def plane(cfg):
import sys,os
from math import sqrt
from utilities import geo2utm
import start as start
#
#
cubit = start.start_cubit()
#
#
command = "reset"
cubit.cmd(command)
#
#
for p in [cfg.x1,cfg.x2,cfg.x3,cfg.x4]:
x_current,y_current=geo2utm(p[0],p[1],cfg.unit)
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( p[2] )
cubit.cmd(cubitcommand)
#
cubitcommand= 'create surface vertex 1 2 3 4'
cubit.cmd(cubitcommand)
command = "del vertex all"
cubit.cmd(command)
command = "save as 'plane.cub' overwrite"
cubit.cmd(command)
#
#
#
cubit.cmd("set info "+cfg.cubit_info)
cubit.cmd("set echo "+cfg.echo_info)
cubit.cmd("set journal "+cfg.jou_info)
def process_surfacefiles(iproc, nx, ny, nstep, grdfile, unit, lat_orientation):
from utilities import geo2utm
numpy = start.start_numpy()
elev = numpy.zeros([nx, ny], float)
coordx = numpy.zeros([nx, ny], float)
coordy = numpy.zeros([nx, ny], float)
icoord = 0
lat_orientation = check_orientation(grdfile)
try:
grdfile = open(grdfile, 'r')
# print 'reading ',grdfile
except:
txt = 'error reading: ' + str(grdfile)
raise Exception(txt)
if lat_orientation is 'SOUTH2NORTH':
rangey = range(0, ny)
else:
rangey = range(ny - 1, -1, -1)
lat_orientation = 'NORTH2SOUTH'
print lat_orientation
for iy in rangey:
for ix in range(0, nx):
txt = grdfile.readline()
try:
if len(txt) != 0:
x, y, z = map(float, txt.split())
if iy % nstep == 0 and ix % nstep == 0:
icoord = icoord + 1
x_current, y_current = geo2utm(x, y, unit)
jx = min(nx - 1, ix / nstep)
jy = min(ny - 1, iy / nstep)
coordx[jx, jy] = x_current
coordy[jx, jy] = y_current
elev[jx, jy] = z
except:
print 'error reading point ', iy * nx + ix, txt, \
grdfile.name, ' proc '
raise NameError('error reading point')
if (nx) * (ny) != icoord:
if iproc == 0:
print 'error in the surface file ' + grdfile.name
if iproc == 0:
print 'x points ' + str(nx) + ' y points ' + str(ny) + \
' tot points ' + str((nx) * (ny))
if iproc == 0:
print 'points read in ' + grdfile.name + ': ' + str(icoord)
raise NameError
grdfile.close()
return coordx, coordy, elev
def process_surfacefiles(iproc, nx, ny, nstep, grdfile, unit, lat_orientation):
from utilities import geo2utm
numpy = start.start_numpy()
elev = numpy.zeros([nx, ny], float)
coordx = numpy.zeros([nx, ny], float)
coordy = numpy.zeros([nx, ny], float)
icoord = 0
lat_orientation = check_orientation(grdfile)
try:
grdfile = open(grdfile, 'r')
# print 'reading ',grdfile
except:
txt = 'error reading: ' + str(grdfile)
raise Exception(txt)
if lat_orientation is 'SOUTH2NORTH':
rangey = range(0, ny)
else:
rangey = range(ny - 1, -1, -1)
lat_orientation = 'NORTH2SOUTH'
print lat_orientation
for iy in rangey:
for ix in range(0, nx):
txt = grdfile.readline()
try:
if len(txt) != 0:
x, y, z = map(float, txt.split())
if iy % nstep == 0 and ix % nstep == 0:
icoord = icoord + 1
x_current, y_current = geo2utm(x, y, unit)
jx = min(nx - 1, ix / nstep)
jy = min(ny - 1, iy / nstep)
coordx[jx, jy] = x_current
coordy[jx, jy] = y_current
elev[jx, jy] = z
except:
print 'error reading point ', iy * nx + ix, txt, \
grdfile.name, ' proc '
raise NameError('error reading point')
if (nx) * (ny) != icoord:
if iproc == 0:
print 'error in the surface file ' + grdfile.name
if iproc == 0:
print 'x points ' + str(nx) + ' y points ' + str(ny) + \
' tot points ' + str((nx) * (ny))
if iproc == 0:
print 'points read in ' + grdfile.name + ': ' + str(icoord)
raise NameError
grdfile.close()
return coordx, coordy, elev
def create_line_v(ind,n,n2,step,data,unit):
last_curve_store=cubit.get_last_id("curve")
command='create curve spline '
for i in range(0,n):
if i%step == 0:
lon,lat,z=data[n2*i+ind][0],data[n2*i+ind][1],data[n2*i+ind][2]
x,y=geo2utm(lon,lat,unit)
txt=' Position ' + str(x) +' '+ str(y) +' '+ str(z)
command=command+txt
#print command
cubit.silent_cmd(command)
last_curve=cubit.get_last_id("curve")
if last_curve != last_curve_store:
return last_curve
else:
return 0
def layercake_volume_ascii_regulargrid_mpiregularmap(filename=None,verticalsandwich=False,onlysurface=False):
import sys
import start as start
#
mpiflag,iproc,numproc,mpi = start.start_mpi()
#
numpy = start.start_numpy()
cfg = start.start_cfg(filename=filename)
from utilities import geo2utm, savegeometry,savesurf,cubit_command_check
from math import sqrt
#
try:
mpi.barrier()
except:
pass
#
#
command = "comment '"+"PROC: "+str(iproc)+"/"+str(numproc)+" '"
cubit_command_check(iproc,command,stop=True)
if verticalsandwich: cubit.cmd("comment 'Starting Vertical Sandwich'")
#
#get icpuy,icpux values
if mpiflag:
icpux = iproc % cfg.nproc_xi
icpuy = int(iproc / cfg.nproc_xi)
else:
icpuy=int(cfg.id_proc/cfg.nproc_xi)
icpux=cfg.id_proc%cfg.nproc_xi
#
if cfg.geometry_format == 'ascii':
#for the original surfaces
#number of points in the files that describe the topography
import local_volume
if cfg.localdir_is_globaldir:
if iproc == 0 or not mpiflag:
coordx_0,coordy_0,elev_0,nx_0,ny_0=local_volume.read_grid(filename)
print 'end of reading grd files '+str(nx_0*ny_0)+ ' points'
else:
pass
if iproc == 0 or not mpiflag:
coordx=mpi.bcast(coordx_0)
else:
coordx=mpi.bcast()
if iproc == 0 or not mpiflag:
coordy=mpi.bcast(coordy_0)
else:
coordy=mpi.bcast()
if iproc == 0 or not mpiflag:
elev=mpi.bcast(elev_0)
else:
elev=mpi.bcast()
if iproc == 0 or not mpiflag:
nx=mpi.bcast(nx_0)
else:
nx=mpi.bcast()
if iproc == 0 or not mpiflag:
ny=mpi.bcast(ny_0)
else:
ny=mpi.bcast()
else:
coordx,coordy,elev,nx,ny=local_volume.read_grid(filename)
print str(iproc)+ ' end of receving grd files '
nx_segment=int(nx/cfg.nproc_xi)+1
ny_segment=int(ny/cfg.nproc_eta)+1
elif cfg.geometry_format=='regmesh': # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
if cfg.depth_bottom != cfg.zdepth[0]:
if iproc == 0: print 'the bottom of the block is at different depth than depth[0] in the configuration file'
nx= cfg.nproc_xi+1
ny= cfg.nproc_eta+1
nx_segment=2
ny_segment=2
#if iproc == 0: print nx,ny,cfg.cpux,cfg.cpuy
xp=(cfg.xmax-cfg.xmin)/float((nx-1))
yp=(cfg.ymax-cfg.ymin)/float((ny-1))
#
elev=numpy.zeros([nx,ny,cfg.nz],float)
coordx=numpy.zeros([nx,ny],float)
coordy=numpy.zeros([nx,ny],float)
#
#
xlength=(cfg.xmax-cfg.xmin)/float(cfg.nproc_xi) #length of x slide for chunk
ylength=(cfg.ymax-cfg.ymin)/float(cfg.nproc_eta) #length of y slide for chunk
nelem_chunk_x=1
nelem_chunk_y=1
ivxtot=nelem_chunk_x+1
ivytot=nelem_chunk_y+1
xstep=xlength #distance between vertex on x
ystep=ylength
for i in range(0,cfg.nz):
elev[:,:,i] = cfg.zdepth[i]
icoord=0
for iy in range(0,ny):
for ix in range(0,nx):
icoord=icoord+1
coordx[ix,iy]=cfg.xmin+xlength*(ix)
coordy[ix,iy]=cfg.ymin+ylength*(iy)
#print coordx,coordy,nx,ny
#
print 'end of building grid '+str(iproc)
print 'number of point: ', len(coordx)*len(coordy)
#
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
#for each processor
#
nxmin_cpu=(nx_segment-1)*(icpux)
nymin_cpu=(ny_segment-1)*(icpuy)
nxmax_cpu=min(nx-1,(nx_segment-1)*(icpux+1))
nymax_cpu=min(ny-1,(ny_segment-1)*(icpuy+1))
#if iproc == 0:
# print nx_segment,ny_segment,nx,ny
# print icpux,icpuy,nxmin_cpu,nxmax_cpu
# print icpux,icpuy,nymin_cpu,nymax_cpu
# print coordx[0,0],coordx[nx-1,ny-1]
# print coordy[0,0],coordy[nx-1,ny-1]
#
#
icurve=0
isurf=0
ivertex=0
#
#create vertex
for inz in range(0,cfg.nz):
if cfg.sea and inz==cfg.nz-1: #sea layer
sealevel=True
bathymetry=False
elif cfg.sea and inz==cfg.nz-2: #bathymetry layer
sealevel=False
bathymetry=True
else:
sealevel=False
bathymetry=False
print sealevel,bathymetry
if cfg.bottomflat and inz == 0: #bottom layer
#
if cfg.geometry_format == 'ascii':
lv=cubit.get_last_id("vertex")
x_current,y_current=(coordx[nxmin_cpu,nymin_cpu],coordy[nxmin_cpu,nymin_cpu])
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=(coordx[nxmin_cpu,nymax_cpu],coordy[nxmin_cpu,nymax_cpu])
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=(coordx[nxmax_cpu,nymax_cpu],coordy[nxmax_cpu,nymax_cpu])
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=(coordx[nxmax_cpu,nymin_cpu],coordy[nxmax_cpu,nymin_cpu])
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
lv2=cubit.get_last_id("vertex")
cubitcommand= 'create surface vertex '+str(lv+1)+' to '+str(lv2)
cubit.cmd(cubitcommand)
#
isurf = isurf + 1
else:
lv=cubit.get_last_id("vertex")
x_current,y_current=geo2utm(coordx[nxmin_cpu,nymin_cpu],coordy[nxmin_cpu,nymin_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmin_cpu,nymax_cpu],coordy[nxmin_cpu,nymax_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymax_cpu],coordy[nxmax_cpu,nymax_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymin_cpu],coordy[nxmax_cpu,nymin_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
lv2=cubit.get_last_id("vertex")
cubitcommand= 'create surface vertex '+str(lv+1)+' to '+str(lv2)
cubit.cmd(cubitcommand)
#
isurf = isurf + 1
else:
if cfg.geometry_format == 'regmesh':
zvertex=cfg.zdepth[inz]
lv=cubit.get_last_id("vertex")
x_current,y_current=geo2utm(coordx[nxmin_cpu,nymin_cpu],coordy[nxmin_cpu,nymin_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( zvertex )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmin_cpu,nymax_cpu],coordy[nxmin_cpu,nymax_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( zvertex )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymax_cpu],coordy[nxmax_cpu,nymax_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( zvertex )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymin_cpu],coordy[nxmax_cpu,nymin_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( zvertex )
cubit.cmd(cubitcommand)
#
cubitcommand= 'create surface vertex '+str(lv+1)+' '+str(lv+2)+' '+str(lv+3)+' '+str(lv+4)
cubit.cmd(cubitcommand)
#
isurf = isurf + 1
elif cfg.geometry_format == 'ascii':
vertex=[]
for iy in range(nymin_cpu,nymax_cpu+1):
ivx=0
for ix in range(nxmin_cpu,nxmax_cpu+1):
zvertex=elev[ix,iy,inz]
#zvertex=adjust_sea_layers(zvertex,sealevel,bathymetry,cfg)
x_current,y_current=(coordx[ix,iy],coordy[ix,iy])
#
vertex.append(' Position '+ str( x_current ) +' '+ str( y_current )+' '+ str( zvertex ) )
#
print 'proc',iproc, 'vertex list created....',len(vertex)
n=max(nx,ny)
uline=[]
vline=[]
iv=0
cubit.cmd("set info off")
cubit.cmd("set echo off")
cubit.cmd("set journal off")
for iy in range(0,nymax_cpu-nymin_cpu+1):
positionx=''
for ix in range(0,nxmax_cpu-nxmin_cpu+1):
positionx=positionx+vertex[iv]
iv=iv+1
command='create curve spline '+positionx
cubit.cmd(command)
#print command
uline.append( cubit.get_last_id("curve") )
for ix in range(0,nxmax_cpu-nxmin_cpu+1):
positiony=''
for iy in range(0,nymax_cpu-nymin_cpu+1):
positiony=positiony+vertex[ix+iy*(nxmax_cpu-nxmin_cpu+1)]
command='create curve spline '+positiony
cubit.cmd(command)
#print command
vline.append( cubit.get_last_id("curve") )
#
cubit.cmd("set info "+cfg.cubit_info)
cubit.cmd("set echo "+cfg.echo_info)
cubit.cmd("set journal "+cfg.jou_info)
#
#
print 'proc',iproc, 'lines created....',len(uline),'*',len(vline)
umax=max(uline)
umin=min(uline)
vmax=max(vline)
vmin=min(vline)
ner=cubit.get_error_count()
cubitcommand= 'create surface net u curve '+ str( umin )+' to '+str( umax )+ ' v curve '+ str( vmin )+ ' to '+str( vmax )+' heal'
cubit.cmd(cubitcommand)
ner2=cubit.get_error_count()
if ner == ner2:
command = "del curve all"
cubit.cmd(command)
isurf=isurf+1
#
else:
raise NameError, 'error, check geometry_format, it should be ascii or regmesh' #
#
cubitcommand= 'del vertex all'
cubit.cmd(cubitcommand)
if cfg.save_surface_cubit:
savegeometry(iproc=iproc,surf=True,filename=filename)
#
#
#!create volume
if not onlysurface:
if cfg.nz == 1:
nsurface=2
else:
nsurface=cfg.nz
for inz in range(1,nsurface):
ner=cubit.get_error_count()
create_volume(inz,inz+1,method=cfg.volumecreation_method)
ner2=cubit.get_error_count()
if ner == ner2 and not cfg.debug_geometry:
#cubitcommand= 'del surface 1 to '+ str( cfg.nz )
cubitcommand= 'del surface all'
cubit.cmd(cubitcommand)
list_vol=cubit.parse_cubit_list("volume","all")
if len(list_vol) > 1:
cubitcommand= 'imprint volume all'
cubit.cmd(cubitcommand)
cubitcommand= 'merge all'
cubit.cmd(cubitcommand)
#ner=cubit.get_error_count()
#cubitcommand= 'composite create curve in vol all'
#cubit.cmd(cubitcommand)
savegeometry(iproc,filename=filename)
#if cfg.geological_imprint:
# curvesname=[cfg.outlinebasin_curve,cfg.transition_curve,cfg.faulttrace_curve]
# outdir=cfg.working_dir
# imprint_topography_with_geological_outline(curvesname,outdir)
#
#
cubit.cmd("set info "+cfg.cubit_info)
cubit.cmd("set echo "+cfg.echo_info)
cubit.cmd("set journal "+cfg.jou_info)
def readcfg(filename=None,importmenu=False,mpiflag=False):
"""
read the configuration file, filename is defined in the command line arguments (see menu.py)
"""
if importmenu:
import menu as menu
cfgname=menu.cfg_name
id_proc=menu.id_proc
create_plane=menu.create_plane
menusurface=menu.surface
single=menu.single
elif filename:
cfgname=filename
id_proc=0
menu=False
create_plane=False
menusurface=False
single=False
else:
print 'error: no configuration file'
import sys
sys.exit()
#
from utilities import geo2utm,get_cubit_version #here I can use pyproj but I prefere to include a function in pure python in order to avoid an additional installation
#
#
import ConfigParser
config = ConfigParser.ConfigParser()
#
#
def converter(s):
if s == 'True':
value=True
elif s == 'False':
value=False
elif s == 'None':
value= None
else:
if s.count(',') != 0:
value=s.split(',')
while value.count(''):
value.remove('')
else:
value=s
try:
if type(value).__name__ == 'str':
if str(value).count('.') != 0:
value=float(value)
else:
value=int(value)
else:
if str(value).count('.') != 0:
value=map(float,value)
else:
value=map(int,value)
except:
pass
return value
#
def section_dict(section):
dict_o = {}
options = config.options(section)
for option in options:
try:
value=converter(config.get(section, option))
dict_o[option] = value
except:
dict_o[option] = None
return dict_o
class attrdict(dict):
def __init__(self, *args, **kwargs):
dict.__init__(self, *args, **kwargs)
self.__dict__ = self
def __str__(self):
names=[]
values=[]
for name,value in self.items():
names.append(name)
values.append(value)
print names,values
a=zip(names,values)
a.sort()
arc=''
for o in a:
if o[0][0] != arc: print
print o[0],' -> ',o[1]
arc=o[0][0]
return '____'
#
dcfg={}
#
#CONSTANTS
dcfg['osystem'] = 'linux'
dcfg['debug_cfg']=False
dcfg['version_cubit']=get_cubit_version()
dcfg['checkbound']=False
dcfg['top_partitioner'] = 10000
dcfg['tres']=0.3 #if n is the vertical component of the normal at a surface pointing horizontally, when -tres < n < tres then the surface is vertical
dcfg['precision'] =0.02 #precision for the boundary check (0.02 m)
#
#INIT
dcfg['debug']=True
dcfg['cubit_info']="on"
dcfg['echo_info']="on"
dcfg['jou_info']="on"
dcfg['jer_info']="on"
dcfg['monitored_cpu']=0
dcfg['parallel_import']=True
dcfg['save_geometry_cubit']=True
dcfg['save_surface_cubit']=False
dcfg['save_geometry_paraview'] = False #not implemented
dcfg['save_geometry_ACIS'] = False #not implemented
dcfg['export_exodus_mesh']=False
dcfg['manual_adj'] =False
dcfg['play_adj'] =False
dcfg['no_adj'] =False
dcfg['nx']=False
dcfg['ny']=False
dcfg['nstep']=False
dcfg['localdir_is_globaldir']=True
dcfg['refinement_depth']=[]
dcfg['scratchdir']=None
dcfg['map_meshing_type']='regularmap'
dcfg['4sideparallel']=True
dcfg["outlinebasin_curve"]=False
dcfg["transition_curve"]=False
dcfg["faulttrace_curve"]=False
dcfg['geological_imprint']=False
dcfg['number_processor_xi']=1
dcfg['number_processor_eta']=1
dcfg['filename']=None
dcfg['actual_vertical_interval_top_layer']=1
dcfg['coarsening_top_layer']=False
dcfg['refineinsidevol']=False
dcfg['sea']=False
dcfg['seaup']=False
dcfg['sea_level']=False
dcfg['sea_threshold']=False
dcfg['subduction']=True
dcfg['subduction_thres']=500
dcfg['debugsurface']=False #if true it creates only the surface not the lofted volumes
dcfg['lat_orientation']=False
dcfg['irregulargridded_surf']=False
dcfg['chktop']=False
dcfg['smoothing']=False
dcfg['ntripl']=0
dcfg['debug_geometry']=False
if float(dcfg['version_cubit']) >= 13.1:
dcfg['volumecreation_method']=None
else:
dcfg['volumecreation_method']='loft'
dcfg['nsurf'] = None
if cfgname:
config.read(cfgname)
sections=['cubit.options','simulation.cpu_parameters','geometry.surfaces','geometry.volumes','geometry.volumes.layercake','geometry.volumes.flatcake','geometry.volumes.partitioner','geometry.partitioner','meshing']
for section in sections:
try:
d=section_dict(section)
dcfg.update(d)
except:
pass
if dcfg['nsurf']:
surface_name=[]
num_x=[]
num_y=[]
xstep=[]
ystep=[]
step=[]
directionx=[]
directiony=[]
unit2=[]
surf_type=[]
delimiter=[]
nsurf=int(dcfg['nsurf'])
for i in range(1,nsurf+1):
section='surface'+str(i)+'.parameters'
d=section_dict(section)
surface_name.append(d['name'])
surf_type.append(d['surf_type'])
unit2.append(d['unit_surf'])
if d['surf_type'] == 'regular_grid':
xstep.append(d['step_along_x'])
ystep.append(d['step_along_y'])
num_x.append(d['number_point_along_x'])
num_y.append(d['number_point_along_y'])
elif d['surf_type'] == 'skin':
step.append(d['step'])
try:
delimiter.append(d['delimiter'])
except:
pass
directionx.append(d['directionx'])
directiony.append(d['directiony'])
dcfg['surface_name']=surface_name
dcfg['num_x']=num_x
dcfg['num_y']=num_y
dcfg['xstep']=xstep
dcfg['ystep']=ystep
dcfg['step']=step
dcfg['directionx']=directionx
dcfg['directiony']=directiony
dcfg['unit2']=unit2
dcfg['surf_type']=surf_type
dcfg['delimiter']=delimiter
try:
tres=0
xmin,ymin=geo2utm(dcfg['longitude_min'],dcfg['latitude_min'],dcfg['unit'])
xmax,ymax=geo2utm(dcfg['longitude_max'],dcfg['latitude_max'],dcfg['unit'])
dcfg['xmin']=xmin
dcfg['ymin']=ymin
dcfg['xmax']=xmax
dcfg['ymax']=ymax
x1,y1=geo2utm(dcfg['longitude_min'],dcfg['latitude_min'],dcfg['unit'])
x2,y2=geo2utm(dcfg['longitude_max'],dcfg['latitude_min'],dcfg['unit'])
x3,y3=geo2utm(dcfg['longitude_max'],dcfg['latitude_max'],dcfg['unit'])
x4,y4=geo2utm(dcfg['longitude_min'],dcfg['latitude_max'],dcfg['unit'])
dcfg['x1_box']=x1
dcfg['y1_box']=y1
dcfg['x2_box']=x2
dcfg['y2_box']=y2
dcfg['x3_box']=x3
dcfg['y3_box']=y3
dcfg['x4_box']=x4
dcfg['y4_box']=y4
dcfg['tres_boundarydetection']=tres
except:
pass
if dcfg['sea']:
if not dcfg['sea_level']: dcfg['sea_level']=0
if not dcfg['sea_threshold']: dcfg['sea_threshold']=-200
dcfg['actual_vertical_interval_top_layer']=1
dcfg['coarsening_top_layer']=True
dcfg['optionsea']={'sea':dcfg['sea'],'seaup':dcfg['seaup'],'sealevel':dcfg['sea_level'],'seathres':dcfg['sea_threshold']}
cfg=attrdict(dcfg)
if menu:
try:
if cfg.working_dir[-1] == '/': cfg.working_dir=cfg.working_dir[:-1]
if cfg.working_dir[0] != '/': cfg.working_dir='./'+cfg.working_dir
except:
cfg.working_dir=os.getcwd()
try:
if cfg.output_dir[-1] == '/': cfg.output_dir=cfg.output_dir[:-1]
if cfg.output_dir[0] != '/': cfg.output_dir='./'+cfg.output_dir
except:
cfg.output_dir=os.getcwd()
try:
if cfg.SPECFEM3D_output_dir[-1] == '/': cfg.SPECFEM3D_output_dir=cfg.SPECFEM3D_output_dir[:-1]
if cfg.SPECFEM3D_output_dir[0] != '/': cfg.SPECFEM3D_output_dir='./'+cfg.SPECFEM3D_output_dir
except:
cfg.SPECFEM3D_output_dir=os.getcwd()
cfg.single=single
if menusurface:
cfg.nsurf=1
cfg.name=[menu.surface_name]
cfg.num_x=[menu.num_x]
cfg.num_y=[menu.num_x]
cfg.unit=[menu.unit]
cfg.surf_type=[menu.surf_type]
try:
cfg.delimiter=[menu.delimiter]
except:
cfg.delimiter=[' ']
cfg.directionx=[menu.directionx]
cfg.directiony=[menu.directiony]
else:
cfg.SPECFEM3D_output_dir=os.getcwd()
if not cfg.number_processor_eta and cfg.nodes:
cfg.number_processor_xi,cfg.number_processor_eta=split(cfg.nodes)
if isinstance(cfg.filename,str): cfg.filename=[cfg.filename]
try:
cfg.nproc_eta=cfg.number_processor_eta
cfg.nproc_xi=cfg.number_processor_xi
cfg.cpuy=cfg.number_processor_eta
cfg.cpux=cfg.number_processor_xi
except:
pass
if create_plane:
cfg.x1=map(float,menu.x1.split(','))
cfg.x2=map(float,menu.x2.split(','))
cfg.x3=map(float,menu.x3.split(','))
cfg.x4=map(float,menu.x4.split(','))
cfg.unit=menu.unit
#
if menu:
cfg.id_proc=menu.id_proc
else:
cfg.id_proc=id_proc
#
try:
if isinstance(cfg.tripl,int): cfg.tripl=[cfg.tripl]
except:
pass
try:
if isinstance(cfg.iv_interval,int): cfg.iv_interval=[cfg.iv_interval]
except:
pass
try:
if isinstance(cfg.refinement_depth,int): cfg.refinement_depth=[cfg.refinement_depth]
except:
pass
return cfg
def layercake_volume_ascii_regulargrid_mpiregularmap(filename=None,
verticalsandwich=False,
onlysurface=False):
import sys
import start as start
#
mpiflag, iproc, numproc, mpi = start.start_mpi()
#
numpy = start.start_numpy()
cfg = start.start_cfg(filename=filename)
from utilities import geo2utm, savegeometry, savesurf, cubit_command_check
from math import sqrt
#
try:
mpi.barrier()
except:
pass
#
#
command = "comment '" + "PROC: " + str(iproc) + "/" + str(numproc) + " '"
cubit_command_check(iproc, command, stop=True)
if verticalsandwich: cubit.cmd("comment 'Starting Vertical Sandwich'")
#
#get icpuy,icpux values
if mpiflag:
icpux = iproc % cfg.nproc_xi
icpuy = int(iproc / cfg.nproc_xi)
else:
icpuy = int(cfg.id_proc / cfg.nproc_xi)
icpux = cfg.id_proc % cfg.nproc_xi
#
if cfg.geometry_format == 'ascii':
#for the original surfaces
#number of points in the files that describe the topography
import local_volume
if cfg.localdir_is_globaldir:
if iproc == 0 or not mpiflag:
coordx_0, coordy_0, elev_0, nx_0, ny_0 = local_volume.read_grid(
filename)
print 'end of reading grd files ' + str(
nx_0 * ny_0) + ' points'
else:
pass
if iproc == 0 or not mpiflag:
coordx = mpi.bcast(coordx_0)
else:
coordx = mpi.bcast()
if iproc == 0 or not mpiflag:
coordy = mpi.bcast(coordy_0)
else:
coordy = mpi.bcast()
if iproc == 0 or not mpiflag:
elev = mpi.bcast(elev_0)
else:
elev = mpi.bcast()
if iproc == 0 or not mpiflag:
nx = mpi.bcast(nx_0)
else:
nx = mpi.bcast()
if iproc == 0 or not mpiflag:
ny = mpi.bcast(ny_0)
else:
ny = mpi.bcast()
else:
coordx, coordy, elev, nx, ny = local_volume.read_grid(filename)
print str(iproc) + ' end of receving grd files '
nx_segment = int(nx / cfg.nproc_xi) + 1
ny_segment = int(ny / cfg.nproc_eta) + 1
elif cfg.geometry_format == 'regmesh': # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
if cfg.depth_bottom != cfg.zdepth[0]:
if iproc == 0:
print 'the bottom of the block is at different depth than depth[0] in the configuration file'
nx = cfg.nproc_xi + 1
ny = cfg.nproc_eta + 1
nx_segment = 2
ny_segment = 2
#if iproc == 0: print nx,ny,cfg.cpux,cfg.cpuy
xp = (cfg.xmax - cfg.xmin) / float((nx - 1))
yp = (cfg.ymax - cfg.ymin) / float((ny - 1))
#
elev = numpy.zeros([nx, ny, cfg.nz], float)
coordx = numpy.zeros([nx, ny], float)
coordy = numpy.zeros([nx, ny], float)
#
#
xlength = (cfg.xmax - cfg.xmin) / float(
cfg.nproc_xi) #length of x slide for chunk
ylength = (cfg.ymax - cfg.ymin) / float(
cfg.nproc_eta) #length of y slide for chunk
nelem_chunk_x = 1
nelem_chunk_y = 1
ivxtot = nelem_chunk_x + 1
ivytot = nelem_chunk_y + 1
xstep = xlength #distance between vertex on x
ystep = ylength
for i in range(0, cfg.nz):
elev[:, :, i] = cfg.zdepth[i]
icoord = 0
for iy in range(0, ny):
for ix in range(0, nx):
icoord = icoord + 1
coordx[ix, iy] = cfg.xmin + xlength * (ix)
coordy[ix, iy] = cfg.ymin + ylength * (iy)
#print coordx,coordy,nx,ny
#
print 'end of building grid ' + str(iproc)
print 'number of point: ', len(coordx) * len(coordy)
#
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
#for each processor
#
nxmin_cpu = (nx_segment - 1) * (icpux)
nymin_cpu = (ny_segment - 1) * (icpuy)
nxmax_cpu = min(nx - 1, (nx_segment - 1) * (icpux + 1))
nymax_cpu = min(ny - 1, (ny_segment - 1) * (icpuy + 1))
#if iproc == 0:
# print nx_segment,ny_segment,nx,ny
# print icpux,icpuy,nxmin_cpu,nxmax_cpu
# print icpux,icpuy,nymin_cpu,nymax_cpu
# print coordx[0,0],coordx[nx-1,ny-1]
# print coordy[0,0],coordy[nx-1,ny-1]
#
#
icurve = 0
isurf = 0
ivertex = 0
#
#create vertex
for inz in range(0, cfg.nz):
if cfg.sea and inz == cfg.nz - 1: #sea layer
sealevel = True
bathymetry = False
elif cfg.sea and inz == cfg.nz - 2: #bathymetry layer
sealevel = False
bathymetry = True
else:
sealevel = False
bathymetry = False
print sealevel, bathymetry
if cfg.bottomflat and inz == 0: #bottom layer
#
if cfg.geometry_format == 'ascii':
lv = cubit.get_last_id("vertex")
x_current, y_current = (coordx[nxmin_cpu,
nymin_cpu], coordy[nxmin_cpu,
nymin_cpu])
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(cfg.depth_bottom)
cubit.cmd(cubitcommand)
#
x_current, y_current = (coordx[nxmin_cpu,
nymax_cpu], coordy[nxmin_cpu,
nymax_cpu])
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(cfg.depth_bottom)
cubit.cmd(cubitcommand)
#
x_current, y_current = (coordx[nxmax_cpu,
nymax_cpu], coordy[nxmax_cpu,
nymax_cpu])
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(cfg.depth_bottom)
cubit.cmd(cubitcommand)
#
x_current, y_current = (coordx[nxmax_cpu,
nymin_cpu], coordy[nxmax_cpu,
nymin_cpu])
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(cfg.depth_bottom)
cubit.cmd(cubitcommand)
#
lv2 = cubit.get_last_id("vertex")
cubitcommand = 'create surface vertex ' + str(
lv + 1) + ' to ' + str(lv2)
cubit.cmd(cubitcommand)
#
isurf = isurf + 1
else:
lv = cubit.get_last_id("vertex")
x_current, y_current = geo2utm(coordx[nxmin_cpu, nymin_cpu],
coordy[nxmin_cpu,
nymin_cpu], 'utm')
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(cfg.depth_bottom)
cubit.cmd(cubitcommand)
#
x_current, y_current = geo2utm(coordx[nxmin_cpu, nymax_cpu],
coordy[nxmin_cpu,
nymax_cpu], 'utm')
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(cfg.depth_bottom)
cubit.cmd(cubitcommand)
#
x_current, y_current = geo2utm(coordx[nxmax_cpu, nymax_cpu],
coordy[nxmax_cpu,
nymax_cpu], 'utm')
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(cfg.depth_bottom)
cubit.cmd(cubitcommand)
#
x_current, y_current = geo2utm(coordx[nxmax_cpu, nymin_cpu],
coordy[nxmax_cpu,
nymin_cpu], 'utm')
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(cfg.depth_bottom)
cubit.cmd(cubitcommand)
#
lv2 = cubit.get_last_id("vertex")
cubitcommand = 'create surface vertex ' + str(
lv + 1) + ' to ' + str(lv2)
cubit.cmd(cubitcommand)
#
isurf = isurf + 1
else:
if cfg.geometry_format == 'regmesh':
zvertex = cfg.zdepth[inz]
lv = cubit.get_last_id("vertex")
x_current, y_current = geo2utm(coordx[nxmin_cpu, nymin_cpu],
coordy[nxmin_cpu,
nymin_cpu], 'utm')
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(zvertex)
cubit.cmd(cubitcommand)
#
x_current, y_current = geo2utm(coordx[nxmin_cpu, nymax_cpu],
coordy[nxmin_cpu,
nymax_cpu], 'utm')
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(zvertex)
cubit.cmd(cubitcommand)
#
x_current, y_current = geo2utm(coordx[nxmax_cpu, nymax_cpu],
coordy[nxmax_cpu,
nymax_cpu], 'utm')
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(zvertex)
cubit.cmd(cubitcommand)
#
x_current, y_current = geo2utm(coordx[nxmax_cpu, nymin_cpu],
coordy[nxmax_cpu,
nymin_cpu], 'utm')
cubitcommand = 'create vertex ' + str(x_current) + ' ' + str(
y_current) + ' ' + str(zvertex)
cubit.cmd(cubitcommand)
#
cubitcommand = 'create surface vertex ' + str(
lv + 1) + ' ' + str(lv + 2) + ' ' + str(lv +
3) + ' ' + str(lv +
4)
cubit.cmd(cubitcommand)
#
isurf = isurf + 1
elif cfg.geometry_format == 'ascii':
vertex = []
for iy in range(nymin_cpu, nymax_cpu + 1):
ivx = 0
for ix in range(nxmin_cpu, nxmax_cpu + 1):
zvertex = elev[ix, iy, inz]
#zvertex=adjust_sea_layers(zvertex,sealevel,bathymetry,cfg)
x_current, y_current = (coordx[ix, iy], coordy[ix, iy])
#
vertex.append(' Position ' + str(x_current) + ' ' +
str(y_current) + ' ' + str(zvertex))
#
print 'proc', iproc, 'vertex list created....', len(vertex)
n = max(nx, ny)
uline = []
vline = []
iv = 0
cubit.cmd("set info off")
cubit.cmd("set echo off")
cubit.cmd("set journal off")
for iy in range(0, nymax_cpu - nymin_cpu + 1):
positionx = ''
for ix in range(0, nxmax_cpu - nxmin_cpu + 1):
positionx = positionx + vertex[iv]
iv = iv + 1
command = 'create curve spline ' + positionx
cubit.cmd(command)
#print command
uline.append(cubit.get_last_id("curve"))
for ix in range(0, nxmax_cpu - nxmin_cpu + 1):
positiony = ''
for iy in range(0, nymax_cpu - nymin_cpu + 1):
positiony = positiony + vertex[
ix + iy * (nxmax_cpu - nxmin_cpu + 1)]
command = 'create curve spline ' + positiony
cubit.cmd(command)
#print command
vline.append(cubit.get_last_id("curve"))
#
cubit.cmd("set info " + cfg.cubit_info)
cubit.cmd("set echo " + cfg.echo_info)
cubit.cmd("set journal " + cfg.jou_info)
#
#
print 'proc', iproc, 'lines created....', len(uline), '*', len(
vline)
umax = max(uline)
umin = min(uline)
vmax = max(vline)
vmin = min(vline)
ner = cubit.get_error_count()
cubitcommand = 'create surface net u curve ' + str(
umin) + ' to ' + str(umax) + ' v curve ' + str(
vmin) + ' to ' + str(vmax) + ' heal'
cubit.cmd(cubitcommand)
ner2 = cubit.get_error_count()
if ner == ner2:
command = "del curve all"
cubit.cmd(command)
isurf = isurf + 1
#
else:
raise NameError, 'error, check geometry_format, it should be ascii or regmesh' #
#
cubitcommand = 'del vertex all'
cubit.cmd(cubitcommand)
if cfg.save_surface_cubit:
savegeometry(iproc=iproc, surf=True, filename=filename)
#
#
#!create volume
if not onlysurface:
if cfg.nz == 1:
nsurface = 2
else:
nsurface = cfg.nz
for inz in range(1, nsurface):
ner = cubit.get_error_count()
create_volume(inz, inz + 1, method=cfg.volumecreation_method)
ner2 = cubit.get_error_count()
if ner == ner2 and not cfg.debug_geometry:
#cubitcommand= 'del surface 1 to '+ str( cfg.nz )
cubitcommand = 'del surface all'
cubit.cmd(cubitcommand)
list_vol = cubit.parse_cubit_list("volume", "all")
if len(list_vol) > 1:
cubitcommand = 'imprint volume all'
cubit.cmd(cubitcommand)
cubitcommand = 'merge all'
cubit.cmd(cubitcommand)
#ner=cubit.get_error_count()
#cubitcommand= 'composite create curve in vol all'
#cubit.cmd(cubitcommand)
savegeometry(iproc, filename=filename)
#if cfg.geological_imprint:
# curvesname=[cfg.outlinebasin_curve,cfg.transition_curve,cfg.faulttrace_curve]
# outdir=cfg.working_dir
# imprint_topography_with_geological_outline(curvesname,outdir)
#
#
cubit.cmd("set info " + cfg.cubit_info)
cubit.cmd("set echo " + cfg.echo_info)
cubit.cmd("set journal " + cfg.jou_info)
def readcfg(filename=None, importmenu=False, mpiflag=False):
"""
read the configuration file, filename is defined in the command line arguments (see menu.py)
"""
if importmenu:
import menu as menu
cfgname = menu.cfg_name
id_proc = menu.id_proc
create_plane = menu.create_plane
menusurface = menu.surface
single = menu.single
elif filename:
cfgname = filename
id_proc = 0
menu = False
create_plane = False
menusurface = False
single = False
else:
print "error: no configuration file"
import sys
sys.exit()
#
from utilities import (
geo2utm,
get_cubit_version,
) # here I can use pyproj but I prefere to include a function in pure python in order to avoid an additional installation
#
#
import ConfigParser
config = ConfigParser.ConfigParser()
#
#
def converter(s):
if s == "True":
value = True
elif s == "False":
value = False
elif s == "None":
value = None
else:
if s.count(",") != 0:
value = s.split(",")
while value.count(""):
value.remove("")
else:
value = s
try:
if type(value).__name__ == "str":
if str(value).count(".") != 0:
value = float(value)
else:
value = int(value)
else:
if str(value).count(".") != 0:
value = map(float, value)
else:
value = map(int, value)
except:
pass
return value
#
def section_dict(section):
dict_o = {}
options = config.options(section)
for option in options:
try:
value = converter(config.get(section, option))
dict_o[option] = value
except:
dict_o[option] = None
return dict_o
class attrdict(dict):
def __init__(self, *args, **kwargs):
dict.__init__(self, *args, **kwargs)
self.__dict__ = self
def __str__(self):
names = []
values = []
for name, value in self.items():
names.append(name)
values.append(value)
print names, values
a = zip(names, values)
a.sort()
arc = ""
for o in a:
if o[0][0] != arc:
print
print o[0], " -> ", o[1]
arc = o[0][0]
print __name__
return "____"
#
dcfg = {}
#
# CONSTANTS
dcfg["osystem"] = "linux"
dcfg["debug_cfg"] = False
dcfg["version_cubit"] = get_cubit_version()
dcfg["checkbound"] = False
dcfg["top_partitioner"] = 10000
dcfg[
"tres"
] = (
0.3
) # if n is the vertical component of the normal at a surface pointing horizontally, when -tres < n < tres then the surface is vertical
dcfg["precision"] = 0.02 # precision for the boundary check (0.02 m)
#
# INIT
dcfg["debug"] = True
dcfg["cubit_info"] = "on"
dcfg["echo_info"] = "on"
dcfg["jou_info"] = "on"
dcfg["jer_info"] = "on"
dcfg["monitored_cpu"] = 0
dcfg["parallel_import"] = True
dcfg["save_geometry_cubit"] = True
dcfg["save_surface_cubit"] = False
dcfg["save_geometry_paraview"] = False # not implemented
dcfg["save_geometry_ACIS"] = False # not implemented
dcfg["export_exodus_mesh"] = False
dcfg["manual_adj"] = False
dcfg["play_adj"] = False
dcfg["no_adj"] = False
dcfg["nx"] = False
dcfg["ny"] = False
dcfg["nstep"] = False
dcfg["localdir_is_globaldir"] = True
dcfg["refinement_depth"] = []
dcfg["scratchdir"] = None
dcfg["map_meshing_type"] = "regularmap"
dcfg["4sideparallel"] = True
dcfg["outlinebasin_curve"] = False
dcfg["transition_curve"] = False
dcfg["faulttrace_curve"] = False
dcfg["geological_imprint"] = False
dcfg["number_processor_xi"] = 1
dcfg["number_processor_eta"] = 1
dcfg["filename"] = None
dcfg["actual_vertical_interval_top_layer"] = 1
dcfg["coarsening_top_layer"] = False
dcfg["refineinsidevol"] = False
dcfg["sea"] = False
dcfg["seaup"] = False
dcfg["sea_level"] = False
dcfg["sea_threshold"] = False
dcfg["subduction"] = False
dcfg["subduction_thres"] = 500
dcfg["debugsurface"] = False # if true it creates only the surface not the lofted volumes
dcfg["lat_orientation"] = False
dcfg["irregulargridded_surf"] = False
dcfg["chktop"] = False
dcfg["smoothing"] = False
dcfg["ntripl"] = 0
dcfg["debug_geometry"] = False
dcfg["topflat"] = False
if float(dcfg["version_cubit"]) >= 13.1:
dcfg["volumecreation_method"] = None
else:
dcfg["volumecreation_method"] = "loft"
dcfg["nsurf"] = None
if cfgname:
config.read(cfgname)
sections = [
"cubit.options",
"simulation.cpu_parameters",
"geometry.surfaces",
"geometry.volumes",
"geometry.volumes.layercake",
"geometry.volumes.flatcake",
"geometry.volumes.partitioner",
"geometry.partitioner",
"meshing",
]
for section in sections:
try:
d = section_dict(section)
dcfg.update(d)
except:
pass
# print dcfg
if dcfg["nsurf"]:
surface_name = []
num_x = []
num_y = []
xstep = []
ystep = []
step = []
directionx = []
directiony = []
unit2 = []
surf_type = []
delimiter = []
nsurf = int(dcfg["nsurf"])
for i in range(1, nsurf + 1):
section = "surface" + str(i) + ".parameters"
d = section_dict(section)
surface_name.append(d["name"])
surf_type.append(d["surf_type"])
unit2.append(d["unit_surf"])
if d["surf_type"] == "regular_grid":
xstep.append(d["step_along_x"])
ystep.append(d["step_along_y"])
num_x.append(d["number_point_along_x"])
num_y.append(d["number_point_along_y"])
elif d["surf_type"] == "skin":
step.append(d["step"])
try:
delimiter.append(d["delimiter"])
except:
pass
directionx.append(d["directionx"])
directiony.append(d["directiony"])
dcfg["surface_name"] = surface_name
dcfg["num_x"] = num_x
dcfg["num_y"] = num_y
dcfg["xstep"] = xstep
dcfg["ystep"] = ystep
dcfg["step"] = step
dcfg["directionx"] = directionx
dcfg["directiony"] = directiony
dcfg["unit2"] = unit2
dcfg["surf_type"] = surf_type
dcfg["delimiter"] = delimiter
try:
tres = 0
xmin, ymin = geo2utm(dcfg["longitude_min"], dcfg["latitude_min"], dcfg["unit"])
xmax, ymax = geo2utm(dcfg["longitude_max"], dcfg["latitude_max"], dcfg["unit"])
dcfg["xmin"] = xmin
dcfg["ymin"] = ymin
dcfg["xmax"] = xmax
dcfg["ymax"] = ymax
x1, y1 = geo2utm(dcfg["longitude_min"], dcfg["latitude_min"], dcfg["unit"])
x2, y2 = geo2utm(dcfg["longitude_max"], dcfg["latitude_min"], dcfg["unit"])
x3, y3 = geo2utm(dcfg["longitude_max"], dcfg["latitude_max"], dcfg["unit"])
x4, y4 = geo2utm(dcfg["longitude_min"], dcfg["latitude_max"], dcfg["unit"])
dcfg["x1_box"] = x1
dcfg["y1_box"] = y1
dcfg["x2_box"] = x2
dcfg["y2_box"] = y2
dcfg["x3_box"] = x3
dcfg["y3_box"] = y3
dcfg["x4_box"] = x4
dcfg["y4_box"] = y4
dcfg["tres_boundarydetection"] = tres
except:
pass
if dcfg["irregulargridded_surf"]:
print "test"
dcfg["xmin"] = dcfg["longitude_min"]
dcfg["ymin"] = dcfg["latitude_min"]
dcfg["xmax"] = dcfg["longitude_max"]
dcfg["ymax"] = dcfg["latitude_max"]
if dcfg["sea"]:
if not dcfg["sea_level"]:
dcfg["sea_level"] = 0
if not dcfg["sea_threshold"]:
dcfg["sea_threshold"] = -200
dcfg["actual_vertical_interval_top_layer"] = 1
dcfg["coarsening_top_layer"] = True
dcfg["optionsea"] = {
"sea": dcfg["sea"],
"seaup": dcfg["seaup"],
"sealevel": dcfg["sea_level"],
"seathres": dcfg["sea_threshold"],
}
cfg = attrdict(dcfg)
if menu:
try:
if cfg.working_dir[-1] == "/":
cfg.working_dir = cfg.working_dir[:-1]
if cfg.working_dir[0] != "/":
cfg.working_dir = "./" + cfg.working_dir
except:
cfg.working_dir = os.getcwd()
try:
if cfg.output_dir[-1] == "/":
cfg.output_dir = cfg.output_dir[:-1]
if cfg.output_dir[0] != "/":
cfg.output_dir = "./" + cfg.output_dir
except:
cfg.output_dir = os.getcwd()
try:
if cfg.SPECFEM3D_output_dir[-1] == "/":
cfg.SPECFEM3D_output_dir = cfg.SPECFEM3D_output_dir[:-1]
if cfg.SPECFEM3D_output_dir[0] != "/":
cfg.SPECFEM3D_output_dir = "./" + cfg.SPECFEM3D_output_dir
except:
cfg.SPECFEM3D_output_dir = os.getcwd()
cfg.single = single
if menusurface:
cfg.nsurf = 1
cfg.name = [menu.surface_name]
cfg.num_x = [menu.num_x]
cfg.num_y = [menu.num_x]
cfg.unit = [menu.unit]
cfg.surf_type = [menu.surf_type]
try:
cfg.delimiter = [menu.delimiter]
except:
cfg.delimiter = [" "]
cfg.directionx = [menu.directionx]
cfg.directiony = [menu.directiony]
else:
cfg.SPECFEM3D_output_dir = os.getcwd()
if not cfg.number_processor_eta and cfg.nodes:
cfg.number_processor_xi, cfg.number_processor_eta = split(cfg.nodes)
if isinstance(cfg.filename, str):
cfg.filename = [cfg.filename]
try:
cfg.nproc_eta = cfg.number_processor_eta
cfg.nproc_xi = cfg.number_processor_xi
cfg.cpuy = cfg.number_processor_eta
cfg.cpux = cfg.number_processor_xi
except:
pass
if create_plane:
cfg.x1 = map(float, menu.x1.split(","))
cfg.x2 = map(float, menu.x2.split(","))
cfg.x3 = map(float, menu.x3.split(","))
cfg.x4 = map(float, menu.x4.split(","))
cfg.unit = menu.unit
#
if menu:
cfg.id_proc = menu.id_proc
else:
cfg.id_proc = id_proc
#
try:
if isinstance(cfg.tripl, int):
cfg.tripl = [cfg.tripl]
except:
pass
try:
if isinstance(cfg.iv_interval, int):
cfg.iv_interval = [cfg.iv_interval]
except:
pass
try:
if isinstance(cfg.refinement_depth, int):
cfg.refinement_depth = [cfg.refinement_depth]
except:
pass
return cfg