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Merge commit '5631ce1e56cda328e8efac33a0ee998a7fd27489'

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Darth Vader 2020-08-18 19:59:27 +00:00
commit 57cf38ddb0
5 changed files with 237 additions and 204 deletions
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11
phreeqcpp/PBasic.cpp
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@ -1612,6 +1612,9 @@ listtokens(FILE * f, tokenrec * l_buf)
case tokdh_a: case tokdh_a:
output_msg("DH_A"); // Debye-Hueckel A output_msg("DH_A"); // Debye-Hueckel A
break; break;
case tokdebye_length:
output_msg("DEBYE_LENGTH"); // Debye-Hueckel length
break;
case tokdh_b: case tokdh_b:
output_msg("DH_B"); // Debye-Hueckel B output_msg("DH_B"); // Debye-Hueckel B
break; break;
@ -3706,6 +3709,13 @@ factor(struct LOC_exec * LINK)
n.UU.val = PhreeqcPtr->DH_A; n.UU.val = PhreeqcPtr->DH_A;
} }
break; break;
case tokdebye_length:
{
double debye_length = (PhreeqcPtr->eps_r * EPSILON_ZERO * R_KJ_DEG_MOL * 1000.0 * PhreeqcPtr->tk_x)
/ (2. * F_C_MOL * F_C_MOL * PhreeqcPtr->mu_x * 1000.);
n.UU.val = sqrt(debye_length);
break;
}
case tokdh_b: case tokdh_b:
if (PhreeqcPtr->llnl_count_temp > 0) if (PhreeqcPtr->llnl_count_temp > 0)
{ {
@ -7377,6 +7387,7 @@ const std::map<const std::string, PBasic::BASIC_TOKEN>::value_type temp_tokens[]
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("eps_r", PBasic::tokeps_r), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("eps_r", PBasic::tokeps_r),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("vm", PBasic::tokvm), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("vm", PBasic::tokvm),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("dh_a", PBasic::tokdh_a), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("dh_a", PBasic::tokdh_a),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("debye_length", PBasic::tokdebye_length),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("dh_b", PBasic::tokdh_b), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("dh_b", PBasic::tokdh_b),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("dh_av", PBasic::tokdh_av), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("dh_av", PBasic::tokdh_av),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("qbrn", PBasic::tokqbrn), std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("qbrn", PBasic::tokqbrn),

1
phreeqcpp/PBasic.h
View File

@ -317,6 +317,7 @@ public:
tokvm, tokvm,
tokphase_vm, tokphase_vm,
tokdh_a, tokdh_a,
tokdebye_length,
tokdh_b, tokdh_b,
tokdh_av, tokdh_av,
tokqbrn, tokqbrn,

1
phreeqcpp/Phreeqc.h
View File

@ -1070,6 +1070,7 @@ public:
LDBLE calc_vm_Cl(void); LDBLE calc_vm_Cl(void);
int multi_D(LDBLE DDt, int mobile_cell, int stagnant); int multi_D(LDBLE DDt, int mobile_cell, int stagnant);
LDBLE find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant); LDBLE find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant);
void calc_b_ij(int icell, int jcell, int k, LDBLE b_i, LDBLE b_j, LDBLE g_i, LDBLE g_j, LDBLE free_i, LDBLE free_j, int stagnant);
void diffuse_implicit(LDBLE DDt, int stagnant); void diffuse_implicit(LDBLE DDt, int stagnant);
int fill_spec(int cell_no, int ref_cell); int fill_spec(int cell_no, int ref_cell);
LDBLE moles_from_redox_states(cxxSolution *sptr, const char *name); LDBLE moles_from_redox_states(cxxSolution *sptr, const char *name);

59
phreeqcpp/tidy.cpp
View File

@ -3613,10 +3613,10 @@ tidy_kin_exchange(void)
assert(false); assert(false);
} }
cxxExchange * exchange_ptr = &(it->second); cxxExchange * exchange_ptr = &(it->second);
//if (!exchange_ptr->Get_new_def()) if (!exchange_ptr->Get_new_def())
// continue; continue;
//if (exchange_ptr->Get_n_user() < 0) if (exchange_ptr->Get_n_user() < 0)
// continue; continue;
// check elements // check elements
for (size_t j = 0; j < exchange_ptr->Get_exchange_comps().size(); j++) for (size_t j = 0; j < exchange_ptr->Get_exchange_comps().size(); j++)
{ {
@ -3846,10 +3846,10 @@ tidy_min_exchange(void)
assert(false); assert(false);
} }
cxxExchange * exchange_ptr = &(it->second); cxxExchange * exchange_ptr = &(it->second);
//if (!exchange_ptr->Get_new_def()) if (!exchange_ptr->Get_new_def())
// continue; continue;
//if (exchange_ptr->Get_n_user() < 0) if (exchange_ptr->Get_n_user() < 0)
// continue; continue;
n = exchange_ptr->Get_n_user(); n = exchange_ptr->Get_n_user();
// check elements // check elements
for (size_t j = 0; j < exchange_ptr->Get_exchange_comps().size(); j++) for (size_t j = 0; j < exchange_ptr->Get_exchange_comps().size(); j++)
@ -4166,7 +4166,6 @@ tidy_min_surface(void)
assert(false); assert(false);
} }
cxxSurface *surface_ptr = &(kit->second); cxxSurface *surface_ptr = &(kit->second);
if (!surface_ptr->Get_new_def()) continue;
if (!surface_ptr->Get_new_def()) if (!surface_ptr->Get_new_def())
continue; continue;
if (surface_ptr->Get_n_user() < 0) if (surface_ptr->Get_n_user() < 0)
@ -4414,7 +4413,20 @@ update_min_surface(void)
double comp_moles = 0.0; double comp_moles = 0.0;
cxxSurfaceComp* surface_comp_ptr = &(surface_ptr->Get_surface_comps()[j]); cxxSurfaceComp* surface_comp_ptr = &(surface_ptr->Get_surface_comps()[j]);
if (surface_comp_ptr->Get_phase_name().size() == 0) continue; if (surface_comp_ptr->Get_phase_name().size() == 0) continue;
cxxSurfaceCharge* surface_charge_ptr = surface_ptr->Find_charge(surface_comp_ptr->Get_charge_name()); cxxSurfaceCharge* surface_charge_ptr = NULL;
if (surface_ptr->Get_type() != cxxSurface::SURFACE_TYPE::NO_EDL)
{
surface_charge_ptr = surface_ptr->Find_charge(surface_comp_ptr->Get_charge_name());
if (surface_charge_ptr == NULL)
{
input_error++;
error_string = sformatf("Data structure for surface charge not found "
"for %s ",
surface_comp_ptr->Get_formula().c_str());
error_msg(error_string, CONTINUE);
continue;
}
}
int n = surface_ptr->Get_n_user(); int n = surface_ptr->Get_n_user();
/* First find surface master species */ /* First find surface master species */
@ -4493,7 +4505,11 @@ update_min_surface(void)
surface_comp_ptr->Set_phase_name(phase_ptr->name); surface_comp_ptr->Set_phase_name(phase_ptr->name);
/* make surface concentration proportional to mineral ... */ /* make surface concentration proportional to mineral ... */
LDBLE conc = jit->second.Get_moles() * surface_comp_ptr->Get_phase_proportion(); LDBLE conc = jit->second.Get_moles() * surface_comp_ptr->Get_phase_proportion();
double grams = surface_charge_ptr->Get_grams(); double grams = 0.0;
if (surface_charge_ptr != NULL)
{
grams = surface_charge_ptr->Get_grams();
}
if (comp_moles > 0.0) if (comp_moles > 0.0)
{ {
surface_comp_ptr->multiply(conc / comp_moles); surface_comp_ptr->multiply(conc / comp_moles);
@ -4514,7 +4530,7 @@ update_min_surface(void)
{ {
surface_charge_ptr->multiply(jit->second.Get_moles() / grams); surface_charge_ptr->multiply(jit->second.Get_moles() / grams);
} }
else /* need to generate from scratch */ else if (surface_charge_ptr != NULL) /* need to generate from scratch */
{ {
surface_charge_ptr->Set_grams(jit->second.Get_moles()); surface_charge_ptr->Set_grams(jit->second.Get_moles());
surface_charge_ptr->Set_charge_balance(0.0); surface_charge_ptr->Set_charge_balance(0.0);
@ -4897,10 +4913,23 @@ update_kin_surface(void)
/* use database name for rate */ /* use database name for rate */
comp_ptr->Set_rate_name(kin_comp_ptr->Get_rate_name().c_str()); comp_ptr->Set_rate_name(kin_comp_ptr->Get_rate_name().c_str());
cxxSurfaceCharge* charge_ptr = surface_ptr->Find_charge(comp_ptr->Get_charge_name()); cxxSurfaceCharge* charge_ptr = surface_ptr->Find_charge(comp_ptr->Get_charge_name());
if (surface_ptr->Get_type() != cxxSurface::SURFACE_TYPE::NO_EDL)
{
charge_ptr = surface_ptr->Find_charge(comp_ptr->Get_charge_name());
if (charge_ptr == NULL)
{
input_error++;
error_string = sformatf("Data structure for surface charge not found "
"for %s ",
comp_ptr->Get_formula().c_str());
error_msg(error_string, CONTINUE);
continue;
}
}
/* make surface concentration proportional to mineral ... */ /* make surface concentration proportional to mineral ... */
LDBLE conc = kin_comp_ptr->Get_m() * comp_ptr->Get_phase_proportion(); LDBLE conc = kin_comp_ptr->Get_m() * comp_ptr->Get_phase_proportion();
double grams = charge_ptr->Get_grams(); double grams = 0.0;
if (charge_ptr != NULL) charge_ptr->Get_grams();
if (comp_moles > 0.0) if (comp_moles > 0.0)
{ {
comp_ptr->multiply(conc / comp_moles); comp_ptr->multiply(conc / comp_moles);
@ -4922,7 +4951,7 @@ update_kin_surface(void)
{ {
charge_ptr->multiply(kin_comp_ptr->Get_m() / grams); charge_ptr->multiply(kin_comp_ptr->Get_m() / grams);
} }
else /* need to generate from scratch */ else if (charge_ptr != NULL) /* need to generate from scratch */
{ {
charge_ptr->Set_grams(kin_comp_ptr->Get_m()); charge_ptr->Set_grams(kin_comp_ptr->Get_m());
charge_ptr->Set_charge_balance(0.0); charge_ptr->Set_charge_balance(0.0);

363
phreeqcpp/transport.cpp
View File

@ -585,7 +585,6 @@ transport(void)
if (overall_iterations > max_iter) if (overall_iterations > max_iter)
max_iter = overall_iterations; max_iter = overall_iterations;
cell_no = i; cell_no = i;
mixrun = j;
if (multi_Dflag) if (multi_Dflag)
sprintf(token, sprintf(token,
"Transport step %3d. MCDrun %3d. Cell %3d. (Max. iter %3d)", "Transport step %3d. MCDrun %3d. Cell %3d. (Max. iter %3d)",
@ -746,7 +745,6 @@ transport(void)
if (i == first_c && count_cells > 1) if (i == first_c && count_cells > 1)
kin_time /= 2; kin_time /= 2;
cell_no = i; cell_no = i;
mixrun = 0;
if (multi_Dflag) if (multi_Dflag)
sprintf(token, sprintf(token,
"Transport step %3d. MCDrun %3d. Cell %3d. (Max. iter %3d)", "Transport step %3d. MCDrun %3d. Cell %3d. (Max. iter %3d)",
@ -794,6 +792,7 @@ transport(void)
j = 1; j = 1;
for (; j <= nmix; j++) // loop on j for (; j <= nmix; j++) // loop on j
{ {
mixrun = j;
if (multi_Dflag && j == nmix && (transport_step % print_modulus == 0)) if (multi_Dflag && j == nmix && (transport_step % print_modulus == 0))
{ {
sprintf(token, sprintf(token,
@ -850,7 +849,6 @@ transport(void)
if (overall_iterations > max_iter) if (overall_iterations > max_iter)
max_iter = overall_iterations; max_iter = overall_iterations;
cell_no = i; cell_no = i;
mixrun = j;
if (multi_Dflag) if (multi_Dflag)
sprintf(token, sprintf(token,
"Transport step %3d. MCDrun %3d. Cell %3d. (Max. iter %3d)", "Transport step %3d. MCDrun %3d. Cell %3d. (Max. iter %3d)",
@ -2827,7 +2825,7 @@ diffuse_implicit(LDBLE DDt, int stagnant)
} }
current_A = current_x / DDt * F_C_MOL; current_A = current_x / DDt * F_C_MOL;
for (i = ifirst; i <= ilast + stagnant + (bcon_last == 2 ? 1 : 0); i++) for (i = ifirst; i <= ilast + stagnant + ((bcon_last == 2 || (dV_dcell && stagnant)) ? 1 : 0); i++)
{ {
if (i <= ilast + 1) if (i <= ilast + 1)
{ {
@ -2879,10 +2877,12 @@ diffuse_implicit(LDBLE DDt, int stagnant)
for (icell = if1; icell != il1; icell += incr) for (icell = if1; icell != il1; icell += incr)
{ {
min_mol = min_dif_M * ct[icell].kgw; min_mol = min_dif_M * ct[icell].kgw;
if (min_mol < 1e-13)
min_mol = 1e-13;
dum1 = dum2 = 0; dum1 = dum2 = 0;
sptr1 = Utilities::Rxn_find(Rxn_solution_map, icell); sptr1 = Utilities::Rxn_find(Rxn_solution_map, icell);
sptr2 = Utilities::Rxn_find(Rxn_solution_map, icell + 1); sptr2 = Utilities::Rxn_find(Rxn_solution_map, icell + 1);
if (stagnant) if (stagnant && mixf_stag[icell][cp])
{ {
i1 = (icell == 0 ? c1 + 1 : icell == c1 ? cc1 : icell + c1); i1 = (icell == 0 ? c1 + 1 : icell == c1 ? cc1 : icell + c1);
sptr_stag = Utilities::Rxn_find(Rxn_solution_map, i1); sptr_stag = Utilities::Rxn_find(Rxn_solution_map, i1);
@ -2890,6 +2890,13 @@ diffuse_implicit(LDBLE DDt, int stagnant)
else else
sptr_stag = NULL; sptr_stag = NULL;
//if (!cp)
//{
// ct[icell].J_ij_sum = ct[icell + 1].J_ij_sum = 0.0;
// if (sptr_stag)
// ct[i1].J_ij_sum = 0.0;
//}
if (!strcmp(ct[icell].m_s[cp].name, "H")) if (!strcmp(ct[icell].m_s[cp].name, "H"))
{ {
dummy = ct[icell].m_s[cp].tot1; dummy = ct[icell].m_s[cp].tot1;
@ -2933,7 +2940,7 @@ diffuse_implicit(LDBLE DDt, int stagnant)
} }
sptr_stag->Set_total_o(sptr_stag->Get_total_o() + dummy); sptr_stag->Set_total_o(sptr_stag->Get_total_o() + dummy);
} }
//if (cp == count_m_s - 1) // transport the charge imbalance (but doesn't improve the change of H2 or O2). //if (cp == count_m_s - 1) // transport the charge imbalance
//{ //{
// sptr1->Set_cb(sptr1->Get_cb() + ct[icell].J_ij_sum); // sptr1->Set_cb(sptr1->Get_cb() + ct[icell].J_ij_sum);
// sptr2->Set_cb(sptr2->Get_cb() + ct[icell + 1].J_ij_sum); // sptr2->Set_cb(sptr2->Get_cb() + ct[icell + 1].J_ij_sum);
@ -2942,180 +2949,166 @@ diffuse_implicit(LDBLE DDt, int stagnant)
//} //}
continue; continue;
} }
// see if icell - incr has negative moles, subtract it, so that it is canceled...
if (icell > 0 && icell <= ilast &&
(it1 = neg_moles.find(icell - incr)) != neg_moles.end()
&& (it2 = (els = it1->second).find(ct[icell].m_s[cp].name)) != els.end())
{
ct[icell].m_s[cp].tot1 += it2->second;
neg_moles.erase(it1);
els.erase(it2);
neg_moles.insert(std::make_pair(icell - incr, els));
}
dum1 = sptr1->Get_totals()[ct[icell].m_s[cp].name]; dum1 = sptr1->Get_totals()[ct[icell].m_s[cp].name];
if (!dum1) dum2 = sptr2->Get_totals()[ct[icell].m_s[cp].name];
if (sptr_stag)
dum_stag = sptr_stag->Get_totals()[ct[icell].m_s[cp].name];
// check for negative moles, add moles from other redox states and the donnan layer when necessary and available...
if (dum1 - ct[icell].m_s[cp].tot1 - ct[icell].m_s[cp].tot_stag < min_mol &&
(dV_dcell || (icell > 0 && icell <= ilast)))
{ {
dum1 = moles_from_redox_states(sptr1, ct[icell].m_s[cp].name); dum1 = moles_from_redox_states(sptr1, ct[icell].m_s[cp].name);
if (dum1) if (ct[icell].dl_s > 1e-8)
sptr1->Get_totals()[ct[icell].m_s[cp].name] = dum1;
}
dum2 = sptr2->Get_totals()[ct[icell].m_s[cp].name];
if (!dum2)
{
dum2 = moles_from_redox_states(sptr2, ct[icell].m_s[cp].name);
if (dum2)
sptr2->Get_totals()[ct[icell].m_s[cp].name] = dum2;
}
if (sptr_stag)
{
dum_stag = sptr_stag->Get_totals()[ct[icell].m_s[cp].name];
if (!dum_stag)
{
dum_stag = moles_from_redox_states(sptr_stag, ct[icell].m_s[cp].name);
if (dum_stag)
sptr_stag->Get_totals()[ct[icell].m_s[cp].name] = dum_stag;
}
}
// check for negative moles, add moles from the donnan layer when necessary and available...
if (ct[icell].m_s[cp].tot1 > dum1 &&
(dV_dcell || (icell > 0 && icell <= ilast)))
{
if (!ct[icell].dl_s)
ct[icell].m_s[cp].tot1 = dum1;
else
{ {
cxxSurface * s_ptr = Utilities::Rxn_find(Rxn_surface_map, icell); cxxSurface * s_ptr = Utilities::Rxn_find(Rxn_surface_map, icell);
if (s_ptr) if (s_ptr)
{ {
dum1 += moles_from_donnan_layer(s_ptr, ct[icell].m_s[cp].name, ct[icell].m_s[cp].tot1 - dum1 + min_mol); dum1 += moles_from_donnan_layer(s_ptr, ct[icell].m_s[cp].name, ct[icell].m_s[cp].tot1 + ct[icell].m_s[cp].tot_stag - dum1 + min_mol);
} }
} }
sptr1->Get_totals()[ct[icell].m_s[cp].name] = dum1; sptr1->Get_totals()[ct[icell].m_s[cp].name] = dum1;
if (dum1 - ct[icell].m_s[cp].tot1 - ct[icell].m_s[cp].tot_stag < min_mol)
ct[icell].m_s[cp].tot1 = dum1 - ct[icell].m_s[cp].tot_stag - min_mol;
} }
// check for negative moles, in the other cell... // check for negative moles, in the other cell...
ct[icell].m_s[cp].tot2 = ct[icell].m_s[cp].tot1; ct[icell].m_s[cp].tot2 = ct[icell].m_s[cp].tot1;
if (-ct[icell].m_s[cp].tot2 > dum2 && dum = 0;
(dV_dcell || (icell >= 0 && icell < ilast) || (icell == ilast && bcon_last == 2))) if (icell == c && sptr_stag && ct[c1].m_s[cp].tot_stag)
dum = ct[c1].m_s[cp].tot_stag;
if (dum2 + ct[icell].m_s[cp].tot2 - dum < min_mol &&
(dV_dcell || (icell >= 0 && icell <= ilast)/* || (icell == ilast && bcon_last == 2)*/))
{ {
if (!ct[icell + 1].dl_s) dum2 = moles_from_redox_states(sptr2, ct[icell].m_s[cp].name);
ct[icell].m_s[cp].tot2 = -dum2; if (ct[icell + 1].dl_s > 1e-8)
else
{ {
cxxSurface * s_ptr = Utilities::Rxn_find(Rxn_surface_map, icell + 1); cxxSurface * s_ptr = Utilities::Rxn_find(Rxn_surface_map, icell + 1);
if (s_ptr) if (s_ptr)
{ {
dum2 += moles_from_donnan_layer(s_ptr, ct[icell].m_s[cp].name, -(ct[icell].m_s[cp].tot2 + dum2 - min_mol)); dum2 += moles_from_donnan_layer(s_ptr, ct[icell].m_s[cp].name, -(ct[icell].m_s[cp].tot2 + dum2 - min_mol));
} }
sptr2->Get_totals()[ct[icell].m_s[cp].name] = dum2;
if (-ct[icell].m_s[cp].tot2 > dum2)
ct[icell].m_s[cp].tot2 = -dum2;
} }
sptr2->Get_totals()[ct[icell].m_s[cp].name] = dum2;
if (dum2 + ct[icell].m_s[cp].tot2 - dum < min_mol)
ct[icell].m_s[cp].tot2 = -dum2 + min_mol + dum;
} }
if (fabs(ct[icell].m_s[cp].tot2) < fabs(ct[icell].m_s[cp].tot1)) if (fabs(ct[icell].m_s[cp].tot2) < fabs(ct[icell].m_s[cp].tot1))
ct[icell].m_s[cp].tot1 = ct[icell].m_s[cp].tot2; ct[icell].m_s[cp].tot1 = ct[icell].m_s[cp].tot2;
if (!cp)
{
ct[icell].J_ij_sum = ct[icell + 1].J_ij_sum = 0.0;
if (sptr_stag)
ct[i1].J_ij_sum = 0.0;
}
if (dV_dcell || (icell > 0 && icell <= ilast)) if (dV_dcell || (icell > 0 && icell <= ilast))
{ {
dum1 -= ct[icell].m_s[cp].tot1; dum = ct[icell].m_s[cp].tot1;
if (sptr_stag) if (stagnant)
dum1 -= ct[icell].m_s[cp].tot_stag; dum += ct[icell].m_s[cp].tot_stag;
sptr1->Get_totals()[ct[icell].m_s[cp].name] = (dum1 > 0 ? dum1 : 0e-16); dum1 -= dum;
if (dum1 < -min_mol && incr > 0) sptr1->Get_totals()[ct[icell].m_s[cp].name] = (dum1 > 0 ? dum1 : min_mol);
if (dum1 < 0)
{ {
dum += dum1 - min_mol;
if ((it1 = neg_moles.find(icell)) != neg_moles.end()
&& (it2 = (els = it1->second).find(ct[icell].m_s[cp].name)) != els.end())
dum1 += it2->second;
els.clear(); els.clear();
els.insert(std::make_pair(ct[icell].m_s[cp].name, dum1)); els.insert(std::make_pair(ct[icell].m_s[cp].name, dum1));
neg_moles.erase(icell); neg_moles.erase(icell);
neg_moles.insert(std::make_pair(icell, els)); neg_moles.insert(std::make_pair(icell, els));
} }
else //ct[icell].J_ij_sum -= dum * ct[icell].m_s[cp].charge;
ct[icell].J_ij_sum += dum1 * ct[icell].m_s[cp].charge;
} }
if (dV_dcell || (icell >= 0 && icell < ilast) || (icell == ilast && bcon_last == 2)) if (dV_dcell || (icell >= 0 && icell < ilast)/* || (icell == ilast && bcon_last == 2)*/)
{ {
dum2 += ct[icell].m_s[cp].tot1; dum = ct[icell].m_s[cp].tot1;
sptr2->Get_totals()[ct[icell].m_s[cp].name] = (dum2 > 0 ? dum2 : 0e-16); if (stagnant && icell == c && dV_dcell)
if (dum2 < -min_mol && incr < 0) dum -= ct[c1].m_s[cp].tot_stag;
dum2 += dum;
sptr2->Get_totals()[ct[icell].m_s[cp].name] = (dum2 > 0 ? dum2 : min_mol);
if (dum2 < 0)
{ {
dum -= dum2 - min_mol;
if ((it1 = neg_moles.find(icell + 1)) != neg_moles.end()
&& (it2 = (els = it1->second).find(ct[icell].m_s[cp].name)) != els.end())
dum2 += it2->second;
els.clear(); els.clear();
els.insert(std::make_pair(ct[icell].m_s[cp].name, dum2)); els.insert(std::make_pair(ct[icell].m_s[cp].name, dum2));
neg_moles.erase(icell + 1); neg_moles.erase(icell + 1);
neg_moles.insert(std::make_pair(icell + 1, els)); neg_moles.insert(std::make_pair(icell + 1, els));
} }
else //ct[icell + 1].J_ij_sum += dum * ct[icell].m_s[cp].charge;
ct[icell + 1].J_ij_sum += dum2 * ct[icell].m_s[cp].charge;
} }
if (sptr_stag) if (sptr_stag)
{ {
if ((it1 = neg_moles.find(i1)) != neg_moles.end() dum = ct[icell].m_s[cp].tot_stag;
&& (it2 = (els = it1->second).find(ct[icell].m_s[cp].name)) != els.end())
{
ct[icell].m_s[cp].tot_stag += it2->second;
// the negative moles are canceled...
neg_moles.erase(it1);
els.erase(it2);
neg_moles.insert(std::make_pair(i1, els));
}
dummy = ct[icell].m_s[cp].tot_stag;
if (icell == c) if (icell == c)
dum += ct[c1].m_s[cp].tot_stag;
if (dum_stag + dum < 0)
{ {
if (dV_dcell) dum_stag = moles_from_redox_states(sptr_stag, ct[icell].m_s[cp].name);
{
if ((dum = sptr2->Get_totals()[ct[icell + 1].m_s[cp].name] - ct[icell + 1].m_s[cp].tot_stag) > 0)
{
sptr2->Get_totals()[ct[icell].m_s[cp].name] = dum;
dummy += ct[icell + 1].m_s[cp].tot_stag;
}
else
{
dummy += sptr2->Get_totals()[ct[icell].m_s[cp].name];
sptr2->Get_totals()[ct[icell].m_s[cp].name] = 0.0;
if (dum < -min_mol)
{
els.clear();
els.insert(std::make_pair(ct[icell].m_s[cp].name, dum));
neg_moles.erase(icell);
neg_moles.insert(std::make_pair(icell, els));
}
}
}
else
dummy += ct[icell + 1].m_s[cp].tot_stag;
}
if (-dummy > dum_stag)
{
if (ct[i1].dl_s) if (ct[i1].dl_s)
{ {
cxxSurface * s_ptr = Utilities::Rxn_find(Rxn_surface_map, i1); cxxSurface * s_ptr = Utilities::Rxn_find(Rxn_surface_map, i1);
if (s_ptr) if (s_ptr)
{ {
dum_stag += moles_from_donnan_layer(s_ptr, ct[icell].m_s[cp].name, -(dummy + dum_stag - min_mol)); dum_stag += moles_from_donnan_layer(s_ptr, ct[icell].m_s[cp].name, -(dum + dum_stag - min_mol));
} }
sptr_stag->Get_totals()[ct[icell].m_s[cp].name] = dum_stag; sptr_stag->Get_totals()[ct[icell].m_s[cp].name] = dum_stag;
} }
} }
dum_stag += dummy; dum_stag += dum;
sptr_stag->Get_totals()[ct[icell].m_s[cp].name] = (dum_stag > 0 ? dum_stag : 0e-16); sptr_stag->Get_totals()[ct[icell].m_s[cp].name] = (dum_stag > 0 ? dum_stag : min_mol);
if (dum_stag < -min_mol) if (dum_stag < 0)
{ {
dum -= dum_stag - min_mol;
if ((it1 = neg_moles.find(i1)) != neg_moles.end()
&& (it2 = (els = it1->second).find(ct[icell].m_s[cp].name)) != els.end())
dum_stag += it2->second;
els.clear(); els.clear();
els.insert(std::make_pair(ct[icell].m_s[cp].name, dum_stag)); els.insert(std::make_pair(ct[icell].m_s[cp].name, dum_stag));
neg_moles.erase(i1); neg_moles.erase(i1);
neg_moles.insert(std::make_pair(i1, els)); neg_moles.insert(std::make_pair(i1, els));
} }
else //ct[i1].J_ij_sum += dum * ct[icell].m_s[cp].charge;
ct[i1].J_ij_sum += dum_stag * ct[icell].m_s[cp].charge;
} }
//if (cp == count_m_s - 1)
// reduce oscillations in the column-boundary cells, but not for H and O, and current_A is not adjusted...
if (icell == il1 - incr && dV_dcell * ct[0].m_s[cp].charge < 0 && strcmp(ct[0].m_s[cp].name, "H") && strcmp(ct[0].m_s[cp].name, "O") && c > 3 && mixrun > 1)
{
dummy = Utilities::Rxn_find(Rxn_solution_map, 0)->Get_totals()[ct[0].m_s[cp].name] / ct[0].kgw * (1 - ct[0].dl_s);
if (dummy > 1e-6)
{
sptr1 = Utilities::Rxn_find(Rxn_solution_map, 1);
sptr2 = Utilities::Rxn_find(Rxn_solution_map, 2);
dum1 = sptr1->Get_totals()[ct[0].m_s[cp].name] / ct[1].kgw * (1 - ct[1].dl_s) - dummy;
dum2 = sptr2->Get_totals()[ct[0].m_s[cp].name] / ct[2].kgw * (1 - ct[2].dl_s) - dummy;
if (dum1 / dum2 < 0 || dum1 / dum2 > 1)
{
dum = cell_data[1].mid_cell_x / cell_data[2].mid_cell_x;
//ct[1].J_ij_sum -= sptr1->Get_totals()[ct[0].m_s[cp].name] * ct[1].m_s[cp].charge;
dum1 = (dummy + dum * dum2) * ct[1].kgw / (1 - ct[1].dl_s);
sptr1->Get_totals()[ct[0].m_s[cp].name] = dum1;
//ct[1].J_ij_sum += dum1 * ct[1].m_s[cp].charge;
}
}
dummy = Utilities::Rxn_find(Rxn_solution_map, c1)->Get_totals()[ct[0].m_s[cp].name] / ct[c1].kgw * (1 - ct[c1].dl_s);
if (dummy > 1e-6)
{
sptr1 = Utilities::Rxn_find(Rxn_solution_map, c);
sptr2 = Utilities::Rxn_find(Rxn_solution_map, c_1);
dum1 = sptr1->Get_totals()[ct[0].m_s[cp].name] / ct[c].kgw * (1 - ct[c].dl_s) - dummy;
dum2 = sptr2->Get_totals()[ct[0].m_s[cp].name] / ct[c_1].kgw * (1 - ct[c_1].dl_s) - dummy;
if (dum1 / dum2 < 0 || dum1 / dum2 > 1)
{
dum = (cell_data[c].mid_cell_x - cell_data[c_1].mid_cell_x) /
(cell_data[c1].mid_cell_x - cell_data[c_1].mid_cell_x);
//ct[c].J_ij_sum -= sptr1->Get_totals()[ct[0].m_s[cp].name] * ct[c].m_s[cp].charge;
dum1 = (dummy + (1 - dum) * dum2) * ct[c].kgw / (1 - ct[c].dl_s);
sptr1->Get_totals()[ct[0].m_s[cp].name] = dum1;
//ct[c].J_ij_sum += dum1 * ct[c].m_s[cp].charge;
}
}
}
//if (cp == count_m_s - 1)
//{ //{
// sptr1->Set_cb(sptr1->Get_cb() + ct[icell].J_ij_sum); // sptr1->Set_cb(sptr1->Get_cb() + ct[icell].J_ij_sum);
// sptr2->Set_cb(sptr2->Get_cb() + ct[icell + 1].J_ij_sum); // sptr2->Set_cb(sptr2->Get_cb() + ct[icell + 1].J_ij_sum);
@ -3664,6 +3657,46 @@ fill_m_s(struct J_ij *l_J_ij, int l_J_ij_count_spec, int icell, int stagnant)
} }
return (OK); return (OK);
} }
/* ---------------------------------------------------------------------- */
void Phreeqc::
calc_b_ij(int icell, int jcell, int k, LDBLE b_i, LDBLE b_j, LDBLE g_i, LDBLE g_j, LDBLE free_i, LDBLE free_j, int stagnant)
/* ---------------------------------------------------------------------- */
{
ct[icell].v_m[k].b_ij = b_i * (free_i + g_i) * b_j * (free_j + g_j) / (b_i * (free_i + g_i) + b_j * (free_j + g_j));
// At filterends, concentrations of ions change step-wise to the DL.
// We take the harmonic mean for f_free, the average for the DL.
if (ct[icell].v_m[k].z)
{
if (!g_i && g_j)
{
ct[icell].v_m[k].b_ij = free_j * b_i * b_j / (b_i + b_j) +
b_i * (1 - free_j) / 4 + b_j * g_j / 4;
}
else if (g_i && !g_j)
ct[icell].v_m[k].b_ij = free_i * b_i * b_j / (b_i + b_j) +
b_j * (1 - free_i) / 4 + b_i * g_i / 4;
}
// for boundary cells...
if (stagnant > 1)
{ /* for a diffusion experiment with well-mixed reservoir in cell 3 and the last stagnant cell,
and with the mixf * 2 for the boundary cells in the input... */
if (icell == 3 && !g_i && g_j)
ct[icell].v_m[k].b_ij = b_j * (free_j + g_j) / 2;
else if (jcell == all_cells - 1 && !g_j && g_i)
ct[icell].v_m[k].b_ij = b_i * (free_i + g_i) / 2;
}
else
{
if (icell == 0 || (icell == count_cells + 1 && jcell == count_cells + count_cells + 1))
ct[icell].v_m[k].b_ij = b_j * (free_j + g_j);
else if (icell == count_cells && jcell == count_cells + 1)
ct[icell].v_m[k].b_ij = b_i * (free_i + g_i);
}
if (ct[icell].v_m[k].z)
ct[icell].Dz2c += ct[icell].v_m[k].b_ij * ct[icell].v_m[k].zc * ct[icell].v_m[k].z;
return;
}
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
LDBLE Phreeqc:: LDBLE Phreeqc::
find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant) find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
@ -3848,7 +3881,11 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
if (dl_aq1 > 0) if (dl_aq1 > 0)
ct[icell].dl_s = dl_aq1 / t_aq1; ct[icell].dl_s = dl_aq1 / t_aq1;
if (dl_aq2 > 0) if (dl_aq2 > 0)
ct[icell].dl_s = ct[jcell].dl_s = dl_aq2 / t_aq2; {
ct[jcell].dl_s = dl_aq2 / t_aq2;
if (!ct[icell].dl_s)
ct[icell].dl_s = 1e-8; // used in implicit appt
}
if (il_calcs) if (il_calcs)
{ {
@ -4142,7 +4179,7 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
g_j += it_sc->Get_z_gMCD_map()[ct[icell].v_m[k].z]; g_j += it_sc->Get_z_gMCD_map()[ct[icell].v_m[k].z];
else else
{ {
dum1 = it_sc->Get_mass_water() / mass_water_bulk_x; dum1 = it_sc->Get_mass_water() / t_aq2;
dum2 = it_sc->Get_z_gMCD_map()[1] / dum1; dum2 = it_sc->Get_z_gMCD_map()[1] / dum1;
g_j += pow(dum2, ct[icell].v_m[k].z) * dum1; g_j += pow(dum2, ct[icell].v_m[k].z) * dum1;
} }
@ -4152,32 +4189,18 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
} }
} }
b_i = A1 * sol_D[icell].spec[i].Dwt * (f_free_i + g_i / ct[icell].visc1); b_i = A1 * sol_D[icell].spec[i].Dwt;
b_j = A2 * (f_free_j + g_j / ct[icell].visc2); b_j = A2;
if (icell == count_cells && !stagnant) if (sol_D[icell].tk_x == sol_D[jcell].tk_x)
ct[icell].v_m[k].b_ij = b_i; b_j *= sol_D[icell].spec[i].Dwt;
else if (icell == all_cells - 1 && stagnant)
ct[icell].v_m[k].b_ij = b_i / 2; /* with the mixf *= 2 for this 'reservoir' cell in the input */
else else
{ {
if (sol_D[icell].tk_x == sol_D[jcell].tk_x) dum2 = sol_D[icell].spec[i].Dwt / sol_D[icell].viscos_f;
b_j *= sol_D[icell].spec[i].Dwt; dum2 *= exp(sol_D[icell].spec[i].dw_t / sol_D[jcell].tk_x - sol_D[icell].spec[i].dw_t / sol_D[icell].tk_x);
else dum2 *= sol_D[jcell].viscos_f;
{ b_j *= dum2;
dum2 = sol_D[icell].spec[i].Dwt / sol_D[icell].viscos_f;
dum2 *= exp(sol_D[icell].spec[i].dw_t / sol_D[jcell].tk_x - sol_D[icell].spec[i].dw_t / sol_D[icell].tk_x);
dum2 *= sol_D[jcell].viscos_f;
b_j *= dum2;
}
ct[icell].v_m[k].b_ij = b_i * b_j / (b_i + b_j);
if (icell == 0 && !stagnant)
ct[icell].v_m[k].b_ij = b_j;
else if (icell == 3 && stagnant && !g_i && g_j)
ct[icell].v_m[k].b_ij = b_j / 2; /* with the mixf *= 2 for stagnant cell 3 in the input */
} }
calc_b_ij(icell, jcell, k, b_i, b_j, g_i, g_j, f_free_i, f_free_j, stagnant);
if (ct[icell].v_m[k].z)
ct[icell].Dz2c += ct[icell].v_m[k].b_ij * ct[icell].v_m[k].zc * ct[icell].v_m[k].z;
k++; k++;
} }
@ -4249,7 +4272,7 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
g_i += it_sc->Get_z_gMCD_map()[ct[icell].v_m[k].z]; g_i += it_sc->Get_z_gMCD_map()[ct[icell].v_m[k].z];
else else
{ {
dum1 = it_sc->Get_mass_water() / mass_water_bulk_x; dum1 = it_sc->Get_mass_water() / t_aq1;
dum2 = it_sc->Get_z_gMCD_map()[1] / dum1; dum2 = it_sc->Get_z_gMCD_map()[1] / dum1;
g_i += pow(dum2, ct[icell].v_m[k].z) * dum1; g_i += pow(dum2, ct[icell].v_m[k].z) * dum1;
} }
@ -4266,31 +4289,18 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
g_j *= sol_D[jcell].spec[j].erm_ddl; g_j *= sol_D[jcell].spec[j].erm_ddl;
} }
} }
b_i = A1 * (f_free_i + g_i / ct[icell].visc1); b_i = A1;
b_j = A2 * sol_D[jcell].spec[j].Dwt * (f_free_j + g_j / ct[icell].visc2); b_j = A2 * sol_D[jcell].spec[j].Dwt;
if (icell == 0 && !stagnant) if (sol_D[icell].tk_x == sol_D[jcell].tk_x)
ct[icell].v_m[k].b_ij = b_j; b_i *= sol_D[jcell].spec[j].Dwt;
else if (icell == 3 && stagnant && g_j && !g_i)
ct[icell].v_m[k].b_ij = b_j / 2; /* with the mixf *= 2 for 'reservoir' cell 3 in the input */
else else
{ {
if (sol_D[icell].tk_x == sol_D[jcell].tk_x) dum2 = sol_D[jcell].spec[j].Dwt / sol_D[jcell].viscos_f;
b_i *= sol_D[jcell].spec[j].Dwt; dum2 *= exp(sol_D[jcell].spec[j].dw_t / sol_D[icell].tk_x - sol_D[jcell].spec[j].dw_t / sol_D[jcell].tk_x);
else dum2 *= sol_D[icell].viscos_f;
{ b_i *= dum2;
dum2 = sol_D[jcell].spec[j].Dwt / sol_D[jcell].viscos_f;
dum2 *= exp(sol_D[jcell].spec[j].dw_t / sol_D[icell].tk_x - sol_D[jcell].spec[j].dw_t / sol_D[jcell].tk_x);
dum2 *= sol_D[icell].viscos_f;
b_i *= dum2;
}
ct[icell].v_m[k].b_ij = b_i * b_j / (b_i + b_j);
if (icell == count_cells && !stagnant)
ct[icell].v_m[k].b_ij = b_i;
else if (jcell == all_cells - 1 && stagnant && !g_j && g_i)
ct[icell].v_m[k].b_ij = b_i / 2; /* with the mixf * 2 for this 'reservoir' cell in the input */
} }
if (ct[icell].v_m[k].z) calc_b_ij(icell, jcell, k, b_i, b_j, g_i, g_j, f_free_i, f_free_j, stagnant);
ct[icell].Dz2c += ct[icell].v_m[k].b_ij * ct[icell].v_m[k].zc * ct[icell].v_m[k].z;
k++; k++;
} }
@ -4373,28 +4383,9 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
g_j *= sol_D[jcell].spec[j].erm_ddl; g_j *= sol_D[jcell].spec[j].erm_ddl;
} }
} }
b_i = A1 * sol_D[icell].spec[i].Dwt * (f_free_i + g_i / ct[icell].visc1); b_i = A1 * sol_D[icell].spec[i].Dwt;
b_j = A2 * sol_D[jcell].spec[j].Dwt * (f_free_j + g_j / ct[icell].visc2); b_j = A2 * sol_D[jcell].spec[j].Dwt;
ct[icell].v_m[k].b_ij = b_i * b_j / (b_i + b_j); calc_b_ij(icell, jcell, k, b_i, b_j, g_i, g_j, f_free_i, f_free_j, stagnant);
// but for boundary cells...
if (stagnant > 1)
{ /* for a diffusion experiment with well-mixed reservoir in cell 3 and the last stagnant cell,
and with the mixf * 2 for the boundary cells in the input... */
if (icell == 3 && !g_i && g_j)
ct[icell].v_m[k].b_ij = b_j / 2;
else if (jcell == all_cells - 1 && !g_j && g_i)
ct[icell].v_m[k].b_ij = b_i / 2;
}
else
{
if (icell == 0 || (icell == count_cells + 1 && jcell == count_cells + count_cells + 1))
ct[icell].v_m[k].b_ij = b_j;
else if (icell == count_cells && jcell == count_cells + 1)
ct[icell].v_m[k].b_ij = b_i;
}
if (ct[icell].v_m[k].z)
ct[icell].Dz2c += ct[icell].v_m[k].b_ij * ct[icell].v_m[k].zc * ct[icell].v_m[k].z;
//ddlm = sol_D[jcell].spec[j].lm - sol_D[icell].spec[i].lm; // appt: this could give an incorrect large factor for implicit //ddlm = sol_D[jcell].spec[j].lm - sol_D[icell].spec[i].lm; // appt: this could give an incorrect large factor for implicit
//if (fabs(ddlm) > 1e-10) //if (fabs(ddlm) > 1e-10)