Remove shifting of zero frequency component

- Rather than directly shifting the zero frequency component of the fft,
  generate_fractal3D shifts the positional vector of each index as if
  the zero frequency had been shifted to the centre
- Changing generate_fractal3D to do this will make the MPI
  implementation easier

gprMax/cython/fractals_generate.pyx

@@ -72,6 +72,7 @@ cpdef void generate_fractal3D(
     int nz,
     int nthreads,
     float D,
+    np.int32_t[:] global_size,
     np.float64_t[:] weighting,
     np.float64_t[:] v1,
     np.complex128_t[:, :, ::1] A,
@@ -94,14 +95,19 @@ cpdef void generate_fractal3D(
 
     cdef Py_ssize_t i, j, k
     cdef double v2x, v2y, v2z, rr, B
+    cdef int sx, sy, sz
+
+    sx = global_size[0] // 2
+    sy = global_size[1] // 2
+    sz = global_size[2] // 2
 
     for i in prange(nx, nogil=True, schedule='static', num_threads=nthreads):
         for j in range(ny):
             for k in range(nz):
                 # Positional vector for current position
-                v2x = weighting[0] * i
-                v2y = weighting[1] * j
-                v2z = weighting[2] * k
+                v2x = ((weighting[0] * i) + sx) % global_size[0]
+                v2y = ((weighting[1] * j) + sy) % global_size[1]
+                v2z = ((weighting[2] * k) + sz) % global_size[2]
 
                 # Calulate norm of v2 - v1
                 rr = ((v2x - v1[0])**2 + (v2y - v1[1])**2 + (v2z - v1[2])**2)**(1/2)

gprMax/fractals.py

@@ -16,6 +16,8 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
+from typing import Optional
+
 import numpy as np
 from scipy import fftpack
 
@@ -135,7 +137,17 @@ class FractalSurface:
 class FractalVolume:
     """Fractal volumes."""
 
-    def __init__(self, xs, xf, ys, yf, zs, zf, dimension, seed):
+    def __init__(
+        self,
+        xs: int,
+        xf: int,
+        ys: int,
+        yf: int,
+        zs: int,
+        zf: int,
+        dimension: float,
+        seed: Optional[int],
+    ):
         """
         Args:
             xs, xf, ys, yf, zs, zf: floats for the extent of the fractal volume.