initial upload

PyLaGriT/examples/arctic_2D/mesh_pylagrit.py

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+from pylagrit import PyLaGriT
+import numpy
+
+# Variables
+nx = 50 # Number of points in x direction
+dy = 0.25 # width of cells in y direction
+distance = 12.34364319 # distance in x direction
+
+l = PyLaGriT()
+
+# Create base layer
+layer = l.create_qua()
+layer.createpts_xyz((nx,2,1),[0.,0.,0.],[distance,dy,0.],rz_switch=[1,1,1],connect=True)
+layer.setatt('itetclr',1)
+layer.minmax_xyz()
+
+# Create top of mesh
+# Collapse y values
+layer.addatt('y_save',vtype='vdouble',rank='scalar')
+layer.copyatt('yic','y_save')
+layer.setatt('yic',0.)
+
+# Read in lidar top elevations
+peat_surf_pts = l.read('surface_coords2.avs')
+peat_surf_pts.addatt('z_save',vtype='vdouble',rank='scalar')
+peat_surf_pts.copyatt('zic','z_save')
+peat_surf_pts.setatt('zic',0.)
+
+# Interpolate surface elevations to layer mo
+layer.addatt('z_val',vtype='vdouble',rank='scalar')
+layer.interpolate_voronoi('z_val',peat_surf_pts,'z_save')
+layer.copyatt('y_save','yic')
+layer.copyatt('z_val','zic')
+
+# Save peat top
+layer.setatt('imt',1)
+layer.setatt('itetclr',1)
+layer.dump('tmp_lay_peat_top.inp')
+peat_surf_pts.delete()
+
+# Read in peat bottom elevations
+peat_bot_pts = l.read('bottom_peat2.avs')
+peat_bot_pts.addatt('z_save',vtype='vdouble',rank='scalar')
+peat_bot_pts.copyatt('zic','z_save')
+peat_bot_pts.setatt('zic',0.)
+
+# Interpolate peat bottom elevations to layer mo
+layer.setatt('yic',0.)
+layer.addatt('z_val',vtype='vdouble',rank='scalar')
+layer.interpolate_voronoi('z_val',peat_bot_pts,'z_save')
+layer.copyatt('y_save','yic')
+layer.delatt('y_save')
+layer.copyatt('z_val','zic')
+layer.delatt('z_val')
+
+# Save peat bot
+layer.dump('tmp_lay_peat_bot.inp')
+
+# Copy layer to peat_bot for use in generating additional layers
+peat_bot = layer.copy()
+
+stack_files = ['tmp_lay_peat_top.inp 1,5']
+stack_files.append('tmp_lay_peat_bot.inp 1,33')
+
+# Layer depths?
+#           1   2   3    4    5    6    7   8    9   10
+layers = [ 1.0, 0.16, 0.32, 0.64, 1.28, 3.2, 6.4, 8.0]
+addnum = [   3,    3,    3,    3,    4,   4,   3,   5]
+matnum = [2]*len(layers) 
+
+layer_interfaces = numpy.cumsum(layers)
+i = 1
+for li,m,a in zip(layer_interfaces,matnum,addnum):
+    layer.math('sub','zic',li,cmosrc=peat_bot)
+    stack_files.append('tmp_lay'+str(i)+'.inp '+str(int(m))+', '+str(a))
+    layer.dump('tmp_lay'+str(i)+'.inp')
+    i += 1
+
+layer.setatt('zic',-45.)
+layer.dump('tmp_lay_bot.inp')
+stack_files.append('tmp_lay_bot.inp 2')
+stack_files.reverse()
+
+# Create stacked layer mesh and fill
+stack = l.create()
+stack.stack_layers(stack_files,file_type='avs',flip_opt=True)
+stack_hex = stack.stack_fill()
+
+# Create boundary facesets, dictionary of PyLaGriT faceset objects is returned
+fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=True,reorder=True)
+
+# Should add this to PyLaGriT, but I'm feeling lazy ;-)
+stack_hex.sendline('quality volume itetclr')
+
+# Write exo file with boundary facesets
+stack_hex.dump_exo('arctic_siteb_2d.exo',facesets=fs.values())
+
+# Write region and faceset identifier file for ats_xml 
+matnames = {10000:'computational domain peat',
+            20000:'computational domain upper mineral'}
+facenames = {1:'bottom face',
+             2:'surface',
+             3:'front',
+             4:'right',
+             5:'back',
+             6:'left'}
+
+stack_hex.dump_ats_xml('arctic_siteb_2d_mesh.xml','/scratch/tundra/dharp/arctic/geophysics/mesh/from_lucia/arctic_siteb_2d.exo',matnames=matnames,facenames=facenames)
+stack_hex.dump_ats_xml('arctic_siteb_2d_par4_mesh.xml','/scratch/tundra/dharp/arctic/geophysics/mesh/from_lucia/arctic_siteb_2d.par',matnames=matnames,facenames=facenames)