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Merge commit '3cc84da8ceac5d4a819fc0a6779b7ca361c17226'

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This commit is contained in:
Scott R Charlton 2018-11-07 14:39:33 -07:00
commit dbefc44f31
3 changed files with 78 additions and 35 deletions
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79
phreeqcpp/basicsubs.cpp
View File

@ -2445,46 +2445,61 @@ surf_total(const char *total_name, const char *surface_name)
// surface matches, now match element or redox state
struct rxn_token *rxn_ptr;
for (rxn_ptr = s_x[j]->rxn_s->token + 1; rxn_ptr->s != NULL; rxn_ptr++)
if (s_x[j]->mole_balance == NULL)
{
if (redox && rxn_ptr->s->secondary)
for (rxn_ptr = s_x[j]->rxn_s->token + 1; rxn_ptr->s != NULL; rxn_ptr++)
{
token = rxn_ptr->s->secondary->elt->name;
}
else if (!redox && rxn_ptr->s->secondary)
{
token = rxn_ptr->s->secondary->elt->primary->elt->name;
}
else if (!redox && rxn_ptr->s->primary)
{
token = rxn_ptr->s->primary->elt->name;
}
else
{
continue;
}
if (strcmp(token.c_str(), total_name) == 0)
{
t += rxn_ptr->coef * s_x[j]->moles;
break;
}
else
// sum all sites in case total_name is a surface name without underscore surf ("Hfo_w", "Hfo")
{
if (rxn_ptr->s->type == SURF)
if (redox && rxn_ptr->s->secondary)
{
if (token.find("_") != std::string::npos)
token = rxn_ptr->s->secondary->elt->name;
}
else if (!redox && rxn_ptr->s->secondary)
{
token = rxn_ptr->s->secondary->elt->primary->elt->name;
}
else if (!redox && rxn_ptr->s->primary)
{
token = rxn_ptr->s->primary->elt->name;
}
else
{
continue;
}
if (strcmp(token.c_str(), total_name) == 0)
{
t += rxn_ptr->coef * s_x[j]->moles;
break;
}
else
// sum all sites in case total_name is a surface name without underscore surf ("Hfo_w", "Hfo")
{
if (rxn_ptr->s->type == SURF)
{
token = token.substr(0, token.find("_"));
}
if (strcmp(token.c_str(), total_name) == 0)
{
t += rxn_ptr->coef * s_x[j]->moles;
break;
if (token.find("_") != std::string::npos)
{
token = token.substr(0, token.find("_"));
}
if (strcmp(token.c_str(), total_name) == 0)
{
t += rxn_ptr->coef * s_x[j]->moles;
break;
}
}
}
}
}
else
{
for (int i = 0; s_x[j]->next_secondary[i].elt != NULL; i++)
{
token = s_x[j]->next_secondary[i].elt->name;
if (strcmp(token.c_str(), total_name) == 0)
{
t += s_x[j]->next_secondary[i].coef * s_x[j]->moles;
break;
}
}
}
}
return t;
}

21
phreeqcpp/model.cpp
View File

@ -532,7 +532,7 @@ check_residuals(void)
{
if (x[i]->ss_in == FALSE)
continue;
if (x[i]->moles <= MIN_TOTAL_SS)
if (x[i]->moles <= 1e2*MIN_TOTAL)
continue;
if (residual[i] >= epsilon
|| residual[i] <= -epsilon /* || stop_program == TRUE */ )
@ -1597,7 +1597,9 @@ ineq(int in_kode)
(size_t) (count_unknowns + 1) * sizeof(LDBLE));
ineq_array[l_count_rows * max_column_count + i] = 1.0;
ineq_array[l_count_rows * max_column_count + count_unknowns] =
0.99 * x[i]->moles - MIN_TOTAL_SS;
x[i]->moles;
//0.99 * x[i]->moles - MIN_TOTAL_SS;
//0.9 * x[i]->moles;
back_eq[l_count_rows] = i;
l_count_rows++;
}
@ -3264,6 +3266,20 @@ reset(void)
}
factor = f0;
}
if (x[i]->moles > 0 && -delta[i] > 1e1*x[i]->moles)
{
f0 = (-delta[i])/(1e1*x[i]->moles);
if (f0 > factor)
{
if (debug_model == TRUE)
{
output_msg(sformatf(
"%-10.10s, Precipitating too much mineral.\t%f\n",
x[i]->description, (double)f0));
}
factor = f0;
}
}
}
}
}
@ -4207,6 +4223,7 @@ residuals(void)
else if (x[i]->type == SS_MOLES)
{
residual[i] = x[i]->f * LOG_10;
if (x[i]->moles <= 1e2*MIN_TOTAL) continue;
if (fabs(residual[i]) > l_toler && x[i]->ss_in == TRUE)
{
if (print_fail)

13
phreeqcpp/transport.cpp
View File

@ -7,6 +7,7 @@
#include "SSassemblage.h"
#include "cxxKinetics.h"
#include "Solution.h"
#include <limits>
LDBLE F_Re3 = F_C_MOL / (R_KJ_DEG_MOL * 1e3);
LDBLE tk_x2; // average tx_x of icell and jcell
@ -1107,8 +1108,15 @@ init_mix(void)
}
else
{
const int max_int = (int) (std::numeric_limits<int>::max)();
if ((int)round(2.25 * maxmix) > max_int)
{
char token[MAX_LENGTH];
sprintf(token, "Calculated number of mixes %g, is beyond program limit,\nERROR: please decrease time_step.", 2.25 * maxmix);
error_msg(token, STOP);
}
if (bcon_first == 1 || bcon_last == 1)
l_nmix = 1 + (int) floor(2.25 * maxmix);
l_nmix = 1 + (long int) floorl(2.25 * maxmix);
else
l_nmix = 1 + (int) floor(1.5 * maxmix);
@ -2046,6 +2054,7 @@ multi_D(LDBLE DDt, int mobile_cell, int stagnant)
* 1. obtain J_ij...
*/
il_calcs = find_J(icell, jcell, mixf, DDt, stagnant);
if (find_current)
{
if (i < last_c)
@ -2078,6 +2087,8 @@ multi_D(LDBLE DDt, int mobile_cell, int stagnant)
continue;
}
}
if (!ct[icell].J_ij_count_spec)
continue;
/*
* 2. sum up the primary or secondary master_species