def _validate(conditions, rsys, symbols, odesys, backend=None, transform=None, ignore=('time',)):
""" For use with create_odesys
Parameters
----------
conditions : OrderedDict
Parameters, values with units from ``chempy.units``.
rsys : ReactionSystem
symbols : dict
Mapping variable name to symbols.
backend : module
Module for symbolic mathematics. (defaults to SymPy)
transform : callable for rewriting expressions
Raises
------
``KeyError`` if a key in conditions is not in odesys.names or odesys.param_names
"""
if backend is None:
from sym import Backend
backend = Backend(backend)
if transform is None:
if backend.__name__ != 'sympy':
warnings.warn("Backend != SymPy, provide your own transform function.")
def transform(arg):
expr = backend.logcombine(arg, force=True)
v, w = map(backend.Wild, 'v w'.split())
expr = expr.replace(backend.log(w**v), v*backend.log(w))
return expr
args = [symbols[key] for key in conditions]
seen = [False]*len(args)
rates = {}
for k, v in rsys.rates(symbols).items():
expr = transform(v)
if expr == 0:
rate = 0 * u.molar/u.second
else:
rate = backend.lambdify(args, expr)(*conditions.values())
to_unitless(rate, u.molar/u.second)
rates[k] = rate
seen = [b or a in expr.free_symbols for b, a in zip(seen, args)]
not_seen = [a for s, a in zip(seen, args) if not s]
for k in conditions:
if k not in odesys.param_names and k not in odesys.names and k not in ignore:
raise KeyError("Unknown param: %s" % k)
return {'not_seen': not_seen, 'rates': rates}
def _validate(
conditions,
rsys,
symbols,
odesys,
backend=None,
transform=None,
ignore=("time", ),
check_conditions_no_extra=False,
):
"""For use with create_odesys
Parameters
----------
conditions : OrderedDict
Parameters, values with units from ``chempy.units``.
rsys : ReactionSystem
symbols : dict
Mapping variable name to symbols.
backend : module
Module for symbolic mathematics. (defaults to SymPy)
transform : callable for rewriting expressions
check_conditions_no_extra : bool
When True, conditions may not contain keys not referenced in any expression.
Raises
------
``KeyError`` if a key in conditions is not in odesys.names or odesys.param_names
"""
if backend is None:
from sym import Backend
backend = Backend(backend)
if transform is None:
if backend.__name__ != "sympy":
warnings.warn(
"Backend != SymPy, provide your own transform function.")
def transform(arg):
expr = backend.logcombine(arg, force=True)
v, w = map(backend.Wild, "v w".split())
return expr.replace(backend.log(w**v), v * backend.log(w))
rates = {}
seen = set()
for k, v in rsys.rates(symbols).items():
expr = transform(v)
if expr == 0:
rate = 0 * u.molar / u.second
else:
rate = None
for term in (expr.args if hasattr(expr, "is_Add") and expr.is_Add
else (expr, )):
args = sorted(expr.free_symbols, key=lambda e: e.name)
values = [conditions[s.name] for s in args]
result = backend.lambdify(args, term)(*map(_exact, values))
to_unitless(result, u.molar /
u.second) # raises an exception upon unit error
if rate is None:
rate = result
else:
rate += result
rates[k] = rate
seen |= set([s.name for s in expr.free_symbols])
if check_conditions_no_extra:
for k in conditions:
if (k not in odesys.param_names and k not in odesys.names
and k not in ignore):
raise KeyError("Unknown param: %s" % k)
return {
"not_seen": (set(rsys.substances) | set(conditions)) - seen,
"rates": rates
}
