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iphreeqc/phreeqcpp/sit.cpp
Darth Vader 622bc5fb4c Squashed 'src/' changes from ac393756..d6a74675 
d6a74675 Merge commit '4e80a54467a084df3b666c7d6fc56a4798fd3301'
4e80a544 Squashed 'phreeqcpp/' changes from 7c7fafd..c876219
0209fdf9 Merge commit 'b537589773f4819fe97ff8e5322bcd38c54b63f7'
b5375897 Squashed 'phreeqcpp/' changes from e317dd0..7c7fafd

git-subtree-dir: src
git-subtree-split: d6a74675d73985977ceac1601b57463c1ee8c331
2024-10-08 20:05:43 +00:00

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#include "Phreeqc.h"
#include "phqalloc.h"
#include "Exchange.h"
#include "Solution.h"
#if defined(PHREEQCI_GUI)
#ifdef _DEBUG
#define new DEBUG_NEW
#undef THIS_FILE
static char THIS_FILE[] = __FILE__;
#endif
#endif
/* ---------------------------------------------------------------------- */
int Phreeqc::
sit_init(void)
/* ---------------------------------------------------------------------- */
{
/*
* Initialization for SIT
*/
sit_model = FALSE;
sit_params.clear();
OTEMP = -100.;
OPRESS = -100.;
return OK;
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
sit_tidy(void)
/* ---------------------------------------------------------------------- */
{
/*
* Make lists of species for cations, anions, neutral
*/
int i, j;
/*
* Ensure new parameters are calculated
*/
OTEMP = -100.;
OPRESS = -100.;
/*
* allocate pointers to species structures
*/
spec.clear();
spec.resize(3 * s.size(), NULL);
cations = &spec[0];
neutrals = &(spec[s.size()]);
anions = &(spec[2 * s.size()]);
sit_MAXCATIONS = (int)s.size();
sit_FIRSTANION = 2 * (int)s.size();
sit_MAXNEUTRAL = (int)s.size();
sit_count_cations = 0;
sit_count_anions = 0;
sit_count_neutrals = 0;
if (itmax < 200) itmax = 200;
/*
* allocate other arrays for SIT
*/
sit_IPRSNT.resize(3 * s.size());
sit_M.resize(3 * s.size());
sit_LGAMMA.resize(3 * s.size());
for (i = 0; i < (int)s.size(); i++)
{
if (s[i] == s_eminus)
continue;
if (s[i] == s_h2o)
continue;
if (s[i]->type == EX || s[i]->type == SURF)
continue;
if (s[i]->z < -.001)
{
anions[sit_count_anions++] = s[i];
}
else if (s[i]->z > .001)
{
cations[sit_count_cations++] = s[i];
}
else
{
neutrals[sit_count_neutrals++] = s[i];
}
}
/*
* no ethetas
*/
/*
* put species numbers in sit_params
*/
for (i = 0; i < (int)sit_params.size(); i++)
{
for (j = 0; j < 3; j++)
{
if (sit_params[i]->species[j] == NULL)
continue;
sit_params[i]->ispec[j] = sit_ISPEC(sit_params[i]->species[j]);
if ((j < 2 && sit_params[i]->ispec[j] == -1) ||
(j == 3
&& (sit_params[i]->type == TYPE_PSI
|| sit_params[i]->type == TYPE_ZETA)
&& sit_params[i]->ispec[j] == -1))
{
input_error++;
error_string = sformatf(
"Species for Pitzer parameter not defined in SOLUTION_SPECIES, %s",
sit_params[i]->species[j]);
error_msg(error_string, CONTINUE);
}
}
} /* remake map */
{
sit_param_map.clear();
for (int j = 0; j < (int)sit_params.size(); j++)
{
std::set< std::string > header;
for (int i = 0; i < 3; i++)
{
if (sit_params[j]->species[i] != NULL) header.insert(sit_params[j]->species[i]);
}
std::ostringstream key_str;
key_str << sit_params[j]->type << " ";
std::set< std::string >::iterator it = header.begin();
for(; it != header.end(); ++it)
{
key_str << *it << " ";
}
std::string key = key_str.str().c_str();
sit_param_map[key] = j;
}
assert ((int) sit_param_map.size() == (int)sit_params.size());
}
if (get_input_errors() > 0) return (ERROR);
return OK;
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
sit_ISPEC(const char *name)
/* ---------------------------------------------------------------------- */
/*
* Find species number in spec for character string species name
*/
{
int i;
for (i = 0; i < 3 * (int)s.size(); i++)
{
if (spec[i] == NULL)
continue;
if (name == spec[i]->name)
{
return (i);
}
}
return (-1);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
read_sit(void)
/* ---------------------------------------------------------------------- */
{
/*
* Reads advection information
*
* Arguments:
* none
*
* Returns:
* KEYWORD if keyword encountered, input_error may be incremented if
* a keyword is encountered in an unexpected position
* EOF if eof encountered while reading mass balance concentrations
* ERROR if error occurred reading data
*
*/
/*
* Read advection parameters:
* number of cells;
* number of shifts;
*/
int n;
class pitz_param *pzp_ptr;
pitz_param_type pzp_type;
int return_value, opt, opt_save;
const char* next_char;
const char *opt_list[] = {
"epsilon", /* 0 */
"epsilon1" /* 1 */
};
int count_opt_list = 2;
/*
* Read lines
*/
opt_save = OPTION_ERROR;
return_value = UNKNOWN;
n = -1;
pzp_type = TYPE_Other;
pitzer_pe = TRUE;
for (;;)
{
opt = get_option(opt_list, count_opt_list, &next_char);
if (opt == OPTION_DEFAULT)
{
opt = opt_save;
}
switch (opt)
{
case OPTION_EOF: /* end of file */
return_value = EOF;
break;
case OPTION_KEYWORD: /* keyword */
return_value = KEYWORD;
break;
case OPTION_DEFAULT:
pzp_ptr = pitz_param_read(line, n);
if (pzp_ptr != NULL)
{
pzp_ptr->type = pzp_type;
sit_param_store(pzp_ptr);
}
break;
case OPTION_ERROR:
input_error++;
error_msg("Unknown input in SIT keyword.", CONTINUE);
error_msg(line_save, CONTINUE);
break;
case 0: /* epsilon */
pzp_type = TYPE_SIT_EPSILON;
n = 2;
opt_save = OPTION_DEFAULT;
break;
case 1: /* epsilon1 */
pzp_type = TYPE_SIT_EPSILON_MU;
n = 2;
opt_save = OPTION_DEFAULT;
break;
}
if (return_value == EOF || return_value == KEYWORD)
break;
}
sit_model = TRUE;
return (return_value);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
calc_sit_param(class pitz_param *pz_ptr, LDBLE TK, LDBLE TR)
/* ---------------------------------------------------------------------- */
{
LDBLE param;
/*
*/
if (fabs(TK - TR) < 0.01)
{
param = pz_ptr->a[0];
}
else
{
param = (pz_ptr->a[0] +
pz_ptr->a[1] * (1.e0 / TK - 1.e0 / TR) +
pz_ptr->a[2] * log(TK / TR) +
pz_ptr->a[3] * (TK - TR) +
pz_ptr->a[4] * (TK * TK - TR * TR));
}
pz_ptr->p = param;
switch (pz_ptr->type)
{
case TYPE_SIT_EPSILON:
pz_ptr->U.eps = param;
break;
case TYPE_SIT_EPSILON_MU:
pz_ptr->U.eps1 = param;
break;
case TYPE_Other:
default:
error_msg("Should not be TYPE_Other in function calc_sit_param",
STOP);
break;
}
return OK;
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
sit(void)
/* ---------------------------------------------------------------------- */
{
int i, i0, i1;
LDBLE param, z0, z1;
LDBLE A, AGAMMA, T;
/*
LDBLE CONV, XI, XX, OSUM, BIGZ, DI, F, XXX, GAMCLM,
CSUM, PHIMAC, OSMOT, BMXP, ETHEAP, CMX, BMX, PHI,
BMXPHI, PHIPHI, AW, A, B;
*/
/*
LDBLE CONV, XI, XX, OSUM, BIGZ, DI, F, XXX, GAMCLM, CSUM, PHIMAC, OSMOT,
B;
*/
LDBLE XI, XX, OSUM, DI, F, OSMOT, B;
LDBLE I, TK;
/*
C
C INITIALIZE
C
*/
//CONV = 1.0 / LOG_10;
XI = 0.0e0;
XX = 0.0e0;
OSUM = 0.0e0;
/*n
I = *I_X;
TK = *TK_X;
*/
I = mu_x;
TK = tk_x;
/* DH_AB(TK, &A, &B); */
/*
C
C TRANSFER DATA FROM TO sit_M
C
*/
double log_min = log10(MIN_TOTAL);
for (size_t j = 0; j < s_list.size(); j++)
{
i = s_list[j];
if (spec[i]->lm > log_min)
{
sit_M[i] = under(spec[i]->lm);
}
else
{
sit_M[i] = 0.0;
}
}
//for (i = 0; i < 3 * (int)s.size(); i++)
//{
// sit_IPRSNT[i] = FALSE;
// sit_M[i] = 0.0;
// if (spec[i] != NULL && spec[i]->in == TRUE)
// {
// if (spec[i]->type == EX ||
// spec[i]->type == SURF || spec[i]->type == SURF_PSI)
// continue;
// sit_M[i] = under(spec[i]->lm);
// if (sit_M[i] > MIN_TOTAL)
// sit_IPRSNT[i] = TRUE;
// }
//}
/*
C
C COMPUTE SIT COEFFICIENTS' TEMPERATURE DEPENDENCE
C
*/
PTEMP_SIT(TK);
for (size_t j = 0; j < s_list.size(); j++)
{
int i = s_list[j];
sit_LGAMMA[i] = 0.0;
XX = XX + sit_M[i] * fabs(spec[i]->z);
XI = XI + sit_M[i] * spec[i]->z * spec[i]->z;
OSUM = OSUM + sit_M[i];
}
//for (i = 0; i < 2 * (int)s.size() + sit_count_anions; i++)
//{
// sit_LGAMMA[i] = 0.0;
// if (sit_IPRSNT[i] == TRUE)
// {
// XX = XX + sit_M[i] * fabs(spec[i]->z);
// XI = XI + sit_M[i] * spec[i]->z * spec[i]->z;
// OSUM = OSUM + sit_M[i];
// }
//}
I = XI / 2.0e0;
I = mu_x; // Added equation for MU
DI = sqrt(I);
/*
C
C CALCULATE F & GAMCLM
C
*/
AGAMMA = 3*sit_A0; /* Grenthe p 379 */
A = AGAMMA / LOG_10;
/*
* F is now for log10 gamma
*/
B = 1.5;
F = -A * (DI / (1.0e0 + B * DI));
/*OSMOT = -(sit_A0) * pow(I, 1.5e0) / (1.0e0 + B * DI);*/
T = 1.0 + B*DI;
OSMOT = -2.0*A/(B*B*B)*(T - 2.0*log(T) - 1.0/T);
/*
* Sums for sit_LGAMMA, and OSMOT
* epsilons are tabulated for log10 gamma (not ln gamma)
*/
for (size_t j = 0; j < param_list.size(); j++)
{
int i = param_list[j];
i0 = sit_params[i]->ispec[0];
i1 = sit_params[i]->ispec[1];
//if (sit_IPRSNT[i0] == FALSE || sit_IPRSNT[i1] == FALSE) continue;
z0 = spec[i0]->z;
z1 = spec[i1]->z;
param = sit_params[i]->p;
switch (sit_params[i]->type)
{
case TYPE_SIT_EPSILON:
sit_LGAMMA[i0] += sit_M[i1] * param;
sit_LGAMMA[i1] += sit_M[i0] * param;
if (z0 == 0.0 && z1 == 0.0)
{
OSMOT += sit_M[i0] * sit_M[i1] * param / 2.0;
}
else
{
OSMOT += sit_M[i0] * sit_M[i1] * param;
}
break;
case TYPE_SIT_EPSILON_MU:
sit_LGAMMA[i0] += sit_M[i1] * I * param;
sit_LGAMMA[i1] += sit_M[i0] * I * param;
OSMOT += sit_M[i0] * sit_M[i1] * param;
if (z0 == 0.0 && z1 == 0.0)
{
OSMOT += sit_M[i0] * sit_M[i1] * param * I / 2.0;
}
else
{
OSMOT += sit_M[i0] * sit_M[i1] * param * I;
}
break;
default:
case TYPE_Other:
error_msg("TYPE_Other in pitz_param list.", STOP);
break;
}
}
/*
* Add F and CSUM terms to sit_LGAMMA
*/
for (size_t j = 0; j < ion_list.size(); j++)
{
int i = ion_list[j];
z0 = spec[i]->z;
sit_LGAMMA[i] += z0 * z0 * F;
}
//for (i = 0; i < sit_count_cations; i++)
//{
// z0 = spec[i]->z;
// sit_LGAMMA[i] += z0 * z0 * F;
//}
//for (i = 2 * (int)s.size(); i < 2 * (int)s.size() + sit_count_anions; i++)
//{
// z0 = spec[i]->z;
// sit_LGAMMA[i] += z0 * z0 * F;
//}
/*
C
C CONVERT TO MACINNES CONVENTION
C
*/
/*COSMOT = 1.0e0 + 2.0e0 * OSMOT / OSUM;*/
COSMOT = 1.0e0 + OSMOT*LOG_10 / OSUM;
/*
C
C CALCULATE THE ACTIVITY OF WATER
C
*/
AW = exp(-OSUM * COSMOT / 55.50837e0);
/*if (AW > 1.0) AW = 1.0;*/
/*s_h2o->la=log10(AW); */
mu_x = I;
for (size_t j = 0; j < s_list.size(); j++)
{
int i = s_list[j];
spec[i]->lg_pitzer = sit_LGAMMA[i];
}
// for (i = 0; i < 2 * (int)s.size() + sit_count_anions; i++)
// {
// if (sit_IPRSNT[i] == FALSE) continue;
// spec[i]->lg_pitzer = sit_LGAMMA[i];
///*
// output_msg(sformatf( "%d %s:\t%e\t%e\t%e\t%e \n", i, spec[i]->name, sit_M[i], spec[i]->la, spec[i]->lg_pitzer, spec[i]->lg));
//*/
// }
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
sit_clean_up(void)
/* ---------------------------------------------------------------------- */
{
/*
* Free all allocated memory, except strings
*/
int i;
for (i = 0; i < (int)sit_params.size(); i++)
{
delete sit_params[i];
}
sit_params.clear();
sit_param_map.clear();
sit_LGAMMA.clear();
sit_IPRSNT.clear();
spec.clear();
//delete aphi;
sit_M.clear();
return OK;
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
set_sit(int initial)
/* ---------------------------------------------------------------------- */
{
/*
* Sets initial guesses for unknowns if initial == TRUE
* Revises guesses whether initial is true or not
*/
int i;
cxxSolution *solution_ptr;
/*
* Set initial log concentrations to zero
*/
iterations = -1;
solution_ptr = use.Get_solution_ptr();
for (i = 0; i < (int)this->s_x.size(); i++)
{
s_x[i]->lm = LOG_ZERO_MOLALITY;
s_x[i]->lg_pitzer = 0.0;
}
if (initial == TRUE || set_and_run_attempt > 0)
{
for (i = 0; i < (int)this->s_x.size(); i++)
{
s_x[i]->lg = 0.0;
}
}
/*
* Set master species activities
*/
tc_x = solution_ptr->Get_tc();
tk_x = tc_x + 273.15;
patm_x = solution_ptr->Get_patm(); // done in calc_rho_0(tc, pa)
potV_x = solution_ptr->Get_potV();
/*
* H+, e-, H2O
*/
mass_water_aq_x = solution_ptr->Get_mass_water();
mu_x = solution_ptr->Get_mu();
s_h2o->moles = mass_water_aq_x / gfw_water;
s_h2o->la = log10(solution_ptr->Get_ah2o());
AW = pow((LDBLE) 10.0E0, s_h2o->la);
s_hplus->la = -solution_ptr->Get_ph();
s_hplus->lm = s_hplus->la;
s_hplus->moles = exp(s_hplus->lm * LOG_10) * mass_water_aq_x;
s_eminus->la = -solution_ptr->Get_pe();
if (initial == TRUE) sit_initial_guesses();
if (dl_type_x != cxxSurface::NO_DL) initial_surface_water();
sit_revise_guesses();
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
sit_initial_guesses(void)
/* ---------------------------------------------------------------------- */
{
/*
* Make initial guesses for activities of master species and
* ionic strength
*/
int i;
cxxSolution *solution_ptr;
solution_ptr = use.Get_solution_ptr();
mu_x =
s_hplus->moles +
exp((solution_ptr->Get_ph() - 14.) * LOG_10) * mass_water_aq_x;
mu_x /= mass_water_aq_x;
s_h2o->la = 0.0;
for (i = 0; i < count_unknowns; i++)
{
if (x[i] == ph_unknown || x[i] == pe_unknown)
continue;
if (x[i]->type < CB)
{
mu_x +=
x[i]->moles / mass_water_aq_x * 0.5 * x[i]->master[0]->s->z *
x[i]->master[0]->s->z;
x[i]->master[0]->s->la = log10(x[i]->moles / mass_water_aq_x);
}
else if (x[i]->type == CB)
{
x[i]->master[0]->s->la =
log10(0.001 * x[i]->moles / mass_water_aq_x);
}
else if (x[i]->type == SOLUTION_PHASE_BOUNDARY)
{
x[i]->master[0]->s->la =
log10(0.001 * x[i]->moles / mass_water_aq_x);
}
else if (x[i]->type == EXCH)
{
if (x[i]->moles <= 0)
{
x[i]->master[0]->s->la = MIN_RELATED_LOG_ACTIVITY;
}
else
{
x[i]->master[0]->s->la = log10(x[i]->moles);
}
}
else if (x[i]->type == SURFACE)
{
if (x[i]->moles <= 0)
{
x[i]->master[0]->s->la = MIN_RELATED_LOG_ACTIVITY;
}
else
{
x[i]->master[0]->s->la = log10(0.1 * x[i]->moles);
}
}
else if (x[i]->type == SURFACE_CB)
{
x[i]->master[0]->s->la = 0.0;
}
}
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
sit_revise_guesses(void)
/* ---------------------------------------------------------------------- */
{
/*
* Revise molalities species
*/
int i;
int l_iter, max_iter, repeat, fail;
LDBLE weight, f;
max_iter = 100;
/* gammas(mu_x); */
l_iter = 0;
repeat = TRUE;
fail = FALSE;
double d = 2;
double logd = log10(d);
while (repeat == TRUE && fail == FALSE)
{
l_iter++;
if (debug_set == TRUE)
{
output_msg(sformatf( "\nBeginning set iteration %d.\n",
l_iter));
}
if (l_iter == max_iter + 1)
{
log_msg(sformatf(
"Did not converge in set, iteration %d.\n",
iterations));
fail = TRUE;
}
if (l_iter > 2 * max_iter)
{
log_msg(sformatf(
"Did not converge with relaxed criteria in set.\n"));
return (OK);
}
molalities(TRUE);
/*pitzer(); */
/*s_h2o->la = 0.0; */
/*molalities(TRUE); */
mb_sums();
if (state < REACTION)
{
sum_species();
}
else
{
for (i = 0; i < count_unknowns; i++)
{
x[i]->sum = x[i]->f;
}
}
/*n
if (debug_set == TRUE) {
pr.species = TRUE;
pr.all = TRUE;
print_species();
}
*/
repeat = FALSE;
for (i = 0; i < count_unknowns; i++)
{
if (x[i] == ph_unknown || x[i] == pe_unknown)
continue;
if (x[i]->type == MB ||
/* x[i]->type == ALK || */
x[i]->type == CB ||
x[i]->type == SOLUTION_PHASE_BOUNDARY ||
x[i]->type == EXCH || x[i]->type == SURFACE)
{
if (debug_set == TRUE)
{
output_msg(sformatf(
"\n\t%5s at beginning of set %d: %e\t%e\t%e\n",
x[i]->description, l_iter, (double) x[i]->sum,
(double) x[i]->moles,
(double) x[i]->master[0]->s->la));
}
if (fabs(x[i]->moles) < 1e-30)
x[i]->moles = 0;
f = fabs(x[i]->sum);
if (f == 0 && x[i]->moles == 0)
{
x[i]->master[0]->s->la = MIN_RELATED_LOG_ACTIVITY;
continue;
}
else if (f == 0)
{
repeat = TRUE;
x[i]->master[0]->s->la += logd;
/*!!!!*/ if (x[i]->master[0]->s->la < -999.)
x[i]->master[0]->s->la = MIN_RELATED_LOG_ACTIVITY;
}
else if (f > d * fabs(x[i]->moles)
|| f < 1.0/d * fabs(x[i]->moles))
{
weight = (f < 1.0/d * fabs(x[i]->moles)) ? 0.3 : 1.0;
if (x[i]->moles <= 0)
{
x[i]->master[0]->s->la = MIN_RELATED_LOG_ACTIVITY;
}
else
{
repeat = TRUE;
x[i]->master[0]->s->la +=
weight * log10(fabs(x[i]->moles / x[i]->sum));
}
if (debug_set == TRUE)
{
output_msg(sformatf(
"\t%5s not converged in set %d: %e\t%e\t%e\n",
x[i]->description, l_iter,
(double) x[i]->sum, (double) x[i]->moles,
(double) x[i]->master[0]->s->la));
}
}
}
else if (x[i]->type == ALK)
{
f = total_co2;
if (fail == TRUE && f < 1.5 * fabs(x[i]->moles))
{
continue;
}
if (f > 1.5 * fabs(x[i]->moles)
|| f < 1.0/d * fabs(x[i]->moles))
{
repeat = TRUE;
weight = (f < 1.0/d * fabs(x[i]->moles)) ? 0.3 : 1.0;
x[i]->master[0]->s->la += weight *
log10(fabs(x[i]->moles / x[i]->sum));
if (debug_set == TRUE)
{
output_msg(sformatf(
"%s not converged in set. %e\t%e\t%e\n",
x[i]->description, (double) x[i]->sum,
(double) x[i]->moles,
(double) x[i]->master[0]->s->la));
}
}
}
}
}
log_msg(sformatf( "Iterations in sit_revise_guesses: %d\n", l_iter));
/*mu_x = mu_unknown->f * 0.5 / mass_water_aq_x; */
if (mu_x <= 1e-8)
{
mu_x = 1e-8;
}
/*gammas(mu_x); */
return (OK);
}
//#define ORIGINAL
#ifdef ORIGINAL
/* ---------------------------------------------------------------------- */
int Phreeqc::
jacobian_sit(void)
/* ---------------------------------------------------------------------- */
{
std::vector<double> base;
LDBLE d, d1, d2;
int i, j;
Restart:
size_t pz_max_unknowns = max_unknowns;
//k_temp(tc_x, patm_x);
if (full_pitzer == TRUE)
{
molalities(TRUE);
sit();
residuals();
}
base = residual; // std::vectors
d = 0.0001;
d1 = d * LOG_10;
d2 = 0;
for (i = 0; i < count_unknowns; i++)
{
switch (x[i]->type)
{
case MB:
case ALK:
case CB:
case SOLUTION_PHASE_BOUNDARY:
case EXCH:
case SURFACE:
case SURFACE_CB:
case SURFACE_CB1:
case SURFACE_CB2:
x[i]->master[0]->s->la += d;
d2 = d1;
break;
case AH2O:
x[i]->master[0]->s->la += d;
d2 = d1;
break;
case PITZER_GAMMA:
if (!full_pitzer)
continue;
x[i]->s->lg += d;
d2 = d;
break;
case MH2O:
mass_water_aq_x *= (1.0 + d);
x[i]->master[0]->s->moles = mass_water_aq_x / gfw_water;
d2 = log(1.0 + d);
break;
case MH:
s_eminus->la += d;
d2 = d1;
break;
/*
if (pitzer_pe == TRUE)
{
s_eminus->la += d;
d2 = d1;
break;
}
else
{
continue;
}
*/
case GAS_MOLES:
if (gas_in == FALSE)
continue;
d2 = (x[i]->moles > 1 ? 1 : 20);
d2 *= d * x[i]->moles;
if (d2 < 1e-14)
d2 = 1e-14;
x[i]->moles += d2;
break;
case MU:
//continue;
d2 = d * mu_x;
mu_x += d2;
//k_temp(tc_x, patm_x);
gammas(mu_x);
break;
case PP:
case SS_MOLES:
continue;
break;
}
molalities(TRUE);
if (max_unknowns > pz_max_unknowns)
{
gammas_sit();
jacobian_sums();
goto Restart;
}
if (full_pitzer == TRUE)
sit();
mb_sums();
residuals();
for (j = 0; j < count_unknowns; j++)
{
my_array[(size_t)j * (count_unknowns + 1) + (size_t)i] =
-(residual[j] - base[j]) / d2;
}
switch (x[i]->type)
{
case MB:
case ALK:
case CB:
case SOLUTION_PHASE_BOUNDARY:
case EXCH:
case SURFACE:
case SURFACE_CB:
case SURFACE_CB1:
case SURFACE_CB2:
case AH2O:
x[i]->master[0]->s->la -= d;
break;
case MH:
s_eminus->la -= d;
if (my_array[(size_t)i * (count_unknowns + 1) + (size_t)i] == 0)
{
my_array[(size_t)i * (count_unknowns + 1) + (size_t)i] =
exp(s_h2->lm * LOG_10) * 2;
}
break;
case PITZER_GAMMA:
x[i]->s->lg -= d;
break;
case MH2O:
mass_water_aq_x /= (1 + d);
x[i]->master[0]->s->moles = mass_water_aq_x / gfw_water;
break;
case MU:
mu_x -= d2;
//k_temp(tc_x, patm_x);
gammas(mu_x);
break;
case GAS_MOLES:
if (gas_in == FALSE)
continue;
x[i]->moles -= d2;
break;
}
}
molalities(TRUE);
if (full_pitzer == TRUE)
sit();
mb_sums();
residuals();
return OK;
}
#else
/* ---------------------------------------------------------------------- */
int Phreeqc::
jacobian_sit(void)
/* ---------------------------------------------------------------------- */
{
std::vector<double> base;
LDBLE d, d1, d2;
int i, j;
std::vector<class phase*> phase_ptrs;
std::vector<class phase> base_phases;
cxxGasPhase base_gas_phase;
cxxSurface base_surface;
Restart:
if (use.Get_surface_ptr() != NULL)
{
base_surface = *use.Get_surface_ptr();
}
if (use.Get_gas_phase_ptr() != NULL)
{
cxxGasPhase* gas_phase_ptr = use.Get_gas_phase_ptr();
base_gas_phase = *gas_phase_ptr;
base_phases.resize(gas_phase_ptr->Get_gas_comps().size());
for (size_t i = 0; i < gas_phase_ptr->Get_gas_comps().size(); i++)
{
const cxxGasComp* gas_comp_ptr = &(gas_phase_ptr->Get_gas_comps()[i]);
class phase* phase_ptr = phase_bsearch(gas_comp_ptr->Get_phase_name().c_str(), &j, FALSE);
phase_ptrs.push_back(phase_ptr);
base_phases[i] = *phase_ptr;
}
}
calculating_deriv = 1;
size_t pz_max_unknowns = max_unknowns;
//k_temp(tc_x, patm_x);
molalities(TRUE);
if (full_pitzer == TRUE)
{
sit();
}
mb_sums();
residuals();
base = residual; // std::vectors
d = 0.0001;
d1 = d * LOG_10;
d2 = 0;
for (i = 0; i < count_unknowns; i++)
{
switch (x[i]->type)
{
case MB:
case ALK:
case CB:
case SOLUTION_PHASE_BOUNDARY:
case EXCH:
case SURFACE:
case SURFACE_CB:
case SURFACE_CB1:
case SURFACE_CB2:
x[i]->master[0]->s->la += d;
d2 = d1;
break;
case AH2O:
x[i]->master[0]->s->la += d;
d2 = d1;
break;
case PITZER_GAMMA:
if (!full_pitzer)
continue;
x[i]->s->lg += d;
d2 = d;
break;
case MH2O:
mass_water_aq_x *= (1.0 + d);
x[i]->master[0]->s->moles = mass_water_aq_x / gfw_water;
d2 = log(1.0 + d);
break;
case MH:
s_eminus->la += d;
d2 = d1;
break;
/*
if (pitzer_pe == TRUE)
{
s_eminus->la += d;
d2 = d1;
break;
}
else
{
continue;
}
*/
case GAS_MOLES:
if (gas_in == FALSE)
continue;
d2 = (x[i]->moles > 1 ? 1 : 20);
d2 *= d * x[i]->moles;
if (d2 < 1e-14)
d2 = 1e-14;
x[i]->moles += d2;
break;
case MU:
//continue;
d2 = d * mu_x;
mu_x += d2;
//k_temp(tc_x, patm_x);
gammas_sit();
break;
case PP:
case SS_MOLES:
continue;
break;
}
molalities(TRUE);
if (max_unknowns > pz_max_unknowns)
{
gammas_sit();
jacobian_sums();
goto Restart;
}
if (full_pitzer == TRUE)
sit();
mb_sums();
residuals();
for (j = 0; j < count_unknowns; j++)
{
my_array[(size_t)j * (count_unknowns + 1) + (size_t)i] =
-(residual[j] - base[j]) / d2;
}
switch (x[i]->type)
{
case MB:
case ALK:
case CB:
case SOLUTION_PHASE_BOUNDARY:
case EXCH:
case SURFACE:
case SURFACE_CB:
case SURFACE_CB1:
case SURFACE_CB2:
case AH2O:
x[i]->master[0]->s->la -= d;
break;
case MH:
s_eminus->la -= d;
if (my_array[(size_t)i * (count_unknowns + 1) + (size_t)i] == 0)
{
my_array[(size_t)i * (count_unknowns + 1) + (size_t)i] =
exp(s_h2->lm * LOG_10) * 2;
}
break;
case PITZER_GAMMA:
x[i]->s->lg -= d;
break;
case MH2O:
mass_water_aq_x /= (1 + d);
x[i]->master[0]->s->moles = mass_water_aq_x / gfw_water;
break;
case MU:
mu_x -= d2;
//k_temp(tc_x, patm_x);
gammas_sit();
break;
case GAS_MOLES:
if (gas_in == FALSE)
continue;
x[i]->moles -= d2;
break;
}
if (use.Get_surface_ptr() != NULL)
{
*use.Get_surface_ptr() = base_surface;
}
if (use.Get_gas_phase_ptr() != NULL)
{
*use.Get_gas_phase_ptr() = base_gas_phase;
for (size_t g = 0; g < base_phases.size(); g++)
{
*phase_ptrs[g] = base_phases[g];
}
}
}
molalities(TRUE);
if (full_pitzer == TRUE)
sit();
mb_sums();
residuals();
//for (i = 0; i < count_unknowns; i++)
//{
// //Debugging
// if (fabs(2.0 * (residual[i] - base[i]) / (residual[i] + base[i])) > 1e-2 &&
// fabs(residual[i]) + fabs(base[i]) > 1e-8)
// {
// std::cerr << i << ": " << x[i]->description << " " << residual[i] << " " << base[i] << std::endl;
// }
//}
calculating_deriv = 0;
return OK;
}
#endif
/* ---------------------------------------------------------------------- */
int Phreeqc::
model_sit(void)
/* ---------------------------------------------------------------------- */
{
/*
* model is called after the equations have been set up by prep
* and initial guesses have been made in set.
*
* Here is the outline of the calculation sequence:
* residuals--residuals are calculated, if small we are done
* sum_jacobian--jacobian is calculated
* ineq--inequality solver is called
* reset--estimates of unknowns revised, if changes are small solution
* has been found, usually convergence is found in residuals.
* gammas--new activity coefficients
* molalities--calculate molalities
* mb_sums--calculate mass-balance sums
* mb_gases--decide if gas_phase exists
* mb_ss--decide if solid_solutions exists
* switch_bases--check to see if new basis species is needed
* reprep--rewrite equations with new basis species if needed
* sit_revise_guesses--revise unknowns to get initial mole balance
* check_residuals--check convergence one last time
* sum_species--calculate sums of elements from species concentrations
*
* An additional pass through may be needed if unstable phases still exist
* in the phase assemblage.
*/
int l_kode, return_kode;
int r;
int count_infeasible, count_basis_change;
int debug_model_save;
int mass_water_switch_save;
/* debug_model = TRUE; */
/* debug_prep = TRUE; */
/* debug_set = TRUE; */
/* mass_water_switch == TRUE, mass of water is constant */
mass_water_switch_save = mass_water_switch;
if (mass_water_switch_save == FALSE && delay_mass_water == TRUE)
{
mass_water_switch = TRUE;
}
debug_model_save = debug_model;
pe_step_size_now = pe_step_size;
step_size_now = step_size;
#ifdef NPP
if (!use.Get_kinetics_in()) status(0, NULL);
#else
status(0, NULL);
#endif
iterations = 0;
gamma_iterations = 0;
count_basis_change = count_infeasible = 0;
stop_program = FALSE;
remove_unstable_phases = FALSE;
if (always_full_pitzer == TRUE)
{
full_pitzer = TRUE;
}
else
{
full_pitzer = FALSE;
}
//sit_make_lists();
for (;;)
{
mb_gases();
mb_ss();
l_kode = 1;
while ((r = residuals()) != CONVERGED
|| remove_unstable_phases == TRUE)
{
#if defined(PHREEQCI_GUI)
PhreeqcIWait(this);
#endif
iterations++;
overall_iterations++;
if (iterations > itmax - 1 && debug_model == FALSE
&& pr.logfile == TRUE)
{
set_forward_output_to_log(TRUE);
debug_model = TRUE;
}
if (debug_model == TRUE)
{
output_msg(sformatf(
"\nIteration %d\tStep_size = %f\n", iterations,
(double) step_size_now));
output_msg(sformatf( "\t\tPe_step_size = %f\n\n",
(double) pe_step_size_now));
}
/*
* Iterations exceeded
*/
if (iterations > itmax)
{
error_string = sformatf( "Maximum iterations exceeded, %d\n",
itmax);
warning_msg(error_string);
stop_program = TRUE;
break;
}
/*
* Calculate jacobian
*/
gammas_sit();
jacobian_sums();
jacobian_sit();
/*
* Full matrix with pure phases
*/
if (r == OK || remove_unstable_phases == TRUE)
{
return_kode = ineq(l_kode);
if (return_kode != OK)
{
if (debug_model == TRUE)
{
output_msg(sformatf(
"Ineq had infeasible solution, "
"kode %d, iteration %d\n", return_kode,
iterations));
}
log_msg(sformatf( "Ineq had infeasible solution, "
"kode %d, iteration %d\n", return_kode,
iterations));
count_infeasible++;
}
if (return_kode == 2)
{
ineq(0);
}
reset();
}
gammas_sit();
if (full_pitzer == TRUE)
sit();
if (always_full_pitzer == TRUE)
{
full_pitzer = TRUE;
}
else
{
full_pitzer = FALSE;
}
if (molalities(FALSE) == ERROR)
{
sit_revise_guesses();
}
if (use.Get_surface_ptr() != NULL &&
use.Get_surface_ptr()->Get_dl_type() != cxxSurface::NO_DL &&
use.Get_surface_ptr()->Get_related_phases() == TRUE)
initial_surface_water();
mb_sums();
mb_gases();
mb_ss();
/*
* Switch bases if necessary
*/
if (switch_bases() == TRUE)
{
count_basis_change++;
//count_unknowns -= (int)this->s_x.size();
count_unknowns -= sit_aqueous_unknowns;
reprep();
full_pitzer = false;
}
/* debug
species_list_sort();
sum_species();
print_species();
print_exchange();
print_surface();
*/
if (stop_program == TRUE)
{
break;
}
}
/*
* Check for stop_program
*/
if (stop_program == TRUE)
{
break;
}
if (check_residuals() == ERROR)
{
stop_program = TRUE;
break;
}
/* remove_unstable_phases is set in check_residuals */
if (remove_unstable_phases == FALSE && mass_water_switch_save == FALSE
&& mass_water_switch == TRUE)
{
log_msg(sformatf(
"\nChanging water switch to FALSE. Iteration %d.\n",
iterations));
mass_water_switch = FALSE;
continue;
}
gamma_iterations++;
if (gamma_iterations > itmax)
{
error_string = sformatf( "Maximum gamma iterations exceeded, %d\n",
itmax);
warning_msg(error_string);
stop_program = TRUE;
break;
}
if (check_gammas_sit() != TRUE)
{
full_pitzer = TRUE;
continue;
}
if (remove_unstable_phases == FALSE)
break;
if (debug_model == TRUE)
{
output_msg(sformatf(
"\nRemoving unstable phases. Iteration %d.\n",
iterations));
}
log_msg(sformatf( "\nRemoving unstable phases. Iteration %d.\n",
iterations));
}
log_msg(sformatf( "\nNumber of infeasible solutions: %d\n",
count_infeasible));
log_msg(sformatf( "Number of basis changes: %d\n\n",
count_basis_change));
log_msg(sformatf( "Number of iterations: %d\n", iterations));
log_msg(sformatf( "Number of gamma iterations: %d\n\n", gamma_iterations));
debug_model = debug_model_save;
set_forward_output_to_log(FALSE);
if (stop_program == TRUE)
{
return (ERROR);
}
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
check_gammas_sit(void)
/* ---------------------------------------------------------------------- */
{
LDBLE old_mu, tol;
int converge, i;
old_mu = mu_x;
sit();
molalities(TRUE);
mb_sums();
converge = TRUE;
tol = convergence_tolerance * 10.;
for (i = 0; i < count_unknowns; i++)
{
if (x[i]->type != PITZER_GAMMA)
continue;
if (fabs(x[i]->s->lg - x[i]->s->lg_pitzer) > tol)
{
converge = FALSE;
}
}
if (fabs(old_mu - mu_x) > tol)
{
converge = FALSE;
}
if ((pow((LDBLE) 10.0, s_h2o->la) - AW) > tol)
{
converge = FALSE;
}
return converge;
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
gammas_sit()
/* ---------------------------------------------------------------------- */
{
/*
* Need exchange gammas for pitzer
*/
int i, j;
LDBLE coef;
/* Initialize */
k_temp(tc_x, patm_x);
/*
* Calculate activity coefficients
*/
for (i = 0; i < (int)this->s_x.size(); i++)
{
switch (s_x[i]->gflag)
{
case 0: /* uncharged */
case 1: /* Davies */
case 2: /* Extended D-H, WATEQ D-H */
case 3: /* Always 1.0 */
break;
case 4: /* Exchange */
/* Now calculated in next loop */
break;
case 5: /* Always 1.0 */
break;
case 6: /* Surface */
/*
* Find moles of sites.
* s_x[i]->equiv is stoichiometric coefficient of sites in species
*/
for (j = 1; s_x[i]->rxn_x.token[j].s != NULL; j++)
{
if (s_x[i]->rxn_x.token[j].s->type == SURF)
{
s_x[i]->alk =
s_x[i]->rxn_x.token[j].s->primary->unknown->moles;
break;
}
}
if (s_x[i]->alk > 0)
{
s_x[i]->lg = log10(s_x[i]->equiv / s_x[i]->alk);
s_x[i]->dg = 0.0;
}
else
{
s_x[i]->lg = 0.0;
s_x[i]->dg = 0.0;
}
break;
case 7: /* LLNL */
break;
case 8: /* LLNL CO2 */
break;
case 9: /* activity water */
s_x[i]->lg = log10(exp(s_h2o->la * LOG_10) * gfw_water);
s_x[i]->dg = 0.0;
break;
}
/*
if (mu_unknown != NULL) {
if (fabs(residual[mu_unknown->number]) > 0.1 &&
fabs(residual[mu_unknown->number])/mu_x > 0.5) {
s_x[i]->dg = 0.0;
}
}
*/
}
/*
* calculate exchange gammas
*/
if (use.Get_exchange_ptr() != NULL)
{
for (i = 0; i < (int)this->s_x.size(); i++)
{
switch (s_x[i]->gflag)
{
case 0: /* uncharged */
case 1: /* Davies */
case 2: /* Extended D-H, WATEQ D-H */
case 3: /* Always 1.0 */
case 5: /* Always 1.0 */
case 6: /* Surface */
case 7: /* LLNL */
case 8: /* LLNL CO2 */
case 9: /* activity water */
break;
case 4: /* Exchange */
/*
* Find CEC
* z contains valence of cation for exchange species, alk contains cec
*/
/* !!!!! */
for (j = 1; s_x[i]->rxn_x.token[j].s != NULL; j++)
{
if (s_x[i]->rxn_x.token[j].s->type == EX)
{
s_x[i]->alk =
s_x[i]->rxn_x.token[j].s->primary->unknown->
moles;
break;
}
}
/*
* Master species is a dummy variable with meaningless activity and mass
*/
s_x[i]->lg = 0.0;
s_x[i]->dg = 0.0;
if (s_x[i]->primary != NULL)
{
break;
}
/*
* All other species
*/
/* modific 29 july 2005... */
if (s_x[i]->equiv != 0 && s_x[i]->alk > 0)
{
s_x[i]->lg = log10(fabs(s_x[i]->equiv) / s_x[i]->alk);
}
if (use.Get_exchange_ptr()->Get_pitzer_exchange_gammas())
{
/* Assume equal gamma's of solute and exchangeable species... */
for (j = 1; s_x[i]->rxn_x.token[j].s != NULL; j++)
{
if (s_x[i]->rxn_x.token[j].s->type == EX)
continue;
coef = s_x[i]->rxn_x.token[j].coef;
s_x[i]->lg += coef * s_x[i]->rxn_x.token[j].s->lg;
s_x[i]->dg += coef * s_x[i]->rxn_x.token[j].s->dg;
}
}
}
}
}
/* ...end modific 29 july 2005 */
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
PTEMP_SIT(LDBLE TK)
/* ---------------------------------------------------------------------- */
{
/*
C
C SUBROUTINE TO CALCULATE TEMPERATURE DEPENDENCE OF PITZER PARAMETER
C
*/
LDBLE TR = 298.15;
if (fabs(TK - OTEMP) < 0.001 && fabs(patm_x - OPRESS) < 0.1) return OK;
/*
C Set DW0
*/
DW0 = rho_0 = calc_rho_0(TK - 273.15, patm_x);
VP = patm_x;
for (size_t j = 0; j < param_list.size(); j++)
{
int i = param_list[j];
calc_sit_param(sit_params[i], TK, TR);
}
calc_dielectrics(TK - 273.15, patm_x);
sit_A0 = A0;
OTEMP = TK;
OPRESS = patm_x;
return OK;
}
/* ---------------------------------------------------------------------- */
void Phreeqc::
sit_make_lists(void)
/* ---------------------------------------------------------------------- */
{
double log_min = log10(MIN_TOTAL);
s_list.clear();
cation_list.clear();
neutral_list.clear();
anion_list.clear();
ion_list.clear();
param_list.clear();
OTEMP = -100.0;
for (int j = 0; j < 3; j++)
{
int min, max;
switch (j)
{
case 0:
min = 0;
max = sit_count_cations;
break;
case 1:
min = (int)s.size();
max = (int)s.size() + sit_count_neutrals;
break;
case 2:
min = 2*(int)s.size();
max = 2*(int)s.size() + sit_count_anions;
break;
}
for (int i = min; i < max; i++)
{
sit_IPRSNT[i] = FALSE;
sit_M[i] = 0.0;
if (spec[i] != NULL && spec[i]->in == TRUE)
{
if (spec[i]->type == EX ||
spec[i]->type == SURF || spec[i]->type == SURF_PSI)
continue;
sit_IPRSNT[i] = TRUE;
s_list.push_back(i);
if (i < (int)s.size())
{
cation_list.push_back(i);
}
if (i >= (int)s.size() && i < 2*(int)s.size())
{
neutral_list.push_back(i);
}
if (i >= 2*(int)s.size())
{
anion_list.push_back(i);
}
if (i < (int)s.size() || i >= 2*(int)s.size())
{
ion_list.push_back(i);
}
if (spec[i]->lm > log_min)
{
sit_M[i] = under(spec[i]->lm);
}
}
}
}
for (int i = 0; i < (int)sit_params.size(); i++)
{
int i0 = sit_params[i]->ispec[0];
int i1 = sit_params[i]->ispec[1];
if (sit_IPRSNT[i0] == FALSE || sit_IPRSNT[i1] == FALSE) continue;
param_list.push_back(i);
}
}
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