merged develop into main for 1.0.1

Author: tylerflex

.gitattributes

@@ -4,3 +4,5 @@ tests/* linguist-vendored
 
 *.ipynb linguist-detectable=false
 *.ipynb linguist-generated=true
+
+CHANGELOG.md merge=union

CHANGELOG.md

@@ -6,13 +6,31 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### Added
+
+### Changed
+
+## [1.0.1] - 2021-2-16
+
+### Added
+- `Selmeier.from_dispersion()` method to quickly make a single-pole fit for lossless weakly dispersive materials.
 - Stable dispersive material fits via webservice.
+- Allow to load dispersive data directly by providing URL to txt or csv file
 - Validates simulation based on discretized size.
 
 ### Changed
-- Refined and updated documentation.
+- `Polyslab.from_gds` returns a list of `PolySlab` objects imported from all polygons in given layer and dtype, can optionally specify single dtype.
+- Warning about structure close to PML disabled if Absorber type.
+- Source dft now ignores insignificant time amplitudes for speed.
 - New color schemes for plots.
 
+## [1.0.0] - 2021-1-31
+
+### Added
+- Stable dispersive material fits via webservice.
+
+### Changed
+- Refined and updated documentation.
+
 ## [0.2.0] - 2021-1-29
 
 ### Added
@@ -45,7 +63,99 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Web API implemented by converting simulations to old tidy3D
 
-[Unreleased]: https://github.com/flexcompute/Tidy3D-client-revamp/compare/v0.2.0...develop
+## Alpha Release Changes
+
+### 22.1.1
+- Solver speed improvement (gain depending on simulation + hardware details).
+- Bringing the speed of the non-angled mode solver back to pre-21.4.2 levels.
+
+### 21.4.4
+- Improvements to subpixel averaging for dispersive materials.
+- Enabled web login using environment variables ``TIDY3D_USER`` and ``TIDY3D_PASS``.
+
+### 21.4.3
+- Bugfix when running simulation with zero ``run_time``.
+- More internal logging.
+- Fixed unstable ``'Li1993_293K'`` variant of ``cSi`` in the material library.
+
+### 21.4.2.2
+- Bugfix when downloading data on Windows.
+- Bugfix in material fitting tool when target tolerance is not reached.
+
+### 21.4.2
+- New Gaussian beam source and `example usage <examples/GratingCoupler.html>`__.
+- Modal sources and monitors in bent and in angled waveguides with `tutorial <examples/Modes_bent_angled.html>`__.
+- Nyquist-limit sampling in frequency-domain monitors (much faster without loss of accuracy).
+- Support for Drude model of material dispersion.
+- Small bugfixes to some of the other dispersion models.
+- PEC boundaries applied by default at the truncation of any boundary with PML, avoiding potential
+   issues with using periodic boundaries under the PML instead.
+- Source normalization no longer adding a spurious frequency-dependent phase to the fields.
+- Fixed bug in unpacking monitor fields with symmetries and ``interpolate=False``.
+- Lots of streamlining on the backend side.
+
+### 21.4.1
+- Fixed bug with zero-size monitor plotting.
+- Fixed bug with empty simulation run introduced in 21.4.0.
+
+### 21.4.0
+- A few small fixes.
+
+
+### 21.3.1.6
+- Fixed nonlinear constraint in dispersive material fitting tool.
+- Fixed potential issue when a monitor stores neither `'E'` nor `'H'`.
+- Fixed some backwards compatibility issues introduced in 21.3.1.5.
+
+
+### 21.3.1.5
+ - Frequency monitors can now optionally store the complex permittivity at the same locations where 
+   the E-fields are recorded, at the monitor frequencies.
+ - Frequency monitors now also have an `'interpolate'` keyword, which defaults to `True` and 
+   reproduces the behavior of previous versions. If set to `False`, however, the raw fields 
+   evaluated at their corresponding Yee grid locations are returned, instead of the fields interpolated 
+   to the Yee cell centers. This also affects the returned permittivity, if requested.
+ - Reorganized internal source time dependence handling, enabling more complicated functionality 
+   in the future, like custom source time.
+ - Total field in the simulation now sampled at the time step of the peak of the source time dependence,
+   for better estimation of the shutoff factor.
+ - A number of bug fixes, especially in the new plotting introduced in 21.3.1.4.
+
+### 21.3.1.4
+- Reorganized plotting:
+- Speeding up structure visualizations.
+- Structures now shown based on primitive definitions rather than grid discretization. This 
+    then shows the physical structures but not what the simulation "sees". Will add an option to 
+    display the grid lines in next version.
+- Bumped down matplotlib version requirement to 3.2 and python version requirement to 3.6.
+- Improved handling of PEC interfaces.- Reorganized and extended internal logging.
+- Added ``tidy3d.__version__``.
+- A number of fixes to the example notebooks and the colab integration.
+
+### 21.3.1.3
+- Bumping back python version requirement from 3.8 to 3.7.
+
+### 21.3.1.2
+- Hotfix to an internal bug in some simulation runs.
+
+### 21.3.1.1
+- New dispersion fitting tool for material data and accompanying `tutorial <examples/Fitting.html>`__.
+- (`beta`) Non-uniform Cartesian meshing now supported. The grid coordinates are provided
+   by hand to `Simulation`. Next step is implementing auto-meshing.
+- `DispersionModel` objects can now be directly used as materials.
+- Fixed bug to `Cylinder` subpixel averaging.
+- Small bugs fixes/added checks for some edge cases.
+
+### 21.3.1.0
+- Rehash of symmetries and support for mode sources and monitors with symmetries.
+- Anisotropic materials (diagonal epsilon tensor).
+- Rehashed error handling to output more runtime errors to tidy3d.log.
+- Job and Batch classes for better simulation handling (eventually to fully replace webapi functions).
+- A large number of small improvements and bug fixes.
+
+[Unreleased]: https://github.com/flexcompute/Tidy3D-client-revamp/compare/v1.0.1...develop
+[1.0.1]: https://github.com/flexcompute/Tidy3D-client-revamp/compare/v1.0.0...v1.0.1
+[1.0.0]: https://github.com/flexcompute/Tidy3D-client-revamp/compare/v0.2.0...v1.0.0
 [0.2.0]: https://github.com/flexcompute/Tidy3D-client-revamp/compare/0.1.1...v0.2.0
 [0.1.1]: https://github.com/flexcompute/Tidy3D-client-revamp/compare/0.1.0...0.1.1
 [0.1.0]: https://github.com/flexcompute/Tidy3D-client-revamp/releases/tag/0.1.0

README.md

@@ -39,7 +39,7 @@ The easiest way to install this beta version of tidy3d is through [pip](https://
 pip install tidy3d-beta
 ```
 
-Note that whikle our old version is still currently pip installable as `tidy3d`, both versions are imoprted in python as `tidy3d`, eg. `import tidy3d as td`.
+Note that while our old version is still currently pip installable as `tidy3d`, both versions are imoprted in python as `tidy3d`, eg. `import tidy3d as td`.
 
 ### (Alternativelty) installing from source
 

lint.py

@@ -3,6 +3,9 @@
 import logging
 from pylint.lint import Run
 
+# wont pass until score (out of 10.0) is greater than this
+DEFAULT_THRESHOLD = 10.0
+
 
 def main():
     logging.getLogger().setLevel(logging.INFO)
@@ -23,7 +26,7 @@ def main():
         "-t",
         "--threshold",
         help="score threshold to fail pylint runner | " "Default: %(default)s | " "Type: %(type)s ",
-        default=9.0,
+        default=DEFAULT_THRESHOLD,
         type=float,
     )
 

tests/_test_fit_web.py

@@ -1,16 +1,14 @@
 import numpy as np
-import sys
 
-sys.path.append("../tidy3d_client_revamp")
-from tidy3d.plugins import StableDispersionFitter
+from tidy3d.plugins import StableDispersionFitter, AdvancedFitterParam
 
 
 def test_dispersion_load_list():
     """performs a fit on some random data"""
     num_data = 10
     n_data = np.random.random(num_data)
     wvls = np.linspace(1, 2, num_data)
-    fitter = StableDispersionFitter(wvls, n_data)
+    fitter = StableDispersionFitter(wvl_um=wvls, n_data=n_data)
 
     num_poles = 3
     num_tries = 10
@@ -27,7 +25,7 @@ def test_dispersion_load_file():
     fitter = StableDispersionFitter.from_file("tests/data/nk_data.csv", skiprows=1, delimiter=",")
 
     num_poles = 3
-    num_tries = 30
+    num_tries = 10
     tolerance_rms = 1e-3
     best_medium, best_rms = fitter.fit(
         num_tries=num_tries, num_poles=num_poles, tolerance_rms=tolerance_rms
@@ -36,5 +34,30 @@ def test_dispersion_load_file():
     print(best_medium.eps_model(1e12))
 
 
-if __name__ == "__main__":
-    test_dispersion_load_file()
+def test_dispersion_load_url():
+
+    url_csv = "https://refractiveindex.info/data_csv.php?datafile=data/main/Ag/Johnson.yml"
+    fitter = StableDispersionFitter.from_url(url_csv)
+
+    num_poles = 2
+    num_tries = 10
+    tolerance_rms = 1e-3
+    best_medium, best_rms = fitter.fit(
+        num_tries=num_tries,
+        num_poles=num_poles,
+        tolerance_rms=tolerance_rms,
+        advanced_param=AdvancedFitterParam(constraint="hard", bound_eps_inf=10),
+    )
+    print(best_rms)
+    print(best_medium.eps_inf)
+
+    fitter.wvl_range = [1.0, 1.3]
+    print(len(fitter.freqs))
+    best_medium, best_rms = fitter.fit(
+        num_tries=num_tries,
+        num_poles=num_poles,
+        tolerance_rms=tolerance_rms,
+        advanced_param=AdvancedFitterParam(constraint="hard", bound_eps_inf=10),
+    )
+    print(best_rms)
+    print(best_medium.eps_inf)

tests/requirements.txt

@@ -1,5 +1,5 @@
 # required for development
-black
+black==22.1.0
 pylint
 tox
-pytest
+pytest

tests/test_components.py

@@ -173,20 +173,37 @@ def _test_monitor_size():
         s.validate_contents()
 
 
-@pytest.mark.parametrize("fwidth,log_level", [(0.001, None), (3, 30)])
-def test_sim_frequency_range(caplog, fwidth, log_level):
-    # small fwidth should be inside range, large one should throw warning
+@pytest.mark.parametrize("freq, log_level", [(1.5, 30), (2.5, None), (3.5, 30)])
+def test_monitor_medium_frequency_range(caplog, freq, log_level):
+    # monitor frequency above or below a given medium's range should throw a warning
 
     size = (1, 1, 1)
     medium = Medium(frequency_range=(2, 3))
     box = Structure(geometry=Box(size=(0.1, 0.1, 0.1)), medium=medium)
+    mnt = FieldMonitor(size=(0, 0, 0), name="freq", freqs=[freq])
     src = VolumeSource(
-        source_time=GaussianPulse(freq0=2.4, fwidth=fwidth),
+        source_time=GaussianPulse(freq0=2.5, fwidth=0.5),
         size=(0, 0, 0),
         polarization="Ex",
     )
-    _ = Simulation(size=(1, 1, 1), grid_size=(0.1, 0.1, 0.1), structures=[box], sources=[src])
+    sim = Simulation(
+        size=(1, 1, 1), grid_size=(0.1, 0.1, 0.1), structures=[box], monitors=[mnt], sources=[src]
+    )
+    assert_log_level(caplog, log_level)
+
 
+@pytest.mark.parametrize("fwidth, log_level", [(0.1, 30), (2, None)])
+def test_monitor_simulation_frequency_range(caplog, fwidth, log_level):
+    # monitor frequency outside of the simulation's frequency range should throw a warning
+
+    size = (1, 1, 1)
+    src = VolumeSource(
+        source_time=GaussianPulse(freq0=2.0, fwidth=fwidth),
+        size=(0, 0, 0),
+        polarization="Ex",
+    )
+    mnt = FieldMonitor(size=(0, 0, 0), name="freq", freqs=[1.5])
+    sim = Simulation(size=(1, 1, 1), grid_size=(0.1, 0.1, 0.1), monitors=[mnt], sources=[src])
     assert_log_level(caplog, log_level)
 
 
@@ -273,8 +290,13 @@ def test_sim_plane_wave_error():
 def test_sim_structure_extent(caplog, box_size, log_level):
     """Make sure we warn if structure extends exactly to simulation edges."""
 
+    src = VolumeSource(
+        source_time=GaussianPulse(freq0=3e14, fwidth=1e13),
+        size=(0, 0, 0),
+        polarization="Ex",
+    )
     box = Structure(geometry=Box(size=box_size), medium=Medium(permittivity=2))
-    sim = Simulation(size=(1, 1, 1), grid_size=(0.1, 0.1, 0.1), structures=[box])
+    sim = Simulation(size=(1, 1, 1), grid_size=(0.1, 0.1, 0.1), structures=[box], sources=[src])
 
     assert_log_level(caplog, log_level)
 
@@ -449,6 +471,25 @@ def test_medium_dispersion_create():
         struct = Structure(geometry=Box(size=(1, 1, 1)), medium=medium)
 
 
+def test_sellmeier_from_dispersion():
+    n = 3.5
+    wvl = 0.5
+    freq = C_0 / wvl
+    dn_dwvl = -0.1
+    with pytest.raises(ValidationError) as e:
+        # Check that postivie dispersion raises an error
+        medium = Sellmeier.from_dispersion(n=n, freq=freq, dn_dwvl=-dn_dwvl)
+
+    # Check that medium properties are as epected
+    medium = Sellmeier.from_dispersion(n=n, freq=freq, dn_dwvl=dn_dwvl)
+    epses = [medium.eps_model(f) for f in [0.99 * freq, freq, 1.01 * freq]]
+    ns = np.sqrt(epses)
+    dn_df = (ns[2] - ns[0]) / 0.02 / freq
+
+    assert np.allclose(ns[1], n)
+    assert np.allclose(-dn_df * C_0 / wvl**2, dn_dwvl)
+
+
 def eps_compare(medium: Medium, expected: Dict, tol: float = 1e-5):
 
     for freq, val in expected.items():
@@ -479,15 +520,15 @@ def test_epsilon_eval():
     eps_compare(material, expected)
 
     # Constant and eps, zero sigma
-    material = Medium(permittivity=1.5 ** 2)
+    material = Medium(permittivity=1.5**2)
     expected = {
         2e14: 2.25,
         5e14: 2.25,
     }
     eps_compare(material, expected)
 
     # Constant eps and sigma
-    material = Medium(permittivity=1.5 ** 2, conductivity=0.1)
+    material = Medium(permittivity=1.5**2, conductivity=0.1)
     expected = {
         2e14: 2.25 + 8.987552009401353j,
         5e14: 2.25 + 3.5950208037605416j,

tests/test_plugins.py

@@ -5,8 +5,6 @@
 import tidy3d as td
 
 from tidy3d.plugins import DispersionFitter
-from tidy3d.plugins.dispersion.fit import _poles_to_coeffs, _coeffs_to_poles
-from tidy3d.plugins.dispersion.fit import _pack_coeffs, _unpack_coeffs
 
 from tidy3d.plugins import ModeSolver
 from tidy3d.plugins import Near2Far
@@ -84,11 +82,14 @@ def test_dispersion():
     num_data = 10
     n_data = np.random.random(num_data)
     wvls = np.linspace(1, 2, num_data)
-    fitter = DispersionFitter(wvls, n_data)
-    medium, rms = fitter.fit_single()
+    fitter = DispersionFitter(wvl_um=wvls, n_data=n_data)
+    medium, rms = fitter._fit_single()
     medium, rms = fitter.fit(num_tries=2)
     medium.to_file("tests/tmp/medium_fit.json")
 
+    k_data = np.random.random(num_data)
+    fitter = DispersionFitter(wvl_um=wvls, n_data=n_data, k_data=k_data)
+
 
 def test_dispersion_load():
     """loads dispersion model from nk data file"""
@@ -101,3 +102,17 @@ def test_dispersion_plot():
     fitter = DispersionFitter.from_file("tests/data/nk_data.csv", skiprows=1, delimiter=",")
     medium, rms = fitter.fit(num_tries=20)
     fitter.plot(medium)
+
+
+def test_dispersion_set_wvg_range():
+    """set wavelength range function"""
+    num_data = 50
+    n_data = np.random.random(num_data)
+    wvls = np.linspace(1, 2, num_data)
+    fitter = DispersionFitter(wvl_um=wvls, n_data=n_data)
+
+    wvl_min = np.random.random(1)[0] * 0.5 + 1
+    wvl_max = wvl_min + 0.5
+    fitter.wvl_range = [wvl_min, wvl_max]
+    assert len(fitter.freqs) < num_data
+    medium, rms = fitter.fit(num_tries=2)