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flake8 compliance openQCD.py
This commit is contained in:
jkuhl-uni
parent
302a7ae439
commit
5f156e4821
2 changed files with 144 additions and 107 deletions
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@ -8,7 +8,6 @@ import struct
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import numpy as np # Thinly-wrapped numpy
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from ..obs import Obs
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from ..fits import fit_lin
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from . import utils
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def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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@ -67,7 +66,8 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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else:
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r_stop = [None] * replica
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print('Read reweighting factors from', prefix[:-1], ',', replica, 'replica', end='')
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print('Read reweighting factors from', prefix[:-1], ',',
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replica, 'replica', end='')
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# Adjust replica names to new bookmarking system
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if names is None:
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@ -75,7 +75,8 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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for entry in ls:
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truncated_entry = entry.split('.')[0]
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idx = truncated_entry.index('r')
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rep_names.append(truncated_entry[:idx] + '|' + truncated_entry[idx:])
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rep_names.append(truncated_entry[:idx] + '|'
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+ truncated_entry[idx:])
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print_err = 0
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if 'print_err' in kwargs:
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@ -97,8 +98,13 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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for k in range(nrw):
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deltas.append([])
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else:
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if ((nrw != struct.unpack('i', t)[0] and (not version == '2.0')) or (nrw != struct.unpack('i', t)[0] / 2 and version == '2.0')): # little weird if-clause due to the /2 operation needed.
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raise Exception('Error: different number of reweighting factors for replicum', rep)
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# little weird if-clause due to the /2 operation needed.
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if ((nrw != struct.unpack('i', t)[0] and
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(not version == '2.0')) or
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(nrw != struct.unpack('i', t)[0] / 2 and
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version == '2.0')):
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raise Exception('Error: different number of reweighting\
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factors for replicum', rep)
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for k in range(nrw):
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tmp_array.append([])
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@ -109,7 +115,8 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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for i in range(nrw):
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t = fp.read(4)
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nfct.append(struct.unpack('i', t)[0])
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# print('nfct: ', nfct) # Hasenbusch factor, 1 for rat reweighting
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# print('nfct: ', nfct) # Hasenbusch factor,
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# 1 for rat reweighting
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else:
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for i in range(nrw):
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nfct.append(1)
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@ -138,8 +145,11 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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for j in range(tmpd['n'][0]):
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tmp_nfct *= np.mean(np.exp(-np.asarray(tmp_rw[j])))
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if print_err:
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print(config_no, i, j, np.mean(np.exp(-np.asarray(tmp_rw[j]))), np.std(np.exp(-np.asarray(tmp_rw[j]))))
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print('Sources:', np.exp(-np.asarray(tmp_rw[j])))
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print(config_no, i, j,
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np.mean(np.exp(-np.asarray(tmp_rw[j]))),
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np.std(np.exp(-np.asarray(tmp_rw[j]))))
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print('Sources:',
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np.exp(-np.asarray(tmp_rw[j])))
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print('Partial factor:', tmp_nfct)
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elif version == '1.6' or version == '1.4':
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tmp_nfct = 1.0
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@ -149,7 +159,9 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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tmp_rw = struct.unpack('d' * nsrc[i], t)
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tmp_nfct *= np.mean(np.exp(-np.asarray(tmp_rw)))
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if print_err:
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print(config_no, i, j, np.mean(np.exp(-np.asarray(tmp_rw))), np.std(np.exp(-np.asarray(tmp_rw))))
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print(config_no, i, j,
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np.mean(np.exp(-np.asarray(tmp_rw))),
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np.std(np.exp(-np.asarray(tmp_rw))))
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print('Sources:', np.exp(-np.asarray(tmp_rw)))
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print('Partial factor:', tmp_nfct)
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tmp_array[i].append(tmp_nfct)
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@ -168,11 +180,14 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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return result
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def extract_t0(path, prefix, dtr_read, xmin, spatial_extent, fit_range=5, **kwargs):
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def extract_t0(path, prefix, dtr_read, xmin,
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spatial_extent, fit_range=5, **kwargs):
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"""Extract t0 from given .ms.dat files. Returns t0 as Obs.
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It is assumed that all boundary effects have sufficiently decayed at x0=xmin.
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The data around the zero crossing of t^2<E> - 0.3 is fitted with a linear function
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It is assumed that all boundary effects have
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sufficiently decayed at x0=xmin.
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The data around the zero crossing of t^2<E> - 0.3
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is fitted with a linear function
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from which the exact root is extracted.
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Only works with openQCD v 1.2.
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@ -183,14 +198,17 @@ def extract_t0(path, prefix, dtr_read, xmin, spatial_extent, fit_range=5, **kwar
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prefix : str
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Ensemble prefix
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dtr_read : int
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Determines how many trajectories should be skipped when reading the ms.dat files.
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Determines how many trajectories should be skipped
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when reading the ms.dat files.
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Corresponds to dtr_cnfg / dtr_ms in the openQCD input file.
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xmin : int
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First timeslice where the boundary effects have sufficiently decayed.
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First timeslice where the boundary
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effects have sufficiently decayed.
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spatial_extent : int
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spatial extent of the lattice, required for normalization.
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fit_range : int
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Number of data points left and right of the zero crossing to be included in the linear fit. (Default: 5)
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Number of data points left and right of the zero
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crossing to be included in the linear fit. (Default: 5)
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r_start : list
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list which contains the first config to be read for each replicum.
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r_stop: list
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@ -276,7 +294,9 @@ def extract_t0(path, prefix, dtr_read, xmin, spatial_extent, fit_range=5, **kwar
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Ysum.append([])
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for i, item in enumerate(Ysl):
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Ysum[-1].append([np.mean(item[current + xmin:current + tmax - xmin]) for current in range(0, len(item), tmax)])
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Ysum[-1].append([np.mean(item[current + xmin:
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current + tmax - xmin])
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for current in range(0, len(item), tmax)])
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t2E_dict = {}
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for n in range(nn + 1):
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@ -287,12 +307,16 @@ def extract_t0(path, prefix, dtr_read, xmin, spatial_extent, fit_range=5, **kwar
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samples[-1].append(cnfg[n])
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samples[-1] = samples[-1][r_start[nrep]:r_stop[nrep]]
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new_obs = Obs(samples, [(w.split('.'))[0] for w in ls])
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t2E_dict[n * dn * eps] = (n * dn * eps) ** 2 * new_obs / (spatial_extent ** 3) - 0.3
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t2E_dict[n * dn * eps] = (n * dn * eps) ** 2 * new_obs \
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/ (spatial_extent ** 3) - 0.3
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zero_crossing = np.argmax(np.array([o.value for o in t2E_dict.values()]) > 0.0)
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zero_crossing = np.argmax(np.array(
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[o.value for o in t2E_dict.values()]) > 0.0)
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x = list(t2E_dict.keys())[zero_crossing - fit_range: zero_crossing + fit_range]
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y = list(t2E_dict.values())[zero_crossing - fit_range: zero_crossing + fit_range]
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x = list(t2E_dict.keys())[zero_crossing - fit_range:
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zero_crossing + fit_range]
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y = list(t2E_dict.values())[zero_crossing - fit_range:
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zero_crossing + fit_range]
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[o.gamma_method() for o in y]
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fit_result = fit_lin(x, y)
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@ -348,7 +372,7 @@ def _read_array_openQCD2(fp):
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return {'d': d, 'n': n, 'size': size, 'arr': arr}
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def read_qtop(path, prefix,c, dtr_cnfg = 1, version = "1.2",**kwargs):
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def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
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"""Read qtop format from given folder structure.
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Parameters
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@ -360,144 +384,150 @@ def read_qtop(path, prefix,c, dtr_cnfg = 1, version = "1.2",**kwargs):
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c: double
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Smearing radius in units of the lattice extent, c = sqrt(8 t0) / L
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dtr_cnfg: int
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(optional) parameter that specifies the number of trajectories between two configs.
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if it is not set, the distance between two measurements in the file is assumed to be
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(optional) parameter that specifies the number of trajectories
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between two configs.
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if it is not set, the distance between two measurements
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in the file is assumed to be
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the distance between two configurations.
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steps: int
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(optional) (maybe only necessary for openQCD2.0)
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nt step size, guessed if not given
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version: str
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version string of the openQCD (sfqcd) version used to create the ensemble
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version string of the openQCD (sfqcd) version used to create
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the ensemble
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L: int
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spatial length of the lattice in L/a. HAS to be set if version != sfqcd, since openQCD does not provide this in the header
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spatial length of the lattice in L/a.
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HAS to be set if version != sfqcd, since openQCD does not provide
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this in the header
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r_start: list
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offset of the first ensemble, making it easier to match later on with other Obs
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offset of the first ensemble, making it easier to match
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later on with other Obs
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r_stop: list
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last configurations that need to be read (per replicum)
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r_meas_start: list
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offset of the first measured ensemble, if there is any
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files: list
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specify the exact files that need to be read from path, pratical if e.g. only one replicum is needed
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specify the exact files that need to be read
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from path, pratical if e.g. only one replicum is needed
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names: list
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Alternative labeling for replicas/ensembles. Has to have the appropriate length
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Alternative labeling for replicas/ensembles.
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Has to have the appropriate length
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"""
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#one could read L from the header in case of sfQCD
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#c = 0.35
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known_versions = ["1.0","1.2","1.4","1.6","2.0", "sfqcd"]
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if not version in known_versions:
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# one could read L from the header in case of sfQCD
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# c = 0.35
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known_versions = ["1.0", "1.2", "1.4", "1.6", "2.0", "sfqcd"]
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if version not in known_versions:
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raise Exception("Unknown openQCD version.")
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target = 0
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if "steps" in kwargs:
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steps = kwargs.get("steps")
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if 'target' in kwargs:
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target = kwargs.get('target')
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if version == "sfqcd":
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if "L" in kwargs:
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supposed_L = kwargs.get("L")
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supposed_L = kwargs.get("L")
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else:
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if not "L" in kwargs:
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raise Exception("This version of openQCD needs you to provide the spatial length of the lattice as parameter 'L'.")
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if "L" not in kwargs:
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raise Exception("This version of openQCD needs you \
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to provide the spatial length of the \
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lattice as parameter 'L'.")
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else:
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L = kwargs.get("L")
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r_start = 1
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r_meas_start = 1
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if "r_meas_start" in kwargs:
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r_meas_start = kwargs.get("r_meas_start")
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if "r_start" in kwargs:
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r_start = kwargs.get("r_start")
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if "r_stop" in kwargs:
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r_stop = kwargs.get("r_stop")
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#if one wants to read specific files with this method...
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# if one wants to read specific files with this method...
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if "files" in kwargs:
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files = kwargs.get("files")
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else:
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#find files in path
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# find files in path
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found = []
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files = []
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for (dirpath, dirnames, filenames) in os.walk(path+"/"):
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#print(filenames)
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# print(filenames)
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found.extend(filenames)
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break
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for f in found:
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if fnmatch.fnmatch(f, prefix+"*"+".ms.dat"):
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files.append(f)
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print(files)
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#now that we found our files, we dechiffer them...
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# now that we found our files, we dechiffer them...
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rep_names = []
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deltas = []
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idl = []
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for rep,file in enumerate(files):
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for rep, file in enumerate(files):
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with open(path+"/"+file, "rb") as fp:
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#this, for now, is for version 1.2,1.4,1.6 and 2.0, but needs to be tested for the last 3, isncethe doc says its the same
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#header
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# header
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t = fp.read(12)
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header = struct.unpack('<iii', t)
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dn = header[0] # step size in integration steps "dnms"
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nn = header[1] # number of measurements, so "ntot"/dn
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tmax = header[2]# lattice T/a
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# step size in integration steps "dnms"
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dn = header[0]
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# number of measurements, so "ntot"/dn
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nn = header[1]
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# lattice T/a
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tmax = header[2]
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if version == "sfqcd":
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t = fp.read(12)
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Ls = struct.unpack('<iii', t)
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if(Ls[0] == Ls[1] and Ls[1] == Ls[2]):
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L = Ls[0]
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if not (supposed_L == L):
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raise Exception("It seems the length given in the header and by you contradict each other")
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raise Exception("It seems the length given\
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in the header and by you \
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contradict each other")
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else:
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raise Exception("Found more than one spatial length in header!")
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raise Exception("Found more than one \
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spatial length in header!")
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print('dnms:', dn)
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print('nn:', nn)
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print('tmax:', tmax)
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t = fp.read(8) #header4 wird mit 16 bytes ausgelesen... cmax fehlt also als Angabe
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eps = struct.unpack('d', t)[0]# das hier ist vllt. tol
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t = fp.read(8)
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eps = struct.unpack('d', t)[0]
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print('eps:', eps)
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Q = []
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ncs = []
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while 0 < 1:
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t = fp.read(4) #int nt
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# int nt
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t = fp.read(4)
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if(len(t) < 4):
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break
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ncs.append(struct.unpack('i',t)[0])
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t = fp.read(8 * tmax * (nn + 1))#Wsl
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t = fp.read(8 * tmax * (nn + 1))#Ysl
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t = fp.read(8 * tmax * (nn + 1))#Qsl, which is asked for in this method
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#unpack the array of Qtops, on each timeslice t=0,...,tmax-1 and the
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#measurement number in = 0...nn (see README.qcd1)
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ncs.append(struct.unpack('i', t)[0])
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# Wsl
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t = fp.read(8 * tmax * (nn + 1))
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# Ysl
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t = fp.read(8 * tmax * (nn + 1))
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# Qsl, which is asked for in this method
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t = fp.read(8 * tmax * (nn + 1))
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# unpack the array of Qtops,
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# on each timeslice t=0,...,tmax-1 and the
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# measurement number in = 0...nn (see README.qcd1)
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tmpd = struct.unpack('d' * tmax * (nn + 1), t)
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Q.append(tmpd)
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#set step by reading all entries, then set stepsize, then check if everything is there
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#make a dtr_config param, which is checked against difference...
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#difference != step
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if not len(set([ncs[i]-ncs[i-1] for i in range(1,len(ncs))])):
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if not len(set([ncs[i]-ncs[i-1] for i in range(1, len(ncs))])):
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raise Exception("Irregularities in stepsize found")
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else:
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if 'steps' in kwargs:
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if steps != ncs[1]-ncs[0]:
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raise Exception("steps and the found stepsize are not the same")
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raise Exception("steps and the found stepsize \
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are not the same")
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else:
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steps = ncs[1]-ncs[0]
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if ncs[0]//steps == ncs[0]/steps:
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r_meas_start = ncs[0]//steps
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print(len(Q))
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print('max_t:', dn * (nn) * eps)
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t_aim = (c * L) ** 2 / 8
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print('t_aim:', t_aim)
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index_aim = round(t_aim / eps / dn)
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print('index_aim:', index_aim)
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Q_sum = []
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for i, item in enumerate(Q):
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Q_sum.append([sum(item[current:current + tmax]) for current in range(0, len(item), tmax)])
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Q_sum.append([sum(item[current:current + tmax])
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for current in range(0, len(item), tmax)])
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print(len(Q_sum))
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print(len(Q_sum[0]))
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Q_round = []
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@ -505,26 +535,27 @@ def read_qtop(path, prefix,c, dtr_cnfg = 1, version = "1.2",**kwargs):
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Q_round.append(round(Q_sum[dtr_cnfg * i][index_aim]))
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if len(Q_round) != len(ncs)//dtr_cnfg:
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raise Exception("qtops and ncs dont have the same length")
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#replica = len(files)
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# replica = len(files)
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truncated_file = file[:-7]
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print(truncated_file)
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idl_start = 1
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if "r_start" in kwargs:
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Q_round = Q_round[r_start[rep]:]
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idl_start = r_start[rep]
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if "r_stop" in kwargs:
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Q_round = Q_round[:r_stop[rep]]
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idl_stop = idl_start+len(Q_round)
|
||||
#keyword "names" prevails over "ens_name"
|
||||
if not "names" in kwargs:
|
||||
# keyword "names" prevails over "ens_name"
|
||||
if "names" not in kwargs:
|
||||
try:
|
||||
idx = truncated_file.index('r')
|
||||
except:
|
||||
if not "names" in kwargs:
|
||||
raise Exception("Automatic recognition of replicum failed, please enter the key word 'names'.")
|
||||
except Exception:
|
||||
if "names" not in kwargs:
|
||||
raise Exception("Automatic recognition of replicum failed,\
|
||||
please enter the key word 'names'.")
|
||||
if "ens_name" in kwargs:
|
||||
ens_name = kwargs.get("ens_name")
|
||||
else:
|
||||
|
|
@ -534,12 +565,13 @@ def read_qtop(path, prefix,c, dtr_cnfg = 1, version = "1.2",**kwargs):
|
|||
names = kwargs.get("names")
|
||||
rep_names = names
|
||||
deltas.append(np.array(Q_round))
|
||||
idl.append(range(idl_start,idl_stop))
|
||||
#print(idl)
|
||||
result = Obs(deltas, rep_names, idl = idl)
|
||||
idl.append(range(idl_start, idl_stop))
|
||||
# print(idl)
|
||||
result = Obs(deltas, rep_names, idl=idl)
|
||||
return result
|
||||
|
||||
def read_qtop_sector(target = 0, **kwargs):
|
||||
|
||||
def read_qtop_sector(target=0, **kwargs):
|
||||
"""target: int
|
||||
specifies the topological sector to be reweighted to (default 0)
|
||||
q_top: Obs
|
||||
|
|
@ -552,12 +584,14 @@ def read_qtop_sector(target = 0, **kwargs):
|
|||
path = kwargs.get("path")
|
||||
del kwargs["path"]
|
||||
else:
|
||||
raise Exception("If you are not providing q_top, please provide path")
|
||||
raise Exception("If you are not providing q_top,\
|
||||
please provide path")
|
||||
if "prefix" in kwargs:
|
||||
prefix = kwargs.get("prefix")
|
||||
del kwargs["prefix"]
|
||||
else:
|
||||
raise Exception("If you are not providing q_top, please provide prefix")
|
||||
raise Exception("If you are not providing q_top,\
|
||||
please provide prefix")
|
||||
if "c" in kwargs:
|
||||
c = kwargs.get("c")
|
||||
del kwargs["c"]
|
||||
|
|
@ -573,14 +607,16 @@ def read_qtop_sector(target = 0, **kwargs):
|
|||
del kwargs["dtr_cnfg"]
|
||||
else:
|
||||
dtr_cnfg = 1
|
||||
qtop = read_qtop(path, prefix,c, dtr_cnfg = dtr_cnfg, version = version,**kwargs)
|
||||
#unpack to original values, project onto target sector
|
||||
qtop = read_qtop(path, prefix, c, dtr_cnfg=dtr_cnfg,
|
||||
version=version, **kwargs)
|
||||
# unpack to original values, project onto target sector
|
||||
names = qtop.names
|
||||
print(names)
|
||||
print(qtop.deltas.keys())
|
||||
proj_qtop = []
|
||||
for n in qtop.deltas:
|
||||
proj_qtop.append(np.array([1 if int(qtop.value+q) == target else 0 for q in qtop.deltas[n]]))
|
||||
|
||||
proj_qtop.append(np.array([1 if int(qtop.value+q) ==
|
||||
target else 0 for q in qtop.deltas[n]]))
|
||||
|
||||
result = Obs(proj_qtop, qtop.names)
|
||||
return result
|
||||
|
|
|
|||
|
|
@ -76,8 +76,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
|
|||
single = 0
|
||||
if "replica" in kwargs:
|
||||
reps = kwargs.get("replica")
|
||||
if "files" in kwargs:
|
||||
files = kwargs.get("files")
|
||||
|
||||
# due to higher usage in current projects,
|
||||
# compact file format is default
|
||||
|
|
@ -339,10 +337,13 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
|
|||
floats[1 + im - single]
|
||||
|
||||
else:
|
||||
for exc in ls:
|
||||
if not fnmatch.fnmatch(exc, prefix + '*.'+name):
|
||||
ls = list(set(ls) - set([exc]))
|
||||
ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
|
||||
if "files" in kwargs:
|
||||
ls = kwargs.get("files")
|
||||
else:
|
||||
for exc in ls:
|
||||
if not fnmatch.fnmatch(exc, prefix + '*.'+name):
|
||||
ls = list(set(ls) - set([exc]))
|
||||
ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
|
||||
# print(ls)
|
||||
pattern = 'name ' + name + '\nquarks '\
|
||||
+ quarks + '\noffset ' + str(noffset)\
|
||||
|
|
@ -358,9 +359,9 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
|
|||
if "[run]" in line:
|
||||
data_starts.append(linenumber)
|
||||
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")
|
||||
not all runs have the same output length")
|
||||
# first chunk of data
|
||||
chunk = content[:data_starts[1]]
|
||||
for linenumber, line in enumerate(chunk):
|
||||
|
|
@ -397,7 +398,7 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
|
|||
found_pat += li
|
||||
if re.search(pattern, found_pat):
|
||||
for t, line in \
|
||||
enumerate(chunk[start_read:start_read+T]):
|
||||
enumerate(chunk[start_read:start_read+T]):
|
||||
floats = list(map(float, line.split()))
|
||||
deltas[t][rep][cnfg] = floats[-2:][im]
|
||||
idl.append(rep_idl)
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue