Merge branch 'main' into schematic_editor_holoviews

gdsfactory · Aug 31, 2023 · 9b6d871 · 9b6d871
2 parents 35e0438 + fda3c3c
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.0
+current_version = 0.3.1
 commit = True
 tag = True
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -48,3 +48,9 @@ repos:
     hooks:
       - id: j2lint
         args: [--ignore, jinja-statements-delimiter, jinja-statements-indentation, --]
+
+  - repo: https://github.com/markdownlint/markdownlint.git
+    rev: v0.12.0
+    hooks:
+      - id: markdownlint
+        args: [--rules, '~MD007,~MD012,~MD013,~MD026,~MD029,~MD033,~MD034']
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# gplugins 0.3.0
+# gplugins 0.3.1
 
 [![docs](https://github.com/gdsfactory/gplugins/actions/workflows/pages.yml/badge.svg)](https://gdsfactory.github.io/gplugins/)
 [![PyPI](https://img.shields.io/pypi/v/gplugins)](https://pypi.org/project/gplugins/)
@@ -18,24 +18,31 @@ gdsfactory plugins:
 - `klayout` for fill, dataprep and testing.
 - `ray` for distributed computing and optimization.
 - `sax` S-parameter circuit solver.
-- `schematic`: for bokeh schematic editor and `path_length_analysis`
+- `schematic`: for bokeh schematic editor and `path_length_analysis`.
 - `meep` for FDTD.
 - `mpb` for MPB mode solver.
-- `web`: for gdsfactory webapp
+- `elmer` for electrostatic (capacitive) simulations.
+- `palace` for electrostatic (capacitive) simulations.
+- `web` for gdsfactory webapp.
 
 ## Installation
 
-You can install all plugins with:
+You can install most plugins with:
 
 ```
 pip install "gplugins[database,devsim,femwell,gmsh,schematic,meow,meshwell,ray,sax,tidy3d]" --upgrade
 ```
 
-Or Install only the plugins you need `pip install gplugins[schematic,femwell,meow,sax,tidy3d]` from the available plugins:
+Or install only the plugins you need with for example `pip install gplugins[schematic,femwell,meow,sax,tidy3d]` from the available plugins.
 
-Separate installation (not using pip):
+### Non-pip plugins
+
+The following plugins require special installation without pip:
 
 - For Meep and MPB you need to use `conda` or `mamba` on MacOS, Linux or [Windows WSL (Windows Subsystem for Linux)](https://learn.microsoft.com/en-us/windows/wsl/install) with `conda install pymeep=*=mpi_mpich_* -c conda-forge -y`
+- For Elmer, refer to [Elmer FEM – Installation](https://www.elmerfem.org/blog/binaries/) for installation or compilation instructions each platform. Gplugins assumes `ElmerSolver`, `ElmerSolver_mpi`, and `ElmerGrid` are available in your PATH environment variable.
+- For Palace, refer to [Palace – Installation](https://awslabs.github.io/palace/stable/install/) for compilation instructions using Spack or Singularity. Gplugins assumes `palace` is available in your PATH environment variable.
+
 
 ## Getting started
 

diff --git a/docs/_config.yml b/docs/_config.yml
@@ -21,6 +21,7 @@ execute:
     - "*ray_optimiser*"
     - "*03_numerical_implantation*"
     - "*02_model_extraction*"
+    - "*palace*"
     # - "*20_schematic_driven_layout*"
     # - "*001_meep_sparameters*"
     # - "*00_tidy3d.ipynb"
@@ -48,6 +49,9 @@ launch_buttons:
   notebook_interface: jupyterlab
   colab_url: "https://colab.research.google.com"
 
+bibtex_bibfiles:
+  - bibliography.bib
+
 sphinx:
   extra_extensions:
     - "sphinx.ext.autodoc"
@@ -57,6 +61,7 @@ sphinx:
     - "sphinx.ext.viewcode"
     - "matplotlib.sphinxext.plot_directive"
     - "sphinxcontrib.autodoc_pydantic"
+    - "sphinxcontrib.bibtex"
   config:
     #autodoc_typehints: description
     autodoc_type_aliases:
@@ -66,5 +71,3 @@ sphinx:
         .py:
             - jupytext.reads
             - fmt: py
-    bibtex_reference_style: author_year
-    bibtex_bibfiles: "bibliography.bib"
diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -23,6 +23,7 @@ parts:
           - file: notebooks/tcad_02_analytical_process
           - file: notebooks/tcad_03_numerical_implantation
           - file: notebooks/elmer_01_electrostatic
+          - file: notebooks/palace_01_electrostatic
       - file: plugins_mode_solver
         sections:
           - file: notebooks/femwell_01_modes

diff --git a/docs/api_design.rst b/docs/api_design.rst
@@ -195,3 +195,26 @@ Circuit solver
     send_to_interconnect
     run_wavelength_sweep
     plot_wavelength_sweep
+
+**************
+Electrostatics
+**************
+
+.. currentmodule:: gplugins.elmer
+
+.. rubric:: Elmer
+
+.. autosummary::
+   :toctree: _autosummary/
+
+   run_capacitive_simulation_elmer
+
+
+.. currentmodule:: gplugins.palace
+
+.. rubric:: Palace
+
+.. autosummary::
+   :toctree: _autosummary/
+
+   run_capacitive_simulation_palace
diff --git a/docs/bibliography.bib b/docs/bibliography.bib
@@ -1,31 +1,31 @@
-
-@article{smolic_capacitance_2021,
-	title = {Capacitance matrix revisited},
-	volume = {92},
-	issn = {1937-6472},
-	url = {http://www.jpier.org/PIERB/pier.php?paper=21011501},
-	doi = {10.2528/PIERB21011501},
-	pages = {1--18},
-	journaltitle = {Progress In Electromagnetics Research B},
-	shortjournal = {{PIER} B},
-	author = {Smolić, Ivica and Klajn, Bruno},
-	urldate = {2023-08-17},
-	date = {2021},
-	langid = {english},
-}
-
 @article{marxer_long-distance_2023,
-	title = {Long-Distance Transmon Coupler with cz-Gate Fidelity above 99.8 \%},
-	volume = {4},
-	issn = {2691-3399},
-	url = {https://link.aps.org/doi/10.1103/PRXQuantum.4.010314},
-	doi = {10.1103/PRXQuantum.4.010314},
-	pages = {010314},
-	number = {1},
-	journaltitle = {{PRX} Quantum},
-	shortjournal = {{PRX} Quantum},
-	author = {Marxer, Fabian and Vepsäläinen, Antti and Jolin, Shan W. and Tuorila, Jani and Landra, Alessandro and Ockeloen-Korppi, Caspar and Liu, Wei and Ahonen, Olli and Auer, Adrian and Belzane, Lucien and Bergholm, Ville and Chan, Chun Fai and Chan, Kok Wai and Hiltunen, Tuukka and Hotari, Juho and Hyyppä, Eric and Ikonen, Joni and Janzso, David and Koistinen, Miikka and Kotilahti, Janne and Li, Tianyi and Luus, Jyrgen and Papic, Miha and Partanen, Matti and Räbinä, Jukka and Rosti, Jari and Savytskyi, Mykhailo and Seppälä, Marko and Sevriuk, Vasilii and Takala, Eelis and Tarasinski, Brian and Thapa, Manish J. and Tosto, Francesca and Vorobeva, Natalia and Yu, Liuqi and Tan, Kuan Yen and Hassel, Juha and Möttönen, Mikko and Heinsoo, Johannes},
-	urldate = {2023-08-17},
-	date = {2023-02-06},
-	langid = {english},
+    title         = {Long-Distance Transmon Coupler with cz-Gate Fidelity above 99.8 \%},
+    author        = {Marxer, Fabian and Veps\"{a}l\"{a}inen, Antti and Jolin, Shan W. and Tuorila, Jani and Landra, Alessandro and Ockeloen-Korppi, Caspar and Liu, Wei and Ahonen, Olli and Auer, Adrian and Belzane, Lucien and Bergholm, Ville and Chan, Chun Fai and Chan, Kok Wai and Hiltunen, Tuukka and Hotari, Juho and Hyypp\"{a}, Eric and Ikonen, Joni and Janzso, David and Koistinen, Miikka and Kotilahti, Janne and Li, Tianyi and Luus, Jyrgen and Papic, Miha and Partanen, Matti and R\"{a}bin\"{a}, Jukka and Rosti, Jari and Savytskyi, Mykhailo and Sepp\"{a}l\"{a}, Marko and Sevriuk, Vasilii and Takala, Eelis and Tarasinski, Brian and Thapa, Manish J. and Tosto, Francesca and Vorobeva, Natalia and Yu, Liuqi and Tan, Kuan Yen and Hassel, Juha and M\"{o}tt\"{o}nen, Mikko and Heinsoo, Johannes},
+    year          = {2023},
+    journal       = {{PRX} Quantum},
+    volume        = {4},
+    number        = {1},
+    pages         = {010314},
+    doi           = {10.1103/PRXQuantum.4.010314},
+    issn          = {2691-3399},
+    url           = {https://link.aps.org/doi/10.1103/PRXQuantum.4.010314},
+    urldate       = {2023-08-17},
+    shortjournal  = {{PRX} Quantum},
+    date          = {2023-02-06},
+    langid        = {english}
+}
+@article{smolic_capacitance_2021,
+    title         = {Capacitance matrix revisited},
+    author        = {Smoli\'{c}, Ivica and Klajn, Bruno},
+    year          = {2021},
+    journal       = {Progress In Electromagnetics Research B},
+    volume        = {92},
+    pages         = {1--18},
+    doi           = {10.2528/PIERB21011501},
+    issn          = {1937-6472},
+    url           = {http://www.jpier.org/PIERB/pier.php?paper=21011501},
+    urldate       = {2023-08-17},
+    shortjournal  = {{PIER} B},
+    date          = {2021},
+    langid        = {english}
 }
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -1,8 +1,8 @@
 # [CHANGELOG](https://keepachangelog.com/en/1.0.0/)
 
-## [Unreleased](https://github.com/gdsfactory/gplugins/compare/v0.2.0...main)
+## [Unreleased](https://github.com/gdsfactory/gplugins/compare/v0.3.0...main)
 
-## [0.3.0](https://github.com/gdsfactory/gplugins/compare/v0.2.0...v0.2.0)
+## [0.3.0](https://github.com/gdsfactory/gplugins/compare/v0.3.0...v0.2.0)
 
 - improve meshing
 - add verification