Adding 'diverged' to SimulationData and the hdf5 attributes

tests/test_components.py

@@ -419,7 +419,7 @@ def test_VolumeSource_directional():
     s = PlaneWave(size=(0, 1, 1), source_time=g, polarization="Ez", direction="+")
 
     # test we can make planewave
-    s = GaussianBeam(size=(0,1,1), source_time=g, polarization='Ez', direction='+')
+    s = GaussianBeam(size=(0, 1, 1), source_time=g, polarization="Ez", direction="+")
 
     # test that non-planar geometry crashes plane wave
     with pytest.raises(ValidationError) as e_info:
@@ -429,7 +429,7 @@ def test_VolumeSource_directional():
     with pytest.raises(ValidationError) as e_info:
         s = PlaneWave(size=(1, 1, 0), source_time=g, polarization="Ez", direction="+")
     with pytest.raises(ValidationError) as e_info:
-        s = GaussianBeam(size=(1,1,1), source_time=g, polarization='Ez', direction='+')
+        s = GaussianBeam(size=(1, 1, 1), source_time=g, polarization="Ez", direction="+")
 
 
 def test_VolumeSource_modal():

tidy3d/__init__.py

@@ -1,7 +1,7 @@
 """ Tidy3d package imports"""
 __version__ = "0.0.0"
 
-from concurrent.futures import ProcessPoolExecutor
+from concurrent.futures import ProcessPoolExecutor, process
 
 from rich import pretty, traceback
 
@@ -63,4 +63,4 @@
 
 # make all stdout and errors pretty
 pretty.install()
-# traceback.install(suppress=[ProcessPoolExecutor])
+# traceback.install()

tidy3d/components/__init__.py

@@ -14,7 +14,7 @@
 
 # medium
 from .medium import Medium, PoleResidue, Sellmeier, Debye, Drude, Lorentz, AnisotropicMedium, PEC
-from .medium import AbstractMedium
+from .medium import AbstractMedium, DispersiveMedium
 
 # structure
 from .structure import Structure
@@ -27,8 +27,8 @@
 from .source import VolumeSource, PlaneWave, ModeSource, GaussianBeam
 
 # monitor
-from .monitor import FieldMonitor, FieldTimeMonitor, FluxMonitor, FluxTimeMonitor
-from .monitor import ModeMonitor
+from .monitor import AbstractFieldMonitor, FreqMonitor, TimeMonitor, FieldMonitor, FieldTimeMonitor
+from .monitor import AbstractFluxMonitor, FluxMonitor, FluxTimeMonitor, ModeMonitor
 
 # simulation
 from .simulation import Simulation

tidy3d/components/data.py

@@ -3,6 +3,7 @@
 
 from abc import ABC, abstractmethod
 from typing import Dict, List, Union
+import logging
 
 import xarray as xr
 import numpy as np
@@ -627,11 +628,14 @@ class SimulationData(Tidy3dBaseModel):
         Mapping of monitor name to :class:`Tidy3dData` intance.
     log_string : str = None
         A string containing the log information from the simulation run.
+    diverged : bool = False
+        A boolean flag denoting if the simulation run diverged.
     """
 
     simulation: Simulation
     monitor_data: Dict[str, Tidy3dData]
     log_string: str = None
+    diverged: bool = False
 
     @property
     def log(self):
@@ -825,12 +829,16 @@ def to_file(self, fname: str) -> None:
 
         with h5py.File(fname, "a") as f_handle:
 
-            # save json string as an attribute
+            # save json string as a dataset
             Tidy3dData.save_string(f_handle, "sim_json", self.simulation.json())
 
+            # save log string as a dataset
             if self.log_string:
                 Tidy3dData.save_string(f_handle, "log_string", self.log_string)
 
+            # save diverged flag as an attribute
+            f_handle.attrs["diverged"] = self.diverged
+
             # make a group for monitor_data
             mon_data_grp = f_handle.create_group("monitor_data")
             for mon_name, mon_data in self.monitor_data.items():
@@ -864,6 +872,12 @@ def from_file(cls, fname: str):
             # get the log if exists
             log_string = Tidy3dData.load_string(f_handle, "log_string")
 
+            # set the diverged flag
+            # TODO: add link to documentation discussing divergence
+            diverged = f_handle.attrs["diverged"]
+            if diverged:
+                logging.warning("Simulation run has diverged!")
+
             # loop through monitor dataset and create all MonitorData instances
             monitor_data_dict = {}
             for monitor_name, monitor_data in f_handle["monitor_data"].items():
@@ -877,6 +891,7 @@ def from_file(cls, fname: str):
             simulation=simulation,
             monitor_data=monitor_data_dict,
             log_string=log_string,
+            diverged=diverged,
         )
 
     def __eq__(self, other):

tidy3d/components/pml.py

@@ -151,6 +151,7 @@ class PML(AbsorberSpec):
     >>> pml = PML(num_layers=10)
     """
 
+    type: Literal["PML"] = "PML"
     num_layers: pydantic.NonNegativeInt = 12
     parameters: PMLParams = DefaultPMLParameters
 
@@ -172,8 +173,9 @@ class StablePML(AbsorberSpec):
     >>> pml = StablePML(num_layers=40)
     """
 
+    type: Literal["StablePML"] = "StablePML"
     num_layers: pydantic.NonNegativeInt = 40
-    parameters: Literal[DefaultStablePMLParameters] = DefaultStablePMLParameters
+    parameters: PMLParams = DefaultStablePMLParameters
 
 
 class Absorber(AbsorberSpec):
@@ -193,6 +195,7 @@ class Absorber(AbsorberSpec):
     >>> pml = Absorber(num_layers=40)
     """
 
+    type: Literal["Absorber"] = "Absorber"
     num_layers: pydantic.NonNegativeInt = 40
     parameters: AbsorberParams = DefaultAbsorberParameters
 

tidy3d/convert.py

@@ -118,7 +118,7 @@ def old_json_structures(sim: Simulation) -> Tuple[List[Dict], List[Dict]]:
         elif isinstance(medium, DispersiveMedium):
             poles = []
             for (a, c) in medium.pole_residue.poles:
-                poles.append([a[0], a[1], c[0], c[1]])
+                poles.append([a.real, a.imag, c.real, c.imag])
             med.update(
                 {
                     "type": "PoleResidue",
@@ -295,8 +295,8 @@ def old_json_sources(sim: Simulation) -> List[Dict]:
                 "waist_radius": float(source.waist_radius),
                 "waist_distance": float(source.waist_distance),
                 "pol_angle": float(source.pol_angle),
-                "amplitude": source.source_time.amplitude
-                }
+                "amplitude": source.source_time.amplitude,
+            }
 
         if src:
             src_list.append(src)

tidy3d/log.py

@@ -25,7 +25,7 @@
 """ Tidy3d custom exceptions """
 
 
-class Tidy3DError(Exception):
+class Tidy3dError(Exception):
     """Any error in tidy3d"""
 
     def __init__(self, message: str = None):
@@ -34,35 +34,35 @@ def __init__(self, message: str = None):
         super().__init__(self, message)
 
 
-class ConfigError(Tidy3DError):
+class ConfigError(Tidy3dError):
     """Error when configuring Tidy3d."""
 
 
-class Tidy3dKeyError(Tidy3DError):
+class Tidy3dKeyError(Tidy3dError):
     """Could not find a key in a Tidy3d dictionary."""
 
 
-class ValidationError(Tidy3DError):
+class ValidationError(Tidy3dError):
     """eError when constructing Tidy3d components."""
 
 
-class SetupError(Tidy3DError):
+class SetupError(Tidy3dError):
     """Error regarding the setup of the components (outside of domains, etc)."""
 
 
-class FileError(Tidy3DError):
+class FileError(Tidy3dError):
     """Error reading or writing to file."""
 
 
-class WebError(Tidy3DError):
+class WebError(Tidy3dError):
     """Error with the webAPI."""
 
 
-class AuthenticationError(Tidy3DError):
+class AuthenticationError(Tidy3dError):
     """Error authenticating a user through webapi webAPI."""
 
 
-class DataError(Tidy3DError):
+class DataError(Tidy3dError):
     """Error accessing data."""