def cubit_command_check(iproc, command, stop=True):
"""
Run a cubit command, checking if it performs correctly.
If the command fails, it writes the result on a file "error_[processor number]" and stop the meshing process
iproc = process number
command = cubit command
stop = if command fails, stop the meshing process (Default: True)
return status variable (0 ok, -1 fail)
"""
er = cubit.get_error_count()
cubit.cmd(command)
ner = cubit.get_error_count()
flag = 0
if ner > er:
text = '"Proc: ' + str(iproc) + ' ERROR ' + str(
command) + ' number of error ' + str(er) + '/' + str(ner) + '"'
cubitcommand = 'comment ' + text
cubit.cmd(cubitcommand)
f = open('error_' + str(iproc) + '.log', 'a')
f.write("CUBIT ERROR: \n" + text)
f.close()
if stop: raise Exception("CUBIT ERROR: " + text)
flag = -1
return flag
def cubit_command_check(iproc, command, stop=True):
"""
Run a cubit command, checking if it performs correctly.
If the command fails, it writes the result on a file
"error_[processor number]" and stop the meshing process
iproc = process number
command = cubit command
stop = if command fails, stop the meshing process (Default: True)
return status variable (0 ok, -1 fail)
"""
flag = True
er = cubit.get_error_count()
cubit.cmd(command)
print command
ner = cubit.get_error_count()
if ner > er:
text = '"Proc: ' + str(iproc) + ' ERROR ' + str(command) + \
' number of error ' + str(er) + '/' + str(ner) + '"'
cubitcommand = 'comment ' + text
cubit.cmd(cubitcommand)
f = open('error_' + str(iproc) + '.log', 'a')
f.write("CUBIT ERROR: \n" + text)
f.close()
if stop:
raise Exception("CUBIT ERROR: " + text)
flag = False
return flag
def runsave(geometryfile,iproc,filename=None):
import start as start
cubit = start.start_cubit()
cfg = start.start_cfg(filename=filename)
flag=[0]
ner=cubit.get_error_count()
cubitcommand= 'save as "'+ cfg.output_dir+'/'+geometryfile+ '" overwrite'
cubit.cmd(cubitcommand)
ner2=cubit.get_error_count()
if ner == ner2:
flag=[1]
return flag
def runsave(geometryfile, iproc, filename=None):
import start as start
cubit = start.start_cubit()
cfg = start.start_cfg(filename=filename)
flag = [0]
ner = cubit.get_error_count()
cubitcommand = 'save as "' + cfg.output_dir + '/' + geometryfile + '" overwrite'
cubit.cmd(cubitcommand)
ner2 = cubit.get_error_count()
if ner == ner2:
flag = [1]
return flag
def runsave(meshfile,iproc,filename=None):
import start as start
cubit = start.start_cubit()
cfg = start.start_cfg(filename=filename)
flag=0
ner=cubit.get_error_count()
cubitcommand= 'save as "'+ cfg.output_dir+'/'+meshfile+'.cub'+ '" overwrite'
cubit.cmd(cubitcommand)
ner2=cubit.get_error_count()
if ner == ner2:
cubitcommand= 'export mesh "'+ cfg.output_dir+'/'+meshfile+'.e'+ '" dimension 3 block all overwrite'
cubit.cmd(cubitcommand)
ner2=cubit.get_error_count()
if ner == ner2:
flag=1
return flag
def runsave(meshfile, iproc, filename=None):
import start as start
cubit = start.start_cubit()
cfg = start.start_cfg(filename=filename)
flag = 0
ner = cubit.get_error_count()
cubitcommand = 'save as "' + cfg.output_dir + '/' + meshfile + '.cub' + '" overwrite'
cubit.cmd(cubitcommand)
ner2 = cubit.get_error_count()
if ner == ner2:
cubitcommand = 'export mesh "' + cfg.output_dir + '/' + meshfile + '.e' + '" dimension 3 block all overwrite'
cubit.cmd(cubitcommand)
ner2 = cubit.get_error_count()
if ner == ner2:
flag = 1
return flag
def cubit_error_stop(iproc,command,ner):
"""obsolete"""
er=cubit.get_error_count()
if er > ner:
text='"Proc: '+str(iproc)+' ERROR '+str(command)+' number of error '+str(er)+'/'+str(ner)+'"'
cubitcommand = 'comment '+text
cubit.cmd(cubitcommand)
raise NameError, text
def cubit_error_continue(iproc,command,n_er):
"""obsolete"""
er=cubit.get_error_count()
if er >= n_er:
text='"Proc: '+str(iproc)+' ERROR continue '+str(command)+' number of error '+str(er)+' '+str(n_er)+'"'
cubit.cmd('comment '+ text)
print 'error: ',text
return er
def cubit_error_stop(iproc, command, ner):
"""obsolete"""
er = cubit.get_error_count()
if er > ner:
text = '"Proc: ' + str(iproc) + ' ERROR ' + str(
command) + ' number of error ' + str(er) + '/' + str(ner) + '"'
cubitcommand = 'comment ' + text
cubit.cmd(cubitcommand)
raise NameError, text
def cubit_error_continue(iproc, command, n_er):
"""obsolete"""
er = cubit.get_error_count()
if er >= n_er:
text = '"Proc: ' + str(iproc) + ' ERROR continue ' + str(
command) + ' number of error ' + str(er) + ' ' + str(n_er) + '"'
cubit.cmd('comment ' + text)
print 'error: ', text
return er
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 layercake_volume_fromacis_mpiregularmap(filename=None):
import sys
import start as start
#
mpiflag,iproc,numproc,mpi = start.start_mpi()
#
cfg = start.start_cfg(filename=filename)
#
from utilities import geo2utm, savegeometry
#
from math import sqrt
#
try:
mpi.barrier()
except:
pass
#
#
command = "comment '"+"PROC: "+str(iproc)+"/"+str(numproc)+" '"
cubit.cmd(command)
#
#get the limit of the volume considering the cpu
def xwebcut(x):
command='create planar surface with plane xplane offset '+str(x)
cubit.cmd(command)
last_surface=cubit.get_last_id("surface")
command="webcut volume all tool volume in surf "+str(last_surface)
cubit.cmd(command)
command="del surf "+str(last_surface)
cubit.cmd(command)
def ywebcut(x):
command='create planar surface with plane yplane offset '+str(x)
cubit.cmd(command)
last_surface=cubit.get_last_id("surface")
command="webcut volume all tool volume in surf "+str(last_surface)
cubit.cmd(command)
command="del surf "+str(last_surface)
cubit.cmd(command)
def translate2zero():
ss=cubit.parse_cubit_list('surface','all')
box = cubit.get_total_bounding_box("surface", ss)
xmin=box[0]
ymin=box[3]
cubit.cmd('move surface all x '+str(-1*xmin)+' y '+str(-1*ymin))
return xmin,ymin
def translate2original(xmin,ymin):
cubit.cmd('move surface all x '+str(xmin)+' y '+str(ymin))
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
#
ner=cubit.get_error_count()
#
icurve=0
isurf=0
ivertex=0
#
xlength=(cfg.xmax-cfg.xmin)/float(cfg.cpux) #length of x slide for chunk
ylength=(cfg.ymax-cfg.ymin)/float(cfg.cpuy) #length of y slide for chunk
xmin_cpu=cfg.xmin+(xlength*(icpux))
ymin_cpu=cfg.ymin+(ylength*(icpuy))
xmax_cpu=xmin_cpu+xlength
ymax_cpu=ymin_cpu+ylength
#
#importing the surfaces
for inz in range(cfg.nz-2,-2,-1):
if cfg.bottomflat and inz==-1:
command = "create planar surface with plane zplane offset "+str(cfg.depth_bottom)
cubit.cmd(command)
else:
command = "import cubit '"+cfg.filename[inz]+"'"
cubit.cmd(command)
#translate
xmin,ymin=translate2zero()
print 'translate ...', -xmin,-ymin
xmin_cpu=xmin_cpu-xmin
ymin_cpu=ymin_cpu-ymin
xmax_cpu=xmax_cpu-xmin
ymax_cpu=ymax_cpu-ymin
ss=cubit.parse_cubit_list('surface','all')
box = cubit.get_total_bounding_box("surface", ss)
print 'dimension... ', box
#cutting the surfaces
xwebcut(xmin_cpu)
xwebcut(xmax_cpu)
ywebcut(ymin_cpu)
ywebcut(ymax_cpu)
#
list_surface_all=cubit.parse_cubit_list("surface","all")
#condisidering only the surfaces inside the boundaries
dict_surf={}
for isurf in list_surface_all:
p=cubit.get_center_point("surface",isurf)
if p[0] < xmin_cpu or p[0] > xmax_cpu or p[1] > ymax_cpu or p[1] < ymin_cpu:
command = "del surf "+str(isurf)
cubit.cmd(command)
else:
dict_surf[str(isurf)]=p[2]
z=dict_surf.values()
z.sort()
list_surf=[]
for val in z:
isurf=[k for k, v in dict_surf.iteritems() if v == val][0]
list_surf.append(int(isurf))
#
#lofting the volume
for i,j in zip(list_surf,list_surf[1:]):
ner=cubit.get_error_count()
create_volume(i,j,method=cfg.volumecreation_method)
#cubitcommand= 'create volume loft surface '+ str(i)+' '+str(j)
#cubit.cmd(cubitcommand)
ner2=cubit.get_error_count()
#
translate2original(xmin,ymin)
if ner == ner2:
cubitcommand= 'del surface all'
cubit.cmd(cubitcommand)
#
#
#cubitcommand= 'composite create curve in vol all'
#cubit.cmd(cubitcommand)
list_vol=cubit.parse_cubit_list("volume","all")
if len(list_vol) > 1:
cubitcommand= 'imprint volume all'
cubit.cmd(cubitcommand)
#cubit_error_stop(iproc,cubitcommand,ner)
#
cubitcommand= 'merge all'
cubit.cmd(cubitcommand)
#
savegeometry(iproc,filename=filename)
# name element blocks for master earth...
blockCount = 1
cubit.cmd ('block ' + str (blockCount) + ' volume with name "masters*"')
cubit.cmd ('block ' + str (blockCount) + ' name "master"')
# and nodesets...
cubit.cmd ('Nodeset ' + str (blockCount) + ' volume with name "masters*"')
cubit.cmd ('Nodeset ' + str (blockCount) + ' name "master"')
# now go through and group the rest of the regions into blocks and nodesets
blockCount = 2
for region in names:
cubit.cmd ('block ' + str (blockCount) + ' volume with name "' + region + '*"')
cubit.cmd ('block ' + str (blockCount) + ' name "' + region + '"')
cubit.cmd ('Nodeset ' + str (blockCount) + ' volume with name "' + region + '*"')
cubit.cmd ('Nodeset ' + str (blockCount) + ' name "' + region + '"')
blockCount = blockCount + 1
cubit.cmd ('Surface all scheme trimesh')
# write and reset for next file.
cubit.cmd ('save as "' + geomPath + 'regions/' + file + '" overwrite')
cubit.cmd ('reset')
if cubit.get_error_count () != 0:
print "Unfortunately, I found some errors"
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 layercake_volume_fromacis_mpiregularmap(filename=None):
import sys
import start as start
#
mpiflag, iproc, numproc, mpi = start.start_mpi()
#
cfg = start.start_cfg(filename=filename)
#
from utilities import geo2utm, savegeometry
#
from math import sqrt
#
try:
mpi.barrier()
except:
pass
#
#
command = "comment '" + "PROC: " + str(iproc) + "/" + str(numproc) + " '"
cubit.cmd(command)
#
#get the limit of the volume considering the cpu
def xwebcut(x):
command = 'create planar surface with plane xplane offset ' + str(x)
cubit.cmd(command)
last_surface = cubit.get_last_id("surface")
command = "webcut volume all tool volume in surf " + str(last_surface)
cubit.cmd(command)
command = "del surf " + str(last_surface)
cubit.cmd(command)
def ywebcut(x):
command = 'create planar surface with plane yplane offset ' + str(x)
cubit.cmd(command)
last_surface = cubit.get_last_id("surface")
command = "webcut volume all tool volume in surf " + str(last_surface)
cubit.cmd(command)
command = "del surf " + str(last_surface)
cubit.cmd(command)
def translate2zero():
ss = cubit.parse_cubit_list('surface', 'all')
box = cubit.get_total_bounding_box("surface", ss)
xmin = box[0]
ymin = box[3]
cubit.cmd('move surface all x ' + str(-1 * xmin) + ' y ' +
str(-1 * ymin))
return xmin, ymin
def translate2original(xmin, ymin):
cubit.cmd('move surface all x ' + str(xmin) + ' y ' + str(ymin))
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
#
ner = cubit.get_error_count()
#
icurve = 0
isurf = 0
ivertex = 0
#
xlength = (cfg.xmax - cfg.xmin) / float(
cfg.cpux) #length of x slide for chunk
ylength = (cfg.ymax - cfg.ymin) / float(
cfg.cpuy) #length of y slide for chunk
xmin_cpu = cfg.xmin + (xlength * (icpux))
ymin_cpu = cfg.ymin + (ylength * (icpuy))
xmax_cpu = xmin_cpu + xlength
ymax_cpu = ymin_cpu + ylength
#
#importing the surfaces
for inz in range(cfg.nz - 2, -2, -1):
if cfg.bottomflat and inz == -1:
command = "create planar surface with plane zplane offset " + str(
cfg.depth_bottom)
cubit.cmd(command)
else:
command = "import cubit '" + cfg.filename[inz] + "'"
cubit.cmd(command)
#translate
xmin, ymin = translate2zero()
print 'translate ...', -xmin, -ymin
xmin_cpu = xmin_cpu - xmin
ymin_cpu = ymin_cpu - ymin
xmax_cpu = xmax_cpu - xmin
ymax_cpu = ymax_cpu - ymin
ss = cubit.parse_cubit_list('surface', 'all')
box = cubit.get_total_bounding_box("surface", ss)
print 'dimension... ', box
#cutting the surfaces
xwebcut(xmin_cpu)
xwebcut(xmax_cpu)
ywebcut(ymin_cpu)
ywebcut(ymax_cpu)
#
list_surface_all = cubit.parse_cubit_list("surface", "all")
#condisidering only the surfaces inside the boundaries
dict_surf = {}
for isurf in list_surface_all:
p = cubit.get_center_point("surface", isurf)
if p[0] < xmin_cpu or p[0] > xmax_cpu or p[1] > ymax_cpu or p[
1] < ymin_cpu:
command = "del surf " + str(isurf)
cubit.cmd(command)
else:
dict_surf[str(isurf)] = p[2]
z = dict_surf.values()
z.sort()
list_surf = []
for val in z:
isurf = [k for k, v in dict_surf.iteritems() if v == val][0]
list_surf.append(int(isurf))
#
#lofting the volume
for i, j in zip(list_surf, list_surf[1:]):
ner = cubit.get_error_count()
create_volume(i, j, method=cfg.volumecreation_method)
#cubitcommand= 'create volume loft surface '+ str(i)+' '+str(j)
#cubit.cmd(cubitcommand)
ner2 = cubit.get_error_count()
#
translate2original(xmin, ymin)
if ner == ner2:
cubitcommand = 'del surface all'
cubit.cmd(cubitcommand)
#
#
#cubitcommand= 'composite create curve in vol all'
#cubit.cmd(cubitcommand)
list_vol = cubit.parse_cubit_list("volume", "all")
if len(list_vol) > 1:
cubitcommand = 'imprint volume all'
cubit.cmd(cubitcommand)
#cubit_error_stop(iproc,cubitcommand,ner)
#
cubitcommand = 'merge all'
cubit.cmd(cubitcommand)
#
savegeometry(iproc, filename=filename)
'xpositive ypositive zpositive' )
fSub = '.rad' + str(rad-abs(dis)).zfill(4) + '-' + str(rad).zfill(4) + \
'.000.cub" overwrite journal'
cubit.cmd ( 'vol 1 name "masters"' )
cubit.cmd ( "group 'Masters' equals Volume all\n" )
cubit.cmd ( fNameBase + 'col000-090.lon000-090' + fSub + '\n' )
cubit.cmd ( 'rotate volume all angle 90 about z include_merged\n' )
cubit.cmd ( fNameBase + 'col000-090.lon090-180' + fSub + '\n' )
cubit.cmd ( 'rotate volume all angle 90 about z include_merged\n' )
cubit.cmd ( fNameBase + 'col000-090.lon180-270' + fSub + '\n' )
cubit.cmd ( 'rotate volume all angle 90 about z include_merged\n' )
cubit.cmd ( fNameBase + 'col000-090.lon270-360' + fSub + '\n' )
cubit.cmd ( 'rotate volume all angle 90 about z include_merged\n' )
cubit.cmd ( 'volume all reflect Z\n' )
cubit.cmd ( fNameBase + 'col090-180.lon000-090' + fSub + '\n' )
cubit.cmd ( 'rotate volume all angle 90 about z include_merged\n' )
cubit.cmd ( fNameBase + 'col090-180.lon090-180' + fSub + '\n' )
cubit.cmd ( 'rotate volume all angle 90 about z include_merged\n' )
cubit.cmd ( fNameBase + 'col090-180.lon180-270' + fSub + '\n' )
cubit.cmd ( 'rotate volume all angle 90 about z include_merged\n' )
cubit.cmd ( fNameBase + 'col090-180.lon270-360' + fSub + '\n' )
cubit.cmd ( 'reset' )
if ( cubit.get_error_count () != 0 ):
print "I'm so sorry, but I've detected errors. Check."
cubit.cmd ( 'quit' )