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t2data.py
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t2data.py
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"""Class for TOUGH2 data.
Copyright 2011 University of Auckland.
This file is part of PyTOUGH.
PyTOUGH is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
PyTOUGH is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with PyTOUGH. If not, see <http://www.gnu.org/licenses/>."""
from __future__ import print_function
import sys
from fixed_format_file import *
from t2grids import *
from t2incons import *
from math import ceil
import struct
from os.path import splitext
def primary_to_region_we(primary):
"""Returns thermodynamic region deduced from primary variables for EOS we."""
from t2thermo import region
if primary[1] < 1.: return 4
else: return region(primary[1], primary[0])
def primary_to_region_wge(primary):
"""Returns thermodynamic region deduced from primary variables for wge
(NCG) EOS (wce, wae)."""
pwater = primary[0] - primary[2]
return primary_to_region_we([pwater, primary[1]])
primary_to_region_funcs = {'w': primary_to_region_we, 'we': primary_to_region_we,
'wce': primary_to_region_wge, 'wae': primary_to_region_wge}
waiwera_eos_num_primary = {'w': 1, 'we': 2, 'wce': 3, 'wae': 3}
def trim_trailing_nones(vals):
"""Trim trailing None values from a list."""
while vals and vals[-1] is None:
vals.pop()
return vals
t2data_format_specification = {
'title': [['title'], ['80s']],
'simulator': [['simulator'], ['80s']],
'rocks1': [['name', 'nad', 'density', 'porosity',
'k1', 'k2', 'k3', 'conductivity', 'specific_heat'],
['5s', '5d'] + ['10.4e'] * 7],
'rocks1.1': [['compressibility', 'expansivity', 'dry_conductivity',
'tortuosity', 'klinkenberg', 'xkd3', 'xkd4'],
['10.4e'] * 7],
'rocks1.2': [['type', ''] + ['parameter'] * 7, ['5d', '5x'] + ['10.3e'] * 7],
'rocks1.3': [['type', ''] + ['parameter'] * 7, ['5d', '5x'] + ['10.3e'] * 7],
'param1_autough2': [['max_iterations', 'print_level', 'max_timesteps',
'max_duration', 'print_interval',
'_option_str', 'diff0', 'texp', 'be'],
['2d'] * 2 + ['4d'] * 3 + ['24s'] + ['10.3e'] * 3],
'param1': [['max_iterations', 'print_level', 'max_timesteps',
'max_duration', 'print_interval', '_option_str', 'texp', 'be'],
['2d'] * 2 + ['4d'] * 3 + ['24s'] + ['10.3e'] * 2],
'param2': [['tstart', 'tstop', 'const_timestep', 'max_timestep',
'print_block', '', 'gravity', 'timestep_reduction', 'scale'],
['10.3e'] * 4 + ['5s', '5x'] + ['10.4e'] * 3],
'param3': [['relative_error', 'absolute_error', 'pivot', 'upstream_weight',
'newton_weight', 'derivative_increment'],
['10.4e'] * 6],
'_more_option_str': [['_more_option_str'], ['21s']],
'timestep': [['timestep'] * 8, ['10.4e'] * 8],
'multi': [['num_components', 'num_equations', 'num_phases',
'num_secondary_parameters', 'num_inc'], ['5d'] * 5],
'multi_autough2': [['num_components', 'num_equations', 'num_phases',
'num_secondary_parameters', 'eos'], ['5d'] * 4 + ['4s']],
'lineq': [['type', 'epsilon', 'max_iterations', 'gauss', 'num_orthog'],
['2d', '10.4e', '4d', '1d', '4d']],
'default_incons': [['incon'] * 4, ['20.14e'] * 4],
'output_times1': [['num_times_specified', 'num_times', 'max_timestep', 'time_increment'],
['5d'] * 2 + ['10.4e'] * 2],
'output_times2': [['time'] * 8, ['10.4e'] * 8],
'relative_permeability': [['type', ''] + ['parameter'] * 7, ['5d', '5x'] + ['10.3e'] * 7],
'capillarity': [['type', ''] + ['parameter'] * 7, ['5d', '5x'] + ['10.3e'] * 7],
'blocks': [['name', 'nseq', 'nadd', 'rocktype', 'volume',
'ahtx', 'pmx', 'x', 'y', 'z'],
['5s', '5d', '5d', '5s'] + ['10.4e'] * 3 + ['10.3e'] * 3],
'connections': [['block1', 'block2', 'nseq', 'nad1', 'nad2',
'direction', 'distance1', 'distance2', 'area', 'dircos', 'sigma'],
['5s'] * 2 + ['5d'] * 4 + ['10.4e'] * 3 + ['10.7f', '10.3e']],
'generator': [['block', 'name', 'nseq', 'nadd', 'nads', 'ltab',
'', 'type', 'itab', 'gx', 'ex', 'hg', 'fg'],
['5s'] * 2 + ['5d'] * 3 + ['5d', '5x', '4s', '1s'] + ['10.3e'] * 4],
'generation_times': [['time'] * 4, ['14.7e'] * 4],
'generation_rates': [['rate'] * 4, ['14.7e'] * 4],
'generation_enthalpy': [['enthalpy'] * 4, ['14.7e'] * 4],
'short': [['', 'frequency'], ['5x', '2d']],
'incon1': [['block', 'nseq', 'nadd', 'porosity'], ['5s'] + ['5d'] * 2 + ['15.9e']],
'incon2': [['incon'] * 4, ['20.14e'] * 4],
'solver': [['type', '', 'z_precond', '', 'o_precond', 'relative_max_iterations', 'closure'],
['1d', '2x', '2s', '3x', '2s'] + ['10.4e'] * 2],
'indom2': [['indom'] * 4, ['20.13e'] * 4],
'diffusion': [['diff'] * 8, ['10.3e'] * 8],
'selec1': [['int_selec'] * 16, ['5d'] * 16],
'selec2': [['float_selec'] * 8, ['10.3e'] * 8],
'radii1': [['nrad'], ['5d']],
'radii2': [['radius'] * 8, ['10.4e'] * 8],
'equid' : [['nequ', '', 'dr'], ['5d', '5x', '10.4e']],
'logar' : [['nlog', '', 'rlog', 'dr'], ['5d', '5x'] + ['10.4e'] * 2],
'layer1': [['nlay'], ['5d']],
'layer2': [['layer'] * 8, ['10.4e'] * 8],
'xyz1' : [['deg'], ['10.4e']],
'xyz2' : [['ntype', '', 'no', 'del'], ['2s', '3x', '5d', '10.4e']],
'xyz3' : [['deli'] * 8, ['10.4e'] * 8],
'minc' : [['part', 'type', '', 'dual'], ['5s'] * 2 + ['5x', '5s']],
'part1' : [['num_continua', 'nvol', 'where'] + ['spacing'] * 7,
['3d'] * 2 + ['-4s'] + ['10.4e'] * 7],
'part2' : [['vol'] * 8, ['10.4e'] * 8]
}
t2data_extra_precision_format_specification = {
'rocks1': [['name', 'nad', 'density', 'porosity', 'k1', 'k2', 'k3',
'conductivity', 'specific_heat'],
['5s', '5d'] + ['15.8e'] * 7],
'rocks1.1': [['compressibility', 'expansivity', 'dry_conductivity',
'tortuosity', 'klinkenberg', 'xkd3', 'xkd4'], ['15.8e'] * 7],
'rocks1.2': [['type', ''] + ['parameter'] * 7, ['5d', '5x'] + ['15.8e'] * 7],
'rocks1.3': [['type', ''] + ['parameter'] * 7, ['5d', '5x'] + ['15.8e'] * 7],
'blocks': [['name', 'nseq', 'nadd', 'rocktype', 'volume',
'ahtx', 'pmx', 'x', 'y', 'z'],
['5s', '5d', '5d', '5s'] + ['15.8e'] * 3 + ['15.8e'] * 3],
'connections': [['block1', 'block2', 'nseq', 'nad1', 'nad2',
'direction', 'distance1', 'distance2', 'area', 'dircos', 'sigma'],
['5s'] * 2 + ['5d'] * 4 + ['15.8e'] * 3 + ['15.8f', '15.8e']],
'relative_permeability': [['type', ''] + ['parameter'] * 7, ['5d', '5x'] + ['15.8e'] * 7],
'capillarity': [['type', ''] + ['parameter'] * 7, ['5d', '5x'] + ['15.8e'] * 7],
'generator': [['block', 'name', 'nseq', 'nadd', 'nads', 'ltab',
'', 'type', 'itab', 'gx', 'ex', 'hg', 'fg'],
['5s'] * 2 + ['5d'] * 3 + ['5d', '5x', '4s', '1s'] + ['15.8e'] * 4],
'generation_times': [['time'] * 4, ['15.8e'] * 4],
'generation_rates': [['rate'] * 4, ['15.8e'] * 4],
'generation_enthalpy': [['enthalpy'] * 4, ['15.8e'] * 4]}
class t2data_parser(fixed_format_file):
"""Class for parsing TOUGH2 data file."""
def __init__(self, filename, mode, read_function = default_read_function):
super(t2data_parser,self).__init__(filename, mode,
t2data_format_specification, read_function)
class t2_extra_precision_data_parser(fixed_format_file):
"""Class for parsing AUTOUGH2 extra-precision auxiliary data file."""
def __init__(self, filename, mode, read_function = default_read_function):
super(t2_extra_precision_data_parser,
self).__init__(filename, mode,
t2data_extra_precision_format_specification,
read_function)
class fortran_unformatted_file(object):
"""Class for 'unformatted' binary file written by Fortran. These are
different from plain binary files in that the byte length of each
'record' is written at its start and end.
"""
def __init__(self, filename, mode):
self.file = open(filename, mode)
def close(self):
self.file.close()
def readrec(self, fmt):
nb, = struct.unpack('i', self.file.read(4))
packed = self.file.read(nb)
self.file.read(4)
return struct.unpack(fmt, packed)
def writerec(self, fmt, val):
nb = struct.calcsize(fmt)
if isinstance(val, (tuple, list, np.ndarray)):
packed = struct.pack(fmt, *val)
else: packed = struct.pack(fmt, val)
head = struct.pack('i', nb)
self.file.write(head)
self.file.write(packed)
self.file.write(head)
class t2generator(object):
"""TOUGH2 generator (source or sink)"""
def __init__(self, name = ' ', block = ' ',
nseq = None, nadd = None, nads = None, type = 'MASS',
ltab = 0, itab = '', gx = 0.0, ex = 0.0, hg = 0.0, fg = 0.0,
time = None, rate = None, enthalpy = None):
if time is None: time = []
if rate is None: rate = []
if enthalpy is None: enthalpy = []
self.name = name
self.block = block
self.nseq, self.nadd, self.nads = nseq, nadd, nads
self.type = type
self.ltab = ltab
self.itab = itab
self.gx = gx
self.ex = ex
self.hg = hg
self.fg = fg
self.time = time
self.rate = rate
self.enthalpy = enthalpy
def __repr__(self): return self.block + ':' + self.name
default_parameters = {
'max_iterations': None,
'print_level': None,
'max_timesteps': None,
'max_duration': None,
'print_interval': None,
'_option_str': '0' * 24,
'option': np.zeros(25, int8),
'diff0': None,
'texp': None,
'tstart': 0.0,
'tstop': None,
'const_timestep': 0.0,
'timestep': [],
'max_timestep': None,
'print_block': None,
'gravity': 0.0,
'timestep_reduction': None,
'scale': None,
'relative_error': None,
'absolute_error': None,
'pivot': None,
'upstream_weight': None,
'newton_weight': None,
'derivative_increment': None,
'default_incons': []}
t2data_sections = [
'SIMUL', 'ROCKS', 'PARAM', 'MOMOP', 'START', 'NOVER', 'RPCAP',
'LINEQ', 'SOLVR', 'MULTI', 'TIMES', 'SELEC', 'DIFFU',
'ELEME', 'CONNE', 'MESHM', 'GENER', 'SHORT', 'FOFT',
'COFT', 'GOFT', 'INCON', 'INDOM']
t2_extra_precision_sections = ['ROCKS', 'ELEME', 'CONNE', 'RPCAP', 'GENER']
class t2data(object):
"""Class for TOUGH2 data."""
def __init__(self, filename = '', meshfilename = '',
read_function = default_read_function):
from copy import deepcopy
self.filename = filename
self.meshfilename = meshfilename
self.title = ''
self.simulator = ''
self.parameter = deepcopy(default_parameters)
self._more_option_str = '0' * 21,
self.more_option = np.zeros(22, int8)
self.multi = {}
self.start = False
self.relative_permeability = {}
self.capillarity = {}
self.lineq = {}
self.output_times = {}
self.grid = t2grid()
self.generatorlist = []
self.generator = {}
self.short_output = {}
self.incon = {}
self.solver = {}
self.history_block = []
self.history_connection = []
self.history_generator = []
self.indom = {}
self.noversion = False
self.diffusion = []
self.selection = {}
self.meshmaker = []
self._sections = []
self.end_keyword = 'ENDCY'
self._extra_precision, self._echo_extra_precision = [], True
self.update_read_write_functions()
self.read_function = read_function
if self.filename: self.read(filename, meshfilename)
def get_extra_precision(self): return self._extra_precision
def set_extra_precision(self, value):
if value is False: value = []
elif value is True: value = t2_extra_precision_sections
elif isinstance(value, str): value = [value]
# check if removing any extra precision sections:
for section in set(self._extra_precision) - set(value):
self.insert_section(section)
self._extra_precision = value
self.update_read_write_functions()
extra_precision = property(get_extra_precision, set_extra_precision)
def get_echo_extra_precision(self): return self._echo_extra_precision
def set_echo_extra_precision(self, value):
if value != self._echo_extra_precision:
if value is False: # remove previously echoed sections from section list
for section in self._extra_precision:
self.delete_section(section)
else: # add sections previously not echoed to section list
for section in self._extra_precision:
self.insert_section(section)
self._echo_extra_precision = value
self.update_read_write_functions()
echo_extra_precision = property(get_echo_extra_precision, set_echo_extra_precision)
def update_read_write_functions(self):
"""Updates functions for reading and writing sections of data file."""
self.read_fn = dict(zip(
t2data_sections,
[self.read_simulator,
self.read_rocktypes,
self.read_parameters,
self.read_more_options,
self.read_start,
self.read_noversion,
self.read_rpcap,
self.read_lineq,
self.read_solver,
self.read_multi,
self.read_times,
self.read_selection,
self.read_diffusion,
self.read_blocks,
self.read_connections,
self.read_meshmaker,
self.read_generators,
self.read_short_output,
self.read_history_blocks,
self.read_history_connections,
self.read_history_generators,
self.read_incons,
self.read_indom]))
self.write_fn = dict(zip(
t2data_sections,
[self.write_simulator,
self.write_rocktypes,
self.write_parameters,
self.write_more_options,
self.write_start,
self.write_noversion,
self.write_rpcap,
self.write_lineq,
self.write_solver,
self.write_multi,
self.write_times,
self.write_selection,
self.write_diffusion,
self.write_blocks,
self.write_connections,
self.write_meshmaker,
self.write_generators,
self.write_short_output,
self.write_history_blocks,
self.write_history_connections,
self.write_history_generators,
self.write_incons,
self.write_indom]))
skip_fn = dict(zip(
t2_extra_precision_sections,
[self.skip_rocktypes,
self.skip_blocks,
self.skip_connections,
self.skip_rpcap,
self.skip_generators]))
if not self.echo_extra_precision:
for section in self.extra_precision: self.read_fn[section] = skip_fn[section]
def get_present_sections(self):
"""Returns a list of TOUGH2 section keywords for which there are
corresponding data in the t2data object."""
data_present = dict(zip(
t2data_sections,
[self.simulator,
self.grid and self.grid.rocktypelist,
self.parameter,
np.any(self.more_option),
self.start,
self.noversion,
self.relative_permeability or self.capillarity,
self.lineq,
self.solver,
self.multi,
self.output_times,
self.selection,
self.diffusion,
self.grid,
self.grid,
self.meshmaker,
self.generatorlist,
self.short_output,
self.history_block,
self.history_connection,
self.history_generator,
self.incon,
self.indom]))
return [keyword for keyword in t2data_sections if data_present[keyword]]
present_sections = property(get_present_sections)
def insert_section(self, section):
"""Inserts a new section into the internal list of data file
sections."""
if section not in self._sections:
i = self.section_insertion_index(section)
self._sections.insert(i, section)
def delete_section(self, section):
"""Deletes a section from the internal list of data file sections."""
try: self._sections.remove(section)
except ValueError: pass
def section_insertion_index(self, section):
"""Determines an appropriate position to insert the specified section
in the internal list of data file sections.
"""
try:
listindex = t2data_sections.index(section)
if listindex == 0: return 0 # SIMUL section
else:
# first look for sections above the one specified,
# and put new one just after the last found:
for i in reversed(range(listindex)):
try:
section_index = self._sections.index(t2data_sections[i])
return section_index + 1
except ValueError: pass
# look for sections below the one specified,
# and put new one just before the first found:
for i in range(listindex, len(t2data_sections)):
try:
section_index = self._sections.index(t2data_sections[i])
return section_index
except ValueError: pass
return len(self._sections)
except ValueError: return len(self._sections)
def update_sections(self):
"""Updates internal section list, based on which properties are present."""
present = self.present_sections
missing = [keyword for keyword in present if keyword not in self._sections]
for keyword in missing: self.insert_section(keyword)
extra = [keyword for keyword in self._sections if keyword not in present]
for keyword in extra: self.delete_section(keyword)
def __repr__(self): return self.title
def run(self, save_filename = '', incon_filename = '', simulator = 'AUTOUGH2_2',
silent = False, output_filename = ''):
"""Runs simulation using TOUGH2 or AUTOUGH2. It's assumed that the
data object has been written to file using write(). For
AUTOUGH2, if the filenames for the save file or initial
conditions file are not specified, they are constructed by
changing the extensions of the data filename. Set silent to
True to suppress screen output. The output_filename applies
only to TOUGH2, and specifies the name of the main output
listing file."""
if self.filename:
from os.path import splitext, basename
from os import devnull, remove
from subprocess import call
datbase, ext = splitext(self.filename)
if (self.type == 'AUTOUGH2'):
if save_filename == '': save_filename = datbase + '.save'
if incon_filename == '': incon_filename = datbase + '.incon'
savebase, ext = splitext(save_filename)
inconbase, ext = splitext(incon_filename)
runfilename = datbase + '_' + basename(simulator) + '.in'
open(runfilename, 'w').write('\n'.join([savebase, inconbase, datbase]))
infile = open(runfilename, 'r')
cmd = [simulator]
if silent: outfile = open(devnull, 'w')
else: outfile = None
# run AUTOUGH2:
call(cmd, stdin = infile, stdout = outfile)
infile.close()
remove(runfilename)
else: # run TOUGH2 (need to specify simulator executable name)
cmd = [simulator]
infile = open(self.filename, 'r')
if silent: outfile = None
else:
if output_filename == '': outfilename = datbase + '.listing'
else: outfilename = output_filename
outfile = open(outfilename, 'w')
call(cmd, stdin = infile, stdout = outfile)
def get_type(self):
"""Returns type (TOUGH2 or AUTOUGH2) based on whether the simulator
has been set."""
if self.simulator: return 'AUTOUGH2'
else: return 'TOUGH2'
def set_type(self, value):
"""Sets type (TOUGH2 or AUTOUGH2), and runs conversion if needed (with
default options)."""
if value in ['AUTOUGH2', 'TOUGH2']:
oldtype = self.type
if oldtype != value:
if oldtype == 'AUTOUGH2': self.convert_to_TOUGH2()
elif oldtype == 'TOUGH2': self.convert_to_AUTOUGH2()
else: raise Exception('Data file type ' + value + ' is not supported.')
type = property(get_type, set_type)
def get_extra_precision_filename(self):
"""Returns name of extra precision data file name, based on the name
of the data file."""
from os.path import splitext
base, ext = splitext(self.filename)
if base[0].isupper(): pext = 'PDAT'
else: pext = 'pdat'
return '.'.join((base, pext))
extra_precision_filename = property(get_extra_precision_filename)
def get_num_generators(self):
return len(self.generatorlist)
num_generators = property(get_num_generators)
def generator_index(self, blocksourcenames):
"""Returns index of generator with specified tuple of block and source
names."""
if blocksourcenames in self.generator:
return self.generatorlist.index(self.generator[blocksourcenames])
else: return None
def total_generation(self, type = 'MASS', name = ''):
"""Returns array containing total generation in each block of the
specified generator type and name. The name parameter
specifies a regular expression to be matched.
"""
import re
tg = np.zeros(self.grid.num_blocks, float64)
gens = [g for g in self.generatorlist if ((type == g.type) and re.search(name, g.name))]
for g in gens: tg[self.grid.block_index(g.block)] += g.gx
return tg
def specific_generation(self, type = 'MASS', name = ''):
"""Returns array containing total specific generation (i.e. generation
per unit volume) in each block of the specified generator type
and name. The name parameter specifies a regular expression
to be matched.
"""
import re
tg = np.zeros(self.grid.num_blocks, float64)
gens = [g for g in self.generatorlist if
((g.type == type) and (re.search(name, g.name)))]
for g in gens:
blkindex = self.grid.block_index(g.block)
tg[blkindex] += g.gx / self.grid.blocklist[blkindex].volume
return tg
def read_title(self, infile):
"""Reads simulation title"""
infile.read_value_line(self.__dict__, 'title')
def write_title(self, outfile):
outfile.write(self.title.strip() + '\n')
def read_simulator(self, infile):
"""Reads simulator and EOS type. If the SIMUL section is present,
check for extra precision data in auxiliary file, and modify
functions accordingly for reading the main data file.
"""
infile.read_value_line(self.__dict__, 'simulator')
if self.type == 'AUTOUGH2': self.read_extra_precision()
def write_simulator(self, outfile):
if self.simulator:
outfile.write('SIMUL\n')
outfile.write(self.simulator.strip() + '\n')
def read_rocktypes(self, infile):
"""Reads grid rock types"""
self.grid.rocktypelist = []
self.grid.rocktype = {}
line = padstring(infile.readline())
while line.strip():
[name, nad, density, porosity,
k1, k2, k3, conductivity, specific_heat] = infile.parse_string(line, 'rocks1')
self.grid.add_rocktype(rocktype(name, nad,
density, porosity,
[k1, k2, k3],
conductivity, specific_heat))
if nad is None: nad = 0
if nad >= 1: # additional lines:
infile.read_value_line(self.grid.rocktype[name].__dict__, 'rocks1.1')
if nad >=2 :
vals = infile.read_values('rocks1.2')
self.grid.rocktype[name].relative_permeability['type'] = vals[0]
self.grid.rocktype[name].relative_permeability['parameters'] = vals[2: -1]
vals = infile.read_values('rocks1.3')
self.grid.rocktype[name].capillarity['type'] = vals[0]
self.grid.rocktype[name].capillarity['parameters'] = vals[2: -1]
line = padstring(infile.readline())
def skip_rocktypes(self, infile):
"""Skips rock type section"""
while infile.readline().strip(): pass
def write_rocktypes(self, outfile):
outfile.write('ROCKS\n')
for rt in self.grid.rocktypelist:
vals = [rt.name, rt.nad, rt.density, rt.porosity] + \
list(rt.permeability) + [rt.conductivity, rt.specific_heat]
outfile.write_values(vals, 'rocks1')
if rt.nad is not None:
if rt.nad >= 1:
outfile.write_value_line(rt.__dict__, 'rocks1.1')
if rt.nad >= 2:
vals = [rt.relative_permeability['type'], None] + \
rt.relative_permeability['parameters']
outfile.write_values(vals, 'rocks1.2')
vals = [rt.capillarity['type'], None] + rt.capillarity['parameters']
outfile.write_values(vals, 'rocks1.2')
outfile.write('\n')
def read_parameters(self, infile):
"""Reads simulation parameters"""
spec = ['param1', 'param1_autough2'][self.type == 'AUTOUGH2']
infile.read_value_line(self.parameter, spec)
mops = self.parameter['_option_str'].rstrip().ljust(24).replace(' ', '0')
self.parameter['option'] = np.array([0] + [int(mop) for mop in mops], int8)
infile.read_value_line(self.parameter, 'param2')
if (self.parameter['print_block'] is not None) and \
(self.parameter['print_block'].strip() == ''):
self.parameter['print_block'] = None
self.read_timesteps(infile)
infile.read_value_line(self.parameter, 'param3')
for val in infile.read_values('default_incons'):
self.parameter['default_incons'].append(val)
self.parameter['default_incons'] = trim_trailing_nones(self.parameter['default_incons'])
# read any additional lines of default incons:
more = True
while more:
line = padstring(infile.readline())
if line.strip():
section = any([line.startswith(keyword) for keyword in t2data_sections])
if section: more = False
else:
more_incons = infile.parse_string(line, 'default_incons')
more_incons = trim_trailing_nones(more_incons)
self.parameter['default_incons'] += more_incons
else: more, line = False, None
return line
def write_parameters(self, outfile):
outfile.write('PARAM\n')
from copy import copy
paramw = copy(self.parameter)
if paramw['print_block'] is not None:
paramw['print_block'] = unfix_blockname(paramw['print_block'])
self.parameter['_option_str'] = ''.join([str(m) for m in self.parameter['option'][1:]])
spec = ['param1', 'param1_autough2'][self.type == 'AUTOUGH2']
outfile.write_value_line(self.parameter, spec)
outfile.write_value_line(paramw, 'param2')
self.write_timesteps(outfile)
outfile.write_value_line(self.parameter, 'param3')
num_vars = len(self.parameter['default_incons'])
if num_vars > 0:
nlines = int(ceil(num_vars / 4.))
for i in range(nlines):
i1, i2 = i * 4, min((i + 1) * 4, num_vars)
vals = list(self.parameter['default_incons'][i1: i2])
if len(vals) < 4: vals += [None] * (4 - len(vals))
outfile.write_values(vals, 'default_incons')
else: outfile.write('\n')
def read_more_options(self, infile):
"""Reads additional parameter options"""
infile.read_value_line(self.__dict__, '_more_option_str')
momops = self._more_option_str.rstrip().ljust(21).replace(' ', '0')
self.more_option = np.array([0] + [int(mop) for mop in momops], int8)
def write_more_options(self, outfile):
"""Writes additional parameter options"""
outfile.write('MOMOP\n')
self._more_option_str = ''.join([str(m) for m in self.more_option[1:]])
outfile.write_value_line(self.__dict__, '_more_option_str')
def read_timesteps(self, infile):
"""Reads time step sizes from file"""
if self.parameter['const_timestep'] >= 0.0:
self.parameter['timestep'] = [self.parameter['const_timestep']]
else:
nlines = -int(self.parameter['const_timestep'])
self.parameter['timestep'] = []
for i in range(nlines):
for val in infile.read_values('timestep'):
if val is not None: self.parameter['timestep'].append(val)
def write_timesteps(self, outfile):
if self.parameter['const_timestep'] < 0.0:
nlines = -int(self.parameter['const_timestep'])
for i in range(nlines):
i1, i2 = i * 8, min((i + 1) * 8, len(self.parameter['timestep']))
vals = self.parameter['timestep'][i1: i2]
if len(vals) < 8: vals += [None] * (8 - len(vals))
outfile.write_values(vals, 'timestep')
def read_multi(self, infile):
"""Reads EOS parameters"""
spec = ['multi', 'multi_autough2'][self.type == 'AUTOUGH2']
infile.read_value_line(self.multi, spec)
if 'eos' in self.multi: self.multi['eos'] = self.multi['eos'].strip()
def write_multi(self, outfile):
if self.multi != {}:
outfile.write('MULTI\n')
spec = ['multi', 'multi_autough2'][self.type == 'AUTOUGH2']
outfile.write_value_line(self.multi, spec)
def read_start(self, infile):
"""Sets start parameter"""
self.start = True
def write_start(self, outfile):
if self.start: outfile.write('START\n')
def read_rpcap(self, infile):
"""Reads relative permeability and capillarity parameters"""
vals = infile.read_values('relative_permeability')
self.relative_permeability['type'] = vals[0]
self.relative_permeability['parameters'] = vals[2:]
vals = infile.read_values('capillarity')
self.capillarity['type']= vals[0]
self.capillarity['parameters'] = vals[2:]
def skip_rpcap(self, infile):
"""Skips relative permeability and capillarity parameter section."""
for i in range(2): infile.readline()
def write_rpcap(self, outfile):
if self.relative_permeability:
outfile.write('RPCAP\n')
vals = [self.relative_permeability['type'], None] + \
self.relative_permeability['parameters']
outfile.write_values(vals, 'relative_permeability')
vals = [self.capillarity['type'], None] + \
self.capillarity['parameters']
outfile.write_values(vals, 'capillarity')
def read_lineq(self, infile):
"""Reads linear equation parameters (AUTOUGH2)"""
infile.read_value_line(self.lineq, 'lineq')
def write_lineq(self, outfile):
if self.lineq:
outfile.write('LINEQ\n')
outfile.write_value_line(self.lineq, 'lineq')
def read_solver(self, infile):
"""Reads linear equation parameters (TOUGH2)"""
infile.read_value_line(self.solver, 'solver')
def write_solver(self, outfile):
if self.solver:
outfile.write('SOLVR\n')
outfile.write_value_line(self.solver, 'solver')
def read_blocks(self, infile):
"""Reads grid blocks"""
self.grid.block, self.grid.blocklist = {}, []
line = padstring(infile.readline())
while line.strip():
[name, nseq, nadd, rockname,
volume, ahtx, pmx, x, y, z] = infile.parse_string(line, 'blocks')
name = fix_blockname(name)
if rockname in self.grid.rocktype:
rocktype = self.grid.rocktype[rockname]
elif rockname.strip() == '' and self.grid.num_rocktypes > 0:
rocktype = self.grid.rocktypelist[0] # default
else:
try: # check if rocktype index specified:
rockindex = int(rockname) - 1
rocktype = self.grid.rocktypelist[rockindex]
except:
raise RuntimeError("Unknown rocktype " + rockname + " in block " + name)
if (x is not None) and (y is not None) and (z is not None):
centre = np.array([x, y, z])
else: centre = None
if nseq == 0: nseq = None
if nadd == 0: nadd = None
self.grid.add_block(t2block(name, volume, rocktype,
centre = centre, ahtx = ahtx,
pmx = pmx, nseq = nseq, nadd = nadd))
line = padstring(infile.readline())
def skip_blocks(self, infile):
"""Skips blocks section in file"""
while infile.readline().strip(): pass
def write_blocks(self, outfile):
outfile.write('ELEME\n')
if self.grid.num_blocks > 0:
from copy import copy
for blk in self.grid.blocklist:
blkw = copy(blk.__dict__)
blkw['name'] = unfix_blockname(blkw['name'])
if blk.centre is None: outfile.write_value_line(blkw, 'blocks')
else:
vals = [blkw['name'], blk.nseq, blk.nadd,
blk.rocktype.name, blk.volume,
blk.ahtx, blk.pmx] + list(blk.centre)
outfile.write_values(vals, 'blocks')
outfile.write('\n')
def read_connections(self, infile):
"""Reads grid connections"""
self.grid.connectionlist, self.grid.connection = [], {}
line = padstring(infile.readline())
while line.strip() and not line.startswith('+++'):
[name1, name2, nseq,
nad1, nad2, isot, d1, d2,
areax, betax, sigx] = infile.parse_string(line, 'connections')
name1, name2 = fix_blockname(name1), fix_blockname(name2)
if nseq == 0: nseq = None
if nad1 == 0: nad1 = None
if nad2 == 0: nad2 = None
self.grid.add_connection(t2connection([self.grid.block[name1],
self.grid.block[name2]],
isot, [d1, d2], areax, betax,
sigx, nseq, nad1, nad2))
line = padstring(infile.readline())
def skip_connections(self, infile):
"""Skips connections section in file"""
while infile.readline().strip(): pass
def write_connections(self, outfile):
outfile.write('CONNE\n')
if self.grid.num_connections > 0:
for con in self.grid.connectionlist:
vals = [unfix_blockname(con.block[0].name),
unfix_blockname(con.block[1].name),
con.nseq, con.nad1, con.nad2, con.direction] + \
con.distance + [con.area, con.dircos, con.sigma]
outfile.write_values(vals, 'connections')
outfile.write('\n')
def add_generator(self, generator = None):
"""Adds a generator."""
if generator is None: generator = t2generator()
self.generatorlist.append(generator)
self.generator[(generator.block, generator.name)] = self.generatorlist[-1]
def delete_generator(self, blocksourcenames):
i = self.generator_index(blocksourcenames)
del self.generator[blocksourcenames]
del self.generatorlist[i]
def clear_generators(self):
self.generator.clear()
del self.generatorlist[:]
def delete_orphan_generators(self):
"""Deletes any generators specified in blocks which do not exist in
the grid."""
delgenindices, delgens = [], set([])
# Delete items from the generator list and dictionary
# separately (rather than using self.delete_generator() in
# case there are multiple generators in the list with the same
# dictionary key.
for i, gen in enumerate(self.generatorlist):
if not (gen.block in self.grid.block):
delgenindices.append(i)
delgens.add((gen.block, gen.name))
for bg in delgens: del self.generator[bg]
for i in reversed(delgenindices):
del self.generatorlist[i]
def read_generator(self, line, infile):
"""Returns generator read from line in file"""
[block, name, nseq, nadd, nads,
ltab, empty, gentype, itab,
gx, ex, hg, fg] = infile.parse_string(line, 'generator')
block, name = fix_blockname(block), fix_blockname(name)
time, rate, enthalpy = [], [], []
if ltab and gentype != 'DELV':
ntimes = abs(ltab)
if ntimes > 1:
nlines = int(ceil(ntimes / 4.))
for i in range(nlines):
for val in infile.read_values('generation_times'):
if val is not None: time.append(val)
for i in range(nlines):
for val in infile.read_values('generation_rates'):
if val is not None: rate.append(val)
if itab.strip():
for i in range(nlines):
for val in infile.read_values('generation_enthalpy'):
if val is not None: enthalpy.append(val)
return t2generator(name = name, block = block,
nseq = nseq, nadd = nadd, nads = nads,
type = gentype, ltab = ltab, itab = itab,
gx = gx, ex = ex, hg = hg, fg = fg,
time = time, rate = rate, enthalpy = enthalpy)
def write_generator(self, gen, outfile):
from copy import copy
genw = copy(gen.__dict__)
genw['name'] = unfix_blockname(genw['name'])
genw['block'] = unfix_blockname(genw['block'])
outfile.write_value_line(genw, 'generator')
if gen.ltab and gen.type != 'DELV': ntimes = abs(gen.ltab)
else: ntimes = 1
if ntimes > 1:
nlines = int(ceil(ntimes / 4.))
for i in range(nlines):
i1, i2 = i * 4, min((i + 1) * 4, ntimes)
vals = list(gen.time[i1: i2])
if len(vals) < 4: vals += [None] * (4 - len(vals))
outfile.write_values(vals, 'generation_times')
for i in range(nlines):
i1, i2 = i * 4, min((i + 1) * 4, ntimes)
vals = list(gen.rate[i1: i2])
if len(vals) < 4: vals += [None] * (4 - len(vals))
outfile.write_values(vals, 'generation_rates')
if gen.enthalpy:
for i in range(nlines):
i1, i2 = i * 4, min((i + 1) * 4, ntimes)
vals = list(gen.enthalpy[i1: i2])
if len(vals) < 4: vals += [None] * (4 - len(vals))
outfile.write_values(vals, 'generation_enthalpy')
def read_generators(self, infile):
"""Reads generators from file"""
self.generatorlist = []
line = infile.readline()
while line.strip():
self.add_generator(self.read_generator(line, infile))
line = infile.readline()
def skip_generators(self, infile):
"""Skips generator section in file"""
while infile.readline().strip(): pass
def write_generators(self, outfile):
if self.generatorlist:
outfile.write('GENER\n')
for generator in self.generatorlist:
self.write_generator(generator, outfile)
outfile.write('\n')
def read_times(self, infile):
"""Reads output times from file"""
infile.read_value_line(self.output_times, 'output_times1')
self.output_times['time'] = []
nlines = int(ceil(self.output_times['num_times_specified'] / 8.))
for i in range(nlines):
for val in infile.read_values('output_times2'):
if val is not None: self.output_times['time'].append(val)
def write_times(self, outfile):
if self.output_times:
outfile.write('TIMES\n')
outfile.write_value_line(self.output_times, 'output_times1')
nlines = int(ceil(self.output_times['num_times_specified'] / 8.))
for i in range(nlines):
i1, i2 = i * 8, min((i + 1) * 8, len(self.output_times['time']))
vals = self.output_times['time'][i1: i2]
if len(vals) < 8: vals += [None] * (8 - len(vals))
outfile.write_values(vals, 'output_times2')
def read_incons(self, infile):
"""Reads initial conditions from file"""
line = infile.readline()
while line.strip():
[blockname, nseq, nadd,
porosity] = infile.parse_string(line, 'incon1')
blockname = fix_blockname(blockname)
variables = infile.read_values('incon2')
variables = trim_trailing_nones(variables)
if nseq == 0: nseq = None
if nadd == 0: nadd = None
if nseq is None:
self.incon[blockname] = [porosity, variables]
else:
self.incon[blockname] = [porosity, variables, nseq, nadd]
line = infile.readline()
def write_incons(self, outfile):
if self.incon:
outfile.write('INCON\n')
for blk in self.grid.blocklist:
blkname = blk.name
try:
inc = self.incon[blkname]
except:
continue
if len(inc) >= 4: nseq, nadd = inc[2], inc[3]
else: nseq, nadd = None, None
vals = [unfix_blockname(blkname), nseq, nadd, inc[0]]
outfile.write_values(vals, 'incon1')
outfile.write_values(inc[1], 'incon2')
outfile.write('\n')