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src/geometry/blockGeometryView3D.cpp | 35 + src/geometry/blockGeometryView3D.h | 113 + src/geometry/blockGeometryView3D.hh | 185 ++ src/geometry/cuboid2D.cpp | 35 + src/geometry/cuboid2D.h | 166 ++ src/geometry/cuboid2D.hh | 425 ++++ src/geometry/cuboid3D.cpp | 35 + src/geometry/cuboid3D.h | 175 ++ src/geometry/cuboid3D.hh | 758 +++++++ src/geometry/cuboidGeometry2D.cpp | 35 + src/geometry/cuboidGeometry2D.h | 165 ++ src/geometry/cuboidGeometry2D.hh | 677 ++++++ src/geometry/cuboidGeometry3D.cpp | 35 + src/geometry/cuboidGeometry3D.h | 273 +++ src/geometry/cuboidGeometry3D.hh | 1233 +++++++++++ src/geometry/geometry2D.h | 38 + src/geometry/geometry2D.hh | 38 + src/geometry/geometry3D.h | 38 + src/geometry/geometry3D.hh | 40 + src/geometry/module.mk | 27 + src/geometry/superGeometry2D.cpp | 37 + src/geometry/superGeometry2D.h | 198 ++ src/geometry/superGeometry2D.hh | 504 +++++ src/geometry/superGeometry3D.cpp | 37 + src/geometry/superGeometry3D.h | 203 ++ src/geometry/superGeometry3D.hh | 557 +++++ src/geometry/superGeometryStatistics2D.cpp | 34 + src/geometry/superGeometryStatistics2D.h | 128 ++ src/geometry/superGeometryStatistics2D.hh | 392 ++++ src/geometry/superGeometryStatistics3D.cpp | 34 + src/geometry/superGeometryStatistics3D.h | 140 ++ src/geometry/superGeometryStatistics3D.hh | 467 ++++ src/io/MakeHeader | 48 + src/io/base64.cpp | 72 + src/io/base64.h | 82 + src/io/base64.hh | 200 ++ src/io/blockGifWriter.cpp | 32 + src/io/blockGifWriter.h | 90 + src/io/blockGifWriter.hh | 202 ++ src/io/blockVtkWriter2D.cpp | 37 + src/io/blockVtkWriter2D.h | 86 + src/io/blockVtkWriter2D.hh | 281 +++ src/io/blockVtkWriter3D.cpp | 37 + src/io/blockVtkWriter3D.h | 88 + src/io/blockVtkWriter3D.hh | 289 +++ src/io/colormaps.cpp | 46 + src/io/colormaps.h | 135 ++ src/io/colormaps.hh | 432 ++++ src/io/fileName.cpp | 98 + src/io/fileName.h | 59 + src/io/gnuplotHeatMapWriter.cpp | 33 + src/io/gnuplotHeatMapWriter.h | 127 ++ src/io/gnuplotHeatMapWriter.hh | 250 +++ src/io/gnuplotWriter.cpp | 32 + src/io/gnuplotWriter.h | 108 + src/io/gnuplotWriter.hh | 296 +++ src/io/io2D.h | 39 + src/io/io2D.hh | 35 + src/io/io3D.h | 42 + src/io/io3D.hh | 39 + src/io/module.mk | 27 + src/io/octree.h | 157 ++ src/io/octree.hh | 756 +++++++ src/io/ostreamManager.cpp | 133 ++ src/io/ostreamManager.h | 106 + src/io/parallelIO.cpp | 335 +++ src/io/parallelIO.h | 108 + src/io/serializerIO.cpp | 33 + src/io/serializerIO.h | 42 + src/io/serializerIO.hh | 94 + src/io/stlReader.cpp | 35 + src/io/stlReader.h | 290 +++ src/io/stlReader.hh | 1258 +++++++++++ src/io/superVtmWriter2D.cpp | 39 + src/io/superVtmWriter2D.h | 115 + src/io/superVtmWriter2D.hh | 448 ++++ src/io/superVtmWriter3D.cpp | 39 + src/io/superVtmWriter3D.h | 115 + src/io/superVtmWriter3D.hh | 439 ++++ src/io/vtiReader.cpp | 44 + src/io/vtiReader.h | 189 ++ src/io/vtiReader.hh | 534 +++++ src/io/vtiWriter.cpp | 38 + src/io/vtiWriter.h | 75 + src/io/vtiWriter.hh | 225 ++ src/io/xmlReader.cpp | 329 +++ src/io/xmlReader.h | 161 ++ src/olb2D.h | 9 + src/olb2D.hh | 9 + src/olb3D.h | 14 + src/olb3D.hh | 13 + src/particles/MakeHeader | 32 + src/particles/boundaries/MakeHeader | 29 + src/particles/boundaries/boundaries.h | 36 + src/particles/boundaries/boundaries.hh | 33 + src/particles/boundaries/boundary3D.cpp | 34 + src/particles/boundaries/boundary3D.h | 57 + src/particles/boundaries/boundary3D.hh | 48 + .../boundaries/boundarySimpleReflection3D.cpp | 35 + .../boundaries/boundarySimpleReflection3D.h | 56 + .../boundaries/boundarySimpleReflection3D.hh | 206 ++ src/particles/boundaries/materialBoundary3D.cpp | 34 + src/particles/boundaries/materialBoundary3D.h | 84 + src/particles/boundaries/materialBoundary3D.hh | 83 + src/particles/boundaries/module.mk | 27 + src/particles/boundaries/periodicBoundary3D.h | 136 ++ src/particles/boundaries/wireBoundaryForMagP3D.cpp | 33 + src/particles/boundaries/wireBoundaryForMagP3D.h | 80 + src/particles/boundaries/wireBoundaryForMagP3D.hh | 88 + src/particles/contactDetection/contactDetection.h | 66 + src/particles/contactDetection/nanoflann.hpp | 1634 ++++++++++++++ .../contactDetection/nanoflann_adaptor.hpp | 127 ++ src/particles/contactDetection/pLattice.h | 205 ++ src/particles/contactDetection/sortAlgorithms.h | 31 + src/particles/forces/MakeHeader | 36 + src/particles/forces/buoyancyForce3D.cpp | 35 + src/particles/forces/buoyancyForce3D.h | 58 + src/particles/forces/buoyancyForce3D.hh | 67 + src/particles/forces/force3D.cpp | 34 + src/particles/forces/force3D.h | 58 + src/particles/forces/force3D.hh | 50 + src/particles/forces/forceFromExtField3D.cpp | 35 + src/particles/forces/forceFromExtField3D.h | 57 + src/particles/forces/forceFromExtField3D.hh | 66 + src/particles/forces/forces.h | 42 + src/particles/forces/forces.hh | 40 + src/particles/forces/hertzMindlinDeresiewicz3D.cpp | 36 + src/particles/forces/hertzMindlinDeresiewicz3D.h | 75 + src/particles/forces/hertzMindlinDeresiewicz3D.hh | 202 ++ ...ndlinDeresiewiczForCombWithCollisionModel3D.cpp | 36 + ...MindlinDeresiewiczForCombWithCollisionModel3D.h | 76 + ...indlinDeresiewiczForCombWithCollisionModel3D.hh | 235 ++ src/particles/forces/interpMagForceForMagP3D.cpp | 40 + src/particles/forces/interpMagForceForMagP3D.h | 59 + src/particles/forces/interpMagForceForMagP3D.hh | 158 ++ src/particles/forces/linearContactForce3D.cpp | 36 + src/particles/forces/linearContactForce3D.h | 76 + src/particles/forces/linearContactForce3D.hh | 208 ++ .../linearDampingForceForMagDipoleMoment3D.cpp | 37 + .../linearDampingForceForMagDipoleMoment3D.h | 55 + .../linearDampingForceForMagDipoleMoment3D.hh | 63 + src/particles/forces/magneticForceForMagP3D.cpp | 35 + src/particles/forces/magneticForceForMagP3D.h | 64 + src/particles/forces/magneticForceForMagP3D.hh | 85 + src/particles/forces/magneticForceFromHField3D.cpp | 35 + src/particles/forces/magneticForceFromHField3D.h | 57 + src/particles/forces/magneticForceFromHField3D.hh | 119 + src/particles/forces/module.mk | 27 + src/particles/forces/stokesDragForce3D.cpp | 36 + src/particles/forces/stokesDragForce3D.h | 71 + src/particles/forces/stokesDragForce3D.hh | 127 ++ .../forces/stokesDragForceForHomVelField3D.cpp | 38 + .../forces/stokesDragForceForHomVelField3D.h | 54 + .../forces/stokesDragForceForHomVelField3D.hh | 57 + src/particles/forces/transferExternalForce3D.cpp | 33 + src/particles/forces/transferExternalForce3D.h | 48 + src/particles/forces/transferExternalForce3D.hh | 54 + src/particles/forces/weightForce3D.cpp | 34 + src/particles/forces/weightForce3D.h | 50 + src/particles/forces/weightForce3D.hh | 50 + src/particles/hlbm/hlbmDynamics2D.h | 110 + src/particles/hlbm/hlbmDynamics2D.hh | 261 +++ src/particles/hlbm/hlbmDynamics3D.h | 108 + src/particles/hlbm/hlbmDynamics3D.hh | 317 +++ src/particles/module.mk | 27 + src/particles/particle3D.cpp | 32 + src/particles/particle3D.h | 407 ++++ src/particles/particle3D.hh | 537 +++++ src/particles/particleSystem3D.cpp | 95 +