pyEQL 1.4.0rc9__cp310-cp310-macosx_10_9_x86_64.whl

pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/parse.cpp

@@ -0,0 +1,1044 @@
+#include "Phreeqc.h"
+#include "phqalloc.h"
+#include "Utils.h"
+
+#if defined(PHREEQCI_GUI)
+#ifdef _DEBUG
+#define new DEBUG_NEW
+#undef THIS_FILE
+static char THIS_FILE[] = __FILE__;
+#endif
+#endif
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+parse_eq(char* eqn, std::vector<class elt_list>& new_elt_list, int association)
+/* ---------------------------------------------------------------------- */
+/*
+ *   function to break equation up into component species
+ *   returns species name, coefficient, and charge in global variable "rxn_list".
+ *   Also returns pointer to elt_list structure array with list of elements
+ *   and coefficients in species.
+ *   rxn_list     global variable, output with contiguous rxn_list structures,
+ *                      which is the reaction.  Target species is first in
+ *                      list, coefficient is -1.0.
+ *
+ *   Argurments:
+ *      *eqn         input,  pointer to equation to be parsed.
+ *     **elt_ptr     output, pointer to contiguous elt_list structures,
+ *                           which is list of elements and coefficients in the
+ *                           target species.
+ *       association input, TRUE or FALSE if reaction is an association reaction
+ */
+{
+	int i;
+	LDBLE coef, l_z;
+	char c;
+	const char* cptr;
+	char token[MAX_LENGTH];
+
+	paren_count = 0;
+	/*
+	 *   Remove white space
+	 */
+	squeeze_white(eqn);
+	/*
+	 *   Check for illegal characters
+	 */
+	for (i = 0; (c = eqn[i]) != '\0'; i++)
+	{
+		if (islegit(c) == FALSE)
+		{
+			error_string = sformatf("Character is not allowed,\
+ %c (octal: %o).", c, c);
+			error_msg(error_string, CONTINUE);
+			return (ERROR);
+		}
+	}
+
+	/*
+	 *   Find coefficients, name, and charge for each species for lhs
+	 */
+	count_trxn = 0;
+	trxn.dz[0] = trxn.dz[1] = trxn.dz[2] = 0.0;
+	cptr = eqn;
+	c = cptr[0];
+	for (;;)
+	{
+		if (c == '=')
+			break;
+		if (c == '\0')
+		{
+			error_string = sformatf("Equation has no equal sign.\n\t%s", eqn);
+			error_msg(error_string, CONTINUE);
+			return (ERROR);
+		}
+		if (get_species(&cptr) == ERROR)
+		{
+			return (ERROR);
+		}
+		c = cptr[0];
+		if (association == FALSE)
+		{
+			trxn.token[count_trxn].coef *= -1.0;
+		}
+		count_trxn++;
+	}
+	/*
+	 *   Get coefficient, name, and charge of species for dissociation reaction
+	 */
+	cptr++;
+	if (association == TRUE)
+	{
+		if (get_species(&cptr) == ERROR)
+		{
+			return (ERROR);
+		}
+		trxn.token[count_trxn].coef *= -1.0;
+		/*   Swap species into first structure position */
+		const char* char_ptr = trxn.token[0].name;
+		coef = trxn.token[0].coef;
+		l_z = trxn.token[0].z;
+		trxn.token[0].name = trxn.token[count_trxn].name;
+		trxn.token[0].coef = trxn.token[count_trxn].coef;
+		trxn.token[0].z = trxn.token[count_trxn].z;
+		trxn.token[count_trxn].name = char_ptr;
+		trxn.token[count_trxn].coef = coef;
+		trxn.token[count_trxn].z = l_z;
+		count_trxn++;
+	}
+	/*
+	 *   Get reaction species from rhs of equation
+	 */
+	c = cptr[0];
+	for (;;)
+	{
+		if (c == '\0')
+			break;
+		if (get_species(&cptr) == ERROR)
+		{
+			return (ERROR);
+		}
+		c = cptr[0];
+		if (association == TRUE)
+		{
+			trxn.token[count_trxn].coef *= -1.0;
+		}
+		count_trxn++;
+	}
+	/*
+	 *   Sort list of reaction species
+	 */
+	trxn_sort();
+	/*
+	 *   Get elements in species or mineral formula
+	 */
+	count_elts = 0;
+	Utilities::strcpy_safe(token, MAX_LENGTH, trxn.token[0].name);
+	replace("(s)", "", token);
+	replace("(S)", "", token);
+	replace("(g)", "", token);
+	replace("(G)", "", token);
+	const char* char_ptr = token;
+
+	if (get_elts_in_species(&char_ptr, trxn.token[0].coef) == ERROR)
+	{
+		return (ERROR);
+	}
+	/*
+	 *   Sort elements in reaction and combine
+	 */
+	if (elt_list_combine() == ERROR)
+		return (ERROR);
+	/*
+	 *   Malloc space and store element data for return
+	 */
+	new_elt_list.resize(count_elts + 1);
+	for (i = 0; i < count_elts; i++)
+	{
+		new_elt_list[i].elt = elt_list[i].elt;
+		new_elt_list[i].coef = -elt_list[i].coef;
+	}
+	new_elt_list[count_elts].elt = NULL;
+
+	/*
+	 *   Debugging print of parsed equation
+		trxn_print();
+	 */
+	return (OK);
+}
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+check_eqn(int association)
+/* ---------------------------------------------------------------------- */
+/*
+ *   Check that equation is balanced reaction. Uses array "trxn.token" and
+ *   assumes "count_trxn" is set to number of species in reaction.
+ *   Charge and elements are checked.
+ *
+ *   Arguments:
+ *
+ *      association  input, TRUE or FALSE if reaction is an association reaction.
+ */
+{
+	int i;
+	int oops = 0;
+	LDBLE sumcharge;
+
+	paren_count = 0;
+	count_elts = 0;
+/*
+ *   Check that coefficient of first species is -1.0
+ */
+	if (equal(trxn.token[0].coef, -1.0, TOL) == FALSE)
+	{
+		if (association == TRUE)
+		{
+			error_string = sformatf(
+					"Coefficient of first species on rhs is not equal to 1.0.");
+			error_msg(error_string, CONTINUE);
+		}
+		else
+		{
+			error_string = sformatf(
+					"Coefficient of mineral (first on lhs) is not equal to 1.0.");
+			error_msg(error_string, CONTINUE);
+		}
+		return (ERROR);
+	}
+/*
+ *   Go through all species in the reaction; sum the charge and store elements
+ */
+	sumcharge = 0.0;
+	for (i = 0; i < count_trxn; i++)
+	{
+		sumcharge += (trxn.token[i].coef) * (trxn.token[i].z);
+		const char* t_ptr = trxn.token[i].name;
+		if (get_elts_in_species(&t_ptr, trxn.token[i].coef) == ERROR)
+		{
+			return (ERROR);
+		}
+	}
+/*
+ *   Sort elements in reaction and combine
+ */
+	if (elt_list_combine() == ERROR)
+		return (ERROR);
+/*
+ *   Check charge
+ */
+	if (equal(sumcharge, 0.0, TOL) == FALSE)
+	{
+		error_string = sformatf( "Equation is not charge balanced, right - left = %7.4f moles charge", sumcharge);
+		error_msg(error_string, CONTINUE);
+		oops++;
+	}
+/*
+ *   Check mass balance
+ */
+	for (i = 0; i < count_elts; i++)
+	{
+		if ((equal(elt_list[i].coef, 0.0, TOL) == FALSE) &&
+			strncmp((elt_list[i].elt)->name, "e", MAX_LENGTH) != 0)
+		{
+			error_string = sformatf(
+				"Equation does not balance for element, %s: right - left = %7.4f moles",
+				(elt_list[i].elt)->name, elt_list[i].coef);
+			error_msg(error_string, CONTINUE);
+			oops++;
+		}
+	}
+	if (oops == 0)
+	{
+		return (OK);
+	}
+	else
+	{
+		return (ERROR);
+	}
+}
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+get_charge(char *charge, size_t charge_size, LDBLE * l_z)
+/* ---------------------------------------------------------------------- */
+/*
+ *   Function takes character string and calculates the charge on
+ *   the species.  Charge can be in two forms: (1) string of "+" or "-"
+ *   or (2) + or - followed by an integer. Charge is reduced to form (2)
+ *   and stored in the pointer location *charge.
+ *
+ *   Arguments:
+ *      *charge    input, string containing charge
+ *                 output, string containing charge of the form + or -
+ *                    followed by an integer, if integer greater than 1.
+ *      *z         output, value of charge.
+ *
+ *   Returns:
+ *      ERROR,
+ *      OK.
+ */
+{
+	int i;
+	char* ptr;
+	char c, c1;
+/*
+ *   Charge is zero
+ */
+	if ((c = charge[0]) == '\0')
+	{
+		*l_z = 0.0;
+		return (OK);
+	}
+/*
+ *   Error check for + or - at start of string
+ */
+	if (c != '+' && c != '-')
+	{
+		error_string = sformatf(
+				"Character string for charge does not start with + or -,\t%s.",
+				charge);
+		error_msg(error_string, CONTINUE);
+		return (ERROR);
+	}
+/*
+ *   Count string of +'s or -'s
+ */
+	i = 0;
+	while (c == (c1 = charge[i++]));
+	i--;
+	if (c1 == '\0')
+	{
+		if (c == '-')
+			i = -i;
+	}
+	else
+	{
+/*
+ *   + or - followed by a number
+ */
+		errno = 0;
+		i = strtol(charge, &ptr, 0);
+/*
+ *   Truncate fractional part of charge if all zeros
+ */
+		if (*ptr != '\0')
+		{
+			if (*ptr == '.')
+			{
+				while (*(++ptr) != '\0')
+				{
+					if (*ptr != '0')
+					{
+						char* ptr;
+						*l_z = strtod(charge, &ptr);
+						return (OK);
+					}
+				}
+/*
+ *   Non-numeric characters
+ */
+			}
+			else
+			{
+				error_string = sformatf(
+						"Error in character string for charge, %s.", charge);
+				error_msg(error_string, CONTINUE);
+				return (ERROR);
+			}
+		}
+	}
+/*
+ *   Charge is zero, must have had +0 or -0 in eqn
+ */
+	if (i == 0)
+	{
+		charge[0] = '\0';
+	}
+/*
+ *   Charge is +1 or -1, single + or -
+ */
+	if (abs(i) == 1)
+	{
+		charge[0] = c;
+		charge[1] = '\0';
+	}
+/*
+ *   Abs(z)>1, set charge to + or - plus integer
+ */
+	if (abs(i) > 1)
+	{
+		if (snprintf(charge, charge_size, "%-+d", i) == EOF)
+		{
+			error_string = sformatf(
+					"Error converting charge to character string, %s.",
+					charge);
+			error_msg(error_string, CONTINUE);
+			return (ERROR);
+		}
+	}
+	*l_z = i;
+	return (OK);
+}
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+get_coef(LDBLE * coef, const char **eqnaddr)
+/* ---------------------------------------------------------------------- */
+/*
+ *   Function reads through eqn and determines the coefficient of the next
+ *   species.
+ *
+ *   Arguments:
+ *       *coef    output, coefficient of next species.
+ *
+ *      **eqnaddr input, pointer to a position in eqn to start parsing
+ *                output, pointer to next position after coefficient
+ *
+ *   Returns:
+ *      ERROR,
+ *      OK.
+ */
+{
+	int i;
+	char c, c1;
+	const char* cptr;
+	const char* rest;
+	char* ptr1;
+	char token[MAX_LENGTH];;
+
+	rest = *eqnaddr;
+	cptr = *eqnaddr;				/* address of a position in eqn */
+	c = *cptr;					/* character in eqn */
+	*coef = 0.0;
+/*
+ *   No leading sign or number
+ */
+	if (isalpha((int) c) ||
+		(c == '(') || (c == ')') || (c == '[') || (c == ']'))
+	{
+		*coef = 1.0;
+		return (OK);
+	}
+/*
+ *   Leading +, no digits
+ */
+	c1 = *(cptr + 1);
+	if (c == '+' &&
+		(isalpha((int) c1) ||
+		 (c1 == '(') || (c1 == ')') || (c1 == '[') || (c1 == ']')))
+	{
+		*eqnaddr = ++cptr;
+		*coef = 1.0;
+		return (OK);
+	}
+/*
+ *   Leading -, no digits
+ */
+	if (c == '-' &&
+		(isalpha((int) c1) ||
+		 (c1 == '(') || (c1 == ')') || (c1 == '[') || (c1 == ']')))
+	{
+		*eqnaddr = ++cptr;
+		*coef = -1.0;
+		return (OK);
+	}
+	i = 0;
+/*
+ *   Has number coefficient
+ */
+	if (isdigit((int) c) || c == '+' || c == '-' || c == '.')
+	{
+		while (isdigit((int) c) || c == '+' || c == '-' || c == '.')
+		{
+			token[i++] = c;
+			if (i >= MAX_LENGTH)
+			{
+				error_string = sformatf(
+						"Coefficient has more than MAX_LENGTH characters.");
+				error_msg(error_string, CONTINUE);
+				return (ERROR);
+			}
+			c = *(++cptr);
+		}
+		token[i] = '\0';
+		*eqnaddr = cptr;
+		errno = 0;
+		*coef = strtod(token, &ptr1);
+		if ((errno == ERANGE) || (*ptr1 != '\0'))
+		{
+			error_string = sformatf(
+					"Error converting coefficient in get_coef, %s.", token);
+			error_msg(error_string, CONTINUE);
+			return (ERROR);
+		}
+		return (OK);
+	}
+/*
+ *   None of the above, unknown construct
+ */
+	error_string = sformatf(
+			"Illegal equation construct detected in get_coef.\n\t%s.", rest);
+	error_msg(error_string, CONTINUE);
+	return (ERROR);
+}
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+get_elt(const char** t_ptr, std::string& element, int* i)
+/* ---------------------------------------------------------------------- */
+/*
+ *      Function reads an element name out of the equation string.
+ *      An element name is composed of a capital letter followed by any number
+ *      of lower case characters.
+ *
+ *      Arguments:
+ *         **t_ptr   input, points to position in the equation to begin
+ *                   output, points to next character of equation after
+ *                      element name.
+ *         *element  input pointer to place to return element character string
+ */
+{
+	char c;
+
+	element.clear();
+	c = *(*t_ptr)++;
+	if (c == '\0')
+	{
+		error_string = sformatf(
+			"Empty string in get_elt.  Expected an element name.");
+		error_msg(error_string, CONTINUE);
+		return (ERROR);
+	}
+	/*
+	 *   Load name into char array element
+	 */
+	element.push_back(c);
+	*i = 1;
+	if (c == '[')
+	{
+		while ((c = (**t_ptr)) != ']')
+		{
+			element.push_back(c);
+			(*i)++;
+			(*t_ptr)++;
+			if ((c = (**t_ptr)) == ']')
+			{
+				element.push_back(c);
+				(*i)++;
+				(*t_ptr)++;
+				break;
+			}
+			else if (**t_ptr == '\0')
+			{
+				error_msg("No ending bracket (]) for element name", CONTINUE);
+				input_error++;
+				break;
+			}
+		}
+		while (islower((int)(c = (**t_ptr))) || c == '_')
+		{
+			element.push_back(c);
+			(*i)++;
+			(*t_ptr)++;
+		}
+	}
+	else
+	{
+		while (islower((int)(c = (**t_ptr))) || c == '_')
+		{
+			element.push_back(c);
+			(*i)++;
+			(*t_ptr)++;
+		}
+	}
+	return (OK);
+}
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+get_elts_in_species(const char **t_ptr, LDBLE coef)
+/* ---------------------------------------------------------------------- */
+{
+/*
+ *    Makes a list of elements with their coefficients, stores elements
+ *    in elt_list at position count_elts.  Global variable count_elts is
+ *    updated with each stored element.  Also uses static global variable
+ *    paren_count.
+ *
+ *    Arguments:
+ *       **t_ptr    input, point in token string to start looking
+ *                  output, is next position to start looking
+ *         coef     input, coefficient to multiply subscripts by
+ */
+	int l;
+	size_t count;
+	char c, c1;
+	LDBLE d;
+	std::string element;
+	const char** t_ptr_save = t_ptr;
+	while (((c = **t_ptr) != '+') && (c != '-') && (c != '\0'))
+	{
+		/* close parenthesis */
+		if (c == ')')
+		{
+			paren_count--;
+			if (paren_count < 0)
+			{
+				error_string = sformatf( "Too many right parentheses.");
+				error_msg(error_string, CONTINUE);
+				return (ERROR);
+			}
+			(*t_ptr)++;
+			return (OK);
+		}
+		c1 = *((*t_ptr) + 1);
+		/* beginning of element name */
+		if (isupper((int) c) || (c == 'e' && c1 == '-') || (c == '['))
+		{
+/*
+ *   Get new element and subscript
+ */
+			if (get_elt(t_ptr, element, &l) == ERROR)
+			{
+				return (ERROR);
+			}
+			if (count_elts >= (int)elt_list.size())
+			{
+				elt_list.resize(count_elts + 1);
+			}
+			elt_list[count_elts].elt = element_store(element.c_str());
+			if (get_num(t_ptr, &d) == ERROR)
+			{
+				return (ERROR);
+			}
+			elt_list[count_elts].coef = d * coef;
+			count_elts++;
+/*
+ *   Expand working space for elements if necessary
+ */
+			if (count_elts >= (int)elt_list.size())
+			{
+				elt_list.resize(count_elts + 1);
+			}
+			continue;
+		}
+/*
+ *   Open parentheses
+ */
+		if (c == '(')
+		{
+			count = count_elts;
+			if (c1 == ')')
+			{
+				error_string = sformatf( "Empty parentheses.");
+				warning_msg(error_string);
+			}
+			paren_count++;
+			(*t_ptr)++;
+			if (get_elts_in_species(t_ptr, coef) == ERROR)
+			{
+				return (ERROR);
+			}
+			if (get_num(t_ptr, &d) == ERROR)
+			{
+				return (ERROR);
+			}
+			for (size_t i = count; i < count_elts; i++)
+			{
+				elt_list[i].coef *= d;
+			}
+			continue;
+		}
+/*
+ *   Colon
+ */
+		if (c == ':')
+		{
+			count = count_elts;
+			(*t_ptr)++;
+			if (get_num(t_ptr, &d) == ERROR)
+			{
+				return (ERROR);
+			}
+			if (get_elts_in_species(t_ptr, coef) == ERROR)
+			{
+				return (ERROR);
+			}
+			for (size_t i = count; i < count_elts; i++)
+			{
+				elt_list[i].coef *= d;
+			}
+			continue;
+		}
+/*
+ *   Not beginning of element and not opening paren
+ */
+		error_string = sformatf(
+				"Parsing error in get_elts_in_species, unexpected character, %c.",
+				c);
+		error_msg(error_string, CONTINUE);
+		input_error++;
+		return (ERROR);
+	}
+	if (paren_count != 0)
+	{
+		error_string = sformatf( "Unbalanced parentheses: %s", *t_ptr_save);
+		error_msg(error_string, CONTINUE);
+		input_error++;
+		return (ERROR);
+	}
+	return (OK);
+}
+
+/* ---------------------------------------------------------------------- */
+ int Phreeqc::
+get_secondary(const char **t_ptr, char *element, int *i)
+/* ---------------------------------------------------------------------- */
+/*
+ *      Function reads an element name out of the equation string.
+ *      An element name is composed of a capital letter followed by any number
+ *      of lower case characters.
+ *
+ *      Arguments:
+ *         **t_ptr   input, points to position in the equation to begin
+ *                   output, points to next character of equation after
+ *                      element name.
+ *         *element  input pointer to place to return element character string
+ */
+{
+	int j;
+	char c;
+	const char* cptr;
+
+	c = *(*t_ptr)++;
+	if (c == '\0')
+	{
+		error_string = sformatf(
+				"Empty string in get_elt.  Expected an element name.");
+		error_msg(error_string, CONTINUE);
+		input_error++;
+		return (ERROR);
+	}
+/*
+ *   Load name into char array element
+ */
+	element[0] = c;
+	*i = 1;
+	if (c == '[')
+	{
+		while ((c = (**t_ptr)) != ']')
+		{
+			element[*i] = c;
+			(*i)++;
+			(*t_ptr)++;
+			if ((c = (**t_ptr)) == ']')
+			{
+				element[*i] = c;
+				(*i)++;
+				(*t_ptr)++;
+				c = (**t_ptr);
+				break;
+			}
+			else if ((c = (**t_ptr)) == '\0')
+			{
+				error_msg("Did not find ending bracket (])", CONTINUE);
+				input_error++;
+				return (ERROR);
+			}
+		}
+		while (islower((int) (c = (**t_ptr))) || c == '_')
+		{
+			element[*i] = c;
+			(*i)++;
+			(*t_ptr)++;
+		}
+	}
+	else
+	{
+		while (islower((int) (c = (**t_ptr))) || c == '_')
+		{
+			element[*i] = c;
+			(*i)++;
+			(*t_ptr)++;
+		}
+	}
+/*
+ *   Check if secondary master species element
+ */
+	j = *i;
+	cptr = *t_ptr;
+	if (c == '(')
+	{
+		/* copy parenthesis */
+		element[*i] = c;
+		(*i)++;
+		(*t_ptr)++;
+		/* copy number */
+		for (;;)
+		{
+			c = **t_ptr;
+			if (isdigit((int) c) || c == '-' || c == '.')
+			{
+				element[*i] = c;
+				(*i)++;
+				(*t_ptr)++;
+			}
+			else if (c == '+')
+			{
+				(*t_ptr)++;
+			}
+			else
+			{
+				break;
+			}
+		}
+		/* go back to before parenthesis */
+		if (c != ')')
+		{
+			*i = j;
+			*t_ptr = cptr;
+			/* put in closing parenthesis */
+		}
+		else
+		{
+			element[*i] = c;
+			(*i)++;
+			(*t_ptr)++;
+		}
+	}
+	element[*i] = '\0';
+	return (OK);
+}
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+get_secondary_in_species(const char **t_ptr, LDBLE coef)
+/* ---------------------------------------------------------------------- */
+{
+/*
+ *    Makes a list of elements with their coefficients, stores elements
+ *    in elt_list at position count_elts.  Global variable count_elts is
+ *    updated with each stored element.  Also uses static global variable
+ *    paren_count.
+ *
+ *    Arguments:
+ *       **t_ptr    input, point in token string to start looking
+ *                  output, is next position to start looking
+ *         coef     input, coefficient to multiply subscripts by
+ */
+	int l;
+	size_t count;
+	char c, c1;
+	LDBLE d;
+	char element[MAX_LENGTH];
+	const char** t_ptr_save = t_ptr;
+	while (((c = **t_ptr) != '+') && (c != '-') && (c != '\0'))
+	{
+		/* close parenthesis */
+		if (c == ')')
+		{
+			paren_count--;
+			if (paren_count < 0)
+			{
+				error_string = sformatf( "Too many right parentheses.");
+				error_msg(error_string, CONTINUE);
+				input_error++;
+				return (ERROR);
+			}
+			(*t_ptr)++;
+			return (OK);
+		}
+		c1 = *((*t_ptr) + 1);
+		/* beginning of element name */
+		if (isupper((int) c) || c == '[' || (c == 'e' && c1 == '-'))
+		{
+/*
+ *   Get new element and subscript
+ */
+			if (get_secondary(t_ptr, element, &l) == ERROR)
+			{
+				return (ERROR);
+			}
+			elt_list[count_elts].elt = element_store(element);
+			if (get_num(t_ptr, &d) == ERROR)
+			{
+				return (ERROR);
+			}
+			elt_list[count_elts].coef = d * coef;
+			count_elts++;
+/*
+ *   Expand working space for elements if necessary
+ */
+			if (count_elts >= (int)elt_list.size())
+			{
+				elt_list.resize(count_elts + 1);
+			}
+			continue;
+		}
+/*
+ *   Open parentheses
+ */
+		if (c == '(')
+		{
+			count = count_elts;
+			if (c1 == ')')
+			{
+				error_string = sformatf( "Empty parentheses.");
+				warning_msg(error_string);
+			}
+			paren_count++;
+			(*t_ptr)++;
+			if (get_secondary_in_species(t_ptr, coef) == ERROR)
+			{
+				return (ERROR);
+			}
+			if (get_num(t_ptr, &d) == ERROR)
+			{
+				return (ERROR);
+			}
+			for (size_t i = count; i < count_elts; i++)
+			{
+				elt_list[i].coef *= d;
+			}
+			continue;
+		}
+/*
+ *   Colon
+ */
+		if (c == ':')
+		{
+			count = count_elts;
+			(*t_ptr)++;
+			if (get_num(t_ptr, &d) == ERROR)
+			{
+				return (ERROR);
+			}
+			if (get_secondary_in_species(t_ptr, coef) == ERROR)
+			{
+				return (ERROR);
+			}
+			for (size_t i = count; i < count_elts; i++)
+			{
+				elt_list[i].coef *= d;
+			}
+			continue;
+		}
+/*
+ *   Not beginning of element and not opening paren
+ */
+		error_string = sformatf(
+				"Parsing error in get_secondary_in_species, unexpected character, %c.",
+				c);
+		error_msg(error_string, CONTINUE);
+		return (ERROR);
+	}
+	if (paren_count != 0)
+	{
+		error_string = sformatf("Unbalanced parentheses: %s", *t_ptr_save);
+		error_msg(error_string, CONTINUE);
+		return (ERROR);
+	}
+	return (OK);
+}
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+get_num(const char **t_ptr, LDBLE * num)
+/* ---------------------------------------------------------------------- */
+/*
+ *      Function reads through a string looking for leading numeric field
+ *      if no numeric field is found, the number is set to 1.0.
+ *
+ *      Arguments:
+ *
+ *       **t_ptr     input, points to a position in a character string from which
+ *                      a number is to be extracted.
+ *                   output, points to next position to be parsed.
+ *        *num       address where the number is to be stored.
+ *
+ *      Returns:
+ *         ERROR,
+ *         OK.
+ */
+{
+	int i, decimal;
+	char c;
+	char* ptr1;
+	char token[MAX_LENGTH];
+
+	*num = 1.0;
+	i = 0;
+	c = **t_ptr;
+	decimal = 0;
+	if (isdigit((int) c) || (c == '.'))
+	{
+		while (isdigit((int) c) || (c == '.'))
+		{
+			if (c == '.')
+				decimal++;
+			if (decimal > 1)
+				break;
+			token[i++] = c;
+			/* check number length */
+			if (i >= MAX_LENGTH)
+			{
+				error_string = sformatf(
+						"Number was greater than MAX_LENGTH characters.");
+				error_msg(error_string, CONTINUE);
+				input_error++;
+				return (ERROR);
+			}
+			c = *(++(*t_ptr));
+		}
+		token[i] = '\0';
+		errno = 0;
+		*num = strtod(token, &ptr1);
+		if (errno == ERANGE)
+		{
+			error_string = sformatf( "Converting number in get_num, %s.", token);
+			input_error++;
+			error_msg(error_string, CONTINUE);
+			return (ERROR);
+		}
+	}
+	return (OK);
+}
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+get_species(const char **cptr)
+/* ---------------------------------------------------------------------- */
+{
+/*   Function reads next species out of the equation, including optional
+ *   preceding coefficient and optional trailing charge. Data are
+ *   store in trxn.token[count].
+ *
+ *   Arguments:
+ *    **cptr       input, points to the position in the equation to pick up the species.
+ *                output, points to the next character after the species charge.
+ *
+ */
+	std::string string;
+	int l;
+
+	if ((size_t) count_trxn + 1 > trxn.token.size()) 
+		trxn.token.resize(count_trxn + 1);
+	/* coefficient */
+	if (get_coef(&(trxn.token[count_trxn].coef), cptr) == ERROR)
+	{
+		return (ERROR);
+	}
+	/* name and charge */
+	if (get_token(cptr, string, &trxn.token[count_trxn].z, &l) == ERROR)
+	{
+		return (ERROR);
+	}
+	trxn.token[count_trxn].name = string_hsave(string.c_str());
+	/*
+	   trxn.token[count_trxn].z = 0;
+	   trxn.token[count_trxn].s = NULL;
+	   trxn.token[count_trxn].unknown = NULL;
+	 */
+	return (OK);
+}