def _readArray(self, fp, which, nelm, format):
#print 'Reading %d values with format %s' % (nelm, format)
fmt = FortranRecordReader(format)
ind = 0
while ind < nelm-1:
fdata = fmt.read(fp.readline())
ind2 = min(ind + len(fdata), nelm)
which[ind:ind2] = fdata[:ind2-ind]
ind = ind2
# Read last line, if any.
if ind < nelm:
fdata = fmt.read(fp.readline())
which[ind:] = fdata[:nelm-ind]
return
class FortranLineParser(object):
def __init__(self, pattern, name=None,
skip=None, strip_whitespace=True, map_values=None,
after_read_hook=None):
self._reader = FortranRecordReader(pattern)
self.name = name
self._skip = [skip] if isinstance(skip, int) else skip
self._strip_whitespace = strip_whitespace
self._map_values = map_values if isinstance(map_values, dict) else None
self._after_read_hook = after_read_hook
def __call__(self, line):
data = self._reader.read(line)
if self._skip:
skip = self._skip
data = [_ for i, _ in enumerate(data) if i not in skip]
if self._strip_whitespace:
data = [(_.strip() if isinstance(_, str) else _) for _ in data]
if self._map_values:
_map = self._map_values
data = [(_map[_] if _ in _map else _) for _ in data]
if self._after_read_hook:
data = self._after_read_hook(data)
return data
class FortranFormat(object):
"""
Processes Fortran format strings according to the Fortran specification for
such formats. This object handles reading and writing data with any valid
Fortran format. It does this by using the `fortranformat` project
[https://bitbucket.org/brendanarnold/py-fortranformat].
However, while `fortranformat` is very general and adheres well to the
standard, it is very slow. As a result, simple, common format strings have
been optimized and processes reads and writes between 3 and 5 times faster.
The format strings (case-insensitive) of the following form (where # can be
replaced by any number) are optimized:
- #E#.#
- #D#.#
- #F#.#
- #(F#.#)
- #a#
- #I#
Parameters
----------
format_string : str
The Fortran Format string to process
strip_strings : bool=True
If True, strings are stripped before being processed by stripping
(only) trailing whitespace
"""
strre = re.compile(r'(\d+)?a(\d+)$', re.I)
intre = re.compile(r'(\d+)?i(\d+)$', re.I)
floatre = re.compile(r'(\d+)?[edf](\d+)\.(\d+)$', re.I)
floatre2 = re.compile(r'(\d+)?\([edf](\d+)\.(\d+)\)$', re.I)
#===================================================
def __init__(self, format_string, strip_strings=True):
"""
Sets the format string and determines how we will read and write
strings using this format
"""
self.format = format_string
self.strip_strings = strip_strings # for ease of copying
# Define a function that processes all arguments prior to adding them to
# the returned list. By default, do nothing, but this allows us to
# optionally strip whitespace from strings.
self.process_method = lambda x: x
if FortranFormat.strre.match(format_string):
rematch = FortranFormat.strre.match(format_string)
# replace our write() method with write_string to force left-justify
self.type, self.write = str, self._write_string
nitems, itemlen = rematch.groups()
if nitems is None:
self.nitems = 1
else:
self.nitems = int(nitems)
self.itemlen = int(itemlen)
self.fmt = '%s'
# See if we want to strip the strings
if strip_strings: self.process_method = lambda x: x.strip()
elif FortranFormat.intre.match(format_string):
self.type = int
rematch = FortranFormat.intre.match(format_string)
nitems, itemlen = rematch.groups()
if nitems is None:
self.nitems = 1
else:
self.nitems = int(nitems)
self.itemlen = int(itemlen)
self.fmt = '%%%dd' % self.itemlen
elif FortranFormat.floatre.match(format_string):
self.type = float
rematch = FortranFormat.floatre.match(format_string)
nitems, itemlen, num_decimals = rematch.groups()
if nitems is None:
self.nitems = 1
else:
self.nitems = int(nitems)
self.itemlen = int(itemlen)
self.num_decimals = int(num_decimals)
if 'F' in format_string.upper():
self.fmt = '%%%s.%sF' % (self.itemlen, self.num_decimals)
else:
self.fmt = '%%%s.%sE' % (self.itemlen, self.num_decimals)
elif FortranFormat.floatre2.match(format_string):
self.type = float
rematch = FortranFormat.floatre2.match(format_string)
nitems, itemlen, num_decimals = rematch.groups()
if nitems is None:
self.nitems = 1
else:
self.nitems = int(nitems)
self.itemlen = int(itemlen)
self.num_decimals = int(num_decimals)
if 'F' in format_string.upper():
self.fmt = '%%%s.%sF' % (self.itemlen, self.num_decimals)
else:
self.fmt = '%%%s.%sE' % (self.itemlen, self.num_decimals)
else:
# We tried... now just use the fortranformat package
self._reader = FortranRecordReader(format_string)
self._writer = FortranRecordWriter(format_string)
self.write = self._write_ffwriter
self.read = self._read_ffreader
#===================================================
def __copy__(self):
return type(self)(self.format, self.strip_strings)
#===================================================
def __str__(self):
return self.format
#===================================================
def write(self, items, dest):
"""
Writes an iterable of data (or a single item) to the passed file-like
object
Parameters
----------
items : iterable or single float/str/int
These are the objects to write in this format. The types of each
item should match the type specified in this Format for that
argument
dest : file or file-like
This is the file to write the data to. It must have a `write` method
or an AttributeError will be raised
Notes
-----
This method may be replaced with _write_string (for #a#-style formats)
or _write_ffwriter in the class initializer if no optimization is
provided for this format, but the call signatures and behavior are the
same for each of those functions.
"""
if hasattr(items, '__iter__') and not isinstance(items, string_types):
mod = self.nitems - 1
for i, item in enumerate(items):
dest.write(self.fmt % item)
if i % self.nitems == mod:
dest.write('\n')
if i % self.nitems != mod:
dest.write('\n')
else:
dest.write(self.fmt % item)
dest.write('\n')
#===================================================
def _write_string(self, items, dest):
""" Writes a list/tuple of strings """
if hasattr(items, '__iter__') and not isinstance(items, string_types):
mod = self.nitems - 1
for i, item in enumerate(items):
dest.write((self.fmt % item).ljust(self.itemlen))
if i % self.nitems == mod:
dest.write('\n')
if i % self.nitems != mod:
dest.write('\n')
else:
dest.write((self.fmt % item).ljust(self.itemlen))
dest.write('\n')
#===================================================
def _read_nostrip(self, line):
"""
Reads the line and returns converted data. Special-cased for flags that
may contain 'blank' data. ugh.
"""
line = line.rstrip('\n')
nitems = int(ceil(len(line) / self.itemlen))
ret = [0 for i in range(nitems)]
start, end = 0, self.itemlen
for i in range(nitems):
ret[i] = self.process_method(self.type(line[start:end]))
start = end
end += self.itemlen
return ret
#===================================================
def read(self, line):
""" Reads the line and returns the converted data """
line = line.rstrip()
nitems = int(ceil(len(line) / self.itemlen))
ret = [0 for i in range(nitems)]
start, end = 0, self.itemlen
for i in range(nitems):
ret[i] = self.process_method(self.type(line[start:end]))
start = end
end += self.itemlen
return ret
#===================================================
def _read_ffreader(self, line):
""" Reads the line and returns the converted data """
return self._reader.read(line.rstrip())
#===================================================
def _write_ffwriter(self, items, dest):
dest.write('%s\n' % self._writer.write(items))
def _fortranRead(self, stream, format):
fmt = FortranRecordReader(format)
fdata = fmt.read(stream)
return fdata
def config_test_1(self):
'''Default RET_UNWRITTEN_VARS_NONE (True)'''
ff = FortranRecordReader('(3G10.2)')
result = ff.read(' 0 0')
self.assertEqual(result, [0.0, 0.0, None])
def config_test_5(self):
'''Custom G_INPUT_TRIAL_EDS'''
config.G_INPUT_TRIAL_EDS = ['A']
ff = FortranRecordReader('(G10.2)')
result = ff.read(' 0')
self.assertEqual(result, [' 0'])
def config_test_4(self):
'''Default G_INPUT_TRIAL_EDS'''
ff = FortranRecordReader('(G10.2)')
result = ff.read(' STR')
self.assertEqual(result, [' STR'])
def import_qeinput(fname):
"""
This function imports a AiiDA structure from a Quantum ESPRESSO
input file.
:param fname: the file name that should be read
"""
import aiida.orm.data.structure as struct
bohr = 0.52917720859
one_over_bohr = 1.0 / bohr
cell_types = ["alat", "bohr", "angstrom"]
pos_types = ["alat", "bohr", "angstrom", "crystal"]
def generate_cell(ibrav, parameters):
cellAlat = np.zeros((3, 3))
if ibrav == 1:
cellAlat[0][0] = 1
cellAlat[0][1] = 0
cellAlat[0][2] = 0
cellAlat[1][0] = 0
cellAlat[1][1] = 1
cellAlat[1][2] = 0
cellAlat[2][0] = 0
cellAlat[2][1] = 0
cellAlat[2][2] = 1
elif ibrav == 2:
cellAlat[0][0] = -0.5
cellAlat[0][1] = 0
cellAlat[0][2] = 0.5
cellAlat[1][0] = 0
cellAlat[1][1] = 0.5
cellAlat[1][2] = 0.5
cellAlat[2][0] = -0.5
cellAlat[2][1] = 0.5
cellAlat[2][2] = 0
elif ibrav == 3:
cellAlat[0][0] = 0.5
cellAlat[0][1] = 0.5
cellAlat[0][2] = 0.5
cellAlat[1][0] = -0.5
cellAlat[1][1] = 0.5
cellAlat[1][2] = 0.5
cellAlat[2][0] = -0.5
cellAlat[2][1] = -0.5
cellAlat[2][2] = 0.5
elif ibrav == 4:
cellAlat[0][0] = 1
cellAlat[0][1] = 0
cellAlat[0][2] = 0
cellAlat[1][0] = -0.5
cellAlat[1][1] = np.sqrt(3) / 2
cellAlat[1][2] = 0
cellAlat[2][0] = 0
cellAlat[2][1] = 0
cellAlat[2][2] = parameters[2]
elif ibrav == 5:
tx = np.sqrt((1 - parameters[3]) / 2)
ty = np.sqrt((1 - parameters[3]) / 6)
tz = np.sqrt((1 + 2 * parameters[3]) / 3)
cellAlat[0][0] = tx
cellAlat[0][1] = -ty
cellAlat[0][2] = tz
cellAlat[1][0] = 0
cellAlat[1][1] = 2 * ty
cellAlat[1][2] = tz
cellAlat[2][0] = -tx
cellAlat[2][1] = -ty
cellAlat[2][2] = tz
elif ibrav == -5:
tx = np.sqrt((1 - parameters[3]) / 2)
ty = np.sqrt((1 - parameters[3]) / 6)
tz = np.sqrt((1 + 2 * parameters[3]) / 3)
u = tz - 2.0 * np.sqrt(2.0) * ty
v = tz + np.sqrt(2.0) * ty
a1 = 1 / np.sqrt(3.0)
cellAlat[0][0] = a1 * u
cellAlat[0][1] = a1 * v
cellAlat[0][2] = a1 * v
cellAlat[1][0] = a1 * v
cellAlat[1][1] = a1 * u
cellAlat[1][2] = a1 * v
cellAlat[2][0] = a1 * v
cellAlat[2][1] = a1 * v
cellAlat[2][2] = a1 * u
elif ibrav == 6:
cellAlat[0][0] = 1
cellAlat[0][1] = 0
cellAlat[0][2] = 0
cellAlat[1][0] = 0
cellAlat[1][1] = 1
cellAlat[1][2] = 0
cellAlat[2][0] = 0
cellAlat[2][1] = 0
cellAlat[2][2] = parameters[2]
elif ibrav == 7:
cellAlat[0][0] = 0.5
cellAlat[0][1] = -0.5
cellAlat[0][2] = parameters[2] / 2
cellAlat[1][0] = 0.5
cellAlat[1][1] = 0.5
cellAlat[1][2] = parameters[2] / 2
cellAlat[2][0] = -0.5
cellAlat[2][1] = -0.5
cellAlat[2][2] = parameters[2] / 2
elif ibrav == 8:
cellAlat[0][0] = 1
cellAlat[0][1] = 0
cellAlat[0][2] = 0
cellAlat[1][0] = 0
cellAlat[1][1] = parameters[1]
cellAlat[1][2] = 0
cellAlat[2][0] = 0
cellAlat[2][1] = 0
cellAlat[2][2] = parameters[2]
elif ibrav == 9:
cellAlat[0][0] = 0.5
cellAlat[0][1] = parameters[1] / 2
cellAlat[0][2] = 0
cellAlat[1][0] = -0.5
cellAlat[1][1] = parameters[1] / 2
cellAlat[1][2] = 0
cellAlat[2][0] = 0
cellAlat[2][1] = 0
cellAlat[2][2] = parameters[1]
elif ibrav == -9:
cellAlat[0][0] = 0.5
cellAlat[0][1] = -parameters[1] / 2
cellAlat[0][2] = 0
cellAlat[1][0] = 0.5
cellAlat[1][1] = -parameters[1] / 2
cellAlat[1][2] = 0
cellAlat[2][0] = 0
cellAlat[2][1] = 0
cellAlat[2][2] = parameters[1]
elif ibrav == 10:
cellAlat[0][0] = 0.5
cellAlat[0][1] = 0
cellAlat[0][2] = parameters[2] / 2
cellAlat[1][0] = 0.5
cellAlat[1][1] = parameters[1] / 2
cellAlat[1][2] = 0
cellAlat[2][0] = 0
cellAlat[2][1] = parameters[1] / 2
cellAlat[2][2] = parameters[1] / 2
elif ibrav == 11:
cellAlat[0][0] = 0.5
cellAlat[0][1] = parameters[1] / 2
cellAlat[0][2] = parameters[2] / 2
cellAlat[1][0] = -0.5
cellAlat[1][1] = parameters[1] / 2
cellAlat[1][2] = parameters[2] / 2
cellAlat[2][0] = -0.5
cellAlat[2][1] = -parameters[1] / 2
cellAlat[2][2] = parameters[2] / 2
elif ibrav == 12:
gamma = np.arccos(parameters[3])
cellAlat[0][0] = 1
cellAlat[0][1] = 0
cellAlat[0][2] = 0
cellAlat[1][0] = parameters[1] * np.cos(gamma)
cellAlat[1][1] = parameters[1] * np.sin(gamma)
cellAlat[1][2] = 0
cellAlat[2][0] = 0
cellAlat[2][1] = 0
cellAlat[2][2] = parameters[2]
elif ibrav == -12:
beta = np.arccos(parameters[4])
cellAlat[0][0] = 1
cellAlat[0][1] = 0
cellAlat[0][2] = 0
cellAlat[1][0] = 0
cellAlat[1][1] = parameters[1]
cellAlat[1][2] = 0
cellAlat[2][0] = parameters[2] * np.sin(beta)
cellAlat[2][1] = 0
cellAlat[2][2] = parameters[2] * np.cos(beta)
elif ibrav == 13:
gamma = np.arccos(parameters[3])
cellAlat[0][0] = 0.5
cellAlat[0][1] = 0
cellAlat[0][2] = -parameters[2] / 2
cellAlat[1][0] = parameters[1] * np.cos(gamma)
cellAlat[1][1] = parameters[1] * np.sin(gamma)
cellAlat[1][2] = 0
cellAlat[2][0] = 0.5
cellAlat[2][1] = 0
cellAlat[2][2] = parameters[2] / 2
elif ibrav == 14:
alpha = np.arccos(parameters[3])
beta = np.arccos(parameters[4])
gamma = np.arccos(parameters[5])
cellAlat[0][0] = 1
cellAlat[0][1] = 0
cellAlat[0][2] = 0
cellAlat[1][0] = parameters[1] * np.cos(gamma)
cellAlat[1][1] = parameters[1] * np.sin(gamma)
cellAlat[1][2] = 0
cellAlat[2][0] = parameters[2] * np.cos(beta)
cellAlat[2][1] = parameters[2] * (
np.cos(alpha) - np.cos(beta) * np.cos(gamma)) / (np.sin(gamma))
cellAlat[2][2] = parameters[2] * np.sqrt(
1 + 2 * np.cos(alpha) * np.cos(beta) * np.cos(gamma) -
(np.cos(beta) * np.cos(beta)) -
(np.cos(alpha) * np.cos(alpha)) -
(np.cos(gamma) * np.cos(gamma))) / (np.sin(gamma))
else:
raise Exception("ibrav [{0}] is not defined !".format(ibrav))
cell_angstrom = cellAlat * parameters[0] * bohr
return cell_angstrom
def get_pos(pos, coord_type, alat, cell):
if coord_type == pos_types[0]: return np.array(pos) * alat * bohr
if coord_type == pos_types[1]: return np.array(pos) * alat
if coord_type == pos_types[3]:
return np.dot(np.array(pos), np.array(cell))
return pos
def get_num_from_name(name):
"""
Return the atomic number given a symbol string, or return zero if
the symbol is not recognized
"""
from aiida.orm.data.structure import _atomic_numbers
return _atomic_numbers.get(name, 0)
def get_name_from_num(num):
"""
Return the atomic symbol given an atomic number (if num=0, return "X")
:raise ValueError: if the number is not valid
"""
from aiida.common.constants import elements
try:
return elements[num]['symbol']
except (IndexError, TypeError):
raise ValueError("'{}' is not a valid atomic number".format(num))
def sanitize(line_raw, sec=None):
if sec is not None:
return line_raw.split("!")[0].split(sec)[0]
else:
return line_raw.split("!")[0]
import re
import numpy as np
from fortranformat import FortranRecordReader
nat = 0
ntyp = 0
ibrav = 0
celldm = None
a = None
b = None
c = None
cosab = None
cosac = None
cosbc = None
cell = None
atomic_raw_kinds = None
atomic_kinds = None
atomic_kindnames = None
atomic_pos = None
atomic_masses_table = None
#group(3)
nat_search = re.compile(
r'(?:^|[^A-Za-z0-9_])nat([\t ]+)?=([\t ]+)?([0-9]+)', re.IGNORECASE)
ntyp_search = re.compile(
r'(?:^|[^A-Za-z0-9_])ntyp([\t ]+)?=([\t ]+)?([0-9]+)', re.IGNORECASE)
ibrav_search = re.compile(
r'(?:^|[^A-Za-z0-9_])ibrav([\t ]+)?=([\t ]+)?(-?[0-9]+)',
re.IGNORECASE)
celldm_search = re.compile(
r'(?:^|[^A-Za-z0-9_])celldm([\t ]+)?\(([\t ]+)?([0-9]+)([\t ]+)?\)([\t ]+)?=([\t ]+)?([0-9\.DdeE-]*)',
re.IGNORECASE)
a_search = re.compile(r'(?:^|[^A-Za-z0-9_])a([\t ]+)?=([\t ]+)?(-?[0-9]+)',
re.IGNORECASE)
b_search = re.compile(r'(?:^|[^A-Za-z0-9_])b([\t ]+)?=([\t ]+)?(-?[0-9]+)',
re.IGNORECASE)
c_search = re.compile(r'(?:^|[^A-Za-z0-9_])c([\t ]+)?=([\t ]+)?(-?[0-9]+)',
re.IGNORECASE)
cosab_search = re.compile(
r'(?:^|[^A-Za-z0-9_])cosab([\t ]+)?=([\t ]+)?(-?[0-9]+)',
re.IGNORECASE)
cosac_search = re.compile(
r'(?:^|[^A-Za-z0-9_])cosac([\t ]+)?=([\t ]+)?(-?[0-9]+)',
re.IGNORECASE)
cosbc_search = re.compile(
r'(?:^|[^A-Za-z0-9_])cosbc([\t ]+)?=([\t ]+)?(-?[0-9]+)',
re.IGNORECASE)
atomic_species = re.compile(r'ATOMIC_SPECIES', re.IGNORECASE)
atomic_position = re.compile(r'ATOMIC_POSITIONS', re.IGNORECASE)
cell_parameters = re.compile(r'CELL_PARAMETERS', re.IGNORECASE)
#group(3) e group(7)
ff_float = FortranRecordReader('F15.9')
f = open(fname, "rw+")
line = sanitize(f.readline())
while line:
if nat_search.search(line): nat = int(nat_search.search(line).group(3))
if ntyp_search.search(line):
ntyp = int(ntyp_search.search(line).group(3))
if ibrav_search.search(line):
ibrav = int(ibrav_search.search(line).group(3))
if celldm_search.search(line) and cell is None:
if celldm is None: celldm = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
for c in celldm_search.findall(line):
celldm[int(c[2]) - 1] = ff_float.read(c[6])[0]
if a_search.search(line): a = float(a_search.search(line).group(3))
if b_search.search(line): b = float(b_search.search(line).group(3))
if c_search.search(line): c = float(c_search.search(line).group(3))
if cosab_search.search(line):
cosab = float(cosab_search.search(line).group(3))
if cosac_search.search(line):
cosac = float(cosac_search.search(line).group(3))
if cosbc_search.search(line):
cosbc = float(cosbc_search.search(line).group(3))
if cell_parameters.search(
line) and nat > 0 and ibrav == 0 and cell is None:
if celldm is not None and a is not None:
raise Exception(
"Cannot declare both celldm and A, B, C, cosAB, cosAC, cosBC (a={}, celldm={})"
.format(a, celldm))
if a is not None:
alat = a
else:
if celldm is None:
celldm = [one_over_bohr, 0.0, 0.0, 0.0, 0.0, 0.0]
alat = celldm[0]
cell_type = cell_types[0] #Alat
for ct in cell_types:
if ct in line.lower(): cell_type = ct
cell = np.zeros((3, 3))
cell_ax = 0
while cell_ax < 3:
line = sanitize(f.readline())
while (line.strip() == ""
or line.strip().startswith("!")) == "":
line = sanitize(f.readline(), sec="#")
cell_ax_val = np.array(
[ff_float.read(p)[0] for p in line.strip().split()])
if cell_type == cell_types[0]: cell_ax_val *= alat * bohr
if cell_type == cell_types[1]: cell_ax_val *= alat
cell[cell_ax] = cell_ax_val
cell_ax += 1
if atomic_species.search(line) and ntyp > 0:
atomic_raw_kinds = [None] * ntyp
atomic_kinds = [None] * ntyp
atomic_masses_table = {}
type_count = 0
while type_count < ntyp:
line = sanitize(f.readline())
while (line.strip() == "" or line.strip().startswith("!")):
line = sanitize(f.readline(), sec="#")
p = line.strip().split()
raw = {
'symbols': p[0],
'weights': 1.0,
'name': p[0],
'mass': float(p[1])
}
_n = get_num_from_name(p[0])
atomic_masses_table[_n] = float(p[1])
atomic_raw_kinds[type_count] = raw
atomic_kinds[type_count] = struct.Kind(symbols=p[0],
weights=1.0,
name=p[0],
mass=float(p[1]))
type_count += 1
if atomic_position.search(line) and nat > 0:
pos_type = "alat"
for pt in pos_types:
if pt in line.lower(): pos_type = pt
atomic_pos = [[0] * 3] * nat
atomic_kindnames = [0] * nat
pos_count = 0
while pos_count < nat:
line = sanitize(f.readline())
while (line.strip() == "" or line.strip().startswith("!")):
line = sanitize(f.readline(), sec="#")
p = line.strip().split()
atomic_kindnames[pos_count] = p[0]
atomic_pos[pos_count] = [
ff_float.read(p[i])[0] for i in range(1, 4)
]
pos_count += 1
line = sanitize(f.readline())
# Cell generation
if celldm is not None and a is not None:
raise Exception(
"Cannot declare both celldm and A, B, C, cosAB, cosAC, cosBC (a={}, celldm={})"
.format(a, celldm))
if a is not None and \
b is not None and \
c is not None and \
cosbc is not None and \
cosac is not None and \
cosbc is not None and \
cell is None:
celldm = [a, b / a, c / a, cosab, cosac, cosbc, 0.0]
cell = generate_cell(ibrav, celldm)
if celldm is not None and ibrav > 0 and cell is None:
cell = generate_cell(ibrav, celldm)
# Positions generation
for i in range(len(atomic_pos)):
atomic_pos[i] = get_pos(atomic_pos[i], pos_type, celldm[0], cell)
the_struc = struct.StructureData(cell=cell, pbc=True)
for k in atomic_kinds:
the_struc.append_kind(k)
sites = zip(atomic_kindnames, atomic_pos)
for kindname, pos in sites:
the_struc.append_site(struct.Site(kind_name=kindname, position=pos))
return the_struc
def config_test_3(self):
'''RET_WRITTEN_VARS_ONLY = False'''
config.RET_WRITTEN_VARS_ONLY = False
ff = FortranRecordReader('(3G10.2)')
result = ff.read(' 0 0')
self.assertEqual(result, [0.0, 0.0, None])
class DataCard:
""" Class to implement a line of generalized ATP/Fortran style input records
format is a format string suitable for the fortranformat module.
fields is a list of field names for indexing the data dict. Field names
will usually be strings, but could be integers or floats in the
case of matching fixed_fields.
fixed_fields is an iterable of field indices that have fixed values.
The expected value for the field should be the field name in the
fields list.
post_read_hook is an optional parameter indicating a function to be
called after reading lines into the DataCard.
Data in the line is internally represented using a dict.
format and fields should not be changed after initialization.
Reads only one line, but should be passed an interable of lines.
"""
def __init__(self, format, fields, fixed_fields=(), name=None,
post_read_hook=None):
self._fields = fields
self._fixed_fields = tuple(fixed_fields)
self._reader = FortranRecordReader(format)
self._writer = FortranRecordWriter(format)
self.name = name
self.post_read_hook = post_read_hook
self.data = {}
for f in fields:
if f is not None:
self.data[f] = None
def read(self, lines):
""" Read in datalines with validation prior to populating data. """
if not self.match(lines):
# This should raise an exception and will help
# identify where in the stack the exception occured.
tmp = copy.deepcopy(self)
tmp._read(lines)
self._read(lines)
def _read(self, lines):
line = lines[0]
data = self._reader.read(line)
for f in self._fixed_fields:
if data[f] != self._fields[f]:
raise ValueError('Fixed field with wrong value: ' + data[f] +
'/' + self._fields[f])
for f, d in zip(self._fields, data):
if f is not None:
self.data[f] = d
if self.post_read_hook is not None:
self.post_read_hook(self)
return self
def write(self):
data = [self.data[f] if f is not None else None for f in self._fields]
return self._writer.write(data)
def match(self, lines):
""" Checks if text lines match record type. Does not modify card data.
"""
tmp = copy.deepcopy(self)
try:
tmp._read(lines)
except ValueError:
return False
return True
def num_lines(self):
return 1
def processsolar():
solarfile = '/var/lib/odindata/' + 'sw.txt'
solar = open(solarfile, 'r')
line = solar.readline(-1)
while line != "BEGIN OBSERVED\n":
line = solar.readline(-1)
res = FortranRecordReader(
'I4,I3,I3,I5,I3,8I3,I4,8I4,I4,F4.1,I2,I4,F6.1,I2,5F6.1')
solardata = []
line = solar.readline(-1)
while line != "END OBSERVED\n":
solardata.append(res.read(line))
line = solar.readline(-1)
solardata = np.array(solardata)
dates = []
for i in range(solardata.shape[0]):
dates.append(
DT.date(
solardata[i, 0].astype(int),
solardata[i, 1].astype(int),
solardata[i, 2].astype(int),
), )
# solardata 13=Kpsum 22=APavg 26=f10.7
while line != "BEGIN DAILY_PREDICTED\n":
line = solar.readline(-1)
solardatapred = []
line = solar.readline(-1)
while line != "END DAILY_PREDICTED\n":
solardatapred.append(res.read(line))
line = solar.readline(-1)
while line != "BEGIN MONTHLY_PREDICTED\n":
line = solar.readline(-1)
line = solar.readline(-1)
while line != "END MONTHLY_PREDICTED\n":
solardatapred.append(res.read(line))
line = solar.readline(-1)
solardatapred = np.array(solardatapred)
datespred = []
for i in range(solardatapred.shape[0]):
datespred.append(
DT.date(
solardatapred[i, 0].astype(int),
solardatapred[i, 1].astype(int),
solardatapred[i, 2].astype(int),
))
solar.close()
dbfile = '/var/lib/odindata/' + 'Solardata2.db'
db = sqlite.connect(dbfile)
cur = db.cursor()
# cur.execute('create table solardata (ID BIGINT, yy shortint, mm shortint,
# dd shortint, BSRN shortint, ND shortint, Kp1 shortint, Kp2 shortint,
# Kp3 shortint, Kp4 shortint, Kp5 shortint, Kp6 shortint, Kp7 short int,
# Kp8 shortint, KpSum shortint, Ap1 shortint, Ap2 shortint,
# Ap3 shortint, Ap4 shortint, Ap5 shortint, Ap6 shortint,
# Ap7 shortint, Ap8 shortint, ApAvg shortint, Cp float, C9 shortint,
# ISN Integer, AdjF10_7 float, Q shortint, AdjCtr81 float,
# AdjLst81 float, ObsF10_7 float, ObsCtr81 float, ObsLst81 float )')
instr = 'insert or replace into solardata values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )' # noqa
for i in range(solardata.shape[0]):
ids = (solardata[i, 0].astype(int) * 10000 +
solardata[i, 1].astype(int) * 100 + solardata[i, 2].astype(int))
cur.execute(instr, np.r_[ids, solardata[i, :]])
# cur.execute('create table solardatapred (ID BIGINT, pred_date bigint,
# yy shortint, mm shortint, dd shortint, BSRN shortint, ND shortint,
# Kp1 shortint, Kp2 shortint, Kp3 shortint, Kp4 shortint, Kp5 shortint
# Kp6 shortint, Kp7 short int, Kp8 shortint, KpSum shortint, Ap1 shortint,
# Ap2 shortint, Ap3 shortint, Ap4 shortint, Ap5 shortint, Ap6 shortint,
# Ap7 shortint, Ap8 shortint, ApAvg shortint, Cp float, C9 shortint,
# ISN Integer, AdjF10_7 float, Q shortint, AdjCtr81 float,
# AdjLst81 float, ObsF10_7 float, ObsCtr81 float, ObsLst81 float )')
instr = 'insert or replace into solardatapred values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )' # noqa
idp = ids
for i in range(solardatapred.shape[0]):
ids = (idp * 100000000 + solardatapred[i, 0].astype(int) * 10000 +
solardatapred[i, 1].astype(int) * 100 +
solardatapred[i, 2].astype(int))
cur.execute(instr, np.r_[ids, idp, solardatapred[i, :]])
db.commit()
db.close()