mirror of
https://github.com/fjosw/pyerrors.git
synced 2025-03-19 00:30:24 +01:00
628 lines
23 KiB
Python
628 lines
23 KiB
Python
#!/usr/bin/env python
|
|
# coding: utf-8
|
|
|
|
import ctypes
|
|
import hashlib
|
|
import autograd.numpy as np # Thinly-wrapped numpy
|
|
from ..pyerrors import Obs
|
|
|
|
|
|
def read_ADerrors(file_path, bdio_path='./libbdio.so', **kwargs):
|
|
""" Extract generic MCMC data from a bdio file
|
|
|
|
read_ADerrors requires bdio to be compiled into a shared library. This can be achieved by
|
|
adding the flag -fPIC to CC and changing the all target to
|
|
|
|
all: bdio.o $(LIBDIR)
|
|
gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o
|
|
cp $(BUILDDIR)/libbdio.so $(LIBDIR)/
|
|
|
|
Parameters
|
|
----------
|
|
file_path -- path to the bdio file
|
|
bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)
|
|
"""
|
|
bdio = ctypes.cdll.LoadLibrary(bdio_path)
|
|
|
|
bdio_open = bdio.bdio_open
|
|
bdio_open.restype = ctypes.c_void_p
|
|
|
|
bdio_close = bdio.bdio_close
|
|
bdio_close.restype = ctypes.c_int
|
|
bdio_close.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_seek_record = bdio.bdio_seek_record
|
|
bdio_seek_record.restype = ctypes.c_int
|
|
bdio_seek_record.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_get_rlen = bdio.bdio_get_rlen
|
|
bdio_get_rlen.restype = ctypes.c_int
|
|
bdio_get_rlen.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_get_ruinfo = bdio.bdio_get_ruinfo
|
|
bdio_get_ruinfo.restype = ctypes.c_int
|
|
bdio_get_ruinfo.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_read = bdio.bdio_read
|
|
bdio_read.restype = ctypes.c_size_t
|
|
bdio_read.argtypes = [ctypes.c_char_p, ctypes.c_size_t, ctypes.c_void_p]
|
|
|
|
bdio_read_f64 = bdio.bdio_read_f64
|
|
bdio_read_f64.restype = ctypes.c_size_t
|
|
bdio_read_f64.argtypes = [ctypes.c_void_p, ctypes.c_size_t, ctypes.c_void_p]
|
|
|
|
bdio_read_int32 = bdio.bdio_read_int32
|
|
bdio_read_int32.restype = ctypes.c_size_t
|
|
bdio_read_int32.argtypes = [ctypes.c_void_p, ctypes.c_size_t, ctypes.c_void_p]
|
|
|
|
b_path = file_path.encode('utf-8')
|
|
read = 'r'
|
|
b_read = read.encode('utf-8')
|
|
|
|
fbdio = bdio_open(ctypes.c_char_p(b_path), ctypes.c_char_p(b_read), None)
|
|
|
|
return_list = []
|
|
|
|
print('Reading of bdio file started')
|
|
while 1 > 0:
|
|
record = bdio_seek_record(fbdio)
|
|
ruinfo = bdio_get_ruinfo(fbdio)
|
|
|
|
if ruinfo == 7:
|
|
print('MD5sum found') # For now we just ignore these entries and do not perform any checks on them
|
|
continue
|
|
|
|
if ruinfo < 0:
|
|
# EOF reached
|
|
break
|
|
rlen = bdio_get_rlen(fbdio)
|
|
|
|
def read_c_double():
|
|
d_buf = ctypes.c_double
|
|
pd_buf = d_buf()
|
|
ppd_buf = ctypes.c_void_p(ctypes.addressof(pd_buf))
|
|
iread = bdio_read_f64(ppd_buf, ctypes.c_size_t(8), ctypes.c_void_p(fbdio))
|
|
return pd_buf.value
|
|
|
|
mean = read_c_double()
|
|
print('mean', mean)
|
|
|
|
def read_c_size_t():
|
|
d_buf = ctypes.c_size_t
|
|
pd_buf = d_buf()
|
|
ppd_buf = ctypes.c_void_p(ctypes.addressof(pd_buf))
|
|
iread = bdio_read_int32(ppd_buf, ctypes.c_size_t(4), ctypes.c_void_p(fbdio))
|
|
return pd_buf.value
|
|
|
|
neid = read_c_size_t()
|
|
print('neid', neid)
|
|
|
|
ndata = []
|
|
for index in range(neid):
|
|
ndata.append(read_c_size_t())
|
|
print('ndata', ndata)
|
|
|
|
nrep = []
|
|
for index in range(neid):
|
|
nrep.append(read_c_size_t())
|
|
print('nrep', nrep)
|
|
|
|
vrep = []
|
|
for index in range(neid):
|
|
vrep.append([])
|
|
for jndex in range(nrep[index]):
|
|
vrep[-1].append(read_c_size_t())
|
|
print('vrep', vrep)
|
|
|
|
ids = []
|
|
for index in range(neid):
|
|
ids.append(read_c_size_t())
|
|
print('ids', ids)
|
|
|
|
nt = []
|
|
for index in range(neid):
|
|
nt.append(read_c_size_t())
|
|
print('nt', nt)
|
|
|
|
zero = []
|
|
for index in range(neid):
|
|
zero.append(read_c_double())
|
|
print('zero', zero)
|
|
|
|
four = []
|
|
for index in range(neid):
|
|
four.append(read_c_double())
|
|
print('four', four)
|
|
|
|
d_buf = ctypes.c_double * np.sum(ndata)
|
|
pd_buf = d_buf()
|
|
ppd_buf = ctypes.c_void_p(ctypes.addressof(pd_buf))
|
|
iread = bdio_read_f64(ppd_buf, ctypes.c_size_t(8 * np.sum(ndata)), ctypes.c_void_p(fbdio))
|
|
delta = pd_buf[:]
|
|
|
|
samples = np.split(np.asarray(delta) + mean, np.cumsum([a for su in vrep for a in su])[:-1])
|
|
no_reps = [len(o) for o in vrep]
|
|
assert len(ids) == len(no_reps)
|
|
tmp_names = []
|
|
ens_length = max([len(str(o)) for o in ids])
|
|
for loc_id, reps in zip(ids, no_reps):
|
|
for index in range(reps):
|
|
missing_chars = ens_length - len(str(loc_id))
|
|
tmp_names.append(str(loc_id) + ' ' * missing_chars + 'r' + '{0:03d}'.format(index))
|
|
|
|
return_list.append(Obs(samples, tmp_names))
|
|
|
|
bdio_close(fbdio)
|
|
print()
|
|
print(len(return_list), 'observable(s) extracted.')
|
|
return return_list
|
|
|
|
|
|
def write_ADerrors(obs_list, file_path, bdio_path='./libbdio.so', **kwargs):
|
|
""" Write Obs to a bdio file according to ADerrors conventions
|
|
|
|
read_mesons requires bdio to be compiled into a shared library. This can be achieved by
|
|
adding the flag -fPIC to CC and changing the all target to
|
|
|
|
all: bdio.o $(LIBDIR)
|
|
gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o
|
|
cp $(BUILDDIR)/libbdio.so $(LIBDIR)/
|
|
|
|
Parameters
|
|
----------
|
|
file_path -- path to the bdio file
|
|
bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)
|
|
"""
|
|
|
|
for obs in obs_list:
|
|
if not obs.e_names:
|
|
raise Exception('Run the gamma method first for all obs.')
|
|
|
|
bdio = ctypes.cdll.LoadLibrary(bdio_path)
|
|
|
|
bdio_open = bdio.bdio_open
|
|
bdio_open.restype = ctypes.c_void_p
|
|
|
|
bdio_close = bdio.bdio_close
|
|
bdio_close.restype = ctypes.c_int
|
|
bdio_close.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_start_record = bdio.bdio_start_record
|
|
bdio_start_record.restype = ctypes.c_int
|
|
bdio_start_record.argtypes = [ctypes.c_size_t, ctypes.c_size_t, ctypes.c_void_p]
|
|
|
|
bdio_flush_record = bdio.bdio_flush_record
|
|
bdio_flush_record.restype = ctypes.c_int
|
|
bdio_flush_record.argytpes = [ctypes.c_void_p]
|
|
|
|
bdio_write_f64 = bdio.bdio_write_f64
|
|
bdio_write_f64.restype = ctypes.c_size_t
|
|
bdio_write_f64.argtypes = [ctypes.c_void_p, ctypes.c_size_t, ctypes.c_void_p]
|
|
|
|
bdio_write_int32 = bdio.bdio_write_int32
|
|
bdio_write_int32.restype = ctypes.c_size_t
|
|
bdio_write_int32.argtypes = [ctypes.c_void_p, ctypes.c_size_t, ctypes.c_void_p]
|
|
|
|
b_path = file_path.encode('utf-8')
|
|
write = 'w'
|
|
b_write = write.encode('utf-8')
|
|
form = 'pyerrors ADerror export'
|
|
b_form = form.encode('utf-8')
|
|
|
|
fbdio = bdio_open(ctypes.c_char_p(b_path), ctypes.c_char_p(b_write), b_form)
|
|
|
|
for obs in obs_list:
|
|
|
|
mean = obs.value
|
|
neid = len(obs.e_names)
|
|
vrep = [[obs.shape[o] for o in sl] for sl in list(obs.e_content.values())]
|
|
vrep_write = [item for sublist in vrep for item in sublist]
|
|
ndata = [np.sum(o) for o in vrep]
|
|
nrep = [len(o) for o in vrep]
|
|
print('ndata', ndata)
|
|
print('nrep', nrep)
|
|
print('vrep', vrep)
|
|
keys = list(obs.e_content.keys())
|
|
ids = []
|
|
for key in keys:
|
|
try: # Try to convert key to integer
|
|
ids.append(int(key))
|
|
except: # If not possible construct a hash
|
|
ids.append(int(hashlib.sha256(key.encode('utf-8')).hexdigest(), 16) % 10 ** 8)
|
|
print('ids', ids)
|
|
nt = []
|
|
for e, e_name in enumerate(obs.e_names):
|
|
|
|
r_length = []
|
|
for r_name in obs.e_content[e_name]:
|
|
r_length.append(len(obs.deltas[r_name]))
|
|
|
|
# e_N = np.sum(r_length)
|
|
nt.append(max(r_length) // 2)
|
|
print('nt', nt)
|
|
zero = neid * [0.0]
|
|
four = neid * [4.0]
|
|
print('zero', zero)
|
|
print('four', four)
|
|
delta = np.concatenate([item for sublist in [[obs.deltas[o] for o in sl] for sl in list(obs.e_content.values())] for item in sublist])
|
|
|
|
bdio_start_record(0x00, 8, fbdio)
|
|
|
|
def write_c_double(double):
|
|
pd_buf = ctypes.c_double(double)
|
|
ppd_buf = ctypes.c_void_p(ctypes.addressof(pd_buf))
|
|
iwrite = bdio_write_f64(ppd_buf, ctypes.c_size_t(8), ctypes.c_void_p(fbdio))
|
|
|
|
def write_c_size_t(int32):
|
|
pd_buf = ctypes.c_size_t(int32)
|
|
ppd_buf = ctypes.c_void_p(ctypes.addressof(pd_buf))
|
|
iwrite = bdio_write_int32(ppd_buf, ctypes.c_size_t(4), ctypes.c_void_p(fbdio))
|
|
|
|
write_c_double(obs.value)
|
|
write_c_size_t(neid)
|
|
|
|
for element in ndata:
|
|
write_c_size_t(element)
|
|
for element in nrep:
|
|
write_c_size_t(element)
|
|
for element in vrep_write:
|
|
write_c_size_t(element)
|
|
for element in ids:
|
|
write_c_size_t(element)
|
|
for element in nt:
|
|
write_c_size_t(element)
|
|
|
|
for element in zero:
|
|
write_c_double(element)
|
|
for element in four:
|
|
write_c_double(element)
|
|
|
|
for element in delta:
|
|
write_c_double(element)
|
|
|
|
bdio_close(fbdio)
|
|
return 0
|
|
|
|
|
|
def _get_kwd(string, key):
|
|
return (string.split(key, 1)[1]).split(" ", 1)[0]
|
|
|
|
|
|
def _get_corr_name(string, key):
|
|
return (string.split(key, 1)[1]).split(' NDIM=', 1)[0]
|
|
|
|
|
|
def read_mesons(file_path, bdio_path='./libbdio.so', **kwargs):
|
|
""" Extract mesons data from a bdio file and return it as a dictionary
|
|
|
|
The dictionary can be accessed with a tuple consisting of (type, source_position, kappa1, kappa2)
|
|
|
|
read_mesons requires bdio to be compiled into a shared library. This can be achieved by
|
|
adding the flag -fPIC to CC and changing the all target to
|
|
|
|
all: bdio.o $(LIBDIR)
|
|
gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o
|
|
cp $(BUILDDIR)/libbdio.so $(LIBDIR)/
|
|
|
|
Parameters
|
|
----------
|
|
file_path -- path to the bdio file
|
|
bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)
|
|
stop -- stops reading at given configuration number (default None)
|
|
alternative_ensemble_name -- Manually overwrite ensemble name
|
|
"""
|
|
bdio = ctypes.cdll.LoadLibrary(bdio_path)
|
|
|
|
bdio_open = bdio.bdio_open
|
|
bdio_open.restype = ctypes.c_void_p
|
|
|
|
bdio_close = bdio.bdio_close
|
|
bdio_close.restype = ctypes.c_int
|
|
bdio_close.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_seek_record = bdio.bdio_seek_record
|
|
bdio_seek_record.restype = ctypes.c_int
|
|
bdio_seek_record.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_get_rlen = bdio.bdio_get_rlen
|
|
bdio_get_rlen.restype = ctypes.c_int
|
|
bdio_get_rlen.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_get_ruinfo = bdio.bdio_get_ruinfo
|
|
bdio_get_ruinfo.restype = ctypes.c_int
|
|
bdio_get_ruinfo.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_read = bdio.bdio_read
|
|
bdio_read.restype = ctypes.c_size_t
|
|
bdio_read.argtypes = [ctypes.c_char_p, ctypes.c_size_t, ctypes.c_void_p]
|
|
|
|
bdio_read_f64 = bdio.bdio_read_f64
|
|
bdio_read_f64.restype = ctypes.c_size_t
|
|
bdio_read_f64.argtypes = [ctypes.c_void_p, ctypes.c_size_t, ctypes.c_void_p]
|
|
|
|
b_path = file_path.encode('utf-8')
|
|
read = 'r'
|
|
b_read = read.encode('utf-8')
|
|
form = 'Generic Correlator Format 1.0'
|
|
b_form = form.encode('utf-8')
|
|
|
|
ensemble_name = ''
|
|
volume = [] # lattice volume
|
|
boundary_conditions = []
|
|
corr_name = [] # Contains correlator names
|
|
corr_type = [] # Contains correlator data type (important for reading out numerical data)
|
|
corr_props = [] # Contanis propagator types (Component of corr_kappa)
|
|
d0 = 0 # tvals
|
|
d1 = 0 # nnoise
|
|
prop_kappa = [] # Contains propagator kappas (Component of corr_kappa)
|
|
prop_source = [] # Contains propagator source positions
|
|
# Check noise type for multiple replica?
|
|
cnfg_no = -1
|
|
corr_no = -1
|
|
data = []
|
|
|
|
fbdio = bdio_open(ctypes.c_char_p(b_path), ctypes.c_char_p(b_read), ctypes.c_char_p(b_form))
|
|
|
|
print('Reading of bdio file started')
|
|
while 1 > 0:
|
|
record = bdio_seek_record(fbdio)
|
|
ruinfo = bdio_get_ruinfo(fbdio)
|
|
if ruinfo < 0:
|
|
# EOF reached
|
|
break
|
|
rlen = bdio_get_rlen(fbdio)
|
|
if ruinfo == 5:
|
|
d_buf = ctypes.c_double * (2 + d0 * d1 * 2)
|
|
pd_buf = d_buf()
|
|
ppd_buf = ctypes.c_void_p(ctypes.addressof(pd_buf))
|
|
iread = bdio_read_f64(ppd_buf, ctypes.c_size_t(rlen), ctypes.c_void_p(fbdio))
|
|
if corr_type[corr_no] == 'complex':
|
|
tmp_mean = np.mean(np.asarray(np.split(np.asarray(pd_buf[2 + 2 * d1:-2 * d1:2]), d0 - 2)), axis=1)
|
|
else:
|
|
tmp_mean = np.mean(np.asarray(np.split(np.asarray(pd_buf[2 + d1:-d0 * d1 - d1]), d0 - 2)), axis=1)
|
|
|
|
data[corr_no].append(tmp_mean)
|
|
corr_no += 1
|
|
else:
|
|
alt_buf = ctypes.create_string_buffer(1024)
|
|
palt_buf = ctypes.c_char_p(ctypes.addressof(alt_buf))
|
|
iread = bdio_read(palt_buf, ctypes.c_size_t(rlen), ctypes.c_void_p(fbdio))
|
|
if rlen != iread:
|
|
print('Error')
|
|
for i, item in enumerate(alt_buf):
|
|
if item == b'\x00':
|
|
alt_buf[i] = b' '
|
|
tmp_string = (alt_buf[:].decode("utf-8")).rstrip()
|
|
if ruinfo == 0:
|
|
ensemble_name = _get_kwd(tmp_string, 'ENSEMBLE=')
|
|
volume.append(int(_get_kwd(tmp_string, 'L0=')))
|
|
volume.append(int(_get_kwd(tmp_string, 'L1=')))
|
|
volume.append(int(_get_kwd(tmp_string, 'L2=')))
|
|
volume.append(int(_get_kwd(tmp_string, 'L3=')))
|
|
boundary_conditions.append(_get_kwd(tmp_string, 'BC0='))
|
|
boundary_conditions.append(_get_kwd(tmp_string, 'BC1='))
|
|
boundary_conditions.append(_get_kwd(tmp_string, 'BC2='))
|
|
boundary_conditions.append(_get_kwd(tmp_string, 'BC3='))
|
|
|
|
if ruinfo == 1:
|
|
corr_name.append(_get_corr_name(tmp_string, 'CORR_NAME='))
|
|
corr_type.append(_get_kwd(tmp_string, 'DATATYPE='))
|
|
corr_props.append([_get_kwd(tmp_string, 'PROP0='), _get_kwd(tmp_string, 'PROP1=')])
|
|
if d0 == 0:
|
|
d0 = int(_get_kwd(tmp_string, 'D0='))
|
|
else:
|
|
if d0 != int(_get_kwd(tmp_string, 'D0=')):
|
|
print('Error: Varying number of time values')
|
|
if d1 == 0:
|
|
d1 = int(_get_kwd(tmp_string, 'D1='))
|
|
else:
|
|
if d1 != int(_get_kwd(tmp_string, 'D1=')):
|
|
print('Error: Varying number of random sources')
|
|
if ruinfo == 2:
|
|
prop_kappa.append(_get_kwd(tmp_string, 'KAPPA='))
|
|
prop_source.append(_get_kwd(tmp_string, 'x0='))
|
|
if ruinfo == 4:
|
|
if 'stop' in kwargs:
|
|
if cnfg_no >= kwargs.get('stop') - 1:
|
|
break
|
|
cnfg_no += 1
|
|
print('\r%s %i' % ('Reading configuration', cnfg_no + 1), end='\r')
|
|
if cnfg_no == 0:
|
|
no_corrs = len(corr_name)
|
|
data = []
|
|
for c in range(no_corrs):
|
|
data.append([])
|
|
|
|
corr_no = 0
|
|
bdio_close(fbdio)
|
|
|
|
print('\nEnsemble: ', ensemble_name)
|
|
if 'alternative_ensemble_name' in kwargs:
|
|
ensemble_name = kwargs.get('alternative_ensemble_name')
|
|
print('Ensemble name overwritten to', ensemble_name)
|
|
print('Lattice volume: ', volume)
|
|
print('Boundary conditions: ', boundary_conditions)
|
|
print('Number of time values: ', d0)
|
|
print('Number of random sources: ', d1)
|
|
print('Number of corrs: ', len(corr_name))
|
|
print('Number of configurations: ', cnfg_no + 1)
|
|
|
|
corr_kappa = [] # Contains kappa values for both propagators of given correlation function
|
|
corr_source = []
|
|
for item in corr_props:
|
|
corr_kappa.append([float(prop_kappa[int(item[0])]), float(prop_kappa[int(item[1])])])
|
|
if prop_source[int(item[0])] != prop_source[int(item[1])]:
|
|
raise Exception('Source position do not match for correlator' + str(item))
|
|
else:
|
|
corr_source.append(int(prop_source[int(item[0])]))
|
|
|
|
result = {}
|
|
for c in range(no_corrs):
|
|
tmp_corr = []
|
|
for t in range(d0 - 2):
|
|
tmp_corr.append(Obs([np.asarray(data[c])[:, t]], [ensemble_name]))
|
|
result[(corr_name[c], corr_source[c]) + tuple(sorted(corr_kappa[c]))] = tmp_corr
|
|
|
|
# Check that all data entries have the same number of configurations
|
|
if len(set([o[0].N for o in list(result.values())])) != 1:
|
|
raise Exception('Error: Not all correlators have the same number of configurations. bdio file is possibly corrupted.')
|
|
|
|
return result
|
|
|
|
|
|
def read_dSdm(file_path, bdio_path='./libbdio.so', **kwargs):
|
|
""" Extract dSdm data from a bdio file and return it as a dictionary
|
|
|
|
The dictionary can be accessed with a tuple consisting of (type, kappa)
|
|
|
|
read_dSdm requires bdio to be compiled into a shared library. This can be achieved by
|
|
adding the flag -fPIC to CC and changing the all target to
|
|
|
|
all: bdio.o $(LIBDIR)
|
|
gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o
|
|
cp $(BUILDDIR)/libbdio.so $(LIBDIR)/
|
|
|
|
Parameters
|
|
----------
|
|
file_path -- path to the bdio file
|
|
bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)
|
|
stop -- stops reading at given configuration number (default None)
|
|
"""
|
|
bdio = ctypes.cdll.LoadLibrary(bdio_path)
|
|
|
|
bdio_open = bdio.bdio_open
|
|
bdio_open.restype = ctypes.c_void_p
|
|
|
|
bdio_close = bdio.bdio_close
|
|
bdio_close.restype = ctypes.c_int
|
|
bdio_close.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_seek_record = bdio.bdio_seek_record
|
|
bdio_seek_record.restype = ctypes.c_int
|
|
bdio_seek_record.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_get_rlen = bdio.bdio_get_rlen
|
|
bdio_get_rlen.restype = ctypes.c_int
|
|
bdio_get_rlen.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_get_ruinfo = bdio.bdio_get_ruinfo
|
|
bdio_get_ruinfo.restype = ctypes.c_int
|
|
bdio_get_ruinfo.argtypes = [ctypes.c_void_p]
|
|
|
|
bdio_read = bdio.bdio_read
|
|
bdio_read.restype = ctypes.c_size_t
|
|
bdio_read.argtypes = [ctypes.c_char_p, ctypes.c_size_t, ctypes.c_void_p]
|
|
|
|
bdio_read_f64 = bdio.bdio_read_f64
|
|
bdio_read_f64.restype = ctypes.c_size_t
|
|
bdio_read_f64.argtypes = [ctypes.c_void_p, ctypes.c_size_t, ctypes.c_void_p]
|
|
|
|
b_path = file_path.encode('utf-8')
|
|
read = 'r'
|
|
b_read = read.encode('utf-8')
|
|
form = 'Generic Correlator Format 1.0'
|
|
b_form = form.encode('utf-8')
|
|
|
|
ensemble_name = ''
|
|
volume = [] # lattice volume
|
|
boundary_conditions = []
|
|
corr_name = [] # Contains correlator names
|
|
corr_type = [] # Contains correlator data type (important for reading out numerical data)
|
|
corr_props = [] # Contains propagator types (Component of corr_kappa)
|
|
d0 = 0 # tvals
|
|
d1 = 0 # nnoise
|
|
prop_kappa = [] # Contains propagator kappas (Component of corr_kappa)
|
|
# Check noise type for multiple replica?
|
|
cnfg_no = -1
|
|
corr_no = -1
|
|
data = []
|
|
|
|
fbdio = bdio_open(ctypes.c_char_p(b_path), ctypes.c_char_p(b_read), ctypes.c_char_p(b_form))
|
|
|
|
print('Reading of bdio file started')
|
|
while 1 > 0:
|
|
record = bdio_seek_record(fbdio)
|
|
ruinfo = bdio_get_ruinfo(fbdio)
|
|
if ruinfo < 0:
|
|
# EOF reached
|
|
break
|
|
rlen = bdio_get_rlen(fbdio)
|
|
if ruinfo == 5:
|
|
d_buf = ctypes.c_double * (2 + d0)
|
|
pd_buf = d_buf()
|
|
ppd_buf = ctypes.c_void_p(ctypes.addressof(pd_buf))
|
|
iread = bdio_read_f64(ppd_buf, ctypes.c_size_t(rlen), ctypes.c_void_p(fbdio))
|
|
tmp_mean = np.mean(np.asarray(pd_buf[2:]))
|
|
|
|
data[corr_no].append(tmp_mean)
|
|
corr_no += 1
|
|
else:
|
|
alt_buf = ctypes.create_string_buffer(1024)
|
|
palt_buf = ctypes.c_char_p(ctypes.addressof(alt_buf))
|
|
iread = bdio_read(palt_buf, ctypes.c_size_t(rlen), ctypes.c_void_p(fbdio))
|
|
if rlen != iread:
|
|
print('Error')
|
|
for i, item in enumerate(alt_buf):
|
|
if item == b'\x00':
|
|
alt_buf[i] = b' '
|
|
tmp_string = (alt_buf[:].decode("utf-8")).rstrip()
|
|
if ruinfo == 0:
|
|
creator = _get_kwd(tmp_string, 'CREATOR=')
|
|
ensemble_name = _get_kwd(tmp_string, 'ENSEMBLE=')
|
|
volume.append(int(_get_kwd(tmp_string, 'L0=')))
|
|
volume.append(int(_get_kwd(tmp_string, 'L1=')))
|
|
volume.append(int(_get_kwd(tmp_string, 'L2=')))
|
|
volume.append(int(_get_kwd(tmp_string, 'L3=')))
|
|
boundary_conditions.append(_get_kwd(tmp_string, 'BC0='))
|
|
boundary_conditions.append(_get_kwd(tmp_string, 'BC1='))
|
|
boundary_conditions.append(_get_kwd(tmp_string, 'BC2='))
|
|
boundary_conditions.append(_get_kwd(tmp_string, 'BC3='))
|
|
|
|
if ruinfo == 1:
|
|
corr_name.append(_get_corr_name(tmp_string, 'CORR_NAME='))
|
|
corr_type.append(_get_kwd(tmp_string, 'DATATYPE='))
|
|
corr_props.append(_get_kwd(tmp_string, 'PROP0='))
|
|
if d0 == 0:
|
|
d0 = int(_get_kwd(tmp_string, 'D0='))
|
|
else:
|
|
if d0 != int(_get_kwd(tmp_string, 'D0=')):
|
|
print('Error: Varying number of time values')
|
|
if ruinfo == 2:
|
|
prop_kappa.append(_get_kwd(tmp_string, 'KAPPA='))
|
|
if ruinfo == 4:
|
|
if 'stop' in kwargs:
|
|
if cnfg_no >= kwargs.get('stop') - 1:
|
|
break
|
|
cnfg_no += 1
|
|
print('\r%s %i' % ('Reading configuration', cnfg_no + 1), end='\r')
|
|
if cnfg_no == 0:
|
|
no_corrs = len(corr_name)
|
|
data = []
|
|
for c in range(no_corrs):
|
|
data.append([])
|
|
|
|
corr_no = 0
|
|
bdio_close(fbdio)
|
|
|
|
print('\nCreator: ', creator)
|
|
print('Ensemble: ', ensemble_name)
|
|
print('Lattice volume: ', volume)
|
|
print('Boundary conditions: ', boundary_conditions)
|
|
print('Number of random sources: ', d0)
|
|
print('Number of corrs: ', len(corr_name))
|
|
print('Number of configurations: ', cnfg_no + 1)
|
|
|
|
corr_kappa = [] # Contains kappa values for both propagators of given correlation function
|
|
corr_source = []
|
|
for item in corr_props:
|
|
corr_kappa.append(float(prop_kappa[int(item)]))
|
|
|
|
result = {}
|
|
for c in range(no_corrs):
|
|
result[(corr_name[c], str(corr_kappa[c]))] = Obs([np.asarray(data[c])], [ensemble_name])
|
|
|
|
# Check that all data entries have the same number of configurations
|
|
if len(set([o.N for o in list(result.values())])) != 1:
|
|
raise Exception('Error: Not all correlators have the same number of configurations. bdio file is possibly corrupted.')
|
|
|
|
return result
|