From 3ef9e7d48b9b19e2df76731ebf329874ca142ad5 Mon Sep 17 00:00:00 2001
From: Craig Warren <craig_warren@me.com>
Date: Tue, 21 Feb 2017 12:35:57 +0000
Subject: [PATCH] Changed solid and rigid array sizes to nx x ny x nz, and all
 field arrays to (nx + 1) x (ny + 1)  x (nz + 1)

---
 gprMax/grid.py | 34 ++++++++++++++++++----------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/gprMax/grid.py b/gprMax/grid.py
index 3868222f..4b7d792e 100644
--- a/gprMax/grid.py
+++ b/gprMax/grid.py
@@ -80,6 +80,9 @@ class FDTDGrid(Grid):
         self.messages = True
         self.tqdmdisable = False
 
+        # CPU - OpenMP threads
+        self.nthreads = 0
+
         # Threshold (dB) down from maximum power (0dB) of main frequency used to calculate highest frequency for disperion analysis
         self.highestfreqthres = 60
         # Maximum allowable percentage physical phase-velocity phase error
@@ -97,11 +100,10 @@ class FDTDGrid(Grid):
         self.dimension = None
         self.iterations = 0
         self.timewindow = 0
-        self.nthreads = 0
-        self.cfs = []
-        
+
         # Ordered dictionary required so that PMLs are always updated in the same order. The order itself does not matter, however, if must be the same from model to model otherwise the numerical precision from adding the PML corrections will be different.
         self.pmlthickness = OrderedDict((key, 10) for key in PML.boundaryIDs)
+        self.cfs = []
         self.pmls = []
 
         self.materials = []
@@ -124,20 +126,20 @@ class FDTDGrid(Grid):
         """Initialise an array for volumetric material IDs (solid); boolean arrays for specifying whether materials can have dielectric smoothing (rigid);
             and an array for cell edge IDs (ID). Solid and ID arrays are initialised to free_space (one); rigid arrays to allow dielectric smoothing (zero).
         """
-        self.solid = np.ones((self.nx + 1, self.ny + 1, self.nz + 1), dtype=np.uint32)
-        self.rigidE = np.zeros((12, self.nx + 1, self.ny + 1, self.nz + 1), dtype=np.int8)
-        self.rigidH = np.zeros((6, self.nx + 1, self.ny + 1, self.nz + 1), dtype=np.int8)
-        self.IDlookup = {'Ex': 0, 'Ey': 1, 'Ez': 2, 'Hx': 3, 'Hy': 4, 'Hz': 5}
+        self.solid = np.ones((self.nx, self.ny, self.nz), dtype=np.uint32)
+        self.rigidE = np.zeros((12, self.nx, self.ny, self.nz), dtype=np.int8)
+        self.rigidH = np.zeros((6, self.nx, self.ny, self.nz), dtype=np.int8)
         self.ID = np.ones((6, self.nx + 1, self.ny + 1, self.nz + 1), dtype=np.uint32)
+        self.IDlookup = {'Ex': 0, 'Ey': 1, 'Ez': 2, 'Hx': 3, 'Hy': 4, 'Hz': 5}
 
     def initialise_field_arrays(self):
         """Initialise arrays for the electric and magnetic field components."""
-        self.Ex = np.zeros((self.nx, self.ny + 1, self.nz + 1), dtype=floattype)
-        self.Ey = np.zeros((self.nx + 1, self.ny, self.nz + 1), dtype=floattype)
-        self.Ez = np.zeros((self.nx + 1, self.ny + 1, self.nz), dtype=floattype)
-        self.Hx = np.zeros((self.nx + 1, self.ny, self.nz), dtype=floattype)
-        self.Hy = np.zeros((self.nx, self.ny + 1, self.nz), dtype=floattype)
-        self.Hz = np.zeros((self.nx, self.ny, self.nz + 1), dtype=floattype)
+        self.Ex = np.zeros((self.nx + 1, self.ny + 1, self.nz + 1), dtype=floattype)
+        self.Ey = np.zeros((self.nx + 1, self.ny + 1, self.nz + 1), dtype=floattype)
+        self.Ez = np.zeros((self.nx + 1, self.ny + 1, self.nz + 1), dtype=floattype)
+        self.Hx = np.zeros((self.nx + 1, self.ny + 1, self.nz + 1), dtype=floattype)
+        self.Hy = np.zeros((self.nx + 1, self.ny + 1, self.nz + 1), dtype=floattype)
+        self.Hz = np.zeros((self.nx + 1, self.ny + 1, self.nz + 1), dtype=floattype)
 
     def initialise_std_update_coeff_arrays(self):
         """Initialise arrays for storing update coefficients."""
@@ -146,9 +148,9 @@ class FDTDGrid(Grid):
 
     def initialise_dispersive_arrays(self):
         """Initialise arrays for storing coefficients when there are dispersive materials present."""
-        self.Tx = np.zeros((Material.maxpoles, self.nx, self.ny + 1, self.nz + 1), dtype=complextype)
-        self.Ty = np.zeros((Material.maxpoles, self.nx + 1, self.ny, self.nz + 1), dtype=complextype)
-        self.Tz = np.zeros((Material.maxpoles, self.nx + 1, self.ny + 1, self.nz), dtype=complextype)
+        self.Tx = np.zeros((Material.maxpoles, self.nx + 1, self.ny + 1, self.nz + 1), dtype=complextype)
+        self.Ty = np.zeros((Material.maxpoles, self.nx + 1, self.ny + 1, self.nz + 1), dtype=complextype)
+        self.Tz = np.zeros((Material.maxpoles, self.nx + 1, self.ny + 1, self.nz + 1), dtype=complextype)
         self.updatecoeffsdispersive = np.zeros((len(self.materials), 3 * Material.maxpoles), dtype=complextype)