save subgrid fields on each timestep

gprMax/fields_outputs.py

@@ -24,7 +24,7 @@ import h5py
 from ._version import __version__
 
 
-def store_outputs(iteration, Ex, Ey, Ez, Hx, Hy, Hz, G):
+def store_outputs(G):
     """Stores field component values for every receiver and transmission line.
 
     Args:
@@ -35,6 +35,10 @@ def store_outputs(iteration, Ex, Ey, Ez, Hx, Hy, Hz, G):
                     the model.
     """
 
+    iteration = G.iteration
+    #import pdb; pdb.set_trace()
+
+    Ex, Ey, Ez, Hx, Hy, Hz = G.Ex, G.Ey, G.Ez, G.Hx, G.Hy, G.Hz
     for rx in G.rxs:
         for output in rx.outputs:
             # Store electric or magnetic field components

gprMax/grid.py

@@ -151,6 +151,7 @@ class FDTDGrid(Grid):
         self.gpu = None
         self.name = 'Main'
         self.outputdirectory = ''
+        self.iteration = 0
 
     def initialise_geometry_arrays(self):
         """

gprMax/solvers.py

@@ -79,7 +79,8 @@ class Solver:
         """Time step the FDTD model."""
         tsolvestart = timer()
         for iteration in iterator:
-            self.updates.store_outputs(iteration)
+            self.updates.grid.iteration = iteration
+            self.updates.store_outputs()
             self.updates.store_snapshots(iteration)
             self.updates.update_magnetic()
             self.updates.update_magnetic_pml()

gprMax/subgrids/solver.py

@@ -54,12 +54,6 @@ class SubgridUpdates(CPUUpdates):
         for sg_updater in self.updaters:
             sg_updater.hsg_2()
 
-    def store_outputs(self, iteration):
-        super().store_outputs(iteration)
-        """Method to store field outputs for all grid for each main grid iteration."""
-        for updater in self.updaters:
-            updater.store_outputs(iteration)
-
 class SubGridSolver:
     """Solver for subgridding simulations."""
 
@@ -95,8 +89,8 @@ class SubGridSolver:
 
         # The main grid FDTD loop
         for iteration in self.iterations:
-
+            self.updates.grid.iteration = iteration
-            self.updates.store_outputs(iteration)
+            self.updates.store_outputs()
             #self.updates.store_snapshots(iteration)
             self.updates.update_magnetic()
             self.updates.update_magnetic_pml()
@@ -168,6 +162,7 @@ class SubgridUpdater(CPUUpdates):
         for m in range(1, upper_m + 1):
 
             # STD update, interpolate inc. field in time, apply correction
+            self.store_outputs()
             self.update_electric_a()
             self.update_electric_pml()
             precursors.interpolate_magnetic_in_time(int(m + sub_grid.ratio / 2 - 0.5))
@@ -183,6 +178,7 @@ class SubgridUpdater(CPUUpdates):
             sub_grid.update_magnetic_is(precursors)
             self.update_sub_grid_magnetic_sources()
 
+        self.store_outputs()
         self.update_electric_a()
         self.update_electric_pml()
         precursors.calc_exact_magnetic_in_time()
@@ -211,6 +207,7 @@ class SubgridUpdater(CPUUpdates):
             sub_grid.update_magnetic_is(precursors)
             self.update_sub_grid_magnetic_sources()
 
+            self.store_outputs()
             self.update_electric_a()
             self.update_electric_pml()
 
@@ -234,6 +231,7 @@ class SubgridUpdater(CPUUpdates):
             source.update_electric(self.source_iteration, sg.updatecoeffsE, sg.ID,
                                    sg.Ex, sg.Ey, sg.Ez, sg)
         self.source_iteration += 1
+        self.grid.iteration = self.source_iteration
 
     def update_sub_grid_magnetic_sources(self):
         """Update any magnetic sources in the subgrid"""

gprMax/subgrids/updates.py

@@ -1,313 +0,0 @@
-# Copyright (C) 2015-2019: The University of Edinburgh
-#                 Authors: Craig Warren and Antonis Giannopoulos
-#
-# This file is part of gprMax.
-#
-# gprMax 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 3 of the License, or
-# (at your option) any later version.
-#
-# gprMax 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 gprMax.  If not, see <http://www.gnu.org/licenses/>.
-from ..updates import CPUUpdates
-from gprMax.utilities import timer
-from ..cython.fields_updates_normal import update_electric
-from ..cython.fields_updates_normal import update_magnetic
-
-
-def create_subgrid_updates(G):
-    # collection responsible for updating each subgrid
-    updaters = []
-
-    # precursor nodes can use low pass filtering at the IS. Filters are either
-    # on or off for all subgrids
-    if G.subgrids[0].filter:
-        from .precursor_nodes import PrecursorNodesFiltered as PrecursorNodes
-    else:
-        from .precursor_nodes import PrecursorNodes
-
-    # make an updater and precursor nodes for each sub grid
-    for sg in G.subgrids:
-        precursors = PrecursorNodes(G, sg)
-        sgu = SubgridUpdater(sg, precursors, G)
-        updaters.append(sgu)
-
-    # responsible for updating the subgridding simulation as a whole
-    updates = SubgridUpdates(G, updaters)
-
-    return updates
-
-
-class SubgridSolver:
-
-    """Generic solver for Update objects"""
-
-    def __init__(self, updates):
-        """Context for the model to run in. Sub-class this with contexts
-        i.e. an MPI context.
-
-        Args:
-            updates (Updates): updates contains methods to run FDTD algorithm
-            iterator (iterator): can be range() or tqdm()
-        """
-        self.updates = updates
-
-    def get_G(self):
-        return self.updates.grid
-
-    def update_electric_1(self):
-        """Method to update E fields, PML and electric sources"""
-        G = self.get_G()
-        update_electric(G.nx, G.ny, G.nz, G.nthreads, G.updatecoeffsE, G.ID, G.Ex, G.Ey, G.Ez, G.Hx, G.Hy, G.Hz)
-
-        # Update electric field components with the PML correction
-        for pml in G.pmls:
-            pml.update_electric(G)
-        # Update electric field components from sources (update any Hertzian dipole sources last)
-        for source in G.voltagesources + G.transmissionlines + G.hertziandipoles:
-            source.update_electric(G.iteration, G.updatecoeffsE, G.ID, G.Ex, G.Ey, G.Ez, G)
-
-    def update_electric_2(self):
-        return
-
-    def update_magnetic(self):
-        """Method to update H fields, PML and magnetic sources"""
-        # Update magnetic field components
-        G = self.get_G()
-
-        update_magnetic(G.nx, G.ny, G.nz, G.nthreads, G.updatecoeffsH, G.ID, G.Ex, G.Ey, G.Ez, G.Hx, G.Hy, G.Hz)
-
-        # Update magnetic field components with the PML correction
-        for pml in G.pmls:
-            pml.update_magnetic(G)
-
-        # Update magnetic field components from sources
-        for source in G.transmissionlines + G.magneticdipoles:
-            source.update_magnetic(G.iteration, G.updatecoeffsH, G.ID, G.Hx, G.Hy, G.Hz, G)
-
-    def solve(self, iterator):
-        """Time step the FDTD model."""
-        tsolvestart = timer()
-
-        for iteration in iterator:
-            # Update main grid electric field components including sources
-            self.updates.store_outputs(iteration)
-            self.update_electric_1()
-            #self.updates.update_electric_pml()
-            #self.updates.update_electric_sources(iteration)
-            # Update the fields in the subgrids / main grid
-            self.updates.hsg_1()
-            # apply 2nd dispersive update after OS updates
-            #self.updates.update_electric_b()
-            # Update main grid electric field components including sources
-            self.update_magnetic()
-            #self.updates.update_magnetic_pml()
-            #self.updates.update_magnetic_sources(iteration)
-            # Update the fields in the subgrids / main grid
-            self.updates.hsg_2()
-
-        tsolve = timer() - tsolvestart
-        return tsolve
-
-
-class SubgridUpdates(CPUUpdates):
-    """Top level subgrid updater. Manages the collection of subgrids."""
-
-    def __init__(self, G, subgrid_updaters):
-        super().__init__(G)
-        self.subgrid_updaters = subgrid_updaters
-
-    def store_outputs(self, iteration):
-        super().store_outputs(iteration)
-        for updater in self.subgrid_updaters:
-            updater.store_outputs(iteration)
-
-    def hsg_1(self):
-        """Method to update the subgrids over the first phase"""
-        for sg_updater in self.subgrid_updaters:
-            sg_updater.hsg_1()
-
-    def hsg_2(self):
-        """Method to update the subgrids over the second phase"""
-        for sg_updater in self.subgrid_updaters:
-            sg_updater.hsg_2()
-
-    def set_dispersive_updates(self, props):
-        # set the dispersive update functions for the main grid updates
-        super().set_dispersive_updates(props)
-        # set the same dispersive update functions for all fields in the subgrids
-        for updater in self.subgrid_updaters:
-            updater.set_dispersive_updates(props)
-
-
-class SubgridUpdater(CPUUpdates):
-    """Class to handle updating the electric and magnetic fields of an HSG
-    subgrid. The IS, OS, subgrid region and the electric/magnetic sources are updated
-    using the precursor regions.
-    """
-
-    def __init__(self, subgrid, precursors, G):
-        """
-        Args:
-            subgrid (SubGrid3d): Subgrid to be updated
-            precursors (PrecursorNodes): Precursor nodes associated with
-            the subgrid
-            G (class): Grid class instance - holds essential parameters
-            describing the model.
-        """
-        super().__init__(subgrid)
-        self.precursors = precursors
-        self.source_iteration = 0
-        self.G = G
-
-    def update_electric_2(self):
-        return
-
-    def update_electric_1(self):
-        subgrid = self.grid
-        # Update electric field components
-        # All materials are non-dispersive so do standard update
-        update_electric(subgrid.nx, subgrid.ny, subgrid.nz, subgrid.nthreads, subgrid.updatecoeffsE, subgrid.ID, subgrid.Ex, subgrid.Ey, subgrid.Ez, subgrid.Hx, subgrid.Hy, subgrid.Hz)
-
-    def hsg_1(self):
-        G = self.G
-        sub_grid = self.grid
-
-        precursors = self.precursors
-
-        precursors.update_electric()
-
-        upper_m = int(sub_grid.ratio / 2 - 0.5)
-
-        for m in range(1, upper_m + 1):
-
-            # store_outputs(self.grid)
-            # STD update, interpolate inc. field in time, apply correction
-            self.update_electric_1()
-
-            for pml in sub_grid.pmls:
-                pml.update_electric(sub_grid)
-            self.update_sub_grid_electric_sources()
-            precursors.interpolate_magnetic_in_time(int(m + sub_grid.ratio / 2 - 0.5))
-            sub_grid.update_electric_is(precursors)
-            self.update_electric_2()
-
-            # STD update, interpolate inc. field in time, apply correction
-            update_magnetic(sub_grid.nx,
-                            sub_grid.ny,
-                            sub_grid.nz,
-                            G.nthreads,
-                            sub_grid.updatecoeffsH,
-                            sub_grid.ID,
-                            sub_grid.Ex,
-                            sub_grid.Ey,
-                            sub_grid.Ez,
-                            sub_grid.Hx,
-                            sub_grid.Hy,
-                            sub_grid.Hz)
-
-            for pml in sub_grid.pmls:
-                pml.update_magnetic(sub_grid)
-            precursors.interpolate_electric_in_time(m)
-            sub_grid.update_magnetic_is(precursors)
-            self.update_sub_grid_magnetic_sources()
-
-        # store_outputs(self.grid)
-        self.update_electric_1()
-        for pml in sub_grid.pmls:
-            pml.update_electric(sub_grid)
-
-        self.update_sub_grid_electric_sources()
-
-        precursors.calc_exact_magnetic_in_time()
-        sub_grid.update_electric_is(precursors)
-        self.update_electric_2()
-
-        sub_grid.update_electric_os(G)
-
-    def hsg_2(self):
-        G = self.G
-        sub_grid = self.grid
-        precursors = self.precursors
-
-        precursors.update_magnetic()
-
-        upper_m = int(sub_grid.ratio / 2 - 0.5)
-
-        for m in range(1, upper_m + 1):
-
-            update_magnetic(sub_grid.nx,
-                            sub_grid.ny,
-                            sub_grid.nz,
-                            G.nthreads,
-                            sub_grid.updatecoeffsH,
-                            sub_grid.ID,
-                            sub_grid.Ex,
-                            sub_grid.Ey,
-                            sub_grid.Ez,
-                            sub_grid.Hx,
-                            sub_grid.Hy,
-                            sub_grid.Hz)
-
-            for pml in sub_grid.pmls:
-                pml.update_magnetic(sub_grid)
-            precursors.interpolate_electric_in_time(int(m + sub_grid.ratio / 2 - 0.5))
-            sub_grid.update_magnetic_is(precursors)
-
-            self.update_sub_grid_magnetic_sources()
-
-            # store_outputs(self.grid)
-            self.update_electric_1()
-
-            for pml in sub_grid.pmls:
-                pml.update_electric(sub_grid)
-            self.update_sub_grid_electric_sources()
-
-            precursors.interpolate_magnetic_in_time(m)
-            sub_grid.update_electric_is(precursors)
-            self.update_electric_2()
-
-        #sub_grid.update_magnetic_os(G)
-
-        update_magnetic(sub_grid.nx,
-                        sub_grid.ny,
-                        sub_grid.nz,
-                        G.nthreads,
-                        sub_grid.updatecoeffsH,
-                        sub_grid.ID,
-                        sub_grid.Ex,
-                        sub_grid.Ey,
-                        sub_grid.Ez,
-                        sub_grid.Hx,
-                        sub_grid.Hy,
-                        sub_grid.Hz)
-
-        for pml in sub_grid.pmls:
-            pml.update_magnetic(sub_grid)
-
-        precursors.calc_exact_electric_in_time()
-        sub_grid.update_magnetic_is(precursors)
-        self.update_sub_grid_magnetic_sources()
-
-        sub_grid.update_magnetic_os(G)
-
-    def update_sub_grid_electric_sources(self):
-        """Update any electric sources in the subgrid"""
-        sg = self.grid
-        for source in sg.voltagesources + sg.transmissionlines + sg.hertziandipoles:
-            source.update_electric(self.source_iteration, sg.updatecoeffsE, sg.ID, sg.Ex, sg.Ey, sg.Ez, sg)
-
-        self.source_iteration += 1
-
-    def update_sub_grid_magnetic_sources(self):
-        """Update any magnetic sources in the subgrid"""
-        sg = self.grid
-        for source in sg.transmissionlines + sg.magneticdipoles:
-            source.update_magnetic(self.source_iteration, sg.updatecoeffsH, sg.ID,
-                                   sg.Hx, sg.Hy, sg.Hz, sg)

gprMax/subgrids/user_objects.py

@@ -156,6 +156,8 @@ class SubGridHSG(SubGridBase):
                  **kwargs):
         """Constructor."""
 
+        pml_separation = ratio // 2 + 2
+
         # copy over the optional parameters
         kwargs['p1'] = p1
         kwargs['p2'] = p2

gprMax/updates.py

@@ -29,16 +29,9 @@ class CPUUpdates:
         self.dispersive_update_a = None
         self.dispersive_update_b = None
 
-    def store_outputs(self, iteration):
+    def store_outputs(self):
         # Store field component values for every receiver and transmission line
-        store_outputs(iteration,
+        store_outputs(self.grid)
-                      self.grid.Ex,
-                      self.grid.Ey,
-                      self.grid.Ez,
-                      self.grid.Hx,
-                      self.grid.Hy,
-                      self.grid.Hz,
-                      self.grid)
 
     def store_snapshots(self, iteration):
         # Store any snapshots