static void propagate_debug (Treelog& msg, int nest, const std::string& text)
{
switch (nest)
{
case is_unknown:
case is_debug:
case is_plain:
case is_warning:
case is_error:
case is_bug:
msg.debug (text);
break;
case is_close:
msg.close ();
break;
case is_touch:
msg.touch ();
break;
case is_flush:
msg.flush ();
break;
default:
msg.open (text);
}
}
void
Horizon::Implementation::initialize (Hydraulic& hydraulic,
const Texture& texture,
const double quarts,
int som_size,
const bool top_soil,
const double center_z,
Treelog& msg)
{
if (CEC < 0.0)
{
CEC = default_CEC (texture);
std::ostringstream tmp;
tmp << "(CEC " << CEC
<< " [cmolc/kg]) ; Estimated from clay and humus.";
msg.debug (tmp.str ());
}
hydraulic.initialize (texture, dry_bulk_density, top_soil, CEC, center_z, msg);
if (som_size > 0)
{
// Fill out SOM_fractions and SOM_C_per_N.
if (SOM_C_per_N.size () > 0 && SOM_C_per_N.size () < som_size + 0U)
SOM_C_per_N.insert (SOM_C_per_N.end (),
som_size - SOM_C_per_N.size (),
SOM_C_per_N.back ());
if (SOM_fractions.size () > 0 && SOM_fractions.size () < som_size + 0U)
SOM_fractions.insert (SOM_fractions.end (),
som_size - SOM_fractions.size (),
0.0);
}
// Did we specify 'dry_bulk_density'? Else calculate it now.
if (dry_bulk_density < 0.0)
{
dry_bulk_density = texture.rho_soil_particles ()
* (1.0 - hydraulic.porosity ());
std::ostringstream tmp;
tmp << "(dry_bulk_density " << dry_bulk_density
<< " [g/cm^3]) ; Estimated from porosity and texture.";
msg.debug (tmp.str ());
}
hor_heat.initialize (hydraulic, texture, quarts, msg);
}
void initialize (const Texture& texture,
double rho_b, const bool top_soil, const double CEC,
const double center_z, Treelog& msg)
{
TREELOG_MODEL (msg);
std::ostringstream tmp;
// Find Theta_sat.
if (Theta_sat < 0.0)
{
if (rho_b < 0.0)
{
msg.error ("You must specify either dry bulk density or porosity");
rho_b = 1.5;
tmp << "Forcing rho_b = " << rho_b << " g/cm^3\n";
}
Theta_sat = 1.0 - rho_b / texture.rho_soil_particles ();
tmp << "(Theta_sat " << Theta_sat << " [])\n";
daisy_assert (Theta_sat < 1.0);
}
if (Theta_sat <= Theta_fc)
{
msg.error ("Field capacity must be below saturation point");
Theta_sat = (1.0 + 4.0 * Theta_fc) / 5.0;
tmp << "Forcing Theta_sat = " << Theta_sat << " []\n";
}
// Find Theta_wp.
if (Theta_wp < 0.0)
{
const double clay_lim // USDA Clay
= texture.fraction_of_minerals_smaller_than ( 2.0 /* [um] */);
const double silt_lim // USDA Silt
= texture.fraction_of_minerals_smaller_than (50.0 /* [um] */);
daisy_assert (clay_lim >= 0.0);
daisy_assert (silt_lim >= clay_lim);
daisy_assert (silt_lim <= 1.0);
const double mineral = texture.mineral ();
const double clay = mineral * clay_lim * 100 /* [%] */;
const double silt = mineral * (silt_lim - clay_lim) * 100 /* [%] */;
const double humus = texture.humus * 100 /* [%] */;
// Madsen and Platou (1983).
Theta_wp = 0.758 * humus + 0.520 * clay + 0.075 * silt + 0.42;
Theta_wp /= 100.0; // [%] -> []
}
b = find_b (Theta_wp, Theta_fc);
h_b = find_h_b (Theta_wp, Theta_fc, Theta_sat, b);
tmp << "(b " << b << " [])\n"
<< "(h_b " << h_b << " [cm])";
msg.debug (tmp.str ());
// Must be called last (K_init depends on the other parameters).
Hydraulic::initialize (texture, rho_b, top_soil, CEC, center_z, msg);
}
void
SoilWater::drain (const std::vector<double>& v, Treelog& msg)
{
forward_sink (v, v);
daisy_assert (S_sum_.size () == v.size ());
daisy_assert (S_drain_.size () == v.size ());
daisy_assert (S_soil_drain_.size () == v.size ());
for (unsigned i = 0; i < v.size (); i++)
{
if (v[i] < -1e-8)
{
std::ostringstream tmp;
tmp << "draining " << v[i] << " [h^-1] from cell " << i;
msg.debug (tmp.str ());
}
S_sum_[i] += v[i];
S_drain_[i] += v[i];
S_soil_drain_[i] += v[i];
}
}
void
UZRectMollerup::tick (const GeometryRect& geo,
const std::vector<size_t>& drain_cell,
const double drain_water_level,
const Soil& soil,
SoilWater& soil_water, const SoilHeat& soil_heat,
const Surface& surface, const Groundwater& groundwater,
const double dt, Treelog& msg)
{
daisy_assert (K_average.get ());
const size_t edge_size = geo.edge_size (); // number of edges
const size_t cell_size = geo.cell_size (); // number of cells
// Insert magic here.
ublas::vector<double> Theta (cell_size); // water content
ublas::vector<double> Theta_previous (cell_size); // at start of small t-step
ublas::vector<double> h (cell_size); // matrix pressure
ublas::vector<double> h_previous (cell_size); // at start of small timestep
ublas::vector<double> h_ice (cell_size); //
ublas::vector<double> S (cell_size); // sink term
ublas::vector<double> S_vol (cell_size); // sink term
#ifdef TEST_OM_DEN_ER_BRUGT
ublas::vector<double> S_macro (cell_size); // sink term
std::vector<double> S_drain (cell_size, 0.0); // matrix-> macro -> drain flow
std::vector<double> S_drain_sum (cell_size, 0.0); // For large timestep
const std::vector<double> S_matrix (cell_size, 0.0); // matrix -> macro
std::vector<double> S_matrix_sum (cell_size, 0.0); // for large timestep
#endif
ublas::vector<double> T (cell_size); // temperature
ublas::vector<double> Kold (edge_size); // old hydraulic conductivity
ublas::vector<double> Ksum (edge_size); // Hansen hydraulic conductivity
ublas::vector<double> Kcell (cell_size); // hydraulic conductivity
ublas::vector<double> Kold_cell (cell_size); // old hydraulic conductivity
ublas::vector<double> Ksum_cell (cell_size); // Hansen hydraulic conductivity
ublas::vector<double> h_lysimeter (cell_size);
std::vector<bool> active_lysimeter (cell_size);
const std::vector<size_t>& edge_above = geo.cell_edges (Geometry::cell_above);
const size_t edge_above_size = edge_above.size ();
ublas::vector<double> remaining_water (edge_above_size);
std::vector<bool> drain_cell_on (drain_cell.size (),false);
for (size_t i = 0; i < edge_above_size; i++)
{
const size_t edge = edge_above[i];
remaining_water (i) = surface.h_top (geo, edge);
}
ublas::vector<double> q; // Accumulated flux
q = ublas::zero_vector<double> (edge_size);
ublas::vector<double> dq (edge_size); // Flux in small timestep.
dq = ublas::zero_vector<double> (edge_size);
//Make Qmat area diagonal matrix
//Note: This only needs to be calculated once...
ublas::banded_matrix<double> Qmat (cell_size, cell_size, 0, 0);
for (int c = 0; c < cell_size; c++)
Qmat (c, c) = geo.cell_volume (c);
// make vectors
for (size_t cell = 0; cell != cell_size ; ++cell)
{
Theta (cell) = soil_water.Theta (cell);
h (cell) = soil_water.h (cell);
h_ice (cell) = soil_water.h_ice (cell);
S (cell) = soil_water.S_sum (cell);
S_vol (cell) = S (cell) * geo.cell_volume (cell);
if (use_forced_T)
T (cell) = forced_T;
else
T (cell) = soil_heat.T (cell);
h_lysimeter (cell) = geo.zplus (cell) - geo.cell_z (cell);
}
// Remember old value.
Theta_error = Theta;
// Start time loop
double time_left = dt; // How much of the large time step left.
double ddt = dt; // We start with small == large time step.
int number_of_time_step_reductions = 0;
int iterations_with_this_time_step = 0;
int n_small_time_steps = 0;
while (time_left > 0.0)
{
if (ddt > time_left)
ddt = time_left;
std::ostringstream tmp_ddt;
tmp_ddt << "Time t = " << (dt - time_left)
<< "; ddt = " << ddt
<< "; steps " << n_small_time_steps
<< "; time left = " << time_left;
Treelog::Open nest (msg, tmp_ddt.str ());
if (n_small_time_steps > 0
&& (n_small_time_steps%msg_number_of_small_time_steps) == 0)
{
msg.touch ();
msg.flush ();
}
n_small_time_steps++;
if (n_small_time_steps > max_number_of_small_time_steps)
{
msg.debug ("Too many small timesteps");
throw "Too many small timesteps";
}
// Initialization for each small time step.
if (debug > 0)
{
std::ostringstream tmp;
tmp << "h = " << h << "\n";
tmp << "Theta = " << Theta;
msg.message (tmp.str ());
}
int iterations_used = 0;
h_previous = h;
Theta_previous = Theta;
if (debug == 5)
{
std::ostringstream tmp;
tmp << "Remaining water at start: " << remaining_water;
msg.message (tmp.str ());
}
ublas::vector<double> h_conv;
for (size_t cell = 0; cell != cell_size ; ++cell)
active_lysimeter[cell] = h (cell) > h_lysimeter (cell);
for (size_t edge = 0; edge != edge_size ; ++edge)
{
Kold[edge] = find_K_edge (soil, geo, edge, h, h_ice, h_previous, T);
Ksum [edge] = 0.0;
}
std::vector<top_state> state (edge_above.size (), top_undecided);
// We try harder with smaller timesteps.
const int max_loop_iter
= max_iterations * (number_of_time_step_reductions
* max_iterations_timestep_reduction_factor + 1);
do // Start iteration loop
{
h_conv = h;
iterations_used++;
std::ostringstream tmp_conv;
tmp_conv << "Convergence " << iterations_used;
Treelog::Open nest (msg, tmp_conv.str ());
if (debug == 7)
msg.touch ();
// Calculate conductivity - The Hansen method
for (size_t e = 0; e < edge_size; e++)
{
Ksum[e] += find_K_edge (soil, geo, e, h, h_ice, h_previous, T);
Kedge[e] = (Ksum[e] / (iterations_used + 0.0)+ Kold[e]) / 2.0;
}
//Initialize diffusive matrix
Solver::Matrix diff (cell_size);
// diff = ublas::zero_matrix<double> (cell_size, cell_size);
diffusion (geo, Kedge, diff);
//Initialize gravitational matrix
ublas::vector<double> grav (cell_size); //ublass compatibility
grav = ublas::zero_vector<double> (cell_size);
gravitation (geo, Kedge, grav);
// Boundary matrices and vectors
ublas::banded_matrix<double> Dm_mat (cell_size, cell_size,
0, 0); // Dir bc
Dm_mat = ublas::zero_matrix<double> (cell_size, cell_size);
ublas::vector<double> Dm_vec (cell_size); // Dir bc
Dm_vec = ublas::zero_vector<double> (cell_size);
ublas::vector<double> Gm (cell_size); // Dir bc
Gm = ublas::zero_vector<double> (cell_size);
ublas::vector<double> B (cell_size); // Neu bc
B = ublas::zero_vector<double> (cell_size);
lowerboundary (geo, groundwater, active_lysimeter, h,
Kedge,
dq, Dm_mat, Dm_vec, Gm, B, msg);
upperboundary (geo, soil, T, surface, state, remaining_water, h,
Kedge,
dq, Dm_mat, Dm_vec, Gm, B, ddt, debug, msg, dt);
Darcy (geo, Kedge, h, dq); //for calculating drain fluxes
//Initialize water capacity matrix
ublas::banded_matrix<double> Cw (cell_size, cell_size, 0, 0);
for (size_t c = 0; c < cell_size; c++)
Cw (c, c) = soil.Cw2 (c, h[c]);
std::vector<double> h_std (cell_size);
//ublas vector -> std vector
std::copy(h.begin (), h.end (), h_std.begin ());
#ifdef TEST_OM_DEN_ER_BRUGT
for (size_t cell = 0; cell != cell_size ; ++cell)
{
S_macro (cell) = (S_matrix[cell] + S_drain[cell])
* geo.cell_volume (cell);
}
#endif
//Initialize sum matrix
Solver::Matrix summat (cell_size);
noalias (summat) = diff + Dm_mat;
//Initialize sum vector
ublas::vector<double> sumvec (cell_size);
sumvec = grav + B + Gm + Dm_vec - S_vol
#ifdef TEST_OM_DEN_ER_BRUGT
- S_macro
#endif
;
// QCw is shorthand for Qmatrix * Cw
Solver::Matrix Q_Cw (cell_size);
noalias (Q_Cw) = prod (Qmat, Cw);
//Initialize A-matrix
Solver::Matrix A (cell_size);
noalias (A) = (1.0 / ddt) * Q_Cw - summat;
// Q_Cw_h is shorthand for Qmatrix * Cw * h
const ublas::vector<double> Q_Cw_h = prod (Q_Cw, h);
//Initialize b-vector
ublas::vector<double> b (cell_size);
//b = sumvec + (1.0 / ddt) * (Qmatrix * Cw * h + Qmatrix *(Wxx-Wyy));
b = sumvec + (1.0 / ddt) * (Q_Cw_h
+ prod (Qmat, Theta_previous-Theta));
// Force active drains to zero h.
drain (geo, drain_cell, drain_water_level,
h, Theta_previous, Theta, S_vol,
#ifdef TEST_OM_DEN_ER_BRUGT
S_macro,
#endif
dq, ddt, drain_cell_on, A, b, debug, msg);
try {
solver->solve (A, b, h); // Solve Ah=b with regard to h.
} catch (const char *const error) {
std::ostringstream tmp;
tmp << "Could not solve equation system: " << error;
msg.warning (tmp.str ());
// Try smaller timestep.
iterations_used = max_loop_iter + 100;
break;
}
for (int c=0; c < cell_size; c++) // update Theta
Theta (c) = soil.Theta (c, h (c), h_ice (c));
if (debug > 1)
{
std::ostringstream tmp;
tmp << "Time left = " << time_left << ", ddt = " << ddt
<< ", iteration = " << iterations_used << "\n";
tmp << "B = " << B << "\n";
tmp << "h = " << h << "\n";
tmp << "Theta = " << Theta;
msg.message (tmp.str ());
}
for (int c=0; c < cell_size; c++)
{
if (h (c) < min_pressure_potential || h (c) > max_pressure_potential)
{
std::ostringstream tmp;
tmp << "Pressure potential out of realistic range, h["
<< c << "] = " << h (c);
msg.debug (tmp.str ());
iterations_used = max_loop_iter + 100;
break;
}
}
}
while (!converges (h_conv, h) && iterations_used <= max_loop_iter);
if (iterations_used > max_loop_iter)
{
number_of_time_step_reductions++;
if (number_of_time_step_reductions > max_time_step_reductions)
{
msg.debug ("Could not find solution");
throw "Could not find solution";
}
iterations_with_this_time_step = 0;
ddt /= time_step_reduction;
h = h_previous;
Theta = Theta_previous;
}
else
{
// Update dq for new h.
ublas::banded_matrix<double> Dm_mat (cell_size, cell_size,
0, 0); // Dir bc
Dm_mat = ublas::zero_matrix<double> (cell_size, cell_size);
ublas::vector<double> Dm_vec (cell_size); // Dir bc
Dm_vec = ublas::zero_vector<double> (cell_size);
ublas::vector<double> Gm (cell_size); // Dir bc
Gm = ublas::zero_vector<double> (cell_size);
ublas::vector<double> B (cell_size); // Neu bc
B = ublas::zero_vector<double> (cell_size);
lowerboundary (geo, groundwater, active_lysimeter, h,
Kedge,
dq, Dm_mat, Dm_vec, Gm, B, msg);
upperboundary (geo, soil, T, surface, state, remaining_water, h,
Kedge,
dq, Dm_mat, Dm_vec, Gm, B, ddt, debug, msg, dt);
Darcy (geo, Kedge, h, dq);
#ifdef TEST_OM_DEN_ER_BRUGT
// update macropore flow components
for (int c = 0; c < cell_size; c++)
{
S_drain_sum[c] += S_drain[c] * ddt/dt;
S_matrix_sum[c] += S_matrix[c] * ddt/dt;
}
#endif
std::vector<double> h_std_new (cell_size);
std::copy(h.begin (), h.end (), h_std_new.begin ());
// Update remaining_water.
for (size_t i = 0; i < edge_above.size (); i++)
{
const int edge = edge_above[i];
const int cell = geo.edge_other (edge, Geometry::cell_above);
const double out_sign = (cell == geo.edge_from (edge))
? 1.0 : -1.0;
remaining_water[i] += out_sign * dq (edge) * ddt;
daisy_assert (std::isfinite (dq (edge)));
}
if (debug == 5)
{
std::ostringstream tmp;
tmp << "Remaining water at end: " << remaining_water;
msg.message (tmp.str ());
}
// Contribution to large time step.
daisy_assert (std::isnormal (dt));
daisy_assert (std::isnormal (ddt));
q += dq * ddt / dt;
for (size_t e = 0; e < edge_size; e++)
{
daisy_assert (std::isfinite (dq (e)));
daisy_assert (std::isfinite (q (e)));
}
for (size_t e = 0; e < edge_size; e++)
{
daisy_assert (std::isfinite (dq (e)));
daisy_assert (std::isfinite (q (e)));
}
time_left -= ddt;
iterations_with_this_time_step++;
if (iterations_with_this_time_step > time_step_reduction)
{
number_of_time_step_reductions--;
iterations_with_this_time_step = 0;
ddt *= time_step_reduction;
}
}
// End of small time step.
}
// Mass balance.
// New = Old - S * dt + q_in * dt - q_out * dt + Error =>
// 0 = Old - New - S * dt + q_in * dt - q_out * dt + Error
Theta_error -= Theta; // Old - New
Theta_error -= S * dt;
#ifdef TEST_OM_DEN_ER_BRUGT
for (size_t c = 0; c < cell_size; c++)
Theta_error (c) -= (S_matrix_sum[c] + S_drain_sum[c]) * dt;
#endif
for (size_t edge = 0; edge != edge_size; ++edge)
{
const int from = geo.edge_from (edge);
const int to = geo.edge_to (edge);
const double flux = q (edge) * geo.edge_area (edge) * dt;
if (geo.cell_is_internal (from))
Theta_error (from) -= flux / geo.cell_volume (from);
if (geo.cell_is_internal (to))
Theta_error (to) += flux / geo.cell_volume (to);
}
// Find drain sink from mass balance.
#ifdef TEST_OM_DEN_ER_BRUGT
std::fill(S_drain.begin (), S_drain.end (), 0.0);
#else
std::vector<double> S_drain (cell_size);
#endif
for (size_t i = 0; i < drain_cell.size (); i++)
{
const size_t cell = drain_cell[i];
S_drain[cell] = Theta_error (cell) / dt;
Theta_error (cell) -= S_drain[cell] * dt;
}
if (debug == 2)
{
double total_error = 0.0;
double total_abs_error = 0.0;
double max_error = 0.0;
int max_cell = -1;
for (size_t cell = 0; cell != cell_size; ++cell)
{
const double volume = geo.cell_volume (cell);
const double error = Theta_error (cell);
total_error += volume * error;
total_abs_error += std::fabs (volume * error);
if (std::fabs (error) > std::fabs (max_error))
{
max_error = error;
max_cell = cell;
}
}
std::ostringstream tmp;
tmp << "Total error = " << total_error << " [cm^3], abs = "
<< total_abs_error << " [cm^3], max = " << max_error << " [] in cell "
<< max_cell;
msg.message (tmp.str ());
}
// Make it official.
for (size_t cell = 0; cell != cell_size; ++cell)
soil_water.set_content (cell, h (cell), Theta (cell));
#ifdef TEST_OM_DEN_ER_BRUGT
soil_water.add_tertiary_sink (S_matrix_sum);
soil_water.drain (S_drain_sum, msg);
#endif
for (size_t edge = 0; edge != edge_size; ++edge)
{
daisy_assert (std::isfinite (q[edge]));
soil_water.set_flux (edge, q[edge]);
}
soil_water.drain (S_drain, msg);
// End of large time step.
}
void
Horizon::initialize_base (const bool top_soil,
const int som_size, const double center_z,
const Texture& texture, Treelog& msg)
{
TREELOG_MODEL (msg);
const double clay_lim = texture_below ( 2.0 /* [um] USDA Clay */);
fast_clay = texture.mineral () * clay_lim;
fast_humus = texture.humus;
impl->initialize (*hydraulic, texture, quartz () * texture.mineral (),
som_size, top_soil, center_z, msg);
impl->secondary->initialize (msg);
std::ostringstream tmp;
const double h_lim = secondary_domain ().h_lim ();
if (h_lim >= 0.0)
impl->primary_sorption_fraction = 1.0;
else
{
const double h_sat = 0.0;
const double Theta_sat = hydraulic->Theta (h_sat);
// Integrate h over Theta.
PLF h_int;
const double h_min = Hydraulic::r2h (impl->r_pore_min);
const double Theta_min =hydraulic->Theta (h_min);
h_int.add (Theta_min, 0.0);
static const int intervals = 100;
double delta = (Theta_sat - Theta_min) / (intervals + 0.0);
double sum = 0.0;
for (double Theta = Theta_min + delta; Theta < Theta_sat; Theta += delta)
{
double my_h = hydraulic->h (Theta);
sum += my_h * delta;
h_int.add (Theta, sum);
}
const double h_wp = -15000.0;
const double Theta_wp = hydraulic->Theta (h_wp);
const double Theta_lim = hydraulic->Theta (h_lim);
tmp << "A saturated secondary domain contain "
<< 100.0 * (Theta_sat - Theta_lim) / (Theta_sat - Theta_wp)
<< " % of plant available water\n";
impl->primary_sorption_fraction = h_int (Theta_lim) / h_int (Theta_sat);
tmp << "Primary domain contains "
<< 100.0 * impl->primary_sorption_fraction
<< " % of the available sorption sites\n";
}
tmp << "h\th\tTheta\tK\n"
<< "cm\tpF\t\tcm/h\n";
const double h_Sat = 0;
tmp << h_Sat << "\t" << "\t" << hydraulic->Theta (h_Sat)
<< "\t" << hydraulic->K (h_Sat) << "\n";
const double pF_Zero = 0;
const double h_Zero = pF2h (pF_Zero);
tmp << h_Zero << "\t" << pF_Zero << "\t" << hydraulic->Theta (h_Zero)
<< "\t" << hydraulic->K (h_Zero) << "\n";
const double pF_One = 1;
const double h_One = pF2h (pF_One);
tmp << h_One << "\t" << pF_One << "\t" << hydraulic->Theta (h_One)
<< "\t" << hydraulic->K (h_One) << "\n";
const double pF_FC = 2.0;
const double h_FC = pF2h (pF_FC);
tmp << h_FC << "\t" << pF_FC << "\t" << hydraulic->Theta (h_FC)
<< "\t" << hydraulic->K (h_FC) << "\n";
const double pF_Three = 3;
const double h_Three = pF2h (pF_Three);
tmp << h_Three << "\t" << pF_Three << "\t" << hydraulic->Theta (h_Three)
<< "\t" << hydraulic->K (h_Three) << "\n";
const double pF_WP = 4.2;
const double h_WP = pF2h (pF_WP);
tmp << h_WP << "\t" << pF_WP << "\t" << hydraulic->Theta (h_WP)
<< "\t" << hydraulic->K (h_WP);
msg.debug (tmp.str ());
}
void
MovementSolute::solute (const Soil& soil, const SoilWater& soil_water,
const double J_above, Chemical& chemical,
const double dt,
const Scope& scope, Treelog& msg)
{
daisy_assert (std::isfinite (J_above));
const size_t cell_size = geometry ().cell_size ();
const size_t edge_size = geometry ().edge_size ();
// Source term transfered from secondary to primary domain.
std::vector<double> S_extra (cell_size, 0.0);
// Divide top solute flux according to water.
std::map<size_t, double> J_tertiary;
std::map<size_t, double> J_secondary;
std::map<size_t, double> J_primary;
if (J_above > 0.0)
// Outgoing, divide according to content in primary domain only.
divide_top_outgoing (geometry (), chemical, J_above,
J_primary, J_secondary, J_tertiary);
else if (J_above < 0.0)
// Incomming, divide according to all incomming water.
divide_top_incomming (geometry (), soil_water, J_above,
J_primary, J_secondary, J_tertiary);
else
// No flux.
zero_top (geometry (), J_primary, J_secondary, J_tertiary);
// Check result.
{
const std::vector<size_t>& edge_above
= geometry ().cell_edges (Geometry::cell_above);
const size_t edge_above_size = edge_above.size ();
double J_sum = 0.0;
for (size_t i = 0; i < edge_above_size; i++)
{
const size_t edge = edge_above[i];
const double in_sign
= geometry ().cell_is_internal (geometry ().edge_to (edge))
? 1.0 : -1.0;
const double area = geometry ().edge_area (edge); // [cm^2 S]
const double J_edge // [g/cm^2 S/h]
= J_tertiary[edge] + J_secondary[edge] + J_primary[edge];
J_sum += in_sign * J_edge * area; // [g/h]
if (in_sign * J_tertiary[edge] < 0.0)
{
std::ostringstream tmp;
tmp << "J_tertiary[" << edge << "] = " << J_tertiary[edge]
<< ", in_sign = " << in_sign << ", J_above = " << J_above;
msg.bug (tmp.str ());
}
if (in_sign * J_secondary[edge] < 0.0)
{
std::ostringstream tmp;
tmp << "J_secondary[" << edge << "] = " << J_secondary[edge]
<< ", in_sign = " << in_sign << ", J_above = " << J_above;
msg.bug (tmp.str ());
}
}
J_sum /= geometry ().surface_area (); // [g/cm^2 S/h]
daisy_approximate (-J_above, J_sum);
}
// We set a fixed concentration below lower boundary, if specified.
std::map<size_t, double> C_border;
const double C_below = chemical.C_below ();
if (C_below >= 0.0)
{
const std::vector<size_t>& edge_below
= geometry ().cell_edges (Geometry::cell_below);
const size_t edge_below_size = edge_below.size ();
for (size_t i = 0; i < edge_below_size; i++)
{
const size_t edge = edge_below[i];
C_border[edge] = C_below;
}
}
// Tertiary transport.
tertiary->solute (geometry (), soil_water, J_tertiary, dt, chemical, msg);
// Fully adsorbed.
if (chemical.adsorption ().full ())
{
static const symbol solid_name ("immobile transport");
Treelog::Open nest (msg, solid_name);
if (!iszero (J_above))
{
std::ostringstream tmp;
tmp << "J_above = " << J_above << ", expected 0 for full sorbtion";
msg.error (tmp.str ());
}
// Secondary "transport".
std::vector<double> J2 (edge_size, 0.0); // Flux delivered by flow.
std::vector<double> Mn (cell_size); // New content.
for (size_t c = 0; c < cell_size; c++)
{
Mn[c] = chemical.M_secondary (c) + chemical.S_secondary (c) * dt;
if (Mn[c] < 0.0)
{
S_extra[c] = Mn[c] / dt;
Mn[c] = 0.0;
}
else
S_extra[c] = 0.0;
}
chemical.set_secondary (soil, soil_water, Mn, J2);
// Primary "transport".
primary_transport (geometry (), soil, soil_water,
*matrix_solid, sink_sorbed, 0, J_primary, C_border,
chemical, S_extra, dt, scope, msg);
return;
}
// Secondary transport activated.
secondary_transport (geometry (), soil, soil_water, J_secondary, C_border,
chemical, S_extra, dt, scope, msg);
// Solute primary transport.
for (size_t transport_iteration = 0;
transport_iteration < 2;
transport_iteration++)
for (size_t i = 0; i < matrix_solute.size (); i++)
{
solute_attempt (i);
static const symbol solute_name ("solute");
Treelog::Open nest (msg, solute_name, i, matrix_solute[i]->objid);
try
{
primary_transport (geometry (), soil, soil_water,
*matrix_solute[i], sink_sorbed,
transport_iteration,
J_primary, C_border,
chemical, S_extra, dt, scope, msg);
if (i > 0)
msg.debug ("Succeeded");
return;
}
catch (const char* error)
{
msg.debug (std::string ("Solute problem: ") + error);
}
catch (const std::string& error)
{
msg.debug(std::string ("Solute trouble: ") + error);
}
solute_failure (i);
}
throw "Matrix solute transport failed";
}
void
MovementSolute::primary_transport (const Geometry& geo, const Soil& soil,
const SoilWater& soil_water,
const Transport& transport,
const bool sink_sorbed,
const size_t transport_iteration,
const std::map<size_t, double>& J_forced,
const std::map<size_t, double>& C_border,
Chemical& solute,
const std::vector<double>& S_extra,
const double dt,
const Scope& scope, Treelog& msg)
{
// Edges.
const size_t edge_size = geo.edge_size ();
std::vector<double> q (edge_size); // Water flux [cm].
std::vector<double> J (edge_size); // Flux delivered by flow.
for (size_t e = 0; e < edge_size; e++)
{
q[e] = soil_water.q_primary (e);
daisy_assert (std::isfinite (q[e]));
J[e] = 0.0;
}
// Cells.
const size_t cell_size = geo.cell_size ();
std::vector<double> Theta_old (cell_size); // Water content at start...
std::vector<double> Theta_new (cell_size); // ...and end of timestep.
std::vector<double> C (cell_size); // Concentration given to flow.
std::vector<double> A (cell_size); // Sorbed mass not given to flow.
std::vector<double> S (cell_size); // Source given to flow.
for (size_t c = 0; c < cell_size; c++)
{
Theta_old[c] = soil_water.Theta_primary_old (c);
daisy_assert (Theta_old[c] > 0.0);
Theta_new[c] = soil_water.Theta_primary (c);
daisy_assert (Theta_new[c] > 0.0);
C[c] = solute.C_primary (c);
daisy_assert (C[c] >= 0.0);
const double M = solute.M_primary (c);
daisy_assert (M >= 0.0);
A[c] = M - C[c] * Theta_old[c];
daisy_assert (std::isfinite (A[c]));
if (A[c] < 0.0)
{
daisy_approximate (M, C[c] * Theta_old[c]);
A[c] = 0.0;
}
daisy_assert (A[c] >= 0.0);
S[c] = solute.S_primary (c) + S_extra[c];
if (sink_sorbed && S[c] < 0.0)
{
A[c] += S[c] * dt;
S[c] = 0.0;
if (A[c] < 0.0)
{
S[c] = A[c] / dt;
A[c] = 0.0;
}
}
daisy_assert (std::isfinite (S[c]));
}
// Flow.
transport.flow (geo, soil, Theta_old, Theta_new, q, solute.objid,
S, J_forced, C_border, C, J,
solute.diffusion_coefficient (),
dt, msg);
// Check fluxes.
for (size_t e = 0; e < edge_size; e++)
daisy_assert (std::isfinite (J[e]));
// Update with new content.
std::vector<double> M (cell_size);
for (size_t c = 0; c < cell_size; c++)
{
daisy_assert (std::isfinite (C[c]));
M[c] = A[c] + C[c] * Theta_new[c];
if (M[c] < 0.0)
{
std::ostringstream tmp;
tmp << "M[" << c << "] = " << M[c]
<< " @ " << geo.cell_name (c)
<< ", C = " << C[c]
<< ", A = " << A[c]
<< ", M_new = " << M[c]
<< ", M_old = " << solute.M_primary (c) << ", dt " << dt
<< ", S = " << S[c]
<< ", S_extra = " << S_extra[c];
solute.debug_cell (tmp, c);
tmp << ", Theta_old " << Theta_old[c]
<< ", Theta_new " << Theta_new[c]
<< ", root " << soil_water.S_root (c)
<< ", drain " << soil_water.S_drain (c)
<< ", B2M " << soil_water.S_B2M (c)
<< ", M2B " << soil_water.S_M2B (c)
<< ", forward_total " << soil_water.S_forward_total (c)
<< ", forward_sink " << soil_water.S_forward_sink (c)
<< ", sum " << soil_water.S_sum (c)
<< ", v1 " << soil_water.velocity_cell_primary (geo, c)
<< ", v2 " << soil_water.velocity_cell_secondary (geo, c);
const std::vector<size_t>& edges = geo.cell_edges (c);
for (size_t i = 0; i < edges.size (); i++)
{
const size_t e = edges[i];
tmp << "\n" << geo.edge_name (e)
<< ": q = " << q[e] << ", J = " << J[e];
}
msg.debug (tmp.str ());
if (transport_iteration == 0)
throw "Negative concentration";
}
}
solute.set_primary (soil, soil_water, M, J);
}
double
PhotoFarquhar::assimilate (const Units& units,
const double ABA, const double psi_c,
const double ec /* Canopy Vapour Pressure [Pa] */,
const double gbw_ms /* Boundary layer [m/s] */,
const double CO2_atm, const double O2_atm,
const double Ptot /* [Pa] */,
const double, const double Tc, const double Tl,
const double cropN,
const std::vector<double>& PAR,
const std::vector<double>& PAR_height,
const double PAR_LAI,
const std::vector<double>& fraction,
const double,
CanopyStandard& canopy,
Phenology& development,
Treelog& msg)
{
const double h_x = std::fabs (psi_c) * 1.0e-4 /* [MPa/cm] */; // MPa
// sugar production [gCH2O/m2/h] by canopy photosynthesis.
const PLF& LAIvsH = canopy.LAIvsH;
const double DS = development.DS;
// One crop: daisy_assert (approximate (canopy.CAI, bioclimate.CAI ()));
if (!approximate (LAIvsH (canopy.Height), canopy.CAI))
{
std::ostringstream tmp;
tmp << "Bug: CAI below top: " << LAIvsH (canopy.Height)
<< " Total CAI: " << canopy.CAI << "\n";
canopy.CanopyStructure (DS);
tmp << "Adjusted: CAI below top: " << LAIvsH (canopy.Height)
<< " Total CAI: " << canopy.CAI;
msg.error (tmp.str ());
}
// CAI (total) below the current leaf layer.
double prevLA = LAIvsH (PAR_height[0]);
// Assimilate produced by canopy photosynthesis
double Ass_ = 0.0;
// Accumulated CAI, for testing purposes.
double accCAI =0.0;
// Number of computational intervals in the canopy.
const int No = PAR.size () - 1;
daisy_assert (No > 0);
daisy_assert (No == PAR_height.size () - 1);
// N-distribution and photosynthetical capacity
std::vector<double> rubisco_Ndist (No, 0.0);
std::vector<double> crop_Vm_total (No, 0.0);
// Photosynthetic capacity (for logging)
while (Vm_vector.size () < No)
Vm_vector.push_back (0.0);
// Potential electron transport rate (for logging)
while (Jm_vector.size () < No)
Jm_vector.push_back (0.0);
// Photosynthetic N-leaf distribution (for logging)
while (Nleaf_vector.size () < No)
Nleaf_vector.push_back (0.0);
// Brutto assimilate production (for logging)
while (Ass_vector.size () < No)
Ass_vector.push_back (0.0);
// LAI (for logging)
while (LAI_vector.size () < No)
LAI_vector.push_back (0.0);
rubiscoNdist->rubiscoN_distribution (units,
PAR_height, prevLA, DS,
rubisco_Ndist/*[mol/m²leaf]*/,
cropN /*[g/m²area]*/, msg);
crop_Vmax_total (rubisco_Ndist, crop_Vm_total);
// Net photosynthesis (for logging)
while (pn_vector.size () < No)
pn_vector.push_back (0.0);//
// Stomata CO2 pressure (for logging)
while (ci_vector.size () < No)
ci_vector.push_back (0.0);//[Pa]
// Leaf surface CO2 pressure (for logging)
while (cs_vector.size () < No)
cs_vector.push_back (0.0);//
// Leaf surface relative humidity (for logging)
while (hs_vector.size () < No)
hs_vector.push_back (0.0);//[]
// Stomata conductance (for logging)
while (gs_vector.size () < No)
gs_vector.push_back (0.0);//[m/s]
// Photosynthetic effect of Xylem ABA and crown water potential.
Gamma = Arrhenius (Gamma25, Ea_Gamma, Tl); // [Pa]
const double estar = FAO::SaturationVapourPressure (Tl); // [Pa]
daisy_assert (gbw_ms >= 0.0);
gbw = Resistance::ms2molly (Tl, Ptot, gbw_ms);
daisy_assert (gbw >= 0.0);
// CAI in each interval.
const double dCAI = PAR_LAI / No;
for (int i = 0; i < No; i++)
{
const double height = PAR_height[i+1];
daisy_assert (height < PAR_height[i]);
// Leaf Area index for a given leaf layer
const double LA = prevLA - LAIvsH (height);
daisy_assert (LA >= 0.0);
prevLA = LAIvsH (height);
accCAI += LA;
if (LA * fraction [i] > 0)
{
// PAR in mol/m2/s = PAR in W/m2 * 0.0000046
const double dPAR = (PAR[i] - PAR[i+1])/dCAI * 0.0000046; //W/m2->mol/m²leaf/s
if (dPAR < 0)
{
std::stringstream tmp;
tmp << "Negative dPAR (" << dPAR
<< " [mol/m^2 leaf/h])" << " PAR[" << i << "] = " << PAR[i]
<< " PAR[" << i+1 << "] = " << PAR[i+1]
<< " dCAI = " << dCAI
<< " LA = " << LA
<< " fraction[" << i << "] = " << fraction [i];
msg.debug (tmp.str ());
continue;
}
// log variable
PAR_ += dPAR * dCAI * 3600.0; //mol/m²area/h/fraction
// Photosynthetic rubisco capacity
const double vmax25 = crop_Vm_total[i]*fraction[i];//[mol/m²leaf/s/fracti.]
daisy_assert (vmax25 >= 0.0);
// leaf respiration
const double rd = respiration_rate(vmax25, Tl);
daisy_assert (rd >= 0.0);
//solving photosynthesis and stomatacondctance model for each layer
double& pn = pn_vector[i];
double ci = 0.5 * CO2_atm;//first guess for ci, [Pa]
double& hs = hs_vector[i];
hs = 0.5; // first guess of hs []
double& cs = cs_vector[i];
//first gues for stomatal cond,[mol/s/m²leaf]
double gsw = Stomatacon->minimum () * 2.0;
// double gsw = 2 * b; // old value
const int maxiter = 150;
int iter = 0;
double lastci;
double lasths;
double lastgs;
do
{
lastci = ci; //Stomata CO2 pressure
lasths = hs;
lastgs = gs;
//Calculating ci and "net"photosynthesis
CxModel(CO2_atm, O2_atm, Ptot,
pn, ci, dPAR /*[mol/m²leaf/s]*/,
gsw, gbw, Tl, vmax25, rd, msg);//[mol/m²leaf/s/fraction]
// Vapour pressure at leaf surface. [Pa]
const double es = (gsw * estar + gbw * ec) / (gsw + gbw);
// Vapour defecit at leaf surface. [Pa]
const double Ds = bound (0.0, estar - es, estar);
// Relative humidity at leaf surface. []
hs = es / estar;
const double hs_use = bound (0.0, hs, 1.0);
// Boundary layer resistance. [s*m2 leaf/mol]
daisy_assert (gbw >0.0);
const double rbw = 1./gbw; //[s*m2 leaf/mol]
// leaf surface CO2 [Pa]
// We really should use CO2_canopy instead of CO2_atm
// below. Adding the resitence from canopy point to
// atmostphere is not a good workaround, as it will
// ignore sources such as the soil and stored CO2 from
// night respiration.
cs = CO2_atm - (1.4 * pn * Ptot * rbw); //[Pa]
daisy_assert (cs > 0.0);
//stomatal conductance
gsw = Stomatacon->stomata_con (ABA /*g/cm^3*/,
h_x /* MPa */,
hs_use /*[]*/,
pn /*[mol/m²leaf/s]*/,
Ptot /*[Pa]*/,
cs /*[Pa]*/, Gamma /*[Pa]*/,
Ds/*[Pa]*/,
msg); //[mol/m²leaf/s]
iter++;
if(iter > maxiter)
{
std::ostringstream tmp;
tmp << "total iterations in assimilation model exceed "
<< maxiter;
msg.warning (tmp.str ());
break;
}
}
// while (std::fabs (lastci-ci)> 0.01);
while (std::fabs (lastci-ci)> 0.01
|| std::fabs (lasths-hs)> 0.01
|| std::fabs (lastgs-gs)> 0.01);
// Leaf brutto photosynthesis [gCO2/m2/h]
/*const*/ double pn_ = (pn+rd) * molWeightCO2 * 3600.0;//mol CO2/m²leaf/s->g CO2/m²leaf/h
const double rd_ = (rd) * molWeightCO2 * 3600.0; //mol CO2/m²/s->g CO2/m²/h
const double Vm_ = V_m(vmax25, Tl); //[mol/m² leaf/s/fraction]
const double Jm_ = J_m(vmax25, Tl); //[mol/m² leaf/s/fraction]
if (pn_ < 0.0)
{
std::stringstream tmp;
tmp << "Negative brutto photosynthesis (" << pn_
<< " [g CO2/m²leaf/h])" << " pn " << pn << " rd " << rd
<< " CO2_atm " << CO2_atm << " O2_atm " << O2_atm
<< " Ptot " << Ptot << " pn " << pn << " ci " << ci
<< " dPAR " << dPAR << " gsw " << gsw
<< " gbw " << gbw << " Tl " << Tl
<< " vmax25 " << vmax25 << " rd " << rd;
msg.error (tmp.str ());
pn_ = 0.0;
}
Ass_ += LA * pn_; // [g/m²area/h]
Res += LA * rd_; // [g/m²area/h]
daisy_assert (Ass_ >= 0.0);
//log variables:
Ass_vector[i]+= pn_* (molWeightCH2O / molWeightCO2) * LA;//[g CH2O/m²area/h]
Nleaf_vector[i]+= rubisco_Ndist[i] * LA * fraction[i]; //[mol N/m²area]OK
gs_vector[i]+= gsw /* * LA * fraction[i] */; //[mol/m² area/s]
ci_vector[i]+= ci /* * fraction[i] */; //[Pa] OK
Vm_vector[i]+= Vm_ * 1000.0 * LA * fraction[i]; //[mmol/m² area/s]OK
Jm_vector[i]+= Jm_ * 1000.0 * LA * fraction[i]; //[mmol/m² area/s]OK
LAI_vector[i] += LA * fraction[i];//OK
ci_middel += ci * fraction[i]/(No + 0.0);// [Pa] OK
gs += LA * gsw * fraction[i];
Ass += LA * pn_ * (molWeightCH2O / molWeightCO2);//[g CH2O/m2 area/h] OK
LAI += LA * fraction[i];//OK
Vmax += 1000.0 * LA * fraction[i] * Vm_; //[mmol/m² area/s]
jm += 1000.0 * LA * fraction[i] * Jm_; //[mmol/m² area/s]
leafPhotN += rubisco_Ndist[i] * LA *fraction[i]; //[mol N/m²area];
fraction_total += fraction[i]/(No + 0.0);
}
}
daisy_assert (approximate (accCAI, canopy.CAI));
daisy_assert (Ass_ >= 0.0);
// Omregning af gs(mol/(m2s)) til gs_ms (m/s) foretages ved
// gs_ms = gs * (R * T)/P:
gs_ms = Resistance::molly2ms (Tl, Ptot, gs);
return (molWeightCH2O / molWeightCO2)* Ass_; // Assimilate [g CH2O/m2/h]
}
void
Movement1D::tick_water (const Geometry1D& geo,
const Soil& soil, const SoilHeat& soil_heat,
Surface& surface, Groundwater& groundwater,
const std::vector<double>& S,
std::vector<double>& h_old,
const std::vector<double>& Theta_old,
const std::vector<double>& h_ice,
std::vector<double>& h,
std::vector<double>& Theta,
std::vector<double>& q,
std::vector<double>& q_p,
const double dt,
Treelog& msg)
{
const size_t top_edge = 0U;
const size_t bottom_edge = geo.edge_size () - 1U;
// Limit for groundwater table.
size_t last = soil.size () - 1;
// Limit for ridging.
const size_t first = (surface.top_type (geo, 0U) == Surface::soil)
? surface.last_cell (geo, 0U)
: 0U;
// Calculate matrix flow next.
for (size_t m = 0; m < matrix_water.size (); m++)
{
water_attempt (m);
Treelog::Open nest (msg, matrix_water[m]->name);
try
{
matrix_water[m]->tick (msg, geo, soil, soil_heat,
first, surface, top_edge,
last, groundwater, bottom_edge,
S, h_old, Theta_old, h_ice, h, Theta, 0U, q,
dt);
for (size_t i = last + 2; i <= soil.size (); i++)
{
q[i] = q[i-1];
q_p[i] = q_p[i-1];
}
// Update surface and groundwater reservoirs.
surface.accept_top (q[0] * dt, geo, 0U, dt, msg);
surface.update_pond_average (geo);
const double q_down = q[soil.size ()] + q_p[soil.size ()];
groundwater.accept_bottom (q_down * dt, geo, soil.size ());
if (m > 0)
msg.debug ("Reserve model succeeded");
return;
}
catch (const char* error)
{
msg.debug (std::string ("UZ problem: ") + error);
}
catch (const std::string& error)
{
msg.debug (std::string ("UZ trouble: ") + error);
}
water_failure (m);
}
throw "Water matrix transport failed";
}