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#2331 fix bug in size of yS numpy array when simulation stops early #2337

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Oct 6, 2022
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#2331 fix bug in size of yS numpy array when simulation stops early #2337

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128e02e
#2331 fix bug in size of yS numpy array when simulation stops early
martinjrobins Oct 4, 2022
7f08623
#2331 add test for sens with events, fix bug in python-based idaklu s…
martinjrobins Oct 6, 2022
fe0fb8b
style: pre-commit fixes
pre-commit-ci[bot] Oct 6, 2022
a6bb115
#2331 add changlog entry
martinjrobins Oct 6, 2022
25d1d0b
style: pre-commit fixes
pre-commit-ci[bot] Oct 6, 2022
749019d
Update CHANGELOG.md
valentinsulzer Oct 6, 2022
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13 changes: 6 additions & 7 deletions pybamm/solvers/c_solvers/idaklu.cpp
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -283,7 +283,8 @@ Solution solve_python(np_array t_np, np_array y0_np, np_array yp0_np,
void *ida_mem; // pointer to memory
N_Vector yy, yp, avtol; // y, y', and absolute tolerance
N_Vector *yyS, *ypS; // y, y' for sensitivities
realtype rtol, *yval, *ypval, *atval, *ySval;
realtype rtol, *yval, *ypval, *atval;
std::vector<realtype *> ySval(number_of_parameters);
int retval;
SUNMatrix J;
SUNLinearSolver LS;
Expand All @@ -300,9 +301,6 @@ Solution solve_python(np_array t_np, np_array y0_np, np_array yp0_np,

// set initial value
yval = N_VGetArrayPointer(yy);
if (number_of_parameters > 0) {
ySval = N_VGetArrayPointer(yyS[0]);
}
ypval = N_VGetArrayPointer(yp);
atval = N_VGetArrayPointer(avtol);
int i;
Expand All @@ -314,6 +312,7 @@ Solution solve_python(np_array t_np, np_array y0_np, np_array yp0_np,
}

for (int is = 0 ; is < number_of_parameters; is++) {
ySval[is] = N_VGetArrayPointer(yyS[is]);
N_VConst(RCONST(0.0), yyS[is]);
N_VConst(RCONST(0.0), ypS[is]);
}
Expand Down Expand Up @@ -376,7 +375,7 @@ Solution solve_python(np_array t_np, np_array y0_np, np_array yp0_np,
for (int j = 0; j < number_of_parameters; j++) {
const int base_index = j * number_of_timesteps * number_of_states;
for (int k = 0; k < number_of_states; k++) {
yS_return[base_index + k] = ySval[j * number_of_states + k];
yS_return[base_index + k] = ySval[j][k];
}
}

Expand Down Expand Up @@ -417,7 +416,7 @@ Solution solve_python(np_array t_np, np_array y0_np, np_array yp0_np,
const int base_index = j * number_of_timesteps * number_of_states
+ t_i * number_of_states;
for (int k = 0; k < number_of_states; k++) {
yS_return[base_index + k] = ySval[j * number_of_states + k];
yS_return[base_index + k] = ySval[j][k];
}
}
t_i += 1;
Expand Down Expand Up @@ -445,7 +444,7 @@ Solution solve_python(np_array t_np, np_array y0_np, np_array yp0_np,
np_array t_ret = np_array(t_i, &t_return[0]);
np_array y_ret = np_array(t_i * number_of_states, &y_return[0]);
np_array yS_ret = np_array(
std::vector<ptrdiff_t>{number_of_parameters, t_i, number_of_states},
std::vector<ptrdiff_t>{number_of_parameters, number_of_timesteps, number_of_states},
&yS_return[0]
);

Expand Down
170 changes: 7 additions & 163 deletions pybamm/solvers/c_solvers/idaklu_casadi.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,15 +15,6 @@ class CasadiFunction {
size_t sz_iw;
size_t sz_w;
m_func.sz_work(sz_arg, sz_res, sz_iw, sz_w);
//std::cout << "name = "<< m_func.name() << " arg = " << sz_arg << " res = " << sz_res << " iw = " << sz_iw << " w = " << sz_w << std::endl;
//for (int i = 0; i < sz_arg; i++) {
// std::cout << "Sparsity for input " << i << std::endl;
// const Sparsity& sparsity = m_func.sparsity_in(i);
//}
//for (int i = 0; i < sz_res; i++) {
// std::cout << "Sparsity for output " << i << std::endl;
// const Sparsity& sparsity = m_func.sparsity_out(i);
//}
m_arg.resize(sz_arg);
m_res.resize(sz_res);
m_iw.resize(sz_iw);
Expand Down Expand Up @@ -104,59 +95,25 @@ int residual_casadi(realtype tres, N_Vector yy, N_Vector yp, N_Vector rr,
CasadiFunctions *p_python_functions =
static_cast<CasadiFunctions *>(user_data);

//std::cout << "RESIDUAL t = " << tres << " y = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << NV_DATA_S(yy)[i] << " ";
//}
//std::cout << "] yp = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << NV_DATA_S(yp)[i] << " ";
//}
//std::cout << "]" << std::endl;
// args are t, y, put result in rr

py::buffer_info input_buf = p_python_functions->inputs.request();
p_python_functions->rhs_alg.m_arg[0] = &tres;
p_python_functions->rhs_alg.m_arg[1] = NV_DATA_S(yy);
p_python_functions->rhs_alg.m_arg[2] = static_cast<realtype *>(input_buf.ptr);
p_python_functions->rhs_alg.m_res[0] = NV_DATA_S(rr);
p_python_functions->rhs_alg();

//std::cout << "rhs_alg = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << NV_DATA_S(rr)[i] << " ";
//}
//std::cout << "]" << std::endl;

realtype *tmp = p_python_functions->get_tmp();
//std::cout << "tmp before = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << tmp[i] << " ";
//}
//std::cout << "]" << std::endl;

// args is yp, put result in tmp
p_python_functions->mass_action.m_arg[0] = NV_DATA_S(yp);
p_python_functions->mass_action.m_res[0] = tmp;
p_python_functions->mass_action();

//std::cout << "tmp = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << tmp[i] << " ";
//}
//std::cout << "]" << std::endl;

// AXPY: y <- a*x + y
const int ns = p_python_functions->number_of_states;
casadi_axpy(ns, -1., tmp, NV_DATA_S(rr));

//std::cout << "residual = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << NV_DATA_S(rr)[i] << " ";
//}
//std::cout << "]" << std::endl;

// now rr has rhs_alg(t, y) - mass_matrix * yp

return 0;
}

Expand Down Expand Up @@ -246,16 +203,9 @@ int jacobian_casadi(realtype tt, realtype cj, N_Vector yy, N_Vector yp,
const int n_row_vals = jac_times_cjmass_rowvals.request().size;
auto p_jac_times_cjmass_rowvals = jac_times_cjmass_rowvals.unchecked<1>();

//std::cout << "jac_data = [";
//for (int i = 0; i < p_python_functions->number_of_nnz; i++) {
// std::cout << jac_data[i] << " ";
//}
//std::cout << "]" << std::endl;

// just copy across row vals (do I need to do this every time?)
// (or just in the setup?)
for (int i = 0; i < n_row_vals; i++) {
//std::cout << "check row vals " << jac_rowvals[i] << " " << p_jac_times_cjmass_rowvals[i] << std::endl;
jac_rowvals[i] = p_jac_times_cjmass_rowvals[i];
}

Expand All @@ -265,7 +215,6 @@ int jacobian_casadi(realtype tt, realtype cj, N_Vector yy, N_Vector yp,

// just copy across col ptrs (do I need to do this every time?)
for (int i = 0; i < n_col_ptrs; i++) {
//std::cout << "check col ptrs " << jac_colptrs[i] << " " << p_jac_times_cjmass_colptrs[i] << std::endl;
jac_colptrs[i] = p_jac_times_cjmass_colptrs[i];
}

Expand All @@ -278,17 +227,6 @@ int events_casadi(realtype t, N_Vector yy, N_Vector yp, realtype *events_ptr,
CasadiFunctions *p_python_functions =
static_cast<CasadiFunctions *>(user_data);

//std::cout << "EVENTS" << std::endl;
//std::cout << "t = " << t << " y = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << NV_DATA_S(yy)[i] << " ";
//}
//std::cout << "] yp = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << NV_DATA_S(yp)[i] << " ";
//}
//std::cout << "]" << std::endl;

// args are t, y, put result in events_ptr
py::buffer_info input_buf = p_python_functions->inputs.request();
p_python_functions->events.m_arg[0] = &t;
Expand All @@ -297,12 +235,6 @@ int events_casadi(realtype t, N_Vector yy, N_Vector yp, realtype *events_ptr,
p_python_functions->events.m_res[0] = events_ptr;
p_python_functions->events();

//std::cout << "events = [";
//for (int i = 0; i < p_python_functions->number_of_events; i++) {
// std::cout << events_ptr[i] << " ";
//}
//std::cout << "]" << std::endl;

return (0);
}

Expand Down Expand Up @@ -336,32 +268,6 @@ int sensitivities_casadi(int Ns, realtype t, N_Vector yy, N_Vector yp,

const int np = p_python_functions->number_of_parameters;

//std::cout << "SENS t = " << t << " y = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << NV_DATA_S(yy)[i] << " ";
//}
//std::cout << "] yp = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << NV_DATA_S(yp)[i] << " ";
//}
//std::cout << "] yS = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << NV_DATA_S(yS[0])[i] << " ";
//}
//std::cout << "] ypS = [";
//for (int i = 0; i < p_python_functions->number_of_states; i++) {
// std::cout << NV_DATA_S(ypS[0])[i] << " ";
//}
//std::cout << "]" << std::endl;

//for (int i = 0; i < np; i++) {
// std::cout << "dF/dp before = [" << i << "] = [";
// for (int j = 0; j < p_python_functions->number_of_states; j++) {
// std::cout << NV_DATA_S(resvalS[i])[j] << " ";
// }
// std::cout << "]" << std::endl;
//}

// args are t, y put result in rr
py::buffer_info input_buf = p_python_functions->inputs.request();
p_python_functions->sens.m_arg[0] = &t;
Expand All @@ -374,13 +280,6 @@ int sensitivities_casadi(int Ns, realtype t, N_Vector yy, N_Vector yp,
p_python_functions->sens();

for (int i = 0; i < np; i++) {
//std::cout << "dF/dp = [" << i << "] = [";
//for (int j = 0; j < p_python_functions->number_of_states; j++) {
// std::cout << NV_DATA_S(resvalS[i])[j] << " ";
//}
//std::cout << "]" << std::endl;


// put (∂F/∂y)s i (t) in tmp
realtype *tmp = p_python_functions->get_tmp();
p_python_functions->jac_action.m_arg[0] = &t;
Expand All @@ -390,12 +289,6 @@ int sensitivities_casadi(int Ns, realtype t, N_Vector yy, N_Vector yp,
p_python_functions->jac_action.m_res[0] = tmp;
p_python_functions->jac_action();

//std::cout << "jac_action = [" << i << "] = [";
//for (int j = 0; j < p_python_functions->number_of_states; j++) {
// std::cout << tmp[j] << " ";
//}
//std::cout << "]" << std::endl;

const int ns = p_python_functions->number_of_states;
casadi_axpy(ns, 1., tmp, NV_DATA_S(resvalS[i]));

Expand All @@ -404,22 +297,9 @@ int sensitivities_casadi(int Ns, realtype t, N_Vector yy, N_Vector yp,
p_python_functions->mass_action.m_res[0] = tmp;
p_python_functions->mass_action();

//std::cout << "mass_Action = [" << i << "] = [";
//for (int j = 0; j < p_python_functions->number_of_states; j++) {
// std::cout << tmp[j] << " ";
//}
//std::cout << "]" << std::endl;


// (∂F/∂y)s i (t)+(∂F/∂ ẏ) ṡ i (t)+(∂F/∂p i )
// AXPY: y <- a*x + y
casadi_axpy(ns, -1., tmp, NV_DATA_S(resvalS[i]));

//std::cout << "resvalS[" << i << "] = [";
//for (int j = 0; j < p_python_functions->number_of_states; j++) {
// std::cout << NV_DATA_S(resvalS[i])[j] << " ";
//}
//std::cout << "]" << std::endl;
}

return 0;
Expand Down Expand Up @@ -457,7 +337,8 @@ Solution solve_casadi(np_array t_np, np_array y0_np, np_array yp0_np,
void *ida_mem; // pointer to memory
N_Vector yy, yp, avtol; // y, y', and absolute tolerance
N_Vector *yyS, *ypS; // y, y' for sensitivities
realtype rtol, *yval, *ypval, *atval, *ySval;
realtype rtol, *yval, *ypval, *atval;
std::vector<realtype *> ySval(number_of_parameters);
int retval;
SUNMatrix J;
SUNLinearSolver LS;
Expand All @@ -474,9 +355,6 @@ Solution solve_casadi(np_array t_np, np_array y0_np, np_array yp0_np,

// set initial value
yval = N_VGetArrayPointer(yy);
if (number_of_parameters > 0) {
ySval = N_VGetArrayPointer(yyS[0]);
}
ypval = N_VGetArrayPointer(yp);
atval = N_VGetArrayPointer(avtol);
int i;
Expand All @@ -488,6 +366,7 @@ Solution solve_casadi(np_array t_np, np_array y0_np, np_array yp0_np,
}

for (int is = 0 ; is < number_of_parameters; is++) {
ySval[is] = N_VGetArrayPointer(yyS[is]);
N_VConst(RCONST(0.0), yyS[is]);
N_VConst(RCONST(0.0), ypS[is]);
}
Expand Down Expand Up @@ -547,37 +426,6 @@ Solution solve_casadi(np_array t_np, np_array y0_np, np_array yp0_np,

SUNLinSolInitialize(LS);

//std::cout << "number of jacobian nz = " << jac_times_cjmass_nnz << std::endl;
//N_Vector rr, tmp1, tmp2, tmp3;
//rr = N_VNew_Serial(number_of_states);
//tmp1 = N_VNew_Serial(number_of_states);
//tmp2 = N_VNew_Serial(number_of_states);
//tmp3 = N_VNew_Serial(number_of_states);
//std::vector<realtype> events_vect(number_of_events);
//auto start = std::chrono::high_resolution_clock::now();
//for (int i = 0; i < 10; i++) {
// residual_casadi(0, yy, yp, rr, user_data);
//}
//auto end = std::chrono::high_resolution_clock::now();
//std::chrono::duration<double> diff = end - start;
//std::cout << "Time to call residual " << diff.count() << " s\n";

//start = std::chrono::high_resolution_clock::now();
//for (int i = 0; i < 10; i++) {
// events_casadi(0, yy, yp, events_vect.data(), user_data);
//}
//end = std::chrono::high_resolution_clock::now();
//diff = end - start;
//std::cout << "Time to call events " << diff.count() << " s\n";

//start = std::chrono::high_resolution_clock::now();
//for (int i = 0; i < 10; i++) {
// jacobian_casadi(0, 1, yy, yp, rr, J, user_data, tmp1, tmp2, tmp3);
//}
//end = std::chrono::high_resolution_clock::now();
//diff = end - start;
//std::cout << "Time to call jacobian " << diff.count() << " s\n";

int t_i = 1;
realtype tret;
realtype t_next;
Expand Down Expand Up @@ -609,7 +457,7 @@ Solution solve_casadi(np_array t_np, np_array y0_np, np_array yp0_np,
for (int j = 0; j < number_of_parameters; j++) {
const int base_index = j * number_of_timesteps * number_of_states;
for (int k = 0; k < number_of_states; k++) {
yS_return[base_index + k] = ySval[j * number_of_states + k];
yS_return[base_index + k] = ySval[j][k];
}
}

Expand Down Expand Up @@ -649,7 +497,7 @@ Solution solve_casadi(np_array t_np, np_array y0_np, np_array yp0_np,
const int base_index = j * number_of_timesteps * number_of_states
+ t_i * number_of_states;
for (int k = 0; k < number_of_states; k++) {
yS_return[base_index + k] = ySval[j * number_of_states + k];
yS_return[base_index + k] = ySval[j][k];
}
}
t_i += 1;
Expand All @@ -665,7 +513,7 @@ Solution solve_casadi(np_array t_np, np_array y0_np, np_array yp0_np,
np_array t_ret = np_array(t_i, &t_return[0], free_t_when_done);
np_array y_ret = np_array(t_i * number_of_states, &y_return[0], free_y_when_done);
np_array yS_ret = np_array(
std::vector<ptrdiff_t>{number_of_parameters, t_i, number_of_states},
std::vector<ptrdiff_t>{number_of_parameters, number_of_timesteps, number_of_states},
&yS_return[0], free_yS_when_done
);

Expand Down Expand Up @@ -729,10 +577,6 @@ Solution solve_casadi(np_array t_np, np_array y0_np, np_array yp0_np,

IDAFree(&ida_mem);

//std::cout << "finished solving 9" << std::endl;

//std::cout << "finished solving 10" << std::endl;

return sol;
}

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