def create_gmsh_geo(shpfile, scalefile, geofile,
startpoly=0, ndmin=8, scalefac=1.0,\
r=1.08, lcmax=2000.0, sigmoid=0,\
linetype='BSpline'):
"""
Generate a gmsh *.geo file using a boundary from a shpfile
Inputs:
---
- shpfile : a polygon shapefile with the domain boundaries. Make sure
that the first polygon is the outer ring. If not change 'startpoly' parameter.
- scalefile : a line shapefile with field 'scale' specifying the target grid
resolution for that region.
- geofile: output geo ascii file.
*Optional*
- startpoly [default=0] - the index of the outer polygon in the shapefile.
- ndmin [default=8] - the minimum range of the scale = ndmin*scale
- r : expansion factor
- lcmax [default=2000] - the maximum grid cell size.
- sigmoid [default=0]
- linetype - 'BSpline' or 'Line'
"""
# Load the polygon shape file
xy, field = readShpPoly(shpfile, FIELDNAME='FID')
# Load the scale shape file
xyscale, scale = readShpPointLine(scalefile, FIELDNAME='scale')
# Load the 'embed' flag to see if the scale layer should be embedded
#try:
# exyscale,embed = readShpPointLine(scalefile,FIELDNAME='embed')
#except:
# print 'Warning - could not find "embed" field in shapefile. Setting embed = 0.'
# embed = [ss*0 for ss in scale]
exyscale, embed = readShpPointLine(scalefile, FIELDNAME='embed')
if embed == []:
embed = [ss * 0 for ss in scale]
## output geo and svg file
fgeo = open(geofile, 'w')
fgeo.write("""IP = newp;
IL = newl;
IS = news;
IF = newf;
""")
ip = 0 # Point counter
il = 0 # Line counter
rp = 0
lines = []
for loop in xy:
firstp = ip
for p in range(loop.shape[0]):
rp = rp + 1
fgeo.write("Point(IP + %i) = {%.16e, %.16e, %.16e}; // %i\n" %
(ip, loop[p, 0], loop[p, 1], 0., rp - 1))
ip = ip + 1
if linetype == 'Line' and ip > 1:
fgeo.write("Line(IL + %i) = {IP + %i , IP + %i};\n" % \
(il, ip-2, ip-1))
il = il + 1
lines.append(il - 1)
if linetype == 'BSpline':
fgeo.write("BSpline(IL + %i) = {IP + %i : IP + %i, IP + %i};\n" % \
(il, firstp, ip - 1, firstp))
il = il + 1
lines.append(il - 1)
# Create the surface polygon
fgeo.write('\n//%s\n//Surface Polygon Definition\n//%s\n\n' %
(72 * '#', 72 * '#'))
surfstart = il
fgeo.write("Line Loop(IL + %i) = {IL + %s};\n" % (il, startpoly))
il += 1
for ll in lines:
if ll != startpoly:
fgeo.write("Line Loop(IL + %i) = {IL + %s};\n" % (il, ll))
il += 1
surfend = il - 1
fgeo.write("Plane Surface(IL + %i) = {IL + %i : IL + %i};\n" %
(il, surfstart, surfend))
fgeo.write('Physical Surface("Ocean") = {IL + %i};\n' % il)
surface_id = il # Keep this to embed lines into
il += 1
# Create the grid scale lines and fields
fgeo.write('\n//%s\n//Grid Scale Definition\n//%s\n\n' %
(72 * '#', 72 * '#'))
slines = [] # Reference to scale lines
for loop, ss, ee in zip(xyscale, scale, embed):
firstp = ip
ss *= scalefac # Applies scale factor
for p in range(loop.shape[0]):
rp = rp + 1
#fgeo.write("Point(IP + %i) = {%.16e, %.16e, %.16e}; // %i\n" % (ip, loop[p,0], loop[p,1], 0., rp -1))
fgeo.write(
"Point(IP + %i) = {%.16e, %.16e, %.16e,%.16e}; // %i\n" %
(ip, loop[p, 0], loop[p, 1], 0., rp - 1, float(ss)))
ip = ip + 1
if ee:
#fgeo.write("BSpline(IL + %i) = {IP + %i : IP + %i};\n" % (il, firstp, ip - 1))
fgeo.write("%s(IL + %i) = {IP + %i : IP + %i};\n" %
(linetpye, il, firstp, ip - 1))
# Embed this line in the main surface so that cells are aligned
fgeo.write("Line{IL + %i} In Surface{IL + %i};\n" %
(il, surface_id))
else:
# Don't embed (can set as BSpline)
fgeo.write("%s(IL + %i) = {IP + %i : IP + %i};\n" %
(linetype, il, firstp, ip - 1))
slines.append(il)
il = il + 1
ifield = 0 # Field counter
fids = []
ii = 0
for ss, line in zip(scale, slines):
fgeo.write("Field[IF + %i] = Attractor;\n" % ifield)
fgeo.write("Field[IF + %i].EdgesList = {IL + %i};\n" % (ifield, line))
nodesperedge = get_nnodes_from_line(xyscale[ii], 2.0 * float(ss))
fgeo.write("Field[IF + %i].NNodesByEdge = %i;\n" %
(ifield, nodesperedge))
ifield += 1
fgeo.write("Field[IF + %i] = Threshold;\n" % ifield)
# Find the maximum distance
Nk = np.log(lcmax / ss) / np.log(r)
print(ss, Nk)
lmin = float(ndmin) * float(ss)
lmax = lmin + Nk * ss
fgeo.write("Field[IF + %i].DistMax = %6.2f;\n" % (ifield, lmax))
fgeo.write("Field[IF + %i].DistMin = %6.2f;\n" % (ifield, lmin))
fgeo.write("Field[IF + %i].IField = IF + %i;\n" % (ifield, ifield - 1))
fgeo.write("Field[IF + %i].LcMax = %6.2f;\n" % (ifield, lcmax))
fgeo.write("Field[IF + %i].LcMin = %6.2f;\n" % (ifield, float(ss)))
fgeo.write("Field[IF + %i].Sigmoid = %d;\n" % (ifield, sigmoid))
fids.append(ifield)
ifield += 1
ii += 1
fieldlist = '{'
for ff in fids:
fieldlist += 'IF + %d, ' % ff
fieldlist = fieldlist[:-2] + '}'
fgeo.write("Field[IF + %i] = Min;\n" % ifield)
fgeo.write("Field[IF + %i].FieldsList = %s;\n" % (ifield, fieldlist))
fgeo.write("Background Field = IF + %i;\n" % ifield)
# Set Quad options by default
fgeo.write("Mesh.CharacteristicLengthMax=%.16e;//Max cell size\n" % lcmax)
fgeo.write("Mesh.RecombineAll=0;//recombine all defined surfaces\n")
fgeo.write("Mesh.Algorithm=6;//front\n")
fgeo.write("Mesh.Smoothing=10;//10 smoothing steps\n")
fgeo.write("Mesh.Remove4Triangles = 1;\n")
fgeo.close()
print('Complete. GMSH geo file written to:\n\t %s' % geofile)
def create_gmsh_geo(shpfile, scalefile, geofile,
startpoly=0, ndmin=8, scalefac=1.0,\
r=1.08, lcmax=2000.0, sigmoid=0,\
linetype='BSpline'):
"""
Generate a gmsh *.geo file using a boundary from a shpfile
Inputs:
---
- shpfile : a polygon shapefile with the domain boundaries. Make sure
that the first polygon is the outer ring. If not change 'startpoly' parameter.
- scalefile : a line shapefile with field 'scale' specifying the target grid
resolution for that region.
- geofile: output geo ascii file.
*Optional*
- startpoly [default=0] - the index of the outer polygon in the shapefile.
- ndmin [default=8] - the minimum range of the scale = ndmin*scale
- r : expansion factor
- lcmax [default=2000] - the maximum grid cell size.
- sigmoid [default=0]
- linetype - 'BSpline' or 'Line'
"""
# Load the polygon shape file
xy,field = readShpPoly(shpfile,FIELDNAME='FID')
# Load the scale shape file
xyscale,scale = readShpPointLine(scalefile,FIELDNAME='scale')
# Load the 'embed' flag to see if the scale layer should be embedded
#try:
# exyscale,embed = readShpPointLine(scalefile,FIELDNAME='embed')
#except:
# print 'Warning - could not find "embed" field in shapefile. Setting embed = 0.'
# embed = [ss*0 for ss in scale]
exyscale,embed = readShpPointLine(scalefile,FIELDNAME='embed')
if embed == []:
embed = [ss*0 for ss in scale]
## output geo and svg file
fgeo = open(geofile,'w')
fgeo.write("""IP = newp;
IL = newl;
IS = news;
IF = newf;
""" )
ip = 0 # Point counter
il = 0 # Line counter
rp = 0
lines=[]
for loop in xy:
firstp = ip
for p in range(loop.shape[0]):
rp = rp + 1
fgeo.write("Point(IP + %i) = {%.16e, %.16e, %.16e}; // %i\n" % (ip, loop[p,0], loop[p,1], 0., rp -1))
ip = ip + 1
if linetype == 'Line' and ip > 1:
fgeo.write("Line(IL + %i) = {IP + %i , IP + %i};\n" % \
(il, ip-2, ip-1))
il = il + 1
lines.append(il-1)
if linetype =='BSpline':
fgeo.write("BSpline(IL + %i) = {IP + %i : IP + %i, IP + %i};\n" % \
(il, firstp, ip - 1, firstp))
il = il + 1
lines.append(il-1)
# Create the surface polygon
fgeo.write('\n//%s\n//Surface Polygon Definition\n//%s\n\n'%(72*'#',72*'#'))
surfstart=il
fgeo.write("Line Loop(IL + %i) = {IL + %s};\n" % (il,startpoly) )
il += 1
for ll in lines:
if ll != startpoly:
fgeo.write("Line Loop(IL + %i) = {IL + %s};\n" % (il,ll) )
il += 1
surfend = il - 1
fgeo.write("Plane Surface(IL + %i) = {IL + %i : IL + %i};\n"%(il,surfstart,surfend))
fgeo.write('Physical Surface("Ocean") = {IL + %i};\n'%il)
surface_id = il # Keep this to embed lines into
il += 1
# Create the grid scale lines and fields
fgeo.write('\n//%s\n//Grid Scale Definition\n//%s\n\n'%(72*'#',72*'#'))
slines=[] # Reference to scale lines
for loop,ss,ee in zip(xyscale,scale,embed):
firstp = ip
ss *= scalefac # Applies scale factor
for p in range(loop.shape[0]):
rp = rp + 1
#fgeo.write("Point(IP + %i) = {%.16e, %.16e, %.16e}; // %i\n" % (ip, loop[p,0], loop[p,1], 0., rp -1))
fgeo.write("Point(IP + %i) = {%.16e, %.16e, %.16e,%.16e}; // %i\n" % (ip, loop[p,0], loop[p,1], 0., rp -1,float(ss)))
ip = ip + 1
if ee:
#fgeo.write("BSpline(IL + %i) = {IP + %i : IP + %i};\n" % (il, firstp, ip - 1))
fgeo.write("%s(IL + %i) = {IP + %i : IP + %i};\n" % (linetpye,il, firstp, ip - 1))
# Embed this line in the main surface so that cells are aligned
fgeo.write("Line{IL + %i} In Surface{IL + %i};\n"%(il,surface_id))
else:
# Don't embed (can set as BSpline)
fgeo.write("%s(IL + %i) = {IP + %i : IP + %i};\n" % (linetype,il, firstp, ip - 1))
slines.append(il)
il = il + 1
ifield = 0 # Field counter
fids = []
ii=0
for ss,line in zip(scale,slines):
fgeo.write("Field[IF + %i] = Attractor;\n"%ifield)
fgeo.write("Field[IF + %i].EdgesList = {IL + %i};\n"%(ifield,line))
nodesperedge = get_nnodes_from_line(xyscale[ii],2.0*float(ss))
fgeo.write("Field[IF + %i].NNodesByEdge = %i;\n"%(ifield,nodesperedge))
ifield+=1
fgeo.write("Field[IF + %i] = Threshold;\n"%ifield)
# Find the maximum distance
Nk = np.log(lcmax/ss)/np.log(r)
print ss,Nk
lmin = float(ndmin)*float(ss)
lmax = lmin + Nk * ss
fgeo.write("Field[IF + %i].DistMax = %6.2f;\n"%(ifield,lmax))
fgeo.write("Field[IF + %i].DistMin = %6.2f;\n"%(ifield,lmin))
fgeo.write("Field[IF + %i].IField = IF + %i;\n"%(ifield,ifield-1))
fgeo.write("Field[IF + %i].LcMax = %6.2f;\n"%(ifield,lcmax))
fgeo.write("Field[IF + %i].LcMin = %6.2f;\n"%(ifield,float(ss)))
fgeo.write("Field[IF + %i].Sigmoid = %d;\n"%(ifield,sigmoid))
fids.append(ifield)
ifield+=1
ii+=1
fieldlist = '{'
for ff in fids:
fieldlist += 'IF + %d, '%ff
fieldlist = fieldlist[:-2]+'}'
fgeo.write("Field[IF + %i] = Min;\n"%ifield)
fgeo.write("Field[IF + %i].FieldsList = %s;\n"%(ifield,fieldlist))
fgeo.write("Background Field = IF + %i;\n"%ifield)
# Set Quad options by default
fgeo.write("Mesh.CharacteristicLengthMax=%.16e;//Max cell size\n"%lcmax)
fgeo.write("Mesh.RecombineAll=0;//recombine all defined surfaces\n")
fgeo.write("Mesh.Algorithm=6;//front\n")
fgeo.write("Mesh.Smoothing=10;//10 smoothing steps\n")
fgeo.write("Mesh.Remove4Triangles = 1;\n")
fgeo.close()
print 'Complete. GMSH geo file written to:\n\t %s'%geofile
def create_pos_file(posfile,scalefile, xlims,ylims,dx,\
geofile=None,ndmin=5, lcmax=2000.,r=1.05, scalefac=1.0):
"""
Generates a gmsh background scale file (*.pos)
If a geofile is specified the mesh is embedded
"""
from shapely import geometry, speedups
import pandas as pd
if speedups.available:
speedups.enable()
X, Y = np.meshgrid(np.arange(xlims[0], xlims[1], dx),
np.arange(ylims[0], ylims[1], dx))
xy = np.vstack((X.ravel(), Y.ravel())).T
Np = xy.shape[0]
nj, ni = X.shape
# Load the scalefile
xyscale, gridscale = readShpPointLine(scalefile, FIELDNAME='scale')
# Load all of the points into shapely type geometry
# Distance method won't work with numpy array
#P = geometry.asPoint(xy)
P = [geometry.Point(xy[i, 0], xy[i, 1]) for i in range(Np)]
L = []
for ll in xyscale:
L.append(geometry.asLineString(ll))
# Vectorize operations using pandas
geo_points = pd.DataFrame({'single_column':xy.tolist()}).single_column.\
apply(lambda x: geometry.Point(x[0],x[1])).values
geo_lines = pd.DataFrame({'single_column':xyscale}).single_column.\
apply(lambda x: geometry.LineString(x)).values
def distance(a_point, a_line):
return a_point.distance(a_line)
distance_vec = np.vectorize(distance)
dist_all = distance_vec(geo_points[..., np.newaxis], geo_lines)
nlines = len(L)
scale_all = np.zeros((nj, ni, nlines))
for n in range(nlines):
print('Calculating distance from line %d...' % n)
ss = gridscale[n] * scalefac
lmin = ndmin * ss
# Find the maximum distance
Nk = np.log(lcmax / ss) / np.log(r)
print(ss, Nk)
lmax = lmin + Nk * ss
#dist = [L[n].distance(P[i]) for i in range(Np)]
#dist = np.array(dist).reshape((nj,ni))
dist = dist_all[:, n].reshape((nj, ni))
# Calculate the scale
N = (dist - lmin) / ss
scale = ss * r**N
ind = dist <= lmin
if ind.any():
scale[ind] = ss
ind = scale > lcmax
if ind.any():
scale[ind] = lcmax
scale_all[:, :, n] = scale
scale_min = scale_all.min(axis=-1)
write_pos_file(posfile, X, Y, scale_min)
if not geofile is None:
fgeo = open(geofile, 'a')
fgeo.write(
"// Merge a post-processing view containing the target mesh sizes\n"
)
fgeo.write('Merge "%s";' % posfile)
fgeo.write("// Apply the view as the current background mesh\n")
fgeo.write("Background Mesh View[0];\n")
fgeo.close()
def create_pos_file(posfile,scalefile, xlims,ylims,dx,\
geofile=None,ndmin=5, lcmax=2000.,r=1.05, scalefac=1.0):
"""
Generates a gmsh background scale file (*.pos)
If a geofile is specified the mesh is embedded
"""
from shapely import geometry, speedups
import pandas as pd
if speedups.available:
speedups.enable()
X,Y = np.meshgrid(np.arange(xlims[0],xlims[1],dx),np.arange(ylims[0],ylims[1],dx))
xy = np.vstack((X.ravel(),Y.ravel())).T
Np = xy.shape[0]
nj,ni=X.shape
# Load the scalefile
xyscale,gridscale = readShpPointLine(scalefile,FIELDNAME='scale')
# Load all of the points into shapely type geometry
# Distance method won't work with numpy array
#P = geometry.asPoint(xy)
P = [geometry.Point(xy[i,0],xy[i,1]) for i in range(Np)]
L=[]
for ll in xyscale:
L.append(geometry.asLineString(ll))
# Vectorize operations using pandas
geo_points = pd.DataFrame({'single_column':xy.tolist()}).single_column.\
apply(lambda x: geometry.Point(x[0],x[1])).values
geo_lines = pd.DataFrame({'single_column':xyscale}).single_column.\
apply(lambda x: geometry.LineString(x)).values
def distance(a_point, a_line):
return a_point.distance(a_line)
distance_vec = np.vectorize(distance)
dist_all = distance_vec(geo_points[...,np.newaxis], geo_lines)
nlines = len(L)
scale_all = np.zeros((nj,ni,nlines))
for n in range(nlines):
print 'Calculating distance from line %d...'%n
ss = gridscale[n] * scalefac
lmin = ndmin * ss
# Find the maximum distance
Nk = np.log(lcmax/ss)/np.log(r)
print ss,Nk
lmax = lmin + Nk * ss
#dist = [L[n].distance(P[i]) for i in range(Np)]
#dist = np.array(dist).reshape((nj,ni))
dist = dist_all[:,n].reshape((nj,ni))
# Calculate the scale
N = (dist-lmin)/ss
scale = ss*r**N
ind = dist<=lmin
if ind.any():
scale[ind] = ss
ind = scale>lcmax
if ind.any():
scale[ind] = lcmax
scale_all[:,:,n] = scale
scale_min = scale_all.min(axis=-1)
write_pos_file(posfile,X,Y,scale_min)
if not geofile is None:
fgeo = open(geofile,'a')
fgeo.write("// Merge a post-processing view containing the target mesh sizes\n")
fgeo.write('Merge "%s";'%posfile)
fgeo.write("// Apply the view as the current background mesh\n")
fgeo.write("Background Mesh View[0];\n")
fgeo.close()