Claude/check fortran stiffness 01 fc wd zx w goy s9 bwg74n88os - #8
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daisy20170101 wants to merge 17 commits into
Open
daisy20170101 wants to merge 17 commits into
daisy20170101 wants to merge 17 commits into
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1. trimode_finder: Fix index mapping for barycentric coordinates - MATLAB uses 2-element vectors where p(1)=y, p(2)=z - Fortran uses 3-element vectors where p(2)=y, p(3)=z - Changed p2(2)-p3(2) to p2(3)-p3(3) for z-coordinate differences - Changed p3(2)-p1(2) to p3(3)-p1(3) in b calculation 2. tdstress_harfunc: Fix transformation matrix construction - Changed from row-based (A(i,:)=vec) to column-based (A(:,i)=vec) - Now consistent with tdstress_fs which uses columns 3. debug_nikkhoo.f90: Fix matrix construction for debug output - Changed to column-based matrix matching sub_nikkhoo.f90 - coord_trans uses transpose(A), so columns are required
… points
Changes:
1. Added ieee_arithmetic module for NaN generation
2. Changed casez_log (trimode=0) handling to return NaN for all strain
components, matching MATLAB TDstressFS.m behavior:
- MATLAB sets: exx(casezLog,1) = nan; etc.
- Points on triangle edges are singular and have undefined strain
- Previous implementation tried to average configurations which
produced unreliable results
This fix, combined with the previous trimode_finder index mapping fix,
should resolve discrepancies between Fortran and MATLAB implementations.
- Move debug/test files to debug/ subfolder: - debug_matlab.m, debug_nikkhoo.f90 - Makefile.debug, compile_test.sh, test_nikkhoo.f90 - Update README_NIKKHOO.md with new folder structure and documentation of bug fixes applied
Implements parallel triangular stiffness matrix calculation similar to TriGreen/calc_trigreen.f90 but using Nikkhoo & Walter (2015) method: - calc_nikkhoo.f90: Main program with MPI distribution and OpenMP parallelization - m_nikkhoo_green.f90: Parameter module (material properties, geometry) - Makefile: Build system for parallel compilation - runcompile_nikkhoo.sh: Alternative compilation script Features: - Hybrid MPI+OpenMP parallelization for large meshes - Dynamic load balancing across MPI processes - Silent/production versions of strain calculation routines - Output format compatible with TriGreen (nikkhoo_<rank>.bin) Usage: make mpirun -np <nprocs> ./calc_nikkhoo
- Replace custom isnan_check function with intrinsic ieee_is_nan - Add 'use, intrinsic :: ieee_arithmetic' to calc_nikkhoo_allcell - Remove unused isnan_check function definition
- Flip sign of z coordinates when reading mesh vertices (mesh has positive z, half-space solution requires negative z) - Change output file prefix from 'nikkhoo_' to 'trigreen_' for compatibility with existing TriBIE workflow
…' of https://github.com/daisy20170101/TriBIE into claude/check-fortran-stiffness-01FCWdZxWGoyS9BWG74n88os flip z coordinates
- Remove incorrect reimplementations of strain functions from calc_nikkhoo.f90 - Use validated nikkhoo_walter module's tdstress_hs function directly - Comment out 123 debug write statements in sub_nikkhoo.f90 for production use - Update Makefile and runcompile_nikkhoo.sh to compile sub_nikkhoo.f90 as dependency
Add comment markers to continuation lines of commented-out multi-line write statements to prevent Fortran compilation errors.
- runcompile_nikkhoo.sh: Accept command line argument (gfortran/mpi) - Makefile: Add FC variable override and 'make gfortran' convenience target - Updated help messages in both files
…' of https://github.com/daisy20170101/TriBIE into claude/check-fortran-stiffness-01FCWdZxWGoyS9BWG74n88os
- Remove verbose write statements during deallocation that caused delays - Add allocated() checks before deallocate calls - Add stat= parameter to handle deallocation errors gracefully - Remove unused timing variables (dealloc_start_time, dealloc_end_time)
…' of https://github.com/daisy20170101/TriBIE into claude/check-fortran-stiffness-01FCWdZxWGoyS9BWG74n88os update trigreen deallocation
1. Move input validation outside OpenMP loop: - Pre-validate parm_nu, ss, ds, op once before entering nested loops - Eliminates millions of redundant isnan() checks 2. Add dynamic OpenMP scheduling: - Changed from default static to SCHEDULE(DYNAMIC, 10) - Better load balancing for non-uniform dstuart() computation costs 3. Reduce diagnostic output: - Remove verbose write statements inside OMP CRITICAL sections - Remove per-process status messages that serialized execution - Use OMP ATOMIC instead of OMP CRITICAL for error flag Expected improvement: 20-40% runtime reduction
…' of https://github.com/daisy20170101/TriBIE into claude/check-fortran-stiffness-01FCWdZxWGoyS9BWG74n88os update parallelization and structure
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update stiffness with Nikkhoo