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https://git.gfz-potsdam.de/naaice/iphreeqc.git
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vector kinetics arrays
This commit is contained in:
David Parkhurst
parent
1850c32c93
commit
bd0cad9434
@ -1061,11 +1061,7 @@ void Phreeqc::init(void)
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kinetics_cvode_mem = NULL;
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cvode_pp_assemblage_save= NULL;
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cvode_ss_assemblage_save= NULL;
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m_original = NULL;
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m_temp = NULL;
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rk_moles = NULL;
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set_and_run_attempt = 0;
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x0_moles = NULL;
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/* model.cpp ------------------------------- */
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gas_in = FALSE;
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min_value = 1e-10;
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@ -1775,11 +1775,8 @@ public:
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cxxSSassemblage *cvode_ss_assemblage_save;
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cxxPPassemblage *cvode_pp_assemblage_save;
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protected:
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LDBLE *m_original;
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LDBLE *m_temp;
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LDBLE *rk_moles;
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std::vector<double> m_temp, m_original, rk_moles, x0_moles;
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int set_and_run_attempt;
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LDBLE *x0_moles;
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/* model.cpp ------------------------------- */
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int gas_in;
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@ -236,17 +236,8 @@ read_calculate_values(void)
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case OPT_1: /* read command */
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if (calculate_value_ptr)
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{
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//length = (int) strlen(calculate_value_ptr->commands);
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//line_length = (int) strlen(line);
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//calculate_value_ptr->commands = (char *)PHRQ_realloc(calculate_value_ptr->commands,
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// ((size_t)length + (size_t)line_length + 2) * sizeof(char));
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//if (calculate_value_ptr->commands == NULL)
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// malloc_error();
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calculate_value_ptr->commands.append(";\0");
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calculate_value_ptr->commands.append(line);
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//calculate_value_ptr->commands[length] = ';';
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//calculate_value_ptr->commands[length + 1] = '\0';
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//strcat((calculate_value_ptr->commands), line);
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opt_save = OPT_1;
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}
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else
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49
kinetics.cpp
49
kinetics.cpp
@ -338,9 +338,7 @@ rk_kinetics(int i, LDBLE kin_time, int use_mix, int nsaver,
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if (kinetics_ptr == NULL)
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return (OK);
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n_reactions = (int) kinetics_ptr->Get_kinetics_comps().size();
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rk_moles = (LDBLE *) free_check_null(rk_moles);
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rk_moles = (LDBLE *) PHRQ_malloc((size_t) 6 * n_reactions * sizeof(LDBLE));
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if (rk_moles == NULL) malloc_error();
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rk_moles.resize(6 * (size_t)n_reactions);
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/*if (use_mix != NOMIX) last_model.force_prep = TRUE; */
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set_and_run_wrapper(i, use_mix, FALSE, i, step_fraction);
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@ -1112,7 +1110,7 @@ rk_kinetics(int i, LDBLE kin_time, int use_mix, int nsaver,
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{
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Utilities::Rxn_copy(Rxn_solution_map, save_old, i);
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}
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rk_moles = (LDBLE *) free_check_null(rk_moles);
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rk_moles.clear();
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rate_sim_time = rate_sim_time_start + kin_time;
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use.Set_kinetics_in(true);
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@ -2040,14 +2038,8 @@ run_reactions(int i, LDBLE kin_time, int use_mix, LDBLE step_fraction)
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* Save moles of kinetic reactants for printout...
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*/
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size_t count_comps = kinetics_ptr->Get_kinetics_comps().size();
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m_temp = (LDBLE *) PHRQ_malloc(count_comps * sizeof(LDBLE));
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if (m_temp == NULL)
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malloc_error();
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m_original =
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(LDBLE *) PHRQ_malloc(count_comps * sizeof(LDBLE));
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if (m_original == NULL)
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malloc_error();
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m_temp.resize(count_comps);
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m_original.resize(count_comps);
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for (size_t j = 0; j < kinetics_ptr->Get_kinetics_comps().size(); j++)
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{
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@ -2244,8 +2236,8 @@ run_reactions(int i, LDBLE kin_time, int use_mix, LDBLE step_fraction)
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cvode_last_good_time = 0;
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if (++m_iter >= kinetics_ptr->Get_bad_step_max())
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{
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m_temp = (LDBLE *) free_check_null(m_temp);
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m_original = (LDBLE *) free_check_null(m_original);
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m_temp.clear();
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m_original.clear();
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error_string = sformatf(
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"CVode is at maximum calls: %d. Cell: %d. Time: %8.2e s\nERROR: Please increase the maximum calls with -bad_step_max.",
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m_iter, cell_no, (double)sum_t);
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@ -2349,8 +2341,8 @@ run_reactions(int i, LDBLE kin_time, int use_mix, LDBLE step_fraction)
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kinetics_comp_ptr->Set_moles(m_original[j] - kinetics_comp_ptr->Get_m());
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/* if (kinetics_ptr->comps[j].moles < 1.e-15) kinetics_ptr->comps[j].moles = 0.0;
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*/ }
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m_temp = (LDBLE *) free_check_null(m_temp);
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m_original = (LDBLE *) free_check_null(m_original);
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m_temp.clear();
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m_original.clear();
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}
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iterations = run_reactions_iterations;
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if (cvode_pp_assemblage_save != NULL)
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@ -2651,13 +2643,8 @@ store_get_equi_reactants(int l, int kin_end)
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if (k == 0)
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return (OK);
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x0_moles = (LDBLE *) free_check_null(x0_moles);
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x0_moles = (LDBLE *) PHRQ_malloc((size_t) k * sizeof(LDBLE));
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if (x0_moles == NULL) malloc_error();
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for (i = 0; i < k; i++)
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{
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x0_moles[i] = 0.0;
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}
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x0_moles.resize(k);
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for (i = 0; i < k; i++) x0_moles[i] = 0.0;
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k = -1;
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if (pp_assemblage_ptr)
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{
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@ -2740,7 +2727,7 @@ store_get_equi_reactants(int l, int kin_end)
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* This condition makes output equal for incremental_reactions TRUE/FALSE...
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* if (incremental_reactions == FALSE || reaction_step == count_total_steps)
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*/
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x0_moles = (LDBLE *) free_check_null(x0_moles);
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x0_moles.clear();
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}
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return (OK);
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}
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@ -2849,7 +2836,8 @@ Jac(integertype N, DenseMat J, RhsFn f, void *f_data,
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{
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int count_cvode_errors;
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int n_reactions, n_user;
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LDBLE *initial_rates, del;
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LDBLE del;
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std::vector<double> initial_rates;
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cxxKinetics *kinetics_ptr;
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LDBLE step_fraction;
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@ -2862,10 +2850,7 @@ Jac(integertype N, DenseMat J, RhsFn f, void *f_data,
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step_fraction = pThis->cvode_step_fraction;
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pThis->rate_sim_time = pThis->cvode_rate_sim_time;
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initial_rates =
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(LDBLE *) pThis->PHRQ_malloc ((size_t) n_reactions * sizeof(LDBLE));
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if (initial_rates == NULL)
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pThis->malloc_error();
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initial_rates.resize(n_reactions);
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for (size_t i = 0; i < kinetics_ptr->Get_kinetics_comps().size(); i++)
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{
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@ -2907,7 +2892,7 @@ Jac(integertype N, DenseMat J, RhsFn f, void *f_data,
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/*
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error_msg("Mass balance error in jacobian", CONTINUE);
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*/
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initial_rates = (LDBLE *) pThis->free_check_null(initial_rates);
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initial_rates.clear();
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return;
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}
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pThis->run_reactions_iterations += pThis->iterations;
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@ -2979,7 +2964,7 @@ Jac(integertype N, DenseMat J, RhsFn f, void *f_data,
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pThis->cvode_error = TRUE;
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if (count_cvode_errors > 30)
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{
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initial_rates = (LDBLE *) pThis->free_check_null(initial_rates);
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initial_rates.clear();
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return;
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}
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pThis->run_reactions_iterations += pThis->iterations;
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@ -3010,7 +2995,7 @@ Jac(integertype N, DenseMat J, RhsFn f, void *f_data,
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cxxKineticsComp * kinetics_comp_ptr = &(kinetics_ptr->Get_kinetics_comps()[i]);
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kinetics_comp_ptr->Set_moles(0);
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}
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initial_rates = (LDBLE *) pThis->free_check_null(initial_rates);
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initial_rates.clear();
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return;
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}
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@ -127,10 +127,10 @@ clean_up(void)
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Rxn_gas_phase_map.clear();
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/* kinetics */
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Rxn_kinetics_map.clear();
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x0_moles = (LDBLE*)free_check_null(x0_moles);
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m_temp = (LDBLE*)free_check_null(m_temp);
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m_original = (LDBLE*)free_check_null(m_original);
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rk_moles = (LDBLE*)free_check_null(rk_moles);
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x0_moles.clear();
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m_temp.clear();
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m_original.clear();
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rk_moles.clear();
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/* rates */
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for (j = 0; j < (int)rates.size(); j++)
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{
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