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https://gitee.com/sunhf/gprMax.git
已同步 2025-08-06 12:36:51 +08:00
hdf5 xdmf support
这个提交包含在：
jasminium
@@ -19,13 +19,14 @@
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import sys
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import numpy as np
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from struct import pack
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from gprMax.xdmf import write_output_file
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from gprMax.utilities import round_value
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class GeometryView:
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"""Views of the geometry of the model."""
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if sys.byteorder == 'little':
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byteorder = 'LittleEndian'
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else:
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@@ -39,7 +40,7 @@ class GeometryView:
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filename (str): Filename to save to.
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type (str): Either 'n' for a per cell geometry view, or 'f' for a per cell edge geometry view.
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"""
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self.xs = xs
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self.ys = ys
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self.zs = zs
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@@ -55,26 +56,30 @@ class GeometryView:
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self.filename = filename
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self.type = type
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def write_xdmf(self, modelrun, numbermodelruns, G):
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filename = self.filename[:-4]
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write_output_file(filename, G)
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def write_vtk(self, modelrun, numbermodelruns, G):
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"""Writes the geometry information to a VTK file. Either ImageData (.vti) for a per-cell geometry view, or PolygonalData (.vtp) for a per-cell-edge geometry view.
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N.B. No Python 3 support for VTK at time of writing (03/2015)
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Args:
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modelrun (int): Current model run number.
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numbermodelruns (int): Total number of model runs.
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G (class): Grid class instance - holds essential parameters describing the model.
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"""
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# Construct filename from user-supplied name and model run number
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if numbermodelruns == 1:
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self.filename = G.inputdirectory + self.filename
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else:
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self.filename = G.inputdirectory + self.filename + str(modelrun)
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if self.type == 'n':
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self.filename += '.vti'
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# Calculate number of cells according to requested sampling for geometry view
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self.vtk_xscells = round_value(self.xs / self.dx)
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self.vtk_xfcells = round_value(self.xf / self.dx)
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@@ -85,16 +90,16 @@ class GeometryView:
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self.vtk_nxcells = self.vtk_xfcells - self.vtk_xscells
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self.vtk_nycells = self.vtk_yfcells - self.vtk_yscells
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self.vtk_nzcells = self.vtk_zfcells - self.vtk_zscells
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# Create an array and add numeric IDs for PML, sources and receivers
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self.srcs_rxs_pml = np.zeros((G.nx + 1, G.ny + 1, G.nz + 1), dtype=np.int8)
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for pml in G.pmls:
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self.srcs_rxs_pml[pml.xs:pml.xf, pml.ys:pml.yf, pml.zs:pml.zf] = 1
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for index, srcrx in enumerate(G.rxs + G.hertziandipoles + G.magneticdipoles + G.voltagesources + G.transmissionlines):
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self.srcs_rxs_pml[srcrx.xcoord, srcrx.ycoord, srcrx.zcoord] = index + 2
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vtk_srcs_rxs_pml_offset = round_value((np.dtype(np.uint32).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells) + np.dtype(np.uint32).itemsize)
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with open(self.filename, 'wb') as f:
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f.write('<?xml version="1.0"?>\n'.encode('utf-8'))
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f.write('<VTKFile type="ImageData" version="1.0" byte_order="{}">\n'.format(GeometryView.byteorder).encode('utf-8'))
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@@ -105,7 +110,7 @@ class GeometryView:
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f.write('<DataArray type="Int8" Name="Sources_Receivers_PML" format="appended" offset="{}" />\n'.format(vtk_srcs_rxs_pml_offset).encode('utf-8'))
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f.write('</CellData>\n'.encode('utf-8'))
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f.write('</Piece>\n</ImageData>\n<AppendedData encoding="raw">\n_'.encode('utf-8'))
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# Write material IDs
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datasize = int(np.dtype(np.uint32).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells)
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# Write number of bytes of appended data as UInt32
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@@ -114,7 +119,7 @@ class GeometryView:
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for j in range(self.ys, self.yf, self.dy):
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for i in range(self.xs, self.xf, self.dx):
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f.write(pack('I', G.solid[i, j, k]))
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# Write source/receiver IDs
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datasize = int(np.dtype(np.int8).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells)
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f.write(pack('I', datasize))
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@@ -124,34 +129,34 @@ class GeometryView:
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f.write(pack('b', self.srcs_rxs_pml[i, j, k]))
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f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8'))
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self.write_gprmax_info(f, G)
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elif self.type == 'f':
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self.filename += '.vtp'
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vtk_numpoints = (self.nx + 1) * (self.ny + 1) * (self.nz + 1)
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vtk_numpoint_components = 3
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vtk_numlines = 2 * self.nx * self.ny + 2 * self.ny * self.nz + 2 * self.nx * self.nz + 3 * self.nx * self.ny * self.nz + self.nx + self.ny + self.nz
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vtk_numline_components = 2;
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vtk_connectivity_offset = round_value((vtk_numpoints * vtk_numpoint_components * np.dtype(np.float32).itemsize) + np.dtype(np.uint32).itemsize)
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vtk_offsets_offset = round_value(vtk_connectivity_offset + (vtk_numlines * vtk_numline_components * np.dtype(np.uint32).itemsize) + np.dtype(np.uint32).itemsize)
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vtk_materials_offset = round_value(vtk_offsets_offset + (vtk_numlines * np.dtype(np.uint32).itemsize) + np.dtype(np.uint32).itemsize)
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with open(self.filename, 'wb') as f:
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f.write('<?xml version="1.0"?>\n'.encode('utf-8'))
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f.write('<VTKFile type="PolyData" version="1.0" byte_order="{}">\n'.format(GeometryView.byteorder).encode('utf-8'))
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f.write('<PolyData>\n<Piece NumberOfPoints="{}" NumberOfVerts="0" NumberOfLines="{}" NumberOfStrips="0" NumberOfPolys="0">\n'.format(vtk_numpoints, vtk_numlines).encode('utf-8'))
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f.write('<Points>\n<DataArray type="Float32" NumberOfComponents="3" format="appended" offset="0" />\n</Points>\n'.encode('utf-8'))
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f.write('<Lines>\n<DataArray type="UInt32" Name="connectivity" format="appended" offset="{}" />\n'.format(vtk_connectivity_offset).encode('utf-8'))
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f.write('<DataArray type="UInt32" Name="offsets" format="appended" offset="{}" />\n</Lines>\n'.format(vtk_offsets_offset).encode('utf-8'))
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f.write('<CellData Scalars="Material">\n'.encode('utf-8'))
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f.write('<DataArray type="UInt32" Name="Material" format="appended" offset="{}" />\n'.format(vtk_materials_offset).encode('utf-8'))
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f.write('</CellData>\n'.encode('utf-8'))
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f.write('</Piece>\n</PolyData>\n<AppendedData encoding="raw">\n_'.encode('utf-8'))
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# Write points
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@@ -209,7 +214,7 @@ class GeometryView:
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for j in range(self.ys, self.yf + 1):
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for k in range(self.zs, self.zf + 1):
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f.write(pack('I', G.ID[0, i, j, k]))
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for i in range(self.xs, self.xf + 1):
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for j in range(self.ys, self.yf):
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for k in range(self.zs, self.zf + 1):
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@@ -227,7 +232,7 @@ class GeometryView:
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def write_gprmax_info(self, f, G, materialsonly=False):
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"""Writes gprMax specific information relating material, source, and receiver names to numeric identifiers.
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Args:
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f (filehandle): VTK file.
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G (class): Grid class instance - holds essential parameters describing the model.
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@@ -42,7 +42,7 @@ from gprMax.yee_cell_build import build_electric_components, build_magnetic_comp
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def main():
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"""This is the main function for gprMax."""
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# Print gprMax logo, version, and licencing/copyright information
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logo(gprMax.__version__ + ' (Bowmore)')
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@@ -59,7 +59,7 @@ def main():
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numbermodelruns = args.n
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inputdirectory = os.path.dirname(os.path.abspath(args.inputfile)) + os.sep
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inputfile = inputdirectory + os.path.basename(args.inputfile)
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# Create a separate namespace that users can access in any Python code blocks in the input file
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usernamespace = {'c': c, 'e0': e0, 'm0': m0, 'z0': z0, 'number_model_runs': numbermodelruns, 'inputdirectory': inputdirectory}
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@@ -92,7 +92,7 @@ def main():
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def run_std_sim(args, numbermodelruns, inputfile, usernamespace, optparams=None):
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"""Run standard simulation - models are run one after another and each model is parallelised with OpenMP
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Args:
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args (dict): Namespace with command line arguments
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numbermodelruns (int): Total number of model runs.
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@@ -100,7 +100,7 @@ def run_std_sim(args, numbermodelruns, inputfile, usernamespace, optparams=None)
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usernamespace (dict): Namespace that can be accessed by user in any Python code blocks in input file.
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optparams (dict): Optional argument. For Taguchi optimisation it provides the parameters to optimise and their values.
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"""
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tsimstart = perf_counter()
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for modelrun in range(1, numbermodelruns + 1):
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if optparams: # If Taguchi optimistaion, add specific value for each parameter to optimise for each experiment to user accessible namespace
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@@ -117,20 +117,20 @@ def run_std_sim(args, numbermodelruns, inputfile, usernamespace, optparams=None)
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def run_benchmark_sim(args, inputfile, usernamespace):
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"""Run standard simulation in benchmarking mode - models are run one after another and each model is parallelised with OpenMP
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Args:
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args (dict): Namespace with command line arguments
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inputfile (str): Name of the input file to open.
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usernamespace (dict): Namespace that can be accessed by user in any Python code blocks in input file.
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"""
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# Number of threads to test - start from max physical CPU cores and divide in half until 1
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thread = psutil.cpu_count(logical=False)
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threads = [thread]
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while not thread%2:
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thread /= 2
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threads.append(int(thread))
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benchtimes = np.zeros(len(threads))
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numbermodelruns = len(threads)
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@@ -150,7 +150,7 @@ def run_benchmark_sim(args, inputfile, usernamespace):
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def run_mpi_sim(args, numbermodelruns, inputfile, usernamespace, optparams=None):
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"""Run mixed mode MPI/OpenMP simulation - MPI task farm for models with each model parallelised with OpenMP
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Args:
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args (dict): Namespace with command line arguments
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numbermodelruns (int): Total number of model runs.
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@@ -180,7 +180,7 @@ def run_mpi_sim(args, numbermodelruns, inputfile, usernamespace, optparams=None)
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data = comm.recv(source=MPI.ANY_SOURCE, tag=MPI.ANY_TAG, status=status)
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source = status.Get_source()
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tag = status.Get_tag()
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if tag == tags.READY.value: # Worker is ready, so send it a task
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if modelrun < numbermodelruns + 1:
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comm.send(modelrun, dest=source, tag=tags.START.value)
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@@ -188,10 +188,10 @@ def run_mpi_sim(args, numbermodelruns, inputfile, usernamespace, optparams=None)
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modelrun += 1
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else:
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comm.send(None, dest=source, tag=tags.EXIT.value)
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elif tag == tags.DONE.value:
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print('Worker {}: completed.'.format(source))
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elif tag == tags.EXIT.value:
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print('Worker {}: exited.'.format(source))
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closedworkers += 1
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@@ -202,7 +202,7 @@ def run_mpi_sim(args, numbermodelruns, inputfile, usernamespace, optparams=None)
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comm.send(None, dest=0, tag=tags.READY.value)
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modelrun = comm.recv(source=0, tag=MPI.ANY_TAG, status=status) # Receive a model number to run from the master
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tag = status.Get_tag()
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# Run a model
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if tag == tags.START.value:
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if optparams: # If Taguchi optimistaion, add specific value for each parameter to optimise for each experiment to user accessible namespace
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@@ -212,10 +212,10 @@ def run_mpi_sim(args, numbermodelruns, inputfile, usernamespace, optparams=None)
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modelusernamespace.update({'optparams': tmp})
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else:
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modelusernamespace = usernamespace
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run_model(args, modelrun, numbermodelruns, inputfile, modelusernamespace)
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comm.send(None, dest=0, tag=tags.DONE.value)
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elif tag == tags.EXIT.value:
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break
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@@ -224,34 +224,34 @@ def run_mpi_sim(args, numbermodelruns, inputfile, usernamespace, optparams=None)
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def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
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"""Runs a model - processes the input file; builds the Yee cells; calculates update coefficients; runs main FDTD loop.
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Args:
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args (dict): Namespace with command line arguments
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modelrun (int): Current model run number.
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numbermodelruns (int): Total number of model runs.
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inputfile (str): Name of the input file to open.
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usernamespace (dict): Namespace that can be accessed by user in any Python code blocks in input file.
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Returns:
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tsolve (int): Length of time (seconds) of main FDTD calculations
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"""
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# Monitor memory usage
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p = psutil.Process()
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print('\n{}\n\nModel input file: {}\n'.format(68*'*', inputfile))
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# Add the current model run to namespace that can be accessed by user in any Python code blocks in input file
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usernamespace['current_model_run'] = modelrun
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print('Constants/variables available for Python scripting: {}\n'.format(usernamespace))
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# Process any user input Python commands
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processedlines = process_python_include_code(inputfile, usernamespace)
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# Write a file containing the input commands after Python blocks have been processed
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if args.write_processed:
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write_processed_file(inputfile, modelrun, numbermodelruns, processedlines)
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# Check validity of command names & that essential commands are present
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singlecmds, multicmds, geometry = check_cmd_names(processedlines)
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@@ -284,7 +284,7 @@ def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
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# Build the PML and calculate initial coefficients
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build_pmls(G)
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# Build the model, i.e. set the material properties (ID) for every edge of every Yee cell
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tbuildstart = perf_counter()
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build_electric_components(G.solid, G.rigidE, G.ID, G)
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@@ -295,7 +295,7 @@ def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
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# Process any voltage sources (that have resistance) to create a new material at the source location
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for voltagesource in G.voltagesources:
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voltagesource.create_material(G)
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# Initialise arrays of update coefficients to pass to update functions
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G.initialise_std_updatecoeff_arrays()
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@@ -309,22 +309,22 @@ def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
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print('ID\tName\t\tProperties')
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print('{}'.format('-'*50))
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for material in G.materials:
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# Calculate update coefficients for material
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material.calculate_update_coeffsE(G)
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material.calculate_update_coeffsH(G)
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# Store all update coefficients together
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G.updatecoeffsE[material.numID, :] = material.CA, material.CBx, material.CBy, material.CBz, material.srce
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G.updatecoeffsH[material.numID, :] = material.DA, material.DBx, material.DBy, material.DBz, material.srcm
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# Store coefficients for any dispersive materials
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if Material.maxpoles != 0:
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z = 0
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for pole in range(Material.maxpoles):
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G.updatecoeffsdispersive[material.numID, z:z+3] = e0 * material.eqt2[pole], material.eqt[pole], material.zt[pole]
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z += 3
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if G.messages:
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if material.deltaer and material.tau:
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tmp = 'delta_epsr={}, tau={} secs; '.format(', '.join('{:g}'.format(deltaer) for deltaer in material.deltaer), ', '.join('{:g}'.format(tau) for tau in material.tau))
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@@ -340,7 +340,7 @@ def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
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resolution = dispersion_check(G)
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if resolution != 0 and max((G.dx, G.dy, G.dz)) > resolution:
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print('\nWARNING: Potential numerical dispersion in the simulation. Check the spatial discretisation against the smallest wavelength present. Suggested resolution should be less than {:g}m'.format(resolution))
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# Write files for any geometry views
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if not G.geometryviews and args.geometry_only:
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raise GeneralError('No geometry views found.')
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@@ -348,16 +348,17 @@ def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
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tgeostart = perf_counter()
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for geometryview in G.geometryviews:
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geometryview.write_vtk(modelrun, numbermodelruns, G)
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geometryview.write_xdmf(modelrun, numbermodelruns, G)
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tgeoend = perf_counter()
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print('\nGeometry file(s) written in [HH:MM:SS]: {}'.format(datetime.timedelta(seconds=int(tgeoend - tgeostart))))
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# Run simulation if not doing only geometry
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if not args.geometry_only:
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# Prepare any snapshot files
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for snapshot in G.snapshots:
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snapshot.prepare_vtk_imagedata(modelrun, numbermodelruns, G)
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# Adjust position of sources and receivers if required
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if G.srcstepx > 0 or G.srcstepy > 0 or G.srcstepz > 0:
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for source in itertools.chain(G.hertziandipoles, G.magneticdipoles, G.voltagesources, G.transmissionlines):
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@@ -396,10 +397,10 @@ def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
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for timestep in range(G.iterations):
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if timestep == 0:
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tstepstart = perf_counter()
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# Write field outputs to file
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||||
write_hdf5(f, timestep, G.Ex, G.Ey, G.Ez, G.Hx, G.Hy, G.Hz, G)
|
||||
|
||||
|
||||
# Write any snapshots to file
|
||||
for snapshot in G.snapshots:
|
||||
if snapshot.time == timestep + 1:
|
||||
@@ -432,7 +433,7 @@ def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
|
||||
|
||||
# Increment absolute time value
|
||||
abstime += 0.5 * G.dt
|
||||
|
||||
|
||||
# Update magnetic field components
|
||||
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)
|
||||
|
||||
@@ -447,7 +448,7 @@ def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
|
||||
|
||||
# Increment absolute time value
|
||||
abstime += 0.5 * G.dt
|
||||
|
||||
|
||||
# Calculate time for two iterations, used to estimate overall runtime
|
||||
if timestep == 1:
|
||||
tstepend = perf_counter()
|
||||
@@ -457,7 +458,7 @@ def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
|
||||
sys.stdout.flush()
|
||||
elif timestep > 1:
|
||||
update_progress((timestep + 1) / G.iterations)
|
||||
|
||||
|
||||
# Close output file
|
||||
f.close()
|
||||
|
||||
|
||||
@@ -22,10 +22,33 @@ import matplotlib.pyplot as plt
|
||||
from gprMax.constants import c, floattype, complextype
|
||||
from gprMax.materials import Material
|
||||
|
||||
class Grid():
|
||||
|
||||
class FDTDGrid:
|
||||
def __init__(self, grid):
|
||||
self.nx = grid.shape[0]
|
||||
self.ny = grid.shape[1]
|
||||
self.nz = grid.shape[2]
|
||||
self.grid = grid
|
||||
|
||||
def n_edges(self):
|
||||
l = self.nx
|
||||
m = self.ny
|
||||
n = self.nz
|
||||
e = (l * m * (n - 1)) + (m * n * (l - 1)) + (l * n * (m - 1))
|
||||
return e
|
||||
|
||||
def n_nodes(self):
|
||||
return self.nx * self.ny * self.nz
|
||||
|
||||
def n_cells(self):
|
||||
return (self.nx - 1) * (self.ny - 1) * (self.nz - 1)
|
||||
|
||||
def get(self, i, j, k):
|
||||
return self.grid[i, j, k]
|
||||
|
||||
class FDTDGrid(Grid):
|
||||
"""Holds attributes associated with the entire grid. A convenient way for accessing regularly used parameters."""
|
||||
|
||||
|
||||
def __init__(self):
|
||||
self.inputdirectory = ''
|
||||
self.title = ''
|
||||
@@ -61,7 +84,7 @@ class FDTDGrid:
|
||||
self.rxstepz = 0
|
||||
self.rxs = []
|
||||
self.snapshots = []
|
||||
|
||||
|
||||
def initialise_std_arrays(self):
|
||||
"""Initialise an array for volumetric material IDs (solid); boolean arrays for specifying whether materials can have dielectric smoothing (rigid);
|
||||
an array for cell edge IDs (ID); and arrays for the electric and magnetic field components. Solid and ID arrays are initialised to free_space (one); rigid arrays
|
||||
@@ -78,7 +101,7 @@ class FDTDGrid:
|
||||
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)
|
||||
|
||||
|
||||
def initialise_std_updatecoeff_arrays(self):
|
||||
"""Initialise arrays for storing update coefficients."""
|
||||
self.updatecoeffsE = np.zeros((len(self.materials), 5), dtype=floattype)
|
||||
@@ -94,25 +117,25 @@ class FDTDGrid:
|
||||
|
||||
def dispersion_check(G):
|
||||
"""Check for potential numerical dispersion. Is the smallest wavelength present in the simulation discretised by at least a factor of 10
|
||||
|
||||
|
||||
Args:
|
||||
G (class): Grid class instance - holds essential parameters describing the model.
|
||||
|
||||
|
||||
Returns:
|
||||
resolution (float): Potential numerical dispersion
|
||||
"""
|
||||
|
||||
|
||||
# Minimum number of spatial steps to resolve smallest wavelength
|
||||
resolvedsteps = 10
|
||||
|
||||
|
||||
# Find maximum frequency
|
||||
maxfreqs = []
|
||||
for waveform in G.waveforms:
|
||||
|
||||
|
||||
# User-defined waveform
|
||||
if waveform.uservalues is not None:
|
||||
waveformvalues = waveform.uservalues
|
||||
|
||||
|
||||
# Built-in waveform
|
||||
else:
|
||||
time = np.linspace(0, 1, G.iterations)
|
||||
@@ -130,24 +153,24 @@ def dispersion_check(G):
|
||||
|
||||
# Shift powers so that frequency with maximum power is at zero decibels
|
||||
power -= np.amax(power)
|
||||
|
||||
|
||||
# Set maximum frequency to -60dB from maximum power
|
||||
freq = np.where((np.amax(power[1::]) - power[1::]) > 60)[0][0] + 1
|
||||
maxfreqs.append(freqs[freq])
|
||||
|
||||
if maxfreqs:
|
||||
maxfreq = max(maxfreqs)
|
||||
|
||||
|
||||
# Find minimum wavelength
|
||||
ers = [material.er for material in G.materials]
|
||||
maxer = max(ers)
|
||||
|
||||
# Minimum velocity
|
||||
minvelocity = c / np.sqrt(maxer)
|
||||
|
||||
|
||||
# Minimum wavelength
|
||||
minwavelength = minvelocity / maxfreq
|
||||
|
||||
|
||||
# Resolution of minimum wavelength
|
||||
resolution = minwavelength / resolvedsteps
|
||||
|
||||
@@ -159,10 +182,10 @@ def dispersion_check(G):
|
||||
|
||||
def get_other_directions(direction):
|
||||
"""Return the two other directions from x, y, z given a single direction
|
||||
|
||||
|
||||
Args:
|
||||
direction (str): Component x, y or z
|
||||
|
||||
|
||||
Returns:
|
||||
(tuple): Two directions from x, y, z
|
||||
"""
|
||||
@@ -174,7 +197,7 @@ def get_other_directions(direction):
|
||||
|
||||
def Ix(x, y, z, Hy, Hz, G):
|
||||
"""Calculates the x-component of current at a grid position.
|
||||
|
||||
|
||||
Args:
|
||||
x, y, z (float): Coordinates of position in grid.
|
||||
Hy, Hz (memory view): numpy array of magnetic field values.
|
||||
@@ -184,14 +207,14 @@ def Ix(x, y, z, Hy, Hz, G):
|
||||
if y == 0 or z == 0:
|
||||
Ix = 0
|
||||
return Ix
|
||||
|
||||
|
||||
else:
|
||||
Ix = G.dy * (Hy[x, y, z - 1] - Hy[x, y, z]) + G.dz * (Hz[x, y, z] - Hz[x, y - 1, z])
|
||||
return Ix
|
||||
|
||||
def Iy(x, y, z, Hx, Hz, G):
|
||||
"""Calculates the y-component of current at a grid position.
|
||||
|
||||
|
||||
Args:
|
||||
x, y, z (float): Coordinates of position in grid.
|
||||
Hx, Hz (memory view): numpy array of magnetic field values.
|
||||
@@ -201,14 +224,14 @@ def Iy(x, y, z, Hx, Hz, G):
|
||||
if x == 0 or z == 0:
|
||||
Iy = 0
|
||||
return Iy
|
||||
|
||||
|
||||
else:
|
||||
Iy = G.dx * (Hx[x, y, z] - Hx[x, y, z - 1]) + G.dz * (Hz[x - 1, y, z] - Hz[x, y, z])
|
||||
return Iy
|
||||
|
||||
def Iz(x, y, z, Hx, Hy, G):
|
||||
"""Calculates the z-component of current at a grid position.
|
||||
|
||||
|
||||
Args:
|
||||
x, y, z (float): Coordinates of position in grid.
|
||||
Hx, Hy (memory view): numpy array of magnetic field values.
|
||||
@@ -218,7 +241,7 @@ def Iz(x, y, z, Hx, Hy, G):
|
||||
if x == 0 or y == 0:
|
||||
Iz = 0
|
||||
return Iz
|
||||
|
||||
|
||||
else:
|
||||
Iz = G.dx * (Hx[x, y - 1, z] - Hx[x, y, z]) + G.dy * (Hy[x, y, z] - Hy[x - 1, y, z])
|
||||
return Iz
|
||||
|
||||
361
gprMax/xdmf.py
普通文件
361
gprMax/xdmf.py
普通文件
@@ -0,0 +1,361 @@
|
||||
import numpy as np
|
||||
import h5py
|
||||
from lxml import etree
|
||||
from gprMax.grid import Grid
|
||||
import copy
|
||||
|
||||
class Edges:
|
||||
|
||||
def __init__(self, grid):
|
||||
|
||||
"""
|
||||
Class to define some connectivity of for an n x l x m
|
||||
grid
|
||||
"""
|
||||
self.total_edges = grid.n_edges()
|
||||
self.edges = np.zeros((self.total_edges, 2), np.float32)
|
||||
self.edge_count = 0
|
||||
self.grid = grid
|
||||
"""
|
||||
Adds the the edge specified by in_node and the i,j,k position of the outnode
|
||||
"""
|
||||
def add_edge(self, in_label, i, j, k):
|
||||
|
||||
out_label = self.grid.get(i, j, k)
|
||||
self.edges[self.edge_count] = np.array([in_label, out_label])
|
||||
self.edge_count += 1
|
||||
|
||||
class Coordinates:
|
||||
|
||||
def __init__(self, grid):
|
||||
self.total_coordinates = grid.nx * grid.ny * grid.nz
|
||||
self.coordinate_count = 0
|
||||
self.coordinates = np.zeros((self.total_coordinates, 3), np.float32)
|
||||
|
||||
def add_coordinate(self, x, y, z):
|
||||
self.coordinates[self.coordinate_count] = np.array([x, y, z])
|
||||
self.coordinate_count += 1
|
||||
|
||||
def hexCellPicker(grid, i, j, k):
|
||||
"""
|
||||
This is the ordering of nodes in the hexahedron cell.
|
||||
|
||||
7 --------- 6
|
||||
/ /|
|
||||
4 --------- 5 2
|
||||
| 3 | /
|
||||
| / |/
|
||||
0 --------- 1
|
||||
|
||||
0 1 2 3 4 5 6 7
|
||||
"""
|
||||
|
||||
cell = [
|
||||
grid[i][j][k],
|
||||
# 1
|
||||
grid[i + 1][j][k],
|
||||
# 2
|
||||
grid[i + 1][j + 1][k],
|
||||
# 3
|
||||
grid[i][j + 1][k],
|
||||
# 4
|
||||
grid[i][j][k + 1],
|
||||
# 5
|
||||
grid[i + 1][j][k + 1],
|
||||
# 6
|
||||
grid[i + 1][j + 1][k + 1],
|
||||
# 7
|
||||
grid[i][j + 1][k + 1]
|
||||
]
|
||||
|
||||
return cell
|
||||
|
||||
class Solids:
|
||||
|
||||
def __init__(self, fdtd_grid):
|
||||
self.count = 0
|
||||
self.fdtd_grid = fdtd_grid
|
||||
self.total_solids = fdtd_grid.n_cells()
|
||||
self.solids = np.zeros((self.total_solids), np.float32)
|
||||
|
||||
def add_solid(self, i, j, k):
|
||||
|
||||
self.solids[self.count] = self.fdtd_grid.solid[i][j][k]
|
||||
self.count += 1
|
||||
|
||||
class SolidLabels():
|
||||
|
||||
def __init__(self, label_grid):
|
||||
self.count = 0
|
||||
self.label_grid = label_grid
|
||||
self.total_solids = label_grid.n_cells()
|
||||
self.solid_labels = np.zeros((self.total_solids, 8), np.float32)
|
||||
|
||||
def add(self, i, j, k):
|
||||
|
||||
solid_labels = hexCellPicker(self.label_grid.grid, i, j, k)
|
||||
self.solid_labels[self.count] = solid_labels
|
||||
self.count += 1
|
||||
|
||||
|
||||
class Materials:
|
||||
|
||||
def __init__(self, fdtd_grid):
|
||||
self.fdtd_grid = fdtd_grid
|
||||
self.n_edges = fdtd_grid.n_edges()
|
||||
self.materials = np.zeros((self.n_edges), np.float32)
|
||||
self.material_count = 0
|
||||
|
||||
# direction x->0 y->1 z->2
|
||||
def add_material(self, i, j, k, direction):
|
||||
|
||||
material = self.fdtd_grid.ID[direction, i, j, k]
|
||||
self.materials[self.material_count] = material
|
||||
|
||||
self.material_count += 1
|
||||
|
||||
def process_grid(fdtd_grid):
|
||||
|
||||
# Dimensions of the problem domain.
|
||||
nx = fdtd_grid.nx
|
||||
ny = fdtd_grid.ny
|
||||
nz = fdtd_grid.nz
|
||||
|
||||
# label each node in the space
|
||||
labels = np.arange(nx * ny * nz).reshape(nx, ny, nz)
|
||||
|
||||
label_grid = Grid(labels)
|
||||
|
||||
# Edges define the connectivity of the grid.
|
||||
edges = Edges(label_grid)
|
||||
|
||||
# Material for each edge
|
||||
edge_materials = Materials(fdtd_grid)
|
||||
|
||||
# Define coordinates for each node
|
||||
coordinates = Coordinates(fdtd_grid)
|
||||
|
||||
# Material for each solid
|
||||
solids = Solids(fdtd_grid)
|
||||
|
||||
# Connectivity for hexhahedron grid
|
||||
solid_labels = SolidLabels(label_grid)
|
||||
|
||||
i_max = nx - 1
|
||||
j_max = ny - 1
|
||||
k_max = nz - 1
|
||||
|
||||
for i, ix in enumerate(labels):
|
||||
for j, jx in enumerate(ix):
|
||||
for k, kx in enumerate(jx):
|
||||
|
||||
label = labels[i][j][k]
|
||||
|
||||
# Each vertex can have varying numbers of edges
|
||||
|
||||
# Type 1 vertex
|
||||
if i < i_max and j < j_max and k < k_max:
|
||||
edges.add_edge(label, i + 1, j, k)
|
||||
edges.add_edge(label, i, j + 1, k)
|
||||
edges.add_edge(label, i, j, k + 1)
|
||||
|
||||
edge_materials.add_material(i, j, k, 0)
|
||||
edge_materials.add_material(i, j, k, 1)
|
||||
edge_materials.add_material(i, j, k, 2)
|
||||
|
||||
# Only this node can support a cell
|
||||
solids.add_solid(i, j, k)
|
||||
solid_labels.add(i, j, k)
|
||||
|
||||
# Type 2 vertex
|
||||
elif i < i_max and j == j_max and k == k_max:
|
||||
edges.add_edge(label, i + 1, j, k)
|
||||
edge_materials.add_material(i, j, k, 0)
|
||||
|
||||
# Type 7 vertex
|
||||
elif i < i_max and j == j_max and k < k_max:
|
||||
edges.add_edge(label, i + 1, j, k)
|
||||
edges.add_edge(label, i, j, k + 1)
|
||||
edge_materials.add_material(i, j, k, 0)
|
||||
edge_materials.add_material(i, j, k, 2)
|
||||
|
||||
# Type 6 vertex
|
||||
elif i == i_max and j == j_max and k < k_max:
|
||||
edges.add_edge(label, i, j, k + 1)
|
||||
edge_materials.add_material(i, j, k, 2)
|
||||
|
||||
# Type 5 vertex
|
||||
elif i == i_max and j < j_max and k < k_max:
|
||||
edges.add_edge(label, i, j, k + 1)
|
||||
edges.add_edge(label, i, j + 1, k)
|
||||
edge_materials.add_material(i, j, k, 2)
|
||||
edge_materials.add_material(i, j, k, 1)
|
||||
|
||||
# Type 4 vertex
|
||||
elif i == i_max and j < j_max and k == k_max:
|
||||
edges.add_edge(label, i, j + 1, k)
|
||||
edge_materials.add_material(i, j, k, 1)
|
||||
|
||||
# Type 8 vertex
|
||||
elif i < i_max and j < j_max and k == k_max:
|
||||
edges.add_edge(label, i, j + 1, k)
|
||||
edges.add_edge(label, i + 1, j, k)
|
||||
edge_materials.add_material(i, j, k, 1)
|
||||
edge_materials.add_material(i, j, k, 0)
|
||||
|
||||
# Type 3 vertex
|
||||
# Has no new connectivity
|
||||
elif i == i_max and j == j_max and k == k_max:
|
||||
pass
|
||||
else:
|
||||
print('oh no')
|
||||
|
||||
# Add the coordinates
|
||||
coordinates.add_coordinate(i, j, k)
|
||||
|
||||
#x = np.arange(fdtd_grid.nx)
|
||||
#y = np.arange(fdtd_grid.ny)
|
||||
#z = np.arange(fdtd_grid.nz)
|
||||
|
||||
return {
|
||||
'coordinates': coordinates,
|
||||
'solids': solids,
|
||||
'solid_labels': solid_labels,
|
||||
'edges': edges,
|
||||
'edge_materials': edge_materials,
|
||||
#'x': x,
|
||||
#'y': y,
|
||||
#'z': z
|
||||
}
|
||||
|
||||
def write_output_file(filename, grid):
|
||||
|
||||
data = process_grid(grid)
|
||||
data['filename'] = filename
|
||||
data['xml_doc'] = create_xdmf_markup(data)
|
||||
|
||||
write_H5file(data)
|
||||
write_xml_doc(data)
|
||||
|
||||
def write_xml_doc(options):
|
||||
#write xml to file
|
||||
with open(options['filename'] + '.xdmf', 'wb') as xdmf_f:
|
||||
xdmf_f.write(options['xml_doc'])
|
||||
|
||||
def write_H5file(options):
|
||||
|
||||
f = h5py.File(options['filename'] + '.h5', "w")
|
||||
coords = f.create_group("mesh")
|
||||
coords.create_dataset('coordinates', data=options['coordinates'].coordinates)
|
||||
coords.create_dataset('connectivity', data=options['edges'].edges)
|
||||
coords.create_dataset('solid_connectivity', data=options['solid_labels'].solid_labels)
|
||||
#coords.create_dataset('x', data=options['x'])
|
||||
#coords.create_dataset('y', data=options['y'])
|
||||
#coords.create_dataset('z', data=options['z'])
|
||||
data = f.create_group("data")
|
||||
data.create_dataset('materials', data=options['edge_materials'].materials)
|
||||
data.create_dataset('solids', data=options['solids'].solids)
|
||||
|
||||
def create_xdmf_markup(options):
|
||||
|
||||
# Write the XDMF markup for edge style grid
|
||||
xdmf_el = etree.Element("Xdmf", Version="2.0")
|
||||
|
||||
domain_el = etree.Element("Domain")
|
||||
xdmf_el.append(domain_el)
|
||||
|
||||
grid_el = etree.Element("Grid", Name="Edges", GridType="Uniform")
|
||||
domain_el.append(grid_el)
|
||||
|
||||
# Create the grid node
|
||||
topology_el = etree.Element("Topology", TopologyType="Polyline", NumberOfElements=str(options['edges'].total_edges))
|
||||
grid_el.append(topology_el)
|
||||
|
||||
topology_dimensions = "{} 2".format(options['edges'].total_edges)
|
||||
top_data_el = etree.Element("DataItem", Dimensions=topology_dimensions, NumberType="Float", Precision="8", Format="HDF")
|
||||
top_data_el.text = "{}:/mesh/connectivity".format(options['filename'] + '.h5')
|
||||
topology_el.append(top_data_el)
|
||||
|
||||
# Create the Geometry node
|
||||
geometry_el = etree.Element("Geometry", GeometryType="XYZ")
|
||||
grid_el.append(geometry_el)
|
||||
|
||||
# Create the origin coordinates
|
||||
coordinates_dimensions = "{} 3".format(options['coordinates'].total_coordinates)
|
||||
origin_el = etree.Element("DataItem", Dimensions=coordinates_dimensions, NumberType="Float", Precision="8", Format="HDF")
|
||||
origin_el.text = "{}:/mesh/coordinates".format(options['filename'] + '.h5')
|
||||
geometry_el.append(origin_el)
|
||||
|
||||
# Create the materials attribute
|
||||
attr_el = etree.Element("Attribute", Center="Cell", Name="Edge_Materials")
|
||||
grid_el.append(attr_el)
|
||||
|
||||
materials_dimensions = "{} 1".format(options['edge_materials'].material_count)
|
||||
materials_el = etree.Element("DataItem", Dimensions=materials_dimensions, NumberType="Float", Precision="8", Format="HDF")
|
||||
materials_el.text = "{}:/data/materials".format(options['filename'] + '.h5')
|
||||
attr_el.append(materials_el)
|
||||
|
||||
"""
|
||||
# VOXEL style markup
|
||||
v_grid_el = etree.Element("Grid", Name="Voxel", GridType="Uniform")
|
||||
domain_el.append(v_grid_el)
|
||||
|
||||
noe = "{} {} {}".format(options['x'].size, options['y'].size, options['y'].size)
|
||||
v_topology_el = etree.Element("Topology", TopologyType="3DRectMesh", NumberOfElements=noe)
|
||||
v_grid_el.append(v_topology_el)
|
||||
|
||||
v_geometry = etree.Element("Geometry", GeometryType="VXVYVZ")
|
||||
v_grid_el.append(v_geometry)
|
||||
|
||||
d1 = etree.Element("DataItem", Dimensions=str(options['x'].size), NumberType="Float", Precision="4", Format="HDF")
|
||||
d1.text = "{}:/mesh/x".format(options['filename'] + '.h5')
|
||||
v_geometry.append(d1)
|
||||
|
||||
d2 = etree.Element("DataItem", Dimensions=str(options['y'].size), NumberType="Float", Precision="4", Format="HDF")
|
||||
d2.text = "{}:/mesh/y".format(options['filename'] + '.h5')
|
||||
v_geometry.append(d2)
|
||||
|
||||
d3 = etree.Element("DataItem", Dimensions=str(options['z'].size), NumberType="Float", Precision="4", Format="HDF")
|
||||
d3.text = "{}:/mesh/z".format(options['filename'] + '.h5')
|
||||
v_geometry.append(d3)
|
||||
|
||||
v_attr = etree.Element("Attribute", Name="material-blocks", Center="Cell")
|
||||
v_grid_el.append(v_attr)
|
||||
|
||||
d4 = etree.Element("DataItem", Format="HDF", NumberType="Float", Precision="4", Dimensions=str(options['solids'].solids.size))
|
||||
d4.text = "{}:/data/solids".format(options['filename'] + '.h5')
|
||||
v_attr.append(d4)
|
||||
|
||||
"""
|
||||
|
||||
v_grid_el = etree.Element("Grid", Name="Voxel", GridType="Uniform")
|
||||
domain_el.append(v_grid_el)
|
||||
|
||||
n_solids = str(options['solids'].solids.size)
|
||||
v_topology_el = etree.Element("Topology", TopologyType="Hexahedron", NumberOfElements=str(options['solids'].solids.size))
|
||||
v_grid_el.append(v_topology_el)
|
||||
|
||||
solid_label_d = "{} {}".format(n_solids, 8)
|
||||
solid_labels_el = etree.Element("DataItem", Dimensions=solid_label_d, Format="HDF")
|
||||
solid_labels_el.text = "{}:/mesh/solid_connectivity".format(options['filename'] + '.h5')
|
||||
v_topology_el.append(solid_labels_el)
|
||||
|
||||
# Same geometry as edges
|
||||
v_grid_el.append(copy.deepcopy(geometry_el))
|
||||
|
||||
v_attr = etree.Element("Attribute", Name="Voxel_Materials", Center="Cell")
|
||||
v_grid_el.append(v_attr)
|
||||
|
||||
d4 = etree.Element("DataItem", Format="HDF", NumberType="Float", Precision="4", Dimensions=str(options['solids'].solids.size))
|
||||
d4.text = "{}:/data/solids".format(options['filename'] + '.h5')
|
||||
v_attr.append(d4)
|
||||
|
||||
# Define a doctype - useful for parsers
|
||||
doc_type = '<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>'
|
||||
|
||||
# Serialize elements
|
||||
xml_doc = etree.tostring(xdmf_el, xml_declaration=True,
|
||||
encoding="utf-8", doctype=doc_type, pretty_print=True)
|
||||
|
||||
return xml_doc
|
||||
|
||||
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