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Allow definition of log() functions #181

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Merged
jorgensd merged 1 commit into from
Sep 3, 2025
Merged

Allow definition of log() functions #181

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22 changes: 12 additions & 10 deletions smart/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -756,14 +756,14 @@ def _init_4_0_initialize_dolfin_parameters(self):
if parameter.type == ParameterType.constant:
parameter.dolfin_constant = d.Constant(parameter.value, name=parameter.name)
elif parameter.type == ParameterType.expression and parameter.is_space_dependent:
c_code = sym.printing.ccode(parameter.sym_expr)
c_code = c_code.replace("log(", "std::log(")
# use higher degree to avoid interpolation error
parameter.dolfin_expression = d.Expression(
sym.printing.ccode(parameter.sym_expr), t=self.T, degree=3
)
parameter.dolfin_expression = d.Expression(c_code, t=self.T, degree=3)
elif parameter.type == ParameterType.expression and not parameter.use_preintegration:
parameter.dolfin_expression = d.Expression(
sym.printing.ccode(parameter.sym_expr), t=self.T, degree=1
)
c_code = sym.printing.ccode(parameter.sym_expr)
c_code = c_code.replace("log(", "std::log(")
parameter.dolfin_expression = d.Expression(c_code, t=self.T, degree=1)
elif parameter.type == ParameterType.expression and parameter.use_preintegration:
parameter.dolfin_constant = d.Constant(parameter.value, name=parameter.name)
elif parameter.type == ParameterType.from_file:
Expand Down Expand Up @@ -1909,9 +1909,9 @@ def update_time_dependent_parameters(self):
a = parameter.preint_sym_expr.subs({"t": tn}).evalf()
b = parameter.preint_sym_expr.subs({"t": t}).evalf()
if parameter.is_space_dependent:
parameter.dolfin_expression = d.Expression(
sym.printing.ccode((b - a) / dt), degree=3
)
c_code = sym.printing.ccode((b - a) / dt)
c_code = c_code.replace("log(", "std::log(")
parameter.dolfin_expression = d.Expression(c_code, degree=3)
logger.debug(
f"Time-dependent parameter {parameter_name} updated by "
f"pre-integrated expression",
Expand Down Expand Up @@ -2006,7 +2006,9 @@ def dolfin_set_function_values(self, sp, ukey, unew):
else:
x = d.SpatialCoordinate(sp.compartment.dolfin_mesh)
curv = sp.compartment.curv_func
full_expr = d.Expression(sym.printing.ccode(sym_expr), curv=curv, degree=1)
c_code = sym.printing.ccode(sym_expr)
c_code = c_code.replace("log(", "std::log(")
full_expr = d.Expression(c_code, curv=curv, degree=1)
ufunc = d.interpolate(full_expr, sp.V)
d.assign(sp.u[ukey], ufunc)
elif isinstance(unew, d.Expression):
Expand Down
10 changes: 6 additions & 4 deletions smart/model_assembly.py
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Original file line number Diff line number Diff line change
Expand Up @@ -775,7 +775,9 @@ def from_expression(
if is_time_dependent and not is_space_dependent:
value = float(sym_expr.subs({"t": 0.0}))
else:
dolfin_expression = d.Expression(sym.printing.ccode(sym_expr), t=0.0, degree=3)
c_code = sym.printing.ccode(sym_expr)
c_code = c_code.replace("log(", "std::log(")
dolfin_expression = d.Expression(c_code, t=0.0, degree=3)
value = float(sym_expr.subs({"t": 0.0, "x[0]": 0.0, "x[1]": 0.0, "x[2]": 0.0}))

parameter = cls(
Expand Down Expand Up @@ -1002,9 +1004,9 @@ def __post_init__(self):
f"Creating dolfin object for space-dependent initial condition {self.name}",
extra=dict(format_type="log"),
)
self.initial_condition_expression = d.Expression(
sym.printing.ccode(sym_expr), degree=1
)
c_code = sym.printing.ccode(sym_expr)
c_code = c_code.replace("log(", "std::log(")
self.initial_condition_expression = d.Expression(c_code, degree=1)
elif isinstance(self.initial_condition, Path):
pass # keep as path
else:
Expand Down