def write_to_file(self, output_fn, molecule, write_coords_in_bohr=True):
# Numeric formats specified in resp input specification
# http://upjv.q4md-forcefieldtools.org/RED/resp/#other3
header_format = FortranRecordWriter('2I5')
atoms_format = FortranRecordWriter('17X,3E16.7')
esp_points_format = FortranRecordWriter('1X,4E16.7')
with open(output_fn, 'x') as f:
f.write(
header_format.write([len(molecule),
len(self.points)]) + "\n")
for atom in molecule:
if write_coords_in_bohr:
coords = [
atom_coord / angstrom_per_bohr
for atom_coord in atom.coords
]
else:
coords = atom.coords
f.write(atoms_format.write(coords) + "\n")
for point_coords, esp_val in zip(self.points, self.values):
if write_coords_in_bohr:
point_coords = [
point_coord / angstrom_per_bohr
for point_coord in point_coords
]
f.write(
esp_points_format.write([esp_val] + point_coords) + "\n")
def default_hitran(ExoCrossline):
"""
Function formats line into default HITRAN format
:param line: input line from file that comes from ExoMol to HITRAN format (ExoCross)
:return: line in HITRAN format
"""
# Following lines get parameters
molecule_id, iso_id = get_id(ExoCrossline)
frequency = get_freq_exo(ExoCrossline)
intensity = get_intensity(ExoCrossline)
einstein_coeff = get_einstein_coeff(ExoCrossline)
broadening_air, broadeing_self = get_broadening(ExoCrossline)
energy = get_energy_exo(ExoCrossline)
n_air = get_n_air(ExoCrossline)
delta_air = get_delta_air(ExoCrossline)
global_upper, global_lower = get_global_qn(ExoCrossline)
local_upper, local_lower = get_local_qn(ExoCrossline)
branch = get_branch_exo(ExoCrossline)
upper_parity, lower_parity = get_parity_exo(ExoCrossline)
error_indices1, error_indices2, error_indices3, error_indices4, error_indices5, error_indices6 = set_error(
)
ref1, ref2, ref3, ref4, ref5, ref6 = set_ref()
g_upper, g_lower = get_g(ExoCrossline)
test1 = ' '
test2 = ' '
line_mixing_flag = ' '
newline = FortranRecordWriter(
'(I2,I1,F12.6,E10.3,E10.3,F5.4,F5.3,F10.4,F4.2,F8.6,A15,A15,10X,A5,5X,A1,I3,A1,A5,6I1,6I2,A1,F7.1,F7.1)'
)
line1 = molecule_id, iso_id, frequency, intensity, einstein_coeff, broadening_air, broadeing_self, energy, n_air,\
delta_air, global_upper,global_lower,test1,branch,local_lower,lower_parity,test2,error_indices1, error_indices2,\
error_indices3, error_indices4, error_indices5, error_indices6,ref1, ref2, ref3, ref4,\
ref5, ref6, line_mixing_flag, g_upper,g_lower
# #
string1 = str(newline.write(line1))
new_string = string1 + '\n'
return new_string
def config_test_1(self):
'''Set config after-creation of format'''
ff = FortranRecordWriter('(2I10)')
result = ff.write([0, 0, 0, 0])
self.assertEqual(result, ' 0 0\n 0 0')
config.RECORD_SEPARATOR = '|'
result = ff.write([0, 0, 0, 0])
self.assertEqual(result, ' 0 0| 0 0')
def _write_modified_respin(respin_type, molecule, ivary_list, charge, iuniq,
fn_out, read_input_charges):
with open(fn_out, 'w') as out:
out.write(_get_respin_content(respin_type, read_input_charges))
numbers = FortranRecordWriter('2I5')
# `charge, iuniq` line
print(numbers.write([charge, iuniq]), file=out)
for atom, ivary in zip(molecule, ivary_list):
print(numbers.write([atom.atomic_no, ivary]), file=out)
print(file=out)
def _read_top(self, fn, f, line):
top_line_format_in_esp = FortranRecordWriter('2I5')
if line == " ESP FILE - ATOMIC UNITS":
return 'Gaussian'
try:
_a, _b = line.split()
except ValueError:
self.raiseInputFormatError(fn)
if line == top_line_format_in_esp.write([int(_a), int(_b)]):
return 'repESP'
else:
self.raiseInputFormatError(fn)
def fort_write(fobj, formatstr, values, debug=False):
vals = list(flatten(values))
vals = [v for v in vals if v is not None]
if debug:
print('--- writing ---')
try:
print('file: ' + fobj.name)
except AttributeError:
print('file: console')
print('fmt: ' + formatstr)
print('values: ')
print(vals)
frw = FortranRecordWriter(formatstr)
line = frw.write(vals)
if fobj is None:
print(line)
else:
fobj.write(line + '\n')
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 fortranWriteLine(data, stream, fformat):
"Write `data` to `stream` according to Fortran format `fformat`."
fmt = FortranRecordWriter(fformat)
stream.write(fmt.write(data))
stream.write('\n')
return
def config_test_2(self):
'''RECORD_SEPARATOR = |'''
config.RECORD_SEPARATOR = '|'
result = FortranRecordWriter('(2I10)').write([0, 0, 0, 0])
self.assertEqual(result, ' 0 0| 0 0')
def config_test_1(self):
'''Default RECORD_SEPARATOR ('\n')'''
ff = FortranRecordWriter('(2I10)')
result = ff.write([0, 0, 0, 0])
self.assertEqual(result, ' 0 0\n 0 0')
def reversion_output_test_4(self):
line = FortranRecordWriter("('[', 3F4.1, ']')")
result = """[ 1.0 1.0 1.0]
[ 1.0 1.0 1.0]"""
self.assertEqual(line.write([1.0, 1.0, 1.0, 1.0, 1.0, 1.0]), result)
def dump_charges_to_qout(molecule, charge_type, filename):
line = FortranRecordWriter("8F10.6")
charges = [atom.charges[charge_type] for atom in molecule]
with open(filename, 'w') as f:
print(line.write(charges), file=f)
emis7 = 0
emis8 = df_emissions.ix[idx, 'ETHYLBENZEN ']
emis9 = df_emissions.ix[idx, 'FORMALDEHYD ']
emis10 = df_emissions.ix[idx, 'LEAD ']
emis11 = df_emissions.ix[idx, 'MANGANESE']
emis12 = df_emissions.ix[idx, 'NAPHTHALENE']
emis13 = df_emissions.ix[idx, ' NH3 ']
emis14 = df_emissions.ix[idx, 'NOX ']
emis15 = df_emissions.ix[idx, 'PAH']
emis16 = df_emissions.ix[idx, ' PM10']
emis17 = df_emissions.ix[idx, ' PM2_5 ']
emis18 = df_emissions.ix[idx, 'SO2']
emis19 = df_emissions.ix[idx, ' TOLUENE ']
emis20 = df_emissions.ix[idx, 'VOC']
emis21 = df_emissions.ix[idx, ' XYLENE']
line = FortranRecordWriter('(I2, A3, A15, 41X, A40, A10, 8X, I4, F6.2, I4, 10X, F9.2, 74X, I4, F9.5, F9.5, 1X, 20(E13.7, 39X), E13.7, 39X)')
# line = FortranRecordWriter('(I2, A3, A15, 81X, A10, 8X, I4, F6.2, I4, 10X, F9.2, 74X, I4, F9.5, F9.5, 1X, E13.7, 39X, E13.7, 39X,E13.7, 39X, E13.7, 39X, E13.7, 39X,E13.7, 39X, E13.7, 39X,E13.7, 39X,E13.7, 39X, E13.7, 39X,E13.7, 39X,E13.7, 39X, E13.7, 39X,E13.7, 39X,E13.7, 39X, E13.7, 39X,E13.7, 39X,E13.7, 39X, E13.7, 39X,E13.7, 39X,E13.7, 39X, E13.7, 39X,E13.7, 39X,E13.7, 39X, E13.7, 39X,E13.7, 39X,E13.7, 39X, E13.7, 39X,E13.7, 39X,E13.7, 39X, E13.7, 39X,E13.7, 39X)\n')
lineOut = line.write([int(state_id), county_id, plant_id, plant_nm, scc_code, stkHeight, stkDia, stkGasTmp, stkGasVel, sic_code,\
latitude, longitude, emis1, emis2, emis3, emis4, emis5, emis6, emis7, emis8, emis9, emis10, emis11, \
emis12, emis13, emis14, emis15, emis16, emis17, emis18, emis19, emis20, emis21])
lineOut = lineOut + ' '*39 + '\n'
outFile.write(lineOut)
outFile.close()
#%%
outputFile = "C:/Users/vik/Documents/Projects/NARA/NARA_files_4_Biorefinery/pt_NARA_biorefinery_2xEmis_tpy.txt"
outFile = open(outputFile, 'w')
lineOut = '%s\n'*6%("#IDA",
"#TYPE Point Source Inventory",
"#COUNTRY US",
"#YEAR 2011",
"#DESC NARA Biorefinery Point Source Inventory with twice original emissions",