fix merge conflict in .github/workflows/build-ci.yml

Author: oskooi

.github/workflows/build-ci.yml

@@ -69,12 +69,6 @@ jobs:
         repository: NanoComp/mpb
         path: mpb-src
 
-    - name: Checkout libGDSII repository
-      uses: actions/checkout@v7
-      with:
-        repository: HomerReid/libGDSII
-        path: libGDSII-src
-
     - name: Cache dependency builds
       uses: actions/cache@v6
       id: deps-cache
@@ -94,10 +88,6 @@ jobs:
       if: steps.deps-cache.outputs.cache-hit != 'true'
       run: cd mpb-src && sh autogen.sh --prefix=${HOME}/local --enable-shared LIBS=-ldl --with-libctl=${HOME}/local/share/libctl --with-hermitian-eps && make -j $(nproc) && make install
 
-    - name: Build and install libGDSII
-      if: steps.deps-cache.outputs.cache-hit != 'true'
-      run: cd libGDSII-src && sh autogen.sh --prefix=${HOME}/local && make install
-
     - name: Define environment variables for serial build
       if: ${{ matrix.enable-mpi == false }}
       run: |

.github/workflows/build-san.yml

@@ -39,7 +39,7 @@ jobs:
       run: |
         sudo apt-get update -y
         sudo apt-get install -y autoconf automake clang libaec-dev libctl-dev \
-          libfftw3-dev libgdsii-dev libgsl-dev libharminv-dev libhdf5-dev \
+          libfftw3-dev libgsl-dev libharminv-dev libhdf5-dev \
           libtool mpb mpb-dev ccache
         mkdir -p ~/apt-cache
         cp /var/cache/apt/archives/*.deb ~/apt-cache/ 2>/dev/null || true

README.md

@@ -23,8 +23,8 @@
 -   [Custom current sources](https://meep.readthedocs.io/en/latest/Python_Tutorials/Custom_Source/) with arbitrary time and spatial profile as well as a [mode launcher](https://meep.readthedocs.io/en/latest/Python_Tutorials/Eigenmode_Source/) for waveguides and planewaves, and [Gaussian beams](https://meep.readthedocs.io/en/latest/Python_User_Interface/#gaussianbeam3dsource).
 -   [Frequency-domain solver](https://meep.readthedocs.io/en/latest/Python_User_Interface/#frequency-domain-solver) for finding the response to a [continuous-wave](https://en.wikipedia.org/wiki/Continuous_wave) (CW) source as well as a [frequency-domain eigensolver](https://meep.readthedocs.io/en/latest/Python_User_Interface/#frequency-domain-eigensolver) for finding resonant modes.
 -   ε/μ and field import/export in the [HDF5](https://en.wikipedia.org/wiki/HDF5) data format.
--   [GDSII](https://meep.readthedocs.io/en/latest/Python_User_Interface/#gdsii-support) file import for planar geometries.
--   Field analyses including [discrete-time Fourier transform (DTFT)](https://meep.readthedocs.io/en/latest/Python_User_Interface/#field-computations), [Poynting flux](https://meep.readthedocs.io/en/latest/Python_Tutorials/Basics/#transmittance-spectrum-of-a-waveguide-bend), [mode decomposition](https://meep.readthedocs.io/en/latest/Python_Tutorials/Mode_Decomposition/) (for [S-parameters](https://meep.readthedocs.io/en/latest/Python_Tutorials/GDSII_Import/#s-parameters-of-a-directional-coupler)), [energy density](https://meep.readthedocs.io/en/latest/Python_User_Interface/#energy-density-spectra), [near to far transformation](https://meep.readthedocs.io/en/latest/Python_Tutorials/Near_to_Far_Field_Spectra/), [frequency extraction](https://meep.readthedocs.io/en/latest/Python_Tutorials/Basics/#modes-of-a-ring-resonator), [local density of states](https://meep.readthedocs.io/en/latest/Python_Tutorials/Local_Density_of_States/) (LDOS), [modal volume](https://meep.readthedocs.io/en/latest/Python_User_Interface/#field-computations), [scattering cross section](https://meep.readthedocs.io/en/latest/Python_Tutorials/Basics/#mie-scattering-of-a-lossless-dielectric-sphere), [Maxwell stress tensor](https://meep.readthedocs.io/en/latest/Python_Tutorials/Optical_Forces/), [absorbed power density](https://meep.readthedocs.io/en/latest/Python_Tutorials/Basics/#absorbed-power-density-map-of-a-lossy-cylinder), [arbitrary functions](https://meep.readthedocs.io/en/latest/Field_Functions/); completely programmable.
+-   [GDS](https://meep.readthedocs.io/en/latest/Python_Tutorials/GDS_Import/) file import for planar geometries (via [gdstk](https://github.com/heitzmann/gdstk)).
+-   Field analyses including [discrete-time Fourier transform (DTFT)](https://meep.readthedocs.io/en/latest/Python_User_Interface/#field-computations), [Poynting flux](https://meep.readthedocs.io/en/latest/Python_Tutorials/Basics/#transmittance-spectrum-of-a-waveguide-bend), [mode decomposition](https://meep.readthedocs.io/en/latest/Python_Tutorials/Mode_Decomposition/) (for [S-parameters](https://meep.readthedocs.io/en/latest/Python_Tutorials/GDS_Import/#s-parameters-of-a-directional-coupler)), [energy density](https://meep.readthedocs.io/en/latest/Python_User_Interface/#energy-density-spectra), [near to far transformation](https://meep.readthedocs.io/en/latest/Python_Tutorials/Near_to_Far_Field_Spectra/), [frequency extraction](https://meep.readthedocs.io/en/latest/Python_Tutorials/Basics/#modes-of-a-ring-resonator), [local density of states](https://meep.readthedocs.io/en/latest/Python_Tutorials/Local_Density_of_States/) (LDOS), [modal volume](https://meep.readthedocs.io/en/latest/Python_User_Interface/#field-computations), [scattering cross section](https://meep.readthedocs.io/en/latest/Python_Tutorials/Basics/#mie-scattering-of-a-lossless-dielectric-sphere), [Maxwell stress tensor](https://meep.readthedocs.io/en/latest/Python_Tutorials/Optical_Forces/), [absorbed power density](https://meep.readthedocs.io/en/latest/Python_Tutorials/Basics/#absorbed-power-density-map-of-a-lossy-cylinder), [arbitrary functions](https://meep.readthedocs.io/en/latest/Field_Functions/); completely programmable.
 -   [Adjoint solver](https://meep.readthedocs.io/en/latest/Python_Tutorials/Adjoint_Solver/) for **inverse design** and **topology optimization**.
 -   [Visualization routines](https://meep.readthedocs.io/en/latest/Python_User_Interface/#data-visualization) for the simulation domain involving geometries, fields, boundary layers, sources, and monitors.
 

configure.ac

@@ -482,22 +482,6 @@ AM_CONDITIONAL(WITH_LIBCTLGEOM, test x"$have_libctlgeom" = "xyes")
 AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <ctlgeom.h>]], [ctl_printf_callback = 0;])],
   AC_DEFINE([HAVE_CTL_PRINTF_CALLBACK], [1], [If we have the ctl_printf_callback variable]))
 
-##############################################################################
-# check for libGDSII
-AC_CHECK_HEADER(libGDSII.h, [have_gdsii=maybe], [have_gdsii=no])
-if test "x$have_gdsii" = xmaybe; then
-  AC_CHECK_LIB(GDSII, libGDSIIExists)
-  if test "x$ac_cv_lib_GDSII_libGDSIIExists" = xyes; then
-    AC_MSG_CHECKING([for libGDSII::GetLayers])
-    have_gdsii_getlayers=no
-    AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <libGDSII.h>]], [libGDSII::GetLayers("foo")])],
-      [have_gdsii_getlayers=yes
-       AC_DEFINE([HAVE_GDSII_GETLAYERS], [1], [If we have libGDSII::GetLayers])])
-    AC_MSG_RESULT($have_gdsii_getlayers)
-  fi
-fi
-AM_CONDITIONAL(WITH_LIBGDSII, test "x$ac_cv_lib_GDSII_libGDSIIExists" = "xyes")
-
 ##############################################################################
 # The following function is used only for debugging.  Note that
 # we must test for it *after* setting the compiler flags (which

contrib/build-meep.sh

@@ -250,12 +250,6 @@ cd mpb/
 autogensh CC=mpicc --with-hermitian-eps
 make -j && $SUDO make install
 
-cd $SRCDIR
-gitclone https://github.com/HomerReid/libGDSII.git
-cd libGDSII/
-autogensh
-make -j && $SUDO make install
-
 cd $SRCDIR
 gitclone https://github.com/NanoComp/meep.git
 cd meep/

doc/docs/Acknowledgements.md

@@ -5,7 +5,7 @@
 Authors
 -------
 
-Meep originated as part of graduate research at [MIT](https://en.wikipedia.org/wiki/Massachusetts_Institute_of_Technology) in the mid 2000s with initial contributions by [Steven G. Johnson](http://math.mit.edu/~stevenj/), [Ardavan Oskooi](http://ab-initio.mit.edu/~oskooi/), [David Roundy](http://physics.oregonstate.edu/~roundyd/), [Mihai Ibanescu](https://www.linkedin.com/in/mihai-ibanescu-2b147825/), and [Peter Bermel](http://web.ics.purdue.edu/~pbermel/). The project has been under continuous development for nearly 20 years. Currently, the Meep project is maintained by an active developer community on [GitHub](https://github.com/NanoComp/meep). [Christopher Hogan](https://github.com/ChristopherHogan) and [M.T. Homer Reid](http://homerreid.dyndns.org/) lead the development of the [Python interface](Python_User_Interface.md), [mode-decomposition feature](Python_Tutorials/Mode_Decomposition.md), and [GDSII import routines](Python_Tutorials/GDSII_Import.md). M.T. Homer Reid and [Alec Hammond](https://github.com/smartalecH/) developed the [adjoint solver](Python_Tutorials/Adjoint_Solver.md). [Alex Cerjan](http://www.alexcerjan.com/) assisted with adding support for saturable absorption via [multilevel atomic gain media](Materials.md#saturable-gain-and-absorption). Alec Hammond developed the [visualization module](Python_User_Interface.md#data-visualization). [Yidong Chong](http://www1.spms.ntu.edu.sg/~ydchong/bio.html) and Alex Cerjan added support for [gyrotropic media](Materials.md#gyrotropic-media). [Andreas Hoenselaar](https://github.com/ahoenselaar) contributed to several performance enhancements. [Krishna Gadepalli](https://github.com/kkg4theweb) added support for checkpointing the simulation state.
+Meep originated as part of graduate research at [MIT](https://en.wikipedia.org/wiki/Massachusetts_Institute_of_Technology) in the mid 2000s with initial contributions by [Steven G. Johnson](http://math.mit.edu/~stevenj/), [Ardavan Oskooi](http://ab-initio.mit.edu/~oskooi/), [David Roundy](http://physics.oregonstate.edu/~roundyd/), [Mihai Ibanescu](https://www.linkedin.com/in/mihai-ibanescu-2b147825/), and [Peter Bermel](http://web.ics.purdue.edu/~pbermel/). The project has been under continuous development for nearly 20 years. Currently, the Meep project is maintained by an active developer community on [GitHub](https://github.com/NanoComp/meep). [Christopher Hogan](https://github.com/ChristopherHogan) and [M.T. Homer Reid](http://homerreid.dyndns.org/) lead the development of the [Python interface](Python_User_Interface.md) and [mode-decomposition feature](Python_Tutorials/Mode_Decomposition.md). M.T. Homer Reid and [Alec Hammond](https://github.com/smartalecH/) developed the [adjoint solver](Python_Tutorials/Adjoint_Solver.md). [Alex Cerjan](http://www.alexcerjan.com/) assisted with adding support for saturable absorption via [multilevel atomic gain media](Materials.md#saturable-gain-and-absorption). Alec Hammond developed the [visualization module](Python_User_Interface.md#data-visualization). [Yidong Chong](http://www1.spms.ntu.edu.sg/~ydchong/bio.html) and Alex Cerjan added support for [gyrotropic media](Materials.md#gyrotropic-media). [Andreas Hoenselaar](https://github.com/ahoenselaar) contributed to several performance enhancements. [Krishna Gadepalli](https://github.com/kkg4theweb) added support for checkpointing the simulation state.
 
 Referencing
 -----------

doc/docs/Build_From_Source.md

@@ -158,10 +158,6 @@ HDF5 supports parallel I/O under MPI which can be enabled by configuring it with
 
 **Note:** If you have a version of HDF5 compiled with MPI parallel I/O support, then you need to use the MPI compilers to link to it, even when you are compiling the serial version of Meep.  Just use `./configure CC=mpicc CXX=mpic++` or whatever your MPI compilers are when configuring.
 
-### libGDSII
-
-[libGDSII](https://github.com/HomerReid/libGDSII) is a library for reading [GDSII](https://en.wikipedia.org/wiki/GDSII) binary data files. GDSII is a widely-used format for 2d/planar geometries supported by [electronic design automation](https://en.wikipedia.org/wiki/Electronic_design_automation) (EDA) circuit-layout editors (e.g., Cadence Virtuoso Layout, Silvaco Expert, KLayout, etc.) and semiconductor foundries.
-
 ### Guile
 
 Guile is required in order to use the Scheme interface. If you don't install it, you can only use the C++ and/or Python interfaces.
@@ -353,12 +349,6 @@ cd mpb/
 sh autogen.sh --enable-shared CC=mpicc LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}" --with-hermitian-eps
 make && sudo make install
 
-cd ~/install
-git clone https://github.com/HomerReid/libGDSII.git
-cd libGDSII/
-sh autogen.sh
-make && sudo make install
-
 # The next line is only required on Ubuntu  16.04
 sudo pip3 install --upgrade pip
 
@@ -517,12 +507,6 @@ sh autogen.sh --enable-shared CC=/usr/local/bin/mpicc LDFLAGS="${MY_LDFLAGS}" CP
 make -j
 sudo make -j install
 
-cd ~/install
-git clone https://github.com/HomerReid/libGDSII.git
-cd libGDSII/
-sh autogen.sh
-sudo make -j install
-
 cd ~/install
 wget https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-3.0.0.tar.gz
 tar xvf mpi4py-3.0.0.tar.gz

doc/docs/FAQ.md

@@ -213,7 +213,7 @@ The "steady-state" response is defined as the exp(-iωt) response field (ω=2πf
 
 ### How do I compute S-parameters?
 
-Meep contains a [mode-decomposition feature](Mode_Decomposition.md) which can be used to compute complex-valued [S-parameters](https://en.wikipedia.org/wiki/Scattering_parameters). An example is provided for a [two-port network](https://en.wikipedia.org/wiki/Two-port_network#Scattering_parameters_(S-parameters)) based on a silicon directional coupler in [Tutorial/GDSII Import](Python_Tutorials/GDSII_Import.md). Additional examples are available for a [waveguide mode converter](Python_Tutorials/Mode_Decomposition.md#reflectance-of-a-waveguide-taper) and [subwavelength grating](Python_Tutorials/Mode_Decomposition.md#phase-map-of-a-subwavelength-binary-grating).
+Meep contains a [mode-decomposition feature](Mode_Decomposition.md) which can be used to compute complex-valued [S-parameters](https://en.wikipedia.org/wiki/Scattering_parameters). An example is provided for a [two-port network](https://en.wikipedia.org/wiki/Two-port_network#Scattering_parameters_(S-parameters)) based on a silicon directional coupler in [Tutorial/GDS Import](Python_Tutorials/GDS_Import.md). Additional examples are available for a [waveguide mode converter](Python_Tutorials/Mode_Decomposition.md#reflectance-of-a-waveguide-taper) and [subwavelength grating](Python_Tutorials/Mode_Decomposition.md#phase-map-of-a-subwavelength-binary-grating).
 
 ### Harminv is unable to find the resonant modes of my structure
 
@@ -336,11 +336,11 @@ Usage: Structures
 
 ### What are the different ways to define a structure?
 
-There are six ways to define a structure: (1) the [`GeometricObject`](Python_User_Interface.md#geometricobject) (Python) or [`geometric-object`](Scheme_User_Interface.md#geometric-object) (Scheme) class used to specify a collection of predefined shapes including `Prism`, `Sphere`, `Cylinder`, `Cone`, `Block`, and `Ellipsoid`, (2) [`material_function`](Python_User_Interface.md#medium) (Python) or [`material-function`](Scheme_User_Interface.md#material-function) (Scheme) used to define an arbitrary function: for a given position in the cell, return the $\varepsilon$/$\mu$ at that point, (3) import the scalar, real-valued, frequency-independent permittivity from an HDF5 file (which can be created using e.g., [h5py](http://docs.h5py.org/en/stable/)) via the `epsilon_input_file` (Python) or `epsilon-input-file` (Scheme) input parameter, (4) import planar geometries from a [GDSII file](Python_User_Interface.md#gdsii-support), (5) load the raw $\varepsilon$/$\mu$ saved from a previous simulation using [`load_structure`](Python_User_Interface.md#load-and-dump-structure) (Python) or [`meep-structure-load`](Scheme_User_Interface.md#load-and-dump-structure) (Scheme), or (6) a [`MaterialGrid`](Python_User_Interface.md#materialgrid) used to specify a pixel grid. Combinations of (1), (2), (4), and (6) are allowed but not (3) or (5).
+There are six ways to define a structure: (1) the [`GeometricObject`](Python_User_Interface.md#geometricobject) (Python) or [`geometric-object`](Scheme_User_Interface.md#geometric-object) (Scheme) class used to specify a collection of predefined shapes including `Prism`, `Sphere`, `Cylinder`, `Cone`, `Block`, and `Ellipsoid`, (2) [`material_function`](Python_User_Interface.md#medium) (Python) or [`material-function`](Scheme_User_Interface.md#material-function) (Scheme) used to define an arbitrary function: for a given position in the cell, return the $\varepsilon$/$\mu$ at that point, (3) import the scalar, real-valued, frequency-independent permittivity from an HDF5 file (which can be created using e.g., [h5py](http://docs.h5py.org/en/stable/)) via the `epsilon_input_file` (Python) or `epsilon-input-file` (Scheme) input parameter, (4) import planar geometries from a [GDS file](Python_Tutorials/GDS_Import.md), (5) load the raw $\varepsilon$/$\mu$ saved from a previous simulation using [`load_structure`](Python_User_Interface.md#load-and-dump-structure) (Python) or [`meep-structure-load`](Scheme_User_Interface.md#load-and-dump-structure) (Scheme), or (6) a [`MaterialGrid`](Python_User_Interface.md#materialgrid) used to specify a pixel grid. Combinations of (1), (2), (4), and (6) are allowed but not (3) or (5).
 
-### Does Meep support importing GDSII files?
+### Does Meep support importing GDS files?
 
-Yes. The [`get_GDSII_prisms`](Python_User_Interface.md#gdsii-support) routine is used to import [GDSII](https://en.wikipedia.org/wiki/GDSII) files. See [Tutorial/GDSII Import](Python_Tutorials/GDSII_Import.md) for examples. This feature facilitates the simulation of 2d/planar structures which are fabricated using semiconductor foundries. Also, it enables Meep's plug-and-play capability with [electronic design automation](https://en.wikipedia.org/wiki/Electronic_design_automation) (EDA) circuit-layout editors (e.g., Cadence Virtuoso Layout, Silvaco Expert, KLayout, etc.). EDA is used for the synthesis and verification of large and complex integrated circuits. A useful tool for creating GDS files of simple geometries (e.g., curved waveguides, ring resonators, directional couplers, etc.) is [gdspy](https://gdspy.readthedocs.io/en/stable/).
+Yes. [GDS](https://en.wikipedia.org/wiki/GDSII) files can be imported using the [gdstk](https://github.com/heitzmann/gdstk) Python package to read the layout polygons, which are then converted into Meep [`Prism`](Python_User_Interface.md#prism) objects (and [`Volume`](Python_User_Interface.md#volume)s for source/flux regions). See [Tutorial/GDS Import](Python_Tutorials/GDS_Import.md) for examples. This feature facilitates the simulation of 2d/planar structures which are fabricated using semiconductor foundries. Also, it enables Meep's plug-and-play capability with [electronic design automation](https://en.wikipedia.org/wiki/Electronic_design_automation) (EDA) circuit-layout editors (e.g., Cadence Virtuoso Layout, Silvaco Expert, KLayout, etc.). EDA is used for the synthesis and verification of large and complex integrated circuits. `gdstk` can also be used to create GDS files of simple geometries (e.g., curved waveguides, ring resonators, directional couplers, etc.)
 
 ### Can Meep simulate time-varying structures?