Updated synthetic turbulent inflow generator. #183
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samoliverowens
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Aug 27, 2024
* Update 2decomp-fft. * Enable compilation on ARCHER2. * Add switch for ibm. * Add statsdump. * Add initstatsdump. * Progress on IBM. * Wall functions. * Don't write start. * IBM tweaks - increased dependence on facet sections. * Enable constant heat flux at surfaces. * Field output changes. * Fix netcdf output indexing mistake. * Don't allocate stats arrays if not doing statsdump. * Don't write IBM file info. * Change from v0 to vouttot in convective outflow BC for y. * Add moisture to IBM. * Restructure IBM and SEB. * Clean up IBM. * Start on non-aligned IBM. * Add modtimedep for time-varying surface fluxes and nudging profiles. * Use non-conservative heat conservation scheme as default. * Scalars. * Restructure startup. * Enable fixed streamwise & spanwise velocities at top. * Changes for Cai validation. * Changes to wall functions. * Correct luvolflowr. * More corrections to luvolflowr. * Remove write statement. * More correction to luvolflowr. * Fix mistake. * Add IBM pre-processing. * Change ARCHER2 project account. * Add 1024^3 example simulation. * trying to figure out how to branch of ecse * Testing push * Pushing to ecse * Remove files * Correct changes to writeIBMfiles.m. * Remove .info.txt. * Allow driver inflow rotation. * Nudge streamwise velocity. * Allow driver inflow rotation. * Finalise wall function implementation. * Simplify pressure gradient pre-processing. * Shifted periodic boundary conditions. * Read nudging profiles even if doing warmstart. * Correct warmstart EB interaction. * Fix mistake with warmstart EB interaction. * Allow use of both IBM and bottom wall functions simultaneously. * Specify ground temperature seperately, read facet temperature in layers. * Add surface energy balance pre-processing. * Fix bugs in matchFacetsToCells, add scripts for writing facet areas & View3D input. * Fix bug in non-aligned case. * Fix another bug in non-aligned cases. * Use distance to NEAREST cell edge when finding reconstruction point ids. * Don't zero statsdump arrays. * Don't copy bound_info. * Complete pre-processing. * Allow geometry to be set from path. * Fix bug in conservative advection correction. * Shift fluid boundary points when calculating distance to facet sections. * Transpose z-grid when stretching. * Fix write header. * Tril different point2trimesh. * Fix latent heat flux. * Use fastPoint2TriMesh. * Allow option to not have geometry, and remove reference to blocks. * Tweak fastPoint2TriMesh. * Max facet size. * Fix bug. * Remove unnecessary -cpp flag. * Update debug flags. * Merge master into ecse. (#155) * Try to clean commit history. (#156) * Install FFTW for running tests. (#152) * Try including submodules when running tests. * Use recursive flag in git submodule loading. * Fixed bug in max_facet_size and updated hpc_build. (#154) * Fixed bug in indexing in max_facet_size calculation * Updated hpc_build for Imperial HPC with latest available modules * Only rank 0 checks for exit file (#151) * Only rank 0 checks for exit file * Only print Broadcast error from rank 0 Calls MPI_Abort to kill the simulation * Try to find submodules. * Update .gitmodules to include View3D. * Try removing update submodule. * Update namoptions.103 * Rename walltypes.inp.103 to factypes.inp.103 * Update namoptions.103 * Update namoptions.103 * Remove unnecessary files. * Update namoptions.103 * Update 2decomp-fft. * Don't run test simulation. * Fix bug with nfcts in preprocessing. * Fix bug with Sdir dimensions. * Update 2decomp-fft. * Included tolerence in in_mypoly functions and fixed bugs (#158) * Start on getting tkedump working. * Remove debugging evidence from fastPoint2TriMesh. * Fix bug defining grid size. * Fix potential (but unlikely) bug with z-grid. * Pre-processing improvements. * Account for x parallelisation in shifted periodic boundary conditions. * Increase precision for writing large-scale forcing. * Gather outputs. * Don't write number of IBM points on each rank to terminal. * Change archer execution parameters. * Modify sbatch parameters. * Fix mistake. * Fix mistake in shifted PBCs. * Implemented in_mypoly_fortran. (#159) * Implemented in_mypoly_fortran. * Fixed bug. * Fixed if else alignment. * Moved solid_u/v/w/c.txt writing in fortran. * Fixed bug in facet_sections_x_3 writing. * Corrected writing format of solid_x.txt in in_mypoly_fortran. * Fix bug writing driver files with nprocx>1. * Write facet normals with more precision. * Load nco. * Remove requirement to always read temperature driver file. * Set cell ib temperature directly. * Build and execute changes. * Nudge v as well as u. * Fix mistake. * Fix mistake in pre-processing with large-scale forcing. * Included boundary masking part in fortran preprocessing. * Add option to not reconstruct in non-aligned cases. * Testing use of kappa advection scheme for temperature. * Try different approach to solid boundary points. * Allow zero roughness length. * Don't nudge v to profile. * Fixed bug. * Various pre-processing changes. * Fix mistakes with PR. * Added matchFacetsToCells.f90 for testing Fortran implementation. * Bug fixed in write_inputs, writeIBMFiles and write_pre_info. (#162) * Bug fixed in write_inputs, writeIBMFiles and write_pre_info. * Fixed issues with in_mypoly path. * More bug fixes in pre-processing. * Work on matchFacetsToCells Fortran. * Rename facets file. * Implemented all grids in matchFacetsToCells. * Fix bugs associated with matchFacetsToCells.m * Work on Fortran matchFacetsToCells. * Incorporated Fortran matchFacetsToCells and improved workflow. * Don't read boundary masks, just index lists. * Remove debugging artifacts. * Clean up matchFacetsToCells Fortran. * Debugging. * Remove unnecessary files. * Move lwindows switch. * Improved MATLAB direct shortwave. * Direct shortwave Fortran. * Implemented new functionality - synthetic inflow turbulence generator. (#163) * Fortran direct solar done and time-varying started. * Modified initd/s file naming to account for nprocx and nprocy. (#164) * Increase tolerance in matchFacetsToCells. * Negate subgrid terms when wall functions not in use. * Re-add forgotten modules. * Misc changes and bug fixes to matchFacetsToCells. * Add lwritefac switch to write stresses and pressures on facets. * Add outgoing longwave to EB output, and change sign of heat fluxes. * Add errors/warnings at startup. * Modified timee writing format to accomodate more decimal places. (#166) * Always write facet area and use Matlab shortwave by default. * Change definition of heat transfer coefficient. * Reverse change of sign and name change in SEB for now. * Fix heat transfer coefficient and time-average facet output. * Misc minor changes. * Rename poly2MaskIDs.m to poly2maskIDs.m * Fix bug with writing facet sections. * Update writeIBMFiles.m * Update account in archer_execute.sh. * Fix bugs with time-dependent shortwave. * Add generator for infinite canyons. * Fix bugs with vfsparse, Sdir I/O. * Modifed cold and warm started dirver file writing and reading (#167) * Modified driver writing, reading, and drivergen call. Also, added few check messages to handle cold and warm start driver simulations better. * Bug fixed with drivergen call in modstartup for idriver==2. * Bug fixed with nturn reading from startfile name. * Bug fixed. Removed unnecessary output message. * Modified printing format of time and storetdriver to accomodate more digits. * Modified printing format at a few more places. * Commented unnecessery redundent check of tdriverstart with respect to timee. * Commented redundant output message. * Added a script to link driver files from driver output directory to target case director. * Merged uDALES/u-dales/ecse into madDipanjan/u-dales/ecse * Bug fixes with merging branches. * Added functionality for reading driverfiles chunkwise. (#172) * Incorporated trees and purifiers module. (#173) * Modified driver writing, reading, and drivergen call. Also, added few check messages to handle cold and warm start driver simulations better. * Bug fixed with drivergen call in modstartup for idriver==2. * Bug fixed with nturn reading from startfile name. * Bug fixed. Removed unnecessary output message. * Modified printing format of time and storetdriver to accomodate more digits. * Modified printing format at a few more places. * Commented unnecessery redundent check of tdriverstart with respect to timee. * Commented redundant output message. * Added a script to link driver files from driver output directory to target case director. * Merged uDALES/u-dales/ecse into madDipanjan/u-dales/ecse * Modified preprocessing to include tree form trees.inp files. * Declared tree parameter variables and add tree namelist. * Avoided creating tree variables during preprocessing if trees.inp file available. * Declared tree field variables. * Corrected file name format in 'for loop' in nco_concatenate_field_x for xmparam==xm * Modified modstatsdump to output treedump. * Incorporated trees and purifiers modules. * Modified array allocation index for a few tree variables from 1 to kb. * Corrected writeIBMFiles to account for flat ground stl without any building. * Reset defaults in write_inputs.m * Update preprocessing.m * Minor update pdate gather_outputs.sh * Minor update writeIBMFiles.m * Reduce memory usage in IBM and SEB. (#171) * More use of local arrays. * Only allocate nfcts arrays when necessary. * Update memory branch with latest changes from ecse. (#168) * Rename poly2MaskIDs.m to poly2maskIDs.m * Fix bug with writing facet sections. * Update memory with changes from ecse. (#169) * Rename poly2MaskIDs.m to poly2maskIDs.m * Fix bug with writing facet sections. * Update writeIBMFiles.m * Update account in archer_execute.sh. * Update memory with changes from ecse. (#170) * Rename poly2MaskIDs.m to poly2maskIDs.m * Fix bug with writing facet sections. * Update writeIBMFiles.m * Update account in archer_execute.sh. * Fix bugs with time-dependent shortwave. * Add generator for infinite canyons. * Only allocate view factor array on rank 0. * Only allocate arrays (dimension nfts) on rank 0 unless needed locally. * Update View3D. * Incorporate changes in View3D. * Remove debugging write statements. * Remove write statements. * Debugging time-dependent shortwave pre-processing. * Add scripts for facet visualisation using vtk, and other misc changes. * Only do time-dependent shortwave on rank 0. * Don't write non-useful info. * Remove write statements. * Remove more write statements. * Nudge temperature and humidity to profiles. * Updated synthetic inflow generation script and few bug fixes. (#174) * Updated synthetic inflow generation script and few bug fixes. * Bug fixes. * Update View3D. * Write initial profiles when doing warmstart. * Remove terminal output when doing warmstart. * Edit formatting. * Update udales-namoptions-overview.md * Update udales-pre-processing.md * Add option to read facet types from text file. * Add unit cube STL to repo. * Edit path to unit cube STL. * Add switch around nudging velocities. * Update udales-simulation-setup.md * Add docs for 2decomp. * Fix bug in matchFacetsToCells. * Add options for pre-processing in Matlab or Fortran. * Fix minor bug in matchFacetsToCells. * Minor changes in pre-processing. * Increase options for shortwave. * Minor changes to matchFacetsToCells.m * No need to always determine reconstruction points. * Add tolerance for using inpolyhedron. * Re-add constant outflow forcing. * Bug fix for y outlet forcing. * Bug fixes (MPI) for outflow rate forcing. * Minor changes and warnings. * Add option to not use view factors. * Don't use 3D arrays for plotting - memory issues. * Update udales-pre-processing.md * Update udales-namoptions-overview.md * Remove redundant code, keeping only what lbottom uses. * Change default month. * Update udales-getting-started.md * Bug fix with volume flow forcing in y direction. * Simplify volume/outflow forcings. * Don't always read temp and moist driver files. * Remove output from driver chunk reading. * Only allocate driver arrays on inlet ranks. * Minor formatting changes. * Updated scalar point/line source module. (#175) * Updated scalar point/line source module. * Added plot_scalarsources to preprocessing. --------- Co-authored-by: samoliverowens <[email protected]> * Do reconstruction depending on wall function distance. * Fix bugs due to scalar merge. * Updated in_mypoly_fortran algorithm for ray-facet intersection counting. (#176) * Updated solid points plot. Important for flat geometry. * Updated in_mypoly_fortran algorithm for counting ray-facet intersections. * Resolved the issue with empty solid_IB_ijk in writeIBMFiles. * Check for too sharp solid corners (MATLAB implementation only). * Fix bug with view factor writing. * Fix mistake in sharp corner detection. * Load gsl for merging on Imperial HPC. * Re-add checks for bounding walls. * Misc IBM debugging. * Only write facet areas if needed, and set type of unused facets to zero. * Don't need to read emissivity. * Update View3D for single row view factor calculation. * Correct SEB for non-homogeneous surfaces. * SEB conductivities defined on layer interfaces. * Added functionality of z-grid stretching with worrying about stretch constant. (#179) * Shortwave radiation set to zero if parameters indicate night-time. * Minor modification in file handling scripts in tools. (#180) * Adding scalar sink (#181) * Adding scalar sink * Changing flags in CMakelists * Added check message for setting trestart while running target simulation. (#182) * Add options to output minimal tdump (mintdump) and i/j/k slicedumps. * Update dependencies. * Update install_deps.sh * Update ci.yml * Update install_deps.sh * Updated synthetic turbulent inflow generator. (#183) * Write unused facets to file. --------- Co-authored-by: cedwardwilson <[email protected]> Co-authored-by: Dipanjan Majumdar <[email protected]> Co-authored-by: Paul Bartholomew <[email protected]> Co-authored-by: Dipanjan Majumdar <[email protected]> Co-authored-by: cedwardwilson <[email protected]>
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