def plot_errors(self,
concs,
init_concs,
varied_data,
varied,
axes=None,
compositions=True,
Q=True,
subplot_kwargs=None):
if axes is None:
import matplotlib.pyplot as plt
if subplot_kwargs is None:
subplot_kwargs = dict(xscale='log')
fig, axes = plt.subplots(1,
2,
figsize=(10, 4),
subplot_kw=subplot_kwargs)
varied_idx = self.as_substance_index(varied)
ls, c = '- -- : -.'.split(), 'krgbcmy'
all_inits = np.tile(self.as_per_substance_array(init_concs),
(len(varied_data), 1))
all_inits[:, varied_idx] = varied_data
if compositions:
cmp_nrs, m1, m2 = self.composition_conservation(concs, all_inits)
for cidx, (cmp_nr, a1, a2) in enumerate(zip(cmp_nrs, m1, m2)):
axes[0].plot(concs[:, varied_idx],
a1 - a2,
label='Comp ' + str(cmp_nr),
ls=ls[cidx % len(ls)],
c=c[cidx % len(c)])
axes[1].plot(concs[:, varied_idx], (a1 - a2) / np.abs(a2),
label='Comp ' + str(cmp_nr),
ls=ls[cidx % len(ls)],
c=c[cidx % len(c)])
if Q:
# TODO: handle precipitate phases in plotting Q error
qs = self.equilibrium_quotients(concs)
ks = [rxn.param for rxn in self.rxns]
for idx, (q, k) in enumerate(zip(qs, ks)):
axes[0].plot(concs[:, varied_idx],
q - k,
label='K R:' + str(idx),
ls=ls[(idx + cidx) % len(ls)],
c=c[(idx + cidx) % len(c)])
axes[1].plot(concs[:, varied_idx], (q - k) / k,
label='K R:' + str(idx),
ls=ls[(idx + cidx) % len(ls)],
c=c[(idx + cidx) % len(c)])
from pyneqsys.plotting import mpl_outside_legend
mpl_outside_legend(axes[0])
mpl_outside_legend(axes[1])
axes[0].set_title("Absolute errors")
axes[1].set_title("Relative errors")
def plot_errors(self, concs, init_concs, varied_data, varied, axes=None,
compositions=True, Q=True, subplot_kwargs=None):
if axes is None:
import matplotlib.pyplot as plt
if subplot_kwargs is None:
subplot_kwargs = dict(xscale='log')
fig, axes = plt.subplots(1, 2, figsize=(10, 4),
subplot_kw=subplot_kwargs)
varied_idx = self.as_substance_index(varied)
ls, c = '- -- : -.'.split(), 'krgbcmy'
all_inits = np.tile(self.as_per_substance_array(init_concs),
(len(varied_data), 1))
all_inits[:, varied_idx] = varied_data
if compositions:
cmp_nrs, m1, m2 = self.composition_conservation(concs, all_inits)
for cidx, (cmp_nr, a1, a2) in enumerate(zip(cmp_nrs, m1, m2)):
axes[0].plot(concs[:, varied_idx],
a1-a2, label='Comp ' + str(cmp_nr),
ls=ls[cidx % len(ls)], c=c[cidx % len(c)])
axes[1].plot(concs[:, varied_idx],
(a1-a2)/np.abs(a2), label='Comp ' + str(cmp_nr),
ls=ls[cidx % len(ls)], c=c[cidx % len(c)])
if Q:
# TODO: handle precipitate phases in plotting Q error
qs = self.equilibrium_quotients(concs)
ks = [rxn.param for rxn in self.rxns]
for idx, (q, k) in enumerate(zip(qs, ks)):
axes[0].plot(concs[:, varied_idx],
q-k, label='K R:' + str(idx),
ls=ls[(idx+cidx) % len(ls)],
c=c[(idx+cidx) % len(c)])
axes[1].plot(concs[:, varied_idx],
(q-k)/k, label='K R:' + str(idx),
ls=ls[(idx+cidx) % len(ls)],
c=c[(idx+cidx) % len(c)])
from pyneqsys.plotting import mpl_outside_legend
mpl_outside_legend(axes[0])
mpl_outside_legend(axes[1])
axes[0].set_title("Absolute errors")
axes[1].set_title("Relative errors")
def roots(
self,
init_concs,
varied_data,
varied,
x0=None,
NumSys=NumSysLog,
plot_kwargs=None,
neqsys_type="chained_conditional",
**kwargs
):
"""
Parameters
----------
init_concs : array or dict
varied_data : array
varied_idx : int or str
x0 : array
NumSys : _NumSys subclass
See :class:`NumSysLin`, :class:`NumSysLog`, etc.
plot_kwargs : dict
See py:meth:`pyneqsys.NeqSys.solve`. Two additional keys
are intercepted here:
latex_names: bool (default: False)
conc_unit_str: str (default: 'M')
neqsys_type : str
what method to use for NeqSys construction (get_neqsys_*)
\\*\\*kwargs :
Keyword argumetns passed on to py:meth:`pyneqsys.NeqSys.solve_series`.
"""
_plot = plot_kwargs is not None
if _plot:
latex_names = plot_kwargs.pop("latex_names", False)
conc_unit_str = plot_kwargs.pop("conc_unit_str", "M")
if "ax" not in plot_kwargs:
plot_kwargs["ax"] = self._get_default_plot_ax()
init_concs = self.as_per_substance_array(init_concs)
neqsys = self.get_neqsys(
neqsys_type,
NumSys=NumSys,
rref_equil=kwargs.pop("rref_equil", False),
rref_preserv=kwargs.pop("rref_preserv", False),
precipitates=kwargs.pop("precipitates", None),
)
if x0 is None:
x0 = init_concs
if _plot:
cb = neqsys.solve_and_plot_series
if "plot_kwargs" not in kwargs:
kwargs["plot_kwargs"] = plot_kwargs
if "labels" not in kwargs["plot_kwargs"]:
kwargs["plot_kwargs"]["labels"] = self.substance_labels(latex_names)
if "substances" in plot_kwargs:
if "indices" in plot_kwargs:
raise ValueError("Now I am confused..")
kwargs["plot_kwargs"]["indices"] = map(
self.as_substance_index, plot_kwargs.pop("substances")
)
print(kwargs["plot_kwargs"]["indices"])
else:
cb = neqsys.solve_series
params = np.concatenate((init_concs, self.eq_constants()))
xvecs, info_dicts = cb(
x0,
params,
varied_data,
self.as_substance_index(varied),
propagate=False,
**kwargs
)
sanity = [self._result_is_sane(init_concs, x) for x in xvecs]
if _plot:
import matplotlib.pyplot as plt
from pyneqsys.plotting import mpl_outside_legend
mpl_outside_legend(plt.gca())
varied_subst = self.substances[varied]
xlbl = (
"$[" + varied_subst.latex_name + "]_0$"
if latex_names
else str(varied_subst)
)
plt.gca().set_xlabel(xlbl + " / " + conc_unit_str)
plt.gca().set_ylabel("Concentration / " + conc_unit_str)
return xvecs, info_dicts, sanity
def roots(self, init_concs, varied_data, varied, x0=None,
NumSys=NumSysLog, plot_kwargs=None,
neqsys_type='chained_conditional', **kwargs):
"""
Parameters
----------
init_concs : array or dict
varied_data : array
varied_idx : int or str
x0 : array
NumSys : _NumSys subclass
See :class:`NumSysLin`, :class:`NumSysLog`, etc.
plot_kwargs : dict
See py:meth:`pyneqsys.NeqSys.solve`. Two additional keys
are intercepted here:
latex_names: bool (default: False)
conc_unit_str: str (default: 'M')
neqsys_type : str
what method to use for NeqSys construction (get_neqsys_*)
\*\*kwargs :
kwargs passed on to py:meth:`pyneqsys.NeqSys.solve_series`
"""
_plot = plot_kwargs is not None
if _plot:
latex_names = plot_kwargs.pop('latex_names', False)
conc_unit_str = plot_kwargs.pop('conc_unit_str', 'M')
if 'ax' not in plot_kwargs:
plot_kwargs['ax'] = self._get_default_plot_ax()
init_concs = self.as_per_substance_array(init_concs)
neqsys = self.get_neqsys(
neqsys_type, init_concs, NumSys=NumSys,
rref_equil=kwargs.pop('rref_equil', False),
rref_preserv=kwargs.pop('rref_preserv', False),
precipitates=kwargs.pop('precipitates', None))
if x0 is None:
x0 = init_concs
if _plot:
cb = neqsys.solve_and_plot_series
if 'plot_kwargs' not in kwargs:
kwargs['plot_kwargs'] = {}
if 'labels' not in kwargs['plot_kwargs']:
kwargs['plot_kwargs']['labels'] = (
self.substance_labels(latex_names))
if 'substances' in plot_kwargs:
if 'indices' in plot_kwargs:
raise ValueError("Now I am confused..")
kwargs['plot_kwargs']['indices'] = map(
self.as_substance_index, plot_kwargs.pop('substances'))
print(kwargs['plot_kwargs']['indices'])
else:
cb = neqsys.solve_series
params = np.concatenate((init_concs, self.eq_constants()))
xvecs, info_dicts = cb(
x0, params, varied_data, self.as_substance_index(varied),
propagate=False, **kwargs)
sanity = [self._result_is_sane(init_concs, x) for x in xvecs]
if _plot:
import matplotlib.pyplot as plt
from pyneqsys.plotting import mpl_outside_legend
mpl_outside_legend(plt.gca())
varied_subst = self.substances[varied]
xlbl = ('$[' + varied_subst.latex_name + ']_0$' if latex_names
else str(varied_subst))
plt.gca().set_xlabel(xlbl + ' / ' + conc_unit_str)
plt.gca().set_ylabel('Concentration / ' + conc_unit_str)
return xvecs, info_dicts, sanity
def roots(self, init_concs, varied_data, varied, x0=None,
NumSys=NumSysLog, plot_kwargs=None,
neqsys_type='chained_conditional', **kwargs):
"""
Parameters
----------
init_concs : array or dict
varied_data : array
varied_idx : int or str
x0 : array
NumSys : _NumSys subclass
See :class:`NumSysLin`, :class:`NumSysLog`, etc.
plot_kwargs : dict
See py:meth:`pyneqsys.NeqSys.solve`. Two additional keys
are intercepted here:
latex_names: bool (default: False)
conc_unit_str: str (default: 'M')
neqsys_type : str
what method to use for NeqSys construction (get_neqsys_*)
\\*\\*kwargs :
Keyword argumetns passed on to py:meth:`pyneqsys.NeqSys.solve_series`.
"""
_plot = plot_kwargs is not None
if _plot:
latex_names = plot_kwargs.pop('latex_names', False)
conc_unit_str = plot_kwargs.pop('conc_unit_str', 'M')
if 'ax' not in plot_kwargs:
plot_kwargs['ax'] = self._get_default_plot_ax()
init_concs = self.as_per_substance_array(init_concs)
neqsys = self.get_neqsys(
neqsys_type, NumSys=NumSys,
rref_equil=kwargs.pop('rref_equil', False),
rref_preserv=kwargs.pop('rref_preserv', False),
precipitates=kwargs.pop('precipitates', None))
if x0 is None:
x0 = init_concs
if _plot:
cb = neqsys.solve_and_plot_series
if 'plot_kwargs' not in kwargs:
kwargs['plot_kwargs'] = plot_kwargs
if 'labels' not in kwargs['plot_kwargs']:
kwargs['plot_kwargs']['labels'] = (
self.substance_labels(latex_names))
if 'substances' in plot_kwargs:
if 'indices' in plot_kwargs:
raise ValueError("Now I am confused..")
kwargs['plot_kwargs']['indices'] = map(
self.as_substance_index, plot_kwargs.pop('substances'))
print(kwargs['plot_kwargs']['indices'])
else:
cb = neqsys.solve_series
params = np.concatenate((init_concs, self.eq_constants()))
xvecs, info_dicts = cb(
x0, params, varied_data, self.as_substance_index(varied),
propagate=False, **kwargs)
sanity = [self._result_is_sane(init_concs, x) for x in xvecs]
if _plot:
import matplotlib.pyplot as plt
from pyneqsys.plotting import mpl_outside_legend
mpl_outside_legend(plt.gca())
varied_subst = self.substances[varied]
xlbl = ('$[' + varied_subst.latex_name + ']_0$' if latex_names
else str(varied_subst))
plt.gca().set_xlabel(xlbl + ' / ' + conc_unit_str)
plt.gca().set_ylabel('Concentration / ' + conc_unit_str)
return xvecs, info_dicts, sanity