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Squashed 'phreeqcpp/' changes from 798f8f9..e4c4cf3
e4c4cf3 Added functions SPECIES_EQUATION and PHASE_EQUATION, and species_equation test case. git-subtree-dir: phreeqcpp git-subtree-split: e4c4cf31fb54a3546e6bdbb1fda762952803fd82
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Darth Vader
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a9c4ef8324
commit
2abb0b0bcd
208
PBasic.cpp
208
PBasic.cpp
@ -1548,6 +1548,14 @@ listtokens(FILE * f, tokenrec * l_buf)
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case tokspecies_formula_:
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output_msg("SPECIES_FORMULA$");
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break;
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case tokphase_equation:
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case tokphase_equation_:
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output_msg("PHASE_EQUATION$");
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break;
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case tokspecies_equation:
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case tokspecies_equation_:
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output_msg("SPECIES_EQUATION$");
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break;
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case toksr:
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output_msg("SR");
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break;
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@ -4080,6 +4088,202 @@ factor(struct LOC_exec * LINK)
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}
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break;
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case tokphase_equation:
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case tokphase_equation_:
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{
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require(toklp, LINK);
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std::string phase_name(stringfactor(STR1, LINK));
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varrec* elts_varrec = NULL, * coef_varrec = NULL;
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std::vector<std::pair<std::string, double> > stoichiometry;
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/*
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* Parse arguments
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*/
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require(tokcomma, LINK);
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count_varrec = LINK->t->UU.vp;
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if (LINK->t->kind != tokvar || count_varrec->stringvar != 0)
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snerr(": Cannot find count variable");
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/* return number of names of species */
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LINK->t = LINK->t->next;
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require(tokcomma, LINK);
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elts_varrec = LINK->t->UU.vp;
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if (LINK->t->kind != tokvar || elts_varrec->stringvar != 1)
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snerr(": Cannot find species string variable");
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/* return coefficients of species */
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LINK->t = LINK->t->next;
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require(tokcomma, LINK);
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coef_varrec = LINK->t->UU.vp;
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if (LINK->t->kind != tokvar || coef_varrec->stringvar != 0)
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snerr(": Cannot find coefficient variable");
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LINK->t = LINK->t->next;
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require(tokrp, LINK);
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free_dim_stringvar(elts_varrec);
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PhreeqcPtr->free_check_null(coef_varrec->UU.U0.arr);
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coef_varrec->UU.U0.arr = NULL;
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/*
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* Call subroutine
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*/
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std::string eq = PhreeqcPtr->phase_equation(phase_name, stoichiometry);
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// put type as return value
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n.stringval = true;
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n.UU.sval = PhreeqcPtr->string_duplicate(eq.c_str());
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/*
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* fill in varrec structure
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*/
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size_t count = stoichiometry.size();
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*count_varrec->UU.U0.val = (LDBLE)count;
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/*
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* malloc space
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*/
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elts_varrec->UU.U1.sarr = (char**)PhreeqcPtr->PHRQ_malloc((count + 1) * sizeof(char*));
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if (elts_varrec->UU.U1.sarr == NULL)
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{
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PhreeqcPtr->malloc_error();
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#if !defined(R_SO)
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exit(4);
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#endif
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}
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coef_varrec->UU.U0.arr = (LDBLE*)PhreeqcPtr->PHRQ_malloc((count + 1) * sizeof(LDBLE));
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if (coef_varrec->UU.U0.arr == NULL)
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{
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PhreeqcPtr->malloc_error();
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#if !defined(R_SO)
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exit(4);
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#endif
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}
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// first position not used
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elts_varrec->UU.U1.sarr[0] = NULL;
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coef_varrec->UU.U0.arr[0] = 0;
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// set dims for Basic array
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for (i = 0; i < maxdims; i++)
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{
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elts_varrec->dims[i] = 0;
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coef_varrec->dims[i] = 0;
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}
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// set dims for first dimension and number of dims
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elts_varrec->dims[0] = (long)(count + 1);
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coef_varrec->dims[0] = (long)(count + 1);
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elts_varrec->numdims = 1;
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coef_varrec->numdims = 1;
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// fill in arrays
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i = 1;
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for (std::vector<std::pair<std::string, double > >::iterator it = stoichiometry.begin(); it != stoichiometry.end(); it++)
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{
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elts_varrec->UU.U1.sarr[i] = PhreeqcPtr->string_duplicate((it->first).c_str());
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coef_varrec->UU.U0.arr[i] = it->second;
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i++;
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}
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}
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break;
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case tokspecies_equation:
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case tokspecies_equation_:
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{
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require(toklp, LINK);
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std::string species_name(stringfactor(STR1, LINK));
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varrec* elts_varrec = NULL, * coef_varrec = NULL;
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std::vector<std::pair<std::string, double> > stoichiometry;
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/*
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* Parse arguments
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*/
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require(tokcomma, LINK);
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count_varrec = LINK->t->UU.vp;
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if (LINK->t->kind != tokvar || count_varrec->stringvar != 0)
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snerr(": Cannot find count variable");
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/* return number of names of species */
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LINK->t = LINK->t->next;
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require(tokcomma, LINK);
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elts_varrec = LINK->t->UU.vp;
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if (LINK->t->kind != tokvar || elts_varrec->stringvar != 1)
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snerr(": Cannot find species string variable");
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/* return coefficients of species */
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LINK->t = LINK->t->next;
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require(tokcomma, LINK);
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coef_varrec = LINK->t->UU.vp;
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if (LINK->t->kind != tokvar || coef_varrec->stringvar != 0)
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snerr(": Cannot find coefficient variable");
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LINK->t = LINK->t->next;
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require(tokrp, LINK);
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free_dim_stringvar(elts_varrec);
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PhreeqcPtr->free_check_null(coef_varrec->UU.U0.arr);
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coef_varrec->UU.U0.arr = NULL;
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/*
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* Call subroutine
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*/
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std::string eq = PhreeqcPtr->species_equation(species_name, stoichiometry);
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// put type as return value
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n.stringval = true;
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n.UU.sval = PhreeqcPtr->string_duplicate(eq.c_str());
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/*
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* fill in varrec structure
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*/
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size_t count = stoichiometry.size();
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*count_varrec->UU.U0.val = (LDBLE)count;
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/*
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* malloc space
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*/
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elts_varrec->UU.U1.sarr = (char**)PhreeqcPtr->PHRQ_malloc((count + 1) * sizeof(char*));
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if (elts_varrec->UU.U1.sarr == NULL)
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{
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PhreeqcPtr->malloc_error();
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#if !defined(R_SO)
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exit(4);
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#endif
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}
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coef_varrec->UU.U0.arr = (LDBLE*)PhreeqcPtr->PHRQ_malloc((count + 1) * sizeof(LDBLE));
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if (coef_varrec->UU.U0.arr == NULL)
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{
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PhreeqcPtr->malloc_error();
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#if !defined(R_SO)
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exit(4);
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#endif
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}
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// first position not used
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elts_varrec->UU.U1.sarr[0] = NULL;
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coef_varrec->UU.U0.arr[0] = 0;
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// set dims for Basic array
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for (i = 0; i < maxdims; i++)
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{
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elts_varrec->dims[i] = 0;
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coef_varrec->dims[i] = 0;
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}
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// set dims for first dimension and number of dims
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elts_varrec->dims[0] = (long)(count + 1);
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coef_varrec->dims[0] = (long)(count + 1);
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elts_varrec->numdims = 1;
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coef_varrec->numdims = 1;
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// fill in arrays
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i = 1;
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for (std::vector<std::pair<std::string, double > >::iterator it = stoichiometry.begin(); it != stoichiometry.end(); it++)
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{
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elts_varrec->UU.U1.sarr[i] = PhreeqcPtr->string_duplicate((it->first).c_str());
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coef_varrec->UU.U0.arr[i] = it->second;
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i++;
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}
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}
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break;
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case toksr:
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{
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const char* str = stringfactor(STR1, LINK);
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@ -8088,6 +8292,10 @@ const std::map<const std::string, PBasic::BASIC_TOKEN>::value_type temp_tokens[]
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std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("soln_vol", PBasic::toksoln_vol),
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std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("species_formula", PBasic::tokspecies_formula),
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std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("species_formula$", PBasic::tokspecies_formula_),
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std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("phase_equation", PBasic::tokphase_equation),
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std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("phase_equation$", PBasic::tokphase_equation_),
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std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("species_equation", PBasic::tokspecies_equation),
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std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("species_equation$", PBasic::tokspecies_equation_),
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std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("sr", PBasic::toksr),
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std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("step_no", PBasic::tokstep_no),
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std::map<const std::string, PBasic::BASIC_TOKEN>::value_type("str_e$", PBasic::tokstr_e_),
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4
PBasic.h
4
PBasic.h
@ -323,6 +323,10 @@ public:
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toksoln_vol,
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tokspecies_formula,
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tokspecies_formula_,
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tokphase_equation,
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tokphase_equation_,
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tokspecies_equation,
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tokspecies_equation_,
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toksr,
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tokstep_no,
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tokstr_e_,
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@ -167,6 +167,8 @@ public:
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std::string kinetics_formula(std::string kinetics_name, cxxNameDouble& stoichiometry);
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std::string phase_formula(std::string phase_name, cxxNameDouble& stoichiometry);
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std::string species_formula(std::string phase_name, cxxNameDouble& stoichiometry);
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std::string phase_equation(std::string phase_name, std::vector<std::pair<std::string, double> >& stoichiometry);
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std::string species_equation(std::string species_name, std::vector<std::pair<std::string, double> >& stoichiometry);
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LDBLE list_ss(std::string ss_name, cxxNameDouble& composition);
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int system_total_elements(void);
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int system_total_si(void);
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103
basicsubs.cpp
103
basicsubs.cpp
@ -3009,6 +3009,109 @@ species_formula(std::string phase_name, cxxNameDouble& stoichiometry)
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return (formula);
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}
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/* ---------------------------------------------------------------------- */
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std::string Phreeqc::
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phase_equation(std::string phase_name, std::vector<std::pair<std::string, double> >& stoichiometry)
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/* ---------------------------------------------------------------------- */
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{
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/*
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* Returns equation
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* Also returns arrays of species and stoichiometry in stoichiometry
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*/
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stoichiometry.clear();
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std::ostringstream eq, lhs, rhs;
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int j = -1;
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class phase* phase_ptr = phase_bsearch(phase_name.c_str(), &j, FALSE);
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bool rhs_started = false;
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bool lhs_started = false;
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if (phase_ptr != NULL)
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{
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std::vector<rxn_token>::iterator it = phase_ptr->rxn.Get_tokens().begin();
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for (; it->name != NULL; it++)
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{
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if (!lhs_started)
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{
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std::pair<std::string, double> item(phase_ptr->formula, it->coef);
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stoichiometry.push_back(item);
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}
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else
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{
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std::pair<std::string, double> item(it->name, it->coef);
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stoichiometry.push_back(item);
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}
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if (it->coef < 0.0)
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{
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if (lhs_started) lhs << "+ ";
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if (it->coef != -1.0)
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{
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lhs << -it->coef;
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}
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lhs << it->name << " ";
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lhs_started = true;
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}
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else if (it->coef > 0.0)
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{
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if (rhs_started) rhs << "+ ";
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if (it->coef != 1.0)
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{
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rhs << it->coef;
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}
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rhs << it->name << " ";
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rhs_started = true;
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}
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}
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}
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eq << lhs.str() << "= " << rhs.str();
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return (eq.str());
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}
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/* ---------------------------------------------------------------------- */
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std::string Phreeqc::
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species_equation(std::string species_name, std::vector<std::pair<std::string, double> >& stoichiometry)
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/* ---------------------------------------------------------------------- */
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{
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/*
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* Returns equation
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* Also returns arrays of species and stoichiometry in stoichiometry
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*/
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stoichiometry.clear();
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std::ostringstream eq, lhs, rhs;;
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class species* s_ptr = s_search(species_name.c_str());
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bool rhs_started = false;
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bool lhs_started = false;
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if (s_ptr != NULL)
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{
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std::vector<rxn_token>::iterator it = s_ptr->rxn.Get_tokens().begin();
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for ( ; it->name != NULL; it++)
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{
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std::pair<std::string, double> item(it->name, it->coef);
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stoichiometry.push_back(item);
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if (it->coef > 0.0)
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{
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if (lhs_started) lhs << "+ ";
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if (it->coef != 1.0)
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{
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lhs << it->coef;
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}
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lhs << it->name << " ";
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lhs_started = true;
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}
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else if (it->coef < 0.0)
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{
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if (rhs_started) rhs << "+ ";
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if (it->coef != -1.0)
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{
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rhs << -it->coef;
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}
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rhs << it->name << " ";
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rhs_started = true;
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}
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}
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}
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eq << lhs.str() << "= " << rhs.str();
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return (eq.str());
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}
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/* ---------------------------------------------------------------------- */
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int Phreeqc::
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system_total_elements(void)
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