├── .gitignore ├── LICENSE ├── Makefile ├── README ├── benchmarking ├── cylinder2Pa.geom ├── cylinder2PaPlunge.geom └── runbenchmarks.sh ├── config ├── make.inc ├── make.inc.clang ├── make.inc.gcc ├── make.inc.gccjoshy ├── make.inc.joshy └── make.inc.ystone ├── doc ├── Doxyfile ├── Figures │ ├── IBFSDesign.graffle │ ├── IBFSDesign.pdf │ ├── IBPMDesign.graffle │ ├── IBPMDesign.pdf │ ├── grid.graffle │ └── grid.pdf ├── Library.dox ├── Makefile ├── Overview.dox ├── References.dox ├── examples │ ├── Makefile │ ├── cylinder.cc │ ├── cylinder.lay │ ├── hello.cc │ └── plot_cylinder.mcr ├── ibpm_design.tex ├── ibpm_manual.tex ├── references.bib └── snippets │ ├── Makefile │ ├── hello_snippet.cc │ ├── setup_grid.cc │ └── template.cc.tpl ├── examples ├── Makefile ├── Oseen.cc ├── RigidBodyLoad.cc ├── bin2plt.cc ├── bininfo.cc ├── cylinder.geom ├── pitching.cc └── plunging.cc ├── ibpm.geom ├── src ├── Array.h ├── BC.cc ├── BC.h ├── BaseFlow.cc ├── BaseFlow.h ├── BoundaryVector.cc ├── BoundaryVector.h ├── CholeskySolver.cc ├── CholeskySolver.h ├── ConjugateGradientSolver.cc ├── ConjugateGradientSolver.h ├── Direction.h ├── Eldredge1.h ├── Eldredge2.h ├── EldredgeCombined2.h ├── EldredgeManeuver.h ├── EllipticSolver.cc ├── EllipticSolver.h ├── EllipticSolver2d.cc ├── EllipticSolver2d.h ├── Field.cc ├── Field.h ├── FixedPosition.h ├── FixedVelocity.h ├── Flux.cc ├── Flux.h ├── Geometry.cc ├── Geometry.h ├── Grid.cc ├── Grid.h ├── IBSolver.cc ├── IBSolver.h ├── LagStep1.h ├── LagStep2.h ├── Logger.cc ├── Logger.h ├── Motion.h ├── MotionFile.h ├── MotionFilePeriodic.h ├── NavierStokesModel.cc ├── NavierStokesModel.h ├── Output.h ├── OutputEnergy.cc ├── OutputEnergy.h ├── OutputForce.cc ├── OutputForce.h ├── OutputProbes.cc ├── OutputProbes.h ├── OutputRestart.cc ├── OutputRestart.h ├── OutputTecplot.cc ├── OutputTecplot.h ├── ParmParser.cc ├── ParmParser.h ├── PitchPlunge.h ├── ProjectionSolver.cc ├── ProjectionSolver.h ├── RandomNumber.h ├── Regularizer.cc ├── Regularizer.h ├── RigidBody.cc ├── RigidBody.h ├── Scalar.cc ├── Scalar.h ├── ScalarToTecplot.cc ├── ScalarToTecplot.h ├── Scheme.h ├── SigmoidalStep.h ├── State.cc ├── State.h ├── StateVector.cc ├── StateVector.h ├── TangentSE2.h ├── VectorOperations.cc ├── VectorOperations.h ├── checkgeom.cc ├── ibpm.cc ├── ibpm.h ├── utils.cc └── utils.h ├── test ├── BCTest.cc ├── BoundaryVectorTest.cc ├── CheckAdjoint.cc ├── CheckCurl.cc ├── CheckFluxToX.cc ├── CheckLaplacian.cc ├── EllipticSolver2dTest.cc ├── EllipticSolverTest.cc ├── FluxTest.cc ├── GeometryTest.cc ├── GridTest.cc ├── Makefile ├── MotionTest.cc ├── NavierStokesModelTest.cc ├── OutputProbesTest.cc ├── ParmParserTest.cc ├── ProjectionSolverTest.cc ├── RegularizerTest.cc ├── RigidBodyTest.cc ├── ScalarTest.cc ├── SingleWavenumber.h ├── StateTest.cc ├── TangentSE2Test.cc ├── VectorOperationsTest.cc └── gtest-1.6.0 │ ├── COPYING │ ├── include │ └── gtest │ │ ├── gtest-death-test.h │ │ ├── gtest-message.h │ │ ├── gtest-param-test.h │ │ ├── gtest-param-test.h.pump │ │ ├── gtest-printers.h │ │ ├── gtest-spi.h │ │ ├── gtest-test-part.h │ │ ├── gtest-typed-test.h │ │ ├── gtest.h │ │ ├── gtest_pred_impl.h │ │ ├── gtest_prod.h │ │ └── internal │ │ ├── gtest-death-test-internal.h │ │ ├── gtest-filepath.h │ │ ├── gtest-internal.h │ │ ├── gtest-linked_ptr.h │ │ ├── gtest-param-util-generated.h │ │ ├── gtest-param-util-generated.h.pump │ │ ├── gtest-param-util.h │ │ ├── gtest-port.h │ │ ├── gtest-string.h │ │ ├── gtest-tuple.h │ │ ├── gtest-tuple.h.pump │ │ ├── gtest-type-util.h │ │ └── gtest-type-util.h.pump │ └── src │ ├── gtest-all.cc │ ├── gtest-death-test.cc │ ├── gtest-filepath.cc │ ├── gtest-internal-inl.h │ ├── gtest-port.cc │ ├── gtest-printers.cc │ ├── gtest-test-part.cc │ ├── gtest-typed-test.cc │ ├── gtest.cc │ └── gtest_main.cc └── xcode └── IBPM.xcodeproj ├── clancy.pbxuser └── project.pbxproj /.gitignore: -------------------------------------------------------------------------------- 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