phi));
     62  Matrix.set(2,2, cos(theta));
    6363  helper.MatrixMultiplication(Matrix);
    6464  helper.ScaleAll(InverseLength);
    … …  
    7474  phi = -EllipsoidAngle[2];
    7575  helper.ScaleAll(EllipsoidLength);
    76   Matrix.at(0,0) = cos(psi)*cos(phi) - sin(psi)*cos(theta)*sin(phi);
    77   Matrix.at(1,0) = -cos(psi)*sin(phi) - sin(psi)*cos(theta)*cos(phi);
    78   Matrix.at(2,0) = sin(psi)*sin(theta);
    79   Matrix.at(0,1) = sin(psi)*cos(phi) + cos(psi)*cos(theta)*sin(phi);
    80   Matrix.at(1,1) = cos(psi)*cos(theta)*cos(phi) - sin(psi)*sin(phi);
    81   Matrix.at(2,1) = -cos(psi)*sin(theta);
    82   Matrix.at(0,2) = sin(theta)*sin(phi);
    83   Matrix.at(1,2) = sin(theta)*cos(phi);
    84   Matrix.at(2,2) = cos(theta);
     76  Matrix.set(0,0, cos(psi)*cos(phi) - sin(psi)*cos(theta)*sin(phi));
     77  Matrix.set(1,0, -cos(psi)*sin(phi) - sin(psi)*cos(theta)*cos(phi));
     78  Matrix.set(2,0, sin(psi)*sin(theta));
     79  Matrix.set(0,1, sin(psi)*cos(phi) + cos(psi)*cos(theta)*sin(phi));
     80  Matrix.set(1,1, cos(psi)*cos(theta)*cos(phi) - sin(psi)*sin(phi));
     81  Matrix.set(2,1, -cos(psi)*sin(theta));
     82  Matrix.set(0,2, sin(theta)*sin(phi));
     83  Matrix.set(1,2, sin(theta)*cos(phi));
     84  Matrix.set(2,2, cos(theta));
    8585  helper.MatrixMultiplication(Matrix);
    8686  //Log() << Verbose(4) << "Intersection is at " << helper << "." << endl;

  • src/vector.cpp

    r436f04 ra679d1  
    105105double Vector::PeriodicDistance(const Vector &y, const double * const cell_size) const
    106106{
    107   double res = distance(y), tmp;
    108   Matrix matrix;
     107  return sqrt(PeriodicDistanceSquared);
     108};
     109
     110/** Calculates distance between this and another vector in a periodic cell.
     111 * \param *y array to second vector
     112 * \param *cell_size 6-dimensional array with (xx, xy, yy, xz, yz, zz) entries specifying the periodic cell
     113 * \return \f$| x - y |^2\f$
     114 */
     115double Vector::PeriodicDistanceSquared(const Vector &y, const double * const cell_size) const
     116{
     117  double res = DistanceSquared(y), tmp;
     118  Matrix matrix = ReturnFullMatrixforSymmetric(cell_size);
    109119    Vector Shiftedy, TranslationVector;
    110120    int N[NDIM];
    111     matrix.at(0,0) = cell_size[0];
    112     matrix.at(1,0) = cell_size[1];
    113     matrix.at(2,0) = cell_size[3];
    114     matrix.at(0,1) = cell_size[1];
    115     matrix.at(1,1) = cell_size[2];
    116     matrix.at(2,1) = cell_size[4];
    117     matrix.at(0,2) = cell_size[3];
    118     matrix.at(1,2) = cell_size[4];
    119     matrix.at(2,2) = cell_size[5];
    120     // in order to check the periodic distance, translate one of the vectors into each of the 27 neighbouring cells
    121     for (N[0]=-1;N[0]<=1;N[0]++)
    122       for (N[1]=-1;N[1]<=1;N[1]++)
    123         for (N[2]=-1;N[2]<=1;N[2]++) {
    124           // create the translation vector
    125           TranslationVector.Zero();
    126           for (int i=NDIM;i--;)
    127             TranslationVector[i] = (double)N[i];
    128           TranslationVector.MatrixMultiplication(matrix);
    129           // add onto the original vector to compare with
    130           Shiftedy = y + TranslationVector;
    131           // get distance and compare with minimum so far
    132           tmp = distance(Shiftedy);
    133           if (tmp < res) res = tmp;
    134         }
    135     return (res);
    136 };
    137 
    138 /** Calculates distance between this and another vector in a periodic cell.
    139  * \param *y array to second vector
    140  * \param *cell_size 6-dimensional array with (xx, xy, yy, xz, yz, zz) entries specifying the periodic cell
    141  * \return \f$| x - y |^2\f$
    142  */
    143 double Vector::PeriodicDistanceSquared(const Vector &y, const double * const cell_size) const
    144 {
    145   double res = DistanceSquared(y), tmp;
    146   Matrix matrix;
    147     Vector Shiftedy, TranslationVector;
    148     int N[NDIM];
    149     matrix.at(0,0) = cell_size[0];
    150     matrix.at(1,0) = cell_size[1];
    151     matrix.at(2,0) = cell_size[3];
    152     matrix.at(0,1) = cell_size[1];
    153     matrix.at(1,1) = cell_size[2];
    154     matrix.at(2,1) = cell_size[4];
    155     matrix.at(0,2) = cell_size[3];
    156     matrix.at(1,2) = cell_size[4];
    157     matrix.at(2,2) = cell_size[5];
     121
    158122    // in order to check the periodic distance, translate one of the vectors into each of the 27 neighbouring cells
    159123    for (N[0]=-1;N[0]<=1;N[0]++)
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