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iphreeqc/phreeqcpp/kinetics.cpp
Darth Vader 21df9497a0 Squashed 'src/' changes from 57b3a6cd..ce34aa5e 
ce34aa5e Merge commit '8184121c90728d5026fa0485302e4584a559ffd8'
8184121c Squashed 'phreeqcpp/' changes from f5587da..b576c75

git-subtree-dir: src
git-subtree-split: ce34aa5e05ddf53f5b3b7ae2240437d31a736f4a
2024-11-18 21:29:52 +00:00

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#include "Utils.h"
#include "Phreeqc.h"
#include "phqalloc.h"
#include <time.h>
#include "StorageBin.h"
#include "Reaction.h"
#include "cxxKinetics.h"
#include "Solution.h"
#include "cxxMix.h"
#include "PPassemblage.h"
#include "Surface.h"
#include "Exchange.h"
#include "GasPhase.h"
#include "SSassemblage.h"
#include "Temperature.h"
#include "cxxKinetics.h"
#include <map>
#include <fstream>
#include <memory>
#include "nvector_serial.h" /* definitions of type N_Vector and macro */
/* NV_Ith_S, prototypes for N_VNew, N_VFree */
/* These macros are defined in order to write code which exactly matches
the mathematical problem description given above.
Ith(v,i) references the ith component of the vector v, where i is in
the range [1..NEQ] and NEQ is defined below. The Ith macro is defined
using the N_VIth macro in nvector.h. N_VIth numbers the components of
a vector starting from 0.
IJth(A,i,j) references the (i,j)th element of the dense matrix A, where
i and j are in the range [1..NEQ]. The IJth macro is defined using the
DENSE_ELEM macro in dense.h. DENSE_ELEM numbers rows and columns of a
dense matrix starting from 0. */
#define Ith(v,i) NV_Ith_S(v,i-1) /* Ith numbers components 1..NEQ */
#define IJth(A,i,j) DENSE_ELEM(A,i-1,j-1) /* IJth numbers rows,cols 1..NEQ */
#define MAX_DIVIDE 2
#define KINETICS_TOL 1e-8;
#if defined(PHREEQCI_GUI)
#ifdef _DEBUG
#define new DEBUG_NEW
#undef THIS_FILE
static char THIS_FILE[] = __FILE__;
#endif
#endif
/* ---------------------------------------------------------------------- */
int Phreeqc::
calc_kinetic_reaction(cxxKinetics *kinetics_ptr, LDBLE time_step)
/* ---------------------------------------------------------------------- */
{
/*
* Go through kinetic components to
* determine rates and
* a list of elements and amounts in
* the reaction.
*/
int j, return_value;
LDBLE coef;
char l_command[] = "run";
class rate *rate_ptr;
/*
* Go through list and generate list of elements and
* coefficient of elements in reaction
*/
return_value = OK;
count_elts = 0;
paren_count = 0;
rate_time = time_step;
/* t1 = clock(); */
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
coef = 0.0;
/*
* Send command to basic interpreter
*/
rate_ptr = rate_search(kinetics_comp_ptr->Get_rate_name().c_str(), &j);
if (rate_ptr == NULL)
{
error_string = sformatf( "Rate not found for %s",
kinetics_comp_ptr->Get_rate_name().c_str());
error_msg(error_string, STOP);
}
else
{
rate_moles = NAN;
rate_m = kinetics_comp_ptr->Get_m();
rate_m0 = kinetics_comp_ptr->Get_m0();
rate_p = kinetics_comp_ptr->Get_d_params();
count_rate_p = (int) kinetics_comp_ptr->Get_d_params().size();
if (rate_ptr->new_def == TRUE)
{
if (basic_compile
(rates[j].commands.c_str(), &rates[j].linebase, &rates[j].varbase,
&rates[j].loopbase) != 0)
{
error_string = sformatf( "Fatal Basic error in rate %s.",
kinetics_comp_ptr->Get_rate_name().c_str());
error_msg(error_string, STOP);
}
rate_ptr->new_def = FALSE;
}
if (basic_run
(l_command, rates[j].linebase, rates[j].varbase,
rates[j].loopbase) != 0)
{
error_string = sformatf( "Fatal Basic error in rate %s.",
kinetics_comp_ptr->Get_rate_name().c_str());
error_msg(error_string, STOP);
}
if (std::isnan(rate_moles))
{
error_string = sformatf( "Moles of reaction not SAVEed for %s.",
kinetics_comp_ptr->Get_rate_name().c_str());
error_msg(error_string, STOP);
}
else
{
coef = rate_moles;
}
}
/*
* Accumulate moles of reaction for component
*/
kinetics_comp_ptr->Set_moles(kinetics_comp_ptr->Get_moles() + coef);
if (coef == 0.0)
continue;
}
/* t2=clock();
printf("secs in reac %e, t2 %e\n", t2-t1, t1);
*/
return (return_value);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
calc_final_kinetic_reaction(cxxKinetics *kinetics_ptr)
/* ---------------------------------------------------------------------- */
{
/*
* Go through kinetic components to
* using extrapolated values, which were
* stored in moles in run_kinetics
*/
LDBLE coef;
class phase *phase_ptr;
class master *master_ptr;
int count= 0;
/*
* Go through list and generate list of elements and
* coefficient of elements in reaction
*/
RESTART: // if limiting rates, jump to here
count++;
kinetics_ptr->Get_totals().clear();
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
count_elts = 0;
paren_count = 0;
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
if (kinetics_comp_ptr->Get_moles() > m_temp[i])
{
kinetics_comp_ptr->Set_moles(m_temp[i]);
kinetics_comp_ptr->Set_m(0);
}
coef = kinetics_comp_ptr->Get_moles();
if (coef == 0.0)
continue;
/*
* Reactant is a pure phase, copy formula into token
*/
cxxNameDouble::iterator it = kinetics_comp_ptr->Get_namecoef().begin();
for ( ; it != kinetics_comp_ptr->Get_namecoef().end(); it++)
{
std::string name = it->first;
LDBLE coef1 = it->second;
phase_ptr = NULL;
int k;
phase_ptr = phase_bsearch(name.c_str(), &k, FALSE);
if (phase_ptr != NULL)
{
add_elt_list(phase_ptr->next_elt,
coef *coef1);
}
else
{
const char* ptr = name.c_str();
if (get_elts_in_species(&ptr, coef * coef1) == ERROR)
{
error_string = sformatf("Error in -formula: %s", name.c_str());
error_msg(error_string, CONTINUE);
}
}
}
if (use.Get_exchange_ptr() != NULL
&& use.Get_exchange_ptr()->Get_related_rate())
{
cxxExchange * exchange_ptr = use.Get_exchange_ptr();
for(size_t j = 0; j < exchange_ptr->Get_exchange_comps().size(); j++)
{
std::string name(exchange_ptr->Get_exchange_comps()[j].Get_rate_name());
if (name.size() > 0)
{
if (strcmp_nocase
(kinetics_comp_ptr->Get_rate_name().c_str(),
name.c_str()) == 0)
{
/* found kinetics component */
std::string formula = exchange_ptr->Get_exchange_comps()[j].Get_formula().c_str();
const char* ptr = formula.c_str();
if (get_elts_in_species(&ptr, -coef*exchange_ptr->Get_exchange_comps()[j].Get_phase_proportion()) == ERROR)
{
error_string = sformatf("Error in -formula: %s", formula.c_str());
error_msg(error_string, CONTINUE);
}
}
}
}
}
if (use.Get_surface_ptr() != NULL && use.Get_surface_ptr()->Get_related_rate())
{
for (size_t j = 0; j < use.Get_surface_ptr()->Get_surface_comps().size(); j++)
{
cxxSurfaceComp *surface_comp_ptr = &(use.Get_surface_ptr()->Get_surface_comps()[j]);
if (surface_comp_ptr->Get_rate_name().size() > 0)
{
if (strcmp_nocase
(kinetics_comp_ptr->Get_rate_name().c_str(),
surface_comp_ptr->Get_rate_name().c_str()) == 0)
{
/* found kinetics component */
std::string temp_formula = surface_comp_ptr->Get_formula().c_str();
const char* cptr = temp_formula.c_str();
/* Surface = 0 when m becomes low ...
*/
if (0.9 * surface_comp_ptr->Get_phase_proportion() *
(kinetics_comp_ptr->Get_m()) < MIN_RELATED_SURFACE)
{
master_ptr = master_bsearch(surface_comp_ptr->Get_master_element().c_str());
if (master_ptr != NULL)
{
master_ptr->total = 0.0;
}
}
else
{
if (get_elts_in_species(&cptr, -coef * surface_comp_ptr->Get_phase_proportion()) == ERROR)
{
error_string = sformatf("Error in -formula: %s", temp_formula.c_str());
error_msg(error_string, CONTINUE);
}
}
}
}
}
}
kinetics_comp_ptr->Set_moles_of_reaction(elt_list_NameDouble());
kinetics_ptr->Get_totals().add_extensive(kinetics_comp_ptr->Get_moles_of_reaction(), 1.0);
}
if (count > 2)
{
#if !defined(R_SO)
fprintf(stderr, "Too many limit_rates-.\n");
#else
error_msg("Too many limit_rates-.\n");
#endif
}
else
{
if (limit_rates(kinetics_ptr))
goto RESTART;
}
if (count > 2)
{
#if !defined(R_SO)
fprintf(stderr, "Too many limit_rates+.\n");
#else
error_msg("Too many limit_rates+.\n");
#endif
}
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
rk_kinetics(int i, LDBLE kin_time, int use_mix, int nsaver,
LDBLE step_fraction)
/* ---------------------------------------------------------------------- */
{
/*
* Runge-Kutta-Fehlberg method; 6 evaluations of the derivative
* give O(h^5) global error and error estimate
* calc_kinetic_reaction(.., ..) calculates moles of intermediate derivatives;
* these are calc'd for the whole step h.
* calc_final_kinetic reaction(..) translates moles to PHREEQC reaction.
*/
int k, save_old;
int l_bad, step_bad, step_ok;
int n_reactions;
LDBLE h, h_old, h_sum;
LDBLE l_error, error_max, safety, moles_max, moles_reduction;
cxxKinetics *kinetics_ptr;
int equal_rate, zero_rate;
cxxPPassemblage *pp_assemblage_save = NULL;
cxxSSassemblage *ss_assemblage_save = NULL;
LDBLE b31 = 3. / 40., b32 = 9. / 40.,
b51 = -11. / 54., b53 = -70. / 27., b54 = 35. / 27.,
b61 = 1631. / 55296., b62 = 175. / 512., b63 = 575. / 13824., b64 =
44275. / 110592., b65 = 253. / 4096., c1 = 37. / 378., c3 =
250. / 621., c4 = 125. / 594., c6 = 512. / 1771., dc5 =
-277. / 14336.;
LDBLE dc1 = c1 - 2825. / 27648., dc3 = c3 - 18575. / 48384., dc4 =
c4 - 13525. / 55296., dc6 = c6 - 0.25;
/*
* Save kinetics i and solution i, if necessary
*/
save_old = -2 - (count_cells * (1 + stag_data.count_stag) + 2);
Utilities::Rxn_copy(Rxn_kinetics_map, i, save_old);
if (nsaver != i)
{
Utilities::Rxn_copy(Rxn_solution_map, i, save_old);
}
/*
* Malloc some space
*/
kinetics_ptr = Utilities::Rxn_find(Rxn_kinetics_map, i);
if (kinetics_ptr == NULL)
return (OK);
n_reactions = (int) kinetics_ptr->Get_kinetics_comps().size();
rk_moles.resize(6 * (size_t)n_reactions);
/*if (use_mix != NOMIX) last_model.force_prep = TRUE; */
set_and_run_wrapper(i, use_mix, FALSE, i, step_fraction);
run_reactions_iterations += iterations;
saver();
if (state == TRANSPORT || state == PHAST)
{
set_transport(i, NOMIX, TRUE, i);
}
else if (state == ADVECTION)
{
set_advection(i, NOMIX, TRUE, i);
}
else if (state == REACTION)
{
set_reaction(i, NOMIX, TRUE);
}
kinetics_ptr = Utilities::Rxn_find(Rxn_kinetics_map, i);
step_bad = step_ok = 0;
l_bad = FALSE;
h_sum = 0.;
h = h_old = kin_time;
moles_max = 0.1;
moles_reduction = 1.0;
safety = 0.7;
if (kinetics_ptr->Get_rk() < 1)
kinetics_ptr->Set_rk(1);
else if (kinetics_ptr->Get_rk() > 3)
kinetics_ptr->Set_rk(6);
if (kinetics_ptr->Get_rk() == 6)
equal_rate = FALSE;
else
equal_rate = TRUE;
/*
* if step_divide > 1, initial timestep is divided
* if < 1, step_divide indicates maximal reaction...
*/
if (kinetics_ptr->Get_step_divide() > 1.0)
{
h = h_old = kin_time / kinetics_ptr->Get_step_divide();
equal_rate = FALSE;
}
else if (kinetics_ptr->Get_step_divide() < 1.0)
moles_max = kinetics_ptr->Get_step_divide();
rate_sim_time = rate_sim_time_start + h_sum;
status(0, NULL);
while (h_sum < kin_time)
{
if (step_bad > kinetics_ptr->Get_bad_step_max())
{
error_string = sformatf(
"Bad RK steps > %d in cell %d. Please decrease (time)step or increase -bad_step_max.",
kinetics_ptr->Get_bad_step_max(), cell_no);
error_msg(error_string, STOP);
}
MOLES_TOO_LARGE:
if (moles_reduction > 1.0)
{
h_old = h;
h = safety * h / (1.0 + moles_reduction);
moles_reduction = 1.0;
equal_rate = FALSE;
l_bad = TRUE;
}
/*
* find k1
*/
if (l_bad == TRUE)
{
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
rk_moles[j] *= (h / h_old);
kinetics_comp_ptr->Set_moles(rk_moles[j] * 0.2);
kinetics_comp_ptr->Set_m(m_temp[j]);
}
l_bad = FALSE;
}
else
{
/*
* define pointers for calc_kinetic_, they are lost after saver()...
*/
if (state == TRANSPORT || state == PHAST)
{
set_transport(i, NOMIX, TRUE, i);
}
else if (state == ADVECTION)
{
set_advection(i, NOMIX, TRUE, i);
}
else if (state == REACTION)
{
set_reaction(i, NOMIX, TRUE);
}
/*
* Moles of minerals and solid solutions may change to make positive
* concentrations. Reactions may take out more than is present in
* solution.
*/
if (use.Get_pp_assemblage_ptr() != NULL)
{
cxxPPassemblage * pp_assemblage_ptr = Utilities::Rxn_find(Rxn_pp_assemblage_map, use.Get_pp_assemblage_ptr()->Get_n_user());
assert(pp_assemblage_ptr);
pp_assemblage_save = new cxxPPassemblage(*pp_assemblage_ptr);
}
if (use.Get_ss_assemblage_ptr() != NULL)
{
cxxSSassemblage * ss_assemblage_ptr = Utilities::Rxn_find(Rxn_ss_assemblage_map, use.Get_ss_assemblage_ptr()->Get_n_user());
assert(ss_assemblage_ptr);
ss_assemblage_save = new cxxSSassemblage(*ss_assemblage_ptr);
}
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_moles(0.);
m_temp[j] = kinetics_comp_ptr->Get_m();
}
rate_sim_time = rate_sim_time_start + h_sum;
calc_kinetic_reaction(kinetics_ptr, h);
/* store k1 in rk_moles ... */
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
if (moles_reduction * moles_max < fabs(kinetics_comp_ptr->Get_moles()))
{
moles_reduction = fabs(kinetics_comp_ptr->Get_moles()) / moles_max;
}
/* define reaction for calculating k2 ... */
rk_moles[j] = kinetics_comp_ptr->Get_moles();
kinetics_comp_ptr->Set_moles(kinetics_comp_ptr->Get_moles() * 0.2);
}
if (moles_reduction > 1.0)
goto MOLES_TOO_LARGE;
}
/*
* Quit rk with rk = 1 and equal rates ...
*/
if (kinetics_ptr->Get_rk() == 1 && equal_rate)
{
zero_rate = TRUE;
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_moles(rk_moles[j]);
if (fabs(kinetics_comp_ptr->Get_moles()) > MIN_TOTAL)
zero_rate = FALSE;
}
if (zero_rate == FALSE)
{
calc_final_kinetic_reaction(kinetics_ptr);
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_m(m_temp[j] - kinetics_comp_ptr->Get_moles());
if (kinetics_comp_ptr->Get_m() < 1.e-30)
kinetics_comp_ptr->Set_m(0);
kinetics_comp_ptr->Set_moles(0.);
}
if (set_and_run_wrapper(i, NOMIX, TRUE, i, 0.) ==
MASS_BALANCE)
{
run_reactions_iterations += iterations;
moles_reduction = 9;
goto MOLES_TOO_LARGE;
}
run_reactions_iterations += iterations;
calc_kinetic_reaction(kinetics_ptr, h);
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
if (fabs(rk_moles[j] - kinetics_comp_ptr->Get_moles()) >
kinetics_comp_ptr->Get_tol())
{
equal_rate = FALSE;
break;
}
}
}
if (zero_rate || equal_rate)
{
/* removing the following line causes different results for
example 6 distributed with the program */
saver();
/* Free space */
if (pp_assemblage_save != NULL)
{
delete pp_assemblage_save;
pp_assemblage_save = NULL;
}
if (ss_assemblage_save != NULL)
{
delete ss_assemblage_save;
ss_assemblage_save = NULL;
}
goto EQUAL_RATE_OUT;
}
else
{
kinetics_ptr->Set_rk(3);
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_moles(0.2 * rk_moles[j]);
}
}
}
/*
* Continue with rk ...
*/
calc_final_kinetic_reaction(kinetics_ptr);
if (set_and_run_wrapper(i, NOMIX, TRUE, i, 0.) == MASS_BALANCE)
{
run_reactions_iterations += iterations;
moles_reduction = 9;
goto MOLES_TOO_LARGE;
}
run_reactions_iterations += iterations;
/*
* find k2
*/
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_m(m_temp[j] - kinetics_comp_ptr->Get_moles());
kinetics_comp_ptr->Set_moles(0.);
}
rate_sim_time = rate_sim_time_start + h_sum + 0.2 * h;
calc_kinetic_reaction(kinetics_ptr, h);
/* Reset to values of last saver() */
if (pp_assemblage_save != NULL)
{
Rxn_pp_assemblage_map[pp_assemblage_save->Get_n_user()] = *pp_assemblage_save;
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, pp_assemblage_save->Get_n_user()));
}
if (ss_assemblage_save != NULL)
{
Rxn_ss_assemblage_map[ss_assemblage_save->Get_n_user()] = *ss_assemblage_save;
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, ss_assemblage_save->Get_n_user()));
}
/* store k2 in rk_moles */
k = n_reactions;
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
if (moles_reduction * moles_max <
fabs(kinetics_comp_ptr->Get_moles()))
{
moles_reduction =
fabs(kinetics_comp_ptr->Get_moles()) / moles_max;
}
/* define reaction for calculating k3 */
rk_moles[k + j] = kinetics_comp_ptr->Get_moles();
kinetics_comp_ptr->Set_moles(b31 * rk_moles[j]
+ b32 * rk_moles[k + j]);
/*
* check for equal_rate ...
*/
if (equal_rate
&& fabs(rk_moles[j] - rk_moles[k + j]) >
kinetics_comp_ptr->Get_tol())
{
equal_rate = FALSE;
}
}
if (moles_reduction > 1.0)
goto MOLES_TOO_LARGE;
/*
* Quit rk with rk = 2 and equal rates ...
*/
if (kinetics_ptr->Get_rk() == 2 && equal_rate)
{
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_moles(
0.3 * rk_moles[j] + 0.7 * rk_moles[k + j]);
}
calc_final_kinetic_reaction(kinetics_ptr);
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_m(m_temp[j] - kinetics_comp_ptr->Get_moles());
if (kinetics_comp_ptr->Get_m() < 1.e-30)
kinetics_comp_ptr->Set_m(0);
kinetics_comp_ptr->Set_moles(0.);
}
if (set_and_run_wrapper(i, NOMIX, TRUE, i, 0.) == MASS_BALANCE)
{
run_reactions_iterations += iterations;
moles_reduction = 9;
goto MOLES_TOO_LARGE;
}
run_reactions_iterations += iterations;
/*
* Move next calc'n to rk = 1 when initial rate equals final rate ...
*/
calc_kinetic_reaction(kinetics_ptr, h);
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
if (fabs(rk_moles[j] - kinetics_comp_ptr->Get_moles()) >
kinetics_comp_ptr->Get_tol())
{
equal_rate = FALSE;
break;
}
}
if (equal_rate)
kinetics_ptr->Set_rk(1);
saver();
/* Free space */
if (pp_assemblage_save != NULL)
{
delete pp_assemblage_save;
pp_assemblage_save = NULL;
}
if (ss_assemblage_save != NULL)
{
Rxn_ss_assemblage_map[ss_assemblage_save->Get_n_user()] = *ss_assemblage_save;
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, ss_assemblage_save->Get_n_user()));
}
goto EQUAL_RATE_OUT;
}
/*
* Continue runge_kutta..
*/
calc_final_kinetic_reaction(kinetics_ptr);
if (set_and_run_wrapper(i, NOMIX, TRUE, i, 0.) == MASS_BALANCE)
{
run_reactions_iterations += iterations;
moles_reduction = 9;
goto MOLES_TOO_LARGE;
}
run_reactions_iterations += iterations;
/*
* find k3
*/
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_m (m_temp[j] - kinetics_comp_ptr->Get_moles());
kinetics_comp_ptr->Set_moles(0.);
}
rate_sim_time = rate_sim_time_start + h_sum + 0.3 * h;
calc_kinetic_reaction(kinetics_ptr, h);
/* Reset to values of last saver() */
if (pp_assemblage_save != NULL)
{
Rxn_pp_assemblage_map[pp_assemblage_save->Get_n_user()] = *pp_assemblage_save;
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, pp_assemblage_save->Get_n_user()));
}
if (ss_assemblage_save != NULL)
{
Rxn_ss_assemblage_map[ss_assemblage_save->Get_n_user()] = *ss_assemblage_save;
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, ss_assemblage_save->Get_n_user()));
}
/* store k3 in rk_moles */
k = 2 * n_reactions;
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
if (moles_reduction * moles_max <
fabs(kinetics_comp_ptr->Get_moles()))
{
moles_reduction =
fabs(kinetics_comp_ptr->Get_moles()) / moles_max;
}
/* define reaction for calculating k4 ... */
rk_moles[k + j] = kinetics_comp_ptr->Get_moles();
kinetics_comp_ptr->Set_moles(0.3 * rk_moles[j]
- 0.9 * rk_moles[n_reactions + j] + 1.2 * rk_moles[k + j]);
/*
* check for equal_rate ...
*/
if (equal_rate
&& fabs(rk_moles[j] - rk_moles[k + j]) >
kinetics_comp_ptr->Get_tol())
equal_rate = FALSE;
}
if (moles_reduction > 1.0)
goto MOLES_TOO_LARGE;
/*
* Quit rk with rk = 3 and equal rates ...
*/
if (kinetics_ptr->Get_rk() == 3 && equal_rate)
{
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_moles(0.5 * rk_moles[j]
- 1.5 * rk_moles[n_reactions + j] + 2 * rk_moles[k + j]);
}
calc_final_kinetic_reaction(kinetics_ptr);
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_m(m_temp[j] - kinetics_comp_ptr->Get_moles());
if (kinetics_comp_ptr->Get_m() < 1.e-30)
kinetics_comp_ptr->Set_m(0.);
kinetics_comp_ptr->Set_moles(0.);
}
if (set_and_run_wrapper(i, NOMIX, TRUE, i, 0.) == MASS_BALANCE)
{
run_reactions_iterations += iterations;
moles_reduction = 9;
goto MOLES_TOO_LARGE;
}
run_reactions_iterations += iterations;
/*
* Move next calc'n to rk = 1 when initial rate equals final rate ...
*/
calc_kinetic_reaction(kinetics_ptr, h);
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
if (fabs(rk_moles[j] - kinetics_comp_ptr->Get_moles()) >
kinetics_comp_ptr->Get_tol())
{
equal_rate = FALSE;
break;
}
}
if (equal_rate)
kinetics_ptr->Set_rk(1);
saver();
/* Free space */
if (pp_assemblage_save != NULL)
{
delete pp_assemblage_save;
pp_assemblage_save = NULL;
}
if (ss_assemblage_save != NULL)
{
delete ss_assemblage_save;
ss_assemblage_save = NULL;
}
goto EQUAL_RATE_OUT;
}
/*
* Continue runge_kutta..
*/
calc_final_kinetic_reaction(kinetics_ptr);
if (set_and_run_wrapper(i, NOMIX, TRUE, i, 0.) == MASS_BALANCE)
{
run_reactions_iterations += iterations;
moles_reduction = 9;
goto MOLES_TOO_LARGE;
}
run_reactions_iterations += iterations;
/*
* find k4
*/
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_m(m_temp[j] - kinetics_comp_ptr->Get_moles());
kinetics_comp_ptr->Set_moles(0.);
}
rate_sim_time = rate_sim_time_start + h_sum + 0.6 * h;
calc_kinetic_reaction(kinetics_ptr, h);
/* Reset to values of last saver() */
if (pp_assemblage_save != NULL)
{
Rxn_pp_assemblage_map[pp_assemblage_save->Get_n_user()] = *pp_assemblage_save;
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, pp_assemblage_save->Get_n_user()));
}
if (ss_assemblage_save != NULL)
{
Rxn_ss_assemblage_map[ss_assemblage_save->Get_n_user()] = *ss_assemblage_save;
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, ss_assemblage_save->Get_n_user()));
}
/* store k4 in rk_moles */
k = 3 * n_reactions;
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
if (moles_reduction * moles_max <
fabs(kinetics_comp_ptr->Get_moles()))
{
moles_reduction =
fabs(kinetics_comp_ptr->Get_moles()) / moles_max;
}
/* define reaction for calculating k5 */
rk_moles[k + j] = kinetics_comp_ptr->Get_moles();
kinetics_comp_ptr->Set_moles(b51 * rk_moles[j]
+ 2.5 * rk_moles[(size_t)n_reactions + j]
+ b53 * rk_moles[2 * (size_t)n_reactions + j]
+ b54 * rk_moles[(size_t)k + (size_t)j]);
}
if (moles_reduction > 1.0)
goto MOLES_TOO_LARGE;
calc_final_kinetic_reaction(kinetics_ptr);
if (set_and_run_wrapper(i, NOMIX, TRUE, i, 0.) == MASS_BALANCE)
{
run_reactions_iterations += iterations;
moles_reduction = 9;
goto MOLES_TOO_LARGE;
}
run_reactions_iterations += iterations;
/*
* find k5
*/
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_m(m_temp[j] - kinetics_comp_ptr->Get_moles());
kinetics_comp_ptr->Set_moles(0.);
}
rate_sim_time = rate_sim_time_start + h_sum + h;
calc_kinetic_reaction(kinetics_ptr, h);
/* Reset to values of last saver() */
if (pp_assemblage_save != NULL)
{
Rxn_pp_assemblage_map[pp_assemblage_save->Get_n_user()] = *pp_assemblage_save;
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, pp_assemblage_save->Get_n_user()));
}
if (ss_assemblage_save != NULL)
{
Rxn_ss_assemblage_map[ss_assemblage_save->Get_n_user()] = *ss_assemblage_save;
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, ss_assemblage_save->Get_n_user()));
}
/* store k5 in rk_moles */
k = 4 * n_reactions;
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
if (moles_reduction * moles_max <
fabs(kinetics_comp_ptr->Get_moles()))
{
moles_reduction =
fabs(kinetics_comp_ptr->Get_moles()) / moles_max;
}
/* define reaction for calculating k6 */
rk_moles[k + j] = kinetics_comp_ptr->Get_moles();
kinetics_comp_ptr->Set_moles(b61 * rk_moles[j]
+ b62 * rk_moles[(size_t)n_reactions + j]
+ b63 * rk_moles[2 * (size_t)n_reactions + j]
+ b64 * rk_moles[3 * (size_t)n_reactions + j]
+ b65 * rk_moles[(size_t)k + (size_t)j]);
}
if (moles_reduction > 1.0)
goto MOLES_TOO_LARGE;
calc_final_kinetic_reaction(kinetics_ptr);
if (set_and_run_wrapper(i, NOMIX, TRUE, i, 0.) == MASS_BALANCE)
{
run_reactions_iterations += iterations;
moles_reduction = 9;
goto MOLES_TOO_LARGE;
}
run_reactions_iterations += iterations;
/*
* find k6
*/
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_m(m_temp[j] - kinetics_comp_ptr->Get_moles());
kinetics_comp_ptr->Set_moles(0.);
}
rate_sim_time = rate_sim_time_start + h_sum + 0.875 * h;
calc_kinetic_reaction(kinetics_ptr, h);
/* Reset to values of last saver() */
if (pp_assemblage_save != NULL)
{
Rxn_pp_assemblage_map[pp_assemblage_save->Get_n_user()] = *pp_assemblage_save;
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, pp_assemblage_save->Get_n_user()));
}
if (ss_assemblage_save != NULL)
{
Rxn_ss_assemblage_map[ss_assemblage_save->Get_n_user()] = *ss_assemblage_save;
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, ss_assemblage_save->Get_n_user()));
}
/* store k6 in rk_moles */
k = 5 * n_reactions;
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
rk_moles[k + j] = kinetics_comp_ptr->Get_moles();
}
/*
* Evaluate error
*/
error_max = 0.;
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
l_error = fabs(dc1 * rk_moles[j]
+ dc3 * rk_moles[2 * (size_t)n_reactions + (size_t)j]
+ dc4 * rk_moles[3 * (size_t)n_reactions + (size_t)j]
+ dc5 * rk_moles[4 * (size_t)n_reactions + (size_t)j]
+ dc6 * rk_moles[5 * (size_t)n_reactions + (size_t)j]);
/* tol is in moles/l */
l_error /= kinetics_comp_ptr->Get_tol();
if (l_error > error_max)
error_max = l_error;
}
/*
* repeat with smaller step
*/
/* printf("timest %g ; error_max %g\n", h, error_max); */
if (error_max > 1)
{
h_old = h;
if (step_ok == 0)
h = h * safety / error_max;
else
h = h * safety * pow(error_max, (LDBLE) -0.25);
l_bad = TRUE;
step_bad++;
}
else
{
/*
* OK, calculate result
*/
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_moles(c1 * rk_moles[j]
+ c3 * rk_moles[2 * (size_t)n_reactions + (size_t)j]
+ c4 * rk_moles[3 * (size_t)n_reactions + (size_t)j]
+ c6 * rk_moles[5 * (size_t)n_reactions + (size_t)j]);
}
calc_final_kinetic_reaction(kinetics_ptr);
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_m(m_temp[j] - kinetics_comp_ptr->Get_moles());
if (kinetics_comp_ptr->Get_m() < 1.e-30)
kinetics_comp_ptr->Set_m(0);
kinetics_comp_ptr->Set_moles(0.);
}
if (set_and_run_wrapper(i, NOMIX, TRUE, i, 0.) == MASS_BALANCE)
{
run_reactions_iterations += iterations;
moles_reduction = 9;
goto MOLES_TOO_LARGE;
}
run_reactions_iterations += iterations;
/*
* Move next calc'n to rk = 1 when initial rate equals final rate ...
*/
calc_kinetic_reaction(kinetics_ptr, h);
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
if (fabs(rk_moles[j] - kinetics_comp_ptr->Get_moles()) >
kinetics_comp_ptr->Get_tol())
{
equal_rate = FALSE;
break;
}
}
if (equal_rate && kinetics_ptr->Get_rk() < 6)
kinetics_ptr->Set_rk(1);
saver();
step_ok++;
h_sum += h;
/* Free space */
if (pp_assemblage_save != NULL)
{
delete pp_assemblage_save;
pp_assemblage_save = NULL;
}
if (ss_assemblage_save != NULL)
{
delete ss_assemblage_save;
ss_assemblage_save = NULL;
}
/*
* and increase step size ...
*/
if (h_sum < kin_time)
{
if (error_max > 0.000577)
{
h = h * safety * pow(error_max, (LDBLE) -0.2e0);
}
else
{
h *= 4;
}
if (h > (kin_time - h_sum))
h = (kin_time - h_sum);
}
}
{
char str[MAX_LENGTH];
snprintf(str, sizeof(str), "RK-steps: Bad%4d. OK%5d. Time %3d%%", step_bad,
step_ok, (int) (100 * h_sum / kin_time));
status(0, str, true);
}
}
EQUAL_RATE_OUT:
/*
* Run one more time to get distribution of species
*/
if (state >= REACTION || nsaver != i)
{
set_and_run_wrapper(i, NOMIX, FALSE, nsaver, 0.);
run_reactions_iterations += iterations;
}
/* saver(); */ /* reset for printing */
if (use_mix == DISP)
{
use.Set_mix_ptr(Utilities::Rxn_find(Dispersion_mix_map, i));
use.Set_mix_in(true);
use.Set_n_mix_user(i);
}
else if ((use_mix == STAG || use_mix == TRUE) && state == TRANSPORT)
{
use.Set_mix_ptr(Utilities::Rxn_find(Rxn_mix_map, i));
if (use.Get_mix_ptr() != NULL)
{
use.Set_mix_in(true);
use.Set_n_mix_user(i);
}
}
/*
* Restore solution i, if necessary
*/
if (nsaver != i)
{
Utilities::Rxn_copy(Rxn_solution_map, save_old, i);
}
rk_moles.clear();
rate_sim_time = rate_sim_time_start + kin_time;
use.Set_kinetics_in(true);
/* Free space */
if (pp_assemblage_save != NULL)
{
delete pp_assemblage_save;
pp_assemblage_save = NULL;
}
if (ss_assemblage_save != NULL)
{
delete ss_assemblage_save;
ss_assemblage_save = NULL;
}
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
set_and_run_wrapper(int i, int use_mix, int use_kinetics, int nsaver,
LDBLE step_fraction)
/* ---------------------------------------------------------------------- */
{
int j, converge, max_try;
int old_diag, old_itmax;
LDBLE old_tol, old_min_value, old_step, old_pe, old_pp_column_scale;
LDBLE small_pe_step, small_step;
#if (__GNUC__ && (__cplusplus >= 201103L)) || (_MSC_VER >= 1600)
std::unique_ptr<cxxPPassemblage> pp_assemblage_save=NULL;
std::unique_ptr<cxxSSassemblage> ss_assemblage_save=NULL;
std::unique_ptr<cxxKinetics> kinetics_save=NULL;
#else
std::auto_ptr<cxxPPassemblage> pp_assemblage_save(NULL);
std::auto_ptr<cxxSSassemblage> ss_assemblage_save(NULL);
std::auto_ptr<cxxKinetics> kinetics_save(NULL);
#endif
int restart = 0;
small_pe_step = 5.;
small_step = 10.;
converge = FALSE;
old_diag = diagonal_scale;
old_itmax = itmax;
old_tol = ineq_tol;
old_step = step_size;
old_pe = pe_step_size;
old_min_value = min_value;
old_pp_column_scale = pp_column_scale;
int old_equi_delay = equi_delay;
if (state == TRANSPORT || state == PHAST)
{
set_transport(i, use_mix, use_kinetics, i);
}
else if (state == ADVECTION)
{
set_advection(i, use_mix, use_kinetics, i);
}
else if (state == REACTION)
{
set_reaction(i, use_mix, use_kinetics);
}
if (use.Get_pp_assemblage_ptr() != NULL)
{
cxxPPassemblage * pp_assemblage_ptr = use.Get_pp_assemblage_ptr();
pp_assemblage_save.reset(new cxxPPassemblage(*pp_assemblage_ptr));
}
if (use.Get_ss_assemblage_ptr() != NULL)
{
cxxSSassemblage * ss_assemblage_ptr = use.Get_ss_assemblage_ptr();
ss_assemblage_save.reset(new cxxSSassemblage(*ss_assemblage_ptr));
}
if (use.Get_kinetics_ptr() != NULL)
{
kinetics_save.reset(new cxxKinetics(*use.Get_kinetics_ptr()));
}
if (pitzer_model == TRUE || sit_model == TRUE)
{
diagonal_scale = TRUE;
always_full_pitzer = FALSE;
max_try = 14;
}
else
{
max_try = 14;
}
max_try = (max_tries < max_try) ? max_tries : max_try;
/*max_try = 1; */
restart:
for (j = 0; j < max_try; j++)
{
if (j == 1)
{
/*always_full_pitzer = TRUE;*/
if (pe_step_size <= small_pe_step && step_size <= small_step)
continue;
itmax *= 2;
step_size = small_step;
pe_step_size = small_pe_step;
error_string = sformatf(
"Trying smaller step size, pe step size %g, %g ... \n",
(double) step_size, (double) pe_step_size);
warning_msg(error_string);
}
else if (j == 2)
{
itmax *= 2;
ineq_tol /= 10.;
error_string = sformatf( "Trying reduced tolerance %g ...\n",
(double) ineq_tol);
warning_msg(error_string);
}
else if (j == 3)
{
itmax *= 2;
ineq_tol *= 10.;
error_string = sformatf( "Trying increased tolerance %g ...\n",
(double) ineq_tol);
warning_msg(error_string);
}
else if (j == 4)
{
always_full_pitzer = TRUE;
itmax *= 2;
if (diagonal_scale == TRUE)
{
diagonal_scale = FALSE;
}
else
{
diagonal_scale = TRUE;
}
error_string = sformatf( "Trying diagonal scaling ...\n");
warning_msg(error_string);
}
else if (j == 5)
{
itmax *= 2;
if (diagonal_scale == TRUE)
{
diagonal_scale = FALSE;
}
else
{
diagonal_scale = TRUE;
}
ineq_tol /= 10.;
error_string = sformatf(
"Trying diagonal scaling and reduced tolerance %g ...\n",
(double) ineq_tol);
warning_msg(error_string);
}
else if (j == 6)
{
if (pitzer_model == TRUE || sit_model == TRUE) continue;
itmax *= 2;
pp_column_scale = 1e-10;
error_string = sformatf(
"Trying scaling pure_phase columns %g ...\n",
(double) pp_column_scale);
warning_msg(error_string);
}
else if (j == 7)
{
if (pitzer_model == TRUE || sit_model == TRUE) continue;
itmax *= 2;
pp_column_scale = 1e-10;
if (diagonal_scale == TRUE)
{
diagonal_scale = FALSE;
}
else
{
diagonal_scale = TRUE;
}
error_string = sformatf(
"Trying scaling pure_phase columns and diagonal scale %g ...\n",
(double) pp_column_scale);
warning_msg(error_string);
}
else if (j == 8)
{
if (use.Get_pp_assemblage_ptr() == NULL) continue;
if (equi_delay > 0)
{
equi_delay = 0;
}
else
{
equi_delay = 1;
}
error_string = sformatf( "Trying delay removal of equilibrium phases %g ...\n",
(double) equi_delay);
warning_msg(error_string);
}
else if (j == 9)
{
if (pitzer_model == TRUE || sit_model == TRUE) continue;
itmax *= 2;
min_value *= 10;
error_string = sformatf( "Trying increased scaling %g ...\n",
(double) min_value);
warning_msg(error_string);
}
else if (j == 10)
{
if (pitzer_model == TRUE || sit_model == TRUE) continue;
aqueous_only = 5;
error_string = sformatf(
"Skipping optimize equations for first %d iterations ...\n",
aqueous_only);
warning_msg(error_string);
}
else if (j == 11)
{
if (pitzer_model == TRUE || sit_model == TRUE) continue;
negative_concentrations = TRUE;
error_string = sformatf(
"Adding inequality to make concentrations greater than zero.\n");
warning_msg(error_string);
}
else if (j == 12)
{
itmax *= 2;
ineq_tol /= 100.;
error_string = sformatf( "Trying reduced tolerance %g ...\n",
(double) ineq_tol);
warning_msg(error_string);
}
else if (j == 13)
{
itmax *= 2;
ineq_tol /= 1000.;
error_string = sformatf( "Trying reduced tolerance %g ...\n",
(double) ineq_tol);
warning_msg(error_string);
}
else if (j == 14 && use.Get_ss_assemblage_in())
{
//cxxStorageBin error_bin;
//Use2cxxStorageBin(error_bin);
//std::ostringstream error_input;
//error_bin.dump_raw(error_input, 0);
//cxxStorageBin reread;
//std::istringstream is(error_input.str());
//CParser cp(is);
//cp.set_echo_stream(CParser::EO_NONE);
//reread.read_raw(cp);
//cxxStorageBin2phreeqc(reread);
//error_string = sformatf("Trying restarting ...\n");
//warning_msg(error_string);
//if (restart < 2)
//{
// restart++;
// goto restart;
//}
}
if (j > 0)
{
if (pp_assemblage_save.get() != NULL)
{
Rxn_pp_assemblage_map[pp_assemblage_save->Get_n_user()] = *pp_assemblage_save;
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, pp_assemblage_save->Get_n_user()));
}
if (ss_assemblage_save.get() != NULL)
{
Rxn_ss_assemblage_map[ss_assemblage_save->Get_n_user()] = *ss_assemblage_save;
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, ss_assemblage_save->Get_n_user()));
}
if (kinetics_save.get() != NULL)
{
Rxn_kinetics_map[kinetics_save->Get_n_user()] = *kinetics_save;
use.Set_kinetics_ptr(Utilities::Rxn_find(Rxn_kinetics_map, kinetics_save->Get_n_user()));
}
}
if (j == 14)
{
cxxStorageBin error_bin(this->Get_phrq_io());
Use2cxxStorageBin(error_bin);
std::ostringstream error_input;
error_bin.dump_raw(error_input, 0);
cxxStorageBin reread(this->Get_phrq_io());
std::istringstream is(error_input.str());
CParser cp(is);
cp.set_echo_stream(CParser::EO_NONE);
cp.set_echo_file(CParser::EO_NONE);
reread.read_raw(cp);
cxxStorageBin2phreeqc(reread);
error_string = sformatf("Trying restarting ...\n");
warning_msg(error_string);
step_size = 1.0 + (small_step - 1.0)/((double) restart + 1.0);
pe_step_size = 1.0 + (small_pe_step - 1)/ ((double)restart + 1.0);
if (restart < 2)
{
restart++;
goto restart;
}
}
set_and_run_attempt = j;
converge =
set_and_run(i, use_mix, use_kinetics, nsaver, step_fraction);
/* reset values */
diagonal_scale = old_diag;
itmax = old_itmax;
ineq_tol = old_tol;
step_size = old_step;
pe_step_size = old_pe;
min_value = old_min_value;
pp_column_scale = old_pp_column_scale;
equi_delay = old_equi_delay;
aqueous_only = 0;
negative_concentrations = FALSE;
always_full_pitzer = FALSE;
if (converge == TRUE)
{
break;
}
else if (converge == MASS_BALANCE)
{
break;
}
warning_msg
("Numerical method failed with this set of convergence parameters.\n");
}
if (converge == FALSE && use.Get_kinetics_ptr() != NULL
&& use.Get_kinetics_ptr()->Get_use_cvode())
{
error_string = sformatf(
"Numerical method failed on all parameter combinations, retrying integration, cell/soln %d", this->solution_number());
warning_msg(error_string);
converge = MASS_BALANCE;
}
if (converge == FALSE)
{
/*
* write to error.inp what failed to converge.
*/
std::ofstream error_input("error.inp");
cxxStorageBin error_bin(this->Get_phrq_io());
Use2cxxStorageBin(error_bin);
error_bin.dump_raw(error_input, 0);
error_input.close();
/* if (state == TRANSPORT && dump_modulus == 0) dump(); */
check_residuals();
pr.all = TRUE;
pr.gas_phase = use.Get_gas_phase_in();
pr.pp_assemblage = use.Get_pp_assemblage_in();
pr.ss_assemblage = use.Get_ss_assemblage_in();
pr.surface = use.Get_surface_in();
pr.exchange = use.Get_exchange_in();
pr.totals = TRUE;
pr.species = TRUE;
pr.saturation_indices = TRUE;
pr.irrev = use.Get_reaction_in();
pr.mix = use.Get_mix_in();
pr.reaction = TRUE;
pr.use = TRUE;
sum_species();
print_all();
error_string = sformatf(
"Numerical method failed on all combinations of convergence parameters, cell/soln/mix %d", this->solution_number());
error_msg(error_string, STOP);
}
numerical_fixed_volume = false;
if (converge == MASS_BALANCE)
{
return (MASS_BALANCE);
}
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
set_and_run(int i, int use_mix, int use_kinetics, int nsaver,
LDBLE step_fraction)
/* ---------------------------------------------------------------------- */
{
/*
* i --user number for soln, reaction, etc.
* use_mix --integer flag
state == TRANSPORT: DISP, STAG, NOMIX
state == REACTION: TRUE, FALSE
* use_kinetics --true or false flag to calculate kinetic reactions
* nsaver --user number to store solution
* step_fraction--fraction of irreversible reaction to add
*/
int converge;
if (state == TRANSPORT || state == PHAST)
{
set_transport(i, use_mix, use_kinetics, nsaver);
}
else if (state == ADVECTION)
{
set_advection(i, use_mix, use_kinetics, nsaver);
}
else if (state == REACTION)
{
set_reaction(i, use_mix, use_kinetics);
}
cell = i;
/*
* Take step
*/
if (state >= REACTION)
{
if (step(step_fraction) == MASS_BALANCE)
{
return (MASS_BALANCE);
}
/*
* Always use solution, exchange, and surface -1
*/
use.Set_solution_ptr(Utilities::Rxn_find(Rxn_solution_map, -1));
/* new */
if (use.Get_exchange_ptr() != NULL)
{
use.Set_exchange_ptr(Utilities::Rxn_find(Rxn_exchange_map, -1));
}
if (use.Get_surface_ptr() != NULL)
{
use.Set_surface_ptr(Utilities::Rxn_find(Rxn_surface_map, -1));
}
/*
* Adjust the total pressure to the gas pressure
*/
if (use.Get_gas_phase_ptr() != NULL)
{
cxxGasPhase *gas_phase_ptr = use.Get_gas_phase_ptr();
if (gas_phase_ptr->Get_type() == cxxGasPhase::GP_PRESSURE)
{
/*
* Fixed-pressure Gas phase and solution will react
* Change total pressure of current simulation to pressure
* of gas phase
*/
patm_x = gas_phase_ptr->Get_total_p();
}
/* fixed volume gas phase is handled in calc_gas_pressures */
}
}
/* end new */
if (use.Get_surface_ptr() != NULL)
{
dl_type_x = use.Get_surface_ptr()->Get_dl_type();
}
if (use.Get_surface_ptr() != NULL && dl_type_x != cxxSurface::NO_DL)
{
converge = surface_model();
}
else
{
prep();
k_temp(use.Get_solution_ptr()->Get_tc(), use.Get_solution_ptr()->Get_patm());
set(FALSE);
converge = model();
}
sum_species();
viscos = viscosity(NULL);
use.Get_solution_ptr()->Set_viscosity(viscos);
use.Get_solution_ptr()->Set_viscos_0(viscos_0);
if (use.Get_surface_ptr() != NULL && dl_type_x != cxxSurface::NO_DL && use.Get_surface_ptr()->Get_calc_viscosity())
use.Get_surface_ptr()->Set_DDL_viscosity(viscosity(use.Get_surface_ptr()));
return (converge);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
set_transport(int i, int use_mix, int use_kinetics, int nsaver)
/* ---------------------------------------------------------------------- */
{
/*
* i --user number for soln, reaction, etc.
* use_mix --integer flag
state == TRANSPORT: DISP, STAG, NOMIX, MIX_BS
state == REACTION: TRUE, FALSE
* use_kinetics --true or false flag to calculate kinetic reactions
* nsaver --user number to store solution
*/
cell = i;
reaction_step = 1;
/*
* Find mixture or solution
*/
use.Set_mix_ptr(NULL);
use.Set_mix_in(false);
if (use_mix == DISP)
{
use.Set_mix_ptr(Utilities::Rxn_find(Dispersion_mix_map, i));
use.Set_mix_in(true);
use.Set_n_mix_user(i);
use.Set_n_mix_user_orig(i);
}
else if ((use_mix == STAG && multi_Dflag != TRUE) || use_mix == MIX_BS)
{
use.Set_mix_ptr(Utilities::Rxn_find(Rxn_mix_map, i));
if (use.Get_mix_ptr() != NULL)
{
use.Set_mix_in(true);
use.Set_n_mix_user(i);
use.Set_n_mix_user_orig(i);
}
else
{
use.Set_solution_ptr(Utilities::Rxn_find(Rxn_solution_map, i));
if (use.Get_solution_ptr() == NULL)
{
error_string = sformatf( "Solution %d not found, while searching mix structure for solution %d.",
i, use.Get_n_solution_user());
error_msg(error_string, STOP);
}
use.Set_n_solution_user(i);
use.Set_solution_in(true);
}
}
else
{
use.Set_solution_ptr(Utilities::Rxn_find(Rxn_solution_map, i));
if (use.Get_solution_ptr() == NULL)
{
error_string = sformatf( "Solution %d not found, while searching mix structure for solution %d.",
i, use.Get_n_solution_user());
error_msg(error_string, STOP);
}
use.Set_n_solution_user(i);
use.Set_solution_in(true);
}
save.solution = TRUE;
save.n_solution_user = nsaver;
save.n_solution_user_end = nsaver;
/*
* Find pure phase assemblage
*/
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, i));
if (use.Get_pp_assemblage_ptr() != NULL)
{
use.Set_pp_assemblage_in(true);
use.Set_n_pp_assemblage_user(i);
save.pp_assemblage = TRUE;
save.n_pp_assemblage_user = i;
save.n_pp_assemblage_user_end = i;
}
else
{
use.Set_pp_assemblage_in(false);
save.pp_assemblage = FALSE;
}
/*
* Find irreversible reaction
*/
use.Set_reaction_ptr(Utilities::Rxn_find(Rxn_reaction_map, i));
if (use.Get_reaction_ptr() != NULL)
{
use.Set_reaction_in(true);
use.Set_n_reaction_user(i);
}
else
{
use.Set_reaction_in(false);
}
/*
* Find exchange
*/
use.Set_exchange_ptr(Utilities::Rxn_find(Rxn_exchange_map, i));
if (use.Get_exchange_ptr() != NULL)
{
use.Set_exchange_in(true);
use.Set_n_exchange_user(i);
save.exchange = TRUE;
save.n_exchange_user = i;
save.n_exchange_user_end = i;
}
else
{
use.Set_exchange_in(false);
save.exchange = FALSE;
}
/*
* Find surface
*/
use.Set_surface_ptr(Utilities::Rxn_find(Rxn_surface_map, i));
if (use.Get_surface_ptr() != NULL)
{
use.Set_surface_in(true);
use.Set_n_surface_user(i);
save.surface = TRUE;
save.n_surface_user = i;
save.n_surface_user_end = i;
}
else
{
use.Set_surface_in(false);
save.surface = FALSE;
dl_type_x = cxxSurface::NO_DL;
}
/*
* Find temperature; temp retardation is done in step
*/
use.Set_temperature_ptr(Utilities::Rxn_find(Rxn_temperature_map, i));
if (use.Get_temperature_ptr() != NULL)
{
use.Set_temperature_in(true);
use.Set_n_temperature_user(i);
}
else
{
use.Set_temperature_in(false);
}
/*
* Find pressure
*/
use.Set_pressure_ptr(Utilities::Rxn_find(Rxn_pressure_map, i));
if (use.Get_pressure_ptr() != NULL)
{
use.Set_pressure_in(true);
use.Set_n_pressure_user(i);
}
else
{
use.Set_pressure_in(false);
}
/*
* Find gas
*/
use.Set_gas_phase_ptr(Utilities::Rxn_find(Rxn_gas_phase_map, i));
if (use.Get_gas_phase_ptr() != NULL)
{
use.Set_gas_phase_in(true);
use.Set_n_gas_phase_user(i);
save.gas_phase = TRUE;
save.n_gas_phase_user = i;
save.n_gas_phase_user_end = i;
}
else
{
use.Set_gas_phase_in(false);
save.gas_phase = FALSE;
}
/*
* Find ss_assemblage
*/
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, i));
if (use.Get_ss_assemblage_ptr() != NULL)
{
use.Set_ss_assemblage_in(true);
use.Set_n_ss_assemblage_user(i);
save.ss_assemblage = TRUE;
save.n_ss_assemblage_user = i;
save.n_ss_assemblage_user_end = i;
}
else
{
use.Set_ss_assemblage_in(false);
save.ss_assemblage = FALSE;
}
/*
* Find kinetics
*/
use.Set_kinetics_ptr(NULL);
use.Set_kinetics_in(false);
save.kinetics = FALSE;
if (use_kinetics == TRUE)
{
use.Set_kinetics_ptr(Utilities::Rxn_find(Rxn_kinetics_map, i));
if (use.Get_kinetics_ptr() != NULL)
{
use.Set_n_kinetics_user(i);
use.Set_kinetics_in(true);
save.kinetics = TRUE;
save.n_kinetics_user = i;
save.n_kinetics_user_end = i;
}
}
/*
if (use.irrev_ptr != NULL && use.Get_kinetics_ptr() != NULL)
{
warning_msg("Should not use REACTION in same simulation with KINETICS.");
}
*/
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
set_reaction(int i, int use_mix, int use_kinetics)
/* ---------------------------------------------------------------------- */
{
/*
* i --user number for soln, reaction, etc.
* use_mix --integer flag
state == TRANSPORT: DISP, STAG, NOMIX
state == REACTION: TRUE, FALSE
* use_kinetics --true or false flag to calculate kinetic reactions
*/
/*
* Find mixture or solution
*/
use.Set_mix_ptr(NULL);
use.Set_solution_ptr(NULL);
if (use_mix == TRUE && use.Get_mix_in() == TRUE)
{
use.Set_mix_ptr(Utilities::Rxn_find(Rxn_mix_map, i));
if (use.Get_mix_ptr() == NULL)
{
error_string = sformatf( "MIX %d not found.", i);
error_msg(error_string, STOP);
}
}
else
{
use.Set_solution_ptr(Utilities::Rxn_find(Rxn_solution_map, i));
if (use.Get_solution_ptr() == NULL)
{
error_string = sformatf( "Solution %d not found.", i);
error_msg(error_string, STOP);
}
}
/*
* Find pure phase assemblage
*/
if (use.Get_pp_assemblage_in() == TRUE)
{
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, i));
if (use.Get_pp_assemblage_ptr() == NULL)
{
error_string = sformatf( "PP_ASSEMBLAGE %d not found.", i);
error_msg(error_string, STOP);
}
}
/*
* Find irreversible reaction
*/
if (use.Get_reaction_in() == TRUE)
{
use.Set_reaction_ptr(Utilities::Rxn_find(Rxn_reaction_map, i));
if (use.Get_reaction_ptr() == NULL)
{
error_string = sformatf( "REACTION %d not found.", i);
error_msg(error_string, STOP);
}
}
/*
* Find exchange
*/
if (use.Get_exchange_in() == TRUE)
{
use.Set_exchange_ptr(Utilities::Rxn_find(Rxn_exchange_map, i));
if (use.Get_exchange_ptr() == NULL)
{
error_string = sformatf( "EXCHANGE %d not found.", i);
error_msg(error_string, STOP);
}
}
/*
* Find surface
*/
//if (use.Get_surface_in() && use.Get_kinetics_in() && use.Get_kinetics_ptr() && !use.Get_kinetics_ptr()->Get_use_cvode() && reaction_step > 1)
//{
// // use.Set_surface_ptr(Utilities::Rxn_find(Rxn_surface_map, i));
// // appt: we may come here with zero kinetic reaction, but surface may have to keep DONNAN_DL
//}
//else
// dl_type_x = cxxSurface::NO_DL;
if (use.Get_surface_in() == TRUE)
{
use.Set_surface_ptr(Utilities::Rxn_find(Rxn_surface_map, i));
if (use.Get_surface_ptr() == NULL)
{
error_string = sformatf( "SURFACE %d not found.", i);
error_msg(error_string, STOP);
}
}
/*
* Find temperature; temp retardation is done in step
*/
if (use.Get_temperature_in() == TRUE)
{
use.Set_temperature_ptr(Utilities::Rxn_find(Rxn_temperature_map, i));
if (use.Get_temperature_ptr() == NULL)
{
error_string = sformatf( "TEMPERATURE %d not found.", i);
error_msg(error_string, STOP);
}
}
/*
* Find pressure
*/
if (use.Get_pressure_in() == TRUE)
{
use.Set_pressure_ptr(Utilities::Rxn_find(Rxn_pressure_map, i));
if (use.Get_pressure_ptr() == NULL)
{
error_string = sformatf( "PRESSURE %d not found.", i);
error_msg(error_string, STOP);
}
}
/*
* Find gas
*/
if (use.Get_gas_phase_in() == TRUE)
{
use.Set_gas_phase_ptr(Utilities::Rxn_find(Rxn_gas_phase_map, i));
if (use.Get_gas_phase_ptr() == NULL)
{
error_string = sformatf( "GAS_PHASE %d not found.", i);
error_msg(error_string, STOP);
}
}
/*
* Find ss_assemblage
*/
if (use.Get_ss_assemblage_in() == TRUE)
{
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, i));
if (use.Get_ss_assemblage_ptr() == NULL)
{
error_string = sformatf( "Solid-solution Assemblage %d not found.",
i);
error_msg(error_string, STOP);
}
}
/*
* Find kinetics
*/
if (use_kinetics == TRUE && use.Get_kinetics_in() == TRUE)
{
use.Set_kinetics_ptr(Utilities::Rxn_find(Rxn_kinetics_map, i));
if (use.Get_kinetics_ptr() == NULL)
{
error_string = sformatf( "KINETICS %d not found.", i);
error_msg(error_string, STOP);
}
}
else
{
use.Set_kinetics_ptr(NULL);
}
/*
if (use.irrev_ptr != NULL && use.Get_kinetics_ptr() != NULL)
{
warning_msg("Should not use REACTION in same simulation with KINETICS.");
}
*/
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
run_reactions(int i, LDBLE kin_time, int use_mix, LDBLE step_fraction)
/* ---------------------------------------------------------------------- */
{
/*
* Kinetics calculations
* Rates and moles of each reaction are calculated in calc_kinetic_reaction
* Total number of moles in reaction is stored in kinetics[i].totals
*/
//int increase_tol = 0; // appt
int converge, m_iter;
int pr_all_save;
int nsaver;
cxxKinetics *kinetics_ptr;
cxxPPassemblage *pp_assemblage_ptr;
cxxSSassemblage *ss_assemblage_ptr;
cxxUse use_save;
int save_old, n_reactions /*, nok, nbad */ ;
/* CVODE definitions */
realtype ropt[OPT_SIZE], reltol, t, tout, tout1, sum_t;
long int iopt[OPT_SIZE];
int flag;
/*
* Set nsaver
*/
run_reactions_iterations = 0;
overall_iterations = 0;
kin_time_x = kin_time;
rate_kin_time = kin_time;
nsaver = i;
if (state == TRANSPORT || state == PHAST)
{
if (use_mix == DISP)
{
nsaver = -2;
}
else if (use_mix == STAG)
{
nsaver = -2 - i;
}
}
if (state == ADVECTION)
{
nsaver = -2;
}
/*
* Check that reaction exists for this cell ..
*/
kinetics_ptr = Utilities::Rxn_find(Rxn_kinetics_map, i);
if (kin_time <= 0 ||
(kinetics_ptr && kinetics_ptr->Get_kinetics_comps().size() == 0) ||
(state == REACTION && use.Get_kinetics_in() == FALSE) ||
(state == TRANSPORT && kinetics_ptr == NULL) ||
(state == PHAST && kinetics_ptr == NULL) ||
(state == ADVECTION && kinetics_ptr == NULL))
{
converge =
set_and_run_wrapper(i, use_mix, FALSE, nsaver, step_fraction);
if (converge == MASS_BALANCE)
{
error_string = sformatf("Negative concentration in solution %d. Stopping calculation.", cell_no);
error_msg(error_string, STOP);
}
run_reactions_iterations += iterations;
}
else
{
/*
* Save moles of kinetic reactants for printout...
*/
size_t count_comps = kinetics_ptr->Get_kinetics_comps().size();
m_temp.resize(count_comps);
m_original.resize(count_comps);
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
m_original[j] = kinetics_comp_ptr->Get_m();
m_temp[j] = kinetics_comp_ptr->Get_m();
}
/*
* Start the loop for timestepping ...
* Use either Runge-Kutta-Fehlberg, or final result extrapolation
*/
pr_all_save = pr.all;
pr.all = FALSE;
/*
* This condition makes output equal for incremental_reactions TRUE/FALSE...
* (if (incremental_reactions == FALSE || reaction_step == 1)
*/
store_get_equi_reactants(i, FALSE);
if (!kinetics_ptr->Get_use_cvode())
{
/* in case dispersivity is not wanted..
if (multi_Dflag)
rk_kinetics(i, kin_time, NOMIX, nsaver, step_fraction);
else
*/
rk_kinetics(i, kin_time, use_mix, nsaver, step_fraction);
}
else
{
save_old = -2 - (count_cells * (1 + stag_data.count_stag) + 2);
if (nsaver != i)
{
Utilities::Rxn_copy(Rxn_solution_map, i, save_old);
}
for (int j = 0; j < OPT_SIZE; j++)
{
iopt[j] = 0;
ropt[j] = 0;
}
/*
* Do mix first
*/
kinetics_ptr = Utilities::Rxn_find(Rxn_kinetics_map, i);
n_reactions = (int) kinetics_ptr->Get_kinetics_comps().size();
cvode_n_user = i;
cvode_kinetics_ptr = (void *) kinetics_ptr;
cvode_n_reactions = n_reactions;
cvode_rate_sim_time_start = rate_sim_time_start;
cvode_rate_sim_time = rate_sim_time;
if (multi_Dflag)
converge = set_and_run_wrapper(i, NOMIX, FALSE, i, step_fraction);
else
converge = set_and_run_wrapper(i, use_mix, FALSE, i, step_fraction);
if (converge == MASS_BALANCE)
{
error_string = sformatf("Negative concentration in solution %d. Stopping calculation.", cell_no);
error_msg(error_string, STOP);
}
saver();
pp_assemblage_ptr = Utilities::Rxn_find(Rxn_pp_assemblage_map, i);
ss_assemblage_ptr = Utilities::Rxn_find(Rxn_ss_assemblage_map, i);
if (pp_assemblage_ptr != NULL)
{
cvode_pp_assemblage_save = new cxxPPassemblage(*pp_assemblage_ptr);
}
if (ss_assemblage_ptr != NULL)
{
cvode_ss_assemblage_save = new cxxSSassemblage(*ss_assemblage_ptr);
}
/* allocate space for CVODE */
kinetics_machEnv = M_EnvInit_Serial(n_reactions);
kinetics_machEnv->phreeqc_ptr = this;
kinetics_y = N_VNew(n_reactions, kinetics_machEnv); /* Allocate y, abstol vectors */
if (kinetics_y == NULL)
malloc_error();
cvode_last_good_y = N_VNew(n_reactions, kinetics_machEnv); /* Allocate y, abstol vectors */
if (cvode_last_good_y == NULL)
malloc_error();
cvode_prev_good_y = N_VNew(n_reactions, kinetics_machEnv); /* Allocate y, abstol vectors */
if (cvode_prev_good_y == NULL)
malloc_error();
kinetics_abstol = N_VNew(n_reactions, kinetics_machEnv);
if (kinetics_abstol == NULL)
malloc_error();
for (int j = 0; j < n_reactions; j++)
{
Ith(cvode_last_good_y, j + 1) = 0.0;
Ith(cvode_prev_good_y, j + 1) = 0.0;
Ith(kinetics_abstol, j + 1) = 0.0;
}
/*
* Set y to 0.0
*/
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_moles(0.0);
Ith(kinetics_y, j + 1) = 0.0;
Ith(kinetics_abstol, j + 1) = kinetics_comp_ptr->Get_tol();
/*Ith(abstol,j+1) = 1e-8; */
/* m_temp[j] = kinetics_ptr->comps[j].m; */
}
reltol = 0.0;
/* Call CVodeMalloc to initialize CVODE:
NEQ is the problem size = number of equations
f is the user's right hand side function in y'=f(t,y)
T0 is the initial time
y is the initial dependent variable vector
BDF specifies the Backward Differentiation Formula
NEWTON specifies a Newton iteration
SV specifies scalar relative and vector absolute tolerances
&reltol is a pointer to the scalar relative tolerance
abstol is the absolute tolerance vector
FALSE indicates there are no optional inputs in iopt and ropt
iopt is an array used to communicate optional integer input and output
ropt is an array used to communicate optional real input and output
A pointer to CVODE problem memory is returned and stored in cvode_mem. */
/* Don`t know what this does */
/*
iopt[SLDET] = TRUE;
cvode_mem = CVodeMalloc(n_reactions, f, 0.0, y, BDF, NEWTON, SV, &reltol, abstol, NULL, NULL, TRUE, iopt, ropt, machEnv);
cvode_mem = CVodeMalloc(n_reactions, f, 0.0, y, ADAMS, FUNCTIONAL, SV, &reltol, abstol, NULL, NULL, FALSE, iopt, ropt, machEnv);
iopt[MXSTEP] is maximum number of steps that CVODE tries.
*/
//iopt[SLDET] = TRUE; // appt
iopt[MXSTEP] = kinetics_ptr->Get_cvode_steps();
iopt[MAXORD] = kinetics_ptr->Get_cvode_order();
kinetics_cvode_mem =
CVodeMalloc(n_reactions, f, 0.0, kinetics_y, BDF, NEWTON, SV,
&reltol, kinetics_abstol, this, NULL, TRUE, iopt,
ropt, kinetics_machEnv);
if (kinetics_cvode_mem == NULL)
malloc_error();
/* Call CVDense to specify the CVODE dense linear solver with the
user-supplied Jacobian routine Jac. */
flag = CVDense(kinetics_cvode_mem, Jac, this);
if (flag != SUCCESS)
{
error_msg("CVDense failed.", STOP);
}
t = 0;
tout = kin_time;
/*ropt[HMAX] = tout/10.; */
/*ropt[HMIN] = 1e-17; */
use_save = use;
flag = CVode(kinetics_cvode_mem, tout, kinetics_y, &t, NORMAL);
rate_sim_time = rate_sim_time_start + t;
/*
printf("At t = %0.4e y =%14.6e %14.6e %14.6e\n",
t, Ith(y,1), Ith(y,2), Ith(y,3));
*/
m_iter = 0;
sum_t = 0;
RESTART:
while (flag != SUCCESS)
{
sum_t += cvode_last_good_time;
{
error_string = sformatf("CV_ODE: Time: %8.2e s. Delta t: %8.2e s. Calls: %d.", (double)(sum_t), (double) cvode_last_good_time, m_iter);
status(0, error_string, true);
}
//if (state != TRANSPORT)
//{
// error_string = sformatf(
// "CVode incomplete at cvode_steps %d. Cell: %d. Time: %8.2e s. Cvode calls: %d, continuing...\n",
// (int)iopt[NST], cell_no, (double)sum_t, m_iter + 1);
// warning_msg(error_string);
//}
#ifdef DEBUG_KINETICS
if (m_iter > 5)
dump_kinetics_stderr(cell_no);
#endif
//if (m_iter > 0.5 * kinetics_ptr->Get_bad_step_max() &&
// (cvode_last_good_time < 1e-6 || cvode_last_good_time < 1e-6 * tout)) // appt
//{
// if (increase_tol < 3)
// {
// increase_tol += 1;
// for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
// {
// cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
// LDBLE tr = kinetics_comp_ptr->Get_tol() * 10.0;
// kinetics_comp_ptr->Set_tol(tr);
// tr += 0;
// }
// }
//}
cvode_last_good_time = 0;
if (++m_iter >= kinetics_ptr->Get_bad_step_max())
{
m_temp.clear();
m_original.clear();
error_string = sformatf(
"CVode is at maximum calls: %d. Cell: %d. Time: %8.2e s\nERROR: Please increase the maximum calls with -bad_step_max.",
m_iter, cell_no, (double)sum_t);
error_msg(error_string, STOP);
}
tout1 = tout - sum_t;
t = 0;
N_VScale(1.0, cvode_last_good_y, kinetics_y);
for (int j = 0; j < OPT_SIZE; j++)
{
iopt[j] = 0;
ropt[j] = 0;
}
CVodeFree(kinetics_cvode_mem); /* Free the CVODE problem memory */
iopt[MXSTEP] = kinetics_ptr->Get_cvode_steps();
iopt[MAXORD] = kinetics_ptr->Get_cvode_order();
kinetics_cvode_mem =
CVodeMalloc(n_reactions, f, 0.0, kinetics_y, BDF, NEWTON,
SV, &reltol, kinetics_abstol, this, NULL,
TRUE, iopt, ropt, kinetics_machEnv);
if (kinetics_cvode_mem == NULL)
malloc_error();
/* Call CVDense to specify the CVODE dense linear solver with the
user-supplied Jacobian routine Jac. */
flag = CVDense(kinetics_cvode_mem, Jac, this);
if (flag != SUCCESS)
{
error_msg("CVDense failed.", STOP);
}
flag =
CVode(kinetics_cvode_mem, tout1, kinetics_y, &t, NORMAL);
/*
error_string = sformatf( "CVode failed, flag=%d.\n", flag);
error_msg(error_string, STOP);
*/
}
/*
odeint(&ystart[-1], n_reactions, 0, kin_time, kinetics_ptr->comps[0].tol, kin_time/kinetics_ptr->step_divide, 0.0, &nok, &nbad, i, nsaver );
*/
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_moles(Ith(kinetics_y, j + 1));
kinetics_comp_ptr->Set_m(m_original[j] - kinetics_comp_ptr->Get_moles());
if (kinetics_comp_ptr->Get_m() < 0)
{
kinetics_comp_ptr->Set_moles(m_original[j]);
kinetics_comp_ptr->Set_m(0.0);
}
}
if (use.Get_pp_assemblage_ptr() != NULL)
{
Rxn_pp_assemblage_map[cvode_pp_assemblage_save->Get_n_user()] = *cvode_pp_assemblage_save;
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, cvode_pp_assemblage_save->Get_n_user()));
}
if (use.Get_ss_assemblage_ptr() != NULL)
{
Rxn_ss_assemblage_map[cvode_ss_assemblage_save->Get_n_user()] = *cvode_ss_assemblage_save;
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, cvode_ss_assemblage_save->Get_n_user()));
}
calc_final_kinetic_reaction(kinetics_ptr);
if (set_and_run_wrapper(i, NOMIX, TRUE, nsaver, 0) ==
MASS_BALANCE)
{
/*error_msg("FAIL 2 after successful integration in CVode", CONTINUE); */
warning_msg("FAIL 2 after successful integration in CVode");
flag = -1;
goto RESTART;
}
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_m(m_original[j] - kinetics_comp_ptr->Get_moles());
}
/*
* Restore solution i, if necessary
*/
if (nsaver != i)
{
Utilities::Rxn_copy(Rxn_solution_map, save_old, i);
}
free_cvode();
use.Set_mix_in(use_save.Get_mix_in());
use.Set_mix_ptr(use_save.Get_mix_ptr());
error_string = sformatf("CV_ODE: Final Delta t: %8.2e s. Calls: %d. ", (double)cvode_last_good_time, m_iter);
status(0, error_string, true);
//status(0, NULL);
}
rate_sim_time = rate_sim_time_start + kin_time;
store_get_equi_reactants(i, TRUE);
pr.all = pr_all_save;
kinetics_ptr = Utilities::Rxn_find(Rxn_kinetics_map, i);
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_moles(m_original[j] - kinetics_comp_ptr->Get_m());
/* if (kinetics_ptr->comps[j].moles < 1.e-15) kinetics_ptr->comps[j].moles = 0.0;
*/ }
m_temp.clear();
m_original.clear();
}
iterations = run_reactions_iterations;
if (cvode_pp_assemblage_save != NULL)
{
delete cvode_pp_assemblage_save;
cvode_pp_assemblage_save = NULL;
}
if (cvode_ss_assemblage_save != NULL)
{
delete cvode_ss_assemblage_save;
cvode_ss_assemblage_save = NULL;
}
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
free_cvode(void)
/* ---------------------------------------------------------------------- */
{
if (kinetics_y != NULL)
N_VFree(kinetics_y); /* Free vector */
kinetics_y = NULL;
if (cvode_last_good_y != NULL)
N_VFree(cvode_last_good_y); /* Free vector */
cvode_last_good_y = NULL;
if (cvode_prev_good_y != NULL)
N_VFree(cvode_prev_good_y); /* Free vector */
cvode_prev_good_y = NULL;
if (kinetics_abstol != NULL)
N_VFree(kinetics_abstol); /* Free vector */
kinetics_abstol = NULL;
if (kinetics_cvode_mem != NULL)
CVodeFree(kinetics_cvode_mem); /* Free the CVODE problem memory */
kinetics_cvode_mem = NULL;
if (kinetics_machEnv != NULL)
M_EnvFree_Serial(kinetics_machEnv); /* Free the machine environment memory */
kinetics_machEnv = NULL;
if (cvode_pp_assemblage_save != NULL)
{
delete cvode_pp_assemblage_save;
cvode_pp_assemblage_save = NULL;
}
if (cvode_ss_assemblage_save != NULL)
{
delete cvode_ss_assemblage_save;
cvode_ss_assemblage_save = NULL;
}
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
set_advection(int i, int use_mix, int use_kinetics, int nsaver)
/* ---------------------------------------------------------------------- */
{
/*
* i --user number for soln, reaction, etc.
* use_mix --integer flag
state == TRANSPORT: DISP, STAG, NOMIX
state == REACTION: TRUE, FALSE
state == ADVECTION: TRUE, FALSE
* use_kinetics --true or false flag to calculate kinetic reactions
* nsaver --user number to store solution
*/
cell = i;
reaction_step = 1;
/*
* Find mixture or solution
*/
use.Set_mix_ptr(NULL);
use.Set_mix_in(false);
use.Set_mix_ptr(Utilities::Rxn_find(Rxn_mix_map, i));
if (use_mix == TRUE && use.Get_mix_ptr() != NULL)
{
use.Set_mix_in(true);
use.Set_n_mix_user(i);
use.Set_n_mix_user_orig(i);
use.Set_n_solution_user(i);
}
else
{
use.Set_solution_ptr(Utilities::Rxn_find(Rxn_solution_map, i));
if (use.Get_solution_ptr() == NULL)
{
error_string = sformatf( "Solution %d not found.",
use.Get_n_solution_user());
error_msg(error_string, STOP);
}
use.Set_n_solution_user(i);
use.Set_solution_in(true);
}
save.solution = TRUE;
save.n_solution_user = nsaver;
save.n_solution_user_end = nsaver;
/*
* Find pure phase assemblage
*/
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, i));
if (use.Get_pp_assemblage_ptr() != NULL)
{
use.Set_pp_assemblage_in(true);
use.Set_n_pp_assemblage_user(i);
save.pp_assemblage = TRUE;
save.n_pp_assemblage_user = i;
save.n_pp_assemblage_user_end = i;
}
else
{
use.Set_pp_assemblage_in(false);
save.pp_assemblage = FALSE;
}
/*
* Find irreversible reaction
*/
use.Set_reaction_ptr(Utilities::Rxn_find(Rxn_reaction_map, i));
if (use.Get_reaction_ptr() != NULL)
{
use.Set_reaction_in(true);
use.Set_n_reaction_user(i);
}
else
{
use.Set_reaction_in(false);
}
/*
* Find exchange
*/
use.Set_exchange_ptr(Utilities::Rxn_find(Rxn_exchange_map, i));
if (use.Get_exchange_ptr() != NULL)
{
use.Set_exchange_in(true);
use.Set_n_exchange_user(i);
save.exchange = TRUE;
save.n_exchange_user = i;
save.n_exchange_user_end = i;
}
else
{
use.Set_exchange_in(false);
save.exchange = FALSE;
}
/*
* Find surface
*/
use.Set_surface_ptr(Utilities::Rxn_find(Rxn_surface_map, i));
if (use.Get_surface_ptr() != NULL)
{
use.Set_surface_in(true);
use.Set_n_surface_user(i);
save.surface = TRUE;
save.n_surface_user = i;
save.n_surface_user_end = i;
}
else
{
use.Set_surface_in(false);
save.surface = FALSE;
dl_type_x = cxxSurface::NO_DL;
}
/*
* Find temperature; temp retardation is done in step
*/
use.Set_temperature_ptr(Utilities::Rxn_find(Rxn_temperature_map, i));
if (use.Get_temperature_ptr() != NULL)
{
use.Set_temperature_in(true);
use.Set_n_temperature_user(i);
}
else
{
use.Set_temperature_in(false);
}
/*
* Find pressure
*/
use.Set_pressure_ptr(Utilities::Rxn_find(Rxn_pressure_map, i));
if (use.Get_pressure_ptr() != NULL)
{
use.Set_pressure_in(true);
use.Set_n_pressure_user(i);
}
else
{
use.Set_pressure_in(false);
}
/*
* Find gas
*/
use.Set_gas_phase_ptr(Utilities::Rxn_find(Rxn_gas_phase_map, i));
if (use.Get_gas_phase_ptr() != NULL)
{
use.Set_gas_phase_in(true);
use.Set_n_gas_phase_user(i);
save.gas_phase = TRUE;
save.n_gas_phase_user = i;
save.n_gas_phase_user_end = i;
}
else
{
use.Set_gas_phase_in(false);
save.gas_phase = FALSE;
}
/*
* Find ss_assemblage
*/
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, i));
if (use.Get_ss_assemblage_ptr() != NULL)
{
use.Set_ss_assemblage_in(true);
use.Set_n_ss_assemblage_user(i);
save.ss_assemblage = TRUE;
save.n_ss_assemblage_user = i;
save.n_ss_assemblage_user_end = i;
}
else
{
use.Set_ss_assemblage_in(false);
save.ss_assemblage = FALSE;
}
/*
* Find kinetics
*/
use.Set_kinetics_ptr(NULL);
use.Set_kinetics_in(false);
save.kinetics = FALSE;
if (use_kinetics == TRUE)
{
use.Set_kinetics_ptr(Utilities::Rxn_find(Rxn_kinetics_map, i));
if (use.Get_kinetics_ptr() != NULL)
{
use.Set_n_kinetics_user(i);
use.Set_kinetics_in(true);
save.kinetics = TRUE;
save.n_kinetics_user = i;
save.n_kinetics_user_end = i;
}
}
/*
if (use.irrev_ptr != NULL && use.Get_kinetics_ptr() != NULL)
{
warning_msg("Should not use REACTION in same simulation with KINETICS.");
}
*/
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
store_get_equi_reactants(int l, int kin_end)
/* ---------------------------------------------------------------------- */
{
int i, k;
if (use.Get_pp_assemblage_in() == TRUE)
{
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, l));
}
else
use.Set_pp_assemblage_ptr(NULL);
cxxPPassemblage * pp_assemblage_ptr = use.Get_pp_assemblage_ptr();
if (use.Get_gas_phase_in() == TRUE)
{
use.Set_gas_phase_ptr(Utilities::Rxn_find(Rxn_gas_phase_map, l));
}
else
use.Set_gas_phase_ptr(NULL);
if (use.Get_ss_assemblage_in() == TRUE)
{
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, l));
}
else
use.Set_ss_assemblage_ptr(NULL);
if (kin_end == FALSE)
{
count_pp = count_ss = count_pg = 0;
if (use.Get_pp_assemblage_ptr() != NULL)
count_pp = (int) pp_assemblage_ptr->Get_pp_assemblage_comps().size();
if (use.Get_gas_phase_ptr() != NULL)
{
cxxGasPhase *gas_phase_ptr = use.Get_gas_phase_ptr();
count_pg = (int) gas_phase_ptr->Get_gas_comps().size();
}
if (use.Get_ss_assemblage_ptr() != NULL)
{
std::vector<cxxSS *> ss_ptrs = use.Get_ss_assemblage_ptr()->Vectorize();
for (size_t i = 0; i < ss_ptrs.size(); i++)
{
cxxSS *ss_ptr = ss_ptrs[i];
count_ss += (int) ss_ptr->Get_ss_comps().size();
}
}
k = count_pp + count_ss + count_pg;
if (k == 0)
return (OK);
x0_moles.resize(k);
for (i = 0; i < k; i++) x0_moles[i] = 0.0;
k = -1;
if (pp_assemblage_ptr)
{
std::map<std::string, cxxPPassemblageComp>::iterator it;
it = pp_assemblage_ptr->Get_pp_assemblage_comps().begin();
for ( ; it != pp_assemblage_ptr->Get_pp_assemblage_comps().end(); it++)
{
x0_moles[++k] = it->second.Get_moles();
}
}
{
cxxGasPhase *gas_phase_ptr = use.Get_gas_phase_ptr();
if (gas_phase_ptr)
{
for (size_t l = 0; l < gas_phase_ptr->Get_gas_comps().size(); l++)
{
x0_moles[++k] += gas_phase_ptr->Get_gas_comps()[l].Get_moles();
}
}
}
if (count_ss != 0)
{
std::vector<cxxSS *> ss_ptrs = use.Get_ss_assemblage_ptr()->Vectorize();
for (size_t i = 0; i < ss_ptrs.size(); i++)
{
cxxSS *ss_ptr = ss_ptrs[i];
for (size_t j = 0; j < ss_ptr->Get_ss_comps().size(); j++)
{
cxxSScomp *comp_ptr = &(ss_ptr->Get_ss_comps()[j]);
x0_moles[++k] = comp_ptr->Get_moles();
}
/*!!!! also miscibility gap comps ??
*/
}
}
}
else
{
k = -1;
if (pp_assemblage_ptr && count_pp > 0)
{
std::map<std::string, cxxPPassemblageComp>::iterator it;
it = pp_assemblage_ptr->Get_pp_assemblage_comps().begin();
for ( ; it != pp_assemblage_ptr->Get_pp_assemblage_comps().end(); it++)
{
it->second.Set_moles(x0_moles[++k]);
it->second.Set_delta(0.0);
}
}
{
cxxGasPhase *gas_phase_ptr = use.Get_gas_phase_ptr();
if (gas_phase_ptr && count_pg)
{
std::vector<cxxGasComp> temp_comps(gas_phase_ptr->Get_gas_comps());
for (size_t l = 0; l < temp_comps.size(); l++)
{
temp_comps[l].Set_moles(x0_moles[++k]);
}
gas_phase_ptr->Set_gas_comps(temp_comps);
}
}
if (count_ss != 0)
{
std::vector<cxxSS *> ss_ptrs = use.Get_ss_assemblage_ptr()->Vectorize();
for (size_t i = 0; i < ss_ptrs.size(); i++)
{
cxxSS *ss_ptr = ss_ptrs[i];
for (size_t j = 0; j < ss_ptr->Get_ss_comps().size(); j++)
{
cxxSScomp *comp_ptr = &(ss_ptr->Get_ss_comps()[j]);
comp_ptr->Set_initial_moles(x0_moles[++k]);
}
/*!!!! also miscibility gap comps ??
*/
}
}
/*
* This condition makes output equal for incremental_reactions TRUE/FALSE...
* if (incremental_reactions == FALSE || reaction_step == count_total_steps)
*/
x0_moles.clear();
}
return (OK);
}
void Phreeqc::
f(integertype N, realtype t, N_Vector y, N_Vector ydot,
void *f_data)
{
int n_user;
//LDBLE step_fraction;
cxxKinetics *kinetics_ptr;
Phreeqc *pThis = (Phreeqc *) f_data;
pThis->cvode_error = FALSE;
n_user = pThis->cvode_n_user;
kinetics_ptr = (cxxKinetics *) pThis->cvode_kinetics_ptr;
//step_fraction = pThis->cvode_step_fraction;
pThis->rate_sim_time = pThis->cvode_rate_sim_time;
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
/*
kinetics_ptr->comps[i].moles = y[i + 1];
kinetics_ptr->comps[i].m = m_original[i] - y[i + 1];
*/
kinetics_comp_ptr->Set_moles(Ith(y, i + 1));
kinetics_comp_ptr->Set_m(pThis->m_original[i] - Ith(y, i + 1));
if (kinetics_comp_ptr->Get_m() < 0)
{
/*
NOTE: y is not correct if it is greater than m_original
However, it seems to work to let y wander off, but use
.moles as the correct integral.
It does not work to reset Y to m_original, presumably
because the rational extrapolation gets screwed up.
*/
/*
Ith(y,i + 1) = m_original[i];
*/
//if (kinetics_ptr->Get_use_cvode())
//{
// pThis->cvode_error = TRUE;
// return;
//}
kinetics_comp_ptr->Set_moles(pThis->m_original[i]);
kinetics_comp_ptr->Set_m(0.0);
}
}
pThis->calc_final_kinetic_reaction(kinetics_ptr);
/* if (set_and_run(n_user, FALSE, TRUE, n_user, step_fraction) == MASS_BALANCE) { */
if (pThis->use.Get_pp_assemblage_ptr() != NULL)
{
pThis->Rxn_pp_assemblage_map[pThis->cvode_pp_assemblage_save->Get_n_user()] = *pThis->cvode_pp_assemblage_save;
pThis->use.Set_pp_assemblage_ptr(Utilities::Rxn_find(pThis->Rxn_pp_assemblage_map, pThis->cvode_pp_assemblage_save->Get_n_user()));
}
if (pThis->use.Get_ss_assemblage_ptr() != NULL)
{
pThis->Rxn_ss_assemblage_map[pThis->cvode_ss_assemblage_save->Get_n_user()] = *pThis->cvode_ss_assemblage_save;
pThis->use.Set_ss_assemblage_ptr(Utilities::Rxn_find(pThis->Rxn_ss_assemblage_map, pThis->cvode_ss_assemblage_save->Get_n_user()));
}
if (pThis->set_and_run_wrapper(n_user, FALSE, TRUE, n_user, 0.0) == MASS_BALANCE)
{
pThis->run_reactions_iterations += pThis->iterations;
pThis->cvode_error = TRUE;
/*
error_msg("Mass balance error in f", CONTINUE);
*/
return;
}
if (pThis->cvode_test == TRUE)
{
return;
}
pThis->run_reactions_iterations += pThis->iterations;
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
kinetics_comp_ptr->Set_moles(0.0);
}
pThis->calc_kinetic_reaction(kinetics_ptr, 1.0);
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
/*
dydx[i + 1] = kinetics_ptr->comps[i].moles;
*/
Ith(ydot, i + 1) = kinetics_comp_ptr->Get_moles();
}
return;
}
/*
static void Jac(integertype N, DenseMat J, RhsFn f, void *f_data, realtype t,
N_Vector y, N_Vector fy, N_Vector ewt, realtype h,
realtype uround, void *jac_data, long int *nfePtr,
N_Vector vtemp1, N_Vector vtemp2, N_Vector vtemp3);
*/
void Phreeqc::
Jac(integertype N, DenseMat J, RhsFn f, void *f_data,
realtype t, N_Vector y, N_Vector fy, N_Vector ewt,
realtype h, realtype uround, void *jac_data,
long int *nfePtr, N_Vector vtemp1, N_Vector vtemp2,
N_Vector vtemp3)
{
int count_cvode_errors;
int n_reactions, n_user;
LDBLE del;
std::vector<double> initial_rates;
cxxKinetics *kinetics_ptr;
LDBLE step_fraction;
Phreeqc *pThis = (Phreeqc *) f_data;
pThis->cvode_error = FALSE;
n_reactions = pThis->cvode_n_reactions;
n_user = pThis->cvode_n_user;
kinetics_ptr = (cxxKinetics *) pThis->cvode_kinetics_ptr;
step_fraction = pThis->cvode_step_fraction;
pThis->rate_sim_time = pThis->cvode_rate_sim_time;
initial_rates.resize(n_reactions);
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
/*
kinetics_ptr->comps[i].moles = y[i + 1];
kinetics_ptr->comps[i].m = m_original[i] - y[i + 1];
*/
kinetics_comp_ptr->Set_moles(Ith(y, i + 1));
kinetics_comp_ptr->Set_m(pThis->m_original[i] - Ith(y, i + 1));
if (kinetics_comp_ptr->Get_m() < 0)
{
/*
NOTE: y is not correct if it is greater than m_original
However, it seems to work to let y wander off, but use
.moles as the correct integral.
It does not work to reset Y to m_original, presumably
because the rational extrapolation gets screwed up.
*/
/*
Ith(y,i + 1) = m_original[i];
*/
kinetics_comp_ptr->Set_moles(pThis->m_original[i]);
kinetics_comp_ptr->Set_m(0.0);
}
}
pThis->calc_final_kinetic_reaction(kinetics_ptr);
/* if (set_and_run(n_user, FALSE, TRUE, n_user, step_fraction) == MASS_BALANCE) { */
if (pThis->use.Get_pp_assemblage_ptr() != NULL)
{
pThis->Rxn_pp_assemblage_map[pThis->cvode_pp_assemblage_save->Get_n_user()] = *pThis->cvode_pp_assemblage_save;
pThis->use.Set_pp_assemblage_ptr(Utilities::Rxn_find(pThis->Rxn_pp_assemblage_map, pThis->cvode_pp_assemblage_save->Get_n_user()));
}
if (pThis->set_and_run_wrapper(n_user, FALSE, TRUE, n_user, 0.0) == MASS_BALANCE)
{
pThis->run_reactions_iterations += pThis->iterations;
pThis->cvode_error = TRUE;
/*
error_msg("Mass balance error in jacobian", CONTINUE);
*/
initial_rates.clear();
return;
}
pThis->run_reactions_iterations += pThis->iterations;
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
kinetics_comp_ptr->Set_moles(0.0);
}
pThis->calc_kinetic_reaction(kinetics_ptr, 1.0);
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
initial_rates[i] = kinetics_comp_ptr->Get_moles();
}
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
cxxKineticsComp * kinetics_comp_i_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
/* calculate reaction up to current time */
del = 1e-12;
pThis->cvode_error = TRUE;
count_cvode_errors = 0;
while (pThis->cvode_error == TRUE)
{
del /= 10.;
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_j_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
/*
kinetics_ptr->comps[j].moles = y[j + 1];
kinetics_ptr->comps[j].m = m_original[j] - y[j + 1];
*/
kinetics_comp_j_ptr->Set_moles(Ith(y, j + 1));
kinetics_comp_j_ptr->Set_m(pThis->m_original[j] - Ith(y, j + 1));
if (kinetics_comp_i_ptr->Get_m() < 0)
{
/*
NOTE: y is not correct if it is greater than m_original
However, it seems to work to let y wander off, but use
.moles as the correct integral.
It does not work to reset Y to m_original, presumably
because the rational extrapolation gets screwed up.
*/
/*
Ith(y,i + 1) = m_original[i];
*/
kinetics_comp_i_ptr->Set_moles(pThis->m_original[i]);
kinetics_comp_i_ptr->Set_m(0.0);
}
}
/* Add small amount of ith reaction */
kinetics_comp_i_ptr->Set_m(kinetics_comp_i_ptr->Get_m() - del);
if (kinetics_comp_i_ptr->Get_m() < 0)
{
kinetics_comp_i_ptr->Set_m(0);
}
kinetics_comp_i_ptr->Set_moles(kinetics_comp_i_ptr->Get_moles() + del);
pThis->calc_final_kinetic_reaction(kinetics_ptr);
if (pThis->use.Get_pp_assemblage_ptr() != NULL)
{
pThis->Rxn_pp_assemblage_map[pThis->cvode_pp_assemblage_save->Get_n_user()] = *pThis->cvode_pp_assemblage_save;
pThis->use.Set_pp_assemblage_ptr(Utilities::Rxn_find(pThis->Rxn_pp_assemblage_map, pThis->cvode_pp_assemblage_save->Get_n_user()));
}
if (pThis->set_and_run_wrapper
(n_user, FALSE, TRUE, n_user, step_fraction) == MASS_BALANCE)
{
count_cvode_errors++;
pThis->cvode_error = TRUE;
if (count_cvode_errors > 30)
{
initial_rates.clear();
return;
}
pThis->run_reactions_iterations += pThis->iterations;
continue;
}
pThis->cvode_error = FALSE;
pThis->run_reactions_iterations += pThis->iterations;
/*kinetics_ptr->comps[i].moles -= del; */
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
kinetics_comp_ptr->Set_moles(0.0);
}
pThis->calc_kinetic_reaction(kinetics_ptr, 1.0);
/* calculate new rates for df/dy[i] */
/* dfdx[i + 1] = 0.0; */
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
IJth(J, j + 1, i + 1) =
(kinetics_comp_ptr->Get_moles() - initial_rates[j]) / del;
}
}
}
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
kinetics_comp_ptr->Set_moles(0);
}
initial_rates.clear();
return;
}
void Phreeqc::
cvode_init(void)
{
cvode_kinetics_ptr = NULL;
cvode_test = 0;
cvode_error = 0;
cvode_n_user = -99;
cvode_n_reactions = -99;
cvode_step_fraction = 0.0;
cvode_rate_sim_time = 0.0;
cvode_rate_sim_time_start = 0.0;
cvode_last_good_time = 0.0;
cvode_prev_good_time = 0.0;
cvode_last_good_y = NULL;
cvode_prev_good_y = NULL;
kinetics_machEnv = NULL;
kinetics_y = kinetics_abstol = NULL;
kinetics_cvode_mem = NULL;
cvode_pp_assemblage_save = NULL;
cvode_ss_assemblage_save = NULL;
return;
}
bool Phreeqc::
cvode_update_reactants(int i, int nsaver, bool save_it)
{
cxxKinetics *kinetics_ptr = use.Get_kinetics_ptr();
int n_reactions = (int) kinetics_ptr->Get_kinetics_comps().size();
for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
// Adds reaction defined by last_good_y
kinetics_comp_ptr->Set_moles(Ith(cvode_last_good_y, j + 1));
// Reduces m
kinetics_comp_ptr->Set_m(m_original[j] - kinetics_comp_ptr->Get_moles());
// Don't update until after calc_final_reaction
//m_original[j] = kinetics_comp_ptr->Get_m();
//m_temp[j] = kinetics_comp_ptr->Get_m();
if (kinetics_comp_ptr->Get_m() < 0)
{
kinetics_comp_ptr->Set_moles(m_original[j]);
kinetics_comp_ptr->Set_m(0.0);
}
}
// calculates net reaction
calc_final_kinetic_reaction(kinetics_ptr);
if (use.Get_pp_assemblage_ptr() != NULL)
{
Rxn_pp_assemblage_map[cvode_pp_assemblage_save->Get_n_user()] = *cvode_pp_assemblage_save;
use.Set_pp_assemblage_ptr(Utilities::Rxn_find(Rxn_pp_assemblage_map, cvode_pp_assemblage_save->Get_n_user()));
}
if (use.Get_ss_assemblage_ptr() != NULL)
{
Rxn_ss_assemblage_map[cvode_ss_assemblage_save->Get_n_user()] = *cvode_ss_assemblage_save;
use.Set_ss_assemblage_ptr(Utilities::Rxn_find(Rxn_ss_assemblage_map, cvode_ss_assemblage_save->Get_n_user()));
}
// runs previous solution plus net reaction
if (set_and_run_wrapper(i, NOMIX, TRUE, nsaver, 1.0) == MASS_BALANCE)
{
error_msg("CVODE step was bad", STOP);
return false;
}
// saves result to reactants defined by saver
if (save_it)
{
saver();
cxxPPassemblage *pp_assemblage_ptr = Utilities::Rxn_find(Rxn_pp_assemblage_map, nsaver);
cxxSSassemblage *ss_assemblage_ptr = Utilities::Rxn_find(Rxn_ss_assemblage_map, nsaver);
if (cvode_pp_assemblage_save != NULL)
{
delete cvode_pp_assemblage_save;
cvode_pp_assemblage_save = new cxxPPassemblage(*pp_assemblage_ptr);
}
if (cvode_ss_assemblage_save != NULL)
{
delete cvode_ss_assemblage_save;
cvode_ss_assemblage_save = new cxxSSassemblage(*ss_assemblage_ptr);
}
for (int j = 0; j < n_reactions; j++)
{
Ith(cvode_last_good_y, j + 1) = 0.0;
Ith(cvode_prev_good_y, j + 1) = 0.0;
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[j]);
m_original[j] = kinetics_comp_ptr->Get_m();
m_temp[j] = kinetics_comp_ptr->Get_m();
}
}
return true;
}
/* ---------------------------------------------------------------------- */
bool Phreeqc::
limit_rates(cxxKinetics *kinetics_ptr)
/* ---------------------------------------------------------------------- */
{
/*
* Go through kinetic components to
* determine rates and
* a list of elements and amounts in
* the reaction.
*/
// check if any small concentrations with negative rates
if (!use_kinetics_limiter)
{
return false;
}
std::vector<std::string> negative_rate;
cxxNameDouble::iterator it = kinetics_ptr->Get_totals().begin();
for ( ; it != kinetics_ptr->Get_totals().end(); it++)
{
if (total(it->first.c_str()) < 1e-10 && it->second < -1e-20)
{
//if (total(it->first.c_str()) > fabs(it->second))
// continue;
negative_rate.push_back(it->first);
}
}
if (negative_rate.size() == 0) return false;
for (size_t j = 0; j < negative_rate.size(); j++)
{
std::string elt = negative_rate[j];
LDBLE positive_rates = 0;
LDBLE negative_rates = 0;
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
cxxNameDouble::iterator it = kinetics_comp_ptr->Get_moles_of_reaction().find(elt);
if (it != kinetics_comp_ptr->Get_moles_of_reaction().end())
{
if (it->second >= 0.0)
{
positive_rates += it->second;
}
else
{
negative_rates += it->second;
}
}
}
// factor to reduce precipitation to equal dissolution
LDBLE limiter_fraction = 1.0;
if (negative_rates < 0.0)
{
limiter_fraction = fabs(positive_rates / negative_rates);
//limiter_fraction = fabs((0.9*total(elt.c_str()) + positive_rates) / negative_rates);
}
else
{
assert(false);
}
// Now limit precipitation
for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
{
cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
cxxNameDouble::iterator it = kinetics_comp_ptr->Get_moles_of_reaction().find(elt);
if (it != kinetics_comp_ptr->Get_moles_of_reaction().end())
{
if (it->second < 0.0)
{
kinetics_comp_ptr->Set_moles(kinetics_comp_ptr->Get_moles() * limiter_fraction);
}
}
}
}
return true;
}
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