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Merge pull request #56 from jkuhl-uni/feature/input_2.0

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Feature/input 2.0
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Fabian Joswig 2022-02-08 13:37:32 +00:00 • committed by GitHub
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230
data/sfcf_test/data_o/test_r0/cfg2/F_V0 Normal file
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data/sfcf_test/data_o/test_r0/cfg3/f_1 Normal file
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80
data/sfcf_test/data_o/test_r0/cfg3/f_A Normal file
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[run]
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230
data/sfcf_test/data_o/test_r0/cfg4/F_V0 Normal file
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[run]
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194
data/sfcf_test/data_o/test_r0/cfg4/f_1 Normal file
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[run]
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80
data/sfcf_test/data_o/test_r0/cfg4/f_A Normal file
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@ -0,0 +1,80 @@
[run]
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230
data/sfcf_test/data_o/test_r0/cfg5/F_V0 Normal file
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[run]
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194
data/sfcf_test/data_o/test_r0/cfg5/f_1 Normal file
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[run]
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80
data/sfcf_test/data_o/test_r0/cfg5/f_A Normal file
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230
data/sfcf_test/data_o/test_r1/cfg1/F_V0 Normal file
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[run]
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194
data/sfcf_test/data_o/test_r1/cfg1/f_1 Normal file
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[run]
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80
data/sfcf_test/data_o/test_r1/cfg1/f_A Normal file
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3 -4.1025142768037739e+01 +5.9315333178954509e-17

230
data/sfcf_test/data_o/test_r2/cfg1/F_V0 Normal file
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@ -0,0 +1,230 @@
[run]
version 2.1
date 2022-01-19 11:04:00 +0100
host r04n07.palma.wwu
dir /scratch/tmp/j_kuhl19
user j_kuhl19
gauge_name /unity
gauge_md5 1ea28326e4090996111a320b8372811d
param_name sfcf_unity_test.in
param_md5 d881e90d41188a33b8b0f1bd0bc53ea5
param_hash 686af5e712ee2902180f5428af94c6e7
data_name ./output_10519905/data_oF_V0
[correlator]
name F_V0
quarks lquark lquark
offset 0
wf 0
wf_2 0
corr_t
1 +6.8367760900851147e+02 +3.0531839956225539e-10
2 +6.6131885855823339e+02 +3.9736225045852382e-12
3 +6.8367760900810049e+02 -2.5611665964422843e-10
[correlator]
name F_V0
quarks lquark lquark
offset 0
wf 0
wf_2 1
corr_t
1 +6.8370283168793060e+02 +3.0532966356282939e-10
2 +6.6134325636407561e+02 +3.9737690976212336e-12
3 +6.8370283168751973e+02 -2.5612610847134760e-10
[correlator]
name F_V0
quarks lquark lquark
offset 0
wf 0
wf_2 2
corr_t
1 +6.8370484437212463e+02 +3.0533056232915147e-10
2 +6.6134520322615822e+02 +3.9737807346122766e-12
3 +6.8370484437171353e+02 -2.5612686251836130e-10
[correlator]
name F_V0
quarks lquark lquark
offset 0
wf 1
wf_2 0
corr_t
1 +6.8370283168792889e+02 +3.0532890521977295e-10
2 +6.6134325636407402e+02 +3.9730355551484655e-12
3 +6.8370283168751791e+02 -2.5612686681440218e-10
[correlator]
name F_V0
quarks lquark lquark
offset 0
wf 1
wf_2 1
corr_t
1 +6.8372805529787934e+02 +3.0534016954586185e-10
2 +6.6136765507001564e+02 +3.9731820664935325e-12
3 +6.8372805529746825e+02 -2.5613631608015786e-10
[correlator]
name F_V0
quarks lquark lquark
offset 0
wf 1
wf_2 2
corr_t
1 +6.8373006805632656e+02 +3.0534106842445933e-10
2 +6.6136960200392332e+02 +3.9731937804440792e-12
3 +6.8373006805591558e+02 -2.5613707007587266e-10
[correlator]
name F_V0
quarks lquark lquark
offset 0
wf 2
wf_2 0
corr_t
1 +6.8370484437212156e+02 +3.0532220084664646e-10
2 +6.6134520322615526e+02 +3.9656927030717790e-12
3 +6.8370484437171069e+02 -2.5613522400086377e-10
[correlator]
name F_V0
quarks lquark lquark
offset 0
wf 2
wf_2 1
corr_t
1 +6.8373006805632599e+02 +3.0533346499198999e-10
2 +6.6136960200392275e+02 +3.9658390079382195e-12
3 +6.8373006805591490e+02 -2.5614467350834153e-10
[correlator]
name F_V0
quarks lquark lquark
offset 0
wf 2
wf_2 2
corr_t
1 +6.8373208082069789e+02 +3.0533436384459901e-10
2 +6.6137154894356127e+02 +3.9658506942251639e-12
3 +6.8373208082028680e+02 -2.5614542753491032e-10
[correlator]
name F_V0
quarks lquark lquark
offset 1
wf 0
wf_2 0
corr_t
1 +6.8367760900918211e+02 -9.5149222536505804e-10
2 +6.6131885855810310e+02 +3.2960434859595585e-10
3 +6.8367760900806934e+02 -2.3744430846347533e-10
[correlator]
name F_V0
quarks lquark lquark
offset 1
wf 0
wf_2 1
corr_t
1 +6.8370283168860135e+02 -9.5152732859532533e-10
2 +6.6134325636394544e+02 +3.2961650841969937e-10
3 +6.8370283168748858e+02 -2.3745306857315358e-10
[correlator]
name F_V0
quarks lquark lquark
offset 1
wf 0
wf_2 2
corr_t
1 +6.8370484437279526e+02 -9.5153012965274573e-10
2 +6.6134520322602793e+02 +3.2961747879154288e-10
3 +6.8370484437168250e+02 -2.3745376753897864e-10
[correlator]
name F_V0
quarks lquark lquark
offset 1
wf 1
wf_2 0
corr_t
1 +6.8370283168859953e+02 -9.5151770701795658e-10
2 +6.6134325636394351e+02 +3.2962581533640458e-10
3 +6.8370283168748665e+02 -2.3744344699578737e-10
[correlator]
name F_V0
quarks lquark lquark
offset 1
wf 1
wf_2 1
corr_t
1 +6.8372805529855032e+02 -9.5155281099707234e-10
2 +6.6136765506988547e+02 +3.2963797613709602e-10
3 +6.8372805529743755e+02 -2.3745220688244645e-10
[correlator]
name F_V0
quarks lquark lquark
offset 1
wf 1
wf_2 2
corr_t
1 +6.8373006805699742e+02 -9.5155561220425917e-10
2 +6.6136960200379315e+02 +3.2963894649982994e-10
3 +6.8373006805588454e+02 -2.3745290592048597e-10
[correlator]
name F_V0
quarks lquark lquark
offset 1
wf 2
wf_2 0
corr_t
1 +6.8370484437279174e+02 -9.5153224647433932e-10
2 +6.6134520322602452e+02 +3.2961543119772646e-10
3 +6.8370484437167897e+02 -2.3745588436057620e-10
[correlator]
name F_V0
quarks lquark lquark
offset 1
wf 2
wf_2 1
corr_t
1 +6.8373006805699617e+02 -9.5156735103669992e-10
2 +6.6136960200379178e+02 +3.2962759157000606e-10
3 +6.8373006805588329e+02 -2.3746464475292832e-10
[correlator]
name F_V0
quarks lquark lquark
offset 1
wf 2
wf_2 2
corr_t
1 +6.8373208082136819e+02 -9.5157015223999714e-10
2 +6.6137154894343041e+02 +3.2962856194733528e-10
3 +6.8373208082025531e+02 -2.3746534378088984e-10

194
data/sfcf_test/data_o/test_r2/cfg1/f_1 Normal file
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@ -0,0 +1,194 @@
[run]
version 2.1
date 2022-01-19 11:04:00 +0100
host r04n07.palma.wwu
dir /scratch/tmp/j_kuhl19
user j_kuhl19
gauge_name /unity
gauge_md5 1ea28326e4090996111a320b8372811d
param_name sfcf_unity_test.in
param_md5 d881e90d41188a33b8b0f1bd0bc53ea5
param_hash 686af5e712ee2902180f5428af94c6e7
data_name ./output_10519905/data_of_1
[correlator]
name f_1
quarks lquark lquark
offset 0
wf 0
wf_2 0
corr
+3.5119415254545021e+02 +6.7620978057264750e-15
[correlator]
name f_1
quarks lquark lquark
offset 0
wf 0
wf_2 1
corr
+3.5120703575855339e+02 +6.5026340956203663e-15
[correlator]
name f_1
quarks lquark lquark
offset 0
wf 0
wf_2 2
corr
+3.5120808902177868e+02 +6.5443496235264788e-15
[correlator]
name f_1
quarks lquark lquark
offset 0
wf 1
wf_2 0
corr
+3.5120703575855515e+02 +6.9706500417651470e-15
[correlator]
name f_1
quarks lquark lquark
offset 0
wf 1
wf_2 1
corr
+3.5122001235609065e+02 +6.9516150897757419e-15
[correlator]
name f_1
quarks lquark lquark
offset 0
wf 1
wf_2 2
corr
+3.5122104108046199e+02 +6.9232860455434941e-15
[correlator]
name f_1
quarks lquark lquark
offset 0
wf 2
wf_2 0
corr
+3.5120808902177447e+02 +1.0849949614595719e-14
[correlator]
name f_1
quarks lquark lquark
offset 0
wf 2
wf_2 1
corr
+3.5122104108046182e+02 +1.0866063643253473e-14
[correlator]
name f_1
quarks lquark lquark
offset 0
wf 2
wf_2 2
corr
+3.5122207631098047e+02 +1.0827277318679030e-14
[correlator]
name f_1
quarks lquark lquark
offset 1
wf 0
wf_2 0
corr
+3.5119415254545038e+02 +3.0143306723935508e-15
[correlator]
name f_1
quarks lquark lquark
offset 1
wf 0
wf_2 1
corr
+3.5120703575855367e+02 +4.3340379505972648e-15
[correlator]
name f_1
quarks lquark lquark
offset 1
wf 0
wf_2 2
corr
+3.5120808902177902e+02 +3.9652247575094006e-15
[correlator]
name f_1
quarks lquark lquark
offset 1
wf 1
wf_2 0
corr
+3.5120703575855526e+02 -8.2540994138261318e-16
[correlator]
name f_1
quarks lquark lquark
offset 1
wf 1
wf_2 1
corr
+3.5122001235609082e+02 -9.7121215247039609e-16
[correlator]
name f_1
quarks lquark lquark
offset 1
wf 1
wf_2 2
corr
+3.5122104108046227e+02 -9.0872484903683497e-16
[correlator]
name f_1
quarks lquark lquark
offset 1
wf 2
wf_2 0
corr
+3.5120808902177453e+02 +5.1331372776616026e-15
[correlator]
name f_1
quarks lquark lquark
offset 1
wf 2
wf_2 1
corr
+3.5122104108046193e+02 +5.0816653044831932e-15
[correlator]
name f_1
quarks lquark lquark
offset 1
wf 2
wf_2 2
corr
+3.5122207631098064e+02 +5.1165649253001659e-15

80
data/sfcf_test/data_o/test_r2/cfg1/f_A Normal file
View file

@ -0,0 +1,80 @@
[run]
version 2.1
date 2022-01-19 11:04:00 +0100
host r04n07.palma.wwu
dir /scratch/tmp/j_kuhl19
user j_kuhl19
gauge_name /unity
gauge_md5 1ea28326e4090996111a320b8372811d
param_name sfcf_unity_test.in
param_md5 d881e90d41188a33b8b0f1bd0bc53ea5
param_hash 686af5e712ee2902180f5428af94c6e7
data_name ./output_10519905/data_of_A
[correlator]
name f_A
quarks lquark lquark
offset 0
wf 0
corr_t
1 +6.5471188727972304e+01 -6.1214214711790100e-12
2 +1.0447210336915187e+00 +8.9219487930753188e-13
3 -4.1025094911185178e+01 -4.8315634170546161e-14
[correlator]
name f_A
quarks lquark lquark
offset 0
wf 1
corr_t
1 +6.5551520722862705e+01 +2.0963356863957609e-13
2 +1.0542820240851569e+00 +2.3989756974599379e-15
3 -4.1024441815729936e+01 -5.7107484666182308e-15
[correlator]
name f_A
quarks lquark lquark
offset 0
wf 2
corr_t
1 +6.5529951269442847e+01 -6.6512260271334321e-14
2 +1.0516822345055969e+00 -2.2935262162529075e-15
3 -4.1025142768037746e+01 +3.7566377680004518e-16
[correlator]
name f_A
quarks lquark lquark
offset 1
wf 0
corr_t
1 +6.5471188727965909e+01 -1.6112786177915427e-11
2 +1.0447210337411881e+00 -7.0387528705692678e-13
3 -4.1025094911167137e+01 +4.6509152745618223e-13
[correlator]
name f_A
quarks lquark lquark
offset 1
wf 1
corr_t
1 +6.5551520722842213e+01 -8.1976426690345305e-13
2 +1.0542820240843382e+00 +2.1626370477046812e-13
3 -4.1024441815730086e+01 -2.4147931196409923e-14
[correlator]
name f_A
quarks lquark lquark
offset 1
wf 2
corr_t
1 +6.5529951269443117e+01 +7.9192560386479701e-14
2 +1.0516822345055870e+00 -1.2443038782429568e-14
3 -4.1025142768037739e+01 +5.9315333178954509e-17

3
pyerrors/input/openQCD.py
View file

@ -217,8 +217,7 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
return result return result
def extract_t0(path, prefix, dtr_read, xmin, def extract_t0(path, prefix, dtr_read, xmin, spatial_extent, fit_range=5, **kwargs):
spatial_extent, fit_range=5, **kwargs):
"""Extract t0 from given .ms.dat files. Returns t0 as Obs. """Extract t0 from given .ms.dat files. Returns t0 as Obs.
It is assumed that all boundary effects have It is assumed that all boundary effects have

208
pyerrors/input/sfcf.py
View file

@ -9,57 +9,46 @@ from ..obs import Obs
from . import utils from . import utils
def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=0, wf2=0, version="1.0c", **kwargs):
version="1.0c", **kwargs): """Read sfcf c format from given folder structure.
"""Read sfcf format from given folder structure.
Parameters Parameters
---------- ----------
path : str quarks: str
Path to the measurement files.
prefix : str
Ensemble prefix for which the data is to be extracted.
name : str
Name of the correlation function to be extracted from the file
quarks: str, optional
Label of the quarks used in the sfcf input file. e.g. "quark quark" Label of the quarks used in the sfcf input file. e.g. "quark quark"
for version 0.0 this does NOT need to be given with the typical " - " for version 0.0 this does NOT need to be given with the typical " - "
that is present in the output file, that is present in the output file,
this is done automatically for this version this is done automatically for this version
noffset: int, optional noffset: int
Offset of the source (only relevant when wavefunctions are used) Offset of the source (only relevant when wavefunctions are used)
wf: int, optional wf: int
ID of wave function ID of wave function
wf2: int, optional wf2: int
ID of the second wavefunction ID of the second wavefunction
(only relevant for boundary-to-boundary correlation functions) (only relevant for boundary-to-boundary correlation functions)
im: bool, optional im: bool
if True, read imaginary instead of real part if True, read imaginary instead of real part
of the correlation function. of the correlation function.
b2b: bool, optional corr_type : str
if True, read a time-dependent boundary-to-boundary change between bi (boundary - inner) (default) bib (boundary - inner - boundary) and bb (boundary - boundary)
correlation function correlator types
single: bool, optional names : list
if True, read time independent boundary to boundary
correlation function
names: list, optional
Alternative labeling for replicas/ensembles. Alternative labeling for replicas/ensembles.
Has to have the appropriate length Has to have the appropriate length
ens_name : str, optional ens_name : str
replaces the name of the ensemble replaces the name of the ensemble
version: str, optional version: str
version of SFCF, with which the measurement was done. version of SFCF, with which the measurement was done.
if the compact output option (-c) was specified, if the compact output option (-c) was spectified,
append a "c" to the version (e.g. "1.0c") append a "c" to the version (e.g. "1.0c")
if the append output option (-a) was specified, if the append output option (-a) was specified,
append an "a" to the version. Currently supported versions append an "a" to the version
are "0.0", "1.0", "2.0", "1.0c", "2.0c", "1.0a" and "2.0a". replica: list
replica: list, optional
list of replica to be read, default is all list of replica to be read, default is all
files: list, optional files: list
list of files to be read per replica, default is all. list of files to be read per replica, default is all.
for non-compact output format, hand the folders to be read here. for non-conpact ouztput format, hand the folders to be read here.
check_configs: list, optional check_configs:
list of list of supposed configs, eg. [range(1,1000)] list of list of supposed configs, eg. [range(1,1000)]
for one replicum with 1000 configs for one replicum with 1000 configs
""" """
@ -69,25 +58,28 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
else: else:
im = 0 im = 0
part = 'real' part = 'real'
if kwargs.get('single'):
b2b = 1
single = 1
else:
if kwargs.get('b2b'):
b2b = 1
else:
b2b = 0
single = 0
if "replica" in kwargs: if "replica" in kwargs:
reps = kwargs.get("replica") reps = kwargs.get("replica")
if corr_type == 'bb':
b2b = True
single = True
elif corr_type == 'bib':
b2b = True
single = False
else:
b2b = False
single = False
# due to higher usage in current projects,
# compact file format is default
compact = True compact = True
appended = False appended = False
# get version string
known_versions = ["0.0", "1.0", "2.0", "1.0c", "2.0c", "1.0a", "2.0a"] known_versions = ["0.0", "1.0", "2.0", "1.0c", "2.0c", "1.0a", "2.0a"]
if version not in known_versions: if version not in known_versions:
raise Exception("This version is not known!") raise Exception("This version is not known!")
# if the letter c is appended to the version,
# the compact fileformat is used (former read_sfcf_c)
if(version[-1] == "c"): if(version[-1] == "c"):
appended = False appended = False
compact = True compact = True
@ -112,20 +104,22 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
else: else:
ls.extend(filenames) ls.extend(filenames)
break break
if not ls:
raise Exception('Error, directory not found')
# Exclude folders with different names # Exclude folders with different names
for exc in ls: for exc in ls:
if not fnmatch.fnmatch(exc, prefix + '*'): if not fnmatch.fnmatch(exc, prefix + '*'):
ls = list(set(ls) - set([exc])) ls = list(set(ls) - set([exc]))
if not ls:
raise Exception('No matching directories found.')
if len(ls) > 1:
ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0]))
if not appended: if not appended:
if len(ls) > 1:
# New version, to cope with ids, etc.
ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0]))
replica = len(ls) replica = len(ls)
else: else:
replica = len([file.split(".")[-1] for file in ls]) // len(set([file.split(".")[-1] for file in ls])) replica = len([file.split(".")[-1] for file in ls]) // len(set([file.split(".")[-1] for file in ls]))
print("Read", part, "part of '" + str(name) + "' with prefix '" + str(prefix) + "' (" + str(replica) + " replica)") print('Read', part, 'part of', name, 'from', prefix[:-1],
',', replica, 'replica')
if 'names' in kwargs: if 'names' in kwargs:
new_names = kwargs.get('names') new_names = kwargs.get('names')
if len(new_names) != len(set(new_names)): if len(new_names) != len(set(new_names)):
@ -133,6 +127,8 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
if len(new_names) != replica: if len(new_names) != replica:
raise Exception('Names does not have the required length', replica) raise Exception('Names does not have the required length', replica)
else: else:
# Adjust replica names to new bookmarking system
new_names = [] new_names = []
if not appended: if not appended:
for entry in ls: for entry in ls:
@ -153,6 +149,7 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1])) ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
for entry in ls: for entry in ls:
myentry = entry[:-len(name) - 1] myentry = entry[:-len(name) - 1]
# print(myentry)
try: try:
idx = myentry.index('r') idx = myentry.index('r')
except Exception: except Exception:
@ -162,6 +159,7 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
new_names.append(kwargs.get('ens_name') + '|' + myentry[idx:]) new_names.append(kwargs.get('ens_name') + '|' + myentry[idx:])
else: else:
new_names.append(myentry[:idx] + '|' + myentry[idx:]) new_names.append(myentry[:idx] + '|' + myentry[idx:])
# print(new_names)
idl = [] idl = []
if not appended: if not appended:
for i, item in enumerate(ls): for i, item in enumerate(ls):
@ -177,16 +175,18 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
sub_ls.extend(dirnames) sub_ls.extend(dirnames)
break break
for exc in sub_ls: # print(sub_ls)
if compact: if compact:
for exc in sub_ls:
if not fnmatch.fnmatch(exc, prefix + '*'): if not fnmatch.fnmatch(exc, prefix + '*'):
sub_ls = list(set(sub_ls) - set([exc])) sub_ls = list(set(sub_ls) - set([exc]))
sub_ls.sort(key=lambda x: sub_ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
int(re.findall(r'\d+', x)[-1]))
else: else:
for exc in sub_ls:
if not fnmatch.fnmatch(exc, 'cfg*'): if not fnmatch.fnmatch(exc, 'cfg*'):
sub_ls = list(set(sub_ls) - set([exc])) sub_ls = list(set(sub_ls) - set([exc]))
sub_ls.sort(key=lambda x: int(x[3:])) sub_ls.sort(key=lambda x: int(x[3:]))
# print(sub_ls)
rep_idl = [] rep_idl = []
no_cfg = len(sub_ls) no_cfg = len(sub_ls)
for cfg in sub_ls: for cfg in sub_ls:
@ -198,20 +198,46 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
except Exception: except Exception:
raise Exception("Couldn't parse idl from directroy, problem with file " + cfg) raise Exception("Couldn't parse idl from directroy, problem with file " + cfg)
rep_idl.sort() rep_idl.sort()
# maybe there is a better way to print the idls
print(item, ':', no_cfg, ' configurations') print(item, ':', no_cfg, ' configurations')
idl.append(rep_idl) idl.append(rep_idl)
# here we have found all the files we need to look into.
if i == 0: if i == 0:
if compact: # here, we want to find the place within the file,
# where the correlator we need is stored.
# to do so, the pattern needed is put together
# from the input values
if version == "0.0":
pattern = "# " + name + " : offset " + str(noffset) + ", wf " + str(wf)
# if b2b, a second wf is needed
if b2b:
pattern += ", wf_2 " + str(wf2)
qs = quarks.split(" ")
pattern += " : " + qs[0] + " - " + qs[1]
file = open(path + '/' + item + '/' + sub_ls[0] + '/' + name, "r")
for k, line in enumerate(file):
if read == 1 and not line.strip() and k > start + 1:
break
if read == 1 and k >= start:
T += 1
if pattern in line:
read = 1
start = k + 1
print(str(T) + " entries found.")
else:
pattern = 'name ' + name + '\nquarks ' + quarks + '\noffset ' + str(noffset) + '\nwf ' + str(wf) pattern = 'name ' + name + '\nquarks ' + quarks + '\noffset ' + str(noffset) + '\nwf ' + str(wf)
if b2b: if b2b:
pattern += '\nwf_2 ' + str(wf2) pattern += '\nwf_2 ' + str(wf2)
with open(path + '/' + item + '/' + sub_ls[0], 'r') as file: # and the file is parsed through to find the pattern
if compact:
file = open(path + '/' + item + '/' + sub_ls[0], "r")
else:
# for non-compactified versions of the files
file = open(path + '/' + item + '/' + sub_ls[0] + '/' + name, "r")
content = file.read() content = file.read()
match = re.search(pattern, content) match = re.search(pattern, content)
if match: if match:
# the start and end point of the correlator
# in question is extracted for later use in
# the other files
start_read = content.count('\n', 0, match.start()) + 5 + b2b start_read = content.count('\n', 0, match.start()) + 5 + b2b
end_match = re.search(r'\n\s*\n', content[match.start():]) end_match = re.search(r'\n\s*\n', content[match.start():])
T = content[match.start():].count('\n', 0, end_match.start()) - 4 - b2b T = content[match.start():].count('\n', 0, end_match.start()) - 4 - b2b
@ -219,67 +245,51 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
print(T, 'entries, starting to read in line', start_read) print(T, 'entries, starting to read in line', start_read)
else: else:
raise Exception('Correlator with pattern\n' + pattern + '\nnot found.') raise Exception('Correlator with pattern\n' + pattern + '\nnot found.')
else: # we found where the correlator
# this part does the same as above, # that is to be read is in the files
# but for non-compactified versions of the files # after preparing the datastructure
with open(path + '/' + item + '/' + sub_ls[0] + '/' + name) as fp: # the correlators get parsed into...
for k, line in enumerate(fp):
if version == "0.0":
# check if this is really the right file
# by matching pattern similar to above
pattern = "# " + name + " : offset " + str(noffset) + ", wf " + str(wf)
# if b2b, a second wf is needed
if b2b:
pattern += ", wf_2 " + str(wf2)
qs = quarks.split(" ")
pattern += " : " + qs[0] + " - " + qs[1]
if read == 1 and not line.strip() and k > start + 1:
break
if read == 1 and k >= start:
T += 1
if version == "0.0":
if pattern in line:
# print(line)
read = 1
start = k + 1
else:
if '[correlator]' in line:
read = 1
start = k + 7 + b2b
T -= b2b
print(str(T) + " entries found.")
deltas = [] deltas = []
for j in range(T): for j in range(T):
deltas.append([]) deltas.append([])
for t in range(T): for t in range(T):
deltas[t].append(np.zeros(no_cfg)) deltas[t].append(np.zeros(no_cfg))
# ...the actual parsing can start.
# we iterate through all measurement files in the path given... # we iterate through all measurement files in the path given...
if compact: if compact:
for cfg in range(no_cfg): for cfg in range(no_cfg):
with open(path + '/' + item + '/' + sub_ls[cfg]) as fp: with open(path + '/' + item + '/' + sub_ls[cfg]) as fp:
lines = fp.readlines() lines = fp.readlines()
# check, if the correlator is in fact
# printed completely
if(start_read + T > len(lines)): if(start_read + T > len(lines)):
raise Exception("EOF before end of correlator data! Maybe " + path + '/' + item + '/' + sub_ls[cfg] + " is corrupted?") raise Exception("EOF before end of correlator data! Maybe " + path + '/' + item + '/' + sub_ls[cfg] + " is corrupted?")
# and start to read the correlator.
# the range here is chosen like this,
# since this allows for implementing
# a security check for every read correlator later...
for k in range(start_read - 6, start_read + T): for k in range(start_read - 6, start_read + T):
if k == start_read - 5 - b2b: if k == start_read - 5 - b2b:
if lines[k].strip() != 'name ' + name: if lines[k].strip() != 'name ' + name:
raise Exception('Wrong format', raise Exception('Wrong format', sub_ls[cfg])
sub_ls[cfg])
if(k >= start_read and k < start_read + T): if(k >= start_read and k < start_read + T):
floats = list(map(float, lines[k].split())) floats = list(map(float, lines[k].split()))
deltas[k - start_read][i][cfg] = floats[-2:][im] deltas[k - start_read][i][cfg] = floats[-2:][im]
else: else:
for cnfg, subitem in enumerate(sub_ls): for cnfg, subitem in enumerate(sub_ls):
with open(path + '/' + item + '/' + subitem + '/' + name) as fp: with open(path + '/' + item + '/' + subitem + '/' + name) as fp:
# since the non-compatified files
# are typically not so long,
# we can iterate over the whole file.
# here one can also implement the chekc from above.
for k, line in enumerate(fp): for k, line in enumerate(fp):
if(k >= start and k < start + T): if(k >= start_read and k < start_read + T):
floats = list(map(float, line.split())) floats = list(map(float, line.split()))
if version == "0.0": if version == "0.0":
deltas[k - start][i][cnfg] = floats[im] deltas[k - start][i][cnfg] = floats[im - single]
else: else:
deltas[k - start][i][cnfg] = floats[1 + im - single] deltas[k - start_read][i][cnfg] = floats[1 + im - single]
else: else:
if "files" in kwargs: if "files" in kwargs:
@ -289,8 +299,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
if not fnmatch.fnmatch(exc, prefix + '*.' + name): if not fnmatch.fnmatch(exc, prefix + '*.' + name):
ls = list(set(ls) - set([exc])) ls = list(set(ls) - set([exc]))
ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1])) ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
if len(ls) == 0:
raise Exception('File(s) for correlator ' + name + ' not found.')
pattern = 'name ' + name + '\nquarks ' + quarks + '\noffset ' + str(noffset) + '\nwf ' + str(wf) pattern = 'name ' + name + '\nquarks ' + quarks + '\noffset ' + str(noffset) + '\nwf ' + str(wf)
if b2b: if b2b:
pattern += '\nwf_2 ' + str(wf2) pattern += '\nwf_2 ' + str(wf2)
@ -302,9 +310,9 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
for linenumber, line in enumerate(content): for linenumber, line in enumerate(content):
if "[run]" in line: if "[run]" in line:
data_starts.append(linenumber) data_starts.append(linenumber)
if len(set([data_starts[i] - data_starts[i - 1] for i in if len(set([data_starts[i] - data_starts[i - 1] for i in range(1, len(data_starts))])) > 1:
range(1, len(data_starts))])) > 1:
raise Exception("Irregularities in file structure found, not all runs have the same output length") raise Exception("Irregularities in file structure found, not all runs have the same output length")
# first chunk of data
chunk = content[:data_starts[1]] chunk = content[:data_starts[1]]
for linenumber, line in enumerate(chunk): for linenumber, line in enumerate(chunk):
if line.startswith("gauge_name"): if line.startswith("gauge_name"):
@ -312,25 +320,31 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
elif line.startswith("[correlator]"): elif line.startswith("[correlator]"):
corr_line = linenumber corr_line = linenumber
found_pat = "" found_pat = ""
for li in chunk[corr_line + 1:corr_line + 6 + b2b]: for li in chunk[corr_line + 1: corr_line + 6 + b2b]:
found_pat += li found_pat += li
if re.search(pattern, found_pat): if re.search(pattern, found_pat):
start_read = corr_line + 7 + b2b start_read = corr_line + 7 + b2b
T = len(chunk) - 1 - start_read break
endline = corr_line + 6 + b2b
while not chunk[endline] == "\n":
endline += 1
T = endline - start_read
if rep == 0: if rep == 0:
deltas = [] deltas = []
for t in range(T): for t in range(T):
deltas.append([]) deltas.append([])
for t in range(T): for t in range(T):
deltas[t].append(np.zeros(len(data_starts))) deltas[t].append(np.zeros(len(data_starts)))
# all other chunks should follow the same structure
for cnfg in range(len(data_starts)): for cnfg in range(len(data_starts)):
start = data_starts[cnfg] start = data_starts[cnfg]
stop = start + data_starts[1] stop = start + data_starts[1]
chunk = content[start:stop] chunk = content[start:stop]
# meta_data = {}
try: try:
rep_idl.append(int(chunk[gauge_line].split("n")[-1])) rep_idl.append(int(chunk[gauge_line].split("n")[-1]))
except Exception: except Exception:
raise Exception("Couldn't parse idl from directroy, problem with chunk around line " + gauge_line) raise Exception("Couldn't parse idl from directory, problem with chunk around line ", gauge_line)
found_pat = "" found_pat = ""
for li in chunk[corr_line + 1:corr_line + 6 + b2b]: for li in chunk[corr_line + 1:corr_line + 6 + b2b]:
@ -338,7 +352,7 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
if re.search(pattern, found_pat): if re.search(pattern, found_pat):
for t, line in enumerate(chunk[start_read:start_read + T]): for t, line in enumerate(chunk[start_read:start_read + T]):
floats = list(map(float, line.split())) floats = list(map(float, line.split()))
deltas[t][rep][cnfg] = floats[-2:][im] deltas[t][rep][cnfg] = floats[im + 1 - single]
idl.append(rep_idl) idl.append(rep_idl)
if "check_configs" in kwargs: if "check_configs" in kwargs:

1150
tests/data/sfcf_test/data_a/data_a_r0.F_V0 Normal file
View file

File diff suppressed because it is too large Load diff

970
tests/data/sfcf_test/data_a/data_a_r0.f_1 Normal file
View file

@ -0,0 +1,970 @@
[run]
version 2.1
date 2022-01-19 11:04:03 +0100
host r04n07.palma.wwu
dir /scratch/tmp/j_kuhl19
user j_kuhl19
gauge_name /data_a_r0_n1
gauge_md5 1ea28326e4090996111a320b8372811d
param_name sfcf_unity_test.in
param_md5 d881e90d41188a33b8b0f1bd0bc53ea5
param_hash 686af5e712ee2902180f5428af94c6e7
data_name ./output_10519905/data_af_1
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version 2.1
date 2022-01-19 11:04:05 +0100
host r04n07.palma.wwu
dir /scratch/tmp/j_kuhl19
user j_kuhl19
gauge_name /data_a_r0_n2
gauge_md5 1ea28326e4090996111a320b8372811d
param_name sfcf_unity_test.in
param_md5 d881e90d41188a33b8b0f1bd0bc53ea5
param_hash 686af5e712ee2902180f5428af94c6e7
data_name ./output_10519905/data_af_1
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version 2.1
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host r04n07.palma.wwu
dir /scratch/tmp/j_kuhl19
user j_kuhl19
gauge_name /data_a_r0_n3
gauge_md5 1ea28326e4090996111a320b8372811d
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name f_1
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[run]
version 2.1
date 2022-01-19 11:04:09 +0100
host r04n07.palma.wwu
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wf 1
corr_t
1 +6.5551520722842213e+01 -8.1976426690345305e-13
2 +1.0542820240843382e+00 +2.1626370477046812e-13
3 -4.1024441815730086e+01 -2.4147931196409923e-14
[correlator]
name f_A
quarks lquark lquark
offset 1
wf 2
corr_t
1 +6.5529951269443117e+01 +7.9192560386479701e-14
2 +1.0516822345055870e+00 -1.2443038782429568e-14
3 -4.1025142768037739e+01 +5.9315333178954509e-17

3273
tests/data/sfcf_test/param/out.out Normal file
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102
tests/data/sfcf_test/param/parameters_a Normal file
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@ -0,0 +1,102 @@
tsize 4
l1 4
l2 4
l3 4
nf 3
beta +3.5522000000000000e+00
ct +1.0551857440459433e+00
cttilde +9.7457913405776697e-01
csw +1.8228459568314139e+00
isw 0
errsq +1.0000000000000001e-18
nmax 4096
oqcd_solver_select -1
oqcd_solver_param 3844
[Solver 0]
solver DFL_SAP_GCR
nkv 24
isolv 1
nmr 4
ncy 5
nmx 2048
res +1.0000000000000000e-10
istop 0
[Solver 1]
solver CGNE
nkv 0
isolv 0
nmr 0
ncy 0
nmx 4096
res +1.0000000000000000e-10
istop 0
[Solver 2]
solver SAP_GCR
nkv 24
isolv 1
nmr 4
ncy 5
nmx 2048
res +1.0000000000000000e-10
istop 0
[Solver 3]
solver CGNE_NO_EO
nkv 0
isolv 0
nmr 0
ncy 0
nmx 4096
res +1.0000000000000000e-10
istop 0
[SAP]
bs 4 4 4 4
[Deflation subspace]
bs 4 4 4 4
Ns 20
[Deflation subspace generation]
kappa +1.3713790000000001e-01
mu +0.0000000000000000e+00
ninv 10
nmr 4
ncy 5
[Deflation projection]
nkv 18
nmx 2048
res +1.0000000000000000e-02
wf_offsets 2
+0.0000000000000000e+00 +0.0000000000000000e+00 +0.0000000000000000e+00
+0.0000000000000000e+00 +0.0000000000000000e+00 +5.0000000000000000e-01
wf_basis 3
+0.0000000000000000e+00 +2.6666666666666665e+00
+1.0000000000000000e+00 +2.6666666666666665e+00
+0.0000000000000000e+00 +5.3333333333333330e+00
wf_coeff 3
+1.0000000000000000e+00 +0.0000000000000000e+00 +0.0000000000000000e+00
+0.0000000000000000e+00 +1.0000000000000000e+00 +0.0000000000000000e+00
+0.0000000000000000e+00 +0.0000000000000000e+00 +1.0000000000000000e+00
qr 1
lquark +1.3713790000000001e-01 +5.0000000000000000e-01 +5.0000000000000000e-01 +5.0000000000000000e-01 persistent
mrr 1
lquark lquark
crr 3
f_A
f_1
F_V0
sg 0
qs 0
mrs 0
crs 0
# param_hash 686af5e712ee2902180f5428af94c6e7

102
tests/data/sfcf_test/param/parameters_c Normal file
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tsize 4
l1 4
l2 4
l3 4
nf 3
beta +3.5522000000000000e+00
ct +1.0551857440459433e+00
cttilde +9.7457913405776697e-01
csw +1.8228459568314139e+00
isw 0
errsq +1.0000000000000001e-18
nmax 4096
oqcd_solver_select -1
oqcd_solver_param 3844
[Solver 0]
solver DFL_SAP_GCR
nkv 24
isolv 1
nmr 4
ncy 5
nmx 2048
res +1.0000000000000000e-10
istop 0
[Solver 1]
solver CGNE
nkv 0
isolv 0
nmr 0
ncy 0
nmx 4096
res +1.0000000000000000e-10
istop 0
[Solver 2]
solver SAP_GCR
nkv 24
isolv 1
nmr 4
ncy 5
nmx 2048
res +1.0000000000000000e-10
istop 0
[Solver 3]
solver CGNE_NO_EO
nkv 0
isolv 0
nmr 0
ncy 0
nmx 4096
res +1.0000000000000000e-10
istop 0
[SAP]
bs 4 4 4 4
[Deflation subspace]
bs 4 4 4 4
Ns 20
[Deflation subspace generation]
kappa +1.3713790000000001e-01
mu +0.0000000000000000e+00
ninv 10
nmr 4
ncy 5
[Deflation projection]
nkv 18
nmx 2048
res +1.0000000000000000e-02
wf_offsets 2
+0.0000000000000000e+00 +0.0000000000000000e+00 +0.0000000000000000e+00
+0.0000000000000000e+00 +0.0000000000000000e+00 +5.0000000000000000e-01
wf_basis 3
+0.0000000000000000e+00 +2.6666666666666665e+00
+1.0000000000000000e+00 +2.6666666666666665e+00
+0.0000000000000000e+00 +5.3333333333333330e+00
wf_coeff 3
+1.0000000000000000e+00 +0.0000000000000000e+00 +0.0000000000000000e+00
+0.0000000000000000e+00 +1.0000000000000000e+00 +0.0000000000000000e+00
+0.0000000000000000e+00 +0.0000000000000000e+00 +1.0000000000000000e+00
qr 1
lquark +1.3713790000000001e-01 +5.0000000000000000e-01 +5.0000000000000000e-01 +5.0000000000000000e-01 persistent
mrr 1
lquark lquark
crr 3
f_A
f_1
F_V0
sg 0
qs 0
mrs 0
crs 0
# param_hash 686af5e712ee2902180f5428af94c6e7

102
tests/data/sfcf_test/param/parameters_o Normal file
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@ -0,0 +1,102 @@
tsize 4
l1 4
l2 4
l3 4
nf 3
beta +3.5522000000000000e+00
ct +1.0551857440459433e+00
cttilde +9.7457913405776697e-01
csw +1.8228459568314139e+00
isw 0
errsq +1.0000000000000001e-18
nmax 4096
oqcd_solver_select -1
oqcd_solver_param 3844
[Solver 0]
solver DFL_SAP_GCR
nkv 24
isolv 1
nmr 4
ncy 5
nmx 2048
res +1.0000000000000000e-10
istop 0
[Solver 1]
solver CGNE
nkv 0
isolv 0
nmr 0
ncy 0
nmx 4096
res +1.0000000000000000e-10
istop 0
[Solver 2]
solver SAP_GCR
nkv 24
isolv 1
nmr 4
ncy 5
nmx 2048
res +1.0000000000000000e-10
istop 0
[Solver 3]
solver CGNE_NO_EO
nkv 0
isolv 0
nmr 0
ncy 0
nmx 4096
res +1.0000000000000000e-10
istop 0
[SAP]
bs 4 4 4 4
[Deflation subspace]
bs 4 4 4 4
Ns 20
[Deflation subspace generation]
kappa +1.3713790000000001e-01
mu +0.0000000000000000e+00
ninv 10
nmr 4
ncy 5
[Deflation projection]
nkv 18
nmx 2048
res +1.0000000000000000e-02
wf_offsets 2
+0.0000000000000000e+00 +0.0000000000000000e+00 +0.0000000000000000e+00
+0.0000000000000000e+00 +0.0000000000000000e+00 +5.0000000000000000e-01
wf_basis 3
+0.0000000000000000e+00 +2.6666666666666665e+00
+1.0000000000000000e+00 +2.6666666666666665e+00
+0.0000000000000000e+00 +5.3333333333333330e+00
wf_coeff 3
+1.0000000000000000e+00 +0.0000000000000000e+00 +0.0000000000000000e+00
+0.0000000000000000e+00 +1.0000000000000000e+00 +0.0000000000000000e+00
+0.0000000000000000e+00 +0.0000000000000000e+00 +1.0000000000000000e+00
qr 1
lquark +1.3713790000000001e-01 +5.0000000000000000e-01 +5.0000000000000000e-01 +5.0000000000000000e-01 persistent
mrr 1
lquark lquark
crr 3
f_A
f_1
F_V0
sg 0
qs 0
mrs 0
crs 0
# param_hash 686af5e712ee2902180f5428af94c6e7

125
tests/sfcf_in_test.py Normal file
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import os,sys,inspect
current_dir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
parent_dir = os.path.dirname(current_dir)
sys.path.insert(0, parent_dir)
import pyerrors as pe
import pyerrors.input.openQCD as qcdin
import pyerrors.input.sfcf as sfin
import shutil
from time import sleep
def build_test_environment(env_type, cfgs, reps):
if env_type == "o":
for i in range(2,cfgs+1):
shutil.copytree("tests/data/sfcf_test/data_o/test_r0/cfg1","tests/data/sfcf_test/data_o/test_r0/cfg"+str(i))
for i in range(1,reps):
shutil.copytree("tests/data/sfcf_test/data_o/test_r0", "tests/data/sfcf_test/data_o/test_r"+str(i))
elif env_type == "c":
for i in range(2,cfgs+1):
shutil.copy("tests/data/sfcf_test/data_c/data_c_r0/data_c_r0_n1","tests/data/sfcf_test/data_c/data_c_r0/data_c_r0_n"+str(i))
for i in range(1,reps):
os.mkdir("tests/data/sfcf_test/data_c/data_c_r"+str(i))
for j in range(1,cfgs+1):
shutil.copy("tests/data/sfcf_test/data_c/data_c_r0/data_c_r0_n1","tests/data/sfcf_test/data_c/data_c_r"+str(i)+"/data_c_r"+str(i)+"_n"+str(j))
def clean_test_environment(env_type, cfgs, reps):
if env_type == "o":
for i in range(1,reps):
shutil.rmtree("tests/data/sfcf_test/data_o/test_r"+str(i))
for i in range(2,cfgs+1):
shutil.rmtree("tests/data/sfcf_test/data_o/test_r0/cfg"+str(i))
elif env_type == "c":
for i in range(1,reps):
shutil.rmtree("tests/data/sfcf_test/data_c/data_c_r"+str(i))
for i in range(2,cfgs+1):
os.remove("tests/data/sfcf_test/data_c/data_c_r0/data_c_r0_n"+str(i))
def test_o_bb():
build_test_environment("o",5,3)
f_1 = sfin.read_sfcf("tests/data/sfcf_test/data_o", "test", "f_1",quarks="lquark lquark", wf = 0, wf2=0, version = "2.0", corr_type="bb")
print(f_1)
clean_test_environment("o",5,3)
assert len(f_1) == 1
assert f_1[0].value == 351.1941525454502
def test_o_bi():
build_test_environment("o",5,3)
f_A = sfin.read_sfcf("tests/data/sfcf_test/data_o", "test", "f_A",quarks="lquark lquark", wf = 0, version = "2.0")
print(f_A)
clean_test_environment("o",5,3)
assert len(f_A) == 3
assert f_A[0].value == 65.4711887279723
assert f_A[1].value == 1.0447210336915187
assert f_A[2].value == -41.025094911185185
def test_o_bib():
build_test_environment("o",5,3)
f_V0 = sfin.read_sfcf("tests/data/sfcf_test/data_o", "test", "F_V0",quarks="lquark lquark", wf = 0, wf2 = 0, version = "2.0", corr_type="bib")
print(f_V0)
clean_test_environment("o",5,3)
assert len(f_V0) == 3
assert f_V0[0] == 683.6776090085115
assert f_V0[1] == 661.3188585582334
assert f_V0[2] == 683.6776090081005
def test_c_bb():
build_test_environment("c",5,3)
f_1 = sfin.read_sfcf("tests/data/sfcf_test/data_c", "data_c", "f_1", quarks="lquark lquark", wf = 0, wf2=0, version = "2.0c", corr_type="bb")
print(f_1)
clean_test_environment("c",5,3)
assert len(f_1) == 1
assert f_1[0].value == 351.1941525454502
def test_c_bi():
build_test_environment("c",5,3)
f_A = sfin.read_sfcf("tests/data/sfcf_test/data_c", "data_c", "f_A", quarks="lquark lquark", wf = 0, version = "2.0c")
print(f_A)
clean_test_environment("c",5,3)
assert len(f_A) == 3
assert f_A[0].value == 65.4711887279723
assert f_A[1].value == 1.0447210336915187
assert f_A[2].value == -41.025094911185185
def test_c_bib():
build_test_environment("c",5,3)
f_V0 = sfin.read_sfcf("tests/data/sfcf_test/data_c", "data_c", "F_V0",quarks="lquark lquark", wf = 0, wf2 = 0, version = "2.0c", corr_type="bib")
print(f_V0)
clean_test_environment("c",5,3)
assert len(f_V0) == 3
assert f_V0[0] == 683.6776090085115
assert f_V0[1] == 661.3188585582334
assert f_V0[2] == 683.6776090081005
def test_a_bb():
build_test_environment("a",5,3)
f_1 = sfin.read_sfcf("tests/data/sfcf_test/data_a", "data_a", "f_1", quarks="lquark lquark", wf = 0, wf2=0, version = "2.0a", corr_type="bb")
print(f_1)
clean_test_environment("a",5,3)
assert len(f_1) == 1
assert f_1[0].value == 351.1941525454502
def test_a_bi():
build_test_environment("a",5,3)
f_A = sfin.read_sfcf("tests/data/sfcf_test/data_a", "data_a", "f_A", quarks="lquark lquark", wf = 0, version = "2.0a")
print(f_A)
clean_test_environment("a",5,3)
assert len(f_A) == 3
assert f_A[0].value == 65.4711887279723
assert f_A[1].value == 1.0447210336915187
assert f_A[2].value == -41.02509491118518
def test_a_bib():
build_test_environment("a",5,3)
f_V0 = sfin.read_sfcf("tests/data/sfcf_test/data_a", "data_a", "F_V0",quarks="lquark lquark", wf = 0, wf2 = 0, version = "2.0a", corr_type="bib")
print(f_V0)
clean_test_environment("a",5,3)
assert len(f_V0) == 3
assert f_V0[0] == 683.6776090085115
assert f_V0[1] == 661.3188585582334
assert f_V0[2] == 683.6776090081005