fly.write("Tags\n")
fly.close()
mph.close()
print("escript file %s generated." % (args.fly))
if args.points:
nodes = diracpoints['nodes']
tags = diracpoints['tags']
f = open(args.points, 'w')
for k in range(len(tags)):
idx = nodes[k][0]
x = nodesX[idx, :]
if sdim == 2:
f.write("%d %g %g %g\n" % (tags[k], x[0], x[1], 0.))
else:
f.write("%d %g %g %g\n" % (tags[k], x[0], x[1], x[2]))
f.close()
print("source points have been written to " + args.points)
if args.silofile is not None:
mesh = ReadMesh(args.fly)
saveSilo(args.silofile, tags=makeTagField(ReducedFunction(mesh)))
print(args.silofile + ".silo with tags has been generated.")
if args.points:
print(
"***WARNING: in COMSOL tags/ids for geometrical node IDs for sources are shown with an offset by 1 to the qIDs in the file. "
)
f.close()
print(n, " measurement written to file " + config.datafile)
if args.silofile is not None:
sigma_true.expand()
gamma_true.expand()
if args.plotA is not None:
A = int(args.plotA)
else:
A = t[0]
if args.plotB is not None:
B = int(args.plotB)
else:
B = t[1]
Es = secondary_field_field[A] - secondary_field_field[B]
Es_hat = (secondary_field_field_hat[A] -
secondary_field_field_hat[B]) / (1 - ETA0)
E = primary_field_field[A] - primary_field_field[B] + Es
gamma = inner(Es_hat, E) / inner(E, E)
saveSilo(args.silofile,
tag=makeTagField(ReducedFunction(domain)),
sigma_true=sigma_true,
gamma_true=gamma_true,
gamma=gamma,
Es=Es,
Es_hat=Es_hat,
E=E)
print(args.silofile +
".silo with tags has been generated for injection [%d, %d]" % (A, B))
if args.query:
sigma, potentials, dV=costf.getArguments(m)
if getMPIRankWorld() == 0:
f=open(args.query,'w')
for t in survey.tokenIterator(): # t=(A,B,M,N) (or so)
f.write("%s, %e, %e\n"%(str(t)[1:-1], survey.getResistenceData(t), dV[t]))
f.close()
print("Data query/result file %s written."%args.query)
else:
sigma=costf.getSigma(m)
if args.vtk:
saveVTK(config.outfile, sigma=sigma, tag=makeTagField(Function(domain)))
if getMPIRankWorld() == 0:
print("result written to %s.vtu"%config.outfile)
else:
saveSilo(config.outfile, sigma=sigma, tag=makeTagField(Function(domain)))
if getMPIRankWorld() == 0:
print("result written to %s.silo"%config.outfile)
if args.xyz:
sigmas=interpolate(sigma, ReducedFunction(domain))
X=sigmas.getFunctionSpace().getX()
if isinstance(config.core, list):
m=insertTaggedValues(Scalar(0., sigmas.getFunctionSpace()), **{ t: 1 for t in config.core })
saveDataCSV(config.outfile+".csv", d0=X[0], d1=X[1], d2=X[2], sigma =sigmas, mask=m)
if getMPIRankWorld() == 0:
print("result written to %s.csv. Core region is %s."%(config.outfile, config.core))
import argparse
from fingal import makeTagField
parser = argparse.ArgumentParser(
description='creates a silo/vtk file from fly.')
parser.add_argument(dest='meshfile',
metavar='meshfile',
type=str,
help='fly file')
parser.add_argument('--silo',
'-s',
dest='silo',
metavar='SILO',
help="silo file to write.")
parser.add_argument('--vtk',
'-v',
dest='vtk',
metavar='SILO',
help="vtk file to write.")
args = parser.parse_args()
domain = ReadMesh(args.meshfile)
print("mesh read from " + args.meshfile)
if args.silo is not None:
saveSilo(args.silo, tag=makeTagField(ReducedFunction(domain)))
print(args.silo + ".silo with tags has been generate")
if args.vtk is not None:
saveSilo(args.vtk, tag=makeTagField(ReducedFunction(domain)))
print(args.vtk + ".vtk with tags has been generated.")
print("\ttotal domain = %s"%R2)
print("\tlog, total domain = %s"%R2log)
if config.core:
mask=insertTaggedValues(Scalar(0., gammai.getFunctionSpace()), **{ t: 1 for t in config.core })
R2=getR2(gamma_true, gammai, chi=mask)
R2log=getR2(log(gamma_true), log(gammai), chi=mask)
if getMPIRankWorld() == 0:
print("\tcore = %s"%R2)
print("\tlog, core = %s"%R2log)
# assemblage of output:
sigma.expand()
outargs={ "tag" : makeTagField(Function(domain)), "sigma":sigma }
if not config.true_properties is None:
outargs['sigma_error']=sigma/sigma_true
sigma_true.expand()
outargs['sigma_true']=sigma_true
if not args.sigmaonly:
outargs['gamma']=gamma
if not config.true_properties is None:
outargs['gamma_error']=gamma/gamma_true
gamma_true.expand()
outargs['gamma_true']=gamma_true
if args.vtk:
saveVTK(config.outfile, **outargs)