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Tony's changes.

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Call calc_delta_v always.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10930 1feff8c3-07ed-0310-ac33-dd36852eb9cd
This commit is contained in:
David L Parkhurst 2016-03-09 19:59:35 +00:00
parent 4405e60e4e
commit d5e7aa0ab3
4 changed files with 97 additions and 25 deletions
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1
SurfaceCharge.h
View File

@ -101,6 +101,7 @@ public:
void Set_sigma2(LDBLE d) {this->sigma2 = d;}
LDBLE Get_sigmaddl() const {return this->sigmaddl;}
void Set_sigmaddl(LDBLE d) {this->sigmaddl = d;}
cxxNameDouble & Get_diffuse_layer_totals(void) { return this->diffuse_layer_totals; }
const cxxNameDouble & Get_diffuse_layer_totals(void)const { return this->diffuse_layer_totals; }
void Set_diffuse_layer_totals(cxxNameDouble & nd) {this->diffuse_layer_totals = nd;}
std::map<LDBLE, cxxSurfDL> &Get_g_map(void) {return g_map;}

2
basicsubs.cpp
View File

@ -684,7 +684,7 @@ calc_logk_s(const char *name)
s_ptr = s_search(token);
if (s_ptr != NULL)
{
if (s_ptr->logk[vm_tc])
//if (s_ptr->logk[vm_tc])
/* calculate delta_v for the reaction... */
s_ptr->logk[delta_v] = calc_delta_v(s_ptr->rxn, false);
for (i = 0; i < MAX_LOG_K_INDICES; i++)

4
prep.cpp
View File

@ -5717,8 +5717,8 @@ k_temp(LDBLE tc, LDBLE pa) /* pa - pressure in atm */
mu_terms_in_logk = false;
for (i = 0; i < count_s_x; i++)
{
if (s_x[i]->rxn_x->logk[vm_tc])
/* calculate delta_v for the reaction... */
//if (s_x[i]->rxn_x->logk[vm_tc])
/* calculate delta_v for the reaction, assume Vm = 0 if not defined for a species... */
s_x[i]->rxn_x->logk[delta_v] = calc_delta_v(s_x[i]->rxn_x, false);
if (tc == current_tc && s_x[i]->rxn_x->logk[delta_v] == 0)
continue;

109
transport.cpp
View File

@ -188,16 +188,31 @@ transport(void)
if (dV_dcell)
{
if (stag_data->count_stag || !multi_Dflag || ishift)
if (/*stag_data->count_stag || */!multi_Dflag || ishift)
{
input_error++;
error_string = sformatf(
"Electrical Field (potential) was defined, but needs -multi_D, \n\t and is not possible with -stagnant or with advective flow.");
//"Electrical Field (potential) was defined, but needs -multi_D, \n\t and is not possible with -stagnant or with advective flow.");
"Electrical Field (potential) was defined, but needs -multi_D, \n\t and is not possible with advective flow.");
error_msg(error_string, CONTINUE);
free_check_null(sol_D);
}
else
{
if (bcon_first != 1)
{
bcon_first = 1;
error_string = sformatf(
"Electrical Field (potential) was defined, assuming constant boundary condition for first cell.");
warning_msg(error_string);
}
if (bcon_last != 1)
{
bcon_last = 1;
error_string = sformatf(
"Electrical Field (potential) was defined, assuming constant boundary condition for last cell.");
warning_msg(error_string);
}
current_cells = (struct CURRENT_CELLS *) PHRQ_malloc((size_t)
(count_cells + 1) * sizeof(struct CURRENT_CELLS));
if (current_cells == NULL)
@ -512,12 +527,12 @@ transport(void)
run_reactions(i, kin_time, NOMIX, step_fraction);
else
run_reactions(i, kin_time, DISP, step_fraction);
if (multi_Dflag)
if (multi_Dflag && j < nmix)
fill_spec(i);
/* punch and output file */
if ((ishift == 0) && (j == nmix)
&& ((stag_data->count_stag == 0)
&& ((stag_data->count_stag == 0) || i == 0
|| Utilities::Rxn_find(Rxn_solution_map, i + 1 + count_cells) == 0))
{
if ((cell_data[i].punch == TRUE)
@ -569,8 +584,18 @@ transport(void)
else
punch_boolean = FALSE;
for (i = 1; i <= count_cells; i++)
mix_stag(i, stagkin_time, punch_boolean,
step_fraction);
mix_stag(i, stagkin_time, punch_boolean, step_fraction);
if (punch_boolean
&& ((cell_data[i].punch == TRUE && transport_step % punch_modulus == 0)
|| (cell_data[i].print == TRUE && transport_step % print_modulus == 0)))
{
cell_no = i;
run_reactions(i, 0, NOMIX, 0);
if (cell_data[i].punch == TRUE)
punch_all();
if (cell_data[i].print == TRUE)
print_all();
}
}
}
}
@ -682,7 +707,7 @@ transport(void)
transport_step, 0, i, max_iter);
status(0, token);
run_reactions(i, kin_time, NOMIX, step_fraction);
if (multi_Dflag == TRUE)
if (multi_Dflag == TRUE && j < nmix)
fill_spec(i);
if (iterations > max_iter)
max_iter = iterations;
@ -800,10 +825,10 @@ transport(void)
run_reactions(i, kin_time, NOMIX, step_fraction);
else
run_reactions(i, kin_time, DISP, step_fraction);
if (multi_Dflag == TRUE)
if (multi_Dflag == TRUE && j < nmix)
fill_spec(i);
if ((j == nmix) && ((stag_data->count_stag == 0) ||
(Utilities::Rxn_find(Rxn_solution_map, i + 1 + count_cells) == 0)))
if ((j == nmix) && (stag_data->count_stag == 0 || i == 0
|| (i != 1 + count_cells && Utilities::Rxn_find(Rxn_solution_map, i + 1 + count_cells) == 0)))
{
if ((cell_data[i].punch == TRUE)
&& (transport_step % punch_modulus == 0))
@ -817,8 +842,8 @@ transport(void)
saver();
/* maybe sorb a surface component... */
if ((j == nmix) && ((stag_data->count_stag == 0) ||
(Utilities::Rxn_find(Rxn_solution_map, i + 1 + count_cells) == 0)))
if ((j == nmix) && ((stag_data->count_stag == 0)
|| (Utilities::Rxn_find(Rxn_solution_map, i + 1 + count_cells) == 0)))
{
if (change_surf_count > 0)
{
@ -853,6 +878,17 @@ transport(void)
punch_boolean = FALSE;
for (i = 1; i <= count_cells; i++)
mix_stag(i, stagkin_time, punch_boolean, step_fraction);
if (punch_boolean
&& ((cell_data[i].punch == TRUE && transport_step % punch_modulus == 0)
|| (cell_data[i].print == TRUE && transport_step % print_modulus == 0)))
{
cell_no = i;
run_reactions(i, 0, NOMIX, 0);
if (cell_data[i].punch == TRUE)
punch_all();
if (cell_data[i].print == TRUE)
print_all();
}
}
}
if (dump_modulus != 0 && (transport_step % dump_modulus) == 0)
@ -1861,7 +1897,7 @@ multi_D(LDBLE DDt, int mobile_cell, int stagnant)
il_calcs = -1;
current_x = sum_R = sum_Rd = 0.0;
if (dV_dcell)
if (dV_dcell && !stagnant)
find_current = loop_f_c = 1; // calculate J_ij once for all cells, find smallest j_x, next with this j_x.
else
find_current = loop_f_c = 0;
@ -1956,11 +1992,13 @@ multi_D(LDBLE DDt, int mobile_cell, int stagnant)
{
tot1_h = tot1_o = tot2_h = tot2_o = 0.0;
m_s = (struct M_S *) free_check_null(m_s);
m_s = (struct M_S *) PHRQ_malloc((size_t)count_elements *
count_m_s = (ct[icell].J_ij_count_spec < count_elements ?
ct[icell].J_ij_count_spec : count_elements);
m_s = (struct M_S *) PHRQ_malloc((size_t)count_m_s *
sizeof(struct M_S));
if (m_s == NULL)
malloc_error();
for (i1 = 0; i1 < count_elements; i1++)
for (i1 = 0; i1 < count_m_s; i1++)
{
m_s[i1].name = NULL;
m_s[i1].tot1 = 0;
@ -1978,7 +2016,7 @@ multi_D(LDBLE DDt, int mobile_cell, int stagnant)
use.Set_solution_ptr(Utilities::Rxn_find(Rxn_solution_map, icell));
use.Get_solution_ptr()->Set_total_h(use.Get_solution_ptr()->Get_total_h() - tot1_h);
use.Get_solution_ptr()->Set_total_o(use.Get_solution_ptr()->Get_total_o() - tot1_o);
if (dV_dcell && i > 0)
if (dV_dcell && i > 0 && !stagnant)
{
use.Get_solution_ptr()->Set_potV(cell_data[icell].potV);
}
@ -2043,7 +2081,37 @@ multi_D(LDBLE DDt, int mobile_cell, int stagnant)
for (it = use.Get_solution_ptr()->Get_totals().begin();
it != use.Get_solution_ptr()->Get_totals().end(); it++)
{
if (strcmp(it->first.c_str(), "H(0)") == 0)
continue;
if (strcmp(it->first.c_str(), "O(0)") == 0)
continue;
LDBLE moles = it->second;
if (moles < 0 && ct[i].dl_s)
{
use.Set_surface_ptr(Utilities::Rxn_find(Rxn_surface_map, i));
cxxSurface * s_ptr = use.Get_surface_ptr();
cxxSurfaceCharge * charge_ptr;
for (size_t j = 0; j < s_ptr->Get_surface_charges().size(); j++)
{
if (s_ptr->Get_dl_type() == cxxSurface::DONNAN_DL)
{
charge_ptr = &(s_ptr->Get_surface_charges()[j]);
break;
}
}
cxxNameDouble::iterator jit;
for (jit = charge_ptr->Get_diffuse_layer_totals().begin(); jit != charge_ptr->Get_diffuse_layer_totals().end(); jit++)
{
if (strcmp(jit->first.c_str(), "H") == 0 || strcmp(jit->first.c_str(), "O") == 0)
continue;
if (strcmp(jit->first.c_str(), it->first.c_str()) == 0)
{
moles += jit->second;
it->second += jit->second;
jit->second = 0;
}
}
}
if (moles < 0)
{
temp = moles;
@ -2241,7 +2309,7 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
else
il_calcs = 0;
if (dV_dcell && !find_current)
if (dV_dcell && !find_current && !stagnant)
goto dV_dcell2;
ct[icell].v_m = (struct V_M *) free_check_null(ct[icell].v_m);
@ -3129,7 +3197,7 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
ct[icell].J_ij_count_spec = i_max = k;
ct[icell].J_ij_il_count_spec = k_il;
if (dV_dcell)
if (dV_dcell && !stagnant)
{
current_cells[icell].ele = current_cells[icell].dif = 0;
dum = dV_dcell * F_Re3 / tk_x2;
@ -3201,8 +3269,11 @@ dV_dcell2:
ct[icell].J_ij_sum += ct[icell].v_m[i].z * ct[icell].J_ij[i].tot1;
}
}
// ensure that icell has dl water when checking negative conc's in MCD
ct[icell].dl_s = dl_aq_i;
ct[jcell].dl_s = dl_aq_j;
if (dV_dcell)
if (dV_dcell && !stagnant)
{
// perhaps adapt dV for getting equal current...
current_cells[icell].ele = current_cells[icell].dif = 0;