/* ---------------------------------------------------------------------- */
static int
reaction_calc (struct irrev *irrev_ptr)
/* ---------------------------------------------------------------------- */
{
/*
* Go through irreversible reaction initially to
* determine a list of elements and amounts in
* the reaction.
*/
int i, j, return_value;
LDBLE coef;
char token[MAX_LENGTH];
char *ptr;
struct phase *phase_ptr;
/*
* Go through list and generate list of elements and
* coefficient of elements in reaction
*/
return_value = OK;
count_elts = 0;
paren_count = 0;
for (i = 0; i < irrev_ptr->count_list; i++)
{
coef = irrev_ptr->list[i].coef;
strcpy (token, irrev_ptr->list[i].name);
phase_ptr = phase_bsearch (token, &j, FALSE);
/*
* Reactant is a pure phase, copy formula into token
*/
if (phase_ptr != NULL)
{
add_elt_list (phase_ptr->next_elt, coef);
}
else
{
ptr = &(token[0]);
get_elts_in_species (&ptr, coef);
}
}
/*
* Check that all elements are in database
*/
for (i = 0; i < count_elts; i++)
{
if (elt_list[i].elt->master == NULL)
{
sprintf (error_string, "Element or phase not defined in database, %s.",
elt_list[i].elt->name);
error_msg (error_string, CONTINUE);
input_error++;
return_value = ERROR;
}
}
irrev_ptr->elts = elt_list_save ();
return (return_value);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
setup_fixed_volume_gas(void)
/* ---------------------------------------------------------------------- */
{
/*
* Fill in data for gas phase unknown (sum of partial pressures)
* in unknown structure
*/
if (use.Get_gas_phase_ptr() == NULL)
return (OK);
cxxGasPhase *gas_phase_ptr = use.Get_gas_phase_ptr();
/*
* One for each gas component
*/
gas_unknowns.clear();
gas_unknown = NULL;
gas_phase_ptr->Set_total_moles(0);
for (size_t i = 0; i < gas_phase_ptr->Get_gas_comps().size(); i++)
{
const cxxGasComp *comp_ptr = &(gas_phase_ptr->Get_gas_comps()[i]);
int j;
struct phase *phase_ptr = phase_bsearch(comp_ptr->Get_phase_name().c_str(), &j, FALSE);
x[count_unknowns]->type = GAS_MOLES;
x[count_unknowns]->description = phase_ptr->name;
x[count_unknowns]->phase = phase_ptr;
x[count_unknowns]->moles = comp_ptr->Get_moles();
if (x[count_unknowns]->moles <= 0)
{
x[count_unknowns]->moles = MIN_TOTAL;
}
x[count_unknowns]->ln_moles = log(x[count_unknowns]->moles);
gas_unknowns.push_back(x[count_unknowns]);
gas_phase_ptr->Set_total_moles(gas_phase_ptr->Get_total_moles() + x[count_unknowns]->moles);
x[count_unknowns]->phase->moles_x = x[count_unknowns]->moles;
count_unknowns++;
}
if (gas_unknowns.size() > 0)
{
gas_unknown = gas_unknowns[0];
}
return (OK);
}
/* ---------------------------------------------------------------------- */
int Phreeqc::
build_fixed_volume_gas(void)
/* ---------------------------------------------------------------------- */
{
/*
* Put coefficients into lists to sum iaps to test for equilibrium
* Put coefficients into lists to build jacobian for
* sum of partial pressures equation and
* mass balance equations for elements contained in gases
*/
int row, col;
struct master *master_ptr;
struct rxn_token *rxn_ptr;
struct unknown *unknown_ptr;
LDBLE coef, coef_elt;
if (gas_unknown == NULL)
return (OK);
cxxGasPhase *gas_phase_ptr = use.Get_gas_phase_ptr();
for (size_t i = 0; i < gas_phase_ptr->Get_gas_comps().size(); i++)
{
const cxxGasComp *comp_ptr = &(gas_phase_ptr->Get_gas_comps()[i]);
int j;
struct phase *phase_ptr = phase_bsearch(comp_ptr->Get_phase_name().c_str(), &j, FALSE);
/*
* Determine elements in gas component
*/
count_elts = 0;
paren_count = 0;
if (phase_ptr->rxn_x == NULL)
continue;
add_elt_list(phase_ptr->next_elt, 1.0);
#define COMBINE
#ifdef COMBINE
change_hydrogen_in_elt_list(0);
#endif
/*
* Build mass balance sums for each element in gas
*/
if (debug_prep == TRUE)
{
output_msg(sformatf( "\n\tMass balance summations %s.\n\n",
phase_ptr->name));
}
/* All elements in gas */
for (j = 0; j < count_elts; j++)
{
unknown_ptr = NULL;
if (strcmp(elt_list[j].elt->name, "H") == 0)
{
unknown_ptr = mass_hydrogen_unknown;
}
else if (strcmp(elt_list[j].elt->name, "O") == 0)
{
unknown_ptr = mass_oxygen_unknown;
}
else
{
if (elt_list[j].elt->primary->in == TRUE)
{
unknown_ptr = elt_list[j].elt->primary->unknown;
}
else if (elt_list[j].elt->primary->s->secondary != NULL)
{
unknown_ptr =
elt_list[j].elt->primary->s->secondary->unknown;
}
}
if (unknown_ptr != NULL)
{
coef = elt_list[j].coef;
store_mb(&(gas_unknowns[i]->moles), &(unknown_ptr->f), coef);
if (debug_prep == TRUE)
{
output_msg(sformatf( "\t\t%-24s%10.3f\n",
unknown_ptr->description, (double) coef));
}
}
}
if (gas_phase_ptr->Get_type() == cxxGasPhase::GP_PRESSURE)
{
/* Total pressure of gases */
store_mb(&(phase_ptr->p_soln_x), &(gas_unknown->f),
1.0);
}
/*
* Build jacobian sums for mass balance equations
*/
if (debug_prep == TRUE)
{
output_msg(sformatf( "\n\tJacobian summations %s.\n\n",
phase_ptr->name));
}
for (j = 0; j < count_elts; j++)
{
unknown_ptr = NULL;
if (strcmp(elt_list[j].elt->name, "H") == 0)
{
unknown_ptr = mass_hydrogen_unknown;
}
else if (strcmp(elt_list[j].elt->name, "O") == 0)
{
unknown_ptr = mass_oxygen_unknown;
}
else
{
if (elt_list[j].elt->primary->in == TRUE)
{
unknown_ptr = elt_list[j].elt->primary->unknown;
}
else if (elt_list[j].elt->primary->s->secondary != NULL)
{
unknown_ptr =
elt_list[j].elt->primary->s->secondary->unknown;
}
}
if (unknown_ptr == NULL)
{
continue;
}
if (debug_prep == TRUE)
{
output_msg(sformatf( "\n\t%s.\n",
unknown_ptr->description));
}
row = unknown_ptr->number * (count_unknowns + 1);
coef_elt = elt_list[j].coef;
for (rxn_ptr = phase_ptr->rxn_x->token + 1;
rxn_ptr->s != NULL; rxn_ptr++)
{
if (rxn_ptr->s->secondary != NULL
&& rxn_ptr->s->secondary->in == TRUE)
{
master_ptr = rxn_ptr->s->secondary;
}
else if (rxn_ptr->s->primary != NULL && rxn_ptr->s->primary->in == TRUE)
{
master_ptr = rxn_ptr->s->primary;
}
else
{
master_ptr = master_bsearch_primary(rxn_ptr->s->name);
master_ptr->s->la = -999.0;
}
if (debug_prep == TRUE)
{
output_msg(sformatf( "\t\t%s\n",
master_ptr->s->name));
}
if (master_ptr->unknown == NULL)
{
continue;
}
if (master_ptr->in == FALSE)
{
error_string = sformatf(
"Element, %s, in phase, %s, is not in model.",
master_ptr->elt->name, phase_ptr->name);
error_msg(error_string, CONTINUE);
input_error++;
}
col = master_ptr->unknown->number;
coef = coef_elt * rxn_ptr->coef;
store_jacob(&(gas_unknowns[i]->moles),
&(array[row + col]), coef);
if (debug_prep == TRUE)
{
output_msg(sformatf( "\t\t%-24s%10.3f\t%d\t%d\n",
master_ptr->s->name, (double) coef,
row / (count_unknowns + 1), col));
}
}
if (gas_phase_ptr->Get_type() == cxxGasPhase::GP_PRESSURE)
{
/* derivative wrt total moles of gas */
store_jacob(&(phase_ptr->fraction_x),
&(array[row + gas_unknown->number]), coef_elt);
if (debug_prep == TRUE)
{
output_msg(sformatf( "\t\t%-24s%10.3f\t%d\t%d\n",
"gas moles", (double) elt_list[j].coef,
row / (count_unknowns + 1),
gas_unknown->number));
}
}
}
/*
* Build jacobian sums for sum of partial pressures equation
*/
if (gas_phase_ptr->Get_type() != cxxGasPhase::GP_PRESSURE)
continue;
if (debug_prep == TRUE)
{
output_msg(sformatf( "\n\tPartial pressure eqn %s.\n\n",
phase_ptr->name));
}
unknown_ptr = gas_unknown;
row = unknown_ptr->number * (count_unknowns + 1);
for (rxn_ptr = phase_ptr->rxn_x->token + 1; rxn_ptr->s != NULL; rxn_ptr++)
{
if (rxn_ptr->s != s_eminus && rxn_ptr->s->in == FALSE)
{
error_string = sformatf(
"Element in species, %s, in phase, %s, is not in model.",
rxn_ptr->s->name, phase_ptr->name);
warning_msg(error_string);
}
else
{
if (rxn_ptr->s->secondary != NULL
&& rxn_ptr->s->secondary->in == TRUE)
{
master_ptr = rxn_ptr->s->secondary;
}
else if (rxn_ptr->s->primary != NULL && rxn_ptr->s->primary->in == TRUE)
{
master_ptr = rxn_ptr->s->primary;
}
else
{
master_ptr = master_bsearch_primary(rxn_ptr->s->name);
if (master_ptr && master_ptr->s)
{
master_ptr->s->la = -999.0;
}
}
if (master_ptr == NULL)
{
error_string = sformatf(
"Master species for %s, in phase, %s, is not in model.",
rxn_ptr->s->name, phase_ptr->name);
error_msg(error_string, CONTINUE);
input_error++;
}
else
{
if (debug_prep == TRUE)
{
output_msg(sformatf( "\t\t%s\n", master_ptr->s->name));
}
if (master_ptr->unknown == NULL)
{
assert(false);
continue;
}
if (master_ptr->in == FALSE)
{
error_string = sformatf(
"Element, %s, in phase, %s, is not in model.",
master_ptr->elt->name, phase_ptr->name);
warning_msg(error_string);
}
col = master_ptr->unknown->number;
coef = rxn_ptr->coef;
store_jacob(&(phase_ptr->p_soln_x), &(array[row + col]), coef);
if (debug_prep == TRUE)
{
output_msg(sformatf( "\t\t%-24s%10.3f\t%d\t%d\n",
master_ptr->s->name, (double) coef,
row / (count_unknowns + 1), col));
}
}
}
}
}
return (OK);
}