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Squashed 'src/phast/PhreeqcRM/' changes from dc6c23c4..5d6f7175
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5d6f7175 Merge commit 'b28e985ea9b4a9f72a07fa133f35af3206a6a7a0'
b28e985e Squashed 'src/' changes from 1a20b699..0e2eed5c
eacdcf9b Merge commit '77cf3260302368bd56c16403497db4caaee7849b'
77cf3260 Squashed 'database/' changes from b5394351..307253d3

git-subtree-dir: src/phast/PhreeqcRM
git-subtree-split: 5d6f71754ccf7f39c70cffad45bd8c51428d5558
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Darth Vader committed Jun 20, 2024
1 parent b46b371 commit 7edbbfa
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Showing 7 changed files with 320 additions and 3 deletions.
2 changes: 1 addition & 1 deletion database/Amm.dat
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ N(+5) NO3- 0 NO3
N(+3) NO2- 0 NO2
N(0) N2 0 N
#N(-3) NH4+ 0 NH4 14.0067
Amm AmmH+ 0 AmmH 17.031
Amm AmmH+ 0 Amm 17.031
B H3BO3 0 B 10.81
P PO4-3 2 P 30.9738
F F- 0 F 18.9984
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2 changes: 1 addition & 1 deletion database/phreeqc.dat
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ N(+5) NO3- 0 N
N(+3) NO2- 0 N
N(0) N2 0 N
N(-3) NH4+ 0 N 14.0067
#Amm AmmH+ 0 AmmH 17.031
#Amm AmmH+ 0 Amm 17.031
B H3BO3 0 B 10.81
P PO4-3 2 P 30.9738
F F- 0 F 18.9984
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2 changes: 1 addition & 1 deletion database/phreeqc_rates.dat
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ N(+5) NO3- 0 N
N(+3) NO2- 0 N
N(0) N2 0 N
N(-3) NH4+ 0 N 14.0067
#Amm AmmH+ 0 AmmH 17.031
#Amm AmmH+ 0 Amm 17.031
B H3BO3 0 B 10.81
P PO4-3 2 P 30.9738
F F- 0 F 18.9984
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208 changes: 208 additions & 0 deletions src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PBasic.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1548,6 +1548,14 @@ listtokens(FILE * f, tokenrec * l_buf)
case tokspecies_formula_:
output_msg("SPECIES_FORMULA$");
break;
case tokphase_equation:
case tokphase_equation_:
output_msg("PHASE_EQUATION$");
break;
case tokspecies_equation:
case tokspecies_equation_:
output_msg("SPECIES_EQUATION$");
break;
case toksr:
output_msg("SR");
break;
Expand Down Expand Up @@ -4080,6 +4088,202 @@ factor(struct LOC_exec * LINK)
}
break;

case tokphase_equation:
case tokphase_equation_:
{
require(toklp, LINK);
std::string phase_name(stringfactor(STR1, LINK));
varrec* elts_varrec = NULL, * coef_varrec = NULL;
std::vector<std::pair<std::string, double> > stoichiometry;
/*
* Parse arguments
*/
require(tokcomma, LINK);

count_varrec = LINK->t->UU.vp;
if (LINK->t->kind != tokvar || count_varrec->stringvar != 0)
snerr(": Cannot find count variable");

/* return number of names of species */
LINK->t = LINK->t->next;
require(tokcomma, LINK);
elts_varrec = LINK->t->UU.vp;
if (LINK->t->kind != tokvar || elts_varrec->stringvar != 1)
snerr(": Cannot find species string variable");

/* return coefficients of species */
LINK->t = LINK->t->next;
require(tokcomma, LINK);
coef_varrec = LINK->t->UU.vp;
if (LINK->t->kind != tokvar || coef_varrec->stringvar != 0)
snerr(": Cannot find coefficient variable");
LINK->t = LINK->t->next;

require(tokrp, LINK);

free_dim_stringvar(elts_varrec);
PhreeqcPtr->free_check_null(coef_varrec->UU.U0.arr);
coef_varrec->UU.U0.arr = NULL;
/*
* Call subroutine
*/
std::string eq = PhreeqcPtr->phase_equation(phase_name, stoichiometry);

// put type as return value
n.stringval = true;
n.UU.sval = PhreeqcPtr->string_duplicate(eq.c_str());

/*
* fill in varrec structure
*/

size_t count = stoichiometry.size();
*count_varrec->UU.U0.val = (LDBLE)count;
/*
* malloc space
*/
elts_varrec->UU.U1.sarr = (char**)PhreeqcPtr->PHRQ_malloc((count + 1) * sizeof(char*));
if (elts_varrec->UU.U1.sarr == NULL)
{
PhreeqcPtr->malloc_error();
#if !defined(R_SO)
exit(4);
#endif
}
coef_varrec->UU.U0.arr = (LDBLE*)PhreeqcPtr->PHRQ_malloc((count + 1) * sizeof(LDBLE));
if (coef_varrec->UU.U0.arr == NULL)
{
PhreeqcPtr->malloc_error();
#if !defined(R_SO)
exit(4);
#endif
}

// first position not used
elts_varrec->UU.U1.sarr[0] = NULL;
coef_varrec->UU.U0.arr[0] = 0;

// set dims for Basic array
for (i = 0; i < maxdims; i++)
{
elts_varrec->dims[i] = 0;
coef_varrec->dims[i] = 0;
}
// set dims for first dimension and number of dims
elts_varrec->dims[0] = (long)(count + 1);
coef_varrec->dims[0] = (long)(count + 1);
elts_varrec->numdims = 1;
coef_varrec->numdims = 1;

// fill in arrays
i = 1;
for (std::vector<std::pair<std::string, double > >::iterator it = stoichiometry.begin(); it != stoichiometry.end(); it++)
{
elts_varrec->UU.U1.sarr[i] = PhreeqcPtr->string_duplicate((it->first).c_str());
coef_varrec->UU.U0.arr[i] = it->second;
i++;
}
}
break;

case tokspecies_equation:
case tokspecies_equation_:
{
require(toklp, LINK);
std::string species_name(stringfactor(STR1, LINK));
varrec* elts_varrec = NULL, * coef_varrec = NULL;
std::vector<std::pair<std::string, double> > stoichiometry;
/*
* Parse arguments
*/
require(tokcomma, LINK);

count_varrec = LINK->t->UU.vp;
if (LINK->t->kind != tokvar || count_varrec->stringvar != 0)
snerr(": Cannot find count variable");

/* return number of names of species */
LINK->t = LINK->t->next;
require(tokcomma, LINK);
elts_varrec = LINK->t->UU.vp;
if (LINK->t->kind != tokvar || elts_varrec->stringvar != 1)
snerr(": Cannot find species string variable");

/* return coefficients of species */
LINK->t = LINK->t->next;
require(tokcomma, LINK);
coef_varrec = LINK->t->UU.vp;
if (LINK->t->kind != tokvar || coef_varrec->stringvar != 0)
snerr(": Cannot find coefficient variable");
LINK->t = LINK->t->next;

require(tokrp, LINK);

free_dim_stringvar(elts_varrec);
PhreeqcPtr->free_check_null(coef_varrec->UU.U0.arr);
coef_varrec->UU.U0.arr = NULL;
/*
* Call subroutine
*/
std::string eq = PhreeqcPtr->species_equation(species_name, stoichiometry);

// put type as return value
n.stringval = true;
n.UU.sval = PhreeqcPtr->string_duplicate(eq.c_str());

/*
* fill in varrec structure
*/

size_t count = stoichiometry.size();
*count_varrec->UU.U0.val = (LDBLE)count;
/*
* malloc space
*/
elts_varrec->UU.U1.sarr = (char**)PhreeqcPtr->PHRQ_malloc((count + 1) * sizeof(char*));
if (elts_varrec->UU.U1.sarr == NULL)
{
PhreeqcPtr->malloc_error();
#if !defined(R_SO)
exit(4);
#endif
}
coef_varrec->UU.U0.arr = (LDBLE*)PhreeqcPtr->PHRQ_malloc((count + 1) * sizeof(LDBLE));
if (coef_varrec->UU.U0.arr == NULL)
{
PhreeqcPtr->malloc_error();
#if !defined(R_SO)
exit(4);
#endif
}

// first position not used
elts_varrec->UU.U1.sarr[0] = NULL;
coef_varrec->UU.U0.arr[0] = 0;

// set dims for Basic array
for (i = 0; i < maxdims; i++)
{
elts_varrec->dims[i] = 0;
coef_varrec->dims[i] = 0;
}
// set dims for first dimension and number of dims
elts_varrec->dims[0] = (long)(count + 1);
coef_varrec->dims[0] = (long)(count + 1);
elts_varrec->numdims = 1;
coef_varrec->numdims = 1;

// fill in arrays
i = 1;
for (std::vector<std::pair<std::string, double > >::iterator it = stoichiometry.begin(); it != stoichiometry.end(); it++)
{
elts_varrec->UU.U1.sarr[i] = PhreeqcPtr->string_duplicate((it->first).c_str());
coef_varrec->UU.U0.arr[i] = it->second;
i++;
}
}
break;

case toksr:
{
const char* str = stringfactor(STR1, LINK);
Expand Down Expand Up @@ -8088,6 +8292,10 @@ const std::map<const std::string, PBasic::BASIC_TOKEN>::value_type temp_tokens[]
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("soln_vol", PBasic::toksoln_vol),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("species_formula", PBasic::tokspecies_formula),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("species_formula$", PBasic::tokspecies_formula_),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("phase_equation", PBasic::tokphase_equation),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("phase_equation$", PBasic::tokphase_equation_),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("species_equation", PBasic::tokspecies_equation),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("species_equation$", PBasic::tokspecies_equation_),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("sr", PBasic::toksr),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("step_no", PBasic::tokstep_no),
std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("str_e$", PBasic::tokstr_e_),
Expand Down
4 changes: 4 additions & 0 deletions src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PBasic.h
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Original file line number Diff line number Diff line change
Expand Up @@ -323,6 +323,10 @@ class PBasic: public PHRQ_base
toksoln_vol,
tokspecies_formula,
tokspecies_formula_,
tokphase_equation,
tokphase_equation_,
tokspecies_equation,
tokspecies_equation_,
toksr,
tokstep_no,
tokstr_e_,
Expand Down
2 changes: 2 additions & 0 deletions src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Phreeqc.h
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Original file line number Diff line number Diff line change
Expand Up @@ -167,6 +167,8 @@ class Phreeqc
std::string kinetics_formula(std::string kinetics_name, cxxNameDouble& stoichiometry);
std::string phase_formula(std::string phase_name, cxxNameDouble& stoichiometry);
std::string species_formula(std::string phase_name, cxxNameDouble& stoichiometry);
std::string phase_equation(std::string phase_name, std::vector<std::pair<std::string, double> >& stoichiometry);
std::string species_equation(std::string species_name, std::vector<std::pair<std::string, double> >& stoichiometry);
LDBLE list_ss(std::string ss_name, cxxNameDouble& composition);
int system_total_elements(void);
int system_total_si(void);
Expand Down
103 changes: 103 additions & 0 deletions src/IPhreeqcPhast/IPhreeqc/phreeqcpp/basicsubs.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3009,6 +3009,109 @@ species_formula(std::string phase_name, cxxNameDouble& stoichiometry)
return (formula);
}

/* ---------------------------------------------------------------------- */
std::string Phreeqc::
phase_equation(std::string phase_name, std::vector<std::pair<std::string, double> >& stoichiometry)
/* ---------------------------------------------------------------------- */
{
/*
* Returns equation
* Also returns arrays of species and stoichiometry in stoichiometry
*/
stoichiometry.clear();
std::ostringstream eq, lhs, rhs;
int j = -1;
class phase* phase_ptr = phase_bsearch(phase_name.c_str(), &j, FALSE);
bool rhs_started = false;
bool lhs_started = false;
if (phase_ptr != NULL)
{
std::vector<rxn_token>::iterator it = phase_ptr->rxn.Get_tokens().begin();
for (; it->name != NULL; it++)
{
if (!lhs_started)
{
std::pair<std::string, double> item(phase_ptr->formula, it->coef);
stoichiometry.push_back(item);
}
else
{
std::pair<std::string, double> item(it->name, it->coef);
stoichiometry.push_back(item);
}
if (it->coef < 0.0)
{
if (lhs_started) lhs << "+ ";
if (it->coef != -1.0)
{
lhs << -it->coef;
}
lhs << it->name << " ";
lhs_started = true;
}
else if (it->coef > 0.0)
{
if (rhs_started) rhs << "+ ";
if (it->coef != 1.0)
{
rhs << it->coef;
}
rhs << it->name << " ";
rhs_started = true;
}
}
}
eq << lhs.str() << "= " << rhs.str();
return (eq.str());
}

/* ---------------------------------------------------------------------- */
std::string Phreeqc::
species_equation(std::string species_name, std::vector<std::pair<std::string, double> >& stoichiometry)
/* ---------------------------------------------------------------------- */
{
/*
* Returns equation
* Also returns arrays of species and stoichiometry in stoichiometry
*/
stoichiometry.clear();
std::ostringstream eq, lhs, rhs;;
class species* s_ptr = s_search(species_name.c_str());
bool rhs_started = false;
bool lhs_started = false;
if (s_ptr != NULL)
{
std::vector<rxn_token>::iterator it = s_ptr->rxn.Get_tokens().begin();
for ( ; it->name != NULL; it++)
{
std::pair<std::string, double> item(it->name, it->coef);
stoichiometry.push_back(item);
if (it->coef > 0.0)
{
if (lhs_started) lhs << "+ ";
if (it->coef != 1.0)
{
lhs << it->coef;
}
lhs << it->name << " ";
lhs_started = true;
}
else if (it->coef < 0.0)
{
if (rhs_started) rhs << "+ ";
if (it->coef != -1.0)
{
rhs << -it->coef;
}
rhs << it->name << " ";
rhs_started = true;
}
}
}
eq << lhs.str() << "= " << rhs.str();
return (eq.str());
}

/* ---------------------------------------------------------------------- */
int Phreeqc::
system_total_elements(void)
Expand Down

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