emerge 0.4.7__py3-none-any.whl → 0.4.9__py3-none-any.whl

emerge/_emerge/simmodel.py

@@ -0,0 +1,444 @@
+# EMerge is an open source Python based FEM EM simulation module.
+# Copyright (C) 2025  Robert Fennis.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see
+# <https://www.gnu.org/licenses/>.
+
+from __future__ import annotations
+from .mesher import Mesher, unpack_lists
+from .geometry import GeoObject, _GEOMANAGER
+from .geo.modeler import Modeler
+from .physics.microwave.microwave_3d import Microwave3D
+from .mesh3d import Mesh3D
+from .selection import Selector, FaceSelection, Selection
+from .logsettings import logger_format
+from .plot.display import BaseDisplay
+from .plot.pyvista import PVDisplay
+from .dataset import SimulationDataset
+from .periodic import PeriodicCell
+from .bc import BoundaryCondition
+from typing import Literal, Type, Generator, Any
+from loguru import logger
+import numpy as np
+import sys
+import gmsh
+import joblib
+import os
+import inspect
+from pathlib import Path
+from atexit import register
+import signal
+
+_GMSH_ERROR_TEXT = """
+--------------------------
+Known problems/solutions:
+(1) - PLC Error:  A segment and a facet intersect at point
+    This can be caused when approximating thin curved volumes. Try to decrease the mesh size for that region.
+--------------------------
+"""
+
+class SimulationError(Exception):
+    pass
+
+
+class Simulation3D:
+
+    def __init__(self, 
+                 modelname: str, 
+                 loglevel: Literal['DEBUG','INFO','WARNING','ERROR'] = 'INFO',
+                 load_file: bool = False,
+                 save_file: bool = False,
+                 logfile: bool = False,
+                 path_suffix: str = ".EMResults"):
+        """Generate a Simulation3D class object.
+
+        As a minimum a file name should be provided. Additionally you may provide it with any
+        class that inherits from BaseDisplay. This will then be used for geometry displaying.
+
+        Args:
+            modelname (str): The name of the simulation model. This will be used for filenames and path names when saving data.
+            loglevel ("DEBUG","INFO","WARNING","ERROR", optional): The loglevel to use for loguru. Defaults to 'INFO'.
+            load_file (bool, optional): If the simulatio model should be loaded from a file. Defaults to False.
+            save_file (bool, optional): if the simulation file should be stored to a file. Defaults to False.
+            logfile (bool, optional): If a file should be created that contains the entire log of the simulation. Defaults to False.
+            path_suffix (str, optional): The suffix that will be added to the results directory. Defaults to ".EMResults".
+        """
+        caller_file = Path(inspect.stack()[1].filename).resolve()
+        base_path = caller_file.parent
+
+        self.modelname = modelname
+        self.modelpath = base_path / (modelname.lower()+path_suffix)
+        self.mesher: Mesher = Mesher()
+        self.modeler: Modeler = Modeler()
+        
+        self.mesh: Mesh3D = Mesh3D(self.mesher)
+        self.select: Selector = Selector()
+        self.display: PVDisplay = None
+        self.set_loglevel(loglevel)
+
+        ## STATES
+        self.__active: bool = False
+        self._defined_geometries: bool = False
+        self._cell: PeriodicCell = None
+
+        self.display = PVDisplay(self.mesh)
+        if logfile:
+            self.set_logfile(logfile)
+
+        self.save_file: bool = save_file
+        self.load_file: bool = load_file
+
+        self.data: SimulationDataset = SimulationDataset()
+
+        ## Physics
+        self.mw: Microwave3D = Microwave3D(self.mesher, self.data.mw)
+
+        self._initialize_simulation()
+
+        self._update_data()
+
+    def __setitem__(self, name: str, value: Any) -> None:
+        """Store data in the current data container"""
+        self.data.sim[name] = value
+
+    def __getitem__(self, name: str) -> Any:
+        """Get the data from the current data container"""
+        return self.data.sim[name]
+    
+    def _update_data(self) -> None:
+        """Writes the stored physics data to each phyics class insatnce"""
+        self.mw.data = self.data.mw
+
+    def all_geometries(self) -> list[GeoObject]:
+        """Returns all geometries stored in the simulation file."""
+        return [obj for obj in self.sim.default.values() if isinstance(obj, GeoObject)]
+    
+    def all_bcs(self) -> list[BoundaryCondition]:
+        """Returns all boundary condition objects stored in the simulation file"""
+        return [obj for obj in self.sim.default.values() if isinstance(obj, BoundaryCondition)]
+    
+    @property
+    def passed_geometries(self) -> list[GeoObject]:
+        """"""
+        return self.data.sim['geometries']
+    
+    def set_mesh(self, mesh: Mesh3D) -> None:
+        """Set the current model mesh to a given mesh."""
+        self.mesh = mesh
+        self.mw.mesh = mesh
+        self.mesher.mesh = mesh
+        self.display._mesh = mesh
+    
+    def save(self) -> None:
+        """Saves the current model in the provided project directory."""
+        # Ensure directory exists
+        if not self.modelpath.exists():
+            self.modelpath.mkdir(parents=True, exist_ok=True)
+            logger.info(f"Created directory: {self.modelpath}")
+
+        # Save mesh
+        mesh_path = self.modelpath / 'mesh.msh'
+        brep_path = self.modelpath / 'model.brep'
+
+        gmsh.option.setNumber('Mesh.SaveParametric', 1)
+        gmsh.option.setNumber('Mesh.SaveAll', 1)
+        gmsh.model.geo.synchronize()
+        gmsh.model.occ.synchronize()
+
+        gmsh.write(str(mesh_path))
+        gmsh.write(str(brep_path))
+        logger.info(f"Saved mesh to: {mesh_path}")
+
+        # Pack and save data
+        dataset = dict(simdata=self.data, mesh=self.mesh)
+        data_path = self.modelpath / 'simdata.emerge'
+        joblib.dump(dataset, str(data_path))
+        logger.info(f"Saved simulation data to: {data_path}")
+
+    def load(self) -> None:
+        """Loads the model from the project directory."""
+        mesh_path = self.modelpath / 'mesh.msh'
+        brep_path = self.modelpath / 'model.brep'
+        data_path = self.modelpath / 'simdata.emerge'
+
+        if not mesh_path.exists() or not data_path.exists():
+            raise FileNotFoundError("Missing required mesh or data file.")
+
+        # Load mesh
+        gmsh.open(str(brep_path))
+        gmsh.merge(str(mesh_path))
+        gmsh.model.geo.synchronize()
+        gmsh.model.occ.synchronize()
+        logger.info(f"Loaded mesh from: {mesh_path}")
+        #self.mesh.update([])
+
+        # Load data
+        datapack = joblib.load(str(data_path))
+        self.data = datapack['simdata']
+        self.set_mesh(datapack['mesh'])
+        logger.info(f"Loaded simulation data from: {data_path}")
+
+    def load_data(self, key: str) -> Any:
+        return self.save_data[key]
+    
+    def set_loglevel(self, loglevel: Literal['DEBUG','INFO','WARNING','ERROR']) -> None:
+        """Set the loglevel for loguru.
+
+        Args:
+            loglevel ('DEBUG','INFO','WARNING','ERROR'): The loglevel
+        """
+        handler = {"sink": sys.stdout, "level": loglevel, "format": logger_format}
+        logger.configure(handlers=[handler])
+
+    def set_logfile(self) -> None:
+        """Adds a file output for the logger."""
+        logger.add(str(self.modelpath / 'logging.log'), mode='w', level='DEBUG', format=logger_format, colorize=False, backtrace=True, diagnose=True)
+        
+    def view(self, 
+             selections: list[Selection] = None, 
+             use_gmsh: bool = False,
+             volume_opacity: float = 0.1,
+             surface_opacity: float = 1,
+             show_edges: bool = True) -> None:
+        """View the current geometry in either the BaseDisplay object (PVDisplay only) or
+        the GMSH viewer.
+
+        Args:
+            selections (list[Selection], optional): Additional selections to highlight. Defaults to None.
+            use_gmsh (bool, optional): Whether to use the GMSH display. Defaults to False.
+            opacity (float, optional): The global opacity of all objects.. Defaults to None.
+            show_edges (bool, optional): Whether to show the geometry edges. Defaults to None.
+        """
+        if not (self.display is not None and self.mesh.defined) or use_gmsh:
+            gmsh.model.occ.synchronize()
+            gmsh.fltk.run()
+            return
+        try:
+            for obj in self.data.sim['geometries']:
+                if obj.dim==2:
+                    opacity=surface_opacity
+                elif obj.dim==3:
+                    opacity=volume_opacity
+                self.display.add_object(obj, show_edges=show_edges, opacity=opacity)
+            if selections:
+                [self.display.add_object(sel, color='red', opacity=0.7) for sel in selections]
+            self.display.show()
+            return
+        except NotImplementedError as e:
+            logger.warning('The provided BaseDisplay class does not support object display. Please make' \
+            'sure that this method is properly implemented.')
+    
+    def set_periodic_cell(self, cell: PeriodicCell, excluded_faces: list[FaceSelection] = None):
+        """Sets the periodic cell information based on the PeriodicCell class object"""
+        self.mw.bc._cell = cell
+        self._cell = cell
+
+    def define_geometry(self, *geometries: list[GeoObject]) -> None:
+        """Provide the physics engine with the geometries that are contained and ought to be included
+        in the simulation. Please make sure to include all geometries. Its currently unclear how the
+        system behaves if only a part of all geometries are included.
+
+        """
+        if not geometries:
+            geometries = _GEOMANAGER.all_geometries()
+        else:
+            geometries = unpack_lists(geometries + tuple([item for item in self.data.sim.default.values() if isinstance(item, GeoObject)]))
+        self.data.sim['geometries'] = geometries
+        self.mesher.submit_objects(geometries)
+        self._defined_geometries = True
+        self.display._facetags = [dt[1] for dt in gmsh.model.get_entities(2)]
+        # Set the cell periodicity in GMSH
+        if self._cell is not None:
+            self.mesher.set_periodic_cell(self._cell)
+            
+        self.mw._initialize_bcs()
+    
+    def generate_mesh(self):
+        """Generate the mesh. 
+        This can only be done after define_geometry(...) is called and if frequencies are defined.
+
+        Args:
+            name (str, optional): The mesh file name. Defaults to "meshname.msh".
+
+        Raises:
+            ValueError: ValueError if no frequencies are defined.
+        """
+        if not self._defined_geometries:
+            self.define_geometry()
+        
+        
+        
+        # Check if frequencies are defined: TODO: Replace with a more generic check
+        if self.mw.frequencies is None:
+            raise ValueError('No frequencies defined for the simulation. Please set frequencies before generating the mesh.')
+
+        gmsh.model.occ.synchronize()
+
+        # Set the mesh size
+        self.mesher.set_mesh_size(self.mw.get_discretizer(), self.mw.resolution)
+        
+        try:
+            gmsh.model.mesh.generate(3)
+        except Exception:
+            logger.error('GMSH Mesh error detected.')
+            print(_GMSH_ERROR_TEXT)
+            raise
+        
+        self.mesh.update(self.mesher._get_periodic_bcs())
+        gmsh.model.occ.synchronize()
+        self.set_mesh(self.mesh)
+
+    def get_boundary(self, face: FaceSelection = None, tags: list[int] = None) -> tuple[np.ndarray, np.ndarray]:
+        ''' Return boundary data. 
+        
+        Parameters
+        ----------
+        obj: GeoObject
+        tags: list[int]
+        
+        Returns:
+        ----------
+        nodes: np.ndarray
+        triangles: np.ndarray
+        '''
+        if tags is None:
+            tags = face.tags
+        tri_ids = self.mesh.get_triangles(tags)
+        return self.mesh.nodes, self.mesh.tris[:,tri_ids]
+
+    def parameter_sweep(self, clear_mesh: bool = True, **parameters: np.ndarray) -> Generator[tuple[float,...], None, None]:
+        """Executes a parameteric sweep iteration.
+
+        The first argument clear_mesh determines if the mesh should be cleared and rebuild in between sweeps. This is usually needed
+        except when you change only port-properties or material properties. The parameters of the sweep can be provided as a set of 
+        keyword arguments. As an example if you defined the axes: width=np.linspace(...) and height=np.linspace(...). You can
+        add them as arguments using .parameter_sweep(True, width=width, height=height).
+
+        The rest of the simulation commands should be inside the iteration scope
+
+        Args:
+            clear_mesh (bool, optional): Wether to clear the mesh in between sweeps. Defaults to True.
+
+        Yields:
+            Generator[tuple[float,...], None, None]: The parameters provided
+
+        Example:
+         >>> for W, H in model.parameter_sweep(True, width=widths, height=heights):
+         >>>    // build simulation
+         >>>    data = model.frequency_domain()
+         >>> // Extract the data
+         >>> widths, heights, frequencies, S21 = data.ax('width','height','freq').S(2,1)
+        """
+        paramlist = sorted(list(parameters.keys()))
+        dims = np.meshgrid(*[parameters[key] for key in paramlist], indexing='ij')
+        dims_flat = [dim.flatten() for dim in dims]
+        self.mw.cache_matrices = False
+        for i_iter in range(dims_flat[0].shape[0]):
+            if clear_mesh:
+                logger.info('Cleaning up mesh.')
+                gmsh.clear()
+                mesh = Mesh3D(self.mesher)
+                _GEOMANAGER.reset(self.modelname)
+                self.set_mesh(mesh)
+                self.mw.reset()
+            
+            params = {key: dim[i_iter] for key,dim in zip(paramlist, dims_flat)}
+            self.mw._params = params
+            self.data.sim.new(**params)
+
+            logger.info(f'Iterating: {params}')
+            if len(dims_flat)==1:
+                yield dims_flat[0][i_iter]
+            else:
+                yield (dim[i_iter] for dim in dims_flat)
+        self.mw.cache_matrices = True
+
+    def __enter__(self) -> Simulation3D:
+        """This method is depricated with the new atexit system. It still exists for backwards compatibility.
+
+        Returns:
+            Simulation3D: the Simulation3D object
+        """
+        return self
+
+    def __exit__(self, type, value, tb):
+        """This method no longer does something. It only serves as backwards compatibility."""
+        self._exit_gmsh()
+        return False
+    
+    def _install_signal_handlers(self):
+        # on SIGINT (Ctrl-C) or SIGTERM, call our exit routine
+        for sig in (signal.SIGINT, signal.SIGTERM):
+            signal.signal(sig, self._handle_signal)
+    
+    def _handle_signal(self, signum, frame):
+        """
+        Signal handler: do our cleanup, then re-raise
+        the default handler so that exit code / traceback
+        is as expected.
+        """
+        try:
+            # run your atexit-style cleanup
+            self._exit_gmsh()
+        except Exception:
+            # log but don’t block shutdown
+            logger.exception("Error during signal cleanup")
+        finally:
+            # restore default handler and re‐send the signal
+            signal.signal(signum, signal.SIG_DFL)
+            os.kill(os.getpid(), signum)
+
+ 
+    def _initialize_simulation(self):
+        """Initializes the Simulation data and GMSH API with proper shutdown routines.
+        """
+        _GEOMANAGER.sign_in(self.modelname)
+        
+        # If GMSH is not yet initialized (Two simulation in a file)
+        if gmsh.isInitialized() == 0:
+            logger.debug('Initializing GMSH')
+            gmsh.initialize()
+            
+            # Set an exit handler for Ctrl+C cases
+            self._install_signal_handlers()
+
+            # Restier the Exit GMSH function on proper program abortion
+            register(self._exit_gmsh)
+
+        # Create a new GMSH model or load it
+        if not self.load_file:
+            gmsh.model.add(self.modelname)
+            self.data: SimulationDataset = SimulationDataset()
+        else:
+            self.load()
+
+        # Set the Simulation state to active
+        self.__active = True
+        return self
+
+    def _exit_gmsh(self):
+        # If the simulation object state is still active (GMSH is running)
+        if not self.__active:
+            return
+        logger.debug('Exiting program')
+        # Save the file first
+        if self.save_file:
+            self.save()
+        # Finalize GMSH
+        gmsh.finalize()
+        logger.debug('GMSH Shut down successful')
+        # set the state to active
+        self.__active = False
+
+