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Compare commits
No commits in common. "develop" and "v2.15.1" have entirely different histories.
17 changed files with 52 additions and 5321 deletions
2
.github/workflows/docs.yml
vendored
2
.github/workflows/docs.yml
vendored
|
|
@ -13,7 +13,7 @@ jobs:
|
|||
- name: Set up Python environment
|
||||
uses: actions/setup-python@v5
|
||||
with:
|
||||
python-version: "3.12"
|
||||
python-version: "3.10"
|
||||
- uses: actions/checkout@v4
|
||||
- name: Updated documentation
|
||||
run: |
|
||||
|
|
|
|||
2
.github/workflows/flake8.yml
vendored
2
.github/workflows/flake8.yml
vendored
|
|
@ -17,7 +17,7 @@ jobs:
|
|||
- name: Set up Python environment
|
||||
uses: actions/setup-python@v5
|
||||
with:
|
||||
python-version: "3.12"
|
||||
python-version: "3.10"
|
||||
- name: flake8 Lint
|
||||
uses: py-actions/flake8@v2
|
||||
with:
|
||||
|
|
|
|||
9
.github/workflows/pytest.yml
vendored
9
.github/workflows/pytest.yml
vendored
|
|
@ -17,7 +17,7 @@ jobs:
|
|||
fail-fast: false
|
||||
matrix:
|
||||
os: [ubuntu-latest]
|
||||
python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
|
||||
python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
|
||||
include:
|
||||
- os: macos-latest
|
||||
python-version: "3.12"
|
||||
|
|
@ -42,10 +42,5 @@ jobs:
|
|||
uv pip install pytest pytest-cov pytest-benchmark hypothesis --system
|
||||
uv pip freeze --system
|
||||
|
||||
- name: Run tests with -Werror
|
||||
if: matrix.python-version != '3.14'
|
||||
- name: Run tests
|
||||
run: pytest --cov=pyerrors -vv -Werror
|
||||
|
||||
- name: Run tests without -Werror for python 3.14
|
||||
if: matrix.python-version == '3.14'
|
||||
run: pytest --cov=pyerrors -vv
|
||||
|
|
|
|||
11
CHANGELOG.md
11
CHANGELOG.md
|
|
@ -2,17 +2,6 @@
|
|||
|
||||
All notable changes to this project will be documented in this file.
|
||||
|
||||
## [2.16.0] - 2025-10-30
|
||||
|
||||
### Added
|
||||
- Support for custom configuration number extraction in the sfcf input module.
|
||||
|
||||
### Fixed
|
||||
- Calculation of expected chisquare in connection with priors.
|
||||
|
||||
### Changed
|
||||
- Support for python<3.10 was dropped.
|
||||
|
||||
## [2.15.1] - 2025-10-19
|
||||
|
||||
### Fixed
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
[](https://www.python.org/downloads/) [](https://opensource.org/licenses/MIT) [](https://arxiv.org/abs/2209.14371) [](https://doi.org/10.1016/j.cpc.2023.108750)
|
||||
[](https://www.python.org/downloads/) [](https://opensource.org/licenses/MIT) [](https://arxiv.org/abs/2209.14371) [](https://doi.org/10.1016/j.cpc.2023.108750)
|
||||
# pyerrors
|
||||
`pyerrors` is a python framework for error computation and propagation of Markov chain Monte Carlo data from lattice field theory and statistical mechanics simulations.
|
||||
|
||||
|
|
|
|||
|
|
@ -472,7 +472,7 @@ def least_squares(x, y, func, priors=None, silent=False, **kwargs):
|
|||
hat_vector = prepare_hat_matrix()
|
||||
A = W @ hat_vector
|
||||
P_phi = A @ np.linalg.pinv(A.T @ A) @ A.T
|
||||
expected_chisquare = np.trace((np.identity(y_all.shape[-1]) - P_phi) @ W @ cov @ W) + len(loc_priors)
|
||||
expected_chisquare = np.trace((np.identity(y_all.shape[-1]) - P_phi) @ W @ cov @ W)
|
||||
output.chisquare_by_expected_chisquare = output.chisquare / expected_chisquare
|
||||
if not silent:
|
||||
print('chisquare/expected_chisquare:', output.chisquare_by_expected_chisquare)
|
||||
|
|
|
|||
|
|
@ -5,13 +5,12 @@ import numpy as np # Thinly-wrapped numpy
|
|||
from ..obs import Obs
|
||||
from .utils import sort_names, check_idl
|
||||
import itertools
|
||||
import warnings
|
||||
|
||||
|
||||
sep = "/"
|
||||
|
||||
|
||||
def read_sfcf(path, prefix, name, quarks='.*', corr_type="bi", noffset=0, wf=0, wf2=0, version="1.0c", cfg_separator="n", cfg_func=None, silent=False, **kwargs):
|
||||
def read_sfcf(path, prefix, name, quarks='.*', corr_type="bi", noffset=0, wf=0, wf2=0, version="1.0c", cfg_separator="n", silent=False, **kwargs):
|
||||
"""Read sfcf files from given folder structure.
|
||||
|
||||
Parameters
|
||||
|
|
@ -72,11 +71,11 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type="bi", noffset=0, wf=0,
|
|||
"""
|
||||
ret = read_sfcf_multi(path, prefix, [name], quarks_list=[quarks], corr_type_list=[corr_type],
|
||||
noffset_list=[noffset], wf_list=[wf], wf2_list=[wf2], version=version,
|
||||
cfg_separator=cfg_separator, cfg_func=cfg_func, silent=silent, **kwargs)
|
||||
cfg_separator=cfg_separator, silent=silent, **kwargs)
|
||||
return ret[name][quarks][str(noffset)][str(wf)][str(wf2)]
|
||||
|
||||
|
||||
def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=['bi'], noffset_list=[0], wf_list=[0], wf2_list=[0], version="1.0c", cfg_separator="n", cfg_func=None, silent=False, keyed_out=False, **kwargs):
|
||||
def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=['bi'], noffset_list=[0], wf_list=[0], wf2_list=[0], version="1.0c", cfg_separator="n", silent=False, keyed_out=False, **kwargs):
|
||||
"""Read sfcf files from given folder structure.
|
||||
|
||||
Parameters
|
||||
|
|
@ -246,16 +245,6 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
|
|||
for key in needed_keys:
|
||||
internal_ret_dict[key] = []
|
||||
|
||||
def _default_idl_func(cfg_string, cfg_sep):
|
||||
return int(cfg_string.split(cfg_sep)[-1])
|
||||
|
||||
if cfg_func is None:
|
||||
print("Default idl function in use.")
|
||||
cfg_func = _default_idl_func
|
||||
cfg_func_args = [cfg_separator]
|
||||
else:
|
||||
cfg_func_args = kwargs.get("cfg_func_args", [])
|
||||
|
||||
if not appended:
|
||||
for i, item in enumerate(ls):
|
||||
rep_path = path + '/' + item
|
||||
|
|
@ -279,7 +268,7 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
|
|||
for cfg in sub_ls:
|
||||
try:
|
||||
if compact:
|
||||
rep_idl.append(cfg_func(cfg, *cfg_func_args))
|
||||
rep_idl.append(int(cfg.split(cfg_separator)[-1]))
|
||||
else:
|
||||
rep_idl.append(int(cfg[3:]))
|
||||
except Exception:
|
||||
|
|
@ -362,7 +351,7 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
|
|||
for rep, file in enumerate(name_ls):
|
||||
rep_idl = []
|
||||
filename = path + '/' + file
|
||||
T, rep_idl, rep_data = _read_append_rep(filename, pattern, intern[name]['b2b'], im, intern[name]['single'], cfg_func, cfg_func_args)
|
||||
T, rep_idl, rep_data = _read_append_rep(filename, pattern, intern[name]['b2b'], cfg_separator, im, intern[name]['single'])
|
||||
if rep == 0:
|
||||
intern[name]['T'] = T
|
||||
for t in range(intern[name]['T']):
|
||||
|
|
@ -592,7 +581,12 @@ def _read_compact_rep(path, rep, sub_ls, intern, needed_keys, im):
|
|||
return return_vals
|
||||
|
||||
|
||||
def _read_chunk_data(chunk, start_read, T, corr_line, b2b, pattern, im, single):
|
||||
def _read_chunk(chunk, gauge_line, cfg_sep, start_read, T, corr_line, b2b, pattern, im, single):
|
||||
try:
|
||||
idl = int(chunk[gauge_line].split(cfg_sep)[-1])
|
||||
except Exception:
|
||||
raise Exception("Couldn't parse idl from directory, problem with chunk around line ", gauge_line)
|
||||
|
||||
found_pat = ""
|
||||
data = []
|
||||
for li in chunk[corr_line + 1:corr_line + 6 + b2b]:
|
||||
|
|
@ -601,90 +595,46 @@ def _read_chunk_data(chunk, start_read, T, corr_line, b2b, pattern, im, single):
|
|||
for t, line in enumerate(chunk[start_read:start_read + T]):
|
||||
floats = list(map(float, line.split()))
|
||||
data.append(floats[im + 1 - single])
|
||||
return data
|
||||
return idl, data
|
||||
|
||||
|
||||
def _check_append_rep(content, start_list):
|
||||
data_len_list = []
|
||||
header_len_list = []
|
||||
has_regular_len_heads = True
|
||||
for chunk_num in range(len(start_list)):
|
||||
start = start_list[chunk_num]
|
||||
if chunk_num == len(start_list) - 1:
|
||||
stop = len(content)
|
||||
else:
|
||||
stop = start_list[chunk_num + 1]
|
||||
chunk = content[start:stop]
|
||||
for linenumber, line in enumerate(chunk):
|
||||
if line.startswith("[correlator]"):
|
||||
header_len = linenumber
|
||||
break
|
||||
header_len_list.append(header_len)
|
||||
data_len_list.append(len(chunk) - header_len)
|
||||
|
||||
if len(set(header_len_list)) > 1:
|
||||
warnings.warn("Not all headers have the same length. Data parts do.")
|
||||
has_regular_len_heads = False
|
||||
|
||||
if len(set(data_len_list)) > 1:
|
||||
raise Exception("Irregularities in file structure found, not all run data are of the same output length")
|
||||
return has_regular_len_heads
|
||||
|
||||
|
||||
def _read_chunk_structure(chunk, pattern, b2b):
|
||||
start_read = 0
|
||||
for linenumber, line in enumerate(chunk):
|
||||
if line.startswith("gauge_name"):
|
||||
gauge_line = linenumber
|
||||
elif line.startswith("[correlator]"):
|
||||
corr_line = linenumber
|
||||
found_pat = ""
|
||||
for li in chunk[corr_line + 1: corr_line + 6 + b2b]:
|
||||
found_pat += li
|
||||
if re.search(pattern, found_pat):
|
||||
start_read = corr_line + 7 + b2b
|
||||
break
|
||||
if start_read == 0:
|
||||
raise ValueError("Did not find pattern\n", pattern)
|
||||
endline = corr_line + 6 + b2b
|
||||
while not chunk[endline] == "\n":
|
||||
endline += 1
|
||||
T = endline - start_read
|
||||
return gauge_line, corr_line, start_read, T
|
||||
|
||||
|
||||
def _read_append_rep(filename, pattern, b2b, im, single, idl_func, cfg_func_args):
|
||||
def _read_append_rep(filename, pattern, b2b, cfg_separator, im, single):
|
||||
with open(filename, 'r') as fp:
|
||||
content = fp.readlines()
|
||||
chunk_start_lines = []
|
||||
data_starts = []
|
||||
for linenumber, line in enumerate(content):
|
||||
if "[run]" in line:
|
||||
chunk_start_lines.append(linenumber)
|
||||
has_regular_len_heads = _check_append_rep(content, chunk_start_lines)
|
||||
if has_regular_len_heads:
|
||||
chunk = content[:chunk_start_lines[1]]
|
||||
try:
|
||||
gauge_line, corr_line, start_read, T = _read_chunk_structure(chunk, pattern, b2b)
|
||||
except ValueError:
|
||||
raise ValueError("Did not find pattern\n", pattern, "\nin\n", filename, "lines", 1, "to", chunk_start_lines[1] + 1)
|
||||
# if has_regular_len_heads is true, all other chunks should follow the same structure
|
||||
data_starts.append(linenumber)
|
||||
if len(set([data_starts[i] - data_starts[i - 1] for i in range(1, len(data_starts))])) > 1:
|
||||
raise Exception("Irregularities in file structure found, not all runs have the same output length")
|
||||
chunk = content[:data_starts[1]]
|
||||
for linenumber, line in enumerate(chunk):
|
||||
if line.startswith("gauge_name"):
|
||||
gauge_line = linenumber
|
||||
elif line.startswith("[correlator]"):
|
||||
corr_line = linenumber
|
||||
found_pat = ""
|
||||
for li in chunk[corr_line + 1: corr_line + 6 + b2b]:
|
||||
found_pat += li
|
||||
if re.search(pattern, found_pat):
|
||||
start_read = corr_line + 7 + b2b
|
||||
break
|
||||
else:
|
||||
raise ValueError("Did not find pattern\n", pattern, "\nin\n", filename)
|
||||
endline = corr_line + 6 + b2b
|
||||
while not chunk[endline] == "\n":
|
||||
endline += 1
|
||||
T = endline - start_read
|
||||
|
||||
# all other chunks should follow the same structure
|
||||
rep_idl = []
|
||||
rep_data = []
|
||||
|
||||
for chunk_num in range(len(chunk_start_lines)):
|
||||
start = chunk_start_lines[chunk_num]
|
||||
if chunk_num == len(chunk_start_lines) - 1:
|
||||
stop = len(content)
|
||||
else:
|
||||
stop = chunk_start_lines[chunk_num + 1]
|
||||
for cnfg in range(len(data_starts)):
|
||||
start = data_starts[cnfg]
|
||||
stop = start + data_starts[1]
|
||||
chunk = content[start:stop]
|
||||
if not has_regular_len_heads:
|
||||
gauge_line, corr_line, start_read, T = _read_chunk_structure(chunk, pattern, b2b)
|
||||
try:
|
||||
idl = idl_func(chunk[gauge_line], *cfg_func_args)
|
||||
except Exception:
|
||||
raise Exception("Couldn't parse idl from file", filename, ", problem with chunk of lines", start + 1, "to", stop + 1)
|
||||
data = _read_chunk_data(chunk, start_read, T, corr_line, b2b, pattern, im, single)
|
||||
idl, data = _read_chunk(chunk, gauge_line, cfg_separator, start_read, T, corr_line, b2b, pattern, im, single)
|
||||
rep_idl.append(idl)
|
||||
rep_data.append(data)
|
||||
|
||||
|
|
|
|||
|
|
@ -1 +1 @@
|
|||
__version__ = "2.17.0-dev"
|
||||
__version__ = "2.15.1"
|
||||
|
|
|
|||
4
setup.py
4
setup.py
|
|
@ -24,18 +24,18 @@ setup(name='pyerrors',
|
|||
author_email='fabian.joswig@ed.ac.uk',
|
||||
license="MIT",
|
||||
packages=find_packages(),
|
||||
python_requires='>=3.10.0',
|
||||
python_requires='>=3.9.0',
|
||||
install_requires=['numpy>=2.0', 'autograd>=1.7.0', 'numdifftools>=0.9.41', 'matplotlib>=3.9', 'scipy>=1.13', 'iminuit>=2.28', 'h5py>=3.11', 'lxml>=5.0', 'python-rapidjson>=1.20', 'pandas>=2.2'],
|
||||
extras_require={'test': ['pytest', 'pytest-cov', 'pytest-benchmark', 'hypothesis', 'nbmake', 'flake8']},
|
||||
classifiers=[
|
||||
'Development Status :: 5 - Production/Stable',
|
||||
'Intended Audience :: Science/Research',
|
||||
'Programming Language :: Python :: 3',
|
||||
'Programming Language :: Python :: 3.9',
|
||||
'Programming Language :: Python :: 3.10',
|
||||
'Programming Language :: Python :: 3.11',
|
||||
'Programming Language :: Python :: 3.12',
|
||||
'Programming Language :: Python :: 3.13',
|
||||
'Programming Language :: Python :: 3.14',
|
||||
'Topic :: Scientific/Engineering :: Physics'
|
||||
],
|
||||
)
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load diff
|
|
@ -1,966 +0,0 @@
|
|||
[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
|
||||
|
||||
[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]
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@ -1,395 +0,0 @@
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|||
[run]
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|
||||
name f_1
|
||||
quarks lquark lquark
|
||||
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|
||||
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|
||||
wf_2 1
|
||||
corr
|
||||
+3.5122104108046193e+02 +5.0816653044831932e-15
|
||||
|
||||
[correlator]
|
||||
|
||||
name f_1
|
||||
quarks lquark lquark
|
||||
offset 1
|
||||
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|
||||
wf_2 2
|
||||
corr
|
||||
+3.5122207631098064e+02 +5.1165649253001659e-15
|
||||
|
||||
|
|
@ -1,400 +0,0 @@
|
|||
[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.lex
|
||||
gauge_md5 1ea28326e4090996111a320b8372811d
|
||||
param_name sfcf_unity_test.in
|
||||
param_md5 d881e90d41188a33b8b0f1bd0bc53ea5
|
||||
param_hash 686af5e712ee2902180f5428af94c6e7
|
||||
data_name ./output_10519905/data_af_A
|
||||
|
||||
[correlator]
|
||||
|
||||
name f_A
|
||||
quarks lquark lquark
|
||||
offset 0
|
||||
wf 0
|
||||
corr_t
|
||||
1 +6.5471188727972304e+01 -6.1214214711790100e-12
|
||||
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|
||||
3 -4.1025094911185178e+01 -4.8315634170546161e-14
|
||||
|
||||
[correlator]
|
||||
|
||||
name f_A
|
||||
quarks lquark lquark
|
||||
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|
||||
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|
||||
corr_t
|
||||
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|
||||
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|
||||
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|
||||
|
||||
[correlator]
|
||||
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
[correlator]
|
||||
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
[correlator]
|
||||
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
[correlator]
|
||||
|
||||
name f_A
|
||||
quarks lquark lquark
|
||||
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|
||||
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|
||||
corr_t
|
||||
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|
||||
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|
||||
3 -4.1025142768037739e+01 +5.9315333178954509e-17
|
||||
|
||||
[run]
|
||||
|
||||
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.lex
|
||||
gauge_md5 1ea28326e4090996111a320b8372811d
|
||||
param_name sfcf_unity_test.in
|
||||
param_md5 d881e90d41188a33b8b0f1bd0bc53ea5
|
||||
param_hash 686af5e712ee2902180f5428af94c6e7
|
||||
data_name ./output_10519905/data_af_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
|
||||
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|
||||
2 +1.0542820240851569e+00 +2.3989756974599379e-15
|
||||
3 -4.1024441815729936e+01 -5.7107484666182308e-15
|
||||
|
||||
[correlator]
|
||||
|
||||
name f_A
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
[correlator]
|
||||
|
||||
name f_A
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
[correlator]
|
||||
|
||||
name f_A
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
[correlator]
|
||||
|
||||
name f_A
|
||||
quarks lquark lquark
|
||||
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|
||||
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|
||||
corr_t
|
||||
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|
||||
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|
||||
3 -4.1025142768037739e+01 +5.9315333178954509e-17
|
||||
|
||||
[run]
|
||||
|
||||
version 2.1
|
||||
date 2022-01-19 11:04:07 +0100
|
||||
host r04n07.palma.wwu
|
||||
dir /scratch/tmp/j_kuhl19
|
||||
user j_kuhl19
|
||||
gauge_name /data_a_r0_n3.lex
|
||||
gauge_md5 1ea28326e4090996111a320b8372811d
|
||||
param_name sfcf_unity_test.in
|
||||
param_md5 d881e90d41188a33b8b0f1bd0bc53ea5
|
||||
param_hash 686af5e712ee2902180f5428af94c6e7
|
||||
data_name ./output_10519905/data_af_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
|
||||
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|
||||
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
|
||||
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|
||||
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|
||||
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
|
||||
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|
||||
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|
||||
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|
||||
|
||||
[correlator]
|
||||
|
||||
name f_A
|
||||
quarks lquark lquark
|
||||
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|
||||
wf 1
|
||||
corr_t
|
||||
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|
||||
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
|
||||
|
||||
[run]
|
||||
|
||||
version 2.1
|
||||
date 2022-01-19 11:04:09 +0100
|
||||
host r04n07.palma.wwu
|
||||
dir /scratch/tmp/j_kuhl19
|
||||
user j_kuhl19
|
||||
gauge_name /data_a_r0_n4.lex
|
||||
gauge_md5 1ea28326e4090996111a320b8372811d
|
||||
param_name sfcf_unity_test.in
|
||||
param_md5 d881e90d41188a33b8b0f1bd0bc53ea5
|
||||
param_hash 686af5e712ee2902180f5428af94c6e7
|
||||
data_name ./output_10519905/data_af_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
|
||||
|
||||
[run]
|
||||
|
||||
version 2.1
|
||||
date 2022-01-19 11:04:11 +0100
|
||||
host r04n07.palma.wwu
|
||||
dir /scratch/tmp/j_kuhl19
|
||||
user j_kuhl19
|
||||
gauge_name /data_a_r0_n5.lex
|
||||
gauge_md5 1ea28326e4090996111a320b8372811d
|
||||
param_name sfcf_unity_test.in
|
||||
param_md5 d881e90d41188a33b8b0f1bd0bc53ea5
|
||||
param_hash 686af5e712ee2902180f5428af94c6e7
|
||||
data_name ./output_10519905/data_af_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
|
||||
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|
||||
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
|
||||
|
||||
|
|
@ -1611,81 +1611,3 @@ def old_prior_fit(x, y, func, priors, silent=False, **kwargs):
|
|||
qqplot(x, y, func, result)
|
||||
|
||||
return output
|
||||
|
||||
def test_dof_prior_fit():
|
||||
"""Performs an uncorrelated fit with a prior to uncorrelated data then
|
||||
the expected chisquare and the usual dof need to agree"""
|
||||
N = 5
|
||||
|
||||
def fitf(a, x):
|
||||
return a[0] + 0 * x
|
||||
|
||||
x = [1. for i in range(N)]
|
||||
y = [pe.cov_Obs(i, .1, '%d' % (i)) for i in range(N)]
|
||||
[o.gm() for o in y]
|
||||
res = pe.fits.least_squares(x, y, fitf, expected_chisquare=True, priors=[pe.cov_Obs(3, 1, 'p')])
|
||||
assert res.chisquare_by_expected_chisquare == res.chisquare_by_dof
|
||||
|
||||
num_samples = 400
|
||||
N = 10
|
||||
|
||||
x = norm.rvs(size=(N, num_samples)) # generate random numbers
|
||||
|
||||
r = np.zeros((N, N))
|
||||
for i in range(N):
|
||||
for j in range(N):
|
||||
if(i==j):
|
||||
r[i, j] = 1.0 # element in correlation matrix
|
||||
|
||||
errl = np.sqrt([3.4, 2.5, 3.6, 2.8, 4.2, 4.7, 4.9, 5.1, 3.2, 4.2]) # set y errors
|
||||
for i in range(N):
|
||||
for j in range(N):
|
||||
if(i==j):
|
||||
r[i, j] *= errl[i] * errl[j] # element in covariance matrix
|
||||
|
||||
c = cholesky(r, lower=True)
|
||||
y = np.dot(c, x)
|
||||
x = np.arange(N)
|
||||
x_dict = {}
|
||||
y_dict = {}
|
||||
for i,item in enumerate(x):
|
||||
x_dict[str(item)] = [x[i]]
|
||||
|
||||
for linear in [True, False]:
|
||||
data = []
|
||||
for i in range(N):
|
||||
if linear:
|
||||
data.append(pe.Obs([[i + 1 + o for o in y[i]]], ['ens'+str(i)]))
|
||||
else:
|
||||
data.append(pe.Obs([[np.exp(-(i + 1)) + np.exp(-(i + 1)) * o for o in y[i]]], ['ens'+str(i)]))
|
||||
|
||||
[o.gamma_method() for o in data]
|
||||
|
||||
data_dict = {}
|
||||
for i,item in enumerate(x):
|
||||
data_dict[str(item)] = [data[i]]
|
||||
|
||||
corr = pe.covariance(data, correlation=True)
|
||||
chol = np.linalg.cholesky(corr)
|
||||
covdiag = np.diag(1 / np.asarray([o.dvalue for o in data]))
|
||||
chol_inv = scipy.linalg.solve_triangular(chol, covdiag, lower=True)
|
||||
chol_inv_keys = [""]
|
||||
chol_inv_keys_combined_fit = [str(item) for i,item in enumerate(x)]
|
||||
|
||||
if linear:
|
||||
def fitf(p, x):
|
||||
return p[1] + p[0] * x
|
||||
fitf_dict = {}
|
||||
for i,item in enumerate(x):
|
||||
fitf_dict[str(item)] = fitf
|
||||
else:
|
||||
def fitf(p, x):
|
||||
return p[1] * anp.exp(-p[0] * x)
|
||||
fitf_dict = {}
|
||||
for i,item in enumerate(x):
|
||||
fitf_dict[str(item)] = fitf
|
||||
|
||||
fit_exp = pe.least_squares(x, data, fitf, expected_chisquare=True, priors = {0:pe.cov_Obs(1.0, 1, 'p')})
|
||||
fit_cov = pe.least_squares(x, data, fitf, correlated_fit = True, inv_chol_cov_matrix = [chol_inv,chol_inv_keys], priors = {0:pe.cov_Obs(1.0, 1, 'p')})
|
||||
assert np.isclose(fit_exp.chisquare_by_expected_chisquare,fit_exp.chisquare_by_dof,atol=1e-8)
|
||||
assert np.isclose(fit_exp.chisquare_by_expected_chisquare,fit_cov.chisquare_by_dof,atol=1e-8)
|
||||
|
|
@ -24,10 +24,10 @@ def build_test_environment(path, env_type, cfgs, reps):
|
|||
os.mkdir(path + "/data_c/data_c_r"+str(i))
|
||||
for j in range(1, cfgs+1):
|
||||
shutil.copy(path + "/data_c/data_c_r0/data_c_r0_n1", path + "/data_c/data_c_r"+str(i)+"/data_c_r"+str(i)+"_n"+str(j))
|
||||
elif env_type in ["a", "apf", "ah"]:
|
||||
elif env_type == "a":
|
||||
for i in range(1, reps):
|
||||
for corr in ["f_1", "f_A", "F_V0"]:
|
||||
shutil.copy(path + "/data_" + env_type + "/data_" + env_type + "_r0." + corr, path + "/data_" + env_type + "/data_" + env_type + "_r" + str(i) + "." + corr)
|
||||
shutil.copy(path + "/data_a/data_a_r0." + corr, path + "/data_a/data_a_r" + str(i) + "." + corr)
|
||||
|
||||
|
||||
def test_o_bb(tmp_path):
|
||||
|
|
@ -276,28 +276,6 @@ def test_a_bb(tmp_path):
|
|||
assert f_1[0].value == 351.1941525454502
|
||||
|
||||
|
||||
def test_a_bb_external_idl_func(tmp_path):
|
||||
build_test_environment(str(tmp_path), "a", 5, 3)
|
||||
def extract_idl(s: str) -> int:
|
||||
return int(s.split("n")[-1])
|
||||
f_1 = sfin.read_sfcf(str(tmp_path) + "/data_a", "data_a", "f_1", quarks="lquark lquark", wf=0, wf2=0, version="2.0a", corr_type="bb", cfg_func=extract_idl)
|
||||
print(f_1)
|
||||
assert len(f_1) == 1
|
||||
assert list(f_1[0].shape.keys()) == ["data_a_|r0", "data_a_|r1", "data_a_|r2"]
|
||||
assert f_1[0].value == 351.1941525454502
|
||||
|
||||
|
||||
def test_a_bb_external_idl_func_postfix(tmp_path):
|
||||
build_test_environment(str(tmp_path), "apf", 5, 3)
|
||||
def extract_idl(s: str) -> int:
|
||||
return int(s.split("n")[-1][:-5])
|
||||
f_1 = sfin.read_sfcf(str(tmp_path) + "/data_apf", "data_apf", "f_1", quarks="lquark lquark", wf=0, wf2=0, version="2.0a", corr_type="bb", cfg_func=extract_idl)
|
||||
print(f_1)
|
||||
assert len(f_1) == 1
|
||||
assert list(f_1[0].shape.keys()) == ["data_apf_|r0", "data_apf_|r1", "data_apf_|r2"]
|
||||
assert f_1[0].value == 351.1941525454502
|
||||
|
||||
|
||||
def test_a_bi(tmp_path):
|
||||
build_test_environment(str(tmp_path), "a", 5, 3)
|
||||
f_A = sfin.read_sfcf(str(tmp_path) + "/data_a", "data_a", "f_A", quarks="lquark lquark", wf=0, version="2.0a")
|
||||
|
|
@ -309,32 +287,6 @@ def test_a_bi(tmp_path):
|
|||
assert f_A[2].value == -41.025094911185185
|
||||
|
||||
|
||||
def test_a_bi_external_idl_func(tmp_path):
|
||||
build_test_environment(str(tmp_path), "a", 5, 3)
|
||||
def extract_idl(s: str) -> int:
|
||||
return int(s.split("n")[-1])
|
||||
f_A = sfin.read_sfcf(str(tmp_path) + "/data_a", "data_a", "f_A", quarks="lquark lquark", wf=0, version="2.0a", cfg_func=extract_idl)
|
||||
print(f_A)
|
||||
assert len(f_A) == 3
|
||||
assert list(f_A[0].shape.keys()) == ["data_a_|r0", "data_a_|r1", "data_a_|r2"]
|
||||
assert f_A[0].value == 65.4711887279723
|
||||
assert f_A[1].value == 1.0447210336915187
|
||||
assert f_A[2].value == -41.025094911185185
|
||||
|
||||
|
||||
def test_a_bi_external_idl_func_postfix(tmp_path):
|
||||
build_test_environment(str(tmp_path), "apf", 5, 3)
|
||||
def extract_idl(s: str) -> int:
|
||||
return int(s.split("n")[-1][:-5])
|
||||
f_A = sfin.read_sfcf(str(tmp_path) + "/data_apf", "data_apf", "f_A", quarks="lquark lquark", wf=0, version="2.0a", cfg_func=extract_idl)
|
||||
print(f_A)
|
||||
assert len(f_A) == 3
|
||||
assert list(f_A[0].shape.keys()) == ["data_apf_|r0", "data_apf_|r1", "data_apf_|r2"]
|
||||
assert f_A[0].value == 65.4711887279723
|
||||
assert f_A[1].value == 1.0447210336915187
|
||||
assert f_A[2].value == -41.025094911185185
|
||||
|
||||
|
||||
def test_a_bi_files(tmp_path):
|
||||
build_test_environment(str(tmp_path), "a", 5, 3)
|
||||
f_A = sfin.read_sfcf(str(tmp_path) + "/data_a", "data_a", "f_A", quarks="lquark lquark", wf=0, version="2.0a", files=["data_a_r0.f_A", "data_a_r1.f_A", "data_a_r2.f_A"])
|
||||
|
|
@ -364,55 +316,6 @@ def test_a_bib(tmp_path):
|
|||
assert f_V0[2] == 683.6776090081005
|
||||
|
||||
|
||||
def test_a_bib_external_idl_func(tmp_path):
|
||||
build_test_environment(str(tmp_path), "a", 5, 3)
|
||||
def extract_idl(s: str) -> int:
|
||||
return int(s.split("n")[-1])
|
||||
f_V0 = sfin.read_sfcf(str(tmp_path) + "/data_a", "data_a", "F_V0", quarks="lquark lquark", wf=0, wf2=0, version="2.0a", corr_type="bib", cfg_func=extract_idl)
|
||||
print(f_V0)
|
||||
assert len(f_V0) == 3
|
||||
assert list(f_V0[0].shape.keys()) == ["data_a_|r0", "data_a_|r1", "data_a_|r2"]
|
||||
assert f_V0[0] == 683.6776090085115
|
||||
assert f_V0[1] == 661.3188585582334
|
||||
assert f_V0[2] == 683.6776090081005
|
||||
|
||||
def test_a_bib_external_idl_func_postfix(tmp_path):
|
||||
build_test_environment(str(tmp_path), "apf", 5, 3)
|
||||
def extract_idl(s: str) -> int:
|
||||
return int(s.split("n")[-1][:-5])
|
||||
f_V0 = sfin.read_sfcf(str(tmp_path) + "/data_apf", "data_apf", "F_V0", quarks="lquark lquark", wf=0, wf2=0, version="2.0a", corr_type="bib", cfg_func=extract_idl)
|
||||
print(f_V0)
|
||||
assert len(f_V0) == 3
|
||||
assert list(f_V0[0].shape.keys()) == ["data_apf_|r0", "data_apf_|r1", "data_apf_|r2"]
|
||||
assert f_V0[0] == 683.6776090085115
|
||||
assert f_V0[1] == 661.3188585582334
|
||||
assert f_V0[2] == 683.6776090081005
|
||||
|
||||
|
||||
def test_a_bib_irreg_header(tmp_path):
|
||||
build_test_environment(str(tmp_path), "ah", 5, 3)
|
||||
with pytest.warns(UserWarning):
|
||||
f_V0 = sfin.read_sfcf(str(tmp_path) + "/data_ah", "data_ah", "F_V0", quarks="lquark lquark", wf=0, wf2=0, version="2.0a", corr_type="bib")
|
||||
print(f_V0)
|
||||
assert len(f_V0) == 3
|
||||
assert list(f_V0[0].shape.keys()) == ["data_ah_|r0", "data_ah_|r1", "data_ah_|r2"]
|
||||
assert f_V0[0] == 683.6776090085115
|
||||
assert f_V0[1] == 661.3188585582334
|
||||
assert f_V0[2] == 683.6776090081005
|
||||
|
||||
|
||||
def test_a_bi_irreg_header(tmp_path):
|
||||
build_test_environment(str(tmp_path), "ah", 5, 3)
|
||||
with pytest.warns(UserWarning):
|
||||
f_A = sfin.read_sfcf(str(tmp_path) + "/data_ah", "data_ah", "f_A", quarks="lquark lquark", wf=0, version="2.0a", corr_type="bi")
|
||||
print(f_A)
|
||||
assert len(f_A) == 3
|
||||
assert list(f_A[0].shape.keys()) == ["data_ah_|r0", "data_ah_|r1", "data_ah_|r2"]
|
||||
assert f_A[0].value == 65.4711887279723
|
||||
assert f_A[1].value == 1.0447210336915187
|
||||
assert f_A[2].value == -41.025094911185185
|
||||
|
||||
|
||||
def test_simple_multi_a(tmp_path):
|
||||
build_test_environment(str(tmp_path), "a", 5, 3)
|
||||
corrs = sfin.read_sfcf_multi(str(tmp_path) + "/data_a", "data_a", ["F_V0"], quarks_list=["lquark lquark"], wf1_list=[0], wf2_list=[0], version="2.0a", corr_type_list=["bib"])
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue