initial upload

PyLaGriT/examples/ideas_mesh/ideas_mesh.py

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+import optparse
+import shutil, distutils.dir_util, os, sys, glob
+
+import numpy
+import math
+import matplotlib.pyplot as plt
+from pylagrit import PyLaGriT
+
+#
+#  Create parser and options
+#
+p = optparse.OptionParser()
+p.add_option('--dem-file', help='DEM data file name including path', type='string', dest='dem_filename' )
+p.add_option('--exo-file', help='Exodus II mesh output including path', type='string', dest='exo_filename')
+p.add_option('--dry-run', help='Show commands and diagnostics but no execution', default=False, dest='dry_run', action='store_true')
+p.add_option('--plot', help='Show commands and diagnostics but no execution', default=False, dest='plot', action='store_true')
+#
+(opts,args) = p.parse_args()
+
+print(opts.dem_filename)
+print(opts.dry_run)
+
+# Input: DEM data
+dem_file_fullname=opts.dem_filename
+dem_file_noext, dem_file_ext=os.path.splitext(opts.dem_filename)
+dem_file_base=os.path.basename(opts.dem_filename).rstrip(dem_file_ext)
+dem_file_path=os.path.dirname(opts.dem_filename)
+
+# Output: Exodus II mesh
+exo_file_fullname=opts.exo_filename
+exo_file_noext, exo_file_ext=os.path.splitext(opts.exo_filename)
+exo_file_base=os.path.basename(opts.exo_filename).rstrip(exo_file_ext)
+exo_file_path=os.path.dirname(opts.exo_filename)
+
+# Output: XML region specifications for the new mesh
+xml_file_fullname=exo_file_path+exo_file_base+'.xml'
+
+# DEM parsing
+# 
+with open(dem_file_fullname) as dem_header:
+    for line in dem_header:
+        if ("ncols" in line):
+            nx=int(line.split()[1])
+        elif ("nrows" in line):
+            ny=int(line.split()[1])
+        elif ("xllcorner" in line):
+            xll_corner=float(line.split()[1])
+        elif ("yllcorner" in line):
+            yll_corner=float(line.split()[1])
+        elif ("cellsize" in line):
+            dx=float(line.split()[1])
+            dy=dx
+        elif ("NODATA_value" in line):
+            no_data_value=int(line.split()[1])
+            break
+
+print(nx, ny, xll_corner, yll_corner, dx, dy, no_data_value)
+dem_header.close()
+
+d = numpy.flipud(numpy.genfromtxt(dem_file_fullname,skip_header=6))
+#plt.matshow(d)
+
+# Create mesh based on ncols and nrows in file, could automatically read
+x = numpy.linspace(xll_corner,dx*(nx-1),nx)
+y = numpy.linspace(yll_corner,dy*(ny-1),ny)
+
+x=numpy.arange(xll_corner,dx*nx,dx)
+y=numpy.arange(yll_corner,dy*ny,dy)
+
+xx, yy = numpy.meshgrid(x,y)
+
+# Write avs file
+fh = open(dem_file_base+'.avs','w')
+# Find number of data values and write avs header
+N = numpy.where(numpy.isnan(d)==False)[0].shape[0]
+fh.write(str(N)+' 0 0 0 0\n')
+# Collect data into avs format
+# JDM:  Not sure if this should be nx*ny? 
+davs = numpy.zeros([nx*ny,4])
+ind = 0
+for i,row in enumerate(d):
+    for j,v in enumerate(row):
+        davs[ind,:] = [ind + 1, xx[i,j], yy[i,j], v]
+        ind += 1
+# Write data to avs file 
+numpy.savetxt(fh,davs,fmt=['%4d','%.1lf','%.1lf','%.8lf'])   
+fh.close()
+
+# Crank up pylagrit
+lg = PyLaGriT()
+# Read in elevations in avs fromat
+m = lg.read(dem_file_base+'.avs')
+# Take a look, change paraview exe
+# Will need to use glyph filter to view points
+#m.paraview(exe='paraview')
+
+# Copy z values over to attribute
+m.addatt('z_save',vtype='vdouble',rank='scalar')
+m.copyatt('zic','z_save')
+# Not sure why this has to be done, but not data elements don't get removed otherwise
+m.setatt('zic',0.)
+
+# Create connected quad mesh surface
+m2 = lg.create()
+#m2.createpts_xyz((nx,ny,1),[xx.min(),yy.min(),0.],[xx.max(),yy.max(),0],rz_switch=[1,1,1],connect=True)
+m2.createpts_xyz((nx,ny,1),[xx.min(),yy.min(),0.],[xx.max(),yy.max(),0],rz_switch=[1,1,1])
+# Create temporary z value attribute
+m2.addatt('z_save',vtype='vdouble',rank='scalar')
+# Interpolate elevations to z_save
+m2.interpolate_voronoi('z_save',m,'z_save')
+# Find nodes associated with nodata
+pdel = m2.pset_attribute('z_save',-9999)
+# Create element set from these nodes and remove elements
+edel = pdel.eltset()
+m2.rmpoint_eltset(edel)
+# Copy temp z values over to actual a values
+#m2.copyatt('z_save','zic')
+# Take a look to make sure everything is ok
+#m2.paraview(exe='paraview')
+
+
+
+m3 = m2.copypts(elem_type='triplane')
+m3.connect()
+# To lazy to add to pylagrit now, and don't know how to make it intuitive
+# Creates edge_max element attribute containing max edge length
+m3.sendline('quality/edge_max/y')
+# Query created attribute
+#m3.printatt('edgemax')
+m3.minmax('edgemax')
+# Figure out max desired edge length
+max_edge = numpy.sqrt(dx**2+dy**2)
+# Identify elements with longer edges
+edel = m3.eltset_attribute('edgemax',max_edge*2.05,'gt')
+m3.rmpoint_eltset(edel)
+
+#m3 = m2.grid2grid_quadtotri2()
+#m3=m2
+# Create temporary z value attribute
+m3.addatt('z_save',vtype='vdouble',rank='scalar')
+# Interpolate elevations to z_save
+m3.interpolate_voronoi('z_save',m,'z_save')
+
+# Find nodes associated with nodata
+pdel = m3.pset_attribute('z_save',-9999)
+# Create element set from these nodes and remove elements
+edel = pdel.eltset()
+m3.rmpoint_eltset(edel)
+# Copy temp z values over to actual a values
+m3.copyatt('z_save','zic')
+# Take a look to make sure everything is ok
+#m2.paraview(exe='paraview')
+
+# Create top surface avs
+m3.dump('top.inp')
+## Subtract 1 from z values of top and dump into bottom surface avs
+m3.math('sub',1,'zic',cmosrc=m3)
+m3.dump('mid.inp')
+m3.setatt('zic',0.0)
+m3.dump('bot.inp')
+
+# Stack the layers in a new mesh object
+stack = lg.create()
+stack.stack_layers('avs',['bot.inp 1','mid.inp 1,3','top.inp 1,0'],flip_opt=True)
+stack_hex = stack.stack_fill()
+# Automatically create face sets based on normal vectors and layer id
+#fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=True)
+#fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=False)
+# Diagnostic
+#stack_hex.sendline('quality volume itetclr')
+
+# Write exo file with boundary facesets
+#stack_hex.dump_exo(exo_file_fullname,facesets=fs.values())
+stack_hex.dump_exo(exo_file_fullname)
+
+# Write region and faceset identifier file for ats_xml
+matnames = {10000:'computational domain peat'}
+facenames = {1:'bottom face',
+             2:'surface',
+             3:'front',
+             4:'right',
+             5:'back',
+             6:'left'}
+
+# Dump ats style xml for mesh, can provide options for other schemas easily also
+#stack_hex.dump_ats_xml(xml_file_fullname,exo_file_fullname,matnames=matnames,facenames=facenames)
+stack_hex.dump_ats_xml(xml_file_fullname,exo_file_fullname,matnames=matnames,facenames=facenames)
+
+# Take a look
+if opts.plot: 
+    stack_hex.paraview(exe='/Applications/paraview.app/Contents/MacOS/paraview')
+
+
+