[Python] Add function to write CSV file from SolutionArray
This commit is contained in:
Ray Speth
parent
faa4c36e1d
commit
00d254a1c2
3 changed files with 186 additions and 80 deletions
|
|
@ -1,5 +1,6 @@
|
|||
from ._cantera import *
|
||||
import numpy as np
|
||||
import csv as _csv
|
||||
|
||||
class Quantity(object):
|
||||
"""
|
||||
|
|
@ -269,6 +270,11 @@ class SolutionArray(object):
|
|||
>>> s.reaction_equation(10)
|
||||
'CH4 + O <=> CH3 + OH'
|
||||
|
||||
Data represnted by a SolutionArray can be extracted and saved to a CSV file
|
||||
using the `write_csv` method:
|
||||
|
||||
>>> states.write_csv('somefile.csv', cols=('T','P','X','net_rates_of_progress'))
|
||||
|
||||
:param phase: The `Solution` object used to compute the thermodynamic,
|
||||
kinetic, and transport properties
|
||||
:param shape: A tuple or integer indicating the dimensions of the
|
||||
|
|
@ -278,6 +284,71 @@ class SolutionArray(object):
|
|||
slicing support.
|
||||
"""
|
||||
|
||||
_scalar = [
|
||||
# From ThermoPhase
|
||||
'mean_molecular_weight', 'P', 'T', 'density', 'density_mass',
|
||||
'density_mole', 'v', 'volume_mass', 'volume_mole', 'u',
|
||||
'int_energy_mole', 'int_energy_mass', 'h', 'enthalpy_mole',
|
||||
'enthalpy_mass', 's', 'entropy_mole', 'entropy_mass', 'g', 'gibbs_mole',
|
||||
'gibbs_mass', 'cv', 'cv_mole', 'cv_mass', 'cp', 'cp_mole', 'cp_mass',
|
||||
'critical_temperature', 'critical_pressure', 'critical_density',
|
||||
'P_sat', 'T_sat', 'isothermal_compressibility',
|
||||
'thermal_expansion_coeff', 'electric_potential',
|
||||
# From Transport
|
||||
'viscosity', 'electrical_conductivity', 'thermal_conductivity',
|
||||
]
|
||||
_n_species = [
|
||||
# from ThermoPhase
|
||||
'Y', 'X', 'concentrations', 'partial_molar_enthalpies',
|
||||
'partial_molar_entropies', 'partial_molar_int_energies',
|
||||
'chemical_potentials', 'electrochemical_potentials', 'partial_molar_cp',
|
||||
'partial_molar_volumes', 'standard_enthalpies_RT',
|
||||
'standard_entropies_R', 'standard_int_energies_RT', 'standard_gibbs_RT',
|
||||
'standard_cp_R',
|
||||
# From Transport
|
||||
'mix_diff_coeffs', 'mix_diff_coeffs_mass', 'mix_diff_coeffs_mole',
|
||||
'thermal_diff_coeffs'
|
||||
]
|
||||
|
||||
# From Kinetics (differs from Solution.n_species for Interface phases)
|
||||
_n_total_species = [
|
||||
'creation_rates', 'destruction_rates', 'net_production_rates',
|
||||
]
|
||||
|
||||
_n_species2 = ['multi_diff_coeffs', 'binary_diff_coeffs']
|
||||
|
||||
_n_reactions = [
|
||||
'forward_rates_of_progress', 'reverse_rates_of_progress',
|
||||
'net_rates_of_progress', 'equilibrium_constants',
|
||||
'forward_rate_constants', 'reverse_rate_constants',
|
||||
'delta_enthalpy', 'delta_gibbs', 'delta_entropy',
|
||||
'delta_standard_enthalpy', 'delta_standard_gibbs',
|
||||
'delta_standard_entropy'
|
||||
]
|
||||
_state2 = ['TD', 'TP', 'UV', 'DP', 'HP', 'SP', 'SV']
|
||||
_call_scalar = ['elemental_mass_fraction', 'elemental_mole_fraction']
|
||||
|
||||
_passthrough = [
|
||||
# from ThermoPhase
|
||||
'name', 'ID', 'basis', 'n_elements', 'element_index',
|
||||
'element_name', 'element_names', 'atomic_weight', 'atomic_weights',
|
||||
'n_species', 'species_name', 'species_names', 'species_index',
|
||||
'species', 'n_atoms', 'molecular_weights', 'min_temp', 'max_temp',
|
||||
'reference_pressure',
|
||||
# From Kinetics
|
||||
'n_total_species', 'n_reactions', 'n_phases', 'reaction_phase_index',
|
||||
'kinetics_species_index', 'reaction', 'reactions', 'modify_reaction',
|
||||
'is_reversible', 'multiplier', 'set_multiplier', 'reaction_type',
|
||||
'reaction_equation', 'reactants', 'products', 'reaction_equations',
|
||||
'reactant_stoich_coeff', 'product_stoich_coeff',
|
||||
'reactant_stoich_coeffs', 'product_stoich_coeffs',
|
||||
# from Transport
|
||||
'transport_model',
|
||||
]
|
||||
|
||||
_interface_passthrough = ['site_density']
|
||||
_interface_n_species = ['coverages']
|
||||
|
||||
def __init__(self, phase, shape=(0,), states=None, extra=None):
|
||||
self._phase = phase
|
||||
|
||||
|
|
@ -403,75 +474,98 @@ class SolutionArray(object):
|
|||
self._phase.equilibrate(*args, **kwargs)
|
||||
self._states[index][:] = self._phase.state
|
||||
|
||||
def collect_data(self, cols=('extra','T','density','Y'), threshold=0,
|
||||
species='Y'):
|
||||
"""
|
||||
Returns the data specified by *cols* in a single 2D Numpy array, along
|
||||
with a list of column labels.
|
||||
|
||||
:param cols: A list of any properties of the solution that are scalars
|
||||
or which have a value for each species or reaction. If species names
|
||||
are specified, then either the mass or mole fraction of that species
|
||||
will be taken, depending on the value of *species*. *cols* may also
|
||||
include any arrays which were specified as 'extra' variables when
|
||||
defining the SolutionArray object. The special value 'extra' can be
|
||||
used to include all 'extra' variables.
|
||||
:param threshold: Relative tolerance for including a particular column.
|
||||
The tolerance is applied by comparing the maximum absolute value for
|
||||
a particular column to the maximum absolute value in all columns for
|
||||
the same variable (e.g. mass fraction).
|
||||
:param species: Specifies whether to use mass ('Y') or mole ('X')
|
||||
fractions for individual species specified in 'cols'
|
||||
"""
|
||||
if len(self._shape) != 1:
|
||||
raise TypeError("collect_data only works for 1D SolutionArray")
|
||||
data = []
|
||||
labels = []
|
||||
|
||||
# Expand cols to include the individual items in 'extra'
|
||||
expanded_cols = []
|
||||
for c in cols:
|
||||
if c == 'extra':
|
||||
expanded_cols.extend(self._extra_arrays)
|
||||
else:
|
||||
expanded_cols.append(c)
|
||||
|
||||
species_names = set(self.species_names)
|
||||
for c in expanded_cols:
|
||||
single_species = False
|
||||
# Determine labels for the items in the current group of columns
|
||||
if c in self._extra_arrays:
|
||||
collabels = [c]
|
||||
elif c in self._scalar:
|
||||
collabels = [c]
|
||||
elif c in self._n_species:
|
||||
collabels = ['{}_{}'.format(c, s) for s in self.species_names]
|
||||
elif c in self._n_reactions:
|
||||
collabels = ['{} {}'.format(c, r)
|
||||
for r in self.reaction_equations()]
|
||||
elif c in species_names:
|
||||
single_species = True
|
||||
collabels = ['{}_{}'.format(species, c)]
|
||||
else:
|
||||
raise Exception('property "{}" not supported'.format(c))
|
||||
|
||||
# Get the data for the current group of columns
|
||||
if single_species:
|
||||
d = getattr(self(c), species)
|
||||
else:
|
||||
d = getattr(self, c)
|
||||
|
||||
if d.ndim == 1:
|
||||
d = d[:, np.newaxis]
|
||||
elif threshold:
|
||||
# Determine threshold value and select columns to keep
|
||||
maxval = abs(d).max()
|
||||
keep = (abs(d) > threshold * maxval).any(axis=0)
|
||||
d = d[:, keep]
|
||||
collabels = [label for label, k in zip(collabels, keep) if k]
|
||||
|
||||
data.append(d)
|
||||
labels.extend(collabels)
|
||||
|
||||
return np.hstack(data), labels
|
||||
|
||||
def write_csv(self, filename, cols=('extra','T','density','Y'),
|
||||
*args, **kwargs):
|
||||
"""
|
||||
Write a CSV file named *filename* containing the data specified by
|
||||
*cols*. The first row of the CSV file will contain column labels.
|
||||
|
||||
Additional arguments are passed on to `collect_data`. This method works
|
||||
only with 1D SolutionArray objects.
|
||||
"""
|
||||
data, labels = self.collect_data(cols, *args, **kwargs)
|
||||
with open(filename, 'w') as outfile:
|
||||
writer = _csv.writer(outfile)
|
||||
writer.writerow(labels)
|
||||
for row in data:
|
||||
writer.writerow(row)
|
||||
|
||||
|
||||
def _make_functions():
|
||||
# this is wrapped in a function to avoid polluting the module namespace
|
||||
|
||||
scalar = [
|
||||
# From ThermoPhase
|
||||
'mean_molecular_weight', 'P', 'T', 'density', 'density_mass',
|
||||
'density_mole', 'v', 'volume_mass', 'volume_mole', 'u',
|
||||
'int_energy_mole', 'int_energy_mass', 'h', 'enthalpy_mole',
|
||||
'enthalpy_mass', 's', 'entropy_mole', 'entropy_mass', 'g', 'gibbs_mole',
|
||||
'gibbs_mass', 'cv', 'cv_mole', 'cv_mass', 'cp', 'cp_mole', 'cp_mass',
|
||||
'critical_temperature', 'critical_pressure', 'critical_density',
|
||||
'P_sat', 'T_sat', 'isothermal_compressibility',
|
||||
'thermal_expansion_coeff', 'electric_potential',
|
||||
# From Transport
|
||||
'viscosity', 'electrical_conductivity', 'thermal_conductivity',
|
||||
]
|
||||
n_species = [
|
||||
# from ThermoPhase
|
||||
'Y', 'X', 'concentrations', 'partial_molar_enthalpies',
|
||||
'partial_molar_entropies', 'partial_molar_int_energies',
|
||||
'chemical_potentials', 'electrochemical_potentials', 'partial_molar_cp',
|
||||
'partial_molar_volumes', 'standard_enthalpies_RT',
|
||||
'standard_entropies_R', 'standard_int_energies_RT', 'standard_gibbs_RT',
|
||||
'standard_cp_R',
|
||||
# From Transport
|
||||
'mix_diff_coeffs', 'mix_diff_coeffs_mass', 'mix_diff_coeffs_mole',
|
||||
'thermal_diff_coeffs'
|
||||
]
|
||||
|
||||
# From Kinetics (differs from Solution.n_species for Interface phases)
|
||||
n_total_species = [
|
||||
'creation_rates', 'destruction_rates', 'net_production_rates',
|
||||
]
|
||||
|
||||
n_species2 = ['multi_diff_coeffs', 'binary_diff_coeffs']
|
||||
|
||||
n_reactions = [
|
||||
'forward_rates_of_progress', 'reverse_rates_of_progress',
|
||||
'net_rates_of_progress', 'equilibrium_constants',
|
||||
'forward_rate_constants', 'reverse_rate_constants',
|
||||
'delta_enthalpy', 'delta_gibbs', 'delta_entropy',
|
||||
'delta_standard_enthalpy', 'delta_standard_gibbs',
|
||||
'delta_standard_entropy'
|
||||
]
|
||||
state2 = ['TD', 'TP', 'UV', 'DP', 'HP', 'SP', 'SV']
|
||||
call_scalar = ['elemental_mass_fraction', 'elemental_mole_fraction']
|
||||
|
||||
passthrough = [
|
||||
# from ThermoPhase
|
||||
'name', 'ID', 'basis', 'n_elements', 'element_index',
|
||||
'element_name', 'element_names', 'atomic_weight', 'atomic_weights',
|
||||
'n_species', 'species_name', 'species_names', 'species_index',
|
||||
'species', 'n_atoms', 'molecular_weights', 'min_temp', 'max_temp',
|
||||
'reference_pressure',
|
||||
# From Kinetics
|
||||
'n_total_species', 'n_reactions', 'n_phases', 'reaction_phase_index',
|
||||
'kinetics_species_index', 'reaction', 'reactions', 'modify_reaction',
|
||||
'is_reversible', 'multiplier', 'set_multiplier', 'reaction_type',
|
||||
'reaction_equation', 'reactants', 'products', 'reaction_equations',
|
||||
'reactant_stoich_coeff', 'product_stoich_coeff',
|
||||
'reactant_stoich_coeffs', 'product_stoich_coeffs',
|
||||
# from Transport
|
||||
'transport_model',
|
||||
]
|
||||
|
||||
interface_passthrough = ['site_density']
|
||||
interface_n_species = ['coverages']
|
||||
|
||||
# Factory for creating properties which consist of a tuple of two variables,
|
||||
# e.g. 'TP' or 'SV'
|
||||
def state2_prop(name, doc_source):
|
||||
|
|
@ -493,7 +587,7 @@ def _make_functions():
|
|||
|
||||
return property(getter, setter, doc=getattr(doc_source, name).__doc__)
|
||||
|
||||
for name in state2:
|
||||
for name in SolutionArray._state2:
|
||||
setattr(SolutionArray, name, state2_prop(name, Solution))
|
||||
|
||||
for name in PureFluid._full_states.values():
|
||||
|
|
@ -563,23 +657,23 @@ def _make_functions():
|
|||
return v
|
||||
return property(getter, doc=getattr(doc_source, name).__doc__)
|
||||
|
||||
for name in scalar:
|
||||
for name in SolutionArray._scalar:
|
||||
setattr(SolutionArray, name, make_prop(name, empty_scalar, Solution))
|
||||
|
||||
for name in n_species:
|
||||
for name in SolutionArray._n_species:
|
||||
setattr(SolutionArray, name, make_prop(name, empty_species, Solution))
|
||||
|
||||
for name in interface_n_species:
|
||||
for name in SolutionArray._interface_n_species:
|
||||
setattr(SolutionArray, name, make_prop(name, empty_species, Interface))
|
||||
|
||||
for name in n_total_species:
|
||||
for name in SolutionArray._n_total_species:
|
||||
setattr(SolutionArray, name,
|
||||
make_prop(name, empty_total_species, Solution))
|
||||
|
||||
for name in n_species2:
|
||||
for name in SolutionArray._n_species2:
|
||||
setattr(SolutionArray, name, make_prop(name, empty_species2, Solution))
|
||||
|
||||
for name in n_reactions:
|
||||
for name in SolutionArray._n_reactions:
|
||||
setattr(SolutionArray, name, make_prop(name, empty_reactions, Solution))
|
||||
|
||||
# Factory for creating wrappers for functions which return a value
|
||||
|
|
@ -592,7 +686,7 @@ def _make_functions():
|
|||
return v
|
||||
return wrapper
|
||||
|
||||
for name in call_scalar:
|
||||
for name in SolutionArray._call_scalar:
|
||||
setattr(SolutionArray, name, caller(name, empty_scalar))
|
||||
|
||||
# Factory for creating properties to pass through state-independent
|
||||
|
|
@ -607,10 +701,10 @@ def _make_functions():
|
|||
|
||||
return property(getter, setter, doc=getattr(doc_source, name).__doc__)
|
||||
|
||||
for name in passthrough:
|
||||
for name in SolutionArray._passthrough:
|
||||
setattr(SolutionArray, name, passthrough_prop(name, Solution))
|
||||
|
||||
for name in interface_passthrough:
|
||||
for name in SolutionArray._interface_passthrough:
|
||||
setattr(SolutionArray, name, passthrough_prop(name, Interface))
|
||||
|
||||
_make_functions()
|
||||
|
|
|
|||
|
|
@ -77,8 +77,7 @@ tfinal = 6.0
|
|||
tnow = 0.0
|
||||
Tprev = combustor.T
|
||||
tprev = tnow
|
||||
outfile = open('combustor.csv','w')
|
||||
csvwriter = csv.writer(outfile)
|
||||
states = ct.SolutionArray(gas, extra=['t','tres'])
|
||||
|
||||
while tnow < tfinal:
|
||||
tnow = sim.step()
|
||||
|
|
@ -87,6 +86,6 @@ while tnow < tfinal:
|
|||
if abs(Tnow - Tprev) > 1.0 or tnow-tprev > 2e-2:
|
||||
tprev = tnow
|
||||
Tprev = Tnow
|
||||
csvwriter.writerow([tnow, combustor.T, tres] +
|
||||
list(combustor.thermo.X))
|
||||
outfile.close()
|
||||
states.append(gas.state, t=tnow, tres=tres)
|
||||
|
||||
states.write_csv('combustor.csv', cols=('t','T','tres','X'))
|
||||
|
|
|
|||
|
|
@ -1307,3 +1307,16 @@ class TestSolutionArray(utilities.CanteraTest):
|
|||
kk = (self.gas.species_index('OH'), self.gas.species_index('O'))
|
||||
self.assertArrayNear(states('OH','O').partial_molar_cp,
|
||||
states.partial_molar_cp[...,kk])
|
||||
|
||||
def test_write_csv(self):
|
||||
states = ct.SolutionArray(self.gas, 7)
|
||||
states.TPX = np.linspace(300, 1000, 7), 2e5, 'H2:0.5, O2:0.4'
|
||||
states.equilibrate('HP')
|
||||
|
||||
outfile = 'solutionarray{}.csv'.format(utilities.python_version)
|
||||
states.write_csv(outfile)
|
||||
|
||||
data = np.genfromtxt(outfile, names=True, delimiter=',')
|
||||
self.assertEqual(len(data), 7)
|
||||
self.assertEqual(len(data.dtype), self.gas.n_species + 2)
|
||||
self.assertIn('Y_H2', data.dtype.fields)
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue