def porfsOpt(x):
global dedge
vx = int(x)
vy = vx
vz = vx
if os.path.isfile(filenameBox + '.vtk'):
os.remove(filenameBox + '.vtk')
if not os.path.isfile(filenameBox + '.ply'):
raise SystemError(".ply file is missing. Nothing to binarize.")
os.system("binvox -e -d {0:d} -rotz -rotx -rotz -rotz -t vtk ".format(vx) +
filenameBox + ".ply >binvox.out")
filenameIn = filenameBox + ".vtk"
filenameOut = filenameBoxAscii + ".vtk"
origin = [dx, dy, dz]
spacing = [dx / vx, dy / vy, dz / vz]
vtkconv.main(filenameIn, filenameOut, origin, spacing)
f = open("foamreconstr.in", "w")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("{0:f}\n".format(dedge))
f.write("{0:f}\n".format(1 - strutContent * (1 - porosity)))
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write(filenameBoxStruts + "\n")
f.write(filenameBoxAscii + ".vtk\n")
f.write(filename + ".gnu\n")
f.write("name\n")
f.write(filenameDescriptors + "\n")
f.write(filenameParameters + "\n")
f.close()
os.system("./foamreconstr/foamreconstr")
f = open(filenameDescriptors, "r")
eps = float(f.readline())
fs = float(f.readline())
f.close()
f = open(filenameParameters, "r")
dedge = float(f.readline())
f.close()
resid = ((eps - porosity) / porosity)**2
print "dimension: {0:f}, porosity: {1:f}".format(vx,eps)+\
", strut content: {0:f}".format(fs)
return resid
def porfsOpt(x):
global dedge
vx=int(x)
vy=vx
vz=vx
if os.path.isfile(filenameBox+'.vtk'):
os.remove(filenameBox+'.vtk')
if not os.path.isfile(filenameBox+'.ply'):
raise SystemError(".ply file is missing. Nothing to binarize.")
os.system("binvox -e -d {0:d} -rotz -rotx -rotz -rotz -t vtk ".format(vx)+
filenameBox+".ply >binvox.out")
filenameIn = filenameBox+".vtk"
filenameOut = filenameBoxAscii+".vtk"
origin=[dx,dy,dz]
spacing=[dx/vx,dy/vy,dz/vz]
vtkconv.main(filenameIn,filenameOut,origin,spacing)
f=open("foamreconstr.in","w")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("{0:f}\n".format(dedge))
f.write("{0:f}\n".format(1-strutContent*(1-porosity)))
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write(filenameBoxStruts+"\n")
f.write(filenameBoxAscii+".vtk\n")
f.write(filename+".gnu\n")
f.write("name\n")
f.write(filenameDescriptors+"\n")
f.write(filenameParameters+"\n")
f.close()
os.system("./foamreconstr/foamreconstr")
f=open(filenameDescriptors,"r")
eps=float(f.readline())
fs=float(f.readline())
f.close()
f=open(filenameParameters,"r")
dedge=float(f.readline())
f.close()
resid=((eps-porosity)/porosity)**2
print "dimension: {0:f}, porosity: {1:f}".format(vx,eps)+\
", strut content: {0:f}".format(fs)
return resid
vx = int(vx)
print 'box size: {0:d}'.format(vx)
vy = vx
vz = vx
print(term.yellow + "Creating and saving optimal foam" + term.normal)
porOpt(vx) # Call it with the optimized box size
if deleteFiles:
os.remove("binvox.out")
os.remove(filename + ".ply")
######### Convert binary .vtk to ascii .vtk
print(term.yellow + "Convert binary .vtk to ascii .vtk" + term.normal)
filenameIn = filenameBox + ".vtk"
filenameOut = filenameBoxAscii + ".vtk"
origin = [dx, dy, dz]
spacing = [dx / vx, dy / vy, dz / vz]
vtkconv.main(filenameIn, filenameOut, origin, spacing)
if deleteFiles:
os.remove(filenameIn)
else:
print(term.yellow + "Optimizing porosity and strut content" +
term.normal)
res = minimize_scalar(porfsOpt,
bracket=[150, 200],
method='Brent',
tol=1e-2)
# res=minimize_scalar(porfsOpt,bounds=[200,250],method='bounded',tol=2e0)
vx = res.x
vx = int(vx)
print 'optimal box size: {0:d}'.format(vx)
vy = vx
vz = vx
def main():
"""Main function.
Executed when running the script from command line.
"""
ts = datetime.datetime.now()
########## Create periodic RVE of foam
print(
term.yellow +
"Create periodic RVE of foam" +
term.normal
)
FoamGeometryConstruction_Periodic.main(
MU,SIGMA,NumOfCells,filename,packing,
alternativePackingAlgorithm,tesselation,visualizeTesselation,geometry,
statistics,hypermesh,deleteFiles,dx,dy,dz
)
if moveToPeriodicBox:
########## Convert .geo to .stl
print(
term.yellow +
"Convert .geo to .stl" +
term.normal
)
os.system("gmsh -n -2 -format stl "+filename+".geo >gmsh.out")
if deleteFiles:
os.remove("gmsh.out")
########## Move to periodic box
print(
term.yellow +
"Move to periodic box" +
term.normal
)
filenameIn = filename+".stl"
filenameOut = filenameBox+".stl"
xmin=dx
ymin=dy
zmin=dz
periodicBox.main(
filenameIn,filenameOut,xmin,ymin,zmin,dx,dy,dz,renderBox
)
if deleteFiles:
os.remove(filenameIn)
########## Convert .stl to .ply
print(
term.yellow +
"Convert .stl to .ply" +
term.normal
)
os.system("meshconv "+filenameBox+".stl -c ply")
if deleteFiles:
os.remove(filenameBox+'.stl')
if binarizeBox:
########## Binarize and save as .vtk
if strutContent==0:
# Find the size of box, which would give desired porosity
# This method is not optimal, since the solver doesn't know that the
# function takes only integer arguments
print(
term.yellow +
"Optimizing porosity" +
term.normal
)
res=minimize_scalar(
porOpt,bracket=[100,120],method='Brent',tol=1e-2
)
vx=res.x
vx=int(vx)
print 'box size: {0:d}'.format(vx)
vy=vx
vz=vx
print(
term.yellow +
"Creating and saving optimal foam" +
term.normal
)
porOpt(vx) # Call it with the optimized box size
if deleteFiles:
os.remove("binvox.out")
os.remove(filename+".ply")
######### Convert binary .vtk to ascii .vtk
print(
term.yellow +
"Convert binary .vtk to ascii .vtk" +
term.normal
)
filenameIn = filenameBox+".vtk"
filenameOut = filenameBoxAscii+".vtk"
origin=[dx,dy,dz]
spacing=[dx/vx,dy/vy,dz/vz]
vtkconv.main(filenameIn,filenameOut,origin,spacing)
if deleteFiles:
os.remove(filenameIn)
else:
print(
term.yellow +
"Optimizing porosity and strut content" +
term.normal
)
res=minimize_scalar(
porfsOpt,bracket=[150,200],method='Brent',tol=1e-2
)
# res=minimize_scalar(
# porfsOpt,bounds=[200,250],method='bounded',tol=2e0
# )
vx=res.x
vx=int(vx)
print 'optimal box size: {0:d}'.format(vx)
vy=vx
vz=vx
print(
term.yellow +
"Creating and saving optimal foam" +
term.normal
)
if os.path.isfile(filenameBox+'.vtk'):
os.remove(filenameBox+'.vtk')
if not os.path.isfile(filenameBox+'.ply'):
raise SystemError(".ply file is missing. Nothing to binarize.")
os.system(
"binvox -e -d {0:d}".format(vx)+" -rotz -rotx -rotz -rotz "
+"-t vtk "+filenameBox+".ply >binvox.out"
)
filenameIn = filenameBox+".vtk"
filenameOut = filenameBoxAscii+".vtk"
origin=[dx,dy,dz]
spacing=[dx/vx,dy/vy,dz/vz]
vtkconv.main(filenameIn,filenameOut,origin,spacing)
f=open("foamreconstr.in","w")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("{0:f}\n".format(dedge))
f.write("{0:f}\n".format(1-strutContent*(1-porosity)))
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write(filenameBoxStruts+"\n")
f.write(filenameBoxAscii+".vtk\n")
f.write(filename+".gnu\n")
f.write("name\n")
f.write(filenameDescriptors+"\n")
f.write(filenameParameters+"\n")
f.close()
os.system("./foamreconstr/foamreconstr")
if deleteFiles:
os.remove(filenameBoxAscii+".vtk")
os.remove(filenameDescriptors)
os.remove(filenameParameters)
os.remove("binvox.out")
os.remove(filenameBox+".vtk")
os.remove("foamreconstr.in")
tf = datetime.datetime.now()
te = tf - ts
print "Foam created in: ",te
def main():
"""Main function.
Executed when running the script from command line.
"""
ts = datetime.datetime.now()
########## Create periodic RVE of foam
print(term.yellow + "Create periodic RVE of foam" + term.normal)
FoamGeometryConstruction_Periodic.main(MU, SIGMA, NumOfCells, filename,
packing,
alternativePackingAlgorithm,
tesselation, visualizeTesselation,
geometry, statistics, hypermesh,
deleteFiles, dx, dy, dz)
if moveToPeriodicBox:
########## Convert .geo to .stl
print(term.yellow + "Convert .geo to .stl" + term.normal)
os.system("gmsh -n -2 -format stl " + filename + ".geo >gmsh.out")
if deleteFiles:
os.remove("gmsh.out")
########## Move to periodic box
print(term.yellow + "Move to periodic box" + term.normal)
filenameIn = filename + ".stl"
filenameOut = filenameBox + ".stl"
xmin = dx
ymin = dy
zmin = dz
periodicBox.main(filenameIn, filenameOut, xmin, ymin, zmin, dx, dy, dz,
renderBox)
if deleteFiles:
os.remove(filenameIn)
########## Convert .stl to .ply
print(term.yellow + "Convert .stl to .ply" + term.normal)
os.system("meshconv " + filenameBox + ".stl -c ply")
if deleteFiles:
os.remove(filenameBox + '.stl')
if binarizeBox:
########## Binarize and save as .vtk
if strutContent == 0:
# Find the size of box, which would give desired porosity
# This method is not optimal, since the solver doesn't know that the
# function takes only integer arguments
print(term.yellow + "Optimizing porosity" + term.normal)
res = minimize_scalar(porOpt,
bracket=[100, 120],
method='Brent',
tol=1e-2)
vx = res.x
vx = int(vx)
print 'box size: {0:d}'.format(vx)
vy = vx
vz = vx
print(term.yellow + "Creating and saving optimal foam" +
term.normal)
porOpt(vx) # Call it with the optimized box size
if deleteFiles:
os.remove("binvox.out")
os.remove(filename + ".ply")
######### Convert binary .vtk to ascii .vtk
print(term.yellow + "Convert binary .vtk to ascii .vtk" +
term.normal)
filenameIn = filenameBox + ".vtk"
filenameOut = filenameBoxAscii + ".vtk"
origin = [dx, dy, dz]
spacing = [dx / vx, dy / vy, dz / vz]
vtkconv.main(filenameIn, filenameOut, origin, spacing)
if deleteFiles:
os.remove(filenameIn)
else:
print(term.yellow + "Optimizing porosity and strut content" +
term.normal)
res = minimize_scalar(porfsOpt,
bracket=[150, 200],
method='Brent',
tol=1e-2)
# res=minimize_scalar(
# porfsOpt,bounds=[200,250],method='bounded',tol=2e0
# )
vx = res.x
vx = int(vx)
print 'optimal box size: {0:d}'.format(vx)
vy = vx
vz = vx
print(term.yellow + "Creating and saving optimal foam" +
term.normal)
if os.path.isfile(filenameBox + '.vtk'):
os.remove(filenameBox + '.vtk')
if not os.path.isfile(filenameBox + '.ply'):
raise SystemError(".ply file is missing. Nothing to binarize.")
os.system("binvox -e -d {0:d}".format(vx) +
" -rotz -rotx -rotz -rotz " + "-t vtk " + filenameBox +
".ply >binvox.out")
filenameIn = filenameBox + ".vtk"
filenameOut = filenameBoxAscii + ".vtk"
origin = [dx, dy, dz]
spacing = [dx / vx, dy / vy, dz / vz]
vtkconv.main(filenameIn, filenameOut, origin, spacing)
f = open("foamreconstr.in", "w")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("{0:f}\n".format(dedge))
f.write("{0:f}\n".format(1 - strutContent * (1 - porosity)))
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write(filenameBoxStruts + "\n")
f.write(filenameBoxAscii + ".vtk\n")
f.write(filename + ".gnu\n")
f.write("name\n")
f.write(filenameDescriptors + "\n")
f.write(filenameParameters + "\n")
f.close()
os.system("./foamreconstr/foamreconstr")
if deleteFiles:
os.remove(filenameBoxAscii + ".vtk")
os.remove(filenameDescriptors)
os.remove(filenameParameters)
os.remove("binvox.out")
os.remove(filenameBox + ".vtk")
os.remove("foamreconstr.in")
tf = datetime.datetime.now()
te = tf - ts
print "Foam created in: ", te
)
porOpt(vx) # Call it with the optimized box size
if deleteFiles:
os.remove("binvox.out")
os.remove(filename+".ply")
######### Convert binary .vtk to ascii .vtk
print(
term.yellow +
"Convert binary .vtk to ascii .vtk" +
term.normal
)
filenameIn = filenameBox+".vtk"
filenameOut = filenameBoxAscii+".vtk"
origin=[dx,dy,dz]
spacing=[dx/vx,dy/vy,dz/vz]
vtkconv.main(filenameIn,filenameOut,origin,spacing)
if deleteFiles:
os.remove(filenameIn)
else:
print(
term.yellow +
"Optimizing porosity and strut content" +
term.normal
)
res=minimize_scalar(porfsOpt,bracket=[150,200],method='Brent',tol=1e-2)
# res=minimize_scalar(porfsOpt,bounds=[200,250],method='bounded',tol=2e0)
vx=res.x
vx=int(vx)
print 'optimal box size: {0:d}'.format(vx)
vy=vx
vz=vx
def porfsOpt(x):
"""Objective function.
For finding size of box, which would give desired porosity and
strut content.
@param[in] x Box size
"""
global DEDGE
filename = INPUTS["filename"]
porosity = INPUTS["structured_grid_options"]["porosity"]
strut_content = INPUTS["structured_grid_options"]["strut_content"]
vx = int(x)
vy = vx
vz = vx
if os.path.isfile(filename + 'Box.vtk'):
os.remove(filename + 'Box.vtk')
if not os.path.isfile(filename + 'Box.ply'):
raise SystemError(".ply file is missing. Nothing to binarize.")
os.system(
"binvox -e -d {0:d} -rotz -rotx -rotz -rotz -t vtk ".format(vx)
+ filename + "Box.ply >binvox.out"
)
filenameIn = filename + "Box.vtk"
filenameOut = filename + "Box-ascii.vtk"
dx = dy = dz = INPUTS["packing_options"]["domain_size"]
origin = [dx, dy, dz]
spacing = [dx / vx, dy / vy, dz / vz]
vtkconv.main(filenameIn, filenameOut, origin, spacing)
f = open("foamreconstr.in", "w")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("{0:f}\n".format(DEDGE))
f.write("{0:f}\n".format(1 - strut_content * (1 - porosity)))
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write(filename + "Box_structured\n")
f.write(filename + "Box-ascii.vtk\n")
f.write(filename + ".gnu\n")
f.write("name\n")
f.write("descriptors.txt" + "\n")
f.write("parameters.txt" + "\n")
f.close()
os.system("./foamreconstr/foamreconstr")
f = open("descriptors.txt", "r")
eps = float(f.readline())
fs = float(f.readline())
f.close()
f = open("parameters.txt", "r")
DEDGE = float(f.readline())
f.close()
resid = ((eps - porosity) / porosity)**2
print("dimension: {0:4d}, porosity: {1:f}".format(
vx, eps) + ", strut content: {0:f}".format(fs))
return resid
def binarize_box(filename, dx, dy, dz, porosity, strut_content):
"""Creates foam with desired porosity and strut content on structured grid."""
# Binarize and save as .vtk
if strut_content == 0:
# Find the size of box, which would give desired porosity
# This method is not optimal, since the solver doesn't know that the
# function takes only integer arguments
print(
TERM.yellow +
"Optimizing porosity" +
TERM.normal
)
res = minimize_scalar(
porOpt, bracket=[100, 120], method='Brent', tol=1e-2
)
vx = vy = vz = int(res.x)
print('box size: {0:d}'.format(vx))
print(
TERM.yellow +
"Creating and saving optimal foam" +
TERM.normal
)
porOpt(vx) # Call it with the optimized box size
# Convert binary .vtk to ascii .vtk
print(
TERM.yellow +
"Convert binary .vtk to ascii .vtk" +
TERM.normal
)
origin = [dx, dy, dz]
spacing = [dx / vx, dy / vy, dz / vz]
vtkconv.main(filename + "Box.vtk", filename +
"_str.vtk", origin, spacing)
else:
print(
TERM.yellow +
"Optimizing porosity and strut content" +
TERM.normal
)
res = minimize_scalar(
porfsOpt, bracket=[150, 200], method='Brent', tol=1e-2
)
# res=minimize_scalar(
# porfsOpt,bounds=[200,250],method='bounded',tol=2e0
# )
vx = vy = vz = int(res.x)
print('optimal box size: {0:d}'.format(vx))
print(
TERM.yellow +
"Creating and saving optimal foam" +
TERM.normal
)
if os.path.isfile(filename + 'Box.vtk'):
os.remove(filename + 'Box.vtk')
if not os.path.isfile(filename + 'Box.ply'):
raise SystemError(".ply file is missing. Nothing to binarize.")
os.system(
"binvox -e -d {0:d}".format(vx) + " -rotz -rotx -rotz -rotz "
+ "-t vtk " + filename + "Box.ply >binvox.out"
)
origin = [dx, dy, dz]
spacing = [dx / vx, dy / vy, dz / vz]
vtkconv.main(filename + "Box.vtk", filename +
"Box-ascii.vtk", origin, spacing)
f = open("foamreconstr.in", "w")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("{0:f}\n".format(DEDGE))
f.write("{0:f}\n".format(1 - strut_content * (1 - porosity)))
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write("1\n")
f.write("0\n")
f.write(filename + "_str\n")
f.write(filename + "Box-ascii.vtk\n")
f.write(filename + ".gnu\n")
f.write("name\n")
f.write("descriptors.txt" + "\n")
f.write("parameters.txt" + "\n")
f.close()
os.system("./foamreconstr/foamreconstr")