def main(argv=None):
if argv == None:
argv = sys.argv
parser = argparse.ArgumentParser(description = "Convert Modflow to Amanzi")
parser.add_argument("-p", "--pfile", help="name of parameter file", default=PARAMETER_FILE)
parser.add_argument("-v", "--view", help="view in Paraview", action="store_true", default = False)
args = parser.parse_args()
PFILE = args.pfile
VIEW_IN_PARAVIEW = args.view
# Initialize LaGriT
l = PyLaGriT()
# Load parameters file & check for missing values
params = load_params(PFILE)
verify_params(params)
# Assign parameters to variables
input_bnds = params['input_bnds']
export_name = params['export_name']
nrows = int(params['nrows'])
ncols = int(params['ncols'])
llcorner = [float(params['minx']),float(params['miny'])]
D_XY=[float(params['dx']),float(params['dy'])]
# IBND and IMAT materials properties
ibnd = {"active": int(params['ibnd_active']), "noflow": int(params['ibnd_noflow']),\
"head": int(params['ibnd_head']), "edge": int(params['ibnd_edge']), "halite": int(params['ibnd_halite'])}
imat = {"active": int(params['imat_active']), "noflow": int(params['imat_noflow']),\
"head": int(params['imat_head']), "edge": int(params['imat_edge']), "halite": int(params['imat_halite'])}
# Cycle through these keys instead of dictionary to preserve sequence
mat_keys = ['active','noflow','head','edge','halite']
fs_bottom = int(params['fs_bottom'])
fs_top = int(params['fs_top'])
fs_east = int(params['fs_east'])
fs_north = int(params['fs_north'])
fs_west = int(params['fs_west'])
fs_south = int(params['fs_south'])
fs_halite = int(params['fs_halite'])
fs_head = int(params['fs_head'])
fs_noflow = int(params['fs_noflow'])
rmmat_edge = int(params['rmmat_edge'])
maxmat = int(params['maxmat'])
EXO_FILE=params['exo_file']
# Generate hexmesh with cell-centered materials and optional elevation
hexmesh = l.read_modflow(input_bnds, nrows, ncols, DXY=D_XY, name=MESH_NAME)
# Eltset stuff
for i, key in enumerate(mat_keys):
hexmesh.eltset_attribute("mod_bnds", ibnd[key], boolstr='eq', name="e{}".format(i+1))
hexmesh.setatt("itetclr",imat[key],stride=["eltset","get","e{}".format(i+1)])
l.sendline('cmo/select/{}'.format(hexmesh.name)) # tmp ---------------------------------------------------
# Remove edge cells
hexmesh.eltset_attribute("itetclr",rmmat_edge,boolstr='eq',name="eremove") # Find edge cells
hexmesh.rmpoint_eltset("eremove") # Remove edge cells
hexmesh.rmpoint_compress(filter_bool=False, resetpts_itp=True) # compress and reset
# Temp facesets for internal side interfaces
mo_sides = l.extract_surfmesh(name="mo_sides",cmo_in=hexmesh,stride=[1,0,0],append='-all-',reorder=False,resetpts_itp=False)
l.sendline("cmo/select/mo_sides")
# Create psets from attributes 1 & 2
ptop = mo_sides.pset_attribute("pts_topbot",2,comparison='eq',stride=(1,0,0),name="ptop")
pbot = mo_sides.pset_attribute("pts_topbot",1,comparison='eq',stride=(1,0,0),name="pbot")
# Generate eltsets from psets
etop = ptop.eltset(membership='exclusive',name='etop')
ebot = pbot.eltset(membership='exclusive',name='ebot')
# Create a single eltset from the above two & remove
e_delete = mo_sides.eltset_bool([etop,ebot],boolstr='union',name='e_delete')
mo_sides.rmpoint_eltset("e_delete",compress=True,resetpts_itp=False)
# NOFLOW faces (west corner)
mo_tmp = l.copy(mo_sides, name="mo_tmp")
edel = mo_tmp.eltset_attribute("itetclr0",imat["noflow"],boolstr='ne',name='edel')
mo_tmp.rmpoint_eltset("edel",compress=True,resetpts_itp=True)
mo_fs1 = l.copy(mo_tmp,name="mo_fs1")
mo_tmp.delete()
# Halite faces (eastern curve)
mo_tmp = l.copy(mo_sides,name="mo_tmp")
l.sendline("cmo/select/mo_tmp")
edel = mo_tmp.eltset_attribute("itetclr0",imat["halite"],boolstr='ne',name='edel')
mo_tmp.rmpoint_eltset("edel",compress=True,resetpts_itp=True)
mo_fs2 = l.copy(mo_tmp,name="mo_fs2")
mo_tmp.delete()
mo_sides.delete()
l.sendline("cmo/select/{}".format(hexmesh.name))
edel = hexmesh.eltset_attribute("itetclr",maxmat,boolstr='gt',name='edel')
hexmesh.rmpoint_eltset("edel",compress=True,resetpts_itp=True)
# Final facesets for cropped mesh
mo_surf = l.extract_surfmesh(name="mo_surf",cmo_in=hexmesh,stride=[1,0,0],append='external',reorder=False,resetpts_itp=False)
mo_surf.addatt("id_normal",vtype='vint',rank='scalar',length='nelements',interpolate='',persistence='',ioflag='',value='')
mo_surf.addatt("id_tmp",vtype='vint',rank='scalar',length='nelements',interpolate='',persistence='',ioflag='',value='')
l.sendline("cmo/select/mo_surf")
mo_surf.settets(method='normal')
mo_surf.copyatt('itetclr',attname_sink='id_normal',mo_src=mo_surf)
# Tag top and bottom face sets
ptop = mo_surf.pset_attribute("pts_topbot",2,comparison='eq',stride=(1,0,0),name="ptop")
pbot = mo_surf.pset_attribute("pts_topbot",1,comparison='eq',stride=(1,0,0),name="pbot")
etop = ptop.eltset(membership='exclusive',name='etop')
ebot = pbot.eltset(membership='exclusive',name='ebot')
mo_surf.setatt("itetclr",2,stride=["eltset","get","etop"])
mo_surf.setatt("itetclr",1,stride=["eltset","get","ebot"])
mo_fs1.setatt("itetclr",1)
mo_surf.setatt("id_tmp",0)
mo_surf.interpolate('map','id_tmp',mo_fs1,'itetclr',stride=[1,0,0])
etmp = mo_surf.eltset_attribute('id_tmp',1,boolstr='eq',name='etmp')
mo_surf.setatt('itetclr',fs_noflow,stride=['eltset','get','etmp'])
etmp.delete()
# Interface between material 1 and halite and head cells
mo_fs2.setatt('itetclr',1)
mo_surf.setatt('id_tmp',0)
mo_surf.interpolate('map','id_tmp',mo_fs2,'itetclr',stride=[1,0,0])
etmp = mo_surf.eltset_attribute('id_tmp',1,boolstr='eq',name='etmp')
mo_surf.setatt('itetclr',fs_halite,stride=['eltset','get','etmp'])
etmp.delete()
mo_surf.addatt('id_side',vtype='VINT',rank='scalar',length='nelements',interpolate='',persistence='',ioflag='',value='')
mo_surf.copyatt('itetclr',attname_sink='id_side',mo_src=mo_surf)
# Check for continuous connected boundary of 1
mo_chk = l.copy(mo_surf,name='mo_chk')
l.boundary_components(style='element',reset=False)
mo_chk.delete()
# Make sure to remove all attributes except idelem1 and idface1
bad_atts = ['id_normal','itetclr0','idnode0','idelem0','facecol','itetclr1','idface0','id_tmp','ncon50','nconbnd','icontab']
for att in bad_atts:
mo_surf.delatt(att)
l.sendline("cmo/select/mo_surf")
filenames = ['bottom','top','east','north','west','south','head','noflow']
ss_ids = [1,2,3,4,5,6,7,8]
# WRITE ALL FACESET FILES
for i in range(0,len(ss_ids)):
l.sendline('define/FILENAME/fs_{}.faceset'.format(filenames[i]))
l.sendline('define/SS_ID/{}'.format(ss_ids[i]))
write_fs_file(l)
#hexmesh.dump_exo(EXO_FILE,facesets=['fs_bottom.faceset','fs_top.faceset','fs_east.faceset'])
l.sendline('dump / exo / {} / {} / / / facesets &\n fs_bottom.faceset fs_top.faceset fs_east.faceset &\n fs_north.faceset fs_west.faceset fs_south.faceset &\n fs_head.faceset fs_noflow.faceset'.format(EXO_FILE, hexmesh.name))
hexmesh.dump_avs2(export_name)
if (VIEW_IN_PARAVIEW == True):
hexmesh.paraview()
# y = np.arange(0,yl/2+dy,dy) #quarter-model
y = np.arange(0,yl+dy,dy) #quarter-model
z = np.arange(-zl, 0.+dz, dz)
# z = np.concatenate((np.arange(-zl/2.,0+dz,dz), np.arange(dz,zl/2+dz,dz)))
mins = np.array([min(x), min(y), min(z)])
maxs = np.array([max(x), max(y), max(z)])
# m = l.gridder(telx,y,z,connect=True) #refines toward fracture plane
m = l.gridder(telx,y,z,connect=False) #refines toward fracture plane #NEW
m.setatt('imt',2) #matrix nodes material set to '2'
l.sendline('filter / 1 0 0 /; rmpoint compress')
l.sendline('cmo printatt mo1 -all- minmax')
m.connect()
m.setatt('imt',2) #matrix nodes material set to '2'
#----------------------------------------------------------------------
# FRACTURE PLANE
#----------------------------------------------------------------------
fmins = np.array([min(x),min(y),min(z)])
