diff --git a/MeshGenerator/Partitioner/Partition.c b/MeshGenerator/Partitioner/Partition.c new file mode 100644 index 0000000..e012dd0 --- /dev/null +++ b/MeshGenerator/Partitioner/Partition.c @@ -0,0 +1,50 @@ +#include +#include + + +__declspec(dllexport) int Partition(int ne, int nn, idx_t *eind, int nparts, idx_t *epart) +{ + idx_t nee = ne; + idx_t nnn = nn; + idx_t nnparts = nparts; + // create eptr array of idx_t with the number of elements + 1 + idx_t *eptr = (idx_t *)malloc((ne + 1) * sizeof(idx_t)); + eptr[0] = 0; + int j = 0; + for (int i = 1; i < ne + 1; i++) + { + j += 8; + eptr[i] = j; + } + + + // Create array of idx_t with the number of elements + 1 + idx_t *vwgt = NULL; + idx_t *vsize = NULL; + + // // define the number of common nodes + idx_t ncommon = 1; + + + + + // This is an array of size nparts that specifies the desired weight for each partition. The target partition + // weight for the ith partition is specified at tpwgts[i] (the numbering for the partitions starts from + // 0). The sum of the tpwgts[] entries must be 1.0. + real_t *tpwgts = NULL; + idx_t objval; + + // idx_t options[METIS_NOPTIONS] + idx_t *options = (idx_t *)malloc(METIS_NOPTIONS * sizeof(idx_t)); + METIS_SetDefaultOptions(options); + + // define the partition vector + + // print somthing + idx_t *npart = (idx_t *)malloc(nn * sizeof(idx_t)); + int res= METIS_PartMeshDual(&nee, &nnn, eptr, eind, vwgt, NULL, &ncommon, &nnparts, tpwgts, options, &objval, epart, npart); + return res; +} + + + diff --git a/PML/PML3/Matlabcode/M.txt b/PML/PML3/Matlabcode/M.txt new file mode 100644 index 0000000..807abba --- /dev/null +++ b/PML/PML3/Matlabcode/M.txt @@ -0,0 +1,11 @@ +(a*b*rho*(10*L_PML_x^2 + alpha_0_x*a^2 + 5*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 6*alpha_0_y*b^2 + 15*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(900*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + alpha_0_x*a^2 + 5*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 3*alpha_0_y*b^2 + 10*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(1800*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + 3*alpha_0_x*a^2 + 10*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 3*alpha_0_y*b^2 + 10*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(3600*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + 3*alpha_0_x*a^2 + 10*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 6*alpha_0_y*b^2 + 15*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(1800*L_PML_x^2*L_PML_y^2), 0, 0, 0, 0, + 0, (a*b*rho*(10*L_PML_x^2 + alpha_0_x*a^2 + 5*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 6*alpha_0_y*b^2 + 15*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(900*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + alpha_0_x*a^2 + 5*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 3*alpha_0_y*b^2 + 10*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(1800*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + 3*alpha_0_x*a^2 + 10*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 3*alpha_0_y*b^2 + 10*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(3600*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + 3*alpha_0_x*a^2 + 10*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 6*alpha_0_y*b^2 + 15*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(1800*L_PML_x^2*L_PML_y^2), 0, 0, 0, + (a*b*rho*(10*L_PML_x^2 + alpha_0_x*a^2 + 5*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 3*alpha_0_y*b^2 + 10*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(1800*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + alpha_0_x*a^2 + 5*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + alpha_0_y*b^2 + 5*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(900*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + 3*alpha_0_x*a^2 + 10*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + alpha_0_y*b^2 + 5*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(1800*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + 3*alpha_0_x*a^2 + 10*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 3*alpha_0_y*b^2 + 10*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(3600*L_PML_x^2*L_PML_y^2), 0, 0, 0, 0, + 0, (a*b*rho*(10*L_PML_x^2 + alpha_0_x*a^2 + 5*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 3*alpha_0_y*b^2 + 10*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(1800*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + alpha_0_x*a^2 + 5*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + alpha_0_y*b^2 + 5*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(900*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + 3*alpha_0_x*a^2 + 10*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + alpha_0_y*b^2 + 5*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(1800*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + 3*alpha_0_x*a^2 + 10*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 3*alpha_0_y*b^2 + 10*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(3600*L_PML_x^2*L_PML_y^2), 0, 0, 0, + (a*b*rho*(10*L_PML_x^2 + 3*alpha_0_x*a^2 + 10*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + 3*alpha_0_y*b^2 + 10*alpha_0_y*b*yj + 10*alpha_0_y*yj^2))/(3600*L_PML_x^2*L_PML_y^2), 0, (a*b*rho*(10*L_PML_x^2 + 3*alpha_0_x*a^2 + 10*alpha_0_x*a*xi + 10*alpha_0_x*xi^2)*(10*L_PML_y^2 + alpha_0_y*b^2 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-0.0625 diff --git a/pyVista/meshcreator-Centrifuge.py b/pyVista/meshcreator-Centrifuge.py new file mode 100644 index 0000000..73e39e4 --- /dev/null +++ b/pyVista/meshcreator-Centrifuge.py @@ -0,0 +1,87 @@ +#%% +import numpy as np +import pyvista as pv +import time +#%% +time1 = time.time() +# create a strucrured grid +# xwidth = 500 +# ywidth = 500 +# zwidth = 500 +# eps = 1e-6 + +# Create Davis Centrifuge container +xwidth = 0.6 +ywidth = 1.7 +zwidth = 0.7 +eps = 1e-6 + +# Xmeshsize, Ymeshsize, Zmeshsize = (2.5, 2.5, 2.5) +# Xmeshsize, Ymeshsize, Zmeshsize = (5, 5, 5) + +# Davis Centrifuge container +Xmeshsize, Ymeshsize, Zmeshsize = (0.025, 0.025, 0.025) + +x = np.arange(-xwidth/2., xwidth/2.+eps, Xmeshsize) +y = np.arange(-ywidth/2., ywidth/2.+eps, Ymeshsize) +z = np.arange(-zwidth, 0+eps, Zmeshsize) + +x, y, z = np.meshgrid(x, y, z) + +mesh = pv.StructuredGrid(x, y, z) + + +PMLthickness = 5.0 +PMLXmeshsize, PMLYmeshsize, PMLZmeshsize = (2.5, 2.5, 2.5) + +# Davis centrifuge containes +PMLthickness = 0.07 +PMLXmeshsize, PMLYmeshsize, PMLZmeshsize = (0.035, 0.035, 0.035) + +# sperate PML layer +xmin = -xwidth/2. + PMLthickness +xmax = xwidth/2. - PMLthickness +ymin = -ywidth/2. + PMLthickness +ymax = ywidth/2. - PMLthickness +zmin = -zwidth + PMLthickness +zmax = 0 +cube = pv.Cube(bounds=[xmin,xmax,ymin,ymax,zmin,zmax]) +PML = mesh.clip_box(cube,invert=True,crinkle=True,progress_bar = True) +PML.cell_data["PML"] = np.ones(PML.n_cells,dtype=bool) + + +# seperate regular mesh +reg = mesh.clip_box(cube,invert=False,crinkle=True,progress_bar = True) +reg.cell_data["PML"] = np.zeros(reg.n_cells,dtype=bool) + +numreg = reg.n_cells +numpml = PML.n_cells + +mesh = reg.merge(PML,merge_points=False,tolerance=1e-6,progress_bar = True) +print(mesh.n_cells,mesh.n_points) +mapping = mesh.clean(produce_merge_map=True)["PointMergeMap"] + +regindicies = np.where(mapping[PML.n_points:]0,True,False) +pl = pv.Plotter() +pl.add_mesh(mesh,scalars="boundary",show_edges=True, style="surface", opacity=1.0, color="#2ca02c") +pl.show() + + +# pl.add_mesh(drm, show_edges=False, style="surface", opacity=1.0, color="#2ca02c") + + + +# %% diff --git a/pyVista/meshcreator.py b/pyVista/meshcreator.py new file mode 100644 index 0000000..988c2d4 --- /dev/null +++ b/pyVista/meshcreator.py @@ -0,0 +1,76 @@ +#%% +import numpy as np +import pyvista as pv +import time +#%% +time1 = time.time() +# create a strucrured grid +xwidth = 500 +ywidth = 500 +zwidth = 500 +eps = 1e-6 + +# Xmeshsize, Ymeshsize, Zmeshsize = (2.5, 2.5, 2.5) +Xmeshsize, Ymeshsize, Zmeshsize = (25, 25, 25) + +x = np.arange(-xwidth/2., xwidth/2.+eps, Xmeshsize) +y = np.arange(-ywidth/2., ywidth/2.+eps, Ymeshsize) +z = np.arange(-zwidth, 0+eps, Zmeshsize) + +x, y, z = np.meshgrid(x, y, z) + +mesh = pv.StructuredGrid(x, y, z) + +PMLthickness = 5.0 + +PMLXmeshsize, PMLYmeshsize, PMLZmeshsize = (2.5, 2.5, 2.5) + +# sperate PML layer +xmin = -xwidth/2. + PMLthickness +xmax = xwidth/2. - PMLthickness +ymin = -ywidth/2. + PMLthickness +ymax = ywidth/2. - PMLthickness +zmin = -zwidth + PMLthickness +zmax = 0 +cube = pv.Cube(bounds=[xmin,xmax,ymin,ymax,zmin,zmax]) +PML = mesh.clip_box(cube,invert=True,crinkle=True,progress_bar = True) +PML.cell_data["PML"] = np.ones(PML.n_cells,dtype=bool) + + +# seperate regular mesh +reg = mesh.clip_box(cube,invert=False,crinkle=True,progress_bar = True) +reg.cell_data["PML"] = np.zeros(reg.n_cells,dtype=bool) + +numreg = reg.n_cells +numpml = PML.n_cells + +mesh = reg.merge(PML,merge_points=False,tolerance=1e-6,progress_bar = True) +print(mesh.n_cells,mesh.n_points) +mapping = mesh.clean(produce_merge_map=True)["PointMergeMap"] + + +regindicies = np.where(mapping[PML.n_points:]0,True,False) +pl = pv.Plotter() +pl.add_mesh(mesh,scalars="boundary",show_edges=True,opacity=1.0) +pl.show() +# %% diff --git a/pyVista/postprocess_Stress.py b/pyVista/postprocess_Stress.py new file mode 100644 index 0000000..34075d8 --- /dev/null +++ b/pyVista/postprocess_Stress.py @@ -0,0 +1,207 @@ +# %% +import numpy as np +import pandas as pd +import pyvista as pv +import os +import matplotlib.pyplot as plt +from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor +# ================================================================== +# load nodes and elements dataframes +# ================================================================== +nodes = pd.read_hdf("nodes.h5") +elements = pd.read_hdf("elements.h5") +pv.set_jupyter_backend('client') + +# ================================================================== +# create PML mesh +# ================================================================== +nodes_in_mesh = nodes[nodes['Domain'] == "pml"] +elements_in_mesh = elements[elements['Domain'] == "pml"] +nodetoint = dict(zip(nodes_in_mesh['tag'], range(nodes_in_mesh.shape[0]))) +cells = elements_in_mesh[['node1', 'node2', 'node3', 'node4', 'node5', 'node6', 'node7', 'node8']] +cells = cells.applymap(nodetoint.get) +cells = cells.to_numpy(dtype=int) +points = nodes_in_mesh[['x', 'y', 'z']].to_numpy(dtype=float) +celltypes = np.ones(cells.shape[0],dtype= int) * pv.CellType.HEXAHEDRON +cells = np.insert(cells, 0, 8, axis=1) +pmlgrid = pv.UnstructuredGrid(cells, celltypes.tolist(), points.tolist()) +pmlgrid = pmlgrid.clip_box([-100,100,-100,100,-40, 0 ], invert=False,crinkle=True) +pmlgrid.clear_data() + + +# ================================================================== +# create whole grid mesh +# ================================================================== + +nodes_in_mesh = nodes[nodes['Domain'] == "reg"] +elements_in_mesh = elements[elements['Domain'] == "reg"] +nodetoint = dict(zip(nodes_in_mesh['tag'], range(nodes_in_mesh.shape[0]))) +cells = elements_in_mesh[['node1', 'node2', 'node3', 'node4', 'node5', 'node6', 'node7', 'node8']] +cells = cells.applymap(nodetoint.get) +cells = cells.to_numpy(dtype=int) +points = nodes_in_mesh[['x', 'y', 'z']].to_numpy(dtype=float) +celltypes = np.ones(cells.shape[0],dtype= int) * pv.CellType.HEXAHEDRON +cells = np.insert(cells, 0, 8, axis=1) +grid = pv.UnstructuredGrid(cells, celltypes.tolist(), points.tolist()) + + +# ================================================================== +# create regular mesh +# ================================================================== +indexes = grid.find_cells_within_bounds([-37.4,37.4,-1.25,1.3,-77.4,5.0]) +reg = grid.extract_cells(indexes) + + + +# ================================================================== +# create DRM mesh +# ================================================================== +cube = pv.Cube(center=(0,0,0), x_length=80, y_length=80, z_length=55) +grid = grid.clip_box(cube,invert=False, crinkle=True) +cube = pv.Cube(center=(0,0,0), x_length=75, y_length=75, z_length=47.5) +drm = grid.clip_box(cube,invert=True, crinkle=True) +# indicies = drm.find_cells_within_bounds([-100,100,-1.25,1.3,-80,5.0]) +# drm = drm.extract_cells(indicies) +reg = grid.clip_box(cube,invert=False, crinkle=True) + +# ================================================================== +# create interface mesh +# ================================================================== +data = np.loadtxt("interfaceInfo.dat") +interface = pv.PolyData(data[:,1:4]) + + + +# create pile mesh +# ================================================================== + +zstart = -30 +zend = 20 +x = 0.0 +y = 0.0 +dz = 0.5 +pile = pv.PolyData() +for z in np.arange(zstart,zend,dz): + cube = pv.Cube(center=(x,y,z), x_length=0.5, y_length=0.5, z_length=dz) + pile = pile + cube +pile = pile.clip_box([-100,100,-100,100,-20, 20 ], invert=False,crinkle=True) +pile.clear_data() + + +# create big mass add the head of the pile +mass = pv.Cube(center=(0,0,zend+2.5), x_length=5, y_length=5, z_length=5) +mass = pv.Sphere(center=(0,0,zend+1.5), radius=2.5) + +# set the camera position and width of the view window the same for all plots +# ================================================================== +pl = pv.Plotter(off_screen=False,window_size=[600,600]) +pl.set_background('white') +# pl.set_position([0,0,0]) +# pl.set_window_size(1920,1080) +# pl.set_scale(1,1,1) +# pl.set_focus([0,0,0]) +# pl.camera_position = [(0, 0, 100), (0, 0, 0), (0, 1, 0)] +# pl.camera_set = True +# pl.camera = pl.camera +# pl.camera.zoom(1.5) +# matplotlib default color +# matplot lib defulat colors #1f77b4, #ff7f0e, #2ca02c, #d62728, #9467bd, #8c564b, #e377c2, #7f7f7f, #bcbd22, #17becf + + +pl.add_mesh(reg, show_edges=False, style="surface", opacity=0.7, color="#1f77b4") +pl.add_mesh(drm, show_edges=False, style="surface", opacity=1.0, color="#2ca02c") +pl.add_mesh(pmlgrid, show_edges=False, style="surface", opacity=1.0, color="#ff7f0e") +pl.add_mesh(interface, opacity=1.0, color="red", point_size=5) +pl.add_mesh(pile, show_edges=False, style="surface", opacity=1.0, color="blue") +pl.add_mesh(mass, show_edges=False, style="surface", opacity=1.0, color="blue") +# adding legend +pl.add_legend(labels=[["Soil mesh", "#1f77b4"], ["DRM mesh", "#2ca02c"], ["PML mesh", "#ff7f0e"], ["Interface", "red"], ["Pile", "blue"]], border=True, bcolor="white", size=[0.3,0.3]) +pl.show() + + + +# # %% +# cube = pv.Cube(center=(0,0,30), x_length=20, y_length=20, z_length=60) +# # create a building mesh +# xrng = np.arange(-10, 10, 2.5, dtype=np.float32) +# yrng = np.arange(-10, 10, 2.5, dtype=np.float32) +# zrng = np.arange(0, 60, 5, dtype=np.float32) +# x, y, z = np.meshgrid(xrng, yrng, zrng, indexing='ij') +# cube = pv.StructuredGrid(x, y, z) + +# zrange = np.arange(0, 2.1, 2., dtype=np.float32) +# x,y,z = np.meshgrid(xrng,yrng,zrange,indexing='ij') +# floor =pv.StructuredGrid(x,y,z) + +# pl = pv.Plotter(off_screen=False) +# pl.set_background('white') +# # pl.add_mesh(cube, show_edges=True, style="wireframe", opacity=1.0, color="green", line_width=0.5) +# # pl.add_mesh(reg, show_edges=True, style="surface", opacity=1.0, color="#1f77b4") + +# # make the points of the rego border red + +# # crere columns of the building +# X , Y = np.meshgrid(xrng,yrng,indexing='ij') +# z = [0,55] +# for x in xrng[::2]: +# for y in yrng[::2]: +# clindeer = pv.Cylinder(center=(x,y,55/2.), direction=(0,0,1), radius=0.5, height=55) +# # pl.add_mesh(pv.Line([x,y,z[0]],[x,y,z[1]]), color="blue", line_width=2.0) +# pl.add_mesh(clindeer, show_edges=False, style="surface", opacity=1.0, color="red") + +# for i in range(1,11): +# f = floor.copy() +# f.points[:,2] += 5 + 5 * i +# pl.add_mesh(f, show_edges=False, style="surface", opacity=1.0) + + + +# xrng = np.arange(-60, 40.1, 20, dtype=np.float32) +# yrng = np.arange(-60, 40.1, 20, dtype=np.float32) +# zrng = np.arange(-60, 0.1, 20, dtype=np.float32) +# x, y, z = np.meshgrid(xrng, yrng, zrng, indexing='ij') +# reg = pv.StructuredGrid(x, y, z) +# pl.add_mesh(reg, show_edges=False, style="Surface", opacity=0.25, color="purple",show_vertices=False) +# pl.add_mesh(reg.extract_feature_edges()) +# # shrink the rego mesh +# xrng = np.arange(-30, 10.1, 10, dtype=np.float32) +# yrng = np.arange(-30, 10.1, 10, dtype=np.float32) +# zrng = np.arange(-30, 0.1, 10, dtype=np.float32) +# x, y, z = np.meshgrid(xrng, yrng, zrng, indexing='ij') +# reg2 = pv.StructuredGrid(x, y, z) +# pl.add_mesh(reg2, show_edges=False, style="Surface", opacity=0.5, color="#1f77b4",show_vertices=False,smooth_shading=True, split_sharp_edges=True) +# # show outer boundary +# surf = reg2.extract_surface() +# pl.add_mesh(surf, show_edges=False, style="points", opacity=1.0, color="red", point_size=5) +# pl.enable_ssao(kernel_size=512) + +# # adding legend +# pl.add_legend(labels=[["DRM Boundary", "#1f77b4"], ["HDF5 Container","pink"]], border=False, bcolor="white", size=[0.3,0.3],face="rectangle") + + +# # increase render quality +# pl.enable_eye_dome_lighting() +# pl.renderer.use_depth_peeling=True +# pl.save_graphic("building.pdf") +# pl.screenshot("building.png") +# pl.show() + +# # +# # %% +# #================================================================== +# from pyvista import examples +# structure, air = examples.download_electronics_cooling() +# # view plot +# jpeg = pv.read("build.png") +# # view the plot +# pl = pv.Plotter(off_screen=False) +# pl.add_mesh(reg, show_edges=True, style="surface", opacity=1.0, color="#1f77b4") +# pl.enable_ssao(kernel_size=128) +# pl.show() + + + + +# # %% + +# %% diff --git a/pyVista/scene-export-centrifuge.html b/pyVista/scene-export-centrifuge.html new file mode 100644 index 0000000..f55fe52 --- /dev/null +++ b/pyVista/scene-export-centrifuge.html @@ -0,0 +1,19 @@ + + + + + + + +
+ + + + diff --git a/pyVista/scene-export.html b/pyVista/scene-export.html new file mode 100644 index 0000000..530580a --- /dev/null +++ b/pyVista/scene-export.html @@ -0,0 +1,19 @@ + + + + + + + +
+ + + +