Merge commit '622bc5fb4cc8f67f9303e45c98397b97fe30822f'

phreeqcpp/Form1.h

@@ -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 )
 			{

phreeqcpp/Makefile.old

@@ -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

phreeqcpp/PBasic.cpp

@@ -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.");
+			snerr(": Missing or wrong type area variable.");
-		// varaiable for thickness
+		// 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);

phreeqcpp/Phreeqc.cpp

@@ -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;

phreeqcpp/Solution.cxx

@@ -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;

phreeqcpp/cl1.cpp

@@ -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;
 	}

phreeqcpp/cl1mp.cpp

@@ -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;
 	}

phreeqcpp/common/Parser.h

@@ -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

phreeqcpp/common/Utils.cxx

@@ -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.;

phreeqcpp/cvode.cpp

@@ -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.
 
 ******************************************************************/

phreeqcpp/global_structures.h

@@ -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;

phreeqcpp/input.cpp

@@ -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

phreeqcpp/inverse.cpp

@@ -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]);

phreeqcpp/mainsubs.cpp

@@ -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).

phreeqcpp/model.cpp

@@ -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

phreeqcpp/nvector_serial.cpp

@@ -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.                *
  *                                                                        *

phreeqcpp/nvector_serial.h

@@ -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

phreeqcpp/pitzer.cpp

@@ -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;

phreeqcpp/prep.cpp

@@ -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++;
 	}

phreeqcpp/read.cpp

@@ -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);

phreeqcpp/sit.cpp

@@ -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;

phreeqcpp/step.cpp

@@ -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)
@@ -646,7 +722,7 @@ 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.",
+			error_string = sformatf("Mix solution not found, %d.",
 				it->first);
 			error_msg(error_string, CONTINUE);
 			input_error++;
@@ -654,7 +730,7 @@ add_mix(cxxMix *mix_ptr)
 		}
 		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)

phreeqcpp/structures.cpp

@@ -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++)

phreeqcpp/tally.cpp

@@ -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;
 /*

phreeqcpp/tidy.cpp

@@ -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
 			{

phreeqcpp/transport.cpp

@@ -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);
+				if (print_viscosity)
-				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);
+					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.
 */

phreeqcpp/utilities.cpp

@@ -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'))
 	{