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WIP: loop_in_chunks over owned points (#1895)
* first draft of loop_in_chunks using grid_vol calculations * try to only use owned points in loop_in_chunks * don't unpad if !use_symmetry * stop vscode from complaining about comments * rm hack to loop over centered grid * fix and example * almost fix * before fix * one more loop over num_chunk * include set * different approach * minor * include climits * include climits * fix retval * clean up * using flipped * add missing changes * fix bug * fix pml * Fix memory leaks in SWIG wrappers. (#1826) * Fix memory leaks in SWIG wrappers. * move delete into material_free Co-authored-by: Steven G. Johnson <stevenj@alum.mit.edu> * Fix adjoint gradient with conductivities (#1830) * damp_fix * increase run time Co-authored-by: Mo Chen <mochen@Mos-MacBook-Pro.local> * plot geometry for dispersive materials without initializing structure object (#1827) * plot geometry without initializing structure class * update docstrings * rotate epsilon grid by 90 degrees to properly orient axes * add support for dispersive ε * update markdown pages from docstrings * make frequency and resolution parameters of plot2D dictionary keys of eps_parameters * reinstate frequency parameter of plot2D and add warning that it is deprecated * fix order of frequency check * unit test for `get_epsilon_grid` (#1835) * unit test for get_epsilon_grid * fix * limit test points to homogeneous regions (i.e. no material interfaces) and away from potential chunk boundaries * support for single-precision floating point for fields array functions (#1833) * switch dft-related functions to using realnum from double * more fixes * more type conversions from double to realnum * adjust check tolerance of tests/integrate.cpp based on floating-point precision * more fixes * rebase from master from fix merge conflicts * slight adjustment to tolerances in unit tests and update docs * remove type check in test_adjoint_solver.py * revert return types of integration functions to double * revert return type of process_dft_component to double * cleanup * Fix memory leaks (#1839) * Fix memory leaks * Add kkg to authors list * Fix for Issue #1834 (#1840) * Fix memory leaks * Add kkg to authors list * Expose set_default_material and use it in libpympb/pympb.cpp * use unique_ptr (C++11) instead of make_unique (C++14) (#1844) * Use None instead of empty list in constructors (#1846) * use None * minor fix Co-authored-by: Mo Chen <mochen@Mos-MacBook-Pro.local> * Define what happens when `β=∞` and `u=η` (#1842) * define what happens when beta=inf and u=0.5 * use eta not 0.5 * Update src/meepgeom.cpp Co-authored-by: Steven G. Johnson <stevenj@mit.edu> * fix for arrays (#1845) * minor improvements to docs (#1848) * update homebrew instructions for hdf5 and openblas (fixes #1850) * recommend python3 on macos * silence compiler warnings * whoops, missing commit * tests need scipy and autograd * missing sudo * parameterized package is also used for tests * h5py and jax on mac * note on autogen.sh for git clone * xcode installation shortcut * bug fix for get_epsilon_point and cell boundary in parallel simulation (#1849) * bug fix for get_epsilon_point and cell boundary in parallel simulation * check for six digits in test_material_grid.py because of single precision * unit test for conductivity (#1857) * unit test for conductivity * describe in the docs how to model the attenutation coefficient using conductivity * Update python/tests/test_conductivity.py Co-authored-by: Steven G. Johnson <stevenj@mit.edu> * Fix the failure message for absorber 1D test (#1859) * add missing fixed field phase to MPB unit test (#1860) * fix memory leak in array-slice-ll.cpp (#1865) * fix memory leak in array-slice-ll.cpp * reinstate line break * fix memory leak in cyl-ellipsoid-ll.cpp (#1866) * level parameter for contour plot calls epsilon data (#1869) * fix heap buffer overflow error for update E from D in cylindrical coordinates (#1871) * Add cylindrical coordinates support for `plot2d` (#1873) * add visualization support for plot2d * bug fix with cartesian plotting * fix near-field monitor position in cylindrical coordinate tutorial (#1874) * fix memory leaks in structure and fields load during checkpointing (#1872) * fix memory leaks in structure and fields load during checkpointing * delete the chi1inv and fields array if it exists and reallocate * in unit test, set gaussian source cutoff to 0 due to off-by-1 timestep counter bug * remove cutoff=0 from unit tests * lazily allocate H only if B is not NULL * allocate fields array for H in PML region * fix two memory leaks in geom_epsilon class (#1877) * fix two memory leaks in geom_epsilon class * delete global variable default_material at the end of unit tests * add unset_default_material function to class meep_geom * include ring-ll.cpp in C++ unit tests (#1878) * include ring-ll.cpp in C++ unit tests * only validate Harminv modes with error below some threshold * fix and example * first draft of loop_in_chunks using grid_vol calculations * try to only use owned points in loop_in_chunks * don't unpad if !use_symmetry * stop vscode from complaining about comments * rm hack to loop over centered grid * almost fix * before fix * one more loop over num_chunk * include set * different approach * minor * include climits * include climits * fix retval * clean up * using flipped * add missing changes * fix bug * fix pml * Fix memory leaks in SWIG wrappers. (#1826) * Fix memory leaks in SWIG wrappers. * move delete into material_free Co-authored-by: Steven G. Johnson <stevenj@alum.mit.edu> * Fix adjoint gradient with conductivities (#1830) * damp_fix * increase run time Co-authored-by: Mo Chen <mochen@Mos-MacBook-Pro.local> * plot geometry for dispersive materials without initializing structure object (#1827) * plot geometry without initializing structure class * update docstrings * rotate epsilon grid by 90 degrees to properly orient axes * add support for dispersive ε * update markdown pages from docstrings * make frequency and resolution parameters of plot2D dictionary keys of eps_parameters * reinstate frequency parameter of plot2D and add warning that it is deprecated * fix order of frequency check * unit test for `get_epsilon_grid` (#1835) * unit test for get_epsilon_grid * fix * limit test points to homogeneous regions (i.e. no material interfaces) and away from potential chunk boundaries * support for single-precision floating point for fields array functions (#1833) * switch dft-related functions to using realnum from double * more fixes * more type conversions from double to realnum * adjust check tolerance of tests/integrate.cpp based on floating-point precision * more fixes * rebase from master from fix merge conflicts * slight adjustment to tolerances in unit tests and update docs * remove type check in test_adjoint_solver.py * revert return types of integration functions to double * revert return type of process_dft_component to double * cleanup * Fix memory leaks (#1839) * Fix memory leaks * Add kkg to authors list * Fix for Issue #1834 (#1840) * Fix memory leaks * Add kkg to authors list * Expose set_default_material and use it in libpympb/pympb.cpp * use unique_ptr (C++11) instead of make_unique (C++14) (#1844) * Use None instead of empty list in constructors (#1846) * use None * minor fix Co-authored-by: Mo Chen <mochen@Mos-MacBook-Pro.local> * Define what happens when `β=∞` and `u=η` (#1842) * define what happens when beta=inf and u=0.5 * use eta not 0.5 * Update src/meepgeom.cpp Co-authored-by: Steven G. Johnson <stevenj@mit.edu> * fix for arrays (#1845) * minor improvements to docs (#1848) * update homebrew instructions for hdf5 and openblas (fixes #1850) * recommend python3 on macos * silence compiler warnings * whoops, missing commit * tests need scipy and autograd * missing sudo * parameterized package is also used for tests * h5py and jax on mac * note on autogen.sh for git clone * xcode installation shortcut * bug fix for get_epsilon_point and cell boundary in parallel simulation (#1849) * bug fix for get_epsilon_point and cell boundary in parallel simulation * check for six digits in test_material_grid.py because of single precision * unit test for conductivity (#1857) * unit test for conductivity * describe in the docs how to model the attenutation coefficient using conductivity * Update python/tests/test_conductivity.py Co-authored-by: Steven G. Johnson <stevenj@mit.edu> * Fix the failure message for absorber 1D test (#1859) * add missing fixed field phase to MPB unit test (#1860) * fix memory leak in array-slice-ll.cpp (#1865) * fix memory leak in array-slice-ll.cpp * reinstate line break * fix memory leak in cyl-ellipsoid-ll.cpp (#1866) * level parameter for contour plot calls epsilon data (#1869) * fix heap buffer overflow error for update E from D in cylindrical coordinates (#1871) * Add cylindrical coordinates support for `plot2d` (#1873) * add visualization support for plot2d * bug fix with cartesian plotting * fix near-field monitor position in cylindrical coordinate tutorial (#1874) * fix memory leaks in structure and fields load during checkpointing (#1872) * fix memory leaks in structure and fields load during checkpointing * delete the chi1inv and fields array if it exists and reallocate * in unit test, set gaussian source cutoff to 0 due to off-by-1 timestep counter bug * remove cutoff=0 from unit tests * lazily allocate H only if B is not NULL * allocate fields array for H in PML region * fix two memory leaks in geom_epsilon class (#1877) * fix two memory leaks in geom_epsilon class * delete global variable default_material at the end of unit tests * add unset_default_material function to class meep_geom * include ring-ll.cpp in C++ unit tests (#1878) * include ring-ll.cpp in C++ unit tests * only validate Harminv modes with error below some threshold * fix and example * first draft of loop_in_chunks using grid_vol calculations * try to only use owned points in loop_in_chunks * don't unpad if !use_symmetry * stop vscode from complaining about comments * rm hack to loop over centered grid * almost fix * before fix * one more loop over num_chunk * include set * different approach * minor * include climits * include climits * fix retval * clean up * using flipped * add missing changes * fix bug * fix pml * Fix adjoint gradient with conductivities (#1830) * damp_fix * increase run time Co-authored-by: Mo Chen <mochen@Mos-MacBook-Pro.local> * plot geometry for dispersive materials without initializing structure object (#1827) * plot geometry without initializing structure class * update docstrings * rotate epsilon grid by 90 degrees to properly orient axes * add support for dispersive ε * update markdown pages from docstrings * make frequency and resolution parameters of plot2D dictionary keys of eps_parameters * reinstate frequency parameter of plot2D and add warning that it is deprecated * fix order of frequency check * support for single-precision floating point for fields array functions (#1833) * switch dft-related functions to using realnum from double * more fixes * more type conversions from double to realnum * adjust check tolerance of tests/integrate.cpp based on floating-point precision * more fixes * rebase from master from fix merge conflicts * slight adjustment to tolerances in unit tests and update docs * remove type check in test_adjoint_solver.py * revert return types of integration functions to double * revert return type of process_dft_component to double * cleanup * Fix memory leaks (#1839) * Fix memory leaks * Add kkg to authors list * Fix for Issue #1834 (#1840) * Fix memory leaks * Add kkg to authors list * Expose set_default_material and use it in libpympb/pympb.cpp * use unique_ptr (C++11) instead of make_unique (C++14) (#1844) * update homebrew instructions for hdf5 and openblas (fixes #1850) * rm hack to loop over centered grid * almost fix * one more loop over num_chunk * different approach * include climits * include climits * clean up * using flipped * Revert "fix pml" This reverts commit 9ed741e. * fix rebase * fix rebase * fix rebase * fix rebase * fix rebase * fix error * increase tol * cleanup * cleanup Co-authored-by: Steven G. Johnson <stevenj@alum.mit.edu> Co-authored-by: Mo Chen <mochen@Mos-MacBook-Pro.local> Co-authored-by: Mo Chen <mochen@dhcp-10-29-91-247.dyn.MIT.EDU> Co-authored-by: Krishna Gadepalli <34969407+kkg4theweb@users.noreply.github.com> Co-authored-by: Ardavan Oskooi <ardavano@google.com> Co-authored-by: Steven G. Johnson <stevenj@mit.edu> Co-authored-by: Alec Hammond <alec.m.hammond@gmail.com> Co-authored-by: Andreas Hoenselaar <ahoens@google.com> Co-authored-by: simbilod <46427609+simbilod@users.noreply.github.com>
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