void
Fetch::initialize (std::vector<Select*>& select, Treelog& msg)
{
Treelog::Open nest (msg, this->tag);
bool found = false;
for (size_t j = 0; j != select.size (); j++)
{
Treelog::Open nest (msg, select[j]->tag ());
if (this->tag == select[j]->tag ())
{
if (found)
msg.warning ("Duplicate tag ignored");
else
{
select[j]->add_dest (this);
this->select_dimension = select[j]->dimension ();
this->type = ((select[j]->handle != Select::Handle::current)
&& !select[j]->accumulate)
? Fetch::Flux
: Fetch::NewContent;
found = true;
}
}
}
if (!found)
msg.warning ("No tag found");
}
void
MovementSolute::element (const Soil& soil, const SoilWater& soil_water,
DOE& element,
const double diffusion_coefficient, double dt,
Treelog& msg)
{
for (size_t i = 0; i < matrix_solute.size (); i++)
{
Treelog::Open nest (msg, "element", i, matrix_solute[i]->library_id ());
try
{
matrix_solute[i]->element (geometry (), soil, soil_water, element,
diffusion_coefficient, dt,
msg);
if (i > 0)
msg.message ("Succeeded");
return;
}
catch (const char* error)
{
msg.warning (std::string ("DOM problem: ") + error);
}
catch (const std::string& error)
{
msg.warning (std::string ("DOM trouble: ") + error);
}
}
throw "Matrix element transport failed";
}
static void propagate (Treelog& msg, int nest, const std::string& text)
{
switch (nest)
{
case is_unknown:
msg.entry (text);
break;
case is_debug:
msg.debug (text);
break;
case is_plain:
msg.message (text);
break;
case is_warning:
msg.warning (text);
break;
case is_error:
msg.error (text);
break;
case is_bug:
msg.bug (text);
break;
case is_close:
msg.close ();
break;
case is_touch:
msg.touch ();
break;
case is_flush:
msg.flush ();
break;
default:
msg.open (text);
}
}
bool
GnuplotProfile::plot (std::ostream& out, Treelog& msg)
{
if (xplus.size () < 1 || zplus.size () < 1)
{
msg.warning ("Nothing to plot");
return false;
}
// Header.
plot_header (out);
out << "\
set pm3d map\n\
set pm3d corners2color c4\n\
unset colorbox\n";
// Same size axes.
out << "\
set size ratio -1\n";
// Legend.
if (legend != "auto")
out << "set key " << legend_table[legend] << "\n";
// Extra.
for (size_t i = 0; i < extra.size (); i++)
out << extra[i].name () << "\n";
// Plot.
out << "splot '-' using 2:1:3 title \"\"\n";
// Data.
daisy_assert (value.size () == xplus.size () * zplus.size ());
// Cell corners only.
daisy_assert (value.size () > 0);
out << "0 0 " << value[0] << "\n";
daisy_assert (value.size () >= zplus.size ());
for (size_t iz = 0; iz < zplus.size (); iz++)
out << zplus[iz] << " 0 " << value[iz * xplus.size ()] << "\n";
for (size_t ix = 0; ix < xplus.size (); ix++)
{
out << "\n0 " << xplus[ix] << " " << value[ix] << "\n";
for (size_t iz = 0; iz < zplus.size (); iz++)
{
const size_t c = ix + iz * xplus.size ();
daisy_assert (c < value.size ());
out << zplus[iz] << " " << xplus[ix] << " " << value[c] << "\n";
}
}
out << "e\n";
// The end.
if (interactive ())
out << "pause mouse\n";
return true;
}
void
ABAProdUptake::production (const Units& units,
const Geometry& geo, const SoilWater& soil_water,
const std::vector<double>& S /* [cm^3/cm^3/h] */,
const std::vector<double>& /* l [cm/cm^3] */,
std::vector<double>& ABA /* [g/cm^3/h] */,
Treelog& msg) const
{
// Check input.
const size_t cell_size = geo.cell_size ();
daisy_assert (ABA.size () == cell_size);
daisy_assert (S.size () == cell_size);
// For all cells.
for (size_t c = 0; c < cell_size; c++)
{
const double h = soil_water.h (c);
// Set up 'h' in scope.
scope.set (h_name, soil_water.h (c));
// Find soil value.
double value = 0.0;
if (!expr->tick_value (units, value, ABA_unit, scope, msg))
msg.error ("No ABA production value found");
if (!std::isfinite (value) || value < 0.0)
{
if (h > -14000) // We are not concerned with ABA below wilting point.
{
std::ostringstream tmp;
tmp << "ABA in cell " << c << " with h = " << h
<< " was " << value << " [" << ABA_unit << "], using 0 instead";
msg.warning (tmp.str ());
}
value = 0.0;
}
daisy_assert (std::isfinite (S[c]));
// Find ABA uptake.
ABA[c] = value * S[c];
// [g/cm^3 S/h] = [g/cm^3 W] * [cm^3 W/cm^3 S/h]
daisy_assert (std::isfinite (ABA[c]));
}
}
void
Rootdens_G_P::set_density (const Geometry& geo,
double SoilDepth, double CropDepth,
const double /* CropWidth [cm] */,
double WRoot, double /* DS */,
std::vector<double>& Density, Treelog& msg)
{
const double Depth = std::min (SoilDepth, CropDepth);
// Dimensional conversion.
static const double m_per_cm = 0.01;
const double MinLengthPrArea = (DensRtTip * 1.2) * CropDepth;
const double LengthPrArea
= std::max (m_per_cm * SpRtLength * WRoot, MinLengthPrArea); // [cm/cm^2]
// We find a * depth first.
const double ad = density_distribution_parameter (LengthPrArea /
(CropDepth * DensRtTip));
// We find L0 from a d.
//
// L0 * exp (-a d) = DensRtTip
// => L0 = DensRtTip / exp (-a d)
L0 = DensRtTip * exp (ad); // 1 / exp (-x) = exp (x)
a = ad / CropDepth;
if (Depth < CropDepth)
{
double Lz = L0 * exp (-a * Depth);
a = density_distribution_parameter (LengthPrArea / (Depth * Lz)) / Depth;
}
// Check minimum density
double extra = 0.0;
if (MinDens > 0.0 && WRoot > 0.0)
{
daisy_assert (L0 > 0.0);
daisy_assert (a > 0.0);
const double too_low = -log (MinDens / L0) / a; // [cm]
if (too_low < Depth)
{
// We don't have MinDens all the way down.
const double NewLengthPrArea
= LengthPrArea - MinDens * Depth; // [cm/cm^2]
#if 1
Treelog::Open nest (msg, "RootDens G+P");
std::ostringstream tmp;
tmp << "too_low = " << too_low
<< ", NewLengthPrArea = " << NewLengthPrArea
<< "MinLengthPrArea = " << MinLengthPrArea;
msg.warning (tmp.str ());
#endif
if (too_low > 0.0 && NewLengthPrArea > too_low * DensRtTip * 1.2)
{
// There is enough to have MinDens all the way, spend
// the rest using the standard model until the point
// where the standard model would give too little..
a = density_distribution_parameter (NewLengthPrArea
/ (too_low * DensRtTip));
L0 = DensRtTip * exp (a);
a /= too_low;
extra = MinDens;
}
else
{
// There is too little, use uniform density all the way.
L0 = 0.0;
extra = LengthPrArea / Depth;
}
}
}
const size_t size = geo.cell_size ();
daisy_assert (Density.size () == size);
#if 1
for (size_t i = 0; i < size; i++)
{
const double f = geo.fraction_in_z_interval (i, 0.0, -Depth);
const double d = -geo.cell_z (i);
if (f > 0.01)
Density[i] = f * (extra + L0 * exp (- a * d));
else
Density[i] = 0.0;
}
#else // 0
unsigned int i = 0;
for (; i == 0 || -geo.zplus (i-1) < Depth; i++)
{
daisy_assert (i < geo.size ());
Density[i] = extra + L0 * exp (a * geo.cell_z (i));
}
for (; i < geo.size (); i++)
Density[i] = 0.0;
#endif // 0
}
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
MovementSolute::secondary_flow (const Geometry& geo,
const std::vector<double>& Theta_old,
const std::vector<double>& Theta_new,
const std::vector<double>& q,
const symbol name,
const std::vector<double>& S,
const std::map<size_t, double>& J_forced,
const std::map<size_t, double>& C_border,
std::vector<double>& M,
std::vector<double>& J,
const double dt,
Treelog& msg)
{
const size_t cell_size = geo.cell_size ();
const size_t edge_size = geo.edge_size ();
// Full timstep left.
daisy_assert (dt > 0.0);
double time_left = dt;
// Initial water content.
std::vector<double> Theta (cell_size);
for (size_t c = 0; c < cell_size; c++)
Theta[c] = Theta_old[c];
// Small timesteps.
for (;;)
{
// Are we done yet?
const double min_timestep_factor = 1e-19;
if (time_left < 0.1 * min_timestep_factor * dt)
break;
// Find new timestep.
double ddt = time_left;
// Limit timestep based on water flux.
for (size_t e = 0; e < edge_size; e++)
{
const int cell = (q[e] > 0.0 ? geo.edge_from (e) : geo.edge_to (e));
if (geo.cell_is_internal (cell)
&& Theta[cell] > 1e-6 && M[cell] > 0.0)
{
const double loss_rate = std::fabs (q[e]) * geo.edge_area (e);
const double content = Theta[cell] * geo.cell_volume (cell);
const double time_to_empty = content / loss_rate;
if (time_to_empty < min_timestep_factor * dt)
{
msg.warning ("Too fast water movement in secondary domain");
ddt = min_timestep_factor * dt;
break;
}
// Go down in timestep while it takes less than two to empty cell.
while (time_to_empty < 2.0 * ddt)
ddt *= 0.5;
}
}
// Cell source. Must be before transport to avoid negative values.
for (size_t c = 0; c < cell_size; c++)
M[c] += S[c] * ddt;
// Find fluxes using new values (more stable).
std::vector<double> dJ (edge_size, -42.42e42);
for (size_t e = 0; e < edge_size; e++)
{
std::map<size_t, double>::const_iterator i = J_forced.find (e);
if (i != J_forced.end ())
// Forced flux.
{
dJ[e] = (*i).second;
daisy_assert (std::isfinite (dJ[e]));
continue;
}
const int edge_from = geo.edge_from (e);
const int edge_to = geo.edge_to (e);
const bool in_flux = q[e] > 0.0;
int flux_from = in_flux ? edge_from : edge_to;
double C_flux_from = -42.42e42;
if (geo.cell_is_internal (flux_from))
// Internal cell, use its concentration.
{
if (Theta[flux_from] > 1e-6 && M[flux_from] > 0.0)
// Positive content in positive water.
C_flux_from = M[flux_from] / Theta[flux_from];
else
// You can't cut the hair of a bald guy.
C_flux_from = 0.0;
}
else
{
i = C_border.find (e);
if (i != C_border.end ())
// Specified by C_border.
C_flux_from = (*i).second;
else
// Assume no gradient.
{
const int flux_to = in_flux ? edge_to : edge_from;
daisy_assert (geo.cell_is_internal (flux_to));
if (Theta[flux_to] > 1e-6 && M[flux_to] > 0.0)
// Positive content in positive water.
C_flux_from = M[flux_to] / Theta[flux_to];
else
// You can't cut the hair of a bald guy.
C_flux_from = 0.0;
}
}
// Convection.
daisy_assert (std::isfinite (q[e]));
daisy_assert (C_flux_from >= 0.0);
dJ[e] = q[e] * C_flux_from;
daisy_assert (std::isfinite (dJ[e]));
}
// Update values for fluxes.
for (size_t e = 0; e < edge_size; e++)
{
const double value = ddt * dJ[e] * geo.edge_area (e);
const int from = geo.edge_from (e);
if (geo.cell_is_internal (from))
M[from] -= value / geo.cell_volume (from);
const int to = geo.edge_to (e);
if (geo.cell_is_internal (to))
M[to] += value / geo.cell_volume (to);
J[e] += dJ[e] * ddt / dt;
}
// Update time left.
time_left -= ddt;
// Interpolate Theta.
for (size_t c = 0; c < cell_size; c++)
{
const double left = time_left / dt;
const double done = 1.0 - left;
Theta[c] = left * Theta_old[c] + done * Theta_new[c];
}
}
}
void doIt (Daisy&, const Scope&, Treelog& out)
{
out.warning (message.name ());
}
void
UZlr::tick (Treelog& msg, const GeometryVert& geo,
const Soil& soil, const SoilHeat& soil_heat,
unsigned int first, const Surface& top,
const size_t top_edge,
unsigned int last, const Groundwater& bottom,
const size_t bottom_edge,
const std::vector<double>& S,
const 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,
const size_t q_offset,
std::vector<double>& q_base,
const double dt)
{
double *const q = &q_base[q_offset];
double q_up = 0.0;
double q_down = 0.0;
const Surface::top_t top_type = top.top_type (geo, top_edge);
if (top_type == Surface::soil)
{
// We have a forced pressure top, in the form of a ridge system.
// Since LR only works with flux top, we use Darcy to simulate a
// flux top between the first cell (with a forced pressure) and
// the second cell, and then continue calculating with a flux
// top from the second cell.
const double dz = geo.cell_z (first) - geo.cell_z (first+1);
const double dh = (h_old[first] - h_old[first+1]);
const double K = std::min (soil.K (first, h_old[first], h_ice[first],
soil_heat.T (first)),
soil.K (first, h_old[first+1], h_ice[first+1],
soil_heat.T (first+1)));
q_up = -K * (dh/dz + 1.0);
// We can safely ignore S[first], since the ridge system has
// already incorporated it.
first++;
// New upper limit.
q[first] = q_up;
}
else
{
// Limit flux by soil capacity.
const double K_sat = soil.K (first, 0.0, h_ice[first],
soil_heat.T (first));
daisy_assert (K_sat > 0.0);
if (top_type == Surface::forced_pressure)
{
const double dz = 0.0 - geo.cell_z (first);
const double dh = top.h_top (geo, top_edge) - h_old[first];
q_up = q[first] = -K_sat * (dh/dz + 1.0);
}
else
// Limited water or forced flux.
q_up = q[first] = std::max (top.q_top (geo, top_edge, dt), -K_sat);
}
// Use darcy for upward movement in the top.
const bool use_darcy = (h_old[first] < h_fc) && (q_up > 0.0);
// Intermediate cells.
for (int i = first; i <= last; i++)
{
const double z = geo.cell_z (i);
const double dz = geo.dz (i);
const double Theta_sat = soil.Theta (i, 0.0, h_ice[i]);
const double Theta_res = soil.Theta_res (i);
const double h_min = pF2h (10.0);
const double Theta_min = soil.Theta (i, h_min, h_ice[i]);
double Theta_new = Theta_old[i] - q[i] * dt / dz - S[i] * dt;
if (Theta_new < Theta_min)
{
// Extreme dryness.
q[i+1] = (Theta_min - Theta_new) * dz / dt;
Theta[i] = Theta_min;
h[i] = h_min;
daisy_assert (std::isfinite (h[i]));
continue;
}
daisy_assert (std::isfinite (h_old[i]));
const double h_new = Theta_new >= Theta_sat
? std::max (h_old[i], 0.0)
: soil.h (i, Theta_new);
daisy_assert (std::isfinite (h_new));
double K_new = soil.K (i, h_new, h_ice[i], soil_heat.T (i));
// If we have free drainage bottom, we go for field capacity all
// the way. Otherwise, we assume groundwater start at the
// bottom of the last cell, and attempt equilibrium from there.
// This asumption is correct for lysimeter bottom, adequate for
// pressure bottom (where groundwater table is in the last
// cell), and wrong for forced flux (= pipe drained soil) where
// the groundwater is usually much higher. Still, it is better
// than using h_fc.
double h_lim;
switch (bottom.bottom_type ())
{
case Groundwater::free_drainage:
h_lim = h_fc;
break;
case Groundwater::pressure:
h_lim = std::max (bottom.table () - z, h_fc);
break;
case Groundwater::lysimeter:
default:
h_lim = std::max (geo.zplus (last) - z, h_fc);
break;
}
if (use_darcy && z > z_top && i < last && h_fc < h_ice[i] )
// Dry earth, near top. Use darcy to move water up.
{
const double dist = z - geo.cell_z (i+1);
q[i+1] = std::max (K_new * ((h_old[i+1] - h_new) / dist - 1.0), 0.0);
const double Theta_next = Theta_new + q[i+1] * dt / dz;
if (Theta_next > Theta_sat)
{
q[i+1] = (Theta_sat - Theta_new) * dz / dt;
Theta[i] = Theta_sat;
h[i] = std::max (0.0, h_new);
daisy_assert (std::isfinite (h[i]));
}
else
{
Theta[i] = Theta_next;
h[i] = soil.h (i, Theta[i]);
daisy_assert (std::isfinite (h[i]));
}
}
else if (h_new <= h_lim)
// Dry earth, no water movement.
{
if (Theta_new <= Theta_sat)
{
q[i+1] = 0.0;
Theta[i] = Theta_new;
h[i] = h_new;
daisy_assert (std::isfinite (h[i]));
}
else
{
q[i+1] = (Theta_sat - Theta_new) * dz / dt;
Theta[i] = Theta_sat;
h[i] = std::max (0.0, h_new);
daisy_assert (std::isfinite (h[i]));
}
}
else
// Gravitational water movement.
{
if (i < last)
{
// Geometric average K.
if (h_ice[i+1] < h_fc) // Blocked by ice.
K_new = 0.0;
else
K_new = sqrt (K_new * soil.K (i+1, h_old[i+1], h_ice[i+1],
soil_heat.T (i+1)));
}
else if (bottom.bottom_type () == Groundwater::forced_flux)
K_new = -bottom.q_bottom (bottom_edge);
// else keep K_new from the node.
const double Theta_lim = soil.Theta (i, h_lim, h_ice[i]);
const double Theta_next = Theta_new - K_new * dt / dz;
if (Theta_next < Theta_lim)
{
if (Theta_lim < Theta_new)
{
q[i+1] = (Theta_lim - Theta_new) * dz / dt;
Theta[i] = Theta_lim;
h[i] = h_lim;
daisy_assert (std::isfinite (h[i]));
}
else
{
q[i+1] = 0.0;
Theta[i] = Theta_new;
h[i] = h_new;
daisy_assert (std::isfinite (h[i]));
}
}
else if (Theta_next >= Theta_sat)
{
q[i+1] = (Theta_sat - Theta_new) * dz / dt;
Theta[i] = Theta_sat;
h[i] = std::max (h_old[i], 0.0);
daisy_assert (std::isfinite (h[i]));
}
else
{
q[i+1] = -K_new;
Theta[i] = Theta_next;
h[i] = soil.h (i, Theta[i]);
daisy_assert (std::isfinite (h[i]));
}
}
daisy_assert (std::isfinite (h[i]));
daisy_assert (std::isfinite (Theta[i]));
daisy_assert (std::isfinite (q[i+1]));
daisy_assert (Theta[i] <= Theta_sat);
daisy_assert (Theta[i] > Theta_res);
}
// Lower border.
q_down = q[last + 1];
if (bottom.bottom_type () == Groundwater::forced_flux)
// Ensure forced bottom.
{
double extra_water = (bottom.q_bottom (bottom_edge) - q_down) * dt;
for (int i = last; true; i--)
{
q[i+1] += extra_water / dt;
if (i < static_cast<int> (first))
{
if (extra_water > 0.0 && overflow_warn)
{
msg.warning ("Soil profile saturated, water flow to surface");
overflow_warn = false;
}
break;
}
const double dz = geo.dz (i);
const double h_min = pF2h (10.0);
const double Theta_min = soil.Theta (i, h_min, h_ice[i]);
const double Theta_sat = soil.Theta (i, 0.0, h_ice[i]);
Theta[i] += extra_water / dz;
if (Theta[i] <= Theta_min)
{
extra_water = (Theta[i] - Theta_min) * dz;
Theta[i] = Theta_min;
h[i] = h_min;
}
else if (Theta[i] <= Theta_sat)
{
extra_water = 0;
h[i] = soil.h (i, Theta[i]);
break;
}
else
{
extra_water = (Theta[i] - Theta_sat) * dz;
Theta[i] = Theta_sat;
h[i] = 0.0;
}
}
q_up = q[first];
q_down = q[last + 1];
}
// Saturated pressure.
double table = geo.cell_z (last) + h[last];
for (int i = last; i > first; i--)
if (h[i] < 0.0)
{
table = geo.cell_z (i) + h[i];
break;
}
for (int i = last; i > first; i--)
if (geo.cell_z (i) < table)
{
daisy_assert (h[i] >= 0.0);
h[i] = table - geo.cell_z (i);
daisy_assert (h[i] >= 0.0);
}
else
break;
// Check mass conservation.
double total_old = 0.0;
double total_new = 0.0;
double total_S = 0.0;
for (unsigned int i = first; i <= last; i++)
{
const double Theta_sat = soil.Theta (i, 0.0, 0.0);
daisy_assert (Theta[i] <= Theta_sat + 1e-10);
total_old += geo.dz (i) * Theta_old[i];
total_new += geo.dz (i) * Theta[i];
total_S += geo.dz (i) * S[i];
daisy_assert (std::isfinite (Theta[i]));
if (Theta[i] <= 0.0)
{
std::ostringstream tmp;
tmp << "Theta[" << i << "] = " << Theta[i];
daisy_bug (tmp.str ());
Theta[i] = 1e-9;
}
}
daisy_balance (total_old, total_new, (-q_up + q_down - total_S) * dt);
}
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]
}