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Description Consider a MOD file glia__dbbs_mod_collection__Na__granule_cell.mod which has:
FUNCTION alfa (v (mV ))(/ ms ){
alfa = Q10 * Aalfa * exp (v / Valfa )
}
FUNCTION beta (v (mV ))(/ ms ){
beta = Q10 * Abeta * exp (- v / Vbeta )
}
FUNCTION teta (v (mV ))(/ ms ){
teta = Q10 * Ateta * exp (- v / Vteta )
}
KINETIC kstates {
: 1 riga
~ C1 < - > C2 (n1 * alfa (v ),n4 * beta (v ))
~ C2 < - > C3 (n2 * alfa (v ),n3 * beta (v ))
~ C3 < - > C4 (n3 * alfa (v ),n2 * beta (v ))
~ C4 < - > C5 (n4 * alfa (v ),n1 * beta (v ))
~ C5 < - > O (gamma ,delta )
~ O < - > OB (epsilon ,teta (v ))
: 2 riga
~ I1 < - > I2 (n1 * alfa (v )* a ,n4 * beta (v )* b )
~ I2 < - > I3 (n2 * alfa (v )* a ,n3 * beta (v )* b )
~ I3 < - > I4 (n3 * alfa (v )* a ,n2 * beta (v )* b )
~ I4 < - > I5 (n4 * alfa (v )* a ,n1 * beta (v )* b )
~ I5 < - > I6 (gamma ,delta )
: connette 1 riga con 2 riga
~ C1 < - > I1 (Con ,Coff )
~ C2 < - > I2 (Con * a ,Coff * b )
~ C3 < - > I3 (Con * a ^ 2 ,Coff * b ^ 2 )
~ C4 < - > I4 (Con * a ^ 3 ,Coff * b ^ 3 )
~ C5 < - > I5 (Con * a ^ 4 ,Coff * b ^ 4 )
~ O < - > I6 (Oon ,Ooff )
CONSERVE C1 + C2 + C3 + C4 + C5 + O + OB + I1 + I2 + I3 + I4 + I5 + I6 = 1
}when we run this via NMODl we get:
./bin/nmodl mod2c/glia__dbbs_mod_collection__Na__granule_cell.mod host --c passes --inline
[NMODL] [info] :: Processing ../../../build_nmodl/x86_64/corenrn/mod2c/glia__dbbs_mod_collection__Na__granule_cell.mod
[NMODL] [info] :: Running semantic analysis visitor
[NMODL] [info] :: Running symtab visitor
[NMODL] [info] :: Running CVode to cnexp visitor
[NMODL] [info] :: Running code compatibility checker
[NMODL] [info] :: Running verbatim rename visitor
[NMODL] [info] :: Running KINETIC block visitor
[NMODL] [info] :: Running STEADYSTATE visitor
[NMODL] [info] :: Parsing Units
[NMODL] [info] :: Running nmodl inline visitor
[NMODL] [info] :: Running local variable rename visitor
[NMODL] [info] :: Automatically enable sympy_analytic because it exists solver of type sparse
[NMODL] [info] :: Running sympy solve visitor
[NMODL] [warning] :: SympySolverVisitor :: solve_non_lin_system python exception: 'Symbol' object is not callable
[NMODL] [info] :: Running cnexp visitor
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [error] :: NeuronSolveVisitor :: solver method 'sparse' not supported
[NMODL] [info] :: Running C backend code generator
[NMODL] [warning] :: RenameVisitor :: Renaming variable v at 121.15 to arg_v
[NMODL] [warning] :: RenameVisitor :: Renaming variable v at 122.23 to arg_v
[NMODL] [warning] :: RenameVisitor :: Renaming variable v at 125.15 to arg_v
[NMODL] [warning] :: RenameVisitor :: Renaming variable v at 126.24 to arg_v
[NMODL] [warning] :: RenameVisitor :: Renaming variable v at 129.15 to arg_v
[NMODL] [warning] :: RenameVisitor :: Renaming variable v at 130.24 to arg_v
[NMODL] [warning] :: RenameVisitor :: Renaming variable alfa at 122.2-5 to ret_alfa
[NMODL] [warning] :: RenameVisitor :: Renaming variable beta at 126.2-5 to ret_beta
[NMODL] [warning] :: RenameVisitor :: Renaming variable teta at 130.2-5 to ret_teta
libc++abi: terminating with uncaught exception of type std::runtime_error: PRIME encountered during code generation, ODEs not solved? Here some quick comments:
note the function calls alpha, beta and teta. I think they are not inlined in the above example and probably make sense
but, if we pass the statements with function calls to sympy, it won't be able to do right thing in the absence of function definition?
The above needs to be verified. Calling sympy / solver expert @cattabiani !
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Consider a MOD file glia__dbbs_mod_collection__Na__granule_cell.mod which has:
when we run this via NMODl we get:
Here some quick comments:
alpha,betaandteta. I think they are not inlined in the above example and probably make senseThe above needs to be verified. Calling sympy / solver expert @cattabiani !