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Merge branch 'master' into demo/linear-wave-body (#83)
* Waves: enable wave direction in the sinusoid wave model (#80) * Waves: enable wave direction in the sinusoid wave model - Allow wave direction to be set for regular waves. - Add test for a wave direction not parallel to the x-axis Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: rename monochromatic_waves model - Rename to regular waves. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves simulation optimisation - part 1 (#82) * Waves: add classes for spreading functions - Add classes for directional spreading functions. - Add vectorised calculations using Eigen. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: update classes for spreading functions - Update classes for directional spreading functions - use Eigen::MatrixXd rather than VectorXd. - Update tests including broadcasting to arrays. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: add classes for omni-directional spectrum functions - Add classes for omni-directional wave spectra. - Add test case for vectorised spectrum calculation using Eigen. - Add regression test and check limits (k = 0, u19 = 0) Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: update classes for omni-directional spectrum functions - Implement ECVK omni-directional spectra. - Add test case for vectorised spectrum calculation using Eigen. - Add regression test and check limits (k = 0, u10 = 0) Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: add regression tests for spectra. - Add regression test against spectrum calculation used in FFT2. - Make spectrum functions in FFT2 static. - Add ECKV spectrum tests. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: fix spreading function test. - Fix segfault caused by missing arg. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: remove unused wave simulation classes - Remove FFTW and OpenCL simulation classes. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: reset test values after physical constant updates. - Update buoyancy regression values after fluid density and gravity value update. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: fix failing static test in gz_waves_bridge - Disable flake8 and fix docstring. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: replace std::vector with Eigen in WaveSimulation - Migration from std::vector to Eigen::VectorXf. Not efficient as involved heap allocation each update. - Replace std::vector for interface calls in OceanTile. - Remove unused code from WaveSpectrum. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: fixes post cherry-pick - Revert interface change in WaveSimulation. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: replace std::vector with Eigen in WaveSimulation - Remove interface using std::vector<double> from WaveSimulation classes. - Update waves plugin classes to use new interfaces. - Update test Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: replace std::vector with Eigen in WaveSimulation - Remove internal interface using std::vector<double> from WaveSimulation classes. - Update tests Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: replace std::vector with Eigen in FFT WaveSimulation - Remove internal interface using std::vector<double> from WaveSimulation classes. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: correct typos in derivative calculations for sinusoid and trochoid waves - Ensure Eigen vector workspace is initialised in WavesVisual. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: visual lighting workaround - Tangent space calculation not correct - environment mapping looks incorrect unless dhdx <---> dhdx? Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: update sinusoid wave interface - Allow x and y to be set independently in wave grid. - Streamline class declarations. - Update tests. - Add vectorise option for sinusoid waves. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: remove unused functions. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: add tests for vectorised sinusoid wave sim - Cross check vectorised code against non-vectorised version. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: remove unused include from WaveSimulationSinusoid Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: refactor WaveSimulation method names. - Rename ComputeHeights to ComputeElevation. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: refactor update indentation formatting. - Add vectorisation method to FFT wave simulation. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: refactor update member variable names in FFT wave simulation - Standardise caps convention for naming member variables (using underscores). - Update interface to allow different nx and ny for grid. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: temp workaround for wave derivatives used in lighting tangent space - Workaround mixed conventions for matrix-ij vs matrix-xy storage in tangent space calcs. Signed-off-by: Rhys Mainwaring <[email protected]> Signed-off-by: Rhys Mainwaring <[email protected]> * Waves simulation optimisation - part 2 (#84) * Waves: update FFT wave simulation tests for non-square grids (nx != ny) Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: apply google coding standards Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: apply google coding standards Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: apply google coding standards Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: apply google coding standards Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: apply google coding standards Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: apply google coding standards Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: update FFT test namesWaves Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: preparation for vectorising FFT wave simulation update - Add placeholders for vectorised versions of functions - Replace hardcoded gravity constants with params. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: preparation for vectorising FFT wave simulation update - Add cross-check tests for vectorised versions of base and current amplitude calculations. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: progress vectorising FFT wave simulation update - Change capitalisation of Cos2sSpreadingFunction. - Update comments in WaveSpectrum. - WaveSimulationFFT - Consolidate initialisation code. - Update variable names (nyquist) - Delay allocation of storage for Eigen member variables. - Update tests to use nearest for cross checks on vectorised version. - Remove use of auto for Eigen references (use Eigen::Ref instead) - Factor out wavenumber initialisation. - Partial vectorisation. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: vectorise base amplitude calc for FFT wave simulation - Leave initialisation of IID random normals un-vectorised for testing against original versions. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: add unit test for Eigen and FFTW - Add test skeleton. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: add unit test for Eigen and FFTW - Add examples using different storage choices. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: add unit test for Eigen and FFTW - Add examples for row vs column major storage. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: add Eigen alignment macro Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: use Eigen types for FFTW storage - reduce copies - Use Eigen types instead of fftw_complex* for FFT workspace. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: remove unused code from FFWT wave simulation Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: use row-major Eigen matrix storage for FFT wave simulation - Intermediate step moving from Eigen::VectorXcd to Eigen::MatrixXcdRowMajor. - FFTW requires row-major ordering, Eigen is column major by default. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: use row-major Eigen matrix storage for FFT wave simulation - Change to matrix indexing in FFT wave storage (from a single column). Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: update output mapping from row to col major storage in FFT wave simulation - Replace loops with vector calls using reshaped to flatten. Signed-off-by: Rhys Mainwaring <[email protected]> * Set up CI using GitHub Actions (#85) - CI: remove travis integration - Add codeowners and gazebo ci.yml - Minimal version - checkout only. - Change checkout actions/checkout@v3 - Add CI workflows for ubuntu and macos - Rename and split macOS into separate workflow. - Install Gazebo Garden. - Test caching - Add brew install script. - Add build script. - Update macos-ci - Add test step. - Add GitHub Actions status badge, remove travis badges. - Update ci install scripts - Update the brew installation script to force relinking on all dependencies of the installed packages. - Fix relink step. - Update ubunti-ci workflow. - Add install, build and test steps. - Rename macos scripts. - Update ubunti-ci workflow. - Install additional build dependencies. - Update ubunti-ci workflow. - Fix colcon build command line. - Move macOS to colcon build. - Update workflow for ubuntu 20.04 - Ensure cgal etc are linked as well as deps. - Split Ubuntu jobs to separate workflow - Update macos workflow - add build tools - Fix EigenFFTW breaking on Ubuntu. - Update macos workflow - reenable build and test - Fix timer in CGAL test and disable triangulation tests failing on Ubuntu. - Fix errors in WaveSimulationFFT2 tests and set tolerances for variance comparisons. - Check colcon install on macOS workflow - Disable trochoid wave test - Investigate why colcon not found in macOS CI workflow - Add workflow to check build tools are installed. - Use pip3 - Use full path to colcon - Add pip install checks - Update path to Python scripts - Update path to Python scripts - Pip install colcon and vcstool with --user flag Signed-off-by: Rhys Mainwaring <[email protected]> * Waves simulation optimisation - part 3 (#87) * Waves: optimise current amplitude calculation for FFT wave simulation - Investigate optimisation options for the current amplitude calculation. - vectorised assignment to fft worlspace is not faster than a single loop. - pre-calculate the fourier amplitude coefficients (reduce index lookup) - marginal gain? Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: label indices in ocean tile to distinguish between vertex indices and wave indices - Vertex array index: v_idx_cm: v - vertex, cm - column major - Wave array index: w_idx_cm: v - vertex, cm - column major - Wave array index: w_idx_rm: v - vertex, rm - row major Signed-off-by: Rhys Mainwaring <[email protected]> * CI: only run macOS workflow on PR Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: rename FFT wave simulation class Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: duplicate FFT wave simulation class to factor out reference version Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: duplicate FFT wave simulation class to factor out reference version - Complete split of reference implementation into separate class. - Remove unused code from the separated FFT wave simulation classes. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: remove commented code - Remove code referring to reference versions of the spectrum calculations. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: add performance checks for spectrum and FFT amplitude calculations - Initial performance tests. Contain debugging and timing info. - Eigen component-wise array versions are not performant... Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: replace slow array versions of spectrum calcs. - Eigen component-wise array versions are not performant - replace with calls using std::transform on unary / binary versions. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: refactor wave simulation and spectrum test names - Functions are not truly vectorised - use Eigen array type to label tests instead. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: satisfy Eigen check that range iterators in STL algorithms are from the same expression. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves simulation optimisation - part 4 (#88) * Waves: restructure wave spectrum performance test for instrumenting - Move initialisation into test fixture Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: remove c-wise amplitude update - Remove inefficient component wise amplitude update and associated data. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: remove c-wise cos / sin update in current amplitude calc - Remove inefficient component wise amplitude update. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: restructure FFT wave amplitude performance test for instrumenting - Move initialisation into test fixture. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: update FFT wave simulation - Consolidate storage (shape depends whether loop is flattened or not). - Make test fixture class names consistent. - Remove array allocation in current amplitude update Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: use previously calculated wave numbers Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: remove two loops from FFT base amplitude calculation Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: remove component-wise array amplitude calculations - Abandon using c-wise amplitude calculations as the loop based update has better performance. - Remove unnecessary storage from the FFT class to reduce memory footprint. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: remove WaveSimulationFFTRef from public interface Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: add performance checks for elevation and displacement calculations - Add performance check for main update loop - elevations, displacements and derivatives. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves simulation optimisation - part 5 (#89) * Waves: update FFTW check - Modify check to transform hermitian amplitudes back to real values. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: create FFTW plans before initialising arrays - FFTW may overwrite data in arrays while planning. Allocate, plan, initialise. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: use complex to real version of FFTW - Change outputs to real arrays. - Change size of input complex arrays to nx * ny/2+1 - Output in Compute* functions is now real. - Add example in the Eigen FFTW test using a c2r plan. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: use complex to real version of FFTW - Flattened index must be calculated as loops do not cover full range. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: use complex to real version of FFTW - Disable hermitian tests for optimised FFT wave sim (arrays truncated using symmetry) Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: temp disable tests broken because of switch to real DFT The following tests require further review - restructuring - ParsevalsIdentityTimeZero - ParsevalsIdentityTimeNonZero - Displacement Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: additional Hermitian tests - Add placeholder tests to check derivative and displacement amplitudes are Hermitian. Signed-off-by: Rhys Mainwaring <[email protected]> * Waves: fix Hermitian symmetry for derivatives (#90) - Correct Nyquist term in derivative amplitudes (must be zero). - Enable tests to check derivative and displacement amplitudes are Hermitian. Signed-off-by: Rhys Mainwaring <[email protected]> * CI: clean build warnings (#91) * CI: enable all warnings and enforce as errors - Clean build of all warnings. - Disable unused variables from tests (primarily present for printing info). - Comment unused parameters in function sigs. - Fix int type comparison warnings in loops. - Fix initialisation order errors in constructors. Signed-off-by: Rhys Mainwaring <[email protected]> * CI: enable all warnings and enforce as errors - Remove GZ_ASSERT raising a warning on Ubuntu Signed-off-by: Rhys Mainwaring <[email protected]> * CI: enable all warnings and enforce as errors - Renaming shadowing variables. Signed-off-by: Rhys Mainwaring <[email protected]> * Wave Body: update cmake dependencies - Use FetchContent to retrieve dependency HighFive. - Fix typo in documentation. - Remove cpp style header for mlinterp Signed-off-by: Rhys Mainwaring <[email protected]> * Wave Body: update ci workflow - Add build flag for HighFive dependency Signed-off-by: Rhys Mainwaring <[email protected]> * Wave Body: update waves bridge tests - Remove breaking tests inherited from ROS project template. Signed-off-by: Rhys Mainwaring <[email protected]>
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