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Squashed 'phreeqcpp/' changes from e317dd0..7c7fafd

Browse Source 
7c7fafd Merge pull request #78 from dlparkhurst/mix_error
eb0591c Merge pull request #74 from mwtoews/fix-typos
334df5e Tony's fix in heat transport
bf897a2 Marked old error in mix. Updated test case.
58566a6 Fix ah2o in adding a solution. Fixed bad_graph database.
75effd0 Merge branch 'viscosity' into mix_error
f4708df account for water mass in addition to mixing fractions
70954c6 mixing by water mass times mixing fraction
84b59ab Fix typos

git-subtree-dir: phreeqcpp
git-subtree-split: 7c7fafd686d7c41753132a978a1d55d4d25b601b
This commit is contained in:
Darth Vader 2024-10-08 20:04:33 +00:00
parent c155685f63
commit b537589773
27 changed files with 131 additions and 51 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
Form1.h
View File

@ -673,7 +673,7 @@ namespace zdg_ui2 {
// Respond to a Zoom Event
void MyZoomEvent( ZedGraphControl ^control, ZoomState ^oldState, ZoomState ^newState )
{
// Here we get notification everytime the user zooms
// Here we get notification every time the user zooms
}
void SetChartOptions( System::Object ^sender, System::EventArgs ^e )
{

2
Makefile.old
View File

@ -4,7 +4,7 @@
# Release
# Debug
#
# Serial verisons: Release Debug
# Serial versions: Release Debug
#
# Makefile sets CFG variable, cd's to appropriate directory, runs Makefile recursively
# Recursive make sets appropriate compiler, objects, options, libraries, and compiles PHREEQC

8
PBasic.cpp
View File

@ -2441,8 +2441,8 @@ factor(struct LOC_exec * LINK)
require(tokcomma, LINK);
varrec* area_varrec = LINK->t->UU.vp;
if (LINK->t->kind != tokvar || area_varrec->stringvar != 0)
snerr(": Missing or wrong type area varaiable.");
// varaiable for thickness
snerr(": Missing or wrong type area variable.");
// variable for thickness
LINK->t = LINK->t->next;
require(tokcomma, LINK);
varrec* thickness_varrec = LINK->t->UU.vp;
@ -5595,7 +5595,7 @@ cmdput(struct LOC_exec *LINK)
/* get parentheses */
require(toklp, LINK);
/* get first argumen */
/* get first argument */
double value = realexpr(LINK);
for (;;)
@ -5628,7 +5628,7 @@ cmdput_(struct LOC_exec* LINK)
/* get parentheses */
require(toklp, LINK);
/* get first argumen */
/* get first argument */
char* str = strexpr(LINK);
std::string s_value = str;
PhreeqcPtr->PHRQ_free(str);

2
Phreeqc.cpp
View File

@ -1966,7 +1966,7 @@ Phreeqc::InternalCopy(const Phreeqc* pSrc)
//count_tally_table_rows = 0;
/* transport.cpp ------------------------------- */
/* storage is created and freed in tranport.cpp */
/* storage is created and freed in transport.cpp */
sol_D = NULL;
sol_D_dbg = NULL;
J_ij = NULL;

2
Solution.cxx
View File

@ -1409,7 +1409,7 @@ cxxSolution::add(const cxxSolution & addee, LDBLE extensive)
this->ph = f1 * this->ph + f2 * addee.ph;
this->pe = f1 * this->pe + f2 * addee.pe;
this->mu = f1 * this->mu + f2 * addee.mu;
this->ah2o = f1 * this->mu + f2 * addee.ah2o;
this->ah2o = f1 * this->ah2o + f2 * addee.ah2o;
this->total_h += addee.total_h * extensive;
this->total_o += addee.total_o * extensive;
this->cb += addee.cb * extensive;

2
cl1.cpp
View File

@ -460,7 +460,7 @@ cl1(int k, int l, int m, int n,
#endif
if (kk < 0)
{
/* no positive value found in L340 or bypass intermediate verticies */
/* no positive value found in L340 or bypass intermediate vertices */
*l_kode = 2;
goto L590;
}

2
cl1mp.cpp
View File

@ -603,7 +603,7 @@ cl1mp(int k, int l, int m, int n,
#endif
if (kk < 0)
{
/* no positive value found in L340 or bypass intermediate verticies */
/* no positive value found in L340 or bypass intermediate vertices */
*kode = 2;
goto L590;
}

2
common/Parser.h
View File

@ -83,7 +83,7 @@ class CParser: public PHRQ_base
Arguments:
string Input, character string used in printing error message
allow_empty Input, True or false, if a blank line is accepable
allow_empty Input, True or false, if a blank line is acceptable
if false, another line is read
allow_eof Input, True or false, if EOF is acceptable
allow_keyword Input, True or false, if a keyword is acceptable

2
common/Utils.cxx
View File

@ -155,7 +155,7 @@ Utilities::convert_time(double t, std::string in, std::string out)
{
t = t * 3600. * 24. * 365.25;
}
// convert to ouput units
// convert to output units
if (out.substr(0,1) == "m")
{
t = t / 60.;

8
cvode.cpp
View File

@ -1672,7 +1672,7 @@ CVEwtSet(CVodeMem cv_mem, N_Vector ycur)
/*********************** CVEwtSetSS *********************************
This routine sets ewt as decribed above in the case tol_type = SS.
This routine sets ewt as described above in the case tol_type = SS.
It tests for non-positive components before inverting. CVEwtSetSS
returns TRUE if ewt is successfully set to a positive vector
and FALSE otherwise. In the latter case, ewt is considered
@ -1698,7 +1698,7 @@ CVEwtSetSS(CVodeMem cv_mem, N_Vector ycur)
/*********************** CVEwtSetSV *********************************
This routine sets ewt as decribed above in the case tol_type = SV.
This routine sets ewt as described above in the case tol_type = SV.
It tests for non-positive components before inverting. CVEwtSetSV
returns TRUE if ewt is successfully set to a positive vector
and FALSE otherwise. In the latter case, ewt is considered
@ -3249,7 +3249,7 @@ static void
CVSetEta(CVodeMem cv_mem)
{
/* If eta below the threshhold THRESH, reject a change of step size */
/* If eta below the threshold THRESH, reject a change of step size */
if (eta < THRESH)
{
eta = ONE;
@ -3320,7 +3320,7 @@ CVComputeEtaqp1(CVodeMem cv_mem)
corresponding value of q. If there is a tie, the preference
order is to (1) keep the same order, then (2) decrease the order,
and finally (3) increase the order. If the maximum eta value
is below the threshhold THRESH, the order is kept unchanged and
is below the threshold THRESH, the order is kept unchanged and
eta is set to 1.
******************************************************************/

4
global_structures.h
View File

@ -109,7 +109,7 @@
#define TRANSPORT 8
#define PHAST 9
/* constaints in mass balance */
/* constants in mass balance */
#define EITHER 0
#define DISSOLVE 1
#define PRECIPITATE -1
@ -981,7 +981,7 @@ public:
alk = 0;
// default gfw for species
gfw = 1;
// formula from which to calcuate gfw
// formula from which to calculate gfw
gfw_formula = NULL;
// pointer to unknown structure
unknown = NULL;

2
input.cpp
View File

@ -55,7 +55,7 @@ check_line_impl(const char *string, int allow_empty, int allow_eof,
*
* Arguments:
* string Input, character string used in printing error message
* allow_empty Input, True or false, if a blank line is accepable
* allow_empty Input, True or false, if a blank line is acceptable
* if false, another line is read
* allow_eof Input, True or false, if EOF is acceptable
* allow_keyword Input, True or false, if a keyword is acceptable

2
inverse.cpp
View File

@ -74,7 +74,7 @@ inverse_models(void)
fprintf(netpath_file, "2.14 # File format\n");
}
/*
* Fill in stucture "use".
* Fill in structure "use".
*/
use.Set_inverse_in(true);
use.Set_inverse_ptr(&inverse[n]);

2
mainsubs.cpp
View File

@ -931,7 +931,7 @@ saver(void)
/* ---------------------------------------------------------------------- */
{
/*
* Save results of calcuations (data in variables with _x,
* Save results of calculations (data in variables with _x,
* in unknown structure x, in master, or s) into structure
* arrays. Structure "save" has info on whether to save
* data for each entity (solution, ex, surf, pp, gas, or s_s).

2
model.cpp
View File

@ -1964,7 +1964,7 @@ jacobian_sums(void)
*sum_jacob2[k].target += *sum_jacob2[k].source * sum_jacob2[k].coef;
}
/*
* Make final adustments to jacobian array
* Make final adjustments to jacobian array
*/
/*
* Ionic strength

2
nvector_serial.cpp
View File

@ -12,7 +12,7 @@
*------------------------------------------------------------------------*
* This is the implementation file for a serial implementation *
* of the NVECTOR package. It contains the implementation of *
* the serial machine environment intialization and free *
* the serial machine environment initialization and free *
* routines (and of the Fortran callable interfaces to them) *
* and of the N_Vector kernels listed in nvector_serial.h. *
* *

2
nvector_serial.h
View File

@ -107,7 +107,7 @@
/****************************************************************
* PART I: *
* Serial implementaion of M_Env and N_Vector *
* Serial implementation of M_Env and N_Vector *
****************************************************************/
/* The serial implementation of the machine environment has

2
pitzer.cpp
View File

@ -737,7 +737,7 @@ PTEMP(LDBLE TK)
{
/*
C
C SUBROUTINE TO CALUCLATE TEMPERATURE DEPENDENCE OF PITZER PARAMETER
C SUBROUTINE TO CALCULATE TEMPERATURE DEPENDENCE OF PITZER PARAMETER
C
*/
LDBLE TR = 298.15;

4
prep.cpp
View File

@ -674,7 +674,7 @@ build_ss_assemblage(void)
/* include mole fraction */
store_mb(&(x[i]->phase->log10_fraction_x), &(x[i]->f), 1.0);
/* include activity coeficient */
/* include activity coefficient */
store_mb(&(x[i]->phase->log10_lambda), &(x[i]->f), 1.0);
/*
* Put coefficients into mass action equations
@ -4478,7 +4478,7 @@ setup_solution(void)
(ph_unknown == charge_balance_unknown)
&& (alkalinity_unknown != NULL))
{
error_msg("pH adustment cannot attain charge balance"
error_msg("pH adjustment cannot attain charge balance"
" when alkalinity is fixed.", CONTINUE);
input_error++;
}

4
read.cpp
View File

@ -7477,7 +7477,7 @@ read_title(void)
}
/*
* Read additonal lines
* Read additional lines
*/
for (;;)
{
@ -9161,7 +9161,7 @@ read_solid_solutions(void)
if (j != 1)
{
error_string = sformatf(
"Expected temperature (Celcius) for parameters, assemblage %d, solid solution %s, using 25 C",
"Expected temperature (Celsius) for parameters, assemblage %d, solid solution %s, using 25 C",
n_user,
ss_ptr->Get_name().c_str());
warning_msg(error_string);

2
sit.cpp
View File

@ -1586,7 +1586,7 @@ PTEMP_SIT(LDBLE TK)
{
/*
C
C SUBROUTINE TO CALUCLATE TEMPERATURE DEPENDENCE OF PITZER PARAMETER
C SUBROUTINE TO CALCULATE TEMPERATURE DEPENDENCE OF PITZER PARAMETER
C
*/
LDBLE TR = 298.15;

83
step.cpp
View File

@ -620,10 +620,86 @@ add_mix(cxxMix *mix_ptr)
* and other variables.
*/
LDBLE sum_fractions, intensive, extensive;
LDBLE sum_fractions_water=0, sum_positive_water=0, intensive_water=0, extensive_water=0;
cxxSolution *solution_ptr;
int count_positive;
LDBLE sum_positive;
if (mix_ptr == NULL)
return (OK);
if (mix_ptr->Get_mixComps().size() == 0)
return (OK);
sum_fractions = 0.0;
sum_positive = 0.0;
count_positive = 0;
std::map<int, LDBLE>::const_iterator it;
for (it = mix_ptr->Get_mixComps().begin(); it != mix_ptr->Get_mixComps().end(); it++)
{
solution_ptr = Utilities::Rxn_find(Rxn_solution_map, it->first);
if (solution_ptr == NULL)
{
error_string = sformatf("Mix solution not found, %d.",
it->first);
error_msg(error_string, CONTINUE);
input_error++;
continue;
}
sum_fractions += it->second;
sum_fractions_water += it->second * solution_ptr->Get_mass_water();
if (it->second > 0)
{
sum_positive += it->second;
sum_positive_water += it->second * solution_ptr->Get_mass_water();
count_positive++;
}
}
for (it = mix_ptr->Get_mixComps().begin(); it != mix_ptr->Get_mixComps().end(); it++)
{
solution_ptr = Utilities::Rxn_find(Rxn_solution_map, it->first);
if (solution_ptr == NULL)
{
error_string = sformatf( "Mix solution not found, %d.",
it->first);
error_msg(error_string, CONTINUE);
input_error++;
continue;
}
extensive = it->second;
extensive_water = it->second * solution_ptr->Get_mass_water();
intensive = extensive / sum_fractions;
intensive_water = extensive_water / sum_fractions_water;
if (count_positive < (int) mix_ptr->Get_mixComps().size())
{
if (it->second > 0)
{
intensive = extensive / sum_positive;
intensive_water = extensive_water / sum_positive;
}
else
{
intensive = 0;
}
}
add_solution(solution_ptr, extensive, intensive_water);
}
return (OK);
}
#ifdef SKIP_ERROR
/* ---------------------------------------------------------------------- */
int Phreeqc::
add_mix(cxxMix* mix_ptr)
/* ---------------------------------------------------------------------- */
{
/*
* calls add_solution to accumulate all data in master->totals
* and other variables.
*/
LDBLE sum_fractions, intensive, extensive;
cxxSolution* solution_ptr;
int count_positive;
LDBLE sum_positive;
if (mix_ptr == NULL)
return (OK);
if (mix_ptr->Get_mixComps().size() == 0)
@ -646,15 +722,15 @@ add_mix(cxxMix *mix_ptr)
solution_ptr = Utilities::Rxn_find(Rxn_solution_map, it->first);
if (solution_ptr == NULL)
{
error_string = sformatf( "Mix solution not found, %d.",
it->first);
error_string = sformatf("Mix solution not found, %d.",
it->first);
error_msg(error_string, CONTINUE);
input_error++;
continue;
}
extensive = it->second;
intensive = extensive / sum_fractions;
if (count_positive < (int) mix_ptr->Get_mixComps().size())
if (count_positive < (int)mix_ptr->Get_mixComps().size())
{
if (it->second > 0)
{
@ -669,6 +745,7 @@ add_mix(cxxMix *mix_ptr)
}
return (OK);
}
#endif
/* ---------------------------------------------------------------------- */
int Phreeqc::
add_pp_assemblage(cxxPPassemblage *pp_assemblage_ptr)

4
structures.cpp
View File

@ -2488,7 +2488,7 @@ unknown_delete(int i)
/* ---------------------------------------------------------------------- */
{
/*
* Delete unknow from list x
* Delete unknown from list x
*/
unknown_free(x[i]);
x.erase(x.begin() + (size_t)i);
@ -2636,7 +2636,7 @@ logk_init(class logk *logk_ptr)
*/
logk_ptr->name = NULL;
/*
* set varibles = 0
* set variables = 0
*/
logk_ptr->lk = 0.0;
for (i = 0; i < MAX_LOG_K_INDICES; i++)

6
tally.cpp
View File

@ -31,7 +31,7 @@ get_tally_table_rows_columns(int *rows, int *columns)
returns number of rows and columns in table
get_tally_table_row_heading(int row, char *string)
row is C row number
returns row descripter for row
returns row descriptor for row
get_tally_table_column_heading(int column, int *type, char *string)
column is C column number
returns column heading for column
@ -803,7 +803,7 @@ build_tally_table(void)
char token[MAX_LENGTH];
const char* cptr;
/*
* make list of all elements in all entitites
* make list of all elements in all entities
* defines the number of rows in the table
*/
get_all_components();
@ -811,7 +811,7 @@ build_tally_table(void)
save_print_use = pr.use;
pr.use = FALSE;
/*
* find nuber of columns
* find number of columns
*/
count_tally_table_columns = 0;
/*

2
tidy.cpp
View File

@ -4661,7 +4661,7 @@ ss_prep(LDBLE t, cxxSS *ss_ptr, int print)
{
if (print == TRUE)
output_msg(sformatf(
"\nLocal minimum in the solidus curve coresponding to a maximum\nin the minimum stoichiometric saturation curve.\n\n"));
"\nLocal minimum in the solidus curve corresponding to a maximum\nin the minimum stoichiometric saturation curve.\n\n"));
}
else
{

25
transport.cpp
View File

@ -28,7 +28,7 @@ struct CURRENT_CELLS
LDBLE dif, ele, R; // diffusive and electric components, relative cell resistance
} *current_cells;
LDBLE sum_R, sum_Rd; // sum of R, sum of (current_cells[0].dif - current_cells[i].dif) * R
struct V_M // For calculating Vinograd and McBain's zero-charge, diffusive tranfer of individual solutes
struct V_M // For calculating Vinograd and McBain's zero-charge, diffusive transfer of individual solutes
{
LDBLE grad, D, z, c, zc, Dz, Dzc;
LDBLE b_ij; // harmonic mean of cell properties, with EDL enrichment
@ -1653,14 +1653,17 @@ init_heat_mix(int l_nmix)
{
if (implicit)
{
LDBLE viscos_f0;
LDBLE viscos_f;
l_heat_nmix = l_nmix;
for (i = 1; i <= count_cells + 1; i++)
{
heat_mix_array[i - 1] = heat_mix_array[i] / l_heat_nmix; /* for implicit, m[i] has mixf with higher cell */
viscos_f0 = sol_D[i - 1].viscos_f0 * exp(heat_diffc / sol_D[i - 1].tk_x - heat_diffc / 298.15);
viscos_f0 += sol_D[i].viscos_f0 * exp(heat_diffc / sol_D[i].tk_x - heat_diffc / 298.15);
heat_mix_array[i - 1] *= (viscos_f0 / 2);
if (print_viscosity)
{
viscos_f = sol_D[i - 1].viscos_f * exp(heat_diffc / sol_D[i - 1].tk_x - heat_diffc / 298.15);
viscos_f += sol_D[i].viscos_f * exp(heat_diffc / sol_D[i].tk_x - heat_diffc / 298.15);
heat_mix_array[i - 1] *= (viscos_f / 2);
}
}
}
else
@ -3871,7 +3874,7 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
for IL: A * por_il / por.
por_il should be entered for the cell with the maximal cec.
IL water is related to X-, thus the cec (eq/L IL water) is the same for all cells if X is difined.
IL water is related to X-, thus the cec (eq/L IL water) is the same for all cells if X is defined.
IL-water = (free + DL porewater) * por_il / por.
for IL: A * aq_il / t_aq.
*/
@ -4352,9 +4355,9 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
b_j *= sol_D[icell].spec[i].Dwt;
else
{
dum2 = sol_D[icell].spec[i].Dwt / sol_D[icell].viscos_f0;
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_f0;
dum2 *= sol_D[jcell].viscos_f;
b_j *= dum2;
}
if (sol_D[icell].spec[i].dw_a_v_dif)
@ -4463,9 +4466,9 @@ find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant)
b_i *= sol_D[jcell].spec[j].Dwt;
else
{
dum2 = sol_D[jcell].spec[j].Dwt / sol_D[jcell].viscos_f0;
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_f0;
dum2 *= sol_D[icell].viscos_f;
b_i *= dum2;
}
if (sol_D[icell].spec[i].dw_a_v_dif)
@ -5602,7 +5605,7 @@ diff_stag_surf(int mobile_cell)
* Diffuse stagnant and mobile surfaces, following the steps of disp_surf.
* First the mobile/stagnant surfaces are mixed, then the stagnant surfaces
* when not already done.
* If mixing factors among the cells are defined expicitly, it is assumed that
* If mixing factors among the cells are defined explicitly, it is assumed that
* mixing with a lower numbered cell was done when that cell was processed:
* for any cell in MCD, need only include the mixing factors for higher numbered cells.
*/

2
utilities.cpp
View File

@ -483,7 +483,7 @@ get_token(const char** eqnaddr, std::string& string, LDBLE* l_z, int* l)
cptr = *eqnaddr;
i = 0;
/*
* Find end of token or begining of charge
* Find end of token or beginning of charge
*/
while (((c = *cptr) != '+') && (c != '-') && (c != '=') && (c != '\0'))
{