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Sensitivities for AlgebraicRule models #2101

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Sensitivities for AlgebraicRule models #2101

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b3325e2
Sensitivities for AlgebraicRule models
dweindl May 22, 2023
74b9d3d
test
dweindl May 22, 2023
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42 changes: 35 additions & 7 deletions src/model_dae.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -164,14 +164,36 @@
const realtype t, const const_N_Vector x, const const_N_Vector dx
) {
auto x_pos = computeX_pos(x);
fdwdp(t, N_VGetArrayPointerConst(x_pos));

if (pythonGenerated) {
// python generated, not yet implemented for DAEs
throw AmiException("Wrapping of DAEs is not yet implemented from Python"
);
// python generated
derived_state_.dxdotdp_explicit.zero();
derived_state_.dxdotdp_implicit.zero();
if (derived_state_.dxdotdp_explicit.capacity()) {
fdxdotdp_explicit_colptrs(derived_state_.dxdotdp_explicit);
fdxdotdp_explicit_rowvals(derived_state_.dxdotdp_explicit);
fdxdotdp_explicit(

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derived_state_.dxdotdp_explicit.data(), t,
N_VGetArrayPointerConst(x_pos),
state_.unscaledParameters.data(), state_.fixedParameters.data(),
state_.h.data(), N_VGetArrayPointerConst(dx), derived_state_.w_.data()

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);
}

fdxdotdw(t, x_pos, dx);

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/* Sparse matrix multiplication
dxdotdp_implicit += dxdotdw * dwdp */
derived_state_.dxdotdw_.sparse_multiply(
derived_state_.dxdotdp_implicit, derived_state_.dwdp_

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);

derived_state_.dxdotdp_full.sparse_add(
derived_state_.dxdotdp_explicit, 1.0,
derived_state_.dxdotdp_implicit, 1.0

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);
} else {
// matlab generated
fdwdp(t, N_VGetArrayPointerConst(x_pos));

for (int ip = 0; ip < nplist(); ip++) {
N_VConst(0.0, derived_state_.dxdotdp.getNVector(ip));
Expand Down Expand Up @@ -496,9 +518,15 @@
}

if (pythonGenerated) {
// python generated, not yet implemented for DAEs
throw AmiException("Wrapping of DAEs is not yet implemented from Python"
);
/* copy dxdotdp and the implicit version over */
// initialize
N_VConst(0.0, sxdot);
realtype* sxdot_tmp = N_VGetArrayPointer(sxdot);

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derived_state_.dxdotdp_full.scatter(
plist(ip), 1.0, nullptr, gsl::make_span(sxdot_tmp, nx_solver), 0,

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nullptr, 0
);
} else {
/* copy dxdotdp over */
N_VScale(1.0, derived_state_.dxdotdp.getNVector(ip), sxdot);
Expand Down
7 changes: 4 additions & 3 deletions tests/testSBMLSuite.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,12 +76,15 @@ def test_sbml_testsuite_case(test_number, result_path, sbml_semantic_cases_dir):
current_test_path,
test_id,
model_dir,
generate_sensitivity_code=test_id in sensitivity_check_cases,
generate_sensitivity_code=True,
)
settings = read_settings_file(current_test_path, test_id)

atol, rtol = apply_settings(settings, solver, model, test_id)

solver.setSensitivityOrder(amici.SensitivityOrder.first)
solver.setSensitivityMethod(amici.SensitivityMethod.forward)

# simulate model
rdata = amici.runAmiciSimulation(model, solver)
if rdata["status"] != amici.AMICI_SUCCESS:
Expand All @@ -98,8 +101,6 @@ def test_sbml_testsuite_case(test_number, result_path, sbml_semantic_cases_dir):

# check sensitivities for selected models
if epsilon := sensitivity_check_cases.get(test_id):
solver.setSensitivityOrder(amici.SensitivityOrder.first)
solver.setSensitivityMethod(amici.SensitivityMethod.forward)
check_derivatives(model, solver, epsilon=epsilon)

except amici.sbml_import.SBMLException as err:
Expand Down
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