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 read_grid(filename=None):
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
#if cfg.irregulargridded_surf==True then cfg.nx and cfg.ny are the desired number of point along the axis....
if cfg.nx and cfg.ny:
nx=cfg.nx
ny=cfg.ny
if cfg.nstep:
nx=min(cfg.nx,int(cfg.nx/cfg.nstep)+1)
ny=min(cfg.ny,int(cfg.ny/cfg.nstep)+1)
nstep=cfg.nstep
else:
nstep=1
else:
try:
xstep=cfg.step
ystep=cfg.step
except:
xstep=cfg.xstep
ystep=cfg.ystep
nx= int((cfg.longitude_max-cfg.longitude_min)/xstep)+1
ny= int((cfg.latitude_max-cfg.latitude_min)/ystep)+1
nstep=1
#
if cfg.irregulargridded_surf:
xt,xstep=numpy.linspace(cfg.xmin, cfg.xmax, num=nx, retstep=True)
yt,ystep=numpy.linspace(cfg.ymin, cfg.ymax, num=ny, retstep=True)
elev=numpy.zeros([nx,ny,cfg.nz],float)
#
if cfg.bottomflat:
elev[:,:,0] = cfg.depth_bottom
bottomsurface=1
else:
bottomsurface=0
for inz in range(bottomsurface,cfg.nz-1):
grdfilename=cfg.filename[inz-bottomsurface]
if cfg.irregulargridded_surf:
coordx,coordy,elev_1=process_irregular_surfacefiles(iproc,nx,ny,cfg.xmin,cfg.xmax,cfg.ymin,cfg.ymax,xstep,ystep,grdfilename)
else:
coordx,coordy,elev_1=process_surfacefiles(iproc,nx,ny,nstep,grdfilename,cfg.unit,cfg.lat_orientation)
elev[:,:,inz]=elev_1[:,:]
#
inz=cfg.nz-1 #last surface
if cfg.sea:
elev[:,:,inz]=elev[:,:,inz-1]
else:
#try:
grdfile = cfg.filename[inz-bottomsurface]
print 'reading ',cfg.filename[inz-bottomsurface]
if cfg.irregulargridded_surf:
coordx,coordy,elev_1=process_irregular_surfacefiles(iproc,nx,ny,cfg.xmin,cfg.xmax,cfg.ymin,cfg.ymax,xstep,ystep,grdfile)
else:
coordx,coordy,elev_1=process_surfacefiles(iproc,nx,ny,nstep,grdfile,cfg.unit,cfg.lat_orientation)
elev[:,:,inz]=elev_1[:,:]
#except:
# txt='error reading: '+ str( cfg.filename[inz-bottomsurface] )
# raise NameError, txt
if cfg.subduction:
print 'subduction'
top=elev[:,:,inz]
slab=elev[:,:,inz-1]
subcrit=numpy.abs(top-slab)<cfg.subduction_thres
top[subcrit]=slab[subcrit]+cfg.subduction_thres
print len(top[subcrit])
elev[:,:,inz]=top
return coordx,coordy,elev,nx,ny
# #
# You should have received a copy of the GNU General Public License #
# along with GEOCUBIT. If not, see <http://www.gnu.org/licenses/>. #
# #
#############################################################################
try:
import start as start
cubit = start.start_cubit()
except:
try:
import cubit
except:
print 'error importing cubit, check if cubit is installed'
pass
numpy = start.start_numpy()
def check_orientation(grdfileNAME):
try:
grdfile = open(grdfileNAME, 'r')
print 'reading ',grdfileNAME
except:
txt='check_orintation ->error reading: '+ str( grdfile )
raise Exception(txt)
diff=1
txt=grdfile.readline()
x0,y0,z=map(float,txt.split())
while diff>0:
try:
txt=grdfile.readline()
def read_grid(filename=None):
import start as start
mpiflag, iproc, numproc, mpi = start.start_mpi()
#
numpy = start.start_numpy()
cfg = start.start_cfg(filename=filename)
# if cfg.irregulargridded_surf==True then cfg.nx and cfg.ny are the
# desired number of point along the axis....
if cfg.nx and cfg.ny:
nx = cfg.nx
ny = cfg.ny
if cfg.nstep:
nx = min(cfg.nx, int(cfg.nx / cfg.nstep) + 1)
ny = min(cfg.ny, int(cfg.ny / cfg.nstep) + 1)
nstep = cfg.nstep
else:
nstep = 1
else:
try:
xstep = cfg.step
ystep = cfg.step
except:
xstep = cfg.xstep
ystep = cfg.ystep
nx = int((cfg.longitude_max - cfg.longitude_min) / xstep) + 1
ny = int((cfg.latitude_max - cfg.latitude_min) / ystep) + 1
nstep = 1
#
if cfg.irregulargridded_surf:
xt, xstep = numpy.linspace(cfg.xmin, cfg.xmax, num=nx, retstep=True)
yt, ystep = numpy.linspace(cfg.ymin, cfg.ymax, num=ny, retstep=True)
elev = numpy.zeros([nx, ny, cfg.nz], float)
#
if cfg.bottomflat:
elev[:, :, 0] = cfg.depth_bottom
bottomsurface = 1
else:
bottomsurface = 0
for inz in range(bottomsurface, cfg.nz - 1):
grdfilename = cfg.filename[inz - bottomsurface]
if cfg.irregulargridded_surf:
coordx, coordy, elev_1 = process_irregular_surfacefiles(
iproc, nx, ny, cfg.xmin, cfg.xmax, cfg.ymin, cfg.ymax,
xstep, ystep, grdfilename)
else:
coordx, coordy, elev_1 = process_surfacefiles(
iproc, nx, ny, nstep, grdfilename, cfg.unit,
cfg.lat_orientation)
elev[:, :, inz] = elev_1[:, :]
#
inz = cfg.nz - 1 # last surface
if cfg.sea:
elev[:, :, inz] = elev[:, :, inz - 1]
else:
if cfg.topflat:
elev[:, :, inz] = cfg.depth_top
else:
grdfile = cfg.filename[inz - bottomsurface]
print 'reading ', cfg.filename[inz - bottomsurface]
if cfg.irregulargridded_surf:
coordx, coordy, elev_1 = process_irregular_surfacefiles(
iproc, nx, ny, cfg.xmin, cfg.xmax, cfg.ymin, cfg.ymax,
xstep, ystep, grdfile)
else:
coordx, coordy, elev_1 = process_surfacefiles(
iproc, nx, ny, nstep, grdfile, cfg.unit,
cfg.lat_orientation)
elev[:, :, inz] = elev_1[:, :]
if cfg.subduction:
print 'subduction'
top = elev[:, :, inz]
slab = elev[:, :, inz - 1]
subcrit = numpy.abs(top - slab) < cfg.subduction_thres
top[subcrit] = slab[subcrit] + cfg.subduction_thres
print len(top[subcrit])
elev[:, :, inz] = top
return coordx, coordy, elev, nx, ny
# You should have received a copy of the GNU General Public License along #
# with this program; if not, write to the Free Software Foundation, Inc., #
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. #
# #
#############################################################################
try:
import start as start
cubit = start.start_cubit()
except:
try:
import cubit
except:
print 'error importing cubit, check if cubit is installed'
pass
numpy = start.start_numpy()
def check_orientation(grdfileNAME):
try:
grdfile = open(grdfileNAME, 'r')
print 'reading ', grdfileNAME
except:
txt = 'check_orintation ->error reading: ' + str(grdfileNAME)
raise Exception(txt)
diff = 1
txt = grdfile.readline()
x0, y0, z = map(float, txt.split())
while diff > 0:
try:
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 surface_regular_grid(isurface=0,cfgname=None):
"""
create an acis surface from a regular lon/lat/z grid
"""
import sys,os
from math import sqrt
from utilities import geo2utm
import start as start
#
#
cfg = start.start_cfg(cfgname)
numpy = start.start_numpy()
#
def create_line_u(ind,n,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[i+ind][0],data[i+ind][1],data[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 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
#
#
cubit.cmd("reset")
#
position=True
#
#
nu= cfg.num_x[isurface]
nv= cfg.num_y[isurface]
ustep= cfg.xstep[isurface]
vstep= cfg.ystep[isurface]
exag=1.
unit=cfg.unit2[isurface]
#
#
data=numpy.loadtxt(cfg.surface_name[isurface])
if len(data) > 100:
command = "set echo off"
cubit.cmd(command)
command = "set journal off"
cubit.cmd(command)
#
u_curve=[]
v_curve=[]
#
for iv in range(0,nv):
if iv%vstep == 0.:
u=create_line_u(iv*(nu),nu,ustep,data,unit)
u_curve.append(u)
for iu in range(0,nu):
if iu%ustep == 0.:
v=create_line_v(iu,nv,nu,ustep,data,unit)
v_curve.append(v)
#
umax=max(u_curve)
umin=min(u_curve)
vmax=max(v_curve)
vmin=min(v_curve)
cubitcommand= 'create surface net u curve '+ str( umin )+' to '+str( umax )+ ' v curve '+ str( vmin )+ ' to '+str( vmax )+' heal'
cubit.cmd(cubitcommand)
command = "del curve all"
cubit.cmd(command)
suff=cfg.surface_name[isurface].split('/')
command = "save as '"+cfg.working_dir+"/surf_"+suff[-1]+".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 mesh_layercake_regularmap(filename=None):
import sys,os
import start as start
mpiflag,iproc,numproc,mpi = start.start_mpi()
from utilities import importgeometry,savemesh,get_v_h_list,cubit_command_check
#
numpy = start.start_numpy()
cfg = start.start_cfg(filename=filename)
from math import sqrt
from sets import Set
#
class cubitvolume:
def __init__(self,ID,intervalv,centerpoint,dimension):
self.ID=ID
self.intervalv=intervalv
self.centerpoint=centerpoint
self.dim=dimension
def __repr__(self):
msg="(vol:%3i, vertical interval: %4i, centerpoint: %8.2f)" % (self.ID, self.intervalv,self.centerpoint)
return msg
#
def by_z(x,y):
return cmp(x.centerpoint,y.centerpoint)
#
#
#
list_vol=cubit.parse_cubit_list("volume","all")
if len(list_vol) != 0:
pass
else:
geometryfile='geometry_vol_'+str(iproc)+'.cub'
importgeometry(geometryfile,iproc=iproc)
#
command = 'composite create curve all'
cubit.cmd(command)
print '###"No valid composites can be created from the specified curves." is NOT a critical ERROR.'
#
command = "compress all"
cubit.cmd(command)
list_vol=cubit.parse_cubit_list("volume","all")
nvol=len(list_vol)
vol=[]
for id_vol in list_vol:
p=cubit.get_center_point("volume",id_vol)
vol.append(cubitvolume(id_vol,1,p[2],0))
vol.sort(by_z)
#
for id_vol in range(0,nvol):
vol[id_vol].intervalv=cfg.iv_interval[id_vol]
#
#
surf_vertical=[]
surf_or=[]
top_surface=0
top_surface_add=''
bottom_surface=0
#
zmin_box=cubit.get_total_bounding_box("volume",list_vol)[6]
xmin_box=cubit.get_total_bounding_box("volume",list_vol)[0]
xmax_box=cubit.get_total_bounding_box("volume",list_vol)[1]
ymin_box=cubit.get_total_bounding_box("volume",list_vol)[3]
ymax_box=cubit.get_total_bounding_box("volume",list_vol)[4]
#
#
#interval assignement
surf_or,surf_vertical,list_curve_or,list_curve_vertical,bottom,top = get_v_h_list(list_vol,chktop=cfg.chktop)
print 'vertical surfaces: ',surf_vertical
for k in surf_vertical:
command = "surface "+str(k)+" scheme submap"
cubit.cmd(command)
for k in surf_or:
command = "surface "+str(k)+" scheme "+cfg.or_mesh_scheme
cubit.cmd(command)
#
ucurve,vcurve=get_uv_curve(list_curve_or)
schemepave=False
#
ucurve_interval={}
for k in ucurve:
length=cubit.get_curve_length(k)
interval=int(2*round(.5*length/cfg.size,0))
ucurve_interval[k]=interval
command = "curve "+str(k)+" interval "+str(interval)
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
command = "curve "+str(k)+" scheme equal"
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
if max(ucurve_interval.values()) != min(ucurve_interval.values()):
schemepave=True
print 'mesh scheme is set to pave'
for sk in surf_or:
command = "surface "+str(sk)+" scheme pave"
cubit.cmd(command)
#
vcurve_interval={}
for k in vcurve:
length=cubit.get_curve_length(k)
interval=int(2*round(.5*length/cfg.size,0))
vcurve_interval[k]=interval
command = "curve "+str(k)+" interval "+str(interval)
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
command = "curve "+str(k)+" scheme equal"
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
if max(vcurve_interval.values()) != min(vcurve_interval.values()):
print 'mesh scheme is set to pave'
schemepave=True
for sk in surf_or:
command = "surface "+str(sk)+" scheme pave"
cubit.cmd(command)
#
for s in surf_vertical:
lcurve=cubit.get_relatives("surface",s,"curve")
interval_store=[]
for k in lcurve:
interval_curve=cubit.get_mesh_intervals('curve',k)
if k in list_curve_vertical:
volume_id = cubit.get_owning_volume("curve", k)
for idv in range(0,nvol):
if vol[idv].ID == volume_id:
int_v=vol[idv].intervalv
command = "curve "+str(k)+" interval "+str(int_v)
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
command = "curve "+str(k)+" scheme equal"
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
else:
interval_store.append((k,interval_curve))
if len(interval_store) != 0:
interval_min=min([iv[1] for iv in interval_store])
command = "curve "+' '.join(str(iv[0]) for iv in interval_store)+" interval "+str(interval_min)
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
command = "curve "+' '.join(str(iv[0]) for iv in interval_store)+" scheme equal"
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
command = "surface "+str(s)+" scheme submap"
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
#
#meshing
if cfg.or_mesh_scheme == 'pave' or schemepave:
command='mesh surf '+' '.join(str(t) for t in top)
status=cubit_command_check(iproc,command,stop=True)
#cubit.cmd(command)
elif cfg.or_mesh_scheme == 'map':
command='mesh surf '+' '.join(str(t) for t in bottom)
status=cubit_command_check(iproc,command,stop=True)
#cubit.cmd(command)
for id_volume in range(nvol-1,-1,-1):
command = "mesh vol "+str(vol[id_volume].ID)
status=cubit_command_check(iproc,command,stop=False)
if not status:
for s in surf_vertical:
command_surf="mesh surf "+str(s)
cubit.cmd(command_surf)
command_set_meshvol='volume all redistribute nodes on\nvolume all autosmooth target off\nvolume all scheme Sweep Vector 0 0 -1\nvolume all sweep smooth Auto\n'
status=cubit_command_check(iproc,command_set_meshvol,stop=False)
status=cubit_command_check(iproc,command,stop=True)
#
#smoothing
print iproc, 'untangling...'
cmd="volume all smooth scheme untangle beta 0.02 cpu 10"
cubit.cmd(cmd)
cmd="smooth volume all"
cubit.cmd(cmd)
if cfg.smoothing:
print 'smoothing .... '+str(cfg.smoothing)
cubitcommand= 'surf all smooth scheme laplacian '
cubit.cmd(cubitcommand)
cubitcommand= 'smooth surf all'
cubit.cmd(cubitcommand)
#
cubitcommand= 'vol all smooth scheme laplacian '
cubit.cmd(cubitcommand)
cubitcommand= 'smooth vol all'
cubit.cmd(cubitcommand)
#
#
##vertical refinement
##for nvol = 3
##
##___________________________ interface 4
##
##vol 2
##___________________________ interface 3
##
##vol 1
##___________________________ interface 2
##
##vol 0
##___________________________ interface 1
##
refinement(nvol,vol,filename=filename)
#
#top layer vertical coarsening
print 'coarsening top layer... ',cfg.coarsening_top_layer
if cfg.coarsening_top_layer:
from sets import Set
cubitcommand= 'del mesh vol '+str(vol[-1].ID)+ ' propagate'
cubit.cmd(cubitcommand)
s1=Set(list_curve_vertical)
command = "group 'list_curve_tmp' add curve "+"in vol "+str(vol[-1].ID)
cubit.cmd(command)
group=cubit.get_id_from_name("list_curve_tmp")
list_curve_tmp=cubit.get_group_curves(group)
command = "delete group "+ str(group)
cubit.cmd(command)
s2=Set(list_curve_tmp)
lc=list(s1 & s2)
#
cubitcommand= 'curve '+' '.join(str(x) for x in lc)+' interval '+str(cfg.actual_vertical_interval_top_layer)
cubit.cmd(cubitcommand)
cubitcommand= 'mesh vol '+str(vol[-1].ID)
cubit.cmd(cubitcommand)
#
n=cubit.get_sideset_id_list()
if len(n) != 0:
command = "del sideset all"
cubit.cmd(command)
n=cubit.get_block_id_list()
if len(n) != 0:
command = "del block all"
cubit.cmd(command)
#
import boundary_definition
entities=['face']
print iproc, 'hex block definition...'
boundary_definition.define_bc(entities,parallel=True,cpux=cfg.cpux,cpuy=cfg.cpuy,cpuxmin=0,cpuymin=0,optionsea=False)
#save mesh
print iproc, 'untangling...'
cmd="volume all smooth scheme untangle beta 0.02 cpu 10"
cubit.cmd(cmd)
cmd="smooth volume all"
cubit.cmd(cmd)
print iproc, 'saving...'
savemesh(mpiflag,iproc=iproc,filename=filename)
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)
