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jkuhl-uni 2022-02-08 11:16:20 +01:00
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pyerrors/input/openQCD.py
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@ -1,11 +1,11 @@
#!/usr/bin/env python
# coding: utf-8
import os
import fnmatch
import re
import struct
import numpy as np # Thinly-wrapped numpy
import warnings
import matplotlib.pyplot as plt
from matplotlib import gridspec
from ..obs import Obs
from ..fits import fit_lin
@ -15,16 +15,31 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
Parameters
----------
path : str
path that contains the data files
prefix : str
all files in path that start with prefix are considered as input files.
May be used together postfix to consider only special file endings.
Prefix is ignored, if the keyword 'files' is used.
version : str
version of openQCD, default 2.0
names : list
list of names that is assigned to the data according according
to the order in the file list. Use careful, if you do not provide file names!
r_start : list
list which contains the first config to be read for each replicum
r_stop : list
list which contains the last config to be read for each replicum
r_step : int
integer that defines a fixed step size between two measurements (in units of configs)
If not given, r_step=1 is assumed.
postfix : str
postfix of the file to read, e.g. '.ms1' for openQCD-files
idl_offsets : list
offsets to the idl range of obs. Useful for the case that the measurements of rwms are only starting at cfg. 20
files : list
list which contains the filenames to be read. No automatic detection of
files performed if given.
print_err : bool
Print additional information that is useful for debugging.
"""
known_oqcd_versions = ['1.4', '1.6', '2.0']
if not (version in known_oqcd_versions):
@ -44,7 +59,6 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
if 'files' in kwargs:
ls = kwargs.get('files')
else:
# Exclude files with different names
for exc in ls:
if not fnmatch.fnmatch(exc, prefix + '*' + postfix + '.dat'):
ls = list(set(ls) - set([exc]))
@ -56,8 +70,7 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
r_start = kwargs.get('r_start')
if len(r_start) != replica:
raise Exception('r_start does not match number of replicas')
# Adjust Configuration numbering to python index
r_start = [o - 1 if o else None for o in r_start]
r_start = [o if o else None for o in r_start]
else:
r_start = [None] * replica
@ -68,16 +81,22 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
else:
r_stop = [None] * replica
if 'r_step' in kwargs:
r_step = kwargs.get('r_step')
else:
r_step = 1
print('Read reweighting factors from', prefix[:-1], ',',
replica, 'replica', end='')
# Adjust replica names to new bookmarking system
if names is None:
rep_names = []
for entry in ls:
truncated_entry = entry.split('.')[0]
idx = truncated_entry.index('r')
rep_names.append(truncated_entry[:idx] + '|' + truncated_entry[idx:])
else:
rep_names = names
print_err = 0
if 'print_err' in kwargs:
@ -86,11 +105,14 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
deltas = []
configlist = []
r_start_index = []
r_stop_index = []
for rep in range(replica):
tmp_array = []
with open(path + '/' + ls[rep], 'rb') as fp:
# header
t = fp.read(4) # number of reweighting factors
if rep == 0:
nrw = struct.unpack('i', t)[0]
@ -99,7 +121,6 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
for k in range(nrw):
deltas.append([])
else:
# little weird if-clause due to the /2 operation needed.
if ((nrw != struct.unpack('i', t)[0] and (not version == '2.0')) or (nrw != struct.unpack('i', t)[0] / 2 and version == '2.0')):
raise Exception('Error: different number of reweighting factors for replicum', rep)
@ -112,8 +133,6 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
for i in range(nrw):
t = fp.read(4)
nfct.append(struct.unpack('i', t)[0])
# print('nfct: ', nfct) # Hasenbusch factor,
# 1 for rat reweighting
else:
for i in range(nrw):
nfct.append(1)
@ -126,13 +145,13 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
if not struct.unpack('i', fp.read(4))[0] == 0:
print('something is wrong!')
# body
configlist.append([])
while 0 < 1:
t = fp.read(4)
if len(t) < 4:
break
if print_err:
config_no = struct.unpack('i', t)
config_no = struct.unpack('i', t)[0]
configlist[-1].append(config_no)
for i in range(nrw):
if(version == '2.0'):
tmpd = _read_array_openQCD2(fp)
@ -163,8 +182,32 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
print('Partial factor:', tmp_nfct)
tmp_array[i].append(tmp_nfct)
if r_start[rep] is None:
r_start_index.append(0)
else:
try:
r_start_index.append(configlist[-1].index(r_start[rep]))
except ValueError:
raise Exception('Config %d not in file with range [%d, %d]' % (
r_start[rep], configlist[-1][0], configlist[-1][-1])) from None
if r_stop[rep] is None:
r_stop_index.append(len(configlist[-1]) - 1)
else:
try:
r_stop_index.append(configlist[-1].index(r_stop[rep]))
except ValueError:
raise Exception('Config %d not in file with range [%d, %d]' % (
r_stop[rep], configlist[-1][0], configlist[-1][-1])) from None
for k in range(nrw):
deltas[k].append(tmp_array[k][r_start[rep]:r_stop[rep]])
deltas[k].append(tmp_array[k][r_start_index[rep]:r_stop_index[rep]][::r_step])
if np.any([len(np.unique(np.diff(cl))) != 1 for cl in configlist]):
raise Exception('Irregular spaced data in input file!', [len(np.unique(np.diff(cl))) for cl in configlist])
stepsizes = [list(np.unique(np.diff(cl)))[0] for cl in configlist]
if np.any([step != 1 for step in stepsizes]):
warnings.warn('Stepsize between configurations is greater than one!' + str(stepsizes), RuntimeWarning)
print(',', nrw, 'reweighting factors with', nsrc, 'sources')
if "idl_offsets" in kwargs:
@ -172,15 +215,9 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
else:
idl_offsets = np.ones(nrw, dtype=int)
result = []
idl = [range(configlist[rep][r_start_index[rep]], configlist[rep][r_stop_index[rep]], r_step) for rep in range(replica)]
for t in range(nrw):
idl = []
for rep in range(replica):
idl.append(range(idl_offsets[rep], len(deltas[t][rep] + idl_offsets[rep])))
if names is None:
result.append(Obs(deltas[t], rep_names, idl=idl))
else:
print(names)
result.append(Obs(deltas[t], names, idl=idl))
result.append(Obs(deltas[t], rep_names, idl=idl))
return result
@ -193,7 +230,12 @@ def extract_t0(path, prefix, dtr_read, xmin,
The data around the zero crossing of t^2<E> - 0.3
is fitted with a linear function
from which the exact root is extracted.
Only works with openQCD v 1.2.
Only works with openQCD
It is assumed that one measurement is performed for each config.
If this is not the case, the resulting idl, as well as the handling
of r_start, r_stop and r_step is wrong and the user has to correct
this in the resulting observable.
Parameters
----------
@ -215,10 +257,26 @@ def extract_t0(path, prefix, dtr_read, xmin,
crossing to be included in the linear fit. (Default: 5)
r_start : list
list which contains the first config to be read for each replicum.
r_stop: list
r_stop : list
list which contains the last config to be read for each replicum.
r_step : int
integer that defines a fixed step size between two measurements (in units of configs)
If not given, r_step=1 is assumed.
plaquette : bool
If true extract the plaquette estimate of t0 instead.
names : list
list of names that is assigned to the data according according
to the order in the file list. Use careful, if you do not provide file names!
files : list
list which contains the filenames to be read. No automatic detection of
files performed if given.
plot_fit : bool
If true, the fit for the extraction of t0 is shown together with the data.
assume_thermalization : bool
If True: If the first record divided by the distance between two measurements is larger than
1, it is assumed that this is due to thermalization and the first measurement belongs
to the first config (default).
If False: The config numbers are assumed to be traj_number // difference
"""
ls = []
@ -229,20 +287,21 @@ def extract_t0(path, prefix, dtr_read, xmin,
if not ls:
raise Exception('Error, directory not found')
# Exclude files with different names
for exc in ls:
if not fnmatch.fnmatch(exc, prefix + '*.ms.dat'):
ls = list(set(ls) - set([exc]))
if len(ls) > 1:
ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0]))
if 'files' in kwargs:
ls = kwargs.get('files')
else:
for exc in ls:
if not fnmatch.fnmatch(exc, prefix + '*.ms.dat'):
ls = list(set(ls) - set([exc]))
if len(ls) > 1:
ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0]))
replica = len(ls)
if 'r_start' in kwargs:
r_start = kwargs.get('r_start')
if len(r_start) != replica:
raise Exception('r_start does not match number of replicas')
# Adjust Configuration numbering to python index
r_start = [o - 1 if o else None for o in r_start]
r_start = [o if o else None for o in r_start]
else:
r_start = [None] * replica
@ -253,14 +312,31 @@ def extract_t0(path, prefix, dtr_read, xmin,
else:
r_stop = [None] * replica
if 'r_step' in kwargs:
r_step = kwargs.get('r_step')
else:
r_step = 1
print('Extract t0 from', prefix, ',', replica, 'replica')
if 'names' in kwargs:
rep_names = kwargs.get('names')
else:
rep_names = []
for entry in ls:
truncated_entry = entry.split('.')[0]
idx = truncated_entry.index('r')
rep_names.append(truncated_entry[:idx] + '|' + truncated_entry[idx:])
Ysum = []
configlist = []
r_start_index = []
r_stop_index = []
for rep in range(replica):
with open(path + '/' + ls[rep], 'rb') as fp:
# Read header
t = fp.read(12)
header = struct.unpack('iii', t)
if rep == 0:
@ -279,12 +355,13 @@ def extract_t0(path, prefix, dtr_read, xmin,
Ysl = []
# Read body
configlist.append([])
while 0 < 1:
t = fp.read(4)
if(len(t) < 4):
break
nc = struct.unpack('i', t)[0]
configlist[-1].append(nc)
t = fp.read(8 * tmax * (nn + 1))
if kwargs.get('plaquette'):
@ -302,6 +379,38 @@ def extract_t0(path, prefix, dtr_read, xmin,
current + tmax - xmin])
for current in range(0, len(item), tmax)])
diffmeas = configlist[-1][-1] - configlist[-1][-2]
configlist[-1] = [item // diffmeas for item in configlist[-1]]
if kwargs.get('assume_thermalization', True) and configlist[-1][0] > 1:
warnings.warn('Assume thermalization and that the first measurement belongs to the first config.')
offset = configlist[-1][0] - 1
configlist[-1] = [item - offset for item in configlist[-1]]
if r_start[rep] is None:
r_start_index.append(0)
else:
try:
r_start_index.append(configlist[-1].index(r_start[rep]))
except ValueError:
raise Exception('Config %d not in file with range [%d, %d]' % (
r_start[rep], configlist[-1][0], configlist[-1][-1])) from None
if r_stop[rep] is None:
r_stop_index.append(len(configlist[-1]) - 1)
else:
try:
r_stop_index.append(configlist[-1].index(r_stop[rep]))
except ValueError:
raise Exception('Config %d not in file with range [%d, %d]' % (
r_stop[rep], configlist[-1][0], configlist[-1][-1])) from None
if np.any([len(np.unique(np.diff(cl))) != 1 for cl in configlist]):
raise Exception('Irregular spaced data in input file!', [len(np.unique(np.diff(cl))) for cl in configlist])
stepsizes = [list(np.unique(np.diff(cl)))[0] for cl in configlist]
if np.any([step != 1 for step in stepsizes]):
warnings.warn('Stepsize between configurations is greater than one!' + str(stepsizes), RuntimeWarning)
idl = [range(configlist[rep][r_start_index[rep]], configlist[rep][r_stop_index[rep]], r_step) for rep in range(replica)]
t2E_dict = {}
for n in range(nn + 1):
samples = []
@ -309,8 +418,8 @@ def extract_t0(path, prefix, dtr_read, xmin,
samples.append([])
for cnfg in rep:
samples[-1].append(cnfg[n])
samples[-1] = samples[-1][r_start[nrep]:r_stop[nrep]]
new_obs = Obs(samples, [(w.split('.'))[0] for w in ls])
samples[-1] = samples[-1][r_start_index[nrep]:r_stop_index[nrep]][::r_step]
new_obs = Obs(samples, rep_names, idl=idl)
t2E_dict[n * dn * eps] = (n * dn * eps) ** 2 * new_obs / (spatial_extent ** 3) - 0.3
zero_crossing = np.argmax(np.array(
@ -323,32 +432,62 @@ def extract_t0(path, prefix, dtr_read, xmin,
[o.gamma_method() for o in y]
fit_result = fit_lin(x, y)
if kwargs.get('plot_fit'):
plt.figure()
gs = gridspec.GridSpec(2, 1, height_ratios=[3, 1], wspace=0.0, hspace=0.0)
ax0 = plt.subplot(gs[0])
xmore = list(t2E_dict.keys())[zero_crossing - fit_range - 2: zero_crossing + fit_range + 2]
ymore = list(t2E_dict.values())[zero_crossing - fit_range - 2: zero_crossing + fit_range + 2]
[o.gamma_method() for o in ymore]
ax0.errorbar(xmore, [yi.value for yi in ymore], yerr=[yi.dvalue for yi in ymore], fmt='x')
xplot = np.linspace(np.min(x), np.max(x))
yplot = [fit_result[0] + fit_result[1] * xi for xi in xplot]
[yi.gamma_method() for yi in yplot]
ax0.fill_between(xplot, y1=[yi.value - yi.dvalue for yi in yplot], y2=[yi.value + yi.dvalue for yi in yplot])
retval = (-fit_result[0] / fit_result[1])
retval.gamma_method()
ylim = ax0.get_ylim()
ax0.fill_betweenx(ylim, x1=retval.value - retval.dvalue, x2=retval.value + retval.dvalue, color='gray', alpha=0.4)
ax0.set_ylim(ylim)
ax0.set_ylabel(r'$t^2 \langle E(t) \rangle - 0.3 $')
xlim = ax0.get_xlim()
fit_res = [fit_result[0] + fit_result[1] * xi for xi in x]
residuals = (np.asarray([o.value for o in y]) - [o.value for o in fit_res]) / np.asarray([o.dvalue for o in y])
ax1 = plt.subplot(gs[1])
ax1.plot(x, residuals, 'ko', ls='none', markersize=5)
ax1.tick_params(direction='out')
ax1.tick_params(axis="x", bottom=True, top=True, labelbottom=True)
ax1.axhline(y=0.0, ls='--', color='k')
ax1.fill_between(xlim, -1.0, 1.0, alpha=0.1, facecolor='k')
ax1.set_xlim(xlim)
ax1.set_ylabel('Residuals')
ax1.set_xlabel(r'$t/a^2$')
plt.show()
return -fit_result[0] / fit_result[1]
def _parse_array_openQCD2(d, n, size, wa, quadrupel=False):
arr = []
if d == 2:
tot = 0
for i in range(n[d - 1] - 1):
for i in range(n[0]):
tmp = wa[i * n[1]:(i + 1) * n[1]]
if quadrupel:
tmp = wa[tot:n[d - 1]]
tmp2 = []
for i in range(len(tmp)):
if i % 2 == 0:
tmp2.append(tmp[i])
for j in range(0, len(tmp), 2):
tmp2.append(tmp[j])
arr.append(tmp2)
else:
arr.append(np.asarray(wa[tot:n[d - 1]]))
arr.append(np.asarray(tmp))
else:
raise Exception('Only two-dimensional arrays supported!')
return arr
# mimic the read_array routine of openQCD-2.0.
# fp is the opened file handle
# returns the dict array
# at this point we only parse a 2d array
# d = 2
# n = [nfct[irw], 2*nsrc[irw]]
def _read_array_openQCD2(fp):
t = fp.read(4)
d = struct.unpack('i', t)[0]
@ -380,42 +519,40 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
Parameters
----------
path:
path : str
path of the measurement files
prefix:
prefix : str
prefix of the measurement files, e.g. <prefix>_id0_r0.ms.dat
c: double
c : double
Smearing radius in units of the lattice extent, c = sqrt(8 t0) / L
dtr_cnfg: int
dtr_cnfg : int
(optional) parameter that specifies the number of trajectories
between two configs.
if it is not set, the distance between two measurements
in the file is assumed to be
the distance between two configurations.
steps: int
steps : int
(optional) (maybe only necessary for openQCD2.0)
nt step size, guessed if not given
version: str
version : str
version string of the openQCD (sfqcd) version used to create
the ensemble
L: int
L : int
spatial length of the lattice in L/a.
HAS to be set if version != sfqcd, since openQCD does not provide
this in the header
r_start: list
r_start : list
offset of the first ensemble, making it easier to match
later on with other Obs
r_stop: list
r_stop : list
last configurations that need to be read (per replicum)
files: list
files : list
specify the exact files that need to be read
from path, pratical if e.g. only one replicum is needed
names: list
from path, practical if e.g. only one replicum is needed
names : list
Alternative labeling for replicas/ensembles.
Has to have the appropriate length
"""
# one could read L from the header in case of sfQCD
# c = 0.35
known_versions = ["1.0", "1.2", "1.4", "1.6", "2.0", "sfqcd"]
if version not in known_versions:
@ -435,11 +572,9 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
r_start = kwargs.get("r_start")
if "r_stop" in kwargs:
r_stop = kwargs.get("r_stop")
# if one wants to read specific files with this method...
if "files" in kwargs:
files = kwargs.get("files")
else:
# find files in path
found = []
files = []
for (dirpath, dirnames, filenames) in os.walk(path + "/"):
@ -450,14 +585,12 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
if fnmatch.fnmatch(f, prefix + "*" + ".ms.dat"):
files.append(f)
print(files)
# now that we found our files, we dechiffer them...
rep_names = []
deltas = []
idl = []
for rep, file in enumerate(files):
with open(path + "/" + file, "rb") as fp:
# header
t = fp.read(12)
header = struct.unpack('<iii', t)
# step size in integration steps "dnms"
@ -486,7 +619,6 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
Q = []
ncs = []
while 0 < 1:
# int nt
t = fp.read(4)
if(len(t) < 4):
break
@ -533,8 +665,6 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
if len(Q_round) != len(ncs) // dtr_cnfg:
raise Exception("qtops and ncs dont have the same length")
# replica = len(files)
truncated_file = file[:-7]
print(truncated_file)
idl_start = 1
@ -562,17 +692,24 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
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)
return result
def read_qtop_sector(target=0, **kwargs):
"""target: int
specifies the topological sector to be reweighted to (default 0)
q_top: Obs
alternatively takes args of read_qtop method as kwargs
"""Constructs reweighting factors to a specified topological sector.
Parameters
----------
target : int
Specifies the topological sector to be reweighted to (default 0)
q_top : Obs
Alternatively takes args of read_qtop method as kwargs
"""
if not isinstance(target, int):
raise Exception("'target' has to be an integer.")
if "q_top" in kwargs:
qtop = kwargs.get("q_top")
else:
@ -603,7 +740,6 @@ def read_qtop_sector(target=0, **kwargs):
dtr_cnfg = 1
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())