def load_fields_3D(file,field_id):
coords, fields = io.ReadDatFile(infile)
nfields = fields.shape[-1]
if field_id>nfields:
print('Warning No Field!')
else:
singlefield = fields[:,:,:,field_id]
return coords,fields,singlefield
zeropadded=str("{val:0>{width}}".format(val=outfile_digits,width=maxdigit))
outfile = outfile_notdigits + zeropadded + ".vtk"
# check if vtk dont already exist?
# IMPLEMENT ME
if args.verbose:
logging.basicConfig(format='%(levelname)s:%(message)s', level=logging.DEBUG)
else:
logging.basicConfig(format='%(levelname)s:%(message)s', level=logging.WARNING)
orthorhombic = True
# Check whether the input file exits, and whether it is a binary PolyFTS file or a formatted on.
# Dispatch reading to relevant function.
# Open as binary first
print("Reading input file {}".format(infile))
# if iotools.TestBinFile(infile):
#ndim, Nx, orthorhombic, M, nfields, AllCoords, AllFields = iotools.ReadBinFile(infile)
# AllCoords, AllFields = iotools.ReadBinFile(infile)
# else:
#ndim, Nx, orthorhombic, M, nfields, AllCoords, AllFields = iotools.ReadDatFile(infile)
AllCoords, AllFields = iotools.ReadDatFile(infile)
logging.info("Orthorhombic cell? {}".format(orthorhombic))
print ("Outputting to Legacy VTK formatted file {}".format(outfile))
#viztools.writeVTK(outfile, Nx, orthorhombic, M, AllCoords, AllFields)
viztools.writeVTK(outfile, AllCoords, AllFields)
default='epsilon.h5',
type=str,
help='Output h5 file to be read by MPB code')
# Parse the command-line arguments
args = parser.parse_args()
# setup and parse input file name
# use iotools to load density.bin to get coords and fields
if args.input != '':
infile = args.input
suffix = infile.split('.')[-1]
if suffix == 'bin':
coords, fields = io.ReadBinFile(infile)
fields_have_imag = True
elif suffix == 'dat':
coords, fields = io.ReadDatFile(infile)
fields_have_imag = False
else:
raise RuntimeError(f"invalid suffix of args.input: {suffix}")
else: # args.input not specified, try density.bin and density.dat
if os.path.isfile('density.bin'):
coords, fields = io.ReadBinFile('density.bin')
fields_have_imag = True
elif os.path.isfile('density.dat'):
coords, fields = io.ReadDatFile('density.dat')
fields_have_imag = False
else:
raise RuntimeError(
"Default inputs density.bin and density.dat not found")
if newDim == 3:
Nz = args.Nz # number of plane waves in new dimension
Lz = args.Lz # length of box in new dimension
infiletype = infilename.split('.')[-1]
outfiletype = outfilename.split('.')[-1]
if (infiletype != "bin" and infiletype != 'dat'):
raise RuntimeError(
f"input file ({infilename}) must have file type of .bin or .dat")
if (outfiletype != "bin" and outfiletype != 'dat' and outfiletype != 'in'):
raise RuntimeError(
f"output file ({outfilename}) must have file type of .bin, .dat or .in"
)
if infiletype == 'dat':
coords, fields = io.ReadDatFile(infilename)
else:
coords, fields = io.ReadBinFile(infilename)
#cb, fb = io.ReadBinFile('density.bin')
#cd, fd = io.ReadDatFile('density.dat')
#pdb.set_trace()
# check newDim relative to origDim
origDim = len(coords.shape) - 1
assert (origDim <
newDim), "output dimension must be greater than input dimension"
if origDim == 1:
# convert from 1d to 2d
#in order to change this expand the box by a factor, so the relative
#tolerance is tighter
box_multiplier = 0.5 / args.tolerance
# if not os.path.isfile('structure.cif') and not args.overwrite:
# make_domains(args.filename)
# else:
# print('Found an existing structure.cif skipping domain calculation, disable this feature with -o')
#======================================================================
#this section finds the domains, using domaintools with meshing enabled
#======================================================================
filetype = re.split('\.', args.filename)[-1]
if filetype == 'bin':
AllCoords, AllFields = io.ReadBinFile(args.filename)
elif filetype == 'dat':
AllCoords, AllFields = io.ReadDatFile(args.filename)
else:
raise NotImplementedError('This only supports .bin and .dat files')
#normalize by box length
#extra AllCoords[1,1,1] is because boxes are mesured by lower left corner
box_length = AllCoords[-1, -1, -1] + AllCoords[1, 1, 1]
AllCoords = AllCoords / (box_length)
domainanalyzer = DomainAnalyzer(AllCoords, AllFields)
ndomains, com, area, vol, IQ = domainanalyzer.getDomainStats(
plotMesh=False, add_periodic_domains=True)
domainanalyzer.meshAllDomains(plotfile="mesh_all.png")
stats = np.vstack((com.T, area, vol, IQ)).T
np.savetxt("stats_mesh.dat", stats, header="comx comy comz area vol IQ")
#======================================================================
#this section makes a crystalography file for platon (.cif)