def _sampling_mp(ismp, skip_title=False, skip_fend=False):
global init, pnu, pxs, plpc, pchi, pfy, tape
t0 = time.time()
mat = tape.mat[0]
newtape = Endf6(tape.copy())
extra_points = np.logspace(-5, 7, init.energy_sequence)
if not pxs.empty:
xs = newtape.get_xs()
if not xs.empty:
xspert = xs.perturb(pxs[ismp])
newtape = newtape.update_xs(xspert)
if not pnu.empty:
nubar = newtape.get_nubar()
if not nubar.empty:
nubarpert = nubar.perturb(pnu[ismp])
newtape = newtape.update_nubar(nubarpert)
if not pchi.empty:
edistr = pfns.from_endf6(newtape).add_points(extra_points)
if not edistr.empty:
edistrpert = edistr.perturb(pchi[ismp])
newtape = newtape.update_edistr(edistrpert)
if not plpc.empty:
lpc = newtape.get_lpc().add_points(extra_points)
if not lpc.empty:
lpcpert = lpc.perturb(plpc[ismp])
newtape = newtape.update_lpc(lpcpert)
if not pfy.empty:
fy = newtape.get_fy()
if not fy.empty:
fypert = fy.perturb(pfy[ismp])
newtape = newtape.update_fy(fypert)
print("Created sample {} for MAT {} in {:.2f} sec".format(ismp, mat, time.time()-t0,))
descr = ["perturbed file No.{} created by SANDY".format(ismp)]
return newtape.delete_cov().update_info(descr=descr).write_string(skip_title=skip_title, skip_fend=skip_fend)
def test_update_info(testPu9):
testPu9.loc[9437, 3, 1].TEXT = "\n".join(
testPu9.loc[9437, 3, 1].TEXT.splitlines()[:10]) + "\n"
testPu9 = Endf6(testPu9.drop([(9437, 3, 102)]))
new = testPu9.update_info()
recordsold = testPu9.read_section(9437, 1, 451)["RECORDS"]
recordsnew = new.read_section(9437, 1, 451)["RECORDS"]
assert (3, 102, 147, 1) in recordsold
assert (3, 102, 147, 1) not in recordsnew
assert (3, 1, 188, 1) in recordsold
assert (3, 1, 10, 1) in recordsnew
def test_sample_fy():
tape = Endf6.from_text("\n".join(FY.endf6))
nsmp = 1000
ismp = randint(1, nsmp)
fyu5 = tape.get_fy(listenergy=[4e5]).filter_by("MAT", 9228)
fyall = tape.get_fy()
cov = fyu5.get_cov(mat=9228, mt=454, energy=4e5)
perts = cov.get_samples(nsmp)
pert = perts[ismp]
fynew = fyall.perturb(pert)
assert (fyall.query("MAT!=9228 & MT!=454 & E!=4e5") == fynew.query(
"MAT!=9228 & MT!=454 & E!=4e5")).all().all()
fy = fynew.query("MAT==9228 & MT==454 & E==4e5")
assert not (fyall.query("MAT==9228 & MT==454 & E==4e5") == fy).all().all()
assert (fy.YI >= 0).all()
assert (fy.YI <= fy.YI * 2).all()
def test_sample_xs():
errtape = Errorr.from_text("\n".join(H1.errorr))
nsmp = 1000
perts = XsCov.from_errorr(
errtape.filter_by(listmt=[102, 451])).get_samples(nsmp, eig=10)
pendftape = Endf6.from_text("\n".join(H1.pendf))
xs = pendftape.get_xs()
ismp = randint(1, nsmp)
pert = perts[ismp]
pxs = xs.perturb(pert)
newtape = pendftape.update_xs(pxs)
assert perts.shape[1] == nsmp
mat = 125
mt = 102
ratio = pxs / xs.values
pert = pert.loc[125, 102]
ugrid = pert.index
pert = pert.reindex(pert.index.union(
ratio.index)).ffill().fillna(1).reindex(ratio.index)
assert np.allclose(ratio[mat, mt], pert)
assert newtape.loc[125, 3, 102].TEXT != pendftape.loc[125, 3, 102].TEXT
def sampling(iargs=None):
"""Construct multivariate normal distributions with a unit vector for
mean and with relative covariances taken from the evaluated files.
Perturbation factors are sampled with the same multigroup structure of
the covariance matrix, and are applied to the pointwise data to produce
the perturbed files.
"""
global init, pnu, pxs, plpc, pchi, pfy, tape
init = parse(iargs)
ftape = read_formatted_file(init.file)
covtape = read_formatted_file(init.cov) if init.cov else ftape
# nsub = ftape.get_nsub()
# INITIALIZE PERT DF
pnu = pd.DataFrame()
pxs = pd.DataFrame()
plpc = pd.DataFrame()
pchi = pd.DataFrame()
pfy = pd.DataFrame()
ftape, covtape, pnu, pxs, plpc, pchi, pfy = extract_samples(ftape, covtape)
df = {}
if pnu.empty and pxs.empty and plpc.empty and pchi.empty and pfy.empty:
logging.warn("no covariance section was selected/found")
return ftape, covtape, df
# APPLY PERTURBATIONS BY MAT
for imat,(mat, tape) in enumerate(sorted(ftape.groupby('MAT'))):
skip_title = False if imat == 0 else True
skip_fend = False if imat == len(ftape.mat) - 1 else True
tape = Endf6(tape)
kw = dict(skip_title=skip_title, skip_fend=skip_fend)
if init.processes == 1:
outs = {i : _sampling_mp(i, **kw) for i in range(1,init.samples+1)}
else:
pool = mp.Pool(processes=init.processes)
outs = {i : pool.apply_async(_sampling_mp, (i,), kw) for i in range(1,init.samples+1)}
outs = {i : out.get() for i,out in outs.items()}
pool.close()
pool.join()
df.update({mat : outs})
# DUMP TO FILES
frame = pd.DataFrame(df)
frame.index.name = "SMP"
frame.columns.name = "MAT"
frame = frame.stack()
outname = init.outname if init.outname else os.path.split(init.file)[1]
for ismp,dfsmp in frame.groupby("SMP"):
output = os.path.join(init.outdir, '{}-{}'.format(outname, ismp))
with open(output, 'w') as f:
for mat,dfmat in dfsmp.groupby("MAT"):
f.write(frame[ismp,mat])
# PRODUCE ACE FILES
if init.acer:
if init.processes == 1:
for i in range(1,init.samples+1):
_process_into_ace(ismp)
else:
pool = mp.Pool(processes=init.processes)
outs = {i : pool.apply_async(_process_into_ace, (i,)) for i in range(1,init.samples+1)}
pool.close()
pool.join()
return ftape, covtape, df
pdb.set_trace()
df = {}
if init.fission_yields:
# EXTRACT FY PERTURBATIONS FROM COV FILE
fy = ftape.get_fy(listmat=init.mat, listmt=init.mt)
if fy.empty:
logging.warn("no fission yield section was selected/found")
return
index = fy.index.to_frame(index=False)
dfperts = []
for mat,dfmat in index.groupby("MAT"):
for mt,dfmt in dfmat.groupby("MT"):
for e,dfe in dfmt.groupby("E"):
fycov = fy.get_cov(mat, mt, e)
pert = fycov.get_samples(init.samples, eig=0)
dfperts.append(pert)
PertFy = FySamples(pd.concat(dfperts))
if init.debug: PertFy.to_csv("perts_mf8.csv")
# DELETE LOCAL VARIABLES
for k in locals().keys():
del locals()[k]
# APPLY PERTURBATIONS BY MAT
for imat,(mat, tape) in enumerate(sorted(ftape.groupby('MAT'))):
skip_title = False if imat == 0 else True
skip_fend = False if imat == ftape.index.get_level_values("MAT").unique().size -1 else True
tape = Endf6(tape)
kw = dict(skip_title=skip_title, skip_fend=skip_fend)
if mat not in init.mat:
out = tape.write_string(**kw)
outs = {i : out for i in range(1,init.samples+1)}
else:
if init.processes == 1:
outs = {i : _sampling_fy_mp(i, **kw) for i in range(1,init.samples+1)}
else:
pool = mp.Pool(processes=init.processes)
outs = {i : pool.apply_async(_sampling_fy_mp, (i,), kw) for i in range(1,init.samples+1)}
outs = {i : out.get() for i,out in outs.items()}
pool.close()
pool.join()
df.update({ mat : outs })
else:
# EXTRACT NUBAR PERTURBATIONS FROM ENDF6 FILE
PertNubar = pd.DataFrame()
if 31 in init.mf and 31 in ftape.mf:
nubarcov = XsCov.from_endf6(covtape.filter_by(listmat=init.mat, listmf=[31], listmt=listmt))
if not nubarcov.empty:
PertNubar = nubarcov.get_samples(init.samples, eig=init.eig)
if init.debug:
PertNubar.to_csv("perts_mf31.csv")
# EXTRACT PERTURBATIONS FROM EDISTR COV FILE
PertEdistr = pd.DataFrame()
if 35 in init.mf and 35 in ftape.mf:
edistrcov = ftape.get_edistr_cov()
if not edistrcov.empty:
PertEdistr = edistrcov.get_samples(init.samples, eig=init.eig)
if init.debug:
PertEdistr.to_csv("perts_mf35.csv")
# EXTRACT PERTURBATIONS FROM LPC COV FILE
PertLpc = pd.DataFrame()
if 34 in init.mf and 34 in covtape.mf:
lpccov = ftape.get_lpc_cov()
if not lpccov.empty:
if init.max_polynomial:
lpccov = lpccov.filter_p(init.max_polynomial)
PertLpc = lpccov.get_samples(init.samples, eig=init.eig)
if init.debug:
PertLpc.to_csv("perts_mf34.csv")
# EXTRACT XS PERTURBATIONS FROM COV FILE
PertXs = pd.DataFrame()
if 33 in init.mf and 33 in covtape.mf:
if init.errorr and len(ftape.mat) > 1: # Limit imposed by running ERRORR to get covariance matrices
raise SandyError("More than one MAT number was found")
if ftape.get_file_format() == "endf6":
with tempfile.TemporaryDirectory() as td:
outputs = njoy.process(init.file, broadr=False, thermr=False,
unresr=False, heatr=False, gaspr=False,
purr=False, errorr=init.errorr, acer=False,
wdir=td, keep_pendf=True,
temperatures=[0], suffixes=[0], err=0.005)[2]
ptape = read_formatted_file(outputs["tape30"])
if init.errorr:
covtape = read_formatted_file(outputs["tape33"]) # WARNING: by doing this we delete the original covtape
ftape = ftape.delete_sections((None, 3, None)). \
add_sections(ptape.filter_by(listmf=[3])). \
add_sections(ptape.filter_by(listmf=[1], listmt=[451]))
listmterr = init.mt if init.mt is None else [451].extend(init.mt) # ERRORR needs MF1/MT451 to get the energy grid
covtape = covtape.filter_by(listmat=init.mat, listmf=[1,33], listmt=listmterr)
covtype = covtape.get_file_format()
xscov = XsCov.from_errorr(covtape) if covtype == "errorr" else XsCov.from_endf6(covtape)
if not xscov.empty:
PertXs = xscov.get_samples(init.samples, eig=init.eig, seed=init.seed33)
if init.debug:
PertXs.to_csv(os.path.join(init.outdir, "perts_mf33.csv"))
if PertLpc.empty and PertEdistr.empty and PertXs.empty and PertNubar.empty:
sys.exit("no covariance section was selected/found")
return
pdb.set_trace()
# DELETE LOCAL VARIABLES
for k in locals().keys():
del locals()[k]
# APPLY PERTURBATIONS BY MAT
for imat,(mat, tape) in enumerate(sorted(ftape.groupby('MAT'))):
skip_title = False if imat == 0 else True
skip_fend = False if imat == ftape.index.get_level_values("MAT").unique().size -1 else True
tape = Endf6(tape)
kw = dict(skip_title=skip_title, skip_fend=skip_fend)
if init.processes == 1:
outs = {i : _sampling_mp(i, **kw) for i in range(1,init.samples+1)}
else:
pool = mp.Pool(processes=init.processes)
outs = {i : pool.apply_async(_sampling_mp, (i,), kw) for i in range(1,init.samples+1)}
outs = {i : out.get() for i,out in outs.items()}
pool.close()
pool.join()
df.update({ mat : outs })
# DUMP TO FILES
frame = pd.DataFrame(df)
frame.index.name = "SMP"
frame.columns.name = "MAT"
frame = frame.stack()
outname = init.outname if init.outname else os.path.split(init.file)[1]
for ismp,dfsmp in frame.groupby("SMP"):
output = os.path.join(init.outdir, '{}-{}'.format(outname, ismp))
with open(output, 'w') as f:
for mat,dfmat in dfsmp.groupby("MAT"):
f.write(frame[ismp,mat])
def process_proton(endftape, wdir="", dryrun=False, tag="", exe=None, route="0", **kwargs):
"""Run sequence to process proton file with njoy.
Parameters
----------
wdir : `str`
working directory (absolute or relative) where all output files are
saved
.. note:
`wdir` will appear as part of the `filename` in
any `xsdir` file
dryrun : `bool`
option to produce the njoy input file without running njoy
tag : `str`
tag to append to each output filename beofre the extension (default is `None`)
.. hint:
to process JEFF-3.3 files you could set `tag = "_j33"`
exe : `str`
njoy executable (with path)
.. note:
If no executable is given, SANDY looks for a default executable in `PATH`
route : `str`
xsdir "route" parameter (default is "0")
Returns
-------
input : `str`
njoy input text
inputs : `map`
map of {`tape` : `file`) for input files
outputs : `map`
map of {`tape` : `file`) for ouptut files
"""
tape = Endf6.from_file(endftape)
mat = tape.mat[0]
info = tape.read_section(mat, 1, 451)
meta = info["LISO"]
za = int(info["ZA"])
za_new = za + meta*100 + 300 if meta else za
inputs = {}
outputs = {}
kwargs["mat"] = mat
inputs["tape20"] = endftape
kwargs["temp"] = 0
kwargs["suff"] = suff = ".00"
text = _acer_input(20, 20, 50, 70, **kwargs)
outputs["tape50"] = os.path.join(wdir, "{}{}{}h".format(za_new, tag, suff))
outputs["tape70"] = os.path.join(wdir, "{}{}{}h.xsd".format(za_new, tag, suff))
text += "stop"
if not dryrun:
_run_njoy(text, inputs, outputs, exe=exe)
# Change route and filename in xsdir file.
acefile = outputs["tape50"]
xsdfile = outputs["tape70"]
text_xsd = open(xsdfile).read(). \
replace("route", route). \
replace("filename", acefile)
text_xsd = " ".join(text_xsd.split())
# If isotope is metatable rewrite ZA in xsdir and ace as ZA = Z*1000 + 300 + A + META*100.
if meta:
pattern = '{:d}'.format(za) + '\.(?P<ext>\d{2}[ct])'
found = re.search(pattern, text_xsd)
ext = found.group("ext")
text_xsd = text_xsd.replace("{:d}.{}".format(za, ext), "{:d}.{}".format(za_new, ext), 1)
text_ace = open(acefile).read()
text_ace = text_ace.replace("{:d}.{}".format(za, ext), "{:d}.{}".format(za_new, ext), 1)
with open(acefile, 'w') as f:
f.write(text_ace)
with open(xsdfile, 'w') as f:
f.write(text_xsd)
return text, inputs, outputs
def process(endftape,
pendftape=None,
kermas=[302, 303, 304, 318, 402, 442, 443, 444, 445, 446, 447],
temperatures=[293.6],
suffixes=None,
broadr=True,
thermr=True,
unresr=False,
heatr=True,
gaspr=True,
purr=True,
errorr=False,
acer=True,
wdir="",
dryrun=False,
tag="",
method=None,
exe=None,
keep_pendf=True,
route="0",
addpath=None,
**kwargs):
"""
Run sequence to process file with njoy.
Parameters
----------
pendftape : `str`, optional, default is `None`
skip module reconr and use this PENDF file
kermas : iterable of `int`, optional, default is `[302, 303, 304, 318, 402, 442, 443, 444, 445, 446, 447]`
MT numbers for partial kermas to pass to heatr.
.. note:: `MT=301` is the KERMA total (energy balance) and is always calculated
temperatures : iterable of `float`, optional, default is [293.6]
iterable of temperature values in K
suffixes : iterable of `int`, optional, default is `None`
iterable of suffix values for ACE files: if `None` is given, use internal routine to determine suffixes
.. warning:: `suffixes` must match the number of entries in `temperatures`
broadr : `bool`, optional, default is `True`
option to run module broadr
thermr : `bool`, optional, default is `True`
option to run module thermr
unresr : `bool`, optional, default is `False`
option to run module unresr
heatr : `bool`, optional, default is `True`
option to run module heatr
gaspr : `bool`, optional, default is `True`
option to run module gapr
purr : `bool`, optional, default is `True`
option to run module purr
errorr : `bool`, optional, default is `False`
option to run module errorr
acer : `bool`, optional, default is `True`
option to run module acer
wdir : `str`, optional, default is `""`
working directory (absolute or relative) where all output files are saved
.. note:: `wdir` will appear as part of the `filename` in any `xsdir` file if `addpath` is not set
addpath : `str`, optional, default is `None`
path to add in xsdir, by default use `wdir`
dryrun : `bool`, optional, default is `False`
option to produce the njoy input file without running njoy
tag : `str`, optional, default is `""`
tag to append to each output filename before the extension (default is `None`)
.. hint:: to process JEFF-3.3 files you could set `tag = "_j33"`
exe : `str`, optional, default is `None`
njoy executable (with path)
.. note:: if no executable is given, SANDY looks for a default executable in `PATH` and in env variable `NJOY`
keep_pendf : `bool`, optional, default is `True`
save output PENDF file
route : `str`, optional, default is `0`
xsdir "route" parameter
Returns
-------
input : `str`
njoy input text
inputs : `map`
map of {`tape` : `file`) for input files
outputs : `map`
map of {`tape` : `file`) for ouptut files
"""
tape = Endf6.from_file(endftape)
mat = tape.mat[0]
info = tape.read_section(mat, 1, 451)
meta = info["LISO"]
za = int(info["ZA"])
zam = za*10 + meta
za_new = za + meta*100 + 300 if meta else za
outprefix = zam if method == "aleph" else za_new
inputs = {}
outputs = {}
# Only kwargs are passed to NJOY inputs, therefore add temperatures and mat
kwargs.update({"temperatures" : temperatures, "mat" : mat})
# Check input args
if not suffixes:
suffixes = [get_suffix(temp, meta, method) for temp in temperatures]
if len(suffixes) != len(temperatures):
raise SandyError("number of suffixes must match number of temperatures")
inputs["tape20"] = endftape
e = 21
p = e + 1
text = _moder_input(20, -e)
if pendftape:
inputs["tape99"] = pendftape
text += _moder_input(99, -p)
else:
text += _reconr_input(-e, -p, **kwargs)
if broadr:
o = p + 1
text += _broadr_input(-e, -p, -o, **kwargs)
p = o
if thermr:
o = p + 1
text += _thermr_input(0, -p, -o, **kwargs)
p = o
if unresr:
o = p + 1
text += _unresr_input(-e, -p, -o, **kwargs)
p = o
if heatr:
for i in range(0, len(kermas), 7):
o = p + 1
kwargs["pks"] = kermas[i:i+7]
text += _heatr_input(-e, -p, -o, **kwargs)
p = o
if gaspr:
o = p + 1
text += _gaspr_input(-e, -p, -o, **kwargs)
p = o
if purr:
o = p + 1
text += _purr_input(-e, -p, -o, **kwargs)
p = o
if keep_pendf:
o = 30
text += _moder_input(-p, o)
outputs["tape{}".format(o)] = os.path.join(wdir, "{}{}.pendf".format(outprefix, tag))
if errorr:
for i,(temp,suff) in enumerate(zip(temperatures, suffixes)):
o = 33 + i
kwargs["temp"] = temp
kwargs["suff"] = suff = ".{}".format(suff)
text += _errorr_input(-e, -p, o, **kwargs)
outputs["tape{}".format(o)] = os.path.join(wdir, "{}{}{}.errorr".format(outprefix, tag, suff))
if acer:
for i,(temp,suff) in enumerate(zip(temperatures, suffixes)):
a = 50 + i
x = 70 + i
kwargs["temp"] = temp
kwargs["suff"] = suff = ".{}".format(suff)
text += _acer_input(-e, -p, a, x, **kwargs)
outputs["tape{}".format(a)] = os.path.join(wdir, "{}{}{}c".format(outprefix, tag, suff))
outputs["tape{}".format(x)] = os.path.join(wdir, "{}{}{}c.xsd".format(outprefix, tag, suff))
text += "stop"
if not dryrun:
_run_njoy(text, inputs, outputs, exe=exe)
if acer:
# Change route and filename in xsdir file.
for i,(temp,suff) in enumerate(zip(temperatures, suffixes)):
a = 50 + i
x = 70 + i
acefile = outputs["tape{}".format(a)]
if addpath is None:
filename = acefile
else:
filename = os.path.basename(acefile)
if addpath:
filename = os.path.join(addpath, filename)
xsdfile = outputs["tape{}".format(x)]
text_xsd = open(xsdfile).read(). \
replace("route", route). \
replace("filename", filename)
text_xsd = " ".join(text_xsd.split())
# If isotope is metatable rewrite ZA in xsdir and ace as ZA = Z*1000 + 300 + A + META*100.
if meta and method != "aleph":
pattern = '{:d}'.format(za) + '\.(?P<ext>\d{2}[ct])'
found = re.search(pattern, text_xsd)
ext = found.group("ext")
text_xsd = text_xsd.replace("{:d}.{}".format(za, ext), "{:d}.{}".format(za_new, ext), 1)
text_ace = open(acefile).read()
text_ace = text_ace.replace("{:d}.{}".format(za, ext), "{:d}.{}".format(za_new, ext), 1)
with open(acefile, 'w') as f:
f.write(text_ace)
with open(xsdfile, 'w') as f:
f.write(text_xsd)
return text, inputs, outputs
def testU8():
tape = Endf6.from_text("\n".join(U8.endf6))
assert (tape.index.get_level_values("MAT").unique() == 9237).all()
return tape
def testU5():
tape = Endf6.from_text("\n".join(U5.nfy))
assert (tape.index.get_level_values("MAT").unique() == 9228).all()
return tape
def test_write_to_string(testH1):
string = testH1.write_string()
newtape = Endf6.from_text(string)
assert testH1.equals(newtape)
def testFe56():
tape = Endf6.from_text("\n".join(Fe56.endf6))
assert (tape.index.get_level_values("MAT").unique() == 2631).all()
return tape
def testH1():
tape = Endf6.from_text("\n".join(H1.pendf))
assert (tape.index.get_level_values("MAT").unique() == 125).all()
return tape