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vector species_list

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This commit is contained in:
David Parkhurst 2021-03-16 17:12:41 -06:00
parent 449a54f61e
commit 41b9965576
8 changed files with 128 additions and 193 deletions
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3
Phreeqc.cpp
View File

@ -570,9 +570,6 @@ void Phreeqc::init(void)
/*----------------------------------------------------------------------
* Species_list
*---------------------------------------------------------------------- */
count_species_list = 0;
max_species_list = 0;
species_list = NULL;
/*----------------------------------------------------------------------
* Jacobian and Mass balance lists
*---------------------------------------------------------------------- */

4
Phreeqc.h
View File

@ -1314,9 +1314,7 @@ protected:
/*----------------------------------------------------------------------
* Species_list
*---------------------------------------------------------------------- */
int count_species_list;
int max_species_list;
struct species_list *species_list;
std::vector<struct species_list> species_list;
/*----------------------------------------------------------------------
* Jacobian and Mass balance lists

4
mainsubs.cpp
View File

@ -1140,7 +1140,7 @@ xexchange_save(int n_user)
count_elts = 0;
paren_count = 0;
charge = 0.0;
for (j = 0; j < count_species_list; j++)
for (j = 0; j < (int)species_list.size(); j++)
{
if (species_list[j].master_s == x[i]->master[0]->s)
{
@ -1530,7 +1530,7 @@ xsurface_save(int n_user)
count_elts = 0;
paren_count = 0;
charge = 0.0;
for (int j = 0; j < count_species_list; j++)
for (int j = 0; j < (int)species_list.size(); j++)
{
if (species_list[j].master_s == x[i]->master[0]->s)
{

2
model.cpp
View File

@ -4952,7 +4952,7 @@ sum_species(void)
master[i]->total = 0.0;
master[i]->total_primary = 0.0;
}
for (i = 0; i < count_species_list; i++)
for (i = 0; i < (int)species_list.size(); i++)
{
if (species_list[i].master_s->secondary != NULL)
{

33
prep.cpp
View File

@ -1129,13 +1129,7 @@ build_model(void)
sum_jacob1.clear();
sum_jacob2.clear();
sum_delta.clear();
max_species_list = 5 * MAX_S;
count_species_list = 0;
species_list = (struct species_list *) free_check_null(species_list);
space((void **) ((void *) &species_list), INIT, &max_species_list,
sizeof(struct species_list));
species_list.clear();
/*
* Pick species in the model, determine reaction for model, build jacobian
*/
@ -1358,8 +1352,8 @@ build_model(void)
/*
* Sort species list, by master only
*/
qsort(&species_list[0], (size_t) count_species_list,
(size_t) sizeof(struct species_list), species_list_compare_master);
qsort(&species_list[0], (int)species_list.size(),
sizeof(struct species_list), species_list_compare_master);
/*
* Save model description
*/
@ -1640,24 +1634,16 @@ build_species_list(int n)
*/
int j;
struct master *master_ptr;
/*
* Check space and store reaction token name and pointer to species
*/
if (count_species_list + count_elts >= max_species_list)
{
space((void **) ((void *) &species_list),
count_species_list + count_elts, &max_species_list,
sizeof(struct species_list));
}
/*
* Treat species made only with H+, e-, and H2O specially
*/
if (is_special(s[n]) == TRUE)
{
size_t count_species_list = species_list.size();
species_list.resize(count_species_list + 1);
species_list[count_species_list].master_s = s_hplus;
species_list[count_species_list].s = s[n];
species_list[count_species_list].coef = 0.0;
count_species_list++;
return (OK);
}
/*
@ -1672,12 +1658,13 @@ build_species_list(int n)
if (elt_list[j].elt->master->s->type != EX)
continue;
master_ptr = elt_list[j].elt->master;
size_t count_species_list = species_list.size();
species_list.resize(count_species_list + 1);
species_list[count_species_list].master_s =
elt_list[j].elt->master->s;
species_list[count_species_list].s = s[n];
species_list[count_species_list].coef = master_ptr->coef *
elt_list[j].coef;
count_species_list++;
}
return (OK);
}
@ -1693,12 +1680,13 @@ build_species_list(int n)
if (elt_list[j].elt->master->s->type != SURF)
continue;
master_ptr = elt_list[j].elt->master;
size_t count_species_list = species_list.size();
species_list.resize(count_species_list + 1);
species_list[count_species_list].master_s =
elt_list[j].elt->master->s;
species_list[count_species_list].s = s[n];
species_list[count_species_list].coef = master_ptr->coef *
elt_list[j].coef;
count_species_list++;
}
return (OK);
}
@ -1717,6 +1705,8 @@ build_species_list(int n)
{
master_ptr = elt_list[j].elt->master->s->primary;
}
size_t count_species_list = species_list.size();
species_list.resize(count_species_list + 1);
species_list[count_species_list].master_s = master_ptr->s;
species_list[count_species_list].s = s[n];
/*
@ -1724,7 +1714,6 @@ build_species_list(int n)
*/
species_list[count_species_list].coef = master_ptr->coef *
elt_list[j].coef;
count_species_list++;
}
return (OK);
}

10
print.cpp
View File

@ -455,7 +455,7 @@ print_exchange(void)
s_h2o->lm = s_h2o->la;
name = s_hplus->secondary->elt->name;
for (i = 0; i < count_species_list; i++)
for (i = 0; i < (int)species_list.size(); i++)
{
/*
* Get name of master species
@ -1486,7 +1486,7 @@ print_species(void)
*/
s_h2o->lm = s_h2o->la;
name = s_hplus->secondary->elt->name;
for (i = 0; i < count_species_list; i++)
for (i = 0; i < (int)species_list.size(); i++)
{
/*
* Get name of master species
@ -1774,7 +1774,7 @@ print_surface(void)
output_msg(sformatf("\t%-15s%12s%12s%12s%12s\n\n",
"Species", "Moles", "Fraction", "Molality",
"Molality"));
for (int i = 0; i < count_species_list; i++)
for (int i = 0; i < (int)species_list.size(); i++)
{
if (species_list[i].master_s != master_ptr->s)
continue;
@ -1816,7 +1816,7 @@ print_surface(void)
output_msg(sformatf("\t%-15s%12s%12s%12s%12s\n\n",
"Species", "Moles", "Fraction", "Molality",
"Molality"));
for (int i = 0; i < count_species_list; i++)
for (int i = 0; i < (int)species_list.size(); i++)
{
if (species_list[i].master_s != master_ptr->s)
continue;
@ -2072,7 +2072,7 @@ print_surface_cd_music(void)
output_msg(sformatf("\t%-20s%12s%12s%12s%12s\n\n",
"Species", "Moles", "Fraction", "Molality",
"Molality"));
for (int i = 0; i < count_species_list; i++)
for (int i = 0; i < (int)species_list.size(); i++)
{
if (species_list[i].master_s != master_ptr->s)
continue;

245
structures.cpp
View File

@ -21,9 +21,9 @@ int Phreeqc::
clean_up(void)
/* ---------------------------------------------------------------------- */
{
/*
* Free all allocated memory, except strings
*/
/*
* Free all allocated memory, except strings
*/
int i, j;
#if defined MULTICHART
chart_handler.End_timer();
@ -37,169 +37,144 @@ clean_up(void)
#endif
#endif
description_x = (char *) free_check_null(description_x);
description_x = (char*)free_check_null(description_x);
isotopes_x.clear();
moles_per_kilogram_string =
(char *) free_check_null(moles_per_kilogram_string);
pe_string = (char *) free_check_null(pe_string);
/* model */
(char*)free_check_null(moles_per_kilogram_string);
pe_string = (char*)free_check_null(pe_string);
/* model */
last_model.exchange =
(struct master **) free_check_null(last_model.exchange);
(struct master**)free_check_null(last_model.exchange);
last_model.gas_phase =
(struct phase **) free_check_null(last_model.gas_phase);
(struct phase**)free_check_null(last_model.gas_phase);
last_model.pp_assemblage =
(struct phase **) free_check_null(last_model.pp_assemblage);
(struct phase**)free_check_null(last_model.pp_assemblage);
last_model.ss_assemblage =
(const char **) free_check_null(last_model.ss_assemblage);
(const char**)free_check_null(last_model.ss_assemblage);
last_model.add_formula =
(const char **) free_check_null(last_model.add_formula);
last_model.si = (LDBLE *) free_check_null(last_model.si);
(const char**)free_check_null(last_model.add_formula);
last_model.si = (LDBLE*)free_check_null(last_model.si);
last_model.surface_comp =
(const char **) free_check_null(last_model.surface_comp);
(const char**)free_check_null(last_model.surface_comp);
last_model.surface_charge =
(const char **) free_check_null(last_model.surface_charge);
(const char**)free_check_null(last_model.surface_charge);
/* model */
free_model_allocs();
/* species */
/* species */
for (j = 0; j < (int)s.size(); j++)
{
s_free(s[j]);
s[j] = (struct species *) free_check_null(s[j]);
s[j] = (struct species*)free_check_null(s[j]);
}
s.clear();
/* master species */
/* master species */
for (j = 0; j < (int)master.size(); j++)
{
master_free(master[j]);
}
master.clear();
/* elements */
/* elements */
for (j = 0; j < (int)elements.size(); j++)
{
elements[j] = (struct element *) free_check_null(elements[j]);
elements[j] = (struct element*)free_check_null(elements[j]);
}
/* solutions */
elements.clear();
/* solutions */
Rxn_solution_map.clear();
/* surfaces */
/* surfaces */
Rxn_surface_map.clear();
/* exchange */
/* exchange */
Rxn_exchange_map.clear();
/* pp assemblages */
/* pp assemblages */
Rxn_pp_assemblage_map.clear();
/* s_s assemblages */
/* s_s assemblages */
Rxn_ss_assemblage_map.clear();
/* irreversible reactions */
/* irreversible reactions */
Rxn_reaction_map.clear();
/* temperature */
/* temperature */
Rxn_temperature_map.clear();
/* pressure */
/* pressure */
Rxn_pressure_map.clear();
/* unknowns */
/* unknowns */
for (j = 0; j < max_unknowns; j++)
{
unknown_free(x[j]);
}
x = (struct unknown **) free_check_null(x);
/* mixtures */
x = (struct unknown**)free_check_null(x);
/* mixtures */
Rxn_mix_map.clear();
/* phases */
/* phases */
for (j = 0; j < (int)phases.size(); j++)
{
phase_free(phases[j]);
phases[j] = (struct phase *) free_check_null(phases[j]);
phases[j] = (struct phase*)free_check_null(phases[j]);
}
/* inverse */
phases.clear();
/* inverse */
for (j = 0; j < count_inverse; j++)
{
inverse_free(&(inverse[j]));
}
inverse = (struct inverse *) free_check_null(inverse);
/* gases */
inverse = (struct inverse*)free_check_null(inverse);
/* gases */
Rxn_gas_phase_map.clear();
/* kinetics */
/* kinetics */
Rxn_kinetics_map.clear();
x0_moles = (LDBLE *) free_check_null(x0_moles);
m_temp = (LDBLE *) free_check_null(m_temp);
m_original = (LDBLE *) free_check_null(m_original);
rk_moles = (LDBLE *) free_check_null(rk_moles);
/* rates */
x0_moles = (LDBLE*)free_check_null(x0_moles);
m_temp = (LDBLE*)free_check_null(m_temp);
m_original = (LDBLE*)free_check_null(m_original);
rk_moles = (LDBLE*)free_check_null(rk_moles);
/* rates */
for (j = 0; j < count_rates; j++)
{
rate_free(&rates[j]);
}
rates = (struct rate *) free_check_null(rates);
/* logk hash table */
rates = (struct rate*)free_check_null(rates);
/* logk hash table */
for (j = 0; j < (int)logk.size(); j++)
{
free_check_null(logk[j]->add_logk);
logk[j] = (struct logk *) free_check_null(logk[j]);
logk[j] = (struct logk*)free_check_null(logk[j]);
}
logk.clear();
/* save_values */
/* save_values */
for (j = 0; j < count_save_values; j++)
{
save_values[j].subscripts =
(int *) free_check_null(save_values[j].subscripts);
(int*)free_check_null(save_values[j].subscripts);
}
save_values = (struct save_values *) free_check_null(save_values);
/* model */
/* global solution */
save_values = (struct save_values*)free_check_null(save_values);
/* working pe*/
pe_x.clear();
/* species_list */
species_list = (struct species_list *) free_check_null(species_list);
/* transport data */
stag_data = (struct stag_data *) free_check_null(stag_data);
cell_data = (struct cell_data *) free_check_null(cell_data);
/* punch */
advection_punch = (int *) free_check_null(advection_punch);
advection_print = (int *) free_check_null(advection_print);
/*species_list*/
species_list.clear();
/* transport data */
stag_data = (struct stag_data*)free_check_null(stag_data);
cell_data = (struct cell_data*)free_check_null(cell_data);
/* advection */
advection_punch = (int*)free_check_null(advection_punch);
advection_print = (int*)free_check_null(advection_print);
/* selected_output */
SelectedOutput_map.clear();
/* user_print and user_punch */
UserPunch_map.clear();
/* user_print and user_punch */
rate_free(user_print);
user_print = (struct rate *) free_check_null(user_print);
user_print = (struct rate*)free_check_null(user_print);
/*
Free llnl aqueous model parameters
*/
llnl_temp = (LDBLE *) free_check_null(llnl_temp);
llnl_adh = (LDBLE *) free_check_null(llnl_adh);
llnl_bdh = (LDBLE *) free_check_null(llnl_bdh);
llnl_bdot = (LDBLE *) free_check_null(llnl_bdot);
llnl_co2_coefs = (LDBLE *) free_check_null(llnl_co2_coefs);
llnl_temp = (LDBLE*)free_check_null(llnl_temp);
llnl_adh = (LDBLE*)free_check_null(llnl_adh);
llnl_bdh = (LDBLE*)free_check_null(llnl_bdh);
llnl_bdot = (LDBLE*)free_check_null(llnl_bdot);
llnl_co2_coefs = (LDBLE*)free_check_null(llnl_co2_coefs);
/*
* Copier space
*/
@ -214,93 +189,76 @@ clean_up(void)
copier_free(&copy_reaction);
copier_free(&copy_temperature);
copier_free(&copy_pressure);
#if defined PHREEQ98
rate_free(user_graph);
user_graph = (struct rate *) free_check_null(user_graph);
user_graph_headings = (char **) free_check_null(user_graph_headings);
#endif
/* master_isotope */
for (i = 0; i < (int)master_isotope.size(); i++)
{
master_isotope[i] = (struct master_isotope *) free_check_null(master_isotope[i]);
master_isotope[i] = (struct master_isotope*)free_check_null(master_isotope[i]);
}
//master_isotope = (struct master_isotope **) free_check_null(master_isotope);
master_isotope.clear();
hdestroy_multi(master_isotope_hash_table);
master_isotope_hash_table = NULL;
/* calculate_value */
for (i = 0; i < (int) calculate_value.size(); i++)
for (i = 0; i < (int)calculate_value.size(); i++)
{
calculate_value_free(calculate_value[i]);
calculate_value[i] = (struct calculate_value*)free_check_null(calculate_value[i]);
}
calculate_value.clear();
hdestroy_multi(calculate_value_hash_table);
calculate_value_hash_table = NULL;
/* isotope_ratio */
for (i = 0; i < (int)isotope_ratio.size(); i++)
{
isotope_ratio[i] =
(struct isotope_ratio *) free_check_null(isotope_ratio[i]);
(struct isotope_ratio*)free_check_null(isotope_ratio[i]);
}
//isotope_ratio = (struct isotope_ratio **) free_check_null(isotope_ratio);
isotope_ratio.clear();
hdestroy_multi(isotope_ratio_hash_table);
isotope_ratio_hash_table = NULL;
/* isotope_alpha */
for (i = 0; i < (int)isotope_alpha.size(); i++)
{
isotope_alpha[i] =
(struct isotope_alpha *) free_check_null(isotope_alpha[i]);
(struct isotope_alpha*)free_check_null(isotope_alpha[i]);
}
isotope_alpha.clear();
hdestroy_multi(isotope_alpha_hash_table);
isotope_alpha_hash_table = NULL;
/* tally table */
free_tally_table();
/* CVODE memory */
free_cvode();
/* pitzer */
pitzer_clean_up();
/* sit */
sit_clean_up();
/* hash tables */
/* hash tables */
hdestroy_multi(elements_hash_table);
hdestroy_multi(species_hash_table);
hdestroy_multi(logk_hash_table);
hdestroy_multi(phases_hash_table);
elements_hash_table = NULL;
species_hash_table = NULL;
logk_hash_table = NULL;
phases_hash_table = NULL;
/* strings */
/* strings */
#ifdef HASH
strings_hash_clear();
#else
strings_map_clear();
#endif
/* delete basic interpreter */
/* delete basic interpreter */
basic_free();
/* change_surf */
change_surf = (struct Change_Surf *) free_check_null(change_surf);
/* miscellaneous work space */
/* miscellaneous work space */
elt_list.clear();
trxn.token.clear();
mb_unknowns.clear();
line = (char *) free_check_null(line);
line_save = (char *) free_check_null(line_save);
/* free user database name if defined */
/* free user database name if defined */
user_database = (char *) free_check_null(user_database);
//selected_output_file_name =
// (char *) free_check_null(selected_output_file_name);
dump_file_name = (char *) free_check_null(dump_file_name);
#ifdef PHREEQCI_GUI
free_spread();
@ -326,33 +284,24 @@ int Phreeqc::
reinitialize(void)
/* ---------------------------------------------------------------------- */
{
/* solutions */
/* solutions */
Rxn_solution_map.clear();
/* surfaces */
/* surfaces */
Rxn_surface_map.clear();
/* exchange */
/* exchange */
Rxn_exchange_map.clear();
/* pp assemblages */
/* pp assemblages */
Rxn_pp_assemblage_map.clear();
/* s_s assemblages */
/* s_s assemblages */
Rxn_ss_assemblage_map.clear();
/* gases */
/* gases */
Rxn_gas_phase_map.clear();
/* kinetics */
/* kinetics */
Rxn_kinetics_map.clear();
/* irreversible reactions */
/* irreversible reactions */
Rxn_reaction_map.clear();
// Temperature
Rxn_temperature_map.clear();
// Pressure
Rxn_pressure_map.clear();
return (OK);
@ -2494,10 +2443,10 @@ species_list_sort(void)
/*
* Sort list using rules in species_list_compare
*/
if (count_species_list > 0)
if (species_list.size() > 0)
{
qsort(&species_list[0], (size_t) count_species_list,
(size_t) sizeof(struct species_list), species_list_compare);
qsort(&species_list[0], species_list.size(),
sizeof(struct species_list), species_list_compare);
}
return (OK);
}

20
transport.cpp
View File

@ -1812,13 +1812,13 @@ fill_spec(int l_cell_no, int ref_cell)
//sol_D[l_cell_no].spec = (struct spec *) free_check_null(sol_D[l_cell_no].spec);
if (sol_D[l_cell_no].spec == NULL)
{
sol_D[l_cell_no].spec = (struct spec *) PHRQ_malloc((size_t)(count_species_list + size_xt) * sizeof(struct spec));
sol_D[l_cell_no].spec_size = count_species_list + size_xt;
sol_D[l_cell_no].spec = (struct spec *) PHRQ_malloc((species_list.size() + (size_t)size_xt) * sizeof(struct spec));
sol_D[l_cell_no].spec_size = (int)species_list.size() + size_xt;
}
else if (count_species_list + size_xt > sol_D[l_cell_no].spec_size)
else if ((int)species_list.size() + size_xt > sol_D[l_cell_no].spec_size)
{
sol_D[l_cell_no].spec = (struct spec *) PHRQ_realloc(sol_D[l_cell_no].spec, (size_t)(count_species_list + size_xt) * sizeof(struct spec));
sol_D[l_cell_no].spec_size = count_species_list + size_xt;
sol_D[l_cell_no].spec = (struct spec *) PHRQ_realloc(sol_D[l_cell_no].spec, (species_list.size() + (size_t)size_xt) * sizeof(struct spec));
sol_D[l_cell_no].spec_size = (int)species_list.size() + size_xt;
}
if (sol_D[l_cell_no].spec == NULL)
malloc_error();
@ -1878,11 +1878,13 @@ fill_spec(int l_cell_no, int ref_cell)
/*
* sort species by name...
*/
if (count_species_list > 0)
qsort(&species_list[0], (size_t) count_species_list,
(size_t) sizeof(struct species_list), sort_species_name);
if (species_list.size() > 1)
{
qsort(&species_list[0], species_list.size(),
sizeof(struct species_list), sort_species_name);
}
for (i = 0; i < count_species_list; i++)
for (i = 0; i < (int)species_list.size(); i++)
{
/*
* copy species data