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Merge commit '5c53fb207238bc0e846123a7e0d71a48bd9976ab'

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This commit is contained in:
Scott R Charlton 2019-06-17 17:34:25 -06:00
commit 8412823930
2 changed files with 25 additions and 6 deletions
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2
phreeqcpp/Phreeqc.cpp
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@ -1689,6 +1689,8 @@ Phreeqc::InternalCopy(const Phreeqc *pSrc)
max_cells = pSrc->max_cells;
multi_Dflag = pSrc->multi_Dflag;
interlayer_Dflag = pSrc->interlayer_Dflag;
implicit = pSrc->implicit;
max_mixf = pSrc->max_mixf;
default_Dw = pSrc->default_Dw;
correct_Dw = pSrc->correct_Dw;
multi_Dpor = pSrc->multi_Dpor;

29
phreeqcpp/transport.cpp
View File

@ -20,7 +20,8 @@ std::set <std::string> dif_spec_names;
std::set <std::string> dif_els_names;
std::map<int, std::map<std::string, double> > neg_moles;
std::map<std::string, double> els;
double *y, *Ct1, *Ct2, *l_tk_x2, **A, **mixf, mixf_comp_size = 0;
double *y, *Ct1, *Ct2, *l_tk_x2, **A, **mixf;
int mixf_comp_size = 0;
struct CURRENT_CELLS
{
@ -263,6 +264,13 @@ transport(void)
"Implicit diffusion needs diffusion coefficients for individual species. Please add -multi_d true");
error_msg(error_string, CONTINUE);
}
if (implicit && !timest)
{
error_string = sformatf(
"Time step not defined for diffusion, using -time_step 1 # seconds");
warning_msg(error_string);
timest = 1;
}
if (implicit && current_cells == NULL)
{
current_cells = (struct CURRENT_CELLS *) PHRQ_malloc((size_t)
@ -2267,13 +2275,22 @@ diffuse_implicit(LDBLE max_mixf, LDBLE DDt, int stagnant)
}
}
if (mixf == NULL)
{
mixf = (LDBLE **)PHRQ_malloc((size_t)(count_cells + 2) * sizeof(LDBLE *));
if (mixf == NULL) malloc_error();
if (mixf == NULL) malloc_error();
for (i = 0; i < count_cells + 2; i++)
{
mixf[i] = NULL;
}
}
if (comp + 2 > mixf_comp_size)
{
for (i = 0; i < count_cells + 2; i++)
{
mixf[i] = (LDBLE *)PHRQ_malloc((size_t)(comp + 2) * sizeof(LDBLE));
if (mixf[i] == NULL)
mixf[i] = (LDBLE *)PHRQ_malloc((size_t)(comp + 2) * sizeof(LDBLE));
else
mixf[i] = (LDBLE *)PHRQ_realloc(mixf[i], (size_t)(comp + 2) * sizeof(LDBLE));
if (mixf[i] == NULL) malloc_error();
mixf_comp_size = comp + 2;
}
@ -2572,7 +2589,7 @@ diffuse_implicit(LDBLE max_mixf, LDBLE DDt, int stagnant)
}
for (icell = if1; icell != il1; icell += incr)
{
min_mol = 1e-12 * ct[i].kgw;
min_mol = 1e-12 * ct[icell].kgw;
if (fabs(ct[icell].m_s[cp].tot1) < min_mol)
continue;
dum1 = dum2 = 0;
@ -3120,7 +3137,7 @@ fill_m_s(struct J_ij *l_J_ij, int l_J_ij_count_spec, int icell, int stagnant)
for (j = 0; j < l_J_ij_count_spec; j++)
{
if (abs(l_J_ij[j].tot1) < 1e-15)
if (fabs(l_J_ij[j].tot1) < 1e-15)
continue;
{
char * temp_name = string_duplicate(l_J_ij[j].name);
@ -3869,7 +3886,7 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
dum2 = (cell_data[jcell].potV - cell_data[icell].potV) / ((cell_data[jcell].length + cell_data[icell].length) / 2);
dum2 *= F_Re3 / tk_x2 * ct[icell].v_m[k].z * (c1 + c2);
// don't transport unavailable moles against the gradient
if (abs(dum) < abs(dum2) &&
if (fabs(dum) < fabs(dum2) &&
((dum2 >= 0 && sol_D[jcell].spec[j].c * aq2 < 1e-12) ||
(dum2 <= 0 && sol_D[icell].spec[i].c * aq1 < 1e-12)))
{