def automeshWithMaxCells(infile, outfile, meshing_factor, MAXCELLS, Lambda, a):
sim = bfdtd.readBristolFDTD(infile)
sim.autoMeshGeometry(meshing_factor)
sim.writeInpFile(outfile)
sim = bfdtd.readBristolFDTD(infile)
sim.autoMeshGeometry(Lambda / a)
while (sim.getNcells() > MAXCELLS and a > 1):
a = a - 1
sim.autoMeshGeometry(Lambda / a)
sim.writeInpFile(outfile)
def automeshWithMaxCells(infile, outfile, meshing_factor, MAXCELLS, Lambda, a):
sim = bfdtd.readBristolFDTD(infile)
sim.autoMeshGeometry(meshing_factor)
sim.writeInpFile(outfile)
sim = bfdtd.readBristolFDTD(infile)
sim.autoMeshGeometry(Lambda / a)
while sim.getNcells() > MAXCELLS and a > 1:
a = a - 1
sim.autoMeshGeometry(Lambda / a)
sim.writeInpFile(outfile)
def efficiency_run(src, dst):
""" Copy src to dst while removing the geometry """
src = os.path.abspath(src).rstrip(os.sep)
dst = os.path.abspath(dst).rstrip(os.sep)
if os.path.isdir(src):
print(src + " is a directory")
FDTDobj = bfdtd.readBristolFDTD(src + os.sep + os.path.basename(src) + ".in")
fileBaseName = os.path.basename(src)
else:
print(src + " is not a directory")
FDTDobj = bfdtd.readBristolFDTD(src)
fileBaseName = os.path.splitext(os.path.basename(src))[0]
FDTDobj.geometry_object_list[:] = []
FDTDobj.writeAll(dst, fileBaseName)
def efficiency_run(src, dst):
''' Copy src to dst while removing the geometry '''
src = os.path.abspath(src).rstrip(os.sep)
dst = os.path.abspath(dst).rstrip(os.sep)
if os.path.isdir(src):
print(src +' is a directory')
FDTDobj = bfdtd.readBristolFDTD(src+os.sep+os.path.basename(src)+'.in')
fileBaseName = os.path.basename(src)
else:
print(src +' is not a directory')
FDTDobj = bfdtd.readBristolFDTD(src)
fileBaseName = os.path.splitext(os.path.basename(src))[0]
FDTDobj.geometry_object_list[:] = []
FDTDobj.writeAll(dst,fileBaseName)
def copyBFDTD(src, dst):
""" Copy src to dst """
src = src.rstrip(os.sep)
dst = dst.rstrip(os.sep)
if os.path.isdir(src):
print(src + " is a directory")
FDTDobj = bfdtd.readBristolFDTD(src + os.sep + os.path.basename(src) + ".in")
fileBaseName = os.path.basename(src)
else:
print(src + " is not a directory")
FDTDobj = bfdtd.readBristolFDTD(src)
fileBaseName = os.path.splitext(os.path.basename(src))[0]
FDTDobj.writeAll(dst, fileBaseName)
bfdtd.GEOshellscript(dst + os.sep + fileBaseName + ".sh", fileBaseName, "$HOME/bin/fdtd", "$JOBDIR", WALLTIME=360)
def copyBFDTD(src,dst):
''' Copy src to dst '''
src = src.rstrip(os.sep)
dst = dst.rstrip(os.sep)
if os.path.isdir(src):
print(src +' is a directory')
FDTDobj = bfdtd.readBristolFDTD(src+os.sep+os.path.basename(src)+'.in')
fileBaseName = os.path.basename(src)
else:
print(src +' is not a directory')
FDTDobj = bfdtd.readBristolFDTD(src)
fileBaseName = os.path.splitext(os.path.basename(src))[0]
FDTDobj.writeAll(dst,fileBaseName)
bfdtd.GEOshellscript(dst+os.sep+fileBaseName+'.sh', fileBaseName,'$HOME/bin/fdtd', '$JOBDIR', WALLTIME = 360)
def fixSnapshots(infile, newbasename):
'''
-read infile
-remove any time snapshots
-set frequency snapshots to first=3200, repetition=32000
-move snapshots 1 grid away from excitation.P1
-write to ./fixedSnapshots/newbasename
'''
sim = bfdtd.readBristolFDTD(infile)
sim.fileList = []
sim.clearTimeSnapshots()
for s in sim.snapshot_list:
s.first = 3200
s.repetition = 32000
refP = sim.excitation_list[0].P1
(idxX, valX) = findNearest(sim.mesh.getXmesh(), refP[0])
(idxY, valY) = findNearest(sim.mesh.getYmesh(), refP[1])
(idxZ, valZ) = findNearest(sim.mesh.getZmesh(), refP[2])
sim.snapshot_list[0].P1[0] = sim.snapshot_list[0].P2[
0] = sim.mesh.getXmesh()[idxX - 1]
sim.snapshot_list[1].P1[1] = sim.snapshot_list[1].P2[
1] = sim.mesh.getYmesh()[idxY - 1]
sim.snapshot_list[2].P1[2] = sim.snapshot_list[2].P2[
2] = sim.mesh.getZmesh()[idxZ - 1]
sim.writeAll('./fixedSnapshots', newbasename)
def addCentralXYZSnapshots(arguments):
FDTDobj = bfdtd.readBristolFDTD(arguments.infile, arguments.verbosity)
# hack: remove epsilon snapshots and probes to increase speed
FDTDobj.clearEpsilonSnapshots()
FDTDobj.clearProbes()
FDTDobj.clearAllSnapshots()
(size, res) = FDTDobj.mesh.getSizeAndResolution()
if arguments.verbosity > 0:
print("res = ", res)
frequency_vector = []
if arguments.freqListFile is not None:
frequency_vector.extend(getFrequencies(arguments.freqListFile))
if arguments.wavelength_mum is not None:
frequency_vector.extend([get_c0() / i for i in arguments.wavelength_mum])
if arguments.frequency_MHz is not None:
frequency_vector.extend(arguments.frequency_MHz)
if len(frequency_vector) <= 0:
print("ERROR: Great scot! You forgot to specify frequencies.", file=sys.stderr)
sys.exit(-1)
FDTDobj.flag.iterations = arguments.iterations
# hack: Make sure there will be at least one long duration snapshot at the end
arguments.repetition = FDTDobj.flag.iterations - arguments.first
# Add full X,Y,Z central snapshots
pos = FDTDobj.box.getCentro()
for i in [0, 1, 2]:
letter = ["X", "Y", "Z"][i]
f = FDTDobj.addFrequencySnapshot(letter, pos[i])
f.name = "central." + letter + ".fsnap"
f.first = arguments.first
f.repetition = arguments.repetition
f.frequency_vector = frequency_vector
if arguments.outdir is None:
print("ERROR: no outdir specified", file=sys.stderr)
sys.exit(-1)
if arguments.basename is None:
arguments.basename = os.path.basename(os.path.abspath(arguments.outdir))
FDTDobj.fileList = []
FDTDobj.writeAll(arguments.outdir, arguments.basename)
FDTDobj.writeShellScript(
arguments.outdir + os.path.sep + arguments.basename + ".sh",
arguments.basename,
arguments.executable,
"$JOBDIR",
WALLTIME=arguments.walltime,
)
return
def clearOutputs(arguments):
if arguments.infile is None:
print('ERROR: No infile specified.')
sys.exit(-1)
if arguments.outdir is None:
print('ERROR: no outdir specified', file=sys.stderr)
sys.exit(-1)
if arguments.basename is None:
arguments.basename = os.path.basename(os.path.abspath(
arguments.outdir))
FDTDobj = bfdtd.readBristolFDTD(arguments.infile, arguments.verbosity)
FDTDobj.clearProbes()
FDTDobj.clearAllSnapshots()
FDTDobj.fileList = []
FDTDobj.writeAll(arguments.outdir, arguments.basename)
FDTDobj.writeShellScript(arguments.outdir + os.path.sep +
arguments.basename + '.sh',
arguments.basename,
arguments.executable,
'$JOBDIR',
WALLTIME=arguments.walltime)
return
def clearOutputs(arguments):
if arguments.infile is None:
print("ERROR: No infile specified.")
sys.exit(-1)
if arguments.outdir is None:
print("ERROR: no outdir specified", file=sys.stderr)
sys.exit(-1)
if arguments.basename is None:
arguments.basename = os.path.basename(os.path.abspath(arguments.outdir))
FDTDobj = bfdtd.readBristolFDTD(arguments.infile, arguments.verbosity)
FDTDobj.clearProbes()
FDTDobj.clearAllSnapshots()
FDTDobj.fileList = []
FDTDobj.writeAll(arguments.outdir, arguments.basename)
FDTDobj.writeShellScript(
arguments.outdir + os.path.sep + arguments.basename + ".sh",
arguments.basename,
arguments.executable,
"$JOBDIR",
WALLTIME=arguments.walltime,
)
return
def fixSnapshots(infile, newbasename):
"""
-read infile
-remove any time snapshots
-set frequency snapshots to first=3200, repetition=32000
-move snapshots 1 grid away from excitation.P1
-write to ./fixedSnapshots/newbasename
"""
sim = bfdtd.readBristolFDTD(infile)
sim.fileList = []
sim.clearTimeSnapshots()
for s in sim.snapshot_list:
s.first = 3200
s.repetition = 32000
refP = sim.excitation_list[0].P1
(idxX, valX) = findNearest(sim.mesh.getXmesh(), refP[0])
(idxY, valY) = findNearest(sim.mesh.getYmesh(), refP[1])
(idxZ, valZ) = findNearest(sim.mesh.getZmesh(), refP[2])
sim.snapshot_list[0].P1[0] = sim.snapshot_list[0].P2[0] = sim.mesh.getXmesh()[idxX - 1]
sim.snapshot_list[1].P1[1] = sim.snapshot_list[1].P2[1] = sim.mesh.getYmesh()[idxY - 1]
sim.snapshot_list[2].P1[2] = sim.snapshot_list[2].P2[2] = sim.mesh.getZmesh()[idxZ - 1]
sim.writeAll("./fixedSnapshots", newbasename)
def rerun_with_new_excitation(src, dst, excitation_wavelength_nm, excitation_time_constant):
''' Copy src to dst, only changing excitation_wavelength_nm and excitation_time_constant'''
src = os.path.abspath(src).rstrip(os.sep)
dst = os.path.abspath(dst).rstrip(os.sep)
if os.path.isdir(src):
print(src +' is a directory')
FDTDobj = bfdtd.readBristolFDTD(src+os.sep+os.path.basename(src)+'.in')
fileBaseName = os.path.basename(src)
else:
print(src +' is not a directory')
FDTDobj = bfdtd.readBristolFDTD(src)
fileBaseName = os.path.splitext(os.path.basename(src))[0]
FDTDobj.excitation_list[0].time_constant = excitation_time_constant
FDTDobj.excitation_list[0].frequency = get_c0()/(1e-3*excitation_wavelength_nm)
FDTDobj.writeAll(dst,fileBaseName)
bfdtd.GEOshellscript(dst+os.sep+fileBaseName+'.sh', fileBaseName,'$HOME/bin/fdtd', '$JOBDIR', WALLTIME = 360)
def rerun_with_new_excitation(src, dst, excitation_wavelength_nm, excitation_time_constant):
""" Copy src to dst, only changing excitation_wavelength_nm and excitation_time_constant"""
src = os.path.abspath(src).rstrip(os.sep)
dst = os.path.abspath(dst).rstrip(os.sep)
if os.path.isdir(src):
print(src + " is a directory")
FDTDobj = bfdtd.readBristolFDTD(src + os.sep + os.path.basename(src) + ".in")
fileBaseName = os.path.basename(src)
else:
print(src + " is not a directory")
FDTDobj = bfdtd.readBristolFDTD(src)
fileBaseName = os.path.splitext(os.path.basename(src))[0]
FDTDobj.excitation_list[0].time_constant = excitation_time_constant
FDTDobj.excitation_list[0].frequency = get_c0() / (1e-3 * excitation_wavelength_nm)
FDTDobj.writeAll(dst, fileBaseName)
bfdtd.GEOshellscript(dst + os.sep + fileBaseName + ".sh", fileBaseName, "$HOME/bin/fdtd", "$JOBDIR", WALLTIME=360)
def printFrequencySnapshotInfo(arguments):
FDTDobj = bfdtd.readBristolFDTD(*arguments.infile,
verbosity=arguments.BFDTDreader_verbosity)
for idx, fsnap in enumerate(FDTDobj.getFrequencySnapshots()):
print('idx+1={}, name={}, plane={}, f={}, centro={}, pos:{}={}'.format(
idx + 1, fsnap.getName(), fsnap.getPlaneLetter(),
fsnap.getFrequencies(), fsnap.getCentro(), fsnap.getPlaneLetter(),
fsnap.getCentro()[fsnap.getPlanePythonIndex()]))
return
def resonance_run(src, dst, freqListFile):
""" Copy src to dst with added frequency snapshots from freqListFile """
src = os.path.abspath(src).rstrip(os.sep)
dst = os.path.abspath(dst).rstrip(os.sep)
if os.path.isdir(src):
print(src + " is a directory")
FDTDobj = bfdtd.readBristolFDTD(src + os.sep + os.path.basename(src) + ".in")
fileBaseName = os.path.basename(src)
else:
print(src + " is not a directory")
FDTDobj = bfdtd.readBristolFDTD(src)
fileBaseName = os.path.splitext(os.path.basename(src))[0]
freq_snapshots = getFrequencies(freqListFile)
for obj in FDTDobj.frequency_snapshot_list:
obj.frequency_vector = freq_snapshots
FDTDobj.writeAll(dst, fileBaseName)
FDTDobj.writeShellScript(dst + os.path.sep + fileBaseName + ".sh")
def resonance_run(src, dst, freqListFile):
''' Copy src to dst with added frequency snapshots from freqListFile '''
src = os.path.abspath(src).rstrip(os.sep)
dst = os.path.abspath(dst).rstrip(os.sep)
if os.path.isdir(src):
print(src +' is a directory')
FDTDobj = bfdtd.readBristolFDTD(src+os.sep+os.path.basename(src)+'.in')
fileBaseName = os.path.basename(src)
else:
print(src +' is not a directory')
FDTDobj = bfdtd.readBristolFDTD(src)
fileBaseName = os.path.splitext(os.path.basename(src))[0]
freq_snapshots = getFrequencies(freqListFile)
for obj in FDTDobj.frequency_snapshot_list:
obj.frequency_vector = freq_snapshots
FDTDobj.writeAll(dst,fileBaseName)
FDTDobj.writeShellScript(dst+os.path.sep+fileBaseName+'.sh')
def addCentralXYZSnapshots(arguments):
FDTDobj = bfdtd.readBristolFDTD(arguments.infile, arguments.verbosity)
# hack: remove epsilon snapshots and probes to increase speed
FDTDobj.clearEpsilonSnapshots()
FDTDobj.clearProbes()
FDTDobj.clearAllSnapshots()
(size,res) = FDTDobj.mesh.getSizeAndResolution()
if arguments.verbosity>0:
print('res = ',res)
frequency_vector = []
if arguments.freqListFile is not None:
frequency_vector.extend(getFrequencies(arguments.freqListFile))
if arguments.wavelength_mum is not None:
frequency_vector.extend([get_c0()/i for i in arguments.wavelength_mum])
if arguments.frequency_MHz is not None:
frequency_vector.extend(arguments.frequency_MHz)
if len(frequency_vector)<=0:
print('ERROR: Great scot! You forgot to specify frequencies.', file=sys.stderr)
sys.exit(-1)
FDTDobj.flag.iterations = arguments.iterations
# hack: Make sure there will be at least one long duration snapshot at the end
arguments.repetition = FDTDobj.flag.iterations - arguments.first
# Add full X,Y,Z central snapshots
pos = FDTDobj.box.getCentro()
for i in [0,1,2]:
letter = ['X','Y','Z'][i]
f = FDTDobj.addFrequencySnapshot(letter,pos[i]);
f.name = 'central.'+letter+'.fsnap'
f.first = arguments.first
f.repetition = arguments.repetition
f.frequency_vector = frequency_vector
if arguments.outdir is None:
print('ERROR: no outdir specified', file=sys.stderr)
sys.exit(-1)
if arguments.basename is None:
arguments.basename = os.path.basename(os.path.abspath(arguments.outdir))
FDTDobj.fileList = []
FDTDobj.writeAll(arguments.outdir, arguments.basename)
FDTDobj.writeShellScript(arguments.outdir + os.path.sep + arguments.basename + '.sh', arguments.basename, arguments.executable, '$JOBDIR', WALLTIME = arguments.walltime)
return
def calculateModeVolume(arguments):
# .. todo:: Finish this
# NOTE: Add way to specify snapshots, epsilon/frequency snapshot pairs
# read in mesh
if arguments.meshfile is None:
print('ERROR: No meshfile specified.', file=sys.stderr)
sys.exit(-1)
sim_mesh = bfdtd.readBristolFDTD(arguments.meshfile, arguments.verbosity)
# read in snapshot files from the various input files
if len(arguments.infile) <= 0:
print('ERROR: No infile(s) specified.', file=sys.stderr)
sys.exit(-1)
sim_in = bfdtd.BFDTDobject()
sim_in.verbosity = arguments.verbosity
for infile in arguments.infile:
sim_in.readBristolFDTD(infile)
# .. todo:: add path of file based on where it was read from
# .. todo:: read in .prn files
# calculate mode volume
snaplist = sim_in.getFrequencySnapshots()
for numID in range(len(snaplist)):
snapshot = snaplist[numID]
#print(['x','y','z'][snapshot.plane-1])
#print(sim_in.flag.id_string)
fsnap_filename, alphaID, pair = brisFDTD_ID_info.numID_to_alphaID_FrequencySnapshot(
numID + 1, ['x', 'y', 'z'][snapshot.plane - 1],
sim_in.flag.id_string.strip('"'),
snap_time_number=1)
print(fsnap_filename)
esnap_filename, alphaID, pair = brisFDTD_ID_info.numID_to_alphaID_EpsilonSnapshot(
numID + 1, ['x', 'y', 'z'][snapshot.plane - 1],
sim_in.flag.id_string.strip('"'),
snap_time_number=1)
print(esnap_filename)
#if arguments.fsnapfiles is None:
#arguments.fsnapfiles = sim_in.getFrequencySnapshots():
#if arguments.esnapfiles is None:
#arguments.esnapfiles = sim_in.getEpsilonSnapshots()
#if len(arguments.fsnapfiles) != len(arguments.esnapfiles):
#print('ERROR: number of frequency snapshots and epsilon snapshots do not match', file=sys.stderr)
#sys.exit(-1)
#else:
#print('OK')
#print(arguments.fsnapfiles)
#print(arguments.esnapfiles)
return
def calculateModeVolume(arguments):
# TODO: Finish this
# NOTE: Add way to specify snapshots, epsilon/frequency snapshot pairs
# read in mesh
if arguments.meshfile is None:
print("ERROR: No meshfile specified.", file=sys.stderr)
sys.exit(-1)
sim_mesh = bfdtd.readBristolFDTD(arguments.meshfile, arguments.verbosity)
# read in snapshot files from the various input files
if len(arguments.infile) <= 0:
print("ERROR: No infile(s) specified.", file=sys.stderr)
sys.exit(-1)
sim_in = bfdtd.BFDTDobject()
sim_in.verbosity = arguments.verbosity
for infile in arguments.infile:
sim_in.readBristolFDTD(infile)
# TODO: add path of file based on where it was read from
# TODO: read in .prn files
# calculate mode volume
snaplist = sim_in.getFrequencySnapshots()
for numID in range(len(snaplist)):
snapshot = snaplist[numID]
# print(['x','y','z'][snapshot.plane-1])
# print(sim_in.flag.id_string)
fsnap_filename, alphaID, pair = brisFDTD_ID_info.numID_to_alphaID_FrequencySnapshot(
numID + 1, ["x", "y", "z"][snapshot.plane - 1], sim_in.flag.id_string.strip('"'), snap_time_number=1
)
print(fsnap_filename)
esnap_filename, alphaID, pair = brisFDTD_ID_info.numID_to_alphaID_EpsilonSnapshot(
numID + 1, ["x", "y", "z"][snapshot.plane - 1], sim_in.flag.id_string.strip('"'), snap_time_number=1
)
print(esnap_filename)
# if arguments.fsnapfiles is None:
# arguments.fsnapfiles = sim_in.getFrequencySnapshots():
# if arguments.esnapfiles is None:
# arguments.esnapfiles = sim_in.getEpsilonSnapshots()
# if len(arguments.fsnapfiles) != len(arguments.esnapfiles):
# print('ERROR: number of frequency snapshots and epsilon snapshots do not match', file=sys.stderr)
# sys.exit(-1)
# else:
# print('OK')
# print(arguments.fsnapfiles)
# print(arguments.esnapfiles)
return
def printFormattedString(arguments):
FDTDobj = bfdtd.readBristolFDTD(*arguments.infile,
verbosity=arguments.BFDTDreader_verbosity)
dt = FDTDobj.getTimeStep()
iterations = FDTDobj.getIterations()
total_time = FDTDobj.getSimulationTime()
lmin = []
lcen = []
lmax = []
fmin = []
fcen = []
fmax = []
eloc = []
for E in FDTDobj.getExcitations():
lmin.append(E.getWavelengthMin())
lcen.append(E.getWavelength())
lmax.append(E.getWavelengthMax())
fmin.append(E.getFrequencyMin())
fcen.append(E.getFrequency())
fmax.append(E.getFrequencyMax())
eloc.append(E.getLocation())
print(
arguments.FORMAT.format(dt=dt,
total_time=total_time,
iterations=iterations,
lmin=lmin,
lcen=lcen,
lmax=lmax,
fmin=fmin,
fcen=fcen,
fmax=fmax,
eloc=eloc))
return
def rotate(infile, outfile, axis_point, axis_direction, angle_degrees):
sim = bfdtd.readBristolFDTD(infile)
sim.rotate(axis_point, axis_direction, angle_degrees)
sim.writeGeoFile(outfile)
def rotate(infile, outfile, axis_point, axis_direction, angle_degrees):
sim = bfdtd.readBristolFDTD(infile)
sim.rotate(axis_point, axis_direction, angle_degrees)
sim.writeGeoFile(outfile)
def automeshWithMeshingFactor(infile, outfile, meshing_factor):
sim = bfdtd.readBristolFDTD(infile)
sim.autoMeshGeometry(meshing_factor)
sim.writeInpFile(outfile)
def process(maindir,
destdir,
overwrite,
dry_run,
disabled_epsilon=False,
disabled_directions=[]):
print('maindir = {}'.format(maindir))
print('destdir = {}'.format(destdir))
print('overwrite = {}'.format(overwrite))
print('dry_run = {}'.format(dry_run))
print('disabled_epsilon = {}'.format(disabled_epsilon))
print('disabled_directions = {}'.format(disabled_directions))
for direction in ['Ex', 'Ey', 'Ez']:
if direction not in disabled_directions:
# get the frequency list, to fail quickly in case of problems
flist = os.path.join(maindir, direction, 'frequency-selection.txt')
freq_MHz_list = getFrequencies(flist)
# read in base file
infile = os.path.join(maindir, direction, 'RCD111.in')
sim = readBristolFDTD(infile, verbosity=0)
sim.setFileBaseName('RCD111')
# clean sim
sim.clearProbes()
sim.clearAllSnapshots()
sim.clearFileList()
# get excitation location
excitation = sim.getExcitations()[0]
excitation_location = excitation.getLocation()
# get min/max param values
dt = sim.getTimeStep()
time_offset = max(
excitation.getTimeOffset(),
MIN_TIME_OFFSET_TIME_CONSTANT_RATIO * excitation.getTimeConstant())
starting_sample_min = int(
ceil((time_offset + MIN_TIME_OFFSET_TIME_CONSTANT_RATIO *
excitation.getTimeConstant()) / dt))
#print(dt)
#print(starting_sample_min)
Npoints_per_period_min = int(
floor((1 / excitation.getFrequencyMax()) / dt))
#print(Npoints_per_period_min)
repetition_min_1 = int(
ceil((MIN_SAMPLINGTIME_MAXPERIOD_RATIO /
excitation.getFrequencyMin()) / dt))
repetition_min_2 = int(
ceil(
(MIN_NFFT_POINTS_IN_EXCITATION_RANGE /
(excitation.getFrequencyMax() - excitation.getFrequencyMin()))
/ dt))
#print(repetition_min_1)
#print(repetition_min_2)
first_min = starting_sample_min + max(repetition_min_1,
repetition_min_2)
#print(first_min)
repetition = max([repetition_min_1, repetition_min_2] + REPETITION)
starting_sample = max([starting_sample_min] + STARTING_SAMPLE)
first = max([starting_sample + repetition] + FIRST)
print('starting_sample = {}, first = {}, repetition = {}'.format(
starting_sample, first, repetition))
#print('starting_sample = {}'.format(starting_sample))
#print('first = {}'.format(first))
#print('repetition = {}'.format(repetition))
# set up the volume box
partial_box = SnapshotBoxVolume()
# set up the XYZ box
xyz_box = SnapshotBoxXYZ()
xyz_box.setIntersectionPoint(excitation_location)
# MV box size is chosen so that it will cover 1+2*47 = 95 mesh lines (we want Nsnaps<=99, but that includes 3 x/y/z snaps)
xmesh = sim.getXmesh()
(idx, val) = findNearestInSortedArray(xmesh, excitation_location[0], 0)
MV_box_size = (xmesh[idx + 42] + xmesh[idx + 43]) / 2 - (
xmesh[idx - 42] + xmesh[idx - 43]) / 2
print('MV_box_size = {} = {}*sim.getSize()'.format(
MV_box_size, MV_box_size / (sim.getSize()[0])))
# set up base frequency snapshot (we need two at the moment because one has full extension and the other one does not)
fsnap_base_partial = FrequencySnapshot()
fsnap_base_partial.setCentro(excitation_location)
fsnap_base_partial.setSize([MV_box_size, MV_box_size, MV_box_size])
fsnap_base_partial.setPlaneOrientationX()
fsnap_base_partial.setFullExtensionOn()
fsnap_base_partial.setStartingSample(starting_sample)
fsnap_base_partial.setFirst(first)
fsnap_base_partial.setRepetition(repetition)
fsnap_base_full = FrequencySnapshot()
fsnap_base_full.setFromSnapshot(fsnap_base_partial)
fsnap_base_full.setFullExtensionOn()
#fsnap_base_full.setCentro(excitation_location)
#fsnap_base_full.setSize(MV_box_size)
#fsnap_base_full.setPlaneOrientationX()
# custom snapshots
fsnap_custom = FrequencySnapshot()
fsnap_custom.setPlaneOrientationZ()
fsnap_custom.setFullExtensionOn()
fsnap_custom.setStartingSample(starting_sample)
fsnap_custom.setFirst(first)
fsnap_custom.setRepetition(repetition)
f1 = copy.deepcopy(fsnap_custom)
f1.setCentro([6.216506, 6.216506, 1.121651E+01])
f2 = copy.deepcopy(fsnap_custom)
f2.setCentro([6.216506, 6.216506, 1.021651E+01])
f3 = copy.deepcopy(fsnap_custom)
f3.setCentro([6.216506, 6.216506, 9.216510E+00])
f4 = copy.deepcopy(fsnap_custom)
f4.setCentro([6.216506, 6.216506, 8.216510E+00])
f5 = copy.deepcopy(fsnap_custom)
f5.setCentro([6.216506, 6.216506, 7.216510E+00])
# f6 = copy.deepcopy(fsnap_custom); f6.setCentro([6.216506,6.216506,6.216510E+00])
f7 = copy.deepcopy(fsnap_custom)
f7.setCentro([6.216506, 6.216506, 5.216510E+00])
f8 = copy.deepcopy(fsnap_custom)
f8.setCentro([6.216506, 6.216506, 4.216510E+00])
f9 = copy.deepcopy(fsnap_custom)
f9.setCentro([6.216506, 6.216506, 3.216510E+00])
f10 = copy.deepcopy(fsnap_custom)
f10.setCentro([6.216506, 6.216506, 2.216510E+00])
f11 = copy.deepcopy(fsnap_custom)
f11.setCentro([6.216506, 6.216506, 1.216510E+00])
if direction == 'Ex':
# create epsilon run
outdir_epsilon = os.path.join(destdir, 'epsilon')
print('outdir_epsilon = {}'.format(outdir_epsilon))
# set up base epsilon snapshots
esnap_base_partial = EpsilonSnapshot()
esnap_base_partial.setFromSnapshot(fsnap_base_partial)
esnap_base_full = EpsilonSnapshot()
esnap_base_full.setFromSnapshot(fsnap_base_full)
#esnap_base_partial.setCentro(excitation_location)
#esnap_base_partial.setSize(sim.getSize()/2)
#esnap_base_partial.setPlaneOrientationY()
## set up base frequency snapshot
#fsnap_base = FrequencySnapshot()
#fsnap_base.setFromSnapshot(esnap_base)
# attach base snapshots to boxes
partial_box.setBaseSnapshot(esnap_base_partial)
xyz_box.setBaseSnapshot(esnap_base_full)
# add the snapshots
sim.setSnapshots([partial_box, xyz_box])
# set up a short simulation
sim.setIterations(1)
sim.setWallTime(120)
# write
if not dry_run and not disabled_epsilon:
sim.writeTorqueJobDirectory(outdir_epsilon,
overwrite=overwrite)
checkSnapshotNumber(os.path.join(
outdir_epsilon,
sim.getFileBaseName() + '.inp'),
verbose=True)
if direction not in disabled_directions:
for freq_MHz in freq_MHz_list:
print('freq_MHz = {}'.format(freq_MHz))
wavelength_mum = get_c0() / freq_MHz
outdir_MV = os.path.join(
destdir, direction,
'MV-freq-{:.0f}-MHz-lambda-{:.6f}-mum'.format(
freq_MHz, wavelength_mum))
print('outdir_MV = {}'.format(outdir_MV))
# set snapshot frequency
fsnap_base_partial.setFrequencies([freq_MHz])
fsnap_base_full.setFrequencies([freq_MHz])
fsnap_custom.setFrequencies([freq_MHz])
# attach base snapshots to boxes
partial_box.setBaseSnapshot(fsnap_base_partial)
xyz_box.setBaseSnapshot(fsnap_base_full)
# add the snapshots
sim.setSnapshots([
partial_box, xyz_box, f1, f2, f3, f4, f5, f7, f8, f9, f10,
f11
])
# set up a long simulation
sim.setIterations(1e9)
sim.setWallTime(360)
# write
if not dry_run:
sim.writeTorqueJobDirectory(outdir_MV, overwrite=overwrite)
checkSnapshotNumber(os.path.join(
outdir_MV,
sim.getFileBaseName() + '.inp'),
verbose=True)
return
def automeshWithMeshingFactor(infile, outfile, meshing_factor):
sim = bfdtd.readBristolFDTD(infile)
sim.autoMeshGeometry(meshing_factor)
sim.writeInpFile(outfile)
